Multiple sequence alignment - TraesCS1B01G095700

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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 TraesCS1B01G095700 chr1B 100.000 6093 0 0 1 6093 99600799 99594707 0.000000e+00 11252
1 TraesCS1B01G095700 chr1D 93.942 5348 200 60 830 6093 62419789 62414482 0.000000e+00 7967
2 TraesCS1B01G095700 chr1D 89.387 848 76 10 1 844 62420642 62419805 0.000000e+00 1055
3 TraesCS1B01G095700 chr1A 94.584 3619 162 21 784 4390 60359051 60355455 0.000000e+00 5566
4 TraesCS1B01G095700 chr1A 91.520 684 38 8 4390 5064 60355375 60354703 0.000000e+00 924
5 TraesCS1B01G095700 chr1A 87.420 779 39 18 5095 5832 60354710 60353950 0.000000e+00 841
6 TraesCS1B01G095700 chr1A 92.453 106 4 3 5990 6093 60353793 60353690 1.370000e-31 148


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 TraesCS1B01G095700 chr1B 99594707 99600799 6092 True 11252.00 11252 100.00000 1 6093 1 chr1B.!!$R1 6092
1 TraesCS1B01G095700 chr1D 62414482 62420642 6160 True 4511.00 7967 91.66450 1 6093 2 chr1D.!!$R1 6092
2 TraesCS1B01G095700 chr1A 60353690 60359051 5361 True 1869.75 5566 91.49425 784 6093 4 chr1A.!!$R1 5309

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
549 553 0.099791 CGTTTGCCCACACGAACTTT 59.900 50.000 1.01 0.0 38.76 2.66 F
612 616 0.178891 TCTTTGAGAGCCCCTGGAGT 60.179 55.000 0.00 0.0 0.00 3.85 F
613 617 0.251634 CTTTGAGAGCCCCTGGAGTC 59.748 60.000 0.00 0.0 0.00 3.36 F
2131 2179 0.040499 GGTCCAATGGGCCAAACCTA 59.960 55.000 19.69 0.0 39.10 3.08 F
2148 2196 0.325602 CTACCCCGCAACCACCTTTA 59.674 55.000 0.00 0.0 0.00 1.85 F
2182 2230 0.390472 GGAAGAGGTGACTTGGAGCG 60.390 60.000 0.00 0.0 44.43 5.03 F
2823 2872 1.134098 GGGCATGCAAGAGTAAGCCTA 60.134 52.381 21.36 0.0 41.71 3.93 F
4348 4400 1.275010 TGGCTAACATCAACTCAGCGA 59.725 47.619 0.00 0.0 32.97 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2138 0.106918 AGCGACCTGTCCCACAAAAA 60.107 50.000 0.00 0.0 0.00 1.94 R
2131 2179 0.993470 TATAAAGGTGGTTGCGGGGT 59.007 50.000 0.00 0.0 0.00 4.95 R
2251 2300 1.620822 AGAACCAACCAACAGGATGC 58.379 50.000 0.00 0.0 42.53 3.91 R
3584 3633 1.061131 GTGTCGTGCCAAGAATCATCG 59.939 52.381 0.00 0.0 0.00 3.84 R
3948 3997 2.623416 GTCTCCAACTTTGAAACTGGGG 59.377 50.000 2.44 0.0 0.00 4.96 R
4045 4094 4.634883 GCAAGTAGGTTTAGGACTTTAGGC 59.365 45.833 0.00 0.0 31.04 3.93 R
4649 4781 1.360551 CATACGAGAGAGGCACGGG 59.639 63.158 0.00 0.0 34.76 5.28 R
5606 5797 0.250513 CTCACCTAACCCACAGCTCC 59.749 60.000 0.00 0.0 0.00 4.70 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
86 87 9.829507 AAACATTCATGTCTTTTGGAATACAAA 57.170 25.926 0.00 0.00 42.82 2.83
113 114 8.273780 AGCTGATTGAAAATCACTAAACTAGG 57.726 34.615 0.00 0.00 0.00 3.02
158 159 7.712797 TCAAAGTAACAGAAAGAAAATCACCC 58.287 34.615 0.00 0.00 0.00 4.61
162 163 7.166167 AGTAACAGAAAGAAAATCACCCGTAT 58.834 34.615 0.00 0.00 0.00 3.06
182 183 1.472878 TGCTAACTCCACTCGCTACAG 59.527 52.381 0.00 0.00 0.00 2.74
189 190 1.066587 CACTCGCTACAGCCCTAGC 59.933 63.158 0.00 0.89 37.91 3.42
200 201 2.712984 GCCCTAGCTCCAATGAAGC 58.287 57.895 0.00 0.00 35.50 3.86
214 215 2.506962 AAGCGACCCGGTTGTGAA 59.493 55.556 6.67 0.00 45.71 3.18
215 216 1.153127 AAGCGACCCGGTTGTGAAA 60.153 52.632 6.67 0.00 45.71 2.69
221 222 1.288752 CCCGGTTGTGAAACCATGC 59.711 57.895 0.00 0.00 42.97 4.06
225 226 0.939106 GGTTGTGAAACCATGCGCAC 60.939 55.000 14.90 0.00 42.38 5.34
229 230 1.135915 TGTGAAACCATGCGCACTTTT 59.864 42.857 14.90 12.63 34.36 2.27
234 235 1.135315 CCATGCGCACTTTTCCTCG 59.865 57.895 14.90 0.00 0.00 4.63
240 241 1.796459 GCGCACTTTTCCTCGAGTTAA 59.204 47.619 12.31 2.35 0.00 2.01
241 242 2.415512 GCGCACTTTTCCTCGAGTTAAT 59.584 45.455 12.31 0.00 0.00 1.40
250 252 7.282450 ACTTTTCCTCGAGTTAATGAAACAAGT 59.718 33.333 12.31 10.99 40.83 3.16
251 253 6.780706 TTCCTCGAGTTAATGAAACAAGTC 57.219 37.500 12.31 0.00 40.83 3.01
255 257 4.380678 TCGAGTTAATGAAACAAGTCGTCG 59.619 41.667 10.33 0.00 44.23 5.12
310 312 3.146847 CCCTGGTTGTAGTCCTTGTTTC 58.853 50.000 0.00 0.00 0.00 2.78
345 347 4.536364 AGATTTGTTCATATCCGCAACG 57.464 40.909 0.96 0.00 0.00 4.10
355 357 5.834169 TCATATCCGCAACGATTACAAGTA 58.166 37.500 0.00 0.00 0.00 2.24
383 385 7.072263 TGCTTTGGATCCAAAATTTAGGAAA 57.928 32.000 33.74 13.44 44.07 3.13
395 397 9.406828 CCAAAATTTAGGAAACTACAAAGTAGC 57.593 33.333 4.20 0.00 44.30 3.58
436 438 1.470098 CAATGAGGCCTTTTGGAGTCG 59.530 52.381 6.77 0.00 44.07 4.18
439 441 0.673956 GAGGCCTTTTGGAGTCGTCC 60.674 60.000 6.77 0.00 44.07 4.79
444 446 1.896465 CCTTTTGGAGTCGTCCTCTCT 59.104 52.381 5.16 0.00 44.30 3.10
450 452 4.498894 TGGAGTCGTCCTCTCTGTAATA 57.501 45.455 5.16 0.00 44.30 0.98
456 458 6.797454 AGTCGTCCTCTCTGTAATATCAAAC 58.203 40.000 0.00 0.00 0.00 2.93
475 478 3.719268 ACTATCAATCCCTGCAACACA 57.281 42.857 0.00 0.00 0.00 3.72
483 486 6.164876 TCAATCCCTGCAACACAAAATATTG 58.835 36.000 0.00 0.00 42.46 1.90
500 503 7.951530 AAATATTGCCAAGACTTCAAAACTG 57.048 32.000 0.00 0.00 0.00 3.16
511 514 0.958091 TCAAAACTGCCAATGGACCG 59.042 50.000 2.05 0.00 0.00 4.79
512 515 0.667184 CAAAACTGCCAATGGACCGC 60.667 55.000 2.05 0.00 0.00 5.68
515 518 3.818787 CTGCCAATGGACCGCAGC 61.819 66.667 2.05 0.00 43.12 5.25
527 530 0.955428 ACCGCAGCAACGATGATGTT 60.955 50.000 12.62 0.00 44.75 2.71
528 531 0.247814 CCGCAGCAACGATGATGTTC 60.248 55.000 12.62 0.00 44.75 3.18
539 543 0.251564 ATGATGTTCCCGTTTGCCCA 60.252 50.000 0.00 0.00 0.00 5.36
549 553 0.099791 CGTTTGCCCACACGAACTTT 59.900 50.000 1.01 0.00 38.76 2.66
556 560 2.286772 GCCCACACGAACTTTACAACTG 60.287 50.000 0.00 0.00 0.00 3.16
606 610 3.653835 ATAAAGGTCTTTGAGAGCCCC 57.346 47.619 6.24 0.00 43.38 5.80
608 612 0.695347 AAGGTCTTTGAGAGCCCCTG 59.305 55.000 3.72 0.00 43.38 4.45
609 613 1.204113 AGGTCTTTGAGAGCCCCTGG 61.204 60.000 3.72 0.00 43.38 4.45
610 614 1.201429 GGTCTTTGAGAGCCCCTGGA 61.201 60.000 0.00 0.00 36.78 3.86
611 615 0.251634 GTCTTTGAGAGCCCCTGGAG 59.748 60.000 0.00 0.00 0.00 3.86
612 616 0.178891 TCTTTGAGAGCCCCTGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
613 617 0.251634 CTTTGAGAGCCCCTGGAGTC 59.748 60.000 0.00 0.00 0.00 3.36
614 618 1.544825 TTTGAGAGCCCCTGGAGTCG 61.545 60.000 0.00 0.00 0.00 4.18
657 661 9.548208 GAAAACTTTGAGCTATGAATGTACTTC 57.452 33.333 0.00 0.00 0.00 3.01
668 672 4.650734 TGAATGTACTTCAGCATGGAACA 58.349 39.130 0.00 0.00 40.43 3.18
702 706 2.224744 TGCAGGCCATTGAACTACAAGA 60.225 45.455 5.01 0.00 42.02 3.02
719 723 9.698309 AACTACAAGATCACCATAATATCGAAG 57.302 33.333 0.00 0.00 0.00 3.79
738 742 5.466728 TCGAAGAAAGATTTCAACTCCACAG 59.533 40.000 7.97 0.00 39.61 3.66
833 839 5.034554 AGACAAAATAACACGATGCACTG 57.965 39.130 0.00 0.00 0.00 3.66
877 913 1.670791 CCAAATTGCATGGGCCAATC 58.329 50.000 11.89 5.79 40.13 2.67
878 914 1.065345 CCAAATTGCATGGGCCAATCA 60.065 47.619 11.89 8.86 40.13 2.57
891 927 2.154462 GCCAATCATCATCTTACCCGG 58.846 52.381 0.00 0.00 0.00 5.73
982 1018 1.955495 GCCCCCAAAATAGCCCAACG 61.955 60.000 0.00 0.00 0.00 4.10
1037 1074 3.723348 GCCGACCCACGCTTTGTC 61.723 66.667 0.00 0.00 41.07 3.18
1204 1248 3.081409 GCCTCCAACGAGCCCCTA 61.081 66.667 0.00 0.00 34.49 3.53
1510 1554 2.126463 CTGGTCGCGCTCTTCGAA 60.126 61.111 5.56 0.00 41.67 3.71
1511 1555 1.733041 CTGGTCGCGCTCTTCGAAA 60.733 57.895 5.56 0.00 41.67 3.46
1543 1587 3.396570 CCGGGGCTAGGGTTTCGT 61.397 66.667 0.00 0.00 0.00 3.85
1550 1594 1.290955 CTAGGGTTTCGTGCGGACA 59.709 57.895 8.11 0.00 0.00 4.02
1570 1614 1.885163 GCGGGAAGAAGGAGGACGAA 61.885 60.000 0.00 0.00 0.00 3.85
1734 1778 8.012241 GCTGAACTCTGTTATTTACTTTGACAG 58.988 37.037 0.00 0.00 39.16 3.51
1753 1798 8.958119 TTGACAGTTTTGTAGTCTAGATGTTT 57.042 30.769 0.00 0.00 37.76 2.83
1874 1920 8.985315 TTTATGTGGATTGATCTGAATAAGCT 57.015 30.769 0.00 0.00 0.00 3.74
1899 1945 5.952347 AGATATATTATCGTCTCAGGGTGCA 59.048 40.000 0.00 0.00 0.00 4.57
1900 1946 6.609212 AGATATATTATCGTCTCAGGGTGCAT 59.391 38.462 0.00 0.00 0.00 3.96
1960 2006 5.923733 TTGCAATTTTGGAATATACGGGT 57.076 34.783 0.00 0.00 33.44 5.28
1997 2043 4.919774 TGTAGAATTAGCCTCCAACCAA 57.080 40.909 0.00 0.00 0.00 3.67
1998 2044 4.585879 TGTAGAATTAGCCTCCAACCAAC 58.414 43.478 0.00 0.00 0.00 3.77
2018 2064 4.508551 ACTGAATACATGCAATCCTGGA 57.491 40.909 0.00 0.00 0.00 3.86
2019 2065 4.858850 ACTGAATACATGCAATCCTGGAA 58.141 39.130 0.00 0.00 0.00 3.53
2054 2100 9.554724 AAATTATGCTGTGTCTACAATAAAACG 57.445 29.630 0.00 0.00 36.14 3.60
2060 2106 6.073980 GCTGTGTCTACAATAAAACGAAGTGA 60.074 38.462 0.00 0.00 37.26 3.41
2092 2138 4.264172 TGGTTATTACAACCATCAAGGCCT 60.264 41.667 0.00 0.00 44.74 5.19
2097 2143 3.473923 ACAACCATCAAGGCCTTTTTG 57.526 42.857 17.61 15.91 43.14 2.44
2102 2150 1.969923 CATCAAGGCCTTTTTGTGGGA 59.030 47.619 17.61 8.71 0.00 4.37
2123 2171 3.134127 GTCGCTGGTCCAATGGGC 61.134 66.667 0.00 0.00 0.00 5.36
2131 2179 0.040499 GGTCCAATGGGCCAAACCTA 59.960 55.000 19.69 0.00 39.10 3.08
2134 2182 0.975556 CCAATGGGCCAAACCTACCC 60.976 60.000 11.89 0.00 44.52 3.69
2138 2186 4.354162 GGCCAAACCTACCCCGCA 62.354 66.667 0.00 0.00 34.51 5.69
2147 2195 1.074248 CTACCCCGCAACCACCTTT 59.926 57.895 0.00 0.00 0.00 3.11
2148 2196 0.325602 CTACCCCGCAACCACCTTTA 59.674 55.000 0.00 0.00 0.00 1.85
2149 2197 0.993470 TACCCCGCAACCACCTTTAT 59.007 50.000 0.00 0.00 0.00 1.40
2150 2198 0.993470 ACCCCGCAACCACCTTTATA 59.007 50.000 0.00 0.00 0.00 0.98
2176 2224 5.788014 AGGAATTTAGAGGAAGAGGTGACTT 59.212 40.000 0.00 0.00 44.43 3.01
2182 2230 0.390472 GGAAGAGGTGACTTGGAGCG 60.390 60.000 0.00 0.00 44.43 5.03
2271 2320 2.107378 TGCATCCTGTTGGTTGGTTCTA 59.893 45.455 0.00 0.00 34.46 2.10
2272 2321 2.488153 GCATCCTGTTGGTTGGTTCTAC 59.512 50.000 0.00 0.00 34.46 2.59
2273 2322 3.810743 GCATCCTGTTGGTTGGTTCTACT 60.811 47.826 0.00 0.00 34.46 2.57
2285 2334 8.220755 TGGTTGGTTCTACTATTCAATAATGC 57.779 34.615 0.00 0.00 0.00 3.56
2545 2594 1.209261 TCTTGGCGAACATAGCATGGA 59.791 47.619 0.00 0.00 36.08 3.41
2635 2684 5.598005 TGGTCCTTCATGAGAACACAAAAAT 59.402 36.000 0.00 0.00 0.00 1.82
2693 2742 7.405292 AGATTTTCCAACAGGATGAAGATACA 58.595 34.615 0.00 0.00 39.69 2.29
2764 2813 7.336427 AGAGCATGTAATTTTGGAAGAGAGAAG 59.664 37.037 0.00 0.00 0.00 2.85
2823 2872 1.134098 GGGCATGCAAGAGTAAGCCTA 60.134 52.381 21.36 0.00 41.71 3.93
2916 2965 2.438021 TCGGTAAAGATGGATCAAGGGG 59.562 50.000 0.00 0.00 0.00 4.79
3077 3126 6.677781 AAAAATGAGACAAGTGACGAGAAA 57.322 33.333 0.00 0.00 0.00 2.52
3373 3422 5.957774 ACCTTGTGGTCCTTTAATATGCAAT 59.042 36.000 0.00 0.00 44.78 3.56
3474 3523 2.997980 TGCTTCACCAGAAACAGTTCA 58.002 42.857 0.00 0.00 36.09 3.18
3489 3538 2.086869 AGTTCAAGAATGTCCATGGCG 58.913 47.619 6.96 0.00 0.00 5.69
3584 3633 3.876914 TGGACACTGACATGTTTGAAGTC 59.123 43.478 0.00 5.41 31.24 3.01
3645 3694 8.134895 TCAGTTTAACAGTAAGCATTTTTGAGG 58.865 33.333 0.00 0.00 0.00 3.86
3946 3995 5.889853 ACTTGTATCAAACATGAGGATGCAT 59.110 36.000 0.00 0.00 38.10 3.96
3948 3997 6.866010 TGTATCAAACATGAGGATGCATAC 57.134 37.500 0.00 0.00 31.43 2.39
3983 4032 5.197451 AGTTGGAGACTACTCTGGTATGAG 58.803 45.833 0.00 0.00 43.00 2.90
4045 4094 8.131100 CAGTTGGTCCAAATATATACTTTGCTG 58.869 37.037 5.69 0.94 33.27 4.41
4061 4110 3.067684 TGCTGCCTAAAGTCCTAAACC 57.932 47.619 0.00 0.00 0.00 3.27
4135 4187 4.451096 CACTACTATCGGCAAACAACAGTT 59.549 41.667 0.00 0.00 0.00 3.16
4221 4273 4.265073 AGGGTAGAATGTGCACATTTCTC 58.735 43.478 37.99 29.63 45.72 2.87
4233 4285 8.470657 TGTGCACATTTCTCTACTAGATAGAT 57.529 34.615 17.42 0.00 39.28 1.98
4250 4302 9.674068 CTAGATAGATATAAGACTAGTGGCACA 57.326 37.037 21.41 5.00 0.00 4.57
4348 4400 1.275010 TGGCTAACATCAACTCAGCGA 59.725 47.619 0.00 0.00 32.97 4.93
4361 4413 4.983671 ACTCAGCGAAAAAGAAAAGGTT 57.016 36.364 0.00 0.00 0.00 3.50
4649 4781 1.335051 GCAGAAGGTGGCGTTTCTTTC 60.335 52.381 0.00 0.00 31.53 2.62
4654 4786 1.281656 GTGGCGTTTCTTTCCCGTG 59.718 57.895 0.00 0.00 0.00 4.94
4662 4794 0.608640 TTCTTTCCCGTGCCTCTCTC 59.391 55.000 0.00 0.00 0.00 3.20
4669 4801 1.433471 CGTGCCTCTCTCGTATGCA 59.567 57.895 0.00 0.00 0.00 3.96
4670 4802 0.179137 CGTGCCTCTCTCGTATGCAA 60.179 55.000 0.00 0.00 33.11 4.08
4683 4815 8.201464 TCTCTCGTATGCAAAAATACAAGGATA 58.799 33.333 0.00 0.00 33.40 2.59
4687 4819 7.011950 TCGTATGCAAAAATACAAGGATACCTG 59.988 37.037 0.00 0.00 33.44 4.00
4713 4852 6.593382 TGTGTTTCTTGATTGTTTTTCCTTGG 59.407 34.615 0.00 0.00 0.00 3.61
4985 5133 0.540365 CACAGTGACAGCCCCCATTT 60.540 55.000 0.00 0.00 0.00 2.32
4987 5135 1.077265 AGTGACAGCCCCCATTTGG 59.923 57.895 0.00 0.00 0.00 3.28
5033 5184 3.057315 TCTTGCTGCTTTACCATTGCTTC 60.057 43.478 0.00 0.00 0.00 3.86
5064 5215 1.444383 CTCGCGTTGCTGTCAGCTA 60.444 57.895 24.76 15.50 42.97 3.32
5065 5216 0.803768 CTCGCGTTGCTGTCAGCTAT 60.804 55.000 24.76 0.00 42.97 2.97
5074 5225 1.709147 CTGTCAGCTATGTTGCGGGC 61.709 60.000 0.00 0.00 38.13 6.13
5098 5249 0.109597 GGCAGGCTTGTTTCATGTCG 60.110 55.000 0.00 0.00 0.00 4.35
5100 5251 0.592637 CAGGCTTGTTTCATGTCGCA 59.407 50.000 0.00 0.00 0.00 5.10
5161 5312 1.135915 AGATAACTGCCACGAGAGCTG 59.864 52.381 0.00 0.00 35.51 4.24
5250 5409 2.737252 GTCTGTAGCTGTTGTTACCTGC 59.263 50.000 0.00 0.00 0.00 4.85
5399 5569 5.149973 TGGCTCAATACATTTGTGCATTT 57.850 34.783 12.62 0.00 39.76 2.32
5400 5570 4.930405 TGGCTCAATACATTTGTGCATTTG 59.070 37.500 12.62 0.00 39.76 2.32
5402 5572 4.201744 GCTCAATACATTTGTGCATTTGCC 60.202 41.667 0.00 0.00 41.18 4.52
5403 5573 5.149973 TCAATACATTTGTGCATTTGCCT 57.850 34.783 0.00 0.00 41.18 4.75
5523 5694 2.684927 GCATTGAACCCACCTGCTATCT 60.685 50.000 0.00 0.00 31.81 1.98
5548 5719 2.029728 CAGCTGATTTTTAGGCGTCTCG 59.970 50.000 8.42 0.00 0.00 4.04
5557 5745 4.707030 TTTAGGCGTCTCGTCAGATTTA 57.293 40.909 0.00 0.00 32.13 1.40
5560 5748 1.536284 GGCGTCTCGTCAGATTTAGGG 60.536 57.143 0.00 0.00 0.00 3.53
5565 5753 2.431057 TCTCGTCAGATTTAGGGAAGGC 59.569 50.000 0.00 0.00 0.00 4.35
5606 5797 1.548719 GGGATTGGGTTCCGGAAAAAG 59.451 52.381 20.79 0.00 36.58 2.27
5637 5836 1.866483 TAGGTGAGGGGGCGTGTCTA 61.866 60.000 0.00 0.00 0.00 2.59
5665 5864 1.683365 GTGCCAGCCATTCCACCAT 60.683 57.895 0.00 0.00 0.00 3.55
5707 5906 3.428999 CGGATCGAGACAGTGGTATGTTT 60.429 47.826 0.00 0.00 32.25 2.83
5718 5917 8.730680 AGACAGTGGTATGTTTAGCTAAATTTG 58.269 33.333 21.28 12.58 32.25 2.32
5724 5923 6.751888 GGTATGTTTAGCTAAATTTGCCACTG 59.248 38.462 21.28 0.00 0.00 3.66
5739 5938 1.338200 CCACTGCCGCTAAGTCTTCTT 60.338 52.381 0.00 0.00 37.65 2.52
5768 5971 4.016706 ACCACGGCACCTGCTACC 62.017 66.667 0.00 0.00 41.70 3.18
5788 5991 4.352009 ACCCTATGATCTCTAGCTGATGG 58.648 47.826 0.00 0.00 0.00 3.51
5789 5992 3.132646 CCCTATGATCTCTAGCTGATGGC 59.867 52.174 0.00 0.00 42.19 4.40
5866 6138 1.298859 GCAACAGTCGCCCCAGTAAG 61.299 60.000 0.00 0.00 0.00 2.34
5893 6165 4.075682 ACTCACACTTCTCTGAATCGAGA 58.924 43.478 0.00 1.76 38.23 4.04
5907 6179 2.818132 GAGATGACCAGAGCCCCG 59.182 66.667 0.00 0.00 0.00 5.73
5923 6195 2.614983 GCCCCGCGAATATTTCTGTTAA 59.385 45.455 8.23 0.00 0.00 2.01
5963 6238 2.484287 AAAGCAGGTCCATCCGTGGG 62.484 60.000 0.00 0.00 46.06 4.61
5977 6252 2.125310 TGGGCGCAACGGATGTAG 60.125 61.111 10.83 0.00 0.00 2.74
6075 6354 4.079253 GAGAATGCCCCTACAAAAACTGA 58.921 43.478 0.00 0.00 0.00 3.41
6076 6355 4.677182 AGAATGCCCCTACAAAAACTGAT 58.323 39.130 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 9.829507 TGTATTCCAAAAGACATGAATGTTTTT 57.170 25.926 0.00 6.21 44.02 1.94
59 60 9.829507 TTGTATTCCAAAAGACATGAATGTTTT 57.170 25.926 0.00 0.00 41.95 2.43
134 135 6.636850 CGGGTGATTTTCTTTCTGTTACTTTG 59.363 38.462 0.00 0.00 0.00 2.77
142 143 4.396166 AGCATACGGGTGATTTTCTTTCTG 59.604 41.667 0.00 0.00 0.00 3.02
158 159 1.065701 AGCGAGTGGAGTTAGCATACG 59.934 52.381 0.00 0.00 0.00 3.06
162 163 1.472878 CTGTAGCGAGTGGAGTTAGCA 59.527 52.381 0.00 0.00 0.00 3.49
182 183 1.162800 CGCTTCATTGGAGCTAGGGC 61.163 60.000 14.91 0.00 39.06 5.19
189 190 1.815421 CCGGGTCGCTTCATTGGAG 60.815 63.158 0.00 0.00 0.00 3.86
190 191 2.119484 AACCGGGTCGCTTCATTGGA 62.119 55.000 6.32 0.00 0.00 3.53
199 200 2.635338 GTTTCACAACCGGGTCGC 59.365 61.111 6.32 0.00 0.00 5.19
200 201 3.336566 GGTTTCACAACCGGGTCG 58.663 61.111 6.32 0.00 43.40 4.79
214 215 0.598065 GAGGAAAAGTGCGCATGGTT 59.402 50.000 15.91 7.85 0.00 3.67
215 216 1.577328 CGAGGAAAAGTGCGCATGGT 61.577 55.000 15.91 0.00 0.00 3.55
221 222 3.678072 TCATTAACTCGAGGAAAAGTGCG 59.322 43.478 18.41 0.00 0.00 5.34
225 226 7.639945 ACTTGTTTCATTAACTCGAGGAAAAG 58.360 34.615 18.41 12.64 37.64 2.27
229 230 4.921515 CGACTTGTTTCATTAACTCGAGGA 59.078 41.667 18.41 0.58 35.27 3.71
234 235 5.817616 TCGACGACTTGTTTCATTAACTC 57.182 39.130 0.00 0.00 37.64 3.01
240 241 5.068234 TCCTATTCGACGACTTGTTTCAT 57.932 39.130 0.00 0.00 0.00 2.57
241 242 4.508461 TCCTATTCGACGACTTGTTTCA 57.492 40.909 0.00 0.00 0.00 2.69
250 252 2.809696 TGCGATACATCCTATTCGACGA 59.190 45.455 0.00 0.00 0.00 4.20
251 253 3.197434 TGCGATACATCCTATTCGACG 57.803 47.619 0.00 0.00 0.00 5.12
255 257 8.935844 TGATGTTTATTGCGATACATCCTATTC 58.064 33.333 20.23 4.13 43.82 1.75
325 327 4.530094 TCGTTGCGGATATGAACAAATC 57.470 40.909 0.00 0.00 0.00 2.17
330 332 5.006358 ACTTGTAATCGTTGCGGATATGAAC 59.994 40.000 0.00 0.00 0.00 3.18
333 335 5.460748 TGTACTTGTAATCGTTGCGGATATG 59.539 40.000 0.00 0.00 0.00 1.78
345 347 7.148086 TGGATCCAAAGCATTGTACTTGTAATC 60.148 37.037 13.46 0.00 34.60 1.75
355 357 6.880529 CCTAAATTTTGGATCCAAAGCATTGT 59.119 34.615 32.77 22.40 45.15 2.71
422 424 0.673956 GAGGACGACTCCAAAAGGCC 60.674 60.000 0.00 0.00 40.49 5.19
423 425 2.842320 GAGGACGACTCCAAAAGGC 58.158 57.895 0.00 0.00 40.49 4.35
444 446 8.217111 TGCAGGGATTGATAGTTTGATATTACA 58.783 33.333 0.00 0.00 0.00 2.41
450 452 5.126061 GTGTTGCAGGGATTGATAGTTTGAT 59.874 40.000 0.00 0.00 0.00 2.57
456 458 5.389859 TTTTGTGTTGCAGGGATTGATAG 57.610 39.130 0.00 0.00 0.00 2.08
475 478 7.041848 GCAGTTTTGAAGTCTTGGCAATATTTT 60.042 33.333 0.00 0.00 0.00 1.82
483 486 1.408702 TGGCAGTTTTGAAGTCTTGGC 59.591 47.619 0.00 0.00 0.00 4.52
500 503 3.372730 TTGCTGCGGTCCATTGGC 61.373 61.111 0.00 0.00 0.00 4.52
511 514 0.099436 GGGAACATCATCGTTGCTGC 59.901 55.000 0.00 0.00 37.38 5.25
512 515 0.374758 CGGGAACATCATCGTTGCTG 59.625 55.000 0.00 0.00 37.38 4.41
515 518 2.850321 CAAACGGGAACATCATCGTTG 58.150 47.619 10.01 0.00 43.65 4.10
527 530 3.402095 TTCGTGTGGGCAAACGGGA 62.402 57.895 0.00 0.00 40.18 5.14
528 531 2.902846 TTCGTGTGGGCAAACGGG 60.903 61.111 0.00 0.00 40.18 5.28
539 543 6.764560 ACCTTTATCAGTTGTAAAGTTCGTGT 59.235 34.615 0.00 0.00 37.42 4.49
593 597 0.178891 ACTCCAGGGGCTCTCAAAGA 60.179 55.000 0.00 0.00 0.00 2.52
604 608 3.787001 GGAAGGGCGACTCCAGGG 61.787 72.222 0.00 0.00 36.21 4.45
606 610 0.250727 TTTTGGAAGGGCGACTCCAG 60.251 55.000 0.00 0.00 36.21 3.86
608 612 0.881796 CTTTTTGGAAGGGCGACTCC 59.118 55.000 0.00 0.00 0.00 3.85
609 613 1.892209 TCTTTTTGGAAGGGCGACTC 58.108 50.000 0.00 0.00 0.00 3.36
610 614 2.162681 CATCTTTTTGGAAGGGCGACT 58.837 47.619 0.00 0.00 0.00 4.18
611 615 1.202348 CCATCTTTTTGGAAGGGCGAC 59.798 52.381 0.00 0.00 39.25 5.19
612 616 1.074727 TCCATCTTTTTGGAAGGGCGA 59.925 47.619 0.00 0.00 42.82 5.54
613 617 1.544724 TCCATCTTTTTGGAAGGGCG 58.455 50.000 0.00 0.00 42.82 6.13
657 661 3.135348 TCCTAGAGGATTGTTCCATGCTG 59.865 47.826 0.00 0.00 45.30 4.41
668 672 1.127343 GCCTGCACTCCTAGAGGATT 58.873 55.000 0.00 0.00 44.46 3.01
719 723 6.867662 TTCTCTGTGGAGTTGAAATCTTTC 57.132 37.500 0.00 0.00 40.29 2.62
725 729 5.299279 GGTTTGATTCTCTGTGGAGTTGAAA 59.701 40.000 0.00 0.00 40.29 2.69
828 834 5.515626 CGGTCTAGTAAGTTTATGTCAGTGC 59.484 44.000 0.00 0.00 0.00 4.40
833 839 6.183360 GGTTTGCGGTCTAGTAAGTTTATGTC 60.183 42.308 0.00 0.00 0.00 3.06
877 913 0.180171 TGTGGCCGGGTAAGATGATG 59.820 55.000 2.18 0.00 0.00 3.07
878 914 0.180406 GTGTGGCCGGGTAAGATGAT 59.820 55.000 2.18 0.00 0.00 2.45
1034 1071 1.203428 TGGAGATTGGGGAGGAAGACA 60.203 52.381 0.00 0.00 0.00 3.41
1035 1072 1.584724 TGGAGATTGGGGAGGAAGAC 58.415 55.000 0.00 0.00 0.00 3.01
1036 1073 2.308866 GTTTGGAGATTGGGGAGGAAGA 59.691 50.000 0.00 0.00 0.00 2.87
1037 1074 2.310052 AGTTTGGAGATTGGGGAGGAAG 59.690 50.000 0.00 0.00 0.00 3.46
1543 1587 3.589654 CTTCTTCCCGCTGTCCGCA 62.590 63.158 0.00 0.00 39.08 5.69
1550 1594 2.352032 CGTCCTCCTTCTTCCCGCT 61.352 63.158 0.00 0.00 0.00 5.52
1570 1614 1.203492 ACAATCTCCACCTTCCTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
1753 1798 7.554211 TGGCAACATAATCAAATGCAAGAATA 58.446 30.769 0.00 0.00 46.17 1.75
1874 1920 7.116736 TGCACCCTGAGACGATAATATATCTA 58.883 38.462 0.00 0.00 0.00 1.98
1881 1927 4.152647 TCTATGCACCCTGAGACGATAAT 58.847 43.478 0.00 0.00 0.00 1.28
1899 1945 7.904558 TCCACATAGAATGACAGAACTCTAT 57.095 36.000 0.00 0.00 32.52 1.98
1900 1946 7.343057 ACATCCACATAGAATGACAGAACTCTA 59.657 37.037 0.00 0.00 0.00 2.43
1997 2043 4.508551 TCCAGGATTGCATGTATTCAGT 57.491 40.909 7.78 0.00 0.00 3.41
1998 2044 5.840243 TTTCCAGGATTGCATGTATTCAG 57.160 39.130 7.78 0.82 0.00 3.02
2033 2079 6.426937 ACTTCGTTTTATTGTAGACACAGCAT 59.573 34.615 0.00 0.00 35.67 3.79
2036 2082 7.381408 TCTCACTTCGTTTTATTGTAGACACAG 59.619 37.037 0.00 0.00 35.67 3.66
2040 2086 6.586844 AGCTCTCACTTCGTTTTATTGTAGAC 59.413 38.462 0.00 0.00 0.00 2.59
2054 2100 5.948992 AATAACCAACAAGCTCTCACTTC 57.051 39.130 0.00 0.00 0.00 3.01
2060 2106 5.959618 GGTTGTAATAACCAACAAGCTCT 57.040 39.130 9.45 0.00 45.81 4.09
2083 2129 1.970640 GTCCCACAAAAAGGCCTTGAT 59.029 47.619 21.33 8.68 0.00 2.57
2090 2136 0.951558 CGACCTGTCCCACAAAAAGG 59.048 55.000 0.00 0.00 0.00 3.11
2092 2138 0.106918 AGCGACCTGTCCCACAAAAA 60.107 50.000 0.00 0.00 0.00 1.94
2097 2143 3.591254 GACCAGCGACCTGTCCCAC 62.591 68.421 0.00 0.00 37.38 4.61
2102 2150 1.003355 CATTGGACCAGCGACCTGT 60.003 57.895 0.00 0.00 37.38 4.00
2123 2171 1.974875 GGTTGCGGGGTAGGTTTGG 60.975 63.158 0.00 0.00 0.00 3.28
2131 2179 0.993470 TATAAAGGTGGTTGCGGGGT 59.007 50.000 0.00 0.00 0.00 4.95
2134 2182 4.345859 TCCTATATAAAGGTGGTTGCGG 57.654 45.455 0.00 0.00 37.91 5.69
2148 2196 9.095700 GTCACCTCTTCCTCTAAATTCCTATAT 57.904 37.037 0.00 0.00 0.00 0.86
2149 2197 8.290277 AGTCACCTCTTCCTCTAAATTCCTATA 58.710 37.037 0.00 0.00 0.00 1.31
2150 2198 7.136203 AGTCACCTCTTCCTCTAAATTCCTAT 58.864 38.462 0.00 0.00 0.00 2.57
2176 2224 4.553330 ATTTCTAAAGAAGACCGCTCCA 57.447 40.909 0.00 0.00 35.21 3.86
2182 2230 8.397575 AGAACCTGAAATTTCTAAAGAAGACC 57.602 34.615 18.64 1.09 35.21 3.85
2251 2300 1.620822 AGAACCAACCAACAGGATGC 58.379 50.000 0.00 0.00 42.53 3.91
2271 2320 9.113838 CCAGTTTCTACAGCATTATTGAATAGT 57.886 33.333 0.00 0.00 0.00 2.12
2272 2321 9.113838 ACCAGTTTCTACAGCATTATTGAATAG 57.886 33.333 0.00 0.00 0.00 1.73
2273 2322 8.892723 CACCAGTTTCTACAGCATTATTGAATA 58.107 33.333 0.00 0.00 0.00 1.75
2330 2379 2.586425 ACAGTAATGTGCCTGCAAGTT 58.414 42.857 0.00 0.00 31.76 2.66
2492 2541 5.448654 CCAGAATCCACATTCTTATTCCCA 58.551 41.667 0.00 0.00 45.68 4.37
2693 2742 7.720957 TCAGTTATGCAAGGCAATAACATATCT 59.279 33.333 17.44 0.00 43.62 1.98
2748 2797 6.595682 TCTTGTCACTTCTCTCTTCCAAAAT 58.404 36.000 0.00 0.00 0.00 1.82
2764 2813 8.917415 AGTTGATTTCTTTTTCTTCTTGTCAC 57.083 30.769 0.00 0.00 0.00 3.67
2823 2872 3.018423 ACTTCCAGCAGGTTTTCTTGT 57.982 42.857 0.00 0.00 35.89 3.16
3386 3435 5.283457 AGCTTCAGGTCAGTATATCAACC 57.717 43.478 0.00 0.00 0.00 3.77
3474 3523 2.787473 TCTTCGCCATGGACATTCTT 57.213 45.000 18.40 0.00 0.00 2.52
3489 3538 8.697292 AGATACTACCTTTTCCACTGTATCTTC 58.303 37.037 0.00 0.00 40.91 2.87
3584 3633 1.061131 GTGTCGTGCCAAGAATCATCG 59.939 52.381 0.00 0.00 0.00 3.84
3946 3995 3.460340 TCTCCAACTTTGAAACTGGGGTA 59.540 43.478 2.13 0.00 30.89 3.69
3948 3997 2.623416 GTCTCCAACTTTGAAACTGGGG 59.377 50.000 2.44 0.00 0.00 4.96
4045 4094 4.634883 GCAAGTAGGTTTAGGACTTTAGGC 59.365 45.833 0.00 0.00 31.04 3.93
4061 4110 8.408601 AGCCTAAAAACATTGATATGCAAGTAG 58.591 33.333 0.00 0.00 40.42 2.57
4135 4187 8.375506 ACCAGAGTAATTTCTCAAATGTACTGA 58.624 33.333 13.77 0.00 36.97 3.41
4199 4251 4.018960 AGAGAAATGTGCACATTCTACCCT 60.019 41.667 37.80 27.96 45.06 4.34
4233 4285 5.932619 ACACATGTGCCACTAGTCTTATA 57.067 39.130 25.68 0.00 0.00 0.98
4250 4302 3.939740 AGCCAATGAGGACATACACAT 57.060 42.857 0.00 0.00 41.22 3.21
4348 4400 8.755028 TCAAGCTAACCTAAACCTTTTCTTTTT 58.245 29.630 0.00 0.00 0.00 1.94
4649 4781 1.360551 CATACGAGAGAGGCACGGG 59.639 63.158 0.00 0.00 34.76 5.28
4654 4786 4.570772 TGTATTTTTGCATACGAGAGAGGC 59.429 41.667 0.00 0.00 32.95 4.70
4662 4794 7.132213 CAGGTATCCTTGTATTTTTGCATACG 58.868 38.462 0.00 0.00 32.95 3.06
4669 4801 7.833285 AACACACAGGTATCCTTGTATTTTT 57.167 32.000 0.00 0.00 0.00 1.94
4670 4802 7.724061 AGAAACACACAGGTATCCTTGTATTTT 59.276 33.333 7.91 8.02 29.06 1.82
4683 4815 5.659440 AAACAATCAAGAAACACACAGGT 57.341 34.783 0.00 0.00 0.00 4.00
4687 4819 7.412891 CCAAGGAAAAACAATCAAGAAACACAC 60.413 37.037 0.00 0.00 0.00 3.82
4810 4949 2.105134 TCCACGGGTTAACTTGACATGT 59.895 45.455 0.00 0.00 0.00 3.21
4985 5133 3.004839 GTGATGTTCTAGATAGCGAGCCA 59.995 47.826 0.00 0.00 0.00 4.75
4987 5135 4.230314 TGTGATGTTCTAGATAGCGAGC 57.770 45.455 0.00 0.00 0.00 5.03
4988 5136 7.144661 AGATTTGTGATGTTCTAGATAGCGAG 58.855 38.462 0.00 0.00 0.00 5.03
4990 5138 7.562412 CAAGATTTGTGATGTTCTAGATAGCG 58.438 38.462 0.00 0.00 0.00 4.26
5033 5184 3.722082 GCAACGCGAGAGAAACATACAAG 60.722 47.826 15.93 0.00 0.00 3.16
5074 5225 3.273080 GAAACAAGCCTGCCCTGCG 62.273 63.158 0.00 0.00 0.00 5.18
5078 5229 0.244721 GACATGAAACAAGCCTGCCC 59.755 55.000 0.00 0.00 0.00 5.36
5098 5249 1.523758 AAGGTGAAATCCACGAGTGC 58.476 50.000 0.00 0.00 46.62 4.40
5100 5251 3.335579 GCTAAAGGTGAAATCCACGAGT 58.664 45.455 0.00 0.00 46.62 4.18
5161 5312 1.212616 GATGTGACGCTGCTATCCAC 58.787 55.000 0.00 1.23 0.00 4.02
5165 5316 1.676529 ACTACGATGTGACGCTGCTAT 59.323 47.619 0.00 0.00 36.70 2.97
5166 5317 1.092348 ACTACGATGTGACGCTGCTA 58.908 50.000 0.00 0.00 36.70 3.49
5173 5324 6.802348 GGTGATATGATACACTACGATGTGAC 59.198 42.308 16.53 9.41 40.12 3.67
5250 5409 2.958355 ACCCACAAGAGTCAAATGGTTG 59.042 45.455 0.00 0.00 35.95 3.77
5321 5487 3.655211 CTGGCCTGCAGGAACCCT 61.655 66.667 37.21 0.00 37.39 4.34
5322 5488 3.971702 ACTGGCCTGCAGGAACCC 61.972 66.667 37.21 26.80 37.39 4.11
5323 5489 2.674380 CACTGGCCTGCAGGAACC 60.674 66.667 37.21 27.54 37.39 3.62
5324 5490 1.968540 GTCACTGGCCTGCAGGAAC 60.969 63.158 37.21 26.55 37.39 3.62
5325 5491 2.149383 AGTCACTGGCCTGCAGGAA 61.149 57.895 37.21 21.71 37.39 3.36
5326 5492 2.527624 AGTCACTGGCCTGCAGGA 60.528 61.111 37.21 15.88 37.39 3.86
5327 5493 2.359602 CAGTCACTGGCCTGCAGG 60.360 66.667 29.34 29.34 38.53 4.85
5328 5494 2.359602 CCAGTCACTGGCCTGCAG 60.360 66.667 12.03 6.78 45.13 4.41
5399 5569 1.564348 GGAAGGGAAGGTGATAAGGCA 59.436 52.381 0.00 0.00 0.00 4.75
5400 5570 1.475213 CGGAAGGGAAGGTGATAAGGC 60.475 57.143 0.00 0.00 0.00 4.35
5402 5572 2.420129 CCACGGAAGGGAAGGTGATAAG 60.420 54.545 0.00 0.00 35.60 1.73
5403 5573 1.557832 CCACGGAAGGGAAGGTGATAA 59.442 52.381 0.00 0.00 35.60 1.75
5523 5694 1.739466 CGCCTAAAAATCAGCTGCAGA 59.261 47.619 20.43 0.00 0.00 4.26
5548 5719 3.914426 TCTGCCTTCCCTAAATCTGAC 57.086 47.619 0.00 0.00 0.00 3.51
5606 5797 0.250513 CTCACCTAACCCACAGCTCC 59.749 60.000 0.00 0.00 0.00 4.70
5695 5894 6.751888 GGCAAATTTAGCTAAACATACCACTG 59.248 38.462 20.85 8.94 0.00 3.66
5707 5906 1.742831 CGGCAGTGGCAAATTTAGCTA 59.257 47.619 17.80 0.00 43.71 3.32
5718 5917 1.362406 GAAGACTTAGCGGCAGTGGC 61.362 60.000 6.62 6.62 40.13 5.01
5724 5923 0.448197 GCCAAAGAAGACTTAGCGGC 59.552 55.000 0.00 0.00 38.19 6.53
5739 5938 1.523154 GCCGTGGTGAATGAAGCCAA 61.523 55.000 0.00 0.00 33.66 4.52
5768 5971 3.181488 CGCCATCAGCTAGAGATCATAGG 60.181 52.174 0.00 0.00 40.39 2.57
5794 5997 6.591834 ACTCTTCATGAAAAACTAGGACGATG 59.408 38.462 9.88 0.00 0.00 3.84
5795 5998 6.702329 ACTCTTCATGAAAAACTAGGACGAT 58.298 36.000 9.88 0.00 0.00 3.73
5796 5999 6.097915 ACTCTTCATGAAAAACTAGGACGA 57.902 37.500 9.88 0.00 0.00 4.20
5797 6000 6.787085 AACTCTTCATGAAAAACTAGGACG 57.213 37.500 9.88 0.00 0.00 4.79
5854 6126 1.547372 GAGTGTTACTTACTGGGGCGA 59.453 52.381 0.00 0.00 0.00 5.54
5857 6129 3.323979 AGTGTGAGTGTTACTTACTGGGG 59.676 47.826 5.64 0.00 35.92 4.96
5861 6133 6.546403 TCAGAGAAGTGTGAGTGTTACTTACT 59.454 38.462 5.64 0.00 35.92 2.24
5862 6134 6.736123 TCAGAGAAGTGTGAGTGTTACTTAC 58.264 40.000 0.00 0.00 35.53 2.34
5866 6138 5.343593 CGATTCAGAGAAGTGTGAGTGTTAC 59.656 44.000 0.00 0.00 0.00 2.50
5963 6238 0.458889 TGGTACTACATCCGTTGCGC 60.459 55.000 0.00 0.00 0.00 6.09
5977 6252 6.334989 TGCTGTTGTACATAGTACATGGTAC 58.665 40.000 10.44 11.70 37.28 3.34


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

AutoCloner maintained by Alex Coulton.