Multiple sequence alignment - TraesCS5A01G163200

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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 TraesCS5A01G163200 chr5A 100.000 5514 0 0 1 5514 349633793 349628280 0 10183
1 TraesCS5A01G163200 chr5D 97.374 5522 104 13 1 5514 263153876 263159364 0 9356
2 TraesCS5A01G163200 chr5B 97.922 4620 88 8 113 4730 295653179 295657792 0 7993
3 TraesCS5A01G163200 chr5B 95.929 737 18 5 4790 5514 295657811 295658547 0 1184


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 TraesCS5A01G163200 chr5A 349628280 349633793 5513 True 10183.0 10183 100.0000 1 5514 1 chr5A.!!$R1 5513
1 TraesCS5A01G163200 chr5D 263153876 263159364 5488 False 9356.0 9356 97.3740 1 5514 1 chr5D.!!$F1 5513
2 TraesCS5A01G163200 chr5B 295653179 295658547 5368 False 4588.5 7993 96.9255 113 5514 2 chr5B.!!$F1 5401

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
413 418 0.319125 TTGATGCGCACGTAGTCACA 60.319 50.000 14.90 0.48 41.61 3.58 F
1404 1409 2.529744 GGATTATGAGGGGGCGGCT 61.530 63.158 9.56 0.00 0.00 5.52 F
2423 2428 0.437678 CAGAAGCGCGCATATGCTAG 59.562 55.000 35.10 18.25 41.46 3.42 F
3027 3032 2.346803 GGCAACATACACATGTCTCGT 58.653 47.619 0.00 0.00 44.83 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 2322 0.102481 CCACGACTAGTATGCCGCTT 59.898 55.000 0.0 0.0 0.00 4.68 R
3150 3155 2.386661 AGTCTGGCTTTACATCCACG 57.613 50.000 0.0 0.0 0.00 4.94 R
3997 4005 4.823989 ACTATGGCAGATCCTAATGTTTGC 59.176 41.667 0.0 0.0 35.26 3.68 R
5025 5044 0.874390 CCACCCACTGTTGTCATTCG 59.126 55.000 0.0 0.0 0.00 3.34 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
188 192 4.142687 CGCTTTCATGTCGATTTTACCCTT 60.143 41.667 0.00 0.00 0.00 3.95
189 193 5.332707 GCTTTCATGTCGATTTTACCCTTC 58.667 41.667 0.00 0.00 0.00 3.46
413 418 0.319125 TTGATGCGCACGTAGTCACA 60.319 50.000 14.90 0.48 41.61 3.58
553 558 3.710722 CCCTTCTGCTCGCACCCT 61.711 66.667 0.00 0.00 0.00 4.34
674 679 5.050159 CCTTGCATTTACTTTCTTGCCAAAC 60.050 40.000 0.00 0.00 34.20 2.93
684 689 3.857157 TCTTGCCAAACTTAGGACAGT 57.143 42.857 0.00 0.00 0.00 3.55
975 980 3.766051 CCTCTTCCTTGATTTGGGGAAAG 59.234 47.826 0.00 0.00 38.45 2.62
1216 1221 2.904434 GACTTGAAGGAGGAGGGTACAA 59.096 50.000 0.00 0.00 0.00 2.41
1310 1315 4.848562 AAACCGAATTGGAGGAAAAGAC 57.151 40.909 0.00 0.00 42.00 3.01
1370 1375 2.552367 ACTTAAGGGAGAGGGGACAAG 58.448 52.381 7.53 0.00 0.00 3.16
1404 1409 2.529744 GGATTATGAGGGGGCGGCT 61.530 63.158 9.56 0.00 0.00 5.52
1431 1436 7.466746 TGAGTTTGATAAGGCAATAAAGCTT 57.533 32.000 0.00 0.00 34.17 3.74
1920 1925 5.241506 TGAAGAAAACCACATGGAGAATGAC 59.758 40.000 4.53 0.00 38.72 3.06
2114 2119 7.857885 CCACAAAGAAACAGAGAGTCAAAATAC 59.142 37.037 0.00 0.00 0.00 1.89
2266 2271 3.502211 CCGTAGCAACCAAGAAATTCACT 59.498 43.478 0.00 0.00 0.00 3.41
2423 2428 0.437678 CAGAAGCGCGCATATGCTAG 59.562 55.000 35.10 18.25 41.46 3.42
2517 2522 3.454371 AGTCTACGGCAAGCGATAAAT 57.546 42.857 0.00 0.00 0.00 1.40
2595 2600 2.391926 TAGAGGGTGACTTGGTGACA 57.608 50.000 0.00 0.00 39.83 3.58
2886 2891 2.526888 TAGTGGATCTCCGTGACCTT 57.473 50.000 0.00 0.00 39.43 3.50
3027 3032 2.346803 GGCAACATACACATGTCTCGT 58.653 47.619 0.00 0.00 44.83 4.18
3150 3155 5.707764 AGCTGGAAAGAAGTTTGAAGATACC 59.292 40.000 0.00 0.00 0.00 2.73
3867 3874 3.648067 CCTAACATAGGGAGCCATCTTCA 59.352 47.826 0.00 0.00 42.42 3.02
3899 3906 3.323979 AGTGGACCACTAGTGTTAACCAG 59.676 47.826 26.08 6.79 43.46 4.00
3928 3935 7.984475 TGGTGGATGGCTATTTGTAATAGTAT 58.016 34.615 7.93 4.16 0.00 2.12
3997 4005 4.748503 TGTATGTTATCGCGAAGAAACG 57.251 40.909 15.24 0.00 0.00 3.60
4147 4155 6.147164 CGGAAGCAACTTCAGTATTACTTCAA 59.853 38.462 9.38 0.00 41.77 2.69
4242 4250 8.872845 CAAAAATTACATTTAATCCTGGTGCTC 58.127 33.333 0.00 0.00 0.00 4.26
4551 4559 2.610433 GACTTGATGCTGTCGACATGA 58.390 47.619 20.40 8.97 0.00 3.07
4828 4836 1.321474 ATGAAGTGTTGTGGGCACTG 58.679 50.000 0.00 0.00 45.36 3.66
4989 5002 1.153745 CGTCCACTAGCACTGGAGC 60.154 63.158 0.87 0.00 38.54 4.70
4991 5004 1.475403 GTCCACTAGCACTGGAGCTA 58.525 55.000 0.87 4.43 44.50 3.32
5025 5044 4.650377 GGCATCGCCCCTGGGATC 62.650 72.222 16.20 4.49 44.06 3.36
5027 5046 3.233980 CATCGCCCCTGGGATCGA 61.234 66.667 24.71 24.71 41.79 3.59
5128 5147 1.221840 GGGCGGAGATGCTTTGAGA 59.778 57.895 0.00 0.00 34.52 3.27
5136 5155 0.449388 GATGCTTTGAGAAGGCCACG 59.551 55.000 5.01 0.00 33.34 4.94
5192 5211 1.549620 CAGAGCAGATCAGTGGACAGT 59.450 52.381 0.00 0.00 0.00 3.55
5253 5272 2.908351 AGGGCTAAAAACCGGACTTCTA 59.092 45.455 9.46 0.00 0.00 2.10
5416 5437 6.276091 AGATGACCAAAGAAACAAAGCTTTC 58.724 36.000 9.23 0.00 32.36 2.62
5460 5486 9.920946 AGAATTGAGCAAAGGGTATTAGAATAA 57.079 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.021396 CGTACATCTGCTTATTACTAGCACATA 58.979 37.037 0.00 0.00 43.30 2.29
14 15 5.117287 GCGTACATCTGCTTATTACTAGCAC 59.883 44.000 0.00 0.00 43.30 4.40
120 124 8.218338 ACATCCTAGAAAATGATGTGTGATTC 57.782 34.615 9.84 0.00 45.39 2.52
139 143 3.675995 TGCATGGAAGCAACATCCT 57.324 47.368 0.00 0.00 42.46 3.24
165 169 3.374058 AGGGTAAAATCGACATGAAAGCG 59.626 43.478 0.00 0.00 0.00 4.68
188 192 2.688446 CTCACTAGCCGTAGATTGGTGA 59.312 50.000 0.00 0.00 0.00 4.02
189 193 2.223829 CCTCACTAGCCGTAGATTGGTG 60.224 54.545 0.00 0.00 0.00 4.17
413 418 2.162681 GTGGCTTCTGTGGTTAGCATT 58.837 47.619 0.00 0.00 36.64 3.56
553 558 1.912763 GCAAAGGGTTGGATGGGCA 60.913 57.895 0.00 0.00 35.10 5.36
674 679 0.905357 CTGGTGGGGACTGTCCTAAG 59.095 60.000 25.01 12.15 36.57 2.18
684 689 1.229529 GAGGAGGAACTGGTGGGGA 60.230 63.158 0.00 0.00 41.55 4.81
975 980 1.066645 CAGAATTTGCAAGCCTTCCCC 60.067 52.381 0.00 0.00 0.00 4.81
1191 1196 1.137872 CCCTCCTCCTTCAAGTCGATG 59.862 57.143 0.00 0.00 0.00 3.84
1216 1221 0.401395 TCCTCCTTCAGTTGGGTGGT 60.401 55.000 0.00 0.00 37.48 4.16
1310 1315 4.582656 AGTCTCTCTTCTGGGATAACATCG 59.417 45.833 0.00 0.00 0.00 3.84
1370 1375 1.484444 ATCCCGCCTCTGGAATAGCC 61.484 60.000 0.00 0.00 35.03 3.93
1404 1409 7.394359 AGCTTTATTGCCTTATCAAACTCAAGA 59.606 33.333 0.00 0.00 0.00 3.02
1722 1727 4.074970 GTGACACAACCTGATTCTCCAAT 58.925 43.478 0.00 0.00 0.00 3.16
1920 1925 7.428826 GGGTATCATTTCCTTCATTGCTTAAG 58.571 38.462 0.00 0.00 0.00 1.85
2068 2073 0.611618 TGCATTTGTTCCGCATCCCT 60.612 50.000 0.00 0.00 0.00 4.20
2114 2119 0.602562 TTTGAGGGGCTTTTCATGCG 59.397 50.000 0.00 0.00 0.00 4.73
2317 2322 0.102481 CCACGACTAGTATGCCGCTT 59.898 55.000 0.00 0.00 0.00 4.68
2423 2428 2.808543 ACAGTCTTTGTTTCTCCATCGC 59.191 45.455 0.00 0.00 36.31 4.58
2517 2522 3.415212 ACTGTACTTACACCGAGCTACA 58.585 45.455 0.00 0.00 31.93 2.74
2595 2600 7.607991 CACCTTAGTTCCTCAGTTGATGTAATT 59.392 37.037 0.00 0.00 0.00 1.40
2886 2891 3.892740 AATGCACAGCCGCGTACCA 62.893 57.895 4.92 0.00 33.35 3.25
3027 3032 7.817478 TCTGATAAAGATAGTCGTTTCTTTGCA 59.183 33.333 7.89 0.00 41.15 4.08
3150 3155 2.386661 AGTCTGGCTTTACATCCACG 57.613 50.000 0.00 0.00 0.00 4.94
3867 3874 9.582648 AACACTAGTGGTCCACTAAAAATATTT 57.417 29.630 27.88 13.71 44.80 1.40
3899 3906 6.463995 TTACAAATAGCCATCCACCAATTC 57.536 37.500 0.00 0.00 0.00 2.17
3997 4005 4.823989 ACTATGGCAGATCCTAATGTTTGC 59.176 41.667 0.00 0.00 35.26 3.68
4341 4349 7.448161 TGAAGCTCAATCCTGAATAACAAAGAA 59.552 33.333 0.00 0.00 0.00 2.52
4478 4486 8.956533 TTTATGTGCTCTAGTACATTATGCAA 57.043 30.769 17.07 4.59 46.66 4.08
4770 4778 4.157656 TGGTATTATTGCTTTGGTCACTGC 59.842 41.667 0.00 0.00 0.00 4.40
4828 4836 2.507407 TTAGAGTGAAATGTGGCCCC 57.493 50.000 0.00 0.00 0.00 5.80
4922 4935 4.175337 CCCCGGCATGACCATCGT 62.175 66.667 0.00 0.00 39.03 3.73
4989 5002 2.233431 GCCCTGATCTAGATGCCACTAG 59.767 54.545 10.74 7.64 40.59 2.57
4991 5004 1.055040 GCCCTGATCTAGATGCCACT 58.945 55.000 10.74 0.00 0.00 4.00
5025 5044 0.874390 CCACCCACTGTTGTCATTCG 59.126 55.000 0.00 0.00 0.00 3.34
5027 5046 0.827507 GGCCACCCACTGTTGTCATT 60.828 55.000 0.00 0.00 0.00 2.57
5128 5147 1.608717 CTGAGGTAGCTCGTGGCCTT 61.609 60.000 16.71 0.00 43.05 4.35
5136 5155 5.948992 ACAATGAAAAACTGAGGTAGCTC 57.051 39.130 15.12 15.12 0.00 4.09
5253 5272 5.472820 CCATCTTCTTTTCAGCTCTTCTTGT 59.527 40.000 0.00 0.00 0.00 3.16
5460 5486 8.918961 TTGATGAACGAAACATGTAACTTTTT 57.081 26.923 0.00 0.00 0.00 1.94
5461 5487 9.528018 AATTGATGAACGAAACATGTAACTTTT 57.472 25.926 0.00 0.00 0.00 2.27
5467 5493 9.781834 GGAAATAATTGATGAACGAAACATGTA 57.218 29.630 0.00 0.00 0.00 2.29
5468 5494 7.484641 CGGAAATAATTGATGAACGAAACATGT 59.515 33.333 0.00 0.00 0.00 3.21
5469 5495 7.513505 GCGGAAATAATTGATGAACGAAACATG 60.514 37.037 0.00 0.00 0.00 3.21
5476 5502 3.288242 CCGCGGAAATAATTGATGAACG 58.712 45.455 24.07 0.00 0.00 3.95
5491 5517 1.456196 TTGCAATTTGAACCCGCGGA 61.456 50.000 30.73 5.29 0.00 5.54


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

AutoCloner maintained by Alex Coulton.