Multiple sequence alignment - TraesCS5D01G197200

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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 TraesCS5D01G197200 chr5D 100.000 2276 0 0 1 2276 300148878 300146603 0.000000e+00 4204
1 TraesCS5D01G197200 chr5D 96.819 1383 43 1 1 1383 300324808 300323427 0.000000e+00 2309
2 TraesCS5D01G197200 chr5D 94.889 900 41 2 1382 2276 300323396 300322497 0.000000e+00 1402
3 TraesCS5D01G197200 chr5D 88.989 890 68 17 1406 2276 300955517 300956395 0.000000e+00 1074
4 TraesCS5D01G197200 chr5D 87.429 883 70 14 1413 2276 299388744 299389604 0.000000e+00 977
5 TraesCS5D01G197200 chr5D 85.836 939 73 23 1382 2275 299068429 299069352 0.000000e+00 942
6 TraesCS5D01G197200 chr5D 86.318 899 77 24 1409 2276 300160915 300160032 0.000000e+00 937
7 TraesCS5D01G197200 chr5D 84.711 641 60 15 1382 2003 299004328 299004949 6.950000e-170 606
8 TraesCS5D01G197200 chr4D 90.015 1322 127 5 1 1320 59513426 59512108 0.000000e+00 1705
9 TraesCS5D01G197200 chr5B 86.249 1309 173 5 1 1304 543261381 543260075 0.000000e+00 1413
10 TraesCS5D01G197200 chr5B 89.542 918 60 19 1382 2276 344241076 344240172 0.000000e+00 1131
11 TraesCS5D01G197200 chr5B 89.195 907 64 13 1382 2276 343952809 343951925 0.000000e+00 1101
12 TraesCS5D01G197200 chr5B 88.985 808 55 15 1487 2275 340609804 340610596 0.000000e+00 968
13 TraesCS5D01G197200 chr5B 87.075 882 68 14 1413 2276 340134534 340135387 0.000000e+00 955
14 TraesCS5D01G197200 chr5B 87.075 882 68 14 1413 2276 340324607 340325460 0.000000e+00 955
15 TraesCS5D01G197200 chr5B 90.711 689 49 5 1591 2276 339977862 339978538 0.000000e+00 904
16 TraesCS5D01G197200 chr3A 85.474 1308 184 6 1 1304 440509550 440510855 0.000000e+00 1358
17 TraesCS5D01G197200 chr7B 85.222 1306 190 3 1 1304 26210387 26209083 0.000000e+00 1339
18 TraesCS5D01G197200 chr6B 85.222 1306 190 3 1 1304 583194316 583193012 0.000000e+00 1339
19 TraesCS5D01G197200 chr6B 85.157 1307 190 4 1 1304 16962028 16960723 0.000000e+00 1336
20 TraesCS5D01G197200 chr1B 85.394 1294 183 6 1 1291 487940104 487941394 0.000000e+00 1338
21 TraesCS5D01G197200 chr1B 84.126 1304 199 8 3 1303 518791395 518792693 0.000000e+00 1254
22 TraesCS5D01G197200 chr5A 89.306 879 61 8 1413 2276 396415632 396416492 0.000000e+00 1072
23 TraesCS5D01G197200 chr5A 87.443 884 78 15 1409 2276 398051287 398050421 0.000000e+00 987
24 TraesCS5D01G197200 chr5A 89.117 781 66 11 1504 2276 397786949 397786180 0.000000e+00 953


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 TraesCS5D01G197200 chr5D 300146603 300148878 2275 True 4204.0 4204 100.000 1 2276 1 chr5D.!!$R1 2275
1 TraesCS5D01G197200 chr5D 300322497 300324808 2311 True 1855.5 2309 95.854 1 2276 2 chr5D.!!$R3 2275
2 TraesCS5D01G197200 chr5D 300955517 300956395 878 False 1074.0 1074 88.989 1406 2276 1 chr5D.!!$F4 870
3 TraesCS5D01G197200 chr5D 299388744 299389604 860 False 977.0 977 87.429 1413 2276 1 chr5D.!!$F3 863
4 TraesCS5D01G197200 chr5D 299068429 299069352 923 False 942.0 942 85.836 1382 2275 1 chr5D.!!$F2 893
5 TraesCS5D01G197200 chr5D 300160032 300160915 883 True 937.0 937 86.318 1409 2276 1 chr5D.!!$R2 867
6 TraesCS5D01G197200 chr5D 299004328 299004949 621 False 606.0 606 84.711 1382 2003 1 chr5D.!!$F1 621
7 TraesCS5D01G197200 chr4D 59512108 59513426 1318 True 1705.0 1705 90.015 1 1320 1 chr4D.!!$R1 1319
8 TraesCS5D01G197200 chr5B 543260075 543261381 1306 True 1413.0 1413 86.249 1 1304 1 chr5B.!!$R3 1303
9 TraesCS5D01G197200 chr5B 344240172 344241076 904 True 1131.0 1131 89.542 1382 2276 1 chr5B.!!$R2 894
10 TraesCS5D01G197200 chr5B 343951925 343952809 884 True 1101.0 1101 89.195 1382 2276 1 chr5B.!!$R1 894
11 TraesCS5D01G197200 chr5B 340609804 340610596 792 False 968.0 968 88.985 1487 2275 1 chr5B.!!$F4 788
12 TraesCS5D01G197200 chr5B 340134534 340135387 853 False 955.0 955 87.075 1413 2276 1 chr5B.!!$F2 863
13 TraesCS5D01G197200 chr5B 340324607 340325460 853 False 955.0 955 87.075 1413 2276 1 chr5B.!!$F3 863
14 TraesCS5D01G197200 chr5B 339977862 339978538 676 False 904.0 904 90.711 1591 2276 1 chr5B.!!$F1 685
15 TraesCS5D01G197200 chr3A 440509550 440510855 1305 False 1358.0 1358 85.474 1 1304 1 chr3A.!!$F1 1303
16 TraesCS5D01G197200 chr7B 26209083 26210387 1304 True 1339.0 1339 85.222 1 1304 1 chr7B.!!$R1 1303
17 TraesCS5D01G197200 chr6B 583193012 583194316 1304 True 1339.0 1339 85.222 1 1304 1 chr6B.!!$R2 1303
18 TraesCS5D01G197200 chr6B 16960723 16962028 1305 True 1336.0 1336 85.157 1 1304 1 chr6B.!!$R1 1303
19 TraesCS5D01G197200 chr1B 487940104 487941394 1290 False 1338.0 1338 85.394 1 1291 1 chr1B.!!$F1 1290
20 TraesCS5D01G197200 chr1B 518791395 518792693 1298 False 1254.0 1254 84.126 3 1303 1 chr1B.!!$F2 1300
21 TraesCS5D01G197200 chr5A 396415632 396416492 860 False 1072.0 1072 89.306 1413 2276 1 chr5A.!!$F1 863
22 TraesCS5D01G197200 chr5A 398050421 398051287 866 True 987.0 987 87.443 1409 2276 1 chr5A.!!$R2 867
23 TraesCS5D01G197200 chr5A 397786180 397786949 769 True 953.0 953 89.117 1504 2276 1 chr5A.!!$R1 772

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
66 67 1.734477 CGCTTGAGACAGTGGACCG 60.734 63.158 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1517 1.331447 TGATTCCAAATCGAGCATGCG 59.669 47.619 13.01 0.0 0.0 4.73 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
66 67 1.734477 CGCTTGAGACAGTGGACCG 60.734 63.158 0.00 0.00 0.00 4.79
312 314 6.207213 CGGTACCTCATATACTGAAGAACAC 58.793 44.000 10.90 0.00 32.14 3.32
1081 1086 8.927675 TTCTGTTATGGCTCCTTTACTTTTAA 57.072 30.769 0.00 0.00 0.00 1.52
1295 1302 2.403252 AAGCTACCAGATTGGAACGG 57.597 50.000 1.40 0.00 40.96 4.44
1339 1346 1.446099 CCGATGGGATACGCCGATG 60.446 63.158 0.00 0.00 34.93 3.84
1342 1349 2.521958 GATGGGATACGCCGATGGGG 62.522 65.000 0.00 0.00 41.67 4.96
1343 1350 2.920912 GGGATACGCCGATGGGGA 60.921 66.667 6.92 0.00 39.07 4.81
1369 1376 1.202533 CCAATCGCAACGATAGGAGGT 60.203 52.381 2.52 0.00 46.30 3.85
1370 1377 1.860950 CAATCGCAACGATAGGAGGTG 59.139 52.381 2.52 0.00 46.30 4.00
1449 1490 4.439700 CGCAAGCAAATCTGATTTCCTGAT 60.440 41.667 12.50 0.00 35.32 2.90
1469 1517 2.549926 TGGATCACATCACATACGCAC 58.450 47.619 0.00 0.00 0.00 5.34
1470 1518 1.522676 GGATCACATCACATACGCACG 59.477 52.381 0.00 0.00 0.00 5.34
1489 1556 1.331447 CGCATGCTCGATTTGGAATCA 59.669 47.619 17.13 0.00 0.00 2.57
1501 1568 2.118313 TGGAATCAGCATCACACCTG 57.882 50.000 0.00 0.00 0.00 4.00
1502 1569 1.340308 TGGAATCAGCATCACACCTGG 60.340 52.381 0.00 0.00 0.00 4.45
1953 2132 2.168106 CTCCTCCAGTTCCTGTGATCAG 59.832 54.545 0.00 0.00 41.01 2.90
1955 2134 2.304180 CCTCCAGTTCCTGTGATCAGTT 59.696 50.000 0.00 0.00 39.82 3.16
1973 2152 2.434359 GCAAGAAGGCGCCTACGT 60.434 61.111 33.07 15.67 42.83 3.57
2159 2338 2.490903 GTCGAGTTACAGGAGCAGGTTA 59.509 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 7.761409 TGAACAATTGTCTGTATCAATTAGCC 58.239 34.615 12.39 0.00 41.58 3.93
300 302 5.290493 ACTTCCACATGTGTTCTTCAGTA 57.710 39.130 23.79 0.67 0.00 2.74
312 314 2.602257 TCCATAGCGACTTCCACATG 57.398 50.000 0.00 0.00 0.00 3.21
693 696 5.120399 TGAATCCGCTTAACCGATGTAAAT 58.880 37.500 0.00 0.00 0.00 1.40
824 829 7.432869 CACCTTATTGAAGTCCAAATTCACAA 58.567 34.615 0.00 0.00 38.43 3.33
1006 1011 1.489481 ACGATCTCCAGGCAATCTGA 58.511 50.000 0.00 0.00 46.18 3.27
1081 1086 5.814481 AGAGGAAGCTAGCTCTTCAATTTT 58.186 37.500 19.65 0.00 43.14 1.82
1339 1346 4.833811 GCGATTGGCATTTTCCCC 57.166 55.556 0.00 0.00 42.87 4.81
1369 1376 2.042842 TGAGGCCATCATTTCTTTCCCA 59.957 45.455 5.01 0.00 31.12 4.37
1370 1377 2.738743 TGAGGCCATCATTTCTTTCCC 58.261 47.619 5.01 0.00 31.12 3.97
1449 1490 2.549926 GTGCGTATGTGATGTGATCCA 58.450 47.619 0.00 0.00 0.00 3.41
1469 1517 1.331447 TGATTCCAAATCGAGCATGCG 59.669 47.619 13.01 0.00 0.00 4.73
1470 1518 2.857489 GCTGATTCCAAATCGAGCATGC 60.857 50.000 10.51 10.51 0.00 4.06
1489 1556 2.194388 CTCAGGCCAGGTGTGATGCT 62.194 60.000 5.01 0.00 0.00 3.79
1501 1568 3.317430 CCTTTTATTGATCAGCTCAGGCC 59.683 47.826 0.00 0.00 39.73 5.19
1502 1569 3.243334 GCCTTTTATTGATCAGCTCAGGC 60.243 47.826 15.28 15.28 34.68 4.85
1669 1845 1.827399 GCTTCCTCGTGAACTCCCCA 61.827 60.000 0.00 0.00 0.00 4.96
1953 2132 1.502190 GTAGGCGCCTTCTTGCAAC 59.498 57.895 37.74 21.34 0.00 4.17
1955 2134 1.879737 TACGTAGGCGCCTTCTTGCA 61.880 55.000 37.74 13.33 42.83 4.08
1973 2152 2.690497 CAGAGGCCGTCATCTTCTTCTA 59.310 50.000 0.00 0.00 0.00 2.10
2159 2338 2.293677 TCTTCTCTCGAGCGAACTTGTT 59.706 45.455 13.66 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.