Multiple sequence alignment - TraesCS2D01G261600

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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 TraesCS2D01G261600 chr2D 100.000 2677 0 0 1 2677 318247349 318250025 0 4944
1 TraesCS2D01G261600 chr2B 92.092 2529 101 39 200 2677 385888296 385890776 0 3470
2 TraesCS2D01G261600 chr2A 94.419 1720 56 16 1 1699 413489980 413488280 0 2608
3 TraesCS2D01G261600 chr2A 86.378 925 51 23 1786 2677 413487993 413487111 0 941


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 TraesCS2D01G261600 chr2D 318247349 318250025 2676 False 4944.0 4944 100.0000 1 2677 1 chr2D.!!$F1 2676
1 TraesCS2D01G261600 chr2B 385888296 385890776 2480 False 3470.0 3470 92.0920 200 2677 1 chr2B.!!$F1 2477
2 TraesCS2D01G261600 chr2A 413487111 413489980 2869 True 1774.5 2608 90.3985 1 2677 2 chr2A.!!$R1 2676

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
898 915 1.152756 AGCCACCAACAACCTCACC 60.153 57.895 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2414 0.626916 TGGCAAACCATACCCTACCC 59.373 55.0 0.0 0.0 42.67 3.69 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
83 84 7.275999 ACTTACTACTAGTCGGTAAACGTAGAC 59.724 40.741 16.75 0.00 44.69 2.59
95 96 8.079203 TCGGTAAACGTAGACAGTTTAATGTTA 58.921 33.333 3.52 0.00 43.13 2.41
198 200 2.663119 GCGTTGCATTCTGAATTGGAAC 59.337 45.455 18.10 18.10 0.00 3.62
397 401 2.507886 TGATGTACCCCACCCATACAAG 59.492 50.000 0.00 0.00 32.80 3.16
478 489 4.944962 TGATTAGACCAAACAGCAATCG 57.055 40.909 0.00 0.00 0.00 3.34
482 493 1.523154 GACCAAACAGCAATCGCCCA 61.523 55.000 0.00 0.00 39.83 5.36
543 554 1.904287 ATCTAGCAGCTCGACCTAGG 58.096 55.000 7.41 7.41 31.66 3.02
553 564 1.338337 CTCGACCTAGGCACGAATCAT 59.662 52.381 24.63 0.00 35.70 2.45
594 605 9.880157 AATGAAGTGCATTCTTTAGCAAATAAT 57.120 25.926 0.00 0.00 43.64 1.28
613 624 8.851145 CAAATAATACTACAGAGTCAGGAGCTA 58.149 37.037 0.00 0.00 37.10 3.32
620 631 5.690464 ACAGAGTCAGGAGCTAAATTCAT 57.310 39.130 0.00 0.00 0.00 2.57
622 633 6.578023 ACAGAGTCAGGAGCTAAATTCATAC 58.422 40.000 0.00 0.00 0.00 2.39
654 665 9.836864 AGTTGATTAATGTGCATTAGATCAGTA 57.163 29.630 17.96 10.16 35.23 2.74
656 667 9.612066 TTGATTAATGTGCATTAGATCAGTACA 57.388 29.630 17.96 0.00 35.23 2.90
660 671 3.452264 TGTGCATTAGATCAGTACAGCCT 59.548 43.478 0.00 0.00 0.00 4.58
672 683 6.956202 TCAGTACAGCCTAGGTAGATTTAC 57.044 41.667 11.31 4.15 0.00 2.01
736 751 3.498397 GCTCTGCTGTACTTTGTAGCAAA 59.502 43.478 6.33 0.00 45.73 3.68
826 843 2.891580 AGACAGTGGTACAGTACACCAG 59.108 50.000 12.89 7.21 46.56 4.00
898 915 1.152756 AGCCACCAACAACCTCACC 60.153 57.895 0.00 0.00 0.00 4.02
932 949 5.162947 ACTCCCCACCCGTAATATAGACTAA 60.163 44.000 0.00 0.00 0.00 2.24
933 950 5.079643 TCCCCACCCGTAATATAGACTAAC 58.920 45.833 0.00 0.00 0.00 2.34
934 951 5.082425 CCCCACCCGTAATATAGACTAACT 58.918 45.833 0.00 0.00 0.00 2.24
935 952 6.045459 TCCCCACCCGTAATATAGACTAACTA 59.955 42.308 0.00 0.00 35.42 2.24
1324 1341 1.048160 AGCTTGGTTGGTTGGTTGGG 61.048 55.000 0.00 0.00 0.00 4.12
1668 1706 2.903357 CCGCCATGCTACTCAGGT 59.097 61.111 0.00 0.00 0.00 4.00
1746 1784 5.647225 GGCTCAGATCTTGTCAGATTTTCTT 59.353 40.000 0.00 0.00 40.14 2.52
1828 2067 3.860378 GCGCTTGATTGTTCCATTTTCCA 60.860 43.478 0.00 0.00 0.00 3.53
1858 2097 7.960738 TCTTATTTTGTCGATTTGATTCCGAAC 59.039 33.333 0.00 0.00 33.91 3.95
1932 2176 3.647771 AAGAACTCCCCGGGTGCC 61.648 66.667 21.85 7.59 0.00 5.01
1957 2201 7.101054 CCTGGTTGATGATTTGTTGATTGATT 58.899 34.615 0.00 0.00 0.00 2.57
1958 2202 7.064134 CCTGGTTGATGATTTGTTGATTGATTG 59.936 37.037 0.00 0.00 0.00 2.67
1960 2204 8.583296 TGGTTGATGATTTGTTGATTGATTGTA 58.417 29.630 0.00 0.00 0.00 2.41
1961 2205 8.863049 GGTTGATGATTTGTTGATTGATTGTAC 58.137 33.333 0.00 0.00 0.00 2.90
1962 2206 9.630098 GTTGATGATTTGTTGATTGATTGTACT 57.370 29.630 0.00 0.00 0.00 2.73
2029 2309 1.137086 GCATGTGATGGTCGAGGTAGT 59.863 52.381 0.00 0.00 0.00 2.73
2030 2310 2.361119 GCATGTGATGGTCGAGGTAGTA 59.639 50.000 0.00 0.00 0.00 1.82
2031 2311 3.181479 GCATGTGATGGTCGAGGTAGTAA 60.181 47.826 0.00 0.00 0.00 2.24
2032 2312 4.360563 CATGTGATGGTCGAGGTAGTAAC 58.639 47.826 0.00 0.00 0.00 2.50
2033 2313 3.423749 TGTGATGGTCGAGGTAGTAACA 58.576 45.455 0.00 0.00 0.00 2.41
2034 2314 4.021229 TGTGATGGTCGAGGTAGTAACAT 58.979 43.478 0.00 0.00 0.00 2.71
2035 2315 4.142249 TGTGATGGTCGAGGTAGTAACATG 60.142 45.833 0.00 0.00 0.00 3.21
2036 2316 3.383505 TGATGGTCGAGGTAGTAACATGG 59.616 47.826 0.00 0.00 0.00 3.66
2037 2317 3.090210 TGGTCGAGGTAGTAACATGGA 57.910 47.619 0.00 0.00 0.00 3.41
2038 2318 3.638860 TGGTCGAGGTAGTAACATGGAT 58.361 45.455 0.00 0.00 0.00 3.41
2039 2319 3.383505 TGGTCGAGGTAGTAACATGGATG 59.616 47.826 0.00 0.00 0.00 3.51
2094 2382 3.003480 GCTCTCGTACATCTTGCCTTTT 58.997 45.455 0.00 0.00 0.00 2.27
2126 2414 3.429141 CACTGCCGCTCCTGCAAG 61.429 66.667 0.00 0.00 38.46 4.01
2156 2444 1.112315 GGTTTGCCACCATGTCCACA 61.112 55.000 0.00 0.00 46.42 4.17
2167 2456 3.254060 CCATGTCCACACTACTCTTTCG 58.746 50.000 0.00 0.00 0.00 3.46
2206 2495 5.305139 TGATGATGAAACTTCACATGCTG 57.695 39.130 10.33 0.00 40.49 4.41
2240 2551 4.948621 AGGCATTCCTCTCTGAATTTCAAG 59.051 41.667 0.01 2.19 38.72 3.02
2251 2562 4.943705 TCTGAATTTCAAGGTAGACCATGC 59.056 41.667 0.66 0.00 38.89 4.06
2443 2757 3.251479 TCACGGCTACTAGTTACTCGA 57.749 47.619 0.00 0.00 0.00 4.04
2524 2847 0.248296 GCGCACGTTTGGTCAAGAAA 60.248 50.000 0.30 0.00 0.00 2.52
2554 2877 4.582701 TTCTCACCGCACAAAATGAATT 57.417 36.364 0.00 0.00 0.00 2.17
2573 2896 3.374042 TTCCAACTTGTCTCCAACCAA 57.626 42.857 0.00 0.00 0.00 3.67
2626 2950 2.479837 CAGTTTGAGCTACCGACAACA 58.520 47.619 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 4.935885 ACTGTCTACGTTTACCGACTAG 57.064 45.455 0.00 0.00 40.70 2.57
66 67 5.689383 AAACTGTCTACGTTTACCGACTA 57.311 39.130 0.00 0.00 40.70 2.59
67 68 4.574599 AAACTGTCTACGTTTACCGACT 57.425 40.909 0.00 0.00 40.70 4.18
95 96 7.386573 GGGAAACACCAACGATAATGAAAATTT 59.613 33.333 0.00 0.00 41.20 1.82
105 106 2.235402 GGAGAGGGAAACACCAACGATA 59.765 50.000 0.00 0.00 41.20 2.92
106 107 1.003233 GGAGAGGGAAACACCAACGAT 59.997 52.381 0.00 0.00 41.20 3.73
280 282 5.830912 TGGGCATTTTCTATTTGATAAGCG 58.169 37.500 0.00 0.00 0.00 4.68
381 384 2.414612 GATCCTTGTATGGGTGGGGTA 58.585 52.381 0.00 0.00 0.00 3.69
397 401 3.499338 TGATGCATGGTTTATGGGATCC 58.501 45.455 2.46 1.92 37.26 3.36
478 489 2.417586 GCATTTCATTTCTTTGCTGGGC 59.582 45.455 0.00 0.00 0.00 5.36
482 493 6.523840 TGGTTTAGCATTTCATTTCTTTGCT 58.476 32.000 1.08 1.08 45.10 3.91
553 564 6.975197 TGCACTTCATTTTACAACGAAAATCA 59.025 30.769 0.00 0.00 36.99 2.57
594 605 6.890268 TGAATTTAGCTCCTGACTCTGTAGTA 59.110 38.462 0.00 0.00 35.56 1.82
606 617 7.349412 ACTAACTCGTATGAATTTAGCTCCT 57.651 36.000 10.81 0.00 0.00 3.69
620 631 8.487313 AATGCACATTAATCAACTAACTCGTA 57.513 30.769 0.00 0.00 0.00 3.43
622 633 8.817100 TCTAATGCACATTAATCAACTAACTCG 58.183 33.333 4.74 0.00 33.34 4.18
641 652 4.282195 ACCTAGGCTGTACTGATCTAATGC 59.718 45.833 9.30 0.00 0.00 3.56
654 665 3.181478 GCACGTAAATCTACCTAGGCTGT 60.181 47.826 9.30 0.00 0.00 4.40
656 667 3.028850 TGCACGTAAATCTACCTAGGCT 58.971 45.455 9.30 0.00 0.00 4.58
743 758 0.464554 GCCTGTAAGATCTGGTGGCC 60.465 60.000 14.62 0.00 34.07 5.36
744 759 0.464554 GGCCTGTAAGATCTGGTGGC 60.465 60.000 16.33 16.33 34.07 5.01
796 813 5.185249 TACTGTACCACTGTCTGAAGGATTC 59.815 44.000 0.00 0.00 37.26 2.52
826 843 2.658707 GGCGTCTTGTCTGTCACGC 61.659 63.158 6.75 6.75 44.51 5.34
898 915 2.122729 TGGGGAGTGAGTGAGGGG 59.877 66.667 0.00 0.00 0.00 4.79
932 949 1.546476 CTGGACTTCGCTCCAAGTAGT 59.454 52.381 0.00 0.00 39.97 2.73
933 950 1.737363 GCTGGACTTCGCTCCAAGTAG 60.737 57.143 0.00 0.00 39.97 2.57
934 951 0.246635 GCTGGACTTCGCTCCAAGTA 59.753 55.000 0.00 0.00 39.97 2.24
935 952 1.004440 GCTGGACTTCGCTCCAAGT 60.004 57.895 0.00 0.00 39.97 3.16
1324 1341 1.000607 TCTGGTACTCGAACACTGCAC 60.001 52.381 0.00 0.00 0.00 4.57
1746 1784 7.036132 AGGGGGAGGAATAAATTAACAGAGAAA 60.036 37.037 0.00 0.00 0.00 2.52
1858 2097 1.014044 CAACCATCGACCAGACACCG 61.014 60.000 0.00 0.00 0.00 4.94
1932 2176 6.028146 TCAATCAACAAATCATCAACCAGG 57.972 37.500 0.00 0.00 0.00 4.45
1982 2226 9.103048 GCGCACAAATACAATATAAGTACAATC 57.897 33.333 0.30 0.00 0.00 2.67
1983 2227 7.796660 CGCGCACAAATACAATATAAGTACAAT 59.203 33.333 8.75 0.00 0.00 2.71
1984 2228 7.120634 CGCGCACAAATACAATATAAGTACAA 58.879 34.615 8.75 0.00 0.00 2.41
1985 2229 6.641989 CGCGCACAAATACAATATAAGTACA 58.358 36.000 8.75 0.00 0.00 2.90
1990 2234 4.537936 TGCGCGCACAAATACAATATAA 57.462 36.364 33.09 0.00 0.00 0.98
2061 2341 2.086054 ACGAGAGCTTGCTTAACTGG 57.914 50.000 0.00 0.00 0.00 4.00
2124 2412 1.286849 GGCAAACCATACCCTACCCTT 59.713 52.381 0.00 0.00 35.26 3.95
2125 2413 0.924090 GGCAAACCATACCCTACCCT 59.076 55.000 0.00 0.00 35.26 4.34
2126 2414 0.626916 TGGCAAACCATACCCTACCC 59.373 55.000 0.00 0.00 42.67 3.69
2156 2444 3.996480 AGCAAAAGAGCGAAAGAGTAGT 58.004 40.909 0.00 0.00 40.15 2.73
2167 2456 6.588756 TCATCATCATCAAAAAGCAAAAGAGC 59.411 34.615 0.00 0.00 0.00 4.09
2240 2551 5.989777 ACGAATAAATACTGCATGGTCTACC 59.010 40.000 0.00 0.00 0.00 3.18
2270 2584 4.458989 GCAATCTGTATGTCTGTTTTCCCA 59.541 41.667 0.00 0.00 0.00 4.37
2443 2757 2.470057 GAGAGATCCACCCTCTCCTT 57.530 55.000 8.53 0.00 46.71 3.36
2524 2847 2.095161 TGTGCGGTGAGAAAACGTTTTT 60.095 40.909 25.86 15.95 0.00 1.94
2573 2896 4.697756 CGGGCCACGTCCACATGT 62.698 66.667 4.39 0.00 37.93 3.21
2597 2920 2.299326 AGCTCAAACTGGCAGGAATT 57.701 45.000 20.34 8.01 0.00 2.17
2626 2950 1.491670 CGCATCTACGCAGCATAGTT 58.508 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.