Multiple sequence alignment - TraesCS5A01G262800

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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 TraesCS5A01G262800 chr5A 100.000 2802 0 0 1 2802 475832982 475830181 0.000000e+00 5175
1 TraesCS5A01G262800 chr5D 88.093 2108 148 50 770 2802 374131172 374129093 0.000000e+00 2407
2 TraesCS5A01G262800 chr5D 84.696 477 68 5 2329 2802 24370212 24369738 3.270000e-129 472
3 TraesCS5A01G262800 chr5D 83.173 416 56 12 2388 2799 345490182 345490587 4.410000e-98 368
4 TraesCS5A01G262800 chr5D 79.930 284 53 4 2518 2799 63483467 63483748 3.660000e-49 206
5 TraesCS5A01G262800 chr5B 89.299 1112 69 20 757 1844 445763542 445762457 0.000000e+00 1349
6 TraesCS5A01G262800 chr5B 87.669 1111 77 29 776 1849 445652158 445651071 0.000000e+00 1238
7 TraesCS5A01G262800 chr5B 82.708 879 110 17 1954 2802 445650651 445649785 0.000000e+00 743
8 TraesCS5A01G262800 chr1B 84.961 645 67 15 76 704 254450345 254449715 6.590000e-176 627
9 TraesCS5A01G262800 chr2B 80.556 432 82 2 2372 2802 91486195 91485765 5.790000e-87 331
10 TraesCS5A01G262800 chr2B 77.014 422 87 8 2382 2799 249950197 249950612 1.680000e-57 233
11 TraesCS5A01G262800 chr2B 77.055 292 63 4 2467 2756 29862705 29862416 6.210000e-37 165
12 TraesCS5A01G262800 chr7A 84.314 204 30 2 2578 2780 611539430 611539228 6.120000e-47 198
13 TraesCS5A01G262800 chrUn 89.691 97 4 2 79 175 717889 717799 4.900000e-23 119
14 TraesCS5A01G262800 chrUn 89.000 100 5 2 76 175 229409075 229409168 4.900000e-23 119


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 TraesCS5A01G262800 chr5A 475830181 475832982 2801 True 5175.0 5175 100.0000 1 2802 1 chr5A.!!$R1 2801
1 TraesCS5A01G262800 chr5D 374129093 374131172 2079 True 2407.0 2407 88.0930 770 2802 1 chr5D.!!$R2 2032
2 TraesCS5A01G262800 chr5B 445762457 445763542 1085 True 1349.0 1349 89.2990 757 1844 1 chr5B.!!$R1 1087
3 TraesCS5A01G262800 chr5B 445649785 445652158 2373 True 990.5 1238 85.1885 776 2802 2 chr5B.!!$R2 2026
4 TraesCS5A01G262800 chr1B 254449715 254450345 630 True 627.0 627 84.9610 76 704 1 chr1B.!!$R1 628

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
503 520 0.038166 GAGCATGGGGGACAGAACAA 59.962 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2011 0.177141 GCCGGCTGGTGTGACTAATA 59.823 55.0 22.15 0.0 37.67 0.98 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
22 23 2.280119 GGCACGAGCACAGTGTGA 60.280 61.111 27.37 0.00 44.61 3.58
23 24 1.669115 GGCACGAGCACAGTGTGAT 60.669 57.895 27.37 21.77 44.61 3.06
24 25 1.494628 GCACGAGCACAGTGTGATG 59.505 57.895 27.37 17.73 41.36 3.07
25 26 1.904852 GCACGAGCACAGTGTGATGG 61.905 60.000 27.37 23.54 41.36 3.51
26 27 0.601046 CACGAGCACAGTGTGATGGT 60.601 55.000 27.37 24.24 41.08 3.55
27 28 0.601046 ACGAGCACAGTGTGATGGTG 60.601 55.000 25.41 14.34 39.19 4.17
28 29 0.601046 CGAGCACAGTGTGATGGTGT 60.601 55.000 27.37 3.08 35.23 4.16
29 30 0.870393 GAGCACAGTGTGATGGTGTG 59.130 55.000 27.37 0.00 43.70 3.82
30 31 0.181114 AGCACAGTGTGATGGTGTGT 59.819 50.000 27.37 0.00 42.96 3.72
31 32 0.588252 GCACAGTGTGATGGTGTGTC 59.412 55.000 27.37 1.65 42.96 3.67
32 33 1.952193 CACAGTGTGATGGTGTGTCA 58.048 50.000 18.83 0.00 37.41 3.58
33 34 1.869132 CACAGTGTGATGGTGTGTCAG 59.131 52.381 18.83 0.00 37.41 3.51
34 35 1.202687 ACAGTGTGATGGTGTGTCAGG 60.203 52.381 0.00 0.00 0.00 3.86
35 36 0.250467 AGTGTGATGGTGTGTCAGGC 60.250 55.000 0.00 0.00 0.00 4.85
36 37 1.073025 TGTGATGGTGTGTCAGGCC 59.927 57.895 0.00 0.00 0.00 5.19
37 38 1.675641 GTGATGGTGTGTCAGGCCC 60.676 63.158 0.00 0.00 0.00 5.80
38 39 1.847506 TGATGGTGTGTCAGGCCCT 60.848 57.895 0.00 0.00 0.00 5.19
39 40 1.380302 GATGGTGTGTCAGGCCCTT 59.620 57.895 0.00 0.00 0.00 3.95
40 41 0.962356 GATGGTGTGTCAGGCCCTTG 60.962 60.000 0.00 0.00 0.00 3.61
41 42 2.985847 GGTGTGTCAGGCCCTTGC 60.986 66.667 0.00 0.00 0.00 4.01
42 43 3.357079 GTGTGTCAGGCCCTTGCG 61.357 66.667 0.00 0.00 38.85 4.85
43 44 4.641645 TGTGTCAGGCCCTTGCGG 62.642 66.667 0.00 0.00 38.85 5.69
44 45 4.643387 GTGTCAGGCCCTTGCGGT 62.643 66.667 0.00 0.00 38.85 5.68
45 46 4.329545 TGTCAGGCCCTTGCGGTC 62.330 66.667 0.00 0.00 38.85 4.79
50 51 3.056328 GGCCCTTGCGGTCTTGAC 61.056 66.667 0.00 0.00 38.85 3.18
51 52 2.032681 GCCCTTGCGGTCTTGACT 59.967 61.111 0.61 0.00 0.00 3.41
52 53 1.295423 GCCCTTGCGGTCTTGACTA 59.705 57.895 0.61 0.00 0.00 2.59
53 54 0.321298 GCCCTTGCGGTCTTGACTAA 60.321 55.000 0.61 0.00 0.00 2.24
54 55 1.880646 GCCCTTGCGGTCTTGACTAAA 60.881 52.381 0.61 0.00 0.00 1.85
55 56 2.076863 CCCTTGCGGTCTTGACTAAAG 58.923 52.381 0.61 3.15 37.22 1.85
56 57 2.289444 CCCTTGCGGTCTTGACTAAAGA 60.289 50.000 0.61 0.00 42.83 2.52
57 58 3.399330 CCTTGCGGTCTTGACTAAAGAA 58.601 45.455 0.61 0.00 46.51 2.52
58 59 3.813166 CCTTGCGGTCTTGACTAAAGAAA 59.187 43.478 0.61 0.00 46.51 2.52
59 60 4.455877 CCTTGCGGTCTTGACTAAAGAAAT 59.544 41.667 0.61 0.00 46.51 2.17
60 61 5.390991 CCTTGCGGTCTTGACTAAAGAAATC 60.391 44.000 0.61 0.00 46.51 2.17
61 62 3.678072 TGCGGTCTTGACTAAAGAAATCG 59.322 43.478 0.61 0.00 46.51 3.34
62 63 3.924686 GCGGTCTTGACTAAAGAAATCGA 59.075 43.478 0.61 0.00 46.51 3.59
63 64 4.201599 GCGGTCTTGACTAAAGAAATCGAC 60.202 45.833 0.00 0.00 46.51 4.20
64 65 4.921515 CGGTCTTGACTAAAGAAATCGACA 59.078 41.667 0.00 0.00 46.51 4.35
65 66 5.061064 CGGTCTTGACTAAAGAAATCGACAG 59.939 44.000 0.00 0.00 46.51 3.51
66 67 5.927115 GGTCTTGACTAAAGAAATCGACAGT 59.073 40.000 0.00 0.00 46.51 3.55
67 68 6.424207 GGTCTTGACTAAAGAAATCGACAGTT 59.576 38.462 0.00 0.00 46.51 3.16
68 69 7.041984 GGTCTTGACTAAAGAAATCGACAGTTT 60.042 37.037 0.00 0.00 46.51 2.66
69 70 8.336080 GTCTTGACTAAAGAAATCGACAGTTTT 58.664 33.333 0.00 0.00 46.51 2.43
70 71 9.537192 TCTTGACTAAAGAAATCGACAGTTTTA 57.463 29.630 0.00 0.00 42.09 1.52
126 127 1.426251 ATCAAGAGCCACCACACCCA 61.426 55.000 0.00 0.00 0.00 4.51
131 132 1.000993 AGCCACCACACCCAAAACA 59.999 52.632 0.00 0.00 0.00 2.83
132 133 1.042559 AGCCACCACACCCAAAACAG 61.043 55.000 0.00 0.00 0.00 3.16
133 134 1.441311 CCACCACACCCAAAACAGC 59.559 57.895 0.00 0.00 0.00 4.40
134 135 1.042559 CCACCACACCCAAAACAGCT 61.043 55.000 0.00 0.00 0.00 4.24
135 136 0.823460 CACCACACCCAAAACAGCTT 59.177 50.000 0.00 0.00 0.00 3.74
137 138 1.480545 ACCACACCCAAAACAGCTTTC 59.519 47.619 0.00 0.00 0.00 2.62
168 170 8.922058 ATTAACAAAAATAGCAGCATCAGAAG 57.078 30.769 0.00 0.00 0.00 2.85
181 183 5.350914 CAGCATCAGAAGAAACTAGAACAGG 59.649 44.000 0.00 0.00 0.00 4.00
182 184 5.247110 AGCATCAGAAGAAACTAGAACAGGA 59.753 40.000 0.00 0.00 0.00 3.86
228 230 3.633525 AGAGCTAGAAGCATGAGTCTCAG 59.366 47.826 8.82 2.21 45.56 3.35
233 235 3.974719 AGAAGCATGAGTCTCAGGTCTA 58.025 45.455 15.47 0.00 29.72 2.59
238 240 6.992664 AGCATGAGTCTCAGGTCTATTAAT 57.007 37.500 15.47 0.00 29.72 1.40
240 242 8.121305 AGCATGAGTCTCAGGTCTATTAATAG 57.879 38.462 15.47 15.25 29.72 1.73
248 250 9.310449 GTCTCAGGTCTATTAATAGGTATTGGA 57.690 37.037 19.98 10.70 0.00 3.53
282 289 7.940178 TGCATTAGTATCAACATAAGTACGG 57.060 36.000 0.00 0.00 0.00 4.02
288 295 7.179076 AGTATCAACATAAGTACGGACCTTT 57.821 36.000 0.00 0.00 0.00 3.11
292 299 3.596214 ACATAAGTACGGACCTTTGCAG 58.404 45.455 0.00 0.00 0.00 4.41
293 300 3.007614 ACATAAGTACGGACCTTTGCAGT 59.992 43.478 0.00 0.00 0.00 4.40
302 309 2.223377 GGACCTTTGCAGTAGAAACACG 59.777 50.000 0.00 0.00 0.00 4.49
321 329 5.050490 ACACGTGGATGTGATAAATAGCTC 58.950 41.667 21.57 0.00 42.55 4.09
332 340 6.830324 TGTGATAAATAGCTCCATTTCTTGCT 59.170 34.615 0.00 0.00 39.30 3.91
339 347 2.928116 GCTCCATTTCTTGCTGCATTTC 59.072 45.455 1.84 0.00 0.00 2.17
345 353 1.624336 TCTTGCTGCATTTCTGGCTT 58.376 45.000 1.84 0.00 0.00 4.35
346 354 1.542915 TCTTGCTGCATTTCTGGCTTC 59.457 47.619 1.84 0.00 0.00 3.86
352 360 3.228453 CTGCATTTCTGGCTTCCCATAT 58.772 45.455 0.00 0.00 41.21 1.78
364 372 3.869912 GCTTCCCATATGTGCCATATCGT 60.870 47.826 1.24 0.00 0.00 3.73
366 374 3.673902 TCCCATATGTGCCATATCGTTG 58.326 45.455 1.24 0.00 0.00 4.10
376 384 1.268032 CCATATCGTTGCCGCAAGAAC 60.268 52.381 5.91 0.00 43.02 3.01
377 385 0.650512 ATATCGTTGCCGCAAGAACG 59.349 50.000 5.91 7.93 44.97 3.95
389 397 0.391130 CAAGAACGATGGCTTCCCGA 60.391 55.000 0.00 0.00 0.00 5.14
400 408 0.179070 GCTTCCCGATCAGAAGACCC 60.179 60.000 21.09 5.24 42.80 4.46
401 409 0.103208 CTTCCCGATCAGAAGACCCG 59.897 60.000 14.53 0.00 42.80 5.28
402 410 0.613853 TTCCCGATCAGAAGACCCGT 60.614 55.000 0.00 0.00 0.00 5.28
407 415 1.469940 CGATCAGAAGACCCGTGAAGG 60.470 57.143 0.00 0.00 40.63 3.46
423 431 4.327680 GTGAAGGAAGTCAAATAGCCACT 58.672 43.478 0.00 0.00 0.00 4.00
424 432 4.154918 GTGAAGGAAGTCAAATAGCCACTG 59.845 45.833 0.00 0.00 0.00 3.66
425 433 4.202461 TGAAGGAAGTCAAATAGCCACTGT 60.202 41.667 0.00 0.00 0.00 3.55
428 436 3.189287 GGAAGTCAAATAGCCACTGTGTG 59.811 47.826 7.08 0.00 0.00 3.82
438 455 1.738099 CACTGTGTGGTAGAGCGGC 60.738 63.158 0.00 0.00 0.00 6.53
459 476 7.489113 AGCGGCACAAATTAATATTGAAAGAAG 59.511 33.333 1.45 5.19 0.00 2.85
481 498 0.916086 TTTACGCCATCCCAGATGGT 59.084 50.000 21.53 8.35 41.17 3.55
495 512 1.067295 GATGGTATGAGCATGGGGGA 58.933 55.000 0.00 0.00 36.31 4.81
496 513 0.773644 ATGGTATGAGCATGGGGGAC 59.226 55.000 0.00 0.00 34.64 4.46
497 514 0.623031 TGGTATGAGCATGGGGGACA 60.623 55.000 0.00 0.00 0.00 4.02
503 520 0.038166 GAGCATGGGGGACAGAACAA 59.962 55.000 0.00 0.00 0.00 2.83
508 525 1.741028 TGGGGGACAGAACAAGATGA 58.259 50.000 0.00 0.00 0.00 2.92
512 529 3.012518 GGGGACAGAACAAGATGATGTG 58.987 50.000 0.00 0.00 32.81 3.21
524 541 7.672983 ACAAGATGATGTGTTCGATACTTTT 57.327 32.000 0.00 0.00 30.82 2.27
525 542 8.099364 ACAAGATGATGTGTTCGATACTTTTT 57.901 30.769 0.00 0.00 30.82 1.94
531 548 7.156000 TGATGTGTTCGATACTTTTTGGTCTA 58.844 34.615 0.00 0.00 0.00 2.59
535 552 7.442969 TGTGTTCGATACTTTTTGGTCTACAAT 59.557 33.333 0.00 0.00 39.21 2.71
537 554 8.928733 TGTTCGATACTTTTTGGTCTACAATAC 58.071 33.333 0.00 0.00 39.21 1.89
540 557 9.661563 TCGATACTTTTTGGTCTACAATACAAT 57.338 29.630 0.00 0.00 39.21 2.71
550 567 8.246908 TGGTCTACAATACAATAGAAACAACG 57.753 34.615 0.00 0.00 0.00 4.10
551 568 8.089597 TGGTCTACAATACAATAGAAACAACGA 58.910 33.333 0.00 0.00 0.00 3.85
552 569 9.095065 GGTCTACAATACAATAGAAACAACGAT 57.905 33.333 0.00 0.00 0.00 3.73
558 575 9.767684 CAATACAATAGAAACAACGATTTGCTA 57.232 29.630 0.00 0.00 36.00 3.49
576 593 0.612174 TAGAGCTGGAACCTGACGCT 60.612 55.000 0.00 0.00 0.00 5.07
591 608 2.607635 TGACGCTGAAGAAGTTGTTCAC 59.392 45.455 11.18 7.95 34.82 3.18
632 649 1.950472 CGAAACGCCAGAACACAATC 58.050 50.000 0.00 0.00 0.00 2.67
642 659 5.295292 CGCCAGAACACAATCTTCATCTTAT 59.705 40.000 0.00 0.00 0.00 1.73
643 660 6.493116 GCCAGAACACAATCTTCATCTTATG 58.507 40.000 0.00 0.00 0.00 1.90
665 682 3.300388 AGGAGCTTTGATCGACCAGATA 58.700 45.455 0.00 0.00 40.26 1.98
674 691 5.869649 TGATCGACCAGATAGATTTCCAA 57.130 39.130 0.00 0.00 40.26 3.53
681 698 6.907212 CGACCAGATAGATTTCCAAAATTTCG 59.093 38.462 0.00 0.00 0.00 3.46
689 706 7.967890 AGATTTCCAAAATTTCGCTTCATTT 57.032 28.000 0.00 0.00 0.00 2.32
704 721 4.395542 GCTTCATTTGCTCTGTCAGAAGAT 59.604 41.667 3.67 0.00 34.47 2.40
705 722 5.106237 GCTTCATTTGCTCTGTCAGAAGATT 60.106 40.000 3.67 0.00 34.47 2.40
706 723 5.874895 TCATTTGCTCTGTCAGAAGATTG 57.125 39.130 3.67 0.00 0.00 2.67
707 724 5.311265 TCATTTGCTCTGTCAGAAGATTGT 58.689 37.500 3.67 0.00 0.00 2.71
708 725 5.410746 TCATTTGCTCTGTCAGAAGATTGTC 59.589 40.000 3.67 0.00 0.00 3.18
709 726 3.325293 TGCTCTGTCAGAAGATTGTCC 57.675 47.619 3.67 0.00 0.00 4.02
710 727 2.634453 TGCTCTGTCAGAAGATTGTCCA 59.366 45.455 3.67 0.00 0.00 4.02
711 728 2.999355 GCTCTGTCAGAAGATTGTCCAC 59.001 50.000 3.67 0.00 0.00 4.02
712 729 3.249091 CTCTGTCAGAAGATTGTCCACG 58.751 50.000 3.67 0.00 0.00 4.94
713 730 2.628178 TCTGTCAGAAGATTGTCCACGT 59.372 45.455 0.00 0.00 0.00 4.49
714 731 2.989840 CTGTCAGAAGATTGTCCACGTC 59.010 50.000 0.00 0.00 0.00 4.34
715 732 2.288825 TGTCAGAAGATTGTCCACGTCC 60.289 50.000 0.00 0.00 0.00 4.79
716 733 1.275291 TCAGAAGATTGTCCACGTCCC 59.725 52.381 0.00 0.00 0.00 4.46
717 734 0.613777 AGAAGATTGTCCACGTCCCC 59.386 55.000 0.00 0.00 0.00 4.81
718 735 0.613777 GAAGATTGTCCACGTCCCCT 59.386 55.000 0.00 0.00 0.00 4.79
719 736 0.613777 AAGATTGTCCACGTCCCCTC 59.386 55.000 0.00 0.00 0.00 4.30
720 737 0.252284 AGATTGTCCACGTCCCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
721 738 0.108138 GATTGTCCACGTCCCCTCTG 60.108 60.000 0.00 0.00 0.00 3.35
722 739 1.553690 ATTGTCCACGTCCCCTCTGG 61.554 60.000 0.00 0.00 0.00 3.86
732 749 4.461119 CCCTCTGGGTGTGAGCTA 57.539 61.111 0.00 0.00 38.25 3.32
733 750 1.901085 CCCTCTGGGTGTGAGCTAC 59.099 63.158 0.00 0.00 38.25 3.58
734 751 0.616111 CCCTCTGGGTGTGAGCTACT 60.616 60.000 0.00 0.00 38.25 2.57
735 752 1.342076 CCCTCTGGGTGTGAGCTACTA 60.342 57.143 0.00 0.00 38.25 1.82
736 753 2.028130 CCTCTGGGTGTGAGCTACTAG 58.972 57.143 0.00 0.00 0.00 2.57
737 754 2.621929 CCTCTGGGTGTGAGCTACTAGT 60.622 54.545 0.00 0.00 0.00 2.57
738 755 3.371702 CCTCTGGGTGTGAGCTACTAGTA 60.372 52.174 1.89 1.89 0.00 1.82
739 756 4.270834 CTCTGGGTGTGAGCTACTAGTAA 58.729 47.826 3.76 0.00 0.00 2.24
740 757 4.270834 TCTGGGTGTGAGCTACTAGTAAG 58.729 47.826 3.76 0.00 0.00 2.34
741 758 4.018688 TCTGGGTGTGAGCTACTAGTAAGA 60.019 45.833 3.76 0.00 0.00 2.10
742 759 4.669700 TGGGTGTGAGCTACTAGTAAGAA 58.330 43.478 3.76 0.00 0.00 2.52
743 760 5.081728 TGGGTGTGAGCTACTAGTAAGAAA 58.918 41.667 3.76 0.00 0.00 2.52
744 761 5.720041 TGGGTGTGAGCTACTAGTAAGAAAT 59.280 40.000 3.76 0.00 0.00 2.17
745 762 6.127423 TGGGTGTGAGCTACTAGTAAGAAATC 60.127 42.308 3.76 0.00 0.00 2.17
746 763 6.127423 GGGTGTGAGCTACTAGTAAGAAATCA 60.127 42.308 3.76 1.80 0.00 2.57
747 764 7.321153 GGTGTGAGCTACTAGTAAGAAATCAA 58.679 38.462 3.76 0.00 0.00 2.57
748 765 7.982354 GGTGTGAGCTACTAGTAAGAAATCAAT 59.018 37.037 3.76 0.00 0.00 2.57
749 766 9.372369 GTGTGAGCTACTAGTAAGAAATCAATT 57.628 33.333 3.76 0.00 0.00 2.32
770 787 7.662258 TCAATTATGAGTAAAGGAAAACGTGGA 59.338 33.333 0.00 0.00 0.00 4.02
846 863 2.593436 CGCGGACCAACCAAACCT 60.593 61.111 0.00 0.00 38.90 3.50
854 876 1.520600 CCAACCAAACCTACCGTGGC 61.521 60.000 0.00 0.00 35.72 5.01
970 1012 2.833957 CCCCCGCCCCTACAATAC 59.166 66.667 0.00 0.00 0.00 1.89
973 1015 2.073716 CCCGCCCCTACAATACCCA 61.074 63.158 0.00 0.00 0.00 4.51
975 1017 1.628238 CCGCCCCTACAATACCCACA 61.628 60.000 0.00 0.00 0.00 4.17
980 1022 2.093128 CCCCTACAATACCCACACTCAC 60.093 54.545 0.00 0.00 0.00 3.51
1004 1046 1.475280 CATTCCATTCCCACACAGCAG 59.525 52.381 0.00 0.00 0.00 4.24
1053 1102 1.872197 CTCTCTCCGATCGCCCATCC 61.872 65.000 10.32 0.00 0.00 3.51
1074 1123 0.104120 CGTTCATATGGCCACCGAGA 59.896 55.000 8.16 0.24 0.00 4.04
1100 1149 2.562912 CCGCACAACATCCTGCAC 59.437 61.111 0.00 0.00 32.57 4.57
1184 1233 3.237741 CCTCCTCCATCGGCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
1225 1283 1.450491 GGCGGCCTTCCTCTTCTTC 60.450 63.158 12.87 0.00 0.00 2.87
1226 1284 1.599576 GCGGCCTTCCTCTTCTTCT 59.400 57.895 0.00 0.00 0.00 2.85
1227 1285 0.035915 GCGGCCTTCCTCTTCTTCTT 60.036 55.000 0.00 0.00 0.00 2.52
1256 1320 2.741092 GGGAAGGTGACGTCTGCA 59.259 61.111 17.92 0.00 39.00 4.41
1301 1365 4.382320 GAAGTGTACGCCGGCCCA 62.382 66.667 23.46 12.75 0.00 5.36
1450 1535 2.040009 GCTATCCCGGTGCCAGCTAA 62.040 60.000 0.00 0.00 0.00 3.09
1484 1569 6.973474 AGCTGTATGTTAGTTTAGTTCTAGCG 59.027 38.462 0.00 0.00 0.00 4.26
1503 1588 1.132640 GCAATCGTCGTTGAGTGGC 59.867 57.895 10.45 0.00 34.68 5.01
1659 1753 7.223971 GGCGTGATGTAATTACAAGTAGAATCA 59.776 37.037 21.57 15.25 39.99 2.57
1721 1816 0.471617 ATCGATCCCCTTTGCCTCTG 59.528 55.000 0.00 0.00 0.00 3.35
1779 1876 8.934825 TGGCTAAATTTTAATTTCTGTTCATGC 58.065 29.630 0.00 0.00 39.24 4.06
1859 1990 7.978982 AGGATAAAGTTGATTTCAATCAGTCG 58.021 34.615 2.57 0.00 45.35 4.18
1880 2011 6.319658 AGTCGCATCCAAGATAATGTTGATTT 59.680 34.615 0.00 0.00 0.00 2.17
1927 2064 0.323360 TGGCCAACCTACATGCCTTC 60.323 55.000 0.61 0.00 44.32 3.46
1952 2089 0.601057 GCTACCCGGCATGTTTGTTT 59.399 50.000 0.00 0.00 0.00 2.83
1963 2375 3.120786 GCATGTTTGTTTGCAGCTGAATC 60.121 43.478 20.43 4.03 38.72 2.52
1992 2404 7.325338 TCGTCTCAGTCGTCTTATTTTTGTTAG 59.675 37.037 0.00 0.00 0.00 2.34
1993 2405 7.114529 CGTCTCAGTCGTCTTATTTTTGTTAGT 59.885 37.037 0.00 0.00 0.00 2.24
1994 2406 9.403110 GTCTCAGTCGTCTTATTTTTGTTAGTA 57.597 33.333 0.00 0.00 0.00 1.82
1996 2408 8.524870 TCAGTCGTCTTATTTTTGTTAGTACC 57.475 34.615 0.00 0.00 0.00 3.34
1997 2409 8.362639 TCAGTCGTCTTATTTTTGTTAGTACCT 58.637 33.333 0.00 0.00 0.00 3.08
2002 2415 9.852091 CGTCTTATTTTTGTTAGTACCTCTACT 57.148 33.333 0.00 0.00 37.04 2.57
2009 2422 3.693085 TGTTAGTACCTCTACTTGCCTCG 59.307 47.826 0.00 0.00 34.79 4.63
2012 2425 1.063764 GTACCTCTACTTGCCTCGTCG 59.936 57.143 0.00 0.00 0.00 5.12
2014 2427 0.526662 CCTCTACTTGCCTCGTCGTT 59.473 55.000 0.00 0.00 0.00 3.85
2039 2452 1.004745 CATAGCCTCCAACCAACCTGT 59.995 52.381 0.00 0.00 0.00 4.00
2054 2467 1.066858 ACCTGTGGTTAGTGCATCTCG 60.067 52.381 0.00 0.00 27.29 4.04
2101 2520 3.897239 TGCGGATCAATAAGGACCATTT 58.103 40.909 0.00 0.00 0.00 2.32
2106 2525 5.123227 GGATCAATAAGGACCATTTCGTGA 58.877 41.667 0.00 0.00 0.00 4.35
2123 2542 2.915463 CGTGAACCGTGATGTAGAAGTC 59.085 50.000 0.00 0.00 0.00 3.01
2139 2558 4.843728 AGAAGTCGGCCATTCAAAATAGA 58.156 39.130 2.24 0.00 0.00 1.98
2142 2561 3.054361 AGTCGGCCATTCAAAATAGACCT 60.054 43.478 2.24 0.00 0.00 3.85
2145 2564 2.101415 GGCCATTCAAAATAGACCTGGC 59.899 50.000 0.00 2.10 42.03 4.85
2156 2575 7.875554 TCAAAATAGACCTGGCCAATTTAAAAC 59.124 33.333 7.01 0.00 0.00 2.43
2163 2596 6.230472 ACCTGGCCAATTTAAAACTCAAATC 58.770 36.000 7.01 0.00 0.00 2.17
2164 2597 5.643348 CCTGGCCAATTTAAAACTCAAATCC 59.357 40.000 7.01 0.00 0.00 3.01
2165 2598 5.233988 TGGCCAATTTAAAACTCAAATCCG 58.766 37.500 0.61 0.00 0.00 4.18
2166 2599 5.011125 TGGCCAATTTAAAACTCAAATCCGA 59.989 36.000 0.61 0.00 0.00 4.55
2167 2600 5.347635 GGCCAATTTAAAACTCAAATCCGAC 59.652 40.000 0.00 0.00 0.00 4.79
2168 2601 5.347635 GCCAATTTAAAACTCAAATCCGACC 59.652 40.000 0.00 0.00 0.00 4.79
2169 2602 6.451393 CCAATTTAAAACTCAAATCCGACCA 58.549 36.000 0.00 0.00 0.00 4.02
2170 2603 7.096551 CCAATTTAAAACTCAAATCCGACCAT 58.903 34.615 0.00 0.00 0.00 3.55
2171 2604 8.247562 CCAATTTAAAACTCAAATCCGACCATA 58.752 33.333 0.00 0.00 0.00 2.74
2172 2605 9.801873 CAATTTAAAACTCAAATCCGACCATAT 57.198 29.630 0.00 0.00 0.00 1.78
2175 2608 9.675464 TTTAAAACTCAAATCCGACCATATAGT 57.325 29.630 0.00 0.00 0.00 2.12
2176 2609 7.553881 AAAACTCAAATCCGACCATATAGTG 57.446 36.000 0.00 0.00 0.00 2.74
2177 2610 4.632153 ACTCAAATCCGACCATATAGTGC 58.368 43.478 0.00 0.00 0.00 4.40
2248 2681 3.777478 TCGCAGAAAAATACTAGTCCGG 58.223 45.455 0.00 0.00 0.00 5.14
2288 2721 9.875691 AAAGAAAATATTGATTTCTGCCTTACC 57.124 29.630 2.59 0.00 44.22 2.85
2321 2754 0.614979 GAGCCTCCACACTCACCCTA 60.615 60.000 0.00 0.00 32.98 3.53
2323 2756 1.900545 GCCTCCACACTCACCCTACC 61.901 65.000 0.00 0.00 0.00 3.18
2324 2757 0.544357 CCTCCACACTCACCCTACCA 60.544 60.000 0.00 0.00 0.00 3.25
2326 2759 0.190069 TCCACACTCACCCTACCACT 59.810 55.000 0.00 0.00 0.00 4.00
2350 2806 2.810439 CCTTCTCGGCTGATCCTTAG 57.190 55.000 0.00 0.00 0.00 2.18
2370 2826 1.006086 TGCGCTTCAACGTCATATGG 58.994 50.000 9.73 0.00 34.88 2.74
2372 2828 1.006086 CGCTTCAACGTCATATGGCA 58.994 50.000 8.28 0.00 0.00 4.92
2374 2830 2.279741 GCTTCAACGTCATATGGCAGA 58.720 47.619 8.28 0.00 0.00 4.26
2386 2842 3.499737 GGCAGACGGATTGCACGG 61.500 66.667 9.68 0.00 43.28 4.94
2395 2851 1.472552 CGGATTGCACGGTCATCCTTA 60.473 52.381 11.62 0.00 0.00 2.69
2414 2871 4.444876 CCTTACATCGTCATCCAAATCCCT 60.445 45.833 0.00 0.00 0.00 4.20
2415 2872 3.199880 ACATCGTCATCCAAATCCCTC 57.800 47.619 0.00 0.00 0.00 4.30
2416 2873 2.138320 CATCGTCATCCAAATCCCTCG 58.862 52.381 0.00 0.00 0.00 4.63
2438 2895 4.434330 CGTCTTTAAGGTCAACATCTTCGC 60.434 45.833 0.00 0.00 0.00 4.70
2445 2902 0.537188 TCAACATCTTCGCCTCCTCC 59.463 55.000 0.00 0.00 0.00 4.30
2465 2922 1.398041 CGAAGCGGATGCAATCTCAAA 59.602 47.619 0.00 0.00 44.71 2.69
2485 2942 8.642432 TCTCAAACTTCTTCTCTTCAAGTATGA 58.358 33.333 0.00 0.00 30.00 2.15
2527 2984 0.457851 CTTCTTCTCGATCGCCACCT 59.542 55.000 11.09 0.00 0.00 4.00
2547 3004 4.202326 ACCTTCAACATGTTAACCTCTCGT 60.202 41.667 11.53 0.00 0.00 4.18
2568 3025 3.065925 GTCCTTACATGCCTTCTTGATGC 59.934 47.826 0.00 0.00 0.00 3.91
2571 3028 0.035152 ACATGCCTTCTTGATGCCGA 60.035 50.000 0.00 0.00 0.00 5.54
2574 3031 0.036732 TGCCTTCTTGATGCCGAAGT 59.963 50.000 0.00 0.00 35.91 3.01
2575 3032 0.449388 GCCTTCTTGATGCCGAAGTG 59.551 55.000 0.00 0.00 35.91 3.16
2580 3037 1.159285 CTTGATGCCGAAGTGCTTGA 58.841 50.000 0.00 0.00 0.00 3.02
2603 3060 1.069358 CATACCTCCTCCTTCTTCGCC 59.931 57.143 0.00 0.00 0.00 5.54
2615 3072 3.181516 CCTTCTTCGCCAAGATTTTCTCG 60.182 47.826 0.00 0.00 38.50 4.04
2669 3126 0.617935 GCTTTGCCTTCTCCTCCTCT 59.382 55.000 0.00 0.00 0.00 3.69
2682 3139 5.588845 TCTCCTCCTCTCATTTCTTTCTCT 58.411 41.667 0.00 0.00 0.00 3.10
2683 3140 6.736581 TCTCCTCCTCTCATTTCTTTCTCTA 58.263 40.000 0.00 0.00 0.00 2.43
2684 3141 6.833416 TCTCCTCCTCTCATTTCTTTCTCTAG 59.167 42.308 0.00 0.00 0.00 2.43
2712 3169 2.396590 TCTAACCTTCATTGTCGGCC 57.603 50.000 0.00 0.00 0.00 6.13
2735 3192 3.304911 TTTGTTGGGTCAGTTGGATCA 57.695 42.857 0.00 0.00 0.00 2.92
2760 3217 2.819984 TTCTTCCTCGGTGCCCATGC 62.820 60.000 0.00 0.00 38.26 4.06
2781 3238 2.342279 CGGTCTTGGCGGAGTTGA 59.658 61.111 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.664677 ACTGTGCTCGTGCCGTCC 62.665 66.667 7.05 0.00 38.71 4.79
2 3 3.406361 CACTGTGCTCGTGCCGTC 61.406 66.667 7.05 0.00 38.71 4.79
3 4 4.221422 ACACTGTGCTCGTGCCGT 62.221 61.111 7.90 0.00 38.71 5.68
4 5 3.705638 CACACTGTGCTCGTGCCG 61.706 66.667 7.90 0.00 38.71 5.69
6 7 1.494628 CATCACACTGTGCTCGTGC 59.505 57.895 7.90 1.71 35.84 5.34
7 8 0.601046 ACCATCACACTGTGCTCGTG 60.601 55.000 7.90 0.00 38.32 4.35
8 9 0.601046 CACCATCACACTGTGCTCGT 60.601 55.000 7.90 0.00 32.98 4.18
9 10 0.601046 ACACCATCACACTGTGCTCG 60.601 55.000 7.90 0.00 32.98 5.03
10 11 0.870393 CACACCATCACACTGTGCTC 59.130 55.000 7.90 0.00 32.98 4.26
11 12 0.181114 ACACACCATCACACTGTGCT 59.819 50.000 7.90 0.00 39.16 4.40
12 13 0.588252 GACACACCATCACACTGTGC 59.412 55.000 7.90 0.00 39.16 4.57
13 14 1.869132 CTGACACACCATCACACTGTG 59.131 52.381 6.19 6.19 40.98 3.66
14 15 1.202687 CCTGACACACCATCACACTGT 60.203 52.381 0.00 0.00 0.00 3.55
15 16 1.516161 CCTGACACACCATCACACTG 58.484 55.000 0.00 0.00 0.00 3.66
16 17 0.250467 GCCTGACACACCATCACACT 60.250 55.000 0.00 0.00 0.00 3.55
17 18 1.237285 GGCCTGACACACCATCACAC 61.237 60.000 0.00 0.00 0.00 3.82
18 19 1.073025 GGCCTGACACACCATCACA 59.927 57.895 0.00 0.00 0.00 3.58
19 20 1.675641 GGGCCTGACACACCATCAC 60.676 63.158 0.84 0.00 0.00 3.06
20 21 1.426251 AAGGGCCTGACACACCATCA 61.426 55.000 6.92 0.00 0.00 3.07
21 22 0.962356 CAAGGGCCTGACACACCATC 60.962 60.000 6.92 0.00 0.00 3.51
22 23 1.075482 CAAGGGCCTGACACACCAT 59.925 57.895 6.92 0.00 0.00 3.55
23 24 2.515398 CAAGGGCCTGACACACCA 59.485 61.111 6.92 0.00 0.00 4.17
24 25 2.985847 GCAAGGGCCTGACACACC 60.986 66.667 6.92 0.00 0.00 4.16
25 26 3.357079 CGCAAGGGCCTGACACAC 61.357 66.667 6.92 0.00 36.38 3.82
37 38 5.613358 ATTTCTTTAGTCAAGACCGCAAG 57.387 39.130 0.00 0.00 41.56 4.01
38 39 4.151689 CGATTTCTTTAGTCAAGACCGCAA 59.848 41.667 0.00 0.00 41.56 4.85
39 40 3.678072 CGATTTCTTTAGTCAAGACCGCA 59.322 43.478 0.00 0.00 41.56 5.69
40 41 3.924686 TCGATTTCTTTAGTCAAGACCGC 59.075 43.478 0.00 0.00 41.56 5.68
41 42 4.921515 TGTCGATTTCTTTAGTCAAGACCG 59.078 41.667 0.00 0.00 41.56 4.79
42 43 5.927115 ACTGTCGATTTCTTTAGTCAAGACC 59.073 40.000 0.00 0.00 41.56 3.85
43 44 7.409465 AACTGTCGATTTCTTTAGTCAAGAC 57.591 36.000 0.00 0.00 41.56 3.01
44 45 8.433421 AAAACTGTCGATTTCTTTAGTCAAGA 57.567 30.769 0.00 0.00 39.99 3.02
59 60 8.175069 GCATGTTCTGAATAATAAAACTGTCGA 58.825 33.333 0.00 0.00 0.00 4.20
60 61 7.429340 GGCATGTTCTGAATAATAAAACTGTCG 59.571 37.037 0.00 0.00 0.00 4.35
61 62 8.243426 TGGCATGTTCTGAATAATAAAACTGTC 58.757 33.333 0.00 0.00 0.00 3.51
62 63 8.028938 GTGGCATGTTCTGAATAATAAAACTGT 58.971 33.333 0.00 0.00 0.00 3.55
63 64 7.218773 CGTGGCATGTTCTGAATAATAAAACTG 59.781 37.037 0.00 0.00 0.00 3.16
64 65 7.120579 TCGTGGCATGTTCTGAATAATAAAACT 59.879 33.333 6.60 0.00 0.00 2.66
65 66 7.247728 TCGTGGCATGTTCTGAATAATAAAAC 58.752 34.615 6.60 0.00 0.00 2.43
66 67 7.384439 TCGTGGCATGTTCTGAATAATAAAA 57.616 32.000 6.60 0.00 0.00 1.52
67 68 6.038161 CCTCGTGGCATGTTCTGAATAATAAA 59.962 38.462 6.60 0.00 0.00 1.40
68 69 5.527214 CCTCGTGGCATGTTCTGAATAATAA 59.473 40.000 6.60 0.00 0.00 1.40
69 70 5.056480 CCTCGTGGCATGTTCTGAATAATA 58.944 41.667 6.60 0.00 0.00 0.98
70 71 3.879295 CCTCGTGGCATGTTCTGAATAAT 59.121 43.478 6.60 0.00 0.00 1.28
71 72 3.270027 CCTCGTGGCATGTTCTGAATAA 58.730 45.455 6.60 0.00 0.00 1.40
72 73 2.905075 CCTCGTGGCATGTTCTGAATA 58.095 47.619 6.60 0.00 0.00 1.75
73 74 1.742761 CCTCGTGGCATGTTCTGAAT 58.257 50.000 6.60 0.00 0.00 2.57
74 75 3.231734 CCTCGTGGCATGTTCTGAA 57.768 52.632 6.60 0.00 0.00 3.02
96 97 4.142790 GTGGCTCTTGATCATGATGGAAT 58.857 43.478 14.30 0.00 0.00 3.01
126 127 9.651913 TTTTGTTAATCTCAAGAAAGCTGTTTT 57.348 25.926 0.00 0.00 0.00 2.43
131 132 9.631452 GCTATTTTTGTTAATCTCAAGAAAGCT 57.369 29.630 0.00 0.00 30.64 3.74
132 133 9.410556 TGCTATTTTTGTTAATCTCAAGAAAGC 57.589 29.630 0.00 0.00 31.95 3.51
134 135 9.410556 GCTGCTATTTTTGTTAATCTCAAGAAA 57.589 29.630 0.00 0.00 0.00 2.52
135 136 8.575589 TGCTGCTATTTTTGTTAATCTCAAGAA 58.424 29.630 0.00 0.00 0.00 2.52
137 138 8.922058 ATGCTGCTATTTTTGTTAATCTCAAG 57.078 30.769 0.00 0.00 0.00 3.02
168 170 2.701107 GGCAGGTCCTGTTCTAGTTTC 58.299 52.381 20.24 0.00 33.43 2.78
197 199 2.289694 TGCTTCTAGCTCTTGTTGGTCC 60.290 50.000 0.00 0.00 42.97 4.46
200 202 3.603532 TCATGCTTCTAGCTCTTGTTGG 58.396 45.455 0.00 0.00 42.97 3.77
261 263 8.474710 AGGTCCGTACTTATGTTGATACTAAT 57.525 34.615 0.00 0.00 0.00 1.73
263 265 7.886629 AAGGTCCGTACTTATGTTGATACTA 57.113 36.000 0.00 0.00 0.00 1.82
277 284 3.308438 TTCTACTGCAAAGGTCCGTAC 57.692 47.619 0.00 0.00 0.00 3.67
278 285 3.069872 TGTTTCTACTGCAAAGGTCCGTA 59.930 43.478 0.00 0.00 0.00 4.02
281 288 2.223377 CGTGTTTCTACTGCAAAGGTCC 59.777 50.000 0.00 0.00 0.00 4.46
282 289 2.870411 ACGTGTTTCTACTGCAAAGGTC 59.130 45.455 0.00 0.00 0.00 3.85
288 295 2.224185 ACATCCACGTGTTTCTACTGCA 60.224 45.455 15.65 0.00 0.00 4.41
292 299 6.715344 TTTATCACATCCACGTGTTTCTAC 57.285 37.500 15.65 0.00 38.12 2.59
293 300 7.223971 GCTATTTATCACATCCACGTGTTTCTA 59.776 37.037 15.65 0.00 38.12 2.10
302 309 7.446625 AGAAATGGAGCTATTTATCACATCCAC 59.553 37.037 0.00 0.00 38.13 4.02
321 329 3.259064 CCAGAAATGCAGCAAGAAATGG 58.741 45.455 0.00 0.62 0.00 3.16
332 340 2.824689 TATGGGAAGCCAGAAATGCA 57.175 45.000 0.00 0.00 0.00 3.96
339 347 2.724520 GGCACATATGGGAAGCCAG 58.275 57.895 9.80 0.00 44.59 4.85
364 372 2.976840 GCCATCGTTCTTGCGGCAA 61.977 57.895 15.55 15.55 42.50 4.52
366 374 2.583685 GAAGCCATCGTTCTTGCGGC 62.584 60.000 0.00 0.00 43.31 6.53
376 384 0.104855 TTCTGATCGGGAAGCCATCG 59.895 55.000 0.62 0.00 0.00 3.84
377 385 1.414181 TCTTCTGATCGGGAAGCCATC 59.586 52.381 17.92 0.00 39.75 3.51
378 386 1.139853 GTCTTCTGATCGGGAAGCCAT 59.860 52.381 17.92 0.00 39.75 4.40
389 397 1.938585 TCCTTCACGGGTCTTCTGAT 58.061 50.000 0.00 0.00 0.00 2.90
400 408 3.125316 GTGGCTATTTGACTTCCTTCACG 59.875 47.826 0.00 0.00 0.00 4.35
401 409 4.154918 CAGTGGCTATTTGACTTCCTTCAC 59.845 45.833 0.00 0.00 0.00 3.18
402 410 4.202461 ACAGTGGCTATTTGACTTCCTTCA 60.202 41.667 0.00 0.00 0.00 3.02
407 415 4.410492 CACACAGTGGCTATTTGACTTC 57.590 45.455 5.31 0.00 0.00 3.01
423 431 2.034048 TTGTGCCGCTCTACCACACA 62.034 55.000 0.00 0.00 39.01 3.72
424 432 0.882927 TTTGTGCCGCTCTACCACAC 60.883 55.000 0.00 0.00 39.01 3.82
425 433 0.036164 ATTTGTGCCGCTCTACCACA 59.964 50.000 0.00 0.00 37.67 4.17
428 436 5.941948 ATATTAATTTGTGCCGCTCTACC 57.058 39.130 0.00 0.00 0.00 3.18
430 438 7.561021 TTCAATATTAATTTGTGCCGCTCTA 57.439 32.000 0.00 0.00 0.00 2.43
432 440 6.972328 TCTTTCAATATTAATTTGTGCCGCTC 59.028 34.615 0.00 0.00 0.00 5.03
459 476 2.554032 CCATCTGGGATGGCGTAAAATC 59.446 50.000 12.74 0.00 40.01 2.17
481 498 1.490490 GTTCTGTCCCCCATGCTCATA 59.510 52.381 0.00 0.00 0.00 2.15
495 512 4.631131 TCGAACACATCATCTTGTTCTGT 58.369 39.130 11.52 0.00 46.32 3.41
496 513 5.791367 ATCGAACACATCATCTTGTTCTG 57.209 39.130 11.52 6.48 46.32 3.02
497 514 6.634805 AGTATCGAACACATCATCTTGTTCT 58.365 36.000 11.52 0.00 46.32 3.01
503 520 6.655003 ACCAAAAAGTATCGAACACATCATCT 59.345 34.615 0.00 0.00 0.00 2.90
508 525 6.932400 TGTAGACCAAAAAGTATCGAACACAT 59.068 34.615 0.00 0.00 0.00 3.21
512 529 8.928733 TGTATTGTAGACCAAAAAGTATCGAAC 58.071 33.333 0.00 0.00 36.44 3.95
524 541 8.714179 CGTTGTTTCTATTGTATTGTAGACCAA 58.286 33.333 0.00 0.00 37.49 3.67
525 542 8.089597 TCGTTGTTTCTATTGTATTGTAGACCA 58.910 33.333 0.00 0.00 0.00 4.02
531 548 8.296713 AGCAAATCGTTGTTTCTATTGTATTGT 58.703 29.630 0.00 0.00 37.06 2.71
535 552 8.766000 TCTAGCAAATCGTTGTTTCTATTGTA 57.234 30.769 0.00 0.00 37.06 2.41
537 554 6.684555 GCTCTAGCAAATCGTTGTTTCTATTG 59.315 38.462 0.00 0.00 41.59 1.90
540 557 5.348724 CAGCTCTAGCAAATCGTTGTTTCTA 59.651 40.000 4.54 0.00 45.16 2.10
541 558 4.153117 CAGCTCTAGCAAATCGTTGTTTCT 59.847 41.667 4.54 0.00 45.16 2.52
542 559 4.398247 CAGCTCTAGCAAATCGTTGTTTC 58.602 43.478 4.54 0.00 45.16 2.78
544 561 2.744202 CCAGCTCTAGCAAATCGTTGTT 59.256 45.455 4.54 0.00 45.16 2.83
545 562 2.028112 TCCAGCTCTAGCAAATCGTTGT 60.028 45.455 4.54 0.00 45.16 3.32
546 563 2.621338 TCCAGCTCTAGCAAATCGTTG 58.379 47.619 4.54 0.00 45.16 4.10
547 564 3.003480 GTTCCAGCTCTAGCAAATCGTT 58.997 45.455 4.54 0.00 45.16 3.85
548 565 2.622436 GTTCCAGCTCTAGCAAATCGT 58.378 47.619 4.54 0.00 45.16 3.73
549 566 1.936547 GGTTCCAGCTCTAGCAAATCG 59.063 52.381 4.54 0.00 45.16 3.34
550 567 2.941720 CAGGTTCCAGCTCTAGCAAATC 59.058 50.000 4.54 0.00 45.16 2.17
551 568 2.573462 TCAGGTTCCAGCTCTAGCAAAT 59.427 45.455 4.54 0.00 45.16 2.32
552 569 1.977854 TCAGGTTCCAGCTCTAGCAAA 59.022 47.619 4.54 0.00 45.16 3.68
553 570 1.276421 GTCAGGTTCCAGCTCTAGCAA 59.724 52.381 4.54 0.00 45.16 3.91
554 571 0.898320 GTCAGGTTCCAGCTCTAGCA 59.102 55.000 4.54 0.00 45.16 3.49
558 575 1.910772 AGCGTCAGGTTCCAGCTCT 60.911 57.895 0.00 0.00 31.94 4.09
576 593 2.992124 TCCGGTGAACAACTTCTTCA 57.008 45.000 0.00 0.00 0.00 3.02
591 608 1.750778 ACATAATTGCTTGCCTTCCGG 59.249 47.619 0.00 0.00 0.00 5.14
625 642 6.054295 GCTCCTCATAAGATGAAGATTGTGT 58.946 40.000 0.00 0.00 39.11 3.72
632 649 6.145858 CGATCAAAGCTCCTCATAAGATGAAG 59.854 42.308 0.00 0.00 39.11 3.02
642 659 1.205655 CTGGTCGATCAAAGCTCCTCA 59.794 52.381 0.00 0.00 0.00 3.86
643 660 1.478510 TCTGGTCGATCAAAGCTCCTC 59.521 52.381 0.00 0.00 0.00 3.71
665 682 7.571798 GCAAATGAAGCGAAATTTTGGAAATCT 60.572 33.333 7.54 0.00 0.00 2.40
674 691 4.874970 ACAGAGCAAATGAAGCGAAATTT 58.125 34.783 0.00 0.00 37.01 1.82
681 698 3.750130 TCTTCTGACAGAGCAAATGAAGC 59.250 43.478 5.10 0.00 32.19 3.86
689 706 2.634453 TGGACAATCTTCTGACAGAGCA 59.366 45.455 5.10 0.00 0.00 4.26
704 721 2.214216 CCAGAGGGGACGTGGACAA 61.214 63.158 0.00 0.00 40.68 3.18
705 722 2.603473 CCAGAGGGGACGTGGACA 60.603 66.667 0.00 0.00 40.68 4.02
716 733 2.028130 CTAGTAGCTCACACCCAGAGG 58.972 57.143 0.00 0.00 40.04 3.69
717 734 2.729194 ACTAGTAGCTCACACCCAGAG 58.271 52.381 0.00 0.00 36.21 3.35
718 735 2.901338 ACTAGTAGCTCACACCCAGA 57.099 50.000 0.00 0.00 0.00 3.86
719 736 4.270834 TCTTACTAGTAGCTCACACCCAG 58.729 47.826 2.23 0.00 0.00 4.45
720 737 4.311520 TCTTACTAGTAGCTCACACCCA 57.688 45.455 2.23 0.00 0.00 4.51
721 738 5.656213 TTTCTTACTAGTAGCTCACACCC 57.344 43.478 2.23 0.00 0.00 4.61
722 739 6.864342 TGATTTCTTACTAGTAGCTCACACC 58.136 40.000 2.23 0.00 0.00 4.16
723 740 8.934507 ATTGATTTCTTACTAGTAGCTCACAC 57.065 34.615 2.23 0.00 0.00 3.82
742 759 9.840427 CACGTTTTCCTTTACTCATAATTGATT 57.160 29.630 0.00 0.00 0.00 2.57
743 760 8.458843 CCACGTTTTCCTTTACTCATAATTGAT 58.541 33.333 0.00 0.00 0.00 2.57
744 761 7.662258 TCCACGTTTTCCTTTACTCATAATTGA 59.338 33.333 0.00 0.00 0.00 2.57
745 762 7.812648 TCCACGTTTTCCTTTACTCATAATTG 58.187 34.615 0.00 0.00 0.00 2.32
746 763 7.989416 TCCACGTTTTCCTTTACTCATAATT 57.011 32.000 0.00 0.00 0.00 1.40
747 764 7.094506 GGTTCCACGTTTTCCTTTACTCATAAT 60.095 37.037 0.00 0.00 0.00 1.28
748 765 6.205270 GGTTCCACGTTTTCCTTTACTCATAA 59.795 38.462 0.00 0.00 0.00 1.90
749 766 5.702209 GGTTCCACGTTTTCCTTTACTCATA 59.298 40.000 0.00 0.00 0.00 2.15
750 767 4.517832 GGTTCCACGTTTTCCTTTACTCAT 59.482 41.667 0.00 0.00 0.00 2.90
751 768 3.878699 GGTTCCACGTTTTCCTTTACTCA 59.121 43.478 0.00 0.00 0.00 3.41
752 769 4.024302 CAGGTTCCACGTTTTCCTTTACTC 60.024 45.833 0.00 0.00 0.00 2.59
753 770 3.881089 CAGGTTCCACGTTTTCCTTTACT 59.119 43.478 0.00 0.00 0.00 2.24
754 771 3.628942 ACAGGTTCCACGTTTTCCTTTAC 59.371 43.478 0.00 0.00 0.00 2.01
755 772 3.888583 ACAGGTTCCACGTTTTCCTTTA 58.111 40.909 0.00 0.00 0.00 1.85
756 773 2.730382 ACAGGTTCCACGTTTTCCTTT 58.270 42.857 0.00 0.00 0.00 3.11
757 774 2.430248 ACAGGTTCCACGTTTTCCTT 57.570 45.000 0.00 0.00 0.00 3.36
758 775 3.564053 TTACAGGTTCCACGTTTTCCT 57.436 42.857 0.00 0.00 0.00 3.36
759 776 3.004002 CCTTTACAGGTTCCACGTTTTCC 59.996 47.826 0.00 0.00 35.06 3.13
760 777 3.004002 CCCTTTACAGGTTCCACGTTTTC 59.996 47.826 0.00 0.00 38.79 2.29
770 787 4.142026 GCTTTGTTGTTCCCTTTACAGGTT 60.142 41.667 0.00 0.00 38.79 3.50
846 863 2.208619 TTTCGGTCCTGCCACGGTA 61.209 57.895 0.00 0.00 36.97 4.02
854 876 1.192146 TCCTCCCAGTTTCGGTCCTG 61.192 60.000 0.00 0.00 0.00 3.86
965 1007 1.024579 GCGGGTGAGTGTGGGTATTG 61.025 60.000 0.00 0.00 0.00 1.90
970 1012 2.034066 AATGCGGGTGAGTGTGGG 59.966 61.111 0.00 0.00 0.00 4.61
973 1015 0.038166 AATGGAATGCGGGTGAGTGT 59.962 50.000 0.00 0.00 0.00 3.55
975 1017 0.394352 GGAATGGAATGCGGGTGAGT 60.394 55.000 0.00 0.00 0.00 3.41
980 1022 1.379710 TGTGGGAATGGAATGCGGG 60.380 57.895 0.00 0.00 0.00 6.13
1004 1046 1.282930 GAGTGGAGAACGCGGTTGAC 61.283 60.000 12.47 0.00 33.90 3.18
1053 1102 1.891919 CGGTGGCCATATGAACGGG 60.892 63.158 9.72 0.00 0.00 5.28
1057 1106 1.347707 GGATCTCGGTGGCCATATGAA 59.652 52.381 9.72 0.00 0.00 2.57
1074 1123 4.778143 GTTGTGCGGGCGGAGGAT 62.778 66.667 0.00 0.00 0.00 3.24
1274 1338 2.601067 TACACTTCCACCGCGGGA 60.601 61.111 31.76 15.75 34.36 5.14
1435 1504 2.589540 CATTAGCTGGCACCGGGA 59.410 61.111 6.32 0.00 0.00 5.14
1450 1535 3.447586 ACTAACATACAGCTCGTGTCCAT 59.552 43.478 0.00 0.00 40.94 3.41
1484 1569 1.787847 CCACTCAACGACGATTGCC 59.212 57.895 0.00 0.00 0.00 4.52
1659 1753 3.494332 ACGTAGGTACTCTTGGACTTGT 58.506 45.455 0.00 0.00 41.75 3.16
1753 1850 8.934825 GCATGAACAGAAATTAAAATTTAGCCA 58.065 29.630 0.00 1.46 38.64 4.75
1789 1886 7.549839 CATCATGATTGGGACACATAAAACTT 58.450 34.615 5.16 0.00 39.29 2.66
1791 1888 5.750067 GCATCATGATTGGGACACATAAAAC 59.250 40.000 5.16 0.00 39.29 2.43
1792 1889 5.657745 AGCATCATGATTGGGACACATAAAA 59.342 36.000 5.16 0.00 39.29 1.52
1802 1899 5.163447 ACTCATTCAAAGCATCATGATTGGG 60.163 40.000 5.16 1.65 34.91 4.12
1880 2011 0.177141 GCCGGCTGGTGTGACTAATA 59.823 55.000 22.15 0.00 37.67 0.98
1952 2089 1.446099 GACGACCGATTCAGCTGCA 60.446 57.895 9.47 0.00 0.00 4.41
1963 2375 1.073964 TAAGACGACTGAGACGACCG 58.926 55.000 11.75 0.00 34.70 4.79
1992 2404 1.063764 CGACGAGGCAAGTAGAGGTAC 59.936 57.143 0.00 0.00 0.00 3.34
1993 2405 1.339438 ACGACGAGGCAAGTAGAGGTA 60.339 52.381 0.00 0.00 0.00 3.08
1994 2406 0.608582 ACGACGAGGCAAGTAGAGGT 60.609 55.000 0.00 0.00 0.00 3.85
1996 2408 3.169733 GTTAACGACGAGGCAAGTAGAG 58.830 50.000 0.00 0.00 0.00 2.43
1997 2409 3.207474 GTTAACGACGAGGCAAGTAGA 57.793 47.619 0.00 0.00 0.00 2.59
2009 2422 1.206523 GGAGGCTATGCGTTAACGAC 58.793 55.000 31.03 21.07 43.02 4.34
2012 2425 1.669265 GGTTGGAGGCTATGCGTTAAC 59.331 52.381 0.00 0.00 0.00 2.01
2014 2427 0.906066 TGGTTGGAGGCTATGCGTTA 59.094 50.000 0.00 0.00 0.00 3.18
2023 2436 1.903404 CCACAGGTTGGTTGGAGGC 60.903 63.158 0.00 0.00 41.10 4.70
2039 2452 1.990799 CGTTCGAGATGCACTAACCA 58.009 50.000 0.00 0.00 0.00 3.67
2054 2467 2.741211 GACTTGGGGTCGGCGTTC 60.741 66.667 6.85 1.15 35.07 3.95
2106 2525 1.403780 GCCGACTTCTACATCACGGTT 60.404 52.381 0.00 0.00 41.92 4.44
2123 2542 2.358898 CCAGGTCTATTTTGAATGGCCG 59.641 50.000 0.00 0.00 0.00 6.13
2139 2558 5.622346 TTTGAGTTTTAAATTGGCCAGGT 57.378 34.783 5.11 0.00 0.00 4.00
2142 2561 5.011125 TCGGATTTGAGTTTTAAATTGGCCA 59.989 36.000 0.00 0.00 0.00 5.36
2145 2564 6.451393 TGGTCGGATTTGAGTTTTAAATTGG 58.549 36.000 0.00 0.00 0.00 3.16
2156 2575 3.997021 GGCACTATATGGTCGGATTTGAG 59.003 47.826 0.00 0.00 0.00 3.02
2163 2596 0.895530 ATCGGGCACTATATGGTCGG 59.104 55.000 0.00 0.00 0.00 4.79
2164 2597 1.544246 TGATCGGGCACTATATGGTCG 59.456 52.381 0.00 0.00 0.00 4.79
2165 2598 2.299013 TGTGATCGGGCACTATATGGTC 59.701 50.000 9.39 0.00 39.49 4.02
2166 2599 2.325484 TGTGATCGGGCACTATATGGT 58.675 47.619 9.39 0.00 39.49 3.55
2167 2600 3.067106 GTTGTGATCGGGCACTATATGG 58.933 50.000 9.39 0.00 39.49 2.74
2168 2601 3.067106 GGTTGTGATCGGGCACTATATG 58.933 50.000 9.39 0.00 39.49 1.78
2169 2602 2.703536 TGGTTGTGATCGGGCACTATAT 59.296 45.455 9.39 0.00 39.49 0.86
2170 2603 2.112190 TGGTTGTGATCGGGCACTATA 58.888 47.619 9.39 0.00 39.49 1.31
2171 2604 0.908910 TGGTTGTGATCGGGCACTAT 59.091 50.000 9.39 0.00 39.49 2.12
2172 2605 0.687920 TTGGTTGTGATCGGGCACTA 59.312 50.000 9.39 0.53 39.49 2.74
2173 2606 0.179004 TTTGGTTGTGATCGGGCACT 60.179 50.000 9.39 0.00 39.49 4.40
2174 2607 0.671251 TTTTGGTTGTGATCGGGCAC 59.329 50.000 2.23 2.23 39.22 5.01
2175 2608 1.403814 TTTTTGGTTGTGATCGGGCA 58.596 45.000 0.00 0.00 0.00 5.36
2195 2628 6.862209 TGTGAAAACTATGCAAACTTGTCTT 58.138 32.000 0.00 0.00 0.00 3.01
2211 2644 1.199789 TGCGATCAGGCATGTGAAAAC 59.800 47.619 0.00 0.00 38.17 2.43
2265 2698 8.686334 TCTGGTAAGGCAGAAATCAATATTTTC 58.314 33.333 0.00 0.00 35.41 2.29
2271 2704 4.263905 TGGTCTGGTAAGGCAGAAATCAAT 60.264 41.667 0.00 0.00 0.00 2.57
2273 2706 2.642311 TGGTCTGGTAAGGCAGAAATCA 59.358 45.455 0.00 0.00 0.00 2.57
2284 2717 1.553248 CTCGGATTGGTGGTCTGGTAA 59.447 52.381 0.00 0.00 0.00 2.85
2288 2721 1.450312 GGCTCGGATTGGTGGTCTG 60.450 63.158 0.00 0.00 0.00 3.51
2321 2754 4.379243 CGAGAAGGCGGCAGTGGT 62.379 66.667 13.08 0.00 0.00 4.16
2349 2805 1.660607 CATATGACGTTGAAGCGCACT 59.339 47.619 11.47 0.00 34.88 4.40
2350 2806 1.267532 CCATATGACGTTGAAGCGCAC 60.268 52.381 11.47 3.52 34.88 5.34
2370 2826 2.740714 GACCGTGCAATCCGTCTGC 61.741 63.158 0.00 0.00 40.35 4.26
2372 2828 0.460284 GATGACCGTGCAATCCGTCT 60.460 55.000 0.00 0.00 0.00 4.18
2374 2830 1.449601 GGATGACCGTGCAATCCGT 60.450 57.895 0.00 0.00 0.00 4.69
2378 2834 2.779755 TGTAAGGATGACCGTGCAAT 57.220 45.000 0.00 0.00 37.33 3.56
2386 2842 4.322080 TGGATGACGATGTAAGGATGAC 57.678 45.455 0.00 0.00 0.00 3.06
2395 2851 2.483714 CGAGGGATTTGGATGACGATGT 60.484 50.000 0.00 0.00 0.00 3.06
2414 2871 4.921515 CGAAGATGTTGACCTTAAAGACGA 59.078 41.667 0.00 0.00 0.00 4.20
2415 2872 4.434330 GCGAAGATGTTGACCTTAAAGACG 60.434 45.833 0.00 0.00 0.00 4.18
2416 2873 4.142881 GGCGAAGATGTTGACCTTAAAGAC 60.143 45.833 0.00 0.00 0.00 3.01
2445 2902 1.009078 TTGAGATTGCATCCGCTTCG 58.991 50.000 0.00 0.00 39.64 3.79
2453 2910 6.713903 TGAAGAGAAGAAGTTTGAGATTGCAT 59.286 34.615 0.00 0.00 0.00 3.96
2465 2922 8.592809 AGAATGTCATACTTGAAGAGAAGAAGT 58.407 33.333 0.00 0.00 32.48 3.01
2485 2942 6.493449 GCTCAAGCTTTTAGAGAAGAATGT 57.507 37.500 14.68 0.00 38.21 2.71
2527 2984 4.039973 AGGACGAGAGGTTAACATGTTGAA 59.960 41.667 21.42 8.59 0.00 2.69
2547 3004 3.282021 GCATCAAGAAGGCATGTAAGGA 58.718 45.455 0.00 0.00 0.00 3.36
2574 3031 1.555075 GGAGGAGGTATGTGTCAAGCA 59.445 52.381 0.00 0.00 0.00 3.91
2575 3032 1.834263 AGGAGGAGGTATGTGTCAAGC 59.166 52.381 0.00 0.00 0.00 4.01
2580 3037 2.761208 CGAAGAAGGAGGAGGTATGTGT 59.239 50.000 0.00 0.00 0.00 3.72
2586 3043 0.836400 TTGGCGAAGAAGGAGGAGGT 60.836 55.000 0.00 0.00 0.00 3.85
2590 3047 2.409948 AATCTTGGCGAAGAAGGAGG 57.590 50.000 15.48 0.00 41.64 4.30
2603 3060 5.233988 ACAGAGAGGTTCGAGAAAATCTTG 58.766 41.667 3.55 0.00 0.00 3.02
2615 3072 2.626840 GCCAAGATGACAGAGAGGTTC 58.373 52.381 0.00 0.00 0.00 3.62
2669 3126 7.456269 AGAAGAGGGTTCTAGAGAAAGAAATGA 59.544 37.037 0.00 0.00 37.24 2.57
2682 3139 6.500751 ACAATGAAGGTTAGAAGAGGGTTCTA 59.499 38.462 0.00 0.00 31.96 2.10
2683 3140 5.310857 ACAATGAAGGTTAGAAGAGGGTTCT 59.689 40.000 0.00 0.00 34.29 3.01
2684 3141 5.561679 ACAATGAAGGTTAGAAGAGGGTTC 58.438 41.667 0.00 0.00 0.00 3.62
2712 3169 2.383855 TCCAACTGACCCAACAAAAGG 58.616 47.619 0.00 0.00 0.00 3.11
2726 3183 2.552373 GGAAGAAACGGGTGATCCAACT 60.552 50.000 0.00 0.00 34.36 3.16
2764 3221 2.027625 GTCAACTCCGCCAAGACCG 61.028 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.