Multiple sequence alignment - TraesCS5A01G510100

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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 TraesCS5A01G510100 chr5A 100.000 5595 0 0 1 5595 673780030 673774436 0.000000e+00 10333.0
1 TraesCS5A01G510100 chr4D 92.342 5145 205 61 528 5595 494273607 494268575 0.000000e+00 7143.0
2 TraesCS5A01G510100 chr4D 85.185 378 17 15 3 343 494274258 494273883 8.920000e-93 351.0
3 TraesCS5A01G510100 chr4B 92.230 4479 199 60 530 4914 633766527 633762104 0.000000e+00 6205.0
4 TraesCS5A01G510100 chr4B 92.422 673 26 12 4944 5595 633762108 633761440 0.000000e+00 937.0
5 TraesCS5A01G510100 chr4B 82.632 380 16 14 3 342 633767207 633766838 1.970000e-74 291.0
6 TraesCS5A01G510100 chr7D 89.091 55 4 2 415 467 564159839 564159785 3.620000e-07 67.6
7 TraesCS5A01G510100 chr7A 87.273 55 5 2 400 452 215323131 215323185 1.680000e-05 62.1
8 TraesCS5A01G510100 chr4A 82.857 70 7 3 401 470 192629410 192629474 2.180000e-04 58.4
9 TraesCS5A01G510100 chr1D 96.970 33 1 0 417 449 483132988 483133020 7.830000e-04 56.5


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 TraesCS5A01G510100 chr5A 673774436 673780030 5594 True 10333.000000 10333 100.000000 1 5595 1 chr5A.!!$R1 5594
1 TraesCS5A01G510100 chr4D 494268575 494274258 5683 True 3747.000000 7143 88.763500 3 5595 2 chr4D.!!$R1 5592
2 TraesCS5A01G510100 chr4B 633761440 633767207 5767 True 2477.666667 6205 89.094667 3 5595 3 chr4B.!!$R1 5592

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
224 254 0.108329 CATTGTCGACCCGCTAACCT 60.108 55.000 14.12 0.0 0.0 3.50 F
228 258 0.175073 GTCGACCCGCTAACCTCATT 59.825 55.000 3.51 0.0 0.0 2.57 F
1171 1447 0.179171 CATCTCGCTTGCCTTGCTTG 60.179 55.000 0.00 0.0 0.0 4.01 F
2164 2496 0.393077 CCCATCTTCCTCGCCGTATT 59.607 55.000 0.00 0.0 0.0 1.89 F
3253 3606 1.002087 CCGTTACCCTGCTTTGACTCT 59.998 52.381 0.00 0.0 0.0 3.24 F
3927 4286 0.476771 GGGGAACAACCAAGACCTGA 59.523 55.000 0.00 0.0 41.2 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 1336 0.252558 TTAAGGGCGAAGAGGGAGGT 60.253 55.0 0.00 0.00 0.00 3.85 R
1382 1697 0.800631 TGCAGAATCTTCAGCAAGCG 59.199 50.0 7.45 0.00 44.94 4.68 R
3085 3438 0.689412 TATCACCCAGGCCGTCATCA 60.689 55.0 0.00 0.00 0.00 3.07 R
3302 3658 0.469917 TTGATCGGGGGAATGAGCTC 59.530 55.0 6.82 6.82 0.00 4.09 R
4502 4863 0.317160 TCGGACGAGTCAAGCATGTT 59.683 50.0 5.55 0.00 0.00 2.71 R
4933 5294 0.955919 CTTCCACGCCTTGTTCTCCC 60.956 60.0 0.00 0.00 0.00 4.30 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
47 48 1.581447 GGCGGTGAAAGGAAAGCTG 59.419 57.895 0.00 0.00 0.00 4.24
48 49 1.081175 GCGGTGAAAGGAAAGCTGC 60.081 57.895 0.00 0.00 0.00 5.25
78 80 0.962489 ATAGGGCTCGTCGATCCTTG 59.038 55.000 18.44 0.00 0.00 3.61
80 82 1.066587 GGGCTCGTCGATCCTTGAG 59.933 63.158 14.40 0.00 0.00 3.02
81 83 1.066587 GGCTCGTCGATCCTTGAGG 59.933 63.158 7.88 0.00 0.00 3.86
223 253 0.390735 ACATTGTCGACCCGCTAACC 60.391 55.000 14.12 0.00 0.00 2.85
224 254 0.108329 CATTGTCGACCCGCTAACCT 60.108 55.000 14.12 0.00 0.00 3.50
228 258 0.175073 GTCGACCCGCTAACCTCATT 59.825 55.000 3.51 0.00 0.00 2.57
229 259 0.899720 TCGACCCGCTAACCTCATTT 59.100 50.000 0.00 0.00 0.00 2.32
230 260 1.134907 TCGACCCGCTAACCTCATTTC 60.135 52.381 0.00 0.00 0.00 2.17
262 314 2.220133 GTCACGCGTAATCACAACAGTT 59.780 45.455 13.44 0.00 0.00 3.16
272 324 7.369800 GCGTAATCACAACAGTTATAATCAACG 59.630 37.037 0.00 0.00 33.50 4.10
275 327 6.164408 TCACAACAGTTATAATCAACGCAG 57.836 37.500 0.00 0.00 33.50 5.18
290 342 0.510359 CGCAGACTCAAACTCACTGC 59.490 55.000 0.00 0.00 46.69 4.40
308 367 4.535786 GCCCGGCCGTTACCTACC 62.536 72.222 26.12 0.00 0.00 3.18
327 386 7.025620 ACCTACCTACCATCATCCAGATTATT 58.974 38.462 0.00 0.00 33.72 1.40
343 402 6.126768 CCAGATTATTACTCCCTCTTTGGTGA 60.127 42.308 0.00 0.00 0.00 4.02
345 404 7.659390 CAGATTATTACTCCCTCTTTGGTGATC 59.341 40.741 0.00 0.00 0.00 2.92
347 406 8.798975 ATTATTACTCCCTCTTTGGTGATCTA 57.201 34.615 0.00 0.00 0.00 1.98
349 408 9.892444 TTATTACTCCCTCTTTGGTGATCTATA 57.108 33.333 0.00 0.00 0.00 1.31
427 655 7.979444 TCTTAACTCTGTCCCAAATTACTTG 57.021 36.000 0.00 0.00 34.52 3.16
429 657 7.996644 TCTTAACTCTGTCCCAAATTACTTGTT 59.003 33.333 0.00 0.00 32.65 2.83
462 694 7.433680 TGTCTAGATACGTACGAATGTACCTA 58.566 38.462 24.41 3.38 46.71 3.08
470 702 6.546395 ACGTACGAATGTACCTAACACTAAG 58.454 40.000 24.41 0.00 46.71 2.18
473 705 5.634896 ACGAATGTACCTAACACTAAGACG 58.365 41.667 0.00 0.00 42.09 4.18
474 706 5.182001 ACGAATGTACCTAACACTAAGACGT 59.818 40.000 0.00 0.00 42.09 4.34
475 707 5.510674 CGAATGTACCTAACACTAAGACGTG 59.489 44.000 0.00 0.00 42.09 4.49
477 709 5.362556 TGTACCTAACACTAAGACGTGTC 57.637 43.478 0.00 0.00 46.71 3.67
480 712 4.139786 ACCTAACACTAAGACGTGTCTGA 58.860 43.478 2.78 0.00 46.71 3.27
481 713 4.581824 ACCTAACACTAAGACGTGTCTGAA 59.418 41.667 2.78 0.00 46.71 3.02
482 714 4.916249 CCTAACACTAAGACGTGTCTGAAC 59.084 45.833 2.78 0.00 46.71 3.18
483 715 4.650754 AACACTAAGACGTGTCTGAACT 57.349 40.909 2.78 0.00 46.71 3.01
484 716 5.762825 AACACTAAGACGTGTCTGAACTA 57.237 39.130 2.78 0.00 46.71 2.24
486 718 4.577693 ACACTAAGACGTGTCTGAACTACA 59.422 41.667 2.78 0.00 44.32 2.74
488 720 5.975344 CACTAAGACGTGTCTGAACTACAAA 59.025 40.000 2.78 0.00 40.36 2.83
490 722 7.009815 CACTAAGACGTGTCTGAACTACAAAAA 59.990 37.037 2.78 0.00 40.36 1.94
491 723 6.920569 AAGACGTGTCTGAACTACAAAAAT 57.079 33.333 2.78 0.00 40.36 1.82
492 724 6.287107 AGACGTGTCTGAACTACAAAAATG 57.713 37.500 0.86 0.00 38.75 2.32
493 725 5.815740 AGACGTGTCTGAACTACAAAAATGT 59.184 36.000 0.86 0.00 38.75 2.71
494 726 6.018994 AGACGTGTCTGAACTACAAAAATGTC 60.019 38.462 0.86 0.00 38.75 3.06
495 727 5.815740 ACGTGTCTGAACTACAAAAATGTCT 59.184 36.000 0.00 0.00 0.00 3.41
496 728 6.315393 ACGTGTCTGAACTACAAAAATGTCTT 59.685 34.615 0.00 0.00 0.00 3.01
497 729 7.493320 ACGTGTCTGAACTACAAAAATGTCTTA 59.507 33.333 0.00 0.00 0.00 2.10
498 730 8.495949 CGTGTCTGAACTACAAAAATGTCTTAT 58.504 33.333 0.00 0.00 0.00 1.73
512 744 8.848474 AAAATGTCTTATATTATGAGACGGGG 57.152 34.615 18.44 0.00 45.74 5.73
513 745 7.554959 AATGTCTTATATTATGAGACGGGGT 57.445 36.000 18.44 6.84 45.74 4.95
514 746 6.989155 TGTCTTATATTATGAGACGGGGTT 57.011 37.500 18.44 0.00 45.74 4.11
515 747 8.660295 ATGTCTTATATTATGAGACGGGGTTA 57.340 34.615 18.44 5.69 45.74 2.85
516 748 7.889469 TGTCTTATATTATGAGACGGGGTTAC 58.111 38.462 18.44 0.61 45.74 2.50
517 749 7.727186 TGTCTTATATTATGAGACGGGGTTACT 59.273 37.037 18.44 0.00 45.74 2.24
518 750 9.236006 GTCTTATATTATGAGACGGGGTTACTA 57.764 37.037 11.50 0.00 36.39 1.82
519 751 9.986157 TCTTATATTATGAGACGGGGTTACTAT 57.014 33.333 0.00 0.00 0.00 2.12
525 757 8.716674 TTATGAGACGGGGTTACTATTATTCT 57.283 34.615 0.00 0.00 0.00 2.40
526 758 6.645790 TGAGACGGGGTTACTATTATTCTC 57.354 41.667 0.00 0.00 0.00 2.87
563 795 6.997655 TCCTGATAGATAATCATTGAACGCT 58.002 36.000 0.00 0.00 43.70 5.07
569 801 9.209175 GATAGATAATCATTGAACGCTAAAGGT 57.791 33.333 0.00 0.00 34.46 3.50
573 810 2.881513 TCATTGAACGCTAAAGGTTGCA 59.118 40.909 0.00 0.00 0.00 4.08
669 907 4.215908 TGATCGAGACAGGGTTTAGCTAT 58.784 43.478 0.00 0.00 0.00 2.97
671 909 4.386867 TCGAGACAGGGTTTAGCTATTG 57.613 45.455 0.00 0.00 0.00 1.90
715 959 5.163343 TGGTTAATTCAGTTCCGCTAGCTAT 60.163 40.000 13.93 0.00 0.00 2.97
716 960 5.758784 GGTTAATTCAGTTCCGCTAGCTATT 59.241 40.000 13.93 2.60 0.00 1.73
738 984 9.462174 CTATTAGCTAATGATATCAGCTGTAGC 57.538 37.037 25.99 21.68 45.04 3.58
744 990 1.795286 GATATCAGCTGTAGCCGTTGC 59.205 52.381 14.67 0.00 43.38 4.17
745 991 0.527600 TATCAGCTGTAGCCGTTGCG 60.528 55.000 14.67 0.00 44.33 4.85
747 993 2.030562 AGCTGTAGCCGTTGCGTT 59.969 55.556 0.00 0.00 44.33 4.84
748 994 2.173382 GCTGTAGCCGTTGCGTTG 59.827 61.111 0.00 0.00 44.33 4.10
785 1039 2.290134 GGAGGCGGTTCCCCTATAAATC 60.290 54.545 0.18 0.00 34.51 2.17
840 1094 1.653115 CTAGCACGTACCTAGGCGG 59.347 63.158 9.30 0.11 39.35 6.13
872 1126 3.585289 GACCCTTCTTCTTCTTCCTCCTT 59.415 47.826 0.00 0.00 0.00 3.36
873 1127 4.764491 ACCCTTCTTCTTCTTCCTCCTTA 58.236 43.478 0.00 0.00 0.00 2.69
875 1129 5.190726 ACCCTTCTTCTTCTTCCTCCTTATG 59.809 44.000 0.00 0.00 0.00 1.90
901 1162 2.223409 CGGCTCGGCTATATATACGCAA 60.223 50.000 12.98 3.97 0.00 4.85
904 1165 3.791887 GCTCGGCTATATATACGCAACAG 59.208 47.826 12.98 8.14 0.00 3.16
940 1201 4.039245 TCCCTAGCTATCTTCAATTCACCG 59.961 45.833 0.00 0.00 0.00 4.94
941 1202 4.039245 CCCTAGCTATCTTCAATTCACCGA 59.961 45.833 0.00 0.00 0.00 4.69
944 1205 7.378966 CCTAGCTATCTTCAATTCACCGATAA 58.621 38.462 0.00 0.00 0.00 1.75
946 1207 7.484035 AGCTATCTTCAATTCACCGATAAAC 57.516 36.000 0.00 0.00 0.00 2.01
977 1242 0.761187 CAGCCCCTTCATAGCTAGCA 59.239 55.000 18.83 3.19 34.38 3.49
1051 1318 1.518133 CAGCCAGACGAGCAGCTAC 60.518 63.158 0.00 0.00 33.33 3.58
1069 1336 4.992319 AGCTACGCATTGTAAGTACACAAA 59.008 37.500 3.18 0.00 41.50 2.83
1072 1339 4.131596 ACGCATTGTAAGTACACAAACCT 58.868 39.130 3.18 0.00 41.50 3.50
1073 1340 4.212636 ACGCATTGTAAGTACACAAACCTC 59.787 41.667 3.18 0.00 41.50 3.85
1081 1349 2.299297 AGTACACAAACCTCCCTCTTCG 59.701 50.000 0.00 0.00 0.00 3.79
1082 1350 0.250338 ACACAAACCTCCCTCTTCGC 60.250 55.000 0.00 0.00 0.00 4.70
1144 1420 9.999660 ATGCTTCTATATATATGCAAGGAGATG 57.000 33.333 11.20 3.28 34.07 2.90
1171 1447 0.179171 CATCTCGCTTGCCTTGCTTG 60.179 55.000 0.00 0.00 0.00 4.01
1193 1488 8.229137 GCTTGCTTTGTATAAATTTTTGCATCA 58.771 29.630 0.00 0.00 0.00 3.07
1195 1490 8.027440 TGCTTTGTATAAATTTTTGCATCACC 57.973 30.769 0.00 0.00 0.00 4.02
1215 1510 1.855978 CAACGTAACGTGTCTTCAGCA 59.144 47.619 0.00 0.00 39.99 4.41
1229 1524 6.853362 GTGTCTTCAGCAAAAACTTGATAGAC 59.147 38.462 0.00 0.00 33.97 2.59
1241 1536 6.414408 AACTTGATAGACTGAAATTGAGCG 57.586 37.500 0.00 0.00 0.00 5.03
1291 1594 3.426525 CGCTTGTTTGGCTTCTTGATTTC 59.573 43.478 0.00 0.00 0.00 2.17
1301 1605 6.866480 TGGCTTCTTGATTTCATTTATCCAC 58.134 36.000 0.00 0.00 0.00 4.02
1330 1637 9.467258 CTTGAAAATTCTGATGCTTGTTTAAGA 57.533 29.630 0.00 0.00 35.92 2.10
1333 1640 9.248291 GAAAATTCTGATGCTTGTTTAAGAACA 57.752 29.630 0.00 0.00 43.73 3.18
1368 1683 1.480954 ACGTACCTCGAGAATTGCCAT 59.519 47.619 15.71 0.00 42.86 4.40
1369 1684 2.691526 ACGTACCTCGAGAATTGCCATA 59.308 45.455 15.71 0.00 42.86 2.74
1370 1685 3.243434 ACGTACCTCGAGAATTGCCATAG 60.243 47.826 15.71 0.00 42.86 2.23
1371 1686 3.243434 CGTACCTCGAGAATTGCCATAGT 60.243 47.826 15.71 1.21 42.86 2.12
1372 1687 4.023450 CGTACCTCGAGAATTGCCATAGTA 60.023 45.833 15.71 0.16 42.86 1.82
1373 1688 4.323553 ACCTCGAGAATTGCCATAGTAC 57.676 45.455 15.71 0.00 0.00 2.73
1374 1689 3.069729 ACCTCGAGAATTGCCATAGTACC 59.930 47.826 15.71 0.00 0.00 3.34
1375 1690 3.069586 CCTCGAGAATTGCCATAGTACCA 59.930 47.826 15.71 0.00 0.00 3.25
1376 1691 4.262635 CCTCGAGAATTGCCATAGTACCAT 60.263 45.833 15.71 0.00 0.00 3.55
1377 1692 5.290493 TCGAGAATTGCCATAGTACCATT 57.710 39.130 0.00 0.00 0.00 3.16
1378 1693 6.413783 TCGAGAATTGCCATAGTACCATTA 57.586 37.500 0.00 0.00 0.00 1.90
1379 1694 6.822442 TCGAGAATTGCCATAGTACCATTAA 58.178 36.000 0.00 0.00 0.00 1.40
1380 1695 7.450074 TCGAGAATTGCCATAGTACCATTAAT 58.550 34.615 0.00 0.00 0.00 1.40
1381 1696 7.936847 TCGAGAATTGCCATAGTACCATTAATT 59.063 33.333 0.00 0.00 0.00 1.40
1382 1697 8.230486 CGAGAATTGCCATAGTACCATTAATTC 58.770 37.037 0.00 0.00 34.94 2.17
1383 1698 8.099364 AGAATTGCCATAGTACCATTAATTCG 57.901 34.615 0.00 0.00 37.97 3.34
1423 1738 0.457035 CCAGATTGGAAACATGGGCG 59.543 55.000 0.00 0.00 40.96 6.13
1556 1872 4.725790 AATCGATGACATGTCAGACAGA 57.274 40.909 30.63 24.57 43.61 3.41
1557 1873 4.725790 ATCGATGACATGTCAGACAGAA 57.274 40.909 30.63 14.64 43.61 3.02
1558 1874 3.838120 TCGATGACATGTCAGACAGAAC 58.162 45.455 30.63 15.17 43.61 3.01
1559 1875 3.255642 TCGATGACATGTCAGACAGAACA 59.744 43.478 30.63 7.57 43.61 3.18
1560 1876 3.611549 CGATGACATGTCAGACAGAACAG 59.388 47.826 30.63 11.73 43.61 3.16
1561 1877 4.616835 CGATGACATGTCAGACAGAACAGA 60.617 45.833 30.63 5.67 43.61 3.41
1569 1885 3.817647 GTCAGACAGAACAGAAGCCAAAT 59.182 43.478 0.00 0.00 0.00 2.32
1602 1918 0.817654 TGCATAGACAGGACGTCCAG 59.182 55.000 35.00 29.53 46.69 3.86
1717 2040 7.765819 CCATATAATCACAGGATTAAGCGATCA 59.234 37.037 1.70 0.00 46.18 2.92
1741 2064 5.124457 ACGCTTCTATTTCATCTGCAAATGT 59.876 36.000 0.00 0.00 0.00 2.71
1812 2136 9.777297 AACAGATTGTACAAAGCCAATTATTTT 57.223 25.926 13.23 0.00 31.67 1.82
1954 2282 4.743057 ATCCGTCAAATGATCAGAGACA 57.257 40.909 18.96 6.62 0.00 3.41
1991 2319 3.429085 CAGCCGTTGATGCAGAAATAAC 58.571 45.455 0.00 0.00 0.00 1.89
1998 2326 3.088532 TGATGCAGAAATAACACACCCC 58.911 45.455 0.00 0.00 0.00 4.95
2017 2345 0.933097 CGCGCAAGAATAGCATCTGT 59.067 50.000 8.75 0.00 43.02 3.41
2021 2349 2.154580 CGCAAGAATAGCATCTGTAGCG 59.845 50.000 11.42 11.42 38.62 4.26
2042 2370 1.134694 GAAATTGCCGGCGTCTGAC 59.865 57.895 23.90 7.77 0.00 3.51
2073 2401 3.139077 CGCCACCCTATAAAAGGTCATC 58.861 50.000 0.00 0.00 44.90 2.92
2075 2403 4.686122 CGCCACCCTATAAAAGGTCATCTT 60.686 45.833 0.00 0.00 44.90 2.40
2110 2442 4.137543 GAGAAACAGGCTTCTTCTTTCCA 58.862 43.478 8.78 0.00 35.76 3.53
2111 2443 4.140536 AGAAACAGGCTTCTTCTTTCCAG 58.859 43.478 2.65 0.00 31.39 3.86
2112 2444 1.902938 ACAGGCTTCTTCTTTCCAGC 58.097 50.000 0.00 0.00 0.00 4.85
2114 2446 2.572733 GGCTTCTTCTTTCCAGCCC 58.427 57.895 0.00 0.00 45.39 5.19
2115 2447 0.967887 GGCTTCTTCTTTCCAGCCCC 60.968 60.000 0.00 0.00 45.39 5.80
2116 2448 0.967887 GCTTCTTCTTTCCAGCCCCC 60.968 60.000 0.00 0.00 0.00 5.40
2164 2496 0.393077 CCCATCTTCCTCGCCGTATT 59.607 55.000 0.00 0.00 0.00 1.89
2182 2514 3.575858 ATTGCGATTCGATCTTTCACG 57.424 42.857 10.88 0.00 0.00 4.35
2200 2532 2.267961 GCTCCGTCCGGAACCATT 59.732 61.111 5.23 0.00 44.66 3.16
2245 2577 2.232208 CAGTTCCAAGGAATTTGCTCCC 59.768 50.000 4.63 0.00 35.95 4.30
2292 2625 2.432628 GTCGCTGTTGAGGACCGG 60.433 66.667 0.00 0.00 0.00 5.28
2380 2713 8.094798 TCTTTTTCGTATGTAGAAACATGCTT 57.905 30.769 0.00 0.00 45.99 3.91
2381 2714 8.015087 TCTTTTTCGTATGTAGAAACATGCTTG 58.985 33.333 0.00 0.00 45.99 4.01
2382 2715 5.794687 TTCGTATGTAGAAACATGCTTGG 57.205 39.130 4.44 0.00 45.99 3.61
2476 2809 3.191371 GCTTGTTCCTTGGGTGATAACTG 59.809 47.826 0.00 0.00 0.00 3.16
2477 2810 2.790433 TGTTCCTTGGGTGATAACTGC 58.210 47.619 0.00 0.00 0.00 4.40
2479 2812 3.153919 GTTCCTTGGGTGATAACTGCAA 58.846 45.455 0.00 0.00 0.00 4.08
2480 2813 3.737559 TCCTTGGGTGATAACTGCAAT 57.262 42.857 0.00 0.00 0.00 3.56
2482 2815 2.428171 CCTTGGGTGATAACTGCAATGG 59.572 50.000 0.00 0.00 0.00 3.16
2483 2816 3.355378 CTTGGGTGATAACTGCAATGGA 58.645 45.455 0.00 0.00 0.00 3.41
2484 2817 2.722094 TGGGTGATAACTGCAATGGAC 58.278 47.619 0.00 0.00 0.00 4.02
2485 2818 2.040947 TGGGTGATAACTGCAATGGACA 59.959 45.455 0.00 0.00 0.00 4.02
2486 2819 3.290710 GGGTGATAACTGCAATGGACAT 58.709 45.455 0.00 0.00 0.00 3.06
2489 2822 4.440525 GGTGATAACTGCAATGGACATTGG 60.441 45.833 22.33 11.81 46.14 3.16
2490 2823 4.158394 GTGATAACTGCAATGGACATTGGT 59.842 41.667 22.33 12.35 46.14 3.67
2491 2824 5.356751 GTGATAACTGCAATGGACATTGGTA 59.643 40.000 22.33 4.56 46.14 3.25
2492 2825 5.356751 TGATAACTGCAATGGACATTGGTAC 59.643 40.000 22.33 9.73 46.14 3.34
2572 2908 6.554419 CATTCAAAAGCACCAAATCGAGATA 58.446 36.000 0.00 0.00 0.00 1.98
2581 2917 7.830739 AGCACCAAATCGAGATAAAATCTTTT 58.169 30.769 0.00 0.00 40.38 2.27
2882 3230 7.117236 TGCTTTCTCGGTTAACTACATAAACAG 59.883 37.037 5.42 0.00 0.00 3.16
2903 3252 3.247648 AGATTTACGCCATAACGTCATGC 59.752 43.478 0.00 0.00 44.43 4.06
2910 3259 2.290367 GCCATAACGTCATGCATGCTTA 59.710 45.455 22.25 15.72 0.00 3.09
2914 3263 3.957671 AACGTCATGCATGCTTATCAG 57.042 42.857 22.25 8.51 0.00 2.90
2953 3306 8.858003 AGAACATACATGACTTTACTGATACG 57.142 34.615 0.00 0.00 0.00 3.06
2965 3318 9.309516 GACTTTACTGATACGGAATGATGTTAA 57.690 33.333 0.00 0.00 0.00 2.01
2978 3331 9.438291 CGGAATGATGTTAACACAATATTTCTC 57.562 33.333 11.22 1.78 36.16 2.87
3021 3374 8.470805 TGTGGTAAAATGTACTCACATGTTTTT 58.529 29.630 0.00 1.38 44.83 1.94
3085 3438 4.394300 GCTGCTCACATACTTGATTTCTGT 59.606 41.667 0.00 0.00 0.00 3.41
3115 3468 1.561542 CTGGGTGATAACCTCCTTGCT 59.438 52.381 0.00 0.00 0.00 3.91
3139 3492 4.835891 ACCTCTACCTCCGGCCCG 62.836 72.222 0.00 0.00 0.00 6.13
3253 3606 1.002087 CCGTTACCCTGCTTTGACTCT 59.998 52.381 0.00 0.00 0.00 3.24
3298 3654 2.718731 CAAAACGCGTGCCCTGAA 59.281 55.556 14.98 0.00 0.00 3.02
3316 3672 2.536997 AAACCGAGCTCATTCCCCCG 62.537 60.000 15.40 0.00 0.00 5.73
3410 3766 1.201429 ATCACGGCTTCCCCAGAGTT 61.201 55.000 0.00 0.00 0.00 3.01
3415 3774 0.915364 GGCTTCCCCAGAGTTCTGAT 59.085 55.000 10.64 0.00 46.59 2.90
3709 4068 4.291783 GACTGACCAGAACATATAGCGAC 58.708 47.826 3.76 0.00 0.00 5.19
3780 4139 7.339466 GGTAACATCTGGAACCTAACAATCAAT 59.661 37.037 0.00 0.00 0.00 2.57
3781 4140 7.781324 AACATCTGGAACCTAACAATCAATT 57.219 32.000 0.00 0.00 0.00 2.32
3846 4205 2.949644 AGCGCTGGTAAAAGAAAAGTGT 59.050 40.909 10.39 0.00 0.00 3.55
3927 4286 0.476771 GGGGAACAACCAAGACCTGA 59.523 55.000 0.00 0.00 41.20 3.86
3973 4332 4.583073 ACCAACATTACCTCCAACAGAAAC 59.417 41.667 0.00 0.00 0.00 2.78
3980 4339 1.528129 CTCCAACAGAAACCTCAGGC 58.472 55.000 0.00 0.00 0.00 4.85
3981 4340 1.072965 CTCCAACAGAAACCTCAGGCT 59.927 52.381 0.00 0.00 0.00 4.58
4082 4441 3.688673 GGAATGAGAGGAACTTCAGCAAG 59.311 47.826 0.00 0.00 41.55 4.01
4212 4573 4.632974 GCAGATAGCAGGCCCCGG 62.633 72.222 0.00 0.00 44.79 5.73
4239 4600 2.955660 TGGAAGGTTTGCAAAGAACGAT 59.044 40.909 13.26 1.31 0.00 3.73
4287 4648 4.702131 AGCTCCCAAAATCATGAACAGTAC 59.298 41.667 0.00 0.00 0.00 2.73
4502 4863 1.377202 GCGGGTGCAGATGGAGAAA 60.377 57.895 0.00 0.00 42.15 2.52
4639 5000 5.023533 AGTCTGTGTTCTGCTTTCAGTTA 57.976 39.130 0.00 0.00 41.10 2.24
4769 5130 6.756542 TGGTGTATTGTATCAATCTGTTCTCG 59.243 38.462 0.00 0.00 0.00 4.04
4851 5212 9.126151 TGTAAAAATAGAATTGTGTCCTTGTCA 57.874 29.630 0.00 0.00 0.00 3.58
4933 5294 8.637281 TGGTGTACATAATAACAGTATTCACG 57.363 34.615 0.00 0.00 32.10 4.35
5037 5398 3.958147 TCTGGCCGTATGTCAAGAAGATA 59.042 43.478 0.00 0.00 0.00 1.98
5150 5524 8.065473 TGTATCAAATACTGGAAATGCACAAT 57.935 30.769 0.00 0.00 36.70 2.71
5213 5592 4.592942 AGTGCATCACAGACCATTTGTAT 58.407 39.130 0.00 0.00 36.74 2.29
5338 5717 3.181423 ACCAATTAGGCCAAGAACTCCAA 60.181 43.478 5.01 0.00 43.14 3.53
5365 5744 2.808543 AGTTAGTGGCAAAAAGAGAGCG 59.191 45.455 0.00 0.00 0.00 5.03
5368 5747 0.238553 GTGGCAAAAAGAGAGCGACC 59.761 55.000 0.00 0.00 31.91 4.79
5431 5810 5.234116 CAGAAAATGAGAAAAACAAACGGGG 59.766 40.000 0.00 0.00 0.00 5.73
5473 5854 5.219739 AGGATTCTGAACTATTCTAGGCCA 58.780 41.667 5.01 0.00 0.00 5.36
5553 5935 3.181429 CCCATTGTACAGGCCCAAGATAT 60.181 47.826 0.00 0.00 0.00 1.63
5554 5936 4.042809 CCCATTGTACAGGCCCAAGATATA 59.957 45.833 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.395312 ACTTCTTGTACCCACACCCG 59.605 55.000 0.00 0.00 33.30 5.28
48 49 1.190643 GAGCCCTATGCCTAGCTAGG 58.809 60.000 32.12 32.12 46.42 3.02
57 58 1.080434 GGATCGACGAGCCCTATGC 60.080 63.158 21.42 0.00 41.71 3.14
58 59 0.962489 AAGGATCGACGAGCCCTATG 59.038 55.000 27.51 0.00 39.17 2.23
60 61 0.106868 TCAAGGATCGACGAGCCCTA 60.107 55.000 27.51 11.28 39.17 3.53
61 62 1.379977 TCAAGGATCGACGAGCCCT 60.380 57.895 27.51 20.07 39.17 5.19
62 63 1.066587 CTCAAGGATCGACGAGCCC 59.933 63.158 27.51 18.19 39.17 5.19
63 64 1.066587 CCTCAAGGATCGACGAGCC 59.933 63.158 24.29 24.29 38.56 4.70
64 65 1.590259 GCCTCAAGGATCGACGAGC 60.590 63.158 4.11 4.11 37.39 5.03
65 66 0.030101 GAGCCTCAAGGATCGACGAG 59.970 60.000 3.01 0.00 41.12 4.18
78 80 5.378292 TCGACATATGTATCTTGAGCCTC 57.622 43.478 8.71 0.00 0.00 4.70
80 82 3.923461 GCTCGACATATGTATCTTGAGCC 59.077 47.826 22.79 12.81 41.19 4.70
81 83 4.804108 AGCTCGACATATGTATCTTGAGC 58.196 43.478 24.36 24.36 45.90 4.26
114 119 1.529012 GCCGTCTACCTACGTAGCTAC 59.471 57.143 17.41 14.19 41.62 3.58
223 253 2.193248 GGAGGGCGGGGAAATGAG 59.807 66.667 0.00 0.00 0.00 2.90
224 254 3.792736 CGGAGGGCGGGGAAATGA 61.793 66.667 0.00 0.00 0.00 2.57
262 314 6.310467 GTGAGTTTGAGTCTGCGTTGATTATA 59.690 38.462 0.00 0.00 0.00 0.98
272 324 0.510359 CGCAGTGAGTTTGAGTCTGC 59.490 55.000 0.00 0.00 45.13 4.26
275 327 1.569479 GGGCGCAGTGAGTTTGAGTC 61.569 60.000 10.83 0.00 0.00 3.36
290 342 4.878682 GTAGGTAACGGCCGGGCG 62.879 72.222 44.20 44.20 46.39 6.13
308 367 7.401493 AGGGAGTAATAATCTGGATGATGGTAG 59.599 40.741 0.00 0.00 35.21 3.18
401 629 9.667107 CAAGTAATTTGGGACAGAGTTAAGATA 57.333 33.333 0.00 0.00 42.39 1.98
402 630 8.164070 ACAAGTAATTTGGGACAGAGTTAAGAT 58.836 33.333 0.00 0.00 42.39 2.40
403 631 7.514721 ACAAGTAATTTGGGACAGAGTTAAGA 58.485 34.615 0.00 0.00 42.39 2.10
404 632 7.745620 ACAAGTAATTTGGGACAGAGTTAAG 57.254 36.000 0.00 0.00 42.39 1.85
449 681 6.371548 ACGTCTTAGTGTTAGGTACATTCGTA 59.628 38.462 0.00 0.00 39.39 3.43
450 682 5.182001 ACGTCTTAGTGTTAGGTACATTCGT 59.818 40.000 0.00 0.00 39.39 3.85
451 683 5.510674 CACGTCTTAGTGTTAGGTACATTCG 59.489 44.000 0.00 0.00 39.39 3.34
470 702 6.018994 AGACATTTTTGTAGTTCAGACACGTC 60.019 38.462 0.00 0.00 0.00 4.34
486 718 9.284968 CCCCGTCTCATAATATAAGACATTTTT 57.715 33.333 4.59 0.00 39.49 1.94
488 720 7.974504 ACCCCGTCTCATAATATAAGACATTT 58.025 34.615 4.59 0.00 39.49 2.32
490 722 7.554959 AACCCCGTCTCATAATATAAGACAT 57.445 36.000 4.59 0.00 39.49 3.06
491 723 6.989155 AACCCCGTCTCATAATATAAGACA 57.011 37.500 4.59 0.00 39.49 3.41
492 724 8.120140 AGTAACCCCGTCTCATAATATAAGAC 57.880 38.462 0.00 0.00 36.82 3.01
493 725 9.986157 ATAGTAACCCCGTCTCATAATATAAGA 57.014 33.333 0.00 0.00 0.00 2.10
499 731 9.322769 AGAATAATAGTAACCCCGTCTCATAAT 57.677 33.333 0.00 0.00 0.00 1.28
500 732 8.716674 AGAATAATAGTAACCCCGTCTCATAA 57.283 34.615 0.00 0.00 0.00 1.90
501 733 7.395489 GGAGAATAATAGTAACCCCGTCTCATA 59.605 40.741 0.00 0.00 32.45 2.15
502 734 6.210984 GGAGAATAATAGTAACCCCGTCTCAT 59.789 42.308 0.00 0.00 32.45 2.90
503 735 5.537674 GGAGAATAATAGTAACCCCGTCTCA 59.462 44.000 0.00 0.00 32.45 3.27
504 736 5.537674 TGGAGAATAATAGTAACCCCGTCTC 59.462 44.000 0.00 0.00 0.00 3.36
505 737 5.461327 TGGAGAATAATAGTAACCCCGTCT 58.539 41.667 0.00 0.00 0.00 4.18
506 738 5.796424 TGGAGAATAATAGTAACCCCGTC 57.204 43.478 0.00 0.00 0.00 4.79
507 739 7.243824 TCTATGGAGAATAATAGTAACCCCGT 58.756 38.462 0.00 0.00 0.00 5.28
508 740 7.713734 TCTATGGAGAATAATAGTAACCCCG 57.286 40.000 0.00 0.00 0.00 5.73
522 754 9.828691 TCTATCAGGATGTTAATCTATGGAGAA 57.171 33.333 0.00 0.00 37.40 2.87
545 777 8.826710 CAACCTTTAGCGTTCAATGATTATCTA 58.173 33.333 0.00 0.00 0.00 1.98
569 801 3.353029 CGTGATGGGTGCGTGCAA 61.353 61.111 0.00 0.00 0.00 4.08
669 907 1.822990 CGGAGGTTACTAGGTGAGCAA 59.177 52.381 0.00 0.00 0.00 3.91
671 909 1.760192 TCGGAGGTTACTAGGTGAGC 58.240 55.000 0.00 0.00 0.00 4.26
748 994 0.537371 CTCCCATATTTGGTCGGGCC 60.537 60.000 0.00 0.00 41.91 5.80
750 996 0.537371 GCCTCCCATATTTGGTCGGG 60.537 60.000 1.26 0.00 41.91 5.14
840 1094 2.163509 GAAGAAGGGTCAAAAGGGAGC 58.836 52.381 0.00 0.00 34.62 4.70
901 1162 1.484444 GGGAAGTGAGAGGTGGCTGT 61.484 60.000 0.00 0.00 0.00 4.40
904 1165 0.827368 CTAGGGAAGTGAGAGGTGGC 59.173 60.000 0.00 0.00 0.00 5.01
940 1201 3.879892 GGCTGGAGATGTGGAAGTTTATC 59.120 47.826 0.00 0.00 0.00 1.75
941 1202 3.372025 GGGCTGGAGATGTGGAAGTTTAT 60.372 47.826 0.00 0.00 0.00 1.40
944 1205 0.329596 GGGCTGGAGATGTGGAAGTT 59.670 55.000 0.00 0.00 0.00 2.66
946 1207 1.225704 GGGGCTGGAGATGTGGAAG 59.774 63.158 0.00 0.00 0.00 3.46
982 1247 0.520404 ATTTGTGCGCTCAAGCTCTG 59.480 50.000 22.36 0.00 39.32 3.35
983 1248 0.520404 CATTTGTGCGCTCAAGCTCT 59.480 50.000 22.36 8.46 39.32 4.09
1051 1318 4.378046 GGAGGTTTGTGTACTTACAATGCG 60.378 45.833 0.10 0.00 40.00 4.73
1069 1336 0.252558 TTAAGGGCGAAGAGGGAGGT 60.253 55.000 0.00 0.00 0.00 3.85
1072 1339 2.944094 GCAAATTAAGGGCGAAGAGGGA 60.944 50.000 0.00 0.00 0.00 4.20
1073 1340 1.405463 GCAAATTAAGGGCGAAGAGGG 59.595 52.381 0.00 0.00 0.00 4.30
1081 1349 1.751437 ACCGAGAGCAAATTAAGGGC 58.249 50.000 0.00 0.00 0.00 5.19
1082 1350 4.941873 ACTAAACCGAGAGCAAATTAAGGG 59.058 41.667 0.00 0.00 0.00 3.95
1144 1420 1.155042 GCAAGCGAGATGGATCATCC 58.845 55.000 0.00 0.00 41.36 3.51
1171 1447 8.027440 TGGTGATGCAAAAATTTATACAAAGC 57.973 30.769 0.00 0.00 0.00 3.51
1193 1488 2.466846 CTGAAGACACGTTACGTTGGT 58.533 47.619 7.98 3.80 38.32 3.67
1195 1490 1.855978 TGCTGAAGACACGTTACGTTG 59.144 47.619 7.98 6.73 38.32 4.10
1215 1510 7.805071 CGCTCAATTTCAGTCTATCAAGTTTTT 59.195 33.333 0.00 0.00 0.00 1.94
1229 1524 8.383619 GGTAGTATATAATGCGCTCAATTTCAG 58.616 37.037 9.73 0.00 0.00 3.02
1301 1605 8.807667 AAACAAGCATCAGAATTTTCAAGTAG 57.192 30.769 0.00 0.00 0.00 2.57
1330 1637 4.281525 ACGTACGTTTGATTGCTTTGTT 57.718 36.364 16.72 0.00 0.00 2.83
1333 1640 4.060205 AGGTACGTACGTTTGATTGCTTT 58.940 39.130 27.92 0.00 0.00 3.51
1368 1683 5.666462 TCAGCAAGCGAATTAATGGTACTA 58.334 37.500 0.00 0.00 0.00 1.82
1369 1684 4.513442 TCAGCAAGCGAATTAATGGTACT 58.487 39.130 0.00 0.00 0.00 2.73
1370 1685 4.875544 TCAGCAAGCGAATTAATGGTAC 57.124 40.909 0.00 0.00 0.00 3.34
1371 1686 5.182487 TCTTCAGCAAGCGAATTAATGGTA 58.818 37.500 0.00 0.00 0.00 3.25
1372 1687 4.009675 TCTTCAGCAAGCGAATTAATGGT 58.990 39.130 0.00 0.00 0.00 3.55
1373 1688 4.621068 TCTTCAGCAAGCGAATTAATGG 57.379 40.909 0.00 0.00 0.00 3.16
1374 1689 6.414109 CAGAATCTTCAGCAAGCGAATTAATG 59.586 38.462 0.00 0.00 0.00 1.90
1375 1690 6.493116 CAGAATCTTCAGCAAGCGAATTAAT 58.507 36.000 0.00 0.00 0.00 1.40
1376 1691 5.674569 GCAGAATCTTCAGCAAGCGAATTAA 60.675 40.000 2.82 0.00 39.23 1.40
1377 1692 4.201851 GCAGAATCTTCAGCAAGCGAATTA 60.202 41.667 2.82 0.00 39.23 1.40
1378 1693 3.427233 GCAGAATCTTCAGCAAGCGAATT 60.427 43.478 2.82 0.00 39.23 2.17
1379 1694 2.097142 GCAGAATCTTCAGCAAGCGAAT 59.903 45.455 2.82 0.00 39.23 3.34
1380 1695 1.466167 GCAGAATCTTCAGCAAGCGAA 59.534 47.619 2.82 0.00 39.23 4.70
1381 1696 1.081892 GCAGAATCTTCAGCAAGCGA 58.918 50.000 2.82 0.00 39.23 4.93
1382 1697 0.800631 TGCAGAATCTTCAGCAAGCG 59.199 50.000 7.45 0.00 44.94 4.68
1423 1738 5.048921 GTGGGTGCCTAAAGAAAGAACTTAC 60.049 44.000 0.00 0.00 0.00 2.34
1534 1850 5.835113 TCTGTCTGACATGTCATCGATTA 57.165 39.130 28.00 14.42 39.13 1.75
1556 1872 2.488153 GGAGCGTAATTTGGCTTCTGTT 59.512 45.455 4.66 0.00 40.16 3.16
1557 1873 2.084546 GGAGCGTAATTTGGCTTCTGT 58.915 47.619 4.66 0.00 40.16 3.41
1558 1874 1.401905 GGGAGCGTAATTTGGCTTCTG 59.598 52.381 8.20 0.00 40.16 3.02
1559 1875 1.004277 TGGGAGCGTAATTTGGCTTCT 59.996 47.619 8.20 0.00 40.16 2.85
1560 1876 1.132453 GTGGGAGCGTAATTTGGCTTC 59.868 52.381 4.66 2.86 40.16 3.86
1561 1877 1.173913 GTGGGAGCGTAATTTGGCTT 58.826 50.000 4.66 0.00 40.16 4.35
1569 1885 3.005472 GTCTATGCATAGTGGGAGCGTAA 59.995 47.826 28.51 6.93 30.19 3.18
1664 1987 5.839063 TGATCTGGAAGTATCCTATTCCGTT 59.161 40.000 0.00 0.00 46.66 4.44
1667 1990 7.038017 TGGATTGATCTGGAAGTATCCTATTCC 60.038 40.741 0.00 0.00 46.70 3.01
1717 2040 5.124457 ACATTTGCAGATGAAATAGAAGCGT 59.876 36.000 22.94 0.00 0.00 5.07
1954 2282 2.224769 CGGCTGGGATGGTAATATGGTT 60.225 50.000 0.00 0.00 0.00 3.67
1991 2319 1.705337 CTATTCTTGCGCGGGGTGTG 61.705 60.000 8.83 0.00 0.00 3.82
1998 2326 0.933097 ACAGATGCTATTCTTGCGCG 59.067 50.000 0.00 0.00 0.00 6.86
2042 2370 2.535485 TAGGGTGGCGTCCATGCAAG 62.535 60.000 0.00 0.00 35.28 4.01
2113 2445 2.040359 GAAGAGGAGGGGAGGGGG 60.040 72.222 0.00 0.00 0.00 5.40
2114 2446 2.040359 GGAAGAGGAGGGGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
2115 2447 2.040359 GGGAAGAGGAGGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
2116 2448 2.444895 CGGGAAGAGGAGGGGAGG 60.445 72.222 0.00 0.00 0.00 4.30
2117 2449 3.157949 GCGGGAAGAGGAGGGGAG 61.158 72.222 0.00 0.00 0.00 4.30
2118 2450 3.556038 TTGCGGGAAGAGGAGGGGA 62.556 63.158 0.00 0.00 0.00 4.81
2119 2451 3.009115 TTGCGGGAAGAGGAGGGG 61.009 66.667 0.00 0.00 0.00 4.79
2120 2452 2.586792 CTTGCGGGAAGAGGAGGG 59.413 66.667 2.75 0.00 32.82 4.30
2121 2453 2.245438 GACCTTGCGGGAAGAGGAGG 62.245 65.000 11.11 0.00 38.76 4.30
2122 2454 1.219393 GACCTTGCGGGAAGAGGAG 59.781 63.158 11.11 0.00 38.76 3.69
2139 2471 1.416401 GGCGAGGAAGATGGGTTATGA 59.584 52.381 0.00 0.00 0.00 2.15
2164 2496 1.277326 CCGTGAAAGATCGAATCGCA 58.723 50.000 0.00 0.00 0.00 5.10
2292 2625 2.027751 GTCGTCGGGGAGCATAGC 59.972 66.667 0.00 0.00 0.00 2.97
2380 2713 1.799933 ATGCTTGGTTTTTGTCCCCA 58.200 45.000 0.00 0.00 0.00 4.96
2381 2714 2.928801 AATGCTTGGTTTTTGTCCCC 57.071 45.000 0.00 0.00 0.00 4.81
2382 2715 4.195416 TGAAAATGCTTGGTTTTTGTCCC 58.805 39.130 0.00 0.00 0.00 4.46
2476 2809 4.438744 GCAGTTAGTACCAATGTCCATTGC 60.439 45.833 13.34 2.16 45.06 3.56
2477 2810 4.699735 TGCAGTTAGTACCAATGTCCATTG 59.300 41.667 12.10 12.10 45.77 2.82
2479 2812 4.568072 TGCAGTTAGTACCAATGTCCAT 57.432 40.909 0.00 0.00 0.00 3.41
2480 2813 4.260985 CATGCAGTTAGTACCAATGTCCA 58.739 43.478 0.00 0.00 0.00 4.02
2482 2815 5.005394 CGTACATGCAGTTAGTACCAATGTC 59.995 44.000 12.83 0.00 35.80 3.06
2483 2816 4.868171 CGTACATGCAGTTAGTACCAATGT 59.132 41.667 12.83 2.26 35.80 2.71
2484 2817 5.106442 TCGTACATGCAGTTAGTACCAATG 58.894 41.667 12.83 0.00 35.80 2.82
2485 2818 5.333299 TCGTACATGCAGTTAGTACCAAT 57.667 39.130 12.83 0.00 35.80 3.16
2486 2819 4.787260 TCGTACATGCAGTTAGTACCAA 57.213 40.909 12.83 3.23 35.80 3.67
2488 2821 5.824429 TGTATCGTACATGCAGTTAGTACC 58.176 41.667 12.83 3.76 35.80 3.34
2489 2822 7.925703 ATTGTATCGTACATGCAGTTAGTAC 57.074 36.000 9.98 9.98 38.68 2.73
2491 2824 9.193133 GATTATTGTATCGTACATGCAGTTAGT 57.807 33.333 0.00 0.00 38.68 2.24
2492 2825 9.411801 AGATTATTGTATCGTACATGCAGTTAG 57.588 33.333 0.00 0.00 38.68 2.34
2572 2908 7.950124 TCCTCAGGTCCAGAATTAAAAGATTTT 59.050 33.333 0.00 0.00 0.00 1.82
2581 2917 4.715297 GGTACTTCCTCAGGTCCAGAATTA 59.285 45.833 0.00 0.00 0.00 1.40
2589 2925 2.810164 AGTCAGGTACTTCCTCAGGTC 58.190 52.381 0.00 0.00 46.24 3.85
2605 2941 8.333235 ACACTGGGATTTTGGTAATTATAGTCA 58.667 33.333 0.00 0.00 0.00 3.41
2882 3230 3.001838 TGCATGACGTTATGGCGTAAATC 59.998 43.478 20.43 3.22 45.79 2.17
2903 3252 5.847304 TGAGTACTAAGGCTGATAAGCATG 58.153 41.667 3.95 0.00 36.33 4.06
2910 3259 6.360370 TGTTCTTTGAGTACTAAGGCTGAT 57.640 37.500 0.00 0.00 31.73 2.90
2914 3263 7.764443 TCATGTATGTTCTTTGAGTACTAAGGC 59.236 37.037 0.00 0.00 31.73 4.35
2987 3340 7.012044 GTGAGTACATTTTACCACACAACTTCT 59.988 37.037 0.00 0.00 0.00 2.85
2988 3341 7.130269 GTGAGTACATTTTACCACACAACTTC 58.870 38.462 0.00 0.00 0.00 3.01
2991 3344 6.366315 TGTGAGTACATTTTACCACACAAC 57.634 37.500 0.00 0.00 34.75 3.32
3021 3374 5.538433 CCCTCCTGTAAATTTCAAAGGTGAA 59.462 40.000 13.38 0.00 42.12 3.18
3085 3438 0.689412 TATCACCCAGGCCGTCATCA 60.689 55.000 0.00 0.00 0.00 3.07
3115 3468 0.965866 CGGAGGTAGAGGTCACTGCA 60.966 60.000 0.00 0.00 0.00 4.41
3139 3492 2.851798 CTCAGAGGAGGCAGCAAAC 58.148 57.895 0.00 0.00 37.51 2.93
3253 3606 2.103432 CTCGAGTAGGGCTGAGAGAGTA 59.897 54.545 3.62 0.00 33.20 2.59
3289 3645 2.032681 AGCTCGGTTTCAGGGCAC 59.967 61.111 0.00 0.00 0.00 5.01
3298 3654 2.998949 GGGGGAATGAGCTCGGTT 59.001 61.111 9.64 6.55 0.00 4.44
3302 3658 0.469917 TTGATCGGGGGAATGAGCTC 59.530 55.000 6.82 6.82 0.00 4.09
3316 3672 1.127582 GCTGCAAGTGTCTCGTTGATC 59.872 52.381 0.00 0.00 35.30 2.92
3410 3766 0.627451 ATTGCCAGCAAGGGATCAGA 59.373 50.000 11.21 0.00 37.68 3.27
3415 3774 1.533513 TTGCATTGCCAGCAAGGGA 60.534 52.632 17.59 12.77 46.13 4.20
3709 4068 2.025863 GCCCCCTTCATGGAATCTGTG 61.026 57.143 0.00 0.00 38.35 3.66
3763 4122 9.535170 TGGTATTAAATTGATTGTTAGGTTCCA 57.465 29.630 0.00 0.00 0.00 3.53
3787 4146 7.040892 TGGTACTATCGTAGTTAAGCAGTATGG 60.041 40.741 3.56 0.00 40.14 2.74
3802 4161 5.416271 ACATGGAAGTTTGGTACTATCGT 57.584 39.130 0.00 0.00 35.54 3.73
3824 4183 4.131596 ACACTTTTCTTTTACCAGCGCTA 58.868 39.130 10.99 0.00 0.00 4.26
3927 4286 2.362077 GGCTTCCGTTGCATCCATTTAT 59.638 45.455 0.00 0.00 0.00 1.40
3973 4332 3.432890 GGTGGAATCTTCTAAGCCTGAGG 60.433 52.174 0.00 0.00 0.00 3.86
3981 4340 7.510549 CAACTTTGAAGGTGGAATCTTCTAA 57.489 36.000 0.77 0.44 40.06 2.10
4212 4573 1.104577 TTGCAAACCTTCCACGGACC 61.105 55.000 0.00 0.00 0.00 4.46
4239 4600 5.125257 TGATCTTGTTGCTTCACAAAGTTCA 59.875 36.000 0.00 0.00 40.82 3.18
4287 4648 6.197364 ACTAGAAGACTTACAATCTGTCCG 57.803 41.667 0.00 0.00 0.00 4.79
4320 4681 5.938125 GGCTGTTTCTGGTAAGATAAGACAA 59.062 40.000 0.00 0.00 30.72 3.18
4502 4863 0.317160 TCGGACGAGTCAAGCATGTT 59.683 50.000 5.55 0.00 0.00 2.71
4639 5000 5.539955 GGGAAACTATGGATTATGGTTGCAT 59.460 40.000 0.00 0.00 39.27 3.96
4769 5130 2.034179 ACTGTTAAGAACGGCAAAAGGC 59.966 45.455 0.00 0.00 41.56 4.35
4933 5294 0.955919 CTTCCACGCCTTGTTCTCCC 60.956 60.000 0.00 0.00 0.00 4.30
4982 5343 4.600062 TCTCTGTACTGGAGTGCTATTCA 58.400 43.478 13.31 0.00 33.06 2.57
4988 5349 2.480416 CGGATTCTCTGTACTGGAGTGC 60.480 54.545 13.31 6.03 33.06 4.40
5213 5592 3.191162 GGTGATGTGCATAAGCTTTCACA 59.809 43.478 22.38 22.38 41.74 3.58
5338 5717 7.867909 GCTCTCTTTTTGCCACTAACTAAAATT 59.132 33.333 0.00 0.00 0.00 1.82
5365 5744 6.126911 TGGGCAATTATTTTTAAGATGGGGTC 60.127 38.462 0.00 0.00 0.00 4.46
5368 5747 6.936335 GGATGGGCAATTATTTTTAAGATGGG 59.064 38.462 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.