Multiple sequence alignment - TraesCS5A01G179200

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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 TraesCS5A01G179200 chr5A 100.000 2108 0 0 1 2108 377186970 377184863 0.000000e+00 3893.0
1 TraesCS5A01G179200 chr5A 97.500 40 1 0 1392 1431 377185478 377185439 3.750000e-08 69.4
2 TraesCS5A01G179200 chr5A 97.500 40 1 0 1493 1532 377185579 377185540 3.750000e-08 69.4
3 TraesCS5A01G179200 chr5B 96.652 1643 41 3 479 2108 322917209 322915568 0.000000e+00 2717.0
4 TraesCS5A01G179200 chr5B 90.570 509 16 5 1 481 322917769 322917265 0.000000e+00 645.0
5 TraesCS5A01G179200 chr5B 100.000 40 0 0 1493 1532 322916294 322916255 8.070000e-10 75.0
6 TraesCS5A01G179200 chr5B 93.478 46 3 0 1447 1492 37648734 37648779 3.750000e-08 69.4
7 TraesCS5A01G179200 chr5B 97.500 40 1 0 1392 1431 322916193 322916154 3.750000e-08 69.4
8 TraesCS5A01G179200 chr5D 92.899 1197 43 10 245 1431 285468887 285467723 0.000000e+00 1701.0
9 TraesCS5A01G179200 chr5D 92.114 634 25 10 1493 2108 285467762 285467136 0.000000e+00 870.0
10 TraesCS5A01G179200 chr5D 95.872 436 18 0 1 436 285469274 285468839 0.000000e+00 706.0
11 TraesCS5A01G179200 chr7D 93.548 62 3 1 1437 1498 175667708 175667648 8.010000e-15 91.6
12 TraesCS5A01G179200 chr4B 92.857 56 4 0 1437 1492 621965568 621965623 4.820000e-12 82.4
13 TraesCS5A01G179200 chr3B 100.000 31 0 0 637 667 379394969 379394999 8.120000e-05 58.4
14 TraesCS5A01G179200 chr3B 96.774 31 1 0 637 667 129698624 129698594 4.000000e-03 52.8
15 TraesCS5A01G179200 chr1B 100.000 31 0 0 1331 1361 32595880 32595850 8.120000e-05 58.4
16 TraesCS5A01G179200 chr6D 100.000 29 0 0 639 667 82728012 82728040 1.000000e-03 54.7
17 TraesCS5A01G179200 chr1D 100.000 29 0 0 639 667 488753113 488753141 1.000000e-03 54.7


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 TraesCS5A01G179200 chr5A 377184863 377186970 2107 True 1343.933333 3893 98.333333 1 2108 3 chr5A.!!$R1 2107
1 TraesCS5A01G179200 chr5B 322915568 322917769 2201 True 876.600000 2717 96.180500 1 2108 4 chr5B.!!$R1 2107
2 TraesCS5A01G179200 chr5D 285467136 285469274 2138 True 1092.333333 1701 93.628333 1 2108 3 chr5D.!!$R1 2107

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
933 1154 0.615331 CTCATACCACACCAGCCACT 59.385 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 2053 0.623194 TATGCACCAAGCTTAGGGCA 59.377 50.0 23.96 23.96 45.94 5.36 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
50 51 5.139727 AGATGGATCAACAAAACAACCTGA 58.860 37.500 0.00 0.0 0.00 3.86
77 78 8.708742 TGTTTGAGTAAAATGATCTGAAGTACG 58.291 33.333 0.00 0.0 0.00 3.67
134 135 9.750125 AAACAATTTTCTGAGTCCAAGAATTAC 57.250 29.630 0.00 0.0 0.00 1.89
178 179 1.486310 TCCTATGCTGCCGACTTGATT 59.514 47.619 0.00 0.0 0.00 2.57
347 374 2.104967 TGCACTACTACCAGGCGTTAT 58.895 47.619 0.00 0.0 0.00 1.89
358 385 2.609459 CCAGGCGTTATCATCTGTCAAC 59.391 50.000 0.00 0.0 0.00 3.18
600 821 6.547510 GCATTGGTAGGATATCTTTTGGAGTT 59.452 38.462 2.05 0.0 0.00 3.01
678 899 4.564406 GGATGACCACTTGATCTTGTCTGT 60.564 45.833 0.00 0.0 35.97 3.41
926 1147 2.366916 CCCTCTCATCTCATACCACACC 59.633 54.545 0.00 0.0 0.00 4.16
933 1154 0.615331 CTCATACCACACCAGCCACT 59.385 55.000 0.00 0.0 0.00 4.00
1041 1265 0.767375 AGCTCAACAGGGCTTTCAGA 59.233 50.000 0.00 0.0 34.96 3.27
1263 1489 0.322816 TTCTCTCCATGGTTGCCTGC 60.323 55.000 12.58 0.0 0.00 4.85
1435 1666 7.615582 TTGATGACAACCTGAGATTGATAAC 57.384 36.000 0.00 0.0 0.00 1.89
1705 1936 3.165875 CTGGTCCTTTGAGAGGTGACTA 58.834 50.000 0.00 0.0 46.39 2.59
1733 1964 4.952262 TGTTGTTCTCTTGATATGCTGC 57.048 40.909 0.00 0.0 0.00 5.25
1767 1998 7.201758 GCCATTGTTGTTCTCTTGATATGATGA 60.202 37.037 0.00 0.0 0.00 2.92
1791 2022 2.810852 CTGCTCTTTCAGGAACTCAACC 59.189 50.000 0.00 0.0 34.60 3.77
1803 2034 3.314080 GGAACTCAACCGTTTCATGTGAA 59.686 43.478 0.00 0.0 0.00 3.18
1817 2048 3.005684 TCATGTGAAACCATTGCAACTCC 59.994 43.478 0.00 0.0 34.36 3.85
1822 2053 3.387374 TGAAACCATTGCAACTCCAACAT 59.613 39.130 0.00 0.0 0.00 2.71
2031 2287 4.987408 TGCATGAGTTAATGTCAATGGG 57.013 40.909 0.00 0.0 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.756074 TCAAACATCAGGTTGTTTTGTTGATC 59.244 34.615 5.89 0.00 45.14 2.92
77 78 5.269505 AGTCAAGTATATGAGTGCTCCAC 57.730 43.478 0.00 0.00 31.82 4.02
134 135 4.683320 CAGCAGTAGGATATGAACACATCG 59.317 45.833 0.00 0.00 0.00 3.84
376 403 0.908198 GGCATGGAGTTCTCAGTCCT 59.092 55.000 0.00 0.00 42.60 3.85
600 821 5.623956 TGTTTAGTGACTCCAAGAAAGGA 57.376 39.130 0.00 0.00 36.00 3.36
678 899 6.007703 CCCCAGAGAATTACAGTGGTAAAAA 58.992 40.000 0.00 0.00 42.43 1.94
895 1116 3.450096 TGAGATGAGAGGGATGTTGAGTG 59.550 47.826 0.00 0.00 0.00 3.51
926 1147 2.886081 CAGCTTGTAGACTAGTGGCTG 58.114 52.381 0.00 12.82 39.38 4.85
933 1154 2.808919 AGGCAGACAGCTTGTAGACTA 58.191 47.619 0.00 0.00 44.79 2.59
1041 1265 3.269906 TGTAGAACCTAGCCCTCTTCTCT 59.730 47.826 0.00 0.00 0.00 3.10
1263 1489 1.604593 CCCCCTTTGCCTGTGACAG 60.605 63.158 5.42 5.42 0.00 3.51
1421 1652 5.463724 GCGGTAAAGAGTTATCAATCTCAGG 59.536 44.000 0.00 0.00 33.63 3.86
1433 1664 5.479124 TTAAGAGGAAGCGGTAAAGAGTT 57.521 39.130 0.00 0.00 0.00 3.01
1434 1665 5.187186 TCATTAAGAGGAAGCGGTAAAGAGT 59.813 40.000 0.00 0.00 0.00 3.24
1435 1666 5.661458 TCATTAAGAGGAAGCGGTAAAGAG 58.339 41.667 0.00 0.00 0.00 2.85
1705 1936 6.294176 GCATATCAAGAGAACAACAACAGGTT 60.294 38.462 0.00 0.00 41.47 3.50
1733 1964 4.940046 AGAGAACAACAATGGCATAGACAG 59.060 41.667 0.00 0.00 0.00 3.51
1767 1998 2.039480 TGAGTTCCTGAAAGAGCAGCAT 59.961 45.455 0.00 0.00 34.07 3.79
1803 2034 2.548493 GCATGTTGGAGTTGCAATGGTT 60.548 45.455 0.59 0.00 36.40 3.67
1817 2048 1.203052 CACCAAGCTTAGGGCATGTTG 59.797 52.381 16.21 4.16 44.79 3.33
1822 2053 0.623194 TATGCACCAAGCTTAGGGCA 59.377 50.000 23.96 23.96 45.94 5.36
2017 2273 4.142469 CGAGGTTTCCCCATTGACATTAAC 60.142 45.833 0.00 0.00 34.66 2.01
2024 2280 1.003118 CAGTCGAGGTTTCCCCATTGA 59.997 52.381 0.00 0.00 34.66 2.57
2031 2287 2.076863 CATGGTTCAGTCGAGGTTTCC 58.923 52.381 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.