Multiple sequence alignment - TraesCS5A01G505100

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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 TraesCS5A01G505100 chr5A 100.000 3158 0 0 1 3158 670427149 670423992 0.000000e+00 5832.0
1 TraesCS5A01G505100 chr5A 80.528 1325 176 36 991 2276 706678529 706677248 0.000000e+00 942.0
2 TraesCS5A01G505100 chr5A 91.429 140 10 1 654 793 584047757 584047620 1.160000e-44 191.0
3 TraesCS5A01G505100 chr5A 78.832 274 32 19 1240 1488 706706073 706705801 9.060000e-36 161.0
4 TraesCS5A01G505100 chr4D 92.566 1399 90 3 793 2189 488666296 488664910 0.000000e+00 1995.0
5 TraesCS5A01G505100 chr4D 83.283 999 127 17 991 1959 397158338 397157350 0.000000e+00 883.0
6 TraesCS5A01G505100 chr4D 92.692 561 27 2 2611 3157 488664477 488663917 0.000000e+00 797.0
7 TraesCS5A01G505100 chr4D 87.209 688 40 14 1 654 488666967 488666294 0.000000e+00 739.0
8 TraesCS5A01G505100 chr4D 94.949 99 2 2 2292 2388 488664601 488664504 5.460000e-33 152.0
9 TraesCS5A01G505100 chr4D 100.000 31 0 0 2359 2389 397157092 397157062 1.220000e-04 58.4
10 TraesCS5A01G505100 chr4B 91.954 1392 95 7 793 2171 626069071 626067684 0.000000e+00 1934.0
11 TraesCS5A01G505100 chr4B 88.639 757 46 9 2218 2956 626067428 626066694 0.000000e+00 885.0
12 TraesCS5A01G505100 chr4B 83.739 904 118 13 1078 1959 489294392 489293496 0.000000e+00 828.0
13 TraesCS5A01G505100 chr4B 89.640 666 46 8 1 654 626069723 626069069 0.000000e+00 826.0
14 TraesCS5A01G505100 chr4B 80.797 276 26 16 1240 1488 667263235 667263510 1.160000e-44 191.0
15 TraesCS5A01G505100 chr4B 79.121 273 33 11 1240 1490 639268899 639269169 1.950000e-37 167.0
16 TraesCS5A01G505100 chr4A 82.983 999 132 16 991 1962 54405912 54404925 0.000000e+00 869.0
17 TraesCS5A01G505100 chr4A 95.652 46 2 0 2359 2404 54404675 54404630 1.210000e-09 75.0
18 TraesCS5A01G505100 chr5D 93.919 148 7 2 650 795 274146086 274145939 4.100000e-54 222.0
19 TraesCS5A01G505100 chr6D 92.157 153 10 2 651 802 297842986 297842835 6.860000e-52 215.0
20 TraesCS5A01G505100 chr1D 93.617 141 8 1 654 793 487846233 487846093 3.190000e-50 209.0
21 TraesCS5A01G505100 chr2A 92.466 146 10 1 651 795 79301493 79301638 1.150000e-49 207.0
22 TraesCS5A01G505100 chr2B 91.275 149 12 1 650 797 37434922 37434774 5.340000e-48 202.0
23 TraesCS5A01G505100 chr1A 92.199 141 10 1 654 793 59222882 59223022 6.910000e-47 198.0
24 TraesCS5A01G505100 chr7D 91.954 87 7 0 706 792 236837950 236838036 4.280000e-24 122.0


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 TraesCS5A01G505100 chr5A 670423992 670427149 3157 True 5832.00 5832 100.000000 1 3158 1 chr5A.!!$R2 3157
1 TraesCS5A01G505100 chr5A 706677248 706678529 1281 True 942.00 942 80.528000 991 2276 1 chr5A.!!$R3 1285
2 TraesCS5A01G505100 chr4D 488663917 488666967 3050 True 920.75 1995 91.854000 1 3157 4 chr4D.!!$R2 3156
3 TraesCS5A01G505100 chr4D 397157062 397158338 1276 True 470.70 883 91.641500 991 2389 2 chr4D.!!$R1 1398
4 TraesCS5A01G505100 chr4B 626066694 626069723 3029 True 1215.00 1934 90.077667 1 2956 3 chr4B.!!$R2 2955
5 TraesCS5A01G505100 chr4B 489293496 489294392 896 True 828.00 828 83.739000 1078 1959 1 chr4B.!!$R1 881
6 TraesCS5A01G505100 chr4A 54404630 54405912 1282 True 472.00 869 89.317500 991 2404 2 chr4A.!!$R1 1413

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
457 489 0.042448 GAAAACTCGCACGGTGTGTC 60.042 55.0 20.03 7.43 35.75 3.67 F
704 739 0.101399 ATACGAGGAGCTGCGAAGTG 59.899 55.0 11.94 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2203 0.235926 GAGCTCAACTGCGGACAAAC 59.764 55.0 9.40 0.0 38.13 2.93 R
2221 2540 0.537371 AGGCCGGAACTCCTGTTTTG 60.537 55.0 5.05 0.0 36.39 2.44 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
77 78 8.738106 GTGGAGTTCATAACTACTGTACTTACT 58.262 37.037 3.81 0.00 43.07 2.24
132 133 5.416013 CACTAGAGTGTACTCATCCTTCACA 59.584 44.000 13.95 0.00 45.21 3.58
139 140 5.527582 GTGTACTCATCCTTCACAAAGTGTT 59.472 40.000 0.00 0.00 34.79 3.32
171 172 1.433053 CCAACAACTCGCAACCGTCA 61.433 55.000 0.00 0.00 35.54 4.35
197 206 3.644399 GAGACCTCGTCCGGCAACC 62.644 68.421 0.00 0.00 32.18 3.77
231 240 7.378966 GTGCACACTAGCTTTCTATATATCCA 58.621 38.462 13.17 0.00 34.99 3.41
236 245 9.148879 ACACTAGCTTTCTATATATCCAAGTGT 57.851 33.333 0.00 0.00 0.00 3.55
247 256 9.987272 CTATATATCCAAGTGTCACTTTCATCA 57.013 33.333 15.73 1.42 36.03 3.07
291 300 4.379243 AGTTGAGGAGGTGCGCGG 62.379 66.667 8.83 0.00 0.00 6.46
345 377 4.403432 ACGGATCTCTCGGGTGTATTAAAA 59.597 41.667 0.00 0.00 0.00 1.52
346 378 4.982916 CGGATCTCTCGGGTGTATTAAAAG 59.017 45.833 0.00 0.00 0.00 2.27
347 379 5.221185 CGGATCTCTCGGGTGTATTAAAAGA 60.221 44.000 0.00 0.00 0.00 2.52
349 381 7.309012 CGGATCTCTCGGGTGTATTAAAAGATA 60.309 40.741 0.00 0.00 0.00 1.98
430 462 4.024809 CGGAGAGAAAAGGTGTTGAGAAAC 60.025 45.833 0.00 0.00 0.00 2.78
457 489 0.042448 GAAAACTCGCACGGTGTGTC 60.042 55.000 20.03 7.43 35.75 3.67
480 512 1.007387 CTGCGAAACCAAACCTGCC 60.007 57.895 0.00 0.00 0.00 4.85
503 535 6.218025 CAGTACATACTGTTTGCGTTACAA 57.782 37.500 10.38 0.00 46.51 2.41
504 536 6.068931 CAGTACATACTGTTTGCGTTACAAC 58.931 40.000 10.38 0.00 46.51 3.32
505 537 5.987347 AGTACATACTGTTTGCGTTACAACT 59.013 36.000 0.00 0.00 34.73 3.16
506 538 5.744666 ACATACTGTTTGCGTTACAACTT 57.255 34.783 0.00 0.00 38.23 2.66
507 539 6.847956 ACATACTGTTTGCGTTACAACTTA 57.152 33.333 0.00 0.00 38.23 2.24
508 540 6.652245 ACATACTGTTTGCGTTACAACTTAC 58.348 36.000 0.00 0.00 38.23 2.34
509 541 6.258287 ACATACTGTTTGCGTTACAACTTACA 59.742 34.615 0.00 0.00 38.23 2.41
510 542 5.548706 ACTGTTTGCGTTACAACTTACAA 57.451 34.783 0.00 0.00 38.23 2.41
530 562 0.731417 GTGCATGCCTCTGTAAGCAG 59.269 55.000 16.68 0.00 43.38 4.24
600 635 4.102524 ACAGAGGTTTCAGGTATGTGTTCA 59.897 41.667 0.00 0.00 0.00 3.18
614 649 6.879458 GGTATGTGTTCACCAGAAATTCTACT 59.121 38.462 0.00 0.00 35.08 2.57
637 672 4.160329 TGTCTAGATTGGTGTTCCTCTGT 58.840 43.478 0.00 0.00 34.23 3.41
640 675 1.421268 AGATTGGTGTTCCTCTGTGCA 59.579 47.619 0.00 0.00 34.23 4.57
651 686 2.833943 TCCTCTGTGCATGTATGTGTCT 59.166 45.455 0.00 0.00 0.00 3.41
652 687 3.261643 TCCTCTGTGCATGTATGTGTCTT 59.738 43.478 0.00 0.00 0.00 3.01
653 688 4.466015 TCCTCTGTGCATGTATGTGTCTTA 59.534 41.667 0.00 0.00 0.00 2.10
654 689 4.807834 CCTCTGTGCATGTATGTGTCTTAG 59.192 45.833 0.00 0.00 0.00 2.18
655 690 4.758688 TCTGTGCATGTATGTGTCTTAGG 58.241 43.478 0.00 0.00 0.00 2.69
656 691 3.270027 TGTGCATGTATGTGTCTTAGGC 58.730 45.455 0.00 0.00 0.00 3.93
657 692 3.270027 GTGCATGTATGTGTCTTAGGCA 58.730 45.455 0.00 0.00 0.00 4.75
658 693 3.310774 GTGCATGTATGTGTCTTAGGCAG 59.689 47.826 0.00 0.00 0.00 4.85
659 694 3.055167 TGCATGTATGTGTCTTAGGCAGT 60.055 43.478 0.00 0.00 0.00 4.40
660 695 3.310774 GCATGTATGTGTCTTAGGCAGTG 59.689 47.826 0.00 0.00 0.00 3.66
661 696 4.507710 CATGTATGTGTCTTAGGCAGTGT 58.492 43.478 0.00 0.00 0.00 3.55
662 697 4.617253 TGTATGTGTCTTAGGCAGTGTT 57.383 40.909 0.00 0.00 0.00 3.32
663 698 4.566004 TGTATGTGTCTTAGGCAGTGTTC 58.434 43.478 0.00 0.00 0.00 3.18
664 699 2.148916 TGTGTCTTAGGCAGTGTTCG 57.851 50.000 0.00 0.00 0.00 3.95
665 700 1.270094 TGTGTCTTAGGCAGTGTTCGG 60.270 52.381 0.00 0.00 0.00 4.30
666 701 0.320421 TGTCTTAGGCAGTGTTCGGC 60.320 55.000 0.00 0.00 0.00 5.54
667 702 0.320421 GTCTTAGGCAGTGTTCGGCA 60.320 55.000 0.00 0.00 36.53 5.69
668 703 0.394938 TCTTAGGCAGTGTTCGGCAA 59.605 50.000 0.00 0.00 36.53 4.52
669 704 0.517316 CTTAGGCAGTGTTCGGCAAC 59.483 55.000 0.00 0.00 36.53 4.17
670 705 0.887387 TTAGGCAGTGTTCGGCAACC 60.887 55.000 0.00 0.00 36.53 3.77
671 706 2.741486 TAGGCAGTGTTCGGCAACCC 62.741 60.000 0.00 0.00 36.53 4.11
672 707 2.904866 GCAGTGTTCGGCAACCCA 60.905 61.111 0.00 0.00 35.02 4.51
673 708 3.030652 CAGTGTTCGGCAACCCAC 58.969 61.111 0.00 0.00 0.00 4.61
674 709 2.203294 AGTGTTCGGCAACCCACC 60.203 61.111 0.00 0.00 0.00 4.61
675 710 2.517402 GTGTTCGGCAACCCACCA 60.517 61.111 0.00 0.00 0.00 4.17
676 711 2.517402 TGTTCGGCAACCCACCAC 60.517 61.111 0.00 0.00 0.00 4.16
677 712 2.203294 GTTCGGCAACCCACCACT 60.203 61.111 0.00 0.00 0.00 4.00
678 713 2.112297 TTCGGCAACCCACCACTC 59.888 61.111 0.00 0.00 0.00 3.51
679 714 3.485346 TTCGGCAACCCACCACTCC 62.485 63.158 0.00 0.00 0.00 3.85
680 715 3.953775 CGGCAACCCACCACTCCT 61.954 66.667 0.00 0.00 0.00 3.69
681 716 2.589157 CGGCAACCCACCACTCCTA 61.589 63.158 0.00 0.00 0.00 2.94
682 717 1.765074 GGCAACCCACCACTCCTAA 59.235 57.895 0.00 0.00 0.00 2.69
683 718 0.111639 GGCAACCCACCACTCCTAAA 59.888 55.000 0.00 0.00 0.00 1.85
684 719 1.479757 GGCAACCCACCACTCCTAAAA 60.480 52.381 0.00 0.00 0.00 1.52
685 720 2.312390 GCAACCCACCACTCCTAAAAA 58.688 47.619 0.00 0.00 0.00 1.94
686 721 2.897326 GCAACCCACCACTCCTAAAAAT 59.103 45.455 0.00 0.00 0.00 1.82
687 722 4.083565 GCAACCCACCACTCCTAAAAATA 58.916 43.478 0.00 0.00 0.00 1.40
688 723 4.082408 GCAACCCACCACTCCTAAAAATAC 60.082 45.833 0.00 0.00 0.00 1.89
689 724 3.946606 ACCCACCACTCCTAAAAATACG 58.053 45.455 0.00 0.00 0.00 3.06
690 725 3.583966 ACCCACCACTCCTAAAAATACGA 59.416 43.478 0.00 0.00 0.00 3.43
691 726 4.189231 CCCACCACTCCTAAAAATACGAG 58.811 47.826 0.00 0.00 0.00 4.18
692 727 4.189231 CCACCACTCCTAAAAATACGAGG 58.811 47.826 0.00 0.00 0.00 4.63
693 728 4.081309 CCACCACTCCTAAAAATACGAGGA 60.081 45.833 0.00 0.00 37.02 3.71
698 733 3.793559 TCCTAAAAATACGAGGAGCTGC 58.206 45.455 0.00 0.00 34.36 5.25
699 734 2.540101 CCTAAAAATACGAGGAGCTGCG 59.460 50.000 0.00 0.00 31.45 5.18
700 735 2.380084 AAAAATACGAGGAGCTGCGA 57.620 45.000 0.00 0.00 0.00 5.10
701 736 2.380084 AAAATACGAGGAGCTGCGAA 57.620 45.000 0.00 0.00 0.00 4.70
702 737 1.927895 AAATACGAGGAGCTGCGAAG 58.072 50.000 0.00 0.00 0.00 3.79
703 738 0.818296 AATACGAGGAGCTGCGAAGT 59.182 50.000 0.00 4.07 0.00 3.01
704 739 0.101399 ATACGAGGAGCTGCGAAGTG 59.899 55.000 11.94 0.00 0.00 3.16
705 740 1.934220 TACGAGGAGCTGCGAAGTGG 61.934 60.000 11.94 0.00 0.00 4.00
706 741 2.973899 GAGGAGCTGCGAAGTGGA 59.026 61.111 0.00 0.00 0.00 4.02
707 742 1.153667 GAGGAGCTGCGAAGTGGAG 60.154 63.158 0.00 0.00 39.42 3.86
708 743 2.125350 GGAGCTGCGAAGTGGAGG 60.125 66.667 0.00 0.00 36.36 4.30
709 744 2.125350 GAGCTGCGAAGTGGAGGG 60.125 66.667 0.00 0.00 36.36 4.30
710 745 2.604686 AGCTGCGAAGTGGAGGGA 60.605 61.111 0.00 0.00 36.36 4.20
711 746 2.435059 GCTGCGAAGTGGAGGGAC 60.435 66.667 0.00 0.00 36.36 4.46
713 748 1.079543 CTGCGAAGTGGAGGGACTG 60.080 63.158 0.00 0.00 41.55 3.51
722 757 3.386237 GAGGGACTGCAGCTCCGT 61.386 66.667 22.28 22.28 41.55 4.69
723 758 3.655810 GAGGGACTGCAGCTCCGTG 62.656 68.421 25.23 0.90 41.55 4.94
736 771 2.409975 GCTCCGTGCTGTTTAACTACA 58.590 47.619 0.00 0.00 38.95 2.74
737 772 2.412089 GCTCCGTGCTGTTTAACTACAG 59.588 50.000 3.35 3.35 46.55 2.74
745 780 3.335579 CTGTTTAACTACAGCTCCACCC 58.664 50.000 0.00 0.00 39.12 4.61
746 781 2.976882 TGTTTAACTACAGCTCCACCCT 59.023 45.455 0.00 0.00 0.00 4.34
747 782 3.244422 TGTTTAACTACAGCTCCACCCTG 60.244 47.826 0.00 0.00 36.41 4.45
748 783 0.902531 TAACTACAGCTCCACCCTGC 59.097 55.000 0.00 0.00 33.65 4.85
749 784 0.838122 AACTACAGCTCCACCCTGCT 60.838 55.000 0.00 0.00 40.54 4.24
750 785 1.261238 ACTACAGCTCCACCCTGCTC 61.261 60.000 0.00 0.00 37.44 4.26
751 786 1.965754 CTACAGCTCCACCCTGCTCC 61.966 65.000 0.00 0.00 37.44 4.70
752 787 4.106925 CAGCTCCACCCTGCTCCC 62.107 72.222 0.00 0.00 37.44 4.30
758 793 4.087892 CACCCTGCTCCCGGAGTG 62.088 72.222 16.09 9.08 31.39 3.51
771 806 4.803426 GAGTGGAGCGGCGGAGTG 62.803 72.222 9.78 0.00 0.00 3.51
776 811 4.200283 GAGCGGCGGAGTGGAGAG 62.200 72.222 9.78 0.00 0.00 3.20
777 812 4.742649 AGCGGCGGAGTGGAGAGA 62.743 66.667 9.78 0.00 0.00 3.10
778 813 4.500116 GCGGCGGAGTGGAGAGAC 62.500 72.222 9.78 0.00 0.00 3.36
779 814 2.752238 CGGCGGAGTGGAGAGACT 60.752 66.667 0.00 0.00 0.00 3.24
780 815 2.766400 CGGCGGAGTGGAGAGACTC 61.766 68.421 0.00 0.00 41.55 3.36
789 824 2.194460 GGAGAGACTCCGAACAGGG 58.806 63.158 0.00 0.00 41.08 4.45
790 825 1.513622 GAGAGACTCCGAACAGGGC 59.486 63.158 0.00 0.00 41.52 5.19
791 826 0.968393 GAGAGACTCCGAACAGGGCT 60.968 60.000 0.00 0.00 41.52 5.19
810 845 5.105187 AGGGCTTTAATCATCAAGCTTTTCC 60.105 40.000 0.00 0.00 44.20 3.13
858 893 1.000283 CCAAACCAATGGCTTACGCAA 60.000 47.619 0.00 0.00 38.10 4.85
876 911 4.162812 CGCAAACGGTAAGCACATTAATT 58.837 39.130 5.72 0.00 34.97 1.40
925 960 3.934457 TCTACAAGTTCAGATGCGACA 57.066 42.857 0.00 0.00 0.00 4.35
967 1002 5.237344 GTGGATAAGATGCTGCGAGTTAAAT 59.763 40.000 0.00 0.00 0.00 1.40
977 1012 4.084328 GCTGCGAGTTAAATGTAGCTATGG 60.084 45.833 0.00 0.00 38.17 2.74
1060 1108 1.151810 AGCAAGAAGGGGGTCCAGA 60.152 57.895 0.00 0.00 34.83 3.86
1071 1119 2.431683 GTCCAGAGCCACCTTGCA 59.568 61.111 0.00 0.00 0.00 4.08
1072 1120 1.228245 GTCCAGAGCCACCTTGCAA 60.228 57.895 0.00 0.00 0.00 4.08
1074 1122 0.112995 TCCAGAGCCACCTTGCAATT 59.887 50.000 0.00 0.00 0.00 2.32
1075 1123 0.529378 CCAGAGCCACCTTGCAATTC 59.471 55.000 0.00 0.00 0.00 2.17
1076 1124 1.250328 CAGAGCCACCTTGCAATTCA 58.750 50.000 0.00 0.00 0.00 2.57
1165 1219 1.696063 CCCGGCATTCAATCCATCTT 58.304 50.000 0.00 0.00 0.00 2.40
1167 1221 2.026641 CCGGCATTCAATCCATCTTGT 58.973 47.619 0.00 0.00 0.00 3.16
1190 1244 0.887933 TCCAATTTCCCGAGCTTTGC 59.112 50.000 0.00 0.00 0.00 3.68
1204 1258 0.445436 CTTTGCAGGCTCATCGTCAC 59.555 55.000 0.00 0.00 0.00 3.67
1320 1377 1.068121 AGGCTAGCACCCTGAACTTT 58.932 50.000 18.24 0.00 0.00 2.66
1335 1401 4.634703 TTTTCCGGCTGGCAGCGA 62.635 61.111 31.22 21.57 43.62 4.93
1455 1530 2.849007 CAGCAGCAGTTCGTGTCG 59.151 61.111 0.00 0.00 0.00 4.35
1456 1531 3.038417 AGCAGCAGTTCGTGTCGC 61.038 61.111 0.00 0.00 0.00 5.19
1530 1612 2.095853 GCATTTACGTGATCACCAGGTG 59.904 50.000 20.03 14.19 43.05 4.00
1558 1640 3.016736 GGCTGCAGCTTAAATAGTTGGA 58.983 45.455 35.82 0.00 41.70 3.53
1622 1704 3.603532 AGTACCATCGACTACGTGAAGA 58.396 45.455 0.00 0.00 40.69 2.87
1624 1706 3.213249 ACCATCGACTACGTGAAGAAC 57.787 47.619 0.00 0.00 40.69 3.01
1669 1754 3.059982 CAAGGCTCACGGAGGTCA 58.940 61.111 0.00 0.00 0.00 4.02
1882 1976 1.073199 CGAAAACCAGGGCCTGTCT 59.927 57.895 30.68 15.34 0.00 3.41
1985 2089 6.149973 CCCTGGTCATATATACATTGTGCAAG 59.850 42.308 0.00 0.00 0.00 4.01
2143 2253 2.751806 CTGAAAATGGCCCTCAGAAGTC 59.248 50.000 13.33 0.00 39.15 3.01
2198 2308 6.633856 ACAAATGTCAAATGATTAGGCCTTC 58.366 36.000 12.58 3.36 0.00 3.46
2202 2312 2.091333 TCAAATGATTAGGCCTTCCCCC 60.091 50.000 12.58 0.00 0.00 5.40
2221 2540 3.096852 CCCCTTCCCTTGTATTTCAACC 58.903 50.000 0.00 0.00 32.18 3.77
2232 2551 6.183360 CCTTGTATTTCAACCAAAACAGGAGT 60.183 38.462 0.00 0.00 32.18 3.85
2284 2652 6.152661 AGTTTCTGAGTTTGTCAACCATTTCA 59.847 34.615 0.00 0.00 33.60 2.69
2285 2653 5.756195 TCTGAGTTTGTCAACCATTTCAG 57.244 39.130 0.00 0.00 34.78 3.02
2286 2654 5.436175 TCTGAGTTTGTCAACCATTTCAGA 58.564 37.500 8.46 8.46 37.80 3.27
2287 2655 6.064060 TCTGAGTTTGTCAACCATTTCAGAT 58.936 36.000 8.46 0.00 36.38 2.90
2288 2656 6.547141 TCTGAGTTTGTCAACCATTTCAGATT 59.453 34.615 8.46 0.00 36.38 2.40
2392 2762 4.047627 TGTGACTAACCAGATCTCCTCA 57.952 45.455 0.00 0.00 0.00 3.86
2404 2774 3.826157 AGATCTCCTCATCTGATTCCGTC 59.174 47.826 0.00 0.00 31.48 4.79
2407 2780 3.963374 TCTCCTCATCTGATTCCGTCAAT 59.037 43.478 0.00 0.00 36.14 2.57
2417 2790 5.872617 TCTGATTCCGTCAATGTATTTCGTT 59.127 36.000 0.00 0.00 36.14 3.85
2444 2817 8.281212 ACAAGAATATTCCACATACAAGAACC 57.719 34.615 11.92 0.00 0.00 3.62
2445 2818 7.065803 ACAAGAATATTCCACATACAAGAACCG 59.934 37.037 11.92 0.00 0.00 4.44
2449 2822 2.355197 TCCACATACAAGAACCGCATG 58.645 47.619 0.00 0.00 0.00 4.06
2456 2829 2.229792 ACAAGAACCGCATGTGAATGT 58.770 42.857 8.11 2.52 0.00 2.71
2464 2837 4.517285 ACCGCATGTGAATGTTCTAATCT 58.483 39.130 8.11 0.00 0.00 2.40
2504 2877 7.251704 TGAATGTTCTGAAACTTCTTGTCTC 57.748 36.000 11.94 0.00 36.30 3.36
2563 2936 2.806945 TTCTGCCTAAATCCACCTGG 57.193 50.000 0.00 0.00 0.00 4.45
2603 2976 3.115554 GCATATTTTGGCGGAATGTGTC 58.884 45.455 9.77 2.02 30.93 3.67
2604 2977 3.181487 GCATATTTTGGCGGAATGTGTCT 60.181 43.478 9.77 0.00 30.93 3.41
2605 2978 4.036262 GCATATTTTGGCGGAATGTGTCTA 59.964 41.667 9.77 0.00 30.93 2.59
2606 2979 5.278463 GCATATTTTGGCGGAATGTGTCTAT 60.278 40.000 9.77 0.00 30.93 1.98
2607 2980 6.072728 GCATATTTTGGCGGAATGTGTCTATA 60.073 38.462 9.77 0.00 30.93 1.31
2757 3142 6.431234 ACAAAAAGACTGAAGTCCATCCATAC 59.569 38.462 6.84 0.00 45.85 2.39
2768 3153 2.238646 TCCATCCATACCACCACTTGAC 59.761 50.000 0.00 0.00 0.00 3.18
2790 3175 2.596346 TGAAGTTGCCCACATCATTGT 58.404 42.857 0.00 0.00 36.15 2.71
2806 3191 4.385825 TCATTGTGGTCCTTCTTGTACAC 58.614 43.478 0.00 0.00 0.00 2.90
2966 3365 1.424638 TCTGCAGGTATCCCCTAAGC 58.575 55.000 15.13 0.00 43.86 3.09
2988 3387 4.441356 GCCCTTTGTCACATCTGAAAAACA 60.441 41.667 0.00 0.00 31.38 2.83
2993 3392 6.507958 TTGTCACATCTGAAAAACACTGAA 57.492 33.333 0.00 0.00 0.00 3.02
2996 3395 5.916883 GTCACATCTGAAAAACACTGAATGG 59.083 40.000 0.00 0.00 0.00 3.16
2999 3398 5.011329 ACATCTGAAAAACACTGAATGGCAT 59.989 36.000 0.00 0.00 0.00 4.40
3030 3429 7.618137 CCATGAAGATCATATCACCATAGTGA 58.382 38.462 0.00 0.00 45.50 3.41
3045 3444 7.195374 ACCATAGTGAACCAATACTACACAT 57.805 36.000 0.00 0.00 32.68 3.21
3054 3453 6.134535 ACCAATACTACACATTTGAGGGAA 57.865 37.500 0.00 0.00 0.00 3.97
3085 3484 3.620488 TCAGGTCTTGCACTGTTTCTTT 58.380 40.909 2.37 0.00 36.17 2.52
3127 3526 2.626582 GCATATGTGCCTGAGCTCC 58.373 57.895 12.15 0.00 45.76 4.70
3148 3547 6.624861 GCTCCGTTTTGAATTTCCATGTATCA 60.625 38.462 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 3.558321 CCGGATAAGTTTGGTGTTGGAGA 60.558 47.826 0.00 0.00 0.00 3.71
139 140 1.601903 GTTGTTGGAGTGTCGAATGCA 59.398 47.619 0.00 0.00 0.00 3.96
202 211 0.798776 GAAAGCTAGTGTGCACGCAT 59.201 50.000 30.53 18.08 36.20 4.73
231 240 6.260936 CAGTAGGTTTGATGAAAGTGACACTT 59.739 38.462 15.23 15.23 40.80 3.16
236 245 5.763204 GGTTCAGTAGGTTTGATGAAAGTGA 59.237 40.000 0.00 0.00 33.74 3.41
291 300 5.751243 TCTGGTTTACAAAGAAACTCTGC 57.249 39.130 0.00 0.00 38.97 4.26
296 305 8.567948 TGATCTGAATCTGGTTTACAAAGAAAC 58.432 33.333 0.00 0.00 34.68 2.78
297 306 8.567948 GTGATCTGAATCTGGTTTACAAAGAAA 58.432 33.333 0.00 0.00 32.75 2.52
345 377 3.902467 TGAAGATCTCCTGCATGCTATCT 59.098 43.478 20.33 14.88 0.00 1.98
346 378 4.021280 TCTGAAGATCTCCTGCATGCTATC 60.021 45.833 20.33 13.03 27.78 2.08
347 379 3.902467 TCTGAAGATCTCCTGCATGCTAT 59.098 43.478 20.33 4.59 27.78 2.97
349 381 2.103432 CTCTGAAGATCTCCTGCATGCT 59.897 50.000 20.33 0.00 27.78 3.79
376 408 3.503363 GTGCCTGACATCGCAGCC 61.503 66.667 0.00 0.00 35.20 4.85
430 462 2.563976 CGTGCGAGTTTTCAGATTGTG 58.436 47.619 0.00 0.00 0.00 3.33
432 464 1.531149 ACCGTGCGAGTTTTCAGATTG 59.469 47.619 0.00 0.00 0.00 2.67
439 471 1.433837 GGACACACCGTGCGAGTTTT 61.434 55.000 0.00 0.00 36.98 2.43
457 489 1.281656 GTTTGGTTTCGCAGTCCGG 59.718 57.895 0.00 0.00 37.59 5.14
501 533 2.816087 AGAGGCATGCACTTGTAAGTTG 59.184 45.455 21.36 0.00 37.08 3.16
503 535 2.224621 ACAGAGGCATGCACTTGTAAGT 60.225 45.455 21.36 8.78 40.60 2.24
504 536 2.430465 ACAGAGGCATGCACTTGTAAG 58.570 47.619 21.36 8.19 0.00 2.34
505 537 2.566833 ACAGAGGCATGCACTTGTAA 57.433 45.000 21.36 0.00 0.00 2.41
506 538 3.599343 CTTACAGAGGCATGCACTTGTA 58.401 45.455 21.36 19.22 0.00 2.41
507 539 2.430465 CTTACAGAGGCATGCACTTGT 58.570 47.619 21.36 20.20 0.00 3.16
508 540 1.131883 GCTTACAGAGGCATGCACTTG 59.868 52.381 21.36 15.58 0.00 3.16
509 541 1.271543 TGCTTACAGAGGCATGCACTT 60.272 47.619 21.36 3.91 33.23 3.16
510 542 0.325933 TGCTTACAGAGGCATGCACT 59.674 50.000 21.36 15.06 33.23 4.40
530 562 5.368989 TCTTTCTTGACTTCCTTTCTGTCC 58.631 41.667 0.00 0.00 0.00 4.02
536 568 7.066404 GTGTTCTCTTCTTTCTTGACTTCCTTT 59.934 37.037 0.00 0.00 0.00 3.11
600 635 8.043710 CCAATCTAGACAAGTAGAATTTCTGGT 58.956 37.037 9.22 2.46 32.72 4.00
614 649 4.593206 ACAGAGGAACACCAATCTAGACAA 59.407 41.667 0.00 0.00 0.00 3.18
637 672 3.055167 ACTGCCTAAGACACATACATGCA 60.055 43.478 0.00 0.00 0.00 3.96
640 675 4.826274 ACACTGCCTAAGACACATACAT 57.174 40.909 0.00 0.00 0.00 2.29
651 686 0.887387 GGTTGCCGAACACTGCCTAA 60.887 55.000 0.00 0.00 33.27 2.69
652 687 1.302192 GGTTGCCGAACACTGCCTA 60.302 57.895 0.00 0.00 33.27 3.93
653 688 2.594592 GGTTGCCGAACACTGCCT 60.595 61.111 0.00 0.00 33.27 4.75
654 689 3.670377 GGGTTGCCGAACACTGCC 61.670 66.667 0.00 0.00 32.16 4.85
655 690 2.904866 TGGGTTGCCGAACACTGC 60.905 61.111 0.00 0.00 36.34 4.40
656 691 2.551912 GGTGGGTTGCCGAACACTG 61.552 63.158 0.00 0.00 36.34 3.66
657 692 2.203294 GGTGGGTTGCCGAACACT 60.203 61.111 0.00 0.00 36.34 3.55
658 693 2.517402 TGGTGGGTTGCCGAACAC 60.517 61.111 0.00 0.00 35.87 3.32
659 694 2.517402 GTGGTGGGTTGCCGAACA 60.517 61.111 0.00 0.00 33.27 3.18
660 695 2.203294 AGTGGTGGGTTGCCGAAC 60.203 61.111 0.00 0.00 0.00 3.95
661 696 2.112297 GAGTGGTGGGTTGCCGAA 59.888 61.111 0.00 0.00 0.00 4.30
662 697 3.948719 GGAGTGGTGGGTTGCCGA 61.949 66.667 0.00 0.00 0.00 5.54
663 698 2.119484 TTAGGAGTGGTGGGTTGCCG 62.119 60.000 0.00 0.00 0.00 5.69
664 699 0.111639 TTTAGGAGTGGTGGGTTGCC 59.888 55.000 0.00 0.00 0.00 4.52
665 700 1.989706 TTTTAGGAGTGGTGGGTTGC 58.010 50.000 0.00 0.00 0.00 4.17
666 701 4.155280 CGTATTTTTAGGAGTGGTGGGTTG 59.845 45.833 0.00 0.00 0.00 3.77
667 702 4.041938 TCGTATTTTTAGGAGTGGTGGGTT 59.958 41.667 0.00 0.00 0.00 4.11
668 703 3.583966 TCGTATTTTTAGGAGTGGTGGGT 59.416 43.478 0.00 0.00 0.00 4.51
669 704 4.189231 CTCGTATTTTTAGGAGTGGTGGG 58.811 47.826 0.00 0.00 0.00 4.61
670 705 4.081309 TCCTCGTATTTTTAGGAGTGGTGG 60.081 45.833 0.00 0.00 34.46 4.61
671 706 5.080969 TCCTCGTATTTTTAGGAGTGGTG 57.919 43.478 0.00 0.00 34.46 4.17
677 712 3.737047 CGCAGCTCCTCGTATTTTTAGGA 60.737 47.826 0.00 0.00 37.07 2.94
678 713 2.540101 CGCAGCTCCTCGTATTTTTAGG 59.460 50.000 0.00 0.00 0.00 2.69
679 714 3.444916 TCGCAGCTCCTCGTATTTTTAG 58.555 45.455 0.00 0.00 0.00 1.85
680 715 3.513680 TCGCAGCTCCTCGTATTTTTA 57.486 42.857 0.00 0.00 0.00 1.52
681 716 2.380084 TCGCAGCTCCTCGTATTTTT 57.620 45.000 0.00 0.00 0.00 1.94
682 717 2.271800 CTTCGCAGCTCCTCGTATTTT 58.728 47.619 0.00 0.00 0.00 1.82
683 718 1.204941 ACTTCGCAGCTCCTCGTATTT 59.795 47.619 0.00 0.00 0.00 1.40
684 719 0.818296 ACTTCGCAGCTCCTCGTATT 59.182 50.000 0.00 0.00 0.00 1.89
685 720 0.101399 CACTTCGCAGCTCCTCGTAT 59.899 55.000 0.00 0.00 0.00 3.06
686 721 1.506718 CACTTCGCAGCTCCTCGTA 59.493 57.895 0.00 0.00 0.00 3.43
687 722 2.259818 CACTTCGCAGCTCCTCGT 59.740 61.111 0.00 0.00 0.00 4.18
688 723 2.507992 CCACTTCGCAGCTCCTCG 60.508 66.667 0.00 0.00 0.00 4.63
689 724 1.153667 CTCCACTTCGCAGCTCCTC 60.154 63.158 0.00 0.00 0.00 3.71
690 725 2.654079 CCTCCACTTCGCAGCTCCT 61.654 63.158 0.00 0.00 0.00 3.69
691 726 2.125350 CCTCCACTTCGCAGCTCC 60.125 66.667 0.00 0.00 0.00 4.70
692 727 2.125350 CCCTCCACTTCGCAGCTC 60.125 66.667 0.00 0.00 0.00 4.09
693 728 2.604686 TCCCTCCACTTCGCAGCT 60.605 61.111 0.00 0.00 0.00 4.24
694 729 2.435059 GTCCCTCCACTTCGCAGC 60.435 66.667 0.00 0.00 0.00 5.25
695 730 1.079543 CAGTCCCTCCACTTCGCAG 60.080 63.158 0.00 0.00 0.00 5.18
696 731 3.059982 CAGTCCCTCCACTTCGCA 58.940 61.111 0.00 0.00 0.00 5.10
697 732 2.435059 GCAGTCCCTCCACTTCGC 60.435 66.667 0.00 0.00 0.00 4.70
698 733 1.079543 CTGCAGTCCCTCCACTTCG 60.080 63.158 5.25 0.00 0.00 3.79
699 734 1.376553 GCTGCAGTCCCTCCACTTC 60.377 63.158 16.64 0.00 0.00 3.01
700 735 1.835927 GAGCTGCAGTCCCTCCACTT 61.836 60.000 16.64 0.00 0.00 3.16
701 736 2.203907 AGCTGCAGTCCCTCCACT 60.204 61.111 16.64 0.00 0.00 4.00
702 737 2.267324 GAGCTGCAGTCCCTCCAC 59.733 66.667 16.64 0.00 0.00 4.02
703 738 3.005539 GGAGCTGCAGTCCCTCCA 61.006 66.667 25.54 0.00 43.63 3.86
704 739 4.154347 CGGAGCTGCAGTCCCTCC 62.154 72.222 22.37 22.37 41.35 4.30
705 740 3.386237 ACGGAGCTGCAGTCCCTC 61.386 66.667 22.03 16.81 0.00 4.30
706 741 3.699894 CACGGAGCTGCAGTCCCT 61.700 66.667 22.03 10.19 0.00 4.20
716 751 2.409975 TGTAGTTAAACAGCACGGAGC 58.590 47.619 0.00 0.00 46.19 4.70
725 760 2.976882 AGGGTGGAGCTGTAGTTAAACA 59.023 45.455 0.00 0.00 0.00 2.83
726 761 3.335579 CAGGGTGGAGCTGTAGTTAAAC 58.664 50.000 0.00 0.00 0.00 2.01
727 762 2.290071 GCAGGGTGGAGCTGTAGTTAAA 60.290 50.000 0.00 0.00 0.00 1.52
728 763 1.278127 GCAGGGTGGAGCTGTAGTTAA 59.722 52.381 0.00 0.00 0.00 2.01
729 764 0.902531 GCAGGGTGGAGCTGTAGTTA 59.097 55.000 0.00 0.00 0.00 2.24
730 765 0.838122 AGCAGGGTGGAGCTGTAGTT 60.838 55.000 0.00 0.00 40.13 2.24
731 766 1.229336 AGCAGGGTGGAGCTGTAGT 60.229 57.895 0.00 0.00 40.13 2.73
732 767 1.519719 GAGCAGGGTGGAGCTGTAG 59.480 63.158 0.00 0.00 42.04 2.74
733 768 1.990060 GGAGCAGGGTGGAGCTGTA 60.990 63.158 0.00 0.00 42.04 2.74
734 769 3.325753 GGAGCAGGGTGGAGCTGT 61.326 66.667 0.00 0.00 42.04 4.40
735 770 4.106925 GGGAGCAGGGTGGAGCTG 62.107 72.222 0.00 0.00 42.04 4.24
741 776 4.087892 CACTCCGGGAGCAGGGTG 62.088 72.222 23.84 11.20 32.04 4.61
754 789 4.803426 CACTCCGCCGCTCCACTC 62.803 72.222 0.00 0.00 0.00 3.51
759 794 4.200283 CTCTCCACTCCGCCGCTC 62.200 72.222 0.00 0.00 0.00 5.03
760 795 4.742649 TCTCTCCACTCCGCCGCT 62.743 66.667 0.00 0.00 0.00 5.52
761 796 4.500116 GTCTCTCCACTCCGCCGC 62.500 72.222 0.00 0.00 0.00 6.53
762 797 2.752238 AGTCTCTCCACTCCGCCG 60.752 66.667 0.00 0.00 0.00 6.46
763 798 3.202467 GAGTCTCTCCACTCCGCC 58.798 66.667 0.00 0.00 37.43 6.13
771 806 1.950973 GCCCTGTTCGGAGTCTCTCC 61.951 65.000 5.79 5.79 46.44 3.71
772 807 0.968393 AGCCCTGTTCGGAGTCTCTC 60.968 60.000 0.00 0.00 33.16 3.20
773 808 0.543174 AAGCCCTGTTCGGAGTCTCT 60.543 55.000 0.00 0.00 33.16 3.10
774 809 0.321996 AAAGCCCTGTTCGGAGTCTC 59.678 55.000 0.00 0.00 33.16 3.36
775 810 1.640917 TAAAGCCCTGTTCGGAGTCT 58.359 50.000 0.00 0.00 33.16 3.24
776 811 2.467566 TTAAAGCCCTGTTCGGAGTC 57.532 50.000 0.00 0.00 33.16 3.36
777 812 2.304761 TGATTAAAGCCCTGTTCGGAGT 59.695 45.455 0.00 0.00 33.16 3.85
778 813 2.985896 TGATTAAAGCCCTGTTCGGAG 58.014 47.619 0.00 0.00 33.16 4.63
779 814 3.054728 TGATGATTAAAGCCCTGTTCGGA 60.055 43.478 0.00 0.00 33.16 4.55
780 815 3.278574 TGATGATTAAAGCCCTGTTCGG 58.721 45.455 0.00 0.00 0.00 4.30
781 816 4.731773 GCTTGATGATTAAAGCCCTGTTCG 60.732 45.833 3.25 0.00 42.40 3.95
782 817 4.676546 GCTTGATGATTAAAGCCCTGTTC 58.323 43.478 3.25 0.00 42.40 3.18
783 818 4.725790 GCTTGATGATTAAAGCCCTGTT 57.274 40.909 3.25 0.00 42.40 3.16
790 825 7.373493 ACACAGGAAAAGCTTGATGATTAAAG 58.627 34.615 0.00 0.00 0.00 1.85
791 826 7.288810 ACACAGGAAAAGCTTGATGATTAAA 57.711 32.000 0.00 0.00 0.00 1.52
858 893 5.618195 CGACCAAATTAATGTGCTTACCGTT 60.618 40.000 0.00 0.00 0.00 4.44
876 911 5.927689 ACAAGTGATTACGATTTACGACCAA 59.072 36.000 0.00 0.00 45.77 3.67
967 1002 8.023021 AGATCACAAGTTTATCCATAGCTACA 57.977 34.615 0.00 0.00 0.00 2.74
977 1012 9.241317 CCATTGCAATAAGATCACAAGTTTATC 57.759 33.333 12.53 0.00 0.00 1.75
1060 1108 0.112995 TCCTGAATTGCAAGGTGGCT 59.887 50.000 4.94 0.00 34.04 4.75
1064 1112 1.542492 CTGCTCCTGAATTGCAAGGT 58.458 50.000 4.94 0.00 36.22 3.50
1066 1114 0.885879 TGCTGCTCCTGAATTGCAAG 59.114 50.000 4.94 0.00 36.22 4.01
1067 1115 0.885879 CTGCTGCTCCTGAATTGCAA 59.114 50.000 0.00 0.00 36.22 4.08
1068 1116 0.251033 ACTGCTGCTCCTGAATTGCA 60.251 50.000 0.00 0.00 35.30 4.08
1069 1117 0.886563 AACTGCTGCTCCTGAATTGC 59.113 50.000 0.00 0.00 0.00 3.56
1071 1119 1.446907 CGAACTGCTGCTCCTGAATT 58.553 50.000 0.00 0.00 0.00 2.17
1072 1120 1.023513 GCGAACTGCTGCTCCTGAAT 61.024 55.000 0.00 0.00 41.73 2.57
1074 1122 2.047844 GCGAACTGCTGCTCCTGA 60.048 61.111 0.00 0.00 41.73 3.86
1075 1123 2.357881 TGCGAACTGCTGCTCCTG 60.358 61.111 0.00 0.00 46.63 3.86
1076 1124 2.047465 CTGCGAACTGCTGCTCCT 60.047 61.111 0.00 0.00 46.63 3.69
1150 1204 4.023365 GGAGCTACAAGATGGATTGAATGC 60.023 45.833 0.00 0.00 34.20 3.56
1152 1206 5.378230 TGGAGCTACAAGATGGATTGAAT 57.622 39.130 0.00 0.00 34.20 2.57
1165 1219 2.691409 CTCGGGAAATTGGAGCTACA 57.309 50.000 0.00 0.00 0.00 2.74
1190 1244 1.812922 GGCAGTGACGATGAGCCTG 60.813 63.158 0.00 0.00 42.01 4.85
1204 1258 1.135315 CGAATGGCAAGTTCGGCAG 59.865 57.895 13.89 0.00 45.56 4.85
1392 1458 1.738099 GATGACGTGCTCTTGCGGT 60.738 57.895 0.00 0.00 43.34 5.68
1456 1531 4.489771 GGGGACGATGGTGGCCAG 62.490 72.222 5.11 0.00 36.75 4.85
1558 1640 7.056006 TGTCAGTCTGAATAATATGGCAATGT 58.944 34.615 3.51 0.00 0.00 2.71
1622 1704 1.981495 CTTCACCTTCTCCTCCAGGTT 59.019 52.381 0.00 0.00 40.85 3.50
1624 1706 0.908198 CCTTCACCTTCTCCTCCAGG 59.092 60.000 0.00 0.00 36.10 4.45
1669 1754 2.179427 TCGAACACCATGGACTCTGAT 58.821 47.619 21.47 0.00 0.00 2.90
1745 1833 3.834799 GTACCCTGACCCGGAGCG 61.835 72.222 0.73 0.00 0.00 5.03
1756 1850 3.736224 TCCGGGCTCGAGTACCCT 61.736 66.667 21.56 0.00 44.63 4.34
1882 1976 5.749588 CGGTATGACGTTGGTGTTTATGATA 59.250 40.000 0.00 0.00 0.00 2.15
1985 2089 4.439057 TCTCTCACAAGTTGTTACCACAC 58.561 43.478 5.57 0.00 30.32 3.82
2047 2157 6.738832 AGTGAACATGTCAATCTTCTGATG 57.261 37.500 0.00 0.00 38.23 3.07
2093 2203 0.235926 GAGCTCAACTGCGGACAAAC 59.764 55.000 9.40 0.00 38.13 2.93
2143 2253 4.440880 CTTCCATTCTACTTCCAGCTGAG 58.559 47.826 17.39 8.22 0.00 3.35
2202 2312 5.799827 TTTGGTTGAAATACAAGGGAAGG 57.200 39.130 0.00 0.00 39.30 3.46
2203 2313 6.578023 TGTTTTGGTTGAAATACAAGGGAAG 58.422 36.000 0.00 0.00 39.30 3.46
2204 2314 6.407525 CCTGTTTTGGTTGAAATACAAGGGAA 60.408 38.462 0.00 0.00 39.30 3.97
2206 2316 5.069781 TCCTGTTTTGGTTGAAATACAAGGG 59.930 40.000 0.00 0.00 39.30 3.95
2208 2318 6.805713 ACTCCTGTTTTGGTTGAAATACAAG 58.194 36.000 0.00 0.00 39.30 3.16
2209 2319 6.783708 ACTCCTGTTTTGGTTGAAATACAA 57.216 33.333 0.00 0.00 36.02 2.41
2211 2321 6.213677 GGAACTCCTGTTTTGGTTGAAATAC 58.786 40.000 0.00 0.00 36.39 1.89
2216 2326 2.294074 CGGAACTCCTGTTTTGGTTGA 58.706 47.619 0.00 0.00 36.39 3.18
2221 2540 0.537371 AGGCCGGAACTCCTGTTTTG 60.537 55.000 5.05 0.00 36.39 2.44
2232 2551 1.003928 GGTTTTCCTAGAAGGCCGGAA 59.996 52.381 5.05 5.05 34.61 4.30
2287 2655 9.685828 CTCGGAAAAAGAAAACATAAATGGTAA 57.314 29.630 0.00 0.00 0.00 2.85
2288 2656 7.810759 GCTCGGAAAAAGAAAACATAAATGGTA 59.189 33.333 0.00 0.00 0.00 3.25
2392 2762 6.049149 ACGAAATACATTGACGGAATCAGAT 58.951 36.000 0.00 0.00 38.99 2.90
2407 2780 8.447833 GTGGAATATTCTTGTCAACGAAATACA 58.552 33.333 14.95 0.00 0.00 2.29
2417 2790 8.946085 GTTCTTGTATGTGGAATATTCTTGTCA 58.054 33.333 14.95 9.35 0.00 3.58
2427 2800 3.066291 TGCGGTTCTTGTATGTGGAAT 57.934 42.857 0.00 0.00 0.00 3.01
2428 2801 2.552599 TGCGGTTCTTGTATGTGGAA 57.447 45.000 0.00 0.00 0.00 3.53
2444 2817 8.390354 TCTTTTAGATTAGAACATTCACATGCG 58.610 33.333 0.00 0.00 33.05 4.73
2504 2877 0.817654 TCTACTCCAGGACATGCACG 59.182 55.000 0.00 0.00 0.00 5.34
2575 2948 6.991531 ACATTCCGCCAAAATATGCAATTTAT 59.008 30.769 0.00 0.00 0.00 1.40
2576 2949 6.257411 CACATTCCGCCAAAATATGCAATTTA 59.743 34.615 0.00 0.00 0.00 1.40
2585 2958 6.481976 CAGTATAGACACATTCCGCCAAAATA 59.518 38.462 0.00 0.00 0.00 1.40
2593 2966 3.555956 GCCAACAGTATAGACACATTCCG 59.444 47.826 0.00 0.00 0.00 4.30
2603 2976 4.141937 TGAGCCAGTTAGCCAACAGTATAG 60.142 45.833 0.00 0.00 37.10 1.31
2604 2977 3.772572 TGAGCCAGTTAGCCAACAGTATA 59.227 43.478 0.00 0.00 37.10 1.47
2605 2978 2.571653 TGAGCCAGTTAGCCAACAGTAT 59.428 45.455 0.00 0.00 37.10 2.12
2606 2979 1.974957 TGAGCCAGTTAGCCAACAGTA 59.025 47.619 0.00 0.00 37.10 2.74
2607 2980 0.764890 TGAGCCAGTTAGCCAACAGT 59.235 50.000 0.00 0.00 37.10 3.55
2644 3029 0.604780 TCTCAGTTGCTTGAGCTGGC 60.605 55.000 4.44 0.00 43.39 4.85
2757 3142 2.287788 GCAACTTCATGTCAAGTGGTGG 60.288 50.000 0.87 0.00 36.69 4.61
2790 3175 2.960384 TCTTCGTGTACAAGAAGGACCA 59.040 45.455 35.53 22.11 43.78 4.02
2806 3191 3.002791 TGGCAGAATAAGCACTTCTTCG 58.997 45.455 3.69 1.57 36.25 3.79
2956 3355 1.285078 GTGACAAAGGGCTTAGGGGAT 59.715 52.381 0.00 0.00 0.00 3.85
2966 3365 5.043248 GTGTTTTTCAGATGTGACAAAGGG 58.957 41.667 4.54 0.00 33.90 3.95
2996 3395 6.822170 TGATATGATCTTCATGGCTTCTATGC 59.178 38.462 0.30 0.00 37.70 3.14
2999 3398 6.270695 TGGTGATATGATCTTCATGGCTTCTA 59.729 38.462 0.30 0.00 37.70 2.10
3030 3429 6.134535 TCCCTCAAATGTGTAGTATTGGTT 57.865 37.500 0.00 0.00 0.00 3.67
3042 3441 7.123247 CCTGAATTGACTATTTCCCTCAAATGT 59.877 37.037 0.00 0.00 35.34 2.71
3045 3444 6.552008 ACCTGAATTGACTATTTCCCTCAAA 58.448 36.000 0.00 0.00 0.00 2.69
3054 3453 5.413833 CAGTGCAAGACCTGAATTGACTATT 59.586 40.000 0.00 0.00 0.00 1.73
3085 3484 6.404293 GCTCCCGCTTGAAGAATAAAATTGTA 60.404 38.462 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.