Multiple sequence alignment - TraesCS5D01G208600

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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 TraesCS5D01G208600 chr5D 100.000 5149 0 0 1 5149 314898164 314903312 0.000000e+00 9509.0
1 TraesCS5D01G208600 chr5D 93.908 673 34 3 1 673 370445394 370444729 0.000000e+00 1009.0
2 TraesCS5D01G208600 chr5D 90.136 294 25 3 382 674 457021370 457021660 3.760000e-101 379.0
3 TraesCS5D01G208600 chr5D 81.699 153 21 7 4988 5137 318811321 318811469 2.520000e-23 121.0
4 TraesCS5D01G208600 chr5A 97.414 2552 57 6 1810 4358 408929434 408931979 0.000000e+00 4338.0
5 TraesCS5D01G208600 chr5A 95.303 958 31 6 855 1808 408928380 408929327 0.000000e+00 1507.0
6 TraesCS5D01G208600 chr5A 77.564 156 30 5 4989 5142 616022295 616022143 7.100000e-14 89.8
7 TraesCS5D01G208600 chr5B 96.449 1577 49 2 2784 4358 362955801 362957372 0.000000e+00 2595.0
8 TraesCS5D01G208600 chr5B 92.022 915 49 13 1865 2775 362947401 362948295 0.000000e+00 1264.0
9 TraesCS5D01G208600 chr5B 93.472 674 42 1 1 674 137053757 137053086 0.000000e+00 1000.0
10 TraesCS5D01G208600 chr5B 93.214 560 21 3 854 1405 362946390 362946940 0.000000e+00 808.0
11 TraesCS5D01G208600 chr5B 86.567 67 5 4 4987 5051 529283929 529283993 2.570000e-08 71.3
12 TraesCS5D01G208600 chr4A 91.543 674 55 1 1 674 142352782 142352111 0.000000e+00 928.0
13 TraesCS5D01G208600 chr4A 81.448 221 32 9 4923 5139 732115916 732115701 6.850000e-39 172.0
14 TraesCS5D01G208600 chr4A 81.448 221 32 9 4923 5139 732119107 732118892 6.850000e-39 172.0
15 TraesCS5D01G208600 chr4A 79.208 202 32 10 4944 5139 732114342 732114145 1.160000e-26 132.0
16 TraesCS5D01G208600 chr4A 79.208 202 32 10 4944 5139 732117533 732117336 1.160000e-26 132.0
17 TraesCS5D01G208600 chr2D 89.778 675 66 3 1 675 230511154 230510483 0.000000e+00 861.0
18 TraesCS5D01G208600 chr2D 77.969 581 78 28 4581 5145 81946913 81946367 8.320000e-83 318.0
19 TraesCS5D01G208600 chr2D 87.726 277 26 2 404 674 635414697 635414423 2.990000e-82 316.0
20 TraesCS5D01G208600 chr7B 89.747 673 66 2 1 672 155571820 155572490 0.000000e+00 857.0
21 TraesCS5D01G208600 chr7B 85.084 476 55 6 208 669 501761877 501762350 6.030000e-129 472.0
22 TraesCS5D01G208600 chr7D 88.576 674 72 3 1 674 29812769 29812101 0.000000e+00 813.0
23 TraesCS5D01G208600 chr7D 82.474 679 110 7 1 674 388020929 388021603 2.070000e-163 586.0
24 TraesCS5D01G208600 chr2B 84.841 409 37 10 4356 4739 493202056 493202464 6.250000e-104 388.0
25 TraesCS5D01G208600 chr2B 82.168 286 38 7 4351 4628 133811553 133811273 3.100000e-57 233.0
26 TraesCS5D01G208600 chr2A 82.075 318 52 5 4827 5142 82133486 82133172 3.060000e-67 267.0
27 TraesCS5D01G208600 chr2A 77.778 477 68 21 4351 4814 82134202 82133751 5.110000e-65 259.0
28 TraesCS5D01G208600 chr2A 81.579 76 11 3 4345 4418 71673561 71673487 5.570000e-05 60.2
29 TraesCS5D01G208600 chr4D 86.184 152 20 1 4430 4580 483948791 483948640 4.130000e-36 163.0
30 TraesCS5D01G208600 chr4D 93.151 73 4 1 4363 4435 483945493 483945564 7.050000e-19 106.0
31 TraesCS5D01G208600 chr3B 77.729 229 35 13 4355 4571 819291388 819291612 5.410000e-25 126.0
32 TraesCS5D01G208600 chr6B 75.879 199 46 2 80 277 658987408 658987605 3.280000e-17 100.0
33 TraesCS5D01G208600 chr3D 80.992 121 21 2 5019 5139 546808580 546808462 1.530000e-15 95.3
34 TraesCS5D01G208600 chr6D 86.207 58 7 1 4940 4996 460481785 460481842 1.550000e-05 62.1


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 TraesCS5D01G208600 chr5D 314898164 314903312 5148 False 9509.0 9509 100.0000 1 5149 1 chr5D.!!$F1 5148
1 TraesCS5D01G208600 chr5D 370444729 370445394 665 True 1009.0 1009 93.9080 1 673 1 chr5D.!!$R1 672
2 TraesCS5D01G208600 chr5A 408928380 408931979 3599 False 2922.5 4338 96.3585 855 4358 2 chr5A.!!$F1 3503
3 TraesCS5D01G208600 chr5B 362955801 362957372 1571 False 2595.0 2595 96.4490 2784 4358 1 chr5B.!!$F1 1574
4 TraesCS5D01G208600 chr5B 362946390 362948295 1905 False 1036.0 1264 92.6180 854 2775 2 chr5B.!!$F3 1921
5 TraesCS5D01G208600 chr5B 137053086 137053757 671 True 1000.0 1000 93.4720 1 674 1 chr5B.!!$R1 673
6 TraesCS5D01G208600 chr4A 142352111 142352782 671 True 928.0 928 91.5430 1 674 1 chr4A.!!$R1 673
7 TraesCS5D01G208600 chr2D 230510483 230511154 671 True 861.0 861 89.7780 1 675 1 chr2D.!!$R2 674
8 TraesCS5D01G208600 chr2D 81946367 81946913 546 True 318.0 318 77.9690 4581 5145 1 chr2D.!!$R1 564
9 TraesCS5D01G208600 chr7B 155571820 155572490 670 False 857.0 857 89.7470 1 672 1 chr7B.!!$F1 671
10 TraesCS5D01G208600 chr7D 29812101 29812769 668 True 813.0 813 88.5760 1 674 1 chr7D.!!$R1 673
11 TraesCS5D01G208600 chr7D 388020929 388021603 674 False 586.0 586 82.4740 1 674 1 chr7D.!!$F1 673
12 TraesCS5D01G208600 chr2A 82133172 82134202 1030 True 263.0 267 79.9265 4351 5142 2 chr2A.!!$R2 791


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
575 581 0.106116 GGTGGTGTTGGTTAACCCCA 60.106 55.0 21.97 17.8 41.23 4.96 F
844 851 0.111253 CCAAGAGCCCACCTTCACTT 59.889 55.0 0.00 0.0 0.00 3.16 F
851 858 0.397941 CCCACCTTCACTTGCTCTCA 59.602 55.0 0.00 0.0 0.00 3.27 F
2513 2697 0.118346 TTAGAAGGGAGGGCTGGTCA 59.882 55.0 0.00 0.0 0.00 4.02 F
2801 2985 0.757935 TATCCCCGTACAGACCCTGC 60.758 60.0 0.00 0.0 34.37 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1540 0.312102 GCAAAGCGCAAAAGGTCTCT 59.688 50.000 11.47 0.0 41.79 3.10 R
2354 2538 0.623723 TGGCTATTGAACCCCCAGAC 59.376 55.000 0.00 0.0 0.00 3.51 R
2801 2985 3.735591 TGTCAAGAAAAGGTAAGTCCCG 58.264 45.455 0.00 0.0 36.75 5.14 R
4004 4190 0.529337 ATCCAAGTGCATCGCTCTCG 60.529 55.000 0.00 0.0 30.88 4.04 R
4544 4733 0.037605 CGAAGACTTTGGCGGTAGGT 60.038 55.000 0.00 0.0 0.00 3.08 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 0.955919 CGGCTTTCACCTGGAAGTCC 60.956 60.000 0.00 0.00 36.72 3.85
245 246 1.526686 CAAGTGTGGCACTGGCTGA 60.527 57.895 19.83 0.00 44.62 4.26
377 378 1.078709 CCTACTTGTCATGTGGTGCG 58.921 55.000 1.71 0.00 0.00 5.34
388 389 1.106351 TGTGGTGCGTTTGGAAGCAT 61.106 50.000 0.00 0.00 45.69 3.79
432 433 2.282674 TACCCCGTCACTCGCTGT 60.283 61.111 0.00 0.00 38.35 4.40
575 581 0.106116 GGTGGTGTTGGTTAACCCCA 60.106 55.000 21.97 17.80 41.23 4.96
647 654 8.492673 TTCTTCTTTAATGAATGATACGCACT 57.507 30.769 4.42 0.00 0.00 4.40
648 655 8.131455 TCTTCTTTAATGAATGATACGCACTC 57.869 34.615 4.42 0.00 0.00 3.51
649 656 7.981789 TCTTCTTTAATGAATGATACGCACTCT 59.018 33.333 4.42 0.00 0.00 3.24
692 699 5.337578 AAAACCAATATGTATGCCACCAC 57.662 39.130 0.00 0.00 0.00 4.16
693 700 3.660970 ACCAATATGTATGCCACCACA 57.339 42.857 0.00 0.00 0.00 4.17
694 701 4.183223 ACCAATATGTATGCCACCACAT 57.817 40.909 0.10 0.10 38.81 3.21
695 702 4.545678 ACCAATATGTATGCCACCACATT 58.454 39.130 0.00 0.00 36.74 2.71
696 703 5.700183 ACCAATATGTATGCCACCACATTA 58.300 37.500 0.00 0.00 36.74 1.90
697 704 5.534654 ACCAATATGTATGCCACCACATTAC 59.465 40.000 0.00 0.00 36.74 1.89
698 705 5.534278 CCAATATGTATGCCACCACATTACA 59.466 40.000 0.00 0.00 36.74 2.41
699 706 6.437928 CAATATGTATGCCACCACATTACAC 58.562 40.000 0.00 0.00 36.74 2.90
700 707 3.425162 TGTATGCCACCACATTACACA 57.575 42.857 0.00 0.00 0.00 3.72
701 708 3.961849 TGTATGCCACCACATTACACAT 58.038 40.909 0.00 0.00 0.00 3.21
702 709 3.693578 TGTATGCCACCACATTACACATG 59.306 43.478 0.00 0.00 0.00 3.21
703 710 2.284754 TGCCACCACATTACACATGT 57.715 45.000 0.00 0.00 0.00 3.21
704 711 1.885233 TGCCACCACATTACACATGTG 59.115 47.619 24.25 24.25 46.49 3.21
712 719 5.369685 CACATTACACATGTGGTAAGCAA 57.630 39.130 28.64 12.79 44.04 3.91
713 720 5.953183 CACATTACACATGTGGTAAGCAAT 58.047 37.500 28.64 14.26 44.04 3.56
714 721 6.029607 CACATTACACATGTGGTAAGCAATC 58.970 40.000 28.64 0.00 44.04 2.67
715 722 5.709631 ACATTACACATGTGGTAAGCAATCA 59.290 36.000 28.64 0.00 34.50 2.57
716 723 6.208402 ACATTACACATGTGGTAAGCAATCAA 59.792 34.615 28.64 7.69 34.50 2.57
717 724 6.641169 TTACACATGTGGTAAGCAATCAAA 57.359 33.333 28.64 3.96 34.19 2.69
718 725 5.726980 ACACATGTGGTAAGCAATCAAAT 57.273 34.783 28.64 0.31 34.19 2.32
719 726 6.832520 ACACATGTGGTAAGCAATCAAATA 57.167 33.333 28.64 0.00 34.19 1.40
720 727 7.225784 ACACATGTGGTAAGCAATCAAATAA 57.774 32.000 28.64 0.00 34.19 1.40
721 728 7.839907 ACACATGTGGTAAGCAATCAAATAAT 58.160 30.769 28.64 0.00 34.19 1.28
722 729 8.313292 ACACATGTGGTAAGCAATCAAATAATT 58.687 29.630 28.64 0.00 34.19 1.40
723 730 8.810427 CACATGTGGTAAGCAATCAAATAATTC 58.190 33.333 18.51 0.00 0.00 2.17
724 731 8.530311 ACATGTGGTAAGCAATCAAATAATTCA 58.470 29.630 0.00 0.00 0.00 2.57
725 732 9.027129 CATGTGGTAAGCAATCAAATAATTCAG 57.973 33.333 0.00 0.00 0.00 3.02
726 733 7.035004 TGTGGTAAGCAATCAAATAATTCAGC 58.965 34.615 0.00 0.00 0.00 4.26
727 734 7.093814 TGTGGTAAGCAATCAAATAATTCAGCT 60.094 33.333 0.00 0.00 0.00 4.24
728 735 8.405531 GTGGTAAGCAATCAAATAATTCAGCTA 58.594 33.333 0.00 0.00 0.00 3.32
729 736 8.623903 TGGTAAGCAATCAAATAATTCAGCTAG 58.376 33.333 0.00 0.00 0.00 3.42
730 737 8.840321 GGTAAGCAATCAAATAATTCAGCTAGA 58.160 33.333 0.00 0.00 0.00 2.43
731 738 9.657121 GTAAGCAATCAAATAATTCAGCTAGAC 57.343 33.333 0.00 0.00 0.00 2.59
732 739 6.952743 AGCAATCAAATAATTCAGCTAGACG 58.047 36.000 0.00 0.00 0.00 4.18
733 740 6.017605 AGCAATCAAATAATTCAGCTAGACGG 60.018 38.462 0.00 0.00 0.00 4.79
734 741 6.017934 GCAATCAAATAATTCAGCTAGACGGA 60.018 38.462 0.00 0.00 0.00 4.69
735 742 7.571026 CAATCAAATAATTCAGCTAGACGGAG 58.429 38.462 0.00 0.00 0.00 4.63
736 743 6.465439 TCAAATAATTCAGCTAGACGGAGA 57.535 37.500 0.00 0.00 0.00 3.71
737 744 7.055667 TCAAATAATTCAGCTAGACGGAGAT 57.944 36.000 0.00 0.00 0.00 2.75
738 745 7.500992 TCAAATAATTCAGCTAGACGGAGATT 58.499 34.615 0.00 0.00 0.00 2.40
739 746 8.638873 TCAAATAATTCAGCTAGACGGAGATTA 58.361 33.333 0.00 0.83 0.00 1.75
740 747 8.920665 CAAATAATTCAGCTAGACGGAGATTAG 58.079 37.037 0.00 0.00 0.00 1.73
741 748 3.992260 TTCAGCTAGACGGAGATTAGC 57.008 47.619 0.00 0.00 40.91 3.09
743 750 4.353383 TCAGCTAGACGGAGATTAGCTA 57.647 45.455 5.07 0.00 45.59 3.32
744 751 4.912586 TCAGCTAGACGGAGATTAGCTAT 58.087 43.478 5.07 0.00 45.59 2.97
745 752 6.051179 TCAGCTAGACGGAGATTAGCTATA 57.949 41.667 5.07 0.00 45.59 1.31
746 753 6.473758 TCAGCTAGACGGAGATTAGCTATAA 58.526 40.000 5.07 0.00 45.59 0.98
747 754 6.596106 TCAGCTAGACGGAGATTAGCTATAAG 59.404 42.308 5.07 0.00 45.59 1.73
748 755 5.355910 AGCTAGACGGAGATTAGCTATAAGC 59.644 44.000 3.60 0.00 45.54 3.09
788 795 9.838339 TTTCAACTTTGTCTCTATCTCTTTTCT 57.162 29.630 0.00 0.00 0.00 2.52
789 796 9.838339 TTCAACTTTGTCTCTATCTCTTTTCTT 57.162 29.630 0.00 0.00 0.00 2.52
831 838 9.930693 ATTTAAGAGTACACTAAAGACCAAGAG 57.069 33.333 0.00 0.00 0.00 2.85
832 839 5.394224 AGAGTACACTAAAGACCAAGAGC 57.606 43.478 0.00 0.00 0.00 4.09
833 840 4.221041 AGAGTACACTAAAGACCAAGAGCC 59.779 45.833 0.00 0.00 0.00 4.70
834 841 2.861147 ACACTAAAGACCAAGAGCCC 57.139 50.000 0.00 0.00 0.00 5.19
835 842 2.054799 ACACTAAAGACCAAGAGCCCA 58.945 47.619 0.00 0.00 0.00 5.36
836 843 2.224548 ACACTAAAGACCAAGAGCCCAC 60.225 50.000 0.00 0.00 0.00 4.61
837 844 1.351350 ACTAAAGACCAAGAGCCCACC 59.649 52.381 0.00 0.00 0.00 4.61
838 845 1.630878 CTAAAGACCAAGAGCCCACCT 59.369 52.381 0.00 0.00 0.00 4.00
839 846 0.853530 AAAGACCAAGAGCCCACCTT 59.146 50.000 0.00 0.00 0.00 3.50
840 847 0.402121 AAGACCAAGAGCCCACCTTC 59.598 55.000 0.00 0.00 0.00 3.46
841 848 0.768221 AGACCAAGAGCCCACCTTCA 60.768 55.000 0.00 0.00 0.00 3.02
842 849 0.606673 GACCAAGAGCCCACCTTCAC 60.607 60.000 0.00 0.00 0.00 3.18
843 850 1.062488 ACCAAGAGCCCACCTTCACT 61.062 55.000 0.00 0.00 0.00 3.41
844 851 0.111253 CCAAGAGCCCACCTTCACTT 59.889 55.000 0.00 0.00 0.00 3.16
845 852 1.242076 CAAGAGCCCACCTTCACTTG 58.758 55.000 0.00 0.00 0.00 3.16
846 853 0.538287 AAGAGCCCACCTTCACTTGC 60.538 55.000 0.00 0.00 0.00 4.01
847 854 1.073897 GAGCCCACCTTCACTTGCT 59.926 57.895 0.00 0.00 0.00 3.91
848 855 0.957888 GAGCCCACCTTCACTTGCTC 60.958 60.000 0.00 0.00 38.51 4.26
849 856 1.073897 GCCCACCTTCACTTGCTCT 59.926 57.895 0.00 0.00 0.00 4.09
850 857 0.957888 GCCCACCTTCACTTGCTCTC 60.958 60.000 0.00 0.00 0.00 3.20
851 858 0.397941 CCCACCTTCACTTGCTCTCA 59.602 55.000 0.00 0.00 0.00 3.27
852 859 1.202806 CCCACCTTCACTTGCTCTCAA 60.203 52.381 0.00 0.00 0.00 3.02
881 888 1.301401 CCGGCGAAGACTCCAAACA 60.301 57.895 9.30 0.00 0.00 2.83
959 974 3.721706 CAGAGGAAGGGCGGCCTT 61.722 66.667 40.42 40.42 33.84 4.35
1353 1371 3.916392 CTTCGTCGCCGCCTTCAGT 62.916 63.158 0.00 0.00 0.00 3.41
1470 1537 3.058450 CAGAAGTGAAGTGCAGTCTCTG 58.942 50.000 0.00 0.00 33.24 3.35
1471 1538 2.961741 AGAAGTGAAGTGCAGTCTCTGA 59.038 45.455 0.00 0.00 32.44 3.27
1472 1539 3.005684 AGAAGTGAAGTGCAGTCTCTGAG 59.994 47.826 0.00 0.00 32.44 3.35
1473 1540 2.591923 AGTGAAGTGCAGTCTCTGAGA 58.408 47.619 2.58 2.58 32.44 3.27
1592 1659 1.305201 TCCGGCTGTGAAAGAAACAC 58.695 50.000 0.00 0.00 38.55 3.32
1626 1693 1.131883 CGCTCCCTTTGCATCAAGAAG 59.868 52.381 0.00 0.00 0.00 2.85
1647 1714 2.560105 GCCCTTGTTGCTCTGAATTCTT 59.440 45.455 7.05 0.00 0.00 2.52
1721 1788 3.806591 GCTGCAGCAATTGTGTCAT 57.193 47.368 33.36 0.00 41.59 3.06
1747 1814 1.954733 GCAATGGGGTGCAGTCATGTA 60.955 52.381 0.00 0.00 44.29 2.29
1788 1863 2.904434 TGGTTCTGTCTAGAAAGGGACC 59.096 50.000 20.89 20.89 44.12 4.46
1808 1883 3.142174 CCACCTCCTTTTCTTGTCTGAC 58.858 50.000 0.00 0.00 0.00 3.51
1907 2087 7.168972 TCGGTTTTGATTTTCATAGTGCTTTTG 59.831 33.333 0.00 0.00 0.00 2.44
2064 2245 9.158233 CTCCGTGAAAATAGGTAAAATGAACTA 57.842 33.333 0.00 0.00 0.00 2.24
2128 2310 6.092122 CACTGTGATTTAGCAATTCTACCGAA 59.908 38.462 0.32 0.00 0.00 4.30
2132 2314 7.335673 TGTGATTTAGCAATTCTACCGAATTCA 59.664 33.333 6.22 0.00 45.57 2.57
2142 2324 4.566004 TCTACCGAATTCAACTCCACTTG 58.434 43.478 6.22 0.00 0.00 3.16
2191 2373 8.472007 AGACCTTTCATAGTCTTACCTCATAG 57.528 38.462 0.00 0.00 40.43 2.23
2192 2374 8.062536 AGACCTTTCATAGTCTTACCTCATAGT 58.937 37.037 0.00 0.00 40.43 2.12
2193 2375 9.352191 GACCTTTCATAGTCTTACCTCATAGTA 57.648 37.037 0.00 0.00 0.00 1.82
2234 2416 4.833478 ACAGAGTGATAGTCTTGCCATT 57.167 40.909 0.00 0.00 0.00 3.16
2354 2538 0.871722 TCGTTTTCACAGGCCATTCG 59.128 50.000 5.01 0.00 0.00 3.34
2513 2697 0.118346 TTAGAAGGGAGGGCTGGTCA 59.882 55.000 0.00 0.00 0.00 4.02
2801 2985 0.757935 TATCCCCGTACAGACCCTGC 60.758 60.000 0.00 0.00 34.37 4.85
2921 3105 2.481185 CCAACAACAATTGCTTGATGCC 59.519 45.455 20.41 0.00 38.37 4.40
3110 3294 5.690865 TCTTCTTCCATAAACAACTGTGGT 58.309 37.500 0.00 0.00 33.47 4.16
3935 4121 1.503542 GTGCTTCTGGGCAATGTCG 59.496 57.895 0.00 0.00 44.18 4.35
4004 4190 3.181448 TGAAAGACAGGGTGGGTAAACTC 60.181 47.826 0.00 0.00 0.00 3.01
4121 4307 4.662961 CAGCACAGGTCCGCGTCA 62.663 66.667 4.92 0.00 0.00 4.35
4145 4331 1.664649 CGCGAGACTTGTGCCTTCA 60.665 57.895 0.00 0.00 0.00 3.02
4209 4395 2.741486 TAACCGGAACTGCTGCCACC 62.741 60.000 9.46 0.00 0.00 4.61
4271 4459 4.712829 TGTGTAGTATTCTCCGGGATGAAA 59.287 41.667 0.00 0.00 0.00 2.69
4272 4460 5.163447 TGTGTAGTATTCTCCGGGATGAAAG 60.163 44.000 0.00 0.00 0.00 2.62
4314 4502 7.378728 GCTAAACAGTTGTTGTCCAATAAACTC 59.621 37.037 0.00 0.00 39.73 3.01
4329 4518 1.620822 AACTCACAGGCCCATGTTTC 58.379 50.000 0.00 0.00 0.00 2.78
4379 4568 4.754618 GGGGACAATTTTCATGTTTTGACC 59.245 41.667 0.00 3.20 32.84 4.02
4380 4569 4.754618 GGGACAATTTTCATGTTTTGACCC 59.245 41.667 16.79 16.79 43.31 4.46
4396 4585 7.931948 TGTTTTGACCCTTTTGTGAAACTTTAA 59.068 29.630 0.00 0.00 38.04 1.52
4407 4596 6.861065 TGTGAAACTTTAACAGGATCTGAC 57.139 37.500 1.59 0.00 38.04 3.51
4416 4605 0.176680 CAGGATCTGACCCTGGTTCG 59.823 60.000 10.48 0.00 45.66 3.95
4421 4610 3.134081 GGATCTGACCCTGGTTCGAAATA 59.866 47.826 0.00 0.00 0.00 1.40
4423 4612 4.837093 TCTGACCCTGGTTCGAAATAAT 57.163 40.909 0.00 0.00 0.00 1.28
4427 4616 6.019779 TGACCCTGGTTCGAAATAATTTTG 57.980 37.500 0.00 0.00 0.00 2.44
4437 4626 7.148069 GGTTCGAAATAATTTTGGGATCTGACT 60.148 37.037 0.00 0.00 0.00 3.41
4439 4628 7.338710 TCGAAATAATTTTGGGATCTGACTCT 58.661 34.615 0.00 0.00 0.00 3.24
4448 4637 7.554959 TTTGGGATCTGACTCTTTTACTACT 57.445 36.000 0.00 0.00 0.00 2.57
4450 4639 5.105310 TGGGATCTGACTCTTTTACTACTGC 60.105 44.000 0.00 0.00 0.00 4.40
4451 4640 5.128008 GGGATCTGACTCTTTTACTACTGCT 59.872 44.000 0.00 0.00 0.00 4.24
4457 4646 9.111613 TCTGACTCTTTTACTACTGCTATAGTC 57.888 37.037 0.84 0.00 40.89 2.59
4470 4659 2.552591 GCTATAGTCTCTGGCGGTAGGA 60.553 54.545 0.84 0.00 0.00 2.94
4479 4668 0.177141 TGGCGGTAGGATAACACTGC 59.823 55.000 0.00 0.00 44.64 4.40
4502 4691 4.681978 GCCACGGTCTTCGGCAGT 62.682 66.667 2.60 0.00 45.52 4.40
4538 4727 6.721442 CGTTATGACGTCGTTATAACATGA 57.279 37.500 33.72 15.40 41.74 3.07
4539 4728 7.140475 CGTTATGACGTCGTTATAACATGAA 57.860 36.000 33.72 12.81 41.74 2.57
4540 4729 7.602645 CGTTATGACGTCGTTATAACATGAAA 58.397 34.615 33.72 12.26 41.74 2.69
4541 4730 8.103320 CGTTATGACGTCGTTATAACATGAAAA 58.897 33.333 33.72 11.70 41.74 2.29
4542 4731 9.743937 GTTATGACGTCGTTATAACATGAAAAA 57.256 29.630 31.92 9.21 41.48 1.94
4545 4734 9.910511 ATGACGTCGTTATAACATGAAAAATAC 57.089 29.630 15.67 0.00 0.00 1.89
4546 4735 8.382130 TGACGTCGTTATAACATGAAAAATACC 58.618 33.333 15.67 0.00 0.00 2.73
4547 4736 8.483307 ACGTCGTTATAACATGAAAAATACCT 57.517 30.769 15.67 0.00 0.00 3.08
4548 4737 9.585099 ACGTCGTTATAACATGAAAAATACCTA 57.415 29.630 15.67 0.00 0.00 3.08
4551 4740 9.033481 TCGTTATAACATGAAAAATACCTACCG 57.967 33.333 15.67 0.00 0.00 4.02
4555 4744 4.337145 ACATGAAAAATACCTACCGCCAA 58.663 39.130 0.00 0.00 0.00 4.52
4556 4745 4.767928 ACATGAAAAATACCTACCGCCAAA 59.232 37.500 0.00 0.00 0.00 3.28
4562 4751 3.538634 ATACCTACCGCCAAAGTCTTC 57.461 47.619 0.00 0.00 0.00 2.87
4572 4761 1.347320 CAAAGTCTTCGGCGGTAGAC 58.653 55.000 25.28 25.28 39.94 2.59
4573 4762 0.245813 AAAGTCTTCGGCGGTAGACC 59.754 55.000 27.38 16.16 40.35 3.85
4574 4763 0.896940 AAGTCTTCGGCGGTAGACCA 60.897 55.000 27.38 0.00 40.35 4.02
4576 4765 0.175073 GTCTTCGGCGGTAGACCATT 59.825 55.000 23.45 0.00 35.29 3.16
4577 4766 1.406539 GTCTTCGGCGGTAGACCATTA 59.593 52.381 23.45 0.00 35.29 1.90
4578 4767 2.035576 GTCTTCGGCGGTAGACCATTAT 59.964 50.000 23.45 0.00 35.29 1.28
4580 4769 3.504906 TCTTCGGCGGTAGACCATTATAG 59.495 47.826 7.21 0.00 35.14 1.31
4581 4770 2.165167 TCGGCGGTAGACCATTATAGG 58.835 52.381 7.21 0.00 35.14 2.57
4582 4771 1.403780 CGGCGGTAGACCATTATAGGC 60.404 57.143 0.00 0.00 35.14 3.93
4583 4772 1.621814 GGCGGTAGACCATTATAGGCA 59.378 52.381 0.00 0.00 35.14 4.75
4584 4773 2.236395 GGCGGTAGACCATTATAGGCAT 59.764 50.000 0.00 0.00 35.14 4.40
4592 4781 7.942894 GGTAGACCATTATAGGCATTACCTTTT 59.057 37.037 0.00 0.00 42.37 2.27
4611 4800 3.915437 TTCTTTGAAAATGAGGTCGCC 57.085 42.857 0.00 0.00 31.23 5.54
4633 4835 2.334653 CGTGCATGGTGGCGTTTT 59.665 55.556 0.00 0.00 36.28 2.43
4634 4836 2.015627 CGTGCATGGTGGCGTTTTG 61.016 57.895 0.00 0.00 36.28 2.44
4635 4837 2.028778 TGCATGGTGGCGTTTTGC 59.971 55.556 0.00 0.00 45.38 3.68
4646 4848 2.785879 GCGTTTTGCAATTATGTGGC 57.214 45.000 0.00 0.00 45.45 5.01
4669 4871 0.108992 AAATGTGCAGGCTTCATGCG 60.109 50.000 0.00 0.00 46.87 4.73
4704 4917 2.043992 ACCCATGCATCCCATCAATTG 58.956 47.619 0.00 0.00 29.71 2.32
4716 4929 7.173047 GCATCCCATCAATTGTTTAAGTTTGTT 59.827 33.333 5.13 0.00 0.00 2.83
4732 4945 2.857186 TGTTGCATGTCCAAGCTAGA 57.143 45.000 0.00 0.00 0.00 2.43
4772 4985 1.908619 AGTACTGATGCATGTGGGTGA 59.091 47.619 2.46 0.00 0.00 4.02
4773 4986 2.093288 AGTACTGATGCATGTGGGTGAG 60.093 50.000 2.46 0.00 0.00 3.51
4801 5014 1.145945 AGGGAGAGATGGATGCGAGTA 59.854 52.381 0.00 0.00 0.00 2.59
4802 5015 1.964223 GGGAGAGATGGATGCGAGTAA 59.036 52.381 0.00 0.00 0.00 2.24
4808 5021 6.161855 AGAGATGGATGCGAGTAAATGTTA 57.838 37.500 0.00 0.00 0.00 2.41
4809 5022 5.986135 AGAGATGGATGCGAGTAAATGTTAC 59.014 40.000 0.00 0.00 0.00 2.50
4814 5027 4.094294 GGATGCGAGTAAATGTTACTGCAA 59.906 41.667 19.47 10.27 36.23 4.08
4816 5029 5.621197 TGCGAGTAAATGTTACTGCAAAT 57.379 34.783 16.11 0.00 32.75 2.32
4817 5030 5.389778 TGCGAGTAAATGTTACTGCAAATG 58.610 37.500 16.11 0.00 32.75 2.32
4818 5031 5.180304 TGCGAGTAAATGTTACTGCAAATGA 59.820 36.000 16.11 1.99 32.75 2.57
4819 5032 6.083630 GCGAGTAAATGTTACTGCAAATGAA 58.916 36.000 5.42 0.00 0.00 2.57
4820 5033 6.747280 GCGAGTAAATGTTACTGCAAATGAAT 59.253 34.615 5.42 0.00 0.00 2.57
4821 5034 7.253420 GCGAGTAAATGTTACTGCAAATGAATG 60.253 37.037 5.42 0.00 0.00 2.67
4822 5035 7.750458 CGAGTAAATGTTACTGCAAATGAATGT 59.250 33.333 5.42 0.00 0.00 2.71
4823 5036 9.410556 GAGTAAATGTTACTGCAAATGAATGTT 57.589 29.630 5.42 0.00 0.00 2.71
4832 5297 4.548494 TGCAAATGAATGTTACTGCAGTG 58.452 39.130 29.57 8.84 35.02 3.66
4836 5301 5.772825 AATGAATGTTACTGCAGTGTGTT 57.227 34.783 29.57 17.26 0.00 3.32
4840 5305 6.052360 TGAATGTTACTGCAGTGTGTTAGAA 58.948 36.000 29.57 10.77 0.00 2.10
4845 5310 2.943033 ACTGCAGTGTGTTAGAAACCAC 59.057 45.455 20.97 0.00 34.71 4.16
4846 5311 1.937223 TGCAGTGTGTTAGAAACCACG 59.063 47.619 0.00 0.00 37.53 4.94
4847 5312 1.937899 GCAGTGTGTTAGAAACCACGT 59.062 47.619 0.00 0.00 37.53 4.49
4889 5354 5.574830 GCATCTCGTAATAGTGAATAGCCTG 59.425 44.000 0.00 0.00 0.00 4.85
4892 5357 3.639561 TCGTAATAGTGAATAGCCTGCCA 59.360 43.478 0.00 0.00 0.00 4.92
4922 5387 0.688487 TGGTGGTAGGGTTACACAGC 59.312 55.000 0.00 0.00 33.19 4.40
4923 5388 0.035725 GGTGGTAGGGTTACACAGCC 60.036 60.000 0.00 0.00 44.40 4.85
4933 5398 0.036765 TTACACAGCCTACCGCCAAG 60.037 55.000 0.00 0.00 38.78 3.61
4936 5401 0.178068 CACAGCCTACCGCCAAGTAT 59.822 55.000 0.00 0.00 38.78 2.12
4949 5414 1.583054 CAAGTATTCTGGCGGTAGGC 58.417 55.000 0.00 0.00 44.11 3.93
4959 5424 0.380733 GGCGGTAGGCTATTTTGCAC 59.619 55.000 0.00 0.00 42.94 4.57
4967 5433 4.370364 AGGCTATTTTGCACGTTAATGG 57.630 40.909 0.00 0.00 34.04 3.16
4970 5436 1.989430 ATTTTGCACGTTAATGGCCG 58.011 45.000 0.00 0.00 0.00 6.13
4986 5452 2.311701 CCGTGACGGCGCAGTTAAA 61.312 57.895 15.89 0.81 41.17 1.52
4994 5461 0.935196 GGCGCAGTTAAATCCTACCG 59.065 55.000 10.83 0.00 0.00 4.02
4995 5462 1.648504 GCGCAGTTAAATCCTACCGT 58.351 50.000 0.30 0.00 0.00 4.83
4998 5465 3.255725 CGCAGTTAAATCCTACCGTCAA 58.744 45.455 0.00 0.00 0.00 3.18
4999 5466 3.306166 CGCAGTTAAATCCTACCGTCAAG 59.694 47.826 0.00 0.00 0.00 3.02
5000 5467 4.251268 GCAGTTAAATCCTACCGTCAAGT 58.749 43.478 0.00 0.00 0.00 3.16
5003 5470 6.628185 CAGTTAAATCCTACCGTCAAGTACT 58.372 40.000 0.00 0.00 0.00 2.73
5004 5471 6.750963 CAGTTAAATCCTACCGTCAAGTACTC 59.249 42.308 0.00 0.00 0.00 2.59
5008 5475 2.040813 TCCTACCGTCAAGTACTCTGGT 59.959 50.000 0.00 4.74 0.00 4.00
5019 5486 4.393239 AGTACTCTGGTGGTAGGTTGTA 57.607 45.455 0.00 0.00 0.00 2.41
5034 5501 2.830104 GTTGTATAACCCTACCGCCAG 58.170 52.381 0.00 0.00 0.00 4.85
5035 5502 2.431782 GTTGTATAACCCTACCGCCAGA 59.568 50.000 0.00 0.00 0.00 3.86
5037 5504 2.091720 TGTATAACCCTACCGCCAGAGA 60.092 50.000 0.00 0.00 0.00 3.10
5041 5508 0.556747 ACCCTACCGCCAGAGACTAT 59.443 55.000 0.00 0.00 0.00 2.12
5095 5562 5.952526 TTTTTCAAACGAGGGTTAGATCC 57.047 39.130 0.00 0.00 34.62 3.36
5096 5563 4.627284 TTTCAAACGAGGGTTAGATCCA 57.373 40.909 0.00 0.00 34.62 3.41
5103 5570 3.132467 ACGAGGGTTAGATCCAGCTAAAC 59.868 47.826 0.00 0.00 37.34 2.01
5107 5574 6.406624 CGAGGGTTAGATCCAGCTAAACTTTA 60.407 42.308 0.00 0.00 37.99 1.85
5109 5576 7.873195 AGGGTTAGATCCAGCTAAACTTTAAT 58.127 34.615 0.00 0.00 37.99 1.40
5126 5593 8.637281 AACTTTAATAAAAGGGTCAAAACACG 57.363 30.769 3.19 0.00 45.39 4.49
5130 5597 9.649167 TTTAATAAAAGGGTCAAAACACGAAAA 57.351 25.926 0.00 0.00 32.44 2.29
5134 5601 4.729227 AGGGTCAAAACACGAAAATTGT 57.271 36.364 0.00 0.00 32.44 2.71
5137 5604 4.440940 GGGTCAAAACACGAAAATTGTCCT 60.441 41.667 0.00 0.00 33.40 3.85
5142 5609 2.779506 ACACGAAAATTGTCCTCCCTC 58.220 47.619 0.00 0.00 0.00 4.30
5145 5612 2.290323 ACGAAAATTGTCCTCCCTCTGG 60.290 50.000 0.00 0.00 0.00 3.86
5146 5613 2.290323 CGAAAATTGTCCTCCCTCTGGT 60.290 50.000 0.00 0.00 0.00 4.00
5147 5614 3.055385 CGAAAATTGTCCTCCCTCTGGTA 60.055 47.826 0.00 0.00 0.00 3.25
5148 5615 4.518249 GAAAATTGTCCTCCCTCTGGTAG 58.482 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 246 1.367840 GTCTGTTCGTGAGGCCACT 59.632 57.895 5.01 0.00 41.06 4.00
377 378 4.678509 TGTCATTACGATGCTTCCAAAC 57.321 40.909 0.00 0.00 33.14 2.93
388 389 4.896562 GTTGAACACGATGTCATTACGA 57.103 40.909 1.29 0.00 0.00 3.43
432 433 5.788533 TCCTCCTTAATCCTAAGTGAAACCA 59.211 40.000 0.00 0.00 37.80 3.67
575 581 7.958567 CACGGTTACATCGTAAATTTACATGTT 59.041 33.333 29.89 21.24 38.94 2.71
675 682 6.039159 TGTGTAATGTGGTGGCATACATATTG 59.961 38.462 19.66 0.00 36.56 1.90
676 683 6.125719 TGTGTAATGTGGTGGCATACATATT 58.874 36.000 17.11 16.89 36.56 1.28
677 684 5.689835 TGTGTAATGTGGTGGCATACATAT 58.310 37.500 17.11 9.01 36.56 1.78
678 685 5.104259 TGTGTAATGTGGTGGCATACATA 57.896 39.130 17.11 7.27 36.56 2.29
679 686 3.961849 TGTGTAATGTGGTGGCATACAT 58.038 40.909 12.71 12.71 39.08 2.29
680 687 3.425162 TGTGTAATGTGGTGGCATACA 57.575 42.857 9.48 9.48 0.00 2.29
681 688 3.694072 ACATGTGTAATGTGGTGGCATAC 59.306 43.478 0.00 0.00 0.00 2.39
682 689 3.693578 CACATGTGTAATGTGGTGGCATA 59.306 43.478 18.03 0.00 44.04 3.14
683 690 2.492881 CACATGTGTAATGTGGTGGCAT 59.507 45.455 18.03 0.00 44.04 4.40
684 691 1.885233 CACATGTGTAATGTGGTGGCA 59.115 47.619 18.03 0.00 44.04 4.92
685 692 2.634982 CACATGTGTAATGTGGTGGC 57.365 50.000 18.03 0.00 44.04 5.01
690 697 5.369685 TTGCTTACCACATGTGTAATGTG 57.630 39.130 23.79 10.21 46.49 3.21
691 698 5.709631 TGATTGCTTACCACATGTGTAATGT 59.290 36.000 23.79 16.29 0.00 2.71
692 699 6.193514 TGATTGCTTACCACATGTGTAATG 57.806 37.500 23.79 11.29 0.00 1.90
693 700 6.832520 TTGATTGCTTACCACATGTGTAAT 57.167 33.333 23.79 10.22 0.00 1.89
694 701 6.641169 TTTGATTGCTTACCACATGTGTAA 57.359 33.333 23.79 18.81 0.00 2.41
695 702 6.832520 ATTTGATTGCTTACCACATGTGTA 57.167 33.333 23.79 13.34 0.00 2.90
696 703 5.726980 ATTTGATTGCTTACCACATGTGT 57.273 34.783 23.79 14.29 0.00 3.72
697 704 8.706492 AATTATTTGATTGCTTACCACATGTG 57.294 30.769 19.31 19.31 0.00 3.21
698 705 8.530311 TGAATTATTTGATTGCTTACCACATGT 58.470 29.630 0.00 0.00 0.00 3.21
699 706 8.929827 TGAATTATTTGATTGCTTACCACATG 57.070 30.769 0.00 0.00 0.00 3.21
700 707 7.707893 GCTGAATTATTTGATTGCTTACCACAT 59.292 33.333 0.00 0.00 0.00 3.21
701 708 7.035004 GCTGAATTATTTGATTGCTTACCACA 58.965 34.615 0.00 0.00 0.00 4.17
702 709 7.260603 AGCTGAATTATTTGATTGCTTACCAC 58.739 34.615 0.00 0.00 0.00 4.16
703 710 7.408756 AGCTGAATTATTTGATTGCTTACCA 57.591 32.000 0.00 0.00 0.00 3.25
704 711 8.840321 TCTAGCTGAATTATTTGATTGCTTACC 58.160 33.333 0.00 0.00 0.00 2.85
705 712 9.657121 GTCTAGCTGAATTATTTGATTGCTTAC 57.343 33.333 0.00 0.00 0.00 2.34
706 713 8.551205 CGTCTAGCTGAATTATTTGATTGCTTA 58.449 33.333 0.00 0.00 0.00 3.09
707 714 7.412853 CGTCTAGCTGAATTATTTGATTGCTT 58.587 34.615 0.00 0.00 0.00 3.91
708 715 6.017605 CCGTCTAGCTGAATTATTTGATTGCT 60.018 38.462 0.00 0.00 0.00 3.91
709 716 6.017934 TCCGTCTAGCTGAATTATTTGATTGC 60.018 38.462 0.00 0.00 0.00 3.56
710 717 7.439356 TCTCCGTCTAGCTGAATTATTTGATTG 59.561 37.037 0.00 0.00 0.00 2.67
711 718 7.500992 TCTCCGTCTAGCTGAATTATTTGATT 58.499 34.615 0.00 0.00 0.00 2.57
712 719 7.055667 TCTCCGTCTAGCTGAATTATTTGAT 57.944 36.000 0.00 0.00 0.00 2.57
713 720 6.465439 TCTCCGTCTAGCTGAATTATTTGA 57.535 37.500 0.00 0.00 0.00 2.69
714 721 7.721286 AATCTCCGTCTAGCTGAATTATTTG 57.279 36.000 0.00 0.00 0.00 2.32
715 722 7.600752 GCTAATCTCCGTCTAGCTGAATTATTT 59.399 37.037 0.00 0.00 36.06 1.40
716 723 7.039363 AGCTAATCTCCGTCTAGCTGAATTATT 60.039 37.037 0.00 0.00 45.14 1.40
717 724 6.435904 AGCTAATCTCCGTCTAGCTGAATTAT 59.564 38.462 0.00 0.00 45.14 1.28
718 725 5.770663 AGCTAATCTCCGTCTAGCTGAATTA 59.229 40.000 0.00 0.00 45.14 1.40
719 726 4.586841 AGCTAATCTCCGTCTAGCTGAATT 59.413 41.667 0.00 0.00 45.14 2.17
720 727 4.148838 AGCTAATCTCCGTCTAGCTGAAT 58.851 43.478 0.00 0.00 45.14 2.57
721 728 3.556999 AGCTAATCTCCGTCTAGCTGAA 58.443 45.455 0.00 0.00 45.14 3.02
722 729 3.216187 AGCTAATCTCCGTCTAGCTGA 57.784 47.619 0.00 0.00 45.14 4.26
723 730 6.676943 GCTTATAGCTAATCTCCGTCTAGCTG 60.677 46.154 12.01 0.00 46.07 4.24
725 732 5.575019 GCTTATAGCTAATCTCCGTCTAGC 58.425 45.833 0.00 0.00 38.45 3.42
762 769 9.838339 AGAAAAGAGATAGAGACAAAGTTGAAA 57.162 29.630 0.00 0.00 0.00 2.69
763 770 9.838339 AAGAAAAGAGATAGAGACAAAGTTGAA 57.162 29.630 0.00 0.00 0.00 2.69
805 812 9.930693 CTCTTGGTCTTTAGTGTACTCTTAAAT 57.069 33.333 2.25 0.00 0.00 1.40
806 813 7.871463 GCTCTTGGTCTTTAGTGTACTCTTAAA 59.129 37.037 2.25 0.73 0.00 1.52
807 814 7.376615 GCTCTTGGTCTTTAGTGTACTCTTAA 58.623 38.462 2.25 0.00 0.00 1.85
808 815 6.071503 GGCTCTTGGTCTTTAGTGTACTCTTA 60.072 42.308 2.25 0.00 0.00 2.10
809 816 5.279556 GGCTCTTGGTCTTTAGTGTACTCTT 60.280 44.000 2.25 0.00 0.00 2.85
810 817 4.221041 GGCTCTTGGTCTTTAGTGTACTCT 59.779 45.833 2.57 2.57 0.00 3.24
811 818 4.496360 GGCTCTTGGTCTTTAGTGTACTC 58.504 47.826 0.00 0.00 0.00 2.59
812 819 3.261137 GGGCTCTTGGTCTTTAGTGTACT 59.739 47.826 0.00 0.00 0.00 2.73
813 820 3.007614 TGGGCTCTTGGTCTTTAGTGTAC 59.992 47.826 0.00 0.00 0.00 2.90
814 821 3.007614 GTGGGCTCTTGGTCTTTAGTGTA 59.992 47.826 0.00 0.00 0.00 2.90
815 822 2.054799 TGGGCTCTTGGTCTTTAGTGT 58.945 47.619 0.00 0.00 0.00 3.55
816 823 2.427506 GTGGGCTCTTGGTCTTTAGTG 58.572 52.381 0.00 0.00 0.00 2.74
817 824 1.351350 GGTGGGCTCTTGGTCTTTAGT 59.649 52.381 0.00 0.00 0.00 2.24
818 825 1.630878 AGGTGGGCTCTTGGTCTTTAG 59.369 52.381 0.00 0.00 0.00 1.85
819 826 1.742308 AGGTGGGCTCTTGGTCTTTA 58.258 50.000 0.00 0.00 0.00 1.85
820 827 0.853530 AAGGTGGGCTCTTGGTCTTT 59.146 50.000 0.00 0.00 0.00 2.52
821 828 0.402121 GAAGGTGGGCTCTTGGTCTT 59.598 55.000 0.00 0.00 0.00 3.01
822 829 0.768221 TGAAGGTGGGCTCTTGGTCT 60.768 55.000 0.00 0.00 0.00 3.85
823 830 0.606673 GTGAAGGTGGGCTCTTGGTC 60.607 60.000 0.00 0.00 0.00 4.02
824 831 1.062488 AGTGAAGGTGGGCTCTTGGT 61.062 55.000 0.00 0.00 0.00 3.67
825 832 0.111253 AAGTGAAGGTGGGCTCTTGG 59.889 55.000 0.00 0.00 0.00 3.61
826 833 1.242076 CAAGTGAAGGTGGGCTCTTG 58.758 55.000 0.00 0.00 31.83 3.02
827 834 0.538287 GCAAGTGAAGGTGGGCTCTT 60.538 55.000 0.00 0.00 0.00 2.85
828 835 1.073897 GCAAGTGAAGGTGGGCTCT 59.926 57.895 0.00 0.00 0.00 4.09
829 836 0.957888 GAGCAAGTGAAGGTGGGCTC 60.958 60.000 0.00 0.00 40.63 4.70
830 837 1.073897 GAGCAAGTGAAGGTGGGCT 59.926 57.895 0.00 0.00 0.00 5.19
831 838 0.957888 GAGAGCAAGTGAAGGTGGGC 60.958 60.000 0.00 0.00 0.00 5.36
832 839 0.397941 TGAGAGCAAGTGAAGGTGGG 59.602 55.000 0.00 0.00 0.00 4.61
833 840 2.149578 CTTGAGAGCAAGTGAAGGTGG 58.850 52.381 0.00 0.00 45.10 4.61
843 850 2.485479 GGTGGTTGAGACTTGAGAGCAA 60.485 50.000 0.00 0.00 0.00 3.91
844 851 1.070758 GGTGGTTGAGACTTGAGAGCA 59.929 52.381 0.00 0.00 0.00 4.26
845 852 1.802069 GGTGGTTGAGACTTGAGAGC 58.198 55.000 0.00 0.00 0.00 4.09
846 853 1.337260 CCGGTGGTTGAGACTTGAGAG 60.337 57.143 0.00 0.00 0.00 3.20
847 854 0.679505 CCGGTGGTTGAGACTTGAGA 59.320 55.000 0.00 0.00 0.00 3.27
848 855 0.951040 GCCGGTGGTTGAGACTTGAG 60.951 60.000 1.90 0.00 0.00 3.02
849 856 1.070786 GCCGGTGGTTGAGACTTGA 59.929 57.895 1.90 0.00 0.00 3.02
850 857 2.317609 CGCCGGTGGTTGAGACTTG 61.318 63.158 7.26 0.00 0.00 3.16
851 858 2.030562 CGCCGGTGGTTGAGACTT 59.969 61.111 7.26 0.00 0.00 3.01
852 859 2.436087 CTTCGCCGGTGGTTGAGACT 62.436 60.000 16.49 0.00 0.00 3.24
853 860 2.027625 CTTCGCCGGTGGTTGAGAC 61.028 63.158 16.49 0.00 0.00 3.36
881 888 3.241530 TCGCCCCTGTGTTGAGCT 61.242 61.111 0.00 0.00 0.00 4.09
964 979 2.583520 GAGCTGGAGCACCTGGAG 59.416 66.667 0.00 0.00 45.16 3.86
983 1001 1.275666 CATAGTGGTGGGTCAGTGGA 58.724 55.000 0.00 0.00 0.00 4.02
1125 1143 2.683933 TGGAAGGAGGCGGAGGAC 60.684 66.667 0.00 0.00 0.00 3.85
1126 1144 2.364317 CTGGAAGGAGGCGGAGGA 60.364 66.667 0.00 0.00 0.00 3.71
1470 1537 1.802069 AAGCGCAAAAGGTCTCTCTC 58.198 50.000 11.47 0.00 0.00 3.20
1471 1538 1.876156 CAAAGCGCAAAAGGTCTCTCT 59.124 47.619 11.47 0.00 0.00 3.10
1472 1539 1.664302 GCAAAGCGCAAAAGGTCTCTC 60.664 52.381 11.47 0.00 41.79 3.20
1473 1540 0.312102 GCAAAGCGCAAAAGGTCTCT 59.688 50.000 11.47 0.00 41.79 3.10
1546 1613 3.871594 AGCTGTTGTTCTACACACAAGAC 59.128 43.478 0.00 0.00 34.79 3.01
1592 1659 4.243007 AGGGAGCGTTTGAAAATTGAAG 57.757 40.909 0.00 0.00 0.00 3.02
1626 1693 2.165998 AGAATTCAGAGCAACAAGGGC 58.834 47.619 8.44 0.00 0.00 5.19
1743 1810 3.771479 TGCACAGATCTCCAAGTCTACAT 59.229 43.478 0.00 0.00 0.00 2.29
1747 1814 2.028294 CACTGCACAGATCTCCAAGTCT 60.028 50.000 4.31 0.00 0.00 3.24
1788 1863 3.808728 TGTCAGACAAGAAAAGGAGGTG 58.191 45.455 0.00 0.00 0.00 4.00
1866 2046 7.141100 TCAAAACCGACCAAAGAGATAAATC 57.859 36.000 0.00 0.00 0.00 2.17
1870 2050 7.229707 TGAAAATCAAAACCGACCAAAGAGATA 59.770 33.333 0.00 0.00 0.00 1.98
1907 2087 5.915196 GCTCAAATCAAACTAACTGAACCAC 59.085 40.000 0.00 0.00 0.00 4.16
2064 2245 7.615365 TCCTGTCATCAAATTAATAAAGCACCT 59.385 33.333 0.00 0.00 0.00 4.00
2098 2279 2.512692 TGCTAAATCACAGTGGCCAT 57.487 45.000 9.72 0.00 0.00 4.40
2128 2310 4.122046 GCAAAAAGCAAGTGGAGTTGAAT 58.878 39.130 0.00 0.00 44.79 2.57
2142 2324 1.202452 ACCACAGCAAGAGCAAAAAGC 60.202 47.619 0.00 0.00 45.49 3.51
2207 2389 6.098838 TGGCAAGACTATCACTCTGTTGATAT 59.901 38.462 0.00 0.00 37.74 1.63
2339 2523 1.522668 CAGACGAATGGCCTGTGAAA 58.477 50.000 3.32 0.00 0.00 2.69
2354 2538 0.623723 TGGCTATTGAACCCCCAGAC 59.376 55.000 0.00 0.00 0.00 3.51
2513 2697 7.821595 CATGATGAAATGCAAAATACACTGT 57.178 32.000 0.00 0.00 0.00 3.55
2577 2761 7.398618 AGACTGAATTTGTTCTCTAGAGGATGA 59.601 37.037 19.67 1.12 0.00 2.92
2801 2985 3.735591 TGTCAAGAAAAGGTAAGTCCCG 58.264 45.455 0.00 0.00 36.75 5.14
2921 3105 0.165944 CACTTAAACTTCTGGCGGCG 59.834 55.000 0.51 0.51 0.00 6.46
3110 3294 6.264292 ACATAACAGATGTTTACAGTGGCAAA 59.736 34.615 3.14 0.00 39.31 3.68
4004 4190 0.529337 ATCCAAGTGCATCGCTCTCG 60.529 55.000 0.00 0.00 30.88 4.04
4121 4307 1.699656 GCACAAGTCTCGCGATGCAT 61.700 55.000 21.54 0.00 33.27 3.96
4145 4331 4.487714 TGCCACGGAGAAATTCTCTTAT 57.512 40.909 20.82 5.80 42.95 1.73
4209 4395 6.455647 TGATAGTTCAGGCTTACAATATCCG 58.544 40.000 0.00 0.00 0.00 4.18
4271 4459 9.014297 ACTGTTTAGCATTTTAAATAGTCTGCT 57.986 29.630 7.69 7.69 39.34 4.24
4272 4460 9.626045 AACTGTTTAGCATTTTAAATAGTCTGC 57.374 29.630 7.90 0.00 41.28 4.26
4314 4502 1.747355 GAGATGAAACATGGGCCTGTG 59.253 52.381 4.53 6.51 0.00 3.66
4360 4549 7.392953 ACAAAAGGGTCAAAACATGAAAATTGT 59.607 29.630 0.00 0.00 40.50 2.71
4364 4553 6.467677 TCACAAAAGGGTCAAAACATGAAAA 58.532 32.000 0.00 0.00 40.50 2.29
4368 4557 5.874261 AGTTTCACAAAAGGGTCAAAACATG 59.126 36.000 0.00 0.00 31.06 3.21
4369 4558 6.048732 AGTTTCACAAAAGGGTCAAAACAT 57.951 33.333 0.00 0.00 31.06 2.71
4370 4559 5.476091 AGTTTCACAAAAGGGTCAAAACA 57.524 34.783 0.00 0.00 31.06 2.83
4379 4568 7.649306 CAGATCCTGTTAAAGTTTCACAAAAGG 59.351 37.037 4.30 2.45 0.00 3.11
4380 4569 8.405531 TCAGATCCTGTTAAAGTTTCACAAAAG 58.594 33.333 4.30 0.00 32.61 2.27
4407 4596 4.464597 TCCCAAAATTATTTCGAACCAGGG 59.535 41.667 0.00 1.43 0.00 4.45
4421 4610 9.232473 GTAGTAAAAGAGTCAGATCCCAAAATT 57.768 33.333 0.00 0.00 0.00 1.82
4423 4612 7.878127 CAGTAGTAAAAGAGTCAGATCCCAAAA 59.122 37.037 0.00 0.00 0.00 2.44
4427 4616 5.128008 AGCAGTAGTAAAAGAGTCAGATCCC 59.872 44.000 0.00 0.00 0.00 3.85
4437 4626 7.013464 GCCAGAGACTATAGCAGTAGTAAAAGA 59.987 40.741 0.00 0.00 37.72 2.52
4439 4628 6.238676 CGCCAGAGACTATAGCAGTAGTAAAA 60.239 42.308 0.00 0.00 37.72 1.52
4443 4632 3.142951 CGCCAGAGACTATAGCAGTAGT 58.857 50.000 0.00 1.16 37.72 2.73
4448 4637 2.505405 CTACCGCCAGAGACTATAGCA 58.495 52.381 0.00 0.00 0.00 3.49
4450 4639 3.420300 TCCTACCGCCAGAGACTATAG 57.580 52.381 0.00 0.00 0.00 1.31
4451 4640 5.221986 TGTTATCCTACCGCCAGAGACTATA 60.222 44.000 0.00 0.00 0.00 1.31
4457 4646 2.032620 AGTGTTATCCTACCGCCAGAG 58.967 52.381 0.00 0.00 0.00 3.35
4526 4715 7.795272 GCGGTAGGTATTTTTCATGTTATAACG 59.205 37.037 10.92 0.00 0.00 3.18
4529 4718 7.281098 TGGCGGTAGGTATTTTTCATGTTATA 58.719 34.615 0.00 0.00 0.00 0.98
4536 4725 4.400120 ACTTTGGCGGTAGGTATTTTTCA 58.600 39.130 0.00 0.00 0.00 2.69
4537 4726 4.698780 AGACTTTGGCGGTAGGTATTTTTC 59.301 41.667 0.00 0.00 0.00 2.29
4538 4727 4.659115 AGACTTTGGCGGTAGGTATTTTT 58.341 39.130 0.00 0.00 0.00 1.94
4539 4728 4.296621 AGACTTTGGCGGTAGGTATTTT 57.703 40.909 0.00 0.00 0.00 1.82
4540 4729 3.994931 AGACTTTGGCGGTAGGTATTT 57.005 42.857 0.00 0.00 0.00 1.40
4541 4730 3.677976 CGAAGACTTTGGCGGTAGGTATT 60.678 47.826 0.00 0.00 0.00 1.89
4542 4731 2.159142 CGAAGACTTTGGCGGTAGGTAT 60.159 50.000 0.00 0.00 0.00 2.73
4543 4732 1.203052 CGAAGACTTTGGCGGTAGGTA 59.797 52.381 0.00 0.00 0.00 3.08
4544 4733 0.037605 CGAAGACTTTGGCGGTAGGT 60.038 55.000 0.00 0.00 0.00 3.08
4545 4734 0.739813 CCGAAGACTTTGGCGGTAGG 60.740 60.000 8.61 0.00 38.99 3.18
4546 4735 2.750815 CCGAAGACTTTGGCGGTAG 58.249 57.895 8.61 0.00 38.99 3.18
4555 4744 0.896940 TGGTCTACCGCCGAAGACTT 60.897 55.000 15.81 0.00 41.53 3.01
4556 4745 0.683504 ATGGTCTACCGCCGAAGACT 60.684 55.000 15.81 0.00 41.53 3.24
4562 4751 1.403780 GCCTATAATGGTCTACCGCCG 60.404 57.143 0.00 0.00 39.43 6.46
4580 4769 7.118245 CCTCATTTTCAAAGAAAAGGTAATGCC 59.882 37.037 14.12 0.00 37.58 4.40
4581 4770 7.657354 ACCTCATTTTCAAAGAAAAGGTAATGC 59.343 33.333 14.12 0.00 0.00 3.56
4582 4771 9.196552 GACCTCATTTTCAAAGAAAAGGTAATG 57.803 33.333 14.12 6.60 0.00 1.90
4583 4772 8.082242 CGACCTCATTTTCAAAGAAAAGGTAAT 58.918 33.333 14.12 4.03 0.00 1.89
4584 4773 7.422399 CGACCTCATTTTCAAAGAAAAGGTAA 58.578 34.615 14.12 0.00 0.00 2.85
4617 4806 2.309501 GCAAAACGCCACCATGCAC 61.310 57.895 0.00 0.00 37.00 4.57
4624 4813 2.411409 CCACATAATTGCAAAACGCCAC 59.589 45.455 1.71 0.00 41.33 5.01
4633 4835 3.263261 CATTTGCAGCCACATAATTGCA 58.737 40.909 0.00 0.00 44.09 4.08
4634 4836 3.062909 CACATTTGCAGCCACATAATTGC 59.937 43.478 0.00 0.00 37.09 3.56
4635 4837 4.850859 CACATTTGCAGCCACATAATTG 57.149 40.909 0.00 0.00 0.00 2.32
4661 4863 3.020627 GCTAGGCAGCGCATGAAG 58.979 61.111 11.47 0.82 38.22 3.02
4704 4917 5.276820 GCTTGGACATGCAACAAACTTAAAC 60.277 40.000 0.00 0.00 0.00 2.01
4716 4929 1.742761 GCTTCTAGCTTGGACATGCA 58.257 50.000 11.93 0.00 38.45 3.96
4745 4958 6.099701 ACCCACATGCATCAGTACTATTAGAA 59.900 38.462 0.00 0.00 0.00 2.10
4746 4959 5.602561 ACCCACATGCATCAGTACTATTAGA 59.397 40.000 0.00 0.00 0.00 2.10
4747 4960 5.698089 CACCCACATGCATCAGTACTATTAG 59.302 44.000 0.00 0.00 0.00 1.73
4748 4961 5.365314 TCACCCACATGCATCAGTACTATTA 59.635 40.000 0.00 0.00 0.00 0.98
4749 4962 4.164030 TCACCCACATGCATCAGTACTATT 59.836 41.667 0.00 0.00 0.00 1.73
4750 4963 3.711190 TCACCCACATGCATCAGTACTAT 59.289 43.478 0.00 0.00 0.00 2.12
4756 4969 2.014857 CTTCTCACCCACATGCATCAG 58.985 52.381 0.00 0.00 0.00 2.90
4772 4985 4.344938 TCCATCTCTCCCTTTCTCTTCT 57.655 45.455 0.00 0.00 0.00 2.85
4773 4986 4.743348 GCATCCATCTCTCCCTTTCTCTTC 60.743 50.000 0.00 0.00 0.00 2.87
4801 5014 9.195411 CAGTAACATTCATTTGCAGTAACATTT 57.805 29.630 0.00 0.00 0.00 2.32
4802 5015 7.329226 GCAGTAACATTCATTTGCAGTAACATT 59.671 33.333 0.00 0.00 0.00 2.71
4808 5021 4.852134 TGCAGTAACATTCATTTGCAGT 57.148 36.364 0.00 0.00 36.71 4.40
4814 5027 5.772825 AACACACTGCAGTAACATTCATT 57.227 34.783 21.20 2.95 0.00 2.57
4816 5029 5.606505 TCTAACACACTGCAGTAACATTCA 58.393 37.500 21.20 0.00 0.00 2.57
4817 5030 6.539649 TTCTAACACACTGCAGTAACATTC 57.460 37.500 21.20 0.00 0.00 2.67
4818 5031 6.238648 GGTTTCTAACACACTGCAGTAACATT 60.239 38.462 21.20 13.70 0.00 2.71
4819 5032 5.238650 GGTTTCTAACACACTGCAGTAACAT 59.761 40.000 21.20 9.23 0.00 2.71
4820 5033 4.573201 GGTTTCTAACACACTGCAGTAACA 59.427 41.667 21.20 2.37 0.00 2.41
4821 5034 4.573201 TGGTTTCTAACACACTGCAGTAAC 59.427 41.667 21.20 16.72 0.00 2.50
4822 5035 4.573201 GTGGTTTCTAACACACTGCAGTAA 59.427 41.667 21.20 5.35 37.54 2.24
4823 5036 4.124238 GTGGTTTCTAACACACTGCAGTA 58.876 43.478 21.20 1.97 37.54 2.74
4824 5037 2.943033 GTGGTTTCTAACACACTGCAGT 59.057 45.455 15.25 15.25 37.54 4.40
4825 5038 2.032894 CGTGGTTTCTAACACACTGCAG 60.033 50.000 13.48 13.48 37.45 4.41
4832 5297 1.454653 GCGAGACGTGGTTTCTAACAC 59.545 52.381 0.00 0.00 0.00 3.32
4836 5301 1.990799 CATGCGAGACGTGGTTTCTA 58.009 50.000 0.00 0.00 0.00 2.10
4840 5305 2.030412 TGCATGCGAGACGTGGTT 59.970 55.556 14.09 0.00 35.67 3.67
4845 5310 1.080435 ATGTGAGTGCATGCGAGACG 61.080 55.000 14.09 0.00 0.00 4.18
4846 5311 0.372679 CATGTGAGTGCATGCGAGAC 59.627 55.000 14.09 5.82 39.59 3.36
4847 5312 2.758497 CATGTGAGTGCATGCGAGA 58.242 52.632 14.09 0.00 39.59 4.04
4906 5371 2.181975 GTAGGCTGTGTAACCCTACCA 58.818 52.381 0.00 0.00 42.46 3.25
4907 5372 2.975732 GTAGGCTGTGTAACCCTACC 57.024 55.000 0.00 0.00 42.46 3.18
4922 5387 1.810412 GCCAGAATACTTGGCGGTAGG 60.810 57.143 0.00 0.00 39.06 3.18
4923 5388 1.583054 GCCAGAATACTTGGCGGTAG 58.417 55.000 0.00 0.00 39.06 3.18
4933 5398 3.679824 AATAGCCTACCGCCAGAATAC 57.320 47.619 0.00 0.00 38.78 1.89
4936 5401 2.639065 CAAAATAGCCTACCGCCAGAA 58.361 47.619 0.00 0.00 38.78 3.02
4944 5409 5.270853 CCATTAACGTGCAAAATAGCCTAC 58.729 41.667 0.00 0.00 0.00 3.18
4949 5414 3.105203 CGGCCATTAACGTGCAAAATAG 58.895 45.455 2.24 0.00 0.00 1.73
4959 5424 3.086309 CCGTCACGGCCATTAACG 58.914 61.111 1.50 6.77 41.17 3.18
4970 5436 0.096454 GGATTTAACTGCGCCGTCAC 59.904 55.000 4.51 0.00 0.00 3.67
4986 5452 3.288964 CCAGAGTACTTGACGGTAGGAT 58.711 50.000 0.00 0.00 0.00 3.24
4994 5461 3.163467 ACCTACCACCAGAGTACTTGAC 58.837 50.000 0.00 0.00 0.00 3.18
4995 5462 3.537795 ACCTACCACCAGAGTACTTGA 57.462 47.619 0.00 0.00 0.00 3.02
4998 5465 3.255634 ACAACCTACCACCAGAGTACT 57.744 47.619 0.00 0.00 0.00 2.73
4999 5466 6.567959 GTTATACAACCTACCACCAGAGTAC 58.432 44.000 0.00 0.00 0.00 2.73
5000 5467 6.780457 GTTATACAACCTACCACCAGAGTA 57.220 41.667 0.00 0.00 0.00 2.59
5019 5486 1.063114 AGTCTCTGGCGGTAGGGTTAT 60.063 52.381 0.00 0.00 0.00 1.89
5034 5501 3.814005 TTTTCCTACCGCCATAGTCTC 57.186 47.619 0.00 0.00 0.00 3.36
5077 5544 2.093658 GCTGGATCTAACCCTCGTTTGA 60.094 50.000 0.00 0.00 37.97 2.69
5083 5550 5.360649 AAGTTTAGCTGGATCTAACCCTC 57.639 43.478 0.00 0.00 0.00 4.30
5091 5558 8.967918 ACCCTTTTATTAAAGTTTAGCTGGATC 58.032 33.333 0.00 0.00 39.29 3.36
5095 5562 9.974980 TTTGACCCTTTTATTAAAGTTTAGCTG 57.025 29.630 0.00 0.00 39.29 4.24
5103 5570 8.859517 TTCGTGTTTTGACCCTTTTATTAAAG 57.140 30.769 0.00 0.00 40.38 1.85
5107 5574 8.608317 CAATTTTCGTGTTTTGACCCTTTTATT 58.392 29.630 0.00 0.00 0.00 1.40
5109 5576 7.097834 ACAATTTTCGTGTTTTGACCCTTTTA 58.902 30.769 0.00 0.00 0.00 1.52
5126 5593 3.441500 ACCAGAGGGAGGACAATTTTC 57.558 47.619 0.00 0.00 38.05 2.29



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

AutoCloner maintained by Alex Coulton.