Multiple sequence alignment - TraesCS5B01G084700

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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 TraesCS5B01G084700 chr5B 100.000 3089 0 0 1 3089 107195921 107199009 0.000000e+00 5705
1 TraesCS5B01G084700 chr5A 96.717 2406 54 10 1 2404 105690252 105687870 0.000000e+00 3982
2 TraesCS5B01G084700 chr5A 96.063 508 14 3 2588 3089 105687878 105687371 0.000000e+00 822
3 TraesCS5B01G084700 chr5D 95.650 2138 57 10 278 2404 97831839 97833951 0.000000e+00 3400
4 TraesCS5B01G084700 chr5D 97.426 505 9 2 2589 3089 97833944 97834448 0.000000e+00 857
5 TraesCS5B01G084700 chr5D 94.304 316 14 2 1 315 97831416 97831728 5.990000e-132 481
6 TraesCS5B01G084700 chr4D 96.739 184 3 3 2405 2587 84999553 84999372 1.390000e-78 303
7 TraesCS5B01G084700 chr4B 95.187 187 7 2 2404 2589 104815749 104815564 8.380000e-76 294
8 TraesCS5B01G084700 chr4B 94.681 188 7 3 2404 2589 104813107 104812921 3.900000e-74 289
9 TraesCS5B01G084700 chr1B 95.652 184 7 1 2404 2587 481325160 481324978 8.380000e-76 294
10 TraesCS5B01G084700 chr1B 94.505 182 8 2 2406 2586 32992047 32992227 2.350000e-71 279
11 TraesCS5B01G084700 chr1B 93.583 187 10 2 2403 2587 69572670 69572484 8.440000e-71 278
12 TraesCS5B01G084700 chr2B 95.135 185 7 2 2406 2589 371564886 371564703 1.080000e-74 291
13 TraesCS5B01G084700 chr2B 93.750 192 8 3 2404 2592 664210598 664210408 5.040000e-73 285
14 TraesCS5B01G084700 chr3B 94.652 187 8 2 2405 2591 416695985 416695801 3.900000e-74 289


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 TraesCS5B01G084700 chr5B 107195921 107199009 3088 False 5705.000000 5705 100.000000 1 3089 1 chr5B.!!$F1 3088
1 TraesCS5B01G084700 chr5A 105687371 105690252 2881 True 2402.000000 3982 96.390000 1 3089 2 chr5A.!!$R1 3088
2 TraesCS5B01G084700 chr5D 97831416 97834448 3032 False 1579.333333 3400 95.793333 1 3089 3 chr5D.!!$F1 3088
3 TraesCS5B01G084700 chr4B 104812921 104815749 2828 True 291.500000 294 94.934000 2404 2589 2 chr4B.!!$R1 185

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
69 70 0.393448 TGCTGCATTGCCACATGTTT 59.607 45.0 6.12 0.0 0.00 2.83 F
1447 1612 0.541530 TGCTGTGGCTGAGAGAGAGT 60.542 55.0 0.00 0.0 39.59 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1659 1.067846 TCTGTCCTGACGTATGTGTGC 60.068 52.381 0.0 0.0 0.0 4.57 R
2402 2567 0.708209 TGAGTCCTAGCCACACCCTA 59.292 55.000 0.0 0.0 0.0 3.53 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
23 24 3.053828 CGTAACCACTGACGGGGT 58.946 61.111 0.00 0.00 39.65 4.95
29 30 0.838608 ACCACTGACGGGGTAAACAA 59.161 50.000 0.00 0.00 35.09 2.83
36 37 4.202493 ACTGACGGGGTAAACAAACCTAAT 60.202 41.667 0.00 0.00 39.65 1.73
69 70 0.393448 TGCTGCATTGCCACATGTTT 59.607 45.000 6.12 0.00 0.00 2.83
108 109 1.035932 TGATCGGTCCGGTTCCTCTC 61.036 60.000 12.29 5.88 0.00 3.20
237 239 5.735285 TTCATTGCAACCATGGATAACAA 57.265 34.783 21.47 14.85 0.00 2.83
242 244 4.880759 TGCAACCATGGATAACAAAACAG 58.119 39.130 21.47 0.00 0.00 3.16
243 245 4.586421 TGCAACCATGGATAACAAAACAGA 59.414 37.500 21.47 0.00 0.00 3.41
244 246 5.163513 GCAACCATGGATAACAAAACAGAG 58.836 41.667 21.47 0.00 0.00 3.35
447 600 1.446272 GAAAGAGTCCACGAGGCGG 60.446 63.158 0.00 0.00 33.74 6.13
474 627 2.994995 TCCATCGCCACGTGTCCT 60.995 61.111 15.65 0.00 0.00 3.85
523 676 2.046314 CGGGATTTCCACACGCCT 60.046 61.111 0.00 0.00 37.91 5.52
592 745 4.779733 TCTCCACCTCCCCTCGCC 62.780 72.222 0.00 0.00 0.00 5.54
716 881 2.105128 CGCTCTCGATTTCCCGCT 59.895 61.111 0.00 0.00 38.10 5.52
1173 1338 2.507102 CGCTACCTCACGCACCTG 60.507 66.667 0.00 0.00 0.00 4.00
1176 1341 1.982395 CTACCTCACGCACCTGGGA 60.982 63.158 0.00 0.00 0.00 4.37
1341 1506 1.450312 CGTCAAGGACCTCATGGCC 60.450 63.158 0.00 0.00 36.63 5.36
1443 1608 0.604780 GCTTTGCTGTGGCTGAGAGA 60.605 55.000 0.00 0.00 39.59 3.10
1447 1612 0.541530 TGCTGTGGCTGAGAGAGAGT 60.542 55.000 0.00 0.00 39.59 3.24
1464 1629 0.545171 AGTCTGGGATGAGGCATGTG 59.455 55.000 0.00 0.00 0.00 3.21
1563 1728 0.250553 GGGTGGACATGGTCGAACAA 60.251 55.000 7.51 0.00 29.60 2.83
2145 2310 1.102809 TTGCATTATGGCGAGCTGGG 61.103 55.000 0.00 0.00 36.28 4.45
2395 2560 6.296030 GGACAAGGATACCCAACTGTAGTAAA 60.296 42.308 0.00 0.00 33.88 2.01
2396 2561 7.266905 ACAAGGATACCCAACTGTAGTAAAT 57.733 36.000 0.00 0.00 33.88 1.40
2397 2562 8.383374 ACAAGGATACCCAACTGTAGTAAATA 57.617 34.615 0.00 0.00 33.88 1.40
2398 2563 8.828751 ACAAGGATACCCAACTGTAGTAAATAA 58.171 33.333 0.00 0.00 33.88 1.40
2399 2564 9.847224 CAAGGATACCCAACTGTAGTAAATAAT 57.153 33.333 0.00 0.00 33.88 1.28
2401 2566 9.448587 AGGATACCCAACTGTAGTAAATAATCT 57.551 33.333 0.00 0.00 33.88 2.40
2418 2583 1.861982 TCTTAGGGTGTGGCTAGGAC 58.138 55.000 0.00 0.00 0.00 3.85
2419 2584 1.361543 TCTTAGGGTGTGGCTAGGACT 59.638 52.381 0.00 0.00 0.00 3.85
2481 2646 4.805192 ACATCACACAACATCAGCAAAAAC 59.195 37.500 0.00 0.00 0.00 2.43
2482 2647 4.446994 TCACACAACATCAGCAAAAACA 57.553 36.364 0.00 0.00 0.00 2.83
2483 2648 4.172505 TCACACAACATCAGCAAAAACAC 58.827 39.130 0.00 0.00 0.00 3.32
2485 2650 4.388165 CACACAACATCAGCAAAAACACAA 59.612 37.500 0.00 0.00 0.00 3.33
2487 2652 5.642919 ACACAACATCAGCAAAAACACAATT 59.357 32.000 0.00 0.00 0.00 2.32
2492 2657 9.552114 CAACATCAGCAAAAACACAATTAAAAA 57.448 25.926 0.00 0.00 0.00 1.94
2520 2685 4.112634 TGTACAAATCTTGAAGCCCCTT 57.887 40.909 0.00 0.00 0.00 3.95
2530 2695 5.437060 TCTTGAAGCCCCTTATTATGTGAC 58.563 41.667 0.00 0.00 0.00 3.67
2551 2716 6.469595 GTGACGAACTACTTAGATGTGACATC 59.530 42.308 17.46 17.46 0.00 3.06
2552 2717 5.892568 ACGAACTACTTAGATGTGACATCC 58.107 41.667 21.05 4.60 0.00 3.51
2626 2822 2.684374 TGCACTACATGTCGTACGGTAT 59.316 45.455 16.52 7.37 0.00 2.73
2840 5194 7.278461 GTAAGCATAGTCCTGATTACTCTCA 57.722 40.000 5.29 0.00 42.11 3.27
3044 5476 1.464023 CGCACATTAAACGCCTGTCTG 60.464 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.083908 GGCACGTCGAATTAGGTTTGTTTA 60.084 41.667 0.00 0.00 0.00 2.01
29 30 1.274167 TCTGGCACGTCGAATTAGGTT 59.726 47.619 0.00 0.00 0.00 3.50
108 109 4.848357 ACCCATAACAGGATGAACTGAAG 58.152 43.478 0.00 0.00 40.97 3.02
209 211 6.795144 ATCCATGGTTGCAATGAATAAGAA 57.205 33.333 12.58 0.00 0.00 2.52
447 600 2.396157 GGCGATGGACGGTTGGTTC 61.396 63.158 0.00 0.00 42.83 3.62
523 676 4.439700 CGTCCGCTTGACTTTATAGAGGAA 60.440 45.833 0.00 0.00 42.13 3.36
761 926 1.003851 GATTCGAATTCGGTCGGCAA 58.996 50.000 26.47 13.24 41.43 4.52
762 927 0.808453 GGATTCGAATTCGGTCGGCA 60.808 55.000 26.47 4.23 41.43 5.69
1041 1206 2.678934 CTCCCGAACTCGTCCCCA 60.679 66.667 0.00 0.00 37.74 4.96
1341 1506 3.403276 GTCCTTGGAGTCGACGAAG 57.597 57.895 10.46 13.01 0.00 3.79
1443 1608 1.129917 CATGCCTCATCCCAGACTCT 58.870 55.000 0.00 0.00 0.00 3.24
1447 1612 1.225426 GCACATGCCTCATCCCAGA 59.775 57.895 0.00 0.00 34.31 3.86
1494 1659 1.067846 TCTGTCCTGACGTATGTGTGC 60.068 52.381 0.00 0.00 0.00 4.57
1500 1665 1.819288 CACACCTCTGTCCTGACGTAT 59.181 52.381 0.00 0.00 0.00 3.06
1602 1767 2.202570 GCCAATCGCTGCTGCAAG 60.203 61.111 16.29 0.73 39.64 4.01
2145 2310 2.176247 TAGATCCCTTCTCCCACACC 57.824 55.000 0.00 0.00 35.79 4.16
2197 2362 6.065976 TCAACATACCTCAAGATTCCACAT 57.934 37.500 0.00 0.00 0.00 3.21
2395 2560 4.593634 GTCCTAGCCACACCCTAAGATTAT 59.406 45.833 0.00 0.00 0.00 1.28
2396 2561 3.965347 GTCCTAGCCACACCCTAAGATTA 59.035 47.826 0.00 0.00 0.00 1.75
2397 2562 2.772515 GTCCTAGCCACACCCTAAGATT 59.227 50.000 0.00 0.00 0.00 2.40
2398 2563 2.022918 AGTCCTAGCCACACCCTAAGAT 60.023 50.000 0.00 0.00 0.00 2.40
2399 2564 1.361543 AGTCCTAGCCACACCCTAAGA 59.638 52.381 0.00 0.00 0.00 2.10
2400 2565 1.757699 GAGTCCTAGCCACACCCTAAG 59.242 57.143 0.00 0.00 0.00 2.18
2401 2566 1.078159 TGAGTCCTAGCCACACCCTAA 59.922 52.381 0.00 0.00 0.00 2.69
2402 2567 0.708209 TGAGTCCTAGCCACACCCTA 59.292 55.000 0.00 0.00 0.00 3.53
2492 2657 8.040727 GGGGCTTCAAGATTTGTACAAAATATT 58.959 33.333 23.97 15.49 33.56 1.28
2520 2685 9.946165 CACATCTAAGTAGTTCGTCACATAATA 57.054 33.333 0.00 0.00 0.00 0.98
2530 2695 6.137794 AGGATGTCACATCTAAGTAGTTCG 57.862 41.667 17.46 0.00 0.00 3.95
2840 5194 4.345854 TGTTTTGGTCTTAACCCACAACT 58.654 39.130 14.78 0.00 45.83 3.16


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

AutoCloner maintained by Alex Coulton.