Multiple sequence alignment - TraesCS5D01G358100

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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 TraesCS5D01G358100 chr5D 100.000 2561 0 0 1 2561 438455304 438452744 0.000000e+00 4730
1 TraesCS5D01G358100 chr5D 89.481 1521 144 11 46 1554 438559121 438557605 0.000000e+00 1908
2 TraesCS5D01G358100 chr5D 85.406 1576 197 23 1 1554 438545265 438543701 0.000000e+00 1605
3 TraesCS5D01G358100 chr5D 83.544 1501 223 18 71 1554 438605222 438603729 0.000000e+00 1382
4 TraesCS5D01G358100 chr5D 82.368 1554 243 21 23 1554 438521635 438520091 0.000000e+00 1323
5 TraesCS5D01G358100 chr5A 97.724 1362 29 2 194 1554 553538907 553537547 0.000000e+00 2342
6 TraesCS5D01G358100 chr5A 95.182 1017 39 7 1551 2561 553537519 553536507 0.000000e+00 1598
7 TraesCS5D01G358100 chr5A 84.615 1573 213 22 1 1554 554060557 554058995 0.000000e+00 1537
8 TraesCS5D01G358100 chr5A 85.885 1169 145 13 142 1295 554112644 554111481 0.000000e+00 1227
9 TraesCS5D01G358100 chr5B 90.944 1557 120 12 4 1554 533089247 533087706 0.000000e+00 2074
10 TraesCS5D01G358100 chr5B 83.400 1500 226 18 71 1554 533509302 533507810 0.000000e+00 1369
11 TraesCS5D01G358100 chr5B 83.301 1527 199 27 48 1554 533383854 533382364 0.000000e+00 1356
12 TraesCS5D01G358100 chr5B 82.251 1555 240 25 23 1554 533389733 533388192 0.000000e+00 1310
13 TraesCS5D01G358100 chr5B 80.834 1487 231 35 94 1554 533451375 533449917 0.000000e+00 1118
14 TraesCS5D01G358100 chr5B 82.462 1186 174 20 382 1554 533565199 533564035 0.000000e+00 1007
15 TraesCS5D01G358100 chr5B 79.908 652 81 26 1551 2164 533087678 533087039 1.410000e-117 433
16 TraesCS5D01G358100 chr5B 83.010 412 61 7 2150 2560 533085015 533084612 5.210000e-97 364


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 TraesCS5D01G358100 chr5D 438452744 438455304 2560 True 4730 4730 100.000000 1 2561 1 chr5D.!!$R1 2560
1 TraesCS5D01G358100 chr5D 438557605 438559121 1516 True 1908 1908 89.481000 46 1554 1 chr5D.!!$R4 1508
2 TraesCS5D01G358100 chr5D 438543701 438545265 1564 True 1605 1605 85.406000 1 1554 1 chr5D.!!$R3 1553
3 TraesCS5D01G358100 chr5D 438603729 438605222 1493 True 1382 1382 83.544000 71 1554 1 chr5D.!!$R5 1483
4 TraesCS5D01G358100 chr5D 438520091 438521635 1544 True 1323 1323 82.368000 23 1554 1 chr5D.!!$R2 1531
5 TraesCS5D01G358100 chr5A 553536507 553538907 2400 True 1970 2342 96.453000 194 2561 2 chr5A.!!$R3 2367
6 TraesCS5D01G358100 chr5A 554058995 554060557 1562 True 1537 1537 84.615000 1 1554 1 chr5A.!!$R1 1553
7 TraesCS5D01G358100 chr5A 554111481 554112644 1163 True 1227 1227 85.885000 142 1295 1 chr5A.!!$R2 1153
8 TraesCS5D01G358100 chr5B 533507810 533509302 1492 True 1369 1369 83.400000 71 1554 1 chr5B.!!$R4 1483
9 TraesCS5D01G358100 chr5B 533382364 533383854 1490 True 1356 1356 83.301000 48 1554 1 chr5B.!!$R1 1506
10 TraesCS5D01G358100 chr5B 533388192 533389733 1541 True 1310 1310 82.251000 23 1554 1 chr5B.!!$R2 1531
11 TraesCS5D01G358100 chr5B 533449917 533451375 1458 True 1118 1118 80.834000 94 1554 1 chr5B.!!$R3 1460
12 TraesCS5D01G358100 chr5B 533564035 533565199 1164 True 1007 1007 82.462000 382 1554 1 chr5B.!!$R5 1172
13 TraesCS5D01G358100 chr5B 533084612 533089247 4635 True 957 2074 84.620667 4 2560 3 chr5B.!!$R6 2556

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
257 266 2.079170 TGCAACCCACAATTTCTCCA 57.921 45.000 0.0 0.0 0.0 3.86 F
427 453 2.808543 GGTCAAGAAGTCGCAGTCAAAT 59.191 45.455 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1173 1.476833 GCGAGGCTGGAAAATCCCATA 60.477 52.381 0.0 0.0 35.03 2.74 R
2314 4491 0.878416 CCGGCTTTTTGTGATTCCGA 59.122 50.000 0.0 0.0 39.23 4.55 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
257 266 2.079170 TGCAACCCACAATTTCTCCA 57.921 45.000 0.00 0.00 0.00 3.86
427 453 2.808543 GGTCAAGAAGTCGCAGTCAAAT 59.191 45.455 0.00 0.00 0.00 2.32
475 501 7.543756 AGGAACAAAAGAATTCAAGAACGAAA 58.456 30.769 8.44 0.00 0.00 3.46
623 649 7.767250 TTGGTACATATTCCAATGACAAACA 57.233 32.000 0.00 0.00 39.30 2.83
624 650 7.953005 TGGTACATATTCCAATGACAAACAT 57.047 32.000 0.00 0.00 41.45 2.71
625 651 9.467796 TTGGTACATATTCCAATGACAAACATA 57.532 29.630 0.00 0.00 39.30 2.29
626 652 9.639563 TGGTACATATTCCAATGACAAACATAT 57.360 29.630 0.00 0.00 38.38 1.78
643 673 9.131791 ACAAACATATTTTCCTAACACAACTCT 57.868 29.630 0.00 0.00 0.00 3.24
652 684 6.613755 TCCTAACACAACTCTACTTTTTGC 57.386 37.500 0.00 0.00 0.00 3.68
731 766 7.971722 ACAACACGGTTTAATATAATCAAAGGC 59.028 33.333 0.00 0.00 0.00 4.35
992 1049 4.422073 TTCTTTGGGTATGATCGAGCAT 57.578 40.909 21.25 21.25 0.00 3.79
1566 1668 2.038557 GGGACGATGTACCTAATGCCAT 59.961 50.000 0.00 0.00 32.80 4.40
1674 1776 4.775780 ACACAGTATACTTGGCTAAGGTCA 59.224 41.667 14.86 0.00 38.26 4.02
1764 1868 4.097437 CGGCAACTAGATGTAGGTCAAGTA 59.903 45.833 0.00 0.00 0.00 2.24
1808 1912 7.328737 ACTTAACTATAAGCCGAGTGTTGAAT 58.671 34.615 0.00 0.00 41.92 2.57
1824 1928 0.536006 GAATAGGGCTGCTCGGCATT 60.536 55.000 0.00 0.00 38.13 3.56
1886 1990 7.551974 ACAATGTGTTGAAACATTTCATTTGGA 59.448 29.630 7.83 0.00 46.19 3.53
1983 2096 7.238486 AGAGTTCTGAAGCTCTTCTCAATAA 57.762 36.000 13.29 0.00 38.81 1.40
2109 2245 1.675641 GCAACGGCCCTCTTCACAT 60.676 57.895 0.00 0.00 0.00 3.21
2283 4459 0.173935 CCAGTACATGCCGAACCGTA 59.826 55.000 0.00 0.00 0.00 4.02
2288 4464 2.981400 ACATGCCGAACCGTAAAAAG 57.019 45.000 0.00 0.00 0.00 2.27
2310 4487 6.753897 AGAAACAAATTCGACTGAAAATGC 57.246 33.333 0.00 0.00 43.15 3.56
2313 4490 5.200368 ACAAATTCGACTGAAAATGCCTT 57.800 34.783 0.00 0.00 37.71 4.35
2314 4491 5.600696 ACAAATTCGACTGAAAATGCCTTT 58.399 33.333 0.00 0.00 37.71 3.11
2324 4501 3.571828 TGAAAATGCCTTTCGGAATCACA 59.428 39.130 0.00 0.00 45.59 3.58
2335 4513 0.246360 GGAATCACAAAAAGCCGGGG 59.754 55.000 2.18 0.00 0.00 5.73
2462 4643 7.890655 GCAATTAATAAGGATTGGAGGGAGTAT 59.109 37.037 0.00 0.00 34.60 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 8.214721 AGGCATAAGAAAGAAACTGTTATAGC 57.785 34.615 0.00 0.00 0.00 2.97
92 100 1.855213 TTGCCTGCTCGCACAATGTC 61.855 55.000 0.00 0.00 38.83 3.06
139 147 4.516698 GCACTCATACCACCCAATCTTATG 59.483 45.833 0.00 0.00 0.00 1.90
257 266 7.037297 TCCTCCTTGTCCAATCTTAGATTCTTT 60.037 37.037 4.24 0.00 0.00 2.52
427 453 6.351371 CCTTGTTGAGAATCTCTACTTAGCCA 60.351 42.308 21.51 2.24 37.20 4.75
626 652 7.971722 GCAAAAAGTAGAGTTGTGTTAGGAAAA 59.028 33.333 0.00 0.00 0.00 2.29
630 656 6.430451 CAGCAAAAAGTAGAGTTGTGTTAGG 58.570 40.000 0.00 0.00 0.00 2.69
643 673 7.978975 AGAAACAAATGTAAGCAGCAAAAAGTA 59.021 29.630 0.00 0.00 0.00 2.24
645 675 7.237920 AGAAACAAATGTAAGCAGCAAAAAG 57.762 32.000 0.00 0.00 0.00 2.27
731 766 0.394352 ATAGAAGCCCCCTTGCAACG 60.394 55.000 0.00 0.00 0.00 4.10
992 1049 0.543277 CTCAGGAGCCATGTAGCCAA 59.457 55.000 0.00 0.00 0.00 4.52
1116 1173 1.476833 GCGAGGCTGGAAAATCCCATA 60.477 52.381 0.00 0.00 35.03 2.74
1230 1299 9.846248 GACTAAAACAAGCAAGAACATCATATT 57.154 29.630 0.00 0.00 0.00 1.28
1566 1668 4.597404 TTGTGAGCCATACAATTTGCAA 57.403 36.364 0.00 0.00 33.43 4.08
1764 1868 2.883386 AGTCGAGTAGTGGACGAAAAGT 59.117 45.455 7.02 0.00 36.56 2.66
1808 1912 1.639722 TATAATGCCGAGCAGCCCTA 58.360 50.000 4.90 0.00 43.65 3.53
1824 1928 7.494211 TCGGCTTATAGTCAAAGTGCTTTATA 58.506 34.615 0.00 0.00 0.00 0.98
2071 2190 3.244457 TGCATGCATTCTCTCTCCCATAG 60.244 47.826 18.46 0.00 0.00 2.23
2109 2245 1.599606 GCCAGGAGAGAGCGTGAGAA 61.600 60.000 0.00 0.00 0.00 2.87
2283 4459 9.971744 CATTTTCAGTCGAATTTGTTTCTTTTT 57.028 25.926 0.00 0.00 31.73 1.94
2288 4464 5.691754 AGGCATTTTCAGTCGAATTTGTTTC 59.308 36.000 0.00 0.00 0.00 2.78
2313 4490 1.268352 CCGGCTTTTTGTGATTCCGAA 59.732 47.619 0.00 0.00 39.23 4.30
2314 4491 0.878416 CCGGCTTTTTGTGATTCCGA 59.122 50.000 0.00 0.00 39.23 4.55
2324 4501 1.604147 GCATAGCACCCCGGCTTTTT 61.604 55.000 0.00 0.00 42.71 1.94
2335 4513 3.278574 TGTTTGTCCCATAGCATAGCAC 58.721 45.455 0.00 0.00 0.00 4.40
2434 4615 5.103301 TCCCTCCAATCCTTATTAATTGCCA 60.103 40.000 0.00 0.00 32.65 4.92
2482 4663 6.194796 TGAAGTAGGCATAATTTGTTCTGC 57.805 37.500 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.