Multiple sequence alignment - TraesCS6D01G139500

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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 TraesCS6D01G139500 chr6D 100.000 7985 0 0 1 7985 108481782 108489766 0 14746
1 TraesCS6D01G139500 chr4D 97.670 8027 128 8 1 7985 123452410 123444401 0 13732
2 TraesCS6D01G139500 chr2B 97.632 8025 149 6 1 7985 234544602 234536579 0 13729
3 TraesCS6D01G139500 chr3B 97.616 8013 157 8 1 7985 92300162 92292156 0 13708
4 TraesCS6D01G139500 chr3B 97.456 8019 167 7 1 7985 6014203 6006188 0 13644
5 TraesCS6D01G139500 chrUn 97.456 8019 167 7 1 7985 217904231 217912246 0 13644
6 TraesCS6D01G139500 chr7A 97.394 8019 174 5 1 7985 563525536 563517519 0 13618
7 TraesCS6D01G139500 chr1B 97.219 8019 167 6 1 7985 619198749 619190753 0 13522
8 TraesCS6D01G139500 chr7D 97.053 8007 209 5 1 7985 307036639 307044640 0 13453
9 TraesCS6D01G139500 chr7D 97.054 7332 187 8 677 7985 307149372 307142047 0 12316
10 TraesCS6D01G139500 chr7D 98.195 2438 31 3 1 2425 382112633 382115070 0 4246
11 TraesCS6D01G139500 chr3D 96.940 8006 190 8 1 7985 501841773 501833802 0 13376
12 TraesCS6D01G139500 chr3A 97.891 7397 121 5 623 7985 495107576 495100181 0 12763
13 TraesCS6D01G139500 chr4A 97.226 7354 163 7 1 7320 67516066 67523412 0 12412
14 TraesCS6D01G139500 chr4A 92.407 1857 129 3 3 1859 280913916 280912072 0 2638
15 TraesCS6D01G139500 chr1A 97.460 6614 126 8 1395 7985 278519177 278525771 0 11245
16 TraesCS6D01G139500 chr5A 97.095 1205 24 1 1 1194 238907389 238908593 0 2021


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 TraesCS6D01G139500 chr6D 108481782 108489766 7984 False 14746 14746 100.000 1 7985 1 chr6D.!!$F1 7984
1 TraesCS6D01G139500 chr4D 123444401 123452410 8009 True 13732 13732 97.670 1 7985 1 chr4D.!!$R1 7984
2 TraesCS6D01G139500 chr2B 234536579 234544602 8023 True 13729 13729 97.632 1 7985 1 chr2B.!!$R1 7984
3 TraesCS6D01G139500 chr3B 92292156 92300162 8006 True 13708 13708 97.616 1 7985 1 chr3B.!!$R2 7984
4 TraesCS6D01G139500 chr3B 6006188 6014203 8015 True 13644 13644 97.456 1 7985 1 chr3B.!!$R1 7984
5 TraesCS6D01G139500 chrUn 217904231 217912246 8015 False 13644 13644 97.456 1 7985 1 chrUn.!!$F1 7984
6 TraesCS6D01G139500 chr7A 563517519 563525536 8017 True 13618 13618 97.394 1 7985 1 chr7A.!!$R1 7984
7 TraesCS6D01G139500 chr1B 619190753 619198749 7996 True 13522 13522 97.219 1 7985 1 chr1B.!!$R1 7984
8 TraesCS6D01G139500 chr7D 307036639 307044640 8001 False 13453 13453 97.053 1 7985 1 chr7D.!!$F1 7984
9 TraesCS6D01G139500 chr7D 307142047 307149372 7325 True 12316 12316 97.054 677 7985 1 chr7D.!!$R1 7308
10 TraesCS6D01G139500 chr7D 382112633 382115070 2437 False 4246 4246 98.195 1 2425 1 chr7D.!!$F2 2424
11 TraesCS6D01G139500 chr3D 501833802 501841773 7971 True 13376 13376 96.940 1 7985 1 chr3D.!!$R1 7984
12 TraesCS6D01G139500 chr3A 495100181 495107576 7395 True 12763 12763 97.891 623 7985 1 chr3A.!!$R1 7362
13 TraesCS6D01G139500 chr4A 67516066 67523412 7346 False 12412 12412 97.226 1 7320 1 chr4A.!!$F1 7319
14 TraesCS6D01G139500 chr4A 280912072 280913916 1844 True 2638 2638 92.407 3 1859 1 chr4A.!!$R1 1856
15 TraesCS6D01G139500 chr1A 278519177 278525771 6594 False 11245 11245 97.460 1395 7985 1 chr1A.!!$F1 6590
16 TraesCS6D01G139500 chr5A 238907389 238908593 1204 False 2021 2021 97.095 1 1194 1 chr5A.!!$F1 1193

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
761 762 0.389817 CGCGTGGTTGAAGGAGATGA 60.390 55.000 0.00 0.0 0.0 2.92 F
1355 1400 0.533308 CCGACCTGGGTTTTCACGAA 60.533 55.000 0.00 0.0 0.0 3.85 F
2831 2886 0.251354 GCCAGTGATTCTCTGAGCCA 59.749 55.000 15.54 0.0 35.2 4.75 F
4335 4395 1.005984 TCGCCAAATTCGTCGACCA 60.006 52.632 10.58 0.0 0.0 4.02 F
4465 4525 1.052124 ACCCAAGAACGACCTGTGGA 61.052 55.000 0.00 0.0 0.0 4.02 F
5180 5246 1.397390 GGCATGGAGAAGCATTGGGG 61.397 60.000 0.00 0.0 0.0 4.96 F
5726 5792 1.006400 AGGGCAGCCTTTAGAAGCAAT 59.994 47.619 12.43 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1854 0.535335 ACCTCGGAAGCTAATTCGCA 59.465 50.000 4.63 0.00 38.95 5.10 R
2951 3006 0.544697 GGGCTGGGTTCTATTTCCGA 59.455 55.000 0.00 0.00 0.00 4.55 R
4667 4727 0.177141 TTTCCCTTCATACGGCTCGG 59.823 55.000 0.00 0.00 0.00 4.63 R
5374 5440 0.602638 TTGTGCCAGTAGCCAACTCG 60.603 55.000 0.00 0.00 42.71 4.18 R
5581 5647 4.037565 CCGGTCCTTTTCTTTTAGTGCTTT 59.962 41.667 0.00 0.00 0.00 3.51 R
6676 6766 1.480137 CATTTGGCCGGCTATGGAAAA 59.520 47.619 28.56 11.74 0.00 2.29 R
7521 7611 2.757868 AGCTCAGCTCACGAAATAGAGT 59.242 45.455 0.00 0.00 30.62 3.24 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
60 61 2.179424 AGACTTCCGGGTATAGGGTGAT 59.821 50.000 0.00 0.00 0.00 3.06
98 99 4.327680 AGTATTCAGGTGGCAGAGTTTTC 58.672 43.478 0.00 0.00 0.00 2.29
192 193 3.137360 AGGTTTTGATCTGAGGCTATCCC 59.863 47.826 0.00 0.00 0.00 3.85
278 279 0.742281 CCTCTTCCACACGGATGCTG 60.742 60.000 0.00 0.00 42.41 4.41
281 282 1.228094 TTCCACACGGATGCTGCAA 60.228 52.632 6.36 0.00 42.41 4.08
544 545 3.788333 TTCGCTATTGGCTTAGTACGT 57.212 42.857 0.00 0.00 39.13 3.57
570 571 1.351017 ACATAATAGGGCCATGACGGG 59.649 52.381 6.18 0.00 34.06 5.28
712 713 2.738521 CCTCTGTGCGGTGAACGG 60.739 66.667 0.00 0.00 44.51 4.44
761 762 0.389817 CGCGTGGTTGAAGGAGATGA 60.390 55.000 0.00 0.00 0.00 2.92
1289 1334 6.900194 TGACTTTGGATAAAGATAGAAGGGG 58.100 40.000 6.77 0.00 44.87 4.79
1355 1400 0.533308 CCGACCTGGGTTTTCACGAA 60.533 55.000 0.00 0.00 0.00 3.85
1710 1755 3.478540 GGAAATGGAAGGTCCGAGG 57.521 57.895 0.00 0.00 40.17 4.63
1730 1775 4.021916 AGGGGCTCATTCATTCTTGAAAG 58.978 43.478 0.00 0.00 44.70 2.62
1801 1854 0.824109 TAAGACAGCGCTGCCTACAT 59.176 50.000 36.28 18.81 0.00 2.29
1973 2026 4.160626 CCGACTAGAGGGACTGAGAAATTT 59.839 45.833 0.00 0.00 41.55 1.82
1974 2027 5.105752 CGACTAGAGGGACTGAGAAATTTG 58.894 45.833 0.00 0.00 41.55 2.32
2192 2245 3.693085 GACCCACTAAGACTCACGTATCA 59.307 47.826 0.00 0.00 0.00 2.15
2724 2779 6.374417 AGAAAGGCAGAGGTAAATACTTCA 57.626 37.500 5.63 0.00 35.05 3.02
2831 2886 0.251354 GCCAGTGATTCTCTGAGCCA 59.749 55.000 15.54 0.00 35.20 4.75
3288 3345 2.542178 GTGATGCAAGTGAACGTGTACA 59.458 45.455 0.00 0.00 0.00 2.90
3386 3443 3.429547 GCTCATTCTTCAGCCGTAGAGAA 60.430 47.826 0.00 0.00 0.00 2.87
3746 3803 8.974060 AAACAACGATTAGTGGATATTGGTAT 57.026 30.769 0.00 0.00 0.00 2.73
3904 3961 5.566623 CATGCATATGTTGTCAGTGAAGAC 58.433 41.667 0.00 0.00 38.99 3.01
4013 4071 6.408548 CCAGTCAAAGATTCCTATTCTAGGCA 60.409 42.308 0.00 0.00 45.82 4.75
4050 4110 3.370527 CCTTCGAATGGTGTTGGTCCTAT 60.371 47.826 0.00 0.00 0.00 2.57
4237 4297 4.905456 TGGGTAGAGGAAGTCTCAAAAAGA 59.095 41.667 0.00 0.00 44.81 2.52
4250 4310 2.301870 TCAAAAAGAGAAGGCCGAGCTA 59.698 45.455 0.00 0.00 0.00 3.32
4333 4393 1.058903 GCTCGCCAAATTCGTCGAC 59.941 57.895 5.18 5.18 0.00 4.20
4335 4395 1.005984 TCGCCAAATTCGTCGACCA 60.006 52.632 10.58 0.00 0.00 4.02
4446 4506 4.527038 CCTTATGTTTAGGAGCGGGATCTA 59.473 45.833 0.00 0.00 34.56 1.98
4465 4525 1.052124 ACCCAAGAACGACCTGTGGA 61.052 55.000 0.00 0.00 0.00 4.02
4553 4613 7.097192 TCACAAGATAAAGAAGTATGACGCTT 58.903 34.615 0.00 0.00 0.00 4.68
4939 5005 3.111853 AGAGATGCGACAAAGTGTTCA 57.888 42.857 0.00 0.00 0.00 3.18
5102 5168 2.096248 CCGAGACTCAGGTTAAGCTCT 58.904 52.381 3.68 0.00 0.00 4.09
5116 5182 2.995872 GCTCTGTCTCGGAACCGCT 61.996 63.158 8.48 0.00 39.59 5.52
5180 5246 1.397390 GGCATGGAGAAGCATTGGGG 61.397 60.000 0.00 0.00 0.00 4.96
5216 5282 2.930826 TCGGAGCAGTTTCTTTTCCT 57.069 45.000 0.00 0.00 0.00 3.36
5374 5440 3.197983 AGGATAACTAAGCTGACACACCC 59.802 47.826 0.00 0.00 0.00 4.61
5581 5647 3.935024 AGCTATCGCTTCGGGTCA 58.065 55.556 0.00 0.00 46.47 4.02
5726 5792 1.006400 AGGGCAGCCTTTAGAAGCAAT 59.994 47.619 12.43 0.00 0.00 3.56
6580 6670 3.372566 CCTTGGTGGGTAATGGCTCAATA 60.373 47.826 0.00 0.00 0.00 1.90
6636 6726 3.833070 ACGTTAGGTTTGGAGAGAGATGT 59.167 43.478 0.00 0.00 0.00 3.06
6790 6880 2.626743 GCTCCTTCTACCTATACCGCAA 59.373 50.000 0.00 0.00 0.00 4.85
6980 7070 9.386122 AGATATTGTGTTTGGAGAGGTAGATAT 57.614 33.333 0.00 0.00 0.00 1.63
7284 7374 3.848272 TTCAATCATCAACGCCCTTTC 57.152 42.857 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 279 1.068610 TGCAAAAGTGATAGCGGTTGC 60.069 47.619 0.00 0.00 41.28 4.17
281 282 1.003118 TCCTGCAAAAGTGATAGCGGT 59.997 47.619 0.00 0.00 0.00 5.68
761 762 0.106167 AGCATTCCATCCAGCAGCAT 60.106 50.000 0.00 0.00 0.00 3.79
789 790 7.482157 TCTATTCCTGATAGAAGGATCATGGA 58.518 38.462 0.00 0.00 45.84 3.41
998 1043 1.406539 GCCCGTTCCTAGTCGTCATAA 59.593 52.381 0.00 0.00 0.00 1.90
999 1044 1.027357 GCCCGTTCCTAGTCGTCATA 58.973 55.000 0.00 0.00 0.00 2.15
1289 1334 1.179174 GGCCACCTTCACAACCTTCC 61.179 60.000 0.00 0.00 0.00 3.46
1710 1755 5.416952 TCTTCTTTCAAGAATGAATGAGCCC 59.583 40.000 10.38 0.00 45.18 5.19
1801 1854 0.535335 ACCTCGGAAGCTAATTCGCA 59.465 50.000 4.63 0.00 38.95 5.10
1973 2026 7.095774 GCTTGAAGATAAGTTTTGTACTCGACA 60.096 37.037 0.00 0.00 35.54 4.35
1974 2027 7.116519 AGCTTGAAGATAAGTTTTGTACTCGAC 59.883 37.037 0.00 0.00 35.54 4.20
2127 2180 4.457949 TCTTTCTACGACATGCTGTAGTCA 59.542 41.667 18.99 9.00 37.41 3.41
2148 2201 2.769095 GTTGGCTCCACCTCTTATCTCT 59.231 50.000 0.00 0.00 40.22 3.10
2192 2245 1.674817 CCGCTCGGGAATGTAGTTGTT 60.675 52.381 0.00 0.00 38.47 2.83
2724 2779 2.722201 CCTACCGAGCCGCCTCTTT 61.722 63.158 0.00 0.00 35.90 2.52
2831 2886 2.427506 GAGGCGTTGGAAATGAAGACT 58.572 47.619 0.00 0.00 33.73 3.24
2951 3006 0.544697 GGGCTGGGTTCTATTTCCGA 59.455 55.000 0.00 0.00 0.00 4.55
3386 3443 6.976934 ATGGTACCTCACAATTCAAAAGTT 57.023 33.333 14.36 0.00 0.00 2.66
3634 3691 7.179160 TGTGGAGGAATCAATATCTCGACATAT 59.821 37.037 0.00 0.00 39.06 1.78
3746 3803 1.031029 TGCTTGCTGTGCAGTGACAA 61.031 50.000 0.00 0.00 40.61 3.18
3904 3961 2.291741 GTCTCCAAGGCTTCACACAAAG 59.708 50.000 0.00 0.00 0.00 2.77
3960 4017 2.094906 ACACATTCGCTCACTTACGCTA 60.095 45.455 0.00 0.00 0.00 4.26
4013 4071 2.567664 GAAGGTTAATGGCCCGCCCT 62.568 60.000 0.00 0.00 34.56 5.19
4025 4085 3.404899 GACCAACACCATTCGAAGGTTA 58.595 45.455 14.28 0.00 37.23 2.85
4237 4297 1.133450 TGACCTATAGCTCGGCCTTCT 60.133 52.381 0.00 0.00 0.00 2.85
4279 4339 0.839853 AGGAGAAAGCCCAGTCAGCT 60.840 55.000 0.00 0.00 44.19 4.24
4446 4506 1.052124 TCCACAGGTCGTTCTTGGGT 61.052 55.000 0.00 0.00 0.00 4.51
4465 4525 2.283388 TCCGTGCCTTCCGTACCT 60.283 61.111 0.00 0.00 0.00 3.08
4553 4613 5.745312 ATGACCAATAGAGTCAGACACAA 57.255 39.130 2.66 0.00 46.76 3.33
4667 4727 0.177141 TTTCCCTTCATACGGCTCGG 59.823 55.000 0.00 0.00 0.00 4.63
5102 5168 2.338620 CACAGCGGTTCCGAGACA 59.661 61.111 15.69 0.00 0.00 3.41
5116 5182 2.340731 TGCTTTACTCCTAACCCCACA 58.659 47.619 0.00 0.00 0.00 4.17
5180 5246 4.381411 CTCCGAAGAAAGATATTGGGGTC 58.619 47.826 0.00 0.00 0.00 4.46
5374 5440 0.602638 TTGTGCCAGTAGCCAACTCG 60.603 55.000 0.00 0.00 42.71 4.18
5581 5647 4.037565 CCGGTCCTTTTCTTTTAGTGCTTT 59.962 41.667 0.00 0.00 0.00 3.51
6471 6561 5.564848 GCATTATAGCACATAGTCTCCGACA 60.565 44.000 0.00 0.00 34.60 4.35
6580 6670 8.839745 TCCAATCATAAGGCTTTCCATCTATAT 58.160 33.333 4.45 0.00 33.74 0.86
6603 6693 4.128643 CAAACCTAACGTGGTAGTTTCCA 58.871 43.478 0.00 0.00 39.83 3.53
6636 6726 3.040477 CCCCCTAAACTATAACGGGTCA 58.960 50.000 0.00 0.00 32.91 4.02
6676 6766 1.480137 CATTTGGCCGGCTATGGAAAA 59.520 47.619 28.56 11.74 0.00 2.29
6814 6904 5.063204 CCCATTACTGACAAGAAAGACACA 58.937 41.667 0.00 0.00 0.00 3.72
6980 7070 4.063998 TCGAGCAAGACTACGTCCTATA 57.936 45.455 0.00 0.00 32.18 1.31
7223 7313 8.130671 ACCACTAGTAACTATGTCAGCTTTTA 57.869 34.615 0.00 0.00 0.00 1.52
7284 7374 7.381678 GGTATCACGAATAGCAGTTTTAGTAGG 59.618 40.741 0.00 0.00 38.09 3.18
7521 7611 2.757868 AGCTCAGCTCACGAAATAGAGT 59.242 45.455 0.00 0.00 30.62 3.24


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

AutoCloner maintained by Alex Coulton.