Multiple sequence alignment - TraesCS4B01G159300

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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 TraesCS4B01G159300 chr4B 100.000 2250 0 0 1 2250 308696597 308694348 0 4156
1 TraesCS4B01G159300 chr3D 96.776 2264 54 7 1 2249 589279415 589281674 0 3759
2 TraesCS4B01G159300 chr1A 96.512 2265 52 8 1 2249 554512375 554510122 0 3720
3 TraesCS4B01G159300 chr5D 96.421 2263 64 7 1 2249 503278099 503280358 0 3714
4 TraesCS4B01G159300 chr5D 96.332 2263 67 5 1 2249 6189067 6186807 0 3705
5 TraesCS4B01G159300 chr5D 95.451 2264 83 9 1 2249 432403370 432405628 0 3592
6 TraesCS4B01G159300 chr5D 96.517 1579 37 6 1 1564 503218345 503216770 0 2595
7 TraesCS4B01G159300 chr1D 96.336 2265 64 9 1 2249 254397982 254400243 0 3705
8 TraesCS4B01G159300 chr5A 95.104 2267 89 10 1 2250 607274527 607272266 0 3552
9 TraesCS4B01G159300 chr6D 96.392 1580 38 7 1 1564 168255053 168253477 0 2584
10 TraesCS4B01G159300 chr6D 95.925 1595 48 6 671 2249 45519030 45517437 0 2569
11 TraesCS4B01G159300 chrUn 96.329 1580 38 8 1 1564 93409504 93411079 0 2579
12 TraesCS4B01G159300 chrUn 96.266 1580 40 7 1 1564 216518475 216520051 0 2573
13 TraesCS4B01G159300 chrUn 96.098 1512 43 5 1 1497 216521863 216523373 0 2451
14 TraesCS4B01G159300 chrUn 97.109 934 27 0 1316 2249 239345464 239346397 0 1576
15 TraesCS4B01G159300 chr3B 96.203 1580 40 8 1 1564 201527151 201525576 0 2567
16 TraesCS4B01G159300 chr2D 96.139 1580 42 7 1 1564 272793766 272795342 0 2562


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 TraesCS4B01G159300 chr4B 308694348 308696597 2249 True 4156 4156 100.000 1 2250 1 chr4B.!!$R1 2249
1 TraesCS4B01G159300 chr3D 589279415 589281674 2259 False 3759 3759 96.776 1 2249 1 chr3D.!!$F1 2248
2 TraesCS4B01G159300 chr1A 554510122 554512375 2253 True 3720 3720 96.512 1 2249 1 chr1A.!!$R1 2248
3 TraesCS4B01G159300 chr5D 503278099 503280358 2259 False 3714 3714 96.421 1 2249 1 chr5D.!!$F2 2248
4 TraesCS4B01G159300 chr5D 6186807 6189067 2260 True 3705 3705 96.332 1 2249 1 chr5D.!!$R1 2248
5 TraesCS4B01G159300 chr5D 432403370 432405628 2258 False 3592 3592 95.451 1 2249 1 chr5D.!!$F1 2248
6 TraesCS4B01G159300 chr5D 503216770 503218345 1575 True 2595 2595 96.517 1 1564 1 chr5D.!!$R2 1563
7 TraesCS4B01G159300 chr1D 254397982 254400243 2261 False 3705 3705 96.336 1 2249 1 chr1D.!!$F1 2248
8 TraesCS4B01G159300 chr5A 607272266 607274527 2261 True 3552 3552 95.104 1 2250 1 chr5A.!!$R1 2249
9 TraesCS4B01G159300 chr6D 168253477 168255053 1576 True 2584 2584 96.392 1 1564 1 chr6D.!!$R2 1563
10 TraesCS4B01G159300 chr6D 45517437 45519030 1593 True 2569 2569 95.925 671 2249 1 chr6D.!!$R1 1578
11 TraesCS4B01G159300 chrUn 93409504 93411079 1575 False 2579 2579 96.329 1 1564 1 chrUn.!!$F1 1563
12 TraesCS4B01G159300 chrUn 216518475 216523373 4898 False 2512 2573 96.182 1 1564 2 chrUn.!!$F3 1563
13 TraesCS4B01G159300 chrUn 239345464 239346397 933 False 1576 1576 97.109 1316 2249 1 chrUn.!!$F2 933
14 TraesCS4B01G159300 chr3B 201525576 201527151 1575 True 2567 2567 96.203 1 1564 1 chr3B.!!$R1 1563
15 TraesCS4B01G159300 chr2D 272793766 272795342 1576 False 2562 2562 96.139 1 1564 1 chr2D.!!$F1 1563

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
146 147 0.387565 GCGCCCCTTGTTTCAAAGAA 59.612 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 3471 0.460635 TTTCGGCGGTTCCCTATTCG 60.461 55.0 7.21 0.0 0.0 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
48 49 6.017605 CAGCAAGTGATTGAGTTCAGTAGTTT 60.018 38.462 0.00 0.0 0.00 2.66
146 147 0.387565 GCGCCCCTTGTTTCAAAGAA 59.612 50.000 0.00 0.0 0.00 2.52
181 182 9.665719 GGGTTATTCACATTTAATTTGATGGTT 57.334 29.630 0.00 0.0 0.00 3.67
188 189 6.692681 CACATTTAATTTGATGGTTAGAGGCG 59.307 38.462 5.92 0.0 0.00 5.52
333 334 5.164620 TGAAGAACATAAGCCAGATGACA 57.835 39.130 0.00 0.0 0.00 3.58
394 395 2.348872 CGATTCGGCAGATTTGGATTCG 60.349 50.000 0.00 0.0 0.00 3.34
489 490 8.459635 GTCATATACATCTAGAAAGCCGTATGA 58.540 37.037 0.00 4.5 0.00 2.15
668 671 5.975693 AATTGCAAAAGAGGGTAAATCGA 57.024 34.783 1.71 0.0 0.00 3.59
669 672 5.975693 ATTGCAAAAGAGGGTAAATCGAA 57.024 34.783 1.71 0.0 0.00 3.71
677 680 7.668525 AAAGAGGGTAAATCGAACACTTTAG 57.331 36.000 0.00 0.0 28.36 1.85
681 684 7.343833 AGAGGGTAAATCGAACACTTTAGGATA 59.656 37.037 0.00 0.0 28.36 2.59
697 700 2.527057 AGGATAACCATCTGGGGAGGTA 59.473 50.000 0.54 0.0 42.91 3.08
698 701 3.050564 AGGATAACCATCTGGGGAGGTAA 60.051 47.826 0.54 0.0 42.91 2.85
723 726 7.686434 AGTTTAGTATCCCAAAACTGCTTAGA 58.314 34.615 0.00 0.0 40.85 2.10
732 735 4.272504 CCAAAACTGCTTAGAAACAGTCGA 59.727 41.667 0.00 0.0 46.17 4.20
804 807 6.351966 GGATCTAAGTGTTGGCTAGGTAAACT 60.352 42.308 0.00 0.0 0.00 2.66
885 889 4.086457 GGAAAGCTCCCATTGGTAGAAAA 58.914 43.478 0.00 0.0 35.42 2.29
886 890 4.526650 GGAAAGCTCCCATTGGTAGAAAAA 59.473 41.667 0.00 0.0 35.42 1.94
913 919 1.076350 CACAACCCCTTGGGGTTATCA 59.924 52.381 34.97 0.0 42.24 2.15
921 927 1.334869 CTTGGGGTTATCATGCGCTTC 59.665 52.381 9.73 0.0 0.00 3.86
1092 1101 5.186256 TGGATTTACAATCCACTGCCTTA 57.814 39.130 13.25 0.0 42.81 2.69
1121 1130 0.685097 GCTACATCCGCCCCTTATCA 59.315 55.000 0.00 0.0 0.00 2.15
1210 1221 6.694844 CGATCGAGATATTGGACATAGAATGG 59.305 42.308 10.26 0.0 33.60 3.16
1226 1237 7.669722 ACATAGAATGGCACTCTTTAAAAAGGA 59.330 33.333 2.86 0.0 34.00 3.36
1328 1355 7.974504 AGGAGGAGAAAGAAACAATAGTAACA 58.025 34.615 0.00 0.0 0.00 2.41
1337 1364 4.563140 AACAATAGTAACATGGTCCCGT 57.437 40.909 0.00 0.0 0.00 5.28
1771 2029 4.825546 GTTGATGATATCAGCCCAAGTG 57.174 45.455 17.90 0.0 40.94 3.16
1911 2169 5.296780 CAGCCAAGAAGAAGTGTAAAGAACA 59.703 40.000 0.00 0.0 35.06 3.18
1967 2225 2.094286 CGGCCAAAATAACCATGAGCAA 60.094 45.455 2.24 0.0 0.00 3.91
2061 2481 6.945636 TTCCCTGATCAAACTAGAGGTTAA 57.054 37.500 0.00 0.0 37.12 2.01
2082 3471 1.406539 CAAGGAACCATGCATAGCACC 59.593 52.381 0.00 0.0 43.04 5.01
2171 3784 5.221986 TGCTCTGCCTGGAATACAATCATAT 60.222 40.000 0.00 0.0 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 2.262637 TGTGAATAACCCGTCCTCCTT 58.737 47.619 0.00 0.00 0.00 3.36
181 182 3.871594 GCTTAGCTTTCAATTCGCCTCTA 59.128 43.478 0.00 0.00 0.00 2.43
188 189 4.773323 ACCACTGCTTAGCTTTCAATTC 57.227 40.909 5.60 0.00 0.00 2.17
333 334 2.028130 CATCCTAGGTCTCTGCGTTCT 58.972 52.381 9.08 0.00 0.00 3.01
407 408 7.069826 TCATATGATGAAGTACCACATGAGTGA 59.930 37.037 0.00 5.57 41.42 3.41
489 490 6.461509 CCAAACTGTACAAGCTTCTTCCAAAT 60.462 38.462 0.00 0.00 0.00 2.32
638 641 4.022329 ACCCTCTTTTGCAATTAGTTTCGG 60.022 41.667 0.00 3.22 0.00 4.30
646 649 5.975693 TCGATTTACCCTCTTTTGCAATT 57.024 34.783 0.00 0.00 0.00 2.32
668 671 5.340027 CCCCAGATGGTTATCCTAAAGTGTT 60.340 44.000 0.00 0.00 33.64 3.32
669 672 4.166144 CCCCAGATGGTTATCCTAAAGTGT 59.834 45.833 0.00 0.00 33.64 3.55
677 680 1.821088 ACCTCCCCAGATGGTTATCC 58.179 55.000 0.00 0.00 33.64 2.59
681 684 2.361085 ACTTACCTCCCCAGATGGTT 57.639 50.000 0.00 0.00 35.48 3.67
723 726 2.413310 ACCCACTTGTTCGACTGTTT 57.587 45.000 0.00 0.00 0.00 2.83
732 735 2.090999 ACCCCAACATTACCCACTTGTT 60.091 45.455 0.00 0.00 34.03 2.83
886 890 1.208706 CCAAGGGGTTGTGGGTTTTT 58.791 50.000 0.00 0.00 0.00 1.94
913 919 2.086054 AGTTCTTCTTCGAAGCGCAT 57.914 45.000 20.56 0.00 0.00 4.73
921 927 7.492352 TTTTCCTTTTCCTAGTTCTTCTTCG 57.508 36.000 0.00 0.00 0.00 3.79
1076 1085 4.227300 AGTGGATTAAGGCAGTGGATTGTA 59.773 41.667 0.00 0.00 0.00 2.41
1092 1101 1.747206 GCGGATGTAGCCAAGTGGATT 60.747 52.381 0.18 0.00 37.39 3.01
1166 1177 5.449314 CGATCGAAGTACAGAGGTCAGAATT 60.449 44.000 10.26 0.00 0.00 2.17
1178 1189 5.529800 TGTCCAATATCTCGATCGAAGTACA 59.470 40.000 19.92 11.36 0.00 2.90
1328 1355 1.447643 GCTAGATGCACGGGACCAT 59.552 57.895 0.00 0.00 42.31 3.55
1666 1924 3.554934 AGCTGTTGTTGAAGTTCCATCA 58.445 40.909 0.00 0.00 0.00 3.07
1682 1940 4.325084 ACTTCCCTCTAGACTTAGCTGT 57.675 45.455 0.00 0.00 0.00 4.40
1771 2029 5.745294 TGATAGTCAAGGTCGCGTTATTAAC 59.255 40.000 5.77 0.00 0.00 2.01
1911 2169 7.665559 TCCAATATGCTAGTTTCAACAACTCTT 59.334 33.333 0.00 0.00 0.00 2.85
2061 2481 2.094675 GTGCTATGCATGGTTCCTTGT 58.905 47.619 10.16 0.00 41.91 3.16
2082 3471 0.460635 TTTCGGCGGTTCCCTATTCG 60.461 55.000 7.21 0.00 0.00 3.34
2101 3490 3.072476 ACATGTTAGGTGTAGCTGGTGTT 59.928 43.478 0.00 0.00 0.00 3.32
2171 3784 8.660295 TTAGGAATCTCTGGTACTTTCAACTA 57.340 34.615 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.