Multiple sequence alignment - TraesCS4A01G152100

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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 TraesCS4A01G152100 chr4A 100.000 2369 0 0 1 2369 309287792 309290160 0 4375
1 TraesCS4A01G152100 chr4A 96.135 1035 38 2 1334 2368 281750015 281748983 0 1688
2 TraesCS4A01G152100 chr4A 95.455 1034 42 4 1337 2369 175989605 175990634 0 1644
3 TraesCS4A01G152100 chr4A 95.349 1032 46 1 1337 2368 599205740 599206769 0 1639
4 TraesCS4A01G152100 chr2D 97.386 1339 33 2 1 1337 648662256 648663594 0 2278
5 TraesCS4A01G152100 chr2D 97.659 1239 27 2 1 1237 648659916 648661154 0 2126
6 TraesCS4A01G152100 chr5D 97.311 1339 34 2 1 1337 6234853 6236191 0 2272
7 TraesCS4A01G152100 chr7D 95.737 1337 48 3 1 1337 88618041 88619368 0 2145
8 TraesCS4A01G152100 chr1A 97.415 1238 31 1 1 1237 554445091 554446328 0 2108
9 TraesCS4A01G152100 chr1A 97.340 1128 29 1 211 1337 554447109 554448236 0 1916
10 TraesCS4A01G152100 chr1A 95.833 1032 41 2 1338 2368 223889850 223890880 0 1666
11 TraesCS4A01G152100 chr1D 97.346 1055 25 3 285 1337 254477760 254476707 0 1790
12 TraesCS4A01G152100 chr1D 97.497 919 22 1 250 1167 180355095 180356013 0 1568
13 TraesCS4A01G152100 chr1D 95.135 925 43 2 414 1337 244201924 244201001 0 1458
14 TraesCS4A01G152100 chr1D 94.924 926 42 5 414 1337 244769112 244768190 0 1445
15 TraesCS4A01G152100 chr7A 95.640 1032 44 1 1338 2368 80226992 80228023 0 1655
16 TraesCS4A01G152100 chr7A 95.640 1032 44 1 1338 2369 270118051 270119081 0 1655
17 TraesCS4A01G152100 chr2A 95.358 1034 46 2 1337 2369 159754879 159755911 0 1642
18 TraesCS4A01G152100 chr5A 95.096 1040 50 1 1330 2368 647320401 647321440 0 1637
19 TraesCS4A01G152100 chr3A 95.091 1039 48 2 1333 2369 502210602 502211639 0 1633
20 TraesCS4A01G152100 chrUn 97.275 954 25 1 310 1262 457255788 457254835 0 1616


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 TraesCS4A01G152100 chr4A 309287792 309290160 2368 False 4375 4375 100.0000 1 2369 1 chr4A.!!$F2 2368
1 TraesCS4A01G152100 chr4A 281748983 281750015 1032 True 1688 1688 96.1350 1334 2368 1 chr4A.!!$R1 1034
2 TraesCS4A01G152100 chr4A 175989605 175990634 1029 False 1644 1644 95.4550 1337 2369 1 chr4A.!!$F1 1032
3 TraesCS4A01G152100 chr4A 599205740 599206769 1029 False 1639 1639 95.3490 1337 2368 1 chr4A.!!$F3 1031
4 TraesCS4A01G152100 chr2D 648659916 648663594 3678 False 2202 2278 97.5225 1 1337 2 chr2D.!!$F1 1336
5 TraesCS4A01G152100 chr5D 6234853 6236191 1338 False 2272 2272 97.3110 1 1337 1 chr5D.!!$F1 1336
6 TraesCS4A01G152100 chr7D 88618041 88619368 1327 False 2145 2145 95.7370 1 1337 1 chr7D.!!$F1 1336
7 TraesCS4A01G152100 chr1A 554445091 554448236 3145 False 2012 2108 97.3775 1 1337 2 chr1A.!!$F2 1336
8 TraesCS4A01G152100 chr1A 223889850 223890880 1030 False 1666 1666 95.8330 1338 2368 1 chr1A.!!$F1 1030
9 TraesCS4A01G152100 chr1D 254476707 254477760 1053 True 1790 1790 97.3460 285 1337 1 chr1D.!!$R3 1052
10 TraesCS4A01G152100 chr1D 180355095 180356013 918 False 1568 1568 97.4970 250 1167 1 chr1D.!!$F1 917
11 TraesCS4A01G152100 chr1D 244201001 244201924 923 True 1458 1458 95.1350 414 1337 1 chr1D.!!$R1 923
12 TraesCS4A01G152100 chr1D 244768190 244769112 922 True 1445 1445 94.9240 414 1337 1 chr1D.!!$R2 923
13 TraesCS4A01G152100 chr7A 80226992 80228023 1031 False 1655 1655 95.6400 1338 2368 1 chr7A.!!$F1 1030
14 TraesCS4A01G152100 chr7A 270118051 270119081 1030 False 1655 1655 95.6400 1338 2369 1 chr7A.!!$F2 1031
15 TraesCS4A01G152100 chr2A 159754879 159755911 1032 False 1642 1642 95.3580 1337 2369 1 chr2A.!!$F1 1032
16 TraesCS4A01G152100 chr5A 647320401 647321440 1039 False 1637 1637 95.0960 1330 2368 1 chr5A.!!$F1 1038
17 TraesCS4A01G152100 chr3A 502210602 502211639 1037 False 1633 1633 95.0910 1333 2369 1 chr3A.!!$F1 1036
18 TraesCS4A01G152100 chrUn 457254835 457255788 953 True 1616 1616 97.2750 310 1262 1 chrUn.!!$R1 952

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
80 81 1.843368 AGGTCTACGGTTCGAATCCA 58.157 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 5938 0.030092 CCTGGATTAGGGGGTCTCCA 60.03 60.0 0.0 0.0 43.33 3.86 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
80 81 1.843368 AGGTCTACGGTTCGAATCCA 58.157 50.000 0.00 0.0 0.00 3.41
215 216 6.033341 GCCTGCGACATAGAATAGAGATAAG 58.967 44.000 0.00 0.0 0.00 1.73
395 396 8.129161 TGCAATTATTTTATCCATTTTGCGAG 57.871 30.769 0.00 0.0 40.69 5.03
867 2680 4.021981 GCACAGAGGAAACAAAGGCTAAAT 60.022 41.667 0.00 0.0 0.00 1.40
873 2686 6.493458 AGAGGAAACAAAGGCTAAATTAAGCA 59.507 34.615 0.00 0.0 44.64 3.91
874 2687 7.179160 AGAGGAAACAAAGGCTAAATTAAGCAT 59.821 33.333 0.00 0.0 44.64 3.79
948 2761 6.441093 TCTGGATAAATTGACAATGCTGAC 57.559 37.500 0.34 0.0 0.00 3.51
1088 5240 3.153130 TGGCATTTTCGATTTCAGGACA 58.847 40.909 0.00 0.0 0.00 4.02
1092 5244 5.639082 GGCATTTTCGATTTCAGGACATTTT 59.361 36.000 0.00 0.0 0.00 1.82
1114 5266 0.688487 CCCGGTTAGTGAAGGACCAA 59.312 55.000 0.00 0.0 32.95 3.67
1120 5272 4.502604 CGGTTAGTGAAGGACCAAAGAAGA 60.503 45.833 0.00 0.0 32.95 2.87
1124 5276 7.363431 GTTAGTGAAGGACCAAAGAAGATTTG 58.637 38.462 0.00 0.0 0.00 2.32
1196 5350 8.821147 TTCCGAATACGCTATTATATGTTTGT 57.179 30.769 0.00 0.0 38.29 2.83
1232 5386 4.201970 TGTTTTTGATGTGGAAACCGTCTC 60.202 41.667 0.00 0.0 33.49 3.36
1276 5430 2.377073 TCGACGTATTGGGTGTATCCA 58.623 47.619 0.00 0.0 38.11 3.41
1340 5495 4.082300 TGGTTTAGTTTATGCATGGCTGTG 60.082 41.667 10.16 0.0 0.00 3.66
1351 5506 1.619827 CATGGCTGTGGGTGTCAAAAT 59.380 47.619 0.00 0.0 0.00 1.82
1356 5511 1.411977 CTGTGGGTGTCAAAATTGGCA 59.588 47.619 0.00 0.0 41.08 4.92
1373 5528 2.201771 AGATCTCGGGTAGGGGGC 59.798 66.667 0.00 0.0 0.00 5.80
1482 5637 5.494390 AACCCTACGTCCTACTTGATTTT 57.506 39.130 0.00 0.0 0.00 1.82
1595 5750 3.463048 TCCTACGGACTAAAACCCTCT 57.537 47.619 0.00 0.0 0.00 3.69
1653 5808 1.622312 AGGTCGGTTACAAAGGAGGAC 59.378 52.381 0.00 0.0 0.00 3.85
1758 5914 3.427573 TCTTCATAGTCCAACAGTCCGA 58.572 45.455 0.00 0.0 0.00 4.55
2210 6370 2.841881 TGGGGGATAAGCGAGTTTTACT 59.158 45.455 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 216 3.696051 TGAATGAGCCTTTGGTAATGCTC 59.304 43.478 3.51 3.51 46.23 4.26
376 377 7.639113 AGGAACTCGCAAAATGGATAAAATA 57.361 32.000 0.00 0.00 0.00 1.40
508 511 9.296400 GAACTCTATTTCAGAACTATGAGACAC 57.704 37.037 10.97 0.00 31.12 3.67
790 2603 3.052490 TCCCAACTCCCTTTCTTTTGGAA 60.052 43.478 0.12 0.00 39.33 3.53
948 2761 9.346725 GGCAGAACTTAAATTAGTCAATTCAAG 57.653 33.333 0.00 0.00 36.03 3.02
1088 5240 2.167662 CTTCACTAACCGGGGCAAAAT 58.832 47.619 6.32 0.00 0.00 1.82
1092 5244 1.536907 TCCTTCACTAACCGGGGCA 60.537 57.895 6.32 0.00 0.00 5.36
1114 5266 8.047310 ACCCGATTCATAACTACAAATCTTCTT 58.953 33.333 0.00 0.00 0.00 2.52
1156 5310 1.373590 CGGAATTGTACCCAAGCCCG 61.374 60.000 0.00 0.00 40.55 6.13
1196 5350 5.406780 ACATCAAAAACAACAAAAACGAGCA 59.593 32.000 0.00 0.00 0.00 4.26
1232 5386 3.392616 ACTCATTGCCCAAGGGTATAGAG 59.607 47.826 17.66 17.66 37.26 2.43
1276 5430 8.638565 CACGAAAATCAAAGCTTCGATAAAAAT 58.361 29.630 0.00 0.00 43.53 1.82
1340 5495 2.827921 AGATCTGCCAATTTTGACACCC 59.172 45.455 0.00 0.00 0.00 4.61
1351 5506 1.048724 CCCTACCCGAGATCTGCCAA 61.049 60.000 0.00 0.00 0.00 4.52
1356 5511 2.201771 GCCCCCTACCCGAGATCT 59.798 66.667 0.00 0.00 0.00 2.75
1373 5528 0.944386 CTTTGACACACAGTTCGGGG 59.056 55.000 0.00 0.00 0.00 5.73
1482 5637 8.988060 TCTTGTACTACCCATATCATCAAGAAA 58.012 33.333 0.00 0.00 36.78 2.52
1595 5750 3.899360 CCCTCCGGTGTCTATATAAACCA 59.101 47.826 0.00 0.00 32.69 3.67
1653 5808 7.661968 AGCTAGGCAATACGGATATGTATATG 58.338 38.462 0.00 0.00 34.01 1.78
1782 5938 0.030092 CCTGGATTAGGGGGTCTCCA 60.030 60.000 0.00 0.00 43.33 3.86
1934 6092 5.279456 GGAATGTGGAACTTATTTTGCAGGT 60.279 40.000 0.00 0.00 38.04 4.00
2103 6263 3.350833 GGGACACAATCTCTGCTTTGAT 58.649 45.455 0.00 0.00 0.00 2.57
2210 6370 2.666469 TATGCGCCCCCACTAGCCTA 62.666 60.000 4.18 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.