Multiple sequence alignment - TraesCS7A01G164600

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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 TraesCS7A01G164600 chr7A 100.000 1322 0 0 1415 2736 120866205 120864884 0.000000e+00 2442
1 TraesCS7A01G164600 chr7A 95.482 1328 46 14 1416 2736 60254246 60255566 0.000000e+00 2108
2 TraesCS7A01G164600 chr7A 100.000 1114 0 0 1 1114 120867619 120866506 0.000000e+00 2058
3 TraesCS7A01G164600 chr7A 98.474 1114 17 0 1 1114 60253095 60254208 0.000000e+00 1964
4 TraesCS7A01G164600 chr7A 97.941 1117 20 1 1 1114 211222774 211223890 0.000000e+00 1932
5 TraesCS7A01G164600 chr3A 95.870 1356 20 18 1415 2736 633122915 633124268 0.000000e+00 2161
6 TraesCS7A01G164600 chr3A 98.833 1114 13 0 1 1114 633121761 633122874 0.000000e+00 1986
7 TraesCS7A01G164600 chr6A 96.090 1330 36 13 1417 2736 64686385 64685062 0.000000e+00 2154
8 TraesCS7A01G164600 chr6A 98.923 1114 12 0 1 1114 64687536 64686423 0.000000e+00 1991
9 TraesCS7A01G164600 chr4B 95.034 1329 49 17 1417 2736 209134293 209135613 0.000000e+00 2073
10 TraesCS7A01G164600 chr4B 98.384 1114 18 0 1 1114 209133142 209134255 0.000000e+00 1958
11 TraesCS7A01G164600 chr4B 94.203 828 36 12 1418 2239 209063061 209062240 0.000000e+00 1253
12 TraesCS7A01G164600 chr4B 93.742 831 39 13 1415 2239 209283343 209284166 0.000000e+00 1234
13 TraesCS7A01G164600 chr4B 98.501 667 9 1 2071 2736 209284034 209284700 0.000000e+00 1175
14 TraesCS7A01G164600 chr4B 98.051 667 12 1 2071 2736 209062372 209061706 0.000000e+00 1158
15 TraesCS7A01G164600 chr7B 94.494 1344 41 21 1419 2736 52970484 52969148 0.000000e+00 2041
16 TraesCS7A01G164600 chr7B 97.569 576 14 0 2161 2736 139531040 139530465 0.000000e+00 987
17 TraesCS7A01G164600 chrUn 99.102 1114 10 0 1 1114 86467995 86466882 0.000000e+00 2002
18 TraesCS7A01G164600 chrUn 98.569 1118 12 1 1 1114 189419824 189418707 0.000000e+00 1973
19 TraesCS7A01G164600 chrUn 94.329 917 35 13 1417 2322 86466844 86465934 0.000000e+00 1389
20 TraesCS7A01G164600 chr1D 98.205 1114 20 0 1 1114 185789296 185790409 0.000000e+00 1947
21 TraesCS7A01G164600 chr1B 98.205 1114 20 0 1 1114 672580355 672579242 0.000000e+00 1947
22 TraesCS7A01G164600 chr1B 93.848 829 39 12 1417 2239 672579204 672578382 0.000000e+00 1238
23 TraesCS7A01G164600 chr1B 97.901 667 13 1 2071 2736 672578514 672577848 0.000000e+00 1153
24 TraesCS7A01G164600 chr3B 94.961 774 32 5 1467 2239 669841302 669840535 0.000000e+00 1206
25 TraesCS7A01G164600 chr3B 96.736 674 21 1 2063 2736 669815929 669815257 0.000000e+00 1122
26 TraesCS7A01G164600 chr3B 98.440 577 9 0 2160 2736 483376379 483376955 0.000000e+00 1016
27 TraesCS7A01G164600 chr3B 98.225 169 3 0 2071 2239 483376254 483376422 2.060000e-76 296
28 TraesCS7A01G164600 chr6B 97.755 579 11 2 2160 2736 625627444 625626866 0.000000e+00 996
29 TraesCS7A01G164600 chr6B 97.633 169 4 0 2071 2239 625627569 625627401 9.580000e-75 291
30 TraesCS7A01G164600 chr6B 96.450 169 6 0 2071 2239 215778819 215778987 2.070000e-71 279


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 TraesCS7A01G164600 chr7A 120864884 120867619 2735 True 2250.0 2442 100.000000 1 2736 2 chr7A.!!$R1 2735
1 TraesCS7A01G164600 chr7A 60253095 60255566 2471 False 2036.0 2108 96.978000 1 2736 2 chr7A.!!$F2 2735
2 TraesCS7A01G164600 chr7A 211222774 211223890 1116 False 1932.0 1932 97.941000 1 1114 1 chr7A.!!$F1 1113
3 TraesCS7A01G164600 chr3A 633121761 633124268 2507 False 2073.5 2161 97.351500 1 2736 2 chr3A.!!$F1 2735
4 TraesCS7A01G164600 chr6A 64685062 64687536 2474 True 2072.5 2154 97.506500 1 2736 2 chr6A.!!$R1 2735
5 TraesCS7A01G164600 chr4B 209133142 209135613 2471 False 2015.5 2073 96.709000 1 2736 2 chr4B.!!$F1 2735
6 TraesCS7A01G164600 chr4B 209061706 209063061 1355 True 1205.5 1253 96.127000 1418 2736 2 chr4B.!!$R1 1318
7 TraesCS7A01G164600 chr4B 209283343 209284700 1357 False 1204.5 1234 96.121500 1415 2736 2 chr4B.!!$F2 1321
8 TraesCS7A01G164600 chr7B 52969148 52970484 1336 True 2041.0 2041 94.494000 1419 2736 1 chr7B.!!$R1 1317
9 TraesCS7A01G164600 chr7B 139530465 139531040 575 True 987.0 987 97.569000 2161 2736 1 chr7B.!!$R2 575
10 TraesCS7A01G164600 chrUn 189418707 189419824 1117 True 1973.0 1973 98.569000 1 1114 1 chrUn.!!$R1 1113
11 TraesCS7A01G164600 chrUn 86465934 86467995 2061 True 1695.5 2002 96.715500 1 2322 2 chrUn.!!$R2 2321
12 TraesCS7A01G164600 chr1D 185789296 185790409 1113 False 1947.0 1947 98.205000 1 1114 1 chr1D.!!$F1 1113
13 TraesCS7A01G164600 chr1B 672577848 672580355 2507 True 1446.0 1947 96.651333 1 2736 3 chr1B.!!$R1 2735
14 TraesCS7A01G164600 chr3B 669840535 669841302 767 True 1206.0 1206 94.961000 1467 2239 1 chr3B.!!$R2 772
15 TraesCS7A01G164600 chr3B 669815257 669815929 672 True 1122.0 1122 96.736000 2063 2736 1 chr3B.!!$R1 673
16 TraesCS7A01G164600 chr3B 483376254 483376955 701 False 656.0 1016 98.332500 2071 2736 2 chr3B.!!$F1 665
17 TraesCS7A01G164600 chr6B 625626866 625627569 703 True 643.5 996 97.694000 2071 2736 2 chr6B.!!$R1 665

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
38 39 1.821136 CAGGCCTGGAAATGGAAACTC 59.179 52.381 26.14 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2015 0.034767 CCAGAATTCTGCAGCTCCCA 60.035 55.0 27.01 0.0 42.47 4.37 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
38 39 1.821136 CAGGCCTGGAAATGGAAACTC 59.179 52.381 26.14 0.00 0.00 3.01
259 260 5.362430 ACAAGGGAAGTTTTCACATAAGCAA 59.638 36.000 0.00 0.00 34.83 3.91
362 363 4.339814 GGTATCAATATGGCAACCCGAAAA 59.660 41.667 0.00 0.00 0.00 2.29
415 416 5.098211 GCTTATCTGCCAGATGAAAACAAC 58.902 41.667 17.46 0.00 35.37 3.32
483 484 4.133078 GCCAGACTAGAATGGAAGAATGG 58.867 47.826 18.37 0.00 39.02 3.16
691 692 6.881602 GTGGAGTTCTTTGATGGTCTATCTTT 59.118 38.462 0.00 0.00 36.71 2.52
935 936 8.477984 TTTTGGAAAGTCAATCTCTTTTTGTG 57.522 30.769 0.00 0.00 35.62 3.33
1441 1449 0.176680 GCGAGATCCAGAGCAAGGAA 59.823 55.000 0.00 0.00 38.93 3.36
1517 1525 9.923143 CATATATGTACTCCAGTTTATCCGAAA 57.077 33.333 4.43 0.00 0.00 3.46
1760 1768 4.900635 AAATGAATGGAATACTCGGCAC 57.099 40.909 0.00 0.00 0.00 5.01
1765 1773 5.620206 TGAATGGAATACTCGGCACAATAT 58.380 37.500 0.00 0.00 0.00 1.28
1797 1805 8.213518 TCCTATTAATGATTGTGACAGCTTTC 57.786 34.615 0.00 0.00 0.00 2.62
1876 1884 1.540363 GCTTAGCTAGCGCCATACCAA 60.540 52.381 9.55 0.00 40.71 3.67
2006 2015 4.376225 TTGATTTAAACGTTCTCCCCCT 57.624 40.909 0.00 0.00 0.00 4.79
2186 2378 7.511959 ATGATTCATCAACTGATTCATCAGG 57.488 36.000 18.89 4.64 45.33 3.86
2187 2379 6.490381 ATGATTCATCAACTGATTCATCAGGG 59.510 38.462 18.89 11.59 45.33 4.45
2188 2380 7.639534 ATGATTCATCAACTGATTCATCAGGGA 60.640 37.037 18.89 15.64 45.33 4.20
2197 2389 5.032327 TGATTCATCAGGGAGTTCATCTG 57.968 43.478 0.00 0.00 32.11 2.90
2198 2390 4.718276 TGATTCATCAGGGAGTTCATCTGA 59.282 41.667 0.00 0.00 41.09 3.27
2199 2391 5.368816 TGATTCATCAGGGAGTTCATCTGAT 59.631 40.000 9.78 9.78 45.75 2.90
2203 2395 5.908562 ATCAGGGAGTTCATCTGATGATT 57.091 39.130 20.16 12.10 43.92 2.57
2204 2396 5.287674 TCAGGGAGTTCATCTGATGATTC 57.712 43.478 20.16 18.63 39.39 2.52
2205 2397 4.718276 TCAGGGAGTTCATCTGATGATTCA 59.282 41.667 20.16 3.89 39.39 2.57
2206 2398 5.368816 TCAGGGAGTTCATCTGATGATTCAT 59.631 40.000 20.16 10.89 39.39 2.57
2207 2399 5.701750 CAGGGAGTTCATCTGATGATTCATC 59.298 44.000 20.16 17.97 40.88 2.92
2208 2400 5.368816 AGGGAGTTCATCTGATGATTCATCA 59.631 40.000 24.16 24.16 46.84 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
349 350 3.739167 CGAGTTTTCGGGTTGCCA 58.261 55.556 0.00 0.00 43.05 4.92
362 363 5.244178 AGAAGAGACCACTTTGATAACGAGT 59.756 40.000 0.00 0.00 0.00 4.18
415 416 1.734707 CGGCCACCTGTTACTACGAAG 60.735 57.143 2.24 0.00 0.00 3.79
483 484 6.624352 TCTTCTGCATTTCAGTATTATGGC 57.376 37.500 0.00 0.00 43.32 4.40
1441 1449 7.235079 TCGAGATATCTTCCAGATTCTTAGGT 58.765 38.462 6.70 0.00 36.20 3.08
1538 1546 5.045140 TCCTCCTTTTTCCCAAATAGTCGAT 60.045 40.000 0.00 0.00 0.00 3.59
1797 1805 3.006537 CCCAAGGTGGTACGTATCCTATG 59.993 52.174 14.24 13.53 35.17 2.23
1822 1830 0.813821 GCTCCCCAAAAGCTCATCAC 59.186 55.000 0.00 0.00 36.80 3.06
1823 1831 0.405198 TGCTCCCCAAAAGCTCATCA 59.595 50.000 0.00 0.00 40.50 3.07
1876 1884 7.891183 CCAAGTCACTATGGTATCTCCTACTAT 59.109 40.741 0.00 0.00 35.82 2.12
2006 2015 0.034767 CCAGAATTCTGCAGCTCCCA 60.035 55.000 27.01 0.00 42.47 4.37
2183 2375 5.032327 TGAATCATCAGATGAACTCCCTG 57.968 43.478 17.24 0.00 43.50 4.45
2184 2376 5.368816 TGATGAATCATCAGATGAACTCCCT 59.631 40.000 20.85 7.28 44.60 4.20
2185 2377 5.618236 TGATGAATCATCAGATGAACTCCC 58.382 41.667 20.85 11.08 44.60 4.30
2211 2403 4.718276 TCAGATGAACTCCCTGATGAATCA 59.282 41.667 0.00 0.00 32.57 2.57
2212 2404 5.287674 TCAGATGAACTCCCTGATGAATC 57.712 43.478 0.00 0.00 32.57 2.52
2213 2405 5.908562 ATCAGATGAACTCCCTGATGAAT 57.091 39.130 0.00 0.00 43.62 2.57
2217 2409 6.070136 CCATATCATCAGATGAACTCCCTGAT 60.070 42.308 17.24 0.00 45.47 2.90
2218 2410 5.247792 CCATATCATCAGATGAACTCCCTGA 59.752 44.000 17.24 0.00 43.50 3.86
2359 2630 3.044235 TGCTTGCTTCTTCGAATCTCA 57.956 42.857 0.00 0.00 0.00 3.27
2628 2899 9.573166 CCATTTGTTATTGGTGATAGGAAGATA 57.427 33.333 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.