Multiple sequence alignment - TraesCS2D01G506900

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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 TraesCS2D01G506900 chr2D 100.000 2598 0 0 1 2598 600435760 600433163 0.000000e+00 4798
1 TraesCS2D01G506900 chr2B 91.829 2619 100 39 1 2560 730647918 730645355 0.000000e+00 3546
2 TraesCS2D01G506900 chr2A 90.417 1941 74 35 704 2598 734102692 734100818 0.000000e+00 2451
3 TraesCS2D01G506900 chr2A 87.644 348 21 5 175 508 734103166 734102827 4.060000e-103 385
4 TraesCS2D01G506900 chr2A 91.946 149 5 4 1 145 734103306 734103161 4.380000e-48 202


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 TraesCS2D01G506900 chr2D 600433163 600435760 2597 True 4798.000000 4798 100.000000 1 2598 1 chr2D.!!$R1 2597
1 TraesCS2D01G506900 chr2B 730645355 730647918 2563 True 3546.000000 3546 91.829000 1 2560 1 chr2B.!!$R1 2559
2 TraesCS2D01G506900 chr2A 734100818 734103306 2488 True 1012.666667 2451 90.002333 1 2598 3 chr2A.!!$R1 2597

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
731 761 0.109873 AGAGTCGTACGTGAAAGCGG 60.11 55.0 16.05 0.0 35.98 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2107 0.17921 CGATAAAAACACACGGCGGG 60.179 55.0 8.04 8.04 0.0 6.13 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
49 54 1.019278 GTAGTGGTGTCATGGCACGG 61.019 60.000 23.35 0.00 40.08 4.94
50 55 1.476845 TAGTGGTGTCATGGCACGGT 61.477 55.000 23.35 12.86 40.08 4.83
214 222 1.595929 GAACAAACTCCCGCGTCCA 60.596 57.895 4.92 0.00 0.00 4.02
276 294 4.394712 CTCCCCGGGTGAGCACAC 62.395 72.222 21.85 5.63 45.27 3.82
298 316 0.597637 GACACGACCATCTATGCCCG 60.598 60.000 0.00 0.00 0.00 6.13
327 345 1.817099 GAAGCTGTGGCCGATCTGG 60.817 63.158 0.00 0.00 39.73 3.86
494 520 2.367241 TCCGTGTCACCTCTTTCAATGA 59.633 45.455 0.00 0.00 0.00 2.57
498 524 4.084328 CGTGTCACCTCTTTCAATGAGTTC 60.084 45.833 0.00 0.00 0.00 3.01
533 559 3.361786 AGACTGTCTAGAAGGCTTCTCC 58.638 50.000 31.69 20.47 41.14 3.71
534 560 2.096248 ACTGTCTAGAAGGCTTCTCCG 58.904 52.381 31.69 22.86 41.14 4.63
535 561 2.291024 ACTGTCTAGAAGGCTTCTCCGA 60.291 50.000 31.69 24.55 41.14 4.55
581 611 6.363626 GCATGGTACGTATCAGAGTTAATCAG 59.636 42.308 14.85 0.00 0.00 2.90
588 618 3.934457 TCAGAGTTAATCAGCACGTGA 57.066 42.857 22.23 0.00 40.38 4.35
682 712 4.519804 GCATGGTGCTGGTGTTGTACAC 62.520 54.545 0.00 1.39 43.39 2.90
731 761 0.109873 AGAGTCGTACGTGAAAGCGG 60.110 55.000 16.05 0.00 35.98 5.52
776 807 7.703328 TCGGTGAATTATTAAATGAAGGAAGC 58.297 34.615 0.00 0.00 0.00 3.86
889 921 2.719798 CCGCAAAAGAACACAACTGAG 58.280 47.619 0.00 0.00 0.00 3.35
1237 1289 4.479993 ACCGCATCCAGCTCAGCC 62.480 66.667 0.00 0.00 42.61 4.85
1434 1487 3.914312 AGTAATCTCACACTTGACCACG 58.086 45.455 0.00 0.00 0.00 4.94
1435 1488 2.910688 AATCTCACACTTGACCACGT 57.089 45.000 0.00 0.00 0.00 4.49
1436 1489 4.521639 AGTAATCTCACACTTGACCACGTA 59.478 41.667 0.00 0.00 0.00 3.57
1437 1490 2.787601 TCTCACACTTGACCACGTAC 57.212 50.000 0.00 0.00 0.00 3.67
1463 1516 5.471456 GGTCTCACTTGTGACATTGATTTCT 59.529 40.000 12.23 0.00 39.53 2.52
1743 1812 6.148811 GTCGTCAACATCTCCCTAAAAATCAA 59.851 38.462 0.00 0.00 0.00 2.57
1745 1814 8.044309 TCGTCAACATCTCCCTAAAAATCAATA 58.956 33.333 0.00 0.00 0.00 1.90
1767 1836 8.408601 CAATAGAAATCATCGATCCAACCTTTT 58.591 33.333 0.00 0.00 0.00 2.27
1768 1837 6.840780 AGAAATCATCGATCCAACCTTTTT 57.159 33.333 0.00 0.00 0.00 1.94
1809 1878 3.735240 TCAAAAGTTCAATGTCGCATTGC 59.265 39.130 20.66 0.00 0.00 3.56
1818 1887 0.522626 TGTCGCATTGCCACAATGAG 59.477 50.000 21.26 18.17 0.00 2.90
1931 2004 1.290955 CCAGTGTCGCTAACCGGAA 59.709 57.895 9.46 0.00 37.59 4.30
2324 2414 2.943034 GTCGGCGTCGCTCGTAAG 60.943 66.667 18.11 2.46 42.13 2.34
2403 2499 0.319555 CGGGAGTGTGACACAACGAT 60.320 55.000 18.95 0.00 36.74 3.73
2432 2528 1.370414 GCACGCGCACAGTTGATTT 60.370 52.632 5.73 0.00 38.36 2.17
2434 2530 0.998226 CACGCGCACAGTTGATTTGG 60.998 55.000 5.73 0.00 0.00 3.28
2443 2542 3.631686 CACAGTTGATTTGGGACTTGACA 59.368 43.478 0.00 0.00 0.00 3.58
2445 2544 3.254166 CAGTTGATTTGGGACTTGACAGG 59.746 47.826 0.00 0.00 0.00 4.00
2454 2553 1.673168 GACTTGACAGGCATGGATCC 58.327 55.000 4.20 4.20 0.00 3.36
2456 2555 0.816825 CTTGACAGGCATGGATCCCG 60.817 60.000 9.90 1.00 0.00 5.14
2537 2650 7.630944 GCACCATTATTGTTTCCCGGTAAAATA 60.631 37.037 0.00 0.00 0.00 1.40
2568 2681 4.544689 GGTGTGCGTTGCGTGCAA 62.545 61.111 2.58 2.58 45.23 4.08
2589 2702 1.064832 TGCCCATGGATCAACGATCAA 60.065 47.619 15.22 0.00 40.50 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.019278 CCGTGCCATGACACCACTAC 61.019 60.000 6.57 0.00 37.25 2.73
214 222 1.743995 GTTGAATAGTGGGCGCGGT 60.744 57.895 8.83 0.00 0.00 5.68
219 227 1.095807 GCGAGGGTTGAATAGTGGGC 61.096 60.000 0.00 0.00 0.00 5.36
268 282 1.008881 GTCGTGTCTCGTGTGCTCA 60.009 57.895 0.00 0.00 40.80 4.26
273 291 1.817357 TAGATGGTCGTGTCTCGTGT 58.183 50.000 0.00 0.00 40.80 4.49
274 292 2.720933 CATAGATGGTCGTGTCTCGTG 58.279 52.381 0.00 0.00 40.80 4.35
275 293 1.065701 GCATAGATGGTCGTGTCTCGT 59.934 52.381 0.00 0.00 40.80 4.18
276 294 1.600663 GGCATAGATGGTCGTGTCTCG 60.601 57.143 0.00 0.00 41.41 4.04
277 295 1.269831 GGGCATAGATGGTCGTGTCTC 60.270 57.143 0.00 0.00 0.00 3.36
278 296 0.753262 GGGCATAGATGGTCGTGTCT 59.247 55.000 0.00 0.00 0.00 3.41
279 297 0.597637 CGGGCATAGATGGTCGTGTC 60.598 60.000 0.00 0.00 0.00 3.67
327 345 1.737793 CACGGAGACATAAACAAGGCC 59.262 52.381 0.00 0.00 0.00 5.19
476 502 4.214332 GGAACTCATTGAAAGAGGTGACAC 59.786 45.833 2.32 0.00 37.43 3.67
498 524 1.072331 ACAGTCTAGGGCAAACAGTGG 59.928 52.381 0.00 0.00 0.00 4.00
531 557 2.091541 GGAAATGCAACTTGGATCGGA 58.908 47.619 0.00 0.00 0.00 4.55
532 558 2.094675 AGGAAATGCAACTTGGATCGG 58.905 47.619 0.00 0.00 0.00 4.18
533 559 2.749076 TGAGGAAATGCAACTTGGATCG 59.251 45.455 0.00 0.00 0.00 3.69
534 560 4.679662 CATGAGGAAATGCAACTTGGATC 58.320 43.478 0.00 0.00 0.00 3.36
535 561 4.730949 CATGAGGAAATGCAACTTGGAT 57.269 40.909 0.00 0.00 0.00 3.41
581 611 5.448926 AAAAACAACAATTCTTCACGTGC 57.551 34.783 11.67 0.00 0.00 5.34
713 743 0.386478 ACCGCTTTCACGTACGACTC 60.386 55.000 24.41 3.68 0.00 3.36
731 761 8.885722 TCACCGAAATATTCCTACACATAAAAC 58.114 33.333 0.00 0.00 0.00 2.43
769 800 0.322906 GCTAGGGTTGCAGCTTCCTT 60.323 55.000 3.82 2.53 34.86 3.36
776 807 2.517650 GCTACTAGCTAGGGTTGCAG 57.482 55.000 24.35 11.69 38.45 4.41
798 829 0.383949 GGACTGAGACCGAGCTCATC 59.616 60.000 15.40 10.65 43.43 2.92
799 830 1.040339 GGGACTGAGACCGAGCTCAT 61.040 60.000 15.40 0.00 43.43 2.90
800 831 1.679305 GGGACTGAGACCGAGCTCA 60.679 63.158 15.40 6.94 42.31 4.26
807 838 1.500474 TGGATGATGGGACTGAGACC 58.500 55.000 0.00 0.00 0.00 3.85
889 921 4.695928 GGTTTAGTGGACTGGTCTTGATTC 59.304 45.833 0.67 0.00 0.00 2.52
1309 1361 4.773117 GTCCAGCCCGTCGTCGTC 62.773 72.222 0.71 0.00 35.01 4.20
1323 1375 1.153349 GACGGCATTGGAGAGGTCC 60.153 63.158 0.00 0.00 44.24 4.46
1403 1455 5.725362 AGTGTGAGATTACTTACTTCCAGC 58.275 41.667 0.00 0.00 34.39 4.85
1434 1487 1.338973 TGTCACAAGTGAGACCGGTAC 59.661 52.381 7.34 1.33 40.75 3.34
1435 1488 1.694844 TGTCACAAGTGAGACCGGTA 58.305 50.000 7.34 0.00 40.75 4.02
1436 1489 1.048601 ATGTCACAAGTGAGACCGGT 58.951 50.000 6.92 6.92 40.75 5.28
1437 1490 1.800586 CAATGTCACAAGTGAGACCGG 59.199 52.381 0.00 0.00 40.75 5.28
1442 1495 7.805071 GGTAAAGAAATCAATGTCACAAGTGAG 59.195 37.037 2.62 0.00 40.75 3.51
1549 1603 2.484203 CTCCGGGTCGTCGACTTC 59.516 66.667 23.69 15.25 32.47 3.01
1564 1618 1.450531 CCCCGCATTGCTTGATCCTC 61.451 60.000 7.12 0.00 0.00 3.71
1743 1812 8.525290 AAAAAGGTTGGATCGATGATTTCTAT 57.475 30.769 0.54 0.00 0.00 1.98
1745 1814 6.840780 AAAAAGGTTGGATCGATGATTTCT 57.159 33.333 0.54 0.00 0.00 2.52
1768 1837 9.092876 ACTTTTGATACAGCGAAAAATGAAAAA 57.907 25.926 0.00 0.00 0.00 1.94
1769 1838 8.641499 ACTTTTGATACAGCGAAAAATGAAAA 57.359 26.923 0.00 0.00 0.00 2.29
1809 1878 6.462500 TCTCTCTTTTCTCTTCTCATTGTGG 58.538 40.000 0.00 0.00 0.00 4.17
1908 1981 0.806492 GGTTAGCGACACTGGCTAGC 60.806 60.000 6.04 6.04 43.30 3.42
1909 1982 0.525668 CGGTTAGCGACACTGGCTAG 60.526 60.000 0.00 0.00 43.30 3.42
1910 1983 1.509463 CGGTTAGCGACACTGGCTA 59.491 57.895 0.00 0.00 41.80 3.93
1911 1984 2.261671 CGGTTAGCGACACTGGCT 59.738 61.111 0.00 0.00 44.35 4.75
1912 1985 2.775032 TTCCGGTTAGCGACACTGGC 62.775 60.000 5.06 0.00 40.17 4.85
1931 2004 4.539083 TTGACGCCGGCACAGTGT 62.539 61.111 28.98 16.15 0.00 3.55
2031 2104 1.787057 TAAAAACACACGGCGGGCTG 61.787 55.000 10.14 9.79 0.00 4.85
2032 2105 0.891904 ATAAAAACACACGGCGGGCT 60.892 50.000 10.14 0.00 0.00 5.19
2033 2106 0.455464 GATAAAAACACACGGCGGGC 60.455 55.000 10.14 0.00 0.00 6.13
2034 2107 0.179210 CGATAAAAACACACGGCGGG 60.179 55.000 8.04 8.04 0.00 6.13
2035 2108 0.791610 GCGATAAAAACACACGGCGG 60.792 55.000 13.24 2.35 0.00 6.13
2432 2528 1.133181 TCCATGCCTGTCAAGTCCCA 61.133 55.000 0.00 0.00 0.00 4.37
2434 2530 1.673168 GATCCATGCCTGTCAAGTCC 58.327 55.000 0.00 0.00 0.00 3.85
2443 2542 3.125376 GCCTTCGGGATCCATGCCT 62.125 63.158 15.23 0.00 35.94 4.75
2445 2544 2.974698 CGCCTTCGGGATCCATGC 60.975 66.667 15.23 7.08 37.25 4.06
2456 2555 0.745845 ATGACAGTCATGCCGCCTTC 60.746 55.000 15.67 0.00 35.43 3.46
2462 2561 1.376543 CTGTGGATGACAGTCATGCC 58.623 55.000 27.07 22.23 46.30 4.40
2537 2650 3.461773 CACCACCGATCTCCGCCT 61.462 66.667 0.00 0.00 36.84 5.52
2568 2681 1.143481 TGATCGTTGATCCATGGGCAT 59.857 47.619 13.02 0.00 38.20 4.40
2574 2687 2.421952 CCCCACTTGATCGTTGATCCAT 60.422 50.000 4.47 0.00 38.20 3.41


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

AutoCloner maintained by Alex Coulton.