Multiple sequence alignment - TraesCS3A01G182300

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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 TraesCS3A01G182300 chr3A 100.000 2339 0 0 1 2339 211951697 211954035 0 4320
1 TraesCS3A01G182300 chr6D 91.886 1368 104 5 1 1366 48683472 48682110 0 1905
2 TraesCS3A01G182300 chr6D 91.510 1119 88 6 245 1359 32688758 32687643 0 1533
3 TraesCS3A01G182300 chr7B 91.514 1367 110 6 1 1364 651392883 651391520 0 1877
4 TraesCS3A01G182300 chr2D 89.019 1366 138 12 1 1363 574398709 574397353 0 1681
5 TraesCS3A01G182300 chr5A 88.905 1361 143 8 3 1359 592306876 592305520 0 1670
6 TraesCS3A01G182300 chr7D 88.529 1360 147 9 4 1359 439710633 439709279 0 1639
7 TraesCS3A01G182300 chr3D 88.546 1362 143 10 1 1358 300565482 300566834 0 1639
8 TraesCS3A01G182300 chr3D 93.255 682 19 8 1670 2339 173595719 173596385 0 979
9 TraesCS3A01G182300 chr1D 87.170 1364 169 6 1 1362 216023918 216022559 0 1544
10 TraesCS3A01G182300 chr4A 86.743 1305 165 8 1 1301 662511499 662512799 0 1445
11 TraesCS3A01G182300 chr3B 90.828 1003 45 16 1367 2339 252342876 252343861 0 1299


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 TraesCS3A01G182300 chr3A 211951697 211954035 2338 False 4320 4320 100.000 1 2339 1 chr3A.!!$F1 2338
1 TraesCS3A01G182300 chr6D 48682110 48683472 1362 True 1905 1905 91.886 1 1366 1 chr6D.!!$R2 1365
2 TraesCS3A01G182300 chr6D 32687643 32688758 1115 True 1533 1533 91.510 245 1359 1 chr6D.!!$R1 1114
3 TraesCS3A01G182300 chr7B 651391520 651392883 1363 True 1877 1877 91.514 1 1364 1 chr7B.!!$R1 1363
4 TraesCS3A01G182300 chr2D 574397353 574398709 1356 True 1681 1681 89.019 1 1363 1 chr2D.!!$R1 1362
5 TraesCS3A01G182300 chr5A 592305520 592306876 1356 True 1670 1670 88.905 3 1359 1 chr5A.!!$R1 1356
6 TraesCS3A01G182300 chr7D 439709279 439710633 1354 True 1639 1639 88.529 4 1359 1 chr7D.!!$R1 1355
7 TraesCS3A01G182300 chr3D 300565482 300566834 1352 False 1639 1639 88.546 1 1358 1 chr3D.!!$F2 1357
8 TraesCS3A01G182300 chr3D 173595719 173596385 666 False 979 979 93.255 1670 2339 1 chr3D.!!$F1 669
9 TraesCS3A01G182300 chr1D 216022559 216023918 1359 True 1544 1544 87.170 1 1362 1 chr1D.!!$R1 1361
10 TraesCS3A01G182300 chr4A 662511499 662512799 1300 False 1445 1445 86.743 1 1301 1 chr4A.!!$F1 1300
11 TraesCS3A01G182300 chr3B 252342876 252343861 985 False 1299 1299 90.828 1367 2339 1 chr3B.!!$F1 972

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
440 445 0.663153 GGTACGATCAAATGCTGGGC 59.337 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 2036 0.108804 TTTGGTAGGAAGCGAGCGAG 60.109 55.0 0.0 0.0 0.0 5.03 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
27 28 7.069331 GGGGAATGGACACAACATCAATATTTA 59.931 37.037 0.00 0.00 0.00 1.40
139 140 4.755266 TCCTGCTTCTAATACTTGGGAC 57.245 45.455 0.00 0.00 0.00 4.46
249 251 9.434420 TTTCATTGCCTGGAATTATACAAAAAG 57.566 29.630 0.00 0.00 0.00 2.27
250 252 7.555087 TCATTGCCTGGAATTATACAAAAAGG 58.445 34.615 0.00 0.00 0.00 3.11
353 358 2.079158 GGCGAACCAAGTTAACCCTAC 58.921 52.381 0.88 0.00 35.26 3.18
369 374 8.921205 GTTAACCCTACTTGGAGTAAGATATGA 58.079 37.037 0.00 0.00 39.76 2.15
382 387 7.988028 GGAGTAAGATATGAAAGTTAGCCTGTT 59.012 37.037 0.00 0.00 0.00 3.16
430 435 3.610821 GCGTATGCTACATGGTACGATCA 60.611 47.826 15.82 0.00 41.62 2.92
431 436 4.542735 CGTATGCTACATGGTACGATCAA 58.457 43.478 0.00 0.00 41.62 2.57
440 445 0.663153 GGTACGATCAAATGCTGGGC 59.337 55.000 0.00 0.00 0.00 5.36
483 488 1.142688 AGGTTTCACCCATCTGCCCT 61.143 55.000 0.00 0.00 39.75 5.19
492 498 1.490490 CCCATCTGCCCTACTTGCTTA 59.510 52.381 0.00 0.00 0.00 3.09
515 521 9.945904 CTTAGAGGGTTTAGAAGATACAAAACT 57.054 33.333 0.00 0.00 33.40 2.66
549 555 5.690997 GCTGTAGTAAAGCAAAGAAGGTT 57.309 39.130 7.50 0.00 40.52 3.50
613 619 2.599281 TTGACCGTGCGGGAGAGA 60.599 61.111 15.44 0.00 39.97 3.10
621 627 2.432628 GCGGGAGAGACGGTGTTG 60.433 66.667 0.00 0.00 0.00 3.33
693 700 4.631377 CCACAATGTACGTGAGATGATTGT 59.369 41.667 0.00 0.90 37.12 2.71
703 710 5.193216 CGTGAGATGATTGTTATTTCAGCG 58.807 41.667 0.00 0.00 33.62 5.18
710 717 6.751514 TGATTGTTATTTCAGCGTGGTATT 57.248 33.333 0.00 0.00 0.00 1.89
726 733 5.820423 CGTGGTATTTATGATGGGAAAGACA 59.180 40.000 0.00 0.00 30.21 3.41
898 910 8.752766 ACTTAATGTTGATGCTTCTTTTGATG 57.247 30.769 0.88 0.00 0.00 3.07
918 930 3.709587 TGACGATCTTCTTAGGGGTTCT 58.290 45.455 0.48 0.00 0.00 3.01
941 953 3.398353 GAGCGGTCCTTCGAGACGG 62.398 68.421 2.39 7.69 37.66 4.79
948 960 1.183030 TCCTTCGAGACGGCAAAGGA 61.183 55.000 13.95 13.95 43.79 3.36
982 994 5.472820 GCTGGAGGGAATGAGAAAATAGATG 59.527 44.000 0.00 0.00 0.00 2.90
1006 1019 0.880441 CGTGGATGTGTTGATGGCAA 59.120 50.000 0.00 0.00 0.00 4.52
1028 1041 7.593644 GGCAAAAGTTTTAGCTCTAAAATTCGA 59.406 33.333 15.34 0.00 44.01 3.71
1041 1054 7.467267 GCTCTAAAATTCGATCTAACATTGGCA 60.467 37.037 0.00 0.00 0.00 4.92
1078 1091 7.561021 TGCAATCGCCTTACTATAAATTCAA 57.439 32.000 0.00 0.00 37.32 2.69
1184 1197 1.944024 TGCTTGTGGTTTCGTTACTGG 59.056 47.619 0.00 0.00 0.00 4.00
1276 1289 4.836125 TTGACTTCTGATTGGTTTGAGC 57.164 40.909 0.00 0.00 0.00 4.26
1315 1328 9.941664 AAATTGTAATGATCATCAGAAACGATC 57.058 29.630 9.06 0.00 36.82 3.69
1324 1337 8.131731 TGATCATCAGAAACGATCTACTACTTG 58.868 37.037 0.00 0.00 36.32 3.16
1347 1360 9.334693 CTTGTTACAAATGAATAAAGTCTGAGC 57.665 33.333 0.00 0.00 0.00 4.26
1401 1414 0.394899 AGGCTAACTTGGATGGCAGC 60.395 55.000 0.00 0.00 0.00 5.25
1412 1425 2.309613 GGATGGCAGCATAATCACCAA 58.690 47.619 4.64 0.00 33.30 3.67
1414 1427 3.491447 GGATGGCAGCATAATCACCAAAC 60.491 47.826 4.64 0.00 33.30 2.93
1431 1444 1.747444 AACTGGTCCATCACCTCCTT 58.253 50.000 0.00 0.00 46.98 3.36
1432 1445 1.280457 ACTGGTCCATCACCTCCTTC 58.720 55.000 0.00 0.00 46.98 3.46
1433 1446 1.203364 ACTGGTCCATCACCTCCTTCT 60.203 52.381 0.00 0.00 46.98 2.85
1437 1450 2.625617 GGTCCATCACCTCCTTCTCTCT 60.626 54.545 0.00 0.00 42.84 3.10
1438 1451 3.373220 GGTCCATCACCTCCTTCTCTCTA 60.373 52.174 0.00 0.00 42.84 2.43
1446 1459 3.161866 CCTCCTTCTCTCTACATAGGCC 58.838 54.545 0.00 0.00 0.00 5.19
1449 1462 5.249780 TCCTTCTCTCTACATAGGCCTAG 57.750 47.826 19.33 12.53 0.00 3.02
1454 1467 4.412528 TCTCTCTACATAGGCCTAGTGTCA 59.587 45.833 23.02 14.26 0.00 3.58
1474 1487 8.936864 AGTGTCAGTTTTATATGACTTTACTGC 58.063 33.333 6.85 0.00 44.90 4.40
1477 1490 7.905493 GTCAGTTTTATATGACTTTACTGCTGC 59.095 37.037 0.00 0.00 42.06 5.25
1478 1491 7.065803 TCAGTTTTATATGACTTTACTGCTGCC 59.934 37.037 0.00 0.00 33.40 4.85
1483 1496 3.819564 TGACTTTACTGCTGCCGATAT 57.180 42.857 0.00 0.00 0.00 1.63
1487 1500 3.133003 ACTTTACTGCTGCCGATATGTCT 59.867 43.478 0.00 0.00 0.00 3.41
1492 1505 2.279741 TGCTGCCGATATGTCTGTTTC 58.720 47.619 0.00 0.00 0.00 2.78
1499 1512 6.216569 TGCCGATATGTCTGTTTCTATCTTC 58.783 40.000 0.00 0.00 0.00 2.87
1502 1515 7.439655 GCCGATATGTCTGTTTCTATCTTCTTT 59.560 37.037 0.00 0.00 0.00 2.52
1538 1551 0.463620 GGTGGTTGGTTGTGTGCATT 59.536 50.000 0.00 0.00 0.00 3.56
1543 1556 3.181471 TGGTTGGTTGTGTGCATTTTAGG 60.181 43.478 0.00 0.00 0.00 2.69
1551 1564 2.554032 GTGTGCATTTTAGGTCTGCAGT 59.446 45.455 14.67 0.00 45.77 4.40
1581 1594 5.294734 TGTTGCTCATCATGCCTTCTATA 57.705 39.130 0.00 0.00 0.00 1.31
1582 1595 5.872963 TGTTGCTCATCATGCCTTCTATAT 58.127 37.500 0.00 0.00 0.00 0.86
1583 1596 5.704053 TGTTGCTCATCATGCCTTCTATATG 59.296 40.000 0.00 0.00 0.00 1.78
1661 1674 7.895759 TCCCCTCTTTACATTTTCATTTTGAG 58.104 34.615 0.00 0.00 0.00 3.02
1712 1725 2.736192 CCACGTGGAAAATGGAAAATGC 59.264 45.455 31.31 0.00 35.33 3.56
1808 1831 2.146342 CAAGGACACACACAGGATCAC 58.854 52.381 0.00 0.00 0.00 3.06
1831 1854 4.873129 CCGTCCGAGCCATCACCG 62.873 72.222 0.00 0.00 0.00 4.94
1859 1882 1.270625 CGGGACACGGCATAATACCAT 60.271 52.381 0.00 0.00 39.42 3.55
1940 1970 1.400142 TGGCAAGTTGACAACGACAAG 59.600 47.619 9.57 3.91 28.38 3.16
2133 2170 2.658807 AAAGACCACACCCTTCCTTC 57.341 50.000 0.00 0.00 0.00 3.46
2135 2172 1.747444 AGACCACACCCTTCCTTCAT 58.253 50.000 0.00 0.00 0.00 2.57
2255 2297 0.108615 CGCCCAACAGAGAGGTAGTG 60.109 60.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.327867 TGGGATCCAGGCATCTTCCT 60.328 55.000 15.23 0.00 36.78 3.36
139 140 6.147821 ACATAGTTTGTTCAATCAGGTCTTCG 59.852 38.462 0.00 0.00 33.74 3.79
249 251 5.278315 GCTGATCGAACCAATAAAATACCCC 60.278 44.000 0.00 0.00 0.00 4.95
250 252 5.278315 GGCTGATCGAACCAATAAAATACCC 60.278 44.000 0.00 0.00 0.00 3.69
259 262 6.207417 CCATAAAATAGGCTGATCGAACCAAT 59.793 38.462 0.00 0.00 0.00 3.16
261 264 5.063204 CCATAAAATAGGCTGATCGAACCA 58.937 41.667 0.00 0.00 0.00 3.67
353 358 8.207545 AGGCTAACTTTCATATCTTACTCCAAG 58.792 37.037 0.00 0.00 35.38 3.61
382 387 8.983724 CCATAAGAAAATTTTAACTTTTGCCGA 58.016 29.630 2.75 0.00 0.00 5.54
440 445 5.281727 TCATATGTCTGTTTGCTAGCGTAG 58.718 41.667 10.77 5.67 0.00 3.51
483 488 7.735326 ATCTTCTAAACCCTCTAAGCAAGTA 57.265 36.000 0.00 0.00 0.00 2.24
515 521 5.812642 GCTTTACTACAGCAGAAGAGCATAA 59.187 40.000 0.00 0.00 37.22 1.90
526 532 4.714632 ACCTTCTTTGCTTTACTACAGCA 58.285 39.130 0.00 0.00 45.73 4.41
544 550 2.449345 TCCCTAGCCTTTTCCAAACCTT 59.551 45.455 0.00 0.00 0.00 3.50
549 555 2.283834 TCCATCCCTAGCCTTTTCCAA 58.716 47.619 0.00 0.00 0.00 3.53
613 619 3.097342 AGTAGATACTCCCAACACCGT 57.903 47.619 0.00 0.00 0.00 4.83
693 700 7.040755 CCCATCATAAATACCACGCTGAAATAA 60.041 37.037 0.00 0.00 0.00 1.40
703 710 7.054124 TCTGTCTTTCCCATCATAAATACCAC 58.946 38.462 0.00 0.00 0.00 4.16
710 717 5.188434 CAGCTTCTGTCTTTCCCATCATAA 58.812 41.667 0.00 0.00 0.00 1.90
766 777 3.563223 AGCAAGAATCCCCATTGAGATG 58.437 45.455 0.00 0.00 0.00 2.90
898 910 5.279056 CCATAGAACCCCTAAGAAGATCGTC 60.279 48.000 0.00 0.00 0.00 4.20
918 930 1.076559 TCGAAGGACCGCTCCCATA 60.077 57.895 0.00 0.00 37.25 2.74
941 953 2.424956 CCAGCTATGAACCTTCCTTTGC 59.575 50.000 0.00 0.00 0.00 3.68
948 960 2.270434 TCCCTCCAGCTATGAACCTT 57.730 50.000 0.00 0.00 0.00 3.50
982 994 2.318578 CATCAACACATCCACGCAAAC 58.681 47.619 0.00 0.00 0.00 2.93
1028 1041 2.091541 CCCGTTGTGCCAATGTTAGAT 58.908 47.619 6.44 0.00 0.00 1.98
1041 1054 3.936772 ATTGCATCCCGCCCGTTGT 62.937 57.895 0.00 0.00 41.33 3.32
1067 1080 9.953565 TCCCCTCCGTATTATTTGAATTTATAG 57.046 33.333 0.00 0.00 0.00 1.31
1078 1091 8.705594 CATAGTATCAATCCCCTCCGTATTATT 58.294 37.037 0.00 0.00 0.00 1.40
1085 1098 5.187772 TCATTCATAGTATCAATCCCCTCCG 59.812 44.000 0.00 0.00 0.00 4.63
1091 1104 7.768120 GTCCTCCATCATTCATAGTATCAATCC 59.232 40.741 0.00 0.00 0.00 3.01
1158 1171 3.848272 ACGAAACCACAAGCATAATGG 57.152 42.857 0.00 0.00 39.57 3.16
1184 1197 8.677148 TTCCCTATTACAATGCTCAAATCTAC 57.323 34.615 0.00 0.00 0.00 2.59
1245 1258 7.230027 ACCAATCAGAAGTCAAAGAAGATCTT 58.770 34.615 7.95 7.95 38.59 2.40
1250 1263 7.031226 TCAAACCAATCAGAAGTCAAAGAAG 57.969 36.000 0.00 0.00 0.00 2.85
1303 1316 8.737175 TGTAACAAGTAGTAGATCGTTTCTGAT 58.263 33.333 1.64 0.00 35.79 2.90
1307 1320 9.953825 CATTTGTAACAAGTAGTAGATCGTTTC 57.046 33.333 0.00 0.00 0.00 2.78
1324 1337 9.899226 AAAGCTCAGACTTTATTCATTTGTAAC 57.101 29.630 0.00 0.00 38.09 2.50
1377 1390 2.485657 GCCATCCAAGTTAGCCTAGGTC 60.486 54.545 11.31 2.66 0.00 3.85
1379 1392 1.490490 TGCCATCCAAGTTAGCCTAGG 59.510 52.381 3.67 3.67 0.00 3.02
1381 1394 1.134098 GCTGCCATCCAAGTTAGCCTA 60.134 52.381 0.00 0.00 0.00 3.93
1431 1444 4.412528 TGACACTAGGCCTATGTAGAGAGA 59.587 45.833 14.30 0.00 0.00 3.10
1432 1445 4.720046 TGACACTAGGCCTATGTAGAGAG 58.280 47.826 14.30 2.74 0.00 3.20
1433 1446 4.166337 ACTGACACTAGGCCTATGTAGAGA 59.834 45.833 14.30 4.82 0.00 3.10
1437 1450 7.670605 ATAAAACTGACACTAGGCCTATGTA 57.329 36.000 14.30 3.99 0.00 2.29
1438 1451 4.910458 AAAACTGACACTAGGCCTATGT 57.090 40.909 20.92 20.92 0.00 2.29
1449 1462 8.936864 AGCAGTAAAGTCATATAAAACTGACAC 58.063 33.333 6.90 0.00 43.35 3.67
1454 1467 6.037172 CGGCAGCAGTAAAGTCATATAAAACT 59.963 38.462 0.00 0.00 0.00 2.66
1474 1487 5.777802 AGATAGAAACAGACATATCGGCAG 58.222 41.667 0.00 0.00 31.37 4.85
1477 1490 8.879342 AAAGAAGATAGAAACAGACATATCGG 57.121 34.615 0.00 0.00 31.37 4.18
1516 1529 0.463620 GCACACAACCAACCACCAAT 59.536 50.000 0.00 0.00 0.00 3.16
1538 1551 2.325484 TCTGACCACTGCAGACCTAAA 58.675 47.619 23.35 0.00 37.46 1.85
1543 1556 1.802960 CAACATCTGACCACTGCAGAC 59.197 52.381 23.35 9.18 44.39 3.51
1636 1649 7.525360 GCTCAAAATGAAAATGTAAAGAGGGGA 60.525 37.037 0.00 0.00 0.00 4.81
1637 1650 6.591448 GCTCAAAATGAAAATGTAAAGAGGGG 59.409 38.462 0.00 0.00 0.00 4.79
1661 1674 7.176340 ACCCGGTAATAGAGAATATATATCCGC 59.824 40.741 0.00 0.00 32.55 5.54
1712 1725 3.495100 GGTACAACAGCCTGATGGATAGG 60.495 52.174 6.92 0.00 38.39 2.57
1808 1831 2.427540 GATGGCTCGGACGGATCAGG 62.428 65.000 0.00 0.00 0.00 3.86
1940 1970 4.660938 AAGCCACGGCCCCTTGTC 62.661 66.667 3.95 0.00 43.17 3.18
2000 2034 2.652496 GTAGGAAGCGAGCGAGCG 60.652 66.667 0.00 0.00 43.00 5.03
2001 2035 2.278923 GGTAGGAAGCGAGCGAGC 60.279 66.667 0.00 0.00 37.41 5.03
2002 2036 0.108804 TTTGGTAGGAAGCGAGCGAG 60.109 55.000 0.00 0.00 0.00 5.03
2003 2037 0.389426 GTTTGGTAGGAAGCGAGCGA 60.389 55.000 0.00 0.00 0.00 4.93
2133 2170 0.311790 AAATTATGGCGCTGCGGATG 59.688 50.000 24.61 0.00 0.00 3.51
2135 2172 1.444119 GGAAATTATGGCGCTGCGGA 61.444 55.000 24.61 0.00 0.00 5.54
2255 2297 1.456331 CCATCCTCCCAATGGCACC 60.456 63.158 0.00 0.00 37.46 5.01


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

AutoCloner maintained by Alex Coulton.