Multiple sequence alignment - TraesCS5A01G097900

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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 TraesCS5A01G097900 chr5A 100.000 2619 0 0 1 2619 139476833 139474215 0 4837
1 TraesCS5A01G097900 chr2D 98.244 2619 43 2 1 2619 644817772 644820387 0 4578
2 TraesCS5A01G097900 chr4D 97.977 2620 50 2 1 2619 403009002 403011619 0 4542
3 TraesCS5A01G097900 chr7D 97.862 2619 51 3 1 2619 29571715 29569102 0 4521
4 TraesCS5A01G097900 chr1D 97.327 2619 65 3 1 2619 187808478 187811091 0 4444
5 TraesCS5A01G097900 chr4B 95.513 2630 103 6 1 2619 74348791 74351416 0 4189
6 TraesCS5A01G097900 chr2B 95.057 2286 105 3 342 2619 63131876 63129591 0 3589
7 TraesCS5A01G097900 chr3D 95.437 2038 86 5 584 2619 107214418 107216450 0 3241
8 TraesCS5A01G097900 chr3D 96.604 589 17 3 1 588 107205666 107206252 0 974
9 TraesCS5A01G097900 chr6D 92.576 1805 91 13 1 1781 433250906 433252691 0 2551
10 TraesCS5A01G097900 chr6A 98.311 1362 19 4 1 1360 615073839 615072480 0 2385
11 TraesCS5A01G097900 chr6A 98.379 987 15 1 1633 2619 615072488 615071503 0 1733
12 TraesCS5A01G097900 chr2A 92.460 1618 86 12 181 1781 605004802 605003204 0 2279
13 TraesCS5A01G097900 chr7B 95.704 1257 53 1 1363 2619 400417620 400416365 0 2021
14 TraesCS5A01G097900 chr6B 96.198 526 19 1 1 526 128934554 128934030 0 859


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 TraesCS5A01G097900 chr5A 139474215 139476833 2618 True 4837 4837 100.000 1 2619 1 chr5A.!!$R1 2618
1 TraesCS5A01G097900 chr2D 644817772 644820387 2615 False 4578 4578 98.244 1 2619 1 chr2D.!!$F1 2618
2 TraesCS5A01G097900 chr4D 403009002 403011619 2617 False 4542 4542 97.977 1 2619 1 chr4D.!!$F1 2618
3 TraesCS5A01G097900 chr7D 29569102 29571715 2613 True 4521 4521 97.862 1 2619 1 chr7D.!!$R1 2618
4 TraesCS5A01G097900 chr1D 187808478 187811091 2613 False 4444 4444 97.327 1 2619 1 chr1D.!!$F1 2618
5 TraesCS5A01G097900 chr4B 74348791 74351416 2625 False 4189 4189 95.513 1 2619 1 chr4B.!!$F1 2618
6 TraesCS5A01G097900 chr2B 63129591 63131876 2285 True 3589 3589 95.057 342 2619 1 chr2B.!!$R1 2277
7 TraesCS5A01G097900 chr3D 107214418 107216450 2032 False 3241 3241 95.437 584 2619 1 chr3D.!!$F2 2035
8 TraesCS5A01G097900 chr3D 107205666 107206252 586 False 974 974 96.604 1 588 1 chr3D.!!$F1 587
9 TraesCS5A01G097900 chr6D 433250906 433252691 1785 False 2551 2551 92.576 1 1781 1 chr6D.!!$F1 1780
10 TraesCS5A01G097900 chr6A 615071503 615073839 2336 True 2059 2385 98.345 1 2619 2 chr6A.!!$R1 2618
11 TraesCS5A01G097900 chr2A 605003204 605004802 1598 True 2279 2279 92.460 181 1781 1 chr2A.!!$R1 1600
12 TraesCS5A01G097900 chr7B 400416365 400417620 1255 True 2021 2021 95.704 1363 2619 1 chr7B.!!$R1 1256
13 TraesCS5A01G097900 chr6B 128934030 128934554 524 True 859 859 96.198 1 526 1 chr6B.!!$R1 525

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
970 1008 0.618458 GTATGTCCTGGTGCTTCCCA 59.382 55.0 0.0 0.0 34.77 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2419 5.00901 TGACTGCAAGGAATTGTTTCTCTTC 59.991 40.0 0.0 0.0 39.3 2.87 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
32 33 7.304054 AGGAAGATGGGGATATATGTAGAGA 57.696 40.000 0.00 0.00 0.00 3.10
33 34 7.723382 AGGAAGATGGGGATATATGTAGAGAA 58.277 38.462 0.00 0.00 0.00 2.87
70 77 5.370880 GGAAGGGAGATGGGCATATATGTAT 59.629 44.000 14.14 6.75 0.00 2.29
516 529 4.037446 GTGGACTTTACATGGTTTCTTGCA 59.963 41.667 0.00 0.00 0.00 4.08
517 530 4.646945 TGGACTTTACATGGTTTCTTGCAA 59.353 37.500 0.00 0.00 0.00 4.08
661 698 2.032680 TTGTACCTTATTGCCGGCTC 57.967 50.000 29.70 0.00 0.00 4.70
690 727 2.431057 ACACAAGAACCTCGACACTCTT 59.569 45.455 0.00 0.00 0.00 2.85
691 728 3.118738 ACACAAGAACCTCGACACTCTTT 60.119 43.478 0.00 0.00 0.00 2.52
949 987 1.064208 CACGACCACCGAGATGTAGAG 59.936 57.143 0.00 0.00 41.76 2.43
970 1008 0.618458 GTATGTCCTGGTGCTTCCCA 59.382 55.000 0.00 0.00 34.77 4.37
1118 1156 1.003118 AGTGCGGTGATTTCTTGCCTA 59.997 47.619 0.00 0.00 0.00 3.93
1222 1265 9.862371 AATAACTACAACAAAATTGTGACACAA 57.138 25.926 22.61 22.61 42.95 3.33
1345 1388 7.971168 TGGAAAAAGTGTGTAGTTATTGTTGTG 59.029 33.333 0.00 0.00 0.00 3.33
1416 1459 9.278978 AGTACTATGTGTGATATGTGAGAGTAG 57.721 37.037 0.00 0.00 0.00 2.57
1451 1496 0.188342 AACATGGTGGACAGGGCTTT 59.812 50.000 0.00 0.00 34.56 3.51
1465 1510 0.536006 GGCTTTGTGACTGAGCTGGT 60.536 55.000 0.00 0.00 36.66 4.00
1792 1860 4.684242 CACATTGTTGTTGCTACGAGTCTA 59.316 41.667 0.00 0.00 32.34 2.59
1848 1916 4.766891 AGTTGATTGTCGGATTTCACCAAT 59.233 37.500 0.00 0.00 0.00 3.16
1870 1938 9.996554 CCAATAAATAAAAACAGAGGAAAACCT 57.003 29.630 0.00 0.00 0.00 3.50
2057 2125 5.760743 AGGAGCACTCTTAGTTTTGTTCTTC 59.239 40.000 0.00 0.00 0.00 2.87
2351 2419 7.330454 CGATCCTATCCACTATCACAATGAAAG 59.670 40.741 0.00 0.00 0.00 2.62
2406 2474 0.114168 AGCATGTTGGGGCTTGGTTA 59.886 50.000 0.00 0.00 36.92 2.85
2461 2529 6.197842 CGTAAAAGGATCTACGTATCCACAAC 59.802 42.308 17.60 9.80 46.81 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.597304 TCCCTTCCTCCTATCTCCCTTT 59.403 50.000 0.0 0.0 0.00 3.11
33 34 2.181196 CTCCCTTCCTCCTATCTCCCTT 59.819 54.545 0.0 0.0 0.00 3.95
70 77 4.311613 TCCCTCTCTGATCTTCCTCTCTA 58.688 47.826 0.0 0.0 0.00 2.43
661 698 4.857588 GTCGAGGTTCTTGTGTGTATAGTG 59.142 45.833 0.0 0.0 0.00 2.74
949 987 0.107165 GGAAGCACCAGGACATACCC 60.107 60.000 0.0 0.0 40.05 3.69
970 1008 2.305927 TCAAGAGGCGGGAAAGATTCTT 59.694 45.455 0.0 0.0 0.00 2.52
1144 1183 1.153745 GTGCGTGAGAAGAGGCGAT 60.154 57.895 0.0 0.0 0.00 4.58
1222 1265 2.638363 GTTCCTTCTCCCACTAACCACT 59.362 50.000 0.0 0.0 0.00 4.00
1416 1459 8.085296 TCCACCATGTTTCATTTTGTATTACAC 58.915 33.333 0.0 0.0 0.00 2.90
1426 1470 2.899256 CCCTGTCCACCATGTTTCATTT 59.101 45.455 0.0 0.0 0.00 2.32
1451 1496 4.350368 TTTATTCACCAGCTCAGTCACA 57.650 40.909 0.0 0.0 0.00 3.58
1465 1510 6.514212 CGTTTCCACCACTGACATTTTATTCA 60.514 38.462 0.0 0.0 0.00 2.57
2351 2419 5.009010 TGACTGCAAGGAATTGTTTCTCTTC 59.991 40.000 0.0 0.0 39.30 2.87
2461 2529 6.515272 AACTCACATGGGTAAGCAAATTAG 57.485 37.500 0.0 0.0 0.00 1.73


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

AutoCloner maintained by Alex Coulton.