Multiple sequence alignment - TraesCS3D01G206500

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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 TraesCS3D01G206500 chr3D 100.000 2339 0 0 1 2339 269285683 269283345 0 4320
1 TraesCS3D01G206500 chr3A 96.525 2302 50 12 45 2317 346952455 346954755 0 3781


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 TraesCS3D01G206500 chr3D 269283345 269285683 2338 True 4320 4320 100.000 1 2339 1 chr3D.!!$R1 2338
1 TraesCS3D01G206500 chr3A 346952455 346954755 2300 False 3781 3781 96.525 45 2317 1 chr3A.!!$F1 2272

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
516 517 0.31836 TACGTGCTGGTTGTCTCGTG 60.318 55.0 0.0 0.0 33.7 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2268 0.0293 ACACTTGTGCACATTGTCGC 59.971 50.0 22.39 4.81 0.0 5.19 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
29 30 7.724128 CGTACTCGTGTATACACATTTAACA 57.276 36.000 30.17 9.81 46.75 2.41
30 31 7.594850 CGTACTCGTGTATACACATTTAACAC 58.405 38.462 30.17 17.89 46.75 3.32
31 32 7.482743 CGTACTCGTGTATACACATTTAACACT 59.517 37.037 30.17 8.57 46.75 3.55
32 33 9.132521 GTACTCGTGTATACACATTTAACACTT 57.867 33.333 30.17 8.82 46.75 3.16
34 35 9.350357 ACTCGTGTATACACATTTAACACTTAG 57.650 33.333 30.17 12.88 46.75 2.18
35 36 9.563898 CTCGTGTATACACATTTAACACTTAGA 57.436 33.333 30.17 15.81 46.75 2.10
36 37 9.345517 TCGTGTATACACATTTAACACTTAGAC 57.654 33.333 30.17 3.02 46.75 2.59
37 38 9.131416 CGTGTATACACATTTAACACTTAGACA 57.869 33.333 30.17 0.00 46.75 3.41
139 140 8.215736 TGCTATCCTAGACAACATAGTGTAGTA 58.784 37.037 0.00 0.00 34.53 1.82
378 379 3.952675 CAGCAGCGTGCCGTTGTT 61.953 61.111 11.63 4.61 46.52 2.83
389 390 1.083657 CCGTTGTTGTTCGCGTGAG 60.084 57.895 5.77 0.00 0.00 3.51
448 449 1.668419 ACAAGAAGTGGACTGCACAC 58.332 50.000 3.27 0.00 39.10 3.82
452 453 0.947244 GAAGTGGACTGCACACCAAG 59.053 55.000 8.44 0.00 39.63 3.61
463 464 2.288702 TGCACACCAAGCGCAAATAAAT 60.289 40.909 11.47 0.00 31.46 1.40
516 517 0.318360 TACGTGCTGGTTGTCTCGTG 60.318 55.000 0.00 0.00 33.70 4.35
595 596 3.417069 AATGTGACGTTCCATCCTTCA 57.583 42.857 0.00 0.00 0.00 3.02
624 625 8.112822 TCAAAATCACTGGATTAATTAGGACCA 58.887 33.333 0.00 0.00 42.87 4.02
625 626 8.748412 CAAAATCACTGGATTAATTAGGACCAA 58.252 33.333 0.00 0.00 42.87 3.67
628 629 8.697507 ATCACTGGATTAATTAGGACCAATTC 57.302 34.615 0.00 0.00 30.84 2.17
727 729 7.119262 GTCTCAATTGGAAATCGACTTCCTTTA 59.881 37.037 24.71 11.71 44.57 1.85
731 733 9.423061 CAATTGGAAATCGACTTCCTTTATTTT 57.577 29.630 24.71 7.98 44.57 1.82
764 766 2.094762 AAAATTCCCTCACCGACGAG 57.905 50.000 0.00 0.00 0.00 4.18
1203 1216 4.193334 TCGGAGAGCACGGCGATG 62.193 66.667 16.62 9.66 0.00 3.84
1269 1282 4.467107 ACCGCCTCCTCCTCCTCC 62.467 72.222 0.00 0.00 0.00 4.30
1272 1285 2.520741 GCCTCCTCCTCCTCCTCG 60.521 72.222 0.00 0.00 0.00 4.63
1275 1288 1.641552 CCTCCTCCTCCTCCTCGTCT 61.642 65.000 0.00 0.00 0.00 4.18
1377 1390 0.991146 TGATGAAACTGCAGGCCCTA 59.009 50.000 19.93 0.25 0.00 3.53
1488 1501 2.930019 CCCAGGGTGAGCAGACCA 60.930 66.667 0.00 0.00 37.80 4.02
1545 1558 0.889306 GTCGTGGGTGAAGCTAGTCT 59.111 55.000 0.00 0.00 0.00 3.24
1559 1572 8.035984 GTGAAGCTAGTCTGTCTAAAATTAGGT 58.964 37.037 0.00 0.00 0.00 3.08
1849 1862 1.153597 GCCAACTGCAAACCACAAGC 61.154 55.000 0.00 0.00 40.77 4.01
1870 1883 7.335924 ACAAGCCGAGTAATTAACAACACATAT 59.664 33.333 0.00 0.00 0.00 1.78
1898 1911 1.594564 GCCGGCGAGGGAGAAATAC 60.595 63.158 12.58 0.00 41.48 1.89
1899 1912 2.029307 GCCGGCGAGGGAGAAATACT 62.029 60.000 12.58 0.00 41.48 2.12
1900 1913 1.325355 CCGGCGAGGGAGAAATACTA 58.675 55.000 9.30 0.00 35.97 1.82
1901 1914 1.000496 CCGGCGAGGGAGAAATACTAC 60.000 57.143 9.30 0.00 35.97 2.73
1932 1950 5.457686 AGTATACGTAGTTTGGGGTGGATA 58.542 41.667 0.08 0.00 37.78 2.59
1935 1953 1.205417 CGTAGTTTGGGGTGGATACGT 59.795 52.381 0.00 0.00 42.51 3.57
2039 2057 3.554934 AGCATTTCCAGAACTGACACAA 58.445 40.909 3.19 0.00 0.00 3.33
2197 2215 7.013655 CCGATTCAGATCCACTTTAAATTCCAT 59.986 37.037 0.00 0.00 0.00 3.41
2218 2236 9.874205 TTCCATTTTGCCAGAAATAGAAATAAG 57.126 29.630 0.00 0.00 28.44 1.73
2250 2268 2.221169 TCAACACTTGCTGGCTACTTG 58.779 47.619 0.00 0.00 0.00 3.16
2258 2276 0.097674 GCTGGCTACTTGCGACAATG 59.902 55.000 0.00 0.00 44.05 2.82
2268 2286 0.029167 TGCGACAATGTGCACAAGTG 59.971 50.000 26.72 25.67 35.90 3.16
2282 2312 3.735746 GCACAAGTGTTAGCACCAAAATC 59.264 43.478 6.04 0.00 46.35 2.17
2289 2319 4.213482 GTGTTAGCACCAAAATCGAGACTT 59.787 41.667 0.00 0.00 39.61 3.01
2317 2347 5.059404 CGGGAGCATTTCACAAATTAGTT 57.941 39.130 0.00 0.00 0.00 2.24
2318 2348 5.469479 CGGGAGCATTTCACAAATTAGTTT 58.531 37.500 0.00 0.00 0.00 2.66
2319 2349 5.925969 CGGGAGCATTTCACAAATTAGTTTT 59.074 36.000 0.00 0.00 0.00 2.43
2320 2350 6.423604 CGGGAGCATTTCACAAATTAGTTTTT 59.576 34.615 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.825972 CCTGTTATTGTCTAAGTGTTAAATGTG 57.174 33.333 0.00 0.00 0.00 3.21
20 21 9.787435 TCCTGTTATTGTCTAAGTGTTAAATGT 57.213 29.630 0.00 0.00 0.00 2.71
24 25 9.485206 GTTCTCCTGTTATTGTCTAAGTGTTAA 57.515 33.333 0.00 0.00 0.00 2.01
25 26 8.644216 TGTTCTCCTGTTATTGTCTAAGTGTTA 58.356 33.333 0.00 0.00 0.00 2.41
26 27 7.506114 TGTTCTCCTGTTATTGTCTAAGTGTT 58.494 34.615 0.00 0.00 0.00 3.32
27 28 7.062749 TGTTCTCCTGTTATTGTCTAAGTGT 57.937 36.000 0.00 0.00 0.00 3.55
28 29 7.962964 TTGTTCTCCTGTTATTGTCTAAGTG 57.037 36.000 0.00 0.00 0.00 3.16
29 30 9.003658 CAATTGTTCTCCTGTTATTGTCTAAGT 57.996 33.333 0.00 0.00 0.00 2.24
30 31 8.454106 CCAATTGTTCTCCTGTTATTGTCTAAG 58.546 37.037 4.43 0.00 0.00 2.18
31 32 8.160765 TCCAATTGTTCTCCTGTTATTGTCTAA 58.839 33.333 4.43 0.00 0.00 2.10
32 33 7.685481 TCCAATTGTTCTCCTGTTATTGTCTA 58.315 34.615 4.43 0.00 0.00 2.59
33 34 6.542821 TCCAATTGTTCTCCTGTTATTGTCT 58.457 36.000 4.43 0.00 0.00 3.41
34 35 6.817765 TCCAATTGTTCTCCTGTTATTGTC 57.182 37.500 4.43 0.00 0.00 3.18
35 36 6.947733 TCATCCAATTGTTCTCCTGTTATTGT 59.052 34.615 4.43 0.00 0.00 2.71
36 37 7.395190 TCATCCAATTGTTCTCCTGTTATTG 57.605 36.000 4.43 0.00 0.00 1.90
37 38 8.421249 TTTCATCCAATTGTTCTCCTGTTATT 57.579 30.769 4.43 0.00 0.00 1.40
38 39 8.306761 GTTTTCATCCAATTGTTCTCCTGTTAT 58.693 33.333 4.43 0.00 0.00 1.89
39 40 7.286546 TGTTTTCATCCAATTGTTCTCCTGTTA 59.713 33.333 4.43 0.00 0.00 2.41
40 41 6.098124 TGTTTTCATCCAATTGTTCTCCTGTT 59.902 34.615 4.43 0.00 0.00 3.16
41 42 5.598005 TGTTTTCATCCAATTGTTCTCCTGT 59.402 36.000 4.43 0.00 0.00 4.00
42 43 6.088016 TGTTTTCATCCAATTGTTCTCCTG 57.912 37.500 4.43 0.00 0.00 3.86
43 44 6.729690 TTGTTTTCATCCAATTGTTCTCCT 57.270 33.333 4.43 0.00 0.00 3.69
377 378 0.808060 TTGACAGCTCACGCGAACAA 60.808 50.000 15.93 4.17 42.32 2.83
378 379 0.808060 TTTGACAGCTCACGCGAACA 60.808 50.000 15.93 0.00 42.32 3.18
424 425 3.128589 GTGCAGTCCACTTCTTGTTTTGA 59.871 43.478 0.00 0.00 41.35 2.69
426 427 3.088532 TGTGCAGTCCACTTCTTGTTTT 58.911 40.909 0.00 0.00 44.92 2.43
448 449 6.728200 TCAAGATCTATTTATTTGCGCTTGG 58.272 36.000 9.73 0.00 33.12 3.61
452 453 8.566008 ACAAATCAAGATCTATTTATTTGCGC 57.434 30.769 20.64 0.00 37.67 6.09
463 464 7.599171 TGACGACAGTAACAAATCAAGATCTA 58.401 34.615 0.00 0.00 0.00 1.98
516 517 2.563427 GGCGCCTGCTTCTTTGTC 59.437 61.111 22.15 0.00 42.25 3.18
528 529 0.234884 GCTACATTGTTATCGGCGCC 59.765 55.000 19.07 19.07 0.00 6.53
624 625 6.991531 TGCTGCCAGAAAATACAAAAAGAATT 59.008 30.769 0.00 0.00 0.00 2.17
625 626 6.523840 TGCTGCCAGAAAATACAAAAAGAAT 58.476 32.000 0.00 0.00 0.00 2.40
628 629 5.984926 TCTTGCTGCCAGAAAATACAAAAAG 59.015 36.000 0.29 0.00 0.00 2.27
727 729 9.373603 GGGAATTTTAACCGCATAAACTAAAAT 57.626 29.630 0.00 0.00 34.98 1.82
731 733 6.885376 TGAGGGAATTTTAACCGCATAAACTA 59.115 34.615 0.00 0.00 0.00 2.24
764 766 8.915654 GGTAAAAATCATCATTCAGACAAACAC 58.084 33.333 0.00 0.00 0.00 3.32
1203 1216 3.336468 GCTCATCCTCATGACCATCATC 58.664 50.000 0.00 0.00 34.28 2.92
1260 1273 4.571243 GGAGACGAGGAGGAGGAG 57.429 66.667 0.00 0.00 0.00 3.69
1272 1285 2.557372 GGAGATCGAGGGCGGAGAC 61.557 68.421 0.00 0.00 38.28 3.36
1275 1288 2.519541 CAGGAGATCGAGGGCGGA 60.520 66.667 0.00 0.00 38.28 5.54
1377 1390 2.283532 ACGGTGCTGGAGCTCTCT 60.284 61.111 14.64 0.00 42.66 3.10
1488 1501 2.356313 CAAGCGGACGTGAGCACT 60.356 61.111 13.36 0.00 35.48 4.40
1545 1558 6.952773 AGTTGCAACACCTAATTTTAGACA 57.047 33.333 30.11 0.00 32.47 3.41
1576 1589 2.223203 GCATTTCTCAATCTCAGCACCG 60.223 50.000 0.00 0.00 0.00 4.94
1901 1914 6.073548 CCCCAAACTACGTATACTCTACTACG 60.074 46.154 0.00 0.97 44.68 3.51
1910 1928 4.677673 ATCCACCCCAAACTACGTATAC 57.322 45.455 0.00 0.00 0.00 1.47
1932 1950 2.232208 GCCCCACTAGTAAGTAACACGT 59.768 50.000 0.00 0.00 33.48 4.49
1935 1953 2.835764 CTGGCCCCACTAGTAAGTAACA 59.164 50.000 0.00 0.00 33.48 2.41
2039 2057 3.270877 CGGGATGCTTTAACTGTAGCTT 58.729 45.455 0.00 0.00 38.22 3.74
2074 2092 2.947652 GCATTTGCTCCTCTTGCTATCA 59.052 45.455 0.00 0.00 38.21 2.15
2117 2135 0.972471 TCATTCCTCTGGCTGAGCGA 60.972 55.000 15.25 11.14 41.35 4.93
2218 2236 6.968904 CCAGCAAGTGTTGATGTGTTATAATC 59.031 38.462 4.38 0.00 45.11 1.75
2250 2268 0.029300 ACACTTGTGCACATTGTCGC 59.971 50.000 22.39 4.81 0.00 5.19
2268 2286 6.476243 TTAAGTCTCGATTTTGGTGCTAAC 57.524 37.500 0.00 0.00 0.00 2.34
2282 2312 0.931005 GCTCCCGCAATTAAGTCTCG 59.069 55.000 0.00 0.00 35.78 4.04


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

AutoCloner maintained by Alex Coulton.