Multiple sequence alignment - TraesCS2D01G346100

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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 TraesCS2D01G346100 chr2D 100.000 5683 0 0 1 5683 442975861 442981543 0.000000e+00 10495.0
1 TraesCS2D01G346100 chr2D 81.662 758 90 25 4869 5587 542642393 542641646 8.210000e-163 584.0
2 TraesCS2D01G346100 chr2D 86.875 160 17 3 1283 1438 463879040 463878881 5.850000e-40 176.0
3 TraesCS2D01G346100 chr2A 97.142 4863 86 17 1 4835 586445225 586450062 0.000000e+00 8161.0
4 TraesCS2D01G346100 chr2A 77.664 779 120 32 4834 5593 8552519 8551776 5.260000e-115 425.0
5 TraesCS2D01G346100 chr2B 96.792 2930 69 8 774 3696 522079212 522082123 0.000000e+00 4867.0
6 TraesCS2D01G346100 chr2B 94.932 1184 24 7 3683 4830 522082140 522083323 0.000000e+00 1821.0
7 TraesCS2D01G346100 chr2B 90.241 789 44 13 1 776 522078165 522078933 0.000000e+00 1000.0
8 TraesCS2D01G346100 chr2B 81.935 858 103 28 4855 5683 22779850 22780684 0.000000e+00 678.0
9 TraesCS2D01G346100 chr2B 77.175 701 110 25 5017 5682 19387587 19386902 4.190000e-96 363.0
10 TraesCS2D01G346100 chr2B 83.373 415 41 15 1538 1924 182254422 182254008 5.410000e-95 359.0
11 TraesCS2D01G346100 chr2B 90.000 280 24 3 1535 1812 283295414 283295691 5.410000e-95 359.0
12 TraesCS2D01G346100 chr2B 81.728 405 57 13 352 748 283294168 283294563 7.100000e-84 322.0
13 TraesCS2D01G346100 chr2B 85.443 316 33 5 3249 3552 283295961 283296275 3.300000e-82 316.0
14 TraesCS2D01G346100 chr2B 80.300 467 45 16 3096 3550 182254008 182253577 5.530000e-80 309.0
15 TraesCS2D01G346100 chr3B 86.056 710 76 15 4990 5683 471788334 471787632 0.000000e+00 741.0
16 TraesCS2D01G346100 chr3B 84.286 280 35 9 2400 2674 479852440 479852165 1.210000e-66 265.0
17 TraesCS2D01G346100 chr5D 86.115 677 67 16 5017 5683 563982322 563981663 0.000000e+00 704.0
18 TraesCS2D01G346100 chr5D 82.384 755 86 26 4866 5587 327211572 327212312 1.050000e-171 614.0
19 TraesCS2D01G346100 chr5D 81.555 759 88 28 4871 5587 458516795 458517543 3.820000e-161 579.0
20 TraesCS2D01G346100 chr5D 86.038 265 35 2 5324 5587 547688848 547689111 3.350000e-72 283.0
21 TraesCS2D01G346100 chr5B 82.277 773 106 12 4858 5609 706397765 706397003 1.730000e-179 640.0
22 TraesCS2D01G346100 chr1B 85.470 585 60 13 1439 2010 357238307 357238879 2.280000e-163 586.0
23 TraesCS2D01G346100 chr1B 79.462 930 102 42 380 1288 357237444 357238305 1.370000e-160 577.0
24 TraesCS2D01G346100 chr1B 86.473 207 22 1 3353 3553 357239093 357239299 7.410000e-54 222.0
25 TraesCS2D01G346100 chr4B 82.825 623 75 20 4987 5587 428836574 428835962 3.900000e-146 529.0
26 TraesCS2D01G346100 chr4B 83.493 418 39 17 1535 1924 195450940 195451355 4.190000e-96 363.0
27 TraesCS2D01G346100 chr4B 84.227 317 35 7 3249 3552 195451483 195451797 1.550000e-75 294.0
28 TraesCS2D01G346100 chr4A 80.330 666 95 16 5022 5675 69729634 69730275 6.660000e-129 472.0
29 TraesCS2D01G346100 chr4A 80.500 400 58 14 4907 5291 584973489 584973883 7.200000e-74 289.0
30 TraesCS2D01G346100 chr7A 78.454 789 120 29 4834 5587 549724462 549723689 2.400000e-128 470.0
31 TraesCS2D01G346100 chr7A 76.987 478 68 28 4935 5384 680194395 680193932 9.520000e-58 235.0
32 TraesCS2D01G346100 chr7A 86.391 169 19 3 1285 1449 511930528 511930696 1.260000e-41 182.0
33 TraesCS2D01G346100 chr7D 81.141 631 76 25 4987 5587 587296478 587297095 3.100000e-127 466.0
34 TraesCS2D01G346100 chr1D 79.710 690 91 30 4935 5587 451134690 451134013 2.410000e-123 453.0
35 TraesCS2D01G346100 chr1D 77.223 641 88 33 4834 5436 403941194 403941814 7.100000e-84 322.0
36 TraesCS2D01G346100 chr7B 78.095 630 93 22 4987 5587 63565365 63565978 1.950000e-94 357.0
37 TraesCS2D01G346100 chr7B 77.316 626 104 19 4937 5537 622515566 622514954 9.120000e-88 335.0
38 TraesCS2D01G346100 chr3D 89.103 156 15 1 1288 1441 441388819 441388664 5.810000e-45 193.0
39 TraesCS2D01G346100 chr6B 89.103 156 14 2 1288 1441 468734617 468734463 2.090000e-44 191.0
40 TraesCS2D01G346100 chr6B 88.816 152 11 4 1287 1434 641305586 641305437 1.260000e-41 182.0
41 TraesCS2D01G346100 chr6B 88.462 52 6 0 2557 2608 554033901 554033850 4.750000e-06 63.9
42 TraesCS2D01G346100 chr3A 88.462 156 16 1 1288 1441 582283367 582283212 2.700000e-43 187.0
43 TraesCS2D01G346100 chr5A 88.158 152 14 2 1286 1435 321920629 321920778 1.630000e-40 178.0


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 TraesCS2D01G346100 chr2D 442975861 442981543 5682 False 10495.000000 10495 100.000000 1 5683 1 chr2D.!!$F1 5682
1 TraesCS2D01G346100 chr2D 542641646 542642393 747 True 584.000000 584 81.662000 4869 5587 1 chr2D.!!$R2 718
2 TraesCS2D01G346100 chr2A 586445225 586450062 4837 False 8161.000000 8161 97.142000 1 4835 1 chr2A.!!$F1 4834
3 TraesCS2D01G346100 chr2A 8551776 8552519 743 True 425.000000 425 77.664000 4834 5593 1 chr2A.!!$R1 759
4 TraesCS2D01G346100 chr2B 522078165 522083323 5158 False 2562.666667 4867 93.988333 1 4830 3 chr2B.!!$F3 4829
5 TraesCS2D01G346100 chr2B 22779850 22780684 834 False 678.000000 678 81.935000 4855 5683 1 chr2B.!!$F1 828
6 TraesCS2D01G346100 chr2B 19386902 19387587 685 True 363.000000 363 77.175000 5017 5682 1 chr2B.!!$R1 665
7 TraesCS2D01G346100 chr2B 182253577 182254422 845 True 334.000000 359 81.836500 1538 3550 2 chr2B.!!$R2 2012
8 TraesCS2D01G346100 chr2B 283294168 283296275 2107 False 332.333333 359 85.723667 352 3552 3 chr2B.!!$F2 3200
9 TraesCS2D01G346100 chr3B 471787632 471788334 702 True 741.000000 741 86.056000 4990 5683 1 chr3B.!!$R1 693
10 TraesCS2D01G346100 chr5D 563981663 563982322 659 True 704.000000 704 86.115000 5017 5683 1 chr5D.!!$R1 666
11 TraesCS2D01G346100 chr5D 327211572 327212312 740 False 614.000000 614 82.384000 4866 5587 1 chr5D.!!$F1 721
12 TraesCS2D01G346100 chr5D 458516795 458517543 748 False 579.000000 579 81.555000 4871 5587 1 chr5D.!!$F2 716
13 TraesCS2D01G346100 chr5B 706397003 706397765 762 True 640.000000 640 82.277000 4858 5609 1 chr5B.!!$R1 751
14 TraesCS2D01G346100 chr1B 357237444 357239299 1855 False 461.666667 586 83.801667 380 3553 3 chr1B.!!$F1 3173
15 TraesCS2D01G346100 chr4B 428835962 428836574 612 True 529.000000 529 82.825000 4987 5587 1 chr4B.!!$R1 600
16 TraesCS2D01G346100 chr4B 195450940 195451797 857 False 328.500000 363 83.860000 1535 3552 2 chr4B.!!$F1 2017
17 TraesCS2D01G346100 chr4A 69729634 69730275 641 False 472.000000 472 80.330000 5022 5675 1 chr4A.!!$F1 653
18 TraesCS2D01G346100 chr7A 549723689 549724462 773 True 470.000000 470 78.454000 4834 5587 1 chr7A.!!$R1 753
19 TraesCS2D01G346100 chr7D 587296478 587297095 617 False 466.000000 466 81.141000 4987 5587 1 chr7D.!!$F1 600
20 TraesCS2D01G346100 chr1D 451134013 451134690 677 True 453.000000 453 79.710000 4935 5587 1 chr1D.!!$R1 652
21 TraesCS2D01G346100 chr1D 403941194 403941814 620 False 322.000000 322 77.223000 4834 5436 1 chr1D.!!$F1 602
22 TraesCS2D01G346100 chr7B 63565365 63565978 613 False 357.000000 357 78.095000 4987 5587 1 chr7B.!!$F1 600
23 TraesCS2D01G346100 chr7B 622514954 622515566 612 True 335.000000 335 77.316000 4937 5537 1 chr7B.!!$R1 600

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
19 20 1.064824 ATGGGGATTGGAGGAGGAGC 61.065 60.000 0.00 0.0 0.00 4.70 F
517 534 1.200020 GTTGCCGGAGTTTCCATCTTG 59.800 52.381 5.05 0.0 35.91 3.02 F
1860 2474 1.250328 TGCTTGCTCTCCATGTTTGG 58.750 50.000 0.00 0.0 45.15 3.28 F
3386 4017 4.761739 TGCTCTTTTCAGAATAACCCTGTG 59.238 41.667 0.00 0.0 33.57 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 2023 4.752101 CGACAGAGTCAAAGACAGGAAATT 59.248 41.667 0.00 0.0 34.60 1.82 R
2410 3032 4.305539 TTTGCAATCTCTGGGATCTGAA 57.694 40.909 0.00 0.0 32.76 3.02 R
3425 4056 0.326264 ACTCACTGCCCTTGCTTAGG 59.674 55.000 0.00 0.0 44.33 2.69 R
4875 5585 0.107081 TCCACGTCAACCCAAACGAT 59.893 50.000 1.52 0.0 41.29 3.73 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
19 20 1.064824 ATGGGGATTGGAGGAGGAGC 61.065 60.000 0.00 0.00 0.00 4.70
74 75 2.548920 GGGTTCCTCATGGATTAGAGCG 60.549 54.545 0.00 0.00 42.81 5.03
119 120 3.804873 GGAGATGGAATTCGTGTAGCTTC 59.195 47.826 0.00 0.00 0.00 3.86
373 387 2.823196 TGAACACAAACAACTCGCAG 57.177 45.000 0.00 0.00 0.00 5.18
517 534 1.200020 GTTGCCGGAGTTTCCATCTTG 59.800 52.381 5.05 0.00 35.91 3.02
548 566 1.523758 GCATAACTGCGGGGATTAGG 58.476 55.000 0.00 0.00 38.92 2.69
567 597 8.060931 GATTAGGCATCCTTTTTCTTCTTCTT 57.939 34.615 0.00 0.00 34.61 2.52
1093 1583 9.533253 CCTAATTCCACCAAAAGCTATTAATTG 57.467 33.333 0.00 0.00 0.00 2.32
1103 1593 8.196771 CCAAAAGCTATTAATTGAGCAATGGTA 58.803 33.333 11.79 0.00 41.36 3.25
1860 2474 1.250328 TGCTTGCTCTCCATGTTTGG 58.750 50.000 0.00 0.00 45.15 3.28
1993 2612 9.801192 TGGATGTGCCTGATGTTAGAGAACAAA 62.801 40.741 0.00 0.00 42.50 2.83
2104 2723 8.925161 TGTGTTCTTACAAAATTTGAGAAAGG 57.075 30.769 13.19 0.00 35.69 3.11
2331 2950 7.386573 TGATGTAGTCGCTAATTGTTTTCTCAA 59.613 33.333 0.00 0.00 0.00 3.02
2332 2951 7.667043 TGTAGTCGCTAATTGTTTTCTCAAT 57.333 32.000 0.00 0.00 39.35 2.57
2800 3422 5.296283 CCTTCACTTCAATATCCAGCTCAAG 59.704 44.000 0.00 0.00 0.00 3.02
3386 4017 4.761739 TGCTCTTTTCAGAATAACCCTGTG 59.238 41.667 0.00 0.00 33.57 3.66
3722 4389 3.058363 GTCAGAGAAAAGGCTCTTTGCAG 60.058 47.826 7.99 0.05 42.41 4.41
4439 5112 4.717313 CTGGAGCAGCAGCAGCCA 62.717 66.667 13.57 13.57 45.49 4.75
4849 5558 9.569167 GTAAAATAATTTAGAGCAACTCCAACC 57.431 33.333 0.00 0.00 31.81 3.77
4851 5560 3.806949 ATTTAGAGCAACTCCAACCCA 57.193 42.857 0.00 0.00 0.00 4.51
4852 5561 2.561478 TTAGAGCAACTCCAACCCAC 57.439 50.000 0.00 0.00 0.00 4.61
4853 5562 1.729586 TAGAGCAACTCCAACCCACT 58.270 50.000 0.00 0.00 0.00 4.00
4875 5585 0.252761 TCCAAATCATCTGCCTGCGA 59.747 50.000 0.00 0.00 0.00 5.10
4891 5601 1.562575 GCGATCGTTTGGGTTGACGT 61.563 55.000 17.81 0.00 40.03 4.34
4914 5624 2.619646 GACAAAAGTAAAGGCCCAACGA 59.380 45.455 0.00 0.00 0.00 3.85
5012 5755 2.806198 CCGCGCGTTTCCTCGTTA 60.806 61.111 29.95 0.00 0.00 3.18
5082 5828 0.821517 TTATGACGGCCATCGACACT 59.178 50.000 2.24 0.00 44.96 3.55
5112 5858 4.081030 CAGCCAGTGCAAGCGTCG 62.081 66.667 0.00 0.00 41.13 5.12
5200 5973 0.111253 CACCACCTTCCTGCTTCCTT 59.889 55.000 0.00 0.00 0.00 3.36
5212 5986 2.668212 TTCCTTGCCGGCGACAAG 60.668 61.111 26.06 26.06 43.36 3.16
5588 6446 1.714794 CTCGAACACGAGGAGCAAAT 58.285 50.000 11.09 0.00 46.33 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.356270 TGCAAAGTCAGCAGCGTTG 59.644 52.632 0.00 0.00 37.02 4.10
74 75 0.727398 GTATCACCACGAAGCTTGGC 59.273 55.000 2.10 0.00 37.69 4.52
373 387 1.732809 GACCGAAGAGCTAAACTTGGC 59.267 52.381 0.00 0.00 34.56 4.52
548 566 7.776933 AACAAAAGAAGAAGAAAAAGGATGC 57.223 32.000 0.00 0.00 0.00 3.91
1093 1583 8.388484 AGATTACAATCTCATTACCATTGCTC 57.612 34.615 0.00 0.00 41.82 4.26
1103 1593 9.624373 AGATAACAGCAAGATTACAATCTCATT 57.376 29.630 4.98 0.12 44.67 2.57
1231 1728 9.709495 ATGCAATTTTATTTTCTAGCACAAGAA 57.291 25.926 0.00 0.00 33.18 2.52
1522 2021 6.238484 CGACAGAGTCAAAGACAGGAAATTTT 60.238 38.462 0.00 0.00 34.60 1.82
1524 2023 4.752101 CGACAGAGTCAAAGACAGGAAATT 59.248 41.667 0.00 0.00 34.60 1.82
1860 2474 8.950208 ACATAGTCTGATAAGCTTTTACTTCC 57.050 34.615 3.20 0.00 0.00 3.46
2410 3032 4.305539 TTTGCAATCTCTGGGATCTGAA 57.694 40.909 0.00 0.00 32.76 3.02
2821 3443 1.203523 GCAGGAGCTTCTCGAGAGAAA 59.796 52.381 15.94 0.00 45.75 2.52
3184 3809 0.726827 CGTCACCACGCATTTGCTAT 59.273 50.000 0.51 0.00 39.69 2.97
3259 3884 0.375803 AACGTCGGTGTTCAACTTGC 59.624 50.000 0.00 0.00 0.00 4.01
3386 4017 4.154347 CTCTCGGGTGCAGCCTCC 62.154 72.222 30.86 8.03 37.43 4.30
3425 4056 0.326264 ACTCACTGCCCTTGCTTAGG 59.674 55.000 0.00 0.00 44.33 2.69
3722 4389 5.144692 TCATCTGATCTACCTATGCTTGC 57.855 43.478 0.00 0.00 0.00 4.01
3881 4548 0.973632 ACAGGTTGAGGTACATCGCA 59.026 50.000 2.68 0.00 0.00 5.10
4554 5245 3.130160 CTTCTTGCCCTCGCTGCC 61.130 66.667 0.00 0.00 35.36 4.85
4849 5558 2.621998 GGCAGATGATTTGGATCAGTGG 59.378 50.000 0.00 0.00 45.01 4.00
4851 5560 3.552875 CAGGCAGATGATTTGGATCAGT 58.447 45.455 0.00 0.00 45.01 3.41
4852 5561 2.293677 GCAGGCAGATGATTTGGATCAG 59.706 50.000 0.00 0.00 45.01 2.90
4853 5562 2.304092 GCAGGCAGATGATTTGGATCA 58.696 47.619 0.00 0.00 45.81 2.92
4875 5585 0.107081 TCCACGTCAACCCAAACGAT 59.893 50.000 1.52 0.00 41.29 3.73
4891 5601 2.696187 GTTGGGCCTTTACTTTTGTCCA 59.304 45.455 4.53 0.00 0.00 4.02
4914 5624 0.966179 GTTTTGGATTTGGGTCGGCT 59.034 50.000 0.00 0.00 0.00 5.52
5075 5821 1.982395 CTAGTGGGCCCAGTGTCGA 60.982 63.158 38.03 19.92 0.00 4.20
5082 5828 3.009115 GGCTGACTAGTGGGCCCA 61.009 66.667 24.45 24.45 38.77 5.36
5212 5986 1.758122 CCCATGGCTAGGGTTTGGC 60.758 63.158 6.09 0.00 41.61 4.52
5266 6085 3.461773 CACGGGAGGATGAGGCGT 61.462 66.667 0.00 0.00 0.00 5.68
5633 6496 1.533033 TCCTCTGGCTGGACAACGA 60.533 57.895 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.