Multiple sequence alignment - TraesCS4B01G124300

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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 TraesCS4B01G124300 chr4B 100.000 3944 0 0 1 3944 149713526 149717469 0.000000e+00 7284
1 TraesCS4B01G124300 chr4B 89.691 97 9 1 602 698 496549861 496549956 5.350000e-24 122
2 TraesCS4B01G124300 chr4A 93.835 1622 60 10 703 2316 470138447 470136858 0.000000e+00 2405
3 TraesCS4B01G124300 chr4A 98.600 643 9 0 2405 3047 470136839 470136197 0.000000e+00 1138
4 TraesCS4B01G124300 chr4A 92.763 608 14 3 2720 3303 470134113 470133512 0.000000e+00 852
5 TraesCS4B01G124300 chr4A 87.407 135 16 1 3356 3490 100122594 100122727 1.900000e-33 154
6 TraesCS4B01G124300 chr4D 93.316 1496 57 19 824 2316 105897574 105899029 0.000000e+00 2169
7 TraesCS4B01G124300 chr4D 98.326 657 11 0 2405 3061 105899048 105899704 0.000000e+00 1153
8 TraesCS4B01G124300 chr4D 89.171 748 40 5 3043 3790 105899746 105900452 0.000000e+00 894
9 TraesCS4B01G124300 chr4D 89.984 619 53 9 1 614 105896869 105897483 0.000000e+00 791
10 TraesCS4B01G124300 chr4D 84.702 621 82 12 1 614 105895784 105896398 3.370000e-170 608
11 TraesCS4B01G124300 chr4D 95.000 160 7 1 3786 3944 105904360 105904519 2.350000e-62 250
12 TraesCS4B01G124300 chr4D 83.658 257 27 4 696 941 105896397 105896649 1.100000e-55 228
13 TraesCS4B01G124300 chr4D 85.333 150 19 3 3344 3490 481792069 481792218 6.830000e-33 152
14 TraesCS4B01G124300 chr2D 85.673 342 46 3 3333 3672 474180142 474180482 1.350000e-94 357
15 TraesCS4B01G124300 chr2D 92.683 82 6 0 2315 2396 525600399 525600480 6.920000e-23 119
16 TraesCS4B01G124300 chr7A 88.028 142 16 1 3356 3496 721664409 721664550 2.440000e-37 167
17 TraesCS4B01G124300 chr5A 84.177 158 22 3 3332 3488 664491340 664491185 2.460000e-32 150
18 TraesCS4B01G124300 chr5A 85.039 127 18 1 3364 3490 693131970 693131845 1.150000e-25 128
19 TraesCS4B01G124300 chr5A 92.683 82 6 0 2315 2396 446318191 446318272 6.920000e-23 119
20 TraesCS4B01G124300 chr5A 89.247 93 10 0 609 701 302308523 302308431 2.490000e-22 117
21 TraesCS4B01G124300 chr5A 89.247 93 10 0 612 704 555623048 555622956 2.490000e-22 117
22 TraesCS4B01G124300 chr7D 86.260 131 17 1 3368 3497 626054690 626054820 1.480000e-29 141
23 TraesCS4B01G124300 chr7B 91.398 93 8 0 613 705 14062895 14062803 1.150000e-25 128
24 TraesCS4B01G124300 chr1D 82.759 145 22 2 3347 3490 431815653 431815511 4.140000e-25 126
25 TraesCS4B01G124300 chr1D 92.941 85 6 0 613 697 291791958 291792042 1.490000e-24 124
26 TraesCS4B01G124300 chr1D 92.683 82 6 0 2315 2396 194875459 194875540 6.920000e-23 119
27 TraesCS4B01G124300 chr6D 93.902 82 5 0 2315 2396 190909275 190909356 1.490000e-24 124
28 TraesCS4B01G124300 chr6D 90.805 87 8 0 2315 2401 142577112 142577026 2.490000e-22 117
29 TraesCS4B01G124300 chr3D 92.683 82 6 0 2315 2396 429950710 429950791 6.920000e-23 119
30 TraesCS4B01G124300 chr3B 91.765 85 7 0 2315 2399 539241229 539241145 6.920000e-23 119
31 TraesCS4B01G124300 chr3B 88.660 97 8 3 603 697 340781503 340781408 8.960000e-22 115
32 TraesCS4B01G124300 chr3B 84.545 110 17 0 599 708 277392838 277392947 4.170000e-20 110
33 TraesCS4B01G124300 chr5D 90.805 87 8 0 2315 2401 118417913 118417999 2.490000e-22 117
34 TraesCS4B01G124300 chr5D 88.660 97 9 2 612 707 381563918 381563823 2.490000e-22 117
35 TraesCS4B01G124300 chr5B 87.500 104 9 4 606 708 689103485 689103385 2.490000e-22 117
36 TraesCS4B01G124300 chr1A 88.172 93 11 0 2308 2400 474384741 474384833 1.160000e-20 111


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 TraesCS4B01G124300 chr4B 149713526 149717469 3943 False 7284.000000 7284 100.000000 1 3944 1 chr4B.!!$F1 3943
1 TraesCS4B01G124300 chr4A 470133512 470138447 4935 True 1465.000000 2405 95.066000 703 3303 3 chr4A.!!$R1 2600
2 TraesCS4B01G124300 chr4D 105895784 105904519 8735 False 870.428571 2169 90.593857 1 3944 7 chr4D.!!$F2 3943

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
435 1524 0.965363 AATCCCCGTTGCCACATGTC 60.965 55.0 0.0 0.0 0.0 3.06 F
1530 2622 0.251386 AGTCCTTCTGCACGGAGAGA 60.251 55.0 0.0 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 3441 0.035458 AGGCTAGCTTGCAGAAACGT 59.965 50.0 21.53 0.00 34.04 3.99 R
3232 6763 0.107312 GATGATGGTGGCTGTCAGCT 60.107 55.0 23.68 3.88 43.76 4.24 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
51 1137 7.854557 TGGATAATCTTGTTTGAGTGATCTG 57.145 36.000 0.00 0.00 0.00 2.90
75 1161 8.862325 TGTTTATGTATGTGAATCCACTTCTT 57.138 30.769 0.00 0.00 43.55 2.52
88 1174 6.727824 ATCCACTTCTTATGTTGTTTCTCG 57.272 37.500 0.00 0.00 0.00 4.04
93 1179 7.284351 CACTTCTTATGTTGTTTCTCGACTTC 58.716 38.462 0.00 0.00 0.00 3.01
186 1273 3.788227 TCTACCAACAGAGGCATTGTT 57.212 42.857 1.39 1.39 39.23 2.83
191 1278 2.361757 CCAACAGAGGCATTGTTTGACA 59.638 45.455 4.19 0.00 36.67 3.58
210 1297 3.422796 ACACAGTCAGAGTCGGTCTTAT 58.577 45.455 0.00 0.00 30.64 1.73
212 1299 3.440522 CACAGTCAGAGTCGGTCTTATCA 59.559 47.826 0.00 0.00 30.64 2.15
215 1302 2.423892 GTCAGAGTCGGTCTTATCAGCA 59.576 50.000 0.00 0.00 30.64 4.41
218 1305 3.614616 CAGAGTCGGTCTTATCAGCAAAC 59.385 47.826 0.00 0.00 30.64 2.93
220 1307 2.567615 AGTCGGTCTTATCAGCAAACCT 59.432 45.455 0.00 0.00 0.00 3.50
331 1419 2.636647 TGTCCAATGAGTGCTTGTCA 57.363 45.000 0.00 0.00 0.00 3.58
332 1420 2.497138 TGTCCAATGAGTGCTTGTCAG 58.503 47.619 0.00 0.00 0.00 3.51
381 1470 1.423845 GCAACTTGTCGCCATACGG 59.576 57.895 0.00 0.00 43.89 4.02
423 1512 8.561738 AAACATAGTATAGCATTTAATCCCCG 57.438 34.615 0.00 0.00 0.00 5.73
430 1519 1.470805 GCATTTAATCCCCGTTGCCAC 60.471 52.381 0.00 0.00 0.00 5.01
435 1524 0.965363 AATCCCCGTTGCCACATGTC 60.965 55.000 0.00 0.00 0.00 3.06
436 1525 2.837031 ATCCCCGTTGCCACATGTCC 62.837 60.000 0.00 0.00 0.00 4.02
439 1528 2.034066 CGTTGCCACATGTCCCCT 59.966 61.111 0.00 0.00 0.00 4.79
495 1586 9.881649 TTAGCCATTTGATTAATGCAATACAAA 57.118 25.926 0.00 0.36 41.93 2.83
497 1588 7.011669 AGCCATTTGATTAATGCAATACAAAGC 59.988 33.333 0.00 1.65 41.93 3.51
552 1643 6.710744 ACATTAACACGACCTCAAATCTCTTT 59.289 34.615 0.00 0.00 0.00 2.52
563 1654 4.330250 TCAAATCTCTTTGAGGCTTCCAG 58.670 43.478 0.00 0.00 44.46 3.86
568 1659 5.599999 TCTCTTTGAGGCTTCCAGTATAC 57.400 43.478 0.00 0.00 0.00 1.47
572 1663 5.361285 TCTTTGAGGCTTCCAGTATACTCTC 59.639 44.000 1.26 6.27 0.00 3.20
591 1682 9.706691 ATACTCTCTCACTTATTTTTCGTTTCA 57.293 29.630 0.00 0.00 0.00 2.69
614 1705 8.932945 TCATCTAGACTTCATGTGTCATTTAC 57.067 34.615 18.44 0.00 36.94 2.01
616 1707 9.029243 CATCTAGACTTCATGTGTCATTTACTC 57.971 37.037 18.44 0.00 36.94 2.59
619 1710 5.249393 AGACTTCATGTGTCATTTACTCCCT 59.751 40.000 18.44 0.00 36.94 4.20
620 1711 5.491982 ACTTCATGTGTCATTTACTCCCTC 58.508 41.667 0.00 0.00 0.00 4.30
621 1712 4.487714 TCATGTGTCATTTACTCCCTCC 57.512 45.455 0.00 0.00 0.00 4.30
622 1713 3.118775 TCATGTGTCATTTACTCCCTCCG 60.119 47.826 0.00 0.00 0.00 4.63
623 1714 2.253610 TGTGTCATTTACTCCCTCCGT 58.746 47.619 0.00 0.00 0.00 4.69
624 1715 2.232941 TGTGTCATTTACTCCCTCCGTC 59.767 50.000 0.00 0.00 0.00 4.79
625 1716 1.829222 TGTCATTTACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
626 1717 1.138464 GTCATTTACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
627 1718 1.200519 CATTTACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
628 1719 1.557832 CATTTACTCCCTCCGTCCCAA 59.442 52.381 0.00 0.00 0.00 4.12
629 1720 1.732117 TTTACTCCCTCCGTCCCAAA 58.268 50.000 0.00 0.00 0.00 3.28
630 1721 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
631 1722 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
632 1723 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
633 1724 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
634 1725 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
635 1726 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
636 1727 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
637 1728 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
638 1729 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
639 1730 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
640 1731 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
641 1732 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
642 1733 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
643 1734 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
644 1735 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
645 1736 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
646 1737 7.061326 CCGTCCCAAAATATAAGAACGTTTTTG 59.939 37.037 13.87 12.16 37.14 2.44
647 1738 7.804129 CGTCCCAAAATATAAGAACGTTTTTGA 59.196 33.333 13.87 2.81 38.79 2.69
648 1739 8.908678 GTCCCAAAATATAAGAACGTTTTTGAC 58.091 33.333 13.87 5.89 38.79 3.18
649 1740 8.630917 TCCCAAAATATAAGAACGTTTTTGACA 58.369 29.630 13.87 0.01 38.79 3.58
650 1741 9.418045 CCCAAAATATAAGAACGTTTTTGACAT 57.582 29.630 13.87 2.89 38.79 3.06
687 1778 8.644619 TCAAAAACGTTCTTATATCTTGAGACG 58.355 33.333 0.00 0.00 0.00 4.18
688 1779 6.570690 AAACGTTCTTATATCTTGAGACGC 57.429 37.500 0.00 0.00 0.00 5.19
689 1780 5.244785 ACGTTCTTATATCTTGAGACGCA 57.755 39.130 0.00 0.00 0.00 5.24
690 1781 5.274718 ACGTTCTTATATCTTGAGACGCAG 58.725 41.667 0.00 0.00 0.00 5.18
691 1782 4.677378 CGTTCTTATATCTTGAGACGCAGG 59.323 45.833 0.00 0.00 0.00 4.85
692 1783 4.855715 TCTTATATCTTGAGACGCAGGG 57.144 45.455 0.00 0.00 0.00 4.45
693 1784 4.470602 TCTTATATCTTGAGACGCAGGGA 58.529 43.478 0.00 0.00 0.00 4.20
694 1785 4.520874 TCTTATATCTTGAGACGCAGGGAG 59.479 45.833 0.00 0.00 0.00 4.30
695 1786 2.145397 TATCTTGAGACGCAGGGAGT 57.855 50.000 0.00 0.00 0.00 3.85
696 1787 2.145397 ATCTTGAGACGCAGGGAGTA 57.855 50.000 0.00 0.00 0.00 2.59
697 1788 1.464734 TCTTGAGACGCAGGGAGTAG 58.535 55.000 0.00 0.00 0.00 2.57
698 1789 1.004394 TCTTGAGACGCAGGGAGTAGA 59.996 52.381 0.00 0.00 0.00 2.59
699 1790 2.028130 CTTGAGACGCAGGGAGTAGAT 58.972 52.381 0.00 0.00 0.00 1.98
700 1791 1.681538 TGAGACGCAGGGAGTAGATC 58.318 55.000 0.00 0.00 0.00 2.75
701 1792 1.213182 TGAGACGCAGGGAGTAGATCT 59.787 52.381 0.00 0.00 0.00 2.75
714 1805 7.928706 CAGGGAGTAGATCTTATGTTTCGAATT 59.071 37.037 0.00 0.00 0.00 2.17
826 1917 6.643770 AGCAGACAACAATTGCATAAGAAAAG 59.356 34.615 5.05 0.00 40.22 2.27
1009 2101 3.353029 CCACCGTCATGTTGCGCA 61.353 61.111 5.66 5.66 0.00 6.09
1329 2421 4.552365 CGGGCCATGGATGACGCT 62.552 66.667 18.40 0.00 0.00 5.07
1347 2439 0.946221 CTGGCGTCGTGCTTCTCTTT 60.946 55.000 0.00 0.00 45.43 2.52
1405 2497 5.917462 ACATTTTGCTCTTGCTAGGTTTTT 58.083 33.333 0.00 0.00 40.48 1.94
1413 2505 5.561725 GCTCTTGCTAGGTTTTTCTTCACTG 60.562 44.000 0.00 0.00 36.03 3.66
1416 2508 2.884639 GCTAGGTTTTTCTTCACTGGCA 59.115 45.455 0.00 0.00 35.96 4.92
1429 2521 0.402121 ACTGGCACCTTCCCTCTTTC 59.598 55.000 0.00 0.00 0.00 2.62
1430 2522 0.674895 CTGGCACCTTCCCTCTTTCG 60.675 60.000 0.00 0.00 0.00 3.46
1431 2523 1.375326 GGCACCTTCCCTCTTTCGT 59.625 57.895 0.00 0.00 0.00 3.85
1432 2524 0.611714 GGCACCTTCCCTCTTTCGTA 59.388 55.000 0.00 0.00 0.00 3.43
1433 2525 1.675116 GGCACCTTCCCTCTTTCGTAC 60.675 57.143 0.00 0.00 0.00 3.67
1514 2606 6.848296 GCAGCATTTATTTAGTGATTCGAGTC 59.152 38.462 0.13 0.13 0.00 3.36
1518 2610 8.064814 GCATTTATTTAGTGATTCGAGTCCTTC 58.935 37.037 5.38 0.00 0.00 3.46
1530 2622 0.251386 AGTCCTTCTGCACGGAGAGA 60.251 55.000 0.00 0.00 0.00 3.10
1559 2651 3.539401 CGTGAAAGCGCAAACTTTTTGAC 60.539 43.478 11.47 3.49 39.93 3.18
1565 2657 5.091910 AGCGCAAACTTTTTGACTACTAC 57.908 39.130 11.47 0.00 0.00 2.73
1628 2724 9.698309 CACTAATTTACCAGATCACTACATAGG 57.302 37.037 0.00 0.00 0.00 2.57
1639 2735 8.424918 CAGATCACTACATAGGTTGAATAGGTT 58.575 37.037 0.00 0.00 0.00 3.50
1711 2807 7.495901 TGCAATTTCATTCACCTCAGTTTTTA 58.504 30.769 0.00 0.00 0.00 1.52
1712 2808 8.149647 TGCAATTTCATTCACCTCAGTTTTTAT 58.850 29.630 0.00 0.00 0.00 1.40
1713 2809 8.992073 GCAATTTCATTCACCTCAGTTTTTATT 58.008 29.630 0.00 0.00 0.00 1.40
1717 2813 8.795786 TTCATTCACCTCAGTTTTTATTTTCG 57.204 30.769 0.00 0.00 0.00 3.46
1718 2814 7.367285 TCATTCACCTCAGTTTTTATTTTCGG 58.633 34.615 0.00 0.00 0.00 4.30
1719 2815 5.116069 TCACCTCAGTTTTTATTTTCGGC 57.884 39.130 0.00 0.00 0.00 5.54
1720 2816 4.022676 TCACCTCAGTTTTTATTTTCGGCC 60.023 41.667 0.00 0.00 0.00 6.13
1721 2817 4.022329 CACCTCAGTTTTTATTTTCGGCCT 60.022 41.667 0.00 0.00 0.00 5.19
1722 2818 5.182380 CACCTCAGTTTTTATTTTCGGCCTA 59.818 40.000 0.00 0.00 0.00 3.93
1723 2819 5.949952 ACCTCAGTTTTTATTTTCGGCCTAT 59.050 36.000 0.00 0.00 0.00 2.57
1724 2820 7.066525 CACCTCAGTTTTTATTTTCGGCCTATA 59.933 37.037 0.00 0.00 0.00 1.31
1725 2821 7.612633 ACCTCAGTTTTTATTTTCGGCCTATAA 59.387 33.333 0.00 0.00 0.00 0.98
1726 2822 8.630037 CCTCAGTTTTTATTTTCGGCCTATAAT 58.370 33.333 0.00 0.00 0.00 1.28
1768 2864 4.826733 TGTATGTATTGGGGTCATGCATTC 59.173 41.667 0.00 0.00 31.53 2.67
1799 2895 3.094062 GCTGCGCCATAGGGAGTCA 62.094 63.158 4.18 0.00 36.19 3.41
1800 2896 1.750930 CTGCGCCATAGGGAGTCAT 59.249 57.895 4.18 0.00 36.19 3.06
1817 2913 4.871993 GTCATGTAGACTGATTTGCTGG 57.128 45.455 0.00 0.00 44.09 4.85
1820 2916 1.009829 GTAGACTGATTTGCTGGCCG 58.990 55.000 0.00 0.00 0.00 6.13
1824 2920 1.064654 GACTGATTTGCTGGCCGAATC 59.935 52.381 0.00 6.16 42.41 2.52
1833 2932 4.350368 TGCTGGCCGAATCAATTAGATA 57.650 40.909 0.00 0.00 35.39 1.98
2168 3270 1.471287 CAAGCATCCACCTCACATGTG 59.529 52.381 20.18 20.18 0.00 3.21
2192 3294 8.664798 GTGGGCAATAAATCCAAAAACTTTATC 58.335 33.333 0.00 0.00 31.73 1.75
2294 3396 6.208644 ACTTTGAAATCTTTTGTGGTGATCG 58.791 36.000 0.00 0.00 0.00 3.69
2295 3397 5.766150 TTGAAATCTTTTGTGGTGATCGT 57.234 34.783 0.00 0.00 0.00 3.73
2316 3418 7.585286 TCGTTTATGTATGGTTGTGAGTTAC 57.415 36.000 0.00 0.00 0.00 2.50
2318 3420 7.543172 TCGTTTATGTATGGTTGTGAGTTACTC 59.457 37.037 5.27 5.27 0.00 2.59
2319 3421 7.201496 CGTTTATGTATGGTTGTGAGTTACTCC 60.201 40.741 10.10 2.16 0.00 3.85
2320 3422 4.546829 TGTATGGTTGTGAGTTACTCCC 57.453 45.455 10.10 4.29 0.00 4.30
2322 3424 3.983044 ATGGTTGTGAGTTACTCCCTC 57.017 47.619 10.10 1.62 0.00 4.30
2323 3425 2.972348 TGGTTGTGAGTTACTCCCTCT 58.028 47.619 10.10 0.00 0.00 3.69
2325 3427 2.633481 GGTTGTGAGTTACTCCCTCTGT 59.367 50.000 10.10 0.00 0.00 3.41
2326 3428 3.306156 GGTTGTGAGTTACTCCCTCTGTC 60.306 52.174 10.10 0.00 0.00 3.51
2327 3429 2.526432 TGTGAGTTACTCCCTCTGTCC 58.474 52.381 10.10 0.00 0.00 4.02
2328 3430 1.826096 GTGAGTTACTCCCTCTGTCCC 59.174 57.143 10.10 0.00 0.00 4.46
2329 3431 1.431633 TGAGTTACTCCCTCTGTCCCA 59.568 52.381 10.10 0.00 0.00 4.37
2330 3432 1.826096 GAGTTACTCCCTCTGTCCCAC 59.174 57.143 0.00 0.00 0.00 4.61
2331 3433 1.149288 AGTTACTCCCTCTGTCCCACA 59.851 52.381 0.00 0.00 0.00 4.17
2332 3434 1.975680 GTTACTCCCTCTGTCCCACAA 59.024 52.381 0.00 0.00 0.00 3.33
2333 3435 2.572104 GTTACTCCCTCTGTCCCACAAT 59.428 50.000 0.00 0.00 0.00 2.71
2334 3436 2.642171 ACTCCCTCTGTCCCACAATA 57.358 50.000 0.00 0.00 0.00 1.90
2335 3437 3.136641 ACTCCCTCTGTCCCACAATAT 57.863 47.619 0.00 0.00 0.00 1.28
2336 3438 4.280789 ACTCCCTCTGTCCCACAATATA 57.719 45.455 0.00 0.00 0.00 0.86
2337 3439 4.631234 ACTCCCTCTGTCCCACAATATAA 58.369 43.478 0.00 0.00 0.00 0.98
2338 3440 4.409247 ACTCCCTCTGTCCCACAATATAAC 59.591 45.833 0.00 0.00 0.00 1.89
2339 3441 4.367166 TCCCTCTGTCCCACAATATAACA 58.633 43.478 0.00 0.00 0.00 2.41
2340 3442 4.163458 TCCCTCTGTCCCACAATATAACAC 59.837 45.833 0.00 0.00 0.00 3.32
2341 3443 4.119862 CCTCTGTCCCACAATATAACACG 58.880 47.826 0.00 0.00 0.00 4.49
2342 3444 4.382685 CCTCTGTCCCACAATATAACACGT 60.383 45.833 0.00 0.00 0.00 4.49
2343 3445 5.155278 TCTGTCCCACAATATAACACGTT 57.845 39.130 0.00 0.00 0.00 3.99
2344 3446 5.553123 TCTGTCCCACAATATAACACGTTT 58.447 37.500 0.00 0.00 0.00 3.60
2345 3447 5.640357 TCTGTCCCACAATATAACACGTTTC 59.360 40.000 0.00 0.00 0.00 2.78
2346 3448 5.553123 TGTCCCACAATATAACACGTTTCT 58.447 37.500 0.00 0.00 0.00 2.52
2347 3449 5.410132 TGTCCCACAATATAACACGTTTCTG 59.590 40.000 0.00 0.00 0.00 3.02
2348 3450 4.393680 TCCCACAATATAACACGTTTCTGC 59.606 41.667 0.00 0.00 0.00 4.26
2349 3451 4.155099 CCCACAATATAACACGTTTCTGCA 59.845 41.667 0.00 0.00 0.00 4.41
2350 3452 5.335269 CCCACAATATAACACGTTTCTGCAA 60.335 40.000 0.00 0.00 0.00 4.08
2351 3453 5.794945 CCACAATATAACACGTTTCTGCAAG 59.205 40.000 0.00 0.00 0.00 4.01
2352 3454 5.283717 CACAATATAACACGTTTCTGCAAGC 59.716 40.000 0.00 0.00 0.00 4.01
2353 3455 5.181245 ACAATATAACACGTTTCTGCAAGCT 59.819 36.000 0.00 0.00 0.00 3.74
2354 3456 6.370442 ACAATATAACACGTTTCTGCAAGCTA 59.630 34.615 0.00 0.00 0.00 3.32
2355 3457 4.928661 ATAACACGTTTCTGCAAGCTAG 57.071 40.909 0.00 0.00 0.00 3.42
2356 3458 0.868406 ACACGTTTCTGCAAGCTAGC 59.132 50.000 6.62 6.62 0.00 3.42
2357 3459 0.166814 CACGTTTCTGCAAGCTAGCC 59.833 55.000 12.13 0.00 0.00 3.93
2358 3460 0.035458 ACGTTTCTGCAAGCTAGCCT 59.965 50.000 12.13 0.00 0.00 4.58
2359 3461 1.275291 ACGTTTCTGCAAGCTAGCCTA 59.725 47.619 12.13 0.00 0.00 3.93
2360 3462 1.929836 CGTTTCTGCAAGCTAGCCTAG 59.070 52.381 12.13 4.98 0.00 3.02
2373 3475 4.708726 CTAGCCTAGCTTGCAAAAACAT 57.291 40.909 0.00 0.00 40.44 2.71
2374 3476 3.582714 AGCCTAGCTTGCAAAAACATC 57.417 42.857 0.00 0.00 33.89 3.06
2375 3477 3.160269 AGCCTAGCTTGCAAAAACATCT 58.840 40.909 0.00 0.00 33.89 2.90
2376 3478 3.575687 AGCCTAGCTTGCAAAAACATCTT 59.424 39.130 0.00 0.00 33.89 2.40
2377 3479 4.766891 AGCCTAGCTTGCAAAAACATCTTA 59.233 37.500 0.00 0.00 33.89 2.10
2378 3480 5.420104 AGCCTAGCTTGCAAAAACATCTTAT 59.580 36.000 0.00 0.00 33.89 1.73
2379 3481 6.603201 AGCCTAGCTTGCAAAAACATCTTATA 59.397 34.615 0.00 0.00 33.89 0.98
2380 3482 7.286316 AGCCTAGCTTGCAAAAACATCTTATAT 59.714 33.333 0.00 0.00 33.89 0.86
2381 3483 7.922811 GCCTAGCTTGCAAAAACATCTTATATT 59.077 33.333 0.00 0.00 0.00 1.28
2385 3487 9.754382 AGCTTGCAAAAACATCTTATATTATGG 57.246 29.630 0.00 0.00 0.00 2.74
2386 3488 8.981647 GCTTGCAAAAACATCTTATATTATGGG 58.018 33.333 0.00 0.00 0.00 4.00
2389 3491 8.349245 TGCAAAAACATCTTATATTATGGGACG 58.651 33.333 0.00 0.00 0.00 4.79
2390 3492 7.807907 GCAAAAACATCTTATATTATGGGACGG 59.192 37.037 0.00 0.00 0.00 4.79
2391 3493 9.062524 CAAAAACATCTTATATTATGGGACGGA 57.937 33.333 0.00 0.00 0.00 4.69
2392 3494 8.848474 AAAACATCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
2393 3495 6.546428 ACATCTTATATTATGGGACGGAGG 57.454 41.667 0.00 0.00 0.00 4.30
2394 3496 5.425539 ACATCTTATATTATGGGACGGAGGG 59.574 44.000 0.00 0.00 0.00 4.30
2395 3497 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2396 3498 5.657446 TCTTATATTATGGGACGGAGGGAA 58.343 41.667 0.00 0.00 0.00 3.97
2397 3499 6.269194 TCTTATATTATGGGACGGAGGGAAT 58.731 40.000 0.00 0.00 0.00 3.01
2398 3500 7.424172 TCTTATATTATGGGACGGAGGGAATA 58.576 38.462 0.00 0.00 0.00 1.75
2399 3501 8.071854 TCTTATATTATGGGACGGAGGGAATAT 58.928 37.037 0.00 0.00 0.00 1.28
2400 3502 6.749036 ATATTATGGGACGGAGGGAATATC 57.251 41.667 0.00 0.00 0.00 1.63
2401 3503 2.723530 ATGGGACGGAGGGAATATCT 57.276 50.000 0.00 0.00 0.00 1.98
2402 3504 1.717032 TGGGACGGAGGGAATATCTG 58.283 55.000 0.00 0.00 0.00 2.90
2403 3505 0.977395 GGGACGGAGGGAATATCTGG 59.023 60.000 0.00 0.00 0.00 3.86
2443 3545 0.598065 AAAAGGCGGACATGCAGTTC 59.402 50.000 0.00 0.00 36.28 3.01
2647 3749 2.912956 ACTGGCTTAGGGTTCTTCATGA 59.087 45.455 0.00 0.00 0.00 3.07
2903 4005 1.376466 GCAAGTGCCCTCTGGAAGA 59.624 57.895 0.00 0.00 36.11 2.87
3322 6860 8.877864 TGTAAACAGGATACAAATTTGGAGAT 57.122 30.769 21.74 11.80 41.41 2.75
3323 6861 8.739039 TGTAAACAGGATACAAATTTGGAGATG 58.261 33.333 21.74 14.93 41.41 2.90
3324 6862 7.781324 AAACAGGATACAAATTTGGAGATGT 57.219 32.000 21.74 15.51 41.41 3.06
3325 6863 8.877864 AAACAGGATACAAATTTGGAGATGTA 57.122 30.769 21.74 5.57 41.41 2.29
3326 6864 8.877864 AACAGGATACAAATTTGGAGATGTAA 57.122 30.769 21.74 0.00 41.41 2.41
3327 6865 8.877864 ACAGGATACAAATTTGGAGATGTAAA 57.122 30.769 21.74 0.00 41.41 2.01
3328 6866 8.739972 ACAGGATACAAATTTGGAGATGTAAAC 58.260 33.333 21.74 3.29 41.41 2.01
3329 6867 8.739039 CAGGATACAAATTTGGAGATGTAAACA 58.261 33.333 21.74 0.00 41.41 2.83
3330 6868 8.960591 AGGATACAAATTTGGAGATGTAAACAG 58.039 33.333 21.74 0.00 41.41 3.16
3331 6869 8.190784 GGATACAAATTTGGAGATGTAAACAGG 58.809 37.037 21.74 0.00 32.53 4.00
3332 6870 8.877864 ATACAAATTTGGAGATGTAAACAGGA 57.122 30.769 21.74 0.00 32.53 3.86
3333 6871 7.781324 ACAAATTTGGAGATGTAAACAGGAT 57.219 32.000 21.74 0.00 0.00 3.24
3334 6872 8.877864 ACAAATTTGGAGATGTAAACAGGATA 57.122 30.769 21.74 0.00 0.00 2.59
3335 6873 8.739972 ACAAATTTGGAGATGTAAACAGGATAC 58.260 33.333 21.74 0.00 0.00 2.24
3336 6874 8.739039 CAAATTTGGAGATGTAAACAGGATACA 58.261 33.333 10.49 0.00 37.64 2.29
3337 6875 8.877864 AATTTGGAGATGTAAACAGGATACAA 57.122 30.769 0.00 0.00 36.88 2.41
3338 6876 8.877864 ATTTGGAGATGTAAACAGGATACAAA 57.122 30.769 0.00 0.00 36.88 2.83
3339 6877 8.877864 TTTGGAGATGTAAACAGGATACAAAT 57.122 30.769 0.00 0.00 36.88 2.32
3340 6878 8.877864 TTGGAGATGTAAACAGGATACAAATT 57.122 30.769 0.00 0.00 36.88 1.82
3341 6879 8.877864 TGGAGATGTAAACAGGATACAAATTT 57.122 30.769 0.00 0.00 36.88 1.82
3342 6880 8.739039 TGGAGATGTAAACAGGATACAAATTTG 58.261 33.333 16.67 16.67 36.88 2.32
3343 6881 8.190784 GGAGATGTAAACAGGATACAAATTTGG 58.809 37.037 21.74 5.80 36.88 3.28
3344 6882 8.877864 AGATGTAAACAGGATACAAATTTGGA 57.122 30.769 21.74 14.66 36.88 3.53
3345 6883 9.308000 AGATGTAAACAGGATACAAATTTGGAA 57.692 29.630 21.74 10.18 36.88 3.53
3346 6884 9.921637 GATGTAAACAGGATACAAATTTGGAAA 57.078 29.630 21.74 7.74 36.88 3.13
3367 6905 9.137459 TGGAAATGTAAACAGGAGATGTAAAAA 57.863 29.630 0.00 0.00 43.00 1.94
3386 6924 9.985318 TGTAAAAATTTGCATCTTCAAAAAGTG 57.015 25.926 0.00 0.00 39.13 3.16
3387 6925 7.974243 AAAAATTTGCATCTTCAAAAAGTGC 57.026 28.000 0.00 0.00 39.13 4.40
3388 6926 6.680874 AAATTTGCATCTTCAAAAAGTGCA 57.319 29.167 9.68 9.68 42.45 4.57
3389 6927 6.870971 AATTTGCATCTTCAAAAAGTGCAT 57.129 29.167 12.67 2.10 43.02 3.96
3390 6928 6.870971 ATTTGCATCTTCAAAAAGTGCATT 57.129 29.167 12.67 0.00 43.02 3.56
3391 6929 6.680874 TTTGCATCTTCAAAAAGTGCATTT 57.319 29.167 12.67 0.00 43.02 2.32
3392 6930 6.680874 TTGCATCTTCAAAAAGTGCATTTT 57.319 29.167 0.65 0.65 43.02 1.82
3393 6931 6.050454 TGCATCTTCAAAAAGTGCATTTTG 57.950 33.333 16.12 16.12 46.66 2.44
3394 6932 4.907582 GCATCTTCAAAAAGTGCATTTTGC 59.092 37.500 17.06 7.67 45.51 3.68
3472 7010 4.232221 CAACTCCAACAGATGATGCAAAC 58.768 43.478 0.00 0.00 0.00 2.93
3494 7032 6.686130 ACGAAGATGTAAACTAGTTCAACG 57.314 37.500 8.95 10.47 0.00 4.10
3503 7041 1.705337 CTAGTTCAACGGCGGCATGG 61.705 60.000 13.24 0.00 0.00 3.66
3504 7042 2.173758 TAGTTCAACGGCGGCATGGA 62.174 55.000 13.24 0.00 0.00 3.41
3609 7147 1.270550 CGAGCCTTTGCCTTCAAATGT 59.729 47.619 0.00 0.00 40.97 2.71
3639 7177 1.956629 GCTCAAATGGCCAGCAGCAT 61.957 55.000 13.05 0.00 46.50 3.79
3672 7210 3.937062 GGCGGATTAACAGCGGCG 61.937 66.667 0.51 0.51 40.43 6.46
3673 7211 4.591317 GCGGATTAACAGCGGCGC 62.591 66.667 26.86 26.86 0.00 6.53
3700 7238 0.033601 AATTGGGCGGTGGATTAGCA 60.034 50.000 0.00 0.00 0.00 3.49
3770 7308 2.434185 GTGTGCGGCTCGAATCCA 60.434 61.111 0.00 0.00 0.00 3.41
3774 7312 0.811616 GTGCGGCTCGAATCCAGAAT 60.812 55.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.819582 CCATGCCACCCTAAAAGCAG 59.180 55.000 0.00 0.00 38.89 4.24
111 1197 3.308866 ACCGCATCGCTTCACTATTTAAC 59.691 43.478 0.00 0.00 0.00 2.01
166 1253 3.788227 AACAATGCCTCTGTTGGTAGA 57.212 42.857 0.00 0.00 35.70 2.59
170 1257 2.361757 TGTCAAACAATGCCTCTGTTGG 59.638 45.455 0.00 0.00 37.10 3.77
181 1268 3.804325 CGACTCTGACTGTGTCAAACAAT 59.196 43.478 12.96 0.00 42.26 2.71
186 1273 1.337071 GACCGACTCTGACTGTGTCAA 59.663 52.381 12.96 0.00 42.26 3.18
191 1278 3.687125 TGATAAGACCGACTCTGACTGT 58.313 45.455 0.00 0.00 0.00 3.55
210 1297 3.788227 ATAGTGGTGAAGGTTTGCTGA 57.212 42.857 0.00 0.00 0.00 4.26
212 1299 4.729868 AGAAATAGTGGTGAAGGTTTGCT 58.270 39.130 0.00 0.00 0.00 3.91
215 1302 7.839680 ATTTGAGAAATAGTGGTGAAGGTTT 57.160 32.000 0.00 0.00 0.00 3.27
218 1305 7.921786 TGTATTTGAGAAATAGTGGTGAAGG 57.078 36.000 0.00 0.00 34.23 3.46
220 1307 9.952030 TGTATGTATTTGAGAAATAGTGGTGAA 57.048 29.630 0.00 0.00 34.23 3.18
267 1355 2.876550 AGGTGGCGTGTTTTCTCTAAAC 59.123 45.455 0.00 0.00 45.17 2.01
274 1362 1.890510 ACCGAGGTGGCGTGTTTTC 60.891 57.895 0.00 0.00 43.94 2.29
301 1389 6.485984 AGCACTCATTGGACATATCATTCTTC 59.514 38.462 0.00 0.00 0.00 2.87
350 1439 2.549754 ACAAGTTGCCTTCTTCGTCATG 59.450 45.455 1.81 0.00 0.00 3.07
396 1485 9.515226 GGGGATTAAATGCTATACTATGTTTCA 57.485 33.333 0.00 0.00 0.00 2.69
410 1499 0.820871 TGGCAACGGGGATTAAATGC 59.179 50.000 0.00 0.00 42.51 3.56
420 1509 3.061848 GGGACATGTGGCAACGGG 61.062 66.667 1.15 0.00 42.51 5.28
423 1512 1.047801 AAAAGGGGACATGTGGCAAC 58.952 50.000 1.15 0.00 0.00 4.17
469 1558 9.881649 TTTGTATTGCATTAATCAAATGGCTAA 57.118 25.926 0.00 0.00 44.45 3.09
471 1560 7.011669 GCTTTGTATTGCATTAATCAAATGGCT 59.988 33.333 0.00 0.00 44.45 4.75
472 1561 7.011669 AGCTTTGTATTGCATTAATCAAATGGC 59.988 33.333 0.00 0.00 44.45 4.40
473 1562 8.428186 AGCTTTGTATTGCATTAATCAAATGG 57.572 30.769 0.00 0.00 44.45 3.16
523 1614 7.712797 AGATTTGAGGTCGTGTTAATGTTTTT 58.287 30.769 0.00 0.00 0.00 1.94
552 1643 4.079730 TGAGAGAGTATACTGGAAGCCTCA 60.080 45.833 10.90 9.95 37.60 3.86
568 1659 8.930760 AGATGAAACGAAAAATAAGTGAGAGAG 58.069 33.333 0.00 0.00 0.00 3.20
572 1663 9.959775 GTCTAGATGAAACGAAAAATAAGTGAG 57.040 33.333 0.00 0.00 0.00 3.51
585 1676 5.863935 TGACACATGAAGTCTAGATGAAACG 59.136 40.000 18.77 0.00 36.94 3.60
591 1682 8.200792 GGAGTAAATGACACATGAAGTCTAGAT 58.799 37.037 18.77 6.59 36.94 1.98
602 1693 2.838202 ACGGAGGGAGTAAATGACACAT 59.162 45.455 0.00 0.00 0.00 3.21
614 1705 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
616 1707 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
619 1710 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
620 1711 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
621 1712 7.804129 TCAAAAACGTTCTTATATTTTGGGACG 59.196 33.333 15.53 0.00 39.94 4.79
622 1713 8.908678 GTCAAAAACGTTCTTATATTTTGGGAC 58.091 33.333 15.53 7.20 39.94 4.46
623 1714 8.630917 TGTCAAAAACGTTCTTATATTTTGGGA 58.369 29.630 15.53 4.35 39.94 4.37
624 1715 8.804688 TGTCAAAAACGTTCTTATATTTTGGG 57.195 30.769 15.53 0.00 39.94 4.12
661 1752 8.644619 CGTCTCAAGATATAAGAACGTTTTTGA 58.355 33.333 13.87 2.81 0.00 2.69
662 1753 7.422746 GCGTCTCAAGATATAAGAACGTTTTTG 59.577 37.037 13.87 0.00 0.00 2.44
663 1754 7.117236 TGCGTCTCAAGATATAAGAACGTTTTT 59.883 33.333 9.22 9.22 0.00 1.94
664 1755 6.588756 TGCGTCTCAAGATATAAGAACGTTTT 59.411 34.615 0.46 0.00 0.00 2.43
665 1756 6.097356 TGCGTCTCAAGATATAAGAACGTTT 58.903 36.000 0.46 0.00 0.00 3.60
666 1757 5.647589 TGCGTCTCAAGATATAAGAACGTT 58.352 37.500 0.00 0.00 0.00 3.99
667 1758 5.244785 TGCGTCTCAAGATATAAGAACGT 57.755 39.130 0.00 0.00 0.00 3.99
668 1759 4.677378 CCTGCGTCTCAAGATATAAGAACG 59.323 45.833 0.00 0.00 0.00 3.95
669 1760 4.985409 CCCTGCGTCTCAAGATATAAGAAC 59.015 45.833 0.00 0.00 0.00 3.01
670 1761 4.893524 TCCCTGCGTCTCAAGATATAAGAA 59.106 41.667 0.00 0.00 0.00 2.52
671 1762 4.470602 TCCCTGCGTCTCAAGATATAAGA 58.529 43.478 0.00 0.00 0.00 2.10
672 1763 4.279671 ACTCCCTGCGTCTCAAGATATAAG 59.720 45.833 0.00 0.00 0.00 1.73
673 1764 4.215908 ACTCCCTGCGTCTCAAGATATAA 58.784 43.478 0.00 0.00 0.00 0.98
674 1765 3.833732 ACTCCCTGCGTCTCAAGATATA 58.166 45.455 0.00 0.00 0.00 0.86
675 1766 2.672098 ACTCCCTGCGTCTCAAGATAT 58.328 47.619 0.00 0.00 0.00 1.63
676 1767 2.145397 ACTCCCTGCGTCTCAAGATA 57.855 50.000 0.00 0.00 0.00 1.98
677 1768 2.028130 CTACTCCCTGCGTCTCAAGAT 58.972 52.381 0.00 0.00 0.00 2.40
678 1769 1.004394 TCTACTCCCTGCGTCTCAAGA 59.996 52.381 0.00 0.00 0.00 3.02
679 1770 1.464734 TCTACTCCCTGCGTCTCAAG 58.535 55.000 0.00 0.00 0.00 3.02
680 1771 2.025155 GATCTACTCCCTGCGTCTCAA 58.975 52.381 0.00 0.00 0.00 3.02
681 1772 1.213182 AGATCTACTCCCTGCGTCTCA 59.787 52.381 0.00 0.00 0.00 3.27
682 1773 1.975660 AGATCTACTCCCTGCGTCTC 58.024 55.000 0.00 0.00 0.00 3.36
683 1774 2.445682 AAGATCTACTCCCTGCGTCT 57.554 50.000 0.00 0.00 0.00 4.18
684 1775 3.570550 ACATAAGATCTACTCCCTGCGTC 59.429 47.826 0.00 0.00 0.00 5.19
685 1776 3.567397 ACATAAGATCTACTCCCTGCGT 58.433 45.455 0.00 0.00 0.00 5.24
686 1777 4.592485 AACATAAGATCTACTCCCTGCG 57.408 45.455 0.00 0.00 0.00 5.18
687 1778 4.985409 CGAAACATAAGATCTACTCCCTGC 59.015 45.833 0.00 0.00 0.00 4.85
688 1779 6.392625 TCGAAACATAAGATCTACTCCCTG 57.607 41.667 0.00 0.00 0.00 4.45
689 1780 7.604657 ATTCGAAACATAAGATCTACTCCCT 57.395 36.000 0.00 0.00 0.00 4.20
690 1781 7.926555 TGAATTCGAAACATAAGATCTACTCCC 59.073 37.037 0.00 0.00 0.00 4.30
691 1782 8.873215 TGAATTCGAAACATAAGATCTACTCC 57.127 34.615 0.00 0.00 0.00 3.85
698 1789 8.725148 GCCTCATATGAATTCGAAACATAAGAT 58.275 33.333 22.61 11.69 31.75 2.40
699 1790 7.714813 TGCCTCATATGAATTCGAAACATAAGA 59.285 33.333 22.61 21.71 31.75 2.10
700 1791 7.864686 TGCCTCATATGAATTCGAAACATAAG 58.135 34.615 22.61 19.75 31.75 1.73
701 1792 7.800155 TGCCTCATATGAATTCGAAACATAA 57.200 32.000 22.61 12.54 31.75 1.90
714 1805 9.492730 TTGAGATATATACCTTGCCTCATATGA 57.507 33.333 5.07 5.07 0.00 2.15
998 2090 3.725459 CGGCTGTGCGCAACATGA 61.725 61.111 14.00 0.00 41.67 3.07
1329 2421 0.944311 GAAAGAGAAGCACGACGCCA 60.944 55.000 0.00 0.00 44.04 5.69
1347 2439 2.283388 AGGTACGCCTTGTCCCGA 60.283 61.111 0.00 0.00 44.18 5.14
1405 2497 0.768221 AGGGAAGGTGCCAGTGAAGA 60.768 55.000 0.00 0.00 0.00 2.87
1413 2505 0.611714 TACGAAAGAGGGAAGGTGCC 59.388 55.000 0.00 0.00 0.00 5.01
1416 2508 2.322339 AGGTACGAAAGAGGGAAGGT 57.678 50.000 0.00 0.00 0.00 3.50
1429 2521 6.030228 CCTCGTTTAGTTAGGTTTAGGTACG 58.970 44.000 0.00 0.00 0.00 3.67
1430 2522 6.808704 CACCTCGTTTAGTTAGGTTTAGGTAC 59.191 42.308 0.00 0.00 41.75 3.34
1431 2523 6.572314 GCACCTCGTTTAGTTAGGTTTAGGTA 60.572 42.308 0.00 0.00 41.75 3.08
1432 2524 5.787380 CACCTCGTTTAGTTAGGTTTAGGT 58.213 41.667 0.00 0.00 41.75 3.08
1433 2525 4.628766 GCACCTCGTTTAGTTAGGTTTAGG 59.371 45.833 0.00 0.00 41.75 2.69
1514 2606 2.393271 AAATCTCTCCGTGCAGAAGG 57.607 50.000 0.00 0.00 0.00 3.46
1518 2610 2.159366 ACGAGTAAATCTCTCCGTGCAG 60.159 50.000 0.00 0.00 40.75 4.41
1530 2622 3.250040 AGTTTGCGCTTTCACGAGTAAAT 59.750 39.130 9.73 0.00 34.06 1.40
1565 2657 9.950680 ATCCAATTCGCAAATATTACTAAACTG 57.049 29.630 0.00 0.00 0.00 3.16
1574 2670 8.849168 TCATAGAACATCCAATTCGCAAATATT 58.151 29.630 0.00 0.00 0.00 1.28
1579 2675 5.821995 TGATCATAGAACATCCAATTCGCAA 59.178 36.000 0.00 0.00 0.00 4.85
1628 2724 4.681483 GCTTTGAGTTGCAACCTATTCAAC 59.319 41.667 25.62 13.27 40.08 3.18
1639 2735 4.859304 ATTTGATCAGCTTTGAGTTGCA 57.141 36.364 0.00 0.00 0.00 4.08
1712 2808 9.398538 ACTTACAACATAATTATAGGCCGAAAA 57.601 29.630 0.00 0.00 0.00 2.29
1713 2809 8.832521 CACTTACAACATAATTATAGGCCGAAA 58.167 33.333 0.00 0.00 0.00 3.46
1714 2810 7.442969 CCACTTACAACATAATTATAGGCCGAA 59.557 37.037 0.00 0.00 0.00 4.30
1715 2811 6.932400 CCACTTACAACATAATTATAGGCCGA 59.068 38.462 0.00 0.00 0.00 5.54
1716 2812 6.148811 CCCACTTACAACATAATTATAGGCCG 59.851 42.308 0.00 0.00 0.00 6.13
1717 2813 7.228590 TCCCACTTACAACATAATTATAGGCC 58.771 38.462 0.00 0.00 0.00 5.19
1718 2814 8.685838 TTCCCACTTACAACATAATTATAGGC 57.314 34.615 0.00 0.00 0.00 3.93
1725 2821 9.474313 ACATACATTTCCCACTTACAACATAAT 57.526 29.630 0.00 0.00 0.00 1.28
1726 2822 8.871629 ACATACATTTCCCACTTACAACATAA 57.128 30.769 0.00 0.00 0.00 1.90
1728 2824 9.474313 AATACATACATTTCCCACTTACAACAT 57.526 29.630 0.00 0.00 0.00 2.71
1729 2825 8.735315 CAATACATACATTTCCCACTTACAACA 58.265 33.333 0.00 0.00 0.00 3.33
1730 2826 8.188139 CCAATACATACATTTCCCACTTACAAC 58.812 37.037 0.00 0.00 0.00 3.32
1731 2827 7.340743 CCCAATACATACATTTCCCACTTACAA 59.659 37.037 0.00 0.00 0.00 2.41
1732 2828 6.831353 CCCAATACATACATTTCCCACTTACA 59.169 38.462 0.00 0.00 0.00 2.41
1733 2829 6.264518 CCCCAATACATACATTTCCCACTTAC 59.735 42.308 0.00 0.00 0.00 2.34
1734 2830 6.068735 ACCCCAATACATACATTTCCCACTTA 60.069 38.462 0.00 0.00 0.00 2.24
1735 2831 5.208121 CCCCAATACATACATTTCCCACTT 58.792 41.667 0.00 0.00 0.00 3.16
1736 2832 4.231890 ACCCCAATACATACATTTCCCACT 59.768 41.667 0.00 0.00 0.00 4.00
1768 2864 2.644992 GCAGCGGTTCAAACAGGG 59.355 61.111 0.00 0.00 0.00 4.45
1799 2895 2.648059 GGCCAGCAAATCAGTCTACAT 58.352 47.619 0.00 0.00 0.00 2.29
1800 2896 1.675714 CGGCCAGCAAATCAGTCTACA 60.676 52.381 2.24 0.00 0.00 2.74
1817 2913 8.946085 TGGTCAATATTATCTAATTGATTCGGC 58.054 33.333 1.51 0.00 42.39 5.54
1833 2932 6.151985 TCCGCAATTTAACAGTGGTCAATATT 59.848 34.615 0.00 0.00 34.61 1.28
1849 2948 6.369799 GCAATTAAACACAATTCCGCAATTT 58.630 32.000 0.00 0.00 28.97 1.82
1855 2954 3.363426 CCACGCAATTAAACACAATTCCG 59.637 43.478 0.00 0.00 35.63 4.30
1961 3060 8.204836 ACTCTGATAAAATTAATCTACGCACCT 58.795 33.333 0.00 0.00 0.00 4.00
2168 3270 9.448438 AAGATAAAGTTTTTGGATTTATTGCCC 57.552 29.630 0.00 0.00 31.10 5.36
2192 3294 6.271488 TGAGGCAATCCTTGTTGAATAAAG 57.729 37.500 0.00 0.00 44.46 1.85
2294 3396 7.065443 GGGAGTAACTCACAACCATACATAAAC 59.935 40.741 0.00 0.00 33.47 2.01
2295 3397 7.037873 AGGGAGTAACTCACAACCATACATAAA 60.038 37.037 0.00 0.00 36.16 1.40
2316 3418 4.408921 TGTTATATTGTGGGACAGAGGGAG 59.591 45.833 0.00 0.00 41.80 4.30
2318 3420 4.451900 GTGTTATATTGTGGGACAGAGGG 58.548 47.826 0.00 0.00 41.80 4.30
2319 3421 4.119862 CGTGTTATATTGTGGGACAGAGG 58.880 47.826 0.00 0.00 41.80 3.69
2320 3422 4.755411 ACGTGTTATATTGTGGGACAGAG 58.245 43.478 0.00 0.00 41.80 3.35
2322 3424 5.642063 AGAAACGTGTTATATTGTGGGACAG 59.358 40.000 0.00 0.00 41.80 3.51
2323 3425 5.410132 CAGAAACGTGTTATATTGTGGGACA 59.590 40.000 0.00 0.00 0.00 4.02
2325 3427 4.393680 GCAGAAACGTGTTATATTGTGGGA 59.606 41.667 0.00 0.00 0.00 4.37
2326 3428 4.155099 TGCAGAAACGTGTTATATTGTGGG 59.845 41.667 0.00 0.00 0.00 4.61
2327 3429 5.289917 TGCAGAAACGTGTTATATTGTGG 57.710 39.130 0.00 0.00 0.00 4.17
2328 3430 5.283717 GCTTGCAGAAACGTGTTATATTGTG 59.716 40.000 0.00 0.00 0.00 3.33
2329 3431 5.181245 AGCTTGCAGAAACGTGTTATATTGT 59.819 36.000 0.00 0.00 0.00 2.71
2330 3432 5.631026 AGCTTGCAGAAACGTGTTATATTG 58.369 37.500 0.00 0.00 0.00 1.90
2331 3433 5.880054 AGCTTGCAGAAACGTGTTATATT 57.120 34.783 0.00 0.00 0.00 1.28
2332 3434 5.006746 GCTAGCTTGCAGAAACGTGTTATAT 59.993 40.000 15.53 0.00 0.00 0.86
2333 3435 4.328983 GCTAGCTTGCAGAAACGTGTTATA 59.671 41.667 15.53 0.00 0.00 0.98
2334 3436 3.125316 GCTAGCTTGCAGAAACGTGTTAT 59.875 43.478 15.53 0.00 0.00 1.89
2335 3437 2.478894 GCTAGCTTGCAGAAACGTGTTA 59.521 45.455 15.53 0.00 0.00 2.41
2336 3438 1.264288 GCTAGCTTGCAGAAACGTGTT 59.736 47.619 15.53 0.00 0.00 3.32
2337 3439 0.868406 GCTAGCTTGCAGAAACGTGT 59.132 50.000 15.53 0.00 0.00 4.49
2338 3440 0.166814 GGCTAGCTTGCAGAAACGTG 59.833 55.000 21.53 0.00 34.04 4.49
2339 3441 0.035458 AGGCTAGCTTGCAGAAACGT 59.965 50.000 21.53 0.00 34.04 3.99
2340 3442 1.929836 CTAGGCTAGCTTGCAGAAACG 59.070 52.381 21.53 0.32 34.04 3.60
2352 3454 4.397417 AGATGTTTTTGCAAGCTAGGCTAG 59.603 41.667 17.33 17.33 38.25 3.42
2353 3455 4.335416 AGATGTTTTTGCAAGCTAGGCTA 58.665 39.130 11.13 0.00 38.25 3.93
2354 3456 3.160269 AGATGTTTTTGCAAGCTAGGCT 58.840 40.909 11.13 0.00 42.56 4.58
2355 3457 3.582714 AGATGTTTTTGCAAGCTAGGC 57.417 42.857 0.00 3.45 0.00 3.93
2359 3461 9.754382 CCATAATATAAGATGTTTTTGCAAGCT 57.246 29.630 0.00 0.00 0.00 3.74
2360 3462 8.981647 CCCATAATATAAGATGTTTTTGCAAGC 58.018 33.333 0.00 0.00 0.00 4.01
2363 3465 8.349245 CGTCCCATAATATAAGATGTTTTTGCA 58.651 33.333 0.00 0.00 0.00 4.08
2364 3466 7.807907 CCGTCCCATAATATAAGATGTTTTTGC 59.192 37.037 0.00 0.00 0.00 3.68
2365 3467 9.062524 TCCGTCCCATAATATAAGATGTTTTTG 57.937 33.333 0.00 0.00 0.00 2.44
2366 3468 9.284968 CTCCGTCCCATAATATAAGATGTTTTT 57.715 33.333 0.00 0.00 0.00 1.94
2367 3469 7.883311 CCTCCGTCCCATAATATAAGATGTTTT 59.117 37.037 0.00 0.00 0.00 2.43
2368 3470 7.394816 CCTCCGTCCCATAATATAAGATGTTT 58.605 38.462 0.00 0.00 0.00 2.83
2369 3471 6.070194 CCCTCCGTCCCATAATATAAGATGTT 60.070 42.308 0.00 0.00 0.00 2.71
2370 3472 5.425539 CCCTCCGTCCCATAATATAAGATGT 59.574 44.000 0.00 0.00 0.00 3.06
2371 3473 5.661312 TCCCTCCGTCCCATAATATAAGATG 59.339 44.000 0.00 0.00 0.00 2.90
2372 3474 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
2373 3475 5.279562 TCCCTCCGTCCCATAATATAAGA 57.720 43.478 0.00 0.00 0.00 2.10
2374 3476 6.561519 ATTCCCTCCGTCCCATAATATAAG 57.438 41.667 0.00 0.00 0.00 1.73
2375 3477 8.071854 AGATATTCCCTCCGTCCCATAATATAA 58.928 37.037 0.00 0.00 0.00 0.98
2376 3478 7.509318 CAGATATTCCCTCCGTCCCATAATATA 59.491 40.741 0.00 0.00 0.00 0.86
2377 3479 6.327626 CAGATATTCCCTCCGTCCCATAATAT 59.672 42.308 0.00 0.00 0.00 1.28
2378 3480 5.661312 CAGATATTCCCTCCGTCCCATAATA 59.339 44.000 0.00 0.00 0.00 0.98
2379 3481 4.471386 CAGATATTCCCTCCGTCCCATAAT 59.529 45.833 0.00 0.00 0.00 1.28
2380 3482 3.838317 CAGATATTCCCTCCGTCCCATAA 59.162 47.826 0.00 0.00 0.00 1.90
2381 3483 3.441101 CAGATATTCCCTCCGTCCCATA 58.559 50.000 0.00 0.00 0.00 2.74
2382 3484 2.260822 CAGATATTCCCTCCGTCCCAT 58.739 52.381 0.00 0.00 0.00 4.00
2383 3485 1.717032 CAGATATTCCCTCCGTCCCA 58.283 55.000 0.00 0.00 0.00 4.37
2384 3486 0.977395 CCAGATATTCCCTCCGTCCC 59.023 60.000 0.00 0.00 0.00 4.46
2385 3487 1.718280 ACCAGATATTCCCTCCGTCC 58.282 55.000 0.00 0.00 0.00 4.79
2386 3488 3.840124 AAACCAGATATTCCCTCCGTC 57.160 47.619 0.00 0.00 0.00 4.79
2387 3489 4.227527 AGAAAAACCAGATATTCCCTCCGT 59.772 41.667 0.00 0.00 0.00 4.69
2388 3490 4.781934 AGAAAAACCAGATATTCCCTCCG 58.218 43.478 0.00 0.00 0.00 4.63
2389 3491 7.255625 GCATAAGAAAAACCAGATATTCCCTCC 60.256 40.741 0.00 0.00 0.00 4.30
2390 3492 7.503902 AGCATAAGAAAAACCAGATATTCCCTC 59.496 37.037 0.00 0.00 0.00 4.30
2391 3493 7.357471 AGCATAAGAAAAACCAGATATTCCCT 58.643 34.615 0.00 0.00 0.00 4.20
2392 3494 7.588497 AGCATAAGAAAAACCAGATATTCCC 57.412 36.000 0.00 0.00 0.00 3.97
2398 3500 8.958119 TTCGTATAGCATAAGAAAAACCAGAT 57.042 30.769 0.00 0.00 0.00 2.90
2399 3501 8.780846 TTTCGTATAGCATAAGAAAAACCAGA 57.219 30.769 11.65 0.00 0.00 3.86
2400 3502 9.834628 TTTTTCGTATAGCATAAGAAAAACCAG 57.165 29.630 22.60 0.00 42.29 4.00
2903 4005 1.133575 CATGCCCCTGAGAATGATGGT 60.134 52.381 0.00 0.00 0.00 3.55
3232 6763 0.107312 GATGATGGTGGCTGTCAGCT 60.107 55.000 23.68 3.88 43.76 4.24
3281 6812 9.967451 TCCTGTTTACATCTCCAAATTTGTATA 57.033 29.630 16.73 2.13 0.00 1.47
3322 6860 9.703892 CATTTCCAAATTTGTATCCTGTTTACA 57.296 29.630 16.73 0.00 0.00 2.41
3323 6861 9.705290 ACATTTCCAAATTTGTATCCTGTTTAC 57.295 29.630 16.73 0.00 0.00 2.01
3327 6865 9.705290 GTTTACATTTCCAAATTTGTATCCTGT 57.295 29.630 16.73 14.07 0.00 4.00
3328 6866 9.703892 TGTTTACATTTCCAAATTTGTATCCTG 57.296 29.630 16.73 9.64 0.00 3.86
3329 6867 9.927668 CTGTTTACATTTCCAAATTTGTATCCT 57.072 29.630 16.73 0.00 0.00 3.24
3330 6868 9.150348 CCTGTTTACATTTCCAAATTTGTATCC 57.850 33.333 16.73 0.00 0.00 2.59
3331 6869 9.921637 TCCTGTTTACATTTCCAAATTTGTATC 57.078 29.630 16.73 0.99 0.00 2.24
3332 6870 9.927668 CTCCTGTTTACATTTCCAAATTTGTAT 57.072 29.630 16.73 4.91 0.00 2.29
3333 6871 9.137459 TCTCCTGTTTACATTTCCAAATTTGTA 57.863 29.630 16.73 0.00 0.00 2.41
3334 6872 8.017418 TCTCCTGTTTACATTTCCAAATTTGT 57.983 30.769 16.73 0.49 0.00 2.83
3335 6873 8.928733 CATCTCCTGTTTACATTTCCAAATTTG 58.071 33.333 11.40 11.40 0.00 2.32
3336 6874 8.650490 ACATCTCCTGTTTACATTTCCAAATTT 58.350 29.630 0.00 0.00 32.90 1.82
3337 6875 8.193953 ACATCTCCTGTTTACATTTCCAAATT 57.806 30.769 0.00 0.00 32.90 1.82
3338 6876 7.781324 ACATCTCCTGTTTACATTTCCAAAT 57.219 32.000 0.00 0.00 32.90 2.32
3339 6877 8.698973 TTACATCTCCTGTTTACATTTCCAAA 57.301 30.769 0.00 0.00 39.39 3.28
3340 6878 8.698973 TTTACATCTCCTGTTTACATTTCCAA 57.301 30.769 0.00 0.00 39.39 3.53
3341 6879 8.698973 TTTTACATCTCCTGTTTACATTTCCA 57.301 30.769 0.00 0.00 39.39 3.53
3346 6884 9.423061 GCAAATTTTTACATCTCCTGTTTACAT 57.577 29.630 0.00 0.00 39.39 2.29
3461 6999 6.546395 AGTTTACATCTTCGTTTGCATCATC 58.454 36.000 0.00 0.00 0.00 2.92
3472 7010 5.444218 GCCGTTGAACTAGTTTACATCTTCG 60.444 44.000 10.02 5.91 0.00 3.79
3557 7095 4.514577 CCTCATCGCTCGGCCGTT 62.515 66.667 27.15 3.13 0.00 4.44
3560 7098 4.959596 GCTCCTCATCGCTCGGCC 62.960 72.222 0.00 0.00 0.00 6.13
3588 7126 1.541147 CATTTGAAGGCAAAGGCTCGA 59.459 47.619 0.00 0.00 46.27 4.04
3624 7162 2.363975 CCCATGCTGCTGGCCATTT 61.364 57.895 5.51 0.00 40.92 2.32
3639 7177 4.794648 CCGCCCAATTCGAGCCCA 62.795 66.667 0.00 0.00 0.00 5.36
3672 7210 4.496927 CGCCCAATTTGAGCCCGC 62.497 66.667 0.00 0.00 0.00 6.13
3673 7211 3.825611 CCGCCCAATTTGAGCCCG 61.826 66.667 0.00 0.00 0.00 6.13
3691 7229 4.545706 CCCGCCGCTGCTAATCCA 62.546 66.667 0.00 0.00 34.43 3.41
3714 7252 2.578495 CACTTGATTCGTGCTTCTTGC 58.422 47.619 0.00 0.00 43.25 4.01
3723 7261 2.031919 TGCCGCCACTTGATTCGT 59.968 55.556 0.00 0.00 0.00 3.85
3770 7308 2.364579 TACCACCCCGCCGATTCT 60.365 61.111 0.00 0.00 0.00 2.40
3834 11284 1.927895 CTAGAAAATCGGCTGCGTCT 58.072 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.