Multiple sequence alignment - TraesCS2A01G243100

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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 TraesCS2A01G243100 chr2A 100.000 2321 0 0 1 2321 340609989 340607669 0 4287
1 TraesCS2A01G243100 chr2A 94.211 2332 91 11 1 2310 605786304 605788613 0 3518
2 TraesCS2A01G243100 chr2A 94.293 1139 53 5 3 1138 538629490 538628361 0 1733
3 TraesCS2A01G243100 chr2A 90.909 1177 79 19 1146 2311 538620864 538619705 0 1555
4 TraesCS2A01G243100 chr2A 95.106 899 30 2 1 885 15511946 15511048 0 1404
5 TraesCS2A01G243100 chr4A 94.886 2327 98 8 1 2310 525154200 525151878 0 3618
6 TraesCS2A01G243100 chr4A 93.008 2360 104 17 1 2307 549634083 549636434 0 3387
7 TraesCS2A01G243100 chr4A 95.086 1506 57 7 809 2310 29673360 29671868 0 2355
8 TraesCS2A01G243100 chr4A 94.024 1389 68 5 1 1375 52462309 52460922 0 2091
9 TraesCS2A01G243100 chr3A 94.067 2343 84 11 1 2310 733879830 733877510 0 3506
10 TraesCS2A01G243100 chr3A 94.003 1384 57 8 1 1372 676002754 676004123 0 2073
11 TraesCS2A01G243100 chr1A 92.668 2346 126 19 1 2310 7955949 7958284 0 3338
12 TraesCS2A01G243100 chr5B 94.399 1464 66 8 7 1456 117470887 117472348 0 2235
13 TraesCS2A01G243100 chr7B 94.437 1438 65 5 1 1424 615589542 615588106 0 2198
14 TraesCS2A01G243100 chr7B 93.741 1406 69 8 1 1387 551234888 551236293 0 2091
15 TraesCS2A01G243100 chr5A 93.583 1387 70 8 1 1384 530198246 530196876 0 2050
16 TraesCS2A01G243100 chr2B 91.149 1367 89 13 957 2310 750617348 750618695 0 1825
17 TraesCS2A01G243100 chr4B 90.929 1367 101 14 957 2310 668342812 668341456 0 1816
18 TraesCS2A01G243100 chr4B 89.059 1371 84 21 957 2310 39578742 39577421 0 1640
19 TraesCS2A01G243100 chr3B 90.916 1365 96 13 961 2310 29817209 29818560 0 1808
20 TraesCS2A01G243100 chr3B 94.196 672 36 1 1 669 765162403 765161732 0 1022
21 TraesCS2A01G243100 chr6A 94.874 1112 40 6 1207 2311 136675188 136676289 0 1722
22 TraesCS2A01G243100 chr1D 94.725 853 34 3 1 842 336730259 336729407 0 1315
23 TraesCS2A01G243100 chr2D 93.787 853 42 4 1 842 239256816 239257668 0 1271


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 TraesCS2A01G243100 chr2A 340607669 340609989 2320 True 4287 4287 100.000 1 2321 1 chr2A.!!$R2 2320
1 TraesCS2A01G243100 chr2A 605786304 605788613 2309 False 3518 3518 94.211 1 2310 1 chr2A.!!$F1 2309
2 TraesCS2A01G243100 chr2A 538628361 538629490 1129 True 1733 1733 94.293 3 1138 1 chr2A.!!$R4 1135
3 TraesCS2A01G243100 chr2A 538619705 538620864 1159 True 1555 1555 90.909 1146 2311 1 chr2A.!!$R3 1165
4 TraesCS2A01G243100 chr2A 15511048 15511946 898 True 1404 1404 95.106 1 885 1 chr2A.!!$R1 884
5 TraesCS2A01G243100 chr4A 525151878 525154200 2322 True 3618 3618 94.886 1 2310 1 chr4A.!!$R3 2309
6 TraesCS2A01G243100 chr4A 549634083 549636434 2351 False 3387 3387 93.008 1 2307 1 chr4A.!!$F1 2306
7 TraesCS2A01G243100 chr4A 29671868 29673360 1492 True 2355 2355 95.086 809 2310 1 chr4A.!!$R1 1501
8 TraesCS2A01G243100 chr4A 52460922 52462309 1387 True 2091 2091 94.024 1 1375 1 chr4A.!!$R2 1374
9 TraesCS2A01G243100 chr3A 733877510 733879830 2320 True 3506 3506 94.067 1 2310 1 chr3A.!!$R1 2309
10 TraesCS2A01G243100 chr3A 676002754 676004123 1369 False 2073 2073 94.003 1 1372 1 chr3A.!!$F1 1371
11 TraesCS2A01G243100 chr1A 7955949 7958284 2335 False 3338 3338 92.668 1 2310 1 chr1A.!!$F1 2309
12 TraesCS2A01G243100 chr5B 117470887 117472348 1461 False 2235 2235 94.399 7 1456 1 chr5B.!!$F1 1449
13 TraesCS2A01G243100 chr7B 615588106 615589542 1436 True 2198 2198 94.437 1 1424 1 chr7B.!!$R1 1423
14 TraesCS2A01G243100 chr7B 551234888 551236293 1405 False 2091 2091 93.741 1 1387 1 chr7B.!!$F1 1386
15 TraesCS2A01G243100 chr5A 530196876 530198246 1370 True 2050 2050 93.583 1 1384 1 chr5A.!!$R1 1383
16 TraesCS2A01G243100 chr2B 750617348 750618695 1347 False 1825 1825 91.149 957 2310 1 chr2B.!!$F1 1353
17 TraesCS2A01G243100 chr4B 668341456 668342812 1356 True 1816 1816 90.929 957 2310 1 chr4B.!!$R2 1353
18 TraesCS2A01G243100 chr4B 39577421 39578742 1321 True 1640 1640 89.059 957 2310 1 chr4B.!!$R1 1353
19 TraesCS2A01G243100 chr3B 29817209 29818560 1351 False 1808 1808 90.916 961 2310 1 chr3B.!!$F1 1349
20 TraesCS2A01G243100 chr3B 765161732 765162403 671 True 1022 1022 94.196 1 669 1 chr3B.!!$R1 668
21 TraesCS2A01G243100 chr6A 136675188 136676289 1101 False 1722 1722 94.874 1207 2311 1 chr6A.!!$F1 1104
22 TraesCS2A01G243100 chr1D 336729407 336730259 852 True 1315 1315 94.725 1 842 1 chr1D.!!$R1 841
23 TraesCS2A01G243100 chr2D 239256816 239257668 852 False 1271 1271 93.787 1 842 1 chr2D.!!$F1 841

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
88 92 1.885887 AGCCGCAAATAAAGTCAGCAA 59.114 42.857 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1461 0.79264 CTACCTGCTCAAACTGCACG 59.207 55.0 0.0 0.0 36.37 5.34 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
88 92 1.885887 AGCCGCAAATAAAGTCAGCAA 59.114 42.857 0.00 0.00 0.00 3.91
282 286 3.794028 GTCGAACAAGATGAATCGAGGAG 59.206 47.826 11.21 0.00 38.84 3.69
293 297 5.661056 TGAATCGAGGAGAAGTTGTGTAT 57.339 39.130 0.00 0.00 0.00 2.29
313 317 6.535508 GTGTATAATCAGAGAACTGGTTCCAC 59.464 42.308 9.51 5.33 43.00 4.02
769 814 4.069232 CGGCTCACTCGGGAAGCA 62.069 66.667 14.67 0.00 0.00 3.91
801 846 4.844884 AGAACCACCATTCTAGGCTTAAC 58.155 43.478 0.00 0.00 37.16 2.01
1033 1079 1.735559 GACACGCCGGTACCAGAAC 60.736 63.158 13.54 0.00 0.00 3.01
1034 1080 2.340809 CACGCCGGTACCAGAACA 59.659 61.111 13.54 0.00 0.00 3.18
1140 1186 3.295973 GCTCCAGTCATCTAGGAACTCT 58.704 50.000 0.00 0.00 41.75 3.24
1215 1279 0.612744 AGAGGTCTGAGCTTCAAGCC 59.387 55.000 11.11 0.00 43.77 4.35
1219 1283 1.512926 GTCTGAGCTTCAAGCCGAAA 58.487 50.000 5.53 0.00 43.77 3.46
1220 1284 1.462670 GTCTGAGCTTCAAGCCGAAAG 59.537 52.381 5.53 0.00 43.77 2.62
1265 1329 3.955471 TCAAGATGAAGGCGGAAGAATT 58.045 40.909 0.00 0.00 0.00 2.17
1376 1461 0.457443 GCTAAGGCAGTTTGATGGCC 59.543 55.000 0.00 0.00 46.42 5.36
1422 1518 0.389426 GCTGCCTTGTTTGATGGCTG 60.389 55.000 0.00 0.00 43.90 4.85
1479 1592 3.468770 TGAGCATTTTGTTGCATTGCTT 58.531 36.364 10.49 0.00 43.29 3.91
1647 1841 0.679002 CCTGGGCTTGTGGATCACTG 60.679 60.000 0.00 0.00 35.11 3.66
1648 1842 0.325933 CTGGGCTTGTGGATCACTGA 59.674 55.000 0.00 0.00 35.11 3.41
1664 1858 0.899720 CTGATGCACATGGGCCTTTT 59.100 50.000 19.33 0.00 0.00 2.27
1740 1934 7.598869 CCAAACAAGAATTAGACTAAAAAGGCC 59.401 37.037 0.00 0.00 0.00 5.19
2003 2220 0.978667 TTGGCCCATGTAGACGGCTA 60.979 55.000 0.00 0.00 42.58 3.93
2031 2248 4.448210 GACCGGGCTGATTCTATTTTACA 58.552 43.478 6.32 0.00 0.00 2.41
2060 2277 2.459060 TTCGGTCGTAATTCTGCCAA 57.541 45.000 0.00 0.00 0.00 4.52
2202 2422 4.913924 GTCACTAATGTCAGTTTACGACGT 59.086 41.667 5.52 5.52 36.11 4.34
2215 2435 2.787601 ACGACGTCTAGCTTTTGACA 57.212 45.000 14.70 0.00 33.18 3.58
2311 2531 6.743575 AGTTGACATATTTCTTGTAGTGCC 57.256 37.500 0.00 0.00 0.00 5.01
2312 2532 6.476378 AGTTGACATATTTCTTGTAGTGCCT 58.524 36.000 0.00 0.00 0.00 4.75
2313 2533 6.942576 AGTTGACATATTTCTTGTAGTGCCTT 59.057 34.615 0.00 0.00 0.00 4.35
2314 2534 6.985188 TGACATATTTCTTGTAGTGCCTTC 57.015 37.500 0.00 0.00 0.00 3.46
2315 2535 6.472016 TGACATATTTCTTGTAGTGCCTTCA 58.528 36.000 0.00 0.00 0.00 3.02
2316 2536 6.939730 TGACATATTTCTTGTAGTGCCTTCAA 59.060 34.615 0.00 0.00 0.00 2.69
2317 2537 7.446931 TGACATATTTCTTGTAGTGCCTTCAAA 59.553 33.333 0.00 0.00 0.00 2.69
2318 2538 7.593825 ACATATTTCTTGTAGTGCCTTCAAAC 58.406 34.615 0.00 0.00 0.00 2.93
2319 2539 4.545823 TTTCTTGTAGTGCCTTCAAACG 57.454 40.909 0.00 0.00 0.00 3.60
2320 2540 2.489971 TCTTGTAGTGCCTTCAAACGG 58.510 47.619 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 92 3.387374 CAGATCAGGCACCAGAGACTTAT 59.613 47.826 0.00 0.00 0.00 1.73
282 286 7.819900 ACCAGTTCTCTGATTATACACAACTTC 59.180 37.037 0.00 0.00 43.76 3.01
293 297 3.616560 GCGTGGAACCAGTTCTCTGATTA 60.617 47.826 10.19 0.00 43.76 1.75
313 317 3.332761 AAATGTGTGTTGTGTAGTGCG 57.667 42.857 0.00 0.00 0.00 5.34
555 559 1.412079 TCAAACAGGGCAAAGCATGT 58.588 45.000 0.00 0.00 32.77 3.21
729 774 7.467811 GCCGATCATCAAACTAACATTCAGATT 60.468 37.037 0.00 0.00 0.00 2.40
867 912 2.297701 AGTAACCAAACCAGCACACAG 58.702 47.619 0.00 0.00 0.00 3.66
1033 1079 2.161808 CAGCAGACTTTGGCTCTTCATG 59.838 50.000 0.00 0.00 38.56 3.07
1034 1080 2.224719 ACAGCAGACTTTGGCTCTTCAT 60.225 45.455 0.00 0.00 38.56 2.57
1215 1279 4.418392 CCAATTCTTCTTGCATCCTTTCG 58.582 43.478 0.00 0.00 0.00 3.46
1219 1283 1.747355 CGCCAATTCTTCTTGCATCCT 59.253 47.619 0.00 0.00 0.00 3.24
1220 1284 1.202336 CCGCCAATTCTTCTTGCATCC 60.202 52.381 0.00 0.00 0.00 3.51
1265 1329 2.104770 CTTGTCGCGTGCAGCTTCAA 62.105 55.000 5.77 1.32 45.59 2.69
1291 1355 3.056536 TGAGACTTCTTGCGCAGTAGATT 60.057 43.478 11.31 1.67 0.00 2.40
1293 1357 1.886542 TGAGACTTCTTGCGCAGTAGA 59.113 47.619 11.31 9.27 0.00 2.59
1376 1461 0.792640 CTACCTGCTCAAACTGCACG 59.207 55.000 0.00 0.00 36.37 5.34
1410 1506 2.288948 GCCATCAAACAGCCATCAAACA 60.289 45.455 0.00 0.00 0.00 2.83
1422 1518 2.508526 AGAGGTTCACAGCCATCAAAC 58.491 47.619 0.00 0.00 0.00 2.93
1479 1592 4.102524 ACAGGTTCACATAACTTCACAGGA 59.897 41.667 0.00 0.00 0.00 3.86
1647 1841 1.002315 ACAAAAAGGCCCATGTGCATC 59.998 47.619 0.00 0.00 0.00 3.91
1648 1842 1.058284 ACAAAAAGGCCCATGTGCAT 58.942 45.000 0.00 0.00 0.00 3.96
1654 1848 7.093112 TGCATAACTATAAACAAAAAGGCCCAT 60.093 33.333 0.00 0.00 0.00 4.00
2003 2220 1.005924 AGAATCAGCCCGGTCCATTTT 59.994 47.619 0.00 0.00 0.00 1.82
2031 2248 5.704053 AGAATTACGACCGAATGAAAAGGTT 59.296 36.000 0.00 0.00 38.57 3.50
2043 2260 1.659098 GACTTGGCAGAATTACGACCG 59.341 52.381 0.00 0.00 0.00 4.79
2060 2277 2.281070 CACCGTGGCAAGCTGACT 60.281 61.111 0.00 0.00 0.00 3.41
2149 2369 5.657474 TCTGGAATGGTCGTAGATGTTTAC 58.343 41.667 0.00 0.00 40.67 2.01
2182 2402 5.368256 AGACGTCGTAAACTGACATTAGT 57.632 39.130 10.46 0.00 36.11 2.24
2202 2422 8.637986 ACCAAAAACATAATGTCAAAAGCTAGA 58.362 29.630 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.