Multiple sequence alignment - TraesCS6D01G328300

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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 TraesCS6D01G328300 chr6D 100.000 3113 0 0 1 3113 433156240 433153128 0.000000e+00 5749
1 TraesCS6D01G328300 chr6D 93.145 2626 163 10 122 2734 432932317 432929696 0.000000e+00 3836
2 TraesCS6D01G328300 chr6D 94.204 2398 115 15 1 2383 433281584 433279196 0.000000e+00 3637
3 TraesCS6D01G328300 chr6D 89.202 1880 184 9 711 2585 433259310 433257445 0.000000e+00 2329
4 TraesCS6D01G328300 chr6D 90.348 1782 157 6 809 2586 432914545 432912775 0.000000e+00 2324
5 TraesCS6D01G328300 chr6D 88.245 638 72 3 2379 3015 433279038 433278403 0.000000e+00 760
6 TraesCS6D01G328300 chr6D 81.183 558 85 12 25 579 432915292 432914752 6.170000e-117 431
7 TraesCS6D01G328300 chr6B 93.445 2395 132 14 1 2380 653873556 653871172 0.000000e+00 3530
8 TraesCS6D01G328300 chr6B 91.156 1696 127 18 1416 3102 653698578 653696897 0.000000e+00 2279
9 TraesCS6D01G328300 chr6B 87.805 1886 187 21 711 2586 653715832 653713980 0.000000e+00 2169
10 TraesCS6D01G328300 chr6B 88.081 1787 191 11 809 2585 653856640 653854866 0.000000e+00 2100
11 TraesCS6D01G328300 chr6B 90.286 1400 106 15 1 1395 653699945 653698571 0.000000e+00 1805
12 TraesCS6D01G328300 chr6B 88.006 642 73 4 2375 3015 653871014 653870376 0.000000e+00 756
13 TraesCS6D01G328300 chr6A 93.134 2403 136 15 1 2380 579144056 579141660 0.000000e+00 3496
14 TraesCS6D01G328300 chr6A 87.051 641 81 2 2375 3015 579141502 579140864 0.000000e+00 723
15 TraesCS6D01G328300 chr7D 83.462 520 81 5 2597 3113 461202129 461201612 2.170000e-131 479
16 TraesCS6D01G328300 chr7D 76.389 432 76 14 1 422 500745095 500745510 3.150000e-50 209
17 TraesCS6D01G328300 chr2D 83.205 518 80 7 2601 3113 638304936 638305451 4.700000e-128 468
18 TraesCS6D01G328300 chr2D 82.692 520 79 11 2601 3113 604075054 604074539 4.730000e-123 451
19 TraesCS6D01G328300 chr5D 82.785 517 83 6 2601 3113 487270113 487270627 1.020000e-124 457
20 TraesCS6D01G328300 chr5A 82.819 518 82 7 2601 3113 589001987 589002502 1.020000e-124 457


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 TraesCS6D01G328300 chr6D 433153128 433156240 3112 True 5749.0 5749 100.0000 1 3113 1 chr6D.!!$R2 3112
1 TraesCS6D01G328300 chr6D 432929696 432932317 2621 True 3836.0 3836 93.1450 122 2734 1 chr6D.!!$R1 2612
2 TraesCS6D01G328300 chr6D 433257445 433259310 1865 True 2329.0 2329 89.2020 711 2585 1 chr6D.!!$R3 1874
3 TraesCS6D01G328300 chr6D 433278403 433281584 3181 True 2198.5 3637 91.2245 1 3015 2 chr6D.!!$R5 3014
4 TraesCS6D01G328300 chr6D 432912775 432915292 2517 True 1377.5 2324 85.7655 25 2586 2 chr6D.!!$R4 2561
5 TraesCS6D01G328300 chr6B 653713980 653715832 1852 True 2169.0 2169 87.8050 711 2586 1 chr6B.!!$R1 1875
6 TraesCS6D01G328300 chr6B 653870376 653873556 3180 True 2143.0 3530 90.7255 1 3015 2 chr6B.!!$R4 3014
7 TraesCS6D01G328300 chr6B 653854866 653856640 1774 True 2100.0 2100 88.0810 809 2585 1 chr6B.!!$R2 1776
8 TraesCS6D01G328300 chr6B 653696897 653699945 3048 True 2042.0 2279 90.7210 1 3102 2 chr6B.!!$R3 3101
9 TraesCS6D01G328300 chr6A 579140864 579144056 3192 True 2109.5 3496 90.0925 1 3015 2 chr6A.!!$R1 3014
10 TraesCS6D01G328300 chr7D 461201612 461202129 517 True 479.0 479 83.4620 2597 3113 1 chr7D.!!$R1 516
11 TraesCS6D01G328300 chr2D 638304936 638305451 515 False 468.0 468 83.2050 2601 3113 1 chr2D.!!$F1 512
12 TraesCS6D01G328300 chr2D 604074539 604075054 515 True 451.0 451 82.6920 2601 3113 1 chr2D.!!$R1 512
13 TraesCS6D01G328300 chr5D 487270113 487270627 514 False 457.0 457 82.7850 2601 3113 1 chr5D.!!$F1 512
14 TraesCS6D01G328300 chr5A 589001987 589002502 515 False 457.0 457 82.8190 2601 3113 1 chr5A.!!$F1 512

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
766 811 0.306228 CGTCAACATCACCGTGCAAA 59.694 50.0 0.0 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2655 2895 0.994247 AATCCATGGACTCACCTGCA 59.006 50.0 18.99 0.0 39.86 4.41 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
23 24 3.997681 TCGGTTCTTGCGTATCATTTTCA 59.002 39.130 0.00 0.00 0.00 2.69
179 180 2.600173 CCCAACAACCCGCACCAT 60.600 61.111 0.00 0.00 0.00 3.55
262 272 9.436957 AATACTTCTGTGAAATTGTTAGTCGAT 57.563 29.630 0.00 0.00 0.00 3.59
397 408 3.950397 AGCATTGTTTGGACTCCGAATA 58.050 40.909 0.74 0.00 0.00 1.75
558 570 4.199310 TGGCATGCTACAAGGATTCTTAC 58.801 43.478 18.92 0.00 0.00 2.34
583 595 9.854303 ACCTATATTCTTTGTAGGTACCCATAT 57.146 33.333 8.74 0.00 44.76 1.78
679 715 1.261619 GCATTGCATAGACGGTAGCAC 59.738 52.381 3.15 0.00 36.62 4.40
694 730 7.170998 AGACGGTAGCACACTTATATATTTTGC 59.829 37.037 0.00 0.00 0.00 3.68
766 811 0.306228 CGTCAACATCACCGTGCAAA 59.694 50.000 0.00 0.00 0.00 3.68
835 880 6.312180 CCAGACGGTAAGTACCTTTGATTTAC 59.688 42.308 5.97 0.00 44.25 2.01
1009 1064 4.403432 CCATCAAATATACCATGGCCATCC 59.597 45.833 17.61 0.00 29.71 3.51
1195 1250 1.425066 AGGTCTTCAAGGCCAATGTCA 59.575 47.619 11.62 0.00 44.17 3.58
1203 1258 2.564062 CAAGGCCAATGTCAGGTTCATT 59.436 45.455 5.01 0.00 36.16 2.57
1256 1311 6.131264 TCTATTTGGGCATCAATCAGTTCAT 58.869 36.000 0.00 0.00 34.98 2.57
1332 1387 1.296715 CTTGCAGCGGGTTCCTACT 59.703 57.895 0.00 0.00 0.00 2.57
1539 1596 2.445682 TTGTAGGTTGTTGTTGGGCT 57.554 45.000 0.00 0.00 0.00 5.19
1584 1641 3.254903 AGGGCATCGTTAAACTCAAAACC 59.745 43.478 0.00 0.00 0.00 3.27
1631 1688 4.074259 CAAGAGTTGGTGGATTGTGATGA 58.926 43.478 0.00 0.00 0.00 2.92
1734 1791 5.598830 CACTGAGTCCAACTACCCATATACT 59.401 44.000 0.00 0.00 0.00 2.12
1857 1914 1.869767 GCAAGTCAACCTGTCTCAGTG 59.130 52.381 0.00 0.00 0.00 3.66
1902 1959 3.243267 CGTTCCAGTTTTACAAAGGTGGG 60.243 47.826 5.17 0.00 0.00 4.61
2107 2164 0.992695 GGAGCCTTCTTACCCCACTT 59.007 55.000 0.00 0.00 0.00 3.16
2116 2173 5.425539 CCTTCTTACCCCACTTCATAGAAGA 59.574 44.000 13.23 0.00 39.45 2.87
2136 2193 3.055167 AGAAGTGCCATATGCCGCATATA 60.055 43.478 22.58 7.72 35.18 0.86
2139 2196 3.009723 GTGCCATATGCCGCATATACTT 58.990 45.455 22.58 2.24 35.18 2.24
2145 2202 6.515832 CCATATGCCGCATATACTTCTATGA 58.484 40.000 22.58 0.00 35.18 2.15
2282 2339 9.979578 TCAATGAATACAATGTAAATTATGCCC 57.020 29.630 0.00 0.00 0.00 5.36
2328 2391 9.764363 AGAATTTGTGTTAGCTATATCATTCGA 57.236 29.630 0.00 0.00 0.00 3.71
2499 2735 5.865552 GGTGGAACAAAATGATGAATGTCAG 59.134 40.000 0.00 0.00 44.16 3.51
2591 2828 0.687354 CCCACAACACCAGCTAGACT 59.313 55.000 0.00 0.00 0.00 3.24
2595 2832 3.449018 CCACAACACCAGCTAGACTAGAT 59.551 47.826 13.91 3.71 0.00 1.98
2599 2836 7.268586 CACAACACCAGCTAGACTAGATATTT 58.731 38.462 13.91 0.00 0.00 1.40
2655 2895 1.843206 GCCTTTCTCCCCTCAATCTCT 59.157 52.381 0.00 0.00 0.00 3.10
2771 3013 6.543100 CAGATAGGTAGAGTTTTAGTCCTCGT 59.457 42.308 0.00 0.00 32.88 4.18
2780 3023 2.215451 TTAGTCCTCGTAGGGGCGGT 62.215 60.000 1.76 0.00 35.59 5.68
2860 3103 3.446873 TCAAATTCGTTCATTGGGATGGG 59.553 43.478 0.00 0.00 33.93 4.00
2871 3114 1.887797 TGGGATGGGTTAGACGGAAT 58.112 50.000 0.00 0.00 0.00 3.01
2900 3143 1.065564 AGATTCCTGCCAGCTCTTCAC 60.066 52.381 0.00 0.00 0.00 3.18
2935 3178 1.571919 GTTTCTCGCCGTGCATATCT 58.428 50.000 0.00 0.00 0.00 1.98
3087 3333 2.737180 CAGTATGGGAGCGGCGAT 59.263 61.111 12.98 2.76 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.395941 CTCCCCTTGATTTGTAGGGCTAT 59.604 47.826 0.00 0.00 40.18 2.97
179 180 0.813184 CGGTCACCCTAAGAAGCGTA 59.187 55.000 0.00 0.00 0.00 4.42
245 255 5.051641 CGCTCCTATCGACTAACAATTTCAC 60.052 44.000 0.00 0.00 0.00 3.18
262 272 2.675423 ACCACGCAGACGCTCCTA 60.675 61.111 0.00 0.00 45.53 2.94
279 289 2.034066 ACCGGACGTACTTCCCGA 59.966 61.111 9.46 0.00 45.58 5.14
583 595 0.683973 TACCTACCCCGCAACGAAAA 59.316 50.000 0.00 0.00 0.00 2.29
587 599 2.185093 GGTACCTACCCCGCAACG 59.815 66.667 4.06 0.00 40.53 4.10
674 710 6.007703 GGGGGCAAAATATATAAGTGTGCTA 58.992 40.000 10.31 0.00 0.00 3.49
700 736 8.120538 TCCTATGTATCTTTATAGTGTAGGGGG 58.879 40.741 0.00 0.00 0.00 5.40
701 737 9.543231 TTCCTATGTATCTTTATAGTGTAGGGG 57.457 37.037 0.00 0.00 0.00 4.79
737 782 4.475944 GGTGATGTTGACGGATTTTTCTG 58.524 43.478 0.00 0.00 0.00 3.02
766 811 4.067896 CAAACAGACTTAGCTGGATGTGT 58.932 43.478 0.00 0.00 40.20 3.72
835 880 0.806102 CGTCTAGTGGGCGGATGTTG 60.806 60.000 0.00 0.00 0.00 3.33
976 1026 5.597594 TGGTATATTTGATGGATTGCTTGCA 59.402 36.000 0.00 0.00 0.00 4.08
1009 1064 5.093849 AGGCCAATGATCAAAGATTTTGG 57.906 39.130 16.05 16.05 37.31 3.28
1149 1204 1.409064 CGGTATGCCTTCTCAGTAGCA 59.591 52.381 0.00 0.00 40.00 3.49
1195 1250 3.185797 GCGTTAAACGACTCAATGAACCT 59.814 43.478 0.00 0.00 46.05 3.50
1332 1387 5.892119 ACTTAGATTCTCGTACCTGAATCCA 59.108 40.000 21.79 12.54 45.62 3.41
1520 1577 2.445682 AGCCCAACAACAACCTACAA 57.554 45.000 0.00 0.00 0.00 2.41
1584 1641 1.929836 GACAGTGAGATAAGCTTGCCG 59.070 52.381 9.86 0.00 0.00 5.69
1734 1791 1.007502 GCACTTGTCATTTGCCGCA 60.008 52.632 0.00 0.00 0.00 5.69
1857 1914 2.217510 TATCTCCTCCATCTACGGCC 57.782 55.000 0.00 0.00 0.00 6.13
1902 1959 2.292267 CCACATGAGCCAGTCATTACC 58.708 52.381 0.00 0.00 44.05 2.85
2328 2391 1.539827 GGCGGCACAATTAACAGTCTT 59.460 47.619 3.07 0.00 0.00 3.01
2422 2656 7.717436 TCAACTCCGCCATTTTCACATATTATA 59.283 33.333 0.00 0.00 0.00 0.98
2440 2674 9.619316 TCAACATTTATTTACAAATCAACTCCG 57.381 29.630 0.00 0.00 0.00 4.63
2499 2735 5.862924 TCATTTCCTCAAGATTCACGAAC 57.137 39.130 0.00 0.00 0.00 3.95
2545 2782 3.270027 CGACCAGGACAATAGCAATTCA 58.730 45.455 0.00 0.00 0.00 2.57
2546 2783 3.270877 ACGACCAGGACAATAGCAATTC 58.729 45.455 0.00 0.00 0.00 2.17
2591 2828 8.204836 CGAGAGGGGAAAGAAAAGAAATATCTA 58.795 37.037 0.00 0.00 33.77 1.98
2595 2832 4.941873 GCGAGAGGGGAAAGAAAAGAAATA 59.058 41.667 0.00 0.00 0.00 1.40
2599 2836 1.697432 TGCGAGAGGGGAAAGAAAAGA 59.303 47.619 0.00 0.00 0.00 2.52
2655 2895 0.994247 AATCCATGGACTCACCTGCA 59.006 50.000 18.99 0.00 39.86 4.41
2737 2979 1.424302 TCTACCTATCTGCTAGCCGGT 59.576 52.381 13.29 12.68 0.00 5.28
2757 2999 1.829849 GCCCCTACGAGGACTAAAACT 59.170 52.381 0.00 0.00 37.67 2.66
2771 3013 2.751688 GTCCAAACACCGCCCCTA 59.248 61.111 0.00 0.00 0.00 3.53
2780 3023 0.389757 TGTCGTCATCCGTCCAAACA 59.610 50.000 0.00 0.00 37.94 2.83
2871 3114 0.539986 GGCAGGAATCTACACCGGAA 59.460 55.000 9.46 0.00 0.00 4.30
2900 3143 1.196127 GAAACCTTAACCTCGTTGCCG 59.804 52.381 0.00 0.00 0.00 5.69
2914 3157 0.178068 ATATGCACGGCGAGAAACCT 59.822 50.000 16.62 0.00 0.00 3.50
2935 3178 3.248495 TGACACCAAATATCGCCGTTA 57.752 42.857 0.00 0.00 0.00 3.18
2964 3207 4.612259 GCCATTGAATCCTTGAATCGATCG 60.612 45.833 9.36 9.36 0.00 3.69
3027 3272 0.535102 ACAGCCGGAAGTCTTTGTGG 60.535 55.000 5.05 0.00 0.00 4.17
3071 3317 0.539901 ACTATCGCCGCTCCCATACT 60.540 55.000 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.