Multiple sequence alignment - TraesCS1D01G359800

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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 TraesCS1D01G359800 chr1D 100.000 2477 0 0 1 2477 443113697 443111221 0 4575
1 TraesCS1D01G359800 chr1D 96.867 2458 62 9 2 2449 114311705 114309253 0 4098
2 TraesCS1D01G359800 chr2D 97.299 2481 58 6 1 2477 536995909 536998384 0 4202
3 TraesCS1D01G359800 chr5D 97.027 2489 59 9 1 2477 26829112 26831597 0 4172
4 TraesCS1D01G359800 chr5D 97.015 2479 65 7 2 2476 77882358 77884831 0 4159
5 TraesCS1D01G359800 chr5D 97.234 2458 59 6 26 2477 371071486 371073940 0 4154
6 TraesCS1D01G359800 chr7D 96.663 2487 68 8 1 2477 452961012 452963493 0 4119
7 TraesCS1D01G359800 chr7D 96.577 2483 72 7 1 2477 102563832 102561357 0 4102
8 TraesCS1D01G359800 chr7D 96.301 2487 77 11 1 2477 632553248 632555729 0 4069
9 TraesCS1D01G359800 chr6D 96.499 2485 70 12 1 2477 83549526 83547051 0 4091


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 TraesCS1D01G359800 chr1D 443111221 443113697 2476 True 4575 4575 100.000 1 2477 1 chr1D.!!$R2 2476
1 TraesCS1D01G359800 chr1D 114309253 114311705 2452 True 4098 4098 96.867 2 2449 1 chr1D.!!$R1 2447
2 TraesCS1D01G359800 chr2D 536995909 536998384 2475 False 4202 4202 97.299 1 2477 1 chr2D.!!$F1 2476
3 TraesCS1D01G359800 chr5D 26829112 26831597 2485 False 4172 4172 97.027 1 2477 1 chr5D.!!$F1 2476
4 TraesCS1D01G359800 chr5D 77882358 77884831 2473 False 4159 4159 97.015 2 2476 1 chr5D.!!$F2 2474
5 TraesCS1D01G359800 chr5D 371071486 371073940 2454 False 4154 4154 97.234 26 2477 1 chr5D.!!$F3 2451
6 TraesCS1D01G359800 chr7D 452961012 452963493 2481 False 4119 4119 96.663 1 2477 1 chr7D.!!$F1 2476
7 TraesCS1D01G359800 chr7D 102561357 102563832 2475 True 4102 4102 96.577 1 2477 1 chr7D.!!$R1 2476
8 TraesCS1D01G359800 chr7D 632553248 632555729 2481 False 4069 4069 96.301 1 2477 1 chr7D.!!$F2 2476
9 TraesCS1D01G359800 chr6D 83547051 83549526 2475 True 4091 4091 96.499 1 2477 1 chr6D.!!$R1 2476

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
249 257 1.761784 CACCCCTCTCAGATCTGAAGG 59.238 57.143 28.99 28.99 39.39 3.46 F
1144 1166 0.037790 GAGGCCGGAGATGCATAGTC 60.038 60.000 5.05 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 1496 0.469494 TCTTGCCAGTGAAGTCAGCA 59.531 50.000 0.00 0.0 0.00 4.41 R
2154 2182 1.225475 CTGACGAAACACGCGATGC 60.225 57.895 15.93 0.0 46.94 3.91 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
189 192 4.887748 TCTGAGGAAGTTGCTCTGTTTAG 58.112 43.478 22.93 12.79 35.71 1.85
249 257 1.761784 CACCCCTCTCAGATCTGAAGG 59.238 57.143 28.99 28.99 39.39 3.46
691 713 6.405538 AGAAGGAGATGTTGAGATTCTTGTC 58.594 40.000 0.00 0.00 0.00 3.18
803 825 7.286546 TGTCTGAAATTTGTAAGGATGGTTTGA 59.713 33.333 0.00 0.00 0.00 2.69
918 940 7.631915 ATTTGCCTTACGTTGAAATTTACAC 57.368 32.000 0.00 0.00 0.00 2.90
1016 1038 0.815213 GCCATGCCTTACGATGAGCA 60.815 55.000 0.00 0.00 40.00 4.26
1144 1166 0.037790 GAGGCCGGAGATGCATAGTC 60.038 60.000 5.05 0.00 0.00 2.59
1145 1167 1.004440 GGCCGGAGATGCATAGTCC 60.004 63.158 5.05 15.07 0.00 3.85
1346 1371 4.910913 AGAGAAGAAGAGGGAAAGGAAAGT 59.089 41.667 0.00 0.00 0.00 2.66
1471 1496 3.754323 TGTTGTGTCGAGGACTTTGTTTT 59.246 39.130 0.00 0.00 33.15 2.43
1472 1497 4.095610 GTTGTGTCGAGGACTTTGTTTTG 58.904 43.478 0.00 0.00 33.15 2.44
1479 1504 3.065371 CGAGGACTTTGTTTTGCTGACTT 59.935 43.478 0.00 0.00 0.00 3.01
1628 1654 7.380536 ACTCATTTCTTCATTAGCAATGCAAA 58.619 30.769 8.35 0.00 37.40 3.68
1718 1744 0.243636 GTGCAGGCATTGGTGGTAAC 59.756 55.000 0.00 0.00 0.00 2.50
1912 1938 5.245526 AGAAGTACTTTACCGAGTTGGACAT 59.754 40.000 10.02 0.00 42.00 3.06
2088 2116 2.031919 AACCCGATGTGCTTGCGA 59.968 55.556 0.00 0.00 0.00 5.10
2154 2182 2.053627 GCTGTTGAGTTTCATTTGCCG 58.946 47.619 0.00 0.00 0.00 5.69
2193 2221 0.397941 TTGGTCTGTTCCAGCCTCAG 59.602 55.000 0.00 0.00 38.80 3.35
2271 2299 4.705507 ACTAAGCATCGTCAGTCCTTCTTA 59.294 41.667 0.00 0.00 0.00 2.10
2320 2348 1.059913 CAGGTTGGACAGGAGAAGGT 58.940 55.000 0.00 0.00 0.00 3.50
2344 2372 2.158943 CGGAAGATAAAGGACTGGGACC 60.159 54.545 0.00 0.00 0.00 4.46
2464 2492 9.256477 CTTTTGATAACTACATACGATGGCTTA 57.744 33.333 0.00 0.00 33.60 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 257 0.463833 ATCGAATCCGGGCCTCAAAC 60.464 55.000 0.84 0.00 36.24 2.93
780 802 7.661040 AGTCAAACCATCCTTACAAATTTCAG 58.339 34.615 0.00 0.00 0.00 3.02
803 825 2.614779 TCGTAGACATCGTCGAGAAGT 58.385 47.619 0.00 0.00 37.67 3.01
904 926 2.981400 AGGGCGTGTAAATTTCAACG 57.019 45.000 16.95 16.95 0.00 4.10
918 940 5.354234 ACAAGTAATGACAAATCTTAGGGCG 59.646 40.000 0.00 0.00 0.00 6.13
961 983 3.581755 CGTGGTACCGAATCTTCAAAGA 58.418 45.455 7.57 0.00 39.78 2.52
978 1000 3.391382 GGACCAGAGACCCCGTGG 61.391 72.222 0.00 0.00 37.38 4.94
1089 1111 1.227853 GGACACCAGTGGAGCGTTT 60.228 57.895 18.40 0.00 34.19 3.60
1144 1166 3.861797 CCCGGTCCGAAGATGGGG 61.862 72.222 14.39 0.00 37.06 4.96
1145 1167 3.861797 CCCCGGTCCGAAGATGGG 61.862 72.222 14.39 10.69 39.26 4.00
1471 1496 0.469494 TCTTGCCAGTGAAGTCAGCA 59.531 50.000 0.00 0.00 0.00 4.41
1472 1497 1.265365 GTTCTTGCCAGTGAAGTCAGC 59.735 52.381 0.00 0.00 0.00 4.26
1479 1504 1.301716 GGAGCGTTCTTGCCAGTGA 60.302 57.895 0.00 0.00 34.65 3.41
1718 1744 5.236047 GCTCCATACAGAAAGTAGAAGCATG 59.764 44.000 0.00 0.00 36.35 4.06
1756 1782 2.027625 CTCTTCGGGCGTCCAACAC 61.028 63.158 6.96 0.00 0.00 3.32
1896 1922 4.865925 CGTAATCATGTCCAACTCGGTAAA 59.134 41.667 0.00 0.00 35.57 2.01
1899 1925 2.888594 CGTAATCATGTCCAACTCGGT 58.111 47.619 0.00 0.00 35.57 4.69
2088 2116 3.774216 GCATAAGCCAGAGATCCCTATCT 59.226 47.826 0.00 0.00 38.97 1.98
2154 2182 1.225475 CTGACGAAACACGCGATGC 60.225 57.895 15.93 0.00 46.94 3.91
2320 2348 2.698797 CCCAGTCCTTTATCTTCCGCTA 59.301 50.000 0.00 0.00 0.00 4.26
2357 2385 2.684001 CTGGAAGCGGGTAACATACA 57.316 50.000 0.00 0.00 39.74 2.29


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

AutoCloner maintained by Alex Coulton.