Multiple sequence alignment - TraesCS1B01G065600

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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 TraesCS1B01G065600 chr1B 100.000 2342 0 0 1 2342 49818047 49820388 0 4325
1 TraesCS1B01G065600 chrUn 97.866 2343 48 2 1 2342 257944318 257946659 0 4048
2 TraesCS1B01G065600 chrUn 97.610 2343 49 3 1 2342 233525062 233522726 0 4010
3 TraesCS1B01G065600 chr1D 97.653 2343 53 2 1 2342 212429075 212431416 0 4021
4 TraesCS1B01G065600 chr7B 97.567 2343 49 4 1 2342 698126727 698124392 0 4004
5 TraesCS1B01G065600 chr7B 97.268 2343 57 3 1 2342 716795632 716793296 0 3965
6 TraesCS1B01G065600 chr7B 97.226 2343 54 5 1 2342 742937688 742940020 0 3956
7 TraesCS1B01G065600 chr7A 97.567 2343 50 3 1 2342 60095992 60093656 0 4004
8 TraesCS1B01G065600 chr4D 97.354 2343 60 2 1 2342 123689168 123691509 0 3982
9 TraesCS1B01G065600 chr2D 97.311 2343 59 4 1 2342 637308499 637306160 0 3975


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 TraesCS1B01G065600 chr1B 49818047 49820388 2341 False 4325 4325 100.000 1 2342 1 chr1B.!!$F1 2341
1 TraesCS1B01G065600 chrUn 257944318 257946659 2341 False 4048 4048 97.866 1 2342 1 chrUn.!!$F1 2341
2 TraesCS1B01G065600 chrUn 233522726 233525062 2336 True 4010 4010 97.610 1 2342 1 chrUn.!!$R1 2341
3 TraesCS1B01G065600 chr1D 212429075 212431416 2341 False 4021 4021 97.653 1 2342 1 chr1D.!!$F1 2341
4 TraesCS1B01G065600 chr7B 698124392 698126727 2335 True 4004 4004 97.567 1 2342 1 chr7B.!!$R1 2341
5 TraesCS1B01G065600 chr7B 716793296 716795632 2336 True 3965 3965 97.268 1 2342 1 chr7B.!!$R2 2341
6 TraesCS1B01G065600 chr7B 742937688 742940020 2332 False 3956 3956 97.226 1 2342 1 chr7B.!!$F1 2341
7 TraesCS1B01G065600 chr7A 60093656 60095992 2336 True 4004 4004 97.567 1 2342 1 chr7A.!!$R1 2341
8 TraesCS1B01G065600 chr4D 123689168 123691509 2341 False 3982 3982 97.354 1 2342 1 chr4D.!!$F1 2341
9 TraesCS1B01G065600 chr2D 637306160 637308499 2339 True 3975 3975 97.311 1 2342 1 chr2D.!!$R1 2341

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
598 599 1.000717 GCCTTTGTTAAGCTTCGCCAA 60.001 47.619 0.0 1.45 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2121 0.914902 GGCTTTCCCCTGGTAGTCCT 60.915 60.0 0.0 0.0 34.23 3.85 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
265 266 5.241403 TCAGAAATGAAAGAAGGCTACCA 57.759 39.130 0.00 0.00 0.00 3.25
338 339 3.857157 TCTTGCTCCTTGGTACTTGTT 57.143 42.857 0.00 0.00 0.00 2.83
353 354 7.220740 TGGTACTTGTTTGATCAATCACACTA 58.779 34.615 16.91 11.08 38.10 2.74
484 485 2.658593 CTTCGCCCGCCTATCGTG 60.659 66.667 0.00 0.00 36.19 4.35
525 526 1.375268 GCGACAGCTTCTGCCTCTT 60.375 57.895 0.00 0.00 40.80 2.85
598 599 1.000717 GCCTTTGTTAAGCTTCGCCAA 60.001 47.619 0.00 1.45 0.00 4.52
626 627 3.623806 TCGCTTCCCGAATGCCTA 58.376 55.556 0.00 0.00 44.21 3.93
733 734 1.337074 GCTACCTTGCTTGCATTGCAA 60.337 47.619 21.97 21.97 46.80 4.08
784 785 2.490509 TGCCTGCTTCAATTGATGTGAG 59.509 45.455 19.25 15.27 0.00 3.51
803 804 3.057526 TGAGTGATCGTGTCTTCGACATT 60.058 43.478 0.00 0.00 44.63 2.71
958 959 3.047718 GATGTCTCCGACGCGACCA 62.048 63.158 15.93 0.00 34.95 4.02
1005 1006 5.458215 GGGTCAGGAGGGAAAATATATGCTT 60.458 44.000 0.00 0.00 0.00 3.91
1200 1201 2.076863 GATTGTTGGGAACGTCCTCTG 58.923 52.381 0.00 0.00 36.57 3.35
1219 1220 7.656137 GTCCTCTGTATTCGAAATATGCCTTTA 59.344 37.037 0.00 0.00 0.00 1.85
1232 1233 9.231297 GAAATATGCCTTTATAGGAGCATTACA 57.769 33.333 3.01 0.00 43.17 2.41
1249 1250 5.677852 GCATTACAATCTGCAGCTCAAATGA 60.678 40.000 22.00 2.54 38.28 2.57
1289 1290 9.330063 CTCTATTGGTCTTATTCTTATTGTGCA 57.670 33.333 0.00 0.00 0.00 4.57
1322 1323 1.582610 TTTGGATCCGCGAAGGCAAC 61.583 55.000 8.23 0.00 40.77 4.17
1342 1343 0.750850 CGCTCGGATCTTCCCCTAAA 59.249 55.000 0.00 0.00 31.13 1.85
1547 1548 1.647346 AAACGACGAGCAAACACTCA 58.353 45.000 0.00 0.00 36.42 3.41
1773 1774 4.031636 GGAGTACTCCGGGATATACACT 57.968 50.000 25.83 8.07 40.36 3.55
1778 1779 2.991713 ACTCCGGGATATACACTAGGGA 59.008 50.000 0.00 0.00 0.00 4.20
1809 1810 1.669115 GCATACGATGATGCCGCCT 60.669 57.895 9.56 0.00 45.41 5.52
1939 1941 4.630644 ATAGATGATGATGAAAGGCGGT 57.369 40.909 0.00 0.00 0.00 5.68
1955 1957 2.031465 GTCCGCTTGAACCGGGAA 59.969 61.111 6.32 0.00 45.60 3.97
1959 1961 0.320946 CCGCTTGAACCGGGAACTAA 60.321 55.000 6.32 0.00 41.99 2.24
2001 2003 4.610333 CAAAGCTAAATAGGAAAGGGGGT 58.390 43.478 0.00 0.00 0.00 4.95
2071 2073 4.389374 GAGCTAATATGGCTGGCTACAAA 58.611 43.478 7.99 0.00 40.40 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 246 6.777580 TCTTTTGGTAGCCTTCTTTCATTTCT 59.222 34.615 0.00 0.00 0.00 2.52
265 266 4.041723 CGAAATCCGTTGCTTGTTCTTTT 58.958 39.130 0.00 0.00 0.00 2.27
353 354 9.965824 AACGAAAAATCAAGTGAACTAATGAAT 57.034 25.926 0.00 0.00 0.00 2.57
428 429 1.734477 CAGACGTGGAGTGGCGAAG 60.734 63.158 0.00 0.00 0.00 3.79
525 526 1.385528 TGAGCGATAGTGAAGCCGTA 58.614 50.000 0.00 0.00 39.35 4.02
603 604 1.739371 GCATTCGGGAAGCGACTAGTT 60.739 52.381 0.00 0.00 0.00 2.24
840 841 6.584563 CCGAAAAGAAAACAGAGACAAAACAA 59.415 34.615 0.00 0.00 0.00 2.83
958 959 7.628101 ACCCCTATAAAAATCTAGTGGAAGTCT 59.372 37.037 0.00 0.00 0.00 3.24
1005 1006 3.008594 TCCGCTTGGGACTGATAGAAAAA 59.991 43.478 0.00 0.00 40.94 1.94
1085 1086 0.404040 CCCCAACCCAACTTGCTCTA 59.596 55.000 0.00 0.00 0.00 2.43
1200 1201 8.604890 GCTCCTATAAAGGCATATTTCGAATAC 58.395 37.037 0.00 0.00 43.31 1.89
1219 1220 4.070716 GCTGCAGATTGTAATGCTCCTAT 58.929 43.478 20.43 0.00 42.98 2.57
1232 1233 2.957006 GGGATCATTTGAGCTGCAGATT 59.043 45.455 20.43 4.00 0.00 2.40
1249 1250 7.079048 AGACCAATAGAGACTTCATAAGGGAT 58.921 38.462 0.00 0.00 0.00 3.85
1289 1290 0.107410 TCCAAACGTGCTCACAAGGT 60.107 50.000 0.00 0.00 0.00 3.50
1322 1323 1.113517 TTAGGGGAAGATCCGAGCGG 61.114 60.000 1.74 1.74 37.43 5.52
1370 1371 0.745486 CGGACATTCCTCATGCTGCA 60.745 55.000 4.13 4.13 36.14 4.41
1547 1548 1.347707 TGATCCCTTGCTCTCACGTTT 59.652 47.619 0.00 0.00 0.00 3.60
1716 1717 1.922447 ACCCATACATGAAGGCCTTGA 59.078 47.619 26.25 16.95 0.00 3.02
1773 1774 5.506815 CGTATGCTCGACATTAGTTTCCCTA 60.507 44.000 5.94 0.00 40.38 3.53
1778 1779 5.588240 TCATCGTATGCTCGACATTAGTTT 58.412 37.500 5.94 0.00 42.56 2.66
1901 1903 1.893919 TATACCAGCTGCCACGCACA 61.894 55.000 8.66 0.00 33.79 4.57
1955 1957 5.936956 GCTTGCTGCCTATTATGAGATTAGT 59.063 40.000 0.00 0.00 35.15 2.24
1959 1961 4.362470 TGCTTGCTGCCTATTATGAGAT 57.638 40.909 0.00 0.00 42.00 2.75
2001 2003 2.807967 CGAAAAAGGCAGTCATCAGTCA 59.192 45.455 0.00 0.00 0.00 3.41
2071 2073 7.014711 TCTCGTCTCATCTTTCTTTGGCTATAT 59.985 37.037 0.00 0.00 0.00 0.86
2119 2121 0.914902 GGCTTTCCCCTGGTAGTCCT 60.915 60.000 0.00 0.00 34.23 3.85


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

AutoCloner maintained by Alex Coulton.