Multiple sequence alignment - TraesCS6B01G117800

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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 TraesCS6B01G117800 chr6B 100.000 2297 0 0 1 2297 111692345 111690049 0 4242
1 TraesCS6B01G117800 chrUn 98.346 2298 37 1 1 2297 291535439 291537736 0 4032
2 TraesCS6B01G117800 chrUn 98.303 2298 38 1 1 2297 199874823 199877120 0 4026
3 TraesCS6B01G117800 chrUn 98.303 2298 38 1 1 2297 229310228 229307931 0 4026
4 TraesCS6B01G117800 chrUn 98.259 2298 38 2 1 2297 245706067 245708363 0 4021
5 TraesCS6B01G117800 chrUn 98.217 2299 39 2 1 2297 274341283 274338985 0 4017
6 TraesCS6B01G117800 chrUn 98.129 2298 42 1 1 2297 3845815 3843518 0 4004
7 TraesCS6B01G117800 chrUn 98.129 2298 42 1 1 2297 199904743 199907040 0 4004
8 TraesCS6B01G117800 chr1B 98.303 2298 36 2 1 2297 544593696 544595991 0 4024
9 TraesCS6B01G117800 chr1B 98.172 2298 41 1 1 2297 544623635 544625932 0 4010


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 TraesCS6B01G117800 chr6B 111690049 111692345 2296 True 4242 4242 100.000 1 2297 1 chr6B.!!$R1 2296
1 TraesCS6B01G117800 chrUn 291535439 291537736 2297 False 4032 4032 98.346 1 2297 1 chrUn.!!$F4 2296
2 TraesCS6B01G117800 chrUn 199874823 199877120 2297 False 4026 4026 98.303 1 2297 1 chrUn.!!$F1 2296
3 TraesCS6B01G117800 chrUn 229307931 229310228 2297 True 4026 4026 98.303 1 2297 1 chrUn.!!$R2 2296
4 TraesCS6B01G117800 chrUn 245706067 245708363 2296 False 4021 4021 98.259 1 2297 1 chrUn.!!$F3 2296
5 TraesCS6B01G117800 chrUn 274338985 274341283 2298 True 4017 4017 98.217 1 2297 1 chrUn.!!$R3 2296
6 TraesCS6B01G117800 chrUn 3843518 3845815 2297 True 4004 4004 98.129 1 2297 1 chrUn.!!$R1 2296
7 TraesCS6B01G117800 chrUn 199904743 199907040 2297 False 4004 4004 98.129 1 2297 1 chrUn.!!$F2 2296
8 TraesCS6B01G117800 chr1B 544593696 544595991 2295 False 4024 4024 98.303 1 2297 1 chr1B.!!$F1 2296
9 TraesCS6B01G117800 chr1B 544623635 544625932 2297 False 4010 4010 98.172 1 2297 1 chr1B.!!$F2 2296

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
78 79 0.611714 GTAGCTGGTTCCCTCCGAAA 59.388 55.0 0.00 0.0 30.39 3.46 F
1040 1042 0.250553 AAGTCGGCAAAACGGATCCA 60.251 50.0 13.41 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1115 0.459934 GTGAGCAGCTCGAGCAATCT 60.460 55.000 36.87 28.04 45.16 2.40 R
2183 2187 1.756538 CCACTGGCTTTTCAACCAAGT 59.243 47.619 0.00 0.00 34.96 3.16 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
23 24 1.525197 GTGCAAATCGTTCGTCTGACA 59.475 47.619 8.73 0.00 0.00 3.58
78 79 0.611714 GTAGCTGGTTCCCTCCGAAA 59.388 55.000 0.00 0.00 30.39 3.46
84 85 1.092348 GGTTCCCTCCGAAATTTCCG 58.908 55.000 12.54 6.41 30.39 4.30
196 197 4.969484 ACTTTAAATAGGTAGGATGGCGG 58.031 43.478 0.00 0.00 0.00 6.13
202 203 3.480133 GTAGGATGGCGGGGCTGT 61.480 66.667 0.00 0.00 0.00 4.40
215 217 1.302192 GGCTGTTTGGTGAGCCGTA 60.302 57.895 0.00 0.00 45.25 4.02
225 227 1.408266 GGTGAGCCGTACCATGGAATT 60.408 52.381 21.47 0.00 38.12 2.17
624 626 3.526534 CGAAGAGGAGAAAGGTTCCATC 58.473 50.000 0.00 0.00 37.18 3.51
629 631 4.787534 AGAGGAGAAAGGTTCCATCTGAAT 59.212 41.667 2.70 0.00 37.18 2.57
705 707 4.545706 GATCACGCGCATCCCCCA 62.546 66.667 5.73 0.00 0.00 4.96
827 829 1.750399 CTGCTTAACGGCCTGCCAT 60.750 57.895 9.17 0.00 35.37 4.40
846 848 1.073199 CCCTGGAAACGGTTCAGCT 59.927 57.895 16.38 0.00 35.25 4.24
924 926 2.120909 CGGCGGCCCATGAAAATCT 61.121 57.895 14.55 0.00 0.00 2.40
1040 1042 0.250553 AAGTCGGCAAAACGGATCCA 60.251 50.000 13.41 0.00 0.00 3.41
1234 1236 2.552743 CAGTCGACTCAGAACTGGTACA 59.447 50.000 16.96 0.00 0.00 2.90
1287 1289 1.815421 GCATTGCGATGGTCCTCGT 60.815 57.895 15.85 0.00 40.73 4.18
1315 1317 1.470098 GACGCAATGTGATTTCTGCCT 59.530 47.619 0.00 0.00 0.00 4.75
1624 1626 8.234546 CGCAAGTGAAATACCACTACTTTTAAT 58.765 33.333 0.00 0.00 45.82 1.40
1649 1653 6.598850 TGTTATTTTACTTATTCCGTGGGTCC 59.401 38.462 0.00 0.00 0.00 4.46
1654 1658 1.479323 CTTATTCCGTGGGTCCGAAGA 59.521 52.381 0.00 0.00 0.00 2.87
1792 1796 3.450457 AGGTGTCCTAAGATGAGCTCAAG 59.550 47.826 22.50 13.34 28.47 3.02
1914 1918 5.407407 AGATCTTCGGAGTTTGAAGCTAA 57.593 39.130 0.00 0.00 42.02 3.09
2183 2187 1.889545 TCACACAATTGGTCATCGCA 58.110 45.000 10.83 0.00 0.00 5.10
2239 2243 1.206132 TGCCGGATTATGACTGAACGT 59.794 47.619 5.05 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.697982 GTCTTTCGCCCCTATACCCAT 59.302 52.381 0.00 0.00 0.00 4.00
78 79 2.366916 CTCCAGCTATCCTGACGGAAAT 59.633 50.000 0.00 0.00 44.64 2.17
84 85 1.050988 TGGGCTCCAGCTATCCTGAC 61.051 60.000 0.00 0.00 44.64 3.51
215 217 0.324645 GGAGCACCCAATTCCATGGT 60.325 55.000 12.58 0.00 38.91 3.55
225 227 4.284550 GCCCACTTGGAGCACCCA 62.285 66.667 0.00 0.00 44.93 4.51
407 409 0.974010 TCGGGGCTAGTTGATTCGGT 60.974 55.000 0.00 0.00 0.00 4.69
624 626 1.403647 CCATGTGCAAGTGCCATTCAG 60.404 52.381 0.00 0.00 41.18 3.02
629 631 0.178978 TTACCCATGTGCAAGTGCCA 60.179 50.000 0.00 0.00 41.18 4.92
705 707 5.421056 GGAAATCTTAACCCGATTCCCTTTT 59.579 40.000 0.00 0.00 31.12 2.27
827 829 1.072505 GCTGAACCGTTTCCAGGGA 59.927 57.895 3.01 0.00 0.00 4.20
846 848 1.080354 CCACTGGACCCTACCTCCA 59.920 63.158 0.00 0.00 36.34 3.86
924 926 1.075482 AACGGTACTCGGTCCTCCA 59.925 57.895 8.31 0.00 44.45 3.86
1040 1042 3.699538 GCCAATCCTTTTCCCGAAGTTAT 59.300 43.478 0.00 0.00 0.00 1.89
1113 1115 0.459934 GTGAGCAGCTCGAGCAATCT 60.460 55.000 36.87 28.04 45.16 2.40
1234 1236 0.905357 CAGTCGGATTCCCCTTGTCT 59.095 55.000 0.00 0.00 0.00 3.41
1315 1317 5.213891 TCACTTTGACATTCAGAGCACTA 57.786 39.130 0.00 0.00 32.38 2.74
1624 1626 6.598850 GGACCCACGGAATAAGTAAAATAACA 59.401 38.462 0.00 0.00 0.00 2.41
1792 1796 2.996621 CCACACGAGATTTCTGTTCTCC 59.003 50.000 0.00 0.00 37.00 3.71
1914 1918 4.850680 TGTGGTAACTTTTCTGACACCTT 58.149 39.130 0.00 0.00 37.61 3.50
2126 2130 8.969260 TCTCGTACTAGGTTGAATTACTATCA 57.031 34.615 0.00 0.00 0.00 2.15
2183 2187 1.756538 CCACTGGCTTTTCAACCAAGT 59.243 47.619 0.00 0.00 34.96 3.16
2239 2243 5.068460 GCTAGCTTGGATTCTGACTTAGAGA 59.932 44.000 7.70 0.00 36.61 3.10


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

AutoCloner maintained by Alex Coulton.