Multiple sequence alignment - TraesCS3B01G354000

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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 TraesCS3B01G354000 chr3B 100.000 3197 0 0 1 3197 564343689 564340493 0.000000e+00 5904
1 TraesCS3B01G354000 chr3D 93.125 2531 103 21 15 2514 432142333 432139843 0.000000e+00 3644
2 TraesCS3B01G354000 chr3D 94.527 402 16 3 2794 3195 432139845 432139450 1.630000e-172 616
3 TraesCS3B01G354000 chr3D 92.759 290 18 3 2512 2799 477843376 477843088 1.770000e-112 416
4 TraesCS3B01G354000 chr3A 91.185 2439 134 41 139 2514 569641746 569639326 0.000000e+00 3238
5 TraesCS3B01G354000 chr3A 93.007 286 18 2 2511 2794 703772978 703773263 1.770000e-112 416
6 TraesCS3B01G354000 chr3A 93.939 132 8 0 1 132 569644853 569644722 1.940000e-47 200
7 TraesCS3B01G354000 chr3A 76.449 276 37 15 2946 3197 569638124 569637853 1.200000e-24 124
8 TraesCS3B01G354000 chr7D 94.755 286 13 2 2512 2795 587092459 587092744 8.140000e-121 444
9 TraesCS3B01G354000 chr4D 94.077 287 15 2 2512 2796 454807778 454808064 4.900000e-118 435
10 TraesCS3B01G354000 chr2B 93.471 291 17 2 2511 2799 219575737 219576027 6.340000e-117 431
11 TraesCS3B01G354000 chr4A 93.728 287 16 2 2512 2796 548783069 548783355 2.280000e-116 429
12 TraesCS3B01G354000 chr2D 93.706 286 16 2 2512 2796 6520778 6521062 8.200000e-116 427
13 TraesCS3B01G354000 chr7B 92.857 294 18 3 2512 2803 734380106 734380398 1.060000e-114 424
14 TraesCS3B01G354000 chr1D 93.056 288 17 3 2514 2798 349468687 349468400 4.930000e-113 418


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 TraesCS3B01G354000 chr3B 564340493 564343689 3196 True 5904.000000 5904 100.000 1 3197 1 chr3B.!!$R1 3196
1 TraesCS3B01G354000 chr3D 432139450 432142333 2883 True 2130.000000 3644 93.826 15 3195 2 chr3D.!!$R2 3180
2 TraesCS3B01G354000 chr3A 569637853 569644853 7000 True 1187.333333 3238 87.191 1 3197 3 chr3A.!!$R1 3196

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
709 3694 0.033601 CATTCCCATTCCCGTTCCCA 60.034 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 5547 0.759346 CAGGGCCTTAAGCTACCGAT 59.241 55.0 1.32 0.0 43.05 4.18 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
55 56 7.148755 CCACGTAACGTAATAAATATGTAGCCC 60.149 40.741 0.00 0.00 38.32 5.19
160 3134 2.293677 AGTATGGCCGTCTGATTCTACG 59.706 50.000 0.00 5.49 38.80 3.51
181 3155 4.825085 ACGATTGGGTTCTGTTAAACACAT 59.175 37.500 0.00 0.00 41.92 3.21
188 3162 5.067283 GGGTTCTGTTAAACACATCACTGTT 59.933 40.000 0.00 0.00 35.83 3.16
231 3205 1.426423 TTGCGTAAACGGCGATAACA 58.574 45.000 16.62 5.70 40.23 2.41
282 3256 1.840224 TATGCCTGCACAGCCTGTCA 61.840 55.000 0.00 0.00 0.00 3.58
320 3295 0.670546 CAACTACCCTGGTCAGCACG 60.671 60.000 0.00 0.00 0.00 5.34
344 3319 4.398319 CCACCAGAGACCAGTTAAAATGT 58.602 43.478 0.00 0.00 0.00 2.71
346 3321 5.643777 CCACCAGAGACCAGTTAAAATGTAG 59.356 44.000 0.00 0.00 0.00 2.74
354 3329 2.097466 CAGTTAAAATGTAGGCGCCTGG 59.903 50.000 38.98 9.08 0.00 4.45
451 3426 5.316167 TCGCCAATCTTGCCTTCATATATT 58.684 37.500 0.00 0.00 0.00 1.28
494 3469 5.683681 TCATGGATGTGCAGAAAAGCTATA 58.316 37.500 0.00 0.00 34.99 1.31
703 3688 1.455587 CACCCCATTCCCATTCCCG 60.456 63.158 0.00 0.00 0.00 5.14
704 3689 1.933812 ACCCCATTCCCATTCCCGT 60.934 57.895 0.00 0.00 0.00 5.28
705 3690 1.309688 CCCCATTCCCATTCCCGTT 59.690 57.895 0.00 0.00 0.00 4.44
706 3691 0.755327 CCCCATTCCCATTCCCGTTC 60.755 60.000 0.00 0.00 0.00 3.95
707 3692 0.755327 CCCATTCCCATTCCCGTTCC 60.755 60.000 0.00 0.00 0.00 3.62
708 3693 0.755327 CCATTCCCATTCCCGTTCCC 60.755 60.000 0.00 0.00 0.00 3.97
709 3694 0.033601 CATTCCCATTCCCGTTCCCA 60.034 55.000 0.00 0.00 0.00 4.37
710 3695 0.258774 ATTCCCATTCCCGTTCCCAG 59.741 55.000 0.00 0.00 0.00 4.45
711 3696 2.440247 CCCATTCCCGTTCCCAGC 60.440 66.667 0.00 0.00 0.00 4.85
712 3697 2.677228 CCATTCCCGTTCCCAGCT 59.323 61.111 0.00 0.00 0.00 4.24
782 3772 1.941734 GCTTCTCGACAGCGATCGG 60.942 63.158 18.30 3.26 46.80 4.18
876 3872 2.418609 GCCGGCCAGCAAATTTAATCTT 60.419 45.455 18.11 0.00 0.00 2.40
881 3877 5.111989 GGCCAGCAAATTTAATCTTCTTCC 58.888 41.667 0.00 0.00 0.00 3.46
892 3895 3.526360 ATCTTCTTCCCCTTCCCCTTA 57.474 47.619 0.00 0.00 0.00 2.69
943 3954 2.511145 CGCTTCCTGAGAGCTGCC 60.511 66.667 0.00 0.00 37.99 4.85
969 3980 0.319211 CGTCACGACCAAGCAACCTA 60.319 55.000 0.00 0.00 0.00 3.08
970 3981 1.145803 GTCACGACCAAGCAACCTAC 58.854 55.000 0.00 0.00 0.00 3.18
971 3982 1.045407 TCACGACCAAGCAACCTACT 58.955 50.000 0.00 0.00 0.00 2.57
973 3984 1.531149 CACGACCAAGCAACCTACTTG 59.469 52.381 0.00 0.00 43.36 3.16
981 4007 0.955919 GCAACCTACTTGCGGCTCTT 60.956 55.000 0.00 0.00 45.88 2.85
982 4008 1.079503 CAACCTACTTGCGGCTCTTC 58.920 55.000 0.00 0.00 0.00 2.87
989 4015 2.585791 CTTGCGGCTCTTCTCCTCCC 62.586 65.000 0.00 0.00 0.00 4.30
1018 4044 2.040213 GATGGCATTGGACGTGCTCG 62.040 60.000 8.99 6.63 42.16 5.03
1118 4144 2.479730 CCATCGGGTTCTACGACAAGAG 60.480 54.545 0.00 0.00 43.78 2.85
1318 4348 0.396435 AACCTGAACTGGATGCGTGA 59.604 50.000 4.82 0.00 0.00 4.35
1331 4361 2.665000 CGTGATCTGCAGGGGTGT 59.335 61.111 15.13 0.00 0.00 4.16
1460 4490 4.803426 GAGGACGAGTGCCCGCTG 62.803 72.222 0.00 0.00 0.00 5.18
1593 4624 5.360999 AGCTTTCTTTTTAGCTGACCAAACT 59.639 36.000 0.00 0.00 45.55 2.66
1599 4630 0.037326 TAGCTGACCAAACTGCCTCG 60.037 55.000 0.00 0.00 35.80 4.63
1665 4703 2.741092 GACGGCAAGGTGTCCTCA 59.259 61.111 0.00 0.00 30.89 3.86
1669 4707 2.048603 GGCAAGGTGTCCTCATGCC 61.049 63.158 13.48 13.48 46.18 4.40
1767 4805 1.212229 GTGGAAGGACCTCGTCGTC 59.788 63.158 0.00 0.00 39.86 4.20
1768 4806 1.074423 TGGAAGGACCTCGTCGTCT 59.926 57.895 0.00 0.00 39.86 4.18
1773 4811 0.536687 AGGACCTCGTCGTCTTGTCA 60.537 55.000 0.00 0.00 32.65 3.58
1881 4919 2.261671 CTGGACAAGGCGTACGCT 59.738 61.111 36.24 19.58 41.60 5.07
1931 4969 0.386985 AACGAGAAAGACGAGACGCC 60.387 55.000 0.00 0.00 34.70 5.68
2110 5148 2.426024 GAGTACTTCCATGACTACGCCA 59.574 50.000 0.00 0.00 0.00 5.69
2191 5229 1.683790 AATCTGCAGCGCGTACGTTC 61.684 55.000 17.90 8.88 42.83 3.95
2243 5281 2.028043 GTGGCTTGGTGCAAGTGC 59.972 61.111 0.00 0.00 42.77 4.40
2501 5547 5.668471 CTGAGAGTATTTCAATCAGAGCCA 58.332 41.667 0.00 0.00 39.80 4.75
2514 5560 2.362397 TCAGAGCCATCGGTAGCTTAAG 59.638 50.000 0.00 0.00 40.11 1.85
2515 5561 1.689273 AGAGCCATCGGTAGCTTAAGG 59.311 52.381 4.29 0.00 40.11 2.69
2516 5562 0.106894 AGCCATCGGTAGCTTAAGGC 59.893 55.000 4.29 0.00 35.22 4.35
2517 5563 0.885150 GCCATCGGTAGCTTAAGGCC 60.885 60.000 4.29 0.00 43.05 5.19
2518 5564 0.250338 CCATCGGTAGCTTAAGGCCC 60.250 60.000 0.00 0.00 43.05 5.80
2519 5565 0.759346 CATCGGTAGCTTAAGGCCCT 59.241 55.000 0.00 0.00 43.05 5.19
2520 5566 0.759346 ATCGGTAGCTTAAGGCCCTG 59.241 55.000 0.00 0.00 43.05 4.45
2521 5567 0.616679 TCGGTAGCTTAAGGCCCTGT 60.617 55.000 0.00 0.00 43.05 4.00
2522 5568 0.252197 CGGTAGCTTAAGGCCCTGTT 59.748 55.000 0.00 0.00 43.05 3.16
2523 5569 1.339727 CGGTAGCTTAAGGCCCTGTTT 60.340 52.381 0.00 0.00 43.05 2.83
2524 5570 2.092323 GGTAGCTTAAGGCCCTGTTTG 58.908 52.381 0.00 0.00 43.05 2.93
2525 5571 2.092323 GTAGCTTAAGGCCCTGTTTGG 58.908 52.381 0.00 0.00 43.05 3.28
2526 5572 0.482887 AGCTTAAGGCCCTGTTTGGT 59.517 50.000 0.00 0.00 43.05 3.67
2527 5573 1.133167 AGCTTAAGGCCCTGTTTGGTT 60.133 47.619 0.00 0.00 43.05 3.67
2528 5574 1.272490 GCTTAAGGCCCTGTTTGGTTC 59.728 52.381 0.00 0.00 34.27 3.62
2529 5575 2.593026 CTTAAGGCCCTGTTTGGTTCA 58.407 47.619 0.00 0.00 0.00 3.18
2530 5576 2.990740 TAAGGCCCTGTTTGGTTCAT 57.009 45.000 0.00 0.00 0.00 2.57
2531 5577 2.990740 AAGGCCCTGTTTGGTTCATA 57.009 45.000 0.00 0.00 0.00 2.15
2532 5578 2.990740 AGGCCCTGTTTGGTTCATAA 57.009 45.000 0.00 0.00 0.00 1.90
2533 5579 2.807676 AGGCCCTGTTTGGTTCATAAG 58.192 47.619 0.00 0.00 0.00 1.73
2534 5580 2.110011 AGGCCCTGTTTGGTTCATAAGT 59.890 45.455 0.00 0.00 0.00 2.24
2535 5581 2.492088 GGCCCTGTTTGGTTCATAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
2536 5582 2.492088 GCCCTGTTTGGTTCATAAGTCC 59.508 50.000 0.00 0.00 0.00 3.85
2537 5583 3.814316 GCCCTGTTTGGTTCATAAGTCCT 60.814 47.826 0.00 0.00 0.00 3.85
2538 5584 4.566907 GCCCTGTTTGGTTCATAAGTCCTA 60.567 45.833 0.00 0.00 0.00 2.94
2539 5585 5.566469 CCCTGTTTGGTTCATAAGTCCTAA 58.434 41.667 0.00 0.00 0.00 2.69
2540 5586 5.648092 CCCTGTTTGGTTCATAAGTCCTAAG 59.352 44.000 0.00 0.00 0.00 2.18
2541 5587 6.472887 CCTGTTTGGTTCATAAGTCCTAAGA 58.527 40.000 0.00 0.00 0.00 2.10
2542 5588 6.371825 CCTGTTTGGTTCATAAGTCCTAAGAC 59.628 42.308 0.00 0.00 43.89 3.01
2570 5616 9.504708 TTTTTAGTCCCAATTTATACGTCTCAA 57.495 29.630 0.00 0.00 0.00 3.02
2571 5617 8.712285 TTTAGTCCCAATTTATACGTCTCAAG 57.288 34.615 0.00 0.00 0.00 3.02
2572 5618 6.295719 AGTCCCAATTTATACGTCTCAAGT 57.704 37.500 0.00 0.00 0.00 3.16
2573 5619 7.414222 AGTCCCAATTTATACGTCTCAAGTA 57.586 36.000 0.00 0.00 0.00 2.24
2574 5620 7.263496 AGTCCCAATTTATACGTCTCAAGTAC 58.737 38.462 0.00 0.00 0.00 2.73
2575 5621 6.478016 GTCCCAATTTATACGTCTCAAGTACC 59.522 42.308 0.00 0.00 0.00 3.34
2576 5622 6.381994 TCCCAATTTATACGTCTCAAGTACCT 59.618 38.462 0.00 0.00 0.00 3.08
2577 5623 7.560991 TCCCAATTTATACGTCTCAAGTACCTA 59.439 37.037 0.00 0.00 0.00 3.08
2578 5624 8.199449 CCCAATTTATACGTCTCAAGTACCTAA 58.801 37.037 0.00 0.00 0.00 2.69
2579 5625 9.590451 CCAATTTATACGTCTCAAGTACCTAAA 57.410 33.333 0.00 0.00 0.00 1.85
2584 5630 9.846248 TTATACGTCTCAAGTACCTAAAAAGTC 57.154 33.333 0.00 0.00 0.00 3.01
2585 5631 5.536260 ACGTCTCAAGTACCTAAAAAGTCC 58.464 41.667 0.00 0.00 0.00 3.85
2586 5632 4.928020 CGTCTCAAGTACCTAAAAAGTCCC 59.072 45.833 0.00 0.00 0.00 4.46
2587 5633 5.279356 CGTCTCAAGTACCTAAAAAGTCCCT 60.279 44.000 0.00 0.00 0.00 4.20
2588 5634 6.071728 CGTCTCAAGTACCTAAAAAGTCCCTA 60.072 42.308 0.00 0.00 0.00 3.53
2589 5635 7.095910 GTCTCAAGTACCTAAAAAGTCCCTAC 58.904 42.308 0.00 0.00 0.00 3.18
2590 5636 6.783977 TCTCAAGTACCTAAAAAGTCCCTACA 59.216 38.462 0.00 0.00 0.00 2.74
2591 5637 7.456902 TCTCAAGTACCTAAAAAGTCCCTACAT 59.543 37.037 0.00 0.00 0.00 2.29
2592 5638 7.391620 TCAAGTACCTAAAAAGTCCCTACATG 58.608 38.462 0.00 0.00 0.00 3.21
2593 5639 6.947376 AGTACCTAAAAAGTCCCTACATGT 57.053 37.500 2.69 2.69 0.00 3.21
2594 5640 7.325725 AGTACCTAAAAAGTCCCTACATGTT 57.674 36.000 2.30 0.00 0.00 2.71
2595 5641 7.752638 AGTACCTAAAAAGTCCCTACATGTTT 58.247 34.615 2.30 0.00 0.00 2.83
2596 5642 6.894339 ACCTAAAAAGTCCCTACATGTTTG 57.106 37.500 2.30 0.00 0.00 2.93
2597 5643 5.773176 ACCTAAAAAGTCCCTACATGTTTGG 59.227 40.000 2.30 7.15 0.00 3.28
2598 5644 5.773176 CCTAAAAAGTCCCTACATGTTTGGT 59.227 40.000 2.30 0.00 0.00 3.67
2599 5645 6.266786 CCTAAAAAGTCCCTACATGTTTGGTT 59.733 38.462 2.30 0.00 0.00 3.67
2600 5646 5.784578 AAAAGTCCCTACATGTTTGGTTC 57.215 39.130 2.30 3.85 0.00 3.62
2601 5647 3.434940 AGTCCCTACATGTTTGGTTCC 57.565 47.619 2.30 0.00 0.00 3.62
2602 5648 2.986728 AGTCCCTACATGTTTGGTTCCT 59.013 45.455 2.30 1.09 0.00 3.36
2603 5649 3.081804 GTCCCTACATGTTTGGTTCCTG 58.918 50.000 2.30 0.00 0.00 3.86
2604 5650 2.983192 TCCCTACATGTTTGGTTCCTGA 59.017 45.455 2.30 0.00 0.00 3.86
2605 5651 3.009033 TCCCTACATGTTTGGTTCCTGAG 59.991 47.826 2.30 0.00 0.00 3.35
2606 5652 3.009033 CCCTACATGTTTGGTTCCTGAGA 59.991 47.826 2.30 0.00 0.00 3.27
2607 5653 4.003648 CCTACATGTTTGGTTCCTGAGAC 58.996 47.826 2.30 0.00 0.00 3.36
2608 5654 3.864789 ACATGTTTGGTTCCTGAGACT 57.135 42.857 0.00 0.00 0.00 3.24
2609 5655 4.170468 ACATGTTTGGTTCCTGAGACTT 57.830 40.909 0.00 0.00 0.00 3.01
2610 5656 5.304686 ACATGTTTGGTTCCTGAGACTTA 57.695 39.130 0.00 0.00 0.00 2.24
2611 5657 5.690865 ACATGTTTGGTTCCTGAGACTTAA 58.309 37.500 0.00 0.00 0.00 1.85
2612 5658 5.531287 ACATGTTTGGTTCCTGAGACTTAAC 59.469 40.000 0.00 0.00 0.00 2.01
2613 5659 5.105567 TGTTTGGTTCCTGAGACTTAACA 57.894 39.130 0.00 0.00 0.00 2.41
2614 5660 5.690865 TGTTTGGTTCCTGAGACTTAACAT 58.309 37.500 0.00 0.00 0.00 2.71
2615 5661 5.530915 TGTTTGGTTCCTGAGACTTAACATG 59.469 40.000 0.00 0.00 0.00 3.21
2616 5662 4.286297 TGGTTCCTGAGACTTAACATGG 57.714 45.455 0.00 0.00 0.00 3.66
2617 5663 3.907474 TGGTTCCTGAGACTTAACATGGA 59.093 43.478 0.00 0.00 0.00 3.41
2618 5664 4.254492 GGTTCCTGAGACTTAACATGGAC 58.746 47.826 0.00 0.00 0.00 4.02
2619 5665 4.020128 GGTTCCTGAGACTTAACATGGACT 60.020 45.833 0.00 0.00 0.00 3.85
2620 5666 5.187186 GGTTCCTGAGACTTAACATGGACTA 59.813 44.000 0.00 0.00 0.00 2.59
2621 5667 6.334202 GTTCCTGAGACTTAACATGGACTAG 58.666 44.000 0.00 0.00 0.00 2.57
2622 5668 5.827756 TCCTGAGACTTAACATGGACTAGA 58.172 41.667 0.00 0.00 0.00 2.43
2623 5669 6.253758 TCCTGAGACTTAACATGGACTAGAA 58.746 40.000 0.00 0.00 0.00 2.10
2624 5670 6.378564 TCCTGAGACTTAACATGGACTAGAAG 59.621 42.308 0.00 0.00 0.00 2.85
2625 5671 6.406400 CCTGAGACTTAACATGGACTAGAAGG 60.406 46.154 0.00 0.00 0.00 3.46
2626 5672 5.105310 TGAGACTTAACATGGACTAGAAGGC 60.105 44.000 0.00 0.00 0.00 4.35
2627 5673 4.162509 AGACTTAACATGGACTAGAAGGCC 59.837 45.833 0.00 0.00 46.38 5.19
2637 5683 4.844884 GGACTAGAAGGCCAATTACAACT 58.155 43.478 5.01 0.00 45.15 3.16
2638 5684 5.985911 GGACTAGAAGGCCAATTACAACTA 58.014 41.667 5.01 0.00 45.15 2.24
2639 5685 6.592870 GGACTAGAAGGCCAATTACAACTAT 58.407 40.000 5.01 0.00 45.15 2.12
2640 5686 7.732996 GGACTAGAAGGCCAATTACAACTATA 58.267 38.462 5.01 0.00 45.15 1.31
2641 5687 8.208903 GGACTAGAAGGCCAATTACAACTATAA 58.791 37.037 5.01 0.00 45.15 0.98
2642 5688 9.262358 GACTAGAAGGCCAATTACAACTATAAG 57.738 37.037 5.01 0.00 0.00 1.73
2643 5689 8.769359 ACTAGAAGGCCAATTACAACTATAAGT 58.231 33.333 5.01 0.00 0.00 2.24
2644 5690 9.262358 CTAGAAGGCCAATTACAACTATAAGTC 57.738 37.037 5.01 0.00 0.00 3.01
2645 5691 7.054751 AGAAGGCCAATTACAACTATAAGTCC 58.945 38.462 5.01 0.00 0.00 3.85
2646 5692 5.691896 AGGCCAATTACAACTATAAGTCCC 58.308 41.667 5.01 0.00 0.00 4.46
2647 5693 5.432060 AGGCCAATTACAACTATAAGTCCCT 59.568 40.000 5.01 0.00 0.00 4.20
2648 5694 6.618196 AGGCCAATTACAACTATAAGTCCCTA 59.382 38.462 5.01 0.00 0.00 3.53
2649 5695 7.294958 AGGCCAATTACAACTATAAGTCCCTAT 59.705 37.037 5.01 0.00 0.00 2.57
2650 5696 8.599792 GGCCAATTACAACTATAAGTCCCTATA 58.400 37.037 0.00 0.00 0.00 1.31
2656 5702 7.852550 ACAACTATAAGTCCCTATAAGTCCC 57.147 40.000 0.00 0.00 0.00 4.46
2657 5703 7.602868 ACAACTATAAGTCCCTATAAGTCCCT 58.397 38.462 0.00 0.00 0.00 4.20
2658 5704 7.729431 ACAACTATAAGTCCCTATAAGTCCCTC 59.271 40.741 0.00 0.00 0.00 4.30
2659 5705 6.803017 ACTATAAGTCCCTATAAGTCCCTCC 58.197 44.000 0.00 0.00 0.00 4.30
2660 5706 5.970692 ATAAGTCCCTATAAGTCCCTCCT 57.029 43.478 0.00 0.00 0.00 3.69
2661 5707 4.645968 AAGTCCCTATAAGTCCCTCCTT 57.354 45.455 0.00 0.00 0.00 3.36
2662 5708 3.930035 AGTCCCTATAAGTCCCTCCTTG 58.070 50.000 0.00 0.00 0.00 3.61
2663 5709 3.536434 AGTCCCTATAAGTCCCTCCTTGA 59.464 47.826 0.00 0.00 0.00 3.02
2664 5710 3.898741 GTCCCTATAAGTCCCTCCTTGAG 59.101 52.174 0.00 0.00 0.00 3.02
2665 5711 3.797845 TCCCTATAAGTCCCTCCTTGAGA 59.202 47.826 0.00 0.00 0.00 3.27
2666 5712 4.140900 TCCCTATAAGTCCCTCCTTGAGAG 60.141 50.000 0.00 0.00 42.83 3.20
2667 5713 4.388118 CCCTATAAGTCCCTCCTTGAGAGT 60.388 50.000 0.00 0.00 41.47 3.24
2668 5714 4.830600 CCTATAAGTCCCTCCTTGAGAGTC 59.169 50.000 0.00 0.00 41.47 3.36
2669 5715 4.618378 ATAAGTCCCTCCTTGAGAGTCT 57.382 45.455 0.00 0.00 41.47 3.24
2670 5716 3.268034 AAGTCCCTCCTTGAGAGTCTT 57.732 47.619 0.00 0.00 41.47 3.01
2671 5717 4.405756 AAGTCCCTCCTTGAGAGTCTTA 57.594 45.455 0.00 0.00 41.47 2.10
2672 5718 4.618378 AGTCCCTCCTTGAGAGTCTTAT 57.382 45.455 0.00 0.00 41.47 1.73
2673 5719 4.954089 AGTCCCTCCTTGAGAGTCTTATT 58.046 43.478 0.00 0.00 41.47 1.40
2674 5720 5.346270 AGTCCCTCCTTGAGAGTCTTATTT 58.654 41.667 0.00 0.00 41.47 1.40
2675 5721 5.423931 AGTCCCTCCTTGAGAGTCTTATTTC 59.576 44.000 0.00 0.00 41.47 2.17
2676 5722 5.187967 GTCCCTCCTTGAGAGTCTTATTTCA 59.812 44.000 0.00 0.00 41.47 2.69
2677 5723 5.966935 TCCCTCCTTGAGAGTCTTATTTCAT 59.033 40.000 0.00 0.00 41.47 2.57
2678 5724 7.070074 GTCCCTCCTTGAGAGTCTTATTTCATA 59.930 40.741 0.00 0.00 41.47 2.15
2679 5725 7.623677 TCCCTCCTTGAGAGTCTTATTTCATAA 59.376 37.037 0.00 0.00 41.47 1.90
2680 5726 7.930865 CCCTCCTTGAGAGTCTTATTTCATAAG 59.069 40.741 0.00 0.00 41.47 1.73
2681 5727 8.482128 CCTCCTTGAGAGTCTTATTTCATAAGT 58.518 37.037 0.00 0.00 41.47 2.24
2682 5728 9.528018 CTCCTTGAGAGTCTTATTTCATAAGTC 57.472 37.037 0.00 0.00 37.60 3.01
2683 5729 8.478877 TCCTTGAGAGTCTTATTTCATAAGTCC 58.521 37.037 0.00 0.00 42.21 3.85
2684 5730 7.713073 CCTTGAGAGTCTTATTTCATAAGTCCC 59.287 40.741 0.00 0.00 42.21 4.46
2685 5731 7.733773 TGAGAGTCTTATTTCATAAGTCCCA 57.266 36.000 0.00 0.00 42.21 4.37
2686 5732 8.146053 TGAGAGTCTTATTTCATAAGTCCCAA 57.854 34.615 0.00 0.00 42.21 4.12
2687 5733 8.602424 TGAGAGTCTTATTTCATAAGTCCCAAA 58.398 33.333 0.00 0.00 42.21 3.28
2688 5734 9.620259 GAGAGTCTTATTTCATAAGTCCCAAAT 57.380 33.333 0.00 0.00 42.21 2.32
2689 5735 9.401058 AGAGTCTTATTTCATAAGTCCCAAATG 57.599 33.333 3.93 0.00 42.21 2.32
2690 5736 8.000780 AGTCTTATTTCATAAGTCCCAAATGC 57.999 34.615 3.93 0.00 42.21 3.56
2691 5737 7.068716 AGTCTTATTTCATAAGTCCCAAATGCC 59.931 37.037 3.93 0.00 42.21 4.40
2692 5738 6.323739 TCTTATTTCATAAGTCCCAAATGCCC 59.676 38.462 3.93 0.00 42.21 5.36
2693 5739 3.464720 TTCATAAGTCCCAAATGCCCA 57.535 42.857 0.00 0.00 0.00 5.36
2694 5740 2.733956 TCATAAGTCCCAAATGCCCAC 58.266 47.619 0.00 0.00 0.00 4.61
2695 5741 2.311542 TCATAAGTCCCAAATGCCCACT 59.688 45.455 0.00 0.00 0.00 4.00
2696 5742 2.990740 TAAGTCCCAAATGCCCACTT 57.009 45.000 0.00 0.00 0.00 3.16
2697 5743 2.101640 AAGTCCCAAATGCCCACTTT 57.898 45.000 0.00 0.00 0.00 2.66
2698 5744 2.990740 AGTCCCAAATGCCCACTTTA 57.009 45.000 0.00 0.00 0.00 1.85
2699 5745 3.252554 AGTCCCAAATGCCCACTTTAA 57.747 42.857 0.00 0.00 0.00 1.52
2700 5746 3.165071 AGTCCCAAATGCCCACTTTAAG 58.835 45.455 0.00 0.00 0.00 1.85
2701 5747 2.897326 GTCCCAAATGCCCACTTTAAGT 59.103 45.455 0.00 0.00 0.00 2.24
2702 5748 3.056821 GTCCCAAATGCCCACTTTAAGTC 60.057 47.826 0.00 0.00 0.00 3.01
2703 5749 2.233676 CCCAAATGCCCACTTTAAGTCC 59.766 50.000 0.00 0.00 0.00 3.85
2704 5750 2.233676 CCAAATGCCCACTTTAAGTCCC 59.766 50.000 0.00 0.00 0.00 4.46
2705 5751 3.165071 CAAATGCCCACTTTAAGTCCCT 58.835 45.455 0.00 0.00 0.00 4.20
2706 5752 4.340617 CAAATGCCCACTTTAAGTCCCTA 58.659 43.478 0.00 0.00 0.00 3.53
2707 5753 4.881157 AATGCCCACTTTAAGTCCCTAT 57.119 40.909 0.00 0.00 0.00 2.57
2708 5754 5.987019 AATGCCCACTTTAAGTCCCTATA 57.013 39.130 0.00 0.00 0.00 1.31
2709 5755 5.987019 ATGCCCACTTTAAGTCCCTATAA 57.013 39.130 0.00 0.00 0.00 0.98
2710 5756 5.782677 TGCCCACTTTAAGTCCCTATAAA 57.217 39.130 0.00 0.00 0.00 1.40
2711 5757 6.335781 TGCCCACTTTAAGTCCCTATAAAT 57.664 37.500 0.00 0.00 0.00 1.40
2712 5758 6.362248 TGCCCACTTTAAGTCCCTATAAATC 58.638 40.000 0.00 0.00 0.00 2.17
2713 5759 5.768662 GCCCACTTTAAGTCCCTATAAATCC 59.231 44.000 0.00 0.00 0.00 3.01
2714 5760 6.304624 CCCACTTTAAGTCCCTATAAATCCC 58.695 44.000 0.00 0.00 0.00 3.85
2715 5761 6.102762 CCCACTTTAAGTCCCTATAAATCCCT 59.897 42.308 0.00 0.00 0.00 4.20
2716 5762 7.225011 CCACTTTAAGTCCCTATAAATCCCTC 58.775 42.308 0.00 0.00 0.00 4.30
2717 5763 7.225011 CACTTTAAGTCCCTATAAATCCCTCC 58.775 42.308 0.00 0.00 0.00 4.30
2718 5764 7.072581 CACTTTAAGTCCCTATAAATCCCTCCT 59.927 40.741 0.00 0.00 0.00 3.69
2719 5765 7.072581 ACTTTAAGTCCCTATAAATCCCTCCTG 59.927 40.741 0.00 0.00 0.00 3.86
2720 5766 4.578149 AGTCCCTATAAATCCCTCCTGT 57.422 45.455 0.00 0.00 0.00 4.00
2721 5767 4.909284 AGTCCCTATAAATCCCTCCTGTT 58.091 43.478 0.00 0.00 0.00 3.16
2722 5768 5.297799 AGTCCCTATAAATCCCTCCTGTTT 58.702 41.667 0.00 0.00 0.00 2.83
2723 5769 5.132816 AGTCCCTATAAATCCCTCCTGTTTG 59.867 44.000 0.00 0.00 0.00 2.93
2724 5770 4.415512 TCCCTATAAATCCCTCCTGTTTGG 59.584 45.833 0.00 0.00 37.10 3.28
2725 5771 4.168088 CCCTATAAATCCCTCCTGTTTGGT 59.832 45.833 0.00 0.00 37.07 3.67
2726 5772 5.340863 CCCTATAAATCCCTCCTGTTTGGTT 60.341 44.000 0.00 0.00 37.07 3.67
2727 5773 6.194967 CCTATAAATCCCTCCTGTTTGGTTT 58.805 40.000 0.00 0.00 37.07 3.27
2728 5774 7.351166 CCTATAAATCCCTCCTGTTTGGTTTA 58.649 38.462 0.00 0.00 37.07 2.01
2729 5775 7.502561 CCTATAAATCCCTCCTGTTTGGTTTAG 59.497 40.741 0.00 0.00 37.07 1.85
2730 5776 5.333566 AAATCCCTCCTGTTTGGTTTAGA 57.666 39.130 0.00 0.00 37.07 2.10
2731 5777 5.536497 AATCCCTCCTGTTTGGTTTAGAT 57.464 39.130 0.00 0.00 37.07 1.98
2732 5778 4.301072 TCCCTCCTGTTTGGTTTAGATG 57.699 45.455 0.00 0.00 37.07 2.90
2733 5779 3.010138 TCCCTCCTGTTTGGTTTAGATGG 59.990 47.826 0.00 0.00 37.07 3.51
2734 5780 3.356290 CCTCCTGTTTGGTTTAGATGGG 58.644 50.000 0.00 0.00 37.07 4.00
2735 5781 3.010138 CCTCCTGTTTGGTTTAGATGGGA 59.990 47.826 0.00 0.00 37.07 4.37
2736 5782 4.010349 CTCCTGTTTGGTTTAGATGGGAC 58.990 47.826 0.00 0.00 37.07 4.46
2737 5783 3.655777 TCCTGTTTGGTTTAGATGGGACT 59.344 43.478 0.00 0.00 37.07 3.85
2738 5784 4.105697 TCCTGTTTGGTTTAGATGGGACTT 59.894 41.667 0.00 0.00 37.07 3.01
2739 5785 5.311121 TCCTGTTTGGTTTAGATGGGACTTA 59.689 40.000 0.00 0.00 37.07 2.24
2740 5786 6.011981 TCCTGTTTGGTTTAGATGGGACTTAT 60.012 38.462 0.00 0.00 37.07 1.73
2741 5787 7.183112 TCCTGTTTGGTTTAGATGGGACTTATA 59.817 37.037 0.00 0.00 37.07 0.98
2742 5788 7.998964 CCTGTTTGGTTTAGATGGGACTTATAT 59.001 37.037 0.00 0.00 0.00 0.86
2747 5793 9.670442 TTGGTTTAGATGGGACTTATATAGACT 57.330 33.333 0.00 0.00 0.00 3.24
2748 5794 9.670442 TGGTTTAGATGGGACTTATATAGACTT 57.330 33.333 0.00 0.00 0.00 3.01
2775 5821 8.726870 TTTAAGTCCCTAAATCAATAAGTCCG 57.273 34.615 0.00 0.00 0.00 4.79
2776 5822 5.952347 AGTCCCTAAATCAATAAGTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
2777 5823 5.671493 AGTCCCTAAATCAATAAGTCCGTG 58.329 41.667 0.00 0.00 0.00 4.94
2778 5824 4.814771 GTCCCTAAATCAATAAGTCCGTGG 59.185 45.833 0.00 0.00 0.00 4.94
2779 5825 4.717778 TCCCTAAATCAATAAGTCCGTGGA 59.282 41.667 0.00 0.00 0.00 4.02
2780 5826 5.190132 TCCCTAAATCAATAAGTCCGTGGAA 59.810 40.000 0.00 0.00 0.00 3.53
2781 5827 5.883673 CCCTAAATCAATAAGTCCGTGGAAA 59.116 40.000 0.00 0.00 0.00 3.13
2782 5828 6.183360 CCCTAAATCAATAAGTCCGTGGAAAC 60.183 42.308 0.00 0.00 0.00 2.78
2783 5829 6.373216 CCTAAATCAATAAGTCCGTGGAAACA 59.627 38.462 0.00 0.00 38.70 2.83
2784 5830 6.642707 AAATCAATAAGTCCGTGGAAACAA 57.357 33.333 0.00 0.00 46.06 2.83
2785 5831 6.642707 AATCAATAAGTCCGTGGAAACAAA 57.357 33.333 0.00 0.00 46.06 2.83
2786 5832 5.427036 TCAATAAGTCCGTGGAAACAAAC 57.573 39.130 0.00 0.00 46.06 2.93
2787 5833 4.882427 TCAATAAGTCCGTGGAAACAAACA 59.118 37.500 0.00 0.00 46.06 2.83
2788 5834 4.823790 ATAAGTCCGTGGAAACAAACAC 57.176 40.909 0.00 0.00 46.06 3.32
2789 5835 1.385528 AGTCCGTGGAAACAAACACC 58.614 50.000 0.00 0.00 46.06 4.16
2790 5836 0.382873 GTCCGTGGAAACAAACACCC 59.617 55.000 0.00 0.00 46.06 4.61
2791 5837 0.256464 TCCGTGGAAACAAACACCCT 59.744 50.000 0.00 0.00 46.06 4.34
2792 5838 0.666374 CCGTGGAAACAAACACCCTC 59.334 55.000 0.00 0.00 46.06 4.30
2793 5839 1.675552 CGTGGAAACAAACACCCTCT 58.324 50.000 0.00 0.00 46.06 3.69
2794 5840 2.485835 CCGTGGAAACAAACACCCTCTA 60.486 50.000 0.00 0.00 46.06 2.43
2795 5841 3.207778 CGTGGAAACAAACACCCTCTAA 58.792 45.455 0.00 0.00 46.06 2.10
2889 5945 8.794335 AAAAGTATCTAACAGATCCCTCAAAC 57.206 34.615 0.00 0.00 36.20 2.93
2955 7063 5.262455 ACCTCCAAGCCTATTTTTCTCTT 57.738 39.130 0.00 0.00 0.00 2.85
3079 7200 2.672996 CCTCCAACCACCGCCTTG 60.673 66.667 0.00 0.00 0.00 3.61
3154 7286 4.516195 GCTTCTCCTCGGCGTCCC 62.516 72.222 6.85 0.00 0.00 4.46
3155 7287 2.756283 CTTCTCCTCGGCGTCCCT 60.756 66.667 6.85 0.00 0.00 4.20
3180 7312 2.729491 CAGCGCTCGTTCGTGTCA 60.729 61.111 7.13 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.455847 ACGTTACGTGGAATAGTTATAAGATTC 57.544 33.333 10.39 9.94 39.18 2.52
83 85 2.497273 GGAATGTCCTTGGTTGGATTGG 59.503 50.000 0.00 0.00 38.52 3.16
160 3134 6.016276 AGTGATGTGTTTAACAGAACCCAATC 60.016 38.462 0.00 0.00 43.64 2.67
181 3155 4.214986 TGTCAAGGTCAAAGAACAGTGA 57.785 40.909 0.00 0.00 0.00 3.41
231 3205 1.196012 GTAAGCTACTCCACCTGCCT 58.804 55.000 0.00 0.00 0.00 4.75
320 3295 0.690762 TTAACTGGTCTCTGGTGGCC 59.309 55.000 0.00 0.00 0.00 5.36
344 3319 2.948979 CAAACAAATATCCAGGCGCCTA 59.051 45.455 32.30 16.51 0.00 3.93
346 3321 1.476488 ACAAACAAATATCCAGGCGCC 59.524 47.619 21.89 21.89 0.00 6.53
354 3329 7.599998 AGCTGACCAAATGAACAAACAAATATC 59.400 33.333 0.00 0.00 0.00 1.63
431 3406 7.591165 CAGTGAATATATGAAGGCAAGATTGG 58.409 38.462 0.00 0.00 0.00 3.16
451 3426 2.346766 ACAGTTGAACATGGCAGTGA 57.653 45.000 0.00 0.00 0.00 3.41
494 3469 3.593794 GCCTCGGCCGACTACGAT 61.594 66.667 27.28 0.00 42.66 3.73
644 3628 1.266989 CGAGCAGAAGGGAACAAAACC 59.733 52.381 0.00 0.00 0.00 3.27
645 3629 1.335051 GCGAGCAGAAGGGAACAAAAC 60.335 52.381 0.00 0.00 0.00 2.43
684 3669 1.075301 GGGAATGGGAATGGGGTGG 60.075 63.158 0.00 0.00 0.00 4.61
876 3872 0.117742 ACGTAAGGGGAAGGGGAAGA 59.882 55.000 0.00 0.00 46.39 2.87
881 3877 0.981943 AACTCACGTAAGGGGAAGGG 59.018 55.000 0.00 0.00 44.90 3.95
892 3895 2.915659 TCAGCCGGGAACTCACGT 60.916 61.111 2.18 0.00 42.08 4.49
918 3928 2.483876 CTCTCAGGAAGCGTTGAAACA 58.516 47.619 0.00 0.00 0.00 2.83
943 3954 2.214181 CTTGGTCGTGACGAGGGGAG 62.214 65.000 8.41 0.35 36.23 4.30
969 3980 1.594310 GAGGAGAAGAGCCGCAAGT 59.406 57.895 0.00 0.00 0.00 3.16
970 3981 1.153469 GGAGGAGAAGAGCCGCAAG 60.153 63.158 0.00 0.00 0.00 4.01
971 3982 2.660064 GGGAGGAGAAGAGCCGCAA 61.660 63.158 0.00 0.00 0.00 4.85
973 3984 4.214327 CGGGAGGAGAAGAGCCGC 62.214 72.222 0.00 0.00 0.00 6.53
1236 4262 0.437295 GCAAAGAAAGCAGCGCAATG 59.563 50.000 11.47 0.00 0.00 2.82
1237 4263 0.668401 GGCAAAGAAAGCAGCGCAAT 60.668 50.000 11.47 0.00 0.00 3.56
1318 4348 2.665000 CGTCACACCCCTGCAGAT 59.335 61.111 17.39 0.00 0.00 2.90
1331 4361 1.141665 CAGCATGATCGACCCGTCA 59.858 57.895 0.00 0.00 39.69 4.35
1460 4490 4.994201 TCTGCGCACGACACGGTC 62.994 66.667 5.66 0.00 0.00 4.79
1469 4499 1.292992 TGATGATGATGTCTGCGCAC 58.707 50.000 5.66 0.00 0.00 5.34
1550 4580 3.056322 AGCTTGAGAAAATCCATGGTTGC 60.056 43.478 12.58 0.00 0.00 4.17
1552 4582 5.541484 AGAAAGCTTGAGAAAATCCATGGTT 59.459 36.000 12.58 0.00 32.16 3.67
1553 4583 5.082425 AGAAAGCTTGAGAAAATCCATGGT 58.918 37.500 12.58 0.00 0.00 3.55
1593 4624 1.070786 GGTCTGGAACAACGAGGCA 59.929 57.895 0.00 0.00 38.70 4.75
1761 4799 1.444553 GCTCCCTGACAAGACGACG 60.445 63.158 0.00 0.00 0.00 5.12
1767 4805 1.669115 CGTGTGGCTCCCTGACAAG 60.669 63.158 0.00 0.00 34.07 3.16
1768 4806 1.480212 ATCGTGTGGCTCCCTGACAA 61.480 55.000 0.00 0.00 34.07 3.18
1773 4811 3.461773 CCGATCGTGTGGCTCCCT 61.462 66.667 15.09 0.00 0.00 4.20
1931 4969 2.819984 CTTGGGGTCCATGTCCACGG 62.820 65.000 6.53 0.00 31.53 4.94
2191 5229 4.827481 CCACCGGGTCGATTAGTG 57.173 61.111 6.32 0.00 0.00 2.74
2501 5547 0.759346 CAGGGCCTTAAGCTACCGAT 59.241 55.000 1.32 0.00 43.05 4.18
2514 5560 2.492088 GACTTATGAACCAAACAGGGCC 59.508 50.000 0.00 0.00 43.89 5.80
2515 5561 2.492088 GGACTTATGAACCAAACAGGGC 59.508 50.000 0.00 0.00 43.89 5.19
2516 5562 4.034285 AGGACTTATGAACCAAACAGGG 57.966 45.455 0.00 0.00 43.89 4.45
2517 5563 6.371825 GTCTTAGGACTTATGAACCAAACAGG 59.628 42.308 0.00 0.00 40.36 4.00
2518 5564 7.365840 GTCTTAGGACTTATGAACCAAACAG 57.634 40.000 0.00 0.00 39.24 3.16
2544 5590 9.504708 TTGAGACGTATAAATTGGGACTAAAAA 57.495 29.630 0.00 0.00 0.00 1.94
2545 5591 9.158233 CTTGAGACGTATAAATTGGGACTAAAA 57.842 33.333 0.00 0.00 0.00 1.52
2546 5592 8.316214 ACTTGAGACGTATAAATTGGGACTAAA 58.684 33.333 0.00 0.00 0.00 1.85
2547 5593 7.844009 ACTTGAGACGTATAAATTGGGACTAA 58.156 34.615 0.00 0.00 0.00 2.24
2548 5594 7.414222 ACTTGAGACGTATAAATTGGGACTA 57.586 36.000 0.00 0.00 0.00 2.59
2549 5595 6.295719 ACTTGAGACGTATAAATTGGGACT 57.704 37.500 0.00 0.00 0.00 3.85
2550 5596 6.478016 GGTACTTGAGACGTATAAATTGGGAC 59.522 42.308 0.00 0.00 0.00 4.46
2551 5597 6.381994 AGGTACTTGAGACGTATAAATTGGGA 59.618 38.462 0.00 0.00 27.25 4.37
2552 5598 6.579865 AGGTACTTGAGACGTATAAATTGGG 58.420 40.000 0.00 0.00 27.25 4.12
2553 5599 9.590451 TTTAGGTACTTGAGACGTATAAATTGG 57.410 33.333 0.00 0.00 41.75 3.16
2558 5604 9.846248 GACTTTTTAGGTACTTGAGACGTATAA 57.154 33.333 0.00 0.00 41.75 0.98
2559 5605 8.462016 GGACTTTTTAGGTACTTGAGACGTATA 58.538 37.037 0.00 0.00 41.75 1.47
2560 5606 7.318893 GGACTTTTTAGGTACTTGAGACGTAT 58.681 38.462 0.00 0.00 41.75 3.06
2561 5607 6.294731 GGGACTTTTTAGGTACTTGAGACGTA 60.295 42.308 0.00 0.00 41.75 3.57
2562 5608 5.510349 GGGACTTTTTAGGTACTTGAGACGT 60.510 44.000 0.00 0.00 41.75 4.34
2563 5609 4.928020 GGGACTTTTTAGGTACTTGAGACG 59.072 45.833 0.00 0.00 41.75 4.18
2564 5610 6.111669 AGGGACTTTTTAGGTACTTGAGAC 57.888 41.667 0.00 0.00 34.75 3.36
2565 5611 6.783977 TGTAGGGACTTTTTAGGTACTTGAGA 59.216 38.462 0.00 0.00 39.49 3.27
2566 5612 7.001099 TGTAGGGACTTTTTAGGTACTTGAG 57.999 40.000 0.00 0.00 39.49 3.02
2567 5613 6.999705 TGTAGGGACTTTTTAGGTACTTGA 57.000 37.500 0.00 0.00 39.49 3.02
2568 5614 7.166167 ACATGTAGGGACTTTTTAGGTACTTG 58.834 38.462 0.00 0.00 39.49 3.16
2569 5615 7.325725 ACATGTAGGGACTTTTTAGGTACTT 57.674 36.000 0.00 0.00 39.49 2.24
2570 5616 6.947376 ACATGTAGGGACTTTTTAGGTACT 57.053 37.500 0.00 0.00 41.75 2.73
2571 5617 7.094506 CCAAACATGTAGGGACTTTTTAGGTAC 60.095 40.741 9.55 0.00 41.75 3.34
2572 5618 6.943718 CCAAACATGTAGGGACTTTTTAGGTA 59.056 38.462 9.55 0.00 41.75 3.08
2573 5619 5.773176 CCAAACATGTAGGGACTTTTTAGGT 59.227 40.000 9.55 0.00 41.75 3.08
2574 5620 5.773176 ACCAAACATGTAGGGACTTTTTAGG 59.227 40.000 19.48 5.71 41.75 2.69
2575 5621 6.894339 ACCAAACATGTAGGGACTTTTTAG 57.106 37.500 19.48 0.00 41.75 1.85
2576 5622 6.265876 GGAACCAAACATGTAGGGACTTTTTA 59.734 38.462 19.48 0.00 41.75 1.52
2577 5623 5.069914 GGAACCAAACATGTAGGGACTTTTT 59.930 40.000 19.48 5.69 41.75 1.94
2578 5624 4.587262 GGAACCAAACATGTAGGGACTTTT 59.413 41.667 19.48 6.31 41.75 2.27
2579 5625 4.141018 AGGAACCAAACATGTAGGGACTTT 60.141 41.667 19.48 6.62 41.75 2.66
2580 5626 3.397955 AGGAACCAAACATGTAGGGACTT 59.602 43.478 19.48 6.91 41.75 3.01
2581 5627 2.986728 AGGAACCAAACATGTAGGGACT 59.013 45.455 19.48 11.76 46.37 3.85
2582 5628 3.081804 CAGGAACCAAACATGTAGGGAC 58.918 50.000 19.48 12.61 0.00 4.46
2583 5629 2.983192 TCAGGAACCAAACATGTAGGGA 59.017 45.455 19.48 6.04 0.00 4.20
2584 5630 3.009033 TCTCAGGAACCAAACATGTAGGG 59.991 47.826 18.43 15.73 0.00 3.53
2585 5631 4.003648 GTCTCAGGAACCAAACATGTAGG 58.996 47.826 14.04 14.04 0.00 3.18
2586 5632 4.899502 AGTCTCAGGAACCAAACATGTAG 58.100 43.478 0.00 0.00 0.00 2.74
2587 5633 4.974645 AGTCTCAGGAACCAAACATGTA 57.025 40.909 0.00 0.00 0.00 2.29
2588 5634 3.864789 AGTCTCAGGAACCAAACATGT 57.135 42.857 0.00 0.00 0.00 3.21
2589 5635 5.530915 TGTTAAGTCTCAGGAACCAAACATG 59.469 40.000 0.00 0.00 0.00 3.21
2590 5636 5.690865 TGTTAAGTCTCAGGAACCAAACAT 58.309 37.500 0.00 0.00 0.00 2.71
2591 5637 5.105567 TGTTAAGTCTCAGGAACCAAACA 57.894 39.130 0.00 0.00 0.00 2.83
2592 5638 5.048713 CCATGTTAAGTCTCAGGAACCAAAC 60.049 44.000 0.00 0.00 0.00 2.93
2593 5639 5.070001 CCATGTTAAGTCTCAGGAACCAAA 58.930 41.667 0.00 0.00 0.00 3.28
2594 5640 4.349636 TCCATGTTAAGTCTCAGGAACCAA 59.650 41.667 0.00 0.00 0.00 3.67
2595 5641 3.907474 TCCATGTTAAGTCTCAGGAACCA 59.093 43.478 0.00 0.00 0.00 3.67
2596 5642 4.020128 AGTCCATGTTAAGTCTCAGGAACC 60.020 45.833 0.00 0.00 0.00 3.62
2597 5643 5.153950 AGTCCATGTTAAGTCTCAGGAAC 57.846 43.478 0.00 0.00 0.00 3.62
2598 5644 6.253758 TCTAGTCCATGTTAAGTCTCAGGAA 58.746 40.000 0.00 0.00 0.00 3.36
2599 5645 5.827756 TCTAGTCCATGTTAAGTCTCAGGA 58.172 41.667 0.00 0.00 0.00 3.86
2600 5646 6.406400 CCTTCTAGTCCATGTTAAGTCTCAGG 60.406 46.154 0.00 0.00 0.00 3.86
2601 5647 6.568869 CCTTCTAGTCCATGTTAAGTCTCAG 58.431 44.000 0.00 0.00 0.00 3.35
2602 5648 5.105310 GCCTTCTAGTCCATGTTAAGTCTCA 60.105 44.000 0.00 0.00 0.00 3.27
2603 5649 5.353111 GCCTTCTAGTCCATGTTAAGTCTC 58.647 45.833 0.00 0.00 0.00 3.36
2604 5650 4.162509 GGCCTTCTAGTCCATGTTAAGTCT 59.837 45.833 0.00 0.00 0.00 3.24
2605 5651 4.081087 TGGCCTTCTAGTCCATGTTAAGTC 60.081 45.833 3.32 0.00 0.00 3.01
2606 5652 3.844211 TGGCCTTCTAGTCCATGTTAAGT 59.156 43.478 3.32 0.00 0.00 2.24
2607 5653 4.487714 TGGCCTTCTAGTCCATGTTAAG 57.512 45.455 3.32 0.00 0.00 1.85
2608 5654 4.919774 TTGGCCTTCTAGTCCATGTTAA 57.080 40.909 3.32 0.00 0.00 2.01
2609 5655 5.450818 AATTGGCCTTCTAGTCCATGTTA 57.549 39.130 3.32 0.00 0.00 2.41
2610 5656 4.322057 AATTGGCCTTCTAGTCCATGTT 57.678 40.909 3.32 0.00 0.00 2.71
2611 5657 4.227300 TGTAATTGGCCTTCTAGTCCATGT 59.773 41.667 3.32 0.00 0.00 3.21
2612 5658 4.780815 TGTAATTGGCCTTCTAGTCCATG 58.219 43.478 3.32 0.00 0.00 3.66
2613 5659 5.044846 AGTTGTAATTGGCCTTCTAGTCCAT 60.045 40.000 3.32 0.00 0.00 3.41
2614 5660 4.288626 AGTTGTAATTGGCCTTCTAGTCCA 59.711 41.667 3.32 0.00 0.00 4.02
2615 5661 4.844884 AGTTGTAATTGGCCTTCTAGTCC 58.155 43.478 3.32 0.00 0.00 3.85
2616 5662 9.262358 CTTATAGTTGTAATTGGCCTTCTAGTC 57.738 37.037 3.32 0.00 0.00 2.59
2617 5663 8.769359 ACTTATAGTTGTAATTGGCCTTCTAGT 58.231 33.333 3.32 0.00 0.00 2.57
2618 5664 9.262358 GACTTATAGTTGTAATTGGCCTTCTAG 57.738 37.037 3.32 0.00 0.00 2.43
2619 5665 8.208903 GGACTTATAGTTGTAATTGGCCTTCTA 58.791 37.037 3.32 0.00 0.00 2.10
2620 5666 7.054751 GGACTTATAGTTGTAATTGGCCTTCT 58.945 38.462 3.32 0.00 0.00 2.85
2621 5667 6.262496 GGGACTTATAGTTGTAATTGGCCTTC 59.738 42.308 3.32 0.00 0.00 3.46
2622 5668 6.069029 AGGGACTTATAGTTGTAATTGGCCTT 60.069 38.462 3.32 0.00 27.25 4.35
2623 5669 5.432060 AGGGACTTATAGTTGTAATTGGCCT 59.568 40.000 3.32 0.00 27.25 5.19
2624 5670 5.691896 AGGGACTTATAGTTGTAATTGGCC 58.308 41.667 0.00 0.00 27.25 5.36
2630 5676 9.372189 GGGACTTATAGGGACTTATAGTTGTAA 57.628 37.037 0.00 0.00 41.75 2.41
2631 5677 8.740512 AGGGACTTATAGGGACTTATAGTTGTA 58.259 37.037 0.00 0.00 34.75 2.41
2632 5678 7.602868 AGGGACTTATAGGGACTTATAGTTGT 58.397 38.462 0.00 0.00 34.75 3.32
2633 5679 7.178805 GGAGGGACTTATAGGGACTTATAGTTG 59.821 44.444 0.00 0.00 41.55 3.16
2634 5680 7.076566 AGGAGGGACTTATAGGGACTTATAGTT 59.923 40.741 0.00 0.00 41.55 2.24
2635 5681 6.571180 AGGAGGGACTTATAGGGACTTATAGT 59.429 42.308 0.00 0.00 41.55 2.12
2636 5682 7.046891 AGGAGGGACTTATAGGGACTTATAG 57.953 44.000 0.00 0.00 41.55 1.31
2637 5683 7.075915 TCAAGGAGGGACTTATAGGGACTTATA 59.924 40.741 0.00 0.00 41.55 0.98
2638 5684 5.970692 AGGAGGGACTTATAGGGACTTAT 57.029 43.478 0.00 0.00 41.55 1.73
2639 5685 5.197189 TCAAGGAGGGACTTATAGGGACTTA 59.803 44.000 0.00 0.00 41.55 2.24
2640 5686 4.015541 TCAAGGAGGGACTTATAGGGACTT 60.016 45.833 0.00 0.00 41.55 3.01
2641 5687 3.536434 TCAAGGAGGGACTTATAGGGACT 59.464 47.826 0.00 0.00 41.55 3.85
2642 5688 3.898741 CTCAAGGAGGGACTTATAGGGAC 59.101 52.174 0.00 0.00 41.55 4.46
2643 5689 3.797845 TCTCAAGGAGGGACTTATAGGGA 59.202 47.826 0.00 0.00 41.55 4.20
2644 5690 4.156477 CTCTCAAGGAGGGACTTATAGGG 58.844 52.174 0.00 0.00 41.55 3.53
2645 5691 4.810345 ACTCTCAAGGAGGGACTTATAGG 58.190 47.826 0.00 0.00 45.83 2.57
2646 5692 5.701224 AGACTCTCAAGGAGGGACTTATAG 58.299 45.833 0.00 0.00 45.83 1.31
2647 5693 5.735733 AGACTCTCAAGGAGGGACTTATA 57.264 43.478 0.00 0.00 45.83 0.98
2648 5694 4.618378 AGACTCTCAAGGAGGGACTTAT 57.382 45.455 0.00 0.00 45.83 1.73
2649 5695 4.405756 AAGACTCTCAAGGAGGGACTTA 57.594 45.455 8.68 0.00 41.64 2.24
2650 5696 3.268034 AAGACTCTCAAGGAGGGACTT 57.732 47.619 5.25 5.25 45.83 3.01
2651 5697 4.618378 ATAAGACTCTCAAGGAGGGACT 57.382 45.455 0.00 0.00 45.83 3.85
2652 5698 5.187967 TGAAATAAGACTCTCAAGGAGGGAC 59.812 44.000 0.00 0.00 45.83 4.46
2653 5699 5.342017 TGAAATAAGACTCTCAAGGAGGGA 58.658 41.667 0.00 0.00 45.83 4.20
2654 5700 5.683876 TGAAATAAGACTCTCAAGGAGGG 57.316 43.478 0.00 0.00 45.83 4.30
2669 5715 5.960811 TGGGCATTTGGGACTTATGAAATAA 59.039 36.000 0.00 0.00 36.20 1.40
2670 5716 5.362430 GTGGGCATTTGGGACTTATGAAATA 59.638 40.000 0.00 0.00 0.00 1.40
2671 5717 4.162131 GTGGGCATTTGGGACTTATGAAAT 59.838 41.667 0.00 0.00 0.00 2.17
2672 5718 3.513515 GTGGGCATTTGGGACTTATGAAA 59.486 43.478 0.00 0.00 0.00 2.69
2673 5719 3.096092 GTGGGCATTTGGGACTTATGAA 58.904 45.455 0.00 0.00 0.00 2.57
2674 5720 2.311542 AGTGGGCATTTGGGACTTATGA 59.688 45.455 0.00 0.00 0.00 2.15
2675 5721 2.738743 AGTGGGCATTTGGGACTTATG 58.261 47.619 0.00 0.00 0.00 1.90
2676 5722 3.473113 AAGTGGGCATTTGGGACTTAT 57.527 42.857 0.00 0.00 0.00 1.73
2677 5723 2.990740 AAGTGGGCATTTGGGACTTA 57.009 45.000 0.00 0.00 0.00 2.24
2678 5724 2.101640 AAAGTGGGCATTTGGGACTT 57.898 45.000 0.00 0.00 0.00 3.01
2679 5725 2.990740 TAAAGTGGGCATTTGGGACT 57.009 45.000 0.00 0.00 0.00 3.85
2680 5726 2.897326 ACTTAAAGTGGGCATTTGGGAC 59.103 45.455 0.00 0.00 0.00 4.46
2681 5727 3.161866 GACTTAAAGTGGGCATTTGGGA 58.838 45.455 0.00 0.00 0.00 4.37
2682 5728 2.233676 GGACTTAAAGTGGGCATTTGGG 59.766 50.000 0.00 0.00 0.00 4.12
2683 5729 2.233676 GGGACTTAAAGTGGGCATTTGG 59.766 50.000 0.00 0.00 0.00 3.28
2684 5730 3.165071 AGGGACTTAAAGTGGGCATTTG 58.835 45.455 0.00 0.00 27.25 2.32
2685 5731 3.542969 AGGGACTTAAAGTGGGCATTT 57.457 42.857 0.00 0.00 27.25 2.32
2686 5732 4.881157 ATAGGGACTTAAAGTGGGCATT 57.119 40.909 0.00 0.00 41.75 3.56
2687 5733 5.987019 TTATAGGGACTTAAAGTGGGCAT 57.013 39.130 0.00 0.00 41.75 4.40
2688 5734 5.782677 TTTATAGGGACTTAAAGTGGGCA 57.217 39.130 0.00 0.00 41.75 5.36
2689 5735 5.768662 GGATTTATAGGGACTTAAAGTGGGC 59.231 44.000 0.00 0.00 41.75 5.36
2690 5736 6.102762 AGGGATTTATAGGGACTTAAAGTGGG 59.897 42.308 0.00 0.00 41.75 4.61
2691 5737 7.150447 AGGGATTTATAGGGACTTAAAGTGG 57.850 40.000 0.00 0.00 41.75 4.00
2692 5738 7.072581 AGGAGGGATTTATAGGGACTTAAAGTG 59.927 40.741 0.00 0.00 41.75 3.16
2693 5739 7.072581 CAGGAGGGATTTATAGGGACTTAAAGT 59.927 40.741 0.00 0.00 41.75 2.66
2694 5740 7.072581 ACAGGAGGGATTTATAGGGACTTAAAG 59.927 40.741 0.00 0.00 41.75 1.85
2695 5741 6.912561 ACAGGAGGGATTTATAGGGACTTAAA 59.087 38.462 0.00 0.00 41.75 1.52
2696 5742 6.458784 ACAGGAGGGATTTATAGGGACTTAA 58.541 40.000 0.00 0.00 41.75 1.85
2697 5743 6.051946 ACAGGAGGGATTTATAGGGACTTA 57.948 41.667 0.00 0.00 41.75 2.24
2698 5744 4.909284 ACAGGAGGGATTTATAGGGACTT 58.091 43.478 0.00 0.00 41.75 3.01
2699 5745 4.578149 ACAGGAGGGATTTATAGGGACT 57.422 45.455 0.00 0.00 46.37 3.85
2700 5746 5.377478 CAAACAGGAGGGATTTATAGGGAC 58.623 45.833 0.00 0.00 0.00 4.46
2701 5747 4.415512 CCAAACAGGAGGGATTTATAGGGA 59.584 45.833 0.00 0.00 41.22 4.20
2702 5748 4.168088 ACCAAACAGGAGGGATTTATAGGG 59.832 45.833 0.00 0.00 41.22 3.53
2703 5749 5.388599 ACCAAACAGGAGGGATTTATAGG 57.611 43.478 0.00 0.00 41.22 2.57
2704 5750 8.272173 TCTAAACCAAACAGGAGGGATTTATAG 58.728 37.037 0.00 0.00 41.22 1.31
2705 5751 8.165267 TCTAAACCAAACAGGAGGGATTTATA 57.835 34.615 0.00 0.00 41.22 0.98
2706 5752 7.039722 TCTAAACCAAACAGGAGGGATTTAT 57.960 36.000 0.00 0.00 41.22 1.40
2707 5753 6.457159 TCTAAACCAAACAGGAGGGATTTA 57.543 37.500 0.00 0.00 41.22 1.40
2708 5754 5.333566 TCTAAACCAAACAGGAGGGATTT 57.666 39.130 0.00 0.00 41.22 2.17
2709 5755 5.264395 CATCTAAACCAAACAGGAGGGATT 58.736 41.667 0.00 0.00 41.22 3.01
2710 5756 4.325344 CCATCTAAACCAAACAGGAGGGAT 60.325 45.833 0.00 0.00 41.22 3.85
2711 5757 3.010138 CCATCTAAACCAAACAGGAGGGA 59.990 47.826 0.00 0.00 41.22 4.20
2712 5758 3.356290 CCATCTAAACCAAACAGGAGGG 58.644 50.000 0.00 0.00 41.22 4.30
2713 5759 3.010138 TCCCATCTAAACCAAACAGGAGG 59.990 47.826 0.00 0.00 41.22 4.30
2714 5760 4.010349 GTCCCATCTAAACCAAACAGGAG 58.990 47.826 0.00 0.00 41.22 3.69
2715 5761 3.655777 AGTCCCATCTAAACCAAACAGGA 59.344 43.478 0.00 0.00 41.22 3.86
2716 5762 4.034285 AGTCCCATCTAAACCAAACAGG 57.966 45.455 0.00 0.00 45.67 4.00
2717 5763 8.980481 ATATAAGTCCCATCTAAACCAAACAG 57.020 34.615 0.00 0.00 0.00 3.16
2721 5767 9.670442 AGTCTATATAAGTCCCATCTAAACCAA 57.330 33.333 0.00 0.00 0.00 3.67
2722 5768 9.670442 AAGTCTATATAAGTCCCATCTAAACCA 57.330 33.333 0.00 0.00 0.00 3.67
2749 5795 9.169592 CGGACTTATTGATTTAGGGACTTAAAA 57.830 33.333 0.00 0.00 41.75 1.52
2750 5796 8.323567 ACGGACTTATTGATTTAGGGACTTAAA 58.676 33.333 0.00 0.00 41.75 1.52
2751 5797 7.767198 CACGGACTTATTGATTTAGGGACTTAA 59.233 37.037 0.00 0.00 41.75 1.85
2752 5798 7.270047 CACGGACTTATTGATTTAGGGACTTA 58.730 38.462 0.00 0.00 41.75 2.24
2753 5799 6.113411 CACGGACTTATTGATTTAGGGACTT 58.887 40.000 0.00 0.00 41.75 3.01
2754 5800 5.396436 CCACGGACTTATTGATTTAGGGACT 60.396 44.000 0.00 0.00 46.37 3.85
2755 5801 4.814771 CCACGGACTTATTGATTTAGGGAC 59.185 45.833 0.00 0.00 0.00 4.46
2756 5802 4.717778 TCCACGGACTTATTGATTTAGGGA 59.282 41.667 0.00 0.00 0.00 4.20
2757 5803 5.031066 TCCACGGACTTATTGATTTAGGG 57.969 43.478 0.00 0.00 0.00 3.53
2758 5804 6.373216 TGTTTCCACGGACTTATTGATTTAGG 59.627 38.462 0.00 0.00 0.00 2.69
2759 5805 7.372451 TGTTTCCACGGACTTATTGATTTAG 57.628 36.000 0.00 0.00 0.00 1.85
2760 5806 7.747155 TTGTTTCCACGGACTTATTGATTTA 57.253 32.000 0.00 0.00 0.00 1.40
2761 5807 6.642707 TTGTTTCCACGGACTTATTGATTT 57.357 33.333 0.00 0.00 0.00 2.17
2762 5808 6.039941 TGTTTGTTTCCACGGACTTATTGATT 59.960 34.615 0.00 0.00 0.00 2.57
2763 5809 5.533154 TGTTTGTTTCCACGGACTTATTGAT 59.467 36.000 0.00 0.00 0.00 2.57
2764 5810 4.882427 TGTTTGTTTCCACGGACTTATTGA 59.118 37.500 0.00 0.00 0.00 2.57
2765 5811 4.973663 GTGTTTGTTTCCACGGACTTATTG 59.026 41.667 0.00 0.00 0.00 1.90
2766 5812 4.037089 GGTGTTTGTTTCCACGGACTTATT 59.963 41.667 0.00 0.00 32.30 1.40
2767 5813 3.566742 GGTGTTTGTTTCCACGGACTTAT 59.433 43.478 0.00 0.00 32.30 1.73
2768 5814 2.944349 GGTGTTTGTTTCCACGGACTTA 59.056 45.455 0.00 0.00 32.30 2.24
2769 5815 1.746787 GGTGTTTGTTTCCACGGACTT 59.253 47.619 0.00 0.00 32.30 3.01
2770 5816 1.385528 GGTGTTTGTTTCCACGGACT 58.614 50.000 0.00 0.00 32.30 3.85
2771 5817 0.382873 GGGTGTTTGTTTCCACGGAC 59.617 55.000 0.00 0.00 32.30 4.79
2772 5818 0.256464 AGGGTGTTTGTTTCCACGGA 59.744 50.000 0.00 0.00 32.30 4.69
2773 5819 0.666374 GAGGGTGTTTGTTTCCACGG 59.334 55.000 0.00 0.00 32.30 4.94
2774 5820 1.675552 AGAGGGTGTTTGTTTCCACG 58.324 50.000 0.00 0.00 32.30 4.94
2775 5821 4.204799 AGTTAGAGGGTGTTTGTTTCCAC 58.795 43.478 0.00 0.00 0.00 4.02
2776 5822 4.513406 AGTTAGAGGGTGTTTGTTTCCA 57.487 40.909 0.00 0.00 0.00 3.53
2777 5823 6.544931 ACTTAAGTTAGAGGGTGTTTGTTTCC 59.455 38.462 1.12 0.00 0.00 3.13
2778 5824 7.281549 TCACTTAAGTTAGAGGGTGTTTGTTTC 59.718 37.037 5.07 0.00 0.00 2.78
2779 5825 7.114095 TCACTTAAGTTAGAGGGTGTTTGTTT 58.886 34.615 5.07 0.00 0.00 2.83
2780 5826 6.655930 TCACTTAAGTTAGAGGGTGTTTGTT 58.344 36.000 5.07 0.00 0.00 2.83
2781 5827 6.099269 TCTCACTTAAGTTAGAGGGTGTTTGT 59.901 38.462 14.22 0.00 0.00 2.83
2782 5828 6.522054 TCTCACTTAAGTTAGAGGGTGTTTG 58.478 40.000 14.22 0.00 0.00 2.93
2783 5829 6.553852 TCTCTCACTTAAGTTAGAGGGTGTTT 59.446 38.462 32.08 0.00 43.22 2.83
2784 5830 6.075984 TCTCTCACTTAAGTTAGAGGGTGTT 58.924 40.000 32.08 0.00 43.22 3.32
2785 5831 5.642165 TCTCTCACTTAAGTTAGAGGGTGT 58.358 41.667 32.08 0.00 43.22 4.16
2786 5832 6.783708 ATCTCTCACTTAAGTTAGAGGGTG 57.216 41.667 32.08 17.27 43.22 4.61
2787 5833 9.138596 GATAATCTCTCACTTAAGTTAGAGGGT 57.861 37.037 32.08 25.06 43.22 4.34
2788 5834 9.362151 AGATAATCTCTCACTTAAGTTAGAGGG 57.638 37.037 32.08 23.88 43.22 4.30
2955 7063 1.344065 TACCGAGAAGTGGCTTTCCA 58.656 50.000 0.00 0.00 40.85 3.53
3079 7200 7.881775 AAATATGTTTACTGGAATCTCACCC 57.118 36.000 0.00 0.00 0.00 4.61
3165 7297 1.057361 GAATGACACGAACGAGCGC 59.943 57.895 0.00 0.00 33.86 5.92


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

AutoCloner maintained by Alex Coulton.