Multiple sequence alignment - TraesCS7B01G205300

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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 TraesCS7B01G205300 chr7B 100.000 3296 0 0 1 3296 375766942 375763647 0 6087
1 TraesCS7B01G205300 chr5B 93.750 3296 204 2 1 3296 464748726 464752019 0 4944
2 TraesCS7B01G205300 chr5B 92.963 3297 229 3 1 3296 231885374 231888668 0 4800
3 TraesCS7B01G205300 chr2B 93.604 3299 203 8 1 3296 163954942 163951649 0 4916
4 TraesCS7B01G205300 chr2B 92.809 3296 232 5 1 3295 659452336 659449045 0 4769
5 TraesCS7B01G205300 chr2B 92.630 3297 235 7 1 3296 381088064 381091353 0 4735
6 TraesCS7B01G205300 chr6B 93.267 3297 214 8 1 3296 373832149 373828860 0 4852
7 TraesCS7B01G205300 chr6B 93.085 3297 225 3 1 3296 471401471 471404765 0 4822
8 TraesCS7B01G205300 chr4B 93.087 3298 224 4 1 3296 434146925 434150220 0 4824
9 TraesCS7B01G205300 chr1B 93.024 3297 221 9 1 3296 303748808 303745520 0 4806


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 TraesCS7B01G205300 chr7B 375763647 375766942 3295 True 6087 6087 100.000 1 3296 1 chr7B.!!$R1 3295
1 TraesCS7B01G205300 chr5B 464748726 464752019 3293 False 4944 4944 93.750 1 3296 1 chr5B.!!$F2 3295
2 TraesCS7B01G205300 chr5B 231885374 231888668 3294 False 4800 4800 92.963 1 3296 1 chr5B.!!$F1 3295
3 TraesCS7B01G205300 chr2B 163951649 163954942 3293 True 4916 4916 93.604 1 3296 1 chr2B.!!$R1 3295
4 TraesCS7B01G205300 chr2B 659449045 659452336 3291 True 4769 4769 92.809 1 3295 1 chr2B.!!$R2 3294
5 TraesCS7B01G205300 chr2B 381088064 381091353 3289 False 4735 4735 92.630 1 3296 1 chr2B.!!$F1 3295
6 TraesCS7B01G205300 chr6B 373828860 373832149 3289 True 4852 4852 93.267 1 3296 1 chr6B.!!$R1 3295
7 TraesCS7B01G205300 chr6B 471401471 471404765 3294 False 4822 4822 93.085 1 3296 1 chr6B.!!$F1 3295
8 TraesCS7B01G205300 chr4B 434146925 434150220 3295 False 4824 4824 93.087 1 3296 1 chr4B.!!$F1 3295
9 TraesCS7B01G205300 chr1B 303745520 303748808 3288 True 4806 4806 93.024 1 3296 1 chr1B.!!$R1 3295

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
62 63 0.106967 GGGAGTTCAATCTGGAGGGC 60.107 60.0 0.00 0.0 0.00 5.19 F
849 853 0.181350 GGAGTCCGGATCTGCCAAAT 59.819 55.0 7.81 0.0 35.94 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 1809 0.035630 AATCTGCAGGACTCCAGTGC 60.036 55.0 15.13 0.0 37.73 4.4 R
2381 2391 0.519961 GACATAAAAACGGCCGCACT 59.480 50.0 28.58 7.2 0.00 4.4 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
56 57 2.283298 CGGATGTGGGAGTTCAATCTG 58.717 52.381 0.00 0.00 0.00 2.90
62 63 0.106967 GGGAGTTCAATCTGGAGGGC 60.107 60.000 0.00 0.00 0.00 5.19
163 164 2.298158 GACACCATCGAGGATGCGGT 62.298 60.000 0.00 0.97 41.22 5.68
197 198 1.541233 CGCCTAGATGCCCAAGTAAGG 60.541 57.143 0.00 0.00 0.00 2.69
428 432 0.441533 CTTCACACACTGCGCATCTC 59.558 55.000 12.24 0.00 0.00 2.75
571 575 0.250989 AAAGAAAATGTCGCCGGGGA 60.251 50.000 18.63 18.63 0.00 4.81
679 683 2.416972 GGTACTGCGTTTCTCCGAGATT 60.417 50.000 0.00 0.00 0.00 2.40
697 701 5.634020 CGAGATTAATAACCAGGATTCGTCC 59.366 44.000 0.00 0.00 0.00 4.79
714 718 1.192146 TCCTTTGCAGTCCGGCTAGT 61.192 55.000 0.00 0.00 34.04 2.57
813 817 2.741985 CATGAAGCGGGCGACACA 60.742 61.111 0.00 0.00 0.00 3.72
849 853 0.181350 GGAGTCCGGATCTGCCAAAT 59.819 55.000 7.81 0.00 35.94 2.32
851 855 1.139853 GAGTCCGGATCTGCCAAATCT 59.860 52.381 7.81 0.00 35.94 2.40
861 865 3.772060 CTGCCAAATCTGGAAGCTAAC 57.228 47.619 0.00 0.00 46.92 2.34
866 870 3.120199 CCAAATCTGGAAGCTAACACGTG 60.120 47.826 15.48 15.48 46.92 4.49
875 879 4.382320 TAACACGTGAGCCGCCCC 62.382 66.667 25.01 0.00 41.42 5.80
919 924 1.764854 GGGGGCGATGAGAAGGGTA 60.765 63.158 0.00 0.00 0.00 3.69
925 930 1.067212 GCGATGAGAAGGGTACGACAT 59.933 52.381 0.00 0.00 0.00 3.06
1023 1028 2.846039 GCATGGTGCTCAAGAAGATG 57.154 50.000 0.00 0.00 40.96 2.90
1029 1034 3.262660 TGGTGCTCAAGAAGATGTCATCT 59.737 43.478 9.68 9.68 42.61 2.90
1052 1057 3.058224 GCTACAAGCGGTTTGAATGAAGT 60.058 43.478 11.67 0.00 39.21 3.01
1061 1066 5.731263 GCGGTTTGAATGAAGTATTTACGAC 59.269 40.000 0.00 0.00 0.00 4.34
1165 1173 3.331294 GGATAGTAGCCCCTGAGACTCTA 59.669 52.174 3.68 0.00 0.00 2.43
1210 1218 6.485830 ACGGGGGATCATATAGTAATGATG 57.514 41.667 4.16 0.16 44.69 3.07
1245 1253 1.538950 CGTAGGTATCTAAGGGTCCGC 59.461 57.143 0.00 0.00 0.00 5.54
1272 1280 1.133513 ACCAGTCCATTGAAGTTGCCA 60.134 47.619 0.00 0.00 0.00 4.92
1276 1284 1.340889 GTCCATTGAAGTTGCCAAGCA 59.659 47.619 0.00 0.00 36.47 3.91
1320 1328 2.598632 GCCGATATCACGCTGGTGC 61.599 63.158 3.12 0.00 44.03 5.01
1370 1378 7.878127 GGTATGTGCTCTGCTTTCCTTATTATA 59.122 37.037 0.00 0.00 0.00 0.98
1514 1522 2.499303 AATGCGGCTGCCCTAAAGGT 62.499 55.000 16.57 0.00 41.78 3.50
1544 1552 0.250234 TTGAGAGCCGAACAGGATGG 59.750 55.000 0.00 0.00 39.82 3.51
1735 1744 2.570415 TCAACAGGCCGGTAAAATCA 57.430 45.000 9.60 0.00 0.00 2.57
1849 1858 2.163815 GACTTGGCGAAGAGTACAGCTA 59.836 50.000 16.00 0.00 32.98 3.32
1884 1893 6.595716 AGTTTTTCGAGGATCAAGGTGATAAG 59.404 38.462 0.00 0.00 37.20 1.73
1906 1915 1.902938 AGTGGAGAAGCTTTTCTGGC 58.097 50.000 15.87 7.25 0.00 4.85
1923 1932 1.669999 GGCCGCAATTCAATGCTCCT 61.670 55.000 0.00 0.00 44.21 3.69
2049 2059 2.612672 GCCCAAGCCGAATAGTTACTTC 59.387 50.000 0.00 0.00 0.00 3.01
2181 2191 2.158564 AGATATGGAGGCCACCATTGTG 60.159 50.000 35.52 0.00 47.00 3.33
2270 2280 0.179056 TGCTTAATAGGGGCGCAGTC 60.179 55.000 10.83 0.00 0.00 3.51
2284 2294 1.363744 GCAGTCCTCGAAGAATGTGG 58.636 55.000 12.58 0.00 34.41 4.17
2286 2296 2.872038 GCAGTCCTCGAAGAATGTGGTT 60.872 50.000 12.58 0.00 34.41 3.67
2311 2321 5.167845 TCGAGTGACAAATCGAATCATTGA 58.832 37.500 10.65 0.00 44.36 2.57
2381 2391 5.652014 CCTGAAAGTATTATTTGTGCCTCCA 59.348 40.000 0.00 0.00 0.00 3.86
2631 2641 2.756760 CCTGGTACTTTTGCATGCATCT 59.243 45.455 23.37 6.68 0.00 2.90
2694 2704 5.601662 TCGTTAATGCAGAGGAATCCTAAG 58.398 41.667 0.00 0.00 31.76 2.18
2733 2743 1.754803 AGTGGTTGAACAGTCTCACGA 59.245 47.619 0.00 0.00 0.00 4.35
2745 2755 4.642437 ACAGTCTCACGATGTATCATGACT 59.358 41.667 0.00 0.00 34.38 3.41
2746 2756 5.823045 ACAGTCTCACGATGTATCATGACTA 59.177 40.000 0.00 0.00 33.04 2.59
2774 2784 6.551227 AGTTTTTGGCTTTCTCTATTGAGGTT 59.449 34.615 4.29 0.00 40.58 3.50
2777 2787 5.505181 TGGCTTTCTCTATTGAGGTTCTT 57.495 39.130 4.29 0.00 40.58 2.52
2859 2869 1.232621 GGAACGTAAGGCGGCAAACT 61.233 55.000 13.08 0.00 46.52 2.66
2936 2946 2.660258 AAGGCCAAACTCGTGACGCT 62.660 55.000 5.01 0.00 0.00 5.07
2950 2960 1.068895 TGACGCTAAACACTCCCGAAA 59.931 47.619 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.761702 TAATAGTCCGTGGGCCCTCC 60.762 60.000 25.70 12.90 0.00 4.30
62 63 2.981859 AGTGCTTAATAGTCCGTGGG 57.018 50.000 0.00 0.00 0.00 4.61
163 164 1.069204 CTAGGCGATTGCAGCTTAGGA 59.931 52.381 7.38 0.00 45.35 2.94
197 198 4.096833 ACAAAGTGTCCGGTTTTAAGGTTC 59.903 41.667 0.00 0.00 0.00 3.62
238 242 5.418840 GGCCATGGAGAGTTTTCAGAATAAA 59.581 40.000 18.40 0.00 0.00 1.40
428 432 2.045340 AAGCAATTCCCCCGGTCG 60.045 61.111 0.00 0.00 0.00 4.79
465 469 4.872574 TCGGATTCCCCTCCCCGG 62.873 72.222 0.00 0.00 42.03 5.73
598 602 2.028484 CATTGGCGGGCATGATGC 59.972 61.111 9.33 9.33 44.08 3.91
697 701 1.927895 CTACTAGCCGGACTGCAAAG 58.072 55.000 5.05 0.00 0.00 2.77
714 718 4.945246 ACGAACTCTGTTGAGAAAAGCTA 58.055 39.130 0.00 0.00 42.73 3.32
813 817 0.039764 TCCTCCGTGATGACACCTCT 59.960 55.000 0.00 0.00 43.34 3.69
849 853 1.336887 GCTCACGTGTTAGCTTCCAGA 60.337 52.381 19.03 0.00 35.80 3.86
851 855 0.320421 GGCTCACGTGTTAGCTTCCA 60.320 55.000 23.59 0.00 38.80 3.53
925 930 0.681887 TCCGGCCAGACATCGAACTA 60.682 55.000 2.24 0.00 0.00 2.24
1023 1028 1.726853 AACCGCTTGTAGCAGATGAC 58.273 50.000 0.00 0.00 42.58 3.06
1029 1034 2.499197 TCATTCAAACCGCTTGTAGCA 58.501 42.857 0.00 0.00 42.58 3.49
1052 1057 2.693591 CCTCTGAGCAGGGTCGTAAATA 59.306 50.000 0.00 0.00 0.00 1.40
1061 1066 0.392729 CTCAAAGCCTCTGAGCAGGG 60.393 60.000 0.00 0.00 34.32 4.45
1245 1253 1.746615 CAATGGACTGGTCGGCTGG 60.747 63.158 0.00 0.00 0.00 4.85
1272 1280 0.393537 CCGATCTGCCTCCTTTGCTT 60.394 55.000 0.00 0.00 0.00 3.91
1276 1284 1.799933 AGATCCGATCTGCCTCCTTT 58.200 50.000 10.23 0.00 38.44 3.11
1320 1328 3.175240 CTCGTTCAGCCGCTCGTG 61.175 66.667 0.00 0.00 0.00 4.35
1450 1458 3.056328 GGCAAGTTCCGCCCTCAC 61.056 66.667 0.00 0.00 44.22 3.51
1514 1522 0.392998 GGCTCTCAATTCTTCGGCCA 60.393 55.000 2.24 0.00 38.16 5.36
1680 1688 2.579201 CTGACCTCGGTCCGCATT 59.421 61.111 13.22 0.00 43.97 3.56
1800 1809 0.035630 AATCTGCAGGACTCCAGTGC 60.036 55.000 15.13 0.00 37.73 4.40
1802 1811 0.534412 CGAATCTGCAGGACTCCAGT 59.466 55.000 15.13 0.00 0.00 4.00
1819 1828 2.202690 CGCCAAGTCCGCATACGA 60.203 61.111 0.00 0.00 43.93 3.43
1849 1858 2.288395 CCTCGAAAAACTTGGCTGCATT 60.288 45.455 0.50 0.00 0.00 3.56
1884 1893 2.816672 CCAGAAAAGCTTCTCCACTTCC 59.183 50.000 0.00 0.00 40.05 3.46
1978 1988 2.568090 CATTGCAAGCCCGGACAC 59.432 61.111 0.73 0.00 0.00 3.67
2038 2048 4.391155 TGCACCAAACCGAAGTAACTATT 58.609 39.130 0.00 0.00 0.00 1.73
2049 2059 1.068434 AGGAATTGTTGCACCAAACCG 59.932 47.619 0.00 0.00 33.26 4.44
2085 2095 1.337071 GACCTTCTCATGGCGTCGATA 59.663 52.381 0.00 0.00 0.00 2.92
2270 2280 3.064207 TCGAAAACCACATTCTTCGAGG 58.936 45.455 1.91 0.00 43.29 4.63
2334 2344 5.123344 GGCACAAAGTATAAATATAGCCCCG 59.877 44.000 0.00 0.00 32.50 5.73
2336 2346 6.940298 TCAGGCACAAAGTATAAATATAGCCC 59.060 38.462 0.00 0.00 39.15 5.19
2381 2391 0.519961 GACATAAAAACGGCCGCACT 59.480 50.000 28.58 7.20 0.00 4.40
2631 2641 2.036089 TGTACATATGCGCCCGTATTCA 59.964 45.455 4.18 0.00 0.00 2.57
2666 2676 1.906574 TCCTCTGCATTAACGAAGGGT 59.093 47.619 0.00 0.00 0.00 4.34
2694 2704 2.426381 ACTCGAAGACTTACCGGAATCC 59.574 50.000 9.46 0.00 0.00 3.01
2733 2743 7.776969 AGCCAAAAACTGATAGTCATGATACAT 59.223 33.333 0.00 0.00 0.00 2.29
2745 2755 8.862325 TCAATAGAGAAAGCCAAAAACTGATA 57.138 30.769 0.00 0.00 0.00 2.15
2746 2756 7.094032 CCTCAATAGAGAAAGCCAAAAACTGAT 60.094 37.037 0.00 0.00 44.98 2.90
2774 2784 2.370849 GCCCTGGTTATTCCGGATAAGA 59.629 50.000 4.15 0.00 45.09 2.10
2777 2787 1.418637 GTGCCCTGGTTATTCCGGATA 59.581 52.381 4.15 0.00 45.09 2.59
2859 2869 4.344865 GGTTTGCCCGGCTCCTGA 62.345 66.667 11.61 0.00 0.00 3.86
2958 2968 5.951747 TCAGCCCATTTTCTGCTATAAAGTT 59.048 36.000 0.00 0.00 33.16 2.66


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

AutoCloner maintained by Alex Coulton.