Multiple sequence alignment - TraesCS5A01G374000

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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 TraesCS5A01G374000 chr5A 100.000 3776 0 0 1 3776 572020504 572024279 0.000000e+00 6974.0
1 TraesCS5A01G374000 chr5A 86.988 1537 179 18 1220 2743 27516306 27517834 0.000000e+00 1711.0
2 TraesCS5A01G374000 chr5D 90.804 3643 179 57 1 3581 453237787 453241335 0.000000e+00 4728.0
3 TraesCS5A01G374000 chr5D 86.996 1538 178 19 1220 2743 38724108 38725637 0.000000e+00 1712.0
4 TraesCS5A01G374000 chr5B 91.642 3338 137 68 2 3255 553724074 553727353 0.000000e+00 4488.0
5 TraesCS5A01G374000 chr5B 86.792 1537 183 17 1220 2743 29337728 29339257 0.000000e+00 1696.0
6 TraesCS5A01G374000 chr5B 88.177 203 19 5 3483 3681 553727473 553727674 1.750000e-58 237.0
7 TraesCS5A01G374000 chr1D 95.556 45 2 0 1306 1350 445097742 445097698 5.230000e-09 73.1
8 TraesCS5A01G374000 chr1B 93.333 45 3 0 1306 1350 606254096 606254052 2.430000e-07 67.6


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 TraesCS5A01G374000 chr5A 572020504 572024279 3775 False 6974.0 6974 100.0000 1 3776 1 chr5A.!!$F2 3775
1 TraesCS5A01G374000 chr5A 27516306 27517834 1528 False 1711.0 1711 86.9880 1220 2743 1 chr5A.!!$F1 1523
2 TraesCS5A01G374000 chr5D 453237787 453241335 3548 False 4728.0 4728 90.8040 1 3581 1 chr5D.!!$F2 3580
3 TraesCS5A01G374000 chr5D 38724108 38725637 1529 False 1712.0 1712 86.9960 1220 2743 1 chr5D.!!$F1 1523
4 TraesCS5A01G374000 chr5B 553724074 553727674 3600 False 2362.5 4488 89.9095 2 3681 2 chr5B.!!$F2 3679
5 TraesCS5A01G374000 chr5B 29337728 29339257 1529 False 1696.0 1696 86.7920 1220 2743 1 chr5B.!!$F1 1523

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
936 1019 0.107214 CACGCTCTCCCTCTCTCTCT 60.107 60.000 0.0 0.0 0.0 3.1 F
937 1020 0.180406 ACGCTCTCCCTCTCTCTCTC 59.820 60.000 0.0 0.0 0.0 3.2 F
938 1021 0.469917 CGCTCTCCCTCTCTCTCTCT 59.530 60.000 0.0 0.0 0.0 3.1 F
1020 1116 1.375268 GCAGACACTCACAGCCTCC 60.375 63.158 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2169 0.819259 GCAGCTTGAACACCACCTGA 60.819 55.000 0.00 0.0 30.21 3.86 R
2234 2351 3.296709 ATCACCACCACCTCGTCGC 62.297 63.158 0.00 0.0 0.00 5.19 R
2661 2784 4.321966 TCGGCGGCATTGACCACA 62.322 61.111 10.53 0.0 0.00 4.17 R
2933 3059 5.447010 CCAACTACGTACTAGTGTGAGCTAC 60.447 48.000 5.39 0.0 35.70 3.58 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
140 152 1.037579 ATGATGCTCCGGTCGAGACA 61.038 55.000 0.00 0.00 41.63 3.41
294 323 2.580867 GCTGAGCCTCGCTGTACG 60.581 66.667 0.00 0.00 39.88 3.67
357 403 1.067974 CGTGCTACATCAACGGGGATA 59.932 52.381 0.00 0.00 0.00 2.59
382 428 7.483307 ACTGTTTAATTATGCTGCTAATGGTG 58.517 34.615 0.00 0.00 0.00 4.17
384 430 6.096705 TGTTTAATTATGCTGCTAATGGTGCT 59.903 34.615 0.00 0.00 0.00 4.40
385 431 4.579454 AATTATGCTGCTAATGGTGCTG 57.421 40.909 0.00 0.00 0.00 4.41
387 433 3.915575 GCTGCTAATGGTGCTGCT 58.084 55.556 0.00 0.00 46.79 4.24
388 434 3.085208 GCTGCTAATGGTGCTGCTA 57.915 52.632 0.00 0.00 46.79 3.49
390 436 1.303309 CTGCTAATGGTGCTGCTACC 58.697 55.000 12.44 12.44 41.24 3.18
391 437 0.461870 TGCTAATGGTGCTGCTACCG 60.462 55.000 13.83 4.15 43.87 4.02
392 438 1.160329 GCTAATGGTGCTGCTACCGG 61.160 60.000 0.00 0.00 43.87 5.28
393 439 0.464036 CTAATGGTGCTGCTACCGGA 59.536 55.000 9.46 0.00 43.87 5.14
394 440 0.464036 TAATGGTGCTGCTACCGGAG 59.536 55.000 9.46 1.84 43.87 4.63
442 491 2.684843 GCGCTGTCCTCCAAGCAAG 61.685 63.158 0.00 0.00 0.00 4.01
443 492 2.684843 CGCTGTCCTCCAAGCAAGC 61.685 63.158 0.00 0.00 0.00 4.01
444 493 1.601759 GCTGTCCTCCAAGCAAGCA 60.602 57.895 0.00 0.00 0.00 3.91
445 494 1.174712 GCTGTCCTCCAAGCAAGCAA 61.175 55.000 0.00 0.00 0.00 3.91
447 496 1.268899 CTGTCCTCCAAGCAAGCAAAG 59.731 52.381 0.00 0.00 0.00 2.77
448 497 0.600057 GTCCTCCAAGCAAGCAAAGG 59.400 55.000 0.00 0.00 0.00 3.11
449 498 0.478072 TCCTCCAAGCAAGCAAAGGA 59.522 50.000 0.00 0.00 0.00 3.36
450 499 1.133513 TCCTCCAAGCAAGCAAAGGAA 60.134 47.619 0.00 0.00 30.19 3.36
451 500 1.271656 CCTCCAAGCAAGCAAAGGAAG 59.728 52.381 0.00 0.00 0.00 3.46
455 504 1.897802 CAAGCAAGCAAAGGAAGGGAT 59.102 47.619 0.00 0.00 0.00 3.85
456 505 3.091545 CAAGCAAGCAAAGGAAGGGATA 58.908 45.455 0.00 0.00 0.00 2.59
457 506 3.010200 AGCAAGCAAAGGAAGGGATAG 57.990 47.619 0.00 0.00 0.00 2.08
458 507 2.027385 GCAAGCAAAGGAAGGGATAGG 58.973 52.381 0.00 0.00 0.00 2.57
469 521 1.143813 AGGGATAGGGCACATGGAAG 58.856 55.000 0.00 0.00 0.00 3.46
527 580 3.264897 CTCCGAATTGGCGCGAGG 61.265 66.667 12.10 0.24 37.80 4.63
626 681 1.876156 AGAAAAGCCAGCAAGAAGACG 59.124 47.619 0.00 0.00 0.00 4.18
627 682 0.312102 AAAAGCCAGCAAGAAGACGC 59.688 50.000 0.00 0.00 0.00 5.19
628 683 0.819259 AAAGCCAGCAAGAAGACGCA 60.819 50.000 0.00 0.00 0.00 5.24
629 684 1.233285 AAGCCAGCAAGAAGACGCAG 61.233 55.000 0.00 0.00 0.00 5.18
630 685 2.866028 CCAGCAAGAAGACGCAGC 59.134 61.111 0.00 0.00 0.00 5.25
631 686 2.473378 CAGCAAGAAGACGCAGCG 59.527 61.111 14.82 14.82 0.00 5.18
672 730 3.626924 GGCACGTCCCAGTCACCT 61.627 66.667 0.00 0.00 0.00 4.00
778 852 4.373116 CCGTCCACCACACTCCCG 62.373 72.222 0.00 0.00 0.00 5.14
804 878 2.073816 CCATCTCTTTTACCAACGCGT 58.926 47.619 5.58 5.58 0.00 6.01
805 879 3.056678 TCCATCTCTTTTACCAACGCGTA 60.057 43.478 14.46 0.00 0.00 4.42
806 880 3.869246 CCATCTCTTTTACCAACGCGTAT 59.131 43.478 14.46 3.61 0.00 3.06
809 883 2.261345 TCTTTTACCAACGCGTATCGG 58.739 47.619 14.46 16.62 43.86 4.18
811 885 1.083242 TTTACCAACGCGTATCGGCC 61.083 55.000 14.46 0.00 43.86 6.13
812 886 1.947597 TTACCAACGCGTATCGGCCT 61.948 55.000 14.46 1.30 43.86 5.19
818 892 4.301027 GCGTATCGGCCTCCCCTG 62.301 72.222 0.00 0.00 0.00 4.45
819 893 4.301027 CGTATCGGCCTCCCCTGC 62.301 72.222 0.00 0.00 0.00 4.85
820 894 3.942439 GTATCGGCCTCCCCTGCC 61.942 72.222 0.00 0.00 45.70 4.85
863 946 1.584380 ATATACGCTCGCCCTCCGAC 61.584 60.000 0.00 0.00 41.89 4.79
929 1012 4.803426 CACCGCACGCTCTCCCTC 62.803 72.222 0.00 0.00 0.00 4.30
931 1014 4.200283 CCGCACGCTCTCCCTCTC 62.200 72.222 0.00 0.00 0.00 3.20
932 1015 3.137459 CGCACGCTCTCCCTCTCT 61.137 66.667 0.00 0.00 0.00 3.10
933 1016 2.804856 GCACGCTCTCCCTCTCTC 59.195 66.667 0.00 0.00 0.00 3.20
934 1017 1.752694 GCACGCTCTCCCTCTCTCT 60.753 63.158 0.00 0.00 0.00 3.10
935 1018 1.724582 GCACGCTCTCCCTCTCTCTC 61.725 65.000 0.00 0.00 0.00 3.20
936 1019 0.107214 CACGCTCTCCCTCTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
937 1020 0.180406 ACGCTCTCCCTCTCTCTCTC 59.820 60.000 0.00 0.00 0.00 3.20
938 1021 0.469917 CGCTCTCCCTCTCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
939 1022 1.541233 CGCTCTCCCTCTCTCTCTCTC 60.541 61.905 0.00 0.00 0.00 3.20
940 1023 1.771255 GCTCTCCCTCTCTCTCTCTCT 59.229 57.143 0.00 0.00 0.00 3.10
976 1059 1.910772 CAATTCCGCCCAAACCCCA 60.911 57.895 0.00 0.00 0.00 4.96
1020 1116 1.375268 GCAGACACTCACAGCCTCC 60.375 63.158 0.00 0.00 0.00 4.30
1048 1144 1.960040 CTCCTCCATACAGCGGCACA 61.960 60.000 1.45 0.00 0.00 4.57
1049 1145 1.815421 CCTCCATACAGCGGCACAC 60.815 63.158 1.45 0.00 0.00 3.82
1434 1551 4.668118 AACGGTGTGTACGCCCGG 62.668 66.667 28.17 15.37 43.41 5.73
2034 2151 3.181465 ACTTCGCCATCACCGAGAATTAT 60.181 43.478 0.00 0.00 35.96 1.28
2046 2163 2.794981 CGAGAATTATGTCGTCGTGCCT 60.795 50.000 0.00 0.00 37.54 4.75
2052 2169 1.888436 ATGTCGTCGTGCCTGACCAT 61.888 55.000 0.00 0.00 35.40 3.55
2133 2250 3.278592 GAAGACGTCCCGCTTCGGT 62.279 63.158 13.01 0.00 46.80 4.69
2234 2351 1.454847 CGTGGGAGGAGGAGGAGAG 60.455 68.421 0.00 0.00 0.00 3.20
2307 2424 2.179517 GAGTCGGACGAGTGCCTG 59.820 66.667 6.80 0.00 0.00 4.85
2661 2784 3.394836 GGCACCTCGGAGCTCCTT 61.395 66.667 29.73 9.10 32.43 3.36
2766 2889 1.142748 CGGCAAGGAGCTCGAATCT 59.857 57.895 7.83 0.00 44.79 2.40
3305 3448 4.954970 CACCACCCGGTTGCTGCT 62.955 66.667 0.00 0.00 46.31 4.24
3317 3460 2.028043 GCTGCTGGTGTTGTTGGC 59.972 61.111 0.00 0.00 0.00 4.52
3318 3461 2.492773 GCTGCTGGTGTTGTTGGCT 61.493 57.895 0.00 0.00 0.00 4.75
3319 3462 2.019897 GCTGCTGGTGTTGTTGGCTT 62.020 55.000 0.00 0.00 0.00 4.35
3320 3463 1.317613 CTGCTGGTGTTGTTGGCTTA 58.682 50.000 0.00 0.00 0.00 3.09
3321 3464 1.888512 CTGCTGGTGTTGTTGGCTTAT 59.111 47.619 0.00 0.00 0.00 1.73
3322 3465 1.612950 TGCTGGTGTTGTTGGCTTATG 59.387 47.619 0.00 0.00 0.00 1.90
3323 3466 1.613437 GCTGGTGTTGTTGGCTTATGT 59.387 47.619 0.00 0.00 0.00 2.29
3324 3467 2.351738 GCTGGTGTTGTTGGCTTATGTC 60.352 50.000 0.00 0.00 0.00 3.06
3325 3468 2.884012 CTGGTGTTGTTGGCTTATGTCA 59.116 45.455 0.00 0.00 0.00 3.58
3326 3469 3.495331 TGGTGTTGTTGGCTTATGTCAT 58.505 40.909 0.00 0.00 0.00 3.06
3327 3470 3.255395 TGGTGTTGTTGGCTTATGTCATG 59.745 43.478 0.00 0.00 0.00 3.07
3328 3471 3.244976 GTGTTGTTGGCTTATGTCATGC 58.755 45.455 0.00 0.00 0.00 4.06
3340 3483 0.676736 TGTCATGCCTCGTGTGTGTA 59.323 50.000 0.00 0.00 0.00 2.90
3387 3530 2.738846 GTGGTGATTGTGCTGACTACAG 59.261 50.000 0.00 0.00 45.91 2.74
3389 3532 2.996621 GGTGATTGTGCTGACTACAGTC 59.003 50.000 2.29 2.29 45.04 3.51
3412 3556 5.048294 TCTCTTGTCATGTGTTCGCTTAGTA 60.048 40.000 0.00 0.00 0.00 1.82
3415 3559 7.317390 TCTTGTCATGTGTTCGCTTAGTATTA 58.683 34.615 0.00 0.00 0.00 0.98
3416 3560 6.880822 TGTCATGTGTTCGCTTAGTATTAC 57.119 37.500 0.00 0.00 0.00 1.89
3417 3561 6.627243 TGTCATGTGTTCGCTTAGTATTACT 58.373 36.000 1.30 1.30 0.00 2.24
3421 3565 8.464404 TCATGTGTTCGCTTAGTATTACTTACT 58.536 33.333 0.85 0.00 43.66 2.24
3425 3569 9.351570 GTGTTCGCTTAGTATTACTTACTTTCT 57.648 33.333 0.85 0.00 41.49 2.52
3451 3595 4.818534 TGAATCTCTGCTTGTGTGTTTC 57.181 40.909 0.00 0.00 0.00 2.78
3452 3596 4.454678 TGAATCTCTGCTTGTGTGTTTCT 58.545 39.130 0.00 0.00 0.00 2.52
3454 3598 5.357878 TGAATCTCTGCTTGTGTGTTTCTTT 59.642 36.000 0.00 0.00 0.00 2.52
3456 3600 4.985413 TCTCTGCTTGTGTGTTTCTTTTG 58.015 39.130 0.00 0.00 0.00 2.44
3459 3603 2.093764 TGCTTGTGTGTTTCTTTTGGGG 60.094 45.455 0.00 0.00 0.00 4.96
3460 3604 2.093711 GCTTGTGTGTTTCTTTTGGGGT 60.094 45.455 0.00 0.00 0.00 4.95
3461 3605 3.520569 CTTGTGTGTTTCTTTTGGGGTG 58.479 45.455 0.00 0.00 0.00 4.61
3463 3607 0.457851 TGTGTTTCTTTTGGGGTGCG 59.542 50.000 0.00 0.00 0.00 5.34
3464 3608 0.249280 GTGTTTCTTTTGGGGTGCGG 60.249 55.000 0.00 0.00 0.00 5.69
3465 3609 0.684805 TGTTTCTTTTGGGGTGCGGT 60.685 50.000 0.00 0.00 0.00 5.68
3466 3610 0.249280 GTTTCTTTTGGGGTGCGGTG 60.249 55.000 0.00 0.00 0.00 4.94
3467 3611 2.022240 TTTCTTTTGGGGTGCGGTGC 62.022 55.000 0.00 0.00 0.00 5.01
3468 3612 3.222855 CTTTTGGGGTGCGGTGCA 61.223 61.111 0.00 0.00 35.60 4.57
3469 3613 3.211564 CTTTTGGGGTGCGGTGCAG 62.212 63.158 0.00 0.00 40.08 4.41
3470 3614 4.514585 TTTGGGGTGCGGTGCAGT 62.515 61.111 0.00 0.00 40.08 4.40
3473 3617 4.947147 GGGGTGCGGTGCAGTGAA 62.947 66.667 0.00 0.00 40.08 3.18
3474 3618 2.672996 GGGTGCGGTGCAGTGAAT 60.673 61.111 0.00 0.00 40.08 2.57
3475 3619 1.376683 GGGTGCGGTGCAGTGAATA 60.377 57.895 0.00 0.00 40.08 1.75
3476 3620 1.369091 GGGTGCGGTGCAGTGAATAG 61.369 60.000 0.00 0.00 40.08 1.73
3477 3621 1.425428 GTGCGGTGCAGTGAATAGC 59.575 57.895 0.00 0.00 40.08 2.97
3478 3622 1.003959 TGCGGTGCAGTGAATAGCA 60.004 52.632 0.00 0.00 38.65 3.49
3479 3623 0.605050 TGCGGTGCAGTGAATAGCAA 60.605 50.000 0.00 0.00 43.20 3.91
3480 3624 0.521291 GCGGTGCAGTGAATAGCAAA 59.479 50.000 0.00 0.00 43.20 3.68
3481 3625 1.133025 GCGGTGCAGTGAATAGCAAAT 59.867 47.619 0.00 0.00 43.20 2.32
3529 3673 5.960113 TCTCTGCTCTGTCAGTAAAAGATC 58.040 41.667 0.00 0.00 35.63 2.75
3561 3705 1.945394 GATTGATCCATTGCTGCGAGT 59.055 47.619 0.00 0.00 0.00 4.18
3576 3720 3.845178 TGCGAGTTACAGTAGTCCAATG 58.155 45.455 0.00 0.00 0.00 2.82
3590 3734 2.710377 TCCAATGTGGAAGAACCGATG 58.290 47.619 0.00 0.00 45.00 3.84
3629 3774 1.270571 CGTTTTGGGTTGAAATGGGGG 60.271 52.381 0.00 0.00 0.00 5.40
3634 3779 0.835971 GGGTTGAAATGGGGGCTTGT 60.836 55.000 0.00 0.00 0.00 3.16
3679 3825 4.124351 GCCCGTCGTCCATCGTCA 62.124 66.667 0.00 0.00 40.80 4.35
3680 3826 2.102357 CCCGTCGTCCATCGTCAG 59.898 66.667 0.00 0.00 40.80 3.51
3681 3827 2.404186 CCCGTCGTCCATCGTCAGA 61.404 63.158 0.00 0.00 40.80 3.27
3682 3828 1.062685 CCGTCGTCCATCGTCAGAG 59.937 63.158 0.00 0.00 40.80 3.35
3683 3829 1.062685 CGTCGTCCATCGTCAGAGG 59.937 63.158 0.00 0.00 40.80 3.69
3684 3830 1.645704 CGTCGTCCATCGTCAGAGGT 61.646 60.000 0.00 0.00 40.80 3.85
3685 3831 0.179161 GTCGTCCATCGTCAGAGGTG 60.179 60.000 0.00 0.00 40.80 4.00
3686 3832 0.322187 TCGTCCATCGTCAGAGGTGA 60.322 55.000 0.00 0.00 40.80 4.02
3687 3833 0.099613 CGTCCATCGTCAGAGGTGAG 59.900 60.000 0.00 0.00 31.53 3.51
3688 3834 1.464734 GTCCATCGTCAGAGGTGAGA 58.535 55.000 0.00 0.00 31.53 3.27
3689 3835 1.403679 GTCCATCGTCAGAGGTGAGAG 59.596 57.143 0.00 0.00 31.53 3.20
3690 3836 0.743688 CCATCGTCAGAGGTGAGAGG 59.256 60.000 0.00 0.00 31.53 3.69
3691 3837 0.743688 CATCGTCAGAGGTGAGAGGG 59.256 60.000 0.00 0.00 31.53 4.30
3692 3838 0.333312 ATCGTCAGAGGTGAGAGGGT 59.667 55.000 0.00 0.00 31.53 4.34
3693 3839 0.609406 TCGTCAGAGGTGAGAGGGTG 60.609 60.000 0.00 0.00 31.53 4.61
3694 3840 1.599606 CGTCAGAGGTGAGAGGGTGG 61.600 65.000 0.00 0.00 31.53 4.61
3695 3841 0.251832 GTCAGAGGTGAGAGGGTGGA 60.252 60.000 0.00 0.00 31.53 4.02
3696 3842 0.251832 TCAGAGGTGAGAGGGTGGAC 60.252 60.000 0.00 0.00 0.00 4.02
3697 3843 1.304547 AGAGGTGAGAGGGTGGACG 60.305 63.158 0.00 0.00 0.00 4.79
3698 3844 2.997897 AGGTGAGAGGGTGGACGC 60.998 66.667 0.00 0.00 0.00 5.19
3699 3845 2.997897 GGTGAGAGGGTGGACGCT 60.998 66.667 0.00 0.00 42.17 5.07
3700 3846 2.262915 GTGAGAGGGTGGACGCTG 59.737 66.667 0.37 0.00 39.39 5.18
3701 3847 2.117423 TGAGAGGGTGGACGCTGA 59.883 61.111 0.37 0.00 39.39 4.26
3702 3848 1.533033 TGAGAGGGTGGACGCTGAA 60.533 57.895 0.37 0.00 39.39 3.02
3703 3849 0.904865 TGAGAGGGTGGACGCTGAAT 60.905 55.000 0.37 0.00 39.39 2.57
3704 3850 0.179097 GAGAGGGTGGACGCTGAATC 60.179 60.000 0.37 0.00 39.39 2.52
3705 3851 0.616111 AGAGGGTGGACGCTGAATCT 60.616 55.000 0.37 0.00 39.39 2.40
3706 3852 0.460987 GAGGGTGGACGCTGAATCTG 60.461 60.000 0.37 0.00 39.39 2.90
3707 3853 0.904865 AGGGTGGACGCTGAATCTGA 60.905 55.000 0.00 0.00 37.77 3.27
3708 3854 0.179000 GGGTGGACGCTGAATCTGAT 59.821 55.000 0.00 0.00 0.00 2.90
3709 3855 1.293924 GGTGGACGCTGAATCTGATG 58.706 55.000 0.00 0.00 0.00 3.07
3710 3856 1.134699 GGTGGACGCTGAATCTGATGA 60.135 52.381 0.00 0.00 0.00 2.92
3711 3857 2.200067 GTGGACGCTGAATCTGATGAG 58.800 52.381 0.00 0.00 0.00 2.90
3712 3858 1.137675 TGGACGCTGAATCTGATGAGG 59.862 52.381 0.00 0.00 0.00 3.86
3713 3859 1.410517 GGACGCTGAATCTGATGAGGA 59.589 52.381 0.00 0.00 0.00 3.71
3714 3860 2.159043 GGACGCTGAATCTGATGAGGAA 60.159 50.000 0.00 0.00 0.00 3.36
3715 3861 3.525537 GACGCTGAATCTGATGAGGAAA 58.474 45.455 0.00 0.00 0.00 3.13
3716 3862 3.935203 GACGCTGAATCTGATGAGGAAAA 59.065 43.478 0.00 0.00 0.00 2.29
3717 3863 4.521146 ACGCTGAATCTGATGAGGAAAAT 58.479 39.130 0.00 0.00 0.00 1.82
3718 3864 4.334759 ACGCTGAATCTGATGAGGAAAATG 59.665 41.667 0.00 0.00 0.00 2.32
3719 3865 4.334759 CGCTGAATCTGATGAGGAAAATGT 59.665 41.667 0.00 0.00 0.00 2.71
3720 3866 5.163683 CGCTGAATCTGATGAGGAAAATGTT 60.164 40.000 0.00 0.00 0.00 2.71
3721 3867 6.034591 GCTGAATCTGATGAGGAAAATGTTG 58.965 40.000 0.00 0.00 0.00 3.33
3722 3868 5.957798 TGAATCTGATGAGGAAAATGTTGC 58.042 37.500 0.00 0.00 0.00 4.17
3723 3869 4.996788 ATCTGATGAGGAAAATGTTGCC 57.003 40.909 0.00 0.00 0.00 4.52
3724 3870 4.038271 TCTGATGAGGAAAATGTTGCCT 57.962 40.909 0.00 0.00 33.97 4.75
3725 3871 4.012374 TCTGATGAGGAAAATGTTGCCTC 58.988 43.478 7.94 7.94 46.60 4.70
3726 3872 3.091545 TGATGAGGAAAATGTTGCCTCC 58.908 45.455 11.76 0.00 46.01 4.30
3727 3873 1.533625 TGAGGAAAATGTTGCCTCCG 58.466 50.000 11.76 0.00 46.01 4.63
3728 3874 1.202879 TGAGGAAAATGTTGCCTCCGT 60.203 47.619 11.76 0.00 46.01 4.69
3729 3875 1.886542 GAGGAAAATGTTGCCTCCGTT 59.113 47.619 3.85 0.00 41.84 4.44
3730 3876 1.613437 AGGAAAATGTTGCCTCCGTTG 59.387 47.619 0.00 0.00 32.91 4.10
3731 3877 1.339929 GGAAAATGTTGCCTCCGTTGT 59.660 47.619 0.00 0.00 0.00 3.32
3732 3878 2.607038 GGAAAATGTTGCCTCCGTTGTC 60.607 50.000 0.00 0.00 0.00 3.18
3733 3879 1.981256 AAATGTTGCCTCCGTTGTCT 58.019 45.000 0.00 0.00 0.00 3.41
3734 3880 1.981256 AATGTTGCCTCCGTTGTCTT 58.019 45.000 0.00 0.00 0.00 3.01
3735 3881 1.981256 ATGTTGCCTCCGTTGTCTTT 58.019 45.000 0.00 0.00 0.00 2.52
3736 3882 1.021202 TGTTGCCTCCGTTGTCTTTG 58.979 50.000 0.00 0.00 0.00 2.77
3737 3883 1.021968 GTTGCCTCCGTTGTCTTTGT 58.978 50.000 0.00 0.00 0.00 2.83
3738 3884 1.404035 GTTGCCTCCGTTGTCTTTGTT 59.596 47.619 0.00 0.00 0.00 2.83
3739 3885 1.021202 TGCCTCCGTTGTCTTTGTTG 58.979 50.000 0.00 0.00 0.00 3.33
3740 3886 1.021968 GCCTCCGTTGTCTTTGTTGT 58.978 50.000 0.00 0.00 0.00 3.32
3741 3887 1.268539 GCCTCCGTTGTCTTTGTTGTG 60.269 52.381 0.00 0.00 0.00 3.33
3742 3888 1.333619 CCTCCGTTGTCTTTGTTGTGG 59.666 52.381 0.00 0.00 0.00 4.17
3743 3889 2.285083 CTCCGTTGTCTTTGTTGTGGA 58.715 47.619 0.00 0.00 0.00 4.02
3744 3890 2.680841 CTCCGTTGTCTTTGTTGTGGAA 59.319 45.455 0.00 0.00 0.00 3.53
3745 3891 2.420722 TCCGTTGTCTTTGTTGTGGAAC 59.579 45.455 0.00 0.00 37.35 3.62
3746 3892 2.422127 CCGTTGTCTTTGTTGTGGAACT 59.578 45.455 0.00 0.00 38.04 3.01
3747 3893 3.119637 CCGTTGTCTTTGTTGTGGAACTT 60.120 43.478 0.00 0.00 38.04 2.66
3748 3894 3.851403 CGTTGTCTTTGTTGTGGAACTTG 59.149 43.478 0.00 0.00 38.04 3.16
3749 3895 4.173256 GTTGTCTTTGTTGTGGAACTTGG 58.827 43.478 0.00 0.00 38.04 3.61
3750 3896 3.426615 TGTCTTTGTTGTGGAACTTGGT 58.573 40.909 0.00 0.00 38.04 3.67
3751 3897 3.829601 TGTCTTTGTTGTGGAACTTGGTT 59.170 39.130 0.00 0.00 38.04 3.67
3752 3898 4.282195 TGTCTTTGTTGTGGAACTTGGTTT 59.718 37.500 0.00 0.00 38.04 3.27
3753 3899 4.862574 GTCTTTGTTGTGGAACTTGGTTTC 59.137 41.667 0.00 0.00 38.04 2.78
3754 3900 3.495670 TTGTTGTGGAACTTGGTTTCG 57.504 42.857 0.00 0.00 38.04 3.46
3755 3901 2.438411 TGTTGTGGAACTTGGTTTCGT 58.562 42.857 0.00 0.00 38.04 3.85
3756 3902 3.607741 TGTTGTGGAACTTGGTTTCGTA 58.392 40.909 0.00 0.00 38.04 3.43
3757 3903 3.374678 TGTTGTGGAACTTGGTTTCGTAC 59.625 43.478 0.00 0.00 38.04 3.67
3758 3904 3.547054 TGTGGAACTTGGTTTCGTACT 57.453 42.857 0.00 0.00 38.04 2.73
3759 3905 4.669206 TGTGGAACTTGGTTTCGTACTA 57.331 40.909 0.00 0.00 38.04 1.82
3760 3906 5.217978 TGTGGAACTTGGTTTCGTACTAT 57.782 39.130 0.00 0.00 38.04 2.12
3761 3907 4.992319 TGTGGAACTTGGTTTCGTACTATG 59.008 41.667 0.00 0.00 38.04 2.23
3762 3908 4.992951 GTGGAACTTGGTTTCGTACTATGT 59.007 41.667 0.00 0.00 0.00 2.29
3763 3909 5.467735 GTGGAACTTGGTTTCGTACTATGTT 59.532 40.000 7.38 7.38 37.99 2.71
3764 3910 5.697633 TGGAACTTGGTTTCGTACTATGTTC 59.302 40.000 17.69 17.69 44.55 3.18
3765 3911 5.930569 GGAACTTGGTTTCGTACTATGTTCT 59.069 40.000 21.30 3.23 44.62 3.01
3766 3912 6.090493 GGAACTTGGTTTCGTACTATGTTCTC 59.910 42.308 21.30 14.25 44.62 2.87
3767 3913 6.342338 ACTTGGTTTCGTACTATGTTCTCT 57.658 37.500 0.00 0.00 0.00 3.10
3768 3914 6.756221 ACTTGGTTTCGTACTATGTTCTCTT 58.244 36.000 0.00 0.00 0.00 2.85
3769 3915 6.867293 ACTTGGTTTCGTACTATGTTCTCTTC 59.133 38.462 0.00 0.00 0.00 2.87
3770 3916 5.717119 TGGTTTCGTACTATGTTCTCTTCC 58.283 41.667 0.00 0.00 0.00 3.46
3771 3917 5.244402 TGGTTTCGTACTATGTTCTCTTCCA 59.756 40.000 0.00 0.00 0.00 3.53
3772 3918 6.161381 GGTTTCGTACTATGTTCTCTTCCAA 58.839 40.000 0.00 0.00 0.00 3.53
3773 3919 6.647895 GGTTTCGTACTATGTTCTCTTCCAAA 59.352 38.462 0.00 0.00 0.00 3.28
3774 3920 7.359849 GGTTTCGTACTATGTTCTCTTCCAAAC 60.360 40.741 0.00 0.00 0.00 2.93
3775 3921 6.335471 TCGTACTATGTTCTCTTCCAAACA 57.665 37.500 0.00 0.00 39.52 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.624697 ACACGTTTTACTTAGATCGTATAACAA 57.375 29.630 10.66 0.00 32.15 2.83
84 88 1.377994 GCTATGCCAGGGGGATCAG 59.622 63.158 0.00 0.00 34.92 2.90
85 89 3.580084 GCTATGCCAGGGGGATCA 58.420 61.111 0.00 0.00 34.92 2.92
111 115 1.103398 GGAGCATCATTTCCCCGGTG 61.103 60.000 0.00 0.00 36.25 4.94
112 116 1.227383 GGAGCATCATTTCCCCGGT 59.773 57.895 0.00 0.00 36.25 5.28
329 358 0.174845 TGATGTAGCACGCAGGGTAC 59.825 55.000 6.94 6.94 41.05 3.34
330 359 0.899019 TTGATGTAGCACGCAGGGTA 59.101 50.000 0.00 0.00 0.00 3.69
331 360 0.673644 GTTGATGTAGCACGCAGGGT 60.674 55.000 0.00 0.00 0.00 4.34
335 364 1.739929 CCCGTTGATGTAGCACGCA 60.740 57.895 0.00 0.00 0.00 5.24
336 365 2.461110 CCCCGTTGATGTAGCACGC 61.461 63.158 0.00 0.00 0.00 5.34
337 366 0.179084 ATCCCCGTTGATGTAGCACG 60.179 55.000 0.00 0.00 0.00 5.34
338 367 2.102588 AGTATCCCCGTTGATGTAGCAC 59.897 50.000 0.00 0.00 0.00 4.40
357 403 7.483307 CACCATTAGCAGCATAATTAAACAGT 58.517 34.615 0.00 0.00 0.00 3.55
386 432 0.902531 TTTTCCCTCAGCTCCGGTAG 59.097 55.000 0.00 0.00 0.00 3.18
387 433 1.354101 TTTTTCCCTCAGCTCCGGTA 58.646 50.000 0.00 0.00 0.00 4.02
388 434 0.698818 ATTTTTCCCTCAGCTCCGGT 59.301 50.000 0.00 0.00 0.00 5.28
390 436 3.812053 CAGATATTTTTCCCTCAGCTCCG 59.188 47.826 0.00 0.00 0.00 4.63
391 437 3.567585 GCAGATATTTTTCCCTCAGCTCC 59.432 47.826 0.00 0.00 0.00 4.70
392 438 4.275443 CAGCAGATATTTTTCCCTCAGCTC 59.725 45.833 0.00 0.00 29.33 4.09
393 439 4.080129 TCAGCAGATATTTTTCCCTCAGCT 60.080 41.667 0.00 0.00 31.59 4.24
394 440 4.202441 TCAGCAGATATTTTTCCCTCAGC 58.798 43.478 0.00 0.00 0.00 4.26
395 441 5.241064 CCATCAGCAGATATTTTTCCCTCAG 59.759 44.000 0.00 0.00 31.88 3.35
396 442 5.135383 CCATCAGCAGATATTTTTCCCTCA 58.865 41.667 0.00 0.00 31.88 3.86
398 444 3.893813 GCCATCAGCAGATATTTTTCCCT 59.106 43.478 0.00 0.00 42.97 4.20
399 445 4.248691 GCCATCAGCAGATATTTTTCCC 57.751 45.455 0.00 0.00 42.97 3.97
442 491 0.258774 TGCCCTATCCCTTCCTTTGC 59.741 55.000 0.00 0.00 0.00 3.68
443 492 1.284785 TGTGCCCTATCCCTTCCTTTG 59.715 52.381 0.00 0.00 0.00 2.77
444 493 1.681229 TGTGCCCTATCCCTTCCTTT 58.319 50.000 0.00 0.00 0.00 3.11
445 494 1.496429 CATGTGCCCTATCCCTTCCTT 59.504 52.381 0.00 0.00 0.00 3.36
447 496 0.111253 CCATGTGCCCTATCCCTTCC 59.889 60.000 0.00 0.00 0.00 3.46
448 497 1.140312 TCCATGTGCCCTATCCCTTC 58.860 55.000 0.00 0.00 0.00 3.46
449 498 1.496429 CTTCCATGTGCCCTATCCCTT 59.504 52.381 0.00 0.00 0.00 3.95
450 499 1.143813 CTTCCATGTGCCCTATCCCT 58.856 55.000 0.00 0.00 0.00 4.20
451 500 1.072965 CTCTTCCATGTGCCCTATCCC 59.927 57.143 0.00 0.00 0.00 3.85
455 504 1.204146 GGACTCTTCCATGTGCCCTA 58.796 55.000 0.00 0.00 42.30 3.53
456 505 1.994463 GGACTCTTCCATGTGCCCT 59.006 57.895 0.00 0.00 42.30 5.19
457 506 4.645809 GGACTCTTCCATGTGCCC 57.354 61.111 0.00 0.00 42.30 5.36
469 521 1.071699 TGGTACTTGCACCTTGGACTC 59.928 52.381 0.00 0.00 39.50 3.36
527 580 4.590226 GACTAACGATCGAGTTTCTCTCC 58.410 47.826 24.34 0.00 39.84 3.71
616 671 4.451652 GCCGCTGCGTCTTCTTGC 62.452 66.667 21.59 11.22 0.00 4.01
627 682 3.667282 ACTTTGCTGCTGCCGCTG 61.667 61.111 16.81 1.71 38.71 5.18
628 683 3.667282 CACTTTGCTGCTGCCGCT 61.667 61.111 16.81 0.00 38.71 5.52
629 684 4.712425 CCACTTTGCTGCTGCCGC 62.712 66.667 13.47 9.23 38.71 6.53
630 685 4.047059 CCCACTTTGCTGCTGCCG 62.047 66.667 13.47 4.26 38.71 5.69
631 686 4.368543 GCCCACTTTGCTGCTGCC 62.369 66.667 13.47 0.00 38.71 4.85
724 783 2.357517 GACTCGCACACACTGGGG 60.358 66.667 0.00 0.00 33.53 4.96
778 852 4.267928 CGTTGGTAAAAGAGATGGATCGAC 59.732 45.833 0.00 0.00 0.00 4.20
835 918 4.948621 AGGGCGAGCGTATATATAGAGTTT 59.051 41.667 0.00 0.00 0.00 2.66
863 946 1.561076 TGGATGGTTGATGTCTGGAGG 59.439 52.381 0.00 0.00 0.00 4.30
926 1009 1.670811 GTTGCGAGAGAGAGAGAGAGG 59.329 57.143 0.00 0.00 0.00 3.69
928 1011 2.481289 TGTTGCGAGAGAGAGAGAGA 57.519 50.000 0.00 0.00 0.00 3.10
929 1012 3.567576 TTTGTTGCGAGAGAGAGAGAG 57.432 47.619 0.00 0.00 0.00 3.20
930 1013 3.553096 GGTTTTGTTGCGAGAGAGAGAGA 60.553 47.826 0.00 0.00 0.00 3.10
931 1014 2.734079 GGTTTTGTTGCGAGAGAGAGAG 59.266 50.000 0.00 0.00 0.00 3.20
932 1015 2.548067 GGGTTTTGTTGCGAGAGAGAGA 60.548 50.000 0.00 0.00 0.00 3.10
933 1016 1.801178 GGGTTTTGTTGCGAGAGAGAG 59.199 52.381 0.00 0.00 0.00 3.20
934 1017 1.140052 TGGGTTTTGTTGCGAGAGAGA 59.860 47.619 0.00 0.00 0.00 3.10
935 1018 1.264288 GTGGGTTTTGTTGCGAGAGAG 59.736 52.381 0.00 0.00 0.00 3.20
936 1019 1.305201 GTGGGTTTTGTTGCGAGAGA 58.695 50.000 0.00 0.00 0.00 3.10
937 1020 0.041312 CGTGGGTTTTGTTGCGAGAG 60.041 55.000 0.00 0.00 0.00 3.20
938 1021 2.018544 CGTGGGTTTTGTTGCGAGA 58.981 52.632 0.00 0.00 0.00 4.04
939 1022 1.657181 GCGTGGGTTTTGTTGCGAG 60.657 57.895 0.00 0.00 0.00 5.03
940 1023 2.409651 GCGTGGGTTTTGTTGCGA 59.590 55.556 0.00 0.00 0.00 5.10
1020 1116 1.033574 GTATGGAGGAGACCGAGGTG 58.966 60.000 0.00 0.00 0.00 4.00
1422 1539 4.360964 CCGTTCCGGGCGTACACA 62.361 66.667 15.86 0.00 44.15 3.72
1725 1842 0.034337 GGTGGCCGTTGAAGTAGACA 59.966 55.000 0.00 0.00 0.00 3.41
2034 2151 2.486636 GATGGTCAGGCACGACGACA 62.487 60.000 0.00 0.00 36.73 4.35
2052 2169 0.819259 GCAGCTTGAACACCACCTGA 60.819 55.000 0.00 0.00 30.21 3.86
2133 2250 4.268939 GCGCACTTTGGCAGCACA 62.269 61.111 0.30 0.00 34.83 4.57
2234 2351 3.296709 ATCACCACCACCTCGTCGC 62.297 63.158 0.00 0.00 0.00 5.19
2661 2784 4.321966 TCGGCGGCATTGACCACA 62.322 61.111 10.53 0.00 0.00 4.17
2933 3059 5.447010 CCAACTACGTACTAGTGTGAGCTAC 60.447 48.000 5.39 0.00 35.70 3.58
3057 3183 5.613116 TCTCTATCTCTAATCCTCACTCCCA 59.387 44.000 0.00 0.00 0.00 4.37
3201 3339 2.702592 ACATATACCAACCCGTGTGG 57.297 50.000 0.00 0.00 41.37 4.17
3299 3442 2.784356 GCCAACAACACCAGCAGCA 61.784 57.895 0.00 0.00 0.00 4.41
3305 3448 2.937519 TGACATAAGCCAACAACACCA 58.062 42.857 0.00 0.00 0.00 4.17
3317 3460 2.349580 CACACACGAGGCATGACATAAG 59.650 50.000 0.00 0.00 0.00 1.73
3318 3461 2.289382 ACACACACGAGGCATGACATAA 60.289 45.455 0.00 0.00 0.00 1.90
3319 3462 1.275010 ACACACACGAGGCATGACATA 59.725 47.619 0.00 0.00 0.00 2.29
3320 3463 0.035317 ACACACACGAGGCATGACAT 59.965 50.000 0.00 0.00 0.00 3.06
3321 3464 0.676736 TACACACACGAGGCATGACA 59.323 50.000 0.00 0.00 0.00 3.58
3322 3465 1.068474 GTACACACACGAGGCATGAC 58.932 55.000 0.00 0.00 0.00 3.06
3323 3466 0.676736 TGTACACACACGAGGCATGA 59.323 50.000 0.00 0.00 0.00 3.07
3324 3467 1.725641 ATGTACACACACGAGGCATG 58.274 50.000 0.00 0.00 37.54 4.06
3325 3468 2.472695 AATGTACACACACGAGGCAT 57.527 45.000 0.00 0.00 37.54 4.40
3326 3469 1.870402 CAAATGTACACACACGAGGCA 59.130 47.619 0.00 0.00 37.54 4.75
3327 3470 1.871039 ACAAATGTACACACACGAGGC 59.129 47.619 0.00 0.00 37.54 4.70
3328 3471 3.558006 TCAACAAATGTACACACACGAGG 59.442 43.478 0.00 0.00 37.54 4.63
3363 3506 2.867624 AGTCAGCACAATCACCACATT 58.132 42.857 0.00 0.00 0.00 2.71
3366 3509 2.738846 CTGTAGTCAGCACAATCACCAC 59.261 50.000 0.00 0.00 34.79 4.16
3387 3530 2.408050 AGCGAACACATGACAAGAGAC 58.592 47.619 0.00 0.00 0.00 3.36
3389 3532 3.990469 ACTAAGCGAACACATGACAAGAG 59.010 43.478 0.00 0.00 0.00 2.85
3415 3559 9.196139 AGCAGAGATTCATACTAGAAAGTAAGT 57.804 33.333 0.00 0.00 41.49 2.24
3417 3561 9.809096 CAAGCAGAGATTCATACTAGAAAGTAA 57.191 33.333 0.00 0.00 41.49 2.24
3421 3565 7.547019 CACACAAGCAGAGATTCATACTAGAAA 59.453 37.037 0.00 0.00 0.00 2.52
3425 3569 6.286240 ACACACAAGCAGAGATTCATACTA 57.714 37.500 0.00 0.00 0.00 1.82
3426 3570 5.157940 ACACACAAGCAGAGATTCATACT 57.842 39.130 0.00 0.00 0.00 2.12
3427 3571 5.869753 AACACACAAGCAGAGATTCATAC 57.130 39.130 0.00 0.00 0.00 2.39
3432 3576 5.841957 AAAGAAACACACAAGCAGAGATT 57.158 34.783 0.00 0.00 0.00 2.40
3434 3578 4.142403 CCAAAAGAAACACACAAGCAGAGA 60.142 41.667 0.00 0.00 0.00 3.10
3451 3595 3.211564 CTGCACCGCACCCCAAAAG 62.212 63.158 0.00 0.00 33.79 2.27
3452 3596 3.222855 CTGCACCGCACCCCAAAA 61.223 61.111 0.00 0.00 33.79 2.44
3456 3600 2.813226 TATTCACTGCACCGCACCCC 62.813 60.000 0.00 0.00 33.79 4.95
3459 3603 1.298157 TGCTATTCACTGCACCGCAC 61.298 55.000 0.00 0.00 33.79 5.34
3460 3604 0.605050 TTGCTATTCACTGCACCGCA 60.605 50.000 0.00 0.00 39.05 5.69
3461 3605 0.521291 TTTGCTATTCACTGCACCGC 59.479 50.000 0.00 0.00 39.05 5.68
3463 3607 5.505173 ACATATTTGCTATTCACTGCACC 57.495 39.130 0.00 0.00 39.05 5.01
3464 3608 8.798153 GTTTTACATATTTGCTATTCACTGCAC 58.202 33.333 0.00 0.00 39.05 4.57
3465 3609 8.739039 AGTTTTACATATTTGCTATTCACTGCA 58.261 29.630 0.00 0.00 37.42 4.41
3466 3610 9.013490 CAGTTTTACATATTTGCTATTCACTGC 57.987 33.333 0.00 0.00 0.00 4.40
3474 3618 8.026607 GCAAGGTTCAGTTTTACATATTTGCTA 58.973 33.333 0.00 0.00 34.74 3.49
3475 3619 6.868339 GCAAGGTTCAGTTTTACATATTTGCT 59.132 34.615 0.00 0.00 34.74 3.91
3476 3620 6.868339 AGCAAGGTTCAGTTTTACATATTTGC 59.132 34.615 0.00 0.00 37.03 3.68
3477 3621 7.271223 CGAGCAAGGTTCAGTTTTACATATTTG 59.729 37.037 0.00 0.00 0.00 2.32
3478 3622 7.040686 ACGAGCAAGGTTCAGTTTTACATATTT 60.041 33.333 0.00 0.00 0.00 1.40
3479 3623 6.430000 ACGAGCAAGGTTCAGTTTTACATATT 59.570 34.615 0.00 0.00 0.00 1.28
3480 3624 5.938125 ACGAGCAAGGTTCAGTTTTACATAT 59.062 36.000 0.00 0.00 0.00 1.78
3481 3625 5.302360 ACGAGCAAGGTTCAGTTTTACATA 58.698 37.500 0.00 0.00 0.00 2.29
3495 3639 0.179140 GAGCAGAGAGACGAGCAAGG 60.179 60.000 0.00 0.00 0.00 3.61
3529 3673 8.577296 AGCAATGGATCAATCTATCTGATTTTG 58.423 33.333 0.00 0.00 43.00 2.44
3540 3684 2.219458 CTCGCAGCAATGGATCAATCT 58.781 47.619 0.00 0.00 0.00 2.40
3576 3720 4.830826 AGAAAAACATCGGTTCTTCCAC 57.169 40.909 0.00 0.00 35.09 4.02
3581 3725 4.918810 AGCAAAGAAAAACATCGGTTCT 57.081 36.364 0.00 0.00 35.82 3.01
3589 3733 3.630312 ACGCCTAGAAGCAAAGAAAAACA 59.370 39.130 0.00 0.00 0.00 2.83
3590 3734 4.224715 ACGCCTAGAAGCAAAGAAAAAC 57.775 40.909 0.00 0.00 0.00 2.43
3665 3811 1.062685 CCTCTGACGATGGACGACG 59.937 63.158 0.00 0.00 45.77 5.12
3666 3812 0.179161 CACCTCTGACGATGGACGAC 60.179 60.000 0.00 0.00 45.77 4.34
3667 3813 0.322187 TCACCTCTGACGATGGACGA 60.322 55.000 0.00 0.00 45.77 4.20
3670 3816 1.683319 CCTCTCACCTCTGACGATGGA 60.683 57.143 0.00 0.00 0.00 3.41
3673 3819 0.333312 ACCCTCTCACCTCTGACGAT 59.667 55.000 0.00 0.00 0.00 3.73
3676 3822 0.251832 TCCACCCTCTCACCTCTGAC 60.252 60.000 0.00 0.00 0.00 3.51
3677 3823 0.251832 GTCCACCCTCTCACCTCTGA 60.252 60.000 0.00 0.00 0.00 3.27
3678 3824 1.599606 CGTCCACCCTCTCACCTCTG 61.600 65.000 0.00 0.00 0.00 3.35
3679 3825 1.304547 CGTCCACCCTCTCACCTCT 60.305 63.158 0.00 0.00 0.00 3.69
3680 3826 3.007973 GCGTCCACCCTCTCACCTC 62.008 68.421 0.00 0.00 0.00 3.85
3681 3827 2.997897 GCGTCCACCCTCTCACCT 60.998 66.667 0.00 0.00 0.00 4.00
3682 3828 2.997897 AGCGTCCACCCTCTCACC 60.998 66.667 0.00 0.00 0.00 4.02
3683 3829 1.816863 TTCAGCGTCCACCCTCTCAC 61.817 60.000 0.00 0.00 0.00 3.51
3684 3830 0.904865 ATTCAGCGTCCACCCTCTCA 60.905 55.000 0.00 0.00 0.00 3.27
3685 3831 0.179097 GATTCAGCGTCCACCCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
3686 3832 0.616111 AGATTCAGCGTCCACCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
3687 3833 0.460987 CAGATTCAGCGTCCACCCTC 60.461 60.000 0.00 0.00 0.00 4.30
3688 3834 0.904865 TCAGATTCAGCGTCCACCCT 60.905 55.000 0.00 0.00 0.00 4.34
3689 3835 0.179000 ATCAGATTCAGCGTCCACCC 59.821 55.000 0.00 0.00 0.00 4.61
3690 3836 1.134699 TCATCAGATTCAGCGTCCACC 60.135 52.381 0.00 0.00 0.00 4.61
3691 3837 2.200067 CTCATCAGATTCAGCGTCCAC 58.800 52.381 0.00 0.00 0.00 4.02
3692 3838 1.137675 CCTCATCAGATTCAGCGTCCA 59.862 52.381 0.00 0.00 0.00 4.02
3693 3839 1.410517 TCCTCATCAGATTCAGCGTCC 59.589 52.381 0.00 0.00 0.00 4.79
3694 3840 2.879002 TCCTCATCAGATTCAGCGTC 57.121 50.000 0.00 0.00 0.00 5.19
3695 3841 3.616956 TTTCCTCATCAGATTCAGCGT 57.383 42.857 0.00 0.00 0.00 5.07
3696 3842 4.334759 ACATTTTCCTCATCAGATTCAGCG 59.665 41.667 0.00 0.00 0.00 5.18
3697 3843 5.831702 ACATTTTCCTCATCAGATTCAGC 57.168 39.130 0.00 0.00 0.00 4.26
3698 3844 6.034591 GCAACATTTTCCTCATCAGATTCAG 58.965 40.000 0.00 0.00 0.00 3.02
3699 3845 5.105635 GGCAACATTTTCCTCATCAGATTCA 60.106 40.000 0.00 0.00 0.00 2.57
3700 3846 5.126707 AGGCAACATTTTCCTCATCAGATTC 59.873 40.000 0.00 0.00 41.41 2.52
3701 3847 5.021458 AGGCAACATTTTCCTCATCAGATT 58.979 37.500 0.00 0.00 41.41 2.40
3702 3848 4.607239 AGGCAACATTTTCCTCATCAGAT 58.393 39.130 0.00 0.00 41.41 2.90
3703 3849 4.012374 GAGGCAACATTTTCCTCATCAGA 58.988 43.478 2.88 0.00 44.38 3.27
3704 3850 3.129988 GGAGGCAACATTTTCCTCATCAG 59.870 47.826 9.40 0.00 46.24 2.90
3705 3851 3.091545 GGAGGCAACATTTTCCTCATCA 58.908 45.455 9.40 0.00 46.24 3.07
3706 3852 2.098117 CGGAGGCAACATTTTCCTCATC 59.902 50.000 9.40 0.00 46.24 2.92
3707 3853 2.094675 CGGAGGCAACATTTTCCTCAT 58.905 47.619 9.40 0.00 46.24 2.90
3708 3854 1.202879 ACGGAGGCAACATTTTCCTCA 60.203 47.619 9.40 0.00 46.24 3.86
3709 3855 1.534729 ACGGAGGCAACATTTTCCTC 58.465 50.000 0.00 0.00 44.28 3.71
3710 3856 1.613437 CAACGGAGGCAACATTTTCCT 59.387 47.619 0.00 0.00 41.41 3.36
3711 3857 1.339929 ACAACGGAGGCAACATTTTCC 59.660 47.619 0.00 0.00 41.41 3.13
3712 3858 2.293399 AGACAACGGAGGCAACATTTTC 59.707 45.455 0.00 0.00 41.41 2.29
3713 3859 2.306847 AGACAACGGAGGCAACATTTT 58.693 42.857 0.00 0.00 41.41 1.82
3714 3860 1.981256 AGACAACGGAGGCAACATTT 58.019 45.000 0.00 0.00 41.41 2.32
3715 3861 1.981256 AAGACAACGGAGGCAACATT 58.019 45.000 0.00 0.00 41.41 2.71
3716 3862 1.608590 CAAAGACAACGGAGGCAACAT 59.391 47.619 0.00 0.00 41.41 2.71
3717 3863 1.021202 CAAAGACAACGGAGGCAACA 58.979 50.000 0.00 0.00 41.41 3.33
3718 3864 1.021968 ACAAAGACAACGGAGGCAAC 58.978 50.000 0.00 0.00 0.00 4.17
3719 3865 1.403679 CAACAAAGACAACGGAGGCAA 59.596 47.619 0.00 0.00 0.00 4.52
3720 3866 1.021202 CAACAAAGACAACGGAGGCA 58.979 50.000 0.00 0.00 0.00 4.75
3721 3867 1.021968 ACAACAAAGACAACGGAGGC 58.978 50.000 0.00 0.00 0.00 4.70
3722 3868 1.333619 CCACAACAAAGACAACGGAGG 59.666 52.381 0.00 0.00 0.00 4.30
3723 3869 2.285083 TCCACAACAAAGACAACGGAG 58.715 47.619 0.00 0.00 0.00 4.63
3724 3870 2.404923 TCCACAACAAAGACAACGGA 57.595 45.000 0.00 0.00 0.00 4.69
3725 3871 2.422127 AGTTCCACAACAAAGACAACGG 59.578 45.455 0.00 0.00 34.60 4.44
3726 3872 3.757745 AGTTCCACAACAAAGACAACG 57.242 42.857 0.00 0.00 34.60 4.10
3727 3873 4.173256 CCAAGTTCCACAACAAAGACAAC 58.827 43.478 0.00 0.00 34.60 3.32
3728 3874 3.829601 ACCAAGTTCCACAACAAAGACAA 59.170 39.130 0.00 0.00 34.60 3.18
3729 3875 3.426615 ACCAAGTTCCACAACAAAGACA 58.573 40.909 0.00 0.00 34.60 3.41
3730 3876 4.450082 AACCAAGTTCCACAACAAAGAC 57.550 40.909 0.00 0.00 34.60 3.01
3731 3877 4.380023 CGAAACCAAGTTCCACAACAAAGA 60.380 41.667 0.00 0.00 34.60 2.52
3732 3878 3.857093 CGAAACCAAGTTCCACAACAAAG 59.143 43.478 0.00 0.00 34.60 2.77
3733 3879 3.256136 ACGAAACCAAGTTCCACAACAAA 59.744 39.130 0.00 0.00 34.60 2.83
3734 3880 2.820787 ACGAAACCAAGTTCCACAACAA 59.179 40.909 0.00 0.00 34.60 2.83
3735 3881 2.438411 ACGAAACCAAGTTCCACAACA 58.562 42.857 0.00 0.00 34.60 3.33
3736 3882 3.624410 AGTACGAAACCAAGTTCCACAAC 59.376 43.478 0.00 0.00 0.00 3.32
3737 3883 3.876341 AGTACGAAACCAAGTTCCACAA 58.124 40.909 0.00 0.00 0.00 3.33
3738 3884 3.547054 AGTACGAAACCAAGTTCCACA 57.453 42.857 0.00 0.00 0.00 4.17
3739 3885 4.992951 ACATAGTACGAAACCAAGTTCCAC 59.007 41.667 0.00 0.00 0.00 4.02
3740 3886 5.217978 ACATAGTACGAAACCAAGTTCCA 57.782 39.130 0.00 0.00 0.00 3.53
3741 3887 5.930569 AGAACATAGTACGAAACCAAGTTCC 59.069 40.000 0.00 0.00 35.02 3.62
3742 3888 6.867293 AGAGAACATAGTACGAAACCAAGTTC 59.133 38.462 0.00 0.00 34.83 3.01
3743 3889 6.756221 AGAGAACATAGTACGAAACCAAGTT 58.244 36.000 0.00 0.00 0.00 2.66
3744 3890 6.342338 AGAGAACATAGTACGAAACCAAGT 57.658 37.500 0.00 0.00 0.00 3.16
3745 3891 6.310711 GGAAGAGAACATAGTACGAAACCAAG 59.689 42.308 0.00 0.00 0.00 3.61
3746 3892 6.161381 GGAAGAGAACATAGTACGAAACCAA 58.839 40.000 0.00 0.00 0.00 3.67
3747 3893 5.244402 TGGAAGAGAACATAGTACGAAACCA 59.756 40.000 0.00 0.00 0.00 3.67
3748 3894 5.717119 TGGAAGAGAACATAGTACGAAACC 58.283 41.667 0.00 0.00 0.00 3.27
3749 3895 7.170320 TGTTTGGAAGAGAACATAGTACGAAAC 59.830 37.037 0.00 0.00 31.30 2.78
3750 3896 7.211573 TGTTTGGAAGAGAACATAGTACGAAA 58.788 34.615 0.00 0.00 31.30 3.46
3751 3897 6.751157 TGTTTGGAAGAGAACATAGTACGAA 58.249 36.000 0.00 0.00 31.30 3.85
3752 3898 6.335471 TGTTTGGAAGAGAACATAGTACGA 57.665 37.500 0.00 0.00 31.30 3.43


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

AutoCloner maintained by Alex Coulton.