Multiple sequence alignment - TraesCS2B01G200600

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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 TraesCS2B01G200600 chr2B 100.000 3446 0 0 1 3446 179064057 179067502 0 6364
1 TraesCS2B01G200600 chr2B 95.200 3458 143 16 1 3446 379155447 379158893 0 5445
2 TraesCS2B01G200600 chr2B 95.056 3459 147 17 1 3446 261018129 261021576 0 5419
3 TraesCS2B01G200600 chr2B 94.994 3456 150 16 1 3446 209875995 209872553 0 5402
4 TraesCS2B01G200600 chr7B 97.073 3451 91 8 1 3446 207971323 207974768 0 5805
5 TraesCS2B01G200600 chr6B 96.903 3455 90 13 1 3446 247392374 247395820 0 5771
6 TraesCS2B01G200600 chr1B 95.343 3457 139 14 1 3446 330756299 330759744 0 5472
7 TraesCS2B01G200600 chr3B 94.996 3457 150 16 1 3446 236260868 236257424 0 5404
8 TraesCS2B01G200600 chr3B 94.828 3461 155 17 1 3446 252185472 252188923 0 5378
9 TraesCS2B01G200600 chr2A 92.177 3464 225 28 1 3446 685104314 685100879 0 4854


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 TraesCS2B01G200600 chr2B 179064057 179067502 3445 False 6364 6364 100.000 1 3446 1 chr2B.!!$F1 3445
1 TraesCS2B01G200600 chr2B 379155447 379158893 3446 False 5445 5445 95.200 1 3446 1 chr2B.!!$F3 3445
2 TraesCS2B01G200600 chr2B 261018129 261021576 3447 False 5419 5419 95.056 1 3446 1 chr2B.!!$F2 3445
3 TraesCS2B01G200600 chr2B 209872553 209875995 3442 True 5402 5402 94.994 1 3446 1 chr2B.!!$R1 3445
4 TraesCS2B01G200600 chr7B 207971323 207974768 3445 False 5805 5805 97.073 1 3446 1 chr7B.!!$F1 3445
5 TraesCS2B01G200600 chr6B 247392374 247395820 3446 False 5771 5771 96.903 1 3446 1 chr6B.!!$F1 3445
6 TraesCS2B01G200600 chr1B 330756299 330759744 3445 False 5472 5472 95.343 1 3446 1 chr1B.!!$F1 3445
7 TraesCS2B01G200600 chr3B 236257424 236260868 3444 True 5404 5404 94.996 1 3446 1 chr3B.!!$R1 3445
8 TraesCS2B01G200600 chr3B 252185472 252188923 3451 False 5378 5378 94.828 1 3446 1 chr3B.!!$F1 3445
9 TraesCS2B01G200600 chr2A 685100879 685104314 3435 True 4854 4854 92.177 1 3446 1 chr2A.!!$R1 3445

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
931 948 1.406065 CCCACAAACCACCATTGCCA 61.406 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2815 2849 2.622436 GCTTACGGACTGATGCTTCTT 58.378 47.619 0.88 0.0 0.0 2.52 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
217 221 4.565564 GTCGGTAGTACAAAAGGCATAGTG 59.434 45.833 2.06 0.00 0.00 2.74
489 503 5.191722 ACATGGTCTCACTGGTATTTGGTAT 59.808 40.000 0.00 0.00 0.00 2.73
596 610 5.545723 AGTGGGATAAGCAGCTGATAAGTAT 59.454 40.000 20.43 6.08 0.00 2.12
717 731 7.491696 ACAAGACTAGTCAGTTCAACAGTAAAC 59.508 37.037 24.44 0.00 34.21 2.01
753 767 2.093341 ACGGTTAGTTATTCCACGCCAT 60.093 45.455 0.00 0.00 0.00 4.40
765 779 3.274586 CGCCATCATCCGTGCCAG 61.275 66.667 0.00 0.00 0.00 4.85
931 948 1.406065 CCCACAAACCACCATTGCCA 61.406 55.000 0.00 0.00 0.00 4.92
944 961 2.302445 CCATTGCCACTTCCATTTCCAA 59.698 45.455 0.00 0.00 0.00 3.53
981 999 2.273619 ACTTCTCTCTCCAAAGCCCAT 58.726 47.619 0.00 0.00 0.00 4.00
1129 1147 0.178992 CAAAGGGGTTGAGCTCCACA 60.179 55.000 18.74 0.00 41.40 4.17
1130 1148 0.555769 AAAGGGGTTGAGCTCCACAA 59.444 50.000 18.74 1.14 41.40 3.33
1151 1169 2.352915 CGAGACGCTGGAGATCGC 60.353 66.667 0.00 0.00 0.00 4.58
1193 1211 1.945354 GCCGACGAGGTGATCTCCAA 61.945 60.000 15.93 0.00 43.70 3.53
1213 1231 1.252904 GCTTTGGAGGATGCTTGGCA 61.253 55.000 0.00 0.00 44.86 4.92
1222 1240 1.616994 GGATGCTTGGCAGTAGGGTTT 60.617 52.381 0.00 0.00 43.65 3.27
1241 1259 1.307355 TGTAGGATCGTCGGCGTTGA 61.307 55.000 10.18 6.53 39.49 3.18
1336 1354 2.813474 TGTACCACATCGCAGCGC 60.813 61.111 10.87 0.00 0.00 5.92
2468 2500 3.201708 AGATAACATCAGAGCCTGCCTTT 59.798 43.478 0.00 0.00 0.00 3.11
2478 2510 3.960755 AGAGCCTGCCTTTGTTTTACTTT 59.039 39.130 0.00 0.00 0.00 2.66
2479 2511 4.405680 AGAGCCTGCCTTTGTTTTACTTTT 59.594 37.500 0.00 0.00 0.00 2.27
3193 3235 0.968393 GGTCAAGAGAGAGGGCGAGT 60.968 60.000 0.00 0.00 0.00 4.18
3269 3311 2.356741 GCTGCCCTTATAAACAGGTCCA 60.357 50.000 10.28 0.00 0.00 4.02
3420 3466 5.654650 CACCAATAAGCCCAGGTATACAAAA 59.345 40.000 5.01 0.00 32.01 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 116 4.085357 TGTTGCTGAGTTACTGGTTGAT 57.915 40.909 0.00 0.00 0.00 2.57
217 221 4.789629 GTCGTTAACTGGTGTGTTTGTTTC 59.210 41.667 3.71 0.00 0.00 2.78
489 503 4.099113 TGGTGATTGAAGTGCAATTGAACA 59.901 37.500 18.97 0.72 46.90 3.18
596 610 5.813672 GGCACCGATTTGTATAGTCAAGTTA 59.186 40.000 0.00 0.00 0.00 2.24
610 624 4.157105 GGTATTTTACTGTGGCACCGATTT 59.843 41.667 16.26 0.00 0.00 2.17
717 731 5.175859 ACTAACCGTCCATGTGAAATAGTG 58.824 41.667 0.00 0.00 0.00 2.74
753 767 3.321648 AGTGGCTGGCACGGATGA 61.322 61.111 25.76 0.00 36.31 2.92
765 779 2.280797 TGTCAACCGCTCAGTGGC 60.281 61.111 3.38 0.00 36.54 5.01
931 948 5.867903 TTGTGTTCATTGGAAATGGAAGT 57.132 34.783 0.42 0.00 34.13 3.01
944 961 6.935167 AGAGAAGTTTTTGGTTTGTGTTCAT 58.065 32.000 0.00 0.00 0.00 2.57
1062 1080 3.818586 GGGGACGTTAATGTCGACA 57.181 52.632 22.48 22.48 39.83 4.35
1129 1147 0.603569 ATCTCCAGCGTCTCGTTGTT 59.396 50.000 5.45 0.00 36.40 2.83
1130 1148 0.171455 GATCTCCAGCGTCTCGTTGT 59.829 55.000 5.45 0.00 36.40 3.32
1151 1169 0.530744 TTCTGGTACGCTAGTGCAGG 59.469 55.000 2.40 0.00 39.64 4.85
1193 1211 0.969409 GCCAAGCATCCTCCAAAGCT 60.969 55.000 0.00 0.00 39.37 3.74
1213 1231 2.686915 CGACGATCCTACAAACCCTACT 59.313 50.000 0.00 0.00 0.00 2.57
1222 1240 1.138036 CAACGCCGACGATCCTACA 59.862 57.895 0.00 0.00 43.93 2.74
1336 1354 8.804358 GAGTAAGATTGCTCACCATTTAGTGGG 61.804 44.444 5.88 0.00 39.95 4.61
1709 1732 4.953579 TGCTTCACCAAGTCCTTAGTTTTT 59.046 37.500 0.00 0.00 31.45 1.94
1986 2017 7.486407 AGGGCAGAGACATTTTGAATATTTT 57.514 32.000 0.00 0.00 0.00 1.82
2468 2500 4.092675 GCAAGCACAAGCAAAAGTAAAACA 59.907 37.500 0.00 0.00 45.49 2.83
2478 2510 3.321682 AGATAAAAGGCAAGCACAAGCAA 59.678 39.130 0.00 0.00 45.49 3.91
2479 2511 2.892852 AGATAAAAGGCAAGCACAAGCA 59.107 40.909 0.00 0.00 45.49 3.91
2814 2848 3.003480 GCTTACGGACTGATGCTTCTTT 58.997 45.455 0.88 0.00 0.00 2.52
2815 2849 2.622436 GCTTACGGACTGATGCTTCTT 58.378 47.619 0.88 0.00 0.00 2.52
2988 3025 9.209175 GATACTTGTTGTTCTAGTTCTTGTCAT 57.791 33.333 0.00 0.00 34.37 3.06
3057 3099 2.350738 ACCTTGGGCGGTCATTTTG 58.649 52.632 0.00 0.00 29.14 2.44
3193 3235 0.527600 CTGAGCGCTTATACACGGCA 60.528 55.000 13.26 0.00 0.00 5.69
3269 3311 2.123640 GCTAGTCGAGGGGGCTCT 60.124 66.667 0.00 0.00 0.00 4.09
3420 3466 0.400213 TTCTTTGTCCCGCCATCTGT 59.600 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.