Multiple sequence alignment - TraesCS6B01G221600

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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 TraesCS6B01G221600 chr6B 100.000 2192 0 0 1 2192 320193157 320195348 0 4048
1 TraesCS6B01G221600 chr3B 94.031 2161 122 4 35 2192 92296697 92294541 0 3269
2 TraesCS6B01G221600 chr3B 93.562 2159 136 3 35 2192 6010731 6008575 0 3214
3 TraesCS6B01G221600 chr2B 93.932 2159 129 2 35 2192 234541125 234538968 0 3260
4 TraesCS6B01G221600 chr3A 93.747 2159 133 2 35 2192 495104725 495102568 0 3238
5 TraesCS6B01G221600 chr1B 93.608 2159 135 3 35 2192 619195296 619193140 0 3219
6 TraesCS6B01G221600 chrUn 93.674 2150 133 3 35 2183 217907703 217909850 0 3214
7 TraesCS6B01G221600 chr1A 93.674 2150 133 3 35 2183 278521229 278523376 0 3214
8 TraesCS6B01G221600 chr4A 93.581 2150 136 2 35 2183 67519533 67521681 0 3205
9 TraesCS6B01G221600 chr6D 93.535 2150 137 2 35 2183 108485243 108487391 0 3199
10 TraesCS6B01G221600 chr6A 94.310 1863 101 3 62 1923 597252931 597251073 0 2848


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 TraesCS6B01G221600 chr6B 320193157 320195348 2191 False 4048 4048 100.000 1 2192 1 chr6B.!!$F1 2191
1 TraesCS6B01G221600 chr3B 92294541 92296697 2156 True 3269 3269 94.031 35 2192 1 chr3B.!!$R2 2157
2 TraesCS6B01G221600 chr3B 6008575 6010731 2156 True 3214 3214 93.562 35 2192 1 chr3B.!!$R1 2157
3 TraesCS6B01G221600 chr2B 234538968 234541125 2157 True 3260 3260 93.932 35 2192 1 chr2B.!!$R1 2157
4 TraesCS6B01G221600 chr3A 495102568 495104725 2157 True 3238 3238 93.747 35 2192 1 chr3A.!!$R1 2157
5 TraesCS6B01G221600 chr1B 619193140 619195296 2156 True 3219 3219 93.608 35 2192 1 chr1B.!!$R1 2157
6 TraesCS6B01G221600 chrUn 217907703 217909850 2147 False 3214 3214 93.674 35 2183 1 chrUn.!!$F1 2148
7 TraesCS6B01G221600 chr1A 278521229 278523376 2147 False 3214 3214 93.674 35 2183 1 chr1A.!!$F1 2148
8 TraesCS6B01G221600 chr4A 67519533 67521681 2148 False 3205 3205 93.581 35 2183 1 chr4A.!!$F1 2148
9 TraesCS6B01G221600 chr6D 108485243 108487391 2148 False 3199 3199 93.535 35 2183 1 chr6D.!!$F1 2148
10 TraesCS6B01G221600 chr6A 597251073 597252931 1858 True 2848 2848 94.310 62 1923 1 chr6A.!!$R1 1861

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
830 831 0.037605 AAAGGCCGAGTTGTAGGTCG 60.038 55.0 0.0 0.0 37.18 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 1871 0.178897 TAGACGGTTCCCTTTCCCCA 60.179 55.0 0.0 0.0 0.0 4.96 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
50 51 4.801891 AGTGTTATCATGCACTTGCTTTG 58.198 39.130 2.33 0.98 42.61 2.77
60 61 4.136796 TGCACTTGCTTTGACTACTCATT 58.863 39.130 2.33 0.00 42.66 2.57
72 73 7.660030 TTGACTACTCATTCTATGGATGTGA 57.340 36.000 0.00 0.00 0.00 3.58
76 77 7.293828 ACTACTCATTCTATGGATGTGAGAGA 58.706 38.462 21.17 11.78 37.68 3.10
94 95 5.245301 TGAGAGAATCAACTCCGTTCCTTTA 59.755 40.000 0.00 0.00 37.82 1.85
141 142 9.525826 AATTGTTGGAATTCTATGAAAGAGTCT 57.474 29.630 5.23 0.00 35.05 3.24
168 169 0.099968 CAGGATGCATGCCAGTTTCG 59.900 55.000 16.68 0.00 0.00 3.46
177 178 1.246649 TGCCAGTTTCGTACGACCTA 58.753 50.000 19.36 0.00 0.00 3.08
189 190 0.614979 ACGACCTAGTGGAGTGGCAT 60.615 55.000 0.00 0.00 37.04 4.40
243 244 5.867903 TGATTCCTCCACACAACAATTTT 57.132 34.783 0.00 0.00 0.00 1.82
252 253 4.970003 CCACACAACAATTTTCTTCTCGTC 59.030 41.667 0.00 0.00 0.00 4.20
280 281 5.105877 ACGAATTAGAAGAGATGTCAACCGA 60.106 40.000 0.00 0.00 0.00 4.69
321 322 8.241497 ACAACGATTAGTGGATATTGGTACTA 57.759 34.615 0.00 0.00 0.00 1.82
332 333 6.043127 TGGATATTGGTACTATCACTGCACAT 59.957 38.462 0.00 0.00 0.00 3.21
341 342 4.703575 ACTATCACTGCACATCAAGCAAAT 59.296 37.500 0.00 0.00 42.17 2.32
380 381 3.991773 GTGTAATGTTAAGAGGTCGTGCA 59.008 43.478 0.00 0.00 0.00 4.57
394 395 3.435327 GGTCGTGCAACATGAAGACATTA 59.565 43.478 0.00 0.00 35.74 1.90
398 399 7.240674 GTCGTGCAACATGAAGACATTAATAA 58.759 34.615 0.00 0.00 35.74 1.40
399 400 7.748683 GTCGTGCAACATGAAGACATTAATAAA 59.251 33.333 0.00 0.00 35.74 1.40
431 432 1.133513 AGTTCCCATCAGGCAACAACA 60.134 47.619 0.00 0.00 41.41 3.33
436 437 1.069022 CCATCAGGCAACAACAGTTCG 60.069 52.381 0.00 0.00 41.41 3.95
488 489 6.507958 TGTCAGTGAAGATTTTGTGTGAAA 57.492 33.333 0.00 0.00 0.00 2.69
501 502 2.104111 TGTGTGAAACCTTGGAGACGAT 59.896 45.455 0.00 0.00 34.36 3.73
562 563 1.270571 TGAGCGAATGTGTGTAAGCCA 60.271 47.619 0.00 0.00 0.00 4.75
563 564 1.394917 GAGCGAATGTGTGTAAGCCAG 59.605 52.381 0.00 0.00 0.00 4.85
583 584 8.102484 AGCCAGGTAAAAGATTCCTATTCTAA 57.898 34.615 0.00 0.00 0.00 2.10
598 599 4.122149 TAAGCGGGGTGGGCCATG 62.122 66.667 10.70 1.05 36.17 3.66
693 694 2.933287 TTCACCGGGGTGGAGCAT 60.933 61.111 17.31 0.00 45.43 3.79
718 719 2.480073 CCGCCAAAATCAGCATAGGTTG 60.480 50.000 0.00 0.00 0.00 3.77
770 771 6.994496 CCATCTTTCTCCATATGAAAGTGCTA 59.006 38.462 3.65 0.00 46.08 3.49
821 822 1.338020 CTCAAAAAGCAAAGGCCGAGT 59.662 47.619 0.00 0.00 42.56 4.18
830 831 0.037605 AAAGGCCGAGTTGTAGGTCG 60.038 55.000 0.00 0.00 37.18 4.79
888 889 1.559219 TCCTGGATCAAAGCGGATCAA 59.441 47.619 14.94 5.90 44.38 2.57
892 893 2.027285 TGGATCAAAGCGGATCAACTCA 60.027 45.455 14.94 4.43 44.38 3.41
935 936 2.186826 GCCCCGGAACATCGAATGG 61.187 63.158 0.73 0.00 33.60 3.16
955 956 3.714798 TGGAAGTGGTCTTTCTACAACCT 59.285 43.478 0.00 0.00 33.64 3.50
981 982 6.538209 TTTATATGATTTTGAGGGCCCCTA 57.462 37.500 21.43 4.37 31.76 3.53
1017 1018 3.181443 CCCTTATGTTTAGGAGCGGGATT 60.181 47.826 0.00 0.00 34.56 3.01
1044 1045 0.390124 GAACGACCTGTGGTGGTACA 59.610 55.000 4.90 0.00 43.58 2.90
1054 1055 1.116536 TGGTGGTACAGAAGGCACGA 61.117 55.000 0.00 0.00 41.80 4.35
1057 1058 0.319211 TGGTACAGAAGGCACGAACG 60.319 55.000 0.00 0.00 0.00 3.95
1123 1124 8.321353 ACCATCACAAGATAAAGAAGTATGACA 58.679 33.333 0.00 0.00 31.88 3.58
1157 1158 8.915036 TCTAACTCTATTGGTCATAGTTCCTTC 58.085 37.037 0.00 0.00 36.87 3.46
1164 1165 3.650942 TGGTCATAGTTCCTTCCTGTTGT 59.349 43.478 0.00 0.00 0.00 3.32
1175 1176 1.829533 CCTGTTGTGGCTGGTGCTT 60.830 57.895 0.00 0.00 39.59 3.91
1205 1206 1.453155 GCGTGAACCACTGGATCATT 58.547 50.000 10.97 0.00 36.89 2.57
1249 1250 2.166459 TCTGAGAATGATTCGAGCCGTT 59.834 45.455 0.00 0.00 34.02 4.44
1325 1329 2.354729 CCATTGACTTGGCCCGGA 59.645 61.111 0.73 0.00 0.00 5.14
1421 1425 3.379372 GCAGCACCTTATGATGTTCATGT 59.621 43.478 0.30 0.00 46.90 3.21
1429 1433 5.759763 CCTTATGATGTTCATGTCCAATCGA 59.240 40.000 0.30 0.00 37.70 3.59
1472 1476 9.477405 AGGTACTAGAGGAGATCGCTATGATCC 62.477 48.148 0.00 0.00 46.99 3.36
1501 1505 3.793797 TCCGTATTGAAGAGATGCGAA 57.206 42.857 0.00 0.00 35.09 4.70
1522 1526 5.514274 AAAAAGTGTTCGGATCATTGTGT 57.486 34.783 0.00 0.00 0.00 3.72
1654 1658 5.784177 ACATAGATCATCGCCGTTCTTAAT 58.216 37.500 0.00 0.00 0.00 1.40
1718 1722 1.120530 GGAGTAAAGCATCCCGAGGA 58.879 55.000 0.00 0.00 35.55 3.71
1746 1750 0.250234 CTCGTTGGGCATGGAGAAGA 59.750 55.000 0.00 0.00 0.00 2.87
1867 1871 4.787534 ACTTCTCCCTTCTTCATTGATCCT 59.212 41.667 0.00 0.00 0.00 3.24
1939 1944 5.602561 TGGCTTGATGAGGATAACTAAGCTA 59.397 40.000 0.00 0.00 39.09 3.32
1944 1949 7.661536 TGATGAGGATAACTAAGCTAACACT 57.338 36.000 0.00 0.00 0.00 3.55
1983 1988 0.110486 CAACAGGGTGGTGCCTTACT 59.890 55.000 0.00 0.00 37.43 2.24
1992 1997 1.305219 GGTGCCTTACTGCATCGCAA 61.305 55.000 0.00 0.00 44.30 4.85
1995 2000 1.647545 GCCTTACTGCATCGCAAGCA 61.648 55.000 0.00 0.00 38.41 3.91
2027 2032 1.680735 GTGTTCATGGTGGTGCTTCAA 59.319 47.619 0.00 0.00 0.00 2.69
2043 2048 5.182001 GTGCTTCAAGATTCCAATGTACTGT 59.818 40.000 0.00 0.00 0.00 3.55
2070 2075 2.172483 ATCAGAACGAGCTTGCCGGT 62.172 55.000 1.90 0.00 0.00 5.28
2123 2128 0.767375 AGCGGTGCCATCTTATCCAT 59.233 50.000 0.00 0.00 0.00 3.41
2132 2137 3.632145 GCCATCTTATCCATGGAAAACGT 59.368 43.478 20.67 3.98 43.32 3.99
2144 2149 3.734463 TGGAAAACGTGTCAAGCTATCA 58.266 40.909 0.00 0.00 0.00 2.15
2151 2156 2.415491 CGTGTCAAGCTATCACTTCGGA 60.415 50.000 11.92 0.00 0.00 4.55
2183 2188 2.740506 AAGAAAAGGACCGGGAAACA 57.259 45.000 6.32 0.00 0.00 2.83
2185 2190 1.213430 AGAAAAGGACCGGGAAACACA 59.787 47.619 6.32 0.00 0.00 3.72
2188 2193 1.990160 AAGGACCGGGAAACACAGCA 61.990 55.000 6.32 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.208022 GCAAGTGCATGATAACACTCTTATATA 57.792 33.333 0.00 0.00 46.17 0.86
21 22 7.935755 AGCAAGTGCATGATAACACTCTTATAT 59.064 33.333 6.00 0.00 46.17 0.86
22 23 7.275183 AGCAAGTGCATGATAACACTCTTATA 58.725 34.615 6.00 0.00 46.17 0.98
23 24 6.118170 AGCAAGTGCATGATAACACTCTTAT 58.882 36.000 6.00 0.00 46.17 1.73
24 25 5.491070 AGCAAGTGCATGATAACACTCTTA 58.509 37.500 6.00 0.00 46.17 2.10
25 26 4.330250 AGCAAGTGCATGATAACACTCTT 58.670 39.130 6.00 0.00 46.17 2.85
26 27 3.947868 AGCAAGTGCATGATAACACTCT 58.052 40.909 6.00 0.00 46.17 3.24
27 28 4.691860 AAGCAAGTGCATGATAACACTC 57.308 40.909 6.00 0.00 46.17 3.51
29 30 4.618489 GTCAAAGCAAGTGCATGATAACAC 59.382 41.667 12.89 0.00 45.16 3.32
30 31 4.520111 AGTCAAAGCAAGTGCATGATAACA 59.480 37.500 12.89 0.00 45.16 2.41
31 32 5.051891 AGTCAAAGCAAGTGCATGATAAC 57.948 39.130 12.89 4.16 45.16 1.89
32 33 5.939883 AGTAGTCAAAGCAAGTGCATGATAA 59.060 36.000 12.89 4.54 45.16 1.75
33 34 5.491070 AGTAGTCAAAGCAAGTGCATGATA 58.509 37.500 12.89 6.29 45.16 2.15
39 40 4.453819 AGAATGAGTAGTCAAAGCAAGTGC 59.546 41.667 3.93 0.00 35.88 4.40
50 51 7.446931 TCTCTCACATCCATAGAATGAGTAGTC 59.553 40.741 5.93 0.00 39.05 2.59
60 61 6.041409 GGAGTTGATTCTCTCACATCCATAGA 59.959 42.308 10.05 0.00 38.11 1.98
94 95 2.190488 CTCCCGCTCCTCAAAAGCCT 62.190 60.000 0.00 0.00 36.36 4.58
141 142 2.769621 ATGCATCCTGGCTCCCGA 60.770 61.111 0.00 0.00 34.04 5.14
168 169 0.455005 GCCACTCCACTAGGTCGTAC 59.545 60.000 0.00 0.00 35.89 3.67
177 178 2.158842 GCAGATCTTATGCCACTCCACT 60.159 50.000 0.00 0.00 37.73 4.00
213 214 5.955961 TGTGTGGAGGAATCAATATCTCA 57.044 39.130 0.00 0.00 0.00 3.27
252 253 5.811588 TGACATCTCTTCTAATTCGTCGAG 58.188 41.667 0.00 0.00 0.00 4.04
280 281 2.803956 CGTTGTTTCCAGATACGGTTGT 59.196 45.455 0.00 0.00 0.00 3.32
321 322 3.508402 TCATTTGCTTGATGTGCAGTGAT 59.492 39.130 0.00 0.00 41.71 3.06
332 333 4.095211 TGAATCCCCAATCATTTGCTTGA 58.905 39.130 0.00 0.00 0.00 3.02
341 342 1.710244 ACACCACTGAATCCCCAATCA 59.290 47.619 0.00 0.00 0.00 2.57
431 432 0.834687 TTGTAGGGTCAGGCCGAACT 60.835 55.000 11.53 9.41 38.44 3.01
436 437 0.251165 TGCTTTTGTAGGGTCAGGCC 60.251 55.000 0.00 0.00 0.00 5.19
488 489 1.192428 GGGTACATCGTCTCCAAGGT 58.808 55.000 0.00 0.00 0.00 3.50
535 536 2.058798 CACACATTCGCTCACTTACGT 58.941 47.619 0.00 0.00 0.00 3.57
562 563 7.217906 CCGCTTAGAATAGGAATCTTTTACCT 58.782 38.462 0.00 0.00 37.76 3.08
563 564 6.427242 CCCGCTTAGAATAGGAATCTTTTACC 59.573 42.308 0.00 0.00 0.00 2.85
598 599 3.626217 GGACCAATACCATTCGAAGGTTC 59.374 47.826 19.76 8.42 40.54 3.62
718 719 2.624838 CCATGTTCCATCAATAGCACCC 59.375 50.000 0.00 0.00 0.00 4.61
843 844 0.178992 CCCAGTCAGCCACCTTTTCA 60.179 55.000 0.00 0.00 0.00 2.69
888 889 3.313012 TGATCGACGAATTTGGTGAGT 57.687 42.857 0.00 0.00 0.00 3.41
935 936 7.981102 AATAAGGTTGTAGAAAGACCACTTC 57.019 36.000 0.00 0.00 35.89 3.01
955 956 7.543755 AGGGGCCCTCAAAATCATATAAATAA 58.456 34.615 22.67 0.00 0.00 1.40
981 982 1.890205 TAAGGGAGGGATAGGGGGAT 58.110 55.000 0.00 0.00 0.00 3.85
1017 1018 0.817634 CACAGGTCGTTCTTGGGCAA 60.818 55.000 0.00 0.00 0.00 4.52
1128 1129 8.643324 GGAACTATGACCAATAGAGTTAGACAT 58.357 37.037 0.00 0.00 40.83 3.06
1134 1135 6.674419 AGGAAGGAACTATGACCAATAGAGTT 59.326 38.462 0.00 0.00 40.83 3.01
1157 1158 1.829533 AAGCACCAGCCACAACAGG 60.830 57.895 0.00 0.00 43.56 4.00
1164 1165 2.813901 GCAAACAAGCACCAGCCA 59.186 55.556 0.00 0.00 43.56 4.75
1187 1188 3.118775 TCCTAATGATCCAGTGGTTCACG 60.119 47.826 22.44 14.32 39.64 4.35
1197 1198 4.662179 AGAGGCATCTTTCCTAATGATCCA 59.338 41.667 0.00 0.00 33.24 3.41
1198 1199 5.221803 TGAGAGGCATCTTTCCTAATGATCC 60.222 44.000 0.76 0.00 35.30 3.36
1205 1206 2.402564 CCCTGAGAGGCATCTTTCCTA 58.597 52.381 0.76 0.00 35.30 2.94
1311 1315 1.128809 TTAGGTCCGGGCCAAGTCAA 61.129 55.000 30.48 9.95 0.00 3.18
1325 1329 4.947388 TCACTTTTGCACTTTCACTTAGGT 59.053 37.500 0.00 0.00 0.00 3.08
1382 1386 1.153549 GCTCTTCGCGAATCCCAGT 60.154 57.895 23.67 0.00 0.00 4.00
1421 1425 3.193903 TGGTACGTCAAGATTCGATTGGA 59.806 43.478 0.00 0.00 0.00 3.53
1472 1476 7.327275 GCATCTCTTCAATACGGATACAGTAAG 59.673 40.741 0.00 0.00 0.00 2.34
1501 1505 6.627395 TTACACAATGATCCGAACACTTTT 57.373 33.333 0.00 0.00 0.00 2.27
1522 1526 7.573710 ACACTAGGCATTTGATTAGGACATTA 58.426 34.615 0.00 0.00 0.00 1.90
1568 1572 4.152647 TCGTGATGGAGGACATAGCTTAT 58.847 43.478 0.00 0.00 40.72 1.73
1654 1658 1.093159 GAGCTTAACCCGAGTCTCGA 58.907 55.000 23.74 0.04 43.74 4.04
1695 1699 3.492829 CCTCGGGATGCTTTACTCCTAAC 60.493 52.174 0.00 0.00 0.00 2.34
1718 1722 2.514592 CCCAACGAGATGCGCCAT 60.515 61.111 4.18 0.00 46.04 4.40
1772 1776 2.361119 GGACGGGAAAAGAAACTGCTTT 59.639 45.455 0.00 0.00 39.65 3.51
1773 1777 1.954382 GGACGGGAAAAGAAACTGCTT 59.046 47.619 0.00 0.00 0.00 3.91
1823 1827 5.178797 AGTCAATTGATTCGTCCGAAGAAT 58.821 37.500 12.12 9.04 37.56 2.40
1833 1837 5.181748 AGAAGGGAGAAGTCAATTGATTCG 58.818 41.667 12.12 0.00 0.00 3.34
1841 1845 5.567037 TCAATGAAGAAGGGAGAAGTCAA 57.433 39.130 0.00 0.00 0.00 3.18
1867 1871 0.178897 TAGACGGTTCCCTTTCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
1939 1944 1.071471 CAGCCAACTCCGGAGTGTT 59.929 57.895 36.87 20.53 41.58 3.32
1944 1949 4.020617 CCAGCAGCCAACTCCGGA 62.021 66.667 2.93 2.93 0.00 5.14
1983 1988 4.388080 GCGTGTGCTTGCGATGCA 62.388 61.111 0.00 0.00 38.39 3.96
1995 2000 2.732094 GAACACTACCGCGCGTGT 60.732 61.111 29.95 26.21 45.55 4.49
2027 2032 4.323792 CCTGGACACAGTACATTGGAATCT 60.324 45.833 0.00 0.00 43.36 2.40
2043 2048 0.532573 GCTCGTTCTGATCCTGGACA 59.467 55.000 0.00 0.00 0.00 4.02
2108 2113 4.498009 CGTTTTCCATGGATAAGATGGCAC 60.498 45.833 17.06 3.17 40.35 5.01
2123 2128 3.496884 GTGATAGCTTGACACGTTTTCCA 59.503 43.478 0.00 0.00 0.00 3.53
2132 2137 3.489229 CGATCCGAAGTGATAGCTTGACA 60.489 47.826 0.00 0.00 0.00 3.58
2151 2156 5.181433 GGTCCTTTTCTTTTAGTGCTTCGAT 59.819 40.000 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.