Multiple sequence alignment - TraesCS4A01G244800

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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 TraesCS4A01G244800 chr4A 100.000 2297 0 0 1 2297 554948269 554950565 0 4242
1 TraesCS4A01G244800 chr1B 97.520 2298 54 2 1 2297 544593696 544595991 0 3925
2 TraesCS4A01G244800 chr1B 97.302 2298 61 1 1 2297 544609338 544611635 0 3899
3 TraesCS4A01G244800 chrUn 97.476 2298 56 2 1 2297 245706067 245708363 0 3921
4 TraesCS4A01G244800 chrUn 97.476 2298 57 1 1 2297 291535439 291537736 0 3921
5 TraesCS4A01G244800 chrUn 97.434 2299 57 2 1 2297 274341283 274338985 0 3917
6 TraesCS4A01G244800 chrUn 97.433 2298 58 1 1 2297 199874823 199877120 0 3916
7 TraesCS4A01G244800 chrUn 97.433 2298 58 1 1 2297 229310228 229307931 0 3916
8 TraesCS4A01G244800 chrUn 97.302 2298 61 1 1 2297 199904743 199907040 0 3899
9 TraesCS4A01G244800 chrUn 97.258 2298 62 1 1 2297 3845815 3843518 0 3893


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 TraesCS4A01G244800 chr4A 554948269 554950565 2296 False 4242 4242 100.000 1 2297 1 chr4A.!!$F1 2296
1 TraesCS4A01G244800 chr1B 544593696 544595991 2295 False 3925 3925 97.520 1 2297 1 chr1B.!!$F1 2296
2 TraesCS4A01G244800 chr1B 544609338 544611635 2297 False 3899 3899 97.302 1 2297 1 chr1B.!!$F2 2296
3 TraesCS4A01G244800 chrUn 245706067 245708363 2296 False 3921 3921 97.476 1 2297 1 chrUn.!!$F3 2296
4 TraesCS4A01G244800 chrUn 291535439 291537736 2297 False 3921 3921 97.476 1 2297 1 chrUn.!!$F4 2296
5 TraesCS4A01G244800 chrUn 274338985 274341283 2298 True 3917 3917 97.434 1 2297 1 chrUn.!!$R3 2296
6 TraesCS4A01G244800 chrUn 199874823 199877120 2297 False 3916 3916 97.433 1 2297 1 chrUn.!!$F1 2296
7 TraesCS4A01G244800 chrUn 229307931 229310228 2297 True 3916 3916 97.433 1 2297 1 chrUn.!!$R2 2296
8 TraesCS4A01G244800 chrUn 199904743 199907040 2297 False 3899 3899 97.302 1 2297 1 chrUn.!!$F2 2296
9 TraesCS4A01G244800 chrUn 3843518 3845815 2297 True 3893 3893 97.258 1 2297 1 chrUn.!!$R1 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
843 845 0.179001 CCAACCCTGGAAACGGTTCT 60.179 55.0 13.88 0.0 46.92 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2202 0.174845 ACAATAGCTTCGCGCCACTA 59.825 50.0 0.0 2.39 40.39 2.74 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
94 95 2.766828 CCGAAGTTTCCCTCAGGATAGT 59.233 50.000 0.00 0.00 43.54 2.12
195 196 7.406916 TCAAACTTTAAATAGGTAGGATGGCA 58.593 34.615 0.00 0.00 0.00 4.92
266 267 4.039124 CCATTTTTGGTAAGCAGAACTGGT 59.961 41.667 0.47 0.47 44.00 4.00
411 412 1.961793 GTGTAACAACTCACCTGCCA 58.038 50.000 0.00 0.00 36.32 4.92
505 506 2.900273 GATGTGTAGGAGGGCGCA 59.100 61.111 10.83 0.00 0.00 6.09
506 507 1.220749 GATGTGTAGGAGGGCGCAA 59.779 57.895 10.83 0.00 0.00 4.85
522 523 3.522731 AACGGCCGCTGCAAAACA 61.523 55.556 28.58 0.00 40.13 2.83
524 525 4.263209 CGGCCGCTGCAAAACACA 62.263 61.111 14.67 0.00 40.13 3.72
843 845 0.179001 CCAACCCTGGAAACGGTTCT 60.179 55.000 13.88 0.00 46.92 3.01
845 847 0.549469 AACCCTGGAAACGGTTCTGT 59.451 50.000 13.88 2.93 37.89 3.41
982 984 1.194781 ACCGCATCAGGTCTCCAAGT 61.195 55.000 0.00 0.00 41.46 3.16
989 991 3.924114 TCAGGTCTCCAAGTTGAACAA 57.076 42.857 3.87 0.00 0.00 2.83
1234 1236 2.552743 CAGTCGACTCAGAACTGGTACA 59.447 50.000 16.96 0.00 0.00 2.90
1333 1335 2.082231 CCCAGTGCTCTGAATGTCAAG 58.918 52.381 17.19 0.00 43.76 3.02
1365 1367 2.739287 CCAAGCGCGGGTAAACGA 60.739 61.111 8.83 0.00 35.47 3.85
1367 1369 2.029369 AAGCGCGGGTAAACGACA 59.971 55.556 8.83 0.00 35.47 4.35
1492 1494 1.632589 GAAACCACAGCCAAGGGAAT 58.367 50.000 0.00 0.00 0.00 3.01
1595 1597 1.204146 GATAAGTGGGAGCCCTCACA 58.796 55.000 0.00 0.00 41.39 3.58
1625 1628 9.398538 ACAAGTGAAATACCACTACTTTTAACA 57.601 29.630 0.00 0.00 45.82 2.41
1762 1766 1.000394 GGGCGGCACAACTGTTAAAAT 60.000 47.619 12.47 0.00 0.00 1.82
1800 1804 3.883830 AGATGAGCTCAACGAGAACAT 57.116 42.857 22.50 0.00 32.97 2.71
1955 1959 1.281867 CAGGGATAACTGGCTTGTGGA 59.718 52.381 0.00 0.00 34.84 4.02
1993 1997 3.628017 CGACGTTGCTTTTTGATCCTTT 58.372 40.909 0.00 0.00 0.00 3.11
2001 2005 4.518590 TGCTTTTTGATCCTTTGATGTCGA 59.481 37.500 0.00 0.00 0.00 4.20
2129 2133 2.646596 CTGATGACAGTGTCGCGAG 58.353 57.895 10.24 9.38 39.11 5.03
2198 2202 1.008538 CGCGCTTGGTTGAAAAGCT 60.009 52.632 5.56 0.00 46.33 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.641906 CCCTATACCCAAGTCAGACGAAT 59.358 47.826 0.00 0.00 0.00 3.34
94 95 1.906574 AGAACTCGTAATGGGCTCCAA 59.093 47.619 0.00 0.00 36.95 3.53
266 267 1.904990 TTCCGGTTCATCCCGCATCA 61.905 55.000 0.00 0.00 46.71 3.07
411 412 3.447229 CCATTTTCGGGGCTAGTTGATTT 59.553 43.478 0.00 0.00 0.00 2.17
492 493 4.077184 CCGTTGCGCCCTCCTACA 62.077 66.667 4.18 0.00 0.00 2.74
505 506 3.522731 TGTTTTGCAGCGGCCGTT 61.523 55.556 28.70 20.13 40.13 4.44
506 507 4.264638 GTGTTTTGCAGCGGCCGT 62.265 61.111 28.70 11.01 40.13 5.68
604 605 3.652869 ACATGGAACCTTTCTCCTCTTCA 59.347 43.478 0.00 0.00 33.77 3.02
843 845 1.000019 CTGGACCCTACCTCCGACA 60.000 63.158 0.00 0.00 0.00 4.35
845 847 1.000019 CACTGGACCCTACCTCCGA 60.000 63.158 0.00 0.00 0.00 4.55
982 984 1.962807 CATTGGCCAGAGGTTGTTCAA 59.037 47.619 5.11 0.00 0.00 2.69
989 991 0.482446 TTGTTCCATTGGCCAGAGGT 59.518 50.000 21.07 1.32 0.00 3.85
1100 1102 3.849951 AATCCGCCGACAGCCGAT 61.850 61.111 0.00 0.00 40.60 4.18
1164 1166 2.058595 CGATTCCTGGTCCGTCCCT 61.059 63.158 0.00 0.00 34.77 4.20
1234 1236 1.985895 ACAGTCGGATTCCCCTTTTCT 59.014 47.619 0.00 0.00 0.00 2.52
1237 1239 2.971901 AAACAGTCGGATTCCCCTTT 57.028 45.000 0.00 0.00 0.00 3.11
1333 1335 3.308530 CGCTTGGTTGAATTTCTTCACC 58.691 45.455 0.00 2.64 41.05 4.02
1365 1367 7.558444 CCTTAAGAGAGTCATAGTTACTCCTGT 59.442 40.741 3.36 0.00 43.64 4.00
1367 1369 7.645002 ACCTTAAGAGAGTCATAGTTACTCCT 58.355 38.462 3.36 0.00 43.64 3.69
1492 1494 2.045045 CTGATTCCGCCAAGCCCA 60.045 61.111 0.00 0.00 0.00 5.36
1595 1597 3.508845 AGTGGTATTTCACTTGTGCCT 57.491 42.857 0.00 0.00 44.74 4.75
1599 1601 9.398538 TGTTAAAAGTAGTGGTATTTCACTTGT 57.601 29.630 2.76 0.00 44.74 3.16
1625 1628 8.269317 TCCGACCCACAGAATAAGTAAAATAAT 58.731 33.333 0.00 0.00 0.00 1.28
1687 1691 2.364579 ATCGGCCCGGTAAGACCA 60.365 61.111 1.90 0.00 38.47 4.02
1752 1756 6.093082 GGACACCTGCGTTATATTTTAACAGT 59.907 38.462 0.00 0.00 0.00 3.55
1762 1766 4.891168 TCATCTTAGGACACCTGCGTTATA 59.109 41.667 0.00 0.00 34.61 0.98
1800 1804 4.517453 CCCTTTTGTTCCACACGAGATTTA 59.483 41.667 0.00 0.00 0.00 1.40
1829 1833 5.551233 ACTGGAAATCAGAATCAAACGAGA 58.449 37.500 0.00 0.00 46.18 4.04
1955 1959 0.391130 TCGCTATGAACGCTTGGCTT 60.391 50.000 0.00 0.00 0.00 4.35
1993 1997 5.360999 ACAATGATAGGAAGAGTCGACATCA 59.639 40.000 19.50 15.65 0.00 3.07
2001 2005 5.188555 TCTGCTTCACAATGATAGGAAGAGT 59.811 40.000 0.00 0.00 39.20 3.24
2084 2088 6.215636 AGGGTAAAACTAACCTGTCTCATGAT 59.784 38.462 0.00 0.00 37.18 2.45
2087 2091 6.729569 AGTAGGGTAAAACTAACCTGTCTCAT 59.270 38.462 0.00 0.00 37.18 2.90
2129 2133 8.466617 TCCTCTCATACTAGGTTGAATTACTC 57.533 38.462 0.00 0.00 34.30 2.59
2198 2202 0.174845 ACAATAGCTTCGCGCCACTA 59.825 50.000 0.00 2.39 40.39 2.74
2214 2218 4.284829 TCAGTCATAATCTGGCACACAA 57.715 40.909 0.00 0.00 34.15 3.33
2215 2219 3.979101 TCAGTCATAATCTGGCACACA 57.021 42.857 0.00 0.00 34.15 3.72
2223 2227 5.361285 ACTTAGAGGCGTTCAGTCATAATCT 59.639 40.000 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.