Multiple sequence alignment - TraesCS3B01G600100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G600100 chr3B 100.000 4957 0 0 3320 8276 820791643 820796599 0.000000e+00 9154.0
1 TraesCS3B01G600100 chr3B 100.000 3055 0 0 1 3055 820788324 820791378 0.000000e+00 5642.0
2 TraesCS3B01G600100 chr3B 94.696 2451 101 7 3675 6120 820672776 820675202 0.000000e+00 3779.0
3 TraesCS3B01G600100 chr3B 95.916 2179 77 7 1 2179 820618949 820621115 0.000000e+00 3520.0
4 TraesCS3B01G600100 chr3B 96.383 2046 64 7 4041 6083 820502726 820504764 0.000000e+00 3360.0
5 TraesCS3B01G600100 chr3B 95.150 1505 69 4 1 1504 820571127 820572628 0.000000e+00 2372.0
6 TraesCS3B01G600100 chr3B 89.761 1885 118 29 6430 8276 820760487 820762334 0.000000e+00 2342.0
7 TraesCS3B01G600100 chr3B 90.409 1783 140 15 6289 8046 820597861 820599637 0.000000e+00 2316.0
8 TraesCS3B01G600100 chr3B 93.351 1534 69 7 1 1504 820698322 820699852 0.000000e+00 2237.0
9 TraesCS3B01G600100 chr3B 88.820 1449 129 8 6600 8038 820675587 820677012 0.000000e+00 1748.0
10 TraesCS3B01G600100 chr3B 95.431 766 32 3 2291 3055 820637630 820638393 0.000000e+00 1218.0
11 TraesCS3B01G600100 chr3B 93.211 707 41 5 6449 7152 820505201 820505903 0.000000e+00 1033.0
12 TraesCS3B01G600100 chr3B 93.713 684 29 4 5384 6056 820716308 820716988 0.000000e+00 1013.0
13 TraesCS3B01G600100 chr3B 87.933 837 78 15 7217 8046 820717877 820718697 0.000000e+00 965.0
14 TraesCS3B01G600100 chr3B 87.772 736 83 2 7315 8046 820505983 820506715 0.000000e+00 854.0
15 TraesCS3B01G600100 chr3B 96.025 478 16 2 5384 5860 820596913 820597388 0.000000e+00 774.0
16 TraesCS3B01G600100 chr3B 88.154 650 70 5 7402 8046 820772041 820772688 0.000000e+00 767.0
17 TraesCS3B01G600100 chr3B 89.799 598 34 10 6508 7102 820717287 820717860 0.000000e+00 741.0
18 TraesCS3B01G600100 chr3B 87.554 466 53 4 7581 8045 820774027 820774488 1.220000e-147 534.0
19 TraesCS3B01G600100 chr3B 84.874 476 69 2 7795 8270 820554849 820555321 2.090000e-130 477.0
20 TraesCS3B01G600100 chr3B 84.232 482 73 2 7795 8276 820718611 820719089 4.520000e-127 466.0
21 TraesCS3B01G600100 chr3B 93.640 283 17 1 3399 3681 820663802 820664083 9.930000e-114 422.0
22 TraesCS3B01G600100 chr3B 91.197 284 21 2 6289 6569 820675310 820675592 4.690000e-102 383.0
23 TraesCS3B01G600100 chr3B 92.803 264 17 2 5862 6124 820597473 820597735 1.690000e-101 381.0
24 TraesCS3B01G600100 chr3B 88.235 323 18 4 3631 3952 826096536 826096839 1.310000e-97 368.0
25 TraesCS3B01G600100 chr3B 94.149 188 10 1 1982 2168 826099506 826099693 1.360000e-72 285.0
26 TraesCS3B01G600100 chr3B 89.151 212 17 3 7243 7454 820554189 820554394 8.240000e-65 259.0
27 TraesCS3B01G600100 chr3B 91.935 186 14 1 6291 6476 820717105 820717289 8.240000e-65 259.0
28 TraesCS3B01G600100 chr3B 85.185 216 32 0 1506 1721 172724958 172724743 1.080000e-53 222.0
29 TraesCS3B01G600100 chr3B 94.545 110 6 0 7259 7368 820771935 820772044 3.970000e-38 171.0
30 TraesCS3B01G600100 chr3B 94.737 38 2 0 6121 6158 820717050 820717087 8.970000e-05 60.2
31 TraesCS3B01G600100 chr3D 95.551 2225 85 5 3974 6197 609623921 609626132 0.000000e+00 3548.0
32 TraesCS3B01G600100 chr3D 91.412 1572 113 10 6487 8046 609626236 609627797 0.000000e+00 2135.0
33 TraesCS3B01G600100 chr3D 95.118 594 24 4 2166 2757 574956636 574957226 0.000000e+00 931.0
34 TraesCS3B01G600100 chr3D 95.230 587 22 6 2172 2757 517441721 517442302 0.000000e+00 924.0
35 TraesCS3B01G600100 chr3D 94.915 590 25 4 2168 2757 8368769 8369353 0.000000e+00 918.0
36 TraesCS3B01G600100 chr3D 91.361 463 38 2 1502 1963 612881986 612881525 4.210000e-177 632.0
37 TraesCS3B01G600100 chr3D 85.000 480 60 8 7795 8271 609627642 609628112 2.090000e-130 477.0
38 TraesCS3B01G600100 chr3D 91.925 322 16 5 3634 3952 612887264 612886950 7.620000e-120 442.0
39 TraesCS3B01G600100 chr3D 90.066 302 30 0 2754 3055 571603818 571603517 7.790000e-105 392.0
40 TraesCS3B01G600100 chr3D 85.098 255 35 2 7795 8046 609627576 609627830 2.960000e-64 257.0
41 TraesCS3B01G600100 chr3D 86.047 215 30 0 1507 1721 581095854 581095640 1.800000e-56 231.0
42 TraesCS3B01G600100 chr3D 78.758 306 53 6 7818 8120 609627632 609627928 2.360000e-45 195.0
43 TraesCS3B01G600100 chr3D 96.226 106 4 0 6192 6297 293614244 293614349 3.070000e-39 174.0
44 TraesCS3B01G600100 chr3D 92.174 115 6 3 6194 6306 23081272 23081159 8.600000e-35 159.0
45 TraesCS3B01G600100 chr3D 79.503 161 28 5 7849 8005 609627564 609627723 8.780000e-20 110.0
46 TraesCS3B01G600100 chr3A 95.284 1887 78 5 3974 5860 743189671 743191546 0.000000e+00 2981.0
47 TraesCS3B01G600100 chr3A 87.618 1478 124 24 6561 8019 743192347 743193784 0.000000e+00 1661.0
48 TraesCS3B01G600100 chr3A 92.165 485 35 1 7795 8276 743193623 743194107 0.000000e+00 682.0
49 TraesCS3B01G600100 chr3A 91.718 326 18 6 3631 3952 747613341 747613021 2.120000e-120 444.0
50 TraesCS3B01G600100 chr3A 91.273 275 20 3 6289 6560 743191987 743192260 1.010000e-98 372.0
51 TraesCS3B01G600100 chr3A 87.912 273 21 2 5862 6124 743191590 743191860 2.240000e-80 311.0
52 TraesCS3B01G600100 chr3A 82.206 281 47 1 7818 8095 743193682 743193962 1.070000e-58 239.0
53 TraesCS3B01G600100 chr3A 86.301 73 6 3 7207 7278 616715087 616715156 8.910000e-10 76.8
54 TraesCS3B01G600100 chr1D 95.392 586 22 5 2172 2757 433024093 433023513 0.000000e+00 928.0
55 TraesCS3B01G600100 chr1D 95.230 587 23 5 2172 2757 443451110 443450528 0.000000e+00 924.0
56 TraesCS3B01G600100 chr1D 84.685 222 27 6 1502 1721 326785999 326785783 1.810000e-51 215.0
57 TraesCS3B01G600100 chr1D 96.000 100 4 0 6193 6292 314718404 314718503 6.650000e-36 163.0
58 TraesCS3B01G600100 chr1D 95.050 101 5 0 6194 6294 2162842 2162742 8.600000e-35 159.0
59 TraesCS3B01G600100 chr1D 94.231 104 6 0 6192 6295 473539121 473539224 8.600000e-35 159.0
60 TraesCS3B01G600100 chr1D 92.381 105 8 0 6193 6297 315817005 315816901 5.170000e-32 150.0
61 TraesCS3B01G600100 chr1D 84.516 155 16 6 5554 5701 372871710 372871863 6.690000e-31 147.0
62 TraesCS3B01G600100 chr2D 95.230 587 23 5 2171 2757 590973078 590973659 0.000000e+00 924.0
63 TraesCS3B01G600100 chr2D 90.397 302 29 0 2754 3055 1647044 1647345 1.670000e-106 398.0
64 TraesCS3B01G600100 chr2D 90.429 303 28 1 2754 3055 422821552 422821854 1.670000e-106 398.0
65 TraesCS3B01G600100 chr2D 92.963 270 18 1 3320 3589 1647120 1647388 7.790000e-105 392.0
66 TraesCS3B01G600100 chr2D 84.862 218 28 5 1507 1721 423119002 423119217 1.810000e-51 215.0
67 TraesCS3B01G600100 chr2D 95.050 101 5 0 6193 6293 133772256 133772356 8.600000e-35 159.0
68 TraesCS3B01G600100 chr2D 94.175 103 6 0 6190 6292 169181079 169180977 3.090000e-34 158.0
69 TraesCS3B01G600100 chr7D 95.068 588 23 6 2171 2757 559792870 559792288 0.000000e+00 920.0
70 TraesCS3B01G600100 chr7D 91.973 299 21 2 2754 3052 541415639 541415344 4.620000e-112 416.0
71 TraesCS3B01G600100 chr7D 91.419 303 25 1 2754 3055 151472854 151472552 1.660000e-111 414.0
72 TraesCS3B01G600100 chr7D 92.364 275 19 1 3320 3592 151472778 151472504 2.800000e-104 390.0
73 TraesCS3B01G600100 chr7D 86.538 208 25 3 1507 1712 586785188 586785394 8.360000e-55 226.0
74 TraesCS3B01G600100 chr6D 93.934 610 28 9 2150 2755 21790926 21790322 0.000000e+00 913.0
75 TraesCS3B01G600100 chr6D 84.862 218 27 6 1507 1721 121158601 121158387 1.810000e-51 215.0
76 TraesCS3B01G600100 chr6D 85.096 208 27 4 1507 1714 315652734 315652531 8.420000e-50 209.0
77 TraesCS3B01G600100 chr6D 84.112 214 32 2 1509 1721 11906388 11906176 1.090000e-48 206.0
78 TraesCS3B01G600100 chr6D 83.333 216 35 1 1507 1721 38883522 38883737 1.820000e-46 198.0
79 TraesCS3B01G600100 chr6D 82.692 208 32 3 1516 1721 460771064 460770859 1.830000e-41 182.0
80 TraesCS3B01G600100 chr6D 82.258 186 29 4 1538 1721 31788734 31788551 3.090000e-34 158.0
81 TraesCS3B01G600100 chr6D 96.809 94 3 0 6195 6288 466538132 466538225 3.090000e-34 158.0
82 TraesCS3B01G600100 chr6D 95.789 95 4 0 6194 6288 362051425 362051519 4.000000e-33 154.0
83 TraesCS3B01G600100 chr6D 93.269 104 7 0 6189 6292 448790857 448790960 4.000000e-33 154.0
84 TraesCS3B01G600100 chr6D 93.137 102 7 0 6194 6295 110277541 110277440 5.170000e-32 150.0
85 TraesCS3B01G600100 chr6D 94.681 94 5 0 6198 6291 52011278 52011185 6.690000e-31 147.0
86 TraesCS3B01G600100 chr6D 93.000 100 7 0 6198 6297 57898689 57898590 6.690000e-31 147.0
87 TraesCS3B01G600100 chr6D 91.262 103 8 1 6190 6291 88883038 88882936 1.120000e-28 139.0
88 TraesCS3B01G600100 chr6D 91.089 101 9 0 6192 6292 91559633 91559533 4.030000e-28 137.0
89 TraesCS3B01G600100 chr6D 89.320 103 11 0 6192 6294 345760565 345760463 6.740000e-26 130.0
90 TraesCS3B01G600100 chr6D 85.833 120 17 0 1603 1722 315192840 315192959 2.420000e-25 128.0
91 TraesCS3B01G600100 chr6D 86.607 112 15 0 1521 1632 405088057 405087946 3.140000e-24 124.0
92 TraesCS3B01G600100 chr6D 80.000 170 29 5 1547 1714 464711127 464710961 4.060000e-23 121.0
93 TraesCS3B01G600100 chr2A 91.749 303 24 1 2754 3055 736219855 736219553 3.570000e-113 420.0
94 TraesCS3B01G600100 chr2A 96.078 102 3 1 6198 6299 619208125 619208025 1.850000e-36 165.0
95 TraesCS3B01G600100 chr5A 93.066 274 18 1 3320 3592 544183846 544184119 4.650000e-107 399.0
96 TraesCS3B01G600100 chr5A 81.925 426 71 4 6584 7007 626250404 626249983 1.020000e-93 355.0
97 TraesCS3B01G600100 chr5B 92.701 274 19 1 3320 3592 501111478 501111205 2.170000e-105 394.0
98 TraesCS3B01G600100 chr5B 84.615 221 32 2 1502 1721 493181507 493181726 1.400000e-52 219.0
99 TraesCS3B01G600100 chr4A 92.701 274 19 1 3320 3592 665482688 665482961 2.170000e-105 394.0
100 TraesCS3B01G600100 chr4A 85.185 216 31 1 1507 1721 37069285 37069070 3.890000e-53 220.0
101 TraesCS3B01G600100 chr4A 84.615 221 30 4 1507 1725 7614493 7614711 5.030000e-52 217.0
102 TraesCS3B01G600100 chr4A 95.000 100 5 0 6198 6297 703218656 703218557 3.090000e-34 158.0
103 TraesCS3B01G600100 chr6B 90.099 303 29 1 2754 3055 29870472 29870774 7.790000e-105 392.0
104 TraesCS3B01G600100 chr6B 92.674 273 19 1 3320 3592 79282404 79282133 7.790000e-105 392.0
105 TraesCS3B01G600100 chr6B 85.388 219 26 5 1507 1721 513140668 513140452 1.080000e-53 222.0
106 TraesCS3B01G600100 chr6B 95.192 104 5 0 6189 6292 336181319 336181216 1.850000e-36 165.0
107 TraesCS3B01G600100 chr6B 95.192 104 5 0 6190 6293 498288911 498289014 1.850000e-36 165.0
108 TraesCS3B01G600100 chr6B 96.000 100 4 0 6194 6293 517836071 517835972 6.650000e-36 163.0
109 TraesCS3B01G600100 chr6B 95.960 99 4 0 6194 6292 718346812 718346910 2.390000e-35 161.0
110 TraesCS3B01G600100 chr6B 93.396 106 7 0 6192 6297 113454845 113454740 3.090000e-34 158.0
111 TraesCS3B01G600100 chr6B 94.949 99 5 0 6194 6292 654640746 654640648 1.110000e-33 156.0
112 TraesCS3B01G600100 chr2B 90.099 303 29 1 2754 3055 106723522 106723220 7.790000e-105 392.0
113 TraesCS3B01G600100 chr2B 94.393 107 5 1 6192 6298 713407069 713407174 6.650000e-36 163.0
114 TraesCS3B01G600100 chr1A 92.963 270 18 1 3320 3589 71436582 71436850 7.790000e-105 392.0
115 TraesCS3B01G600100 chr1A 92.308 273 21 0 3320 3592 23221282 23221010 1.010000e-103 388.0
116 TraesCS3B01G600100 chr1A 85.185 216 30 1 1507 1720 347675097 347674882 3.890000e-53 220.0
117 TraesCS3B01G600100 chr1A 84.163 221 33 2 1502 1721 410441556 410441775 6.510000e-51 213.0
118 TraesCS3B01G600100 chr1A 83.857 223 30 3 1509 1730 513729314 513729097 3.030000e-49 207.0
119 TraesCS3B01G600100 chr1A 97.895 95 2 0 6193 6287 208637558 208637652 1.850000e-36 165.0
120 TraesCS3B01G600100 chr4D 86.977 215 24 4 1507 1721 468288083 468287873 1.070000e-58 239.0
121 TraesCS3B01G600100 chr4D 86.574 216 26 3 1507 1721 382740303 382740090 1.390000e-57 235.0
122 TraesCS3B01G600100 chr4D 84.018 219 29 6 1507 1721 75273384 75273600 1.090000e-48 206.0
123 TraesCS3B01G600100 chr4D 83.796 216 33 2 1507 1721 127149869 127150083 3.920000e-48 204.0
124 TraesCS3B01G600100 chr4D 84.135 208 33 0 1507 1714 490890513 490890306 1.410000e-47 202.0
125 TraesCS3B01G600100 chr4D 94.949 99 5 0 6194 6292 293864546 293864644 1.110000e-33 156.0
126 TraesCS3B01G600100 chr4D 93.269 104 7 0 6194 6297 54799449 54799346 4.000000e-33 154.0
127 TraesCS3B01G600100 chr4D 95.745 94 4 0 6195 6288 64547635 64547728 1.440000e-32 152.0
128 TraesCS3B01G600100 chr4D 93.939 99 6 0 6195 6293 94883332 94883430 5.170000e-32 150.0
129 TraesCS3B01G600100 chr7A 86.175 217 27 2 1507 1721 141624127 141624342 1.800000e-56 231.0
130 TraesCS3B01G600100 chr7A 85.714 217 28 2 1507 1721 141016821 141017036 8.360000e-55 226.0
131 TraesCS3B01G600100 chr4B 85.648 216 28 3 1509 1722 64685722 64685508 3.010000e-54 224.0
132 TraesCS3B01G600100 chr4B 96.907 97 3 0 6198 6294 32922887 32922791 6.650000e-36 163.0
133 TraesCS3B01G600100 chr4B 94.340 106 5 1 6191 6295 186741772 186741667 2.390000e-35 161.0
134 TraesCS3B01G600100 chr7B 85.185 216 27 5 1507 1721 15824191 15824402 5.030000e-52 217.0
135 TraesCS3B01G600100 chr7B 94.444 108 6 0 6190 6297 188953744 188953637 5.140000e-37 167.0
136 TraesCS3B01G600100 chr7B 93.519 108 7 0 6185 6292 41171599 41171706 2.390000e-35 161.0
137 TraesCS3B01G600100 chr6A 97.030 101 3 0 6193 6293 315625264 315625364 3.970000e-38 171.0
138 TraesCS3B01G600100 chr1B 96.040 101 4 0 6195 6295 328139686 328139786 1.850000e-36 165.0
139 TraesCS3B01G600100 chr1B 91.453 117 9 1 6200 6316 679750860 679750745 8.600000e-35 159.0
140 TraesCS3B01G600100 chr1B 92.523 107 6 2 6199 6305 171887408 171887304 1.440000e-32 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G600100 chr3B 820788324 820796599 8275 False 7398.000000 9154 100.000000 1 8276 2 chr3B.!!$F13 8275
1 TraesCS3B01G600100 chr3B 820618949 820621115 2166 False 3520.000000 3520 95.916000 1 2179 1 chr3B.!!$F2 2178
2 TraesCS3B01G600100 chr3B 820571127 820572628 1501 False 2372.000000 2372 95.150000 1 1504 1 chr3B.!!$F1 1503
3 TraesCS3B01G600100 chr3B 820760487 820762334 1847 False 2342.000000 2342 89.761000 6430 8276 1 chr3B.!!$F6 1846
4 TraesCS3B01G600100 chr3B 820698322 820699852 1530 False 2237.000000 2237 93.351000 1 1504 1 chr3B.!!$F5 1503
5 TraesCS3B01G600100 chr3B 820672776 820677012 4236 False 1970.000000 3779 91.571000 3675 8038 3 chr3B.!!$F10 4363
6 TraesCS3B01G600100 chr3B 820502726 820506715 3989 False 1749.000000 3360 92.455333 4041 8046 3 chr3B.!!$F7 4005
7 TraesCS3B01G600100 chr3B 820637630 820638393 763 False 1218.000000 1218 95.431000 2291 3055 1 chr3B.!!$F3 764
8 TraesCS3B01G600100 chr3B 820596913 820599637 2724 False 1157.000000 2316 93.079000 5384 8046 3 chr3B.!!$F9 2662
9 TraesCS3B01G600100 chr3B 820716308 820719089 2781 False 584.033333 1013 90.391500 5384 8276 6 chr3B.!!$F11 2892
10 TraesCS3B01G600100 chr3B 820771935 820774488 2553 False 490.666667 767 90.084333 7259 8046 3 chr3B.!!$F12 787
11 TraesCS3B01G600100 chr3B 820554189 820555321 1132 False 368.000000 477 87.012500 7243 8270 2 chr3B.!!$F8 1027
12 TraesCS3B01G600100 chr3B 826096536 826099693 3157 False 326.500000 368 91.192000 1982 3952 2 chr3B.!!$F14 1970
13 TraesCS3B01G600100 chr3D 609623921 609628112 4191 False 1120.333333 3548 85.887000 3974 8271 6 chr3D.!!$F5 4297
14 TraesCS3B01G600100 chr3D 574956636 574957226 590 False 931.000000 931 95.118000 2166 2757 1 chr3D.!!$F4 591
15 TraesCS3B01G600100 chr3D 517441721 517442302 581 False 924.000000 924 95.230000 2172 2757 1 chr3D.!!$F3 585
16 TraesCS3B01G600100 chr3D 8368769 8369353 584 False 918.000000 918 94.915000 2168 2757 1 chr3D.!!$F1 589
17 TraesCS3B01G600100 chr3A 743189671 743194107 4436 False 1041.000000 2981 89.409667 3974 8276 6 chr3A.!!$F2 4302
18 TraesCS3B01G600100 chr1D 433023513 433024093 580 True 928.000000 928 95.392000 2172 2757 1 chr1D.!!$R4 585
19 TraesCS3B01G600100 chr1D 443450528 443451110 582 True 924.000000 924 95.230000 2172 2757 1 chr1D.!!$R5 585
20 TraesCS3B01G600100 chr2D 590973078 590973659 581 False 924.000000 924 95.230000 2171 2757 1 chr2D.!!$F4 586
21 TraesCS3B01G600100 chr7D 559792288 559792870 582 True 920.000000 920 95.068000 2171 2757 1 chr7D.!!$R2 586
22 TraesCS3B01G600100 chr6D 21790322 21790926 604 True 913.000000 913 93.934000 2150 2755 1 chr6D.!!$R2 605

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
868 873 0.107312 TTTCCCACGAAACCGAACCA 60.107 50.000 0.00 0.0 32.96 3.67 F
2372 2407 0.032952 GCGATGCCCATTAGTACCGA 59.967 55.000 0.00 0.0 0.00 4.69 F
2905 2947 0.251787 AAACCCACAGCAAGATCCCC 60.252 55.000 0.00 0.0 0.00 4.81 F
3341 3383 0.107081 CACCCGGTTGTGTTAGGTCA 59.893 55.000 0.00 0.0 0.00 4.02 F
4190 4526 0.107066 CAGGATGCCATGTGCTACCA 60.107 55.000 16.83 0.0 42.00 3.25 F
5008 6377 3.449018 AGTGAAGCTGGTAGTGATTCGAT 59.551 43.478 0.00 0.0 0.00 3.59 F
5217 6586 0.455410 TGCTGCACCACTTGTTGTTC 59.545 50.000 0.00 0.0 0.00 3.18 F
5218 6587 0.455410 GCTGCACCACTTGTTGTTCA 59.545 50.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2847 2889 1.282157 AGGTGTTTCTATGGGCTGACC 59.718 52.381 0.0 0.0 40.81 4.02 R
3322 3364 0.107081 TGACCTAACACAACCGGGTG 59.893 55.000 20.6 20.6 44.35 4.61 R
3773 3815 1.133853 AGAAGCTGCCTTCCATCCATC 60.134 52.381 0.0 0.0 46.97 3.51 R
5093 6462 0.530650 CAACAGCTCGACCGGCATAT 60.531 55.000 0.0 0.0 0.00 1.78 R
5099 6468 1.428448 TTTCATCAACAGCTCGACCG 58.572 50.000 0.0 0.0 0.00 4.79 R
6767 9023 1.406219 CGTCGATGCTGAAGGTCACG 61.406 60.000 0.0 0.0 0.00 4.35 R
7205 9472 1.004628 ACATTACCATCCAGCAGCACA 59.995 47.619 0.0 0.0 0.00 4.57 R
7445 9724 4.091509 CACGCTTATTCGTTCTAGCAGTTT 59.908 41.667 0.0 0.0 41.21 2.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 7.936847 CCTAGTGATTACAGGCCAAACATTATA 59.063 37.037 5.01 0.00 0.00 0.98
281 282 8.924511 ATATAGGGGATACATTTGAACACAAG 57.075 34.615 0.00 0.00 39.74 3.16
574 575 4.065088 ACTGCGAGCTTGATTTTTACTGA 58.935 39.130 4.70 0.00 0.00 3.41
579 580 6.922957 TGCGAGCTTGATTTTTACTGAAATTT 59.077 30.769 4.70 0.00 29.75 1.82
580 581 7.114811 TGCGAGCTTGATTTTTACTGAAATTTC 59.885 33.333 11.41 11.41 29.75 2.17
619 621 1.370609 TCTTTTGTGTCGGCGTGAAA 58.629 45.000 6.85 0.00 0.00 2.69
741 745 4.838986 GGATAGGTAGTTCTGCATCCCTAA 59.161 45.833 0.00 0.00 0.00 2.69
840 844 2.457813 ATGTTGGCATGCCATTAGGA 57.542 45.000 38.78 21.98 46.64 2.94
868 873 0.107312 TTTCCCACGAAACCGAACCA 60.107 50.000 0.00 0.00 32.96 3.67
906 911 8.141268 CCAATATTGCTGGTTTATTCGGTTTAT 58.859 33.333 10.11 0.00 0.00 1.40
925 930 7.466185 CGGTTTATAGTGAATGATGCGGTTTTA 60.466 37.037 0.00 0.00 0.00 1.52
938 943 3.057104 TGCGGTTTTAAGATCTGTCGAGA 60.057 43.478 0.00 0.00 0.00 4.04
993 998 2.361438 CCGAGAAGCCTAACTAACCGAT 59.639 50.000 0.00 0.00 0.00 4.18
1002 1007 2.981859 AACTAACCGATGCTACCAGG 57.018 50.000 0.00 0.00 0.00 4.45
1170 1175 4.997395 TGAGAAGGTGCTAGCTTGTTTTAG 59.003 41.667 17.23 0.00 35.86 1.85
1179 1184 3.857157 AGCTTGTTTTAGTCCTGGACA 57.143 42.857 27.48 11.67 34.60 4.02
1223 1229 1.794116 CGGATTGCTTTTTGCTTGTGG 59.206 47.619 0.00 0.00 43.37 4.17
1435 1468 7.257722 GTTCGGTGTTGATATTTCAATGGATT 58.742 34.615 1.79 0.00 43.49 3.01
1525 1558 4.989279 AAGGCCTTATTACGACGACTTA 57.011 40.909 18.87 0.00 0.00 2.24
1580 1613 2.919856 CGAGGGAGGGGCGATGAT 60.920 66.667 0.00 0.00 0.00 2.45
1594 1627 0.924090 GATGATGACGACACGCCTTC 59.076 55.000 0.00 0.00 0.00 3.46
1653 1686 7.125659 TGGTCTACTGATCTGGATGTGATTTTA 59.874 37.037 4.49 0.00 0.00 1.52
1699 1732 9.755804 GTACTGTCATGATTGAAGATGAATAGA 57.244 33.333 0.00 0.00 32.48 1.98
1875 1908 7.951530 AACTTGATGGTCAATTTTGAATCAC 57.048 32.000 7.02 0.00 39.21 3.06
1906 1939 8.209917 CCTAAATGCTCTTATTTTTAGGTCGT 57.790 34.615 10.69 0.00 42.73 4.34
1919 1952 6.610075 TTTTAGGTCGTAGGACTAACCATT 57.390 37.500 14.75 0.00 42.97 3.16
1931 1964 4.072131 GACTAACCATTCCAGACAAAGCA 58.928 43.478 0.00 0.00 0.00 3.91
1942 1975 3.623060 CCAGACAAAGCATACATAGCGTT 59.377 43.478 0.00 0.00 37.01 4.84
1961 1994 6.945072 AGCGTTATTACATTTAACTAGCTGC 58.055 36.000 0.00 0.00 30.28 5.25
1963 1996 7.065324 AGCGTTATTACATTTAACTAGCTGCAA 59.935 33.333 1.02 0.00 30.28 4.08
2018 2051 6.584563 GCATTGTTTAGAAGTTCGGCATTTTA 59.415 34.615 0.00 0.00 0.00 1.52
2019 2052 7.275560 GCATTGTTTAGAAGTTCGGCATTTTAT 59.724 33.333 0.00 0.00 0.00 1.40
2020 2053 9.139174 CATTGTTTAGAAGTTCGGCATTTTATT 57.861 29.630 0.00 0.00 0.00 1.40
2021 2054 8.514136 TTGTTTAGAAGTTCGGCATTTTATTG 57.486 30.769 0.00 0.00 0.00 1.90
2022 2055 7.653647 TGTTTAGAAGTTCGGCATTTTATTGT 58.346 30.769 0.00 0.00 0.00 2.71
2023 2056 8.138712 TGTTTAGAAGTTCGGCATTTTATTGTT 58.861 29.630 0.00 0.00 0.00 2.83
2024 2057 8.424731 GTTTAGAAGTTCGGCATTTTATTGTTG 58.575 33.333 0.00 0.00 0.00 3.33
2025 2058 6.325919 AGAAGTTCGGCATTTTATTGTTGA 57.674 33.333 0.00 0.00 0.00 3.18
2026 2059 6.744112 AGAAGTTCGGCATTTTATTGTTGAA 58.256 32.000 0.00 0.00 0.00 2.69
2027 2060 7.378181 AGAAGTTCGGCATTTTATTGTTGAAT 58.622 30.769 0.00 0.00 0.00 2.57
2028 2061 8.519526 AGAAGTTCGGCATTTTATTGTTGAATA 58.480 29.630 0.00 0.00 0.00 1.75
2029 2062 9.301153 GAAGTTCGGCATTTTATTGTTGAATAT 57.699 29.630 0.00 0.00 0.00 1.28
2064 2097 8.279695 TGATTGAAAAACATTGTTCATACACG 57.720 30.769 1.83 0.00 33.90 4.49
2065 2098 7.918033 TGATTGAAAAACATTGTTCATACACGT 59.082 29.630 1.83 0.00 33.90 4.49
2066 2099 7.443218 TTGAAAAACATTGTTCATACACGTG 57.557 32.000 15.48 15.48 33.90 4.49
2067 2100 5.457148 TGAAAAACATTGTTCATACACGTGC 59.543 36.000 17.22 0.00 32.98 5.34
2068 2101 2.873170 ACATTGTTCATACACGTGCG 57.127 45.000 17.22 4.51 32.98 5.34
2069 2102 1.463056 ACATTGTTCATACACGTGCGG 59.537 47.619 17.22 5.34 32.98 5.69
2070 2103 1.729517 CATTGTTCATACACGTGCGGA 59.270 47.619 17.22 7.93 32.98 5.54
2071 2104 2.087501 TTGTTCATACACGTGCGGAT 57.912 45.000 17.22 3.72 32.98 4.18
2072 2105 2.943449 TGTTCATACACGTGCGGATA 57.057 45.000 17.22 0.00 0.00 2.59
2073 2106 3.233684 TGTTCATACACGTGCGGATAA 57.766 42.857 17.22 0.93 0.00 1.75
2074 2107 3.787785 TGTTCATACACGTGCGGATAAT 58.212 40.909 17.22 0.00 0.00 1.28
2075 2108 4.934515 TGTTCATACACGTGCGGATAATA 58.065 39.130 17.22 0.00 0.00 0.98
2076 2109 5.534407 TGTTCATACACGTGCGGATAATAT 58.466 37.500 17.22 0.76 0.00 1.28
2077 2110 5.404066 TGTTCATACACGTGCGGATAATATG 59.596 40.000 17.22 13.79 0.00 1.78
2078 2111 5.128992 TCATACACGTGCGGATAATATGT 57.871 39.130 17.22 0.00 0.00 2.29
2079 2112 4.920927 TCATACACGTGCGGATAATATGTG 59.079 41.667 17.22 1.35 37.36 3.21
2080 2113 3.173668 ACACGTGCGGATAATATGTGT 57.826 42.857 17.22 0.00 39.13 3.72
2081 2114 3.527533 ACACGTGCGGATAATATGTGTT 58.472 40.909 17.22 0.00 40.56 3.32
2082 2115 3.554324 ACACGTGCGGATAATATGTGTTC 59.446 43.478 17.22 0.00 40.56 3.18
2083 2116 3.553917 CACGTGCGGATAATATGTGTTCA 59.446 43.478 0.82 0.00 0.00 3.18
2084 2117 4.211164 CACGTGCGGATAATATGTGTTCAT 59.789 41.667 0.82 0.00 38.00 2.57
2085 2118 5.404066 CACGTGCGGATAATATGTGTTCATA 59.596 40.000 0.82 0.00 40.26 2.15
2086 2119 6.090763 CACGTGCGGATAATATGTGTTCATAT 59.909 38.462 0.82 0.00 45.72 1.78
2087 2120 7.274686 CACGTGCGGATAATATGTGTTCATATA 59.725 37.037 0.82 0.00 43.80 0.86
2088 2121 7.815549 ACGTGCGGATAATATGTGTTCATATAA 59.184 33.333 0.00 0.00 43.80 0.98
2089 2122 8.817100 CGTGCGGATAATATGTGTTCATATAAT 58.183 33.333 1.91 0.00 43.80 1.28
2090 2123 9.920826 GTGCGGATAATATGTGTTCATATAATG 57.079 33.333 1.91 0.00 43.80 1.90
2091 2124 9.665719 TGCGGATAATATGTGTTCATATAATGT 57.334 29.630 1.91 0.00 43.80 2.71
2092 2125 9.920826 GCGGATAATATGTGTTCATATAATGTG 57.079 33.333 1.91 0.00 43.80 3.21
2100 2133 7.994425 TGTGTTCATATAATGTGGAAACAGT 57.006 32.000 0.00 0.00 44.46 3.55
2101 2134 7.815641 TGTGTTCATATAATGTGGAAACAGTG 58.184 34.615 0.00 0.00 44.46 3.66
2102 2135 7.446931 TGTGTTCATATAATGTGGAAACAGTGT 59.553 33.333 0.00 0.00 44.46 3.55
2103 2136 8.296713 GTGTTCATATAATGTGGAAACAGTGTT 58.703 33.333 1.64 1.64 44.46 3.32
2104 2137 8.855110 TGTTCATATAATGTGGAAACAGTGTTT 58.145 29.630 21.00 21.00 44.46 2.83
2105 2138 9.691362 GTTCATATAATGTGGAAACAGTGTTTT 57.309 29.630 21.70 8.01 44.46 2.43
2106 2139 9.906660 TTCATATAATGTGGAAACAGTGTTTTC 57.093 29.630 21.70 20.13 44.46 2.29
2164 2197 8.990163 AAGTAAGTACAAATCTGGAAAAAGGA 57.010 30.769 0.00 0.00 0.00 3.36
2165 2198 8.990163 AGTAAGTACAAATCTGGAAAAAGGAA 57.010 30.769 0.00 0.00 0.00 3.36
2166 2199 8.847196 AGTAAGTACAAATCTGGAAAAAGGAAC 58.153 33.333 0.00 0.00 0.00 3.62
2289 2324 1.265454 GGCTAGGGCACTGTACAGGT 61.265 60.000 26.12 9.70 40.87 4.00
2303 2338 4.095946 TGTACAGGTATTAGTCCCGGTTT 58.904 43.478 0.00 0.00 31.43 3.27
2372 2407 0.032952 GCGATGCCCATTAGTACCGA 59.967 55.000 0.00 0.00 0.00 4.69
2397 2432 1.351683 TGGCACCAACCGGTACTAAAT 59.648 47.619 8.00 0.00 46.94 1.40
2519 2558 4.195225 TCAAACTCTACACACACACACA 57.805 40.909 0.00 0.00 0.00 3.72
2689 2728 6.181908 AGTGTAGGGAAAATATAAAACGGCA 58.818 36.000 0.00 0.00 0.00 5.69
2761 2803 1.084289 AGCACGAAAATCCGCCTAAC 58.916 50.000 0.00 0.00 0.00 2.34
2770 2812 4.530857 CCGCCTAACCCTGGAGCG 62.531 72.222 0.00 1.65 46.04 5.03
2847 2889 0.682852 TCTCCACCCGGTTGTGTTAG 59.317 55.000 9.60 6.99 34.35 2.34
2860 2902 2.827755 TGTGTTAGGTCAGCCCATAGA 58.172 47.619 0.00 0.00 34.66 1.98
2894 2936 1.900981 CATCCGTGCCAAACCCACA 60.901 57.895 0.00 0.00 32.85 4.17
2895 2937 1.603455 ATCCGTGCCAAACCCACAG 60.603 57.895 0.00 0.00 32.85 3.66
2905 2947 0.251787 AAACCCACAGCAAGATCCCC 60.252 55.000 0.00 0.00 0.00 4.81
2994 3036 3.717294 ACCCCGGAGACATGTGCC 61.717 66.667 1.15 3.35 0.00 5.01
3022 3064 0.767375 AGACATGCCAACACACCTCT 59.233 50.000 0.00 0.00 0.00 3.69
3046 3088 4.910585 GTATGAGGGCCCGGTGCG 62.911 72.222 18.44 0.00 42.61 5.34
3337 3379 3.226884 CTCCACCCGGTTGTGTTAG 57.773 57.895 9.60 3.80 34.35 2.34
3338 3380 0.321298 CTCCACCCGGTTGTGTTAGG 60.321 60.000 9.60 0.00 34.35 2.69
3339 3381 1.055551 TCCACCCGGTTGTGTTAGGT 61.056 55.000 9.60 0.00 34.35 3.08
3340 3382 0.604511 CCACCCGGTTGTGTTAGGTC 60.605 60.000 9.60 0.00 34.35 3.85
3341 3383 0.107081 CACCCGGTTGTGTTAGGTCA 59.893 55.000 0.00 0.00 0.00 4.02
3342 3384 0.395312 ACCCGGTTGTGTTAGGTCAG 59.605 55.000 0.00 0.00 0.00 3.51
3343 3385 0.953960 CCCGGTTGTGTTAGGTCAGC 60.954 60.000 0.00 0.00 0.00 4.26
3344 3386 0.953960 CCGGTTGTGTTAGGTCAGCC 60.954 60.000 0.00 0.00 0.00 4.85
3345 3387 0.953960 CGGTTGTGTTAGGTCAGCCC 60.954 60.000 0.00 0.00 32.60 5.19
3346 3388 0.109723 GGTTGTGTTAGGTCAGCCCA 59.890 55.000 0.00 0.00 34.66 5.36
3347 3389 1.271926 GGTTGTGTTAGGTCAGCCCAT 60.272 52.381 0.00 0.00 34.66 4.00
3348 3390 2.026636 GGTTGTGTTAGGTCAGCCCATA 60.027 50.000 0.00 0.00 34.66 2.74
3349 3391 3.371595 GGTTGTGTTAGGTCAGCCCATAT 60.372 47.826 0.00 0.00 34.66 1.78
3350 3392 3.558931 TGTGTTAGGTCAGCCCATATG 57.441 47.619 0.00 0.00 34.66 1.78
3351 3393 3.111484 TGTGTTAGGTCAGCCCATATGA 58.889 45.455 3.65 0.00 34.66 2.15
3352 3394 3.521531 TGTGTTAGGTCAGCCCATATGAA 59.478 43.478 3.65 0.00 34.66 2.57
3353 3395 3.877508 GTGTTAGGTCAGCCCATATGAAC 59.122 47.826 3.65 0.00 34.45 3.18
3354 3396 3.521531 TGTTAGGTCAGCCCATATGAACA 59.478 43.478 3.65 0.57 36.82 3.18
3355 3397 2.717639 AGGTCAGCCCATATGAACAC 57.282 50.000 3.65 0.00 36.82 3.32
3356 3398 2.200081 AGGTCAGCCCATATGAACACT 58.800 47.619 3.65 0.00 36.82 3.55
3357 3399 2.578021 AGGTCAGCCCATATGAACACTT 59.422 45.455 3.65 0.00 36.82 3.16
3358 3400 3.010584 AGGTCAGCCCATATGAACACTTT 59.989 43.478 3.65 0.00 36.82 2.66
3359 3401 3.129287 GGTCAGCCCATATGAACACTTTG 59.871 47.826 3.65 0.00 34.40 2.77
3360 3402 3.129287 GTCAGCCCATATGAACACTTTGG 59.871 47.826 3.65 0.00 0.00 3.28
3361 3403 3.010027 TCAGCCCATATGAACACTTTGGA 59.990 43.478 3.65 0.00 0.00 3.53
3362 3404 3.379372 CAGCCCATATGAACACTTTGGAG 59.621 47.826 3.65 0.00 0.00 3.86
3363 3405 2.099756 GCCCATATGAACACTTTGGAGC 59.900 50.000 3.65 0.00 0.00 4.70
3364 3406 3.355378 CCCATATGAACACTTTGGAGCA 58.645 45.455 3.65 0.00 0.00 4.26
3365 3407 3.763360 CCCATATGAACACTTTGGAGCAA 59.237 43.478 3.65 0.00 0.00 3.91
3366 3408 4.380867 CCCATATGAACACTTTGGAGCAAC 60.381 45.833 3.65 0.00 0.00 4.17
3367 3409 4.218200 CCATATGAACACTTTGGAGCAACA 59.782 41.667 3.65 0.00 0.00 3.33
3368 3410 5.105635 CCATATGAACACTTTGGAGCAACAT 60.106 40.000 3.65 0.00 0.00 2.71
3369 3411 3.988379 TGAACACTTTGGAGCAACATC 57.012 42.857 0.00 0.00 0.00 3.06
3370 3412 2.622942 TGAACACTTTGGAGCAACATCC 59.377 45.455 0.00 0.00 40.03 3.51
3371 3413 1.238439 ACACTTTGGAGCAACATCCG 58.762 50.000 0.00 0.00 42.77 4.18
3372 3414 0.523072 CACTTTGGAGCAACATCCGG 59.477 55.000 0.00 0.00 42.77 5.14
3373 3415 0.609131 ACTTTGGAGCAACATCCGGG 60.609 55.000 0.00 0.00 42.77 5.73
3374 3416 1.937546 CTTTGGAGCAACATCCGGGC 61.938 60.000 0.00 0.00 42.77 6.13
3375 3417 3.936772 TTGGAGCAACATCCGGGCC 62.937 63.158 0.00 0.00 42.77 5.80
3376 3418 4.424711 GGAGCAACATCCGGGCCA 62.425 66.667 4.39 0.00 0.00 5.36
3377 3419 2.361104 GAGCAACATCCGGGCCAA 60.361 61.111 4.39 0.00 0.00 4.52
3378 3420 1.976474 GAGCAACATCCGGGCCAAA 60.976 57.895 4.39 0.00 0.00 3.28
3379 3421 2.212900 GAGCAACATCCGGGCCAAAC 62.213 60.000 4.39 0.00 0.00 2.93
3380 3422 2.969827 CAACATCCGGGCCAAACC 59.030 61.111 4.39 0.00 37.93 3.27
3389 3431 2.736531 GGCCAAACCCACAGCAAG 59.263 61.111 0.00 0.00 0.00 4.01
3390 3432 1.832167 GGCCAAACCCACAGCAAGA 60.832 57.895 0.00 0.00 0.00 3.02
3391 3433 1.187567 GGCCAAACCCACAGCAAGAT 61.188 55.000 0.00 0.00 0.00 2.40
3392 3434 0.244721 GCCAAACCCACAGCAAGATC 59.755 55.000 0.00 0.00 0.00 2.75
3393 3435 0.890683 CCAAACCCACAGCAAGATCC 59.109 55.000 0.00 0.00 0.00 3.36
3394 3436 0.890683 CAAACCCACAGCAAGATCCC 59.109 55.000 0.00 0.00 0.00 3.85
3395 3437 0.251787 AAACCCACAGCAAGATCCCC 60.252 55.000 0.00 0.00 0.00 4.81
3396 3438 1.142688 AACCCACAGCAAGATCCCCT 61.143 55.000 0.00 0.00 0.00 4.79
3397 3439 1.225704 CCCACAGCAAGATCCCCTC 59.774 63.158 0.00 0.00 0.00 4.30
3398 3440 1.225704 CCACAGCAAGATCCCCTCC 59.774 63.158 0.00 0.00 0.00 4.30
3399 3441 1.153289 CACAGCAAGATCCCCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
3400 3442 2.203126 CAGCAAGATCCCCTCCGC 60.203 66.667 0.00 0.00 0.00 5.54
3401 3443 3.854669 AGCAAGATCCCCTCCGCG 61.855 66.667 0.00 0.00 0.00 6.46
3402 3444 4.162690 GCAAGATCCCCTCCGCGT 62.163 66.667 4.92 0.00 0.00 6.01
3403 3445 2.792947 GCAAGATCCCCTCCGCGTA 61.793 63.158 4.92 0.00 0.00 4.42
3404 3446 1.364171 CAAGATCCCCTCCGCGTAG 59.636 63.158 4.92 0.00 0.00 3.51
3405 3447 1.107538 CAAGATCCCCTCCGCGTAGA 61.108 60.000 4.92 0.00 0.00 2.59
3406 3448 1.108132 AAGATCCCCTCCGCGTAGAC 61.108 60.000 4.92 0.00 0.00 2.59
3407 3449 2.521224 ATCCCCTCCGCGTAGACC 60.521 66.667 4.92 0.00 0.00 3.85
3408 3450 4.828296 TCCCCTCCGCGTAGACCC 62.828 72.222 4.92 0.00 0.00 4.46
3411 3453 3.885521 CCTCCGCGTAGACCCGAC 61.886 72.222 4.92 0.00 0.00 4.79
3412 3454 4.233635 CTCCGCGTAGACCCGACG 62.234 72.222 4.92 0.00 43.19 5.12
3417 3459 2.021931 CGTAGACCCGACGCGTAC 59.978 66.667 13.97 3.38 32.89 3.67
3491 3533 4.057428 GAGACGTGTGCCGCCTCT 62.057 66.667 0.00 0.00 42.14 3.69
3492 3534 3.575351 GAGACGTGTGCCGCCTCTT 62.575 63.158 0.00 0.00 42.14 2.85
3493 3535 3.112709 GACGTGTGCCGCCTCTTC 61.113 66.667 0.00 0.00 41.42 2.87
3494 3536 3.858868 GACGTGTGCCGCCTCTTCA 62.859 63.158 0.00 0.00 41.42 3.02
3495 3537 3.114616 CGTGTGCCGCCTCTTCAG 61.115 66.667 0.00 0.00 0.00 3.02
3496 3538 2.343758 GTGTGCCGCCTCTTCAGA 59.656 61.111 0.00 0.00 0.00 3.27
3497 3539 2.029844 GTGTGCCGCCTCTTCAGAC 61.030 63.158 0.00 0.00 0.00 3.51
3498 3540 2.343758 GTGCCGCCTCTTCAGACA 59.656 61.111 0.00 0.00 0.00 3.41
3499 3541 1.078848 GTGCCGCCTCTTCAGACAT 60.079 57.895 0.00 0.00 0.00 3.06
3500 3542 1.078918 TGCCGCCTCTTCAGACATG 60.079 57.895 0.00 0.00 0.00 3.21
3501 3543 2.467826 GCCGCCTCTTCAGACATGC 61.468 63.158 0.00 0.00 0.00 4.06
3502 3544 1.817099 CCGCCTCTTCAGACATGCC 60.817 63.158 0.00 0.00 0.00 4.40
3503 3545 1.220206 CGCCTCTTCAGACATGCCT 59.780 57.895 0.00 0.00 0.00 4.75
3504 3546 0.809241 CGCCTCTTCAGACATGCCTC 60.809 60.000 0.00 0.00 0.00 4.70
3505 3547 0.463474 GCCTCTTCAGACATGCCTCC 60.463 60.000 0.00 0.00 0.00 4.30
3506 3548 1.202330 CCTCTTCAGACATGCCTCCT 58.798 55.000 0.00 0.00 0.00 3.69
3507 3549 1.138661 CCTCTTCAGACATGCCTCCTC 59.861 57.143 0.00 0.00 0.00 3.71
3508 3550 1.829849 CTCTTCAGACATGCCTCCTCA 59.170 52.381 0.00 0.00 0.00 3.86
3509 3551 1.552337 TCTTCAGACATGCCTCCTCAC 59.448 52.381 0.00 0.00 0.00 3.51
3510 3552 0.615331 TTCAGACATGCCTCCTCACC 59.385 55.000 0.00 0.00 0.00 4.02
3511 3553 1.222936 CAGACATGCCTCCTCACCC 59.777 63.158 0.00 0.00 0.00 4.61
3512 3554 1.997874 AGACATGCCTCCTCACCCC 60.998 63.158 0.00 0.00 0.00 4.95
3513 3555 3.017581 ACATGCCTCCTCACCCCC 61.018 66.667 0.00 0.00 0.00 5.40
3532 3574 4.343581 CGCATGTATGAGGACCCG 57.656 61.111 0.00 0.00 0.00 5.28
3533 3575 1.300931 CGCATGTATGAGGACCCGG 60.301 63.158 0.00 0.00 0.00 5.73
3534 3576 1.830145 GCATGTATGAGGACCCGGT 59.170 57.895 0.00 0.00 0.00 5.28
3535 3577 0.532862 GCATGTATGAGGACCCGGTG 60.533 60.000 0.00 0.00 0.00 4.94
3536 3578 0.532862 CATGTATGAGGACCCGGTGC 60.533 60.000 0.00 0.00 0.00 5.01
3537 3579 2.028125 ATGTATGAGGACCCGGTGCG 62.028 60.000 0.00 0.00 0.00 5.34
3538 3580 2.043752 TATGAGGACCCGGTGCGA 60.044 61.111 0.00 0.00 0.00 5.10
3539 3581 2.420568 TATGAGGACCCGGTGCGAC 61.421 63.158 0.00 3.16 0.00 5.19
3554 3596 3.499737 GACGCTCCGGTGGCATTG 61.500 66.667 18.63 7.99 0.00 2.82
3557 3599 2.270850 GCTCCGGTGGCATTGGTA 59.729 61.111 15.08 0.00 0.00 3.25
3558 3600 1.377987 GCTCCGGTGGCATTGGTAA 60.378 57.895 15.08 0.00 0.00 2.85
3559 3601 1.654023 GCTCCGGTGGCATTGGTAAC 61.654 60.000 15.08 0.00 0.00 2.50
3560 3602 1.001887 TCCGGTGGCATTGGTAACC 60.002 57.895 0.00 0.00 0.00 2.85
3561 3603 2.049767 CCGGTGGCATTGGTAACCC 61.050 63.158 0.00 0.00 0.00 4.11
3562 3604 2.049767 CGGTGGCATTGGTAACCCC 61.050 63.158 0.00 0.00 0.00 4.95
3563 3605 1.684391 GGTGGCATTGGTAACCCCC 60.684 63.158 0.00 0.00 0.00 5.40
3564 3606 2.049767 GTGGCATTGGTAACCCCCG 61.050 63.158 0.00 0.00 0.00 5.73
3565 3607 2.441348 GGCATTGGTAACCCCCGG 60.441 66.667 0.00 0.00 0.00 5.73
3566 3608 2.441348 GCATTGGTAACCCCCGGG 60.441 66.667 15.80 15.80 42.03 5.73
3583 3625 3.723922 GGCCCCCGTCTTGCCTAA 61.724 66.667 0.00 0.00 42.01 2.69
3584 3626 2.437895 GCCCCCGTCTTGCCTAAC 60.438 66.667 0.00 0.00 0.00 2.34
3585 3627 2.271173 CCCCCGTCTTGCCTAACC 59.729 66.667 0.00 0.00 0.00 2.85
3586 3628 2.271173 CCCCGTCTTGCCTAACCC 59.729 66.667 0.00 0.00 0.00 4.11
3587 3629 2.298661 CCCCGTCTTGCCTAACCCT 61.299 63.158 0.00 0.00 0.00 4.34
3588 3630 1.078426 CCCGTCTTGCCTAACCCTG 60.078 63.158 0.00 0.00 0.00 4.45
3589 3631 1.078426 CCGTCTTGCCTAACCCTGG 60.078 63.158 0.00 0.00 0.00 4.45
3590 3632 1.550130 CCGTCTTGCCTAACCCTGGA 61.550 60.000 0.00 0.00 0.00 3.86
3591 3633 0.108138 CGTCTTGCCTAACCCTGGAG 60.108 60.000 0.00 0.00 0.00 3.86
3592 3634 0.984995 GTCTTGCCTAACCCTGGAGT 59.015 55.000 0.00 0.00 0.00 3.85
3593 3635 1.351350 GTCTTGCCTAACCCTGGAGTT 59.649 52.381 0.00 0.21 0.00 3.01
3594 3636 2.570302 GTCTTGCCTAACCCTGGAGTTA 59.430 50.000 0.00 1.50 0.00 2.24
3595 3637 2.838202 TCTTGCCTAACCCTGGAGTTAG 59.162 50.000 19.74 19.74 45.82 2.34
3596 3638 2.337359 TGCCTAACCCTGGAGTTAGT 57.663 50.000 22.47 1.68 45.12 2.24
3597 3639 2.185387 TGCCTAACCCTGGAGTTAGTC 58.815 52.381 22.47 15.95 45.12 2.59
3598 3640 2.185387 GCCTAACCCTGGAGTTAGTCA 58.815 52.381 22.47 2.93 45.12 3.41
3599 3641 2.570302 GCCTAACCCTGGAGTTAGTCAA 59.430 50.000 22.47 2.67 45.12 3.18
3600 3642 3.008704 GCCTAACCCTGGAGTTAGTCAAA 59.991 47.826 22.47 2.16 45.12 2.69
3601 3643 4.324331 GCCTAACCCTGGAGTTAGTCAAAT 60.324 45.833 22.47 0.00 45.12 2.32
3602 3644 5.104652 GCCTAACCCTGGAGTTAGTCAAATA 60.105 44.000 22.47 1.14 45.12 1.40
3603 3645 6.577638 GCCTAACCCTGGAGTTAGTCAAATAA 60.578 42.308 22.47 0.64 45.12 1.40
3604 3646 7.574607 CCTAACCCTGGAGTTAGTCAAATAAT 58.425 38.462 22.47 0.00 45.12 1.28
3605 3647 8.711170 CCTAACCCTGGAGTTAGTCAAATAATA 58.289 37.037 22.47 0.00 45.12 0.98
3610 3652 9.204570 CCCTGGAGTTAGTCAAATAATAATACG 57.795 37.037 0.00 0.00 0.00 3.06
3611 3653 9.760077 CCTGGAGTTAGTCAAATAATAATACGT 57.240 33.333 0.00 0.00 0.00 3.57
3773 3815 1.377229 TGGTAACGGAGGGCCAAAG 59.623 57.895 6.18 0.00 42.51 2.77
3793 3835 0.924823 ATGGATGGAAGGCAGCTTCT 59.075 50.000 0.00 0.00 34.06 2.85
3851 3896 3.517901 TGGTCCGACAGAATAGGATTGTT 59.482 43.478 0.00 0.00 36.34 2.83
4065 4401 7.888021 TCTGTGTTGGTGATATTTTCCATAGTT 59.112 33.333 0.00 0.00 0.00 2.24
4190 4526 0.107066 CAGGATGCCATGTGCTACCA 60.107 55.000 16.83 0.00 42.00 3.25
4406 5061 3.567478 AAGTATCTGGCATGGTCCTTC 57.433 47.619 0.00 0.00 0.00 3.46
4795 6164 5.104900 ACAGCAACTACCGGATTTATCTTCT 60.105 40.000 9.46 0.00 0.00 2.85
4894 6263 9.326413 CTTAATTCATAAGACCGTAGAACCAAT 57.674 33.333 0.00 0.00 43.16 3.16
4960 6329 4.141321 TGAATCTGGATCTTCAAGGGATGG 60.141 45.833 0.00 0.00 0.00 3.51
5008 6377 3.449018 AGTGAAGCTGGTAGTGATTCGAT 59.551 43.478 0.00 0.00 0.00 3.59
5009 6378 3.799420 GTGAAGCTGGTAGTGATTCGATC 59.201 47.826 0.00 0.00 0.00 3.69
5016 6385 5.453567 TGGTAGTGATTCGATCGATGATT 57.546 39.130 20.18 4.34 0.00 2.57
5093 6462 7.734942 TGTATGATGGTAATGTAGATCAAGCA 58.265 34.615 0.00 0.00 0.00 3.91
5099 6468 5.939883 TGGTAATGTAGATCAAGCATATGCC 59.060 40.000 23.96 8.39 43.38 4.40
5111 6480 0.530650 CATATGCCGGTCGAGCTGTT 60.531 55.000 13.48 1.34 0.00 3.16
5214 6583 1.102809 TCCTGCTGCACCACTTGTTG 61.103 55.000 0.00 0.00 0.00 3.33
5215 6584 1.386525 CCTGCTGCACCACTTGTTGT 61.387 55.000 0.00 0.00 0.00 3.32
5216 6585 0.457035 CTGCTGCACCACTTGTTGTT 59.543 50.000 0.00 0.00 0.00 2.83
5217 6586 0.455410 TGCTGCACCACTTGTTGTTC 59.545 50.000 0.00 0.00 0.00 3.18
5218 6587 0.455410 GCTGCACCACTTGTTGTTCA 59.545 50.000 0.00 0.00 0.00 3.18
5219 6588 1.135141 GCTGCACCACTTGTTGTTCAA 60.135 47.619 0.00 0.00 34.61 2.69
5320 6689 1.274728 AGATCCATCGGCTAGTGATGC 59.725 52.381 16.97 7.78 41.48 3.91
5368 6737 3.117701 TCTGAGGTTTCACCCAAATCACA 60.118 43.478 0.00 0.00 39.75 3.58
5497 6866 2.787473 ACATCAGAAGGATCCGCAAA 57.213 45.000 5.98 0.00 32.57 3.68
6096 7632 5.163478 GGCTGCTCATTTTTAATGGATCACT 60.163 40.000 0.00 0.00 0.00 3.41
6180 7911 7.993758 GGAAAAGGAGTAAGCAAGTAGGAATAT 59.006 37.037 0.00 0.00 0.00 1.28
6182 7913 6.426646 AGGAGTAAGCAAGTAGGAATATGG 57.573 41.667 0.00 0.00 0.00 2.74
6200 7931 9.232473 GGAATATGGTCTCAGTTTTATATTCCC 57.768 37.037 17.09 5.58 44.34 3.97
6203 7934 6.248569 TGGTCTCAGTTTTATATTCCCTCC 57.751 41.667 0.00 0.00 0.00 4.30
6204 7935 5.163343 TGGTCTCAGTTTTATATTCCCTCCG 60.163 44.000 0.00 0.00 0.00 4.63
6205 7936 5.163332 GGTCTCAGTTTTATATTCCCTCCGT 60.163 44.000 0.00 0.00 0.00 4.69
6206 7937 5.984323 GTCTCAGTTTTATATTCCCTCCGTC 59.016 44.000 0.00 0.00 0.00 4.79
6207 7938 5.070047 TCTCAGTTTTATATTCCCTCCGTCC 59.930 44.000 0.00 0.00 0.00 4.79
6208 7939 4.966805 TCAGTTTTATATTCCCTCCGTCCT 59.033 41.667 0.00 0.00 0.00 3.85
6209 7940 6.138263 TCAGTTTTATATTCCCTCCGTCCTA 58.862 40.000 0.00 0.00 0.00 2.94
6210 7941 6.612456 TCAGTTTTATATTCCCTCCGTCCTAA 59.388 38.462 0.00 0.00 0.00 2.69
6211 7942 7.126115 TCAGTTTTATATTCCCTCCGTCCTAAA 59.874 37.037 0.00 0.00 0.00 1.85
6212 7943 7.771826 CAGTTTTATATTCCCTCCGTCCTAAAA 59.228 37.037 0.00 0.00 0.00 1.52
6213 7944 8.500238 AGTTTTATATTCCCTCCGTCCTAAAAT 58.500 33.333 0.00 0.00 0.00 1.82
6214 7945 9.783081 GTTTTATATTCCCTCCGTCCTAAAATA 57.217 33.333 0.00 0.00 0.00 1.40
6217 7948 5.970501 ATTCCCTCCGTCCTAAAATAAGT 57.029 39.130 0.00 0.00 0.00 2.24
6218 7949 4.748277 TCCCTCCGTCCTAAAATAAGTG 57.252 45.455 0.00 0.00 0.00 3.16
6219 7950 4.098894 TCCCTCCGTCCTAAAATAAGTGT 58.901 43.478 0.00 0.00 0.00 3.55
6220 7951 4.161001 TCCCTCCGTCCTAAAATAAGTGTC 59.839 45.833 0.00 0.00 0.00 3.67
6221 7952 4.161754 CCCTCCGTCCTAAAATAAGTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
6222 7953 5.349809 CCTCCGTCCTAAAATAAGTGTCTC 58.650 45.833 0.00 0.00 0.00 3.36
6223 7954 5.105473 CCTCCGTCCTAAAATAAGTGTCTCA 60.105 44.000 0.00 0.00 0.00 3.27
6224 7955 6.349243 TCCGTCCTAAAATAAGTGTCTCAA 57.651 37.500 0.00 0.00 0.00 3.02
6225 7956 6.161381 TCCGTCCTAAAATAAGTGTCTCAAC 58.839 40.000 0.00 0.00 0.00 3.18
6226 7957 6.014840 TCCGTCCTAAAATAAGTGTCTCAACT 60.015 38.462 0.00 0.00 0.00 3.16
6227 7958 6.649557 CCGTCCTAAAATAAGTGTCTCAACTT 59.350 38.462 0.00 0.00 42.89 2.66
6228 7959 7.172703 CCGTCCTAAAATAAGTGTCTCAACTTT 59.827 37.037 0.00 0.00 40.77 2.66
6229 7960 8.009974 CGTCCTAAAATAAGTGTCTCAACTTTG 58.990 37.037 0.00 0.00 40.77 2.77
6230 7961 8.837389 GTCCTAAAATAAGTGTCTCAACTTTGT 58.163 33.333 0.00 0.00 40.77 2.83
6236 7967 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
6237 7968 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
6238 7969 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
6239 7970 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
6240 7971 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
6241 7972 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
6243 7974 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
6267 7998 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
6268 7999 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
6269 8000 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
6270 8001 8.988934 CAAATTTGTACTAAGCTCAAGACACTA 58.011 33.333 10.15 0.00 0.00 2.74
6271 8002 9.555727 AAATTTGTACTAAGCTCAAGACACTAA 57.444 29.630 3.19 4.72 0.00 2.24
6272 8003 9.726438 AATTTGTACTAAGCTCAAGACACTAAT 57.274 29.630 3.19 6.34 0.00 1.73
6273 8004 9.726438 ATTTGTACTAAGCTCAAGACACTAATT 57.274 29.630 3.19 0.00 0.00 1.40
6274 8005 9.555727 TTTGTACTAAGCTCAAGACACTAATTT 57.444 29.630 3.19 0.00 0.00 1.82
6275 8006 9.555727 TTGTACTAAGCTCAAGACACTAATTTT 57.444 29.630 3.19 0.00 0.00 1.82
6276 8007 8.988934 TGTACTAAGCTCAAGACACTAATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
6277 8008 7.440523 ACTAAGCTCAAGACACTAATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
6278 8009 5.712152 AAGCTCAAGACACTAATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
6279 8010 4.985538 AGCTCAAGACACTAATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
6280 8011 4.762251 AGCTCAAGACACTAATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
6281 8012 4.378459 GCTCAAGACACTAATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
6282 8013 4.069304 TCAAGACACTAATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
6283 8014 4.069304 CAAGACACTAATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
6284 8015 3.939066 AGACACTAATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
6285 8016 3.007635 GACACTAATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
6286 8017 2.290705 ACACTAATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
6287 8018 2.026636 CACTAATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
6288 8019 2.645797 ACTAATTTTGGGACGGAGGGAA 59.354 45.455 0.00 0.00 0.00 3.97
6289 8020 2.919772 AATTTTGGGACGGAGGGAAT 57.080 45.000 0.00 0.00 0.00 3.01
6306 8037 6.015940 GGAGGGAATATTAATTCAGCCACTTG 60.016 42.308 0.00 0.00 42.88 3.16
6435 8561 9.331282 AGACATTTTAAGGCAGATGATACTTAC 57.669 33.333 0.00 0.00 0.00 2.34
6514 8654 8.334263 TGTGCACTAAATTATCTGATTGTTCA 57.666 30.769 19.41 0.00 0.00 3.18
6534 8674 8.982091 TGTTCATCCCCACGATAATTTTATTA 57.018 30.769 0.00 0.00 0.00 0.98
6767 9023 3.073062 ACCTAGTGTCAATGGATATGCCC 59.927 47.826 0.00 0.00 34.97 5.36
6986 9242 3.117663 AGTGAAGGGGCACTTTTGAGTTA 60.118 43.478 2.19 0.00 46.42 2.24
6987 9243 3.253432 GTGAAGGGGCACTTTTGAGTTAG 59.747 47.826 2.19 0.00 40.21 2.34
7035 9291 9.345517 CTTTTGTGGATACTGTAAATCATTGTG 57.654 33.333 0.00 0.00 37.61 3.33
7039 9295 7.134815 GTGGATACTGTAAATCATTGTGCATC 58.865 38.462 0.00 0.00 37.61 3.91
7445 9724 9.765795 CTTCCAAGAAACTAGTAAAGAGAAAGA 57.234 33.333 0.00 0.00 0.00 2.52
7458 9821 6.532365 AAAGAGAAAGAAACTGCTAGAACG 57.468 37.500 0.00 0.00 0.00 3.95
7466 9829 4.563184 AGAAACTGCTAGAACGAATAAGCG 59.437 41.667 0.00 0.00 37.80 4.68
7564 9927 1.873270 GCAACCCCGCCGAATTCTTT 61.873 55.000 3.52 0.00 0.00 2.52
7573 9936 0.447801 CCGAATTCTTTGACAGCCGG 59.552 55.000 0.00 0.00 0.00 6.13
7808 10264 4.434520 GTTCCTCTTTGGTAAGGATCTCG 58.565 47.826 0.00 0.00 41.26 4.04
7869 10331 2.708861 TCTGGCAAGTTCTTGGTAAGGA 59.291 45.455 13.35 0.00 0.00 3.36
7916 10381 4.148128 AGTAAGCATCTCCAATGGACAG 57.852 45.455 0.00 0.00 0.00 3.51
7964 10495 0.897863 GCCATGGCAGGTTGTTGGTA 60.898 55.000 32.08 0.00 41.49 3.25
7979 10543 1.951209 TGGTAAGCATCTCCTGTGGA 58.049 50.000 0.00 0.00 0.00 4.02
8005 10569 2.805671 TCACGTTGTTGGTAAGCATCTG 59.194 45.455 0.00 0.00 0.00 2.90
8017 10581 0.180642 AGCATCTGCAGTGGAGATGG 59.819 55.000 39.28 27.12 44.80 3.51
8019 10583 0.180642 CATCTGCAGTGGAGATGGCT 59.819 55.000 34.94 12.39 42.13 4.75
8023 10587 0.321919 TGCAGTGGAGATGGCTTGTC 60.322 55.000 0.00 0.00 0.00 3.18
8024 10588 1.028868 GCAGTGGAGATGGCTTGTCC 61.029 60.000 9.38 9.38 0.00 4.02
8133 10760 0.033504 TGACTCTGGTTCGTCCTTGC 59.966 55.000 0.00 0.00 37.07 4.01
8163 10790 3.204827 CCAATGGCTCCGGCTTCG 61.205 66.667 0.00 0.00 38.73 3.79
8259 10886 1.227002 CGCCTCTTAGAAGACCGGC 60.227 63.158 0.00 10.94 40.87 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.950397 TGTTTGGCCTGTAATCACTAGG 58.050 45.455 3.32 0.00 34.67 3.02
26 27 5.948162 AGATGCCTATATAATGTTTGGCCTG 59.052 40.000 3.32 0.00 39.60 4.85
41 42 9.387681 ATTCTCCAGAATGCATGAGATGCCTAT 62.388 40.741 13.49 3.62 44.61 2.57
529 530 8.131731 CAGTCAGTTCTCTATCGATAACAATCA 58.868 37.037 6.58 0.00 30.92 2.57
587 589 7.412020 GCCGACACAAAAGAAACAAATACAAAA 60.412 33.333 0.00 0.00 0.00 2.44
600 602 1.062880 GTTTCACGCCGACACAAAAGA 59.937 47.619 0.00 0.00 0.00 2.52
741 745 7.068226 GGTGGTTGTCCAGTTTGCTATATAATT 59.932 37.037 0.00 0.00 45.24 1.40
868 873 4.036734 CAGCAATATTGGCTAATTCGGTGT 59.963 41.667 17.02 0.00 40.23 4.16
906 911 7.011389 CAGATCTTAAAACCGCATCATTCACTA 59.989 37.037 0.00 0.00 0.00 2.74
907 912 5.882557 AGATCTTAAAACCGCATCATTCACT 59.117 36.000 0.00 0.00 0.00 3.41
938 943 8.915036 AGACTAATAACCGATAGAAACACTGAT 58.085 33.333 0.00 0.00 39.76 2.90
1002 1007 4.283467 AGGCCTTTTTATTTGGACCAAGAC 59.717 41.667 7.07 0.00 0.00 3.01
1035 1040 2.888414 GCCTAGACTAGAGGACATGACC 59.112 54.545 11.27 6.05 35.99 4.02
1170 1175 2.234908 AGTCATGTTAGCTGTCCAGGAC 59.765 50.000 13.35 13.35 39.48 3.85
1179 1184 2.636830 GCATGTCCAGTCATGTTAGCT 58.363 47.619 6.72 0.00 44.68 3.32
1250 1259 4.811969 ACTGACCGGTCACATTTATGTA 57.188 40.909 33.23 8.50 39.39 2.29
1594 1627 1.512926 ACAAACACTGAAGCTAGCCG 58.487 50.000 12.13 0.00 0.00 5.52
1657 1690 5.813157 TGACAGTACAACGAACATCAGAAAA 59.187 36.000 0.00 0.00 0.00 2.29
1659 1692 4.939271 TGACAGTACAACGAACATCAGAA 58.061 39.130 0.00 0.00 0.00 3.02
1660 1693 4.577834 TGACAGTACAACGAACATCAGA 57.422 40.909 0.00 0.00 0.00 3.27
1661 1694 4.923281 TCATGACAGTACAACGAACATCAG 59.077 41.667 0.00 0.00 0.00 2.90
1662 1695 4.877282 TCATGACAGTACAACGAACATCA 58.123 39.130 0.00 0.00 0.00 3.07
1663 1696 6.090763 TCAATCATGACAGTACAACGAACATC 59.909 38.462 0.00 0.00 0.00 3.06
1664 1697 5.931724 TCAATCATGACAGTACAACGAACAT 59.068 36.000 0.00 0.00 0.00 2.71
1665 1698 5.293560 TCAATCATGACAGTACAACGAACA 58.706 37.500 0.00 0.00 0.00 3.18
1666 1699 5.839262 TCAATCATGACAGTACAACGAAC 57.161 39.130 0.00 0.00 0.00 3.95
1667 1700 6.220201 TCTTCAATCATGACAGTACAACGAA 58.780 36.000 0.00 0.00 34.61 3.85
1813 1846 8.421784 TGTGGATTAGATATCAGAAAGTACACC 58.578 37.037 5.32 0.00 0.00 4.16
1853 1886 7.949903 TTGTGATTCAAAATTGACCATCAAG 57.050 32.000 10.53 0.00 36.64 3.02
1906 1939 5.570844 GCTTTGTCTGGAATGGTTAGTCCTA 60.571 44.000 0.00 0.00 41.58 2.94
1919 1952 3.118775 ACGCTATGTATGCTTTGTCTGGA 60.119 43.478 0.00 0.00 0.00 3.86
2038 2071 8.914654 CGTGTATGAACAATGTTTTTCAATCAT 58.085 29.630 0.00 0.00 37.36 2.45
2039 2072 7.918033 ACGTGTATGAACAATGTTTTTCAATCA 59.082 29.630 0.00 0.00 37.36 2.57
2040 2073 8.207252 CACGTGTATGAACAATGTTTTTCAATC 58.793 33.333 7.58 0.00 37.36 2.67
2041 2074 7.306515 GCACGTGTATGAACAATGTTTTTCAAT 60.307 33.333 18.38 0.00 37.36 2.57
2042 2075 6.020281 GCACGTGTATGAACAATGTTTTTCAA 60.020 34.615 18.38 0.00 37.36 2.69
2043 2076 5.457148 GCACGTGTATGAACAATGTTTTTCA 59.543 36.000 18.38 0.00 37.36 2.69
2044 2077 5.385918 CGCACGTGTATGAACAATGTTTTTC 60.386 40.000 18.38 0.00 37.36 2.29
2045 2078 4.439449 CGCACGTGTATGAACAATGTTTTT 59.561 37.500 18.38 0.00 37.36 1.94
2046 2079 3.971871 CGCACGTGTATGAACAATGTTTT 59.028 39.130 18.38 0.00 37.36 2.43
2047 2080 3.550561 CGCACGTGTATGAACAATGTTT 58.449 40.909 18.38 0.00 37.36 2.83
2048 2081 2.095969 CCGCACGTGTATGAACAATGTT 60.096 45.455 18.38 0.00 37.36 2.71
2049 2082 1.463056 CCGCACGTGTATGAACAATGT 59.537 47.619 18.38 0.00 37.36 2.71
2050 2083 1.729517 TCCGCACGTGTATGAACAATG 59.270 47.619 18.38 0.00 37.36 2.82
2051 2084 2.087501 TCCGCACGTGTATGAACAAT 57.912 45.000 18.38 0.00 37.36 2.71
2052 2085 2.087501 ATCCGCACGTGTATGAACAA 57.912 45.000 18.38 0.00 37.36 2.83
2053 2086 2.943449 TATCCGCACGTGTATGAACA 57.057 45.000 18.38 1.74 0.00 3.18
2054 2087 5.404366 ACATATTATCCGCACGTGTATGAAC 59.596 40.000 18.38 0.00 0.00 3.18
2055 2088 5.404066 CACATATTATCCGCACGTGTATGAA 59.596 40.000 18.38 6.00 0.00 2.57
2056 2089 4.920927 CACATATTATCCGCACGTGTATGA 59.079 41.667 18.38 11.51 0.00 2.15
2057 2090 4.684242 ACACATATTATCCGCACGTGTATG 59.316 41.667 18.38 16.23 34.55 2.39
2058 2091 4.878439 ACACATATTATCCGCACGTGTAT 58.122 39.130 18.38 10.97 34.55 2.29
2059 2092 4.310357 ACACATATTATCCGCACGTGTA 57.690 40.909 18.38 3.51 34.55 2.90
2060 2093 3.173668 ACACATATTATCCGCACGTGT 57.826 42.857 18.38 0.00 0.00 4.49
2061 2094 3.553917 TGAACACATATTATCCGCACGTG 59.446 43.478 12.28 12.28 0.00 4.49
2062 2095 3.787785 TGAACACATATTATCCGCACGT 58.212 40.909 0.00 0.00 0.00 4.49
2063 2096 4.990543 ATGAACACATATTATCCGCACG 57.009 40.909 0.00 0.00 0.00 5.34
2064 2097 9.920826 CATTATATGAACACATATTATCCGCAC 57.079 33.333 7.80 0.00 37.99 5.34
2065 2098 9.665719 ACATTATATGAACACATATTATCCGCA 57.334 29.630 7.80 0.00 37.99 5.69
2066 2099 9.920826 CACATTATATGAACACATATTATCCGC 57.079 33.333 7.80 0.00 37.99 5.54
2074 2107 9.679661 ACTGTTTCCACATTATATGAACACATA 57.320 29.630 0.00 0.00 30.39 2.29
2075 2108 8.461222 CACTGTTTCCACATTATATGAACACAT 58.539 33.333 0.00 0.00 30.39 3.21
2076 2109 7.446931 ACACTGTTTCCACATTATATGAACACA 59.553 33.333 0.00 0.00 30.39 3.72
2077 2110 7.816640 ACACTGTTTCCACATTATATGAACAC 58.183 34.615 0.00 0.00 30.39 3.32
2078 2111 7.994425 ACACTGTTTCCACATTATATGAACA 57.006 32.000 0.00 0.00 30.39 3.18
2079 2112 9.691362 AAAACACTGTTTCCACATTATATGAAC 57.309 29.630 7.62 0.00 30.39 3.18
2080 2113 9.906660 GAAAACACTGTTTCCACATTATATGAA 57.093 29.630 7.62 0.00 32.36 2.57
2138 2171 9.416284 TCCTTTTTCCAGATTTGTACTTACTTT 57.584 29.630 0.00 0.00 0.00 2.66
2139 2172 8.990163 TCCTTTTTCCAGATTTGTACTTACTT 57.010 30.769 0.00 0.00 0.00 2.24
2140 2173 8.847196 GTTCCTTTTTCCAGATTTGTACTTACT 58.153 33.333 0.00 0.00 0.00 2.24
2141 2174 8.626526 TGTTCCTTTTTCCAGATTTGTACTTAC 58.373 33.333 0.00 0.00 0.00 2.34
2142 2175 8.754991 TGTTCCTTTTTCCAGATTTGTACTTA 57.245 30.769 0.00 0.00 0.00 2.24
2143 2176 7.654022 TGTTCCTTTTTCCAGATTTGTACTT 57.346 32.000 0.00 0.00 0.00 2.24
2144 2177 7.839680 ATGTTCCTTTTTCCAGATTTGTACT 57.160 32.000 0.00 0.00 0.00 2.73
2145 2178 9.406828 GTTATGTTCCTTTTTCCAGATTTGTAC 57.593 33.333 0.00 0.00 0.00 2.90
2146 2179 9.137459 TGTTATGTTCCTTTTTCCAGATTTGTA 57.863 29.630 0.00 0.00 0.00 2.41
2147 2180 7.926018 GTGTTATGTTCCTTTTTCCAGATTTGT 59.074 33.333 0.00 0.00 0.00 2.83
2148 2181 8.143835 AGTGTTATGTTCCTTTTTCCAGATTTG 58.856 33.333 0.00 0.00 0.00 2.32
2153 2186 7.745620 ACTAGTGTTATGTTCCTTTTTCCAG 57.254 36.000 0.00 0.00 0.00 3.86
2162 2195 8.665685 CCATGTTTTCTACTAGTGTTATGTTCC 58.334 37.037 5.39 0.00 0.00 3.62
2163 2196 8.175716 GCCATGTTTTCTACTAGTGTTATGTTC 58.824 37.037 5.39 0.00 0.00 3.18
2164 2197 7.883311 AGCCATGTTTTCTACTAGTGTTATGTT 59.117 33.333 5.39 0.00 0.00 2.71
2165 2198 7.394816 AGCCATGTTTTCTACTAGTGTTATGT 58.605 34.615 5.39 0.00 0.00 2.29
2166 2199 7.849804 AGCCATGTTTTCTACTAGTGTTATG 57.150 36.000 5.39 1.12 0.00 1.90
2259 2294 3.515286 CCTAGCCGCTCGAACCGA 61.515 66.667 0.00 0.00 0.00 4.69
2281 2316 3.386932 ACCGGGACTAATACCTGTACA 57.613 47.619 6.32 0.00 32.38 2.90
2289 2324 5.972327 TCCCATTTAAACCGGGACTAATA 57.028 39.130 19.08 1.47 44.28 0.98
2303 2338 4.098894 ACCGAGACTAAAGGTCCCATTTA 58.901 43.478 0.00 0.00 45.54 1.40
2372 2407 2.671619 CCGGTTGGTGCCACGAAT 60.672 61.111 0.00 0.00 0.00 3.34
2397 2432 2.893424 ACCGGGACTAAAGGTCTAACA 58.107 47.619 6.32 0.00 43.97 2.41
2519 2558 1.303282 GAAAAGGCGATCCAGGGGT 59.697 57.895 0.00 0.00 33.74 4.95
2689 2728 7.609760 TCTGACATCGTATGCAAAAGTTATT 57.390 32.000 0.00 0.00 0.00 1.40
2761 2803 2.971598 ATGGTCAACCGCTCCAGGG 61.972 63.158 0.00 0.00 39.43 4.45
2770 2812 2.019984 GGCAAGATCTCATGGTCAACC 58.980 52.381 0.00 0.00 0.00 3.77
2808 2850 1.966451 GTCCACTGGTCAAAGCCCG 60.966 63.158 0.00 0.00 0.00 6.13
2847 2889 1.282157 AGGTGTTTCTATGGGCTGACC 59.718 52.381 0.00 0.00 40.81 4.02
2860 2902 1.620822 GATGTTGCTCCCAGGTGTTT 58.379 50.000 0.00 0.00 0.00 2.83
2894 2936 2.053244 CTACATGGAGGGGATCTTGCT 58.947 52.381 0.00 0.00 0.00 3.91
2895 2937 2.050144 TCTACATGGAGGGGATCTTGC 58.950 52.381 4.74 0.00 0.00 4.01
2905 2947 1.065928 GCGTCGGGTCTACATGGAG 59.934 63.158 0.00 0.00 0.00 3.86
2963 3005 4.394712 GGGTGTGGCCTCCTCACG 62.395 72.222 3.32 0.00 45.56 4.35
2964 3006 4.035102 GGGGTGTGGCCTCCTCAC 62.035 72.222 3.32 8.26 44.37 3.51
2994 3036 0.674581 TTGGCATGTCTGAAGAGGCG 60.675 55.000 0.00 0.00 0.00 5.52
3022 3064 1.839191 GGGCCCTCATACATGCAGA 59.161 57.895 17.04 0.00 0.00 4.26
3319 3361 0.321298 CCTAACACAACCGGGTGGAG 60.321 60.000 26.30 18.52 43.08 3.86
3320 3362 1.055551 ACCTAACACAACCGGGTGGA 61.056 55.000 26.30 4.88 43.08 4.02
3321 3363 0.604511 GACCTAACACAACCGGGTGG 60.605 60.000 26.30 15.44 43.08 4.61
3322 3364 0.107081 TGACCTAACACAACCGGGTG 59.893 55.000 20.60 20.60 44.35 4.61
3323 3365 0.395312 CTGACCTAACACAACCGGGT 59.605 55.000 6.32 0.00 0.00 5.28
3324 3366 0.953960 GCTGACCTAACACAACCGGG 60.954 60.000 6.32 0.00 0.00 5.73
3325 3367 0.953960 GGCTGACCTAACACAACCGG 60.954 60.000 0.00 0.00 0.00 5.28
3326 3368 0.953960 GGGCTGACCTAACACAACCG 60.954 60.000 0.00 0.00 35.85 4.44
3327 3369 0.109723 TGGGCTGACCTAACACAACC 59.890 55.000 0.00 0.00 41.11 3.77
3328 3370 2.200373 ATGGGCTGACCTAACACAAC 57.800 50.000 0.00 0.00 41.11 3.32
3329 3371 3.521531 TCATATGGGCTGACCTAACACAA 59.478 43.478 0.00 0.00 41.11 3.33
3330 3372 3.111484 TCATATGGGCTGACCTAACACA 58.889 45.455 0.00 0.00 41.11 3.72
3331 3373 3.838244 TCATATGGGCTGACCTAACAC 57.162 47.619 0.00 0.00 41.11 3.32
3332 3374 3.521531 TGTTCATATGGGCTGACCTAACA 59.478 43.478 0.00 1.21 41.11 2.41
3333 3375 3.877508 GTGTTCATATGGGCTGACCTAAC 59.122 47.826 0.00 0.00 41.11 2.34
3334 3376 3.780294 AGTGTTCATATGGGCTGACCTAA 59.220 43.478 0.00 0.00 41.11 2.69
3335 3377 3.384168 AGTGTTCATATGGGCTGACCTA 58.616 45.455 0.00 0.00 41.11 3.08
3336 3378 2.200081 AGTGTTCATATGGGCTGACCT 58.800 47.619 0.00 0.00 41.11 3.85
3337 3379 2.717639 AGTGTTCATATGGGCTGACC 57.282 50.000 2.13 0.00 40.81 4.02
3338 3380 3.129287 CCAAAGTGTTCATATGGGCTGAC 59.871 47.826 2.13 0.00 0.00 3.51
3339 3381 3.010027 TCCAAAGTGTTCATATGGGCTGA 59.990 43.478 2.13 0.00 0.00 4.26
3340 3382 3.355378 TCCAAAGTGTTCATATGGGCTG 58.645 45.455 2.13 0.00 0.00 4.85
3341 3383 3.624777 CTCCAAAGTGTTCATATGGGCT 58.375 45.455 2.13 0.00 0.00 5.19
3342 3384 2.099756 GCTCCAAAGTGTTCATATGGGC 59.900 50.000 2.13 0.00 0.00 5.36
3343 3385 3.355378 TGCTCCAAAGTGTTCATATGGG 58.645 45.455 2.13 0.00 0.00 4.00
3344 3386 4.218200 TGTTGCTCCAAAGTGTTCATATGG 59.782 41.667 2.13 0.00 0.00 2.74
3345 3387 5.375417 TGTTGCTCCAAAGTGTTCATATG 57.625 39.130 0.00 0.00 0.00 1.78
3346 3388 5.126061 GGATGTTGCTCCAAAGTGTTCATAT 59.874 40.000 0.00 0.00 35.24 1.78
3347 3389 4.458989 GGATGTTGCTCCAAAGTGTTCATA 59.541 41.667 0.00 0.00 35.24 2.15
3348 3390 3.256631 GGATGTTGCTCCAAAGTGTTCAT 59.743 43.478 0.00 0.00 35.24 2.57
3349 3391 2.622942 GGATGTTGCTCCAAAGTGTTCA 59.377 45.455 0.00 0.00 35.24 3.18
3350 3392 2.350772 CGGATGTTGCTCCAAAGTGTTC 60.351 50.000 0.00 0.00 34.78 3.18
3351 3393 1.608590 CGGATGTTGCTCCAAAGTGTT 59.391 47.619 0.00 0.00 34.78 3.32
3352 3394 1.238439 CGGATGTTGCTCCAAAGTGT 58.762 50.000 0.00 0.00 34.78 3.55
3353 3395 0.523072 CCGGATGTTGCTCCAAAGTG 59.477 55.000 0.00 0.00 34.78 3.16
3354 3396 0.609131 CCCGGATGTTGCTCCAAAGT 60.609 55.000 0.73 0.00 34.78 2.66
3355 3397 1.937546 GCCCGGATGTTGCTCCAAAG 61.938 60.000 0.73 0.00 34.78 2.77
3356 3398 1.976474 GCCCGGATGTTGCTCCAAA 60.976 57.895 0.73 0.00 34.78 3.28
3357 3399 2.361104 GCCCGGATGTTGCTCCAA 60.361 61.111 0.73 0.00 34.78 3.53
3358 3400 4.424711 GGCCCGGATGTTGCTCCA 62.425 66.667 0.73 0.00 34.78 3.86
3359 3401 3.936772 TTGGCCCGGATGTTGCTCC 62.937 63.158 0.73 0.00 0.00 4.70
3360 3402 1.976474 TTTGGCCCGGATGTTGCTC 60.976 57.895 0.73 0.00 0.00 4.26
3361 3403 2.117206 TTTGGCCCGGATGTTGCT 59.883 55.556 0.73 0.00 0.00 3.91
3362 3404 2.261361 GTTTGGCCCGGATGTTGC 59.739 61.111 0.73 0.00 0.00 4.17
3363 3405 2.969827 GGTTTGGCCCGGATGTTG 59.030 61.111 0.73 0.00 0.00 3.33
3372 3414 1.187567 ATCTTGCTGTGGGTTTGGCC 61.188 55.000 0.00 0.00 0.00 5.36
3373 3415 0.244721 GATCTTGCTGTGGGTTTGGC 59.755 55.000 0.00 0.00 0.00 4.52
3374 3416 0.890683 GGATCTTGCTGTGGGTTTGG 59.109 55.000 0.00 0.00 0.00 3.28
3375 3417 0.890683 GGGATCTTGCTGTGGGTTTG 59.109 55.000 0.00 0.00 0.00 2.93
3376 3418 0.251787 GGGGATCTTGCTGTGGGTTT 60.252 55.000 0.00 0.00 0.00 3.27
3377 3419 1.142688 AGGGGATCTTGCTGTGGGTT 61.143 55.000 0.00 0.00 0.00 4.11
3378 3420 1.542375 AGGGGATCTTGCTGTGGGT 60.542 57.895 0.00 0.00 0.00 4.51
3379 3421 1.225704 GAGGGGATCTTGCTGTGGG 59.774 63.158 0.00 0.00 0.00 4.61
3380 3422 1.225704 GGAGGGGATCTTGCTGTGG 59.774 63.158 0.00 0.00 0.00 4.17
3381 3423 1.153289 CGGAGGGGATCTTGCTGTG 60.153 63.158 0.00 0.00 0.00 3.66
3382 3424 3.036429 GCGGAGGGGATCTTGCTGT 62.036 63.158 0.00 0.00 0.00 4.40
3383 3425 2.203126 GCGGAGGGGATCTTGCTG 60.203 66.667 0.00 0.00 0.00 4.41
3384 3426 3.854669 CGCGGAGGGGATCTTGCT 61.855 66.667 0.00 0.00 36.55 3.91
3400 3442 2.021931 GTACGCGTCGGGTCTACG 59.978 66.667 18.63 1.96 43.12 3.51
3401 3443 2.021931 CGTACGCGTCGGGTCTAC 59.978 66.667 18.63 11.38 0.00 2.59
3464 3506 4.373116 CACGTCTCCGGGGTGTGG 62.373 72.222 18.11 2.48 38.78 4.17
3465 3507 3.612681 ACACGTCTCCGGGGTGTG 61.613 66.667 22.39 22.39 43.48 3.82
3466 3508 3.612681 CACACGTCTCCGGGGTGT 61.613 66.667 0.00 8.44 43.48 4.16
3477 3519 3.865929 CTGAAGAGGCGGCACACGT 62.866 63.158 13.08 0.00 46.52 4.49
3479 3521 2.029844 GTCTGAAGAGGCGGCACAC 61.030 63.158 13.08 4.19 0.00 3.82
3480 3522 1.830587 ATGTCTGAAGAGGCGGCACA 61.831 55.000 13.08 4.97 0.00 4.57
3481 3523 1.078848 ATGTCTGAAGAGGCGGCAC 60.079 57.895 13.08 4.59 0.00 5.01
3482 3524 1.078918 CATGTCTGAAGAGGCGGCA 60.079 57.895 13.08 0.00 0.00 5.69
3483 3525 2.467826 GCATGTCTGAAGAGGCGGC 61.468 63.158 0.00 0.00 0.00 6.53
3484 3526 1.817099 GGCATGTCTGAAGAGGCGG 60.817 63.158 0.00 0.00 0.00 6.13
3485 3527 0.809241 GAGGCATGTCTGAAGAGGCG 60.809 60.000 3.48 0.00 0.00 5.52
3486 3528 0.463474 GGAGGCATGTCTGAAGAGGC 60.463 60.000 3.48 0.00 0.00 4.70
3487 3529 1.138661 GAGGAGGCATGTCTGAAGAGG 59.861 57.143 3.48 0.00 0.00 3.69
3488 3530 1.829849 TGAGGAGGCATGTCTGAAGAG 59.170 52.381 3.48 0.00 0.00 2.85
3489 3531 1.552337 GTGAGGAGGCATGTCTGAAGA 59.448 52.381 3.48 0.00 0.00 2.87
3490 3532 1.406614 GGTGAGGAGGCATGTCTGAAG 60.407 57.143 3.48 0.00 0.00 3.02
3491 3533 0.615331 GGTGAGGAGGCATGTCTGAA 59.385 55.000 3.48 0.00 0.00 3.02
3492 3534 1.267574 GGGTGAGGAGGCATGTCTGA 61.268 60.000 3.48 0.00 0.00 3.27
3493 3535 1.222936 GGGTGAGGAGGCATGTCTG 59.777 63.158 3.48 0.00 0.00 3.51
3494 3536 1.997874 GGGGTGAGGAGGCATGTCT 60.998 63.158 0.00 0.00 0.00 3.41
3495 3537 2.592308 GGGGTGAGGAGGCATGTC 59.408 66.667 0.00 0.00 0.00 3.06
3496 3538 3.017581 GGGGGTGAGGAGGCATGT 61.018 66.667 0.00 0.00 0.00 3.21
3511 3553 1.071471 GTCCTCATACATGCGGGGG 59.929 63.158 0.00 0.00 33.55 5.40
3512 3554 1.071471 GGTCCTCATACATGCGGGG 59.929 63.158 0.00 0.00 33.55 5.73
3513 3555 1.071471 GGGTCCTCATACATGCGGG 59.929 63.158 0.00 0.00 33.55 6.13
3514 3556 1.300931 CGGGTCCTCATACATGCGG 60.301 63.158 0.00 0.00 34.02 5.69
3515 3557 1.300931 CCGGGTCCTCATACATGCG 60.301 63.158 0.00 0.00 0.00 4.73
3516 3558 0.532862 CACCGGGTCCTCATACATGC 60.533 60.000 6.32 0.00 0.00 4.06
3517 3559 0.532862 GCACCGGGTCCTCATACATG 60.533 60.000 6.32 0.00 0.00 3.21
3518 3560 1.830145 GCACCGGGTCCTCATACAT 59.170 57.895 6.32 0.00 0.00 2.29
3519 3561 2.717044 CGCACCGGGTCCTCATACA 61.717 63.158 6.32 0.00 0.00 2.29
3520 3562 2.106332 CGCACCGGGTCCTCATAC 59.894 66.667 6.32 0.00 0.00 2.39
3521 3563 2.043752 TCGCACCGGGTCCTCATA 60.044 61.111 6.32 0.00 0.00 2.15
3522 3564 3.771160 GTCGCACCGGGTCCTCAT 61.771 66.667 6.32 0.00 0.00 2.90
3537 3579 3.499737 CAATGCCACCGGAGCGTC 61.500 66.667 9.46 0.00 0.00 5.19
3539 3581 3.673956 TACCAATGCCACCGGAGCG 62.674 63.158 9.46 0.09 0.00 5.03
3540 3582 1.377987 TTACCAATGCCACCGGAGC 60.378 57.895 9.46 11.93 0.00 4.70
3541 3583 1.029947 GGTTACCAATGCCACCGGAG 61.030 60.000 9.46 0.00 0.00 4.63
3542 3584 1.001887 GGTTACCAATGCCACCGGA 60.002 57.895 9.46 0.00 0.00 5.14
3543 3585 2.049767 GGGTTACCAATGCCACCGG 61.050 63.158 2.98 0.00 36.50 5.28
3544 3586 2.049767 GGGGTTACCAATGCCACCG 61.050 63.158 2.98 0.00 39.85 4.94
3545 3587 1.684391 GGGGGTTACCAATGCCACC 60.684 63.158 2.98 0.00 42.91 4.61
3546 3588 2.049767 CGGGGGTTACCAATGCCAC 61.050 63.158 2.98 0.00 42.91 5.01
3547 3589 2.357056 CGGGGGTTACCAATGCCA 59.643 61.111 2.98 0.00 42.91 4.92
3548 3590 2.441348 CCGGGGGTTACCAATGCC 60.441 66.667 2.98 0.00 42.91 4.40
3549 3591 2.441348 CCCGGGGGTTACCAATGC 60.441 66.667 14.71 0.00 42.91 3.56
3550 3592 2.277404 CCCCGGGGGTTACCAATG 59.723 66.667 34.01 0.70 42.91 2.82
3551 3593 3.746436 GCCCCGGGGGTTACCAAT 61.746 66.667 40.58 0.00 46.51 3.16
3567 3609 2.437895 GTTAGGCAAGACGGGGGC 60.438 66.667 0.00 0.00 0.00 5.80
3568 3610 2.271173 GGTTAGGCAAGACGGGGG 59.729 66.667 0.00 0.00 0.00 5.40
3569 3611 2.271173 GGGTTAGGCAAGACGGGG 59.729 66.667 0.00 0.00 0.00 5.73
3570 3612 1.078426 CAGGGTTAGGCAAGACGGG 60.078 63.158 0.00 0.00 0.00 5.28
3571 3613 1.078426 CCAGGGTTAGGCAAGACGG 60.078 63.158 0.00 0.00 0.00 4.79
3572 3614 0.108138 CTCCAGGGTTAGGCAAGACG 60.108 60.000 0.00 0.00 0.00 4.18
3573 3615 0.984995 ACTCCAGGGTTAGGCAAGAC 59.015 55.000 0.00 0.00 0.00 3.01
3574 3616 1.742308 AACTCCAGGGTTAGGCAAGA 58.258 50.000 0.00 0.00 0.00 3.02
3575 3617 3.268023 CTAACTCCAGGGTTAGGCAAG 57.732 52.381 9.23 0.00 42.67 4.01
3584 3626 9.204570 CGTATTATTATTTGACTAACTCCAGGG 57.795 37.037 0.00 0.00 0.00 4.45
3585 3627 9.760077 ACGTATTATTATTTGACTAACTCCAGG 57.240 33.333 0.00 0.00 0.00 4.45
3614 3656 8.292444 TGCATCAGCTATACCTTTATGTTTTT 57.708 30.769 0.00 0.00 42.74 1.94
3615 3657 7.880160 TGCATCAGCTATACCTTTATGTTTT 57.120 32.000 0.00 0.00 42.74 2.43
3616 3658 7.502120 CTGCATCAGCTATACCTTTATGTTT 57.498 36.000 0.00 0.00 42.74 2.83
3632 3674 1.085091 GTGAAGTGAGGCTGCATCAG 58.915 55.000 18.14 0.00 34.71 2.90
3633 3675 0.321919 GGTGAAGTGAGGCTGCATCA 60.322 55.000 13.56 13.56 33.87 3.07
3634 3676 0.321919 TGGTGAAGTGAGGCTGCATC 60.322 55.000 7.45 7.45 34.71 3.91
3676 3718 9.716556 AAGATCTACCGGACCATAATCTATATT 57.283 33.333 9.46 0.00 0.00 1.28
3685 3727 4.795469 TGTACAAGATCTACCGGACCATA 58.205 43.478 9.46 0.00 0.00 2.74
3773 3815 1.133853 AGAAGCTGCCTTCCATCCATC 60.134 52.381 0.00 0.00 46.97 3.51
3793 3835 1.417517 ACCATGTCTCTGCAGTGACAA 59.582 47.619 39.82 28.20 47.00 3.18
3804 3846 4.045104 CACGAATAGCTGTACCATGTCTC 58.955 47.826 0.00 0.00 0.00 3.36
4190 4526 9.491675 TGTAAATCATGAAAACTGCATTCAAAT 57.508 25.926 0.00 0.90 39.98 2.32
4421 5414 3.625649 AGGATCTGAAGCTTTGTCTCC 57.374 47.619 0.00 5.72 0.00 3.71
4894 6263 3.027412 GAGGAATCAGCTACACCTCTGA 58.973 50.000 16.15 0.00 42.41 3.27
4960 6329 3.118629 TGAATCATACACAGAGCCACTCC 60.119 47.826 0.00 0.00 0.00 3.85
5008 6377 4.149511 TGAAGGTTATGGCAATCATCGA 57.850 40.909 0.00 0.00 37.30 3.59
5009 6378 5.039480 GATGAAGGTTATGGCAATCATCG 57.961 43.478 0.00 0.00 35.40 3.84
5016 6385 3.055458 TCTTGACGATGAAGGTTATGGCA 60.055 43.478 0.00 0.00 0.00 4.92
5093 6462 0.530650 CAACAGCTCGACCGGCATAT 60.531 55.000 0.00 0.00 0.00 1.78
5099 6468 1.428448 TTTCATCAACAGCTCGACCG 58.572 50.000 0.00 0.00 0.00 4.79
5111 6480 6.605995 AGATGAGAGATGCCAAATTTTCATCA 59.394 34.615 22.34 12.26 41.13 3.07
5214 6583 5.168569 TGATGTCTGTACCGAATCTTGAAC 58.831 41.667 0.00 0.00 0.00 3.18
5215 6584 5.400066 TGATGTCTGTACCGAATCTTGAA 57.600 39.130 0.00 0.00 0.00 2.69
5216 6585 5.105351 ACATGATGTCTGTACCGAATCTTGA 60.105 40.000 19.24 0.00 0.00 3.02
5217 6586 5.006068 CACATGATGTCTGTACCGAATCTTG 59.994 44.000 0.00 15.19 0.00 3.02
5218 6587 5.111989 CACATGATGTCTGTACCGAATCTT 58.888 41.667 0.00 0.00 0.00 2.40
5219 6588 4.686972 CACATGATGTCTGTACCGAATCT 58.313 43.478 0.00 0.00 0.00 2.40
5320 6689 5.923204 AGAAGGCATATAGAACACTCAAGG 58.077 41.667 0.00 0.00 0.00 3.61
5368 6737 6.591750 ACAAGTCTACACATACTAGCAAGT 57.408 37.500 0.00 0.00 39.91 3.16
5497 6866 5.419542 ACAGACAATGTAACGATGCATACT 58.580 37.500 0.00 0.00 41.60 2.12
5511 6880 9.467258 AGAAAAACAATCACAATACAGACAATG 57.533 29.630 0.00 0.00 0.00 2.82
5534 6903 7.095607 GCTGAGAAATAAGTTGACGAAGAAGAA 60.096 37.037 0.00 0.00 0.00 2.52
5535 6904 6.366332 GCTGAGAAATAAGTTGACGAAGAAGA 59.634 38.462 0.00 0.00 0.00 2.87
6096 7632 9.117183 CATCATGATGAAAATACTCCTCTTTGA 57.883 33.333 28.37 0.00 41.20 2.69
6155 7864 8.831550 CATATTCCTACTTGCTTACTCCTTTTC 58.168 37.037 0.00 0.00 0.00 2.29
6180 7911 5.163343 CGGAGGGAATATAAAACTGAGACCA 60.163 44.000 0.00 0.00 0.00 4.02
6182 7913 5.915175 ACGGAGGGAATATAAAACTGAGAC 58.085 41.667 0.00 0.00 0.00 3.36
6197 7928 4.098894 ACACTTATTTTAGGACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
6198 7929 4.161754 AGACACTTATTTTAGGACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
6199 7930 5.105473 TGAGACACTTATTTTAGGACGGAGG 60.105 44.000 0.00 0.00 0.00 4.30
6200 7931 5.962433 TGAGACACTTATTTTAGGACGGAG 58.038 41.667 0.00 0.00 0.00 4.63
6201 7932 5.988310 TGAGACACTTATTTTAGGACGGA 57.012 39.130 0.00 0.00 0.00 4.69
6202 7933 6.164176 AGTTGAGACACTTATTTTAGGACGG 58.836 40.000 0.00 0.00 0.00 4.79
6203 7934 7.653767 AAGTTGAGACACTTATTTTAGGACG 57.346 36.000 0.00 0.00 35.10 4.79
6204 7935 8.837389 ACAAAGTTGAGACACTTATTTTAGGAC 58.163 33.333 0.00 0.00 35.87 3.85
6205 7936 8.974060 ACAAAGTTGAGACACTTATTTTAGGA 57.026 30.769 0.00 0.00 35.87 2.94
6210 7941 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
6211 7942 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
6212 7943 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
6213 7944 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
6214 7945 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
6215 7946 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
6216 7947 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
6217 7948 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
6218 7949 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
6242 7973 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
6243 7974 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
6244 7975 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
6245 7976 9.555727 TTAGTGTCTTGAGCTTAGTACAAATTT 57.444 29.630 0.00 0.00 0.00 1.82
6246 7977 9.726438 ATTAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
6247 7978 9.726438 AATTAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
6248 7979 9.555727 AAATTAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
6249 7980 9.555727 AAAATTAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
6250 7981 8.988934 CAAAATTAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
6251 7982 8.443937 CCAAAATTAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
6252 7983 7.606456 CCCAAAATTAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
6253 7984 6.431234 CCCAAAATTAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
6254 7985 6.655003 TCCCAAAATTAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
6255 7986 6.430000 GTCCCAAAATTAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
6256 7987 5.241728 GTCCCAAAATTAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
6257 7988 4.762251 GTCCCAAAATTAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
6258 7989 4.378459 CGTCCCAAAATTAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
6259 7990 4.154195 CCGTCCCAAAATTAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
6260 7991 4.069304 CCGTCCCAAAATTAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
6261 7992 4.069304 TCCGTCCCAAAATTAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
6262 7993 4.324267 CTCCGTCCCAAAATTAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
6263 7994 3.307480 CCTCCGTCCCAAAATTAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
6264 7995 3.007635 CCTCCGTCCCAAAATTAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
6265 7996 2.290705 CCCTCCGTCCCAAAATTAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
6266 7997 2.026636 TCCCTCCGTCCCAAAATTAGTG 60.027 50.000 0.00 0.00 0.00 2.74
6267 7998 2.271777 TCCCTCCGTCCCAAAATTAGT 58.728 47.619 0.00 0.00 0.00 2.24
6268 7999 3.359695 TTCCCTCCGTCCCAAAATTAG 57.640 47.619 0.00 0.00 0.00 1.73
6269 8000 5.656549 ATATTCCCTCCGTCCCAAAATTA 57.343 39.130 0.00 0.00 0.00 1.40
6270 8001 2.919772 ATTCCCTCCGTCCCAAAATT 57.080 45.000 0.00 0.00 0.00 1.82
6271 8002 4.536295 AATATTCCCTCCGTCCCAAAAT 57.464 40.909 0.00 0.00 0.00 1.82
6272 8003 5.453866 TTAATATTCCCTCCGTCCCAAAA 57.546 39.130 0.00 0.00 0.00 2.44
6273 8004 5.656549 ATTAATATTCCCTCCGTCCCAAA 57.343 39.130 0.00 0.00 0.00 3.28
6274 8005 5.132985 TGAATTAATATTCCCTCCGTCCCAA 59.867 40.000 0.00 0.00 39.56 4.12
6275 8006 4.661240 TGAATTAATATTCCCTCCGTCCCA 59.339 41.667 0.00 0.00 39.56 4.37
6276 8007 5.237236 TGAATTAATATTCCCTCCGTCCC 57.763 43.478 0.00 0.00 39.56 4.46
6277 8008 4.695928 GCTGAATTAATATTCCCTCCGTCC 59.304 45.833 0.00 0.00 39.56 4.79
6278 8009 4.695928 GGCTGAATTAATATTCCCTCCGTC 59.304 45.833 0.00 0.00 39.56 4.79
6279 8010 4.104102 TGGCTGAATTAATATTCCCTCCGT 59.896 41.667 0.00 0.00 39.56 4.69
6280 8011 4.455877 GTGGCTGAATTAATATTCCCTCCG 59.544 45.833 0.00 0.00 39.56 4.63
6281 8012 5.635120 AGTGGCTGAATTAATATTCCCTCC 58.365 41.667 0.00 0.00 39.56 4.30
6282 8013 6.772716 TCAAGTGGCTGAATTAATATTCCCTC 59.227 38.462 0.00 0.00 39.56 4.30
6283 8014 6.672593 TCAAGTGGCTGAATTAATATTCCCT 58.327 36.000 0.00 0.00 39.56 4.20
6284 8015 6.959639 TCAAGTGGCTGAATTAATATTCCC 57.040 37.500 0.00 0.00 39.56 3.97
6285 8016 7.771183 TGTTCAAGTGGCTGAATTAATATTCC 58.229 34.615 0.00 0.00 39.56 3.01
6286 8017 9.638239 TTTGTTCAAGTGGCTGAATTAATATTC 57.362 29.630 0.00 0.00 37.63 1.75
6287 8018 9.995003 TTTTGTTCAAGTGGCTGAATTAATATT 57.005 25.926 0.00 0.00 37.63 1.28
6288 8019 9.995003 TTTTTGTTCAAGTGGCTGAATTAATAT 57.005 25.926 0.00 0.00 37.63 1.28
6289 8020 9.995003 ATTTTTGTTCAAGTGGCTGAATTAATA 57.005 25.926 0.00 0.00 37.63 0.98
6372 8103 6.790285 AAATGCAAACAAAAGATGCCTAAG 57.210 33.333 0.00 0.00 39.31 2.18
6534 8674 1.915489 TGATGTGGGCTCAGGTTATGT 59.085 47.619 0.00 0.00 0.00 2.29
6767 9023 1.406219 CGTCGATGCTGAAGGTCACG 61.406 60.000 0.00 0.00 0.00 4.35
6939 9195 2.205074 GATCGCCACGATTCTGTTCAT 58.795 47.619 3.74 0.00 47.00 2.57
6986 9242 4.089408 AGCATTTGAACCAAATTTGCCT 57.911 36.364 12.92 1.29 40.60 4.75
6987 9243 4.996758 AGTAGCATTTGAACCAAATTTGCC 59.003 37.500 12.92 4.81 40.60 4.52
7035 9291 1.268896 CCTCGGCATTCACAATGATGC 60.269 52.381 0.25 0.00 41.46 3.91
7205 9472 1.004628 ACATTACCATCCAGCAGCACA 59.995 47.619 0.00 0.00 0.00 4.57
7445 9724 4.091509 CACGCTTATTCGTTCTAGCAGTTT 59.908 41.667 0.00 0.00 41.21 2.66
7458 9821 4.226761 CCTGGTTTTTGACACGCTTATTC 58.773 43.478 0.00 0.00 0.00 1.75
7466 9829 5.310451 TGGATACTACCTGGTTTTTGACAC 58.690 41.667 3.84 0.00 37.61 3.67
7808 10264 3.129988 CCAAGAACTTGCCATCTCCATTC 59.870 47.826 8.81 0.00 39.16 2.67
7916 10381 1.388547 TGCTCACCAACAAGTTGACC 58.611 50.000 10.54 0.00 42.93 4.02
7979 10543 2.806244 GCTTACCAACAACGTGACATCT 59.194 45.455 0.00 0.00 0.00 2.90
7980 10544 2.546368 TGCTTACCAACAACGTGACATC 59.454 45.455 0.00 0.00 0.00 3.06
7987 10551 1.535028 TGCAGATGCTTACCAACAACG 59.465 47.619 6.35 0.00 42.66 4.10
8005 10569 1.028868 GGACAAGCCATCTCCACTGC 61.029 60.000 0.00 0.00 36.34 4.40
8017 10581 2.357009 CAGATGCTTACCATGGACAAGC 59.643 50.000 31.67 31.67 43.92 4.01
8019 10583 2.290832 TGCAGATGCTTACCATGGACAA 60.291 45.455 21.47 10.97 42.66 3.18
8023 10587 1.674441 CACTGCAGATGCTTACCATGG 59.326 52.381 23.35 11.19 42.66 3.66
8024 10588 1.674441 CCACTGCAGATGCTTACCATG 59.326 52.381 23.35 3.50 42.66 3.66
8025 10589 2.020694 GCCACTGCAGATGCTTACCAT 61.021 52.381 23.35 0.00 42.66 3.55
8133 10760 1.404391 GCCATTGGAGCACATCTTCAG 59.596 52.381 6.95 0.00 30.44 3.02
8163 10790 0.749454 ATGTTTGCGATGGAGGAGGC 60.749 55.000 0.00 0.00 0.00 4.70


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.