Multiple sequence alignment - TraesCS2D01G203900

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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 TraesCS2D01G203900 chr2D 100.000 4811 0 0 1 4811 155737862 155733052 0.000000e+00 8885.0
1 TraesCS2D01G203900 chr2D 93.939 66 4 0 3888 3953 155733910 155733845 3.060000e-17 100.0
2 TraesCS2D01G203900 chr2D 93.939 66 4 0 3953 4018 155733975 155733910 3.060000e-17 100.0
3 TraesCS2D01G203900 chr2A 94.730 4877 164 34 1 4811 165851733 165846884 0.000000e+00 7496.0
4 TraesCS2D01G203900 chr2B 95.677 4441 125 23 1 4391 213256905 213252482 0.000000e+00 7075.0
5 TraesCS2D01G203900 chr2B 89.625 453 16 14 4390 4811 213252378 213251926 9.100000e-152 547.0
6 TraesCS2D01G203900 chr2B 89.394 66 7 0 3888 3953 213252926 213252861 3.090000e-12 84.2
7 TraesCS2D01G203900 chr5D 82.353 153 23 4 1782 1932 231746332 231746482 3.910000e-26 130.0
8 TraesCS2D01G203900 chr5B 82.353 153 23 4 1782 1932 273719013 273718863 3.910000e-26 130.0
9 TraesCS2D01G203900 chr5A 82.353 153 23 4 1782 1932 325373840 325373690 3.910000e-26 130.0


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 TraesCS2D01G203900 chr2D 155733052 155737862 4810 True 8885 8885 100.000 1 4811 1 chr2D.!!$R1 4810
1 TraesCS2D01G203900 chr2A 165846884 165851733 4849 True 7496 7496 94.730 1 4811 1 chr2A.!!$R1 4810
2 TraesCS2D01G203900 chr2B 213251926 213256905 4979 True 3811 7075 92.651 1 4811 2 chr2B.!!$R2 4810

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
366 372 0.608130 AAAATCGGGCTGCCTTTTCC 59.392 50.0 19.68 0.00 0.00 3.13 F
754 786 0.618968 TCCTCCCTCTTCCTTGGCTC 60.619 60.0 0.00 0.00 0.00 4.70 F
1181 1222 0.954449 CATGCCAGATCGCTGATCCC 60.954 60.0 12.81 5.31 45.17 3.85 F
2985 3073 0.746659 TCGCTGACATGATCGATGGT 59.253 50.0 0.54 0.00 36.23 3.55 F
3501 3589 0.528901 TGGACTTCGACAACACCACG 60.529 55.0 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2194 0.032952 TGTCCACCAGCTCGTTGTAC 59.967 55.0 0.00 0.0 0.00 2.90 R
2251 2339 1.985473 TCACAAGAGCTGCAAATGGT 58.015 45.0 1.02 0.0 0.00 3.55 R
3168 3256 0.449388 CTTCATCGGCAGCTTGGAAC 59.551 55.0 0.00 0.0 0.00 3.62 R
3804 3892 0.035152 ATGGCGAAACATCTCAGGCA 60.035 50.0 0.00 0.0 41.46 4.75 R
4517 4747 0.179034 GGTGGAGTGATGGAGATGGC 60.179 60.0 0.00 0.0 0.00 4.40 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
24 25 1.315257 ATCATCAACGGGCAGGCAAC 61.315 55.000 0.00 0.00 0.00 4.17
35 36 2.132996 CAGGCAACACAAAGGGGCA 61.133 57.895 0.00 0.00 41.41 5.36
63 64 4.518970 TCCAACCATTTCCTTTTCTTCTCG 59.481 41.667 0.00 0.00 0.00 4.04
111 112 5.245075 TGTCAAGGACAAGAAAACAAAACCT 59.755 36.000 0.00 0.00 39.78 3.50
198 199 4.340246 GCCGTCCCCTTTCCGGTT 62.340 66.667 0.00 0.00 43.56 4.44
366 372 0.608130 AAAATCGGGCTGCCTTTTCC 59.392 50.000 19.68 0.00 0.00 3.13
430 438 3.696548 GCAATTCCAGTCCCTTTTAGAGG 59.303 47.826 0.00 0.00 45.86 3.69
505 526 6.446909 TGTGGATTAGTATATTGGCATGGA 57.553 37.500 0.00 0.00 0.00 3.41
512 533 3.976654 AGTATATTGGCATGGAGTGAGGT 59.023 43.478 0.00 0.00 0.00 3.85
556 577 0.966875 TTGTAGCCTCGCCCGACTAA 60.967 55.000 0.00 0.00 0.00 2.24
603 624 1.358046 CCCTAGTGCGTACGTAGCC 59.642 63.158 17.90 1.14 0.00 3.93
604 625 1.010350 CCTAGTGCGTACGTAGCCG 60.010 63.158 17.90 7.67 40.83 5.52
705 736 5.250982 TCTAAACTAAACCCAAGCTTAGCC 58.749 41.667 0.00 0.00 0.00 3.93
754 786 0.618968 TCCTCCCTCTTCCTTGGCTC 60.619 60.000 0.00 0.00 0.00 4.70
773 805 3.490348 CTCCTTCCCATCTCTCTCTCTC 58.510 54.545 0.00 0.00 0.00 3.20
776 808 3.139025 CCTTCCCATCTCTCTCTCTCTCT 59.861 52.174 0.00 0.00 0.00 3.10
777 809 4.392940 CTTCCCATCTCTCTCTCTCTCTC 58.607 52.174 0.00 0.00 0.00 3.20
778 810 3.668821 TCCCATCTCTCTCTCTCTCTCT 58.331 50.000 0.00 0.00 0.00 3.10
779 811 3.392285 TCCCATCTCTCTCTCTCTCTCTG 59.608 52.174 0.00 0.00 0.00 3.35
902 940 3.522731 ACTCCTCCTAGCAGCGCG 61.523 66.667 0.00 0.00 0.00 6.86
904 942 3.192954 CTCCTCCTAGCAGCGCGAG 62.193 68.421 12.10 1.41 0.00 5.03
1147 1188 3.589654 CTCCTGCGGCCGTTTCTCA 62.590 63.158 28.70 14.77 0.00 3.27
1181 1222 0.954449 CATGCCAGATCGCTGATCCC 60.954 60.000 12.81 5.31 45.17 3.85
1704 1780 7.344352 AGAAGTATCTTCTCTTCTGTATGCCTT 59.656 37.037 6.24 0.00 45.50 4.35
1717 1793 7.031226 TCTGTATGCCTTAATTGATTGCTTC 57.969 36.000 0.00 0.00 0.00 3.86
1719 1795 7.992608 TCTGTATGCCTTAATTGATTGCTTCTA 59.007 33.333 0.00 0.00 0.00 2.10
1889 1973 1.354101 TCGTCAATGGTAACCAGGGT 58.646 50.000 0.00 0.00 36.75 4.34
1966 2050 2.168496 TCACTGCGTAGGTAAGCTTCT 58.832 47.619 0.00 0.00 0.00 2.85
1967 2051 2.561419 TCACTGCGTAGGTAAGCTTCTT 59.439 45.455 0.00 0.00 0.00 2.52
2046 2134 3.826157 GTGGAAATTTGATGAGGTGGACA 59.174 43.478 0.00 0.00 0.00 4.02
2106 2194 2.772691 GGAGGTGTACGCCGAGGAG 61.773 68.421 19.53 0.00 0.00 3.69
2166 2254 2.079925 GTGCTTGAGATGGTCACCTTC 58.920 52.381 1.18 1.18 33.71 3.46
2251 2339 5.249393 AGAAGTGCCTCTTGGATCTCTTTAA 59.751 40.000 0.00 0.00 36.40 1.52
2556 2644 4.599241 AGGCATGCTTATAGTAATGGGTCT 59.401 41.667 18.92 0.00 0.00 3.85
2880 2968 4.196971 GGGTACGCAACATCTATTTTCCT 58.803 43.478 4.83 0.00 0.00 3.36
2973 3061 2.984458 GAGGTTACTCGTATCGCTGAC 58.016 52.381 0.00 0.00 33.35 3.51
2985 3073 0.746659 TCGCTGACATGATCGATGGT 59.253 50.000 0.54 0.00 36.23 3.55
3159 3247 1.815003 GAACTGCATGGGAGGTTTGAG 59.185 52.381 0.00 0.00 0.00 3.02
3168 3256 1.134670 GGGAGGTTTGAGGAGATCACG 60.135 57.143 0.00 0.00 37.77 4.35
3237 3325 1.664017 CTCTGATGATGGAGGCGCG 60.664 63.158 0.00 0.00 0.00 6.86
3243 3331 1.996786 ATGATGGAGGCGCGCAAAAG 61.997 55.000 34.42 0.00 0.00 2.27
3274 3362 5.255397 TGTCAAAGACAAGGAACCCATAT 57.745 39.130 0.00 0.00 39.78 1.78
3378 3466 4.302455 CAACCGAGAATTATGAGAGCGAT 58.698 43.478 0.00 0.00 0.00 4.58
3501 3589 0.528901 TGGACTTCGACAACACCACG 60.529 55.000 0.00 0.00 0.00 4.94
3804 3892 0.830444 TACCCCTAAGCGCCATCGAT 60.830 55.000 2.29 0.00 38.10 3.59
4034 4124 5.510520 GCCTTGTGAATCTAGAGGATACCAG 60.511 48.000 0.00 0.00 33.71 4.00
4039 4129 7.760607 TGTGAATCTAGAGGATACCAGTCTAT 58.239 38.462 0.00 0.00 33.71 1.98
4090 4180 1.629013 CTGTGTGCGTCGTATGATGT 58.371 50.000 6.05 0.00 33.44 3.06
4099 4189 2.735444 CGTCGTATGATGTTGCAGAGGT 60.735 50.000 0.00 0.00 0.00 3.85
4261 4359 5.994054 CCCATATCTTGATAATAGATGCCGG 59.006 44.000 0.00 0.00 34.35 6.13
4349 4447 0.177836 GGAGCTGGAAGAGAAGAGCC 59.822 60.000 0.00 0.00 34.07 4.70
4517 4747 1.303282 GGCAAGGACAAGGGTAGGG 59.697 63.158 0.00 0.00 0.00 3.53
4578 4808 5.188555 AGAAGACCTGTGCAGATCTCATTTA 59.811 40.000 0.00 0.00 0.00 1.40
4670 4901 0.939419 GCGGTGGTTAAAACACGAGT 59.061 50.000 6.76 0.00 39.69 4.18
4789 5023 7.558807 AGAAAATTCAGACAGGCATTATCATGA 59.441 33.333 0.00 0.00 31.07 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.676967 GGAGAGCTGCCCCTTTGTG 60.677 63.158 0.00 0.00 0.00 3.33
35 36 3.532641 AAAGGAAATGGTTGGAGAGCT 57.467 42.857 0.00 0.00 0.00 4.09
63 64 3.438434 GGCAAATCTGACTCTTGACTTCC 59.562 47.826 0.00 0.00 0.00 3.46
111 112 6.909550 AAATGGCAGTGGTAAATTTACTGA 57.090 33.333 23.89 11.22 43.35 3.41
216 217 2.946990 GAGAACGGGGTGTTTTTCAGAA 59.053 45.455 0.00 0.00 42.09 3.02
217 218 2.567985 GAGAACGGGGTGTTTTTCAGA 58.432 47.619 0.00 0.00 42.09 3.27
218 219 1.263217 CGAGAACGGGGTGTTTTTCAG 59.737 52.381 0.00 0.00 42.09 3.02
219 220 1.134461 TCGAGAACGGGGTGTTTTTCA 60.134 47.619 0.00 0.00 42.09 2.69
419 427 3.133901 GCTCCTCTTCTCCTCTAAAAGGG 59.866 52.174 0.00 0.00 46.23 3.95
430 438 1.965754 ATGGCGTGGCTCCTCTTCTC 61.966 60.000 0.00 0.00 0.00 2.87
505 526 4.062991 GACACGGTCAAATTAACCTCACT 58.937 43.478 7.99 0.00 34.45 3.41
512 533 5.249420 TCCATCATGACACGGTCAAATTAA 58.751 37.500 10.17 0.00 45.96 1.40
556 577 3.890147 GGATCCTAGATACTGTCGTTGGT 59.110 47.826 3.84 0.00 0.00 3.67
603 624 5.172232 CACACGAGATGAGATTTACTAAGCG 59.828 44.000 0.00 0.00 0.00 4.68
604 625 5.460419 CCACACGAGATGAGATTTACTAAGC 59.540 44.000 0.00 0.00 0.00 3.09
705 736 1.072965 GGATGATGAGGCTACCCCAAG 59.927 57.143 0.00 0.00 35.39 3.61
744 775 0.625849 GATGGGAAGGAGCCAAGGAA 59.374 55.000 0.00 0.00 0.00 3.36
754 786 3.139025 AGAGAGAGAGAGAGATGGGAAGG 59.861 52.174 0.00 0.00 0.00 3.46
779 811 1.827789 ACATGGTGTGTGTGGGCAC 60.828 57.895 0.00 0.00 45.44 5.01
804 836 1.269723 GCGGCCTATTTAGGGAAATGC 59.730 52.381 0.00 0.00 43.82 3.56
864 902 0.178918 GATAGGGAGTGAGGAGGGGG 60.179 65.000 0.00 0.00 0.00 5.40
966 1004 3.718210 CTCCGGCTCCGTAACCAGC 62.718 68.421 7.59 0.00 37.81 4.85
1147 1188 0.532115 GCATGGCAGGGAAACGAATT 59.468 50.000 0.00 0.00 0.00 2.17
1704 1780 6.318648 ACCAGCGAATTAGAAGCAATCAATTA 59.681 34.615 0.00 0.00 0.00 1.40
1717 1793 5.597806 TGTACCTAATCACCAGCGAATTAG 58.402 41.667 0.00 0.00 0.00 1.73
1719 1795 4.442706 CTGTACCTAATCACCAGCGAATT 58.557 43.478 0.00 0.00 0.00 2.17
1889 1973 1.511305 GTCGCCGATCTTGACCTCA 59.489 57.895 0.00 0.00 0.00 3.86
1998 2082 3.141398 CCATCACCATTTGGGATCGTAG 58.859 50.000 0.96 0.00 41.15 3.51
2046 2134 2.307686 ACCTACCCAAACAATCCGACAT 59.692 45.455 0.00 0.00 0.00 3.06
2106 2194 0.032952 TGTCCACCAGCTCGTTGTAC 59.967 55.000 0.00 0.00 0.00 2.90
2166 2254 2.847901 CATTCGCTATACGGGTACTCG 58.152 52.381 15.01 15.01 43.89 4.18
2251 2339 1.985473 TCACAAGAGCTGCAAATGGT 58.015 45.000 1.02 0.00 0.00 3.55
2556 2644 2.040145 TGAGAACCCATTGCTCATCACA 59.960 45.455 0.00 0.00 34.02 3.58
2847 2935 3.428282 CGTACCCGGCCTGCAAAC 61.428 66.667 0.00 0.00 0.00 2.93
2880 2968 4.183865 CAGTATCAGCCTCAACATCGAAA 58.816 43.478 0.00 0.00 0.00 3.46
2973 3061 3.739810 CACTAAGCTCACCATCGATCATG 59.260 47.826 0.00 0.00 0.00 3.07
2985 3073 1.374631 CACCAGCGCACTAAGCTCA 60.375 57.895 11.47 0.00 44.06 4.26
2997 3085 1.389609 CCATCCAATCTGGCACCAGC 61.390 60.000 12.03 0.00 43.31 4.85
2998 3086 2.803203 CCATCCAATCTGGCACCAG 58.197 57.895 10.60 10.60 44.86 4.00
3159 3247 1.363744 CAGCTTGGAACGTGATCTCC 58.636 55.000 0.00 0.00 0.00 3.71
3168 3256 0.449388 CTTCATCGGCAGCTTGGAAC 59.551 55.000 0.00 0.00 0.00 3.62
3237 3325 2.798976 TGACATGTTGCTCCTTTTGC 57.201 45.000 0.00 0.00 0.00 3.68
3243 3331 3.304928 CCTTGTCTTTGACATGTTGCTCC 60.305 47.826 0.00 0.00 42.40 4.70
3274 3362 1.969923 CTTTGGAAACCCATTCAGGCA 59.030 47.619 0.00 0.00 39.98 4.75
3288 3376 3.775316 GACCTCTTCTACCCATCTTTGGA 59.225 47.826 0.00 0.00 46.92 3.53
3391 3479 3.203716 GCTTTATGTCGAACCCCTTAGG 58.796 50.000 0.00 0.00 43.78 2.69
3393 3481 3.985019 TGCTTTATGTCGAACCCCTTA 57.015 42.857 0.00 0.00 0.00 2.69
3501 3589 0.391661 TCGTCCTGCTTGCTCCATTC 60.392 55.000 0.00 0.00 0.00 2.67
3555 3643 1.135803 CGGAAATTGTGGTGCTTACCG 60.136 52.381 0.00 0.00 0.00 4.02
3714 3802 4.460263 AGTTTCTGGCTGTGAACATACAA 58.540 39.130 12.71 0.00 0.00 2.41
3804 3892 0.035152 ATGGCGAAACATCTCAGGCA 60.035 50.000 0.00 0.00 41.46 4.75
4034 4124 4.269603 CAGCATACACTCAACAGCATAGAC 59.730 45.833 0.00 0.00 0.00 2.59
4039 4129 1.159285 GCAGCATACACTCAACAGCA 58.841 50.000 0.00 0.00 0.00 4.41
4090 4180 1.005450 GGATAACCCCAACCTCTGCAA 59.995 52.381 0.00 0.00 0.00 4.08
4235 4333 6.302269 GGCATCTATTATCAAGATATGGGGG 58.698 44.000 0.00 0.00 32.40 5.40
4261 4359 6.967199 GCATAATTAACTAACAGCAAGGACAC 59.033 38.462 0.00 0.00 0.00 3.67
4298 4396 3.856521 CGATCTGATTCATAGCTTAGGCG 59.143 47.826 0.00 0.00 44.37 5.52
4349 4447 7.176490 ACTAGGCTGTATTAGTATAGGACTGG 58.824 42.308 0.00 0.00 39.39 4.00
4399 4602 2.014068 GCAAGATGGGCTGTGGAGTAC 61.014 57.143 0.00 0.00 0.00 2.73
4517 4747 0.179034 GGTGGAGTGATGGAGATGGC 60.179 60.000 0.00 0.00 0.00 4.40
4578 4808 4.748798 CCCTGGTCCTGGAGCCCT 62.749 72.222 22.16 0.00 0.00 5.19
4670 4901 1.055849 TGTGAGCCACTTTAGCAGGA 58.944 50.000 6.83 0.00 35.11 3.86
4775 5006 2.287188 GGTGCGTTCATGATAATGCCTG 60.287 50.000 8.73 0.00 40.04 4.85
4789 5023 1.827399 ATCTCCAACCTCGGTGCGTT 61.827 55.000 0.00 0.00 0.00 4.84


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

AutoCloner maintained by Alex Coulton.