Multiple sequence alignment - TraesCS7B01G400100

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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 TraesCS7B01G400100 chr7B 100.000 6784 0 0 1 6784 666533821 666527038 0 12528
1 TraesCS7B01G400100 chr7B 98.616 6791 77 15 1 6784 194120441 194127221 0 12004
2 TraesCS7B01G400100 chr6A 99.043 6791 56 7 1 6784 87933839 87940627 0 12172
3 TraesCS7B01G400100 chr6A 98.793 6791 70 10 1 6784 480630566 480637351 0 12076
4 TraesCS7B01G400100 chr6A 98.521 6626 85 11 167 6784 12700532 12693912 0 11681
5 TraesCS7B01G400100 chr7A 98.586 6789 84 8 1 6784 624766393 624759612 0 11995
6 TraesCS7B01G400100 chr7A 98.220 6799 96 11 1 6784 634123099 634129887 0 11862
7 TraesCS7B01G400100 chr1B 98.394 6787 93 12 1 6784 637607136 637613909 0 11915
8 TraesCS7B01G400100 chr6B 98.202 6785 91 15 1 6784 21371770 21365016 0 11825
9 TraesCS7B01G400100 chr5A 98.468 5416 66 11 1 5412 396395850 396401252 0 9526
10 TraesCS7B01G400100 chr4B 98.254 1947 22 10 1 1942 14719143 14717204 0 3397


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 TraesCS7B01G400100 chr7B 666527038 666533821 6783 True 12528 12528 100.000 1 6784 1 chr7B.!!$R1 6783
1 TraesCS7B01G400100 chr7B 194120441 194127221 6780 False 12004 12004 98.616 1 6784 1 chr7B.!!$F1 6783
2 TraesCS7B01G400100 chr6A 87933839 87940627 6788 False 12172 12172 99.043 1 6784 1 chr6A.!!$F1 6783
3 TraesCS7B01G400100 chr6A 480630566 480637351 6785 False 12076 12076 98.793 1 6784 1 chr6A.!!$F2 6783
4 TraesCS7B01G400100 chr6A 12693912 12700532 6620 True 11681 11681 98.521 167 6784 1 chr6A.!!$R1 6617
5 TraesCS7B01G400100 chr7A 624759612 624766393 6781 True 11995 11995 98.586 1 6784 1 chr7A.!!$R1 6783
6 TraesCS7B01G400100 chr7A 634123099 634129887 6788 False 11862 11862 98.220 1 6784 1 chr7A.!!$F1 6783
7 TraesCS7B01G400100 chr1B 637607136 637613909 6773 False 11915 11915 98.394 1 6784 1 chr1B.!!$F1 6783
8 TraesCS7B01G400100 chr6B 21365016 21371770 6754 True 11825 11825 98.202 1 6784 1 chr6B.!!$R1 6783
9 TraesCS7B01G400100 chr5A 396395850 396401252 5402 False 9526 9526 98.468 1 5412 1 chr5A.!!$F1 5411
10 TraesCS7B01G400100 chr4B 14717204 14719143 1939 True 3397 3397 98.254 1 1942 1 chr4B.!!$R1 1941

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
934 949 1.766494 CCCAGTTGGCTGCATGATTA 58.234 50.000 0.50 0.0 41.26 1.75 F
2470 2518 1.480954 TGGCTAGAAGAACGGATGACC 59.519 52.381 0.00 0.0 0.00 4.02 F
2634 2682 3.395639 ACACATTAACGAAGCTTTCCGA 58.604 40.909 13.82 0.0 0.00 4.55 F
4518 4591 1.675310 CCAATGGAGGCAGCGACAA 60.675 57.895 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2822 2873 1.136891 CTGGGATGTCATGTACGAGCA 59.863 52.381 0.0 0.0 0.00 4.26 R
3469 3525 3.555956 CACTAACCTGCGGATTGTATGTC 59.444 47.826 0.0 0.0 0.00 3.06 R
4523 4596 3.735746 GCGTTGTCATCATCATCGTCATA 59.264 43.478 0.0 0.0 32.75 2.15 R
6428 6517 0.301687 CCGGCTTCATCGAATCAACG 59.698 55.000 0.0 0.0 0.00 4.10 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
340 343 9.662947 GTTTTTGTACTAGGTGGTTGTCTATAT 57.337 33.333 0.00 0.00 0.00 0.86
934 949 1.766494 CCCAGTTGGCTGCATGATTA 58.234 50.000 0.50 0.00 41.26 1.75
1269 1289 3.610114 GCATGTTGATGACACAAGTCCAC 60.610 47.826 0.00 0.00 44.33 4.02
2204 2252 7.547370 GCTATTGAACTTATCAGACACACTTCT 59.453 37.037 0.00 0.00 39.77 2.85
2470 2518 1.480954 TGGCTAGAAGAACGGATGACC 59.519 52.381 0.00 0.00 0.00 4.02
2634 2682 3.395639 ACACATTAACGAAGCTTTCCGA 58.604 40.909 13.82 0.00 0.00 4.55
2822 2873 5.602561 TGGTGCAGATACTATACCTTGATGT 59.397 40.000 0.00 0.00 32.68 3.06
3469 3525 2.824936 TGTGGCATCCAAGTTACCAATG 59.175 45.455 0.00 0.00 34.18 2.82
3900 3958 4.060205 GTGTTGATGCAGAAAAAGGCAAT 58.940 39.130 0.00 0.00 44.20 3.56
4518 4591 1.675310 CCAATGGAGGCAGCGACAA 60.675 57.895 0.00 0.00 0.00 3.18
5230 5304 2.035632 CCACCAAAACCACCTAAGCAA 58.964 47.619 0.00 0.00 0.00 3.91
5824 5911 1.410517 GCTCCAGCAGTAGATACAGCA 59.589 52.381 9.62 0.00 40.63 4.41
5958 6045 0.038744 CCAGAGAATTGCCACACCCT 59.961 55.000 0.00 0.00 0.00 4.34
6428 6517 9.613957 GCTTTCTACATTTCTTTAAAGGAGTTC 57.386 33.333 15.13 0.00 30.99 3.01
6479 6568 7.708752 TGGTTGTCAAAAATTGTTATTGAGACC 59.291 33.333 14.38 14.38 39.05 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1269 1289 7.800155 ATATGACCCAAACAAAACCAAAAAG 57.200 32.000 0.00 0.00 0.00 2.27
1340 1364 4.024387 GCTTTACAACACGGAACTGATCAA 60.024 41.667 0.00 0.00 0.00 2.57
1502 1530 8.691661 ACAAAAGGTTGTTATTGACAGACTAT 57.308 30.769 0.00 0.00 46.01 2.12
1672 1711 1.886313 CTGCTGCGGAAGATGCGAT 60.886 57.895 1.17 0.00 30.86 4.58
2634 2682 1.425066 TGCTTCTCCTGGTCCATGTTT 59.575 47.619 0.00 0.00 0.00 2.83
2710 2760 5.059161 CACAGAAAGAACAGGAACAGATGA 58.941 41.667 0.00 0.00 0.00 2.92
2822 2873 1.136891 CTGGGATGTCATGTACGAGCA 59.863 52.381 0.00 0.00 0.00 4.26
3469 3525 3.555956 CACTAACCTGCGGATTGTATGTC 59.444 47.826 0.00 0.00 0.00 3.06
3900 3958 4.379394 GCTCATTGACCACTTTCGCAATTA 60.379 41.667 0.00 0.00 0.00 1.40
4518 4591 4.038402 TGTCATCATCATCGTCATAGCTGT 59.962 41.667 0.00 0.00 0.00 4.40
4523 4596 3.735746 GCGTTGTCATCATCATCGTCATA 59.264 43.478 0.00 0.00 32.75 2.15
5266 5340 1.608801 CCCAAATCTTTTGTGGCCTGC 60.609 52.381 3.32 0.00 0.00 4.85
5270 5345 2.103941 TGAACCCCAAATCTTTTGTGGC 59.896 45.455 2.00 0.00 0.00 5.01
5486 5561 4.837298 TGAAGCATCTCTATCAGTAGGCAT 59.163 41.667 0.00 0.00 0.00 4.40
5632 5707 3.997762 TCGCAATAGTGTTGTAGTTGGT 58.002 40.909 1.33 0.00 0.00 3.67
5824 5911 3.539604 GATGCTAATCACACTGGCTTCT 58.460 45.455 0.00 0.00 32.61 2.85
5958 6045 2.093500 AGTTCTGGTTCTGCGCATATCA 60.093 45.455 12.24 8.09 0.00 2.15
6334 6422 4.602340 AAAGACAAGTTAGCTCGAAGGA 57.398 40.909 0.00 0.00 0.00 3.36
6428 6517 0.301687 CCGGCTTCATCGAATCAACG 59.698 55.000 0.00 0.00 0.00 4.10
6479 6568 3.159353 TCCGTGATGTGTAAGATTCCG 57.841 47.619 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.