Multiple sequence alignment - TraesCS1D01G389500

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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 TraesCS1D01G389500 chr1D 100.000 4011 0 0 1 4011 461137621 461141631 0.000000e+00 7408
1 TraesCS1D01G389500 chr1D 84.713 157 18 6 3493 3647 478273883 478274035 6.940000e-33 152
2 TraesCS1D01G389500 chr1D 89.691 97 6 4 420 516 415985006 415984914 1.960000e-23 121
3 TraesCS1D01G389500 chr1A 92.097 2733 159 23 492 3189 552210944 552213654 0.000000e+00 3797
4 TraesCS1D01G389500 chr1A 85.304 626 55 14 570 1191 552201133 552201725 2.650000e-171 612
5 TraesCS1D01G389500 chr1A 90.000 440 25 11 3429 3855 552214451 552214884 5.860000e-153 551
6 TraesCS1D01G389500 chr1A 90.206 194 13 3 3237 3430 552213663 552213850 8.610000e-62 248
7 TraesCS1D01G389500 chr1A 87.037 108 9 2 3894 4001 552215122 552215224 2.530000e-22 117
8 TraesCS1D01G389500 chr1B 90.057 1227 83 20 1975 3189 633332256 633333455 0.000000e+00 1554
9 TraesCS1D01G389500 chr1B 92.582 728 33 8 796 1508 633330710 633331431 0.000000e+00 1026
10 TraesCS1D01G389500 chr1B 91.865 504 38 3 1523 2024 633331569 633332071 0.000000e+00 701
11 TraesCS1D01G389500 chr1B 95.767 378 16 0 1526 1903 549465235 549464858 9.530000e-171 610
12 TraesCS1D01G389500 chr1B 89.362 423 31 6 1 422 633329703 633330112 1.650000e-143 520
13 TraesCS1D01G389500 chr1B 86.580 462 41 12 1075 1519 549465728 549465271 1.300000e-134 490
14 TraesCS1D01G389500 chr1B 92.701 274 18 2 3495 3767 633333729 633334001 1.040000e-105 394
15 TraesCS1D01G389500 chr1B 84.943 352 29 8 488 839 633330384 633330711 6.420000e-88 335
16 TraesCS1D01G389500 chr1B 85.161 155 17 6 3495 3647 666072879 666073029 1.930000e-33 154
17 TraesCS1D01G389500 chr5D 91.052 1017 66 13 1075 2073 556407995 556406986 0.000000e+00 1351
18 TraesCS1D01G389500 chr5D 89.899 99 6 4 418 516 464931448 464931354 1.510000e-24 124
19 TraesCS1D01G389500 chr5D 89.583 96 7 3 421 516 388081852 388081944 7.040000e-23 119
20 TraesCS1D01G389500 chr5D 93.056 72 5 0 2982 3053 94447344 94447273 5.480000e-19 106
21 TraesCS1D01G389500 chr7B 95.503 378 17 0 1526 1903 64764781 64764404 4.430000e-169 604
22 TraesCS1D01G389500 chr7B 85.714 462 45 12 1075 1519 64765274 64764817 6.070000e-128 468
23 TraesCS1D01G389500 chr7B 90.099 101 6 4 416 516 723128974 723129070 1.170000e-25 128
24 TraesCS1D01G389500 chr7B 91.304 92 4 4 421 511 469466701 469466789 5.440000e-24 122
25 TraesCS1D01G389500 chr3B 95.503 378 17 0 1526 1903 769345696 769346073 4.430000e-169 604
26 TraesCS1D01G389500 chr3B 86.905 420 34 4 1 419 9089389 9089788 6.110000e-123 451
27 TraesCS1D01G389500 chr6B 94.709 378 20 0 1526 1903 30364505 30364128 4.470000e-164 588
28 TraesCS1D01G389500 chr6B 86.147 462 43 12 1075 1519 30364998 30364541 2.800000e-131 479
29 TraesCS1D01G389500 chr6B 90.909 165 12 3 1075 1238 655258129 655258291 6.750000e-53 219
30 TraesCS1D01G389500 chr6B 77.365 296 53 10 519 807 10220124 10219836 3.210000e-36 163
31 TraesCS1D01G389500 chr4A 88.194 144 14 3 3501 3643 144625338 144625479 6.890000e-38 169
32 TraesCS1D01G389500 chr4A 91.753 97 5 3 420 516 617007221 617007314 9.050000e-27 132
33 TraesCS1D01G389500 chr2D 88.028 142 13 4 3508 3648 103147569 103147707 8.920000e-37 165
34 TraesCS1D01G389500 chr2D 88.406 138 13 3 3508 3645 37250761 37250627 3.210000e-36 163
35 TraesCS1D01G389500 chr4D 87.500 144 12 5 3501 3643 326385178 326385040 1.150000e-35 161
36 TraesCS1D01G389500 chr4D 80.488 164 10 11 3129 3292 196908729 196908870 5.480000e-19 106
37 TraesCS1D01G389500 chr4D 96.721 61 2 0 3129 3189 239797779 239797719 7.090000e-18 102
38 TraesCS1D01G389500 chr4D 96.721 61 2 0 3129 3189 261234842 261234782 7.090000e-18 102
39 TraesCS1D01G389500 chr5A 85.443 158 16 6 3493 3647 10860736 10860583 1.490000e-34 158
40 TraesCS1D01G389500 chr5A 80.488 164 10 2 3129 3292 544971489 544971630 5.480000e-19 106
41 TraesCS1D01G389500 chr6A 90.722 97 6 3 420 516 553935443 553935350 4.210000e-25 126
42 TraesCS1D01G389500 chr5B 89.583 96 7 3 421 516 8190776 8190868 7.040000e-23 119
43 TraesCS1D01G389500 chr5B 96.721 61 2 0 3129 3189 492515597 492515537 7.090000e-18 102
44 TraesCS1D01G389500 chr3A 89.362 94 6 4 419 512 745272720 745272631 9.110000e-22 115
45 TraesCS1D01G389500 chr6D 80.488 164 10 12 3129 3292 46523379 46523238 5.480000e-19 106
46 TraesCS1D01G389500 chr6D 96.721 61 2 0 3129 3189 297173936 297173876 7.090000e-18 102


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 TraesCS1D01G389500 chr1D 461137621 461141631 4010 False 7408.00 7408 100.000000 1 4011 1 chr1D.!!$F1 4010
1 TraesCS1D01G389500 chr1A 552210944 552215224 4280 False 1178.25 3797 89.835000 492 4001 4 chr1A.!!$F2 3509
2 TraesCS1D01G389500 chr1A 552201133 552201725 592 False 612.00 612 85.304000 570 1191 1 chr1A.!!$F1 621
3 TraesCS1D01G389500 chr1B 633329703 633334001 4298 False 755.00 1554 90.251667 1 3767 6 chr1B.!!$F2 3766
4 TraesCS1D01G389500 chr1B 549464858 549465728 870 True 550.00 610 91.173500 1075 1903 2 chr1B.!!$R1 828
5 TraesCS1D01G389500 chr5D 556406986 556407995 1009 True 1351.00 1351 91.052000 1075 2073 1 chr5D.!!$R3 998
6 TraesCS1D01G389500 chr7B 64764404 64765274 870 True 536.00 604 90.608500 1075 1903 2 chr7B.!!$R1 828
7 TraesCS1D01G389500 chr6B 30364128 30364998 870 True 533.50 588 90.428000 1075 1903 2 chr6B.!!$R2 828

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
784 993 0.109504 GGCAAATTTAAGCACGGCGA 60.110 50.0 16.62 0.0 0.0 5.54 F
1375 1640 0.118346 TTAGGGCCTCTCTGGGTGAA 59.882 55.0 10.74 0.0 36.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 2121 0.247145 GCAGGACGTTGAAATACGCG 60.247 55.0 3.53 3.53 45.06 6.01 R
3199 3850 0.179020 CTGCCTTTGACACACCAGGA 60.179 55.0 0.00 0.00 0.00 3.86 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
43 44 7.809226 AAAAATGGTGTTTCAAATTTTGTGC 57.191 28.000 8.89 2.24 33.65 4.57
44 45 6.506500 AAATGGTGTTTCAAATTTTGTGCA 57.493 29.167 8.89 4.50 0.00 4.57
45 46 6.696441 AATGGTGTTTCAAATTTTGTGCAT 57.304 29.167 8.89 0.00 0.00 3.96
46 47 5.481200 TGGTGTTTCAAATTTTGTGCATG 57.519 34.783 8.89 0.00 0.00 4.06
47 48 4.940046 TGGTGTTTCAAATTTTGTGCATGT 59.060 33.333 8.89 0.00 0.00 3.21
48 49 5.413833 TGGTGTTTCAAATTTTGTGCATGTT 59.586 32.000 8.89 0.00 0.00 2.71
49 50 6.072286 TGGTGTTTCAAATTTTGTGCATGTTT 60.072 30.769 8.89 0.00 0.00 2.83
50 51 6.805760 GGTGTTTCAAATTTTGTGCATGTTTT 59.194 30.769 8.89 0.00 0.00 2.43
51 52 7.965107 GGTGTTTCAAATTTTGTGCATGTTTTA 59.035 29.630 8.89 0.00 0.00 1.52
154 156 3.749404 TCGTGTTTCCAAAAGTTGTTCG 58.251 40.909 0.00 0.00 0.00 3.95
164 166 6.966021 TCCAAAAGTTGTTCGGAATTTCTAG 58.034 36.000 0.00 0.00 0.00 2.43
193 195 5.828299 TCATGTTTTCAAAGAAGTTCGGT 57.172 34.783 0.00 0.00 0.00 4.69
202 204 6.202516 TCAAAGAAGTTCGGTGTTTCAAAT 57.797 33.333 0.00 0.00 0.00 2.32
207 209 6.394809 AGAAGTTCGGTGTTTCAAATTTTGT 58.605 32.000 8.89 0.00 0.00 2.83
216 218 6.734617 GGTGTTTCAAATTTTGTTCGTGTTTC 59.265 34.615 8.89 0.00 0.00 2.78
218 220 7.794349 GTGTTTCAAATTTTGTTCGTGTTTCAA 59.206 29.630 8.89 0.00 0.00 2.69
221 223 8.871742 TTCAAATTTTGTTCGTGTTTCAATTG 57.128 26.923 8.89 0.00 0.00 2.32
228 230 4.142665 TGTTCGTGTTTCAATTGTTCGGAA 60.143 37.500 5.13 1.06 0.00 4.30
288 290 7.441017 TCATAATTCCAAAAAGGTGTTCCAAG 58.559 34.615 0.00 0.00 39.02 3.61
306 308 4.698304 TCCAAGTTTTCAAAGAGTGTTCGT 59.302 37.500 0.00 0.00 0.00 3.85
321 323 6.866248 AGAGTGTTCGTGTTTTCAAAACATTT 59.134 30.769 18.54 0.75 38.80 2.32
327 329 4.425401 CGTGTTTTCAAAACATTTTTCGCG 59.575 37.500 18.54 11.44 32.23 5.87
350 352 9.798885 CGCGTTTTGAAAATAAATTGGAATTTA 57.201 25.926 0.00 6.95 42.94 1.40
399 401 7.709947 ACATTGAGTAATGGTCATTTATGCTG 58.290 34.615 1.28 0.00 46.33 4.41
422 424 5.125417 TGCTGCAGTTTGTTCTTTAGACTTT 59.875 36.000 16.64 0.00 0.00 2.66
423 425 6.036470 GCTGCAGTTTGTTCTTTAGACTTTT 58.964 36.000 16.64 0.00 0.00 2.27
444 446 5.726729 TTTTTGCGGAAAAACTTCCAATC 57.273 34.783 21.65 0.00 41.16 2.67
446 448 5.776173 TTTGCGGAAAAACTTCCAATCTA 57.224 34.783 0.00 0.00 41.16 1.98
448 450 5.975693 TGCGGAAAAACTTCCAATCTATT 57.024 34.783 4.85 0.00 41.16 1.73
449 451 5.949735 TGCGGAAAAACTTCCAATCTATTC 58.050 37.500 4.85 0.00 41.16 1.75
451 453 6.152661 TGCGGAAAAACTTCCAATCTATTCAT 59.847 34.615 4.85 0.00 41.16 2.57
452 454 6.693113 GCGGAAAAACTTCCAATCTATTCATC 59.307 38.462 4.85 0.00 41.16 2.92
453 455 7.415653 GCGGAAAAACTTCCAATCTATTCATCT 60.416 37.037 4.85 0.00 41.16 2.90
455 457 9.794685 GGAAAAACTTCCAATCTATTCATCTTC 57.205 33.333 0.00 0.00 40.79 2.87
460 462 9.690913 AACTTCCAATCTATTCATCTTCAATCA 57.309 29.630 0.00 0.00 0.00 2.57
461 463 9.863650 ACTTCCAATCTATTCATCTTCAATCAT 57.136 29.630 0.00 0.00 0.00 2.45
463 465 8.631480 TCCAATCTATTCATCTTCAATCATGG 57.369 34.615 0.00 0.00 0.00 3.66
464 466 7.176165 TCCAATCTATTCATCTTCAATCATGGC 59.824 37.037 0.00 0.00 0.00 4.40
465 467 7.039993 CCAATCTATTCATCTTCAATCATGGCA 60.040 37.037 0.00 0.00 0.00 4.92
467 469 6.598503 TCTATTCATCTTCAATCATGGCAGT 58.401 36.000 0.00 0.00 0.00 4.40
468 470 7.738847 TCTATTCATCTTCAATCATGGCAGTA 58.261 34.615 0.00 0.00 0.00 2.74
470 472 5.101648 TCATCTTCAATCATGGCAGTACA 57.898 39.130 0.00 0.00 0.00 2.90
471 473 5.499313 TCATCTTCAATCATGGCAGTACAA 58.501 37.500 0.00 0.00 0.00 2.41
472 474 5.355071 TCATCTTCAATCATGGCAGTACAAC 59.645 40.000 0.00 0.00 0.00 3.32
473 475 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
474 476 3.326836 TCAATCATGGCAGTACAACGA 57.673 42.857 0.00 0.00 0.00 3.85
475 477 3.669536 TCAATCATGGCAGTACAACGAA 58.330 40.909 0.00 0.00 0.00 3.85
476 478 3.435327 TCAATCATGGCAGTACAACGAAC 59.565 43.478 0.00 0.00 0.00 3.95
480 482 0.178301 TGGCAGTACAACGAACACCA 59.822 50.000 0.00 0.00 0.00 4.17
481 483 0.865769 GGCAGTACAACGAACACCAG 59.134 55.000 0.00 0.00 0.00 4.00
484 486 2.610374 GCAGTACAACGAACACCAGAAA 59.390 45.455 0.00 0.00 0.00 2.52
485 487 3.250040 GCAGTACAACGAACACCAGAAAT 59.750 43.478 0.00 0.00 0.00 2.17
486 488 4.449743 GCAGTACAACGAACACCAGAAATA 59.550 41.667 0.00 0.00 0.00 1.40
489 491 7.411274 CAGTACAACGAACACCAGAAATAAAA 58.589 34.615 0.00 0.00 0.00 1.52
490 492 7.911205 CAGTACAACGAACACCAGAAATAAAAA 59.089 33.333 0.00 0.00 0.00 1.94
493 495 6.635239 ACAACGAACACCAGAAATAAAAATCG 59.365 34.615 0.00 0.00 0.00 3.34
586 794 8.821894 CACTGGACATAGAGACTTTTATAAAGC 58.178 37.037 0.00 0.00 0.00 3.51
596 804 8.267894 AGAGACTTTTATAAAGCAAGCCATCTA 58.732 33.333 0.00 0.00 0.00 1.98
606 814 5.039920 AGCAAGCCATCTATTGTATGTGA 57.960 39.130 0.00 0.00 0.00 3.58
614 822 8.432013 AGCCATCTATTGTATGTGAGTTTCATA 58.568 33.333 0.00 0.00 0.00 2.15
656 864 2.495155 AATACAGTGCCACATGAGCA 57.505 45.000 10.47 10.47 38.08 4.26
672 880 7.820872 CCACATGAGCACATTATACATCTATGA 59.179 37.037 0.00 0.00 34.15 2.15
726 934 8.902806 TGTGTCAAGTTTTAGAATCAGTTTGAT 58.097 29.630 0.00 0.00 39.09 2.57
763 972 6.370718 AGTTTAGGCAGTAAAGTAAACATCGG 59.629 38.462 6.60 0.00 37.68 4.18
770 979 4.822896 AGTAAAGTAAACATCGGTGGCAAA 59.177 37.500 0.00 0.00 0.00 3.68
780 989 1.068885 TCGGTGGCAAATTTAAGCACG 60.069 47.619 3.25 4.63 0.00 5.34
781 990 1.708822 GGTGGCAAATTTAAGCACGG 58.291 50.000 3.25 0.00 0.00 4.94
783 992 0.387878 TGGCAAATTTAAGCACGGCG 60.388 50.000 4.80 4.80 0.00 6.46
784 993 0.109504 GGCAAATTTAAGCACGGCGA 60.110 50.000 16.62 0.00 0.00 5.54
956 1220 1.988406 GCCGTCCTCCTAACCCAGT 60.988 63.158 0.00 0.00 0.00 4.00
1027 1291 3.895704 AGAAAGGAGGTAAAAAGGCCA 57.104 42.857 5.01 0.00 0.00 5.36
1171 1435 1.507141 CCCTCGTTTGACTTGCGCTT 61.507 55.000 9.73 0.00 0.00 4.68
1174 1438 0.531974 TCGTTTGACTTGCGCTTCCT 60.532 50.000 9.73 0.00 0.00 3.36
1362 1627 0.742635 GCAGTCAGAGCTGTTAGGGC 60.743 60.000 0.00 0.00 38.65 5.19
1375 1640 0.118346 TTAGGGCCTCTCTGGGTGAA 59.882 55.000 10.74 0.00 36.00 3.18
1386 1656 2.484264 CTCTGGGTGAAATTCGTTCCAC 59.516 50.000 4.66 0.00 35.12 4.02
1394 1664 3.629855 TGAAATTCGTTCCACTTGCTTGA 59.370 39.130 0.00 0.00 35.12 3.02
1401 1671 1.210931 CCACTTGCTTGACATGCCG 59.789 57.895 10.53 4.86 0.00 5.69
1403 1673 2.180017 CTTGCTTGACATGCCGGC 59.820 61.111 22.73 22.73 0.00 6.13
1407 1677 2.828128 GCTTGACATGCCGGCTAGC 61.828 63.158 29.70 20.50 0.00 3.42
1415 1685 1.450134 TGCCGGCTAGCATCACAAG 60.450 57.895 29.70 0.00 38.00 3.16
1430 1702 6.378280 AGCATCACAAGTTAGGAAAATTAGGG 59.622 38.462 0.00 0.00 0.00 3.53
1495 1775 2.202557 GCATACGTTTTGGCCGCC 60.203 61.111 1.04 1.04 0.00 6.13
1508 1788 2.511373 CCGCCGTATGCAGCAGAA 60.511 61.111 0.00 0.00 41.33 3.02
1512 1792 1.193203 CGCCGTATGCAGCAGAATTAG 59.807 52.381 0.00 0.00 41.33 1.73
1558 1962 0.795085 CTAGTGCTCACTGCTGCAAC 59.205 55.000 12.43 0.00 42.52 4.17
1576 1980 2.947652 CAACTCATGCAGTCCTTATGGG 59.052 50.000 0.00 0.00 32.30 4.00
1713 2121 0.449388 CGCTCAAGGAGAACATTGCC 59.551 55.000 0.00 0.00 37.65 4.52
1815 2223 5.700402 ATATCACTAGTTCTGCAAAGGGT 57.300 39.130 0.00 0.00 0.00 4.34
1852 2260 2.947852 TCTCGTTGTTCAAGCTAGCTC 58.052 47.619 19.65 5.90 0.00 4.09
1986 2544 9.678260 ACTAAACTTGCTGATCTAATCTTCATT 57.322 29.630 0.00 0.00 0.00 2.57
2006 2564 7.611213 TCATTTAGCTAAAGTGGAAACTAGC 57.389 36.000 22.55 0.00 37.60 3.42
2034 2592 7.939039 ACTTACATATCTGGTGGTATTGATTGG 59.061 37.037 0.00 0.00 0.00 3.16
2163 2805 3.334583 AGGTTGCGAGTGTGTTCATAT 57.665 42.857 0.00 0.00 0.00 1.78
2173 2815 5.974158 CGAGTGTGTTCATATAGTTCTGAGG 59.026 44.000 0.00 0.00 0.00 3.86
2177 2819 8.634444 AGTGTGTTCATATAGTTCTGAGGTATC 58.366 37.037 0.00 0.00 0.00 2.24
2187 2831 3.650070 TCTGAGGTATCGTGCATGATC 57.350 47.619 24.44 15.34 0.00 2.92
2191 2835 3.384467 TGAGGTATCGTGCATGATCTTGA 59.616 43.478 24.44 4.81 0.00 3.02
2554 3198 7.447853 ATGAGCTTTTCAGATAAGGATGAATCC 59.552 37.037 0.69 0.69 42.49 3.01
2731 3375 1.342074 CTGAGGACAAGGTGGAGTCA 58.658 55.000 0.00 0.00 36.50 3.41
2797 3441 4.035102 GAGCTTGGGGCCTCCGTT 62.035 66.667 0.00 0.00 43.05 4.44
3021 3665 2.827921 GCCCATCCTGATTGTTGAAGTT 59.172 45.455 0.00 0.00 0.00 2.66
3065 3715 4.246458 CCCTCTAGTTTGTAGCAGTGTTC 58.754 47.826 0.00 0.00 0.00 3.18
3068 3718 4.883083 TCTAGTTTGTAGCAGTGTTCTGG 58.117 43.478 0.00 0.00 41.57 3.86
3089 3739 4.897076 TGGTGTGTCTTCTAGTTGGAGTTA 59.103 41.667 0.00 0.00 0.00 2.24
3100 3750 6.166279 TCTAGTTGGAGTTATGAAGCTTGTG 58.834 40.000 2.10 0.00 0.00 3.33
3106 3756 5.215160 GGAGTTATGAAGCTTGTGTTGTTG 58.785 41.667 2.10 0.00 0.00 3.33
3111 3761 2.822561 TGAAGCTTGTGTTGTTGAACCA 59.177 40.909 2.10 0.00 0.00 3.67
3114 3764 3.584834 AGCTTGTGTTGTTGAACCAAAC 58.415 40.909 0.00 0.00 0.00 2.93
3116 3766 3.827625 CTTGTGTTGTTGAACCAAACGA 58.172 40.909 0.00 0.00 32.47 3.85
3158 3809 6.014584 TCCAGTGAACAAGAGAATGCTTAGTA 60.015 38.462 0.00 0.00 0.00 1.82
3170 3821 6.398918 AGAATGCTTAGTACTTAGTGTGGTG 58.601 40.000 10.40 0.00 0.00 4.17
3189 3840 2.293399 GTGTTGGAATTCCTGGTGTGTC 59.707 50.000 24.73 7.27 36.82 3.67
3190 3841 2.174639 TGTTGGAATTCCTGGTGTGTCT 59.825 45.455 24.73 0.00 36.82 3.41
3191 3842 2.554032 GTTGGAATTCCTGGTGTGTCTG 59.446 50.000 24.73 0.00 36.82 3.51
3192 3843 1.774254 TGGAATTCCTGGTGTGTCTGT 59.226 47.619 24.73 0.00 36.82 3.41
3193 3844 2.174639 TGGAATTCCTGGTGTGTCTGTT 59.825 45.455 24.73 0.00 36.82 3.16
3194 3845 2.554032 GGAATTCCTGGTGTGTCTGTTG 59.446 50.000 17.73 0.00 0.00 3.33
3195 3846 2.276732 ATTCCTGGTGTGTCTGTTGG 57.723 50.000 0.00 0.00 0.00 3.77
3196 3847 1.208706 TTCCTGGTGTGTCTGTTGGA 58.791 50.000 0.00 0.00 0.00 3.53
3197 3848 1.208706 TCCTGGTGTGTCTGTTGGAA 58.791 50.000 0.00 0.00 0.00 3.53
3198 3849 1.774254 TCCTGGTGTGTCTGTTGGAAT 59.226 47.619 0.00 0.00 0.00 3.01
3199 3850 2.174639 TCCTGGTGTGTCTGTTGGAATT 59.825 45.455 0.00 0.00 0.00 2.17
3200 3851 2.554032 CCTGGTGTGTCTGTTGGAATTC 59.446 50.000 0.00 0.00 0.00 2.17
3201 3852 2.554032 CTGGTGTGTCTGTTGGAATTCC 59.446 50.000 18.17 18.17 0.00 3.01
3202 3853 2.174639 TGGTGTGTCTGTTGGAATTCCT 59.825 45.455 24.73 0.00 36.82 3.36
3203 3854 2.554032 GGTGTGTCTGTTGGAATTCCTG 59.446 50.000 24.73 12.33 36.82 3.86
3204 3855 2.554032 GTGTGTCTGTTGGAATTCCTGG 59.446 50.000 24.73 11.97 36.82 4.45
3205 3856 2.174639 TGTGTCTGTTGGAATTCCTGGT 59.825 45.455 24.73 0.00 36.82 4.00
3206 3857 2.554032 GTGTCTGTTGGAATTCCTGGTG 59.446 50.000 24.73 12.66 36.82 4.17
3207 3858 2.174639 TGTCTGTTGGAATTCCTGGTGT 59.825 45.455 24.73 0.00 36.82 4.16
3208 3859 2.554032 GTCTGTTGGAATTCCTGGTGTG 59.446 50.000 24.73 10.42 36.82 3.82
3209 3860 2.174639 TCTGTTGGAATTCCTGGTGTGT 59.825 45.455 24.73 0.00 36.82 3.72
3210 3861 2.554032 CTGTTGGAATTCCTGGTGTGTC 59.446 50.000 24.73 7.27 36.82 3.67
3211 3862 2.092158 TGTTGGAATTCCTGGTGTGTCA 60.092 45.455 24.73 9.44 36.82 3.58
3212 3863 2.955660 GTTGGAATTCCTGGTGTGTCAA 59.044 45.455 24.73 5.10 36.82 3.18
3213 3864 3.304911 TGGAATTCCTGGTGTGTCAAA 57.695 42.857 24.73 0.00 36.82 2.69
3214 3865 3.221771 TGGAATTCCTGGTGTGTCAAAG 58.778 45.455 24.73 0.00 36.82 2.77
3215 3866 2.558359 GGAATTCCTGGTGTGTCAAAGG 59.442 50.000 17.73 0.00 0.00 3.11
3216 3867 1.620822 ATTCCTGGTGTGTCAAAGGC 58.379 50.000 0.00 0.00 0.00 4.35
3217 3868 0.257328 TTCCTGGTGTGTCAAAGGCA 59.743 50.000 0.00 0.00 0.00 4.75
3218 3869 0.179020 TCCTGGTGTGTCAAAGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
3219 3870 0.466189 CCTGGTGTGTCAAAGGCAGT 60.466 55.000 0.00 0.00 0.00 4.40
3220 3871 1.202758 CCTGGTGTGTCAAAGGCAGTA 60.203 52.381 0.00 0.00 0.00 2.74
3221 3872 2.553028 CCTGGTGTGTCAAAGGCAGTAT 60.553 50.000 0.00 0.00 0.00 2.12
3222 3873 2.485426 CTGGTGTGTCAAAGGCAGTATG 59.515 50.000 0.00 0.00 40.87 2.39
3223 3874 2.105649 TGGTGTGTCAAAGGCAGTATGA 59.894 45.455 0.00 0.00 39.69 2.15
3250 3901 8.967664 TGGTTGTAATATATACAAGGTTGGTC 57.032 34.615 1.52 0.00 38.01 4.02
3317 3968 0.822164 CTCTGGTAGTTACCCGGTGG 59.178 60.000 0.00 0.00 45.87 4.61
3343 3994 4.082571 CCTGTCCTGATTGTTGAAATGTCC 60.083 45.833 0.00 0.00 0.00 4.02
3376 4027 5.164051 CGGACTCAACATCGTTATGATATGC 60.164 44.000 0.00 0.00 34.83 3.14
3383 4034 8.147704 TCAACATCGTTATGATATGCCTTTCTA 58.852 33.333 0.00 0.00 34.83 2.10
3394 4045 8.023021 TGATATGCCTTTCTAGTTCATACTGT 57.977 34.615 0.00 0.00 35.78 3.55
3395 4046 9.143155 TGATATGCCTTTCTAGTTCATACTGTA 57.857 33.333 0.00 0.00 35.78 2.74
3396 4047 9.632807 GATATGCCTTTCTAGTTCATACTGTAG 57.367 37.037 0.00 0.00 35.78 2.74
3397 4048 5.661458 TGCCTTTCTAGTTCATACTGTAGC 58.339 41.667 0.00 0.00 35.78 3.58
3398 4049 5.186992 TGCCTTTCTAGTTCATACTGTAGCA 59.813 40.000 0.00 0.00 35.78 3.49
3402 4053 7.254590 CCTTTCTAGTTCATACTGTAGCAATGC 60.255 40.741 0.00 0.00 35.78 3.56
3418 4069 4.156190 AGCAATGCTGAAATCTGTCTTCTG 59.844 41.667 7.07 0.00 37.57 3.02
3424 4075 3.668447 TGAAATCTGTCTTCTGGTCTGC 58.332 45.455 0.00 0.00 0.00 4.26
3444 4697 2.547211 GCAGCCACAATATGAGCACTAG 59.453 50.000 0.00 0.00 0.00 2.57
3452 4705 6.986231 CCACAATATGAGCACTAGTGTCAATA 59.014 38.462 23.44 17.16 0.00 1.90
3453 4707 7.495606 CCACAATATGAGCACTAGTGTCAATAA 59.504 37.037 23.44 14.46 0.00 1.40
3652 4918 1.004560 CTCCGTGCTCTTTGGCAGA 60.005 57.895 0.00 0.00 43.25 4.26
3684 4950 6.706295 CATTCCTTCTTGTATATCTCCCCTC 58.294 44.000 0.00 0.00 0.00 4.30
3687 4953 4.530161 CCTTCTTGTATATCTCCCCTCCAG 59.470 50.000 0.00 0.00 0.00 3.86
3730 4997 7.502696 AGCGGTATGGTACTAATCATAAAACA 58.497 34.615 0.00 0.00 0.00 2.83
3757 5024 2.815647 GCTGCGCGCTTACCTCTT 60.816 61.111 33.29 0.00 35.14 2.85
3786 5053 3.491342 TGCTGTTATTGTGGGCTGTTAA 58.509 40.909 0.00 0.00 0.00 2.01
3787 5054 4.085733 TGCTGTTATTGTGGGCTGTTAAT 58.914 39.130 0.00 0.00 0.00 1.40
3788 5055 4.526262 TGCTGTTATTGTGGGCTGTTAATT 59.474 37.500 0.00 0.00 0.00 1.40
3789 5056 5.712446 TGCTGTTATTGTGGGCTGTTAATTA 59.288 36.000 0.00 0.00 0.00 1.40
3790 5057 6.209589 TGCTGTTATTGTGGGCTGTTAATTAA 59.790 34.615 0.00 0.00 0.00 1.40
3797 5064 5.837437 TGTGGGCTGTTAATTAACAACTTG 58.163 37.500 26.60 17.88 44.67 3.16
3804 5071 6.089417 GCTGTTAATTAACAACTTGCCATGTC 59.911 38.462 26.60 8.81 44.67 3.06
3810 5077 0.896940 CAACTTGCCATGTCCAGCCT 60.897 55.000 0.00 0.00 0.00 4.58
3811 5078 0.178953 AACTTGCCATGTCCAGCCTT 60.179 50.000 0.00 0.00 0.00 4.35
3844 5111 1.027357 ACTCGGATGCATTGATTGGC 58.973 50.000 0.00 0.00 0.00 4.52
3855 5122 1.243342 TTGATTGGCTTGGTCTGCGG 61.243 55.000 0.00 0.00 0.00 5.69
3857 5124 0.960364 GATTGGCTTGGTCTGCGGAA 60.960 55.000 0.00 0.00 0.00 4.30
3858 5125 0.962356 ATTGGCTTGGTCTGCGGAAG 60.962 55.000 0.00 0.00 0.00 3.46
3861 5128 1.578206 GGCTTGGTCTGCGGAAGTTC 61.578 60.000 0.00 0.00 0.00 3.01
3862 5129 1.901650 GCTTGGTCTGCGGAAGTTCG 61.902 60.000 0.00 0.00 0.00 3.95
3863 5130 1.291877 CTTGGTCTGCGGAAGTTCGG 61.292 60.000 0.00 6.09 0.00 4.30
3864 5131 2.434359 GGTCTGCGGAAGTTCGGG 60.434 66.667 11.90 0.83 0.00 5.14
3865 5132 3.119096 GTCTGCGGAAGTTCGGGC 61.119 66.667 11.90 10.81 0.00 6.13
3866 5133 4.388499 TCTGCGGAAGTTCGGGCC 62.388 66.667 11.90 0.00 0.00 5.80
3867 5134 4.697756 CTGCGGAAGTTCGGGCCA 62.698 66.667 4.39 2.36 0.00 5.36
3869 5136 3.508840 GCGGAAGTTCGGGCCATG 61.509 66.667 4.39 0.00 0.00 3.66
3870 5137 3.508840 CGGAAGTTCGGGCCATGC 61.509 66.667 4.39 0.00 0.00 4.06
3871 5138 2.044946 GGAAGTTCGGGCCATGCT 60.045 61.111 4.39 0.00 0.00 3.79
3872 5139 1.223487 GGAAGTTCGGGCCATGCTA 59.777 57.895 4.39 0.00 0.00 3.49
3873 5140 0.815615 GGAAGTTCGGGCCATGCTAG 60.816 60.000 4.39 0.00 0.00 3.42
3875 5142 0.107654 AAGTTCGGGCCATGCTAGAC 60.108 55.000 4.39 0.00 0.00 2.59
3877 5144 0.530870 GTTCGGGCCATGCTAGACTC 60.531 60.000 4.39 0.00 0.00 3.36
3878 5145 0.975556 TTCGGGCCATGCTAGACTCA 60.976 55.000 4.39 0.00 0.00 3.41
3879 5146 0.975556 TCGGGCCATGCTAGACTCAA 60.976 55.000 4.39 0.00 0.00 3.02
3880 5147 0.107703 CGGGCCATGCTAGACTCAAA 60.108 55.000 4.39 0.00 0.00 2.69
3881 5148 1.678728 CGGGCCATGCTAGACTCAAAA 60.679 52.381 4.39 0.00 0.00 2.44
3882 5149 2.446435 GGGCCATGCTAGACTCAAAAA 58.554 47.619 4.39 0.00 0.00 1.94
3930 5396 1.067354 TCGAAAGGCCTTAAGACGGAC 60.067 52.381 20.84 2.53 0.00 4.79
3935 5401 4.772886 AAGGCCTTAAGACGGACAATAT 57.227 40.909 18.87 0.00 29.42 1.28
3937 5403 4.451900 AGGCCTTAAGACGGACAATATTG 58.548 43.478 14.01 14.01 29.42 1.90
3938 5404 3.564225 GGCCTTAAGACGGACAATATTGG 59.436 47.826 19.37 4.67 0.00 3.16
3940 5406 4.638865 GCCTTAAGACGGACAATATTGGTT 59.361 41.667 19.37 0.00 0.00 3.67
3944 5410 7.224167 CCTTAAGACGGACAATATTGGTTCTAC 59.776 40.741 19.37 6.56 0.00 2.59
3945 5411 5.934402 AGACGGACAATATTGGTTCTACT 57.066 39.130 19.37 8.49 0.00 2.57
3946 5412 5.661458 AGACGGACAATATTGGTTCTACTG 58.339 41.667 19.37 10.12 0.00 2.74
3947 5413 4.189231 ACGGACAATATTGGTTCTACTGC 58.811 43.478 19.37 1.37 0.00 4.40
3986 5452 4.209452 TGTCGAATGCTTCAAAGACAAC 57.791 40.909 0.00 0.00 35.94 3.32
3987 5453 3.876914 TGTCGAATGCTTCAAAGACAACT 59.123 39.130 0.00 0.00 35.94 3.16
3988 5454 5.053811 TGTCGAATGCTTCAAAGACAACTA 58.946 37.500 0.00 0.00 35.94 2.24
3989 5455 5.525745 TGTCGAATGCTTCAAAGACAACTAA 59.474 36.000 0.00 0.00 35.94 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 9.554395 TGAAAGTCTCAACATTATAGAAACACA 57.446 29.630 0.00 0.00 0.00 3.72
134 135 2.849473 CCGAACAACTTTTGGAAACACG 59.151 45.455 0.00 0.00 42.67 4.49
135 136 4.099380 TCCGAACAACTTTTGGAAACAC 57.901 40.909 0.00 0.00 42.67 3.32
164 166 9.906111 GAACTTCTTTGAAAACATGAACAAATC 57.094 29.630 0.00 0.00 33.01 2.17
193 195 7.408132 TGAAACACGAACAAAATTTGAAACA 57.592 28.000 13.19 0.00 0.00 2.83
202 204 5.061064 CCGAACAATTGAAACACGAACAAAA 59.939 36.000 13.59 0.00 0.00 2.44
207 209 4.617808 TTCCGAACAATTGAAACACGAA 57.382 36.364 13.59 3.25 0.00 3.85
216 218 9.980780 ACAAAAACTTTAAATTCCGAACAATTG 57.019 25.926 3.24 3.24 0.00 2.32
221 223 9.078753 TGAGAACAAAAACTTTAAATTCCGAAC 57.921 29.630 0.00 0.00 0.00 3.95
260 262 7.288852 TGGAACACCTTTTTGGAATTATGAAGA 59.711 33.333 0.00 0.00 39.71 2.87
288 290 6.361214 TGAAAACACGAACACTCTTTGAAAAC 59.639 34.615 0.00 0.00 0.00 2.43
306 308 5.517037 ACGCGAAAAATGTTTTGAAAACA 57.483 30.435 23.72 23.72 30.55 2.83
321 323 7.464830 TCCAATTTATTTTCAAAACGCGAAA 57.535 28.000 15.93 1.02 0.00 3.46
375 377 6.639686 GCAGCATAAATGACCATTACTCAATG 59.360 38.462 0.00 0.00 41.13 2.82
399 401 4.820284 AGTCTAAAGAACAAACTGCAGC 57.180 40.909 15.27 0.00 0.00 5.25
434 436 9.690913 TGATTGAAGATGAATAGATTGGAAGTT 57.309 29.630 0.00 0.00 0.00 2.66
435 437 9.863650 ATGATTGAAGATGAATAGATTGGAAGT 57.136 29.630 0.00 0.00 0.00 3.01
437 439 9.074576 CCATGATTGAAGATGAATAGATTGGAA 57.925 33.333 0.00 0.00 0.00 3.53
438 440 7.176165 GCCATGATTGAAGATGAATAGATTGGA 59.824 37.037 0.00 0.00 0.00 3.53
440 442 7.882179 TGCCATGATTGAAGATGAATAGATTG 58.118 34.615 0.00 0.00 0.00 2.67
441 443 7.724506 ACTGCCATGATTGAAGATGAATAGATT 59.275 33.333 0.00 0.00 0.00 2.40
442 444 7.232188 ACTGCCATGATTGAAGATGAATAGAT 58.768 34.615 0.00 0.00 0.00 1.98
443 445 6.598503 ACTGCCATGATTGAAGATGAATAGA 58.401 36.000 0.00 0.00 0.00 1.98
444 446 6.879276 ACTGCCATGATTGAAGATGAATAG 57.121 37.500 0.00 0.00 0.00 1.73
446 448 6.124340 TGTACTGCCATGATTGAAGATGAAT 58.876 36.000 0.00 0.00 0.00 2.57
448 450 5.101648 TGTACTGCCATGATTGAAGATGA 57.898 39.130 0.00 0.00 0.00 2.92
449 451 5.575957 GTTGTACTGCCATGATTGAAGATG 58.424 41.667 0.00 0.00 0.00 2.90
451 453 3.684305 CGTTGTACTGCCATGATTGAAGA 59.316 43.478 0.00 0.00 0.00 2.87
452 454 3.684305 TCGTTGTACTGCCATGATTGAAG 59.316 43.478 0.00 0.00 0.00 3.02
453 455 3.669536 TCGTTGTACTGCCATGATTGAA 58.330 40.909 0.00 0.00 0.00 2.69
455 457 3.188254 TGTTCGTTGTACTGCCATGATTG 59.812 43.478 0.00 0.00 0.00 2.67
456 458 3.188460 GTGTTCGTTGTACTGCCATGATT 59.812 43.478 0.00 0.00 0.00 2.57
457 459 2.742053 GTGTTCGTTGTACTGCCATGAT 59.258 45.455 0.00 0.00 0.00 2.45
458 460 2.139917 GTGTTCGTTGTACTGCCATGA 58.860 47.619 0.00 0.00 0.00 3.07
460 462 1.202710 TGGTGTTCGTTGTACTGCCAT 60.203 47.619 0.00 0.00 0.00 4.40
461 463 0.178301 TGGTGTTCGTTGTACTGCCA 59.822 50.000 0.00 0.00 0.00 4.92
463 465 1.860676 TCTGGTGTTCGTTGTACTGC 58.139 50.000 0.00 0.00 0.00 4.40
464 466 6.533819 TTATTTCTGGTGTTCGTTGTACTG 57.466 37.500 0.00 0.00 0.00 2.74
465 467 7.556733 TTTTATTTCTGGTGTTCGTTGTACT 57.443 32.000 0.00 0.00 0.00 2.73
467 469 7.799447 CGATTTTTATTTCTGGTGTTCGTTGTA 59.201 33.333 0.00 0.00 0.00 2.41
468 470 6.635239 CGATTTTTATTTCTGGTGTTCGTTGT 59.365 34.615 0.00 0.00 0.00 3.32
470 472 5.627780 GCGATTTTTATTTCTGGTGTTCGTT 59.372 36.000 0.00 0.00 0.00 3.85
471 473 5.151389 GCGATTTTTATTTCTGGTGTTCGT 58.849 37.500 0.00 0.00 0.00 3.85
472 474 4.259734 CGCGATTTTTATTTCTGGTGTTCG 59.740 41.667 0.00 0.00 0.00 3.95
473 475 5.387279 TCGCGATTTTTATTTCTGGTGTTC 58.613 37.500 3.71 0.00 0.00 3.18
474 476 5.048991 ACTCGCGATTTTTATTTCTGGTGTT 60.049 36.000 10.36 0.00 0.00 3.32
475 477 4.454504 ACTCGCGATTTTTATTTCTGGTGT 59.545 37.500 10.36 0.00 0.00 4.16
476 478 4.969816 ACTCGCGATTTTTATTTCTGGTG 58.030 39.130 10.36 0.00 0.00 4.17
480 482 7.484959 GGATTTGAACTCGCGATTTTTATTTCT 59.515 33.333 10.36 0.00 0.00 2.52
481 483 7.511506 CGGATTTGAACTCGCGATTTTTATTTC 60.512 37.037 10.36 5.54 0.00 2.17
484 486 5.064198 TCGGATTTGAACTCGCGATTTTTAT 59.936 36.000 10.36 5.36 0.00 1.40
485 487 4.389382 TCGGATTTGAACTCGCGATTTTTA 59.611 37.500 10.36 0.00 0.00 1.52
486 488 3.187637 TCGGATTTGAACTCGCGATTTTT 59.812 39.130 10.36 2.92 0.00 1.94
489 491 2.004583 TCGGATTTGAACTCGCGATT 57.995 45.000 10.36 0.00 0.00 3.34
490 492 2.225068 ATCGGATTTGAACTCGCGAT 57.775 45.000 10.36 0.00 0.00 4.58
493 495 1.527311 GCCTATCGGATTTGAACTCGC 59.473 52.381 0.00 0.00 0.00 5.03
528 736 5.596845 TGTCAGCACAAAGGGAAAATAAAC 58.403 37.500 0.00 0.00 0.00 2.01
586 794 6.932356 AACTCACATACAATAGATGGCTTG 57.068 37.500 0.00 0.00 0.00 4.01
596 804 7.549134 ACACGTGATATGAAACTCACATACAAT 59.451 33.333 25.01 0.00 41.46 2.71
602 810 3.431912 GCACACGTGATATGAAACTCACA 59.568 43.478 25.01 0.00 41.46 3.58
606 814 3.181507 GCATGCACACGTGATATGAAACT 60.182 43.478 25.01 0.00 34.49 2.66
614 822 1.456296 AATCAGCATGCACACGTGAT 58.544 45.000 25.01 16.38 34.49 3.06
672 880 9.692749 ACGTGTAAATACGATGATAATCTCATT 57.307 29.630 6.25 0.00 44.83 2.57
697 905 8.911247 AACTGATTCTAAAACTTGACACAAAC 57.089 30.769 0.00 0.00 0.00 2.93
736 944 8.928733 CGATGTTTACTTTACTGCCTAAACTTA 58.071 33.333 0.00 0.00 32.56 2.24
739 947 6.148315 ACCGATGTTTACTTTACTGCCTAAAC 59.852 38.462 0.00 0.00 32.15 2.01
740 948 6.148150 CACCGATGTTTACTTTACTGCCTAAA 59.852 38.462 0.00 0.00 0.00 1.85
743 951 4.000988 CACCGATGTTTACTTTACTGCCT 58.999 43.478 0.00 0.00 0.00 4.75
748 957 4.752661 TTGCCACCGATGTTTACTTTAC 57.247 40.909 0.00 0.00 0.00 2.01
763 972 1.067693 GCCGTGCTTAAATTTGCCAC 58.932 50.000 0.00 4.54 0.00 5.01
770 979 4.638304 AGGTAATATCGCCGTGCTTAAAT 58.362 39.130 0.00 0.00 0.00 1.40
856 1114 0.251386 TTTGGGCCGCCTGATGTTAA 60.251 50.000 9.86 0.00 0.00 2.01
1128 1392 2.107141 GAGCAGGATTAGCGCCGT 59.893 61.111 2.29 0.00 37.01 5.68
1171 1435 1.952990 GACATCATCTGCGAGAGAGGA 59.047 52.381 2.29 2.29 45.32 3.71
1174 1438 0.665298 CCGACATCATCTGCGAGAGA 59.335 55.000 0.00 0.00 34.25 3.10
1362 1627 2.770164 ACGAATTTCACCCAGAGAGG 57.230 50.000 0.00 0.00 37.03 3.69
1375 1640 2.948979 TGTCAAGCAAGTGGAACGAATT 59.051 40.909 0.00 0.00 45.86 2.17
1386 1656 1.026182 TAGCCGGCATGTCAAGCAAG 61.026 55.000 31.54 0.00 0.00 4.01
1401 1671 3.543680 TCCTAACTTGTGATGCTAGCC 57.456 47.619 13.29 0.00 0.00 3.93
1403 1673 8.616076 CCTAATTTTCCTAACTTGTGATGCTAG 58.384 37.037 0.00 0.00 0.00 3.42
1407 1677 6.663523 ACCCCTAATTTTCCTAACTTGTGATG 59.336 38.462 0.00 0.00 0.00 3.07
1415 1685 9.470399 TCAGATAAAACCCCTAATTTTCCTAAC 57.530 33.333 0.00 0.00 31.79 2.34
1430 1702 8.686334 TGAGCAAGGATAAATTCAGATAAAACC 58.314 33.333 0.00 0.00 0.00 3.27
1463 1743 6.978343 AACGTATGCACTTTCAGCTAATTA 57.022 33.333 0.00 0.00 0.00 1.40
1473 1753 1.335506 CGGCCAAAACGTATGCACTTT 60.336 47.619 2.24 0.00 0.00 2.66
1474 1754 0.239879 CGGCCAAAACGTATGCACTT 59.760 50.000 2.24 0.00 0.00 3.16
1478 1758 2.202557 GGCGGCCAAAACGTATGC 60.203 61.111 15.62 0.00 0.00 3.14
1483 1763 2.099446 CATACGGCGGCCAAAACG 59.901 61.111 20.71 6.94 0.00 3.60
1495 1775 7.413475 AATAACTCTAATTCTGCTGCATACG 57.587 36.000 1.31 0.00 0.00 3.06
1524 1928 7.880195 AGTGAGCACTAGACAGAAACAAAATAT 59.120 33.333 0.41 0.00 40.43 1.28
1558 1962 2.092753 ACACCCATAAGGACTGCATGAG 60.093 50.000 0.00 0.00 39.89 2.90
1713 2121 0.247145 GCAGGACGTTGAAATACGCG 60.247 55.000 3.53 3.53 45.06 6.01
1815 2223 1.303561 GAAGCTGGCATCCACCACA 60.304 57.895 0.00 0.00 35.33 4.17
1852 2260 6.820656 GGATATCACATACCATAGGCAGAAAG 59.179 42.308 4.83 0.00 0.00 2.62
1986 2544 6.531021 AGTTGCTAGTTTCCACTTTAGCTAA 58.469 36.000 0.86 0.86 36.10 3.09
2006 2564 8.908786 ATCAATACCACCAGATATGTAAGTTG 57.091 34.615 0.00 0.00 0.00 3.16
2034 2592 4.045636 ACCAGAATCACAACAAAACAGC 57.954 40.909 0.00 0.00 0.00 4.40
2150 2792 6.868622 ACCTCAGAACTATATGAACACACTC 58.131 40.000 0.00 0.00 0.00 3.51
2163 2805 3.951680 TCATGCACGATACCTCAGAACTA 59.048 43.478 0.00 0.00 0.00 2.24
2173 2815 5.614231 GCAGAATCAAGATCATGCACGATAC 60.614 44.000 0.00 0.00 34.34 2.24
2177 2819 2.612672 AGCAGAATCAAGATCATGCACG 59.387 45.455 16.74 0.00 35.72 5.34
2248 2892 6.209391 CCCTGATTCTGACCACTTAAAACATT 59.791 38.462 0.00 0.00 0.00 2.71
2416 3060 5.118203 CAGACATACACATATCTGCGTCATG 59.882 44.000 0.00 0.00 32.76 3.07
2554 3198 6.468333 TCATCTTCCTCAAGATCAGAGAAG 57.532 41.667 14.67 14.41 44.86 2.85
2731 3375 2.494870 GTGGCTCAGCAAATTCTCCATT 59.505 45.455 0.00 0.00 0.00 3.16
2797 3441 3.998913 TCAGATGGGTCTTGTGCATAA 57.001 42.857 0.00 0.00 30.42 1.90
2986 3630 3.073650 AGGATGGGCTGATGGTAAGATTC 59.926 47.826 0.00 0.00 0.00 2.52
3021 3665 5.415701 GGGCATGTCATAAAAGAAGTCTTCA 59.584 40.000 14.97 0.00 34.61 3.02
3039 3683 3.201290 CTGCTACAAACTAGAGGGCATG 58.799 50.000 0.00 0.00 0.00 4.06
3065 3715 3.322254 ACTCCAACTAGAAGACACACCAG 59.678 47.826 0.00 0.00 0.00 4.00
3068 3718 6.688578 TCATAACTCCAACTAGAAGACACAC 58.311 40.000 0.00 0.00 0.00 3.82
3089 3739 3.446873 TGGTTCAACAACACAAGCTTCAT 59.553 39.130 0.00 0.00 33.70 2.57
3100 3750 2.094734 ACTCGTCGTTTGGTTCAACAAC 59.905 45.455 0.00 0.00 0.00 3.32
3106 3756 0.865769 ATGCACTCGTCGTTTGGTTC 59.134 50.000 0.00 0.00 0.00 3.62
3111 3761 3.299340 AGAACTATGCACTCGTCGTTT 57.701 42.857 0.00 0.00 0.00 3.60
3114 3764 2.599082 GGAAAGAACTATGCACTCGTCG 59.401 50.000 0.00 0.00 0.00 5.12
3116 3766 3.006967 ACTGGAAAGAACTATGCACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
3158 3809 4.141251 AGGAATTCCAACACCACACTAAGT 60.141 41.667 26.22 0.00 38.89 2.24
3170 3821 2.554032 CAGACACACCAGGAATTCCAAC 59.446 50.000 26.22 7.91 38.89 3.77
3189 3840 2.554032 GACACACCAGGAATTCCAACAG 59.446 50.000 26.22 14.93 38.89 3.16
3190 3841 2.092158 TGACACACCAGGAATTCCAACA 60.092 45.455 26.22 10.57 38.89 3.33
3191 3842 2.582052 TGACACACCAGGAATTCCAAC 58.418 47.619 26.22 8.37 38.89 3.77
3192 3843 3.304911 TTGACACACCAGGAATTCCAA 57.695 42.857 26.22 5.67 38.89 3.53
3193 3844 3.221771 CTTTGACACACCAGGAATTCCA 58.778 45.455 26.22 0.00 38.89 3.53
3194 3845 2.558359 CCTTTGACACACCAGGAATTCC 59.442 50.000 17.31 17.31 0.00 3.01
3195 3846 2.029918 GCCTTTGACACACCAGGAATTC 60.030 50.000 0.00 0.00 0.00 2.17
3196 3847 1.963515 GCCTTTGACACACCAGGAATT 59.036 47.619 0.00 0.00 0.00 2.17
3197 3848 1.133513 TGCCTTTGACACACCAGGAAT 60.134 47.619 0.00 0.00 0.00 3.01
3198 3849 0.257328 TGCCTTTGACACACCAGGAA 59.743 50.000 0.00 0.00 0.00 3.36
3199 3850 0.179020 CTGCCTTTGACACACCAGGA 60.179 55.000 0.00 0.00 0.00 3.86
3200 3851 0.466189 ACTGCCTTTGACACACCAGG 60.466 55.000 0.00 0.00 0.00 4.45
3201 3852 2.254546 TACTGCCTTTGACACACCAG 57.745 50.000 0.00 0.00 0.00 4.00
3202 3853 2.105649 TCATACTGCCTTTGACACACCA 59.894 45.455 0.00 0.00 0.00 4.17
3203 3854 2.484264 GTCATACTGCCTTTGACACACC 59.516 50.000 0.00 0.00 39.59 4.16
3204 3855 3.187227 CAGTCATACTGCCTTTGACACAC 59.813 47.826 5.23 0.00 39.62 3.82
3205 3856 3.402110 CAGTCATACTGCCTTTGACACA 58.598 45.455 5.23 0.00 39.62 3.72
3206 3857 2.744202 CCAGTCATACTGCCTTTGACAC 59.256 50.000 1.43 0.00 44.63 3.67
3207 3858 2.371841 ACCAGTCATACTGCCTTTGACA 59.628 45.455 1.43 0.00 44.63 3.58
3208 3859 3.059352 ACCAGTCATACTGCCTTTGAC 57.941 47.619 1.43 0.00 44.63 3.18
3209 3860 3.181445 ACAACCAGTCATACTGCCTTTGA 60.181 43.478 15.43 0.00 44.63 2.69
3210 3861 3.149196 ACAACCAGTCATACTGCCTTTG 58.851 45.455 1.43 7.01 44.63 2.77
3211 3862 3.508845 ACAACCAGTCATACTGCCTTT 57.491 42.857 1.43 0.00 44.63 3.11
3212 3863 4.634012 TTACAACCAGTCATACTGCCTT 57.366 40.909 1.43 0.00 44.63 4.35
3213 3864 4.844349 ATTACAACCAGTCATACTGCCT 57.156 40.909 1.43 0.00 44.63 4.75
3214 3865 9.367444 GTATATATTACAACCAGTCATACTGCC 57.633 37.037 1.43 0.00 44.63 4.85
3215 3866 9.923143 TGTATATATTACAACCAGTCATACTGC 57.077 33.333 1.43 0.00 44.63 4.40
3221 3872 9.607988 CAACCTTGTATATATTACAACCAGTCA 57.392 33.333 0.00 0.00 34.21 3.41
3222 3873 9.052759 CCAACCTTGTATATATTACAACCAGTC 57.947 37.037 0.00 0.00 34.21 3.51
3223 3874 8.554011 ACCAACCTTGTATATATTACAACCAGT 58.446 33.333 0.00 0.00 34.21 4.00
3224 3875 8.974060 ACCAACCTTGTATATATTACAACCAG 57.026 34.615 0.00 0.00 34.21 4.00
3225 3876 7.994334 GGACCAACCTTGTATATATTACAACCA 59.006 37.037 0.00 0.00 34.21 3.67
3226 3877 8.387190 GGACCAACCTTGTATATATTACAACC 57.613 38.462 0.00 0.00 34.21 3.77
3250 3901 7.823745 ATTACAGCACCCAAAATTATCTAGG 57.176 36.000 0.00 0.00 0.00 3.02
3317 3968 5.416952 ACATTTCAACAATCAGGACAGGATC 59.583 40.000 0.00 0.00 0.00 3.36
3354 4005 5.928839 AGGCATATCATAACGATGTTGAGTC 59.071 40.000 0.00 0.00 35.39 3.36
3358 4009 7.194607 AGAAAGGCATATCATAACGATGTTG 57.805 36.000 0.00 0.00 35.39 3.33
3376 4027 7.254590 GCATTGCTACAGTATGAACTAGAAAGG 60.255 40.741 0.16 0.00 39.69 3.11
3383 4034 5.089970 TCAGCATTGCTACAGTATGAACT 57.910 39.130 11.55 0.00 35.13 3.01
3391 4042 4.634883 AGACAGATTTCAGCATTGCTACAG 59.365 41.667 11.55 0.00 36.40 2.74
3392 4043 4.582869 AGACAGATTTCAGCATTGCTACA 58.417 39.130 11.55 0.00 36.40 2.74
3393 4044 5.353678 AGAAGACAGATTTCAGCATTGCTAC 59.646 40.000 11.55 1.39 36.40 3.58
3394 4045 5.353400 CAGAAGACAGATTTCAGCATTGCTA 59.647 40.000 11.55 0.00 36.40 3.49
3395 4046 4.156190 CAGAAGACAGATTTCAGCATTGCT 59.844 41.667 5.03 5.03 40.77 3.91
3396 4047 4.413087 CAGAAGACAGATTTCAGCATTGC 58.587 43.478 0.00 0.00 0.00 3.56
3397 4048 4.458295 ACCAGAAGACAGATTTCAGCATTG 59.542 41.667 0.00 0.00 0.00 2.82
3398 4049 4.660168 ACCAGAAGACAGATTTCAGCATT 58.340 39.130 0.00 0.00 0.00 3.56
3402 4053 3.683822 GCAGACCAGAAGACAGATTTCAG 59.316 47.826 0.00 0.00 0.00 3.02
3418 4069 1.945394 CTCATATTGTGGCTGCAGACC 59.055 52.381 19.23 18.04 0.00 3.85
3424 4075 3.558829 CACTAGTGCTCATATTGTGGCTG 59.441 47.826 10.54 0.00 0.00 4.85
3485 4739 7.935520 ACAAAACCAAACTGAAAATGTGTTTT 58.064 26.923 0.00 0.00 40.13 2.43
3488 4742 6.072783 CCAACAAAACCAAACTGAAAATGTGT 60.073 34.615 0.00 0.00 0.00 3.72
3571 4837 0.947180 AAAGAATACCGTGTGCGCGT 60.947 50.000 8.43 0.00 36.67 6.01
3652 4918 1.001641 AAGAAGGAATGCAGCCGCT 60.002 52.632 0.00 0.00 39.64 5.52
3684 4950 1.527844 GCTGCTAAGGATGGGCTGG 60.528 63.158 0.00 0.00 0.00 4.85
3687 4953 1.889545 CTTAGCTGCTAAGGATGGGC 58.110 55.000 32.13 0.00 39.57 5.36
3757 5024 1.267533 CACAATAACAGCAGCAGCACA 59.732 47.619 3.17 0.00 45.49 4.57
3786 5053 3.056607 GCTGGACATGGCAAGTTGTTAAT 60.057 43.478 4.44 0.00 0.00 1.40
3787 5054 2.295909 GCTGGACATGGCAAGTTGTTAA 59.704 45.455 4.44 0.00 0.00 2.01
3788 5055 1.885887 GCTGGACATGGCAAGTTGTTA 59.114 47.619 4.44 0.00 0.00 2.41
3789 5056 0.675633 GCTGGACATGGCAAGTTGTT 59.324 50.000 4.44 0.00 0.00 2.83
3790 5057 1.181098 GGCTGGACATGGCAAGTTGT 61.181 55.000 4.44 0.00 0.00 3.32
3797 5064 2.036256 ACCAAGGCTGGACATGGC 59.964 61.111 9.53 0.00 46.92 4.40
3844 5111 1.291877 CCGAACTTCCGCAGACCAAG 61.292 60.000 0.00 0.00 0.00 3.61
3855 5122 0.178068 TCTAGCATGGCCCGAACTTC 59.822 55.000 0.00 0.00 0.00 3.01
3857 5124 0.978146 AGTCTAGCATGGCCCGAACT 60.978 55.000 0.00 0.00 0.00 3.01
3858 5125 0.530870 GAGTCTAGCATGGCCCGAAC 60.531 60.000 0.00 0.00 0.00 3.95
3861 5128 0.107703 TTTGAGTCTAGCATGGCCCG 60.108 55.000 0.00 0.00 0.00 6.13
3862 5129 2.128771 TTTTGAGTCTAGCATGGCCC 57.871 50.000 0.00 0.00 0.00 5.80
3885 5152 0.476771 TGGCCCGAACTTCCTCTTTT 59.523 50.000 0.00 0.00 0.00 2.27
3886 5153 0.698818 ATGGCCCGAACTTCCTCTTT 59.301 50.000 0.00 0.00 0.00 2.52
3889 5156 2.115291 GCATGGCCCGAACTTCCTC 61.115 63.158 0.00 0.00 0.00 3.71
3890 5157 2.044946 GCATGGCCCGAACTTCCT 60.045 61.111 0.00 0.00 0.00 3.36
3891 5158 3.140814 GGCATGGCCCGAACTTCC 61.141 66.667 8.35 0.00 44.06 3.46
3908 5374 1.933853 CCGTCTTAAGGCCTTTCGATG 59.066 52.381 26.08 22.62 0.00 3.84
3911 5377 1.337447 TGTCCGTCTTAAGGCCTTTCG 60.337 52.381 26.08 21.09 0.00 3.46
3920 5386 7.762615 CAGTAGAACCAATATTGTCCGTCTTAA 59.237 37.037 14.25 0.00 0.00 1.85
3921 5387 7.262772 CAGTAGAACCAATATTGTCCGTCTTA 58.737 38.462 14.25 0.39 0.00 2.10
3930 5396 3.242739 GCGTGGCAGTAGAACCAATATTG 60.243 47.826 8.58 8.58 37.79 1.90
3935 5401 0.970640 TAGCGTGGCAGTAGAACCAA 59.029 50.000 0.00 0.00 37.79 3.67
3937 5403 0.459759 GGTAGCGTGGCAGTAGAACC 60.460 60.000 0.00 0.00 0.00 3.62
3938 5404 0.245539 TGGTAGCGTGGCAGTAGAAC 59.754 55.000 0.00 0.00 0.00 3.01
3940 5406 1.191535 ATTGGTAGCGTGGCAGTAGA 58.808 50.000 0.00 0.00 0.00 2.59
3944 5410 4.515191 ACATTATTATTGGTAGCGTGGCAG 59.485 41.667 0.00 0.00 0.00 4.85
3945 5411 4.456535 ACATTATTATTGGTAGCGTGGCA 58.543 39.130 0.00 0.00 0.00 4.92
3946 5412 4.377022 CGACATTATTATTGGTAGCGTGGC 60.377 45.833 0.00 0.00 0.00 5.01
3947 5413 4.986034 TCGACATTATTATTGGTAGCGTGG 59.014 41.667 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.