Multiple sequence alignment - TraesCS1D01G086000

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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 TraesCS1D01G086000 chr1D 100.000 2303 0 0 1 2303 70458112 70455810 0.000000e+00 4253
1 TraesCS1D01G086000 chr1A 93.033 1995 89 31 1 1969 70907662 70905692 0.000000e+00 2868
2 TraesCS1D01G086000 chr1A 83.578 341 34 12 1965 2303 70904833 70904513 1.340000e-77 300
3 TraesCS1D01G086000 chr1B 93.668 1453 71 14 178 1627 111919140 111917706 0.000000e+00 2154
4 TraesCS1D01G086000 chr1B 93.264 193 12 1 1625 1817 111917506 111917315 1.350000e-72 283
5 TraesCS1D01G086000 chr1B 87.255 204 12 2 1 192 111920342 111920141 1.070000e-53 220
6 TraesCS1D01G086000 chr1B 91.892 111 7 2 1809 1917 111917149 111917039 1.100000e-33 154


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 TraesCS1D01G086000 chr1D 70455810 70458112 2302 True 4253.00 4253 100.00000 1 2303 1 chr1D.!!$R1 2302
1 TraesCS1D01G086000 chr1A 70904513 70907662 3149 True 1584.00 2868 88.30550 1 2303 2 chr1A.!!$R1 2302
2 TraesCS1D01G086000 chr1B 111917039 111920342 3303 True 702.75 2154 91.51975 1 1917 4 chr1B.!!$R1 1916

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
923 1972 0.108774 GCCTCGCTATAAAAGGGGCT 59.891 55.0 0.0 0.0 38.66 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 4424 0.105194 AGAAGTTTTTGGGGTGGGGG 60.105 55.0 0.0 0.0 0.0 5.4 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
34 36 7.950512 TCATTTCCTTTTCTTTCAGTGCATAA 58.049 30.769 0.00 0.00 0.00 1.90
139 160 1.299541 AGGGCATATTTCGTTCGCAG 58.700 50.000 0.00 0.00 0.00 5.18
140 161 1.134521 AGGGCATATTTCGTTCGCAGA 60.135 47.619 0.00 0.00 0.00 4.26
152 173 3.084278 CGTTCGCAGAATTCTAAAAGCG 58.916 45.455 24.27 24.27 45.90 4.68
154 175 1.060553 TCGCAGAATTCTAAAAGCGCG 59.939 47.619 25.02 23.79 44.27 6.86
156 177 1.396996 GCAGAATTCTAAAAGCGCGGA 59.603 47.619 8.83 0.00 0.00 5.54
225 1263 8.000709 ACAGAGGATTGGCAATCATAGAAATTA 58.999 33.333 34.04 0.00 39.71 1.40
229 1267 9.151177 AGGATTGGCAATCATAGAAATTATGTT 57.849 29.630 34.04 0.12 39.71 2.71
230 1268 9.199982 GGATTGGCAATCATAGAAATTATGTTG 57.800 33.333 34.04 0.00 39.71 3.33
291 1329 9.492730 AAGGAATCCTAATTAACATGGTCAAAT 57.507 29.630 0.46 0.00 31.13 2.32
292 1330 9.136323 AGGAATCCTAATTAACATGGTCAAATC 57.864 33.333 0.00 0.00 28.47 2.17
424 1465 7.860373 TGTTAGAATTCATGTGTTTTTCCTTCG 59.140 33.333 8.44 0.00 0.00 3.79
441 1482 8.848474 TTTCCTTCGAACTGAGATAAAAGAAT 57.152 30.769 0.00 0.00 0.00 2.40
442 1483 8.848474 TTCCTTCGAACTGAGATAAAAGAATT 57.152 30.769 0.00 0.00 0.00 2.17
478 1519 5.982890 TTTCTTTGATTGTCCCATTCCTC 57.017 39.130 0.00 0.00 0.00 3.71
489 1531 3.444034 GTCCCATTCCTCTTAACCAAAGC 59.556 47.826 0.00 0.00 34.97 3.51
576 1622 6.512297 TGAACCAAAAGAGGCATAAGTTTTC 58.488 36.000 0.00 0.00 0.00 2.29
596 1644 7.450014 AGTTTTCACATGGTATTATGGTGTTGA 59.550 33.333 0.00 0.00 32.32 3.18
612 1660 5.163513 GGTGTTGAAGATATGCCAAAAGTG 58.836 41.667 0.00 0.00 0.00 3.16
613 1661 4.622740 GTGTTGAAGATATGCCAAAAGTGC 59.377 41.667 0.00 0.00 0.00 4.40
620 1668 0.249996 ATGCCAAAAGTGCCAACTGC 60.250 50.000 0.00 0.00 36.51 4.40
668 1716 8.861033 ATTACAAATCGCTGTCGTATAGTAAA 57.139 30.769 0.00 0.00 36.96 2.01
671 1719 7.618442 ACAAATCGCTGTCGTATAGTAAAATG 58.382 34.615 0.00 0.00 36.96 2.32
851 1900 8.203485 TCATGGTTAATGAGGGAATTTTTATGC 58.797 33.333 0.00 0.00 40.50 3.14
923 1972 0.108774 GCCTCGCTATAAAAGGGGCT 59.891 55.000 0.00 0.00 38.66 5.19
953 2003 2.590821 CATCCCCATTCATCCAACCTC 58.409 52.381 0.00 0.00 0.00 3.85
976 2026 7.230849 TCAGGAAACAAACAAGCATCATATT 57.769 32.000 0.00 0.00 0.00 1.28
977 2027 7.315142 TCAGGAAACAAACAAGCATCATATTC 58.685 34.615 0.00 0.00 0.00 1.75
979 2029 7.762615 CAGGAAACAAACAAGCATCATATTCAT 59.237 33.333 0.00 0.00 0.00 2.57
980 2030 8.970020 AGGAAACAAACAAGCATCATATTCATA 58.030 29.630 0.00 0.00 0.00 2.15
981 2031 9.754382 GGAAACAAACAAGCATCATATTCATAT 57.246 29.630 0.00 0.00 0.00 1.78
1088 2138 1.825474 GGTGGAGAAGATCGAGTTCCA 59.175 52.381 6.67 7.05 35.67 3.53
1113 2163 1.450312 CGTCCACATCAAGCCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
1117 2167 1.450312 CACATCAAGCCTCCCGTCC 60.450 63.158 0.00 0.00 0.00 4.79
1264 2314 3.784701 TCATCGAGGACACTAAGAAGC 57.215 47.619 0.00 0.00 0.00 3.86
1399 2449 4.201656 GCCGTCCTCGTCAGTAAAAATTAC 60.202 45.833 0.00 0.00 35.01 1.89
1400 2450 4.925054 CCGTCCTCGTCAGTAAAAATTACA 59.075 41.667 3.37 0.00 35.01 2.41
1401 2451 5.061808 CCGTCCTCGTCAGTAAAAATTACAG 59.938 44.000 3.37 0.00 35.01 2.74
1402 2452 5.632347 CGTCCTCGTCAGTAAAAATTACAGT 59.368 40.000 3.37 0.00 0.00 3.55
1403 2453 6.803320 CGTCCTCGTCAGTAAAAATTACAGTA 59.197 38.462 3.37 0.00 0.00 2.74
1522 2579 0.594602 ATGCATGCATGATACGGTGC 59.405 50.000 31.74 14.24 41.61 5.01
1583 2641 9.482175 ACCAGCTAAATAATTTGGGTTTGTATA 57.518 29.630 0.00 0.00 33.20 1.47
1643 2902 7.397512 TGTACGTATGTTTTTAGTCACTGTG 57.602 36.000 0.00 0.17 0.00 3.66
1709 2968 4.555511 GCTAATCATCTTCCATTTGCCGAC 60.556 45.833 0.00 0.00 0.00 4.79
1828 3261 9.109533 CAGTTGGTAATAATGTAAACACGTTTC 57.890 33.333 0.00 0.00 34.23 2.78
1888 3321 7.235399 ACTTCCCAGGTTTGAAAATTACATGAT 59.765 33.333 0.00 0.00 0.00 2.45
1921 3356 7.417342 GCCCAATCATTAGTATGCAACCTTAAA 60.417 37.037 0.00 0.00 0.00 1.52
1963 4261 6.817765 ATTGTTAACCCAATCACTGTACTG 57.182 37.500 2.48 0.00 29.02 2.74
1969 4267 3.569701 ACCCAATCACTGTACTGCTTTTG 59.430 43.478 0.00 1.79 0.00 2.44
1974 4272 6.441274 CAATCACTGTACTGCTTTTGACATT 58.559 36.000 0.00 0.00 0.00 2.71
1982 4280 7.548097 TGTACTGCTTTTGACATTACCAAAAA 58.452 30.769 0.00 0.00 41.28 1.94
2025 4323 9.793252 TTCATAAATCTTGAATGCTTTAGCTTC 57.207 29.630 0.00 5.40 42.66 3.86
2048 4346 5.880332 TCGTCCTTGCAAAATTCTAGCTATT 59.120 36.000 0.00 0.00 0.00 1.73
2093 4391 4.870363 TCTCATTTGTGTTTAAAGCTGCC 58.130 39.130 0.00 0.00 0.00 4.85
2100 4398 0.388520 GTTTAAAGCTGCCCCTTGCG 60.389 55.000 0.00 0.00 45.60 4.85
2106 4404 4.047059 CTGCCCCTTGCGCAACAG 62.047 66.667 21.02 20.33 45.60 3.16
2118 4416 4.748144 CAACAGCAGCCCCCTCCC 62.748 72.222 0.00 0.00 0.00 4.30
2150 4448 4.649218 CCCCACCCCAAAAACTTCTATATG 59.351 45.833 0.00 0.00 0.00 1.78
2152 4450 5.719563 CCCACCCCAAAAACTTCTATATGTT 59.280 40.000 0.00 0.00 0.00 2.71
2154 4452 7.256511 CCCACCCCAAAAACTTCTATATGTTTT 60.257 37.037 0.00 0.00 44.91 2.43
2156 4454 9.203421 CACCCCAAAAACTTCTATATGTTTTTC 57.797 33.333 11.89 0.00 46.72 2.29
2158 4456 9.639601 CCCCAAAAACTTCTATATGTTTTTCTC 57.360 33.333 11.89 0.00 46.72 2.87
2159 4457 9.341899 CCCAAAAACTTCTATATGTTTTTCTCG 57.658 33.333 11.89 4.24 46.72 4.04
2174 4478 8.223177 TGTTTTTCTCGATAAAGGGTGTTTTA 57.777 30.769 0.00 0.00 0.00 1.52
2184 4488 9.550811 CGATAAAGGGTGTTTTAATTAACTCAC 57.449 33.333 16.95 16.95 0.00 3.51
2216 4522 1.132640 GCGGACAAACACGATGAGC 59.867 57.895 0.00 0.00 0.00 4.26
2229 4535 5.872635 ACACGATGAGCAAATGTTTCTATG 58.127 37.500 0.00 0.00 0.00 2.23
2276 4582 7.912778 TTCAAGATTTATTTTCCTATGGGGG 57.087 36.000 0.00 0.00 35.33 5.40
2286 4592 0.323360 CCTATGGGGGTGGTGTTGTG 60.323 60.000 0.00 0.00 0.00 3.33
2292 4598 1.756561 GGGTGGTGTTGTGGCAACT 60.757 57.895 12.36 0.00 37.61 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 135 5.703592 TGCGAACGAAATATGCCCTAATATT 59.296 36.000 0.00 0.00 34.83 1.28
115 136 5.242434 TGCGAACGAAATATGCCCTAATAT 58.758 37.500 0.00 0.00 0.00 1.28
116 137 4.633175 TGCGAACGAAATATGCCCTAATA 58.367 39.130 0.00 0.00 0.00 0.98
117 138 3.472652 TGCGAACGAAATATGCCCTAAT 58.527 40.909 0.00 0.00 0.00 1.73
118 139 2.869801 CTGCGAACGAAATATGCCCTAA 59.130 45.455 0.00 0.00 0.00 2.69
119 140 2.101750 TCTGCGAACGAAATATGCCCTA 59.898 45.455 0.00 0.00 0.00 3.53
120 141 1.134521 TCTGCGAACGAAATATGCCCT 60.135 47.619 0.00 0.00 0.00 5.19
139 160 6.044512 TCTATTTCCGCGCTTTTAGAATTC 57.955 37.500 5.56 0.00 0.00 2.17
140 161 6.431198 TTCTATTTCCGCGCTTTTAGAATT 57.569 33.333 5.56 0.00 0.00 2.17
225 1263 5.126869 TGTGAACCAAACATCAAGTCAACAT 59.873 36.000 0.00 0.00 0.00 2.71
229 1267 3.631686 CCTGTGAACCAAACATCAAGTCA 59.368 43.478 0.00 0.00 0.00 3.41
230 1268 3.882888 TCCTGTGAACCAAACATCAAGTC 59.117 43.478 0.00 0.00 0.00 3.01
263 1301 9.983024 TTGACCATGTTAATTAGGATTCCTTTA 57.017 29.630 11.25 1.54 34.61 1.85
291 1329 5.588958 TTTTCATGTGGTGTGACATTTGA 57.411 34.783 0.00 0.00 34.18 2.69
292 1330 9.806203 ATATATTTTCATGTGGTGTGACATTTG 57.194 29.630 0.00 0.00 34.18 2.32
296 1335 9.679661 AACTATATATTTTCATGTGGTGTGACA 57.320 29.630 0.00 0.00 0.00 3.58
366 1407 9.581289 TTGGACCTCTTTTTCAATTTACTATGA 57.419 29.630 0.00 0.00 0.00 2.15
375 1416 4.473444 TCTGCTTGGACCTCTTTTTCAAT 58.527 39.130 0.00 0.00 0.00 2.57
380 1421 3.515602 ACATCTGCTTGGACCTCTTTT 57.484 42.857 0.00 0.00 0.00 2.27
464 1505 5.716703 CTTTGGTTAAGAGGAATGGGACAAT 59.283 40.000 0.00 0.00 37.84 2.71
518 1560 7.613022 TGTAGAGGCAAAAGAGATGAATGAATT 59.387 33.333 0.00 0.00 0.00 2.17
529 1575 6.207417 TCAAAGGAAATGTAGAGGCAAAAGAG 59.793 38.462 0.00 0.00 0.00 2.85
576 1622 7.572523 ATCTTCAACACCATAATACCATGTG 57.427 36.000 0.00 0.00 0.00 3.21
612 1660 1.845809 CGTTGTCTGAGGCAGTTGGC 61.846 60.000 0.00 0.00 43.74 4.52
613 1661 1.230635 CCGTTGTCTGAGGCAGTTGG 61.231 60.000 0.00 0.00 32.61 3.77
620 1668 1.498865 GCACACACCGTTGTCTGAGG 61.499 60.000 0.00 0.00 31.66 3.86
668 1716 5.859648 CGACCGCTTTTATTTTTGTACCATT 59.140 36.000 0.00 0.00 0.00 3.16
671 1719 4.786507 ACGACCGCTTTTATTTTTGTACC 58.213 39.130 0.00 0.00 0.00 3.34
846 1895 8.757789 CCGTAAAGATATAACAGTTTCGCATAA 58.242 33.333 0.00 0.00 0.00 1.90
851 1900 9.454585 TCATACCGTAAAGATATAACAGTTTCG 57.545 33.333 0.00 0.00 0.00 3.46
923 1972 1.628238 AATGGGGATGGCGAACGGTA 61.628 55.000 0.00 0.00 0.00 4.02
953 2003 7.092079 TGAATATGATGCTTGTTTGTTTCCTG 58.908 34.615 0.00 0.00 0.00 3.86
1088 2138 1.878102 GCTTGATGTGGACGAGGTTGT 60.878 52.381 0.00 0.00 0.00 3.32
1170 2220 4.803426 CCGGAGCTGTCGGCACTC 62.803 72.222 11.49 10.06 44.79 3.51
1522 2579 6.036735 AGTCATACCGATGAATTTAACAACCG 59.963 38.462 0.00 0.00 43.77 4.44
1583 2641 1.069296 CGTGCAACCAACGAACATCAT 60.069 47.619 0.00 0.00 0.00 2.45
1584 2642 0.306228 CGTGCAACCAACGAACATCA 59.694 50.000 0.00 0.00 0.00 3.07
1643 2902 2.486472 ATCCAATCATCGATGCCCTC 57.514 50.000 20.81 0.00 0.00 4.30
1709 2968 8.144478 TCTGTGAATCTATCCTTCCGAATAAAG 58.856 37.037 0.00 0.00 0.00 1.85
1828 3261 7.864686 TGAAATTTCATATATGCTCCTCGTTG 58.135 34.615 16.91 0.00 31.01 4.10
1888 3321 7.457561 TGCATACTAATGATTGGGCTATAACA 58.542 34.615 0.00 0.00 34.84 2.41
1940 3375 5.183140 GCAGTACAGTGATTGGGTTAACAAT 59.817 40.000 8.10 0.00 43.36 2.71
1947 3382 3.508845 AAAGCAGTACAGTGATTGGGT 57.491 42.857 0.00 0.00 0.00 4.51
1982 4280 9.657419 GATTTATGAATGGAACTTGACCAAATT 57.343 29.630 0.00 0.00 40.93 1.82
1984 4282 8.421249 AGATTTATGAATGGAACTTGACCAAA 57.579 30.769 0.00 0.00 40.93 3.28
2001 4299 7.912250 ACGAAGCTAAAGCATTCAAGATTTATG 59.088 33.333 4.54 0.00 45.16 1.90
2016 4314 3.896648 TTTGCAAGGACGAAGCTAAAG 57.103 42.857 0.00 0.00 0.00 1.85
2025 4323 5.741388 ATAGCTAGAATTTTGCAAGGACG 57.259 39.130 0.00 0.00 0.00 4.79
2093 4391 4.712425 GCTGCTGTTGCGCAAGGG 62.712 66.667 25.78 19.48 43.34 3.95
2126 4424 0.105194 AGAAGTTTTTGGGGTGGGGG 60.105 55.000 0.00 0.00 0.00 5.40
2127 4425 2.687003 TAGAAGTTTTTGGGGTGGGG 57.313 50.000 0.00 0.00 0.00 4.96
2150 4448 9.687210 ATTAAAACACCCTTTATCGAGAAAAAC 57.313 29.630 6.68 0.00 0.00 2.43
2156 4454 9.983804 GAGTTAATTAAAACACCCTTTATCGAG 57.016 33.333 0.00 0.00 0.00 4.04
2158 4456 9.550811 GTGAGTTAATTAAAACACCCTTTATCG 57.449 33.333 17.76 0.00 0.00 2.92
2162 4460 9.541143 CATTGTGAGTTAATTAAAACACCCTTT 57.459 29.630 22.06 9.92 0.00 3.11
2168 4472 9.979578 ATGCTTCATTGTGAGTTAATTAAAACA 57.020 25.926 0.00 2.88 0.00 2.83
2174 4478 6.810182 GCTTGATGCTTCATTGTGAGTTAATT 59.190 34.615 2.75 0.00 38.95 1.40
2184 4488 1.469703 TGTCCGCTTGATGCTTCATTG 59.530 47.619 2.75 1.52 40.11 2.82
2187 4491 1.266718 GTTTGTCCGCTTGATGCTTCA 59.733 47.619 0.00 0.00 40.11 3.02
2249 4555 9.599866 CCCCATAGGAAAATAAATCTTGAAAAC 57.400 33.333 0.00 0.00 38.24 2.43
2254 4560 6.041979 CCACCCCCATAGGAAAATAAATCTTG 59.958 42.308 0.00 0.00 38.24 3.02
2260 4566 3.598782 ACACCACCCCCATAGGAAAATAA 59.401 43.478 0.00 0.00 38.24 1.40
2273 4579 2.443016 TTGCCACAACACCACCCC 60.443 61.111 0.00 0.00 0.00 4.95
2276 4582 1.675552 ACTAGTTGCCACAACACCAC 58.324 50.000 12.56 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.