Multiple sequence alignment - TraesCS2B01G420200

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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 TraesCS2B01G420200 chr2B 100.000 2549 0 0 1 2549 602077751 602075203 0 4708
1 TraesCS2B01G420200 chr2B 96.425 1986 62 6 564 2549 543889473 543887497 0 3265
2 TraesCS2B01G420200 chr2B 96.233 1991 69 4 561 2549 596962063 596964049 0 3256
3 TraesCS2B01G420200 chr2B 96.274 1986 65 6 564 2549 544319644 544317668 0 3249
4 TraesCS2B01G420200 chr2B 92.933 566 40 0 1 566 704164811 704165376 0 824
5 TraesCS2B01G420200 chr7B 96.576 1986 61 6 565 2548 621924190 621926170 0 3284
6 TraesCS2B01G420200 chr7B 96.171 1985 67 6 566 2549 718488475 718486499 0 3236
7 TraesCS2B01G420200 chr7B 94.523 566 29 1 1 566 583673296 583673859 0 872
8 TraesCS2B01G420200 chr7B 93.816 566 35 0 1 566 168485433 168485998 0 852
9 TraesCS2B01G420200 chr7B 92.756 566 41 0 1 566 335008085 335007520 0 819
10 TraesCS2B01G420200 chr5B 96.474 1985 65 5 566 2549 269389472 269391452 0 3273
11 TraesCS2B01G420200 chr5B 96.382 1990 65 5 562 2549 446193260 446191276 0 3269
12 TraesCS2B01G420200 chr5B 93.463 566 37 0 1 566 648492039 648491474 0 841
13 TraesCS2B01G420200 chr5B 92.756 566 40 1 1 566 588601029 588600465 0 817
14 TraesCS2B01G420200 chr1B 96.376 1987 66 5 564 2549 663786492 663788473 0 3265
15 TraesCS2B01G420200 chr1B 93.286 566 38 0 1 566 38005428 38005993 0 835
16 TraesCS2B01G420200 chr3B 96.131 1990 66 9 562 2549 703251163 703253143 0 3238
17 TraesCS2B01G420200 chr3B 92.933 566 38 2 1 566 640637308 640636745 0 822
18 TraesCS2B01G420200 chr4B 94.170 566 33 0 1 566 672904700 672904135 0 863


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 TraesCS2B01G420200 chr2B 602075203 602077751 2548 True 4708 4708 100.000 1 2549 1 chr2B.!!$R3 2548
1 TraesCS2B01G420200 chr2B 543887497 543889473 1976 True 3265 3265 96.425 564 2549 1 chr2B.!!$R1 1985
2 TraesCS2B01G420200 chr2B 596962063 596964049 1986 False 3256 3256 96.233 561 2549 1 chr2B.!!$F1 1988
3 TraesCS2B01G420200 chr2B 544317668 544319644 1976 True 3249 3249 96.274 564 2549 1 chr2B.!!$R2 1985
4 TraesCS2B01G420200 chr2B 704164811 704165376 565 False 824 824 92.933 1 566 1 chr2B.!!$F2 565
5 TraesCS2B01G420200 chr7B 621924190 621926170 1980 False 3284 3284 96.576 565 2548 1 chr7B.!!$F3 1983
6 TraesCS2B01G420200 chr7B 718486499 718488475 1976 True 3236 3236 96.171 566 2549 1 chr7B.!!$R2 1983
7 TraesCS2B01G420200 chr7B 583673296 583673859 563 False 872 872 94.523 1 566 1 chr7B.!!$F2 565
8 TraesCS2B01G420200 chr7B 168485433 168485998 565 False 852 852 93.816 1 566 1 chr7B.!!$F1 565
9 TraesCS2B01G420200 chr7B 335007520 335008085 565 True 819 819 92.756 1 566 1 chr7B.!!$R1 565
10 TraesCS2B01G420200 chr5B 269389472 269391452 1980 False 3273 3273 96.474 566 2549 1 chr5B.!!$F1 1983
11 TraesCS2B01G420200 chr5B 446191276 446193260 1984 True 3269 3269 96.382 562 2549 1 chr5B.!!$R1 1987
12 TraesCS2B01G420200 chr5B 648491474 648492039 565 True 841 841 93.463 1 566 1 chr5B.!!$R3 565
13 TraesCS2B01G420200 chr5B 588600465 588601029 564 True 817 817 92.756 1 566 1 chr5B.!!$R2 565
14 TraesCS2B01G420200 chr1B 663786492 663788473 1981 False 3265 3265 96.376 564 2549 1 chr1B.!!$F2 1985
15 TraesCS2B01G420200 chr1B 38005428 38005993 565 False 835 835 93.286 1 566 1 chr1B.!!$F1 565
16 TraesCS2B01G420200 chr3B 703251163 703253143 1980 False 3238 3238 96.131 562 2549 1 chr3B.!!$F1 1987
17 TraesCS2B01G420200 chr3B 640636745 640637308 563 True 822 822 92.933 1 566 1 chr3B.!!$R1 565
18 TraesCS2B01G420200 chr4B 672904135 672904700 565 True 863 863 94.170 1 566 1 chr4B.!!$R1 565

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
296 297 0.847373 TTACTTGCCCTGAACCACCA 59.153 50.0 0.00 0.00 0.0 4.17 F
992 994 0.970937 TTGAGATCCCGTTCGGCTCT 60.971 55.0 14.65 13.43 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1353 0.894184 TCTTCTTCCGGAGCTCGTGT 60.894 55.000 3.34 0.0 37.11 4.49 R
1960 1965 2.573340 CCCAGCCGCACCAATTTC 59.427 61.111 0.00 0.0 0.00 2.17 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
103 104 4.820716 TCCTAGCGTAAGGACTTAGTCATC 59.179 45.833 14.72 0.00 40.86 2.92
126 127 1.202533 GCCATCGCAACTAGGAAGCTA 60.203 52.381 0.00 0.00 34.03 3.32
127 128 2.474816 CCATCGCAACTAGGAAGCTAC 58.525 52.381 0.00 0.00 0.00 3.58
166 167 6.350445 GGACAAAGGACACGAGGTTTATACTA 60.350 42.308 0.00 0.00 0.00 1.82
293 294 2.107378 TGATGTTACTTGCCCTGAACCA 59.893 45.455 0.00 0.00 0.00 3.67
296 297 0.847373 TTACTTGCCCTGAACCACCA 59.153 50.000 0.00 0.00 0.00 4.17
348 349 2.644212 CCAGCGGCTCACAGAGTCT 61.644 63.158 0.00 0.00 31.30 3.24
423 424 9.883142 TTCACAATACAAGTCACATACATATGA 57.117 29.630 10.38 0.00 37.15 2.15
444 445 1.537562 CGGTTTATCACTACGGGCCTC 60.538 57.143 0.84 0.00 0.00 4.70
589 591 7.430760 TGGGTTAATTATCCATTTTCCCTTG 57.569 36.000 13.40 0.00 37.41 3.61
648 650 1.108727 TGTGCTCAGTTTTGCCCCTG 61.109 55.000 0.00 0.00 0.00 4.45
788 790 4.966787 GTGGCTTGCGGGACCCAA 62.967 66.667 12.15 0.00 0.00 4.12
798 800 2.224159 GGGACCCAACAGAGAGCCA 61.224 63.158 5.33 0.00 0.00 4.75
992 994 0.970937 TTGAGATCCCGTTCGGCTCT 60.971 55.000 14.65 13.43 0.00 4.09
1076 1078 1.203523 GATGCCTGTCTTCGTCTGTCT 59.796 52.381 0.00 0.00 0.00 3.41
1193 1195 2.353208 GGGCAATTGCACCATTTTCGTA 60.353 45.455 30.32 0.00 44.36 3.43
1197 1199 4.793071 CAATTGCACCATTTTCGTAGTCA 58.207 39.130 0.00 0.00 0.00 3.41
1340 1342 2.990967 CATGCTGCCCCAAACCGT 60.991 61.111 0.00 0.00 0.00 4.83
1351 1353 2.111460 AAACCGTAGTGGCCGCAA 59.889 55.556 20.59 0.00 43.94 4.85
1827 1832 6.362283 CACCGTCATTTAAATCAAAGACCAAC 59.638 38.462 0.00 0.00 0.00 3.77
1960 1965 2.364970 TGAAGGGTGGAAAATGCACAAG 59.635 45.455 4.42 0.00 40.73 3.16
2159 2166 4.452733 GGCTGGGGACTCGAACCG 62.453 72.222 2.86 0.00 0.00 4.44
2387 2397 0.874390 CGTATGTTTGCACTGCCACT 59.126 50.000 0.00 0.00 0.00 4.00
2450 2460 7.996644 AGTCTCACTTGGTTTAGGATTTAAACA 59.003 33.333 10.79 0.00 38.71 2.83
2484 2497 9.979578 TTTGCATGTTAGTTCATGACTTATTTT 57.020 25.926 10.28 0.00 45.41 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 4.789807 TGACTAAGTCCTTACGCTAGGAT 58.210 43.478 9.12 0.00 45.69 3.24
126 127 3.673543 TTGTCCTGTTTAACCCCTTGT 57.326 42.857 0.00 0.00 0.00 3.16
127 128 3.320826 CCTTTGTCCTGTTTAACCCCTTG 59.679 47.826 0.00 0.00 0.00 3.61
348 349 0.892755 ACTGTTTATGAGCCGTCCGA 59.107 50.000 0.00 0.00 0.00 4.55
423 424 0.176449 GGCCCGTAGTGATAAACCGT 59.824 55.000 0.00 0.00 0.00 4.83
579 581 1.219213 TGGACACCACCAAGGGAAAAT 59.781 47.619 0.00 0.00 43.89 1.82
583 585 0.475632 AGATGGACACCACCAAGGGA 60.476 55.000 0.00 0.00 43.47 4.20
589 591 0.392193 CTGAGCAGATGGACACCACC 60.392 60.000 0.00 0.00 35.80 4.61
788 790 3.036819 TCTATGCTCAATGGCTCTCTGT 58.963 45.455 0.00 0.00 0.00 3.41
798 800 1.303309 GCAACGGCTCTATGCTCAAT 58.697 50.000 0.00 0.00 42.39 2.57
907 909 4.096003 GCTAGCTTCCCACCGCCA 62.096 66.667 7.70 0.00 0.00 5.69
948 950 3.775654 GCGCCCTCCACAGCTAGT 61.776 66.667 0.00 0.00 0.00 2.57
992 994 1.219124 GCGGAAGACATGGAGCTCA 59.781 57.895 17.19 1.87 0.00 4.26
1051 1053 1.137872 GACGAAGACAGGCATCTCCAT 59.862 52.381 0.00 0.00 37.29 3.41
1088 1090 1.541310 AACCCTCCGATCAACGCTCA 61.541 55.000 0.00 0.00 41.07 4.26
1193 1195 3.529533 CGATTGCTCAAAGATCCTGACT 58.470 45.455 0.00 0.00 0.00 3.41
1197 1199 3.012518 CAACCGATTGCTCAAAGATCCT 58.987 45.455 0.00 0.00 0.00 3.24
1340 1342 2.048597 CTCGTGTTGCGGCCACTA 60.049 61.111 2.24 0.00 41.72 2.74
1351 1353 0.894184 TCTTCTTCCGGAGCTCGTGT 60.894 55.000 3.34 0.00 37.11 4.49
1827 1832 3.193903 TGAGGCACATTTTCCATGACATG 59.806 43.478 8.56 8.56 0.00 3.21
1938 1943 2.607499 TGTGCATTTTCCACCCTTCAT 58.393 42.857 0.00 0.00 32.30 2.57
1960 1965 2.573340 CCCAGCCGCACCAATTTC 59.427 61.111 0.00 0.00 0.00 2.17
2387 2397 2.691011 GTGCCACTCTAACCAAAACCAA 59.309 45.455 0.00 0.00 0.00 3.67
2484 2497 6.844097 AGCCCTCCGTTTTATTCAAAAATA 57.156 33.333 0.00 0.00 35.46 1.40
2485 2498 5.738619 AGCCCTCCGTTTTATTCAAAAAT 57.261 34.783 0.00 0.00 35.46 1.82
2486 2499 5.303333 AGAAGCCCTCCGTTTTATTCAAAAA 59.697 36.000 0.00 0.00 35.46 1.94


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

AutoCloner maintained by Alex Coulton.