Multiple sequence alignment - TraesCS5D01G322700

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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 TraesCS5D01G322700 chr5D 100.000 4522 0 0 1 4522 414219429 414223950 0.000000e+00 8351.0
1 TraesCS5D01G322700 chr5D 80.843 261 33 10 2651 2897 542278103 542277846 5.970000e-44 189.0
2 TraesCS5D01G322700 chr5A 92.658 2370 106 19 1289 3634 526617508 526619833 0.000000e+00 3350.0
3 TraesCS5D01G322700 chr5A 89.022 1248 83 21 1 1235 526616300 526617506 0.000000e+00 1496.0
4 TraesCS5D01G322700 chr5A 91.167 317 23 3 4186 4498 526620220 526620535 4.180000e-115 425.0
5 TraesCS5D01G322700 chr5A 85.427 199 14 8 3740 3928 526619831 526620024 4.620000e-45 193.0
6 TraesCS5D01G322700 chr5B 92.034 1632 95 14 830 2444 499165948 499167561 0.000000e+00 2261.0
7 TraesCS5D01G322700 chr5B 95.078 833 24 11 1 824 499164646 499165470 0.000000e+00 1295.0
8 TraesCS5D01G322700 chr5B 96.667 720 18 3 2924 3637 499167964 499168683 0.000000e+00 1192.0
9 TraesCS5D01G322700 chr5B 91.593 452 28 6 4056 4498 499168951 499169401 2.310000e-172 616.0
10 TraesCS5D01G322700 chr5B 84.985 333 30 12 3740 4057 499168686 499169013 2.030000e-83 320.0
11 TraesCS5D01G322700 chr2A 80.074 808 108 25 1648 2444 21469087 21469852 6.610000e-153 551.0
12 TraesCS5D01G322700 chr2A 85.950 121 8 5 1548 1663 21468945 21469061 2.210000e-23 121.0
13 TraesCS5D01G322700 chr3B 92.035 113 6 1 3631 3743 41018582 41018473 6.060000e-34 156.0
14 TraesCS5D01G322700 chr3B 91.892 111 6 1 3633 3743 812340464 812340357 7.840000e-33 152.0
15 TraesCS5D01G322700 chr6A 90.678 118 8 1 3626 3743 502244342 502244228 2.180000e-33 154.0
16 TraesCS5D01G322700 chr6A 90.090 111 8 1 3634 3744 295818514 295818407 1.700000e-29 141.0
17 TraesCS5D01G322700 chr2D 90.598 117 7 2 3634 3750 625519656 625519544 7.840000e-33 152.0
18 TraesCS5D01G322700 chr6B 88.710 124 9 3 3624 3746 492505657 492505538 3.650000e-31 147.0
19 TraesCS5D01G322700 chr3A 90.991 111 7 1 3633 3743 734786365 734786258 3.650000e-31 147.0
20 TraesCS5D01G322700 chrUn 90.090 111 8 1 3634 3744 321894324 321894217 1.700000e-29 141.0
21 TraesCS5D01G322700 chr4A 87.805 123 10 3 3629 3749 374717054 374717173 6.100000e-29 139.0
22 TraesCS5D01G322700 chr7B 100.000 28 0 0 2647 2674 618502746 618502719 8.000000e-03 52.8


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 TraesCS5D01G322700 chr5D 414219429 414223950 4521 False 8351.0 8351 100.0000 1 4522 1 chr5D.!!$F1 4521
1 TraesCS5D01G322700 chr5A 526616300 526620535 4235 False 1366.0 3350 89.5685 1 4498 4 chr5A.!!$F1 4497
2 TraesCS5D01G322700 chr5B 499164646 499169401 4755 False 1136.8 2261 92.0714 1 4498 5 chr5B.!!$F1 4497
3 TraesCS5D01G322700 chr2A 21468945 21469852 907 False 336.0 551 83.0120 1548 2444 2 chr2A.!!$F1 896

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
843 1336 0.245266 GGTGTGGGCAAAATAACGGG 59.755 55.0 0.00 0.0 0.0 5.28 F
2696 3470 0.380378 GCGGCGCTTATGATGGAAAA 59.620 50.0 26.86 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2778 3552 0.320374 TCCTCCGCGTGAGTTGAAAT 59.68 50.0 18.94 0.0 39.65 2.17 R
4083 4895 0.039798 TTGTACGACACTGCTCGGTC 60.04 55.0 0.00 0.0 38.02 4.79 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
134 139 2.697751 AGGAGAGGTTTGATGGAGATCG 59.302 50.000 0.00 0.00 0.00 3.69
152 157 3.703286 TCGTGGATAATGTACGTCTGG 57.297 47.619 0.00 0.00 38.80 3.86
354 363 8.765488 TTGAATTCTGGGCATATCATTCTTTA 57.235 30.769 7.05 0.00 0.00 1.85
550 560 4.272489 TCTGCCATTTCTCTACCATTTGG 58.728 43.478 0.00 0.00 42.17 3.28
631 641 2.910482 CGTTCGAAACAAGCCATGAATG 59.090 45.455 0.00 0.00 0.00 2.67
632 642 3.364864 CGTTCGAAACAAGCCATGAATGA 60.365 43.478 0.00 0.00 0.00 2.57
633 643 4.545610 GTTCGAAACAAGCCATGAATGAA 58.454 39.130 0.00 0.00 0.00 2.57
634 644 5.163513 GTTCGAAACAAGCCATGAATGAAT 58.836 37.500 0.00 0.00 0.00 2.57
635 645 4.735985 TCGAAACAAGCCATGAATGAATG 58.264 39.130 0.00 0.00 0.00 2.67
636 646 4.218200 TCGAAACAAGCCATGAATGAATGT 59.782 37.500 0.00 0.00 0.00 2.71
637 647 5.414144 TCGAAACAAGCCATGAATGAATGTA 59.586 36.000 0.00 0.00 0.00 2.29
638 648 6.095300 TCGAAACAAGCCATGAATGAATGTAT 59.905 34.615 0.00 0.00 0.00 2.29
644 654 6.263516 AGCCATGAATGAATGTATGTATGC 57.736 37.500 0.00 0.00 0.00 3.14
796 817 6.739331 ACCCATCTACTCCTATTTCTCTTG 57.261 41.667 0.00 0.00 0.00 3.02
828 1321 2.027285 GCAAAATAATTGGCCCAGGTGT 60.027 45.455 0.00 0.00 28.38 4.16
843 1336 0.245266 GGTGTGGGCAAAATAACGGG 59.755 55.000 0.00 0.00 0.00 5.28
902 1395 3.130160 GCCTGGCTTTCTCCGCAG 61.130 66.667 12.43 0.00 0.00 5.18
997 1490 0.536460 CCCCACACCCCGCATATAAC 60.536 60.000 0.00 0.00 0.00 1.89
1015 1508 1.361204 ACACATGTCCACCTCCATGA 58.639 50.000 0.00 0.00 40.70 3.07
1060 1553 4.101077 CCTCCCTGCCTCCCCTCT 62.101 72.222 0.00 0.00 0.00 3.69
1063 1556 3.093172 CCCTGCCTCCCCTCTTCC 61.093 72.222 0.00 0.00 0.00 3.46
1278 1771 2.746277 GCCCTGGCCAAGTACACG 60.746 66.667 7.01 0.00 34.56 4.49
1365 1858 1.482593 CTCATCTACGCCCTCAGGTTT 59.517 52.381 0.00 0.00 34.57 3.27
1446 1939 1.139853 GCGTGAGGATCCCTGATTTCT 59.860 52.381 8.55 0.00 31.76 2.52
1666 2203 2.512476 TCTACCCATTTAGGCCTTTCCC 59.488 50.000 12.58 0.00 35.39 3.97
1773 2322 4.780815 CCTGGATTTGCTAACAGGTCATA 58.219 43.478 8.71 0.00 44.21 2.15
1845 2394 5.607939 TCCATGCCTAGTAAGAAATTCGA 57.392 39.130 0.00 0.00 0.00 3.71
1847 2396 5.105106 TCCATGCCTAGTAAGAAATTCGACA 60.105 40.000 4.39 0.00 0.00 4.35
1849 2398 6.093495 CCATGCCTAGTAAGAAATTCGACAAA 59.907 38.462 4.39 0.00 0.00 2.83
1913 2462 6.685828 GTGCATTTCTATATAATCATGCGCAG 59.314 38.462 18.32 8.46 44.08 5.18
1946 2495 8.308207 TGGCTACAAAAAGTCATAATTAAACCC 58.692 33.333 0.00 0.00 0.00 4.11
1978 2535 8.903570 TCAATTTATTGTACAAATTGTAGCGG 57.096 30.769 22.05 6.70 46.37 5.52
2005 2562 7.666804 TGCTCATAATCATTTACATGTATGGCT 59.333 33.333 6.36 0.00 29.06 4.75
2114 2676 8.110860 ACATAAGTTCAGTAACATTTGGGAAG 57.889 34.615 0.00 0.00 38.12 3.46
2145 2715 7.286775 ACCCTGTAAATCTGTAGCTTTTTCAAA 59.713 33.333 0.00 0.00 0.00 2.69
2313 2883 2.525629 TGGCTTCCAGTGACGGGA 60.526 61.111 0.00 0.00 0.00 5.14
2323 2893 3.118334 TCCAGTGACGGGAAGTTGTAAAA 60.118 43.478 0.85 0.00 0.00 1.52
2324 2894 3.628487 CCAGTGACGGGAAGTTGTAAAAA 59.372 43.478 0.00 0.00 0.00 1.94
2434 3008 8.271458 TGAGTGTATCCATGCCTTATAAGAAAA 58.729 33.333 14.28 0.00 0.00 2.29
2445 3019 6.036470 GCCTTATAAGAAAATTGGTCAGTGC 58.964 40.000 14.28 0.00 0.00 4.40
2446 3020 6.350110 GCCTTATAAGAAAATTGGTCAGTGCA 60.350 38.462 14.28 0.00 0.00 4.57
2489 3258 7.467267 CGCCATATTTATGTTAGCTTCAGTTGT 60.467 37.037 0.00 0.00 31.82 3.32
2508 3278 3.717707 TGTAAATCATCTAGACAGCCGC 58.282 45.455 0.00 0.00 0.00 6.53
2526 3296 2.032054 CCGCGCAGATAACATGTGATTT 59.968 45.455 8.75 0.00 0.00 2.17
2541 3311 6.941436 ACATGTGATTTTGGCAAAATATGGTT 59.059 30.769 30.93 19.04 40.97 3.67
2637 3411 8.402472 TCAAGATACAACGTTCATTTTCTGTTT 58.598 29.630 0.00 0.00 0.00 2.83
2661 3435 5.013704 TCAAGTTTAGTTAGGGCATCTCCAA 59.986 40.000 0.00 0.00 36.21 3.53
2691 3465 2.250485 GCAGCGGCGCTTATGATG 59.750 61.111 34.51 21.77 36.40 3.07
2696 3470 0.380378 GCGGCGCTTATGATGGAAAA 59.620 50.000 26.86 0.00 0.00 2.29
2733 3507 0.396435 TCTTGCGCTTCCTCTTCCAA 59.604 50.000 9.73 0.00 0.00 3.53
2734 3508 0.519077 CTTGCGCTTCCTCTTCCAAC 59.481 55.000 9.73 0.00 0.00 3.77
2738 3512 2.391389 GCTTCCTCTTCCAACGGCG 61.391 63.158 4.80 4.80 0.00 6.46
2768 3542 2.967615 GGGTGCTTAGCGATCGCC 60.968 66.667 34.89 20.58 43.17 5.54
2777 3551 0.806102 TAGCGATCGCCTGACAAAGC 60.806 55.000 34.89 5.09 43.17 3.51
2778 3552 2.390599 GCGATCGCCTGACAAAGCA 61.391 57.895 29.48 0.00 34.56 3.91
2819 3593 2.076863 GAAAGAAAAGGCTAGCGCTCA 58.923 47.619 16.34 0.00 36.09 4.26
2823 3597 0.391793 AAAAGGCTAGCGCTCACCTC 60.392 55.000 26.33 9.31 36.09 3.85
2833 3607 1.073897 GCTCACCTCCAGCTTTGGT 59.926 57.895 0.00 0.00 33.75 3.67
2854 3640 1.736645 CGACGCCAGGATTTGTCGT 60.737 57.895 13.01 2.22 46.56 4.34
2858 3644 1.156736 CGCCAGGATTTGTCGTTCTT 58.843 50.000 0.00 0.00 0.00 2.52
2860 3646 2.936498 CGCCAGGATTTGTCGTTCTTAT 59.064 45.455 0.00 0.00 0.00 1.73
2864 3650 4.396166 CCAGGATTTGTCGTTCTTATTGCT 59.604 41.667 0.00 0.00 0.00 3.91
2878 3664 4.104579 TCTTATTGCTGATTGGGCAGGATA 59.895 41.667 0.00 0.00 40.90 2.59
2899 3685 0.965866 TAGTCCTGGTGCTCACTCCG 60.966 60.000 0.00 0.00 31.75 4.63
3037 3827 5.308825 AGTCTTTAACTGGGTCATGTCTTG 58.691 41.667 0.00 0.00 36.65 3.02
3092 3882 6.772605 AGTGTATGCTATCAATGATGCCTTA 58.227 36.000 5.91 1.02 0.00 2.69
3101 3891 4.784177 TCAATGATGCCTTATCTGCTGAA 58.216 39.130 0.00 0.00 36.71 3.02
3320 4110 3.850098 AAAGCCGCCACCACAGAGG 62.850 63.158 0.00 0.00 45.67 3.69
3350 4140 1.076332 CGTTTCCGGTGATCAACTCC 58.924 55.000 9.52 0.00 0.00 3.85
3449 4239 3.507162 TCTGATTTGCTCCCTGTTGAA 57.493 42.857 0.00 0.00 0.00 2.69
3536 4326 0.324368 ACTAGTGAGTCCCATGGCGA 60.324 55.000 6.09 2.08 0.00 5.54
3539 4329 1.227674 GTGAGTCCCATGGCGATCC 60.228 63.158 6.09 2.61 0.00 3.36
3576 4367 9.638300 CTCGATCTTAAAATAAAAGTGAATCCG 57.362 33.333 0.00 0.00 0.00 4.18
3634 4425 7.241042 AGGTGAACTTGAGCTTTATGTAGTA 57.759 36.000 0.00 0.00 0.00 1.82
3635 4426 7.097834 AGGTGAACTTGAGCTTTATGTAGTAC 58.902 38.462 0.00 0.00 0.00 2.73
3636 4427 7.038941 AGGTGAACTTGAGCTTTATGTAGTACT 60.039 37.037 0.00 0.00 0.00 2.73
3637 4428 7.275999 GGTGAACTTGAGCTTTATGTAGTACTC 59.724 40.741 0.00 0.00 0.00 2.59
3638 4429 7.275999 GTGAACTTGAGCTTTATGTAGTACTCC 59.724 40.741 0.00 0.00 0.00 3.85
3639 4430 6.223351 ACTTGAGCTTTATGTAGTACTCCC 57.777 41.667 0.00 0.00 0.00 4.30
3640 4431 5.958987 ACTTGAGCTTTATGTAGTACTCCCT 59.041 40.000 0.00 0.00 0.00 4.20
3641 4432 6.097129 ACTTGAGCTTTATGTAGTACTCCCTC 59.903 42.308 0.00 0.00 0.00 4.30
3642 4433 5.767670 TGAGCTTTATGTAGTACTCCCTCT 58.232 41.667 0.00 0.00 0.00 3.69
3643 4434 5.594725 TGAGCTTTATGTAGTACTCCCTCTG 59.405 44.000 0.00 0.00 0.00 3.35
3644 4435 5.520751 AGCTTTATGTAGTACTCCCTCTGT 58.479 41.667 0.00 0.00 0.00 3.41
3645 4436 5.958987 AGCTTTATGTAGTACTCCCTCTGTT 59.041 40.000 0.00 0.00 0.00 3.16
3646 4437 6.097129 AGCTTTATGTAGTACTCCCTCTGTTC 59.903 42.308 0.00 0.00 0.00 3.18
3647 4438 6.683360 GCTTTATGTAGTACTCCCTCTGTTCC 60.683 46.154 0.00 0.00 0.00 3.62
3648 4439 3.820195 TGTAGTACTCCCTCTGTTCCA 57.180 47.619 0.00 0.00 0.00 3.53
3649 4440 4.332683 TGTAGTACTCCCTCTGTTCCAT 57.667 45.455 0.00 0.00 0.00 3.41
3650 4441 5.461516 TGTAGTACTCCCTCTGTTCCATA 57.538 43.478 0.00 0.00 0.00 2.74
3651 4442 6.027025 TGTAGTACTCCCTCTGTTCCATAT 57.973 41.667 0.00 0.00 0.00 1.78
3652 4443 6.441222 TGTAGTACTCCCTCTGTTCCATATT 58.559 40.000 0.00 0.00 0.00 1.28
3653 4444 7.589081 TGTAGTACTCCCTCTGTTCCATATTA 58.411 38.462 0.00 0.00 0.00 0.98
3654 4445 7.724506 TGTAGTACTCCCTCTGTTCCATATTAG 59.275 40.741 0.00 0.00 0.00 1.73
3655 4446 6.684538 AGTACTCCCTCTGTTCCATATTAGT 58.315 40.000 0.00 0.00 0.00 2.24
3656 4447 7.133483 AGTACTCCCTCTGTTCCATATTAGTT 58.867 38.462 0.00 0.00 0.00 2.24
3657 4448 6.240549 ACTCCCTCTGTTCCATATTAGTTG 57.759 41.667 0.00 0.00 0.00 3.16
3658 4449 5.726793 ACTCCCTCTGTTCCATATTAGTTGT 59.273 40.000 0.00 0.00 0.00 3.32
3659 4450 6.127026 ACTCCCTCTGTTCCATATTAGTTGTC 60.127 42.308 0.00 0.00 0.00 3.18
3660 4451 5.050490 CCCTCTGTTCCATATTAGTTGTCG 58.950 45.833 0.00 0.00 0.00 4.35
3661 4452 4.508124 CCTCTGTTCCATATTAGTTGTCGC 59.492 45.833 0.00 0.00 0.00 5.19
3662 4453 5.339008 TCTGTTCCATATTAGTTGTCGCT 57.661 39.130 0.00 0.00 0.00 4.93
3663 4454 5.348986 TCTGTTCCATATTAGTTGTCGCTC 58.651 41.667 0.00 0.00 0.00 5.03
3664 4455 5.079689 TGTTCCATATTAGTTGTCGCTCA 57.920 39.130 0.00 0.00 0.00 4.26
3665 4456 5.483811 TGTTCCATATTAGTTGTCGCTCAA 58.516 37.500 0.00 0.00 0.00 3.02
3666 4457 5.935206 TGTTCCATATTAGTTGTCGCTCAAA 59.065 36.000 0.00 0.00 37.81 2.69
3667 4458 6.128391 TGTTCCATATTAGTTGTCGCTCAAAC 60.128 38.462 0.00 0.00 37.81 2.93
3668 4459 5.483811 TCCATATTAGTTGTCGCTCAAACA 58.516 37.500 0.00 0.00 37.81 2.83
3669 4460 5.580691 TCCATATTAGTTGTCGCTCAAACAG 59.419 40.000 0.00 0.00 37.81 3.16
3670 4461 5.580691 CCATATTAGTTGTCGCTCAAACAGA 59.419 40.000 0.00 0.00 37.81 3.41
3671 4462 6.258727 CCATATTAGTTGTCGCTCAAACAGAT 59.741 38.462 0.00 0.00 37.81 2.90
3672 4463 4.990543 TTAGTTGTCGCTCAAACAGATG 57.009 40.909 0.00 0.00 37.81 2.90
3673 4464 2.838736 AGTTGTCGCTCAAACAGATGT 58.161 42.857 0.00 0.00 37.81 3.06
3674 4465 3.990092 AGTTGTCGCTCAAACAGATGTA 58.010 40.909 0.00 0.00 37.81 2.29
3675 4466 3.741344 AGTTGTCGCTCAAACAGATGTAC 59.259 43.478 0.00 0.00 37.81 2.90
3676 4467 2.683968 TGTCGCTCAAACAGATGTACC 58.316 47.619 0.00 0.00 0.00 3.34
3677 4468 2.299013 TGTCGCTCAAACAGATGTACCT 59.701 45.455 0.00 0.00 0.00 3.08
3678 4469 3.508402 TGTCGCTCAAACAGATGTACCTA 59.492 43.478 0.00 0.00 0.00 3.08
3679 4470 4.106197 GTCGCTCAAACAGATGTACCTAG 58.894 47.826 0.00 0.00 0.00 3.02
3680 4471 2.860735 CGCTCAAACAGATGTACCTAGC 59.139 50.000 0.00 0.00 0.00 3.42
3681 4472 3.676049 CGCTCAAACAGATGTACCTAGCA 60.676 47.826 0.00 0.00 0.00 3.49
3682 4473 3.619038 GCTCAAACAGATGTACCTAGCAC 59.381 47.826 0.00 0.00 0.00 4.40
3683 4474 4.621747 GCTCAAACAGATGTACCTAGCACT 60.622 45.833 0.00 0.00 0.00 4.40
3684 4475 4.820897 TCAAACAGATGTACCTAGCACTG 58.179 43.478 0.00 0.00 0.00 3.66
3685 4476 4.526650 TCAAACAGATGTACCTAGCACTGA 59.473 41.667 0.00 0.00 0.00 3.41
3686 4477 5.011635 TCAAACAGATGTACCTAGCACTGAA 59.988 40.000 0.00 0.00 0.00 3.02
3687 4478 5.483685 AACAGATGTACCTAGCACTGAAA 57.516 39.130 0.00 0.00 0.00 2.69
3688 4479 5.683876 ACAGATGTACCTAGCACTGAAAT 57.316 39.130 0.00 0.00 0.00 2.17
3689 4480 6.791867 ACAGATGTACCTAGCACTGAAATA 57.208 37.500 0.00 0.00 0.00 1.40
3690 4481 6.574350 ACAGATGTACCTAGCACTGAAATAC 58.426 40.000 0.00 0.00 0.00 1.89
3691 4482 5.687730 CAGATGTACCTAGCACTGAAATACG 59.312 44.000 0.00 0.00 0.00 3.06
3692 4483 5.360144 AGATGTACCTAGCACTGAAATACGT 59.640 40.000 0.00 0.00 0.00 3.57
3693 4484 4.990257 TGTACCTAGCACTGAAATACGTC 58.010 43.478 0.00 0.00 0.00 4.34
3694 4485 4.703575 TGTACCTAGCACTGAAATACGTCT 59.296 41.667 0.00 0.00 0.00 4.18
3695 4486 5.882000 TGTACCTAGCACTGAAATACGTCTA 59.118 40.000 0.00 0.00 0.00 2.59
3696 4487 5.909621 ACCTAGCACTGAAATACGTCTAA 57.090 39.130 0.00 0.00 0.00 2.10
3697 4488 6.276832 ACCTAGCACTGAAATACGTCTAAA 57.723 37.500 0.00 0.00 0.00 1.85
3698 4489 6.875076 ACCTAGCACTGAAATACGTCTAAAT 58.125 36.000 0.00 0.00 0.00 1.40
3699 4490 8.004087 ACCTAGCACTGAAATACGTCTAAATA 57.996 34.615 0.00 0.00 0.00 1.40
3700 4491 7.919621 ACCTAGCACTGAAATACGTCTAAATAC 59.080 37.037 0.00 0.00 0.00 1.89
3701 4492 7.919091 CCTAGCACTGAAATACGTCTAAATACA 59.081 37.037 0.00 0.00 0.00 2.29
3702 4493 9.464714 CTAGCACTGAAATACGTCTAAATACAT 57.535 33.333 0.00 0.00 0.00 2.29
3703 4494 8.354011 AGCACTGAAATACGTCTAAATACATC 57.646 34.615 0.00 0.00 0.00 3.06
3704 4495 7.438459 AGCACTGAAATACGTCTAAATACATCC 59.562 37.037 0.00 0.00 0.00 3.51
3705 4496 7.567048 GCACTGAAATACGTCTAAATACATCCG 60.567 40.741 0.00 0.00 0.00 4.18
3706 4497 7.434307 CACTGAAATACGTCTAAATACATCCGT 59.566 37.037 0.00 0.00 0.00 4.69
3707 4498 7.977853 ACTGAAATACGTCTAAATACATCCGTT 59.022 33.333 0.00 0.00 0.00 4.44
3708 4499 8.706492 TGAAATACGTCTAAATACATCCGTTT 57.294 30.769 0.00 0.00 0.00 3.60
3709 4500 9.153721 TGAAATACGTCTAAATACATCCGTTTT 57.846 29.630 0.00 0.00 0.00 2.43
3712 4503 6.579491 ACGTCTAAATACATCCGTTTTAGC 57.421 37.500 0.00 0.00 34.45 3.09
3713 4504 5.230726 ACGTCTAAATACATCCGTTTTAGCG 59.769 40.000 0.00 0.00 37.83 4.26
3714 4505 5.456497 CGTCTAAATACATCCGTTTTAGCGA 59.544 40.000 0.00 0.00 36.15 4.93
3715 4506 6.559158 CGTCTAAATACATCCGTTTTAGCGAC 60.559 42.308 0.00 0.00 36.15 5.19
3716 4507 6.254157 GTCTAAATACATCCGTTTTAGCGACA 59.746 38.462 0.00 0.00 34.45 4.35
3717 4508 5.866335 AAATACATCCGTTTTAGCGACAA 57.134 34.783 0.00 0.00 0.00 3.18
3718 4509 4.852609 ATACATCCGTTTTAGCGACAAC 57.147 40.909 0.00 0.00 0.00 3.32
3719 4510 2.762745 ACATCCGTTTTAGCGACAACT 58.237 42.857 0.00 0.00 0.00 3.16
3720 4511 3.916761 ACATCCGTTTTAGCGACAACTA 58.083 40.909 0.00 0.00 0.00 2.24
3721 4512 3.924686 ACATCCGTTTTAGCGACAACTAG 59.075 43.478 0.00 0.00 0.00 2.57
3722 4513 3.648339 TCCGTTTTAGCGACAACTAGT 57.352 42.857 0.00 0.00 0.00 2.57
3723 4514 4.764679 TCCGTTTTAGCGACAACTAGTA 57.235 40.909 0.00 0.00 0.00 1.82
3724 4515 5.119931 TCCGTTTTAGCGACAACTAGTAA 57.880 39.130 0.00 0.00 0.00 2.24
3725 4516 5.713025 TCCGTTTTAGCGACAACTAGTAAT 58.287 37.500 0.00 0.00 0.00 1.89
3726 4517 6.851609 TCCGTTTTAGCGACAACTAGTAATA 58.148 36.000 0.00 0.00 0.00 0.98
3727 4518 7.483307 TCCGTTTTAGCGACAACTAGTAATAT 58.517 34.615 0.00 0.00 0.00 1.28
3728 4519 7.433131 TCCGTTTTAGCGACAACTAGTAATATG 59.567 37.037 0.00 0.00 0.00 1.78
3729 4520 7.306399 CCGTTTTAGCGACAACTAGTAATATGG 60.306 40.741 0.00 0.00 0.00 2.74
3730 4521 7.433131 CGTTTTAGCGACAACTAGTAATATGGA 59.567 37.037 0.00 0.00 0.00 3.41
3731 4522 9.090692 GTTTTAGCGACAACTAGTAATATGGAA 57.909 33.333 0.00 0.00 0.00 3.53
3732 4523 8.638685 TTTAGCGACAACTAGTAATATGGAAC 57.361 34.615 0.00 0.00 0.00 3.62
3733 4524 5.279384 AGCGACAACTAGTAATATGGAACG 58.721 41.667 0.00 0.79 0.00 3.95
3734 4525 4.443394 GCGACAACTAGTAATATGGAACGG 59.557 45.833 0.00 0.00 0.00 4.44
3735 4526 5.734220 GCGACAACTAGTAATATGGAACGGA 60.734 44.000 0.00 0.00 0.00 4.69
3736 4527 5.913514 CGACAACTAGTAATATGGAACGGAG 59.086 44.000 0.00 0.00 0.00 4.63
3737 4528 6.158023 ACAACTAGTAATATGGAACGGAGG 57.842 41.667 0.00 0.00 0.00 4.30
3738 4529 5.895534 ACAACTAGTAATATGGAACGGAGGA 59.104 40.000 0.00 0.00 0.00 3.71
3745 4536 8.896722 AGTAATATGGAACGGAGGAAGTATAT 57.103 34.615 0.00 0.00 0.00 0.86
3789 4589 0.397941 CACTCCCTCAACTTCCAGCA 59.602 55.000 0.00 0.00 0.00 4.41
3874 4676 2.417651 GCTTTTAAATGTTACGGCCCCC 60.418 50.000 0.00 0.00 0.00 5.40
3928 4740 3.826157 TGTTCCAAGGTGATTTGTGATCC 59.174 43.478 0.00 0.00 0.00 3.36
3930 4742 2.304470 TCCAAGGTGATTTGTGATCCGA 59.696 45.455 0.00 0.00 0.00 4.55
3934 4746 5.336690 CCAAGGTGATTTGTGATCCGAAATT 60.337 40.000 0.00 0.00 0.00 1.82
3935 4747 5.314923 AGGTGATTTGTGATCCGAAATTG 57.685 39.130 0.00 0.00 0.00 2.32
3939 4751 6.460123 GGTGATTTGTGATCCGAAATTGCTAT 60.460 38.462 0.00 0.00 0.00 2.97
3940 4752 6.634436 GTGATTTGTGATCCGAAATTGCTATC 59.366 38.462 0.00 0.00 0.00 2.08
3943 4755 2.480419 GTGATCCGAAATTGCTATCCGG 59.520 50.000 13.05 13.05 41.36 5.14
3945 4757 2.234300 TCCGAAATTGCTATCCGGAC 57.766 50.000 6.12 0.00 43.47 4.79
3950 4762 2.981859 AATTGCTATCCGGACGACTT 57.018 45.000 6.12 0.00 0.00 3.01
3954 4766 5.717078 ATTGCTATCCGGACGACTTTATA 57.283 39.130 6.12 0.00 0.00 0.98
3956 4768 5.055642 TGCTATCCGGACGACTTTATATG 57.944 43.478 6.12 0.00 0.00 1.78
3959 4771 4.537135 ATCCGGACGACTTTATATGCAT 57.463 40.909 6.12 3.79 0.00 3.96
3960 4772 5.654603 ATCCGGACGACTTTATATGCATA 57.345 39.130 6.12 9.27 0.00 3.14
3961 4773 4.801891 TCCGGACGACTTTATATGCATAC 58.198 43.478 8.99 0.00 0.00 2.39
3968 4780 8.721478 GGACGACTTTATATGCATACAATTCAT 58.279 33.333 8.99 0.00 0.00 2.57
3988 4800 2.980568 TGTCCGATGTTGTAATCCCAC 58.019 47.619 0.00 0.00 0.00 4.61
3995 4807 2.993937 TGTTGTAATCCCACGATTCCC 58.006 47.619 0.00 0.00 39.49 3.97
3996 4808 1.937899 GTTGTAATCCCACGATTCCCG 59.062 52.381 0.00 0.00 39.49 5.14
3997 4809 0.179067 TGTAATCCCACGATTCCCGC 60.179 55.000 0.00 0.00 43.32 6.13
4007 4819 1.002430 ACGATTCCCGCTGATGCATAT 59.998 47.619 0.00 0.00 43.32 1.78
4010 4822 3.492383 CGATTCCCGCTGATGCATATATC 59.508 47.826 0.00 0.00 39.64 1.63
4019 4831 5.114780 GCTGATGCATATATCTGACCGAAT 58.885 41.667 0.00 0.00 39.41 3.34
4039 4851 1.616374 TGGTGATTGAGCAGTGTCGTA 59.384 47.619 0.00 0.00 0.00 3.43
4041 4853 2.609491 GGTGATTGAGCAGTGTCGTACA 60.609 50.000 0.00 0.00 0.00 2.90
4044 4856 4.152402 GTGATTGAGCAGTGTCGTACAAAT 59.848 41.667 0.00 0.00 0.00 2.32
4054 4866 6.412460 CAGTGTCGTACAAATGTCGTAAAAA 58.588 36.000 0.00 0.00 0.00 1.94
4075 4887 4.989279 AAATTGGTGCATATGTCTGACC 57.011 40.909 5.17 6.50 0.00 4.02
4076 4888 2.022764 TTGGTGCATATGTCTGACCG 57.977 50.000 5.17 0.00 0.00 4.79
4077 4889 1.190643 TGGTGCATATGTCTGACCGA 58.809 50.000 5.17 0.00 0.00 4.69
4078 4890 1.552792 TGGTGCATATGTCTGACCGAA 59.447 47.619 5.17 0.00 0.00 4.30
4079 4891 2.170397 TGGTGCATATGTCTGACCGAAT 59.830 45.455 5.17 0.00 0.00 3.34
4080 4892 2.545526 GGTGCATATGTCTGACCGAATG 59.454 50.000 5.17 7.42 0.00 2.67
4081 4893 2.545526 GTGCATATGTCTGACCGAATGG 59.454 50.000 5.17 0.00 42.84 3.16
4091 4903 2.264480 CCGAATGGTGACCGAGCA 59.736 61.111 0.00 0.00 36.23 4.26
4092 4904 1.811266 CCGAATGGTGACCGAGCAG 60.811 63.158 0.00 0.00 34.93 4.24
4093 4905 1.079819 CGAATGGTGACCGAGCAGT 60.080 57.895 0.00 0.00 34.93 4.40
4094 4906 1.354337 CGAATGGTGACCGAGCAGTG 61.354 60.000 0.00 0.00 34.93 3.66
4095 4907 0.320771 GAATGGTGACCGAGCAGTGT 60.321 55.000 0.00 0.00 34.93 3.55
4096 4908 0.320771 AATGGTGACCGAGCAGTGTC 60.321 55.000 0.00 0.00 34.93 3.67
4097 4909 2.430921 GGTGACCGAGCAGTGTCG 60.431 66.667 7.78 7.78 39.77 4.35
4098 4910 2.335369 GTGACCGAGCAGTGTCGT 59.665 61.111 12.11 3.49 38.32 4.34
4099 4911 1.577922 GTGACCGAGCAGTGTCGTA 59.422 57.895 12.11 0.00 38.32 3.43
4100 4912 0.728466 GTGACCGAGCAGTGTCGTAC 60.728 60.000 12.11 7.58 38.32 3.67
4101 4913 1.167781 TGACCGAGCAGTGTCGTACA 61.168 55.000 12.11 9.36 38.32 2.90
4102 4914 0.039798 GACCGAGCAGTGTCGTACAA 60.040 55.000 12.11 0.00 38.32 2.41
4103 4915 0.386476 ACCGAGCAGTGTCGTACAAA 59.614 50.000 12.11 0.00 38.32 2.83
4104 4916 0.782384 CCGAGCAGTGTCGTACAAAC 59.218 55.000 12.11 0.00 38.32 2.93
4193 5006 5.255687 TGATGTGTTGCCTATTGAGTCAAT 58.744 37.500 21.57 21.57 37.80 2.57
4198 5171 5.590259 GTGTTGCCTATTGAGTCAATATGGT 59.410 40.000 22.72 3.79 36.03 3.55
4285 5259 3.821033 ACAAGTGAAGCTAAATCACCCAC 59.179 43.478 12.39 0.00 46.60 4.61
4339 5313 2.996631 AGCTGTCCTGCCTAGATTTTG 58.003 47.619 0.00 0.00 0.00 2.44
4410 5387 5.578727 GCAACTACCAGTCACTTATTGAGAG 59.421 44.000 0.00 0.00 33.71 3.20
4412 5389 6.767524 ACTACCAGTCACTTATTGAGAGAG 57.232 41.667 0.00 0.00 33.71 3.20
4461 5442 6.612247 TGAGGCATAAATGTTGGTATAACG 57.388 37.500 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.312918 TCACCGACAAAATATTCTAACTCTGC 59.687 38.462 0.00 0.00 0.00 4.26
27 28 8.297426 GTCAATGAAGATAGTATGTATCACCGA 58.703 37.037 0.00 0.00 0.00 4.69
100 101 8.340618 TCAAACCTCTCCTTTATTCTCAAATG 57.659 34.615 0.00 0.00 0.00 2.32
134 139 2.124903 CGCCAGACGTACATTATCCAC 58.875 52.381 0.00 0.00 36.87 4.02
354 363 5.305386 GGGATAAATGCCCTCAAGCTTTTAT 59.695 40.000 13.83 13.83 46.94 1.40
774 795 5.070981 TGCAAGAGAAATAGGAGTAGATGGG 59.929 44.000 0.00 0.00 0.00 4.00
796 817 5.801444 GCCAATTATTTTGCCAAGAATTTGC 59.199 36.000 6.29 6.29 32.79 3.68
824 845 0.245266 CCCGTTATTTTGCCCACACC 59.755 55.000 0.00 0.00 0.00 4.16
828 1321 2.239681 ATTCCCCGTTATTTTGCCCA 57.760 45.000 0.00 0.00 0.00 5.36
836 1329 6.014156 TCAAAATGTTCCAAATTCCCCGTTAT 60.014 34.615 0.00 0.00 0.00 1.89
837 1330 5.304614 TCAAAATGTTCCAAATTCCCCGTTA 59.695 36.000 0.00 0.00 0.00 3.18
843 1336 5.928264 CACTCCTCAAAATGTTCCAAATTCC 59.072 40.000 0.00 0.00 0.00 3.01
902 1395 4.301027 CCTGATAGACGGCCGGCC 62.301 72.222 36.69 36.69 0.00 6.13
997 1490 1.679944 GGTCATGGAGGTGGACATGTG 60.680 57.143 1.15 0.00 43.68 3.21
1293 1786 3.181967 CTCTCGGCGGCGAACTTG 61.182 66.667 33.90 22.32 0.00 3.16
1457 1950 2.125350 CTCCGTCAGCTTCCTGCC 60.125 66.667 0.00 0.00 44.23 4.85
1666 2203 4.717877 TCATAATGTCCTGCCTTACCATG 58.282 43.478 0.00 0.00 0.00 3.66
1773 2322 5.189736 TCAGAGGTTAACATGGTGAAGCTAT 59.810 40.000 8.10 0.00 35.18 2.97
1847 2396 8.873144 AGGCCATATGCTTTCACAAATATATTT 58.127 29.630 5.01 4.81 40.92 1.40
1849 2398 7.892241 AGAGGCCATATGCTTTCACAAATATAT 59.108 33.333 5.01 0.00 40.92 0.86
1913 2462 5.818136 TGACTTTTTGTAGCCAGATATGC 57.182 39.130 0.00 0.00 0.00 3.14
1978 2535 7.752239 GCCATACATGTAAATGATTATGAGCAC 59.248 37.037 10.14 0.00 0.00 4.40
2114 2676 7.683437 AAGCTACAGATTTACAGGGTTAAAC 57.317 36.000 0.00 0.00 0.00 2.01
2145 2715 8.579006 TCTTGCAGAAAATGAAAGTTGTATCAT 58.421 29.630 0.00 0.00 44.16 2.45
2183 2753 4.751098 CGGTCTACACTATCTACAGGACTC 59.249 50.000 0.00 0.00 0.00 3.36
2336 2906 5.418840 CCTGTTACCAAATCCAAGCATTACT 59.581 40.000 0.00 0.00 0.00 2.24
2434 3008 2.519771 ACATGGATGCACTGACCAAT 57.480 45.000 0.00 0.00 37.24 3.16
2459 3162 7.857569 TGAAGCTAACATAAATATGGCGTTAC 58.142 34.615 5.48 0.00 38.00 2.50
2489 3258 2.862530 GCGCGGCTGTCTAGATGATTTA 60.863 50.000 8.83 0.00 0.00 1.40
2508 3278 3.792956 GCCAAAATCACATGTTATCTGCG 59.207 43.478 0.00 0.00 0.00 5.18
2541 3311 7.120579 CAGGCCACATAACTGAACTTATGTAAA 59.879 37.037 5.01 0.00 42.82 2.01
2637 3411 4.534500 TGGAGATGCCCTAACTAAACTTGA 59.466 41.667 0.00 0.00 34.97 3.02
2661 3435 2.818132 GCTGCTAGCGTCTCCCAT 59.182 61.111 10.77 0.00 0.00 4.00
2696 3470 7.448469 AGCGCAAGATTACTGGGATATTTATTT 59.552 33.333 11.47 0.00 43.02 1.40
2717 3491 1.667830 CGTTGGAAGAGGAAGCGCA 60.668 57.895 11.47 0.00 0.00 6.09
2733 3507 2.027169 GCTATTAGCGTCCGCCGT 59.973 61.111 8.23 0.00 43.17 5.68
2768 3542 3.970610 CGTGAGTTGAAATGCTTTGTCAG 59.029 43.478 0.00 0.00 0.00 3.51
2777 3551 0.443869 CCTCCGCGTGAGTTGAAATG 59.556 55.000 18.94 3.26 39.65 2.32
2778 3552 0.320374 TCCTCCGCGTGAGTTGAAAT 59.680 50.000 18.94 0.00 39.65 2.17
2798 3572 2.289694 TGAGCGCTAGCCTTTTCTTTCT 60.290 45.455 11.50 0.00 46.67 2.52
2819 3593 1.071471 CGACACCAAAGCTGGAGGT 59.929 57.895 0.00 0.00 46.92 3.85
2833 3607 0.669318 GACAAATCCTGGCGTCGACA 60.669 55.000 17.16 0.00 0.00 4.35
2854 3640 3.025978 CCTGCCCAATCAGCAATAAGAA 58.974 45.455 0.00 0.00 40.35 2.52
2858 3644 3.395607 AGTATCCTGCCCAATCAGCAATA 59.604 43.478 0.00 0.00 40.35 1.90
2860 3646 1.565759 AGTATCCTGCCCAATCAGCAA 59.434 47.619 0.00 0.00 40.35 3.91
2864 3650 2.972713 GGACTAGTATCCTGCCCAATCA 59.027 50.000 0.00 0.00 35.68 2.57
2878 3664 1.551452 GAGTGAGCACCAGGACTAGT 58.449 55.000 0.00 0.00 0.00 2.57
3037 3827 5.353400 GCAGGAATTGGTACCTACAAAGTAC 59.647 44.000 14.36 0.00 39.51 2.73
3101 3891 1.112315 CATAGTCCTCTGCCGCTCCT 61.112 60.000 0.00 0.00 0.00 3.69
3107 3897 5.799827 AGATAGTTTCATAGTCCTCTGCC 57.200 43.478 0.00 0.00 0.00 4.85
3416 4206 5.371526 AGCAAATCAGAAGTCTTCTTGTCA 58.628 37.500 12.62 0.00 38.11 3.58
3449 4239 6.692849 TCTCCATCATCAAGTATAGCCATT 57.307 37.500 0.00 0.00 0.00 3.16
3536 4326 4.762289 AGATCGAGCTTAAACCTTGGAT 57.238 40.909 0.00 0.00 0.00 3.41
3576 4367 1.026718 CAGGGAGGAATGCAACCGTC 61.027 60.000 0.00 0.00 0.00 4.79
3639 4430 8.318649 TTGAGCGACAACTAATATGGAACAGAG 61.319 40.741 0.00 0.00 35.89 3.35
3640 4431 6.573485 TTGAGCGACAACTAATATGGAACAGA 60.573 38.462 0.00 0.00 35.89 3.41
3641 4432 5.580691 TTGAGCGACAACTAATATGGAACAG 59.419 40.000 0.00 0.00 35.89 3.16
3642 4433 5.483811 TTGAGCGACAACTAATATGGAACA 58.516 37.500 0.00 0.00 36.63 3.18
3643 4434 6.128391 TGTTTGAGCGACAACTAATATGGAAC 60.128 38.462 0.00 0.00 38.29 3.62
3644 4435 5.935206 TGTTTGAGCGACAACTAATATGGAA 59.065 36.000 0.00 0.00 38.29 3.53
3645 4436 5.483811 TGTTTGAGCGACAACTAATATGGA 58.516 37.500 0.00 0.00 38.29 3.41
3646 4437 5.580691 TCTGTTTGAGCGACAACTAATATGG 59.419 40.000 0.00 0.00 38.29 2.74
3647 4438 6.647212 TCTGTTTGAGCGACAACTAATATG 57.353 37.500 0.00 0.00 38.29 1.78
3648 4439 6.818644 ACATCTGTTTGAGCGACAACTAATAT 59.181 34.615 0.00 0.00 38.29 1.28
3649 4440 6.163476 ACATCTGTTTGAGCGACAACTAATA 58.837 36.000 0.00 0.00 38.29 0.98
3650 4441 4.997395 ACATCTGTTTGAGCGACAACTAAT 59.003 37.500 0.00 0.00 38.29 1.73
3651 4442 4.377021 ACATCTGTTTGAGCGACAACTAA 58.623 39.130 0.00 0.00 38.29 2.24
3652 4443 3.990092 ACATCTGTTTGAGCGACAACTA 58.010 40.909 0.00 0.00 38.29 2.24
3653 4444 2.838736 ACATCTGTTTGAGCGACAACT 58.161 42.857 0.00 0.00 38.29 3.16
3654 4445 3.120649 GGTACATCTGTTTGAGCGACAAC 60.121 47.826 0.00 0.00 38.29 3.32
3655 4446 3.064207 GGTACATCTGTTTGAGCGACAA 58.936 45.455 0.00 0.00 36.65 3.18
3656 4447 2.299013 AGGTACATCTGTTTGAGCGACA 59.701 45.455 0.00 0.00 0.00 4.35
3657 4448 2.960819 AGGTACATCTGTTTGAGCGAC 58.039 47.619 0.00 0.00 0.00 5.19
3658 4449 3.428999 GCTAGGTACATCTGTTTGAGCGA 60.429 47.826 0.00 0.00 0.00 4.93
3659 4450 2.860735 GCTAGGTACATCTGTTTGAGCG 59.139 50.000 0.00 0.00 0.00 5.03
3660 4451 3.619038 GTGCTAGGTACATCTGTTTGAGC 59.381 47.826 0.00 0.00 0.00 4.26
3661 4452 4.867047 CAGTGCTAGGTACATCTGTTTGAG 59.133 45.833 0.00 0.00 0.00 3.02
3662 4453 4.526650 TCAGTGCTAGGTACATCTGTTTGA 59.473 41.667 0.00 0.00 0.00 2.69
3663 4454 4.820897 TCAGTGCTAGGTACATCTGTTTG 58.179 43.478 0.00 0.00 0.00 2.93
3664 4455 5.483685 TTCAGTGCTAGGTACATCTGTTT 57.516 39.130 0.00 0.00 0.00 2.83
3665 4456 5.483685 TTTCAGTGCTAGGTACATCTGTT 57.516 39.130 0.00 0.00 0.00 3.16
3666 4457 5.683876 ATTTCAGTGCTAGGTACATCTGT 57.316 39.130 0.00 0.00 0.00 3.41
3667 4458 5.687730 CGTATTTCAGTGCTAGGTACATCTG 59.312 44.000 0.00 0.00 0.00 2.90
3668 4459 5.360144 ACGTATTTCAGTGCTAGGTACATCT 59.640 40.000 0.00 0.00 0.00 2.90
3669 4460 5.589192 ACGTATTTCAGTGCTAGGTACATC 58.411 41.667 0.00 0.00 0.00 3.06
3670 4461 5.360144 AGACGTATTTCAGTGCTAGGTACAT 59.640 40.000 0.00 0.00 0.00 2.29
3671 4462 4.703575 AGACGTATTTCAGTGCTAGGTACA 59.296 41.667 0.00 0.00 0.00 2.90
3672 4463 5.246145 AGACGTATTTCAGTGCTAGGTAC 57.754 43.478 0.00 0.00 0.00 3.34
3673 4464 7.395190 TTTAGACGTATTTCAGTGCTAGGTA 57.605 36.000 0.00 0.00 0.00 3.08
3674 4465 5.909621 TTAGACGTATTTCAGTGCTAGGT 57.090 39.130 0.00 0.00 0.00 3.08
3675 4466 7.919091 TGTATTTAGACGTATTTCAGTGCTAGG 59.081 37.037 0.00 0.00 0.00 3.02
3676 4467 8.851960 TGTATTTAGACGTATTTCAGTGCTAG 57.148 34.615 0.00 0.00 0.00 3.42
3677 4468 9.459640 GATGTATTTAGACGTATTTCAGTGCTA 57.540 33.333 0.00 0.00 0.00 3.49
3678 4469 7.438459 GGATGTATTTAGACGTATTTCAGTGCT 59.562 37.037 0.00 0.00 0.00 4.40
3679 4470 7.564988 GGATGTATTTAGACGTATTTCAGTGC 58.435 38.462 0.00 0.00 0.00 4.40
3680 4471 7.434307 ACGGATGTATTTAGACGTATTTCAGTG 59.566 37.037 0.00 0.00 32.30 3.66
3681 4472 7.486647 ACGGATGTATTTAGACGTATTTCAGT 58.513 34.615 0.00 0.00 32.30 3.41
3682 4473 7.925703 ACGGATGTATTTAGACGTATTTCAG 57.074 36.000 0.00 0.00 32.30 3.02
3683 4474 8.706492 AAACGGATGTATTTAGACGTATTTCA 57.294 30.769 0.00 0.00 33.85 2.69
3686 4477 8.758715 GCTAAAACGGATGTATTTAGACGTATT 58.241 33.333 8.30 0.00 38.37 1.89
3687 4478 7.113965 CGCTAAAACGGATGTATTTAGACGTAT 59.886 37.037 8.30 0.00 38.37 3.06
3688 4479 6.414694 CGCTAAAACGGATGTATTTAGACGTA 59.585 38.462 8.30 0.00 38.37 3.57
3689 4480 5.230726 CGCTAAAACGGATGTATTTAGACGT 59.769 40.000 8.30 0.00 38.37 4.34
3690 4481 5.456497 TCGCTAAAACGGATGTATTTAGACG 59.544 40.000 8.30 10.14 38.37 4.18
3691 4482 6.254157 TGTCGCTAAAACGGATGTATTTAGAC 59.746 38.462 8.30 1.14 38.37 2.59
3692 4483 6.331845 TGTCGCTAAAACGGATGTATTTAGA 58.668 36.000 8.30 0.00 38.37 2.10
3693 4484 6.578020 TGTCGCTAAAACGGATGTATTTAG 57.422 37.500 0.00 0.00 38.86 1.85
3694 4485 6.591062 AGTTGTCGCTAAAACGGATGTATTTA 59.409 34.615 0.00 0.00 0.00 1.40
3695 4486 5.410439 AGTTGTCGCTAAAACGGATGTATTT 59.590 36.000 0.00 0.00 0.00 1.40
3696 4487 4.933400 AGTTGTCGCTAAAACGGATGTATT 59.067 37.500 0.00 0.00 0.00 1.89
3697 4488 4.501071 AGTTGTCGCTAAAACGGATGTAT 58.499 39.130 0.00 0.00 0.00 2.29
3698 4489 3.916761 AGTTGTCGCTAAAACGGATGTA 58.083 40.909 0.00 0.00 0.00 2.29
3699 4490 2.762745 AGTTGTCGCTAAAACGGATGT 58.237 42.857 0.00 0.00 0.00 3.06
3700 4491 3.924686 ACTAGTTGTCGCTAAAACGGATG 59.075 43.478 0.00 0.00 0.00 3.51
3701 4492 4.184079 ACTAGTTGTCGCTAAAACGGAT 57.816 40.909 0.00 0.00 0.00 4.18
3702 4493 3.648339 ACTAGTTGTCGCTAAAACGGA 57.352 42.857 0.00 0.00 0.00 4.69
3703 4494 7.306399 CCATATTACTAGTTGTCGCTAAAACGG 60.306 40.741 0.00 0.00 0.00 4.44
3704 4495 7.433131 TCCATATTACTAGTTGTCGCTAAAACG 59.567 37.037 0.00 0.00 0.00 3.60
3705 4496 8.638685 TCCATATTACTAGTTGTCGCTAAAAC 57.361 34.615 0.00 0.00 0.00 2.43
3706 4497 9.090692 GTTCCATATTACTAGTTGTCGCTAAAA 57.909 33.333 0.00 0.00 0.00 1.52
3707 4498 7.433131 CGTTCCATATTACTAGTTGTCGCTAAA 59.567 37.037 0.00 0.00 0.00 1.85
3708 4499 6.914215 CGTTCCATATTACTAGTTGTCGCTAA 59.086 38.462 0.00 0.00 0.00 3.09
3709 4500 6.432936 CGTTCCATATTACTAGTTGTCGCTA 58.567 40.000 0.00 0.00 0.00 4.26
3710 4501 5.279384 CGTTCCATATTACTAGTTGTCGCT 58.721 41.667 0.00 0.00 0.00 4.93
3711 4502 4.443394 CCGTTCCATATTACTAGTTGTCGC 59.557 45.833 0.00 0.00 0.00 5.19
3712 4503 5.824429 TCCGTTCCATATTACTAGTTGTCG 58.176 41.667 0.00 0.00 0.00 4.35
3713 4504 6.040166 TCCTCCGTTCCATATTACTAGTTGTC 59.960 42.308 0.00 0.00 0.00 3.18
3714 4505 5.895534 TCCTCCGTTCCATATTACTAGTTGT 59.104 40.000 0.00 0.00 0.00 3.32
3715 4506 6.401047 TCCTCCGTTCCATATTACTAGTTG 57.599 41.667 0.00 0.00 0.00 3.16
3716 4507 6.610425 ACTTCCTCCGTTCCATATTACTAGTT 59.390 38.462 0.00 0.00 0.00 2.24
3717 4508 6.134754 ACTTCCTCCGTTCCATATTACTAGT 58.865 40.000 0.00 0.00 0.00 2.57
3718 4509 6.651975 ACTTCCTCCGTTCCATATTACTAG 57.348 41.667 0.00 0.00 0.00 2.57
3719 4510 9.986157 ATATACTTCCTCCGTTCCATATTACTA 57.014 33.333 0.00 0.00 0.00 1.82
3720 4511 8.896722 ATATACTTCCTCCGTTCCATATTACT 57.103 34.615 0.00 0.00 0.00 2.24
3726 4517 8.656806 TGAAATAATATACTTCCTCCGTTCCAT 58.343 33.333 0.00 0.00 0.00 3.41
3727 4518 8.025270 TGAAATAATATACTTCCTCCGTTCCA 57.975 34.615 0.00 0.00 0.00 3.53
3728 4519 8.365647 TCTGAAATAATATACTTCCTCCGTTCC 58.634 37.037 0.00 0.00 0.00 3.62
3729 4520 9.413048 CTCTGAAATAATATACTTCCTCCGTTC 57.587 37.037 0.00 0.00 0.00 3.95
3730 4521 8.925338 ACTCTGAAATAATATACTTCCTCCGTT 58.075 33.333 0.00 0.00 0.00 4.44
3731 4522 8.480133 ACTCTGAAATAATATACTTCCTCCGT 57.520 34.615 0.00 0.00 0.00 4.69
3745 4536 9.554395 TGTCTGAAACACATTACTCTGAAATAA 57.446 29.630 0.00 0.00 31.20 1.40
3879 4681 5.532406 ACAGTAACAGAATGCAACAGACATT 59.468 36.000 0.00 0.00 42.53 2.71
3883 4685 4.702831 TGACAGTAACAGAATGCAACAGA 58.297 39.130 0.00 0.00 42.53 3.41
3928 4740 1.521423 GTCGTCCGGATAGCAATTTCG 59.479 52.381 7.81 2.69 0.00 3.46
3930 4742 2.981859 AGTCGTCCGGATAGCAATTT 57.018 45.000 7.81 0.00 0.00 1.82
3934 4746 4.617530 GCATATAAAGTCGTCCGGATAGCA 60.618 45.833 7.81 0.00 0.00 3.49
3935 4747 3.858238 GCATATAAAGTCGTCCGGATAGC 59.142 47.826 7.81 0.00 0.00 2.97
3939 4751 4.278919 TGTATGCATATAAAGTCGTCCGGA 59.721 41.667 10.16 0.00 0.00 5.14
3940 4752 4.552355 TGTATGCATATAAAGTCGTCCGG 58.448 43.478 10.16 0.00 0.00 5.14
3943 4755 9.533983 CATGAATTGTATGCATATAAAGTCGTC 57.466 33.333 18.29 11.53 0.00 4.20
3945 4757 9.533983 GACATGAATTGTATGCATATAAAGTCG 57.466 33.333 18.29 11.00 39.18 4.18
3950 4762 8.667463 CATCGGACATGAATTGTATGCATATAA 58.333 33.333 16.95 16.95 39.18 0.98
3954 4766 4.823442 ACATCGGACATGAATTGTATGCAT 59.177 37.500 3.79 3.79 39.18 3.96
3956 4768 4.818534 ACATCGGACATGAATTGTATGC 57.181 40.909 0.00 0.00 39.18 3.14
3959 4771 7.011950 GGATTACAACATCGGACATGAATTGTA 59.988 37.037 0.00 1.02 39.18 2.41
3960 4772 6.183360 GGATTACAACATCGGACATGAATTGT 60.183 38.462 0.00 1.93 42.79 2.71
3961 4773 6.201517 GGATTACAACATCGGACATGAATTG 58.798 40.000 0.00 0.00 0.00 2.32
3968 4780 2.675603 CGTGGGATTACAACATCGGACA 60.676 50.000 0.00 0.00 0.00 4.02
3988 4800 1.730501 ATATGCATCAGCGGGAATCG 58.269 50.000 0.19 0.00 46.23 3.34
3995 4807 2.856557 CGGTCAGATATATGCATCAGCG 59.143 50.000 0.19 0.00 46.23 5.18
3996 4808 4.115401 TCGGTCAGATATATGCATCAGC 57.885 45.455 0.19 0.00 42.57 4.26
3997 4809 5.522824 CCATTCGGTCAGATATATGCATCAG 59.477 44.000 0.19 0.00 0.00 2.90
4007 4819 4.740634 GCTCAATCACCATTCGGTCAGATA 60.741 45.833 0.00 0.00 44.71 1.98
4010 4822 1.667724 GCTCAATCACCATTCGGTCAG 59.332 52.381 0.00 0.00 44.71 3.51
4019 4831 0.392706 ACGACACTGCTCAATCACCA 59.607 50.000 0.00 0.00 0.00 4.17
4054 4866 3.378112 CGGTCAGACATATGCACCAATTT 59.622 43.478 1.58 0.00 0.00 1.82
4055 4867 2.945008 CGGTCAGACATATGCACCAATT 59.055 45.455 1.58 0.00 0.00 2.32
4056 4868 2.170397 TCGGTCAGACATATGCACCAAT 59.830 45.455 1.58 0.00 0.00 3.16
4057 4869 1.552792 TCGGTCAGACATATGCACCAA 59.447 47.619 1.58 0.00 0.00 3.67
4058 4870 1.190643 TCGGTCAGACATATGCACCA 58.809 50.000 1.58 0.00 0.00 4.17
4059 4871 2.309528 TTCGGTCAGACATATGCACC 57.690 50.000 1.58 3.34 0.00 5.01
4060 4872 2.545526 CCATTCGGTCAGACATATGCAC 59.454 50.000 1.58 0.00 0.00 4.57
4061 4873 2.170397 ACCATTCGGTCAGACATATGCA 59.830 45.455 1.58 0.00 44.71 3.96
4062 4874 2.545526 CACCATTCGGTCAGACATATGC 59.454 50.000 1.58 0.00 44.71 3.14
4063 4875 3.804325 GTCACCATTCGGTCAGACATATG 59.196 47.826 2.17 0.00 44.71 1.78
4064 4876 3.181465 GGTCACCATTCGGTCAGACATAT 60.181 47.826 2.17 0.00 44.71 1.78
4065 4877 2.167693 GGTCACCATTCGGTCAGACATA 59.832 50.000 2.17 0.00 44.71 2.29
4066 4878 1.066143 GGTCACCATTCGGTCAGACAT 60.066 52.381 2.17 0.00 44.71 3.06
4067 4879 0.320374 GGTCACCATTCGGTCAGACA 59.680 55.000 2.17 0.00 44.71 3.41
4068 4880 0.736325 CGGTCACCATTCGGTCAGAC 60.736 60.000 0.00 0.00 44.71 3.51
4069 4881 0.896479 TCGGTCACCATTCGGTCAGA 60.896 55.000 0.00 0.00 44.71 3.27
4070 4882 0.458543 CTCGGTCACCATTCGGTCAG 60.459 60.000 0.00 0.00 44.71 3.51
4071 4883 1.589630 CTCGGTCACCATTCGGTCA 59.410 57.895 0.00 0.00 44.71 4.02
4072 4884 1.810030 GCTCGGTCACCATTCGGTC 60.810 63.158 0.00 0.00 44.71 4.79
4074 4886 1.811266 CTGCTCGGTCACCATTCGG 60.811 63.158 0.00 0.00 38.77 4.30
4075 4887 1.079819 ACTGCTCGGTCACCATTCG 60.080 57.895 0.00 0.00 0.00 3.34
4076 4888 0.320771 ACACTGCTCGGTCACCATTC 60.321 55.000 0.00 0.00 0.00 2.67
4077 4889 0.320771 GACACTGCTCGGTCACCATT 60.321 55.000 0.00 0.00 34.22 3.16
4078 4890 1.293498 GACACTGCTCGGTCACCAT 59.707 57.895 0.00 0.00 34.22 3.55
4079 4891 2.734591 GACACTGCTCGGTCACCA 59.265 61.111 0.00 0.00 34.22 4.17
4080 4892 1.859427 TACGACACTGCTCGGTCACC 61.859 60.000 0.00 0.00 38.02 4.02
4081 4893 0.728466 GTACGACACTGCTCGGTCAC 60.728 60.000 0.00 0.00 38.02 3.67
4082 4894 1.167781 TGTACGACACTGCTCGGTCA 61.168 55.000 0.00 0.00 38.02 4.02
4083 4895 0.039798 TTGTACGACACTGCTCGGTC 60.040 55.000 0.00 0.00 38.02 4.79
4084 4896 0.386476 TTTGTACGACACTGCTCGGT 59.614 50.000 0.00 0.00 38.02 4.69
4085 4897 0.782384 GTTTGTACGACACTGCTCGG 59.218 55.000 0.00 0.00 38.02 4.63
4116 4928 0.179045 GTGCTAGGCCCACGATGATT 60.179 55.000 0.00 0.00 0.00 2.57
4126 4938 3.003480 CACAAAAGAGTAGTGCTAGGCC 58.997 50.000 0.00 0.00 0.00 5.19
4193 5006 3.248024 ACCAAGTGAAGTCTCCACCATA 58.752 45.455 0.00 0.00 35.23 2.74
4198 5171 2.771943 AGTGAACCAAGTGAAGTCTCCA 59.228 45.455 0.00 0.00 0.00 3.86
4355 5332 1.081481 TACTCAGGTCCCAGGTCAGA 58.919 55.000 0.00 0.00 0.00 3.27
4461 5442 7.765307 TGAGTAAATGAGAAATTGAGAATGCC 58.235 34.615 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.