Multiple sequence alignment - TraesCS1A01G014700

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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 TraesCS1A01G014700 chr1A 100.000 2324 0 0 1 2324 7955960 7958283 0 4292
1 TraesCS1A01G014700 chr1A 93.560 1646 69 23 1 1633 539843255 539841634 0 2418
2 TraesCS1A01G014700 chr1A 97.121 903 23 3 1425 2324 539841887 539840985 0 1520
3 TraesCS1A01G014700 chr2A 97.376 2325 58 3 1 2324 55069647 55067325 0 3952
4 TraesCS1A01G014700 chr2A 96.817 2325 69 4 1 2324 599672284 599669964 0 3879
5 TraesCS1A01G014700 chr6A 97.246 2324 62 1 1 2324 436398644 436400965 0 3936
6 TraesCS1A01G014700 chr6A 90.974 1119 76 17 1211 2324 136675189 136676287 0 1483
7 TraesCS1A01G014700 chr5A 97.246 2324 60 4 1 2324 345653536 345651217 0 3934
8 TraesCS1A01G014700 chr5A 96.862 2326 65 7 1 2324 634752626 634754945 0 3884
9 TraesCS1A01G014700 chr7A 96.903 2325 69 2 1 2324 639853105 639850783 0 3892
10 TraesCS1A01G014700 chr7A 96.731 2325 73 2 1 2324 578424342 578422020 0 3869
11 TraesCS1A01G014700 chr7A 94.346 1751 72 4 1 1743 734442707 734444438 0 2660
12 TraesCS1A01G014700 chr7A 95.289 934 22 5 1394 2324 493525420 493526334 0 1461


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 TraesCS1A01G014700 chr1A 7955960 7958283 2323 False 4292 4292 100.0000 1 2324 1 chr1A.!!$F1 2323
1 TraesCS1A01G014700 chr1A 539840985 539843255 2270 True 1969 2418 95.3405 1 2324 2 chr1A.!!$R1 2323
2 TraesCS1A01G014700 chr2A 55067325 55069647 2322 True 3952 3952 97.3760 1 2324 1 chr2A.!!$R1 2323
3 TraesCS1A01G014700 chr2A 599669964 599672284 2320 True 3879 3879 96.8170 1 2324 1 chr2A.!!$R2 2323
4 TraesCS1A01G014700 chr6A 436398644 436400965 2321 False 3936 3936 97.2460 1 2324 1 chr6A.!!$F2 2323
5 TraesCS1A01G014700 chr6A 136675189 136676287 1098 False 1483 1483 90.9740 1211 2324 1 chr6A.!!$F1 1113
6 TraesCS1A01G014700 chr5A 345651217 345653536 2319 True 3934 3934 97.2460 1 2324 1 chr5A.!!$R1 2323
7 TraesCS1A01G014700 chr5A 634752626 634754945 2319 False 3884 3884 96.8620 1 2324 1 chr5A.!!$F1 2323
8 TraesCS1A01G014700 chr7A 639850783 639853105 2322 True 3892 3892 96.9030 1 2324 1 chr7A.!!$R2 2323
9 TraesCS1A01G014700 chr7A 578422020 578424342 2322 True 3869 3869 96.7310 1 2324 1 chr7A.!!$R1 2323
10 TraesCS1A01G014700 chr7A 734442707 734444438 1731 False 2660 2660 94.3460 1 1743 1 chr7A.!!$F2 1742
11 TraesCS1A01G014700 chr7A 493525420 493526334 914 False 1461 1461 95.2890 1394 2324 1 chr7A.!!$F1 930

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
531 535 1.91924 TTCGGAGCCAGTCAAGACTA 58.081 50.0 1.86 0.0 40.2 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1409 0.038744 AGGCAGCAATGCAACTACCT 59.961 50.0 8.35 3.32 36.33 3.08 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
531 535 1.919240 TTCGGAGCCAGTCAAGACTA 58.081 50.000 1.86 0.00 40.20 2.59
571 575 2.633967 TGCTTTGCCCTGTTTGATTCAT 59.366 40.909 0.00 0.00 0.00 2.57
594 598 3.380637 AGCTAGCTTTGATGCTTTGATGG 59.619 43.478 12.68 0.00 43.74 3.51
608 612 6.577103 TGCTTTGATGGTTTGATGTTGTTTA 58.423 32.000 0.00 0.00 0.00 2.01
1124 1129 0.622665 CTCAGGAATGTTGGGCTCCT 59.377 55.000 0.00 0.00 40.33 3.69
1209 1214 1.898472 CAGAAGCTGGAGAGGTCTGAA 59.102 52.381 3.67 0.00 31.71 3.02
1321 1326 1.069204 TGCGCAAGAAGTCTCAAGAGT 59.931 47.619 8.16 0.00 43.02 3.24
1371 1376 2.639839 TCTCTTTGGAGCTAAGGCAGTT 59.360 45.455 0.00 0.00 41.70 3.16
1372 1377 3.073062 TCTCTTTGGAGCTAAGGCAGTTT 59.927 43.478 0.00 0.00 41.70 2.66
1373 1378 3.149196 TCTTTGGAGCTAAGGCAGTTTG 58.851 45.455 0.00 0.00 41.70 2.93
1374 1379 2.949177 TTGGAGCTAAGGCAGTTTGA 57.051 45.000 0.00 0.00 41.70 2.69
1375 1380 3.439857 TTGGAGCTAAGGCAGTTTGAT 57.560 42.857 0.00 0.00 41.70 2.57
1376 1381 2.715046 TGGAGCTAAGGCAGTTTGATG 58.285 47.619 0.00 0.00 41.70 3.07
1377 1382 2.019984 GGAGCTAAGGCAGTTTGATGG 58.980 52.381 0.00 0.00 41.70 3.51
1378 1383 1.403323 GAGCTAAGGCAGTTTGATGGC 59.597 52.381 0.00 0.00 45.63 4.40
1386 1391 3.545703 GGCAGTTTGATGGCTATGTAGT 58.454 45.455 0.00 0.00 42.21 2.73
1387 1392 3.947834 GGCAGTTTGATGGCTATGTAGTT 59.052 43.478 0.00 0.00 42.21 2.24
1388 1393 4.399303 GGCAGTTTGATGGCTATGTAGTTT 59.601 41.667 0.00 0.00 42.21 2.66
1389 1394 5.335127 GCAGTTTGATGGCTATGTAGTTTG 58.665 41.667 0.00 0.00 0.00 2.93
1390 1395 5.106157 GCAGTTTGATGGCTATGTAGTTTGT 60.106 40.000 0.00 0.00 0.00 2.83
1391 1396 6.546395 CAGTTTGATGGCTATGTAGTTTGTC 58.454 40.000 0.00 0.00 0.00 3.18
1392 1397 6.372659 CAGTTTGATGGCTATGTAGTTTGTCT 59.627 38.462 0.00 0.00 0.00 3.41
1393 1398 6.942576 AGTTTGATGGCTATGTAGTTTGTCTT 59.057 34.615 0.00 0.00 0.00 3.01
1394 1399 7.448469 AGTTTGATGGCTATGTAGTTTGTCTTT 59.552 33.333 0.00 0.00 0.00 2.52
1395 1400 6.741992 TGATGGCTATGTAGTTTGTCTTTG 57.258 37.500 0.00 0.00 0.00 2.77
1396 1401 6.472016 TGATGGCTATGTAGTTTGTCTTTGA 58.528 36.000 0.00 0.00 0.00 2.69
1397 1402 6.595326 TGATGGCTATGTAGTTTGTCTTTGAG 59.405 38.462 0.00 0.00 0.00 3.02
1398 1403 4.695455 TGGCTATGTAGTTTGTCTTTGAGC 59.305 41.667 0.00 0.00 0.00 4.26
1399 1404 4.938226 GGCTATGTAGTTTGTCTTTGAGCT 59.062 41.667 0.00 0.00 0.00 4.09
1400 1405 6.106673 GGCTATGTAGTTTGTCTTTGAGCTA 58.893 40.000 0.00 0.00 0.00 3.32
1401 1406 6.036191 GGCTATGTAGTTTGTCTTTGAGCTAC 59.964 42.308 0.00 0.00 0.00 3.58
1402 1407 6.814146 GCTATGTAGTTTGTCTTTGAGCTACT 59.186 38.462 0.00 0.00 32.50 2.57
1403 1408 7.974501 GCTATGTAGTTTGTCTTTGAGCTACTA 59.025 37.037 0.00 0.00 32.50 1.82
1404 1409 9.856488 CTATGTAGTTTGTCTTTGAGCTACTAA 57.144 33.333 0.00 0.00 32.50 2.24
1405 1410 8.764524 ATGTAGTTTGTCTTTGAGCTACTAAG 57.235 34.615 0.00 0.00 32.50 2.18
1406 1411 7.152645 TGTAGTTTGTCTTTGAGCTACTAAGG 58.847 38.462 0.00 0.00 33.47 2.69
1407 1412 6.176014 AGTTTGTCTTTGAGCTACTAAGGT 57.824 37.500 0.00 0.00 35.73 3.50
1408 1413 7.299246 AGTTTGTCTTTGAGCTACTAAGGTA 57.701 36.000 0.00 0.00 32.30 3.08
1409 1414 7.379750 AGTTTGTCTTTGAGCTACTAAGGTAG 58.620 38.462 0.00 0.00 45.91 3.18
1410 1415 6.912951 TTGTCTTTGAGCTACTAAGGTAGT 57.087 37.500 0.00 0.00 45.18 2.73
1411 1416 6.912951 TGTCTTTGAGCTACTAAGGTAGTT 57.087 37.500 0.00 0.00 45.18 2.24
1412 1417 6.688578 TGTCTTTGAGCTACTAAGGTAGTTG 58.311 40.000 0.00 0.00 45.18 3.16
1420 1425 5.725110 CTACTAAGGTAGTTGCATTGCTG 57.275 43.478 10.49 0.00 40.21 4.41
1421 1426 3.938963 TACTAAGGTAGTTGCATTGCTGC 59.061 43.478 10.49 2.71 43.19 5.25
1422 1427 5.161249 TACTAAGGTAGTTGCATTGCTGCC 61.161 45.833 10.49 10.91 42.71 4.85
1424 1429 8.038961 TACTAAGGTAGTTGCATTGCTGCCTA 62.039 42.308 18.24 4.56 45.01 3.93
1425 1430 9.723110 TACTAAGGTAGTTGCATTGCTGCCTAG 62.723 44.444 18.24 16.74 45.01 3.02
1489 1569 3.780804 TTGCTGCCTAGTTTGAACCTA 57.219 42.857 0.00 0.00 0.00 3.08
1553 1633 4.452455 CCTGTGAAGTTATGTGAACCTGTC 59.548 45.833 0.00 0.00 0.00 3.51
1656 1736 1.457346 CTGGGCTTGTGGATCACTTC 58.543 55.000 0.00 0.00 35.11 3.01
1687 1767 6.964464 TGGGCCTTTCTGTTTATAGTTATGA 58.036 36.000 4.53 0.00 0.00 2.15
1840 1921 3.713826 AGGCCCAAATTCGAACTAGAA 57.286 42.857 0.00 0.00 34.31 2.10
1867 1948 2.829741 GCTGTGGCCCAAAACAATAA 57.170 45.000 0.00 0.00 0.00 1.40
1922 2004 5.090139 TCCATTCCCAGAAAATAAAAGGCA 58.910 37.500 0.00 0.00 0.00 4.75
2090 2179 1.228245 ACGTCAGCTTGCCATGGTT 60.228 52.632 14.67 0.00 0.00 3.67
2149 2238 7.411274 CAAAACAGTTGGTCGTTAAATCTACA 58.589 34.615 0.00 0.00 0.00 2.74
2151 2240 6.780706 ACAGTTGGTCGTTAAATCTACAAG 57.219 37.500 0.00 0.00 0.00 3.16
2212 2303 7.166691 AGAAAGGTCGCTATAGTCAGTTTAA 57.833 36.000 0.84 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 239 3.070446 TGTTCGACACACAGGTTTCCTAT 59.930 43.478 0.00 0.00 29.64 2.57
531 535 7.268586 CAAAGCATGGAGTGACTTACTATAGT 58.731 38.462 10.87 10.87 40.53 2.12
571 575 4.577693 CCATCAAAGCATCAAAGCTAGCTA 59.422 41.667 19.70 2.19 45.89 3.32
594 598 5.344933 GGCTCCGAATTAAACAACATCAAAC 59.655 40.000 0.00 0.00 0.00 2.93
608 612 2.224523 TGTTCTTGACTGGCTCCGAATT 60.225 45.455 0.00 0.00 0.00 2.17
907 912 3.018423 AGCAAGAGAAACCAAACCAGT 57.982 42.857 0.00 0.00 0.00 4.00
1022 1027 1.623811 GCTCTTCACCTTCTGGTACCA 59.376 52.381 15.39 15.39 46.60 3.25
1124 1129 2.496070 CCGGAGTTGTTCCTAGATGACA 59.504 50.000 0.00 0.00 44.41 3.58
1321 1326 1.831736 GTGGGCTAACTGCTCTTCCTA 59.168 52.381 0.00 0.00 44.09 2.94
1371 1376 6.939730 TCAAAGACAAACTACATAGCCATCAA 59.060 34.615 0.00 0.00 0.00 2.57
1372 1377 6.472016 TCAAAGACAAACTACATAGCCATCA 58.528 36.000 0.00 0.00 0.00 3.07
1373 1378 6.457528 GCTCAAAGACAAACTACATAGCCATC 60.458 42.308 0.00 0.00 0.00 3.51
1374 1379 5.355350 GCTCAAAGACAAACTACATAGCCAT 59.645 40.000 0.00 0.00 0.00 4.40
1375 1380 4.695455 GCTCAAAGACAAACTACATAGCCA 59.305 41.667 0.00 0.00 0.00 4.75
1376 1381 4.938226 AGCTCAAAGACAAACTACATAGCC 59.062 41.667 0.00 0.00 0.00 3.93
1377 1382 6.814146 AGTAGCTCAAAGACAAACTACATAGC 59.186 38.462 0.00 0.00 33.96 2.97
1378 1383 9.856488 TTAGTAGCTCAAAGACAAACTACATAG 57.144 33.333 0.00 0.00 33.96 2.23
1379 1384 9.856488 CTTAGTAGCTCAAAGACAAACTACATA 57.144 33.333 0.00 0.00 33.96 2.29
1380 1385 7.819900 CCTTAGTAGCTCAAAGACAAACTACAT 59.180 37.037 0.00 0.00 33.96 2.29
1381 1386 7.152645 CCTTAGTAGCTCAAAGACAAACTACA 58.847 38.462 0.00 0.00 33.96 2.74
1382 1387 7.153315 ACCTTAGTAGCTCAAAGACAAACTAC 58.847 38.462 0.00 0.00 0.00 2.73
1383 1388 7.299246 ACCTTAGTAGCTCAAAGACAAACTA 57.701 36.000 0.00 0.00 0.00 2.24
1384 1389 6.176014 ACCTTAGTAGCTCAAAGACAAACT 57.824 37.500 0.00 0.00 0.00 2.66
1385 1390 7.583860 CTACCTTAGTAGCTCAAAGACAAAC 57.416 40.000 0.00 0.00 39.66 2.93
1397 1402 7.427138 GCAGCAATGCAACTACCTTAGTAGC 62.427 48.000 8.35 0.00 41.09 3.58
1398 1403 4.034510 GCAGCAATGCAACTACCTTAGTAG 59.965 45.833 8.35 0.00 42.06 2.57
1399 1404 3.938963 GCAGCAATGCAACTACCTTAGTA 59.061 43.478 8.35 0.00 38.26 1.82
1400 1405 2.749621 GCAGCAATGCAACTACCTTAGT 59.250 45.455 8.35 0.00 41.73 2.24
1401 1406 2.098117 GGCAGCAATGCAACTACCTTAG 59.902 50.000 8.35 0.00 36.33 2.18
1402 1407 2.091541 GGCAGCAATGCAACTACCTTA 58.908 47.619 8.35 0.00 36.33 2.69
1403 1408 0.890683 GGCAGCAATGCAACTACCTT 59.109 50.000 8.35 0.00 36.33 3.50
1404 1409 0.038744 AGGCAGCAATGCAACTACCT 59.961 50.000 8.35 3.32 36.33 3.08
1405 1410 1.672881 CTAGGCAGCAATGCAACTACC 59.327 52.381 8.35 0.78 36.33 3.18
1406 1411 2.359900 ACTAGGCAGCAATGCAACTAC 58.640 47.619 8.35 0.00 36.33 2.73
1407 1412 2.787473 ACTAGGCAGCAATGCAACTA 57.213 45.000 8.35 5.74 36.33 2.24
1408 1413 1.915141 AACTAGGCAGCAATGCAACT 58.085 45.000 8.35 4.77 36.33 3.16
1409 1414 2.030007 TCAAACTAGGCAGCAATGCAAC 60.030 45.455 8.35 0.00 36.33 4.17
1410 1415 2.237643 TCAAACTAGGCAGCAATGCAA 58.762 42.857 8.35 0.00 36.33 4.08
1411 1416 1.908344 TCAAACTAGGCAGCAATGCA 58.092 45.000 8.35 0.00 36.33 3.96
1412 1417 2.480759 CCATCAAACTAGGCAGCAATGC 60.481 50.000 0.00 0.00 0.00 3.56
1413 1418 3.431922 CCATCAAACTAGGCAGCAATG 57.568 47.619 0.00 0.00 0.00 2.82
1421 1426 2.749621 GGTTCACAGCCATCAAACTAGG 59.250 50.000 0.00 0.00 0.00 3.02
1422 1427 3.679389 AGGTTCACAGCCATCAAACTAG 58.321 45.455 0.00 0.00 0.00 2.57
1423 1428 3.327757 AGAGGTTCACAGCCATCAAACTA 59.672 43.478 0.00 0.00 0.00 2.24
1424 1429 2.107204 AGAGGTTCACAGCCATCAAACT 59.893 45.455 0.00 0.00 0.00 2.66
1425 1430 2.508526 AGAGGTTCACAGCCATCAAAC 58.491 47.619 0.00 0.00 0.00 2.93
1426 1431 2.957402 AGAGGTTCACAGCCATCAAA 57.043 45.000 0.00 0.00 0.00 2.69
1489 1569 6.299141 ACTTCACAGGTTCACATAACTTCAT 58.701 36.000 0.00 0.00 0.00 2.57
1553 1633 6.652481 AGAGGTTCACAAGATCACATAACTTG 59.348 38.462 0.00 0.00 44.16 3.16
1656 1736 1.975407 CAGAAAGGCCCAGGTGCAG 60.975 63.158 0.00 0.00 0.00 4.41
1687 1767 7.849322 TTTTAGAGCCCAGGTTCTTATTTTT 57.151 32.000 8.45 0.00 36.99 1.94
1891 1973 2.514458 TCTGGGAATGGAGCCTTTTC 57.486 50.000 0.00 0.00 0.00 2.29
2090 2179 0.317160 GACCACACCACGTCAGATCA 59.683 55.000 0.00 0.00 0.00 2.92
2212 2303 1.600916 GGTCAAAAGCTGGCCGTCT 60.601 57.895 0.00 0.00 40.90 4.18


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

AutoCloner maintained by Alex Coulton.