Multiple sequence alignment - TraesCS6A01G185200

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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 TraesCS6A01G185200 chr6A 100.000 2282 0 0 1 2282 216935639 216933358 0.000000e+00 4215.0
1 TraesCS6A01G185200 chr6A 93.103 87 6 0 2195 2281 258045900 258045986 6.620000e-26 128.0
2 TraesCS6A01G185200 chr6A 86.869 99 4 8 2185 2281 216555604 216555695 4.010000e-18 102.0
3 TraesCS6A01G185200 chr6A 90.789 76 7 0 2206 2281 399944038 399943963 4.010000e-18 102.0
4 TraesCS6A01G185200 chr2A 94.989 2215 98 7 1 2203 352651378 352653591 0.000000e+00 3463.0
5 TraesCS6A01G185200 chr2A 94.851 2214 101 7 1 2203 352643368 352645579 0.000000e+00 3445.0
6 TraesCS6A01G185200 chr2A 86.018 987 77 32 1207 2180 261452881 261451943 0.000000e+00 1002.0
7 TraesCS6A01G185200 chr2A 89.390 754 58 16 1207 1957 604016772 604017506 0.000000e+00 929.0
8 TraesCS6A01G185200 chr2A 80.764 733 76 34 1496 2208 271816237 271815550 1.560000e-141 512.0
9 TraesCS6A01G185200 chr2A 100.000 65 0 0 2218 2282 352645722 352645786 1.110000e-23 121.0
10 TraesCS6A01G185200 chr4A 94.357 2215 85 10 1 2203 85922175 85924361 0.000000e+00 3362.0
11 TraesCS6A01G185200 chr4A 94.134 2216 89 11 1 2203 85954388 85956575 0.000000e+00 3334.0
12 TraesCS6A01G185200 chr4A 86.466 532 52 14 1688 2203 374723994 374724521 1.180000e-157 566.0
13 TraesCS6A01G185200 chr4A 92.072 391 22 4 1821 2203 409180869 409181258 1.990000e-150 542.0
14 TraesCS6A01G185200 chr4A 100.000 65 0 0 2218 2282 85956718 85956782 1.110000e-23 121.0
15 TraesCS6A01G185200 chr4A 100.000 63 0 0 2218 2280 380749710 380749648 1.430000e-22 117.0
16 TraesCS6A01G185200 chr4A 92.105 76 4 2 2206 2280 443125811 443125737 3.100000e-19 106.0
17 TraesCS6A01G185200 chr5A 91.953 2212 128 24 1 2197 268814516 268812340 0.000000e+00 3053.0
18 TraesCS6A01G185200 chr5A 91.776 2213 131 24 1 2197 268822490 268820313 0.000000e+00 3031.0
19 TraesCS6A01G185200 chr5A 89.787 656 59 8 1499 2152 133071031 133070382 0.000000e+00 833.0
20 TraesCS6A01G185200 chr5A 85.062 241 21 10 1967 2194 443027378 443027616 4.900000e-57 231.0
21 TraesCS6A01G185200 chr1A 91.414 2213 136 23 1 2197 201752127 201754301 0.000000e+00 2985.0
22 TraesCS6A01G185200 chr1A 90.578 658 55 7 1497 2152 322707998 322707346 0.000000e+00 865.0
23 TraesCS6A01G185200 chr1A 79.146 609 63 34 1613 2203 183475521 183476083 1.670000e-96 363.0
24 TraesCS6A01G185200 chr1A 82.041 245 28 13 1972 2203 202591640 202591881 6.430000e-46 195.0
25 TraesCS6A01G185200 chr1A 80.408 245 32 12 1972 2203 202545401 202545642 3.010000e-39 172.0
26 TraesCS6A01G185200 chr1A 100.000 65 0 0 2218 2282 322707144 322707080 1.110000e-23 121.0
27 TraesCS6A01G185200 chr1A 90.909 77 6 1 2206 2281 264838995 264839071 4.010000e-18 102.0
28 TraesCS6A01G185200 chr3A 95.276 1376 58 7 12 1382 701989674 701988301 0.000000e+00 2174.0
29 TraesCS6A01G185200 chr3A 94.336 1377 68 10 12 1382 701981808 701980436 0.000000e+00 2102.0
30 TraesCS6A01G185200 chr3A 93.421 76 5 0 2206 2281 85958658 85958583 1.850000e-21 113.0
31 TraesCS6A01G185200 chr7A 93.421 76 5 0 2206 2281 340733534 340733459 1.850000e-21 113.0
32 TraesCS6A01G185200 chr7A 90.789 76 7 0 2206 2281 23066235 23066310 4.010000e-18 102.0
33 TraesCS6A01G185200 chr7A 85.567 97 9 5 2185 2281 249267537 249267446 1.870000e-16 97.1


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 TraesCS6A01G185200 chr6A 216933358 216935639 2281 True 4215.0 4215 100.0000 1 2282 1 chr6A.!!$R1 2281
1 TraesCS6A01G185200 chr2A 352651378 352653591 2213 False 3463.0 3463 94.9890 1 2203 1 chr2A.!!$F1 2202
2 TraesCS6A01G185200 chr2A 352643368 352645786 2418 False 1783.0 3445 97.4255 1 2282 2 chr2A.!!$F3 2281
3 TraesCS6A01G185200 chr2A 261451943 261452881 938 True 1002.0 1002 86.0180 1207 2180 1 chr2A.!!$R1 973
4 TraesCS6A01G185200 chr2A 604016772 604017506 734 False 929.0 929 89.3900 1207 1957 1 chr2A.!!$F2 750
5 TraesCS6A01G185200 chr2A 271815550 271816237 687 True 512.0 512 80.7640 1496 2208 1 chr2A.!!$R2 712
6 TraesCS6A01G185200 chr4A 85922175 85924361 2186 False 3362.0 3362 94.3570 1 2203 1 chr4A.!!$F1 2202
7 TraesCS6A01G185200 chr4A 85954388 85956782 2394 False 1727.5 3334 97.0670 1 2282 2 chr4A.!!$F4 2281
8 TraesCS6A01G185200 chr4A 374723994 374724521 527 False 566.0 566 86.4660 1688 2203 1 chr4A.!!$F2 515
9 TraesCS6A01G185200 chr5A 268812340 268814516 2176 True 3053.0 3053 91.9530 1 2197 1 chr5A.!!$R2 2196
10 TraesCS6A01G185200 chr5A 268820313 268822490 2177 True 3031.0 3031 91.7760 1 2197 1 chr5A.!!$R3 2196
11 TraesCS6A01G185200 chr5A 133070382 133071031 649 True 833.0 833 89.7870 1499 2152 1 chr5A.!!$R1 653
12 TraesCS6A01G185200 chr1A 201752127 201754301 2174 False 2985.0 2985 91.4140 1 2197 1 chr1A.!!$F2 2196
13 TraesCS6A01G185200 chr1A 322707080 322707998 918 True 493.0 865 95.2890 1497 2282 2 chr1A.!!$R1 785
14 TraesCS6A01G185200 chr1A 183475521 183476083 562 False 363.0 363 79.1460 1613 2203 1 chr1A.!!$F1 590
15 TraesCS6A01G185200 chr3A 701988301 701989674 1373 True 2174.0 2174 95.2760 12 1382 1 chr3A.!!$R3 1370
16 TraesCS6A01G185200 chr3A 701980436 701981808 1372 True 2102.0 2102 94.3360 12 1382 1 chr3A.!!$R2 1370

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
515 522 0.114168 CCGATCCCATCTCCTCCTCT 59.886 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1447 0.595567 CGGAACCTCGTCAACGTTCA 60.596 55.0 0.0 0.0 38.08 3.18 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
64 65 1.203001 TCCGGAGCTCCACCAAAAATT 60.203 47.619 31.67 0.0 35.14 1.82
515 522 0.114168 CCGATCCCATCTCCTCCTCT 59.886 60.000 0.00 0.0 0.00 3.69
553 560 0.983378 CCTTCTCCCACGATCCCCTT 60.983 60.000 0.00 0.0 0.00 3.95
707 714 3.329889 TCTTCAGGCGGCCATGGT 61.330 61.111 23.09 0.0 0.00 3.55
815 822 1.059098 TGGTGACCTGCATCTTGTCT 58.941 50.000 2.11 0.0 0.00 3.41
905 912 4.595538 TGCGTTGCCGGAGTTCGT 62.596 61.111 5.05 0.0 37.11 3.85
917 924 3.692406 GTTCGTCGGAGCCCCAGT 61.692 66.667 0.00 0.0 0.00 4.00
1153 1161 0.109532 TCGCCATGGTTCTGTCCAAA 59.890 50.000 14.67 0.0 41.09 3.28
1156 1164 1.915141 CCATGGTTCTGTCCAAAGCT 58.085 50.000 2.57 0.0 41.09 3.74
1306 1314 2.740826 CAACCGTCGCCGTGGATT 60.741 61.111 5.21 0.0 0.00 3.01
1350 1358 0.815734 CTCCCACGACGACCTTGTAT 59.184 55.000 0.00 0.0 0.00 2.29
1439 1447 1.144057 GATCGCCAAGGTGGATCGT 59.856 57.895 0.00 0.0 40.96 3.73
1519 1527 1.208358 CACTACCGTCGCTCGAACA 59.792 57.895 0.00 0.0 42.86 3.18
1870 1909 3.334604 ATGACATGCCCCCGTCAT 58.665 55.556 0.00 0.0 45.36 3.06
1876 1915 1.185315 CATGCCCCCGTCATTTTTCT 58.815 50.000 0.00 0.0 0.00 2.52
1878 1917 0.965439 TGCCCCCGTCATTTTTCTTG 59.035 50.000 0.00 0.0 0.00 3.02
2152 2222 7.626390 CATATGGGGTTCTATCGGGTTTATTA 58.374 38.462 0.00 0.0 0.00 0.98
2154 2224 7.817910 ATGGGGTTCTATCGGGTTTATTATA 57.182 36.000 0.00 0.0 0.00 0.98
2155 2225 7.008021 TGGGGTTCTATCGGGTTTATTATAC 57.992 40.000 0.00 0.0 0.00 1.47
2156 2226 6.013466 TGGGGTTCTATCGGGTTTATTATACC 60.013 42.308 0.00 0.0 34.82 2.73
2162 2240 2.955342 GGGTTTATTATACCCGGCCA 57.045 50.000 2.24 0.0 45.42 5.36
2215 2293 6.881602 TGTTATGTATCATACTTGGTTGTGCA 59.118 34.615 0.00 0.0 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.827722 AGGAAGGTCCAAAAATGTTCGA 58.172 40.909 0.00 0.00 39.61 3.71
282 287 6.831353 CACTCCCTCTCTCATCTCTTAAACTA 59.169 42.308 0.00 0.00 0.00 2.24
369 374 1.287739 CTGGGCCTTAGGAAAATGGGA 59.712 52.381 0.69 0.00 0.00 4.37
515 522 2.927856 TGGCTGCGGAAGGGAAGA 60.928 61.111 0.00 0.00 0.00 2.87
553 560 0.250124 GCGAGATCGAGAGGAGAGGA 60.250 60.000 6.39 0.00 43.02 3.71
654 661 1.684734 GGTTGGTAGAGGAGGGCGA 60.685 63.158 0.00 0.00 0.00 5.54
795 802 1.421268 AGACAAGATGCAGGTCACCAA 59.579 47.619 0.00 0.00 34.04 3.67
905 912 0.894184 GATCGATACTGGGGCTCCGA 60.894 60.000 0.00 0.00 35.24 4.55
917 924 1.512996 GACGACGCTGGGGATCGATA 61.513 60.000 10.82 0.00 39.16 2.92
964 971 1.293498 GTTCCTGCCAAGCTCTCGA 59.707 57.895 0.00 0.00 0.00 4.04
1153 1161 2.980233 GGCGTTGGACTTGCAGCT 60.980 61.111 0.00 0.00 0.00 4.24
1156 1164 1.153066 TCTTGGCGTTGGACTTGCA 60.153 52.632 0.00 0.00 0.00 4.08
1350 1358 1.401409 CGGTTCTTGCGACGGTAGTTA 60.401 52.381 0.00 0.00 0.00 2.24
1439 1447 0.595567 CGGAACCTCGTCAACGTTCA 60.596 55.000 0.00 0.00 38.08 3.18
1519 1527 4.860907 GTCGACGGTACATGTTCTGTAAAT 59.139 41.667 16.00 0.00 41.93 1.40
1870 1909 3.354131 GCGGGTGCAACAAGAAAAA 57.646 47.368 3.06 0.00 39.98 1.94
1918 1957 1.837538 CGAAACGGTGCCACGACAAT 61.838 55.000 4.05 0.00 37.61 2.71
2042 2109 7.872163 TGACATGAACAAGTTTTATGCAATC 57.128 32.000 0.00 3.83 0.00 2.67
2215 2293 4.440525 CGGTTTAAAGAAGCATGGCATGAT 60.441 41.667 30.69 22.82 0.00 2.45


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

AutoCloner maintained by Alex Coulton.