Multiple sequence alignment - TraesCS5D01G404100

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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 TraesCS5D01G404100 chr5D 100.000 3012 0 0 452 3463 469463557 469466568 0.000000e+00 5563.0
1 TraesCS5D01G404100 chr5D 82.650 1464 217 20 971 2420 469479645 469481085 0.000000e+00 1262.0
2 TraesCS5D01G404100 chr5D 76.950 1449 290 27 1001 2421 469305968 469307400 0.000000e+00 785.0
3 TraesCS5D01G404100 chr5D 100.000 122 0 0 1 122 469463106 469463227 3.480000e-55 226.0
4 TraesCS5D01G404100 chr5D 94.262 122 7 0 1 122 380847493 380847372 1.640000e-43 187.0
5 TraesCS5D01G404100 chr5D 92.784 97 7 0 3001 3097 426018657 426018561 1.300000e-29 141.0
6 TraesCS5D01G404100 chr5D 91.753 97 8 0 3001 3097 426039465 426039369 6.030000e-28 135.0
7 TraesCS5D01G404100 chr5B 91.587 2080 111 15 498 2544 576902538 576904586 0.000000e+00 2813.0
8 TraesCS5D01G404100 chr5B 89.974 1905 119 36 688 2544 576916073 576917953 0.000000e+00 2394.0
9 TraesCS5D01G404100 chr5B 91.684 938 63 10 2511 3443 577091714 577092641 0.000000e+00 1286.0
10 TraesCS5D01G404100 chr5B 82.292 1457 219 22 992 2420 577212907 577214352 0.000000e+00 1225.0
11 TraesCS5D01G404100 chr5B 92.683 287 21 0 3063 3349 577211818 577212104 6.920000e-112 414.0
12 TraesCS5D01G404100 chr5B 90.722 97 8 1 3001 3097 515701081 515700986 1.010000e-25 128.0
13 TraesCS5D01G404100 chr5A 90.113 1598 120 20 940 2505 590455400 590456991 0.000000e+00 2041.0
14 TraesCS5D01G404100 chr5A 87.571 1593 142 21 1624 3212 590445398 590446938 0.000000e+00 1794.0
15 TraesCS5D01G404100 chr5A 89.059 1243 103 21 1542 2780 590300960 590299747 0.000000e+00 1511.0
16 TraesCS5D01G404100 chr5A 91.251 1063 90 3 1333 2394 590110039 590111099 0.000000e+00 1445.0
17 TraesCS5D01G404100 chr5A 88.617 1063 102 10 1177 2222 590220242 590221302 0.000000e+00 1275.0
18 TraesCS5D01G404100 chr5A 82.467 1443 213 22 992 2420 590526326 590527742 0.000000e+00 1227.0
19 TraesCS5D01G404100 chr5A 92.515 815 51 4 532 1337 590100527 590101340 0.000000e+00 1158.0
20 TraesCS5D01G404100 chr5A 81.492 1448 230 21 992 2420 590452132 590453560 0.000000e+00 1155.0
21 TraesCS5D01G404100 chr5A 86.387 977 99 16 2216 3174 590236666 590237626 0.000000e+00 1037.0
22 TraesCS5D01G404100 chr5A 76.515 1452 298 31 1001 2421 589584058 589585497 0.000000e+00 752.0
23 TraesCS5D01G404100 chr5A 90.192 520 36 7 2656 3173 590465487 590465993 0.000000e+00 664.0
24 TraesCS5D01G404100 chr5A 78.312 936 165 23 999 1914 590240376 590241293 1.390000e-158 569.0
25 TraesCS5D01G404100 chr5A 93.689 206 11 2 3212 3416 590450435 590450639 1.210000e-79 307.0
26 TraesCS5D01G404100 chr5A 88.048 251 17 5 3166 3416 590524344 590524581 5.660000e-73 285.0
27 TraesCS5D01G404100 chr5A 86.853 251 19 3 3168 3416 590238146 590238384 5.700000e-68 268.0
28 TraesCS5D01G404100 chrUn 95.902 122 4 1 1 121 238904439 238904560 2.730000e-46 196.0
29 TraesCS5D01G404100 chrUn 95.082 122 5 1 1 121 264348181 264348060 1.270000e-44 191.0
30 TraesCS5D01G404100 chr3D 94.215 121 7 0 1 121 413673881 413674001 5.900000e-43 185.0
31 TraesCS5D01G404100 chr2D 94.262 122 6 1 1 121 86069302 86069423 5.900000e-43 185.0
32 TraesCS5D01G404100 chr1D 94.215 121 7 0 1 121 216544168 216544288 5.900000e-43 185.0
33 TraesCS5D01G404100 chr1D 93.388 121 8 0 1 121 42988310 42988190 2.750000e-41 180.0
34 TraesCS5D01G404100 chr1D 93.443 122 7 1 1 121 491721106 491721227 2.750000e-41 180.0
35 TraesCS5D01G404100 chr6D 93.443 122 6 2 1 121 450666217 450666337 2.750000e-41 180.0
36 TraesCS5D01G404100 chr7D 78.866 194 29 9 3002 3184 559455051 559454859 1.690000e-23 121.0
37 TraesCS5D01G404100 chr6B 89.362 94 10 0 3002 3095 198404669 198404576 6.070000e-23 119.0
38 TraesCS5D01G404100 chr6B 92.453 53 4 0 2926 2978 352368354 352368302 3.710000e-10 76.8
39 TraesCS5D01G404100 chr4B 95.652 46 2 0 2929 2974 139629590 139629635 1.330000e-09 75.0


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 TraesCS5D01G404100 chr5D 469463106 469466568 3462 False 2894.500000 5563 100.000000 1 3463 2 chr5D.!!$F3 3462
1 TraesCS5D01G404100 chr5D 469479645 469481085 1440 False 1262.000000 1262 82.650000 971 2420 1 chr5D.!!$F2 1449
2 TraesCS5D01G404100 chr5D 469305968 469307400 1432 False 785.000000 785 76.950000 1001 2421 1 chr5D.!!$F1 1420
3 TraesCS5D01G404100 chr5B 576902538 576904586 2048 False 2813.000000 2813 91.587000 498 2544 1 chr5B.!!$F1 2046
4 TraesCS5D01G404100 chr5B 576916073 576917953 1880 False 2394.000000 2394 89.974000 688 2544 1 chr5B.!!$F2 1856
5 TraesCS5D01G404100 chr5B 577091714 577092641 927 False 1286.000000 1286 91.684000 2511 3443 1 chr5B.!!$F3 932
6 TraesCS5D01G404100 chr5B 577211818 577214352 2534 False 819.500000 1225 87.487500 992 3349 2 chr5B.!!$F4 2357
7 TraesCS5D01G404100 chr5A 590299747 590300960 1213 True 1511.000000 1511 89.059000 1542 2780 1 chr5A.!!$R1 1238
8 TraesCS5D01G404100 chr5A 590110039 590111099 1060 False 1445.000000 1445 91.251000 1333 2394 1 chr5A.!!$F3 1061
9 TraesCS5D01G404100 chr5A 590445398 590456991 11593 False 1324.250000 2041 88.216250 940 3416 4 chr5A.!!$F7 2476
10 TraesCS5D01G404100 chr5A 590220242 590221302 1060 False 1275.000000 1275 88.617000 1177 2222 1 chr5A.!!$F4 1045
11 TraesCS5D01G404100 chr5A 590100527 590101340 813 False 1158.000000 1158 92.515000 532 1337 1 chr5A.!!$F2 805
12 TraesCS5D01G404100 chr5A 590524344 590527742 3398 False 756.000000 1227 85.257500 992 3416 2 chr5A.!!$F8 2424
13 TraesCS5D01G404100 chr5A 589584058 589585497 1439 False 752.000000 752 76.515000 1001 2421 1 chr5A.!!$F1 1420
14 TraesCS5D01G404100 chr5A 590465487 590465993 506 False 664.000000 664 90.192000 2656 3173 1 chr5A.!!$F5 517
15 TraesCS5D01G404100 chr5A 590236666 590241293 4627 False 624.666667 1037 83.850667 999 3416 3 chr5A.!!$F6 2417

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
733 734 0.035458 CTTGGTCCACACTCCACTCC 59.965 60.0 0.0 0.0 33.12 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2635 13631 0.105039 GGCCCATAGGACAGTCTTCG 59.895 60.0 0.0 0.0 43.07 3.79 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
19 20 2.176792 CGCGCTTTTCCCTTGAGC 59.823 61.111 5.56 0.00 0.00 4.26
20 21 2.568612 GCGCTTTTCCCTTGAGCC 59.431 61.111 0.00 0.00 32.90 4.70
23 24 1.303317 GCTTTTCCCTTGAGCCGGA 60.303 57.895 5.05 0.00 0.00 5.14
24 25 1.308783 GCTTTTCCCTTGAGCCGGAG 61.309 60.000 5.05 0.00 0.00 4.63
25 26 1.303317 TTTTCCCTTGAGCCGGAGC 60.303 57.895 5.05 0.00 40.32 4.70
33 34 4.570874 GAGCCGGAGCCCCCAATC 62.571 72.222 5.05 0.00 41.25 2.67
43 44 4.820744 CCCCAATCGCCCCCAGTG 62.821 72.222 0.00 0.00 0.00 3.66
100 101 4.439472 CCGAACCGGCGCTTTTCG 62.439 66.667 22.90 22.90 41.17 3.46
110 111 3.431725 GCTTTTCGGCGTCCTGGG 61.432 66.667 6.85 0.00 0.00 4.45
111 112 2.746277 CTTTTCGGCGTCCTGGGG 60.746 66.667 6.85 0.00 0.00 4.96
112 113 4.338710 TTTTCGGCGTCCTGGGGG 62.339 66.667 6.85 0.00 0.00 5.40
474 475 6.730960 GTAGATCACATTTTAACCGTCCAA 57.269 37.500 0.00 0.00 0.00 3.53
475 476 7.316544 GTAGATCACATTTTAACCGTCCAAT 57.683 36.000 0.00 0.00 0.00 3.16
476 477 6.834168 AGATCACATTTTAACCGTCCAATT 57.166 33.333 0.00 0.00 0.00 2.32
477 478 7.227049 AGATCACATTTTAACCGTCCAATTT 57.773 32.000 0.00 0.00 0.00 1.82
478 479 7.666623 AGATCACATTTTAACCGTCCAATTTT 58.333 30.769 0.00 0.00 0.00 1.82
479 480 8.798402 AGATCACATTTTAACCGTCCAATTTTA 58.202 29.630 0.00 0.00 0.00 1.52
481 482 7.942990 TCACATTTTAACCGTCCAATTTTACT 58.057 30.769 0.00 0.00 0.00 2.24
483 484 8.079809 CACATTTTAACCGTCCAATTTTACTCT 58.920 33.333 0.00 0.00 0.00 3.24
485 486 8.512138 CATTTTAACCGTCCAATTTTACTCTCT 58.488 33.333 0.00 0.00 0.00 3.10
486 487 8.454570 TTTTAACCGTCCAATTTTACTCTCTT 57.545 30.769 0.00 0.00 0.00 2.85
488 489 6.954487 AACCGTCCAATTTTACTCTCTTTT 57.046 33.333 0.00 0.00 0.00 2.27
489 490 6.954487 ACCGTCCAATTTTACTCTCTTTTT 57.046 33.333 0.00 0.00 0.00 1.94
592 593 1.660607 CAATGAGATCGTTGTCCCACG 59.339 52.381 6.62 0.00 41.78 4.94
696 697 6.798427 GGAGATGCTCCTGTATATATCCAA 57.202 41.667 6.23 0.00 46.41 3.53
697 698 6.578023 GGAGATGCTCCTGTATATATCCAAC 58.422 44.000 6.23 0.00 46.41 3.77
698 699 6.155221 GGAGATGCTCCTGTATATATCCAACA 59.845 42.308 6.23 0.00 46.41 3.33
702 703 7.500629 TGCTCCTGTATATATCCAACATGAT 57.499 36.000 0.00 0.00 0.00 2.45
703 704 8.608185 TGCTCCTGTATATATCCAACATGATA 57.392 34.615 0.00 0.00 0.00 2.15
704 705 8.699130 TGCTCCTGTATATATCCAACATGATAG 58.301 37.037 0.00 0.00 31.09 2.08
705 706 8.918116 GCTCCTGTATATATCCAACATGATAGA 58.082 37.037 0.00 0.00 31.09 1.98
714 715 4.832248 TCCAACATGATAGAGACAACCAC 58.168 43.478 0.00 0.00 0.00 4.16
715 716 4.532126 TCCAACATGATAGAGACAACCACT 59.468 41.667 0.00 0.00 0.00 4.00
716 717 5.013079 TCCAACATGATAGAGACAACCACTT 59.987 40.000 0.00 0.00 0.00 3.16
718 719 4.836825 ACATGATAGAGACAACCACTTGG 58.163 43.478 0.00 0.00 42.17 3.61
729 730 1.836391 CCACTTGGTCCACACTCCA 59.164 57.895 0.00 0.00 0.00 3.86
730 731 0.535102 CCACTTGGTCCACACTCCAC 60.535 60.000 0.00 0.00 33.12 4.02
731 732 0.469917 CACTTGGTCCACACTCCACT 59.530 55.000 0.00 0.00 33.12 4.00
732 733 0.759346 ACTTGGTCCACACTCCACTC 59.241 55.000 0.00 0.00 33.12 3.51
733 734 0.035458 CTTGGTCCACACTCCACTCC 59.965 60.000 0.00 0.00 33.12 3.85
735 736 1.371558 GGTCCACACTCCACTCCAC 59.628 63.158 0.00 0.00 0.00 4.02
736 737 1.407656 GGTCCACACTCCACTCCACA 61.408 60.000 0.00 0.00 0.00 4.17
738 739 1.072331 GTCCACACTCCACTCCACAAT 59.928 52.381 0.00 0.00 0.00 2.71
739 740 1.774254 TCCACACTCCACTCCACAATT 59.226 47.619 0.00 0.00 0.00 2.32
742 743 3.213506 CACACTCCACTCCACAATTTCA 58.786 45.455 0.00 0.00 0.00 2.69
743 744 3.822735 CACACTCCACTCCACAATTTCAT 59.177 43.478 0.00 0.00 0.00 2.57
745 746 5.473162 CACACTCCACTCCACAATTTCATAA 59.527 40.000 0.00 0.00 0.00 1.90
746 747 6.016360 CACACTCCACTCCACAATTTCATAAA 60.016 38.462 0.00 0.00 0.00 1.40
747 748 6.549364 ACACTCCACTCCACAATTTCATAAAA 59.451 34.615 0.00 0.00 0.00 1.52
748 749 7.069331 ACACTCCACTCCACAATTTCATAAAAA 59.931 33.333 0.00 0.00 0.00 1.94
749 750 8.090214 CACTCCACTCCACAATTTCATAAAAAT 58.910 33.333 0.00 0.00 0.00 1.82
750 751 8.650490 ACTCCACTCCACAATTTCATAAAAATT 58.350 29.630 0.00 0.00 0.00 1.82
751 752 9.492973 CTCCACTCCACAATTTCATAAAAATTT 57.507 29.630 0.00 0.00 0.00 1.82
770 771 8.970691 AAAATTTATCAACAGGATCGTTTGAG 57.029 30.769 14.08 0.00 37.44 3.02
771 772 7.687941 AATTTATCAACAGGATCGTTTGAGT 57.312 32.000 14.08 8.38 37.44 3.41
772 773 6.721571 TTTATCAACAGGATCGTTTGAGTC 57.278 37.500 14.08 0.00 37.44 3.36
773 774 3.744238 TCAACAGGATCGTTTGAGTCA 57.256 42.857 0.00 0.00 0.00 3.41
774 775 4.271696 TCAACAGGATCGTTTGAGTCAT 57.728 40.909 0.00 0.00 0.00 3.06
775 776 4.641396 TCAACAGGATCGTTTGAGTCATT 58.359 39.130 0.00 0.00 0.00 2.57
777 778 5.637810 TCAACAGGATCGTTTGAGTCATTAC 59.362 40.000 0.00 0.00 0.00 1.89
778 779 4.504858 ACAGGATCGTTTGAGTCATTACC 58.495 43.478 0.00 0.00 0.00 2.85
779 780 3.871594 CAGGATCGTTTGAGTCATTACCC 59.128 47.826 0.00 0.00 0.00 3.69
780 781 3.517901 AGGATCGTTTGAGTCATTACCCA 59.482 43.478 0.00 0.00 0.00 4.51
781 782 3.871594 GGATCGTTTGAGTCATTACCCAG 59.128 47.826 0.00 0.00 0.00 4.45
783 784 4.819105 TCGTTTGAGTCATTACCCAGAT 57.181 40.909 0.00 0.00 0.00 2.90
784 785 5.925506 TCGTTTGAGTCATTACCCAGATA 57.074 39.130 0.00 0.00 0.00 1.98
785 786 6.288941 TCGTTTGAGTCATTACCCAGATAA 57.711 37.500 0.00 0.00 0.00 1.75
786 787 6.103997 TCGTTTGAGTCATTACCCAGATAAC 58.896 40.000 0.00 0.00 0.00 1.89
789 790 7.562135 GTTTGAGTCATTACCCAGATAACCTA 58.438 38.462 0.00 0.00 0.00 3.08
790 791 7.931015 TTGAGTCATTACCCAGATAACCTAT 57.069 36.000 0.00 0.00 0.00 2.57
791 792 7.931015 TGAGTCATTACCCAGATAACCTATT 57.069 36.000 0.00 0.00 0.00 1.73
792 793 7.963532 TGAGTCATTACCCAGATAACCTATTC 58.036 38.462 0.00 0.00 0.00 1.75
793 794 7.789831 TGAGTCATTACCCAGATAACCTATTCT 59.210 37.037 0.00 0.00 0.00 2.40
797 798 8.217799 TCATTACCCAGATAACCTATTCTTTGG 58.782 37.037 0.00 0.00 0.00 3.28
798 799 7.758820 TTACCCAGATAACCTATTCTTTGGA 57.241 36.000 0.00 0.00 0.00 3.53
800 801 6.663734 ACCCAGATAACCTATTCTTTGGAAG 58.336 40.000 0.00 0.00 34.70 3.46
801 802 6.447084 ACCCAGATAACCTATTCTTTGGAAGA 59.553 38.462 0.00 0.00 34.70 2.87
802 803 6.995091 CCCAGATAACCTATTCTTTGGAAGAG 59.005 42.308 0.00 0.00 39.64 2.85
803 804 7.147479 CCCAGATAACCTATTCTTTGGAAGAGA 60.147 40.741 2.51 0.00 41.70 3.10
804 805 7.713073 CCAGATAACCTATTCTTTGGAAGAGAC 59.287 40.741 2.51 0.00 41.70 3.36
805 806 8.260818 CAGATAACCTATTCTTTGGAAGAGACA 58.739 37.037 2.51 0.00 41.70 3.41
806 807 8.826765 AGATAACCTATTCTTTGGAAGAGACAA 58.173 33.333 2.51 0.00 41.70 3.18
808 809 7.511959 AACCTATTCTTTGGAAGAGACAAAC 57.488 36.000 2.51 0.00 41.70 2.93
809 810 6.601332 ACCTATTCTTTGGAAGAGACAAACA 58.399 36.000 2.51 0.00 41.70 2.83
810 811 7.234355 ACCTATTCTTTGGAAGAGACAAACAT 58.766 34.615 2.51 0.00 41.70 2.71
812 813 6.966534 ATTCTTTGGAAGAGACAAACATGT 57.033 33.333 0.00 0.00 39.03 3.21
814 815 4.580167 TCTTTGGAAGAGACAAACATGTGG 59.420 41.667 0.00 0.00 34.43 4.17
815 816 3.576078 TGGAAGAGACAAACATGTGGT 57.424 42.857 0.00 0.12 0.00 4.16
816 817 3.476552 TGGAAGAGACAAACATGTGGTC 58.523 45.455 18.47 18.47 0.00 4.02
817 818 3.136443 TGGAAGAGACAAACATGTGGTCT 59.864 43.478 25.29 25.29 44.12 3.85
819 820 3.845781 AGAGACAAACATGTGGTCTGT 57.154 42.857 28.37 23.68 41.68 3.41
821 822 3.879295 AGAGACAAACATGTGGTCTGTTG 59.121 43.478 28.37 17.66 41.68 3.33
822 823 3.876914 GAGACAAACATGTGGTCTGTTGA 59.123 43.478 28.37 0.00 41.68 3.18
824 825 3.620488 ACAAACATGTGGTCTGTTGACT 58.380 40.909 11.62 0.00 42.54 3.41
827 828 6.530120 ACAAACATGTGGTCTGTTGACTATA 58.470 36.000 11.62 0.00 42.54 1.31
828 829 6.995686 ACAAACATGTGGTCTGTTGACTATAA 59.004 34.615 11.62 0.00 42.54 0.98
829 830 7.665559 ACAAACATGTGGTCTGTTGACTATAAT 59.334 33.333 11.62 0.00 42.54 1.28
830 831 7.615582 AACATGTGGTCTGTTGACTATAATG 57.384 36.000 0.00 0.00 42.54 1.90
831 832 6.711277 ACATGTGGTCTGTTGACTATAATGT 58.289 36.000 0.00 0.00 42.54 2.71
832 833 6.595326 ACATGTGGTCTGTTGACTATAATGTG 59.405 38.462 0.00 0.00 39.68 3.21
833 834 4.935205 TGTGGTCTGTTGACTATAATGTGC 59.065 41.667 0.00 0.00 42.54 4.57
834 835 5.178797 GTGGTCTGTTGACTATAATGTGCT 58.821 41.667 0.00 0.00 42.54 4.40
835 836 5.063944 GTGGTCTGTTGACTATAATGTGCTG 59.936 44.000 0.00 0.00 42.54 4.41
836 837 5.046663 TGGTCTGTTGACTATAATGTGCTGA 60.047 40.000 0.00 0.00 42.54 4.26
837 838 6.051717 GGTCTGTTGACTATAATGTGCTGAT 58.948 40.000 0.00 0.00 42.54 2.90
838 839 6.018425 GGTCTGTTGACTATAATGTGCTGATG 60.018 42.308 0.00 0.00 42.54 3.07
839 840 5.525012 TCTGTTGACTATAATGTGCTGATGC 59.475 40.000 0.00 0.00 40.20 3.91
840 841 8.795830 GTCTGTTGACTATAATGTGCTGATGCA 61.796 40.741 0.00 0.00 42.30 3.96
852 853 1.687563 CTGATGCAATCCCTGATGCA 58.312 50.000 2.65 2.65 44.73 3.96
853 854 2.028876 CTGATGCAATCCCTGATGCAA 58.971 47.619 4.41 0.00 44.73 4.08
856 857 2.447408 TGCAATCCCTGATGCAAGAT 57.553 45.000 0.00 0.00 34.08 2.40
857 858 2.304092 TGCAATCCCTGATGCAAGATC 58.696 47.619 0.00 0.00 34.08 2.75
858 859 2.304092 GCAATCCCTGATGCAAGATCA 58.696 47.619 0.00 0.00 0.00 2.92
861 862 4.202223 GCAATCCCTGATGCAAGATCAATT 60.202 41.667 0.00 0.00 0.00 2.32
862 863 5.289595 CAATCCCTGATGCAAGATCAATTG 58.710 41.667 0.00 0.00 0.00 2.32
863 864 3.293337 TCCCTGATGCAAGATCAATTGG 58.707 45.455 5.42 0.00 0.00 3.16
864 865 3.028850 CCCTGATGCAAGATCAATTGGT 58.971 45.455 5.42 0.00 0.00 3.67
866 867 3.952323 CCTGATGCAAGATCAATTGGTCT 59.048 43.478 15.72 15.72 0.00 3.85
868 869 3.697542 TGATGCAAGATCAATTGGTCTGG 59.302 43.478 21.77 19.59 0.00 3.86
869 870 1.820519 TGCAAGATCAATTGGTCTGGC 59.179 47.619 32.86 32.86 40.96 4.85
871 872 2.159282 GCAAGATCAATTGGTCTGGCAG 60.159 50.000 33.96 19.78 40.41 4.85
873 874 3.726557 AGATCAATTGGTCTGGCAGAA 57.273 42.857 20.49 3.95 0.00 3.02
875 876 1.909700 TCAATTGGTCTGGCAGAACC 58.090 50.000 28.61 24.65 39.84 3.62
876 877 1.425066 TCAATTGGTCTGGCAGAACCT 59.575 47.619 28.61 14.05 40.22 3.50
877 878 2.158475 TCAATTGGTCTGGCAGAACCTT 60.158 45.455 28.61 18.94 40.22 3.50
878 879 3.073798 TCAATTGGTCTGGCAGAACCTTA 59.926 43.478 28.61 14.90 40.22 2.69
879 880 4.019174 CAATTGGTCTGGCAGAACCTTAT 58.981 43.478 28.61 16.43 40.22 1.73
880 881 5.045213 TCAATTGGTCTGGCAGAACCTTATA 60.045 40.000 28.61 7.79 40.22 0.98
881 882 5.653255 ATTGGTCTGGCAGAACCTTATAT 57.347 39.130 28.61 11.77 40.22 0.86
882 883 4.422073 TGGTCTGGCAGAACCTTATATG 57.578 45.455 28.61 0.00 40.22 1.78
884 885 3.433598 GGTCTGGCAGAACCTTATATGCA 60.434 47.826 22.05 0.00 40.46 3.96
885 886 3.561725 GTCTGGCAGAACCTTATATGCAC 59.438 47.826 20.62 0.00 40.46 4.57
887 888 4.139786 CTGGCAGAACCTTATATGCACAT 58.860 43.478 9.42 0.00 40.46 3.21
888 889 3.884693 TGGCAGAACCTTATATGCACATG 59.115 43.478 0.00 0.00 40.46 3.21
889 890 3.885297 GGCAGAACCTTATATGCACATGT 59.115 43.478 0.00 0.00 40.46 3.21
890 891 4.261322 GGCAGAACCTTATATGCACATGTG 60.261 45.833 21.83 21.83 40.46 3.21
891 892 4.336433 GCAGAACCTTATATGCACATGTGT 59.664 41.667 26.01 10.78 38.54 3.72
892 893 8.596038 GGCAGAACCTTATATGCACATGTGTG 62.596 46.154 26.01 12.77 41.48 3.82
893 894 4.883585 AGAACCTTATATGCACATGTGTGG 59.116 41.667 26.01 17.33 45.72 4.17
894 895 3.554934 ACCTTATATGCACATGTGTGGG 58.445 45.455 26.01 17.84 45.72 4.61
905 906 5.239359 CACATGTGTGGGCATATATATGC 57.761 43.478 31.34 31.34 45.74 3.14
920 921 7.946207 CATATATATGCCAGACTATCGTCCTT 58.054 38.462 9.75 0.00 41.16 3.36
921 922 2.898729 ATGCCAGACTATCGTCCTTG 57.101 50.000 0.00 0.00 41.16 3.61
922 923 1.557099 TGCCAGACTATCGTCCTTGT 58.443 50.000 0.00 0.00 41.16 3.16
923 924 1.476891 TGCCAGACTATCGTCCTTGTC 59.523 52.381 0.00 0.00 41.16 3.18
924 925 1.476891 GCCAGACTATCGTCCTTGTCA 59.523 52.381 0.00 0.00 41.16 3.58
925 926 2.101582 GCCAGACTATCGTCCTTGTCAT 59.898 50.000 0.00 0.00 41.16 3.06
926 927 3.797184 GCCAGACTATCGTCCTTGTCATC 60.797 52.174 0.00 0.00 41.16 2.92
929 930 3.886505 AGACTATCGTCCTTGTCATCCTC 59.113 47.826 0.00 0.00 41.16 3.71
930 931 2.619177 ACTATCGTCCTTGTCATCCTCG 59.381 50.000 0.00 0.00 0.00 4.63
931 932 1.475403 ATCGTCCTTGTCATCCTCGT 58.525 50.000 0.00 0.00 0.00 4.18
932 933 0.809385 TCGTCCTTGTCATCCTCGTC 59.191 55.000 0.00 0.00 0.00 4.20
933 934 0.179134 CGTCCTTGTCATCCTCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
934 935 0.895530 GTCCTTGTCATCCTCGTCCA 59.104 55.000 0.00 0.00 0.00 4.02
935 936 0.895530 TCCTTGTCATCCTCGTCCAC 59.104 55.000 0.00 0.00 0.00 4.02
936 937 0.458543 CCTTGTCATCCTCGTCCACG 60.459 60.000 0.00 0.00 41.45 4.94
938 939 1.884075 TTGTCATCCTCGTCCACGGG 61.884 60.000 0.00 0.00 40.09 5.28
944 945 2.361357 CTCGTCCACGGGGAGAGT 60.361 66.667 6.67 0.00 46.12 3.24
946 947 2.675423 CGTCCACGGGGAGAGTGA 60.675 66.667 6.67 0.00 46.12 3.41
947 948 2.971452 GTCCACGGGGAGAGTGAC 59.029 66.667 6.67 0.00 46.12 3.67
949 950 1.906824 TCCACGGGGAGAGTGACAC 60.907 63.158 0.00 0.00 41.83 3.67
950 951 2.207229 CCACGGGGAGAGTGACACA 61.207 63.158 0.00 0.00 41.83 3.72
951 952 1.544825 CCACGGGGAGAGTGACACAT 61.545 60.000 0.00 0.00 41.83 3.21
953 954 1.056660 ACGGGGAGAGTGACACATTT 58.943 50.000 8.59 0.00 0.00 2.32
955 956 1.806542 CGGGGAGAGTGACACATTTTG 59.193 52.381 8.59 0.00 0.00 2.44
956 957 1.541588 GGGGAGAGTGACACATTTTGC 59.458 52.381 8.59 0.00 0.00 3.68
958 959 2.485814 GGGAGAGTGACACATTTTGCTC 59.514 50.000 8.59 4.57 0.00 4.26
959 960 3.406764 GGAGAGTGACACATTTTGCTCT 58.593 45.455 8.59 0.00 36.20 4.09
960 961 3.817647 GGAGAGTGACACATTTTGCTCTT 59.182 43.478 8.59 0.00 33.99 2.85
962 963 3.004106 AGAGTGACACATTTTGCTCTTGC 59.996 43.478 8.59 0.00 40.20 4.01
987 988 6.851222 AATTTGTCATACTCCATTCTAGCG 57.149 37.500 0.00 0.00 0.00 4.26
988 989 3.371102 TGTCATACTCCATTCTAGCGC 57.629 47.619 0.00 0.00 0.00 5.92
990 991 2.031069 GTCATACTCCATTCTAGCGCGA 60.031 50.000 12.10 0.00 0.00 5.87
997 998 1.075542 CATTCTAGCGCGAACAACCA 58.924 50.000 12.10 0.00 0.00 3.67
1502 12424 8.811017 TGGTAAGAGCAAATCAAAATTTCCATA 58.189 29.630 0.00 0.00 32.69 2.74
1510 12446 7.550196 GCAAATCAAAATTTCCATATCCACAGT 59.450 33.333 0.00 0.00 32.69 3.55
1522 12458 7.103641 TCCATATCCACAGTTGTACTTTTCTC 58.896 38.462 0.00 0.00 0.00 2.87
1554 12515 3.253188 AGTTTTGGACATGAACATGGACG 59.747 43.478 17.25 0.00 42.91 4.79
2234 13225 2.341257 CAGAGCTACATCTGCAACGTT 58.659 47.619 0.00 0.00 40.26 3.99
2408 13400 1.688772 GGTCCTCGCATGAGTACCTA 58.311 55.000 0.00 0.00 45.30 3.08
2421 13413 3.963428 AGTACCTACTCAAGCTTGTGG 57.037 47.619 27.12 23.31 0.00 4.17
2431 13423 3.754965 TCAAGCTTGTGGATTTGCTAGT 58.245 40.909 25.19 0.00 35.09 2.57
2449 13441 1.221523 AGTAGAGCAGGGATCCCATCA 59.778 52.381 32.69 14.09 38.92 3.07
2451 13443 1.070445 GAGCAGGGATCCCATCACG 59.930 63.158 32.69 15.52 37.89 4.35
2498 13491 0.537188 ATCGGACGGCTCTGAACATT 59.463 50.000 0.00 0.00 35.32 2.71
2505 13498 3.135994 ACGGCTCTGAACATTTACGTTT 58.864 40.909 0.00 0.00 0.00 3.60
2513 13506 9.047871 GCTCTGAACATTTACGTTTACAAATAC 57.952 33.333 0.00 0.00 0.00 1.89
2577 13573 5.994250 ACAATATAGTGAAGTGGTGAGCAT 58.006 37.500 7.27 0.00 0.00 3.79
2606 13602 3.785486 TCTGCATCCGTGTTAGAATGAG 58.215 45.455 0.00 0.00 0.00 2.90
2611 13607 5.088739 GCATCCGTGTTAGAATGAGTTTTG 58.911 41.667 0.00 0.00 0.00 2.44
2629 13625 8.260818 TGAGTTTTGTTTTCATGTTGGGAATTA 58.739 29.630 0.00 0.00 0.00 1.40
2635 13631 7.653647 TGTTTTCATGTTGGGAATTACTACAC 58.346 34.615 0.00 0.00 0.00 2.90
2648 13644 6.094603 GGAATTACTACACGAAGACTGTCCTA 59.905 42.308 3.76 0.00 0.00 2.94
2649 13645 7.201803 GGAATTACTACACGAAGACTGTCCTAT 60.202 40.741 3.76 0.00 0.00 2.57
2650 13646 4.966965 ACTACACGAAGACTGTCCTATG 57.033 45.455 3.76 1.12 0.00 2.23
2651 13647 3.695060 ACTACACGAAGACTGTCCTATGG 59.305 47.826 3.76 0.00 0.00 2.74
2652 13648 1.825474 ACACGAAGACTGTCCTATGGG 59.175 52.381 3.76 0.00 0.00 4.00
2653 13649 0.824759 ACGAAGACTGTCCTATGGGC 59.175 55.000 3.76 0.00 0.00 5.36
2654 13650 0.105039 CGAAGACTGTCCTATGGGCC 59.895 60.000 3.76 0.00 0.00 5.80
2786 13785 6.158598 ACATTTTTGAGCGAAATTACTGCAT 58.841 32.000 0.00 0.00 0.00 3.96
2791 13790 1.811965 AGCGAAATTACTGCATGCACA 59.188 42.857 18.46 4.49 0.00 4.57
2808 13807 4.992688 TGCACAACGTTTCTTTTCAATCT 58.007 34.783 0.00 0.00 0.00 2.40
2809 13808 4.797868 TGCACAACGTTTCTTTTCAATCTG 59.202 37.500 0.00 0.00 0.00 2.90
2832 13831 2.322081 CGATGCCCAACGAACGGTT 61.322 57.895 0.00 0.00 40.22 4.44
2885 13884 3.317149 GTCAGGTGTCATACGTATAGCCA 59.683 47.826 7.96 2.49 0.00 4.75
2901 13900 7.042925 ACGTATAGCCAAACTCTATTTTAAGCG 60.043 37.037 0.00 0.00 0.00 4.68
2914 13914 4.920640 TTTTAAGCGGGAAACACAATGA 57.079 36.364 0.00 0.00 0.00 2.57
2948 13948 2.531912 CGAGTTCATGGATTCGTCTTCG 59.468 50.000 10.60 0.00 38.55 3.79
2949 13949 3.512680 GAGTTCATGGATTCGTCTTCGT 58.487 45.455 0.00 0.00 38.33 3.85
2960 13960 0.663688 CGTCTTCGTCGGATGAGGAT 59.336 55.000 14.16 0.00 38.67 3.24
3178 14180 1.901464 GGTGGCATTTGGTGTCCGT 60.901 57.895 0.00 0.00 0.00 4.69
3207 14209 4.700365 CGCGACTGCTGTCCACGA 62.700 66.667 21.65 0.00 39.88 4.35
3266 14268 2.603953 GTCAGCGGACTACACCTAAAC 58.396 52.381 9.95 0.00 40.99 2.01
3272 14274 2.665052 CGGACTACACCTAAACGAAAGC 59.335 50.000 0.00 0.00 0.00 3.51
3275 14277 4.694037 GGACTACACCTAAACGAAAGCATT 59.306 41.667 0.00 0.00 0.00 3.56
3276 14278 5.390567 GGACTACACCTAAACGAAAGCATTG 60.391 44.000 0.00 0.00 0.00 2.82
3277 14279 3.282831 ACACCTAAACGAAAGCATTGC 57.717 42.857 0.00 0.00 0.00 3.56
3279 14281 2.030363 CACCTAAACGAAAGCATTGCCA 60.030 45.455 4.70 0.00 0.00 4.92
3280 14282 2.825532 ACCTAAACGAAAGCATTGCCAT 59.174 40.909 4.70 0.00 0.00 4.40
3283 14285 4.327087 CCTAAACGAAAGCATTGCCATTTC 59.673 41.667 4.70 8.91 0.00 2.17
3295 14298 3.630892 TGCCATTTCCATCCAATTTGG 57.369 42.857 9.28 9.28 39.43 3.28
3299 14302 1.265236 TTTCCATCCAATTTGGCGCT 58.735 45.000 7.64 0.00 37.47 5.92
3343 14346 4.878397 ACATTTTGGAGCTCCTTAGAATCG 59.122 41.667 32.28 19.47 36.82 3.34
3364 14367 5.979993 TCGGTGACTGCTTATAATGGTTAA 58.020 37.500 0.00 0.00 0.00 2.01
3373 14376 6.132658 TGCTTATAATGGTTAAGAATGCCCA 58.867 36.000 0.00 0.00 0.00 5.36
3420 14423 1.138883 CGATCACACCCGACGACAT 59.861 57.895 0.00 0.00 0.00 3.06
3443 14446 4.344102 TGTACTTCCTGCCCTGTGATATAC 59.656 45.833 0.00 0.00 0.00 1.47
3444 14447 3.658725 ACTTCCTGCCCTGTGATATACT 58.341 45.455 0.00 0.00 0.00 2.12
3445 14448 4.040755 ACTTCCTGCCCTGTGATATACTT 58.959 43.478 0.00 0.00 0.00 2.24
3446 14449 4.101741 ACTTCCTGCCCTGTGATATACTTC 59.898 45.833 0.00 0.00 0.00 3.01
3447 14450 2.972713 TCCTGCCCTGTGATATACTTCC 59.027 50.000 0.00 0.00 0.00 3.46
3448 14451 2.975489 CCTGCCCTGTGATATACTTCCT 59.025 50.000 0.00 0.00 0.00 3.36
3449 14452 3.007398 CCTGCCCTGTGATATACTTCCTC 59.993 52.174 0.00 0.00 0.00 3.71
3450 14453 3.900601 CTGCCCTGTGATATACTTCCTCT 59.099 47.826 0.00 0.00 0.00 3.69
3451 14454 3.643320 TGCCCTGTGATATACTTCCTCTG 59.357 47.826 0.00 0.00 0.00 3.35
3452 14455 3.643792 GCCCTGTGATATACTTCCTCTGT 59.356 47.826 0.00 0.00 0.00 3.41
3453 14456 4.101741 GCCCTGTGATATACTTCCTCTGTT 59.898 45.833 0.00 0.00 0.00 3.16
3454 14457 5.396884 GCCCTGTGATATACTTCCTCTGTTT 60.397 44.000 0.00 0.00 0.00 2.83
3455 14458 6.284459 CCCTGTGATATACTTCCTCTGTTTC 58.716 44.000 0.00 0.00 0.00 2.78
3456 14459 6.127054 CCCTGTGATATACTTCCTCTGTTTCA 60.127 42.308 0.00 0.00 0.00 2.69
3457 14460 7.331026 CCTGTGATATACTTCCTCTGTTTCAA 58.669 38.462 0.00 0.00 0.00 2.69
3458 14461 7.824289 CCTGTGATATACTTCCTCTGTTTCAAA 59.176 37.037 0.00 0.00 0.00 2.69
3459 14462 9.219603 CTGTGATATACTTCCTCTGTTTCAAAA 57.780 33.333 0.00 0.00 0.00 2.44
3460 14463 9.739276 TGTGATATACTTCCTCTGTTTCAAAAT 57.261 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.328288 CTCAAGGGAAAAGCGCGGC 62.328 63.158 8.83 0.00 34.07 6.53
1 2 2.870372 CTCAAGGGAAAAGCGCGG 59.130 61.111 8.83 0.00 34.07 6.46
2 3 2.176792 GCTCAAGGGAAAAGCGCG 59.823 61.111 0.00 0.00 34.07 6.86
5 6 1.303317 TCCGGCTCAAGGGAAAAGC 60.303 57.895 0.00 0.00 35.27 3.51
6 7 1.308783 GCTCCGGCTCAAGGGAAAAG 61.309 60.000 0.00 0.00 35.22 2.27
7 8 1.303317 GCTCCGGCTCAAGGGAAAA 60.303 57.895 0.00 0.00 35.22 2.29
8 9 2.351276 GCTCCGGCTCAAGGGAAA 59.649 61.111 0.00 0.00 35.22 3.13
9 10 3.717294 GGCTCCGGCTCAAGGGAA 61.717 66.667 0.00 0.00 38.73 3.97
16 17 4.570874 GATTGGGGGCTCCGGCTC 62.571 72.222 0.00 0.00 38.76 4.70
85 86 4.753877 GCCGAAAAGCGCCGGTTC 62.754 66.667 21.18 13.43 46.84 3.62
93 94 3.431725 CCCAGGACGCCGAAAAGC 61.432 66.667 0.00 0.00 0.00 3.51
94 95 2.746277 CCCCAGGACGCCGAAAAG 60.746 66.667 0.00 0.00 0.00 2.27
95 96 4.338710 CCCCCAGGACGCCGAAAA 62.339 66.667 0.00 0.00 33.47 2.29
452 453 7.931578 AATTGGACGGTTAAAATGTGATCTA 57.068 32.000 0.00 0.00 0.00 1.98
453 454 6.834168 AATTGGACGGTTAAAATGTGATCT 57.166 33.333 0.00 0.00 0.00 2.75
454 455 7.883229 AAAATTGGACGGTTAAAATGTGATC 57.117 32.000 0.00 0.00 0.00 2.92
455 456 8.581578 AGTAAAATTGGACGGTTAAAATGTGAT 58.418 29.630 0.00 0.00 0.00 3.06
456 457 7.942990 AGTAAAATTGGACGGTTAAAATGTGA 58.057 30.769 0.00 0.00 0.00 3.58
458 459 8.173542 AGAGTAAAATTGGACGGTTAAAATGT 57.826 30.769 0.00 0.00 0.00 2.71
461 462 8.454570 AAGAGAGTAAAATTGGACGGTTAAAA 57.545 30.769 0.00 0.00 0.00 1.52
462 463 8.454570 AAAGAGAGTAAAATTGGACGGTTAAA 57.545 30.769 0.00 0.00 0.00 1.52
463 464 8.454570 AAAAGAGAGTAAAATTGGACGGTTAA 57.545 30.769 0.00 0.00 0.00 2.01
464 465 8.454570 AAAAAGAGAGTAAAATTGGACGGTTA 57.545 30.769 0.00 0.00 0.00 2.85
465 466 6.954487 AAAAGAGAGTAAAATTGGACGGTT 57.046 33.333 0.00 0.00 0.00 4.44
466 467 6.954487 AAAAAGAGAGTAAAATTGGACGGT 57.046 33.333 0.00 0.00 0.00 4.83
488 489 2.668144 ATTGGACGGTTCCCTCAAAA 57.332 45.000 0.00 0.00 42.01 2.44
489 490 2.668144 AATTGGACGGTTCCCTCAAA 57.332 45.000 0.00 0.00 42.01 2.69
490 491 2.668144 AAATTGGACGGTTCCCTCAA 57.332 45.000 0.00 0.00 42.01 3.02
491 492 2.668144 AAAATTGGACGGTTCCCTCA 57.332 45.000 0.00 0.00 42.01 3.86
492 493 3.439129 CAGTAAAATTGGACGGTTCCCTC 59.561 47.826 0.00 0.00 42.01 4.30
493 494 3.181437 ACAGTAAAATTGGACGGTTCCCT 60.181 43.478 0.00 0.00 42.01 4.20
494 495 3.151554 ACAGTAAAATTGGACGGTTCCC 58.848 45.455 0.00 0.00 42.01 3.97
495 496 4.841443 AACAGTAAAATTGGACGGTTCC 57.159 40.909 3.63 0.00 43.19 3.62
496 497 4.979815 CCAAACAGTAAAATTGGACGGTTC 59.020 41.667 8.33 0.00 45.14 3.62
500 501 5.176407 TCACCAAACAGTAAAATTGGACG 57.824 39.130 10.50 2.09 45.14 4.79
562 563 3.955471 ACGATCTCATTGGTCCATTGTT 58.045 40.909 12.41 1.38 0.00 2.83
615 616 1.428448 TTCACTTCGCACCAAGATCG 58.572 50.000 0.00 0.00 0.00 3.69
641 642 1.892209 AAACCTAGGTTTCGCCAGTG 58.108 50.000 30.43 0.00 43.95 3.66
687 688 9.104713 TGGTTGTCTCTATCATGTTGGATATAT 57.895 33.333 0.00 0.00 0.00 0.86
693 694 4.836825 AGTGGTTGTCTCTATCATGTTGG 58.163 43.478 0.00 0.00 0.00 3.77
695 696 5.248640 CCAAGTGGTTGTCTCTATCATGTT 58.751 41.667 0.00 0.00 30.95 2.71
696 697 4.836825 CCAAGTGGTTGTCTCTATCATGT 58.163 43.478 0.00 0.00 30.95 3.21
712 713 0.469917 AGTGGAGTGTGGACCAAGTG 59.530 55.000 0.00 0.00 37.94 3.16
714 715 0.035458 GGAGTGGAGTGTGGACCAAG 59.965 60.000 0.00 0.00 37.94 3.61
715 716 0.692756 TGGAGTGGAGTGTGGACCAA 60.693 55.000 0.00 0.00 37.94 3.67
716 717 1.074850 TGGAGTGGAGTGTGGACCA 60.075 57.895 0.00 0.00 0.00 4.02
718 719 0.468226 TTGTGGAGTGGAGTGTGGAC 59.532 55.000 0.00 0.00 0.00 4.02
719 720 1.434188 ATTGTGGAGTGGAGTGTGGA 58.566 50.000 0.00 0.00 0.00 4.02
720 721 2.276732 AATTGTGGAGTGGAGTGTGG 57.723 50.000 0.00 0.00 0.00 4.17
721 722 3.213506 TGAAATTGTGGAGTGGAGTGTG 58.786 45.455 0.00 0.00 0.00 3.82
722 723 3.576078 TGAAATTGTGGAGTGGAGTGT 57.424 42.857 0.00 0.00 0.00 3.55
723 724 6.573664 TTTATGAAATTGTGGAGTGGAGTG 57.426 37.500 0.00 0.00 0.00 3.51
724 725 7.595819 TTTTTATGAAATTGTGGAGTGGAGT 57.404 32.000 0.00 0.00 0.00 3.85
745 746 8.576442 ACTCAAACGATCCTGTTGATAAATTTT 58.424 29.630 0.00 0.00 32.41 1.82
746 747 8.110860 ACTCAAACGATCCTGTTGATAAATTT 57.889 30.769 0.00 0.00 32.41 1.82
747 748 7.390440 TGACTCAAACGATCCTGTTGATAAATT 59.610 33.333 0.00 0.00 32.41 1.82
748 749 6.878923 TGACTCAAACGATCCTGTTGATAAAT 59.121 34.615 0.00 0.00 32.41 1.40
749 750 6.227522 TGACTCAAACGATCCTGTTGATAAA 58.772 36.000 0.00 0.00 32.41 1.40
750 751 5.789521 TGACTCAAACGATCCTGTTGATAA 58.210 37.500 0.00 0.00 32.41 1.75
751 752 5.400066 TGACTCAAACGATCCTGTTGATA 57.600 39.130 0.00 0.00 32.41 2.15
752 753 4.271696 TGACTCAAACGATCCTGTTGAT 57.728 40.909 0.00 0.00 36.01 2.57
753 754 3.744238 TGACTCAAACGATCCTGTTGA 57.256 42.857 0.00 0.00 31.10 3.18
754 755 5.163854 GGTAATGACTCAAACGATCCTGTTG 60.164 44.000 0.00 0.00 31.10 3.33
755 756 4.935808 GGTAATGACTCAAACGATCCTGTT 59.064 41.667 0.00 0.00 0.00 3.16
756 757 4.504858 GGTAATGACTCAAACGATCCTGT 58.495 43.478 0.00 0.00 0.00 4.00
757 758 3.871594 GGGTAATGACTCAAACGATCCTG 59.128 47.826 0.00 0.00 0.00 3.86
758 759 3.517901 TGGGTAATGACTCAAACGATCCT 59.482 43.478 0.00 0.00 31.17 3.24
759 760 3.869065 TGGGTAATGACTCAAACGATCC 58.131 45.455 0.00 0.00 31.17 3.36
762 763 4.819105 ATCTGGGTAATGACTCAAACGA 57.181 40.909 0.00 0.00 34.93 3.85
763 764 5.293569 GGTTATCTGGGTAATGACTCAAACG 59.706 44.000 0.00 0.00 34.93 3.60
766 767 7.931015 ATAGGTTATCTGGGTAATGACTCAA 57.069 36.000 0.00 0.00 34.93 3.02
767 768 7.789831 AGAATAGGTTATCTGGGTAATGACTCA 59.210 37.037 0.00 0.00 33.91 3.41
769 770 8.568617 AAGAATAGGTTATCTGGGTAATGACT 57.431 34.615 0.00 0.00 0.00 3.41
770 771 9.057089 CAAAGAATAGGTTATCTGGGTAATGAC 57.943 37.037 0.00 0.00 0.00 3.06
771 772 8.217799 CCAAAGAATAGGTTATCTGGGTAATGA 58.782 37.037 0.00 0.00 0.00 2.57
772 773 8.217799 TCCAAAGAATAGGTTATCTGGGTAATG 58.782 37.037 0.00 0.00 0.00 1.90
773 774 8.344939 TCCAAAGAATAGGTTATCTGGGTAAT 57.655 34.615 0.00 0.00 0.00 1.89
774 775 7.758820 TCCAAAGAATAGGTTATCTGGGTAA 57.241 36.000 0.00 0.00 0.00 2.85
775 776 7.626084 TCTTCCAAAGAATAGGTTATCTGGGTA 59.374 37.037 0.00 0.00 33.83 3.69
777 778 6.900194 TCTTCCAAAGAATAGGTTATCTGGG 58.100 40.000 0.00 0.00 33.83 4.45
778 779 7.713073 GTCTCTTCCAAAGAATAGGTTATCTGG 59.287 40.741 0.00 0.00 37.02 3.86
779 780 8.260818 TGTCTCTTCCAAAGAATAGGTTATCTG 58.739 37.037 0.00 0.00 37.02 2.90
780 781 8.380742 TGTCTCTTCCAAAGAATAGGTTATCT 57.619 34.615 0.00 0.00 37.02 1.98
781 782 9.449719 TTTGTCTCTTCCAAAGAATAGGTTATC 57.550 33.333 0.00 0.00 37.02 1.75
783 784 8.215050 TGTTTGTCTCTTCCAAAGAATAGGTTA 58.785 33.333 0.00 0.00 37.02 2.85
784 785 7.060421 TGTTTGTCTCTTCCAAAGAATAGGTT 58.940 34.615 0.00 0.00 37.02 3.50
785 786 6.601332 TGTTTGTCTCTTCCAAAGAATAGGT 58.399 36.000 0.00 0.00 37.02 3.08
786 787 7.175641 ACATGTTTGTCTCTTCCAAAGAATAGG 59.824 37.037 0.00 0.00 37.02 2.57
789 790 6.239120 CCACATGTTTGTCTCTTCCAAAGAAT 60.239 38.462 0.00 0.00 33.21 2.40
790 791 5.067674 CCACATGTTTGTCTCTTCCAAAGAA 59.932 40.000 0.00 0.00 33.21 2.52
791 792 4.580167 CCACATGTTTGTCTCTTCCAAAGA 59.420 41.667 0.00 0.00 32.79 2.52
792 793 4.339247 ACCACATGTTTGTCTCTTCCAAAG 59.661 41.667 0.00 0.00 32.79 2.77
793 794 4.277476 ACCACATGTTTGTCTCTTCCAAA 58.723 39.130 0.00 0.00 32.34 3.28
797 798 4.130118 ACAGACCACATGTTTGTCTCTTC 58.870 43.478 19.95 0.42 37.76 2.87
798 799 4.156455 ACAGACCACATGTTTGTCTCTT 57.844 40.909 19.95 10.72 37.76 2.85
800 801 3.876914 TCAACAGACCACATGTTTGTCTC 59.123 43.478 19.95 1.95 41.13 3.36
801 802 3.627577 GTCAACAGACCACATGTTTGTCT 59.372 43.478 17.96 17.96 41.13 3.41
802 803 3.627577 AGTCAACAGACCACATGTTTGTC 59.372 43.478 14.65 14.65 41.13 3.18
803 804 3.620488 AGTCAACAGACCACATGTTTGT 58.380 40.909 0.00 0.00 43.64 2.83
804 805 5.947228 ATAGTCAACAGACCACATGTTTG 57.053 39.130 0.00 0.00 38.80 2.93
805 806 7.665559 ACATTATAGTCAACAGACCACATGTTT 59.334 33.333 0.00 0.00 38.80 2.83
806 807 7.119699 CACATTATAGTCAACAGACCACATGTT 59.880 37.037 0.00 0.00 41.47 2.71
808 809 6.457392 GCACATTATAGTCAACAGACCACATG 60.457 42.308 0.00 0.00 32.62 3.21
809 810 5.586243 GCACATTATAGTCAACAGACCACAT 59.414 40.000 0.00 0.00 32.62 3.21
810 811 4.935205 GCACATTATAGTCAACAGACCACA 59.065 41.667 0.00 0.00 32.62 4.17
812 813 5.046663 TCAGCACATTATAGTCAACAGACCA 60.047 40.000 0.00 0.00 32.62 4.02
814 815 6.510799 GCATCAGCACATTATAGTCAACAGAC 60.511 42.308 0.00 0.00 41.58 3.51
815 816 5.525012 GCATCAGCACATTATAGTCAACAGA 59.475 40.000 0.00 0.00 41.58 3.41
816 817 5.745514 GCATCAGCACATTATAGTCAACAG 58.254 41.667 0.00 0.00 41.58 3.16
817 818 5.739752 GCATCAGCACATTATAGTCAACA 57.260 39.130 0.00 0.00 41.58 3.33
832 833 0.314302 GCATCAGGGATTGCATCAGC 59.686 55.000 0.00 0.00 42.57 4.26
833 834 1.687563 TGCATCAGGGATTGCATCAG 58.312 50.000 0.00 0.00 31.84 2.90
834 835 2.028876 CTTGCATCAGGGATTGCATCA 58.971 47.619 0.00 0.00 37.13 3.07
835 836 2.304092 TCTTGCATCAGGGATTGCATC 58.696 47.619 0.00 0.00 37.13 3.91
836 837 2.447408 TCTTGCATCAGGGATTGCAT 57.553 45.000 0.00 0.00 37.13 3.96
837 838 2.304092 GATCTTGCATCAGGGATTGCA 58.696 47.619 0.00 0.00 35.31 4.08
838 839 2.304092 TGATCTTGCATCAGGGATTGC 58.696 47.619 0.00 0.00 0.00 3.56
839 840 5.289595 CAATTGATCTTGCATCAGGGATTG 58.710 41.667 0.00 0.00 0.00 2.67
840 841 4.344102 CCAATTGATCTTGCATCAGGGATT 59.656 41.667 7.12 0.00 0.00 3.01
841 842 3.895656 CCAATTGATCTTGCATCAGGGAT 59.104 43.478 7.12 0.00 0.00 3.85
842 843 3.293337 CCAATTGATCTTGCATCAGGGA 58.707 45.455 7.12 0.00 0.00 4.20
844 845 3.952323 AGACCAATTGATCTTGCATCAGG 59.048 43.478 7.12 0.00 0.00 3.86
845 846 4.202020 CCAGACCAATTGATCTTGCATCAG 60.202 45.833 7.12 0.00 0.00 2.90
846 847 3.697542 CCAGACCAATTGATCTTGCATCA 59.302 43.478 7.12 0.00 0.00 3.07
847 848 3.490419 GCCAGACCAATTGATCTTGCATC 60.490 47.826 18.74 0.00 34.55 3.91
848 849 2.429610 GCCAGACCAATTGATCTTGCAT 59.570 45.455 18.74 0.00 34.55 3.96
852 853 3.726557 TCTGCCAGACCAATTGATCTT 57.273 42.857 7.12 0.00 0.00 2.40
853 854 3.350833 GTTCTGCCAGACCAATTGATCT 58.649 45.455 7.12 0.30 0.00 2.75
856 857 1.425066 AGGTTCTGCCAGACCAATTGA 59.575 47.619 7.12 0.00 40.61 2.57
857 858 1.915141 AGGTTCTGCCAGACCAATTG 58.085 50.000 13.47 0.00 40.61 2.32
858 859 2.683211 AAGGTTCTGCCAGACCAATT 57.317 45.000 13.47 0.00 40.61 2.32
861 862 3.433598 GCATATAAGGTTCTGCCAGACCA 60.434 47.826 13.47 0.00 40.61 4.02
862 863 3.142174 GCATATAAGGTTCTGCCAGACC 58.858 50.000 0.00 0.00 40.61 3.85
863 864 3.561725 GTGCATATAAGGTTCTGCCAGAC 59.438 47.826 0.00 0.00 40.61 3.51
864 865 3.199727 TGTGCATATAAGGTTCTGCCAGA 59.800 43.478 0.00 0.00 40.61 3.86
866 867 3.643199 TGTGCATATAAGGTTCTGCCA 57.357 42.857 0.00 0.00 40.61 4.92
868 869 4.336433 ACACATGTGCATATAAGGTTCTGC 59.664 41.667 25.68 0.00 35.21 4.26
869 870 5.220912 CCACACATGTGCATATAAGGTTCTG 60.221 44.000 25.68 10.99 44.34 3.02
871 872 4.036734 CCCACACATGTGCATATAAGGTTC 59.963 45.833 25.68 0.00 44.34 3.62
873 874 3.554934 CCCACACATGTGCATATAAGGT 58.445 45.455 25.68 0.00 44.34 3.50
875 876 2.950975 TGCCCACACATGTGCATATAAG 59.049 45.455 25.68 8.72 44.34 1.73
876 877 3.010200 TGCCCACACATGTGCATATAA 57.990 42.857 25.68 4.75 44.34 0.98
877 878 2.725221 TGCCCACACATGTGCATATA 57.275 45.000 25.68 7.15 44.34 0.86
878 879 2.076207 ATGCCCACACATGTGCATAT 57.924 45.000 25.68 10.28 44.34 1.78
879 880 2.725221 TATGCCCACACATGTGCATA 57.275 45.000 25.68 21.94 44.34 3.14
880 881 2.076207 ATATGCCCACACATGTGCAT 57.924 45.000 25.68 22.93 44.34 3.96
881 882 2.725221 TATATGCCCACACATGTGCA 57.275 45.000 25.68 17.76 44.34 4.57
882 883 5.239359 CATATATATGCCCACACATGTGC 57.761 43.478 25.68 12.27 44.34 4.57
910 911 2.619177 ACGAGGATGACAAGGACGATAG 59.381 50.000 0.00 0.00 46.19 2.08
911 912 2.617308 GACGAGGATGACAAGGACGATA 59.383 50.000 0.00 0.00 0.00 2.92
914 915 0.179134 GGACGAGGATGACAAGGACG 60.179 60.000 0.00 0.00 0.00 4.79
915 916 0.895530 TGGACGAGGATGACAAGGAC 59.104 55.000 0.00 0.00 0.00 3.85
916 917 0.895530 GTGGACGAGGATGACAAGGA 59.104 55.000 0.00 0.00 0.00 3.36
917 918 0.458543 CGTGGACGAGGATGACAAGG 60.459 60.000 0.00 0.00 43.02 3.61
920 921 2.348104 CCCGTGGACGAGGATGACA 61.348 63.158 0.00 0.00 43.02 3.58
921 922 2.494918 CCCGTGGACGAGGATGAC 59.505 66.667 0.00 0.00 43.02 3.06
922 923 2.758327 CCCCGTGGACGAGGATGA 60.758 66.667 0.00 0.00 39.83 2.92
923 924 2.758327 TCCCCGTGGACGAGGATG 60.758 66.667 0.00 0.00 41.40 3.51
924 925 2.442272 CTCCCCGTGGACGAGGAT 60.442 66.667 2.64 0.00 45.14 3.24
925 926 3.640257 CTCTCCCCGTGGACGAGGA 62.640 68.421 2.23 2.23 44.08 3.71
926 927 3.141488 CTCTCCCCGTGGACGAGG 61.141 72.222 0.00 0.00 43.02 4.63
929 930 2.675423 TCACTCTCCCCGTGGACG 60.675 66.667 0.00 0.00 35.03 4.79
930 931 1.906824 TGTCACTCTCCCCGTGGAC 60.907 63.158 0.00 0.00 35.03 4.02
931 932 1.906824 GTGTCACTCTCCCCGTGGA 60.907 63.158 0.00 0.00 38.75 4.02
932 933 1.544825 ATGTGTCACTCTCCCCGTGG 61.545 60.000 4.27 0.00 33.31 4.94
933 934 0.321671 AATGTGTCACTCTCCCCGTG 59.678 55.000 4.27 0.00 0.00 4.94
934 935 1.056660 AAATGTGTCACTCTCCCCGT 58.943 50.000 4.27 0.00 0.00 5.28
935 936 1.806542 CAAAATGTGTCACTCTCCCCG 59.193 52.381 4.27 0.00 0.00 5.73
936 937 1.541588 GCAAAATGTGTCACTCTCCCC 59.458 52.381 4.27 0.00 0.00 4.81
938 939 3.406764 AGAGCAAAATGTGTCACTCTCC 58.593 45.455 4.27 0.00 28.55 3.71
939 940 4.781071 CAAGAGCAAAATGTGTCACTCTC 58.219 43.478 4.27 2.13 33.52 3.20
940 941 3.004106 GCAAGAGCAAAATGTGTCACTCT 59.996 43.478 4.27 0.00 41.58 3.24
941 942 3.303406 GCAAGAGCAAAATGTGTCACTC 58.697 45.455 4.27 0.00 41.58 3.51
955 956 5.098211 GGAGTATGACAAATTTGCAAGAGC 58.902 41.667 18.12 4.86 42.57 4.09
956 957 6.258230 TGGAGTATGACAAATTTGCAAGAG 57.742 37.500 18.12 0.00 0.00 2.85
958 959 7.318141 AGAATGGAGTATGACAAATTTGCAAG 58.682 34.615 18.12 0.00 0.00 4.01
959 960 7.230849 AGAATGGAGTATGACAAATTTGCAA 57.769 32.000 18.12 6.96 0.00 4.08
960 961 6.839124 AGAATGGAGTATGACAAATTTGCA 57.161 33.333 18.12 16.14 0.00 4.08
962 963 7.128331 CGCTAGAATGGAGTATGACAAATTTG 58.872 38.462 16.67 16.67 0.00 2.32
963 964 6.238484 GCGCTAGAATGGAGTATGACAAATTT 60.238 38.462 0.00 0.00 0.00 1.82
964 965 5.237344 GCGCTAGAATGGAGTATGACAAATT 59.763 40.000 0.00 0.00 0.00 1.82
965 966 4.752101 GCGCTAGAATGGAGTATGACAAAT 59.248 41.667 0.00 0.00 0.00 2.32
966 967 4.119862 GCGCTAGAATGGAGTATGACAAA 58.880 43.478 0.00 0.00 0.00 2.83
967 968 3.717707 GCGCTAGAATGGAGTATGACAA 58.282 45.455 0.00 0.00 0.00 3.18
968 969 2.287608 CGCGCTAGAATGGAGTATGACA 60.288 50.000 5.56 0.00 0.00 3.58
969 970 2.031069 TCGCGCTAGAATGGAGTATGAC 60.031 50.000 5.56 0.00 0.00 3.06
987 988 0.664166 CAGCCATTGTGGTTGTTCGC 60.664 55.000 4.85 0.00 42.83 4.70
988 989 3.477504 CAGCCATTGTGGTTGTTCG 57.522 52.632 4.85 0.00 42.83 3.95
997 998 2.282958 AGCAGCAGCAGCCATTGT 60.283 55.556 6.10 0.00 45.49 2.71
1502 12424 4.202326 ACGGAGAAAAGTACAACTGTGGAT 60.202 41.667 0.00 0.00 0.00 3.41
1522 12458 4.457603 TCATGTCCAAAACTCCAAATACGG 59.542 41.667 0.00 0.00 0.00 4.02
1554 12515 3.116531 GTTCCCTGCGTACGTGGC 61.117 66.667 17.90 1.72 0.00 5.01
2173 13164 1.911269 TACGGCCAGCAGAGGAACA 60.911 57.895 2.24 0.00 0.00 3.18
2234 13225 4.292145 TTGATGCCGGTGCCCCAA 62.292 61.111 1.90 0.00 36.33 4.12
2279 13271 0.181587 TCTCGATCTCCTCCTTCGCT 59.818 55.000 0.00 0.00 33.08 4.93
2408 13400 2.590821 AGCAAATCCACAAGCTTGAGT 58.409 42.857 32.50 8.75 32.52 3.41
2431 13423 1.722034 GTGATGGGATCCCTGCTCTA 58.278 55.000 31.05 10.70 36.94 2.43
2449 13441 2.019951 GTGATTCACGCGGTGTCGT 61.020 57.895 12.47 0.00 44.35 4.34
2463 13456 1.515954 GATGTCCCGGTGTCGTGAT 59.484 57.895 0.00 0.00 33.95 3.06
2474 13467 3.148279 AGAGCCGTCCGATGTCCC 61.148 66.667 0.00 0.00 0.00 4.46
2475 13468 1.945354 TTCAGAGCCGTCCGATGTCC 61.945 60.000 0.00 0.00 0.00 4.02
2554 13548 5.420725 TGCTCACCACTTCACTATATTGT 57.579 39.130 0.00 0.00 0.00 2.71
2555 13549 5.237996 CCATGCTCACCACTTCACTATATTG 59.762 44.000 0.00 0.00 0.00 1.90
2556 13550 5.371526 CCATGCTCACCACTTCACTATATT 58.628 41.667 0.00 0.00 0.00 1.28
2606 13602 8.432110 AGTAATTCCCAACATGAAAACAAAAC 57.568 30.769 0.00 0.00 0.00 2.43
2611 13607 6.799925 CGTGTAGTAATTCCCAACATGAAAAC 59.200 38.462 0.00 0.00 30.35 2.43
2629 13625 3.695060 CCATAGGACAGTCTTCGTGTAGT 59.305 47.826 0.00 0.00 0.00 2.73
2635 13631 0.105039 GGCCCATAGGACAGTCTTCG 59.895 60.000 0.00 0.00 43.07 3.79
2648 13644 2.658064 CCAAAACGCCATGGCCCAT 61.658 57.895 30.79 14.05 37.98 4.00
2649 13645 2.715181 TACCAAAACGCCATGGCCCA 62.715 55.000 30.79 4.24 40.51 5.36
2650 13646 1.326951 ATACCAAAACGCCATGGCCC 61.327 55.000 30.79 5.10 40.51 5.80
2651 13647 0.534873 AATACCAAAACGCCATGGCC 59.465 50.000 30.79 13.37 40.51 5.36
2652 13648 2.378445 AAATACCAAAACGCCATGGC 57.622 45.000 27.67 27.67 40.51 4.40
2653 13649 4.310769 TCAAAAATACCAAAACGCCATGG 58.689 39.130 7.63 7.63 42.60 3.66
2654 13650 4.987912 ACTCAAAAATACCAAAACGCCATG 59.012 37.500 0.00 0.00 0.00 3.66
2761 13760 6.673106 TGCAGTAATTTCGCTCAAAAATGTA 58.327 32.000 0.00 0.00 0.00 2.29
2763 13762 6.463478 CATGCAGTAATTTCGCTCAAAAATG 58.537 36.000 0.00 0.00 0.00 2.32
2786 13785 4.797868 CAGATTGAAAAGAAACGTTGTGCA 59.202 37.500 0.00 0.00 0.00 4.57
2791 13790 5.277634 CGTACCCAGATTGAAAAGAAACGTT 60.278 40.000 0.00 0.00 0.00 3.99
2832 13831 4.594123 TTGTCCTGACACATTAGTTCGA 57.406 40.909 0.00 0.00 41.67 3.71
2839 13838 6.183360 ACGTACAATTTTTGTCCTGACACATT 60.183 34.615 0.00 0.00 44.12 2.71
2867 13866 4.690122 AGTTTGGCTATACGTATGACACC 58.310 43.478 18.37 13.24 0.00 4.16
2885 13884 6.263617 TGTGTTTCCCGCTTAAAATAGAGTTT 59.736 34.615 0.00 0.00 0.00 2.66
2897 13896 3.611530 CGAATTCATTGTGTTTCCCGCTT 60.612 43.478 6.22 0.00 0.00 4.68
2901 13900 2.673893 GCCCGAATTCATTGTGTTTCCC 60.674 50.000 6.22 0.00 0.00 3.97
2948 13948 3.648009 GTCATCTTCATCCTCATCCGAC 58.352 50.000 0.00 0.00 0.00 4.79
2949 13949 2.294512 CGTCATCTTCATCCTCATCCGA 59.705 50.000 0.00 0.00 0.00 4.55
2960 13960 1.999735 GCCGTTTCATCGTCATCTTCA 59.000 47.619 0.00 0.00 0.00 3.02
3156 14158 0.039035 GACACCAAATGCCACCCCTA 59.961 55.000 0.00 0.00 0.00 3.53
3192 14194 0.667487 ATGTTCGTGGACAGCAGTCG 60.667 55.000 2.90 0.00 45.92 4.18
3207 14209 3.627577 GGCATCCGATGACACTAAATGTT 59.372 43.478 12.79 0.00 43.56 2.71
3266 14268 2.367030 TGGAAATGGCAATGCTTTCG 57.633 45.000 4.82 0.00 31.21 3.46
3272 14274 4.336993 CCAAATTGGATGGAAATGGCAATG 59.663 41.667 6.04 0.00 40.96 2.82
3275 14277 3.630892 CCAAATTGGATGGAAATGGCA 57.369 42.857 6.04 0.00 40.96 4.92
3276 14278 2.291365 GCCAAATTGGATGGAAATGGC 58.709 47.619 17.47 0.00 40.96 4.40
3277 14279 2.553086 CGCCAAATTGGATGGAAATGG 58.447 47.619 17.47 0.00 40.96 3.16
3279 14281 1.832998 AGCGCCAAATTGGATGGAAAT 59.167 42.857 17.47 0.00 40.96 2.17
3280 14282 1.067000 CAGCGCCAAATTGGATGGAAA 60.067 47.619 17.47 0.00 40.96 3.13
3283 14285 1.519898 GCAGCGCCAAATTGGATGG 60.520 57.895 17.47 5.02 40.96 3.51
3299 14302 0.322975 GGTTCTGAGAAGGCTGAGCA 59.677 55.000 6.82 0.00 0.00 4.26
3328 14331 2.691011 AGTCACCGATTCTAAGGAGCTC 59.309 50.000 4.71 4.71 0.00 4.09
3333 14336 2.969628 AGCAGTCACCGATTCTAAGG 57.030 50.000 0.00 0.00 0.00 2.69
3343 14346 7.859325 TTCTTAACCATTATAAGCAGTCACC 57.141 36.000 0.00 0.00 31.77 4.02
3387 14390 4.684242 GTGTGATCGACATGTGTAGTTTCA 59.316 41.667 1.15 0.71 36.78 2.69
3416 14419 1.279271 ACAGGGCAGGAAGTACATGTC 59.721 52.381 0.00 0.00 33.94 3.06
3420 14423 1.656587 ATCACAGGGCAGGAAGTACA 58.343 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.