Multiple sequence alignment - TraesCS7D01G040900

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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 TraesCS7D01G040900 chr7D 100.000 3881 0 0 1 3881 20546371 20550251 0.000000e+00 7167.0
1 TraesCS7D01G040900 chr7D 84.160 1654 248 10 2235 3879 20948221 20949869 0.000000e+00 1591.0
2 TraesCS7D01G040900 chr7D 83.263 1655 262 13 2235 3879 89531966 89530317 0.000000e+00 1507.0
3 TraesCS7D01G040900 chr7D 83.111 1652 269 9 2235 3879 555195317 555193669 0.000000e+00 1496.0
4 TraesCS7D01G040900 chr7D 82.880 1653 270 11 2235 3880 20311928 20313574 0.000000e+00 1472.0
5 TraesCS7D01G040900 chr7D 82.656 1649 268 16 2235 3872 20599439 20601080 0.000000e+00 1445.0
6 TraesCS7D01G040900 chr7D 82.537 1632 265 16 2235 3857 20443530 20445150 0.000000e+00 1417.0
7 TraesCS7D01G040900 chr7D 80.109 1649 291 30 2243 3870 20584677 20586309 0.000000e+00 1194.0
8 TraesCS7D01G040900 chr7D 83.725 1235 182 15 833 2058 20460277 20461501 0.000000e+00 1149.0
9 TraesCS7D01G040900 chr7D 84.327 1174 179 4 887 2058 89533130 89531960 0.000000e+00 1144.0
10 TraesCS7D01G040900 chr7A 83.705 1657 246 22 2235 3880 20911767 20913410 0.000000e+00 1543.0
11 TraesCS7D01G040900 chr7A 83.303 1653 264 11 2235 3879 20651878 20653526 0.000000e+00 1513.0
12 TraesCS7D01G040900 chr7A 84.988 1219 179 4 839 2055 20588615 20589831 0.000000e+00 1234.0
13 TraesCS7D01G040900 chr7A 84.696 1235 172 14 833 2058 20482660 20483886 0.000000e+00 1218.0
14 TraesCS7D01G040900 chr7A 84.653 1238 171 12 831 2058 20910545 20911773 0.000000e+00 1216.0
15 TraesCS7D01G040900 chr7A 84.622 1216 171 10 844 2057 20650682 20651883 0.000000e+00 1195.0
16 TraesCS7D01G040900 chr7A 83.636 1210 188 8 858 2062 20659531 20660735 0.000000e+00 1129.0
17 TraesCS7D01G040900 chr7A 93.478 46 3 0 109 154 20553675 20553720 6.960000e-08 69.4
18 TraesCS7D01G040900 chr7A 100.000 31 0 0 111 141 20478704 20478734 1.510000e-04 58.4
19 TraesCS7D01G040900 chr4A 83.354 1652 265 10 2235 3879 713033385 713035033 0.000000e+00 1519.0
20 TraesCS7D01G040900 chr4A 81.693 1595 279 13 2235 3822 713039304 713040892 0.000000e+00 1315.0
21 TraesCS7D01G040900 chr4A 83.779 1233 176 19 833 2055 669381923 669383141 0.000000e+00 1147.0
22 TraesCS7D01G040900 chr2A 85.166 1173 167 7 889 2058 733087691 733088859 0.000000e+00 1195.0
23 TraesCS7D01G040900 chr2B 84.402 1154 175 4 906 2058 727685964 727687113 0.000000e+00 1129.0
24 TraesCS7D01G040900 chr3A 97.500 40 0 1 832 870 308690169 308690208 2.500000e-07 67.6


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 TraesCS7D01G040900 chr7D 20546371 20550251 3880 False 7167.0 7167 100.0000 1 3881 1 chr7D.!!$F4 3880
1 TraesCS7D01G040900 chr7D 20948221 20949869 1648 False 1591.0 1591 84.1600 2235 3879 1 chr7D.!!$F7 1644
2 TraesCS7D01G040900 chr7D 555193669 555195317 1648 True 1496.0 1496 83.1110 2235 3879 1 chr7D.!!$R1 1644
3 TraesCS7D01G040900 chr7D 20311928 20313574 1646 False 1472.0 1472 82.8800 2235 3880 1 chr7D.!!$F1 1645
4 TraesCS7D01G040900 chr7D 20599439 20601080 1641 False 1445.0 1445 82.6560 2235 3872 1 chr7D.!!$F6 1637
5 TraesCS7D01G040900 chr7D 20443530 20445150 1620 False 1417.0 1417 82.5370 2235 3857 1 chr7D.!!$F2 1622
6 TraesCS7D01G040900 chr7D 89530317 89533130 2813 True 1325.5 1507 83.7950 887 3879 2 chr7D.!!$R2 2992
7 TraesCS7D01G040900 chr7D 20584677 20586309 1632 False 1194.0 1194 80.1090 2243 3870 1 chr7D.!!$F5 1627
8 TraesCS7D01G040900 chr7D 20460277 20461501 1224 False 1149.0 1149 83.7250 833 2058 1 chr7D.!!$F3 1225
9 TraesCS7D01G040900 chr7A 20910545 20913410 2865 False 1379.5 1543 84.1790 831 3880 2 chr7A.!!$F6 3049
10 TraesCS7D01G040900 chr7A 20650682 20653526 2844 False 1354.0 1513 83.9625 844 3879 2 chr7A.!!$F5 3035
11 TraesCS7D01G040900 chr7A 20588615 20589831 1216 False 1234.0 1234 84.9880 839 2055 1 chr7A.!!$F2 1216
12 TraesCS7D01G040900 chr7A 20659531 20660735 1204 False 1129.0 1129 83.6360 858 2062 1 chr7A.!!$F3 1204
13 TraesCS7D01G040900 chr7A 20478704 20483886 5182 False 638.2 1218 92.3480 111 2058 2 chr7A.!!$F4 1947
14 TraesCS7D01G040900 chr4A 713033385 713035033 1648 False 1519.0 1519 83.3540 2235 3879 1 chr4A.!!$F2 1644
15 TraesCS7D01G040900 chr4A 713039304 713040892 1588 False 1315.0 1315 81.6930 2235 3822 1 chr4A.!!$F3 1587
16 TraesCS7D01G040900 chr4A 669381923 669383141 1218 False 1147.0 1147 83.7790 833 2055 1 chr4A.!!$F1 1222
17 TraesCS7D01G040900 chr2A 733087691 733088859 1168 False 1195.0 1195 85.1660 889 2058 1 chr2A.!!$F1 1169
18 TraesCS7D01G040900 chr2B 727685964 727687113 1149 False 1129.0 1129 84.4020 906 2058 1 chr2B.!!$F1 1152


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
551 1173 0.032515 TCGATCTCCTGGCCTGGTTA 60.033 55.0 26.40 16.58 0.0 2.85 F
585 1207 0.177604 CAACTGCCTCTCTAGCCTGG 59.822 60.0 0.00 0.00 0.0 4.45 F
592 1214 0.251354 CTCTCTAGCCTGGCAAAGCA 59.749 55.0 22.65 6.87 0.0 3.91 F
2090 5375 0.035056 AGAAACGGAGCATGGAAGGG 60.035 55.0 0.00 0.00 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 4825 0.034186 TTTTCTCCGCTGGCATCCAT 60.034 50.0 0.0 0.0 30.82 3.41 R
2071 5356 0.035056 CCCTTCCATGCTCCGTTTCT 60.035 55.0 0.0 0.0 0.00 2.52 R
2094 5379 0.323451 GTTCCATCAACTCCCCACCC 60.323 60.0 0.0 0.0 31.50 4.61 R
3779 7079 0.249676 CCTCTGTCATGCTGCTGAGT 59.750 55.0 0.0 0.0 0.00 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)



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AutoCloner maintained by Alex Coulton.