Multiple sequence alignment - TraesCS6D01G101500

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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 TraesCS6D01G101500 chr6D 100.000 4544 0 0 1 4544 65050672 65055215 0.000000e+00 8392.0
1 TraesCS6D01G101500 chr6D 92.562 3321 174 37 622 3896 65361424 65358131 0.000000e+00 4697.0
2 TraesCS6D01G101500 chr6D 85.482 1412 170 17 968 2354 65095181 65093780 0.000000e+00 1439.0
3 TraesCS6D01G101500 chr6D 82.609 1380 182 35 999 2352 63817296 63815949 0.000000e+00 1166.0
4 TraesCS6D01G101500 chr6D 77.844 1002 171 32 2867 3850 65093658 65092690 1.420000e-159 573.0
5 TraesCS6D01G101500 chr6D 82.982 617 53 19 3250 3837 65341677 65341084 1.130000e-140 510.0
6 TraesCS6D01G101500 chr6D 89.790 333 33 1 135 467 65363301 65362970 4.200000e-115 425.0
7 TraesCS6D01G101500 chr6D 84.562 434 46 14 3976 4390 65358134 65357703 1.180000e-110 411.0
8 TraesCS6D01G101500 chr6D 82.766 441 40 19 3978 4393 65352075 65351646 1.200000e-95 361.0
9 TraesCS6D01G101500 chr6D 87.755 147 14 2 2545 2690 10312267 10312410 7.820000e-38 169.0
10 TraesCS6D01G101500 chr6D 90.984 122 6 3 3720 3836 65357577 65357456 4.710000e-35 159.0
11 TraesCS6D01G101500 chr6D 94.565 92 5 0 3889 3980 41237201 41237292 4.740000e-30 143.0
12 TraesCS6D01G101500 chr6B 97.980 4555 75 10 1 4544 139882778 139887326 0.000000e+00 7886.0
13 TraesCS6D01G101500 chr6B 93.425 1901 75 17 831 2689 140367437 140365545 0.000000e+00 2772.0
14 TraesCS6D01G101500 chr6B 85.020 1502 156 27 966 2433 140333532 140332066 0.000000e+00 1463.0
15 TraesCS6D01G101500 chr6B 85.605 1306 152 23 968 2255 140097446 140096159 0.000000e+00 1338.0
16 TraesCS6D01G101500 chr6B 85.089 845 86 22 1 810 140368261 140367422 0.000000e+00 826.0
17 TraesCS6D01G101500 chr6B 77.358 1060 175 44 2818 3850 140094804 140093783 6.600000e-158 568.0
18 TraesCS6D01G101500 chr6B 82.500 320 27 16 4066 4365 140354589 140354279 2.100000e-63 254.0
19 TraesCS6D01G101500 chr6B 95.455 88 4 0 3892 3979 179236253 179236340 1.700000e-29 141.0
20 TraesCS6D01G101500 chr6A 90.316 1993 126 26 466 2437 83434564 83436510 0.000000e+00 2549.0
21 TraesCS6D01G101500 chr6A 92.954 1249 72 12 2761 3998 83436988 83438231 0.000000e+00 1805.0
22 TraesCS6D01G101500 chr6A 85.231 1449 170 26 957 2373 83644506 83645942 0.000000e+00 1450.0
23 TraesCS6D01G101500 chr6A 84.902 1477 166 24 966 2418 83599499 83600942 0.000000e+00 1439.0
24 TraesCS6D01G101500 chr6A 83.075 1418 196 25 999 2406 81191957 81190574 0.000000e+00 1249.0
25 TraesCS6D01G101500 chr6A 83.745 769 115 6 2782 3544 83600876 83601640 0.000000e+00 719.0
26 TraesCS6D01G101500 chr6A 77.516 1103 179 43 2820 3889 83645988 83647054 2.340000e-167 599.0
27 TraesCS6D01G101500 chr6A 86.627 501 40 18 4053 4543 83438235 83438718 3.110000e-146 529.0
28 TraesCS6D01G101500 chr6A 81.841 391 32 18 3461 3833 83439331 83439700 4.450000e-75 292.0
29 TraesCS6D01G101500 chr6A 92.437 119 7 2 3720 3836 83440281 83440399 7.820000e-38 169.0
30 TraesCS6D01G101500 chrUn 94.077 1165 56 10 2739 3891 388715148 388713985 0.000000e+00 1757.0
31 TraesCS6D01G101500 chrUn 87.079 178 10 3 2636 2800 388715305 388715128 6.000000e-44 189.0
32 TraesCS6D01G101500 chr5B 80.020 1011 149 27 2783 3773 261675472 261674495 0.000000e+00 699.0
33 TraesCS6D01G101500 chr5B 80.911 571 95 6 1866 2432 261675957 261675397 5.400000e-119 438.0
34 TraesCS6D01G101500 chr5B 93.684 95 4 2 3892 3984 554776750 554776656 1.700000e-29 141.0
35 TraesCS6D01G101500 chr4D 85.714 154 19 1 2537 2690 508013196 508013046 4.710000e-35 159.0
36 TraesCS6D01G101500 chr7D 97.727 88 2 0 2430 2517 165657947 165657860 7.870000e-33 152.0
37 TraesCS6D01G101500 chr4A 95.745 94 4 0 3886 3979 511040579 511040486 7.870000e-33 152.0
38 TraesCS6D01G101500 chr3D 84.177 158 21 1 2533 2690 187220266 187220113 2.830000e-32 150.0
39 TraesCS6D01G101500 chr3D 90.741 108 6 4 3879 3986 302930484 302930381 1.700000e-29 141.0
40 TraesCS6D01G101500 chr3D 87.037 54 7 0 390 443 405441974 405442027 1.360000e-05 62.1
41 TraesCS6D01G101500 chr1A 96.703 91 2 1 2428 2518 27361940 27362029 2.830000e-32 150.0
42 TraesCS6D01G101500 chr1A 94.565 92 5 0 3888 3979 527084022 527083931 4.740000e-30 143.0
43 TraesCS6D01G101500 chr1D 95.652 92 3 1 3889 3979 42391712 42391803 3.660000e-31 147.0
44 TraesCS6D01G101500 chr3B 95.556 90 4 0 3895 3984 11070083 11069994 1.320000e-30 145.0
45 TraesCS6D01G101500 chr3B 100.000 32 0 0 261 292 416509443 416509412 4.910000e-05 60.2
46 TraesCS6D01G101500 chr5D 96.341 82 3 0 2435 2516 294637753 294637672 7.930000e-28 135.0
47 TraesCS6D01G101500 chr5D 91.667 84 6 1 2437 2519 294637677 294637760 1.030000e-21 115.0
48 TraesCS6D01G101500 chr2D 92.593 81 5 1 2435 2514 579535336 579535256 1.030000e-21 115.0
49 TraesCS6D01G101500 chr7B 88.043 92 5 2 2432 2518 489866965 489867055 2.240000e-18 104.0
50 TraesCS6D01G101500 chr7A 100.000 29 0 0 222 250 667344295 667344267 2.000000e-03 54.7


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 TraesCS6D01G101500 chr6D 65050672 65055215 4543 False 8392.0 8392 100.0000 1 4544 1 chr6D.!!$F3 4543
1 TraesCS6D01G101500 chr6D 65357456 65363301 5845 True 1423.0 4697 89.4745 135 4390 4 chr6D.!!$R5 4255
2 TraesCS6D01G101500 chr6D 63815949 63817296 1347 True 1166.0 1166 82.6090 999 2352 1 chr6D.!!$R1 1353
3 TraesCS6D01G101500 chr6D 65092690 65095181 2491 True 1006.0 1439 81.6630 968 3850 2 chr6D.!!$R4 2882
4 TraesCS6D01G101500 chr6D 65341084 65341677 593 True 510.0 510 82.9820 3250 3837 1 chr6D.!!$R2 587
5 TraesCS6D01G101500 chr6B 139882778 139887326 4548 False 7886.0 7886 97.9800 1 4544 1 chr6B.!!$F1 4543
6 TraesCS6D01G101500 chr6B 140365545 140368261 2716 True 1799.0 2772 89.2570 1 2689 2 chr6B.!!$R4 2688
7 TraesCS6D01G101500 chr6B 140332066 140333532 1466 True 1463.0 1463 85.0200 966 2433 1 chr6B.!!$R1 1467
8 TraesCS6D01G101500 chr6B 140093783 140097446 3663 True 953.0 1338 81.4815 968 3850 2 chr6B.!!$R3 2882
9 TraesCS6D01G101500 chr6A 81190574 81191957 1383 True 1249.0 1249 83.0750 999 2406 1 chr6A.!!$R1 1407
10 TraesCS6D01G101500 chr6A 83599499 83601640 2141 False 1079.0 1439 84.3235 966 3544 2 chr6A.!!$F2 2578
11 TraesCS6D01G101500 chr6A 83434564 83440399 5835 False 1068.8 2549 88.8350 466 4543 5 chr6A.!!$F1 4077
12 TraesCS6D01G101500 chr6A 83644506 83647054 2548 False 1024.5 1450 81.3735 957 3889 2 chr6A.!!$F3 2932
13 TraesCS6D01G101500 chrUn 388713985 388715305 1320 True 973.0 1757 90.5780 2636 3891 2 chrUn.!!$R1 1255
14 TraesCS6D01G101500 chr5B 261674495 261675957 1462 True 568.5 699 80.4655 1866 3773 2 chr5B.!!$R2 1907

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
383 384 0.249868 CACGTCTGAGGCCAAAGACA 60.250 55.000 27.76 11.06 42.45 3.41 F
722 2114 1.154263 CAGACCGAGAACCGACGTC 60.154 63.158 5.18 5.18 41.76 4.34 F
888 2304 2.264794 CCCGTACAGCCAGTCCAC 59.735 66.667 0.00 0.00 0.00 4.02 F
1765 3269 2.281208 TCGGCCTTTTCCACACCG 60.281 61.111 0.00 0.00 45.15 4.94 F
2572 5369 3.506067 GGGGATGTTTCAACGAACTTCAT 59.494 43.478 0.00 0.00 36.15 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 3269 2.675317 CGACTTCCCTGTCCTTGATGAC 60.675 54.545 0.0 0.0 33.70 3.06 R
2572 5369 2.281484 GCCACGTTCTTCAGCCCA 60.281 61.111 0.0 0.0 0.00 5.36 R
2780 6050 7.591421 TCACCATCGATAAACAAGTATAGGA 57.409 36.000 0.0 0.0 0.00 2.94 R
3258 6530 2.368011 GCCTCCCTCCACTACCACC 61.368 68.421 0.0 0.0 0.00 4.61 R
4457 9410 0.318441 CCGACAGCAAGAGTTCCTCA 59.682 55.000 0.0 0.0 32.06 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
196 197 1.893137 TCACTGCTGGACACGATACTT 59.107 47.619 0.00 0.00 0.00 2.24
205 206 1.549170 GACACGATACTTGACCACCCT 59.451 52.381 0.00 0.00 0.00 4.34
217 218 1.746615 CCACCCTTGCACGATCCAG 60.747 63.158 0.00 0.00 0.00 3.86
329 330 2.748209 CCCCGATAATGGAAGGGTTT 57.252 50.000 0.00 0.00 42.26 3.27
383 384 0.249868 CACGTCTGAGGCCAAAGACA 60.250 55.000 27.76 11.06 42.45 3.41
511 581 3.202595 ACCCCGGCTTATTTAACATACCA 59.797 43.478 0.00 0.00 0.00 3.25
722 2114 1.154263 CAGACCGAGAACCGACGTC 60.154 63.158 5.18 5.18 41.76 4.34
888 2304 2.264794 CCCGTACAGCCAGTCCAC 59.735 66.667 0.00 0.00 0.00 4.02
895 2311 3.941188 AGCCAGTCCACCACGGTG 61.941 66.667 9.36 9.36 45.02 4.94
986 2412 2.736682 CGCCGACAAAACCCTAGCG 61.737 63.158 0.00 0.00 35.82 4.26
1765 3269 2.281208 TCGGCCTTTTCCACACCG 60.281 61.111 0.00 0.00 45.15 4.94
1935 3439 3.877559 TGAAATCATTGTCGAGGATGCT 58.122 40.909 0.00 0.00 0.00 3.79
2418 5201 9.698309 GATATCAGCTTATTCAACTGCTAGTTA 57.302 33.333 0.00 0.00 36.03 2.24
2572 5369 3.506067 GGGGATGTTTCAACGAACTTCAT 59.494 43.478 0.00 0.00 36.15 2.57
2780 6050 9.295825 TCGATAATATGGCATTTTGATACCTTT 57.704 29.630 4.78 0.00 0.00 3.11
3258 6530 2.234661 TGGAAGTAGTGGCAGTGATGAG 59.765 50.000 4.76 0.00 0.00 2.90
3307 6579 1.674962 GTTCTGCTGATGAGGGCAATC 59.325 52.381 0.00 0.00 38.02 2.67
3356 6628 2.845659 TGATGTGGTAATGGAGGGAGT 58.154 47.619 0.00 0.00 0.00 3.85
3781 7093 3.590466 ATGTGGAAGTGCCCTGGCC 62.590 63.158 5.57 0.00 41.09 5.36
4123 7474 1.267806 CACATTTTCAGGCTGCGTTCT 59.732 47.619 10.34 0.00 0.00 3.01
4165 7516 5.988561 TGTTTCCCAAAATTATGCTTGTGTC 59.011 36.000 0.00 0.00 0.00 3.67
4445 9398 1.555075 GGGTGTGTGGCTTGATAGAGA 59.445 52.381 0.00 0.00 0.00 3.10
4457 9410 4.443034 GCTTGATAGAGAACCCCGTGTATT 60.443 45.833 0.00 0.00 0.00 1.89
4496 9449 6.156602 TGTCGGATTGTAACCCTATCCTTTAA 59.843 38.462 0.00 0.00 41.64 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 6.563398 TCGTCGTGTGTATCAATATTGTTC 57.437 37.500 14.97 7.60 0.00 3.18
196 197 1.003839 GATCGTGCAAGGGTGGTCA 60.004 57.895 0.00 0.00 0.00 4.02
205 206 0.537143 AGGCAAACTGGATCGTGCAA 60.537 50.000 0.00 0.00 38.78 4.08
217 218 3.013921 TGGTTTATCCGATGAGGCAAAC 58.986 45.455 0.00 0.00 40.70 2.93
383 384 9.067986 TGAGTGAGTTTCGTAGATCATATGTAT 57.932 33.333 1.90 0.00 35.04 2.29
1765 3269 2.675317 CGACTTCCCTGTCCTTGATGAC 60.675 54.545 0.00 0.00 33.70 3.06
2409 5192 7.841956 ACTATATAGCAATGGGTAACTAGCAG 58.158 38.462 9.78 0.00 0.00 4.24
2418 5201 6.323737 ACAGAGGTACTATATAGCAATGGGT 58.676 40.000 9.78 0.00 41.55 4.51
2467 5258 6.983890 AGACGTTTTGGCAGTTTAATTTGAAT 59.016 30.769 0.00 0.00 0.00 2.57
2572 5369 2.281484 GCCACGTTCTTCAGCCCA 60.281 61.111 0.00 0.00 0.00 5.36
2722 5536 8.548880 AGTATAGGGAAGATAACAAGTGCTAA 57.451 34.615 0.00 0.00 0.00 3.09
2780 6050 7.591421 TCACCATCGATAAACAAGTATAGGA 57.409 36.000 0.00 0.00 0.00 2.94
3258 6530 2.368011 GCCTCCCTCCACTACCACC 61.368 68.421 0.00 0.00 0.00 4.61
3307 6579 4.440802 GCTACTACTTCCACCTGATGACAG 60.441 50.000 0.00 0.00 43.12 3.51
3781 7093 3.547813 GCCAAAAGGCCAAACAATTTTCG 60.548 43.478 5.01 0.00 0.00 3.46
3949 7297 7.844779 TCCCTCTGTAAAGAAATATAGGAGTGT 59.155 37.037 0.00 0.00 0.00 3.55
4123 7474 6.239458 GGGAAACAATGGGAACTACAAATTCA 60.239 38.462 0.00 0.00 0.00 2.57
4165 7516 3.058520 CCGTATCGTTGTTACAACTGTCG 59.941 47.826 23.27 19.72 0.00 4.35
4436 9389 4.712829 TCAATACACGGGGTTCTCTATCAA 59.287 41.667 0.00 0.00 0.00 2.57
4445 9398 1.982958 AGTTCCTCAATACACGGGGTT 59.017 47.619 0.00 0.00 0.00 4.11
4457 9410 0.318441 CCGACAGCAAGAGTTCCTCA 59.682 55.000 0.00 0.00 32.06 3.86
4474 9427 6.823497 TCTTAAAGGATAGGGTTACAATCCG 58.177 40.000 5.41 0.00 43.33 4.18
4496 9449 9.905713 TTGGCAAGATCAATAGTAGTTTATTCT 57.094 29.630 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.