Multiple sequence alignment - TraesCS6B01G267200

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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 TraesCS6B01G267200 chr6B 100.000 2342 0 0 1 2342 480788103 480785762 0.000000e+00 4325
1 TraesCS6B01G267200 chr6D 95.917 1200 27 6 738 1936 340196657 340197835 0.000000e+00 1925
2 TraesCS6B01G267200 chr6D 95.436 745 31 2 1 745 340194884 340195625 0.000000e+00 1184
3 TraesCS6B01G267200 chr6D 88.756 418 41 5 1931 2342 340198670 340199087 7.470000e-140 507
4 TraesCS6B01G267200 chr6A 89.058 658 23 10 737 1368 480197392 480198026 0.000000e+00 771
5 TraesCS6B01G267200 chr6A 84.457 682 89 14 1 676 480194572 480195242 0.000000e+00 656
6 TraesCS6B01G267200 chr6A 88.969 417 23 8 1453 1858 480198029 480198433 5.810000e-136 494
7 TraesCS6B01G267200 chr6A 85.656 244 26 7 1857 2096 480198781 480199019 5.000000e-62 248


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 TraesCS6B01G267200 chr6B 480785762 480788103 2341 True 4325.000000 4325 100.000000 1 2342 1 chr6B.!!$R1 2341
1 TraesCS6B01G267200 chr6D 340194884 340199087 4203 False 1205.333333 1925 93.369667 1 2342 3 chr6D.!!$F1 2341
2 TraesCS6B01G267200 chr6A 480194572 480199019 4447 False 542.250000 771 87.035000 1 2096 4 chr6A.!!$F1 2095

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
650 657 0.179018 GGATGCATTAAGGACCCGCT 60.179 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 6503 0.036388 GGTGAGAACTCCCATCGCAA 60.036 55.0 0.0 0.0 0.0 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
302 308 5.371526 AGCATGGTATGAATCGAAGACATT 58.628 37.500 0.00 0.00 42.51 2.71
425 432 3.233684 AGTAGCGTTCTAAGCTTCCAC 57.766 47.619 0.00 0.00 43.24 4.02
444 451 7.306866 GCTTCCACTCATTGTATAATCGAACTC 60.307 40.741 0.00 0.00 0.00 3.01
476 483 3.055458 TCTTTCCACATTGTCAGGCGATA 60.055 43.478 0.00 0.00 0.00 2.92
588 595 5.635700 GTGATCAAATAGATTAGCCGGTCTC 59.364 44.000 1.90 0.00 37.00 3.36
589 596 4.602340 TCAAATAGATTAGCCGGTCTCC 57.398 45.455 1.90 0.00 0.00 3.71
606 613 6.598064 CCGGTCTCCTTTGACAAATTATAGTT 59.402 38.462 0.05 0.00 38.61 2.24
625 632 3.753272 AGTTATACGGAATGCATCATGGC 59.247 43.478 0.00 0.00 0.00 4.40
639 646 0.821517 CATGGCTGTGTGGATGCATT 59.178 50.000 0.00 0.00 0.00 3.56
650 657 0.179018 GGATGCATTAAGGACCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
676 683 5.637810 TGTATTGAGAAACGTTTGGCTCTAG 59.362 40.000 20.10 0.00 0.00 2.43
715 2774 8.259049 TGTTATGGAATACAACTCCTTTTACG 57.741 34.615 0.00 0.00 33.77 3.18
855 3990 2.712539 CACGCACGGCAAGACAAA 59.287 55.556 0.00 0.00 0.00 2.83
890 4025 2.837591 TGGACCGATGATCAAAGGAGAA 59.162 45.455 22.02 7.55 0.00 2.87
986 4147 2.285368 ATCCCAGTTCCCAGCCGA 60.285 61.111 0.00 0.00 0.00 5.54
988 4149 4.785453 CCCAGTTCCCAGCCGAGC 62.785 72.222 0.00 0.00 0.00 5.03
1284 4452 2.185608 GCCTGGCTCTCCGTCTTC 59.814 66.667 12.43 0.00 34.14 2.87
1374 4542 1.447838 CCACGCATGAAGTACGGCT 60.448 57.895 0.00 0.00 0.00 5.52
1375 4543 1.421410 CCACGCATGAAGTACGGCTC 61.421 60.000 0.00 0.00 0.00 4.70
1376 4544 1.516386 ACGCATGAAGTACGGCTCG 60.516 57.895 0.00 0.00 0.00 5.03
1377 4545 1.516386 CGCATGAAGTACGGCTCGT 60.516 57.895 0.00 5.58 44.35 4.18
1378 4546 1.076533 CGCATGAAGTACGGCTCGTT 61.077 55.000 0.00 0.00 41.54 3.85
1379 4547 1.076332 GCATGAAGTACGGCTCGTTT 58.924 50.000 0.00 0.00 41.54 3.60
1380 4548 1.201921 GCATGAAGTACGGCTCGTTTG 60.202 52.381 0.00 0.00 41.54 2.93
1381 4549 1.393539 CATGAAGTACGGCTCGTTTGG 59.606 52.381 5.57 0.00 41.54 3.28
1382 4550 0.320073 TGAAGTACGGCTCGTTTGGG 60.320 55.000 5.57 0.00 41.54 4.12
1383 4551 1.632948 GAAGTACGGCTCGTTTGGGC 61.633 60.000 5.57 0.00 41.54 5.36
1384 4552 2.047560 GTACGGCTCGTTTGGGCT 60.048 61.111 5.57 0.00 41.54 5.19
1385 4553 2.047655 TACGGCTCGTTTGGGCTG 60.048 61.111 5.57 0.00 41.54 4.85
1558 4731 6.638468 GGATGGTATGAATTTGAGCGAATTTC 59.362 38.462 0.00 0.00 29.75 2.17
1593 4766 3.772572 TCCTTTCCTGATGATGGTAACGA 59.227 43.478 0.00 0.00 42.51 3.85
1642 4820 7.539710 CCATAATTGCCGTCATTATTCTCAATG 59.460 37.037 0.00 0.00 37.27 2.82
1751 4929 2.270352 ACTTTCCACGCTTGATCCAA 57.730 45.000 0.00 0.00 0.00 3.53
1794 4972 2.067091 ATTTCGCGCTCCGTCCGATA 62.067 55.000 5.56 0.00 38.35 2.92
1810 4988 3.255888 TCCGATAGTTTCTCTATGCGCAT 59.744 43.478 28.23 28.23 39.22 4.73
1841 5020 3.009723 CGTAAGCCTGGTCACAATGAAT 58.990 45.455 0.00 0.00 0.00 2.57
1900 5427 3.837213 ATCATTTTTGCTGAGGTGACG 57.163 42.857 0.00 0.00 0.00 4.35
1915 5442 1.128692 GTGACGCACCATTAAGTGAGC 59.871 52.381 0.00 0.00 40.76 4.26
1956 6323 9.159364 GTATCATGATATGTGTAATGCATGACT 57.841 33.333 18.18 0.00 43.10 3.41
2111 6486 0.599060 TGTGACCAGCGTATTCGTGA 59.401 50.000 0.00 0.00 39.49 4.35
2112 6487 1.203758 TGTGACCAGCGTATTCGTGAT 59.796 47.619 0.00 0.00 39.49 3.06
2117 6492 0.846401 CAGCGTATTCGTGATGTCCG 59.154 55.000 0.00 0.00 39.49 4.79
2118 6493 0.454600 AGCGTATTCGTGATGTCCGT 59.545 50.000 0.00 0.00 39.49 4.69
2120 6495 1.474017 CGTATTCGTGATGTCCGTCC 58.526 55.000 0.00 0.00 0.00 4.79
2126 6501 1.517257 GTGATGTCCGTCCTCTGCG 60.517 63.158 0.00 0.00 0.00 5.18
2128 6503 1.037579 TGATGTCCGTCCTCTGCGAT 61.038 55.000 0.00 0.00 0.00 4.58
2153 6528 0.843309 TGGGAGTTCTCACCTTTGCA 59.157 50.000 0.00 0.00 0.00 4.08
2171 6546 1.338200 GCATGAACCGAGTGTCCTTCT 60.338 52.381 0.00 0.00 0.00 2.85
2174 6549 0.680061 GAACCGAGTGTCCTTCTGGT 59.320 55.000 0.00 0.00 34.23 4.00
2195 6570 2.977456 GCATGCACGGTGACCACA 60.977 61.111 14.21 0.00 0.00 4.17
2216 6591 4.402793 ACAGAGGTATCATCACACAGTACC 59.597 45.833 0.00 0.00 36.02 3.34
2233 6608 1.080025 CCTTCGTGTCCCCTTCGAC 60.080 63.158 0.00 0.00 33.38 4.20
2234 6609 1.663739 CTTCGTGTCCCCTTCGACA 59.336 57.895 0.00 0.00 40.44 4.35
2238 6613 1.746517 GTGTCCCCTTCGACAGTGT 59.253 57.895 0.00 0.00 43.26 3.55
2278 6653 5.639082 ACGCTTCATCATATTCGAATATGCA 59.361 36.000 36.94 28.87 44.96 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 94 8.737175 ACATGGATATGCATATTGTTCAATCTC 58.263 33.333 20.00 4.56 37.85 2.75
107 112 4.822685 AATTGCAAGCCAAACATGGATA 57.177 36.364 4.94 0.00 36.92 2.59
230 236 0.319555 GACAGGCGCTAGAACACACA 60.320 55.000 7.64 0.00 0.00 3.72
270 276 8.242729 TCGATTCATACCATGCTATGATCTAT 57.757 34.615 10.78 3.28 33.93 1.98
302 308 4.023792 GCCGCAAATATGATTGTCTCATCA 60.024 41.667 0.00 0.00 43.70 3.07
332 338 7.070322 AGGGCTTCATTGCAATAGAACATAAAT 59.930 33.333 12.53 0.00 34.04 1.40
425 432 7.154656 TCCATGGAGTTCGATTATACAATGAG 58.845 38.462 11.44 0.00 0.00 2.90
444 451 0.329261 TGTGGAAAGAGCCTCCATGG 59.671 55.000 4.97 4.97 44.69 3.66
476 483 2.609737 CGTAGGCCAAACGAGAAAGTCT 60.610 50.000 22.20 0.00 42.90 3.24
606 613 3.244526 ACAGCCATGATGCATTCCGTATA 60.245 43.478 0.00 0.00 0.00 1.47
625 632 2.684881 GGTCCTTAATGCATCCACACAG 59.315 50.000 0.00 0.00 0.00 3.66
639 646 4.476297 TCTCAATACATAGCGGGTCCTTA 58.524 43.478 0.00 0.00 0.00 2.69
650 657 6.170506 AGAGCCAAACGTTTCTCAATACATA 58.829 36.000 23.80 0.00 0.00 2.29
852 3987 0.109781 CCAAGTTGATCGGCGGTTTG 60.110 55.000 7.21 0.42 0.00 2.93
855 3990 1.375523 GTCCAAGTTGATCGGCGGT 60.376 57.895 7.21 0.00 0.00 5.68
961 4122 1.272554 GGGAACTGGGATCGGGAAGT 61.273 60.000 0.00 0.00 0.00 3.01
994 4155 2.364186 TGCAGGCTCCATCGAGGA 60.364 61.111 0.00 0.67 46.75 3.71
1374 4542 0.250684 TCAAGATGCAGCCCAAACGA 60.251 50.000 0.00 0.00 0.00 3.85
1375 4543 0.597568 TTCAAGATGCAGCCCAAACG 59.402 50.000 0.00 0.00 0.00 3.60
1376 4544 3.193267 TGTATTCAAGATGCAGCCCAAAC 59.807 43.478 0.00 0.00 0.00 2.93
1377 4545 3.429492 TGTATTCAAGATGCAGCCCAAA 58.571 40.909 0.00 0.00 0.00 3.28
1378 4546 3.084536 TGTATTCAAGATGCAGCCCAA 57.915 42.857 0.00 0.00 0.00 4.12
1379 4547 2.804986 TGTATTCAAGATGCAGCCCA 57.195 45.000 0.00 0.00 0.00 5.36
1380 4548 4.580167 TGTAATGTATTCAAGATGCAGCCC 59.420 41.667 0.00 0.00 0.00 5.19
1381 4549 5.756195 TGTAATGTATTCAAGATGCAGCC 57.244 39.130 0.00 0.00 0.00 4.85
1382 4550 6.147581 CCATGTAATGTATTCAAGATGCAGC 58.852 40.000 0.00 0.00 44.81 5.25
1383 4551 7.136772 CACCATGTAATGTATTCAAGATGCAG 58.863 38.462 0.00 0.00 44.81 4.41
1384 4552 6.459985 GCACCATGTAATGTATTCAAGATGCA 60.460 38.462 0.00 0.00 44.81 3.96
1385 4553 5.916883 GCACCATGTAATGTATTCAAGATGC 59.083 40.000 0.00 0.00 44.81 3.91
1386 4554 7.268199 AGCACCATGTAATGTATTCAAGATG 57.732 36.000 0.00 0.00 44.81 2.90
1593 4766 4.718961 ACCTTCATGTTGCTAGTCTGTTT 58.281 39.130 0.00 0.00 0.00 2.83
1642 4820 1.136336 CGCGGTAGAAAAAGACAGTGC 60.136 52.381 0.00 0.00 0.00 4.40
1794 4972 2.464865 GTCGATGCGCATAGAGAAACT 58.535 47.619 29.96 3.45 0.00 2.66
1900 5427 3.753272 TCTCTTTGCTCACTTAATGGTGC 59.247 43.478 0.00 0.00 37.16 5.01
1910 5437 8.709386 TGATACTTAATCTTCTCTTTGCTCAC 57.291 34.615 0.00 0.00 35.45 3.51
1946 6313 8.783833 AGCGATCTTATTTATAGTCATGCATT 57.216 30.769 0.00 0.00 0.00 3.56
2075 6448 6.112734 TGGTCACAATCAAGTGTCATATACC 58.887 40.000 0.00 0.00 40.37 2.73
2084 6457 1.229428 ACGCTGGTCACAATCAAGTG 58.771 50.000 0.00 0.00 40.85 3.16
2089 6462 2.029244 CACGAATACGCTGGTCACAATC 59.971 50.000 0.00 0.00 43.96 2.67
2111 6486 0.179100 CAATCGCAGAGGACGGACAT 60.179 55.000 0.00 0.00 43.63 3.06
2112 6487 1.215382 CAATCGCAGAGGACGGACA 59.785 57.895 0.00 0.00 43.63 4.02
2117 6492 1.493950 CCATCGCAATCGCAGAGGAC 61.494 60.000 0.00 0.00 43.63 3.85
2118 6493 1.227350 CCATCGCAATCGCAGAGGA 60.227 57.895 0.00 0.00 43.63 3.71
2120 6495 1.220169 CTCCCATCGCAATCGCAGAG 61.220 60.000 0.00 0.00 43.63 3.35
2126 6501 1.936547 GTGAGAACTCCCATCGCAATC 59.063 52.381 0.00 0.00 0.00 2.67
2128 6503 0.036388 GGTGAGAACTCCCATCGCAA 60.036 55.000 0.00 0.00 0.00 4.85
2153 6528 1.276421 CCAGAAGGACACTCGGTTCAT 59.724 52.381 0.00 0.00 36.89 2.57
2195 6570 4.873010 AGGTACTGTGTGATGATACCTCT 58.127 43.478 0.00 0.00 41.45 3.69
2216 6591 0.388649 CTGTCGAAGGGGACACGAAG 60.389 60.000 0.00 0.00 41.76 3.79
2292 6667 0.896923 TTGGCCCTGATTCATGCAAC 59.103 50.000 0.00 0.00 0.00 4.17
2293 6668 1.551430 CTTTGGCCCTGATTCATGCAA 59.449 47.619 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.