Multiple sequence alignment - TraesCS6D01G074500

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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 TraesCS6D01G074500 chr6D 100.000 2309 0 0 1 2309 38118905 38121213 0.000000e+00 4265.0
1 TraesCS6D01G074500 chr6D 89.491 923 61 18 820 1727 37933935 37934836 0.000000e+00 1134.0
2 TraesCS6D01G074500 chr6D 86.702 940 75 28 812 1727 37927680 37928593 0.000000e+00 998.0
3 TraesCS6D01G074500 chr6D 87.631 857 44 23 9 816 37933056 37933899 0.000000e+00 939.0
4 TraesCS6D01G074500 chr6D 85.987 157 5 4 676 816 37927496 37927651 3.970000e-33 152.0
5 TraesCS6D01G074500 chr6B 89.883 1028 60 20 678 1676 88735818 88736830 0.000000e+00 1282.0
6 TraesCS6D01G074500 chr6B 85.482 737 67 18 669 1385 88781045 88781761 0.000000e+00 732.0
7 TraesCS6D01G074500 chr6B 81.494 616 66 27 9 589 88778759 88779361 1.620000e-126 462.0
8 TraesCS6D01G074500 chr6B 89.489 352 23 7 1381 1727 88816852 88817194 1.270000e-117 433.0
9 TraesCS6D01G074500 chr6B 79.109 651 60 35 9 597 88735187 88735823 1.670000e-101 379.0
10 TraesCS6D01G074500 chr6B 81.651 436 32 28 335 734 88716820 88717243 3.700000e-83 318.0
11 TraesCS6D01G074500 chr6B 94.118 170 10 0 1920 2089 88818852 88819021 2.280000e-65 259.0
12 TraesCS6D01G074500 chr6B 91.176 170 13 2 1757 1925 88818620 88818788 1.780000e-56 230.0
13 TraesCS6D01G074500 chr6B 89.071 183 16 2 2128 2309 88819185 88819364 8.300000e-55 224.0
14 TraesCS6D01G074500 chr6A 89.064 1015 66 20 730 1727 49196576 49197562 0.000000e+00 1218.0
15 TraesCS6D01G074500 chr6A 88.077 931 70 14 812 1727 49550738 49551642 0.000000e+00 1066.0
16 TraesCS6D01G074500 chr6A 82.442 1327 122 43 448 1727 49483312 49484574 0.000000e+00 1057.0
17 TraesCS6D01G074500 chr6A 85.328 1036 75 32 735 1727 49499536 49500537 0.000000e+00 1000.0
18 TraesCS6D01G074500 chr6A 89.216 612 45 10 861 1465 49201970 49202567 0.000000e+00 745.0
19 TraesCS6D01G074500 chr6A 79.456 662 73 39 9 638 49195856 49196486 5.940000e-111 411.0
20 TraesCS6D01G074500 chr6A 83.014 418 35 25 108 503 49550042 49550445 1.700000e-91 346.0
21 TraesCS6D01G074500 chr6A 92.444 225 16 1 2086 2309 49553605 49553829 1.030000e-83 320.0
22 TraesCS6D01G074500 chr6A 96.629 178 5 1 9 185 49483053 49483230 6.240000e-76 294.0
23 TraesCS6D01G074500 chr6A 97.059 170 4 1 1920 2089 49553279 49553447 3.750000e-73 285.0
24 TraesCS6D01G074500 chr6A 94.915 177 8 1 10 185 49498112 49498288 2.260000e-70 276.0
25 TraesCS6D01G074500 chr6A 95.322 171 5 3 1757 1925 49553058 49553227 3.780000e-68 268.0
26 TraesCS6D01G074500 chr6A 92.593 135 10 0 2175 2309 49555519 49555653 6.510000e-46 195.0
27 TraesCS6D01G074500 chr6A 90.805 87 7 1 730 816 49550624 49550709 5.210000e-22 115.0
28 TraesCS6D01G074500 chr5B 83.042 572 58 24 812 1381 511835353 511835887 1.240000e-132 483.0
29 TraesCS6D01G074500 chr7D 82.462 593 60 21 730 1299 587150411 587149840 1.600000e-131 479.0
30 TraesCS6D01G074500 chr7D 93.103 58 3 1 2232 2288 410057938 410057995 1.470000e-12 84.2
31 TraesCS6D01G074500 chr7D 95.652 46 1 1 2238 2282 444363153 444363108 3.180000e-09 73.1
32 TraesCS6D01G074500 chr7D 97.619 42 1 0 2238 2279 444363155 444363196 3.180000e-09 73.1
33 TraesCS6D01G074500 chr7D 90.385 52 4 1 2232 2282 410057950 410057899 1.480000e-07 67.6
34 TraesCS6D01G074500 chr4D 92.453 53 2 2 2232 2282 213422054 213422106 8.850000e-10 75.0
35 TraesCS6D01G074500 chr7A 92.157 51 4 0 2241 2291 472124387 472124337 3.180000e-09 73.1


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 TraesCS6D01G074500 chr6D 38118905 38121213 2308 False 4265.000000 4265 100.000000 1 2309 1 chr6D.!!$F1 2308
1 TraesCS6D01G074500 chr6D 37933056 37934836 1780 False 1036.500000 1134 88.561000 9 1727 2 chr6D.!!$F3 1718
2 TraesCS6D01G074500 chr6D 37927496 37928593 1097 False 575.000000 998 86.344500 676 1727 2 chr6D.!!$F2 1051
3 TraesCS6D01G074500 chr6B 88735187 88736830 1643 False 830.500000 1282 84.496000 9 1676 2 chr6B.!!$F2 1667
4 TraesCS6D01G074500 chr6B 88778759 88781761 3002 False 597.000000 732 83.488000 9 1385 2 chr6B.!!$F3 1376
5 TraesCS6D01G074500 chr6B 88816852 88819364 2512 False 286.500000 433 90.963500 1381 2309 4 chr6B.!!$F4 928
6 TraesCS6D01G074500 chr6A 49195856 49197562 1706 False 814.500000 1218 84.260000 9 1727 2 chr6A.!!$F2 1718
7 TraesCS6D01G074500 chr6A 49201970 49202567 597 False 745.000000 745 89.216000 861 1465 1 chr6A.!!$F1 604
8 TraesCS6D01G074500 chr6A 49483053 49484574 1521 False 675.500000 1057 89.535500 9 1727 2 chr6A.!!$F3 1718
9 TraesCS6D01G074500 chr6A 49498112 49500537 2425 False 638.000000 1000 90.121500 10 1727 2 chr6A.!!$F4 1717
10 TraesCS6D01G074500 chr6A 49550042 49555653 5611 False 370.714286 1066 91.330571 108 2309 7 chr6A.!!$F5 2201
11 TraesCS6D01G074500 chr5B 511835353 511835887 534 False 483.000000 483 83.042000 812 1381 1 chr5B.!!$F1 569
12 TraesCS6D01G074500 chr7D 587149840 587150411 571 True 479.000000 479 82.462000 730 1299 1 chr7D.!!$R3 569

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
578 766 1.003972 CGCAAGAAACAGCAACGAAGA 60.004 47.619 0.0 0.0 43.02 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 6106 1.209504 TCAGGCCATTGTAGTGTAGGC 59.79 52.381 5.01 0.0 44.48 3.93 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
196 221 9.986833 TCACAAATATCAATGTATTTTGTCGAG 57.013 29.630 0.00 0.5 33.24 4.04
218 245 9.878599 TCGAGAAAATAATTCTTGTTGAACTTC 57.121 29.630 0.00 0.0 37.52 3.01
348 479 4.619973 TGAACATTTGCATGGTGAACTTC 58.380 39.130 0.00 0.0 34.27 3.01
409 566 2.806818 TGTGCGGCGAACTTTTTATGTA 59.193 40.909 20.38 0.0 0.00 2.29
410 567 3.437395 TGTGCGGCGAACTTTTTATGTAT 59.563 39.130 20.38 0.0 0.00 2.29
445 603 8.642908 AGAGAACAAAAATAAAAAGGGAAACG 57.357 30.769 0.00 0.0 0.00 3.60
578 766 1.003972 CGCAAGAAACAGCAACGAAGA 60.004 47.619 0.00 0.0 43.02 2.87
646 2458 2.807895 CCCGTGTGAACGTAGCCG 60.808 66.667 0.00 0.0 40.83 5.52
657 2469 1.489824 CGTAGCCGTTCACAAACCG 59.510 57.895 0.00 0.0 31.27 4.44
659 2471 1.219646 GTAGCCGTTCACAAACCGAA 58.780 50.000 0.00 0.0 31.27 4.30
660 2472 1.193874 GTAGCCGTTCACAAACCGAAG 59.806 52.381 0.00 0.0 31.27 3.79
769 3511 1.131315 GTTTTCAAGATCCGCTGGCTC 59.869 52.381 0.00 0.0 0.00 4.70
994 3807 1.447945 GCAGGCAGTTCTTCTCTTCC 58.552 55.000 0.00 0.0 0.00 3.46
1151 3970 1.676014 GGACATCACCAACCTCTTCGG 60.676 57.143 0.00 0.0 39.35 4.30
1336 4188 7.310664 ACTACCGATTGTACATGGATTATACG 58.689 38.462 14.26 3.3 0.00 3.06
1399 4251 9.659135 TTGGTTGGATTGATTATAGGAAATGAT 57.341 29.630 0.00 0.0 0.00 2.45
1587 4486 5.596836 TTGCCCATATTTTTCTCATGTCC 57.403 39.130 0.00 0.0 0.00 4.02
1643 4544 4.695928 AGCGTTTTTCTCCTAGATTTGTCC 59.304 41.667 0.00 0.0 0.00 4.02
1769 6093 9.529823 TGATGTATCTAATAGGAACGGTAGATT 57.470 33.333 0.00 0.0 0.00 2.40
1782 6106 3.118738 ACGGTAGATTTACCTGGCTTCTG 60.119 47.826 10.51 0.0 46.05 3.02
1804 6128 2.555199 CTACACTACAATGGCCTGAGC 58.445 52.381 3.32 0.0 38.76 4.26
1806 6130 0.391661 CACTACAATGGCCTGAGCGT 60.392 55.000 3.32 0.0 41.24 5.07
1809 6133 1.812571 CTACAATGGCCTGAGCGTTTT 59.187 47.619 3.32 0.0 41.24 2.43
1842 6166 0.693092 CGGACCCCAGGGAATTCCTA 60.693 60.000 23.63 0.0 46.12 2.94
1893 6218 2.949644 GTCCTGTACCAGCACTGTTTTT 59.050 45.455 0.00 0.0 0.00 1.94
1996 6391 0.031994 ATTGTCACGCAAAAGGGCAC 59.968 50.000 0.00 0.0 40.91 5.01
2001 6396 0.385390 CACGCAAAAGGGCACTCTTT 59.615 50.000 0.00 0.0 38.48 2.52
2062 6457 3.577415 GAGTACCCATACTATGTGTCCCC 59.423 52.174 0.00 0.0 41.98 4.81
2089 6484 4.499696 GCTTGGCAAACTTCATACACTTGT 60.500 41.667 0.00 0.0 0.00 3.16
2091 6486 6.701145 TTGGCAAACTTCATACACTTGTAA 57.299 33.333 0.00 0.0 33.76 2.41
2092 6487 6.892658 TGGCAAACTTCATACACTTGTAAT 57.107 33.333 0.00 0.0 33.76 1.89
2113 6672 9.494271 TGTAATTGCCTAAAATGCACAAATTTA 57.506 25.926 0.00 0.0 38.72 1.40
2133 6692 9.546428 AAATTTATGACATATCGTGTGATCAGA 57.454 29.630 0.00 0.0 42.36 3.27
2134 6693 9.546428 AATTTATGACATATCGTGTGATCAGAA 57.454 29.630 0.00 0.0 42.36 3.02
2161 6720 2.240160 TGTAGTTGGGTGGTTCTGTGTT 59.760 45.455 0.00 0.0 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.357637 CCACCACCTGTGTTTGTGTTAG 59.642 50.000 0.00 0.00 43.85 2.34
1 2 2.026169 TCCACCACCTGTGTTTGTGTTA 60.026 45.455 0.00 0.00 43.85 2.41
2 3 1.181786 CCACCACCTGTGTTTGTGTT 58.818 50.000 0.00 0.00 43.85 3.32
3 4 0.329931 TCCACCACCTGTGTTTGTGT 59.670 50.000 0.00 0.00 43.85 3.72
5 6 0.751643 GCTCCACCACCTGTGTTTGT 60.752 55.000 0.00 0.00 43.85 2.83
6 7 0.466189 AGCTCCACCACCTGTGTTTG 60.466 55.000 0.00 0.00 43.85 2.93
7 8 1.136828 TAGCTCCACCACCTGTGTTT 58.863 50.000 0.00 0.00 43.85 2.83
348 479 8.830580 AGAAAATGTTCACCGTATATCATGAAG 58.169 33.333 0.00 0.00 36.09 3.02
387 544 2.227865 ACATAAAAAGTTCGCCGCACAT 59.772 40.909 0.00 0.00 0.00 3.21
422 580 9.438228 TTTCGTTTCCCTTTTTATTTTTGTTCT 57.562 25.926 0.00 0.00 0.00 3.01
506 686 3.886505 TGCTTTCGGTTTTTCAGTGGTAT 59.113 39.130 0.00 0.00 0.00 2.73
507 687 3.280295 TGCTTTCGGTTTTTCAGTGGTA 58.720 40.909 0.00 0.00 0.00 3.25
578 766 0.999406 CGATTCGCGTGATGTTCCTT 59.001 50.000 5.77 0.00 34.64 3.36
616 2428 1.819632 CACGGGCCAATCCTACAGC 60.820 63.158 4.39 0.00 34.39 4.40
666 2478 7.018650 AGGGGAGGGAGATTCGAATTTATTTAT 59.981 37.037 12.81 0.00 0.00 1.40
667 2479 6.331837 AGGGGAGGGAGATTCGAATTTATTTA 59.668 38.462 12.81 0.00 0.00 1.40
671 2501 3.665443 AGGGGAGGGAGATTCGAATTTA 58.335 45.455 12.81 0.00 0.00 1.40
733 3475 4.039032 TGAAAACTTCCGCGAAATGTTTC 58.961 39.130 8.23 12.16 31.54 2.78
746 3488 2.414691 GCCAGCGGATCTTGAAAACTTC 60.415 50.000 0.00 0.00 0.00 3.01
769 3511 2.434359 GGTCGGAAGGCTCCAACG 60.434 66.667 0.00 0.00 42.58 4.10
898 3706 0.259938 GTTGGAGCTTGGGATGGGAT 59.740 55.000 0.00 0.00 0.00 3.85
994 3807 1.450312 GGTCAACTGCCATCTCGGG 60.450 63.158 0.00 0.00 34.06 5.14
1227 4055 2.048222 TTCTTCACGGCCAGCTCG 60.048 61.111 2.24 0.00 0.00 5.03
1514 4404 4.564406 GGAGAAGCAGATCTGAAGTCCAAA 60.564 45.833 27.04 0.00 0.00 3.28
1523 4413 2.102925 GAGAAGGGGAGAAGCAGATCTG 59.897 54.545 18.84 18.84 0.00 2.90
1562 4461 7.014615 AGGACATGAGAAAAATATGGGCAATAC 59.985 37.037 0.00 0.00 0.00 1.89
1587 4486 5.284660 GCAGCAATCAAATTTTCGTACAGAG 59.715 40.000 0.00 0.00 0.00 3.35
1643 4544 7.605449 ACAACATGTCCCAAAGAAAATATGAG 58.395 34.615 0.00 0.00 0.00 2.90
1658 4559 6.697019 GCATATTCACCATTTACAACATGTCC 59.303 38.462 0.00 0.00 0.00 4.02
1782 6106 1.209504 TCAGGCCATTGTAGTGTAGGC 59.790 52.381 5.01 0.00 44.48 3.93
1804 6128 4.259135 GTCCGTGACATATCGTGTAAAACG 60.259 45.833 0.00 0.00 42.36 3.60
1806 6130 4.175516 GGTCCGTGACATATCGTGTAAAA 58.824 43.478 6.41 0.00 42.36 1.52
1809 6133 1.677576 GGGTCCGTGACATATCGTGTA 59.322 52.381 6.41 0.00 42.36 2.90
1842 6166 7.492614 GAAACGCAAATTCGATCACTAAAAT 57.507 32.000 0.00 0.00 0.00 1.82
1893 6218 8.952278 ACATCTAAACTACAGTTTTGAACACAA 58.048 29.630 18.31 1.12 46.63 3.33
2062 6457 2.806608 ATGAAGTTTGCCAAGCACAG 57.193 45.000 0.00 0.00 38.71 3.66
2091 6486 8.667463 GTCATAAATTTGTGCATTTTAGGCAAT 58.333 29.630 9.87 0.00 43.91 3.56
2092 6487 7.658982 TGTCATAAATTTGTGCATTTTAGGCAA 59.341 29.630 9.87 0.00 43.91 4.52
2113 6672 7.811713 CAGTATTCTGATCACACGATATGTCAT 59.188 37.037 0.00 0.00 40.98 3.06
2133 6692 4.349930 AGAACCACCCAACTACACAGTATT 59.650 41.667 0.00 0.00 33.48 1.89
2134 6693 3.908103 AGAACCACCCAACTACACAGTAT 59.092 43.478 0.00 0.00 33.48 2.12
2161 6720 2.917713 AAGGGGCATTGTGAACCATA 57.082 45.000 0.00 0.00 0.00 2.74
2188 6747 3.684305 TGTGACCATTGTAAGCAGATTCG 59.316 43.478 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.