Multiple sequence alignment - TraesCS5B01G112400

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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 TraesCS5B01G112400 chr5B 100.000 2336 0 0 1 2336 175704575 175706910 0 4314
1 TraesCS5B01G112400 chr5B 96.855 1399 41 3 941 2336 140795573 140794175 0 2337
2 TraesCS5B01G112400 chr6B 97.353 1398 35 2 941 2336 221951597 221952994 0 2375
3 TraesCS5B01G112400 chr6B 97.353 1398 34 3 941 2336 274703215 274701819 0 2374
4 TraesCS5B01G112400 chr6B 97.137 1397 38 2 941 2336 456389044 456390439 0 2357
5 TraesCS5B01G112400 chr6B 95.903 952 29 5 1 942 409504167 409505118 0 1533
6 TraesCS5B01G112400 chr7B 96.996 1398 40 2 941 2336 278618540 278617143 0 2348
7 TraesCS5B01G112400 chr1A 96.937 1404 35 2 941 2336 382346945 382345542 0 2348
8 TraesCS5B01G112400 chr3B 96.924 1398 40 3 942 2336 247216547 247217944 0 2340
9 TraesCS5B01G112400 chr3B 96.850 1397 42 2 941 2336 171347295 171345900 0 2335
10 TraesCS5B01G112400 chr3B 96.109 951 27 2 2 942 442116823 442117773 0 1543
11 TraesCS5B01G112400 chr2B 96.853 1398 40 4 941 2335 374639523 374640919 0 2335
12 TraesCS5B01G112400 chr4D 86.784 1763 188 25 607 2336 254082350 254080600 0 1923
13 TraesCS5B01G112400 chr4A 96.534 952 23 2 1 942 474093425 474094376 0 1567
14 TraesCS5B01G112400 chr3A 96.534 952 22 3 1 942 19248579 19249529 0 1565
15 TraesCS5B01G112400 chr2A 96.425 951 24 6 1 942 128046339 128045390 0 1559
16 TraesCS5B01G112400 chr2A 96.218 952 26 2 1 942 727750540 727749589 0 1550
17 TraesCS5B01G112400 chr6A 96.017 954 23 7 1 942 415940109 415941059 0 1537
18 TraesCS5B01G112400 chr1B 95.992 948 29 4 3 942 269953372 269954318 0 1531
19 TraesCS5B01G112400 chr1B 95.689 951 30 2 1 942 270048512 270049460 0 1519
20 TraesCS5B01G112400 chr1B 95.948 839 22 3 116 942 519412785 519411947 0 1351
21 TraesCS5B01G112400 chr1B 92.364 956 57 6 1 942 159789626 159790579 0 1347
22 TraesCS5B01G112400 chr4B 93.994 949 45 7 2 942 162831480 162830536 0 1426


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 TraesCS5B01G112400 chr5B 175704575 175706910 2335 False 4314 4314 100.000 1 2336 1 chr5B.!!$F1 2335
1 TraesCS5B01G112400 chr5B 140794175 140795573 1398 True 2337 2337 96.855 941 2336 1 chr5B.!!$R1 1395
2 TraesCS5B01G112400 chr6B 221951597 221952994 1397 False 2375 2375 97.353 941 2336 1 chr6B.!!$F1 1395
3 TraesCS5B01G112400 chr6B 274701819 274703215 1396 True 2374 2374 97.353 941 2336 1 chr6B.!!$R1 1395
4 TraesCS5B01G112400 chr6B 456389044 456390439 1395 False 2357 2357 97.137 941 2336 1 chr6B.!!$F3 1395
5 TraesCS5B01G112400 chr6B 409504167 409505118 951 False 1533 1533 95.903 1 942 1 chr6B.!!$F2 941
6 TraesCS5B01G112400 chr7B 278617143 278618540 1397 True 2348 2348 96.996 941 2336 1 chr7B.!!$R1 1395
7 TraesCS5B01G112400 chr1A 382345542 382346945 1403 True 2348 2348 96.937 941 2336 1 chr1A.!!$R1 1395
8 TraesCS5B01G112400 chr3B 247216547 247217944 1397 False 2340 2340 96.924 942 2336 1 chr3B.!!$F1 1394
9 TraesCS5B01G112400 chr3B 171345900 171347295 1395 True 2335 2335 96.850 941 2336 1 chr3B.!!$R1 1395
10 TraesCS5B01G112400 chr3B 442116823 442117773 950 False 1543 1543 96.109 2 942 1 chr3B.!!$F2 940
11 TraesCS5B01G112400 chr2B 374639523 374640919 1396 False 2335 2335 96.853 941 2335 1 chr2B.!!$F1 1394
12 TraesCS5B01G112400 chr4D 254080600 254082350 1750 True 1923 1923 86.784 607 2336 1 chr4D.!!$R1 1729
13 TraesCS5B01G112400 chr4A 474093425 474094376 951 False 1567 1567 96.534 1 942 1 chr4A.!!$F1 941
14 TraesCS5B01G112400 chr3A 19248579 19249529 950 False 1565 1565 96.534 1 942 1 chr3A.!!$F1 941
15 TraesCS5B01G112400 chr2A 128045390 128046339 949 True 1559 1559 96.425 1 942 1 chr2A.!!$R1 941
16 TraesCS5B01G112400 chr2A 727749589 727750540 951 True 1550 1550 96.218 1 942 1 chr2A.!!$R2 941
17 TraesCS5B01G112400 chr6A 415940109 415941059 950 False 1537 1537 96.017 1 942 1 chr6A.!!$F1 941
18 TraesCS5B01G112400 chr1B 269953372 269954318 946 False 1531 1531 95.992 3 942 1 chr1B.!!$F2 939
19 TraesCS5B01G112400 chr1B 270048512 270049460 948 False 1519 1519 95.689 1 942 1 chr1B.!!$F3 941
20 TraesCS5B01G112400 chr1B 519411947 519412785 838 True 1351 1351 95.948 116 942 1 chr1B.!!$R1 826
21 TraesCS5B01G112400 chr1B 159789626 159790579 953 False 1347 1347 92.364 1 942 1 chr1B.!!$F1 941
22 TraesCS5B01G112400 chr4B 162830536 162831480 944 True 1426 1426 93.994 2 942 1 chr4B.!!$R1 940

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
278 280 0.610687 CAGGCCGAGAGAAGGAGTTT 59.389 55.0 0.0 0.0 0.0 2.66 F
1007 1028 1.673767 ACACAGGATTGGATGGTCCT 58.326 50.0 0.0 0.0 45.6 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1129 1.075482 CACCCTTGGCACCATCTGT 59.925 57.895 0.0 0.0 0.0 3.41 R
2186 2238 1.531423 CTGCCTGCAACTCATCAACT 58.469 50.000 0.0 0.0 0.0 3.16 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
154 156 5.283294 TCGTTTTGAAGTCGATAGTTGTGA 58.717 37.500 0.00 0.00 37.40 3.58
278 280 0.610687 CAGGCCGAGAGAAGGAGTTT 59.389 55.000 0.00 0.00 0.00 2.66
544 550 4.141937 CGAGGGAGGACATCAAGTGAATTA 60.142 45.833 0.00 0.00 0.00 1.40
642 657 5.277825 TCTAGTTCAACATTTTTGTTGCGG 58.722 37.500 12.74 3.32 46.21 5.69
813 831 9.884636 ACATTTATATGTCTAACTGTACTGCAA 57.115 29.630 0.00 0.00 41.07 4.08
960 981 2.872858 GGTCTTGTCTGAAACACAGTCC 59.127 50.000 0.00 0.00 45.86 3.85
1007 1028 1.673767 ACACAGGATTGGATGGTCCT 58.326 50.000 0.00 0.00 45.60 3.85
1056 1077 4.202441 AGCAAAGCAAGAAGAAGTTGAGA 58.798 39.130 0.00 0.00 0.00 3.27
1108 1129 4.534647 AAGGAGAAGCAGAGGAGATCTA 57.465 45.455 0.00 0.00 36.10 1.98
1211 1250 0.532862 AGTCCACGTGTTGCTGGAAG 60.533 55.000 15.65 0.00 38.33 3.46
1266 1305 2.912295 TGGTGGAAGTGATGATCCTCAA 59.088 45.455 1.92 0.00 0.00 3.02
1273 1312 3.005554 AGTGATGATCCTCAACGCAAAG 58.994 45.455 1.92 0.00 32.94 2.77
1568 1620 2.819608 TGCATTTCCCTTTACACAGAGC 59.180 45.455 0.00 0.00 0.00 4.09
1623 1675 4.042884 TGATGGTGAGGGAGATGATTCTT 58.957 43.478 0.00 0.00 30.30 2.52
1723 1775 2.099756 GTGTTAGGGATGCTGGATTTGC 59.900 50.000 0.00 0.00 0.00 3.68
1748 1800 7.308229 GCTGTTGTCTTTGATCTGACAGTAAAT 60.308 37.037 1.59 0.00 42.98 1.40
1913 1965 2.362120 GCACCCATGCCTGCTTCT 60.362 61.111 5.75 0.00 46.97 2.85
2019 2071 3.054728 TGAGAAGTTGAAGGTGTTGGTGA 60.055 43.478 0.00 0.00 0.00 4.02
2307 2359 1.268743 ACTGCTTGAAGCTTCGCAAAC 60.269 47.619 23.53 11.06 42.97 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 156 1.620819 CCCTAGATCCGCATTGCTACT 59.379 52.381 7.12 3.51 0.00 2.57
278 280 4.347000 GGAATAAGCACTCCACATACCCTA 59.653 45.833 0.00 0.00 0.00 3.53
544 550 6.268847 ACTTATAGGAGAAGATTCAATCGGCT 59.731 38.462 0.00 0.00 0.00 5.52
642 657 8.543774 GCTGCATATACTAAAATCACGGATATC 58.456 37.037 0.00 0.00 0.00 1.63
813 831 9.271738 CGTTAAAAATTGCACAAAAAGAACAAT 57.728 25.926 0.00 0.00 32.53 2.71
960 981 3.368843 CCTCTGTACCATCAACAGACTGG 60.369 52.174 7.51 0.40 46.38 4.00
1007 1028 4.183865 CTCATATTGACGAAGCTGTTCCA 58.816 43.478 0.00 0.00 0.00 3.53
1056 1077 8.606602 GCAAACTCTTTTGACTCAATTTCAAAT 58.393 29.630 4.96 0.00 44.38 2.32
1108 1129 1.075482 CACCCTTGGCACCATCTGT 59.925 57.895 0.00 0.00 0.00 3.41
1211 1250 4.583871 TCTCTTGCCAAGATTCTTCTTCC 58.416 43.478 7.75 0.00 40.28 3.46
1568 1620 5.871524 TGCATTGCTCTTACTAGACTTCTTG 59.128 40.000 10.49 0.00 0.00 3.02
1623 1675 5.163703 ACAAACGCACAGTCTTGTTAAATCA 60.164 36.000 0.00 0.00 34.62 2.57
1723 1775 7.482654 TTTACTGTCAGATCAAAGACAACAG 57.517 36.000 6.91 9.50 43.48 3.16
1748 1800 7.536964 CACATAAGAATGCACGACACATTTTTA 59.463 33.333 11.79 11.79 38.02 1.52
1913 1965 3.123050 CAACGATTCATCATGACCGCTA 58.877 45.455 0.00 0.00 0.00 4.26
2019 2071 7.335422 GTCAACACTCACATAATCATCTTCCTT 59.665 37.037 0.00 0.00 0.00 3.36
2186 2238 1.531423 CTGCCTGCAACTCATCAACT 58.469 50.000 0.00 0.00 0.00 3.16
2307 2359 2.287644 TCAACGTGTGCATGACTGAAAG 59.712 45.455 0.00 0.00 42.29 2.62


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

AutoCloner maintained by Alex Coulton.