Multiple sequence alignment - TraesCS6B01G311800

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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 TraesCS6B01G311800 chr6B 100.000 3173 0 0 1 3173 558924270 558921098 0.000000e+00 5860.0
1 TraesCS6B01G311800 chr6B 92.570 646 44 4 2529 3173 149019520 149020162 0.000000e+00 924.0
2 TraesCS6B01G311800 chr6B 87.762 572 51 15 1545 2108 720765106 720765666 0.000000e+00 651.0
3 TraesCS6B01G311800 chr6B 84.615 663 65 12 2533 3171 249496468 249497117 2.690000e-175 625.0
4 TraesCS6B01G311800 chr6B 86.233 523 60 7 1586 2108 300673362 300673872 9.940000e-155 556.0
5 TraesCS6B01G311800 chr6B 79.350 431 66 16 914 1331 300672593 300673013 6.700000e-72 281.0
6 TraesCS6B01G311800 chr6B 77.848 474 72 22 914 1372 720764398 720764853 2.430000e-66 263.0
7 TraesCS6B01G311800 chr6B 84.615 169 14 10 230 393 659955120 659955281 1.180000e-34 158.0
8 TraesCS6B01G311800 chr3D 97.294 2550 42 13 1 2539 23152483 23155016 0.000000e+00 4301.0
9 TraesCS6B01G311800 chr2D 94.792 2554 75 28 1 2539 432771041 432768531 0.000000e+00 3927.0
10 TraesCS6B01G311800 chr7A 98.583 635 9 0 2539 3173 736098838 736099472 0.000000e+00 1123.0
11 TraesCS6B01G311800 chr7A 96.535 635 22 0 2539 3173 191847673 191847039 0.000000e+00 1051.0
12 TraesCS6B01G311800 chr7A 86.233 523 60 7 1586 2108 317896325 317895815 9.940000e-155 556.0
13 TraesCS6B01G311800 chr2B 97.165 635 18 0 2539 3173 4913334 4913968 0.000000e+00 1074.0
14 TraesCS6B01G311800 chr2B 95.604 637 26 2 2538 3173 98132912 98132277 0.000000e+00 1020.0
15 TraesCS6B01G311800 chr6A 96.870 639 19 1 2535 3173 565056989 565056352 0.000000e+00 1068.0
16 TraesCS6B01G311800 chr5D 92.272 647 37 3 2539 3173 294589620 294588975 0.000000e+00 905.0
17 TraesCS6B01G311800 chr5D 81.481 405 55 15 914 1307 553779884 553779489 6.610000e-82 315.0
18 TraesCS6B01G311800 chr5D 91.139 79 6 1 2030 2108 553776933 553776856 4.330000e-19 106.0
19 TraesCS6B01G311800 chr3B 90.139 649 51 3 2538 3173 803620083 803620731 0.000000e+00 832.0
20 TraesCS6B01G311800 chr3B 86.973 522 56 5 1587 2108 85344116 85343607 7.630000e-161 577.0
21 TraesCS6B01G311800 chr3B 86.973 522 56 5 1587 2108 781352083 781351574 7.630000e-161 577.0
22 TraesCS6B01G311800 chr3B 93.333 345 21 2 2526 2869 720201537 720201194 2.820000e-140 508.0
23 TraesCS6B01G311800 chr3B 80.645 558 72 17 2631 3169 153618181 153618721 1.770000e-107 399.0
24 TraesCS6B01G311800 chr3B 79.350 431 66 13 914 1331 781352853 781352433 6.700000e-72 281.0
25 TraesCS6B01G311800 chr4A 88.287 572 48 13 1545 2108 726663622 726664182 0.000000e+00 667.0
26 TraesCS6B01G311800 chr4A 81.233 373 50 17 912 1268 24020427 24020059 1.860000e-72 283.0
27 TraesCS6B01G311800 chr4A 77.637 474 73 22 914 1372 726662911 726663366 1.130000e-64 257.0
28 TraesCS6B01G311800 chr1A 87.809 566 48 14 1551 2108 22855025 22854473 0.000000e+00 643.0
29 TraesCS6B01G311800 chr1A 86.905 84 11 0 2120 2203 498425299 498425382 9.370000e-16 95.3
30 TraesCS6B01G311800 chr3A 87.238 572 53 12 1545 2108 109881890 109882449 4.460000e-178 634.0
31 TraesCS6B01G311800 chr1B 86.782 522 57 5 1587 2108 512627605 512627096 3.550000e-159 571.0
32 TraesCS6B01G311800 chr5B 93.413 334 21 1 2537 2869 703781677 703781344 7.910000e-136 494.0
33 TraesCS6B01G311800 chr4D 80.000 430 63 14 914 1330 211757507 211757926 2.390000e-76 296.0


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 TraesCS6B01G311800 chr6B 558921098 558924270 3172 True 5860.0 5860 100.0000 1 3173 1 chr6B.!!$R1 3172
1 TraesCS6B01G311800 chr6B 149019520 149020162 642 False 924.0 924 92.5700 2529 3173 1 chr6B.!!$F1 644
2 TraesCS6B01G311800 chr6B 249496468 249497117 649 False 625.0 625 84.6150 2533 3171 1 chr6B.!!$F2 638
3 TraesCS6B01G311800 chr6B 720764398 720765666 1268 False 457.0 651 82.8050 914 2108 2 chr6B.!!$F5 1194
4 TraesCS6B01G311800 chr6B 300672593 300673872 1279 False 418.5 556 82.7915 914 2108 2 chr6B.!!$F4 1194
5 TraesCS6B01G311800 chr3D 23152483 23155016 2533 False 4301.0 4301 97.2940 1 2539 1 chr3D.!!$F1 2538
6 TraesCS6B01G311800 chr2D 432768531 432771041 2510 True 3927.0 3927 94.7920 1 2539 1 chr2D.!!$R1 2538
7 TraesCS6B01G311800 chr7A 736098838 736099472 634 False 1123.0 1123 98.5830 2539 3173 1 chr7A.!!$F1 634
8 TraesCS6B01G311800 chr7A 191847039 191847673 634 True 1051.0 1051 96.5350 2539 3173 1 chr7A.!!$R1 634
9 TraesCS6B01G311800 chr7A 317895815 317896325 510 True 556.0 556 86.2330 1586 2108 1 chr7A.!!$R2 522
10 TraesCS6B01G311800 chr2B 4913334 4913968 634 False 1074.0 1074 97.1650 2539 3173 1 chr2B.!!$F1 634
11 TraesCS6B01G311800 chr2B 98132277 98132912 635 True 1020.0 1020 95.6040 2538 3173 1 chr2B.!!$R1 635
12 TraesCS6B01G311800 chr6A 565056352 565056989 637 True 1068.0 1068 96.8700 2535 3173 1 chr6A.!!$R1 638
13 TraesCS6B01G311800 chr5D 294588975 294589620 645 True 905.0 905 92.2720 2539 3173 1 chr5D.!!$R1 634
14 TraesCS6B01G311800 chr5D 553776856 553779884 3028 True 210.5 315 86.3100 914 2108 2 chr5D.!!$R2 1194
15 TraesCS6B01G311800 chr3B 803620083 803620731 648 False 832.0 832 90.1390 2538 3173 1 chr3B.!!$F2 635
16 TraesCS6B01G311800 chr3B 85343607 85344116 509 True 577.0 577 86.9730 1587 2108 1 chr3B.!!$R1 521
17 TraesCS6B01G311800 chr3B 781351574 781352853 1279 True 429.0 577 83.1615 914 2108 2 chr3B.!!$R3 1194
18 TraesCS6B01G311800 chr3B 153618181 153618721 540 False 399.0 399 80.6450 2631 3169 1 chr3B.!!$F1 538
19 TraesCS6B01G311800 chr4A 726662911 726664182 1271 False 462.0 667 82.9620 914 2108 2 chr4A.!!$F1 1194
20 TraesCS6B01G311800 chr1A 22854473 22855025 552 True 643.0 643 87.8090 1551 2108 1 chr1A.!!$R1 557
21 TraesCS6B01G311800 chr3A 109881890 109882449 559 False 634.0 634 87.2380 1545 2108 1 chr3A.!!$F1 563
22 TraesCS6B01G311800 chr1B 512627096 512627605 509 True 571.0 571 86.7820 1587 2108 1 chr1B.!!$R1 521

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
51 52 7.209471 TGATGCTAGTTTACCGTTTGATTTT 57.791 32.000 0.0 0.0 0.00 1.82 F
291 292 7.328277 ACACACTGTATTTCTTAGTGCAAAA 57.672 32.000 0.0 0.0 44.22 2.44 F
1412 3171 4.260375 CGAATTGCCTGAAACGGAAGATAG 60.260 45.833 0.0 0.0 0.00 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 3171 1.300971 TTGCGAGCTCCAACATCTGC 61.301 55.000 8.47 3.47 0.00 4.26 R
1727 3835 3.068307 ACTCTGAAGAACACGTACTTGCT 59.932 43.478 0.00 0.00 0.00 3.91 R
2563 4755 1.234615 GCTTACACTCGGCCTTTGCA 61.235 55.000 0.00 0.00 40.13 4.08 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
51 52 7.209471 TGATGCTAGTTTACCGTTTGATTTT 57.791 32.000 0.00 0.00 0.00 1.82
268 269 8.542497 TTGTCACTGTACATTTTACTGGATAC 57.458 34.615 0.00 0.00 0.00 2.24
291 292 7.328277 ACACACTGTATTTCTTAGTGCAAAA 57.672 32.000 0.00 0.00 44.22 2.44
1005 1013 7.739498 TTCGGAAATAGATTAAAGTATGGGC 57.261 36.000 0.00 0.00 0.00 5.36
1384 3143 8.462589 TCATTGCCTGTTTATATATCTTGCAA 57.537 30.769 0.00 0.00 40.06 4.08
1412 3171 4.260375 CGAATTGCCTGAAACGGAAGATAG 60.260 45.833 0.00 0.00 0.00 2.08
1727 3835 1.841302 ATTGGCGGCTTGTCTCCTCA 61.841 55.000 11.43 0.00 0.00 3.86
1795 3904 0.837691 TGTGAGGACAGAGGTGCCAT 60.838 55.000 0.00 0.00 35.71 4.40
1862 3971 7.613022 TGCTTCAGTGATTCAGATTAGGAAAAT 59.387 33.333 0.00 0.00 0.00 1.82
2114 4306 9.177608 CTTCTTGTGTCCAAATCCAATATTAGA 57.822 33.333 0.00 0.00 0.00 2.10
2446 4638 7.648039 TTTTACAGTGTATTTTCCAAGTGGT 57.352 32.000 3.28 0.00 36.34 4.16
2447 4639 8.749026 TTTTACAGTGTATTTTCCAAGTGGTA 57.251 30.769 3.28 0.00 36.34 3.25
2448 4640 8.927675 TTTACAGTGTATTTTCCAAGTGGTAT 57.072 30.769 3.28 0.00 36.34 2.73
2449 4641 8.927675 TTACAGTGTATTTTCCAAGTGGTATT 57.072 30.769 3.28 0.00 36.34 1.89
2450 4642 7.833285 ACAGTGTATTTTCCAAGTGGTATTT 57.167 32.000 0.00 0.00 36.34 1.40
2451 4643 8.245195 ACAGTGTATTTTCCAAGTGGTATTTT 57.755 30.769 0.00 0.00 36.34 1.82
2452 4644 8.357402 ACAGTGTATTTTCCAAGTGGTATTTTC 58.643 33.333 0.00 0.00 36.34 2.29
2453 4645 7.812669 CAGTGTATTTTCCAAGTGGTATTTTCC 59.187 37.037 0.00 0.00 36.34 3.13
2454 4646 7.507616 AGTGTATTTTCCAAGTGGTATTTTCCA 59.492 33.333 0.00 0.00 36.34 3.53
2455 4647 8.145122 GTGTATTTTCCAAGTGGTATTTTCCAA 58.855 33.333 0.00 0.00 39.34 3.53
2461 4653 5.245075 TCCAAGTGGTATTTTCCAATGGAAC 59.755 40.000 15.24 3.56 44.94 3.62
2563 4755 2.281484 ACTCGTTGCGCCAATGGT 60.281 55.556 4.18 3.04 31.92 3.55
2599 4791 6.267014 AGTGTAAGCCAAGTAGTGAAAGAGTA 59.733 38.462 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 269 8.801715 AATTTTGCACTAAGAAATACAGTGTG 57.198 30.769 5.88 0.00 41.39 3.82
525 526 8.797438 TGCAAATACATCACAGTAAAATAACCA 58.203 29.630 0.00 0.00 0.00 3.67
625 626 4.152223 GCAAAACTATCCAAAACACCATGC 59.848 41.667 0.00 0.00 0.00 4.06
626 627 4.690280 GGCAAAACTATCCAAAACACCATG 59.310 41.667 0.00 0.00 0.00 3.66
627 628 4.592778 AGGCAAAACTATCCAAAACACCAT 59.407 37.500 0.00 0.00 0.00 3.55
628 629 3.964031 AGGCAAAACTATCCAAAACACCA 59.036 39.130 0.00 0.00 0.00 4.17
983 991 6.934645 TCTGCCCATACTTTAATCTATTTCCG 59.065 38.462 0.00 0.00 0.00 4.30
1005 1013 3.960571 ACCAAGACCCTTCATGATTCTG 58.039 45.455 0.00 0.00 0.00 3.02
1384 3143 2.393764 CGTTTCAGGCAATTCGCTTTT 58.606 42.857 0.00 0.00 41.91 2.27
1412 3171 1.300971 TTGCGAGCTCCAACATCTGC 61.301 55.000 8.47 3.47 0.00 4.26
1727 3835 3.068307 ACTCTGAAGAACACGTACTTGCT 59.932 43.478 0.00 0.00 0.00 3.91
1795 3904 4.830046 TGCTAGCCATTTGACAAACCTAAA 59.170 37.500 13.29 0.00 0.00 1.85
1862 3971 7.022055 ACATATTCGCAAATCGGAATAAACA 57.978 32.000 0.00 0.00 39.05 2.83
2334 4526 7.174080 ACACAGCAAAAACCACTAAACAAAATT 59.826 29.630 0.00 0.00 0.00 1.82
2442 4634 6.015434 ACTGAAGTTCCATTGGAAAATACCAC 60.015 38.462 19.57 6.52 43.86 4.16
2443 4635 6.015519 CACTGAAGTTCCATTGGAAAATACCA 60.016 38.462 19.57 11.83 43.86 3.25
2444 4636 6.389906 CACTGAAGTTCCATTGGAAAATACC 58.610 40.000 19.57 7.24 43.86 2.73
2445 4637 5.863935 GCACTGAAGTTCCATTGGAAAATAC 59.136 40.000 19.57 8.33 43.86 1.89
2446 4638 5.538053 TGCACTGAAGTTCCATTGGAAAATA 59.462 36.000 19.57 6.29 43.86 1.40
2447 4639 4.344679 TGCACTGAAGTTCCATTGGAAAAT 59.655 37.500 19.57 11.34 43.86 1.82
2448 4640 3.703556 TGCACTGAAGTTCCATTGGAAAA 59.296 39.130 19.57 5.61 43.86 2.29
2449 4641 3.295093 TGCACTGAAGTTCCATTGGAAA 58.705 40.909 19.57 3.64 43.86 3.13
2450 4642 2.942804 TGCACTGAAGTTCCATTGGAA 58.057 42.857 14.24 14.24 39.66 3.53
2451 4643 2.655090 TGCACTGAAGTTCCATTGGA 57.345 45.000 0.00 0.00 0.00 3.53
2452 4644 3.947910 AATGCACTGAAGTTCCATTGG 57.052 42.857 0.00 0.00 0.00 3.16
2548 4740 4.036804 GCACCATTGGCGCAACGA 62.037 61.111 10.83 0.00 30.18 3.85
2563 4755 1.234615 GCTTACACTCGGCCTTTGCA 61.235 55.000 0.00 0.00 40.13 4.08


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

AutoCloner maintained by Alex Coulton.