Multiple sequence alignment - TraesCS4A01G153800

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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 TraesCS4A01G153800 chr4A 100.000 2162 0 0 1 2162 309514619 309516780 0 3993
1 TraesCS4A01G153800 chr3B 96.764 2163 69 1 1 2162 201526512 201528674 0 3605
2 TraesCS4A01G153800 chr1A 96.764 2163 69 1 1 2162 554511736 554513898 0 3605
3 TraesCS4A01G153800 chr5D 96.718 2163 70 1 1 2162 503217706 503219868 0 3600
4 TraesCS4A01G153800 chr5D 96.579 2163 73 1 1 2162 503278738 503276576 0 3583
5 TraesCS4A01G153800 chr5D 96.301 2163 79 1 1 2162 6188428 6190590 0 3550
6 TraesCS4A01G153800 chr3D 96.486 2163 72 3 1 2162 589280054 589277895 0 3570
7 TraesCS4A01G153800 chrUn 96.301 2163 78 2 1 2162 216519114 216516953 0 3550
8 TraesCS4A01G153800 chr2B 96.024 2163 80 3 1 2162 474907942 474910099 0 3513


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 TraesCS4A01G153800 chr4A 309514619 309516780 2161 False 3993 3993 100.000 1 2162 1 chr4A.!!$F1 2161
1 TraesCS4A01G153800 chr3B 201526512 201528674 2162 False 3605 3605 96.764 1 2162 1 chr3B.!!$F1 2161
2 TraesCS4A01G153800 chr1A 554511736 554513898 2162 False 3605 3605 96.764 1 2162 1 chr1A.!!$F1 2161
3 TraesCS4A01G153800 chr5D 503217706 503219868 2162 False 3600 3600 96.718 1 2162 1 chr5D.!!$F2 2161
4 TraesCS4A01G153800 chr5D 503276576 503278738 2162 True 3583 3583 96.579 1 2162 1 chr5D.!!$R1 2161
5 TraesCS4A01G153800 chr5D 6188428 6190590 2162 False 3550 3550 96.301 1 2162 1 chr5D.!!$F1 2161
6 TraesCS4A01G153800 chr3D 589277895 589280054 2159 True 3570 3570 96.486 1 2162 1 chr3D.!!$R1 2161
7 TraesCS4A01G153800 chrUn 216516953 216519114 2161 True 3550 3550 96.301 1 2162 1 chrUn.!!$R1 2161
8 TraesCS4A01G153800 chr2B 474907942 474910099 2157 False 3513 3513 96.024 1 2162 1 chr2B.!!$F1 2161

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
312 313 0.165944 GGTTTCTGCGTTCCGTCATG 59.834 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1227 3.369175 TGGGCCATACAATGCATTACAA 58.631 40.909 12.53 0.6 0.0 2.41 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
34 35 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.00 0.00 44.23 4.00
261 262 3.099141 GGAAAGGAATCCAAATCTGCCA 58.901 45.455 0.61 0.00 39.42 4.92
276 277 2.677836 TCTGCCAAATCGCTCATGTTAC 59.322 45.455 0.00 0.00 0.00 2.50
296 297 6.832384 TGTTACGATCTTCTACATCCTAGGTT 59.168 38.462 9.08 0.00 0.00 3.50
312 313 0.165944 GGTTTCTGCGTTCCGTCATG 59.834 55.000 0.00 0.00 0.00 3.07
326 327 3.449377 TCCGTCATGTGGCTTATGTTCTA 59.551 43.478 0.00 0.00 0.00 2.10
416 417 3.056832 GGAGACATCCCTATTTTCCCCT 58.943 50.000 0.00 0.00 40.03 4.79
436 437 4.042174 CCTGGGGGTCTTAATTACCACTA 58.958 47.826 8.78 3.08 40.51 2.74
441 442 6.910290 TGGGGGTCTTAATTACCACTACTTAT 59.090 38.462 8.78 0.00 40.51 1.73
485 486 8.820831 ACCATCAAATTAAATGTGAATAACCCA 58.179 29.630 0.00 0.00 0.00 4.51
497 498 5.148502 GTGAATAACCCATCCTCCTCTCTA 58.851 45.833 0.00 0.00 0.00 2.43
540 541 1.330521 TCTCTGCGTGCTTCAAACAAC 59.669 47.619 0.00 0.00 0.00 3.32
553 554 5.163612 GCTTCAAACAACTTTGTCTTCTCCT 60.164 40.000 0.00 0.00 41.31 3.69
628 629 3.990092 TCACTTGCTGTCGTTACTCAAT 58.010 40.909 0.00 0.00 0.00 2.57
654 655 4.760530 TTCTGTTGAGGTCTATCCCATG 57.239 45.455 0.00 0.00 36.75 3.66
673 674 5.203528 CCATGGAGGTAGTCAAATTGGATT 58.796 41.667 5.56 0.00 0.00 3.01
694 695 8.265055 TGGATTAGTGATCGATTTCTAGGTTTT 58.735 33.333 0.00 0.00 35.49 2.43
698 699 6.464222 AGTGATCGATTTCTAGGTTTTGTCA 58.536 36.000 0.00 0.00 0.00 3.58
749 750 5.732647 CGTAAATCAATAGTTCAAACCGCAG 59.267 40.000 0.00 0.00 0.00 5.18
843 847 8.986991 AGCCCTCTAGGATGTAAAATATATCTG 58.013 37.037 0.00 0.00 38.24 2.90
911 915 9.096823 TCAATTAGGGTCGTATTCTATGGTTAT 57.903 33.333 0.00 0.00 0.00 1.89
981 985 0.603569 ATAGGCGCTTATGACCTCCG 59.396 55.000 11.70 0.00 34.92 4.63
982 986 0.466739 TAGGCGCTTATGACCTCCGA 60.467 55.000 7.64 0.00 34.92 4.55
1019 1023 7.152645 GCGGTAATGATTCCTCTAGAATTACA 58.847 38.462 18.02 6.82 45.52 2.41
1127 1131 5.071250 TGCTCGGGATAGGTGTTTTGTATAT 59.929 40.000 0.00 0.00 0.00 0.86
1222 1227 5.820947 GGTTGAAGGGTAATGATCATACGTT 59.179 40.000 9.04 10.09 0.00 3.99
1399 1404 4.963276 TGATTCTTGCCCAATAAACGAG 57.037 40.909 0.00 0.00 0.00 4.18
1460 1465 6.329197 TCCATAAATCGACTTTCCCTCCTATT 59.671 38.462 0.00 0.00 0.00 1.73
1463 1468 5.959583 AATCGACTTTCCCTCCTATTCTT 57.040 39.130 0.00 0.00 0.00 2.52
1471 1476 6.273495 ACTTTCCCTCCTATTCTTTGAGTTCT 59.727 38.462 0.00 0.00 0.00 3.01
1714 1719 4.023107 ACAGGGATCATCGTACATCGTAAG 60.023 45.833 0.00 0.00 40.80 2.34
1819 1824 2.305927 TGAAAACACCTCTCTGGATCCC 59.694 50.000 9.90 0.00 39.71 3.85
1840 1845 4.943705 CCCCGAATTGAAAGAGAGATTGAA 59.056 41.667 0.00 0.00 0.00 2.69
1971 1976 2.442413 TGAACAACCGGGATCCATTTC 58.558 47.619 15.23 6.67 0.00 2.17
1996 2001 6.428159 CCTTATGATACCTAGTTGGCATTGAC 59.572 42.308 0.00 0.00 40.22 3.18
2069 2074 9.561069 AAAGACGTATATTCCTTGCTCATTATT 57.439 29.630 0.00 0.00 0.00 1.40
2122 2127 6.373495 GTGGGACTAATCGTTTTCATTTACCT 59.627 38.462 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.147330 ACATAGAAATCACACGTGGAAGA 57.853 39.130 21.57 14.78 0.00 2.87
74 75 2.622064 ACTTCAACCGATATGCCCTC 57.378 50.000 0.00 0.00 0.00 4.30
117 118 0.774908 TGTACAGTTTGGGAAGGGGG 59.225 55.000 0.00 0.00 0.00 5.40
239 240 2.432146 GGCAGATTTGGATTCCTTTCCC 59.568 50.000 3.95 0.00 34.67 3.97
261 262 5.352284 AGAAGATCGTAACATGAGCGATTT 58.648 37.500 18.67 13.35 44.06 2.17
276 277 6.442952 CAGAAACCTAGGATGTAGAAGATCG 58.557 44.000 17.98 0.00 0.00 3.69
312 313 5.116180 TGCTACATGTAGAACATAAGCCAC 58.884 41.667 32.39 12.97 41.94 5.01
416 417 4.702196 AGTAGTGGTAATTAAGACCCCCA 58.298 43.478 6.83 0.00 35.99 4.96
436 437 6.151817 GGTCAGAGGCAAATTGAAAGATAAGT 59.848 38.462 0.00 0.00 0.00 2.24
441 442 3.831323 TGGTCAGAGGCAAATTGAAAGA 58.169 40.909 0.00 0.00 0.00 2.52
485 486 4.657969 CCCTTGTTTCATAGAGAGGAGGAT 59.342 45.833 0.00 0.00 0.00 3.24
497 498 1.250840 GGAAGCGCCCCTTGTTTCAT 61.251 55.000 2.29 0.00 32.78 2.57
523 524 2.193306 AAGTTGTTTGAAGCACGCAG 57.807 45.000 0.00 0.00 0.00 5.18
628 629 5.783360 TGGGATAGACCTCAACAGAAAACTA 59.217 40.000 0.00 0.00 38.98 2.24
654 655 6.650120 TCACTAATCCAATTTGACTACCTCC 58.350 40.000 0.00 0.00 0.00 4.30
673 674 7.608153 TGACAAAACCTAGAAATCGATCACTA 58.392 34.615 0.00 4.95 0.00 2.74
843 847 2.505819 ACACTATGGGGATGGTGAGAAC 59.494 50.000 5.65 0.00 36.65 3.01
887 891 9.096823 TCATAACCATAGAATACGACCCTAATT 57.903 33.333 0.00 0.00 0.00 1.40
1040 1044 6.777091 TCCACGAAATAATTTGATCCATGGAT 59.223 34.615 27.66 27.66 37.59 3.41
1222 1227 3.369175 TGGGCCATACAATGCATTACAA 58.631 40.909 12.53 0.60 0.00 2.41
1386 1391 4.514781 AAAAAGTCCTCGTTTATTGGGC 57.485 40.909 0.00 0.00 0.00 5.36
1463 1468 9.880064 CGAATTCTTATCGATACTAGAACTCAA 57.120 33.333 20.09 4.45 42.76 3.02
1523 1528 6.708502 TCCATACATAACGAATTGGTATGGTG 59.291 38.462 21.76 7.96 45.91 4.17
1636 1641 7.102346 CCCAACTCATAATTGGTAAATTTGCA 58.898 34.615 8.59 0.00 44.46 4.08
1819 1824 6.404074 CCCTTTCAATCTCTCTTTCAATTCGG 60.404 42.308 0.00 0.00 0.00 4.30
1971 1976 6.428159 GTCAATGCCAACTAGGTATCATAAGG 59.572 42.308 0.00 0.00 42.47 2.69
2069 2074 7.335924 CGAGGTTTGGGAATAAGTGATTTTCTA 59.664 37.037 0.00 0.00 0.00 2.10
2073 2078 5.183140 CACGAGGTTTGGGAATAAGTGATTT 59.817 40.000 0.00 0.00 0.00 2.17
2122 2127 4.211920 ACGAAAAGGGTTTTCCATGAGAA 58.788 39.130 0.00 0.00 44.73 2.87


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

AutoCloner maintained by Alex Coulton.