Multiple sequence alignment - TraesCS6B01G255200

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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 TraesCS6B01G255200 chr6B 100.000 2399 0 0 1 2399 459326314 459328712 0.000000e+00 4431
1 TraesCS6B01G255200 chr6B 96.154 1820 68 2 579 2397 292937385 292935567 0.000000e+00 2972
2 TraesCS6B01G255200 chr6B 96.099 1820 66 3 579 2397 296099150 296097335 0.000000e+00 2963
3 TraesCS6B01G255200 chr6B 96.046 1821 68 4 579 2397 329963634 329961816 0.000000e+00 2961
4 TraesCS6B01G255200 chr6B 95.936 1821 71 3 579 2397 293695585 293697404 0.000000e+00 2950
5 TraesCS6B01G255200 chr4B 96.044 1820 69 3 579 2397 494436635 494438452 0.000000e+00 2959
6 TraesCS6B01G255200 chr4B 96.037 1817 70 2 579 2394 580636224 580638039 0.000000e+00 2955
7 TraesCS6B01G255200 chr4B 98.621 580 5 2 1 578 94549139 94548561 0.000000e+00 1024
8 TraesCS6B01G255200 chr1B 95.987 1819 69 3 579 2394 483331094 483332911 0.000000e+00 2952
9 TraesCS6B01G255200 chr1B 86.726 339 30 11 249 578 218668107 218667775 1.750000e-96 363
10 TraesCS6B01G255200 chr7B 95.884 1822 71 3 579 2397 602005084 602006904 0.000000e+00 2946
11 TraesCS6B01G255200 chr7B 95.824 1820 74 2 579 2397 369288438 369290256 0.000000e+00 2939
12 TraesCS6B01G255200 chr7B 98.448 580 7 1 1 578 319870801 319871380 0.000000e+00 1020
13 TraesCS6B01G255200 chr7B 98.443 578 8 1 1 578 319866267 319866843 0.000000e+00 1016
14 TraesCS6B01G255200 chr7B 81.905 420 53 18 174 578 161602690 161603101 1.370000e-87 333
15 TraesCS6B01G255200 chr3B 98.621 580 6 1 1 578 396979375 396979954 0.000000e+00 1026
16 TraesCS6B01G255200 chrUn 86.798 356 34 10 218 565 41660524 41660874 3.740000e-103 385
17 TraesCS6B01G255200 chrUn 85.955 356 37 10 218 565 41664957 41665307 3.770000e-98 368
18 TraesCS6B01G255200 chr2B 85.984 371 37 11 218 579 724010421 724010057 1.350000e-102 383
19 TraesCS6B01G255200 chr2B 85.405 370 39 11 218 578 724014818 724014455 1.050000e-98 370


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 TraesCS6B01G255200 chr6B 459326314 459328712 2398 False 4431 4431 100.0000 1 2399 1 chr6B.!!$F2 2398
1 TraesCS6B01G255200 chr6B 292935567 292937385 1818 True 2972 2972 96.1540 579 2397 1 chr6B.!!$R1 1818
2 TraesCS6B01G255200 chr6B 296097335 296099150 1815 True 2963 2963 96.0990 579 2397 1 chr6B.!!$R2 1818
3 TraesCS6B01G255200 chr6B 329961816 329963634 1818 True 2961 2961 96.0460 579 2397 1 chr6B.!!$R3 1818
4 TraesCS6B01G255200 chr6B 293695585 293697404 1819 False 2950 2950 95.9360 579 2397 1 chr6B.!!$F1 1818
5 TraesCS6B01G255200 chr4B 494436635 494438452 1817 False 2959 2959 96.0440 579 2397 1 chr4B.!!$F1 1818
6 TraesCS6B01G255200 chr4B 580636224 580638039 1815 False 2955 2955 96.0370 579 2394 1 chr4B.!!$F2 1815
7 TraesCS6B01G255200 chr4B 94548561 94549139 578 True 1024 1024 98.6210 1 578 1 chr4B.!!$R1 577
8 TraesCS6B01G255200 chr1B 483331094 483332911 1817 False 2952 2952 95.9870 579 2394 1 chr1B.!!$F1 1815
9 TraesCS6B01G255200 chr7B 602005084 602006904 1820 False 2946 2946 95.8840 579 2397 1 chr7B.!!$F3 1818
10 TraesCS6B01G255200 chr7B 369288438 369290256 1818 False 2939 2939 95.8240 579 2397 1 chr7B.!!$F2 1818
11 TraesCS6B01G255200 chr7B 319866267 319871380 5113 False 1018 1020 98.4455 1 578 2 chr7B.!!$F4 577
12 TraesCS6B01G255200 chr3B 396979375 396979954 579 False 1026 1026 98.6210 1 578 1 chr3B.!!$F1 577

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
897 2436 0.041839 GCTTTGTCGCGGCATCTATG 60.042 55.0 16.97 2.95 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 5888 0.033504 ACGCATCTGACAACCGACTT 59.966 50.0 0.0 0.0 0.0 3.01 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
219 220 9.786105 TGTGCTATATAAATTCATGTGTGTTTG 57.214 29.630 0.00 0.00 0.00 2.93
554 555 2.142319 TCGTAGTTTGGGGCGTAAAAC 58.858 47.619 1.42 1.42 36.69 2.43
573 574 5.892524 AAACCCCCGCTATATTACAACTA 57.107 39.130 0.00 0.00 0.00 2.24
578 579 5.873164 CCCCCGCTATATTACAACTAATCAC 59.127 44.000 0.00 0.00 0.00 3.06
579 580 5.873164 CCCCGCTATATTACAACTAATCACC 59.127 44.000 0.00 0.00 0.00 4.02
580 581 5.873164 CCCGCTATATTACAACTAATCACCC 59.127 44.000 0.00 0.00 0.00 4.61
581 582 6.460781 CCGCTATATTACAACTAATCACCCA 58.539 40.000 0.00 0.00 0.00 4.51
582 583 6.932400 CCGCTATATTACAACTAATCACCCAA 59.068 38.462 0.00 0.00 0.00 4.12
583 584 7.095355 CCGCTATATTACAACTAATCACCCAAC 60.095 40.741 0.00 0.00 0.00 3.77
584 585 7.656137 CGCTATATTACAACTAATCACCCAACT 59.344 37.037 0.00 0.00 0.00 3.16
715 1260 0.166814 GCAGATGTTGACGGACTTGC 59.833 55.000 0.00 0.00 0.00 4.01
726 1271 1.671742 GGACTTGCTCCGGACAAGA 59.328 57.895 34.02 13.08 45.99 3.02
729 1274 2.427506 GACTTGCTCCGGACAAGAAAT 58.572 47.619 34.02 21.57 45.99 2.17
764 1309 2.930562 AAGGCTGGCGAGAGGGTT 60.931 61.111 0.00 0.00 0.00 4.11
768 1313 1.743252 GCTGGCGAGAGGGTTCTTG 60.743 63.158 0.00 0.00 37.81 3.02
803 1348 3.403968 GGAGAGGAACAAACTCCAAGAC 58.596 50.000 0.00 0.00 46.42 3.01
897 2436 0.041839 GCTTTGTCGCGGCATCTATG 60.042 55.000 16.97 2.95 0.00 2.23
1057 2596 0.027586 GCAACTGCTCGAACGTGTTT 59.972 50.000 0.00 0.00 38.21 2.83
1340 3078 2.102578 AGAGCTGGCCGCAAAATATTT 58.897 42.857 19.30 0.00 42.61 1.40
1384 3122 5.640147 ACAACCTGTTAGATGGGATTGAAA 58.360 37.500 0.00 0.00 0.00 2.69
1459 3463 4.223953 TCCTTCTAGCCGGATTGTAGATT 58.776 43.478 5.05 0.00 0.00 2.40
1584 3588 2.124411 AGGCGTAGGGGTCATAATTGT 58.876 47.619 0.00 0.00 0.00 2.71
1994 4000 1.663643 GCGATCAAAAGGTACATGCGA 59.336 47.619 0.00 0.00 0.00 5.10
2180 5800 5.005682 ACAAAGACAGCGAAAAGAAAAATGC 59.994 36.000 0.00 0.00 0.00 3.56
2268 5888 0.893270 CGTTCCATGGGTTTGGCTCA 60.893 55.000 13.02 0.00 36.66 4.26
2325 5945 1.675219 GCCGGTAAGGACTTGGTCA 59.325 57.895 1.90 0.00 45.00 4.02
2398 6160 1.799548 GCAGGCGTAGAACTAGCTCAC 60.800 57.143 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 210 4.379339 GGTTTACACCACAAACACACAT 57.621 40.909 0.00 0.00 43.61 3.21
554 555 5.873164 GTGATTAGTTGTAATATAGCGGGGG 59.127 44.000 0.00 0.00 0.00 5.40
573 574 1.632589 GGCCTCAAAGTTGGGTGATT 58.367 50.000 0.00 0.00 0.00 2.57
578 579 2.597217 TGCGGCCTCAAAGTTGGG 60.597 61.111 0.00 0.00 0.00 4.12
579 580 1.898574 AGTGCGGCCTCAAAGTTGG 60.899 57.895 0.00 0.00 0.00 3.77
580 581 1.165907 TCAGTGCGGCCTCAAAGTTG 61.166 55.000 0.00 0.00 0.00 3.16
581 582 1.148273 TCAGTGCGGCCTCAAAGTT 59.852 52.632 0.00 0.00 0.00 2.66
582 583 1.598130 GTCAGTGCGGCCTCAAAGT 60.598 57.895 0.00 0.00 0.00 2.66
583 584 2.328099 GGTCAGTGCGGCCTCAAAG 61.328 63.158 0.00 0.00 0.00 2.77
584 585 2.281484 GGTCAGTGCGGCCTCAAA 60.281 61.111 0.00 0.00 0.00 2.69
715 1260 4.363999 CAGTAGCTATTTCTTGTCCGGAG 58.636 47.826 3.06 0.00 0.00 4.63
726 1271 2.009774 CAACTGGCGCAGTAGCTATTT 58.990 47.619 10.83 0.00 44.62 1.40
729 1274 0.606096 TTCAACTGGCGCAGTAGCTA 59.394 50.000 10.83 0.00 44.62 3.32
764 1309 0.535780 CCTGCTGCACCTTCACAAGA 60.536 55.000 0.00 0.00 0.00 3.02
768 1313 0.673022 CTCTCCTGCTGCACCTTCAC 60.673 60.000 0.00 0.00 0.00 3.18
1057 2596 4.783621 GCCACTCATCGCCTGCCA 62.784 66.667 0.00 0.00 0.00 4.92
1297 3035 3.055819 ACTTGGTCGTACATCAAGCTCAT 60.056 43.478 14.45 0.00 40.90 2.90
1340 3078 6.428083 TGTCTAATTTACAGTCCTGTTGGA 57.572 37.500 5.10 0.00 41.83 3.53
1384 3122 8.746530 TCGTCAAACTGACTAATTATACTCCTT 58.253 33.333 5.34 0.00 44.85 3.36
1437 3441 3.308035 TCTACAATCCGGCTAGAAGGA 57.692 47.619 8.74 8.74 41.30 3.36
1459 3463 1.757682 AAGGTCCGCAAAGACAAACA 58.242 45.000 1.50 0.00 38.59 2.83
1584 3588 6.430000 GCTAGTTGGGAACTTGTCTGATAAAA 59.570 38.462 0.00 0.00 42.81 1.52
1680 3684 0.034186 CACTTTAGGGCATGCCTCCA 60.034 55.000 34.70 17.92 36.10 3.86
1705 3709 2.086510 TGCTATTTTCGCAGTCCGC 58.913 52.632 0.00 0.00 36.73 5.54
1937 3943 6.431543 TCGATATGACTTAAGTTTTGGCCAAA 59.568 34.615 27.13 27.13 0.00 3.28
1994 4000 3.255642 GCCCAACACATGTGTCATACTTT 59.744 43.478 30.64 11.51 44.13 2.66
2056 4566 5.295292 GTGCTACTCACACTCGTTATACCTA 59.705 44.000 0.00 0.00 44.98 3.08
2180 5800 1.277557 CTCCTTCCTCTGTCCACCTTG 59.722 57.143 0.00 0.00 0.00 3.61
2248 5868 0.893727 GAGCCAAACCCATGGAACGT 60.894 55.000 15.22 0.00 43.54 3.99
2268 5888 0.033504 ACGCATCTGACAACCGACTT 59.966 50.000 0.00 0.00 0.00 3.01
2343 5963 4.223144 AGGACAAACTTAAGCCCAAATGT 58.777 39.130 1.29 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.