Multiple sequence alignment - TraesCS5A01G531900

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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 TraesCS5A01G531900 chr5A 100.000 2396 0 0 1 2396 689916786 689914391 0.000000e+00 4425.0
1 TraesCS5A01G531900 chr5A 84.699 830 79 23 1554 2353 689891798 689890987 0.000000e+00 785.0
2 TraesCS5A01G531900 chr5A 83.838 198 16 8 938 1134 689892147 689891965 8.800000e-40 174.0
3 TraesCS5A01G531900 chr4D 86.623 1667 116 36 754 2353 505433316 505431690 0.000000e+00 1744.0
4 TraesCS5A01G531900 chr4D 94.809 366 18 1 1 366 505433919 505433555 9.610000e-159 569.0
5 TraesCS5A01G531900 chr4D 98.198 111 1 1 568 678 57472699 57472590 2.430000e-45 193.0
6 TraesCS5A01G531900 chr4D 97.619 42 1 0 698 739 505433356 505433315 3.300000e-09 73.1
7 TraesCS5A01G531900 chr4B 85.404 966 95 20 1419 2353 652284123 652283173 0.000000e+00 961.0
8 TraesCS5A01G531900 chr4B 87.931 638 37 17 768 1369 652284767 652284134 0.000000e+00 715.0
9 TraesCS5A01G531900 chr4B 95.641 390 16 1 1 390 652288816 652288428 2.020000e-175 625.0
10 TraesCS5A01G531900 chr4B 99.057 106 1 0 573 678 565865961 565865856 8.740000e-45 191.0
11 TraesCS5A01G531900 chr4B 100.000 43 0 0 703 745 652284807 652284765 1.970000e-11 80.5
12 TraesCS5A01G531900 chr5B 98.182 110 1 1 569 678 78422389 78422281 8.740000e-45 191.0
13 TraesCS5A01G531900 chr6B 96.491 114 4 0 570 683 159410492 159410605 3.140000e-44 189.0
14 TraesCS5A01G531900 chr6B 94.118 119 7 0 560 678 590562194 590562076 5.260000e-42 182.0
15 TraesCS5A01G531900 chr3B 96.491 114 4 0 565 678 217773160 217773273 3.140000e-44 189.0
16 TraesCS5A01G531900 chr2A 95.000 120 3 3 561 678 448553061 448553179 4.070000e-43 185.0
17 TraesCS5A01G531900 chr1B 96.460 113 3 1 566 678 359907234 359907345 4.070000e-43 185.0
18 TraesCS5A01G531900 chr4A 95.614 114 5 0 565 678 4341147 4341260 1.460000e-42 183.0
19 TraesCS5A01G531900 chrUn 84.404 109 17 0 114 222 83950835 83950727 9.060000e-20 108.0
20 TraesCS5A01G531900 chr7B 84.404 109 17 0 114 222 2101634 2101742 9.060000e-20 108.0
21 TraesCS5A01G531900 chr7B 81.651 109 20 0 114 222 2076788 2076896 9.120000e-15 91.6


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 TraesCS5A01G531900 chr5A 689914391 689916786 2395 True 4425.000000 4425 100.0000 1 2396 1 chr5A.!!$R1 2395
1 TraesCS5A01G531900 chr5A 689890987 689892147 1160 True 479.500000 785 84.2685 938 2353 2 chr5A.!!$R2 1415
2 TraesCS5A01G531900 chr4D 505431690 505433919 2229 True 795.366667 1744 93.0170 1 2353 3 chr4D.!!$R2 2352
3 TraesCS5A01G531900 chr4B 652283173 652288816 5643 True 595.375000 961 92.2440 1 2353 4 chr4B.!!$R2 2352

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
689 4106 0.030908 GAGGGAGTCGATAAGGTGCG 59.969 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 5887 0.700564 ACATGTCTTGATGCCCCAGT 59.299 50.0 0.0 0.0 0.0 4.0 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
112 113 1.597027 CCTGCTCGTGGACGGTTTT 60.597 57.895 0.00 0.00 40.29 2.43
124 125 2.325082 CGGTTTTGGTCTGGAGCCG 61.325 63.158 0.00 0.00 0.00 5.52
175 176 3.266772 TGAAGCATGGGGAGTACTTCATT 59.733 43.478 2.92 0.00 41.20 2.57
295 296 1.372582 AGGTGCAAGCATGTGTATCG 58.627 50.000 0.00 0.00 36.26 2.92
317 318 7.542534 TCGTACGATTAATTGCAATAAGGTT 57.457 32.000 15.28 0.00 0.00 3.50
355 356 6.627953 CGCCATCTCCAATTGTAATCCTTTTT 60.628 38.462 4.43 0.00 0.00 1.94
390 391 5.209944 GCGAGAATTGCCTAGTATAATGC 57.790 43.478 0.00 0.00 40.55 3.56
392 393 4.201628 CGAGAATTGCCTAGTATAATGCGC 60.202 45.833 0.00 0.00 0.00 6.09
393 394 4.899502 AGAATTGCCTAGTATAATGCGCT 58.100 39.130 9.73 0.00 0.00 5.92
396 405 4.594123 TTGCCTAGTATAATGCGCTACA 57.406 40.909 9.73 0.00 0.00 2.74
412 421 3.981416 CGCTACAACATATAGATGTGCGT 59.019 43.478 19.08 14.61 45.93 5.24
430 446 1.303643 TGCCCACACACACACACAA 60.304 52.632 0.00 0.00 0.00 3.33
431 447 0.895559 TGCCCACACACACACACAAA 60.896 50.000 0.00 0.00 0.00 2.83
447 3861 1.333619 ACAAACCGCACTCATTCACAC 59.666 47.619 0.00 0.00 0.00 3.82
463 3877 6.307077 TCATTCACACGTCGTTTACTGAATAG 59.693 38.462 13.15 9.88 31.96 1.73
464 3878 5.112220 TCACACGTCGTTTACTGAATAGT 57.888 39.130 0.00 0.00 40.99 2.12
472 3886 3.546670 CGTTTACTGAATAGTGGAGTCGC 59.453 47.826 0.00 0.00 37.78 5.19
498 3914 3.251487 TCTTCACGACTACGAATGTCACA 59.749 43.478 0.00 0.00 42.66 3.58
505 3921 6.472486 CACGACTACGAATGTCACAATTATCT 59.528 38.462 0.00 0.00 42.66 1.98
560 3977 2.229792 TGGTCTGCCATGAAGAACAAC 58.770 47.619 12.21 0.00 38.42 3.32
565 3982 1.523154 GCCATGAAGAACAACCCGCA 61.523 55.000 0.00 0.00 0.00 5.69
572 3989 3.320541 TGAAGAACAACCCGCAAAATGAT 59.679 39.130 0.00 0.00 0.00 2.45
575 3992 4.079253 AGAACAACCCGCAAAATGATACT 58.921 39.130 0.00 0.00 0.00 2.12
576 3993 4.156008 AGAACAACCCGCAAAATGATACTC 59.844 41.667 0.00 0.00 0.00 2.59
577 3994 2.752903 ACAACCCGCAAAATGATACTCC 59.247 45.455 0.00 0.00 0.00 3.85
578 3995 2.052782 ACCCGCAAAATGATACTCCC 57.947 50.000 0.00 0.00 0.00 4.30
579 3996 1.564348 ACCCGCAAAATGATACTCCCT 59.436 47.619 0.00 0.00 0.00 4.20
580 3997 2.222027 CCCGCAAAATGATACTCCCTC 58.778 52.381 0.00 0.00 0.00 4.30
581 3998 2.222027 CCGCAAAATGATACTCCCTCC 58.778 52.381 0.00 0.00 0.00 4.30
582 3999 1.867233 CGCAAAATGATACTCCCTCCG 59.133 52.381 0.00 0.00 0.00 4.63
583 4000 2.741878 CGCAAAATGATACTCCCTCCGT 60.742 50.000 0.00 0.00 0.00 4.69
584 4001 3.279434 GCAAAATGATACTCCCTCCGTT 58.721 45.455 0.00 0.00 0.00 4.44
585 4002 3.312697 GCAAAATGATACTCCCTCCGTTC 59.687 47.826 0.00 0.00 0.00 3.95
586 4003 3.840124 AAATGATACTCCCTCCGTTCC 57.160 47.619 0.00 0.00 0.00 3.62
587 4004 1.329256 ATGATACTCCCTCCGTTCCG 58.671 55.000 0.00 0.00 0.00 4.30
588 4005 0.256752 TGATACTCCCTCCGTTCCGA 59.743 55.000 0.00 0.00 0.00 4.55
589 4006 1.341285 TGATACTCCCTCCGTTCCGAA 60.341 52.381 0.00 0.00 0.00 4.30
590 4007 1.962100 GATACTCCCTCCGTTCCGAAT 59.038 52.381 0.00 0.00 0.00 3.34
591 4008 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
592 4009 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
593 4010 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
594 4011 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
595 4012 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
596 4013 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
597 4014 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
598 4015 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
599 4016 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
600 4017 2.030007 TCCGTTCCGAATTACTTGTCGT 60.030 45.455 0.00 0.00 35.48 4.34
601 4018 3.190327 TCCGTTCCGAATTACTTGTCGTA 59.810 43.478 0.00 0.00 35.48 3.43
602 4019 3.301642 CCGTTCCGAATTACTTGTCGTAC 59.698 47.826 0.00 0.00 35.48 3.67
603 4020 3.002732 CGTTCCGAATTACTTGTCGTACG 60.003 47.826 9.53 9.53 37.20 3.67
604 4021 3.829886 TCCGAATTACTTGTCGTACGT 57.170 42.857 16.05 0.00 35.48 3.57
605 4022 4.937696 TCCGAATTACTTGTCGTACGTA 57.062 40.909 16.05 2.87 35.48 3.57
606 4023 5.484173 TCCGAATTACTTGTCGTACGTAT 57.516 39.130 16.05 0.22 35.48 3.06
607 4024 5.265477 TCCGAATTACTTGTCGTACGTATG 58.735 41.667 16.05 8.56 35.48 2.39
608 4025 4.438797 CCGAATTACTTGTCGTACGTATGG 59.561 45.833 16.05 7.26 35.48 2.74
609 4026 5.265477 CGAATTACTTGTCGTACGTATGGA 58.735 41.667 16.05 5.16 32.61 3.41
610 4027 5.911280 CGAATTACTTGTCGTACGTATGGAT 59.089 40.000 16.05 0.78 32.61 3.41
611 4028 6.129535 CGAATTACTTGTCGTACGTATGGATG 60.130 42.308 16.05 6.93 32.61 3.51
612 4029 5.565592 TTACTTGTCGTACGTATGGATGT 57.434 39.130 16.05 11.53 0.00 3.06
613 4030 6.676237 TTACTTGTCGTACGTATGGATGTA 57.324 37.500 16.05 10.72 0.00 2.29
614 4031 5.762825 ACTTGTCGTACGTATGGATGTAT 57.237 39.130 16.05 0.00 29.78 2.29
615 4032 5.755813 ACTTGTCGTACGTATGGATGTATC 58.244 41.667 16.05 0.00 29.78 2.24
616 4033 5.530171 ACTTGTCGTACGTATGGATGTATCT 59.470 40.000 16.05 0.00 29.78 1.98
617 4034 6.707608 ACTTGTCGTACGTATGGATGTATCTA 59.292 38.462 16.05 0.00 29.78 1.98
618 4035 6.716898 TGTCGTACGTATGGATGTATCTAG 57.283 41.667 16.05 0.00 29.78 2.43
619 4036 6.458210 TGTCGTACGTATGGATGTATCTAGA 58.542 40.000 16.05 0.00 29.78 2.43
620 4037 7.101700 TGTCGTACGTATGGATGTATCTAGAT 58.898 38.462 16.05 10.73 29.78 1.98
621 4038 7.064253 TGTCGTACGTATGGATGTATCTAGATG 59.936 40.741 15.79 0.00 29.78 2.90
622 4039 7.064371 GTCGTACGTATGGATGTATCTAGATGT 59.936 40.741 15.79 3.16 34.03 3.06
623 4040 8.253113 TCGTACGTATGGATGTATCTAGATGTA 58.747 37.037 15.79 4.44 32.29 2.29
624 4041 9.043079 CGTACGTATGGATGTATCTAGATGTAT 57.957 37.037 15.79 9.11 34.84 2.29
652 4069 9.529325 TTAGTTCTAGATACATCCATTTCAACG 57.471 33.333 0.00 0.00 0.00 4.10
653 4070 7.782049 AGTTCTAGATACATCCATTTCAACGA 58.218 34.615 0.00 0.00 0.00 3.85
654 4071 7.707035 AGTTCTAGATACATCCATTTCAACGAC 59.293 37.037 0.00 0.00 0.00 4.34
655 4072 6.206498 TCTAGATACATCCATTTCAACGACG 58.794 40.000 0.00 0.00 0.00 5.12
656 4073 5.006153 AGATACATCCATTTCAACGACGA 57.994 39.130 0.00 0.00 0.00 4.20
657 4074 5.043903 AGATACATCCATTTCAACGACGAG 58.956 41.667 0.00 0.00 0.00 4.18
658 4075 3.040147 ACATCCATTTCAACGACGAGT 57.960 42.857 0.00 0.00 0.00 4.18
659 4076 4.182693 ACATCCATTTCAACGACGAGTA 57.817 40.909 0.00 0.00 0.00 2.59
660 4077 4.562082 ACATCCATTTCAACGACGAGTAA 58.438 39.130 0.00 0.00 0.00 2.24
661 4078 5.175859 ACATCCATTTCAACGACGAGTAAT 58.824 37.500 0.00 0.00 0.00 1.89
662 4079 5.642063 ACATCCATTTCAACGACGAGTAATT 59.358 36.000 0.00 0.00 0.00 1.40
663 4080 6.148811 ACATCCATTTCAACGACGAGTAATTT 59.851 34.615 0.00 0.00 0.00 1.82
664 4081 5.922546 TCCATTTCAACGACGAGTAATTTG 58.077 37.500 0.00 0.00 0.00 2.32
665 4082 5.086058 CCATTTCAACGACGAGTAATTTGG 58.914 41.667 0.00 0.00 0.00 3.28
666 4083 5.106869 CCATTTCAACGACGAGTAATTTGGA 60.107 40.000 0.00 0.00 0.00 3.53
667 4084 5.987777 TTTCAACGACGAGTAATTTGGAA 57.012 34.783 0.00 0.00 0.00 3.53
668 4085 4.977741 TCAACGACGAGTAATTTGGAAC 57.022 40.909 0.00 0.00 0.00 3.62
669 4086 3.426191 TCAACGACGAGTAATTTGGAACG 59.574 43.478 0.00 0.00 0.00 3.95
670 4087 2.331194 ACGACGAGTAATTTGGAACGG 58.669 47.619 0.00 0.00 0.00 4.44
671 4088 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
672 4089 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
673 4090 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
674 4091 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
675 4092 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
676 4093 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
677 4094 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
689 4106 0.030908 GAGGGAGTCGATAAGGTGCG 59.969 60.000 0.00 0.00 0.00 5.34
690 4107 1.591863 GGGAGTCGATAAGGTGCGC 60.592 63.158 0.00 0.00 0.00 6.09
691 4108 1.944676 GGAGTCGATAAGGTGCGCG 60.945 63.158 0.00 0.00 0.00 6.86
692 4109 2.577785 GAGTCGATAAGGTGCGCGC 61.578 63.158 27.26 27.26 0.00 6.86
693 4110 2.883730 GTCGATAAGGTGCGCGCA 60.884 61.111 33.09 33.09 0.00 6.09
694 4111 2.883730 TCGATAAGGTGCGCGCAC 60.884 61.111 46.90 46.90 45.49 5.34
745 4162 2.839629 CATGCAGTGCAACGGAGTA 58.160 52.632 23.90 0.00 45.00 2.59
746 4163 0.723414 CATGCAGTGCAACGGAGTAG 59.277 55.000 23.90 1.13 45.00 2.57
747 4164 0.608130 ATGCAGTGCAACGGAGTAGA 59.392 50.000 23.90 0.00 45.00 2.59
748 4165 0.608130 TGCAGTGCAACGGAGTAGAT 59.392 50.000 17.26 0.00 45.00 1.98
749 4166 1.002366 GCAGTGCAACGGAGTAGATG 58.998 55.000 11.09 0.00 45.00 2.90
750 4167 1.404181 GCAGTGCAACGGAGTAGATGA 60.404 52.381 11.09 0.00 45.00 2.92
751 4168 2.263077 CAGTGCAACGGAGTAGATGAC 58.737 52.381 0.00 0.00 45.00 3.06
752 4169 1.135373 AGTGCAACGGAGTAGATGACG 60.135 52.381 0.00 0.00 45.00 4.35
753 4170 1.135489 GTGCAACGGAGTAGATGACGA 60.135 52.381 0.00 0.00 45.00 4.20
754 4171 1.542472 TGCAACGGAGTAGATGACGAA 59.458 47.619 0.00 0.00 45.00 3.85
765 4182 5.730550 AGTAGATGACGAATGCCAAAAGTA 58.269 37.500 0.00 0.00 0.00 2.24
790 4207 6.350629 AGTTCAAATTGAGGATTCAAAGGG 57.649 37.500 0.00 0.00 45.82 3.95
811 4231 5.298527 AGGGGTAAGTTTCAGAACGAAAAAG 59.701 40.000 0.00 0.00 45.11 2.27
894 4327 3.815337 CGTAGGAGATCATACACGAGG 57.185 52.381 5.61 0.00 33.15 4.63
940 4374 3.117093 TGAAAATTGACCCAGGGTTACCA 60.117 43.478 14.23 2.98 40.13 3.25
956 4392 1.201429 ACCAGGCCGGATTTCTCAGT 61.201 55.000 18.74 0.00 38.63 3.41
957 4393 0.462759 CCAGGCCGGATTTCTCAGTC 60.463 60.000 5.05 0.00 36.56 3.51
1254 4692 1.775039 AACTCACCGACGACGACGAA 61.775 55.000 20.63 5.44 42.66 3.85
1269 4707 0.037877 ACGAAGACGAGGAGGAGGAA 59.962 55.000 0.00 0.00 42.66 3.36
1338 4791 3.322466 AGGTTCAGCCCCGAGGTG 61.322 66.667 0.00 0.00 45.72 4.00
1358 4814 3.419759 CAAGAAACCGGACGGCGG 61.420 66.667 9.46 0.00 39.32 6.13
1427 4883 1.000717 GTCGGTTGATTGGTTGGTTGG 60.001 52.381 0.00 0.00 0.00 3.77
1476 4932 4.645535 TCCTGCTGCTTAATTATGCCTAG 58.354 43.478 17.85 11.81 0.00 3.02
1477 4933 3.190118 CCTGCTGCTTAATTATGCCTAGC 59.810 47.826 20.18 20.18 0.00 3.42
1478 4934 4.070716 CTGCTGCTTAATTATGCCTAGCT 58.929 43.478 24.04 0.00 31.98 3.32
1479 4935 5.227569 TGCTGCTTAATTATGCCTAGCTA 57.772 39.130 24.04 14.49 31.98 3.32
1481 4937 5.877012 TGCTGCTTAATTATGCCTAGCTATC 59.123 40.000 24.04 9.62 31.98 2.08
1482 4938 5.295540 GCTGCTTAATTATGCCTAGCTATCC 59.704 44.000 19.91 0.00 33.15 2.59
1520 4978 8.393366 CAAGTATGTCCTGTTCTATCATGTTTG 58.607 37.037 0.00 0.00 0.00 2.93
1553 5012 6.535150 CGAATTCTGAAACTGCTGTAGGATAA 59.465 38.462 3.52 0.00 0.00 1.75
1555 5014 7.798596 ATTCTGAAACTGCTGTAGGATAATG 57.201 36.000 0.00 0.00 0.00 1.90
1557 5016 6.711277 TCTGAAACTGCTGTAGGATAATGTT 58.289 36.000 0.00 0.00 0.00 2.71
1568 5052 7.336931 GCTGTAGGATAATGTTATTGGGTATGG 59.663 40.741 0.00 0.00 0.00 2.74
1569 5053 8.513139 TGTAGGATAATGTTATTGGGTATGGA 57.487 34.615 0.00 0.00 0.00 3.41
1662 5151 7.094205 ACTGAAATGGGTATCACTTTGATTGTC 60.094 37.037 0.00 0.00 38.26 3.18
1698 5189 7.859325 ACTGACACTACAAGTTACACAAATT 57.141 32.000 0.00 0.00 0.00 1.82
1722 5213 1.108727 ATGCACACACCACACAAGGG 61.109 55.000 0.00 0.00 0.00 3.95
1723 5214 1.453015 GCACACACCACACAAGGGA 60.453 57.895 0.00 0.00 0.00 4.20
1724 5215 1.724582 GCACACACCACACAAGGGAC 61.725 60.000 0.00 0.00 0.00 4.46
1725 5216 0.393673 CACACACCACACAAGGGACA 60.394 55.000 0.00 0.00 0.00 4.02
1726 5217 0.329931 ACACACCACACAAGGGACAA 59.670 50.000 0.00 0.00 0.00 3.18
1727 5218 1.024271 CACACCACACAAGGGACAAG 58.976 55.000 0.00 0.00 0.00 3.16
1728 5219 0.106719 ACACCACACAAGGGACAAGG 60.107 55.000 0.00 0.00 0.00 3.61
1740 5231 1.963515 GGGACAAGGCACAAGAACAAT 59.036 47.619 0.00 0.00 0.00 2.71
1754 5245 6.035650 CACAAGAACAATATCGTAACCGTCAT 59.964 38.462 0.00 0.00 35.01 3.06
1771 5262 3.795639 CGTCATCTGCACACTATCAAGAG 59.204 47.826 0.00 0.00 0.00 2.85
1813 5320 3.711704 TGCCCTCCCAAACATGTTAAAAA 59.288 39.130 12.39 0.00 0.00 1.94
1814 5321 4.202305 TGCCCTCCCAAACATGTTAAAAAG 60.202 41.667 12.39 7.63 0.00 2.27
1815 5322 4.314961 CCCTCCCAAACATGTTAAAAAGC 58.685 43.478 12.39 0.00 0.00 3.51
1873 5385 1.689273 AGTTGATCGCCCTGATAGACC 59.311 52.381 0.00 0.00 37.47 3.85
1876 5388 1.620323 TGATCGCCCTGATAGACCATG 59.380 52.381 0.00 0.00 37.47 3.66
1914 5426 5.105554 AGCGACATCTTCTAACAGTTCATCT 60.106 40.000 0.00 0.00 0.00 2.90
1917 5429 7.476667 CGACATCTTCTAACAGTTCATCTAGT 58.523 38.462 0.00 0.00 0.00 2.57
1931 5443 8.651389 CAGTTCATCTAGTAAGAATCCCCATAA 58.349 37.037 0.00 0.00 34.73 1.90
1942 5454 5.780731 AGAATCCCCATAAATCCACAACAT 58.219 37.500 0.00 0.00 0.00 2.71
1943 5455 5.599656 AGAATCCCCATAAATCCACAACATG 59.400 40.000 0.00 0.00 0.00 3.21
1991 5511 3.711704 TCCCTCTTCCAGATCCATGTTAC 59.288 47.826 0.00 0.00 0.00 2.50
2015 5535 1.547372 GCTGGTTCAATGTGCTTGGAT 59.453 47.619 0.00 0.00 35.43 3.41
2017 5537 3.428045 GCTGGTTCAATGTGCTTGGATAC 60.428 47.826 0.00 0.00 35.43 2.24
2025 5545 6.653020 TCAATGTGCTTGGATACTGATAACT 58.347 36.000 0.00 0.00 35.43 2.24
2031 5551 7.287696 TGTGCTTGGATACTGATAACTGAGATA 59.712 37.037 0.00 0.00 37.61 1.98
2037 5557 6.439058 GGATACTGATAACTGAGATAGCCCTT 59.561 42.308 0.00 0.00 0.00 3.95
2038 5558 5.543507 ACTGATAACTGAGATAGCCCTTG 57.456 43.478 0.00 0.00 0.00 3.61
2041 5561 7.013220 ACTGATAACTGAGATAGCCCTTGATA 58.987 38.462 0.00 0.00 0.00 2.15
2042 5562 7.039363 ACTGATAACTGAGATAGCCCTTGATAC 60.039 40.741 0.00 0.00 0.00 2.24
2043 5563 6.782494 TGATAACTGAGATAGCCCTTGATACA 59.218 38.462 0.00 0.00 0.00 2.29
2080 5600 3.331889 AGATGAAGTTCTGTCCCATTGGT 59.668 43.478 4.17 0.00 0.00 3.67
2101 5621 4.069304 GTGGTGCCTGTATGTTTTGTCTA 58.931 43.478 0.00 0.00 0.00 2.59
2102 5622 4.154195 GTGGTGCCTGTATGTTTTGTCTAG 59.846 45.833 0.00 0.00 0.00 2.43
2182 5703 2.093941 CAGATGCAGTCAAAGAAGAGCG 59.906 50.000 0.00 0.00 0.00 5.03
2184 5705 1.502231 TGCAGTCAAAGAAGAGCGTC 58.498 50.000 0.00 0.00 0.00 5.19
2193 5714 5.121454 GTCAAAGAAGAGCGTCAAATCATCT 59.879 40.000 0.00 0.00 0.00 2.90
2238 5759 1.419762 TCTTCAAACAGGCAGGTGCTA 59.580 47.619 1.26 0.00 41.70 3.49
2241 5762 1.142870 TCAAACAGGCAGGTGCTAACT 59.857 47.619 1.26 0.00 41.70 2.24
2252 5773 5.220931 GGCAGGTGCTAACTAATTCATCTTG 60.221 44.000 1.26 0.00 41.70 3.02
2265 5786 7.880195 ACTAATTCATCTTGTAGATACCATGCC 59.120 37.037 0.00 0.00 32.12 4.40
2290 5811 6.806751 TCTAAGTTCTGGTATGTGCATAGTC 58.193 40.000 0.00 0.00 0.00 2.59
2360 5891 6.783708 AAGATCTCTTCTTGGTAGTACTGG 57.216 41.667 5.39 0.00 43.21 4.00
2361 5892 5.205056 AGATCTCTTCTTGGTAGTACTGGG 58.795 45.833 5.39 0.00 0.00 4.45
2362 5893 3.709587 TCTCTTCTTGGTAGTACTGGGG 58.290 50.000 5.39 0.00 0.00 4.96
2363 5894 2.168728 CTCTTCTTGGTAGTACTGGGGC 59.831 54.545 5.39 0.00 0.00 5.80
2364 5895 1.906574 CTTCTTGGTAGTACTGGGGCA 59.093 52.381 5.39 0.00 0.00 5.36
2365 5896 2.263895 TCTTGGTAGTACTGGGGCAT 57.736 50.000 5.39 0.00 0.00 4.40
2366 5897 2.116238 TCTTGGTAGTACTGGGGCATC 58.884 52.381 5.39 0.00 0.00 3.91
2367 5898 1.837439 CTTGGTAGTACTGGGGCATCA 59.163 52.381 5.39 0.00 0.00 3.07
2368 5899 1.959710 TGGTAGTACTGGGGCATCAA 58.040 50.000 5.39 0.00 0.00 2.57
2369 5900 1.837439 TGGTAGTACTGGGGCATCAAG 59.163 52.381 5.39 0.00 0.00 3.02
2370 5901 2.116238 GGTAGTACTGGGGCATCAAGA 58.884 52.381 5.39 0.00 0.00 3.02
2371 5902 2.158943 GGTAGTACTGGGGCATCAAGAC 60.159 54.545 5.39 0.00 0.00 3.01
2372 5903 1.656587 AGTACTGGGGCATCAAGACA 58.343 50.000 0.00 0.00 0.00 3.41
2373 5904 2.200081 AGTACTGGGGCATCAAGACAT 58.800 47.619 0.00 0.00 0.00 3.06
2374 5905 2.092753 AGTACTGGGGCATCAAGACATG 60.093 50.000 0.00 0.00 0.00 3.21
2375 5906 0.700564 ACTGGGGCATCAAGACATGT 59.299 50.000 0.00 0.00 0.00 3.21
2376 5907 1.076024 ACTGGGGCATCAAGACATGTT 59.924 47.619 0.00 0.00 0.00 2.71
2377 5908 2.173519 CTGGGGCATCAAGACATGTTT 58.826 47.619 0.00 0.00 0.00 2.83
2378 5909 1.894466 TGGGGCATCAAGACATGTTTG 59.106 47.619 0.00 7.08 0.00 2.93
2379 5910 1.895131 GGGGCATCAAGACATGTTTGT 59.105 47.619 0.00 0.00 39.32 2.83
2380 5911 2.353011 GGGGCATCAAGACATGTTTGTG 60.353 50.000 0.00 8.70 35.79 3.33
2381 5912 2.331194 GGCATCAAGACATGTTTGTGC 58.669 47.619 21.95 21.95 35.79 4.57
2382 5913 2.288334 GGCATCAAGACATGTTTGTGCA 60.288 45.455 25.74 12.17 35.79 4.57
2383 5914 3.382855 GCATCAAGACATGTTTGTGCAA 58.617 40.909 23.28 10.09 35.79 4.08
2384 5915 3.182972 GCATCAAGACATGTTTGTGCAAC 59.817 43.478 23.28 6.29 35.79 4.17
2385 5916 4.613944 CATCAAGACATGTTTGTGCAACT 58.386 39.130 0.00 0.00 35.79 3.16
2386 5917 4.291540 TCAAGACATGTTTGTGCAACTC 57.708 40.909 0.00 0.00 35.79 3.01
2387 5918 3.693578 TCAAGACATGTTTGTGCAACTCA 59.306 39.130 0.00 0.00 35.79 3.41
2388 5919 3.698029 AGACATGTTTGTGCAACTCAC 57.302 42.857 0.00 0.00 45.82 3.51
2389 5920 2.358898 AGACATGTTTGTGCAACTCACC 59.641 45.455 0.00 0.00 45.03 4.02
2390 5921 2.358898 GACATGTTTGTGCAACTCACCT 59.641 45.455 0.00 0.00 45.03 4.00
2391 5922 2.099592 ACATGTTTGTGCAACTCACCTG 59.900 45.455 0.00 0.00 45.03 4.00
2392 5923 1.832883 TGTTTGTGCAACTCACCTGT 58.167 45.000 0.00 0.00 45.03 4.00
2393 5924 2.992593 TGTTTGTGCAACTCACCTGTA 58.007 42.857 0.00 0.00 45.03 2.74
2394 5925 2.942376 TGTTTGTGCAACTCACCTGTAG 59.058 45.455 0.00 0.00 45.03 2.74
2395 5926 2.254546 TTGTGCAACTCACCTGTAGG 57.745 50.000 0.00 0.00 45.03 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.405559 AGATGAGGTCCATGCAGATGA 58.594 47.619 0.00 0.00 35.17 2.92
124 125 1.165270 CCACCGTGATTTCCTTGGTC 58.835 55.000 0.00 0.00 0.00 4.02
317 318 1.417517 AGATGGCGTCCAAGCATATGA 59.582 47.619 6.97 0.00 36.95 2.15
355 356 4.035558 GCAATTCTCGCCACAAAGATGATA 59.964 41.667 0.00 0.00 0.00 2.15
384 385 7.201556 GCACATCTATATGTTGTAGCGCATTAT 60.202 37.037 11.47 0.00 44.07 1.28
390 391 3.981416 ACGCACATCTATATGTTGTAGCG 59.019 43.478 16.80 16.80 44.07 4.26
392 393 4.150627 GGCACGCACATCTATATGTTGTAG 59.849 45.833 0.00 0.00 44.07 2.74
393 394 4.055360 GGCACGCACATCTATATGTTGTA 58.945 43.478 0.00 0.00 44.07 2.41
396 405 2.158827 TGGGCACGCACATCTATATGTT 60.159 45.455 0.00 0.00 44.07 2.71
412 421 0.895559 TTTGTGTGTGTGTGTGGGCA 60.896 50.000 0.00 0.00 0.00 5.36
426 442 1.333308 TGTGAATGAGTGCGGTTTGTG 59.667 47.619 0.00 0.00 0.00 3.33
427 443 1.333619 GTGTGAATGAGTGCGGTTTGT 59.666 47.619 0.00 0.00 0.00 2.83
430 446 0.531974 ACGTGTGAATGAGTGCGGTT 60.532 50.000 0.00 0.00 0.00 4.44
431 447 0.944311 GACGTGTGAATGAGTGCGGT 60.944 55.000 0.00 0.00 0.00 5.68
447 3861 4.730657 ACTCCACTATTCAGTAAACGACG 58.269 43.478 0.00 0.00 32.21 5.12
463 3877 1.006571 TGAAGAACCGCGACTCCAC 60.007 57.895 8.23 1.32 0.00 4.02
464 3878 1.006571 GTGAAGAACCGCGACTCCA 60.007 57.895 8.23 0.00 0.00 3.86
472 3886 2.320805 TTCGTAGTCGTGAAGAACCG 57.679 50.000 0.00 0.00 38.33 4.44
557 3974 2.099098 GGGAGTATCATTTTGCGGGTTG 59.901 50.000 0.00 0.00 36.25 3.77
560 3977 2.222027 GAGGGAGTATCATTTTGCGGG 58.778 52.381 0.00 0.00 36.25 6.13
565 3982 4.152284 GGAACGGAGGGAGTATCATTTT 57.848 45.455 0.00 0.00 36.25 1.82
580 3997 3.301642 GTACGACAAGTAATTCGGAACGG 59.698 47.826 0.00 0.00 45.22 4.44
581 3998 3.002732 CGTACGACAAGTAATTCGGAACG 60.003 47.826 10.44 6.71 46.10 3.95
582 3999 3.914364 ACGTACGACAAGTAATTCGGAAC 59.086 43.478 24.41 0.00 39.63 3.62
583 4000 4.159377 ACGTACGACAAGTAATTCGGAA 57.841 40.909 24.41 0.00 39.63 4.30
584 4001 3.829886 ACGTACGACAAGTAATTCGGA 57.170 42.857 24.41 0.00 39.63 4.55
585 4002 4.438797 CCATACGTACGACAAGTAATTCGG 59.561 45.833 24.41 2.22 39.63 4.30
586 4003 5.265477 TCCATACGTACGACAAGTAATTCG 58.735 41.667 24.41 0.00 41.14 3.34
587 4004 6.694411 ACATCCATACGTACGACAAGTAATTC 59.306 38.462 24.41 0.00 37.02 2.17
588 4005 6.567050 ACATCCATACGTACGACAAGTAATT 58.433 36.000 24.41 0.00 37.02 1.40
589 4006 6.140303 ACATCCATACGTACGACAAGTAAT 57.860 37.500 24.41 0.00 37.02 1.89
590 4007 5.565592 ACATCCATACGTACGACAAGTAA 57.434 39.130 24.41 1.13 37.02 2.24
591 4008 6.707608 AGATACATCCATACGTACGACAAGTA 59.292 38.462 24.41 14.12 0.00 2.24
592 4009 5.530171 AGATACATCCATACGTACGACAAGT 59.470 40.000 24.41 12.48 0.00 3.16
593 4010 5.998553 AGATACATCCATACGTACGACAAG 58.001 41.667 24.41 7.99 0.00 3.16
594 4011 6.930722 TCTAGATACATCCATACGTACGACAA 59.069 38.462 24.41 7.24 0.00 3.18
595 4012 6.458210 TCTAGATACATCCATACGTACGACA 58.542 40.000 24.41 9.64 0.00 4.35
596 4013 6.957984 TCTAGATACATCCATACGTACGAC 57.042 41.667 24.41 0.00 0.00 4.34
597 4014 7.101700 ACATCTAGATACATCCATACGTACGA 58.898 38.462 24.41 6.04 0.00 3.43
598 4015 7.304919 ACATCTAGATACATCCATACGTACG 57.695 40.000 15.01 15.01 0.00 3.67
626 4043 9.529325 CGTTGAAATGGATGTATCTAGAACTAA 57.471 33.333 0.00 0.00 0.00 2.24
627 4044 8.909923 TCGTTGAAATGGATGTATCTAGAACTA 58.090 33.333 0.00 0.00 0.00 2.24
628 4045 7.707035 GTCGTTGAAATGGATGTATCTAGAACT 59.293 37.037 0.00 0.00 0.00 3.01
629 4046 7.306051 CGTCGTTGAAATGGATGTATCTAGAAC 60.306 40.741 0.00 0.00 0.00 3.01
630 4047 6.695713 CGTCGTTGAAATGGATGTATCTAGAA 59.304 38.462 0.00 0.00 0.00 2.10
631 4048 6.038936 TCGTCGTTGAAATGGATGTATCTAGA 59.961 38.462 0.00 0.00 0.00 2.43
632 4049 6.206498 TCGTCGTTGAAATGGATGTATCTAG 58.794 40.000 0.00 0.00 0.00 2.43
633 4050 6.139048 TCGTCGTTGAAATGGATGTATCTA 57.861 37.500 0.00 0.00 0.00 1.98
634 4051 5.006153 TCGTCGTTGAAATGGATGTATCT 57.994 39.130 0.00 0.00 0.00 1.98
635 4052 4.804139 ACTCGTCGTTGAAATGGATGTATC 59.196 41.667 0.00 0.00 0.00 2.24
636 4053 4.755411 ACTCGTCGTTGAAATGGATGTAT 58.245 39.130 0.00 0.00 0.00 2.29
637 4054 4.182693 ACTCGTCGTTGAAATGGATGTA 57.817 40.909 0.00 0.00 0.00 2.29
638 4055 3.040147 ACTCGTCGTTGAAATGGATGT 57.960 42.857 0.00 0.00 0.00 3.06
639 4056 5.718649 ATTACTCGTCGTTGAAATGGATG 57.281 39.130 0.00 0.00 0.00 3.51
640 4057 6.403200 CCAAATTACTCGTCGTTGAAATGGAT 60.403 38.462 0.00 0.00 0.00 3.41
641 4058 5.106869 CCAAATTACTCGTCGTTGAAATGGA 60.107 40.000 0.00 0.00 0.00 3.41
642 4059 5.086058 CCAAATTACTCGTCGTTGAAATGG 58.914 41.667 0.00 0.00 0.00 3.16
643 4060 5.922546 TCCAAATTACTCGTCGTTGAAATG 58.077 37.500 0.00 0.00 0.00 2.32
644 4061 6.368213 GTTCCAAATTACTCGTCGTTGAAAT 58.632 36.000 0.00 0.00 0.00 2.17
645 4062 5.556758 CGTTCCAAATTACTCGTCGTTGAAA 60.557 40.000 0.00 0.00 0.00 2.69
646 4063 4.084952 CGTTCCAAATTACTCGTCGTTGAA 60.085 41.667 0.00 0.00 0.00 2.69
647 4064 3.426191 CGTTCCAAATTACTCGTCGTTGA 59.574 43.478 0.00 0.00 0.00 3.18
648 4065 3.422603 CCGTTCCAAATTACTCGTCGTTG 60.423 47.826 0.00 0.00 0.00 4.10
649 4066 2.733026 CCGTTCCAAATTACTCGTCGTT 59.267 45.455 0.00 0.00 0.00 3.85
650 4067 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
651 4068 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
652 4069 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
653 4070 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
654 4071 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
655 4072 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
656 4073 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
657 4074 3.268330 GACTCCCTCCGTTCCAAATTAC 58.732 50.000 0.00 0.00 0.00 1.89
658 4075 2.093869 CGACTCCCTCCGTTCCAAATTA 60.094 50.000 0.00 0.00 0.00 1.40
659 4076 1.338769 CGACTCCCTCCGTTCCAAATT 60.339 52.381 0.00 0.00 0.00 1.82
660 4077 0.249398 CGACTCCCTCCGTTCCAAAT 59.751 55.000 0.00 0.00 0.00 2.32
661 4078 0.828762 TCGACTCCCTCCGTTCCAAA 60.829 55.000 0.00 0.00 0.00 3.28
662 4079 0.613853 ATCGACTCCCTCCGTTCCAA 60.614 55.000 0.00 0.00 0.00 3.53
663 4080 0.256752 TATCGACTCCCTCCGTTCCA 59.743 55.000 0.00 0.00 0.00 3.53
664 4081 1.337387 CTTATCGACTCCCTCCGTTCC 59.663 57.143 0.00 0.00 0.00 3.62
665 4082 1.337387 CCTTATCGACTCCCTCCGTTC 59.663 57.143 0.00 0.00 0.00 3.95
666 4083 1.341778 ACCTTATCGACTCCCTCCGTT 60.342 52.381 0.00 0.00 0.00 4.44
667 4084 0.258194 ACCTTATCGACTCCCTCCGT 59.742 55.000 0.00 0.00 0.00 4.69
668 4085 0.669077 CACCTTATCGACTCCCTCCG 59.331 60.000 0.00 0.00 0.00 4.63
669 4086 0.389757 GCACCTTATCGACTCCCTCC 59.610 60.000 0.00 0.00 0.00 4.30
670 4087 0.030908 CGCACCTTATCGACTCCCTC 59.969 60.000 0.00 0.00 0.00 4.30
671 4088 2.017559 GCGCACCTTATCGACTCCCT 62.018 60.000 0.30 0.00 0.00 4.20
672 4089 1.591863 GCGCACCTTATCGACTCCC 60.592 63.158 0.30 0.00 0.00 4.30
673 4090 1.944676 CGCGCACCTTATCGACTCC 60.945 63.158 8.75 0.00 0.00 3.85
674 4091 2.577785 GCGCGCACCTTATCGACTC 61.578 63.158 29.10 0.00 0.00 3.36
675 4092 2.582498 GCGCGCACCTTATCGACT 60.582 61.111 29.10 0.00 0.00 4.18
676 4093 2.883730 TGCGCGCACCTTATCGAC 60.884 61.111 33.09 0.00 0.00 4.20
677 4094 2.883730 GTGCGCGCACCTTATCGA 60.884 61.111 45.62 15.78 40.79 3.59
689 4106 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
690 4107 2.021243 CGTGTGTGTGTGTGTGCG 59.979 61.111 0.00 0.00 0.00 5.34
691 4108 2.103647 TCCGTGTGTGTGTGTGTGC 61.104 57.895 0.00 0.00 0.00 4.57
692 4109 1.016653 TGTCCGTGTGTGTGTGTGTG 61.017 55.000 0.00 0.00 0.00 3.82
693 4110 0.107897 ATGTCCGTGTGTGTGTGTGT 60.108 50.000 0.00 0.00 0.00 3.72
694 4111 1.003972 GAATGTCCGTGTGTGTGTGTG 60.004 52.381 0.00 0.00 0.00 3.82
695 4112 1.295792 GAATGTCCGTGTGTGTGTGT 58.704 50.000 0.00 0.00 0.00 3.72
696 4113 0.586319 GGAATGTCCGTGTGTGTGTG 59.414 55.000 0.00 0.00 0.00 3.82
742 4159 4.579869 ACTTTTGGCATTCGTCATCTACT 58.420 39.130 0.00 0.00 0.00 2.57
743 4160 4.946784 ACTTTTGGCATTCGTCATCTAC 57.053 40.909 0.00 0.00 0.00 2.59
744 4161 6.653320 ACTTTACTTTTGGCATTCGTCATCTA 59.347 34.615 0.00 0.00 0.00 1.98
745 4162 5.473504 ACTTTACTTTTGGCATTCGTCATCT 59.526 36.000 0.00 0.00 0.00 2.90
746 4163 5.699839 ACTTTACTTTTGGCATTCGTCATC 58.300 37.500 0.00 0.00 0.00 2.92
747 4164 5.705609 ACTTTACTTTTGGCATTCGTCAT 57.294 34.783 0.00 0.00 0.00 3.06
748 4165 5.066634 TGAACTTTACTTTTGGCATTCGTCA 59.933 36.000 0.00 0.00 0.00 4.35
749 4166 5.516090 TGAACTTTACTTTTGGCATTCGTC 58.484 37.500 0.00 0.00 0.00 4.20
750 4167 5.508200 TGAACTTTACTTTTGGCATTCGT 57.492 34.783 0.00 0.00 0.00 3.85
751 4168 6.820470 TTTGAACTTTACTTTTGGCATTCG 57.180 33.333 0.00 0.00 0.00 3.34
752 4169 8.825745 TCAATTTGAACTTTACTTTTGGCATTC 58.174 29.630 0.00 0.00 0.00 2.67
753 4170 8.729805 TCAATTTGAACTTTACTTTTGGCATT 57.270 26.923 0.00 0.00 0.00 3.56
754 4171 7.442062 CCTCAATTTGAACTTTACTTTTGGCAT 59.558 33.333 0.01 0.00 0.00 4.40
765 4182 7.219322 CCCTTTGAATCCTCAATTTGAACTTT 58.781 34.615 0.01 0.00 41.22 2.66
790 4207 7.966753 ACTTTCTTTTTCGTTCTGAAACTTACC 59.033 33.333 0.00 0.00 45.98 2.85
811 4231 0.467290 TCACTGGTTGGGCCACTTTC 60.467 55.000 5.23 0.00 43.61 2.62
871 4291 1.068472 CGTGTATGATCTCCTACGGGC 60.068 57.143 0.00 0.00 0.00 6.13
892 4325 0.606673 GCTCGGAAGGCAGAAAACCT 60.607 55.000 0.00 0.00 40.02 3.50
894 4327 1.876664 GGCTCGGAAGGCAGAAAAC 59.123 57.895 0.00 0.00 46.99 2.43
918 4352 3.117093 TGGTAACCCTGGGTCAATTTTCA 60.117 43.478 20.85 8.19 33.12 2.69
924 4358 2.470311 CCTGGTAACCCTGGGTCAA 58.530 57.895 20.85 7.89 44.18 3.18
940 4374 0.539051 CTGACTGAGAAATCCGGCCT 59.461 55.000 0.00 0.00 0.00 5.19
956 4392 0.898320 CCGCTCTCCCTTCTTTCTGA 59.102 55.000 0.00 0.00 0.00 3.27
957 4393 0.742635 GCCGCTCTCCCTTCTTTCTG 60.743 60.000 0.00 0.00 0.00 3.02
999 4437 1.592669 GGATGACGAGGTCGCCATG 60.593 63.158 5.88 0.00 42.29 3.66
1007 4445 4.227134 CCGCCTGGGATGACGAGG 62.227 72.222 0.00 0.00 46.95 4.63
1171 4609 1.594331 GCAAGAAACTCCTTGTCCGT 58.406 50.000 0.00 0.00 43.96 4.69
1177 4615 1.966451 CCCGCGCAAGAAACTCCTT 60.966 57.895 8.75 0.00 43.02 3.36
1211 4649 2.048222 CGACGAAGCCCTTCTGCA 60.048 61.111 6.48 0.00 37.44 4.41
1212 4650 1.807573 CTCGACGAAGCCCTTCTGC 60.808 63.158 0.00 0.00 37.44 4.26
1254 4692 0.257616 CCTCTTCCTCCTCCTCGTCT 59.742 60.000 0.00 0.00 0.00 4.18
1269 4707 1.893919 GAGCTGCGTTTCCTCCCTCT 61.894 60.000 0.00 0.00 0.00 3.69
1338 4791 2.322830 GCCGTCCGGTTTCTTGGTC 61.323 63.158 7.66 0.00 37.65 4.02
1427 4883 2.484889 GCCGGATTAAGGATCAGTCAC 58.515 52.381 5.05 0.00 36.43 3.67
1477 4933 6.820656 ACATACTTGACAGAAAGCTTGGATAG 59.179 38.462 0.00 0.00 0.00 2.08
1478 4934 6.711277 ACATACTTGACAGAAAGCTTGGATA 58.289 36.000 0.00 0.00 0.00 2.59
1479 4935 5.564550 ACATACTTGACAGAAAGCTTGGAT 58.435 37.500 0.00 0.00 0.00 3.41
1481 4937 4.154918 GGACATACTTGACAGAAAGCTTGG 59.845 45.833 0.00 0.00 0.00 3.61
1482 4938 4.999950 AGGACATACTTGACAGAAAGCTTG 59.000 41.667 0.00 0.00 0.00 4.01
1486 4944 6.226787 AGAACAGGACATACTTGACAGAAAG 58.773 40.000 0.00 0.00 0.00 2.62
1493 4951 7.423844 ACATGATAGAACAGGACATACTTGA 57.576 36.000 0.00 0.00 0.00 3.02
1520 4978 4.214437 CAGTTTCAGAATTCGACAACAGC 58.786 43.478 14.97 0.00 0.00 4.40
1553 5012 6.018469 CCATTCCATCCATACCCAATAACAT 58.982 40.000 0.00 0.00 0.00 2.71
1555 5014 5.640147 TCCATTCCATCCATACCCAATAAC 58.360 41.667 0.00 0.00 0.00 1.89
1557 5016 5.555144 TCATCCATTCCATCCATACCCAATA 59.445 40.000 0.00 0.00 0.00 1.90
1568 5052 8.370940 ACCGATACATATATCATCCATTCCATC 58.629 37.037 0.00 0.00 37.63 3.51
1569 5053 8.152898 CACCGATACATATATCATCCATTCCAT 58.847 37.037 0.00 0.00 37.63 3.41
1662 5151 7.385205 ACTTGTAGTGTCAGTTAGTTATGCAAG 59.615 37.037 0.00 0.00 34.90 4.01
1698 5189 3.409026 TGTGTGGTGTGTGCATATGTA 57.591 42.857 4.29 0.00 0.00 2.29
1722 5213 4.154195 ACGATATTGTTCTTGTGCCTTGTC 59.846 41.667 0.00 0.00 0.00 3.18
1723 5214 4.072131 ACGATATTGTTCTTGTGCCTTGT 58.928 39.130 0.00 0.00 0.00 3.16
1724 5215 4.685169 ACGATATTGTTCTTGTGCCTTG 57.315 40.909 0.00 0.00 0.00 3.61
1725 5216 5.123344 GGTTACGATATTGTTCTTGTGCCTT 59.877 40.000 0.00 0.00 0.00 4.35
1726 5217 4.634443 GGTTACGATATTGTTCTTGTGCCT 59.366 41.667 0.00 0.00 0.00 4.75
1727 5218 4.493545 CGGTTACGATATTGTTCTTGTGCC 60.494 45.833 0.00 0.00 44.60 5.01
1728 5219 4.092383 ACGGTTACGATATTGTTCTTGTGC 59.908 41.667 0.00 0.00 44.60 4.57
1740 5231 2.424246 TGTGCAGATGACGGTTACGATA 59.576 45.455 0.00 0.00 44.60 2.92
1813 5320 7.816995 GCTTGCTAATGTGAGTATTAGATAGCT 59.183 37.037 16.43 0.00 41.17 3.32
1814 5321 7.600375 TGCTTGCTAATGTGAGTATTAGATAGC 59.400 37.037 16.64 16.64 41.17 2.97
1815 5322 8.920665 GTGCTTGCTAATGTGAGTATTAGATAG 58.079 37.037 9.12 6.42 41.17 2.08
1873 5385 3.062639 GTCGCTTATGACTTGTGGACATG 59.937 47.826 0.00 0.00 35.95 3.21
1876 5388 2.683968 TGTCGCTTATGACTTGTGGAC 58.316 47.619 0.00 0.00 39.64 4.02
1914 5426 7.699709 TGTGGATTTATGGGGATTCTTACTA 57.300 36.000 0.00 0.00 0.00 1.82
1917 5429 6.736581 TGTTGTGGATTTATGGGGATTCTTA 58.263 36.000 0.00 0.00 0.00 2.10
1924 5436 5.418676 GAAACATGTTGTGGATTTATGGGG 58.581 41.667 12.82 0.00 0.00 4.96
1931 5443 3.126858 CGATCGGAAACATGTTGTGGATT 59.873 43.478 12.82 0.00 0.00 3.01
1942 5454 3.492656 GGATGAATCTCCGATCGGAAACA 60.493 47.826 34.77 28.26 44.66 2.83
1943 5455 3.060602 GGATGAATCTCCGATCGGAAAC 58.939 50.000 34.77 24.44 44.66 2.78
1991 5511 2.119801 AGCACATTGAACCAGCTAGG 57.880 50.000 0.00 0.00 45.67 3.02
2015 5535 6.373759 TCAAGGGCTATCTCAGTTATCAGTA 58.626 40.000 0.00 0.00 0.00 2.74
2017 5537 5.798125 TCAAGGGCTATCTCAGTTATCAG 57.202 43.478 0.00 0.00 0.00 2.90
2025 5545 7.618019 AATAAGTGTATCAAGGGCTATCTCA 57.382 36.000 0.00 0.00 0.00 3.27
2031 5551 9.125026 CAGAAATAAATAAGTGTATCAAGGGCT 57.875 33.333 0.00 0.00 0.00 5.19
2080 5600 3.222173 AGACAAAACATACAGGCACCA 57.778 42.857 0.00 0.00 0.00 4.17
2101 5621 2.149973 CCCCCTGCTTATCTTTTGCT 57.850 50.000 0.00 0.00 0.00 3.91
2126 5647 2.295909 GCAATACAGGGCAAACACTTCA 59.704 45.455 0.00 0.00 0.00 3.02
2127 5648 2.558359 AGCAATACAGGGCAAACACTTC 59.442 45.455 0.00 0.00 0.00 3.01
2160 5681 2.159544 GCTCTTCTTTGACTGCATCTGC 60.160 50.000 0.00 0.00 42.50 4.26
2193 5714 2.166870 GCATCAGGGCAATCATCAAACA 59.833 45.455 0.00 0.00 0.00 2.83
2238 5759 9.277783 GCATGGTATCTACAAGATGAATTAGTT 57.722 33.333 0.00 0.00 35.37 2.24
2241 5762 7.977818 AGGCATGGTATCTACAAGATGAATTA 58.022 34.615 0.00 0.00 35.37 1.40
2252 5773 6.451393 CAGAACTTAGAGGCATGGTATCTAC 58.549 44.000 0.00 0.00 0.00 2.59
2263 5784 3.198872 GCACATACCAGAACTTAGAGGC 58.801 50.000 0.00 0.00 0.00 4.70
2265 5786 6.810911 ACTATGCACATACCAGAACTTAGAG 58.189 40.000 0.00 0.00 0.00 2.43
2290 5811 7.873505 GGTTAGGTTACATAGAAAGCTATCAGG 59.126 40.741 0.00 0.00 36.94 3.86
2353 5884 1.656587 TGTCTTGATGCCCCAGTACT 58.343 50.000 0.00 0.00 0.00 2.73
2354 5885 2.292267 CATGTCTTGATGCCCCAGTAC 58.708 52.381 0.00 0.00 0.00 2.73
2355 5886 1.915489 ACATGTCTTGATGCCCCAGTA 59.085 47.619 0.00 0.00 0.00 2.74
2356 5887 0.700564 ACATGTCTTGATGCCCCAGT 59.299 50.000 0.00 0.00 0.00 4.00
2357 5888 1.843368 AACATGTCTTGATGCCCCAG 58.157 50.000 0.00 0.00 0.00 4.45
2358 5889 1.894466 CAAACATGTCTTGATGCCCCA 59.106 47.619 0.00 0.00 0.00 4.96
2359 5890 1.895131 ACAAACATGTCTTGATGCCCC 59.105 47.619 20.41 0.00 0.00 5.80
2360 5891 2.927871 GCACAAACATGTCTTGATGCCC 60.928 50.000 20.41 6.51 30.92 5.36
2361 5892 2.288334 TGCACAAACATGTCTTGATGCC 60.288 45.455 24.06 16.17 33.59 4.40
2362 5893 3.015934 TGCACAAACATGTCTTGATGC 57.984 42.857 20.41 21.64 34.37 3.91
2363 5894 4.613944 AGTTGCACAAACATGTCTTGATG 58.386 39.130 20.41 16.16 41.61 3.07
2364 5895 4.338964 TGAGTTGCACAAACATGTCTTGAT 59.661 37.500 20.41 8.07 41.61 2.57
2365 5896 3.693578 TGAGTTGCACAAACATGTCTTGA 59.306 39.130 20.41 3.49 41.61 3.02
2366 5897 3.792956 GTGAGTTGCACAAACATGTCTTG 59.207 43.478 15.01 15.01 46.91 3.02
2367 5898 4.032703 GTGAGTTGCACAAACATGTCTT 57.967 40.909 0.00 0.00 46.91 3.01
2368 5899 3.698029 GTGAGTTGCACAAACATGTCT 57.302 42.857 0.00 0.00 46.91 3.41


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

AutoCloner maintained by Alex Coulton.