Multiple sequence alignment - TraesCS3D01G247500

Loading Multiple Alignment...

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 TraesCS3D01G247500 chr3D 100.000 2712 0 0 1 2712 346642560 346645271 0.000000e+00 5009
1 TraesCS3D01G247500 chr3A 94.911 1788 37 19 588 2342 457085183 457083417 0.000000e+00 2748
2 TraesCS3D01G247500 chr3A 93.606 563 16 7 11 570 457085715 457085170 0.000000e+00 822
3 TraesCS3D01G247500 chr3A 95.491 377 13 2 2340 2712 457083386 457083010 1.390000e-167 599
4 TraesCS3D01G247500 chr3A 85.377 212 23 6 242 453 550416958 550417161 2.120000e-51 213
5 TraesCS3D01G247500 chr3B 93.975 946 43 6 809 1751 446172525 446173459 0.000000e+00 1419
6 TraesCS3D01G247500 chr3B 86.521 868 57 24 1877 2712 446173531 446174370 0.000000e+00 900
7 TraesCS3D01G247500 chr3B 82.237 304 32 11 244 546 157245935 157245653 2.700000e-60 243
8 TraesCS3D01G247500 chr5A 82.517 286 36 9 264 545 644359601 644359876 3.490000e-59 239
9 TraesCS3D01G247500 chr6D 79.697 330 53 10 242 564 30131298 30130976 2.720000e-55 226
10 TraesCS3D01G247500 chr5B 80.412 291 45 10 264 548 649730527 649730811 7.610000e-51 211
11 TraesCS3D01G247500 chr2B 79.553 313 51 12 242 546 26559424 26559117 7.610000e-51 211
12 TraesCS3D01G247500 chr6B 77.558 303 51 12 250 544 438097990 438098283 1.670000e-37 167
13 TraesCS3D01G247500 chr2D 80.788 203 34 5 242 441 614646701 614646901 1.300000e-33 154
14 TraesCS3D01G247500 chr2A 76.792 293 46 20 242 524 564615786 564615506 7.830000e-31 145
15 TraesCS3D01G247500 chr1A 76.703 279 53 10 242 517 492270531 492270262 7.830000e-31 145


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 TraesCS3D01G247500 chr3D 346642560 346645271 2711 False 5009.000000 5009 100.000000 1 2712 1 chr3D.!!$F1 2711
1 TraesCS3D01G247500 chr3A 457083010 457085715 2705 True 1389.666667 2748 94.669333 11 2712 3 chr3A.!!$R1 2701
2 TraesCS3D01G247500 chr3B 446172525 446174370 1845 False 1159.500000 1419 90.248000 809 2712 2 chr3B.!!$F1 1903

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
661 665 0.59117 CCACCCTTTTAGCACGTGTG 59.409 55.0 18.38 3.68 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2264 0.03438 TCTCGACTCCACTACCCCAG 60.034 60.0 0.0 0.0 0.0 4.45 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
349 351 5.067936 TCCAAAAGTGGTATTTTCGAAAGCA 59.932 36.000 10.98 3.32 46.11 3.91
430 434 4.405116 TTTTGCAGGCACTCAAAAGATT 57.595 36.364 0.00 0.00 39.02 2.40
437 441 4.741676 CAGGCACTCAAAAGATTTGTCAAC 59.258 41.667 3.06 0.00 34.60 3.18
443 447 4.109050 TCAAAAGATTTGTCAACGTTGGC 58.891 39.130 25.54 25.54 0.00 4.52
444 448 2.793278 AAGATTTGTCAACGTTGGCC 57.207 45.000 28.59 18.83 30.03 5.36
445 449 1.686355 AGATTTGTCAACGTTGGCCA 58.314 45.000 28.59 21.01 30.03 5.36
446 450 1.336755 AGATTTGTCAACGTTGGCCAC 59.663 47.619 28.59 19.10 30.03 5.01
447 451 1.066303 GATTTGTCAACGTTGGCCACA 59.934 47.619 28.59 21.36 30.03 4.17
448 452 0.888619 TTTGTCAACGTTGGCCACAA 59.111 45.000 28.59 25.27 30.03 3.33
449 453 0.888619 TTGTCAACGTTGGCCACAAA 59.111 45.000 28.59 14.25 38.54 2.83
510 514 7.922505 TTTTTGGATTTTACTGTTCATCACG 57.077 32.000 0.00 0.00 0.00 4.35
511 515 6.869315 TTTGGATTTTACTGTTCATCACGA 57.131 33.333 0.00 0.00 0.00 4.35
512 516 6.480524 TTGGATTTTACTGTTCATCACGAG 57.519 37.500 0.00 0.00 0.00 4.18
513 517 4.391830 TGGATTTTACTGTTCATCACGAGC 59.608 41.667 0.00 0.00 0.00 5.03
514 518 4.631813 GGATTTTACTGTTCATCACGAGCT 59.368 41.667 0.00 0.00 0.00 4.09
515 519 5.220491 GGATTTTACTGTTCATCACGAGCTC 60.220 44.000 2.73 2.73 0.00 4.09
516 520 3.934457 TTACTGTTCATCACGAGCTCA 57.066 42.857 15.40 0.00 0.00 4.26
517 521 2.820059 ACTGTTCATCACGAGCTCAA 57.180 45.000 15.40 0.00 0.00 3.02
518 522 3.325293 ACTGTTCATCACGAGCTCAAT 57.675 42.857 15.40 0.72 0.00 2.57
559 563 1.247567 CTTTCGGTTCATGGGCAACT 58.752 50.000 0.00 0.00 0.00 3.16
560 564 2.224670 ACTTTCGGTTCATGGGCAACTA 60.225 45.455 0.00 0.00 0.00 2.24
561 565 2.799126 TTCGGTTCATGGGCAACTAT 57.201 45.000 0.00 0.00 39.02 2.12
562 566 2.799126 TCGGTTCATGGGCAACTATT 57.201 45.000 0.00 0.00 34.29 1.73
563 567 3.080300 TCGGTTCATGGGCAACTATTT 57.920 42.857 0.00 0.00 34.29 1.40
564 568 2.752354 TCGGTTCATGGGCAACTATTTG 59.248 45.455 0.00 0.00 34.29 2.32
576 580 4.965042 CAACTATTTGCCAAACGTTTCC 57.035 40.909 11.37 5.92 0.00 3.13
577 581 3.653539 ACTATTTGCCAAACGTTTCCC 57.346 42.857 11.37 5.55 0.00 3.97
578 582 2.030628 ACTATTTGCCAAACGTTTCCCG 60.031 45.455 11.37 2.74 44.03 5.14
579 583 0.598942 ATTTGCCAAACGTTTCCCGC 60.599 50.000 11.37 13.23 41.42 6.13
580 584 1.945354 TTTGCCAAACGTTTCCCGCA 61.945 50.000 18.18 18.18 41.42 5.69
581 585 1.945354 TTGCCAAACGTTTCCCGCAA 61.945 50.000 24.74 24.74 41.42 4.85
582 586 1.227002 GCCAAACGTTTCCCGCAAA 60.227 52.632 11.37 0.00 41.42 3.68
583 587 0.806492 GCCAAACGTTTCCCGCAAAA 60.806 50.000 11.37 0.00 41.42 2.44
584 588 1.641577 CCAAACGTTTCCCGCAAAAA 58.358 45.000 11.37 0.00 41.42 1.94
661 665 0.591170 CCACCCTTTTAGCACGTGTG 59.409 55.000 18.38 3.68 0.00 3.82
829 841 2.287608 CGAGTGTTGGCCTTCCTTTTTC 60.288 50.000 3.32 0.00 0.00 2.29
907 919 6.696441 TGTTTTTGGTAACCGTAGATTTGT 57.304 33.333 0.00 0.00 0.00 2.83
1356 1368 3.589654 CTTCCTTGACGGCGAGCCA 62.590 63.158 16.62 5.51 35.37 4.75
1363 1375 1.810030 GACGGCGAGCCAAAGGTAG 60.810 63.158 16.62 0.00 35.37 3.18
1364 1376 2.264794 CGGCGAGCCAAAGGTAGT 59.735 61.111 15.03 0.00 35.37 2.73
1365 1377 1.810030 CGGCGAGCCAAAGGTAGTC 60.810 63.158 15.03 0.00 35.37 2.59
1366 1378 1.810030 GGCGAGCCAAAGGTAGTCG 60.810 63.158 9.58 0.00 35.81 4.18
1367 1379 3.782042 CGAGCCAAAGGTAGTCGC 58.218 61.111 0.00 0.00 0.00 5.19
1368 1380 1.080093 CGAGCCAAAGGTAGTCGCA 60.080 57.895 0.00 0.00 0.00 5.10
1369 1381 0.669318 CGAGCCAAAGGTAGTCGCAA 60.669 55.000 0.00 0.00 0.00 4.85
1381 1395 3.961414 TCGCAAACCCAGTCCCCC 61.961 66.667 0.00 0.00 0.00 5.40
1394 1408 0.958876 GTCCCCCGTGAAATTTCGCT 60.959 55.000 24.95 0.00 35.61 4.93
1400 1414 2.739913 CCCGTGAAATTTCGCTCAGTTA 59.260 45.455 24.95 0.00 35.61 2.24
1404 1418 5.382303 CGTGAAATTTCGCTCAGTTATGTT 58.618 37.500 24.95 0.00 35.61 2.71
1406 1420 7.012943 CGTGAAATTTCGCTCAGTTATGTTTA 58.987 34.615 24.95 0.00 35.61 2.01
1408 1422 7.270579 GTGAAATTTCGCTCAGTTATGTTTACC 59.729 37.037 21.71 0.00 34.94 2.85
1409 1423 5.813080 ATTTCGCTCAGTTATGTTTACCC 57.187 39.130 0.00 0.00 0.00 3.69
1413 1427 3.617263 CGCTCAGTTATGTTTACCCTGAC 59.383 47.826 0.00 0.00 0.00 3.51
1417 1431 4.525487 TCAGTTATGTTTACCCTGACGTCT 59.475 41.667 17.92 0.00 0.00 4.18
1424 1438 2.725127 TACCCTGACGTCTGCCAGGT 62.725 60.000 17.92 19.22 46.47 4.00
1425 1439 2.262915 CCTGACGTCTGCCAGGTC 59.737 66.667 17.92 0.00 43.71 3.85
1426 1440 2.279069 CCTGACGTCTGCCAGGTCT 61.279 63.158 17.92 0.00 43.71 3.85
1427 1441 0.965866 CCTGACGTCTGCCAGGTCTA 60.966 60.000 17.92 0.00 43.71 2.59
1428 1442 0.171455 CTGACGTCTGCCAGGTCTAC 59.829 60.000 17.92 0.00 40.11 2.59
1429 1443 0.251209 TGACGTCTGCCAGGTCTACT 60.251 55.000 17.92 0.00 40.11 2.57
1431 1445 0.539901 ACGTCTGCCAGGTCTACTGT 60.540 55.000 0.00 0.00 46.06 3.55
1458 1472 9.628500 TCTACTCATAGTTAGCAAGTCTTCATA 57.372 33.333 0.00 0.00 0.00 2.15
1461 1475 8.918116 ACTCATAGTTAGCAAGTCTTCATATGA 58.082 33.333 0.00 0.00 0.00 2.15
1532 1546 0.321034 GGTGATGCTCACTGTCTGCA 60.321 55.000 13.59 6.68 46.19 4.41
1561 1575 2.064014 GTGGTAGTTGCGGTGTTACTC 58.936 52.381 0.00 0.00 0.00 2.59
1761 1775 5.106673 GGTCCTCTCTTTTATGGTTGAAACG 60.107 44.000 0.00 0.00 0.00 3.60
1782 1796 3.255642 CGATTCCTGGTGTTGGTTTGAAT 59.744 43.478 0.00 0.00 0.00 2.57
1928 1978 8.996024 TTAGGGTTTTGCTTTAAATTATCAGC 57.004 30.769 0.00 0.00 0.00 4.26
1986 2036 5.689383 TTGAGATCTGGTACAAAGCAAAC 57.311 39.130 0.00 0.00 38.70 2.93
1993 2044 4.688879 TCTGGTACAAAGCAAACATACTCG 59.311 41.667 0.00 0.00 38.70 4.18
2002 2053 2.677836 GCAAACATACTCGATGCTTCCA 59.322 45.455 0.00 0.00 39.39 3.53
2129 2180 2.400399 CATTAGACCAACGACACGTGT 58.600 47.619 23.64 23.64 39.99 4.49
2130 2181 3.567530 CATTAGACCAACGACACGTGTA 58.432 45.455 23.44 1.44 39.99 2.90
2131 2182 3.921119 TTAGACCAACGACACGTGTAT 57.079 42.857 23.44 10.40 39.99 2.29
2134 2185 4.241590 AGACCAACGACACGTGTATTTA 57.758 40.909 23.44 0.00 39.99 1.40
2241 2294 1.477923 GGAGTCGAGAGCTCCTATGGT 60.478 57.143 10.93 0.00 45.15 3.55
2407 2513 3.677601 CATGCTATGCTTCAACAGTTCG 58.322 45.455 0.00 0.00 0.00 3.95
2506 2612 7.591426 GCACTTCAATTTTTGACAGGTTACTAG 59.409 37.037 0.00 0.00 39.87 2.57
2526 2632 1.950630 GGCAAGCACACTTTTGGCG 60.951 57.895 0.00 0.00 39.54 5.69
2679 2788 1.787012 CCAGTGTGGCATTTTTGCTC 58.213 50.000 0.00 0.00 34.73 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.942850 TCATATGAATCTTGACTTTGAACACTA 57.057 29.630 1.98 0.00 0.00 2.74
3 4 8.853077 TCATATGAATCTTGACTTTGAACACT 57.147 30.769 1.98 0.00 0.00 3.55
105 106 3.976169 GCACCTGCAAAAACTCATTACA 58.024 40.909 0.00 0.00 41.59 2.41
378 382 3.501828 TGAAATGACATTTGTGGGAGTCG 59.498 43.478 18.00 0.00 33.83 4.18
430 434 0.888619 TTTGTGGCCAACGTTGACAA 59.111 45.000 29.35 25.50 0.00 3.18
492 496 5.348724 TGAGCTCGTGATGAACAGTAAAATC 59.651 40.000 9.64 0.00 0.00 2.17
513 517 3.156511 TCTACTCGCAAGCTCATTGAG 57.843 47.619 9.40 9.40 41.83 3.02
514 518 3.193479 TCTTCTACTCGCAAGCTCATTGA 59.807 43.478 0.00 0.00 41.83 2.57
515 519 3.515630 TCTTCTACTCGCAAGCTCATTG 58.484 45.455 0.00 0.00 42.20 2.82
516 520 3.876274 TCTTCTACTCGCAAGCTCATT 57.124 42.857 0.00 0.00 37.18 2.57
517 521 3.382865 TCATCTTCTACTCGCAAGCTCAT 59.617 43.478 0.00 0.00 37.18 2.90
518 522 2.755103 TCATCTTCTACTCGCAAGCTCA 59.245 45.455 0.00 0.00 37.18 4.26
559 563 1.336056 GCGGGAAACGTTTGGCAAATA 60.336 47.619 20.10 0.00 46.52 1.40
560 564 0.598942 GCGGGAAACGTTTGGCAAAT 60.599 50.000 20.10 0.00 46.52 2.32
561 565 1.227002 GCGGGAAACGTTTGGCAAA 60.227 52.632 20.10 8.93 46.52 3.68
562 566 1.945354 TTGCGGGAAACGTTTGGCAA 61.945 50.000 26.66 26.66 46.52 4.52
563 567 1.945354 TTTGCGGGAAACGTTTGGCA 61.945 50.000 20.10 20.39 46.52 4.92
564 568 0.806492 TTTTGCGGGAAACGTTTGGC 60.806 50.000 20.10 18.11 46.52 4.52
565 569 1.641577 TTTTTGCGGGAAACGTTTGG 58.358 45.000 20.10 8.53 46.52 3.28
585 589 8.769891 CGGAAAGTAAATTTGGCAAATAGTTTT 58.230 29.630 24.58 20.02 0.00 2.43
586 590 7.386573 CCGGAAAGTAAATTTGGCAAATAGTTT 59.613 33.333 24.58 22.18 0.00 2.66
587 591 6.871492 CCGGAAAGTAAATTTGGCAAATAGTT 59.129 34.615 24.58 18.07 0.00 2.24
588 592 6.014925 ACCGGAAAGTAAATTTGGCAAATAGT 60.015 34.615 24.58 17.60 0.00 2.12
589 593 6.310224 CACCGGAAAGTAAATTTGGCAAATAG 59.690 38.462 24.58 8.50 0.00 1.73
661 665 6.272822 ACAGAAAGGTATTTTGAATGGAGC 57.727 37.500 0.00 0.00 0.00 4.70
803 808 0.822121 GAAGGCCAACACTCGGGTTT 60.822 55.000 5.01 0.00 0.00 3.27
859 871 6.664428 AAATAGGCAAGTTCTAGGCAAAAA 57.336 33.333 0.00 0.00 0.00 1.94
860 872 6.664428 AAAATAGGCAAGTTCTAGGCAAAA 57.336 33.333 0.00 0.00 0.00 2.44
907 919 3.073062 GGAATTGGGCTGCTTATAGGAGA 59.927 47.826 0.00 0.00 35.49 3.71
1356 1368 1.142262 ACTGGGTTTGCGACTACCTTT 59.858 47.619 0.00 0.00 34.75 3.11
1363 1375 2.671963 GGGGACTGGGTTTGCGAC 60.672 66.667 0.00 0.00 0.00 5.19
1364 1376 3.961414 GGGGGACTGGGTTTGCGA 61.961 66.667 0.00 0.00 0.00 5.10
1366 1378 4.280019 ACGGGGGACTGGGTTTGC 62.280 66.667 0.00 0.00 42.76 3.68
1367 1379 2.282180 CACGGGGGACTGGGTTTG 60.282 66.667 0.00 0.00 42.76 2.93
1368 1380 1.647334 TTTCACGGGGGACTGGGTTT 61.647 55.000 0.00 0.00 42.42 3.27
1369 1381 1.432023 ATTTCACGGGGGACTGGGTT 61.432 55.000 0.00 0.00 42.42 4.11
1381 1395 4.957971 ACATAACTGAGCGAAATTTCACG 58.042 39.130 17.99 6.94 0.00 4.35
1394 1408 4.525487 AGACGTCAGGGTAAACATAACTGA 59.475 41.667 19.50 0.00 35.97 3.41
1400 1414 1.338769 GGCAGACGTCAGGGTAAACAT 60.339 52.381 19.50 0.00 0.00 2.71
1404 1418 1.972198 CTGGCAGACGTCAGGGTAA 59.028 57.895 19.50 0.00 41.42 2.85
1409 1423 0.171455 GTAGACCTGGCAGACGTCAG 59.829 60.000 19.50 11.47 44.93 3.51
1413 1427 0.603569 AACAGTAGACCTGGCAGACG 59.396 55.000 17.94 2.11 46.06 4.18
1417 1431 3.090037 GAGTAGAACAGTAGACCTGGCA 58.910 50.000 0.00 0.00 46.06 4.92
1424 1438 8.803397 TTGCTAACTATGAGTAGAACAGTAGA 57.197 34.615 0.00 0.00 0.00 2.59
1425 1439 8.679100 ACTTGCTAACTATGAGTAGAACAGTAG 58.321 37.037 0.00 0.00 0.00 2.57
1426 1440 8.577048 ACTTGCTAACTATGAGTAGAACAGTA 57.423 34.615 0.00 0.00 0.00 2.74
1427 1441 7.394923 AGACTTGCTAACTATGAGTAGAACAGT 59.605 37.037 0.00 0.00 0.00 3.55
1428 1442 7.767261 AGACTTGCTAACTATGAGTAGAACAG 58.233 38.462 0.00 0.00 0.00 3.16
1429 1443 7.704578 AGACTTGCTAACTATGAGTAGAACA 57.295 36.000 0.00 0.00 0.00 3.18
1430 1444 8.244802 TGAAGACTTGCTAACTATGAGTAGAAC 58.755 37.037 0.00 0.00 0.00 3.01
1431 1445 8.349568 TGAAGACTTGCTAACTATGAGTAGAA 57.650 34.615 0.00 0.00 0.00 2.10
1458 1472 1.608590 CCAAAGAGGCAAACACGTCAT 59.391 47.619 0.00 0.00 0.00 3.06
1461 1475 0.738389 CACCAAAGAGGCAAACACGT 59.262 50.000 0.00 0.00 43.14 4.49
1561 1575 1.228510 GGGCATCTTCCCCTCCTTG 59.771 63.158 0.00 0.00 40.51 3.61
1761 1775 4.559153 CATTCAAACCAACACCAGGAATC 58.441 43.478 0.00 0.00 0.00 2.52
1782 1796 2.938451 CTCATAAGATTTCACGGCAGCA 59.062 45.455 0.00 0.00 0.00 4.41
1818 1832 5.297547 TGAAGCTTTGACAGTAACCTAGTG 58.702 41.667 0.00 0.00 35.25 2.74
1845 1859 6.014647 ACAACTCACTTCCTATGTACTGGTA 58.985 40.000 0.00 0.00 0.00 3.25
1846 1860 4.838986 ACAACTCACTTCCTATGTACTGGT 59.161 41.667 0.00 0.00 0.00 4.00
1847 1861 5.407407 ACAACTCACTTCCTATGTACTGG 57.593 43.478 0.00 0.00 0.00 4.00
1848 1862 9.737427 CTATTACAACTCACTTCCTATGTACTG 57.263 37.037 0.00 0.00 0.00 2.74
1849 1863 8.915036 CCTATTACAACTCACTTCCTATGTACT 58.085 37.037 0.00 0.00 0.00 2.73
1850 1864 8.693625 ACCTATTACAACTCACTTCCTATGTAC 58.306 37.037 0.00 0.00 0.00 2.90
1986 2036 6.628856 CGTTTTAATTGGAAGCATCGAGTATG 59.371 38.462 0.00 0.00 38.74 2.39
1993 2044 8.707839 TCATTTTTCGTTTTAATTGGAAGCATC 58.292 29.630 0.00 0.00 0.00 3.91
2002 2053 8.934507 TGGACAGTTCATTTTTCGTTTTAATT 57.065 26.923 0.00 0.00 0.00 1.40
2134 2185 8.612619 GGATCACTTCGTGTTTTTGTCATATAT 58.387 33.333 0.00 0.00 34.79 0.86
2211 2264 0.034380 TCTCGACTCCACTACCCCAG 60.034 60.000 0.00 0.00 0.00 4.45
2506 2612 1.153597 GCCAAAAGTGTGCTTGCCAC 61.154 55.000 6.24 6.24 44.90 5.01
2526 2632 0.250338 ACGGCAAACTGGAAGGAGTC 60.250 55.000 0.00 0.00 39.30 3.36


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

AutoCloner maintained by Alex Coulton.