Multiple sequence alignment - TraesCS3D01G140600

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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 TraesCS3D01G140600 chr3D 100.000 2633 0 0 1 2633 102189659 102187027 0.000000e+00 4863
1 TraesCS3D01G140600 chr3B 91.741 2676 133 38 1 2633 152963545 152960915 0.000000e+00 3637
2 TraesCS3D01G140600 chr3A 88.345 2677 196 63 28 2633 553559996 553562627 0.000000e+00 3109
3 TraesCS3D01G140600 chr2D 85.549 173 10 4 1294 1466 643732324 643732167 1.620000e-37 167


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 TraesCS3D01G140600 chr3D 102187027 102189659 2632 True 4863 4863 100.000 1 2633 1 chr3D.!!$R1 2632
1 TraesCS3D01G140600 chr3B 152960915 152963545 2630 True 3637 3637 91.741 1 2633 1 chr3B.!!$R1 2632
2 TraesCS3D01G140600 chr3A 553559996 553562627 2631 False 3109 3109 88.345 28 2633 1 chr3A.!!$F1 2605

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
162 163 0.39113 GAGCACATAACACTCCCGCA 60.391 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1725 0.096976 CATTTAGCAGCGACCAACCG 59.903 55.0 0.0 0.0 0.0 4.44 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
86 87 3.305964 GGGCGAAACTAAAGCAGAAAAC 58.694 45.455 0.00 0.00 0.00 2.43
89 90 3.855895 GCGAAACTAAAGCAGAAAACCCC 60.856 47.826 0.00 0.00 0.00 4.95
104 105 3.473923 AACCCCAAAATGAGCAAAGTG 57.526 42.857 0.00 0.00 0.00 3.16
129 130 1.072505 GTGCAGGGTTTCCTCGGAA 59.927 57.895 0.00 0.00 42.67 4.30
138 139 1.993370 GTTTCCTCGGAAGATGACACG 59.007 52.381 0.00 0.00 40.84 4.49
162 163 0.391130 GAGCACATAACACTCCCGCA 60.391 55.000 0.00 0.00 0.00 5.69
206 207 7.836512 TGTTCTTATTTTTGCGATGAAAACAC 58.163 30.769 0.00 0.00 0.00 3.32
209 210 3.422417 TTTTTGCGATGAAAACACGGA 57.578 38.095 0.00 0.00 0.00 4.69
305 308 0.666274 CGAACTTCTGCCACGTAGCA 60.666 55.000 8.71 8.71 41.46 3.49
306 309 1.726853 GAACTTCTGCCACGTAGCAT 58.273 50.000 9.60 0.00 43.09 3.79
332 335 5.740513 GCTTGAAGGGCTACTCCTATTGTAG 60.741 48.000 0.00 0.00 40.05 2.74
373 377 5.202640 GTCGTTTTCTTACGCAAAAGACAT 58.797 37.500 5.80 0.00 39.65 3.06
374 378 5.336209 GTCGTTTTCTTACGCAAAAGACATC 59.664 40.000 5.80 0.00 39.65 3.06
398 402 2.760374 CTTTCTTCAAGGAGTCTGCGT 58.240 47.619 0.00 0.00 0.00 5.24
406 410 2.338015 GGAGTCTGCGTACCGTCCA 61.338 63.158 0.00 0.00 0.00 4.02
412 416 0.671796 CTGCGTACCGTCCATCCATA 59.328 55.000 0.00 0.00 0.00 2.74
450 454 5.662211 GTTTGGTACGAAAAGTTGCTAGA 57.338 39.130 4.49 0.00 0.00 2.43
484 505 4.184079 ACGTAATTCTAACTTCGCAGGT 57.816 40.909 0.00 0.00 0.00 4.00
523 546 1.880340 GTGAGGGCGCTCGATGAAG 60.880 63.158 23.95 0.00 0.00 3.02
611 642 1.598685 TGTTTTCGGAAGGACGGGC 60.599 57.895 0.00 0.00 0.00 6.13
660 692 2.510768 ACAACTCAGTCGTCCAACTC 57.489 50.000 0.00 0.00 0.00 3.01
661 693 1.754803 ACAACTCAGTCGTCCAACTCA 59.245 47.619 0.00 0.00 0.00 3.41
662 694 2.167693 ACAACTCAGTCGTCCAACTCAA 59.832 45.455 0.00 0.00 0.00 3.02
837 869 2.859538 CACAATTGCCAACATATTCCGC 59.140 45.455 5.05 0.00 0.00 5.54
1134 1180 3.314331 CAGGCCGACACCACCTCT 61.314 66.667 0.00 0.00 0.00 3.69
1669 1725 0.253044 TTGGTATGCTCTGCTCACCC 59.747 55.000 9.43 0.00 34.06 4.61
1670 1726 1.227380 GGTATGCTCTGCTCACCCG 60.227 63.158 0.00 0.00 30.67 5.28
1671 1727 1.227380 GTATGCTCTGCTCACCCGG 60.227 63.158 0.00 0.00 0.00 5.73
1672 1728 1.685765 TATGCTCTGCTCACCCGGT 60.686 57.895 0.00 0.00 0.00 5.28
1711 1768 2.575993 CTCCTGGAGTGCGAGGTG 59.424 66.667 15.76 0.00 40.57 4.00
1840 1897 5.440610 GGATTAATTGATCACTCCACCAGT 58.559 41.667 11.86 0.00 34.67 4.00
1898 1958 5.967088 AGTAGTTTCATACTGGCAGTAGTG 58.033 41.667 29.14 24.52 37.73 2.74
2083 2160 7.083875 TCAAAACCTGAACTTGAACTTACTG 57.916 36.000 0.00 0.00 0.00 2.74
2104 2181 4.293494 TGAGGACAGGCTGATTTCTAGAT 58.707 43.478 23.66 0.00 0.00 1.98
2115 2192 5.048643 GCTGATTTCTAGATGACGGCTACTA 60.049 44.000 13.48 0.00 0.00 1.82
2116 2193 6.315091 TGATTTCTAGATGACGGCTACTAC 57.685 41.667 0.00 0.00 0.00 2.73
2117 2194 6.062749 TGATTTCTAGATGACGGCTACTACT 58.937 40.000 0.00 0.00 0.00 2.57
2118 2195 6.205076 TGATTTCTAGATGACGGCTACTACTC 59.795 42.308 0.00 0.00 0.00 2.59
2119 2196 4.005487 TCTAGATGACGGCTACTACTCC 57.995 50.000 0.00 0.00 0.00 3.85
2120 2197 2.730934 AGATGACGGCTACTACTCCA 57.269 50.000 0.00 0.00 0.00 3.86
2121 2198 2.577700 AGATGACGGCTACTACTCCAG 58.422 52.381 0.00 0.00 0.00 3.86
2122 2199 2.092321 AGATGACGGCTACTACTCCAGT 60.092 50.000 0.00 0.00 41.62 4.00
2123 2200 3.136077 AGATGACGGCTACTACTCCAGTA 59.864 47.826 0.00 0.00 38.80 2.74
2152 2229 5.589452 ACTCCAGTACTCCGTATAAGAGTTG 59.411 44.000 10.96 5.75 41.87 3.16
2177 2254 5.572896 GTGCAAATTCAAAGTACTGGTATGC 59.427 40.000 0.00 2.42 0.00 3.14
2204 2287 5.367937 AGAGGCTGCATTTTTATCTCCTCTA 59.632 40.000 0.50 0.00 45.11 2.43
2205 2288 5.619220 AGGCTGCATTTTTATCTCCTCTAG 58.381 41.667 0.50 0.00 0.00 2.43
2285 2375 8.091449 TCAGGATCAGTTAAGAAGAAGAAACTC 58.909 37.037 0.00 0.00 29.93 3.01
2381 2472 5.269554 TCTGAACCCCCTTCAATAATTGT 57.730 39.130 0.00 0.00 38.47 2.71
2404 2495 4.588528 TCCCCTCTTTCCAACAAAATCTTG 59.411 41.667 0.00 0.00 38.61 3.02
2406 2497 4.039609 CCCTCTTTCCAACAAAATCTTGCT 59.960 41.667 0.00 0.00 35.84 3.91
2448 2552 3.127376 CGGAACACATTGATCTGCATTGA 59.873 43.478 0.00 0.00 33.29 2.57
2450 2554 5.657474 GGAACACATTGATCTGCATTGAAT 58.343 37.500 0.00 0.00 33.29 2.57
2451 2555 5.747197 GGAACACATTGATCTGCATTGAATC 59.253 40.000 0.00 0.00 33.29 2.52
2452 2556 4.916870 ACACATTGATCTGCATTGAATCG 58.083 39.130 0.00 0.00 33.29 3.34
2453 2557 4.637091 ACACATTGATCTGCATTGAATCGA 59.363 37.500 0.00 0.00 33.29 3.59
2455 2559 6.031471 CACATTGATCTGCATTGAATCGAAA 58.969 36.000 0.00 0.00 33.29 3.46
2456 2560 6.020916 CACATTGATCTGCATTGAATCGAAAC 60.021 38.462 0.00 0.00 33.29 2.78
2457 2561 5.625921 TTGATCTGCATTGAATCGAAACA 57.374 34.783 0.00 0.00 0.00 2.83
2545 2649 2.693591 GCTACTGCTACTGGTGGTGATA 59.306 50.000 0.00 0.00 36.03 2.15
2546 2650 3.322254 GCTACTGCTACTGGTGGTGATAT 59.678 47.826 0.00 0.00 36.03 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 3.316868 TGGGGTTTTCTGCTTTAGTTTCG 59.683 43.478 0.00 0.00 0.00 3.46
86 87 2.892852 TCTCACTTTGCTCATTTTGGGG 59.107 45.455 0.00 0.00 0.00 4.96
89 90 5.401376 CACATGTCTCACTTTGCTCATTTTG 59.599 40.000 0.00 0.00 0.00 2.44
104 105 1.168714 GGAAACCCTGCACATGTCTC 58.831 55.000 0.00 0.00 0.00 3.36
129 130 2.202492 GCTCGACGCGTGTCATCT 60.202 61.111 27.16 0.00 45.80 2.90
138 139 0.640768 GAGTGTTATGTGCTCGACGC 59.359 55.000 0.00 0.58 39.77 5.19
150 151 0.906066 TATGCCTTGCGGGAGTGTTA 59.094 50.000 0.00 0.00 37.23 2.41
154 155 0.464373 CATGTATGCCTTGCGGGAGT 60.464 55.000 0.00 0.00 37.23 3.85
171 172 6.968904 CGCAAAAATAAGAACATGTCTAGCAT 59.031 34.615 0.00 0.00 34.56 3.79
184 185 5.627367 CCGTGTTTTCATCGCAAAAATAAGA 59.373 36.000 0.00 0.00 0.00 2.10
195 196 6.966413 CAATTTATTGTCCGTGTTTTCATCG 58.034 36.000 0.00 0.00 33.22 3.84
209 210 8.683331 TCGCAACGAGTGAGTACAATTTATTGT 61.683 37.037 12.30 12.30 41.63 2.71
305 308 0.548510 GGAGTAGCCCTTCAAGCCAT 59.451 55.000 0.00 0.00 0.00 4.40
306 309 0.547712 AGGAGTAGCCCTTCAAGCCA 60.548 55.000 0.00 0.00 37.37 4.75
332 335 2.478894 CGACATAAACATATGGACGGCC 59.521 50.000 0.00 0.00 32.42 6.13
333 336 3.128349 ACGACATAAACATATGGACGGC 58.872 45.455 7.80 0.00 36.50 5.68
373 377 2.365617 AGACTCCTTGAAGAAAGCACGA 59.634 45.455 0.00 0.00 34.24 4.35
374 378 2.478134 CAGACTCCTTGAAGAAAGCACG 59.522 50.000 0.00 0.00 34.24 5.34
398 402 4.096833 GCGTGTATATATGGATGGACGGTA 59.903 45.833 0.00 0.00 0.00 4.02
406 410 4.159693 ACGACATGGCGTGTATATATGGAT 59.840 41.667 29.05 0.00 43.79 3.41
412 416 2.869801 CCAAACGACATGGCGTGTATAT 59.130 45.455 30.36 8.73 44.86 0.86
502 525 3.157252 ATCGAGCGCCCTCACCAT 61.157 61.111 2.29 0.00 38.00 3.55
504 527 3.371097 TTCATCGAGCGCCCTCACC 62.371 63.158 2.29 0.00 38.00 4.02
506 529 1.888436 AACTTCATCGAGCGCCCTCA 61.888 55.000 2.29 0.00 38.00 3.86
611 642 5.859521 TTTGAATTTTGATTTGATGCCGG 57.140 34.783 0.00 0.00 0.00 6.13
617 649 8.820933 TGTATGCGTTTTTGAATTTTGATTTGA 58.179 25.926 0.00 0.00 0.00 2.69
668 700 3.680490 TCCGTTTCCAGCACATCATTTA 58.320 40.909 0.00 0.00 0.00 1.40
943 985 1.179174 CGTGACTGTGAGGGAGTCCA 61.179 60.000 12.30 0.00 39.36 4.02
988 1034 0.824109 GCCTCCATGGTAAAAAGGGC 59.176 55.000 12.58 10.98 38.35 5.19
1669 1725 0.096976 CATTTAGCAGCGACCAACCG 59.903 55.000 0.00 0.00 0.00 4.44
1670 1726 0.179163 GCATTTAGCAGCGACCAACC 60.179 55.000 0.00 0.00 44.79 3.77
1671 1727 3.312709 GCATTTAGCAGCGACCAAC 57.687 52.632 0.00 0.00 44.79 3.77
1711 1768 5.471456 AGCAAATAATCCACAGATCGAATCC 59.529 40.000 0.00 0.00 0.00 3.01
1840 1897 6.127168 TGGTAAAGAGACAAAGAACACTCAGA 60.127 38.462 0.00 0.00 32.59 3.27
1898 1958 5.360999 AGGAAAATGCCAAGCTAAATCTACC 59.639 40.000 0.00 0.00 0.00 3.18
2083 2160 4.343526 TCATCTAGAAATCAGCCTGTCCTC 59.656 45.833 0.00 0.00 0.00 3.71
2104 2181 3.972368 ACTGGAGTAGTAGCCGTCA 57.028 52.632 0.00 0.00 38.04 4.35
2115 2192 0.616111 CTGGAGTGGCCTACTGGAGT 60.616 60.000 11.89 0.00 40.53 3.85
2116 2193 0.616111 ACTGGAGTGGCCTACTGGAG 60.616 60.000 11.89 9.52 40.53 3.86
2117 2194 0.708209 TACTGGAGTGGCCTACTGGA 59.292 55.000 11.89 0.00 40.53 3.86
2118 2195 0.824759 GTACTGGAGTGGCCTACTGG 59.175 60.000 11.89 5.64 40.53 4.00
2119 2196 1.751924 GAGTACTGGAGTGGCCTACTG 59.248 57.143 11.89 0.00 40.53 2.74
2120 2197 1.342175 GGAGTACTGGAGTGGCCTACT 60.342 57.143 3.32 5.85 44.02 2.57
2121 2198 1.112950 GGAGTACTGGAGTGGCCTAC 58.887 60.000 3.32 0.00 37.63 3.18
2122 2199 0.395311 CGGAGTACTGGAGTGGCCTA 60.395 60.000 3.32 0.00 37.63 3.93
2123 2200 1.682684 CGGAGTACTGGAGTGGCCT 60.683 63.158 3.32 0.00 37.63 5.19
2124 2201 0.682209 TACGGAGTACTGGAGTGGCC 60.682 60.000 0.00 0.00 45.11 5.36
2125 2202 2.877975 TACGGAGTACTGGAGTGGC 58.122 57.895 0.00 0.00 45.11 5.01
2152 2229 4.584327 ACCAGTACTTTGAATTTGCACC 57.416 40.909 0.00 0.00 0.00 5.01
2177 2254 3.294214 AGATAAAAATGCAGCCTCTGGG 58.706 45.455 0.00 0.00 31.21 4.45
2285 2375 2.420890 GGCCCTCTGCTCAGATCG 59.579 66.667 0.00 0.00 40.92 3.69
2381 2472 4.469469 AGATTTTGTTGGAAAGAGGGGA 57.531 40.909 0.00 0.00 0.00 4.81
2404 2495 7.758495 TCCGAGATTTTAACAGGATTTTTAGC 58.242 34.615 0.00 0.00 0.00 3.09
2406 2497 9.069082 TGTTCCGAGATTTTAACAGGATTTTTA 57.931 29.630 0.00 0.00 0.00 1.52
2426 2518 3.127376 TCAATGCAGATCAATGTGTTCCG 59.873 43.478 0.00 0.00 0.00 4.30
2545 2649 3.392616 GTCTCATATTCCCACTCCCACAT 59.607 47.826 0.00 0.00 0.00 3.21
2546 2650 2.771943 GTCTCATATTCCCACTCCCACA 59.228 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.