Multiple sequence alignment - TraesCS6A01G208700

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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 TraesCS6A01G208700 chr6A 100.000 2900 0 0 1 2900 376478701 376481600 0.000000e+00 5356.0
1 TraesCS6A01G208700 chr6B 93.409 2109 75 21 626 2697 413283688 413285769 0.000000e+00 3066.0
2 TraesCS6A01G208700 chr6B 94.017 117 5 1 2695 2809 413290284 413290400 2.970000e-40 176.0
3 TraesCS6A01G208700 chr6D 94.310 2021 67 19 602 2591 265880404 265882407 0.000000e+00 3051.0
4 TraesCS6A01G208700 chr6D 90.000 590 46 7 1 589 14405306 14405883 0.000000e+00 750.0
5 TraesCS6A01G208700 chr6D 95.954 173 7 0 2576 2748 265883524 265883696 6.120000e-72 281.0
6 TraesCS6A01G208700 chr6D 92.537 67 3 1 2753 2817 265891698 265891764 8.560000e-16 95.3
7 TraesCS6A01G208700 chr7D 89.226 594 49 7 1 592 553077307 553077887 0.000000e+00 728.0
8 TraesCS6A01G208700 chr7D 92.222 90 7 0 2806 2895 287128708 287128797 8.430000e-26 128.0
9 TraesCS6A01G208700 chr3D 89.358 592 46 9 1 589 608970377 608970954 0.000000e+00 728.0
10 TraesCS6A01G208700 chr3D 88.663 591 39 11 1 589 322767971 322768535 0.000000e+00 695.0
11 TraesCS6A01G208700 chr3D 88.176 592 52 13 1 589 19873382 19873958 0.000000e+00 689.0
12 TraesCS6A01G208700 chr3D 87.065 603 39 16 1 601 177351772 177352337 0.000000e+00 645.0
13 TraesCS6A01G208700 chr3D 86.464 591 46 19 1 589 560794627 560794069 4.110000e-173 617.0
14 TraesCS6A01G208700 chr5D 89.340 591 46 10 1 589 61479785 61479210 0.000000e+00 726.0
15 TraesCS6A01G208700 chr5D 87.960 598 61 11 1 589 504928894 504929489 0.000000e+00 695.0
16 TraesCS6A01G208700 chr5D 91.388 418 24 6 1 417 302730437 302730843 1.950000e-156 562.0
17 TraesCS6A01G208700 chr5B 89.020 592 51 5 1 589 121526605 121526025 0.000000e+00 721.0
18 TraesCS6A01G208700 chr5B 92.308 91 7 0 2805 2895 13379122 13379212 2.350000e-26 130.0
19 TraesCS6A01G208700 chr4D 88.663 591 54 7 1 589 488770131 488769552 0.000000e+00 708.0
20 TraesCS6A01G208700 chr5A 88.644 590 54 6 1 589 538325550 538324973 0.000000e+00 706.0
21 TraesCS6A01G208700 chr5A 90.625 96 7 2 2807 2900 689652938 689652843 3.030000e-25 126.0
22 TraesCS6A01G208700 chr2A 87.986 591 58 6 1 589 486280674 486281253 0.000000e+00 686.0
23 TraesCS6A01G208700 chr2A 94.253 87 5 0 2809 2895 499562558 499562644 1.810000e-27 134.0
24 TraesCS6A01G208700 chr2A 88.571 105 8 3 2794 2895 182891159 182891262 1.090000e-24 124.0
25 TraesCS6A01G208700 chr2A 83.571 140 15 6 1102 1237 753116150 753116015 1.090000e-24 124.0
26 TraesCS6A01G208700 chr3A 87.797 590 56 7 1 587 456410908 456410332 0.000000e+00 676.0
27 TraesCS6A01G208700 chrUn 86.054 588 52 15 1 587 43282246 43282804 3.200000e-169 604.0
28 TraesCS6A01G208700 chr7A 86.028 501 55 8 90 587 37787565 37788053 9.210000e-145 523.0
29 TraesCS6A01G208700 chr7A 85.828 501 56 8 90 587 37811698 37812186 4.280000e-143 518.0
30 TraesCS6A01G208700 chr7A 93.750 96 5 1 2801 2895 345765736 345765831 3.010000e-30 143.0
31 TraesCS6A01G208700 chr7B 92.553 94 7 0 2802 2895 553109863 553109956 5.040000e-28 135.0
32 TraesCS6A01G208700 chr1A 91.489 94 8 0 2807 2900 297379108 297379015 2.350000e-26 130.0
33 TraesCS6A01G208700 chr4B 92.222 90 7 0 2806 2895 454440601 454440690 8.430000e-26 128.0
34 TraesCS6A01G208700 chr2B 82.857 140 16 5 1102 1237 762214231 762214096 5.080000e-23 119.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G208700 chr6A 376478701 376481600 2899 False 5356 5356 100.000 1 2900 1 chr6A.!!$F1 2899
1 TraesCS6A01G208700 chr6B 413283688 413285769 2081 False 3066 3066 93.409 626 2697 1 chr6B.!!$F1 2071
2 TraesCS6A01G208700 chr6D 265880404 265883696 3292 False 1666 3051 95.132 602 2748 2 chr6D.!!$F3 2146
3 TraesCS6A01G208700 chr6D 14405306 14405883 577 False 750 750 90.000 1 589 1 chr6D.!!$F1 588
4 TraesCS6A01G208700 chr7D 553077307 553077887 580 False 728 728 89.226 1 592 1 chr7D.!!$F2 591
5 TraesCS6A01G208700 chr3D 608970377 608970954 577 False 728 728 89.358 1 589 1 chr3D.!!$F4 588
6 TraesCS6A01G208700 chr3D 322767971 322768535 564 False 695 695 88.663 1 589 1 chr3D.!!$F3 588
7 TraesCS6A01G208700 chr3D 19873382 19873958 576 False 689 689 88.176 1 589 1 chr3D.!!$F1 588
8 TraesCS6A01G208700 chr3D 177351772 177352337 565 False 645 645 87.065 1 601 1 chr3D.!!$F2 600
9 TraesCS6A01G208700 chr3D 560794069 560794627 558 True 617 617 86.464 1 589 1 chr3D.!!$R1 588
10 TraesCS6A01G208700 chr5D 61479210 61479785 575 True 726 726 89.340 1 589 1 chr5D.!!$R1 588
11 TraesCS6A01G208700 chr5D 504928894 504929489 595 False 695 695 87.960 1 589 1 chr5D.!!$F2 588
12 TraesCS6A01G208700 chr5B 121526025 121526605 580 True 721 721 89.020 1 589 1 chr5B.!!$R1 588
13 TraesCS6A01G208700 chr4D 488769552 488770131 579 True 708 708 88.663 1 589 1 chr4D.!!$R1 588
14 TraesCS6A01G208700 chr5A 538324973 538325550 577 True 706 706 88.644 1 589 1 chr5A.!!$R1 588
15 TraesCS6A01G208700 chr2A 486280674 486281253 579 False 686 686 87.986 1 589 1 chr2A.!!$F2 588
16 TraesCS6A01G208700 chr3A 456410332 456410908 576 True 676 676 87.797 1 587 1 chr3A.!!$R1 586
17 TraesCS6A01G208700 chrUn 43282246 43282804 558 False 604 604 86.054 1 587 1 chrUn.!!$F1 586

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
438 461 0.030908 CGCAAAACTGGCCCGTAAAA 59.969 50.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2263 1.153647 CTTGCGAGGCACCGTCATA 60.154 57.895 0.0 0.0 38.71 2.15 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
40 42 7.461749 AGGAATGAACTTGGAATTCTTCTACA 58.538 34.615 5.23 0.53 32.15 2.74
60 62 0.605319 ACAATGTGGGTAGCCGTGTG 60.605 55.000 6.45 4.47 0.00 3.82
100 103 4.425577 AACCGCATTAGAGCTTTTCTTG 57.574 40.909 0.00 0.00 37.36 3.02
151 154 4.191544 CACACACTTTCAACTTCAGGAGA 58.808 43.478 0.00 0.00 0.00 3.71
159 162 6.878389 ACTTTCAACTTCAGGAGAATCTCATC 59.122 38.462 12.79 0.00 32.31 2.92
169 172 3.256879 GGAGAATCTCATCGAGCACCATA 59.743 47.826 12.79 0.00 33.73 2.74
425 447 0.827368 AAAAAGCAGACCCCGCAAAA 59.173 45.000 0.00 0.00 0.00 2.44
429 451 2.919494 GCAGACCCCGCAAAACTGG 61.919 63.158 0.00 0.00 0.00 4.00
438 461 0.030908 CGCAAAACTGGCCCGTAAAA 59.969 50.000 0.00 0.00 0.00 1.52
483 507 5.390087 TTTTATATGGATCCGTTTGGGGA 57.610 39.130 12.82 0.00 41.17 4.81
592 617 4.340950 GTCTGCTAGAGTTGCTCTAATCCT 59.659 45.833 7.22 0.00 41.74 3.24
593 618 5.533154 GTCTGCTAGAGTTGCTCTAATCCTA 59.467 44.000 7.22 0.00 41.74 2.94
594 619 5.767665 TCTGCTAGAGTTGCTCTAATCCTAG 59.232 44.000 7.22 0.00 41.74 3.02
610 635 9.106977 TCTAATCCTAGAGAGCTTAGTGATAGA 57.893 37.037 0.00 0.00 30.34 1.98
611 636 9.383519 CTAATCCTAGAGAGCTTAGTGATAGAG 57.616 40.741 0.00 0.00 0.00 2.43
612 637 6.757173 TCCTAGAGAGCTTAGTGATAGAGT 57.243 41.667 0.00 0.00 0.00 3.24
613 638 7.859026 TCCTAGAGAGCTTAGTGATAGAGTA 57.141 40.000 0.00 0.00 0.00 2.59
614 639 7.903145 TCCTAGAGAGCTTAGTGATAGAGTAG 58.097 42.308 0.00 0.00 0.00 2.57
645 670 1.808411 AAGTCATACCAAGTGTGCGG 58.192 50.000 0.00 0.00 0.00 5.69
697 722 4.900635 TTTTTGAGGAACTGAAGACAGC 57.099 40.909 0.00 0.00 46.95 4.40
700 725 3.777106 TGAGGAACTGAAGACAGCAAT 57.223 42.857 0.00 0.00 46.95 3.56
727 752 5.841810 AGCCATTTCGAGATTGAAAAACAA 58.158 33.333 0.00 0.00 40.90 2.83
728 753 5.922544 AGCCATTTCGAGATTGAAAAACAAG 59.077 36.000 0.00 0.00 40.90 3.16
729 754 5.691754 GCCATTTCGAGATTGAAAAACAAGT 59.308 36.000 0.00 0.00 40.90 3.16
730 755 6.861055 GCCATTTCGAGATTGAAAAACAAGTA 59.139 34.615 0.00 0.00 40.90 2.24
731 756 7.061094 GCCATTTCGAGATTGAAAAACAAGTAG 59.939 37.037 0.00 0.00 40.90 2.57
732 757 7.538678 CCATTTCGAGATTGAAAAACAAGTAGG 59.461 37.037 0.00 0.00 40.90 3.18
742 767 6.154445 TGAAAAACAAGTAGGAGTAGTAGCG 58.846 40.000 0.00 0.00 0.00 4.26
854 879 5.995282 ACAAAGTCAATATCAAGTGGTTCGA 59.005 36.000 0.00 0.00 0.00 3.71
966 1019 0.923358 ACTCCCAAGTCCCAACACAA 59.077 50.000 0.00 0.00 0.00 3.33
1513 1566 4.609995 CCGCTACGGTCACCATTT 57.390 55.556 0.00 0.00 42.73 2.32
1553 1606 2.623915 CGTCGTCTGTTCCCGGAGT 61.624 63.158 0.73 0.00 0.00 3.85
1558 1611 0.037232 GTCTGTTCCCGGAGTGGAAG 60.037 60.000 0.73 0.00 44.86 3.46
1559 1612 0.178944 TCTGTTCCCGGAGTGGAAGA 60.179 55.000 0.73 0.00 44.86 2.87
1560 1613 0.037232 CTGTTCCCGGAGTGGAAGAC 60.037 60.000 0.73 0.00 44.86 3.01
1689 1742 2.108514 CCATGTTCGCACTGCCGAT 61.109 57.895 0.00 0.00 37.06 4.18
1700 1753 3.989698 CTGCCGATCCTGACGCGTT 62.990 63.158 15.53 0.00 0.00 4.84
1783 1836 2.562912 GCGACAACGGGTACGAGA 59.437 61.111 0.00 0.00 44.60 4.04
2000 2057 1.675552 TAAGATTTGCTTAGCCGCCC 58.324 50.000 0.29 0.00 38.05 6.13
2039 2096 5.468072 CAGTGTCTAATCAATCATGCTACCC 59.532 44.000 0.00 0.00 0.00 3.69
2070 2127 6.939622 AGATCAACTTTTGGGGATTGAAATC 58.060 36.000 0.00 0.00 34.88 2.17
2171 2228 8.042515 CCATGTTGATTTGGTGAAATTCCTTAT 58.957 33.333 0.00 0.00 31.58 1.73
2172 2229 9.090692 CATGTTGATTTGGTGAAATTCCTTATC 57.909 33.333 0.00 0.00 31.58 1.75
2289 2350 8.421784 GGATGGTGTTTCTACTGATTCATACTA 58.578 37.037 0.00 0.00 0.00 1.82
2290 2351 9.469807 GATGGTGTTTCTACTGATTCATACTAG 57.530 37.037 0.00 0.00 0.00 2.57
2291 2352 8.362464 TGGTGTTTCTACTGATTCATACTAGT 57.638 34.615 0.00 0.00 0.00 2.57
2292 2353 9.470399 TGGTGTTTCTACTGATTCATACTAGTA 57.530 33.333 4.77 4.77 0.00 1.82
2293 2354 9.953697 GGTGTTTCTACTGATTCATACTAGTAG 57.046 37.037 8.85 0.00 42.36 2.57
2369 2430 0.384230 CGCAAACGCATGTCGAGTTT 60.384 50.000 14.88 9.78 46.99 2.66
2408 2469 0.440758 CGCCGCTCGTTGTATTTGAA 59.559 50.000 0.00 0.00 0.00 2.69
2481 2542 2.112815 GCCCAGTAATGCCGTGGTC 61.113 63.158 0.00 0.00 0.00 4.02
2594 3788 2.667473 AGTAATACTTTGCCGCTCGT 57.333 45.000 0.00 0.00 0.00 4.18
2737 3931 5.860941 TTTGTTTCTCCACTGCCATAAAA 57.139 34.783 0.00 0.00 0.00 1.52
2753 3947 3.984838 AAAAATGCCTTTGCGCTCA 57.015 42.105 9.73 0.00 41.78 4.26
2754 3948 2.237393 AAAAATGCCTTTGCGCTCAA 57.763 40.000 9.73 0.00 41.78 3.02
2755 3949 1.787012 AAAATGCCTTTGCGCTCAAG 58.213 45.000 9.73 10.95 41.78 3.02
2756 3950 0.675633 AAATGCCTTTGCGCTCAAGT 59.324 45.000 9.73 0.00 41.78 3.16
2757 3951 0.675633 AATGCCTTTGCGCTCAAGTT 59.324 45.000 9.73 0.00 41.78 2.66
2758 3952 1.533625 ATGCCTTTGCGCTCAAGTTA 58.466 45.000 9.73 2.69 41.78 2.24
2759 3953 1.313772 TGCCTTTGCGCTCAAGTTAA 58.686 45.000 9.73 0.00 41.78 2.01
2760 3954 1.885887 TGCCTTTGCGCTCAAGTTAAT 59.114 42.857 9.73 0.00 41.78 1.40
2761 3955 2.253603 GCCTTTGCGCTCAAGTTAATG 58.746 47.619 9.73 0.00 33.12 1.90
2762 3956 2.253603 CCTTTGCGCTCAAGTTAATGC 58.746 47.619 9.73 0.00 33.12 3.56
2766 3960 1.721487 CGCTCAAGTTAATGCGGGG 59.279 57.895 7.99 0.00 43.97 5.73
2767 3961 0.742990 CGCTCAAGTTAATGCGGGGA 60.743 55.000 7.99 0.00 43.97 4.81
2768 3962 1.017387 GCTCAAGTTAATGCGGGGAG 58.983 55.000 0.00 0.00 0.00 4.30
2769 3963 1.668419 CTCAAGTTAATGCGGGGAGG 58.332 55.000 0.00 0.00 0.00 4.30
2770 3964 1.209504 CTCAAGTTAATGCGGGGAGGA 59.790 52.381 0.00 0.00 0.00 3.71
2771 3965 1.209504 TCAAGTTAATGCGGGGAGGAG 59.790 52.381 0.00 0.00 0.00 3.69
2772 3966 1.065418 CAAGTTAATGCGGGGAGGAGT 60.065 52.381 0.00 0.00 0.00 3.85
2773 3967 0.831307 AGTTAATGCGGGGAGGAGTC 59.169 55.000 0.00 0.00 0.00 3.36
2774 3968 0.529992 GTTAATGCGGGGAGGAGTCG 60.530 60.000 0.00 0.00 0.00 4.18
2775 3969 0.685131 TTAATGCGGGGAGGAGTCGA 60.685 55.000 0.00 0.00 0.00 4.20
2776 3970 0.469331 TAATGCGGGGAGGAGTCGAT 60.469 55.000 0.00 0.00 0.00 3.59
2777 3971 2.032860 AATGCGGGGAGGAGTCGATG 62.033 60.000 0.00 0.00 0.00 3.84
2778 3972 4.593864 GCGGGGAGGAGTCGATGC 62.594 72.222 0.00 0.00 0.00 3.91
2779 3973 3.147595 CGGGGAGGAGTCGATGCA 61.148 66.667 0.00 0.00 0.00 3.96
2780 3974 2.501610 GGGGAGGAGTCGATGCAC 59.498 66.667 0.00 0.00 0.00 4.57
2781 3975 2.105128 GGGAGGAGTCGATGCACG 59.895 66.667 0.00 0.00 44.09 5.34
2782 3976 2.711922 GGGAGGAGTCGATGCACGT 61.712 63.158 8.22 0.00 43.13 4.49
2783 3977 1.226717 GGAGGAGTCGATGCACGTC 60.227 63.158 8.22 3.86 43.13 4.34
2784 3978 1.226717 GAGGAGTCGATGCACGTCC 60.227 63.158 8.22 8.66 43.13 4.79
2785 3979 1.658686 GAGGAGTCGATGCACGTCCT 61.659 60.000 15.58 15.58 45.71 3.85
2786 3980 1.226717 GGAGTCGATGCACGTCCTC 60.227 63.158 15.30 15.30 43.13 3.71
2787 3981 1.583967 GAGTCGATGCACGTCCTCG 60.584 63.158 0.20 0.20 43.13 4.63
2801 3995 4.663636 CGTCCTCGTAAAAAGCTTTGAT 57.336 40.909 13.54 7.71 0.00 2.57
2802 3996 4.638963 CGTCCTCGTAAAAAGCTTTGATC 58.361 43.478 13.54 5.19 0.00 2.92
2803 3997 4.151689 CGTCCTCGTAAAAAGCTTTGATCA 59.848 41.667 13.54 0.00 0.00 2.92
2804 3998 5.163854 CGTCCTCGTAAAAAGCTTTGATCAT 60.164 40.000 13.54 0.00 0.00 2.45
2805 3999 6.251549 GTCCTCGTAAAAAGCTTTGATCATC 58.748 40.000 13.54 0.34 0.00 2.92
2806 4000 6.092807 GTCCTCGTAAAAAGCTTTGATCATCT 59.907 38.462 13.54 0.00 0.00 2.90
2807 4001 6.655003 TCCTCGTAAAAAGCTTTGATCATCTT 59.345 34.615 13.54 3.86 0.00 2.40
2808 4002 7.822334 TCCTCGTAAAAAGCTTTGATCATCTTA 59.178 33.333 13.54 2.83 0.00 2.10
2809 4003 8.119226 CCTCGTAAAAAGCTTTGATCATCTTAG 58.881 37.037 13.54 2.38 0.00 2.18
2810 4004 7.974675 TCGTAAAAAGCTTTGATCATCTTAGG 58.025 34.615 13.54 10.88 0.00 2.69
2811 4005 6.688813 CGTAAAAAGCTTTGATCATCTTAGGC 59.311 38.462 13.54 0.00 0.00 3.93
2812 4006 6.847421 AAAAAGCTTTGATCATCTTAGGCT 57.153 33.333 13.54 0.00 0.00 4.58
2813 4007 5.831702 AAAGCTTTGATCATCTTAGGCTG 57.168 39.130 11.80 0.00 0.00 4.85
2814 4008 3.818180 AGCTTTGATCATCTTAGGCTGG 58.182 45.455 0.00 0.00 0.00 4.85
2815 4009 3.201708 AGCTTTGATCATCTTAGGCTGGT 59.798 43.478 0.00 0.00 0.00 4.00
2816 4010 3.563390 GCTTTGATCATCTTAGGCTGGTC 59.437 47.826 0.00 0.00 0.00 4.02
2817 4011 4.774124 CTTTGATCATCTTAGGCTGGTCA 58.226 43.478 0.00 0.00 30.82 4.02
2818 4012 3.827008 TGATCATCTTAGGCTGGTCAC 57.173 47.619 0.00 0.00 27.75 3.67
2819 4013 3.106827 TGATCATCTTAGGCTGGTCACA 58.893 45.455 0.00 0.00 27.75 3.58
2821 4015 2.540383 TCATCTTAGGCTGGTCACAGT 58.460 47.619 0.00 0.00 46.62 3.55
2822 4016 3.708451 TCATCTTAGGCTGGTCACAGTA 58.292 45.455 0.00 0.00 46.62 2.74
2823 4017 3.701542 TCATCTTAGGCTGGTCACAGTAG 59.298 47.826 0.00 0.00 46.62 2.57
2824 4018 2.457598 TCTTAGGCTGGTCACAGTAGG 58.542 52.381 0.00 0.00 46.62 3.18
2825 4019 1.482593 CTTAGGCTGGTCACAGTAGGG 59.517 57.143 0.00 0.00 46.62 3.53
2826 4020 0.708209 TAGGCTGGTCACAGTAGGGA 59.292 55.000 0.00 0.00 46.62 4.20
2827 4021 0.616111 AGGCTGGTCACAGTAGGGAG 60.616 60.000 0.00 0.00 46.62 4.30
2828 4022 0.905337 GGCTGGTCACAGTAGGGAGT 60.905 60.000 0.00 0.00 46.62 3.85
2829 4023 1.618888 GGCTGGTCACAGTAGGGAGTA 60.619 57.143 0.00 0.00 46.62 2.59
2830 4024 2.176889 GCTGGTCACAGTAGGGAGTAA 58.823 52.381 0.00 0.00 46.62 2.24
2831 4025 2.094130 GCTGGTCACAGTAGGGAGTAAC 60.094 54.545 0.00 0.00 46.62 2.50
2832 4026 3.432378 CTGGTCACAGTAGGGAGTAACT 58.568 50.000 0.00 0.00 39.92 2.24
2833 4027 3.833070 CTGGTCACAGTAGGGAGTAACTT 59.167 47.826 0.00 0.00 39.92 2.66
2834 4028 5.001833 TGGTCACAGTAGGGAGTAACTTA 57.998 43.478 0.00 0.00 0.00 2.24
2835 4029 5.396485 TGGTCACAGTAGGGAGTAACTTAA 58.604 41.667 0.00 0.00 0.00 1.85
2836 4030 5.840149 TGGTCACAGTAGGGAGTAACTTAAA 59.160 40.000 0.00 0.00 0.00 1.52
2837 4031 6.162079 GGTCACAGTAGGGAGTAACTTAAAC 58.838 44.000 0.00 0.00 0.00 2.01
2838 4032 6.014755 GGTCACAGTAGGGAGTAACTTAAACT 60.015 42.308 0.00 0.00 0.00 2.66
2839 4033 7.177392 GGTCACAGTAGGGAGTAACTTAAACTA 59.823 40.741 0.00 0.00 0.00 2.24
2840 4034 8.242739 GTCACAGTAGGGAGTAACTTAAACTAG 58.757 40.741 0.00 0.00 0.00 2.57
2841 4035 7.946776 TCACAGTAGGGAGTAACTTAAACTAGT 59.053 37.037 0.00 0.00 0.00 2.57
2842 4036 9.236006 CACAGTAGGGAGTAACTTAAACTAGTA 57.764 37.037 0.00 0.00 0.00 1.82
2843 4037 9.813826 ACAGTAGGGAGTAACTTAAACTAGTAA 57.186 33.333 0.00 0.00 0.00 2.24
2845 4039 9.813826 AGTAGGGAGTAACTTAAACTAGTAACA 57.186 33.333 0.00 0.00 0.00 2.41
2848 4042 9.097946 AGGGAGTAACTTAAACTAGTAACATGT 57.902 33.333 0.00 0.00 0.00 3.21
2885 4079 8.861086 AGTCTATGTTACTACATTCATAGTGGG 58.139 37.037 0.00 0.00 42.29 4.61
2886 4080 8.639761 GTCTATGTTACTACATTCATAGTGGGT 58.360 37.037 0.00 0.00 42.29 4.51
2887 4081 8.638873 TCTATGTTACTACATTCATAGTGGGTG 58.361 37.037 0.00 0.00 42.29 4.61
2888 4082 5.984725 TGTTACTACATTCATAGTGGGTGG 58.015 41.667 0.00 0.00 36.09 4.61
2889 4083 5.486063 TGTTACTACATTCATAGTGGGTGGT 59.514 40.000 0.00 0.00 36.09 4.16
2890 4084 6.668718 TGTTACTACATTCATAGTGGGTGGTA 59.331 38.462 0.00 0.00 36.09 3.25
2891 4085 7.346175 TGTTACTACATTCATAGTGGGTGGTAT 59.654 37.037 0.00 0.00 36.09 2.73
2892 4086 6.420913 ACTACATTCATAGTGGGTGGTATC 57.579 41.667 0.00 0.00 34.02 2.24
2893 4087 5.903010 ACTACATTCATAGTGGGTGGTATCA 59.097 40.000 0.00 0.00 34.02 2.15
2894 4088 5.912149 ACATTCATAGTGGGTGGTATCAT 57.088 39.130 0.00 0.00 0.00 2.45
2895 4089 5.624159 ACATTCATAGTGGGTGGTATCATG 58.376 41.667 0.00 0.00 0.00 3.07
2896 4090 4.705110 TTCATAGTGGGTGGTATCATGG 57.295 45.455 0.00 0.00 0.00 3.66
2897 4091 2.978978 TCATAGTGGGTGGTATCATGGG 59.021 50.000 0.00 0.00 0.00 4.00
2898 4092 2.579624 TAGTGGGTGGTATCATGGGT 57.420 50.000 0.00 0.00 0.00 4.51
2899 4093 0.918983 AGTGGGTGGTATCATGGGTG 59.081 55.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 0.109723 ACACGGCTACCCACATTGTT 59.890 50.000 0.00 0.00 0.00 2.83
60 62 3.118702 GGTTAGGGTCTCTAGCTGGTTTC 60.119 52.174 0.00 0.00 31.00 2.78
100 103 7.148188 TGCATTTTCAATCTCCTTGTATGTCTC 60.148 37.037 0.00 0.00 36.20 3.36
151 154 2.289320 GCCTATGGTGCTCGATGAGATT 60.289 50.000 0.00 0.00 0.00 2.40
159 162 1.097547 CCCTTTGCCTATGGTGCTCG 61.098 60.000 0.00 0.00 0.00 5.03
169 172 2.437897 CTGTCCAGCCCTTTGCCT 59.562 61.111 0.00 0.00 42.71 4.75
374 396 3.626996 CTGCATCTCACCGGCCCAA 62.627 63.158 0.00 0.00 0.00 4.12
471 494 3.071602 CAGATGTAGATCCCCAAACGGAT 59.928 47.826 0.00 0.00 45.72 4.18
483 507 0.753262 GGACGGCCACAGATGTAGAT 59.247 55.000 0.00 0.00 0.00 1.98
514 539 0.883814 TTCGCGGAAAACGGCCTTTA 60.884 50.000 6.13 0.00 44.51 1.85
559 584 1.680735 CTCTAGCAGACTTCGCATCCT 59.319 52.381 0.00 0.00 0.00 3.24
568 593 4.340950 GGATTAGAGCAACTCTAGCAGACT 59.659 45.833 4.64 0.00 42.92 3.24
593 618 9.720769 GTTATCTACTCTATCACTAAGCTCTCT 57.279 37.037 0.00 0.00 0.00 3.10
594 619 9.720769 AGTTATCTACTCTATCACTAAGCTCTC 57.279 37.037 0.00 0.00 28.23 3.20
645 670 5.130311 ACCCCCTCCAATACAAATTAATTGC 59.870 40.000 0.39 0.00 43.13 3.56
688 713 6.238456 CGAAATGGCTATTATTGCTGTCTTCA 60.238 38.462 0.00 0.00 0.00 3.02
697 722 9.734620 TTTTCAATCTCGAAATGGCTATTATTG 57.265 29.630 8.26 8.26 34.94 1.90
700 725 8.735315 TGTTTTTCAATCTCGAAATGGCTATTA 58.265 29.630 0.00 0.00 34.94 0.98
727 752 6.963083 ATGAAAATCGCTACTACTCCTACT 57.037 37.500 0.00 0.00 0.00 2.57
728 753 7.921745 AGAAATGAAAATCGCTACTACTCCTAC 59.078 37.037 0.00 0.00 0.00 3.18
729 754 8.008513 AGAAATGAAAATCGCTACTACTCCTA 57.991 34.615 0.00 0.00 0.00 2.94
730 755 6.879400 AGAAATGAAAATCGCTACTACTCCT 58.121 36.000 0.00 0.00 0.00 3.69
731 756 8.644318 TTAGAAATGAAAATCGCTACTACTCC 57.356 34.615 0.00 0.00 0.00 3.85
742 767 9.727627 ATCGATGCTCTTTTAGAAATGAAAATC 57.272 29.630 0.00 0.00 0.00 2.17
854 879 8.966868 TCTTCTTCTTTTTGACAAAATACACCT 58.033 29.630 13.90 0.00 31.28 4.00
886 939 1.976474 GGGCGATGGGCAAGACAAA 60.976 57.895 3.19 0.00 46.16 2.83
889 942 3.721370 ATGGGGCGATGGGCAAGAC 62.721 63.158 3.19 0.00 46.16 3.01
966 1019 1.315257 GGAATGGCGATGTGCTTGGT 61.315 55.000 0.00 0.00 45.43 3.67
1086 1139 3.071837 TACTGCATGCCCGTCGGA 61.072 61.111 16.68 0.00 0.00 4.55
1260 1313 2.751688 GGTGCGGGGAAGTTGGTA 59.248 61.111 0.00 0.00 0.00 3.25
1553 1606 1.955663 TCGTCGTCGTCGTCTTCCA 60.956 57.895 11.41 0.00 38.33 3.53
1558 1611 2.202146 CCAGTCGTCGTCGTCGTC 60.202 66.667 11.41 6.41 38.33 4.20
1559 1612 3.720193 CCCAGTCGTCGTCGTCGT 61.720 66.667 11.41 0.00 38.33 4.34
1560 1613 3.417224 TCCCAGTCGTCGTCGTCG 61.417 66.667 5.50 5.50 38.33 5.12
1674 1727 2.434185 GGATCGGCAGTGCGAACA 60.434 61.111 9.45 0.00 0.00 3.18
1689 1742 1.215382 CCAGATCAACGCGTCAGGA 59.785 57.895 14.44 11.72 0.00 3.86
1700 1753 2.268920 GGTTCGGCAGCCAGATCA 59.731 61.111 13.30 0.00 0.00 2.92
1736 1789 3.843117 GAAGAGGATACGCCGCCGG 62.843 68.421 0.00 0.00 43.43 6.13
2039 2096 6.049955 TCCCCAAAAGTTGATCTAGTACAG 57.950 41.667 0.00 0.00 0.00 2.74
2070 2127 3.064545 GCATTTGCTAGCTACAAGACCAG 59.935 47.826 17.23 0.00 38.21 4.00
2171 2228 7.255801 CCCCAAAATTTAGCTTTAACACAGAGA 60.256 37.037 0.00 0.00 0.00 3.10
2172 2229 6.868339 CCCCAAAATTTAGCTTTAACACAGAG 59.132 38.462 0.00 0.00 0.00 3.35
2203 2261 1.884075 TTGCGAGGCACCGTCATACT 61.884 55.000 0.00 0.00 38.71 2.12
2204 2262 1.421410 CTTGCGAGGCACCGTCATAC 61.421 60.000 0.00 0.00 38.71 2.39
2205 2263 1.153647 CTTGCGAGGCACCGTCATA 60.154 57.895 0.00 0.00 38.71 2.15
2322 2383 4.986659 CCTTTGGAAAACAAGCTTGATGAG 59.013 41.667 32.50 15.91 40.82 2.90
2369 2430 1.668751 GTTGGGCGCAATAAGATCGAA 59.331 47.619 19.93 0.00 0.00 3.71
2397 2458 6.128661 TGTCGTGATGCTACTTCAAATACAAC 60.129 38.462 0.00 0.00 0.00 3.32
2405 2466 2.672874 GCAATGTCGTGATGCTACTTCA 59.327 45.455 0.00 0.00 37.12 3.02
2408 2469 1.656652 GGCAATGTCGTGATGCTACT 58.343 50.000 0.00 0.00 39.94 2.57
2495 2556 3.733727 GTGAACTGGCCGTGTTATTTTTG 59.266 43.478 12.98 0.00 0.00 2.44
2622 3816 4.476410 CAGAGCGTACGCAGCCGA 62.476 66.667 38.58 0.00 44.88 5.54
2737 3931 0.675633 ACTTGAGCGCAAAGGCATTT 59.324 45.000 22.13 0.00 41.24 2.32
2749 3943 1.017387 CTCCCCGCATTAACTTGAGC 58.983 55.000 0.00 0.00 0.00 4.26
2750 3944 1.209504 TCCTCCCCGCATTAACTTGAG 59.790 52.381 0.00 0.00 0.00 3.02
2751 3945 1.209504 CTCCTCCCCGCATTAACTTGA 59.790 52.381 0.00 0.00 0.00 3.02
2752 3946 1.065418 ACTCCTCCCCGCATTAACTTG 60.065 52.381 0.00 0.00 0.00 3.16
2753 3947 1.209747 GACTCCTCCCCGCATTAACTT 59.790 52.381 0.00 0.00 0.00 2.66
2754 3948 0.831307 GACTCCTCCCCGCATTAACT 59.169 55.000 0.00 0.00 0.00 2.24
2755 3949 0.529992 CGACTCCTCCCCGCATTAAC 60.530 60.000 0.00 0.00 0.00 2.01
2756 3950 0.685131 TCGACTCCTCCCCGCATTAA 60.685 55.000 0.00 0.00 0.00 1.40
2757 3951 0.469331 ATCGACTCCTCCCCGCATTA 60.469 55.000 0.00 0.00 0.00 1.90
2758 3952 1.762460 ATCGACTCCTCCCCGCATT 60.762 57.895 0.00 0.00 0.00 3.56
2759 3953 2.123251 ATCGACTCCTCCCCGCAT 60.123 61.111 0.00 0.00 0.00 4.73
2760 3954 3.147595 CATCGACTCCTCCCCGCA 61.148 66.667 0.00 0.00 0.00 5.69
2761 3955 4.593864 GCATCGACTCCTCCCCGC 62.594 72.222 0.00 0.00 0.00 6.13
2762 3956 3.147595 TGCATCGACTCCTCCCCG 61.148 66.667 0.00 0.00 0.00 5.73
2763 3957 2.501610 GTGCATCGACTCCTCCCC 59.498 66.667 0.00 0.00 0.00 4.81
2764 3958 2.105128 CGTGCATCGACTCCTCCC 59.895 66.667 0.00 0.00 42.86 4.30
2765 3959 1.226717 GACGTGCATCGACTCCTCC 60.227 63.158 14.18 0.00 42.86 4.30
2766 3960 1.226717 GGACGTGCATCGACTCCTC 60.227 63.158 14.18 2.75 42.86 3.71
2767 3961 1.658686 GAGGACGTGCATCGACTCCT 61.659 60.000 10.52 15.58 44.19 3.69
2768 3962 1.226717 GAGGACGTGCATCGACTCC 60.227 63.158 10.52 11.31 42.86 3.85
2769 3963 4.386245 GAGGACGTGCATCGACTC 57.614 61.111 10.52 14.93 42.86 3.36
2780 3974 4.151689 TGATCAAAGCTTTTTACGAGGACG 59.848 41.667 9.53 0.00 45.75 4.79
2781 3975 5.607119 TGATCAAAGCTTTTTACGAGGAC 57.393 39.130 9.53 1.40 0.00 3.85
2782 3976 6.173339 AGATGATCAAAGCTTTTTACGAGGA 58.827 36.000 9.53 2.07 0.00 3.71
2783 3977 6.428385 AGATGATCAAAGCTTTTTACGAGG 57.572 37.500 9.53 0.00 0.00 4.63
2784 3978 8.119226 CCTAAGATGATCAAAGCTTTTTACGAG 58.881 37.037 9.53 0.00 0.00 4.18
2785 3979 7.414098 GCCTAAGATGATCAAAGCTTTTTACGA 60.414 37.037 9.53 4.05 0.00 3.43
2786 3980 6.688813 GCCTAAGATGATCAAAGCTTTTTACG 59.311 38.462 9.53 0.00 0.00 3.18
2787 3981 7.699812 CAGCCTAAGATGATCAAAGCTTTTTAC 59.300 37.037 9.53 4.26 0.00 2.01
2788 3982 7.148018 CCAGCCTAAGATGATCAAAGCTTTTTA 60.148 37.037 9.53 0.72 0.00 1.52
2789 3983 6.350780 CCAGCCTAAGATGATCAAAGCTTTTT 60.351 38.462 9.53 2.01 0.00 1.94
2790 3984 5.126707 CCAGCCTAAGATGATCAAAGCTTTT 59.873 40.000 9.53 0.00 0.00 2.27
2791 3985 4.643784 CCAGCCTAAGATGATCAAAGCTTT 59.356 41.667 5.69 5.69 0.00 3.51
2792 3986 4.205587 CCAGCCTAAGATGATCAAAGCTT 58.794 43.478 0.00 6.78 0.00 3.74
2793 3987 3.201708 ACCAGCCTAAGATGATCAAAGCT 59.798 43.478 0.00 0.00 0.00 3.74
2794 3988 3.549794 ACCAGCCTAAGATGATCAAAGC 58.450 45.455 0.00 0.00 0.00 3.51
2795 3989 4.574013 GTGACCAGCCTAAGATGATCAAAG 59.426 45.833 0.00 0.00 0.00 2.77
2796 3990 4.019411 TGTGACCAGCCTAAGATGATCAAA 60.019 41.667 0.00 0.00 0.00 2.69
2797 3991 3.519107 TGTGACCAGCCTAAGATGATCAA 59.481 43.478 0.00 0.00 0.00 2.57
2798 3992 3.106827 TGTGACCAGCCTAAGATGATCA 58.893 45.455 0.00 0.00 0.00 2.92
2799 3993 3.133721 ACTGTGACCAGCCTAAGATGATC 59.866 47.826 0.00 0.00 42.81 2.92
2800 3994 3.110705 ACTGTGACCAGCCTAAGATGAT 58.889 45.455 0.00 0.00 42.81 2.45
2801 3995 2.540383 ACTGTGACCAGCCTAAGATGA 58.460 47.619 0.00 0.00 42.81 2.92
2802 3996 3.181471 CCTACTGTGACCAGCCTAAGATG 60.181 52.174 0.00 0.00 42.81 2.90
2803 3997 3.034635 CCTACTGTGACCAGCCTAAGAT 58.965 50.000 0.00 0.00 42.81 2.40
2804 3998 2.457598 CCTACTGTGACCAGCCTAAGA 58.542 52.381 0.00 0.00 42.81 2.10
2805 3999 1.482593 CCCTACTGTGACCAGCCTAAG 59.517 57.143 0.00 0.00 42.81 2.18
2806 4000 1.078159 TCCCTACTGTGACCAGCCTAA 59.922 52.381 0.00 0.00 42.81 2.69
2807 4001 0.708209 TCCCTACTGTGACCAGCCTA 59.292 55.000 0.00 0.00 42.81 3.93
2808 4002 0.616111 CTCCCTACTGTGACCAGCCT 60.616 60.000 0.00 0.00 42.81 4.58
2809 4003 0.905337 ACTCCCTACTGTGACCAGCC 60.905 60.000 0.00 0.00 42.81 4.85
2810 4004 1.848652 TACTCCCTACTGTGACCAGC 58.151 55.000 0.00 0.00 42.81 4.85
2811 4005 3.432378 AGTTACTCCCTACTGTGACCAG 58.568 50.000 0.00 0.00 44.68 4.00
2812 4006 3.537795 AGTTACTCCCTACTGTGACCA 57.462 47.619 0.00 0.00 0.00 4.02
2813 4007 5.990120 TTAAGTTACTCCCTACTGTGACC 57.010 43.478 0.00 0.00 0.00 4.02
2814 4008 6.990798 AGTTTAAGTTACTCCCTACTGTGAC 58.009 40.000 0.00 0.00 0.00 3.67
2815 4009 7.946776 ACTAGTTTAAGTTACTCCCTACTGTGA 59.053 37.037 0.00 0.00 0.00 3.58
2816 4010 8.120140 ACTAGTTTAAGTTACTCCCTACTGTG 57.880 38.462 0.00 0.00 0.00 3.66
2817 4011 9.813826 TTACTAGTTTAAGTTACTCCCTACTGT 57.186 33.333 0.00 0.00 0.00 3.55
2819 4013 9.813826 TGTTACTAGTTTAAGTTACTCCCTACT 57.186 33.333 0.00 0.00 31.82 2.57
2822 4016 9.097946 ACATGTTACTAGTTTAAGTTACTCCCT 57.902 33.333 0.00 0.00 31.82 4.20
2859 4053 8.861086 CCCACTATGAATGTAGTAACATAGACT 58.139 37.037 16.37 0.00 45.79 3.24
2860 4054 8.639761 ACCCACTATGAATGTAGTAACATAGAC 58.360 37.037 16.37 0.00 45.79 2.59
2861 4055 8.638873 CACCCACTATGAATGTAGTAACATAGA 58.361 37.037 16.37 0.00 45.79 1.98
2862 4056 7.872993 CCACCCACTATGAATGTAGTAACATAG 59.127 40.741 0.00 0.00 45.79 2.23
2863 4057 7.346175 ACCACCCACTATGAATGTAGTAACATA 59.654 37.037 0.00 0.00 45.79 2.29
2865 4059 5.486063 ACCACCCACTATGAATGTAGTAACA 59.514 40.000 0.00 0.00 40.69 2.41
2866 4060 5.985911 ACCACCCACTATGAATGTAGTAAC 58.014 41.667 0.00 0.00 33.29 2.50
2867 4061 7.565768 TGATACCACCCACTATGAATGTAGTAA 59.434 37.037 0.00 0.00 33.29 2.24
2868 4062 7.070629 TGATACCACCCACTATGAATGTAGTA 58.929 38.462 0.00 0.00 33.29 1.82
2869 4063 5.903010 TGATACCACCCACTATGAATGTAGT 59.097 40.000 0.00 0.00 35.34 2.73
2870 4064 6.419484 TGATACCACCCACTATGAATGTAG 57.581 41.667 0.00 0.00 0.00 2.74
2871 4065 6.239858 CCATGATACCACCCACTATGAATGTA 60.240 42.308 0.00 0.00 0.00 2.29
2872 4066 5.456619 CCATGATACCACCCACTATGAATGT 60.457 44.000 0.00 0.00 0.00 2.71
2873 4067 5.005740 CCATGATACCACCCACTATGAATG 58.994 45.833 0.00 0.00 0.00 2.67
2874 4068 4.043310 CCCATGATACCACCCACTATGAAT 59.957 45.833 0.00 0.00 0.00 2.57
2875 4069 3.394274 CCCATGATACCACCCACTATGAA 59.606 47.826 0.00 0.00 0.00 2.57
2876 4070 2.978978 CCCATGATACCACCCACTATGA 59.021 50.000 0.00 0.00 0.00 2.15
2877 4071 2.711009 ACCCATGATACCACCCACTATG 59.289 50.000 0.00 0.00 0.00 2.23
2878 4072 2.711009 CACCCATGATACCACCCACTAT 59.289 50.000 0.00 0.00 0.00 2.12
2879 4073 2.123589 CACCCATGATACCACCCACTA 58.876 52.381 0.00 0.00 0.00 2.74
2880 4074 0.918983 CACCCATGATACCACCCACT 59.081 55.000 0.00 0.00 0.00 4.00
2881 4075 3.494850 CACCCATGATACCACCCAC 57.505 57.895 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.