Multiple sequence alignment - TraesCS4A01G174200

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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 TraesCS4A01G174200 chr4A 100.000 2626 0 0 1 2626 444377778 444380403 0.000000e+00 4850.0
1 TraesCS4A01G174200 chr4A 91.379 116 6 1 1 112 696175690 696175805 3.500000e-34 156.0
2 TraesCS4A01G174200 chr3A 95.251 2632 112 7 1 2626 720600689 720598065 0.000000e+00 4156.0
3 TraesCS4A01G174200 chr3A 94.144 2493 134 7 141 2626 117786789 117784302 0.000000e+00 3784.0
4 TraesCS4A01G174200 chr5D 94.464 2511 130 7 124 2626 375002114 375004623 0.000000e+00 3858.0
5 TraesCS4A01G174200 chr5D 93.688 2519 139 12 124 2626 184453147 184455661 0.000000e+00 3753.0
6 TraesCS4A01G174200 chr5D 93.776 2378 138 7 127 2498 397473055 397470682 0.000000e+00 3563.0
7 TraesCS4A01G174200 chr5D 93.409 2382 144 9 124 2498 397466695 397469070 0.000000e+00 3517.0
8 TraesCS4A01G174200 chr6B 92.467 2509 180 7 127 2626 666360843 666358335 0.000000e+00 3578.0
9 TraesCS4A01G174200 chr7A 95.076 1970 89 5 124 2089 692229488 692231453 0.000000e+00 3094.0
10 TraesCS4A01G174200 chr7A 86.916 107 12 2 2521 2626 250082453 250082348 4.590000e-23 119.0
11 TraesCS4A01G174200 chr7A 86.792 106 12 1 2523 2626 353019768 353019873 1.650000e-22 117.0
12 TraesCS4A01G174200 chr7A 91.463 82 7 0 2545 2626 287662978 287662897 2.140000e-21 113.0
13 TraesCS4A01G174200 chr7A 85.577 104 15 0 2523 2626 667808412 667808515 2.760000e-20 110.0
14 TraesCS4A01G174200 chr2A 94.114 1665 96 2 130 1792 33472701 33471037 0.000000e+00 2531.0
15 TraesCS4A01G174200 chr2A 94.096 813 42 4 1816 2626 33471048 33470240 0.000000e+00 1230.0
16 TraesCS4A01G174200 chr2A 92.899 507 29 4 2126 2626 478457240 478457745 0.000000e+00 730.0
17 TraesCS4A01G174200 chr7B 94.783 115 6 0 1 115 723722468 723722354 2.080000e-41 180.0
18 TraesCS4A01G174200 chr7B 91.667 120 5 2 1 115 112123121 112123240 7.520000e-36 161.0
19 TraesCS4A01G174200 chr5B 91.597 119 6 1 1 115 643123870 643123752 7.520000e-36 161.0
20 TraesCS4A01G174200 chr2B 92.241 116 5 1 1 112 22678458 22678573 7.520000e-36 161.0
21 TraesCS4A01G174200 chr3B 92.035 113 5 1 1 109 809803527 809803639 3.500000e-34 156.0
22 TraesCS4A01G174200 chr3B 89.916 119 8 1 1 115 799206621 799206503 1.630000e-32 150.0
23 TraesCS4A01G174200 chr6A 100.000 33 0 0 1 33 584479143 584479175 7.850000e-06 62.1


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 TraesCS4A01G174200 chr4A 444377778 444380403 2625 False 4850.0 4850 100.000 1 2626 1 chr4A.!!$F1 2625
1 TraesCS4A01G174200 chr3A 720598065 720600689 2624 True 4156.0 4156 95.251 1 2626 1 chr3A.!!$R2 2625
2 TraesCS4A01G174200 chr3A 117784302 117786789 2487 True 3784.0 3784 94.144 141 2626 1 chr3A.!!$R1 2485
3 TraesCS4A01G174200 chr5D 375002114 375004623 2509 False 3858.0 3858 94.464 124 2626 1 chr5D.!!$F2 2502
4 TraesCS4A01G174200 chr5D 184453147 184455661 2514 False 3753.0 3753 93.688 124 2626 1 chr5D.!!$F1 2502
5 TraesCS4A01G174200 chr5D 397470682 397473055 2373 True 3563.0 3563 93.776 127 2498 1 chr5D.!!$R1 2371
6 TraesCS4A01G174200 chr5D 397466695 397469070 2375 False 3517.0 3517 93.409 124 2498 1 chr5D.!!$F3 2374
7 TraesCS4A01G174200 chr6B 666358335 666360843 2508 True 3578.0 3578 92.467 127 2626 1 chr6B.!!$R1 2499
8 TraesCS4A01G174200 chr7A 692229488 692231453 1965 False 3094.0 3094 95.076 124 2089 1 chr7A.!!$F3 1965
9 TraesCS4A01G174200 chr2A 33470240 33472701 2461 True 1880.5 2531 94.105 130 2626 2 chr2A.!!$R1 2496
10 TraesCS4A01G174200 chr2A 478457240 478457745 505 False 730.0 730 92.899 2126 2626 1 chr2A.!!$F1 500

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
345 346 0.254462 TGACTTTGGCCCGCATGATA 59.746 50.0 0.0 0.0 0.0 2.15 F
1274 1282 0.605319 CTACAAGCCAAACTGCCCGA 60.605 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1607 0.321475 GAGCAAGAGCAGAGCACCTT 60.321 55.000 0.00 0.0 45.49 3.50 R
2477 2508 2.348472 CTTCCATATTAGGGGGCCTCA 58.652 52.381 5.99 0.0 34.61 3.86 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
345 346 0.254462 TGACTTTGGCCCGCATGATA 59.746 50.000 0.00 0.00 0.00 2.15
359 360 3.569277 CGCATGATATTGTGGGGATTTGA 59.431 43.478 0.00 0.00 0.00 2.69
361 362 5.279106 CGCATGATATTGTGGGGATTTGATT 60.279 40.000 0.00 0.00 0.00 2.57
367 368 4.335735 TTGTGGGGATTTGATTCCAGAT 57.664 40.909 0.00 0.00 37.53 2.90
405 406 4.936891 ACAATTTCTTGCTGTTTCAGTCC 58.063 39.130 0.00 0.00 35.69 3.85
432 433 6.806249 GTGCTTGATAGATAGCTGTCTCATAC 59.194 42.308 17.10 7.55 38.22 2.39
470 472 6.936335 CCTAATGGTGCTTTTTCATTTCCTTT 59.064 34.615 0.00 0.00 33.72 3.11
576 581 9.268282 AGGTAGGTTCTTTGTTCTTATCAGATA 57.732 33.333 0.00 0.00 0.00 1.98
631 637 5.227908 AGTGTGTCTACCTGATTGTAAACG 58.772 41.667 0.00 0.00 0.00 3.60
643 649 7.173562 ACCTGATTGTAAACGTAACTGCAATAA 59.826 33.333 8.00 2.33 0.00 1.40
673 679 5.767816 ATGTTGACAGTCTGGTAAAAACC 57.232 39.130 4.53 0.00 0.00 3.27
735 742 9.886132 TCTATCCTTTCCTTACTCATACAAAAC 57.114 33.333 0.00 0.00 0.00 2.43
736 743 7.939784 ATCCTTTCCTTACTCATACAAAACC 57.060 36.000 0.00 0.00 0.00 3.27
1023 1030 2.511600 GAATACCACGCCGCAGCT 60.512 61.111 0.00 0.00 36.60 4.24
1060 1068 5.159209 GTTGCGCTATATACGTGAGGTAAT 58.841 41.667 9.73 0.00 34.09 1.89
1174 1182 9.725019 TGAAAGAAATCTTTGATGCTAACTCTA 57.275 29.630 12.85 0.00 45.37 2.43
1274 1282 0.605319 CTACAAGCCAAACTGCCCGA 60.605 55.000 0.00 0.00 0.00 5.14
1595 1604 5.588648 TCTTGTTCTCTTTTGAAATGGACGT 59.411 36.000 0.00 0.00 0.00 4.34
1598 1607 6.285224 TGTTCTCTTTTGAAATGGACGTAGA 58.715 36.000 0.00 0.00 0.00 2.59
1659 1668 1.827789 GGTGGTGCTTGTTGAGGCA 60.828 57.895 0.00 0.00 36.01 4.75
1691 1701 2.360475 GGCACCACAAGCTCTCCC 60.360 66.667 0.00 0.00 0.00 4.30
1772 1782 4.385825 TGTTGGTTTAGAACACTAGCAGG 58.614 43.478 0.00 0.00 0.00 4.85
1823 1835 2.421424 GCAGGAGCTCAATTACCTTGTG 59.579 50.000 17.19 0.00 37.91 3.33
2062 2076 3.242543 CGTCAATGATGCCTACTTGCTTC 60.243 47.826 0.00 0.00 36.31 3.86
2066 2080 1.480545 TGATGCCTACTTGCTTCGCTA 59.519 47.619 0.00 0.00 38.02 4.26
2077 2091 3.868757 TGCTTCGCTACTACAGTGATT 57.131 42.857 0.00 0.00 43.24 2.57
2102 2116 2.249309 CGGTCAAGCAAGCACACG 59.751 61.111 0.00 0.00 0.00 4.49
2154 2168 4.712476 AGATGTGCCATAATTCCTCTGTC 58.288 43.478 0.00 0.00 0.00 3.51
2299 2313 1.790755 TGGATGCGTGTGTGTAACTC 58.209 50.000 0.00 0.00 38.04 3.01
2316 2330 7.088905 GTGTAACTCGATTAAAGAGGTCTTGA 58.911 38.462 13.61 0.00 39.90 3.02
2340 2354 4.201901 GCCCAAACAATTTTGTCCAAACAG 60.202 41.667 0.00 0.00 41.31 3.16
2505 2537 3.852578 CCCCTAATATGGAAGTATGGCCT 59.147 47.826 3.32 0.00 0.00 5.19
2541 2573 6.319715 ACCAGGAAAAACATACTAAATGGGT 58.680 36.000 0.00 0.00 0.00 4.51
2583 2615 4.770531 CCATATAGACACCTAATCGGACCA 59.229 45.833 0.00 0.00 36.31 4.02
2596 2628 1.757118 TCGGACCAGGCTGAATCTTAG 59.243 52.381 17.94 9.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 6.899393 TCTAAATGAGGAAGTGCACAAATT 57.101 33.333 21.04 4.29 0.00 1.82
125 126 7.953305 ATTATTGTTCGTTCGTTCATTCATG 57.047 32.000 0.00 0.00 0.00 3.07
254 255 5.989477 TGCACTAGTATTGCTGGATAACTT 58.011 37.500 13.03 0.00 40.86 2.66
345 346 4.335735 TCTGGAATCAAATCCCCACAAT 57.664 40.909 0.00 0.00 38.82 2.71
359 360 4.837860 CAGCCTCTACCTCTAATCTGGAAT 59.162 45.833 0.00 0.00 0.00 3.01
361 362 3.463704 TCAGCCTCTACCTCTAATCTGGA 59.536 47.826 0.00 0.00 0.00 3.86
367 368 5.721960 AGAAATTGTCAGCCTCTACCTCTAA 59.278 40.000 0.00 0.00 0.00 2.10
405 406 5.199024 AGACAGCTATCTATCAAGCACTG 57.801 43.478 0.00 0.00 41.32 3.66
432 433 2.422127 ACCATTAGGAACGGAAAATGCG 59.578 45.455 0.00 0.00 38.69 4.73
470 472 5.640147 ACAACATCCTTTATTTGTCCTGGA 58.360 37.500 0.00 0.00 0.00 3.86
476 478 5.768164 ACCGAGAACAACATCCTTTATTTGT 59.232 36.000 0.00 0.00 33.59 2.83
580 585 6.311935 GCATATGCACAACAAATTGAATCTGT 59.688 34.615 22.84 0.00 39.30 3.41
588 593 4.691685 CACTTGGCATATGCACAACAAATT 59.308 37.500 28.07 10.24 44.36 1.82
673 679 0.102844 CACAAACCCAGGCACAACAG 59.897 55.000 0.00 0.00 0.00 3.16
735 742 2.514458 ACAAGAACAATAGCTGGGGG 57.486 50.000 0.00 0.00 0.00 5.40
736 743 6.601613 TGTATTTACAAGAACAATAGCTGGGG 59.398 38.462 0.00 0.00 32.40 4.96
1060 1068 2.637382 TCTCCACTGCCTGTAATGTTCA 59.363 45.455 0.00 0.00 0.00 3.18
1135 1143 6.675987 AGATTTCTTTCAGTTTCAGCACATC 58.324 36.000 0.00 0.00 0.00 3.06
1174 1182 2.289382 TGTCACTGCCATAATCACACGT 60.289 45.455 0.00 0.00 0.00 4.49
1257 1265 1.898574 CTCGGGCAGTTTGGCTTGT 60.899 57.895 2.60 0.00 43.20 3.16
1259 1267 1.302832 CTCTCGGGCAGTTTGGCTT 60.303 57.895 2.60 0.00 43.20 4.35
1412 1420 2.206576 AAATGAACAGGAGGGAGCAC 57.793 50.000 0.00 0.00 0.00 4.40
1580 1589 5.689819 CACCTTCTACGTCCATTTCAAAAG 58.310 41.667 0.00 0.00 0.00 2.27
1595 1604 1.066573 GCAAGAGCAGAGCACCTTCTA 60.067 52.381 0.00 0.00 41.58 2.10
1598 1607 0.321475 GAGCAAGAGCAGAGCACCTT 60.321 55.000 0.00 0.00 45.49 3.50
1651 1660 1.525077 TCACACCGGTTGCCTCAAC 60.525 57.895 2.97 1.33 42.89 3.18
1691 1701 0.526524 GAAGATGGAGCCGACTCACG 60.527 60.000 0.00 0.00 45.42 4.35
1772 1782 5.936956 AGTATGTATACACGGTAGGCTACTC 59.063 44.000 23.01 12.74 35.74 2.59
2062 2076 2.469147 CGCATGAATCACTGTAGTAGCG 59.531 50.000 0.00 0.00 35.42 4.26
2066 2080 1.656652 GGCGCATGAATCACTGTAGT 58.343 50.000 10.83 0.00 0.00 2.73
2077 2091 4.695993 TGCTTGACCGGCGCATGA 62.696 61.111 10.83 0.00 0.00 3.07
2102 2116 8.242053 ACTATCCTAACATGTACGTATATGCAC 58.758 37.037 26.47 4.66 0.00 4.57
2299 2313 3.198872 GGGCTCAAGACCTCTTTAATCG 58.801 50.000 0.00 0.00 41.12 3.34
2477 2508 2.348472 CTTCCATATTAGGGGGCCTCA 58.652 52.381 5.99 0.00 34.61 3.86
2505 2537 5.127845 TGTTTTTCCTGGTAATTTCTGCACA 59.872 36.000 0.00 0.00 0.00 4.57
2583 2615 3.201708 AGGTCATTGCTAAGATTCAGCCT 59.798 43.478 0.00 0.00 38.29 4.58


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

AutoCloner maintained by Alex Coulton.