Multiple sequence alignment - TraesCS5B01G261200

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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 TraesCS5B01G261200 chr5B 100.000 2369 0 0 1 2369 445652869 445650501 0.000000e+00 4375
1 TraesCS5B01G261200 chr5B 85.320 1124 82 32 704 1794 445763530 445762457 0.000000e+00 1085
2 TraesCS5B01G261200 chr5D 88.604 1132 63 31 712 1799 374131167 374130058 0.000000e+00 1315
3 TraesCS5B01G261200 chr5D 85.308 633 76 13 1 624 37121375 37120751 2.570000e-179 638
4 TraesCS5B01G261200 chr5D 89.610 154 13 2 2216 2368 374129956 374129805 2.400000e-45 193
5 TraesCS5B01G261200 chr5D 88.281 128 7 3 1818 1944 374130073 374129953 1.900000e-31 147
6 TraesCS5B01G261200 chr5A 87.702 1114 71 31 712 1799 475832207 475831134 0.000000e+00 1238
7 TraesCS5B01G261200 chr3B 84.765 617 79 14 7 612 783292463 783291851 2.600000e-169 604
8 TraesCS5B01G261200 chr6A 84.219 621 79 14 1 612 502359363 502359973 9.430000e-164 586
9 TraesCS5B01G261200 chr6A 88.172 279 32 1 1941 2219 29206443 29206720 4.880000e-87 331
10 TraesCS5B01G261200 chr7D 83.546 626 84 16 2 622 596307973 596308584 3.420000e-158 568
11 TraesCS5B01G261200 chr2A 83.494 624 83 17 1 613 643022615 643023229 4.420000e-157 564
12 TraesCS5B01G261200 chr2A 81.337 643 97 18 3 631 46079001 46078368 3.520000e-138 501
13 TraesCS5B01G261200 chr2B 82.797 622 86 13 1 612 411881188 411880578 9.640000e-149 536
14 TraesCS5B01G261200 chr2D 81.453 647 95 24 1 631 43656366 43655729 7.560000e-140 507
15 TraesCS5B01G261200 chr1D 82.274 598 89 15 1 589 99698852 99699441 3.520000e-138 501
16 TraesCS5B01G261200 chr1B 87.805 287 34 1 1932 2218 537319081 537319366 3.770000e-88 335
17 TraesCS5B01G261200 chr1B 87.097 279 36 0 1941 2219 601006774 601006496 1.370000e-82 316
18 TraesCS5B01G261200 chr7B 87.500 280 33 2 1940 2218 193926639 193926361 2.940000e-84 322
19 TraesCS5B01G261200 chr7B 87.097 279 36 0 1941 2219 56999750 57000028 1.370000e-82 316
20 TraesCS5B01G261200 chr3D 87.410 278 35 0 1941 2218 145199364 145199641 1.060000e-83 320
21 TraesCS5B01G261200 chr4A 86.972 284 34 3 1940 2222 11601627 11601908 1.370000e-82 316
22 TraesCS5B01G261200 chr4B 87.050 278 36 0 1941 2218 368251105 368250828 4.920000e-82 315
23 TraesCS5B01G261200 chr4B 86.572 283 38 0 1941 2223 189738683 189738965 1.770000e-81 313


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 TraesCS5B01G261200 chr5B 445650501 445652869 2368 True 4375.000000 4375 100.000000 1 2369 1 chr5B.!!$R1 2368
1 TraesCS5B01G261200 chr5B 445762457 445763530 1073 True 1085.000000 1085 85.320000 704 1794 1 chr5B.!!$R2 1090
2 TraesCS5B01G261200 chr5D 37120751 37121375 624 True 638.000000 638 85.308000 1 624 1 chr5D.!!$R1 623
3 TraesCS5B01G261200 chr5D 374129805 374131167 1362 True 551.666667 1315 88.831667 712 2368 3 chr5D.!!$R2 1656
4 TraesCS5B01G261200 chr5A 475831134 475832207 1073 True 1238.000000 1238 87.702000 712 1799 1 chr5A.!!$R1 1087
5 TraesCS5B01G261200 chr3B 783291851 783292463 612 True 604.000000 604 84.765000 7 612 1 chr3B.!!$R1 605
6 TraesCS5B01G261200 chr6A 502359363 502359973 610 False 586.000000 586 84.219000 1 612 1 chr6A.!!$F2 611
7 TraesCS5B01G261200 chr7D 596307973 596308584 611 False 568.000000 568 83.546000 2 622 1 chr7D.!!$F1 620
8 TraesCS5B01G261200 chr2A 643022615 643023229 614 False 564.000000 564 83.494000 1 613 1 chr2A.!!$F1 612
9 TraesCS5B01G261200 chr2A 46078368 46079001 633 True 501.000000 501 81.337000 3 631 1 chr2A.!!$R1 628
10 TraesCS5B01G261200 chr2B 411880578 411881188 610 True 536.000000 536 82.797000 1 612 1 chr2B.!!$R1 611
11 TraesCS5B01G261200 chr2D 43655729 43656366 637 True 507.000000 507 81.453000 1 631 1 chr2D.!!$R1 630
12 TraesCS5B01G261200 chr1D 99698852 99699441 589 False 501.000000 501 82.274000 1 589 1 chr1D.!!$F1 588

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
869 967 0.039437 ACGACGCGTCTTCACTTCAT 60.039 50.0 33.94 7.68 33.69 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2043 0.106519 GCATGTAGGTTGGCCATCCT 60.107 55.0 32.89 32.89 37.19 3.24 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
103 115 8.779354 ATAGACTTTCAGAAATGTCTACCAAC 57.221 34.615 23.48 4.80 46.46 3.77
165 177 7.123190 CCGGTTCAAAAGAAAATGCTTAAAAC 58.877 34.615 0.00 0.00 0.00 2.43
181 193 9.850198 ATGCTTAAAACCCATTTGCAATATAAT 57.150 25.926 0.00 0.00 34.69 1.28
233 286 9.786105 GTTTGTGATTTTTGAAAATGTTCCAAT 57.214 25.926 6.44 0.00 38.64 3.16
302 355 6.471146 AGTAATGCTTCTGAGTCTTTGTGAT 58.529 36.000 0.00 0.00 0.00 3.06
511 579 8.441312 AACATTTTCTTGCATTTCTGAACAAT 57.559 26.923 0.00 0.00 0.00 2.71
559 630 3.181397 CAAAATGTGGTCATCGCCATTC 58.819 45.455 0.00 0.00 41.08 2.67
596 673 0.393132 TTCTCCGGTTGCAACACACA 60.393 50.000 29.55 10.27 0.00 3.72
617 696 3.629398 CAGGCCCTTTTGCTAGTTATGAG 59.371 47.826 0.00 0.00 0.00 2.90
626 705 8.743714 CCTTTTGCTAGTTATGAGAAAAGGAAT 58.256 33.333 13.44 0.00 46.58 3.01
629 708 9.733556 TTTGCTAGTTATGAGAAAAGGAATACA 57.266 29.630 0.00 0.00 0.00 2.29
630 709 8.718102 TGCTAGTTATGAGAAAAGGAATACAC 57.282 34.615 0.00 0.00 0.00 2.90
631 710 7.769044 TGCTAGTTATGAGAAAAGGAATACACC 59.231 37.037 0.00 0.00 0.00 4.16
632 711 7.226918 GCTAGTTATGAGAAAAGGAATACACCC 59.773 40.741 0.00 0.00 0.00 4.61
633 712 7.272144 AGTTATGAGAAAAGGAATACACCCT 57.728 36.000 0.00 0.00 35.03 4.34
634 713 7.339482 AGTTATGAGAAAAGGAATACACCCTC 58.661 38.462 0.00 0.00 32.57 4.30
635 714 4.202245 TGAGAAAAGGAATACACCCTCG 57.798 45.455 0.00 0.00 32.57 4.63
636 715 3.581332 TGAGAAAAGGAATACACCCTCGT 59.419 43.478 0.00 0.00 32.57 4.18
637 716 4.182339 GAGAAAAGGAATACACCCTCGTC 58.818 47.826 0.00 0.00 32.57 4.20
638 717 3.838903 AGAAAAGGAATACACCCTCGTCT 59.161 43.478 0.00 0.00 32.57 4.18
639 718 4.286291 AGAAAAGGAATACACCCTCGTCTT 59.714 41.667 0.00 0.00 32.57 3.01
640 719 5.482878 AGAAAAGGAATACACCCTCGTCTTA 59.517 40.000 0.00 0.00 32.57 2.10
641 720 5.952347 AAAGGAATACACCCTCGTCTTAT 57.048 39.130 0.00 0.00 32.57 1.73
642 721 4.939052 AGGAATACACCCTCGTCTTATG 57.061 45.455 0.00 0.00 0.00 1.90
643 722 4.287552 AGGAATACACCCTCGTCTTATGT 58.712 43.478 0.00 0.00 0.00 2.29
644 723 4.715297 AGGAATACACCCTCGTCTTATGTT 59.285 41.667 0.00 0.00 0.00 2.71
645 724 5.895534 AGGAATACACCCTCGTCTTATGTTA 59.104 40.000 0.00 0.00 0.00 2.41
646 725 6.553852 AGGAATACACCCTCGTCTTATGTTAT 59.446 38.462 0.00 0.00 0.00 1.89
647 726 7.727186 AGGAATACACCCTCGTCTTATGTTATA 59.273 37.037 0.00 0.00 0.00 0.98
648 727 8.027771 GGAATACACCCTCGTCTTATGTTATAG 58.972 40.741 0.00 0.00 0.00 1.31
649 728 5.786264 ACACCCTCGTCTTATGTTATAGG 57.214 43.478 0.00 0.00 0.00 2.57
650 729 5.452255 ACACCCTCGTCTTATGTTATAGGA 58.548 41.667 0.00 0.00 0.00 2.94
651 730 5.301298 ACACCCTCGTCTTATGTTATAGGAC 59.699 44.000 0.00 0.00 0.00 3.85
652 731 5.301045 CACCCTCGTCTTATGTTATAGGACA 59.699 44.000 10.42 0.00 0.00 4.02
653 732 5.535406 ACCCTCGTCTTATGTTATAGGACAG 59.465 44.000 10.42 7.33 32.19 3.51
654 733 5.768662 CCCTCGTCTTATGTTATAGGACAGA 59.231 44.000 10.42 7.93 32.19 3.41
655 734 6.072397 CCCTCGTCTTATGTTATAGGACAGAG 60.072 46.154 16.40 16.40 32.19 3.35
656 735 6.711194 CCTCGTCTTATGTTATAGGACAGAGA 59.289 42.308 20.49 8.98 33.75 3.10
657 736 7.228906 CCTCGTCTTATGTTATAGGACAGAGAA 59.771 40.741 20.49 3.23 33.75 2.87
658 737 8.693120 TCGTCTTATGTTATAGGACAGAGAAT 57.307 34.615 10.42 0.00 31.61 2.40
659 738 8.568794 TCGTCTTATGTTATAGGACAGAGAATG 58.431 37.037 10.42 0.00 31.61 2.67
666 745 9.911788 ATGTTATAGGACAGAGAATGTTTGATT 57.088 29.630 0.00 0.00 44.17 2.57
672 751 8.924511 AGGACAGAGAATGTTTGATTAAGAAA 57.075 30.769 0.00 0.00 44.17 2.52
673 752 8.787852 AGGACAGAGAATGTTTGATTAAGAAAC 58.212 33.333 6.11 6.11 44.17 2.78
674 753 8.567948 GGACAGAGAATGTTTGATTAAGAAACA 58.432 33.333 14.63 14.63 44.17 2.83
698 777 3.188965 GTCACGAGACGGAGGGAG 58.811 66.667 0.00 0.00 34.60 4.30
699 778 1.674980 GTCACGAGACGGAGGGAGT 60.675 63.158 0.00 0.00 34.60 3.85
700 779 0.392193 GTCACGAGACGGAGGGAGTA 60.392 60.000 0.00 0.00 34.60 2.59
701 780 0.392193 TCACGAGACGGAGGGAGTAC 60.392 60.000 0.00 0.00 0.00 2.73
702 781 0.675837 CACGAGACGGAGGGAGTACA 60.676 60.000 0.00 0.00 0.00 2.90
724 803 3.207778 TGGGACACGTAAAAGGAACAAG 58.792 45.455 0.00 0.00 0.00 3.16
736 815 0.875059 GGAACAAGAAAGCGACCCTG 59.125 55.000 0.00 0.00 0.00 4.45
768 847 2.456594 GAACATGCAACGGAAGCGCA 62.457 55.000 11.47 0.00 45.25 6.09
782 871 3.039202 GCGCAGATCAACCAACCGG 62.039 63.158 0.30 0.00 38.77 5.28
784 873 2.700773 GCAGATCAACCAACCGGGC 61.701 63.158 6.32 0.00 42.05 6.13
799 888 1.221021 GGGCGAGGACCGAAGAAAT 59.779 57.895 0.00 0.00 41.76 2.17
825 914 0.680061 GAAGTCGTCCAAGTCCACCT 59.320 55.000 0.00 0.00 0.00 4.00
827 916 1.186267 AGTCGTCCAAGTCCACCTCC 61.186 60.000 0.00 0.00 0.00 4.30
828 917 2.261671 CGTCCAAGTCCACCTCCG 59.738 66.667 0.00 0.00 0.00 4.63
830 919 2.525629 TCCAAGTCCACCTCCGCA 60.526 61.111 0.00 0.00 0.00 5.69
831 920 2.144078 TCCAAGTCCACCTCCGCAA 61.144 57.895 0.00 0.00 0.00 4.85
832 921 1.966451 CCAAGTCCACCTCCGCAAC 60.966 63.158 0.00 0.00 0.00 4.17
833 922 1.227823 CAAGTCCACCTCCGCAACA 60.228 57.895 0.00 0.00 0.00 3.33
834 923 1.227853 AAGTCCACCTCCGCAACAC 60.228 57.895 0.00 0.00 0.00 3.32
835 924 2.668550 GTCCACCTCCGCAACACC 60.669 66.667 0.00 0.00 0.00 4.16
836 925 3.164977 TCCACCTCCGCAACACCA 61.165 61.111 0.00 0.00 0.00 4.17
869 967 0.039437 ACGACGCGTCTTCACTTCAT 60.039 50.000 33.94 7.68 33.69 2.57
871 969 1.698165 GACGCGTCTTCACTTCATCA 58.302 50.000 31.12 0.00 0.00 3.07
872 970 2.263077 GACGCGTCTTCACTTCATCAT 58.737 47.619 31.12 0.00 0.00 2.45
874 972 1.590238 CGCGTCTTCACTTCATCATCC 59.410 52.381 0.00 0.00 0.00 3.51
875 973 1.590238 GCGTCTTCACTTCATCATCCG 59.410 52.381 0.00 0.00 0.00 4.18
877 990 3.254060 CGTCTTCACTTCATCATCCGTT 58.746 45.455 0.00 0.00 0.00 4.44
884 997 1.765314 CTTCATCATCCGTTCTCCCCT 59.235 52.381 0.00 0.00 0.00 4.79
887 1000 1.765314 CATCATCCGTTCTCCCCTCTT 59.235 52.381 0.00 0.00 0.00 2.85
888 1001 1.486211 TCATCCGTTCTCCCCTCTTC 58.514 55.000 0.00 0.00 0.00 2.87
889 1002 0.466124 CATCCGTTCTCCCCTCTTCC 59.534 60.000 0.00 0.00 0.00 3.46
893 1006 1.229853 GTTCTCCCCTCTTCCCCCA 60.230 63.158 0.00 0.00 0.00 4.96
899 1012 2.913617 CTCCCCTCTTCCCCCATATAAC 59.086 54.545 0.00 0.00 0.00 1.89
931 1044 0.687427 CCCCATTCCATTCCCACACC 60.687 60.000 0.00 0.00 0.00 4.16
941 1054 0.179004 TTCCCACACCGCAATCAACT 60.179 50.000 0.00 0.00 0.00 3.16
952 1065 3.207474 GCAATCAACTGCGTTCTCAAT 57.793 42.857 0.00 0.00 31.50 2.57
953 1066 3.166657 GCAATCAACTGCGTTCTCAATC 58.833 45.455 0.00 0.00 31.50 2.67
954 1067 3.120060 GCAATCAACTGCGTTCTCAATCT 60.120 43.478 0.00 0.00 31.50 2.40
955 1068 4.614535 GCAATCAACTGCGTTCTCAATCTT 60.615 41.667 0.00 0.00 31.50 2.40
959 1072 2.417719 ACTGCGTTCTCAATCTTCCAC 58.582 47.619 0.00 0.00 0.00 4.02
967 1080 1.918957 CTCAATCTTCCACTCCCCCTT 59.081 52.381 0.00 0.00 0.00 3.95
972 1085 0.621082 CTTCCACTCCCCCTTTCTCC 59.379 60.000 0.00 0.00 0.00 3.71
973 1086 0.845102 TTCCACTCCCCCTTTCTCCC 60.845 60.000 0.00 0.00 0.00 4.30
974 1087 1.229984 CCACTCCCCCTTTCTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
975 1088 1.275421 CCACTCCCCCTTTCTCCCTC 61.275 65.000 0.00 0.00 0.00 4.30
976 1089 0.252927 CACTCCCCCTTTCTCCCTCT 60.253 60.000 0.00 0.00 0.00 3.69
977 1090 0.043485 ACTCCCCCTTTCTCCCTCTC 59.957 60.000 0.00 0.00 0.00 3.20
978 1091 0.341609 CTCCCCCTTTCTCCCTCTCT 59.658 60.000 0.00 0.00 0.00 3.10
1008 1121 0.760567 TCTCCGCTCATATGGCCACT 60.761 55.000 8.16 0.00 0.00 4.00
1120 1233 2.123077 CTCCTCCTCCATCGGCCT 60.123 66.667 0.00 0.00 0.00 5.19
1170 1292 3.263170 GGCCTTCCTCTTCTTCTTCTTCT 59.737 47.826 0.00 0.00 0.00 2.85
1171 1293 4.263287 GGCCTTCCTCTTCTTCTTCTTCTT 60.263 45.833 0.00 0.00 0.00 2.52
1172 1294 4.935205 GCCTTCCTCTTCTTCTTCTTCTTC 59.065 45.833 0.00 0.00 0.00 2.87
1173 1295 5.279960 GCCTTCCTCTTCTTCTTCTTCTTCT 60.280 44.000 0.00 0.00 0.00 2.85
1415 1547 0.892358 AGTCGCCTAGTGGACACGAA 60.892 55.000 11.60 0.00 35.63 3.85
1507 1643 0.963225 GGTTTTATTGTGTGGCCGGT 59.037 50.000 1.90 0.00 0.00 5.28
1602 1747 4.026393 CGATCGGCGTGATGTAATTACAAA 60.026 41.667 21.57 10.80 37.47 2.83
1745 1894 9.950680 TCTGTTCATGTTGATTAAAAGAAGTTC 57.049 29.630 0.00 0.00 0.00 3.01
1778 1927 4.870221 TCATGATGCTTTGAATGAGTCG 57.130 40.909 0.00 0.00 0.00 4.18
1780 1929 1.394572 TGATGCTTTGAATGAGTCGCG 59.605 47.619 0.00 0.00 0.00 5.87
1783 1932 0.790207 GCTTTGAATGAGTCGCGTCA 59.210 50.000 5.77 3.40 0.00 4.35
1785 1934 2.723010 GCTTTGAATGAGTCGCGTCAAG 60.723 50.000 5.77 0.00 0.00 3.02
1786 1935 1.428448 TTGAATGAGTCGCGTCAAGG 58.572 50.000 5.77 0.00 0.00 3.61
1787 1936 0.601057 TGAATGAGTCGCGTCAAGGA 59.399 50.000 5.77 0.00 0.00 3.36
1788 1937 1.204704 TGAATGAGTCGCGTCAAGGAT 59.795 47.619 5.77 0.00 0.00 3.24
1791 1940 3.520290 ATGAGTCGCGTCAAGGATAAA 57.480 42.857 5.77 0.00 0.00 1.40
1792 1941 2.876091 TGAGTCGCGTCAAGGATAAAG 58.124 47.619 5.77 0.00 0.00 1.85
1793 1942 2.230508 TGAGTCGCGTCAAGGATAAAGT 59.769 45.455 5.77 0.00 0.00 2.66
1794 1943 3.251571 GAGTCGCGTCAAGGATAAAGTT 58.748 45.455 5.77 0.00 0.00 2.66
1795 1944 2.993899 AGTCGCGTCAAGGATAAAGTTG 59.006 45.455 5.77 0.00 0.00 3.16
1796 1945 2.991190 GTCGCGTCAAGGATAAAGTTGA 59.009 45.455 5.77 0.00 0.00 3.18
1797 1946 3.617263 GTCGCGTCAAGGATAAAGTTGAT 59.383 43.478 5.77 0.00 35.22 2.57
1798 1947 4.092968 GTCGCGTCAAGGATAAAGTTGATT 59.907 41.667 5.77 0.00 35.22 2.57
1799 1948 4.328983 TCGCGTCAAGGATAAAGTTGATTC 59.671 41.667 5.77 0.00 35.22 2.52
1800 1949 4.494199 CGCGTCAAGGATAAAGTTGATTCC 60.494 45.833 0.00 0.00 35.22 3.01
1801 1950 4.636206 GCGTCAAGGATAAAGTTGATTCCT 59.364 41.667 0.00 0.00 40.32 3.36
1802 1951 5.123979 GCGTCAAGGATAAAGTTGATTCCTT 59.876 40.000 7.94 7.94 46.88 3.36
1803 1952 6.349363 GCGTCAAGGATAAAGTTGATTCCTTT 60.349 38.462 10.17 0.00 44.27 3.11
1804 1953 7.244192 CGTCAAGGATAAAGTTGATTCCTTTC 58.756 38.462 10.17 7.21 44.27 2.62
1805 1954 7.119846 CGTCAAGGATAAAGTTGATTCCTTTCT 59.880 37.037 10.17 0.00 44.27 2.52
1806 1955 8.797438 GTCAAGGATAAAGTTGATTCCTTTCTT 58.203 33.333 10.17 0.00 44.27 2.52
1807 1956 9.367160 TCAAGGATAAAGTTGATTCCTTTCTTT 57.633 29.630 10.17 0.00 44.27 2.52
1808 1957 9.987272 CAAGGATAAAGTTGATTCCTTTCTTTT 57.013 29.630 10.17 0.00 44.27 2.27
1873 2022 9.599322 CCAAGATAATGTTGATTAATTAGTCGC 57.401 33.333 3.81 0.77 0.00 5.19
1889 2038 3.431725 GCACCAGCCGGCAGTTAC 61.432 66.667 31.54 15.55 34.57 2.50
1890 2039 2.031919 CACCAGCCGGCAGTTACA 59.968 61.111 31.54 0.00 34.57 2.41
1891 2040 1.599518 CACCAGCCGGCAGTTACAA 60.600 57.895 31.54 0.00 34.57 2.41
1892 2041 1.302511 ACCAGCCGGCAGTTACAAG 60.303 57.895 31.54 9.21 34.57 3.16
1893 2042 1.302511 CCAGCCGGCAGTTACAAGT 60.303 57.895 31.54 0.00 0.00 3.16
1894 2043 0.036765 CCAGCCGGCAGTTACAAGTA 60.037 55.000 31.54 0.00 0.00 2.24
1895 2044 1.359848 CAGCCGGCAGTTACAAGTAG 58.640 55.000 31.54 0.00 0.00 2.57
1896 2045 0.249398 AGCCGGCAGTTACAAGTAGG 59.751 55.000 31.54 0.00 0.00 3.18
1897 2046 0.248289 GCCGGCAGTTACAAGTAGGA 59.752 55.000 24.80 0.00 0.00 2.94
1931 2080 2.581409 CTTACGTGCGCTACCCGG 60.581 66.667 9.73 0.00 37.44 5.73
1932 2081 3.055080 CTTACGTGCGCTACCCGGA 62.055 63.158 9.73 0.00 37.44 5.14
1933 2082 2.546645 CTTACGTGCGCTACCCGGAA 62.547 60.000 9.73 7.85 39.61 4.30
1944 2093 2.681344 GCTACCCGGAATGTTTGTTAGG 59.319 50.000 0.73 0.00 0.00 2.69
1945 2094 2.209690 ACCCGGAATGTTTGTTAGGG 57.790 50.000 0.73 0.00 42.82 3.53
1946 2095 0.815095 CCCGGAATGTTTGTTAGGGC 59.185 55.000 0.73 0.00 0.00 5.19
1947 2096 0.450184 CCGGAATGTTTGTTAGGGCG 59.550 55.000 0.00 0.00 0.00 6.13
1948 2097 1.161843 CGGAATGTTTGTTAGGGCGT 58.838 50.000 0.00 0.00 0.00 5.68
1949 2098 1.135803 CGGAATGTTTGTTAGGGCGTG 60.136 52.381 0.00 0.00 0.00 5.34
1950 2099 1.883926 GGAATGTTTGTTAGGGCGTGT 59.116 47.619 0.00 0.00 0.00 4.49
1951 2100 3.075884 GGAATGTTTGTTAGGGCGTGTA 58.924 45.455 0.00 0.00 0.00 2.90
1952 2101 3.120095 GGAATGTTTGTTAGGGCGTGTAC 60.120 47.826 0.00 0.00 0.00 2.90
1953 2102 2.616634 TGTTTGTTAGGGCGTGTACA 57.383 45.000 0.00 0.00 0.00 2.90
1954 2103 2.915349 TGTTTGTTAGGGCGTGTACAA 58.085 42.857 0.00 5.86 0.00 2.41
1955 2104 3.478509 TGTTTGTTAGGGCGTGTACAAT 58.521 40.909 0.00 0.00 31.30 2.71
1956 2105 3.251245 TGTTTGTTAGGGCGTGTACAATG 59.749 43.478 0.00 0.00 31.30 2.82
1957 2106 2.102070 TGTTAGGGCGTGTACAATGG 57.898 50.000 0.00 0.00 0.00 3.16
1958 2107 1.348366 TGTTAGGGCGTGTACAATGGT 59.652 47.619 0.00 0.00 0.00 3.55
1959 2108 2.224572 TGTTAGGGCGTGTACAATGGTT 60.225 45.455 0.00 0.00 0.00 3.67
1960 2109 2.102070 TAGGGCGTGTACAATGGTTG 57.898 50.000 0.00 0.00 0.00 3.77
1961 2110 0.398696 AGGGCGTGTACAATGGTTGA 59.601 50.000 0.00 0.00 0.00 3.18
1962 2111 1.004277 AGGGCGTGTACAATGGTTGAT 59.996 47.619 0.00 0.00 0.00 2.57
1963 2112 2.237643 AGGGCGTGTACAATGGTTGATA 59.762 45.455 0.00 0.00 0.00 2.15
1964 2113 3.011119 GGGCGTGTACAATGGTTGATAA 58.989 45.455 0.00 0.00 0.00 1.75
1965 2114 3.440872 GGGCGTGTACAATGGTTGATAAA 59.559 43.478 0.00 0.00 0.00 1.40
1966 2115 4.082679 GGGCGTGTACAATGGTTGATAAAA 60.083 41.667 0.00 0.00 0.00 1.52
1967 2116 5.393678 GGGCGTGTACAATGGTTGATAAAAT 60.394 40.000 0.00 0.00 0.00 1.82
1968 2117 6.183360 GGGCGTGTACAATGGTTGATAAAATA 60.183 38.462 0.00 0.00 0.00 1.40
1969 2118 6.910433 GGCGTGTACAATGGTTGATAAAATAG 59.090 38.462 0.00 0.00 0.00 1.73
1970 2119 7.414762 GGCGTGTACAATGGTTGATAAAATAGT 60.415 37.037 0.00 0.00 0.00 2.12
1971 2120 7.966204 GCGTGTACAATGGTTGATAAAATAGTT 59.034 33.333 0.00 0.00 0.00 2.24
1972 2121 9.834628 CGTGTACAATGGTTGATAAAATAGTTT 57.165 29.630 0.00 0.00 0.00 2.66
2026 2175 9.941664 GATGACAATAAAGAATGTCTACAATGG 57.058 33.333 7.35 0.00 44.86 3.16
2027 2176 9.685276 ATGACAATAAAGAATGTCTACAATGGA 57.315 29.630 7.35 0.00 44.86 3.41
2028 2177 9.685276 TGACAATAAAGAATGTCTACAATGGAT 57.315 29.630 7.35 0.00 44.86 3.41
2161 2310 6.935240 TTTTTATGAGTTCTCTCTCCTCCA 57.065 37.500 1.53 0.00 40.98 3.86
2162 2311 5.923733 TTTATGAGTTCTCTCTCCTCCAC 57.076 43.478 1.53 0.00 40.98 4.02
2163 2312 2.223803 TGAGTTCTCTCTCCTCCACC 57.776 55.000 1.53 0.00 40.98 4.61
2164 2313 1.713647 TGAGTTCTCTCTCCTCCACCT 59.286 52.381 1.53 0.00 40.98 4.00
2165 2314 2.291282 TGAGTTCTCTCTCCTCCACCTC 60.291 54.545 1.53 0.00 40.98 3.85
2166 2315 1.713647 AGTTCTCTCTCCTCCACCTCA 59.286 52.381 0.00 0.00 0.00 3.86
2167 2316 2.314549 AGTTCTCTCTCCTCCACCTCAT 59.685 50.000 0.00 0.00 0.00 2.90
2168 2317 3.103742 GTTCTCTCTCCTCCACCTCATT 58.896 50.000 0.00 0.00 0.00 2.57
2169 2318 4.017037 AGTTCTCTCTCCTCCACCTCATTA 60.017 45.833 0.00 0.00 0.00 1.90
2170 2319 4.823364 TCTCTCTCCTCCACCTCATTAT 57.177 45.455 0.00 0.00 0.00 1.28
2171 2320 5.149584 TCTCTCTCCTCCACCTCATTATT 57.850 43.478 0.00 0.00 0.00 1.40
2172 2321 5.533112 TCTCTCTCCTCCACCTCATTATTT 58.467 41.667 0.00 0.00 0.00 1.40
2173 2322 6.683537 TCTCTCTCCTCCACCTCATTATTTA 58.316 40.000 0.00 0.00 0.00 1.40
2174 2323 7.309091 TCTCTCTCCTCCACCTCATTATTTAT 58.691 38.462 0.00 0.00 0.00 1.40
2175 2324 7.791766 TCTCTCTCCTCCACCTCATTATTTATT 59.208 37.037 0.00 0.00 0.00 1.40
2176 2325 7.967908 TCTCTCCTCCACCTCATTATTTATTC 58.032 38.462 0.00 0.00 0.00 1.75
2177 2326 7.791766 TCTCTCCTCCACCTCATTATTTATTCT 59.208 37.037 0.00 0.00 0.00 2.40
2178 2327 9.094578 CTCTCCTCCACCTCATTATTTATTCTA 57.905 37.037 0.00 0.00 0.00 2.10
2179 2328 8.871125 TCTCCTCCACCTCATTATTTATTCTAC 58.129 37.037 0.00 0.00 0.00 2.59
2180 2329 8.561536 TCCTCCACCTCATTATTTATTCTACA 57.438 34.615 0.00 0.00 0.00 2.74
2181 2330 9.170890 TCCTCCACCTCATTATTTATTCTACAT 57.829 33.333 0.00 0.00 0.00 2.29
2182 2331 9.224267 CCTCCACCTCATTATTTATTCTACATG 57.776 37.037 0.00 0.00 0.00 3.21
2183 2332 9.784531 CTCCACCTCATTATTTATTCTACATGT 57.215 33.333 2.69 2.69 0.00 3.21
2184 2333 9.778741 TCCACCTCATTATTTATTCTACATGTC 57.221 33.333 0.00 0.00 0.00 3.06
2185 2334 9.559732 CCACCTCATTATTTATTCTACATGTCA 57.440 33.333 0.00 0.00 0.00 3.58
2198 2347 8.894768 ATTCTACATGTCACTCCTAAAATAGC 57.105 34.615 0.00 0.00 0.00 2.97
2199 2348 7.418337 TCTACATGTCACTCCTAAAATAGCA 57.582 36.000 0.00 0.00 0.00 3.49
2200 2349 7.265673 TCTACATGTCACTCCTAAAATAGCAC 58.734 38.462 0.00 0.00 0.00 4.40
2201 2350 5.186198 ACATGTCACTCCTAAAATAGCACC 58.814 41.667 0.00 0.00 0.00 5.01
2202 2351 4.901197 TGTCACTCCTAAAATAGCACCA 57.099 40.909 0.00 0.00 0.00 4.17
2203 2352 5.435686 TGTCACTCCTAAAATAGCACCAT 57.564 39.130 0.00 0.00 0.00 3.55
2204 2353 5.815581 TGTCACTCCTAAAATAGCACCATT 58.184 37.500 0.00 0.00 0.00 3.16
2205 2354 5.647658 TGTCACTCCTAAAATAGCACCATTG 59.352 40.000 0.00 0.00 0.00 2.82
2206 2355 5.648092 GTCACTCCTAAAATAGCACCATTGT 59.352 40.000 0.00 0.00 0.00 2.71
2207 2356 6.821665 GTCACTCCTAAAATAGCACCATTGTA 59.178 38.462 0.00 0.00 0.00 2.41
2208 2357 6.821665 TCACTCCTAAAATAGCACCATTGTAC 59.178 38.462 0.00 0.00 0.00 2.90
2209 2358 6.597672 CACTCCTAAAATAGCACCATTGTACA 59.402 38.462 0.00 0.00 0.00 2.90
2210 2359 7.283127 CACTCCTAAAATAGCACCATTGTACAT 59.717 37.037 0.00 0.00 0.00 2.29
2211 2360 7.283127 ACTCCTAAAATAGCACCATTGTACATG 59.717 37.037 0.00 0.00 0.00 3.21
2212 2361 6.039270 TCCTAAAATAGCACCATTGTACATGC 59.961 38.462 10.53 10.53 38.39 4.06
2213 2362 4.654091 AAATAGCACCATTGTACATGCC 57.346 40.909 14.08 0.00 38.92 4.40
2214 2363 2.051334 TAGCACCATTGTACATGCCC 57.949 50.000 14.08 0.00 38.92 5.36
2215 2364 0.332632 AGCACCATTGTACATGCCCT 59.667 50.000 14.08 0.00 38.92 5.19
2216 2365 1.185315 GCACCATTGTACATGCCCTT 58.815 50.000 7.77 0.00 31.71 3.95
2217 2366 2.025416 AGCACCATTGTACATGCCCTTA 60.025 45.455 14.08 0.00 38.92 2.69
2218 2367 2.358898 GCACCATTGTACATGCCCTTAG 59.641 50.000 7.77 0.00 31.71 2.18
2219 2368 2.358898 CACCATTGTACATGCCCTTAGC 59.641 50.000 0.00 0.00 44.14 3.09
2238 2387 2.143122 GCAACTGAATTGGTCGTCTCA 58.857 47.619 0.00 0.00 38.88 3.27
2240 2389 6.544646 AGCAACTGAATTGGTCGTCTCAGT 62.545 45.833 0.00 0.00 46.11 3.41
2244 2393 1.986378 GAATTGGTCGTCTCAGTCGTG 59.014 52.381 0.00 0.00 0.00 4.35
2273 2422 3.290710 TGTTACCTCGACATACCTACCC 58.709 50.000 0.00 0.00 0.00 3.69
2284 2433 5.557866 GACATACCTACCCCATCATAAACC 58.442 45.833 0.00 0.00 0.00 3.27
2302 2451 0.701731 CCCATACCCTCCAACCAACA 59.298 55.000 0.00 0.00 0.00 3.33
2328 2477 2.572095 TAGTGCATCTCCAACGCCGG 62.572 60.000 0.00 0.00 0.00 6.13
2343 2492 1.358759 CCGGCACCAAGTCAAACAC 59.641 57.895 0.00 0.00 0.00 3.32
2344 2493 1.010125 CGGCACCAAGTCAAACACG 60.010 57.895 0.00 0.00 0.00 4.49
2345 2494 1.711060 CGGCACCAAGTCAAACACGT 61.711 55.000 0.00 0.00 0.00 4.49
2346 2495 1.301423 GGCACCAAGTCAAACACGTA 58.699 50.000 0.00 0.00 0.00 3.57
2347 2496 1.877443 GGCACCAAGTCAAACACGTAT 59.123 47.619 0.00 0.00 0.00 3.06
2348 2497 3.068560 GGCACCAAGTCAAACACGTATA 58.931 45.455 0.00 0.00 0.00 1.47
2349 2498 3.120442 GGCACCAAGTCAAACACGTATAC 60.120 47.826 0.00 0.00 0.00 1.47
2351 2500 4.377022 GCACCAAGTCAAACACGTATACTG 60.377 45.833 0.56 1.45 0.00 2.74
2355 2504 2.984471 AGTCAAACACGTATACTGTGCG 59.016 45.455 20.41 13.00 41.03 5.34
2368 2517 2.906354 ACTGTGCGGATCAATAAGGAC 58.094 47.619 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 85 6.831976 AGTTGGTAGACATTTCTGAAAGTCT 58.168 36.000 24.70 24.70 43.25 3.24
81 86 7.226720 TGAAGTTGGTAGACATTTCTGAAAGTC 59.773 37.037 17.45 17.45 32.75 3.01
83 88 7.496529 TGAAGTTGGTAGACATTTCTGAAAG 57.503 36.000 8.95 3.97 32.75 2.62
84 89 7.873719 TTGAAGTTGGTAGACATTTCTGAAA 57.126 32.000 5.15 5.15 32.75 2.69
85 90 7.873719 TTTGAAGTTGGTAGACATTTCTGAA 57.126 32.000 0.00 0.00 32.75 3.02
86 91 7.873719 TTTTGAAGTTGGTAGACATTTCTGA 57.126 32.000 0.00 0.00 32.75 3.27
206 219 7.459486 TGGAACATTTTCAAAAATCACAAACG 58.541 30.769 0.00 0.00 36.52 3.60
234 287 8.686418 CGATCATTCGTGATTTGTTTTTACAAA 58.314 29.630 5.98 5.98 40.60 2.83
237 290 8.429739 TTCGATCATTCGTGATTTGTTTTTAC 57.570 30.769 0.00 0.00 45.65 2.01
244 297 4.864916 ACCTTCGATCATTCGTGATTTG 57.135 40.909 0.00 0.00 45.65 2.32
247 300 5.201713 ACATACCTTCGATCATTCGTGAT 57.798 39.130 0.00 0.00 45.65 3.06
302 355 9.913310 TTCTTCAACATTCACATGGGTATATAA 57.087 29.630 0.00 0.00 34.27 0.98
320 373 1.067354 CCTGGCAGCCAATTCTTCAAC 60.067 52.381 17.03 0.00 30.80 3.18
425 485 6.370593 TCACATTTTTGAAGAAGTATCGTGC 58.629 36.000 0.00 0.00 0.00 5.34
433 497 9.693157 GAAACAATGTTCACATTTTTGAAGAAG 57.307 29.630 0.00 0.00 43.48 2.85
436 500 9.991388 ATTGAAACAATGTTCACATTTTTGAAG 57.009 25.926 0.00 0.00 43.48 3.02
503 570 6.788458 CACGCATGATTTTGAAAATTGTTCAG 59.212 34.615 4.46 0.00 0.00 3.02
511 579 5.630264 CACATCTCACGCATGATTTTGAAAA 59.370 36.000 0.00 0.00 33.22 2.29
583 660 2.417097 GGCCTGTGTGTTGCAACC 59.583 61.111 26.14 17.38 0.00 3.77
592 669 0.478507 ACTAGCAAAAGGGCCTGTGT 59.521 50.000 6.92 0.00 0.00 3.72
596 673 3.523564 TCTCATAACTAGCAAAAGGGCCT 59.476 43.478 0.00 0.00 0.00 5.19
617 696 4.203654 AGACGAGGGTGTATTCCTTTTC 57.796 45.455 0.00 0.00 34.21 2.29
626 705 6.488006 GTCCTATAACATAAGACGAGGGTGTA 59.512 42.308 0.00 0.00 0.00 2.90
629 708 5.452255 TGTCCTATAACATAAGACGAGGGT 58.548 41.667 0.00 0.00 0.00 4.34
630 709 5.768662 TCTGTCCTATAACATAAGACGAGGG 59.231 44.000 0.00 0.00 0.00 4.30
631 710 6.711194 TCTCTGTCCTATAACATAAGACGAGG 59.289 42.308 0.00 0.00 33.25 4.63
632 711 7.731882 TCTCTGTCCTATAACATAAGACGAG 57.268 40.000 0.00 0.00 33.47 4.18
633 712 8.568794 CATTCTCTGTCCTATAACATAAGACGA 58.431 37.037 0.00 0.00 0.00 4.20
634 713 8.353684 ACATTCTCTGTCCTATAACATAAGACG 58.646 37.037 0.00 0.00 29.94 4.18
640 719 9.911788 AATCAAACATTCTCTGTCCTATAACAT 57.088 29.630 0.00 0.00 36.98 2.71
647 726 8.787852 GTTTCTTAATCAAACATTCTCTGTCCT 58.212 33.333 5.64 0.00 36.98 3.85
648 727 8.567948 TGTTTCTTAATCAAACATTCTCTGTCC 58.432 33.333 8.20 0.00 38.53 4.02
665 744 8.218441 CGTCTCGTGACATAAAATGTTTCTTAA 58.782 33.333 17.02 0.00 45.03 1.85
666 745 7.148705 CCGTCTCGTGACATAAAATGTTTCTTA 60.149 37.037 17.02 0.00 45.03 2.10
667 746 6.347402 CCGTCTCGTGACATAAAATGTTTCTT 60.347 38.462 17.02 0.00 45.03 2.52
668 747 5.120208 CCGTCTCGTGACATAAAATGTTTCT 59.880 40.000 17.02 0.00 45.03 2.52
669 748 5.119588 TCCGTCTCGTGACATAAAATGTTTC 59.880 40.000 17.02 0.00 45.03 2.78
670 749 4.992319 TCCGTCTCGTGACATAAAATGTTT 59.008 37.500 17.02 0.00 45.03 2.83
671 750 4.562082 TCCGTCTCGTGACATAAAATGTT 58.438 39.130 17.02 0.00 45.03 2.71
673 752 3.551890 CCTCCGTCTCGTGACATAAAATG 59.448 47.826 17.02 0.00 43.06 2.32
674 753 3.430374 CCCTCCGTCTCGTGACATAAAAT 60.430 47.826 17.02 0.00 43.06 1.82
675 754 2.094390 CCCTCCGTCTCGTGACATAAAA 60.094 50.000 17.02 0.00 43.06 1.52
676 755 1.475280 CCCTCCGTCTCGTGACATAAA 59.525 52.381 17.02 0.00 43.06 1.40
677 756 1.100510 CCCTCCGTCTCGTGACATAA 58.899 55.000 17.02 1.70 43.06 1.90
678 757 0.253894 TCCCTCCGTCTCGTGACATA 59.746 55.000 17.02 3.96 43.06 2.29
679 758 1.001269 TCCCTCCGTCTCGTGACAT 60.001 57.895 17.02 0.00 43.06 3.06
680 759 1.674651 CTCCCTCCGTCTCGTGACA 60.675 63.158 17.02 0.00 43.06 3.58
681 760 0.392193 TACTCCCTCCGTCTCGTGAC 60.392 60.000 7.56 7.56 39.70 3.67
682 761 0.392193 GTACTCCCTCCGTCTCGTGA 60.392 60.000 0.00 0.00 0.00 4.35
683 762 0.675837 TGTACTCCCTCCGTCTCGTG 60.676 60.000 0.00 0.00 0.00 4.35
684 763 0.255318 ATGTACTCCCTCCGTCTCGT 59.745 55.000 0.00 0.00 0.00 4.18
685 764 0.663688 CATGTACTCCCTCCGTCTCG 59.336 60.000 0.00 0.00 0.00 4.04
686 765 1.033574 CCATGTACTCCCTCCGTCTC 58.966 60.000 0.00 0.00 0.00 3.36
687 766 0.397254 CCCATGTACTCCCTCCGTCT 60.397 60.000 0.00 0.00 0.00 4.18
688 767 0.396695 TCCCATGTACTCCCTCCGTC 60.397 60.000 0.00 0.00 0.00 4.79
689 768 0.686769 GTCCCATGTACTCCCTCCGT 60.687 60.000 0.00 0.00 0.00 4.69
690 769 0.686441 TGTCCCATGTACTCCCTCCG 60.686 60.000 0.00 0.00 0.00 4.63
691 770 0.831307 GTGTCCCATGTACTCCCTCC 59.169 60.000 0.00 0.00 0.00 4.30
692 771 0.460311 CGTGTCCCATGTACTCCCTC 59.540 60.000 0.00 0.00 0.00 4.30
693 772 0.252103 ACGTGTCCCATGTACTCCCT 60.252 55.000 0.00 0.00 31.23 4.20
694 773 1.477553 TACGTGTCCCATGTACTCCC 58.522 55.000 0.00 0.00 35.12 4.30
695 774 3.598019 TTTACGTGTCCCATGTACTCC 57.402 47.619 0.00 0.00 35.86 3.85
696 775 3.930848 CCTTTTACGTGTCCCATGTACTC 59.069 47.826 0.00 0.00 35.86 2.59
697 776 3.579586 TCCTTTTACGTGTCCCATGTACT 59.420 43.478 0.00 0.00 35.86 2.73
698 777 3.929094 TCCTTTTACGTGTCCCATGTAC 58.071 45.455 0.00 0.00 35.86 2.90
699 778 4.202336 TGTTCCTTTTACGTGTCCCATGTA 60.202 41.667 0.00 0.00 35.12 2.29
700 779 3.143728 GTTCCTTTTACGTGTCCCATGT 58.856 45.455 0.00 0.00 37.38 3.21
701 780 3.142951 TGTTCCTTTTACGTGTCCCATG 58.857 45.455 0.00 0.00 0.00 3.66
702 781 3.495434 TGTTCCTTTTACGTGTCCCAT 57.505 42.857 0.00 0.00 0.00 4.00
709 788 3.872771 TCGCTTTCTTGTTCCTTTTACGT 59.127 39.130 0.00 0.00 0.00 3.57
710 789 4.209112 GTCGCTTTCTTGTTCCTTTTACG 58.791 43.478 0.00 0.00 0.00 3.18
716 795 0.765510 AGGGTCGCTTTCTTGTTCCT 59.234 50.000 0.00 0.00 0.00 3.36
724 803 1.206831 GTTTCGCAGGGTCGCTTTC 59.793 57.895 0.00 0.00 0.00 2.62
760 839 0.169009 GTTGGTTGATCTGCGCTTCC 59.831 55.000 9.73 1.17 0.00 3.46
768 847 2.046314 CGCCCGGTTGGTTGATCT 60.046 61.111 0.00 0.00 36.04 2.75
782 871 0.727398 CAATTTCTTCGGTCCTCGCC 59.273 55.000 0.00 0.00 39.05 5.54
784 873 1.066430 TCCCAATTTCTTCGGTCCTCG 60.066 52.381 0.00 0.00 40.90 4.63
792 881 3.676093 ACGACTTCCTCCCAATTTCTTC 58.324 45.455 0.00 0.00 0.00 2.87
793 882 3.559384 GGACGACTTCCTCCCAATTTCTT 60.559 47.826 0.00 0.00 41.95 2.52
794 883 2.027100 GGACGACTTCCTCCCAATTTCT 60.027 50.000 0.00 0.00 41.95 2.52
799 888 0.685097 CTTGGACGACTTCCTCCCAA 59.315 55.000 0.00 0.00 46.10 4.12
828 917 4.659874 CGACGCGGTTGGTGTTGC 62.660 66.667 12.47 0.00 40.09 4.17
849 942 0.248743 TGAAGTGAAGACGCGTCGTT 60.249 50.000 31.56 24.71 41.37 3.85
852 950 1.698165 TGATGAAGTGAAGACGCGTC 58.302 50.000 31.30 31.30 36.04 5.19
869 967 1.486211 GAAGAGGGGAGAACGGATGA 58.514 55.000 0.00 0.00 0.00 2.92
871 969 0.691413 GGGAAGAGGGGAGAACGGAT 60.691 60.000 0.00 0.00 0.00 4.18
872 970 1.305887 GGGAAGAGGGGAGAACGGA 60.306 63.158 0.00 0.00 0.00 4.69
874 972 2.368011 GGGGGAAGAGGGGAGAACG 61.368 68.421 0.00 0.00 0.00 3.95
875 973 0.624795 ATGGGGGAAGAGGGGAGAAC 60.625 60.000 0.00 0.00 0.00 3.01
877 990 1.264869 ATATGGGGGAAGAGGGGAGA 58.735 55.000 0.00 0.00 0.00 3.71
884 997 3.115563 AGGGGATGTTATATGGGGGAAGA 60.116 47.826 0.00 0.00 0.00 2.87
887 1000 2.462688 AGAGGGGATGTTATATGGGGGA 59.537 50.000 0.00 0.00 0.00 4.81
888 1001 2.846827 GAGAGGGGATGTTATATGGGGG 59.153 54.545 0.00 0.00 0.00 5.40
889 1002 3.531059 TGAGAGGGGATGTTATATGGGG 58.469 50.000 0.00 0.00 0.00 4.96
893 1006 4.203045 TGGGGATGAGAGGGGATGTTATAT 60.203 45.833 0.00 0.00 0.00 0.86
899 1012 1.353694 GAATGGGGATGAGAGGGGATG 59.646 57.143 0.00 0.00 0.00 3.51
941 1054 2.612972 GGAGTGGAAGATTGAGAACGCA 60.613 50.000 0.00 0.00 0.00 5.24
950 1063 2.578480 GAGAAAGGGGGAGTGGAAGATT 59.422 50.000 0.00 0.00 0.00 2.40
952 1065 1.657804 GAGAAAGGGGGAGTGGAAGA 58.342 55.000 0.00 0.00 0.00 2.87
953 1066 0.621082 GGAGAAAGGGGGAGTGGAAG 59.379 60.000 0.00 0.00 0.00 3.46
954 1067 0.845102 GGGAGAAAGGGGGAGTGGAA 60.845 60.000 0.00 0.00 0.00 3.53
955 1068 1.229853 GGGAGAAAGGGGGAGTGGA 60.230 63.158 0.00 0.00 0.00 4.02
959 1072 0.341609 AGAGAGGGAGAAAGGGGGAG 59.658 60.000 0.00 0.00 0.00 4.30
975 1088 1.583986 GGAGATGGGCGATCGAGAG 59.416 63.158 21.57 0.00 36.04 3.20
976 1089 2.261586 CGGAGATGGGCGATCGAGA 61.262 63.158 21.57 0.85 36.04 4.04
977 1090 2.256764 CGGAGATGGGCGATCGAG 59.743 66.667 21.57 0.00 36.04 4.04
978 1091 3.978491 GCGGAGATGGGCGATCGA 61.978 66.667 21.57 0.00 36.04 3.59
1125 1247 2.902457 ATGGTTTCTCCGGCCGGTT 61.902 57.895 41.57 15.55 39.52 4.44
1170 1292 1.270550 GTCACCTTCCCGTACGAAGAA 59.729 52.381 18.76 17.33 41.57 2.52
1171 1293 0.883833 GTCACCTTCCCGTACGAAGA 59.116 55.000 18.76 10.45 41.57 2.87
1172 1294 0.455633 CGTCACCTTCCCGTACGAAG 60.456 60.000 18.76 13.11 39.22 3.79
1173 1295 1.172180 ACGTCACCTTCCCGTACGAA 61.172 55.000 18.76 2.67 37.04 3.85
1400 1528 0.317479 ACAGTTCGTGTCCACTAGGC 59.683 55.000 0.00 0.00 31.90 3.93
1415 1547 7.760340 GCTGCTAGAACTAAACTAACATACAGT 59.240 37.037 0.00 0.00 0.00 3.55
1544 1680 1.078918 CTGCGCTCATTCCAGACCA 60.079 57.895 9.73 0.00 0.00 4.02
1602 1747 4.384647 GCACTCTTGGACTTGGGATTCTAT 60.385 45.833 0.00 0.00 0.00 1.98
1745 1894 4.649088 AGCATCATGATTGGAACACATG 57.351 40.909 5.16 0.00 39.29 3.21
1778 1927 4.636206 AGGAATCAACTTTATCCTTGACGC 59.364 41.667 0.00 0.00 39.23 5.19
1806 1955 3.502356 ACTTTATCCTTCCCCGCAAAAA 58.498 40.909 0.00 0.00 0.00 1.94
1807 1956 3.163616 ACTTTATCCTTCCCCGCAAAA 57.836 42.857 0.00 0.00 0.00 2.44
1808 1957 2.823154 CAACTTTATCCTTCCCCGCAAA 59.177 45.455 0.00 0.00 0.00 3.68
1809 1958 2.040545 TCAACTTTATCCTTCCCCGCAA 59.959 45.455 0.00 0.00 0.00 4.85
1810 1959 1.631388 TCAACTTTATCCTTCCCCGCA 59.369 47.619 0.00 0.00 0.00 5.69
1811 1960 2.413310 TCAACTTTATCCTTCCCCGC 57.587 50.000 0.00 0.00 0.00 6.13
1812 1961 4.947388 TGAAATCAACTTTATCCTTCCCCG 59.053 41.667 0.00 0.00 0.00 5.73
1813 1962 6.850752 TTGAAATCAACTTTATCCTTCCCC 57.149 37.500 0.00 0.00 0.00 4.81
1814 1963 8.066612 TGATTGAAATCAACTTTATCCTTCCC 57.933 34.615 3.24 0.00 42.11 3.97
1815 1964 8.743714 ACTGATTGAAATCAACTTTATCCTTCC 58.256 33.333 7.13 0.00 44.20 3.46
1816 1965 9.780413 GACTGATTGAAATCAACTTTATCCTTC 57.220 33.333 7.13 0.00 44.20 3.46
1872 2021 3.431725 GTAACTGCCGGCTGGTGC 61.432 66.667 31.74 27.14 37.67 5.01
1873 2022 1.577328 CTTGTAACTGCCGGCTGGTG 61.577 60.000 31.74 18.82 37.67 4.17
1884 2033 3.308188 GGTTGGCCATCCTACTTGTAACT 60.308 47.826 23.48 0.00 38.05 2.24
1886 2035 2.916934 AGGTTGGCCATCCTACTTGTAA 59.083 45.455 30.47 0.00 38.05 2.41
1888 2037 1.372501 AGGTTGGCCATCCTACTTGT 58.627 50.000 30.47 8.77 38.05 3.16
1893 2042 1.142870 GCATGTAGGTTGGCCATCCTA 59.857 52.381 30.94 30.94 37.19 2.94
1894 2043 0.106519 GCATGTAGGTTGGCCATCCT 60.107 55.000 32.89 32.89 37.19 3.24
1895 2044 1.109323 GGCATGTAGGTTGGCCATCC 61.109 60.000 23.35 23.35 45.70 3.51
1896 2045 2.419057 GGCATGTAGGTTGGCCATC 58.581 57.895 6.09 5.53 45.70 3.51
1897 2046 4.684623 GGCATGTAGGTTGGCCAT 57.315 55.556 6.09 0.00 45.70 4.40
1931 2080 3.499157 TGTACACGCCCTAACAAACATTC 59.501 43.478 0.00 0.00 0.00 2.67
1932 2081 3.478509 TGTACACGCCCTAACAAACATT 58.521 40.909 0.00 0.00 0.00 2.71
1933 2082 3.128852 TGTACACGCCCTAACAAACAT 57.871 42.857 0.00 0.00 0.00 2.71
1944 2093 4.688511 TTTATCAACCATTGTACACGCC 57.311 40.909 0.00 0.00 0.00 5.68
1945 2094 7.469260 ACTATTTTATCAACCATTGTACACGC 58.531 34.615 0.00 0.00 0.00 5.34
1946 2095 9.834628 AAACTATTTTATCAACCATTGTACACG 57.165 29.630 0.00 0.00 0.00 4.49
2000 2149 9.941664 CCATTGTAGACATTCTTTATTGTCATC 57.058 33.333 5.91 0.00 43.72 2.92
2001 2150 9.685276 TCCATTGTAGACATTCTTTATTGTCAT 57.315 29.630 5.91 0.00 43.72 3.06
2002 2151 9.685276 ATCCATTGTAGACATTCTTTATTGTCA 57.315 29.630 5.91 0.00 43.72 3.58
2138 2287 6.295916 GGTGGAGGAGAGAGAACTCATAAAAA 60.296 42.308 4.64 0.00 44.79 1.94
2139 2288 5.187967 GGTGGAGGAGAGAGAACTCATAAAA 59.812 44.000 4.64 0.00 44.79 1.52
2140 2289 4.712337 GGTGGAGGAGAGAGAACTCATAAA 59.288 45.833 4.64 0.00 44.79 1.40
2141 2290 4.017037 AGGTGGAGGAGAGAGAACTCATAA 60.017 45.833 4.64 0.00 44.79 1.90
2142 2291 3.529734 AGGTGGAGGAGAGAGAACTCATA 59.470 47.826 4.64 0.00 44.79 2.15
2143 2292 2.314549 AGGTGGAGGAGAGAGAACTCAT 59.685 50.000 4.64 0.00 44.79 2.90
2144 2293 1.713647 AGGTGGAGGAGAGAGAACTCA 59.286 52.381 4.64 0.00 44.79 3.41
2145 2294 2.291282 TGAGGTGGAGGAGAGAGAACTC 60.291 54.545 0.00 0.00 42.90 3.01
2146 2295 1.713647 TGAGGTGGAGGAGAGAGAACT 59.286 52.381 0.00 0.00 0.00 3.01
2147 2296 2.223803 TGAGGTGGAGGAGAGAGAAC 57.776 55.000 0.00 0.00 0.00 3.01
2148 2297 3.481559 AATGAGGTGGAGGAGAGAGAA 57.518 47.619 0.00 0.00 0.00 2.87
2149 2298 4.823364 ATAATGAGGTGGAGGAGAGAGA 57.177 45.455 0.00 0.00 0.00 3.10
2150 2299 5.885449 AAATAATGAGGTGGAGGAGAGAG 57.115 43.478 0.00 0.00 0.00 3.20
2151 2300 7.791766 AGAATAAATAATGAGGTGGAGGAGAGA 59.208 37.037 0.00 0.00 0.00 3.10
2152 2301 7.972301 AGAATAAATAATGAGGTGGAGGAGAG 58.028 38.462 0.00 0.00 0.00 3.20
2153 2302 7.937700 AGAATAAATAATGAGGTGGAGGAGA 57.062 36.000 0.00 0.00 0.00 3.71
2154 2303 8.651389 TGTAGAATAAATAATGAGGTGGAGGAG 58.349 37.037 0.00 0.00 0.00 3.69
2155 2304 8.561536 TGTAGAATAAATAATGAGGTGGAGGA 57.438 34.615 0.00 0.00 0.00 3.71
2156 2305 9.224267 CATGTAGAATAAATAATGAGGTGGAGG 57.776 37.037 0.00 0.00 0.00 4.30
2157 2306 9.784531 ACATGTAGAATAAATAATGAGGTGGAG 57.215 33.333 0.00 0.00 0.00 3.86
2158 2307 9.778741 GACATGTAGAATAAATAATGAGGTGGA 57.221 33.333 0.00 0.00 0.00 4.02
2159 2308 9.559732 TGACATGTAGAATAAATAATGAGGTGG 57.440 33.333 0.00 0.00 0.00 4.61
2172 2321 9.982651 GCTATTTTAGGAGTGACATGTAGAATA 57.017 33.333 0.00 0.00 0.00 1.75
2173 2322 8.486210 TGCTATTTTAGGAGTGACATGTAGAAT 58.514 33.333 0.00 0.00 0.00 2.40
2174 2323 7.764443 GTGCTATTTTAGGAGTGACATGTAGAA 59.236 37.037 0.00 0.00 0.00 2.10
2175 2324 7.265673 GTGCTATTTTAGGAGTGACATGTAGA 58.734 38.462 0.00 0.00 0.00 2.59
2176 2325 6.480320 GGTGCTATTTTAGGAGTGACATGTAG 59.520 42.308 0.00 0.00 0.00 2.74
2177 2326 6.070481 TGGTGCTATTTTAGGAGTGACATGTA 60.070 38.462 0.00 0.00 0.00 2.29
2178 2327 5.186198 GGTGCTATTTTAGGAGTGACATGT 58.814 41.667 0.00 0.00 0.00 3.21
2179 2328 5.185454 TGGTGCTATTTTAGGAGTGACATG 58.815 41.667 0.00 0.00 0.00 3.21
2180 2329 5.435686 TGGTGCTATTTTAGGAGTGACAT 57.564 39.130 0.00 0.00 0.00 3.06
2181 2330 4.901197 TGGTGCTATTTTAGGAGTGACA 57.099 40.909 0.00 0.00 0.00 3.58
2182 2331 5.648092 ACAATGGTGCTATTTTAGGAGTGAC 59.352 40.000 0.00 0.00 0.00 3.67
2183 2332 5.815581 ACAATGGTGCTATTTTAGGAGTGA 58.184 37.500 0.00 0.00 0.00 3.41
2184 2333 6.597672 TGTACAATGGTGCTATTTTAGGAGTG 59.402 38.462 0.00 0.00 0.00 3.51
2185 2334 6.717289 TGTACAATGGTGCTATTTTAGGAGT 58.283 36.000 0.00 0.00 0.00 3.85
2186 2335 7.642669 CATGTACAATGGTGCTATTTTAGGAG 58.357 38.462 0.00 0.00 0.00 3.69
2187 2336 6.039270 GCATGTACAATGGTGCTATTTTAGGA 59.961 38.462 11.12 0.00 34.85 2.94
2188 2337 6.208644 GCATGTACAATGGTGCTATTTTAGG 58.791 40.000 11.12 0.00 34.85 2.69
2189 2338 6.208644 GGCATGTACAATGGTGCTATTTTAG 58.791 40.000 16.47 0.00 37.70 1.85
2190 2339 5.068460 GGGCATGTACAATGGTGCTATTTTA 59.932 40.000 16.47 0.00 37.70 1.52
2191 2340 4.141959 GGGCATGTACAATGGTGCTATTTT 60.142 41.667 16.47 0.00 37.70 1.82
2192 2341 3.384467 GGGCATGTACAATGGTGCTATTT 59.616 43.478 16.47 0.00 37.70 1.40
2193 2342 2.958355 GGGCATGTACAATGGTGCTATT 59.042 45.455 16.47 0.00 37.70 1.73
2194 2343 2.175499 AGGGCATGTACAATGGTGCTAT 59.825 45.455 16.47 5.35 37.70 2.97
2195 2344 1.563879 AGGGCATGTACAATGGTGCTA 59.436 47.619 16.47 0.00 37.70 3.49
2196 2345 0.332632 AGGGCATGTACAATGGTGCT 59.667 50.000 16.47 0.00 37.70 4.40
2197 2346 1.185315 AAGGGCATGTACAATGGTGC 58.815 50.000 10.12 10.12 36.88 5.01
2198 2347 2.358898 GCTAAGGGCATGTACAATGGTG 59.641 50.000 0.00 0.00 41.35 4.17
2199 2348 2.654863 GCTAAGGGCATGTACAATGGT 58.345 47.619 0.00 0.00 41.35 3.55
2211 2360 2.164422 GACCAATTCAGTTGCTAAGGGC 59.836 50.000 0.00 0.00 42.22 5.19
2212 2361 2.420022 CGACCAATTCAGTTGCTAAGGG 59.580 50.000 0.00 0.00 36.46 3.95
2213 2362 3.074412 ACGACCAATTCAGTTGCTAAGG 58.926 45.455 0.00 0.00 36.46 2.69
2214 2363 3.997021 AGACGACCAATTCAGTTGCTAAG 59.003 43.478 0.00 0.00 36.46 2.18
2215 2364 3.994392 GAGACGACCAATTCAGTTGCTAA 59.006 43.478 0.00 0.00 36.46 3.09
2216 2365 3.006430 TGAGACGACCAATTCAGTTGCTA 59.994 43.478 0.00 0.00 36.46 3.49
2217 2366 2.224281 TGAGACGACCAATTCAGTTGCT 60.224 45.455 0.00 0.00 36.46 3.91
2218 2367 2.143122 TGAGACGACCAATTCAGTTGC 58.857 47.619 0.00 0.00 36.46 4.17
2219 2368 3.393800 ACTGAGACGACCAATTCAGTTG 58.606 45.455 0.45 0.00 45.80 3.16
2220 2369 3.753294 ACTGAGACGACCAATTCAGTT 57.247 42.857 0.45 0.00 45.80 3.16
2238 2387 5.984926 TCGAGGTAACAAAAATAACACGACT 59.015 36.000 0.00 0.00 41.41 4.18
2240 2389 5.752472 TGTCGAGGTAACAAAAATAACACGA 59.248 36.000 0.00 0.00 41.41 4.35
2244 2393 8.260270 AGGTATGTCGAGGTAACAAAAATAAC 57.740 34.615 0.00 0.00 41.41 1.89
2273 2422 3.397618 TGGAGGGTATGGGTTTATGATGG 59.602 47.826 0.00 0.00 0.00 3.51
2284 2433 2.025416 TCATGTTGGTTGGAGGGTATGG 60.025 50.000 0.00 0.00 0.00 2.74
2302 2451 3.679917 CGTTGGAGATGCACTAACCTCAT 60.680 47.826 0.00 0.00 0.00 2.90
2328 2477 3.744426 AGTATACGTGTTTGACTTGGTGC 59.256 43.478 0.00 0.00 0.00 5.01
2330 2479 4.748102 CACAGTATACGTGTTTGACTTGGT 59.252 41.667 15.34 0.00 0.00 3.67
2343 2492 4.621460 CCTTATTGATCCGCACAGTATACG 59.379 45.833 0.00 0.00 0.00 3.06
2344 2493 5.634020 GTCCTTATTGATCCGCACAGTATAC 59.366 44.000 0.00 0.00 0.00 1.47
2345 2494 5.779922 GTCCTTATTGATCCGCACAGTATA 58.220 41.667 0.00 0.00 0.00 1.47
2346 2495 4.632153 GTCCTTATTGATCCGCACAGTAT 58.368 43.478 0.00 0.00 0.00 2.12
2347 2496 4.054780 GTCCTTATTGATCCGCACAGTA 57.945 45.455 0.00 0.00 0.00 2.74
2348 2497 2.906354 GTCCTTATTGATCCGCACAGT 58.094 47.619 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.