Multiple sequence alignment - TraesCS1B01G352800

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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 TraesCS1B01G352800 chr1B 100.000 2830 0 0 1 2830 583536771 583533942 0.000000e+00 5227
1 TraesCS1B01G352800 chr1B 98.588 2832 35 3 1 2830 683734142 683731314 0.000000e+00 5003
2 TraesCS1B01G352800 chr1B 98.095 2834 49 5 1 2830 338892817 338895649 0.000000e+00 4929
3 TraesCS1B01G352800 chrUn 98.729 2832 33 3 1 2830 223706934 223704104 0.000000e+00 5027
4 TraesCS1B01G352800 chr2A 98.691 2827 33 4 1 2825 605912877 605910053 0.000000e+00 5012
5 TraesCS1B01G352800 chr2A 97.952 2832 52 3 1 2830 563256642 563259469 0.000000e+00 4903
6 TraesCS1B01G352800 chr2A 97.897 2711 52 4 123 2830 735136912 735139620 0.000000e+00 4686
7 TraesCS1B01G352800 chr2A 92.737 537 33 6 835 1367 715900117 715900651 0.000000e+00 771
8 TraesCS1B01G352800 chr2A 97.101 138 3 1 2540 2676 588462427 588462290 6.100000e-57 231
9 TraesCS1B01G352800 chr2A 97.638 127 3 0 1 127 735132921 735133047 4.750000e-53 219
10 TraesCS1B01G352800 chr2A 94.231 104 6 0 2232 2335 199191507 199191610 2.920000e-35 159
11 TraesCS1B01G352800 chr2A 100.000 57 0 0 2190 2246 735909509 735909453 3.860000e-19 106
12 TraesCS1B01G352800 chr7B 98.517 2832 38 3 1 2830 698140160 698142989 0.000000e+00 4994
13 TraesCS1B01G352800 chr5B 98.199 2832 44 4 1 2830 713082218 713079392 0.000000e+00 4940


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 TraesCS1B01G352800 chr1B 583533942 583536771 2829 True 5227.0 5227 100.0000 1 2830 1 chr1B.!!$R1 2829
1 TraesCS1B01G352800 chr1B 683731314 683734142 2828 True 5003.0 5003 98.5880 1 2830 1 chr1B.!!$R2 2829
2 TraesCS1B01G352800 chr1B 338892817 338895649 2832 False 4929.0 4929 98.0950 1 2830 1 chr1B.!!$F1 2829
3 TraesCS1B01G352800 chrUn 223704104 223706934 2830 True 5027.0 5027 98.7290 1 2830 1 chrUn.!!$R1 2829
4 TraesCS1B01G352800 chr2A 605910053 605912877 2824 True 5012.0 5012 98.6910 1 2825 1 chr2A.!!$R2 2824
5 TraesCS1B01G352800 chr2A 563256642 563259469 2827 False 4903.0 4903 97.9520 1 2830 1 chr2A.!!$F2 2829
6 TraesCS1B01G352800 chr2A 735132921 735139620 6699 False 2452.5 4686 97.7675 1 2830 2 chr2A.!!$F4 2829
7 TraesCS1B01G352800 chr2A 715900117 715900651 534 False 771.0 771 92.7370 835 1367 1 chr2A.!!$F3 532
8 TraesCS1B01G352800 chr7B 698140160 698142989 2829 False 4994.0 4994 98.5170 1 2830 1 chr7B.!!$F1 2829
9 TraesCS1B01G352800 chr5B 713079392 713082218 2826 True 4940.0 4940 98.1990 1 2830 1 chr5B.!!$R1 2829

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
383 4253 4.858935 TGTTGCTGTAATCAAAGAAGCAC 58.141 39.130 0.0 0.0 43.18 4.40 F
1108 4980 3.945921 CGTCAGTAGAGATGTTCCCACTA 59.054 47.826 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 5455 0.597637 AACAAGCACCACTCGACGAG 60.598 55.000 22.97 22.97 35.52 4.18 R
2371 6247 1.077787 CTTGTGCCCGCCCATTCTA 60.078 57.895 0.00 0.00 0.00 2.10 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
110 111 7.341769 CCTATTATTCAAACCACAAAGGATCCA 59.658 37.037 15.82 0.00 41.22 3.41
311 4181 7.336931 GTGGGGCTATCGAATTGATATGTATTT 59.663 37.037 0.00 0.00 38.85 1.40
383 4253 4.858935 TGTTGCTGTAATCAAAGAAGCAC 58.141 39.130 0.00 0.00 43.18 4.40
754 4625 8.326529 TCGAATCTTAATAAAAGGAAGGGTTCT 58.673 33.333 0.00 0.00 0.00 3.01
970 4842 7.772166 TCATTTTTAGCGTCTCATCTTCTCTA 58.228 34.615 0.00 0.00 0.00 2.43
1108 4980 3.945921 CGTCAGTAGAGATGTTCCCACTA 59.054 47.826 0.00 0.00 0.00 2.74
1497 5370 4.980339 AAGGGGAATGAGCAACAAAATT 57.020 36.364 0.00 0.00 0.00 1.82
1637 5512 2.158549 AGAAAGTGGGCTTGAAGCTCTT 60.159 45.455 19.00 15.61 43.70 2.85
1757 5632 3.576078 ATGTTGGGTGTTCTTCTGTCA 57.424 42.857 0.00 0.00 0.00 3.58
1987 5862 1.448540 CCTCGCTGCTCGGAAACAT 60.449 57.895 0.00 0.00 39.05 2.71
2319 6195 1.078001 ATAAAAGCGGACGTGGGGG 60.078 57.895 0.00 0.00 0.00 5.40
2538 6414 4.545610 GCTTTGTTGCTAAAGTGCATACA 58.454 39.130 0.00 0.00 42.96 2.29
2622 6500 3.330720 CCGCCCCCTTTCCTGTCT 61.331 66.667 0.00 0.00 0.00 3.41
2629 6507 1.481056 CCCTTTCCTGTCTGTCCCGT 61.481 60.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.628178 TGTGGTCTCGATATTGGGCTAG 59.372 50.000 0.00 0.00 0.00 3.42
110 111 5.046529 CGAGAAGATTGGACGATGAAAGAT 58.953 41.667 0.00 0.00 0.00 2.40
311 4181 5.663106 AGTGATTACCAGCTCCTAAGATTCA 59.337 40.000 0.00 0.00 0.00 2.57
383 4253 2.425143 TCTAGAGGCATTTTGGGCAG 57.575 50.000 0.00 0.00 35.46 4.85
970 4842 2.231478 TCCGTTCGATTTGAGCTTCTCT 59.769 45.455 0.00 0.00 0.00 3.10
1578 5453 2.932234 AAGCACCACTCGACGAGGG 61.932 63.158 27.39 24.12 33.35 4.30
1579 5454 1.734477 CAAGCACCACTCGACGAGG 60.734 63.158 27.39 15.05 33.35 4.63
1580 5455 0.597637 AACAAGCACCACTCGACGAG 60.598 55.000 22.97 22.97 35.52 4.18
1622 5497 1.604593 GGCAAGAGCTTCAAGCCCA 60.605 57.895 5.53 0.00 43.77 5.36
1637 5512 2.047655 CGGCTCGTTGGTAAGGCA 60.048 61.111 0.00 0.00 37.91 4.75
1757 5632 0.603707 CATAAGCCATCGGGTCGCAT 60.604 55.000 0.00 0.00 36.17 4.73
1987 5862 3.970332 AGTGTGGTCAGCACTGGA 58.030 55.556 8.76 0.00 44.52 3.86
2319 6195 4.767255 CTGTGCCCTGACCCGAGC 62.767 72.222 0.00 0.00 0.00 5.03
2328 6204 1.204941 CTCTTAGTTACGCTGTGCCCT 59.795 52.381 0.00 0.00 0.00 5.19
2365 6241 2.050269 CCCGCCCATTCTATCTCGT 58.950 57.895 0.00 0.00 0.00 4.18
2371 6247 1.077787 CTTGTGCCCGCCCATTCTA 60.078 57.895 0.00 0.00 0.00 2.10
2538 6414 1.995376 AACCGACCCAGCAAGAAAAT 58.005 45.000 0.00 0.00 0.00 1.82
2629 6507 4.329545 GACCCAACTGCTGCCGGA 62.330 66.667 5.05 0.00 0.00 5.14
2681 6559 1.474330 TTCTGCCTCATACAGCTCGA 58.526 50.000 0.00 0.00 35.04 4.04


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

AutoCloner maintained by Alex Coulton.