Multiple sequence alignment - TraesCS5B01G280200

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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 TraesCS5B01G280200 chr5B 100.000 2210 0 0 1 2210 466000981 466003190 0.000000e+00 4082.0
1 TraesCS5B01G280200 chr5B 94.444 288 12 3 60 345 60961456 60961741 7.240000e-120 440.0
2 TraesCS5B01G280200 chr5D 91.712 929 67 9 531 1452 387628574 387629499 0.000000e+00 1280.0
3 TraesCS5B01G280200 chr5D 91.667 396 19 6 1817 2210 387629781 387630164 8.980000e-149 536.0
4 TraesCS5B01G280200 chr5D 91.579 95 5 2 387 478 387628170 387628264 6.400000e-26 128.0
5 TraesCS5B01G280200 chr5A 91.531 614 40 9 847 1452 490318346 490318955 0.000000e+00 835.0
6 TraesCS5B01G280200 chr5A 88.315 368 27 12 1 360 490317222 490317581 5.640000e-116 427.0
7 TraesCS5B01G280200 chr5A 88.814 295 26 3 1817 2111 490319240 490319527 2.700000e-94 355.0
8 TraesCS5B01G280200 chr5A 94.340 212 8 2 1475 1686 490319032 490319239 2.740000e-84 322.0
9 TraesCS5B01G280200 chr2B 94.769 325 12 4 60 382 118130808 118131129 3.280000e-138 501.0
10 TraesCS5B01G280200 chr2B 91.379 58 5 0 386 443 118131393 118131450 1.820000e-11 80.5
11 TraesCS5B01G280200 chr3B 95.333 300 10 4 60 357 53188027 53187730 7.140000e-130 473.0
12 TraesCS5B01G280200 chr6B 95.833 288 7 3 60 345 233152874 233152590 5.560000e-126 460.0
13 TraesCS5B01G280200 chr7B 95.139 288 10 3 60 345 561773740 561773455 3.350000e-123 451.0
14 TraesCS5B01G280200 chr4B 95.139 288 10 4 60 345 634537370 634537655 3.350000e-123 451.0
15 TraesCS5B01G280200 chr4B 93.333 300 14 4 60 357 396968746 396969041 2.610000e-119 438.0
16 TraesCS5B01G280200 chr4B 94.326 282 12 3 63 343 634901537 634901259 1.570000e-116 429.0


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 TraesCS5B01G280200 chr5B 466000981 466003190 2209 False 4082.00 4082 100.000000 1 2210 1 chr5B.!!$F2 2209
1 TraesCS5B01G280200 chr5D 387628170 387630164 1994 False 648.00 1280 91.652667 387 2210 3 chr5D.!!$F1 1823
2 TraesCS5B01G280200 chr5A 490317222 490319527 2305 False 484.75 835 90.750000 1 2111 4 chr5A.!!$F1 2110
3 TraesCS5B01G280200 chr2B 118130808 118131450 642 False 290.75 501 93.074000 60 443 2 chr2B.!!$F1 383

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
312 321 0.108567 GCACCCCTCTCTTCTTCGTC 60.109 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 2615 0.107831 AGGCACGGTAAGTTGAAGCA 59.892 50.0 0.0 0.0 0.0 3.91 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
19 20 3.535962 CCAGCGCCCCTCTCTCTC 61.536 72.222 2.29 0.00 0.00 3.20
21 22 2.123897 AGCGCCCCTCTCTCTCTC 60.124 66.667 2.29 0.00 0.00 3.20
22 23 2.441164 GCGCCCCTCTCTCTCTCA 60.441 66.667 0.00 0.00 0.00 3.27
24 25 1.379176 CGCCCCTCTCTCTCTCACA 60.379 63.158 0.00 0.00 0.00 3.58
25 26 1.662438 CGCCCCTCTCTCTCTCACAC 61.662 65.000 0.00 0.00 0.00 3.82
26 27 0.613292 GCCCCTCTCTCTCTCACACA 60.613 60.000 0.00 0.00 0.00 3.72
37 38 0.668535 TCTCACACACGAGTCACCAG 59.331 55.000 0.00 0.00 34.46 4.00
39 40 2.027605 ACACACGAGTCACCAGCG 59.972 61.111 0.00 0.00 0.00 5.18
113 116 2.366435 CTCGCCCCCTTCCCCTTA 60.366 66.667 0.00 0.00 0.00 2.69
138 141 1.620259 CTCTGCCCCCTCTCTCTCT 59.380 63.158 0.00 0.00 0.00 3.10
139 142 0.468029 CTCTGCCCCCTCTCTCTCTC 60.468 65.000 0.00 0.00 0.00 3.20
308 317 0.839853 AGCAGCACCCCTCTCTTCTT 60.840 55.000 0.00 0.00 0.00 2.52
312 321 0.108567 GCACCCCTCTCTTCTTCGTC 60.109 60.000 0.00 0.00 0.00 4.20
361 370 2.839486 AGCTGTTCGATCTGTTTGGA 57.161 45.000 0.00 0.00 0.00 3.53
378 387 3.717400 TGGACAGTAGATTCGCTGATC 57.283 47.619 14.99 9.86 36.62 2.92
379 388 3.291584 TGGACAGTAGATTCGCTGATCT 58.708 45.455 14.99 4.42 39.59 2.75
380 389 3.067320 TGGACAGTAGATTCGCTGATCTG 59.933 47.826 14.99 0.00 37.01 2.90
381 390 3.067461 GGACAGTAGATTCGCTGATCTGT 59.933 47.826 14.99 0.00 37.01 3.41
383 392 5.078411 ACAGTAGATTCGCTGATCTGTTT 57.922 39.130 14.99 0.00 37.01 2.83
384 393 4.867047 ACAGTAGATTCGCTGATCTGTTTG 59.133 41.667 14.99 6.81 37.01 2.93
396 726 1.450312 CTGTTTGGGCTCGGCTAGG 60.450 63.158 0.00 0.00 0.00 3.02
429 761 3.190874 GCAGGTGCAGACTATCTGTAAC 58.809 50.000 4.00 4.00 45.46 2.50
431 764 2.427453 AGGTGCAGACTATCTGTAACCG 59.573 50.000 18.88 0.00 46.13 4.44
478 811 6.654582 TCAAAATATGCACTGCTCAGTTCTTA 59.345 34.615 1.98 0.00 40.20 2.10
480 813 6.428385 AATATGCACTGCTCAGTTCTTAAC 57.572 37.500 1.98 0.00 40.20 2.01
481 814 2.494059 TGCACTGCTCAGTTCTTAACC 58.506 47.619 1.98 0.00 40.20 2.85
482 815 2.158827 TGCACTGCTCAGTTCTTAACCA 60.159 45.455 1.98 0.00 40.20 3.67
483 816 2.224314 GCACTGCTCAGTTCTTAACCAC 59.776 50.000 0.00 0.00 40.20 4.16
484 817 2.808543 CACTGCTCAGTTCTTAACCACC 59.191 50.000 0.00 0.00 40.20 4.61
485 818 2.706190 ACTGCTCAGTTCTTAACCACCT 59.294 45.455 0.00 0.00 38.83 4.00
486 819 3.136626 ACTGCTCAGTTCTTAACCACCTT 59.863 43.478 0.00 0.00 38.83 3.50
487 820 4.347000 ACTGCTCAGTTCTTAACCACCTTA 59.653 41.667 0.00 0.00 38.83 2.69
488 821 5.163237 ACTGCTCAGTTCTTAACCACCTTAA 60.163 40.000 0.00 0.00 38.83 1.85
489 822 5.061179 TGCTCAGTTCTTAACCACCTTAAC 58.939 41.667 0.00 0.00 0.00 2.01
490 823 5.061179 GCTCAGTTCTTAACCACCTTAACA 58.939 41.667 0.00 0.00 0.00 2.41
491 824 5.179555 GCTCAGTTCTTAACCACCTTAACAG 59.820 44.000 0.00 0.00 0.00 3.16
492 825 6.488769 TCAGTTCTTAACCACCTTAACAGA 57.511 37.500 0.00 0.00 0.00 3.41
493 826 6.891388 TCAGTTCTTAACCACCTTAACAGAA 58.109 36.000 0.00 0.00 0.00 3.02
495 828 7.660208 TCAGTTCTTAACCACCTTAACAGAATC 59.340 37.037 0.00 0.00 0.00 2.52
496 829 7.444183 CAGTTCTTAACCACCTTAACAGAATCA 59.556 37.037 0.00 0.00 0.00 2.57
497 830 7.661847 AGTTCTTAACCACCTTAACAGAATCAG 59.338 37.037 0.00 0.00 0.00 2.90
498 831 7.311092 TCTTAACCACCTTAACAGAATCAGA 57.689 36.000 0.00 0.00 0.00 3.27
499 832 7.918076 TCTTAACCACCTTAACAGAATCAGAT 58.082 34.615 0.00 0.00 0.00 2.90
500 833 8.041323 TCTTAACCACCTTAACAGAATCAGATC 58.959 37.037 0.00 0.00 0.00 2.75
501 834 5.762179 ACCACCTTAACAGAATCAGATCA 57.238 39.130 0.00 0.00 0.00 2.92
502 835 5.738909 ACCACCTTAACAGAATCAGATCAG 58.261 41.667 0.00 0.00 0.00 2.90
503 836 4.574013 CCACCTTAACAGAATCAGATCAGC 59.426 45.833 0.00 0.00 0.00 4.26
506 1097 4.272991 CCTTAACAGAATCAGATCAGCAGC 59.727 45.833 0.00 0.00 0.00 5.25
508 1099 2.907634 ACAGAATCAGATCAGCAGCAG 58.092 47.619 0.00 0.00 0.00 4.24
521 1112 1.367659 GCAGCAGCTGGAAACTAGAG 58.632 55.000 24.13 0.00 37.91 2.43
522 1113 1.367659 CAGCAGCTGGAAACTAGAGC 58.632 55.000 17.12 0.00 0.00 4.09
523 1114 0.979665 AGCAGCTGGAAACTAGAGCA 59.020 50.000 17.12 0.00 35.03 4.26
524 1115 1.082690 GCAGCTGGAAACTAGAGCAC 58.917 55.000 17.12 0.00 35.03 4.40
526 1117 2.344950 CAGCTGGAAACTAGAGCACAG 58.655 52.381 5.57 0.85 35.03 3.66
527 1118 1.082690 GCTGGAAACTAGAGCACAGC 58.917 55.000 14.68 14.68 43.50 4.40
528 1119 1.354040 CTGGAAACTAGAGCACAGCG 58.646 55.000 0.00 0.00 0.00 5.18
529 1120 0.679505 TGGAAACTAGAGCACAGCGT 59.320 50.000 0.00 0.00 0.00 5.07
530 1121 1.336887 TGGAAACTAGAGCACAGCGTC 60.337 52.381 0.00 0.00 0.00 5.19
531 1122 1.067495 GGAAACTAGAGCACAGCGTCT 60.067 52.381 0.00 0.00 0.00 4.18
532 1123 1.989165 GAAACTAGAGCACAGCGTCTG 59.011 52.381 0.00 5.47 37.52 3.51
533 1124 0.962489 AACTAGAGCACAGCGTCTGT 59.038 50.000 0.00 6.67 46.51 3.41
535 1126 0.179150 CTAGAGCACAGCGTCTGTCC 60.179 60.000 9.15 1.70 43.43 4.02
536 1127 0.893727 TAGAGCACAGCGTCTGTCCA 60.894 55.000 9.15 0.00 43.43 4.02
552 1143 0.758734 TCCAGTAGAATCGCCCATGG 59.241 55.000 4.14 4.14 0.00 3.66
560 1151 2.955022 AATCGCCCATGGAGCTGCTC 62.955 60.000 21.17 21.17 0.00 4.26
573 1164 3.563390 GGAGCTGCTCAAGTCATATTTCC 59.437 47.826 28.95 6.01 31.08 3.13
577 1168 4.337555 GCTGCTCAAGTCATATTTCCATGT 59.662 41.667 0.00 0.00 0.00 3.21
625 1217 2.571212 TGCAACCAAGTGTTCTAGTGG 58.429 47.619 0.00 0.00 34.00 4.00
631 1223 2.293399 CCAAGTGTTCTAGTGGCCAAAC 59.707 50.000 7.24 9.36 0.00 2.93
641 1233 2.730990 TGGCCAAACATGACCACAG 58.269 52.632 0.61 0.00 0.00 3.66
642 1234 1.290009 GGCCAAACATGACCACAGC 59.710 57.895 0.00 0.00 0.00 4.40
651 1243 0.960861 ATGACCACAGCGAGTCGAGA 60.961 55.000 18.61 0.00 35.71 4.04
664 1256 5.575995 AGCGAGTCGAGAATTTTAAAGTACC 59.424 40.000 18.61 0.00 0.00 3.34
694 1286 8.874156 ACCATTTATAGTCTCTCAGCAATCATA 58.126 33.333 0.00 0.00 0.00 2.15
709 1301 4.261197 GCAATCATATGACCGAACCCTTTC 60.261 45.833 7.78 0.00 0.00 2.62
722 1314 4.517453 CGAACCCTTTCTTTGGATGTGTTA 59.483 41.667 0.00 0.00 0.00 2.41
770 1362 9.367444 GGAATAATTGTTATGATAGGTCCTACG 57.633 37.037 0.00 0.00 0.00 3.51
795 1387 7.472543 GTTAACCATGGTGTATGCTTTCTTAG 58.527 38.462 20.60 0.00 35.37 2.18
822 1627 6.785337 AATCATGGTGAATGTTGATCATGT 57.215 33.333 0.00 0.00 37.56 3.21
973 1789 8.057623 ACTATTTCATCCCTTTTGTCTGATGAT 58.942 33.333 0.00 0.00 42.15 2.45
975 1791 4.785301 TCATCCCTTTTGTCTGATGATCC 58.215 43.478 0.00 0.00 38.84 3.36
984 1800 2.036346 TGTCTGATGATCCTGCGTATGG 59.964 50.000 0.00 0.00 0.00 2.74
1011 1827 1.064389 GTTGGAAGGATGAGGAAGGGG 60.064 57.143 0.00 0.00 0.00 4.79
1092 1908 3.010472 TCATGATGACCAAGGTGAACCAT 59.990 43.478 0.00 0.00 38.89 3.55
1101 1917 0.035439 AGGTGAACCATACCGGCAAG 60.035 55.000 0.00 0.00 43.06 4.01
1211 2027 3.833070 GAGGAGAACCAAGACAAGTAGGA 59.167 47.826 0.00 0.00 38.94 2.94
1214 2030 4.308265 GAGAACCAAGACAAGTAGGACAC 58.692 47.826 0.00 0.00 0.00 3.67
1233 2049 3.272031 GCTGTTTGCAGAGGAGCC 58.728 61.111 0.00 0.00 45.28 4.70
1237 2053 2.286872 CTGTTTGCAGAGGAGCCATAG 58.713 52.381 0.00 0.00 45.28 2.23
1370 2186 3.446442 ACTTGCATGTTGGGATTCTCT 57.554 42.857 0.00 0.00 0.00 3.10
1371 2187 4.574674 ACTTGCATGTTGGGATTCTCTA 57.425 40.909 0.00 0.00 0.00 2.43
1374 2190 4.574674 TGCATGTTGGGATTCTCTAAGT 57.425 40.909 0.00 0.00 0.00 2.24
1376 2192 3.557595 GCATGTTGGGATTCTCTAAGTCG 59.442 47.826 0.00 0.00 0.00 4.18
1387 2203 8.562052 GGGATTCTCTAAGTCGTAAAACAAAAA 58.438 33.333 0.00 0.00 0.00 1.94
1389 2205 9.595357 GATTCTCTAAGTCGTAAAACAAAAAGG 57.405 33.333 0.00 0.00 0.00 3.11
1394 2213 8.347035 TCTAAGTCGTAAAACAAAAAGGAATGG 58.653 33.333 0.00 0.00 0.00 3.16
1396 2215 7.102847 AGTCGTAAAACAAAAAGGAATGGAA 57.897 32.000 0.00 0.00 0.00 3.53
1415 2234 9.325198 GAATGGAACCAATTAGTTTCTGTTTTT 57.675 29.630 0.00 0.00 0.00 1.94
1439 2258 1.824230 TCAGTTAATGGTTGGGCATGC 59.176 47.619 9.90 9.90 0.00 4.06
1444 2263 1.126329 AATGGTTGGGCATGCCAACA 61.126 50.000 36.56 26.53 46.35 3.33
1464 2289 7.468631 GCCAACATGTCTTTCTTCTGTTTCTAA 60.469 37.037 0.00 0.00 0.00 2.10
1467 2292 7.588512 ACATGTCTTTCTTCTGTTTCTAATGC 58.411 34.615 0.00 0.00 0.00 3.56
1472 2297 9.766277 GTCTTTCTTCTGTTTCTAATGCATTAG 57.234 33.333 32.08 32.08 40.79 1.73
1489 2362 6.523840 TGCATTAGTTTGCTTGAAATCCTTT 58.476 32.000 0.00 0.00 43.18 3.11
1496 2369 5.528043 TTGCTTGAAATCCTTTGCTGTAA 57.472 34.783 0.00 0.00 0.00 2.41
1566 2440 1.299316 CAGGCTTTGCACAACGTGG 60.299 57.895 0.00 0.00 33.64 4.94
1580 2454 0.318762 ACGTGGGCTTCTGAGAACTC 59.681 55.000 0.00 0.00 0.00 3.01
1672 2546 1.872773 AGTTTAGCCTGGAGGAGGAG 58.127 55.000 0.00 0.00 46.33 3.69
1674 2548 0.716591 TTTAGCCTGGAGGAGGAGGA 59.283 55.000 0.00 0.00 46.33 3.71
1675 2549 0.716591 TTAGCCTGGAGGAGGAGGAA 59.283 55.000 0.00 0.00 46.33 3.36
1676 2550 0.032017 TAGCCTGGAGGAGGAGGAAC 60.032 60.000 0.00 0.00 46.33 3.62
1686 2560 3.966665 GAGGAGGAGGAACATGAAGAGAT 59.033 47.826 0.00 0.00 0.00 2.75
1688 2562 3.181456 GGAGGAGGAACATGAAGAGATGG 60.181 52.174 0.00 0.00 0.00 3.51
1689 2563 3.708631 GAGGAGGAACATGAAGAGATGGA 59.291 47.826 0.00 0.00 0.00 3.41
1690 2564 3.710677 AGGAGGAACATGAAGAGATGGAG 59.289 47.826 0.00 0.00 0.00 3.86
1691 2565 3.181456 GGAGGAACATGAAGAGATGGAGG 60.181 52.174 0.00 0.00 0.00 4.30
1692 2566 2.172293 AGGAACATGAAGAGATGGAGGC 59.828 50.000 0.00 0.00 0.00 4.70
1693 2567 2.092753 GGAACATGAAGAGATGGAGGCA 60.093 50.000 0.00 0.00 0.00 4.75
1694 2568 2.706339 ACATGAAGAGATGGAGGCAC 57.294 50.000 0.00 0.00 0.00 5.01
1696 2570 2.093075 ACATGAAGAGATGGAGGCACTG 60.093 50.000 0.00 0.00 41.55 3.66
1697 2571 1.942776 TGAAGAGATGGAGGCACTGA 58.057 50.000 0.00 0.00 41.55 3.41
1698 2572 2.259917 TGAAGAGATGGAGGCACTGAA 58.740 47.619 0.00 0.00 41.55 3.02
1699 2573 2.235650 TGAAGAGATGGAGGCACTGAAG 59.764 50.000 0.00 0.00 41.55 3.02
1700 2574 0.540923 AGAGATGGAGGCACTGAAGC 59.459 55.000 0.00 0.00 41.55 3.86
1701 2575 0.540923 GAGATGGAGGCACTGAAGCT 59.459 55.000 0.00 0.00 41.55 3.74
1702 2576 0.252479 AGATGGAGGCACTGAAGCTG 59.748 55.000 0.00 0.00 41.55 4.24
1703 2577 0.035630 GATGGAGGCACTGAAGCTGT 60.036 55.000 0.00 0.00 41.55 4.40
1704 2578 0.322277 ATGGAGGCACTGAAGCTGTG 60.322 55.000 0.00 0.00 41.55 3.66
1705 2579 1.673665 GGAGGCACTGAAGCTGTGG 60.674 63.158 4.98 0.00 41.55 4.17
1706 2580 1.372683 GAGGCACTGAAGCTGTGGA 59.627 57.895 4.98 0.00 41.55 4.02
1707 2581 0.673022 GAGGCACTGAAGCTGTGGAG 60.673 60.000 4.98 0.00 41.55 3.86
1708 2582 1.673665 GGCACTGAAGCTGTGGAGG 60.674 63.158 4.98 0.00 34.61 4.30
1709 2583 2.331132 GCACTGAAGCTGTGGAGGC 61.331 63.158 4.98 0.00 34.61 4.70
1710 2584 2.031516 CACTGAAGCTGTGGAGGCG 61.032 63.158 0.00 0.00 31.27 5.52
1711 2585 2.435586 CTGAAGCTGTGGAGGCGG 60.436 66.667 0.00 0.00 34.52 6.13
1712 2586 4.704833 TGAAGCTGTGGAGGCGGC 62.705 66.667 0.00 0.00 40.86 6.53
1713 2587 4.704833 GAAGCTGTGGAGGCGGCA 62.705 66.667 13.08 0.00 42.87 5.69
1714 2588 4.711949 AAGCTGTGGAGGCGGCAG 62.712 66.667 13.08 0.00 42.87 4.85
1717 2591 4.320456 CTGTGGAGGCGGCAGTGT 62.320 66.667 13.08 0.00 0.00 3.55
1718 2592 3.832237 CTGTGGAGGCGGCAGTGTT 62.832 63.158 13.08 0.00 0.00 3.32
1719 2593 3.050275 GTGGAGGCGGCAGTGTTC 61.050 66.667 13.08 0.00 0.00 3.18
1720 2594 3.555324 TGGAGGCGGCAGTGTTCA 61.555 61.111 13.08 0.00 0.00 3.18
1721 2595 3.050275 GGAGGCGGCAGTGTTCAC 61.050 66.667 13.08 0.00 0.00 3.18
1722 2596 2.280797 GAGGCGGCAGTGTTCACA 60.281 61.111 13.08 0.00 0.00 3.58
1723 2597 2.281070 AGGCGGCAGTGTTCACAG 60.281 61.111 13.08 0.00 0.00 3.66
1724 2598 2.591715 GGCGGCAGTGTTCACAGT 60.592 61.111 3.07 0.00 0.00 3.55
1725 2599 2.186826 GGCGGCAGTGTTCACAGTT 61.187 57.895 3.07 0.00 0.00 3.16
1726 2600 1.279840 GCGGCAGTGTTCACAGTTC 59.720 57.895 5.74 0.00 0.00 3.01
1727 2601 1.436195 GCGGCAGTGTTCACAGTTCA 61.436 55.000 5.74 0.00 0.00 3.18
1728 2602 0.304705 CGGCAGTGTTCACAGTTCAC 59.695 55.000 5.74 0.00 0.00 3.18
1729 2603 1.378531 GGCAGTGTTCACAGTTCACA 58.621 50.000 5.74 0.00 34.94 3.58
1730 2604 1.742831 GGCAGTGTTCACAGTTCACAA 59.257 47.619 5.74 0.00 34.94 3.33
1731 2605 2.163412 GGCAGTGTTCACAGTTCACAAA 59.837 45.455 5.74 0.00 34.94 2.83
1732 2606 3.171277 GCAGTGTTCACAGTTCACAAAC 58.829 45.455 5.74 0.00 34.94 2.93
1733 2607 3.758300 CAGTGTTCACAGTTCACAAACC 58.242 45.455 5.74 0.00 35.92 3.27
1734 2608 3.190327 CAGTGTTCACAGTTCACAAACCA 59.810 43.478 5.74 0.00 35.92 3.67
1735 2609 3.440173 AGTGTTCACAGTTCACAAACCAG 59.560 43.478 5.74 0.00 35.92 4.00
1736 2610 3.190535 GTGTTCACAGTTCACAAACCAGT 59.809 43.478 0.00 0.00 35.92 4.00
1737 2611 4.393680 GTGTTCACAGTTCACAAACCAGTA 59.606 41.667 0.00 0.00 35.92 2.74
1738 2612 4.634004 TGTTCACAGTTCACAAACCAGTAG 59.366 41.667 0.00 0.00 35.92 2.57
1739 2613 3.804036 TCACAGTTCACAAACCAGTAGG 58.196 45.455 0.00 0.00 42.21 3.18
1740 2614 3.452990 TCACAGTTCACAAACCAGTAGGA 59.547 43.478 0.00 0.00 38.69 2.94
1741 2615 4.102524 TCACAGTTCACAAACCAGTAGGAT 59.897 41.667 0.00 0.00 38.69 3.24
1742 2616 4.214119 CACAGTTCACAAACCAGTAGGATG 59.786 45.833 0.00 0.00 38.69 3.51
1743 2617 3.189287 CAGTTCACAAACCAGTAGGATGC 59.811 47.826 0.00 0.00 38.69 3.91
1744 2618 3.073062 AGTTCACAAACCAGTAGGATGCT 59.927 43.478 0.00 0.00 38.69 3.79
1745 2619 3.788227 TCACAAACCAGTAGGATGCTT 57.212 42.857 0.00 0.00 38.69 3.91
1746 2620 3.674997 TCACAAACCAGTAGGATGCTTC 58.325 45.455 0.00 0.00 38.69 3.86
1747 2621 3.072330 TCACAAACCAGTAGGATGCTTCA 59.928 43.478 0.00 0.00 38.69 3.02
1748 2622 3.820467 CACAAACCAGTAGGATGCTTCAA 59.180 43.478 0.00 0.00 38.69 2.69
1749 2623 3.821033 ACAAACCAGTAGGATGCTTCAAC 59.179 43.478 0.00 0.00 38.69 3.18
1750 2624 4.074970 CAAACCAGTAGGATGCTTCAACT 58.925 43.478 0.00 1.95 38.69 3.16
1751 2625 4.373156 AACCAGTAGGATGCTTCAACTT 57.627 40.909 0.00 0.00 38.69 2.66
1752 2626 5.499004 AACCAGTAGGATGCTTCAACTTA 57.501 39.130 0.00 0.00 38.69 2.24
1753 2627 4.833390 ACCAGTAGGATGCTTCAACTTAC 58.167 43.478 0.00 0.00 38.69 2.34
1754 2628 4.192317 CCAGTAGGATGCTTCAACTTACC 58.808 47.826 0.00 0.00 36.89 2.85
1755 2629 3.865745 CAGTAGGATGCTTCAACTTACCG 59.134 47.826 0.00 0.00 0.00 4.02
1756 2630 3.514309 AGTAGGATGCTTCAACTTACCGT 59.486 43.478 0.00 0.00 0.00 4.83
1757 2631 2.699954 AGGATGCTTCAACTTACCGTG 58.300 47.619 1.64 0.00 0.00 4.94
1758 2632 1.130561 GGATGCTTCAACTTACCGTGC 59.869 52.381 1.64 0.00 0.00 5.34
1759 2633 1.130561 GATGCTTCAACTTACCGTGCC 59.869 52.381 0.00 0.00 0.00 5.01
1760 2634 0.107831 TGCTTCAACTTACCGTGCCT 59.892 50.000 0.00 0.00 0.00 4.75
1761 2635 1.235724 GCTTCAACTTACCGTGCCTT 58.764 50.000 0.00 0.00 0.00 4.35
1762 2636 1.197036 GCTTCAACTTACCGTGCCTTC 59.803 52.381 0.00 0.00 0.00 3.46
1763 2637 2.767505 CTTCAACTTACCGTGCCTTCT 58.232 47.619 0.00 0.00 0.00 2.85
1764 2638 3.863400 GCTTCAACTTACCGTGCCTTCTA 60.863 47.826 0.00 0.00 0.00 2.10
1765 2639 4.504858 CTTCAACTTACCGTGCCTTCTAT 58.495 43.478 0.00 0.00 0.00 1.98
1766 2640 5.657474 CTTCAACTTACCGTGCCTTCTATA 58.343 41.667 0.00 0.00 0.00 1.31
1767 2641 5.864418 TCAACTTACCGTGCCTTCTATAT 57.136 39.130 0.00 0.00 0.00 0.86
1768 2642 5.839621 TCAACTTACCGTGCCTTCTATATC 58.160 41.667 0.00 0.00 0.00 1.63
1769 2643 4.500603 ACTTACCGTGCCTTCTATATCG 57.499 45.455 0.00 0.00 0.00 2.92
1770 2644 4.139786 ACTTACCGTGCCTTCTATATCGA 58.860 43.478 0.00 0.00 0.00 3.59
1771 2645 4.765856 ACTTACCGTGCCTTCTATATCGAT 59.234 41.667 2.16 2.16 0.00 3.59
1772 2646 3.851976 ACCGTGCCTTCTATATCGATC 57.148 47.619 0.00 0.00 0.00 3.69
1773 2647 3.422796 ACCGTGCCTTCTATATCGATCT 58.577 45.455 0.00 0.00 0.00 2.75
1774 2648 4.586884 ACCGTGCCTTCTATATCGATCTA 58.413 43.478 0.00 0.00 0.00 1.98
1775 2649 5.008331 ACCGTGCCTTCTATATCGATCTAA 58.992 41.667 0.00 0.00 0.00 2.10
1776 2650 5.652891 ACCGTGCCTTCTATATCGATCTAAT 59.347 40.000 0.00 0.00 0.00 1.73
1777 2651 6.183360 ACCGTGCCTTCTATATCGATCTAATC 60.183 42.308 0.00 0.00 0.00 1.75
1778 2652 6.038825 CCGTGCCTTCTATATCGATCTAATCT 59.961 42.308 0.00 0.00 0.00 2.40
1779 2653 7.415765 CCGTGCCTTCTATATCGATCTAATCTT 60.416 40.741 0.00 0.00 0.00 2.40
1780 2654 7.971168 CGTGCCTTCTATATCGATCTAATCTTT 59.029 37.037 0.00 0.00 0.00 2.52
1781 2655 9.646427 GTGCCTTCTATATCGATCTAATCTTTT 57.354 33.333 0.00 0.00 0.00 2.27
1782 2656 9.862371 TGCCTTCTATATCGATCTAATCTTTTC 57.138 33.333 0.00 0.00 0.00 2.29
1783 2657 9.308318 GCCTTCTATATCGATCTAATCTTTTCC 57.692 37.037 0.00 0.00 0.00 3.13
1791 2665 7.953158 TCGATCTAATCTTTTCCATAAGCAG 57.047 36.000 0.00 0.00 0.00 4.24
1792 2666 6.425114 TCGATCTAATCTTTTCCATAAGCAGC 59.575 38.462 0.00 0.00 0.00 5.25
1793 2667 6.426328 CGATCTAATCTTTTCCATAAGCAGCT 59.574 38.462 0.00 0.00 0.00 4.24
1794 2668 7.600375 CGATCTAATCTTTTCCATAAGCAGCTA 59.400 37.037 0.00 0.00 0.00 3.32
1795 2669 9.277783 GATCTAATCTTTTCCATAAGCAGCTAA 57.722 33.333 0.00 0.00 0.00 3.09
1796 2670 8.668510 TCTAATCTTTTCCATAAGCAGCTAAG 57.331 34.615 0.00 0.00 0.00 2.18
1797 2671 8.486210 TCTAATCTTTTCCATAAGCAGCTAAGA 58.514 33.333 0.00 0.00 0.00 2.10
1798 2672 7.944729 AATCTTTTCCATAAGCAGCTAAGAA 57.055 32.000 0.00 0.00 0.00 2.52
1799 2673 7.944729 ATCTTTTCCATAAGCAGCTAAGAAA 57.055 32.000 0.00 0.12 0.00 2.52
1800 2674 7.944729 TCTTTTCCATAAGCAGCTAAGAAAT 57.055 32.000 0.00 0.00 0.00 2.17
1801 2675 7.765307 TCTTTTCCATAAGCAGCTAAGAAATG 58.235 34.615 0.00 5.79 0.00 2.32
1802 2676 5.505173 TTCCATAAGCAGCTAAGAAATGC 57.495 39.130 0.00 0.00 40.29 3.56
1803 2677 4.525996 TCCATAAGCAGCTAAGAAATGCA 58.474 39.130 0.00 0.00 42.45 3.96
1804 2678 4.336433 TCCATAAGCAGCTAAGAAATGCAC 59.664 41.667 0.00 0.00 42.45 4.57
1805 2679 4.498682 CCATAAGCAGCTAAGAAATGCACC 60.499 45.833 0.00 0.00 42.45 5.01
1806 2680 1.089920 AGCAGCTAAGAAATGCACCG 58.910 50.000 0.00 0.00 42.45 4.94
1807 2681 0.524180 GCAGCTAAGAAATGCACCGC 60.524 55.000 0.00 0.00 39.75 5.68
1808 2682 0.804364 CAGCTAAGAAATGCACCGCA 59.196 50.000 0.00 0.00 44.86 5.69
1844 2718 7.850982 GCACAATTATACGAGAACAATTGGTAG 59.149 37.037 10.83 0.94 40.85 3.18
1896 2770 8.144478 CCTCTTCTAATATCGTTCATTTCCTGA 58.856 37.037 0.00 0.00 0.00 3.86
1911 2785 5.371115 TTTCCTGATCATTTTCCAACGTC 57.629 39.130 0.00 0.00 0.00 4.34
1913 2787 4.393834 TCCTGATCATTTTCCAACGTCAA 58.606 39.130 0.00 0.00 0.00 3.18
1914 2788 5.009631 TCCTGATCATTTTCCAACGTCAAT 58.990 37.500 0.00 0.00 0.00 2.57
1915 2789 5.476599 TCCTGATCATTTTCCAACGTCAATT 59.523 36.000 0.00 0.00 0.00 2.32
1916 2790 5.574055 CCTGATCATTTTCCAACGTCAATTG 59.426 40.000 0.00 0.00 0.00 2.32
1917 2791 6.324561 TGATCATTTTCCAACGTCAATTGA 57.675 33.333 3.38 3.38 0.00 2.57
1918 2792 6.743110 TGATCATTTTCCAACGTCAATTGAA 58.257 32.000 10.35 0.00 0.00 2.69
1919 2793 6.640499 TGATCATTTTCCAACGTCAATTGAAC 59.360 34.615 10.35 3.95 0.00 3.18
1948 2822 3.067461 ACAAAATCTTGCGTAACAGCCAA 59.933 39.130 0.00 0.00 35.84 4.52
1992 2866 9.764870 CACTTTATCTGTCTACATGAAACATTG 57.235 33.333 0.00 0.00 0.00 2.82
2023 2898 5.233957 TCACATCATAAAACATTCGGCAG 57.766 39.130 0.00 0.00 0.00 4.85
2072 2947 9.458374 AAACAAAGTACGGTTATCAAATTTCAG 57.542 29.630 0.00 0.00 0.00 3.02
2111 2986 8.815912 GGCCCATTATGATAGTTTGGAAATAAT 58.184 33.333 0.00 0.00 0.00 1.28
2154 3029 3.244112 TGGCATGATTCAACATTGCACAA 60.244 39.130 11.05 0.00 0.00 3.33
2178 3053 9.754382 CAATTGCTAATTAGGCATCTAAATGTT 57.246 29.630 14.28 0.00 38.77 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.737236 CTCGTGTGTGAGAGAGAGAGG 59.263 57.143 0.00 0.00 38.28 3.69
19 20 0.941463 GCTGGTGACTCGTGTGTGAG 60.941 60.000 0.00 0.00 41.86 3.51
21 22 2.302952 CGCTGGTGACTCGTGTGTG 61.303 63.158 0.00 0.00 0.00 3.82
22 23 2.027605 CGCTGGTGACTCGTGTGT 59.972 61.111 0.00 0.00 0.00 3.72
24 25 2.421877 CTTCCGCTGGTGACTCGTGT 62.422 60.000 0.00 0.00 0.00 4.49
25 26 1.734477 CTTCCGCTGGTGACTCGTG 60.734 63.158 0.00 0.00 0.00 4.35
26 27 1.867919 CTCTTCCGCTGGTGACTCGT 61.868 60.000 0.00 0.00 0.00 4.18
308 317 2.056223 GGGGAGGAATCACCGACGA 61.056 63.158 0.00 0.00 44.74 4.20
312 321 0.689745 TACCTGGGGAGGAATCACCG 60.690 60.000 0.00 0.00 44.74 4.94
361 370 4.727507 AACAGATCAGCGAATCTACTGT 57.272 40.909 0.00 0.00 34.21 3.55
378 387 1.450312 CCTAGCCGAGCCCAAACAG 60.450 63.158 0.00 0.00 0.00 3.16
379 388 1.916273 TCCTAGCCGAGCCCAAACA 60.916 57.895 0.00 0.00 0.00 2.83
380 389 1.449778 GTCCTAGCCGAGCCCAAAC 60.450 63.158 0.00 0.00 0.00 2.93
381 390 1.485294 TTGTCCTAGCCGAGCCCAAA 61.485 55.000 0.00 0.00 0.00 3.28
383 392 0.397957 TATTGTCCTAGCCGAGCCCA 60.398 55.000 0.00 0.00 0.00 5.36
384 393 0.756903 TTATTGTCCTAGCCGAGCCC 59.243 55.000 0.00 0.00 0.00 5.19
478 811 6.126863 TGATCTGATTCTGTTAAGGTGGTT 57.873 37.500 0.00 0.00 0.00 3.67
480 813 4.574013 GCTGATCTGATTCTGTTAAGGTGG 59.426 45.833 3.42 0.00 0.00 4.61
481 814 5.181009 TGCTGATCTGATTCTGTTAAGGTG 58.819 41.667 3.42 0.00 0.00 4.00
482 815 5.426504 CTGCTGATCTGATTCTGTTAAGGT 58.573 41.667 3.42 0.00 0.00 3.50
483 816 4.272991 GCTGCTGATCTGATTCTGTTAAGG 59.727 45.833 3.42 0.00 0.00 2.69
484 817 4.874396 TGCTGCTGATCTGATTCTGTTAAG 59.126 41.667 3.42 0.00 0.00 1.85
485 818 4.835678 TGCTGCTGATCTGATTCTGTTAA 58.164 39.130 3.42 0.00 0.00 2.01
486 819 4.439968 CTGCTGCTGATCTGATTCTGTTA 58.560 43.478 3.42 0.00 0.00 2.41
487 820 3.271729 CTGCTGCTGATCTGATTCTGTT 58.728 45.455 3.42 0.00 0.00 3.16
488 821 2.907634 CTGCTGCTGATCTGATTCTGT 58.092 47.619 3.42 0.00 0.00 3.41
489 822 1.600013 GCTGCTGCTGATCTGATTCTG 59.400 52.381 10.92 0.00 36.03 3.02
490 823 1.956297 GCTGCTGCTGATCTGATTCT 58.044 50.000 10.92 0.00 36.03 2.40
502 835 1.367659 CTCTAGTTTCCAGCTGCTGC 58.632 55.000 23.86 7.62 40.05 5.25
503 836 1.338484 TGCTCTAGTTTCCAGCTGCTG 60.338 52.381 22.44 22.44 34.03 4.41
506 1097 2.344950 CTGTGCTCTAGTTTCCAGCTG 58.655 52.381 6.78 6.78 34.03 4.24
508 1099 1.082690 GCTGTGCTCTAGTTTCCAGC 58.917 55.000 10.00 10.00 38.58 4.85
511 1102 1.067495 AGACGCTGTGCTCTAGTTTCC 60.067 52.381 0.00 0.00 0.00 3.13
516 1107 0.179150 GGACAGACGCTGTGCTCTAG 60.179 60.000 18.94 0.00 46.69 2.43
522 1113 0.881796 TCTACTGGACAGACGCTGTG 59.118 55.000 15.61 5.93 45.44 3.66
524 1115 2.792890 CGATTCTACTGGACAGACGCTG 60.793 54.545 6.29 5.47 37.52 5.18
526 1117 1.828832 CGATTCTACTGGACAGACGC 58.171 55.000 6.29 0.00 0.00 5.19
527 1118 1.534175 GGCGATTCTACTGGACAGACG 60.534 57.143 6.29 0.00 0.00 4.18
528 1119 1.202428 GGGCGATTCTACTGGACAGAC 60.202 57.143 6.29 0.00 0.00 3.51
529 1120 1.112113 GGGCGATTCTACTGGACAGA 58.888 55.000 6.29 0.00 0.00 3.41
530 1121 0.824109 TGGGCGATTCTACTGGACAG 59.176 55.000 0.00 0.00 0.00 3.51
531 1122 1.138859 CATGGGCGATTCTACTGGACA 59.861 52.381 0.00 0.00 0.00 4.02
532 1123 1.541233 CCATGGGCGATTCTACTGGAC 60.541 57.143 2.85 0.00 0.00 4.02
533 1124 0.758734 CCATGGGCGATTCTACTGGA 59.241 55.000 2.85 0.00 0.00 3.86
535 1126 1.875576 GCTCCATGGGCGATTCTACTG 60.876 57.143 13.02 0.00 0.00 2.74
536 1127 0.394565 GCTCCATGGGCGATTCTACT 59.605 55.000 13.02 0.00 0.00 2.57
552 1143 4.194640 TGGAAATATGACTTGAGCAGCTC 58.805 43.478 16.21 16.21 0.00 4.09
560 1151 5.007039 CAGACGGACATGGAAATATGACTTG 59.993 44.000 0.00 0.00 0.00 3.16
606 1197 1.266989 GCCACTAGAACACTTGGTTGC 59.733 52.381 0.00 0.00 40.63 4.17
625 1217 1.081242 CGCTGTGGTCATGTTTGGC 60.081 57.895 0.00 0.00 0.00 4.52
631 1223 0.799917 CTCGACTCGCTGTGGTCATG 60.800 60.000 9.42 0.00 33.19 3.07
641 1233 5.346822 TGGTACTTTAAAATTCTCGACTCGC 59.653 40.000 0.00 0.00 0.00 5.03
642 1234 6.585322 ACTGGTACTTTAAAATTCTCGACTCG 59.415 38.462 0.00 0.00 0.00 4.18
664 1256 7.043961 TGCTGAGAGACTATAAATGGTACTG 57.956 40.000 0.00 0.00 0.00 2.74
694 1286 2.107552 TCCAAAGAAAGGGTTCGGTCAT 59.892 45.455 0.00 0.00 38.90 3.06
709 1301 3.679389 AGCAGGAGTAACACATCCAAAG 58.321 45.455 0.00 0.00 38.12 2.77
722 1314 4.641989 CCAAGTTTGCAATATAGCAGGAGT 59.358 41.667 0.00 0.00 46.54 3.85
795 1387 5.127519 TGATCAACATTCACCATGATTTCCC 59.872 40.000 0.00 0.00 36.24 3.97
973 1789 0.907704 ACCTGGAACCATACGCAGGA 60.908 55.000 0.00 0.00 33.34 3.86
975 1791 1.086696 CAACCTGGAACCATACGCAG 58.913 55.000 0.00 0.00 0.00 5.18
1092 1908 4.211893 TGGTACACCTTGCCGGTA 57.788 55.556 1.90 0.00 46.94 4.02
1152 1968 1.169661 ATCGGCGTTTGAACTTGGCA 61.170 50.000 6.85 0.00 0.00 4.92
1232 2048 6.169800 GCTTAAGGCTAAGGAGAATCTATGG 58.830 44.000 4.29 0.00 35.90 2.74
1342 2158 2.050691 CCAACATGCAAGTAACGCAAC 58.949 47.619 0.00 0.00 43.84 4.17
1344 2160 0.595588 CCCAACATGCAAGTAACGCA 59.404 50.000 0.00 0.00 44.94 5.24
1346 2162 3.440173 AGAATCCCAACATGCAAGTAACG 59.560 43.478 0.00 0.00 0.00 3.18
1349 2165 4.574674 AGAGAATCCCAACATGCAAGTA 57.425 40.909 0.00 0.00 33.66 2.24
1370 2186 8.223177 TCCATTCCTTTTTGTTTTACGACTTA 57.777 30.769 0.00 0.00 0.00 2.24
1371 2187 7.102847 TCCATTCCTTTTTGTTTTACGACTT 57.897 32.000 0.00 0.00 0.00 3.01
1374 2190 6.127423 TGGTTCCATTCCTTTTTGTTTTACGA 60.127 34.615 0.00 0.00 0.00 3.43
1376 2192 7.851387 TTGGTTCCATTCCTTTTTGTTTTAC 57.149 32.000 0.00 0.00 0.00 2.01
1387 2203 6.314917 ACAGAAACTAATTGGTTCCATTCCT 58.685 36.000 7.72 0.00 43.16 3.36
1389 2205 8.887036 AAAACAGAAACTAATTGGTTCCATTC 57.113 30.769 7.72 2.11 43.16 2.67
1396 2215 9.965824 CTGATGTAAAAACAGAAACTAATTGGT 57.034 29.630 0.00 0.00 34.07 3.67
1415 2234 4.308526 TGCCCAACCATTAACTGATGTA 57.691 40.909 0.00 0.00 0.00 2.29
1416 2235 3.168035 TGCCCAACCATTAACTGATGT 57.832 42.857 0.00 0.00 0.00 3.06
1439 2258 6.382869 AGAAACAGAAGAAAGACATGTTGG 57.617 37.500 0.00 0.00 34.50 3.77
1444 2263 7.750229 TGCATTAGAAACAGAAGAAAGACAT 57.250 32.000 0.00 0.00 0.00 3.06
1452 2271 8.166367 GCAAACTAATGCATTAGAAACAGAAG 57.834 34.615 40.04 24.15 45.70 2.85
1464 2289 7.118680 CAAAGGATTTCAAGCAAACTAATGCAT 59.881 33.333 0.00 0.00 42.47 3.96
1467 2292 6.647895 AGCAAAGGATTTCAAGCAAACTAATG 59.352 34.615 0.00 0.00 35.03 1.90
1472 2297 4.122046 ACAGCAAAGGATTTCAAGCAAAC 58.878 39.130 0.00 0.00 35.03 2.93
1489 2362 5.045872 CACATCGATCTCTCAATTACAGCA 58.954 41.667 0.00 0.00 0.00 4.41
1496 2369 5.064452 GCTTTGTTCACATCGATCTCTCAAT 59.936 40.000 0.00 0.00 0.00 2.57
1566 2440 3.393089 TGAACTGAGTTCTCAGAAGCC 57.607 47.619 29.07 17.06 42.39 4.35
1580 2454 6.616947 TGAAGTAACCAAAGTTGTTGAACTG 58.383 36.000 0.00 0.00 41.87 3.16
1672 2546 2.092753 TGCCTCCATCTCTTCATGTTCC 60.093 50.000 0.00 0.00 0.00 3.62
1674 2548 2.575279 AGTGCCTCCATCTCTTCATGTT 59.425 45.455 0.00 0.00 0.00 2.71
1675 2549 2.093075 CAGTGCCTCCATCTCTTCATGT 60.093 50.000 0.00 0.00 0.00 3.21
1676 2550 2.169978 TCAGTGCCTCCATCTCTTCATG 59.830 50.000 0.00 0.00 0.00 3.07
1686 2560 1.071987 CACAGCTTCAGTGCCTCCA 59.928 57.895 0.00 0.00 0.00 3.86
1688 2562 0.673022 CTCCACAGCTTCAGTGCCTC 60.673 60.000 0.00 0.00 35.69 4.70
1689 2563 1.374190 CTCCACAGCTTCAGTGCCT 59.626 57.895 0.00 0.00 35.69 4.75
1690 2564 1.673665 CCTCCACAGCTTCAGTGCC 60.674 63.158 0.00 0.00 35.69 5.01
1691 2565 2.331132 GCCTCCACAGCTTCAGTGC 61.331 63.158 0.00 0.00 35.69 4.40
1692 2566 2.031516 CGCCTCCACAGCTTCAGTG 61.032 63.158 0.00 0.00 36.76 3.66
1693 2567 2.345244 CGCCTCCACAGCTTCAGT 59.655 61.111 0.00 0.00 0.00 3.41
1694 2568 2.435586 CCGCCTCCACAGCTTCAG 60.436 66.667 0.00 0.00 0.00 3.02
1695 2569 4.704833 GCCGCCTCCACAGCTTCA 62.705 66.667 0.00 0.00 0.00 3.02
1696 2570 4.704833 TGCCGCCTCCACAGCTTC 62.705 66.667 0.00 0.00 0.00 3.86
1697 2571 4.711949 CTGCCGCCTCCACAGCTT 62.712 66.667 0.00 0.00 0.00 3.74
1700 2574 3.832237 AACACTGCCGCCTCCACAG 62.832 63.158 0.00 0.00 37.45 3.66
1701 2575 3.825160 GAACACTGCCGCCTCCACA 62.825 63.158 0.00 0.00 0.00 4.17
1702 2576 3.050275 GAACACTGCCGCCTCCAC 61.050 66.667 0.00 0.00 0.00 4.02
1703 2577 3.555324 TGAACACTGCCGCCTCCA 61.555 61.111 0.00 0.00 0.00 3.86
1704 2578 3.050275 GTGAACACTGCCGCCTCC 61.050 66.667 0.00 0.00 0.00 4.30
1705 2579 2.280797 TGTGAACACTGCCGCCTC 60.281 61.111 6.51 0.00 0.00 4.70
1706 2580 2.281070 CTGTGAACACTGCCGCCT 60.281 61.111 6.51 0.00 0.00 5.52
1707 2581 2.117941 GAACTGTGAACACTGCCGCC 62.118 60.000 10.78 0.00 34.16 6.13
1708 2582 1.279840 GAACTGTGAACACTGCCGC 59.720 57.895 10.78 0.00 34.16 6.53
1709 2583 0.304705 GTGAACTGTGAACACTGCCG 59.695 55.000 10.78 0.00 34.16 5.69
1710 2584 1.378531 TGTGAACTGTGAACACTGCC 58.621 50.000 10.78 5.28 35.83 4.85
1711 2585 3.171277 GTTTGTGAACTGTGAACACTGC 58.829 45.455 10.78 0.00 35.83 4.40
1712 2586 3.190327 TGGTTTGTGAACTGTGAACACTG 59.810 43.478 9.59 9.59 36.03 3.66
1713 2587 3.417101 TGGTTTGTGAACTGTGAACACT 58.583 40.909 6.51 0.00 36.03 3.55
1714 2588 3.190535 ACTGGTTTGTGAACTGTGAACAC 59.809 43.478 0.00 0.00 36.03 3.32
1715 2589 3.417101 ACTGGTTTGTGAACTGTGAACA 58.583 40.909 0.00 0.00 36.03 3.18
1716 2590 4.035208 CCTACTGGTTTGTGAACTGTGAAC 59.965 45.833 0.00 0.00 36.03 3.18
1717 2591 4.080807 TCCTACTGGTTTGTGAACTGTGAA 60.081 41.667 0.00 0.00 36.03 3.18
1718 2592 3.452990 TCCTACTGGTTTGTGAACTGTGA 59.547 43.478 0.00 0.00 36.03 3.58
1719 2593 3.804036 TCCTACTGGTTTGTGAACTGTG 58.196 45.455 0.00 0.00 36.03 3.66
1720 2594 4.389374 CATCCTACTGGTTTGTGAACTGT 58.611 43.478 0.00 0.00 36.03 3.55
1721 2595 3.189287 GCATCCTACTGGTTTGTGAACTG 59.811 47.826 0.00 0.00 36.03 3.16
1722 2596 3.073062 AGCATCCTACTGGTTTGTGAACT 59.927 43.478 0.00 0.00 36.03 3.01
1723 2597 3.412386 AGCATCCTACTGGTTTGTGAAC 58.588 45.455 0.00 0.00 34.96 3.18
1724 2598 3.788227 AGCATCCTACTGGTTTGTGAA 57.212 42.857 0.00 0.00 34.23 3.18
1725 2599 3.072330 TGAAGCATCCTACTGGTTTGTGA 59.928 43.478 0.00 0.00 37.00 3.58
1726 2600 3.411446 TGAAGCATCCTACTGGTTTGTG 58.589 45.455 0.00 0.00 37.00 3.33
1727 2601 3.788227 TGAAGCATCCTACTGGTTTGT 57.212 42.857 0.00 0.00 37.00 2.83
1728 2602 4.074970 AGTTGAAGCATCCTACTGGTTTG 58.925 43.478 0.00 0.00 37.00 2.93
1729 2603 4.373156 AGTTGAAGCATCCTACTGGTTT 57.627 40.909 0.00 0.00 37.00 3.27
1730 2604 4.373156 AAGTTGAAGCATCCTACTGGTT 57.627 40.909 0.00 0.00 39.42 3.67
1731 2605 4.323562 GGTAAGTTGAAGCATCCTACTGGT 60.324 45.833 0.00 0.00 34.23 4.00
1732 2606 4.192317 GGTAAGTTGAAGCATCCTACTGG 58.808 47.826 0.00 0.00 0.00 4.00
1733 2607 3.865745 CGGTAAGTTGAAGCATCCTACTG 59.134 47.826 0.00 0.00 0.00 2.74
1734 2608 3.514309 ACGGTAAGTTGAAGCATCCTACT 59.486 43.478 0.00 0.00 0.00 2.57
1735 2609 3.617263 CACGGTAAGTTGAAGCATCCTAC 59.383 47.826 0.00 0.00 0.00 3.18
1736 2610 3.857052 CACGGTAAGTTGAAGCATCCTA 58.143 45.455 0.00 0.00 0.00 2.94
1737 2611 2.699954 CACGGTAAGTTGAAGCATCCT 58.300 47.619 0.00 0.00 0.00 3.24
1738 2612 1.130561 GCACGGTAAGTTGAAGCATCC 59.869 52.381 0.00 0.00 0.00 3.51
1739 2613 1.130561 GGCACGGTAAGTTGAAGCATC 59.869 52.381 0.00 0.00 0.00 3.91
1740 2614 1.165270 GGCACGGTAAGTTGAAGCAT 58.835 50.000 0.00 0.00 0.00 3.79
1741 2615 0.107831 AGGCACGGTAAGTTGAAGCA 59.892 50.000 0.00 0.00 0.00 3.91
1742 2616 1.197036 GAAGGCACGGTAAGTTGAAGC 59.803 52.381 0.00 0.00 0.00 3.86
1743 2617 2.767505 AGAAGGCACGGTAAGTTGAAG 58.232 47.619 0.00 0.00 0.00 3.02
1744 2618 2.922740 AGAAGGCACGGTAAGTTGAA 57.077 45.000 0.00 0.00 0.00 2.69
1745 2619 5.506815 CGATATAGAAGGCACGGTAAGTTGA 60.507 44.000 0.00 0.00 0.00 3.18
1746 2620 4.680110 CGATATAGAAGGCACGGTAAGTTG 59.320 45.833 0.00 0.00 0.00 3.16
1747 2621 4.581824 TCGATATAGAAGGCACGGTAAGTT 59.418 41.667 0.00 0.00 0.00 2.66
1748 2622 4.139786 TCGATATAGAAGGCACGGTAAGT 58.860 43.478 0.00 0.00 0.00 2.24
1749 2623 4.761235 TCGATATAGAAGGCACGGTAAG 57.239 45.455 0.00 0.00 0.00 2.34
1750 2624 5.008331 AGATCGATATAGAAGGCACGGTAA 58.992 41.667 0.00 0.00 0.00 2.85
1751 2625 4.586884 AGATCGATATAGAAGGCACGGTA 58.413 43.478 0.00 0.00 0.00 4.02
1752 2626 3.422796 AGATCGATATAGAAGGCACGGT 58.577 45.455 0.00 0.00 0.00 4.83
1753 2627 5.562506 TTAGATCGATATAGAAGGCACGG 57.437 43.478 0.00 0.00 0.00 4.94
1754 2628 7.022055 AGATTAGATCGATATAGAAGGCACG 57.978 40.000 0.00 0.00 0.00 5.34
1755 2629 9.646427 AAAAGATTAGATCGATATAGAAGGCAC 57.354 33.333 0.00 0.00 0.00 5.01
1756 2630 9.862371 GAAAAGATTAGATCGATATAGAAGGCA 57.138 33.333 0.00 0.00 0.00 4.75
1757 2631 9.308318 GGAAAAGATTAGATCGATATAGAAGGC 57.692 37.037 0.00 0.00 0.00 4.35
1765 2639 9.645059 CTGCTTATGGAAAAGATTAGATCGATA 57.355 33.333 0.00 0.00 0.00 2.92
1766 2640 7.118971 GCTGCTTATGGAAAAGATTAGATCGAT 59.881 37.037 0.00 0.00 0.00 3.59
1767 2641 6.425114 GCTGCTTATGGAAAAGATTAGATCGA 59.575 38.462 0.00 0.00 0.00 3.59
1768 2642 6.426328 AGCTGCTTATGGAAAAGATTAGATCG 59.574 38.462 0.00 0.00 0.00 3.69
1769 2643 7.742556 AGCTGCTTATGGAAAAGATTAGATC 57.257 36.000 0.00 0.00 0.00 2.75
1770 2644 9.282569 CTTAGCTGCTTATGGAAAAGATTAGAT 57.717 33.333 7.79 0.00 0.00 1.98
1771 2645 8.486210 TCTTAGCTGCTTATGGAAAAGATTAGA 58.514 33.333 7.79 0.00 0.00 2.10
1772 2646 8.668510 TCTTAGCTGCTTATGGAAAAGATTAG 57.331 34.615 7.79 0.00 0.00 1.73
1773 2647 9.461312 TTTCTTAGCTGCTTATGGAAAAGATTA 57.539 29.630 7.79 0.00 0.00 1.75
1774 2648 7.944729 TTCTTAGCTGCTTATGGAAAAGATT 57.055 32.000 7.79 0.00 0.00 2.40
1775 2649 7.944729 TTTCTTAGCTGCTTATGGAAAAGAT 57.055 32.000 7.79 0.00 0.00 2.40
1776 2650 7.629222 GCATTTCTTAGCTGCTTATGGAAAAGA 60.629 37.037 7.79 6.06 33.15 2.52
1777 2651 6.474751 GCATTTCTTAGCTGCTTATGGAAAAG 59.525 38.462 7.79 11.11 33.15 2.27
1778 2652 6.071447 TGCATTTCTTAGCTGCTTATGGAAAA 60.071 34.615 7.79 1.48 36.84 2.29
1779 2653 5.418524 TGCATTTCTTAGCTGCTTATGGAAA 59.581 36.000 7.79 13.15 36.84 3.13
1780 2654 4.949238 TGCATTTCTTAGCTGCTTATGGAA 59.051 37.500 7.79 4.95 36.84 3.53
1781 2655 4.336433 GTGCATTTCTTAGCTGCTTATGGA 59.664 41.667 7.79 3.29 36.84 3.41
1782 2656 4.498682 GGTGCATTTCTTAGCTGCTTATGG 60.499 45.833 7.79 0.00 36.84 2.74
1783 2657 4.604976 GGTGCATTTCTTAGCTGCTTATG 58.395 43.478 7.79 5.85 36.84 1.90
1784 2658 3.313526 CGGTGCATTTCTTAGCTGCTTAT 59.686 43.478 7.79 0.00 36.84 1.73
1785 2659 2.677836 CGGTGCATTTCTTAGCTGCTTA 59.322 45.455 7.79 0.00 36.84 3.09
1786 2660 1.470098 CGGTGCATTTCTTAGCTGCTT 59.530 47.619 7.79 0.00 36.84 3.91
1787 2661 1.089920 CGGTGCATTTCTTAGCTGCT 58.910 50.000 7.57 7.57 36.84 4.24
1788 2662 0.524180 GCGGTGCATTTCTTAGCTGC 60.524 55.000 0.00 0.00 36.45 5.25
1789 2663 0.804364 TGCGGTGCATTTCTTAGCTG 59.196 50.000 0.00 0.00 31.71 4.24
1790 2664 3.248043 TGCGGTGCATTTCTTAGCT 57.752 47.368 0.00 0.00 31.71 3.32
1800 2674 0.109179 GCTTGAAATGATGCGGTGCA 60.109 50.000 0.00 0.00 44.86 4.57
1801 2675 0.109179 TGCTTGAAATGATGCGGTGC 60.109 50.000 0.00 0.00 0.00 5.01
1802 2676 1.068402 TGTGCTTGAAATGATGCGGTG 60.068 47.619 0.00 0.00 0.00 4.94
1803 2677 1.246649 TGTGCTTGAAATGATGCGGT 58.753 45.000 0.00 0.00 0.00 5.68
1804 2678 2.350899 TTGTGCTTGAAATGATGCGG 57.649 45.000 0.00 0.00 0.00 5.69
1805 2679 6.129639 CGTATAATTGTGCTTGAAATGATGCG 60.130 38.462 0.00 0.00 29.99 4.73
1806 2680 6.912051 TCGTATAATTGTGCTTGAAATGATGC 59.088 34.615 0.00 0.00 0.00 3.91
1807 2681 8.337532 TCTCGTATAATTGTGCTTGAAATGATG 58.662 33.333 0.00 0.00 0.00 3.07
1808 2682 8.437360 TCTCGTATAATTGTGCTTGAAATGAT 57.563 30.769 0.00 0.00 0.00 2.45
1809 2683 7.841915 TCTCGTATAATTGTGCTTGAAATGA 57.158 32.000 0.00 0.00 0.00 2.57
1810 2684 7.962373 TGTTCTCGTATAATTGTGCTTGAAATG 59.038 33.333 0.00 0.00 0.00 2.32
1811 2685 8.039603 TGTTCTCGTATAATTGTGCTTGAAAT 57.960 30.769 0.00 0.00 0.00 2.17
1812 2686 7.428282 TGTTCTCGTATAATTGTGCTTGAAA 57.572 32.000 0.00 0.00 0.00 2.69
1813 2687 7.428282 TTGTTCTCGTATAATTGTGCTTGAA 57.572 32.000 0.00 0.00 0.00 2.69
1814 2688 7.609760 ATTGTTCTCGTATAATTGTGCTTGA 57.390 32.000 0.00 0.00 0.00 3.02
1815 2689 7.218773 CCAATTGTTCTCGTATAATTGTGCTTG 59.781 37.037 4.43 0.00 38.30 4.01
1816 2690 7.094377 ACCAATTGTTCTCGTATAATTGTGCTT 60.094 33.333 4.43 0.00 38.30 3.91
1817 2691 6.374333 ACCAATTGTTCTCGTATAATTGTGCT 59.626 34.615 4.43 0.00 38.30 4.40
1818 2692 6.551736 ACCAATTGTTCTCGTATAATTGTGC 58.448 36.000 4.43 0.00 38.30 4.57
1844 2718 8.072567 GTCAGCATGTTTTACTGATGGATATTC 58.927 37.037 3.71 0.00 42.08 1.75
1847 2721 5.822519 GGTCAGCATGTTTTACTGATGGATA 59.177 40.000 3.71 0.00 42.08 2.59
1864 2738 5.359860 TGAACGATATTAGAAGAGGTCAGCA 59.640 40.000 0.00 0.00 0.00 4.41
1869 2743 7.928706 CAGGAAATGAACGATATTAGAAGAGGT 59.071 37.037 0.00 0.00 0.00 3.85
1896 2770 6.511416 TGTTCAATTGACGTTGGAAAATGAT 58.489 32.000 7.89 0.00 0.00 2.45
1911 2785 8.949953 GCAAGATTTTGTTCATTTGTTCAATTG 58.050 29.630 0.00 0.00 36.65 2.32
1913 2787 7.011295 ACGCAAGATTTTGTTCATTTGTTCAAT 59.989 29.630 0.00 0.00 43.62 2.57
1914 2788 6.312426 ACGCAAGATTTTGTTCATTTGTTCAA 59.688 30.769 0.00 0.00 43.62 2.69
1915 2789 5.809562 ACGCAAGATTTTGTTCATTTGTTCA 59.190 32.000 0.00 0.00 43.62 3.18
1916 2790 6.272698 ACGCAAGATTTTGTTCATTTGTTC 57.727 33.333 0.00 0.00 43.62 3.18
1917 2791 7.276658 TGTTACGCAAGATTTTGTTCATTTGTT 59.723 29.630 0.00 0.00 43.62 2.83
1918 2792 6.754209 TGTTACGCAAGATTTTGTTCATTTGT 59.246 30.769 0.00 0.00 43.62 2.83
1919 2793 7.159437 TGTTACGCAAGATTTTGTTCATTTG 57.841 32.000 0.00 0.00 43.62 2.32
1948 2822 0.482446 TGGGGAAAATGAGCAGGTGT 59.518 50.000 0.00 0.00 0.00 4.16
1992 2866 7.599630 ATGTTTTATGATGTGAAATTGTGCC 57.400 32.000 0.00 0.00 0.00 5.01
2014 2888 1.333308 TCACAACACAACTGCCGAATG 59.667 47.619 0.00 0.00 0.00 2.67
2111 2986 8.005192 TGCCAAAGTATATTGTTTATGATGCA 57.995 30.769 0.00 0.00 0.00 3.96
2127 3002 5.170021 GCAATGTTGAATCATGCCAAAGTA 58.830 37.500 0.00 0.00 0.00 2.24
2178 3053 9.474313 AACATTTAGATGCCTTTGGAAATAGTA 57.526 29.630 0.00 0.00 36.72 1.82
2179 3054 7.961326 ACATTTAGATGCCTTTGGAAATAGT 57.039 32.000 0.00 0.00 36.72 2.12
2180 3055 8.469200 TGAACATTTAGATGCCTTTGGAAATAG 58.531 33.333 0.00 0.00 36.72 1.73


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

AutoCloner maintained by Alex Coulton.