Multiple sequence alignment - TraesCS2A01G231400

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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 TraesCS2A01G231400 chr2A 100.000 2780 0 0 1 2780 271881036 271878257 0 5134
1 TraesCS2A01G231400 chr2A 93.221 2788 174 11 1 2780 418163497 418166277 0 4087
2 TraesCS2A01G231400 chr7A 93.963 2783 160 7 1 2780 197223329 197226106 0 4202
3 TraesCS2A01G231400 chr7A 93.214 2785 173 14 1 2780 135768149 135770922 0 4082
4 TraesCS2A01G231400 chr3A 93.281 2783 182 5 1 2780 471347047 471344267 0 4098
5 TraesCS2A01G231400 chr3A 93.070 2785 177 13 1 2780 485718257 485715484 0 4060
6 TraesCS2A01G231400 chr5A 93.070 2785 180 12 1 2780 231569251 231572027 0 4061
7 TraesCS2A01G231400 chr5A 92.977 2791 173 17 1 2780 455061436 455064214 0 4047
8 TraesCS2A01G231400 chr5A 92.890 2785 184 13 1 2780 331144615 331147390 0 4034
9 TraesCS2A01G231400 chr4A 93.003 2787 184 9 1 2780 561428546 561431328 0 4056


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 TraesCS2A01G231400 chr2A 271878257 271881036 2779 True 5134 5134 100.000 1 2780 1 chr2A.!!$R1 2779
1 TraesCS2A01G231400 chr2A 418163497 418166277 2780 False 4087 4087 93.221 1 2780 1 chr2A.!!$F1 2779
2 TraesCS2A01G231400 chr7A 197223329 197226106 2777 False 4202 4202 93.963 1 2780 1 chr7A.!!$F2 2779
3 TraesCS2A01G231400 chr7A 135768149 135770922 2773 False 4082 4082 93.214 1 2780 1 chr7A.!!$F1 2779
4 TraesCS2A01G231400 chr3A 471344267 471347047 2780 True 4098 4098 93.281 1 2780 1 chr3A.!!$R1 2779
5 TraesCS2A01G231400 chr3A 485715484 485718257 2773 True 4060 4060 93.070 1 2780 1 chr3A.!!$R2 2779
6 TraesCS2A01G231400 chr5A 231569251 231572027 2776 False 4061 4061 93.070 1 2780 1 chr5A.!!$F1 2779
7 TraesCS2A01G231400 chr5A 455061436 455064214 2778 False 4047 4047 92.977 1 2780 1 chr5A.!!$F3 2779
8 TraesCS2A01G231400 chr5A 331144615 331147390 2775 False 4034 4034 92.890 1 2780 1 chr5A.!!$F2 2779
9 TraesCS2A01G231400 chr4A 561428546 561431328 2782 False 4056 4056 93.003 1 2780 1 chr4A.!!$F1 2779

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
929 942 0.452184 CGCTGACTGTAGGACACGAT 59.548 55.0 0.0 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1952 0.106015 TCTCGGAGGCATCTGATGGA 60.106 55.0 18.6 2.56 40.12 3.41 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
40 41 5.734855 TTATTCATGCTAGAAACTTCCGC 57.265 39.130 0.00 0.00 0.00 5.54
190 191 5.959618 TCAGAAAGACTGTGTCTCGAATA 57.040 39.130 0.42 0.00 42.59 1.75
230 231 2.484770 CGAGTCTTGTGGGGAAAAGTGA 60.485 50.000 0.00 0.00 0.00 3.41
310 312 6.351371 GGACATCTTGAGTATCTGGTTCTTGA 60.351 42.308 0.00 0.00 34.92 3.02
340 342 9.713713 ATCATGATTGATCTCATCACTCTTAAG 57.286 33.333 1.18 0.00 38.18 1.85
570 578 3.376859 TGTTACTTTGCCAGCATATTCCG 59.623 43.478 0.00 0.00 0.00 4.30
585 593 2.981977 TTCCGTGTGCTGACCCGTTC 62.982 60.000 0.00 0.00 0.00 3.95
649 661 0.535335 GGAGCCATAGGTCGTTGTCA 59.465 55.000 0.00 0.00 41.62 3.58
678 690 2.236146 AGTGATGCCGTTGGAGTTGATA 59.764 45.455 0.00 0.00 0.00 2.15
703 715 4.003648 CTCACGTTATCTTCCAAGCCTTT 58.996 43.478 0.00 0.00 0.00 3.11
714 726 3.745799 TCCAAGCCTTTCGTTGTTATCA 58.254 40.909 0.00 0.00 0.00 2.15
877 890 3.854666 CACAGAGATCGGACTGTTTGAT 58.145 45.455 16.32 0.00 43.52 2.57
880 893 4.248859 CAGAGATCGGACTGTTTGATGTT 58.751 43.478 8.64 0.00 0.00 2.71
890 903 3.498397 ACTGTTTGATGTTTGGTCGCTAG 59.502 43.478 0.00 0.00 0.00 3.42
929 942 0.452184 CGCTGACTGTAGGACACGAT 59.548 55.000 0.00 0.00 0.00 3.73
943 957 5.978814 AGGACACGATCACTAAGCTAAAAT 58.021 37.500 0.00 0.00 0.00 1.82
946 960 5.116882 ACACGATCACTAAGCTAAAATCCC 58.883 41.667 0.00 0.00 0.00 3.85
959 973 5.071115 AGCTAAAATCCCAGATCACTACTCC 59.929 44.000 0.00 0.00 0.00 3.85
968 982 4.280677 CCAGATCACTACTCCCTTCTCATC 59.719 50.000 0.00 0.00 0.00 2.92
976 990 2.314549 ACTCCCTTCTCATCTCTGACCT 59.685 50.000 0.00 0.00 0.00 3.85
985 1000 5.132502 TCTCATCTCTGACCTCTCTTCATC 58.867 45.833 0.00 0.00 0.00 2.92
1030 1045 2.543653 GCGAGGAACAAGTTTGCACAAT 60.544 45.455 0.00 0.00 0.00 2.71
1033 1048 2.948979 AGGAACAAGTTTGCACAATCGA 59.051 40.909 0.00 0.00 0.00 3.59
1121 1137 1.114722 TTCACCGGGACCTACAACGT 61.115 55.000 6.32 0.00 0.00 3.99
1289 1305 5.385198 ACACATTGGAGAAGTTTACCACAT 58.615 37.500 2.18 0.00 33.20 3.21
1330 1346 2.033448 AGATTTGTGGGCGCCGAA 59.967 55.556 22.54 12.84 0.00 4.30
1335 1351 2.136196 TTTGTGGGCGCCGAAATGAC 62.136 55.000 22.54 10.14 0.00 3.06
1383 1399 6.714356 GGAAGGATAGATCTATTGCAGCTTTT 59.286 38.462 16.37 3.43 0.00 2.27
1410 1426 2.414161 GGAGTTAAACCAGCACATTCGC 60.414 50.000 0.00 0.00 0.00 4.70
1542 1558 6.380274 AGGAAATCATCGTACTAGTGGAGAAA 59.620 38.462 5.39 0.00 0.00 2.52
1567 1583 1.412710 ACGACCTGACAAGAAAGCTGA 59.587 47.619 0.00 0.00 0.00 4.26
1636 1652 3.762823 CACCTACCCGGAGAACTATATCC 59.237 52.174 0.73 0.00 36.31 2.59
1889 1908 5.714333 TCATGTGCATATGGGTAGTGTTTTT 59.286 36.000 21.57 0.00 0.00 1.94
1918 1938 6.502074 AGACCCCATTCTACTCTATTTTCC 57.498 41.667 0.00 0.00 0.00 3.13
1923 1943 6.241645 CCCATTCTACTCTATTTTCCCATCC 58.758 44.000 0.00 0.00 0.00 3.51
1976 1996 3.119029 CGACAATGGATTTGCTTTCCCAT 60.119 43.478 0.00 0.00 40.84 4.00
2042 2062 7.124901 TGCAGATTCTAGTCTAGAACCAGAATT 59.875 37.037 21.92 6.87 43.58 2.17
2068 2088 6.052360 GGGGAACAACAACAATAACAACAAT 58.948 36.000 0.00 0.00 0.00 2.71
2086 2109 4.596585 CCACCACCACCACCACCC 62.597 72.222 0.00 0.00 0.00 4.61
2297 2320 2.119495 ACACTGTCACCTATCCCATCC 58.881 52.381 0.00 0.00 0.00 3.51
2332 2355 1.813178 GACCAGTTTTAGCAGGCCTTC 59.187 52.381 0.00 0.00 0.00 3.46
2416 2439 1.407656 AAGGAGGACGCACTGTTGGA 61.408 55.000 0.00 0.00 0.00 3.53
2419 2442 0.531974 GAGGACGCACTGTTGGACAA 60.532 55.000 0.00 0.00 0.00 3.18
2424 2447 1.468520 ACGCACTGTTGGACAATATGC 59.531 47.619 7.60 7.60 31.81 3.14
2545 2569 1.533625 TGCAGTTGATGGTAGCAACC 58.466 50.000 0.00 0.00 45.05 3.77
2561 2585 7.982224 GGTAGCAACCTTTAATAACTACCAAG 58.018 38.462 10.60 0.00 44.84 3.61
2649 2673 7.133133 AGTATGGACACGGGAAGTATAATTT 57.867 36.000 0.00 0.00 0.00 1.82
2759 2788 1.748879 CACAACCATAGTGGCCCCG 60.749 63.158 0.00 0.00 42.67 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 2.501723 ACAACCCACTACATCTGCTAGG 59.498 50.000 0.00 0.00 0.00 3.02
230 231 0.471617 ACACTCTGCAGAGGTTTGCT 59.528 50.000 39.42 20.43 46.13 3.91
547 555 4.036734 CGGAATATGCTGGCAAAGTAACAT 59.963 41.667 0.00 0.00 0.00 2.71
585 593 3.055719 ATGAACGTTGCAGCCCGG 61.056 61.111 5.00 0.00 0.00 5.73
649 661 2.079158 CAACGGCATCACTGAGTGAAT 58.921 47.619 20.26 5.59 45.96 2.57
703 715 6.119536 AGGCCATCTAAATTGATAACAACGA 58.880 36.000 5.01 0.00 38.90 3.85
744 756 8.495949 TCGAATGTCTCAAAAGAGAACATAAAC 58.504 33.333 0.00 0.93 32.39 2.01
877 890 2.301870 ACCATCTTCTAGCGACCAAACA 59.698 45.455 0.00 0.00 0.00 2.83
880 893 3.958147 TGATACCATCTTCTAGCGACCAA 59.042 43.478 0.00 0.00 0.00 3.67
890 903 3.119291 CGTGTGCTCTGATACCATCTTC 58.881 50.000 0.00 0.00 0.00 2.87
929 942 6.156949 AGTGATCTGGGATTTTAGCTTAGTGA 59.843 38.462 0.00 0.00 0.00 3.41
943 957 2.587777 AGAAGGGAGTAGTGATCTGGGA 59.412 50.000 0.00 0.00 0.00 4.37
946 960 5.139727 AGATGAGAAGGGAGTAGTGATCTG 58.860 45.833 0.00 0.00 0.00 2.90
959 973 3.902218 AGAGAGGTCAGAGATGAGAAGG 58.098 50.000 0.00 0.00 0.00 3.46
968 982 6.122277 AGTAGAAGATGAAGAGAGGTCAGAG 58.878 44.000 0.00 0.00 0.00 3.35
976 990 9.130661 CATCCTAAAGAGTAGAAGATGAAGAGA 57.869 37.037 0.00 0.00 33.16 3.10
985 1000 3.637229 TCCGCCATCCTAAAGAGTAGAAG 59.363 47.826 0.00 0.00 0.00 2.85
1030 1045 3.138304 CAAAGGGTGTGTCTTCATTCGA 58.862 45.455 0.00 0.00 0.00 3.71
1033 1048 3.222603 GTCCAAAGGGTGTGTCTTCATT 58.777 45.455 0.00 0.00 34.93 2.57
1121 1137 3.399330 CGCTCCTCTTTTGGTAAAGTGA 58.601 45.455 0.00 0.00 41.25 3.41
1268 1284 4.766891 CCATGTGGTAAACTTCTCCAATGT 59.233 41.667 0.00 0.00 32.82 2.71
1289 1305 8.010697 TCTGGTAAATAGTATCCTTGAGATCCA 58.989 37.037 0.00 0.00 36.33 3.41
1330 1346 4.583489 GCTGATCATCTTCCATTGGTCATT 59.417 41.667 1.86 0.00 32.80 2.57
1335 1351 2.621998 GGTGCTGATCATCTTCCATTGG 59.378 50.000 0.00 0.00 0.00 3.16
1383 1399 3.585289 TGTGCTGGTTTAACTCCTGGATA 59.415 43.478 0.00 0.00 0.00 2.59
1410 1426 1.153289 CATCTGGTTCTCCTGGCGG 60.153 63.158 0.00 0.00 34.13 6.13
1542 1558 3.251004 GCTTTCTTGTCAGGTCGTCATTT 59.749 43.478 0.00 0.00 0.00 2.32
1587 1603 0.907486 CATCTTCTCCTCCTGGTGCA 59.093 55.000 0.00 0.00 34.23 4.57
1636 1652 0.247735 GAGTCGGTGTCGTCGATGAG 60.248 60.000 7.79 0.00 38.93 2.90
1889 1908 2.179424 GAGTAGAATGGGGTCTAGGGGA 59.821 54.545 0.00 0.00 30.70 4.81
1918 1938 6.072064 GCATCTGATGGATTTAGAAAGGATGG 60.072 42.308 18.60 0.00 31.27 3.51
1923 1943 5.472820 GGAGGCATCTGATGGATTTAGAAAG 59.527 44.000 18.60 0.00 31.27 2.62
1932 1952 0.106015 TCTCGGAGGCATCTGATGGA 60.106 55.000 18.60 2.56 40.12 3.41
1976 1996 2.025155 GATCAACTAGGTGAGCTCCGA 58.975 52.381 18.73 0.00 31.14 4.55
2042 2062 5.892119 TGTTGTTATTGTTGTTGTTCCCCTA 59.108 36.000 0.00 0.00 0.00 3.53
2068 2088 3.494254 GGTGGTGGTGGTGGTGGA 61.494 66.667 0.00 0.00 0.00 4.02
2086 2109 2.225068 ATCGGGCTAAGTGATCAACG 57.775 50.000 0.00 0.00 0.00 4.10
2297 2320 2.224523 ACTGGTCCCATGTAACAGTGTG 60.225 50.000 13.58 0.00 40.56 3.82
2332 2355 1.153188 TGATACATGGGCAGTGCGG 60.153 57.895 9.45 1.01 0.00 5.69
2363 2386 2.550830 AACTCACGCTTCTTCATGGT 57.449 45.000 0.00 0.00 0.00 3.55
2416 2439 4.450976 TGCTAAAGTCATCCGCATATTGT 58.549 39.130 0.00 0.00 0.00 2.71
2419 2442 3.499918 GCTTGCTAAAGTCATCCGCATAT 59.500 43.478 0.00 0.00 35.69 1.78
2424 2447 2.541762 GCTAGCTTGCTAAAGTCATCCG 59.458 50.000 13.17 0.00 35.69 4.18
2561 2585 5.767665 TCATGAGAGCTCTATCTACCAACTC 59.232 44.000 18.25 0.00 0.00 3.01
2649 2673 0.905357 GGGTCTCTGCTAAGCTCCAA 59.095 55.000 0.00 0.00 0.00 3.53
2729 2758 0.109532 TGGTTGTGCGAAATCCCTCA 59.890 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.