Multiple sequence alignment - TraesCS6A01G250000

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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 TraesCS6A01G250000 chr6A 100.000 2359 0 0 1 2359 463541531 463539173 0.000000e+00 4357.0
1 TraesCS6A01G250000 chr6A 93.878 49 1 1 684 730 596304311 596304263 3.250000e-09 73.1
2 TraesCS6A01G250000 chr6B 91.801 2366 148 21 1 2359 497880423 497882749 0.000000e+00 3253.0
3 TraesCS6A01G250000 chr6B 87.571 177 18 4 1588 1764 125173026 125173198 3.980000e-48 202.0
4 TraesCS6A01G250000 chr6B 88.710 62 4 3 674 734 135131116 135131175 3.250000e-09 73.1
5 TraesCS6A01G250000 chr6D 95.480 1637 62 7 732 2359 325403828 325402195 0.000000e+00 2603.0
6 TraesCS6A01G250000 chr6D 89.675 707 53 12 1 691 325404517 325403815 0.000000e+00 883.0
7 TraesCS6A01G250000 chr4D 86.755 302 32 4 1032 1332 397686403 397686109 1.750000e-86 329.0
8 TraesCS6A01G250000 chr2B 94.545 55 1 2 680 732 641645350 641645296 1.500000e-12 84.2
9 TraesCS6A01G250000 chr1D 100.000 44 0 0 688 731 14487868 14487911 5.400000e-12 82.4
10 TraesCS6A01G250000 chr4A 94.000 50 1 2 688 735 313639890 313639841 9.040000e-10 75.0
11 TraesCS6A01G250000 chr2D 97.727 44 0 1 688 730 87598716 87598673 9.040000e-10 75.0
12 TraesCS6A01G250000 chr3A 93.750 48 3 0 683 730 570498958 570498911 3.250000e-09 73.1
13 TraesCS6A01G250000 chr3A 89.655 58 2 4 688 744 32184224 32184278 1.170000e-08 71.3
14 TraesCS6A01G250000 chr2A 90.741 54 4 1 681 733 27494898 27494845 1.170000e-08 71.3


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 TraesCS6A01G250000 chr6A 463539173 463541531 2358 True 4357 4357 100.0000 1 2359 1 chr6A.!!$R1 2358
1 TraesCS6A01G250000 chr6B 497880423 497882749 2326 False 3253 3253 91.8010 1 2359 1 chr6B.!!$F3 2358
2 TraesCS6A01G250000 chr6D 325402195 325404517 2322 True 1743 2603 92.5775 1 2359 2 chr6D.!!$R1 2358

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
428 439 0.179067 GAGTTCCAACGGTGTCACCA 60.179 55.0 21.91 0.0 38.47 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1594 0.506932 CGACAACGACCACACACATC 59.493 55.0 0.0 0.0 42.66 3.06 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
33 34 6.299141 ACTCCACTGTGAACAAGTAATCATT 58.701 36.000 9.86 0.00 0.00 2.57
36 37 6.770303 TCCACTGTGAACAAGTAATCATTCAA 59.230 34.615 9.86 0.00 33.09 2.69
42 43 7.013178 TGTGAACAAGTAATCATTCAAAGCTCA 59.987 33.333 0.00 0.00 33.09 4.26
70 71 2.904866 TCTTGCGCACAACCCCAC 60.905 61.111 11.12 0.00 0.00 4.61
113 114 3.637821 AAGCCATATGACTAGAGGGGA 57.362 47.619 3.65 0.00 0.00 4.81
157 158 2.351276 GCCCAACATGTCTCCCGT 59.649 61.111 0.00 0.00 0.00 5.28
159 160 2.040544 CCCAACATGTCTCCCGTGC 61.041 63.158 0.00 0.00 33.01 5.34
166 167 3.386237 GTCTCCCGTGCAGGCTCT 61.386 66.667 0.00 0.00 39.21 4.09
170 171 3.699894 CCCGTGCAGGCTCTCTGT 61.700 66.667 0.00 0.00 45.08 3.41
241 242 9.213799 GAGTCTTCAAAGTAGATCATCAACTTT 57.786 33.333 0.00 2.84 42.60 2.66
242 243 9.213799 AGTCTTCAAAGTAGATCATCAACTTTC 57.786 33.333 10.66 3.33 40.52 2.62
245 246 7.020827 TCAAAGTAGATCATCAACTTTCCCT 57.979 36.000 10.66 0.00 40.52 4.20
246 247 7.106239 TCAAAGTAGATCATCAACTTTCCCTC 58.894 38.462 10.66 0.00 40.52 4.30
298 309 2.503375 CGTCGTCGCCACCACTAC 60.503 66.667 0.00 0.00 0.00 2.73
311 322 1.151413 ACCACTACCTTCCTCCTCCAA 59.849 52.381 0.00 0.00 0.00 3.53
333 344 2.057137 TGTGAAGGATTAGGCATGCC 57.943 50.000 30.12 30.12 0.00 4.40
360 371 2.480759 GCGATAGAGCCAAAGGACGTTA 60.481 50.000 0.00 0.00 39.76 3.18
428 439 0.179067 GAGTTCCAACGGTGTCACCA 60.179 55.000 21.91 0.00 38.47 4.17
475 486 7.639113 TTTAGGGGCAAAATATTCTGTACAG 57.361 36.000 17.17 17.17 0.00 2.74
504 515 2.019249 CCCTGTTGTATCATGCACCTG 58.981 52.381 0.00 0.00 0.00 4.00
517 528 1.271325 TGCACCTGTCGATGATGGTTT 60.271 47.619 0.00 0.00 0.00 3.27
524 535 4.635765 CCTGTCGATGATGGTTTGTATGTT 59.364 41.667 0.00 0.00 0.00 2.71
525 536 5.123820 CCTGTCGATGATGGTTTGTATGTTT 59.876 40.000 0.00 0.00 0.00 2.83
650 664 9.737427 TCAAAATAACGTTGACACAAAATATGT 57.263 25.926 11.99 0.00 34.69 2.29
715 732 7.954788 TTTTATTGTTTGGATTGCTTACCAC 57.045 32.000 0.00 0.00 35.81 4.16
716 733 6.656632 TTATTGTTTGGATTGCTTACCACA 57.343 33.333 0.00 0.00 35.81 4.17
717 734 5.743636 ATTGTTTGGATTGCTTACCACAT 57.256 34.783 0.00 0.00 35.81 3.21
718 735 4.517952 TGTTTGGATTGCTTACCACATG 57.482 40.909 0.00 0.00 35.81 3.21
719 736 3.894427 TGTTTGGATTGCTTACCACATGT 59.106 39.130 0.00 0.00 35.81 3.21
720 737 4.343526 TGTTTGGATTGCTTACCACATGTT 59.656 37.500 0.00 0.00 35.81 2.71
721 738 5.163364 TGTTTGGATTGCTTACCACATGTTT 60.163 36.000 0.00 0.00 35.81 2.83
722 739 4.782019 TGGATTGCTTACCACATGTTTC 57.218 40.909 0.00 0.00 0.00 2.78
723 740 4.148079 TGGATTGCTTACCACATGTTTCA 58.852 39.130 0.00 0.00 0.00 2.69
724 741 4.771577 TGGATTGCTTACCACATGTTTCAT 59.228 37.500 0.00 0.00 0.00 2.57
725 742 5.104374 GGATTGCTTACCACATGTTTCATG 58.896 41.667 0.00 7.99 0.00 3.07
726 743 5.336690 GGATTGCTTACCACATGTTTCATGT 60.337 40.000 9.21 9.21 0.00 3.21
727 744 4.502171 TGCTTACCACATGTTTCATGTG 57.498 40.909 26.20 26.20 46.49 3.21
738 755 8.673626 CACATGTTTCATGTGGTTAACTATTC 57.326 34.615 25.74 0.00 44.04 1.75
743 760 8.908903 TGTTTCATGTGGTTAACTATTCTGTTT 58.091 29.630 5.42 0.00 0.00 2.83
754 771 5.874895 ACTATTCTGTTTTTAGTTCCGCC 57.125 39.130 0.00 0.00 0.00 6.13
845 870 0.814010 ATCCGCTATTGTTGGGCGTC 60.814 55.000 0.00 0.00 46.23 5.19
860 885 2.750237 GTCCGGCCCAACATGGAC 60.750 66.667 9.17 9.17 40.96 4.02
978 1005 1.082879 TCTCCCTTTCCCATCTCCCTT 59.917 52.381 0.00 0.00 0.00 3.95
985 1013 1.153086 CCCATCTCCCTTGCCTTCG 60.153 63.158 0.00 0.00 0.00 3.79
1432 1460 2.502093 CCCGCCCGTGCATACTTA 59.498 61.111 0.00 0.00 37.32 2.24
1439 1467 3.305539 CGCCCGTGCATACTTATACCTTA 60.306 47.826 0.00 0.00 37.32 2.69
1444 1472 7.436118 CCCGTGCATACTTATACCTTACTTTA 58.564 38.462 0.00 0.00 0.00 1.85
1464 1493 0.657840 ATCTTGCGCGCCATTAGTTC 59.342 50.000 30.77 0.00 0.00 3.01
1476 1505 3.671702 GCCATTAGTTCAGTTGCTTGCTC 60.672 47.826 0.00 0.00 0.00 4.26
1533 1562 1.947456 GTGTCACCCTTTGGTCACTTC 59.053 52.381 0.00 0.00 45.57 3.01
1565 1594 6.618287 TGATTCTGTGTAGTTTTTGTCCAG 57.382 37.500 0.00 0.00 0.00 3.86
1580 1609 0.756294 TCCAGATGTGTGTGGTCGTT 59.244 50.000 0.00 0.00 39.70 3.85
1670 1699 6.194796 TCCAAAAGGAAATTATTCAGCTCG 57.805 37.500 0.00 0.00 37.29 5.03
1719 1748 6.566079 TGGAGAATTAGAGATGTCCATGTT 57.434 37.500 0.00 0.00 0.00 2.71
1781 1810 1.131693 GTATGTAGCACCGTTTTGGCC 59.868 52.381 0.00 0.00 43.94 5.36
1841 1870 2.422479 TGCGTAGTGACATGACTACCTC 59.578 50.000 15.46 10.09 43.73 3.85
1845 1874 5.220989 GCGTAGTGACATGACTACCTCAATA 60.221 44.000 15.46 2.88 43.73 1.90
1931 1960 2.225394 ACCTTTGGGTCTCTCTAGCTGA 60.225 50.000 0.00 0.00 43.38 4.26
1965 1994 8.168725 TCCATACTATACCTCCTTTACCTACAG 58.831 40.741 0.00 0.00 0.00 2.74
1969 1998 3.555117 ACCTCCTTTACCTACAGTCCA 57.445 47.619 0.00 0.00 0.00 4.02
2295 2326 4.929479 TCCCTATGTTTTATGCAGTGGTT 58.071 39.130 0.00 0.00 0.00 3.67
2322 2353 2.489938 TGCTAAGCCTACCTGTTTGG 57.510 50.000 0.00 0.00 42.93 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.526970 AGAGGTGAAGTTTTGAGCTTTGA 58.473 39.130 0.00 0.00 0.00 2.69
36 37 3.067320 GCAAGAGGTGAAGTTTTGAGCTT 59.933 43.478 0.00 0.00 0.00 3.74
42 43 1.065551 GTGCGCAAGAGGTGAAGTTTT 59.934 47.619 14.00 0.00 43.02 2.43
113 114 4.481368 TGATAAGGGTATGCGTGAAAGT 57.519 40.909 0.00 0.00 0.00 2.66
157 158 3.385384 CGGGACAGAGAGCCTGCA 61.385 66.667 0.00 0.00 46.81 4.41
166 167 1.278127 GATCTTTTGGGTCGGGACAGA 59.722 52.381 0.75 0.00 0.00 3.41
170 171 1.422024 TGTTGATCTTTTGGGTCGGGA 59.578 47.619 0.00 0.00 0.00 5.14
241 242 0.689745 ATGGATCCGAAACCGAGGGA 60.690 55.000 7.39 0.00 0.00 4.20
242 243 0.249911 GATGGATCCGAAACCGAGGG 60.250 60.000 7.39 0.00 0.00 4.30
285 296 1.079336 GGAAGGTAGTGGTGGCGAC 60.079 63.158 0.00 0.00 0.00 5.19
288 299 0.910088 AGGAGGAAGGTAGTGGTGGC 60.910 60.000 0.00 0.00 0.00 5.01
298 309 2.191400 TCACATCTTGGAGGAGGAAGG 58.809 52.381 0.00 0.00 0.00 3.46
311 322 3.484407 GCATGCCTAATCCTTCACATCT 58.516 45.455 6.36 0.00 0.00 2.90
333 344 2.954020 TTTGGCTCTATCGCGCGAGG 62.954 60.000 36.99 29.44 0.00 4.63
350 361 5.540400 TCGATATTGGGATAACGTCCTTT 57.460 39.130 0.00 0.00 46.91 3.11
360 371 4.018960 CCTTTCCCTCATCGATATTGGGAT 60.019 45.833 23.99 0.00 45.26 3.85
365 376 3.425162 GGCCTTTCCCTCATCGATATT 57.575 47.619 0.00 0.00 0.00 1.28
391 402 5.276067 GGAACTCATATTTTACCGACGTTCG 60.276 44.000 0.00 0.00 40.07 3.95
406 417 2.289195 GGTGACACCGTTGGAACTCATA 60.289 50.000 9.33 0.00 0.00 2.15
459 470 7.415206 GGTGTAAGGGCTGTACAGAATATTTTG 60.415 40.741 27.08 4.50 32.23 2.44
460 471 6.602009 GGTGTAAGGGCTGTACAGAATATTTT 59.398 38.462 27.08 12.47 32.23 1.82
465 476 2.238898 GGGTGTAAGGGCTGTACAGAAT 59.761 50.000 27.08 10.69 32.23 2.40
475 486 2.026636 TGATACAACAGGGTGTAAGGGC 60.027 50.000 0.70 0.00 37.52 5.19
528 539 7.504924 AATTCAACGTCTATCACCTTGAAAA 57.495 32.000 0.00 0.00 40.91 2.29
533 547 4.156008 GGCAAATTCAACGTCTATCACCTT 59.844 41.667 0.00 0.00 0.00 3.50
611 625 8.476142 CAACGTTATTTTGACGATTTCATGTTT 58.524 29.630 0.00 0.00 42.82 2.83
660 674 9.458374 CAGAATAGTTTGTTCGGTTACAAAAAT 57.542 29.630 11.21 7.17 46.27 1.82
661 675 8.460428 ACAGAATAGTTTGTTCGGTTACAAAAA 58.540 29.630 11.21 5.69 46.27 1.94
694 711 6.210385 ACATGTGGTAAGCAATCCAAACAATA 59.790 34.615 0.00 0.00 35.38 1.90
695 712 5.011943 ACATGTGGTAAGCAATCCAAACAAT 59.988 36.000 0.00 0.00 35.38 2.71
696 713 4.343526 ACATGTGGTAAGCAATCCAAACAA 59.656 37.500 0.00 0.00 35.38 2.83
697 714 3.894427 ACATGTGGTAAGCAATCCAAACA 59.106 39.130 0.00 0.00 35.38 2.83
699 716 5.069648 TGAAACATGTGGTAAGCAATCCAAA 59.930 36.000 0.00 0.00 35.38 3.28
700 717 4.586421 TGAAACATGTGGTAAGCAATCCAA 59.414 37.500 0.00 0.00 35.38 3.53
701 718 4.148079 TGAAACATGTGGTAAGCAATCCA 58.852 39.130 0.00 0.00 0.00 3.41
702 719 4.782019 TGAAACATGTGGTAAGCAATCC 57.218 40.909 0.00 0.00 0.00 3.01
703 720 5.574055 CACATGAAACATGTGGTAAGCAATC 59.426 40.000 26.94 0.00 44.04 2.67
704 721 5.472148 CACATGAAACATGTGGTAAGCAAT 58.528 37.500 26.94 0.00 44.04 3.56
705 722 4.869215 CACATGAAACATGTGGTAAGCAA 58.131 39.130 26.94 0.00 44.04 3.91
706 723 4.502171 CACATGAAACATGTGGTAAGCA 57.498 40.909 26.94 0.00 44.04 3.91
713 730 8.514594 AGAATAGTTAACCACATGAAACATGTG 58.485 33.333 27.39 27.39 46.49 3.21
714 731 8.514594 CAGAATAGTTAACCACATGAAACATGT 58.485 33.333 10.94 10.94 0.00 3.21
715 732 8.514594 ACAGAATAGTTAACCACATGAAACATG 58.485 33.333 0.00 9.72 0.00 3.21
716 733 8.635765 ACAGAATAGTTAACCACATGAAACAT 57.364 30.769 0.00 0.00 0.00 2.71
717 734 8.458573 AACAGAATAGTTAACCACATGAAACA 57.541 30.769 0.00 0.00 0.00 2.83
718 735 9.744468 AAAACAGAATAGTTAACCACATGAAAC 57.256 29.630 0.00 0.00 0.00 2.78
725 742 9.888878 GGAACTAAAAACAGAATAGTTAACCAC 57.111 33.333 0.88 0.00 39.34 4.16
726 743 8.776470 CGGAACTAAAAACAGAATAGTTAACCA 58.224 33.333 0.88 0.00 39.34 3.67
727 744 7.747799 GCGGAACTAAAAACAGAATAGTTAACC 59.252 37.037 0.88 0.00 39.34 2.85
728 745 7.747799 GGCGGAACTAAAAACAGAATAGTTAAC 59.252 37.037 0.00 0.00 39.34 2.01
729 746 7.662669 AGGCGGAACTAAAAACAGAATAGTTAA 59.337 33.333 0.00 0.00 39.34 2.01
730 747 7.163441 AGGCGGAACTAAAAACAGAATAGTTA 58.837 34.615 0.00 0.00 39.34 2.24
738 755 2.500229 TGGAGGCGGAACTAAAAACAG 58.500 47.619 0.00 0.00 0.00 3.16
743 760 1.913419 AGGATTGGAGGCGGAACTAAA 59.087 47.619 0.00 0.00 0.00 1.85
746 763 0.698818 AAAGGATTGGAGGCGGAACT 59.301 50.000 0.00 0.00 0.00 3.01
754 771 2.899256 TCTTGGGCAAAAAGGATTGGAG 59.101 45.455 0.00 0.00 0.00 3.86
860 885 2.887151 AGGAAGGACACATTTCCAGG 57.113 50.000 6.09 0.00 44.26 4.45
985 1013 1.034292 GCCATCTCTGAGGGTTTGGC 61.034 60.000 18.75 18.75 42.40 4.52
1111 1139 5.121768 CACCGTTTGTTTACCTGGAGATTAG 59.878 44.000 0.00 0.00 0.00 1.73
1432 1460 4.025145 GCGCGCAAGATTAAAGTAAGGTAT 60.025 41.667 29.10 0.00 43.02 2.73
1439 1467 1.094785 ATGGCGCGCAAGATTAAAGT 58.905 45.000 34.42 0.00 43.02 2.66
1444 1472 1.064060 GAACTAATGGCGCGCAAGATT 59.936 47.619 34.42 26.44 43.02 2.40
1476 1505 3.243101 GCATCAGATTCTTCACCATGCTG 60.243 47.826 0.00 0.00 32.13 4.41
1533 1562 2.680312 ACACAGAATCATCGACAGGG 57.320 50.000 0.00 0.00 0.00 4.45
1565 1594 0.506932 CGACAACGACCACACACATC 59.493 55.000 0.00 0.00 42.66 3.06
1580 1609 1.066787 TGGCATTTCGGTGATACGACA 60.067 47.619 0.00 0.00 43.37 4.35
1653 1682 3.878778 ACAGCGAGCTGAATAATTTCCT 58.121 40.909 29.11 2.10 46.30 3.36
1670 1699 6.985188 TTCATTAGTCAAACCATCTACAGC 57.015 37.500 0.00 0.00 0.00 4.40
1765 1794 1.525941 TTAGGCCAAAACGGTGCTAC 58.474 50.000 5.01 0.00 36.97 3.58
1768 1797 2.089201 ACTATTAGGCCAAAACGGTGC 58.911 47.619 5.01 0.00 36.97 5.01
1781 1810 6.642950 GTGGAACAGCACTAGCATACTATTAG 59.357 42.308 0.00 0.00 45.49 1.73
1828 1857 7.849804 AACACAATATTGAGGTAGTCATGTC 57.150 36.000 22.16 0.00 34.17 3.06
1841 1870 8.744652 TCCTACCCAAACATAAACACAATATTG 58.255 33.333 14.01 14.01 0.00 1.90
1845 1874 6.551601 TGTTCCTACCCAAACATAAACACAAT 59.448 34.615 0.00 0.00 30.73 2.71
1931 1960 5.020132 GGAGGTATAGTATGGAGTGCTGAT 58.980 45.833 0.00 0.00 0.00 2.90
2001 2032 7.315142 ACAAATGAATCTGCAATCGTTATTGT 58.685 30.769 0.00 0.00 43.75 2.71
2295 2326 4.009675 CAGGTAGGCTTAGCAAAATCACA 58.990 43.478 6.53 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.