Multiple sequence alignment - TraesCS7D01G081200

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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 TraesCS7D01G081200 chr7D 100.000 2448 0 0 1 2448 48126878 48129325 0.000000e+00 4521.0
1 TraesCS7D01G081200 chr7D 96.718 2468 57 10 1 2448 48208837 48211300 0.000000e+00 4087.0
2 TraesCS7D01G081200 chr7D 96.588 2462 55 9 1 2448 48165828 48168274 0.000000e+00 4054.0
3 TraesCS7D01G081200 chr7D 96.588 2462 55 9 1 2448 48172815 48175261 0.000000e+00 4054.0
4 TraesCS7D01G081200 chr7D 92.848 1482 75 18 494 1970 48257036 48258491 0.000000e+00 2121.0
5 TraesCS7D01G081200 chr7D 81.978 910 127 17 794 1697 47809298 47808420 0.000000e+00 737.0
6 TraesCS7D01G081200 chr7A 90.802 1620 86 36 494 2108 50633249 50634810 0.000000e+00 2108.0
7 TraesCS7D01G081200 chr7A 80.440 910 138 18 794 1697 50425652 50424777 0.000000e+00 658.0
8 TraesCS7D01G081200 chr7A 89.665 358 26 6 2100 2446 50816851 50816494 1.730000e-121 446.0
9 TraesCS7D01G081200 chr7A 87.989 358 26 10 2100 2446 50791450 50791801 8.150000e-110 407.0
10 TraesCS7D01G081200 chr7A 87.500 56 1 6 747 802 71037008 71036959 2.630000e-05 60.2
11 TraesCS7D01G081200 chrUn 89.114 1626 112 30 494 2110 49485309 49486878 0.000000e+00 1962.0
12 TraesCS7D01G081200 chrUn 87.546 1638 112 33 494 2121 49452720 49454275 0.000000e+00 1810.0
13 TraesCS7D01G081200 chrUn 95.086 407 11 2 1666 2064 478115711 478116116 1.240000e-177 632.0
14 TraesCS7D01G081200 chrUn 92.920 339 21 2 2112 2448 49462385 49462722 7.870000e-135 490.0
15 TraesCS7D01G081200 chr4A 94.465 795 41 2 995 1787 663211687 663212480 0.000000e+00 1221.0
16 TraesCS7D01G081200 chr4A 92.379 643 40 4 1808 2445 663212471 663213109 0.000000e+00 907.0
17 TraesCS7D01G081200 chr4A 93.333 480 26 5 494 968 663211209 663211687 0.000000e+00 704.0


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 TraesCS7D01G081200 chr7D 48126878 48129325 2447 False 4521 4521 100.000000 1 2448 1 chr7D.!!$F1 2447
1 TraesCS7D01G081200 chr7D 48208837 48211300 2463 False 4087 4087 96.718000 1 2448 1 chr7D.!!$F4 2447
2 TraesCS7D01G081200 chr7D 48165828 48168274 2446 False 4054 4054 96.588000 1 2448 1 chr7D.!!$F2 2447
3 TraesCS7D01G081200 chr7D 48172815 48175261 2446 False 4054 4054 96.588000 1 2448 1 chr7D.!!$F3 2447
4 TraesCS7D01G081200 chr7D 48257036 48258491 1455 False 2121 2121 92.848000 494 1970 1 chr7D.!!$F5 1476
5 TraesCS7D01G081200 chr7D 47808420 47809298 878 True 737 737 81.978000 794 1697 1 chr7D.!!$R1 903
6 TraesCS7D01G081200 chr7A 50633249 50634810 1561 False 2108 2108 90.802000 494 2108 1 chr7A.!!$F1 1614
7 TraesCS7D01G081200 chr7A 50424777 50425652 875 True 658 658 80.440000 794 1697 1 chr7A.!!$R1 903
8 TraesCS7D01G081200 chrUn 49485309 49486878 1569 False 1962 1962 89.114000 494 2110 1 chrUn.!!$F3 1616
9 TraesCS7D01G081200 chrUn 49452720 49454275 1555 False 1810 1810 87.546000 494 2121 1 chrUn.!!$F1 1627
10 TraesCS7D01G081200 chr4A 663211209 663213109 1900 False 944 1221 93.392333 494 2445 3 chr4A.!!$F1 1951

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
332 333 0.028770 GTGAGCGGTCTCGAGATCAG 59.971 60.0 24.78 17.57 42.26 2.90 F
1331 1380 4.586001 AGAAATTTTGCAGCCTCTTTCTCA 59.414 37.5 0.00 0.00 29.44 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1459 0.250209 ACACTTCTGCAGGCACTCAG 60.250 55.000 15.13 3.4 34.60 3.35 R
2288 2373 2.580815 GCTTTTGGGCATGGAGGC 59.419 61.111 0.00 0.0 43.27 4.70 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
87 88 5.112129 ACCTTCCACATATACTGGTTTCC 57.888 43.478 0.00 0.00 0.00 3.13
129 130 0.613260 CTGTGGATCTTCCGTTCCCA 59.387 55.000 0.00 0.00 40.17 4.37
165 166 0.466124 CCTTCCGATCTTGACTCCCC 59.534 60.000 0.00 0.00 0.00 4.81
175 176 1.830477 CTTGACTCCCCTCTTCTCTGG 59.170 57.143 0.00 0.00 0.00 3.86
300 301 1.641577 CTAGCAACACTCGTAAGGCC 58.358 55.000 0.00 0.00 38.47 5.19
332 333 0.028770 GTGAGCGGTCTCGAGATCAG 59.971 60.000 24.78 17.57 42.26 2.90
1149 1188 5.592688 TCTTCGGATCAGACATACATACACA 59.407 40.000 0.00 0.00 0.00 3.72
1150 1189 5.183014 TCGGATCAGACATACATACACAC 57.817 43.478 0.00 0.00 0.00 3.82
1331 1380 4.586001 AGAAATTTTGCAGCCTCTTTCTCA 59.414 37.500 0.00 0.00 29.44 3.27
1342 1391 7.137426 GCAGCCTCTTTCTCATATGTTATTTG 58.863 38.462 1.90 0.00 0.00 2.32
1410 1459 2.978489 CCGACTGTTACAAGACGAAGAC 59.022 50.000 0.00 0.00 37.50 3.01
1429 1478 0.250209 CTGAGTGCCTGCAGAAGTGT 60.250 55.000 17.39 0.00 34.06 3.55
1467 1516 2.046314 CCCACCTTCATCGCGGTT 60.046 61.111 6.13 0.00 0.00 4.44
1772 1828 0.758310 TGATTTGGCAGTTGTGGGCA 60.758 50.000 0.00 0.00 39.24 5.36
1790 1846 6.326323 TGTGGGCAGACAGTCATATAGATTTA 59.674 38.462 2.66 0.00 0.00 1.40
1897 1966 3.932545 ATGGTGCGCAAACTAAATCAA 57.067 38.095 14.00 0.00 0.00 2.57
1949 2018 7.398618 TCAGGACTCTTTCAGATGAAGATAAGT 59.601 37.037 0.00 0.00 35.21 2.24
1989 2058 9.075519 ACAACATGCAGAAACATTTTTATATCG 57.924 29.630 0.00 0.00 0.00 2.92
2157 2241 4.578871 CATTTATGCCCATCCGTCTCATA 58.421 43.478 0.00 0.00 0.00 2.15
2179 2263 8.807118 TCATATTTTGCAACAAAATACCCTACA 58.193 29.630 21.45 6.25 35.63 2.74
2232 2316 1.593209 TGAGGTTCGTCCGTTGTGC 60.593 57.895 0.00 0.00 41.99 4.57
2267 2352 2.015587 AGGAAACGGTTGCGTTTTGTA 58.984 42.857 0.00 0.00 41.42 2.41
2288 2373 7.294676 TGTAAGATTCAAACTCATGATGTCG 57.705 36.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 2.606308 CGATCGGTAAGGTTATGTCCGG 60.606 54.545 7.38 0.00 41.27 5.14
129 130 2.680370 GGGGCGGGTTGAGGAGAAT 61.680 63.158 0.00 0.00 0.00 2.40
165 166 2.421619 GTTGCCAGAACCAGAGAAGAG 58.578 52.381 0.00 0.00 0.00 2.85
175 176 0.317854 GAAGTTGCGGTTGCCAGAAC 60.318 55.000 0.00 0.00 41.78 3.01
300 301 1.308069 CGCTCACCCATCCACCAAAG 61.308 60.000 0.00 0.00 0.00 2.77
392 396 1.954035 AAACCCTAGAGTCCCCTCAC 58.046 55.000 0.00 0.00 40.40 3.51
1149 1188 0.679505 AGTACCGCAGATGTGTGTGT 59.320 50.000 2.44 3.17 31.71 3.72
1150 1189 1.070821 CAGTACCGCAGATGTGTGTG 58.929 55.000 2.44 0.00 31.71 3.82
1342 1391 3.681897 ACTCAGCACGAATCTCAATGTTC 59.318 43.478 0.00 0.00 0.00 3.18
1410 1459 0.250209 ACACTTCTGCAGGCACTCAG 60.250 55.000 15.13 3.40 34.60 3.35
1429 1478 3.942748 GGCATTAACCGTTGTAGGAATGA 59.057 43.478 7.57 0.00 34.73 2.57
1760 1816 1.510480 GACTGTCTGCCCACAACTGC 61.510 60.000 0.00 0.00 0.00 4.40
1897 1966 1.134521 TCTCACTTGTCTTGTGCCGTT 60.135 47.619 0.00 0.00 35.58 4.44
1949 2018 6.760298 TCTGCATGTTGTTTTCTTGCAATTTA 59.240 30.769 0.00 0.00 42.35 1.40
2157 2241 8.916628 AAATGTAGGGTATTTTGTTGCAAAAT 57.083 26.923 19.38 19.38 34.55 1.82
2179 2263 6.028146 ACCGCGGGTTAATTAAAGAAAAAT 57.972 33.333 31.76 0.00 27.29 1.82
2232 2316 3.482110 CGTTTCCTCGTTCTTTGCAAAAG 59.518 43.478 13.84 7.07 0.00 2.27
2267 2352 4.095483 GGCGACATCATGAGTTTGAATCTT 59.905 41.667 0.09 0.00 0.00 2.40
2288 2373 2.580815 GCTTTTGGGCATGGAGGC 59.419 61.111 0.00 0.00 43.27 4.70
2374 2459 6.093357 TGCGTATTCTCATGCAAAGTATCAAA 59.907 34.615 0.00 0.00 37.50 2.69
2426 2511 3.476552 TCGAGTTGGCTTGTTGATTTCT 58.523 40.909 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.