Multiple sequence alignment - TraesCS2D01G357000

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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 TraesCS2D01G357000 chr2D 100.000 2336 0 0 1 2336 459315486 459313151 0.000000e+00 4314
1 TraesCS2D01G357000 chr2B 94.224 1887 72 14 1 1864 540709306 540707434 0.000000e+00 2846
2 TraesCS2D01G357000 chr2B 96.403 417 13 2 1921 2336 540707433 540707018 0.000000e+00 686
3 TraesCS2D01G357000 chr2A 88.939 2197 149 49 1 2134 602483081 602480916 0.000000e+00 2625
4 TraesCS2D01G357000 chr2A 87.907 215 12 5 2127 2334 602480568 602480361 8.340000e-60 241


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 TraesCS2D01G357000 chr2D 459313151 459315486 2335 True 4314 4314 100.0000 1 2336 1 chr2D.!!$R1 2335
1 TraesCS2D01G357000 chr2B 540707018 540709306 2288 True 1766 2846 95.3135 1 2336 2 chr2B.!!$R1 2335
2 TraesCS2D01G357000 chr2A 602480361 602483081 2720 True 1433 2625 88.4230 1 2334 2 chr2A.!!$R1 2333

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
473 477 0.108585 GCTCCCCGAATCTGCCATTA 59.891 55.0 0.0 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2640 2.758423 GGTGGAGTCCCGCAAATAAAAT 59.242 45.455 6.74 0.0 44.7 1.82 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
193 194 1.449601 CCCGGTCAACAAGATCCCG 60.450 63.158 0.00 0.00 36.08 5.14
420 424 3.645268 CTGCCCCCACCAAGGTAGC 62.645 68.421 0.00 0.00 34.66 3.58
441 445 1.379916 CCTGCACATGAACCCCTCA 59.620 57.895 0.00 0.00 38.81 3.86
448 452 2.029649 CACATGAACCCCTCAAAGCTTG 60.030 50.000 0.00 0.00 37.67 4.01
473 477 0.108585 GCTCCCCGAATCTGCCATTA 59.891 55.000 0.00 0.00 0.00 1.90
475 479 0.108585 TCCCCGAATCTGCCATTAGC 59.891 55.000 0.00 0.00 44.14 3.09
618 634 1.745141 GCTTCCAATGCTCTGATCCGT 60.745 52.381 0.00 0.00 0.00 4.69
674 690 9.300681 TCCTTGTTCTTCTGTTTGATTATTGAT 57.699 29.630 0.00 0.00 0.00 2.57
675 691 9.565213 CCTTGTTCTTCTGTTTGATTATTGATC 57.435 33.333 0.00 0.00 35.21 2.92
676 692 9.270576 CTTGTTCTTCTGTTTGATTATTGATCG 57.729 33.333 0.00 0.00 37.60 3.69
677 693 8.546597 TGTTCTTCTGTTTGATTATTGATCGA 57.453 30.769 0.00 0.00 37.60 3.59
735 751 5.408604 GTCAGATCGATGGTTTGTAAGTTGT 59.591 40.000 0.54 0.00 0.00 3.32
789 810 3.125316 CCATTCAGTTTGCGTCCTACTTC 59.875 47.826 0.00 0.00 0.00 3.01
881 903 1.963515 ACTCAAAATCCACCCTGCAAC 59.036 47.619 0.00 0.00 0.00 4.17
896 918 4.638421 CCCTGCAACTCCGTTATAAATTCA 59.362 41.667 0.00 0.00 0.00 2.57
926 948 1.062294 TCGCAACTAAAACAAACGCGT 59.938 42.857 5.58 5.58 41.77 6.01
929 951 2.696255 CAACTAAAACAAACGCGTCGT 58.304 42.857 14.44 10.80 43.97 4.34
970 992 2.032071 ACCTTCCAAGTTCGGCCG 59.968 61.111 22.12 22.12 0.00 6.13
1228 1250 4.731503 CGCAGCAGCAGTTCACGC 62.732 66.667 0.82 0.00 42.27 5.34
1304 1326 2.047274 CGGTGTGCCAAGATCGGT 60.047 61.111 0.00 0.00 34.09 4.69
1366 1388 3.243535 CCTGAACCAGGCTGTTCTTTTTC 60.244 47.826 21.79 12.26 45.13 2.29
1367 1389 3.360867 TGAACCAGGCTGTTCTTTTTCA 58.639 40.909 21.79 14.00 43.96 2.69
1368 1390 3.960102 TGAACCAGGCTGTTCTTTTTCAT 59.040 39.130 21.79 0.00 43.96 2.57
1369 1391 5.136828 TGAACCAGGCTGTTCTTTTTCATA 58.863 37.500 21.79 5.38 43.96 2.15
1370 1392 5.241506 TGAACCAGGCTGTTCTTTTTCATAG 59.758 40.000 21.79 4.75 43.96 2.23
1371 1393 3.507622 ACCAGGCTGTTCTTTTTCATAGC 59.492 43.478 14.43 0.00 0.00 2.97
1372 1394 3.760684 CCAGGCTGTTCTTTTTCATAGCT 59.239 43.478 14.43 0.00 0.00 3.32
1398 1422 6.388278 AGTTCAGAAACTACCGATGTAACTC 58.612 40.000 0.00 0.00 43.98 3.01
1399 1423 5.320549 TCAGAAACTACCGATGTAACTCC 57.679 43.478 0.00 0.00 0.00 3.85
1400 1424 4.103357 CAGAAACTACCGATGTAACTCCG 58.897 47.826 0.00 0.00 0.00 4.63
1405 1429 4.488879 ACTACCGATGTAACTCCGTTTTC 58.511 43.478 0.00 0.00 0.00 2.29
1463 1493 5.246145 ACTAGCACTGTAATCTTACGACC 57.754 43.478 0.00 0.00 36.45 4.79
1519 1575 5.877012 TGCTGAGATACACAGGAAAAATCTC 59.123 40.000 0.00 0.00 41.82 2.75
1672 1728 2.314852 TCTATCTCACCCTCTCCACCAA 59.685 50.000 0.00 0.00 0.00 3.67
1673 1729 1.577736 ATCTCACCCTCTCCACCAAG 58.422 55.000 0.00 0.00 0.00 3.61
1674 1730 0.487325 TCTCACCCTCTCCACCAAGA 59.513 55.000 0.00 0.00 0.00 3.02
1675 1731 1.132849 TCTCACCCTCTCCACCAAGAA 60.133 52.381 0.00 0.00 0.00 2.52
1703 1759 1.149174 GCAATAGCAGCTGCCCCTA 59.851 57.895 34.39 20.94 43.38 3.53
1806 1862 4.729868 AGAAACAAGGCCAGAATTAGTGT 58.270 39.130 5.01 0.00 0.00 3.55
1807 1863 5.876357 AGAAACAAGGCCAGAATTAGTGTA 58.124 37.500 5.01 0.00 0.00 2.90
1840 1896 7.345914 ACCTCTGGATTATTAGACTAAACAGCT 59.654 37.037 0.00 0.00 0.00 4.24
1864 1920 4.785346 ATGTGGATTGTGGAGATTAGCT 57.215 40.909 0.00 0.00 0.00 3.32
1865 1921 4.574674 TGTGGATTGTGGAGATTAGCTT 57.425 40.909 0.00 0.00 0.00 3.74
1866 1922 5.692115 TGTGGATTGTGGAGATTAGCTTA 57.308 39.130 0.00 0.00 0.00 3.09
1878 1936 7.715249 GTGGAGATTAGCTTAATGTGGATTGTA 59.285 37.037 0.00 0.00 0.00 2.41
1894 1952 8.486210 TGTGGATTGTAGAGAATAGCTTAATGT 58.514 33.333 0.00 0.00 0.00 2.71
1899 1957 8.718102 TTGTAGAGAATAGCTTAATGTGGAAC 57.282 34.615 0.00 0.00 37.35 3.62
1905 1963 9.601217 GAGAATAGCTTAATGTGGAACTTCTAA 57.399 33.333 0.00 0.00 38.04 2.10
2007 2065 9.931210 GAAGAAATTATACGTTTACAGAATGGG 57.069 33.333 0.00 0.00 43.62 4.00
2110 2181 1.165270 ATTGACAAACCTAGCGGTGC 58.835 50.000 0.00 0.00 44.73 5.01
2151 2577 6.819397 AAAGATTAACAAAGACTACTGGGC 57.181 37.500 0.00 0.00 0.00 5.36
2207 2640 7.285858 TGCCTGATCAATCATCATCATTTTACA 59.714 33.333 0.00 0.00 40.95 2.41
2283 2716 9.679661 TGTAGAAATCCTGCAGAATATACAAAA 57.320 29.630 17.39 0.00 32.40 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
420 424 1.379044 GGGGTTCATGTGCAGGGAG 60.379 63.158 0.00 0.00 0.00 4.30
448 452 2.028337 GATTCGGGGAGCGAGCTC 59.972 66.667 16.14 16.14 42.04 4.09
453 457 2.947938 AATGGCAGATTCGGGGAGCG 62.948 60.000 0.00 0.00 0.00 5.03
473 477 2.132762 CAACAGAAACCTCGTAACGCT 58.867 47.619 0.00 0.00 0.00 5.07
475 479 1.193874 GCCAACAGAAACCTCGTAACG 59.806 52.381 0.00 0.00 0.00 3.18
676 692 4.348656 TGTACAATACGCTCGAACTCATC 58.651 43.478 0.00 0.00 0.00 2.92
677 693 4.365899 TGTACAATACGCTCGAACTCAT 57.634 40.909 0.00 0.00 0.00 2.90
735 751 6.605471 AACTGGTGATAGTTACATGACAGA 57.395 37.500 0.00 0.00 39.03 3.41
789 810 1.578583 ACCGAAACAAACTGACGGAG 58.421 50.000 0.00 0.00 45.31 4.63
865 887 1.632589 GGAGTTGCAGGGTGGATTTT 58.367 50.000 0.00 0.00 0.00 1.82
881 903 3.558418 CCCACGGTGAATTTATAACGGAG 59.442 47.826 10.28 0.00 0.00 4.63
896 918 0.322322 TTAGTTGCGATTCCCACGGT 59.678 50.000 0.00 0.00 0.00 4.83
926 948 1.000052 TGTCGGCTGTTGTTGATACGA 60.000 47.619 0.00 0.00 0.00 3.43
929 951 3.610040 ATCTGTCGGCTGTTGTTGATA 57.390 42.857 0.00 0.00 0.00 2.15
970 992 2.490685 GGGTCTCTCTCGCGTTCC 59.509 66.667 5.77 0.00 0.00 3.62
984 1006 1.333636 CCATCTTCAGAGCTCCGGGT 61.334 60.000 10.93 0.00 0.00 5.28
1125 1147 3.343788 CTGGCACGAGACCGACCTC 62.344 68.421 0.00 0.00 39.50 3.85
1250 1272 4.933064 GCTGGGACGCCGATCTCG 62.933 72.222 0.00 3.19 39.44 4.04
1366 1388 6.561614 TCGGTAGTTTCTGAACTAAGCTATG 58.438 40.000 0.96 0.00 46.80 2.23
1367 1389 6.770746 TCGGTAGTTTCTGAACTAAGCTAT 57.229 37.500 0.96 0.00 46.80 2.97
1368 1390 6.152323 ACATCGGTAGTTTCTGAACTAAGCTA 59.848 38.462 0.96 0.00 46.80 3.32
1369 1391 5.047235 ACATCGGTAGTTTCTGAACTAAGCT 60.047 40.000 0.96 0.00 46.80 3.74
1370 1392 5.169295 ACATCGGTAGTTTCTGAACTAAGC 58.831 41.667 0.96 0.00 46.80 3.09
1371 1393 8.027771 AGTTACATCGGTAGTTTCTGAACTAAG 58.972 37.037 0.96 0.28 46.80 2.18
1372 1394 7.889469 AGTTACATCGGTAGTTTCTGAACTAA 58.111 34.615 0.96 0.00 46.80 2.24
1428 1452 6.607004 ACAGTGCTAGTTACAACTATCCTT 57.393 37.500 2.43 0.00 40.46 3.36
1430 1454 8.414778 AGATTACAGTGCTAGTTACAACTATCC 58.585 37.037 2.43 0.00 40.46 2.59
1519 1575 4.974103 CTGTTGTTCAGGTTCTTCTACG 57.026 45.455 0.00 0.00 40.23 3.51
1672 1728 4.633565 GCTGCTATTGCTAAGTGTCTTTCT 59.366 41.667 0.00 0.00 40.48 2.52
1673 1729 4.633565 AGCTGCTATTGCTAAGTGTCTTTC 59.366 41.667 0.00 0.00 39.21 2.62
1674 1730 4.394300 CAGCTGCTATTGCTAAGTGTCTTT 59.606 41.667 0.00 0.00 38.92 2.52
1675 1731 3.937706 CAGCTGCTATTGCTAAGTGTCTT 59.062 43.478 0.00 0.00 38.92 3.01
1703 1759 5.468540 TGATAACTCTGCAGTACACTGTT 57.531 39.130 14.67 11.99 45.45 3.16
1840 1896 6.662755 AGCTAATCTCCACAATCCACATTAA 58.337 36.000 0.00 0.00 0.00 1.40
1878 1936 7.856415 AGAAGTTCCACATTAAGCTATTCTCT 58.144 34.615 0.00 0.00 0.00 3.10
1905 1963 8.732746 ATAAATAGATGCTTGGTTACTTCGTT 57.267 30.769 0.00 0.00 0.00 3.85
2007 2065 9.570468 AATGATATGATCCAATATCCATGCTAC 57.430 33.333 9.45 0.00 38.33 3.58
2131 2202 4.501071 TCGCCCAGTAGTCTTTGTTAATC 58.499 43.478 0.00 0.00 0.00 1.75
2141 2567 3.808174 GGTTGAAATATCGCCCAGTAGTC 59.192 47.826 0.00 0.00 0.00 2.59
2151 2577 8.491152 GTTCATAGTCTCATGGTTGAAATATCG 58.509 37.037 0.00 0.00 0.00 2.92
2207 2640 2.758423 GGTGGAGTCCCGCAAATAAAAT 59.242 45.455 6.74 0.00 44.70 1.82
2283 2716 6.110707 CAGCTGCCCTTTCAAATTTATCAAT 58.889 36.000 0.00 0.00 0.00 2.57
2286 2719 4.436332 CCAGCTGCCCTTTCAAATTTATC 58.564 43.478 8.66 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.