Multiple sequence alignment - TraesCS1D01G309600

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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 TraesCS1D01G309600 chr1D 100.000 8377 0 0 1 8377 405373065 405364689 0.000000e+00 15470.0
1 TraesCS1D01G309600 chr1B 95.207 5737 210 31 994 6706 545213201 545207506 0.000000e+00 9010.0
2 TraesCS1D01G309600 chr1B 90.868 1106 73 17 6751 7852 545207493 545206412 0.000000e+00 1458.0
3 TraesCS1D01G309600 chr1B 94.382 534 29 1 7845 8377 545206032 545205499 0.000000e+00 819.0
4 TraesCS1D01G309600 chr1B 84.717 530 45 19 415 942 545213789 545213294 1.620000e-136 497.0
5 TraesCS1D01G309600 chr1B 88.483 356 38 3 1 355 545216417 545216064 2.160000e-115 427.0
6 TraesCS1D01G309600 chr1B 81.013 79 13 2 5204 5281 209132455 209132378 2.520000e-05 62.1
7 TraesCS1D01G309600 chr1A 91.559 3412 190 52 4992 8377 500830154 500826815 0.000000e+00 4615.0
8 TraesCS1D01G309600 chr1A 96.950 1574 44 1 3069 4642 500831886 500830317 0.000000e+00 2638.0
9 TraesCS1D01G309600 chr1A 96.231 1539 32 14 1544 3082 500834370 500832858 0.000000e+00 2497.0
10 TraesCS1D01G309600 chr1A 94.793 1133 39 7 433 1546 500835661 500834530 0.000000e+00 1748.0
11 TraesCS1D01G309600 chr1A 94.648 355 14 2 1 355 500839419 500839070 5.720000e-151 545.0
12 TraesCS1D01G309600 chr1A 93.103 145 5 4 4572 4713 24135937 24135795 3.060000e-49 207.0
13 TraesCS1D01G309600 chr1A 92.771 83 5 1 4790 4871 500830231 500830149 1.480000e-22 119.0
14 TraesCS1D01G309600 chr1A 92.453 53 4 0 5229 5281 52500769 52500717 9.020000e-10 76.8
15 TraesCS1D01G309600 chr1A 83.871 62 8 2 5221 5281 529937884 529937824 3.270000e-04 58.4
16 TraesCS1D01G309600 chr2D 86.669 2468 228 52 444 2846 534358126 534360557 0.000000e+00 2641.0
17 TraesCS1D01G309600 chr2D 88.230 2226 202 39 5285 7492 534362883 534365066 0.000000e+00 2604.0
18 TraesCS1D01G309600 chr2D 87.033 1473 137 21 3141 4573 534360985 534362443 0.000000e+00 1613.0
19 TraesCS1D01G309600 chr2B 90.555 1927 170 9 924 2846 635339277 635341195 0.000000e+00 2540.0
20 TraesCS1D01G309600 chr2B 91.102 1416 107 17 5285 6684 635343507 635344919 0.000000e+00 1899.0
21 TraesCS1D01G309600 chr2B 84.488 1631 170 33 2979 4573 635341478 635343061 0.000000e+00 1533.0
22 TraesCS1D01G309600 chr2B 83.808 772 78 29 6728 7492 635344913 635345644 0.000000e+00 689.0
23 TraesCS1D01G309600 chr2B 79.320 353 30 17 444 764 635338785 635339126 3.060000e-49 207.0
24 TraesCS1D01G309600 chr6A 93.750 144 6 2 4572 4713 381088707 381088849 6.590000e-51 213.0
25 TraesCS1D01G309600 chr7A 93.056 144 7 2 4572 4713 552975528 552975386 3.060000e-49 207.0
26 TraesCS1D01G309600 chr6D 93.056 144 7 2 4572 4713 267532814 267532956 3.060000e-49 207.0
27 TraesCS1D01G309600 chr6D 93.056 144 7 2 4572 4713 269703806 269703948 3.060000e-49 207.0
28 TraesCS1D01G309600 chr6D 93.007 143 6 4 4572 4713 372827512 372827651 1.100000e-48 206.0
29 TraesCS1D01G309600 chr3B 78.370 319 66 3 6313 6629 139410927 139410610 3.960000e-48 204.0
30 TraesCS1D01G309600 chr3A 87.952 166 12 5 4551 4713 70981923 70981763 1.110000e-43 189.0
31 TraesCS1D01G309600 chr3A 95.349 43 2 0 5238 5280 729750734 729750776 1.510000e-07 69.4
32 TraesCS1D01G309600 chr3D 77.500 320 66 5 6313 6629 89899526 89899210 3.990000e-43 187.0
33 TraesCS1D01G309600 chr7B 81.915 94 13 4 5190 5281 734291094 734291003 9.020000e-10 76.8
34 TraesCS1D01G309600 chr7B 92.857 42 3 0 5240 5281 659428330 659428289 2.520000e-05 62.1
35 TraesCS1D01G309600 chr4A 82.540 63 9 2 5220 5281 363453288 363453349 4.000000e-03 54.7


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 TraesCS1D01G309600 chr1D 405364689 405373065 8376 True 15470.0 15470 100.000000 1 8377 1 chr1D.!!$R1 8376
1 TraesCS1D01G309600 chr1B 545205499 545216417 10918 True 2442.2 9010 90.731400 1 8377 5 chr1B.!!$R2 8376
2 TraesCS1D01G309600 chr1A 500826815 500839419 12604 True 2027.0 4615 94.492000 1 8377 6 chr1A.!!$R4 8376
3 TraesCS1D01G309600 chr2D 534358126 534365066 6940 False 2286.0 2641 87.310667 444 7492 3 chr2D.!!$F1 7048
4 TraesCS1D01G309600 chr2B 635338785 635345644 6859 False 1373.6 2540 85.854600 444 7492 5 chr2B.!!$F1 7048

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
669 5344 0.230260 TAAACGCGCGTGTCTGTTTC 59.770 50.000 38.44 0.00 36.14 2.78 F
2034 6943 1.130561 GTTGCTATGGTCACTTTCGGC 59.869 52.381 0.00 0.00 0.00 5.54 F
2565 7474 2.008329 GTCCTTGAAGCATGCTCTCTG 58.992 52.381 22.93 11.77 0.00 3.35 F
3177 9232 2.373169 TCTTGCTTCTGTGTCCATCCTT 59.627 45.455 0.00 0.00 0.00 3.36 F
4145 10228 1.860641 TTGATTCCACTCCTAGCGGA 58.139 50.000 0.00 0.00 37.82 5.54 F
5034 11131 0.841961 TAGCAGTAGTAGAGGGCGGA 59.158 55.000 0.00 0.00 0.00 5.54 F
5922 12036 0.034616 ACTTCACAGAGACAGCTGGC 59.965 55.000 19.93 16.91 40.20 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 7236 3.858135 ACCCTCATTCCCTGTCGTATAT 58.142 45.455 0.00 0.00 0.00 0.86 R
3801 9884 4.507691 CCAGTAGACAATAAACCCAACCCA 60.508 45.833 0.00 0.00 0.00 4.51 R
4096 10179 0.792640 CGGTGCTCGGAATATGCATC 59.207 55.000 0.19 0.00 39.00 3.91 R
4607 10696 2.112190 GTTTCAGCTCTAGCCTACCCT 58.888 52.381 0.00 0.00 43.38 4.34 R
5595 11707 0.107263 TGCCAGCTATTGATTCGGCA 60.107 50.000 6.06 6.06 46.80 5.69 R
6086 12200 0.827368 TTCACCCTTTGTTGGCCAAC 59.173 50.000 36.78 36.78 41.50 3.77 R
7627 13776 0.252197 ACCGGTGAAATCCACTAGCC 59.748 55.000 6.12 0.00 45.03 3.93 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
25 26 0.690762 TTTCTCCCTCCTTGTTCCCG 59.309 55.000 0.00 0.00 0.00 5.14
45 46 2.029244 CGGTCATACATCTCGTTTGCAC 59.971 50.000 0.00 0.00 0.00 4.57
89 91 8.121305 ACTGATGTTTAAGGCATGTTTGATTA 57.879 30.769 0.00 0.00 0.00 1.75
102 104 8.726988 GGCATGTTTGATTAGTGACTAACTTTA 58.273 33.333 7.28 0.00 40.56 1.85
140 142 1.878102 CGCTTGCCTTACTTGAGGTGT 60.878 52.381 0.00 0.00 39.11 4.16
317 319 2.346766 TGAGATGTGGCAAAGTGTGT 57.653 45.000 0.00 0.00 0.00 3.72
318 320 2.653726 TGAGATGTGGCAAAGTGTGTT 58.346 42.857 0.00 0.00 0.00 3.32
355 357 0.820871 GCAAGGTGTGGTTTGGAACA 59.179 50.000 0.00 0.00 0.00 3.18
359 361 2.530701 AGGTGTGGTTTGGAACAACAA 58.469 42.857 2.78 0.00 46.33 2.83
363 365 4.697828 GGTGTGGTTTGGAACAACAATTTT 59.302 37.500 2.78 0.00 46.33 1.82
364 366 5.875359 GGTGTGGTTTGGAACAACAATTTTA 59.125 36.000 2.78 0.00 46.33 1.52
365 367 6.540551 GGTGTGGTTTGGAACAACAATTTTAT 59.459 34.615 2.78 0.00 46.33 1.40
367 369 9.267084 GTGTGGTTTGGAACAACAATTTTATAT 57.733 29.630 2.78 0.00 46.33 0.86
393 423 1.936203 GCATGTTGCGTCAAATTGCCT 60.936 47.619 12.64 0.00 31.71 4.75
613 5269 1.940883 CTGCCTCGCCCGTGTAACTA 61.941 60.000 0.00 0.00 31.75 2.24
623 5279 1.274167 CCGTGTAACTACTCCTTGCCA 59.726 52.381 0.00 0.00 31.75 4.92
669 5344 0.230260 TAAACGCGCGTGTCTGTTTC 59.770 50.000 38.44 0.00 36.14 2.78
782 5475 2.808543 GTTCCAGAAACACGCTCATCTT 59.191 45.455 0.00 0.00 37.82 2.40
819 5512 5.572896 CGCTCTGCTGTTTTTATTTTTAGGG 59.427 40.000 0.00 0.00 0.00 3.53
888 5581 7.148356 TGCATCAGCTGTACTTTCTGAAAATAG 60.148 37.037 14.67 0.00 39.88 1.73
1153 5900 4.116238 CAGAAAGAAACCGCTAGATCTCC 58.884 47.826 0.00 0.00 0.00 3.71
1158 5905 3.068873 AGAAACCGCTAGATCTCCATGAC 59.931 47.826 0.00 0.00 0.00 3.06
1179 5926 2.109126 GCCGTCCTTGGATGACAGC 61.109 63.158 10.25 2.24 32.91 4.40
1281 6028 2.598394 GTCAAGCTGGCCAAGGCA 60.598 61.111 18.35 0.13 44.11 4.75
1426 6173 1.381872 TCCAGCAGAGAGGGCTACC 60.382 63.158 0.00 0.00 40.23 3.18
1702 6611 3.736126 GCAAATTGTTCTAGCCATGCTCC 60.736 47.826 0.00 0.00 40.44 4.70
2034 6943 1.130561 GTTGCTATGGTCACTTTCGGC 59.869 52.381 0.00 0.00 0.00 5.54
2327 7236 2.035961 CTCTCCAAGACGTGAACTTCCA 59.964 50.000 0.00 0.00 0.00 3.53
2502 7411 5.875359 ACAGAGTGGGAAAATCGAAGATAAC 59.125 40.000 0.00 0.00 45.12 1.89
2565 7474 2.008329 GTCCTTGAAGCATGCTCTCTG 58.992 52.381 22.93 11.77 0.00 3.35
3177 9232 2.373169 TCTTGCTTCTGTGTCCATCCTT 59.627 45.455 0.00 0.00 0.00 3.36
3277 9340 7.601856 TGGATTTTGTGATTGATCCAGTTTAC 58.398 34.615 0.02 0.00 42.21 2.01
3481 9564 7.702348 GCTGGAAACAAATGTATAATGTCTTCC 59.298 37.037 0.00 0.00 42.06 3.46
3578 9661 5.192927 CAAGCAGGGGATTACACTGAAATA 58.807 41.667 1.09 0.00 34.21 1.40
3801 9884 2.640284 AGAAGAGAGGGAGAAAGGCT 57.360 50.000 0.00 0.00 0.00 4.58
4096 10179 2.419673 TGCTATTTGACAAGATGCACCG 59.580 45.455 0.00 0.00 0.00 4.94
4145 10228 1.860641 TTGATTCCACTCCTAGCGGA 58.139 50.000 0.00 0.00 37.82 5.54
4215 10298 7.964559 ACAATGATAAATTGAAGTCACATGTCG 59.035 33.333 0.00 0.00 33.51 4.35
4242 10326 6.581166 CGGAGTGCTGTTAAACTTTTTATTCC 59.419 38.462 0.00 0.00 0.00 3.01
4437 10521 8.715998 CCTGTTATTGTTGCATCTCTATCATAC 58.284 37.037 0.00 0.00 0.00 2.39
4502 10587 5.649602 TTGTTCGCATCCATTTTGAAAAC 57.350 34.783 0.00 0.00 0.00 2.43
4607 10696 5.056553 AGCCTTTAGTCCCAAACAAGTTA 57.943 39.130 0.00 0.00 0.00 2.24
4676 10765 5.174395 GGTTCTGCTACATGGATATGCTAG 58.826 45.833 0.00 0.00 37.85 3.42
4690 10779 2.509336 CTAGCTTCCACGCACCCG 60.509 66.667 0.00 0.00 41.14 5.28
4692 10781 3.291101 TAGCTTCCACGCACCCGTC 62.291 63.158 0.00 0.00 46.39 4.79
4694 10783 4.308458 CTTCCACGCACCCGTCCA 62.308 66.667 0.00 0.00 46.39 4.02
4695 10784 3.605749 CTTCCACGCACCCGTCCAT 62.606 63.158 0.00 0.00 46.39 3.41
4696 10785 3.892740 TTCCACGCACCCGTCCATG 62.893 63.158 0.00 0.00 46.39 3.66
4697 10786 4.386951 CCACGCACCCGTCCATGA 62.387 66.667 0.00 0.00 46.39 3.07
4698 10787 2.358125 CACGCACCCGTCCATGAA 60.358 61.111 0.00 0.00 46.39 2.57
4886 10978 7.849804 AATGTGCAGTGTTACTAATTCTAGG 57.150 36.000 0.00 0.00 0.00 3.02
4891 10983 6.605995 TGCAGTGTTACTAATTCTAGGAGCTA 59.394 38.462 0.00 0.00 0.00 3.32
4910 11002 8.548877 AGGAGCTATGTTTCTGTTTCCTTAATA 58.451 33.333 0.00 0.00 29.85 0.98
4963 11055 9.736414 TCATATAGGTCACTGAGTATAACTACC 57.264 37.037 0.00 0.00 0.00 3.18
5031 11125 8.560374 CAATTTAAATTAGCAGTAGTAGAGGGC 58.440 37.037 12.98 0.00 0.00 5.19
5034 11131 0.841961 TAGCAGTAGTAGAGGGCGGA 59.158 55.000 0.00 0.00 0.00 5.54
5210 11312 3.199946 ACTCCCTCTCAAAACAAGTGTCA 59.800 43.478 0.00 0.00 0.00 3.58
5218 11320 7.156876 TCTCAAAACAAGTGTCACAGATTTT 57.843 32.000 5.62 5.64 0.00 1.82
5230 11332 8.250332 AGTGTCACAGATTTTGTACAAATTTGT 58.750 29.630 25.99 25.99 44.86 2.83
5231 11333 9.509855 GTGTCACAGATTTTGTACAAATTTGTA 57.490 29.630 23.91 23.91 42.35 2.41
5255 11357 9.512435 GTACTGACTTTATACTAAATCTGCGAA 57.488 33.333 0.00 0.00 0.00 4.70
5282 11384 2.832201 GGGACGGAGGGAGTACGG 60.832 72.222 0.00 0.00 0.00 4.02
5348 11453 4.037923 AGTGTCACAACTGCAAATTTAGGG 59.962 41.667 5.62 0.00 0.00 3.53
5595 11707 1.203994 GCTCCTGTGATGCAGCATTTT 59.796 47.619 8.41 0.00 43.71 1.82
5636 11748 7.141363 GGCACAACTATAATTAGATGCTTTGG 58.859 38.462 4.06 0.00 35.06 3.28
5922 12036 0.034616 ACTTCACAGAGACAGCTGGC 59.965 55.000 19.93 16.91 40.20 4.85
6010 12124 6.436847 TGCTTTGGAAAACAGAATGATATCCA 59.563 34.615 0.00 0.00 40.52 3.41
6078 12192 6.264744 CCCTTACGATATCAGAAAGTAGACCA 59.735 42.308 3.12 0.00 0.00 4.02
6086 12200 2.932614 CAGAAAGTAGACCAGATTGCCG 59.067 50.000 0.00 0.00 0.00 5.69
6148 12262 9.627395 TTCATGTTCGTTTCTTCAACTTTAAAA 57.373 25.926 0.00 0.00 32.53 1.52
6149 12263 9.796120 TCATGTTCGTTTCTTCAACTTTAAAAT 57.204 25.926 0.00 0.00 32.53 1.82
6607 12737 5.336055 CGACCCTCTGGATGAATATAGTGAC 60.336 48.000 0.00 0.00 34.81 3.67
6685 12815 6.848470 GTCAATTTGACCGCATAACTTAAC 57.152 37.500 17.07 0.00 41.37 2.01
6686 12816 6.608610 GTCAATTTGACCGCATAACTTAACT 58.391 36.000 17.07 0.00 41.37 2.24
6688 12818 5.560966 ATTTGACCGCATAACTTAACTGG 57.439 39.130 0.00 0.00 0.00 4.00
6738 12868 8.925161 TTTGATGGCTAAAGTAATTTATGTGC 57.075 30.769 0.00 0.00 0.00 4.57
6744 12874 7.072030 GGCTAAAGTAATTTATGTGCGATCTG 58.928 38.462 0.00 0.00 0.00 2.90
6766 12896 3.445096 GCATTTTCTAGGCATTGGACTGT 59.555 43.478 0.00 0.00 31.78 3.55
6822 12952 4.664188 CTTAAGCTCGACTCTACAGGTTC 58.336 47.826 0.00 0.00 0.00 3.62
6828 12958 4.377635 GCTCGACTCTACAGGTTCGATATC 60.378 50.000 0.00 0.00 0.00 1.63
6852 12982 9.751542 ATCTATAATAAACTCTCCAGAAACACG 57.248 33.333 0.00 0.00 0.00 4.49
6853 12983 6.663944 ATAATAAACTCTCCAGAAACACGC 57.336 37.500 0.00 0.00 0.00 5.34
6855 12985 2.622064 AACTCTCCAGAAACACGCTT 57.378 45.000 0.00 0.00 0.00 4.68
6856 12986 2.622064 ACTCTCCAGAAACACGCTTT 57.378 45.000 0.00 0.00 0.00 3.51
6857 12987 2.919228 ACTCTCCAGAAACACGCTTTT 58.081 42.857 0.00 0.00 0.00 2.27
6859 12989 3.134458 CTCTCCAGAAACACGCTTTTCT 58.866 45.455 6.12 6.12 44.98 2.52
6862 12992 4.398044 TCTCCAGAAACACGCTTTTCTTTT 59.602 37.500 8.72 0.00 42.09 2.27
6863 12993 5.587043 TCTCCAGAAACACGCTTTTCTTTTA 59.413 36.000 8.72 0.00 42.09 1.52
6865 12995 6.205784 TCCAGAAACACGCTTTTCTTTTATG 58.794 36.000 8.72 0.60 42.09 1.90
6866 12996 6.038825 TCCAGAAACACGCTTTTCTTTTATGA 59.961 34.615 8.72 0.93 42.09 2.15
6868 12998 7.148918 CCAGAAACACGCTTTTCTTTTATGATG 60.149 37.037 8.72 0.00 42.09 3.07
6869 12999 6.363357 AGAAACACGCTTTTCTTTTATGATGC 59.637 34.615 6.12 0.00 42.09 3.91
6870 13000 4.485163 ACACGCTTTTCTTTTATGATGCC 58.515 39.130 0.00 0.00 0.00 4.40
6871 13001 4.022416 ACACGCTTTTCTTTTATGATGCCA 60.022 37.500 0.00 0.00 0.00 4.92
6872 13002 4.560035 CACGCTTTTCTTTTATGATGCCAG 59.440 41.667 0.00 0.00 0.00 4.85
6873 13003 3.549070 CGCTTTTCTTTTATGATGCCAGC 59.451 43.478 0.00 0.00 0.00 4.85
6874 13004 3.549070 GCTTTTCTTTTATGATGCCAGCG 59.451 43.478 0.00 0.00 0.00 5.18
6875 13005 4.675146 GCTTTTCTTTTATGATGCCAGCGA 60.675 41.667 0.00 0.00 0.00 4.93
6876 13006 5.581126 TTTTCTTTTATGATGCCAGCGAT 57.419 34.783 0.00 0.00 0.00 4.58
6877 13007 5.581126 TTTCTTTTATGATGCCAGCGATT 57.419 34.783 0.00 0.00 0.00 3.34
6878 13008 4.556942 TCTTTTATGATGCCAGCGATTG 57.443 40.909 0.00 0.00 0.00 2.67
6879 13009 3.947196 TCTTTTATGATGCCAGCGATTGT 59.053 39.130 0.00 0.00 0.00 2.71
6880 13010 4.398988 TCTTTTATGATGCCAGCGATTGTT 59.601 37.500 0.00 0.00 0.00 2.83
6881 13011 4.717233 TTTATGATGCCAGCGATTGTTT 57.283 36.364 0.00 0.00 0.00 2.83
6882 13012 5.826601 TTTATGATGCCAGCGATTGTTTA 57.173 34.783 0.00 0.00 0.00 2.01
6883 13013 3.976793 ATGATGCCAGCGATTGTTTAG 57.023 42.857 0.00 0.00 0.00 1.85
6884 13014 2.710377 TGATGCCAGCGATTGTTTAGT 58.290 42.857 0.00 0.00 0.00 2.24
6885 13015 2.677836 TGATGCCAGCGATTGTTTAGTC 59.322 45.455 0.00 0.00 0.00 2.59
6886 13016 2.177394 TGCCAGCGATTGTTTAGTCA 57.823 45.000 0.00 0.00 0.00 3.41
6887 13017 2.499197 TGCCAGCGATTGTTTAGTCAA 58.501 42.857 0.00 0.00 0.00 3.18
6900 13032 6.603237 TGTTTAGTCAATTATGATGGCGAG 57.397 37.500 0.00 0.00 38.01 5.03
6946 13079 3.430042 AATGCAGTCACAGAGAATGGT 57.570 42.857 0.00 0.00 42.38 3.55
7141 13276 3.731216 CACATCGTATCACATCGGTTCTC 59.269 47.826 0.00 0.00 0.00 2.87
7214 13355 7.968956 TGCGTTACAGATTTTTAACTGACAAAA 59.031 29.630 0.00 0.00 37.54 2.44
7259 13403 5.704888 TGTTGGTCTGTTTTAACTGTTGTG 58.295 37.500 2.69 0.00 0.00 3.33
7290 13435 5.592282 TGTAAAACAGGTGAAATTGCAGAGA 59.408 36.000 0.00 0.00 0.00 3.10
7379 13524 6.079763 CACGATGGGATCAAAATTATAAGCG 58.920 40.000 0.00 0.00 0.00 4.68
7389 13534 5.239306 TCAAAATTATAAGCGGAGGATGCAG 59.761 40.000 0.00 0.00 33.85 4.41
7392 13537 0.683973 ATAAGCGGAGGATGCAGAGG 59.316 55.000 0.00 0.00 33.85 3.69
7399 13544 2.086251 GAGGATGCAGAGGAGAGCCG 62.086 65.000 0.00 0.00 39.96 5.52
7427 13576 4.431035 CCGATATCGCCGGTGTTT 57.569 55.556 19.78 6.68 41.91 2.83
7493 13642 7.730084 TCAGAACTCCACATATATTTCTCCAG 58.270 38.462 0.00 0.00 0.00 3.86
7523 13672 7.465916 CGTGCATGCAGTTCTTACAGTATAAAT 60.466 37.037 23.41 0.00 0.00 1.40
7558 13707 6.068670 AGTGACCATTAGTTTAAGCTTGGTT 58.931 36.000 14.65 0.22 37.58 3.67
7590 13739 4.124851 ACGGTGGAGATTGATACTTCAC 57.875 45.455 0.00 0.00 41.58 3.18
7627 13776 6.744993 CGAGATTCATACTTCACCGATCATAG 59.255 42.308 0.00 0.00 0.00 2.23
7713 13862 4.675029 CGGGACCCGTTGAGCGTT 62.675 66.667 25.54 0.00 42.73 4.84
7734 13883 1.153881 GAAGTACTCGGCGTCCCAC 60.154 63.158 6.85 1.05 0.00 4.61
7904 14440 2.435938 CGTGCCGGTAATGCTGGT 60.436 61.111 1.90 0.00 45.57 4.00
7907 14443 0.748005 GTGCCGGTAATGCTGGTGAT 60.748 55.000 1.90 0.00 45.57 3.06
8017 14553 4.776322 CGGCGAACTCCATGGCCA 62.776 66.667 8.56 8.56 43.68 5.36
8019 14555 3.134127 GCGAACTCCATGGCCACC 61.134 66.667 8.16 0.00 0.00 4.61
8055 14591 1.526686 GACGTGGGGTTTTTCCGGT 60.527 57.895 0.00 0.00 37.00 5.28
8171 14707 1.478510 CAGTATGTCTCCGAGGTTGCT 59.521 52.381 0.00 0.00 0.00 3.91
8309 14846 3.944650 GCTTGAGAAAGAGGATCCCTTTC 59.055 47.826 29.80 29.80 45.91 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.159156 CGAGATGTATGACCGGGAACAA 60.159 50.000 6.32 0.00 0.00 2.83
25 26 3.000041 TGTGCAAACGAGATGTATGACC 59.000 45.455 0.00 0.00 0.00 4.02
45 46 4.329801 TCAGTAACTAGCGAACATGCATTG 59.670 41.667 0.00 0.00 37.31 2.82
116 118 0.394938 TCAAGTAAGGCAAGCGTGGA 59.605 50.000 0.79 0.00 0.00 4.02
140 142 4.761739 CCAAAGTGTGGCTAAGAATCTGAA 59.238 41.667 0.00 0.00 41.72 3.02
200 202 8.552034 GTGAGTAAAAAGCCTCACATATCATAC 58.448 37.037 13.35 0.00 43.83 2.39
364 366 9.131416 CAATTTGACGCAACATGCATAATATAT 57.869 29.630 0.00 0.00 45.36 0.86
365 367 7.114670 GCAATTTGACGCAACATGCATAATATA 59.885 33.333 0.00 0.00 45.36 0.86
367 369 5.231779 GCAATTTGACGCAACATGCATAATA 59.768 36.000 0.00 0.00 45.36 0.98
369 371 3.367327 GCAATTTGACGCAACATGCATAA 59.633 39.130 0.00 0.00 45.36 1.90
370 372 2.922387 GCAATTTGACGCAACATGCATA 59.078 40.909 0.00 0.00 45.36 3.14
371 373 1.727880 GCAATTTGACGCAACATGCAT 59.272 42.857 16.52 0.00 45.36 3.96
372 374 1.138337 GCAATTTGACGCAACATGCA 58.862 45.000 16.52 0.00 45.36 3.96
373 375 0.439600 GGCAATTTGACGCAACATGC 59.560 50.000 0.00 14.64 40.69 4.06
374 376 1.987770 GAGGCAATTTGACGCAACATG 59.012 47.619 0.60 0.00 0.00 3.21
375 377 1.888512 AGAGGCAATTTGACGCAACAT 59.111 42.857 8.75 0.00 0.00 2.71
376 378 1.001487 CAGAGGCAATTTGACGCAACA 60.001 47.619 8.75 0.00 0.00 3.33
377 379 1.001378 ACAGAGGCAATTTGACGCAAC 60.001 47.619 8.75 0.00 0.00 4.17
382 412 2.287547 TGCGAAACAGAGGCAATTTGAC 60.288 45.455 0.00 0.00 33.01 3.18
406 436 4.184629 GTGTGTGTTATGTCCCTCAGATC 58.815 47.826 0.00 0.00 0.00 2.75
613 5269 0.692476 TGTGCTGTATGGCAAGGAGT 59.308 50.000 0.00 0.00 44.18 3.85
623 5279 8.409358 TCTGTAGATACATGTATGTGCTGTAT 57.591 34.615 22.93 0.00 41.89 2.29
669 5344 0.315382 GCAACATCGAAATCTCGCGG 60.315 55.000 6.13 0.00 45.04 6.46
782 5475 2.185350 GAGCGCTGCAGAGCCTAA 59.815 61.111 34.60 0.00 42.91 2.69
819 5512 1.135199 CAGGCAATGAAGCACATCACC 60.135 52.381 0.00 0.00 38.38 4.02
888 5581 9.021863 CGTCTAAGTTTGACCATAGAACTATTC 57.978 37.037 11.15 0.00 33.54 1.75
893 5586 5.285607 CGTCGTCTAAGTTTGACCATAGAAC 59.714 44.000 11.15 1.60 0.00 3.01
951 5653 6.088085 CCGAAACTGAGAAAAATGCACATTAC 59.912 38.462 0.00 0.00 0.00 1.89
1166 5913 0.036952 ACTGTCGCTGTCATCCAAGG 60.037 55.000 0.00 0.00 0.00 3.61
1179 5926 1.079127 GACCCCATGGACACTGTCG 60.079 63.158 15.22 0.00 32.65 4.35
1281 6028 5.296748 GGTTTCCATGTTGTAAGCACAATT 58.703 37.500 0.00 0.00 46.03 2.32
1426 6173 3.000925 ACAACAAACGTCAACGCTAGAAG 59.999 43.478 1.81 0.00 44.43 2.85
1702 6611 7.510630 CAAAAACCAAGTGTCGAGTATAAGAG 58.489 38.462 0.00 0.00 0.00 2.85
2327 7236 3.858135 ACCCTCATTCCCTGTCGTATAT 58.142 45.455 0.00 0.00 0.00 0.86
2373 7282 5.164061 GCAAGACAATAAACTTGATTTGCCG 60.164 40.000 0.00 0.00 43.98 5.69
2418 7327 7.094762 CCACAAGTTTTAACCTCTCCTGATAAC 60.095 40.741 0.00 0.00 0.00 1.89
2502 7411 5.295431 TCATTTCTGTGCCGAAAAGTATG 57.705 39.130 0.00 0.00 36.57 2.39
2565 7474 7.496346 TGGTAATATATCCAGGTCCTTGATC 57.504 40.000 8.73 0.00 0.00 2.92
3131 9179 6.924060 AGATTAATTACCACTCTCACGCATAC 59.076 38.462 0.00 0.00 0.00 2.39
3177 9232 9.853555 AAATGCAATATGAAGAACATTCGTTAA 57.146 25.926 0.00 0.00 40.07 2.01
3249 9312 5.075858 TGGATCAATCACAAAATCCAAGC 57.924 39.130 0.56 0.00 43.52 4.01
3277 9340 9.696917 GGATATATAAACTCAAAATTGCTTGGG 57.303 33.333 0.00 0.00 32.68 4.12
3591 9674 9.132521 GGACACAATTAATTCAGTGAATTCTTG 57.867 33.333 29.87 29.87 40.77 3.02
3801 9884 4.507691 CCAGTAGACAATAAACCCAACCCA 60.508 45.833 0.00 0.00 0.00 4.51
4096 10179 0.792640 CGGTGCTCGGAATATGCATC 59.207 55.000 0.19 0.00 39.00 3.91
4215 10298 4.547406 AAAAGTTTAACAGCACTCCGAC 57.453 40.909 0.00 0.00 0.00 4.79
4242 10326 7.518161 TGTTTCGACTTTCAGCATTAATACTG 58.482 34.615 9.13 9.13 35.15 2.74
4251 10335 3.796178 GCAATTTGTTTCGACTTTCAGCA 59.204 39.130 0.00 0.00 0.00 4.41
4478 10562 6.092670 TGTTTTCAAAATGGATGCGAACAAAA 59.907 30.769 0.00 0.00 0.00 2.44
4607 10696 2.112190 GTTTCAGCTCTAGCCTACCCT 58.888 52.381 0.00 0.00 43.38 4.34
4660 10749 5.174395 GTGGAAGCTAGCATATCCATGTAG 58.826 45.833 28.55 0.00 43.41 2.74
4784 10875 8.819845 AGTCTATCTATATGAACAATGGCATGA 58.180 33.333 0.00 0.00 0.00 3.07
4785 10876 9.445878 AAGTCTATCTATATGAACAATGGCATG 57.554 33.333 0.00 0.00 0.00 4.06
4823 10914 6.757897 TCTGAACAGATTTTCACAACACTT 57.242 33.333 0.00 0.00 32.02 3.16
4910 11002 2.270352 TGAAAATCTCGGCACACCTT 57.730 45.000 0.00 0.00 0.00 3.50
4917 11009 3.440173 TGAGAAACCATGAAAATCTCGGC 59.560 43.478 0.00 0.00 39.45 5.54
4963 11055 6.313905 AGTCACTTACACAAGTTTGAGTCAAG 59.686 38.462 5.56 0.00 42.51 3.02
5031 11125 6.084277 GTGCTTCAATAAGGTTAAAGTTCCG 58.916 40.000 0.00 0.00 32.98 4.30
5034 11131 7.920682 CACTTGTGCTTCAATAAGGTTAAAGTT 59.079 33.333 0.00 0.00 35.35 2.66
5231 11333 8.870879 GTTTCGCAGATTTAGTATAAAGTCAGT 58.129 33.333 0.00 0.00 35.04 3.41
5232 11334 9.088512 AGTTTCGCAGATTTAGTATAAAGTCAG 57.911 33.333 0.00 0.00 35.04 3.51
5233 11335 8.997621 AGTTTCGCAGATTTAGTATAAAGTCA 57.002 30.769 0.00 0.00 35.04 3.41
5255 11357 2.645797 TCCCTCCGTCCCAAAATAAGTT 59.354 45.455 0.00 0.00 0.00 2.66
5348 11453 4.694982 CCTAACCAAAAATTCACCATTGGC 59.305 41.667 1.54 0.00 44.90 4.52
5595 11707 0.107263 TGCCAGCTATTGATTCGGCA 60.107 50.000 6.06 6.06 46.80 5.69
5636 11748 6.370166 CCAACTGATGAACTCTCTTTCCTTAC 59.630 42.308 0.00 0.00 0.00 2.34
5892 12006 5.540337 TGTCTCTGTGAAGTGTAAGGAGATT 59.460 40.000 0.00 0.00 32.28 2.40
5922 12036 3.340814 AGTCCATAAGTGACTGCAAGG 57.659 47.619 0.00 0.00 41.40 3.61
6010 12124 8.362639 GGTCATGTATTGCAATATTCTTTCCAT 58.637 33.333 21.52 14.65 0.00 3.41
6086 12200 0.827368 TTCACCCTTTGTTGGCCAAC 59.173 50.000 36.78 36.78 41.50 3.77
6200 12319 7.807977 ACTATGTGCCATTAAAACTATCCAG 57.192 36.000 0.00 0.00 0.00 3.86
6202 12321 8.774586 CACTACTATGTGCCATTAAAACTATCC 58.225 37.037 0.00 0.00 0.00 2.59
6254 12376 9.084164 GCAACGTTATATTAGAAGAAACTCAGA 57.916 33.333 0.00 0.00 0.00 3.27
6308 12438 3.057315 GGCGCATATTTTACCTGCATGAT 60.057 43.478 10.83 0.00 35.64 2.45
6607 12737 1.482593 AGTACCTCCCAGATTTGCTCG 59.517 52.381 0.00 0.00 0.00 5.03
6662 12792 6.523201 CAGTTAAGTTATGCGGTCAAATTGAC 59.477 38.462 17.16 17.16 46.23 3.18
6674 12804 6.194796 TGCTGATTTCCAGTTAAGTTATGC 57.805 37.500 0.00 0.00 44.71 3.14
6685 12815 7.330900 AGAAAATACAGATGCTGATTTCCAG 57.669 36.000 0.82 0.00 45.67 3.86
6686 12816 8.985315 ATAGAAAATACAGATGCTGATTTCCA 57.015 30.769 0.82 0.22 35.27 3.53
6714 12844 7.066404 TCGCACATAAATTACTTTAGCCATCAA 59.934 33.333 0.00 0.00 30.61 2.57
6715 12845 6.540551 TCGCACATAAATTACTTTAGCCATCA 59.459 34.615 0.00 0.00 30.61 3.07
6738 12868 4.534168 CAATGCCTAGAAAATGCAGATCG 58.466 43.478 0.00 0.00 38.58 3.69
6744 12874 3.445096 ACAGTCCAATGCCTAGAAAATGC 59.555 43.478 0.00 0.00 0.00 3.56
6746 12876 5.079643 ACAACAGTCCAATGCCTAGAAAAT 58.920 37.500 0.00 0.00 0.00 1.82
6749 12879 3.072330 TGACAACAGTCCAATGCCTAGAA 59.928 43.478 0.00 0.00 0.00 2.10
6784 12914 5.205988 GCTTAAGCTCGTTCTTTCTAACC 57.794 43.478 20.38 0.00 38.21 2.85
6828 12958 7.707035 AGCGTGTTTCTGGAGAGTTTATTATAG 59.293 37.037 0.00 0.00 0.00 1.31
6838 12968 3.134458 AGAAAAGCGTGTTTCTGGAGAG 58.866 45.455 12.76 0.00 44.35 3.20
6839 12969 3.194005 AGAAAAGCGTGTTTCTGGAGA 57.806 42.857 12.76 0.00 44.35 3.71
6840 12970 3.971032 AAGAAAAGCGTGTTTCTGGAG 57.029 42.857 13.85 0.00 45.09 3.86
6841 12971 4.712122 AAAAGAAAAGCGTGTTTCTGGA 57.288 36.364 13.85 0.00 45.09 3.86
6842 12972 6.205784 TCATAAAAGAAAAGCGTGTTTCTGG 58.794 36.000 13.85 5.14 45.09 3.86
6843 12973 7.617935 GCATCATAAAAGAAAAGCGTGTTTCTG 60.618 37.037 13.85 5.12 45.09 3.02
6845 12975 6.399986 GGCATCATAAAAGAAAAGCGTGTTTC 60.400 38.462 5.19 5.19 37.70 2.78
6847 12977 4.923281 GGCATCATAAAAGAAAAGCGTGTT 59.077 37.500 0.00 0.00 0.00 3.32
6848 12978 4.022416 TGGCATCATAAAAGAAAAGCGTGT 60.022 37.500 0.00 0.00 0.00 4.49
6850 12980 4.737054 CTGGCATCATAAAAGAAAAGCGT 58.263 39.130 0.00 0.00 0.00 5.07
6852 12982 3.549070 CGCTGGCATCATAAAAGAAAAGC 59.451 43.478 0.00 0.00 0.00 3.51
6853 12983 4.985413 TCGCTGGCATCATAAAAGAAAAG 58.015 39.130 0.00 0.00 0.00 2.27
6855 12985 5.105797 ACAATCGCTGGCATCATAAAAGAAA 60.106 36.000 0.00 0.00 0.00 2.52
6856 12986 4.398988 ACAATCGCTGGCATCATAAAAGAA 59.601 37.500 0.00 0.00 0.00 2.52
6857 12987 3.947196 ACAATCGCTGGCATCATAAAAGA 59.053 39.130 0.00 0.00 0.00 2.52
6859 12989 4.717233 AACAATCGCTGGCATCATAAAA 57.283 36.364 0.00 0.00 0.00 1.52
6862 12992 4.450976 ACTAAACAATCGCTGGCATCATA 58.549 39.130 0.00 0.00 0.00 2.15
6863 12993 3.282021 ACTAAACAATCGCTGGCATCAT 58.718 40.909 0.00 0.00 0.00 2.45
6865 12995 2.677836 TGACTAAACAATCGCTGGCATC 59.322 45.455 0.00 0.00 0.00 3.91
6866 12996 2.710377 TGACTAAACAATCGCTGGCAT 58.290 42.857 0.00 0.00 0.00 4.40
6868 12998 3.764885 ATTGACTAAACAATCGCTGGC 57.235 42.857 0.00 0.00 35.92 4.85
6869 12999 7.015226 TCATAATTGACTAAACAATCGCTGG 57.985 36.000 0.00 0.00 39.19 4.85
6870 13000 7.588854 CCATCATAATTGACTAAACAATCGCTG 59.411 37.037 0.00 0.00 39.19 5.18
6871 13001 7.642669 CCATCATAATTGACTAAACAATCGCT 58.357 34.615 0.00 0.00 39.19 4.93
6872 13002 6.360681 GCCATCATAATTGACTAAACAATCGC 59.639 38.462 0.00 0.00 39.19 4.58
6873 13003 6.574832 CGCCATCATAATTGACTAAACAATCG 59.425 38.462 0.00 0.00 39.19 3.34
6874 13004 7.639039 TCGCCATCATAATTGACTAAACAATC 58.361 34.615 0.00 0.00 39.19 2.67
6875 13005 7.566760 TCGCCATCATAATTGACTAAACAAT 57.433 32.000 0.00 0.00 41.43 2.71
6876 13006 6.458206 GCTCGCCATCATAATTGACTAAACAA 60.458 38.462 0.00 0.00 33.85 2.83
6877 13007 5.007626 GCTCGCCATCATAATTGACTAAACA 59.992 40.000 0.00 0.00 33.85 2.83
6878 13008 5.444122 GCTCGCCATCATAATTGACTAAAC 58.556 41.667 0.00 0.00 33.85 2.01
6879 13009 4.515191 GGCTCGCCATCATAATTGACTAAA 59.485 41.667 2.41 0.00 33.85 1.85
6880 13010 4.065088 GGCTCGCCATCATAATTGACTAA 58.935 43.478 2.41 0.00 33.85 2.24
6881 13011 3.070878 TGGCTCGCCATCATAATTGACTA 59.929 43.478 6.52 0.00 41.89 2.59
6882 13012 2.158769 TGGCTCGCCATCATAATTGACT 60.159 45.455 6.52 0.00 41.89 3.41
6883 13013 2.221169 TGGCTCGCCATCATAATTGAC 58.779 47.619 6.52 0.00 41.89 3.18
6884 13014 2.636647 TGGCTCGCCATCATAATTGA 57.363 45.000 6.52 0.00 41.89 2.57
6885 13015 3.928727 ATTGGCTCGCCATCATAATTG 57.071 42.857 12.00 0.00 46.64 2.32
6886 13016 5.072741 AGTTATTGGCTCGCCATCATAATT 58.927 37.500 12.00 7.81 46.64 1.40
6887 13017 4.655963 AGTTATTGGCTCGCCATCATAAT 58.344 39.130 12.00 4.45 46.64 1.28
6900 13032 7.370383 TCAGTTCAAAAGATCAAGTTATTGGC 58.630 34.615 0.00 0.00 37.02 4.52
6946 13079 2.668212 CCCGCGCTCCAGTTTTCA 60.668 61.111 5.56 0.00 0.00 2.69
7141 13276 4.216687 AGAAGAATAACCCTCTCGCTATCG 59.783 45.833 0.00 0.00 0.00 2.92
7214 13355 6.318913 ACAGAGGAGAACAGCATATATAGGT 58.681 40.000 0.00 0.00 0.00 3.08
7259 13403 7.516627 GCAATTTCACCTGTTTTACACAACATC 60.517 37.037 0.00 0.00 36.08 3.06
7298 13443 1.086634 CCTCTAGCAACTTCGCTGGC 61.087 60.000 0.00 0.00 43.68 4.85
7331 13476 2.544267 CTCCGACACAAGTTTGGAGAAC 59.456 50.000 10.53 0.00 45.94 3.01
7379 13524 1.747774 GCTCTCCTCTGCATCCTCC 59.252 63.158 0.00 0.00 0.00 4.30
7389 13534 0.753479 TCCATGACTCGGCTCTCCTC 60.753 60.000 0.00 0.00 0.00 3.71
7392 13537 1.067250 GCTCCATGACTCGGCTCTC 59.933 63.158 0.00 0.00 0.00 3.20
7399 13544 1.734047 GCGATATCGGCTCCATGACTC 60.734 57.143 25.51 1.48 40.23 3.36
7493 13642 2.907910 AAGAACTGCATGCACGAATC 57.092 45.000 18.46 12.21 0.00 2.52
7523 13672 8.834004 AAACTAATGGTCACTACTCCTACATA 57.166 34.615 0.00 0.00 0.00 2.29
7529 13678 6.641474 AGCTTAAACTAATGGTCACTACTCC 58.359 40.000 0.00 0.00 0.00 3.85
7530 13679 7.064728 CCAAGCTTAAACTAATGGTCACTACTC 59.935 40.741 0.00 0.00 0.00 2.59
7558 13707 5.542251 TCAATCTCCACCGTAATATGATCCA 59.458 40.000 0.00 0.00 0.00 3.41
7590 13739 2.311463 TGAATCTCGAGCTAAGAGGGG 58.689 52.381 7.81 0.00 36.45 4.79
7627 13776 0.252197 ACCGGTGAAATCCACTAGCC 59.748 55.000 6.12 0.00 45.03 3.93
7646 13795 3.244630 GGACAAGTATGTGGTGTGGGTAA 60.245 47.826 0.00 0.00 40.74 2.85
7889 14425 0.747644 CATCACCAGCATTACCGGCA 60.748 55.000 0.00 0.00 0.00 5.69
7895 14431 1.823470 GGCGGCATCACCAGCATTA 60.823 57.895 3.07 0.00 39.00 1.90
7924 14460 2.434359 GGAGCCGCACAGGTACAC 60.434 66.667 0.00 0.00 43.70 2.90
8234 14770 4.335647 CCAAGCTGGGCCACGTCT 62.336 66.667 0.00 0.00 32.67 4.18
8309 14846 2.435586 CAGCACCTCAAGGCCGAG 60.436 66.667 0.00 0.00 39.32 4.63


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

AutoCloner maintained by Alex Coulton.