Multiple sequence alignment - TraesCS5D01G179700

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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 TraesCS5D01G179700 chr5D 100.000 2644 0 0 966 3609 279156941 279154298 0.000000e+00 4883
1 TraesCS5D01G179700 chr5D 98.286 700 12 0 2910 3609 441909179 441909878 0.000000e+00 1227
2 TraesCS5D01G179700 chr5D 98.143 700 13 0 2910 3609 280546837 280546138 0.000000e+00 1221
3 TraesCS5D01G179700 chr5D 100.000 517 0 0 1 517 279157906 279157390 0.000000e+00 955
4 TraesCS5D01G179700 chr5D 83.103 290 47 2 2281 2569 285839832 285839544 2.760000e-66 263
5 TraesCS5D01G179700 chr5B 97.174 1451 28 4 1466 2913 317060427 317058987 0.000000e+00 2440
6 TraesCS5D01G179700 chr5B 97.030 505 13 2 966 1470 317064271 317063769 0.000000e+00 848
7 TraesCS5D01G179700 chr5B 97.552 286 7 0 232 517 317064665 317064380 1.160000e-134 490
8 TraesCS5D01G179700 chr5B 82.034 295 52 1 2276 2569 324248739 324248445 2.150000e-62 250
9 TraesCS5D01G179700 chr5A 96.386 1162 33 5 1752 2909 368792748 368793904 0.000000e+00 1905
10 TraesCS5D01G179700 chr5A 97.582 703 17 0 966 1668 368791809 368792511 0.000000e+00 1205
11 TraesCS5D01G179700 chr5A 92.655 531 15 5 1 517 368791034 368791554 0.000000e+00 743
12 TraesCS5D01G179700 chr2D 97.845 696 15 0 2912 3607 592281909 592281214 0.000000e+00 1203
13 TraesCS5D01G179700 chr2D 96.903 678 20 1 2932 3609 591547200 591546524 0.000000e+00 1134
14 TraesCS5D01G179700 chr2D 97.878 377 8 0 2909 3285 645845949 645846325 0.000000e+00 652
15 TraesCS5D01G179700 chr2D 98.204 334 6 0 3276 3609 69270305 69270638 5.190000e-163 584
16 TraesCS5D01G179700 chr3D 97.571 700 17 0 2910 3609 402355556 402354857 0.000000e+00 1199
17 TraesCS5D01G179700 chr3D 82.337 368 59 6 2218 2582 478653363 478652999 7.520000e-82 315
18 TraesCS5D01G179700 chr6D 95.863 701 9 1 2909 3609 417474363 417475043 0.000000e+00 1116
19 TraesCS5D01G179700 chr6D 93.562 699 16 2 2910 3608 28333950 28333281 0.000000e+00 1014
20 TraesCS5D01G179700 chr6D 98.138 376 6 1 2910 3285 436110557 436110931 0.000000e+00 654
21 TraesCS5D01G179700 chr4D 93.786 692 22 4 2919 3609 397101412 397102083 0.000000e+00 1020
22 TraesCS5D01G179700 chr7D 97.613 377 9 0 2909 3285 469895959 469895583 0.000000e+00 647
23 TraesCS5D01G179700 chr7D 98.204 334 6 0 3276 3609 469895469 469895136 5.190000e-163 584
24 TraesCS5D01G179700 chr7D 86.932 352 46 0 2218 2569 512747071 512746720 2.610000e-106 396
25 TraesCS5D01G179700 chr7B 87.216 352 45 0 2218 2569 544481052 544480701 5.610000e-108 401
26 TraesCS5D01G179700 chr3B 82.609 368 58 6 2218 2582 638357251 638356887 1.620000e-83 320
27 TraesCS5D01G179700 chr3A 82.240 366 61 4 2219 2582 621893438 621893075 2.710000e-81 313
28 TraesCS5D01G179700 chr1D 84.300 293 44 2 2279 2569 372360679 372360971 5.900000e-73 285
29 TraesCS5D01G179700 chr1B 83.959 293 45 2 2279 2569 497274642 497274934 2.740000e-71 279
30 TraesCS5D01G179700 chr1A 83.959 293 45 2 2279 2569 471730130 471730422 2.740000e-71 279


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 TraesCS5D01G179700 chr5D 279154298 279157906 3608 True 2919.000000 4883 100.0000 1 3609 2 chr5D.!!$R3 3608
1 TraesCS5D01G179700 chr5D 441909179 441909878 699 False 1227.000000 1227 98.2860 2910 3609 1 chr5D.!!$F1 699
2 TraesCS5D01G179700 chr5D 280546138 280546837 699 True 1221.000000 1221 98.1430 2910 3609 1 chr5D.!!$R1 699
3 TraesCS5D01G179700 chr5B 317058987 317064665 5678 True 1259.333333 2440 97.2520 232 2913 3 chr5B.!!$R2 2681
4 TraesCS5D01G179700 chr5A 368791034 368793904 2870 False 1284.333333 1905 95.5410 1 2909 3 chr5A.!!$F1 2908
5 TraesCS5D01G179700 chr2D 592281214 592281909 695 True 1203.000000 1203 97.8450 2912 3607 1 chr2D.!!$R2 695
6 TraesCS5D01G179700 chr2D 591546524 591547200 676 True 1134.000000 1134 96.9030 2932 3609 1 chr2D.!!$R1 677
7 TraesCS5D01G179700 chr3D 402354857 402355556 699 True 1199.000000 1199 97.5710 2910 3609 1 chr3D.!!$R1 699
8 TraesCS5D01G179700 chr6D 417474363 417475043 680 False 1116.000000 1116 95.8630 2909 3609 1 chr6D.!!$F1 700
9 TraesCS5D01G179700 chr6D 28333281 28333950 669 True 1014.000000 1014 93.5620 2910 3608 1 chr6D.!!$R1 698
10 TraesCS5D01G179700 chr4D 397101412 397102083 671 False 1020.000000 1020 93.7860 2919 3609 1 chr4D.!!$F1 690
11 TraesCS5D01G179700 chr7D 469895136 469895959 823 True 615.500000 647 97.9085 2909 3609 2 chr7D.!!$R2 700

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
499 514 0.517316 GGTCACATGAGGAAACACGC 59.483 55.000 0.00 0.0 0.00 5.34 F
1364 1379 1.587054 CGAACGAGCAGGAGGAAGT 59.413 57.895 0.00 0.0 0.00 3.01 F
1967 5479 0.943835 TTGTCACCTCGTGCATGTCG 60.944 55.000 5.68 0.0 32.98 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 5055 0.592148 CCCGTAGCTACAGATCCGTC 59.408 60.000 23.21 0.0 0.0 4.79 R
2422 5934 2.970974 GCACTTGCGGCAGAGGAAC 61.971 63.158 1.67 0.0 0.0 3.62 R
3585 7230 1.306148 CGTCGGAGGAGCACTATACA 58.694 55.000 0.00 0.0 0.0 2.29 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
106 107 9.352784 GTGCAAAATGATAAAACTTATGCTACA 57.647 29.630 0.00 0.00 32.74 2.74
126 127 8.254508 TGCTACAAACCAAAGTTCTTTTTATGT 58.745 29.630 0.00 2.75 34.19 2.29
136 137 8.603181 CAAAGTTCTTTTTATGTGGGAAAACAG 58.397 33.333 0.00 0.00 32.52 3.16
199 200 5.355071 TGTGAGATTCAGCATGTTCATAACC 59.645 40.000 0.00 0.00 37.40 2.85
499 514 0.517316 GGTCACATGAGGAAACACGC 59.483 55.000 0.00 0.00 0.00 5.34
993 1008 3.141767 TCTAGCTAGCTATCAAGGCGA 57.858 47.619 24.36 13.37 34.52 5.54
1147 1162 2.172930 AGCCATGATCACAGCAAGATCT 59.827 45.455 18.27 0.00 41.85 2.75
1364 1379 1.587054 CGAACGAGCAGGAGGAAGT 59.413 57.895 0.00 0.00 0.00 3.01
1695 5055 4.743151 GCATGCATGATCACCATAACAAAG 59.257 41.667 30.64 0.00 33.31 2.77
1810 5322 3.181431 GGGCTATAGTGTAGAGACTGGGA 60.181 52.174 0.84 0.00 0.00 4.37
1907 5419 1.273838 ACAGATGTAGGGCTTCCTCCA 60.274 52.381 0.00 0.00 41.96 3.86
1938 5450 1.447317 CTGGCTTTTGTCGTGCCTGT 61.447 55.000 0.00 0.00 46.23 4.00
1967 5479 0.943835 TTGTCACCTCGTGCATGTCG 60.944 55.000 5.68 0.00 32.98 4.35
1981 5493 1.955778 CATGTCGAGGCTCAGAGAGAT 59.044 52.381 15.95 5.08 0.00 2.75
1996 5508 3.117663 AGAGAGATGGAGAGAGGTACCAC 60.118 52.174 15.94 8.18 36.49 4.16
2149 5661 7.201848 CCATGCATCCACTGTTGTCTAATTAAT 60.202 37.037 0.00 0.00 0.00 1.40
2216 5728 9.256477 TGCAGTTAACTTTGAGGATATAATACG 57.744 33.333 5.07 0.00 0.00 3.06
2495 6007 1.373497 CACGAGAAGAACTGCGGCT 60.373 57.895 0.00 0.00 0.00 5.52
2774 6291 5.065914 TGCTAGCTGAACTCAGTTTGATTT 58.934 37.500 17.23 0.00 45.45 2.17
3296 6938 2.183300 CGCAGCTACCTTACGGCA 59.817 61.111 0.00 0.00 0.00 5.69
3379 7024 3.546009 GGTGGGCCGTATCTAGCA 58.454 61.111 0.00 0.00 0.00 3.49
3585 7230 2.590007 GGCCGATGCGCTGATTCT 60.590 61.111 9.73 0.00 38.85 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.989777 AGGGTACGTGCATATTTCATTCTAC 59.010 40.000 5.86 0.0 0.00 2.59
24 25 3.688694 ACAAATCTAAGGGTACGTGCA 57.311 42.857 5.86 0.0 0.00 4.57
25 26 5.002464 TCTACAAATCTAAGGGTACGTGC 57.998 43.478 0.00 0.0 0.00 5.34
106 107 7.189079 TCCCACATAAAAAGAACTTTGGTTT 57.811 32.000 0.45 0.0 35.58 3.27
126 127 6.478129 AGGTTCGAATAATACTGTTTTCCCA 58.522 36.000 0.00 0.0 0.00 4.37
199 200 6.084326 ACTTGCTTATAAGTGTGGGTTTTG 57.916 37.500 13.91 0.0 39.33 2.44
228 229 3.119849 ACTCTGTCATTATTTGTTGGCGC 60.120 43.478 0.00 0.0 0.00 6.53
230 231 8.986477 ATTAAACTCTGTCATTATTTGTTGGC 57.014 30.769 0.00 0.0 0.00 4.52
993 1008 1.198759 ACGGGTTGGACATGGCTAGT 61.199 55.000 0.00 0.0 0.00 2.57
1147 1162 0.896019 CCGGCATACCCACAACCAAA 60.896 55.000 0.00 0.0 0.00 3.28
1364 1379 2.799562 GCATCATCATCGTCGTCTTCCA 60.800 50.000 0.00 0.0 0.00 3.53
1695 5055 0.592148 CCCGTAGCTACAGATCCGTC 59.408 60.000 23.21 0.0 0.00 4.79
1810 5322 1.102978 AGCTGAAACGCACAAAAGGT 58.897 45.000 0.00 0.0 0.00 3.50
1907 5419 5.297776 CGACAAAAGCCAGGATAGAATGATT 59.702 40.000 0.00 0.0 0.00 2.57
1938 5450 4.553156 GCACGAGGTGACAAAAATACGAAA 60.553 41.667 0.00 0.0 35.23 3.46
1967 5479 2.158623 TCTCTCCATCTCTCTGAGCCTC 60.159 54.545 0.00 0.0 0.00 4.70
1981 5493 2.297698 TTTCGTGGTACCTCTCTCCA 57.702 50.000 14.36 0.0 0.00 3.86
1996 5508 4.034975 GGCAGAATGGAGAGAGAATTTTCG 59.965 45.833 0.00 0.0 35.86 3.46
2149 5661 6.035866 GCAATGTCACTCAAAACATGTCAAAA 59.964 34.615 0.00 0.0 36.28 2.44
2158 5670 7.307694 TGATATTCAGCAATGTCACTCAAAAC 58.692 34.615 0.00 0.0 35.75 2.43
2422 5934 2.970974 GCACTTGCGGCAGAGGAAC 61.971 63.158 1.67 0.0 0.00 3.62
3266 6785 3.118454 CTGCGCGGGATCAAACGT 61.118 61.111 8.83 0.0 0.00 3.99
3296 6938 3.996124 AGCAGAGTTCGCAGCGGT 61.996 61.111 16.42 0.0 0.00 5.68
3375 7020 4.817063 GCGCGACGTACGGTGCTA 62.817 66.667 24.80 0.0 42.83 3.49
3585 7230 1.306148 CGTCGGAGGAGCACTATACA 58.694 55.000 0.00 0.0 0.00 2.29


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

AutoCloner maintained by Alex Coulton.