Multiple sequence alignment - TraesCS4A01G153100

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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 TraesCS4A01G153100 chr4A 100.000 2468 0 0 1 2468 309505713 309503246 0.000000e+00 4558
1 TraesCS4A01G153100 chr5D 96.527 1641 51 5 1 1637 6179512 6177874 0.000000e+00 2710
2 TraesCS4A01G153100 chr5D 95.181 1660 51 7 1 1637 503288747 503290400 0.000000e+00 2595
3 TraesCS4A01G153100 chr5D 92.788 1650 93 15 1 1637 513586948 513585312 0.000000e+00 2364
4 TraesCS4A01G153100 chr2D 95.901 1659 44 6 1 1637 9786578 9788234 0.000000e+00 2665
5 TraesCS4A01G153100 chr6D 95.419 1659 52 7 1 1637 45510134 45508478 0.000000e+00 2621
6 TraesCS4A01G153100 chr1A 94.829 1663 52 10 1 1637 554459902 554461556 0.000000e+00 2564
7 TraesCS4A01G153100 chr2B 94.692 1658 57 9 1 1637 474901771 474903418 0.000000e+00 2545
8 TraesCS4A01G153100 chr7B 93.426 1582 84 11 3 1580 105255171 105253606 0.000000e+00 2327
9 TraesCS4A01G153100 chr4D 92.250 1471 83 7 188 1637 207070648 207069188 0.000000e+00 2056
10 TraesCS4A01G153100 chr1D 95.175 1140 37 1 1 1122 51876634 51875495 0.000000e+00 1784
11 TraesCS4A01G153100 chr1D 94.805 693 14 6 1 673 254418495 254419185 0.000000e+00 1061
12 TraesCS4A01G153100 chr3A 95.427 831 36 2 1638 2468 62339289 62338461 0.000000e+00 1323
13 TraesCS4A01G153100 chr3A 94.946 831 41 1 1638 2468 581957907 581957078 0.000000e+00 1301
14 TraesCS4A01G153100 chr3A 96.491 114 3 1 1525 1637 187128466 187128353 1.170000e-43 187
15 TraesCS4A01G153100 chr5A 95.187 831 39 1 1638 2468 690817154 690817983 0.000000e+00 1312
16 TraesCS4A01G153100 chr5A 94.934 829 41 1 1638 2466 445470257 445471084 0.000000e+00 1297
17 TraesCS4A01G153100 chr5A 94.731 835 41 2 1636 2468 537080388 537079555 0.000000e+00 1295
18 TraesCS4A01G153100 chr6A 94.813 829 42 1 1640 2468 159569470 159570297 0.000000e+00 1291
19 TraesCS4A01G153100 chr6A 94.712 832 41 3 1638 2468 405601335 405602164 0.000000e+00 1290
20 TraesCS4A01G153100 chr6A 94.391 838 45 2 1632 2468 308075581 308074745 0.000000e+00 1286
21 TraesCS4A01G153100 chr7A 94.705 831 43 1 1638 2468 256769735 256768906 0.000000e+00 1290
22 TraesCS4A01G153100 chr7D 94.662 637 13 4 1 616 77240265 77240901 0.000000e+00 968


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 TraesCS4A01G153100 chr4A 309503246 309505713 2467 True 4558 4558 100.000 1 2468 1 chr4A.!!$R1 2467
1 TraesCS4A01G153100 chr5D 6177874 6179512 1638 True 2710 2710 96.527 1 1637 1 chr5D.!!$R1 1636
2 TraesCS4A01G153100 chr5D 503288747 503290400 1653 False 2595 2595 95.181 1 1637 1 chr5D.!!$F1 1636
3 TraesCS4A01G153100 chr5D 513585312 513586948 1636 True 2364 2364 92.788 1 1637 1 chr5D.!!$R2 1636
4 TraesCS4A01G153100 chr2D 9786578 9788234 1656 False 2665 2665 95.901 1 1637 1 chr2D.!!$F1 1636
5 TraesCS4A01G153100 chr6D 45508478 45510134 1656 True 2621 2621 95.419 1 1637 1 chr6D.!!$R1 1636
6 TraesCS4A01G153100 chr1A 554459902 554461556 1654 False 2564 2564 94.829 1 1637 1 chr1A.!!$F1 1636
7 TraesCS4A01G153100 chr2B 474901771 474903418 1647 False 2545 2545 94.692 1 1637 1 chr2B.!!$F1 1636
8 TraesCS4A01G153100 chr7B 105253606 105255171 1565 True 2327 2327 93.426 3 1580 1 chr7B.!!$R1 1577
9 TraesCS4A01G153100 chr4D 207069188 207070648 1460 True 2056 2056 92.250 188 1637 1 chr4D.!!$R1 1449
10 TraesCS4A01G153100 chr1D 51875495 51876634 1139 True 1784 1784 95.175 1 1122 1 chr1D.!!$R1 1121
11 TraesCS4A01G153100 chr1D 254418495 254419185 690 False 1061 1061 94.805 1 673 1 chr1D.!!$F1 672
12 TraesCS4A01G153100 chr3A 62338461 62339289 828 True 1323 1323 95.427 1638 2468 1 chr3A.!!$R1 830
13 TraesCS4A01G153100 chr3A 581957078 581957907 829 True 1301 1301 94.946 1638 2468 1 chr3A.!!$R3 830
14 TraesCS4A01G153100 chr5A 690817154 690817983 829 False 1312 1312 95.187 1638 2468 1 chr5A.!!$F2 830
15 TraesCS4A01G153100 chr5A 445470257 445471084 827 False 1297 1297 94.934 1638 2466 1 chr5A.!!$F1 828
16 TraesCS4A01G153100 chr5A 537079555 537080388 833 True 1295 1295 94.731 1636 2468 1 chr5A.!!$R1 832
17 TraesCS4A01G153100 chr6A 159569470 159570297 827 False 1291 1291 94.813 1640 2468 1 chr6A.!!$F1 828
18 TraesCS4A01G153100 chr6A 405601335 405602164 829 False 1290 1290 94.712 1638 2468 1 chr6A.!!$F2 830
19 TraesCS4A01G153100 chr6A 308074745 308075581 836 True 1286 1286 94.391 1632 2468 1 chr6A.!!$R1 836
20 TraesCS4A01G153100 chr7A 256768906 256769735 829 True 1290 1290 94.705 1638 2468 1 chr7A.!!$R1 830
21 TraesCS4A01G153100 chr7D 77240265 77240901 636 False 968 968 94.662 1 616 1 chr7D.!!$F1 615

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
869 961 0.036875 GCAGCAGTTTCTACCCCTGT 59.963 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1876 1.134491 GGCGGTTTACAGTATCAGGCT 60.134 52.381 0.0 0.0 0.0 4.58 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
118 122 7.241376 AGACAAGAATTTTTCGCTATTTACGG 58.759 34.615 0.00 0.00 34.02 4.02
214 222 5.385509 TGGATTTCGAAGGTCCATTTTTC 57.614 39.130 22.98 4.07 37.12 2.29
219 233 6.709018 TTTCGAAGGTCCATTTTTCTTTCT 57.291 33.333 0.00 0.00 0.00 2.52
253 267 1.620822 AGTTCTTCCACCCATGCAAC 58.379 50.000 0.00 0.00 0.00 4.17
255 269 1.000274 GTTCTTCCACCCATGCAACAC 60.000 52.381 0.00 0.00 0.00 3.32
347 361 6.894103 AGGAGTCTTGGAATAATGCTGAATTT 59.106 34.615 0.00 0.00 0.00 1.82
554 645 8.883731 AGAAATCGTCCACAGATAATAAAACTG 58.116 33.333 0.00 0.00 37.62 3.16
686 777 9.367160 TGATCTGTTTGATACTATGGATGACTA 57.633 33.333 0.00 0.00 35.14 2.59
712 804 2.600556 CGAAGGGACCGTTTCGTTTTTC 60.601 50.000 17.11 0.00 40.79 2.29
869 961 0.036875 GCAGCAGTTTCTACCCCTGT 59.963 55.000 0.00 0.00 0.00 4.00
975 1067 3.685139 TGGACTTTTGTAGCTCTCCAG 57.315 47.619 0.00 0.00 0.00 3.86
1090 1182 6.045955 GGTCCAATTGCTGTTTTTGTTTCTA 58.954 36.000 0.00 0.00 0.00 2.10
1119 1211 5.946377 CCTTATTTATCCACTAGGGCAATCC 59.054 44.000 0.00 0.00 36.21 3.01
1134 1226 1.339610 CAATCCGGTTGGTTCTTTGCA 59.660 47.619 0.00 0.00 36.30 4.08
1147 1239 0.102120 CTTTGCACCGAGTTTTGGCA 59.898 50.000 0.00 0.00 0.00 4.92
1232 1324 4.753516 TTCATATGATGGGAGTTGTCGT 57.246 40.909 6.17 0.00 0.00 4.34
1299 1391 8.943085 ACCATAGAAATCACTCTATTTGAGGAT 58.057 33.333 0.33 0.00 46.72 3.24
1320 1412 3.505386 TGGTGATGGTGCAAATACCTTT 58.495 40.909 0.00 0.00 41.43 3.11
1416 1508 7.278875 TCTTTGGTGTTGCTTTTTCCAATAAT 58.721 30.769 0.00 0.00 37.87 1.28
1418 1510 6.418057 TGGTGTTGCTTTTTCCAATAATCT 57.582 33.333 0.00 0.00 0.00 2.40
1419 1511 6.454795 TGGTGTTGCTTTTTCCAATAATCTC 58.545 36.000 0.00 0.00 0.00 2.75
1424 1516 6.515272 TGCTTTTTCCAATAATCTCTGGTC 57.485 37.500 0.00 0.00 34.11 4.02
1501 1594 0.877743 GTTGGCTTGGCTCTGAACTC 59.122 55.000 0.00 0.00 0.00 3.01
1524 1617 3.074412 CGTGCCTATGACTTTGTTTCCT 58.926 45.455 0.00 0.00 0.00 3.36
1532 1625 7.122799 GCCTATGACTTTGTTTCCTAGGAAATT 59.877 37.037 33.92 18.69 44.52 1.82
1537 1630 5.826208 ACTTTGTTTCCTAGGAAATTCGTGT 59.174 36.000 33.92 24.95 44.52 4.49
1540 1633 6.105397 TGTTTCCTAGGAAATTCGTGTAGT 57.895 37.500 33.92 0.00 44.52 2.73
1616 1710 3.058160 GTGCGTGGATGGCAGCTT 61.058 61.111 1.50 0.00 41.83 3.74
1671 1765 0.618107 TACCAGTATGACCCGCCCAA 60.618 55.000 0.00 0.00 39.69 4.12
1711 1805 4.514066 CCTAATGGCGGGTTACATAAGAAC 59.486 45.833 0.00 0.00 0.00 3.01
1781 1876 2.441505 CCTGGGGGCCGGTTTAAA 59.558 61.111 1.90 0.00 0.00 1.52
1816 1911 0.935196 CCGCCGTATGTAAGGAAAGC 59.065 55.000 0.00 0.00 0.00 3.51
1964 2061 5.587043 ACAAGAAACAACCAAGTCGATAACA 59.413 36.000 0.00 0.00 0.00 2.41
2043 2140 5.161943 AGACGTAGGCTTTTACCTTCATT 57.838 39.130 0.00 0.00 41.50 2.57
2109 2206 2.577105 TCCCGATTAACCCCTTTAAGCA 59.423 45.455 0.00 0.00 36.07 3.91
2118 2215 3.190439 ACCCCTTTAAGCATCCTAGTGT 58.810 45.455 0.00 0.00 0.00 3.55
2136 2233 2.102588 GTGTGATGGCCCTACGACTAAT 59.897 50.000 0.00 0.00 0.00 1.73
2189 2286 4.947147 GACAGTTGGCGCCCACCA 62.947 66.667 25.83 3.07 38.16 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 169 4.530710 ATGTGTAGCGTAAAGGAGTTGA 57.469 40.909 0.00 0.00 0.00 3.18
219 233 8.871125 GGTGGAAGAACTAATATAGAGGATTCA 58.129 37.037 0.00 0.00 0.00 2.57
253 267 3.439857 TCTTTTCCCATTCCCTCTGTG 57.560 47.619 0.00 0.00 0.00 3.66
255 269 3.359950 CCTTCTTTTCCCATTCCCTCTG 58.640 50.000 0.00 0.00 0.00 3.35
491 582 5.532557 CCCTTTTTCAATGGTCTCAAAGAC 58.467 41.667 0.00 0.00 44.32 3.01
496 587 2.956132 TGCCCTTTTTCAATGGTCTCA 58.044 42.857 0.00 0.00 0.00 3.27
554 645 6.712095 TCATATCACTTTCCAAGGCATATGAC 59.288 38.462 6.97 2.74 37.99 3.06
666 757 9.395707 CGTAACTAGTCATCCATAGTATCAAAC 57.604 37.037 0.00 0.00 32.01 2.93
686 777 1.336240 CGAAACGGTCCCTTCGTAACT 60.336 52.381 11.08 0.00 40.18 2.24
712 804 4.464069 GCAATAGGCTAGACCATCCTAG 57.536 50.000 0.00 0.00 43.14 3.02
842 934 1.523758 AGAAACTGCTGCGGTTAAGG 58.476 50.000 25.69 0.00 32.14 2.69
869 961 7.639039 CAACAAAGAGTGTGCTAAACTATTGA 58.361 34.615 13.68 0.00 40.60 2.57
975 1067 2.031870 CCTATTAGTGCAAAAGCCCCC 58.968 52.381 0.00 0.00 0.00 5.40
1090 1182 8.463055 TGCCCTAGTGGATAAATAAGGAATAT 57.537 34.615 1.75 0.00 35.39 1.28
1110 1202 1.304134 GAACCAACCGGATTGCCCT 60.304 57.895 9.46 0.00 36.93 5.19
1119 1211 1.008995 CGGTGCAAAGAACCAACCG 60.009 57.895 0.00 0.00 37.57 4.44
1134 1226 1.453155 CTGCTATGCCAAAACTCGGT 58.547 50.000 0.00 0.00 0.00 4.69
1229 1321 1.605710 GAGCCGCACCTAATACTACGA 59.394 52.381 0.00 0.00 0.00 3.43
1232 1324 1.340248 GCAGAGCCGCACCTAATACTA 59.660 52.381 0.00 0.00 0.00 1.82
1283 1375 5.163269 CCATCACCATCCTCAAATAGAGTGA 60.163 44.000 0.00 0.00 43.12 3.41
1299 1391 2.897271 AGGTATTTGCACCATCACCA 57.103 45.000 0.00 0.00 41.40 4.17
1320 1412 2.920524 TGAGTTGGGTTAAAAGCACGA 58.079 42.857 0.00 0.00 0.00 4.35
1416 1508 5.441718 AGCATAAAGAAATGGACCAGAGA 57.558 39.130 0.00 0.00 0.00 3.10
1418 1510 7.615365 ACAAATAGCATAAAGAAATGGACCAGA 59.385 33.333 0.00 0.00 0.00 3.86
1419 1511 7.775120 ACAAATAGCATAAAGAAATGGACCAG 58.225 34.615 0.00 0.00 0.00 4.00
1424 1516 7.138736 CGGGTACAAATAGCATAAAGAAATGG 58.861 38.462 0.00 0.00 0.00 3.16
1501 1594 3.364964 GGAAACAAAGTCATAGGCACGTG 60.365 47.826 12.28 12.28 0.00 4.49
1524 1617 5.988310 TCTTCCACTACACGAATTTCCTA 57.012 39.130 0.00 0.00 0.00 2.94
1532 1625 3.081710 TCAGGATCTTCCACTACACGA 57.918 47.619 0.00 0.00 39.61 4.35
1537 1630 6.441924 AGTCTCAAATTCAGGATCTTCCACTA 59.558 38.462 0.00 0.00 39.61 2.74
1540 1633 5.768980 AGTCTCAAATTCAGGATCTTCCA 57.231 39.130 0.00 0.00 39.61 3.53
1711 1805 8.915057 ACTATCATCTTGAATGTTTATCAGGG 57.085 34.615 0.00 0.00 0.00 4.45
1771 1866 2.354821 CAGTATCAGGCTTTAAACCGGC 59.645 50.000 0.00 0.00 0.00 6.13
1776 1871 5.122711 GCGGTTTACAGTATCAGGCTTTAAA 59.877 40.000 0.00 0.00 0.00 1.52
1781 1876 1.134491 GGCGGTTTACAGTATCAGGCT 60.134 52.381 0.00 0.00 0.00 4.58
1816 1911 8.062065 TCCTTTACATGCCTTTATTTACAAGG 57.938 34.615 0.00 0.00 43.47 3.61
1825 1920 5.007682 GGTGACTTCCTTTACATGCCTTTA 58.992 41.667 0.00 0.00 0.00 1.85
1964 2061 2.038837 GGCTTAACTCGCCGGCTTT 61.039 57.895 26.68 16.84 37.87 3.51
2043 2140 2.530460 TACTAGTTCGGCCCCTTACA 57.470 50.000 0.00 0.00 0.00 2.41
2109 2206 2.330216 GTAGGGCCATCACACTAGGAT 58.670 52.381 6.18 0.00 0.00 3.24
2118 2215 2.367567 GGAATTAGTCGTAGGGCCATCA 59.632 50.000 6.18 0.00 0.00 3.07
2197 2294 3.039202 CTCAAATCCACCGTGCGCC 62.039 63.158 4.18 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.