Multiple sequence alignment - TraesCS6D01G218800

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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 TraesCS6D01G218800 chr6D 100.000 2798 0 0 1 2798 308902270 308899473 0.000000e+00 5168
1 TraesCS6D01G218800 chr6B 90.795 2879 117 59 1 2797 476127537 476124725 0.000000e+00 3712
2 TraesCS6D01G218800 chr6A 91.829 1689 65 34 816 2450 445561950 445563619 0.000000e+00 2287
3 TraesCS6D01G218800 chr6A 85.235 447 25 23 370 784 445559908 445560345 3.330000e-114 422
4 TraesCS6D01G218800 chr6A 86.757 370 11 4 2438 2798 445569980 445570320 7.320000e-101 377
5 TraesCS6D01G218800 chr6A 86.607 336 12 15 1 323 445558567 445558882 9.600000e-90 340


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 TraesCS6D01G218800 chr6D 308899473 308902270 2797 True 5168.000000 5168 100.000000 1 2798 1 chr6D.!!$R1 2797
1 TraesCS6D01G218800 chr6B 476124725 476127537 2812 True 3712.000000 3712 90.795000 1 2797 1 chr6B.!!$R1 2796
2 TraesCS6D01G218800 chr6A 445558567 445563619 5052 False 1016.333333 2287 87.890333 1 2450 3 chr6A.!!$F2 2449

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
613 1636 0.447801 CCAACCGAATCAGCCTTTCG 59.552 55.0 6.36 6.36 44.17 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 4547 0.249031 AAACCAGCTCGCTTTGTTGC 60.249 50.0 4.83 0.0 0.0 4.17 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
23 24 2.413765 GCACAGCTCATTGCAACTACAG 60.414 50.000 0.00 0.00 45.94 2.74
26 30 3.069289 CAGCTCATTGCAACTACAGACA 58.931 45.455 0.00 0.00 45.94 3.41
58 62 4.552365 ATGGCATCGACCGGCAGG 62.552 66.667 16.49 0.00 42.76 4.85
210 218 4.142381 GCTCCCGTTTTAATCAAGAGCATT 60.142 41.667 4.33 0.00 43.62 3.56
360 1374 1.589196 GCACGCATACGAGTCCTCC 60.589 63.158 0.00 0.00 43.93 4.30
370 1384 0.687757 CGAGTCCTCCATTCCCAGGA 60.688 60.000 0.00 0.00 36.38 3.86
419 1439 2.736721 CGTTTGATGTACCACTCCACAG 59.263 50.000 0.00 0.00 0.00 3.66
476 1498 3.057174 AGTCTACTGAGAAGACGCCAAAG 60.057 47.826 0.00 0.00 46.46 2.77
578 1601 2.289444 CGAAGGGTCCAAAGCTACTCAA 60.289 50.000 0.00 0.00 0.00 3.02
579 1602 3.339141 GAAGGGTCCAAAGCTACTCAAG 58.661 50.000 0.00 0.00 0.00 3.02
580 1603 2.621070 AGGGTCCAAAGCTACTCAAGA 58.379 47.619 0.00 0.00 0.00 3.02
613 1636 0.447801 CCAACCGAATCAGCCTTTCG 59.552 55.000 6.36 6.36 44.17 3.46
621 1644 2.642139 ATCAGCCTTTCGCAAACATG 57.358 45.000 0.00 0.00 41.38 3.21
668 1717 7.876936 TTTGCCCGGTTTATGTACAATTATA 57.123 32.000 0.00 0.00 0.00 0.98
669 1718 6.864360 TGCCCGGTTTATGTACAATTATAC 57.136 37.500 0.00 0.00 0.00 1.47
671 1720 6.707161 TGCCCGGTTTATGTACAATTATACTC 59.293 38.462 0.00 0.00 0.00 2.59
674 1723 7.935210 CCCGGTTTATGTACAATTATACTCCTT 59.065 37.037 0.00 0.00 0.00 3.36
693 1744 6.601613 ACTCCTTTTTGGCGATGATTTATACA 59.398 34.615 0.00 0.00 35.26 2.29
812 3411 7.220683 CGATGCAAGGTGTTGGAATTTATTTAG 59.779 37.037 0.00 0.00 37.57 1.85
813 3412 7.296628 TGCAAGGTGTTGGAATTTATTTAGT 57.703 32.000 0.00 0.00 33.87 2.24
814 3413 8.410673 TGCAAGGTGTTGGAATTTATTTAGTA 57.589 30.769 0.00 0.00 33.87 1.82
815 3414 9.030452 TGCAAGGTGTTGGAATTTATTTAGTAT 57.970 29.630 0.00 0.00 33.87 2.12
1006 3628 3.136443 ACAACTCCTCAAATCTCACCACA 59.864 43.478 0.00 0.00 0.00 4.17
1378 4001 2.393768 CCGCTGCACAACTAGCCTG 61.394 63.158 0.00 0.00 36.60 4.85
1379 4002 1.669115 CGCTGCACAACTAGCCTGT 60.669 57.895 0.00 0.00 36.60 4.00
1380 4003 0.389817 CGCTGCACAACTAGCCTGTA 60.390 55.000 0.00 0.00 36.60 2.74
1381 4004 1.079503 GCTGCACAACTAGCCTGTAC 58.920 55.000 0.00 0.00 33.89 2.90
1382 4005 1.338200 GCTGCACAACTAGCCTGTACT 60.338 52.381 0.00 0.00 33.89 2.73
1392 4015 1.222113 GCCTGTACTGGCCTTCTCC 59.778 63.158 28.40 3.83 46.82 3.71
1477 4104 2.347490 CAGTACCACTGCGCCCTT 59.653 61.111 4.18 0.00 39.62 3.95
1514 4143 0.110486 TTCTCCTTGTCCTTGTGCCC 59.890 55.000 0.00 0.00 0.00 5.36
1619 4265 1.741770 AAGGCCACGCGAGATTGTC 60.742 57.895 15.93 0.00 0.00 3.18
1739 4391 2.814183 TTCCCGCGCTCTTCTTCGAC 62.814 60.000 5.56 0.00 0.00 4.20
1767 4419 3.965379 TGCTCGGTGTTTATTACTCCA 57.035 42.857 0.00 0.00 39.83 3.86
1776 4428 4.508124 GTGTTTATTACTCCATCTGCCTCG 59.492 45.833 0.00 0.00 0.00 4.63
1788 4440 5.540337 TCCATCTGCCTCGAAATATAAGACT 59.460 40.000 0.00 0.00 0.00 3.24
1875 4530 5.548406 TCTTAGGGTAGCAAAGTGTTCTTC 58.452 41.667 0.00 0.00 32.90 2.87
1884 4539 4.814234 AGCAAAGTGTTCTTCGTAACATGA 59.186 37.500 0.00 0.00 41.18 3.07
1888 4543 7.570507 GCAAAGTGTTCTTCGTAACATGATGTA 60.571 37.037 0.00 0.00 41.18 2.29
1892 4547 7.489435 AGTGTTCTTCGTAACATGATGTATGAG 59.511 37.037 0.00 0.00 41.18 2.90
1893 4548 6.255670 TGTTCTTCGTAACATGATGTATGAGC 59.744 38.462 0.00 0.00 39.21 4.26
1894 4549 5.901552 TCTTCGTAACATGATGTATGAGCA 58.098 37.500 0.00 0.00 39.21 4.26
1896 4551 5.966636 TCGTAACATGATGTATGAGCAAC 57.033 39.130 0.00 0.00 39.21 4.17
1897 4552 5.415221 TCGTAACATGATGTATGAGCAACA 58.585 37.500 0.00 0.00 39.21 3.33
2036 4709 1.002868 GGTCCAGTGCTCTGCATGT 60.003 57.895 10.32 0.00 41.91 3.21
2083 4756 2.760092 CCTCAGAGAGAAGAAGGTGAGG 59.240 54.545 0.00 1.94 43.78 3.86
2134 4807 1.070038 GACGAATTTACCGTGGCGAA 58.930 50.000 0.00 0.00 40.67 4.70
2136 4809 0.095762 CGAATTTACCGTGGCGAACC 59.904 55.000 0.00 0.00 0.00 3.62
2241 4914 0.764890 TGTTTGAGGACCACAGGGAG 59.235 55.000 0.00 0.00 38.05 4.30
2340 5017 2.543012 GCGATCAGTCAATGTGAGGATG 59.457 50.000 0.00 0.00 0.00 3.51
2358 5042 7.327032 GTGAGGATGAGCAATAAAAAGTCAAAC 59.673 37.037 0.00 0.00 0.00 2.93
2513 5197 8.560355 TTGCAGATAGCTACAGTTTAAATTCA 57.440 30.769 0.00 0.00 45.94 2.57
2514 5198 7.974675 TGCAGATAGCTACAGTTTAAATTCAC 58.025 34.615 0.00 0.00 45.94 3.18
2515 5199 7.119997 GCAGATAGCTACAGTTTAAATTCACG 58.880 38.462 0.00 0.00 41.15 4.35
2516 5200 7.010183 GCAGATAGCTACAGTTTAAATTCACGA 59.990 37.037 0.00 0.00 41.15 4.35
2517 5201 8.535592 CAGATAGCTACAGTTTAAATTCACGAG 58.464 37.037 0.00 0.00 0.00 4.18
2518 5202 8.251721 AGATAGCTACAGTTTAAATTCACGAGT 58.748 33.333 0.00 0.00 0.00 4.18
2519 5203 9.512435 GATAGCTACAGTTTAAATTCACGAGTA 57.488 33.333 0.00 0.00 0.00 2.59
2520 5204 7.813852 AGCTACAGTTTAAATTCACGAGTAG 57.186 36.000 0.00 0.00 33.31 2.57
2521 5205 7.376615 AGCTACAGTTTAAATTCACGAGTAGT 58.623 34.615 0.00 0.00 33.01 2.73
2522 5206 8.517878 AGCTACAGTTTAAATTCACGAGTAGTA 58.482 33.333 0.00 0.00 33.01 1.82
2523 5207 8.582096 GCTACAGTTTAAATTCACGAGTAGTAC 58.418 37.037 0.00 0.00 33.01 2.73
2524 5208 9.837525 CTACAGTTTAAATTCACGAGTAGTACT 57.162 33.333 1.37 1.37 0.00 2.73
2526 5210 9.837525 ACAGTTTAAATTCACGAGTAGTACTAG 57.162 33.333 1.87 5.79 0.00 2.57
2527 5211 9.837525 CAGTTTAAATTCACGAGTAGTACTAGT 57.162 33.333 10.09 10.09 34.33 2.57
2553 5237 6.318144 ACTTCTAACATGATTGATGAAGCCAG 59.682 38.462 0.00 0.00 35.80 4.85
2557 5241 4.597004 ACATGATTGATGAAGCCAGACTT 58.403 39.130 0.00 0.00 42.98 3.01
2596 5281 7.693969 AGGAACAGATAAAATCCAAAGTGAG 57.306 36.000 0.00 0.00 34.30 3.51
2639 5324 8.076178 AGGAAAAATTGACTGAGTTTCGTATTG 58.924 33.333 0.00 0.00 0.00 1.90
2665 5350 3.284617 TGCATGAGATGGTGATTCAAGG 58.715 45.455 0.00 0.00 0.00 3.61
2696 5381 2.688507 TGACGAGCATCCTTGTTCTTC 58.311 47.619 0.00 0.00 35.80 2.87
2709 5394 2.964740 TGTTCTTCCGAATCTGCTCAG 58.035 47.619 0.00 0.00 0.00 3.35
2797 5482 0.746659 AAGTGTTGCTCAAGGCCAAC 59.253 50.000 5.01 0.00 40.92 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.610741 TGCCATTTAAATTTGGTTTGTGTC 57.389 33.333 9.13 0.00 35.34 3.67
26 30 6.147000 GTCGATGCCATTTAAATTTGGTTTGT 59.853 34.615 9.13 0.00 35.34 2.83
58 62 2.094597 TGCTGCTGTCCAATTTATGTGC 60.095 45.455 0.00 0.00 0.00 4.57
210 218 3.849911 CGAGTGATTAAGCTGGAGTTCA 58.150 45.455 0.00 0.00 0.00 3.18
302 320 5.127491 AGATTTACTCTGCGAGCTACTACT 58.873 41.667 5.63 0.00 32.04 2.57
303 321 5.427036 AGATTTACTCTGCGAGCTACTAC 57.573 43.478 5.63 0.00 32.04 2.73
304 322 5.589050 TGAAGATTTACTCTGCGAGCTACTA 59.411 40.000 5.63 0.00 31.16 1.82
360 1374 1.453379 CCTGCTGCTCCTGGGAATG 60.453 63.158 0.00 0.00 0.00 2.67
370 1384 2.502947 TGATATTGTCTCACCTGCTGCT 59.497 45.455 0.00 0.00 0.00 4.24
371 1385 2.611292 GTGATATTGTCTCACCTGCTGC 59.389 50.000 0.00 0.00 37.61 5.25
419 1439 3.114065 GGAGTATACTGTAAGCGCACAC 58.886 50.000 10.90 7.39 37.60 3.82
453 1475 2.085320 TGGCGTCTTCTCAGTAGACTC 58.915 52.381 9.54 1.64 39.86 3.36
476 1498 3.490759 CGCGCACTGGATGTCCAC 61.491 66.667 8.75 0.00 42.01 4.02
578 1601 1.280421 GTTGGATGGGCTGAGACTTCT 59.720 52.381 0.00 0.00 0.00 2.85
579 1602 1.680249 GGTTGGATGGGCTGAGACTTC 60.680 57.143 0.00 0.00 0.00 3.01
580 1603 0.329596 GGTTGGATGGGCTGAGACTT 59.670 55.000 0.00 0.00 0.00 3.01
642 1691 3.919223 TGTACATAAACCGGGCAAAAC 57.081 42.857 6.32 0.00 0.00 2.43
668 1717 6.601613 TGTATAAATCATCGCCAAAAAGGAGT 59.398 34.615 0.00 0.00 41.22 3.85
669 1718 7.026631 TGTATAAATCATCGCCAAAAAGGAG 57.973 36.000 0.00 0.00 41.22 3.69
671 1720 8.647143 AATTGTATAAATCATCGCCAAAAAGG 57.353 30.769 0.00 0.00 41.84 3.11
693 1744 9.661954 TTACTGAATCTCCCTCTCAGTATAATT 57.338 33.333 10.93 0.00 46.63 1.40
812 3411 3.181537 ACGAAGCAAACGCGTTCTTATAC 60.182 43.478 26.77 13.80 34.12 1.47
813 3412 2.988493 ACGAAGCAAACGCGTTCTTATA 59.012 40.909 26.77 0.00 34.12 0.98
814 3413 1.796459 ACGAAGCAAACGCGTTCTTAT 59.204 42.857 26.77 12.38 34.12 1.73
815 3414 1.210870 ACGAAGCAAACGCGTTCTTA 58.789 45.000 26.77 0.00 34.12 2.10
816 3415 0.375803 AACGAAGCAAACGCGTTCTT 59.624 45.000 26.77 23.77 43.87 2.52
1006 3628 0.396556 GGTGGTGGTTTGGTTGTCCT 60.397 55.000 0.00 0.00 34.23 3.85
1105 3728 1.028868 GTGTCTGGCAATGGAGGAGC 61.029 60.000 0.00 0.00 0.00 4.70
1378 4001 0.827368 CCTGAGGAGAAGGCCAGTAC 59.173 60.000 5.01 0.00 0.00 2.73
1379 4002 3.306902 CCTGAGGAGAAGGCCAGTA 57.693 57.895 5.01 0.00 0.00 2.74
1380 4003 4.143740 CCTGAGGAGAAGGCCAGT 57.856 61.111 5.01 0.00 0.00 4.00
1477 4104 9.762933 CAAGGAGAAAATGATAAACAAAAAGGA 57.237 29.630 0.00 0.00 0.00 3.36
1514 4143 1.858798 GCATTGCTATGCGTGCTCTTG 60.859 52.381 17.11 0.00 46.89 3.02
1581 4227 4.202264 CCTTGATCGATTTGCCCTACTACT 60.202 45.833 0.00 0.00 0.00 2.57
1582 4228 4.058817 CCTTGATCGATTTGCCCTACTAC 58.941 47.826 0.00 0.00 0.00 2.73
1583 4229 3.494398 GCCTTGATCGATTTGCCCTACTA 60.494 47.826 0.00 0.00 0.00 1.82
1619 4265 4.662468 AGATCACATGGCACTAGTACAG 57.338 45.455 0.00 0.00 0.00 2.74
1739 4391 4.701956 ATAAACACCGAGCAAATTCCTG 57.298 40.909 0.00 0.00 0.00 3.86
1767 4419 8.738645 AAAAAGTCTTATATTTCGAGGCAGAT 57.261 30.769 0.00 0.00 0.00 2.90
1875 4530 5.717038 TGTTGCTCATACATCATGTTACG 57.283 39.130 0.00 0.00 35.96 3.18
1884 4539 2.096496 GCTCGCTTTGTTGCTCATACAT 59.904 45.455 0.00 0.00 0.00 2.29
1888 4543 0.520404 CAGCTCGCTTTGTTGCTCAT 59.480 50.000 0.00 0.00 33.03 2.90
1892 4547 0.249031 AAACCAGCTCGCTTTGTTGC 60.249 50.000 4.83 0.00 0.00 4.17
1893 4548 2.548057 TCTAAACCAGCTCGCTTTGTTG 59.452 45.455 4.83 0.00 0.00 3.33
1894 4549 2.846193 TCTAAACCAGCTCGCTTTGTT 58.154 42.857 0.00 0.00 0.00 2.83
1896 4551 3.067106 TCTTCTAAACCAGCTCGCTTTG 58.933 45.455 0.00 0.00 0.00 2.77
1897 4552 3.402628 TCTTCTAAACCAGCTCGCTTT 57.597 42.857 0.00 0.00 0.00 3.51
2028 4701 3.751175 GCAAAAGGTGTAGTACATGCAGA 59.249 43.478 17.08 0.00 0.00 4.26
2036 4709 4.079980 TGAAGCTGCAAAAGGTGTAGTA 57.920 40.909 1.02 0.00 41.70 1.82
2083 4756 3.802866 CAAGATAAACTGAGAGGCCCTC 58.197 50.000 1.26 1.26 42.30 4.30
2134 4807 2.542907 CGTTTGCGTTGGCTCTGGT 61.543 57.895 0.00 0.00 40.82 4.00
2260 4933 3.633986 ACTTTGCAAGAAAAGGGACTGAG 59.366 43.478 0.00 0.00 40.86 3.35
2321 4998 3.808726 GCTCATCCTCACATTGACTGATC 59.191 47.826 0.00 0.00 0.00 2.92
2322 4999 3.199289 TGCTCATCCTCACATTGACTGAT 59.801 43.478 0.00 0.00 0.00 2.90
2323 5000 2.568509 TGCTCATCCTCACATTGACTGA 59.431 45.455 0.00 0.00 0.00 3.41
2340 5017 5.212194 TCTGCGTTTGACTTTTTATTGCTC 58.788 37.500 0.00 0.00 0.00 4.26
2358 5042 4.111375 ACTACACCTATTTGACTCTGCG 57.889 45.455 0.00 0.00 0.00 5.18
2497 5181 7.578169 ACTACTCGTGAATTTAAACTGTAGC 57.422 36.000 0.00 0.00 30.76 3.58
2513 5197 9.311916 CATGTTAGAAGTACTAGTACTACTCGT 57.688 37.037 30.89 17.91 44.96 4.18
2514 5198 9.526713 TCATGTTAGAAGTACTAGTACTACTCG 57.473 37.037 30.89 19.79 44.96 4.18
2524 5208 9.534565 GCTTCATCAATCATGTTAGAAGTACTA 57.465 33.333 0.00 0.00 34.92 1.82
2525 5209 7.497249 GGCTTCATCAATCATGTTAGAAGTACT 59.503 37.037 0.00 0.00 34.92 2.73
2526 5210 7.280876 TGGCTTCATCAATCATGTTAGAAGTAC 59.719 37.037 0.00 0.00 34.92 2.73
2527 5211 7.337938 TGGCTTCATCAATCATGTTAGAAGTA 58.662 34.615 0.00 0.00 34.92 2.24
2553 5237 6.038271 TGTTCCTTTTGAGCTGAAAGTAAGTC 59.962 38.462 14.68 1.97 35.30 3.01
2557 5241 5.680619 TCTGTTCCTTTTGAGCTGAAAGTA 58.319 37.500 14.68 0.91 35.30 2.24
2612 5297 6.451064 ACGAAACTCAGTCAATTTTTCCTT 57.549 33.333 0.00 0.00 0.00 3.36
2639 5324 6.381481 TGAATCACCATCTCATGCAAATAC 57.619 37.500 0.00 0.00 0.00 1.89
2696 5381 0.529337 ATCGCACTGAGCAGATTCGG 60.529 55.000 4.21 0.00 46.13 4.30
2709 5394 0.387239 GTGGCTGGAAACAATCGCAC 60.387 55.000 0.00 0.00 42.06 5.34
2758 5443 6.886459 ACACTTTTATTCTGTATGCAGGATGT 59.114 34.615 14.42 1.66 40.96 3.06
2759 5444 7.325660 ACACTTTTATTCTGTATGCAGGATG 57.674 36.000 14.42 1.04 40.96 3.51


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

AutoCloner maintained by Alex Coulton.