Multiple sequence alignment - TraesCS6A01G181400

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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 TraesCS6A01G181400 chr6A 100.000 2749 0 0 1 2749 206353502 206350754 0.000000e+00 5077.0
1 TraesCS6A01G181400 chr6B 96.465 2376 57 9 384 2749 277625198 277622840 0.000000e+00 3897.0
2 TraesCS6A01G181400 chr6B 96.247 373 13 1 1 372 277625552 277625180 6.510000e-171 610.0
3 TraesCS6A01G181400 chr6D 96.098 2076 42 9 683 2749 153865973 153863928 0.000000e+00 3349.0
4 TraesCS6A01G181400 chr6D 100.000 85 0 0 1 85 153866813 153866729 1.020000e-34 158.0
5 TraesCS6A01G181400 chr6D 90.164 61 6 0 1025 1085 443741328 443741268 2.270000e-11 80.5
6 TraesCS6A01G181400 chr7A 81.579 380 48 18 1216 1574 549357820 549357442 7.440000e-76 294.0
7 TraesCS6A01G181400 chr7A 89.691 97 10 0 1001 1097 549358117 549358021 1.030000e-24 124.0
8 TraesCS6A01G181400 chr7A 87.805 82 10 0 1643 1724 549357345 549357264 2.250000e-16 97.1
9 TraesCS6A01G181400 chr7B 80.637 377 54 14 1216 1574 508195341 508194966 9.700000e-70 274.0
10 TraesCS6A01G181400 chr7B 88.000 100 11 1 992 1090 508195654 508195555 1.730000e-22 117.0
11 TraesCS6A01G181400 chr7B 87.356 87 10 1 1638 1724 508194876 508194791 6.270000e-17 99.0
12 TraesCS6A01G181400 chr7B 94.231 52 3 0 1035 1086 47737301 47737352 2.270000e-11 80.5
13 TraesCS6A01G181400 chr7D 91.111 90 8 0 1001 1090 482134338 482134249 3.720000e-24 122.0
14 TraesCS6A01G181400 chr7D 87.356 87 10 1 1638 1724 482133568 482133483 6.270000e-17 99.0
15 TraesCS6A01G181400 chr7D 94.231 52 3 0 1035 1086 93949351 93949300 2.270000e-11 80.5
16 TraesCS6A01G181400 chr7D 94.231 52 3 0 1035 1086 94005584 94005635 2.270000e-11 80.5


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 TraesCS6A01G181400 chr6A 206350754 206353502 2748 True 5077.0 5077 100.000 1 2749 1 chr6A.!!$R1 2748
1 TraesCS6A01G181400 chr6B 277622840 277625552 2712 True 2253.5 3897 96.356 1 2749 2 chr6B.!!$R1 2748
2 TraesCS6A01G181400 chr6D 153863928 153866813 2885 True 1753.5 3349 98.049 1 2749 2 chr6D.!!$R2 2748

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
665 1267 0.739112 CGCTCTTGTCTTCTGCCTCC 60.739 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 2999 0.528017 TCCTGACGACTGCAGATGAC 59.472 55.0 23.35 12.6 35.39 3.06 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
99 448 6.038356 CCATATTGACAATCCAAACAGAAGC 58.962 40.000 3.36 0.00 0.00 3.86
155 505 2.438975 CATGCGTCCCATGGCACT 60.439 61.111 6.09 0.00 46.09 4.40
218 820 2.096013 GCTACGAAAGAACCAAGATGGC 59.904 50.000 0.00 0.00 42.67 4.40
239 841 3.066064 GCGAGCTCTCTTTCTGTATCTGA 59.934 47.826 12.85 0.00 0.00 3.27
256 858 3.128349 TCTGACTCGGTTTTACTTGCAC 58.872 45.455 0.00 0.00 0.00 4.57
361 963 6.126409 TGACCTGTTGGGCCTTTAATAATAG 58.874 40.000 4.53 0.00 42.00 1.73
362 964 6.087276 ACCTGTTGGGCCTTTAATAATAGT 57.913 37.500 4.53 0.00 39.10 2.12
363 965 7.092354 TGACCTGTTGGGCCTTTAATAATAGTA 60.092 37.037 4.53 0.00 42.00 1.82
364 966 7.287810 ACCTGTTGGGCCTTTAATAATAGTAG 58.712 38.462 4.53 0.00 39.10 2.57
365 967 7.092128 ACCTGTTGGGCCTTTAATAATAGTAGT 60.092 37.037 4.53 0.00 39.10 2.73
366 968 8.434392 CCTGTTGGGCCTTTAATAATAGTAGTA 58.566 37.037 4.53 0.00 0.00 1.82
367 969 9.490379 CTGTTGGGCCTTTAATAATAGTAGTAG 57.510 37.037 4.53 0.00 0.00 2.57
368 970 8.995577 TGTTGGGCCTTTAATAATAGTAGTAGT 58.004 33.333 4.53 0.00 0.00 2.73
419 1021 9.664332 AATAATAATCTCGGGATCTGATCTTTG 57.336 33.333 16.61 7.59 0.00 2.77
428 1030 5.367302 GGGATCTGATCTTTGAGAAGAAGG 58.633 45.833 16.61 0.00 44.61 3.46
544 1146 3.332034 AGGTGAGCGTGTTTATTACCAC 58.668 45.455 0.00 0.00 0.00 4.16
665 1267 0.739112 CGCTCTTGTCTTCTGCCTCC 60.739 60.000 0.00 0.00 0.00 4.30
859 1461 3.454371 ACCTACGCATCTAACCACATC 57.546 47.619 0.00 0.00 0.00 3.06
959 1562 1.227823 CAACACCTTGGCGGACTCA 60.228 57.895 0.00 0.00 36.31 3.41
1150 1759 6.842676 ACTTCCTCTAAAGATCAGTGGTTTT 58.157 36.000 0.00 0.00 0.00 2.43
1152 1761 7.445707 ACTTCCTCTAAAGATCAGTGGTTTTTC 59.554 37.037 0.00 0.00 0.00 2.29
1154 1763 6.003950 CCTCTAAAGATCAGTGGTTTTTCCA 58.996 40.000 0.00 0.00 45.01 3.53
1214 1823 7.406553 CGTGTCTTTGTGAATGAAGTAAAAGA 58.593 34.615 0.00 0.00 32.73 2.52
1235 1844 0.608308 GGGTGTGGCTTGGTACCTTC 60.608 60.000 14.36 1.76 33.71 3.46
1391 2000 2.042025 GGCAGCTCCTCCTCCTCT 60.042 66.667 0.00 0.00 0.00 3.69
2037 2646 3.500448 TTGTGTTACCTCATGCCTTCA 57.500 42.857 0.00 0.00 0.00 3.02
2105 2717 7.943079 ACATGATGAAGGTGATATTTGTGAA 57.057 32.000 0.00 0.00 0.00 3.18
2225 2837 8.513774 TGATGCGATATGTGTATGCATTTATTT 58.486 29.630 3.54 0.00 45.54 1.40
2282 2894 1.300388 CAAGCAGCCAAGCACCAAC 60.300 57.895 0.00 0.00 36.85 3.77
2387 2999 1.662629 CTCAGCTAGCACACAATTCCG 59.337 52.381 18.83 0.00 0.00 4.30
2486 3098 1.279271 GAAGCTCCCTTCTGCCAGTTA 59.721 52.381 0.00 0.00 43.31 2.24
2487 3099 0.615850 AGCTCCCTTCTGCCAGTTAC 59.384 55.000 0.00 0.00 0.00 2.50
2499 3112 2.739913 TGCCAGTTACGTTAGCAATGTC 59.260 45.455 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 448 3.411446 TGCAAAGACTGGTATGTCAAGG 58.589 45.455 0.00 0.00 39.27 3.61
218 820 4.335315 AGTCAGATACAGAAAGAGAGCTCG 59.665 45.833 8.37 0.00 34.09 5.03
239 841 2.632987 AGGTGCAAGTAAAACCGAGT 57.367 45.000 0.00 0.00 39.07 4.18
256 858 5.529581 AATGTTACAAACCAGGACAAAGG 57.470 39.130 0.00 0.00 0.00 3.11
419 1021 2.238395 AGCCATGTCTTCCCTTCTTCTC 59.762 50.000 0.00 0.00 0.00 2.87
428 1030 3.451178 TCCTACAACTAGCCATGTCTTCC 59.549 47.826 0.20 0.00 0.00 3.46
544 1146 1.482593 CCACCTTCCCTGCTAGTACAG 59.517 57.143 0.00 0.00 37.42 2.74
766 1368 2.152016 GTGCCTGGTCTAGTTTTCACC 58.848 52.381 0.00 0.00 0.00 4.02
859 1461 1.016130 CCTCTGCACTGCCGTGTTAG 61.016 60.000 10.12 8.82 43.16 2.34
959 1562 1.596895 GACGAGGGAACGAGCCTCTT 61.597 60.000 0.00 0.00 37.03 2.85
1150 1759 4.459390 TCTTGTAAACCGATCGATGGAA 57.541 40.909 18.66 0.60 0.00 3.53
1152 1761 5.050490 AGAATCTTGTAAACCGATCGATGG 58.950 41.667 18.66 7.51 0.00 3.51
1154 1763 7.262772 TGTTAGAATCTTGTAAACCGATCGAT 58.737 34.615 18.66 0.00 0.00 3.59
1214 1823 1.065997 AGGTACCAAGCCACACCCTT 61.066 55.000 15.94 0.00 0.00 3.95
1235 1844 1.374758 AGCCTCTTCAGCGGTTTCG 60.375 57.895 0.00 0.00 39.81 3.46
1391 2000 4.201523 TGGGACAGGTTGCTCGTA 57.798 55.556 0.00 0.00 0.00 3.43
1859 2468 6.147164 TGCTTTTTGTAACTTGGATCGAGTAG 59.853 38.462 0.00 0.00 0.00 2.57
1865 2474 9.476202 AAACTTATGCTTTTTGTAACTTGGATC 57.524 29.630 0.00 0.00 0.00 3.36
2037 2646 6.382869 CAAGTTTGGAGTCTGAAGTTGAAT 57.617 37.500 15.53 0.00 36.35 2.57
2105 2717 4.131596 GTCGTATAGAGCTGAGGTCTTCT 58.868 47.826 20.11 10.17 40.94 2.85
2178 2790 6.723298 TCAATACAAGAAAATGGTTGGTGT 57.277 33.333 0.00 0.00 0.00 4.16
2387 2999 0.528017 TCCTGACGACTGCAGATGAC 59.472 55.000 23.35 12.60 35.39 3.06
2486 3098 2.475818 TGTTGACGACATTGCTAACGT 58.524 42.857 0.00 0.00 41.57 3.99
2487 3099 3.059868 AGTTGTTGACGACATTGCTAACG 60.060 43.478 0.00 0.00 38.26 3.18
2499 3112 2.413239 GCATGATGTGGAGTTGTTGACG 60.413 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.