Multiple sequence alignment - TraesCS5B01G250400

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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 TraesCS5B01G250400 chr5B 100.000 2201 0 0 1 2201 432871480 432869280 0 4065
1 TraesCS5B01G250400 chr2A 96.642 2204 71 3 1 2201 726901127 726903330 0 3657
2 TraesCS5B01G250400 chr7B 96.459 2203 76 2 1 2201 662732241 662730039 0 3635
3 TraesCS5B01G250400 chr7B 96.278 2203 80 2 1 2201 663094098 663096300 0 3613
4 TraesCS5B01G250400 chr3B 96.461 2204 75 3 1 2201 201569459 201571662 0 3635
5 TraesCS5B01G250400 chr3B 96.187 2203 80 4 1 2201 201544845 201542645 0 3600
6 TraesCS5B01G250400 chr3D 96.325 2204 77 4 1 2201 589258200 589260402 0 3618
7 TraesCS5B01G250400 chr7A 96.143 2204 81 4 1 2201 258305486 258307688 0 3596
8 TraesCS5B01G250400 chr3A 96.096 2203 83 3 1 2201 695645711 695643510 0 3589


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 TraesCS5B01G250400 chr5B 432869280 432871480 2200 True 4065 4065 100.000 1 2201 1 chr5B.!!$R1 2200
1 TraesCS5B01G250400 chr2A 726901127 726903330 2203 False 3657 3657 96.642 1 2201 1 chr2A.!!$F1 2200
2 TraesCS5B01G250400 chr7B 662730039 662732241 2202 True 3635 3635 96.459 1 2201 1 chr7B.!!$R1 2200
3 TraesCS5B01G250400 chr7B 663094098 663096300 2202 False 3613 3613 96.278 1 2201 1 chr7B.!!$F1 2200
4 TraesCS5B01G250400 chr3B 201569459 201571662 2203 False 3635 3635 96.461 1 2201 1 chr3B.!!$F1 2200
5 TraesCS5B01G250400 chr3B 201542645 201544845 2200 True 3600 3600 96.187 1 2201 1 chr3B.!!$R1 2200
6 TraesCS5B01G250400 chr3D 589258200 589260402 2202 False 3618 3618 96.325 1 2201 1 chr3D.!!$F1 2200
7 TraesCS5B01G250400 chr7A 258305486 258307688 2202 False 3596 3596 96.143 1 2201 1 chr7A.!!$F1 2200
8 TraesCS5B01G250400 chr3A 695643510 695645711 2201 True 3589 3589 96.096 1 2201 1 chr3A.!!$R1 2200

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
163 165 0.103572 GCTTTACGTCCGCTATCCCA 59.896 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1318 0.976641 CACTTGGAGCTGTAGGTGGA 59.023 55.0 0.0 0.0 0.0 4.02 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
52 54 2.100418 AGGTAACCGTTCGCTATCCTTC 59.900 50.000 0.00 0.00 37.17 3.46
163 165 0.103572 GCTTTACGTCCGCTATCCCA 59.896 55.000 0.00 0.00 0.00 4.37
296 298 1.068753 CATCTGAGCTACAGGCCCG 59.931 63.158 0.00 0.00 45.76 6.13
329 331 1.344087 GGATCTCTTCCAGGGGGTACA 60.344 57.143 0.00 0.00 44.74 2.90
361 363 4.289672 TCAGGTTAAGAAGATGGGAAAGCT 59.710 41.667 0.00 0.00 0.00 3.74
421 423 0.325671 TGGGAGAGAGGGGATGTGAC 60.326 60.000 0.00 0.00 0.00 3.67
535 537 6.534475 AAGCTTTTTATCATTCTGGCATCA 57.466 33.333 0.00 0.00 0.00 3.07
575 577 2.423088 CCTCCCCTACAGTATCGTCACT 60.423 54.545 0.00 0.00 0.00 3.41
576 578 3.181447 CCTCCCCTACAGTATCGTCACTA 60.181 52.174 0.00 0.00 0.00 2.74
825 828 8.294577 TCATCAAAGAGTTGAACAATGAAGATG 58.705 33.333 0.00 4.52 46.66 2.90
853 856 5.746638 GCAAGTGCCTGATCGATTTGATCT 61.747 45.833 13.79 0.00 43.61 2.75
883 886 6.203338 GTGTAGGAACAAGGTTCAAATCGTTA 59.797 38.462 10.86 0.00 37.36 3.18
949 952 4.274602 TGACACCTATTTAAACGGCTCA 57.725 40.909 5.50 4.54 0.00 4.26
954 957 5.116180 CACCTATTTAAACGGCTCATCTCA 58.884 41.667 5.50 0.00 0.00 3.27
1056 1059 0.395862 CGGAGGCTCTAGGGAAGTCA 60.396 60.000 15.23 0.00 0.00 3.41
1069 1072 2.387757 GGAAGTCAGAGGAGAGAGCAT 58.612 52.381 0.00 0.00 0.00 3.79
1188 1191 3.384532 GGTGCGTCCTTCCCGGTA 61.385 66.667 0.00 0.00 0.00 4.02
1266 1269 3.308053 CCGAACTATCTCACGACGTTCTA 59.692 47.826 0.00 0.00 33.86 2.10
1269 1272 5.448479 CGAACTATCTCACGACGTTCTAAAG 59.552 44.000 0.00 0.00 33.86 1.85
1331 1334 1.204146 GGATCCACCTACAGCTCCAA 58.796 55.000 6.95 0.00 35.41 3.53
1477 1481 2.093658 GGATCACTAAGGCCGACTTTCA 60.094 50.000 0.00 0.00 40.64 2.69
1490 1494 2.159448 CGACTTTCATCTCTGCTCGACT 60.159 50.000 0.00 0.00 0.00 4.18
1536 1540 0.392193 CTGCCTTTGCACTCGAGGAT 60.392 55.000 18.41 0.00 44.23 3.24
1688 1692 3.017442 TCTTCCAGAGTGGTATCTCACG 58.983 50.000 0.00 0.00 42.10 4.35
1700 1705 4.227134 CTCACGGATGGCTCGGGG 62.227 72.222 0.00 0.00 0.00 5.73
1741 1746 1.192146 TCGCCTTCCACCTAAGCTGT 61.192 55.000 0.00 0.00 0.00 4.40
1773 1778 1.623279 CCAAAGCCAATCCCAGGGAAT 60.623 52.381 13.94 0.00 34.34 3.01
1809 1814 1.476833 GGTCTTTCTGTCCAGGTGCAA 60.477 52.381 0.00 0.00 0.00 4.08
1844 1849 6.997655 TCTTCACAGACATGTCTATTTCACT 58.002 36.000 27.44 0.74 37.65 3.41
1877 1882 0.036952 AGACAGTGCCCAGATCGTTG 60.037 55.000 0.00 0.00 0.00 4.10
1921 1926 1.698506 ACCCGACAAGGAATTTTGCA 58.301 45.000 0.00 0.00 45.00 4.08
1967 1972 4.367023 CGTTCACCGGGGCTTCGA 62.367 66.667 6.32 0.00 0.00 3.71
2022 2027 3.637273 GACCTTCCGGCACTGGGT 61.637 66.667 0.00 0.00 0.00 4.51
2141 2146 2.046217 GCACCCCTTCTCCCGAAC 60.046 66.667 0.00 0.00 0.00 3.95
2142 2147 2.669240 CACCCCTTCTCCCGAACC 59.331 66.667 0.00 0.00 0.00 3.62
2159 2164 0.916809 ACCTACGGGGCTATTTTGCT 59.083 50.000 0.00 0.00 39.10 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 165 5.399497 CCCTGAGGGTAGGAAAATCATGATT 60.399 44.000 15.36 15.36 40.42 2.57
218 220 2.822643 AATCCCTCCTCGCCCACAGA 62.823 60.000 0.00 0.00 0.00 3.41
279 281 2.136878 CCGGGCCTGTAGCTCAGAT 61.137 63.158 11.58 0.00 45.13 2.90
320 322 2.308866 CTGAAATGAAGGTGTACCCCCT 59.691 50.000 0.00 0.00 36.42 4.79
361 363 6.590292 CGCACTGTTCTTATAAAGAGAAAGGA 59.410 38.462 0.00 0.00 39.03 3.36
390 392 1.148027 TCTCTCCCACTTCACACCTCT 59.852 52.381 0.00 0.00 0.00 3.69
421 423 6.241385 GTCGTCTTATTCAAAACCTCAATCG 58.759 40.000 0.00 0.00 0.00 3.34
535 537 2.171003 GGTCCTGTGGCAAAATAGCTT 58.829 47.619 0.00 0.00 34.17 3.74
548 550 1.390287 TACTGTAGGGGAGGTCCTGT 58.610 55.000 0.00 0.00 37.75 4.00
575 577 9.590451 CGAATTTGGTGGTTAAACTCTACTATA 57.410 33.333 0.00 0.00 0.00 1.31
576 578 7.551617 CCGAATTTGGTGGTTAAACTCTACTAT 59.448 37.037 3.21 0.00 0.00 2.12
739 741 6.134535 TCTCTTGGATAGATAGAGAGGGAC 57.865 45.833 0.00 0.00 39.46 4.46
853 856 1.373435 CCTTGTTCCTACACGGCCA 59.627 57.895 2.24 0.00 36.94 5.36
883 886 1.134670 GCTGAGGCATCCTAACGAACT 60.135 52.381 0.00 0.00 38.54 3.01
949 952 3.246416 AGGATAAGGTAGCGGTGAGAT 57.754 47.619 0.00 0.00 0.00 2.75
954 957 4.228824 TGGAAATAGGATAAGGTAGCGGT 58.771 43.478 0.00 0.00 0.00 5.68
1056 1059 3.388676 CCAAGATGAATGCTCTCTCCTCT 59.611 47.826 0.00 0.00 0.00 3.69
1069 1072 1.005450 GTAAGCCCACCCCAAGATGAA 59.995 52.381 0.00 0.00 0.00 2.57
1188 1191 3.624456 GGACCTTTCCCTAGTACGAGAGT 60.624 52.174 4.34 0.00 41.63 3.24
1251 1254 2.230508 TGGCTTTAGAACGTCGTGAGAT 59.769 45.455 0.00 0.00 45.19 2.75
1266 1269 1.271543 TGCAGTACATGAGCTGGCTTT 60.272 47.619 17.88 0.00 33.62 3.51
1269 1272 1.386533 AATGCAGTACATGAGCTGGC 58.613 50.000 17.88 12.52 39.60 4.85
1315 1318 0.976641 CACTTGGAGCTGTAGGTGGA 59.023 55.000 0.00 0.00 0.00 4.02
1477 1481 1.102154 CTCACCAGTCGAGCAGAGAT 58.898 55.000 0.00 0.00 0.00 2.75
1536 1540 2.668632 GGGCCAGACGGACATTGA 59.331 61.111 4.39 0.00 45.55 2.57
1715 1720 1.377333 GGTGGAAGGCGAAGAAGGG 60.377 63.158 0.00 0.00 0.00 3.95
1741 1746 2.209315 GCTTTGGGCCTTTCCTGCA 61.209 57.895 4.53 0.00 34.39 4.41
1773 1778 7.180408 ACAGAAAGACCCTATGAAGCTTTACTA 59.820 37.037 0.00 0.00 0.00 1.82
1809 1814 2.164624 GTCTGTGAAGATGCGGACTACT 59.835 50.000 0.00 0.00 37.84 2.57
1895 1900 4.635699 AATTCCTTGTCGGGTAAGTTCT 57.364 40.909 0.00 0.00 0.00 3.01
1921 1926 6.136541 CGTAACTATAACGGTCCTAAGGTT 57.863 41.667 0.00 0.00 36.71 3.50
1967 1972 4.162690 GACAGGGAAGCCGGCGAT 62.163 66.667 23.20 15.02 0.00 4.58
2142 2147 2.213499 CTCAGCAAAATAGCCCCGTAG 58.787 52.381 0.00 0.00 34.23 3.51
2159 2164 5.636123 AGACAACTCTCTCTAAGGAACTCA 58.364 41.667 0.00 0.00 38.49 3.41


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

AutoCloner maintained by Alex Coulton.