Multiple sequence alignment - TraesCS5A01G403300

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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 TraesCS5A01G403300 chr5A 100.000 4293 0 0 1 4293 595555259 595550967 0.000000e+00 7928.0
1 TraesCS5A01G403300 chr5B 90.949 3458 207 55 696 4088 583713200 583709784 0.000000e+00 4554.0
2 TraesCS5A01G403300 chr5B 92.182 307 19 4 1 306 583713515 583713213 3.070000e-116 429.0
3 TraesCS5A01G403300 chr5B 81.250 112 19 1 124 233 583713605 583713494 5.910000e-14 89.8
4 TraesCS5A01G403300 chr5D 92.050 1849 91 28 2269 4088 476196372 476194551 0.000000e+00 2549.0
5 TraesCS5A01G403300 chr5D 88.127 1255 81 27 696 1897 476197812 476196573 0.000000e+00 1430.0
6 TraesCS5A01G403300 chr5D 91.643 347 19 7 1 342 476198372 476198031 5.020000e-129 472.0
7 TraesCS5A01G403300 chr5D 89.103 156 10 2 380 534 476198039 476197890 2.040000e-43 187.0
8 TraesCS5A01G403300 chr5D 92.079 101 8 0 4193 4293 476194108 476194008 4.470000e-30 143.0
9 TraesCS5A01G403300 chr5D 86.408 103 10 4 533 634 332584393 332584294 4.540000e-20 110.0
10 TraesCS5A01G403300 chr6B 91.817 611 41 6 1213 1820 426742889 426743493 0.000000e+00 843.0
11 TraesCS5A01G403300 chr6A 83.682 239 31 5 83 320 66752090 66751859 7.230000e-53 219.0
12 TraesCS5A01G403300 chr6A 80.519 77 11 4 532 607 606977782 606977709 6.000000e-04 56.5
13 TraesCS5A01G403300 chr7B 79.767 257 24 20 83 332 478015786 478015551 1.240000e-35 161.0
14 TraesCS5A01G403300 chrUn 81.651 109 12 5 532 635 240118556 240118451 2.750000e-12 84.2
15 TraesCS5A01G403300 chrUn 81.651 109 12 5 532 635 357457051 357456946 2.750000e-12 84.2
16 TraesCS5A01G403300 chrUn 81.651 109 12 5 532 635 357459188 357459083 2.750000e-12 84.2
17 TraesCS5A01G403300 chr2B 80.734 109 13 5 532 635 77822654 77822549 1.280000e-10 78.7
18 TraesCS5A01G403300 chr2A 80.392 102 12 6 533 631 76520567 76520663 2.140000e-08 71.3
19 TraesCS5A01G403300 chr2A 79.612 103 14 7 537 635 631638178 631638277 2.770000e-07 67.6
20 TraesCS5A01G403300 chr7A 91.667 48 4 0 529 576 66608404 66608451 2.770000e-07 67.6
21 TraesCS5A01G403300 chr1D 79.412 102 15 6 532 631 437988490 437988393 2.770000e-07 67.6
22 TraesCS5A01G403300 chr7D 91.489 47 4 0 336 382 178941449 178941495 9.960000e-07 65.8
23 TraesCS5A01G403300 chr1B 87.500 48 6 0 336 383 70183080 70183127 6.000000e-04 56.5


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 TraesCS5A01G403300 chr5A 595550967 595555259 4292 True 7928.000000 7928 100.0000 1 4293 1 chr5A.!!$R1 4292
1 TraesCS5A01G403300 chr5B 583709784 583713605 3821 True 1690.933333 4554 88.1270 1 4088 3 chr5B.!!$R1 4087
2 TraesCS5A01G403300 chr5D 476194008 476198372 4364 True 956.200000 2549 90.6004 1 4293 5 chr5D.!!$R2 4292
3 TraesCS5A01G403300 chr6B 426742889 426743493 604 False 843.000000 843 91.8170 1213 1820 1 chr6B.!!$F1 607

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
481 574 0.465460 GCGAAGGTGGCAATGGGATA 60.465 55.0 0.0 0.0 0.00 2.59 F
1612 1722 0.038801 GCAGCAAGGAGTTTTCTGCC 60.039 55.0 0.0 0.0 42.98 4.85 F
1871 2023 0.029834 GCCATTGTAGCCATGCTTCG 59.970 55.0 0.0 0.0 40.44 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2003 0.029834 GAAGCATGGCTACAATGGCG 59.970 55.000 0.0 0.0 38.25 5.69 R
3196 3400 2.061773 GCATGAGGTATCGTTGGATCG 58.938 52.381 0.0 0.0 34.00 3.69 R
3705 3918 1.111277 GTGTCAGGGGCAACAAAAGT 58.889 50.000 0.0 0.0 39.74 2.66 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
263 355 8.947115 AGCATAGAAATAACAACAAAGTCCTAC 58.053 33.333 0.00 0.00 0.00 3.18
264 356 8.947115 GCATAGAAATAACAACAAAGTCCTACT 58.053 33.333 0.00 0.00 0.00 2.57
318 410 9.908152 GGTTATGCTTAAGTTAGATGTTGTTTT 57.092 29.630 4.02 0.00 0.00 2.43
353 445 9.820725 AATGATTCAATCTTTGTTCAAAGTTGA 57.179 25.926 22.83 22.83 32.93 3.18
354 446 9.820725 ATGATTCAATCTTTGTTCAAAGTTGAA 57.179 25.926 29.49 29.49 44.31 2.69
382 474 0.466922 TTCCGATCGGAGGGAGTACC 60.467 60.000 33.67 0.00 46.06 3.34
411 503 6.194235 TCAGTTTCATGGGCCTGTAATTTAT 58.806 36.000 4.53 0.00 0.00 1.40
414 506 7.278424 CAGTTTCATGGGCCTGTAATTTATTTG 59.722 37.037 4.53 0.00 0.00 2.32
416 508 5.523588 TCATGGGCCTGTAATTTATTTGGA 58.476 37.500 4.53 0.00 0.00 3.53
418 510 5.867903 TGGGCCTGTAATTTATTTGGATG 57.132 39.130 4.53 0.00 0.00 3.51
481 574 0.465460 GCGAAGGTGGCAATGGGATA 60.465 55.000 0.00 0.00 0.00 2.59
490 583 4.147321 GTGGCAATGGGATAGTGAATGAT 58.853 43.478 0.00 0.00 0.00 2.45
491 584 5.316167 GTGGCAATGGGATAGTGAATGATA 58.684 41.667 0.00 0.00 0.00 2.15
492 585 5.182001 GTGGCAATGGGATAGTGAATGATAC 59.818 44.000 0.00 0.00 0.00 2.24
493 586 4.393062 GGCAATGGGATAGTGAATGATACG 59.607 45.833 0.00 0.00 0.00 3.06
494 587 4.393062 GCAATGGGATAGTGAATGATACGG 59.607 45.833 0.00 0.00 0.00 4.02
495 588 4.826274 ATGGGATAGTGAATGATACGGG 57.174 45.455 0.00 0.00 0.00 5.28
503 596 4.744570 AGTGAATGATACGGGTATATGCG 58.255 43.478 0.00 0.00 0.00 4.73
523 616 2.225727 CGGGATGTGCATCAAGATCATG 59.774 50.000 13.37 0.00 39.54 3.07
524 617 3.220110 GGGATGTGCATCAAGATCATGT 58.780 45.455 13.37 0.00 39.54 3.21
534 627 8.491152 GTGCATCAAGATCATGTAAGTACATAC 58.509 37.037 3.69 1.26 44.57 2.39
535 628 8.424133 TGCATCAAGATCATGTAAGTACATACT 58.576 33.333 9.48 2.49 44.57 2.12
538 631 9.988815 ATCAAGATCATGTAAGTACATACTTCC 57.011 33.333 7.56 0.00 44.57 3.46
540 633 9.469807 CAAGATCATGTAAGTACATACTTCCTC 57.530 37.037 7.56 3.23 44.57 3.71
541 634 8.184304 AGATCATGTAAGTACATACTTCCTCC 57.816 38.462 7.56 0.00 44.57 4.30
543 636 5.889853 TCATGTAAGTACATACTTCCTCCGT 59.110 40.000 7.56 0.00 44.57 4.69
544 637 7.056006 TCATGTAAGTACATACTTCCTCCGTA 58.944 38.462 7.56 0.00 44.57 4.02
545 638 7.722728 TCATGTAAGTACATACTTCCTCCGTAT 59.277 37.037 7.56 0.00 44.57 3.06
546 639 7.886629 TGTAAGTACATACTTCCTCCGTATT 57.113 36.000 7.56 0.00 44.77 1.89
548 641 9.407380 TGTAAGTACATACTTCCTCCGTATTAA 57.593 33.333 7.56 0.00 44.77 1.40
558 651 8.713737 ACTTCCTCCGTATTAAAATAAGTGTC 57.286 34.615 0.00 0.00 0.00 3.67
560 653 8.937634 TTCCTCCGTATTAAAATAAGTGTCTC 57.062 34.615 0.00 0.00 0.00 3.36
562 655 8.533657 TCCTCCGTATTAAAATAAGTGTCTCAA 58.466 33.333 0.00 0.00 0.00 3.02
563 656 8.601476 CCTCCGTATTAAAATAAGTGTCTCAAC 58.399 37.037 0.00 0.00 0.00 3.18
564 657 8.483307 TCCGTATTAAAATAAGTGTCTCAACC 57.517 34.615 0.00 0.00 0.00 3.77
565 658 8.316214 TCCGTATTAAAATAAGTGTCTCAACCT 58.684 33.333 0.00 0.00 0.00 3.50
566 659 8.943002 CCGTATTAAAATAAGTGTCTCAACCTT 58.057 33.333 0.00 0.00 0.00 3.50
578 671 9.531158 AAGTGTCTCAACCTTAGTATAACTACT 57.469 33.333 0.00 0.00 41.19 2.57
619 712 9.793259 ACTAAGGTTGAGACATTTATTTTGAGA 57.207 29.630 0.00 0.00 31.38 3.27
621 714 8.697507 AAGGTTGAGACATTTATTTTGAGACT 57.302 30.769 0.00 0.00 0.00 3.24
622 715 8.103948 AGGTTGAGACATTTATTTTGAGACTG 57.896 34.615 0.00 0.00 0.00 3.51
623 716 7.939039 AGGTTGAGACATTTATTTTGAGACTGA 59.061 33.333 0.00 0.00 0.00 3.41
624 717 8.233190 GGTTGAGACATTTATTTTGAGACTGAG 58.767 37.037 0.00 0.00 0.00 3.35
625 718 7.912056 TGAGACATTTATTTTGAGACTGAGG 57.088 36.000 0.00 0.00 0.00 3.86
626 719 6.881065 TGAGACATTTATTTTGAGACTGAGGG 59.119 38.462 0.00 0.00 0.00 4.30
627 720 7.020827 AGACATTTATTTTGAGACTGAGGGA 57.979 36.000 0.00 0.00 0.00 4.20
628 721 7.108847 AGACATTTATTTTGAGACTGAGGGAG 58.891 38.462 0.00 0.00 0.00 4.30
667 760 9.342308 ACAACTGATATTAACCACTGGAATATG 57.658 33.333 0.71 0.00 0.00 1.78
668 761 9.342308 CAACTGATATTAACCACTGGAATATGT 57.658 33.333 0.71 0.00 0.00 2.29
670 763 9.998106 ACTGATATTAACCACTGGAATATGTAC 57.002 33.333 0.71 0.00 0.00 2.90
677 770 9.607988 TTAACCACTGGAATATGTACTTACATG 57.392 33.333 11.45 0.00 45.77 3.21
678 771 7.432148 ACCACTGGAATATGTACTTACATGA 57.568 36.000 11.45 0.00 45.77 3.07
679 772 8.034313 ACCACTGGAATATGTACTTACATGAT 57.966 34.615 11.45 1.26 45.77 2.45
680 773 8.150945 ACCACTGGAATATGTACTTACATGATC 58.849 37.037 11.45 9.07 45.77 2.92
681 774 8.370940 CCACTGGAATATGTACTTACATGATCT 58.629 37.037 11.45 0.00 45.77 2.75
688 781 8.932945 ATATGTACTTACATGATCTATTGCGG 57.067 34.615 11.45 0.00 45.77 5.69
689 782 6.399639 TGTACTTACATGATCTATTGCGGA 57.600 37.500 0.00 0.00 0.00 5.54
690 783 6.811954 TGTACTTACATGATCTATTGCGGAA 58.188 36.000 0.00 0.00 0.00 4.30
691 784 7.269316 TGTACTTACATGATCTATTGCGGAAA 58.731 34.615 0.00 0.00 0.00 3.13
692 785 7.766738 TGTACTTACATGATCTATTGCGGAAAA 59.233 33.333 0.00 0.00 0.00 2.29
693 786 7.624360 ACTTACATGATCTATTGCGGAAAAA 57.376 32.000 0.00 0.00 0.00 1.94
734 827 5.820423 TGACTATGTTACAATGTATGGGCAC 59.180 40.000 0.00 0.00 0.00 5.01
936 1030 3.494254 TTTGACCCGGCACCCAGT 61.494 61.111 0.00 0.00 0.00 4.00
1196 1290 1.136984 CGGTGAGTCCTCGTAGCAC 59.863 63.158 0.00 0.00 0.00 4.40
1210 1304 4.377021 TCGTAGCACACTCAAACTGATTT 58.623 39.130 0.00 0.00 0.00 2.17
1211 1305 4.211164 TCGTAGCACACTCAAACTGATTTG 59.789 41.667 0.00 0.00 45.67 2.32
1214 1308 2.863704 GCACACTCAAACTGATTTGGCC 60.864 50.000 0.00 0.00 44.61 5.36
1280 1375 8.121305 TCATGCTCATAAAACACCAGTAAAAT 57.879 30.769 0.00 0.00 0.00 1.82
1283 1378 8.810652 TGCTCATAAAACACCAGTAAAATTTC 57.189 30.769 0.00 0.00 0.00 2.17
1322 1422 1.133790 GCATGTGAAGTCATTCCTGCC 59.866 52.381 0.00 0.00 34.28 4.85
1392 1500 3.441290 GCCTCAGCCAAGCAGCAG 61.441 66.667 0.00 0.00 34.23 4.24
1393 1501 3.441290 CCTCAGCCAAGCAGCAGC 61.441 66.667 0.00 0.00 42.56 5.25
1394 1502 2.671963 CTCAGCCAAGCAGCAGCA 60.672 61.111 3.17 0.00 45.49 4.41
1486 1594 0.533531 CTGTGCTCACCACTCTTGCA 60.534 55.000 0.00 0.00 44.92 4.08
1489 1597 1.598962 GCTCACCACTCTTGCAGCA 60.599 57.895 0.00 0.00 0.00 4.41
1552 1660 2.186243 TCTCTCAAGGATCTTGCTGCT 58.814 47.619 0.00 0.00 0.00 4.24
1581 1689 1.801178 GCCATATGAAGAGGTTAGCGC 59.199 52.381 3.65 0.00 0.00 5.92
1612 1722 0.038801 GCAGCAAGGAGTTTTCTGCC 60.039 55.000 0.00 0.00 42.98 4.85
1626 1736 2.933287 TGCCCACCCCTACACTGG 60.933 66.667 0.00 0.00 0.00 4.00
1638 1748 4.656112 CCCCTACACTGGACAAAGAGATAT 59.344 45.833 0.00 0.00 0.00 1.63
1676 1786 3.918591 CAGCTAAATGTCAGCAGCAAAAG 59.081 43.478 0.00 0.00 41.66 2.27
1685 1799 3.067320 GTCAGCAGCAAAAGGAAGTTTCT 59.933 43.478 0.00 0.00 0.00 2.52
1689 1803 3.067320 GCAGCAAAAGGAAGTTTCTCTGT 59.933 43.478 0.87 0.00 33.34 3.41
1695 1809 7.285401 AGCAAAAGGAAGTTTCTCTGTCATTTA 59.715 33.333 0.00 0.00 0.00 1.40
1696 1810 8.084684 GCAAAAGGAAGTTTCTCTGTCATTTAT 58.915 33.333 0.00 0.00 0.00 1.40
1767 1904 5.512753 ACAATTGCAGTATGTGAACAACA 57.487 34.783 5.05 0.00 44.79 3.33
1791 1928 2.426024 GCATGATCCATTGCAGTTCAGT 59.574 45.455 0.00 0.00 0.00 3.41
1806 1943 5.932303 GCAGTTCAGTTCATGGTAGAGTTAA 59.068 40.000 0.00 0.00 0.00 2.01
1851 2003 5.703130 AGAAAGTGCTCCTTCTTTATGACAC 59.297 40.000 0.00 0.00 34.60 3.67
1859 2011 3.440173 CCTTCTTTATGACACGCCATTGT 59.560 43.478 0.00 0.00 0.00 2.71
1871 2023 0.029834 GCCATTGTAGCCATGCTTCG 59.970 55.000 0.00 0.00 40.44 3.79
1880 2032 1.808945 AGCCATGCTTCGTTTCTTCAG 59.191 47.619 0.00 0.00 33.89 3.02
1903 2055 8.249638 TCAGACTTCATCAGAACTTTCTATGAG 58.750 37.037 0.00 1.24 35.34 2.90
1909 2061 9.730705 TTCATCAGAACTTTCTATGAGTCAATT 57.269 29.630 0.00 0.00 35.34 2.32
2021 2187 3.428862 GCCCATTTGTCCGTTAATCCAAG 60.429 47.826 0.00 0.00 0.00 3.61
2023 2189 4.142469 CCCATTTGTCCGTTAATCCAAGAC 60.142 45.833 0.00 0.00 0.00 3.01
2033 2199 5.106157 CCGTTAATCCAAGACATGCTTTCTT 60.106 40.000 0.00 0.00 33.60 2.52
2034 2200 6.093495 CCGTTAATCCAAGACATGCTTTCTTA 59.907 38.462 0.00 0.00 33.60 2.10
2036 2202 7.360861 CGTTAATCCAAGACATGCTTTCTTACA 60.361 37.037 0.00 0.00 33.60 2.41
2038 2204 5.227569 TCCAAGACATGCTTTCTTACAGA 57.772 39.130 0.00 0.00 33.60 3.41
2039 2205 5.240891 TCCAAGACATGCTTTCTTACAGAG 58.759 41.667 0.00 0.00 33.60 3.35
2040 2206 4.999950 CCAAGACATGCTTTCTTACAGAGT 59.000 41.667 0.00 0.00 33.60 3.24
2041 2207 5.471456 CCAAGACATGCTTTCTTACAGAGTT 59.529 40.000 0.00 0.00 33.60 3.01
2042 2208 6.650807 CCAAGACATGCTTTCTTACAGAGTTA 59.349 38.462 0.00 0.00 33.60 2.24
2043 2209 7.360438 CCAAGACATGCTTTCTTACAGAGTTAC 60.360 40.741 0.00 0.00 33.60 2.50
2044 2210 6.759272 AGACATGCTTTCTTACAGAGTTACA 58.241 36.000 0.00 0.00 0.00 2.41
2045 2211 6.647067 AGACATGCTTTCTTACAGAGTTACAC 59.353 38.462 0.00 0.00 0.00 2.90
2087 2253 7.225145 TCAATTTTCAAGATGTTGGCTTTTCTG 59.775 33.333 2.33 0.00 34.09 3.02
2098 2264 2.376518 TGGCTTTTCTGGAGAAGATGGT 59.623 45.455 5.27 0.00 33.93 3.55
2201 2367 6.929606 GCCCATTGGTAAACTAGTACTCATAG 59.070 42.308 0.00 0.00 0.00 2.23
2202 2368 7.201974 GCCCATTGGTAAACTAGTACTCATAGA 60.202 40.741 0.00 0.00 0.00 1.98
2229 2399 6.591448 TCTGTACACTGAATAGCTTTCATGTG 59.409 38.462 21.73 21.73 35.59 3.21
2260 2430 7.395772 TGACAAGCAACCCTATTATGATTGAAA 59.604 33.333 9.61 0.00 41.60 2.69
2264 2434 6.260936 AGCAACCCTATTATGATTGAAACTCG 59.739 38.462 0.00 0.00 0.00 4.18
2593 2771 4.415596 TCCTAAAATGTGCACCTTCCATT 58.584 39.130 15.69 3.87 0.00 3.16
2641 2819 6.323996 AGCTACACTAATCCTGTATAAGTGCA 59.676 38.462 0.00 0.00 40.94 4.57
2662 2840 2.549926 TGCAGTATCATACACTTGCCG 58.450 47.619 5.34 0.00 0.00 5.69
2756 2935 4.707448 ACCACAGTCATTAGTGAGTCTAGG 59.293 45.833 0.00 0.00 35.84 3.02
2759 2938 4.642885 ACAGTCATTAGTGAGTCTAGGAGC 59.357 45.833 0.00 0.00 35.84 4.70
2962 3166 5.360714 ACTGACTGAACCAATGAACACATTT 59.639 36.000 0.00 0.00 32.76 2.32
3196 3400 0.250467 TGGTTGCTCTGTCTTCTGGC 60.250 55.000 0.00 0.00 0.00 4.85
3310 3514 2.778187 AGTAATAGCTCTTCGTCGCC 57.222 50.000 0.00 0.00 0.00 5.54
3401 3606 7.179338 AGTCCAAGTATAGAATGTCTGTTGTCT 59.821 37.037 0.00 0.00 0.00 3.41
3409 3614 6.152932 AGAATGTCTGTTGTCTTTTTGCAT 57.847 33.333 0.00 0.00 0.00 3.96
3413 3618 6.449635 TGTCTGTTGTCTTTTTGCATAAGT 57.550 33.333 8.44 0.00 0.00 2.24
3415 3620 7.414436 TGTCTGTTGTCTTTTTGCATAAGTAC 58.586 34.615 8.44 3.75 0.00 2.73
3416 3621 7.066404 TGTCTGTTGTCTTTTTGCATAAGTACA 59.934 33.333 8.44 5.87 0.00 2.90
3418 3623 9.278978 TCTGTTGTCTTTTTGCATAAGTACATA 57.721 29.630 8.44 0.00 0.00 2.29
3436 3645 7.205992 AGTACATATGCAGTTGATCACTAGTG 58.794 38.462 17.17 17.17 32.76 2.74
3515 3724 5.263599 TGAGGGCTGTTGATGTTGAAATAT 58.736 37.500 0.00 0.00 0.00 1.28
3516 3725 6.422333 TGAGGGCTGTTGATGTTGAAATATA 58.578 36.000 0.00 0.00 0.00 0.86
3517 3726 6.543465 TGAGGGCTGTTGATGTTGAAATATAG 59.457 38.462 0.00 0.00 0.00 1.31
3644 3857 6.378280 AGGCTAGATTTTCACCCAACTTAATG 59.622 38.462 0.00 0.00 0.00 1.90
3667 3880 6.791303 TGTAAAGAGTTAAAACAGCTTGGTG 58.209 36.000 0.00 0.00 0.00 4.17
3683 3896 4.755123 GCTTGGTGTTACACATCTGTTACT 59.245 41.667 17.67 0.00 35.86 2.24
3705 3918 9.904198 TTACTTGATGTTTAATGATCATCTGGA 57.096 29.630 9.06 0.00 38.78 3.86
3735 3948 2.290960 GCCCCTGACACTACTGGATTTT 60.291 50.000 0.00 0.00 0.00 1.82
3829 4042 2.659610 GGCAGAGCTGACCGAGTT 59.340 61.111 0.85 0.00 30.68 3.01
3838 4051 2.564947 AGCTGACCGAGTTCAGAAATCT 59.435 45.455 8.88 0.00 45.19 2.40
3905 4118 2.738314 GCATTGTGCAAGTGGATTTTCC 59.262 45.455 0.00 0.00 44.26 3.13
3968 4181 7.997482 ACTACGAGAATCAGTGTATTGTGTAT 58.003 34.615 0.00 0.00 33.17 2.29
3969 4182 9.117183 ACTACGAGAATCAGTGTATTGTGTATA 57.883 33.333 0.00 0.00 33.17 1.47
4024 4237 7.096106 CGAGAACGTACTGGTGTTAATAAACAA 60.096 37.037 0.00 0.00 39.76 2.83
4094 4313 4.495690 GGAGGTTCCTAGAATGAGCTTT 57.504 45.455 0.00 0.00 32.53 3.51
4095 4314 4.849518 GGAGGTTCCTAGAATGAGCTTTT 58.150 43.478 0.00 0.00 32.53 2.27
4097 4316 5.355630 GGAGGTTCCTAGAATGAGCTTTTTC 59.644 44.000 0.00 0.00 32.53 2.29
4098 4317 5.257262 AGGTTCCTAGAATGAGCTTTTTCC 58.743 41.667 6.09 0.00 0.00 3.13
4099 4318 5.014649 AGGTTCCTAGAATGAGCTTTTTCCT 59.985 40.000 6.09 0.00 0.00 3.36
4101 4320 5.762179 TCCTAGAATGAGCTTTTTCCTGA 57.238 39.130 6.09 0.00 0.00 3.86
4102 4321 5.491982 TCCTAGAATGAGCTTTTTCCTGAC 58.508 41.667 6.09 0.00 0.00 3.51
4103 4322 5.013079 TCCTAGAATGAGCTTTTTCCTGACA 59.987 40.000 6.09 0.00 0.00 3.58
4104 4323 5.353678 CCTAGAATGAGCTTTTTCCTGACAG 59.646 44.000 0.00 0.00 0.00 3.51
4105 4324 4.077822 AGAATGAGCTTTTTCCTGACAGG 58.922 43.478 15.99 15.99 36.46 4.00
4108 4327 3.214328 TGAGCTTTTTCCTGACAGGTTC 58.786 45.455 21.06 9.04 36.53 3.62
4109 4328 2.222027 AGCTTTTTCCTGACAGGTTCG 58.778 47.619 21.06 7.80 36.53 3.95
4110 4329 2.158813 AGCTTTTTCCTGACAGGTTCGA 60.159 45.455 21.06 0.00 36.53 3.71
4111 4330 2.224314 GCTTTTTCCTGACAGGTTCGAG 59.776 50.000 21.06 15.07 36.53 4.04
4112 4331 2.543777 TTTTCCTGACAGGTTCGAGG 57.456 50.000 21.06 0.00 36.53 4.63
4113 4332 0.685097 TTTCCTGACAGGTTCGAGGG 59.315 55.000 21.06 0.00 36.53 4.30
4114 4333 1.192146 TTCCTGACAGGTTCGAGGGG 61.192 60.000 21.06 0.00 36.53 4.79
4115 4334 1.609501 CCTGACAGGTTCGAGGGGA 60.610 63.158 13.84 0.00 0.00 4.81
4116 4335 1.608717 CCTGACAGGTTCGAGGGGAG 61.609 65.000 13.84 0.00 0.00 4.30
4117 4336 2.232298 CTGACAGGTTCGAGGGGAGC 62.232 65.000 0.00 0.00 0.00 4.70
4118 4337 2.203788 ACAGGTTCGAGGGGAGCA 60.204 61.111 0.00 0.00 0.00 4.26
4120 4339 2.685380 AGGTTCGAGGGGAGCAGG 60.685 66.667 0.00 0.00 0.00 4.85
4121 4340 4.475135 GGTTCGAGGGGAGCAGGC 62.475 72.222 0.00 0.00 0.00 4.85
4122 4341 3.706373 GTTCGAGGGGAGCAGGCA 61.706 66.667 0.00 0.00 0.00 4.75
4123 4342 2.927856 TTCGAGGGGAGCAGGCAA 60.928 61.111 0.00 0.00 0.00 4.52
4124 4343 2.525124 TTCGAGGGGAGCAGGCAAA 61.525 57.895 0.00 0.00 0.00 3.68
4125 4344 2.437359 CGAGGGGAGCAGGCAAAG 60.437 66.667 0.00 0.00 0.00 2.77
4127 4346 2.532715 AGGGGAGCAGGCAAAGGA 60.533 61.111 0.00 0.00 0.00 3.36
4128 4347 2.142292 GAGGGGAGCAGGCAAAGGAA 62.142 60.000 0.00 0.00 0.00 3.36
4130 4349 0.615827 GGGGAGCAGGCAAAGGAATT 60.616 55.000 0.00 0.00 0.00 2.17
4131 4350 1.269958 GGGAGCAGGCAAAGGAATTT 58.730 50.000 0.00 0.00 0.00 1.82
4132 4351 1.205655 GGGAGCAGGCAAAGGAATTTC 59.794 52.381 0.00 0.00 0.00 2.17
4133 4352 2.174360 GGAGCAGGCAAAGGAATTTCT 58.826 47.619 0.00 0.00 0.00 2.52
4134 4353 2.094338 GGAGCAGGCAAAGGAATTTCTG 60.094 50.000 0.00 0.00 0.00 3.02
4135 4354 1.274447 AGCAGGCAAAGGAATTTCTGC 59.726 47.619 0.00 0.00 41.98 4.26
4136 4355 1.274447 GCAGGCAAAGGAATTTCTGCT 59.726 47.619 0.00 0.00 40.14 4.24
4137 4356 2.673326 GCAGGCAAAGGAATTTCTGCTC 60.673 50.000 0.00 1.36 40.14 4.26
4140 4359 2.159462 GGCAAAGGAATTTCTGCTCTCG 60.159 50.000 8.47 0.00 35.13 4.04
4141 4360 2.485814 GCAAAGGAATTTCTGCTCTCGT 59.514 45.455 0.00 0.00 0.00 4.18
4143 4362 4.557496 GCAAAGGAATTTCTGCTCTCGTTT 60.557 41.667 0.00 0.00 0.00 3.60
4144 4363 5.523369 CAAAGGAATTTCTGCTCTCGTTTT 58.477 37.500 0.00 0.00 0.00 2.43
4145 4364 5.774498 AAGGAATTTCTGCTCTCGTTTTT 57.226 34.783 0.00 0.00 0.00 1.94
4146 4365 5.363979 AGGAATTTCTGCTCTCGTTTTTC 57.636 39.130 0.00 0.00 0.00 2.29
4148 4367 5.532779 AGGAATTTCTGCTCTCGTTTTTCTT 59.467 36.000 0.00 0.00 0.00 2.52
4149 4368 6.039829 AGGAATTTCTGCTCTCGTTTTTCTTT 59.960 34.615 0.00 0.00 0.00 2.52
4150 4369 7.228706 AGGAATTTCTGCTCTCGTTTTTCTTTA 59.771 33.333 0.00 0.00 0.00 1.85
4151 4370 7.535599 GGAATTTCTGCTCTCGTTTTTCTTTAG 59.464 37.037 0.00 0.00 0.00 1.85
4152 4371 5.924475 TTCTGCTCTCGTTTTTCTTTAGG 57.076 39.130 0.00 0.00 0.00 2.69
4154 4373 4.039973 TCTGCTCTCGTTTTTCTTTAGGGA 59.960 41.667 0.00 0.00 0.00 4.20
4155 4374 4.906618 TGCTCTCGTTTTTCTTTAGGGAT 58.093 39.130 0.00 0.00 0.00 3.85
4156 4375 5.313712 TGCTCTCGTTTTTCTTTAGGGATT 58.686 37.500 0.00 0.00 0.00 3.01
4158 4377 5.181433 GCTCTCGTTTTTCTTTAGGGATTGT 59.819 40.000 0.00 0.00 0.00 2.71
4159 4378 6.370718 GCTCTCGTTTTTCTTTAGGGATTGTA 59.629 38.462 0.00 0.00 0.00 2.41
4160 4379 7.413109 GCTCTCGTTTTTCTTTAGGGATTGTAG 60.413 40.741 0.00 0.00 0.00 2.74
4161 4380 6.370718 TCTCGTTTTTCTTTAGGGATTGTAGC 59.629 38.462 0.00 0.00 0.00 3.58
4162 4381 6.235664 TCGTTTTTCTTTAGGGATTGTAGCT 58.764 36.000 0.00 0.00 0.00 3.32
4163 4382 6.713450 TCGTTTTTCTTTAGGGATTGTAGCTT 59.287 34.615 0.00 0.00 0.00 3.74
4164 4383 7.021790 CGTTTTTCTTTAGGGATTGTAGCTTC 58.978 38.462 0.00 0.00 0.00 3.86
4165 4384 7.313646 GTTTTTCTTTAGGGATTGTAGCTTCC 58.686 38.462 0.00 0.00 0.00 3.46
4166 4385 5.772393 TTCTTTAGGGATTGTAGCTTCCA 57.228 39.130 4.59 0.00 33.43 3.53
4168 4387 5.684704 TCTTTAGGGATTGTAGCTTCCATG 58.315 41.667 4.59 0.00 33.43 3.66
4169 4388 4.437682 TTAGGGATTGTAGCTTCCATGG 57.562 45.455 4.97 4.97 33.43 3.66
4170 4389 1.133668 AGGGATTGTAGCTTCCATGGC 60.134 52.381 6.96 0.00 33.43 4.40
4171 4390 1.322442 GGATTGTAGCTTCCATGGCC 58.678 55.000 6.96 0.00 31.99 5.36
4173 4392 0.255890 ATTGTAGCTTCCATGGCCGT 59.744 50.000 6.96 0.00 0.00 5.68
4178 4581 1.078426 GCTTCCATGGCCGTAGTGT 60.078 57.895 6.96 0.00 0.00 3.55
4180 4583 0.537188 CTTCCATGGCCGTAGTGTCT 59.463 55.000 6.96 0.00 0.00 3.41
4194 4597 7.299586 GCCGTAGTGTCTAGATTATGTCTTAG 58.700 42.308 0.00 0.00 38.42 2.18
4195 4598 7.172875 GCCGTAGTGTCTAGATTATGTCTTAGA 59.827 40.741 0.00 0.00 38.42 2.10
4196 4599 9.221933 CCGTAGTGTCTAGATTATGTCTTAGAT 57.778 37.037 0.00 0.00 38.42 1.98
4213 4770 5.527214 TCTTAGATTGTTGTGTCTTGTGTGG 59.473 40.000 0.00 0.00 0.00 4.17
4235 4792 2.234908 AGTAGTGTCTCACTTCCATGGC 59.765 50.000 6.96 0.00 42.59 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 118 4.141367 TGTTACCTGAAAATCTGGGACACA 60.141 41.667 7.98 4.89 39.50 3.72
237 329 8.947115 GTAGGACTTTGTTGTTATTTCTATGCT 58.053 33.333 0.00 0.00 0.00 3.79
360 452 1.272807 ACTCCCTCCGATCGGAAAAA 58.727 50.000 34.77 21.62 44.66 1.94
361 453 1.753073 GTACTCCCTCCGATCGGAAAA 59.247 52.381 34.77 21.95 44.66 2.29
362 454 1.396653 GTACTCCCTCCGATCGGAAA 58.603 55.000 34.77 22.27 44.66 3.13
363 455 0.466922 GGTACTCCCTCCGATCGGAA 60.467 60.000 34.77 21.03 44.66 4.30
364 456 1.150081 GGTACTCCCTCCGATCGGA 59.850 63.158 33.55 33.55 42.90 4.55
365 457 0.539901 ATGGTACTCCCTCCGATCGG 60.540 60.000 28.62 28.62 0.00 4.18
366 458 1.329256 AATGGTACTCCCTCCGATCG 58.671 55.000 8.51 8.51 0.00 3.69
367 459 3.134081 TGAAAATGGTACTCCCTCCGATC 59.866 47.826 0.00 0.00 0.00 3.69
368 460 3.112263 TGAAAATGGTACTCCCTCCGAT 58.888 45.455 0.00 0.00 0.00 4.18
369 461 2.500098 CTGAAAATGGTACTCCCTCCGA 59.500 50.000 0.00 0.00 0.00 4.55
370 462 2.236395 ACTGAAAATGGTACTCCCTCCG 59.764 50.000 0.00 0.00 0.00 4.63
371 463 4.302559 AACTGAAAATGGTACTCCCTCC 57.697 45.455 0.00 0.00 0.00 4.30
372 464 5.313712 TGAAACTGAAAATGGTACTCCCTC 58.686 41.667 0.00 0.00 0.00 4.30
373 465 5.319043 TGAAACTGAAAATGGTACTCCCT 57.681 39.130 0.00 0.00 0.00 4.20
374 466 5.105756 CCATGAAACTGAAAATGGTACTCCC 60.106 44.000 0.00 0.00 35.78 4.30
375 467 5.105756 CCCATGAAACTGAAAATGGTACTCC 60.106 44.000 0.00 0.00 38.32 3.85
376 468 5.622233 GCCCATGAAACTGAAAATGGTACTC 60.622 44.000 0.00 0.00 38.32 2.59
377 469 4.220602 GCCCATGAAACTGAAAATGGTACT 59.779 41.667 0.00 0.00 38.32 2.73
378 470 4.494484 GCCCATGAAACTGAAAATGGTAC 58.506 43.478 0.00 0.00 38.32 3.34
382 474 3.007182 ACAGGCCCATGAAACTGAAAATG 59.993 43.478 14.59 0.00 35.08 2.32
445 538 1.070758 TCGCTCTTGGGATATGAAGGC 59.929 52.381 0.00 0.00 0.00 4.35
481 574 4.381612 CCGCATATACCCGTATCATTCACT 60.382 45.833 0.00 0.00 0.00 3.41
490 583 1.546923 CACATCCCGCATATACCCGTA 59.453 52.381 0.00 0.00 0.00 4.02
491 584 0.320374 CACATCCCGCATATACCCGT 59.680 55.000 0.00 0.00 0.00 5.28
492 585 1.019278 GCACATCCCGCATATACCCG 61.019 60.000 0.00 0.00 0.00 5.28
493 586 0.036164 TGCACATCCCGCATATACCC 59.964 55.000 0.00 0.00 33.55 3.69
494 587 3.623848 TGCACATCCCGCATATACC 57.376 52.632 0.00 0.00 33.55 2.73
503 596 3.220110 ACATGATCTTGATGCACATCCC 58.780 45.455 15.03 0.00 37.02 3.85
534 627 8.943909 AGACACTTATTTTAATACGGAGGAAG 57.056 34.615 0.00 0.00 0.00 3.46
535 628 8.533657 TGAGACACTTATTTTAATACGGAGGAA 58.466 33.333 0.00 0.00 0.00 3.36
537 630 8.601476 GTTGAGACACTTATTTTAATACGGAGG 58.399 37.037 0.00 0.00 0.00 4.30
538 631 8.601476 GGTTGAGACACTTATTTTAATACGGAG 58.399 37.037 0.00 0.00 0.00 4.63
540 633 8.488651 AGGTTGAGACACTTATTTTAATACGG 57.511 34.615 0.00 0.00 0.00 4.02
593 686 9.793259 TCTCAAAATAAATGTCTCAACCTTAGT 57.207 29.630 0.00 0.00 0.00 2.24
595 688 9.793259 AGTCTCAAAATAAATGTCTCAACCTTA 57.207 29.630 0.00 0.00 0.00 2.69
596 689 8.571336 CAGTCTCAAAATAAATGTCTCAACCTT 58.429 33.333 0.00 0.00 0.00 3.50
597 690 7.939039 TCAGTCTCAAAATAAATGTCTCAACCT 59.061 33.333 0.00 0.00 0.00 3.50
598 691 8.099364 TCAGTCTCAAAATAAATGTCTCAACC 57.901 34.615 0.00 0.00 0.00 3.77
599 692 8.233190 CCTCAGTCTCAAAATAAATGTCTCAAC 58.767 37.037 0.00 0.00 0.00 3.18
600 693 7.391554 CCCTCAGTCTCAAAATAAATGTCTCAA 59.608 37.037 0.00 0.00 0.00 3.02
601 694 6.881065 CCCTCAGTCTCAAAATAAATGTCTCA 59.119 38.462 0.00 0.00 0.00 3.27
602 695 7.106239 TCCCTCAGTCTCAAAATAAATGTCTC 58.894 38.462 0.00 0.00 0.00 3.36
603 696 7.020827 TCCCTCAGTCTCAAAATAAATGTCT 57.979 36.000 0.00 0.00 0.00 3.41
604 697 6.881602 ACTCCCTCAGTCTCAAAATAAATGTC 59.118 38.462 0.00 0.00 0.00 3.06
605 698 6.784031 ACTCCCTCAGTCTCAAAATAAATGT 58.216 36.000 0.00 0.00 0.00 2.71
606 699 8.970859 ATACTCCCTCAGTCTCAAAATAAATG 57.029 34.615 0.00 0.00 36.43 2.32
609 702 9.434275 TCATATACTCCCTCAGTCTCAAAATAA 57.566 33.333 0.00 0.00 36.43 1.40
610 703 9.607333 ATCATATACTCCCTCAGTCTCAAAATA 57.393 33.333 0.00 0.00 36.43 1.40
611 704 7.921041 TCATATACTCCCTCAGTCTCAAAAT 57.079 36.000 0.00 0.00 36.43 1.82
612 705 7.921041 ATCATATACTCCCTCAGTCTCAAAA 57.079 36.000 0.00 0.00 36.43 2.44
613 706 7.202038 CCAATCATATACTCCCTCAGTCTCAAA 60.202 40.741 0.00 0.00 36.43 2.69
614 707 6.268617 CCAATCATATACTCCCTCAGTCTCAA 59.731 42.308 0.00 0.00 36.43 3.02
615 708 5.777223 CCAATCATATACTCCCTCAGTCTCA 59.223 44.000 0.00 0.00 36.43 3.27
616 709 5.337169 GCCAATCATATACTCCCTCAGTCTC 60.337 48.000 0.00 0.00 36.43 3.36
617 710 4.530161 GCCAATCATATACTCCCTCAGTCT 59.470 45.833 0.00 0.00 36.43 3.24
618 711 4.284490 TGCCAATCATATACTCCCTCAGTC 59.716 45.833 0.00 0.00 36.43 3.51
619 712 4.040952 GTGCCAATCATATACTCCCTCAGT 59.959 45.833 0.00 0.00 39.41 3.41
620 713 4.040829 TGTGCCAATCATATACTCCCTCAG 59.959 45.833 0.00 0.00 0.00 3.35
621 714 3.973305 TGTGCCAATCATATACTCCCTCA 59.027 43.478 0.00 0.00 0.00 3.86
622 715 4.623932 TGTGCCAATCATATACTCCCTC 57.376 45.455 0.00 0.00 0.00 4.30
623 716 4.413520 AGTTGTGCCAATCATATACTCCCT 59.586 41.667 0.00 0.00 0.00 4.20
624 717 4.516698 CAGTTGTGCCAATCATATACTCCC 59.483 45.833 0.00 0.00 0.00 4.30
625 718 5.368145 TCAGTTGTGCCAATCATATACTCC 58.632 41.667 0.00 0.00 0.00 3.85
626 719 8.783833 ATATCAGTTGTGCCAATCATATACTC 57.216 34.615 0.00 0.00 0.00 2.59
667 760 7.709269 TTTCCGCAATAGATCATGTAAGTAC 57.291 36.000 0.00 0.00 0.00 2.73
668 761 8.725405 TTTTTCCGCAATAGATCATGTAAGTA 57.275 30.769 0.00 0.00 0.00 2.24
669 762 7.624360 TTTTTCCGCAATAGATCATGTAAGT 57.376 32.000 0.00 0.00 0.00 2.24
692 785 9.920946 ACATAGTCATATATTCCAGTGGTTTTT 57.079 29.630 9.54 0.00 0.00 1.94
693 786 9.920946 AACATAGTCATATATTCCAGTGGTTTT 57.079 29.630 9.54 0.00 0.00 2.43
695 788 9.998106 GTAACATAGTCATATATTCCAGTGGTT 57.002 33.333 9.54 0.58 0.00 3.67
696 789 9.154632 TGTAACATAGTCATATATTCCAGTGGT 57.845 33.333 9.54 0.00 0.00 4.16
697 790 9.996554 TTGTAACATAGTCATATATTCCAGTGG 57.003 33.333 1.40 1.40 0.00 4.00
706 799 9.884636 GCCCATACATTGTAACATAGTCATATA 57.115 33.333 0.00 0.00 0.00 0.86
707 800 8.382405 TGCCCATACATTGTAACATAGTCATAT 58.618 33.333 0.00 0.00 0.00 1.78
708 801 7.659799 GTGCCCATACATTGTAACATAGTCATA 59.340 37.037 0.00 0.00 0.00 2.15
712 805 6.001449 AGTGCCCATACATTGTAACATAGT 57.999 37.500 0.00 0.00 0.00 2.12
715 808 6.437162 AGAAAAGTGCCCATACATTGTAACAT 59.563 34.615 0.00 0.00 0.00 2.71
720 813 5.570320 ACTAGAAAAGTGCCCATACATTGT 58.430 37.500 0.00 0.00 36.93 2.71
726 819 7.195374 ACATAGAACTAGAAAAGTGCCCATA 57.805 36.000 0.00 0.00 38.88 2.74
810 904 2.880963 TTTTCGCAAAAGAAGGTGGG 57.119 45.000 0.00 0.00 0.00 4.61
936 1030 2.559840 GAACTGACGACGAGCCGA 59.440 61.111 0.00 0.00 0.00 5.54
1077 1171 2.445438 CGAAGAAAGCGGAGGCGAC 61.445 63.158 0.00 0.00 46.35 5.19
1082 1176 2.820037 GGGGCGAAGAAAGCGGAG 60.820 66.667 0.00 0.00 35.00 4.63
1196 1290 3.947910 ATGGCCAAATCAGTTTGAGTG 57.052 42.857 10.96 0.00 46.03 3.51
1214 1308 2.092212 AGTCTATCCACTGCCCCAAATG 60.092 50.000 0.00 0.00 0.00 2.32
1271 1366 7.999679 TGCTATCTGATTGGAAATTTTACTGG 58.000 34.615 0.00 0.00 0.00 4.00
1280 1375 8.953313 CATGCTATATTGCTATCTGATTGGAAA 58.047 33.333 10.48 0.00 0.00 3.13
1283 1378 7.551617 TCACATGCTATATTGCTATCTGATTGG 59.448 37.037 10.48 0.00 0.00 3.16
1327 1427 2.031012 TGCTCGTCCTGTGGCAAG 59.969 61.111 0.00 0.00 0.00 4.01
1329 1429 2.506957 TTCTGCTCGTCCTGTGGCA 61.507 57.895 0.00 0.00 0.00 4.92
1330 1430 2.029844 GTTCTGCTCGTCCTGTGGC 61.030 63.158 0.00 0.00 0.00 5.01
1486 1594 1.504275 ATCCAAAGAGGCCCACTGCT 61.504 55.000 0.00 0.00 40.92 4.24
1489 1597 0.915364 GAGATCCAAAGAGGCCCACT 59.085 55.000 0.00 0.00 37.29 4.00
1612 1722 0.768622 TTTGTCCAGTGTAGGGGTGG 59.231 55.000 0.00 0.00 0.00 4.61
1626 1736 9.217278 ACATTATGCATCAGATATCTCTTTGTC 57.783 33.333 0.19 0.00 0.00 3.18
1638 1748 7.283807 ACATTTAGCTGAACATTATGCATCAGA 59.716 33.333 23.79 9.93 37.01 3.27
1704 1818 9.991906 GCAACTAAATTACCCATATCTGTAGTA 57.008 33.333 0.00 0.00 0.00 1.82
1729 1866 6.267817 TGCAATTGTAAGCATCAAATCTAGC 58.732 36.000 7.40 0.00 35.51 3.42
1767 1904 3.512329 TGAACTGCAATGGATCATGCTTT 59.488 39.130 15.52 10.10 0.00 3.51
1791 1928 6.071616 GCAATGGGTTTTAACTCTACCATGAA 60.072 38.462 0.00 0.00 38.61 2.57
1806 1943 5.271598 TCTTGGATCTATTGCAATGGGTTT 58.728 37.500 22.27 7.74 34.90 3.27
1851 2003 0.029834 GAAGCATGGCTACAATGGCG 59.970 55.000 0.00 0.00 38.25 5.69
1859 2011 3.002791 CTGAAGAAACGAAGCATGGCTA 58.997 45.455 0.00 0.00 38.25 3.93
1871 2023 7.489574 AAGTTCTGATGAAGTCTGAAGAAAC 57.510 36.000 0.00 0.00 42.95 2.78
1880 2032 8.031864 TGACTCATAGAAAGTTCTGATGAAGTC 58.968 37.037 3.76 14.29 38.19 3.01
1933 2085 0.402887 TGGTAGAGACCCACGACAGA 59.597 55.000 0.00 0.00 46.32 3.41
1939 2091 1.822990 TGTCGAATGGTAGAGACCCAC 59.177 52.381 0.00 0.00 46.32 4.61
1952 2104 9.764363 TTCAACTTAATATGCTCTATGTCGAAT 57.236 29.630 0.00 0.00 0.00 3.34
1953 2105 9.031360 GTTCAACTTAATATGCTCTATGTCGAA 57.969 33.333 0.00 0.00 0.00 3.71
1955 2107 8.352752 TGTTCAACTTAATATGCTCTATGTCG 57.647 34.615 0.00 0.00 0.00 4.35
1958 2110 9.276590 TGGATGTTCAACTTAATATGCTCTATG 57.723 33.333 0.00 0.00 0.00 2.23
1960 2112 9.851686 ATTGGATGTTCAACTTAATATGCTCTA 57.148 29.630 0.00 0.00 0.00 2.43
1961 2113 8.757982 ATTGGATGTTCAACTTAATATGCTCT 57.242 30.769 0.00 0.00 0.00 4.09
1962 2114 8.623903 TGATTGGATGTTCAACTTAATATGCTC 58.376 33.333 0.00 0.00 0.00 4.26
1998 2164 1.407618 GGATTAACGGACAAATGGGCC 59.592 52.381 0.00 0.00 0.00 5.80
2021 2187 6.822506 GTGTAACTCTGTAAGAAAGCATGTC 58.177 40.000 0.00 0.00 46.34 3.06
2056 2222 7.899973 AGCCAACATCTTGAAAATTGAGTAAT 58.100 30.769 0.00 0.00 0.00 1.89
2068 2234 3.822735 CTCCAGAAAAGCCAACATCTTGA 59.177 43.478 0.00 0.00 0.00 3.02
2087 2253 5.767168 CCCATCATTTTCTACCATCTTCTCC 59.233 44.000 0.00 0.00 0.00 3.71
2124 2290 7.759489 AAAGCAGTACTAAATCAATGAACCA 57.241 32.000 0.00 0.00 0.00 3.67
2201 2367 7.834068 TGAAAGCTATTCAGTGTACAGAATC 57.166 36.000 12.26 2.33 34.56 2.52
2202 2368 7.826252 ACATGAAAGCTATTCAGTGTACAGAAT 59.174 33.333 13.17 13.17 36.33 2.40
2209 2375 6.882610 TTTCACATGAAAGCTATTCAGTGT 57.117 33.333 21.98 18.16 38.94 3.55
2210 2376 8.024865 TCAATTTCACATGAAAGCTATTCAGTG 58.975 33.333 12.30 19.86 45.87 3.66
2229 2399 7.771183 TCATAATAGGGTTGCTTGTCAATTTC 58.229 34.615 0.00 0.00 36.99 2.17
2260 2430 3.244078 TGTGCAACCAGATAAAGACGAGT 60.244 43.478 0.00 0.00 34.36 4.18
2264 2434 5.215160 CAGTTTGTGCAACCAGATAAAGAC 58.785 41.667 0.00 0.00 35.77 3.01
2294 2464 7.003648 GCAATTCAAAGAAAAAGTATGCGAAC 58.996 34.615 0.00 0.00 0.00 3.95
2593 2771 5.616270 TGTCCAGCTACAAAGTTGTATTCA 58.384 37.500 4.43 0.00 42.26 2.57
2641 2819 3.133691 CGGCAAGTGTATGATACTGCAT 58.866 45.455 14.58 0.00 0.00 3.96
2662 2840 6.049790 CCAGAACTTTAGTATTCTGTAGCCC 58.950 44.000 11.80 0.00 46.93 5.19
2756 2935 6.862090 GCAGATCAGAATTGAATTATTGGCTC 59.138 38.462 0.00 0.00 36.78 4.70
2759 2938 7.813148 GGATGCAGATCAGAATTGAATTATTGG 59.187 37.037 0.00 0.00 36.78 3.16
3196 3400 2.061773 GCATGAGGTATCGTTGGATCG 58.938 52.381 0.00 0.00 34.00 3.69
3310 3514 2.492881 TGGCATTATGCTGAAACTGGTG 59.507 45.455 17.13 0.00 44.28 4.17
3409 3614 8.914011 ACTAGTGATCAACTGCATATGTACTTA 58.086 33.333 4.29 0.00 40.26 2.24
3413 3618 5.985530 GCACTAGTGATCAACTGCATATGTA 59.014 40.000 27.08 0.00 40.26 2.29
3415 3620 4.812626 TGCACTAGTGATCAACTGCATATG 59.187 41.667 27.08 0.00 40.26 1.78
3416 3621 5.027293 TGCACTAGTGATCAACTGCATAT 57.973 39.130 27.08 0.00 40.26 1.78
3418 3623 3.339253 TGCACTAGTGATCAACTGCAT 57.661 42.857 27.08 0.00 40.26 3.96
3419 3624 2.837532 TGCACTAGTGATCAACTGCA 57.162 45.000 27.08 11.54 40.26 4.41
3436 3645 4.877823 TCACTAAATCTGGTGACATCATGC 59.122 41.667 0.00 0.00 38.06 4.06
3478 3687 3.826637 CCTCAAAAGGGCATTGCTG 57.173 52.632 8.82 0.00 39.21 4.41
3598 3811 3.084070 CCACAAAAGCTTCAGTGGTTC 57.916 47.619 28.88 0.00 44.95 3.62
3615 3828 2.026262 TGGGTGAAAATCTAGCCTCCAC 60.026 50.000 0.00 0.00 35.54 4.02
3644 3857 6.792326 ACACCAAGCTGTTTTAACTCTTTAC 58.208 36.000 0.00 0.00 0.00 2.01
3683 3896 8.812513 AAGTCCAGATGATCATTAAACATCAA 57.187 30.769 10.14 0.00 41.64 2.57
3705 3918 1.111277 GTGTCAGGGGCAACAAAAGT 58.889 50.000 0.00 0.00 39.74 2.66
3739 3952 2.110578 TCCTGCAGGAATCAGATCGAA 58.889 47.619 33.41 5.54 42.18 3.71
3829 4042 8.849168 TGTTGCTCTTTTTAATGAGATTTCTGA 58.151 29.630 8.95 0.00 33.39 3.27
3838 4051 6.716628 ACTGATCCTGTTGCTCTTTTTAATGA 59.283 34.615 0.00 0.00 0.00 2.57
3905 4118 0.652592 CTAGCCAAACGCCTGAATCG 59.347 55.000 0.00 0.00 38.78 3.34
3929 4142 2.420372 CTCGTAGTCACTAGCAGCTCAA 59.580 50.000 0.00 0.00 0.00 3.02
3968 4181 5.420725 AGCATACATCTGTTTCACCTGTA 57.579 39.130 0.00 0.00 0.00 2.74
3969 4182 4.292186 AGCATACATCTGTTTCACCTGT 57.708 40.909 0.00 0.00 0.00 4.00
4047 4260 9.683069 CTTGCAAAAAGATGAGTAATGTTTACT 57.317 29.630 0.00 0.00 30.81 2.24
4060 4279 3.575687 AGGAACCTCCTTGCAAAAAGATG 59.424 43.478 0.00 0.00 46.91 2.90
4088 4307 2.224314 CGAACCTGTCAGGAAAAAGCTC 59.776 50.000 26.18 8.47 37.67 4.09
4089 4308 2.158813 TCGAACCTGTCAGGAAAAAGCT 60.159 45.455 26.18 0.00 37.67 3.74
4091 4310 2.808543 CCTCGAACCTGTCAGGAAAAAG 59.191 50.000 26.18 15.43 37.67 2.27
4092 4311 2.486548 CCCTCGAACCTGTCAGGAAAAA 60.487 50.000 26.18 7.18 37.67 1.94
4093 4312 1.071699 CCCTCGAACCTGTCAGGAAAA 59.928 52.381 26.18 6.84 37.67 2.29
4094 4313 0.685097 CCCTCGAACCTGTCAGGAAA 59.315 55.000 26.18 6.50 37.67 3.13
4095 4314 1.192146 CCCCTCGAACCTGTCAGGAA 61.192 60.000 26.18 6.84 37.67 3.36
4097 4316 1.608717 CTCCCCTCGAACCTGTCAGG 61.609 65.000 17.88 17.88 42.49 3.86
4098 4317 1.893786 CTCCCCTCGAACCTGTCAG 59.106 63.158 0.00 0.00 0.00 3.51
4099 4318 2.283529 GCTCCCCTCGAACCTGTCA 61.284 63.158 0.00 0.00 0.00 3.58
4101 4320 2.203788 TGCTCCCCTCGAACCTGT 60.204 61.111 0.00 0.00 0.00 4.00
4102 4321 2.581354 CTGCTCCCCTCGAACCTG 59.419 66.667 0.00 0.00 0.00 4.00
4103 4322 2.685380 CCTGCTCCCCTCGAACCT 60.685 66.667 0.00 0.00 0.00 3.50
4104 4323 4.475135 GCCTGCTCCCCTCGAACC 62.475 72.222 0.00 0.00 0.00 3.62
4105 4324 2.748058 TTTGCCTGCTCCCCTCGAAC 62.748 60.000 0.00 0.00 0.00 3.95
4108 4327 2.437359 CTTTGCCTGCTCCCCTCG 60.437 66.667 0.00 0.00 0.00 4.63
4109 4328 2.044551 CCTTTGCCTGCTCCCCTC 60.045 66.667 0.00 0.00 0.00 4.30
4110 4329 1.513087 ATTCCTTTGCCTGCTCCCCT 61.513 55.000 0.00 0.00 0.00 4.79
4111 4330 0.615827 AATTCCTTTGCCTGCTCCCC 60.616 55.000 0.00 0.00 0.00 4.81
4112 4331 1.205655 GAAATTCCTTTGCCTGCTCCC 59.794 52.381 0.00 0.00 0.00 4.30
4113 4332 2.094338 CAGAAATTCCTTTGCCTGCTCC 60.094 50.000 0.00 0.00 0.00 4.70
4114 4333 2.673326 GCAGAAATTCCTTTGCCTGCTC 60.673 50.000 0.00 0.00 39.66 4.26
4115 4334 1.274447 GCAGAAATTCCTTTGCCTGCT 59.726 47.619 0.00 0.00 39.66 4.24
4116 4335 1.274447 AGCAGAAATTCCTTTGCCTGC 59.726 47.619 0.00 0.00 41.46 4.85
4117 4336 2.824341 AGAGCAGAAATTCCTTTGCCTG 59.176 45.455 2.65 0.00 37.26 4.85
4118 4337 3.087781 GAGAGCAGAAATTCCTTTGCCT 58.912 45.455 2.65 0.85 37.26 4.75
4120 4339 2.485814 ACGAGAGCAGAAATTCCTTTGC 59.514 45.455 0.00 0.00 36.83 3.68
4121 4340 4.756084 AACGAGAGCAGAAATTCCTTTG 57.244 40.909 0.00 0.00 0.00 2.77
4122 4341 5.774498 AAAACGAGAGCAGAAATTCCTTT 57.226 34.783 0.00 0.00 0.00 3.11
4123 4342 5.532779 AGAAAAACGAGAGCAGAAATTCCTT 59.467 36.000 0.00 0.00 0.00 3.36
4124 4343 5.066593 AGAAAAACGAGAGCAGAAATTCCT 58.933 37.500 0.00 0.00 0.00 3.36
4125 4344 5.363979 AGAAAAACGAGAGCAGAAATTCC 57.636 39.130 0.00 0.00 0.00 3.01
4127 4346 7.363431 CCTAAAGAAAAACGAGAGCAGAAATT 58.637 34.615 0.00 0.00 0.00 1.82
4128 4347 6.072452 CCCTAAAGAAAAACGAGAGCAGAAAT 60.072 38.462 0.00 0.00 0.00 2.17
4130 4349 4.755123 CCCTAAAGAAAAACGAGAGCAGAA 59.245 41.667 0.00 0.00 0.00 3.02
4131 4350 4.039973 TCCCTAAAGAAAAACGAGAGCAGA 59.960 41.667 0.00 0.00 0.00 4.26
4132 4351 4.315803 TCCCTAAAGAAAAACGAGAGCAG 58.684 43.478 0.00 0.00 0.00 4.24
4133 4352 4.345859 TCCCTAAAGAAAAACGAGAGCA 57.654 40.909 0.00 0.00 0.00 4.26
4134 4353 5.181433 ACAATCCCTAAAGAAAAACGAGAGC 59.819 40.000 0.00 0.00 0.00 4.09
4135 4354 6.803154 ACAATCCCTAAAGAAAAACGAGAG 57.197 37.500 0.00 0.00 0.00 3.20
4136 4355 6.370718 GCTACAATCCCTAAAGAAAAACGAGA 59.629 38.462 0.00 0.00 0.00 4.04
4137 4356 6.371825 AGCTACAATCCCTAAAGAAAAACGAG 59.628 38.462 0.00 0.00 0.00 4.18
4140 4359 7.039993 TGGAAGCTACAATCCCTAAAGAAAAAC 60.040 37.037 0.00 0.00 34.68 2.43
4141 4360 7.007723 TGGAAGCTACAATCCCTAAAGAAAAA 58.992 34.615 0.00 0.00 34.68 1.94
4143 4362 6.134535 TGGAAGCTACAATCCCTAAAGAAA 57.865 37.500 0.00 0.00 34.68 2.52
4144 4363 5.772393 TGGAAGCTACAATCCCTAAAGAA 57.228 39.130 0.00 0.00 34.68 2.52
4145 4364 5.397899 CCATGGAAGCTACAATCCCTAAAGA 60.398 44.000 5.56 0.00 34.68 2.52
4146 4365 4.823989 CCATGGAAGCTACAATCCCTAAAG 59.176 45.833 5.56 0.00 34.68 1.85
4148 4367 3.435026 GCCATGGAAGCTACAATCCCTAA 60.435 47.826 18.40 0.00 34.68 2.69
4149 4368 2.106511 GCCATGGAAGCTACAATCCCTA 59.893 50.000 18.40 0.00 34.68 3.53
4150 4369 1.133668 GCCATGGAAGCTACAATCCCT 60.134 52.381 18.40 0.00 34.68 4.20
4151 4370 1.322442 GCCATGGAAGCTACAATCCC 58.678 55.000 18.40 0.00 34.68 3.85
4152 4371 1.322442 GGCCATGGAAGCTACAATCC 58.678 55.000 18.40 0.00 36.21 3.01
4154 4373 0.255890 ACGGCCATGGAAGCTACAAT 59.744 50.000 18.40 0.00 0.00 2.71
4155 4374 0.906066 TACGGCCATGGAAGCTACAA 59.094 50.000 18.40 0.00 0.00 2.41
4156 4375 0.464036 CTACGGCCATGGAAGCTACA 59.536 55.000 18.40 0.00 0.00 2.74
4158 4377 0.464036 CACTACGGCCATGGAAGCTA 59.536 55.000 18.40 3.01 0.00 3.32
4159 4378 1.221840 CACTACGGCCATGGAAGCT 59.778 57.895 18.40 1.97 0.00 3.74
4160 4379 1.078426 ACACTACGGCCATGGAAGC 60.078 57.895 18.40 0.00 0.00 3.86
4161 4380 0.537188 AGACACTACGGCCATGGAAG 59.463 55.000 18.40 10.84 0.00 3.46
4162 4381 1.754803 CTAGACACTACGGCCATGGAA 59.245 52.381 18.40 0.00 0.00 3.53
4163 4382 1.064240 TCTAGACACTACGGCCATGGA 60.064 52.381 18.40 0.00 0.00 3.41
4164 4383 1.399714 TCTAGACACTACGGCCATGG 58.600 55.000 7.63 7.63 0.00 3.66
4165 4384 3.735237 AATCTAGACACTACGGCCATG 57.265 47.619 2.24 0.00 0.00 3.66
4166 4385 4.833380 ACATAATCTAGACACTACGGCCAT 59.167 41.667 2.24 0.00 0.00 4.40
4168 4387 4.519730 AGACATAATCTAGACACTACGGCC 59.480 45.833 0.00 0.00 35.15 6.13
4169 4388 5.692613 AGACATAATCTAGACACTACGGC 57.307 43.478 0.00 0.00 35.15 5.68
4170 4389 8.604640 TCTAAGACATAATCTAGACACTACGG 57.395 38.462 0.00 0.00 36.27 4.02
4194 4597 3.627577 ACTCCACACAAGACACAACAATC 59.372 43.478 0.00 0.00 0.00 2.67
4195 4598 3.620488 ACTCCACACAAGACACAACAAT 58.380 40.909 0.00 0.00 0.00 2.71
4196 4599 3.066291 ACTCCACACAAGACACAACAA 57.934 42.857 0.00 0.00 0.00 2.83
4197 4600 2.779755 ACTCCACACAAGACACAACA 57.220 45.000 0.00 0.00 0.00 3.33
4198 4601 3.555956 CACTACTCCACACAAGACACAAC 59.444 47.826 0.00 0.00 0.00 3.32
4199 4602 3.196901 ACACTACTCCACACAAGACACAA 59.803 43.478 0.00 0.00 0.00 3.33
4200 4603 2.764010 ACACTACTCCACACAAGACACA 59.236 45.455 0.00 0.00 0.00 3.72
4213 4770 3.677424 GCCATGGAAGTGAGACACTACTC 60.677 52.174 18.40 0.72 44.62 2.59
4258 4815 4.539083 AACTGTGGTCGCGTGCCA 62.539 61.111 18.17 18.17 0.00 4.92
4259 4816 4.012895 CAACTGTGGTCGCGTGCC 62.013 66.667 5.77 10.87 0.00 5.01


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

AutoCloner maintained by Alex Coulton.