Multiple sequence alignment - TraesCS4A01G225500

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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 TraesCS4A01G225500 chr4A 100.000 5372 0 0 1 5372 533443658 533449029 0.000000e+00 9921
1 TraesCS4A01G225500 chr4B 92.883 3892 129 55 720 4541 93291651 93287838 0.000000e+00 5517
2 TraesCS4A01G225500 chr4B 93.590 468 17 7 4540 4998 93287616 93287153 0.000000e+00 686
3 TraesCS4A01G225500 chr4B 86.751 634 40 19 77 672 93292264 93291637 0.000000e+00 665
4 TraesCS4A01G225500 chr4B 94.833 329 14 2 5005 5330 93286947 93286619 1.330000e-140 510
5 TraesCS4A01G225500 chr4D 95.126 2934 85 18 1639 4541 62879884 62876978 0.000000e+00 4573
6 TraesCS4A01G225500 chr4D 95.060 911 19 16 722 1623 62880762 62879869 0.000000e+00 1410
7 TraesCS4A01G225500 chr4D 93.377 453 13 8 4559 4998 62876753 62876305 0.000000e+00 654
8 TraesCS4A01G225500 chr4D 84.087 641 45 20 80 673 62883299 62882669 2.810000e-157 566
9 TraesCS4A01G225500 chr4D 96.746 338 7 2 4997 5330 62876267 62875930 1.310000e-155 560
10 TraesCS4A01G225500 chr4D 85.946 555 37 16 80 598 62881321 62880772 6.080000e-154 555
11 TraesCS4A01G225500 chr5D 100.000 80 0 0 1 80 8060912 8060833 1.210000e-31 148
12 TraesCS4A01G225500 chr7A 98.780 82 1 0 1 82 660485370 660485289 4.340000e-31 147
13 TraesCS4A01G225500 chr2A 100.000 79 0 0 1 79 734392899 734392821 4.340000e-31 147
14 TraesCS4A01G225500 chr2A 95.000 80 4 0 1 80 13918111 13918032 5.650000e-25 126
15 TraesCS4A01G225500 chr3B 96.104 77 3 0 1 77 763235638 763235714 5.650000e-25 126
16 TraesCS4A01G225500 chr3D 93.671 79 5 0 1 79 450238504 450238426 9.450000e-23 119


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G225500 chr4A 533443658 533449029 5371 False 9921.000000 9921 100.000000 1 5372 1 chr4A.!!$F1 5371
1 TraesCS4A01G225500 chr4B 93286619 93292264 5645 True 1844.500000 5517 92.014250 77 5330 4 chr4B.!!$R1 5253
2 TraesCS4A01G225500 chr4D 62875930 62883299 7369 True 1386.333333 4573 91.723667 80 5330 6 chr4D.!!$R1 5250

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
51 52 0.039074 GTCAGGTGAGTGTCGTCCAG 60.039 60.0 0.00 0.00 0.00 3.86 F
674 2694 0.241749 TCAACGCTCGTGTCCGTTAT 59.758 50.0 0.00 0.00 44.83 1.89 F
1899 3937 0.103937 CCAACGGCAAAAAGGAGCAA 59.896 50.0 0.00 0.00 0.00 3.91 F
2483 4580 0.180171 TCTGCGTTACCCCATGATGG 59.820 55.0 3.98 3.98 37.25 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 3606 1.648116 ACCTGGGCATGCTGAAATTT 58.352 45.000 18.92 0.0 0.00 1.82 R
2218 4291 0.809241 TTTTGCAGCTGGCCGTTTTG 60.809 50.000 17.12 0.0 43.89 2.44 R
3557 5654 0.824759 GTATGAGGGTTGAGGAGCGT 59.175 55.000 0.00 0.0 0.00 5.07 R
4441 6543 1.003839 GTCACCGACCCATGCTCAA 60.004 57.895 0.00 0.0 0.00 3.02 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
31 32 4.727235 GTAGCATACGGTTTGATTAGCC 57.273 45.455 2.63 0.00 0.00 3.93
37 38 1.006832 CGGTTTGATTAGCCGTCAGG 58.993 55.000 0.00 0.00 40.53 3.86
38 39 1.674817 CGGTTTGATTAGCCGTCAGGT 60.675 52.381 0.00 0.00 40.53 4.00
39 40 1.737793 GGTTTGATTAGCCGTCAGGTG 59.262 52.381 0.00 0.00 40.50 4.00
40 41 2.614481 GGTTTGATTAGCCGTCAGGTGA 60.614 50.000 0.00 0.00 40.50 4.02
41 42 2.672961 TTGATTAGCCGTCAGGTGAG 57.327 50.000 0.00 0.00 40.50 3.51
42 43 1.557099 TGATTAGCCGTCAGGTGAGT 58.443 50.000 0.00 0.00 40.50 3.41
43 44 1.204704 TGATTAGCCGTCAGGTGAGTG 59.795 52.381 0.00 0.00 40.50 3.51
44 45 1.204941 GATTAGCCGTCAGGTGAGTGT 59.795 52.381 0.00 0.00 40.50 3.55
45 46 0.601558 TTAGCCGTCAGGTGAGTGTC 59.398 55.000 0.00 0.00 40.50 3.67
46 47 1.583495 TAGCCGTCAGGTGAGTGTCG 61.583 60.000 0.00 0.00 40.50 4.35
47 48 3.039988 CCGTCAGGTGAGTGTCGT 58.960 61.111 0.00 0.00 0.00 4.34
48 49 1.081376 CCGTCAGGTGAGTGTCGTC 60.081 63.158 0.00 0.00 0.00 4.20
49 50 1.081376 CGTCAGGTGAGTGTCGTCC 60.081 63.158 0.00 0.00 0.00 4.79
50 51 1.792118 CGTCAGGTGAGTGTCGTCCA 61.792 60.000 0.00 0.00 0.00 4.02
51 52 0.039074 GTCAGGTGAGTGTCGTCCAG 60.039 60.000 0.00 0.00 0.00 3.86
52 53 1.373497 CAGGTGAGTGTCGTCCAGC 60.373 63.158 0.00 0.00 0.00 4.85
53 54 2.048127 GGTGAGTGTCGTCCAGCC 60.048 66.667 0.00 0.00 0.00 4.85
54 55 2.430921 GTGAGTGTCGTCCAGCCG 60.431 66.667 0.00 0.00 0.00 5.52
55 56 2.596338 TGAGTGTCGTCCAGCCGA 60.596 61.111 0.00 0.00 33.79 5.54
56 57 2.197605 TGAGTGTCGTCCAGCCGAA 61.198 57.895 0.00 0.00 38.80 4.30
57 58 1.733399 GAGTGTCGTCCAGCCGAAC 60.733 63.158 0.00 0.00 38.80 3.95
58 59 2.028484 GTGTCGTCCAGCCGAACA 59.972 61.111 0.00 0.00 38.80 3.18
59 60 1.374252 GTGTCGTCCAGCCGAACAT 60.374 57.895 0.00 0.00 38.80 2.71
60 61 1.080093 TGTCGTCCAGCCGAACATC 60.080 57.895 0.00 0.00 38.80 3.06
61 62 2.158959 GTCGTCCAGCCGAACATCG 61.159 63.158 0.00 0.00 38.80 3.84
62 63 2.126071 CGTCCAGCCGAACATCGT 60.126 61.111 0.00 0.00 38.40 3.73
63 64 2.158959 CGTCCAGCCGAACATCGTC 61.159 63.158 0.00 0.00 38.40 4.20
64 65 1.810030 GTCCAGCCGAACATCGTCC 60.810 63.158 0.00 0.00 38.40 4.79
65 66 2.885644 CCAGCCGAACATCGTCCG 60.886 66.667 0.00 0.00 38.40 4.79
66 67 2.126071 CAGCCGAACATCGTCCGT 60.126 61.111 0.00 0.00 38.40 4.69
67 68 2.126071 AGCCGAACATCGTCCGTG 60.126 61.111 0.00 0.00 38.40 4.94
68 69 2.126228 GCCGAACATCGTCCGTGA 60.126 61.111 0.00 0.00 38.40 4.35
69 70 1.735198 GCCGAACATCGTCCGTGAA 60.735 57.895 0.00 0.00 38.40 3.18
70 71 1.683790 GCCGAACATCGTCCGTGAAG 61.684 60.000 0.00 0.00 38.40 3.02
71 72 0.388134 CCGAACATCGTCCGTGAAGT 60.388 55.000 0.00 0.00 38.40 3.01
72 73 1.135603 CCGAACATCGTCCGTGAAGTA 60.136 52.381 0.00 0.00 38.40 2.24
73 74 2.479049 CCGAACATCGTCCGTGAAGTAT 60.479 50.000 0.00 0.00 38.40 2.12
74 75 3.176708 CGAACATCGTCCGTGAAGTATT 58.823 45.455 0.00 0.00 34.72 1.89
75 76 3.611113 CGAACATCGTCCGTGAAGTATTT 59.389 43.478 0.00 0.00 34.72 1.40
76 77 4.259292 CGAACATCGTCCGTGAAGTATTTC 60.259 45.833 0.00 0.00 34.72 2.17
77 78 3.518590 ACATCGTCCGTGAAGTATTTCC 58.481 45.455 0.00 0.00 32.09 3.13
78 79 2.267188 TCGTCCGTGAAGTATTTCCG 57.733 50.000 0.00 0.00 32.09 4.30
135 2114 0.974010 GGTGGATGAGTCACCGGGTA 60.974 60.000 6.32 0.00 44.16 3.69
153 2132 5.359009 CCGGGTAGTCTAGTCAATAAACTCA 59.641 44.000 0.00 0.00 0.00 3.41
219 2215 1.067295 AGGACATCAAGTTCCAGCCA 58.933 50.000 0.00 0.00 0.00 4.75
232 2228 1.339610 TCCAGCCAAAAATGTGGTTCG 59.660 47.619 0.00 0.00 41.12 3.95
253 2249 3.370978 CGCCAAACATGAAGTGGTAGTAG 59.629 47.826 0.00 0.00 34.71 2.57
254 2250 4.324267 GCCAAACATGAAGTGGTAGTAGT 58.676 43.478 0.00 0.00 34.71 2.73
255 2251 5.484715 GCCAAACATGAAGTGGTAGTAGTA 58.515 41.667 0.00 0.00 34.71 1.82
278 2274 1.888512 TCATTGAGAGGCCAACTTTGC 59.111 47.619 5.01 0.00 0.00 3.68
289 2285 1.269206 CCAACTTTGCAGCACGTGAAT 60.269 47.619 22.23 3.35 0.00 2.57
297 2293 1.044725 CAGCACGTGAATTTGCGAAC 58.955 50.000 22.23 0.00 43.87 3.95
300 2296 1.643810 GCACGTGAATTTGCGAACATC 59.356 47.619 22.23 0.00 0.00 3.06
326 2322 7.755373 CGGTAGTATGTGTATGGTGAATGATAG 59.245 40.741 0.00 0.00 0.00 2.08
327 2323 8.585881 GGTAGTATGTGTATGGTGAATGATAGT 58.414 37.037 0.00 0.00 0.00 2.12
407 2408 7.652300 TGCACAAGGAGCGTTAATATATAAG 57.348 36.000 0.00 0.00 33.85 1.73
520 2526 2.280628 AGGATAGTTTAGCGTTGCTGC 58.719 47.619 0.70 0.00 40.10 5.25
542 2559 3.181476 CCAAAGAGGACAACCAACAAAGG 60.181 47.826 0.00 0.00 41.22 3.11
569 2586 7.112779 ACCTTACCAAAATCTGATCTACCAAG 58.887 38.462 0.00 0.00 0.00 3.61
571 2588 3.941483 ACCAAAATCTGATCTACCAAGCG 59.059 43.478 0.00 0.00 0.00 4.68
598 2616 9.520515 AGATATTCCAAATTCAACCGCTATTAT 57.479 29.630 0.00 0.00 0.00 1.28
605 2623 9.912634 CCAAATTCAACCGCTATTATCATATTT 57.087 29.630 0.00 0.00 0.00 1.40
612 2630 4.870426 CCGCTATTATCATATTTGGCGAGT 59.130 41.667 0.00 0.00 43.25 4.18
613 2631 5.351465 CCGCTATTATCATATTTGGCGAGTT 59.649 40.000 0.00 0.00 43.25 3.01
615 2633 7.298122 CGCTATTATCATATTTGGCGAGTTTT 58.702 34.615 0.00 0.00 43.25 2.43
621 2639 5.698832 TCATATTTGGCGAGTTTTGTCTTG 58.301 37.500 0.00 0.00 0.00 3.02
637 2657 3.826157 TGTCTTGCCAAAACCAATAGAGG 59.174 43.478 0.00 0.00 0.00 3.69
660 2680 3.231965 CGATACTATTACCCGCTCAACG 58.768 50.000 0.00 0.00 43.15 4.10
661 2681 2.497107 TACTATTACCCGCTCAACGC 57.503 50.000 0.00 0.00 41.76 4.84
662 2682 0.822164 ACTATTACCCGCTCAACGCT 59.178 50.000 0.00 0.00 41.76 5.07
663 2683 1.202382 ACTATTACCCGCTCAACGCTC 60.202 52.381 0.00 0.00 41.76 5.03
664 2684 0.248743 TATTACCCGCTCAACGCTCG 60.249 55.000 0.00 0.00 41.76 5.03
665 2685 2.221906 ATTACCCGCTCAACGCTCGT 62.222 55.000 0.00 0.00 41.76 4.18
666 2686 3.620300 TACCCGCTCAACGCTCGTG 62.620 63.158 0.00 0.00 41.76 4.35
668 2688 3.470567 CCGCTCAACGCTCGTGTC 61.471 66.667 0.00 0.00 41.76 3.67
669 2689 3.470567 CGCTCAACGCTCGTGTCC 61.471 66.667 0.00 0.00 36.13 4.02
670 2690 3.470567 GCTCAACGCTCGTGTCCG 61.471 66.667 0.00 0.00 35.14 4.79
671 2691 2.050351 CTCAACGCTCGTGTCCGT 60.050 61.111 0.00 0.00 39.70 4.69
673 2693 0.386352 CTCAACGCTCGTGTCCGTTA 60.386 55.000 0.00 0.00 44.83 3.18
674 2694 0.241749 TCAACGCTCGTGTCCGTTAT 59.758 50.000 0.00 0.00 44.83 1.89
675 2695 0.638746 CAACGCTCGTGTCCGTTATC 59.361 55.000 0.00 0.00 44.83 1.75
676 2696 0.457337 AACGCTCGTGTCCGTTATCC 60.457 55.000 0.00 0.00 44.79 2.59
677 2697 1.937846 CGCTCGTGTCCGTTATCCG 60.938 63.158 0.00 0.00 35.01 4.18
678 2698 2.228914 GCTCGTGTCCGTTATCCGC 61.229 63.158 0.00 0.00 35.01 5.54
679 2699 1.138036 CTCGTGTCCGTTATCCGCA 59.862 57.895 0.00 0.00 35.01 5.69
680 2700 0.457166 CTCGTGTCCGTTATCCGCAA 60.457 55.000 0.00 0.00 35.01 4.85
681 2701 0.733566 TCGTGTCCGTTATCCGCAAC 60.734 55.000 0.00 0.00 35.01 4.17
682 2702 1.009903 CGTGTCCGTTATCCGCAACA 61.010 55.000 0.00 0.00 34.38 3.33
683 2703 1.149987 GTGTCCGTTATCCGCAACAA 58.850 50.000 0.00 0.00 34.08 2.83
684 2704 1.532007 GTGTCCGTTATCCGCAACAAA 59.468 47.619 0.00 0.00 34.08 2.83
685 2705 2.031857 GTGTCCGTTATCCGCAACAAAA 60.032 45.455 0.00 0.00 34.08 2.44
686 2706 2.617308 TGTCCGTTATCCGCAACAAAAA 59.383 40.909 0.00 0.00 34.38 1.94
702 2722 4.113681 AAAAACGCTCGTGTCCGT 57.886 50.000 0.00 0.00 39.70 4.69
704 2724 1.569708 AAAAACGCTCGTGTCCGTTA 58.430 45.000 0.00 0.00 45.75 3.18
705 2725 1.787012 AAAACGCTCGTGTCCGTTAT 58.213 45.000 0.00 0.00 45.75 1.89
706 2726 1.343506 AAACGCTCGTGTCCGTTATC 58.656 50.000 0.00 0.00 45.75 1.75
707 2727 0.457337 AACGCTCGTGTCCGTTATCC 60.457 55.000 0.00 0.00 44.79 2.59
708 2728 1.937846 CGCTCGTGTCCGTTATCCG 60.938 63.158 0.00 0.00 35.01 4.18
709 2729 2.228914 GCTCGTGTCCGTTATCCGC 61.229 63.158 0.00 0.00 35.01 5.54
710 2730 1.138036 CTCGTGTCCGTTATCCGCA 59.862 57.895 0.00 0.00 35.01 5.69
711 2731 0.457166 CTCGTGTCCGTTATCCGCAA 60.457 55.000 0.00 0.00 35.01 4.85
712 2732 0.733566 TCGTGTCCGTTATCCGCAAC 60.734 55.000 0.00 0.00 35.01 4.17
713 2733 1.009903 CGTGTCCGTTATCCGCAACA 61.010 55.000 0.00 0.00 34.38 3.33
714 2734 1.149987 GTGTCCGTTATCCGCAACAA 58.850 50.000 0.00 0.00 34.08 2.83
715 2735 1.532007 GTGTCCGTTATCCGCAACAAA 59.468 47.619 0.00 0.00 34.08 2.83
716 2736 2.031857 GTGTCCGTTATCCGCAACAAAA 60.032 45.455 0.00 0.00 34.08 2.44
717 2737 2.617308 TGTCCGTTATCCGCAACAAAAA 59.383 40.909 0.00 0.00 34.38 1.94
763 2783 1.472480 CAACCCGATAACAAGCCCAAG 59.528 52.381 0.00 0.00 0.00 3.61
820 2844 4.100963 AGTTTTCCAGAAAATTCCCGCTTT 59.899 37.500 8.68 0.00 41.64 3.51
850 2874 4.715523 CCCTCTTTTCCCGCGGCA 62.716 66.667 22.85 0.00 0.00 5.69
902 2927 3.762247 CCGAGGGGCGAAACCGTA 61.762 66.667 0.00 0.00 44.57 4.02
921 2946 1.873270 AAATTCCCCGCGAGCCAAAC 61.873 55.000 8.23 0.00 0.00 2.93
928 2953 2.263540 GCGAGCCAAACCGACCTA 59.736 61.111 0.00 0.00 0.00 3.08
929 2954 2.098831 GCGAGCCAAACCGACCTAC 61.099 63.158 0.00 0.00 0.00 3.18
930 2955 1.290955 CGAGCCAAACCGACCTACA 59.709 57.895 0.00 0.00 0.00 2.74
931 2956 0.736325 CGAGCCAAACCGACCTACAG 60.736 60.000 0.00 0.00 0.00 2.74
932 2957 0.391263 GAGCCAAACCGACCTACAGG 60.391 60.000 0.00 0.00 42.17 4.00
1071 3098 1.272480 CCGAAAATCCCCCAAAGTCCT 60.272 52.381 0.00 0.00 0.00 3.85
1099 3126 3.666253 GACCCAACCGCCGGTTTG 61.666 66.667 20.83 16.42 44.33 2.93
1136 3163 4.708968 CGGATCTAGCCGCCTCGC 62.709 72.222 0.00 0.00 45.38 5.03
1579 3606 1.371267 GCGTGCTCGAGTGTGTGTA 60.371 57.895 15.13 0.00 39.71 2.90
1580 3607 0.937699 GCGTGCTCGAGTGTGTGTAA 60.938 55.000 15.13 0.00 39.71 2.41
1606 3634 1.961180 GCATGCCCAGGTAGTCGTCT 61.961 60.000 6.36 0.00 0.00 4.18
1610 3638 3.617368 CCAGGTAGTCGTCTGGGG 58.383 66.667 0.00 0.00 44.99 4.96
1656 3684 5.022282 AGGTGGGAATTTCTTGTTTTGTG 57.978 39.130 0.00 0.00 0.00 3.33
1664 3692 8.027189 GGGAATTTCTTGTTTTGTGTATAGGTC 58.973 37.037 0.00 0.00 0.00 3.85
1685 3713 8.079211 AGGTCTTTGTGTCAGCTATAGATTTA 57.921 34.615 3.21 0.00 0.00 1.40
1691 3719 7.603180 TGTGTCAGCTATAGATTTATCTGGT 57.397 36.000 3.21 0.00 37.76 4.00
1692 3720 8.023021 TGTGTCAGCTATAGATTTATCTGGTT 57.977 34.615 3.21 0.00 37.76 3.67
1761 3797 5.067283 GGGATGCTGTAAAATCCGTGTAAAT 59.933 40.000 0.00 0.00 42.90 1.40
1762 3798 6.405397 GGGATGCTGTAAAATCCGTGTAAATT 60.405 38.462 0.00 0.00 42.90 1.82
1770 3806 6.515272 AAAATCCGTGTAAATTCATGCTCT 57.485 33.333 0.00 0.00 0.00 4.09
1790 3826 8.654230 TGCTCTCATGAATTAGATTTGACTAC 57.346 34.615 0.00 0.00 0.00 2.73
1844 3881 9.460906 GCATTATCCATTTTTCTTGAATCTCTC 57.539 33.333 0.00 0.00 0.00 3.20
1897 3935 4.653555 CCAACGGCAAAAAGGAGC 57.346 55.556 0.00 0.00 0.00 4.70
1899 3937 0.103937 CCAACGGCAAAAAGGAGCAA 59.896 50.000 0.00 0.00 0.00 3.91
2076 4149 2.678336 CGGGAACTTAAAGCCACATCTC 59.322 50.000 0.00 0.00 0.00 2.75
2121 4194 5.647658 TGACCATGACTGTTGAATTACATCC 59.352 40.000 0.00 0.00 0.00 3.51
2218 4291 7.752695 AGTTTCACTTCATAATTCGGAATGAC 58.247 34.615 3.59 0.00 31.99 3.06
2223 4296 8.020819 TCACTTCATAATTCGGAATGACAAAAC 58.979 33.333 3.59 0.00 31.99 2.43
2357 4430 7.208777 TCACTGCAAACAAATGTGACAATAAT 58.791 30.769 0.00 0.00 33.45 1.28
2359 4432 9.142515 CACTGCAAACAAATGTGACAATAATAT 57.857 29.630 0.00 0.00 0.00 1.28
2361 4434 9.356433 CTGCAAACAAATGTGACAATAATATCA 57.644 29.630 0.00 0.00 0.00 2.15
2362 4435 9.872721 TGCAAACAAATGTGACAATAATATCAT 57.127 25.926 0.00 0.00 0.00 2.45
2384 4457 4.213564 TGGAAAAATGGTTGCAACACTT 57.786 36.364 29.55 18.85 0.00 3.16
2483 4580 0.180171 TCTGCGTTACCCCATGATGG 59.820 55.000 3.98 3.98 37.25 3.51
2532 4629 2.243957 CGATCCGCGGCATTTGCTA 61.244 57.895 23.51 0.00 41.70 3.49
2676 4773 6.127026 ACCTAAGAGTCAGGTATAAAAGGCAG 60.127 42.308 0.26 0.00 44.77 4.85
2816 4913 5.272283 AGAAGTTTGAAGTTGACTACCGA 57.728 39.130 0.00 0.00 0.00 4.69
2852 4949 1.523758 CCACTGGCTGTTCTTGGTAC 58.476 55.000 0.00 0.00 0.00 3.34
2873 4970 1.632589 GGCAGTGGGGATTCAAACTT 58.367 50.000 0.00 0.00 0.00 2.66
2920 5017 1.953686 TGAAACCTACAGCAAAGCCAC 59.046 47.619 0.00 0.00 0.00 5.01
2939 5036 3.578716 CCACTGAAAACCTCTCCTCAGTA 59.421 47.826 3.43 0.00 45.15 2.74
2962 5059 1.273886 ACTCTCTCACTTCTTTCCGCC 59.726 52.381 0.00 0.00 0.00 6.13
3002 5099 2.093890 CAACTGCAGGATACCATTGCA 58.906 47.619 19.93 0.00 44.81 4.08
3035 5132 1.004560 CTCAAAGCGCCCTCTCACA 60.005 57.895 2.29 0.00 0.00 3.58
3045 5142 1.066430 GCCCTCTCACAACATTCCGTA 60.066 52.381 0.00 0.00 0.00 4.02
3377 5474 7.671302 ACAGTGAGACAAACACAATAGAGTAT 58.329 34.615 0.00 0.00 40.25 2.12
3493 5590 2.919229 GCTCACAAATGAAATCTTGCCG 59.081 45.455 0.00 0.00 33.30 5.69
3557 5654 6.239036 CCGTGACATCAAGTTCCTCTATGATA 60.239 42.308 0.00 0.00 31.59 2.15
3688 5785 9.565090 CATTATGACATGGAAGAGGATTTCTTA 57.435 33.333 0.00 0.00 46.12 2.10
3901 5998 3.405831 TCTTGATTGTCCAACTGCAGAG 58.594 45.455 23.35 12.34 0.00 3.35
4015 6112 1.688311 CGGATGGAGAGGGGTGTAGAA 60.688 57.143 0.00 0.00 0.00 2.10
4153 6250 1.466167 CAGGTGCCGAAGAGATTTGTG 59.534 52.381 0.00 0.00 0.00 3.33
4391 6491 6.078456 TGAGGTTAATCATTCAGGGTTCAT 57.922 37.500 0.00 0.00 0.00 2.57
4392 6492 5.887598 TGAGGTTAATCATTCAGGGTTCATG 59.112 40.000 0.00 0.00 0.00 3.07
4394 6494 6.676558 AGGTTAATCATTCAGGGTTCATGAT 58.323 36.000 0.00 0.00 38.96 2.45
4396 6496 7.286316 AGGTTAATCATTCAGGGTTCATGATTC 59.714 37.037 9.34 0.00 43.49 2.52
4398 6498 8.636213 GTTAATCATTCAGGGTTCATGATTCAT 58.364 33.333 9.34 0.00 43.49 2.57
4441 6543 6.808321 TTTAGTGTATATTCCAGCAGACCT 57.192 37.500 0.00 0.00 0.00 3.85
4451 6553 1.030488 CAGCAGACCTTGAGCATGGG 61.030 60.000 7.25 0.00 0.00 4.00
4483 6585 1.338020 CTTTGTTCTCTGGCCACCAAC 59.662 52.381 0.00 5.49 30.80 3.77
4531 6633 4.678622 AGCGGAAACTGTTTTAAAACCTG 58.321 39.130 24.55 19.44 38.11 4.00
4536 6638 7.520937 GCGGAAACTGTTTTAAAACCTGAGATA 60.521 37.037 24.55 6.71 38.11 1.98
4565 6892 5.218885 TGTTTGCACAGTTGTATACATTGC 58.781 37.500 6.36 13.00 37.32 3.56
4730 7062 9.926751 CAGTGACTTGACATTAATACATTGATC 57.073 33.333 0.00 0.00 0.00 2.92
4807 7142 7.495934 CAGCAACACTTACTATAGCCTAACAAT 59.504 37.037 0.00 0.00 0.00 2.71
4808 7143 8.047310 AGCAACACTTACTATAGCCTAACAATT 58.953 33.333 0.00 0.00 0.00 2.32
4846 7181 3.973973 TGGATACTGGGGACAATTCCTAG 59.026 47.826 0.00 0.00 42.06 3.02
4849 7184 5.310857 GGATACTGGGGACAATTCCTAGATT 59.689 44.000 2.51 0.00 42.38 2.40
4953 7293 6.436890 AGCTCCACTTATTAGAGTTCTAGGT 58.563 40.000 0.00 0.00 0.00 3.08
4954 7294 7.584532 AGCTCCACTTATTAGAGTTCTAGGTA 58.415 38.462 0.00 0.00 0.00 3.08
4955 7295 8.228905 AGCTCCACTTATTAGAGTTCTAGGTAT 58.771 37.037 0.00 0.00 0.00 2.73
5261 7803 6.655078 ACAAGGCAAGTGAAGAAACAATAT 57.345 33.333 0.00 0.00 0.00 1.28
5306 7849 6.719370 ACAATTGGAGTGTAGCAAATTAAGGA 59.281 34.615 10.83 0.00 0.00 3.36
5330 7873 6.054295 ACAAGCTCAGGATGCTAAATTCTAG 58.946 40.000 0.00 0.00 40.22 2.43
5331 7874 6.126940 ACAAGCTCAGGATGCTAAATTCTAGA 60.127 38.462 0.00 0.00 40.22 2.43
5332 7875 6.491714 AGCTCAGGATGCTAAATTCTAGAA 57.508 37.500 7.82 7.82 39.21 2.10
5333 7876 6.893583 AGCTCAGGATGCTAAATTCTAGAAA 58.106 36.000 9.71 0.00 39.21 2.52
5334 7877 6.765512 AGCTCAGGATGCTAAATTCTAGAAAC 59.234 38.462 9.71 0.00 39.21 2.78
5335 7878 6.017523 GCTCAGGATGCTAAATTCTAGAAACC 60.018 42.308 9.71 3.81 34.76 3.27
5336 7879 6.957631 TCAGGATGCTAAATTCTAGAAACCA 58.042 36.000 9.71 3.18 34.76 3.67
5337 7880 7.402054 TCAGGATGCTAAATTCTAGAAACCAA 58.598 34.615 9.71 0.00 34.76 3.67
5338 7881 7.888021 TCAGGATGCTAAATTCTAGAAACCAAA 59.112 33.333 9.71 0.00 34.76 3.28
5339 7882 8.522830 CAGGATGCTAAATTCTAGAAACCAAAA 58.477 33.333 9.71 0.00 0.00 2.44
5340 7883 8.523658 AGGATGCTAAATTCTAGAAACCAAAAC 58.476 33.333 9.71 0.00 0.00 2.43
5341 7884 8.523658 GGATGCTAAATTCTAGAAACCAAAACT 58.476 33.333 9.71 0.00 0.00 2.66
5342 7885 9.561270 GATGCTAAATTCTAGAAACCAAAACTC 57.439 33.333 9.71 0.00 0.00 3.01
5343 7886 8.691661 TGCTAAATTCTAGAAACCAAAACTCT 57.308 30.769 9.71 0.00 0.00 3.24
5344 7887 8.784043 TGCTAAATTCTAGAAACCAAAACTCTC 58.216 33.333 9.71 0.00 0.00 3.20
5345 7888 7.958025 GCTAAATTCTAGAAACCAAAACTCTCG 59.042 37.037 9.71 0.00 0.00 4.04
5346 7889 5.864628 ATTCTAGAAACCAAAACTCTCGC 57.135 39.130 9.71 0.00 0.00 5.03
5347 7890 3.660865 TCTAGAAACCAAAACTCTCGCC 58.339 45.455 0.00 0.00 0.00 5.54
5348 7891 1.605753 AGAAACCAAAACTCTCGCCC 58.394 50.000 0.00 0.00 0.00 6.13
5349 7892 1.143073 AGAAACCAAAACTCTCGCCCT 59.857 47.619 0.00 0.00 0.00 5.19
5350 7893 1.954382 GAAACCAAAACTCTCGCCCTT 59.046 47.619 0.00 0.00 0.00 3.95
5351 7894 1.605753 AACCAAAACTCTCGCCCTTC 58.394 50.000 0.00 0.00 0.00 3.46
5352 7895 0.250770 ACCAAAACTCTCGCCCTTCC 60.251 55.000 0.00 0.00 0.00 3.46
5353 7896 0.960861 CCAAAACTCTCGCCCTTCCC 60.961 60.000 0.00 0.00 0.00 3.97
5354 7897 0.250727 CAAAACTCTCGCCCTTCCCA 60.251 55.000 0.00 0.00 0.00 4.37
5355 7898 0.476771 AAAACTCTCGCCCTTCCCAA 59.523 50.000 0.00 0.00 0.00 4.12
5356 7899 0.476771 AAACTCTCGCCCTTCCCAAA 59.523 50.000 0.00 0.00 0.00 3.28
5357 7900 0.698818 AACTCTCGCCCTTCCCAAAT 59.301 50.000 0.00 0.00 0.00 2.32
5358 7901 0.698818 ACTCTCGCCCTTCCCAAATT 59.301 50.000 0.00 0.00 0.00 1.82
5359 7902 1.913419 ACTCTCGCCCTTCCCAAATTA 59.087 47.619 0.00 0.00 0.00 1.40
5360 7903 2.307686 ACTCTCGCCCTTCCCAAATTAA 59.692 45.455 0.00 0.00 0.00 1.40
5361 7904 3.053619 ACTCTCGCCCTTCCCAAATTAAT 60.054 43.478 0.00 0.00 0.00 1.40
5362 7905 3.954258 CTCTCGCCCTTCCCAAATTAATT 59.046 43.478 0.00 0.00 0.00 1.40
5363 7906 3.699038 TCTCGCCCTTCCCAAATTAATTG 59.301 43.478 0.39 0.00 38.84 2.32
5364 7907 3.699038 CTCGCCCTTCCCAAATTAATTGA 59.301 43.478 0.39 0.00 41.85 2.57
5365 7908 4.090090 TCGCCCTTCCCAAATTAATTGAA 58.910 39.130 0.39 0.76 41.85 2.69
5366 7909 4.159506 TCGCCCTTCCCAAATTAATTGAAG 59.840 41.667 15.13 15.13 41.85 3.02
5367 7910 4.081697 CGCCCTTCCCAAATTAATTGAAGT 60.082 41.667 18.32 0.00 41.85 3.01
5368 7911 5.568624 CGCCCTTCCCAAATTAATTGAAGTT 60.569 40.000 18.32 0.00 41.85 2.66
5369 7912 5.874810 GCCCTTCCCAAATTAATTGAAGTTC 59.125 40.000 18.32 0.00 41.85 3.01
5370 7913 6.295859 GCCCTTCCCAAATTAATTGAAGTTCT 60.296 38.462 18.32 0.00 41.85 3.01
5371 7914 7.093509 GCCCTTCCCAAATTAATTGAAGTTCTA 60.094 37.037 18.32 0.00 41.85 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.183775 CGGCTAATCAAACCGTATGCTAC 59.816 47.826 0.00 0.00 42.01 3.58
11 12 3.386486 CGGCTAATCAAACCGTATGCTA 58.614 45.455 0.00 0.00 42.01 3.49
12 13 2.210116 CGGCTAATCAAACCGTATGCT 58.790 47.619 0.00 0.00 42.01 3.79
13 14 2.663279 CGGCTAATCAAACCGTATGC 57.337 50.000 0.00 0.00 42.01 3.14
19 20 1.737793 CACCTGACGGCTAATCAAACC 59.262 52.381 0.00 0.00 0.00 3.27
20 21 2.673368 CTCACCTGACGGCTAATCAAAC 59.327 50.000 0.00 0.00 0.00 2.93
21 22 2.301870 ACTCACCTGACGGCTAATCAAA 59.698 45.455 0.00 0.00 0.00 2.69
22 23 1.899814 ACTCACCTGACGGCTAATCAA 59.100 47.619 0.00 0.00 0.00 2.57
23 24 1.204704 CACTCACCTGACGGCTAATCA 59.795 52.381 0.00 0.00 0.00 2.57
24 25 1.204941 ACACTCACCTGACGGCTAATC 59.795 52.381 0.00 0.00 0.00 1.75
25 26 1.204941 GACACTCACCTGACGGCTAAT 59.795 52.381 0.00 0.00 0.00 1.73
26 27 0.601558 GACACTCACCTGACGGCTAA 59.398 55.000 0.00 0.00 0.00 3.09
27 28 1.583495 CGACACTCACCTGACGGCTA 61.583 60.000 0.00 0.00 0.00 3.93
28 29 2.920645 CGACACTCACCTGACGGCT 61.921 63.158 0.00 0.00 0.00 5.52
29 30 2.430921 CGACACTCACCTGACGGC 60.431 66.667 0.00 0.00 0.00 5.68
30 31 1.081376 GACGACACTCACCTGACGG 60.081 63.158 0.00 0.00 34.26 4.79
31 32 1.081376 GGACGACACTCACCTGACG 60.081 63.158 0.00 0.00 35.77 4.35
32 33 0.039074 CTGGACGACACTCACCTGAC 60.039 60.000 0.00 0.00 0.00 3.51
33 34 1.806461 GCTGGACGACACTCACCTGA 61.806 60.000 0.00 0.00 0.00 3.86
34 35 1.373497 GCTGGACGACACTCACCTG 60.373 63.158 0.00 0.00 0.00 4.00
35 36 2.574955 GGCTGGACGACACTCACCT 61.575 63.158 0.00 0.00 0.00 4.00
36 37 2.048127 GGCTGGACGACACTCACC 60.048 66.667 0.00 0.00 0.00 4.02
37 38 2.416244 TTCGGCTGGACGACACTCAC 62.416 60.000 0.00 0.00 43.37 3.51
38 39 2.197605 TTCGGCTGGACGACACTCA 61.198 57.895 0.00 0.00 43.37 3.41
39 40 1.733399 GTTCGGCTGGACGACACTC 60.733 63.158 0.00 0.00 43.37 3.51
40 41 1.816863 ATGTTCGGCTGGACGACACT 61.817 55.000 0.00 0.00 43.37 3.55
41 42 1.352156 GATGTTCGGCTGGACGACAC 61.352 60.000 0.00 1.58 43.37 3.67
42 43 1.080093 GATGTTCGGCTGGACGACA 60.080 57.895 0.00 1.02 43.37 4.35
43 44 2.158959 CGATGTTCGGCTGGACGAC 61.159 63.158 0.00 0.00 43.37 4.34
44 45 2.180769 CGATGTTCGGCTGGACGA 59.819 61.111 0.00 0.00 41.76 4.20
45 46 2.126071 ACGATGTTCGGCTGGACG 60.126 61.111 0.00 0.00 45.59 4.79
46 47 3.782042 GACGATGTTCGGCTGGAC 58.218 61.111 0.00 0.00 46.20 4.02
52 53 0.388134 ACTTCACGGACGATGTTCGG 60.388 55.000 2.37 0.00 45.59 4.30
53 54 2.251869 TACTTCACGGACGATGTTCG 57.748 50.000 0.00 0.00 46.93 3.95
54 55 4.032558 GGAAATACTTCACGGACGATGTTC 59.967 45.833 0.00 0.00 32.75 3.18
55 56 3.930848 GGAAATACTTCACGGACGATGTT 59.069 43.478 0.00 0.00 32.75 2.71
56 57 3.518590 GGAAATACTTCACGGACGATGT 58.481 45.455 0.00 0.00 32.75 3.06
57 58 2.534349 CGGAAATACTTCACGGACGATG 59.466 50.000 0.00 0.00 32.75 3.84
58 59 2.424601 TCGGAAATACTTCACGGACGAT 59.575 45.455 0.00 0.00 32.75 3.73
59 60 1.811965 TCGGAAATACTTCACGGACGA 59.188 47.619 0.00 0.00 32.75 4.20
60 61 1.916000 GTCGGAAATACTTCACGGACG 59.084 52.381 0.00 0.00 32.75 4.79
61 62 3.227810 AGTCGGAAATACTTCACGGAC 57.772 47.619 0.00 0.00 32.75 4.79
62 63 4.012374 ACTAGTCGGAAATACTTCACGGA 58.988 43.478 0.00 0.00 32.75 4.69
63 64 4.103357 CACTAGTCGGAAATACTTCACGG 58.897 47.826 0.00 0.00 32.75 4.94
64 65 4.978186 TCACTAGTCGGAAATACTTCACG 58.022 43.478 0.00 0.00 32.75 4.35
65 66 7.705214 ACTATCACTAGTCGGAAATACTTCAC 58.295 38.462 0.00 0.00 32.56 3.18
66 67 7.876936 ACTATCACTAGTCGGAAATACTTCA 57.123 36.000 0.00 0.00 32.56 3.02
70 71 9.962783 ACAATAACTATCACTAGTCGGAAATAC 57.037 33.333 0.00 0.00 37.20 1.89
122 2101 1.632409 ACTAGACTACCCGGTGACTCA 59.368 52.381 0.00 0.00 0.00 3.41
135 2114 9.965902 ATTTTCCATGAGTTTATTGACTAGACT 57.034 29.630 0.00 0.00 0.00 3.24
190 2169 5.296283 GGAACTTGATGTCCTTGATGATGAG 59.704 44.000 0.00 0.00 0.00 2.90
191 2170 5.188434 GGAACTTGATGTCCTTGATGATGA 58.812 41.667 0.00 0.00 0.00 2.92
232 2228 4.324267 ACTACTACCACTTCATGTTTGGC 58.676 43.478 9.15 0.00 33.25 4.52
253 2249 3.878778 AGTTGGCCTCTCAATGACATAC 58.121 45.455 3.32 0.00 0.00 2.39
254 2250 4.574674 AAGTTGGCCTCTCAATGACATA 57.425 40.909 3.32 0.00 0.00 2.29
255 2251 3.446442 AAGTTGGCCTCTCAATGACAT 57.554 42.857 3.32 0.00 0.00 3.06
278 2274 1.044725 GTTCGCAAATTCACGTGCTG 58.955 50.000 11.67 6.54 38.66 4.41
289 2285 3.615056 CACATACTACCGATGTTCGCAAA 59.385 43.478 0.00 0.00 38.82 3.68
297 2293 5.447624 TCACCATACACATACTACCGATG 57.552 43.478 0.00 0.00 0.00 3.84
300 2296 5.838529 TCATTCACCATACACATACTACCG 58.161 41.667 0.00 0.00 0.00 4.02
466 2470 2.066262 CGGTGCTACCTTAGTTGTGTG 58.934 52.381 4.21 0.00 35.66 3.82
520 2526 3.181476 CCTTTGTTGGTTGTCCTCTTTGG 60.181 47.826 0.00 0.00 34.23 3.28
542 2559 7.110155 TGGTAGATCAGATTTTGGTAAGGTTC 58.890 38.462 0.00 0.00 0.00 3.62
569 2586 4.527564 CGGTTGAATTTGGAATATCTCGC 58.472 43.478 0.00 0.00 0.00 5.03
571 2588 5.757850 AGCGGTTGAATTTGGAATATCTC 57.242 39.130 0.00 0.00 0.00 2.75
598 2616 5.698832 CAAGACAAAACTCGCCAAATATGA 58.301 37.500 0.00 0.00 0.00 2.15
605 2623 0.749818 TGGCAAGACAAAACTCGCCA 60.750 50.000 0.00 0.00 46.00 5.69
612 2630 6.227298 TCTATTGGTTTTGGCAAGACAAAA 57.773 33.333 20.74 9.64 45.20 2.44
613 2631 5.221422 CCTCTATTGGTTTTGGCAAGACAAA 60.221 40.000 20.74 16.77 38.48 2.83
615 2633 3.826157 CCTCTATTGGTTTTGGCAAGACA 59.174 43.478 20.74 9.42 0.00 3.41
621 2639 0.455815 CGGCCTCTATTGGTTTTGGC 59.544 55.000 0.00 0.00 39.61 4.52
637 2657 1.542915 TGAGCGGGTAATAGTATCGGC 59.457 52.381 4.98 4.98 37.03 5.54
660 2680 2.228914 GCGGATAACGGACACGAGC 61.229 63.158 0.00 0.00 44.60 5.03
661 2681 0.457166 TTGCGGATAACGGACACGAG 60.457 55.000 0.00 0.00 44.72 4.18
662 2682 0.733566 GTTGCGGATAACGGACACGA 60.734 55.000 0.00 0.00 44.72 4.35
663 2683 1.009903 TGTTGCGGATAACGGACACG 61.010 55.000 0.00 0.00 44.72 4.49
664 2684 1.149987 TTGTTGCGGATAACGGACAC 58.850 50.000 0.00 0.00 44.72 3.67
665 2685 1.880271 TTTGTTGCGGATAACGGACA 58.120 45.000 0.00 0.00 44.72 4.02
666 2686 2.973419 TTTTGTTGCGGATAACGGAC 57.027 45.000 0.00 0.00 44.72 4.79
685 2705 1.569708 TAACGGACACGAGCGTTTTT 58.430 45.000 0.00 0.00 44.60 1.94
686 2706 1.723003 GATAACGGACACGAGCGTTTT 59.277 47.619 0.00 0.00 44.60 2.43
687 2707 1.343506 GATAACGGACACGAGCGTTT 58.656 50.000 0.00 0.00 44.60 3.60
688 2708 0.457337 GGATAACGGACACGAGCGTT 60.457 55.000 0.00 0.00 44.60 4.84
689 2709 1.138247 GGATAACGGACACGAGCGT 59.862 57.895 0.00 0.00 44.60 5.07
690 2710 1.937846 CGGATAACGGACACGAGCG 60.938 63.158 0.00 0.00 44.60 5.03
691 2711 2.228914 GCGGATAACGGACACGAGC 61.229 63.158 0.00 0.00 44.60 5.03
692 2712 0.457166 TTGCGGATAACGGACACGAG 60.457 55.000 0.00 0.00 44.72 4.18
693 2713 0.733566 GTTGCGGATAACGGACACGA 60.734 55.000 0.00 0.00 44.72 4.35
694 2714 1.009903 TGTTGCGGATAACGGACACG 61.010 55.000 0.00 0.00 44.72 4.49
695 2715 1.149987 TTGTTGCGGATAACGGACAC 58.850 50.000 0.00 0.00 44.72 3.67
696 2716 1.880271 TTTGTTGCGGATAACGGACA 58.120 45.000 0.00 0.00 44.72 4.02
697 2717 2.973419 TTTTGTTGCGGATAACGGAC 57.027 45.000 0.00 0.00 44.72 4.79
716 2736 0.027063 CAACGGACACGAGCGTTTTT 59.973 50.000 0.00 0.00 44.60 1.94
717 2737 1.639534 CAACGGACACGAGCGTTTT 59.360 52.632 0.00 0.00 44.60 2.43
718 2738 2.877974 GCAACGGACACGAGCGTTT 61.878 57.895 0.00 0.00 44.60 3.60
734 2754 2.130821 TTATCGGGTTGGGCTGTGCA 62.131 55.000 0.00 0.00 0.00 4.57
820 2844 3.744940 AAAGAGGGGCTGATTGATTGA 57.255 42.857 0.00 0.00 0.00 2.57
894 2919 0.097499 CGCGGGGAATTTACGGTTTC 59.903 55.000 0.00 0.00 0.00 2.78
902 2927 1.605165 TTTGGCTCGCGGGGAATTT 60.605 52.632 8.71 0.00 0.00 1.82
921 2946 2.017559 GCCTGTAGCCTGTAGGTCGG 62.018 65.000 0.00 0.00 37.57 4.79
923 2948 0.175989 GTGCCTGTAGCCTGTAGGTC 59.824 60.000 0.00 0.00 42.71 3.85
924 2949 0.544357 TGTGCCTGTAGCCTGTAGGT 60.544 55.000 0.00 0.00 42.71 3.08
925 2950 0.176680 CTGTGCCTGTAGCCTGTAGG 59.823 60.000 0.00 0.00 42.71 3.18
927 2952 1.596934 GCTGTGCCTGTAGCCTGTA 59.403 57.895 0.00 0.00 42.71 2.74
928 2953 2.348998 GCTGTGCCTGTAGCCTGT 59.651 61.111 0.00 0.00 42.71 4.00
1071 3098 3.621805 TTGGGTCTGGAAGCGCGA 61.622 61.111 12.10 0.00 0.00 5.87
1099 3126 3.422655 CGATCGGGTTCGGAAAATTTTC 58.577 45.455 20.51 20.51 35.50 2.29
1262 3289 4.504916 CGCAGGTCGAGGAGGCAG 62.505 72.222 0.00 0.00 41.67 4.85
1574 3601 2.896044 TGGGCATGCTGAAATTTACACA 59.104 40.909 18.92 0.00 0.00 3.72
1575 3602 3.514645 CTGGGCATGCTGAAATTTACAC 58.485 45.455 18.92 0.00 0.00 2.90
1579 3606 1.648116 ACCTGGGCATGCTGAAATTT 58.352 45.000 18.92 0.00 0.00 1.82
1580 3607 2.291800 ACTACCTGGGCATGCTGAAATT 60.292 45.455 18.92 0.59 0.00 1.82
1627 3655 6.306643 ACAAGAAATTCCCACCTTTTCAAA 57.693 33.333 0.00 0.00 32.94 2.69
1628 3656 5.948742 ACAAGAAATTCCCACCTTTTCAA 57.051 34.783 0.00 0.00 32.94 2.69
1629 3657 5.948742 AACAAGAAATTCCCACCTTTTCA 57.051 34.783 0.00 0.00 32.94 2.69
1630 3658 6.597672 ACAAAACAAGAAATTCCCACCTTTTC 59.402 34.615 0.00 0.00 0.00 2.29
1631 3659 6.374053 CACAAAACAAGAAATTCCCACCTTTT 59.626 34.615 0.00 0.00 0.00 2.27
1648 3676 6.824196 TGACACAAAGACCTATACACAAAACA 59.176 34.615 0.00 0.00 0.00 2.83
1656 3684 8.167605 TCTATAGCTGACACAAAGACCTATAC 57.832 38.462 0.00 0.00 0.00 1.47
1664 3692 8.986847 CCAGATAAATCTATAGCTGACACAAAG 58.013 37.037 0.00 0.00 40.81 2.77
1685 3713 5.726793 ACTCCATACTCTTTACCAACCAGAT 59.273 40.000 0.00 0.00 0.00 2.90
1691 3719 7.186972 TCTAGGAACTCCATACTCTTTACCAA 58.813 38.462 0.00 0.00 41.75 3.67
1692 3720 6.738635 TCTAGGAACTCCATACTCTTTACCA 58.261 40.000 0.00 0.00 41.75 3.25
1770 3806 6.099125 TCGGGGTAGTCAAATCTAATTCATGA 59.901 38.462 0.00 0.00 0.00 3.07
1790 3826 1.896122 AAGCCTTTACTCCGTCGGGG 61.896 60.000 10.39 10.39 37.02 5.73
1831 3867 2.998670 CAAGCGCAGAGAGATTCAAGAA 59.001 45.455 11.47 0.00 0.00 2.52
1948 4008 3.647636 CCTCTGTTCCCTCTCATTCCTA 58.352 50.000 0.00 0.00 0.00 2.94
1973 4033 9.342308 CTATTAGGAATAGGCTGTTCATTTTGA 57.658 33.333 22.94 0.95 37.74 2.69
2044 4104 4.961438 TTAAGTTCCCGAACAGGTAGTT 57.039 40.909 10.07 0.00 43.47 2.24
2047 4107 3.557686 GGCTTTAAGTTCCCGAACAGGTA 60.558 47.826 10.07 0.00 43.47 3.08
2050 4123 2.225727 GTGGCTTTAAGTTCCCGAACAG 59.774 50.000 10.07 0.19 43.47 3.16
2076 4149 6.072286 GGTCATGCCATTATCTATTTGTCAGG 60.072 42.308 1.78 0.00 37.17 3.86
2105 4178 4.265073 GCTCCAGGATGTAATTCAACAGT 58.735 43.478 0.00 0.00 31.70 3.55
2121 4194 4.730949 AATGACATCAATTTGGCTCCAG 57.269 40.909 0.00 0.00 0.00 3.86
2196 4269 7.680442 TTGTCATTCCGAATTATGAAGTGAA 57.320 32.000 0.00 0.00 32.94 3.18
2218 4291 0.809241 TTTTGCAGCTGGCCGTTTTG 60.809 50.000 17.12 0.00 43.89 2.44
2223 4296 3.297620 AGGTTTTGCAGCTGGCCG 61.298 61.111 17.12 0.00 43.89 6.13
2288 4361 7.459795 TGCAAATACTGAACATTGGTGATAA 57.540 32.000 0.00 0.00 0.00 1.75
2357 4430 6.426328 GTGTTGCAACCATTTTTCCAATGATA 59.574 34.615 26.14 0.00 0.00 2.15
2359 4432 4.574013 GTGTTGCAACCATTTTTCCAATGA 59.426 37.500 26.14 0.00 0.00 2.57
2361 4434 4.779696 AGTGTTGCAACCATTTTTCCAAT 58.220 34.783 26.14 0.99 0.00 3.16
2362 4435 4.213564 AGTGTTGCAACCATTTTTCCAA 57.786 36.364 26.14 0.76 0.00 3.53
2363 4436 3.902881 AGTGTTGCAACCATTTTTCCA 57.097 38.095 26.14 1.62 0.00 3.53
2364 4437 4.187694 TGAAGTGTTGCAACCATTTTTCC 58.812 39.130 26.14 9.52 0.00 3.13
2365 4438 5.351189 AGTTGAAGTGTTGCAACCATTTTTC 59.649 36.000 26.14 19.68 44.03 2.29
2366 4439 5.244755 AGTTGAAGTGTTGCAACCATTTTT 58.755 33.333 26.14 12.84 44.03 1.94
2367 4440 4.831107 AGTTGAAGTGTTGCAACCATTTT 58.169 34.783 26.14 14.50 44.03 1.82
2368 4441 4.470334 AGTTGAAGTGTTGCAACCATTT 57.530 36.364 26.14 16.86 44.03 2.32
2369 4442 4.160252 AGAAGTTGAAGTGTTGCAACCATT 59.840 37.500 26.14 19.69 44.03 3.16
2370 4443 3.701040 AGAAGTTGAAGTGTTGCAACCAT 59.299 39.130 26.14 12.23 44.03 3.55
2371 4444 3.088532 AGAAGTTGAAGTGTTGCAACCA 58.911 40.909 26.14 14.07 44.03 3.67
2483 4580 4.322567 GGCATAGTCCCAATCTTCAGATC 58.677 47.826 0.00 0.00 32.75 2.75
2514 4611 2.243957 TAGCAAATGCCGCGGATCG 61.244 57.895 33.48 12.86 43.38 3.69
2532 4629 5.302568 CCCATTTTCATGTACTATGCCATGT 59.697 40.000 0.00 0.00 39.53 3.21
2816 4913 2.094675 GTGGCAATGGCATGTAGAACT 58.905 47.619 13.81 0.00 43.71 3.01
2852 4949 1.304052 TTTGAATCCCCACTGCCCG 60.304 57.895 0.00 0.00 0.00 6.13
2873 4970 1.125093 TTCCGAAGCTCCCACTTCCA 61.125 55.000 0.00 0.00 42.57 3.53
2920 5017 5.186797 AGTGATACTGAGGAGAGGTTTTCAG 59.813 44.000 0.00 0.00 42.07 3.02
2939 5036 3.367910 GCGGAAAGAAGTGAGAGAGTGAT 60.368 47.826 0.00 0.00 0.00 3.06
3002 5099 5.921004 GCTTTGAGAGCGATTGATAGAAT 57.079 39.130 0.00 0.00 42.46 2.40
3035 5132 5.422214 AGAGGAACAGATTACGGAATGTT 57.578 39.130 0.00 0.00 38.53 2.71
3045 5142 4.164988 CCCCAAGACATAGAGGAACAGATT 59.835 45.833 0.00 0.00 0.00 2.40
3149 5246 2.099141 TCTCATCAGCCCAGTTTTCG 57.901 50.000 0.00 0.00 0.00 3.46
3377 5474 4.954202 ACCAATATCTGAGTCACGAACCTA 59.046 41.667 0.00 0.00 0.00 3.08
3493 5590 1.143969 GCATGCTCGCATTCTTTGGC 61.144 55.000 11.37 0.00 33.90 4.52
3557 5654 0.824759 GTATGAGGGTTGAGGAGCGT 59.175 55.000 0.00 0.00 0.00 5.07
3649 5746 7.068962 TCCATGTCATAATGCTTGATGAATTGT 59.931 33.333 1.21 0.00 33.96 2.71
3652 5749 7.504574 TCTTCCATGTCATAATGCTTGATGAAT 59.495 33.333 1.21 0.00 33.96 2.57
3688 5785 2.624838 CAGCACAGATTGGTTTTGAGGT 59.375 45.455 0.00 0.00 31.87 3.85
3901 5998 2.545946 GAGCTTGACTTGAGTTGTGTCC 59.454 50.000 0.00 0.00 0.00 4.02
4015 6112 7.656948 CCACATGAACAATTAACTGTCCATTTT 59.343 33.333 0.00 0.00 0.00 1.82
4153 6250 6.072728 TGTGGAGTAATTTACAAGATGCACAC 60.073 38.462 13.28 8.62 33.48 3.82
4351 6448 5.441718 ACCTCATACAAACCAGACATCAT 57.558 39.130 0.00 0.00 0.00 2.45
4391 6491 2.516906 TGCTGGTTTGCTCATGAATCA 58.483 42.857 0.00 0.00 0.00 2.57
4392 6492 3.129813 TCATGCTGGTTTGCTCATGAATC 59.870 43.478 0.00 0.00 41.36 2.52
4394 6494 2.516906 TCATGCTGGTTTGCTCATGAA 58.483 42.857 0.00 0.00 41.36 2.57
4396 6496 2.230508 ACTTCATGCTGGTTTGCTCATG 59.769 45.455 0.00 0.00 38.05 3.07
4398 6498 1.985473 ACTTCATGCTGGTTTGCTCA 58.015 45.000 0.00 0.00 0.00 4.26
4401 6501 4.445385 CACTAAAACTTCATGCTGGTTTGC 59.555 41.667 9.89 0.00 34.09 3.68
4402 6502 5.591099 ACACTAAAACTTCATGCTGGTTTG 58.409 37.500 9.89 4.63 34.09 2.93
4403 6503 5.852282 ACACTAAAACTTCATGCTGGTTT 57.148 34.783 6.17 6.17 35.11 3.27
4404 6504 8.807948 ATATACACTAAAACTTCATGCTGGTT 57.192 30.769 0.00 0.00 0.00 3.67
4441 6543 1.003839 GTCACCGACCCATGCTCAA 60.004 57.895 0.00 0.00 0.00 3.02
4451 6553 1.940613 AGAACAAAGCAAGTCACCGAC 59.059 47.619 0.00 0.00 0.00 4.79
4483 6585 9.859427 TTATTTTTCAGTGCCATTTAGAAGATG 57.141 29.630 0.00 0.00 0.00 2.90
4531 6633 7.584987 ACAACTGTGCAAACATACTTTATCTC 58.415 34.615 0.00 0.00 0.00 2.75
4536 6638 8.160521 TGTATACAACTGTGCAAACATACTTT 57.839 30.769 2.20 0.00 0.00 2.66
4600 6927 3.751698 GGATACACTCCTTCGCTTTTGTT 59.248 43.478 0.00 0.00 41.29 2.83
4608 6937 2.099921 CTGGACTGGATACACTCCTTCG 59.900 54.545 5.34 0.00 46.42 3.79
4807 7142 9.349713 CCAGTATCCACCTTATTATTTTGCTAA 57.650 33.333 0.00 0.00 0.00 3.09
4808 7143 7.942341 CCCAGTATCCACCTTATTATTTTGCTA 59.058 37.037 0.00 0.00 0.00 3.49
4879 7219 5.351465 ACTGGATTTCACTGTTATAAGCACG 59.649 40.000 0.00 0.00 0.00 5.34
5064 7603 2.158726 GGACCAAAGTGTGTAGGGTTCA 60.159 50.000 0.00 0.00 30.55 3.18
5077 7616 3.503748 GGACTGTTTCTGATGGACCAAAG 59.496 47.826 0.00 0.00 0.00 2.77
5160 7702 2.409975 TGTCAAACGAACCTCGGAATC 58.590 47.619 0.67 0.00 45.59 2.52
5261 7803 9.806203 CAATTGTCCTCTTGCAATTATAAATGA 57.194 29.630 0.00 0.00 41.62 2.57
5279 7821 5.391312 AATTTGCTACACTCCAATTGTCC 57.609 39.130 4.43 0.00 0.00 4.02
5281 7823 6.719370 TCCTTAATTTGCTACACTCCAATTGT 59.281 34.615 4.43 0.00 0.00 2.71
5282 7824 7.029563 GTCCTTAATTTGCTACACTCCAATTG 58.970 38.462 0.00 0.00 0.00 2.32
5283 7825 6.719370 TGTCCTTAATTTGCTACACTCCAATT 59.281 34.615 0.00 0.00 0.00 2.32
5306 7849 4.853007 AGAATTTAGCATCCTGAGCTTGT 58.147 39.130 0.00 0.00 43.25 3.16
5330 7873 1.605753 AGGGCGAGAGTTTTGGTTTC 58.394 50.000 0.00 0.00 0.00 2.78
5331 7874 1.954382 GAAGGGCGAGAGTTTTGGTTT 59.046 47.619 0.00 0.00 0.00 3.27
5332 7875 1.605753 GAAGGGCGAGAGTTTTGGTT 58.394 50.000 0.00 0.00 0.00 3.67
5333 7876 0.250770 GGAAGGGCGAGAGTTTTGGT 60.251 55.000 0.00 0.00 0.00 3.67
5334 7877 0.960861 GGGAAGGGCGAGAGTTTTGG 60.961 60.000 0.00 0.00 0.00 3.28
5335 7878 0.250727 TGGGAAGGGCGAGAGTTTTG 60.251 55.000 0.00 0.00 0.00 2.44
5336 7879 0.476771 TTGGGAAGGGCGAGAGTTTT 59.523 50.000 0.00 0.00 0.00 2.43
5337 7880 0.476771 TTTGGGAAGGGCGAGAGTTT 59.523 50.000 0.00 0.00 0.00 2.66
5338 7881 0.698818 ATTTGGGAAGGGCGAGAGTT 59.301 50.000 0.00 0.00 0.00 3.01
5339 7882 0.698818 AATTTGGGAAGGGCGAGAGT 59.301 50.000 0.00 0.00 0.00 3.24
5340 7883 2.710096 TAATTTGGGAAGGGCGAGAG 57.290 50.000 0.00 0.00 0.00 3.20
5341 7884 3.662759 ATTAATTTGGGAAGGGCGAGA 57.337 42.857 0.00 0.00 0.00 4.04
5342 7885 3.699038 TCAATTAATTTGGGAAGGGCGAG 59.301 43.478 0.00 0.00 35.92 5.03
5343 7886 3.702792 TCAATTAATTTGGGAAGGGCGA 58.297 40.909 0.00 0.00 35.92 5.54
5344 7887 4.081697 ACTTCAATTAATTTGGGAAGGGCG 60.082 41.667 21.56 6.82 35.92 6.13
5345 7888 5.420725 ACTTCAATTAATTTGGGAAGGGC 57.579 39.130 21.56 0.00 35.92 5.19
5346 7889 7.244886 AGAACTTCAATTAATTTGGGAAGGG 57.755 36.000 21.56 7.55 35.92 3.95


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

AutoCloner maintained by Alex Coulton.