Multiple sequence alignment - TraesCS2A01G419200

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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 TraesCS2A01G419200 chr2A 100.000 5006 0 0 1 5006 674528217 674533222 0.000000e+00 9245.0
1 TraesCS2A01G419200 chr2A 84.298 605 92 2 4 605 182896169 182895565 5.580000e-164 588.0
2 TraesCS2A01G419200 chr2A 81.788 302 53 2 4706 5006 679977365 679977065 8.320000e-63 252.0
3 TraesCS2A01G419200 chr2A 100.000 51 0 0 4323 4373 674532461 674532511 1.480000e-15 95.3
4 TraesCS2A01G419200 chr2A 100.000 51 0 0 4245 4295 674532539 674532589 1.480000e-15 95.3
5 TraesCS2A01G419200 chr2B 93.632 3439 143 43 844 4234 629811327 629814737 0.000000e+00 5068.0
6 TraesCS2A01G419200 chr2B 94.250 713 32 5 4294 5006 629814760 629815463 0.000000e+00 1081.0
7 TraesCS2A01G419200 chr2B 92.373 118 9 0 4724 4841 150891052 150891169 8.620000e-38 169.0
8 TraesCS2A01G419200 chr2B 91.057 123 8 3 723 842 629811088 629811210 4.010000e-36 163.0
9 TraesCS2A01G419200 chr2D 93.801 2807 127 28 904 3686 529680502 529683285 0.000000e+00 4176.0
10 TraesCS2A01G419200 chr2D 94.250 713 32 6 4294 5006 529683740 529684443 0.000000e+00 1081.0
11 TraesCS2A01G419200 chr2D 91.264 435 31 7 3804 4234 529683286 529683717 2.010000e-163 586.0
12 TraesCS2A01G419200 chr2D 83.500 600 94 3 6 601 37640124 37639526 5.660000e-154 555.0
13 TraesCS2A01G419200 chr2D 86.784 227 30 0 4780 5006 537438568 537438342 2.310000e-63 254.0
14 TraesCS2A01G419200 chr4D 85.167 600 86 1 4 600 342831132 342830533 3.310000e-171 612.0
15 TraesCS2A01G419200 chr4D 83.555 602 94 3 1 598 491000608 491001208 4.380000e-155 558.0
16 TraesCS2A01G419200 chr4D 83.196 607 90 9 4 605 360116599 360116000 3.410000e-151 545.0
17 TraesCS2A01G419200 chr6D 85.329 593 82 3 17 604 364845769 364846361 4.290000e-170 608.0
18 TraesCS2A01G419200 chrUn 85.231 562 73 9 14 567 100273906 100274465 2.020000e-158 569.0
19 TraesCS2A01G419200 chr6A 83.306 611 94 5 1 604 506182692 506183301 1.570000e-154 556.0
20 TraesCS2A01G419200 chr1D 83.196 607 94 6 4 605 322162408 322161805 2.630000e-152 549.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G419200 chr2A 674528217 674533222 5005 False 3145.200000 9245 100.000000 1 5006 3 chr2A.!!$F1 5005
1 TraesCS2A01G419200 chr2A 182895565 182896169 604 True 588.000000 588 84.298000 4 605 1 chr2A.!!$R1 601
2 TraesCS2A01G419200 chr2B 629811088 629815463 4375 False 2104.000000 5068 92.979667 723 5006 3 chr2B.!!$F2 4283
3 TraesCS2A01G419200 chr2D 529680502 529684443 3941 False 1947.666667 4176 93.105000 904 5006 3 chr2D.!!$F1 4102
4 TraesCS2A01G419200 chr2D 37639526 37640124 598 True 555.000000 555 83.500000 6 601 1 chr2D.!!$R1 595
5 TraesCS2A01G419200 chr4D 342830533 342831132 599 True 612.000000 612 85.167000 4 600 1 chr4D.!!$R1 596
6 TraesCS2A01G419200 chr4D 491000608 491001208 600 False 558.000000 558 83.555000 1 598 1 chr4D.!!$F1 597
7 TraesCS2A01G419200 chr4D 360116000 360116599 599 True 545.000000 545 83.196000 4 605 1 chr4D.!!$R2 601
8 TraesCS2A01G419200 chr6D 364845769 364846361 592 False 608.000000 608 85.329000 17 604 1 chr6D.!!$F1 587
9 TraesCS2A01G419200 chrUn 100273906 100274465 559 False 569.000000 569 85.231000 14 567 1 chrUn.!!$F1 553
10 TraesCS2A01G419200 chr6A 506182692 506183301 609 False 556.000000 556 83.306000 1 604 1 chr6A.!!$F1 603
11 TraesCS2A01G419200 chr1D 322161805 322162408 603 True 549.000000 549 83.196000 4 605 1 chr1D.!!$R1 601

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
902 1037 0.031994 AGCAAACATGGAAACCGTGC 59.968 50.0 9.55 0.00 43.81 5.34 F
2662 2826 0.107848 AAAATAGTGGGACCGCTCGG 60.108 55.0 7.84 6.79 37.92 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2815 2982 1.557371 TGGGCTGATTCGGTGATTGTA 59.443 47.619 0.00 0.0 0.00 2.41 R
4395 4605 1.067364 CTTGCTGCATGTCAACAACCA 59.933 47.619 1.84 0.0 28.75 3.67 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
58 59 0.183014 ATGATGGCTCAAGCTCCCAG 59.817 55.000 1.46 0.00 41.70 4.45
66 67 2.165167 CTCAAGCTCCCAGCAATCAAA 58.835 47.619 0.00 0.00 45.56 2.69
79 80 2.029470 GCAATCAAATGGGTTGGACGAA 60.029 45.455 0.00 0.00 37.85 3.85
80 81 3.574614 CAATCAAATGGGTTGGACGAAC 58.425 45.455 0.00 0.00 37.85 3.95
89 90 2.552373 GGGTTGGACGAACAAGAGGAAT 60.552 50.000 2.63 0.00 36.12 3.01
95 96 7.282450 GGTTGGACGAACAAGAGGAATATATTT 59.718 37.037 0.00 0.00 36.12 1.40
148 151 2.301346 GATAACCAGCAAGTCATGGGG 58.699 52.381 0.00 0.00 41.13 4.96
154 157 2.173519 CAGCAAGTCATGGGGAACAAT 58.826 47.619 0.00 0.00 0.00 2.71
207 210 4.921470 CGACTACAAAAATGTCGTCCAT 57.079 40.909 6.59 0.00 45.54 3.41
215 218 7.156876 ACAAAAATGTCGTCCATATGAACAT 57.843 32.000 3.65 5.83 31.97 2.71
224 227 6.020440 GTCGTCCATATGAACATGCATTTTTG 60.020 38.462 3.65 0.00 0.00 2.44
269 276 6.299805 AGAGGTACAAGCTCATGTTGAATA 57.700 37.500 8.66 0.00 44.69 1.75
277 284 7.436118 ACAAGCTCATGTTGAATACACAAAAT 58.564 30.769 1.85 0.00 40.19 1.82
281 288 8.796475 AGCTCATGTTGAATACACAAAATAAGT 58.204 29.630 0.00 0.00 40.19 2.24
285 292 9.689976 CATGTTGAATACACAAAATAAGTGGAA 57.310 29.630 0.00 0.00 40.19 3.53
295 302 5.211201 CAAAATAAGTGGAAGGATGGGGAT 58.789 41.667 0.00 0.00 0.00 3.85
299 306 0.394565 GTGGAAGGATGGGGATCGAG 59.605 60.000 0.00 0.00 0.00 4.04
324 331 2.739379 GGACGGAGAAGAAGCTGAAAAG 59.261 50.000 0.00 0.00 0.00 2.27
359 366 2.329267 TCCAGTTGGAGAAGCAAGAGA 58.671 47.619 0.00 0.00 39.78 3.10
401 408 3.463048 AGAAGGCCAAGACATTTGGAT 57.537 42.857 5.01 0.00 42.06 3.41
412 419 6.017275 CCAAGACATTTGGATAGATTGAGCTC 60.017 42.308 6.82 6.82 42.06 4.09
418 425 5.598416 TTGGATAGATTGAGCTCGAGAAA 57.402 39.130 18.75 7.37 0.00 2.52
488 495 2.184533 TGGACGAAAGCCTCTTGGATA 58.815 47.619 0.00 0.00 34.57 2.59
536 550 7.713073 AGAAGAAGAAGAAAAAGATCAACGAGT 59.287 33.333 0.00 0.00 0.00 4.18
544 559 3.870633 AAGATCAACGAGTGTAGGGAC 57.129 47.619 0.00 0.00 0.00 4.46
579 595 2.173669 CGACTATGGCAGCAACGGG 61.174 63.158 0.00 0.00 0.00 5.28
602 619 2.334946 GCAACAAGGATGCAGGCGA 61.335 57.895 0.00 0.00 43.29 5.54
605 622 0.036732 AACAAGGATGCAGGCGAAGA 59.963 50.000 0.00 0.00 0.00 2.87
606 623 0.036732 ACAAGGATGCAGGCGAAGAA 59.963 50.000 0.00 0.00 0.00 2.52
607 624 1.167851 CAAGGATGCAGGCGAAGAAA 58.832 50.000 0.00 0.00 0.00 2.52
608 625 1.541147 CAAGGATGCAGGCGAAGAAAA 59.459 47.619 0.00 0.00 0.00 2.29
609 626 1.457346 AGGATGCAGGCGAAGAAAAG 58.543 50.000 0.00 0.00 0.00 2.27
610 627 0.453390 GGATGCAGGCGAAGAAAAGG 59.547 55.000 0.00 0.00 0.00 3.11
611 628 1.453155 GATGCAGGCGAAGAAAAGGA 58.547 50.000 0.00 0.00 0.00 3.36
612 629 2.019984 GATGCAGGCGAAGAAAAGGAT 58.980 47.619 0.00 0.00 0.00 3.24
613 630 1.167851 TGCAGGCGAAGAAAAGGATG 58.832 50.000 0.00 0.00 0.00 3.51
614 631 0.179153 GCAGGCGAAGAAAAGGATGC 60.179 55.000 0.00 0.00 0.00 3.91
615 632 1.167851 CAGGCGAAGAAAAGGATGCA 58.832 50.000 0.00 0.00 0.00 3.96
616 633 1.131883 CAGGCGAAGAAAAGGATGCAG 59.868 52.381 0.00 0.00 0.00 4.41
617 634 0.453390 GGCGAAGAAAAGGATGCAGG 59.547 55.000 0.00 0.00 0.00 4.85
618 635 0.179153 GCGAAGAAAAGGATGCAGGC 60.179 55.000 0.00 0.00 0.00 4.85
619 636 0.097674 CGAAGAAAAGGATGCAGGCG 59.902 55.000 0.00 0.00 0.00 5.52
620 637 0.179153 GAAGAAAAGGATGCAGGCGC 60.179 55.000 0.00 0.00 39.24 6.53
636 653 4.675029 GCACCCGCGGCCGTATAT 62.675 66.667 28.70 7.73 0.00 0.86
637 654 2.029964 CACCCGCGGCCGTATATT 59.970 61.111 28.70 4.66 0.00 1.28
638 655 1.595929 CACCCGCGGCCGTATATTT 60.596 57.895 28.70 3.44 0.00 1.40
639 656 1.595929 ACCCGCGGCCGTATATTTG 60.596 57.895 28.70 10.91 0.00 2.32
640 657 2.322081 CCCGCGGCCGTATATTTGG 61.322 63.158 28.70 16.05 0.00 3.28
649 666 4.584327 GCCGTATATTTGGCCTGATTTT 57.416 40.909 3.32 0.00 45.73 1.82
650 667 4.546570 GCCGTATATTTGGCCTGATTTTC 58.453 43.478 3.32 0.00 45.73 2.29
651 668 4.558697 GCCGTATATTTGGCCTGATTTTCC 60.559 45.833 3.32 0.00 45.73 3.13
652 669 4.582656 CCGTATATTTGGCCTGATTTTCCA 59.417 41.667 3.32 0.00 0.00 3.53
653 670 5.278463 CCGTATATTTGGCCTGATTTTCCAG 60.278 44.000 3.32 0.00 0.00 3.86
654 671 5.530915 CGTATATTTGGCCTGATTTTCCAGA 59.469 40.000 3.32 0.00 36.29 3.86
655 672 6.207417 CGTATATTTGGCCTGATTTTCCAGAT 59.793 38.462 3.32 0.00 36.29 2.90
656 673 6.661304 ATATTTGGCCTGATTTTCCAGATC 57.339 37.500 3.32 0.00 36.29 2.75
657 674 3.744940 TTGGCCTGATTTTCCAGATCT 57.255 42.857 3.32 0.00 36.29 2.75
658 675 3.008835 TGGCCTGATTTTCCAGATCTG 57.991 47.619 16.24 16.24 36.29 2.90
659 676 2.309755 TGGCCTGATTTTCCAGATCTGT 59.690 45.455 21.11 1.98 36.29 3.41
660 677 2.686915 GGCCTGATTTTCCAGATCTGTG 59.313 50.000 21.11 12.59 36.29 3.66
661 678 3.614092 GCCTGATTTTCCAGATCTGTGA 58.386 45.455 21.11 14.61 36.29 3.58
662 679 4.012374 GCCTGATTTTCCAGATCTGTGAA 58.988 43.478 21.11 19.06 36.29 3.18
663 680 4.643784 GCCTGATTTTCCAGATCTGTGAAT 59.356 41.667 21.11 16.17 36.29 2.57
664 681 5.450137 GCCTGATTTTCCAGATCTGTGAATG 60.450 44.000 21.11 5.81 36.29 2.67
665 682 5.450137 CCTGATTTTCCAGATCTGTGAATGC 60.450 44.000 21.11 14.38 36.29 3.56
666 683 5.258841 TGATTTTCCAGATCTGTGAATGCT 58.741 37.500 21.11 10.91 0.00 3.79
667 684 5.356190 TGATTTTCCAGATCTGTGAATGCTC 59.644 40.000 21.11 17.11 0.00 4.26
668 685 4.564782 TTTCCAGATCTGTGAATGCTCT 57.435 40.909 21.11 0.00 0.00 4.09
669 686 3.538634 TCCAGATCTGTGAATGCTCTG 57.461 47.619 21.11 2.22 34.48 3.35
670 687 3.102204 TCCAGATCTGTGAATGCTCTGA 58.898 45.455 21.11 4.59 36.32 3.27
671 688 3.118847 TCCAGATCTGTGAATGCTCTGAC 60.119 47.826 21.11 0.00 36.32 3.51
672 689 3.196463 CAGATCTGTGAATGCTCTGACC 58.804 50.000 14.95 0.00 36.32 4.02
673 690 2.836372 AGATCTGTGAATGCTCTGACCA 59.164 45.455 0.00 0.00 0.00 4.02
674 691 3.455177 AGATCTGTGAATGCTCTGACCAT 59.545 43.478 0.00 0.00 0.00 3.55
675 692 3.708403 TCTGTGAATGCTCTGACCATT 57.292 42.857 0.00 0.00 35.73 3.16
676 693 3.603532 TCTGTGAATGCTCTGACCATTC 58.396 45.455 15.56 15.56 45.44 2.67
682 699 4.918037 GAATGCTCTGACCATTCAATCAC 58.082 43.478 16.91 0.00 44.89 3.06
683 700 3.421919 TGCTCTGACCATTCAATCACA 57.578 42.857 0.00 0.00 0.00 3.58
684 701 3.959293 TGCTCTGACCATTCAATCACAT 58.041 40.909 0.00 0.00 0.00 3.21
685 702 5.101648 TGCTCTGACCATTCAATCACATA 57.898 39.130 0.00 0.00 0.00 2.29
686 703 5.687780 TGCTCTGACCATTCAATCACATAT 58.312 37.500 0.00 0.00 0.00 1.78
687 704 6.124340 TGCTCTGACCATTCAATCACATATT 58.876 36.000 0.00 0.00 0.00 1.28
688 705 7.281841 TGCTCTGACCATTCAATCACATATTA 58.718 34.615 0.00 0.00 0.00 0.98
689 706 7.774625 TGCTCTGACCATTCAATCACATATTAA 59.225 33.333 0.00 0.00 0.00 1.40
690 707 8.790718 GCTCTGACCATTCAATCACATATTAAT 58.209 33.333 0.00 0.00 0.00 1.40
717 734 9.747293 TTACATAACCGTATCATTTTCGTATGA 57.253 29.630 0.00 0.00 38.78 2.15
718 735 8.294341 ACATAACCGTATCATTTTCGTATGAG 57.706 34.615 0.00 0.00 37.91 2.90
719 736 5.652744 AACCGTATCATTTTCGTATGAGC 57.347 39.130 0.00 0.00 37.91 4.26
720 737 4.056050 ACCGTATCATTTTCGTATGAGCC 58.944 43.478 0.00 0.00 37.91 4.70
721 738 4.202223 ACCGTATCATTTTCGTATGAGCCT 60.202 41.667 0.00 0.00 37.91 4.58
758 775 2.851263 TTTATCTTGTGGGTGCGACT 57.149 45.000 0.00 0.00 0.00 4.18
760 777 0.973632 TATCTTGTGGGTGCGACTGT 59.026 50.000 0.00 0.00 0.00 3.55
766 785 1.217882 GTGGGTGCGACTGTATATGC 58.782 55.000 0.00 0.00 0.00 3.14
772 791 3.309388 GTGCGACTGTATATGCCACTAG 58.691 50.000 0.00 0.00 0.00 2.57
773 792 2.288213 TGCGACTGTATATGCCACTAGC 60.288 50.000 0.00 0.00 44.14 3.42
792 811 4.639135 AGCAGAAGACCAAAAAGACAAC 57.361 40.909 0.00 0.00 0.00 3.32
796 815 5.289434 GCAGAAGACCAAAAAGACAACAAAG 59.711 40.000 0.00 0.00 0.00 2.77
846 866 9.620660 AAAGTAGCGTGAATACAAAATTTTAGG 57.379 29.630 2.44 0.00 0.00 2.69
847 867 8.556213 AGTAGCGTGAATACAAAATTTTAGGA 57.444 30.769 2.44 0.00 0.00 2.94
887 1022 2.071778 AGGAAGCCAAGACAAAGCAA 57.928 45.000 0.00 0.00 0.00 3.91
888 1023 2.387757 AGGAAGCCAAGACAAAGCAAA 58.612 42.857 0.00 0.00 0.00 3.68
902 1037 0.031994 AGCAAACATGGAAACCGTGC 59.968 50.000 9.55 0.00 43.81 5.34
903 1038 1.274798 GCAAACATGGAAACCGTGCG 61.275 55.000 9.55 1.30 43.81 5.34
904 1039 1.007849 AAACATGGAAACCGTGCGC 60.008 52.632 0.00 0.00 43.81 6.09
905 1040 2.725275 AAACATGGAAACCGTGCGCG 62.725 55.000 13.88 13.88 43.81 6.86
968 1117 3.131577 CCAATCCACATCACATCCCAAAG 59.868 47.826 0.00 0.00 0.00 2.77
1144 1296 3.474570 GATGGCGAGGCAGGAGGT 61.475 66.667 5.43 0.00 0.00 3.85
1145 1297 3.746949 GATGGCGAGGCAGGAGGTG 62.747 68.421 5.43 0.00 0.00 4.00
1617 1769 8.210265 GGATTTCTCTGATTTCTCACTAGGATT 58.790 37.037 0.00 0.00 0.00 3.01
1815 1978 2.088104 AGGTGGAGTCTGAACACTCA 57.912 50.000 3.17 0.00 44.18 3.41
1880 2043 6.094742 TGACTGCACTTTCACAAATTTCTGTA 59.905 34.615 0.00 0.00 0.00 2.74
1899 2062 7.342769 TCTGTAAGTTTTAGTGTCACTCTGA 57.657 36.000 9.26 0.00 33.76 3.27
1909 2073 5.808366 AGTGTCACTCTGATGGAAGTTAA 57.192 39.130 0.00 0.00 0.00 2.01
2011 2175 4.520492 CCTGATTGCAAGTCCTGTTAGTTT 59.480 41.667 4.94 0.00 0.00 2.66
2023 2187 7.707104 AGTCCTGTTAGTTTTGTCAATTTCAG 58.293 34.615 0.00 0.00 0.00 3.02
2058 2222 7.599998 ACGATTCGGTACAGTTTTACTTGTATT 59.400 33.333 11.29 0.00 0.00 1.89
2076 2240 6.091718 TGTATTGGGGCTTCAACTAAAAAC 57.908 37.500 0.00 0.00 0.00 2.43
2077 2241 5.598830 TGTATTGGGGCTTCAACTAAAAACA 59.401 36.000 0.00 0.00 0.00 2.83
2108 2272 1.312815 GATAAGGTGATGTGGCTGGC 58.687 55.000 0.00 0.00 0.00 4.85
2124 2288 2.739379 GCTGGCAGACTAACTTGACTTC 59.261 50.000 20.86 0.00 0.00 3.01
2169 2333 6.919721 TGTGATGGGTAGCTAATTTTGAAAC 58.080 36.000 0.00 0.00 0.00 2.78
2188 2352 8.850454 TTGAAACAAAGAAATTTAGAAGACCG 57.150 30.769 0.00 0.00 0.00 4.79
2191 2355 8.446599 AAACAAAGAAATTTAGAAGACCGAGA 57.553 30.769 0.00 0.00 0.00 4.04
2220 2384 4.605640 CCAGATTTGTGGTGATTGGTTT 57.394 40.909 0.00 0.00 32.32 3.27
2221 2385 4.309099 CCAGATTTGTGGTGATTGGTTTG 58.691 43.478 0.00 0.00 32.32 2.93
2228 2392 5.667539 TGTGGTGATTGGTTTGAAAGAAA 57.332 34.783 0.00 0.00 0.00 2.52
2229 2393 5.659463 TGTGGTGATTGGTTTGAAAGAAAG 58.341 37.500 0.00 0.00 0.00 2.62
2241 2405 7.763985 TGGTTTGAAAGAAAGAAAACAAGATCC 59.236 33.333 0.00 0.00 34.85 3.36
2246 2410 5.674933 AGAAAGAAAACAAGATCCGTGAC 57.325 39.130 1.14 0.00 0.00 3.67
2517 2681 9.730705 ACTGGTGAGTATTATCAATCAATATGG 57.269 33.333 0.00 0.00 0.00 2.74
2662 2826 0.107848 AAAATAGTGGGACCGCTCGG 60.108 55.000 7.84 6.79 37.92 4.63
2815 2982 6.305272 TCTTCAAATACTTCCAGCAGATCT 57.695 37.500 0.00 0.00 0.00 2.75
2930 3099 8.100791 TGTCAGTTGCTTACTATGGAAGTATTT 58.899 33.333 0.00 0.00 40.41 1.40
3181 3350 0.460284 CGCCGCTCATTTACAGGTCT 60.460 55.000 0.00 0.00 0.00 3.85
3222 3391 6.718593 ATGGGGGTCTGCTATATTCATTTA 57.281 37.500 0.00 0.00 0.00 1.40
3322 3492 1.337823 ACGGTTGGTCACTATGCTGTC 60.338 52.381 0.00 0.00 0.00 3.51
3696 3893 1.739067 AGCTGGTTTAGTTCATCGGC 58.261 50.000 0.00 0.00 0.00 5.54
3707 3904 1.936547 GTTCATCGGCATGTCTCTTCC 59.063 52.381 0.00 0.00 0.00 3.46
3756 3953 4.044191 GGGGTAATAATTCCTATGCCAGGT 59.956 45.833 1.67 0.00 45.71 4.00
3765 3962 3.653164 TCCTATGCCAGGTCATCTGTTA 58.347 45.455 1.67 0.00 45.71 2.41
3796 3993 2.159612 CGTGTATCGTTGGAGTTCTCGA 60.160 50.000 0.00 0.00 36.77 4.04
4106 4303 9.331282 GCCTAATACTATGTTAATCATGGATCC 57.669 37.037 4.20 4.20 38.21 3.36
4172 4369 5.500645 AAAAAGTCGAAAGGTTTCCTCTG 57.499 39.130 0.00 0.00 33.68 3.35
4204 4410 6.344572 GCAATCCGCATATTATTACGATGA 57.655 37.500 0.00 0.00 41.79 2.92
4206 4412 7.409697 GCAATCCGCATATTATTACGATGAAT 58.590 34.615 0.00 0.00 41.79 2.57
4207 4413 8.547894 GCAATCCGCATATTATTACGATGAATA 58.452 33.333 0.00 0.00 41.79 1.75
4210 4416 8.851960 TCCGCATATTATTACGATGAATAGAC 57.148 34.615 0.00 0.00 0.00 2.59
4212 4418 7.921214 CCGCATATTATTACGATGAATAGACCT 59.079 37.037 0.00 0.00 0.00 3.85
4234 4444 5.045869 CCTTGTGGTTGGTCTATAAAGAGGA 60.046 44.000 0.00 0.00 30.45 3.71
4235 4445 5.416271 TGTGGTTGGTCTATAAAGAGGAC 57.584 43.478 0.00 0.00 30.45 3.85
4236 4446 4.081862 TGTGGTTGGTCTATAAAGAGGACG 60.082 45.833 0.00 0.00 30.45 4.79
4237 4447 4.159135 GTGGTTGGTCTATAAAGAGGACGA 59.841 45.833 0.00 0.00 30.45 4.20
4241 4451 7.146648 GGTTGGTCTATAAAGAGGACGAATAG 58.853 42.308 0.00 0.00 32.34 1.73
4242 4452 7.014038 GGTTGGTCTATAAAGAGGACGAATAGA 59.986 40.741 0.00 0.00 32.34 1.98
4243 4453 7.507733 TGGTCTATAAAGAGGACGAATAGAC 57.492 40.000 10.80 10.80 44.15 2.59
4248 4458 6.793505 ATAAAGAGGACGAATAGACCTTGT 57.206 37.500 0.00 0.00 44.84 3.16
4251 4461 4.345854 AGAGGACGAATAGACCTTGTTCT 58.654 43.478 0.00 0.00 44.84 3.01
4252 4462 4.773149 AGAGGACGAATAGACCTTGTTCTT 59.227 41.667 0.00 0.00 44.84 2.52
4253 4463 5.074584 AGGACGAATAGACCTTGTTCTTC 57.925 43.478 0.00 0.00 42.25 2.87
4254 4464 4.773149 AGGACGAATAGACCTTGTTCTTCT 59.227 41.667 0.00 0.00 42.25 2.85
4255 4465 5.103687 GGACGAATAGACCTTGTTCTTCTC 58.896 45.833 0.00 0.00 0.00 2.87
4256 4466 5.105675 GGACGAATAGACCTTGTTCTTCTCT 60.106 44.000 0.00 0.00 0.00 3.10
4257 4467 5.956642 ACGAATAGACCTTGTTCTTCTCTC 58.043 41.667 0.00 0.00 0.00 3.20
4258 4468 5.712917 ACGAATAGACCTTGTTCTTCTCTCT 59.287 40.000 0.00 0.00 0.00 3.10
4259 4469 6.209788 ACGAATAGACCTTGTTCTTCTCTCTT 59.790 38.462 0.00 0.00 0.00 2.85
4260 4470 6.750039 CGAATAGACCTTGTTCTTCTCTCTTC 59.250 42.308 0.00 0.00 0.00 2.87
4261 4471 7.546250 AATAGACCTTGTTCTTCTCTCTTCA 57.454 36.000 0.00 0.00 0.00 3.02
4262 4472 7.732222 ATAGACCTTGTTCTTCTCTCTTCAT 57.268 36.000 0.00 0.00 0.00 2.57
4263 4473 6.432403 AGACCTTGTTCTTCTCTCTTCATT 57.568 37.500 0.00 0.00 0.00 2.57
4264 4474 6.463360 AGACCTTGTTCTTCTCTCTTCATTC 58.537 40.000 0.00 0.00 0.00 2.67
4265 4475 6.269769 AGACCTTGTTCTTCTCTCTTCATTCT 59.730 38.462 0.00 0.00 0.00 2.40
4266 4476 6.463360 ACCTTGTTCTTCTCTCTTCATTCTC 58.537 40.000 0.00 0.00 0.00 2.87
4267 4477 6.269769 ACCTTGTTCTTCTCTCTTCATTCTCT 59.730 38.462 0.00 0.00 0.00 3.10
4268 4478 6.591062 CCTTGTTCTTCTCTCTTCATTCTCTG 59.409 42.308 0.00 0.00 0.00 3.35
4269 4479 6.035368 TGTTCTTCTCTCTTCATTCTCTGG 57.965 41.667 0.00 0.00 0.00 3.86
4270 4480 5.541868 TGTTCTTCTCTCTTCATTCTCTGGT 59.458 40.000 0.00 0.00 0.00 4.00
4271 4481 6.721668 TGTTCTTCTCTCTTCATTCTCTGGTA 59.278 38.462 0.00 0.00 0.00 3.25
4272 4482 7.093988 TGTTCTTCTCTCTTCATTCTCTGGTAG 60.094 40.741 0.00 0.00 0.00 3.18
4273 4483 6.489603 TCTTCTCTCTTCATTCTCTGGTAGT 58.510 40.000 0.00 0.00 0.00 2.73
4274 4484 6.951198 TCTTCTCTCTTCATTCTCTGGTAGTT 59.049 38.462 0.00 0.00 0.00 2.24
4275 4485 6.767524 TCTCTCTTCATTCTCTGGTAGTTC 57.232 41.667 0.00 0.00 0.00 3.01
4276 4486 5.355630 TCTCTCTTCATTCTCTGGTAGTTCG 59.644 44.000 0.00 0.00 0.00 3.95
4277 4487 4.399618 TCTCTTCATTCTCTGGTAGTTCGG 59.600 45.833 0.00 0.00 0.00 4.30
4278 4488 2.961526 TCATTCTCTGGTAGTTCGGC 57.038 50.000 0.00 0.00 0.00 5.54
4279 4489 1.480954 TCATTCTCTGGTAGTTCGGCC 59.519 52.381 0.00 0.00 0.00 6.13
4280 4490 1.207089 CATTCTCTGGTAGTTCGGCCA 59.793 52.381 2.24 0.00 0.00 5.36
4281 4491 1.568504 TTCTCTGGTAGTTCGGCCAT 58.431 50.000 2.24 0.00 33.84 4.40
4282 4492 1.568504 TCTCTGGTAGTTCGGCCATT 58.431 50.000 2.24 0.00 33.84 3.16
4283 4493 1.906574 TCTCTGGTAGTTCGGCCATTT 59.093 47.619 2.24 0.00 33.84 2.32
4284 4494 2.304761 TCTCTGGTAGTTCGGCCATTTT 59.695 45.455 2.24 0.00 33.84 1.82
4285 4495 2.420022 CTCTGGTAGTTCGGCCATTTTG 59.580 50.000 2.24 0.00 33.84 2.44
4286 4496 2.159382 CTGGTAGTTCGGCCATTTTGT 58.841 47.619 2.24 0.00 33.84 2.83
4287 4497 3.008157 TCTGGTAGTTCGGCCATTTTGTA 59.992 43.478 2.24 0.00 33.84 2.41
4288 4498 3.945285 CTGGTAGTTCGGCCATTTTGTAT 59.055 43.478 2.24 0.00 33.84 2.29
4289 4499 4.337145 TGGTAGTTCGGCCATTTTGTATT 58.663 39.130 2.24 0.00 0.00 1.89
4290 4500 4.767928 TGGTAGTTCGGCCATTTTGTATTT 59.232 37.500 2.24 0.00 0.00 1.40
4291 4501 5.099575 GGTAGTTCGGCCATTTTGTATTTG 58.900 41.667 2.24 0.00 0.00 2.32
4292 4502 4.864704 AGTTCGGCCATTTTGTATTTGT 57.135 36.364 2.24 0.00 0.00 2.83
4299 4509 6.016192 TCGGCCATTTTGTATTTGTTAACTGA 60.016 34.615 2.24 0.00 0.00 3.41
4308 4518 7.744087 TGTATTTGTTAACTGATGCAGTCTT 57.256 32.000 7.22 0.00 44.62 3.01
4323 4533 3.563390 GCAGTCTTTTGCTTCTCAACTCT 59.437 43.478 0.00 0.00 40.89 3.24
4349 4559 6.721668 TGTTCTTCTCTCTTCATTCTCTGGTA 59.278 38.462 0.00 0.00 0.00 3.25
4353 4563 6.767524 TCTCTCTTCATTCTCTGGTAGTTC 57.232 41.667 0.00 0.00 0.00 3.01
4362 4572 2.304761 TCTCTGGTAGTTCGGCCATTTT 59.695 45.455 2.24 0.00 33.84 1.82
4363 4573 2.420022 CTCTGGTAGTTCGGCCATTTTG 59.580 50.000 2.24 0.00 33.84 2.44
4364 4574 2.159382 CTGGTAGTTCGGCCATTTTGT 58.841 47.619 2.24 0.00 33.84 2.83
4365 4575 3.008157 TCTGGTAGTTCGGCCATTTTGTA 59.992 43.478 2.24 0.00 33.84 2.41
4368 4578 4.767928 TGGTAGTTCGGCCATTTTGTATTT 59.232 37.500 2.24 0.00 0.00 1.40
4369 4579 5.099575 GGTAGTTCGGCCATTTTGTATTTG 58.900 41.667 2.24 0.00 0.00 2.32
4370 4580 4.864704 AGTTCGGCCATTTTGTATTTGT 57.135 36.364 2.24 0.00 0.00 2.83
4371 4581 5.208463 AGTTCGGCCATTTTGTATTTGTT 57.792 34.783 2.24 0.00 0.00 2.83
4372 4582 6.334102 AGTTCGGCCATTTTGTATTTGTTA 57.666 33.333 2.24 0.00 0.00 2.41
4373 4583 6.153756 AGTTCGGCCATTTTGTATTTGTTAC 58.846 36.000 2.24 0.00 0.00 2.50
4374 4584 4.724303 TCGGCCATTTTGTATTTGTTACG 58.276 39.130 2.24 0.00 33.15 3.18
4378 4588 6.402334 CGGCCATTTTGTATTTGTTACGTAGA 60.402 38.462 2.24 0.00 33.15 2.59
4395 4605 6.837471 ACGTAGATTCCAGTAGTTCTCTTT 57.163 37.500 0.00 0.00 0.00 2.52
4401 4611 5.367945 TTCCAGTAGTTCTCTTTGGTTGT 57.632 39.130 0.00 0.00 32.59 3.32
4456 4666 0.179056 CCGTGGCCGATTACTGGAAT 60.179 55.000 0.00 0.00 35.63 3.01
4462 4672 0.843984 CCGATTACTGGAATGGGGGT 59.156 55.000 5.79 0.00 39.22 4.95
4619 4829 4.293610 TGGAGAGCACCACTGACA 57.706 55.556 0.00 0.00 34.77 3.58
4628 4838 1.200716 GCACCACTGACAATCACCATG 59.799 52.381 0.00 0.00 0.00 3.66
4629 4839 1.814394 CACCACTGACAATCACCATGG 59.186 52.381 11.19 11.19 0.00 3.66
4630 4840 0.813184 CCACTGACAATCACCATGGC 59.187 55.000 13.04 0.00 0.00 4.40
4631 4841 0.813184 CACTGACAATCACCATGGCC 59.187 55.000 13.04 0.00 0.00 5.36
4632 4842 0.677731 ACTGACAATCACCATGGCCG 60.678 55.000 13.04 3.06 0.00 6.13
4701 4911 1.888436 TTCGAGGACAAGCTCGGCAT 61.888 55.000 0.00 0.00 42.61 4.40
4703 4913 1.817099 GAGGACAAGCTCGGCATGG 60.817 63.158 0.00 0.00 31.12 3.66
4731 4941 0.840722 AAGATCCACCTGTTCCCGGT 60.841 55.000 0.00 0.00 34.38 5.28
4895 5105 1.742880 TCCGTCGAGGAGGTGTACG 60.743 63.158 6.70 0.00 45.98 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.494398 GCCTTGAGATCGCCCATAAGTTA 60.494 47.826 0.00 0.00 0.00 2.24
8 9 2.512896 GGCCTTGAGATCGCCCAT 59.487 61.111 0.00 0.00 36.63 4.00
12 13 1.424493 CTTGTCGGCCTTGAGATCGC 61.424 60.000 0.00 0.00 0.00 4.58
58 59 1.543802 TCGTCCAACCCATTTGATTGC 59.456 47.619 0.00 0.00 37.39 3.56
66 67 1.271379 CCTCTTGTTCGTCCAACCCAT 60.271 52.381 0.00 0.00 33.51 4.00
79 80 7.792032 TCTCCACGAAAATATATTCCTCTTGT 58.208 34.615 0.00 0.00 0.00 3.16
80 81 8.662781 TTCTCCACGAAAATATATTCCTCTTG 57.337 34.615 0.00 3.37 0.00 3.02
89 90 6.706270 GCTCTTCCATTCTCCACGAAAATATA 59.294 38.462 0.00 0.00 34.79 0.86
95 96 1.066143 GGCTCTTCCATTCTCCACGAA 60.066 52.381 0.00 0.00 35.78 3.85
148 151 2.232208 CCTTGCCTTCTCCCAATTGTTC 59.768 50.000 4.43 0.00 0.00 3.18
154 157 2.440599 GCCCTTGCCTTCTCCCAA 59.559 61.111 0.00 0.00 0.00 4.12
207 210 3.925299 CACCGCAAAAATGCATGTTCATA 59.075 39.130 1.67 0.00 34.41 2.15
215 218 0.825425 TCCCTCACCGCAAAAATGCA 60.825 50.000 1.42 0.00 34.41 3.96
224 227 0.034896 TTCTTGTTCTCCCTCACCGC 59.965 55.000 0.00 0.00 0.00 5.68
269 276 4.772100 CCCATCCTTCCACTTATTTTGTGT 59.228 41.667 0.00 0.00 33.92 3.72
277 284 2.047061 CGATCCCCATCCTTCCACTTA 58.953 52.381 0.00 0.00 0.00 2.24
281 288 0.264657 TCTCGATCCCCATCCTTCCA 59.735 55.000 0.00 0.00 0.00 3.53
285 292 0.114168 CCTCTCTCGATCCCCATCCT 59.886 60.000 0.00 0.00 0.00 3.24
295 302 0.903236 TCTTCTCCGTCCTCTCTCGA 59.097 55.000 0.00 0.00 0.00 4.04
299 306 1.134175 CAGCTTCTTCTCCGTCCTCTC 59.866 57.143 0.00 0.00 0.00 3.20
305 312 3.134458 CACTTTTCAGCTTCTTCTCCGT 58.866 45.455 0.00 0.00 0.00 4.69
324 331 2.745968 ACTGGATCTTCTCCCTCTCAC 58.254 52.381 0.00 0.00 44.23 3.51
341 348 2.064762 CGTCTCTTGCTTCTCCAACTG 58.935 52.381 0.00 0.00 0.00 3.16
359 366 0.323725 AGCTCCCATTTGATTGCCGT 60.324 50.000 0.00 0.00 0.00 5.68
401 408 4.578516 CCTCTCTTTCTCGAGCTCAATCTA 59.421 45.833 15.40 0.00 0.00 1.98
412 419 3.181526 CGATTTGCAACCTCTCTTTCTCG 60.182 47.826 0.00 0.00 0.00 4.04
457 464 7.907389 AGAGGCTTTCGTCCATCAATATAATA 58.093 34.615 0.00 0.00 0.00 0.98
460 467 5.808366 AGAGGCTTTCGTCCATCAATATA 57.192 39.130 0.00 0.00 0.00 0.86
468 475 0.984230 ATCCAAGAGGCTTTCGTCCA 59.016 50.000 0.00 0.00 33.74 4.02
536 550 0.745845 GCCGTCTCGTAGTCCCTACA 60.746 60.000 2.66 0.00 36.83 2.74
544 559 4.253257 GCCCTCGCCGTCTCGTAG 62.253 72.222 0.00 0.00 0.00 3.51
579 595 1.592743 TGCATCCTTGTTGCATGCC 59.407 52.632 16.68 0.28 44.73 4.40
602 619 1.885871 GCGCCTGCATCCTTTTCTT 59.114 52.632 0.00 0.00 42.15 2.52
619 636 4.675029 ATATACGGCCGCGGGTGC 62.675 66.667 29.38 12.84 37.91 5.01
620 637 1.595929 AAATATACGGCCGCGGGTG 60.596 57.895 29.38 0.83 0.00 4.61
621 638 1.595929 CAAATATACGGCCGCGGGT 60.596 57.895 29.38 19.83 0.00 5.28
622 639 2.322081 CCAAATATACGGCCGCGGG 61.322 63.158 29.38 14.21 0.00 6.13
623 640 2.961669 GCCAAATATACGGCCGCGG 61.962 63.158 28.58 24.05 42.82 6.46
624 641 2.554272 GCCAAATATACGGCCGCG 59.446 61.111 28.58 1.99 42.82 6.46
629 646 4.582656 TGGAAAATCAGGCCAAATATACGG 59.417 41.667 5.01 0.00 0.00 4.02
630 647 5.530915 TCTGGAAAATCAGGCCAAATATACG 59.469 40.000 5.01 0.00 35.58 3.06
631 648 6.959639 TCTGGAAAATCAGGCCAAATATAC 57.040 37.500 5.01 0.00 35.58 1.47
632 649 7.449395 CAGATCTGGAAAATCAGGCCAAATATA 59.551 37.037 15.38 0.00 35.58 0.86
633 650 6.267014 CAGATCTGGAAAATCAGGCCAAATAT 59.733 38.462 15.38 0.00 35.58 1.28
634 651 5.595542 CAGATCTGGAAAATCAGGCCAAATA 59.404 40.000 15.38 0.00 35.58 1.40
635 652 4.404715 CAGATCTGGAAAATCAGGCCAAAT 59.595 41.667 15.38 0.00 35.58 2.32
636 653 3.765511 CAGATCTGGAAAATCAGGCCAAA 59.234 43.478 15.38 0.00 35.58 3.28
637 654 3.245371 ACAGATCTGGAAAATCAGGCCAA 60.245 43.478 26.08 0.00 35.58 4.52
638 655 2.309755 ACAGATCTGGAAAATCAGGCCA 59.690 45.455 26.08 0.00 35.58 5.36
639 656 2.686915 CACAGATCTGGAAAATCAGGCC 59.313 50.000 26.08 0.00 35.58 5.19
640 657 3.614092 TCACAGATCTGGAAAATCAGGC 58.386 45.455 26.08 0.00 35.58 4.85
641 658 5.450137 GCATTCACAGATCTGGAAAATCAGG 60.450 44.000 26.08 11.34 35.58 3.86
642 659 5.357314 AGCATTCACAGATCTGGAAAATCAG 59.643 40.000 26.08 14.46 36.17 2.90
643 660 5.258841 AGCATTCACAGATCTGGAAAATCA 58.741 37.500 26.08 6.38 34.19 2.57
644 661 5.589452 AGAGCATTCACAGATCTGGAAAATC 59.411 40.000 26.08 20.35 29.28 2.17
645 662 5.357314 CAGAGCATTCACAGATCTGGAAAAT 59.643 40.000 26.08 17.78 43.71 1.82
646 663 4.698780 CAGAGCATTCACAGATCTGGAAAA 59.301 41.667 26.08 16.43 43.71 2.29
647 664 4.019950 TCAGAGCATTCACAGATCTGGAAA 60.020 41.667 26.08 18.76 46.49 3.13
648 665 3.516700 TCAGAGCATTCACAGATCTGGAA 59.483 43.478 26.08 23.36 46.49 3.53
649 666 3.102204 TCAGAGCATTCACAGATCTGGA 58.898 45.455 26.08 16.96 46.49 3.86
650 667 3.196463 GTCAGAGCATTCACAGATCTGG 58.804 50.000 26.08 15.01 46.49 3.86
652 669 2.836372 TGGTCAGAGCATTCACAGATCT 59.164 45.455 0.00 0.00 30.71 2.75
653 670 3.257469 TGGTCAGAGCATTCACAGATC 57.743 47.619 0.00 0.00 0.00 2.75
654 671 3.928005 ATGGTCAGAGCATTCACAGAT 57.072 42.857 9.43 0.00 31.32 2.90
655 672 3.708403 AATGGTCAGAGCATTCACAGA 57.292 42.857 20.11 0.00 41.98 3.41
662 679 3.959293 TGTGATTGAATGGTCAGAGCAT 58.041 40.909 9.43 9.43 38.04 3.79
663 680 3.421919 TGTGATTGAATGGTCAGAGCA 57.578 42.857 4.40 4.40 34.49 4.26
664 681 6.630444 AATATGTGATTGAATGGTCAGAGC 57.370 37.500 0.00 0.00 34.49 4.09
691 708 9.747293 TCATACGAAAATGATACGGTTATGTAA 57.253 29.630 0.00 0.00 30.92 2.41
692 709 9.401873 CTCATACGAAAATGATACGGTTATGTA 57.598 33.333 0.00 0.00 35.40 2.29
693 710 7.095774 GCTCATACGAAAATGATACGGTTATGT 60.096 37.037 0.00 0.00 35.40 2.29
694 711 7.227461 GCTCATACGAAAATGATACGGTTATG 58.773 38.462 0.00 0.00 35.40 1.90
695 712 6.367969 GGCTCATACGAAAATGATACGGTTAT 59.632 38.462 0.00 0.00 35.40 1.89
696 713 5.693104 GGCTCATACGAAAATGATACGGTTA 59.307 40.000 0.00 0.00 35.40 2.85
697 714 4.510340 GGCTCATACGAAAATGATACGGTT 59.490 41.667 0.00 0.00 35.40 4.44
698 715 4.056050 GGCTCATACGAAAATGATACGGT 58.944 43.478 0.00 0.00 35.40 4.83
699 716 4.307432 AGGCTCATACGAAAATGATACGG 58.693 43.478 0.00 0.00 35.40 4.02
700 717 5.907197 AAGGCTCATACGAAAATGATACG 57.093 39.130 0.00 0.00 35.40 3.06
701 718 7.012421 AGGAAAAGGCTCATACGAAAATGATAC 59.988 37.037 0.00 0.00 35.40 2.24
702 719 7.054124 AGGAAAAGGCTCATACGAAAATGATA 58.946 34.615 0.00 0.00 35.40 2.15
703 720 5.888161 AGGAAAAGGCTCATACGAAAATGAT 59.112 36.000 0.00 0.00 35.40 2.45
704 721 5.253330 AGGAAAAGGCTCATACGAAAATGA 58.747 37.500 0.00 0.00 34.72 2.57
705 722 5.567138 AGGAAAAGGCTCATACGAAAATG 57.433 39.130 0.00 0.00 0.00 2.32
706 723 5.589050 GGTAGGAAAAGGCTCATACGAAAAT 59.411 40.000 0.00 0.00 34.23 1.82
707 724 4.939439 GGTAGGAAAAGGCTCATACGAAAA 59.061 41.667 0.00 0.00 34.23 2.29
708 725 4.020039 TGGTAGGAAAAGGCTCATACGAAA 60.020 41.667 0.00 0.00 34.23 3.46
709 726 3.516300 TGGTAGGAAAAGGCTCATACGAA 59.484 43.478 0.00 0.00 34.23 3.85
710 727 3.101437 TGGTAGGAAAAGGCTCATACGA 58.899 45.455 0.00 0.00 34.23 3.43
711 728 3.536956 TGGTAGGAAAAGGCTCATACG 57.463 47.619 0.00 0.00 34.23 3.06
712 729 3.945921 GGTTGGTAGGAAAAGGCTCATAC 59.054 47.826 0.00 0.00 32.97 2.39
713 730 3.053917 GGGTTGGTAGGAAAAGGCTCATA 60.054 47.826 0.00 0.00 0.00 2.15
714 731 2.291605 GGGTTGGTAGGAAAAGGCTCAT 60.292 50.000 0.00 0.00 0.00 2.90
715 732 1.074889 GGGTTGGTAGGAAAAGGCTCA 59.925 52.381 0.00 0.00 0.00 4.26
716 733 1.354705 AGGGTTGGTAGGAAAAGGCTC 59.645 52.381 0.00 0.00 0.00 4.70
717 734 1.456919 AGGGTTGGTAGGAAAAGGCT 58.543 50.000 0.00 0.00 0.00 4.58
718 735 2.304221 AAGGGTTGGTAGGAAAAGGC 57.696 50.000 0.00 0.00 0.00 4.35
719 736 8.059461 AGATAAATAAGGGTTGGTAGGAAAAGG 58.941 37.037 0.00 0.00 0.00 3.11
720 737 9.475620 AAGATAAATAAGGGTTGGTAGGAAAAG 57.524 33.333 0.00 0.00 0.00 2.27
721 738 9.250246 CAAGATAAATAAGGGTTGGTAGGAAAA 57.750 33.333 0.00 0.00 0.00 2.29
766 785 4.214332 GTCTTTTTGGTCTTCTGCTAGTGG 59.786 45.833 0.00 0.00 0.00 4.00
772 791 4.370364 TGTTGTCTTTTTGGTCTTCTGC 57.630 40.909 0.00 0.00 0.00 4.26
773 792 6.620678 TCTTTGTTGTCTTTTTGGTCTTCTG 58.379 36.000 0.00 0.00 0.00 3.02
845 865 7.768582 TCCTTTTCTTTTGTCCATTTTTCTTCC 59.231 33.333 0.00 0.00 0.00 3.46
846 866 8.716646 TCCTTTTCTTTTGTCCATTTTTCTTC 57.283 30.769 0.00 0.00 0.00 2.87
847 867 9.166173 CTTCCTTTTCTTTTGTCCATTTTTCTT 57.834 29.630 0.00 0.00 0.00 2.52
858 993 4.466015 TGTCTTGGCTTCCTTTTCTTTTGT 59.534 37.500 0.00 0.00 0.00 2.83
887 1022 2.642700 GCGCACGGTTTCCATGTT 59.357 55.556 0.30 0.00 0.00 2.71
888 1023 3.722295 CGCGCACGGTTTCCATGT 61.722 61.111 8.75 0.00 34.97 3.21
902 1037 0.171007 ACTCATTTTTCCATGCCGCG 59.829 50.000 0.00 0.00 0.00 6.46
903 1038 1.994779 CAACTCATTTTTCCATGCCGC 59.005 47.619 0.00 0.00 0.00 6.53
904 1039 2.230992 TCCAACTCATTTTTCCATGCCG 59.769 45.455 0.00 0.00 0.00 5.69
905 1040 3.853475 CTCCAACTCATTTTTCCATGCC 58.147 45.455 0.00 0.00 0.00 4.40
992 1141 2.420022 CGATGCGTTCTTTCCTTCCAAT 59.580 45.455 0.00 0.00 0.00 3.16
995 1144 1.439679 ACGATGCGTTCTTTCCTTCC 58.560 50.000 0.00 0.00 36.35 3.46
1181 1333 2.362503 ACGGCCAGGATCTCGTCA 60.363 61.111 2.24 0.00 0.00 4.35
1427 1579 3.836949 CACAAATCTGAATTTCACGGGG 58.163 45.455 0.00 0.00 32.69 5.73
1644 1802 8.523658 GCTTCTAATCAAAATTAACAGGTTCCT 58.476 33.333 0.00 0.00 0.00 3.36
1719 1881 6.016610 AGGCAAATTAAACTAACATGACACGT 60.017 34.615 0.00 0.00 0.00 4.49
1815 1978 5.943349 TCCATCCAATTTCATGAAATGCT 57.057 34.783 29.52 15.45 46.21 3.79
1866 2029 9.997482 GACACTAAAACTTACAGAAATTTGTGA 57.003 29.630 21.09 3.25 32.56 3.58
1880 2043 6.174720 TCCATCAGAGTGACACTAAAACTT 57.825 37.500 8.41 0.00 0.00 2.66
1899 2062 7.555965 AGTCAAACAAAAGCTTTAACTTCCAT 58.444 30.769 13.10 0.00 0.00 3.41
1909 2073 9.696917 CCTTGATAATAAGTCAAACAAAAGCTT 57.303 29.630 0.00 0.00 35.36 3.74
1928 2092 8.756927 TGAAATTTCCATTATGCAACCTTGATA 58.243 29.630 15.48 0.00 0.00 2.15
1929 2093 7.550196 GTGAAATTTCCATTATGCAACCTTGAT 59.450 33.333 15.48 0.00 0.00 2.57
1930 2094 6.873076 GTGAAATTTCCATTATGCAACCTTGA 59.127 34.615 15.48 0.00 0.00 3.02
2011 2175 4.325741 CGTTTGCAACACTGAAATTGACAA 59.674 37.500 0.00 0.00 0.00 3.18
2023 2187 2.032722 TGTACCGAATCGTTTGCAACAC 60.033 45.455 0.00 0.00 0.00 3.32
2034 2198 8.173130 CCAATACAAGTAAAACTGTACCGAATC 58.827 37.037 0.00 0.00 0.00 2.52
2058 2222 2.962421 CCTGTTTTTAGTTGAAGCCCCA 59.038 45.455 0.00 0.00 0.00 4.96
2076 2240 2.549754 CACCTTATCGCTTAATGGCCTG 59.450 50.000 3.32 0.00 0.00 4.85
2077 2241 2.438021 TCACCTTATCGCTTAATGGCCT 59.562 45.455 3.32 0.00 0.00 5.19
2108 2272 4.318121 GCACAACGAAGTCAAGTTAGTCTG 60.318 45.833 0.00 0.00 45.00 3.51
2124 2288 1.732259 GGGTTCACTATGAGCACAACG 59.268 52.381 0.00 0.00 30.87 4.10
2169 2333 9.372369 AGTATCTCGGTCTTCTAAATTTCTTTG 57.628 33.333 0.00 0.00 0.00 2.77
2187 2351 6.036083 CACCACAAATCTGGTTTAGTATCTCG 59.964 42.308 0.00 0.00 42.29 4.04
2188 2352 7.103641 TCACCACAAATCTGGTTTAGTATCTC 58.896 38.462 0.00 0.00 42.29 2.75
2191 2355 7.122650 CCAATCACCACAAATCTGGTTTAGTAT 59.877 37.037 0.00 0.00 42.29 2.12
2220 2384 6.317642 TCACGGATCTTGTTTTCTTTCTTTCA 59.682 34.615 0.00 0.00 0.00 2.69
2221 2385 6.633234 GTCACGGATCTTGTTTTCTTTCTTTC 59.367 38.462 0.00 0.00 0.00 2.62
2228 2392 4.336889 TCAGTCACGGATCTTGTTTTCT 57.663 40.909 0.00 0.00 0.00 2.52
2229 2393 4.690748 TCATCAGTCACGGATCTTGTTTTC 59.309 41.667 0.00 0.00 0.00 2.29
2241 2405 4.389992 ACAGTAAAGCATTCATCAGTCACG 59.610 41.667 0.00 0.00 0.00 4.35
2246 2410 3.935203 ACCGACAGTAAAGCATTCATCAG 59.065 43.478 0.00 0.00 0.00 2.90
2286 2450 5.446860 AGCATTGAGATGAATGGAGACAAT 58.553 37.500 0.00 0.00 38.76 2.71
2492 2656 9.730705 ACCATATTGATTGATAATACTCACCAG 57.269 33.333 0.00 0.00 0.00 4.00
2517 2681 8.261522 AGAAATATCTGAGTAAGTGGGAAAGAC 58.738 37.037 0.00 0.00 33.59 3.01
2763 2930 3.817647 ACTGCTTGAAACTTCATCTGTCC 59.182 43.478 0.00 0.00 37.00 4.02
2815 2982 1.557371 TGGGCTGATTCGGTGATTGTA 59.443 47.619 0.00 0.00 0.00 2.41
2896 3065 2.325583 AAGCAACTGACAGTCGGAAA 57.674 45.000 16.84 0.00 0.00 3.13
2930 3099 5.719563 TGTGATTGAGAACTGGTATCCTGTA 59.280 40.000 0.00 0.00 34.63 2.74
3181 3350 5.445069 CCCCATTGATAATCCACTGTGTAA 58.555 41.667 7.08 0.00 0.00 2.41
3222 3391 8.164070 AGAACAAACATGTTAAGGAACTATCCT 58.836 33.333 12.39 0.00 44.28 3.24
3527 3724 7.278868 GGTGTCCTGTAGAAATTGATCAAGTAG 59.721 40.741 14.54 5.07 0.00 2.57
3559 3756 5.363580 TGTTCCAAAAATCTCCTCTGCTTTT 59.636 36.000 0.00 0.00 0.00 2.27
3765 3962 1.174783 ACGATACACGCTCTCTTGGT 58.825 50.000 0.00 0.00 46.94 3.67
3814 4011 4.164030 TGGCCTATGCACAGATTTCTAAGA 59.836 41.667 3.32 0.00 40.13 2.10
4106 4303 4.202151 CCTGGAGGAACCTTTTCAACTTTG 60.202 45.833 0.00 0.00 39.86 2.77
4210 4416 5.045869 TCCTCTTTATAGACCAACCACAAGG 60.046 44.000 0.00 0.00 42.21 3.61
4212 4418 5.568023 CGTCCTCTTTATAGACCAACCACAA 60.568 44.000 0.00 0.00 0.00 3.33
4216 4422 4.996788 TCGTCCTCTTTATAGACCAACC 57.003 45.455 0.00 0.00 0.00 3.77
4234 4444 5.712917 AGAGAGAAGAACAAGGTCTATTCGT 59.287 40.000 0.00 0.00 0.00 3.85
4235 4445 6.202516 AGAGAGAAGAACAAGGTCTATTCG 57.797 41.667 0.00 0.00 0.00 3.34
4236 4446 7.607250 TGAAGAGAGAAGAACAAGGTCTATTC 58.393 38.462 0.00 0.00 36.47 1.75
4237 4447 7.546250 TGAAGAGAGAAGAACAAGGTCTATT 57.454 36.000 0.00 0.00 0.00 1.73
4241 4451 6.463360 AGAATGAAGAGAGAAGAACAAGGTC 58.537 40.000 0.00 0.00 0.00 3.85
4242 4452 6.269769 AGAGAATGAAGAGAGAAGAACAAGGT 59.730 38.462 0.00 0.00 0.00 3.50
4243 4453 6.591062 CAGAGAATGAAGAGAGAAGAACAAGG 59.409 42.308 0.00 0.00 0.00 3.61
4244 4454 6.591062 CCAGAGAATGAAGAGAGAAGAACAAG 59.409 42.308 0.00 0.00 0.00 3.16
4245 4455 6.042552 ACCAGAGAATGAAGAGAGAAGAACAA 59.957 38.462 0.00 0.00 0.00 2.83
4248 4458 6.951198 ACTACCAGAGAATGAAGAGAGAAGAA 59.049 38.462 0.00 0.00 0.00 2.52
4251 4461 6.127869 CGAACTACCAGAGAATGAAGAGAGAA 60.128 42.308 0.00 0.00 0.00 2.87
4252 4462 5.355630 CGAACTACCAGAGAATGAAGAGAGA 59.644 44.000 0.00 0.00 0.00 3.10
4253 4463 5.449862 CCGAACTACCAGAGAATGAAGAGAG 60.450 48.000 0.00 0.00 0.00 3.20
4254 4464 4.399618 CCGAACTACCAGAGAATGAAGAGA 59.600 45.833 0.00 0.00 0.00 3.10
4255 4465 4.677584 CCGAACTACCAGAGAATGAAGAG 58.322 47.826 0.00 0.00 0.00 2.85
4256 4466 3.119101 GCCGAACTACCAGAGAATGAAGA 60.119 47.826 0.00 0.00 0.00 2.87
4257 4467 3.190874 GCCGAACTACCAGAGAATGAAG 58.809 50.000 0.00 0.00 0.00 3.02
4258 4468 2.093658 GGCCGAACTACCAGAGAATGAA 60.094 50.000 0.00 0.00 0.00 2.57
4259 4469 1.480954 GGCCGAACTACCAGAGAATGA 59.519 52.381 0.00 0.00 0.00 2.57
4260 4470 1.207089 TGGCCGAACTACCAGAGAATG 59.793 52.381 0.00 0.00 0.00 2.67
4261 4471 1.568504 TGGCCGAACTACCAGAGAAT 58.431 50.000 0.00 0.00 0.00 2.40
4262 4472 1.568504 ATGGCCGAACTACCAGAGAA 58.431 50.000 0.00 0.00 39.88 2.87
4263 4473 1.568504 AATGGCCGAACTACCAGAGA 58.431 50.000 0.00 0.00 39.88 3.10
4264 4474 2.403252 AAATGGCCGAACTACCAGAG 57.597 50.000 0.00 0.00 39.88 3.35
4265 4475 2.224670 ACAAAATGGCCGAACTACCAGA 60.225 45.455 0.00 0.00 39.88 3.86
4266 4476 2.159382 ACAAAATGGCCGAACTACCAG 58.841 47.619 0.00 0.00 39.88 4.00
4267 4477 2.279935 ACAAAATGGCCGAACTACCA 57.720 45.000 0.00 0.00 41.06 3.25
4268 4478 4.976224 AATACAAAATGGCCGAACTACC 57.024 40.909 0.00 0.00 0.00 3.18
4269 4479 5.705902 ACAAATACAAAATGGCCGAACTAC 58.294 37.500 0.00 0.00 0.00 2.73
4270 4480 5.968528 ACAAATACAAAATGGCCGAACTA 57.031 34.783 0.00 0.00 0.00 2.24
4271 4481 4.864704 ACAAATACAAAATGGCCGAACT 57.135 36.364 0.00 0.00 0.00 3.01
4272 4482 6.643360 AGTTAACAAATACAAAATGGCCGAAC 59.357 34.615 8.61 0.00 0.00 3.95
4273 4483 6.642950 CAGTTAACAAATACAAAATGGCCGAA 59.357 34.615 8.61 0.00 0.00 4.30
4274 4484 6.016192 TCAGTTAACAAATACAAAATGGCCGA 60.016 34.615 8.61 0.00 0.00 5.54
4275 4485 6.153067 TCAGTTAACAAATACAAAATGGCCG 58.847 36.000 8.61 0.00 0.00 6.13
4276 4486 7.412891 GCATCAGTTAACAAATACAAAATGGCC 60.413 37.037 8.61 0.00 0.00 5.36
4277 4487 7.117523 TGCATCAGTTAACAAATACAAAATGGC 59.882 33.333 8.61 0.00 0.00 4.40
4278 4488 8.531622 TGCATCAGTTAACAAATACAAAATGG 57.468 30.769 8.61 0.00 0.00 3.16
4279 4489 9.195411 ACTGCATCAGTTAACAAATACAAAATG 57.805 29.630 8.61 0.00 42.59 2.32
4280 4490 9.410556 GACTGCATCAGTTAACAAATACAAAAT 57.589 29.630 8.61 0.00 45.44 1.82
4281 4491 8.629158 AGACTGCATCAGTTAACAAATACAAAA 58.371 29.630 8.61 0.00 45.44 2.44
4282 4492 8.165239 AGACTGCATCAGTTAACAAATACAAA 57.835 30.769 8.61 0.00 45.44 2.83
4283 4493 7.744087 AGACTGCATCAGTTAACAAATACAA 57.256 32.000 8.61 0.00 45.44 2.41
4284 4494 7.744087 AAGACTGCATCAGTTAACAAATACA 57.256 32.000 8.61 1.21 45.44 2.29
4285 4495 8.905702 CAAAAGACTGCATCAGTTAACAAATAC 58.094 33.333 8.61 0.00 45.44 1.89
4286 4496 7.594758 GCAAAAGACTGCATCAGTTAACAAATA 59.405 33.333 8.61 0.00 45.44 1.40
4287 4497 6.421801 GCAAAAGACTGCATCAGTTAACAAAT 59.578 34.615 8.61 0.00 45.44 2.32
4288 4498 5.748152 GCAAAAGACTGCATCAGTTAACAAA 59.252 36.000 8.61 0.00 45.44 2.83
4289 4499 5.067674 AGCAAAAGACTGCATCAGTTAACAA 59.932 36.000 8.61 0.00 45.44 2.83
4290 4500 4.580167 AGCAAAAGACTGCATCAGTTAACA 59.420 37.500 8.61 0.00 45.44 2.41
4291 4501 5.113502 AGCAAAAGACTGCATCAGTTAAC 57.886 39.130 0.00 0.00 45.44 2.01
4292 4502 5.532406 AGAAGCAAAAGACTGCATCAGTTAA 59.468 36.000 0.66 0.00 45.44 2.01
4299 4509 3.887716 AGTTGAGAAGCAAAAGACTGCAT 59.112 39.130 0.00 0.00 45.18 3.96
4308 4518 5.882557 AGAAGAACAAGAGTTGAGAAGCAAA 59.117 36.000 0.00 0.00 38.30 3.68
4323 4533 6.042552 ACCAGAGAATGAAGAGAGAAGAACAA 59.957 38.462 0.00 0.00 0.00 2.83
4349 4559 4.864704 ACAAATACAAAATGGCCGAACT 57.135 36.364 0.00 0.00 0.00 3.01
4353 4563 4.477780 ACGTAACAAATACAAAATGGCCG 58.522 39.130 0.00 0.00 33.89 6.13
4362 4572 8.742777 ACTACTGGAATCTACGTAACAAATACA 58.257 33.333 0.00 0.00 33.89 2.29
4363 4573 9.578439 AACTACTGGAATCTACGTAACAAATAC 57.422 33.333 0.00 0.00 0.00 1.89
4364 4574 9.793252 GAACTACTGGAATCTACGTAACAAATA 57.207 33.333 0.00 0.00 0.00 1.40
4365 4575 8.529476 AGAACTACTGGAATCTACGTAACAAAT 58.471 33.333 0.00 0.00 0.00 2.32
4368 4578 6.883217 AGAGAACTACTGGAATCTACGTAACA 59.117 38.462 0.00 0.00 0.00 2.41
4369 4579 7.319142 AGAGAACTACTGGAATCTACGTAAC 57.681 40.000 0.00 0.00 0.00 2.50
4370 4580 7.934855 AAGAGAACTACTGGAATCTACGTAA 57.065 36.000 0.00 0.00 0.00 3.18
4371 4581 7.148120 CCAAAGAGAACTACTGGAATCTACGTA 60.148 40.741 0.00 0.00 33.57 3.57
4372 4582 6.350277 CCAAAGAGAACTACTGGAATCTACGT 60.350 42.308 0.00 0.00 33.57 3.57
4373 4583 6.037098 CCAAAGAGAACTACTGGAATCTACG 58.963 44.000 0.00 0.00 33.57 3.51
4374 4584 6.937392 ACCAAAGAGAACTACTGGAATCTAC 58.063 40.000 0.00 0.00 34.93 2.59
4378 4588 5.941788 ACAACCAAAGAGAACTACTGGAAT 58.058 37.500 0.00 0.00 34.93 3.01
4395 4605 1.067364 CTTGCTGCATGTCAACAACCA 59.933 47.619 1.84 0.00 28.75 3.67
4401 4611 2.566833 AGGTACTTGCTGCATGTCAA 57.433 45.000 22.31 5.82 27.25 3.18
4615 4825 1.378382 CCGGCCATGGTGATTGTCA 60.378 57.895 14.67 0.00 0.00 3.58
4619 4829 1.153249 CGTACCGGCCATGGTGATT 60.153 57.895 14.67 0.00 43.68 2.57
4628 4838 2.588034 GCTCCATTCGTACCGGCC 60.588 66.667 0.00 0.00 0.00 6.13
4629 4839 2.960129 CGCTCCATTCGTACCGGC 60.960 66.667 0.00 0.00 0.00 6.13
4630 4840 2.279252 CCGCTCCATTCGTACCGG 60.279 66.667 0.00 0.00 0.00 5.28
4631 4841 1.588139 GACCGCTCCATTCGTACCG 60.588 63.158 0.00 0.00 0.00 4.02
4632 4842 1.227176 GGACCGCTCCATTCGTACC 60.227 63.158 0.00 0.00 36.42 3.34
4701 4911 1.680989 TGGATCTTCGTCTCCGCCA 60.681 57.895 0.00 0.00 34.05 5.69
4703 4913 1.227002 GGTGGATCTTCGTCTCCGC 60.227 63.158 0.00 0.00 40.58 5.54
4731 4941 2.981302 CGAGGTCCACCATGCTCA 59.019 61.111 0.00 0.00 38.89 4.26


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

AutoCloner maintained by Alex Coulton.