Multiple sequence alignment - TraesCS5D01G169700

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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 TraesCS5D01G169700 chr5D 100.000 2462 0 0 1 2462 266086673 266089134 0.000000e+00 4547
1 TraesCS5D01G169700 chr3D 91.829 2362 168 15 104 2458 385264628 385266971 0.000000e+00 3269
2 TraesCS5D01G169700 chr5A 91.455 2364 169 16 115 2462 354313925 354311579 0.000000e+00 3216
3 TraesCS5D01G169700 chr5A 91.847 1251 88 9 110 1349 227520523 227519276 0.000000e+00 1733
4 TraesCS5D01G169700 chr5A 91.486 1245 92 9 116 1349 227422416 227421175 0.000000e+00 1700
5 TraesCS5D01G169700 chr5A 90.129 932 91 1 1531 2461 475502487 475501556 0.000000e+00 1210
6 TraesCS5D01G169700 chr5A 94.017 117 7 0 1 117 354314652 354314536 7.000000e-41 178
7 TraesCS5D01G169700 chr5B 90.450 2377 172 28 104 2462 543625383 543623044 0.000000e+00 3081
8 TraesCS5D01G169700 chr5B 95.495 111 2 1 1 111 299848346 299848453 9.050000e-40 174
9 TraesCS5D01G169700 chr4D 92.037 1620 115 10 104 1712 121764290 121765906 0.000000e+00 2265
10 TraesCS5D01G169700 chr4D 91.188 749 64 2 1714 2461 121794198 121794945 0.000000e+00 1016
11 TraesCS5D01G169700 chr4B 91.862 1536 122 3 929 2461 621425331 621426866 0.000000e+00 2141
12 TraesCS5D01G169700 chr7A 91.853 1252 86 9 110 1349 730114760 730113513 0.000000e+00 1733
13 TraesCS5D01G169700 chrUn 91.687 1251 90 9 110 1349 184002032 184000785 0.000000e+00 1722
14 TraesCS5D01G169700 chrUn 91.488 1257 93 9 104 1349 191276481 191277734 0.000000e+00 1716
15 TraesCS5D01G169700 chr2B 91.905 210 17 0 2252 2461 61456460 61456251 6.660000e-76 294


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 TraesCS5D01G169700 chr5D 266086673 266089134 2461 False 4547 4547 100.000 1 2462 1 chr5D.!!$F1 2461
1 TraesCS5D01G169700 chr3D 385264628 385266971 2343 False 3269 3269 91.829 104 2458 1 chr3D.!!$F1 2354
2 TraesCS5D01G169700 chr5A 227519276 227520523 1247 True 1733 1733 91.847 110 1349 1 chr5A.!!$R2 1239
3 TraesCS5D01G169700 chr5A 227421175 227422416 1241 True 1700 1700 91.486 116 1349 1 chr5A.!!$R1 1233
4 TraesCS5D01G169700 chr5A 354311579 354314652 3073 True 1697 3216 92.736 1 2462 2 chr5A.!!$R4 2461
5 TraesCS5D01G169700 chr5A 475501556 475502487 931 True 1210 1210 90.129 1531 2461 1 chr5A.!!$R3 930
6 TraesCS5D01G169700 chr5B 543623044 543625383 2339 True 3081 3081 90.450 104 2462 1 chr5B.!!$R1 2358
7 TraesCS5D01G169700 chr4D 121764290 121765906 1616 False 2265 2265 92.037 104 1712 1 chr4D.!!$F1 1608
8 TraesCS5D01G169700 chr4D 121794198 121794945 747 False 1016 1016 91.188 1714 2461 1 chr4D.!!$F2 747
9 TraesCS5D01G169700 chr4B 621425331 621426866 1535 False 2141 2141 91.862 929 2461 1 chr4B.!!$F1 1532
10 TraesCS5D01G169700 chr7A 730113513 730114760 1247 True 1733 1733 91.853 110 1349 1 chr7A.!!$R1 1239
11 TraesCS5D01G169700 chrUn 184000785 184002032 1247 True 1722 1722 91.687 110 1349 1 chrUn.!!$R1 1239
12 TraesCS5D01G169700 chrUn 191276481 191277734 1253 False 1716 1716 91.488 104 1349 1 chrUn.!!$F1 1245

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
987 1610 1.023513 CGGCTGAAGAGCTGGAAAGG 61.024 60.0 0.0 0.0 46.54 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2492 0.117541 TCCCAGTACAGCCAACCCTA 59.882 55.0 0.0 0.0 0.0 3.53 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
64 65 2.031508 CACACGCACCTTTTATTTCCGT 60.032 45.455 0.00 0.0 0.00 4.69
68 69 1.466866 GCACCTTTTATTTCCGTCGCC 60.467 52.381 0.00 0.0 0.00 5.54
224 838 2.838736 TCAAAATGATAGCTCTCCGGC 58.161 47.619 0.00 0.0 0.00 6.13
293 907 1.481871 ACCGGGTCGACTCATTACAT 58.518 50.000 17.19 0.0 0.00 2.29
319 933 6.655078 AACATTTTGTTGGCTTATGAGAGT 57.345 33.333 0.00 0.0 39.45 3.24
327 941 9.851686 TTTGTTGGCTTATGAGAGTATTCATAT 57.148 29.630 0.00 0.0 39.20 1.78
391 1005 5.335127 CAGTTAAACTGGATATGCACAAGC 58.665 41.667 0.00 0.0 42.35 4.01
393 1007 2.814805 AACTGGATATGCACAAGCCT 57.185 45.000 6.72 0.0 41.13 4.58
394 1008 3.931907 AACTGGATATGCACAAGCCTA 57.068 42.857 6.72 0.0 41.13 3.93
414 1028 6.069963 AGCCTATATGATAGGGTTGAATGGAC 60.070 42.308 10.73 0.0 42.22 4.02
441 1056 3.251479 AGCAGAATGATGACACGCTTA 57.749 42.857 0.00 0.0 39.69 3.09
499 1118 6.821665 TGTGTCCAGTCAGTTAAATATAAGGC 59.178 38.462 0.00 0.0 0.00 4.35
633 1253 2.023984 TGGCTCATAGAGAGGAGGTTCA 60.024 50.000 0.00 0.0 44.86 3.18
867 1489 5.276489 GCCGACATATGCACAAAATTGAATG 60.276 40.000 1.58 0.0 0.00 2.67
925 1547 4.875713 GGCTATGGTGGGTGCGGG 62.876 72.222 0.00 0.0 0.00 6.13
935 1557 4.101448 GGTGCGGGCAGGAGTGAT 62.101 66.667 0.00 0.0 0.00 3.06
987 1610 1.023513 CGGCTGAAGAGCTGGAAAGG 61.024 60.000 0.00 0.0 46.54 3.11
1021 1646 8.174085 TGTCTATGGGAGGAAAGGAAATTTTAA 58.826 33.333 0.00 0.0 0.00 1.52
1048 1673 5.765510 AGGCAGTTATACAATCCATTCCAA 58.234 37.500 0.00 0.0 0.00 3.53
1073 1706 9.463443 AATTTTTGCTATGTCTGTCTTTAACAC 57.537 29.630 0.00 0.0 33.24 3.32
1172 1806 0.748450 CATTGGATGGCATGGTGGAC 59.252 55.000 3.81 0.0 0.00 4.02
1229 1863 3.510388 TCGTGATCTGCACTCCTTTAG 57.490 47.619 0.00 0.0 45.49 1.85
1382 2016 0.405585 ACCTGGCAAAGCATAGTGGT 59.594 50.000 0.00 0.0 0.00 4.16
1460 2096 3.994317 TCAACATCTGGGAGGATCACTA 58.006 45.455 0.00 0.0 41.12 2.74
1489 2126 7.851228 TCCAGGAAGTATAAATCGCATGATAT 58.149 34.615 0.00 0.0 33.40 1.63
1522 2159 9.889128 CCAAGGGACAAATAATATTGAAAACAT 57.111 29.630 0.00 0.0 34.38 2.71
1633 2271 3.243068 GCGGATTCCATTAAGCGAACATT 60.243 43.478 3.09 0.0 0.00 2.71
1648 2286 8.561738 AAGCGAACATTAAGAGGAAGATTTTA 57.438 30.769 0.00 0.0 0.00 1.52
1690 2329 7.611213 AATCTTATTCGTTCTCCGTTTGATT 57.389 32.000 0.00 0.0 37.94 2.57
1694 2333 1.533731 TCGTTCTCCGTTTGATTTGCC 59.466 47.619 0.00 0.0 37.94 4.52
1706 2345 8.783093 TCCGTTTGATTTGCCTATTATATTGAG 58.217 33.333 0.00 0.0 0.00 3.02
1761 2400 1.991813 TGGATGGACAAGGGACATCAA 59.008 47.619 0.00 0.0 42.03 2.57
1793 2433 3.071602 CGGTATGGGAGATTCTGTGGAAT 59.928 47.826 0.00 0.0 43.99 3.01
1812 2452 4.040339 GGAATTTGAGGGTTCCACACAAAT 59.960 41.667 0.00 0.0 42.72 2.32
1852 2492 0.106318 GCCTTGCATGGGATTCTCCT 60.106 55.000 19.47 0.0 36.57 3.69
1870 2510 0.541863 CTAGGGTTGGCTGTACTGGG 59.458 60.000 1.65 0.0 0.00 4.45
1891 2531 3.008049 GGAAACAGGCATATCCCGACTAT 59.992 47.826 0.00 0.0 34.51 2.12
1923 2563 1.310904 GGTTTGTACAAAGGGTGCGA 58.689 50.000 21.12 0.0 34.44 5.10
1940 2580 2.168313 TGCGAAGGACATCAAGCATCTA 59.832 45.455 0.00 0.0 0.00 1.98
2014 2655 6.552445 AGACATAATTGAGGAAGCTACAGT 57.448 37.500 0.00 0.0 0.00 3.55
2208 2849 2.736721 TCAGCGTTCAGAATACAAGCAC 59.263 45.455 0.00 0.0 0.00 4.40
2295 2936 3.375922 ACCAAAGAACACGTACAAACTGG 59.624 43.478 0.00 0.0 0.00 4.00
2343 2984 2.044806 AACACGAGGTGCAGGAGCTT 62.045 55.000 0.00 0.0 42.74 3.74
2368 3010 5.878406 ATTCGTAATGATCAGGGAGAAGT 57.122 39.130 0.09 0.0 0.00 3.01
2418 3060 1.825474 ACTTGCTAGATGTGGCTACGT 59.175 47.619 1.04 0.0 0.00 3.57
2419 3061 3.021695 ACTTGCTAGATGTGGCTACGTA 58.978 45.455 1.04 0.0 0.00 3.57
2435 3077 1.429148 CGTATGAAGCAACGGCCCTC 61.429 60.000 0.00 0.0 42.56 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.461897 CGACGGAAATAAAAGGTGCGT 59.538 47.619 0.00 0.00 42.24 5.24
48 49 1.466866 GGCGACGGAAATAAAAGGTGC 60.467 52.381 0.00 0.00 0.00 5.01
51 52 2.352388 TCTGGCGACGGAAATAAAAGG 58.648 47.619 0.00 0.00 44.59 3.11
89 90 5.193216 CGTGTTATTCTTGATTGCTCATCG 58.807 41.667 0.00 0.00 34.08 3.84
143 757 2.194271 GTACTGTGTAATGAGCTCGGC 58.806 52.381 9.64 0.00 0.00 5.54
145 759 3.439293 CCTGTACTGTGTAATGAGCTCG 58.561 50.000 9.64 0.00 0.00 5.03
204 818 2.435805 AGCCGGAGAGCTATCATTTTGA 59.564 45.455 5.05 0.00 42.70 2.69
293 907 9.461312 ACTCTCATAAGCCAACAAAATGTTATA 57.539 29.630 0.00 0.00 38.77 0.98
391 1005 7.502060 AGTCCATTCAACCCTATCATATAGG 57.498 40.000 6.06 6.06 34.52 2.57
441 1056 8.299570 CAATTTACAAACTCTACATGAAAGCCT 58.700 33.333 0.00 0.00 0.00 4.58
633 1253 1.617804 CCCTGACACCTTCAATGCCAT 60.618 52.381 0.00 0.00 32.21 4.40
922 1544 2.403252 AAAACTATCACTCCTGCCCG 57.597 50.000 0.00 0.00 0.00 6.13
925 1547 7.550906 AGAGTTGAATAAAACTATCACTCCTGC 59.449 37.037 0.00 0.00 40.48 4.85
987 1610 6.319911 CCTTTCCTCCCATAGACAGAAATTTC 59.680 42.308 10.33 10.33 0.00 2.17
1021 1646 6.491403 GGAATGGATTGTATAACTGCCTTCAT 59.509 38.462 0.00 0.00 0.00 2.57
1048 1673 8.629158 TGTGTTAAAGACAGACATAGCAAAAAT 58.371 29.630 0.00 0.00 39.39 1.82
1073 1706 7.541783 TCATTTCTTTGCATAATTTCTTCGGTG 59.458 33.333 0.00 0.00 0.00 4.94
1172 1806 2.827322 TCCTTCTTTGGGATGCACATTG 59.173 45.455 0.00 0.00 0.00 2.82
1229 1863 5.390991 GCTTGTTTCACCAACATAGCTAGAC 60.391 44.000 0.00 0.00 45.17 2.59
1252 1886 4.400251 TGGATTTGAAATCAGTCTCCATGC 59.600 41.667 18.55 0.00 30.06 4.06
1382 2016 8.964772 GTCCTCTACAAAAAGTACATAGACCTA 58.035 37.037 0.00 0.00 0.00 3.08
1460 2096 6.174720 TGCGATTTATACTTCCTGGAATCT 57.825 37.500 10.03 0.84 0.00 2.40
1489 2126 7.947782 ATATTATTTGTCCCTTGGGAGTCTA 57.052 36.000 8.93 0.00 0.00 2.59
1522 2159 7.552687 AGTCGTTGGATCAATAAGCTCATTAAA 59.447 33.333 0.00 0.00 0.00 1.52
1587 2225 6.463614 GCAAGATTCTATCCACATCTACAGGT 60.464 42.308 0.00 0.00 0.00 4.00
1633 2271 6.969043 TCCAAGCCATAAAATCTTCCTCTTA 58.031 36.000 0.00 0.00 0.00 2.10
1685 2324 8.224025 TCCCACTCAATATAATAGGCAAATCAA 58.776 33.333 0.00 0.00 0.00 2.57
1686 2325 7.665559 GTCCCACTCAATATAATAGGCAAATCA 59.334 37.037 0.00 0.00 0.00 2.57
1690 2329 5.371176 TGGTCCCACTCAATATAATAGGCAA 59.629 40.000 0.00 0.00 0.00 4.52
1694 2333 8.597167 TGAGAATGGTCCCACTCAATATAATAG 58.403 37.037 4.61 0.00 36.63 1.73
1706 2345 1.207089 TGACGATGAGAATGGTCCCAC 59.793 52.381 0.00 0.00 0.00 4.61
1793 2433 4.026744 TCAATTTGTGTGGAACCCTCAAA 58.973 39.130 0.00 0.00 36.19 2.69
1806 2446 5.570973 TCCACGCGAATATTTTCAATTTGTG 59.429 36.000 15.93 0.00 35.33 3.33
1807 2447 5.704888 TCCACGCGAATATTTTCAATTTGT 58.295 33.333 15.93 0.00 0.00 2.83
1812 2452 3.426963 GCCTTCCACGCGAATATTTTCAA 60.427 43.478 15.93 0.00 0.00 2.69
1852 2492 0.117541 TCCCAGTACAGCCAACCCTA 59.882 55.000 0.00 0.00 0.00 3.53
1870 2510 2.622064 AGTCGGGATATGCCTGTTTC 57.378 50.000 11.91 0.00 44.00 2.78
1923 2563 7.831193 AGTAAACATTAGATGCTTGATGTCCTT 59.169 33.333 0.00 0.00 31.94 3.36
1986 2626 8.198109 TGTAGCTTCCTCAATTATGTCTAGAAC 58.802 37.037 0.00 0.00 0.00 3.01
1991 2632 6.155221 TGACTGTAGCTTCCTCAATTATGTCT 59.845 38.462 0.00 0.00 0.00 3.41
2014 2655 5.305386 ACAATCGATCCAGACCTATCAATGA 59.695 40.000 0.00 0.00 0.00 2.57
2185 2826 4.002982 TGCTTGTATTCTGAACGCTGATT 58.997 39.130 0.00 0.00 0.00 2.57
2208 2849 2.798283 CAGCACCAAAATCACTTGCAAG 59.202 45.455 24.84 24.84 35.57 4.01
2295 2936 2.003301 GAAGAAAGAGGCGTCCACATC 58.997 52.381 2.06 0.00 0.00 3.06
2328 2969 2.029838 ATAAAAGCTCCTGCACCTCG 57.970 50.000 0.00 0.00 42.74 4.63
2343 2984 7.792032 ACTTCTCCCTGATCATTACGAATAAA 58.208 34.615 0.00 0.00 0.00 1.40
2368 3010 3.493699 GGGTATACACGAGCCAGCAATTA 60.494 47.826 5.01 0.00 34.46 1.40
2418 3060 1.223487 GGAGGGCCGTTGCTTCATA 59.777 57.895 0.00 0.00 37.74 2.15
2419 3061 2.044946 GGAGGGCCGTTGCTTCAT 60.045 61.111 0.00 0.00 37.74 2.57
2435 3077 1.301293 GAGCTTGACCCCTTCCTGG 59.699 63.158 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.