Multiple sequence alignment - TraesCS6D01G121200

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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 TraesCS6D01G121200 chr6D 100.000 6163 0 0 1 6163 86148977 86142815 0.000000e+00 11382.0
1 TraesCS6D01G121200 chr6B 94.313 4660 168 33 905 5503 163235283 163230660 0.000000e+00 7047.0
2 TraesCS6D01G121200 chr6B 95.217 669 11 7 5496 6163 163230634 163229986 0.000000e+00 1038.0
3 TraesCS6D01G121200 chr6B 85.714 224 5 8 647 870 163235820 163235624 1.740000e-50 211.0
4 TraesCS6D01G121200 chr6B 86.719 128 17 0 509 636 163236000 163235873 6.440000e-30 143.0
5 TraesCS6D01G121200 chr6A 93.852 2391 99 17 692 3068 103764339 103761983 0.000000e+00 3557.0
6 TraesCS6D01G121200 chr6A 95.165 1634 34 18 3067 4695 103761901 103760308 0.000000e+00 2538.0
7 TraesCS6D01G121200 chr6A 92.149 1452 46 16 4767 6163 103760281 103758843 0.000000e+00 1988.0
8 TraesCS6D01G121200 chr6A 89.151 636 51 9 3 636 103770587 103769968 0.000000e+00 776.0
9 TraesCS6D01G121200 chr5A 90.947 718 56 6 4764 5473 323084048 323084764 0.000000e+00 957.0
10 TraesCS6D01G121200 chr5A 94.144 222 13 0 4474 4695 323083803 323084024 7.650000e-89 339.0
11 TraesCS6D01G121200 chr4A 90.960 708 58 3 4764 5465 113486045 113486752 0.000000e+00 948.0
12 TraesCS6D01G121200 chr4A 94.595 222 12 0 4474 4695 113485800 113486021 1.640000e-90 344.0
13 TraesCS6D01G121200 chrUn 86.253 451 59 3 1 451 34777244 34777691 2.580000e-133 486.0
14 TraesCS6D01G121200 chr7B 91.642 335 28 0 51 385 676995268 676994934 1.210000e-126 464.0
15 TraesCS6D01G121200 chr7B 82.812 448 74 3 5 451 680780311 680779866 1.240000e-106 398.0
16 TraesCS6D01G121200 chr7B 96.774 31 1 0 3032 3062 75793893 75793863 1.100000e-02 52.8
17 TraesCS6D01G121200 chr1B 87.712 236 27 2 1096 1331 113518791 113519024 2.190000e-69 274.0
18 TraesCS6D01G121200 chr1A 83.404 235 37 2 5 238 567540777 567540544 3.740000e-52 217.0
19 TraesCS6D01G121200 chr4D 87.719 171 9 4 1037 1201 24254374 24254210 8.160000e-44 189.0
20 TraesCS6D01G121200 chr1D 76.119 335 61 14 129 451 379465885 379465558 2.300000e-34 158.0
21 TraesCS6D01G121200 chr3A 90.385 52 5 0 25 76 691301713 691301764 1.110000e-07 69.4


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 TraesCS6D01G121200 chr6D 86142815 86148977 6162 True 11382.000000 11382 100.00000 1 6163 1 chr6D.!!$R1 6162
1 TraesCS6D01G121200 chr6B 163229986 163236000 6014 True 2109.750000 7047 90.49075 509 6163 4 chr6B.!!$R1 5654
2 TraesCS6D01G121200 chr6A 103758843 103764339 5496 True 2694.333333 3557 93.72200 692 6163 3 chr6A.!!$R2 5471
3 TraesCS6D01G121200 chr6A 103769968 103770587 619 True 776.000000 776 89.15100 3 636 1 chr6A.!!$R1 633
4 TraesCS6D01G121200 chr5A 323083803 323084764 961 False 648.000000 957 92.54550 4474 5473 2 chr5A.!!$F1 999
5 TraesCS6D01G121200 chr4A 113485800 113486752 952 False 646.000000 948 92.77750 4474 5465 2 chr4A.!!$F1 991

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
212 213 0.036164 CCGTGACCCCTGATTTGTCA 59.964 55.000 0.00 0.00 36.71 3.58 F
293 294 0.250901 GGTGCTTTTCCCAGCTGAGA 60.251 55.000 17.39 3.87 40.79 3.27 F
1249 1599 0.108615 CGACACTTCGCTGATTCCCT 60.109 55.000 0.00 0.00 38.71 4.20 F
1548 1898 0.248743 CTCCGTTTAGGCGCGTCATA 60.249 55.000 15.58 1.60 40.77 2.15 F
1549 1899 0.386476 TCCGTTTAGGCGCGTCATAT 59.614 50.000 15.58 0.00 40.77 1.78 F
1550 1900 0.782384 CCGTTTAGGCGCGTCATATC 59.218 55.000 15.58 0.00 0.00 1.63 F
1793 2150 0.961019 GCTGGATTGCTTGTGGTTGA 59.039 50.000 0.00 0.00 0.00 3.18 F
1826 2183 1.691434 GAGTAGCTTGGATCCTCCTGG 59.309 57.143 14.23 0.00 37.46 4.45 F
3558 4018 1.669779 GAATGCTCTCAGATGCCACAC 59.330 52.381 0.00 0.00 0.00 3.82 F
4701 5165 0.833287 ATGGTCCCAAGATCCACTCG 59.167 55.000 0.00 0.00 33.91 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1584 0.036010 CACCAGGGAATCAGCGAAGT 60.036 55.000 0.0 0.0 0.00 3.01 R
1551 1901 0.038251 CAGCACAGACTAGCGAACCA 60.038 55.000 0.0 0.0 35.48 3.67 R
2783 3154 0.904865 CAGTAGTGGGCTCTGGTCCA 60.905 60.000 0.0 0.0 46.10 4.02 R
3162 3620 3.119884 ACGAACATAACACCGTCGTGATA 60.120 43.478 0.0 0.0 43.14 2.15 R
3261 3719 3.756434 TGTGCATTAAAACTCTAGCCACC 59.244 43.478 0.0 0.0 0.00 4.61 R
3413 3872 6.159575 TCCTGACTGATGTGGGGAAAAATATA 59.840 38.462 0.0 0.0 0.00 0.86 R
3558 4018 9.778741 TTAGTATCTCAATTAATGCTTACAGGG 57.221 33.333 0.0 0.0 0.00 4.45 R
3827 4287 4.457949 ACACGTATTTTGTCTTCATTCCCC 59.542 41.667 0.0 0.0 0.00 4.81 R
4706 5170 0.036010 CTGTGCGGTGGAAGAAGGAT 60.036 55.000 0.0 0.0 0.00 3.24 R
5920 6466 0.453793 TTTGTGTGTTTGGTCGGCAG 59.546 50.000 0.0 0.0 0.00 4.85 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
42 43 1.580845 CCTTGCAGCTCTCCCAAACG 61.581 60.000 0.00 0.00 0.00 3.60
73 74 2.369629 CCGACGTGCACGGTTACAG 61.370 63.158 39.21 22.90 44.57 2.74
77 78 1.219522 ACGTGCACGGTTACAGCTTC 61.220 55.000 39.21 0.00 44.95 3.86
81 82 1.941476 GCACGGTTACAGCTTCGTCG 61.941 60.000 0.00 0.00 33.31 5.12
94 95 4.789031 CGTCGTCGAAGAGCGCGA 62.789 66.667 12.10 0.00 42.78 5.87
109 110 3.108289 CGACTGAGTGCTGCACGG 61.108 66.667 25.39 20.56 39.64 4.94
111 112 1.595382 GACTGAGTGCTGCACGGTT 60.595 57.895 25.39 9.93 39.64 4.44
171 172 3.409026 CCAACTTCTGGTTACAGCTCT 57.591 47.619 0.00 0.00 44.54 4.09
177 178 1.630369 TCTGGTTACAGCTCTGCCAAT 59.370 47.619 0.00 0.00 44.54 3.16
180 181 0.375106 GTTACAGCTCTGCCAATCGC 59.625 55.000 0.00 0.00 38.31 4.58
190 191 4.189188 CCAATCGCTGGCTGCAGC 62.189 66.667 30.88 30.88 44.25 5.25
191 192 3.132139 CAATCGCTGGCTGCAGCT 61.132 61.111 35.82 14.52 45.43 4.24
192 193 2.823147 AATCGCTGGCTGCAGCTC 60.823 61.111 35.82 25.84 45.43 4.09
193 194 4.853050 ATCGCTGGCTGCAGCTCC 62.853 66.667 35.82 21.98 45.43 4.70
211 212 0.676782 CCCGTGACCCCTGATTTGTC 60.677 60.000 0.00 0.00 0.00 3.18
212 213 0.036164 CCGTGACCCCTGATTTGTCA 59.964 55.000 0.00 0.00 36.71 3.58
232 233 2.743928 GAGTGTGGCGCCTCAAGG 60.744 66.667 31.06 0.00 38.53 3.61
261 262 1.028330 ATCACGGCAGCTTGTCCATG 61.028 55.000 0.00 0.00 0.00 3.66
267 268 1.813859 CAGCTTGTCCATGGCCATG 59.186 57.895 34.82 34.82 38.51 3.66
293 294 0.250901 GGTGCTTTTCCCAGCTGAGA 60.251 55.000 17.39 3.87 40.79 3.27
320 321 1.362406 CGGGAGAAAGAAGAAGGCGC 61.362 60.000 0.00 0.00 0.00 6.53
327 328 2.046892 GAAGAAGGCGCTGGAGCA 60.047 61.111 7.64 0.00 42.21 4.26
353 354 7.127955 AGAGAGATAAAAAGGGCAAGAGGATAA 59.872 37.037 0.00 0.00 0.00 1.75
369 371 2.618709 GGATAAGAAGCAAATGGGACGG 59.381 50.000 0.00 0.00 0.00 4.79
382 384 2.343758 GACGGCTCAGCTGGACAA 59.656 61.111 15.13 0.00 39.57 3.18
385 387 1.302033 CGGCTCAGCTGGACAAGTT 60.302 57.895 15.13 0.00 0.00 2.66
400 402 1.069296 CAAGTTGCATGGTACGTGTGG 60.069 52.381 0.00 0.00 0.00 4.17
405 407 4.090588 ATGGTACGTGTGGCCCCG 62.091 66.667 0.00 2.04 0.00 5.73
424 426 4.838486 AGTGCTCGCGTCGCTAGC 62.838 66.667 30.49 30.49 45.59 3.42
460 462 1.559682 AGTTTGGGCCGACATGTAGAT 59.440 47.619 7.62 0.00 0.00 1.98
466 468 1.286501 GCCGACATGTAGATGCGAAA 58.713 50.000 7.62 0.00 33.56 3.46
467 469 1.867233 GCCGACATGTAGATGCGAAAT 59.133 47.619 7.62 0.00 33.56 2.17
468 470 2.348872 GCCGACATGTAGATGCGAAATG 60.349 50.000 7.62 3.60 33.56 2.32
473 475 5.794945 CGACATGTAGATGCGAAATGTTTTT 59.205 36.000 0.00 0.00 33.56 1.94
773 817 1.757682 TATGGGCCGAACACCATTTC 58.242 50.000 0.00 0.00 44.85 2.17
774 818 0.251564 ATGGGCCGAACACCATTTCA 60.252 50.000 0.00 0.00 44.85 2.69
776 820 0.894835 GGGCCGAACACCATTTCATT 59.105 50.000 0.00 0.00 0.00 2.57
777 821 1.135112 GGGCCGAACACCATTTCATTC 60.135 52.381 0.00 0.00 0.00 2.67
778 822 1.467374 GGCCGAACACCATTTCATTCG 60.467 52.381 0.00 0.00 42.71 3.34
781 825 3.610585 GCCGAACACCATTTCATTCGAAA 60.611 43.478 0.00 0.00 45.18 3.46
782 826 4.158384 CCGAACACCATTTCATTCGAAAG 58.842 43.478 0.00 0.00 45.18 2.62
783 827 4.083537 CCGAACACCATTTCATTCGAAAGA 60.084 41.667 0.00 0.00 45.18 2.52
927 1277 1.181786 GGTCCCCGATTTCAAATGCA 58.818 50.000 0.00 0.00 0.00 3.96
933 1283 1.269206 CCGATTTCAAATGCATCCCCG 60.269 52.381 0.00 0.00 0.00 5.73
1238 1588 2.124695 GGGGATGGCCGACACTTC 60.125 66.667 0.00 0.00 33.83 3.01
1247 1597 1.696832 GCCGACACTTCGCTGATTCC 61.697 60.000 0.00 0.00 44.43 3.01
1249 1599 0.108615 CGACACTTCGCTGATTCCCT 60.109 55.000 0.00 0.00 38.71 4.20
1369 1719 1.202687 CCTCAAGCAGGTGAGTGAACA 60.203 52.381 10.17 0.00 43.02 3.18
1543 1893 2.582498 CCTCTCCGTTTAGGCGCG 60.582 66.667 0.00 0.00 40.77 6.86
1544 1894 2.181021 CTCTCCGTTTAGGCGCGT 59.819 61.111 8.43 8.08 40.77 6.01
1545 1895 1.872679 CTCTCCGTTTAGGCGCGTC 60.873 63.158 5.57 0.21 40.77 5.19
1546 1896 2.126228 CTCCGTTTAGGCGCGTCA 60.126 61.111 15.58 0.00 40.77 4.35
1547 1897 1.518572 CTCCGTTTAGGCGCGTCAT 60.519 57.895 15.58 2.75 40.77 3.06
1548 1898 0.248743 CTCCGTTTAGGCGCGTCATA 60.249 55.000 15.58 1.60 40.77 2.15
1549 1899 0.386476 TCCGTTTAGGCGCGTCATAT 59.614 50.000 15.58 0.00 40.77 1.78
1550 1900 0.782384 CCGTTTAGGCGCGTCATATC 59.218 55.000 15.58 0.00 0.00 1.63
1551 1901 1.602165 CCGTTTAGGCGCGTCATATCT 60.602 52.381 15.58 0.00 0.00 1.98
1552 1902 1.452025 CGTTTAGGCGCGTCATATCTG 59.548 52.381 15.58 0.00 0.00 2.90
1581 1931 1.819288 GTCTGTGCTGCTGGTAGTAGA 59.181 52.381 0.00 0.00 28.61 2.59
1596 1953 3.601443 AGTAGAAGATGTGACTGTGCC 57.399 47.619 0.00 0.00 0.00 5.01
1599 1956 1.071605 GAAGATGTGACTGTGCCGTC 58.928 55.000 0.00 0.00 34.52 4.79
1612 1969 1.134694 GCCGTCTTGATGGTTTCGC 59.865 57.895 10.22 0.00 0.00 4.70
1695 2052 1.226262 AAGCGTGAAGGTTGGTGGT 59.774 52.632 0.00 0.00 39.39 4.16
1713 2070 4.323945 GGTGGTACCTTGTATTGATGTGGA 60.324 45.833 14.36 0.00 34.73 4.02
1761 2118 8.846943 TTTTATTTCTGCTGAGTTCATCTGTA 57.153 30.769 0.00 0.00 0.00 2.74
1793 2150 0.961019 GCTGGATTGCTTGTGGTTGA 59.039 50.000 0.00 0.00 0.00 3.18
1815 2172 5.353400 TGATTTTGCAGATCTGAGTAGCTTG 59.647 40.000 27.04 0.00 0.00 4.01
1826 2183 1.691434 GAGTAGCTTGGATCCTCCTGG 59.309 57.143 14.23 0.00 37.46 4.45
1904 2261 7.172868 TCCTGTGTCATTCAATTGCATTTAT 57.827 32.000 0.00 0.00 0.00 1.40
2129 2486 3.152341 CAGCTGGTTCAGTTCCAAATCT 58.848 45.455 5.57 0.00 34.35 2.40
2189 2546 7.306749 CCATTTTCAGTAACTTTGTCATTGCAC 60.307 37.037 0.00 0.00 0.00 4.57
2247 2618 3.627577 CCACTGTAACAAGCTGTCTTTGT 59.372 43.478 0.00 0.00 0.00 2.83
2274 2645 3.947868 AGAGCATGTATTCACAGCAGTT 58.052 40.909 0.00 0.00 38.30 3.16
2512 2883 4.883083 TCCTGAGTGTGTTATTGAGTCAC 58.117 43.478 0.00 0.00 0.00 3.67
2520 2891 6.641314 AGTGTGTTATTGAGTCACTACTTTCG 59.359 38.462 0.00 0.00 37.55 3.46
2649 3020 5.343307 AGCACCTGTTGAAATCAAACTTT 57.657 34.783 0.00 0.00 37.63 2.66
2716 3087 6.909550 TTTTAGCCACACCATCTATTTTGT 57.090 33.333 0.00 0.00 0.00 2.83
2763 3134 5.034852 ACTGCAACTTTAATTGGCCTTTT 57.965 34.783 3.32 0.00 0.00 2.27
2783 3154 6.406624 CCTTTTGAAATGCAGGAGCTCATATT 60.407 38.462 17.19 3.10 42.74 1.28
2813 3184 3.838317 AGCCCACTACTGACAGATTTGTA 59.162 43.478 10.08 0.00 37.76 2.41
2838 3209 3.752747 TGTGATGGTAAGTGTTGCATGAG 59.247 43.478 0.00 0.00 0.00 2.90
3284 3742 4.399303 GGTGGCTAGAGTTTTAATGCACAT 59.601 41.667 0.00 0.00 0.00 3.21
3373 3832 5.417754 TCAATTTGCATTCCCTATTTGCA 57.582 34.783 0.00 0.00 44.12 4.08
3413 3872 7.967908 ACTCGTATTTATCCCATTGATCTCTT 58.032 34.615 0.00 0.00 34.76 2.85
3558 4018 1.669779 GAATGCTCTCAGATGCCACAC 59.330 52.381 0.00 0.00 0.00 3.82
3827 4287 3.432252 AGCGTGTCATTTCTTCTTTACGG 59.568 43.478 0.00 0.00 0.00 4.02
3857 4317 3.211045 AGACAAAATACGTGTGGTGCTT 58.789 40.909 0.00 0.00 0.00 3.91
4135 4596 7.093858 ACGCTTTAGTAATCTTACTTCTGGAGT 60.094 37.037 7.84 0.00 40.96 3.85
4161 4622 7.999545 TCTGAAGGTTGTACAGCTCTAGTATAT 59.000 37.037 9.71 0.00 30.69 0.86
4446 4910 5.575606 CGCCGGGTAAGTAATAATGTATCAG 59.424 44.000 2.18 0.00 0.00 2.90
4448 4912 7.156673 GCCGGGTAAGTAATAATGTATCAGAA 58.843 38.462 2.18 0.00 0.00 3.02
4450 4914 9.151471 CCGGGTAAGTAATAATGTATCAGAATG 57.849 37.037 0.00 0.00 37.54 2.67
4622 5086 2.039462 ATGGGGAAAGCCAAGGCC 59.961 61.111 7.62 0.00 43.17 5.19
4637 5101 2.109126 GGCCCAACAGCGACTCATC 61.109 63.158 0.00 0.00 0.00 2.92
4695 5159 2.562298 TGCAAAACATGGTCCCAAGATC 59.438 45.455 0.00 0.00 0.00 2.75
4696 5160 2.094026 GCAAAACATGGTCCCAAGATCC 60.094 50.000 0.00 0.00 0.00 3.36
4697 5161 3.164268 CAAAACATGGTCCCAAGATCCA 58.836 45.455 0.00 0.00 35.64 3.41
4698 5162 2.514458 AACATGGTCCCAAGATCCAC 57.486 50.000 0.00 0.00 33.91 4.02
4699 5163 1.673767 ACATGGTCCCAAGATCCACT 58.326 50.000 0.00 0.00 33.91 4.00
4700 5164 1.561542 ACATGGTCCCAAGATCCACTC 59.438 52.381 0.00 0.00 33.91 3.51
4701 5165 0.833287 ATGGTCCCAAGATCCACTCG 59.167 55.000 0.00 0.00 33.91 4.18
4704 5168 1.829222 GGTCCCAAGATCCACTCGTTA 59.171 52.381 0.00 0.00 0.00 3.18
4705 5169 2.159085 GGTCCCAAGATCCACTCGTTAG 60.159 54.545 0.00 0.00 0.00 2.34
4706 5170 2.758979 GTCCCAAGATCCACTCGTTAGA 59.241 50.000 0.00 0.00 0.00 2.10
4707 5171 3.385111 GTCCCAAGATCCACTCGTTAGAT 59.615 47.826 0.00 0.00 0.00 1.98
4713 5190 4.798882 AGATCCACTCGTTAGATCCTTCT 58.201 43.478 0.00 0.00 37.69 2.85
4723 5200 0.250513 AGATCCTTCTTCCACCGCAC 59.749 55.000 0.00 0.00 0.00 5.34
4726 5203 2.328099 CCTTCTTCCACCGCACAGC 61.328 63.158 0.00 0.00 0.00 4.40
4801 5279 0.536006 ACTGCCTCCTTTCTGCACAC 60.536 55.000 0.00 0.00 0.00 3.82
5030 5508 1.202891 AGCAACCCTTACCAGTGAACC 60.203 52.381 0.00 0.00 0.00 3.62
5055 5533 1.285950 TGACCTCTCGTCAGTTGCG 59.714 57.895 0.00 0.00 46.80 4.85
5067 5545 1.412710 TCAGTTGCGACTTGTTCCTCT 59.587 47.619 3.02 0.00 32.54 3.69
5075 5553 2.731976 CGACTTGTTCCTCTAGTGTTGC 59.268 50.000 0.00 0.00 32.78 4.17
5178 5678 4.763279 ACACAATGTTCAGAGATGCATTGA 59.237 37.500 18.90 0.00 46.39 2.57
5238 5738 5.565439 GCCTATGCATCTTTGACAACTGTTT 60.565 40.000 0.19 0.00 37.47 2.83
5266 5767 5.365021 AGATACTTGGTGGGAGAATTCAG 57.635 43.478 8.44 0.00 0.00 3.02
5299 5800 5.581085 GGCACTATAGTAGGACTTGTGTTTG 59.419 44.000 4.74 0.00 30.85 2.93
5306 5807 1.006639 AGGACTTGTGTTTGTTGGGGT 59.993 47.619 0.00 0.00 0.00 4.95
5307 5808 1.136110 GGACTTGTGTTTGTTGGGGTG 59.864 52.381 0.00 0.00 0.00 4.61
5337 5838 2.951642 AGAAACATACATGGATTGGCCG 59.048 45.455 0.00 0.00 40.66 6.13
5339 5840 0.823356 ACATACATGGATTGGCCGGC 60.823 55.000 21.18 21.18 40.66 6.13
5342 5843 0.840617 TACATGGATTGGCCGGCTTA 59.159 50.000 28.56 15.26 40.66 3.09
5375 5876 7.805542 GCAGAAATGAAGTTTAGAAGGAAGAAC 59.194 37.037 0.00 0.00 0.00 3.01
5658 6200 1.348064 TCCGTCCATCACAGAAAGGT 58.652 50.000 0.00 0.00 0.00 3.50
5659 6201 1.697432 TCCGTCCATCACAGAAAGGTT 59.303 47.619 0.00 0.00 0.00 3.50
5660 6202 2.105821 TCCGTCCATCACAGAAAGGTTT 59.894 45.455 0.00 0.00 0.00 3.27
5661 6203 2.884639 CCGTCCATCACAGAAAGGTTTT 59.115 45.455 0.00 0.00 0.00 2.43
5662 6204 3.317993 CCGTCCATCACAGAAAGGTTTTT 59.682 43.478 0.00 0.00 0.00 1.94
5663 6205 4.537015 CGTCCATCACAGAAAGGTTTTTC 58.463 43.478 0.00 0.00 42.44 2.29
5664 6206 4.556699 CGTCCATCACAGAAAGGTTTTTCC 60.557 45.833 0.00 0.00 42.99 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.189676 TGGCTGATTTGGGATGCAAAT 58.810 42.857 0.00 0.00 35.24 2.32
1 2 1.642112 TGGCTGATTTGGGATGCAAA 58.358 45.000 0.00 0.00 0.00 3.68
9 10 0.037046 GCAAGGGTTGGCTGATTTGG 60.037 55.000 0.00 0.00 0.00 3.28
17 18 2.282745 AGAGCTGCAAGGGTTGGC 60.283 61.111 1.02 0.00 0.00 4.52
18 19 1.676967 GGAGAGCTGCAAGGGTTGG 60.677 63.158 1.02 0.00 0.00 3.77
57 58 1.219522 AAGCTGTAACCGTGCACGTC 61.220 55.000 34.81 22.05 37.74 4.34
59 60 1.491563 GAAGCTGTAACCGTGCACG 59.508 57.895 31.77 31.77 39.44 5.34
77 78 4.789031 TCGCGCTCTTCGACGACG 62.789 66.667 5.56 0.00 40.02 5.12
92 93 3.108289 CCGTGCAGCACTCAGTCG 61.108 66.667 23.15 8.84 31.34 4.18
94 95 1.889105 CAACCGTGCAGCACTCAGT 60.889 57.895 23.15 14.39 31.34 3.41
184 185 4.767255 GGGTCACGGGAGCTGCAG 62.767 72.222 17.63 10.11 41.29 4.41
187 188 4.087892 CAGGGGTCACGGGAGCTG 62.088 72.222 17.63 4.09 41.29 4.24
188 189 3.625632 ATCAGGGGTCACGGGAGCT 62.626 63.158 17.63 0.00 41.29 4.09
189 190 2.198304 AAATCAGGGGTCACGGGAGC 62.198 60.000 8.75 8.75 40.81 4.70
190 191 0.392998 CAAATCAGGGGTCACGGGAG 60.393 60.000 0.00 0.00 0.00 4.30
191 192 1.131303 ACAAATCAGGGGTCACGGGA 61.131 55.000 0.00 0.00 0.00 5.14
192 193 0.676782 GACAAATCAGGGGTCACGGG 60.677 60.000 0.00 0.00 0.00 5.28
193 194 0.036164 TGACAAATCAGGGGTCACGG 59.964 55.000 0.00 0.00 36.69 4.94
194 195 3.623848 TGACAAATCAGGGGTCACG 57.376 52.632 0.00 0.00 36.69 4.35
196 197 2.038952 CTCAGTGACAAATCAGGGGTCA 59.961 50.000 0.00 0.00 39.09 4.02
197 198 2.039084 ACTCAGTGACAAATCAGGGGTC 59.961 50.000 0.00 0.00 34.75 4.46
198 199 2.057922 ACTCAGTGACAAATCAGGGGT 58.942 47.619 0.00 0.00 34.75 4.95
199 200 2.224621 ACACTCAGTGACAAATCAGGGG 60.225 50.000 13.14 0.00 36.96 4.79
212 213 2.721971 CTTGAGGCGCCACACTCAGT 62.722 60.000 31.54 4.27 43.84 3.41
232 233 0.804989 CTGCCGTGATTTCCTTCCAC 59.195 55.000 0.00 0.00 0.00 4.02
261 262 3.694538 GCACCCAACACCATGGCC 61.695 66.667 13.04 0.00 39.26 5.36
267 268 1.745890 GGGAAAAGCACCCAACACC 59.254 57.895 0.00 0.00 46.05 4.16
288 289 0.173481 TCTCCCGAAACGCATCTCAG 59.827 55.000 0.00 0.00 0.00 3.35
293 294 2.076863 CTTCTTTCTCCCGAAACGCAT 58.923 47.619 0.00 0.00 35.41 4.73
320 321 4.450053 CCCTTTTTATCTCTCTGCTCCAG 58.550 47.826 0.00 0.00 0.00 3.86
327 328 4.785376 TCCTCTTGCCCTTTTTATCTCTCT 59.215 41.667 0.00 0.00 0.00 3.10
353 354 0.678048 GAGCCGTCCCATTTGCTTCT 60.678 55.000 0.00 0.00 33.41 2.85
369 371 1.168407 TGCAACTTGTCCAGCTGAGC 61.168 55.000 17.39 7.95 0.00 4.26
382 384 1.234615 GCCACACGTACCATGCAACT 61.235 55.000 0.00 0.00 0.00 3.16
385 387 2.359354 GGCCACACGTACCATGCA 60.359 61.111 0.00 0.00 0.00 3.96
447 449 1.286501 TTTCGCATCTACATGTCGGC 58.713 50.000 0.00 0.96 33.19 5.54
490 492 1.580059 AGGCCTCCTTCGGTTCATAA 58.420 50.000 0.00 0.00 0.00 1.90
648 651 3.268034 AATGGCTCCCCTAACCAAAAA 57.732 42.857 0.00 0.00 36.94 1.94
651 654 3.564790 GGTAAAATGGCTCCCCTAACCAA 60.565 47.826 0.00 0.00 36.94 3.67
652 655 2.024751 GGTAAAATGGCTCCCCTAACCA 60.025 50.000 0.00 0.00 37.99 3.67
653 656 2.024751 TGGTAAAATGGCTCCCCTAACC 60.025 50.000 0.00 0.00 0.00 2.85
690 734 1.821216 TCTTTTCATCCGGGCTGAAC 58.179 50.000 12.58 0.00 32.57 3.18
744 788 1.629043 TCGGCCCATATGACTAGACC 58.371 55.000 3.65 0.00 0.00 3.85
773 817 7.795431 TTCGAATGGAAATTTCTTTCGAATG 57.205 32.000 35.70 21.06 45.28 2.67
774 818 7.865385 TGTTTCGAATGGAAATTTCTTTCGAAT 59.135 29.630 37.24 18.28 46.90 3.34
776 820 6.730175 TGTTTCGAATGGAAATTTCTTTCGA 58.270 32.000 32.01 32.01 45.80 3.71
777 821 6.984740 TGTTTCGAATGGAAATTTCTTTCG 57.015 33.333 29.96 29.96 45.80 3.46
783 827 8.868916 CGGAATTATTGTTTCGAATGGAAATTT 58.131 29.630 0.00 0.00 45.80 1.82
784 828 8.247562 TCGGAATTATTGTTTCGAATGGAAATT 58.752 29.630 0.00 2.48 45.80 1.82
785 829 7.767261 TCGGAATTATTGTTTCGAATGGAAAT 58.233 30.769 0.00 0.00 45.80 2.17
786 830 7.147143 TCGGAATTATTGTTTCGAATGGAAA 57.853 32.000 0.00 0.00 42.23 3.13
787 831 6.676943 GCTCGGAATTATTGTTTCGAATGGAA 60.677 38.462 0.00 0.00 0.00 3.53
788 832 5.220777 GCTCGGAATTATTGTTTCGAATGGA 60.221 40.000 0.00 0.00 0.00 3.41
789 833 4.970003 GCTCGGAATTATTGTTTCGAATGG 59.030 41.667 0.00 0.00 0.00 3.16
795 839 3.680789 CGGTGCTCGGAATTATTGTTTC 58.319 45.455 0.00 0.00 34.75 2.78
1150 1500 4.314440 GAGCACGCACCTGGGTCA 62.314 66.667 0.00 0.00 39.30 4.02
1234 1584 0.036010 CACCAGGGAATCAGCGAAGT 60.036 55.000 0.00 0.00 0.00 3.01
1238 1588 2.825836 GCCACCAGGGAATCAGCG 60.826 66.667 0.00 0.00 40.01 5.18
1301 1651 4.555709 AACTTGGTGGCGTCGGCA 62.556 61.111 18.58 18.58 42.47 5.69
1521 1871 0.744771 GCCTAAACGGAGAGGGCAAG 60.745 60.000 0.00 0.00 42.08 4.01
1543 1893 4.036971 ACAGACTAGCGAACCAGATATGAC 59.963 45.833 0.00 0.00 0.00 3.06
1544 1894 4.036852 CACAGACTAGCGAACCAGATATGA 59.963 45.833 0.00 0.00 0.00 2.15
1545 1895 4.294232 CACAGACTAGCGAACCAGATATG 58.706 47.826 0.00 0.00 0.00 1.78
1546 1896 3.243569 GCACAGACTAGCGAACCAGATAT 60.244 47.826 0.00 0.00 0.00 1.63
1547 1897 2.099263 GCACAGACTAGCGAACCAGATA 59.901 50.000 0.00 0.00 0.00 1.98
1548 1898 1.134965 GCACAGACTAGCGAACCAGAT 60.135 52.381 0.00 0.00 0.00 2.90
1549 1899 0.243907 GCACAGACTAGCGAACCAGA 59.756 55.000 0.00 0.00 0.00 3.86
1550 1900 0.244994 AGCACAGACTAGCGAACCAG 59.755 55.000 0.00 0.00 35.48 4.00
1551 1901 0.038251 CAGCACAGACTAGCGAACCA 60.038 55.000 0.00 0.00 35.48 3.67
1552 1902 1.355066 GCAGCACAGACTAGCGAACC 61.355 60.000 0.00 0.00 35.48 3.62
1581 1931 0.681733 AGACGGCACAGTCACATCTT 59.318 50.000 0.00 0.00 43.24 2.40
1596 1953 0.443869 CAGGCGAAACCATCAAGACG 59.556 55.000 0.00 0.00 43.14 4.18
1599 1956 1.666888 GCAACAGGCGAAACCATCAAG 60.667 52.381 0.00 0.00 43.14 3.02
1634 1991 2.125350 CCCGCTTGAGCCAGAGAC 60.125 66.667 0.00 0.00 37.91 3.36
1695 2052 5.247337 TCACAGTCCACATCAATACAAGGTA 59.753 40.000 0.00 0.00 0.00 3.08
1703 2060 2.816087 GCAGTTCACAGTCCACATCAAT 59.184 45.455 0.00 0.00 0.00 2.57
1704 2061 2.221169 GCAGTTCACAGTCCACATCAA 58.779 47.619 0.00 0.00 0.00 2.57
1713 2070 0.671781 GATGAGGCGCAGTTCACAGT 60.672 55.000 10.83 0.00 0.00 3.55
1761 2118 3.119245 GCAATCCAGCTCAAACATCACAT 60.119 43.478 0.00 0.00 0.00 3.21
1793 2150 4.639310 CCAAGCTACTCAGATCTGCAAAAT 59.361 41.667 18.36 3.84 0.00 1.82
1826 2183 4.142513 GCAGTTCATCAAGACCTTTCATCC 60.143 45.833 0.00 0.00 0.00 3.51
1904 2261 1.204704 CCATGTTAGTGTGAGAGGCGA 59.795 52.381 0.00 0.00 0.00 5.54
2069 2426 1.302832 CTGAGGGGTGCCTGAACAC 60.303 63.158 0.00 0.00 39.94 3.32
2129 2486 7.097192 CACATAAGTAGAGTACCTTCTTTGCA 58.903 38.462 7.97 0.00 34.80 4.08
2247 2618 6.114767 TGCTGTGAATACATGCTCTAATTGA 58.885 36.000 0.00 0.00 35.97 2.57
2274 2645 6.959639 ATCTACAAAGCACCAAAGAAAGAA 57.040 33.333 0.00 0.00 0.00 2.52
2520 2891 9.754382 AATATGGAAGAATAAATGCAATGACAC 57.246 29.630 0.00 0.00 0.00 3.67
2649 3020 3.268034 AAATAAAGCCCCAAACCTGGA 57.732 42.857 0.00 0.00 46.92 3.86
2689 3060 6.469782 AATAGATGGTGTGGCTAAAAATGG 57.530 37.500 0.00 0.00 0.00 3.16
2716 3087 7.972277 GTCTGATGTTATAGAGAAACGTACCAA 59.028 37.037 0.00 0.00 0.00 3.67
2763 3134 3.887110 CCAATATGAGCTCCTGCATTTCA 59.113 43.478 12.15 0.00 42.74 2.69
2783 3154 0.904865 CAGTAGTGGGCTCTGGTCCA 60.905 60.000 0.00 0.00 46.10 4.02
2813 3184 3.550820 TGCAACACTTACCATCACAACT 58.449 40.909 0.00 0.00 0.00 3.16
2838 3209 6.618287 TCCTTGCTGCATGTACATAAATAC 57.382 37.500 8.32 0.00 0.00 1.89
3162 3620 3.119884 ACGAACATAACACCGTCGTGATA 60.120 43.478 0.00 0.00 43.14 2.15
3177 3635 6.795098 TGTATTTCAGCAAACTACGAACAT 57.205 33.333 0.00 0.00 0.00 2.71
3261 3719 3.756434 TGTGCATTAAAACTCTAGCCACC 59.244 43.478 0.00 0.00 0.00 4.61
3413 3872 6.159575 TCCTGACTGATGTGGGGAAAAATATA 59.840 38.462 0.00 0.00 0.00 0.86
3558 4018 9.778741 TTAGTATCTCAATTAATGCTTACAGGG 57.221 33.333 0.00 0.00 0.00 4.45
3827 4287 4.457949 ACACGTATTTTGTCTTCATTCCCC 59.542 41.667 0.00 0.00 0.00 4.81
3857 4317 3.211045 GTCAACTTGGTCTGCCTTGTTA 58.789 45.455 0.00 0.00 32.73 2.41
3935 4395 1.686800 GCCGGGTTACACCTAGGGA 60.687 63.158 14.81 0.00 38.64 4.20
4110 4570 7.259161 ACTCCAGAAGTAAGATTACTAAAGCG 58.741 38.462 5.71 0.00 42.86 4.68
4135 4596 4.408276 ACTAGAGCTGTACAACCTTCAGA 58.592 43.478 0.00 0.00 0.00 3.27
4637 5101 5.140177 GCAAACTCATCTTGTAAGTTGTCG 58.860 41.667 3.43 0.00 33.68 4.35
4683 5147 0.544357 ACGAGTGGATCTTGGGACCA 60.544 55.000 0.00 0.00 32.04 4.02
4684 5148 0.613777 AACGAGTGGATCTTGGGACC 59.386 55.000 0.00 0.00 32.04 4.46
4695 5159 3.447586 TGGAAGAAGGATCTAACGAGTGG 59.552 47.826 0.00 0.00 33.77 4.00
4696 5160 4.425520 GTGGAAGAAGGATCTAACGAGTG 58.574 47.826 0.00 0.00 33.77 3.51
4697 5161 3.447944 GGTGGAAGAAGGATCTAACGAGT 59.552 47.826 0.00 0.00 33.77 4.18
4698 5162 3.489398 CGGTGGAAGAAGGATCTAACGAG 60.489 52.174 0.00 0.00 40.43 4.18
4699 5163 2.426024 CGGTGGAAGAAGGATCTAACGA 59.574 50.000 0.00 0.00 40.43 3.85
4700 5164 2.810650 CGGTGGAAGAAGGATCTAACG 58.189 52.381 0.00 0.00 33.77 3.18
4701 5165 2.093658 TGCGGTGGAAGAAGGATCTAAC 60.094 50.000 0.00 0.00 33.77 2.34
4704 5168 0.250513 GTGCGGTGGAAGAAGGATCT 59.749 55.000 0.00 0.00 37.57 2.75
4705 5169 0.036388 TGTGCGGTGGAAGAAGGATC 60.036 55.000 0.00 0.00 0.00 3.36
4706 5170 0.036010 CTGTGCGGTGGAAGAAGGAT 60.036 55.000 0.00 0.00 0.00 3.24
4707 5171 1.371183 CTGTGCGGTGGAAGAAGGA 59.629 57.895 0.00 0.00 0.00 3.36
4723 5200 7.751047 ATCTGAAATTCATTTGATTTCGCTG 57.249 32.000 0.00 0.45 37.17 5.18
4731 5208 8.352137 ACACCATGTATCTGAAATTCATTTGA 57.648 30.769 0.00 0.00 0.00 2.69
4811 5289 0.615331 ACATCTCAGGCGTCAATGGT 59.385 50.000 0.00 0.00 0.00 3.55
5030 5508 3.114558 GACGAGAGGTCAGCAACAG 57.885 57.895 0.00 0.00 45.36 3.16
5055 5533 3.991121 GAGCAACACTAGAGGAACAAGTC 59.009 47.826 0.00 0.00 0.00 3.01
5067 5545 0.608130 ATGGCAGACGAGCAACACTA 59.392 50.000 0.00 0.00 35.83 2.74
5075 5553 1.135721 TCATGAGTCATGGCAGACGAG 59.864 52.381 28.54 4.35 41.66 4.18
5178 5678 4.336713 GCACTGAAGACAAAAGGAAAGAGT 59.663 41.667 0.00 0.00 0.00 3.24
5212 5712 3.693085 AGTTGTCAAAGATGCATAGGCTG 59.307 43.478 0.00 0.00 41.91 4.85
5238 5738 4.890988 TCTCCCACCAAGTATCTATTCCA 58.109 43.478 0.00 0.00 0.00 3.53
5266 5767 6.893005 AGTCCTACTATAGTGCCTATTCATCC 59.107 42.308 15.90 0.00 0.00 3.51
5299 5800 1.337118 TCTGCCAAAATCACCCCAAC 58.663 50.000 0.00 0.00 0.00 3.77
5306 5807 5.479724 TCCATGTATGTTTCTGCCAAAATCA 59.520 36.000 0.00 0.00 0.00 2.57
5307 5808 5.964758 TCCATGTATGTTTCTGCCAAAATC 58.035 37.500 0.00 0.00 0.00 2.17
5347 5848 7.667219 TCTTCCTTCTAAACTTCATTTCTGCAT 59.333 33.333 0.00 0.00 0.00 3.96
5920 6466 0.453793 TTTGTGTGTTTGGTCGGCAG 59.546 50.000 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.