Multiple sequence alignment - TraesCS1A01G029700

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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 TraesCS1A01G029700 chr1A 100.000 2375 0 0 1 2375 13859172 13856798 0.000000e+00 4386
1 TraesCS1A01G029700 chr1D 92.214 2389 142 23 1 2375 11779256 11776898 0.000000e+00 3341
2 TraesCS1A01G029700 chr1B 90.543 1840 124 26 566 2375 17620693 17618874 0.000000e+00 2388
3 TraesCS1A01G029700 chr1B 77.723 404 38 24 97 480 17621092 17620721 1.440000e-47 200
4 TraesCS1A01G029700 chr5D 75.592 844 188 13 1001 1835 555660831 555659997 3.680000e-108 401
5 TraesCS1A01G029700 chr7D 75.030 833 180 24 1008 1829 11668055 11668870 6.240000e-96 361
6 TraesCS1A01G029700 chr4A 74.686 877 191 27 955 1820 726296702 726297558 6.240000e-96 361
7 TraesCS1A01G029700 chr5B 74.458 830 189 15 1010 1829 695618546 695619362 1.050000e-88 337


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 TraesCS1A01G029700 chr1A 13856798 13859172 2374 True 4386 4386 100.000 1 2375 1 chr1A.!!$R1 2374
1 TraesCS1A01G029700 chr1D 11776898 11779256 2358 True 3341 3341 92.214 1 2375 1 chr1D.!!$R1 2374
2 TraesCS1A01G029700 chr1B 17618874 17621092 2218 True 1294 2388 84.133 97 2375 2 chr1B.!!$R1 2278
3 TraesCS1A01G029700 chr5D 555659997 555660831 834 True 401 401 75.592 1001 1835 1 chr5D.!!$R1 834
4 TraesCS1A01G029700 chr7D 11668055 11668870 815 False 361 361 75.030 1008 1829 1 chr7D.!!$F1 821
5 TraesCS1A01G029700 chr4A 726296702 726297558 856 False 361 361 74.686 955 1820 1 chr4A.!!$F1 865
6 TraesCS1A01G029700 chr5B 695618546 695619362 816 False 337 337 74.458 1010 1829 1 chr5B.!!$F1 819

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
564 585 0.037697 CTAGTGTACAGTTGCCGCCA 60.038 55.0 8.85 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1693 2.174639 TGATAATGCCCCCGAATCTTGT 59.825 45.455 0.0 0.0 0.0 3.16 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
32 33 1.374252 GAAGGACGTGCACATCGGT 60.374 57.895 18.64 6.20 0.00 4.69
43 44 1.996292 CACATCGGTGGTACAGTCAG 58.004 55.000 0.00 0.00 41.80 3.51
54 55 3.055819 TGGTACAGTCAGGAAATGCTCTC 60.056 47.826 0.00 0.00 0.00 3.20
69 70 1.918467 CTCTCTTCATGCCTGGCCCA 61.918 60.000 17.53 0.00 0.00 5.36
79 80 1.133823 TGCCTGGCCCATACAAGTATG 60.134 52.381 17.53 12.20 41.86 2.39
94 95 9.494271 CATACAAGTATGATACTTAACTGGCAT 57.506 33.333 16.73 0.00 46.66 4.40
196 208 1.731424 GCTACGCGCAAACAGAGTAGA 60.731 52.381 17.09 0.00 42.13 2.59
283 301 4.144297 AGACAGCTGCTGTTTATTTTCCA 58.856 39.130 33.33 0.00 45.44 3.53
343 361 1.076332 CTTGGTTCGTTGACCCGATC 58.924 55.000 3.60 0.00 39.01 3.69
387 405 2.874701 GGCTTGTGGATATGCACTAGTG 59.125 50.000 29.07 18.93 0.00 2.74
390 408 5.116180 GCTTGTGGATATGCACTAGTGTTA 58.884 41.667 29.07 15.60 0.00 2.41
435 453 3.431912 GGTTGAATTTGGATGGCGAAAAC 59.568 43.478 0.00 0.00 0.00 2.43
475 493 5.242393 GGCTTACATACATGATTTCAGCCAT 59.758 40.000 16.50 0.00 37.48 4.40
525 545 2.483876 AGTCGATACATTGGCCATTCG 58.516 47.619 6.09 11.02 0.00 3.34
528 548 2.102420 TCGATACATTGGCCATTCGTCT 59.898 45.455 6.09 0.00 0.00 4.18
540 561 3.551863 GCCATTCGTCTCTGTCCTATCTG 60.552 52.174 0.00 0.00 0.00 2.90
546 567 3.317711 CGTCTCTGTCCTATCTGAATGCT 59.682 47.826 0.00 0.00 0.00 3.79
561 582 2.010145 ATGCTAGTGTACAGTTGCCG 57.990 50.000 27.02 8.92 32.73 5.69
564 585 0.037697 CTAGTGTACAGTTGCCGCCA 60.038 55.000 8.85 0.00 0.00 5.69
592 613 2.099141 TCGAGGTTTGAATCCAGCTG 57.901 50.000 6.78 6.78 0.00 4.24
752 776 1.390565 TACTGCTAACGAGGCTCTCC 58.609 55.000 13.50 0.00 0.00 3.71
863 887 1.375853 GCACATGCCAGCCATCGTTA 61.376 55.000 0.00 0.00 34.31 3.18
865 889 1.677576 CACATGCCAGCCATCGTTATT 59.322 47.619 0.00 0.00 29.71 1.40
897 924 3.788227 ATCTTGCAACTGGTCTGGTAA 57.212 42.857 0.00 0.00 0.00 2.85
941 968 1.694150 CTTGTCTGAGTTCTCCCCACA 59.306 52.381 0.00 0.00 0.00 4.17
1044 1076 4.717313 GGCACGTTGGGTCCCCTC 62.717 72.222 5.13 0.00 36.94 4.30
1172 1213 3.195825 GTCCAGAAGTACACCATGCTAGT 59.804 47.826 0.00 0.00 0.00 2.57
1260 1301 5.702670 AGATTGTGTCGACAAGTTCATTCAT 59.297 36.000 21.95 4.62 45.29 2.57
1295 1336 2.123428 GGCGCCATGGAAGCTTCAT 61.123 57.895 27.02 15.54 0.00 2.57
1362 1404 0.240945 GGCGTGGAATCACAACCAAG 59.759 55.000 0.00 0.00 43.79 3.61
1613 1662 4.444022 CCATTGTTGGTTTTGGTGGATTGA 60.444 41.667 0.00 0.00 38.30 2.57
1644 1693 2.816672 CTCTAGCGCATGAGGTCTATCA 59.183 50.000 11.47 0.00 0.00 2.15
1823 1873 4.460382 GCTGAGAGAGCTGCTAGAAGATAT 59.540 45.833 0.27 0.00 45.21 1.63
1874 1924 4.520078 CGCAAACGTAACATGTGTAGTTT 58.480 39.130 15.59 15.59 33.69 2.66
1875 1925 5.333187 CCGCAAACGTAACATGTGTAGTTTA 60.333 40.000 18.87 0.00 37.70 2.01
1923 1981 5.794687 TCCACTATTAATTTCGCACACAG 57.205 39.130 0.00 0.00 0.00 3.66
1928 1986 6.738200 CACTATTAATTTCGCACACAGTGAAG 59.262 38.462 7.81 0.15 46.51 3.02
1930 1988 5.940192 TTAATTTCGCACACAGTGAAGAT 57.060 34.783 7.81 0.00 46.51 2.40
1932 1990 3.607422 TTTCGCACACAGTGAAGATTG 57.393 42.857 7.81 0.00 46.51 2.67
1933 1991 0.867746 TCGCACACAGTGAAGATTGC 59.132 50.000 7.81 5.25 35.23 3.56
1944 2002 7.085746 CACAGTGAAGATTGCACAATATTTCA 58.914 34.615 14.15 14.15 38.70 2.69
1962 2020 4.699925 TTCACAGCCCTAACAGTACTTT 57.300 40.909 0.00 0.00 0.00 2.66
1963 2021 5.811796 TTCACAGCCCTAACAGTACTTTA 57.188 39.130 0.00 0.00 0.00 1.85
1964 2022 5.401531 TCACAGCCCTAACAGTACTTTAG 57.598 43.478 13.54 13.54 0.00 1.85
1992 2050 6.777091 ACATGGCTTGCATAATTGTAGGAATA 59.223 34.615 0.00 0.00 0.00 1.75
1994 2052 6.364701 TGGCTTGCATAATTGTAGGAATACT 58.635 36.000 0.00 0.00 0.00 2.12
2019 2077 2.819019 CCACACATGCACCATACTGAAA 59.181 45.455 0.00 0.00 0.00 2.69
2068 2126 7.698506 TGTACCTAAGATATTATAGCACGCT 57.301 36.000 0.00 0.00 0.00 5.07
2069 2127 7.535997 TGTACCTAAGATATTATAGCACGCTG 58.464 38.462 0.72 0.00 0.00 5.18
2142 2201 2.806244 CAGTCCACAGGTAAACCTTTCG 59.194 50.000 0.00 0.00 46.09 3.46
2211 2280 4.437682 TCCTTCAGTTCACCATTTCAGT 57.562 40.909 0.00 0.00 0.00 3.41
2219 2288 6.039270 TCAGTTCACCATTTCAGTTTAGTTGG 59.961 38.462 0.00 0.00 0.00 3.77
2226 2295 5.705441 CCATTTCAGTTTAGTTGGTCTGCTA 59.295 40.000 0.00 0.00 0.00 3.49
2235 2304 6.662414 TTAGTTGGTCTGCTATTTTGATCG 57.338 37.500 0.00 0.00 0.00 3.69
2249 2318 7.325821 GCTATTTTGATCGTTGTTTGTGATGAA 59.674 33.333 0.00 0.00 0.00 2.57
2315 2385 8.112183 TCTGCTATCCTCACTGATGATAATCTA 58.888 37.037 5.76 0.00 33.22 1.98
2332 2402 8.201464 TGATAATCTACGAACATGTTGTGGTAT 58.799 33.333 17.58 10.40 0.00 2.73
2343 2413 5.992829 ACATGTTGTGGTATCGTTTGTCTTA 59.007 36.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.351430 CTGTACCACCGATGTGCACG 61.351 60.000 13.13 0.00 41.35 5.34
32 33 2.906389 AGAGCATTTCCTGACTGTACCA 59.094 45.455 0.00 0.00 0.00 3.25
43 44 2.358267 CAGGCATGAAGAGAGCATTTCC 59.642 50.000 0.00 0.00 0.00 3.13
54 55 0.106569 TGTATGGGCCAGGCATGAAG 60.107 55.000 15.19 0.00 0.00 3.02
79 80 3.885297 ACCATGCATGCCAGTTAAGTATC 59.115 43.478 21.69 0.00 0.00 2.24
94 95 4.144297 AGAAGAAACAGCTAAACCATGCA 58.856 39.130 0.00 0.00 0.00 3.96
181 182 2.726066 GCACAATCTACTCTGTTTGCGC 60.726 50.000 0.00 0.00 0.00 6.09
196 208 0.526096 GATGCATTTCGGCGCACAAT 60.526 50.000 10.83 0.21 41.79 2.71
283 301 4.783764 GCCTTAGGCTGTTTTATGTTGT 57.216 40.909 17.16 0.00 46.69 3.32
387 405 8.198778 CCCTCTAGTCACCTTCTCTAAAATAAC 58.801 40.741 0.00 0.00 0.00 1.89
390 408 5.663556 CCCCTCTAGTCACCTTCTCTAAAAT 59.336 44.000 0.00 0.00 0.00 1.82
435 453 1.881602 GCCTCTGCTTGCCTTTCAG 59.118 57.895 0.00 0.00 33.53 3.02
467 485 8.688747 AAATTGGATTTTGTTTTATGGCTGAA 57.311 26.923 0.00 0.00 0.00 3.02
511 531 2.236146 ACAGAGACGAATGGCCAATGTA 59.764 45.455 10.96 0.00 0.00 2.29
517 537 1.112113 TAGGACAGAGACGAATGGCC 58.888 55.000 0.00 0.00 45.77 5.36
521 541 5.508825 GCATTCAGATAGGACAGAGACGAAT 60.509 44.000 0.00 0.00 0.00 3.34
525 545 4.935352 AGCATTCAGATAGGACAGAGAC 57.065 45.455 0.00 0.00 0.00 3.36
528 548 5.204292 ACACTAGCATTCAGATAGGACAGA 58.796 41.667 0.00 0.00 40.53 3.41
540 561 2.348666 CGGCAACTGTACACTAGCATTC 59.651 50.000 9.91 0.00 0.00 2.67
546 567 0.611200 ATGGCGGCAACTGTACACTA 59.389 50.000 18.31 0.00 0.00 2.74
561 582 3.938963 TCAAACCTCGATTAGTCAATGGC 59.061 43.478 0.00 0.00 0.00 4.40
564 585 6.414732 TGGATTCAAACCTCGATTAGTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
592 613 3.362401 CGCGAATCTCATACAAGCATCAC 60.362 47.826 0.00 0.00 0.00 3.06
656 677 5.238868 TCATCTCGATAGCCACTTGTACTAC 59.761 44.000 0.00 0.00 0.00 2.73
657 678 5.374071 TCATCTCGATAGCCACTTGTACTA 58.626 41.667 0.00 0.00 0.00 1.82
658 679 4.207955 TCATCTCGATAGCCACTTGTACT 58.792 43.478 0.00 0.00 0.00 2.73
752 776 1.691976 TGTCAGGTCACAACAGGTAGG 59.308 52.381 0.00 0.00 0.00 3.18
863 887 7.147846 CCAGTTGCAAGATTTACCTTGGATAAT 60.148 37.037 0.00 0.00 42.58 1.28
865 889 5.652014 CCAGTTGCAAGATTTACCTTGGATA 59.348 40.000 0.00 0.00 42.58 2.59
897 924 0.110486 AACACGGATGAAGGCCTTGT 59.890 50.000 26.25 11.58 39.29 3.16
899 926 0.322546 GGAACACGGATGAAGGCCTT 60.323 55.000 20.65 20.65 0.00 4.35
901 928 1.026718 CAGGAACACGGATGAAGGCC 61.027 60.000 0.00 0.00 0.00 5.19
902 929 1.648467 GCAGGAACACGGATGAAGGC 61.648 60.000 0.00 0.00 0.00 4.35
911 938 1.143305 CTCAGACAAGCAGGAACACG 58.857 55.000 0.00 0.00 0.00 4.49
941 968 3.761218 TCTTGTTTGTGTGTGTGATGGTT 59.239 39.130 0.00 0.00 0.00 3.67
1084 1116 2.852075 ACGGACCCCTTTCAGGCA 60.852 61.111 0.00 0.00 32.73 4.75
1172 1213 4.498241 CTTCACTTCGACATCTGGATCAA 58.502 43.478 0.00 0.00 0.00 2.57
1295 1336 2.483876 CAGTCTTGCGAAAGAAGTCCA 58.516 47.619 7.62 0.00 0.00 4.02
1319 1360 6.063461 GAGACCCAAGTGTCTTTAGACGGT 62.063 50.000 5.50 5.89 45.41 4.83
1362 1404 1.596727 GCGAGCCTTCAGATCATCAAC 59.403 52.381 0.00 0.00 0.00 3.18
1613 1662 2.543777 TGCGCTAGAGTTGTTTTCCT 57.456 45.000 9.73 0.00 0.00 3.36
1644 1693 2.174639 TGATAATGCCCCCGAATCTTGT 59.825 45.455 0.00 0.00 0.00 3.16
1816 1866 9.036671 GTAAAAGCTAAGTCACCTCATATCTTC 57.963 37.037 0.00 0.00 0.00 2.87
1823 1873 4.967084 TGGTAAAAGCTAAGTCACCTCA 57.033 40.909 0.00 0.00 0.00 3.86
1875 1925 9.686683 AAGCACTAAAGATACCAGAAATAATGT 57.313 29.630 0.00 0.00 0.00 2.71
1923 1981 6.034256 GCTGTGAAATATTGTGCAATCTTCAC 59.966 38.462 26.01 26.01 44.17 3.18
1928 1986 4.114794 GGGCTGTGAAATATTGTGCAATC 58.885 43.478 0.18 0.00 32.50 2.67
1930 1988 3.164268 AGGGCTGTGAAATATTGTGCAA 58.836 40.909 0.00 0.00 0.00 4.08
1932 1990 4.157656 TGTTAGGGCTGTGAAATATTGTGC 59.842 41.667 0.00 0.00 0.00 4.57
1933 1991 5.415701 ACTGTTAGGGCTGTGAAATATTGTG 59.584 40.000 0.00 0.00 0.00 3.33
1944 2002 3.055312 GGCTAAAGTACTGTTAGGGCTGT 60.055 47.826 18.38 0.00 0.00 4.40
1992 2050 2.356665 TGGTGCATGTGTGGTAAAGT 57.643 45.000 0.00 0.00 0.00 2.66
1994 2052 3.755905 CAGTATGGTGCATGTGTGGTAAA 59.244 43.478 0.00 0.00 0.00 2.01
2043 2101 8.191446 CAGCGTGCTATAATATCTTAGGTACAT 58.809 37.037 0.00 0.00 0.00 2.29
2194 2254 6.039270 CCAACTAAACTGAAATGGTGAACTGA 59.961 38.462 0.00 0.00 0.00 3.41
2195 2255 6.183360 ACCAACTAAACTGAAATGGTGAACTG 60.183 38.462 0.00 0.00 39.57 3.16
2211 2280 6.653320 ACGATCAAAATAGCAGACCAACTAAA 59.347 34.615 0.00 0.00 0.00 1.85
2219 2288 6.086765 CACAAACAACGATCAAAATAGCAGAC 59.913 38.462 0.00 0.00 0.00 3.51
2226 2295 8.417780 TTTTCATCACAAACAACGATCAAAAT 57.582 26.923 0.00 0.00 0.00 1.82
2260 2329 9.941325 AATTGAGTGGTTTAATGCATCATTTTA 57.059 25.926 0.00 0.00 35.54 1.52
2266 2335 8.437742 CAGAAAAATTGAGTGGTTTAATGCATC 58.562 33.333 0.00 0.00 0.00 3.91
2270 2339 7.951530 AGCAGAAAAATTGAGTGGTTTAATG 57.048 32.000 0.00 0.00 0.00 1.90
2315 2385 3.034721 ACGATACCACAACATGTTCGT 57.965 42.857 8.48 10.84 33.92 3.85


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

AutoCloner maintained by Alex Coulton.