Multiple sequence alignment - TraesCS7B01G260300

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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 TraesCS7B01G260300 chr7B 100.000 7069 0 0 1 7069 480428258 480435326 0.000000e+00 13055.0
1 TraesCS7B01G260300 chr7B 85.496 917 89 22 5405 6282 191209974 191209063 0.000000e+00 917.0
2 TraesCS7B01G260300 chr7B 80.020 991 149 34 250 1200 195993151 195992170 0.000000e+00 688.0
3 TraesCS7B01G260300 chr7B 96.992 266 7 1 6805 7069 263174240 263173975 5.030000e-121 446.0
4 TraesCS7B01G260300 chr7B 83.469 490 43 17 5379 5853 530666560 530667026 8.480000e-114 422.0
5 TraesCS7B01G260300 chr7B 89.506 324 27 5 6749 7069 195987184 195986865 3.070000e-108 403.0
6 TraesCS7B01G260300 chr7B 87.143 280 22 8 6275 6551 530667439 530667707 8.910000e-79 305.0
7 TraesCS7B01G260300 chr7B 91.566 166 14 0 6642 6807 191208661 191208496 5.520000e-56 230.0
8 TraesCS7B01G260300 chr2B 96.366 5807 147 27 772 6551 451264669 451270438 0.000000e+00 9496.0
9 TraesCS7B01G260300 chr2B 92.830 795 46 4 1 795 705308700 705307917 0.000000e+00 1142.0
10 TraesCS7B01G260300 chr2B 90.727 798 58 7 1 795 194713852 194714636 0.000000e+00 1050.0
11 TraesCS7B01G260300 chr2B 93.177 469 32 0 778 1246 487736404 487736872 0.000000e+00 689.0
12 TraesCS7B01G260300 chr2B 85.918 632 49 13 5686 6282 410276809 410277435 7.730000e-179 638.0
13 TraesCS7B01G260300 chr2B 84.043 470 50 14 2466 2910 290333472 290333941 5.070000e-116 429.0
14 TraesCS7B01G260300 chr2B 96.498 257 9 0 6549 6805 451270408 451270664 6.550000e-115 425.0
15 TraesCS7B01G260300 chr2B 94.595 74 4 0 2059 2132 183539399 183539326 1.610000e-21 115.0
16 TraesCS7B01G260300 chr2B 82.857 105 8 4 2362 2466 290333357 290333451 1.260000e-12 86.1
17 TraesCS7B01G260300 chr5A 95.995 4844 166 9 1730 6551 425056548 425051711 0.000000e+00 7845.0
18 TraesCS7B01G260300 chr5A 90.161 620 43 4 777 1379 425060728 425060110 0.000000e+00 791.0
19 TraesCS7B01G260300 chr5A 93.519 324 19 1 1415 1738 425060109 425059788 1.380000e-131 481.0
20 TraesCS7B01G260300 chr5A 95.489 266 11 1 6549 6814 425051741 425051477 2.360000e-114 424.0
21 TraesCS7B01G260300 chr5A 81.627 332 42 12 2809 3126 404992417 404992743 2.530000e-64 257.0
22 TraesCS7B01G260300 chr3A 96.087 3501 121 10 2566 6057 446325910 446322417 0.000000e+00 5692.0
23 TraesCS7B01G260300 chr3A 95.540 426 17 2 6127 6551 446322416 446321992 0.000000e+00 680.0
24 TraesCS7B01G260300 chr3A 96.109 257 9 1 6549 6805 446322022 446321767 1.100000e-112 418.0
25 TraesCS7B01G260300 chr1B 93.931 2274 116 9 1755 4014 453034502 453032237 0.000000e+00 3415.0
26 TraesCS7B01G260300 chr1B 91.486 2079 132 13 4512 6551 453031810 453029738 0.000000e+00 2817.0
27 TraesCS7B01G260300 chr1B 93.208 795 43 3 1 795 476400090 476400873 0.000000e+00 1158.0
28 TraesCS7B01G260300 chr1B 92.875 786 42 5 1 783 574508689 574509463 0.000000e+00 1129.0
29 TraesCS7B01G260300 chr1B 89.698 796 67 6 1 795 537267975 537268756 0.000000e+00 1002.0
30 TraesCS7B01G260300 chr1B 86.125 800 101 8 1 795 454931854 454931060 0.000000e+00 854.0
31 TraesCS7B01G260300 chr1B 90.114 526 49 3 4502 5026 72969945 72970468 0.000000e+00 680.0
32 TraesCS7B01G260300 chr1B 89.924 526 50 3 4502 5026 73000481 73001004 0.000000e+00 675.0
33 TraesCS7B01G260300 chr1B 89.544 526 52 3 4502 5026 72982041 72982564 0.000000e+00 664.0
34 TraesCS7B01G260300 chr1B 89.544 526 52 3 4502 5026 72994148 72994671 0.000000e+00 664.0
35 TraesCS7B01G260300 chr1B 89.163 526 54 3 4502 5026 73015946 73016469 0.000000e+00 652.0
36 TraesCS7B01G260300 chr1B 82.517 755 119 11 264 1011 296606877 296606129 0.000000e+00 651.0
37 TraesCS7B01G260300 chr1B 89.150 341 32 5 6732 7069 345521860 345521522 3.050000e-113 420.0
38 TraesCS7B01G260300 chr1B 83.610 482 41 14 2466 2910 496663737 496663257 1.100000e-112 418.0
39 TraesCS7B01G260300 chr1B 91.011 267 22 1 4000 4264 453032072 453031806 6.740000e-95 359.0
40 TraesCS7B01G260300 chr1B 89.531 277 26 3 5041 5316 72994891 72995165 1.460000e-91 348.0
41 TraesCS7B01G260300 chr1B 88.809 277 28 3 5041 5316 73001224 73001498 3.160000e-88 337.0
42 TraesCS7B01G260300 chr1B 79.903 413 39 16 1510 1895 496664494 496664099 5.440000e-66 263.0
43 TraesCS7B01G260300 chr1B 81.056 322 51 5 2809 3128 40257886 40258199 1.520000e-61 248.0
44 TraesCS7B01G260300 chr1B 87.264 212 20 3 1842 2052 496664093 496663888 1.190000e-57 235.0
45 TraesCS7B01G260300 chr1B 91.228 171 12 3 6647 6814 163778113 163778283 5.520000e-56 230.0
46 TraesCS7B01G260300 chr1B 94.595 148 8 0 6637 6784 453029653 453029506 5.520000e-56 230.0
47 TraesCS7B01G260300 chr1B 93.902 82 5 0 6555 6636 453029762 453029681 2.680000e-24 124.0
48 TraesCS7B01G260300 chr1B 92.593 81 6 0 1583 1663 453034600 453034520 4.480000e-22 117.0
49 TraesCS7B01G260300 chr1B 96.154 52 2 0 3630 3681 453032572 453032521 1.260000e-12 86.1
50 TraesCS7B01G260300 chr1B 97.222 36 1 0 2360 2395 496663892 496663857 2.130000e-05 62.1
51 TraesCS7B01G260300 chr5B 84.496 2122 253 42 2958 5026 463003836 463005934 0.000000e+00 2026.0
52 TraesCS7B01G260300 chr5B 92.211 796 47 6 1 795 108280852 108280071 0.000000e+00 1112.0
53 TraesCS7B01G260300 chr5B 90.506 790 59 10 1 788 536944237 536945012 0.000000e+00 1029.0
54 TraesCS7B01G260300 chr5B 92.952 454 31 1 777 1230 339620174 339620626 0.000000e+00 660.0
55 TraesCS7B01G260300 chr5B 85.976 492 49 9 5379 5853 115861164 115860676 6.330000e-140 508.0
56 TraesCS7B01G260300 chr5B 92.398 342 25 1 6729 7069 277766775 277767116 2.960000e-133 486.0
57 TraesCS7B01G260300 chr5B 91.975 324 24 1 4973 5296 191165074 191164753 3.010000e-123 453.0
58 TraesCS7B01G260300 chr5B 83.576 481 43 12 2466 2910 386864132 386864612 1.100000e-112 418.0
59 TraesCS7B01G260300 chr5B 85.423 343 34 8 5041 5381 463006192 463006520 6.790000e-90 342.0
60 TraesCS7B01G260300 chr5B 88.583 254 26 3 5324 5577 191164752 191164502 8.910000e-79 305.0
61 TraesCS7B01G260300 chr5B 79.661 413 40 16 1510 1895 386863375 386863770 2.530000e-64 257.0
62 TraesCS7B01G260300 chr5B 87.736 212 19 3 1842 2052 386863776 386863981 2.550000e-59 241.0
63 TraesCS7B01G260300 chr5B 85.714 154 12 4 5595 5739 191164276 191164124 3.410000e-33 154.0
64 TraesCS7B01G260300 chr5B 94.595 74 4 0 2059 2132 672545742 672545669 1.610000e-21 115.0
65 TraesCS7B01G260300 chr5B 91.304 46 2 2 2350 2395 386863969 386864012 2.130000e-05 62.1
66 TraesCS7B01G260300 chr5D 85.002 2007 219 42 2958 4908 364245630 364247610 0.000000e+00 1964.0
67 TraesCS7B01G260300 chr5D 83.884 1694 202 36 3270 4907 351147 352825 0.000000e+00 1550.0
68 TraesCS7B01G260300 chr5D 86.367 1247 129 24 2989 4209 348002 349233 0.000000e+00 1323.0
69 TraesCS7B01G260300 chr5D 84.927 962 110 24 3270 4209 350192 351140 0.000000e+00 941.0
70 TraesCS7B01G260300 chr5D 84.703 961 111 22 3270 4209 349240 350185 0.000000e+00 928.0
71 TraesCS7B01G260300 chr5D 90.379 343 28 3 5041 5381 353026 353365 5.030000e-121 446.0
72 TraesCS7B01G260300 chr5D 89.655 232 21 2 2958 3187 564868020 564868250 6.940000e-75 292.0
73 TraesCS7B01G260300 chr5D 88.793 232 23 2 2958 3187 409715325 409715555 1.500000e-71 281.0
74 TraesCS7B01G260300 chr5D 90.196 51 3 2 3631 3679 364246351 364246401 1.650000e-06 65.8
75 TraesCS7B01G260300 chr7A 84.704 2007 235 45 2963 4917 99586934 99584948 0.000000e+00 1940.0
76 TraesCS7B01G260300 chr7A 89.474 95 7 3 6553 6644 171753234 171753140 4.480000e-22 117.0
77 TraesCS7B01G260300 chr7A 89.474 95 7 3 6553 6644 171867519 171867425 4.480000e-22 117.0
78 TraesCS7B01G260300 chr6A 84.247 2006 219 47 2958 4908 162188479 162190442 0.000000e+00 1864.0
79 TraesCS7B01G260300 chr6B 92.956 795 46 2 1 795 64468214 64467430 0.000000e+00 1149.0
80 TraesCS7B01G260300 chr6B 92.956 795 46 2 1 795 614502714 614501930 0.000000e+00 1149.0
81 TraesCS7B01G260300 chr6B 90.201 796 68 5 1 795 636338374 636337588 0.000000e+00 1029.0
82 TraesCS7B01G260300 chr6B 85.385 910 89 21 5405 6275 480266158 480267062 0.000000e+00 904.0
83 TraesCS7B01G260300 chr6B 96.992 266 6 2 6805 7069 526784182 526783918 5.030000e-121 446.0
84 TraesCS7B01G260300 chr6B 88.809 277 28 3 5041 5316 22890419 22890693 3.160000e-88 337.0
85 TraesCS7B01G260300 chr6B 86.477 281 32 5 6275 6550 480267096 480267375 3.200000e-78 303.0
86 TraesCS7B01G260300 chr6B 82.857 175 24 4 1684 1853 250334107 250333934 1.230000e-32 152.0
87 TraesCS7B01G260300 chr6B 92.683 41 3 0 2092 2132 599816902 599816942 7.660000e-05 60.2
88 TraesCS7B01G260300 chr3B 88.049 979 75 11 5324 6273 618465671 618464706 0.000000e+00 1122.0
89 TraesCS7B01G260300 chr3B 92.075 795 53 2 1 795 500203445 500204229 0.000000e+00 1110.0
90 TraesCS7B01G260300 chr3B 93.117 741 44 6 4557 5296 618466406 618465672 0.000000e+00 1079.0
91 TraesCS7B01G260300 chr3B 93.313 658 39 2 4202 4859 158635285 158634633 0.000000e+00 966.0
92 TraesCS7B01G260300 chr3B 90.155 711 57 4 4326 5025 414809731 414810439 0.000000e+00 913.0
93 TraesCS7B01G260300 chr3B 93.933 478 29 0 769 1246 631925511 631925034 0.000000e+00 723.0
94 TraesCS7B01G260300 chr3B 92.964 469 33 0 778 1246 631818430 631817962 0.000000e+00 684.0
95 TraesCS7B01G260300 chr3B 96.981 265 6 2 6806 7069 364740141 364739878 1.810000e-120 444.0
96 TraesCS7B01G260300 chr3B 96.981 265 7 1 6806 7069 395574681 395574945 1.810000e-120 444.0
97 TraesCS7B01G260300 chr3B 93.220 295 17 3 6776 7069 33678796 33678504 1.410000e-116 431.0
98 TraesCS7B01G260300 chr3B 91.342 231 19 1 6278 6507 618464670 618464440 1.480000e-81 315.0
99 TraesCS7B01G260300 chr3B 90.058 171 16 1 6637 6807 414811162 414811331 3.320000e-53 220.0
100 TraesCS7B01G260300 chrUn 90.213 797 63 7 1 795 77658924 77658141 0.000000e+00 1026.0
101 TraesCS7B01G260300 chrUn 88.362 232 24 3 2958 3187 70175178 70174948 6.980000e-70 276.0
102 TraesCS7B01G260300 chrUn 89.474 95 7 3 6553 6644 247470991 247471085 4.480000e-22 117.0
103 TraesCS7B01G260300 chrUn 90.909 88 6 2 6553 6638 371710536 371710449 4.480000e-22 117.0
104 TraesCS7B01G260300 chrUn 90.217 92 6 3 6553 6642 447274286 447274376 4.480000e-22 117.0
105 TraesCS7B01G260300 chr4B 89.724 798 69 7 1 795 167286223 167285436 0.000000e+00 1007.0
106 TraesCS7B01G260300 chr4B 89.335 797 61 10 1 795 130326963 130327737 0.000000e+00 979.0
107 TraesCS7B01G260300 chr4B 90.114 526 49 3 4502 5026 414709760 414709237 0.000000e+00 680.0
108 TraesCS7B01G260300 chr4B 84.929 491 54 8 5379 5852 242909976 242909489 4.960000e-131 479.0
109 TraesCS7B01G260300 chr4B 96.992 266 7 1 6805 7069 26677739 26678004 5.030000e-121 446.0
110 TraesCS7B01G260300 chr4B 89.170 277 27 3 5041 5316 414709018 414708744 6.790000e-90 342.0
111 TraesCS7B01G260300 chr4A 78.837 997 164 33 3 979 481751809 481750840 4.650000e-176 628.0
112 TraesCS7B01G260300 chr4A 79.627 643 109 21 258 887 138487682 138487049 6.510000e-120 442.0
113 TraesCS7B01G260300 chr1D 86.885 488 47 10 5379 5853 93832091 93832574 1.350000e-146 531.0
114 TraesCS7B01G260300 chr1D 86.631 374 32 3 5917 6272 93832601 93832974 1.430000e-106 398.0
115 TraesCS7B01G260300 chr6D 87.740 416 29 6 5877 6275 425060239 425060649 3.860000e-127 466.0
116 TraesCS7B01G260300 chr6D 88.530 279 30 2 6275 6551 425060683 425060961 3.160000e-88 337.0
117 TraesCS7B01G260300 chr6D 94.118 170 10 0 6637 6806 425061059 425061228 7.030000e-65 259.0
118 TraesCS7B01G260300 chr2A 90.253 277 20 5 6279 6550 347871987 347872261 8.720000e-94 355.0
119 TraesCS7B01G260300 chr2A 91.765 170 14 0 6637 6806 347872359 347872528 3.300000e-58 237.0
120 TraesCS7B01G260300 chr2A 86.500 200 27 0 2059 2258 21184450 21184649 3.320000e-53 220.0
121 TraesCS7B01G260300 chr7D 83.912 317 47 4 1510 1824 414417276 414417590 4.140000e-77 300.0
122 TraesCS7B01G260300 chr7D 89.224 232 22 2 2958 3187 575649379 575649609 3.230000e-73 287.0
123 TraesCS7B01G260300 chr7D 83.019 318 48 6 1510 1824 468083336 468083650 4.170000e-72 283.0
124 TraesCS7B01G260300 chr3D 83.281 317 49 4 1510 1824 189335205 189335519 8.970000e-74 289.0
125 TraesCS7B01G260300 chr3D 89.224 232 22 2 2958 3187 419635368 419635138 3.230000e-73 287.0
126 TraesCS7B01G260300 chr3D 87.500 232 22 2 2958 3187 355118881 355118655 1.960000e-65 261.0
127 TraesCS7B01G260300 chr4D 82.663 323 52 4 1510 1830 270640617 270640297 4.170000e-72 283.0


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 TraesCS7B01G260300 chr7B 480428258 480435326 7068 False 13055.000000 13055 100.000000 1 7069 1 chr7B.!!$F1 7068
1 TraesCS7B01G260300 chr7B 195992170 195993151 981 True 688.000000 688 80.020000 250 1200 1 chr7B.!!$R2 950
2 TraesCS7B01G260300 chr7B 191208496 191209974 1478 True 573.500000 917 88.531000 5405 6807 2 chr7B.!!$R4 1402
3 TraesCS7B01G260300 chr7B 530666560 530667707 1147 False 363.500000 422 85.306000 5379 6551 2 chr7B.!!$F2 1172
4 TraesCS7B01G260300 chr2B 451264669 451270664 5995 False 4960.500000 9496 96.432000 772 6805 2 chr2B.!!$F5 6033
5 TraesCS7B01G260300 chr2B 705307917 705308700 783 True 1142.000000 1142 92.830000 1 795 1 chr2B.!!$R2 794
6 TraesCS7B01G260300 chr2B 194713852 194714636 784 False 1050.000000 1050 90.727000 1 795 1 chr2B.!!$F1 794
7 TraesCS7B01G260300 chr2B 410276809 410277435 626 False 638.000000 638 85.918000 5686 6282 1 chr2B.!!$F2 596
8 TraesCS7B01G260300 chr2B 290333357 290333941 584 False 257.550000 429 83.450000 2362 2910 2 chr2B.!!$F4 548
9 TraesCS7B01G260300 chr5A 425051477 425060728 9251 True 2385.250000 7845 93.791000 777 6814 4 chr5A.!!$R1 6037
10 TraesCS7B01G260300 chr3A 446321767 446325910 4143 True 2263.333333 5692 95.912000 2566 6805 3 chr3A.!!$R1 4239
11 TraesCS7B01G260300 chr1B 476400090 476400873 783 False 1158.000000 1158 93.208000 1 795 1 chr1B.!!$F6 794
12 TraesCS7B01G260300 chr1B 574508689 574509463 774 False 1129.000000 1129 92.875000 1 783 1 chr1B.!!$F8 782
13 TraesCS7B01G260300 chr1B 453029506 453034600 5094 True 1021.157143 3415 93.381714 1583 6784 7 chr1B.!!$R4 5201
14 TraesCS7B01G260300 chr1B 537267975 537268756 781 False 1002.000000 1002 89.698000 1 795 1 chr1B.!!$F7 794
15 TraesCS7B01G260300 chr1B 454931060 454931854 794 True 854.000000 854 86.125000 1 795 1 chr1B.!!$R3 794
16 TraesCS7B01G260300 chr1B 72969945 72970468 523 False 680.000000 680 90.114000 4502 5026 1 chr1B.!!$F2 524
17 TraesCS7B01G260300 chr1B 72982041 72982564 523 False 664.000000 664 89.544000 4502 5026 1 chr1B.!!$F3 524
18 TraesCS7B01G260300 chr1B 73015946 73016469 523 False 652.000000 652 89.163000 4502 5026 1 chr1B.!!$F4 524
19 TraesCS7B01G260300 chr1B 296606129 296606877 748 True 651.000000 651 82.517000 264 1011 1 chr1B.!!$R1 747
20 TraesCS7B01G260300 chr1B 72994148 72995165 1017 False 506.000000 664 89.537500 4502 5316 2 chr1B.!!$F9 814
21 TraesCS7B01G260300 chr1B 73000481 73001498 1017 False 506.000000 675 89.366500 4502 5316 2 chr1B.!!$F10 814
22 TraesCS7B01G260300 chr1B 496663257 496664494 1237 True 244.525000 418 86.999750 1510 2910 4 chr1B.!!$R5 1400
23 TraesCS7B01G260300 chr5B 463003836 463006520 2684 False 1184.000000 2026 84.959500 2958 5381 2 chr5B.!!$F5 2423
24 TraesCS7B01G260300 chr5B 108280071 108280852 781 True 1112.000000 1112 92.211000 1 795 1 chr5B.!!$R1 794
25 TraesCS7B01G260300 chr5B 536944237 536945012 775 False 1029.000000 1029 90.506000 1 788 1 chr5B.!!$F3 787
26 TraesCS7B01G260300 chr5B 191164124 191165074 950 True 304.000000 453 88.757333 4973 5739 3 chr5B.!!$R4 766
27 TraesCS7B01G260300 chr5B 386863375 386864612 1237 False 244.525000 418 85.569250 1510 2910 4 chr5B.!!$F4 1400
28 TraesCS7B01G260300 chr5D 348002 353365 5363 False 1037.600000 1550 86.052000 2989 5381 5 chr5D.!!$F3 2392
29 TraesCS7B01G260300 chr5D 364245630 364247610 1980 False 1014.900000 1964 87.599000 2958 4908 2 chr5D.!!$F4 1950
30 TraesCS7B01G260300 chr7A 99584948 99586934 1986 True 1940.000000 1940 84.704000 2963 4917 1 chr7A.!!$R1 1954
31 TraesCS7B01G260300 chr6A 162188479 162190442 1963 False 1864.000000 1864 84.247000 2958 4908 1 chr6A.!!$F1 1950
32 TraesCS7B01G260300 chr6B 64467430 64468214 784 True 1149.000000 1149 92.956000 1 795 1 chr6B.!!$R1 794
33 TraesCS7B01G260300 chr6B 614501930 614502714 784 True 1149.000000 1149 92.956000 1 795 1 chr6B.!!$R4 794
34 TraesCS7B01G260300 chr6B 636337588 636338374 786 True 1029.000000 1029 90.201000 1 795 1 chr6B.!!$R5 794
35 TraesCS7B01G260300 chr6B 480266158 480267375 1217 False 603.500000 904 85.931000 5405 6550 2 chr6B.!!$F3 1145
36 TraesCS7B01G260300 chr3B 500203445 500204229 784 False 1110.000000 1110 92.075000 1 795 1 chr3B.!!$F2 794
37 TraesCS7B01G260300 chr3B 158634633 158635285 652 True 966.000000 966 93.313000 4202 4859 1 chr3B.!!$R2 657
38 TraesCS7B01G260300 chr3B 618464440 618466406 1966 True 838.666667 1122 90.836000 4557 6507 3 chr3B.!!$R6 1950
39 TraesCS7B01G260300 chr3B 414809731 414811331 1600 False 566.500000 913 90.106500 4326 6807 2 chr3B.!!$F3 2481
40 TraesCS7B01G260300 chrUn 77658141 77658924 783 True 1026.000000 1026 90.213000 1 795 1 chrUn.!!$R2 794
41 TraesCS7B01G260300 chr4B 167285436 167286223 787 True 1007.000000 1007 89.724000 1 795 1 chr4B.!!$R1 794
42 TraesCS7B01G260300 chr4B 130326963 130327737 774 False 979.000000 979 89.335000 1 795 1 chr4B.!!$F2 794
43 TraesCS7B01G260300 chr4B 414708744 414709760 1016 True 511.000000 680 89.642000 4502 5316 2 chr4B.!!$R3 814
44 TraesCS7B01G260300 chr4A 481750840 481751809 969 True 628.000000 628 78.837000 3 979 1 chr4A.!!$R2 976
45 TraesCS7B01G260300 chr4A 138487049 138487682 633 True 442.000000 442 79.627000 258 887 1 chr4A.!!$R1 629
46 TraesCS7B01G260300 chr1D 93832091 93832974 883 False 464.500000 531 86.758000 5379 6272 2 chr1D.!!$F1 893
47 TraesCS7B01G260300 chr6D 425060239 425061228 989 False 354.000000 466 90.129333 5877 6806 3 chr6D.!!$F1 929
48 TraesCS7B01G260300 chr2A 347871987 347872528 541 False 296.000000 355 91.009000 6279 6806 2 chr2A.!!$F2 527

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
994 1026 2.806198 CGCCCATGTGCAAAAGCG 60.806 61.111 0.00 5.11 37.39 4.68 F
1423 1503 0.962356 GCAGGGACTTGGTGGATGTG 60.962 60.000 0.00 0.00 34.60 3.21 F
1873 5297 1.347378 TGGAGTAGCAGATGTGTGCAA 59.653 47.619 4.91 0.00 46.60 4.08 F
3389 6920 0.811281 AAGCATTTACCTGAAGGCGC 59.189 50.000 0.00 0.00 40.90 6.53 F
3834 10283 1.001378 GTCTGTTGCACGCCTTCATTT 60.001 47.619 0.00 0.00 0.00 2.32 F
4147 10782 1.068741 GTCTATGTAGCCGTCCTTGGG 59.931 57.143 0.00 0.00 0.00 4.12 F
4307 10970 1.463674 CAACTGGTTGTGCCCCTATC 58.536 55.000 5.41 0.00 35.92 2.08 F
4412 11075 4.811969 TTCTCTATTCAACGCCCAGTTA 57.188 40.909 0.00 0.00 42.02 2.24 F
4559 11235 5.819379 TGATCTACCTGATGCATTTCTTCAC 59.181 40.000 0.00 0.00 35.14 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 5770 1.484653 ACATGTAGGCATAGCACCGAA 59.515 47.619 0.00 0.00 33.30 4.30 R
3366 6897 3.191371 CGCCTTCAGGTAAATGCTTCTTT 59.809 43.478 0.00 0.00 37.57 2.52 R
3495 8936 1.063266 TGTCAAGGATAAATGGGGGCC 60.063 52.381 0.00 0.00 0.00 5.80 R
5322 12278 1.130054 TGACAGCCTGCCTTTCCTCT 61.130 55.000 0.00 0.00 0.00 3.69 R
5637 12830 8.712285 ATAGTTCGAATCAGAAATAAAACCGA 57.288 30.769 0.00 0.00 34.91 4.69 R
5853 13069 2.058798 GAACGAACATGCTCTTGTCGA 58.941 47.619 0.00 0.00 0.00 4.20 R
5935 13159 4.466370 TGACATAGACACCTAGGAGTTTGG 59.534 45.833 17.98 8.59 31.59 3.28 R
6029 13258 5.710513 TTGAACAATCAGCAGCACTTTAT 57.289 34.783 0.00 0.00 36.78 1.40 R
6537 13830 1.140252 ACTCCCCGCACATATGGTAAC 59.860 52.381 7.80 0.00 0.00 2.50 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
303 316 8.263854 TCTATCCTTACTTTTATGCCTAGCTT 57.736 34.615 0.00 0.00 0.00 3.74
445 467 7.276658 TGTTTTAATTAGTGTTTGTGCCAAGTG 59.723 33.333 0.00 0.00 0.00 3.16
446 468 6.701145 TTAATTAGTGTTTGTGCCAAGTGA 57.299 33.333 0.00 0.00 0.00 3.41
457 479 3.279434 GTGCCAAGTGAAACCTATAGGG 58.721 50.000 22.91 5.28 37.80 3.53
556 581 4.503734 CACAGAAACGTGATTTTGCATTGT 59.496 37.500 0.00 0.00 39.34 2.71
715 743 7.654923 TGTGTTGTTTGCTTATTTTGATGCATA 59.345 29.630 0.00 0.00 35.27 3.14
913 944 7.590279 ACTTGGTAATATTGTTTTTCACCTCG 58.410 34.615 0.00 0.00 0.00 4.63
942 974 5.643379 TTTTTCTATCCAATGACTGGTGC 57.357 39.130 0.00 0.00 46.51 5.01
994 1026 2.806198 CGCCCATGTGCAAAAGCG 60.806 61.111 0.00 5.11 37.39 4.68
1118 1183 2.042435 CGCTCCTCCTTCCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
1246 1326 4.421554 CCTGCCTCCTCCCTCCCA 62.422 72.222 0.00 0.00 0.00 4.37
1296 1376 4.680237 CTTCACCACAGCCGCCGA 62.680 66.667 0.00 0.00 0.00 5.54
1310 1390 3.851184 CCGATCCCCTCCCTCCCT 61.851 72.222 0.00 0.00 0.00 4.20
1381 1461 4.867599 CCGGGTAGAAGGTCGCGC 62.868 72.222 0.00 0.00 38.37 6.86
1423 1503 0.962356 GCAGGGACTTGGTGGATGTG 60.962 60.000 0.00 0.00 34.60 3.21
1637 1717 4.082523 CGACATCAGCGGGTGGGT 62.083 66.667 7.42 6.26 0.00 4.51
1825 5189 2.869801 TCGTTCTTTTGCTCGTGATGTT 59.130 40.909 0.00 0.00 0.00 2.71
1832 5196 6.734137 TCTTTTGCTCGTGATGTTATTTTGT 58.266 32.000 0.00 0.00 0.00 2.83
1873 5297 1.347378 TGGAGTAGCAGATGTGTGCAA 59.653 47.619 4.91 0.00 46.60 4.08
1898 5323 6.315891 AGTTTACCTAGAGCTTAGTAGACACG 59.684 42.308 0.00 0.00 0.00 4.49
2092 5517 6.051717 GTGTGTCTCCATCTGCTAATACATT 58.948 40.000 0.00 0.00 0.00 2.71
2148 5577 8.877864 ATCTGAAGTGGGTTAATCAAACAATA 57.122 30.769 0.00 0.00 40.08 1.90
2259 5688 4.832248 CAGGTGATTGAAGGTTAGCTGTA 58.168 43.478 0.00 0.00 33.53 2.74
2341 5770 3.084039 CTGTGGTTGAGGCATGTTATGT 58.916 45.455 0.00 0.00 0.00 2.29
3056 6577 4.381185 GGAAAGTGTCTTTGGTCGGTTTTT 60.381 41.667 0.00 0.00 0.00 1.94
3238 6759 6.093495 TGCTATTGCCTGTTAATACTTCACAC 59.907 38.462 0.00 0.00 38.71 3.82
3291 6812 7.290110 TCATCGATTATCTTCTGCCTTTCTA 57.710 36.000 0.00 0.00 0.00 2.10
3389 6920 0.811281 AAGCATTTACCTGAAGGCGC 59.189 50.000 0.00 0.00 40.90 6.53
3495 8936 5.664457 TCAGACTTGGTGCTAGATATGTTG 58.336 41.667 0.00 0.00 0.00 3.33
3592 9036 4.965814 ACAGATGCATCTCGGTCATTTAT 58.034 39.130 26.44 0.00 34.22 1.40
3784 10233 9.342308 CACTTTAATATATCTTCTTGGAAGCCA 57.658 33.333 2.74 0.00 0.00 4.75
3834 10283 1.001378 GTCTGTTGCACGCCTTCATTT 60.001 47.619 0.00 0.00 0.00 2.32
3890 10339 3.441572 AGAATTTTCAGAGGCATGGTTCG 59.558 43.478 0.00 0.00 0.00 3.95
4014 10467 6.414987 GCAAGGCGTCTATAATCATTTTGTTC 59.585 38.462 0.00 0.00 0.00 3.18
4147 10782 1.068741 GTCTATGTAGCCGTCCTTGGG 59.931 57.143 0.00 0.00 0.00 4.12
4228 10871 8.559536 CAAATTTGTTCTCCTATATGTATGCGT 58.440 33.333 10.15 0.00 0.00 5.24
4231 10874 5.538118 TGTTCTCCTATATGTATGCGTTGG 58.462 41.667 0.00 0.00 0.00 3.77
4307 10970 1.463674 CAACTGGTTGTGCCCCTATC 58.536 55.000 5.41 0.00 35.92 2.08
4412 11075 4.811969 TTCTCTATTCAACGCCCAGTTA 57.188 40.909 0.00 0.00 42.02 2.24
4534 11210 9.330063 CTGATACACATTACAATTATGGACTGT 57.670 33.333 0.00 0.00 0.00 3.55
4539 11215 8.677300 ACACATTACAATTATGGACTGTTGATC 58.323 33.333 0.00 0.00 0.00 2.92
4559 11235 5.819379 TGATCTACCTGATGCATTTCTTCAC 59.181 40.000 0.00 0.00 35.14 3.18
4827 11506 9.661563 TGTTTATACTTGAATCAAAGGACGTAT 57.338 29.630 8.98 8.98 0.00 3.06
5853 13069 6.641314 CCGCTGTAAGATCGATAATAACTTGT 59.359 38.462 0.00 0.00 34.07 3.16
6361 13650 9.877178 AGTATACTTCATTTTTCATCTTCGAGT 57.123 29.630 0.00 0.00 0.00 4.18
6370 13659 9.611284 CATTTTTCATCTTCGAGTGTTTGAATA 57.389 29.630 0.00 0.00 0.00 1.75
6508 13801 0.593518 TTCAACGCGCACATGGTTTG 60.594 50.000 5.73 0.00 0.00 2.93
6532 13825 1.295423 GGGCTCTGCGTGGAGTTAA 59.705 57.895 8.17 0.00 35.89 2.01
6533 13826 0.321298 GGGCTCTGCGTGGAGTTAAA 60.321 55.000 8.17 0.00 35.89 1.52
6534 13827 1.679032 GGGCTCTGCGTGGAGTTAAAT 60.679 52.381 8.17 0.00 35.89 1.40
6535 13828 2.084546 GGCTCTGCGTGGAGTTAAATT 58.915 47.619 8.17 0.00 35.89 1.82
6536 13829 2.488153 GGCTCTGCGTGGAGTTAAATTT 59.512 45.455 0.00 0.00 35.89 1.82
6537 13830 3.492313 GCTCTGCGTGGAGTTAAATTTG 58.508 45.455 0.00 0.00 35.89 2.32
6538 13831 3.058224 GCTCTGCGTGGAGTTAAATTTGT 60.058 43.478 0.00 0.00 35.89 2.83
6539 13832 4.556699 GCTCTGCGTGGAGTTAAATTTGTT 60.557 41.667 0.00 0.00 35.89 2.83
6540 13833 5.334569 GCTCTGCGTGGAGTTAAATTTGTTA 60.335 40.000 0.00 0.00 35.89 2.41
6541 13834 5.992729 TCTGCGTGGAGTTAAATTTGTTAC 58.007 37.500 0.00 0.00 0.00 2.50
6542 13835 5.049267 TCTGCGTGGAGTTAAATTTGTTACC 60.049 40.000 0.00 0.62 0.00 2.85
6543 13836 4.579340 TGCGTGGAGTTAAATTTGTTACCA 59.421 37.500 0.00 3.23 0.00 3.25
6544 13837 5.241949 TGCGTGGAGTTAAATTTGTTACCAT 59.758 36.000 0.00 0.00 0.00 3.55
6545 13838 6.430308 TGCGTGGAGTTAAATTTGTTACCATA 59.570 34.615 0.00 0.00 0.00 2.74
6546 13839 7.121463 TGCGTGGAGTTAAATTTGTTACCATAT 59.879 33.333 0.00 0.00 0.00 1.78
6547 13840 7.431084 GCGTGGAGTTAAATTTGTTACCATATG 59.569 37.037 0.00 0.00 0.00 1.78
6548 13841 8.455682 CGTGGAGTTAAATTTGTTACCATATGT 58.544 33.333 0.00 0.00 0.00 2.29
6549 13842 9.567848 GTGGAGTTAAATTTGTTACCATATGTG 57.432 33.333 0.00 0.00 0.00 3.21
6550 13843 8.247562 TGGAGTTAAATTTGTTACCATATGTGC 58.752 33.333 0.00 0.00 0.00 4.57
6551 13844 7.431084 GGAGTTAAATTTGTTACCATATGTGCG 59.569 37.037 0.00 0.00 0.00 5.34
6552 13845 7.254852 AGTTAAATTTGTTACCATATGTGCGG 58.745 34.615 0.00 0.00 0.00 5.69
6553 13846 4.647424 AATTTGTTACCATATGTGCGGG 57.353 40.909 1.24 0.00 0.00 6.13
6554 13847 2.045561 TTGTTACCATATGTGCGGGG 57.954 50.000 1.24 0.00 0.00 5.73
6555 13848 1.205055 TGTTACCATATGTGCGGGGA 58.795 50.000 1.24 0.00 0.00 4.81
6556 13849 1.140052 TGTTACCATATGTGCGGGGAG 59.860 52.381 1.24 0.00 0.00 4.30
6557 13850 1.140252 GTTACCATATGTGCGGGGAGT 59.860 52.381 1.24 0.00 0.00 3.85
6558 13851 1.502690 TACCATATGTGCGGGGAGTT 58.497 50.000 1.24 0.00 0.00 3.01
6559 13852 1.502690 ACCATATGTGCGGGGAGTTA 58.497 50.000 1.24 0.00 0.00 2.24
6744 14080 5.735285 TGTCCATGCAAAATGAAACCATA 57.265 34.783 0.00 0.00 0.00 2.74
6810 14146 4.032104 CGCAACGGGTCAACTAGTATAAAC 59.968 45.833 0.00 0.00 0.00 2.01
6813 14149 6.073112 GCAACGGGTCAACTAGTATAAACAAA 60.073 38.462 0.00 0.00 0.00 2.83
6814 14150 7.515643 CAACGGGTCAACTAGTATAAACAAAG 58.484 38.462 0.00 0.00 0.00 2.77
6815 14151 6.996509 ACGGGTCAACTAGTATAAACAAAGA 58.003 36.000 0.00 0.00 0.00 2.52
6816 14152 7.444299 ACGGGTCAACTAGTATAAACAAAGAA 58.556 34.615 0.00 0.00 0.00 2.52
6817 14153 8.098912 ACGGGTCAACTAGTATAAACAAAGAAT 58.901 33.333 0.00 0.00 0.00 2.40
6818 14154 8.388103 CGGGTCAACTAGTATAAACAAAGAATG 58.612 37.037 0.00 0.00 0.00 2.67
6819 14155 9.444600 GGGTCAACTAGTATAAACAAAGAATGA 57.555 33.333 0.00 0.00 0.00 2.57
6834 14170 8.324163 ACAAAGAATGAGTTCATTACAGTACC 57.676 34.615 7.31 0.00 45.72 3.34
6835 14171 8.157476 ACAAAGAATGAGTTCATTACAGTACCT 58.843 33.333 7.31 0.00 45.72 3.08
6836 14172 9.003658 CAAAGAATGAGTTCATTACAGTACCTT 57.996 33.333 7.31 2.99 45.72 3.50
6839 14175 9.823647 AGAATGAGTTCATTACAGTACCTTATG 57.176 33.333 7.31 0.00 45.72 1.90
6840 14176 9.601217 GAATGAGTTCATTACAGTACCTTATGT 57.399 33.333 7.31 0.00 45.72 2.29
6841 14177 8.948631 ATGAGTTCATTACAGTACCTTATGTG 57.051 34.615 0.00 0.00 31.37 3.21
6842 14178 7.327975 TGAGTTCATTACAGTACCTTATGTGG 58.672 38.462 0.00 0.00 0.00 4.17
6843 14179 7.038587 TGAGTTCATTACAGTACCTTATGTGGT 60.039 37.037 0.00 0.00 43.66 4.16
6844 14180 7.103641 AGTTCATTACAGTACCTTATGTGGTG 58.896 38.462 0.00 0.00 41.05 4.17
6845 14181 5.984725 TCATTACAGTACCTTATGTGGTGG 58.015 41.667 0.00 0.00 41.05 4.61
6846 14182 5.486063 TCATTACAGTACCTTATGTGGTGGT 59.514 40.000 0.00 0.00 41.05 4.16
6847 14183 5.829062 TTACAGTACCTTATGTGGTGGTT 57.171 39.130 0.00 0.00 41.05 3.67
6848 14184 4.717279 ACAGTACCTTATGTGGTGGTTT 57.283 40.909 0.00 0.00 41.05 3.27
6849 14185 5.056553 ACAGTACCTTATGTGGTGGTTTT 57.943 39.130 0.00 0.00 41.05 2.43
6850 14186 5.067954 ACAGTACCTTATGTGGTGGTTTTC 58.932 41.667 0.00 0.00 41.05 2.29
6851 14187 5.163131 ACAGTACCTTATGTGGTGGTTTTCT 60.163 40.000 0.00 0.00 41.05 2.52
6852 14188 5.768164 CAGTACCTTATGTGGTGGTTTTCTT 59.232 40.000 0.00 0.00 41.05 2.52
6853 14189 6.264518 CAGTACCTTATGTGGTGGTTTTCTTT 59.735 38.462 0.00 0.00 41.05 2.52
6854 14190 6.837048 AGTACCTTATGTGGTGGTTTTCTTTT 59.163 34.615 0.00 0.00 41.05 2.27
6855 14191 6.156748 ACCTTATGTGGTGGTTTTCTTTTC 57.843 37.500 0.00 0.00 39.17 2.29
6856 14192 5.897250 ACCTTATGTGGTGGTTTTCTTTTCT 59.103 36.000 0.00 0.00 39.17 2.52
6857 14193 6.382859 ACCTTATGTGGTGGTTTTCTTTTCTT 59.617 34.615 0.00 0.00 39.17 2.52
6858 14194 7.093068 ACCTTATGTGGTGGTTTTCTTTTCTTT 60.093 33.333 0.00 0.00 39.17 2.52
6859 14195 7.438160 CCTTATGTGGTGGTTTTCTTTTCTTTC 59.562 37.037 0.00 0.00 0.00 2.62
6860 14196 5.730296 TGTGGTGGTTTTCTTTTCTTTCA 57.270 34.783 0.00 0.00 0.00 2.69
6861 14197 5.474825 TGTGGTGGTTTTCTTTTCTTTCAC 58.525 37.500 0.00 0.00 0.00 3.18
6862 14198 5.245075 TGTGGTGGTTTTCTTTTCTTTCACT 59.755 36.000 0.00 0.00 0.00 3.41
6863 14199 6.434652 TGTGGTGGTTTTCTTTTCTTTCACTA 59.565 34.615 0.00 0.00 0.00 2.74
6864 14200 7.039644 TGTGGTGGTTTTCTTTTCTTTCACTAA 60.040 33.333 0.00 0.00 0.00 2.24
6865 14201 7.274904 GTGGTGGTTTTCTTTTCTTTCACTAAC 59.725 37.037 0.00 0.00 0.00 2.34
6866 14202 6.471198 GGTGGTTTTCTTTTCTTTCACTAACG 59.529 38.462 0.00 0.00 0.00 3.18
6867 14203 6.471198 GTGGTTTTCTTTTCTTTCACTAACGG 59.529 38.462 0.00 0.00 0.00 4.44
6868 14204 6.374894 TGGTTTTCTTTTCTTTCACTAACGGA 59.625 34.615 0.00 0.00 0.00 4.69
6869 14205 6.910972 GGTTTTCTTTTCTTTCACTAACGGAG 59.089 38.462 0.00 0.00 0.00 4.63
6870 14206 5.668558 TTCTTTTCTTTCACTAACGGAGC 57.331 39.130 0.00 0.00 0.00 4.70
6871 14207 4.957296 TCTTTTCTTTCACTAACGGAGCT 58.043 39.130 0.00 0.00 0.00 4.09
6872 14208 5.365619 TCTTTTCTTTCACTAACGGAGCTT 58.634 37.500 0.00 0.00 0.00 3.74
6873 14209 6.518493 TCTTTTCTTTCACTAACGGAGCTTA 58.482 36.000 0.00 0.00 0.00 3.09
6874 14210 7.159372 TCTTTTCTTTCACTAACGGAGCTTAT 58.841 34.615 0.00 0.00 0.00 1.73
6875 14211 6.721571 TTTCTTTCACTAACGGAGCTTATG 57.278 37.500 0.00 0.00 0.00 1.90
6876 14212 5.654603 TCTTTCACTAACGGAGCTTATGA 57.345 39.130 0.00 0.00 0.00 2.15
6877 14213 5.651530 TCTTTCACTAACGGAGCTTATGAG 58.348 41.667 0.00 0.00 0.00 2.90
6878 14214 5.417894 TCTTTCACTAACGGAGCTTATGAGA 59.582 40.000 0.00 0.00 0.00 3.27
6879 14215 5.854010 TTCACTAACGGAGCTTATGAGAT 57.146 39.130 0.00 0.00 0.00 2.75
6880 14216 5.854010 TCACTAACGGAGCTTATGAGATT 57.146 39.130 0.00 0.00 0.00 2.40
6881 14217 6.222038 TCACTAACGGAGCTTATGAGATTT 57.778 37.500 0.00 0.00 0.00 2.17
6882 14218 6.273825 TCACTAACGGAGCTTATGAGATTTC 58.726 40.000 0.00 0.00 0.00 2.17
6883 14219 5.463724 CACTAACGGAGCTTATGAGATTTCC 59.536 44.000 0.00 0.00 0.00 3.13
6884 14220 4.762289 AACGGAGCTTATGAGATTTCCT 57.238 40.909 0.00 0.00 0.00 3.36
6885 14221 4.065321 ACGGAGCTTATGAGATTTCCTG 57.935 45.455 0.00 0.00 0.00 3.86
6886 14222 3.452627 ACGGAGCTTATGAGATTTCCTGT 59.547 43.478 0.00 0.00 0.00 4.00
6887 14223 4.080863 ACGGAGCTTATGAGATTTCCTGTT 60.081 41.667 0.00 0.00 0.00 3.16
6888 14224 4.272018 CGGAGCTTATGAGATTTCCTGTTG 59.728 45.833 0.00 0.00 0.00 3.33
6889 14225 5.431765 GGAGCTTATGAGATTTCCTGTTGA 58.568 41.667 0.00 0.00 0.00 3.18
6890 14226 5.526846 GGAGCTTATGAGATTTCCTGTTGAG 59.473 44.000 0.00 0.00 0.00 3.02
6891 14227 6.059787 AGCTTATGAGATTTCCTGTTGAGT 57.940 37.500 0.00 0.00 0.00 3.41
6892 14228 6.479884 AGCTTATGAGATTTCCTGTTGAGTT 58.520 36.000 0.00 0.00 0.00 3.01
6893 14229 6.944862 AGCTTATGAGATTTCCTGTTGAGTTT 59.055 34.615 0.00 0.00 0.00 2.66
6894 14230 7.449704 AGCTTATGAGATTTCCTGTTGAGTTTT 59.550 33.333 0.00 0.00 0.00 2.43
6895 14231 7.540055 GCTTATGAGATTTCCTGTTGAGTTTTG 59.460 37.037 0.00 0.00 0.00 2.44
6896 14232 6.966534 ATGAGATTTCCTGTTGAGTTTTGT 57.033 33.333 0.00 0.00 0.00 2.83
6897 14233 6.135290 TGAGATTTCCTGTTGAGTTTTGTG 57.865 37.500 0.00 0.00 0.00 3.33
6898 14234 5.652014 TGAGATTTCCTGTTGAGTTTTGTGT 59.348 36.000 0.00 0.00 0.00 3.72
6899 14235 6.152661 TGAGATTTCCTGTTGAGTTTTGTGTT 59.847 34.615 0.00 0.00 0.00 3.32
6900 14236 6.332630 AGATTTCCTGTTGAGTTTTGTGTTG 58.667 36.000 0.00 0.00 0.00 3.33
6901 14237 5.461032 TTTCCTGTTGAGTTTTGTGTTGT 57.539 34.783 0.00 0.00 0.00 3.32
6902 14238 4.433186 TCCTGTTGAGTTTTGTGTTGTG 57.567 40.909 0.00 0.00 0.00 3.33
6903 14239 4.075682 TCCTGTTGAGTTTTGTGTTGTGA 58.924 39.130 0.00 0.00 0.00 3.58
6904 14240 4.520874 TCCTGTTGAGTTTTGTGTTGTGAA 59.479 37.500 0.00 0.00 0.00 3.18
6905 14241 4.858692 CCTGTTGAGTTTTGTGTTGTGAAG 59.141 41.667 0.00 0.00 0.00 3.02
6906 14242 5.446143 TGTTGAGTTTTGTGTTGTGAAGT 57.554 34.783 0.00 0.00 0.00 3.01
6907 14243 5.837437 TGTTGAGTTTTGTGTTGTGAAGTT 58.163 33.333 0.00 0.00 0.00 2.66
6908 14244 6.276847 TGTTGAGTTTTGTGTTGTGAAGTTT 58.723 32.000 0.00 0.00 0.00 2.66
6909 14245 6.419413 TGTTGAGTTTTGTGTTGTGAAGTTTC 59.581 34.615 0.00 0.00 0.00 2.78
6910 14246 5.465935 TGAGTTTTGTGTTGTGAAGTTTCC 58.534 37.500 0.00 0.00 0.00 3.13
6911 14247 5.010112 TGAGTTTTGTGTTGTGAAGTTTCCA 59.990 36.000 0.00 0.00 0.00 3.53
6912 14248 5.848406 AGTTTTGTGTTGTGAAGTTTCCAA 58.152 33.333 0.00 0.00 0.00 3.53
6913 14249 5.925969 AGTTTTGTGTTGTGAAGTTTCCAAG 59.074 36.000 0.00 0.00 0.00 3.61
6914 14250 5.461032 TTTGTGTTGTGAAGTTTCCAAGT 57.539 34.783 0.00 0.00 0.00 3.16
6915 14251 5.461032 TTGTGTTGTGAAGTTTCCAAGTT 57.539 34.783 0.00 0.00 0.00 2.66
6916 14252 5.461032 TGTGTTGTGAAGTTTCCAAGTTT 57.539 34.783 0.00 0.00 0.00 2.66
6917 14253 5.848406 TGTGTTGTGAAGTTTCCAAGTTTT 58.152 33.333 0.00 0.00 0.00 2.43
6918 14254 5.694006 TGTGTTGTGAAGTTTCCAAGTTTTG 59.306 36.000 0.00 0.00 0.00 2.44
6934 14270 7.656707 CAAGTTTTGGGTAAAGATTTGATGG 57.343 36.000 0.00 0.00 0.00 3.51
6935 14271 7.441017 CAAGTTTTGGGTAAAGATTTGATGGA 58.559 34.615 0.00 0.00 0.00 3.41
6936 14272 6.993079 AGTTTTGGGTAAAGATTTGATGGAC 58.007 36.000 0.00 0.00 0.00 4.02
6937 14273 6.782494 AGTTTTGGGTAAAGATTTGATGGACT 59.218 34.615 0.00 0.00 0.00 3.85
6938 14274 7.947890 AGTTTTGGGTAAAGATTTGATGGACTA 59.052 33.333 0.00 0.00 0.00 2.59
6939 14275 8.749354 GTTTTGGGTAAAGATTTGATGGACTAT 58.251 33.333 0.00 0.00 0.00 2.12
6940 14276 7.880160 TTGGGTAAAGATTTGATGGACTATG 57.120 36.000 0.00 0.00 0.00 2.23
6941 14277 6.364701 TGGGTAAAGATTTGATGGACTATGG 58.635 40.000 0.00 0.00 0.00 2.74
6942 14278 6.159575 TGGGTAAAGATTTGATGGACTATGGA 59.840 38.462 0.00 0.00 0.00 3.41
6943 14279 6.712547 GGGTAAAGATTTGATGGACTATGGAG 59.287 42.308 0.00 0.00 0.00 3.86
6944 14280 7.283329 GGTAAAGATTTGATGGACTATGGAGT 58.717 38.462 0.00 0.00 39.20 3.85
6945 14281 8.429641 GGTAAAGATTTGATGGACTATGGAGTA 58.570 37.037 0.00 0.00 35.45 2.59
6946 14282 9.832445 GTAAAGATTTGATGGACTATGGAGTAA 57.168 33.333 0.00 0.00 35.45 2.24
6947 14283 8.970859 AAAGATTTGATGGACTATGGAGTAAG 57.029 34.615 0.00 0.00 35.45 2.34
6948 14284 7.072263 AGATTTGATGGACTATGGAGTAAGG 57.928 40.000 0.00 0.00 35.45 2.69
6949 14285 6.846505 AGATTTGATGGACTATGGAGTAAGGA 59.153 38.462 0.00 0.00 35.45 3.36
6950 14286 6.485830 TTTGATGGACTATGGAGTAAGGAG 57.514 41.667 0.00 0.00 35.45 3.69
6951 14287 5.144159 TGATGGACTATGGAGTAAGGAGT 57.856 43.478 0.00 0.00 35.45 3.85
6952 14288 4.895889 TGATGGACTATGGAGTAAGGAGTG 59.104 45.833 0.00 0.00 35.45 3.51
6953 14289 3.643237 TGGACTATGGAGTAAGGAGTGG 58.357 50.000 0.00 0.00 35.45 4.00
6954 14290 2.365941 GGACTATGGAGTAAGGAGTGGC 59.634 54.545 0.00 0.00 35.45 5.01
6955 14291 3.031736 GACTATGGAGTAAGGAGTGGCA 58.968 50.000 0.00 0.00 35.45 4.92
6956 14292 3.450904 ACTATGGAGTAAGGAGTGGCAA 58.549 45.455 0.00 0.00 32.65 4.52
6957 14293 3.844211 ACTATGGAGTAAGGAGTGGCAAA 59.156 43.478 0.00 0.00 32.65 3.68
6958 14294 3.806949 ATGGAGTAAGGAGTGGCAAAA 57.193 42.857 0.00 0.00 0.00 2.44
6959 14295 3.140325 TGGAGTAAGGAGTGGCAAAAG 57.860 47.619 0.00 0.00 0.00 2.27
6960 14296 1.813178 GGAGTAAGGAGTGGCAAAAGC 59.187 52.381 0.00 0.00 0.00 3.51
6961 14297 1.813178 GAGTAAGGAGTGGCAAAAGCC 59.187 52.381 0.00 0.00 0.00 4.35
6962 14298 1.425448 AGTAAGGAGTGGCAAAAGCCT 59.575 47.619 8.11 0.00 0.00 4.58
6963 14299 2.642807 AGTAAGGAGTGGCAAAAGCCTA 59.357 45.455 8.11 0.00 0.00 3.93
6964 14300 2.675658 AAGGAGTGGCAAAAGCCTAA 57.324 45.000 8.11 0.00 0.00 2.69
6965 14301 2.206576 AGGAGTGGCAAAAGCCTAAG 57.793 50.000 8.11 0.00 0.00 2.18
6966 14302 0.528017 GGAGTGGCAAAAGCCTAAGC 59.472 55.000 8.11 0.00 40.32 3.09
6976 14312 3.847621 GCCTAAGCTTGGGGATGC 58.152 61.111 28.06 11.54 35.50 3.91
6977 14313 1.829970 GCCTAAGCTTGGGGATGCC 60.830 63.158 28.06 9.13 35.50 4.40
6978 14314 1.152673 CCTAAGCTTGGGGATGCCC 60.153 63.158 20.71 16.99 44.51 5.36
6987 14323 2.123726 GGGATGCCCATGACACCC 60.124 66.667 0.00 2.81 44.65 4.61
6988 14324 2.123726 GGATGCCCATGACACCCC 60.124 66.667 0.00 0.00 0.00 4.95
6989 14325 2.682846 GATGCCCATGACACCCCA 59.317 61.111 0.00 0.00 0.00 4.96
6990 14326 1.000233 GATGCCCATGACACCCCAA 60.000 57.895 0.00 0.00 0.00 4.12
6991 14327 0.614415 GATGCCCATGACACCCCAAA 60.614 55.000 0.00 0.00 0.00 3.28
6992 14328 0.178909 ATGCCCATGACACCCCAAAA 60.179 50.000 0.00 0.00 0.00 2.44
6993 14329 0.178909 TGCCCATGACACCCCAAAAT 60.179 50.000 0.00 0.00 0.00 1.82
6994 14330 1.077828 TGCCCATGACACCCCAAAATA 59.922 47.619 0.00 0.00 0.00 1.40
6995 14331 2.292785 TGCCCATGACACCCCAAAATAT 60.293 45.455 0.00 0.00 0.00 1.28
6996 14332 2.771372 GCCCATGACACCCCAAAATATT 59.229 45.455 0.00 0.00 0.00 1.28
6997 14333 3.181466 GCCCATGACACCCCAAAATATTC 60.181 47.826 0.00 0.00 0.00 1.75
6998 14334 4.029520 CCCATGACACCCCAAAATATTCA 58.970 43.478 0.00 0.00 0.00 2.57
6999 14335 4.469227 CCCATGACACCCCAAAATATTCAA 59.531 41.667 0.00 0.00 0.00 2.69
7000 14336 5.395546 CCCATGACACCCCAAAATATTCAAG 60.396 44.000 0.00 0.00 0.00 3.02
7001 14337 5.421693 CCATGACACCCCAAAATATTCAAGA 59.578 40.000 0.00 0.00 0.00 3.02
7002 14338 6.070881 CCATGACACCCCAAAATATTCAAGAA 60.071 38.462 0.00 0.00 0.00 2.52
7003 14339 7.364939 CCATGACACCCCAAAATATTCAAGAAT 60.365 37.037 0.00 0.52 34.93 2.40
7004 14340 8.694540 CATGACACCCCAAAATATTCAAGAATA 58.305 33.333 5.09 5.09 37.64 1.75
7005 14341 8.292444 TGACACCCCAAAATATTCAAGAATAG 57.708 34.615 8.34 0.00 36.79 1.73
7006 14342 7.112452 ACACCCCAAAATATTCAAGAATAGC 57.888 36.000 8.34 0.00 36.79 2.97
7007 14343 6.098266 ACACCCCAAAATATTCAAGAATAGCC 59.902 38.462 8.34 0.00 36.79 3.93
7008 14344 6.098124 CACCCCAAAATATTCAAGAATAGCCA 59.902 38.462 8.34 0.00 36.79 4.75
7009 14345 6.671779 ACCCCAAAATATTCAAGAATAGCCAA 59.328 34.615 8.34 0.00 36.79 4.52
7010 14346 7.181845 ACCCCAAAATATTCAAGAATAGCCAAA 59.818 33.333 8.34 0.00 36.79 3.28
7011 14347 8.046107 CCCCAAAATATTCAAGAATAGCCAAAA 58.954 33.333 8.34 0.00 36.79 2.44
7012 14348 9.101655 CCCAAAATATTCAAGAATAGCCAAAAG 57.898 33.333 8.34 0.00 36.79 2.27
7013 14349 8.606602 CCAAAATATTCAAGAATAGCCAAAAGC 58.393 33.333 8.34 0.00 36.79 3.51
7014 14350 8.606602 CAAAATATTCAAGAATAGCCAAAAGCC 58.393 33.333 8.34 0.00 36.79 4.35
7015 14351 7.666063 AATATTCAAGAATAGCCAAAAGCCT 57.334 32.000 8.34 0.00 36.79 4.58
7016 14352 8.766994 AATATTCAAGAATAGCCAAAAGCCTA 57.233 30.769 8.34 0.00 36.79 3.93
7017 14353 8.766994 ATATTCAAGAATAGCCAAAAGCCTAA 57.233 30.769 8.34 0.00 36.79 2.69
7018 14354 6.515272 TTCAAGAATAGCCAAAAGCCTAAG 57.485 37.500 0.00 0.00 45.47 2.18
7019 14355 4.399303 TCAAGAATAGCCAAAAGCCTAAGC 59.601 41.667 0.00 0.00 45.47 3.09
7029 14365 3.847621 GCCTAAGCTTGGGATGCC 58.152 61.111 31.20 10.56 35.50 4.40
7030 14366 1.829970 GCCTAAGCTTGGGATGCCC 60.830 63.158 31.20 10.18 39.26 5.36
7051 14387 3.503998 GGAAGGCATCCCCTCTTTC 57.496 57.895 0.00 0.00 45.62 2.62
7052 14388 0.464554 GGAAGGCATCCCCTCTTTCG 60.465 60.000 0.00 0.00 45.62 3.46
7053 14389 0.253327 GAAGGCATCCCCTCTTTCGT 59.747 55.000 0.00 0.00 45.62 3.85
7054 14390 0.253327 AAGGCATCCCCTCTTTCGTC 59.747 55.000 0.00 0.00 45.62 4.20
7055 14391 0.618968 AGGCATCCCCTCTTTCGTCT 60.619 55.000 0.00 0.00 41.21 4.18
7056 14392 0.253327 GGCATCCCCTCTTTCGTCTT 59.747 55.000 0.00 0.00 0.00 3.01
7057 14393 1.657822 GCATCCCCTCTTTCGTCTTC 58.342 55.000 0.00 0.00 0.00 2.87
7058 14394 1.927895 CATCCCCTCTTTCGTCTTCG 58.072 55.000 0.00 0.00 38.55 3.79
7059 14395 1.204941 CATCCCCTCTTTCGTCTTCGT 59.795 52.381 0.00 0.00 38.33 3.85
7060 14396 1.335145 TCCCCTCTTTCGTCTTCGTT 58.665 50.000 0.00 0.00 38.33 3.85
7061 14397 1.271656 TCCCCTCTTTCGTCTTCGTTC 59.728 52.381 0.00 0.00 38.33 3.95
7062 14398 1.000506 CCCCTCTTTCGTCTTCGTTCA 59.999 52.381 0.00 0.00 38.33 3.18
7063 14399 2.353803 CCCCTCTTTCGTCTTCGTTCAT 60.354 50.000 0.00 0.00 38.33 2.57
7064 14400 3.326747 CCCTCTTTCGTCTTCGTTCATT 58.673 45.455 0.00 0.00 38.33 2.57
7065 14401 3.123621 CCCTCTTTCGTCTTCGTTCATTG 59.876 47.826 0.00 0.00 38.33 2.82
7066 14402 3.123621 CCTCTTTCGTCTTCGTTCATTGG 59.876 47.826 0.00 0.00 38.33 3.16
7067 14403 3.724374 TCTTTCGTCTTCGTTCATTGGT 58.276 40.909 0.00 0.00 38.33 3.67
7068 14404 4.873817 TCTTTCGTCTTCGTTCATTGGTA 58.126 39.130 0.00 0.00 38.33 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 169 4.086457 TCCATGCCTTTCCTAAACTTTCC 58.914 43.478 0.00 0.00 0.00 3.13
167 170 5.010617 TGTTCCATGCCTTTCCTAAACTTTC 59.989 40.000 0.00 0.00 0.00 2.62
168 171 4.898861 TGTTCCATGCCTTTCCTAAACTTT 59.101 37.500 0.00 0.00 0.00 2.66
169 172 4.280929 GTGTTCCATGCCTTTCCTAAACTT 59.719 41.667 0.00 0.00 0.00 2.66
170 173 3.826729 GTGTTCCATGCCTTTCCTAAACT 59.173 43.478 0.00 0.00 0.00 2.66
171 174 3.826729 AGTGTTCCATGCCTTTCCTAAAC 59.173 43.478 0.00 0.00 0.00 2.01
172 175 4.112634 AGTGTTCCATGCCTTTCCTAAA 57.887 40.909 0.00 0.00 0.00 1.85
173 176 3.806949 AGTGTTCCATGCCTTTCCTAA 57.193 42.857 0.00 0.00 0.00 2.69
174 177 3.806949 AAGTGTTCCATGCCTTTCCTA 57.193 42.857 0.00 0.00 0.00 2.94
175 178 2.683211 AAGTGTTCCATGCCTTTCCT 57.317 45.000 0.00 0.00 0.00 3.36
235 246 5.118990 GGCACTTGATTCATAAGTAGCTCA 58.881 41.667 0.00 0.00 36.29 4.26
303 316 1.088306 CGCTATTGTTTAACGCCCCA 58.912 50.000 0.00 0.00 0.00 4.96
556 581 9.814899 TGTTTATTGATCAGAAGCAAAAAGAAA 57.185 25.926 0.00 0.00 33.87 2.52
624 650 5.593968 TCTGTAACTAACGCAAACTTCTGA 58.406 37.500 0.00 0.00 0.00 3.27
785 813 5.454755 GGTGAGTTGGCTAGCCTCATTATTA 60.455 44.000 33.07 8.77 37.54 0.98
913 944 8.847444 CAGTCATTGGATAGAAAAATAACTGC 57.153 34.615 0.00 0.00 0.00 4.40
942 974 1.284657 ATGAAAGCGTGAGATGAGCG 58.715 50.000 0.00 0.00 35.78 5.03
999 1031 4.487412 GCGAGCAGTGCATTGGGC 62.487 66.667 19.20 8.88 45.13 5.36
1147 1212 1.681076 GGGCGGAGGTGTAAAGGAA 59.319 57.895 0.00 0.00 0.00 3.36
1246 1326 3.351885 AGGAGGAGGGAGAGGCGT 61.352 66.667 0.00 0.00 0.00 5.68
1296 1376 2.706071 GACAGGGAGGGAGGGGAT 59.294 66.667 0.00 0.00 0.00 3.85
1310 1390 0.106469 CGAGAGGGAGAGGATGGACA 60.106 60.000 0.00 0.00 0.00 4.02
1381 1461 0.250234 TTCCTTCATGGCAGACTCGG 59.750 55.000 0.00 0.00 35.26 4.63
1393 1473 1.130054 AGTCCCTGCTGCTTCCTTCA 61.130 55.000 0.00 0.00 0.00 3.02
1394 1474 0.037447 AAGTCCCTGCTGCTTCCTTC 59.963 55.000 0.00 0.00 0.00 3.46
1423 1503 1.073897 ACTCCCCTGCAGAGCAAAC 59.926 57.895 17.39 0.00 38.41 2.93
1497 1577 1.612991 CCGTCAACCATGTCCCATCAA 60.613 52.381 0.00 0.00 0.00 2.57
1533 1613 0.034767 CCTGGCAGCTCTCAATCCAA 60.035 55.000 9.56 0.00 0.00 3.53
1622 1702 2.927856 TCACCCACCCGCTGATGT 60.928 61.111 0.00 0.00 0.00 3.06
1825 5189 8.912988 CCAGGCTTAATTCATCCTAACAAAATA 58.087 33.333 0.00 0.00 0.00 1.40
1832 5196 4.386312 CCACCCAGGCTTAATTCATCCTAA 60.386 45.833 0.00 0.00 0.00 2.69
1873 5297 6.315891 CGTGTCTACTAAGCTCTAGGTAAACT 59.684 42.308 0.00 0.00 0.00 2.66
1932 5357 8.638873 CCAGGAAAAGGTTGTAACTATTTTTCT 58.361 33.333 19.27 15.46 35.60 2.52
2092 5517 7.394016 CAAGCATATATACCAAGGTATGACCA 58.606 38.462 19.50 2.45 41.95 4.02
2341 5770 1.484653 ACATGTAGGCATAGCACCGAA 59.515 47.619 0.00 0.00 33.30 4.30
3006 6525 7.558807 AGAATGCAACAGATGAGGAAATTATCA 59.441 33.333 0.00 0.00 0.00 2.15
3011 6530 4.401519 CCAGAATGCAACAGATGAGGAAAT 59.598 41.667 0.00 0.00 31.97 2.17
3056 6577 6.526325 CACGATTGAAACAGTGAAAAGAACAA 59.474 34.615 0.00 0.00 36.79 2.83
3173 6694 4.748701 AGGAAGTAAAGTGTGAGACCCTA 58.251 43.478 0.00 0.00 0.00 3.53
3366 6897 3.191371 CGCCTTCAGGTAAATGCTTCTTT 59.809 43.478 0.00 0.00 37.57 2.52
3389 6920 9.988350 ACAAATTCTATGTGAAAACGCTATTAG 57.012 29.630 0.00 0.00 38.29 1.73
3495 8936 1.063266 TGTCAAGGATAAATGGGGGCC 60.063 52.381 0.00 0.00 0.00 5.80
3592 9036 6.349611 GCTGAAGATGCAGATTTTAGTTTCCA 60.350 38.462 0.00 0.00 38.14 3.53
3834 10283 1.821666 GCAGGAAGTAGCCCACCAAAA 60.822 52.381 0.00 0.00 0.00 2.44
3890 10339 3.334272 ACTAAAAGTTGCACGCAAGAC 57.666 42.857 4.35 0.00 43.62 3.01
4228 10871 1.212688 ACGCCTCATCAATCATCCCAA 59.787 47.619 0.00 0.00 0.00 4.12
4231 10874 3.438087 CCAATACGCCTCATCAATCATCC 59.562 47.826 0.00 0.00 0.00 3.51
4307 10970 5.531634 ACAACACAAATATTGAGCAGGTTG 58.468 37.500 0.00 0.00 0.00 3.77
4412 11075 9.847224 AATTTATCTGATTCCTAACCACGTATT 57.153 29.630 0.00 0.00 0.00 1.89
4464 11129 3.735237 AGCTATCTGGACACGGTATTG 57.265 47.619 0.00 0.00 0.00 1.90
4534 11210 6.317140 GTGAAGAAATGCATCAGGTAGATCAA 59.683 38.462 0.00 0.00 33.72 2.57
4539 11215 4.183865 TCGTGAAGAAATGCATCAGGTAG 58.816 43.478 0.00 0.00 33.29 3.18
4944 11632 7.844493 AATGCATATCCATACCAAAGTTCAT 57.156 32.000 0.00 0.00 0.00 2.57
5056 12006 1.135689 CGTCAGCAACAACCATTAGGC 60.136 52.381 0.00 0.00 39.06 3.93
5247 12203 2.162208 CACGGAAATCTTGTGATGGTGG 59.838 50.000 0.00 0.00 35.66 4.61
5322 12278 1.130054 TGACAGCCTGCCTTTCCTCT 61.130 55.000 0.00 0.00 0.00 3.69
5637 12830 8.712285 ATAGTTCGAATCAGAAATAAAACCGA 57.288 30.769 0.00 0.00 34.91 4.69
5853 13069 2.058798 GAACGAACATGCTCTTGTCGA 58.941 47.619 0.00 0.00 0.00 4.20
5935 13159 4.466370 TGACATAGACACCTAGGAGTTTGG 59.534 45.833 17.98 8.59 31.59 3.28
6029 13258 5.710513 TTGAACAATCAGCAGCACTTTAT 57.289 34.783 0.00 0.00 36.78 1.40
6421 13712 6.136541 ACCATCTCAACTTGAAGTGTTTTC 57.863 37.500 0.00 0.00 0.00 2.29
6508 13801 2.409870 CCACGCAGAGCCCCATTTC 61.410 63.158 0.00 0.00 0.00 2.17
6537 13830 1.140252 ACTCCCCGCACATATGGTAAC 59.860 52.381 7.80 0.00 0.00 2.50
6538 13831 1.502690 ACTCCCCGCACATATGGTAA 58.497 50.000 7.80 0.00 0.00 2.85
6539 13832 1.502690 AACTCCCCGCACATATGGTA 58.497 50.000 7.80 0.00 0.00 3.25
6540 13833 1.502690 TAACTCCCCGCACATATGGT 58.497 50.000 7.80 0.00 0.00 3.55
6541 13834 2.631160 TTAACTCCCCGCACATATGG 57.369 50.000 7.80 0.00 0.00 2.74
6542 13835 5.163561 ACAAATTTAACTCCCCGCACATATG 60.164 40.000 0.00 0.00 0.00 1.78
6543 13836 4.953579 ACAAATTTAACTCCCCGCACATAT 59.046 37.500 0.00 0.00 0.00 1.78
6544 13837 4.337145 ACAAATTTAACTCCCCGCACATA 58.663 39.130 0.00 0.00 0.00 2.29
6545 13838 3.161866 ACAAATTTAACTCCCCGCACAT 58.838 40.909 0.00 0.00 0.00 3.21
6546 13839 2.588620 ACAAATTTAACTCCCCGCACA 58.411 42.857 0.00 0.00 0.00 4.57
6547 13840 3.653539 AACAAATTTAACTCCCCGCAC 57.346 42.857 0.00 0.00 0.00 5.34
6548 13841 3.506844 GGTAACAAATTTAACTCCCCGCA 59.493 43.478 0.00 0.00 0.00 5.69
6549 13842 4.100707 GGTAACAAATTTAACTCCCCGC 57.899 45.455 0.00 0.00 0.00 6.13
6744 14080 3.346315 TCAAGCCATGTTGTCGATGAAT 58.654 40.909 0.00 0.00 0.00 2.57
6810 14146 8.553459 AGGTACTGTAATGAACTCATTCTTTG 57.447 34.615 8.19 1.89 41.19 2.77
6813 14149 9.823647 CATAAGGTACTGTAATGAACTCATTCT 57.176 33.333 8.19 0.00 42.05 2.40
6814 14150 9.601217 ACATAAGGTACTGTAATGAACTCATTC 57.399 33.333 8.19 2.51 42.05 2.67
6815 14151 9.383519 CACATAAGGTACTGTAATGAACTCATT 57.616 33.333 9.74 9.74 44.13 2.57
6816 14152 7.987458 CCACATAAGGTACTGTAATGAACTCAT 59.013 37.037 4.66 0.00 40.86 2.90
6817 14153 7.038587 ACCACATAAGGTACTGTAATGAACTCA 60.039 37.037 4.66 0.00 40.98 3.41
6818 14154 7.277981 CACCACATAAGGTACTGTAATGAACTC 59.722 40.741 4.66 0.00 40.77 3.01
6819 14155 7.103641 CACCACATAAGGTACTGTAATGAACT 58.896 38.462 4.66 0.00 40.77 3.01
6820 14156 6.315393 CCACCACATAAGGTACTGTAATGAAC 59.685 42.308 4.66 0.00 40.77 3.18
6821 14157 6.013206 ACCACCACATAAGGTACTGTAATGAA 60.013 38.462 4.66 0.00 40.77 2.57
6822 14158 5.486063 ACCACCACATAAGGTACTGTAATGA 59.514 40.000 4.66 0.00 40.77 2.57
6823 14159 5.741011 ACCACCACATAAGGTACTGTAATG 58.259 41.667 0.00 0.00 40.77 1.90
6824 14160 6.382919 AACCACCACATAAGGTACTGTAAT 57.617 37.500 0.00 0.00 40.77 1.89
6825 14161 5.829062 AACCACCACATAAGGTACTGTAA 57.171 39.130 0.00 0.00 40.77 2.41
6826 14162 5.829062 AAACCACCACATAAGGTACTGTA 57.171 39.130 0.00 0.00 40.77 2.74
6827 14163 4.717279 AAACCACCACATAAGGTACTGT 57.283 40.909 0.00 0.00 40.77 3.55
6828 14164 5.313712 AGAAAACCACCACATAAGGTACTG 58.686 41.667 0.00 0.00 40.77 2.74
6829 14165 5.578157 AGAAAACCACCACATAAGGTACT 57.422 39.130 0.00 0.00 40.77 2.73
6830 14166 6.644248 AAAGAAAACCACCACATAAGGTAC 57.356 37.500 0.00 0.00 40.77 3.34
6831 14167 7.064229 AGAAAAGAAAACCACCACATAAGGTA 58.936 34.615 0.00 0.00 40.77 3.08
6832 14168 5.897250 AGAAAAGAAAACCACCACATAAGGT 59.103 36.000 0.00 0.00 44.48 3.50
6833 14169 6.405278 AGAAAAGAAAACCACCACATAAGG 57.595 37.500 0.00 0.00 0.00 2.69
6834 14170 7.978975 TGAAAGAAAAGAAAACCACCACATAAG 59.021 33.333 0.00 0.00 0.00 1.73
6835 14171 7.762159 GTGAAAGAAAAGAAAACCACCACATAA 59.238 33.333 0.00 0.00 0.00 1.90
6836 14172 7.123547 AGTGAAAGAAAAGAAAACCACCACATA 59.876 33.333 0.00 0.00 0.00 2.29
6837 14173 6.070824 AGTGAAAGAAAAGAAAACCACCACAT 60.071 34.615 0.00 0.00 0.00 3.21
6838 14174 5.245075 AGTGAAAGAAAAGAAAACCACCACA 59.755 36.000 0.00 0.00 0.00 4.17
6839 14175 5.720202 AGTGAAAGAAAAGAAAACCACCAC 58.280 37.500 0.00 0.00 0.00 4.16
6840 14176 5.993748 AGTGAAAGAAAAGAAAACCACCA 57.006 34.783 0.00 0.00 0.00 4.17
6841 14177 6.471198 CGTTAGTGAAAGAAAAGAAAACCACC 59.529 38.462 0.00 0.00 0.00 4.61
6842 14178 6.471198 CCGTTAGTGAAAGAAAAGAAAACCAC 59.529 38.462 0.00 0.00 0.00 4.16
6843 14179 6.374894 TCCGTTAGTGAAAGAAAAGAAAACCA 59.625 34.615 0.00 0.00 0.00 3.67
6844 14180 6.788243 TCCGTTAGTGAAAGAAAAGAAAACC 58.212 36.000 0.00 0.00 0.00 3.27
6845 14181 6.414109 GCTCCGTTAGTGAAAGAAAAGAAAAC 59.586 38.462 0.00 0.00 0.00 2.43
6846 14182 6.317893 AGCTCCGTTAGTGAAAGAAAAGAAAA 59.682 34.615 0.00 0.00 0.00 2.29
6847 14183 5.820947 AGCTCCGTTAGTGAAAGAAAAGAAA 59.179 36.000 0.00 0.00 0.00 2.52
6848 14184 5.365619 AGCTCCGTTAGTGAAAGAAAAGAA 58.634 37.500 0.00 0.00 0.00 2.52
6849 14185 4.957296 AGCTCCGTTAGTGAAAGAAAAGA 58.043 39.130 0.00 0.00 0.00 2.52
6850 14186 5.674933 AAGCTCCGTTAGTGAAAGAAAAG 57.325 39.130 0.00 0.00 0.00 2.27
6851 14187 6.932400 TCATAAGCTCCGTTAGTGAAAGAAAA 59.068 34.615 0.00 0.00 0.00 2.29
6852 14188 6.460781 TCATAAGCTCCGTTAGTGAAAGAAA 58.539 36.000 0.00 0.00 0.00 2.52
6853 14189 6.032956 TCATAAGCTCCGTTAGTGAAAGAA 57.967 37.500 0.00 0.00 0.00 2.52
6854 14190 5.417894 TCTCATAAGCTCCGTTAGTGAAAGA 59.582 40.000 0.00 0.00 0.00 2.52
6855 14191 5.651530 TCTCATAAGCTCCGTTAGTGAAAG 58.348 41.667 0.00 0.00 0.00 2.62
6856 14192 5.654603 TCTCATAAGCTCCGTTAGTGAAA 57.345 39.130 0.00 0.00 0.00 2.69
6857 14193 5.854010 ATCTCATAAGCTCCGTTAGTGAA 57.146 39.130 0.00 0.00 0.00 3.18
6858 14194 5.854010 AATCTCATAAGCTCCGTTAGTGA 57.146 39.130 0.00 0.00 0.00 3.41
6859 14195 5.463724 GGAAATCTCATAAGCTCCGTTAGTG 59.536 44.000 0.00 0.00 0.00 2.74
6860 14196 5.364157 AGGAAATCTCATAAGCTCCGTTAGT 59.636 40.000 0.00 0.00 0.00 2.24
6861 14197 5.694006 CAGGAAATCTCATAAGCTCCGTTAG 59.306 44.000 0.00 0.00 0.00 2.34
6862 14198 5.128827 ACAGGAAATCTCATAAGCTCCGTTA 59.871 40.000 0.00 0.00 0.00 3.18
6863 14199 4.080863 ACAGGAAATCTCATAAGCTCCGTT 60.081 41.667 0.00 0.00 0.00 4.44
6864 14200 3.452627 ACAGGAAATCTCATAAGCTCCGT 59.547 43.478 0.00 0.00 0.00 4.69
6865 14201 4.065321 ACAGGAAATCTCATAAGCTCCG 57.935 45.455 0.00 0.00 0.00 4.63
6866 14202 5.431765 TCAACAGGAAATCTCATAAGCTCC 58.568 41.667 0.00 0.00 0.00 4.70
6867 14203 6.112058 ACTCAACAGGAAATCTCATAAGCTC 58.888 40.000 0.00 0.00 0.00 4.09
6868 14204 6.059787 ACTCAACAGGAAATCTCATAAGCT 57.940 37.500 0.00 0.00 0.00 3.74
6869 14205 6.749923 AACTCAACAGGAAATCTCATAAGC 57.250 37.500 0.00 0.00 0.00 3.09
6870 14206 8.571336 ACAAAACTCAACAGGAAATCTCATAAG 58.429 33.333 0.00 0.00 0.00 1.73
6871 14207 8.352201 CACAAAACTCAACAGGAAATCTCATAA 58.648 33.333 0.00 0.00 0.00 1.90
6872 14208 7.502226 ACACAAAACTCAACAGGAAATCTCATA 59.498 33.333 0.00 0.00 0.00 2.15
6873 14209 6.322201 ACACAAAACTCAACAGGAAATCTCAT 59.678 34.615 0.00 0.00 0.00 2.90
6874 14210 5.652014 ACACAAAACTCAACAGGAAATCTCA 59.348 36.000 0.00 0.00 0.00 3.27
6875 14211 6.136541 ACACAAAACTCAACAGGAAATCTC 57.863 37.500 0.00 0.00 0.00 2.75
6876 14212 6.071391 ACAACACAAAACTCAACAGGAAATCT 60.071 34.615 0.00 0.00 0.00 2.40
6877 14213 6.034898 CACAACACAAAACTCAACAGGAAATC 59.965 38.462 0.00 0.00 0.00 2.17
6878 14214 5.868801 CACAACACAAAACTCAACAGGAAAT 59.131 36.000 0.00 0.00 0.00 2.17
6879 14215 5.010112 TCACAACACAAAACTCAACAGGAAA 59.990 36.000 0.00 0.00 0.00 3.13
6880 14216 4.520874 TCACAACACAAAACTCAACAGGAA 59.479 37.500 0.00 0.00 0.00 3.36
6881 14217 4.075682 TCACAACACAAAACTCAACAGGA 58.924 39.130 0.00 0.00 0.00 3.86
6882 14218 4.433186 TCACAACACAAAACTCAACAGG 57.567 40.909 0.00 0.00 0.00 4.00
6883 14219 5.460646 ACTTCACAACACAAAACTCAACAG 58.539 37.500 0.00 0.00 0.00 3.16
6884 14220 5.446143 ACTTCACAACACAAAACTCAACA 57.554 34.783 0.00 0.00 0.00 3.33
6885 14221 6.128929 GGAAACTTCACAACACAAAACTCAAC 60.129 38.462 0.00 0.00 0.00 3.18
6886 14222 5.923684 GGAAACTTCACAACACAAAACTCAA 59.076 36.000 0.00 0.00 0.00 3.02
6887 14223 5.010112 TGGAAACTTCACAACACAAAACTCA 59.990 36.000 0.00 0.00 0.00 3.41
6888 14224 5.465935 TGGAAACTTCACAACACAAAACTC 58.534 37.500 0.00 0.00 0.00 3.01
6889 14225 5.461032 TGGAAACTTCACAACACAAAACT 57.539 34.783 0.00 0.00 0.00 2.66
6890 14226 5.694458 ACTTGGAAACTTCACAACACAAAAC 59.306 36.000 0.00 0.00 0.00 2.43
6891 14227 5.848406 ACTTGGAAACTTCACAACACAAAA 58.152 33.333 0.00 0.00 0.00 2.44
6892 14228 5.461032 ACTTGGAAACTTCACAACACAAA 57.539 34.783 0.00 0.00 0.00 2.83
6893 14229 5.461032 AACTTGGAAACTTCACAACACAA 57.539 34.783 0.00 0.00 0.00 3.33
6894 14230 5.461032 AAACTTGGAAACTTCACAACACA 57.539 34.783 0.00 0.00 0.00 3.72
6895 14231 6.151975 CAAAACTTGGAAACTTCACAACAC 57.848 37.500 0.00 0.00 0.00 3.32
6910 14246 7.384932 GTCCATCAAATCTTTACCCAAAACTTG 59.615 37.037 0.00 0.00 0.00 3.16
6911 14247 7.290014 AGTCCATCAAATCTTTACCCAAAACTT 59.710 33.333 0.00 0.00 0.00 2.66
6912 14248 6.782494 AGTCCATCAAATCTTTACCCAAAACT 59.218 34.615 0.00 0.00 0.00 2.66
6913 14249 6.993079 AGTCCATCAAATCTTTACCCAAAAC 58.007 36.000 0.00 0.00 0.00 2.43
6914 14250 8.748412 CATAGTCCATCAAATCTTTACCCAAAA 58.252 33.333 0.00 0.00 0.00 2.44
6915 14251 7.341769 CCATAGTCCATCAAATCTTTACCCAAA 59.658 37.037 0.00 0.00 0.00 3.28
6916 14252 6.833416 CCATAGTCCATCAAATCTTTACCCAA 59.167 38.462 0.00 0.00 0.00 4.12
6917 14253 6.159575 TCCATAGTCCATCAAATCTTTACCCA 59.840 38.462 0.00 0.00 0.00 4.51
6918 14254 6.601332 TCCATAGTCCATCAAATCTTTACCC 58.399 40.000 0.00 0.00 0.00 3.69
6919 14255 7.283329 ACTCCATAGTCCATCAAATCTTTACC 58.717 38.462 0.00 0.00 0.00 2.85
6920 14256 9.832445 TTACTCCATAGTCCATCAAATCTTTAC 57.168 33.333 0.00 0.00 37.15 2.01
6922 14258 7.995488 CCTTACTCCATAGTCCATCAAATCTTT 59.005 37.037 0.00 0.00 37.15 2.52
6923 14259 7.348274 TCCTTACTCCATAGTCCATCAAATCTT 59.652 37.037 0.00 0.00 37.15 2.40
6924 14260 6.846505 TCCTTACTCCATAGTCCATCAAATCT 59.153 38.462 0.00 0.00 37.15 2.40
6925 14261 7.067496 TCCTTACTCCATAGTCCATCAAATC 57.933 40.000 0.00 0.00 37.15 2.17
6926 14262 6.617371 ACTCCTTACTCCATAGTCCATCAAAT 59.383 38.462 0.00 0.00 37.15 2.32
6927 14263 5.964477 ACTCCTTACTCCATAGTCCATCAAA 59.036 40.000 0.00 0.00 37.15 2.69
6928 14264 5.363868 CACTCCTTACTCCATAGTCCATCAA 59.636 44.000 0.00 0.00 37.15 2.57
6929 14265 4.895889 CACTCCTTACTCCATAGTCCATCA 59.104 45.833 0.00 0.00 37.15 3.07
6930 14266 4.282195 CCACTCCTTACTCCATAGTCCATC 59.718 50.000 0.00 0.00 37.15 3.51
6931 14267 4.227197 CCACTCCTTACTCCATAGTCCAT 58.773 47.826 0.00 0.00 37.15 3.41
6932 14268 3.643237 CCACTCCTTACTCCATAGTCCA 58.357 50.000 0.00 0.00 37.15 4.02
6933 14269 2.365941 GCCACTCCTTACTCCATAGTCC 59.634 54.545 0.00 0.00 37.15 3.85
6934 14270 3.031736 TGCCACTCCTTACTCCATAGTC 58.968 50.000 0.00 0.00 37.15 2.59
6935 14271 3.116096 TGCCACTCCTTACTCCATAGT 57.884 47.619 0.00 0.00 39.91 2.12
6936 14272 4.487714 TTTGCCACTCCTTACTCCATAG 57.512 45.455 0.00 0.00 0.00 2.23
6937 14273 4.843728 CTTTTGCCACTCCTTACTCCATA 58.156 43.478 0.00 0.00 0.00 2.74
6938 14274 3.690460 CTTTTGCCACTCCTTACTCCAT 58.310 45.455 0.00 0.00 0.00 3.41
6939 14275 2.814097 GCTTTTGCCACTCCTTACTCCA 60.814 50.000 0.00 0.00 40.15 3.86
6940 14276 1.813178 GCTTTTGCCACTCCTTACTCC 59.187 52.381 0.00 0.00 40.15 3.85
6959 14295 1.829970 GGCATCCCCAAGCTTAGGC 60.830 63.158 5.25 0.00 39.06 3.93
6960 14296 4.587056 GGCATCCCCAAGCTTAGG 57.413 61.111 3.60 3.60 0.00 2.69
6970 14306 2.123726 GGGTGTCATGGGCATCCC 60.124 66.667 8.68 9.69 45.71 3.85
6971 14307 2.123726 GGGGTGTCATGGGCATCC 60.124 66.667 10.74 10.74 36.42 3.51
6972 14308 0.614415 TTTGGGGTGTCATGGGCATC 60.614 55.000 0.00 0.00 0.00 3.91
6973 14309 0.178909 TTTTGGGGTGTCATGGGCAT 60.179 50.000 0.00 0.00 0.00 4.40
6974 14310 0.178909 ATTTTGGGGTGTCATGGGCA 60.179 50.000 0.00 0.00 0.00 5.36
6975 14311 1.859302 TATTTTGGGGTGTCATGGGC 58.141 50.000 0.00 0.00 0.00 5.36
6976 14312 4.029520 TGAATATTTTGGGGTGTCATGGG 58.970 43.478 0.00 0.00 0.00 4.00
6977 14313 5.421693 TCTTGAATATTTTGGGGTGTCATGG 59.578 40.000 0.00 0.00 0.00 3.66
6978 14314 6.528537 TCTTGAATATTTTGGGGTGTCATG 57.471 37.500 0.00 0.00 0.00 3.07
6979 14315 7.738437 ATTCTTGAATATTTTGGGGTGTCAT 57.262 32.000 0.00 0.00 0.00 3.06
6980 14316 7.147915 GCTATTCTTGAATATTTTGGGGTGTCA 60.148 37.037 3.86 0.00 0.00 3.58
6981 14317 7.203218 GCTATTCTTGAATATTTTGGGGTGTC 58.797 38.462 3.86 0.00 0.00 3.67
6982 14318 6.098266 GGCTATTCTTGAATATTTTGGGGTGT 59.902 38.462 3.86 0.00 0.00 4.16
6983 14319 6.098124 TGGCTATTCTTGAATATTTTGGGGTG 59.902 38.462 3.86 0.00 0.00 4.61
6984 14320 6.201591 TGGCTATTCTTGAATATTTTGGGGT 58.798 36.000 3.86 0.00 0.00 4.95
6985 14321 6.729690 TGGCTATTCTTGAATATTTTGGGG 57.270 37.500 3.86 0.00 0.00 4.96
6986 14322 9.101655 CTTTTGGCTATTCTTGAATATTTTGGG 57.898 33.333 3.86 0.00 0.00 4.12
6987 14323 8.606602 GCTTTTGGCTATTCTTGAATATTTTGG 58.393 33.333 3.86 0.00 38.06 3.28
6988 14324 8.606602 GGCTTTTGGCTATTCTTGAATATTTTG 58.393 33.333 3.86 0.00 42.31 2.44
6989 14325 8.722480 GGCTTTTGGCTATTCTTGAATATTTT 57.278 30.769 3.86 0.00 42.31 1.82
7011 14347 2.290021 GGGCATCCCAAGCTTAGGCT 62.290 60.000 5.98 0.00 44.65 4.58
7012 14348 1.829970 GGGCATCCCAAGCTTAGGC 60.830 63.158 5.98 0.55 44.65 3.93
7013 14349 4.587056 GGGCATCCCAAGCTTAGG 57.413 61.111 4.29 4.29 44.65 2.69
7033 14369 0.464554 CGAAAGAGGGGATGCCTTCC 60.465 60.000 11.99 0.00 44.62 3.46
7034 14370 0.253327 ACGAAAGAGGGGATGCCTTC 59.747 55.000 7.35 7.35 0.00 3.46
7035 14371 0.253327 GACGAAAGAGGGGATGCCTT 59.747 55.000 2.19 0.00 0.00 4.35
7036 14372 0.618968 AGACGAAAGAGGGGATGCCT 60.619 55.000 2.19 0.00 0.00 4.75
7037 14373 0.253327 AAGACGAAAGAGGGGATGCC 59.747 55.000 0.00 0.00 0.00 4.40
7038 14374 1.657822 GAAGACGAAAGAGGGGATGC 58.342 55.000 0.00 0.00 0.00 3.91
7039 14375 1.204941 ACGAAGACGAAAGAGGGGATG 59.795 52.381 0.00 0.00 42.66 3.51
7040 14376 1.558233 ACGAAGACGAAAGAGGGGAT 58.442 50.000 0.00 0.00 42.66 3.85
7041 14377 1.271656 GAACGAAGACGAAAGAGGGGA 59.728 52.381 0.00 0.00 42.66 4.81
7042 14378 1.000506 TGAACGAAGACGAAAGAGGGG 59.999 52.381 0.00 0.00 42.66 4.79
7043 14379 2.433868 TGAACGAAGACGAAAGAGGG 57.566 50.000 0.00 0.00 42.66 4.30
7044 14380 3.123621 CCAATGAACGAAGACGAAAGAGG 59.876 47.826 0.00 0.00 42.66 3.69
7045 14381 3.741344 ACCAATGAACGAAGACGAAAGAG 59.259 43.478 0.00 0.00 42.66 2.85
7046 14382 3.724374 ACCAATGAACGAAGACGAAAGA 58.276 40.909 0.00 0.00 42.66 2.52


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

AutoCloner maintained by Alex Coulton.