Multiple sequence alignment - TraesCS2B01G295600

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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 TraesCS2B01G295600 chr2B 100.000 3308 0 0 1 3308 412713140 412716447 0.000000e+00 6109.0
1 TraesCS2B01G295600 chr2B 98.461 2079 31 1 1 2079 412659389 412661466 0.000000e+00 3661.0
2 TraesCS2B01G295600 chr2B 98.460 1234 18 1 2076 3308 412661523 412662756 0.000000e+00 2172.0
3 TraesCS2B01G295600 chr2B 83.051 118 19 1 2287 2403 63162366 63162249 4.510000e-19 106.0
4 TraesCS2B01G295600 chr7B 96.863 510 11 2 75 579 223808424 223807915 0.000000e+00 848.0
5 TraesCS2B01G295600 chr7B 98.851 174 2 0 1 174 223808598 223808425 8.910000e-81 311.0
6 TraesCS2B01G295600 chr7B 74.889 450 103 10 2273 2717 610359129 610358685 2.600000e-46 196.0
7 TraesCS2B01G295600 chr3B 90.741 162 14 1 423 583 104722430 104722269 7.190000e-52 215.0
8 TraesCS2B01G295600 chr3B 89.677 155 15 1 423 576 185954767 185954921 2.600000e-46 196.0
9 TraesCS2B01G295600 chr3B 88.679 159 17 1 423 580 184381623 184381781 3.370000e-45 193.0
10 TraesCS2B01G295600 chr3B 96.875 32 1 0 378 409 104722458 104722427 2.000000e-03 54.7
11 TraesCS2B01G295600 chr4B 90.132 152 13 2 433 583 27021450 27021600 2.600000e-46 196.0
12 TraesCS2B01G295600 chr1D 85.890 163 18 4 423 583 274041031 274041190 5.680000e-38 169.0
13 TraesCS2B01G295600 chr3A 81.159 207 20 11 376 580 453202559 453202370 7.400000e-32 148.0
14 TraesCS2B01G295600 chr3D 81.407 199 20 8 382 579 339588563 339588381 2.660000e-31 147.0
15 TraesCS2B01G295600 chr4A 83.117 77 12 1 2312 2387 709029499 709029423 5.920000e-08 69.4
16 TraesCS2B01G295600 chr5D 75.969 129 27 4 2270 2396 347023273 347023147 2.760000e-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 TraesCS2B01G295600 chr2B 412713140 412716447 3307 False 6109.0 6109 100.0000 1 3308 1 chr2B.!!$F1 3307
1 TraesCS2B01G295600 chr2B 412659389 412662756 3367 False 2916.5 3661 98.4605 1 3308 2 chr2B.!!$F2 3307
2 TraesCS2B01G295600 chr7B 223807915 223808598 683 True 579.5 848 97.8570 1 579 2 chr7B.!!$R2 578

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
818 924 1.081442 GTGGCGCTTTTCTTTCCGG 60.081 57.895 7.64 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2742 2908 0.251519 CTGCTTCCCCCTTGCTTCTT 60.252 55.0 0.0 0.0 0.0 2.52 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
108 209 4.320608 TTGGAAGACTGATTTTGTTGGC 57.679 40.909 0.00 0.00 0.00 4.52
113 214 2.035066 AGACTGATTTTGTTGGCAGTGC 59.965 45.455 6.55 6.55 41.30 4.40
202 303 3.860536 GTGTTTTTATGTGCCGTGTTTGT 59.139 39.130 0.00 0.00 0.00 2.83
416 521 3.879998 TGTGTTGGTCCGTTATATGCAT 58.120 40.909 3.79 3.79 0.00 3.96
638 744 3.057547 CTCCACTGTCGAGAGCCCG 62.058 68.421 9.90 0.00 0.00 6.13
773 879 2.266055 CTCCACCCTTGACGGCTC 59.734 66.667 0.00 0.00 0.00 4.70
818 924 1.081442 GTGGCGCTTTTCTTTCCGG 60.081 57.895 7.64 0.00 0.00 5.14
983 1089 2.352805 GAAGGGGGTGCTGGTCTG 59.647 66.667 0.00 0.00 0.00 3.51
1096 1202 0.977627 TGTCGACTCCATGATGGGCT 60.978 55.000 17.92 0.00 38.32 5.19
1116 1222 1.362406 GCCTAAACCTGCTCGCAGAC 61.362 60.000 19.78 0.00 46.30 3.51
1475 1581 4.351874 TCATCAACCTTCCTTTCGAGTT 57.648 40.909 0.00 0.00 0.00 3.01
1484 1590 4.515191 CCTTCCTTTCGAGTTGATGAACAA 59.485 41.667 0.00 0.00 34.17 2.83
1610 1716 0.602562 CCTTTTGCCGAGCCAATTCA 59.397 50.000 0.00 0.00 0.00 2.57
1859 1965 2.097110 TCTTGGTATAGCGACCCCAT 57.903 50.000 0.00 0.00 38.89 4.00
1953 2059 0.317479 AAGGGGAGAACGTCAAGTCG 59.683 55.000 0.00 0.00 0.00 4.18
1957 2063 1.006571 GAGAACGTCAAGTCGGGCA 60.007 57.895 0.00 0.00 34.94 5.36
1964 2070 2.032528 CAAGTCGGGCAAGCAGGA 59.967 61.111 0.00 0.00 0.00 3.86
1965 2071 2.037136 CAAGTCGGGCAAGCAGGAG 61.037 63.158 0.00 0.00 0.00 3.69
1966 2072 3.259633 AAGTCGGGCAAGCAGGAGG 62.260 63.158 0.00 0.00 0.00 4.30
2047 2153 2.098443 GCAAAGAAATTATTCCCGGCGA 59.902 45.455 9.30 0.00 36.12 5.54
2307 2473 2.097036 CAGCCCTGCAAAGATCAATGA 58.903 47.619 0.00 0.00 0.00 2.57
2329 2495 1.743623 TGGTAGCGTGGAATTGCCG 60.744 57.895 0.00 0.00 40.66 5.69
2403 2569 5.743130 GCCGAAGATCCTGATATCCTTTTCA 60.743 44.000 0.00 0.00 0.00 2.69
2404 2570 5.931146 CCGAAGATCCTGATATCCTTTTCAG 59.069 44.000 0.00 0.00 39.25 3.02
2432 2598 6.715347 AAAACAAAGCTTGACAGGAATAGT 57.285 33.333 0.00 0.00 0.00 2.12
2469 2635 3.066380 GGGATGTTGAACATGCAAAACC 58.934 45.455 26.93 15.41 46.96 3.27
2493 2659 1.061546 GGTTAGGGACTGTGTTGGGA 58.938 55.000 0.00 0.00 41.52 4.37
2507 2673 3.373565 GGGAAAAGCGGTGGCCTG 61.374 66.667 3.32 0.00 41.24 4.85
2742 2908 1.270625 ACGAGATCCTGTTTGCCGAAA 60.271 47.619 0.00 0.00 0.00 3.46
2980 3147 0.622738 ATCCCAGGCACTCTGACCAT 60.623 55.000 0.00 0.00 46.18 3.55
3018 3185 4.386312 GGTGATGGAACCTGAATATTCCCA 60.386 45.833 12.90 12.03 43.30 4.37
3023 3190 3.467803 GAACCTGAATATTCCCACGGAG 58.532 50.000 12.90 2.50 31.21 4.63
3044 3211 2.172483 GAGGGCGACTGTGGTGTCAT 62.172 60.000 0.00 0.00 36.82 3.06
3049 3216 1.346365 CGACTGTGGTGTCATAACCG 58.654 55.000 0.00 0.00 43.73 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 209 0.318275 GCTACCTAGCTAGCGCACTG 60.318 60.000 15.74 3.11 45.62 3.66
202 303 4.460263 ACTACAAACATGACTTGCCAAGA 58.540 39.130 12.25 0.00 0.00 3.02
576 682 4.701765 AGTTGATTGCTCGCTCATCTATT 58.298 39.130 0.00 0.00 0.00 1.73
588 694 2.625737 CTGATGGACGAGTTGATTGCT 58.374 47.619 0.00 0.00 0.00 3.91
753 859 4.410400 CCGTCAAGGGTGGAGGGC 62.410 72.222 0.00 0.00 34.00 5.19
818 924 3.181464 GGTAAGGCAAGGTAGATCCAGAC 60.181 52.174 0.00 0.00 39.02 3.51
983 1089 5.119931 TGACATTGTTGTTGTGCCTAATC 57.880 39.130 0.00 0.00 35.79 1.75
1096 1202 1.375908 CTGCGAGCAGGTTTAGGCA 60.376 57.895 16.69 0.00 40.17 4.75
1116 1222 1.179174 TGTCCACCACCTCTGTCTCG 61.179 60.000 0.00 0.00 0.00 4.04
1263 1369 2.750657 CCTTAGCCTGAGCCCCCTG 61.751 68.421 0.00 0.00 41.25 4.45
1475 1581 7.723616 TCTTCAAACCCTTTCTATTGTTCATCA 59.276 33.333 0.00 0.00 0.00 3.07
1484 1590 5.253330 TCGCAATCTTCAAACCCTTTCTAT 58.747 37.500 0.00 0.00 0.00 1.98
1859 1965 0.331137 TCCCCCACCTCCCCTATCTA 60.331 60.000 0.00 0.00 0.00 1.98
2014 2120 9.798994 GAATAATTTCTTTGCAATCTCAGACAT 57.201 29.630 0.00 0.00 0.00 3.06
2047 2153 2.930826 TTCCCTTTTCGCTCAGTCTT 57.069 45.000 0.00 0.00 0.00 3.01
2307 2473 1.539827 GCAATTCCACGCTACCACTTT 59.460 47.619 0.00 0.00 0.00 2.66
2403 2569 4.580580 CCTGTCAAGCTTTGTTTTAGACCT 59.419 41.667 0.00 0.00 0.00 3.85
2404 2570 4.578928 TCCTGTCAAGCTTTGTTTTAGACC 59.421 41.667 0.00 0.00 0.00 3.85
2409 2575 6.715347 ACTATTCCTGTCAAGCTTTGTTTT 57.285 33.333 0.00 0.00 0.00 2.43
2432 2598 3.245586 ACATCCCCTTGAACCTTTGCATA 60.246 43.478 0.00 0.00 0.00 3.14
2469 2635 1.645710 ACACAGTCCCTAACCTCCAG 58.354 55.000 0.00 0.00 0.00 3.86
2493 2659 4.603535 AGCCAGGCCACCGCTTTT 62.604 61.111 8.22 0.00 34.44 2.27
2507 2673 3.333804 CTCTTTCTTCCAGAACAGAGCC 58.666 50.000 10.26 0.00 35.20 4.70
2742 2908 0.251519 CTGCTTCCCCCTTGCTTCTT 60.252 55.000 0.00 0.00 0.00 2.52
2923 3090 4.475135 GCCGGGAAGTGGGCTCTC 62.475 72.222 2.18 0.00 45.93 3.20
2980 3147 1.357137 TCACCACAATCACAGGCCTA 58.643 50.000 3.98 0.00 0.00 3.93
3023 3190 4.394712 CACCACAGTCGCCCTCCC 62.395 72.222 0.00 0.00 0.00 4.30
3044 3211 3.478857 TCTTGCCTCAAACTTCGGTTA 57.521 42.857 0.00 0.00 37.14 2.85
3049 3216 2.094854 CAGCCATCTTGCCTCAAACTTC 60.095 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.