Multiple sequence alignment - TraesCS6A01G163800

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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 TraesCS6A01G163800 chr6A 100.000 9471 0 0 1 9471 158985736 158976266 0 17490
1 TraesCS6A01G163800 chr2A 97.086 9505 222 23 1 9471 685106596 685097113 0 15967
2 TraesCS6A01G163800 chr2A 97.044 9506 233 20 1 9469 284797622 284807116 0 15954
3 TraesCS6A01G163800 chr2A 96.940 9509 237 23 1 9471 572972212 572962720 0 15898
4 TraesCS6A01G163800 chr2A 96.760 9507 238 31 1 9471 80117342 80126814 0 15786
5 TraesCS6A01G163800 chr2A 96.539 9506 264 28 1 9471 716656443 716646968 0 15671
6 TraesCS6A01G163800 chr5A 97.033 9504 237 12 1 9471 541974609 541984100 0 15946
7 TraesCS6A01G163800 chr5A 96.920 9513 234 24 1 9471 34945654 34936159 0 15889
8 TraesCS6A01G163800 chr5A 96.918 9506 225 25 1 9471 465651849 465661321 0 15869
9 TraesCS6A01G163800 chr3A 96.592 9507 258 24 1 9471 554825167 554834643 0 15701
10 TraesCS6A01G163800 chr7B 94.984 7377 301 33 3 7320 300039242 300046608 0 11509
11 TraesCS6A01G163800 chr7B 94.720 6231 279 23 1 6188 192835697 192829474 0 9638
12 TraesCS6A01G163800 chr6B 94.641 7389 313 38 1 7336 85660551 85667909 0 11374
13 TraesCS6A01G163800 chr3B 94.330 7390 355 34 1 7336 545974848 545967469 0 11267
14 TraesCS6A01G163800 chr1A 97.353 6348 136 7 3152 9471 70944907 70938564 0 10763
15 TraesCS6A01G163800 chr2B 94.762 6224 281 20 1 6188 514559300 514553086 0 9646
16 TraesCS6A01G163800 chr4B 94.933 6118 262 16 1 6082 173399794 173393689 0 9537


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 TraesCS6A01G163800 chr6A 158976266 158985736 9470 True 17490 17490 100.000 1 9471 1 chr6A.!!$R1 9470
1 TraesCS6A01G163800 chr2A 685097113 685106596 9483 True 15967 15967 97.086 1 9471 1 chr2A.!!$R2 9470
2 TraesCS6A01G163800 chr2A 284797622 284807116 9494 False 15954 15954 97.044 1 9469 1 chr2A.!!$F2 9468
3 TraesCS6A01G163800 chr2A 572962720 572972212 9492 True 15898 15898 96.940 1 9471 1 chr2A.!!$R1 9470
4 TraesCS6A01G163800 chr2A 80117342 80126814 9472 False 15786 15786 96.760 1 9471 1 chr2A.!!$F1 9470
5 TraesCS6A01G163800 chr2A 716646968 716656443 9475 True 15671 15671 96.539 1 9471 1 chr2A.!!$R3 9470
6 TraesCS6A01G163800 chr5A 541974609 541984100 9491 False 15946 15946 97.033 1 9471 1 chr5A.!!$F2 9470
7 TraesCS6A01G163800 chr5A 34936159 34945654 9495 True 15889 15889 96.920 1 9471 1 chr5A.!!$R1 9470
8 TraesCS6A01G163800 chr5A 465651849 465661321 9472 False 15869 15869 96.918 1 9471 1 chr5A.!!$F1 9470
9 TraesCS6A01G163800 chr3A 554825167 554834643 9476 False 15701 15701 96.592 1 9471 1 chr3A.!!$F1 9470
10 TraesCS6A01G163800 chr7B 300039242 300046608 7366 False 11509 11509 94.984 3 7320 1 chr7B.!!$F1 7317
11 TraesCS6A01G163800 chr7B 192829474 192835697 6223 True 9638 9638 94.720 1 6188 1 chr7B.!!$R1 6187
12 TraesCS6A01G163800 chr6B 85660551 85667909 7358 False 11374 11374 94.641 1 7336 1 chr6B.!!$F1 7335
13 TraesCS6A01G163800 chr3B 545967469 545974848 7379 True 11267 11267 94.330 1 7336 1 chr3B.!!$R1 7335
14 TraesCS6A01G163800 chr1A 70938564 70944907 6343 True 10763 10763 97.353 3152 9471 1 chr1A.!!$R1 6319
15 TraesCS6A01G163800 chr2B 514553086 514559300 6214 True 9646 9646 94.762 1 6188 1 chr2B.!!$R1 6187
16 TraesCS6A01G163800 chr4B 173393689 173399794 6105 True 9537 9537 94.933 1 6082 1 chr4B.!!$R1 6081

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
790 797 1.264020 GTCTTTTCTGCGTGCATGTCA 59.736 47.619 7.93 5.39 0.00 3.58 F
1058 1065 0.247814 GAACTCGACGCCATGCATTG 60.248 55.000 0.00 0.00 0.00 2.82 F
1463 1506 0.535102 GGGGTAAGGTCATGCGGATG 60.535 60.000 11.15 11.15 0.00 3.51 F
2953 3012 0.246360 CACCACCATAGAGACGTGCA 59.754 55.000 0.00 0.00 0.00 4.57 F
3211 3288 0.251165 CCCTCGTTCCCACAAACCAT 60.251 55.000 0.00 0.00 0.00 3.55 F
3271 3348 1.072331 GTCTCTCTCCAAAGCCCACAA 59.928 52.381 0.00 0.00 0.00 3.33 F
3371 3448 1.216178 CGACATTAACGTCCCCGGT 59.784 57.895 0.00 0.00 38.78 5.28 F
3561 3638 1.279271 CCAACGAAGATGAACCTCCCT 59.721 52.381 0.00 0.00 29.10 4.20 F
4389 4476 4.745125 CGACAAAGAGAAGCTGAAGTTGTA 59.255 41.667 0.00 0.00 0.00 2.41 F
6493 6731 3.096092 AGTTTTGAGCAACAACTCCCAA 58.904 40.909 0.00 0.00 38.29 4.12 F
7165 7426 0.466372 AGGCCGACGAGATGATGAGA 60.466 55.000 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 1884 0.893270 CCCCGAATGTTGTGCCTTGA 60.893 55.000 0.00 0.0 0.00 3.02 R
2941 3000 1.066143 CCCCACTTTGCACGTCTCTAT 60.066 52.381 0.00 0.0 0.00 1.98 R
3211 3288 0.817013 GGAAATGGAAGCGGCAATGA 59.183 50.000 1.45 0.0 0.00 2.57 R
4347 4434 1.069296 CGCTTTCAATGCTGAAACCGA 60.069 47.619 9.39 0.0 46.51 4.69 R
4389 4476 1.129058 GGGGTTGATCTCCATACCGT 58.871 55.000 9.12 0.0 36.51 4.83 R
4538 4629 3.305813 CCGCACAGTTTGTAGTCTTCCTA 60.306 47.826 0.00 0.0 0.00 2.94 R
4955 5049 5.401531 ACGTTCCATTCAGAAGCTACTTA 57.598 39.130 0.00 0.0 0.00 2.24 R
6188 6422 1.639534 GTTCGTTGTGGTGTGGACG 59.360 57.895 0.00 0.0 36.89 4.79 R
6714 6969 1.001633 TGTCCTGGAAGAACTAACCGC 59.998 52.381 0.00 0.0 34.07 5.68 R
8452 8721 2.041251 TTCATGCATCTTCATCCGCA 57.959 45.000 0.00 0.0 39.01 5.69 R
9331 9606 6.815641 TGTTTGTGTTGTTTGATGCTTGTATT 59.184 30.769 0.00 0.0 0.00 1.89 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
114 115 8.223330 AGAAATGGATATCAGCCTACTTCAAAT 58.777 33.333 4.83 0.00 0.00 2.32
196 197 7.489757 GCTCAAGAAGAACTACGTAAATGAGAT 59.510 37.037 0.00 0.00 34.06 2.75
282 283 2.632537 ACCAGGAGACAATGGGTAACT 58.367 47.619 0.00 0.00 41.13 2.24
397 401 6.469410 ACAATTTGGTCATCATTCTTGCATT 58.531 32.000 0.78 0.00 0.00 3.56
501 505 6.072397 GCGAGATCAGAGATAGGCTAAAACTA 60.072 42.308 0.00 0.00 0.00 2.24
769 776 6.045955 GCACCTCTTCCAAAAACAAATACAA 58.954 36.000 0.00 0.00 0.00 2.41
790 797 1.264020 GTCTTTTCTGCGTGCATGTCA 59.736 47.619 7.93 5.39 0.00 3.58
1036 1043 3.314080 GGTCGTCATGGACAAACTTGAAA 59.686 43.478 4.76 0.00 38.70 2.69
1058 1065 0.247814 GAACTCGACGCCATGCATTG 60.248 55.000 0.00 0.00 0.00 2.82
1063 1070 1.704387 CGACGCCATGCATTGTGCTA 61.704 55.000 11.01 0.00 45.31 3.49
1192 1199 2.113986 AGCAGCAACCGGAGCTTT 59.886 55.556 20.63 11.20 41.14 3.51
1354 1361 0.701147 AAAGGGGAGGAAGAGCAAGG 59.299 55.000 0.00 0.00 0.00 3.61
1463 1506 0.535102 GGGGTAAGGTCATGCGGATG 60.535 60.000 11.15 11.15 0.00 3.51
1656 1699 1.115326 GCAAAGTGGGCAAGGAGGTT 61.115 55.000 0.00 0.00 0.00 3.50
1745 1788 6.030548 AGAAGAGTTTGATGAGAATGACGA 57.969 37.500 0.00 0.00 0.00 4.20
1841 1884 3.178540 AACCTGGAAAGAGCGCCGT 62.179 57.895 2.29 0.00 0.00 5.68
2580 2635 1.799933 AAGCTATGCCTGCTCCTACT 58.200 50.000 0.00 0.00 40.22 2.57
2941 3000 2.234896 AAATGCCATCATCACCACCA 57.765 45.000 0.00 0.00 31.27 4.17
2953 3012 0.246360 CACCACCATAGAGACGTGCA 59.754 55.000 0.00 0.00 0.00 4.57
3007 3067 4.607955 TGACAAGACTAGTCAGTTCAACG 58.392 43.478 24.44 6.09 40.80 4.10
3211 3288 0.251165 CCCTCGTTCCCACAAACCAT 60.251 55.000 0.00 0.00 0.00 3.55
3271 3348 1.072331 GTCTCTCTCCAAAGCCCACAA 59.928 52.381 0.00 0.00 0.00 3.33
3301 3378 1.504275 AAGGCCATGGCAGAGGAACT 61.504 55.000 36.56 20.19 43.35 3.01
3371 3448 1.216178 CGACATTAACGTCCCCGGT 59.784 57.895 0.00 0.00 38.78 5.28
3561 3638 1.279271 CCAACGAAGATGAACCTCCCT 59.721 52.381 0.00 0.00 29.10 4.20
3765 3842 5.222079 TGTGAAAAGTGGATGCACTACTA 57.778 39.130 21.06 4.96 39.36 1.82
4347 4434 4.805192 GCATGACAAGTTGTTCACATTTGT 59.195 37.500 10.45 9.06 37.00 2.83
4389 4476 4.745125 CGACAAAGAGAAGCTGAAGTTGTA 59.255 41.667 0.00 0.00 0.00 2.41
4538 4629 5.336213 GGCATGAAGAACAAGATCAACACAT 60.336 40.000 0.00 0.00 0.00 3.21
4558 4649 5.120830 CACATAGGAAGACTACAAACTGTGC 59.879 44.000 0.00 0.00 33.45 4.57
6229 6463 6.382821 CGATCTGCTCGTAAAATAATCTCC 57.617 41.667 0.00 0.00 42.56 3.71
6493 6731 3.096092 AGTTTTGAGCAACAACTCCCAA 58.904 40.909 0.00 0.00 38.29 4.12
6592 6830 6.244654 TGGAAAAACATCACAGATCCATACA 58.755 36.000 0.00 0.00 30.90 2.29
6635 6890 3.882444 CCATCATCACAACCACAGAGAT 58.118 45.455 0.00 0.00 0.00 2.75
6732 6987 0.611714 GGCGGTTAGTTCTTCCAGGA 59.388 55.000 0.00 0.00 0.00 3.86
7048 7309 3.187700 GAGCAACCTCGTCGACATTAAT 58.812 45.455 17.16 0.00 0.00 1.40
7165 7426 0.466372 AGGCCGACGAGATGATGAGA 60.466 55.000 0.00 0.00 0.00 3.27
8393 8662 4.001618 TGGAAGACAATCGACAACATCA 57.998 40.909 0.00 0.00 0.00 3.07
8452 8721 2.039879 CCCCTACTACCACTGCAACTTT 59.960 50.000 0.00 0.00 0.00 2.66
8534 8803 6.259167 TGTGTGTGTCCTTAGTATTGTTGTTC 59.741 38.462 0.00 0.00 0.00 3.18
8537 8806 6.430000 GTGTGTCCTTAGTATTGTTGTTCCAT 59.570 38.462 0.00 0.00 0.00 3.41
9331 9606 6.757897 ATCACAAGAAACACAACAGAAGAA 57.242 33.333 0.00 0.00 0.00 2.52
9336 9611 7.967854 CACAAGAAACACAACAGAAGAAATACA 59.032 33.333 0.00 0.00 0.00 2.29
9430 9706 4.814771 AGTTTATTCGGTAAGTGCTATGCC 59.185 41.667 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.192212 GTCTTTTCCAGGCATCCTCAAAG 59.808 47.826 0.00 0.00 0.00 2.77
114 115 5.292765 TGTCATTTTGGCGCAGAAAATTTA 58.707 33.333 20.66 12.59 31.96 1.40
282 283 4.519350 CGACAAGTGATAGAGCTATACCCA 59.481 45.833 0.00 0.00 0.00 4.51
397 401 2.733858 GCGTGTTTTGTTCCTTCTGCAA 60.734 45.455 0.00 0.00 0.00 4.08
501 505 1.373497 CGCCGTGAAGAGAGTGCTT 60.373 57.895 0.00 0.00 0.00 3.91
743 750 3.799281 TTGTTTTTGGAAGAGGTGCAG 57.201 42.857 0.00 0.00 0.00 4.41
769 776 1.532868 GACATGCACGCAGAAAAGACT 59.467 47.619 0.00 0.00 0.00 3.24
952 959 3.044059 GCACCCTCATGTTCAGCGC 62.044 63.158 0.00 0.00 0.00 5.92
1036 1043 0.602638 TGCATGGCGTCGAGTTCTTT 60.603 50.000 0.00 0.00 0.00 2.52
1058 1065 3.364964 CGTGACACCTCCATTTTTAGCAC 60.365 47.826 0.00 0.00 0.00 4.40
1063 1070 2.227194 GTCCGTGACACCTCCATTTTT 58.773 47.619 0.00 0.00 32.09 1.94
1389 1432 4.740822 ATGGGGCGTGGTGGCTTC 62.741 66.667 0.00 0.00 44.11 3.86
1453 1496 2.752939 CGTTGCAGCATCCGCATGA 61.753 57.895 0.00 0.00 42.27 3.07
1463 1506 0.727122 GTTGCTCATGACGTTGCAGC 60.727 55.000 7.34 6.61 36.75 5.25
1656 1699 4.323485 CCCTGTTTATGTTCAGCTCCACTA 60.323 45.833 0.00 0.00 0.00 2.74
1745 1788 4.271696 TCATTGTCTTCGTCTGATTGGT 57.728 40.909 0.00 0.00 0.00 3.67
1841 1884 0.893270 CCCCGAATGTTGTGCCTTGA 60.893 55.000 0.00 0.00 0.00 3.02
2304 2348 2.741759 TAATGTCACTGCTTCAGCGA 57.258 45.000 0.00 0.00 45.83 4.93
2484 2534 2.069273 CTTTTGTACTGCCGACTGAGG 58.931 52.381 0.00 0.00 0.00 3.86
2580 2635 5.250543 TGATGGTCTTTCTGAATTGGGACTA 59.749 40.000 0.00 0.00 0.00 2.59
2941 3000 1.066143 CCCCACTTTGCACGTCTCTAT 60.066 52.381 0.00 0.00 0.00 1.98
2953 3012 1.119684 GACCTGCAAAACCCCACTTT 58.880 50.000 0.00 0.00 0.00 2.66
3007 3067 5.921976 CCGTCCAAGTTAAATGGTTTTTACC 59.078 40.000 8.08 0.00 39.09 2.85
3068 3128 4.893601 TTCGTCGTGGCAACCGCA 62.894 61.111 0.00 0.00 41.24 5.69
3211 3288 0.817013 GGAAATGGAAGCGGCAATGA 59.183 50.000 1.45 0.00 0.00 2.57
3371 3448 2.260434 GTGTACCCGCGCTTCTCA 59.740 61.111 5.56 0.00 0.00 3.27
3382 3459 1.798813 CTTTGAGCGTTCTGGTGTACC 59.201 52.381 0.00 0.00 0.00 3.34
3561 3638 3.220222 CAGGACTGCCGCCATCTA 58.780 61.111 0.00 0.00 39.96 1.98
3709 3786 7.549147 AGTACATCTAGTTGGGAAACAAGTA 57.451 36.000 5.80 0.00 42.58 2.24
4347 4434 1.069296 CGCTTTCAATGCTGAAACCGA 60.069 47.619 9.39 0.00 46.51 4.69
4389 4476 1.129058 GGGGTTGATCTCCATACCGT 58.871 55.000 9.12 0.00 36.51 4.83
4538 4629 3.305813 CCGCACAGTTTGTAGTCTTCCTA 60.306 47.826 0.00 0.00 0.00 2.94
4955 5049 5.401531 ACGTTCCATTCAGAAGCTACTTA 57.598 39.130 0.00 0.00 0.00 2.24
6188 6422 1.639534 GTTCGTTGTGGTGTGGACG 59.360 57.895 0.00 0.00 36.89 4.79
6229 6463 4.631740 GGTTGGGGGTGGGGGTTG 62.632 72.222 0.00 0.00 0.00 3.77
6592 6830 4.559153 GCATTTTGCACTGTTTAGGTGAT 58.441 39.130 0.00 0.00 44.26 3.06
6635 6890 2.161855 CTGCTAAATCCCACTTGCACA 58.838 47.619 0.00 0.00 0.00 4.57
6714 6969 1.001633 TGTCCTGGAAGAACTAACCGC 59.998 52.381 0.00 0.00 34.07 5.68
6781 7036 1.079621 TAGTGGTCGTGGGGGTCAT 59.920 57.895 0.00 0.00 0.00 3.06
7165 7426 1.611965 GCCCTTCATCCTGAGCCTT 59.388 57.895 0.00 0.00 0.00 4.35
7700 7966 4.083110 AGTGCTTGATACATCTTTGTGCAC 60.083 41.667 10.75 10.75 45.62 4.57
8393 8662 6.953520 TCTTTTGAAATATCCCAACCTGTCAT 59.046 34.615 0.00 0.00 0.00 3.06
8452 8721 2.041251 TTCATGCATCTTCATCCGCA 57.959 45.000 0.00 0.00 39.01 5.69
8534 8803 9.009327 CATAACGAAAGCAAACTACAAATATGG 57.991 33.333 0.00 0.00 0.00 2.74
8537 8806 9.388346 CAACATAACGAAAGCAAACTACAAATA 57.612 29.630 0.00 0.00 0.00 1.40
9331 9606 6.815641 TGTTTGTGTTGTTTGATGCTTGTATT 59.184 30.769 0.00 0.00 0.00 1.89
9336 9611 7.840342 TTATTGTTTGTGTTGTTTGATGCTT 57.160 28.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.