Multiple sequence alignment - TraesCS5A01G260900

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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 TraesCS5A01G260900 chr5A 100.000 2567 0 0 1 2567 474827814 474830380 0.000000e+00 4741
1 TraesCS5A01G260900 chr5D 95.924 2576 91 10 1 2565 371796309 371798881 0.000000e+00 4163
2 TraesCS5A01G260900 chr5B 93.970 1509 66 12 1065 2565 441646868 441648359 0.000000e+00 2259
3 TraesCS5A01G260900 chr5B 93.901 1197 46 15 1 1186 441645767 441646947 0.000000e+00 1781
4 TraesCS5A01G260900 chr5B 92.473 93 7 0 1 93 403708628 403708720 1.600000e-27 134
5 TraesCS5A01G260900 chr5B 95.181 83 4 0 1065 1147 441646910 441646992 5.760000e-27 132
6 TraesCS5A01G260900 chr5B 92.500 80 6 0 1107 1186 441646826 441646905 5.800000e-22 115
7 TraesCS5A01G260900 chr6A 92.473 93 7 0 1 93 538097728 538097820 1.600000e-27 134
8 TraesCS5A01G260900 chr3B 92.473 93 7 0 1 93 521797874 521797782 1.600000e-27 134
9 TraesCS5A01G260900 chr2D 92.473 93 7 0 1 93 122864214 122864122 1.600000e-27 134
10 TraesCS5A01G260900 chr1B 92.473 93 7 0 1 93 136627474 136627382 1.600000e-27 134
11 TraesCS5A01G260900 chr1B 92.391 92 6 1 1 92 632021029 632020939 2.070000e-26 130
12 TraesCS5A01G260900 chr1A 92.473 93 7 0 1 93 155857756 155857848 1.600000e-27 134
13 TraesCS5A01G260900 chr1D 89.216 102 11 0 1 102 81742290 81742189 7.460000e-26 128


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 TraesCS5A01G260900 chr5A 474827814 474830380 2566 False 4741.00 4741 100.000 1 2567 1 chr5A.!!$F1 2566
1 TraesCS5A01G260900 chr5D 371796309 371798881 2572 False 4163.00 4163 95.924 1 2565 1 chr5D.!!$F1 2564
2 TraesCS5A01G260900 chr5B 441645767 441648359 2592 False 1071.75 2259 93.888 1 2565 4 chr5B.!!$F2 2564

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
998 1010 1.236708 CCTAAGAGAGGGAGGGAGGA 58.763 60.0 0.0 0.0 42.39 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2450 2523 0.341961 ACTGACACCCCCTAGCCATA 59.658 55.0 0.0 0.0 0.0 2.74 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
47 48 4.946772 TGTTTGTTCACTCATTTCAGTCCA 59.053 37.500 0.00 0.0 0.00 4.02
289 298 2.443255 AGAAGGCAAGAACAGAAAGGGA 59.557 45.455 0.00 0.0 0.00 4.20
291 300 2.800250 AGGCAAGAACAGAAAGGGATG 58.200 47.619 0.00 0.0 0.00 3.51
423 434 7.718334 AACATCTAAAGGAAAAATACCAGGG 57.282 36.000 0.00 0.0 0.00 4.45
509 520 1.237285 CCCTGTACAAGTGGCAGCAC 61.237 60.000 0.00 0.0 0.00 4.40
637 649 8.148351 CAGGATTCCAAAATAGGTCTTCGTATA 58.852 37.037 5.29 0.0 0.00 1.47
854 866 2.293399 CTGGTTTGTCCTACTTTGGCAC 59.707 50.000 0.00 0.0 37.07 5.01
856 868 1.265905 GTTTGTCCTACTTTGGCACGG 59.734 52.381 0.00 0.0 0.00 4.94
878 890 2.575532 CAAGGTCTGACAAAGCCAAGA 58.424 47.619 10.38 0.0 0.00 3.02
896 908 4.298332 CAAGACCAACAAATACCAAGCAC 58.702 43.478 0.00 0.0 0.00 4.40
988 1000 4.284746 ACTTCCTTTCACCACCTAAGAGAG 59.715 45.833 0.00 0.0 0.00 3.20
998 1010 1.236708 CCTAAGAGAGGGAGGGAGGA 58.763 60.000 0.00 0.0 42.39 3.71
1331 1385 4.792068 CTTAACCTGGATTGCCCTTATGA 58.208 43.478 0.00 0.0 35.38 2.15
1523 1577 5.066634 CCACAGAGAGTATAAGCGAAGAAGA 59.933 44.000 0.00 0.0 0.00 2.87
1533 1587 0.179215 GCGAAGAAGACATTGGTGCG 60.179 55.000 0.00 0.0 0.00 5.34
1544 1598 0.976641 ATTGGTGCGAAGAGACCTCA 59.023 50.000 0.00 0.0 32.98 3.86
1551 1605 1.674221 GCGAAGAGACCTCATTGTGCT 60.674 52.381 0.00 0.0 0.00 4.40
1554 1608 4.437239 CGAAGAGACCTCATTGTGCTATT 58.563 43.478 0.00 0.0 0.00 1.73
1634 1690 2.034179 GGAAGAAAAGGGGTTCACAACG 59.966 50.000 0.00 0.0 0.00 4.10
1666 1722 7.307493 TCATTGTTCAGGATATTTCTTCACG 57.693 36.000 0.00 0.0 0.00 4.35
1667 1723 5.545658 TTGTTCAGGATATTTCTTCACGC 57.454 39.130 0.00 0.0 0.00 5.34
1668 1724 3.938963 TGTTCAGGATATTTCTTCACGCC 59.061 43.478 0.00 0.0 0.00 5.68
1695 1751 9.113838 AGATACTTAAATGGTACTGAAGCAATG 57.886 33.333 0.00 0.0 39.48 2.82
1735 1804 6.071728 CCCAGGAATATGATATTTGCCACTTC 60.072 42.308 0.00 0.0 0.00 3.01
1739 1808 9.812347 AGGAATATGATATTTGCCACTTCATAA 57.188 29.630 0.00 0.0 34.12 1.90
1763 1832 5.938322 TCACGAAAAGATATTTGCCACTTC 58.062 37.500 0.00 0.0 0.00 3.01
1820 1889 3.518634 TTTGTGTTTCTTGCCCTTCAC 57.481 42.857 0.00 0.0 0.00 3.18
2252 2322 7.791029 TGATAGTTTTGGTCAGATATGTAGCA 58.209 34.615 0.00 0.0 0.00 3.49
2261 2333 6.539826 TGGTCAGATATGTAGCATTTTCACAG 59.460 38.462 0.00 0.0 0.00 3.66
2262 2334 6.540189 GGTCAGATATGTAGCATTTTCACAGT 59.460 38.462 0.00 0.0 0.00 3.55
2281 2353 6.041637 TCACAGTAGTTTGATAGTTCACTGGT 59.958 38.462 0.00 0.0 29.62 4.00
2404 2477 9.435570 AGGGTTTATGTTAGTGACTGATAGTAT 57.564 33.333 0.00 0.0 0.00 2.12
2450 2523 3.795688 TCAGAATTGTCCCAAAGCTCT 57.204 42.857 0.00 0.0 0.00 4.09
2478 2556 1.286248 GGGGTGTCAGTATGGGAACT 58.714 55.000 0.00 0.0 36.16 3.01
2565 2643 2.549064 AGGTTGCCTGCCAAAATTTC 57.451 45.000 0.00 0.0 34.68 2.17
2566 2644 1.767681 AGGTTGCCTGCCAAAATTTCA 59.232 42.857 0.00 0.0 34.68 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.760660 GTGAACAAACACAATAGAATATGTCTC 57.239 33.333 0.00 0.00 40.11 3.36
18 19 8.131100 ACTGAAATGAGTGAACAAACACAATAG 58.869 33.333 0.00 0.00 42.45 1.73
21 22 6.266168 ACTGAAATGAGTGAACAAACACAA 57.734 33.333 0.00 0.00 42.45 3.33
289 298 5.240891 ACTCTGACATCATCGTTGTTTCAT 58.759 37.500 0.00 0.00 0.00 2.57
291 300 5.377358 CAACTCTGACATCATCGTTGTTTC 58.623 41.667 12.02 0.00 34.29 2.78
423 434 3.417690 ACGCCGTTGTTATCTAGTCTC 57.582 47.619 0.00 0.00 0.00 3.36
509 520 5.512060 CCAGGTGAACACATAGGATATCCAG 60.512 48.000 23.81 14.69 38.89 3.86
637 649 3.154710 TCAATATAGACATCCGCGGAGT 58.845 45.455 33.87 28.33 0.00 3.85
854 866 1.856265 GCTTTGTCAGACCTTGGCCG 61.856 60.000 0.00 0.00 0.00 6.13
856 868 0.823356 TGGCTTTGTCAGACCTTGGC 60.823 55.000 0.00 1.07 0.00 4.52
878 890 3.492482 GCTTGTGCTTGGTATTTGTTGGT 60.492 43.478 0.00 0.00 36.03 3.67
896 908 5.236263 TGTTTATAGATACGGCATGTGCTTG 59.764 40.000 4.84 0.98 41.70 4.01
988 1000 2.000825 GAGCCCATTTCCTCCCTCCC 62.001 65.000 0.00 0.00 0.00 4.30
998 1010 0.606401 CTGTGACCGTGAGCCCATTT 60.606 55.000 0.00 0.00 0.00 2.32
1095 1107 4.519437 CATCTGGCGCCGCTCTCA 62.519 66.667 23.90 0.87 0.00 3.27
1331 1385 2.136026 GGATATTGGGGGAGTTGTCCT 58.864 52.381 0.00 0.00 43.36 3.85
1523 1577 0.687354 AGGTCTCTTCGCACCAATGT 59.313 50.000 0.00 0.00 34.80 2.71
1533 1587 5.755861 GGTAATAGCACAATGAGGTCTCTTC 59.244 44.000 0.00 0.00 0.00 2.87
1544 1598 9.561069 CCTTTTAGTATCTGGTAATAGCACAAT 57.439 33.333 0.00 0.00 0.00 2.71
1551 1605 6.329197 AGCAGGCCTTTTAGTATCTGGTAATA 59.671 38.462 0.00 0.00 32.27 0.98
1554 1608 4.037927 AGCAGGCCTTTTAGTATCTGGTA 58.962 43.478 0.00 0.00 32.27 3.25
1648 1704 4.081142 TCTGGCGTGAAGAAATATCCTGAA 60.081 41.667 0.00 0.00 0.00 3.02
1666 1722 6.017852 GCTTCAGTACCATTTAAGTATCTGGC 60.018 42.308 0.00 0.00 31.72 4.85
1667 1723 7.047891 TGCTTCAGTACCATTTAAGTATCTGG 58.952 38.462 0.00 0.00 34.84 3.86
1668 1724 8.492673 TTGCTTCAGTACCATTTAAGTATCTG 57.507 34.615 0.00 0.00 0.00 2.90
1735 1804 8.131100 AGTGGCAAATATCTTTTCGTGATTATG 58.869 33.333 0.00 0.00 0.00 1.90
1739 1808 6.150976 TGAAGTGGCAAATATCTTTTCGTGAT 59.849 34.615 0.00 0.00 0.00 3.06
1742 1811 5.957842 TGAAGTGGCAAATATCTTTTCGT 57.042 34.783 0.00 0.00 0.00 3.85
1763 1832 6.576185 ACTGCATGAAATTTATTAGGCCTTG 58.424 36.000 12.58 0.00 0.00 3.61
1893 1963 8.870116 ACTTGCATATGTAGGATATTCTGTACA 58.130 33.333 9.88 0.00 0.00 2.90
2042 2112 2.687935 ACTGCCACTTTGTTGACGAATT 59.312 40.909 0.00 0.00 0.00 2.17
2252 2322 9.561069 AGTGAACTATCAAACTACTGTGAAAAT 57.439 29.630 0.00 0.00 37.30 1.82
2261 2333 8.773404 ATGTAACCAGTGAACTATCAAACTAC 57.227 34.615 0.00 0.00 37.30 2.73
2262 2334 9.865321 GTATGTAACCAGTGAACTATCAAACTA 57.135 33.333 0.00 0.00 37.30 2.24
2316 2388 9.905713 TTTAGAAATGAGGCAATTATACTCACT 57.094 29.630 7.74 4.85 43.29 3.41
2412 2485 9.286170 CAATTCTGATGATGAGGAGATATTTGT 57.714 33.333 0.00 0.00 0.00 2.83
2436 2509 1.635487 AGCCATAGAGCTTTGGGACAA 59.365 47.619 11.81 0.00 41.41 3.18
2450 2523 0.341961 ACTGACACCCCCTAGCCATA 59.658 55.000 0.00 0.00 0.00 2.74
2478 2556 5.453762 CCACATGCATCTGTCTGAGGTAATA 60.454 44.000 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.