Multiple sequence alignment - TraesCS6D01G118300

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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 TraesCS6D01G118300 chr6D 100.000 2723 0 0 1 2723 83975173 83972451 0 5029
1 TraesCS6D01G118300 chr6D 97.970 591 11 1 2133 2723 168780187 168779598 0 1024
2 TraesCS6D01G118300 chr5B 98.501 2135 31 1 1 2134 679660393 679662527 0 3764
3 TraesCS6D01G118300 chrUn 98.409 2137 31 2 1 2134 189394035 189396171 0 3755
4 TraesCS6D01G118300 chrUn 97.647 595 9 2 2133 2723 222675288 222675881 0 1016
5 TraesCS6D01G118300 chr4D 98.360 2134 34 1 1 2134 123414378 123416510 0 3746
6 TraesCS6D01G118300 chr4D 97.800 591 12 1 2133 2723 123437138 123436549 0 1018
7 TraesCS6D01G118300 chr7D 98.315 2136 33 2 2 2134 203554849 203552714 0 3742
8 TraesCS6D01G118300 chr7B 98.220 2135 37 1 1 2134 743087695 743089829 0 3731
9 TraesCS6D01G118300 chr5A 98.220 2135 37 1 1 2134 16601427 16599293 0 3731
10 TraesCS6D01G118300 chr5A 98.220 2135 37 1 1 2134 300074475 300076609 0 3731
11 TraesCS6D01G118300 chr5A 97.631 591 13 1 2133 2723 492851169 492850580 0 1013
12 TraesCS6D01G118300 chr7A 98.084 2140 35 2 1 2134 4961333 4963472 0 3720
13 TraesCS6D01G118300 chr6A 98.080 2135 40 1 1 2134 289130126 289132260 0 3714
14 TraesCS6D01G118300 chr6A 98.308 591 9 1 2133 2723 608871168 608871757 0 1035
15 TraesCS6D01G118300 chr2D 98.646 591 7 1 2133 2723 322916032 322915443 0 1046
16 TraesCS6D01G118300 chr4A 98.308 591 9 1 2133 2723 67564610 67565199 0 1035
17 TraesCS6D01G118300 chr5D 97.973 592 10 2 2133 2723 324462060 324461470 0 1026
18 TraesCS6D01G118300 chr6B 97.647 595 9 2 2133 2723 596633714 596633121 0 1016


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 TraesCS6D01G118300 chr6D 83972451 83975173 2722 True 5029 5029 100.000 1 2723 1 chr6D.!!$R1 2722
1 TraesCS6D01G118300 chr6D 168779598 168780187 589 True 1024 1024 97.970 2133 2723 1 chr6D.!!$R2 590
2 TraesCS6D01G118300 chr5B 679660393 679662527 2134 False 3764 3764 98.501 1 2134 1 chr5B.!!$F1 2133
3 TraesCS6D01G118300 chrUn 189394035 189396171 2136 False 3755 3755 98.409 1 2134 1 chrUn.!!$F1 2133
4 TraesCS6D01G118300 chrUn 222675288 222675881 593 False 1016 1016 97.647 2133 2723 1 chrUn.!!$F2 590
5 TraesCS6D01G118300 chr4D 123414378 123416510 2132 False 3746 3746 98.360 1 2134 1 chr4D.!!$F1 2133
6 TraesCS6D01G118300 chr4D 123436549 123437138 589 True 1018 1018 97.800 2133 2723 1 chr4D.!!$R1 590
7 TraesCS6D01G118300 chr7D 203552714 203554849 2135 True 3742 3742 98.315 2 2134 1 chr7D.!!$R1 2132
8 TraesCS6D01G118300 chr7B 743087695 743089829 2134 False 3731 3731 98.220 1 2134 1 chr7B.!!$F1 2133
9 TraesCS6D01G118300 chr5A 16599293 16601427 2134 True 3731 3731 98.220 1 2134 1 chr5A.!!$R1 2133
10 TraesCS6D01G118300 chr5A 300074475 300076609 2134 False 3731 3731 98.220 1 2134 1 chr5A.!!$F1 2133
11 TraesCS6D01G118300 chr5A 492850580 492851169 589 True 1013 1013 97.631 2133 2723 1 chr5A.!!$R2 590
12 TraesCS6D01G118300 chr7A 4961333 4963472 2139 False 3720 3720 98.084 1 2134 1 chr7A.!!$F1 2133
13 TraesCS6D01G118300 chr6A 289130126 289132260 2134 False 3714 3714 98.080 1 2134 1 chr6A.!!$F1 2133
14 TraesCS6D01G118300 chr6A 608871168 608871757 589 False 1035 1035 98.308 2133 2723 1 chr6A.!!$F2 590
15 TraesCS6D01G118300 chr2D 322915443 322916032 589 True 1046 1046 98.646 2133 2723 1 chr2D.!!$R1 590
16 TraesCS6D01G118300 chr4A 67564610 67565199 589 False 1035 1035 98.308 2133 2723 1 chr4A.!!$F1 590
17 TraesCS6D01G118300 chr5D 324461470 324462060 590 True 1026 1026 97.973 2133 2723 1 chr5D.!!$R1 590
18 TraesCS6D01G118300 chr6B 596633121 596633714 593 True 1016 1016 97.647 2133 2723 1 chr6B.!!$R1 590

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
33 34 1.153449 CCGCCCGCTCTCAATACAA 60.153 57.895 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1829 2.267642 CCGGCAGGAATCGAACCA 59.732 61.111 13.17 0.0 41.02 3.67 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
33 34 1.153449 CCGCCCGCTCTCAATACAA 60.153 57.895 0.00 0.0 0.00 2.41
137 143 5.553123 TGTATAGCGAAACCTTTCCTTGAA 58.447 37.500 0.00 0.0 33.68 2.69
180 186 2.722094 AGCCGAGCTATCTATCCAGAG 58.278 52.381 0.00 0.0 36.99 3.35
207 213 4.226761 GTTGAACGAAGCGAATGGAAAAT 58.773 39.130 0.00 0.0 0.00 1.82
295 301 6.647067 CGATGTAAGATAGAAAGAATGGGGAC 59.353 42.308 0.00 0.0 0.00 4.46
348 354 5.341872 TCAATTCCAAATCATTTGCCGAT 57.658 34.783 4.40 0.0 39.31 4.18
427 433 3.059188 CGTGGGTGAATCAAGTACAACAC 60.059 47.826 0.00 0.0 0.00 3.32
513 519 5.243954 AGAAGTACACATTGCTGACTGACTA 59.756 40.000 0.00 0.0 0.00 2.59
615 621 1.169577 AGCACAGACTCTACTCACCG 58.830 55.000 0.00 0.0 0.00 4.94
1069 1076 2.420022 AGCTACGCGCAAATTCTCATTT 59.580 40.909 5.73 0.0 42.61 2.32
1070 1077 3.119849 AGCTACGCGCAAATTCTCATTTT 60.120 39.130 5.73 0.0 42.61 1.82
1071 1078 3.608073 GCTACGCGCAAATTCTCATTTTT 59.392 39.130 5.73 0.0 38.92 1.94
1096 1103 2.734606 CGGTTGTTCTTAACAGCGATGA 59.265 45.455 8.12 0.0 42.68 2.92
1127 1134 0.830444 AGTCTTCGGGTAGCACCACA 60.830 55.000 7.49 0.0 41.02 4.17
1421 1429 0.112218 ATTTACCTGGGTGCACTGCA 59.888 50.000 17.98 0.0 35.60 4.41
1643 1651 3.601435 TCTTGTTCGTTCTGGAAACACA 58.399 40.909 0.00 0.0 35.60 3.72
1753 1761 9.273016 CTCTCAAATAAAAACCTAGTTCACTCA 57.727 33.333 0.00 0.0 0.00 3.41
1821 1829 4.502105 AGGCAAAATGGGTCAAAAAGTT 57.498 36.364 0.00 0.0 0.00 2.66
2356 2370 6.228273 TCAATTCTCTGTCTTGCTAAAACG 57.772 37.500 0.00 0.0 0.00 3.60
2540 2554 1.675310 CTCAGGTGCGGCCAAATCA 60.675 57.895 2.24 0.0 40.61 2.57
2623 2637 8.594550 AGCTGGTACTAGTTTCATTCTTTCTAA 58.405 33.333 8.16 0.0 0.00 2.10
2719 2741 0.976641 TCTCATCCGGTTGAGCTGTT 59.023 50.000 29.99 0.0 42.37 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.037446 GTCTTGTGAGAGAGAGTCACTTGT 59.963 45.833 4.96 0.00 44.02 3.16
137 143 7.148000 GGCTTCTATTAGCTGAGAATGGTTTTT 60.148 37.037 0.00 0.00 40.99 1.94
180 186 1.503818 TTCGCTTCGTTCAACCCTGC 61.504 55.000 0.00 0.00 0.00 4.85
207 213 8.646004 TCACAATGGATTTATGTTTTCTTTGGA 58.354 29.630 0.00 0.00 0.00 3.53
231 237 6.572509 GCTGTAGAGTCACTGGTTTCTAATCA 60.573 42.308 0.00 0.00 0.00 2.57
295 301 1.555533 AGAGGAAACCGAAGCCCTAAG 59.444 52.381 0.00 0.00 0.00 2.18
348 354 4.537135 AAAAGAGAAGTGAGTCCGCATA 57.463 40.909 0.00 0.00 0.00 3.14
427 433 0.668706 CCACAAGCTCTGACCTGACG 60.669 60.000 0.00 0.00 0.00 4.35
513 519 8.351461 GCTACTAGTAACTAGGATCGTTCAAAT 58.649 37.037 3.76 0.00 38.30 2.32
615 621 1.777199 CGTAGGTGGAAAACGCGTC 59.223 57.895 14.44 0.00 0.00 5.19
865 871 4.656117 TTTCGCTCCGCTCGTGCA 62.656 61.111 10.43 0.00 39.64 4.57
963 969 4.038402 CCTTGCAAGTGGAACAAGAAAGAT 59.962 41.667 24.35 0.00 44.16 2.40
1069 1076 4.260456 CGCTGTTAAGAACAACCGAGAAAA 60.260 41.667 6.32 0.00 41.61 2.29
1070 1077 3.246699 CGCTGTTAAGAACAACCGAGAAA 59.753 43.478 6.32 0.00 41.61 2.52
1071 1078 2.798283 CGCTGTTAAGAACAACCGAGAA 59.202 45.455 6.32 0.00 41.61 2.87
1096 1103 6.985059 GCTACCCGAAGACTTAAATGAATAGT 59.015 38.462 0.00 0.00 0.00 2.12
1127 1134 6.779539 AGAATTTCCACCTTGTTGAAGATCTT 59.220 34.615 7.95 7.95 0.00 2.40
1206 1213 4.890088 AGGAACTGTTTATAACTGTCGCA 58.110 39.130 0.00 0.00 41.84 5.10
1421 1429 5.281727 GTTCGACAGGAAGCTTTTGAAAAT 58.718 37.500 16.11 0.00 34.69 1.82
1498 1506 2.778299 TGTATTCCACCAGTTGACTGC 58.222 47.619 5.62 0.00 42.47 4.40
1643 1651 5.369699 TCGGGAAAAGATGGAATAGGAAGAT 59.630 40.000 0.00 0.00 0.00 2.40
1753 1761 3.370840 TTCAGCCATGGATGCTTTAGT 57.629 42.857 25.40 0.00 36.81 2.24
1821 1829 2.267642 CCGGCAGGAATCGAACCA 59.732 61.111 13.17 0.00 41.02 3.67
2354 2368 4.918810 ACAAGAAAAGAAGGATTTGCGT 57.081 36.364 0.00 0.00 0.00 5.24
2355 2369 7.905493 GTCTATACAAGAAAAGAAGGATTTGCG 59.095 37.037 0.00 0.00 35.47 4.85
2356 2370 7.905493 CGTCTATACAAGAAAAGAAGGATTTGC 59.095 37.037 0.00 0.00 35.47 3.68
2474 2488 0.946221 CTTCTTGTGCCGACTTCGCT 60.946 55.000 0.00 0.00 38.18 4.93
2534 2548 6.914215 CAGACGGGAATATTGATTGTGATTTG 59.086 38.462 0.00 0.00 0.00 2.32
2623 2637 3.958147 GTTCCGGGTATTGGATTTTGGAT 59.042 43.478 0.00 0.00 34.91 3.41


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

AutoCloner maintained by Alex Coulton.