Multiple sequence alignment - TraesCS5B01G572800

Loading Multiple Alignment...

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 TraesCS5B01G572800 chr5B 100.000 2261 0 0 1 2261 713025930 713023670 0.000000e+00 4176
1 TraesCS5B01G572800 chr5B 96.166 939 34 2 1324 2261 474114225 474113288 0.000000e+00 1533
2 TraesCS5B01G572800 chr5B 95.634 939 39 2 1324 2261 487565640 487564703 0.000000e+00 1506
3 TraesCS5B01G572800 chr5B 95.421 939 41 2 1324 2261 25433738 25432801 0.000000e+00 1495
4 TraesCS5B01G572800 chr5B 97.814 183 4 0 1123 1305 679660078 679660260 1.300000e-82 316
5 TraesCS5B01G572800 chr5A 98.848 1128 10 2 1 1125 300072977 300074104 0.000000e+00 2008
6 TraesCS5B01G572800 chr5A 98.579 1126 13 2 1 1125 16602921 16601798 0.000000e+00 1988
7 TraesCS5B01G572800 chr5A 98.361 183 3 0 1123 1305 16601742 16601560 2.800000e-84 322
8 TraesCS5B01G572800 chr5A 98.361 183 3 0 1123 1305 600278556 600278374 2.800000e-84 322
9 TraesCS5B01G572800 chr5A 97.814 183 4 0 1123 1305 300074160 300074342 1.300000e-82 316
10 TraesCS5B01G572800 chr2A 98.848 1128 10 2 1 1125 618279958 618278831 0.000000e+00 2008
11 TraesCS5B01G572800 chr7B 98.759 1128 11 3 1 1125 743086197 743087324 0.000000e+00 2002
12 TraesCS5B01G572800 chr7B 95.527 939 37 3 1324 2261 497016520 497015586 0.000000e+00 1496
13 TraesCS5B01G572800 chrUn 98.670 1128 12 2 1 1125 189392537 189393664 0.000000e+00 1997
14 TraesCS5B01G572800 chr6A 98.669 1127 12 3 1 1125 289128630 289129755 0.000000e+00 1995
15 TraesCS5B01G572800 chr6A 97.814 183 4 0 1123 1305 289129811 289129993 1.300000e-82 316
16 TraesCS5B01G572800 chr6A 97.814 183 4 0 1123 1305 608883641 608883459 1.300000e-82 316
17 TraesCS5B01G572800 chr7D 98.582 1128 13 2 1 1125 626698492 626697365 0.000000e+00 1991
18 TraesCS5B01G572800 chr7D 98.361 183 3 0 1123 1305 626697309 626697127 2.800000e-84 322
19 TraesCS5B01G572800 chr7D 97.814 183 4 0 1123 1305 203555165 203554983 1.300000e-82 316
20 TraesCS5B01G572800 chr7A 98.492 1127 15 2 1 1125 4959836 4960962 0.000000e+00 1986
21 TraesCS5B01G572800 chr3B 98.492 1127 14 3 1 1125 92199602 92200727 0.000000e+00 1984
22 TraesCS5B01G572800 chr3B 96.805 939 26 3 1324 2261 311150071 311151006 0.000000e+00 1565
23 TraesCS5B01G572800 chr1B 96.375 938 33 1 1324 2261 652228041 652227105 0.000000e+00 1543
24 TraesCS5B01G572800 chr4B 95.745 940 37 3 1324 2261 411403701 411402763 0.000000e+00 1511
25 TraesCS5B01G572800 chr4B 95.634 939 39 2 1324 2261 457780974 457780037 0.000000e+00 1506
26 TraesCS5B01G572800 chr6B 95.634 939 39 2 1324 2261 106401260 106402197 0.000000e+00 1506
27 TraesCS5B01G572800 chr1D 98.343 181 3 0 1123 1303 185770636 185770816 3.620000e-83 318


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 TraesCS5B01G572800 chr5B 713023670 713025930 2260 True 4176.0 4176 100.0000 1 2261 1 chr5B.!!$R4 2260
1 TraesCS5B01G572800 chr5B 474113288 474114225 937 True 1533.0 1533 96.1660 1324 2261 1 chr5B.!!$R2 937
2 TraesCS5B01G572800 chr5B 487564703 487565640 937 True 1506.0 1506 95.6340 1324 2261 1 chr5B.!!$R3 937
3 TraesCS5B01G572800 chr5B 25432801 25433738 937 True 1495.0 1495 95.4210 1324 2261 1 chr5B.!!$R1 937
4 TraesCS5B01G572800 chr5A 300072977 300074342 1365 False 1162.0 2008 98.3310 1 1305 2 chr5A.!!$F1 1304
5 TraesCS5B01G572800 chr5A 16601560 16602921 1361 True 1155.0 1988 98.4700 1 1305 2 chr5A.!!$R2 1304
6 TraesCS5B01G572800 chr2A 618278831 618279958 1127 True 2008.0 2008 98.8480 1 1125 1 chr2A.!!$R1 1124
7 TraesCS5B01G572800 chr7B 743086197 743087324 1127 False 2002.0 2002 98.7590 1 1125 1 chr7B.!!$F1 1124
8 TraesCS5B01G572800 chr7B 497015586 497016520 934 True 1496.0 1496 95.5270 1324 2261 1 chr7B.!!$R1 937
9 TraesCS5B01G572800 chrUn 189392537 189393664 1127 False 1997.0 1997 98.6700 1 1125 1 chrUn.!!$F1 1124
10 TraesCS5B01G572800 chr6A 289128630 289129993 1363 False 1155.5 1995 98.2415 1 1305 2 chr6A.!!$F1 1304
11 TraesCS5B01G572800 chr7D 626697127 626698492 1365 True 1156.5 1991 98.4715 1 1305 2 chr7D.!!$R2 1304
12 TraesCS5B01G572800 chr7A 4959836 4960962 1126 False 1986.0 1986 98.4920 1 1125 1 chr7A.!!$F1 1124
13 TraesCS5B01G572800 chr3B 92199602 92200727 1125 False 1984.0 1984 98.4920 1 1125 1 chr3B.!!$F1 1124
14 TraesCS5B01G572800 chr3B 311150071 311151006 935 False 1565.0 1565 96.8050 1324 2261 1 chr3B.!!$F2 937
15 TraesCS5B01G572800 chr1B 652227105 652228041 936 True 1543.0 1543 96.3750 1324 2261 1 chr1B.!!$R1 937
16 TraesCS5B01G572800 chr4B 411402763 411403701 938 True 1511.0 1511 95.7450 1324 2261 1 chr4B.!!$R1 937
17 TraesCS5B01G572800 chr4B 457780037 457780974 937 True 1506.0 1506 95.6340 1324 2261 1 chr4B.!!$R2 937
18 TraesCS5B01G572800 chr6B 106401260 106402197 937 False 1506.0 1506 95.6340 1324 2261 1 chr6B.!!$F1 937

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
174 175 0.473326 GCCCAGCATCTCTCCTGAAT 59.527 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 1380 0.250989 TAGGTTCCAAAAGTGCCGGG 60.251 55.0 2.18 0.0 0.0 5.73 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
174 175 0.473326 GCCCAGCATCTCTCCTGAAT 59.527 55.000 0.00 0.00 0.00 2.57
375 376 6.279513 TGACAAAAGAAGAAAAAGAAGCCA 57.720 33.333 0.00 0.00 0.00 4.75
663 668 3.710209 AGACAGCAGCAAGTTCCTATT 57.290 42.857 0.00 0.00 0.00 1.73
724 729 2.933495 TCTCGGGTGAATACGTGAAG 57.067 50.000 0.00 0.00 30.88 3.02
945 951 2.760385 GTCCCCCTACGAGCAGCT 60.760 66.667 0.00 0.00 0.00 4.24
998 1004 0.658829 CCGAGCGAGCGTAGATTCAG 60.659 60.000 0.00 0.00 0.00 3.02
1139 1203 1.548809 CCCCTCAGAGCGGATCTATCA 60.549 57.143 0.00 0.00 36.10 2.15
1175 1239 3.805108 GCTGGCGGATGTGATCTATTCTT 60.805 47.826 0.00 0.00 0.00 2.52
1187 1251 5.807520 GTGATCTATTCTTGTGTCACATCGT 59.192 40.000 6.48 0.00 36.78 3.73
1305 1369 3.892284 TGTTCTTAGTGAAAGGGTTGCA 58.108 40.909 0.00 0.00 36.30 4.08
1306 1370 3.882888 TGTTCTTAGTGAAAGGGTTGCAG 59.117 43.478 0.00 0.00 36.30 4.41
1307 1371 4.134563 GTTCTTAGTGAAAGGGTTGCAGA 58.865 43.478 0.00 0.00 36.30 4.26
1308 1372 4.431416 TCTTAGTGAAAGGGTTGCAGAA 57.569 40.909 0.00 0.00 35.75 3.02
1309 1373 4.134563 TCTTAGTGAAAGGGTTGCAGAAC 58.865 43.478 0.00 0.00 35.75 3.01
1310 1374 8.386125 GTTCTTAGTGAAAGGGTTGCAGAACC 62.386 46.154 0.00 0.00 42.61 3.62
1317 1381 1.745890 GGTTGCAGAACCCAAACCC 59.254 57.895 0.00 0.00 45.48 4.11
1318 1382 1.745890 GTTGCAGAACCCAAACCCC 59.254 57.895 0.00 0.00 0.00 4.95
1319 1383 1.830408 TTGCAGAACCCAAACCCCG 60.830 57.895 0.00 0.00 0.00 5.73
1320 1384 2.989253 GCAGAACCCAAACCCCGG 60.989 66.667 0.00 0.00 0.00 5.73
1321 1385 2.989253 CAGAACCCAAACCCCGGC 60.989 66.667 0.00 0.00 0.00 6.13
1322 1386 3.503839 AGAACCCAAACCCCGGCA 61.504 61.111 0.00 0.00 0.00 5.69
1356 1420 1.824852 TCTTCGCCAAGTCATCAGCTA 59.175 47.619 0.00 0.00 0.00 3.32
1622 1687 6.493115 AGTGAATCTGGAGTACATATCTGAGG 59.507 42.308 0.00 0.00 0.00 3.86
1703 1768 4.922206 AGCCATCAAAGAACATAGTCCAA 58.078 39.130 0.00 0.00 0.00 3.53
1826 1893 6.851836 TGATATCTAGGGGAAGGAGTTCAATT 59.148 38.462 3.98 0.00 33.93 2.32
2034 2103 2.289756 TGTAATACACTGGGCGCTGAAA 60.290 45.455 14.63 0.00 0.00 2.69
2085 2154 4.314961 TCGACCGTAAGTACTGTACTGAA 58.685 43.478 20.34 9.76 39.39 3.02
2086 2155 4.754618 TCGACCGTAAGTACTGTACTGAAA 59.245 41.667 20.34 7.41 39.39 2.69
2122 2191 3.803778 GCTGCAATGTAAAGCAACAAAGT 59.196 39.130 0.00 0.00 40.73 2.66
2188 2257 2.159296 GGGTTTTCAACTCTGCAAACGT 60.159 45.455 0.00 0.00 38.93 3.99
2217 2286 1.613925 CTTCAGGAGTCCACTCGAACA 59.386 52.381 12.86 0.00 43.76 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 1.709578 AGAGTCTGCAGAAGGTGTCA 58.290 50.000 20.19 0.00 0.00 3.58
663 668 4.584327 TTGATCTGTCGTCTTGTTCTCA 57.416 40.909 0.00 0.00 0.00 3.27
724 729 3.393800 TCACTGAGCTAAGCAACACTTC 58.606 45.455 0.00 0.00 39.97 3.01
945 951 4.551702 TGAACTCCTTCATTGATTCCGA 57.448 40.909 0.00 0.00 31.00 4.55
998 1004 5.220340 CCTTCGTTCGGTACAATCAACATAC 60.220 44.000 0.00 0.00 0.00 2.39
1139 1203 2.363975 CCAGCCAGCCATGCCATTT 61.364 57.895 0.00 0.00 0.00 2.32
1175 1239 5.584649 AGAAGAAAGAAAACGATGTGACACA 59.415 36.000 11.41 11.41 0.00 3.72
1187 1251 7.069344 AGAAAATGGAGGGAGAAGAAAGAAAA 58.931 34.615 0.00 0.00 0.00 2.29
1305 1369 3.503839 TGCCGGGGTTTGGGTTCT 61.504 61.111 2.18 0.00 0.00 3.01
1306 1370 3.299977 GTGCCGGGGTTTGGGTTC 61.300 66.667 2.18 0.00 0.00 3.62
1307 1371 2.882403 AAAGTGCCGGGGTTTGGGTT 62.882 55.000 2.18 0.00 0.00 4.11
1308 1372 2.882403 AAAAGTGCCGGGGTTTGGGT 62.882 55.000 2.18 0.00 0.00 4.51
1309 1373 2.137528 AAAAGTGCCGGGGTTTGGG 61.138 57.895 2.18 0.00 0.00 4.12
1310 1374 1.068921 CAAAAGTGCCGGGGTTTGG 59.931 57.895 2.18 0.00 0.00 3.28
1311 1375 1.068921 CCAAAAGTGCCGGGGTTTG 59.931 57.895 2.18 0.00 0.00 2.93
1312 1376 0.688087 TTCCAAAAGTGCCGGGGTTT 60.688 50.000 2.18 0.00 0.00 3.27
1313 1377 1.075896 TTCCAAAAGTGCCGGGGTT 60.076 52.632 2.18 0.00 0.00 4.11
1314 1378 1.830847 GTTCCAAAAGTGCCGGGGT 60.831 57.895 2.18 0.00 0.00 4.95
1315 1379 2.570284 GGTTCCAAAAGTGCCGGGG 61.570 63.158 2.18 0.00 0.00 5.73
1316 1380 0.250989 TAGGTTCCAAAAGTGCCGGG 60.251 55.000 2.18 0.00 0.00 5.73
1317 1381 1.743394 GATAGGTTCCAAAAGTGCCGG 59.257 52.381 0.00 0.00 0.00 6.13
1318 1382 2.711542 AGATAGGTTCCAAAAGTGCCG 58.288 47.619 0.00 0.00 0.00 5.69
1319 1383 3.127030 CGAAGATAGGTTCCAAAAGTGCC 59.873 47.826 0.00 0.00 0.00 5.01
1320 1384 3.426292 GCGAAGATAGGTTCCAAAAGTGC 60.426 47.826 0.00 0.00 0.00 4.40
1321 1385 3.127030 GGCGAAGATAGGTTCCAAAAGTG 59.873 47.826 0.00 0.00 0.00 3.16
1322 1386 3.244770 TGGCGAAGATAGGTTCCAAAAGT 60.245 43.478 0.00 0.00 0.00 2.66
1356 1420 2.107552 TCCCCCGACTGAAAAATCAAGT 59.892 45.455 0.00 0.00 0.00 3.16
1703 1768 1.620819 ACTCAAGTTCACTCGGAGCAT 59.379 47.619 4.58 0.00 33.30 3.79
1826 1893 1.228398 TCGAGTGGCAAAATGGGCA 60.228 52.632 0.00 0.00 41.50 5.36
2034 2103 4.745351 AGAAGAAGGGAAAGCCTTCAAAT 58.255 39.130 3.95 0.00 44.15 2.32
2058 2127 0.674895 AGTACTTACGGTCGAGCGGT 60.675 55.000 36.44 26.94 34.85 5.68
2085 2154 0.536006 GCAGCCACAGGACAAGTCTT 60.536 55.000 0.00 0.00 0.00 3.01
2086 2155 1.072159 GCAGCCACAGGACAAGTCT 59.928 57.895 0.00 0.00 0.00 3.24
2122 2191 1.221840 GCCCCGATCAGCAAAGAGA 59.778 57.895 0.00 0.00 0.00 3.10
2188 2257 1.339438 GGACTCCTGAAGCTGATGCAA 60.339 52.381 0.00 0.00 42.74 4.08
2217 2286 4.381398 CCGACTGATGAAGAAGTCAGACAT 60.381 45.833 2.66 0.00 43.50 3.06


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

AutoCloner maintained by Alex Coulton.