Multiple sequence alignment - TraesCS7B01G125900

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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 TraesCS7B01G125900 chr7B 100.000 7039 0 0 1 7039 147706499 147713537 0 12999
1 TraesCS7B01G125900 chr3A 98.567 7048 86 13 1 7039 212705093 212712134 0 12441
2 TraesCS7B01G125900 chr2A 98.354 7049 100 14 1 7039 742784338 742791380 0 12360
3 TraesCS7B01G125900 chr2A 98.197 7045 111 15 1 7039 306618788 306625822 0 12292
4 TraesCS7B01G125900 chr7A 98.241 7048 110 13 1 7039 549409741 549402699 0 12316
5 TraesCS7B01G125900 chr3B 98.214 7056 98 17 1 7039 798422229 798429273 0 12307
6 TraesCS7B01G125900 chr3B 97.556 6056 100 23 1 6024 642076068 642082107 0 10320
7 TraesCS7B01G125900 chr6A 98.034 7071 100 21 1 7039 90756946 90764009 0 12251
8 TraesCS7B01G125900 chr5A 97.753 7077 113 20 1 7039 687730710 687723642 0 12146
9 TraesCS7B01G125900 chr1A 97.752 7074 110 25 1 7039 531033314 531040373 0 12137
10 TraesCS7B01G125900 chr1A 97.709 7070 114 24 1 7039 521305229 521312281 0 12115
11 TraesCS7B01G125900 chr1B 97.665 7067 116 24 1 7039 65600593 65593548 0 12091
12 TraesCS7B01G125900 chr6B 97.042 5949 110 36 1 5938 69680196 69686089 0 9950


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 TraesCS7B01G125900 chr7B 147706499 147713537 7038 False 12999 12999 100.000 1 7039 1 chr7B.!!$F1 7038
1 TraesCS7B01G125900 chr3A 212705093 212712134 7041 False 12441 12441 98.567 1 7039 1 chr3A.!!$F1 7038
2 TraesCS7B01G125900 chr2A 742784338 742791380 7042 False 12360 12360 98.354 1 7039 1 chr2A.!!$F2 7038
3 TraesCS7B01G125900 chr2A 306618788 306625822 7034 False 12292 12292 98.197 1 7039 1 chr2A.!!$F1 7038
4 TraesCS7B01G125900 chr7A 549402699 549409741 7042 True 12316 12316 98.241 1 7039 1 chr7A.!!$R1 7038
5 TraesCS7B01G125900 chr3B 798422229 798429273 7044 False 12307 12307 98.214 1 7039 1 chr3B.!!$F2 7038
6 TraesCS7B01G125900 chr3B 642076068 642082107 6039 False 10320 10320 97.556 1 6024 1 chr3B.!!$F1 6023
7 TraesCS7B01G125900 chr6A 90756946 90764009 7063 False 12251 12251 98.034 1 7039 1 chr6A.!!$F1 7038
8 TraesCS7B01G125900 chr5A 687723642 687730710 7068 True 12146 12146 97.753 1 7039 1 chr5A.!!$R1 7038
9 TraesCS7B01G125900 chr1A 531033314 531040373 7059 False 12137 12137 97.752 1 7039 1 chr1A.!!$F2 7038
10 TraesCS7B01G125900 chr1A 521305229 521312281 7052 False 12115 12115 97.709 1 7039 1 chr1A.!!$F1 7038
11 TraesCS7B01G125900 chr1B 65593548 65600593 7045 True 12091 12091 97.665 1 7039 1 chr1B.!!$R1 7038
12 TraesCS7B01G125900 chr6B 69680196 69686089 5893 False 9950 9950 97.042 1 5938 1 chr6B.!!$F1 5937

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
128 131 0.107263 TGAAACTGCAGACTGTGGCA 60.107 50.000 23.35 5.45 38.52 4.92 F
1011 1034 0.541392 TCAGCATAATGGCTCGTGGT 59.459 50.000 0.00 0.00 43.68 4.16 F
2388 2443 0.108585 ACCATCAGCGTTGTCAAGGT 59.891 50.000 7.09 0.85 0.00 3.50 F
3024 3084 1.208358 GACGACGACGATGACACCA 59.792 57.895 15.32 0.00 42.66 4.17 F
3461 3523 2.143122 CTGCTCGCTTGAACAAAGGTA 58.857 47.619 0.00 0.00 36.30 3.08 F
4614 4691 2.297597 GTGGAGATACTGCTAAGGCGAT 59.702 50.000 0.00 0.00 42.25 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1567 1.003233 GGGCGAACAGCTCTTCCTT 60.003 57.895 0.00 0.0 44.82 3.36 R
2930 2990 2.165845 GGAGCTGTTGTAGTCATACCGT 59.834 50.000 0.00 0.0 0.00 4.83 R
3629 3693 1.024271 TGTGACAAAAGCAGACCAGC 58.976 50.000 0.00 0.0 0.00 4.85 R
5227 5304 2.669133 CCTGCCCTCGACCATTGGA 61.669 63.158 10.37 0.0 0.00 3.53 R
5456 5534 0.940519 CACGTGCTTGCCCAAATGTG 60.941 55.000 0.82 0.0 0.00 3.21 R
6068 6151 0.395311 TCGGGCTCGTAGTCTTCCAT 60.395 55.000 5.57 0.0 37.69 3.41 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
26 27 2.289382 GGTTCGAAATTTGGGGTTGCAT 60.289 45.455 0.00 0.00 0.00 3.96
128 131 0.107263 TGAAACTGCAGACTGTGGCA 60.107 50.000 23.35 5.45 38.52 4.92
179 183 2.536761 TGTGCGGCAACTAAACTACT 57.463 45.000 3.23 0.00 0.00 2.57
273 286 3.039134 CACCCCAAAACGAGGTGC 58.961 61.111 0.00 0.00 44.21 5.01
449 464 3.818210 TGTGTGGCAACTAAACTACATGG 59.182 43.478 0.00 0.00 37.61 3.66
609 626 2.009774 GCCACATACACGCTCTTGAAT 58.990 47.619 0.00 0.00 0.00 2.57
1011 1034 0.541392 TCAGCATAATGGCTCGTGGT 59.459 50.000 0.00 0.00 43.68 4.16
1392 1416 1.061546 ACCTTGTCAACCCGGTATGT 58.938 50.000 0.00 0.00 0.00 2.29
1476 1500 6.324601 AGACTTCCATTGAATGAGGAATCT 57.675 37.500 6.76 5.42 40.39 2.40
1543 1567 6.294342 CCCGTACGAGGTTAATAATGAGATCA 60.294 42.308 18.76 0.00 0.00 2.92
1600 1624 1.017177 GGCAATGCCGAACACGTCTA 61.017 55.000 9.14 0.00 39.62 2.59
1725 1749 1.261089 CGCCCAAGCAACAAATGTTTG 59.739 47.619 4.04 4.04 46.39 2.93
1950 1976 1.438651 TGTCGTCTGCACTTAATGGC 58.561 50.000 0.00 0.00 0.00 4.40
2201 2254 6.291648 TGGATCATACATTATCCTGCTCTC 57.708 41.667 0.00 0.00 41.94 3.20
2379 2434 3.939837 CTGCGTGGACCATCAGCGT 62.940 63.158 12.07 0.00 0.00 5.07
2388 2443 0.108585 ACCATCAGCGTTGTCAAGGT 59.891 50.000 7.09 0.85 0.00 3.50
2491 2547 4.679197 GCATGCTTACAAATTTGACACGAA 59.321 37.500 24.64 4.88 0.00 3.85
2678 2738 2.365941 TGTCCACATCTACGGTTTGTCA 59.634 45.455 0.00 0.00 0.00 3.58
2930 2990 4.939368 CCAACCGGTTGCCGTGGA 62.939 66.667 36.83 0.00 46.80 4.02
3024 3084 1.208358 GACGACGACGATGACACCA 59.792 57.895 15.32 0.00 42.66 4.17
3240 3300 2.724454 CCAGGAAGAGGTTCGACTCTA 58.276 52.381 6.03 0.00 46.70 2.43
3241 3301 3.292460 CCAGGAAGAGGTTCGACTCTAT 58.708 50.000 6.03 0.00 46.70 1.98
3348 3408 2.772568 TTGTTGTCTGACAATTGCCG 57.227 45.000 24.44 0.00 40.59 5.69
3376 3438 2.885135 TCCTTCCATCTGTTGCATGT 57.115 45.000 0.00 0.00 0.00 3.21
3461 3523 2.143122 CTGCTCGCTTGAACAAAGGTA 58.857 47.619 0.00 0.00 36.30 3.08
4000 4072 3.222603 ACTACCAGCTTTTTCCACTTGG 58.777 45.455 0.00 0.00 0.00 3.61
4614 4691 2.297597 GTGGAGATACTGCTAAGGCGAT 59.702 50.000 0.00 0.00 42.25 4.58
5065 5142 2.376518 TCTTTCACCCTTGGATTCTGCT 59.623 45.455 0.00 0.00 0.00 4.24
5351 5428 5.712152 GACTTTTGTCCCAATCACATTCT 57.288 39.130 0.00 0.00 43.37 2.40
5354 5431 6.282930 ACTTTTGTCCCAATCACATTCTTTG 58.717 36.000 0.00 0.00 0.00 2.77
5456 5534 2.505557 GCTGCCATGCTGCGTTTC 60.506 61.111 2.22 0.00 42.83 2.78
5545 5623 5.181245 GGCAAATACAGTTCAGTACACATGT 59.819 40.000 0.00 0.00 0.00 3.21
5934 6016 0.316522 CCGCATGATCGAGGAGACAT 59.683 55.000 0.00 0.00 0.00 3.06
6116 6199 1.978580 CCACTAAGGAACAGACCCAGT 59.021 52.381 0.00 0.00 41.22 4.00
6587 6674 4.180057 GAGGAACAATTTTGCACAACACA 58.820 39.130 0.00 0.00 0.00 3.72
6818 6906 6.389091 GCTCATTTTGTTCATACAATGGACA 58.611 36.000 0.00 0.00 46.71 4.02
6912 7002 5.576384 TGTTGTTCTTTCATGTGAACTTTGC 59.424 36.000 20.41 12.74 41.99 3.68
6992 7082 1.139308 ACACGACCGACACGACAAA 59.861 52.632 0.00 0.00 34.70 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.373370 CAATTCTCGCGCGAAATGGA 59.627 50.000 33.99 23.76 0.00 3.41
128 131 7.095910 TCACGTTCAATCATATTGCCAATTTT 58.904 30.769 0.00 0.00 0.00 1.82
179 183 2.614983 GGCAACTACCACGTTTCTTCAA 59.385 45.455 0.00 0.00 0.00 2.69
273 286 7.086376 CACAGGAGTTCAATGAAATTAGTTGG 58.914 38.462 0.00 0.00 32.46 3.77
318 332 5.559148 TTAAAATTTGCCACATGGGAAGT 57.441 34.783 4.94 0.00 46.23 3.01
1253 1277 1.202698 GGGAGGCTCTGTTGCGAATAT 60.203 52.381 15.23 0.00 0.00 1.28
1392 1416 3.068165 CGTATATCTCACCAAGCCAGTCA 59.932 47.826 0.00 0.00 0.00 3.41
1543 1567 1.003233 GGGCGAACAGCTCTTCCTT 60.003 57.895 0.00 0.00 44.82 3.36
2678 2738 4.576053 CCGTGACATCAACATGTAATCCAT 59.424 41.667 0.00 0.00 43.79 3.41
2930 2990 2.165845 GGAGCTGTTGTAGTCATACCGT 59.834 50.000 0.00 0.00 0.00 4.83
3024 3084 2.078849 TCAGCGTGTTCATCGTCATT 57.921 45.000 0.00 0.00 0.00 2.57
3253 3313 6.707440 TTCCAAAGAAAAGATACACAGCAA 57.293 33.333 0.00 0.00 0.00 3.91
3373 3435 2.494918 GCGGTCGGCTCACTACAT 59.505 61.111 0.00 0.00 39.11 2.29
3461 3523 4.360405 GTCACCGGCAATGGGGGT 62.360 66.667 0.00 0.00 31.39 4.95
3629 3693 1.024271 TGTGACAAAAGCAGACCAGC 58.976 50.000 0.00 0.00 0.00 4.85
5227 5304 2.669133 CCTGCCCTCGACCATTGGA 61.669 63.158 10.37 0.00 0.00 3.53
5390 5467 2.874014 TCAAATCCAGTTGCCATGTCA 58.126 42.857 0.00 0.00 0.00 3.58
5456 5534 0.940519 CACGTGCTTGCCCAAATGTG 60.941 55.000 0.82 0.00 0.00 3.21
6068 6151 0.395311 TCGGGCTCGTAGTCTTCCAT 60.395 55.000 5.57 0.00 37.69 3.41
6069 6152 0.609957 TTCGGGCTCGTAGTCTTCCA 60.610 55.000 5.57 0.00 37.69 3.53
6587 6674 2.432146 TCAGTGTGAGCTTGAAGTCACT 59.568 45.455 20.36 14.48 43.03 3.41
6818 6906 5.299531 GGGAGTAGTTGAAAAGAAAGTTGCT 59.700 40.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.