Multiple sequence alignment - TraesCS5B01G369400

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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 TraesCS5B01G369400 chr5B 100.000 2348 0 0 1 2348 548384031 548381684 0.000000e+00 4337
1 TraesCS5B01G369400 chr5B 96.682 663 21 1 1687 2348 643534276 643533614 0.000000e+00 1101
2 TraesCS5B01G369400 chr6B 93.365 1688 99 6 1 1686 695921008 695922684 0.000000e+00 2484
3 TraesCS5B01G369400 chr6B 90.076 1703 146 11 1 1687 544397850 544396155 0.000000e+00 2187
4 TraesCS5B01G369400 chr6B 86.733 1696 210 12 1 1686 232073916 232075606 0.000000e+00 1871
5 TraesCS5B01G369400 chr6B 85.875 1600 209 15 97 1688 79247719 79246129 0.000000e+00 1687
6 TraesCS5B01G369400 chr6B 95.633 664 26 3 1687 2348 586664960 586664298 0.000000e+00 1062
7 TraesCS5B01G369400 chr3B 92.481 1689 120 5 2 1687 106936235 106937919 0.000000e+00 2409
8 TraesCS5B01G369400 chr3B 96.078 663 25 1 1687 2348 239894384 239893722 0.000000e+00 1079
9 TraesCS5B01G369400 chr3B 95.815 669 26 2 1681 2348 829516392 829517059 0.000000e+00 1079
10 TraesCS5B01G369400 chr1B 91.681 1695 132 7 1 1687 613010099 613008406 0.000000e+00 2340
11 TraesCS5B01G369400 chr1B 91.538 1690 131 4 7 1687 592573619 592571933 0.000000e+00 2318
12 TraesCS5B01G369400 chr7B 87.750 1698 187 16 1 1685 38632619 38630930 0.000000e+00 1964
13 TraesCS5B01G369400 chr7B 96.983 663 19 1 1687 2348 741685780 741686442 0.000000e+00 1112
14 TraesCS5B01G369400 chr7B 95.928 663 26 1 1687 2348 467442463 467443125 0.000000e+00 1074
15 TraesCS5B01G369400 chr2B 81.417 1609 281 14 91 1687 748211383 748212985 0.000000e+00 1299
16 TraesCS5B01G369400 chr2B 96.682 663 21 1 1687 2348 175650029 175650691 0.000000e+00 1101
17 TraesCS5B01G369400 chr2B 95.777 663 27 1 1687 2348 78419884 78420546 0.000000e+00 1068
18 TraesCS5B01G369400 chr2B 80.769 546 92 9 1151 1687 748363422 748363963 4.670000e-112 414
19 TraesCS5B01G369400 chr4B 95.764 661 27 1 1687 2346 18142361 18143021 0.000000e+00 1064


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 TraesCS5B01G369400 chr5B 548381684 548384031 2347 True 4337 4337 100.000 1 2348 1 chr5B.!!$R1 2347
1 TraesCS5B01G369400 chr5B 643533614 643534276 662 True 1101 1101 96.682 1687 2348 1 chr5B.!!$R2 661
2 TraesCS5B01G369400 chr6B 695921008 695922684 1676 False 2484 2484 93.365 1 1686 1 chr6B.!!$F2 1685
3 TraesCS5B01G369400 chr6B 544396155 544397850 1695 True 2187 2187 90.076 1 1687 1 chr6B.!!$R2 1686
4 TraesCS5B01G369400 chr6B 232073916 232075606 1690 False 1871 1871 86.733 1 1686 1 chr6B.!!$F1 1685
5 TraesCS5B01G369400 chr6B 79246129 79247719 1590 True 1687 1687 85.875 97 1688 1 chr6B.!!$R1 1591
6 TraesCS5B01G369400 chr6B 586664298 586664960 662 True 1062 1062 95.633 1687 2348 1 chr6B.!!$R3 661
7 TraesCS5B01G369400 chr3B 106936235 106937919 1684 False 2409 2409 92.481 2 1687 1 chr3B.!!$F1 1685
8 TraesCS5B01G369400 chr3B 239893722 239894384 662 True 1079 1079 96.078 1687 2348 1 chr3B.!!$R1 661
9 TraesCS5B01G369400 chr3B 829516392 829517059 667 False 1079 1079 95.815 1681 2348 1 chr3B.!!$F2 667
10 TraesCS5B01G369400 chr1B 613008406 613010099 1693 True 2340 2340 91.681 1 1687 1 chr1B.!!$R2 1686
11 TraesCS5B01G369400 chr1B 592571933 592573619 1686 True 2318 2318 91.538 7 1687 1 chr1B.!!$R1 1680
12 TraesCS5B01G369400 chr7B 38630930 38632619 1689 True 1964 1964 87.750 1 1685 1 chr7B.!!$R1 1684
13 TraesCS5B01G369400 chr7B 741685780 741686442 662 False 1112 1112 96.983 1687 2348 1 chr7B.!!$F2 661
14 TraesCS5B01G369400 chr7B 467442463 467443125 662 False 1074 1074 95.928 1687 2348 1 chr7B.!!$F1 661
15 TraesCS5B01G369400 chr2B 748211383 748212985 1602 False 1299 1299 81.417 91 1687 1 chr2B.!!$F3 1596
16 TraesCS5B01G369400 chr2B 175650029 175650691 662 False 1101 1101 96.682 1687 2348 1 chr2B.!!$F2 661
17 TraesCS5B01G369400 chr2B 78419884 78420546 662 False 1068 1068 95.777 1687 2348 1 chr2B.!!$F1 661
18 TraesCS5B01G369400 chr2B 748363422 748363963 541 False 414 414 80.769 1151 1687 1 chr2B.!!$F4 536
19 TraesCS5B01G369400 chr4B 18142361 18143021 660 False 1064 1064 95.764 1687 2346 1 chr4B.!!$F1 659

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
924 933 0.037734 GGAGACGGAATTGGTTGGGT 59.962 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
1974 2010 1.557371 TGGTGTGCTTCAATCCCGATA 59.443 47.619 0.0 0.0 0.0 2.92 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
49 50 3.572642 TCCTCAAGTGTTGTGAGTCCTA 58.427 45.455 1.14 0.00 40.83 2.94
54 55 4.832823 TCAAGTGTTGTGAGTCCTAGATCA 59.167 41.667 0.00 0.00 0.00 2.92
479 482 0.854039 TCTACCTGGTGGGGAGGAGA 60.854 60.000 10.23 0.00 46.19 3.71
599 604 1.897473 ATGATGGGGATCACTGTGGA 58.103 50.000 8.11 0.00 32.79 4.02
605 610 2.771943 TGGGGATCACTGTGGATAGTTC 59.228 50.000 8.11 0.00 0.00 3.01
627 634 6.381498 TCTAAGAATGGTGTGGGTGATAAA 57.619 37.500 0.00 0.00 0.00 1.40
628 635 6.785076 TCTAAGAATGGTGTGGGTGATAAAA 58.215 36.000 0.00 0.00 0.00 1.52
629 636 7.235079 TCTAAGAATGGTGTGGGTGATAAAAA 58.765 34.615 0.00 0.00 0.00 1.94
679 687 2.042464 GTGAGCAGTGGAGGGATATGA 58.958 52.381 0.00 0.00 0.00 2.15
865 874 9.748708 CACTTAAGATTCAAATTTTCTTGTGGA 57.251 29.630 10.09 0.00 32.28 4.02
924 933 0.037734 GGAGACGGAATTGGTTGGGT 59.962 55.000 0.00 0.00 0.00 4.51
963 972 6.826231 CCTTCTGTGAGTATAGAGAGACTTCA 59.174 42.308 0.00 0.00 0.00 3.02
964 973 7.338196 CCTTCTGTGAGTATAGAGAGACTTCAA 59.662 40.741 0.00 0.00 0.00 2.69
1033 1042 0.759812 TGGGTGTGTACTGGGAACGA 60.760 55.000 0.00 0.00 0.00 3.85
1087 1096 4.919774 TCCTGGTGTTATTGCTTCCTTA 57.080 40.909 0.00 0.00 0.00 2.69
1259 1268 1.661463 ATGCTGAAGGGAGAAGACCA 58.339 50.000 0.00 0.00 0.00 4.02
1378 1411 1.948144 GCTGCTTCCCCAACTTCTCTC 60.948 57.143 0.00 0.00 0.00 3.20
1381 1414 0.977395 CTTCCCCAACTTCTCTCCGT 59.023 55.000 0.00 0.00 0.00 4.69
1431 1464 2.875933 CCTTTTGGTGTCGCTAGTTTGA 59.124 45.455 0.00 0.00 34.07 2.69
1490 1524 6.382859 TGACTTTGATTAGCCTGATGGTACTA 59.617 38.462 0.00 0.00 35.27 1.82
1592 1627 1.303236 CAGGGATGCGTTGAACCCA 60.303 57.895 0.00 0.00 44.25 4.51
1896 1932 0.924090 GTCCTCGACGATCATGTTGC 59.076 55.000 0.00 0.00 0.00 4.17
1913 1949 1.581912 GCGCATGATCACACAAGCG 60.582 57.895 18.12 18.12 43.07 4.68
1921 1957 2.283298 GATCACACAAGCGGTCATCAT 58.717 47.619 0.00 0.00 0.00 2.45
2115 2152 6.805150 ACCACTGAGGATATATACCATCAGA 58.195 40.000 22.65 0.00 41.22 3.27
2169 2206 2.503765 TGACCTCAAAGTTGACAGGTGA 59.496 45.455 9.12 0.00 36.30 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.141158 ACACTTGAGGAACCTCTTTTCCAT 60.141 41.667 19.61 0.12 46.76 3.41
21 22 3.199946 TCACAACACTTGAGGAACCTCTT 59.800 43.478 19.61 4.77 43.12 2.85
49 50 1.094073 GGACGCTGCATTGCTGATCT 61.094 55.000 18.44 0.46 0.00 2.75
54 55 2.816958 CGAGGACGCTGCATTGCT 60.817 61.111 10.49 0.00 0.00 3.91
319 322 1.675552 CGTTTCCAACTTCCACCACT 58.324 50.000 0.00 0.00 0.00 4.00
479 482 9.392259 GCAAGGTTACCAGAATTAAGTAATACT 57.608 33.333 3.51 0.00 0.00 2.12
599 604 5.487488 TCACCCACACCATTCTTAGAACTAT 59.513 40.000 0.00 0.00 0.00 2.12
605 610 7.461182 TTTTTATCACCCACACCATTCTTAG 57.539 36.000 0.00 0.00 0.00 2.18
679 687 2.159382 CCACGAGGCTACCACATTTTT 58.841 47.619 0.00 0.00 0.00 1.94
865 874 7.780271 AGTAAGAATGGAGTCTTGGAAAAGTTT 59.220 33.333 0.00 0.00 38.33 2.66
924 933 4.410883 TCACAGAAGGAACAAGAAGGGTTA 59.589 41.667 0.00 0.00 0.00 2.85
963 972 2.831526 ACAGGTGAAAAACAGGTGCTTT 59.168 40.909 0.00 0.00 0.00 3.51
964 973 2.427095 GACAGGTGAAAAACAGGTGCTT 59.573 45.455 0.00 0.00 0.00 3.91
1033 1042 1.408969 ATGTTGTTCGGGCAAAGGTT 58.591 45.000 0.00 0.00 0.00 3.50
1087 1096 3.551635 ATAGAATCTCTCCCCATCGGT 57.448 47.619 0.00 0.00 0.00 4.69
1259 1268 0.909610 TCCCCTCTCCATTGCTTCGT 60.910 55.000 0.00 0.00 0.00 3.85
1381 1414 1.476845 TACAGACAGCAAAGCCCGGA 61.477 55.000 0.73 0.00 0.00 5.14
1431 1464 1.439228 CTCCCATCGCTCGACACAT 59.561 57.895 0.00 0.00 0.00 3.21
1490 1524 8.168058 ACACCAAAATATCCAAGGTAAACTACT 58.832 33.333 0.00 0.00 0.00 2.57
1592 1627 4.405680 CAGGAAACAAAGAAAGGGGAAAGT 59.594 41.667 0.00 0.00 0.00 2.66
1913 1949 3.876320 GGAAGCTTTGAGAGATGATGACC 59.124 47.826 0.00 0.00 0.00 4.02
1921 1957 4.566488 GGGATGAAAGGAAGCTTTGAGAGA 60.566 45.833 0.00 0.00 0.00 3.10
1974 2010 1.557371 TGGTGTGCTTCAATCCCGATA 59.443 47.619 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.