Multiple sequence alignment - TraesCS6B01G145800

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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 TraesCS6B01G145800 chr6B 100.000 3000 0 0 1 3000 145897701 145900700 0.000000e+00 5541.0
1 TraesCS6B01G145800 chr6B 95.036 826 34 4 1223 2047 145891417 145892236 0.000000e+00 1291.0
2 TraesCS6B01G145800 chr6B 94.356 815 46 0 1 815 145889527 145890341 0.000000e+00 1251.0
3 TraesCS6B01G145800 chr6B 95.261 422 16 4 808 1226 145890875 145891295 0.000000e+00 665.0
4 TraesCS6B01G145800 chr6B 85.843 332 29 7 2380 2696 145892507 145892835 1.330000e-88 337.0
5 TraesCS6B01G145800 chr6B 93.478 92 5 1 2114 2205 145892234 145892324 5.220000e-28 135.0
6 TraesCS6B01G145800 chr6B 90.698 43 4 0 2045 2087 85383763 85383721 1.160000e-04 58.4
7 TraesCS6B01G145800 chr6B 97.059 34 1 0 2912 2945 138634657 138634624 1.160000e-04 58.4
8 TraesCS6B01G145800 chr6B 97.059 34 1 0 2912 2945 138673495 138673462 1.160000e-04 58.4
9 TraesCS6B01G145800 chr6D 95.560 1802 61 9 828 2612 71143471 71145270 0.000000e+00 2867.0
10 TraesCS6B01G145800 chr6D 94.293 1244 64 6 808 2047 71135388 71136628 0.000000e+00 1897.0
11 TraesCS6B01G145800 chr6D 97.178 815 23 0 1 815 71142085 71142899 0.000000e+00 1378.0
12 TraesCS6B01G145800 chr6D 93.608 704 45 0 112 815 71134151 71134854 0.000000e+00 1051.0
13 TraesCS6B01G145800 chr6D 91.197 284 20 3 2114 2393 71136626 71136908 6.070000e-102 381.0
14 TraesCS6B01G145800 chr6D 85.915 71 7 2 2045 2112 404329077 404329007 4.150000e-09 73.1
15 TraesCS6B01G145800 chr6A 95.944 1208 47 2 838 2044 87930723 87931929 0.000000e+00 1958.0
16 TraesCS6B01G145800 chr6A 96.476 823 20 2 1 815 87929308 87930129 0.000000e+00 1351.0
17 TraesCS6B01G145800 chr6A 85.581 645 39 25 2115 2710 87931931 87932570 7.060000e-176 627.0
18 TraesCS6B01G145800 chr6A 95.455 44 0 2 2074 2115 263872842 263872885 5.370000e-08 69.4
19 TraesCS6B01G145800 chr6A 90.698 43 4 0 2045 2087 263872885 263872843 1.160000e-04 58.4
20 TraesCS6B01G145800 chr3D 90.512 1191 101 10 834 2017 360334828 360336013 0.000000e+00 1563.0
21 TraesCS6B01G145800 chr3D 88.433 1219 112 14 808 2017 360558268 360559466 0.000000e+00 1443.0
22 TraesCS6B01G145800 chr3D 93.620 815 51 1 1 815 360333424 360334237 0.000000e+00 1216.0
23 TraesCS6B01G145800 chr3D 90.196 816 64 7 1 815 360556848 360557648 0.000000e+00 1050.0
24 TraesCS6B01G145800 chr3B 90.480 1187 101 9 834 2014 466265152 466266332 0.000000e+00 1555.0
25 TraesCS6B01G145800 chr3B 93.006 815 57 0 1 815 466263751 466264565 0.000000e+00 1190.0
26 TraesCS6B01G145800 chr3B 89.828 816 67 7 1 815 466609569 466610369 0.000000e+00 1033.0
27 TraesCS6B01G145800 chr3B 90.698 43 4 0 2045 2087 312156993 312156951 1.160000e-04 58.4
28 TraesCS6B01G145800 chr3A 90.099 1212 98 15 839 2045 479772814 479774008 0.000000e+00 1554.0
29 TraesCS6B01G145800 chr3A 89.298 1196 116 9 833 2024 480051121 480052308 0.000000e+00 1489.0
30 TraesCS6B01G145800 chr3A 92.270 815 61 1 1 815 479771409 479772221 0.000000e+00 1155.0
31 TraesCS6B01G145800 chr3A 88.767 819 73 10 1 815 480049730 480050533 0.000000e+00 985.0
32 TraesCS6B01G145800 chr3A 92.857 42 3 0 2045 2086 100417846 100417805 8.980000e-06 62.1
33 TraesCS6B01G145800 chr5D 92.308 65 5 0 2901 2965 52054544 52054608 3.180000e-15 93.5
34 TraesCS6B01G145800 chr5D 93.182 44 1 2 2074 2115 28479991 28480034 2.500000e-06 63.9
35 TraesCS6B01G145800 chr5D 91.111 45 4 0 2043 2087 421531411 421531367 8.980000e-06 62.1
36 TraesCS6B01G145800 chr5B 90.769 65 6 0 2901 2965 55179467 55179531 1.480000e-13 87.9
37 TraesCS6B01G145800 chr5A 94.118 51 3 0 2915 2965 41302765 41302815 8.920000e-11 78.7
38 TraesCS6B01G145800 chr5A 93.182 44 1 2 2074 2115 19105034 19105077 2.500000e-06 63.9
39 TraesCS6B01G145800 chr4D 93.333 45 1 2 2074 2116 5067867 5067911 6.940000e-07 65.8
40 TraesCS6B01G145800 chr2B 95.238 42 0 2 2076 2115 526778362 526778403 6.940000e-07 65.8
41 TraesCS6B01G145800 chr2B 94.872 39 1 1 2040 2078 526778407 526778370 3.230000e-05 60.2
42 TraesCS6B01G145800 chr2B 97.059 34 1 0 2045 2078 247368538 247368571 1.160000e-04 58.4
43 TraesCS6B01G145800 chr1B 93.333 45 1 2 2074 2116 56061763 56061719 6.940000e-07 65.8
44 TraesCS6B01G145800 chr1A 93.023 43 2 1 2074 2115 498055344 498055386 8.980000e-06 62.1
45 TraesCS6B01G145800 chrUn 97.059 34 1 0 2912 2945 194970051 194970084 1.160000e-04 58.4


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 TraesCS6B01G145800 chr6B 145897701 145900700 2999 False 5541.000000 5541 100.000000 1 3000 1 chr6B.!!$F1 2999
1 TraesCS6B01G145800 chr6B 145889527 145892835 3308 False 735.800000 1291 92.794800 1 2696 5 chr6B.!!$F2 2695
2 TraesCS6B01G145800 chr6D 71142085 71145270 3185 False 2122.500000 2867 96.369000 1 2612 2 chr6D.!!$F2 2611
3 TraesCS6B01G145800 chr6D 71134151 71136908 2757 False 1109.666667 1897 93.032667 112 2393 3 chr6D.!!$F1 2281
4 TraesCS6B01G145800 chr6A 87929308 87932570 3262 False 1312.000000 1958 92.667000 1 2710 3 chr6A.!!$F2 2709
5 TraesCS6B01G145800 chr3D 360333424 360336013 2589 False 1389.500000 1563 92.066000 1 2017 2 chr3D.!!$F1 2016
6 TraesCS6B01G145800 chr3D 360556848 360559466 2618 False 1246.500000 1443 89.314500 1 2017 2 chr3D.!!$F2 2016
7 TraesCS6B01G145800 chr3B 466263751 466266332 2581 False 1372.500000 1555 91.743000 1 2014 2 chr3B.!!$F2 2013
8 TraesCS6B01G145800 chr3B 466609569 466610369 800 False 1033.000000 1033 89.828000 1 815 1 chr3B.!!$F1 814
9 TraesCS6B01G145800 chr3A 479771409 479774008 2599 False 1354.500000 1554 91.184500 1 2045 2 chr3A.!!$F1 2044
10 TraesCS6B01G145800 chr3A 480049730 480052308 2578 False 1237.000000 1489 89.032500 1 2024 2 chr3A.!!$F2 2023

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
771 785 4.433022 CGACTCTCAGTTGACGCATTAAAC 60.433 45.833 0.0 0.0 31.05 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2752 3696 0.179081 AGATTTTACTCGGCCGCCTC 60.179 55.0 23.51 8.64 0.0 4.7 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
113 114 7.605410 TGAAAGACGTAAAATACAGGATTCC 57.395 36.000 0.00 0.00 0.00 3.01
771 785 4.433022 CGACTCTCAGTTGACGCATTAAAC 60.433 45.833 0.00 0.00 31.05 2.01
810 824 5.077441 AGGAGATAACCTGGGCCTTATAGTA 59.923 44.000 4.53 0.00 39.01 1.82
986 1686 8.792633 AGATCGGAAGTCAAAAATCAATACAAA 58.207 29.630 0.00 0.00 0.00 2.83
1065 1765 2.742053 CAGTTTCAAGTACCCATCACGG 59.258 50.000 0.00 0.00 0.00 4.94
1476 2309 3.381908 GGAGTCGAGATTAAGAGCCTGAA 59.618 47.826 0.00 0.00 0.00 3.02
1949 2782 3.543536 GAGGCCCTGATGCGGATCC 62.544 68.421 14.82 0.00 0.00 3.36
2058 2894 3.567478 TCTTACTACTCCCTCCGTACC 57.433 52.381 0.00 0.00 0.00 3.34
2073 2909 6.239008 CCCTCCGTACCAAAATATAAGACGTA 60.239 42.308 0.00 0.00 0.00 3.57
2078 2914 9.033481 CCGTACCAAAATATAAGACGTATTTGA 57.967 33.333 0.00 0.00 33.35 2.69
2111 2960 7.427989 AACGTCTTATATTTTGGTAGAGGGA 57.572 36.000 0.00 0.00 0.00 4.20
2186 3035 5.522456 TGTGATTTGAGAAGTGAATGCAAC 58.478 37.500 0.00 0.00 0.00 4.17
2189 3038 6.089016 GTGATTTGAGAAGTGAATGCAACATG 59.911 38.462 0.00 0.00 0.00 3.21
2316 3178 2.545731 GATTTCGAGCTCTGACCCTTC 58.454 52.381 12.85 2.37 0.00 3.46
2440 3355 4.117685 ACTACGAACACACAGGTTTCTTC 58.882 43.478 0.00 0.00 0.00 2.87
2441 3356 2.980568 ACGAACACACAGGTTTCTTCA 58.019 42.857 0.00 0.00 0.00 3.02
2541 3456 6.255020 CAGAATCCATGCAAATTTTAGAGCAC 59.745 38.462 3.31 0.00 40.14 4.40
2545 3460 1.885887 TGCAAATTTTAGAGCACCGCT 59.114 42.857 0.00 0.00 43.88 5.52
2560 3475 3.081409 GCTTACCTCTGGGCCGGA 61.081 66.667 15.74 15.74 35.63 5.14
2612 3529 1.361668 CCATCTTCACCGGCGAGTTG 61.362 60.000 9.30 2.14 0.00 3.16
2613 3530 1.079127 ATCTTCACCGGCGAGTTGG 60.079 57.895 9.30 0.00 0.00 3.77
2614 3531 1.541310 ATCTTCACCGGCGAGTTGGA 61.541 55.000 9.30 0.97 0.00 3.53
2615 3532 1.301401 CTTCACCGGCGAGTTGGAA 60.301 57.895 9.30 4.94 0.00 3.53
2616 3533 1.566018 CTTCACCGGCGAGTTGGAAC 61.566 60.000 9.30 0.00 0.00 3.62
2670 3612 2.614057 CCGAAATGGACCTGCATAACTC 59.386 50.000 0.00 0.00 42.00 3.01
2710 3654 7.118825 CCTTAGACCGGTTAAAGGAGTAAAAAG 59.881 40.741 31.07 10.91 40.85 2.27
2711 3655 5.933617 AGACCGGTTAAAGGAGTAAAAAGT 58.066 37.500 9.42 0.00 0.00 2.66
2712 3656 6.359804 AGACCGGTTAAAGGAGTAAAAAGTT 58.640 36.000 9.42 0.00 0.00 2.66
2713 3657 6.830324 AGACCGGTTAAAGGAGTAAAAAGTTT 59.170 34.615 9.42 0.00 0.00 2.66
2714 3658 7.992608 AGACCGGTTAAAGGAGTAAAAAGTTTA 59.007 33.333 9.42 0.00 0.00 2.01
2715 3659 8.158169 ACCGGTTAAAGGAGTAAAAAGTTTAG 57.842 34.615 0.00 0.00 0.00 1.85
2716 3660 7.775093 ACCGGTTAAAGGAGTAAAAAGTTTAGT 59.225 33.333 0.00 0.00 0.00 2.24
2717 3661 9.271828 CCGGTTAAAGGAGTAAAAAGTTTAGTA 57.728 33.333 0.00 0.00 0.00 1.82
2722 3666 8.599055 AAAGGAGTAAAAAGTTTAGTACTCGG 57.401 34.615 21.61 0.00 42.17 4.63
2723 3667 6.162079 AGGAGTAAAAAGTTTAGTACTCGGC 58.838 40.000 21.61 14.39 42.17 5.54
2724 3668 5.349817 GGAGTAAAAAGTTTAGTACTCGGCC 59.650 44.000 21.61 12.49 42.17 6.13
2725 3669 5.240891 AGTAAAAAGTTTAGTACTCGGCCC 58.759 41.667 0.00 0.00 35.54 5.80
2726 3670 2.375173 AAAGTTTAGTACTCGGCCCG 57.625 50.000 0.00 0.00 35.54 6.13
2727 3671 0.108472 AAGTTTAGTACTCGGCCCGC 60.108 55.000 0.00 0.00 35.54 6.13
2728 3672 1.875364 GTTTAGTACTCGGCCCGCG 60.875 63.158 0.00 0.00 0.00 6.46
2729 3673 3.067480 TTTAGTACTCGGCCCGCGG 62.067 63.158 21.04 21.04 0.00 6.46
2730 3674 3.993614 TTAGTACTCGGCCCGCGGA 62.994 63.158 30.73 5.11 0.00 5.54
2738 3682 3.777910 GGCCCGCGGAGGAGTAAA 61.778 66.667 30.73 0.00 45.00 2.01
2739 3683 2.266689 GCCCGCGGAGGAGTAAAA 59.733 61.111 30.73 0.00 45.00 1.52
2740 3684 1.376295 GCCCGCGGAGGAGTAAAAA 60.376 57.895 30.73 0.00 45.00 1.94
2741 3685 0.746923 GCCCGCGGAGGAGTAAAAAT 60.747 55.000 30.73 0.00 45.00 1.82
2742 3686 1.473788 GCCCGCGGAGGAGTAAAAATA 60.474 52.381 30.73 0.00 45.00 1.40
2743 3687 2.207590 CCCGCGGAGGAGTAAAAATAC 58.792 52.381 30.73 0.00 45.00 1.89
2744 3688 2.159000 CCCGCGGAGGAGTAAAAATACT 60.159 50.000 30.73 0.00 45.00 2.12
2745 3689 3.121544 CCGCGGAGGAGTAAAAATACTC 58.878 50.000 24.07 7.34 45.00 2.59
2746 3690 2.787680 CGCGGAGGAGTAAAAATACTCG 59.212 50.000 0.00 1.51 45.51 4.18
2747 3691 3.121544 GCGGAGGAGTAAAAATACTCGG 58.878 50.000 9.25 0.00 45.51 4.63
2748 3692 3.181483 GCGGAGGAGTAAAAATACTCGGA 60.181 47.826 9.25 0.00 45.51 4.55
2749 3693 4.357996 CGGAGGAGTAAAAATACTCGGAC 58.642 47.826 9.25 4.42 45.51 4.79
2750 3694 4.097589 CGGAGGAGTAAAAATACTCGGACT 59.902 45.833 9.25 2.56 45.51 3.85
2751 3695 5.590145 GGAGGAGTAAAAATACTCGGACTC 58.410 45.833 9.25 9.70 45.51 3.36
2752 3696 5.246145 AGGAGTAAAAATACTCGGACTCG 57.754 43.478 9.25 0.00 45.51 4.18
2753 3697 4.946157 AGGAGTAAAAATACTCGGACTCGA 59.054 41.667 9.25 0.00 45.51 4.04
2766 3710 3.515286 CTCGAGGCGGCCGAGTAA 61.515 66.667 33.48 8.52 45.89 2.24
2767 3711 3.060020 CTCGAGGCGGCCGAGTAAA 62.060 63.158 33.48 9.74 45.89 2.01
2768 3712 2.125832 CGAGGCGGCCGAGTAAAA 60.126 61.111 33.48 0.00 0.00 1.52
2769 3713 1.520787 CGAGGCGGCCGAGTAAAAT 60.521 57.895 33.48 4.94 0.00 1.82
2770 3714 1.488261 CGAGGCGGCCGAGTAAAATC 61.488 60.000 33.48 13.41 0.00 2.17
2771 3715 0.179081 GAGGCGGCCGAGTAAAATCT 60.179 55.000 33.48 11.61 0.00 2.40
2772 3716 0.179081 AGGCGGCCGAGTAAAATCTC 60.179 55.000 33.48 6.40 0.00 2.75
2782 3726 2.937149 GAGTAAAATCTCGTTGCTCCCC 59.063 50.000 0.00 0.00 33.17 4.81
2783 3727 2.572104 AGTAAAATCTCGTTGCTCCCCT 59.428 45.455 0.00 0.00 0.00 4.79
2784 3728 2.115343 AAAATCTCGTTGCTCCCCTC 57.885 50.000 0.00 0.00 0.00 4.30
2785 3729 0.253327 AAATCTCGTTGCTCCCCTCC 59.747 55.000 0.00 0.00 0.00 4.30
2786 3730 0.909610 AATCTCGTTGCTCCCCTCCA 60.910 55.000 0.00 0.00 0.00 3.86
2787 3731 0.909610 ATCTCGTTGCTCCCCTCCAA 60.910 55.000 0.00 0.00 0.00 3.53
2788 3732 1.376037 CTCGTTGCTCCCCTCCAAC 60.376 63.158 0.00 0.00 38.30 3.77
2789 3733 2.359975 CGTTGCTCCCCTCCAACC 60.360 66.667 0.00 0.00 38.41 3.77
2790 3734 2.035783 GTTGCTCCCCTCCAACCC 59.964 66.667 0.00 0.00 36.27 4.11
2791 3735 3.264845 TTGCTCCCCTCCAACCCC 61.265 66.667 0.00 0.00 0.00 4.95
2794 3738 2.609610 CTCCCCTCCAACCCCGAA 60.610 66.667 0.00 0.00 0.00 4.30
2795 3739 2.001269 CTCCCCTCCAACCCCGAAT 61.001 63.158 0.00 0.00 0.00 3.34
2796 3740 1.984288 CTCCCCTCCAACCCCGAATC 61.984 65.000 0.00 0.00 0.00 2.52
2797 3741 2.595655 CCCTCCAACCCCGAATCC 59.404 66.667 0.00 0.00 0.00 3.01
2798 3742 2.189521 CCTCCAACCCCGAATCCG 59.810 66.667 0.00 0.00 0.00 4.18
2799 3743 2.666098 CCTCCAACCCCGAATCCGT 61.666 63.158 0.00 0.00 0.00 4.69
2800 3744 1.153429 CTCCAACCCCGAATCCGTC 60.153 63.158 0.00 0.00 0.00 4.79
2801 3745 1.895020 CTCCAACCCCGAATCCGTCA 61.895 60.000 0.00 0.00 0.00 4.35
2802 3746 1.743995 CCAACCCCGAATCCGTCAC 60.744 63.158 0.00 0.00 0.00 3.67
2803 3747 1.743995 CAACCCCGAATCCGTCACC 60.744 63.158 0.00 0.00 0.00 4.02
2804 3748 3.305177 AACCCCGAATCCGTCACCG 62.305 63.158 0.00 0.00 0.00 4.94
2806 3750 4.143333 CCCGAATCCGTCACCGCT 62.143 66.667 0.00 0.00 0.00 5.52
2807 3751 2.885644 CCGAATCCGTCACCGCTG 60.886 66.667 0.00 0.00 0.00 5.18
2808 3752 3.554692 CGAATCCGTCACCGCTGC 61.555 66.667 0.00 0.00 0.00 5.25
2809 3753 3.195698 GAATCCGTCACCGCTGCC 61.196 66.667 0.00 0.00 0.00 4.85
2810 3754 3.950794 GAATCCGTCACCGCTGCCA 62.951 63.158 0.00 0.00 0.00 4.92
2811 3755 4.760047 ATCCGTCACCGCTGCCAC 62.760 66.667 0.00 0.00 0.00 5.01
2814 3758 3.490759 CGTCACCGCTGCCACATC 61.491 66.667 0.00 0.00 0.00 3.06
2815 3759 3.127533 GTCACCGCTGCCACATCC 61.128 66.667 0.00 0.00 0.00 3.51
2816 3760 3.635191 TCACCGCTGCCACATCCA 61.635 61.111 0.00 0.00 0.00 3.41
2817 3761 2.672651 CACCGCTGCCACATCCAA 60.673 61.111 0.00 0.00 0.00 3.53
2818 3762 2.672996 ACCGCTGCCACATCCAAC 60.673 61.111 0.00 0.00 0.00 3.77
2819 3763 3.443045 CCGCTGCCACATCCAACC 61.443 66.667 0.00 0.00 0.00 3.77
2820 3764 3.443045 CGCTGCCACATCCAACCC 61.443 66.667 0.00 0.00 0.00 4.11
2821 3765 3.070576 GCTGCCACATCCAACCCC 61.071 66.667 0.00 0.00 0.00 4.95
2822 3766 2.440147 CTGCCACATCCAACCCCA 59.560 61.111 0.00 0.00 0.00 4.96
2823 3767 1.228831 CTGCCACATCCAACCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
2824 3768 1.532794 TGCCACATCCAACCCCAAC 60.533 57.895 0.00 0.00 0.00 3.77
2825 3769 2.282783 GCCACATCCAACCCCAACC 61.283 63.158 0.00 0.00 0.00 3.77
2826 3770 1.609210 CCACATCCAACCCCAACCC 60.609 63.158 0.00 0.00 0.00 4.11
2827 3771 1.609210 CACATCCAACCCCAACCCC 60.609 63.158 0.00 0.00 0.00 4.95
2828 3772 2.038813 CATCCAACCCCAACCCCC 59.961 66.667 0.00 0.00 0.00 5.40
2829 3773 3.668142 ATCCAACCCCAACCCCCG 61.668 66.667 0.00 0.00 0.00 5.73
2832 3776 4.671590 CAACCCCAACCCCCGGTC 62.672 72.222 0.00 0.00 33.12 4.79
2854 3798 4.729918 CCACCACCAGCTCAGCCC 62.730 72.222 0.00 0.00 0.00 5.19
2855 3799 4.729918 CACCACCAGCTCAGCCCC 62.730 72.222 0.00 0.00 0.00 5.80
2893 3837 3.470888 CGTCCCACCCCTAGGCTG 61.471 72.222 2.05 0.03 36.11 4.85
2894 3838 3.798511 GTCCCACCCCTAGGCTGC 61.799 72.222 2.05 0.00 36.11 5.25
2912 3856 2.745884 CGCTGCCGGATTTCACCA 60.746 61.111 5.05 0.00 0.00 4.17
2913 3857 2.331893 CGCTGCCGGATTTCACCAA 61.332 57.895 5.05 0.00 0.00 3.67
2914 3858 1.656818 CGCTGCCGGATTTCACCAAT 61.657 55.000 5.05 0.00 0.00 3.16
2915 3859 0.101219 GCTGCCGGATTTCACCAATC 59.899 55.000 5.05 0.00 40.79 2.67
2916 3860 1.755179 CTGCCGGATTTCACCAATCT 58.245 50.000 5.05 0.00 41.22 2.40
2917 3861 1.402968 CTGCCGGATTTCACCAATCTG 59.597 52.381 5.05 0.00 45.05 2.90
2928 3872 3.657956 CCAATCTGGTCGAGCTCTC 57.342 57.895 16.64 4.71 31.35 3.20
2938 3882 4.742201 GAGCTCTCGCGGTTGCCA 62.742 66.667 6.13 0.00 42.32 4.92
2939 3883 4.087892 AGCTCTCGCGGTTGCCAT 62.088 61.111 6.13 0.00 42.32 4.40
2940 3884 3.869272 GCTCTCGCGGTTGCCATG 61.869 66.667 6.13 0.00 38.08 3.66
2941 3885 3.197790 CTCTCGCGGTTGCCATGG 61.198 66.667 7.63 7.63 38.08 3.66
2947 3891 3.140141 CGGTTGCCATGGCGGATT 61.140 61.111 30.87 0.00 45.51 3.01
2948 3892 2.709883 CGGTTGCCATGGCGGATTT 61.710 57.895 30.87 0.00 45.51 2.17
2949 3893 1.153588 GGTTGCCATGGCGGATTTG 60.154 57.895 30.87 0.00 45.51 2.32
2950 3894 1.153588 GTTGCCATGGCGGATTTGG 60.154 57.895 30.87 0.00 45.51 3.28
2951 3895 2.357575 TTGCCATGGCGGATTTGGG 61.358 57.895 30.87 0.00 45.51 4.12
2952 3896 3.539791 GCCATGGCGGATTTGGGG 61.540 66.667 23.48 0.00 36.56 4.96
2953 3897 3.539791 CCATGGCGGATTTGGGGC 61.540 66.667 0.00 0.00 36.56 5.80
2954 3898 2.442643 CATGGCGGATTTGGGGCT 60.443 61.111 0.00 0.00 0.00 5.19
2955 3899 2.123726 ATGGCGGATTTGGGGCTC 60.124 61.111 0.00 0.00 0.00 4.70
2956 3900 2.693871 ATGGCGGATTTGGGGCTCT 61.694 57.895 0.00 0.00 0.00 4.09
2957 3901 2.830370 GGCGGATTTGGGGCTCTG 60.830 66.667 0.00 0.00 0.00 3.35
2958 3902 2.830370 GCGGATTTGGGGCTCTGG 60.830 66.667 0.00 0.00 0.00 3.86
2959 3903 2.998097 CGGATTTGGGGCTCTGGA 59.002 61.111 0.00 0.00 0.00 3.86
2960 3904 1.302949 CGGATTTGGGGCTCTGGAA 59.697 57.895 0.00 0.00 0.00 3.53
2961 3905 1.032114 CGGATTTGGGGCTCTGGAAC 61.032 60.000 0.00 0.00 0.00 3.62
2962 3906 0.684479 GGATTTGGGGCTCTGGAACC 60.684 60.000 0.00 0.00 0.00 3.62
2963 3907 0.039618 GATTTGGGGCTCTGGAACCA 59.960 55.000 0.00 0.00 0.00 3.67
2964 3908 0.040204 ATTTGGGGCTCTGGAACCAG 59.960 55.000 14.01 14.01 44.86 4.00
2965 3909 1.360393 TTTGGGGCTCTGGAACCAGT 61.360 55.000 18.60 0.00 43.96 4.00
2966 3910 2.067932 TTGGGGCTCTGGAACCAGTG 62.068 60.000 18.60 17.11 43.96 3.66
2967 3911 2.224159 GGGGCTCTGGAACCAGTGA 61.224 63.158 21.92 5.15 43.96 3.41
2968 3912 1.003233 GGGCTCTGGAACCAGTGAC 60.003 63.158 21.92 19.71 42.85 3.67
2969 3913 1.374758 GGCTCTGGAACCAGTGACG 60.375 63.158 21.92 10.74 43.96 4.35
2970 3914 1.374758 GCTCTGGAACCAGTGACGG 60.375 63.158 21.92 10.04 43.96 4.79
2971 3915 1.816863 GCTCTGGAACCAGTGACGGA 61.817 60.000 21.92 3.27 43.96 4.69
2972 3916 0.038159 CTCTGGAACCAGTGACGGAC 60.038 60.000 18.60 0.00 43.96 4.79
2973 3917 0.757561 TCTGGAACCAGTGACGGACA 60.758 55.000 18.60 0.00 43.96 4.02
2974 3918 0.321671 CTGGAACCAGTGACGGACAT 59.678 55.000 12.21 0.00 39.10 3.06
2975 3919 0.034756 TGGAACCAGTGACGGACATG 59.965 55.000 0.00 0.00 0.00 3.21
2976 3920 0.673644 GGAACCAGTGACGGACATGG 60.674 60.000 0.00 7.13 38.83 3.66
2977 3921 1.298859 GAACCAGTGACGGACATGGC 61.299 60.000 0.00 0.00 36.21 4.40
2978 3922 2.815211 CCAGTGACGGACATGGCG 60.815 66.667 0.00 0.00 0.00 5.69
2979 3923 2.815211 CAGTGACGGACATGGCGG 60.815 66.667 4.24 4.24 0.00 6.13
2980 3924 4.760047 AGTGACGGACATGGCGGC 62.760 66.667 5.94 0.00 0.00 6.53
2998 3942 3.140814 GGGCTGCGGAATTGGGTC 61.141 66.667 0.00 0.00 0.00 4.46
2999 3943 2.361104 GGCTGCGGAATTGGGTCA 60.361 61.111 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.586001 GGATCCTTTACCAATGCATGATGT 59.414 41.667 3.84 0.14 0.00 3.06
113 114 3.278574 TGATAAGGAATTGGGCACTTCG 58.721 45.455 0.00 0.00 0.00 3.79
810 824 9.793252 GATTGTTAATTCTCATATGCAAACTGT 57.207 29.630 0.00 0.00 0.00 3.55
986 1686 1.678123 GCATCATGCCCTCATCGCTAT 60.678 52.381 0.00 0.00 37.42 2.97
1065 1765 4.883585 TCACTGAATATTTGGACATCAGGC 59.116 41.667 6.11 0.00 41.34 4.85
1120 1820 6.857964 ACAAGACTACAAAAGATTGCAAATCG 59.142 34.615 1.71 0.00 40.34 3.34
1476 2309 6.327386 TCTGATCCCTTAACCAGCTAATTT 57.673 37.500 0.00 0.00 0.00 1.82
1810 2643 2.544685 CTCACCATGACTCGATCCAAC 58.455 52.381 0.00 0.00 0.00 3.77
1949 2782 3.023946 CGAAGCATAGACTCCATCCTG 57.976 52.381 0.00 0.00 0.00 3.86
2044 2880 7.014615 GTCTTATATTTTGGTACGGAGGGAGTA 59.985 40.741 0.00 0.00 0.00 2.59
2091 2940 9.670442 ATGTACTCCCTCTACCAAAATATAAGA 57.330 33.333 0.00 0.00 0.00 2.10
2111 2960 5.477984 TGTACTAGGAACAAACGGATGTACT 59.522 40.000 0.00 1.62 32.02 2.73
2336 3199 5.133221 ACCTGCAGTTTTTGTGAAGTAGAT 58.867 37.500 13.81 0.00 0.00 1.98
2440 3355 4.914291 GACGTTGTCGCCCTTTTG 57.086 55.556 0.00 0.00 41.18 2.44
2541 3456 4.530857 CGGCCCAGAGGTAAGCGG 62.531 72.222 0.00 0.00 34.57 5.52
2545 3460 3.072468 CGTCCGGCCCAGAGGTAA 61.072 66.667 0.00 0.00 34.57 2.85
2613 3530 2.047179 AGCCCGCGGAAAGAGTTC 60.047 61.111 30.73 4.65 0.00 3.01
2614 3531 2.358737 CAGCCCGCGGAAAGAGTT 60.359 61.111 30.73 3.83 0.00 3.01
2615 3532 4.394712 CCAGCCCGCGGAAAGAGT 62.395 66.667 30.73 0.15 0.00 3.24
2644 3585 2.046285 CAGGTCCATTTCGGCCCAC 61.046 63.158 0.00 0.00 32.87 4.61
2646 3587 3.140814 GCAGGTCCATTTCGGCCC 61.141 66.667 0.00 0.00 32.87 5.80
2686 3630 7.508687 ACTTTTTACTCCTTTAACCGGTCTAA 58.491 34.615 8.04 6.34 0.00 2.10
2689 3633 6.624352 AACTTTTTACTCCTTTAACCGGTC 57.376 37.500 8.04 0.00 0.00 4.79
2710 3654 1.875364 CGCGGGCCGAGTACTAAAC 60.875 63.158 33.44 7.29 40.02 2.01
2711 3655 2.491152 CGCGGGCCGAGTACTAAA 59.509 61.111 33.44 0.00 40.02 1.85
2712 3656 3.520862 CCGCGGGCCGAGTACTAA 61.521 66.667 33.44 0.00 40.02 2.24
2713 3657 4.488136 TCCGCGGGCCGAGTACTA 62.488 66.667 33.44 8.72 40.02 1.82
2721 3665 2.808181 TTTTTACTCCTCCGCGGGCC 62.808 60.000 27.83 0.00 0.00 5.80
2722 3666 0.746923 ATTTTTACTCCTCCGCGGGC 60.747 55.000 27.83 0.00 0.00 6.13
2723 3667 2.159000 AGTATTTTTACTCCTCCGCGGG 60.159 50.000 27.83 16.14 0.00 6.13
2724 3668 3.121544 GAGTATTTTTACTCCTCCGCGG 58.878 50.000 22.12 22.12 40.31 6.46
2725 3669 2.787680 CGAGTATTTTTACTCCTCCGCG 59.212 50.000 0.00 0.00 42.52 6.46
2726 3670 3.121544 CCGAGTATTTTTACTCCTCCGC 58.878 50.000 7.40 0.00 42.52 5.54
2727 3671 4.097589 AGTCCGAGTATTTTTACTCCTCCG 59.902 45.833 7.40 0.00 42.52 4.63
2728 3672 5.590145 GAGTCCGAGTATTTTTACTCCTCC 58.410 45.833 7.40 0.00 42.52 4.30
2729 3673 5.065731 TCGAGTCCGAGTATTTTTACTCCTC 59.934 44.000 7.40 7.38 42.52 3.71
2730 3674 4.946157 TCGAGTCCGAGTATTTTTACTCCT 59.054 41.667 7.40 0.43 42.52 3.69
2731 3675 5.240713 TCGAGTCCGAGTATTTTTACTCC 57.759 43.478 7.40 0.00 42.52 3.85
2750 3694 1.952102 ATTTTACTCGGCCGCCTCGA 61.952 55.000 23.51 0.55 35.24 4.04
2751 3695 1.488261 GATTTTACTCGGCCGCCTCG 61.488 60.000 23.51 11.17 0.00 4.63
2752 3696 0.179081 AGATTTTACTCGGCCGCCTC 60.179 55.000 23.51 8.64 0.00 4.70
2753 3697 0.179081 GAGATTTTACTCGGCCGCCT 60.179 55.000 23.51 10.25 0.00 5.52
2754 3698 2.308344 GAGATTTTACTCGGCCGCC 58.692 57.895 23.51 0.00 0.00 6.13
2761 3705 2.937149 GGGGAGCAACGAGATTTTACTC 59.063 50.000 0.00 0.00 0.00 2.59
2762 3706 2.572104 AGGGGAGCAACGAGATTTTACT 59.428 45.455 0.00 0.00 0.00 2.24
2763 3707 2.937149 GAGGGGAGCAACGAGATTTTAC 59.063 50.000 0.00 0.00 0.00 2.01
2764 3708 2.093128 GGAGGGGAGCAACGAGATTTTA 60.093 50.000 0.00 0.00 0.00 1.52
2765 3709 1.340114 GGAGGGGAGCAACGAGATTTT 60.340 52.381 0.00 0.00 0.00 1.82
2766 3710 0.253327 GGAGGGGAGCAACGAGATTT 59.747 55.000 0.00 0.00 0.00 2.17
2767 3711 0.909610 TGGAGGGGAGCAACGAGATT 60.910 55.000 0.00 0.00 0.00 2.40
2768 3712 0.909610 TTGGAGGGGAGCAACGAGAT 60.910 55.000 0.00 0.00 0.00 2.75
2769 3713 1.535444 TTGGAGGGGAGCAACGAGA 60.535 57.895 0.00 0.00 0.00 4.04
2770 3714 1.376037 GTTGGAGGGGAGCAACGAG 60.376 63.158 0.00 0.00 0.00 4.18
2771 3715 2.747686 GTTGGAGGGGAGCAACGA 59.252 61.111 0.00 0.00 0.00 3.85
2772 3716 2.359975 GGTTGGAGGGGAGCAACG 60.360 66.667 0.00 0.00 0.00 4.10
2773 3717 2.035783 GGGTTGGAGGGGAGCAAC 59.964 66.667 0.00 0.00 0.00 4.17
2774 3718 3.264845 GGGGTTGGAGGGGAGCAA 61.265 66.667 0.00 0.00 0.00 3.91
2777 3721 1.984288 GATTCGGGGTTGGAGGGGAG 61.984 65.000 0.00 0.00 0.00 4.30
2778 3722 1.999002 GATTCGGGGTTGGAGGGGA 60.999 63.158 0.00 0.00 0.00 4.81
2779 3723 2.595655 GATTCGGGGTTGGAGGGG 59.404 66.667 0.00 0.00 0.00 4.79
2780 3724 2.595655 GGATTCGGGGTTGGAGGG 59.404 66.667 0.00 0.00 0.00 4.30
2781 3725 2.189521 CGGATTCGGGGTTGGAGG 59.810 66.667 0.00 0.00 0.00 4.30
2782 3726 1.153429 GACGGATTCGGGGTTGGAG 60.153 63.158 0.00 0.00 41.39 3.86
2783 3727 1.914263 TGACGGATTCGGGGTTGGA 60.914 57.895 0.00 0.00 41.39 3.53
2784 3728 1.743995 GTGACGGATTCGGGGTTGG 60.744 63.158 0.00 0.00 41.39 3.77
2785 3729 1.743995 GGTGACGGATTCGGGGTTG 60.744 63.158 0.00 0.00 41.39 3.77
2786 3730 2.666812 GGTGACGGATTCGGGGTT 59.333 61.111 0.00 0.00 41.39 4.11
2798 3742 3.127533 GGATGTGGCAGCGGTGAC 61.128 66.667 20.69 17.95 0.00 3.67
2799 3743 3.189376 TTGGATGTGGCAGCGGTGA 62.189 57.895 20.69 0.00 0.00 4.02
2800 3744 2.672651 TTGGATGTGGCAGCGGTG 60.673 61.111 10.98 10.98 0.00 4.94
2801 3745 2.672996 GTTGGATGTGGCAGCGGT 60.673 61.111 0.00 0.00 0.00 5.68
2802 3746 3.443045 GGTTGGATGTGGCAGCGG 61.443 66.667 0.00 0.00 0.00 5.52
2803 3747 3.443045 GGGTTGGATGTGGCAGCG 61.443 66.667 0.00 0.00 0.00 5.18
2804 3748 3.070576 GGGGTTGGATGTGGCAGC 61.071 66.667 0.00 0.00 0.00 5.25
2805 3749 1.228831 TTGGGGTTGGATGTGGCAG 60.229 57.895 0.00 0.00 0.00 4.85
2806 3750 1.532794 GTTGGGGTTGGATGTGGCA 60.533 57.895 0.00 0.00 0.00 4.92
2807 3751 2.282783 GGTTGGGGTTGGATGTGGC 61.283 63.158 0.00 0.00 0.00 5.01
2808 3752 1.609210 GGGTTGGGGTTGGATGTGG 60.609 63.158 0.00 0.00 0.00 4.17
2809 3753 1.609210 GGGGTTGGGGTTGGATGTG 60.609 63.158 0.00 0.00 0.00 3.21
2810 3754 2.858655 GGGGTTGGGGTTGGATGT 59.141 61.111 0.00 0.00 0.00 3.06
2811 3755 2.038813 GGGGGTTGGGGTTGGATG 59.961 66.667 0.00 0.00 0.00 3.51
2812 3756 3.668142 CGGGGGTTGGGGTTGGAT 61.668 66.667 0.00 0.00 0.00 3.41
2815 3759 4.671590 GACCGGGGGTTGGGGTTG 62.672 72.222 6.32 0.00 35.25 3.77
2837 3781 4.729918 GGGCTGAGCTGGTGGTGG 62.730 72.222 3.72 0.00 0.00 4.61
2838 3782 4.729918 GGGGCTGAGCTGGTGGTG 62.730 72.222 3.72 0.00 0.00 4.17
2876 3820 3.470888 CAGCCTAGGGGTGGGACG 61.471 72.222 11.72 0.00 46.19 4.79
2891 3835 3.880846 GAAATCCGGCAGCGGCAG 61.881 66.667 11.88 6.58 43.71 4.85
2892 3836 4.713735 TGAAATCCGGCAGCGGCA 62.714 61.111 11.88 0.00 43.71 5.69
2893 3837 4.179579 GTGAAATCCGGCAGCGGC 62.180 66.667 0.00 0.00 40.13 6.53
2894 3838 3.508840 GGTGAAATCCGGCAGCGG 61.509 66.667 0.00 0.00 0.00 5.52
2895 3839 1.656818 ATTGGTGAAATCCGGCAGCG 61.657 55.000 0.00 0.00 35.41 5.18
2896 3840 0.101219 GATTGGTGAAATCCGGCAGC 59.899 55.000 0.00 0.00 39.08 5.25
2897 3841 1.402968 CAGATTGGTGAAATCCGGCAG 59.597 52.381 0.00 0.00 45.10 4.85
2898 3842 1.462616 CAGATTGGTGAAATCCGGCA 58.537 50.000 0.00 0.00 45.10 5.69
2899 3843 0.740737 CCAGATTGGTGAAATCCGGC 59.259 55.000 0.00 0.00 45.10 6.13
2910 3854 3.657956 GAGAGCTCGACCAGATTGG 57.342 57.895 8.37 0.00 45.02 3.16
2924 3868 3.197790 CCATGGCAACCGCGAGAG 61.198 66.667 8.23 0.00 39.92 3.20
2930 3874 2.709883 AAATCCGCCATGGCAACCG 61.710 57.895 34.93 19.06 42.06 4.44
2931 3875 1.153588 CAAATCCGCCATGGCAACC 60.154 57.895 34.93 7.30 42.06 3.77
2932 3876 1.153588 CCAAATCCGCCATGGCAAC 60.154 57.895 34.93 7.70 42.06 4.17
2933 3877 2.357575 CCCAAATCCGCCATGGCAA 61.358 57.895 34.93 23.09 42.06 4.52
2934 3878 2.759149 CCCAAATCCGCCATGGCA 60.759 61.111 34.93 18.52 42.06 4.92
2935 3879 3.539791 CCCCAAATCCGCCATGGC 61.540 66.667 27.67 27.67 37.80 4.40
2936 3880 3.539791 GCCCCAAATCCGCCATGG 61.540 66.667 7.63 7.63 40.09 3.66
2937 3881 2.442643 AGCCCCAAATCCGCCATG 60.443 61.111 0.00 0.00 0.00 3.66
2938 3882 2.123726 GAGCCCCAAATCCGCCAT 60.124 61.111 0.00 0.00 0.00 4.40
2939 3883 3.338250 AGAGCCCCAAATCCGCCA 61.338 61.111 0.00 0.00 0.00 5.69
2940 3884 2.830370 CAGAGCCCCAAATCCGCC 60.830 66.667 0.00 0.00 0.00 6.13
2941 3885 2.830370 CCAGAGCCCCAAATCCGC 60.830 66.667 0.00 0.00 0.00 5.54
2942 3886 1.032114 GTTCCAGAGCCCCAAATCCG 61.032 60.000 0.00 0.00 0.00 4.18
2943 3887 0.684479 GGTTCCAGAGCCCCAAATCC 60.684 60.000 0.00 0.00 0.00 3.01
2944 3888 0.039618 TGGTTCCAGAGCCCCAAATC 59.960 55.000 0.00 0.00 0.00 2.17
2945 3889 0.040204 CTGGTTCCAGAGCCCCAAAT 59.960 55.000 13.02 0.00 36.24 2.32
2946 3890 1.360393 ACTGGTTCCAGAGCCCCAAA 61.360 55.000 23.45 0.00 37.49 3.28
2947 3891 1.774217 ACTGGTTCCAGAGCCCCAA 60.774 57.895 23.45 0.00 37.49 4.12
2948 3892 2.121963 ACTGGTTCCAGAGCCCCA 60.122 61.111 23.45 0.00 37.49 4.96
2949 3893 2.224159 TCACTGGTTCCAGAGCCCC 61.224 63.158 23.45 0.00 37.49 5.80
2950 3894 1.003233 GTCACTGGTTCCAGAGCCC 60.003 63.158 23.45 7.67 37.49 5.19
2951 3895 1.374758 CGTCACTGGTTCCAGAGCC 60.375 63.158 23.45 6.56 37.49 4.70
2952 3896 1.374758 CCGTCACTGGTTCCAGAGC 60.375 63.158 23.45 11.61 37.49 4.09
2953 3897 0.038159 GTCCGTCACTGGTTCCAGAG 60.038 60.000 23.45 16.33 37.49 3.35
2954 3898 0.757561 TGTCCGTCACTGGTTCCAGA 60.758 55.000 23.45 1.49 37.49 3.86
2955 3899 0.321671 ATGTCCGTCACTGGTTCCAG 59.678 55.000 16.25 16.25 39.74 3.86
2956 3900 0.034756 CATGTCCGTCACTGGTTCCA 59.965 55.000 0.00 0.00 0.00 3.53
2957 3901 0.673644 CCATGTCCGTCACTGGTTCC 60.674 60.000 0.00 0.00 0.00 3.62
2958 3902 1.298859 GCCATGTCCGTCACTGGTTC 61.299 60.000 0.00 0.00 31.82 3.62
2959 3903 1.302511 GCCATGTCCGTCACTGGTT 60.303 57.895 0.00 0.00 31.82 3.67
2960 3904 2.347490 GCCATGTCCGTCACTGGT 59.653 61.111 0.00 0.00 31.82 4.00
2961 3905 2.815211 CGCCATGTCCGTCACTGG 60.815 66.667 0.00 0.00 0.00 4.00
2962 3906 2.815211 CCGCCATGTCCGTCACTG 60.815 66.667 0.00 0.00 0.00 3.66
2963 3907 4.760047 GCCGCCATGTCCGTCACT 62.760 66.667 0.00 0.00 0.00 3.41
2981 3925 3.140814 GACCCAATTCCGCAGCCC 61.141 66.667 0.00 0.00 0.00 5.19
2982 3926 2.361104 TGACCCAATTCCGCAGCC 60.361 61.111 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.