Multiple sequence alignment - TraesCS5B01G017200

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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 TraesCS5B01G017200 chr5B 100.000 2270 0 0 1 2270 16010575 16012844 0 4193
1 TraesCS5B01G017200 chr5B 93.920 1546 86 3 1 1545 426532763 426534301 0 2327
2 TraesCS5B01G017200 chr5B 93.532 1546 91 4 1 1545 658084103 658085640 0 2292
3 TraesCS5B01G017200 chr5B 98.760 726 9 0 1545 2270 16028322 16029047 0 1291
4 TraesCS5B01G017200 chr5B 98.345 725 12 0 1546 2270 446954790 446954066 0 1273
5 TraesCS5B01G017200 chr4B 96.505 1545 51 2 1 1545 598448944 598447403 0 2551
6 TraesCS5B01G017200 chr4B 98.347 726 12 0 1545 2270 498358441 498359166 0 1275
7 TraesCS5B01G017200 chr4B 98.347 726 12 0 1545 2270 537849421 537848696 0 1275
8 TraesCS5B01G017200 chr2B 95.487 1551 58 3 1 1545 579908105 579909649 0 2466
9 TraesCS5B01G017200 chr2B 92.492 1545 104 7 1 1545 649657455 649655923 0 2200
10 TraesCS5B01G017200 chr6A 93.596 1546 91 5 1 1545 387215232 387216770 0 2300
11 TraesCS5B01G017200 chr7D 93.528 1545 88 6 1 1545 16799691 16798159 0 2289
12 TraesCS5B01G017200 chr4A 93.467 1546 93 5 1 1545 514407624 514406086 0 2289
13 TraesCS5B01G017200 chr3B 92.621 1545 101 8 1 1545 40993580 40992049 0 2209
14 TraesCS5B01G017200 chr3B 98.485 726 10 1 1545 2270 127999874 127999150 0 1279
15 TraesCS5B01G017200 chr3B 98.082 730 14 0 1541 2270 128006912 128006183 0 1271
16 TraesCS5B01G017200 chr7B 98.483 725 11 0 1546 2270 638388467 638387743 0 1279
17 TraesCS5B01G017200 chr7B 98.345 725 12 0 1546 2270 658304963 658305687 0 1273
18 TraesCS5B01G017200 chr6B 97.954 733 13 2 1538 2270 345844594 345845324 0 1269


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 TraesCS5B01G017200 chr5B 16010575 16012844 2269 False 4193 4193 100.000 1 2270 1 chr5B.!!$F1 2269
1 TraesCS5B01G017200 chr5B 426532763 426534301 1538 False 2327 2327 93.920 1 1545 1 chr5B.!!$F3 1544
2 TraesCS5B01G017200 chr5B 658084103 658085640 1537 False 2292 2292 93.532 1 1545 1 chr5B.!!$F4 1544
3 TraesCS5B01G017200 chr5B 16028322 16029047 725 False 1291 1291 98.760 1545 2270 1 chr5B.!!$F2 725
4 TraesCS5B01G017200 chr5B 446954066 446954790 724 True 1273 1273 98.345 1546 2270 1 chr5B.!!$R1 724
5 TraesCS5B01G017200 chr4B 598447403 598448944 1541 True 2551 2551 96.505 1 1545 1 chr4B.!!$R2 1544
6 TraesCS5B01G017200 chr4B 498358441 498359166 725 False 1275 1275 98.347 1545 2270 1 chr4B.!!$F1 725
7 TraesCS5B01G017200 chr4B 537848696 537849421 725 True 1275 1275 98.347 1545 2270 1 chr4B.!!$R1 725
8 TraesCS5B01G017200 chr2B 579908105 579909649 1544 False 2466 2466 95.487 1 1545 1 chr2B.!!$F1 1544
9 TraesCS5B01G017200 chr2B 649655923 649657455 1532 True 2200 2200 92.492 1 1545 1 chr2B.!!$R1 1544
10 TraesCS5B01G017200 chr6A 387215232 387216770 1538 False 2300 2300 93.596 1 1545 1 chr6A.!!$F1 1544
11 TraesCS5B01G017200 chr7D 16798159 16799691 1532 True 2289 2289 93.528 1 1545 1 chr7D.!!$R1 1544
12 TraesCS5B01G017200 chr4A 514406086 514407624 1538 True 2289 2289 93.467 1 1545 1 chr4A.!!$R1 1544
13 TraesCS5B01G017200 chr3B 40992049 40993580 1531 True 2209 2209 92.621 1 1545 1 chr3B.!!$R1 1544
14 TraesCS5B01G017200 chr3B 127999150 127999874 724 True 1279 1279 98.485 1545 2270 1 chr3B.!!$R2 725
15 TraesCS5B01G017200 chr3B 128006183 128006912 729 True 1271 1271 98.082 1541 2270 1 chr3B.!!$R3 729
16 TraesCS5B01G017200 chr7B 638387743 638388467 724 True 1279 1279 98.483 1546 2270 1 chr7B.!!$R1 724
17 TraesCS5B01G017200 chr7B 658304963 658305687 724 False 1273 1273 98.345 1546 2270 1 chr7B.!!$F1 724
18 TraesCS5B01G017200 chr6B 345844594 345845324 730 False 1269 1269 97.954 1538 2270 1 chr6B.!!$F1 732

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
797 866 0.89694 GGTGGTGGTGGTCGTAGAGA 60.897 60.0 0.0 0.0 36.95 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2118 0.399233 GGGCCCAGTGATACCTCTCT 60.399 60.0 19.95 0.0 0.0 3.1 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
146 147 5.415077 GCGAGAGGCCTAGTAAGTATCATTA 59.585 44.000 4.42 0.00 34.80 1.90
162 163 2.689471 TCATTAGCCATGCTCGCATTTT 59.311 40.909 0.85 0.00 40.44 1.82
431 432 3.574614 GCATGAAACAATTTGGTAGCGT 58.425 40.909 0.00 0.00 0.00 5.07
579 581 2.632996 TGAACGAGTTGGAAGAGGTGAT 59.367 45.455 0.00 0.00 0.00 3.06
584 586 2.303022 GAGTTGGAAGAGGTGATGGTGA 59.697 50.000 0.00 0.00 0.00 4.02
636 638 1.154454 TGGTGGTGGTCGTAGAGGT 59.846 57.895 0.00 0.00 36.95 3.85
797 866 0.896940 GGTGGTGGTGGTCGTAGAGA 60.897 60.000 0.00 0.00 36.95 3.10
859 928 3.476552 GTTGATAATGGATCGGCCTTCA 58.523 45.455 0.00 0.00 37.38 3.02
1093 1168 1.545651 CCAGGTTGGACAAGGAGAACC 60.546 57.143 0.00 0.00 40.96 3.62
1101 1176 2.573915 GGACAAGGAGAACCAGAAGGAT 59.426 50.000 0.00 0.00 38.69 3.24
1175 1250 0.468226 TCCACTGACCGCAAGAAGTT 59.532 50.000 0.00 0.00 43.02 2.66
1193 1268 6.937392 AGAAGTTATGGACAGAAGGTAGAAC 58.063 40.000 0.00 0.00 0.00 3.01
1201 1276 4.812626 GGACAGAAGGTAGAACGTTTTTCA 59.187 41.667 0.46 0.00 0.00 2.69
1212 1287 4.340950 AGAACGTTTTTCATGTGTCCCAAT 59.659 37.500 0.46 0.00 0.00 3.16
1258 1333 5.700832 CCAACTAACGCATATGACATACCAT 59.299 40.000 6.97 0.00 0.00 3.55
1424 1499 3.187700 GACCAACGTCGAGATTGCTTAT 58.812 45.455 0.00 0.00 0.00 1.73
1457 1532 2.363680 CTGTTCGAGGAGTCCTATGCAT 59.636 50.000 12.99 3.79 31.76 3.96
1467 1542 0.779358 TCCTATGCATGGGGATTGGG 59.221 55.000 27.02 3.15 38.08 4.12
1524 1599 0.251832 AAGCGTGAGGAAGAGAGGGA 60.252 55.000 0.00 0.00 0.00 4.20
1801 1876 4.210120 GTCATTAGGAGAATGACGTGATGC 59.790 45.833 13.07 0.00 44.56 3.91
1824 1899 5.192927 CACAAGACCCAATCCTAAGCATAA 58.807 41.667 0.00 0.00 0.00 1.90
2043 2118 3.517901 AGGATTTGTCACTCCGGATTACA 59.482 43.478 3.57 7.12 36.62 2.41
2067 2142 1.271840 GGTATCACTGGGCCCACTCA 61.272 60.000 24.45 7.42 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 4.321452 CCATTATAAAATGCGAGCATGGCT 60.321 41.667 11.64 2.15 41.95 4.75
162 163 1.666553 CGCCTTCGCCGCCATTATA 60.667 57.895 0.00 0.00 0.00 0.98
579 581 0.834261 TTCCTCGACCACCATCACCA 60.834 55.000 0.00 0.00 0.00 4.17
584 586 1.296715 GTGCTTCCTCGACCACCAT 59.703 57.895 0.00 0.00 0.00 3.55
636 638 1.066858 GCACCTCTAGCACTTGTGCTA 60.067 52.381 27.11 27.11 46.56 3.49
797 866 2.498167 CACCTCTAGCACTTGTGCTTT 58.502 47.619 29.37 12.30 43.52 3.51
1035 1104 1.296392 CATGTCCTCTTGGTCCGCA 59.704 57.895 0.00 0.00 34.23 5.69
1093 1168 2.173356 TGGGCACATCCTTATCCTTCTG 59.827 50.000 0.00 0.00 34.39 3.02
1101 1176 0.037590 GTGGTGTGGGCACATCCTTA 59.962 55.000 13.04 0.00 46.95 2.69
1175 1250 5.733620 AAACGTTCTACCTTCTGTCCATA 57.266 39.130 0.00 0.00 0.00 2.74
1193 1268 5.062058 GCATAATTGGGACACATGAAAAACG 59.938 40.000 0.00 0.00 39.29 3.60
1212 1287 3.123050 CCTTCGACGATCATGTGCATAA 58.877 45.455 0.00 0.00 0.00 1.90
1434 1509 2.379972 CATAGGACTCCTCGAACAGGT 58.620 52.381 0.00 0.00 43.95 4.00
1524 1599 0.398318 AGCCTCCTTCTCTTTGCGTT 59.602 50.000 0.00 0.00 0.00 4.84
1801 1876 3.071874 TGCTTAGGATTGGGTCTTGTG 57.928 47.619 0.00 0.00 0.00 3.33
2043 2118 0.399233 GGGCCCAGTGATACCTCTCT 60.399 60.000 19.95 0.00 0.00 3.10
2067 2142 6.111669 AGCTCATTATGATGATGCACTACT 57.888 37.500 17.69 2.05 41.28 2.57


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

AutoCloner maintained by Alex Coulton.