Multiple sequence alignment - TraesCS6B01G150500

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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 TraesCS6B01G150500 chr6B 100.000 2318 0 0 1 2318 151387192 151384875 0 4281
1 TraesCS6B01G150500 chr7B 96.134 1345 48 4 1 1343 192798492 192797150 0 2193
2 TraesCS6B01G150500 chr7B 91.443 1344 114 1 1 1343 552700430 552699087 0 1844
3 TraesCS6B01G150500 chr7B 91.026 1326 118 1 1 1325 552747419 552746094 0 1788
4 TraesCS6B01G150500 chr1D 94.118 1343 77 2 1 1342 475891461 475892802 0 2041
5 TraesCS6B01G150500 chr7D 93.894 1343 80 2 1 1342 615912062 615910721 0 2025
6 TraesCS6B01G150500 chr5A 92.852 1343 94 2 1 1342 71139705 71141046 0 1947
7 TraesCS6B01G150500 chr5B 92.628 1343 96 2 1 1342 348576110 348574770 0 1929
8 TraesCS6B01G150500 chr4A 88.039 1346 156 5 1 1343 669052074 669050731 0 1589
9 TraesCS6B01G150500 chr4A 87.509 1345 162 4 1 1343 676915479 676914139 0 1548
10 TraesCS6B01G150500 chr6D 92.432 991 45 18 1342 2318 78766992 78766018 0 1387


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 TraesCS6B01G150500 chr6B 151384875 151387192 2317 True 4281 4281 100.000 1 2318 1 chr6B.!!$R1 2317
1 TraesCS6B01G150500 chr7B 192797150 192798492 1342 True 2193 2193 96.134 1 1343 1 chr7B.!!$R1 1342
2 TraesCS6B01G150500 chr7B 552699087 552700430 1343 True 1844 1844 91.443 1 1343 1 chr7B.!!$R2 1342
3 TraesCS6B01G150500 chr7B 552746094 552747419 1325 True 1788 1788 91.026 1 1325 1 chr7B.!!$R3 1324
4 TraesCS6B01G150500 chr1D 475891461 475892802 1341 False 2041 2041 94.118 1 1342 1 chr1D.!!$F1 1341
5 TraesCS6B01G150500 chr7D 615910721 615912062 1341 True 2025 2025 93.894 1 1342 1 chr7D.!!$R1 1341
6 TraesCS6B01G150500 chr5A 71139705 71141046 1341 False 1947 1947 92.852 1 1342 1 chr5A.!!$F1 1341
7 TraesCS6B01G150500 chr5B 348574770 348576110 1340 True 1929 1929 92.628 1 1342 1 chr5B.!!$R1 1341
8 TraesCS6B01G150500 chr4A 669050731 669052074 1343 True 1589 1589 88.039 1 1343 1 chr4A.!!$R1 1342
9 TraesCS6B01G150500 chr4A 676914139 676915479 1340 True 1548 1548 87.509 1 1343 1 chr4A.!!$R2 1342
10 TraesCS6B01G150500 chr6D 78766018 78766992 974 True 1387 1387 92.432 1342 2318 1 chr6D.!!$R1 976

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
659 663 0.522705 CGCAATGAGCTGACACATGC 60.523 55.0 0.0 0.0 42.61 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1520 0.43883 GCGTGATCGGTTGTCTTGTC 59.561 55.0 0.0 0.0 37.56 3.18 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
52 53 0.738975 GCCGCTTCAATAGGGTTTCC 59.261 55.000 0.00 0.00 35.13 3.13
252 253 2.096980 CGCATGATCAGAATGTTGCAGT 59.903 45.455 15.05 0.00 37.40 4.40
468 472 5.279156 GGAAGACTCATTTCATGCTTTGGTT 60.279 40.000 0.00 0.00 0.00 3.67
659 663 0.522705 CGCAATGAGCTGACACATGC 60.523 55.000 0.00 0.00 42.61 4.06
849 853 2.030562 CCGTGCCAAGGACGACTT 59.969 61.111 10.32 0.00 39.21 3.01
1129 1133 3.585862 GCTTACGGACAGATTGTCTTGA 58.414 45.455 8.89 0.00 46.19 3.02
1276 1280 1.481871 GGTTCCACCCTGTATCGAGA 58.518 55.000 0.00 0.00 30.04 4.04
1361 1365 4.755266 AAATCACATACTTAGCGAGGGT 57.245 40.909 0.00 0.00 0.00 4.34
1366 1370 2.963101 ACATACTTAGCGAGGGTGCATA 59.037 45.455 0.00 0.00 37.31 3.14
1367 1371 3.578716 ACATACTTAGCGAGGGTGCATAT 59.421 43.478 0.00 0.00 37.31 1.78
1368 1372 2.821991 ACTTAGCGAGGGTGCATATC 57.178 50.000 0.00 0.00 37.31 1.63
1369 1373 2.039418 ACTTAGCGAGGGTGCATATCA 58.961 47.619 0.00 0.00 37.31 2.15
1382 1386 4.024556 GGTGCATATCATGAAGAAGTTCGG 60.025 45.833 0.00 0.00 35.17 4.30
1387 1391 6.347240 GCATATCATGAAGAAGTTCGGATCAC 60.347 42.308 0.00 0.00 35.17 3.06
1400 1409 2.695666 TCGGATCACATTCTTCTCTCCC 59.304 50.000 0.00 0.00 0.00 4.30
1414 1423 3.947132 CTCCCACGCAGCCAGACAG 62.947 68.421 0.00 0.00 0.00 3.51
1416 1425 2.031012 CCACGCAGCCAGACAGAA 59.969 61.111 0.00 0.00 0.00 3.02
1418 1427 1.571460 CACGCAGCCAGACAGAAAC 59.429 57.895 0.00 0.00 0.00 2.78
1419 1428 1.146041 ACGCAGCCAGACAGAAACA 59.854 52.632 0.00 0.00 0.00 2.83
1420 1429 1.160329 ACGCAGCCAGACAGAAACAC 61.160 55.000 0.00 0.00 0.00 3.32
1447 1457 2.364324 AGCACTAGAGTTTGAACGGACA 59.636 45.455 0.00 0.00 0.00 4.02
1510 1520 4.081406 TCCATTTGGGTCATCAAGTTCAG 58.919 43.478 0.00 0.00 38.11 3.02
1522 1532 3.194861 TCAAGTTCAGACAAGACAACCG 58.805 45.455 0.00 0.00 0.00 4.44
1534 1544 1.135373 AGACAACCGATCACGCACTAG 60.135 52.381 0.00 0.00 38.29 2.57
1545 1555 4.991153 TCACGCACTAGAGATTCTTGAT 57.009 40.909 0.00 0.00 0.00 2.57
1589 1599 7.229907 GTCACTGTTCTTTATAAAAGTTGGGGA 59.770 37.037 0.00 0.00 0.00 4.81
1592 1602 9.154632 ACTGTTCTTTATAAAAGTTGGGGAAAT 57.845 29.630 0.00 0.00 0.00 2.17
1619 1634 8.846423 ATATCCTTAGTCCCTCGATTATGAAT 57.154 34.615 0.00 0.00 0.00 2.57
1621 1636 7.704578 TCCTTAGTCCCTCGATTATGAATAG 57.295 40.000 0.00 0.00 0.00 1.73
1640 1655 6.097554 TGAATAGGTCTTCAATCTGGTCTCTC 59.902 42.308 0.00 0.00 32.35 3.20
1655 1670 2.753452 GTCTCTCGATTCCAGTACCACA 59.247 50.000 0.00 0.00 0.00 4.17
1656 1671 3.017442 TCTCTCGATTCCAGTACCACAG 58.983 50.000 0.00 0.00 0.00 3.66
1657 1672 1.476891 TCTCGATTCCAGTACCACAGC 59.523 52.381 0.00 0.00 0.00 4.40
1658 1673 1.204704 CTCGATTCCAGTACCACAGCA 59.795 52.381 0.00 0.00 0.00 4.41
1659 1674 1.067142 TCGATTCCAGTACCACAGCAC 60.067 52.381 0.00 0.00 0.00 4.40
1740 1755 4.276926 AGAGAGTGGTTTTGACAATCAAGC 59.723 41.667 0.00 0.00 37.70 4.01
1832 1847 9.491675 GGGGAAATTAAATTAAACGGAGAAAAA 57.508 29.630 0.00 0.00 0.00 1.94
1998 2014 9.634021 AACTTCCTTGGATATTAGATTTTCCTC 57.366 33.333 0.00 0.00 0.00 3.71
2299 2316 4.525874 TGTGTGAAATGCCAACCATCAATA 59.474 37.500 0.00 0.00 31.43 1.90
2302 2319 6.036300 GTGTGAAATGCCAACCATCAATATTG 59.964 38.462 9.29 9.29 31.43 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 0.378257 CGTTGCCATCCAGGAAATCG 59.622 55.000 0.00 0.00 37.23 3.34
80 81 2.895680 GCTGAGTCGATCCTGCCA 59.104 61.111 0.00 0.00 0.00 4.92
296 298 1.071699 CCTTCCAGACGAGGTTCCAAA 59.928 52.381 0.00 0.00 0.00 3.28
422 426 0.467384 CTCAATCCCACAGAGCCGAT 59.533 55.000 0.00 0.00 0.00 4.18
468 472 5.940192 AAATTCTCGCATGAGTACAAACA 57.060 34.783 0.00 0.00 43.09 2.83
659 663 0.320771 CACTGGTGGGACTTCCTTCG 60.321 60.000 0.00 0.00 36.20 3.79
1276 1280 1.212935 ACAGTCAAGAGGCCACAAGTT 59.787 47.619 5.01 0.00 0.00 2.66
1361 1365 5.022282 TCCGAACTTCTTCATGATATGCA 57.978 39.130 0.00 0.00 0.00 3.96
1366 1370 5.089970 TGTGATCCGAACTTCTTCATGAT 57.910 39.130 0.00 0.00 0.00 2.45
1367 1371 4.535526 TGTGATCCGAACTTCTTCATGA 57.464 40.909 0.00 0.00 0.00 3.07
1368 1372 5.583854 AGAATGTGATCCGAACTTCTTCATG 59.416 40.000 0.00 0.00 0.00 3.07
1369 1373 5.738909 AGAATGTGATCCGAACTTCTTCAT 58.261 37.500 0.00 0.00 0.00 2.57
1382 1386 3.452474 CGTGGGAGAGAAGAATGTGATC 58.548 50.000 0.00 0.00 0.00 2.92
1387 1391 1.649664 CTGCGTGGGAGAGAAGAATG 58.350 55.000 0.00 0.00 0.00 2.67
1400 1409 1.159713 TGTTTCTGTCTGGCTGCGTG 61.160 55.000 0.00 0.00 0.00 5.34
1414 1423 3.244249 ACTCTAGTGCTCCCTTGTGTTTC 60.244 47.826 0.00 0.00 0.00 2.78
1416 1425 2.330216 ACTCTAGTGCTCCCTTGTGTT 58.670 47.619 0.00 0.00 0.00 3.32
1418 1427 3.070018 CAAACTCTAGTGCTCCCTTGTG 58.930 50.000 0.00 0.00 0.00 3.33
1419 1428 2.972713 TCAAACTCTAGTGCTCCCTTGT 59.027 45.455 0.00 0.00 0.00 3.16
1420 1429 3.685139 TCAAACTCTAGTGCTCCCTTG 57.315 47.619 0.00 0.00 0.00 3.61
1447 1457 0.036010 ACGCCACTTGAGCTAGCAAT 60.036 50.000 18.83 0.00 0.00 3.56
1473 1483 1.435256 ATGGAGGGGGTATAGCACAC 58.565 55.000 6.50 0.00 0.00 3.82
1476 1486 1.780309 CCAAATGGAGGGGGTATAGCA 59.220 52.381 4.02 0.00 37.39 3.49
1510 1520 0.438830 GCGTGATCGGTTGTCTTGTC 59.561 55.000 0.00 0.00 37.56 3.18
1522 1532 4.926244 TCAAGAATCTCTAGTGCGTGATC 58.074 43.478 0.00 0.00 0.00 2.92
1583 1593 6.860480 AGGGACTAAGGATATAATTTCCCCAA 59.140 38.462 0.00 0.00 42.27 4.12
1592 1602 9.763837 TTCATAATCGAGGGACTAAGGATATAA 57.236 33.333 0.00 0.00 41.55 0.98
1594 1604 8.846423 ATTCATAATCGAGGGACTAAGGATAT 57.154 34.615 0.00 0.00 41.55 1.63
1595 1605 9.409918 CTATTCATAATCGAGGGACTAAGGATA 57.590 37.037 0.00 0.00 41.55 2.59
1596 1606 7.343316 CCTATTCATAATCGAGGGACTAAGGAT 59.657 40.741 0.00 0.00 41.55 3.24
1597 1607 6.663953 CCTATTCATAATCGAGGGACTAAGGA 59.336 42.308 0.00 0.00 41.55 3.36
1598 1608 6.437793 ACCTATTCATAATCGAGGGACTAAGG 59.562 42.308 0.00 0.00 41.55 2.69
1599 1609 7.394923 AGACCTATTCATAATCGAGGGACTAAG 59.605 40.741 0.00 0.00 41.55 2.18
1619 1634 3.948473 CGAGAGACCAGATTGAAGACCTA 59.052 47.826 0.00 0.00 0.00 3.08
1621 1636 2.755655 TCGAGAGACCAGATTGAAGACC 59.244 50.000 0.00 0.00 33.31 3.85
1640 1655 1.337728 TGTGCTGTGGTACTGGAATCG 60.338 52.381 0.00 0.00 0.00 3.34
1655 1670 3.260380 GCATCTCTATCACCCTATGTGCT 59.740 47.826 0.00 0.00 45.03 4.40
1656 1671 3.594134 GCATCTCTATCACCCTATGTGC 58.406 50.000 0.00 0.00 45.03 4.57
1657 1672 3.580022 TGGCATCTCTATCACCCTATGTG 59.420 47.826 0.00 0.00 46.88 3.21
1658 1673 3.580458 GTGGCATCTCTATCACCCTATGT 59.420 47.826 0.00 0.00 0.00 2.29
1659 1674 3.580022 TGTGGCATCTCTATCACCCTATG 59.420 47.826 0.00 0.00 0.00 2.23
1731 1746 1.180029 GACCATGGCTGCTTGATTGT 58.820 50.000 13.04 0.00 0.00 2.71
1740 1755 2.046988 TGCACGAGACCATGGCTG 60.047 61.111 13.04 1.20 0.00 4.85
1832 1847 3.829601 TGGCCTTTTCGGAATGTTTATGT 59.170 39.130 3.32 0.00 33.16 2.29
1918 1933 4.751600 CCACAAATTGAGGAAAAGAAAGCC 59.248 41.667 3.23 0.00 28.90 4.35
1995 2011 6.007703 TGTGGTAAAAATGGGAACTTAGAGG 58.992 40.000 0.00 0.00 0.00 3.69
1996 2012 7.703058 ATGTGGTAAAAATGGGAACTTAGAG 57.297 36.000 0.00 0.00 0.00 2.43
1997 2013 8.485578 AAATGTGGTAAAAATGGGAACTTAGA 57.514 30.769 0.00 0.00 0.00 2.10
1998 2014 9.554395 AAAAATGTGGTAAAAATGGGAACTTAG 57.446 29.630 0.00 0.00 0.00 2.18
2002 2018 9.278978 ACATAAAAATGTGGTAAAAATGGGAAC 57.721 29.630 0.00 0.00 32.79 3.62
2282 2299 7.166851 TGAAACAATATTGATGGTTGGCATTT 58.833 30.769 22.16 7.62 29.01 2.32
2290 2307 8.428063 TGAAAACCTTGAAACAATATTGATGGT 58.572 29.630 22.16 13.12 0.00 3.55


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

AutoCloner maintained by Alex Coulton.