Multiple sequence alignment - TraesCS4B01G119900

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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 TraesCS4B01G119900 chr4B 100.000 2339 0 0 1 2339 140437445 140435107 0.000000e+00 4320.0
1 TraesCS4B01G119900 chr4B 94.147 1794 57 12 418 2205 139940781 139939030 0.000000e+00 2687.0
2 TraesCS4B01G119900 chr4B 97.474 1544 39 0 794 2337 140233711 140232168 0.000000e+00 2636.0
3 TraesCS4B01G119900 chr4B 94.322 1356 40 5 995 2337 62433505 62432174 0.000000e+00 2043.0
4 TraesCS4B01G119900 chr4B 93.266 1381 50 10 966 2339 61495530 61494186 0.000000e+00 1995.0
5 TraesCS4B01G119900 chr4B 91.660 1163 48 8 1178 2337 62049987 62048871 0.000000e+00 1565.0
6 TraesCS4B01G119900 chr4B 96.893 708 14 1 1630 2337 61323755 61323056 0.000000e+00 1179.0
7 TraesCS4B01G119900 chr4B 96.751 708 15 1 1630 2337 61537185 61537884 0.000000e+00 1173.0
8 TraesCS4B01G119900 chr4B 96.469 708 16 2 1630 2337 61524112 61524810 0.000000e+00 1160.0
9 TraesCS4B01G119900 chr4B 95.211 710 24 3 1630 2337 62868452 62867751 0.000000e+00 1114.0
10 TraesCS4B01G119900 chr4B 89.035 839 51 19 1 807 140234559 140233730 0.000000e+00 1002.0
11 TraesCS4B01G119900 chr4B 81.919 1167 108 53 418 1515 61522812 61523944 0.000000e+00 891.0
12 TraesCS4B01G119900 chr4B 80.584 1164 111 64 418 1515 61325037 61323923 0.000000e+00 791.0
13 TraesCS4B01G119900 chr4B 87.500 624 38 15 1 593 139945906 139945292 0.000000e+00 684.0
14 TraesCS4B01G119900 chr4B 93.719 398 17 6 1 394 61520885 61521278 7.200000e-165 590.0
15 TraesCS4B01G119900 chr4B 93.467 398 20 5 1 394 61325951 61325556 9.310000e-164 586.0
16 TraesCS4B01G119900 chr4B 83.871 434 42 16 538 947 61889229 61889658 2.820000e-104 388.0
17 TraesCS4B01G119900 chr4B 82.506 423 39 14 1 394 62058128 62057712 2.880000e-89 339.0
18 TraesCS4B01G119900 chr4B 82.311 424 38 18 1 394 62041146 62040730 1.340000e-87 333.0
19 TraesCS4B01G119900 chr4B 81.797 423 40 14 1 394 61534519 61534933 1.040000e-83 320.0
20 TraesCS4B01G119900 chr4B 80.140 428 37 24 7 394 62436743 62436324 2.290000e-70 276.0
21 TraesCS4B01G119900 chr4B 82.675 329 36 15 420 743 62040051 62039739 2.960000e-69 272.0
22 TraesCS4B01G119900 chr4B 79.907 428 38 24 7 394 62435088 62434669 1.070000e-68 270.0
23 TraesCS4B01G119900 chr4B 90.244 41 4 0 334 374 166707421 166707381 1.000000e-03 54.7
24 TraesCS4B01G119900 chr4D 94.278 1136 43 11 384 1508 43077434 43076310 0.000000e+00 1718.0
25 TraesCS4B01G119900 chr4D 92.995 728 20 5 1630 2339 43075991 43075277 0.000000e+00 1033.0
26 TraesCS4B01G119900 chr4D 91.862 725 25 5 1630 2336 43150340 43149632 0.000000e+00 981.0
27 TraesCS4B01G119900 chr4D 80.685 1139 138 54 418 1515 43151687 43150590 0.000000e+00 809.0
28 TraesCS4B01G119900 chr4D 82.840 338 25 13 20 330 43079007 43078676 2.960000e-69 272.0
29 TraesCS4B01G119900 chr4D 88.489 139 11 5 258 394 43153350 43153215 1.860000e-36 163.0
30 TraesCS4B01G119900 chr1B 96.536 664 16 7 1 660 647241328 647241988 0.000000e+00 1092.0
31 TraesCS4B01G119900 chr4A 84.468 1146 112 43 418 1515 556781026 556782153 0.000000e+00 1070.0
32 TraesCS4B01G119900 chr4A 89.051 274 20 6 384 655 556804179 556804444 4.820000e-87 331.0
33 TraesCS4B01G119900 chr4A 96.250 80 2 1 1 79 556803852 556803931 1.890000e-26 130.0
34 TraesCS4B01G119900 chr4A 83.333 132 12 9 20 146 624865292 624865166 1.900000e-21 113.0
35 TraesCS4B01G119900 chr4A 82.576 132 13 9 20 146 624887497 624887371 8.840000e-20 108.0
36 TraesCS4B01G119900 chr1D 80.260 1155 142 58 426 1515 55609704 55610837 0.000000e+00 791.0
37 TraesCS4B01G119900 chr1A 80.795 151 17 10 1 146 569202852 569202995 8.840000e-20 108.0
38 TraesCS4B01G119900 chr1A 80.921 152 16 11 1 146 570190954 570191098 8.840000e-20 108.0


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 TraesCS4B01G119900 chr4B 140435107 140437445 2338 True 4320.000000 4320 100.000000 1 2339 1 chr4B.!!$R7 2338
1 TraesCS4B01G119900 chr4B 139939030 139940781 1751 True 2687.000000 2687 94.147000 418 2205 1 chr4B.!!$R5 1787
2 TraesCS4B01G119900 chr4B 61494186 61495530 1344 True 1995.000000 1995 93.266000 966 2339 1 chr4B.!!$R1 1373
3 TraesCS4B01G119900 chr4B 140232168 140234559 2391 True 1819.000000 2636 93.254500 1 2337 2 chr4B.!!$R12 2336
4 TraesCS4B01G119900 chr4B 62048871 62049987 1116 True 1565.000000 1565 91.660000 1178 2337 1 chr4B.!!$R2 1159
5 TraesCS4B01G119900 chr4B 62867751 62868452 701 True 1114.000000 1114 95.211000 1630 2337 1 chr4B.!!$R4 707
6 TraesCS4B01G119900 chr4B 61520885 61524810 3925 False 880.333333 1160 90.702333 1 2337 3 chr4B.!!$F2 2336
7 TraesCS4B01G119900 chr4B 62432174 62436743 4569 True 863.000000 2043 84.789667 7 2337 3 chr4B.!!$R11 2330
8 TraesCS4B01G119900 chr4B 61323056 61325951 2895 True 852.000000 1179 90.314667 1 2337 3 chr4B.!!$R9 2336
9 TraesCS4B01G119900 chr4B 61534519 61537884 3365 False 746.500000 1173 89.274000 1 2337 2 chr4B.!!$F3 2336
10 TraesCS4B01G119900 chr4B 139945292 139945906 614 True 684.000000 684 87.500000 1 593 1 chr4B.!!$R6 592
11 TraesCS4B01G119900 chr4B 62039739 62041146 1407 True 302.500000 333 82.493000 1 743 2 chr4B.!!$R10 742
12 TraesCS4B01G119900 chr4D 43075277 43079007 3730 True 1007.666667 1718 90.037667 20 2339 3 chr4D.!!$R1 2319
13 TraesCS4B01G119900 chr4D 43149632 43153350 3718 True 651.000000 981 87.012000 258 2336 3 chr4D.!!$R2 2078
14 TraesCS4B01G119900 chr1B 647241328 647241988 660 False 1092.000000 1092 96.536000 1 660 1 chr1B.!!$F1 659
15 TraesCS4B01G119900 chr4A 556781026 556782153 1127 False 1070.000000 1070 84.468000 418 1515 1 chr4A.!!$F1 1097
16 TraesCS4B01G119900 chr4A 556803852 556804444 592 False 230.500000 331 92.650500 1 655 2 chr4A.!!$F2 654
17 TraesCS4B01G119900 chr1D 55609704 55610837 1133 False 791.000000 791 80.260000 426 1515 1 chr1D.!!$F1 1089

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
485 4636 2.073816 ACGCCGACAATCTTTTAGTGG 58.926 47.619 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 5866 0.034186 TGACATTCCAGCACATCCCC 60.034 55.0 0.0 0.0 0.0 4.81 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
469 4619 6.201234 TGCTTTGAACCTTTTAAAAATACGCC 59.799 34.615 1.66 0.0 0.00 5.68
485 4636 2.073816 ACGCCGACAATCTTTTAGTGG 58.926 47.619 0.00 0.0 0.00 4.00
486 4637 2.073816 CGCCGACAATCTTTTAGTGGT 58.926 47.619 0.00 0.0 0.00 4.16
487 4638 3.255725 CGCCGACAATCTTTTAGTGGTA 58.744 45.455 0.00 0.0 0.00 3.25
488 4639 3.869246 CGCCGACAATCTTTTAGTGGTAT 59.131 43.478 0.00 0.0 0.00 2.73
495 4646 5.812642 ACAATCTTTTAGTGGTATCTGAGCG 59.187 40.000 0.00 0.0 0.00 5.03
1399 5696 2.037772 TCTGAAGAAGGTCAGCCTGTTC 59.962 50.000 0.00 0.0 46.33 3.18
1535 5866 5.799213 AGTAATCAAGTCAGAAGTCAAGGG 58.201 41.667 0.00 0.0 0.00 3.95
1897 6423 0.321653 AACAGTTCATCGGCAGACCC 60.322 55.000 0.00 0.0 0.00 4.46
2117 6653 1.066573 AGTCGAATCAGCCCAGAACTG 60.067 52.381 0.00 0.0 36.44 3.16
2134 6670 6.079763 CAGAACTGTTTCGATGTGTTTATGG 58.920 40.000 0.00 0.0 36.78 2.74
2251 6787 9.692749 TTCTACAAAGTAGTGTAAGACTGAATG 57.307 33.333 4.30 0.0 35.96 2.67
2285 6825 2.949106 CTCGCTGTTTGGCTGTGG 59.051 61.111 0.00 0.0 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
363 2956 3.074412 CAGGTCTTTGGAACGTATGCTT 58.926 45.455 0.00 0.0 33.70 3.91
469 4619 6.019479 GCTCAGATACCACTAAAAGATTGTCG 60.019 42.308 0.00 0.0 0.00 4.35
487 4638 9.507280 CAATATGTATTTTGAAAACGCTCAGAT 57.493 29.630 0.00 0.0 0.00 2.90
488 4639 8.726068 TCAATATGTATTTTGAAAACGCTCAGA 58.274 29.630 0.00 0.0 0.00 3.27
626 4785 4.806342 AGTTCACCATGTGTTACGAAAC 57.194 40.909 0.00 0.0 34.79 2.78
892 5145 2.206223 GGAAAGGGGATTAGGTCAGGT 58.794 52.381 0.00 0.0 0.00 4.00
1399 5696 3.525537 ACTCTGCAATCCAATAGACACG 58.474 45.455 0.00 0.0 0.00 4.49
1535 5866 0.034186 TGACATTCCAGCACATCCCC 60.034 55.000 0.00 0.0 0.00 4.81
1897 6423 4.402474 ACAAGGTGAAAGGAGAGGTTTTTG 59.598 41.667 0.00 0.0 0.00 2.44
2117 6653 6.020678 GCATAAAGCCATAAACACATCGAAAC 60.021 38.462 0.00 0.0 37.23 2.78
2134 6670 2.877043 CCCATCACTTGGCATAAAGC 57.123 50.000 0.00 0.0 44.97 3.51
2251 6787 2.541762 GCGAGCCAGTCATTATCAGAAC 59.458 50.000 0.00 0.0 0.00 3.01
2285 6825 8.594881 ATTCATATTTGTAGTACAGCAGTAGC 57.405 34.615 2.68 0.0 42.56 3.58


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

AutoCloner maintained by Alex Coulton.