Multiple sequence alignment - TraesCS2D01G250300

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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 TraesCS2D01G250300 chr2D 100.000 2597 0 0 1 2597 298836437 298839033 0.000000e+00 4796.0
1 TraesCS2D01G250300 chr2B 96.450 2338 34 13 261 2597 363488077 363485788 0.000000e+00 3812.0
2 TraesCS2D01G250300 chr2B 94.074 270 16 0 1 270 363489115 363488846 6.690000e-111 411.0
3 TraesCS2D01G250300 chr2A 96.692 2146 54 7 452 2597 372370732 372372860 0.000000e+00 3554.0
4 TraesCS2D01G250300 chr3B 92.593 54 2 2 175 227 825556975 825557027 2.770000e-10 76.8
5 TraesCS2D01G250300 chr1D 97.727 44 1 0 1024 1067 474282835 474282792 2.770000e-10 76.8
6 TraesCS2D01G250300 chr1A 93.182 44 3 0 1024 1067 568638184 568638141 6.000000e-07 65.8


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 TraesCS2D01G250300 chr2D 298836437 298839033 2596 False 4796.0 4796 100.000 1 2597 1 chr2D.!!$F1 2596
1 TraesCS2D01G250300 chr2B 363485788 363489115 3327 True 2111.5 3812 95.262 1 2597 2 chr2B.!!$R1 2596
2 TraesCS2D01G250300 chr2A 372370732 372372860 2128 False 3554.0 3554 96.692 452 2597 1 chr2A.!!$F1 2145

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
302 1081 0.033228 CATGGACAGAGATCCTCGCC 59.967 60.0 0.0 0.0 39.75 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 2575 0.308993 GGCGAGCATAAGCATCAACC 59.691 55.0 0.0 0.0 45.49 3.77 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
31 32 0.035439 TCAAAACGGCCTCTGGATCC 60.035 55.000 4.20 4.20 0.00 3.36
48 49 7.052873 TCTGGATCCAGTACTGTTACTACTAC 58.947 42.308 35.34 3.00 43.96 2.73
154 155 1.217916 TTCAGGGGAGGTTCACACAA 58.782 50.000 0.00 0.00 0.00 3.33
157 158 1.352352 CAGGGGAGGTTCACACAATCT 59.648 52.381 0.00 0.00 0.00 2.40
184 185 2.871096 TGAACCACCCTACCACAATC 57.129 50.000 0.00 0.00 0.00 2.67
210 211 3.906846 ACAGAAGTGAGGGACTTTCTCAT 59.093 43.478 0.00 0.00 45.48 2.90
236 237 4.100653 TGAAAATCAAACCATGTGCCTTCA 59.899 37.500 0.00 0.00 0.00 3.02
237 238 3.665745 AATCAAACCATGTGCCTTCAC 57.334 42.857 0.00 0.00 43.40 3.18
252 253 2.224066 CCTTCACTGTCGTCTTTGGACT 60.224 50.000 0.00 0.00 40.10 3.85
254 255 2.821546 TCACTGTCGTCTTTGGACTTG 58.178 47.619 0.00 0.00 40.10 3.16
259 260 1.070776 GTCGTCTTTGGACTTGTTCGC 60.071 52.381 0.00 0.00 40.10 4.70
270 271 1.404035 ACTTGTTCGCCTTGAAACCAC 59.596 47.619 0.00 0.00 38.60 4.16
271 272 0.378962 TTGTTCGCCTTGAAACCACG 59.621 50.000 0.00 0.00 38.60 4.94
272 273 0.462225 TGTTCGCCTTGAAACCACGA 60.462 50.000 0.00 0.00 38.60 4.35
301 1080 1.035923 TCATGGACAGAGATCCTCGC 58.964 55.000 0.00 0.00 39.75 5.03
302 1081 0.033228 CATGGACAGAGATCCTCGCC 59.967 60.000 0.00 0.00 39.75 5.54
303 1082 1.118356 ATGGACAGAGATCCTCGCCC 61.118 60.000 0.00 0.00 39.75 6.13
312 1091 1.807495 GATCCTCGCCCTAACCCTCG 61.807 65.000 0.00 0.00 0.00 4.63
313 1092 3.537874 CCTCGCCCTAACCCTCGG 61.538 72.222 0.00 0.00 0.00 4.63
324 1103 1.196012 AACCCTCGGTTGAGATCCTC 58.804 55.000 0.00 0.00 45.07 3.71
347 1126 5.471797 TCGAGCAAAACCATCTTTATCAACA 59.528 36.000 0.00 0.00 0.00 3.33
379 1158 2.677875 CTCCCCAAGCCAGTTGCC 60.678 66.667 0.00 0.00 42.71 4.52
381 1160 1.850289 TCCCCAAGCCAGTTGCCTA 60.850 57.895 0.00 0.00 42.71 3.93
403 1182 3.650461 AGGGCTCTTTCAAAAGTCTCTCT 59.350 43.478 2.63 0.00 37.31 3.10
434 1213 0.165944 GAGCGCTTGCGTGTGTAAAT 59.834 50.000 13.26 0.00 45.69 1.40
456 1235 2.582636 AGGGCTGGTAGTTGATGGAAAT 59.417 45.455 0.00 0.00 0.00 2.17
581 1360 7.692705 GTGATTTCGCTTTAAGAAATGTAGGTC 59.307 37.037 8.64 0.00 45.18 3.85
595 1374 2.167398 TAGGTCCGTGCTTGTGCTCC 62.167 60.000 0.00 0.00 40.48 4.70
596 1375 2.031163 GTCCGTGCTTGTGCTCCT 59.969 61.111 0.00 0.00 40.48 3.69
597 1376 2.031012 TCCGTGCTTGTGCTCCTG 59.969 61.111 0.00 0.00 40.48 3.86
643 1422 4.767255 CTGCCACCGCCTCCACTC 62.767 72.222 0.00 0.00 0.00 3.51
736 1515 1.699656 CGCTCAGCCACAGATTTCCG 61.700 60.000 0.00 0.00 0.00 4.30
754 1533 4.238761 TCCGTATTAATCTCTCGCCTTG 57.761 45.455 0.00 0.00 0.00 3.61
1484 2264 4.379813 CCAAGGATGCACAAACTATGACAC 60.380 45.833 0.00 0.00 0.00 3.67
1492 2272 4.335416 CACAAACTATGACACTGGGGATT 58.665 43.478 0.00 0.00 0.00 3.01
1504 2284 1.228276 GGGGATTTGCCGAGGATCC 60.228 63.158 2.48 2.48 38.87 3.36
1795 2575 1.660560 CCCTCATTTCCTTGCGCAGG 61.661 60.000 13.36 13.36 45.64 4.85
1832 2612 2.352030 CGCCCTCTGTTTACGAGTGTAA 60.352 50.000 0.00 0.00 38.77 2.41
1833 2613 3.656559 GCCCTCTGTTTACGAGTGTAAA 58.343 45.455 0.00 0.00 45.76 2.01
2238 3018 6.587990 CCAGAATTGATAGCGAGAAATATCGT 59.412 38.462 0.00 0.00 44.53 3.73
2478 3258 4.542697 AGTTTTGGAACTTGTGGGTGTAT 58.457 39.130 0.00 0.00 43.48 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.336806 GTGCAGATAGTAGTAGTAACAGTACTG 58.663 40.741 21.44 21.44 40.89 2.74
48 49 0.904649 TCAGTGGGTGGTGCAGATAG 59.095 55.000 0.00 0.00 0.00 2.08
53 54 3.884774 GGGTCAGTGGGTGGTGCA 61.885 66.667 0.00 0.00 0.00 4.57
87 88 1.616628 GAGCTTCCCCAGGGAGGAA 60.617 63.158 18.56 8.06 46.06 3.36
108 109 2.276740 CCAATGGGGAGAGTGGCC 59.723 66.667 0.00 0.00 40.01 5.36
126 127 1.700042 CCTCCCCTGAATTCCTCCGG 61.700 65.000 2.27 0.00 0.00 5.14
154 155 2.127708 GGGTGGTTCATGTAGGGAGAT 58.872 52.381 0.00 0.00 0.00 2.75
157 158 2.474112 GTAGGGTGGTTCATGTAGGGA 58.526 52.381 0.00 0.00 0.00 4.20
184 185 4.884164 AGAAAGTCCCTCACTTCTGTTTTG 59.116 41.667 0.00 0.00 45.32 2.44
210 211 4.832266 AGGCACATGGTTTGATTTTCACTA 59.168 37.500 0.00 0.00 0.00 2.74
252 253 0.378962 CGTGGTTTCAAGGCGAACAA 59.621 50.000 0.00 0.00 31.73 2.83
254 255 0.658897 TTCGTGGTTTCAAGGCGAAC 59.341 50.000 0.00 0.00 36.78 3.95
259 260 2.812011 CCCTTAGTTCGTGGTTTCAAGG 59.188 50.000 0.00 0.00 0.00 3.61
271 272 9.729256 GGATCTCTGTCCATGAACCCTTAGTTC 62.729 48.148 0.00 0.00 44.83 3.01
272 273 4.168101 TCTCTGTCCATGAACCCTTAGTT 58.832 43.478 0.00 0.00 43.07 2.24
286 1065 0.178987 TAGGGCGAGGATCTCTGTCC 60.179 60.000 0.00 0.00 38.62 4.02
301 1080 1.413077 GATCTCAACCGAGGGTTAGGG 59.587 57.143 0.00 0.00 45.01 3.53
302 1081 1.413077 GGATCTCAACCGAGGGTTAGG 59.587 57.143 0.00 0.00 45.01 2.69
303 1082 2.362717 GAGGATCTCAACCGAGGGTTAG 59.637 54.545 0.00 0.00 45.01 2.34
312 1091 2.386661 TTTGCTCGAGGATCTCAACC 57.613 50.000 15.58 0.00 0.00 3.77
313 1092 2.416893 GGTTTTGCTCGAGGATCTCAAC 59.583 50.000 15.58 11.54 0.00 3.18
324 1103 5.698832 TGTTGATAAAGATGGTTTTGCTCG 58.301 37.500 0.00 0.00 0.00 5.03
347 1126 2.122768 GGGGAGGTGATCAGAGTTGAT 58.877 52.381 0.00 0.00 46.61 2.57
379 1158 5.046663 AGAGAGACTTTTGAAAGAGCCCTAG 60.047 44.000 10.26 0.00 39.31 3.02
381 1160 3.650461 AGAGAGACTTTTGAAAGAGCCCT 59.350 43.478 10.26 2.43 39.31 5.19
403 1182 4.082733 ACGCAAGCGCTCATATAAGAGATA 60.083 41.667 12.06 0.00 44.19 1.98
434 1213 2.561209 TCCATCAACTACCAGCCCTA 57.439 50.000 0.00 0.00 0.00 3.53
456 1235 0.320374 CCAGCGGGGCGATTCTATTA 59.680 55.000 0.00 0.00 0.00 0.98
581 1360 3.730761 GCAGGAGCACAAGCACGG 61.731 66.667 0.00 0.00 45.49 4.94
641 1420 4.544689 CTCGCCGTGCTCGAGGAG 62.545 72.222 15.58 11.25 46.82 3.69
736 1515 4.446051 GCAGACAAGGCGAGAGATTAATAC 59.554 45.833 0.00 0.00 0.00 1.89
754 1533 2.003301 GATCCGACAAAAGGAGCAGAC 58.997 52.381 0.00 0.00 43.19 3.51
1484 2264 0.536006 GATCCTCGGCAAATCCCCAG 60.536 60.000 0.00 0.00 0.00 4.45
1492 2272 1.198094 TCCACAAGGATCCTCGGCAA 61.198 55.000 16.52 0.00 39.61 4.52
1504 2284 1.734163 GGGTCCGTTGTATCCACAAG 58.266 55.000 0.00 0.00 45.18 3.16
1795 2575 0.308993 GGCGAGCATAAGCATCAACC 59.691 55.000 0.00 0.00 45.49 3.77
1832 2612 3.378339 CGTTTGAGGTACTGAGAACGTT 58.622 45.455 0.00 0.00 41.55 3.99
1833 2613 2.360165 ACGTTTGAGGTACTGAGAACGT 59.640 45.455 18.02 18.02 45.74 3.99
2182 2962 6.699575 AATAGCCACTGAAATGTTATGACC 57.300 37.500 0.00 0.00 0.00 4.02
2238 3018 8.908786 ACATCTGAGTTGTAAGAGAAAAATGA 57.091 30.769 0.00 0.00 0.00 2.57
2478 3258 1.268640 GCACCGGCGAGTTTTAAAACA 60.269 47.619 28.03 0.00 41.30 2.83


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

AutoCloner maintained by Alex Coulton.