Multiple sequence alignment - TraesCS2A01G333800

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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 TraesCS2A01G333800 chr2A 100.000 4580 0 0 1 4580 567383219 567378640 0.000000e+00 8458.0
1 TraesCS2A01G333800 chr2A 99.106 2462 10 2 2119 4580 547411986 547414435 0.000000e+00 4414.0
2 TraesCS2A01G333800 chr2A 99.278 970 7 0 1159 2128 547410135 547411104 0.000000e+00 1753.0
3 TraesCS2A01G333800 chr2A 95.254 590 24 3 263 848 547409015 547409604 0.000000e+00 931.0
4 TraesCS2A01G333800 chr2A 99.603 252 1 0 857 1108 547409668 547409919 1.160000e-125 460.0
5 TraesCS2A01G333800 chr2A 95.259 232 4 2 1 225 547408785 547409016 1.210000e-95 361.0
6 TraesCS2A01G333800 chr2A 97.110 173 5 0 1 173 547408039 547408211 4.480000e-75 292.0
7 TraesCS2A01G333800 chr2D 95.288 2504 88 9 2100 4580 421143219 421140723 0.000000e+00 3943.0
8 TraesCS2A01G333800 chr2D 90.313 991 70 17 1122 2093 421144242 421143259 0.000000e+00 1275.0
9 TraesCS2A01G333800 chr2D 91.727 822 52 9 1 811 421145721 421144905 0.000000e+00 1127.0
10 TraesCS2A01G333800 chr2D 95.547 247 11 0 857 1103 421144834 421144588 3.320000e-106 396.0
11 TraesCS2A01G333800 chr2B 94.015 1888 78 10 2100 3970 493716903 493715034 0.000000e+00 2828.0
12 TraesCS2A01G333800 chr2B 94.415 931 32 4 857 1785 493718144 493717232 0.000000e+00 1413.0
13 TraesCS2A01G333800 chr2B 97.222 612 17 0 3969 4580 493714818 493714207 0.000000e+00 1037.0
14 TraesCS2A01G333800 chr7A 95.122 41 1 1 721 760 650862771 650862731 3.830000e-06 63.9


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 TraesCS2A01G333800 chr2A 567378640 567383219 4579 True 8458.000000 8458 100.000000 1 4580 1 chr2A.!!$R1 4579
1 TraesCS2A01G333800 chr2A 547408039 547414435 6396 False 1368.500000 4414 97.601667 1 4580 6 chr2A.!!$F1 4579
2 TraesCS2A01G333800 chr2D 421140723 421145721 4998 True 1685.250000 3943 93.218750 1 4580 4 chr2D.!!$R1 4579
3 TraesCS2A01G333800 chr2B 493714207 493718144 3937 True 1759.333333 2828 95.217333 857 4580 3 chr2B.!!$R1 3723

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
423 1178 2.360801 ACGCCATTTATTTTGGATCGGG 59.639 45.455 0.0 0.0 36.26 5.14 F
463 1219 4.723248 GCTAGCTGCAAGTTAAATTCGTT 58.277 39.130 7.7 0.0 42.31 3.85 F
694 1453 6.198216 CCACATAAAGACAAAACCAGAAAACG 59.802 38.462 0.0 0.0 0.00 3.60 F
2437 4550 0.034186 TTTCCTGGGCAATCTCGCAT 60.034 50.000 0.0 0.0 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 3040 7.613022 TGGCTGAAATCTTTTACTCAGATGATT 59.387 33.333 2.21 0.00 38.02 2.57 R
2437 4550 0.955428 GATGCCGAACCACTGCTTCA 60.955 55.000 0.00 0.00 34.71 3.02 R
2546 4659 5.148785 CAAGCACTTGAAGGTTCCGAAGG 62.149 52.174 4.31 0.00 47.00 3.46 R
3786 5908 7.748691 TCAAACATCAATTCTGATCAGTGAA 57.251 32.000 21.92 10.96 40.49 3.18 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
30 31 8.998989 GTTTGATATCACACGTTTCAATATGTG 58.001 33.333 4.48 0.00 43.08 3.21
372 1126 2.851263 TGAACTGGCCTCGTTAACAT 57.149 45.000 3.32 0.00 0.00 2.71
381 1135 4.067896 GGCCTCGTTAACATCATGATGAT 58.932 43.478 36.37 28.47 41.20 2.45
421 1176 3.181491 ACCACGCCATTTATTTTGGATCG 60.181 43.478 0.00 0.00 36.26 3.69
423 1178 2.360801 ACGCCATTTATTTTGGATCGGG 59.639 45.455 0.00 0.00 36.26 5.14
463 1219 4.723248 GCTAGCTGCAAGTTAAATTCGTT 58.277 39.130 7.70 0.00 42.31 3.85
557 1313 8.895845 CAGTGTTTCACGAATTTTCAGAAATAG 58.104 33.333 0.00 0.00 39.64 1.73
694 1453 6.198216 CCACATAAAGACAAAACCAGAAAACG 59.802 38.462 0.00 0.00 0.00 3.60
752 1511 8.253810 TGTTTCTCCATGTGTGTTTTGAATTTA 58.746 29.630 0.00 0.00 0.00 1.40
851 1610 9.635520 ATTTGTTGAAAATTGAAATGTTGCAAA 57.364 22.222 0.00 0.00 0.00 3.68
852 1611 9.467258 TTTGTTGAAAATTGAAATGTTGCAAAA 57.533 22.222 0.00 0.00 0.00 2.44
1868 3039 7.072076 AGGGATTCCTTAAACGTATGGACTATT 59.928 37.037 2.01 0.00 41.56 1.73
1869 3040 8.370182 GGGATTCCTTAAACGTATGGACTATTA 58.630 37.037 2.01 0.00 34.19 0.98
2437 4550 0.034186 TTTCCTGGGCAATCTCGCAT 60.034 50.000 0.00 0.00 0.00 4.73
3107 5229 7.312899 CAACCAAAATAAGCGGAGTAGATTTT 58.687 34.615 0.00 0.00 31.55 1.82
3741 5863 7.279758 TGAAAAATGGTTTTTGTGGAGATGAAC 59.720 33.333 5.25 0.00 42.51 3.18
3950 6074 3.930336 ACAGGTCATCACAGTACACATG 58.070 45.455 0.00 0.00 0.00 3.21
4151 6500 3.527253 TCCACATATCAATTGGTCCTGGT 59.473 43.478 5.42 0.00 0.00 4.00
4530 6879 3.902881 ACACCCTCTGAATAGCTGAAG 57.097 47.619 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.718940 AAATAGGGCACTACAATTGCAC 57.281 40.909 5.05 0.00 44.28 4.57
59 806 4.885426 CACCAGTGCTCCAACAGT 57.115 55.556 0.00 0.00 0.00 3.55
97 844 5.098211 GGCATCAATTTTTCTTCTTCTCCG 58.902 41.667 0.00 0.00 0.00 4.63
381 1135 7.977853 TGGCGTGGTTTTAGTTAAATTACAAAA 59.022 29.630 0.00 0.00 0.00 2.44
391 1146 7.599245 CCAAAATAAATGGCGTGGTTTTAGTTA 59.401 33.333 0.00 0.00 0.00 2.24
423 1178 7.147976 CAGCTAGCATAACAAAAATATTCCCC 58.852 38.462 18.83 0.00 0.00 4.81
460 1216 6.366332 GGAGCACCTGATATATTTCAGTAACG 59.634 42.308 18.31 8.38 41.30 3.18
557 1313 6.432607 ACATGACTCATGAACATTCACATC 57.567 37.500 23.30 0.00 43.81 3.06
694 1453 5.824904 ACAAATCTGGATGTGAATAGTGC 57.175 39.130 7.66 0.00 30.60 4.40
852 1611 3.365265 CGGCCAGGCTCGCTTTTT 61.365 61.111 12.43 0.00 0.00 1.94
1113 1927 4.179599 GAGGGGGAGGGGGAGGAG 62.180 77.778 0.00 0.00 0.00 3.69
1868 3039 9.113838 GGCTGAAATCTTTTACTCAGATGATTA 57.886 33.333 2.21 0.00 38.02 1.75
1869 3040 7.613022 TGGCTGAAATCTTTTACTCAGATGATT 59.387 33.333 2.21 0.00 38.02 2.57
2437 4550 0.955428 GATGCCGAACCACTGCTTCA 60.955 55.000 0.00 0.00 34.71 3.02
2546 4659 5.148785 CAAGCACTTGAAGGTTCCGAAGG 62.149 52.174 4.31 0.00 47.00 3.46
3786 5908 7.748691 TCAAACATCAATTCTGATCAGTGAA 57.251 32.000 21.92 10.96 40.49 3.18
4530 6879 2.287915 ACATCACAAGTTTCAGCGTCAC 59.712 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.