Multiple sequence alignment - TraesCS6B01G241900

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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 TraesCS6B01G241900 chr6B 100.000 2264 0 0 1 2264 425587416 425589679 0 4181
1 TraesCS6B01G241900 chr6B 96.570 933 31 1 1332 2264 417720056 417719125 0 1544
2 TraesCS6B01G241900 chr7B 95.662 1337 49 5 1 1335 34282301 34280972 0 2139
3 TraesCS6B01G241900 chr7B 96.563 931 32 0 1334 2264 137834137 137835067 0 1543
4 TraesCS6B01G241900 chr5D 95.160 1343 48 8 1 1335 387840676 387839343 0 2104
5 TraesCS6B01G241900 chr4A 94.577 1346 55 9 1 1335 737660736 737662074 0 2065
6 TraesCS6B01G241900 chr2A 94.619 1338 60 10 1 1335 372742769 372744097 0 2061
7 TraesCS6B01G241900 chr1B 94.407 1341 61 7 1 1333 623645163 623646497 0 2049
8 TraesCS6B01G241900 chr1B 96.774 930 29 1 1335 2264 470915246 470916174 0 1550
9 TraesCS6B01G241900 chr1B 96.663 929 30 1 1336 2264 480377172 480378099 0 1543
10 TraesCS6B01G241900 chr5B 94.007 1335 70 10 1 1333 578837545 578836219 0 2013
11 TraesCS6B01G241900 chr5B 93.333 1335 80 7 1 1333 641182743 641181416 0 1964
12 TraesCS6B01G241900 chr5B 96.667 930 30 1 1335 2264 337390166 337389238 0 1544
13 TraesCS6B01G241900 chr3A 93.862 1336 72 6 1 1333 44774219 44772891 0 2004
14 TraesCS6B01G241900 chr7A 93.304 1344 62 20 1 1335 124062130 124060806 0 1958
15 TraesCS6B01G241900 chr2B 96.771 929 28 2 1336 2264 475259842 475260768 0 1548
16 TraesCS6B01G241900 chr2B 96.563 931 31 1 1334 2264 178179024 178178095 0 1541
17 TraesCS6B01G241900 chrUn 96.559 930 32 0 1335 2264 290240094 290239165 0 1541
18 TraesCS6B01G241900 chr4B 96.348 931 32 2 1336 2264 179999613 179998683 0 1530


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 TraesCS6B01G241900 chr6B 425587416 425589679 2263 False 4181 4181 100.000 1 2264 1 chr6B.!!$F1 2263
1 TraesCS6B01G241900 chr6B 417719125 417720056 931 True 1544 1544 96.570 1332 2264 1 chr6B.!!$R1 932
2 TraesCS6B01G241900 chr7B 34280972 34282301 1329 True 2139 2139 95.662 1 1335 1 chr7B.!!$R1 1334
3 TraesCS6B01G241900 chr7B 137834137 137835067 930 False 1543 1543 96.563 1334 2264 1 chr7B.!!$F1 930
4 TraesCS6B01G241900 chr5D 387839343 387840676 1333 True 2104 2104 95.160 1 1335 1 chr5D.!!$R1 1334
5 TraesCS6B01G241900 chr4A 737660736 737662074 1338 False 2065 2065 94.577 1 1335 1 chr4A.!!$F1 1334
6 TraesCS6B01G241900 chr2A 372742769 372744097 1328 False 2061 2061 94.619 1 1335 1 chr2A.!!$F1 1334
7 TraesCS6B01G241900 chr1B 623645163 623646497 1334 False 2049 2049 94.407 1 1333 1 chr1B.!!$F3 1332
8 TraesCS6B01G241900 chr1B 470915246 470916174 928 False 1550 1550 96.774 1335 2264 1 chr1B.!!$F1 929
9 TraesCS6B01G241900 chr1B 480377172 480378099 927 False 1543 1543 96.663 1336 2264 1 chr1B.!!$F2 928
10 TraesCS6B01G241900 chr5B 578836219 578837545 1326 True 2013 2013 94.007 1 1333 1 chr5B.!!$R2 1332
11 TraesCS6B01G241900 chr5B 641181416 641182743 1327 True 1964 1964 93.333 1 1333 1 chr5B.!!$R3 1332
12 TraesCS6B01G241900 chr5B 337389238 337390166 928 True 1544 1544 96.667 1335 2264 1 chr5B.!!$R1 929
13 TraesCS6B01G241900 chr3A 44772891 44774219 1328 True 2004 2004 93.862 1 1333 1 chr3A.!!$R1 1332
14 TraesCS6B01G241900 chr7A 124060806 124062130 1324 True 1958 1958 93.304 1 1335 1 chr7A.!!$R1 1334
15 TraesCS6B01G241900 chr2B 475259842 475260768 926 False 1548 1548 96.771 1336 2264 1 chr2B.!!$F1 928
16 TraesCS6B01G241900 chr2B 178178095 178179024 929 True 1541 1541 96.563 1334 2264 1 chr2B.!!$R1 930
17 TraesCS6B01G241900 chrUn 290239165 290240094 929 True 1541 1541 96.559 1335 2264 1 chrUn.!!$R1 929
18 TraesCS6B01G241900 chr4B 179998683 179999613 930 True 1530 1530 96.348 1336 2264 1 chr4B.!!$R1 928

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
662 675 0.90158 GGTGGTGGTCGTAGAGGGAA 60.902 60.0 0.0 0.0 36.95 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1542 0.109458 CGGTCGGATCGTGAAGACAA 60.109 55.0 1.71 0.0 35.49 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
103 105 2.676342 ACGAGACGGTTTTCAATATGGC 59.324 45.455 0.00 0.00 0.00 4.40
392 394 2.907042 ACCAAGGGTAGAAGGAGAACTG 59.093 50.000 0.00 0.00 32.11 3.16
423 425 2.057922 GGGTGATATGGATGACCTGGT 58.942 52.381 0.00 0.00 39.21 4.00
546 550 5.294734 ACATGCAAGAAAGGAAAACCAAT 57.705 34.783 0.00 0.00 0.00 3.16
551 555 8.619546 CATGCAAGAAAGGAAAACCAATAAAAA 58.380 29.630 0.00 0.00 0.00 1.94
572 576 1.002792 GAAAACAAGTCGTGGAGGTGC 60.003 52.381 0.00 0.00 0.00 5.01
662 675 0.901580 GGTGGTGGTCGTAGAGGGAA 60.902 60.000 0.00 0.00 36.95 3.97
706 719 1.629043 TCGTAGAGGGAGCACAAGTT 58.371 50.000 0.00 0.00 0.00 2.66
721 734 4.489810 CACAAGTTCTAGAGGTGCTAGTG 58.510 47.826 0.00 0.00 45.60 2.74
722 735 4.021894 CACAAGTTCTAGAGGTGCTAGTGT 60.022 45.833 0.00 0.00 45.60 3.55
723 736 4.589374 ACAAGTTCTAGAGGTGCTAGTGTT 59.411 41.667 0.00 0.00 45.60 3.32
724 737 5.070580 ACAAGTTCTAGAGGTGCTAGTGTTT 59.929 40.000 0.00 0.00 45.60 2.83
725 738 5.140747 AGTTCTAGAGGTGCTAGTGTTTG 57.859 43.478 0.00 0.00 45.60 2.93
726 739 4.589374 AGTTCTAGAGGTGCTAGTGTTTGT 59.411 41.667 0.00 0.00 45.60 2.83
727 740 5.773680 AGTTCTAGAGGTGCTAGTGTTTGTA 59.226 40.000 0.00 0.00 45.60 2.41
731 744 3.511934 AGAGGTGCTAGTGTTTGTAGAGG 59.488 47.826 0.00 0.00 0.00 3.69
735 748 3.258622 GTGCTAGTGTTTGTAGAGGGAGT 59.741 47.826 0.00 0.00 0.00 3.85
752 765 2.826725 GGAGTACAAGTGCTAGAGGTGT 59.173 50.000 0.00 0.00 0.00 4.16
773 792 1.160329 GGTCGAGCAAGCACAAGTGT 61.160 55.000 10.30 0.00 0.00 3.55
785 804 2.484770 GCACAAGTGTTAGAGGTGGTGA 60.485 50.000 1.79 0.00 0.00 4.02
852 907 6.520021 AGAGGAATGGTTGATAATGGATCA 57.480 37.500 0.00 0.00 43.11 2.92
869 924 2.192664 TCAGCCTTCGGTTATTTGCA 57.807 45.000 0.00 0.00 0.00 4.08
1105 1166 3.197927 AGGAGAAGGAGAAGGATGTGT 57.802 47.619 0.00 0.00 0.00 3.72
1210 1271 4.756135 GGTTTTTCGTGTGTCCCAACTATA 59.244 41.667 0.00 0.00 0.00 1.31
1221 1282 3.741344 GTCCCAACTATACACATGATCGC 59.259 47.826 0.00 0.00 0.00 4.58
1393 1454 3.541996 ACACGCAAGATCATGGTGATA 57.458 42.857 19.56 0.00 37.20 2.15
1481 1542 0.038892 ACGCGGTTGATGTAGTCGTT 60.039 50.000 12.47 0.00 0.00 3.85
1482 1543 1.065358 CGCGGTTGATGTAGTCGTTT 58.935 50.000 0.00 0.00 0.00 3.60
1507 1568 0.179121 CACGATCCGACCGATCCAAA 60.179 55.000 0.00 0.00 44.07 3.28
1570 1631 3.758133 ATGACGATCCCCGGGCTCT 62.758 63.158 17.73 0.00 43.93 4.09
1641 1702 1.270826 CGATGATGATGCTCTACCGGT 59.729 52.381 13.98 13.98 0.00 5.28
1689 1750 4.158025 ACGATATGACCGAGGTGGAATATC 59.842 45.833 0.00 8.80 42.00 1.63
1726 1787 2.905075 CACACGGCTAAGGAATGATCA 58.095 47.619 0.00 0.00 0.00 2.92
1777 1843 2.262637 CCCTGCCCCCGTATATAAAGA 58.737 52.381 0.00 0.00 0.00 2.52
1873 1939 1.290134 AGGATTCCACCTCCCTTGTC 58.710 55.000 5.29 0.00 34.98 3.18
2010 2076 1.809133 TCCCGTATGGCCCAATAAGA 58.191 50.000 0.00 0.00 0.00 2.10
2047 2113 1.402968 CGAATTCCCGTAACTCTCCGA 59.597 52.381 0.00 0.00 0.00 4.55
2243 2309 0.318869 TCGAAACCTTAAGCGTGCGA 60.319 50.000 13.27 13.27 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 1.210931 CACCTCAAATGCAGCACCG 59.789 57.895 0.00 0.0 0.00 4.94
392 394 2.370189 CCATATCACCCCTGAACCTCTC 59.630 54.545 0.00 0.0 0.00 3.20
423 425 3.760738 TGTTTCATGCCAGTGTATCCAA 58.239 40.909 0.00 0.0 0.00 3.53
504 507 1.021390 CCGCTCATTGTGTCCACCTC 61.021 60.000 0.00 0.0 0.00 3.85
508 511 0.324614 ATGTCCGCTCATTGTGTCCA 59.675 50.000 0.00 0.0 0.00 4.02
546 550 5.648960 ACCTCCACGACTTGTTTTCTTTTTA 59.351 36.000 0.00 0.0 0.00 1.52
551 555 2.561569 CACCTCCACGACTTGTTTTCT 58.438 47.619 0.00 0.0 0.00 2.52
662 675 1.051812 AGCACCTCTAGCACTTGTGT 58.948 50.000 2.61 0.0 0.00 3.72
706 719 5.567430 TCTACAAACACTAGCACCTCTAGA 58.433 41.667 6.02 0.0 46.12 2.43
716 729 6.208994 ACTTGTACTCCCTCTACAAACACTAG 59.791 42.308 0.00 0.0 34.46 2.57
718 731 4.900054 ACTTGTACTCCCTCTACAAACACT 59.100 41.667 0.00 0.0 34.46 3.55
721 734 3.995048 GCACTTGTACTCCCTCTACAAAC 59.005 47.826 0.00 0.0 34.46 2.93
722 735 3.901844 AGCACTTGTACTCCCTCTACAAA 59.098 43.478 0.00 0.0 34.46 2.83
723 736 3.507411 AGCACTTGTACTCCCTCTACAA 58.493 45.455 0.00 0.0 33.88 2.41
724 737 3.170991 AGCACTTGTACTCCCTCTACA 57.829 47.619 0.00 0.0 0.00 2.74
725 738 4.525024 TCTAGCACTTGTACTCCCTCTAC 58.475 47.826 0.00 0.0 0.00 2.59
726 739 4.385421 CCTCTAGCACTTGTACTCCCTCTA 60.385 50.000 0.00 0.0 0.00 2.43
727 740 3.626222 CCTCTAGCACTTGTACTCCCTCT 60.626 52.174 0.00 0.0 0.00 3.69
731 744 2.826725 ACACCTCTAGCACTTGTACTCC 59.173 50.000 0.00 0.0 0.00 3.85
735 748 2.969950 ACCAACACCTCTAGCACTTGTA 59.030 45.455 0.00 0.0 0.00 2.41
752 765 0.463654 ACTTGTGCTTGCTCGACCAA 60.464 50.000 0.00 0.0 0.00 3.67
773 792 1.933021 ACGACCATCACCACCTCTAA 58.067 50.000 0.00 0.0 0.00 2.10
785 804 1.557099 TGTGCTTCCTCTACGACCAT 58.443 50.000 0.00 0.0 0.00 3.55
1105 1166 4.918592 CCAACATGGTGGTGTGGA 57.081 55.556 22.48 0.0 31.91 4.02
1210 1271 1.815421 GCCTTCGGCGATCATGTGT 60.815 57.895 11.76 0.0 39.62 3.72
1221 1282 1.392589 ATGCATTAGTTGGCCTTCGG 58.607 50.000 3.32 0.0 0.00 4.30
1312 1373 8.487313 ACAGCGACTACATAAAAATCATGTTA 57.513 30.769 0.00 0.0 37.74 2.41
1393 1454 1.211457 CTCCCCTCTTGTTGCTATGCT 59.789 52.381 0.00 0.0 0.00 3.79
1481 1542 0.109458 CGGTCGGATCGTGAAGACAA 60.109 55.000 1.71 0.0 35.49 3.18
1482 1543 0.956902 TCGGTCGGATCGTGAAGACA 60.957 55.000 10.85 0.0 35.49 3.41
1507 1568 1.398390 GAGGTGTCGTACGTTCGGTAT 59.602 52.381 16.05 0.0 32.74 2.73
1570 1631 0.677731 CCCGAAGCTTTGCTGGATCA 60.678 55.000 8.32 0.0 39.62 2.92
1726 1787 5.707298 CCCATGACACAAAAGTTGATCTACT 59.293 40.000 3.80 3.8 0.00 2.57
1873 1939 1.757699 CTTTCCCCTTCTCCTACTCCG 59.242 57.143 0.00 0.0 0.00 4.63
2010 2076 1.911766 CGCCGGGGAGTATATGGGT 60.912 63.158 14.46 0.0 0.00 4.51
2047 2113 5.756833 GTGATTCGGGTATTTTTCGGAGTAT 59.243 40.000 0.00 0.0 0.00 2.12


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

AutoCloner maintained by Alex Coulton.