Multiple sequence alignment - TraesCS4A01G445600

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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 TraesCS4A01G445600 chr4A 100.000 8343 0 0 1 8343 713515952 713524294 0.000000e+00 15407.0
1 TraesCS4A01G445600 chr4A 98.300 1059 14 3 1 1056 457569082 457570139 0.000000e+00 1853.0
2 TraesCS4A01G445600 chr4A 90.631 491 41 2 7858 8343 634360830 634360340 0.000000e+00 647.0
3 TraesCS4A01G445600 chr4A 89.668 271 22 5 4138 4402 614570390 614570660 2.880000e-89 340.0
4 TraesCS4A01G445600 chr4A 91.667 240 15 1 3695 3929 713517687 713517926 2.250000e-85 327.0
5 TraesCS4A01G445600 chr4A 91.667 240 15 1 1736 1975 713519646 713519880 2.250000e-85 327.0
6 TraesCS4A01G445600 chr4A 91.139 237 19 2 2588 2823 241019515 241019280 3.760000e-83 320.0
7 TraesCS4A01G445600 chr4A 89.231 195 20 1 5499 5693 713519009 713519202 8.370000e-60 243.0
8 TraesCS4A01G445600 chr4A 89.231 195 20 1 3058 3251 713521450 713521644 8.370000e-60 243.0
9 TraesCS4A01G445600 chr4A 80.000 230 45 1 1996 2225 562186961 562186733 1.440000e-37 169.0
10 TraesCS4A01G445600 chr4A 86.000 100 14 0 6856 6955 620951993 620952092 3.180000e-19 108.0
11 TraesCS4A01G445600 chr7A 90.904 1935 115 31 5700 7600 19900917 19899010 0.000000e+00 2542.0
12 TraesCS4A01G445600 chr7A 93.671 632 27 8 1048 1678 19906458 19905839 0.000000e+00 933.0
13 TraesCS4A01G445600 chr7A 85.822 529 62 9 1699 2225 19905848 19905331 4.400000e-152 549.0
14 TraesCS4A01G445600 chr7A 92.330 352 19 2 5356 5700 19901301 19900951 2.090000e-135 494.0
15 TraesCS4A01G445600 chr7A 86.493 422 29 11 4962 5373 19901718 19901315 9.940000e-119 438.0
16 TraesCS4A01G445600 chr7A 90.717 237 22 0 2587 2823 674358095 674358331 4.860000e-82 316.0
17 TraesCS4A01G445600 chr7A 90.717 237 22 0 2587 2823 674406676 674406912 4.860000e-82 316.0
18 TraesCS4A01G445600 chr7A 83.143 350 36 5 3058 3385 19901158 19900810 1.760000e-76 298.0
19 TraesCS4A01G445600 chr7A 84.516 310 39 6 4662 4970 39122225 39122526 1.760000e-76 298.0
20 TraesCS4A01G445600 chr7A 83.404 235 34 5 1995 2225 592296490 592296257 6.560000e-51 213.0
21 TraesCS4A01G445600 chr7A 91.333 150 13 0 1787 1936 19905277 19905128 1.100000e-48 206.0
22 TraesCS4A01G445600 chr7A 90.435 115 9 1 4393 4507 446681385 446681497 5.220000e-32 150.0
23 TraesCS4A01G445600 chr7A 83.051 118 13 7 5017 5128 280283663 280283779 5.330000e-17 100.0
24 TraesCS4A01G445600 chr3A 98.667 1050 12 2 2 1050 371159261 371158213 0.000000e+00 1860.0
25 TraesCS4A01G445600 chr3A 89.474 266 22 5 4135 4394 739916697 739916962 1.740000e-86 331.0
26 TraesCS4A01G445600 chr3A 97.297 37 0 1 4579 4614 511632936 511632900 2.510000e-05 62.1
27 TraesCS4A01G445600 chr4B 96.503 1058 28 6 1 1050 96269417 96268361 0.000000e+00 1740.0
28 TraesCS4A01G445600 chr4B 89.299 271 24 4 4139 4404 494016341 494016611 1.340000e-87 335.0
29 TraesCS4A01G445600 chr4B 84.810 316 39 5 4660 4974 628118964 628118657 8.130000e-80 309.0
30 TraesCS4A01G445600 chr4B 74.919 614 139 10 6715 7322 665612336 665612940 4.960000e-67 267.0
31 TraesCS4A01G445600 chr4B 89.844 128 11 2 4014 4140 457411809 457411935 6.700000e-36 163.0
32 TraesCS4A01G445600 chr4B 88.034 117 14 0 4024 4140 621989491 621989375 1.130000e-28 139.0
33 TraesCS4A01G445600 chr1B 96.378 1049 33 4 3 1049 7370414 7369369 0.000000e+00 1722.0
34 TraesCS4A01G445600 chr1B 92.724 536 35 1 7812 8343 143112344 143112879 0.000000e+00 771.0
35 TraesCS4A01G445600 chr1B 90.152 132 13 0 7668 7799 37646848 37646717 1.110000e-38 172.0
36 TraesCS4A01G445600 chr1B 91.892 111 7 1 4393 4503 558919725 558919617 4.030000e-33 154.0
37 TraesCS4A01G445600 chr1B 83.088 136 23 0 2090 2225 632774519 632774384 3.160000e-24 124.0
38 TraesCS4A01G445600 chr1B 87.500 72 8 1 5011 5082 225788041 225787971 1.930000e-11 82.4
39 TraesCS4A01G445600 chr1B 87.273 55 6 1 4585 4639 225788147 225788094 2.510000e-05 62.1
40 TraesCS4A01G445600 chr5B 95.862 1015 31 6 1 1011 534992215 534991208 0.000000e+00 1631.0
41 TraesCS4A01G445600 chr5B 95.113 532 20 3 7812 8343 196472901 196473426 0.000000e+00 833.0
42 TraesCS4A01G445600 chr5B 83.713 307 42 7 6387 6687 562759537 562759841 4.930000e-72 283.0
43 TraesCS4A01G445600 chr5B 80.645 310 49 9 4662 4970 293241242 293241541 6.510000e-56 230.0
44 TraesCS4A01G445600 chr7D 94.092 914 48 3 6544 7456 19405918 19405010 0.000000e+00 1384.0
45 TraesCS4A01G445600 chr7D 94.963 814 36 3 5742 6552 19406880 19406069 0.000000e+00 1271.0
46 TraesCS4A01G445600 chr7D 89.468 959 63 17 1047 1983 19410888 19409946 0.000000e+00 1177.0
47 TraesCS4A01G445600 chr7D 93.433 533 34 1 7812 8343 2171992 2172524 0.000000e+00 789.0
48 TraesCS4A01G445600 chr7D 85.621 612 51 18 5098 5700 19407643 19407060 7.160000e-170 608.0
49 TraesCS4A01G445600 chr7D 91.691 337 21 7 2226 2557 99616349 99616683 2.120000e-125 460.0
50 TraesCS4A01G445600 chr7D 83.066 437 54 10 3272 3702 19408998 19408576 6.110000e-101 379.0
51 TraesCS4A01G445600 chr7D 84.267 375 42 11 1623 1992 19408299 19407937 4.790000e-92 350.0
52 TraesCS4A01G445600 chr7D 87.255 306 25 6 3696 3990 19408189 19407887 3.730000e-88 337.0
53 TraesCS4A01G445600 chr7D 90.717 237 22 0 2587 2823 99616329 99616565 4.860000e-82 316.0
54 TraesCS4A01G445600 chr7D 84.936 312 28 8 3696 3990 19410196 19409887 1.760000e-76 298.0
55 TraesCS4A01G445600 chr7D 84.615 221 33 1 2005 2225 568947875 568947656 1.410000e-52 219.0
56 TraesCS4A01G445600 chr7D 85.859 198 22 4 3058 3250 19409249 19409053 1.100000e-48 206.0
57 TraesCS4A01G445600 chr7D 91.892 111 7 1 4393 4503 535083259 535083151 4.030000e-33 154.0
58 TraesCS4A01G445600 chr7D 89.565 115 12 0 4017 4131 105290352 105290466 6.750000e-31 147.0
59 TraesCS4A01G445600 chr7D 80.469 128 19 4 4013 4140 25579290 25579411 8.920000e-15 93.5
60 TraesCS4A01G445600 chr6D 90.646 1037 43 14 1 1011 448570534 448571542 0.000000e+00 1328.0
61 TraesCS4A01G445600 chr6D 91.089 101 6 3 4041 4140 68581302 68581204 5.250000e-27 134.0
62 TraesCS4A01G445600 chr6D 84.956 113 16 1 4020 4132 455313357 455313246 6.840000e-21 113.0
63 TraesCS4A01G445600 chrUn 93.939 660 29 5 391 1050 112561344 112561992 0.000000e+00 987.0
64 TraesCS4A01G445600 chrUn 91.667 360 14 5 1 355 112560993 112561341 1.260000e-132 484.0
65 TraesCS4A01G445600 chrUn 81.901 547 88 9 1049 1590 282501315 282500775 1.280000e-122 451.0
66 TraesCS4A01G445600 chrUn 81.901 547 88 9 1049 1590 282508087 282507547 1.280000e-122 451.0
67 TraesCS4A01G445600 chrUn 81.901 547 88 9 1049 1590 296567130 296566590 1.280000e-122 451.0
68 TraesCS4A01G445600 chrUn 75.523 621 135 13 6715 7328 108414322 108413712 1.060000e-73 289.0
69 TraesCS4A01G445600 chrUn 89.677 155 8 4 2821 2969 65754774 65754622 3.070000e-44 191.0
70 TraesCS4A01G445600 chrUn 90.351 114 9 1 4393 4506 212973130 212973019 1.880000e-31 148.0
71 TraesCS4A01G445600 chr3B 95.857 531 21 1 7812 8342 232646190 232646719 0.000000e+00 857.0
72 TraesCS4A01G445600 chr3B 82.649 536 79 10 7812 8342 61566463 61566989 5.900000e-126 462.0
73 TraesCS4A01G445600 chr3B 89.275 345 29 8 2224 2564 650059146 650058806 7.740000e-115 425.0
74 TraesCS4A01G445600 chr3B 84.076 314 40 8 4660 4973 456987687 456987990 2.280000e-75 294.0
75 TraesCS4A01G445600 chr3B 81.595 326 45 13 4652 4974 748861209 748861522 1.070000e-63 255.0
76 TraesCS4A01G445600 chr3B 80.368 326 50 11 4652 4974 295711111 295711425 1.400000e-57 235.0
77 TraesCS4A01G445600 chr3B 87.879 132 15 1 7668 7799 741972811 741972941 4.030000e-33 154.0
78 TraesCS4A01G445600 chr3B 87.069 116 15 0 4025 4140 803661666 803661781 1.890000e-26 132.0
79 TraesCS4A01G445600 chr1A 91.370 533 45 1 7811 8342 517522060 517522592 0.000000e+00 728.0
80 TraesCS4A01G445600 chr1A 89.850 532 53 1 7812 8343 549165335 549165865 0.000000e+00 682.0
81 TraesCS4A01G445600 chr1A 87.963 324 12 13 1 321 507755124 507754825 2.860000e-94 357.0
82 TraesCS4A01G445600 chr1A 84.142 309 42 6 6386 6687 521708480 521708172 8.190000e-75 292.0
83 TraesCS4A01G445600 chr1A 89.216 102 10 1 4040 4140 577660243 577660344 8.790000e-25 126.0
84 TraesCS4A01G445600 chr1A 83.478 115 19 0 4017 4131 453769775 453769889 3.180000e-19 108.0
85 TraesCS4A01G445600 chr3D 87.005 631 54 14 2221 2830 590228360 590228983 0.000000e+00 686.0
86 TraesCS4A01G445600 chr3D 88.761 347 28 10 2221 2561 590228753 590229094 1.680000e-111 414.0
87 TraesCS4A01G445600 chr3D 88.400 250 18 6 2821 3061 579075548 579075795 2.950000e-74 291.0
88 TraesCS4A01G445600 chr3D 84.328 134 17 3 1990 2120 410998351 410998483 2.440000e-25 128.0
89 TraesCS4A01G445600 chr3D 84.000 125 18 2 4017 4140 355714310 355714433 1.470000e-22 119.0
90 TraesCS4A01G445600 chr3D 79.137 139 29 0 4013 4151 6024178 6024316 6.890000e-16 97.1
91 TraesCS4A01G445600 chr4D 89.098 532 54 2 7812 8343 497082284 497082811 0.000000e+00 658.0
92 TraesCS4A01G445600 chr4D 89.299 271 22 6 4139 4403 7924765 7925034 4.830000e-87 333.0
93 TraesCS4A01G445600 chr4D 91.561 237 20 0 2587 2823 366321232 366320996 2.250000e-85 327.0
94 TraesCS4A01G445600 chr4D 85.099 302 36 6 4670 4970 20134000 20134293 4.890000e-77 300.0
95 TraesCS4A01G445600 chr4D 87.952 249 21 4 2821 3061 438110772 438110525 1.370000e-72 285.0
96 TraesCS4A01G445600 chr4D 82.906 117 14 5 4022 4135 49243209 49243096 5.330000e-17 100.0
97 TraesCS4A01G445600 chr4D 92.157 51 4 0 1007 1057 3913736 3913686 1.160000e-08 73.1
98 TraesCS4A01G445600 chr7B 83.384 662 76 22 1 645 64843075 64843719 4.340000e-162 582.0
99 TraesCS4A01G445600 chr7B 87.912 364 33 10 2221 2579 374982256 374982613 1.300000e-112 418.0
100 TraesCS4A01G445600 chr7B 84.539 304 41 4 6389 6687 9699127 9699429 6.330000e-76 296.0
101 TraesCS4A01G445600 chr7B 84.194 310 41 6 6387 6690 587018622 587018315 2.280000e-75 294.0
102 TraesCS4A01G445600 chr7B 87.923 207 18 3 2821 3021 130740764 130740969 3.890000e-58 237.0
103 TraesCS4A01G445600 chr7B 82.734 139 20 4 4014 4150 397222109 397222245 4.090000e-23 121.0
104 TraesCS4A01G445600 chr7B 97.727 44 1 0 1007 1050 720140006 720139963 8.980000e-10 76.8
105 TraesCS4A01G445600 chr7B 97.674 43 1 0 1007 1049 742143668 742143626 3.230000e-09 75.0
106 TraesCS4A01G445600 chr2A 85.897 546 64 13 1049 1592 9057902 9058436 3.380000e-158 569.0
107 TraesCS4A01G445600 chr2A 79.126 618 122 6 6714 7329 9059471 9060083 3.600000e-113 420.0
108 TraesCS4A01G445600 chr2A 80.992 242 36 10 1990 2225 733154418 733154655 5.140000e-42 183.0
109 TraesCS4A01G445600 chr2A 89.831 118 10 1 4393 4510 705274976 705274861 5.220000e-32 150.0
110 TraesCS4A01G445600 chr2A 87.603 121 15 0 4020 4140 123130104 123129984 3.140000e-29 141.0
111 TraesCS4A01G445600 chr2B 81.716 536 87 9 1068 1598 13040324 13040853 3.580000e-118 436.0
112 TraesCS4A01G445600 chr2B 84.688 320 41 6 4659 4977 65959461 65959773 6.290000e-81 313.0
113 TraesCS4A01G445600 chr2B 85.065 308 38 6 6386 6687 378599 378294 2.930000e-79 307.0
114 TraesCS4A01G445600 chr2B 83.871 310 40 8 6385 6687 118159813 118160119 3.810000e-73 287.0
115 TraesCS4A01G445600 chr2B 88.430 121 14 0 4020 4140 776136253 776136133 6.750000e-31 147.0
116 TraesCS4A01G445600 chr2B 84.874 119 18 0 4022 4140 315239 315121 4.090000e-23 121.0
117 TraesCS4A01G445600 chr2B 86.916 107 14 0 2005 2111 525254165 525254059 4.090000e-23 121.0
118 TraesCS4A01G445600 chr5A 87.637 364 31 12 2224 2580 444261997 444261641 2.170000e-110 411.0
119 TraesCS4A01G445600 chr5A 88.116 345 33 8 2221 2561 594951611 594951951 3.630000e-108 403.0
120 TraesCS4A01G445600 chr5A 88.768 276 23 7 4124 4394 597832018 597832290 1.740000e-86 331.0
121 TraesCS4A01G445600 chr5A 84.858 317 39 6 4658 4973 28234348 28234040 2.260000e-80 311.0
122 TraesCS4A01G445600 chr5A 90.000 240 22 2 2584 2823 594951594 594951831 8.130000e-80 309.0
123 TraesCS4A01G445600 chr5A 74.756 614 140 10 6715 7322 705594093 705594697 2.310000e-65 261.0
124 TraesCS4A01G445600 chr5A 81.818 220 39 1 2004 2223 384180547 384180329 5.140000e-42 183.0
125 TraesCS4A01G445600 chr5A 80.357 224 44 0 2002 2225 295059762 295059539 4.000000e-38 171.0
126 TraesCS4A01G445600 chr5A 91.228 114 8 1 4393 4506 643493316 643493205 4.030000e-33 154.0
127 TraesCS4A01G445600 chr2D 88.439 346 29 11 2221 2561 500694754 500695093 2.800000e-109 407.0
128 TraesCS4A01G445600 chr2D 87.861 346 34 7 2224 2564 197037828 197037486 4.690000e-107 399.0
129 TraesCS4A01G445600 chr2D 79.839 496 88 10 1049 1539 9738620 9739108 1.330000e-92 351.0
130 TraesCS4A01G445600 chr2D 77.184 618 118 10 6714 7329 9742519 9743115 1.040000e-88 339.0
131 TraesCS4A01G445600 chr2D 88.421 285 27 5 4134 4412 357895099 357894815 1.040000e-88 339.0
132 TraesCS4A01G445600 chr2D 81.590 239 41 2 1989 2225 353161494 353161731 2.380000e-45 195.0
133 TraesCS4A01G445600 chr2D 100.000 28 0 0 5017 5044 592628979 592628952 1.500000e-02 52.8
134 TraesCS4A01G445600 chr6B 91.221 262 17 4 4139 4395 536831432 536831172 1.330000e-92 351.0
135 TraesCS4A01G445600 chr6B 89.888 267 22 4 4137 4398 455461304 455461038 1.040000e-88 339.0
136 TraesCS4A01G445600 chr6B 88.755 249 19 4 2821 3061 79718029 79718276 6.330000e-76 296.0
137 TraesCS4A01G445600 chr6B 84.039 307 41 6 6387 6687 202527757 202528061 1.060000e-73 289.0
138 TraesCS4A01G445600 chr6B 97.674 43 1 0 1007 1049 508616081 508616123 3.230000e-09 75.0
139 TraesCS4A01G445600 chr1D 89.925 268 21 3 4133 4394 422067132 422066865 2.880000e-89 340.0
140 TraesCS4A01G445600 chr1D 89.958 239 24 0 2584 2822 488109099 488109337 8.130000e-80 309.0
141 TraesCS4A01G445600 chr1D 91.304 115 7 2 4393 4506 168351651 168351763 4.030000e-33 154.0
142 TraesCS4A01G445600 chr1D 90.517 116 9 2 4393 4508 88614869 88614756 1.450000e-32 152.0
143 TraesCS4A01G445600 chr1D 79.545 132 18 8 5011 5135 164446060 164446189 1.490000e-12 86.1
144 TraesCS4A01G445600 chr1D 97.143 35 1 0 4582 4616 164445950 164445984 9.040000e-05 60.2
145 TraesCS4A01G445600 chr5D 91.176 238 17 3 2587 2823 30974034 30973800 3.760000e-83 320.0
146 TraesCS4A01G445600 chr5D 90.678 118 9 1 4393 4510 432081494 432081379 1.120000e-33 156.0
147 TraesCS4A01G445600 chr5D 85.000 100 15 0 6856 6955 549325021 549325120 1.480000e-17 102.0
148 TraesCS4A01G445600 chr6A 90.000 100 10 0 4041 4140 86302335 86302236 6.800000e-26 130.0
149 TraesCS4A01G445600 chr6A 82.946 129 20 2 4013 4140 399644468 399644341 1.900000e-21 115.0


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 TraesCS4A01G445600 chr4A 713515952 713524294 8342 False 15407.000000 15407 100.000000 1 8343 1 chr4A.!!$F4 8342
1 TraesCS4A01G445600 chr4A 457569082 457570139 1057 False 1853.000000 1853 98.300000 1 1056 1 chr4A.!!$F1 1055
2 TraesCS4A01G445600 chr4A 713517687 713521644 3957 False 285.000000 327 90.449000 1736 5693 4 chr4A.!!$F5 3957
3 TraesCS4A01G445600 chr7A 19899010 19906458 7448 True 780.000000 2542 89.099429 1048 7600 7 chr7A.!!$R2 6552
4 TraesCS4A01G445600 chr3A 371158213 371159261 1048 True 1860.000000 1860 98.667000 2 1050 1 chr3A.!!$R1 1048
5 TraesCS4A01G445600 chr4B 96268361 96269417 1056 True 1740.000000 1740 96.503000 1 1050 1 chr4B.!!$R1 1049
6 TraesCS4A01G445600 chr4B 665612336 665612940 604 False 267.000000 267 74.919000 6715 7322 1 chr4B.!!$F3 607
7 TraesCS4A01G445600 chr1B 7369369 7370414 1045 True 1722.000000 1722 96.378000 3 1049 1 chr1B.!!$R1 1046
8 TraesCS4A01G445600 chr1B 143112344 143112879 535 False 771.000000 771 92.724000 7812 8343 1 chr1B.!!$F1 531
9 TraesCS4A01G445600 chr5B 534991208 534992215 1007 True 1631.000000 1631 95.862000 1 1011 1 chr5B.!!$R1 1010
10 TraesCS4A01G445600 chr5B 196472901 196473426 525 False 833.000000 833 95.113000 7812 8343 1 chr5B.!!$F1 531
11 TraesCS4A01G445600 chr7D 2171992 2172524 532 False 789.000000 789 93.433000 7812 8343 1 chr7D.!!$F1 531
12 TraesCS4A01G445600 chr7D 19405010 19410888 5878 True 667.777778 1384 87.725222 1047 7456 9 chr7D.!!$R3 6409
13 TraesCS4A01G445600 chr6D 448570534 448571542 1008 False 1328.000000 1328 90.646000 1 1011 1 chr6D.!!$F1 1010
14 TraesCS4A01G445600 chrUn 112560993 112561992 999 False 735.500000 987 92.803000 1 1050 2 chrUn.!!$F1 1049
15 TraesCS4A01G445600 chrUn 282500775 282501315 540 True 451.000000 451 81.901000 1049 1590 1 chrUn.!!$R4 541
16 TraesCS4A01G445600 chrUn 282507547 282508087 540 True 451.000000 451 81.901000 1049 1590 1 chrUn.!!$R5 541
17 TraesCS4A01G445600 chrUn 296566590 296567130 540 True 451.000000 451 81.901000 1049 1590 1 chrUn.!!$R6 541
18 TraesCS4A01G445600 chrUn 108413712 108414322 610 True 289.000000 289 75.523000 6715 7328 1 chrUn.!!$R2 613
19 TraesCS4A01G445600 chr3B 232646190 232646719 529 False 857.000000 857 95.857000 7812 8342 1 chr3B.!!$F2 530
20 TraesCS4A01G445600 chr3B 61566463 61566989 526 False 462.000000 462 82.649000 7812 8342 1 chr3B.!!$F1 530
21 TraesCS4A01G445600 chr1A 517522060 517522592 532 False 728.000000 728 91.370000 7811 8342 1 chr1A.!!$F2 531
22 TraesCS4A01G445600 chr1A 549165335 549165865 530 False 682.000000 682 89.850000 7812 8343 1 chr1A.!!$F3 531
23 TraesCS4A01G445600 chr3D 590228360 590229094 734 False 550.000000 686 87.883000 2221 2830 2 chr3D.!!$F5 609
24 TraesCS4A01G445600 chr4D 497082284 497082811 527 False 658.000000 658 89.098000 7812 8343 1 chr4D.!!$F3 531
25 TraesCS4A01G445600 chr7B 64843075 64843719 644 False 582.000000 582 83.384000 1 645 1 chr7B.!!$F2 644
26 TraesCS4A01G445600 chr2A 9057902 9060083 2181 False 494.500000 569 82.511500 1049 7329 2 chr2A.!!$F2 6280
27 TraesCS4A01G445600 chr2B 13040324 13040853 529 False 436.000000 436 81.716000 1068 1598 1 chr2B.!!$F1 530
28 TraesCS4A01G445600 chr5A 705594093 705594697 604 False 261.000000 261 74.756000 6715 7322 1 chr5A.!!$F2 607
29 TraesCS4A01G445600 chr2D 9738620 9743115 4495 False 345.000000 351 78.511500 1049 7329 2 chr2D.!!$F3 6280

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
570 652 2.385315 GAGCGGTTCAAGCAAGAAAAC 58.615 47.619 0.0 0.0 37.01 2.43 F
1159 1272 0.245539 CCAACAATGGCAGCTCCTTG 59.754 55.000 0.0 0.0 40.58 3.61 F
1725 2390 0.323629 AAAGAAAGATGACGGGGCGA 59.676 50.000 0.0 0.0 0.00 5.54 F
5986 11627 0.109919 GCCTTTGGCGAAAACTACGG 60.110 55.000 0.0 0.0 39.62 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 2372 0.391263 GTCGCCCCGTCATCTTTCTT 60.391 55.000 0.0 0.0 0.00 2.52 R
5762 11402 8.311395 TCACTGGTTCAGTTCTATATGAAGAT 57.689 34.615 0.0 0.0 42.59 2.40 R
6057 11698 1.071857 GTTGGGAAAGAAGTCCTCGGT 59.928 52.381 0.0 0.0 37.85 4.69 R
7762 13651 0.035439 TGATCCTTCCCGCCAAAGTC 60.035 55.000 0.0 0.0 0.00 3.01 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
570 652 2.385315 GAGCGGTTCAAGCAAGAAAAC 58.615 47.619 0.00 0.00 37.01 2.43
836 942 5.416639 CCATGGATGAAGTGATTTGAGACAA 59.583 40.000 5.56 0.00 0.00 3.18
941 1047 2.623418 TAAGGTGAGAGGCAGGAAGA 57.377 50.000 0.00 0.00 0.00 2.87
1126 1239 2.509336 GGCGCGCTTCTCAGCTTA 60.509 61.111 32.29 0.00 44.85 3.09
1127 1240 2.698020 GCGCGCTTCTCAGCTTAC 59.302 61.111 26.67 0.00 44.85 2.34
1159 1272 0.245539 CCAACAATGGCAGCTCCTTG 59.754 55.000 0.00 0.00 40.58 3.61
1196 1312 2.668144 ATCTCCCTCCTCTTCCTACG 57.332 55.000 0.00 0.00 0.00 3.51
1207 1323 2.088674 CTTCCTACGCCGGAGATGGG 62.089 65.000 13.83 10.64 33.89 4.00
1307 1423 3.068691 CCACCGGAGCCTCTCGAA 61.069 66.667 9.46 0.00 0.00 3.71
1314 1430 4.186433 AGCCTCTCGAAGCTCGCG 62.186 66.667 0.00 0.00 40.21 5.87
1405 1521 1.153349 GTGCGGGAGGCTCTAAAGG 60.153 63.158 15.23 0.79 44.05 3.11
1666 2328 2.107950 TTTCGGCATACCTGAACTGG 57.892 50.000 0.00 0.00 31.26 4.00
1725 2390 0.323629 AAAGAAAGATGACGGGGCGA 59.676 50.000 0.00 0.00 0.00 5.54
5726 11262 5.012664 ACCCACGGATGCATATTCATAAGTA 59.987 40.000 0.00 0.00 0.00 2.24
5762 11402 9.836864 AATATTGCAACACAGACTATGAGATTA 57.163 29.630 0.00 0.00 0.00 1.75
5766 11406 7.559486 TGCAACACAGACTATGAGATTATCTT 58.441 34.615 0.00 0.00 0.00 2.40
5872 11513 1.204941 ACTTGTCCGTGACTAGATGGC 59.795 52.381 17.33 0.00 37.54 4.40
5986 11627 0.109919 GCCTTTGGCGAAAACTACGG 60.110 55.000 0.00 0.00 39.62 4.02
6057 11698 0.103755 CATGCTGAGCGGCTTCTCTA 59.896 55.000 2.97 0.00 34.29 2.43
6071 11712 3.193903 GCTTCTCTACCGAGGACTTCTTT 59.806 47.826 0.00 0.00 37.86 2.52
6083 11724 1.531578 GACTTCTTTCCCAACAGCGTC 59.468 52.381 0.00 0.00 0.00 5.19
6174 11815 4.511454 CCTTCTTTGAACAAGTCATCGACA 59.489 41.667 0.00 0.00 35.70 4.35
6189 11830 4.578898 ACAAGTGCGTCGGCGACA 62.579 61.111 35.62 17.97 44.10 4.35
6357 12004 9.862371 AACCTCATCATTACATATACTCGAATC 57.138 33.333 0.00 0.00 0.00 2.52
6432 12105 6.147821 CGGTCACTATGAGAAAGACATTTTGT 59.852 38.462 0.00 0.00 0.00 2.83
6436 12109 9.383519 TCACTATGAGAAAGACATTTTGTATCC 57.616 33.333 0.00 0.00 0.00 2.59
6453 12126 5.100811 TGTATCCATATAGGGCCATCAACT 58.899 41.667 6.18 0.00 38.24 3.16
6456 12129 3.072915 TCCATATAGGGCCATCAACTGTG 59.927 47.826 6.18 0.00 38.24 3.66
6513 12186 5.424121 AGCAACTTGTTTAGTACTTGCAG 57.576 39.130 12.92 1.47 37.70 4.41
6587 12438 2.416547 GCATGCGGCGTATTAATGATCT 59.583 45.455 8.02 0.00 0.00 2.75
6588 12439 3.616821 GCATGCGGCGTATTAATGATCTA 59.383 43.478 8.02 0.00 0.00 1.98
6703 12557 7.716998 GGATGGAGTAATTAGTTCATCACATGT 59.283 37.037 30.25 6.21 41.45 3.21
6754 12608 1.002366 GTGGCAATCACACTAGCTCG 58.998 55.000 0.00 0.00 45.39 5.03
6982 12838 0.608640 GGATTCGGGTCGCAGGATAT 59.391 55.000 0.00 0.00 0.00 1.63
6994 12850 1.072806 GCAGGATATGACATCCCAGCA 59.927 52.381 14.99 0.00 38.68 4.41
7031 12887 1.160137 GAATGCATGGGCTATCGGTC 58.840 55.000 0.00 0.00 41.91 4.79
7060 12916 1.210234 AGCGTGTGGAATGATGATCCA 59.790 47.619 0.00 0.00 44.58 3.41
7159 13031 3.148279 GGACGACGGATCTGCCCT 61.148 66.667 0.00 0.00 0.00 5.19
7256 13128 0.042581 TGGGGTGAGCTGTGAGGATA 59.957 55.000 0.00 0.00 0.00 2.59
7279 13151 4.765970 ATGGAGGAGGCAGGGGCA 62.766 66.667 0.00 0.00 43.71 5.36
7358 13230 7.871973 TGTGTCCTTGATTGAAATTAATGGTTG 59.128 33.333 0.00 0.00 0.00 3.77
7388 13260 4.094887 CAGAGCCATTAACTTATGTGCGTT 59.905 41.667 0.00 0.00 31.32 4.84
7406 13280 2.222508 CGTTGCATTCGCTGTACAGTAC 60.223 50.000 23.44 7.53 39.64 2.73
7443 13317 5.831702 TCCTTTTACGTTTGCCTGTTTTA 57.168 34.783 0.00 0.00 0.00 1.52
7446 13320 7.586747 TCCTTTTACGTTTGCCTGTTTTATAG 58.413 34.615 0.00 0.00 0.00 1.31
7450 13324 4.648651 ACGTTTGCCTGTTTTATAGTCCT 58.351 39.130 0.00 0.00 0.00 3.85
7453 13327 6.084277 CGTTTGCCTGTTTTATAGTCCTTTC 58.916 40.000 0.00 0.00 0.00 2.62
7454 13328 6.072673 CGTTTGCCTGTTTTATAGTCCTTTCT 60.073 38.462 0.00 0.00 0.00 2.52
7455 13329 7.118680 CGTTTGCCTGTTTTATAGTCCTTTCTA 59.881 37.037 0.00 0.00 0.00 2.10
7456 13330 7.916914 TTGCCTGTTTTATAGTCCTTTCTAC 57.083 36.000 0.00 0.00 0.00 2.59
7458 13332 7.630082 TGCCTGTTTTATAGTCCTTTCTACAT 58.370 34.615 0.00 0.00 0.00 2.29
7459 13333 8.764558 TGCCTGTTTTATAGTCCTTTCTACATA 58.235 33.333 0.00 0.00 0.00 2.29
7460 13334 9.043079 GCCTGTTTTATAGTCCTTTCTACATAC 57.957 37.037 0.00 0.00 0.00 2.39
7469 13343 6.592870 AGTCCTTTCTACATACAATAAGGGC 58.407 40.000 0.00 0.00 37.58 5.19
7470 13344 6.157994 AGTCCTTTCTACATACAATAAGGGCA 59.842 38.462 0.00 0.00 39.28 5.36
7471 13345 6.260271 GTCCTTTCTACATACAATAAGGGCAC 59.740 42.308 0.00 0.00 37.34 5.01
7472 13346 6.157994 TCCTTTCTACATACAATAAGGGCACT 59.842 38.462 0.00 0.00 34.35 4.40
7476 13365 4.584638 ACATACAATAAGGGCACTCCAA 57.415 40.909 0.00 0.00 38.24 3.53
7480 13369 3.421844 ACAATAAGGGCACTCCAAGTTC 58.578 45.455 0.00 0.00 38.24 3.01
7484 13373 2.032681 GGCACTCCAAGTTCGCCT 59.967 61.111 0.00 0.00 35.20 5.52
7500 13389 5.531287 AGTTCGCCTTGTTACTTTTCTTGAT 59.469 36.000 0.00 0.00 0.00 2.57
7504 13393 6.038825 TCGCCTTGTTACTTTTCTTGATTGAA 59.961 34.615 0.00 0.00 0.00 2.69
7505 13394 6.142320 CGCCTTGTTACTTTTCTTGATTGAAC 59.858 38.462 0.00 0.00 0.00 3.18
7506 13395 7.203218 GCCTTGTTACTTTTCTTGATTGAACT 58.797 34.615 0.00 0.00 0.00 3.01
7507 13396 7.168135 GCCTTGTTACTTTTCTTGATTGAACTG 59.832 37.037 0.00 0.00 0.00 3.16
7508 13397 7.168135 CCTTGTTACTTTTCTTGATTGAACTGC 59.832 37.037 0.00 0.00 0.00 4.40
7509 13398 7.333528 TGTTACTTTTCTTGATTGAACTGCT 57.666 32.000 0.00 0.00 0.00 4.24
7510 13399 7.417612 TGTTACTTTTCTTGATTGAACTGCTC 58.582 34.615 0.00 0.00 0.00 4.26
7511 13400 7.283127 TGTTACTTTTCTTGATTGAACTGCTCT 59.717 33.333 0.00 0.00 0.00 4.09
7512 13401 6.069684 ACTTTTCTTGATTGAACTGCTCTG 57.930 37.500 0.00 0.00 0.00 3.35
7513 13402 4.494350 TTTCTTGATTGAACTGCTCTGC 57.506 40.909 0.00 0.00 0.00 4.26
7514 13403 3.413846 TCTTGATTGAACTGCTCTGCT 57.586 42.857 0.00 0.00 0.00 4.24
7515 13404 3.332919 TCTTGATTGAACTGCTCTGCTC 58.667 45.455 0.00 0.00 0.00 4.26
7516 13405 1.718396 TGATTGAACTGCTCTGCTCG 58.282 50.000 0.00 0.00 0.00 5.03
7518 13407 2.231235 TGATTGAACTGCTCTGCTCGTA 59.769 45.455 0.00 0.00 0.00 3.43
7519 13408 3.118992 TGATTGAACTGCTCTGCTCGTAT 60.119 43.478 0.00 0.00 0.00 3.06
7521 13410 4.450082 TTGAACTGCTCTGCTCGTATAA 57.550 40.909 0.00 0.00 0.00 0.98
7522 13411 4.033990 TGAACTGCTCTGCTCGTATAAG 57.966 45.455 0.00 0.00 0.00 1.73
7523 13412 3.694566 TGAACTGCTCTGCTCGTATAAGA 59.305 43.478 0.00 0.00 0.00 2.10
7547 13436 4.011698 CTGACATGGATGATGTGGTTTCA 58.988 43.478 0.00 0.00 45.90 2.69
7550 13439 6.186234 TGACATGGATGATGTGGTTTCATTA 58.814 36.000 0.00 0.00 45.90 1.90
7553 13442 8.400184 ACATGGATGATGTGGTTTCATTATAG 57.600 34.615 0.00 0.00 44.12 1.31
7576 13465 2.762043 GAGCCGGGAAGAGCCTCT 60.762 66.667 2.18 0.00 36.66 3.69
7583 13472 2.035632 CGGGAAGAGCCTCTCTGTTAT 58.964 52.381 0.00 0.00 40.28 1.89
7584 13473 2.223923 CGGGAAGAGCCTCTCTGTTATG 60.224 54.545 0.00 0.00 40.28 1.90
7585 13474 2.769095 GGGAAGAGCCTCTCTGTTATGT 59.231 50.000 0.00 0.00 40.28 2.29
7587 13476 4.187694 GGAAGAGCCTCTCTGTTATGTTG 58.812 47.826 0.00 0.00 40.28 3.33
7594 13483 6.711277 AGCCTCTCTGTTATGTTGTTATTCA 58.289 36.000 0.00 0.00 0.00 2.57
7606 13495 3.651803 TGTTATTCAACAAAAGGGCCG 57.348 42.857 0.00 0.00 41.69 6.13
7607 13496 2.959707 TGTTATTCAACAAAAGGGCCGT 59.040 40.909 0.00 0.00 41.69 5.68
7608 13497 3.243569 TGTTATTCAACAAAAGGGCCGTG 60.244 43.478 0.00 0.00 41.69 4.94
7609 13498 0.678950 ATTCAACAAAAGGGCCGTGG 59.321 50.000 0.00 0.00 0.00 4.94
7610 13499 0.684805 TTCAACAAAAGGGCCGTGGT 60.685 50.000 0.00 0.00 0.00 4.16
7611 13500 0.684805 TCAACAAAAGGGCCGTGGTT 60.685 50.000 0.00 1.44 0.00 3.67
7612 13501 0.176910 CAACAAAAGGGCCGTGGTTT 59.823 50.000 0.00 0.00 0.00 3.27
7613 13502 0.462375 AACAAAAGGGCCGTGGTTTC 59.538 50.000 0.00 0.00 0.00 2.78
7614 13503 1.007849 CAAAAGGGCCGTGGTTTCG 60.008 57.895 0.00 0.00 0.00 3.46
7615 13504 1.454295 AAAAGGGCCGTGGTTTCGT 60.454 52.632 0.00 0.00 0.00 3.85
7616 13505 1.038681 AAAAGGGCCGTGGTTTCGTT 61.039 50.000 0.00 0.00 0.00 3.85
7617 13506 1.449726 AAAGGGCCGTGGTTTCGTTC 61.450 55.000 0.00 0.00 0.00 3.95
7618 13507 3.719144 GGGCCGTGGTTTCGTTCG 61.719 66.667 0.00 0.00 0.00 3.95
7619 13508 2.662527 GGCCGTGGTTTCGTTCGA 60.663 61.111 0.00 0.00 0.00 3.71
7620 13509 2.664436 GGCCGTGGTTTCGTTCGAG 61.664 63.158 0.00 0.00 0.00 4.04
7621 13510 1.952635 GCCGTGGTTTCGTTCGAGT 60.953 57.895 0.00 0.00 0.00 4.18
7622 13511 0.664166 GCCGTGGTTTCGTTCGAGTA 60.664 55.000 0.00 0.00 0.00 2.59
7623 13512 1.334054 CCGTGGTTTCGTTCGAGTAG 58.666 55.000 0.00 0.00 0.00 2.57
7624 13513 1.335324 CCGTGGTTTCGTTCGAGTAGT 60.335 52.381 0.00 0.00 0.00 2.73
7625 13514 2.095768 CCGTGGTTTCGTTCGAGTAGTA 60.096 50.000 0.00 0.00 0.00 1.82
7626 13515 3.554524 CGTGGTTTCGTTCGAGTAGTAA 58.445 45.455 0.00 0.00 0.00 2.24
7627 13516 4.161333 CGTGGTTTCGTTCGAGTAGTAAT 58.839 43.478 0.00 0.00 0.00 1.89
7628 13517 4.618489 CGTGGTTTCGTTCGAGTAGTAATT 59.382 41.667 0.00 0.00 0.00 1.40
7629 13518 5.794945 CGTGGTTTCGTTCGAGTAGTAATTA 59.205 40.000 0.00 0.00 0.00 1.40
7630 13519 6.470235 CGTGGTTTCGTTCGAGTAGTAATTAT 59.530 38.462 0.00 0.00 0.00 1.28
7631 13520 7.008628 CGTGGTTTCGTTCGAGTAGTAATTATT 59.991 37.037 0.00 0.00 0.00 1.40
7632 13521 8.316753 GTGGTTTCGTTCGAGTAGTAATTATTC 58.683 37.037 0.00 0.00 0.00 1.75
7633 13522 8.246180 TGGTTTCGTTCGAGTAGTAATTATTCT 58.754 33.333 0.00 0.00 0.00 2.40
7634 13523 9.722056 GGTTTCGTTCGAGTAGTAATTATTCTA 57.278 33.333 0.00 0.00 0.00 2.10
7673 13562 6.699895 GCATATGCATGTCCAACAATATTG 57.300 37.500 22.84 14.01 41.59 1.90
7674 13563 6.218019 GCATATGCATGTCCAACAATATTGT 58.782 36.000 22.84 15.47 41.46 2.71
7675 13564 6.144886 GCATATGCATGTCCAACAATATTGTG 59.855 38.462 22.84 14.56 40.33 3.33
7676 13565 3.847542 TGCATGTCCAACAATATTGTGC 58.152 40.909 21.46 17.52 41.31 4.57
7677 13566 3.257624 TGCATGTCCAACAATATTGTGCA 59.742 39.130 21.46 19.66 41.31 4.57
7678 13567 3.861113 GCATGTCCAACAATATTGTGCAG 59.139 43.478 21.46 13.86 41.31 4.41
7679 13568 4.426416 CATGTCCAACAATATTGTGCAGG 58.574 43.478 21.46 21.01 41.31 4.85
7680 13569 3.760738 TGTCCAACAATATTGTGCAGGA 58.239 40.909 21.46 22.65 41.31 3.86
7681 13570 3.505680 TGTCCAACAATATTGTGCAGGAC 59.494 43.478 34.21 34.21 46.88 3.85
7682 13571 3.088532 TCCAACAATATTGTGCAGGACC 58.911 45.455 21.46 0.00 41.31 4.46
7683 13572 2.824936 CCAACAATATTGTGCAGGACCA 59.175 45.455 21.46 0.00 41.31 4.02
7684 13573 3.448301 CCAACAATATTGTGCAGGACCAT 59.552 43.478 21.46 0.00 41.31 3.55
7685 13574 4.426416 CAACAATATTGTGCAGGACCATG 58.574 43.478 21.46 8.98 41.31 3.66
7686 13575 3.966979 ACAATATTGTGCAGGACCATGA 58.033 40.909 20.19 0.00 40.49 3.07
7687 13576 4.539726 ACAATATTGTGCAGGACCATGAT 58.460 39.130 20.19 0.00 40.49 2.45
7688 13577 4.957954 ACAATATTGTGCAGGACCATGATT 59.042 37.500 20.19 0.00 40.49 2.57
7689 13578 5.068198 ACAATATTGTGCAGGACCATGATTC 59.932 40.000 20.19 0.00 40.49 2.52
7690 13579 2.885135 TTGTGCAGGACCATGATTCT 57.115 45.000 0.00 0.00 0.00 2.40
7691 13580 2.118313 TGTGCAGGACCATGATTCTG 57.882 50.000 0.00 0.00 0.00 3.02
7693 13582 2.412605 GCAGGACCATGATTCTGCC 58.587 57.895 9.53 0.00 44.70 4.85
7694 13583 1.442526 GCAGGACCATGATTCTGCCG 61.443 60.000 9.53 0.00 44.70 5.69
7695 13584 0.178767 CAGGACCATGATTCTGCCGA 59.821 55.000 0.00 0.00 0.00 5.54
7696 13585 0.911769 AGGACCATGATTCTGCCGAA 59.088 50.000 0.00 0.00 0.00 4.30
7697 13586 1.017387 GGACCATGATTCTGCCGAAC 58.983 55.000 0.00 0.00 30.67 3.95
7698 13587 1.407437 GGACCATGATTCTGCCGAACT 60.407 52.381 0.00 0.00 30.67 3.01
7699 13588 2.359900 GACCATGATTCTGCCGAACTT 58.640 47.619 0.00 0.00 30.67 2.66
7700 13589 3.531538 GACCATGATTCTGCCGAACTTA 58.468 45.455 0.00 0.00 30.67 2.24
7701 13590 4.130118 GACCATGATTCTGCCGAACTTAT 58.870 43.478 0.00 0.00 30.67 1.73
7702 13591 5.290493 ACCATGATTCTGCCGAACTTATA 57.710 39.130 0.00 0.00 30.67 0.98
7703 13592 5.057149 ACCATGATTCTGCCGAACTTATAC 58.943 41.667 0.00 0.00 30.67 1.47
7704 13593 5.163301 ACCATGATTCTGCCGAACTTATACT 60.163 40.000 0.00 0.00 30.67 2.12
7705 13594 5.406780 CCATGATTCTGCCGAACTTATACTC 59.593 44.000 0.00 0.00 30.67 2.59
7706 13595 4.607955 TGATTCTGCCGAACTTATACTCG 58.392 43.478 0.00 0.00 34.83 4.18
7714 13603 4.100707 CGAACTTATACTCGGTTCCACA 57.899 45.455 0.00 0.00 36.85 4.17
7715 13604 3.855950 CGAACTTATACTCGGTTCCACAC 59.144 47.826 0.00 0.00 36.85 3.82
7716 13605 4.616604 CGAACTTATACTCGGTTCCACACA 60.617 45.833 0.00 0.00 36.85 3.72
7717 13606 5.416271 AACTTATACTCGGTTCCACACAT 57.584 39.130 0.00 0.00 0.00 3.21
7718 13607 5.007385 ACTTATACTCGGTTCCACACATC 57.993 43.478 0.00 0.00 0.00 3.06
7719 13608 4.464951 ACTTATACTCGGTTCCACACATCA 59.535 41.667 0.00 0.00 0.00 3.07
7720 13609 2.736144 TACTCGGTTCCACACATCAC 57.264 50.000 0.00 0.00 0.00 3.06
7721 13610 0.756294 ACTCGGTTCCACACATCACA 59.244 50.000 0.00 0.00 0.00 3.58
7722 13611 1.347707 ACTCGGTTCCACACATCACAT 59.652 47.619 0.00 0.00 0.00 3.21
7723 13612 1.733912 CTCGGTTCCACACATCACATG 59.266 52.381 0.00 0.00 0.00 3.21
7724 13613 1.346068 TCGGTTCCACACATCACATGA 59.654 47.619 0.00 0.00 0.00 3.07
7725 13614 1.464608 CGGTTCCACACATCACATGAC 59.535 52.381 0.00 0.00 0.00 3.06
7726 13615 2.503331 GGTTCCACACATCACATGACA 58.497 47.619 0.00 0.00 0.00 3.58
7727 13616 2.884012 GGTTCCACACATCACATGACAA 59.116 45.455 0.00 0.00 0.00 3.18
7728 13617 3.304659 GGTTCCACACATCACATGACAAC 60.305 47.826 0.00 0.00 0.00 3.32
7729 13618 3.205784 TCCACACATCACATGACAACA 57.794 42.857 0.00 0.00 0.00 3.33
7730 13619 3.753815 TCCACACATCACATGACAACAT 58.246 40.909 0.00 0.00 37.19 2.71
7731 13620 4.143543 TCCACACATCACATGACAACATT 58.856 39.130 0.00 0.00 34.15 2.71
7732 13621 4.583907 TCCACACATCACATGACAACATTT 59.416 37.500 0.00 0.00 34.15 2.32
7733 13622 4.682401 CCACACATCACATGACAACATTTG 59.318 41.667 0.00 0.00 36.05 2.32
7746 13635 5.221891 ACAACATTTGTCGAGATATGTGC 57.778 39.130 17.12 0.00 40.56 4.57
7747 13636 4.694982 ACAACATTTGTCGAGATATGTGCA 59.305 37.500 17.12 0.00 40.56 4.57
7748 13637 5.355071 ACAACATTTGTCGAGATATGTGCAT 59.645 36.000 17.12 5.61 40.56 3.96
7749 13638 5.413969 ACATTTGTCGAGATATGTGCATG 57.586 39.130 15.98 0.00 30.51 4.06
7750 13639 4.274214 ACATTTGTCGAGATATGTGCATGG 59.726 41.667 15.98 0.00 30.51 3.66
7751 13640 1.869774 TGTCGAGATATGTGCATGGC 58.130 50.000 0.00 0.00 0.00 4.40
7752 13641 0.786581 GTCGAGATATGTGCATGGCG 59.213 55.000 0.00 0.00 0.00 5.69
7753 13642 0.319813 TCGAGATATGTGCATGGCGG 60.320 55.000 0.00 0.00 0.00 6.13
7754 13643 0.601046 CGAGATATGTGCATGGCGGT 60.601 55.000 0.00 0.00 0.00 5.68
7755 13644 1.597742 GAGATATGTGCATGGCGGTT 58.402 50.000 0.00 0.00 0.00 4.44
7756 13645 1.265095 GAGATATGTGCATGGCGGTTG 59.735 52.381 0.00 0.00 0.00 3.77
7757 13646 1.024271 GATATGTGCATGGCGGTTGT 58.976 50.000 0.00 0.00 0.00 3.32
7758 13647 0.740149 ATATGTGCATGGCGGTTGTG 59.260 50.000 0.00 0.00 0.00 3.33
7759 13648 1.311651 TATGTGCATGGCGGTTGTGG 61.312 55.000 0.00 0.00 0.00 4.17
7760 13649 3.294493 GTGCATGGCGGTTGTGGT 61.294 61.111 0.00 0.00 0.00 4.16
7761 13650 1.969064 GTGCATGGCGGTTGTGGTA 60.969 57.895 0.00 0.00 0.00 3.25
7762 13651 1.673993 TGCATGGCGGTTGTGGTAG 60.674 57.895 0.00 0.00 0.00 3.18
7763 13652 1.376683 GCATGGCGGTTGTGGTAGA 60.377 57.895 0.00 0.00 0.00 2.59
7764 13653 1.644786 GCATGGCGGTTGTGGTAGAC 61.645 60.000 0.00 0.00 0.00 2.59
7765 13654 0.036388 CATGGCGGTTGTGGTAGACT 60.036 55.000 0.00 0.00 0.00 3.24
7766 13655 0.690762 ATGGCGGTTGTGGTAGACTT 59.309 50.000 0.00 0.00 0.00 3.01
7767 13656 0.470766 TGGCGGTTGTGGTAGACTTT 59.529 50.000 0.00 0.00 0.00 2.66
7768 13657 0.872388 GGCGGTTGTGGTAGACTTTG 59.128 55.000 0.00 0.00 0.00 2.77
7769 13658 0.872388 GCGGTTGTGGTAGACTTTGG 59.128 55.000 0.00 0.00 0.00 3.28
7770 13659 0.872388 CGGTTGTGGTAGACTTTGGC 59.128 55.000 0.00 0.00 0.00 4.52
7771 13660 0.872388 GGTTGTGGTAGACTTTGGCG 59.128 55.000 0.00 0.00 0.00 5.69
7772 13661 0.872388 GTTGTGGTAGACTTTGGCGG 59.128 55.000 0.00 0.00 0.00 6.13
7773 13662 0.250553 TTGTGGTAGACTTTGGCGGG 60.251 55.000 0.00 0.00 0.00 6.13
7774 13663 1.122632 TGTGGTAGACTTTGGCGGGA 61.123 55.000 0.00 0.00 0.00 5.14
7775 13664 0.035739 GTGGTAGACTTTGGCGGGAA 59.964 55.000 0.00 0.00 0.00 3.97
7776 13665 0.323629 TGGTAGACTTTGGCGGGAAG 59.676 55.000 0.00 0.00 0.00 3.46
7777 13666 0.392595 GGTAGACTTTGGCGGGAAGG 60.393 60.000 0.00 0.00 0.00 3.46
7778 13667 0.611714 GTAGACTTTGGCGGGAAGGA 59.388 55.000 0.00 0.00 0.00 3.36
7779 13668 1.209747 GTAGACTTTGGCGGGAAGGAT 59.790 52.381 0.00 0.00 0.00 3.24
7780 13669 0.253327 AGACTTTGGCGGGAAGGATC 59.747 55.000 0.00 0.00 0.00 3.36
7781 13670 0.035439 GACTTTGGCGGGAAGGATCA 60.035 55.000 0.00 0.00 0.00 2.92
7782 13671 0.404040 ACTTTGGCGGGAAGGATCAA 59.596 50.000 0.00 0.00 0.00 2.57
7783 13672 0.811281 CTTTGGCGGGAAGGATCAAC 59.189 55.000 0.00 0.00 0.00 3.18
7784 13673 0.958382 TTTGGCGGGAAGGATCAACG 60.958 55.000 0.00 0.00 0.00 4.10
7785 13674 2.513897 GGCGGGAAGGATCAACGG 60.514 66.667 0.00 0.00 0.00 4.44
7786 13675 2.582436 GCGGGAAGGATCAACGGA 59.418 61.111 0.00 0.00 0.00 4.69
7787 13676 1.814169 GCGGGAAGGATCAACGGAC 60.814 63.158 0.00 0.00 0.00 4.79
7788 13677 1.594833 CGGGAAGGATCAACGGACA 59.405 57.895 0.00 0.00 0.00 4.02
7789 13678 0.178068 CGGGAAGGATCAACGGACAT 59.822 55.000 0.00 0.00 0.00 3.06
7790 13679 1.806623 CGGGAAGGATCAACGGACATC 60.807 57.143 0.00 0.00 0.00 3.06
7791 13680 1.475213 GGGAAGGATCAACGGACATCC 60.475 57.143 0.00 1.49 39.24 3.51
7792 13681 1.475213 GGAAGGATCAACGGACATCCC 60.475 57.143 0.00 0.00 39.73 3.85
7793 13682 1.209504 GAAGGATCAACGGACATCCCA 59.790 52.381 0.00 0.00 39.73 4.37
7794 13683 0.541863 AGGATCAACGGACATCCCAC 59.458 55.000 0.00 0.00 39.73 4.61
7795 13684 0.810031 GGATCAACGGACATCCCACG 60.810 60.000 0.00 0.00 33.55 4.94
7796 13685 0.108329 GATCAACGGACATCCCACGT 60.108 55.000 0.00 0.00 43.43 4.49
7800 13689 1.895238 ACGGACATCCCACGTTAGG 59.105 57.895 0.00 0.00 37.61 2.69
7801 13690 1.520787 CGGACATCCCACGTTAGGC 60.521 63.158 0.00 0.00 34.14 3.93
7802 13691 1.153229 GGACATCCCACGTTAGGCC 60.153 63.158 0.00 0.00 34.14 5.19
7803 13692 1.153229 GACATCCCACGTTAGGCCC 60.153 63.158 0.00 0.00 0.00 5.80
7804 13693 1.615424 ACATCCCACGTTAGGCCCT 60.615 57.895 0.00 0.00 0.00 5.19
7805 13694 1.146263 CATCCCACGTTAGGCCCTC 59.854 63.158 0.00 0.00 0.00 4.30
7806 13695 2.070650 ATCCCACGTTAGGCCCTCC 61.071 63.158 0.00 0.00 0.00 4.30
7807 13696 3.793888 CCCACGTTAGGCCCTCCC 61.794 72.222 0.00 0.00 0.00 4.30
7808 13697 3.793888 CCACGTTAGGCCCTCCCC 61.794 72.222 0.00 0.00 0.00 4.81
7809 13698 3.006728 CACGTTAGGCCCTCCCCA 61.007 66.667 0.00 0.00 0.00 4.96
7964 13859 3.931907 ACACAGGTGTACATGCCATAT 57.068 42.857 2.68 0.00 42.90 1.78
8140 14035 1.064296 GAGCGACACGATCACGGAT 59.936 57.895 4.60 0.00 42.09 4.18
8187 14082 1.237533 TGTGCGCTGATGTTGAACAT 58.762 45.000 11.10 11.10 42.43 2.71
8278 14173 2.634453 TGAGCTCATGGAGAAGTTGTCA 59.366 45.455 13.74 0.00 0.00 3.58
8293 14188 1.279496 TGTCATAGCCAGCAGGACTT 58.721 50.000 0.00 0.00 36.89 3.01
8317 14212 0.743688 ACACAATTTGCAACTCCGCA 59.256 45.000 0.00 0.00 41.03 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
836 942 2.620108 GCATTCCCTCCTCTGCTTCTTT 60.620 50.000 0.00 0.00 0.00 2.52
879 985 2.304180 CCACTCATTCTGTCCTCCACTT 59.696 50.000 0.00 0.00 0.00 3.16
941 1047 3.314331 CTCTGGTCCCACGCACCT 61.314 66.667 0.00 0.00 34.66 4.00
1126 1239 1.717032 TGTTGGTGTAGGAGCTCTGT 58.283 50.000 14.64 3.93 0.00 3.41
1127 1240 2.839486 TTGTTGGTGTAGGAGCTCTG 57.161 50.000 14.64 0.00 0.00 3.35
1139 1252 0.178953 AAGGAGCTGCCATTGTTGGT 60.179 50.000 0.00 0.00 45.57 3.67
1159 1272 6.271159 AGGGAGATAAGTGGGAGAATGAATAC 59.729 42.308 0.00 0.00 0.00 1.89
1196 1312 3.083997 ACCTGTCCCATCTCCGGC 61.084 66.667 0.00 0.00 0.00 6.13
1207 1323 2.240162 CTAAGGCCACCGGACCTGTC 62.240 65.000 9.46 0.00 36.07 3.51
1388 1504 1.612442 ACCTTTAGAGCCTCCCGCA 60.612 57.895 0.00 0.00 41.38 5.69
1604 1720 9.851686 TTGCTGATTCAGAAATACTATAACCAT 57.148 29.630 17.87 0.00 32.44 3.55
1697 2362 6.039270 CCCCGTCATCTTTCTTTATGCATAAA 59.961 38.462 26.14 26.14 0.00 1.40
1702 2367 2.033424 GCCCCGTCATCTTTCTTTATGC 59.967 50.000 0.00 0.00 0.00 3.14
1707 2372 0.391263 GTCGCCCCGTCATCTTTCTT 60.391 55.000 0.00 0.00 0.00 2.52
1718 2383 1.241315 ATCAAGTTTTGGTCGCCCCG 61.241 55.000 0.00 0.00 35.15 5.73
1725 2390 7.823745 ATTCTGACACTAATCAAGTTTTGGT 57.176 32.000 0.00 0.00 35.76 3.67
5762 11402 8.311395 TCACTGGTTCAGTTCTATATGAAGAT 57.689 34.615 0.00 0.00 42.59 2.40
5766 11406 9.739276 ATTTTTCACTGGTTCAGTTCTATATGA 57.261 29.630 0.00 0.00 42.59 2.15
5986 11627 2.747855 CCTTGAACTGCTCCGCCC 60.748 66.667 0.00 0.00 0.00 6.13
6057 11698 1.071857 GTTGGGAAAGAAGTCCTCGGT 59.928 52.381 0.00 0.00 37.85 4.69
6071 11712 4.351938 CGACCGACGCTGTTGGGA 62.352 66.667 16.20 0.00 41.22 4.37
6093 11734 2.396590 ATGCCCGTAACTTTGTCGAT 57.603 45.000 0.00 0.00 0.00 3.59
6122 11763 4.849518 TCTTCTTGAAGATCCTCTCTCGA 58.150 43.478 8.80 0.00 31.03 4.04
6174 11815 2.357034 ATTGTCGCCGACGCACTT 60.357 55.556 13.18 0.00 39.84 3.16
6189 11830 1.078143 GCCTTCTGCGACTGGGATT 60.078 57.895 0.00 0.00 0.00 3.01
6432 12105 5.045651 CACAGTTGATGGCCCTATATGGATA 60.046 44.000 0.00 0.00 38.35 2.59
6436 12109 4.356405 TCACAGTTGATGGCCCTATATG 57.644 45.455 0.00 0.00 0.00 1.78
6453 12126 5.000591 TCACTAATTTTTGCCTCGATCACA 58.999 37.500 0.00 0.00 0.00 3.58
6456 12129 6.124088 ACATCACTAATTTTTGCCTCGATC 57.876 37.500 0.00 0.00 0.00 3.69
6534 12207 8.093927 AGAAAGGAATGAGAAGAAAGTAGTGAG 58.906 37.037 0.00 0.00 0.00 3.51
6537 12210 7.093992 CGAGAAAGGAATGAGAAGAAAGTAGT 58.906 38.462 0.00 0.00 0.00 2.73
6671 12525 6.601332 TGAACTAATTACTCCATCCATTCCC 58.399 40.000 0.00 0.00 0.00 3.97
6703 12557 7.275888 AGTGTTCTGAAACATTAGCAATTGA 57.724 32.000 10.34 0.00 46.58 2.57
6754 12608 3.368323 CCATTGCCCAGTTTATTGTCACC 60.368 47.826 0.00 0.00 0.00 4.02
6969 12825 1.338200 GGATGTCATATCCTGCGACCC 60.338 57.143 0.00 0.00 35.36 4.46
6982 12838 2.655090 TTGTCTTTGCTGGGATGTCA 57.345 45.000 0.00 0.00 0.00 3.58
6994 12850 5.181811 TGCATTCACGATGATCTTTGTCTTT 59.818 36.000 0.00 0.00 38.03 2.52
7031 12887 4.838152 CCACACGCTGGGATCCCG 62.838 72.222 26.03 20.32 39.42 5.14
7060 12916 1.544246 CTTTCCGGGCGAAATTCCTTT 59.456 47.619 0.00 0.00 39.73 3.11
7061 12917 1.173913 CTTTCCGGGCGAAATTCCTT 58.826 50.000 0.00 0.00 39.73 3.36
7141 13013 3.148279 GGGCAGATCCGTCGTCCT 61.148 66.667 0.00 0.00 34.94 3.85
7256 13128 0.549950 CCTGCCTCCTCCATGTTGAT 59.450 55.000 0.00 0.00 0.00 2.57
7279 13151 3.381949 CGTCTTCTTTCGGAAAGTCAGT 58.618 45.455 25.21 0.00 39.52 3.41
7350 13222 2.436417 GCTCTGCCAGTTCAACCATTA 58.564 47.619 0.00 0.00 0.00 1.90
7351 13223 1.251251 GCTCTGCCAGTTCAACCATT 58.749 50.000 0.00 0.00 0.00 3.16
7352 13224 2.952714 GCTCTGCCAGTTCAACCAT 58.047 52.632 0.00 0.00 0.00 3.55
7353 13225 4.481195 GCTCTGCCAGTTCAACCA 57.519 55.556 0.00 0.00 0.00 3.67
7371 13243 5.053091 CGAATGCAACGCACATAAGTTAATG 60.053 40.000 0.00 0.00 43.04 1.90
7374 13246 3.997276 CGAATGCAACGCACATAAGTTA 58.003 40.909 0.00 0.00 43.04 2.24
7388 13260 1.068125 ACGTACTGTACAGCGAATGCA 60.068 47.619 22.90 0.00 46.23 3.96
7406 13280 5.167628 CGTAAAAGGAAACACAAAACGTACG 59.832 40.000 15.01 15.01 0.00 3.67
7443 13317 8.376270 GCCCTTATTGTATGTAGAAAGGACTAT 58.624 37.037 0.00 0.00 36.42 2.12
7446 13320 6.260271 GTGCCCTTATTGTATGTAGAAAGGAC 59.740 42.308 0.00 0.00 36.42 3.85
7450 13324 6.069905 TGGAGTGCCCTTATTGTATGTAGAAA 60.070 38.462 0.00 0.00 35.38 2.52
7453 13327 5.290493 TGGAGTGCCCTTATTGTATGTAG 57.710 43.478 0.00 0.00 35.38 2.74
7454 13328 5.190925 ACTTGGAGTGCCCTTATTGTATGTA 59.809 40.000 0.00 0.00 35.38 2.29
7455 13329 4.018415 ACTTGGAGTGCCCTTATTGTATGT 60.018 41.667 0.00 0.00 35.38 2.29
7456 13330 4.526970 ACTTGGAGTGCCCTTATTGTATG 58.473 43.478 0.00 0.00 35.38 2.39
7458 13332 4.585879 GAACTTGGAGTGCCCTTATTGTA 58.414 43.478 0.00 0.00 35.38 2.41
7459 13333 3.421844 GAACTTGGAGTGCCCTTATTGT 58.578 45.455 0.00 0.00 35.38 2.71
7460 13334 2.420022 CGAACTTGGAGTGCCCTTATTG 59.580 50.000 0.00 0.00 35.38 1.90
7461 13335 2.711542 CGAACTTGGAGTGCCCTTATT 58.288 47.619 0.00 0.00 35.38 1.40
7462 13336 1.679032 GCGAACTTGGAGTGCCCTTAT 60.679 52.381 0.00 0.00 35.38 1.73
7463 13337 0.321298 GCGAACTTGGAGTGCCCTTA 60.321 55.000 0.00 0.00 35.38 2.69
7464 13338 1.600916 GCGAACTTGGAGTGCCCTT 60.601 57.895 0.00 0.00 35.38 3.95
7465 13339 2.032681 GCGAACTTGGAGTGCCCT 59.967 61.111 0.00 0.00 35.38 5.19
7467 13341 1.600916 AAGGCGAACTTGGAGTGCC 60.601 57.895 2.21 2.21 46.07 5.01
7468 13342 4.065110 AAGGCGAACTTGGAGTGC 57.935 55.556 0.00 0.00 38.21 4.40
7476 13365 4.879545 TCAAGAAAAGTAACAAGGCGAACT 59.120 37.500 0.00 0.00 0.00 3.01
7480 13369 5.757886 TCAATCAAGAAAAGTAACAAGGCG 58.242 37.500 0.00 0.00 0.00 5.52
7484 13373 7.771183 AGCAGTTCAATCAAGAAAAGTAACAA 58.229 30.769 0.00 0.00 0.00 2.83
7500 13389 4.157840 TCTTATACGAGCAGAGCAGTTCAA 59.842 41.667 0.00 0.00 0.00 2.69
7504 13393 3.980646 CTCTTATACGAGCAGAGCAGT 57.019 47.619 0.00 0.00 0.00 4.40
7513 13402 4.837896 TCCATGTCAGCTCTTATACGAG 57.162 45.455 1.89 1.89 0.00 4.18
7514 13403 4.827284 TCATCCATGTCAGCTCTTATACGA 59.173 41.667 0.00 0.00 0.00 3.43
7515 13404 5.126396 TCATCCATGTCAGCTCTTATACG 57.874 43.478 0.00 0.00 0.00 3.06
7516 13405 6.368243 CACATCATCCATGTCAGCTCTTATAC 59.632 42.308 0.00 0.00 44.60 1.47
7518 13407 5.306394 CACATCATCCATGTCAGCTCTTAT 58.694 41.667 0.00 0.00 44.60 1.73
7519 13408 4.443881 CCACATCATCCATGTCAGCTCTTA 60.444 45.833 0.00 0.00 44.60 2.10
7521 13410 2.158798 CCACATCATCCATGTCAGCTCT 60.159 50.000 0.00 0.00 44.60 4.09
7522 13411 2.219458 CCACATCATCCATGTCAGCTC 58.781 52.381 0.00 0.00 44.60 4.09
7523 13412 1.562942 ACCACATCATCCATGTCAGCT 59.437 47.619 0.00 0.00 44.60 4.24
7525 13414 4.011698 TGAAACCACATCATCCATGTCAG 58.988 43.478 0.00 0.00 44.60 3.51
7527 13416 5.587388 AATGAAACCACATCATCCATGTC 57.413 39.130 0.00 0.00 44.60 3.06
7529 13418 8.400184 ACTATAATGAAACCACATCATCCATG 57.600 34.615 0.00 0.00 36.53 3.66
7547 13436 5.091552 TCTTCCCGGCTCCATTACTATAAT 58.908 41.667 0.00 0.00 0.00 1.28
7550 13439 2.900546 CTCTTCCCGGCTCCATTACTAT 59.099 50.000 0.00 0.00 0.00 2.12
7553 13442 0.533085 GCTCTTCCCGGCTCCATTAC 60.533 60.000 0.00 0.00 0.00 1.89
7587 13476 3.313690 CACGGCCCTTTTGTTGAATAAC 58.686 45.455 0.00 0.00 37.32 1.89
7594 13483 0.462375 GAAACCACGGCCCTTTTGTT 59.538 50.000 0.00 0.00 0.00 2.83
7600 13489 2.281276 GAACGAAACCACGGCCCT 60.281 61.111 0.00 0.00 37.61 5.19
7601 13490 3.719144 CGAACGAAACCACGGCCC 61.719 66.667 0.00 0.00 37.61 5.80
7602 13491 2.662527 TCGAACGAAACCACGGCC 60.663 61.111 0.00 0.00 37.61 6.13
7603 13492 0.664166 TACTCGAACGAAACCACGGC 60.664 55.000 0.00 0.00 37.61 5.68
7604 13493 1.334054 CTACTCGAACGAAACCACGG 58.666 55.000 0.00 0.00 37.61 4.94
7605 13494 2.042104 ACTACTCGAACGAAACCACG 57.958 50.000 0.00 0.00 39.31 4.94
7606 13495 7.746526 ATAATTACTACTCGAACGAAACCAC 57.253 36.000 0.00 0.00 0.00 4.16
7607 13496 8.246180 AGAATAATTACTACTCGAACGAAACCA 58.754 33.333 0.00 0.00 0.00 3.67
7608 13497 8.626093 AGAATAATTACTACTCGAACGAAACC 57.374 34.615 0.00 0.00 0.00 3.27
7648 13537 7.633116 ACAATATTGTTGGACATGCATATGCAA 60.633 33.333 32.59 14.50 46.76 4.08
7650 13539 6.144886 CACAATATTGTTGGACATGCATATGC 59.855 38.462 21.09 21.09 39.91 3.14
7651 13540 6.144886 GCACAATATTGTTGGACATGCATATG 59.855 38.462 18.50 0.00 39.91 1.78
7652 13541 6.183360 TGCACAATATTGTTGGACATGCATAT 60.183 34.615 18.50 0.00 39.91 1.78
7653 13542 5.126707 TGCACAATATTGTTGGACATGCATA 59.873 36.000 18.50 0.41 39.91 3.14
7654 13543 4.081586 TGCACAATATTGTTGGACATGCAT 60.082 37.500 18.50 0.00 39.91 3.96
7655 13544 3.257624 TGCACAATATTGTTGGACATGCA 59.742 39.130 18.50 18.43 39.91 3.96
7656 13545 3.847542 TGCACAATATTGTTGGACATGC 58.152 40.909 18.50 16.24 39.91 4.06
7657 13546 4.158209 TCCTGCACAATATTGTTGGACATG 59.842 41.667 18.50 11.09 39.91 3.21
7658 13547 4.158394 GTCCTGCACAATATTGTTGGACAT 59.842 41.667 33.28 11.44 44.26 3.06
7659 13548 3.505680 GTCCTGCACAATATTGTTGGACA 59.494 43.478 33.28 22.93 44.26 4.02
7660 13549 3.119495 GGTCCTGCACAATATTGTTGGAC 60.119 47.826 32.06 32.06 44.20 4.02
7661 13550 3.088532 GGTCCTGCACAATATTGTTGGA 58.911 45.455 18.50 20.33 39.91 3.53
7662 13551 2.824936 TGGTCCTGCACAATATTGTTGG 59.175 45.455 18.50 18.64 39.91 3.77
7663 13552 4.158209 TCATGGTCCTGCACAATATTGTTG 59.842 41.667 18.50 14.29 39.91 3.33
7664 13553 4.343231 TCATGGTCCTGCACAATATTGTT 58.657 39.130 18.50 1.72 39.91 2.83
7665 13554 3.966979 TCATGGTCCTGCACAATATTGT 58.033 40.909 15.47 15.47 43.36 2.71
7666 13555 5.301045 AGAATCATGGTCCTGCACAATATTG 59.699 40.000 14.01 14.01 0.00 1.90
7667 13556 5.301045 CAGAATCATGGTCCTGCACAATATT 59.699 40.000 0.00 0.00 0.00 1.28
7668 13557 4.825634 CAGAATCATGGTCCTGCACAATAT 59.174 41.667 0.00 0.00 0.00 1.28
7669 13558 4.201657 CAGAATCATGGTCCTGCACAATA 58.798 43.478 0.00 0.00 0.00 1.90
7670 13559 3.021695 CAGAATCATGGTCCTGCACAAT 58.978 45.455 0.00 0.00 0.00 2.71
7671 13560 2.439409 CAGAATCATGGTCCTGCACAA 58.561 47.619 0.00 0.00 0.00 3.33
7672 13561 2.118313 CAGAATCATGGTCCTGCACA 57.882 50.000 0.00 0.00 0.00 4.57
7676 13565 0.178767 TCGGCAGAATCATGGTCCTG 59.821 55.000 0.00 0.00 0.00 3.86
7677 13566 0.911769 TTCGGCAGAATCATGGTCCT 59.088 50.000 0.00 0.00 0.00 3.85
7678 13567 1.017387 GTTCGGCAGAATCATGGTCC 58.983 55.000 1.73 0.00 38.80 4.46
7679 13568 2.029838 AGTTCGGCAGAATCATGGTC 57.970 50.000 1.73 0.00 38.80 4.02
7680 13569 2.496899 AAGTTCGGCAGAATCATGGT 57.503 45.000 1.73 0.00 38.80 3.55
7681 13570 5.300752 AGTATAAGTTCGGCAGAATCATGG 58.699 41.667 1.73 0.00 38.80 3.66
7682 13571 5.117745 CGAGTATAAGTTCGGCAGAATCATG 59.882 44.000 1.73 0.00 38.80 3.07
7683 13572 5.223382 CGAGTATAAGTTCGGCAGAATCAT 58.777 41.667 1.73 0.00 38.80 2.45
7684 13573 4.607955 CGAGTATAAGTTCGGCAGAATCA 58.392 43.478 1.73 0.00 38.80 2.57
7693 13582 3.855950 GTGTGGAACCGAGTATAAGTTCG 59.144 47.826 0.00 0.00 40.62 3.95
7694 13583 4.813027 TGTGTGGAACCGAGTATAAGTTC 58.187 43.478 0.00 0.00 39.31 3.01
7695 13584 4.877378 TGTGTGGAACCGAGTATAAGTT 57.123 40.909 0.00 0.00 34.36 2.66
7696 13585 4.464951 TGATGTGTGGAACCGAGTATAAGT 59.535 41.667 0.00 0.00 34.36 2.24
7697 13586 4.804139 GTGATGTGTGGAACCGAGTATAAG 59.196 45.833 0.00 0.00 34.36 1.73
7698 13587 4.221041 TGTGATGTGTGGAACCGAGTATAA 59.779 41.667 0.00 0.00 34.36 0.98
7699 13588 3.764972 TGTGATGTGTGGAACCGAGTATA 59.235 43.478 0.00 0.00 34.36 1.47
7700 13589 2.565391 TGTGATGTGTGGAACCGAGTAT 59.435 45.455 0.00 0.00 34.36 2.12
7701 13590 1.964933 TGTGATGTGTGGAACCGAGTA 59.035 47.619 0.00 0.00 34.36 2.59
7702 13591 0.756294 TGTGATGTGTGGAACCGAGT 59.244 50.000 0.00 0.00 34.36 4.18
7703 13592 1.733912 CATGTGATGTGTGGAACCGAG 59.266 52.381 0.00 0.00 34.36 4.63
7704 13593 1.346068 TCATGTGATGTGTGGAACCGA 59.654 47.619 0.00 0.00 34.36 4.69
7705 13594 1.464608 GTCATGTGATGTGTGGAACCG 59.535 52.381 0.00 0.00 34.36 4.44
7706 13595 2.503331 TGTCATGTGATGTGTGGAACC 58.497 47.619 0.00 0.00 34.36 3.62
7707 13596 3.314913 TGTTGTCATGTGATGTGTGGAAC 59.685 43.478 0.00 0.00 37.35 3.62
7708 13597 3.549794 TGTTGTCATGTGATGTGTGGAA 58.450 40.909 0.00 0.00 0.00 3.53
7709 13598 3.205784 TGTTGTCATGTGATGTGTGGA 57.794 42.857 0.00 0.00 0.00 4.02
7710 13599 4.508461 AATGTTGTCATGTGATGTGTGG 57.492 40.909 0.00 0.00 34.19 4.17
7711 13600 5.283294 ACAAATGTTGTCATGTGATGTGTG 58.717 37.500 5.53 0.00 40.56 3.82
7712 13601 5.518848 ACAAATGTTGTCATGTGATGTGT 57.481 34.783 5.53 0.00 40.56 3.72
7725 13614 5.220557 TGCACATATCTCGACAAATGTTG 57.779 39.130 0.27 0.00 30.32 3.33
7726 13615 5.220912 CCATGCACATATCTCGACAAATGTT 60.221 40.000 0.00 0.00 30.32 2.71
7727 13616 4.274214 CCATGCACATATCTCGACAAATGT 59.726 41.667 0.00 0.00 32.91 2.71
7728 13617 4.779987 CCATGCACATATCTCGACAAATG 58.220 43.478 0.00 0.00 0.00 2.32
7729 13618 3.251729 GCCATGCACATATCTCGACAAAT 59.748 43.478 0.00 0.00 0.00 2.32
7730 13619 2.613595 GCCATGCACATATCTCGACAAA 59.386 45.455 0.00 0.00 0.00 2.83
7731 13620 2.212652 GCCATGCACATATCTCGACAA 58.787 47.619 0.00 0.00 0.00 3.18
7732 13621 1.869342 CGCCATGCACATATCTCGACA 60.869 52.381 0.00 0.00 0.00 4.35
7733 13622 0.786581 CGCCATGCACATATCTCGAC 59.213 55.000 0.00 0.00 0.00 4.20
7734 13623 0.319813 CCGCCATGCACATATCTCGA 60.320 55.000 0.00 0.00 0.00 4.04
7735 13624 0.601046 ACCGCCATGCACATATCTCG 60.601 55.000 0.00 0.00 0.00 4.04
7736 13625 1.265095 CAACCGCCATGCACATATCTC 59.735 52.381 0.00 0.00 0.00 2.75
7737 13626 1.311859 CAACCGCCATGCACATATCT 58.688 50.000 0.00 0.00 0.00 1.98
7738 13627 1.024271 ACAACCGCCATGCACATATC 58.976 50.000 0.00 0.00 0.00 1.63
7739 13628 0.740149 CACAACCGCCATGCACATAT 59.260 50.000 0.00 0.00 0.00 1.78
7740 13629 1.311651 CCACAACCGCCATGCACATA 61.312 55.000 0.00 0.00 0.00 2.29
7741 13630 2.638354 CCACAACCGCCATGCACAT 61.638 57.895 0.00 0.00 0.00 3.21
7742 13631 2.682582 TACCACAACCGCCATGCACA 62.683 55.000 0.00 0.00 0.00 4.57
7743 13632 1.922135 CTACCACAACCGCCATGCAC 61.922 60.000 0.00 0.00 0.00 4.57
7744 13633 1.673993 CTACCACAACCGCCATGCA 60.674 57.895 0.00 0.00 0.00 3.96
7745 13634 1.376683 TCTACCACAACCGCCATGC 60.377 57.895 0.00 0.00 0.00 4.06
7746 13635 0.036388 AGTCTACCACAACCGCCATG 60.036 55.000 0.00 0.00 0.00 3.66
7747 13636 0.690762 AAGTCTACCACAACCGCCAT 59.309 50.000 0.00 0.00 0.00 4.40
7748 13637 0.470766 AAAGTCTACCACAACCGCCA 59.529 50.000 0.00 0.00 0.00 5.69
7749 13638 0.872388 CAAAGTCTACCACAACCGCC 59.128 55.000 0.00 0.00 0.00 6.13
7750 13639 0.872388 CCAAAGTCTACCACAACCGC 59.128 55.000 0.00 0.00 0.00 5.68
7751 13640 0.872388 GCCAAAGTCTACCACAACCG 59.128 55.000 0.00 0.00 0.00 4.44
7752 13641 0.872388 CGCCAAAGTCTACCACAACC 59.128 55.000 0.00 0.00 0.00 3.77
7753 13642 0.872388 CCGCCAAAGTCTACCACAAC 59.128 55.000 0.00 0.00 0.00 3.32
7754 13643 0.250553 CCCGCCAAAGTCTACCACAA 60.251 55.000 0.00 0.00 0.00 3.33
7755 13644 1.122632 TCCCGCCAAAGTCTACCACA 61.123 55.000 0.00 0.00 0.00 4.17
7756 13645 0.035739 TTCCCGCCAAAGTCTACCAC 59.964 55.000 0.00 0.00 0.00 4.16
7757 13646 0.323629 CTTCCCGCCAAAGTCTACCA 59.676 55.000 0.00 0.00 0.00 3.25
7758 13647 0.392595 CCTTCCCGCCAAAGTCTACC 60.393 60.000 0.00 0.00 0.00 3.18
7759 13648 0.611714 TCCTTCCCGCCAAAGTCTAC 59.388 55.000 0.00 0.00 0.00 2.59
7760 13649 1.485066 GATCCTTCCCGCCAAAGTCTA 59.515 52.381 0.00 0.00 0.00 2.59
7761 13650 0.253327 GATCCTTCCCGCCAAAGTCT 59.747 55.000 0.00 0.00 0.00 3.24
7762 13651 0.035439 TGATCCTTCCCGCCAAAGTC 60.035 55.000 0.00 0.00 0.00 3.01
7763 13652 0.404040 TTGATCCTTCCCGCCAAAGT 59.596 50.000 0.00 0.00 0.00 2.66
7764 13653 0.811281 GTTGATCCTTCCCGCCAAAG 59.189 55.000 0.00 0.00 0.00 2.77
7765 13654 0.958382 CGTTGATCCTTCCCGCCAAA 60.958 55.000 0.00 0.00 0.00 3.28
7766 13655 1.376683 CGTTGATCCTTCCCGCCAA 60.377 57.895 0.00 0.00 0.00 4.52
7767 13656 2.267642 CGTTGATCCTTCCCGCCA 59.732 61.111 0.00 0.00 0.00 5.69
7768 13657 2.513897 CCGTTGATCCTTCCCGCC 60.514 66.667 0.00 0.00 0.00 6.13
7769 13658 1.814169 GTCCGTTGATCCTTCCCGC 60.814 63.158 0.00 0.00 0.00 6.13
7770 13659 0.178068 ATGTCCGTTGATCCTTCCCG 59.822 55.000 0.00 0.00 0.00 5.14
7771 13660 1.475213 GGATGTCCGTTGATCCTTCCC 60.475 57.143 0.00 0.00 36.04 3.97
7772 13661 1.475213 GGGATGTCCGTTGATCCTTCC 60.475 57.143 0.00 0.00 38.61 3.46
7773 13662 1.209504 TGGGATGTCCGTTGATCCTTC 59.790 52.381 0.00 0.00 38.61 3.46
7774 13663 1.065418 GTGGGATGTCCGTTGATCCTT 60.065 52.381 0.00 0.00 38.61 3.36
7775 13664 0.541863 GTGGGATGTCCGTTGATCCT 59.458 55.000 0.00 0.00 38.61 3.24
7776 13665 0.810031 CGTGGGATGTCCGTTGATCC 60.810 60.000 0.00 0.00 37.94 3.36
7777 13666 0.108329 ACGTGGGATGTCCGTTGATC 60.108 55.000 0.00 0.00 38.76 2.92
7778 13667 0.323629 AACGTGGGATGTCCGTTGAT 59.676 50.000 0.00 0.00 42.59 2.57
7779 13668 0.967662 TAACGTGGGATGTCCGTTGA 59.032 50.000 6.89 0.00 43.81 3.18
7780 13669 1.355971 CTAACGTGGGATGTCCGTTG 58.644 55.000 6.89 0.00 43.81 4.10
7781 13670 0.248289 CCTAACGTGGGATGTCCGTT 59.752 55.000 2.01 0.00 45.65 4.44
7782 13671 1.895238 CCTAACGTGGGATGTCCGT 59.105 57.895 2.01 0.00 38.76 4.69
7783 13672 1.520787 GCCTAACGTGGGATGTCCG 60.521 63.158 11.41 0.00 38.76 4.79
7784 13673 1.153229 GGCCTAACGTGGGATGTCC 60.153 63.158 11.41 0.00 0.00 4.02
7785 13674 1.153229 GGGCCTAACGTGGGATGTC 60.153 63.158 0.84 0.00 0.00 3.06
7786 13675 1.615424 AGGGCCTAACGTGGGATGT 60.615 57.895 2.82 0.00 0.00 3.06
7787 13676 1.146263 GAGGGCCTAACGTGGGATG 59.854 63.158 5.73 0.00 0.00 3.51
7788 13677 2.070650 GGAGGGCCTAACGTGGGAT 61.071 63.158 5.73 0.00 0.00 3.85
7789 13678 2.686106 GGAGGGCCTAACGTGGGA 60.686 66.667 5.73 0.00 0.00 4.37
7790 13679 3.793888 GGGAGGGCCTAACGTGGG 61.794 72.222 5.73 0.00 0.00 4.61
7791 13680 3.793888 GGGGAGGGCCTAACGTGG 61.794 72.222 5.73 0.00 0.00 4.94
7792 13681 2.132089 TTTGGGGAGGGCCTAACGTG 62.132 60.000 5.73 0.00 0.00 4.49
7793 13682 1.848886 CTTTGGGGAGGGCCTAACGT 61.849 60.000 5.73 0.00 0.00 3.99
7794 13683 1.077716 CTTTGGGGAGGGCCTAACG 60.078 63.158 5.73 0.00 0.00 3.18
7795 13684 0.408309 AACTTTGGGGAGGGCCTAAC 59.592 55.000 5.73 1.76 0.00 2.34
7796 13685 0.407918 CAACTTTGGGGAGGGCCTAA 59.592 55.000 5.73 0.00 0.00 2.69
7797 13686 1.506028 CCAACTTTGGGGAGGGCCTA 61.506 60.000 5.73 0.00 44.70 3.93
7798 13687 2.854076 CAACTTTGGGGAGGGCCT 59.146 61.111 5.25 5.25 0.00 5.19
7799 13688 2.283894 CCAACTTTGGGGAGGGCC 60.284 66.667 0.00 0.00 44.70 5.80
8140 14035 4.696877 ACATTGAGATCGACTTGCATTTCA 59.303 37.500 0.00 0.00 0.00 2.69
8187 14082 5.528690 GTGCTTCATATCTTGCCAGTAATCA 59.471 40.000 0.00 0.00 0.00 2.57
8278 14173 1.500474 TGCTAAGTCCTGCTGGCTAT 58.500 50.000 4.42 0.00 0.00 2.97
8317 14212 4.110493 GCGCCGAAGCTGAATACT 57.890 55.556 0.00 0.00 36.60 2.12


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

AutoCloner maintained by Alex Coulton.