Multiple sequence alignment - TraesCS4D01G119900

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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 TraesCS4D01G119900 chr4D 100.000 3496 0 0 1 3496 101020500 101023995 0.000000e+00 6457
1 TraesCS4D01G119900 chr4B 94.998 3059 88 24 491 3496 144744792 144747838 0.000000e+00 4741
2 TraesCS4D01G119900 chr4B 97.468 158 2 1 161 318 144744377 144744532 5.750000e-68 268
3 TraesCS4D01G119900 chr4B 97.386 153 3 1 8 160 144744190 144744341 3.460000e-65 259
4 TraesCS4D01G119900 chr4B 94.805 154 8 0 316 469 144744649 144744802 1.250000e-59 241
5 TraesCS4D01G119900 chr4A 95.513 2184 66 14 1333 3496 474744129 474741958 0.000000e+00 3461
6 TraesCS4D01G119900 chr4A 91.842 809 36 8 490 1273 474744933 474744130 0.000000e+00 1101
7 TraesCS4D01G119900 chr4A 95.425 153 7 0 8 160 474745373 474745221 9.690000e-61 244
8 TraesCS4D01G119900 chr4A 95.370 108 5 0 362 469 474745029 474744922 4.640000e-39 172


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 TraesCS4D01G119900 chr4D 101020500 101023995 3495 False 6457.00 6457 100.00000 1 3496 1 chr4D.!!$F1 3495
1 TraesCS4D01G119900 chr4B 144744190 144747838 3648 False 1377.25 4741 96.16425 8 3496 4 chr4B.!!$F1 3488
2 TraesCS4D01G119900 chr4A 474741958 474745373 3415 True 1244.50 3461 94.53750 8 3496 4 chr4A.!!$R1 3488

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
475 632 0.038526 AGTGAAGTCGGCAGGTTACG 60.039 55.000 0.00 0.0 0.00 3.18 F
482 639 0.249953 TCGGCAGGTTACGCTCAAAA 60.250 50.000 0.00 0.0 0.00 2.44 F
483 640 0.589223 CGGCAGGTTACGCTCAAAAA 59.411 50.000 0.00 0.0 0.00 1.94 F
588 747 0.882927 CACGTGTGGTACAACCCTGG 60.883 60.000 7.58 0.0 44.16 4.45 F
2175 2390 1.063616 CAACGCTGAATCATCTGCCAG 59.936 52.381 2.72 0.0 44.93 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2239 0.612732 AGGTCATACACGTCCCCGAA 60.613 55.000 0.00 0.0 37.88 4.30 R
2175 2390 3.002246 CACGACCATGGCATATAACACAC 59.998 47.826 13.04 0.0 0.00 3.82 R
2210 2425 4.320057 GCAGAGTCCTGAACAAACATCTTG 60.320 45.833 0.00 0.0 43.02 3.02 R
2491 2706 1.798223 CATGGTGTACAAGTGGTCACG 59.202 52.381 0.00 0.0 36.20 4.35 R
3304 3539 9.999883 GAAATTCGATCAAAATGAGTTTCAAAG 57.000 29.630 9.24 0.0 37.90 2.77 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
114 115 3.199442 TGGTTGGACCTCCTGAAGATA 57.801 47.619 7.57 0.00 39.58 1.98
176 212 0.038618 GGCGTTGGACCATTTGGAAC 60.039 55.000 3.01 0.00 38.94 3.62
201 237 8.204160 ACACCAGAGATTCGACATATTTTGATA 58.796 33.333 0.00 0.00 0.00 2.15
341 498 2.554032 CGATGAGGAGGCTTGTTGTTTT 59.446 45.455 0.00 0.00 0.00 2.43
368 525 8.879342 AAAAATGAATCAATACGTTGGACAAA 57.121 26.923 0.00 0.00 35.99 2.83
456 613 3.419943 TGGCATGCATGTGTTTTCTAGA 58.580 40.909 26.79 0.00 0.00 2.43
457 614 3.441222 TGGCATGCATGTGTTTTCTAGAG 59.559 43.478 26.79 0.00 0.00 2.43
458 615 3.441572 GGCATGCATGTGTTTTCTAGAGT 59.558 43.478 26.79 0.00 0.00 3.24
459 616 4.409570 GCATGCATGTGTTTTCTAGAGTG 58.590 43.478 26.79 0.00 0.00 3.51
460 617 4.154737 GCATGCATGTGTTTTCTAGAGTGA 59.845 41.667 26.79 0.00 0.00 3.41
461 618 5.335113 GCATGCATGTGTTTTCTAGAGTGAA 60.335 40.000 26.79 0.00 0.00 3.18
462 619 5.929697 TGCATGTGTTTTCTAGAGTGAAG 57.070 39.130 0.00 0.00 0.00 3.02
463 620 5.368145 TGCATGTGTTTTCTAGAGTGAAGT 58.632 37.500 0.00 0.00 0.00 3.01
464 621 5.466728 TGCATGTGTTTTCTAGAGTGAAGTC 59.533 40.000 0.00 0.00 0.00 3.01
465 622 5.388890 GCATGTGTTTTCTAGAGTGAAGTCG 60.389 44.000 0.00 0.00 0.00 4.18
466 623 4.617959 TGTGTTTTCTAGAGTGAAGTCGG 58.382 43.478 0.00 0.00 0.00 4.79
467 624 3.429207 GTGTTTTCTAGAGTGAAGTCGGC 59.571 47.826 0.00 0.00 0.00 5.54
468 625 3.069016 TGTTTTCTAGAGTGAAGTCGGCA 59.931 43.478 0.00 0.00 0.00 5.69
469 626 3.577649 TTTCTAGAGTGAAGTCGGCAG 57.422 47.619 0.00 0.00 0.00 4.85
470 627 1.464734 TCTAGAGTGAAGTCGGCAGG 58.535 55.000 0.00 0.00 0.00 4.85
471 628 1.178276 CTAGAGTGAAGTCGGCAGGT 58.822 55.000 0.00 0.00 0.00 4.00
472 629 1.546476 CTAGAGTGAAGTCGGCAGGTT 59.454 52.381 0.00 0.00 0.00 3.50
473 630 1.629043 AGAGTGAAGTCGGCAGGTTA 58.371 50.000 0.00 0.00 0.00 2.85
474 631 1.272769 AGAGTGAAGTCGGCAGGTTAC 59.727 52.381 0.00 0.00 0.00 2.50
475 632 0.038526 AGTGAAGTCGGCAGGTTACG 60.039 55.000 0.00 0.00 0.00 3.18
476 633 1.373748 TGAAGTCGGCAGGTTACGC 60.374 57.895 0.00 0.00 0.00 4.42
477 634 1.080025 GAAGTCGGCAGGTTACGCT 60.080 57.895 0.00 0.00 0.00 5.07
478 635 1.077089 GAAGTCGGCAGGTTACGCTC 61.077 60.000 0.00 0.00 0.00 5.03
479 636 1.812686 AAGTCGGCAGGTTACGCTCA 61.813 55.000 0.00 0.00 0.00 4.26
480 637 1.373748 GTCGGCAGGTTACGCTCAA 60.374 57.895 0.00 0.00 0.00 3.02
481 638 0.947180 GTCGGCAGGTTACGCTCAAA 60.947 55.000 0.00 0.00 0.00 2.69
482 639 0.249953 TCGGCAGGTTACGCTCAAAA 60.250 50.000 0.00 0.00 0.00 2.44
483 640 0.589223 CGGCAGGTTACGCTCAAAAA 59.411 50.000 0.00 0.00 0.00 1.94
527 685 6.304683 GCATGTACGTGGAACAAGATAAAAAC 59.695 38.462 16.68 0.00 44.16 2.43
530 688 2.900046 CGTGGAACAAGATAAAAACGCG 59.100 45.455 3.53 3.53 44.16 6.01
532 690 2.550606 TGGAACAAGATAAAAACGCGCT 59.449 40.909 5.73 0.00 31.92 5.92
533 691 3.747010 TGGAACAAGATAAAAACGCGCTA 59.253 39.130 5.73 0.00 31.92 4.26
534 692 4.086574 GGAACAAGATAAAAACGCGCTAC 58.913 43.478 5.73 0.00 0.00 3.58
535 693 4.142966 GGAACAAGATAAAAACGCGCTACT 60.143 41.667 5.73 0.00 0.00 2.57
536 694 5.062558 GGAACAAGATAAAAACGCGCTACTA 59.937 40.000 5.73 0.00 0.00 1.82
537 695 5.697848 ACAAGATAAAAACGCGCTACTAG 57.302 39.130 5.73 0.00 0.00 2.57
552 710 4.499357 CGCTACTAGTAGAAATCCACCCAC 60.499 50.000 30.09 9.32 35.21 4.61
576 735 5.170625 CGAAATAAAGGACAAAACACGTGTG 59.829 40.000 24.16 12.72 0.00 3.82
588 747 0.882927 CACGTGTGGTACAACCCTGG 60.883 60.000 7.58 0.00 44.16 4.45
611 770 3.111038 GCAAGTTATGCGGAGGCC 58.889 61.111 0.00 0.00 46.87 5.19
635 799 2.188837 TTCTAGTGCGTGCATAGACG 57.811 50.000 0.00 0.00 42.42 4.18
664 831 2.668945 CGTGACAAATGGCGTACATACA 59.331 45.455 0.00 0.00 39.40 2.29
770 958 1.089920 GTGATGTGCTGTGGACATCC 58.910 55.000 22.70 13.81 46.21 3.51
807 1012 1.559682 TGGGAGGTAGCAGGTGATTTC 59.440 52.381 0.00 0.00 0.00 2.17
982 1190 2.222729 GGCGCACAAACAATCGTAGTAG 60.223 50.000 10.83 0.00 0.00 2.57
1380 1590 8.749354 AGGGGAACAAAATATAGCTTTAAACTG 58.251 33.333 0.00 0.00 0.00 3.16
1381 1591 8.528643 GGGGAACAAAATATAGCTTTAAACTGT 58.471 33.333 0.00 0.00 0.00 3.55
1448 1658 7.044966 GCCGTTTTATGATCACACTTATTTTCG 60.045 37.037 0.00 0.00 0.00 3.46
1585 1797 4.965062 TCCGTCGAAATAAGAAATTGTGC 58.035 39.130 0.00 0.00 0.00 4.57
1586 1798 3.778718 CCGTCGAAATAAGAAATTGTGCG 59.221 43.478 0.00 0.00 0.00 5.34
1961 2176 1.749634 CCGGTTACAGTAGCAGCTACT 59.250 52.381 26.87 26.87 46.75 2.57
2024 2239 2.035576 GGCGTACCTGATTTATCCGAGT 59.964 50.000 0.00 0.00 0.00 4.18
2174 2389 1.089112 CAACGCTGAATCATCTGCCA 58.911 50.000 2.72 0.00 44.93 4.92
2175 2390 1.063616 CAACGCTGAATCATCTGCCAG 59.936 52.381 2.72 0.00 44.93 4.85
2199 2414 2.436173 TGTTATATGCCATGGTCGTGGA 59.564 45.455 14.67 0.00 42.02 4.02
2210 2425 3.648339 TGGTCGTGGAACTGTAACTAC 57.352 47.619 0.00 0.00 31.75 2.73
2395 2610 4.863707 GCAGGAGGCGATGATTCA 57.136 55.556 0.00 0.00 0.00 2.57
2480 2695 2.758736 AGCGTCTCTTTCAGCTCATT 57.241 45.000 0.00 0.00 34.48 2.57
2491 2706 5.470098 TCTTTCAGCTCATTGTCAAGTTACC 59.530 40.000 0.00 0.00 0.00 2.85
2886 3105 1.523154 GGAACTGGCCGCACAAATGA 61.523 55.000 0.00 0.00 0.00 2.57
2946 3167 1.123077 ATAGGCAGATGCTGAACGGA 58.877 50.000 4.59 0.00 41.70 4.69
3145 3366 2.795110 GCTCCTGCGCCTCATCTCT 61.795 63.158 4.18 0.00 0.00 3.10
3304 3539 2.538512 ATAGGCGATTCGGTTTACCC 57.461 50.000 8.34 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.604511 TGCATGACCTCAGTGCACAG 60.605 55.000 21.04 11.93 43.30 3.66
1 2 1.451072 TGCATGACCTCAGTGCACA 59.549 52.632 21.04 0.00 43.30 4.57
2 3 4.384599 TGCATGACCTCAGTGCAC 57.615 55.556 9.40 9.40 43.30 4.57
3 4 1.202794 TCTTTGCATGACCTCAGTGCA 60.203 47.619 0.00 7.77 46.15 4.57
4 5 1.198637 GTCTTTGCATGACCTCAGTGC 59.801 52.381 0.00 0.00 39.26 4.40
5 6 2.497138 TGTCTTTGCATGACCTCAGTG 58.503 47.619 14.98 0.00 33.83 3.66
6 7 2.936919 TGTCTTTGCATGACCTCAGT 57.063 45.000 14.98 0.00 33.83 3.41
10 11 5.733620 ATGATTTTGTCTTTGCATGACCT 57.266 34.783 14.98 1.58 33.83 3.85
114 115 3.004752 AGCACGAATTAAGCCCTGAAT 57.995 42.857 0.00 0.00 0.00 2.57
129 130 1.525995 ACAGGGTCCACAAAGCACG 60.526 57.895 0.00 0.00 0.00 5.34
176 212 6.908870 TCAAAATATGTCGAATCTCTGGTG 57.091 37.500 0.00 0.00 0.00 4.17
368 525 2.092914 CCTCGGGCTAAGAATCAAAGGT 60.093 50.000 0.00 0.00 0.00 3.50
456 613 0.038526 CGTAACCTGCCGACTTCACT 60.039 55.000 0.00 0.00 0.00 3.41
457 614 1.623973 GCGTAACCTGCCGACTTCAC 61.624 60.000 0.00 0.00 0.00 3.18
458 615 1.373748 GCGTAACCTGCCGACTTCA 60.374 57.895 0.00 0.00 0.00 3.02
459 616 1.077089 GAGCGTAACCTGCCGACTTC 61.077 60.000 0.00 0.00 0.00 3.01
460 617 1.080025 GAGCGTAACCTGCCGACTT 60.080 57.895 0.00 0.00 0.00 3.01
461 618 1.812686 TTGAGCGTAACCTGCCGACT 61.813 55.000 0.00 0.00 0.00 4.18
462 619 0.947180 TTTGAGCGTAACCTGCCGAC 60.947 55.000 0.00 0.00 0.00 4.79
463 620 0.249953 TTTTGAGCGTAACCTGCCGA 60.250 50.000 0.00 0.00 0.00 5.54
464 621 0.589223 TTTTTGAGCGTAACCTGCCG 59.411 50.000 0.00 0.00 0.00 5.69
480 637 4.142600 GCATGCCGACTTCACTCTATTTTT 60.143 41.667 6.36 0.00 0.00 1.94
481 638 3.375299 GCATGCCGACTTCACTCTATTTT 59.625 43.478 6.36 0.00 0.00 1.82
482 639 2.939103 GCATGCCGACTTCACTCTATTT 59.061 45.455 6.36 0.00 0.00 1.40
483 640 2.093500 TGCATGCCGACTTCACTCTATT 60.093 45.455 16.68 0.00 0.00 1.73
484 641 1.482182 TGCATGCCGACTTCACTCTAT 59.518 47.619 16.68 0.00 0.00 1.98
485 642 0.894835 TGCATGCCGACTTCACTCTA 59.105 50.000 16.68 0.00 0.00 2.43
486 643 0.251354 ATGCATGCCGACTTCACTCT 59.749 50.000 16.68 0.00 0.00 3.24
487 644 0.376152 CATGCATGCCGACTTCACTC 59.624 55.000 14.93 0.00 0.00 3.51
488 645 0.321919 ACATGCATGCCGACTTCACT 60.322 50.000 26.53 0.00 0.00 3.41
527 685 3.298317 GTGGATTTCTACTAGTAGCGCG 58.702 50.000 22.87 0.00 33.32 6.86
530 688 4.499357 CGTGGGTGGATTTCTACTAGTAGC 60.499 50.000 22.87 10.26 33.32 3.58
532 690 4.858850 TCGTGGGTGGATTTCTACTAGTA 58.141 43.478 1.89 1.89 0.00 1.82
533 691 3.705051 TCGTGGGTGGATTTCTACTAGT 58.295 45.455 0.00 0.00 0.00 2.57
534 692 4.730949 TTCGTGGGTGGATTTCTACTAG 57.269 45.455 0.00 0.00 0.00 2.57
535 693 5.687166 ATTTCGTGGGTGGATTTCTACTA 57.313 39.130 0.00 0.00 0.00 1.82
536 694 4.569719 ATTTCGTGGGTGGATTTCTACT 57.430 40.909 0.00 0.00 0.00 2.57
537 695 6.183360 CCTTTATTTCGTGGGTGGATTTCTAC 60.183 42.308 0.00 0.00 0.00 2.59
552 710 5.170625 CACACGTGTTTTGTCCTTTATTTCG 59.829 40.000 20.79 0.00 0.00 3.46
576 735 0.679960 GCATCACCCAGGGTTGTACC 60.680 60.000 9.12 0.00 37.60 3.34
635 799 1.391144 GCCATTTGTCACGTACGGTAC 59.609 52.381 21.06 16.70 0.00 3.34
664 831 3.300032 TCCAACGGACAGAGGCTAT 57.700 52.632 0.00 0.00 0.00 2.97
770 958 9.289782 CTACCTCCCATAAATCTTAGGAAAATG 57.710 37.037 0.00 0.00 0.00 2.32
807 1012 0.179111 TCGCGAGTCTAAATGCAGGG 60.179 55.000 3.71 0.00 0.00 4.45
862 1067 4.183865 GTTTATTTCCAGAAGCATTGGCC 58.816 43.478 0.00 0.00 42.56 5.36
911 1116 7.275999 GCCCTTTAGTGACGAGCTATTTATATC 59.724 40.741 0.00 0.00 0.00 1.63
947 1152 0.831711 TGCGCCTGCCTATCTATCCA 60.832 55.000 4.18 0.00 41.78 3.41
982 1190 5.229469 CGTCCATCTCGTCAATAACTTGTAC 59.771 44.000 0.00 0.00 33.87 2.90
1313 1521 7.033185 GTGCAGTAACCAAAAAGAAGAAGAAA 58.967 34.615 0.00 0.00 0.00 2.52
1316 1524 6.136541 AGTGCAGTAACCAAAAAGAAGAAG 57.863 37.500 0.00 0.00 0.00 2.85
1322 1530 6.619801 AAGAGTAGTGCAGTAACCAAAAAG 57.380 37.500 1.96 0.00 0.00 2.27
1397 1607 7.513560 TTATAAAAGCTTACAGAGGGGGTAA 57.486 36.000 0.00 0.00 0.00 2.85
1423 1633 7.428183 CCGAAAATAAGTGTGATCATAAAACGG 59.572 37.037 0.00 0.00 0.00 4.44
1448 1658 7.215719 AGTGGTTTTCTAATAAAGAGCAACC 57.784 36.000 9.61 9.61 43.52 3.77
1585 1797 6.820152 TCATCTATCATGATTTCCATAAGGCG 59.180 38.462 14.65 0.00 33.31 5.52
1586 1798 8.571461 TTCATCTATCATGATTTCCATAAGGC 57.429 34.615 14.65 0.00 33.31 4.35
2024 2239 0.612732 AGGTCATACACGTCCCCGAA 60.613 55.000 0.00 0.00 37.88 4.30
2174 2389 3.118408 ACGACCATGGCATATAACACACT 60.118 43.478 13.04 0.00 0.00 3.55
2175 2390 3.002246 CACGACCATGGCATATAACACAC 59.998 47.826 13.04 0.00 0.00 3.82
2199 2414 8.500753 TGAACAAACATCTTGTAGTTACAGTT 57.499 30.769 0.00 0.00 37.52 3.16
2210 2425 4.320057 GCAGAGTCCTGAACAAACATCTTG 60.320 45.833 0.00 0.00 43.02 3.02
2491 2706 1.798223 CATGGTGTACAAGTGGTCACG 59.202 52.381 0.00 0.00 36.20 4.35
2886 3105 0.476771 ACCAATCACCGGGACAACTT 59.523 50.000 6.32 0.00 0.00 2.66
2946 3167 0.974010 CAAATGCTCCCCTGCCATGT 60.974 55.000 0.00 0.00 0.00 3.21
3304 3539 9.999883 GAAATTCGATCAAAATGAGTTTCAAAG 57.000 29.630 9.24 0.00 37.90 2.77


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

AutoCloner maintained by Alex Coulton.