Multiple sequence alignment - TraesCS2D01G149000

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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 TraesCS2D01G149000 chr2D 100.000 3311 0 0 1 3311 90500191 90503501 0.000000e+00 6115
1 TraesCS2D01G149000 chr2A 95.665 3299 115 9 30 3310 90415860 90419148 0.000000e+00 5275
2 TraesCS2D01G149000 chr2B 96.277 3116 93 10 210 3310 143272650 143275757 0.000000e+00 5090
3 TraesCS2D01G149000 chr1D 91.686 2153 173 4 263 2409 476255828 476253676 0.000000e+00 2979
4 TraesCS2D01G149000 chr1D 79.287 589 61 35 2702 3245 476259107 476258535 4.060000e-94 355
5 TraesCS2D01G149000 chr1B 91.454 2153 178 4 263 2409 662555084 662552932 0.000000e+00 2952
6 TraesCS2D01G149000 chr1B 79.117 589 62 35 2702 3245 662558330 662557758 1.890000e-92 350
7 TraesCS2D01G149000 chr1A 91.314 2153 181 4 263 2409 572019135 572016983 0.000000e+00 2935
8 TraesCS2D01G149000 chr1A 77.721 588 69 36 2702 3245 572022397 572021828 1.490000e-78 303


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 TraesCS2D01G149000 chr2D 90500191 90503501 3310 False 6115 6115 100.0000 1 3311 1 chr2D.!!$F1 3310
1 TraesCS2D01G149000 chr2A 90415860 90419148 3288 False 5275 5275 95.6650 30 3310 1 chr2A.!!$F1 3280
2 TraesCS2D01G149000 chr2B 143272650 143275757 3107 False 5090 5090 96.2770 210 3310 1 chr2B.!!$F1 3100
3 TraesCS2D01G149000 chr1D 476253676 476259107 5431 True 1667 2979 85.4865 263 3245 2 chr1D.!!$R1 2982
4 TraesCS2D01G149000 chr1B 662552932 662558330 5398 True 1651 2952 85.2855 263 3245 2 chr1B.!!$R1 2982
5 TraesCS2D01G149000 chr1A 572016983 572022397 5414 True 1619 2935 84.5175 263 3245 2 chr1A.!!$R1 2982

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
223 229 0.254462 TCACTGCGCCATTCCCATTA 59.746 50.000 4.18 0.0 0.00 1.90 F
1239 4358 1.152902 TTGTGCTGGTCTTGCAGCT 60.153 52.632 0.00 0.0 44.19 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 4448 2.063156 TTATGCTGCCACTTTTTGCG 57.937 45.0 0.00 0.00 0.0 4.85 R
3093 6220 0.029300 CAAACTGCACACAACCGGAG 59.971 55.0 9.46 1.96 0.0 4.63 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 3.754976 TGGTATTCCAAGATTACCCCCT 58.245 45.455 11.31 0.00 41.25 4.79
25 26 3.462205 GGTATTCCAAGATTACCCCCTGT 59.538 47.826 4.92 0.00 34.40 4.00
26 27 3.953542 ATTCCAAGATTACCCCCTGTC 57.046 47.619 0.00 0.00 0.00 3.51
27 28 2.352561 TCCAAGATTACCCCCTGTCA 57.647 50.000 0.00 0.00 0.00 3.58
148 154 3.148279 CTAGTTCCGCCGCCCTCT 61.148 66.667 0.00 0.00 0.00 3.69
156 162 2.034221 GCCGCCCTCTCTTGGTTT 59.966 61.111 0.00 0.00 0.00 3.27
158 164 1.866853 GCCGCCCTCTCTTGGTTTTG 61.867 60.000 0.00 0.00 0.00 2.44
223 229 0.254462 TCACTGCGCCATTCCCATTA 59.746 50.000 4.18 0.00 0.00 1.90
234 240 3.323243 CATTCCCATTATCCGGTCGTAC 58.677 50.000 0.00 0.00 0.00 3.67
257 268 6.543735 ACTTTTCCATTCTTGTTAGCTACCT 58.456 36.000 0.00 0.00 0.00 3.08
678 3794 1.230635 ATGTGCACGCTGTCAAGTCC 61.231 55.000 13.13 0.00 0.00 3.85
1239 4358 1.152902 TTGTGCTGGTCTTGCAGCT 60.153 52.632 0.00 0.00 44.19 4.24
1329 4448 6.039270 TCTGCAATGCCCTAATTAACATGTAC 59.961 38.462 1.53 0.00 0.00 2.90
1445 4564 1.147824 ATCATGGCCTTGCGAGAGG 59.852 57.895 13.75 0.00 39.93 3.69
1644 4766 0.109412 GTTTGCTGTGCAGAGATGGC 60.109 55.000 16.28 0.00 40.61 4.40
1676 4798 5.559770 TGAGGCAGAACACTTCATATTGAA 58.440 37.500 0.00 0.00 34.79 2.69
1926 5048 4.827284 CCTGGTGTTAGTTGGATTCAAGTT 59.173 41.667 0.00 0.00 37.65 2.66
2061 5183 4.744631 CCAAATTTTGCAGTTGTCCTACAC 59.255 41.667 3.50 0.00 0.00 2.90
2254 5376 6.631962 AGAAGAAGAATAGTTGTAAGGGACG 58.368 40.000 0.00 0.00 0.00 4.79
2270 5392 0.872388 GACGCTGTCCGGTTTCATTT 59.128 50.000 0.00 0.00 42.52 2.32
2322 5444 3.269381 ACCATTGGTGATCCATACCTTGT 59.731 43.478 7.76 0.00 43.91 3.16
2385 5507 9.888878 CATCAACATGGTATGTCATCTAATTTC 57.111 33.333 0.00 0.00 44.07 2.17
2416 5538 4.755266 AGGTTATACTCTGTTTCCGCAT 57.245 40.909 0.00 0.00 0.00 4.73
2511 5633 6.552859 TCATATTCAATGTTGTGTTGTCGT 57.447 33.333 0.00 0.00 0.00 4.34
2512 5634 6.598525 TCATATTCAATGTTGTGTTGTCGTC 58.401 36.000 0.00 0.00 0.00 4.20
2529 5653 9.599866 TGTTGTCGTCTCTCATGATATAAATTT 57.400 29.630 0.00 0.00 0.00 1.82
2595 5719 2.598192 CGCTGAATTAAAATGTTGCCGG 59.402 45.455 0.00 0.00 0.00 6.13
2641 5765 5.016831 TCAGACAGTTAAGCCTAGTGATCA 58.983 41.667 0.00 0.00 0.00 2.92
2645 5769 6.663953 AGACAGTTAAGCCTAGTGATCAAGTA 59.336 38.462 0.00 0.00 0.00 2.24
2677 5801 4.860907 GCCATGCAAATCTAAAAGTCACTG 59.139 41.667 0.00 0.00 0.00 3.66
2708 5832 5.022021 GGCGATATTTTCTTCTTTGACACG 58.978 41.667 0.00 0.00 0.00 4.49
2788 5912 1.039785 AGCGCTGTAGCAGATCCAGA 61.040 55.000 10.39 0.00 42.21 3.86
2810 5934 1.747325 TTGGCAAAGCAGGGCAGAAC 61.747 55.000 0.00 0.00 42.10 3.01
2927 6054 1.474077 GCCAGTACAGAAGCCAAATGG 59.526 52.381 0.00 0.00 38.53 3.16
2988 6115 2.401568 TGCTGGATCCTCTTATCAGCA 58.598 47.619 14.23 14.56 37.52 4.41
3093 6220 7.224949 CCATTTATTCTTCTTTACTCTCCGGTC 59.775 40.741 0.00 0.00 0.00 4.79
3095 6222 5.585820 ATTCTTCTTTACTCTCCGGTCTC 57.414 43.478 0.00 0.00 0.00 3.36
3096 6223 3.354467 TCTTCTTTACTCTCCGGTCTCC 58.646 50.000 0.00 0.00 0.00 3.71
3295 6422 7.795534 AGGAAGATATGACTGATCTGCTATT 57.204 36.000 0.00 0.00 33.85 1.73
3310 6437 4.079844 TCTGCTATTCATGTTGGGAATCCA 60.080 41.667 0.09 0.00 42.25 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.461831 CAGGGGGTAATCTTGGAATACCA 59.538 47.826 12.15 0.00 39.21 3.25
3 4 3.462205 ACAGGGGGTAATCTTGGAATACC 59.538 47.826 3.85 3.85 37.36 2.73
4 5 4.165372 TGACAGGGGGTAATCTTGGAATAC 59.835 45.833 0.00 0.00 0.00 1.89
5 6 4.376223 TGACAGGGGGTAATCTTGGAATA 58.624 43.478 0.00 0.00 0.00 1.75
6 7 3.197983 TGACAGGGGGTAATCTTGGAAT 58.802 45.455 0.00 0.00 0.00 3.01
7 8 2.638325 TGACAGGGGGTAATCTTGGAA 58.362 47.619 0.00 0.00 0.00 3.53
9 10 2.620627 GGTTGACAGGGGGTAATCTTGG 60.621 54.545 0.00 0.00 0.00 3.61
10 11 2.308866 AGGTTGACAGGGGGTAATCTTG 59.691 50.000 0.00 0.00 0.00 3.02
11 12 2.644151 AGGTTGACAGGGGGTAATCTT 58.356 47.619 0.00 0.00 0.00 2.40
12 13 2.361085 AGGTTGACAGGGGGTAATCT 57.639 50.000 0.00 0.00 0.00 2.40
13 14 3.371273 GGTTAGGTTGACAGGGGGTAATC 60.371 52.174 0.00 0.00 0.00 1.75
14 15 2.579400 GGTTAGGTTGACAGGGGGTAAT 59.421 50.000 0.00 0.00 0.00 1.89
17 18 0.402272 TGGTTAGGTTGACAGGGGGT 60.402 55.000 0.00 0.00 0.00 4.95
18 19 0.774908 TTGGTTAGGTTGACAGGGGG 59.225 55.000 0.00 0.00 0.00 5.40
19 20 2.668144 TTTGGTTAGGTTGACAGGGG 57.332 50.000 0.00 0.00 0.00 4.79
115 121 0.897863 CTAGAGAGGGAGGATGGCCG 60.898 65.000 0.00 0.00 39.96 6.13
148 154 1.901464 GCGGGAGGCAAAACCAAGA 60.901 57.895 0.00 0.00 43.14 3.02
223 229 3.197116 AGAATGGAAAAGTACGACCGGAT 59.803 43.478 9.46 0.00 0.00 4.18
234 240 6.183360 CGAGGTAGCTAACAAGAATGGAAAAG 60.183 42.308 12.26 0.00 0.00 2.27
334 3449 4.778143 GGACAGATTGCCGGCGGT 62.778 66.667 28.82 13.23 0.00 5.68
498 3613 1.265454 ACATGAGGAGGTTCCCGGAC 61.265 60.000 0.73 0.00 37.19 4.79
662 3778 2.661537 CGGACTTGACAGCGTGCA 60.662 61.111 0.00 0.00 0.00 4.57
1239 4358 3.321396 TGAGTGCATTGCCATTTTTCAGA 59.679 39.130 6.12 0.00 0.00 3.27
1329 4448 2.063156 TTATGCTGCCACTTTTTGCG 57.937 45.000 0.00 0.00 0.00 4.85
1445 4564 7.389884 ACATATCATGAAATACAGACATGGCTC 59.610 37.037 0.00 0.00 40.86 4.70
1676 4798 5.414454 ACAACGTCTGTGCCAATATAATTGT 59.586 36.000 0.00 0.00 36.69 2.71
1926 5048 3.053991 TGAAAACTTGGACCTCACTTCCA 60.054 43.478 0.00 0.00 41.64 3.53
2061 5183 4.455533 TCCTTTTGTTCATCCTCAACATCG 59.544 41.667 0.00 0.00 33.76 3.84
2254 5376 6.315393 TCTTCTATAAAATGAAACCGGACAGC 59.685 38.462 9.46 0.00 0.00 4.40
2270 5392 7.496920 CACATGAGCAAACTCCATCTTCTATAA 59.503 37.037 0.00 0.00 42.74 0.98
2385 5507 6.793505 ACAGAGTATAACCTTTCCACTAGG 57.206 41.667 0.00 0.00 38.79 3.02
2416 5538 4.462834 TCAAAGCTATCGGAGTTCTCTCAA 59.537 41.667 0.00 0.00 42.05 3.02
2507 5629 7.360438 GGCCAAATTTATATCATGAGAGACGAC 60.360 40.741 0.09 0.00 0.00 4.34
2511 5633 6.183361 TGGGGCCAAATTTATATCATGAGAGA 60.183 38.462 4.39 0.00 0.00 3.10
2512 5634 6.012113 TGGGGCCAAATTTATATCATGAGAG 58.988 40.000 4.39 0.00 0.00 3.20
2529 5653 2.516702 TGATCTAGTAGTACTGGGGCCA 59.483 50.000 13.29 6.32 0.00 5.36
2575 5699 2.929398 CCCGGCAACATTTTAATTCAGC 59.071 45.455 0.00 0.00 0.00 4.26
2595 5719 6.644592 TGAAATTAAGTTTGCATGCAAGTACC 59.355 34.615 30.25 19.65 37.24 3.34
2641 5765 1.271934 TGCATGGCAATTGCGTTACTT 59.728 42.857 23.48 5.74 43.10 2.24
2677 5801 0.317020 GAAAATATCGCCGCTGGTGC 60.317 55.000 3.64 0.00 32.51 5.01
2708 5832 9.578439 CTATCCTGAATTCAAAAGGAAATCAAC 57.422 33.333 16.39 0.00 43.08 3.18
2788 5912 1.823169 CTGCCCTGCTTTGCCAACAT 61.823 55.000 0.00 0.00 0.00 2.71
2810 5934 2.186076 GTGTTAAGATCTGTCTCGCCG 58.814 52.381 0.00 0.00 32.15 6.46
2865 5992 1.547372 CCTTTGTTCTCAGCAATGGGG 59.453 52.381 0.00 0.00 37.44 4.96
2927 6054 0.521291 TTGCTGTGCCGTTATCTTGC 59.479 50.000 0.00 0.00 0.00 4.01
2937 6064 0.242017 GAGGATGTTGTTGCTGTGCC 59.758 55.000 0.00 0.00 0.00 5.01
3093 6220 0.029300 CAAACTGCACACAACCGGAG 59.971 55.000 9.46 1.96 0.00 4.63
3095 6222 1.588667 GCAAACTGCACACAACCGG 60.589 57.895 0.00 0.00 44.26 5.28
3096 6223 3.996073 GCAAACTGCACACAACCG 58.004 55.556 0.00 0.00 44.26 4.44
3162 6289 4.639755 CCATGGCAAACCTTCAAAAGTTTT 59.360 37.500 0.00 0.00 36.63 2.43
3230 6357 9.559958 AGCATAACTGAAAACTTTTGAATATCG 57.440 29.630 0.00 0.00 0.00 2.92
3281 6408 4.514441 CCCAACATGAATAGCAGATCAGTC 59.486 45.833 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.