Multiple sequence alignment - TraesCS5A01G337300

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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 TraesCS5A01G337300 chr5A 100.000 2472 0 0 1 2472 545752450 545749979 0.000000e+00 4566
1 TraesCS5A01G337300 chr5A 95.263 1161 45 6 741 1892 643381327 643382486 0.000000e+00 1831
2 TraesCS5A01G337300 chr5A 94.078 743 39 5 1 742 457423232 457423970 0.000000e+00 1123
3 TraesCS5A01G337300 chr5A 93.935 742 43 1 1 742 73751027 73750288 0.000000e+00 1120
4 TraesCS5A01G337300 chr5A 93.261 742 43 3 1 742 73802934 73802200 0.000000e+00 1086
5 TraesCS5A01G337300 chr5A 92.722 742 47 2 1 742 73768081 73767347 0.000000e+00 1064
6 TraesCS5A01G337300 chr5A 92.608 744 45 5 1 741 452517069 452516333 0.000000e+00 1061
7 TraesCS5A01G337300 chr2B 95.147 1154 35 7 744 1891 229826552 229827690 0.000000e+00 1801
8 TraesCS5A01G337300 chr2B 93.460 1162 48 8 743 1893 454009433 454010577 0.000000e+00 1700
9 TraesCS5A01G337300 chr2B 91.372 1159 58 15 746 1892 82490453 82489325 0.000000e+00 1548
10 TraesCS5A01G337300 chr2B 79.891 368 47 18 744 1092 543339005 543339364 6.830000e-61 244
11 TraesCS5A01G337300 chr1D 94.965 1152 40 6 744 1887 400879438 400880579 0.000000e+00 1790
12 TraesCS5A01G337300 chr6D 94.870 1150 43 5 752 1891 380812554 380811411 0.000000e+00 1783
13 TraesCS5A01G337300 chr7B 93.615 1159 46 8 744 1891 58077364 58078505 0.000000e+00 1705
14 TraesCS5A01G337300 chr7B 97.595 582 14 0 1891 2472 86800205 86800786 0.000000e+00 998
15 TraesCS5A01G337300 chr5B 92.235 1159 52 8 744 1891 278897266 278896135 0.000000e+00 1607
16 TraesCS5A01G337300 chr5B 97.595 582 14 0 1891 2472 513958325 513957744 0.000000e+00 998
17 TraesCS5A01G337300 chr3B 91.042 1161 57 19 744 1891 777850394 777849268 0.000000e+00 1524
18 TraesCS5A01G337300 chr3B 97.766 582 13 0 1891 2472 814696565 814695984 0.000000e+00 1003
19 TraesCS5A01G337300 chr2A 93.666 742 40 5 1 742 746633602 746634336 0.000000e+00 1103
20 TraesCS5A01G337300 chr2A 92.637 747 43 7 1 742 746646940 746647679 0.000000e+00 1064
21 TraesCS5A01G337300 chr2A 97.759 580 13 0 1891 2470 5161055 5160476 0.000000e+00 1000
22 TraesCS5A01G337300 chr7A 93.011 744 47 3 1 742 154373278 154374018 0.000000e+00 1081
23 TraesCS5A01G337300 chr7A 91.812 745 49 7 1 742 657148156 657147421 0.000000e+00 1027
24 TraesCS5A01G337300 chr7A 97.766 582 13 0 1891 2472 631494856 631494275 0.000000e+00 1003
25 TraesCS5A01G337300 chr4A 97.766 582 13 0 1891 2472 665113859 665113278 0.000000e+00 1003
26 TraesCS5A01G337300 chr3A 97.595 582 14 0 1891 2472 733930392 733930973 0.000000e+00 998
27 TraesCS5A01G337300 chr1A 97.595 582 14 0 1891 2472 471983414 471983995 0.000000e+00 998
28 TraesCS5A01G337300 chr6A 97.595 582 13 1 1891 2472 181426592 181427172 0.000000e+00 996


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 TraesCS5A01G337300 chr5A 545749979 545752450 2471 True 4566 4566 100.000 1 2472 1 chr5A.!!$R5 2471
1 TraesCS5A01G337300 chr5A 643381327 643382486 1159 False 1831 1831 95.263 741 1892 1 chr5A.!!$F2 1151
2 TraesCS5A01G337300 chr5A 457423232 457423970 738 False 1123 1123 94.078 1 742 1 chr5A.!!$F1 741
3 TraesCS5A01G337300 chr5A 73750288 73751027 739 True 1120 1120 93.935 1 742 1 chr5A.!!$R1 741
4 TraesCS5A01G337300 chr5A 73802200 73802934 734 True 1086 1086 93.261 1 742 1 chr5A.!!$R3 741
5 TraesCS5A01G337300 chr5A 73767347 73768081 734 True 1064 1064 92.722 1 742 1 chr5A.!!$R2 741
6 TraesCS5A01G337300 chr5A 452516333 452517069 736 True 1061 1061 92.608 1 741 1 chr5A.!!$R4 740
7 TraesCS5A01G337300 chr2B 229826552 229827690 1138 False 1801 1801 95.147 744 1891 1 chr2B.!!$F1 1147
8 TraesCS5A01G337300 chr2B 454009433 454010577 1144 False 1700 1700 93.460 743 1893 1 chr2B.!!$F2 1150
9 TraesCS5A01G337300 chr2B 82489325 82490453 1128 True 1548 1548 91.372 746 1892 1 chr2B.!!$R1 1146
10 TraesCS5A01G337300 chr1D 400879438 400880579 1141 False 1790 1790 94.965 744 1887 1 chr1D.!!$F1 1143
11 TraesCS5A01G337300 chr6D 380811411 380812554 1143 True 1783 1783 94.870 752 1891 1 chr6D.!!$R1 1139
12 TraesCS5A01G337300 chr7B 58077364 58078505 1141 False 1705 1705 93.615 744 1891 1 chr7B.!!$F1 1147
13 TraesCS5A01G337300 chr7B 86800205 86800786 581 False 998 998 97.595 1891 2472 1 chr7B.!!$F2 581
14 TraesCS5A01G337300 chr5B 278896135 278897266 1131 True 1607 1607 92.235 744 1891 1 chr5B.!!$R1 1147
15 TraesCS5A01G337300 chr5B 513957744 513958325 581 True 998 998 97.595 1891 2472 1 chr5B.!!$R2 581
16 TraesCS5A01G337300 chr3B 777849268 777850394 1126 True 1524 1524 91.042 744 1891 1 chr3B.!!$R1 1147
17 TraesCS5A01G337300 chr3B 814695984 814696565 581 True 1003 1003 97.766 1891 2472 1 chr3B.!!$R2 581
18 TraesCS5A01G337300 chr2A 746633602 746634336 734 False 1103 1103 93.666 1 742 1 chr2A.!!$F1 741
19 TraesCS5A01G337300 chr2A 746646940 746647679 739 False 1064 1064 92.637 1 742 1 chr2A.!!$F2 741
20 TraesCS5A01G337300 chr2A 5160476 5161055 579 True 1000 1000 97.759 1891 2470 1 chr2A.!!$R1 579
21 TraesCS5A01G337300 chr7A 154373278 154374018 740 False 1081 1081 93.011 1 742 1 chr7A.!!$F1 741
22 TraesCS5A01G337300 chr7A 657147421 657148156 735 True 1027 1027 91.812 1 742 1 chr7A.!!$R2 741
23 TraesCS5A01G337300 chr7A 631494275 631494856 581 True 1003 1003 97.766 1891 2472 1 chr7A.!!$R1 581
24 TraesCS5A01G337300 chr4A 665113278 665113859 581 True 1003 1003 97.766 1891 2472 1 chr4A.!!$R1 581
25 TraesCS5A01G337300 chr3A 733930392 733930973 581 False 998 998 97.595 1891 2472 1 chr3A.!!$F1 581
26 TraesCS5A01G337300 chr1A 471983414 471983995 581 False 998 998 97.595 1891 2472 1 chr1A.!!$F1 581
27 TraesCS5A01G337300 chr6A 181426592 181427172 580 False 996 996 97.595 1891 2472 1 chr6A.!!$F1 581

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
547 559 0.035439 CACGAATGGGCTAAGTGGGT 60.035 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2020 0.819582 CCCCACGGTAGACACGTATT 59.18 55.0 0.0 0.0 43.58 1.89 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
196 197 2.768698 ACGAAGAGACAGAGACGAAGA 58.231 47.619 0.00 0.00 0.00 2.87
283 285 0.859232 CTTCCGTGTGACCTTTCGTG 59.141 55.000 0.00 0.00 0.00 4.35
295 297 1.541147 CCTTTCGTGTACCCGTAGTGA 59.459 52.381 0.00 0.00 0.00 3.41
370 382 3.735029 GTCGTGACGAGGCGAGGT 61.735 66.667 8.41 0.00 36.23 3.85
490 502 5.152934 AGGTCCAACTTCCACTAAACTAGA 58.847 41.667 0.00 0.00 0.00 2.43
518 530 8.654485 TGTGGGACTAAACTTTAGTAGTATCA 57.346 34.615 13.18 7.64 35.54 2.15
531 543 1.442769 AGTATCACTTGCCTTGCACG 58.557 50.000 0.00 0.00 38.71 5.34
547 559 0.035439 CACGAATGGGCTAAGTGGGT 60.035 55.000 0.00 0.00 0.00 4.51
569 581 8.881262 TGGGTCTCTAGGATTTATTAGGAATTC 58.119 37.037 0.00 0.00 0.00 2.17
611 625 6.350949 GCTGCCCAAAATAGACTAAATTCCAA 60.351 38.462 0.00 0.00 0.00 3.53
649 663 2.629617 CCCAGAGGCACACAGAAATTTT 59.370 45.455 0.00 0.00 0.00 1.82
669 683 6.607004 TTTTCCTTTGGTTCCAAAACACTA 57.393 33.333 16.25 2.46 37.10 2.74
984 1003 3.615709 GCAGCCCACAACCCAACC 61.616 66.667 0.00 0.00 0.00 3.77
986 1005 2.198426 AGCCCACAACCCAACCAG 59.802 61.111 0.00 0.00 0.00 4.00
1233 1281 1.003839 CCACGCCAAGCAGAAGGTA 60.004 57.895 0.00 0.00 0.00 3.08
1373 1421 1.217511 CATCTGACGGCAGTGCTCT 59.782 57.895 19.93 0.00 42.84 4.09
1490 1538 5.333566 TGGAATAAAGAAGGAAGTGGGTT 57.666 39.130 0.00 0.00 0.00 4.11
1684 1734 6.017192 ACTTACCCTCAAGACTGTGATTCTA 58.983 40.000 0.00 0.00 0.00 2.10
1716 1766 3.006672 ACCGAAGTTGGTCTTGCAG 57.993 52.632 0.00 0.00 37.91 4.41
1970 2020 2.819608 GCTTCACATAAAGCCTTGACCA 59.180 45.455 0.00 0.00 44.75 4.02
1978 2028 2.561478 AAGCCTTGACCAATACGTGT 57.439 45.000 0.00 0.00 0.00 4.49
1989 2039 0.819582 AATACGTGTCTACCGTGGGG 59.180 55.000 0.00 0.00 39.22 4.96
2267 2317 3.244215 CCTCTCAGTTGACCAACAGCTTA 60.244 47.826 14.42 0.00 43.47 3.09
2410 2460 2.649816 ACCCTTGGTAAAAGGATCTGCT 59.350 45.455 5.69 0.00 39.81 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 197 0.886490 CTTCGGCTGCTGGTTGTTCT 60.886 55.000 8.89 0.00 0.00 3.01
283 285 0.604578 TTGCCACTCACTACGGGTAC 59.395 55.000 0.00 0.00 0.00 3.34
295 297 5.594317 AGCCGATATCTAAATTTTTGCCACT 59.406 36.000 0.00 0.00 0.00 4.00
404 416 0.389391 CAAGAGGGATATCCACGCGT 59.611 55.000 23.27 5.58 38.24 6.01
518 530 1.526575 CCCATTCGTGCAAGGCAAGT 61.527 55.000 0.00 0.00 41.47 3.16
531 543 1.840635 AGAGACCCACTTAGCCCATTC 59.159 52.381 0.00 0.00 0.00 2.67
547 559 9.898576 TCAGGAATTCCTAATAAATCCTAGAGA 57.101 33.333 26.61 11.45 46.65 3.10
569 581 3.319122 GGCAGCCCAATAACTATTTCAGG 59.681 47.826 0.00 0.00 0.00 3.86
611 625 1.216990 GGGATCTGGTGGGAGATTGT 58.783 55.000 0.00 0.00 32.57 2.71
617 631 1.003442 CCTCTGGGATCTGGTGGGA 59.997 63.158 0.00 0.00 33.58 4.37
649 663 6.800072 AAATAGTGTTTTGGAACCAAAGGA 57.200 33.333 16.72 7.06 45.15 3.36
984 1003 2.125350 GGCTCTTGAGGCCGACTG 60.125 66.667 12.43 0.00 40.19 3.51
1068 1099 0.528017 CAGCGGTCAAGAGAGTAGCA 59.472 55.000 0.00 0.00 0.00 3.49
1210 1258 3.057548 CTGCTTGGCGTGGATGCA 61.058 61.111 0.00 0.00 36.28 3.96
1233 1281 4.078516 GCGTTGTAGGCGAGGGGT 62.079 66.667 0.00 0.00 0.00 4.95
1373 1421 1.266178 TCTTCCATCTCCACGAGCAA 58.734 50.000 0.00 0.00 0.00 3.91
1490 1538 4.193893 CCCCAGATCCATGCGCCA 62.194 66.667 4.18 0.00 0.00 5.69
1684 1734 5.810074 CCAACTTCGGTCTCAAAAACAAAAT 59.190 36.000 0.00 0.00 0.00 1.82
1970 2020 0.819582 CCCCACGGTAGACACGTATT 59.180 55.000 0.00 0.00 43.58 1.89
2267 2317 4.408921 TCCCGTGAATTAGATGTGGAAGAT 59.591 41.667 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.