Multiple sequence alignment - TraesCS7B01G114000

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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 TraesCS7B01G114000 chr7B 100.000 2393 0 0 1 2393 131957995 131955603 0.000000e+00 4420
1 TraesCS7B01G114000 chr7B 82.168 286 44 5 1114 1394 131947699 131947416 3.070000e-59 239
2 TraesCS7B01G114000 chr7A 90.047 1075 78 18 733 1790 169038760 169037698 0.000000e+00 1365
3 TraesCS7B01G114000 chr7A 86.078 747 81 20 1 733 169042196 169041459 0.000000e+00 782
4 TraesCS7B01G114000 chr7A 92.251 542 30 5 1787 2317 169037397 169036857 0.000000e+00 758
5 TraesCS7B01G114000 chr7A 77.847 483 69 30 134 603 42505433 42504976 5.070000e-67 265
6 TraesCS7B01G114000 chr7A 81.818 286 45 5 1114 1394 169026244 169025961 1.430000e-57 233
7 TraesCS7B01G114000 chr7A 92.045 88 7 0 2304 2391 169036517 169036430 8.980000e-25 124
8 TraesCS7B01G114000 chr7D 95.501 778 34 1 781 1558 167551474 167550698 0.000000e+00 1242
9 TraesCS7B01G114000 chr7D 92.545 550 28 6 1604 2146 167549736 167549193 0.000000e+00 776
10 TraesCS7B01G114000 chr7D 82.303 825 87 33 1 810 167552486 167551706 0.000000e+00 660
11 TraesCS7B01G114000 chr7D 81.119 286 47 5 1114 1394 167531928 167531645 3.100000e-54 222
12 TraesCS7B01G114000 chr7D 93.617 94 5 1 2207 2299 167549193 167549100 3.210000e-29 139
13 TraesCS7B01G114000 chr1A 79.462 409 56 21 65 461 97821779 97822171 5.070000e-67 265
14 TraesCS7B01G114000 chr3D 81.272 283 35 12 272 547 147606689 147606960 1.860000e-51 213
15 TraesCS7B01G114000 chr1B 73.964 603 88 49 65 651 130106278 130106827 1.890000e-41 180


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 TraesCS7B01G114000 chr7B 131955603 131957995 2392 True 4420.00 4420 100.00000 1 2393 1 chr7B.!!$R2 2392
1 TraesCS7B01G114000 chr7A 169036430 169042196 5766 True 757.25 1365 90.10525 1 2391 4 chr7A.!!$R3 2390
2 TraesCS7B01G114000 chr7D 167549100 167552486 3386 True 704.25 1242 90.99150 1 2299 4 chr7D.!!$R2 2298

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
849 3831 1.08023 CGTGTGACAGCAGGGAGAG 60.08 63.158 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 6380 0.733223 GACTGTCGGCTCTTCGGAAC 60.733 60.0 0.0 0.0 0.0 3.62 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
120 130 7.316393 ACTGATATCCTCGGGATAAAAATGA 57.684 36.000 14.24 0.00 46.18 2.57
129 139 6.039717 CCTCGGGATAAAAATGACATGAACAT 59.960 38.462 0.00 1.80 0.00 2.71
131 141 8.153479 TCGGGATAAAAATGACATGAACATAG 57.847 34.615 0.00 0.00 0.00 2.23
132 142 7.228507 TCGGGATAAAAATGACATGAACATAGG 59.771 37.037 0.00 0.00 0.00 2.57
210 221 7.168135 CGTCGTACTTTATAAAACTACCATCCC 59.832 40.741 0.00 0.00 0.00 3.85
257 268 5.585047 ACGCCTCATAAATAAAACTGTCCTC 59.415 40.000 0.00 0.00 0.00 3.71
406 421 6.400579 TTGTTAATAAAAATGCCATGCACG 57.599 33.333 0.00 0.00 43.04 5.34
417 432 8.885494 AAAATGCCATGCACGTAATAATAAAT 57.115 26.923 0.00 0.00 43.04 1.40
418 433 8.519492 AAATGCCATGCACGTAATAATAAATC 57.481 30.769 0.00 0.00 43.04 2.17
426 441 8.432110 TGCACGTAATAATAAATCTGTCATGT 57.568 30.769 0.00 0.00 0.00 3.21
428 443 8.765219 GCACGTAATAATAAATCTGTCATGTCT 58.235 33.333 0.00 0.00 0.00 3.41
446 461 9.585099 GTCATGTCTCAAAAATAAAATGCCATA 57.415 29.630 0.00 0.00 0.00 2.74
462 477 9.467258 AAAATGCCATATCTCAATCATAAAACG 57.533 29.630 0.00 0.00 0.00 3.60
515 531 4.175516 AGTGTTGATAAAAATGCCATGCG 58.824 39.130 0.00 0.00 0.00 4.73
529 545 7.749539 AATGCCATGCGTTTAGTAATAAAAC 57.250 32.000 0.00 0.00 33.67 2.43
532 548 6.149640 TGCCATGCGTTTAGTAATAAAACTGA 59.850 34.615 0.00 0.00 35.20 3.41
651 670 8.082242 CAGGATTTCCGGGATTGAAAAATATAC 58.918 37.037 0.00 0.00 42.08 1.47
692 711 2.242043 ACAGATTCACAAAAGGCCCTG 58.758 47.619 0.00 0.00 0.00 4.45
723 744 2.722487 CTCGGTTCGATCCCTCGG 59.278 66.667 6.94 0.00 45.10 4.63
744 3464 5.328886 GGCTCACGAATTTTTGAAAAAGG 57.671 39.130 9.13 3.80 0.00 3.11
745 3465 4.808895 GGCTCACGAATTTTTGAAAAAGGT 59.191 37.500 9.13 4.37 0.00 3.50
752 3472 8.608317 CACGAATTTTTGAAAAAGGTAAACCAT 58.392 29.630 9.13 0.00 38.89 3.55
835 3817 2.507102 CTGCGCCGAGATTCGTGT 60.507 61.111 4.18 0.00 38.40 4.49
839 3821 1.443702 CGCCGAGATTCGTGTGACA 60.444 57.895 0.00 0.00 38.40 3.58
849 3831 1.080230 CGTGTGACAGCAGGGAGAG 60.080 63.158 0.00 0.00 0.00 3.20
853 3835 2.183046 GACAGCAGGGAGAGCGTC 59.817 66.667 0.00 0.00 37.01 5.19
987 3969 2.762535 TCTCTGAAATCCGAACACCC 57.237 50.000 0.00 0.00 0.00 4.61
1164 4146 2.970639 CAGGGCGTCTTCTTCCGA 59.029 61.111 0.00 0.00 0.00 4.55
1403 4385 2.821366 CGCCTGATGACCACTGGC 60.821 66.667 0.00 0.00 44.81 4.85
1437 4419 7.390718 AGTGACATGGTAATAAAACCTCTGAAC 59.609 37.037 0.00 0.00 40.44 3.18
1492 4474 4.202192 TGAGCGAGATGTCAGCTTATTGAT 60.202 41.667 9.76 0.00 41.84 2.57
1530 4512 2.548920 GGAATTCCTAGTGGCAGGATCG 60.549 54.545 17.73 0.00 44.26 3.69
1558 4540 5.060816 GTGTGGTGTTTATTGAATCAATGCG 59.939 40.000 17.93 0.00 35.54 4.73
1623 5522 9.959749 GATCAGTAGAAACAACCAAACAAAATA 57.040 29.630 0.00 0.00 0.00 1.40
1624 5523 9.744468 ATCAGTAGAAACAACCAAACAAAATAC 57.256 29.630 0.00 0.00 0.00 1.89
1625 5524 8.962679 TCAGTAGAAACAACCAAACAAAATACT 58.037 29.630 0.00 0.00 0.00 2.12
1674 5574 5.314718 TCCATTCTCTGCCATTCATATGT 57.685 39.130 1.90 0.00 0.00 2.29
1730 5630 8.526978 TGATATAGATTAGCAAGCGAATCTCTT 58.473 33.333 26.25 19.21 43.70 2.85
1747 5647 9.689976 CGAATCTCTTATATCACTCAATCTGTT 57.310 33.333 0.00 0.00 0.00 3.16
1792 5692 7.617723 AGGCCAAGGAAAATAAATGTGTACATA 59.382 33.333 5.01 0.00 35.10 2.29
1808 6011 6.014070 TGTGTACATAGGCTTCTCTTGGTAAA 60.014 38.462 0.00 0.00 0.00 2.01
1811 6014 7.606456 TGTACATAGGCTTCTCTTGGTAAAAAG 59.394 37.037 0.00 0.00 0.00 2.27
1852 6056 1.216941 CGTTACCACTCGTTGCCGTT 61.217 55.000 0.00 0.00 35.01 4.44
1904 6111 2.854420 AATGGCCTCTCCTCTGCCCT 62.854 60.000 3.32 0.00 44.72 5.19
1935 6142 2.429930 CCCAGCCTCCGTTCAACA 59.570 61.111 0.00 0.00 0.00 3.33
2104 6317 2.168313 CCCCAATGGTTTAATCACTGGC 59.832 50.000 0.00 0.00 0.00 4.85
2111 6324 4.580868 TGGTTTAATCACTGGCGTTCATA 58.419 39.130 0.00 0.00 0.00 2.15
2160 6373 3.887621 TCTGGGTGTACTATGTCTTGC 57.112 47.619 0.00 0.00 0.00 4.01
2166 6379 4.891756 GGGTGTACTATGTCTTGCTACCTA 59.108 45.833 0.00 0.00 0.00 3.08
2167 6380 5.009811 GGGTGTACTATGTCTTGCTACCTAG 59.990 48.000 0.00 0.00 0.00 3.02
2171 6384 5.855740 ACTATGTCTTGCTACCTAGTTCC 57.144 43.478 0.00 0.00 29.71 3.62
2182 6395 0.100861 CCTAGTTCCGAAGAGCCGAC 59.899 60.000 0.00 0.00 0.00 4.79
2193 6406 3.650139 GAAGAGCCGACAGTCTAAAACA 58.350 45.455 0.00 0.00 0.00 2.83
2271 6485 3.349022 ACCAAAGTTTTTGGACGACTGA 58.651 40.909 23.36 0.00 42.06 3.41
2272 6486 3.759618 ACCAAAGTTTTTGGACGACTGAA 59.240 39.130 23.36 0.00 42.06 3.02
2316 6883 4.811557 GTGTGTACTTGTCAGCTTCTCTTT 59.188 41.667 0.00 0.00 0.00 2.52
2322 6889 3.777106 TGTCAGCTTCTCTTTCCATGT 57.223 42.857 0.00 0.00 0.00 3.21
2350 6917 7.832685 TGGAGTTGATGTGTAGTAGTGTATAGT 59.167 37.037 0.00 0.00 0.00 2.12
2352 6919 8.803397 AGTTGATGTGTAGTAGTGTATAGTGA 57.197 34.615 0.00 0.00 0.00 3.41
2391 6958 5.186409 AGCTTATGTTGTGCTGGATGAAAAT 59.814 36.000 0.00 0.00 35.54 1.82
2392 6959 5.290158 GCTTATGTTGTGCTGGATGAAAATG 59.710 40.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.529084 TGTTTATTATCCCAGGGATGACAT 57.471 37.500 29.46 19.65 43.06 3.06
92 102 7.801716 TTTTATCCCGAGGATATCAGTTTTG 57.198 36.000 11.86 0.00 43.26 2.44
180 191 8.243426 TGGTAGTTTTATAAAGTACGACGACAT 58.757 33.333 0.00 0.00 0.00 3.06
187 198 7.503549 AGGGGATGGTAGTTTTATAAAGTACG 58.496 38.462 9.72 0.00 0.00 3.67
188 199 9.993454 CTAGGGGATGGTAGTTTTATAAAGTAC 57.007 37.037 8.09 8.09 0.00 2.73
325 340 6.894654 TGGCATTTTAATTATTGAGAGGGTGA 59.105 34.615 0.00 0.00 0.00 4.02
417 432 7.814107 GGCATTTTATTTTTGAGACATGACAGA 59.186 33.333 0.00 0.00 0.00 3.41
418 433 7.599621 TGGCATTTTATTTTTGAGACATGACAG 59.400 33.333 0.00 0.00 0.00 3.51
461 476 9.180678 GGAGTTTTTATCAACAATATAATGCCG 57.819 33.333 0.00 0.00 0.00 5.69
484 500 7.864379 GGCATTTTTATCAACACTATGATGGAG 59.136 37.037 0.23 0.00 40.21 3.86
494 510 3.925913 ACGCATGGCATTTTTATCAACAC 59.074 39.130 0.00 0.00 0.00 3.32
503 519 8.652463 GTTTTATTACTAAACGCATGGCATTTT 58.348 29.630 0.00 0.00 0.00 1.82
508 524 6.468000 GTCAGTTTTATTACTAAACGCATGGC 59.532 38.462 0.00 0.00 39.77 4.40
515 531 9.855021 AATGGCATGTCAGTTTTATTACTAAAC 57.145 29.630 6.04 0.00 36.08 2.01
529 545 9.643693 ACTTCTTTATTTTTAATGGCATGTCAG 57.356 29.630 6.04 0.00 0.00 3.51
532 548 8.592809 TGGACTTCTTTATTTTTAATGGCATGT 58.407 29.630 0.00 0.00 0.00 3.21
633 652 8.621286 GCCATATAGTATATTTTTCAATCCCGG 58.379 37.037 0.00 0.00 0.00 5.73
668 687 3.572255 GGGCCTTTTGTGAATCTGTTGTA 59.428 43.478 0.84 0.00 0.00 2.41
692 711 2.740055 CGAGCACCACTGGCTGAC 60.740 66.667 0.00 0.00 42.78 3.51
723 744 5.966636 ACCTTTTTCAAAAATTCGTGAGC 57.033 34.783 0.00 0.00 0.00 4.26
744 3464 1.977594 CTGGCGGACGCATGGTTTAC 61.978 60.000 18.95 0.00 44.11 2.01
745 3465 1.743623 CTGGCGGACGCATGGTTTA 60.744 57.895 18.95 0.00 44.11 2.01
768 3488 1.540363 GGAGTGGTTCGCTGTTCAGAA 60.540 52.381 3.84 0.00 0.00 3.02
835 3817 2.601666 ACGCTCTCCCTGCTGTCA 60.602 61.111 0.00 0.00 0.00 3.58
987 3969 3.379452 AGGGAACATTCTGGAGGAGTAG 58.621 50.000 0.00 0.00 0.00 2.57
1164 4146 1.972223 CGTCTCCACCGTCCAGTCT 60.972 63.158 0.00 0.00 0.00 3.24
1403 4385 7.905604 TTTATTACCATGTCACTGACAAGAG 57.094 36.000 15.80 9.79 45.96 2.85
1437 4419 7.677309 TGCTAAAAATCATTGAATGCGAAATG 58.323 30.769 0.00 0.00 35.52 2.32
1492 4474 6.598753 GAATTCCGATTCCAATAGTTCGAA 57.401 37.500 0.00 0.00 36.47 3.71
1522 4504 2.887568 CCACACTCGCGATCCTGC 60.888 66.667 10.36 0.00 0.00 4.85
1530 4512 3.889196 TTCAATAAACACCACACTCGC 57.111 42.857 0.00 0.00 0.00 5.03
1595 4663 5.690865 TGTTTGGTTGTTTCTACTGATCCT 58.309 37.500 0.00 0.00 0.00 3.24
1645 5545 3.063510 TGGCAGAGAATGGAAGAACAG 57.936 47.619 0.00 0.00 0.00 3.16
1674 5574 9.823647 GAGAAGTTATTTTGGTAGATCATCAGA 57.176 33.333 0.00 0.00 0.00 3.27
1716 5616 5.923114 TGAGTGATATAAGAGATTCGCTTGC 59.077 40.000 12.29 1.40 0.00 4.01
1792 5692 3.832527 TGCTTTTTACCAAGAGAAGCCT 58.167 40.909 4.20 0.00 41.40 4.58
1808 6011 4.020039 TGATGAAATCTGGCCATTTGCTTT 60.020 37.500 5.51 0.00 45.81 3.51
1811 6014 3.530265 TGATGAAATCTGGCCATTTGC 57.470 42.857 5.51 2.27 45.81 3.68
1852 6056 3.068165 CGACTGGTACATCTGCAGGATAA 59.932 47.826 15.13 0.00 38.20 1.75
1935 6142 1.283613 TGTTGGTGACAGTTGGAGGTT 59.716 47.619 0.00 0.00 44.54 3.50
2111 6324 1.459450 AACCACAGTTCAACGCTGTT 58.541 45.000 0.00 0.00 43.87 3.16
2160 6373 1.334243 CGGCTCTTCGGAACTAGGTAG 59.666 57.143 0.00 0.00 0.00 3.18
2166 6379 1.179814 ACTGTCGGCTCTTCGGAACT 61.180 55.000 0.00 0.00 0.00 3.01
2167 6380 0.733223 GACTGTCGGCTCTTCGGAAC 60.733 60.000 0.00 0.00 0.00 3.62
2171 6384 2.631418 TTTAGACTGTCGGCTCTTCG 57.369 50.000 1.52 0.00 0.00 3.79
2193 6406 9.343539 GTCATAGTGGGCTCTAAAGAATATTTT 57.656 33.333 0.00 0.00 0.00 1.82
2271 6485 1.600916 GTCTTGGGCGGTTCAGCTT 60.601 57.895 0.00 0.00 37.29 3.74
2272 6486 2.032681 GTCTTGGGCGGTTCAGCT 59.967 61.111 0.00 0.00 37.29 4.24
2322 6889 8.762481 ATACACTACTACACATCAACTCCATA 57.238 34.615 0.00 0.00 0.00 2.74
2326 6893 8.890718 TCACTATACACTACTACACATCAACTC 58.109 37.037 0.00 0.00 0.00 3.01
2332 6899 8.007405 TGCAATCACTATACACTACTACACAT 57.993 34.615 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.