Multiple sequence alignment - TraesCS6A01G226100

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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 TraesCS6A01G226100 chr6A 100.000 6743 0 0 1 6743 425740848 425747590 0.000000e+00 12453.0
1 TraesCS6A01G226100 chr6A 80.513 195 32 4 3997 4186 595166934 595167127 1.960000e-30 145.0
2 TraesCS6A01G226100 chr6A 96.429 56 1 1 6285 6340 425747079 425747133 2.590000e-14 91.6
3 TraesCS6A01G226100 chr6B 95.163 3742 120 22 2565 6271 459564056 459560341 0.000000e+00 5851.0
4 TraesCS6A01G226100 chr6B 94.189 1239 38 11 929 2137 459565862 459564628 0.000000e+00 1858.0
5 TraesCS6A01G226100 chr6B 89.569 882 63 12 2 877 168772627 168773485 0.000000e+00 1092.0
6 TraesCS6A01G226100 chr6B 97.506 441 9 2 2133 2572 459564529 459564090 0.000000e+00 752.0
7 TraesCS6A01G226100 chr6B 87.931 290 28 6 6312 6597 459560335 459560049 1.080000e-87 335.0
8 TraesCS6A01G226100 chr6B 92.241 116 9 0 6628 6743 459560077 459559962 1.500000e-36 165.0
9 TraesCS6A01G226100 chr6D 98.126 3362 51 9 2565 5922 295274404 295271051 0.000000e+00 5849.0
10 TraesCS6A01G226100 chr6D 93.829 1734 44 15 892 2572 295276161 295274438 0.000000e+00 2551.0
11 TraesCS6A01G226100 chr6D 95.312 320 15 0 5921 6240 295270813 295270494 6.030000e-140 508.0
12 TraesCS6A01G226100 chr6D 87.761 335 28 4 6271 6597 295270375 295270046 4.940000e-101 379.0
13 TraesCS6A01G226100 chr1A 98.885 807 8 1 1 806 520856100 520856906 0.000000e+00 1439.0
14 TraesCS6A01G226100 chr1A 85.612 139 17 3 6151 6286 452043809 452043671 7.050000e-30 143.0
15 TraesCS6A01G226100 chr1A 96.721 61 2 0 807 867 520856891 520856951 1.200000e-17 102.0
16 TraesCS6A01G226100 chr3A 98.391 808 11 1 1 806 703928563 703927756 0.000000e+00 1419.0
17 TraesCS6A01G226100 chr3A 96.721 61 2 0 807 867 703927771 703927711 1.200000e-17 102.0
18 TraesCS6A01G226100 chr3A 93.750 64 3 1 6285 6347 603266460 603266523 2.000000e-15 95.3
19 TraesCS6A01G226100 chr3A 94.872 39 2 0 829 867 699999450 699999488 2.030000e-05 62.1
20 TraesCS6A01G226100 chr3A 87.037 54 3 2 829 878 6709795 6709848 2.630000e-04 58.4
21 TraesCS6A01G226100 chr3A 87.037 54 3 2 829 878 6764366 6764419 2.630000e-04 58.4
22 TraesCS6A01G226100 chr2B 92.099 886 40 13 1 876 609285942 609285077 0.000000e+00 1221.0
23 TraesCS6A01G226100 chr2B 90.126 871 57 13 1 867 282451481 282452326 0.000000e+00 1105.0
24 TraesCS6A01G226100 chr2B 91.358 810 58 8 2 806 57157806 57157004 0.000000e+00 1098.0
25 TraesCS6A01G226100 chr2B 84.507 142 19 3 6148 6286 243784810 243784669 3.280000e-28 137.0
26 TraesCS6A01G226100 chr2B 79.286 140 25 4 4026 4162 653584890 653584752 2.000000e-15 95.3
27 TraesCS6A01G226100 chr2B 89.552 67 6 1 6285 6350 243784725 243784659 4.330000e-12 84.2
28 TraesCS6A01G226100 chr2A 91.369 811 58 8 2 807 395711601 395710798 0.000000e+00 1099.0
29 TraesCS6A01G226100 chr2A 91.224 809 60 7 2 806 405468994 405469795 0.000000e+00 1090.0
30 TraesCS6A01G226100 chr2A 81.522 184 29 5 3976 4157 28248295 28248115 5.450000e-31 147.0
31 TraesCS6A01G226100 chr7B 91.358 810 58 8 2 806 49029375 49028573 0.000000e+00 1098.0
32 TraesCS6A01G226100 chr5A 90.988 810 67 4 2 806 119067183 119067991 0.000000e+00 1086.0
33 TraesCS6A01G226100 chr5A 84.058 138 18 4 6153 6286 535139082 535139219 5.490000e-26 130.0
34 TraesCS6A01G226100 chr5D 91.826 783 57 6 2 779 390800630 390799850 0.000000e+00 1085.0
35 TraesCS6A01G226100 chr5D 94.643 56 3 0 1052 1107 332433749 332433694 3.350000e-13 87.9
36 TraesCS6A01G226100 chr5D 89.831 59 3 3 819 876 458311813 458311869 9.380000e-09 73.1
37 TraesCS6A01G226100 chr7D 82.796 186 30 2 3974 4158 318392477 318392661 1.500000e-36 165.0
38 TraesCS6A01G226100 chr7D 81.046 153 25 4 6144 6292 93783579 93783731 1.190000e-22 119.0
39 TraesCS6A01G226100 chr1D 83.425 181 27 3 3970 4149 435536473 435536651 1.500000e-36 165.0
40 TraesCS6A01G226100 chr1D 85.612 139 17 3 6151 6286 351254859 351254721 7.050000e-30 143.0
41 TraesCS6A01G226100 chr1D 93.548 62 3 1 6290 6350 351254772 351254711 2.590000e-14 91.6
42 TraesCS6A01G226100 chr3D 86.207 145 16 4 6145 6286 482599409 482599266 3.260000e-33 154.0
43 TraesCS6A01G226100 chr3D 91.045 67 5 1 6285 6350 482599322 482599256 9.310000e-14 89.8
44 TraesCS6A01G226100 chr3D 88.679 53 1 5 829 878 141380772 141380822 7.300000e-05 60.2
45 TraesCS6A01G226100 chr4A 78.922 204 32 7 3981 4177 477943040 477943239 1.970000e-25 128.0
46 TraesCS6A01G226100 chr7A 82.192 146 23 3 6144 6286 96559112 96559257 9.180000e-24 122.0
47 TraesCS6A01G226100 chr7A 94.030 67 3 1 6285 6350 96559201 96559267 4.300000e-17 100.0
48 TraesCS6A01G226100 chr1B 81.560 141 18 6 3976 4115 476947702 476947835 7.150000e-20 110.0
49 TraesCS6A01G226100 chr1B 89.855 69 4 2 6285 6350 136627456 136627524 1.200000e-12 86.1


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 TraesCS6A01G226100 chr6A 425740848 425747590 6742 False 6272.30 12453 98.2145 1 6743 2 chr6A.!!$F2 6742
1 TraesCS6A01G226100 chr6B 459559962 459565862 5900 True 1792.20 5851 93.4060 929 6743 5 chr6B.!!$R1 5814
2 TraesCS6A01G226100 chr6B 168772627 168773485 858 False 1092.00 1092 89.5690 2 877 1 chr6B.!!$F1 875
3 TraesCS6A01G226100 chr6D 295270046 295276161 6115 True 2321.75 5849 93.7570 892 6597 4 chr6D.!!$R1 5705
4 TraesCS6A01G226100 chr1A 520856100 520856951 851 False 770.50 1439 97.8030 1 867 2 chr1A.!!$F1 866
5 TraesCS6A01G226100 chr3A 703927711 703928563 852 True 760.50 1419 97.5560 1 867 2 chr3A.!!$R1 866
6 TraesCS6A01G226100 chr2B 609285077 609285942 865 True 1221.00 1221 92.0990 1 876 1 chr2B.!!$R2 875
7 TraesCS6A01G226100 chr2B 282451481 282452326 845 False 1105.00 1105 90.1260 1 867 1 chr2B.!!$F1 866
8 TraesCS6A01G226100 chr2B 57157004 57157806 802 True 1098.00 1098 91.3580 2 806 1 chr2B.!!$R1 804
9 TraesCS6A01G226100 chr2A 395710798 395711601 803 True 1099.00 1099 91.3690 2 807 1 chr2A.!!$R2 805
10 TraesCS6A01G226100 chr2A 405468994 405469795 801 False 1090.00 1090 91.2240 2 806 1 chr2A.!!$F1 804
11 TraesCS6A01G226100 chr7B 49028573 49029375 802 True 1098.00 1098 91.3580 2 806 1 chr7B.!!$R1 804
12 TraesCS6A01G226100 chr5A 119067183 119067991 808 False 1086.00 1086 90.9880 2 806 1 chr5A.!!$F1 804
13 TraesCS6A01G226100 chr5D 390799850 390800630 780 True 1085.00 1085 91.8260 2 779 1 chr5D.!!$R2 777

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
867 883 1.821216 CACGGGCATGTTTCCTAGTT 58.179 50.000 0.00 0.00 0.00 2.24 F
1813 1881 0.035881 TGTCTTGCAGGGAGCTTCTG 59.964 55.000 12.09 12.09 45.94 3.02 F
2372 2543 1.806247 GCTGTTGGCTTTGGTTTGGAC 60.806 52.381 0.00 0.00 38.06 4.02 F
2785 2997 3.582208 ACAATTCAGAGCAAGAGAGGAGT 59.418 43.478 0.00 0.00 0.00 3.85 F
3758 3979 4.335315 GTGTGTGTCAGGAACTCATTGAAA 59.665 41.667 0.00 0.00 34.60 2.69 F
4304 4539 1.897560 ACAAAACAGTAGCAGAGGCC 58.102 50.000 0.00 0.00 42.56 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2543 0.179062 GCAGGCATAGTGAGGGACAG 60.179 60.000 0.0 0.0 0.00 3.51 R
2939 3151 1.260544 AGCTTGTTGCCCCAATCTTC 58.739 50.000 0.0 0.0 44.23 2.87 R
3896 4117 1.162698 CCACACCATGCTTCTCAGTG 58.837 55.000 0.0 0.0 34.61 3.66 R
4304 4539 2.579201 CCACAGGGGTGCGAGTAG 59.421 66.667 0.0 0.0 43.88 2.57 R
5586 5824 2.904319 CGCGTCAAACAGTGATGAATTG 59.096 45.455 0.0 0.0 44.89 2.32 R
5776 6014 0.393537 CTCGCTCCCCAAATCAGCTT 60.394 55.000 0.0 0.0 0.00 3.74 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
205 212 7.857734 TTCTGATAAAAACGCTATCCATCAA 57.142 32.000 0.00 0.00 0.00 2.57
421 431 5.422331 TGAGAAGACCGAGTTCCATTATCTT 59.578 40.000 0.00 0.00 0.00 2.40
807 822 9.734620 CGTTCAAAAATTATATGGTCATGTGAT 57.265 29.630 0.00 0.00 0.00 3.06
819 834 7.933215 ATGGTCATGTGATTATATGGTCATG 57.067 36.000 0.00 0.00 35.47 3.07
820 835 6.840527 TGGTCATGTGATTATATGGTCATGT 58.159 36.000 0.00 0.00 35.60 3.21
821 836 6.711645 TGGTCATGTGATTATATGGTCATGTG 59.288 38.462 0.00 0.00 35.60 3.21
846 861 3.896888 TGGATTGTTTCTCCTGTTGCAAT 59.103 39.130 0.59 0.00 33.69 3.56
867 883 1.821216 CACGGGCATGTTTCCTAGTT 58.179 50.000 0.00 0.00 0.00 2.24
869 885 3.340034 CACGGGCATGTTTCCTAGTTAA 58.660 45.455 0.00 0.00 0.00 2.01
877 893 7.491372 GGGCATGTTTCCTAGTTAAAATAAAGC 59.509 37.037 0.00 0.00 0.00 3.51
878 894 7.220108 GGCATGTTTCCTAGTTAAAATAAAGCG 59.780 37.037 0.00 0.00 0.00 4.68
879 895 7.220108 GCATGTTTCCTAGTTAAAATAAAGCGG 59.780 37.037 0.00 0.00 0.00 5.52
880 896 6.614160 TGTTTCCTAGTTAAAATAAAGCGGC 58.386 36.000 0.00 0.00 0.00 6.53
881 897 6.207025 TGTTTCCTAGTTAAAATAAAGCGGCA 59.793 34.615 1.45 0.00 0.00 5.69
882 898 7.094118 TGTTTCCTAGTTAAAATAAAGCGGCAT 60.094 33.333 1.45 0.00 0.00 4.40
883 899 7.399245 TTCCTAGTTAAAATAAAGCGGCATT 57.601 32.000 1.45 0.00 0.00 3.56
884 900 7.399245 TCCTAGTTAAAATAAAGCGGCATTT 57.601 32.000 1.45 2.82 0.00 2.32
885 901 8.508883 TCCTAGTTAAAATAAAGCGGCATTTA 57.491 30.769 1.45 5.03 0.00 1.40
886 902 8.400186 TCCTAGTTAAAATAAAGCGGCATTTAC 58.600 33.333 1.45 0.00 0.00 2.01
887 903 7.646526 CCTAGTTAAAATAAAGCGGCATTTACC 59.353 37.037 1.45 0.00 0.00 2.85
888 904 6.334989 AGTTAAAATAAAGCGGCATTTACCC 58.665 36.000 1.45 0.00 0.00 3.69
889 905 6.153851 AGTTAAAATAAAGCGGCATTTACCCT 59.846 34.615 1.45 0.00 0.00 4.34
890 906 7.339976 AGTTAAAATAAAGCGGCATTTACCCTA 59.660 33.333 1.45 0.00 0.00 3.53
926 942 5.470098 CGGAGTACAAATTGGGAAGGATATG 59.530 44.000 0.00 0.00 0.00 1.78
927 943 5.770162 GGAGTACAAATTGGGAAGGATATGG 59.230 44.000 0.00 0.00 0.00 2.74
938 956 4.325501 GGGAAGGATATGGTTTTGTGGGTA 60.326 45.833 0.00 0.00 0.00 3.69
1150 1184 2.974698 GCAGAATCCCCATCCGCG 60.975 66.667 0.00 0.00 0.00 6.46
1228 1262 0.326143 GGAGAAGAAGGAGGAGGCCT 60.326 60.000 3.86 3.86 40.93 5.19
1342 1376 3.068691 CCTCCTCTCCGTTGGCGA 61.069 66.667 0.00 0.00 41.33 5.54
1373 1407 1.557443 GCCGAATAATCTCCCGCGTG 61.557 60.000 4.92 0.00 0.00 5.34
1410 1452 2.257286 CTTGGCTGCTTATTGCGCGT 62.257 55.000 8.43 0.00 46.63 6.01
1454 1496 2.119801 TGGGTCCTACTGTACTCGTC 57.880 55.000 0.00 0.00 0.00 4.20
1476 1518 1.215382 CTCGATGTTCGGTGCCAGA 59.785 57.895 0.00 0.00 40.88 3.86
1490 1537 3.119245 GGTGCCAGAAACTCGTGACTATA 60.119 47.826 0.00 0.00 0.00 1.31
1547 1594 4.067913 CATTTGGGTGGCCACGGC 62.068 66.667 29.08 16.40 41.06 5.68
1571 1618 5.911280 CACTATGCGAGGCTTAATTGATTTG 59.089 40.000 0.00 0.00 0.00 2.32
1594 1641 0.322997 CGGCTTAATTCCACACCCCA 60.323 55.000 0.00 0.00 0.00 4.96
1596 1643 1.272480 GGCTTAATTCCACACCCCACT 60.272 52.381 0.00 0.00 0.00 4.00
1597 1644 2.525368 GCTTAATTCCACACCCCACTT 58.475 47.619 0.00 0.00 0.00 3.16
1607 1654 3.497763 CCACACCCCACTTGACATTAAGA 60.498 47.826 0.00 0.00 0.00 2.10
1656 1706 1.888215 ATTGCGGTAGATGCCTGATG 58.112 50.000 0.00 0.00 0.00 3.07
1661 1711 1.807755 CGGTAGATGCCTGATGGTGTG 60.808 57.143 0.00 0.00 35.27 3.82
1678 1728 1.490621 GTGGTGAAACAACATGCTGC 58.509 50.000 0.00 0.00 41.66 5.25
1786 1854 7.969536 ATGTGCTAATAATCTCGTATGCTTT 57.030 32.000 0.00 0.00 0.00 3.51
1813 1881 0.035881 TGTCTTGCAGGGAGCTTCTG 59.964 55.000 12.09 12.09 45.94 3.02
1947 2015 2.422597 TGTTTCTGGTGCGTCCATAAG 58.577 47.619 0.94 0.00 46.12 1.73
2372 2543 1.806247 GCTGTTGGCTTTGGTTTGGAC 60.806 52.381 0.00 0.00 38.06 4.02
2785 2997 3.582208 ACAATTCAGAGCAAGAGAGGAGT 59.418 43.478 0.00 0.00 0.00 3.85
2939 3151 6.907206 TTGCACTTTTTCAAGAAAATGGAG 57.093 33.333 19.07 12.29 39.69 3.86
3006 3218 4.590647 AGGAGAAGTCTCAGTTGATGACAA 59.409 41.667 10.39 0.00 44.60 3.18
3140 3352 9.185680 TCTAAATTTAGAATAAGAAGGGTTGGC 57.814 33.333 22.73 0.00 36.88 4.52
3468 3687 9.988815 ATAGCTCTCTACCTTAACAACATAATG 57.011 33.333 0.00 0.00 0.00 1.90
3495 3714 6.127563 TGTGCATCAAGTTCATCATGCTAATT 60.128 34.615 0.00 0.00 41.89 1.40
3758 3979 4.335315 GTGTGTGTCAGGAACTCATTGAAA 59.665 41.667 0.00 0.00 34.60 2.69
3896 4117 5.685511 AGTCAATGTCGTTAATTTTGTGCAC 59.314 36.000 10.75 10.75 0.00 4.57
3904 4125 5.065346 TCGTTAATTTTGTGCACACTGAGAA 59.935 36.000 21.56 8.05 0.00 2.87
4044 4277 9.313118 GTGAAACTAAAAAGACAAATCCAACAT 57.687 29.630 0.00 0.00 0.00 2.71
4068 4301 8.745837 CATGAATAGTGTCACAAAAAGACAAAC 58.254 33.333 5.62 0.00 46.50 2.93
4304 4539 1.897560 ACAAAACAGTAGCAGAGGCC 58.102 50.000 0.00 0.00 42.56 5.19
4382 4618 3.320826 GGGCAATTTCTACCACAAACTGT 59.679 43.478 0.00 0.00 0.00 3.55
5204 5441 7.951591 ACTAGAAATTTGGTTGCAACATTAGT 58.048 30.769 29.55 17.05 0.00 2.24
5351 5589 7.119846 GCAAATCATAGTGGGAGGTATTGATAC 59.880 40.741 0.00 0.00 0.00 2.24
5367 5605 5.993748 TTGATACGCATCCATGTATCCTA 57.006 39.130 9.22 0.00 43.99 2.94
5408 5646 5.165961 TGAGTTACTCTGATCCTTTTGGG 57.834 43.478 13.86 0.00 40.87 4.12
5409 5647 3.942115 GAGTTACTCTGATCCTTTTGGGC 59.058 47.826 4.94 0.00 40.87 5.36
5412 5650 3.243359 ACTCTGATCCTTTTGGGCAAA 57.757 42.857 0.00 0.00 40.87 3.68
5415 5653 4.594491 ACTCTGATCCTTTTGGGCAAAATT 59.406 37.500 0.00 0.00 39.29 1.82
5417 5655 4.004982 CTGATCCTTTTGGGCAAAATTGG 58.995 43.478 0.00 0.00 39.29 3.16
5419 5657 4.289148 TGATCCTTTTGGGCAAAATTGGAT 59.711 37.500 17.19 17.19 42.79 3.41
5776 6014 3.321682 ACCAAGCAAGCATTTCTAGCAAA 59.678 39.130 0.00 0.00 0.00 3.68
5840 6086 5.444122 GGATTAAATGAATGTAGCGTGCTC 58.556 41.667 0.00 0.00 0.00 4.26
6094 6579 6.715344 TCCACGTCACATAACTTGATAAAC 57.285 37.500 0.00 0.00 0.00 2.01
6181 6669 8.906867 CCATTCATAGACATAAGATGTTTTGGT 58.093 33.333 0.00 0.00 45.03 3.67
6227 6715 3.428746 TTGAATGGGTGAACAAACACG 57.571 42.857 0.00 0.00 41.12 4.49
6240 6728 6.635239 GTGAACAAACACGCTAAAACATGTAT 59.365 34.615 0.00 0.00 0.00 2.29
6241 6729 7.799447 GTGAACAAACACGCTAAAACATGTATA 59.201 33.333 0.00 0.00 0.00 1.47
6242 6730 8.508062 TGAACAAACACGCTAAAACATGTATAT 58.492 29.630 0.00 0.00 0.00 0.86
6243 6731 9.976255 GAACAAACACGCTAAAACATGTATATA 57.024 29.630 0.00 0.00 0.00 0.86
6346 6938 5.588648 ACATCTTATATTTGTGAACGGTGGG 59.411 40.000 0.00 0.00 0.00 4.61
6350 6942 1.892209 ATTTGTGAACGGTGGGAGTC 58.108 50.000 0.00 0.00 0.00 3.36
6440 7040 5.511234 ACGTGTGTACTAAAGAAGACACT 57.489 39.130 5.68 0.00 42.16 3.55
6527 7128 3.314693 TCTTTTCTATCCCACCCGCTAT 58.685 45.455 0.00 0.00 0.00 2.97
6547 7149 7.254761 CCGCTATTCTTATGTGACAATGCTAAA 60.255 37.037 0.00 0.00 0.00 1.85
6584 7186 4.676924 GGAGTTCATCTTTCTTTTGCAACG 59.323 41.667 0.00 0.00 0.00 4.10
6587 7189 3.631144 TCATCTTTCTTTTGCAACGCTG 58.369 40.909 0.00 0.00 0.00 5.18
6597 7199 1.225475 GCAACGCTGATGTTCGACG 60.225 57.895 0.00 0.00 0.00 5.12
6598 7200 1.225475 CAACGCTGATGTTCGACGC 60.225 57.895 0.00 0.00 0.00 5.19
6599 7201 1.372997 AACGCTGATGTTCGACGCT 60.373 52.632 0.00 0.00 0.00 5.07
6600 7202 0.944311 AACGCTGATGTTCGACGCTT 60.944 50.000 0.00 0.00 0.00 4.68
6601 7203 0.109458 ACGCTGATGTTCGACGCTTA 60.109 50.000 0.00 0.00 0.00 3.09
6602 7204 1.200483 CGCTGATGTTCGACGCTTAT 58.800 50.000 0.00 0.00 0.00 1.73
6603 7205 2.223409 ACGCTGATGTTCGACGCTTATA 60.223 45.455 0.00 0.00 0.00 0.98
6604 7206 2.980476 CGCTGATGTTCGACGCTTATAT 59.020 45.455 0.00 0.00 0.00 0.86
6605 7207 3.425525 CGCTGATGTTCGACGCTTATATT 59.574 43.478 0.00 0.00 0.00 1.28
6606 7208 4.085055 CGCTGATGTTCGACGCTTATATTT 60.085 41.667 0.00 0.00 0.00 1.40
6607 7209 5.133264 GCTGATGTTCGACGCTTATATTTG 58.867 41.667 0.00 0.00 0.00 2.32
6608 7210 5.276868 GCTGATGTTCGACGCTTATATTTGT 60.277 40.000 0.00 0.00 0.00 2.83
6609 7211 6.656314 TGATGTTCGACGCTTATATTTGTT 57.344 33.333 0.00 0.00 0.00 2.83
6610 7212 6.474364 TGATGTTCGACGCTTATATTTGTTG 58.526 36.000 0.00 0.00 0.00 3.33
6611 7213 4.643953 TGTTCGACGCTTATATTTGTTGC 58.356 39.130 0.00 0.00 0.00 4.17
6612 7214 4.390603 TGTTCGACGCTTATATTTGTTGCT 59.609 37.500 0.00 0.00 0.00 3.91
6613 7215 4.772046 TCGACGCTTATATTTGTTGCTC 57.228 40.909 0.00 0.00 0.00 4.26
6614 7216 4.430007 TCGACGCTTATATTTGTTGCTCT 58.570 39.130 0.00 0.00 0.00 4.09
6615 7217 4.868171 TCGACGCTTATATTTGTTGCTCTT 59.132 37.500 0.00 0.00 0.00 2.85
6616 7218 5.005394 TCGACGCTTATATTTGTTGCTCTTC 59.995 40.000 0.00 0.00 0.00 2.87
6617 7219 5.005779 CGACGCTTATATTTGTTGCTCTTCT 59.994 40.000 0.00 0.00 0.00 2.85
6618 7220 6.111768 ACGCTTATATTTGTTGCTCTTCTG 57.888 37.500 0.00 0.00 0.00 3.02
6619 7221 4.966366 CGCTTATATTTGTTGCTCTTCTGC 59.034 41.667 0.00 0.00 0.00 4.26
6620 7222 5.447683 CGCTTATATTTGTTGCTCTTCTGCA 60.448 40.000 0.00 0.00 41.65 4.41
6681 7283 4.630644 ACTTTCATCTCCTCAAGAGCAA 57.369 40.909 0.00 0.00 42.90 3.91
6684 7286 4.564782 TTCATCTCCTCAAGAGCAACAT 57.435 40.909 0.00 0.00 42.90 2.71
6739 7341 0.036306 TTCTGCCCCGGAAAGACTTC 59.964 55.000 0.73 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 212 9.920946 TCTAGAAGGCAATTAATTAAGTCCAAT 57.079 29.630 0.00 0.00 0.00 3.16
421 431 4.657814 AATGGGAAACTTCTGGCTTCTA 57.342 40.909 0.00 0.00 0.00 2.10
807 822 5.103728 ACAATCCACCCACATGACCATATAA 60.104 40.000 0.00 0.00 0.00 0.98
808 823 4.415179 ACAATCCACCCACATGACCATATA 59.585 41.667 0.00 0.00 0.00 0.86
809 824 3.205056 ACAATCCACCCACATGACCATAT 59.795 43.478 0.00 0.00 0.00 1.78
810 825 2.580322 ACAATCCACCCACATGACCATA 59.420 45.455 0.00 0.00 0.00 2.74
811 826 1.358787 ACAATCCACCCACATGACCAT 59.641 47.619 0.00 0.00 0.00 3.55
812 827 0.776810 ACAATCCACCCACATGACCA 59.223 50.000 0.00 0.00 0.00 4.02
813 828 1.923356 AACAATCCACCCACATGACC 58.077 50.000 0.00 0.00 0.00 4.02
814 829 3.157087 AGAAACAATCCACCCACATGAC 58.843 45.455 0.00 0.00 0.00 3.06
815 830 3.420893 GAGAAACAATCCACCCACATGA 58.579 45.455 0.00 0.00 0.00 3.07
816 831 2.493278 GGAGAAACAATCCACCCACATG 59.507 50.000 0.00 0.00 36.79 3.21
817 832 2.379907 AGGAGAAACAATCCACCCACAT 59.620 45.455 0.00 0.00 39.47 3.21
818 833 1.780309 AGGAGAAACAATCCACCCACA 59.220 47.619 0.00 0.00 39.47 4.17
819 834 2.162681 CAGGAGAAACAATCCACCCAC 58.837 52.381 0.00 0.00 39.47 4.61
820 835 1.780309 ACAGGAGAAACAATCCACCCA 59.220 47.619 0.00 0.00 39.47 4.51
821 836 2.558359 CAACAGGAGAAACAATCCACCC 59.442 50.000 0.00 0.00 39.47 4.61
867 883 7.642082 TTAGGGTAAATGCCGCTTTATTTTA 57.358 32.000 0.00 0.00 0.00 1.52
869 885 6.532988 TTTAGGGTAAATGCCGCTTTATTT 57.467 33.333 0.00 0.00 0.00 1.40
903 919 5.770162 CCATATCCTTCCCAATTTGTACTCC 59.230 44.000 0.00 0.00 0.00 3.85
904 920 6.365520 ACCATATCCTTCCCAATTTGTACTC 58.634 40.000 0.00 0.00 0.00 2.59
905 921 6.341408 ACCATATCCTTCCCAATTTGTACT 57.659 37.500 0.00 0.00 0.00 2.73
906 922 7.418337 AAACCATATCCTTCCCAATTTGTAC 57.582 36.000 0.00 0.00 0.00 2.90
910 926 6.296374 CCACAAAACCATATCCTTCCCAATTT 60.296 38.462 0.00 0.00 0.00 1.82
916 932 3.708451 ACCCACAAAACCATATCCTTCC 58.292 45.455 0.00 0.00 0.00 3.46
926 942 2.501261 GTCCAGTCTACCCACAAAACC 58.499 52.381 0.00 0.00 0.00 3.27
927 943 2.140717 CGTCCAGTCTACCCACAAAAC 58.859 52.381 0.00 0.00 0.00 2.43
938 956 2.480845 GTGTTTTAGTGCGTCCAGTCT 58.519 47.619 0.00 0.00 0.00 3.24
1150 1184 1.671379 GCCTCGGTGGAAGTGGAAC 60.671 63.158 0.00 0.00 38.35 3.62
1373 1407 2.112815 GCAGGCGTATCCACAACCC 61.113 63.158 0.00 0.00 37.29 4.11
1410 1452 1.032794 CATCGGATCAAGACGAGGGA 58.967 55.000 0.00 0.00 42.89 4.20
1454 1496 1.519455 GCACCGAACATCGAGGAGG 60.519 63.158 3.06 6.77 43.74 4.30
1490 1537 9.634021 TGATCGGTATTGCTAGATAGATTAGAT 57.366 33.333 0.00 0.00 0.00 1.98
1547 1594 5.679734 AATCAATTAAGCCTCGCATAGTG 57.320 39.130 0.00 0.00 0.00 2.74
1571 1618 1.467342 GGTGTGGAATTAAGCCGACAC 59.533 52.381 13.19 13.19 37.04 3.67
1656 1706 1.408702 AGCATGTTGTTTCACCACACC 59.591 47.619 0.00 0.00 0.00 4.16
1661 1711 0.388659 TGGCAGCATGTTGTTTCACC 59.611 50.000 11.44 4.00 39.31 4.02
1778 1846 7.221452 CCTGCAAGACATATTGAAAAAGCATAC 59.779 37.037 0.00 0.00 34.07 2.39
1786 1854 3.696051 GCTCCCTGCAAGACATATTGAAA 59.304 43.478 0.00 0.00 42.31 2.69
1813 1881 9.234827 ACCTTACCAATAACAACTGGTTTATAC 57.765 33.333 0.00 0.00 43.62 1.47
2257 2428 4.433186 TGAAAACAACTTGTGGAGTGTG 57.567 40.909 0.00 0.00 39.00 3.82
2363 2534 0.472471 GTGAGGGACAGTCCAAACCA 59.528 55.000 21.75 9.72 38.64 3.67
2372 2543 0.179062 GCAGGCATAGTGAGGGACAG 60.179 60.000 0.00 0.00 0.00 3.51
2664 2876 6.688637 AACTAGTGTTTGGTGGAAAGTAAC 57.311 37.500 0.00 0.00 31.37 2.50
2939 3151 1.260544 AGCTTGTTGCCCCAATCTTC 58.739 50.000 0.00 0.00 44.23 2.87
3169 3381 9.179909 TCACAAAACCAAAGATAAGTCAGTTTA 57.820 29.630 0.00 0.00 0.00 2.01
3468 3687 3.435566 CATGATGAACTTGATGCACAGC 58.564 45.455 0.00 0.00 0.00 4.40
3495 3714 6.601613 AGAGTAAGTCAAACACCAATTTCACA 59.398 34.615 0.00 0.00 0.00 3.58
3583 3802 7.325097 ACAAAAATTAATAGCGGACGAAAACTG 59.675 33.333 0.00 0.00 0.00 3.16
3857 4078 2.341846 TGACTAATGCCGGAAATCCC 57.658 50.000 5.05 0.00 0.00 3.85
3896 4117 1.162698 CCACACCATGCTTCTCAGTG 58.837 55.000 0.00 0.00 34.61 3.66
3904 4125 4.080356 ACATATCAGTAACCACACCATGCT 60.080 41.667 0.00 0.00 0.00 3.79
4044 4277 6.964370 CGTTTGTCTTTTTGTGACACTATTCA 59.036 34.615 7.20 0.00 43.13 2.57
4068 4301 4.091509 GGTGTGAATAGTGTAGTTTCTGCG 59.908 45.833 0.00 0.00 0.00 5.18
4304 4539 2.579201 CCACAGGGGTGCGAGTAG 59.421 66.667 0.00 0.00 43.88 2.57
4382 4618 5.724370 TGAACTTATGTCTGATTAGGGACCA 59.276 40.000 0.00 0.00 0.00 4.02
4526 4762 6.419484 TCTGTGACTCAAGGATAAAACTCA 57.581 37.500 0.00 0.00 0.00 3.41
4527 4763 7.913674 ATTCTGTGACTCAAGGATAAAACTC 57.086 36.000 0.00 0.00 0.00 3.01
4631 4868 5.592282 ACACAAAACACAGGAATCATGTACA 59.408 36.000 0.00 0.00 0.00 2.90
5351 5589 3.257393 GAAGCTAGGATACATGGATGCG 58.743 50.000 3.46 0.00 41.41 4.73
5367 5605 4.015084 CTCAAGACATGGGAAATGAAGCT 58.985 43.478 0.00 0.00 0.00 3.74
5408 5646 6.431198 AAGCATTCATCAATCCAATTTTGC 57.569 33.333 0.00 0.00 0.00 3.68
5409 5647 6.745450 GCAAAGCATTCATCAATCCAATTTTG 59.255 34.615 0.00 0.00 0.00 2.44
5412 5650 5.492895 TGCAAAGCATTCATCAATCCAATT 58.507 33.333 0.00 0.00 31.71 2.32
5415 5653 3.118920 CCTGCAAAGCATTCATCAATCCA 60.119 43.478 0.00 0.00 38.13 3.41
5417 5655 4.110482 GACCTGCAAAGCATTCATCAATC 58.890 43.478 0.00 0.00 38.13 2.67
5419 5657 3.159472 AGACCTGCAAAGCATTCATCAA 58.841 40.909 0.00 0.00 38.13 2.57
5586 5824 2.904319 CGCGTCAAACAGTGATGAATTG 59.096 45.455 0.00 0.00 44.89 2.32
5776 6014 0.393537 CTCGCTCCCCAAATCAGCTT 60.394 55.000 0.00 0.00 0.00 3.74
5840 6086 4.322953 CCCAAAAGGAATCAAGGACAATGG 60.323 45.833 0.00 0.00 38.24 3.16
6318 6910 7.904977 CACCGTTCACAAATATAAGATGTTCTG 59.095 37.037 0.00 0.00 0.00 3.02
6410 7002 9.585099 TCTTCTTTAGTACACACGTTTTCTAAA 57.415 29.630 0.00 0.00 0.00 1.85
6411 7003 9.023967 GTCTTCTTTAGTACACACGTTTTCTAA 57.976 33.333 0.00 0.00 0.00 2.10
6419 7013 5.115171 CGAAGTGTCTTCTTTAGTACACACG 59.885 44.000 7.15 7.99 43.65 4.49
6513 7114 4.020573 CACATAAGAATAGCGGGTGGGATA 60.021 45.833 0.00 0.00 0.00 2.59
6527 7128 7.035004 GCCATTTTAGCATTGTCACATAAGAA 58.965 34.615 0.00 0.00 0.00 2.52
6547 7149 0.960364 AACTCCGCGTTCATGCCATT 60.960 50.000 4.92 0.00 0.00 3.16
6584 7186 4.974103 AATATAAGCGTCGAACATCAGC 57.026 40.909 0.00 0.00 0.00 4.26
6587 7189 5.392585 GCAACAAATATAAGCGTCGAACATC 59.607 40.000 0.00 0.00 0.00 3.06
6597 7199 5.883661 TGCAGAAGAGCAACAAATATAAGC 58.116 37.500 0.00 0.00 42.46 3.09
6623 7225 5.296780 TCAGCGTCACAGAAGAAAGATTTTT 59.703 36.000 0.00 0.00 0.00 1.94
6624 7226 4.816385 TCAGCGTCACAGAAGAAAGATTTT 59.184 37.500 0.00 0.00 0.00 1.82
6625 7227 4.380531 TCAGCGTCACAGAAGAAAGATTT 58.619 39.130 0.00 0.00 0.00 2.17
6626 7228 3.995199 TCAGCGTCACAGAAGAAAGATT 58.005 40.909 0.00 0.00 0.00 2.40
6627 7229 3.667497 TCAGCGTCACAGAAGAAAGAT 57.333 42.857 0.00 0.00 0.00 2.40
6628 7230 3.243873 ACATCAGCGTCACAGAAGAAAGA 60.244 43.478 0.00 0.00 0.00 2.52
6629 7231 3.062763 ACATCAGCGTCACAGAAGAAAG 58.937 45.455 0.00 0.00 0.00 2.62
6630 7232 3.111853 ACATCAGCGTCACAGAAGAAA 57.888 42.857 0.00 0.00 0.00 2.52
6631 7233 2.820059 ACATCAGCGTCACAGAAGAA 57.180 45.000 0.00 0.00 0.00 2.52
6632 7234 2.677199 GAACATCAGCGTCACAGAAGA 58.323 47.619 0.00 0.00 0.00 2.87
6633 7235 1.388093 CGAACATCAGCGTCACAGAAG 59.612 52.381 0.00 0.00 0.00 2.85
6634 7236 1.000717 TCGAACATCAGCGTCACAGAA 60.001 47.619 0.00 0.00 0.00 3.02
6635 7237 0.596082 TCGAACATCAGCGTCACAGA 59.404 50.000 0.00 0.00 0.00 3.41
6636 7238 0.710567 GTCGAACATCAGCGTCACAG 59.289 55.000 0.00 0.00 0.00 3.66
6637 7239 0.666274 GGTCGAACATCAGCGTCACA 60.666 55.000 0.00 0.00 0.00 3.58
6638 7240 0.666274 TGGTCGAACATCAGCGTCAC 60.666 55.000 0.00 0.00 0.00 3.67
6639 7241 0.666274 GTGGTCGAACATCAGCGTCA 60.666 55.000 6.36 0.00 0.00 4.35
6640 7242 0.388649 AGTGGTCGAACATCAGCGTC 60.389 55.000 6.36 0.00 0.00 5.19
6641 7243 0.885879 TAGTGGTCGAACATCAGCGT 59.114 50.000 6.36 0.00 0.00 5.07
6642 7244 1.135373 AGTAGTGGTCGAACATCAGCG 60.135 52.381 6.36 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.