Multiple sequence alignment - TraesCS6A01G310700

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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 TraesCS6A01G310700 chr6A 100.000 4777 0 0 1 4777 546926004 546930780 0.000000e+00 8822.0
1 TraesCS6A01G310700 chr6D 96.429 3276 65 20 707 3963 400699193 400702435 0.000000e+00 5354.0
2 TraesCS6A01G310700 chr6D 93.460 581 36 2 4198 4777 400706197 400706776 0.000000e+00 861.0
3 TraesCS6A01G310700 chr6B 95.497 3309 106 16 707 4003 599755950 599759227 0.000000e+00 5245.0
4 TraesCS6A01G310700 chr6B 93.363 663 28 6 4128 4777 599767317 599767976 0.000000e+00 966.0
5 TraesCS6A01G310700 chr5A 92.640 625 27 1 1 606 700671566 700670942 0.000000e+00 881.0
6 TraesCS6A01G310700 chr5A 90.217 552 35 1 74 606 510491056 510491607 0.000000e+00 702.0
7 TraesCS6A01G310700 chr4A 92.173 626 29 2 1 606 65714514 65715139 0.000000e+00 867.0
8 TraesCS6A01G310700 chr3D 92.147 624 28 2 1 605 300680024 300680645 0.000000e+00 861.0
9 TraesCS6A01G310700 chr3D 92.110 545 20 2 85 606 23089594 23089050 0.000000e+00 747.0
10 TraesCS6A01G310700 chr2A 91.026 624 36 2 1 605 29274035 29273413 0.000000e+00 824.0
11 TraesCS6A01G310700 chr2A 86.356 623 59 5 1 604 166635450 166634835 0.000000e+00 656.0
12 TraesCS6A01G310700 chr4D 90.989 455 19 4 172 606 465182958 465183410 1.140000e-165 593.0
13 TraesCS6A01G310700 chr5D 89.169 397 26 3 226 605 519644724 519644328 3.340000e-131 479.0
14 TraesCS6A01G310700 chr7A 90.244 246 24 0 359 604 462335799 462336044 5.960000e-84 322.0
15 TraesCS6A01G310700 chr1A 74.737 285 62 9 2926 3208 497241656 497241380 8.400000e-23 119.0
16 TraesCS6A01G310700 chr1A 80.357 112 16 5 3507 3615 497241033 497240925 3.960000e-11 80.5
17 TraesCS6A01G310700 chr1A 88.525 61 5 2 3517 3576 492801084 492801143 6.630000e-09 73.1
18 TraesCS6A01G310700 chr1B 90.741 54 3 2 3517 3569 530052942 530052994 2.390000e-08 71.3


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 TraesCS6A01G310700 chr6A 546926004 546930780 4776 False 8822.0 8822 100.0000 1 4777 1 chr6A.!!$F1 4776
1 TraesCS6A01G310700 chr6D 400699193 400706776 7583 False 3107.5 5354 94.9445 707 4777 2 chr6D.!!$F1 4070
2 TraesCS6A01G310700 chr6B 599755950 599759227 3277 False 5245.0 5245 95.4970 707 4003 1 chr6B.!!$F1 3296
3 TraesCS6A01G310700 chr6B 599767317 599767976 659 False 966.0 966 93.3630 4128 4777 1 chr6B.!!$F2 649
4 TraesCS6A01G310700 chr5A 700670942 700671566 624 True 881.0 881 92.6400 1 606 1 chr5A.!!$R1 605
5 TraesCS6A01G310700 chr5A 510491056 510491607 551 False 702.0 702 90.2170 74 606 1 chr5A.!!$F1 532
6 TraesCS6A01G310700 chr4A 65714514 65715139 625 False 867.0 867 92.1730 1 606 1 chr4A.!!$F1 605
7 TraesCS6A01G310700 chr3D 300680024 300680645 621 False 861.0 861 92.1470 1 605 1 chr3D.!!$F1 604
8 TraesCS6A01G310700 chr3D 23089050 23089594 544 True 747.0 747 92.1100 85 606 1 chr3D.!!$R1 521
9 TraesCS6A01G310700 chr2A 29273413 29274035 622 True 824.0 824 91.0260 1 605 1 chr2A.!!$R1 604
10 TraesCS6A01G310700 chr2A 166634835 166635450 615 True 656.0 656 86.3560 1 604 1 chr2A.!!$R2 603

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
658 683 0.041238 AGAGGACGGTGGAGATTGGA 59.959 55.000 0.00 0.00 0.00 3.53 F
747 772 0.604243 TACGCATGTGGTGTGGGAAC 60.604 55.000 11.65 0.00 42.69 3.62 F
828 859 0.813184 ATGCATCCGGCTGAAACAAG 59.187 50.000 10.06 0.00 45.15 3.16 F
1259 1300 1.203563 CGGAGATACTCGTACGCCG 59.796 63.158 11.24 12.02 38.13 6.46 F
2040 2081 1.298859 GGGGCACACACGTCATCTTC 61.299 60.000 0.00 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 2476 0.166597 AAGACATGCACGCACGAATG 59.833 50.000 0.00 0.65 0.00 2.67 R
2539 2582 0.518636 CTTGACAACCATGGTCAGCG 59.481 55.000 20.07 9.83 45.20 5.18 R
2937 2980 2.261671 GTCCTCGTGCATGGACGT 59.738 61.111 33.95 0.00 42.51 4.34 R
3053 3096 3.084579 GCGTTCAGCGACTGGATG 58.915 61.111 6.95 5.29 44.77 3.51 R
4105 4450 0.168128 GTACTGTTGGCGATGTTGGC 59.832 55.000 0.00 0.00 0.00 4.52 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
71 73 5.601583 ATCATGTGATAATTTTGCTGCCA 57.398 34.783 0.00 0.00 32.01 4.92
72 74 5.001237 TCATGTGATAATTTTGCTGCCAG 57.999 39.130 0.00 0.00 0.00 4.85
98 100 7.224557 GGCCACATGCGATAATAAAAGAAAATT 59.775 33.333 0.00 0.00 42.61 1.82
173 179 2.433970 TCATATGGTGATGACGGCTCAA 59.566 45.455 2.13 0.00 30.75 3.02
229 235 6.057533 AGGTGCGATCATATTTTCTTCATGA 58.942 36.000 0.00 0.00 33.47 3.07
233 239 6.767423 TGCGATCATATTTTCTTCATGAAGGA 59.233 34.615 30.33 22.67 38.88 3.36
279 285 2.365617 TCGAAGAGGAGTTGAGTGCTTT 59.634 45.455 0.00 0.00 0.00 3.51
302 308 1.009389 GGAAGGACTGTCGTTCGCAG 61.009 60.000 27.15 12.29 40.91 5.18
338 344 7.068839 GTGACCTTCTAGTGGAGATAGAAATGA 59.931 40.741 10.62 0.00 38.46 2.57
566 591 9.645059 GCTAGCTATGATTGATTGTATGAACTA 57.355 33.333 7.70 0.00 0.00 2.24
644 669 8.746052 TCATCACAGTTTTAAAAGAAAGAGGA 57.254 30.769 0.00 2.80 0.00 3.71
645 670 8.621286 TCATCACAGTTTTAAAAGAAAGAGGAC 58.379 33.333 0.00 0.00 0.00 3.85
646 671 7.011828 TCACAGTTTTAAAAGAAAGAGGACG 57.988 36.000 0.00 0.00 0.00 4.79
647 672 6.037830 TCACAGTTTTAAAAGAAAGAGGACGG 59.962 38.462 0.00 0.00 0.00 4.79
648 673 5.884232 ACAGTTTTAAAAGAAAGAGGACGGT 59.116 36.000 0.00 0.00 0.00 4.83
649 674 6.183360 ACAGTTTTAAAAGAAAGAGGACGGTG 60.183 38.462 0.00 0.00 0.00 4.94
650 675 5.298527 AGTTTTAAAAGAAAGAGGACGGTGG 59.701 40.000 0.00 0.00 0.00 4.61
651 676 4.693042 TTAAAAGAAAGAGGACGGTGGA 57.307 40.909 0.00 0.00 0.00 4.02
652 677 2.841442 AAAGAAAGAGGACGGTGGAG 57.159 50.000 0.00 0.00 0.00 3.86
653 678 2.011122 AAGAAAGAGGACGGTGGAGA 57.989 50.000 0.00 0.00 0.00 3.71
654 679 2.239681 AGAAAGAGGACGGTGGAGAT 57.760 50.000 0.00 0.00 0.00 2.75
655 680 2.541466 AGAAAGAGGACGGTGGAGATT 58.459 47.619 0.00 0.00 0.00 2.40
656 681 2.234908 AGAAAGAGGACGGTGGAGATTG 59.765 50.000 0.00 0.00 0.00 2.67
657 682 0.905357 AAGAGGACGGTGGAGATTGG 59.095 55.000 0.00 0.00 0.00 3.16
658 683 0.041238 AGAGGACGGTGGAGATTGGA 59.959 55.000 0.00 0.00 0.00 3.53
659 684 1.123928 GAGGACGGTGGAGATTGGAT 58.876 55.000 0.00 0.00 0.00 3.41
660 685 1.069358 GAGGACGGTGGAGATTGGATC 59.931 57.143 0.00 0.00 0.00 3.36
661 686 0.830648 GGACGGTGGAGATTGGATCA 59.169 55.000 0.00 0.00 0.00 2.92
662 687 1.209504 GGACGGTGGAGATTGGATCAA 59.790 52.381 0.00 0.00 0.00 2.57
663 688 2.355716 GGACGGTGGAGATTGGATCAAA 60.356 50.000 0.00 0.00 0.00 2.69
664 689 3.343617 GACGGTGGAGATTGGATCAAAA 58.656 45.455 0.00 0.00 0.00 2.44
665 690 3.947834 GACGGTGGAGATTGGATCAAAAT 59.052 43.478 0.00 0.00 0.00 1.82
666 691 4.344104 ACGGTGGAGATTGGATCAAAATT 58.656 39.130 0.00 0.00 0.00 1.82
667 692 4.772100 ACGGTGGAGATTGGATCAAAATTT 59.228 37.500 0.00 0.00 0.00 1.82
668 693 5.105756 ACGGTGGAGATTGGATCAAAATTTC 60.106 40.000 0.00 0.00 0.00 2.17
669 694 5.343249 GGTGGAGATTGGATCAAAATTTCG 58.657 41.667 0.00 0.00 0.00 3.46
670 695 5.125417 GGTGGAGATTGGATCAAAATTTCGA 59.875 40.000 0.00 0.00 0.00 3.71
671 696 6.183360 GGTGGAGATTGGATCAAAATTTCGAT 60.183 38.462 0.00 0.00 0.00 3.59
672 697 7.260603 GTGGAGATTGGATCAAAATTTCGATT 58.739 34.615 0.00 0.00 0.00 3.34
673 698 7.433425 GTGGAGATTGGATCAAAATTTCGATTC 59.567 37.037 0.00 0.00 0.00 2.52
674 699 7.122501 TGGAGATTGGATCAAAATTTCGATTCA 59.877 33.333 0.00 0.00 0.00 2.57
675 700 7.433425 GGAGATTGGATCAAAATTTCGATTCAC 59.567 37.037 0.00 0.00 26.50 3.18
676 701 6.968904 AGATTGGATCAAAATTTCGATTCACG 59.031 34.615 0.00 0.00 44.09 4.35
677 702 4.411327 TGGATCAAAATTTCGATTCACGC 58.589 39.130 0.00 0.00 42.26 5.34
678 703 4.155826 TGGATCAAAATTTCGATTCACGCT 59.844 37.500 0.00 0.00 42.26 5.07
679 704 5.352846 TGGATCAAAATTTCGATTCACGCTA 59.647 36.000 0.00 0.00 42.26 4.26
680 705 6.038161 TGGATCAAAATTTCGATTCACGCTAT 59.962 34.615 0.00 0.00 42.26 2.97
681 706 7.225734 TGGATCAAAATTTCGATTCACGCTATA 59.774 33.333 0.00 0.00 42.26 1.31
682 707 7.530861 GGATCAAAATTTCGATTCACGCTATAC 59.469 37.037 0.00 0.00 42.26 1.47
700 725 8.146885 CGCTATACGGAAAAAGAAAAGAAAAG 57.853 34.615 0.00 0.00 38.44 2.27
701 726 8.013378 CGCTATACGGAAAAAGAAAAGAAAAGA 58.987 33.333 0.00 0.00 38.44 2.52
702 727 9.673454 GCTATACGGAAAAAGAAAAGAAAAGAA 57.327 29.630 0.00 0.00 0.00 2.52
721 746 2.649331 AAACATTCATGCTGCAGCTC 57.351 45.000 36.61 12.36 42.66 4.09
729 754 2.369532 TCATGCTGCAGCTCCATGTATA 59.630 45.455 36.61 15.85 42.66 1.47
731 756 1.143305 GCTGCAGCTCCATGTATACG 58.857 55.000 31.33 0.00 38.21 3.06
732 757 1.143305 CTGCAGCTCCATGTATACGC 58.857 55.000 0.00 0.00 0.00 4.42
736 761 2.759191 CAGCTCCATGTATACGCATGT 58.241 47.619 0.00 0.00 43.33 3.21
747 772 0.604243 TACGCATGTGGTGTGGGAAC 60.604 55.000 11.65 0.00 42.69 3.62
789 820 0.944386 GGCATCGGCATGTCGTTATT 59.056 50.000 20.64 0.39 43.71 1.40
790 821 2.139917 GGCATCGGCATGTCGTTATTA 58.860 47.619 20.64 0.00 43.71 0.98
791 822 2.742053 GGCATCGGCATGTCGTTATTAT 59.258 45.455 20.64 1.85 43.71 1.28
826 857 1.936436 GCATGCATCCGGCTGAAACA 61.936 55.000 14.21 0.00 45.15 2.83
828 859 0.813184 ATGCATCCGGCTGAAACAAG 59.187 50.000 10.06 0.00 45.15 3.16
895 932 3.792736 GTCCCCCGGCATGCAGTA 61.793 66.667 21.36 0.00 0.00 2.74
899 936 1.893808 CCCCGGCATGCAGTACATC 60.894 63.158 21.36 0.00 36.64 3.06
1257 1298 1.495878 TCTCGGAGATACTCGTACGC 58.504 55.000 11.24 0.00 33.89 4.42
1259 1300 1.203563 CGGAGATACTCGTACGCCG 59.796 63.158 11.24 12.02 38.13 6.46
1410 1451 1.662309 CCGCACTATACCGACATCGTC 60.662 57.143 0.00 0.00 37.74 4.20
1628 1669 1.303309 GATTCCCGTCAGAATGCTGG 58.697 55.000 0.00 0.00 42.53 4.85
1698 1739 4.379243 ACCGCCTTCTCCGTGCTG 62.379 66.667 0.00 0.00 0.00 4.41
2040 2081 1.298859 GGGGCACACACGTCATCTTC 61.299 60.000 0.00 0.00 0.00 2.87
2420 2463 7.118723 ACCATAGTGTATTGTTGGACAATCAT 58.881 34.615 9.37 0.00 44.91 2.45
2421 2464 7.283127 ACCATAGTGTATTGTTGGACAATCATC 59.717 37.037 9.37 3.94 44.91 2.92
2422 2465 7.282901 CCATAGTGTATTGTTGGACAATCATCA 59.717 37.037 9.37 6.05 44.91 3.07
2433 2476 5.472148 TGGACAATCATCAATTTGTTGCTC 58.528 37.500 3.09 0.00 0.00 4.26
3360 3403 2.045926 GGTGCATGCGGGAGTTCT 60.046 61.111 14.09 0.00 0.00 3.01
3620 3663 1.200760 TGCTGGTGGTGCAGTCCTAT 61.201 55.000 0.00 0.00 35.31 2.57
3659 3708 4.755614 GCCGCGTCGACGTCTTCT 62.756 66.667 35.48 0.00 42.22 2.85
3780 3829 7.281774 CACATTCTGACCTTATGCTTTGATAGT 59.718 37.037 0.00 0.00 0.00 2.12
3781 3830 8.486210 ACATTCTGACCTTATGCTTTGATAGTA 58.514 33.333 0.00 0.00 0.00 1.82
3782 3831 8.986847 CATTCTGACCTTATGCTTTGATAGTAG 58.013 37.037 0.00 0.00 0.00 2.57
3823 3872 9.252962 GCTTGCTAGCACATTGATTAATTAATT 57.747 29.630 19.17 5.89 46.95 1.40
3872 3921 3.878778 CAGGGGAATTAGGAAGTGTCTG 58.121 50.000 0.00 0.00 0.00 3.51
3885 3934 4.350346 GAAGTGTCTGATGATCAGTCGAG 58.650 47.826 20.82 0.00 44.58 4.04
4003 4053 5.856455 CCAACGGAAACTTTGATTCACATAC 59.144 40.000 0.00 0.00 41.80 2.39
4004 4054 5.277601 ACGGAAACTTTGATTCACATACG 57.722 39.130 0.00 0.00 0.00 3.06
4007 4057 6.592607 ACGGAAACTTTGATTCACATACGTAT 59.407 34.615 1.14 1.14 0.00 3.06
4008 4058 7.760794 ACGGAAACTTTGATTCACATACGTATA 59.239 33.333 7.96 0.00 0.00 1.47
4010 4060 9.698617 GGAAACTTTGATTCACATACGTATAAC 57.301 33.333 7.96 0.00 0.00 1.89
4014 4064 9.378551 ACTTTGATTCACATACGTATAACACAT 57.621 29.630 7.96 0.00 0.00 3.21
4015 4065 9.636965 CTTTGATTCACATACGTATAACACATG 57.363 33.333 7.96 0.00 0.00 3.21
4016 4066 7.172654 TGATTCACATACGTATAACACATGC 57.827 36.000 7.96 0.00 0.00 4.06
4018 4068 6.582437 TTCACATACGTATAACACATGCAG 57.418 37.500 7.96 0.00 0.00 4.41
4043 4388 4.772046 TGCTATCGAAGTATGAAAACGC 57.228 40.909 0.00 0.00 0.00 4.84
4045 4390 4.868171 TGCTATCGAAGTATGAAAACGCTT 59.132 37.500 0.00 0.00 0.00 4.68
4047 4392 4.859629 ATCGAAGTATGAAAACGCTTCC 57.140 40.909 0.00 0.00 35.28 3.46
4048 4393 2.997986 TCGAAGTATGAAAACGCTTCCC 59.002 45.455 0.00 0.00 35.28 3.97
4049 4394 3.000727 CGAAGTATGAAAACGCTTCCCT 58.999 45.455 0.00 0.00 35.28 4.20
4050 4395 4.082081 TCGAAGTATGAAAACGCTTCCCTA 60.082 41.667 0.00 0.00 35.28 3.53
4052 4397 5.293569 CGAAGTATGAAAACGCTTCCCTATT 59.706 40.000 0.00 0.00 35.28 1.73
4053 4398 6.477688 CGAAGTATGAAAACGCTTCCCTATTA 59.522 38.462 0.00 0.00 35.28 0.98
4054 4399 7.306632 CGAAGTATGAAAACGCTTCCCTATTAG 60.307 40.741 0.00 0.00 35.28 1.73
4057 4402 4.328536 TGAAAACGCTTCCCTATTAGCAA 58.671 39.130 0.00 0.00 37.23 3.91
4058 4403 4.947388 TGAAAACGCTTCCCTATTAGCAAT 59.053 37.500 0.00 0.00 37.23 3.56
4059 4404 4.900635 AAACGCTTCCCTATTAGCAATG 57.099 40.909 0.00 0.00 37.23 2.82
4060 4405 3.560636 ACGCTTCCCTATTAGCAATGT 57.439 42.857 0.00 0.00 37.23 2.71
4061 4406 4.682778 ACGCTTCCCTATTAGCAATGTA 57.317 40.909 0.00 0.00 37.23 2.29
4062 4407 5.228945 ACGCTTCCCTATTAGCAATGTAT 57.771 39.130 0.00 0.00 37.23 2.29
4063 4408 6.354794 ACGCTTCCCTATTAGCAATGTATA 57.645 37.500 0.00 0.00 37.23 1.47
4064 4409 6.765403 ACGCTTCCCTATTAGCAATGTATAA 58.235 36.000 0.00 0.00 37.23 0.98
4065 4410 6.649557 ACGCTTCCCTATTAGCAATGTATAAC 59.350 38.462 0.00 0.00 37.23 1.89
4066 4411 6.649141 CGCTTCCCTATTAGCAATGTATAACA 59.351 38.462 0.00 0.00 37.23 2.41
4067 4412 7.360101 CGCTTCCCTATTAGCAATGTATAACAC 60.360 40.741 0.00 0.00 37.23 3.32
4068 4413 7.661847 GCTTCCCTATTAGCAATGTATAACACT 59.338 37.037 0.00 0.00 37.35 3.55
4069 4414 8.902540 TTCCCTATTAGCAATGTATAACACTG 57.097 34.615 0.00 0.00 0.00 3.66
4070 4415 8.257602 TCCCTATTAGCAATGTATAACACTGA 57.742 34.615 0.00 0.00 24.12 3.41
4071 4416 8.710239 TCCCTATTAGCAATGTATAACACTGAA 58.290 33.333 0.00 0.00 24.12 3.02
4072 4417 8.993121 CCCTATTAGCAATGTATAACACTGAAG 58.007 37.037 0.00 0.00 24.12 3.02
4073 4418 9.764363 CCTATTAGCAATGTATAACACTGAAGA 57.236 33.333 0.00 0.00 24.12 2.87
4079 4424 9.448438 AGCAATGTATAACACTGAAGAAATACA 57.552 29.630 0.00 0.00 35.11 2.29
4080 4425 9.708222 GCAATGTATAACACTGAAGAAATACAG 57.292 33.333 0.00 0.00 34.38 2.74
4083 4428 9.823647 ATGTATAACACTGAAGAAATACAGAGG 57.176 33.333 0.00 0.00 34.38 3.69
4084 4429 9.031537 TGTATAACACTGAAGAAATACAGAGGA 57.968 33.333 0.00 0.00 37.54 3.71
4085 4430 9.303537 GTATAACACTGAAGAAATACAGAGGAC 57.696 37.037 0.00 0.00 37.54 3.85
4086 4431 5.808366 ACACTGAAGAAATACAGAGGACA 57.192 39.130 0.00 0.00 37.54 4.02
4087 4432 5.542779 ACACTGAAGAAATACAGAGGACAC 58.457 41.667 0.00 0.00 37.54 3.67
4088 4433 5.070446 ACACTGAAGAAATACAGAGGACACA 59.930 40.000 0.00 0.00 37.54 3.72
4089 4434 5.636965 CACTGAAGAAATACAGAGGACACAG 59.363 44.000 0.00 0.00 37.54 3.66
4090 4435 5.152623 TGAAGAAATACAGAGGACACAGG 57.847 43.478 0.00 0.00 0.00 4.00
4091 4436 4.838423 TGAAGAAATACAGAGGACACAGGA 59.162 41.667 0.00 0.00 0.00 3.86
4092 4437 5.306937 TGAAGAAATACAGAGGACACAGGAA 59.693 40.000 0.00 0.00 0.00 3.36
4093 4438 5.825593 AGAAATACAGAGGACACAGGAAA 57.174 39.130 0.00 0.00 0.00 3.13
4094 4439 6.380079 AGAAATACAGAGGACACAGGAAAT 57.620 37.500 0.00 0.00 0.00 2.17
4095 4440 6.410540 AGAAATACAGAGGACACAGGAAATC 58.589 40.000 0.00 0.00 0.00 2.17
4096 4441 5.762179 AATACAGAGGACACAGGAAATCA 57.238 39.130 0.00 0.00 0.00 2.57
4097 4442 5.965033 ATACAGAGGACACAGGAAATCAT 57.035 39.130 0.00 0.00 0.00 2.45
4098 4443 4.647564 ACAGAGGACACAGGAAATCATT 57.352 40.909 0.00 0.00 0.00 2.57
4099 4444 4.330250 ACAGAGGACACAGGAAATCATTG 58.670 43.478 0.00 0.00 0.00 2.82
4100 4445 4.042062 ACAGAGGACACAGGAAATCATTGA 59.958 41.667 0.00 0.00 0.00 2.57
4101 4446 4.394300 CAGAGGACACAGGAAATCATTGAC 59.606 45.833 0.00 0.00 0.00 3.18
4102 4447 3.690460 AGGACACAGGAAATCATTGACC 58.310 45.455 0.00 0.00 0.00 4.02
4103 4448 3.331889 AGGACACAGGAAATCATTGACCT 59.668 43.478 0.00 0.00 0.00 3.85
4104 4449 4.082125 GGACACAGGAAATCATTGACCTT 58.918 43.478 0.00 0.00 0.00 3.50
4105 4450 4.082571 GGACACAGGAAATCATTGACCTTG 60.083 45.833 0.00 0.00 0.00 3.61
4106 4451 3.256631 ACACAGGAAATCATTGACCTTGC 59.743 43.478 0.00 0.00 0.00 4.01
4107 4452 2.827921 ACAGGAAATCATTGACCTTGCC 59.172 45.455 0.00 0.00 0.00 4.52
4108 4453 2.827322 CAGGAAATCATTGACCTTGCCA 59.173 45.455 0.81 0.00 0.00 4.92
4109 4454 3.258872 CAGGAAATCATTGACCTTGCCAA 59.741 43.478 0.81 0.00 0.00 4.52
4110 4455 3.259123 AGGAAATCATTGACCTTGCCAAC 59.741 43.478 0.81 0.00 0.00 3.77
4111 4456 3.006752 GGAAATCATTGACCTTGCCAACA 59.993 43.478 0.00 0.00 0.00 3.33
4112 4457 4.322953 GGAAATCATTGACCTTGCCAACAT 60.323 41.667 0.00 0.00 0.00 2.71
4113 4458 4.460948 AATCATTGACCTTGCCAACATC 57.539 40.909 0.00 0.00 0.00 3.06
4114 4459 1.811965 TCATTGACCTTGCCAACATCG 59.188 47.619 0.00 0.00 0.00 3.84
4115 4460 0.527565 ATTGACCTTGCCAACATCGC 59.472 50.000 0.00 0.00 0.00 4.58
4116 4461 1.523154 TTGACCTTGCCAACATCGCC 61.523 55.000 0.00 0.00 0.00 5.54
4117 4462 1.971167 GACCTTGCCAACATCGCCA 60.971 57.895 0.00 0.00 0.00 5.69
4118 4463 1.523154 GACCTTGCCAACATCGCCAA 61.523 55.000 0.00 0.00 0.00 4.52
4119 4464 1.080569 CCTTGCCAACATCGCCAAC 60.081 57.895 0.00 0.00 0.00 3.77
4120 4465 1.659233 CTTGCCAACATCGCCAACA 59.341 52.632 0.00 0.00 0.00 3.33
4121 4466 0.387622 CTTGCCAACATCGCCAACAG 60.388 55.000 0.00 0.00 0.00 3.16
4122 4467 1.106351 TTGCCAACATCGCCAACAGT 61.106 50.000 0.00 0.00 0.00 3.55
4123 4468 0.250510 TGCCAACATCGCCAACAGTA 60.251 50.000 0.00 0.00 0.00 2.74
4124 4469 0.168128 GCCAACATCGCCAACAGTAC 59.832 55.000 0.00 0.00 0.00 2.73
4125 4470 1.808411 CCAACATCGCCAACAGTACT 58.192 50.000 0.00 0.00 0.00 2.73
4126 4471 1.464608 CCAACATCGCCAACAGTACTG 59.535 52.381 21.44 21.44 0.00 2.74
4146 4491 5.700846 ACTGAACGGATGATCGATGTATAC 58.299 41.667 0.54 0.00 0.00 1.47
4157 4502 3.946606 TCGATGTATACCCTCGCATAGA 58.053 45.455 16.12 0.42 32.62 1.98
4170 4515 4.770287 CTCGCATAGAAAATGTGAGCATC 58.230 43.478 13.74 0.00 45.71 3.91
4186 4531 4.133078 GAGCATCCTTGATGAACCTAAGG 58.867 47.826 8.21 0.00 42.09 2.69
4207 7872 2.755469 GTGCAACATCCCGGGCAT 60.755 61.111 18.49 7.71 38.68 4.40
4214 7879 0.916086 ACATCCCGGGCATAGTTCAA 59.084 50.000 18.49 0.00 0.00 2.69
4229 7894 4.813296 AGTTCAAGCGAAGGTAACAAAG 57.187 40.909 0.00 0.00 37.06 2.77
4249 7914 4.891992 AGTAGGCTTGAAGCTGAAAGTA 57.108 40.909 17.59 0.00 41.99 2.24
4250 7915 5.428184 AGTAGGCTTGAAGCTGAAAGTAT 57.572 39.130 17.59 3.04 41.99 2.12
4251 7916 6.546428 AGTAGGCTTGAAGCTGAAAGTATA 57.454 37.500 17.59 2.29 41.99 1.47
4257 7923 8.049721 AGGCTTGAAGCTGAAAGTATACTAAAT 58.950 33.333 17.59 0.00 41.99 1.40
4322 7988 0.887387 TGCAAACTTGGCGTCCCTAC 60.887 55.000 0.00 0.00 0.00 3.18
4330 7996 3.845259 GCGTCCCTACCGGCATCA 61.845 66.667 0.00 0.00 0.00 3.07
4365 8031 3.891977 TCCTCCTCACATATGTCTACAGC 59.108 47.826 5.07 0.00 0.00 4.40
4438 8104 4.201679 CGGTCACCGCGAGCCATA 62.202 66.667 8.23 0.00 41.17 2.74
4505 8171 5.163713 GGATGTACAATCTTTGCACCTTCTC 60.164 44.000 0.00 0.00 0.00 2.87
4570 8236 4.170292 AGCAATCATCAGTTCAAGCAAC 57.830 40.909 0.00 0.00 34.86 4.17
4590 8257 7.889469 AGCAACAAGAAAATATCTGTGTGAAT 58.111 30.769 0.00 0.00 38.79 2.57
4617 8284 8.618702 AAAGATTATCATCACTTCATAGCCTG 57.381 34.615 0.00 0.00 0.00 4.85
4620 8287 3.851458 TCATCACTTCATAGCCTGCAT 57.149 42.857 0.00 0.00 0.00 3.96
4649 8326 8.929487 AGATAAGAAGAGGTAAATCCCTAACAG 58.071 37.037 0.00 0.00 34.03 3.16
4761 8438 3.825014 AGCATGCTCAGAATGTTTCTTGT 59.175 39.130 16.30 0.00 38.11 3.16
4764 8441 6.152323 AGCATGCTCAGAATGTTTCTTGTAAT 59.848 34.615 16.30 0.00 38.11 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 4.460263 TCTTTTATTATCGCATGTGGCCT 58.540 39.130 3.32 0.00 40.31 5.19
72 74 4.829064 TCTTTTATTATCGCATGTGGCC 57.171 40.909 6.39 0.00 40.31 5.36
154 160 2.170397 TGTTGAGCCGTCATCACCATAT 59.830 45.455 0.00 0.00 30.85 1.78
173 179 3.194968 CGAAGTACCATACCAGAACCTGT 59.805 47.826 0.00 0.00 0.00 4.00
229 235 5.566469 TCCCGACATGAAAATAGTTTCCTT 58.434 37.500 12.73 0.00 42.20 3.36
233 239 7.112779 AGAGAATCCCGACATGAAAATAGTTT 58.887 34.615 0.00 0.00 33.66 2.66
264 270 4.640771 TCCATAAAAGCACTCAACTCCT 57.359 40.909 0.00 0.00 0.00 3.69
269 275 4.761739 CAGTCCTTCCATAAAAGCACTCAA 59.238 41.667 0.00 0.00 24.22 3.02
279 285 2.673043 GCGAACGACAGTCCTTCCATAA 60.673 50.000 6.69 0.00 0.00 1.90
321 327 9.481340 CGATTGAATTCATTTCTATCTCCACTA 57.519 33.333 9.40 0.00 41.55 2.74
338 344 6.272318 TCAACTTGAAAGCAACGATTGAATT 58.728 32.000 0.00 0.00 0.00 2.17
618 643 9.354673 TCCTCTTTCTTTTAAAACTGTGATGAT 57.645 29.630 0.00 0.00 0.00 2.45
619 644 8.621286 GTCCTCTTTCTTTTAAAACTGTGATGA 58.379 33.333 0.00 0.00 0.00 2.92
620 645 7.587757 CGTCCTCTTTCTTTTAAAACTGTGATG 59.412 37.037 0.00 0.00 0.00 3.07
621 646 7.255139 CCGTCCTCTTTCTTTTAAAACTGTGAT 60.255 37.037 0.00 0.00 0.00 3.06
622 647 6.037830 CCGTCCTCTTTCTTTTAAAACTGTGA 59.962 38.462 0.00 0.00 0.00 3.58
623 648 6.183360 ACCGTCCTCTTTCTTTTAAAACTGTG 60.183 38.462 0.00 0.00 0.00 3.66
624 649 5.884232 ACCGTCCTCTTTCTTTTAAAACTGT 59.116 36.000 0.00 0.00 0.00 3.55
625 650 6.199393 CACCGTCCTCTTTCTTTTAAAACTG 58.801 40.000 0.00 0.00 0.00 3.16
626 651 5.298527 CCACCGTCCTCTTTCTTTTAAAACT 59.701 40.000 0.00 0.00 0.00 2.66
627 652 5.297527 TCCACCGTCCTCTTTCTTTTAAAAC 59.702 40.000 0.00 0.00 0.00 2.43
628 653 5.438833 TCCACCGTCCTCTTTCTTTTAAAA 58.561 37.500 0.00 0.00 0.00 1.52
629 654 5.038651 TCCACCGTCCTCTTTCTTTTAAA 57.961 39.130 0.00 0.00 0.00 1.52
630 655 4.345837 TCTCCACCGTCCTCTTTCTTTTAA 59.654 41.667 0.00 0.00 0.00 1.52
631 656 3.899360 TCTCCACCGTCCTCTTTCTTTTA 59.101 43.478 0.00 0.00 0.00 1.52
632 657 2.704065 TCTCCACCGTCCTCTTTCTTTT 59.296 45.455 0.00 0.00 0.00 2.27
633 658 2.326428 TCTCCACCGTCCTCTTTCTTT 58.674 47.619 0.00 0.00 0.00 2.52
634 659 2.011122 TCTCCACCGTCCTCTTTCTT 57.989 50.000 0.00 0.00 0.00 2.52
635 660 2.234908 CAATCTCCACCGTCCTCTTTCT 59.765 50.000 0.00 0.00 0.00 2.52
636 661 2.622436 CAATCTCCACCGTCCTCTTTC 58.378 52.381 0.00 0.00 0.00 2.62
637 662 1.279271 CCAATCTCCACCGTCCTCTTT 59.721 52.381 0.00 0.00 0.00 2.52
638 663 0.905357 CCAATCTCCACCGTCCTCTT 59.095 55.000 0.00 0.00 0.00 2.85
639 664 0.041238 TCCAATCTCCACCGTCCTCT 59.959 55.000 0.00 0.00 0.00 3.69
640 665 1.069358 GATCCAATCTCCACCGTCCTC 59.931 57.143 0.00 0.00 0.00 3.71
641 666 1.123928 GATCCAATCTCCACCGTCCT 58.876 55.000 0.00 0.00 0.00 3.85
642 667 0.830648 TGATCCAATCTCCACCGTCC 59.169 55.000 0.00 0.00 0.00 4.79
643 668 2.691409 TTGATCCAATCTCCACCGTC 57.309 50.000 0.00 0.00 0.00 4.79
644 669 3.433306 TTTTGATCCAATCTCCACCGT 57.567 42.857 0.00 0.00 0.00 4.83
645 670 4.989279 AATTTTGATCCAATCTCCACCG 57.011 40.909 0.00 0.00 0.00 4.94
646 671 5.125417 TCGAAATTTTGATCCAATCTCCACC 59.875 40.000 3.86 0.00 0.00 4.61
647 672 6.194796 TCGAAATTTTGATCCAATCTCCAC 57.805 37.500 3.86 0.00 0.00 4.02
648 673 7.122501 TGAATCGAAATTTTGATCCAATCTCCA 59.877 33.333 19.16 6.88 30.98 3.86
649 674 7.433425 GTGAATCGAAATTTTGATCCAATCTCC 59.567 37.037 19.16 0.00 30.98 3.71
650 675 7.164826 CGTGAATCGAAATTTTGATCCAATCTC 59.835 37.037 19.16 12.93 42.86 2.75
651 676 6.968904 CGTGAATCGAAATTTTGATCCAATCT 59.031 34.615 19.16 4.82 42.86 2.40
652 677 6.291269 GCGTGAATCGAAATTTTGATCCAATC 60.291 38.462 19.16 13.82 42.86 2.67
653 678 5.516339 GCGTGAATCGAAATTTTGATCCAAT 59.484 36.000 19.16 5.82 42.86 3.16
654 679 4.856487 GCGTGAATCGAAATTTTGATCCAA 59.144 37.500 19.16 7.29 42.86 3.53
655 680 4.155826 AGCGTGAATCGAAATTTTGATCCA 59.844 37.500 19.16 11.78 42.86 3.41
656 681 4.662145 AGCGTGAATCGAAATTTTGATCC 58.338 39.130 19.16 9.29 42.86 3.36
657 682 7.264242 CGTATAGCGTGAATCGAAATTTTGATC 59.736 37.037 19.16 13.49 42.86 2.92
658 683 7.063456 CGTATAGCGTGAATCGAAATTTTGAT 58.937 34.615 14.21 14.21 42.86 2.57
659 684 6.407623 CGTATAGCGTGAATCGAAATTTTGA 58.592 36.000 10.57 10.57 42.86 2.69
660 685 5.615581 CCGTATAGCGTGAATCGAAATTTTG 59.384 40.000 0.00 0.00 42.86 2.44
661 686 5.521010 TCCGTATAGCGTGAATCGAAATTTT 59.479 36.000 0.00 0.00 42.86 1.82
662 687 5.045215 TCCGTATAGCGTGAATCGAAATTT 58.955 37.500 0.00 0.00 42.86 1.82
663 688 4.613944 TCCGTATAGCGTGAATCGAAATT 58.386 39.130 0.00 0.00 42.86 1.82
664 689 4.233123 TCCGTATAGCGTGAATCGAAAT 57.767 40.909 0.00 0.00 42.86 2.17
665 690 3.696281 TCCGTATAGCGTGAATCGAAA 57.304 42.857 0.00 0.00 42.86 3.46
666 691 3.696281 TTCCGTATAGCGTGAATCGAA 57.304 42.857 0.00 0.00 42.86 3.71
667 692 3.696281 TTTCCGTATAGCGTGAATCGA 57.304 42.857 0.00 0.00 42.86 3.59
668 693 4.501559 TCTTTTTCCGTATAGCGTGAATCG 59.498 41.667 0.00 0.00 43.12 3.34
669 694 5.961395 TCTTTTTCCGTATAGCGTGAATC 57.039 39.130 0.00 0.00 39.32 2.52
670 695 6.730960 TTTCTTTTTCCGTATAGCGTGAAT 57.269 33.333 0.00 0.00 39.32 2.57
671 696 6.424509 TCTTTTCTTTTTCCGTATAGCGTGAA 59.575 34.615 0.00 0.00 39.32 3.18
672 697 5.927689 TCTTTTCTTTTTCCGTATAGCGTGA 59.072 36.000 0.00 0.00 39.32 4.35
673 698 6.160664 TCTTTTCTTTTTCCGTATAGCGTG 57.839 37.500 0.00 0.00 39.32 5.34
674 699 6.790285 TTCTTTTCTTTTTCCGTATAGCGT 57.210 33.333 0.00 0.00 39.32 5.07
675 700 8.013378 TCTTTTCTTTTCTTTTTCCGTATAGCG 58.987 33.333 0.00 0.00 40.95 4.26
676 701 9.673454 TTCTTTTCTTTTCTTTTTCCGTATAGC 57.327 29.630 0.00 0.00 0.00 2.97
680 705 9.694137 TGTTTTCTTTTCTTTTCTTTTTCCGTA 57.306 25.926 0.00 0.00 0.00 4.02
681 706 8.596271 TGTTTTCTTTTCTTTTCTTTTTCCGT 57.404 26.923 0.00 0.00 0.00 4.69
687 712 9.992910 GCATGAATGTTTTCTTTTCTTTTCTTT 57.007 25.926 0.00 0.00 32.78 2.52
688 713 9.387257 AGCATGAATGTTTTCTTTTCTTTTCTT 57.613 25.926 0.00 0.00 32.78 2.52
689 714 8.823818 CAGCATGAATGTTTTCTTTTCTTTTCT 58.176 29.630 0.00 0.00 39.69 2.52
690 715 7.585210 GCAGCATGAATGTTTTCTTTTCTTTTC 59.415 33.333 0.00 0.00 39.69 2.29
691 716 7.066043 TGCAGCATGAATGTTTTCTTTTCTTTT 59.934 29.630 0.00 0.00 39.69 2.27
692 717 6.539464 TGCAGCATGAATGTTTTCTTTTCTTT 59.461 30.769 0.00 0.00 39.69 2.52
693 718 6.050432 TGCAGCATGAATGTTTTCTTTTCTT 58.950 32.000 0.00 0.00 39.69 2.52
694 719 5.603596 TGCAGCATGAATGTTTTCTTTTCT 58.396 33.333 0.00 0.00 39.69 2.52
695 720 5.614013 GCTGCAGCATGAATGTTTTCTTTTC 60.614 40.000 33.36 0.00 39.69 2.29
696 721 4.212636 GCTGCAGCATGAATGTTTTCTTTT 59.787 37.500 33.36 0.00 39.69 2.27
697 722 3.744426 GCTGCAGCATGAATGTTTTCTTT 59.256 39.130 33.36 0.00 39.69 2.52
698 723 3.006537 AGCTGCAGCATGAATGTTTTCTT 59.993 39.130 38.24 11.50 45.16 2.52
699 724 2.561419 AGCTGCAGCATGAATGTTTTCT 59.439 40.909 38.24 11.97 45.16 2.52
700 725 2.921754 GAGCTGCAGCATGAATGTTTTC 59.078 45.455 38.24 19.91 45.16 2.29
701 726 2.353406 GGAGCTGCAGCATGAATGTTTT 60.353 45.455 38.24 15.47 45.16 2.43
702 727 1.203994 GGAGCTGCAGCATGAATGTTT 59.796 47.619 38.24 16.27 45.16 2.83
703 728 0.815734 GGAGCTGCAGCATGAATGTT 59.184 50.000 38.24 17.06 45.16 2.71
704 729 0.323087 TGGAGCTGCAGCATGAATGT 60.323 50.000 38.24 17.87 45.16 2.71
705 730 1.032794 ATGGAGCTGCAGCATGAATG 58.967 50.000 38.24 0.46 45.16 2.67
711 736 1.538849 CGTATACATGGAGCTGCAGCA 60.539 52.381 38.24 20.45 45.16 4.41
729 754 1.896660 GTTCCCACACCACATGCGT 60.897 57.895 0.00 0.00 0.00 5.24
731 756 2.275380 GGGTTCCCACACCACATGC 61.275 63.158 2.59 0.00 38.79 4.06
732 757 0.251742 ATGGGTTCCCACACCACATG 60.252 55.000 13.19 0.00 38.79 3.21
736 761 0.178975 GTGAATGGGTTCCCACACCA 60.179 55.000 13.19 8.39 38.79 4.17
769 800 0.884704 ATAACGACATGCCGATGCCC 60.885 55.000 8.88 0.00 36.33 5.36
826 857 3.883489 GGCCGTAATTTTGATAGCTCCTT 59.117 43.478 0.00 0.00 0.00 3.36
828 859 2.552743 GGGCCGTAATTTTGATAGCTCC 59.447 50.000 0.00 0.00 0.00 4.70
880 917 3.420206 ATGTACTGCATGCCGGGGG 62.420 63.158 16.68 2.82 36.26 5.40
1029 1070 0.181350 GCTCCCATAGGTCCAACAGG 59.819 60.000 0.00 0.00 0.00 4.00
1034 1075 0.982852 CAGGTGCTCCCATAGGTCCA 60.983 60.000 0.00 0.00 34.66 4.02
1257 1298 3.521529 GATCATGGAGACGGGCCGG 62.522 68.421 31.78 12.53 0.00 6.13
1259 1300 1.227674 GTGATCATGGAGACGGGCC 60.228 63.158 0.00 0.00 0.00 5.80
1628 1669 0.179184 GGAGAGTCTGTCGACGAAGC 60.179 60.000 11.62 6.82 44.93 3.86
1953 1994 4.193334 TCGCGCTCCTCACCGATG 62.193 66.667 5.56 0.00 0.00 3.84
2040 2081 3.361977 CCAAACACGAAGGCCCCG 61.362 66.667 12.92 12.92 0.00 5.73
2334 2375 1.256812 TGTTGAGGATGACGAGCTCA 58.743 50.000 15.40 0.00 0.00 4.26
2420 2463 3.307674 GCACGAATGAGCAACAAATTGA 58.692 40.909 0.00 0.00 38.15 2.57
2421 2464 2.089427 CGCACGAATGAGCAACAAATTG 59.911 45.455 0.00 0.00 38.99 2.32
2422 2465 2.287547 ACGCACGAATGAGCAACAAATT 60.288 40.909 0.00 0.00 0.00 1.82
2433 2476 0.166597 AAGACATGCACGCACGAATG 59.833 50.000 0.00 0.65 0.00 2.67
2539 2582 0.518636 CTTGACAACCATGGTCAGCG 59.481 55.000 20.07 9.83 45.20 5.18
2937 2980 2.261671 GTCCTCGTGCATGGACGT 59.738 61.111 33.95 0.00 42.51 4.34
3053 3096 3.084579 GCGTTCAGCGACTGGATG 58.915 61.111 6.95 5.29 44.77 3.51
3092 3135 4.722700 AGGATGGCCACCGTGCAC 62.723 66.667 8.16 6.82 33.12 4.57
3341 3384 3.918253 GAACTCCCGCATGCACCCA 62.918 63.158 19.57 0.00 0.00 4.51
3515 3558 3.095347 GCTCCAGTCCGACATCCCC 62.095 68.421 0.40 0.00 0.00 4.81
3644 3693 0.793478 ATTCAGAAGACGTCGACGCG 60.793 55.000 35.92 16.05 44.43 6.01
3651 3700 3.003689 CCAACAGCAAATTCAGAAGACGT 59.996 43.478 0.00 0.00 0.00 4.34
3659 3708 0.597568 CCTCGCCAACAGCAAATTCA 59.402 50.000 0.00 0.00 44.04 2.57
3780 3829 7.709613 GCTAGCAAGCTTTACCAAACTATACTA 59.290 37.037 10.63 0.00 45.85 1.82
3781 3830 6.539103 GCTAGCAAGCTTTACCAAACTATACT 59.461 38.462 10.63 0.00 45.85 2.12
3782 3831 6.716438 GCTAGCAAGCTTTACCAAACTATAC 58.284 40.000 10.63 0.00 45.85 1.47
3872 3921 7.706281 AATTAACATCACTCGACTGATCATC 57.294 36.000 4.76 0.00 0.00 2.92
3885 3934 5.240623 TGACTGTCACCCAAATTAACATCAC 59.759 40.000 6.36 0.00 0.00 3.06
4016 4066 7.340699 GTTTTCATACTTCGATAGCATGTCTG 58.659 38.462 0.00 0.00 0.00 3.51
4018 4068 6.347881 CGTTTTCATACTTCGATAGCATGTC 58.652 40.000 0.00 0.00 0.00 3.06
4029 4374 6.679327 AATAGGGAAGCGTTTTCATACTTC 57.321 37.500 0.00 0.00 38.22 3.01
4035 4380 3.945346 TGCTAATAGGGAAGCGTTTTCA 58.055 40.909 0.00 0.00 41.77 2.69
4042 4387 7.661847 AGTGTTATACATTGCTAATAGGGAAGC 59.338 37.037 0.00 0.00 39.25 3.86
4043 4388 8.993121 CAGTGTTATACATTGCTAATAGGGAAG 58.007 37.037 0.00 0.00 29.25 3.46
4045 4390 8.257602 TCAGTGTTATACATTGCTAATAGGGA 57.742 34.615 0.00 0.00 36.01 4.20
4047 4392 9.764363 TCTTCAGTGTTATACATTGCTAATAGG 57.236 33.333 0.00 0.00 36.01 2.57
4053 4398 9.448438 TGTATTTCTTCAGTGTTATACATTGCT 57.552 29.630 0.00 0.00 36.01 3.91
4054 4399 9.708222 CTGTATTTCTTCAGTGTTATACATTGC 57.292 33.333 0.00 0.00 36.01 3.56
4057 4402 9.823647 CCTCTGTATTTCTTCAGTGTTATACAT 57.176 33.333 0.00 0.00 33.89 2.29
4058 4403 9.031537 TCCTCTGTATTTCTTCAGTGTTATACA 57.968 33.333 0.00 0.00 33.89 2.29
4059 4404 9.303537 GTCCTCTGTATTTCTTCAGTGTTATAC 57.696 37.037 0.00 0.00 33.89 1.47
4060 4405 9.031537 TGTCCTCTGTATTTCTTCAGTGTTATA 57.968 33.333 0.00 0.00 33.89 0.98
4061 4406 7.819900 GTGTCCTCTGTATTTCTTCAGTGTTAT 59.180 37.037 0.00 0.00 33.89 1.89
4062 4407 7.152645 GTGTCCTCTGTATTTCTTCAGTGTTA 58.847 38.462 0.00 0.00 33.89 2.41
4063 4408 5.992217 GTGTCCTCTGTATTTCTTCAGTGTT 59.008 40.000 0.00 0.00 33.89 3.32
4064 4409 5.070446 TGTGTCCTCTGTATTTCTTCAGTGT 59.930 40.000 0.00 0.00 33.89 3.55
4065 4410 5.541845 TGTGTCCTCTGTATTTCTTCAGTG 58.458 41.667 0.00 0.00 33.89 3.66
4066 4411 5.279708 CCTGTGTCCTCTGTATTTCTTCAGT 60.280 44.000 0.00 0.00 33.89 3.41
4067 4412 5.047021 TCCTGTGTCCTCTGTATTTCTTCAG 60.047 44.000 0.00 0.00 0.00 3.02
4068 4413 4.838423 TCCTGTGTCCTCTGTATTTCTTCA 59.162 41.667 0.00 0.00 0.00 3.02
4069 4414 5.407407 TCCTGTGTCCTCTGTATTTCTTC 57.593 43.478 0.00 0.00 0.00 2.87
4070 4415 5.825593 TTCCTGTGTCCTCTGTATTTCTT 57.174 39.130 0.00 0.00 0.00 2.52
4071 4416 5.825593 TTTCCTGTGTCCTCTGTATTTCT 57.174 39.130 0.00 0.00 0.00 2.52
4072 4417 6.173339 TGATTTCCTGTGTCCTCTGTATTTC 58.827 40.000 0.00 0.00 0.00 2.17
4073 4418 6.126863 TGATTTCCTGTGTCCTCTGTATTT 57.873 37.500 0.00 0.00 0.00 1.40
4074 4419 5.762179 TGATTTCCTGTGTCCTCTGTATT 57.238 39.130 0.00 0.00 0.00 1.89
4075 4420 5.965033 ATGATTTCCTGTGTCCTCTGTAT 57.035 39.130 0.00 0.00 0.00 2.29
4076 4421 5.248248 TCAATGATTTCCTGTGTCCTCTGTA 59.752 40.000 0.00 0.00 0.00 2.74
4077 4422 4.042062 TCAATGATTTCCTGTGTCCTCTGT 59.958 41.667 0.00 0.00 0.00 3.41
4078 4423 4.394300 GTCAATGATTTCCTGTGTCCTCTG 59.606 45.833 0.00 0.00 0.00 3.35
4079 4424 4.566488 GGTCAATGATTTCCTGTGTCCTCT 60.566 45.833 0.00 0.00 0.00 3.69
4080 4425 3.691609 GGTCAATGATTTCCTGTGTCCTC 59.308 47.826 0.00 0.00 0.00 3.71
4081 4426 3.331889 AGGTCAATGATTTCCTGTGTCCT 59.668 43.478 0.00 0.00 0.00 3.85
4082 4427 3.690460 AGGTCAATGATTTCCTGTGTCC 58.310 45.455 0.00 0.00 0.00 4.02
4083 4428 4.616835 GCAAGGTCAATGATTTCCTGTGTC 60.617 45.833 0.43 0.00 0.00 3.67
4084 4429 3.256631 GCAAGGTCAATGATTTCCTGTGT 59.743 43.478 0.43 0.00 0.00 3.72
4085 4430 3.367703 GGCAAGGTCAATGATTTCCTGTG 60.368 47.826 0.43 3.29 0.00 3.66
4086 4431 2.827921 GGCAAGGTCAATGATTTCCTGT 59.172 45.455 0.43 0.00 0.00 4.00
4087 4432 2.827322 TGGCAAGGTCAATGATTTCCTG 59.173 45.455 0.43 0.00 0.00 3.86
4088 4433 3.173953 TGGCAAGGTCAATGATTTCCT 57.826 42.857 0.00 0.00 0.00 3.36
4089 4434 3.006752 TGTTGGCAAGGTCAATGATTTCC 59.993 43.478 0.00 0.00 27.28 3.13
4090 4435 4.255833 TGTTGGCAAGGTCAATGATTTC 57.744 40.909 0.00 0.00 27.28 2.17
4091 4436 4.618927 CGATGTTGGCAAGGTCAATGATTT 60.619 41.667 0.00 0.00 27.28 2.17
4092 4437 3.119388 CGATGTTGGCAAGGTCAATGATT 60.119 43.478 0.00 0.00 27.28 2.57
4093 4438 2.424601 CGATGTTGGCAAGGTCAATGAT 59.575 45.455 0.00 0.00 27.28 2.45
4094 4439 1.811965 CGATGTTGGCAAGGTCAATGA 59.188 47.619 0.00 0.00 27.28 2.57
4095 4440 1.733389 GCGATGTTGGCAAGGTCAATG 60.733 52.381 0.00 0.00 27.28 2.82
4096 4441 0.527565 GCGATGTTGGCAAGGTCAAT 59.472 50.000 0.00 0.00 27.28 2.57
4097 4442 1.523154 GGCGATGTTGGCAAGGTCAA 61.523 55.000 0.00 0.00 0.00 3.18
4098 4443 1.971167 GGCGATGTTGGCAAGGTCA 60.971 57.895 0.00 0.00 0.00 4.02
4099 4444 1.971167 TGGCGATGTTGGCAAGGTC 60.971 57.895 0.00 0.54 41.96 3.85
4100 4445 2.115052 TGGCGATGTTGGCAAGGT 59.885 55.556 0.00 0.00 41.96 3.50
4104 4449 0.250510 TACTGTTGGCGATGTTGGCA 60.251 50.000 0.00 0.00 43.36 4.92
4105 4450 0.168128 GTACTGTTGGCGATGTTGGC 59.832 55.000 0.00 0.00 0.00 4.52
4106 4451 1.464608 CAGTACTGTTGGCGATGTTGG 59.535 52.381 15.06 0.00 0.00 3.77
4107 4452 2.412870 TCAGTACTGTTGGCGATGTTG 58.587 47.619 21.99 0.00 0.00 3.33
4108 4453 2.806244 GTTCAGTACTGTTGGCGATGTT 59.194 45.455 21.99 0.00 0.00 2.71
4109 4454 2.413837 GTTCAGTACTGTTGGCGATGT 58.586 47.619 21.99 0.00 0.00 3.06
4110 4455 1.390123 CGTTCAGTACTGTTGGCGATG 59.610 52.381 21.99 5.21 0.00 3.84
4111 4456 1.671850 CCGTTCAGTACTGTTGGCGAT 60.672 52.381 21.99 0.00 0.00 4.58
4112 4457 0.319211 CCGTTCAGTACTGTTGGCGA 60.319 55.000 21.99 0.00 0.00 5.54
4113 4458 0.319211 TCCGTTCAGTACTGTTGGCG 60.319 55.000 21.99 19.10 0.00 5.69
4114 4459 1.732259 CATCCGTTCAGTACTGTTGGC 59.268 52.381 21.99 9.95 0.00 4.52
4115 4460 3.313012 TCATCCGTTCAGTACTGTTGG 57.687 47.619 21.99 19.98 0.00 3.77
4116 4461 3.547868 CGATCATCCGTTCAGTACTGTTG 59.452 47.826 21.99 12.62 0.00 3.33
4117 4462 3.442625 TCGATCATCCGTTCAGTACTGTT 59.557 43.478 21.99 0.00 0.00 3.16
4118 4463 3.014623 TCGATCATCCGTTCAGTACTGT 58.985 45.455 21.99 0.00 0.00 3.55
4119 4464 3.692791 TCGATCATCCGTTCAGTACTG 57.307 47.619 17.17 17.17 0.00 2.74
4120 4465 3.632604 ACATCGATCATCCGTTCAGTACT 59.367 43.478 0.00 0.00 0.00 2.73
4121 4466 3.966154 ACATCGATCATCCGTTCAGTAC 58.034 45.455 0.00 0.00 0.00 2.73
4122 4467 5.959618 ATACATCGATCATCCGTTCAGTA 57.040 39.130 0.00 0.00 0.00 2.74
4123 4468 4.855715 ATACATCGATCATCCGTTCAGT 57.144 40.909 0.00 0.00 0.00 3.41
4124 4469 5.096169 GGTATACATCGATCATCCGTTCAG 58.904 45.833 5.01 0.00 0.00 3.02
4125 4470 4.082408 GGGTATACATCGATCATCCGTTCA 60.082 45.833 5.01 0.00 0.00 3.18
4126 4471 4.158025 AGGGTATACATCGATCATCCGTTC 59.842 45.833 5.01 0.00 0.00 3.95
4146 4491 2.289002 GCTCACATTTTCTATGCGAGGG 59.711 50.000 0.00 0.00 31.03 4.30
4157 4502 5.337009 GGTTCATCAAGGATGCTCACATTTT 60.337 40.000 1.37 0.00 39.63 1.82
4170 4515 4.256920 CACAGACCTTAGGTTCATCAAGG 58.743 47.826 4.99 0.00 43.73 3.61
4186 4531 2.040544 CCCGGGATGTTGCACAGAC 61.041 63.158 18.48 0.00 0.00 3.51
4207 7872 5.362263 ACTTTGTTACCTTCGCTTGAACTA 58.638 37.500 0.00 0.00 0.00 2.24
4214 7879 2.302157 AGCCTACTTTGTTACCTTCGCT 59.698 45.455 0.00 0.00 0.00 4.93
4229 7894 6.342111 AGTATACTTTCAGCTTCAAGCCTAC 58.658 40.000 5.53 4.60 43.77 3.18
4249 7914 4.656112 CAGGGTCCCAGACTCATTTAGTAT 59.344 45.833 11.55 0.00 39.07 2.12
4250 7915 4.030913 CAGGGTCCCAGACTCATTTAGTA 58.969 47.826 11.55 0.00 39.07 1.82
4251 7916 2.840651 CAGGGTCCCAGACTCATTTAGT 59.159 50.000 11.55 0.00 42.80 2.24
4257 7923 0.042581 TATGCAGGGTCCCAGACTCA 59.957 55.000 11.55 0.33 35.11 3.41
4330 7996 5.759059 TGTGAGGAGGATTGCATCTATTTT 58.241 37.500 0.00 0.00 0.00 1.82
4356 8022 9.890629 AGTTTATAATTGATTCTGCTGTAGACA 57.109 29.630 0.00 0.00 34.43 3.41
4365 8031 7.800380 GTGATGGCGAGTTTATAATTGATTCTG 59.200 37.037 0.00 0.00 0.00 3.02
4408 8074 2.506438 GACCGCAGTAGCACGACC 60.506 66.667 0.00 0.00 42.27 4.79
4438 8104 0.874607 GTGACACCGACTTTGAGCGT 60.875 55.000 0.00 0.00 0.00 5.07
4505 8171 3.617263 GGCCGTTGTTATTACTGTGAGAG 59.383 47.826 0.00 0.00 0.00 3.20
4617 8284 9.004717 GGGATTTACCTCTTCTTATCTTAATGC 57.995 37.037 0.00 0.00 38.98 3.56
4649 8326 4.212214 GTCTGCACTTTAGCTATATGGTGC 59.788 45.833 22.39 22.39 46.65 5.01


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

AutoCloner maintained by Alex Coulton.