Multiple sequence alignment - TraesCS6A01G038200

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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 TraesCS6A01G038200 chr6A 100.000 3202 0 0 1 3202 18793086 18789885 0.000000e+00 5914
1 TraesCS6A01G038200 chr6A 96.019 3215 95 8 1 3202 575506505 575509699 0.000000e+00 5197
2 TraesCS6A01G038200 chr6B 96.263 3211 103 6 1 3202 70703175 70706377 0.000000e+00 5249
3 TraesCS6A01G038200 chr5B 96.233 3212 105 6 1 3202 127791147 127787942 0.000000e+00 5247
4 TraesCS6A01G038200 chr5B 95.951 3211 114 6 1 3202 708888186 708891389 0.000000e+00 5195
5 TraesCS6A01G038200 chr5B 95.951 3211 108 8 1 3202 689153781 689156978 0.000000e+00 5190
6 TraesCS6A01G038200 chr4A 96.228 3208 105 6 4 3202 701547924 701544724 0.000000e+00 5240
7 TraesCS6A01G038200 chr4A 95.951 3211 115 6 1 3202 718590776 718587572 0.000000e+00 5195
8 TraesCS6A01G038200 chr4B 96.171 3212 109 5 1 3202 664138274 664141481 0.000000e+00 5238
9 TraesCS6A01G038200 chr4B 96.221 3202 106 5 10 3202 664113355 664116550 0.000000e+00 5228
10 TraesCS6A01G038200 chrUn 96.167 3209 103 8 1 3200 194097419 194100616 0.000000e+00 5227
11 TraesCS6A01G038200 chrUn 96.230 1777 57 3 1435 3202 344447650 344445875 0.000000e+00 2902
12 TraesCS6A01G038200 chrUn 96.772 1704 50 3 1 1704 345189777 345188079 0.000000e+00 2837
13 TraesCS6A01G038200 chrUn 96.655 1704 52 3 1 1704 345187368 345185670 0.000000e+00 2826
14 TraesCS6A01G038200 chr3B 95.823 3208 99 7 3 3201 766123650 766120469 0.000000e+00 5149
15 TraesCS6A01G038200 chr2A 95.467 3221 106 12 4 3202 3028653 3025451 0.000000e+00 5103
16 TraesCS6A01G038200 chr2A 95.034 3222 107 25 1 3202 772273915 772277103 0.000000e+00 5014
17 TraesCS6A01G038200 chr3A 89.625 1041 46 21 1395 2387 733180471 733179445 0.000000e+00 1267
18 TraesCS6A01G038200 chr7A 87.749 1004 85 32 1395 2387 538320532 538321508 0.000000e+00 1138
19 TraesCS6A01G038200 chr7A 90.377 478 31 11 1482 1952 705514357 705514826 5.870000e-172 614


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 TraesCS6A01G038200 chr6A 18789885 18793086 3201 True 5914.0 5914 100.0000 1 3202 1 chr6A.!!$R1 3201
1 TraesCS6A01G038200 chr6A 575506505 575509699 3194 False 5197.0 5197 96.0190 1 3202 1 chr6A.!!$F1 3201
2 TraesCS6A01G038200 chr6B 70703175 70706377 3202 False 5249.0 5249 96.2630 1 3202 1 chr6B.!!$F1 3201
3 TraesCS6A01G038200 chr5B 127787942 127791147 3205 True 5247.0 5247 96.2330 1 3202 1 chr5B.!!$R1 3201
4 TraesCS6A01G038200 chr5B 708888186 708891389 3203 False 5195.0 5195 95.9510 1 3202 1 chr5B.!!$F2 3201
5 TraesCS6A01G038200 chr5B 689153781 689156978 3197 False 5190.0 5190 95.9510 1 3202 1 chr5B.!!$F1 3201
6 TraesCS6A01G038200 chr4A 701544724 701547924 3200 True 5240.0 5240 96.2280 4 3202 1 chr4A.!!$R1 3198
7 TraesCS6A01G038200 chr4A 718587572 718590776 3204 True 5195.0 5195 95.9510 1 3202 1 chr4A.!!$R2 3201
8 TraesCS6A01G038200 chr4B 664138274 664141481 3207 False 5238.0 5238 96.1710 1 3202 1 chr4B.!!$F2 3201
9 TraesCS6A01G038200 chr4B 664113355 664116550 3195 False 5228.0 5228 96.2210 10 3202 1 chr4B.!!$F1 3192
10 TraesCS6A01G038200 chrUn 194097419 194100616 3197 False 5227.0 5227 96.1670 1 3200 1 chrUn.!!$F1 3199
11 TraesCS6A01G038200 chrUn 344445875 344447650 1775 True 2902.0 2902 96.2300 1435 3202 1 chrUn.!!$R1 1767
12 TraesCS6A01G038200 chrUn 345185670 345189777 4107 True 2831.5 2837 96.7135 1 1704 2 chrUn.!!$R2 1703
13 TraesCS6A01G038200 chr3B 766120469 766123650 3181 True 5149.0 5149 95.8230 3 3201 1 chr3B.!!$R1 3198
14 TraesCS6A01G038200 chr2A 3025451 3028653 3202 True 5103.0 5103 95.4670 4 3202 1 chr2A.!!$R1 3198
15 TraesCS6A01G038200 chr2A 772273915 772277103 3188 False 5014.0 5014 95.0340 1 3202 1 chr2A.!!$F1 3201
16 TraesCS6A01G038200 chr3A 733179445 733180471 1026 True 1267.0 1267 89.6250 1395 2387 1 chr3A.!!$R1 992
17 TraesCS6A01G038200 chr7A 538320532 538321508 976 False 1138.0 1138 87.7490 1395 2387 1 chr7A.!!$F1 992

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
121 122 0.734309 ACACGACATACGACGGCATA 59.266 50.0 0.0 0.0 45.77 3.14 F
942 980 0.760567 ATCTGCCTCCACCATCGCTA 60.761 55.0 0.0 0.0 0.00 4.26 F
974 1012 1.550130 AAGGCGGAGGAATCGTGGAA 61.550 55.0 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 4474 0.251341 GTTTGGCAGTGGGATGTCCT 60.251 55.000 0.0 0.0 36.2 3.85 R
2098 4480 0.467290 GAGGTTGTTTGGCAGTGGGA 60.467 55.000 0.0 0.0 0.0 4.37 R
2204 4586 1.072159 CCAATGATCCTCCGCCTCC 59.928 63.158 0.0 0.0 0.0 4.30 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
121 122 0.734309 ACACGACATACGACGGCATA 59.266 50.000 0.00 0.00 45.77 3.14
197 198 7.469181 GCAACAAAAGGATCAGAAGAGAAAAGA 60.469 37.037 0.00 0.00 0.00 2.52
266 267 7.977904 TCGATTACATCTAAGTTGAACGACTA 58.022 34.615 0.00 0.00 0.00 2.59
380 381 2.284625 ACTCATGGGACCGGAGCA 60.285 61.111 9.46 0.00 31.88 4.26
421 422 2.093021 TCCTGATGGTCATGAAATCGCA 60.093 45.455 0.00 0.00 34.23 5.10
446 447 3.994392 CGTTGTCAGCCTACATTTGTAGT 59.006 43.478 14.81 0.00 44.88 2.73
627 632 6.381133 TCTCTTAATATGGTTGCAGTGAGAGA 59.619 38.462 0.00 0.00 35.03 3.10
637 642 5.183904 GGTTGCAGTGAGAGAAAAATATGGT 59.816 40.000 0.00 0.00 0.00 3.55
699 713 2.365635 CCCACGTCTCCCCTCCAT 60.366 66.667 0.00 0.00 0.00 3.41
707 721 3.521937 ACGTCTCCCCTCCATATTTTTCA 59.478 43.478 0.00 0.00 0.00 2.69
898 936 1.211456 CTGCTCCATCTTCCTCCCTT 58.789 55.000 0.00 0.00 0.00 3.95
915 953 1.272092 CCTTTGCCTCCACCATCAAGA 60.272 52.381 0.00 0.00 0.00 3.02
923 961 2.040278 CTCCACCATCAAGAAACTCCCA 59.960 50.000 0.00 0.00 0.00 4.37
942 980 0.760567 ATCTGCCTCCACCATCGCTA 60.761 55.000 0.00 0.00 0.00 4.26
974 1012 1.550130 AAGGCGGAGGAATCGTGGAA 61.550 55.000 0.00 0.00 0.00 3.53
1141 1179 3.499737 CCGTGCCGCTCATGGTTC 61.500 66.667 6.05 0.00 45.01 3.62
1463 1510 4.174009 TGAAGTAGACGCAATAGTTCTGC 58.826 43.478 9.68 0.00 34.85 4.26
1960 4341 1.978542 GACAAGTACGTCGACATGCT 58.021 50.000 17.16 6.35 0.00 3.79
1967 4348 2.097160 GTCGACATGCTGCGCAAG 59.903 61.111 13.05 7.04 43.62 4.01
2092 4474 4.340617 GAATTGGACCACAAACTATGGGA 58.659 43.478 0.00 0.00 43.46 4.37
2098 4480 2.919602 ACCACAAACTATGGGAGGACAT 59.080 45.455 0.00 0.00 41.97 3.06
2200 4582 5.302568 TCGTCAAAGAAGGTTTGGAGTACTA 59.697 40.000 0.00 0.00 0.00 1.82
2204 4586 4.810191 AGAAGGTTTGGAGTACTAGCAG 57.190 45.455 0.00 0.00 0.00 4.24
2253 4635 5.607171 CCCTACTACTGGGGATATTGAGTTT 59.393 44.000 0.00 0.00 45.18 2.66
2351 4757 8.546597 AGCTTTTGTTATGTTGAACAAGTTTT 57.453 26.923 0.62 0.00 46.88 2.43
2442 4848 7.825761 AGAACACTTATGATTGTGATGTGATGA 59.174 33.333 5.51 0.00 37.59 2.92
2452 4858 7.815549 TGATTGTGATGTGATGAAAAATCCTTG 59.184 33.333 0.00 0.00 0.00 3.61
3051 5461 1.694169 AGTGGGGGATCTGGCGATT 60.694 57.895 0.00 0.00 0.00 3.34
3131 5541 2.028020 CCTACTTCGGATGGGCCTAATC 60.028 54.545 4.53 6.56 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 3.573538 TGTTGTTTGGCTTGTGCATAGAT 59.426 39.130 0.00 0.00 41.91 1.98
197 198 8.752187 ACCATGAATTGTGCTATTAATGTCTTT 58.248 29.630 0.00 0.00 28.16 2.52
266 267 7.451255 TGAATTGTATGTCTCTTTGGTTTGGAT 59.549 33.333 0.00 0.00 0.00 3.41
380 381 2.203070 GACGGCGGCTTCATCCAT 60.203 61.111 13.24 0.00 0.00 3.41
446 447 3.069443 TGTGCAGTGAGATAGACACAACA 59.931 43.478 0.00 0.00 40.25 3.33
488 489 6.551736 CATCCATCGACCGTTCTTTATTTTT 58.448 36.000 0.00 0.00 0.00 1.94
599 604 6.888105 TCACTGCAACCATATTAAGAGATCA 58.112 36.000 0.00 0.00 0.00 2.92
826 844 2.880890 AGATTGAGCGGCAATGGAATAC 59.119 45.455 11.73 0.00 46.90 1.89
898 936 2.158475 AGTTTCTTGATGGTGGAGGCAA 60.158 45.455 0.00 0.00 0.00 4.52
915 953 0.329596 GTGGAGGCAGATGGGAGTTT 59.670 55.000 0.00 0.00 0.00 2.66
923 961 0.760567 TAGCGATGGTGGAGGCAGAT 60.761 55.000 0.00 0.00 0.00 2.90
956 994 1.987855 TTCCACGATTCCTCCGCCT 60.988 57.895 0.00 0.00 0.00 5.52
974 1012 2.584391 GCAGACGGAGGGGAGTTGT 61.584 63.158 0.00 0.00 0.00 3.32
1141 1179 5.609423 CTTCTCCTTCTTCAGGTGGATATG 58.391 45.833 0.00 0.00 44.37 1.78
1463 1510 8.194104 ACTAGTATTGCATCTACTTCAGAACTG 58.806 37.037 13.00 0.00 36.67 3.16
1960 4341 1.301716 GGAACTCTCCACTTGCGCA 60.302 57.895 5.66 5.66 41.96 6.09
2092 4474 0.251341 GTTTGGCAGTGGGATGTCCT 60.251 55.000 0.00 0.00 36.20 3.85
2098 4480 0.467290 GAGGTTGTTTGGCAGTGGGA 60.467 55.000 0.00 0.00 0.00 4.37
2200 4582 2.841988 GATCCTCCGCCTCCTGCT 60.842 66.667 0.00 0.00 38.05 4.24
2204 4586 1.072159 CCAATGATCCTCCGCCTCC 59.928 63.158 0.00 0.00 0.00 4.30
2253 4635 8.349245 CAAACTGAGACACATAATACCACAAAA 58.651 33.333 0.00 0.00 0.00 2.44
2351 4757 8.196771 AGCAAACTTGTTCATCATTACAAAAGA 58.803 29.630 0.00 0.00 34.17 2.52
2428 4834 7.898918 TCAAGGATTTTTCATCACATCACAAT 58.101 30.769 0.00 0.00 0.00 2.71
2442 4848 7.563906 TGATCACCAAAAGTTCAAGGATTTTT 58.436 30.769 0.00 0.00 0.00 1.94
2452 4858 9.185192 CTTGAACTAAATGATCACCAAAAGTTC 57.815 33.333 20.48 20.48 39.58 3.01
2638 5046 3.620472 GCCAAATTGGATGCATTCAGGTT 60.620 43.478 17.47 4.90 40.96 3.50
2707 5115 7.013369 CACTATTGGACACATACAGTAGAGCTA 59.987 40.741 0.00 0.00 33.56 3.32
2976 5386 4.798682 CTCCACCCCCGCTACCCT 62.799 72.222 0.00 0.00 0.00 4.34
3051 5461 3.931631 CTGTGGCCTCCCTCCCTCA 62.932 68.421 3.32 0.00 0.00 3.86
3131 5541 0.184933 TCCAAATTAGGCCCATCCGG 59.815 55.000 0.00 0.00 40.77 5.14


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

AutoCloner maintained by Alex Coulton.