Multiple sequence alignment - TraesCS6B01G348400

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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 TraesCS6B01G348400 chr6B 100.000 2948 0 0 1 2948 613162225 613159278 0 5445
1 TraesCS6B01G348400 chr6B 96.557 1946 62 5 1 1941 306995911 306993966 0 3217
2 TraesCS6B01G348400 chr6B 98.037 1019 19 1 1930 2948 613189129 613188112 0 1770
3 TraesCS6B01G348400 chr6B 96.762 1019 30 2 1930 2948 306993653 306992638 0 1696
4 TraesCS6B01G348400 chrUn 97.260 1934 50 3 1 1932 275330183 275328251 0 3275
5 TraesCS6B01G348400 chrUn 96.860 1019 29 2 1930 2948 391007211 391008226 0 1701
6 TraesCS6B01G348400 chr4D 97.260 1934 50 3 1 1932 123299969 123301901 0 3275
7 TraesCS6B01G348400 chr4D 97.448 1019 24 2 1930 2948 123302224 123303240 0 1736
8 TraesCS6B01G348400 chr7D 97.209 1935 51 3 1 1932 203515555 203517489 0 3271
9 TraesCS6B01G348400 chr7D 97.154 1019 27 2 1930 2948 203517812 203518828 0 1720
10 TraesCS6B01G348400 chr1D 97.208 1934 51 3 1 1932 141313057 141311125 0 3269
11 TraesCS6B01G348400 chr7B 97.054 1935 52 4 1 1932 644467523 644469455 0 3253
12 TraesCS6B01G348400 chr7B 97.448 1019 23 2 1930 2948 644469778 644470793 0 1735
13 TraesCS6B01G348400 chr3A 97.001 1934 54 3 1 1932 633111333 633113264 0 3247
14 TraesCS6B01G348400 chr3A 96.958 1019 27 2 1930 2948 633113586 633114600 0 1707
15 TraesCS6B01G348400 chr1B 96.440 1938 61 8 1 1932 638700587 638698652 0 3190
16 TraesCS6B01G348400 chr4B 96.329 1934 67 3 1 1932 209077439 209075508 0 3175
17 TraesCS6B01G348400 chr7A 96.860 1019 29 2 1930 2948 60121231 60120216 0 1701
18 TraesCS6B01G348400 chr2B 96.565 1019 32 2 1930 2948 391110505 391109490 0 1685


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 TraesCS6B01G348400 chr6B 613159278 613162225 2947 True 5445.0 5445 100.0000 1 2948 1 chr6B.!!$R1 2947
1 TraesCS6B01G348400 chr6B 306992638 306995911 3273 True 2456.5 3217 96.6595 1 2948 2 chr6B.!!$R3 2947
2 TraesCS6B01G348400 chr6B 613188112 613189129 1017 True 1770.0 1770 98.0370 1930 2948 1 chr6B.!!$R2 1018
3 TraesCS6B01G348400 chrUn 275328251 275330183 1932 True 3275.0 3275 97.2600 1 1932 1 chrUn.!!$R1 1931
4 TraesCS6B01G348400 chrUn 391007211 391008226 1015 False 1701.0 1701 96.8600 1930 2948 1 chrUn.!!$F1 1018
5 TraesCS6B01G348400 chr4D 123299969 123303240 3271 False 2505.5 3275 97.3540 1 2948 2 chr4D.!!$F1 2947
6 TraesCS6B01G348400 chr7D 203515555 203518828 3273 False 2495.5 3271 97.1815 1 2948 2 chr7D.!!$F1 2947
7 TraesCS6B01G348400 chr1D 141311125 141313057 1932 True 3269.0 3269 97.2080 1 1932 1 chr1D.!!$R1 1931
8 TraesCS6B01G348400 chr7B 644467523 644470793 3270 False 2494.0 3253 97.2510 1 2948 2 chr7B.!!$F1 2947
9 TraesCS6B01G348400 chr3A 633111333 633114600 3267 False 2477.0 3247 96.9795 1 2948 2 chr3A.!!$F1 2947
10 TraesCS6B01G348400 chr1B 638698652 638700587 1935 True 3190.0 3190 96.4400 1 1932 1 chr1B.!!$R1 1931
11 TraesCS6B01G348400 chr4B 209075508 209077439 1931 True 3175.0 3175 96.3290 1 1932 1 chr4B.!!$R1 1931
12 TraesCS6B01G348400 chr7A 60120216 60121231 1015 True 1701.0 1701 96.8600 1930 2948 1 chr7A.!!$R1 1018
13 TraesCS6B01G348400 chr2B 391109490 391110505 1015 True 1685.0 1685 96.5650 1930 2948 1 chr2B.!!$R1 1018

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
309 312 0.036952 CCAGACACATCGCACTTCCT 60.037 55.0 0.0 0.0 0.00 3.36 F
314 317 0.171231 CACATCGCACTTCCTCTCGA 59.829 55.0 0.0 0.0 35.34 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1508 1.634459 TCCAGTAGACGACCTCTTCCT 59.366 52.381 0.0 0.0 0.00 3.36 R
2309 2649 1.262950 CGTGAGACTCTCGCCTCATAG 59.737 57.143 13.4 0.0 40.95 2.23 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
105 107 4.345859 TCCTTAAAGAGCCTTTCGTTCA 57.654 40.909 3.80 0.00 0.00 3.18
206 209 6.361768 AGAAAGAAGGGTCGAAGTTTAGAT 57.638 37.500 0.00 0.00 0.00 1.98
282 285 3.830744 ACCCGAATCCATTTACGATCA 57.169 42.857 0.00 0.00 0.00 2.92
309 312 0.036952 CCAGACACATCGCACTTCCT 60.037 55.000 0.00 0.00 0.00 3.36
314 317 0.171231 CACATCGCACTTCCTCTCGA 59.829 55.000 0.00 0.00 35.34 4.04
393 396 5.713025 CTGGTTTTTGGAATTCGACATCAT 58.287 37.500 0.00 0.00 0.00 2.45
589 593 5.453339 GGCAATATCTACCTACACAAGCTCA 60.453 44.000 0.00 0.00 0.00 4.26
636 640 3.499918 AGAAGCACGAAATTCCTCTTGTG 59.500 43.478 0.00 0.00 0.00 3.33
650 654 8.655935 ATTCCTCTTGTGGTGAAAATAAGATT 57.344 30.769 0.00 0.00 0.00 2.40
776 780 1.896220 AAGAGCATCCAACGCAAAGA 58.104 45.000 0.00 0.00 33.66 2.52
799 803 2.890945 ACCTTTCATTCCCTTGTTTCGG 59.109 45.455 0.00 0.00 0.00 4.30
922 935 3.655810 CTCGAGCCTCCTTTGCGCT 62.656 63.158 9.73 0.00 34.97 5.92
993 1007 9.620259 AATGGTAGAGAAGGCTTTAATAAGAAG 57.380 33.333 0.00 0.00 32.92 2.85
1022 1036 7.202011 GGCCATGAGAGACCTTCTTAAGTATTA 60.202 40.741 0.00 0.00 35.87 0.98
1041 1055 0.777446 ACAAAAGAAGGGGCCTGCTA 59.223 50.000 0.84 0.00 30.21 3.49
1104 1118 4.858680 GGCCTGGCCCGTAAGCTC 62.859 72.222 27.77 0.00 44.06 4.09
1158 1172 1.282817 TTTGTTACGCGCGATATGCT 58.717 45.000 39.36 16.04 43.27 3.79
1189 1203 3.253061 TGGGAATCGTGGGTGCCA 61.253 61.111 0.00 0.00 32.07 4.92
1263 1277 1.630878 CTGAACCTTTGGGTAGGCTCT 59.369 52.381 0.00 0.00 46.67 4.09
1393 1407 1.831736 AGCGTCTATGGGTAAAGCACT 59.168 47.619 0.00 0.00 0.00 4.40
1452 1466 3.660669 TCCATTCCAAGTTTAGGGACCTT 59.339 43.478 0.00 0.00 31.59 3.50
1481 1495 9.775539 TTATAGTATCCCTATCAAAGAGCTGAT 57.224 33.333 0.00 0.00 37.54 2.90
1494 1508 2.045524 GAGCTGATGAAGGGGATGAGA 58.954 52.381 0.00 0.00 0.00 3.27
1611 1625 0.035152 AGCACATCCGGCAAAGATCA 60.035 50.000 0.00 0.00 0.00 2.92
1689 1703 2.711922 GGCAGTCTCACGATCGGGT 61.712 63.158 18.47 0.00 0.00 5.28
1736 1750 0.767060 ACTCCCTTTGGTCGGAAGGT 60.767 55.000 2.57 0.00 41.70 3.50
1764 1779 3.256960 GGAAGGGGACACTGGGCA 61.257 66.667 0.00 0.00 0.00 5.36
1850 1865 2.228059 TCGGGATCGAGGTCTCATTAC 58.772 52.381 0.00 0.00 40.88 1.89
1876 1891 1.434513 AAGACCCAGGCCAATCCACA 61.435 55.000 5.01 0.00 37.29 4.17
1932 2272 1.135228 GTAAATTGGTTCGCGGGCATT 60.135 47.619 6.13 0.00 0.00 3.56
2151 2491 6.514376 GCGTCAGAAAAATAGAACCTTTCCAA 60.514 38.462 0.00 0.00 30.83 3.53
2196 2536 3.949031 GCGACTAGCTTCTACCCAG 57.051 57.895 0.00 0.00 44.04 4.45
2333 2673 2.168947 GGCGAGAGTCTCACGTACA 58.831 57.895 19.99 0.00 33.10 2.90
2603 2943 0.181587 TGGCCGGAAAGTGTTCTTGA 59.818 50.000 5.05 0.00 33.79 3.02
2771 3111 2.882927 TGCTCGTTCTGCGGTTATAT 57.117 45.000 0.00 0.00 41.72 0.86
2776 3116 4.684703 GCTCGTTCTGCGGTTATATGTAAT 59.315 41.667 0.00 0.00 41.72 1.89
2810 3150 7.527868 GCCTAATTTCTAGAATAGGGATGCAGA 60.528 40.741 24.27 1.91 39.78 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.366396 GGAAGTAGTCCCATCACTCTCA 58.634 50.000 0.00 0.00 41.10 3.27
206 209 2.089980 GGGTAGAACTACTGTGAGCGA 58.910 52.381 11.04 0.00 36.36 4.93
282 285 1.935300 GCGATGTGTCTGGAAACTCGT 60.935 52.381 11.35 0.00 0.00 4.18
393 396 3.311322 GTCGATGGTGTGAAAACACTTCA 59.689 43.478 8.73 0.52 40.28 3.02
589 593 3.565449 CGGATCCTCCCTATCTCCTGATT 60.565 52.174 10.75 0.00 31.63 2.57
650 654 6.319658 ACGACGACCTATTCTTAATAGAACCA 59.680 38.462 0.00 0.00 42.91 3.67
776 780 3.821033 CGAAACAAGGGAATGAAAGGTCT 59.179 43.478 0.00 0.00 0.00 3.85
843 855 4.211164 GGAAAACGAAAGGCATTTTCTTGG 59.789 41.667 0.00 0.00 42.47 3.61
845 857 4.377021 GGGAAAACGAAAGGCATTTTCTT 58.623 39.130 0.00 0.00 42.47 2.52
887 900 1.003233 CGAGGGCTTGTTAAGGAAGGT 59.997 52.381 0.00 0.00 0.00 3.50
993 1007 1.280421 AGAAGGTCTCTCATGGCCAAC 59.720 52.381 10.96 0.83 0.00 3.77
1022 1036 0.777446 TAGCAGGCCCCTTCTTTTGT 59.223 50.000 0.00 0.00 0.00 2.83
1041 1055 2.040884 TCCCCGCCCAGCTCTATT 60.041 61.111 0.00 0.00 0.00 1.73
1104 1118 0.901827 AATGGCTTTTAAAGGGGGCG 59.098 50.000 6.84 0.00 0.00 6.13
1137 1151 2.635444 GCATATCGCGCGTAACAAATT 58.365 42.857 30.98 7.94 0.00 1.82
1158 1172 3.376234 CGATTCCCAGTAGTAAGTCGTCA 59.624 47.826 0.00 0.00 0.00 4.35
1263 1277 2.025981 AGCTATGGTTGTTGATCCTGCA 60.026 45.455 0.00 0.00 0.00 4.41
1452 1466 7.956315 AGCTCTTTGATAGGGATACTATAACCA 59.044 37.037 0.00 0.00 42.43 3.67
1481 1495 2.628021 CCTCTTCCTCTCATCCCCTTCA 60.628 54.545 0.00 0.00 0.00 3.02
1494 1508 1.634459 TCCAGTAGACGACCTCTTCCT 59.366 52.381 0.00 0.00 0.00 3.36
1689 1703 7.453393 ACAATTTCTTCTTCAGGACACTCATA 58.547 34.615 0.00 0.00 0.00 2.15
1764 1779 2.706339 ATTCGCTGCTGAAAGATCCT 57.294 45.000 10.06 0.00 34.07 3.24
1850 1865 2.359975 GCCTGGGTCTTGTTCGGG 60.360 66.667 0.00 0.00 0.00 5.14
1898 1913 8.883731 CGAACCAATTTACTATGTCTCTTTCAT 58.116 33.333 0.00 0.00 0.00 2.57
1902 1917 5.291128 CGCGAACCAATTTACTATGTCTCTT 59.709 40.000 0.00 0.00 0.00 2.85
2151 2491 2.017559 GAAGCAGCGATCTACCGGGT 62.018 60.000 6.32 4.46 0.00 5.28
2196 2536 5.590259 TGATTCAAGGTAGCTTTAGCCATTC 59.410 40.000 3.96 0.00 43.38 2.67
2309 2649 1.262950 CGTGAGACTCTCGCCTCATAG 59.737 57.143 13.40 0.00 40.95 2.23
2603 2943 4.988029 ACTACCCGAGCTAATGATAGAGT 58.012 43.478 0.00 0.00 0.00 3.24
2771 3111 6.001449 AGAAATTAGGCTGGCTACATTACA 57.999 37.500 10.81 0.00 0.00 2.41
2776 3116 5.950544 TTCTAGAAATTAGGCTGGCTACA 57.049 39.130 10.81 3.31 0.00 2.74
2810 3150 1.402787 CACAAACAAAGCCCTCCTGT 58.597 50.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.