Multiple sequence alignment - TraesCS7A01G293800

Loading Multiple Alignment...

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 TraesCS7A01G293800 chr7A 100.000 2438 0 0 1 2438 377335225 377332788 0 4503
1 TraesCS7A01G293800 chr7A 96.152 2443 87 4 2 2438 271652635 271650194 0 3984
2 TraesCS7A01G293800 chr6A 96.357 2443 82 4 2 2438 411709540 411707099 0 4012
3 TraesCS7A01G293800 chr6A 96.275 2443 83 6 2 2438 203854671 203852231 0 4000
4 TraesCS7A01G293800 chr6A 96.193 2443 83 6 2 2438 202721569 202724007 0 3988
5 TraesCS7A01G293800 chr2A 96.355 2442 82 5 2 2438 647969062 647971501 0 4010
6 TraesCS7A01G293800 chr2A 96.152 2443 87 5 2 2438 517765564 517763123 0 3984
7 TraesCS7A01G293800 chr2A 96.152 2443 86 6 2 2438 594479288 594476848 0 3984
8 TraesCS7A01G293800 chr1A 96.313 2441 85 3 2 2438 80773546 80775985 0 4004
9 TraesCS7A01G293800 chr4A 96.263 2435 85 5 2 2432 475494023 475491591 0 3988


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 TraesCS7A01G293800 chr7A 377332788 377335225 2437 True 4503 4503 100.000 1 2438 1 chr7A.!!$R2 2437
1 TraesCS7A01G293800 chr7A 271650194 271652635 2441 True 3984 3984 96.152 2 2438 1 chr7A.!!$R1 2436
2 TraesCS7A01G293800 chr6A 411707099 411709540 2441 True 4012 4012 96.357 2 2438 1 chr6A.!!$R2 2436
3 TraesCS7A01G293800 chr6A 203852231 203854671 2440 True 4000 4000 96.275 2 2438 1 chr6A.!!$R1 2436
4 TraesCS7A01G293800 chr6A 202721569 202724007 2438 False 3988 3988 96.193 2 2438 1 chr6A.!!$F1 2436
5 TraesCS7A01G293800 chr2A 647969062 647971501 2439 False 4010 4010 96.355 2 2438 1 chr2A.!!$F1 2436
6 TraesCS7A01G293800 chr2A 517763123 517765564 2441 True 3984 3984 96.152 2 2438 1 chr2A.!!$R1 2436
7 TraesCS7A01G293800 chr2A 594476848 594479288 2440 True 3984 3984 96.152 2 2438 1 chr2A.!!$R2 2436
8 TraesCS7A01G293800 chr1A 80773546 80775985 2439 False 4004 4004 96.313 2 2438 1 chr1A.!!$F1 2436
9 TraesCS7A01G293800 chr4A 475491591 475494023 2432 True 3988 3988 96.263 2 2432 1 chr4A.!!$R1 2430

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
217 218 0.961753 ACAAGCTTGTTTGGCTAGCC 59.038 50.0 26.36 27.71 45.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2210 0.519961 GTGGCACGTATTCAACCCAC 59.48 55.0 0.0 0.0 36.36 4.61 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
109 110 6.775142 CCACTATGATAAACTGAGGAGAGAGA 59.225 42.308 0.00 0.00 0.00 3.10
110 111 7.451255 CCACTATGATAAACTGAGGAGAGAGAT 59.549 40.741 0.00 0.00 0.00 2.75
217 218 0.961753 ACAAGCTTGTTTGGCTAGCC 59.038 50.000 26.36 27.71 45.00 3.93
273 274 3.737559 AAATGGGCAGTGAACCTCATA 57.262 42.857 0.00 0.00 0.00 2.15
274 275 2.717639 ATGGGCAGTGAACCTCATAC 57.282 50.000 0.00 0.00 0.00 2.39
412 415 9.667107 CTAACCTCCAAGAAATTAACATCTGTA 57.333 33.333 0.00 0.00 0.00 2.74
496 499 9.890915 TTATTGCCCATAAATACCTAGGAAATT 57.109 29.630 17.98 11.80 0.00 1.82
497 500 8.797436 ATTGCCCATAAATACCTAGGAAATTT 57.203 30.769 17.98 20.71 0.00 1.82
586 589 1.070289 TGCATGCTGTGAAATTTGGCA 59.930 42.857 20.33 1.38 37.32 4.92
709 712 4.037446 TCCGCAATGAGCTTAACAAAAGTT 59.963 37.500 0.00 0.00 42.61 2.66
888 892 3.577919 GAAGTATTCCTCCAGCTCCCTA 58.422 50.000 0.00 0.00 39.83 3.53
1031 1040 5.105877 GGGATAACCTTAGGCAAAGAAACAC 60.106 44.000 0.00 0.00 37.38 3.32
1121 1130 8.834004 TGTATAGTTACTAAACATCTCTGGGT 57.166 34.615 0.00 0.00 38.12 4.51
1251 1260 0.401738 TCCTTTGGTGCCTCTGGAAG 59.598 55.000 0.00 0.00 0.00 3.46
1420 1429 0.322546 ATCCCTCCAGAAACCGTTGC 60.323 55.000 0.00 0.00 0.00 4.17
1460 1469 3.071206 GCTCGACCTGCTCTGGGA 61.071 66.667 0.00 0.00 0.00 4.37
1479 1488 4.682334 TGGACCCGTGGGCTCGTA 62.682 66.667 4.41 0.00 39.32 3.43
1492 1501 2.625790 GGGCTCGTATCAAGATCTCTGT 59.374 50.000 0.00 0.00 0.00 3.41
1511 1520 7.375753 CTCTGTTGAAGATGATGGGCACCTA 62.376 48.000 0.00 0.00 42.02 3.08
1541 1550 1.152881 GAGGGACATCCACCATGCC 60.153 63.158 0.00 0.00 35.65 4.40
1576 1585 1.203994 GGTGTCTCCGCTTGCTTACTA 59.796 52.381 0.00 0.00 0.00 1.82
1798 1811 7.915293 ATCAGAATATGTTGTGGTTTCGTTA 57.085 32.000 0.00 0.00 0.00 3.18
1825 1838 2.367202 GGAACCGGGGAGATGCTCA 61.367 63.158 6.32 0.00 31.08 4.26
1826 1839 1.700042 GGAACCGGGGAGATGCTCAT 61.700 60.000 6.32 0.00 31.08 2.90
1954 1971 2.295909 ACAAAATGCTCAGCGCCTTTTA 59.704 40.909 2.29 0.00 42.18 1.52
2074 2091 8.463456 TTTTTAGGAAATAAAATAAACGGGCG 57.537 30.769 0.00 0.00 41.74 6.13
2432 2454 3.914312 GCTATGAAGCGCTAATCTACCA 58.086 45.455 12.05 0.58 39.39 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.285020 AGTCAGCTAACTCCTGATCATCA 58.715 43.478 0.00 0.0 41.01 3.07
110 111 9.009675 TGATTTTATCTAGAAGGGGTTGGATAA 57.990 33.333 0.00 0.0 0.00 1.75
217 218 3.909732 AGGAGAGGAGATACACTGGAAG 58.090 50.000 0.00 0.0 42.29 3.46
273 274 5.100344 AGCAATGAGACATCTGAGAATGT 57.900 39.130 0.00 0.0 42.49 2.71
274 275 5.354513 ACAAGCAATGAGACATCTGAGAATG 59.645 40.000 0.00 0.0 0.00 2.67
412 415 9.634021 GAATCTTTTAATCCAAGACCCTAGAAT 57.366 33.333 0.00 0.0 33.04 2.40
496 499 8.057011 GGAGGAAGGGACAAAAATATTAGGTAA 58.943 37.037 0.00 0.0 0.00 2.85
497 500 7.184936 TGGAGGAAGGGACAAAAATATTAGGTA 59.815 37.037 0.00 0.0 0.00 3.08
564 567 2.095213 GCCAAATTTCACAGCATGCATG 59.905 45.455 22.70 22.7 42.53 4.06
586 589 3.139025 CCATCCCCTATGTTCCATCTGTT 59.861 47.826 0.00 0.0 33.34 3.16
709 712 2.882137 GACCGTCCCAAACTTCATTGAA 59.118 45.455 0.00 0.0 31.84 2.69
840 844 0.401356 TGTCCAGCTGCCAAATCAGA 59.599 50.000 8.66 0.0 36.19 3.27
888 892 8.949421 ACCCCTCTAAAGTTGATAACATGATAT 58.051 33.333 0.00 0.0 0.00 1.63
1021 1030 3.387699 AGGGGTTTGATGGTGTTTCTTTG 59.612 43.478 0.00 0.0 0.00 2.77
1023 1032 3.328535 AGGGGTTTGATGGTGTTTCTT 57.671 42.857 0.00 0.0 0.00 2.52
1027 1036 2.765689 TCAAGGGGTTTGATGGTGTT 57.234 45.000 0.00 0.0 40.82 3.32
1105 1114 3.248024 TGTGGACCCAGAGATGTTTAGT 58.752 45.455 0.00 0.0 0.00 2.24
1121 1130 8.324191 ACTAGAGAAATATTCCTCAATGTGGA 57.676 34.615 4.38 0.0 32.07 4.02
1420 1429 2.217750 TGTTCAACCACAAGTGATCGG 58.782 47.619 0.94 0.0 0.00 4.18
1479 1488 6.993308 CCATCATCTTCAACAGAGATCTTGAT 59.007 38.462 0.00 0.0 33.87 2.57
1492 1501 2.421952 GCTAGGTGCCCATCATCTTCAA 60.422 50.000 0.00 0.0 37.35 2.69
1511 1520 1.671379 GTCCCTCTTTTTCGGCGCT 60.671 57.895 7.64 0.0 0.00 5.92
1678 1687 4.647611 TGAATAACACAAATCACCCGAGT 58.352 39.130 0.00 0.0 0.00 4.18
1798 1811 0.701731 TCCCCGGTTCCATTGTTGAT 59.298 50.000 0.00 0.0 0.00 2.57
2074 2091 5.835113 ACAAATAATGTAGTGTCCATGCC 57.165 39.130 0.00 0.0 41.63 4.40
2145 2163 4.485024 TTTTGCGCGGTAGAATTTACAA 57.515 36.364 8.83 0.0 0.00 2.41
2188 2210 0.519961 GTGGCACGTATTCAACCCAC 59.480 55.000 0.00 0.0 36.36 4.61


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

AutoCloner maintained by Alex Coulton.