Multiple sequence alignment - TraesCS2D01G260200

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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 TraesCS2D01G260200 chr2D 100.000 2423 0 0 1 2423 316288724 316286302 0.000000e+00 4475.0
1 TraesCS2D01G260200 chr2A 90.559 1949 78 40 1 1903 418820796 418822684 0.000000e+00 2483.0
2 TraesCS2D01G260200 chr2A 91.379 348 26 1 2076 2423 418822874 418823217 7.840000e-130 473.0
3 TraesCS2D01G260200 chr2B 92.372 1783 72 30 1 1748 384343442 384341689 0.000000e+00 2481.0
4 TraesCS2D01G260200 chr2B 92.857 56 4 0 2359 2414 384338630 384338575 5.550000e-12 82.4


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 TraesCS2D01G260200 chr2D 316286302 316288724 2422 True 4475.0 4475 100.0000 1 2423 1 chr2D.!!$R1 2422
1 TraesCS2D01G260200 chr2A 418820796 418823217 2421 False 1478.0 2483 90.9690 1 2423 2 chr2A.!!$F1 2422
2 TraesCS2D01G260200 chr2B 384338575 384343442 4867 True 1281.7 2481 92.6145 1 2414 2 chr2B.!!$R1 2413

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
202 203 0.107945 TGGCGTGCATGCATGTACTA 60.108 50.0 34.88 22.69 40.59 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1598 0.456995 CACTTCTTCCTCCGTCTCGC 60.457 60.0 0.0 0.0 0.0 5.03 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
85 86 0.670546 CCTCCACACTAACACGGCTG 60.671 60.000 0.00 0.00 0.00 4.85
87 88 2.667318 CCACACTAACACGGCTGCG 61.667 63.158 0.00 0.00 0.00 5.18
171 172 4.155280 CCGGAAAATATTTGTGTCTCCGTT 59.845 41.667 25.48 0.73 42.12 4.44
178 179 6.668541 ATATTTGTGTCTCCGTTCATCTTG 57.331 37.500 0.00 0.00 0.00 3.02
202 203 0.107945 TGGCGTGCATGCATGTACTA 60.108 50.000 34.88 22.69 40.59 1.82
203 204 0.583438 GGCGTGCATGCATGTACTAG 59.417 55.000 34.88 25.12 40.59 2.57
222 223 6.770746 ACTAGCTCGGTAAAGATCTAAACA 57.229 37.500 0.00 0.00 0.00 2.83
225 226 5.652518 AGCTCGGTAAAGATCTAAACACTC 58.347 41.667 0.00 0.00 0.00 3.51
262 272 6.545298 ACAAGGGAGTACTACCTAATCGTAAG 59.455 42.308 27.61 11.56 45.16 2.34
313 323 4.440802 CGGGAAGACCAACAATTTGTTTCA 60.441 41.667 12.02 0.00 38.77 2.69
337 347 9.631452 TCAGAAATCGAATGATCATATGTACTC 57.369 33.333 9.04 0.53 32.24 2.59
338 348 9.636879 CAGAAATCGAATGATCATATGTACTCT 57.363 33.333 9.04 5.18 32.24 3.24
350 360 8.833231 ATCATATGTACTCTTATTTTGGGACG 57.167 34.615 1.90 0.00 0.00 4.79
352 362 5.687166 ATGTACTCTTATTTTGGGACGGA 57.313 39.130 0.00 0.00 0.00 4.69
355 365 3.951663 ACTCTTATTTTGGGACGGAAGG 58.048 45.455 0.00 0.00 0.00 3.46
357 367 4.192317 CTCTTATTTTGGGACGGAAGGAG 58.808 47.826 0.00 0.00 0.00 3.69
360 370 2.845363 TTTTGGGACGGAAGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
367 377 3.318557 GGGACGGAAGGAGTACTTATGAG 59.681 52.174 0.00 0.00 40.21 2.90
477 492 1.593196 TCCTGCAACTGAAAACGGAG 58.407 50.000 0.00 0.00 0.00 4.63
561 584 4.511527 ACAGTGATGTTCAGCTAATCCTG 58.488 43.478 0.00 1.28 0.00 3.86
661 692 2.167219 ATCCACGTGCTCAATCGCG 61.167 57.895 10.91 0.00 44.61 5.87
666 697 2.434185 GTGCTCAATCGCGGGACA 60.434 61.111 6.13 0.00 0.00 4.02
700 731 0.179001 TCAGACGGTCAGGTCAGTGA 60.179 55.000 11.27 0.41 39.42 3.41
728 759 1.429423 CCGTACGTCCGGTAAGACC 59.571 63.158 11.95 0.00 43.07 3.85
762 796 3.606846 CGCAACAGCAAGAAAGAAATCGA 60.607 43.478 0.00 0.00 0.00 3.59
776 810 3.702045 AGAAATCGATCGGTCCTCTTCTT 59.298 43.478 16.41 0.00 0.00 2.52
778 812 1.390565 TCGATCGGTCCTCTTCTTCC 58.609 55.000 16.41 0.00 0.00 3.46
779 813 1.064611 TCGATCGGTCCTCTTCTTCCT 60.065 52.381 16.41 0.00 0.00 3.36
853 893 5.426509 AGAATCAGAGACAGAGAGAGAGAGA 59.573 44.000 0.00 0.00 0.00 3.10
855 895 4.352893 TCAGAGACAGAGAGAGAGAGAGA 58.647 47.826 0.00 0.00 0.00 3.10
1157 1204 0.596083 CGTGGACGATGGAGCTGATC 60.596 60.000 0.00 0.00 43.02 2.92
1165 1212 1.209019 GATGGAGCTGATCAGTGGTGT 59.791 52.381 23.38 8.02 0.00 4.16
1295 1342 4.130281 GCGGAAGTACGTGCACGC 62.130 66.667 37.35 22.81 44.43 5.34
1533 1580 1.544246 ACCGCGTGCAGCTATGATATA 59.456 47.619 4.92 0.00 45.59 0.86
1543 1591 6.192234 GCAGCTATGATATAAAGCAGCAAT 57.808 37.500 12.86 0.00 45.06 3.56
1548 1598 5.618056 ATGATATAAAGCAGCAATCGTGG 57.382 39.130 0.00 0.00 0.00 4.94
1549 1599 3.250762 TGATATAAAGCAGCAATCGTGGC 59.749 43.478 0.00 0.00 0.00 5.01
1560 1610 3.989838 ATCGTGGCGAGACGGAGGA 62.990 63.158 6.78 0.00 39.91 3.71
1658 1719 6.730960 TCCATTTTGATGTAGTAAACCGAC 57.269 37.500 0.00 0.00 0.00 4.79
1727 1798 5.791367 TCGTGTGCTAGTACAGTAAGTAG 57.209 43.478 14.45 1.04 32.19 2.57
1844 2075 2.895372 GCGGGTGCCATCGTAAGG 60.895 66.667 0.00 0.00 33.85 2.69
1866 2097 3.685836 ACAAACGCCTAGTTGACAAAC 57.314 42.857 0.00 0.00 43.37 2.93
1903 2134 6.220930 TGTATTTTGGATATGTAGCGAGGTC 58.779 40.000 0.00 0.00 0.00 3.85
1908 2139 3.181469 TGGATATGTAGCGAGGTCCAAAC 60.181 47.826 0.00 0.00 33.15 2.93
1971 3340 6.827762 TGAGCATTGGTGTATTTGACATGATA 59.172 34.615 0.00 0.00 41.14 2.15
2060 3439 9.698309 TTTAACCACATGTACAATGTAAAATGG 57.302 29.630 16.73 14.94 0.00 3.16
2061 3440 6.279513 ACCACATGTACAATGTAAAATGGG 57.720 37.500 16.87 13.97 0.00 4.00
2062 3441 5.777732 ACCACATGTACAATGTAAAATGGGT 59.222 36.000 16.87 16.44 0.00 4.51
2063 3442 6.268847 ACCACATGTACAATGTAAAATGGGTT 59.731 34.615 16.87 3.90 0.00 4.11
2064 3443 7.158021 CCACATGTACAATGTAAAATGGGTTT 58.842 34.615 16.73 0.06 0.00 3.27
2065 3444 7.659390 CCACATGTACAATGTAAAATGGGTTTT 59.341 33.333 16.73 0.00 40.48 2.43
2066 3445 9.050601 CACATGTACAATGTAAAATGGGTTTTT 57.949 29.630 16.73 0.00 40.59 1.94
2109 3488 9.553418 GTTAGTTCCTTTTCTCTAGTTACTACG 57.447 37.037 0.00 0.00 0.00 3.51
2111 3490 7.592051 AGTTCCTTTTCTCTAGTTACTACGTG 58.408 38.462 0.00 0.00 0.00 4.49
2141 3563 7.431376 GGTTTAAACTGTAGTTCAACTCTTTGC 59.569 37.037 17.50 0.00 37.25 3.68
2143 3565 6.509418 AAACTGTAGTTCAACTCTTTGCAA 57.491 33.333 0.00 0.00 37.25 4.08
2225 3653 6.594788 AGCTGAAATAAACCACACATGAAT 57.405 33.333 0.00 0.00 0.00 2.57
2231 3659 9.039870 TGAAATAAACCACACATGAATTGAAAC 57.960 29.630 0.00 0.00 0.00 2.78
2288 4901 2.029307 GCTAGGTTGGGGCGTAGAGG 62.029 65.000 0.00 0.00 0.00 3.69
2354 4967 3.938963 CTGGAGCGCAATAGGAGTTTTTA 59.061 43.478 11.47 0.00 0.00 1.52
2355 4968 4.523083 TGGAGCGCAATAGGAGTTTTTAT 58.477 39.130 11.47 0.00 0.00 1.40
2356 4969 4.947388 TGGAGCGCAATAGGAGTTTTTATT 59.053 37.500 11.47 0.00 0.00 1.40
2357 4970 6.116806 TGGAGCGCAATAGGAGTTTTTATTA 58.883 36.000 11.47 0.00 0.00 0.98
2417 5030 3.306710 GGGCAACATTAAACTCCCCTTTG 60.307 47.826 0.00 0.00 39.74 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.217001 TCGATTCCATACATGCACGC 58.783 50.000 0.00 0.00 0.00 5.34
87 88 4.966249 CATGATCGATTCCATACATGCAC 58.034 43.478 0.00 0.00 0.00 4.57
171 172 1.296392 CACGCCACCCTCAAGATGA 59.704 57.895 0.00 0.00 0.00 2.92
202 203 5.419471 AGAGTGTTTAGATCTTTACCGAGCT 59.581 40.000 0.00 0.00 33.64 4.09
203 204 5.652518 AGAGTGTTTAGATCTTTACCGAGC 58.347 41.667 0.00 0.00 0.00 5.03
233 234 7.067981 ACGATTAGGTAGTACTCCCTTGTAAAG 59.932 40.741 12.85 3.26 45.69 1.85
237 238 4.864726 ACGATTAGGTAGTACTCCCTTGT 58.135 43.478 12.85 1.73 32.08 3.16
238 239 6.769822 TCTTACGATTAGGTAGTACTCCCTTG 59.230 42.308 12.85 3.62 32.08 3.61
239 240 6.904626 TCTTACGATTAGGTAGTACTCCCTT 58.095 40.000 12.85 0.00 32.08 3.95
240 241 6.506538 TCTTACGATTAGGTAGTACTCCCT 57.493 41.667 12.22 12.22 34.74 4.20
262 272 7.301868 TGATAATTTGGCCCCTTTGATAATC 57.698 36.000 0.00 0.00 0.00 1.75
271 281 1.756538 CGCTTTGATAATTTGGCCCCT 59.243 47.619 0.00 0.00 0.00 4.79
337 347 3.951663 ACTCCTTCCGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
338 348 4.533311 AGTACTCCTTCCGTCCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
339 349 4.098894 AGTACTCCTTCCGTCCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
340 350 2.910977 AGTACTCCTTCCGTCCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
341 351 2.332117 AGTACTCCTTCCGTCCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
342 352 2.019807 AGTACTCCTTCCGTCCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
343 353 2.019807 AAGTACTCCTTCCGTCCCAA 57.980 50.000 0.00 0.00 0.00 4.12
344 354 2.905415 TAAGTACTCCTTCCGTCCCA 57.095 50.000 0.00 0.00 34.46 4.37
345 355 3.294214 TCATAAGTACTCCTTCCGTCCC 58.706 50.000 0.00 0.00 34.46 4.46
346 356 3.318557 CCTCATAAGTACTCCTTCCGTCC 59.681 52.174 0.00 0.00 34.46 4.79
347 357 4.205587 TCCTCATAAGTACTCCTTCCGTC 58.794 47.826 0.00 0.00 34.46 4.79
348 358 4.208746 CTCCTCATAAGTACTCCTTCCGT 58.791 47.826 0.00 0.00 34.46 4.69
350 360 5.239087 CGTACTCCTCATAAGTACTCCTTCC 59.761 48.000 0.00 0.00 44.46 3.46
352 362 5.589452 CACGTACTCCTCATAAGTACTCCTT 59.411 44.000 0.00 0.00 44.46 3.36
355 365 4.261114 GCCACGTACTCCTCATAAGTACTC 60.261 50.000 0.00 0.00 44.46 2.59
357 367 3.631227 AGCCACGTACTCCTCATAAGTAC 59.369 47.826 0.00 3.84 43.63 2.73
360 370 2.223829 CCAGCCACGTACTCCTCATAAG 60.224 54.545 0.00 0.00 0.00 1.73
367 377 3.702048 TGGCCAGCCACGTACTCC 61.702 66.667 7.43 0.00 41.89 3.85
447 462 3.477224 TTGCAGGAAAACGCGCACC 62.477 57.895 5.73 4.52 33.09 5.01
561 584 3.016474 GCGTCTGAACAAGCGGCTC 62.016 63.158 1.45 0.00 0.00 4.70
594 625 0.601558 GTACGTCTCTCTTGGCCACA 59.398 55.000 3.88 0.00 0.00 4.17
596 627 1.255667 GGGTACGTCTCTCTTGGCCA 61.256 60.000 0.00 0.00 0.00 5.36
601 632 0.608582 ACGCTGGGTACGTCTCTCTT 60.609 55.000 0.00 0.00 40.28 2.85
728 759 1.969256 GCTGTTGCGATGTTTGTTACG 59.031 47.619 0.00 0.00 0.00 3.18
734 765 3.066621 TCTTTCTTGCTGTTGCGATGTTT 59.933 39.130 0.00 0.00 43.34 2.83
739 772 3.606846 CGATTTCTTTCTTGCTGTTGCGA 60.607 43.478 0.00 0.00 43.34 5.10
762 796 3.028130 GAGAAGGAAGAAGAGGACCGAT 58.972 50.000 0.00 0.00 0.00 4.18
776 810 0.967887 CGAGCTGGGTGAGAGAAGGA 60.968 60.000 0.00 0.00 0.00 3.36
778 812 1.153667 GCGAGCTGGGTGAGAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
779 813 2.650116 GGCGAGCTGGGTGAGAGAA 61.650 63.158 0.00 0.00 0.00 2.87
853 893 1.762522 CTCCAGCACACACACCCTCT 61.763 60.000 0.00 0.00 0.00 3.69
855 895 2.831770 CTCCAGCACACACACCCT 59.168 61.111 0.00 0.00 0.00 4.34
918 965 3.430929 GCCGAGAGAAATCTTTGCCTCTA 60.431 47.826 0.00 0.00 36.25 2.43
993 1040 0.686441 AGGGGTACGACATGCTGCTA 60.686 55.000 0.00 0.00 0.00 3.49
1157 1204 3.415212 ACTCATGGATGAAACACCACTG 58.585 45.455 0.00 0.00 39.06 3.66
1165 1212 3.084039 GACCTGCAACTCATGGATGAAA 58.916 45.455 0.00 0.00 36.18 2.69
1533 1580 1.915614 CTCGCCACGATTGCTGCTTT 61.916 55.000 0.00 0.00 34.61 3.51
1543 1591 4.710167 TCCTCCGTCTCGCCACGA 62.710 66.667 7.46 0.00 42.69 4.35
1548 1598 0.456995 CACTTCTTCCTCCGTCTCGC 60.457 60.000 0.00 0.00 0.00 5.03
1549 1599 1.166129 TCACTTCTTCCTCCGTCTCG 58.834 55.000 0.00 0.00 0.00 4.04
1560 1610 3.409026 GACAGTGGGTCATCACTTCTT 57.591 47.619 0.00 0.00 44.74 2.52
1658 1719 7.339212 TGATGATGGTAAACTCTTTTACATGGG 59.661 37.037 8.99 0.00 46.24 4.00
1727 1798 5.872070 TGAACTTTCAAATGGACAACCAAAC 59.128 36.000 0.00 0.00 41.06 2.93
1777 2008 6.720012 AGCAGATTTGTTTTCGTTGTTTTT 57.280 29.167 0.00 0.00 0.00 1.94
1778 2009 6.720012 AAGCAGATTTGTTTTCGTTGTTTT 57.280 29.167 0.00 0.00 0.00 2.43
1779 2010 8.419076 AATAAGCAGATTTGTTTTCGTTGTTT 57.581 26.923 0.00 0.00 0.00 2.83
1780 2011 8.419076 AAATAAGCAGATTTGTTTTCGTTGTT 57.581 26.923 0.00 0.00 0.00 2.83
1781 2012 7.096640 CGAAATAAGCAGATTTGTTTTCGTTGT 60.097 33.333 12.03 0.00 0.00 3.32
1782 2013 7.096640 ACGAAATAAGCAGATTTGTTTTCGTTG 60.097 33.333 16.79 2.49 29.95 4.10
1844 2075 3.955771 TTGTCAACTAGGCGTTTGTTC 57.044 42.857 0.00 0.00 32.27 3.18
1866 2097 6.875948 TCCAAAATACATTATCGGATGGTG 57.124 37.500 0.00 2.10 0.00 4.17
1912 2143 4.208686 GGTGCCTCGTAGCCGGAG 62.209 72.222 5.05 0.00 33.95 4.63
1916 2147 2.125512 CAGTGGTGCCTCGTAGCC 60.126 66.667 0.00 0.00 0.00 3.93
1930 2161 2.152297 CTCAGTGGTCAGAGCGCAGT 62.152 60.000 11.47 0.00 0.00 4.40
2070 3449 9.772973 GAAAAGGAACTAACCCATTTTAATTGT 57.227 29.630 0.00 0.00 38.49 2.71
2071 3450 9.996554 AGAAAAGGAACTAACCCATTTTAATTG 57.003 29.630 0.00 0.00 38.49 2.32
2073 3452 9.601810 AGAGAAAAGGAACTAACCCATTTTAAT 57.398 29.630 0.00 0.00 38.49 1.40
2091 3470 6.522510 CCGTTCACGTAGTAACTAGAGAAAAG 59.477 42.308 0.00 0.00 41.61 2.27
2109 3488 6.348621 TGAACTACAGTTTAAACCGTTCAC 57.651 37.500 24.07 12.40 38.56 3.18
2111 3490 7.008440 AGTTGAACTACAGTTTAAACCGTTC 57.992 36.000 21.26 21.26 38.56 3.95
2141 3563 6.925165 ACAATAAGATGAGGCAACAAAAGTTG 59.075 34.615 4.10 4.10 41.41 3.16
2143 3565 6.655078 ACAATAAGATGAGGCAACAAAAGT 57.345 33.333 0.00 0.00 41.41 2.66
2165 3587 6.492254 AGATTTTTCACCAAACAACTCGTAC 58.508 36.000 0.00 0.00 0.00 3.67
2201 3629 6.403866 TTCATGTGTGGTTTATTTCAGCTT 57.596 33.333 0.00 0.00 0.00 3.74
2203 3631 6.867816 TCAATTCATGTGTGGTTTATTTCAGC 59.132 34.615 0.00 0.00 0.00 4.26
2225 3653 4.090090 TCCAAAAACCCAGACAGTTTCAA 58.910 39.130 0.00 0.00 36.44 2.69
2231 3659 2.755103 GCCTATCCAAAAACCCAGACAG 59.245 50.000 0.00 0.00 0.00 3.51
2357 4970 9.685276 TCTGTGGTGTTGAGAATTATTGATAAT 57.315 29.630 0.00 0.00 34.59 1.28


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

AutoCloner maintained by Alex Coulton.