Multiple sequence alignment - TraesCS2B01G279300

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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 TraesCS2B01G279300 chr2B 100.000 2432 0 0 1 2432 385563353 385560922 0.000000e+00 4492.0
1 TraesCS2B01G279300 chr2D 95.226 2451 72 15 1 2432 317943366 317940942 0.000000e+00 3836.0
2 TraesCS2B01G279300 chr2D 88.453 433 31 5 1993 2418 610708929 610709349 2.790000e-139 505.0
3 TraesCS2B01G279300 chr2D 93.519 216 14 0 1268 1483 610707318 610707533 3.020000e-84 322.0
4 TraesCS2B01G279300 chr2D 94.595 37 2 0 1222 1258 12523790 12523826 9.390000e-05 58.4
5 TraesCS2B01G279300 chr2A 95.012 1604 58 13 844 2432 415062088 415063684 0.000000e+00 2499.0
6 TraesCS2B01G279300 chr2A 90.140 1501 97 27 976 2430 750149895 750148400 0.000000e+00 1905.0
7 TraesCS2B01G279300 chr2A 92.890 858 54 5 2 858 414994553 414995404 0.000000e+00 1240.0
8 TraesCS2B01G279300 chr7D 89.881 1512 80 24 964 2432 498275151 498273670 0.000000e+00 1877.0
9 TraesCS2B01G279300 chr5B 75.446 505 105 15 1102 1601 579810053 579809563 6.760000e-56 228.0
10 TraesCS2B01G279300 chrUn 77.297 185 36 6 1229 1410 293161165 293161346 1.190000e-18 104.0
11 TraesCS2B01G279300 chrUn 77.297 185 36 6 1229 1410 409868967 409868786 1.190000e-18 104.0
12 TraesCS2B01G279300 chr6D 80.556 108 17 4 1229 1334 97520251 97520356 2.000000e-11 80.5


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 TraesCS2B01G279300 chr2B 385560922 385563353 2431 True 4492.0 4492 100.000 1 2432 1 chr2B.!!$R1 2431
1 TraesCS2B01G279300 chr2D 317940942 317943366 2424 True 3836.0 3836 95.226 1 2432 1 chr2D.!!$R1 2431
2 TraesCS2B01G279300 chr2D 610707318 610709349 2031 False 413.5 505 90.986 1268 2418 2 chr2D.!!$F2 1150
3 TraesCS2B01G279300 chr2A 415062088 415063684 1596 False 2499.0 2499 95.012 844 2432 1 chr2A.!!$F2 1588
4 TraesCS2B01G279300 chr2A 750148400 750149895 1495 True 1905.0 1905 90.140 976 2430 1 chr2A.!!$R1 1454
5 TraesCS2B01G279300 chr2A 414994553 414995404 851 False 1240.0 1240 92.890 2 858 1 chr2A.!!$F1 856
6 TraesCS2B01G279300 chr7D 498273670 498275151 1481 True 1877.0 1877 89.881 964 2432 1 chr7D.!!$R1 1468

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
287 289 0.108472 CGAAGATGCTCAGGTGCTCA 60.108 55.000 0.0 0.0 0.0 4.26 F
566 569 1.202533 CCGAATCGCCACACTCCTTAT 60.203 52.381 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1192 0.252513 TGTCCTTCGGGATGGGAAGA 60.253 55.000 3.26 0.0 46.96 2.87 R
1954 3203 1.218316 GCGGGAGATGAAGGACGTT 59.782 57.895 0.00 0.0 0.00 3.99 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
76 77 9.476202 AGCTGTAAACTCATTTTTAATTTGGAC 57.524 29.630 0.00 0.00 0.00 4.02
108 109 2.614057 CGATCCTGAATGTGGCTTTACC 59.386 50.000 0.00 0.00 39.84 2.85
116 117 6.418057 TGAATGTGGCTTTACCTTTTGAAT 57.582 33.333 0.00 0.00 40.22 2.57
155 156 4.463891 CCCTTGAGTTTGTTCCAGCATTAT 59.536 41.667 0.00 0.00 0.00 1.28
231 232 0.745845 CCGGGCTCATCTCACTTTGG 60.746 60.000 0.00 0.00 0.00 3.28
287 289 0.108472 CGAAGATGCTCAGGTGCTCA 60.108 55.000 0.00 0.00 0.00 4.26
339 341 6.443849 TGGACATTCTAGGACCTTAGACAAAT 59.556 38.462 0.00 0.00 29.67 2.32
340 342 7.037586 TGGACATTCTAGGACCTTAGACAAATT 60.038 37.037 0.00 0.00 29.67 1.82
341 343 7.829706 GGACATTCTAGGACCTTAGACAAATTT 59.170 37.037 0.00 0.00 29.67 1.82
342 344 9.232473 GACATTCTAGGACCTTAGACAAATTTT 57.768 33.333 0.00 0.00 29.67 1.82
343 345 9.588096 ACATTCTAGGACCTTAGACAAATTTTT 57.412 29.630 0.00 0.00 29.67 1.94
368 370 9.425248 TTTTTCCGGATCCTAATAGTACTCTTA 57.575 33.333 4.15 0.00 0.00 2.10
372 374 8.388589 TCCGGATCCTAATAGTACTCTTATTCA 58.611 37.037 10.75 0.00 0.00 2.57
566 569 1.202533 CCGAATCGCCACACTCCTTAT 60.203 52.381 0.00 0.00 0.00 1.73
637 640 8.570488 CCATTGCAATATGCTACTCTTTTCATA 58.430 33.333 12.53 0.00 45.31 2.15
667 670 9.661563 AACATTATACTTTCGGTAAGTGATTCA 57.338 29.630 9.90 0.00 46.46 2.57
741 744 3.873952 GCAACTCATATTCTCACACCTCC 59.126 47.826 0.00 0.00 0.00 4.30
743 746 5.114780 CAACTCATATTCTCACACCTCCTG 58.885 45.833 0.00 0.00 0.00 3.86
744 747 4.357325 ACTCATATTCTCACACCTCCTGT 58.643 43.478 0.00 0.00 0.00 4.00
745 748 4.780021 ACTCATATTCTCACACCTCCTGTT 59.220 41.667 0.00 0.00 0.00 3.16
746 749 5.249393 ACTCATATTCTCACACCTCCTGTTT 59.751 40.000 0.00 0.00 0.00 2.83
747 750 6.126863 TCATATTCTCACACCTCCTGTTTT 57.873 37.500 0.00 0.00 0.00 2.43
748 751 6.542821 TCATATTCTCACACCTCCTGTTTTT 58.457 36.000 0.00 0.00 0.00 1.94
785 797 8.962884 AAATTGTGAAATAATTTAGGGATGCC 57.037 30.769 0.00 0.00 44.27 4.40
800 812 3.293311 GATGCCATACAATGTGCATCC 57.707 47.619 20.04 7.82 46.50 3.51
864 876 9.613428 AGTACAAACTATGCAATGTGTACATAT 57.387 29.630 22.02 0.00 42.30 1.78
1503 2696 1.514228 GTGCGCGTCGATCTCTTCA 60.514 57.895 8.43 0.00 0.00 3.02
1624 2817 6.202516 TCCATCCAAAATTCCAAATACGAC 57.797 37.500 0.00 0.00 0.00 4.34
1771 3002 2.041762 ATGCCCTGCTCCTCCTCA 59.958 61.111 0.00 0.00 0.00 3.86
1776 3013 1.446791 CCTGCTCCTCCTCATGCTC 59.553 63.158 0.00 0.00 0.00 4.26
1825 3074 2.363680 CTCCCTGTCGATGAGCTTGTAT 59.636 50.000 0.00 0.00 0.00 2.29
1850 3099 2.879907 CGTTCCTCCGGCTCGTTA 59.120 61.111 0.00 0.00 0.00 3.18
2086 3335 2.435586 CGCTTCAGCTCCACCCTG 60.436 66.667 0.00 0.00 39.32 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.096335 CAGCTGCGTAAGATCAAATGCA 59.904 45.455 0.00 12.13 43.02 3.96
76 77 5.006068 CACATTCAGGATCGTAACTGATGTG 59.994 44.000 19.42 19.42 42.73 3.21
116 117 7.787623 ACTCAAGGGCTTAACTTAGTAGTAA 57.212 36.000 0.00 0.00 33.17 2.24
287 289 0.238289 CGAACATTTGCACGCTCCTT 59.762 50.000 0.00 0.00 0.00 3.36
308 310 3.910627 AGGTCCTAGAATGTCCAAACACT 59.089 43.478 0.00 0.00 38.48 3.55
342 344 7.909485 AGAGTACTATTAGGATCCGGAAAAA 57.091 36.000 9.01 0.30 0.00 1.94
343 345 7.909485 AAGAGTACTATTAGGATCCGGAAAA 57.091 36.000 9.01 0.71 0.00 2.29
344 346 9.597681 AATAAGAGTACTATTAGGATCCGGAAA 57.402 33.333 9.01 0.00 0.00 3.13
347 349 8.577048 TGAATAAGAGTACTATTAGGATCCGG 57.423 38.462 14.76 0.00 0.00 5.14
785 797 0.936600 TCGCGGATGCACATTGTATG 59.063 50.000 6.13 0.00 42.97 2.39
800 812 6.510746 TGTTCTTGTGAATATATCTTCGCG 57.489 37.500 0.00 0.00 38.25 5.87
1179 1192 0.252513 TGTCCTTCGGGATGGGAAGA 60.253 55.000 3.26 0.00 46.96 2.87
1624 2817 9.769093 CCGTTACCTTATTTCAAACTAATCTTG 57.231 33.333 0.00 0.00 0.00 3.02
1903 3152 1.946984 CCAACCTGTGGGACTACCTA 58.053 55.000 0.00 0.00 44.64 3.08
1954 3203 1.218316 GCGGGAGATGAAGGACGTT 59.782 57.895 0.00 0.00 0.00 3.99
1981 3230 2.579787 GACGGAGCGGACATGTCG 60.580 66.667 19.33 15.06 0.00 4.35
2162 3411 2.795973 CCGCGTCGACCTCATGTA 59.204 61.111 10.58 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.