Multiple sequence alignment - TraesCS1A01G267500

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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 TraesCS1A01G267500 chr1A 100.000 2736 0 0 1 2736 462533264 462530529 0 5053
1 TraesCS1A01G267500 chr1A 95.210 2046 85 9 1 2036 547459992 547457950 0 3223
2 TraesCS1A01G267500 chr1A 95.059 2044 84 12 1 2036 531496244 531498278 0 3199
3 TraesCS1A01G267500 chr1A 94.580 2048 88 12 1 2036 38376105 38374069 0 3145
4 TraesCS1A01G267500 chr1A 95.983 722 26 2 2016 2736 531498289 531499008 0 1170
5 TraesCS1A01G267500 chr2A 92.847 2754 135 40 1 2736 613870164 613867455 0 3938
6 TraesCS1A01G267500 chr2A 95.983 722 27 2 2016 2736 374683090 374682370 0 1171
7 TraesCS1A01G267500 chr3B 91.367 2780 167 32 1 2736 440315075 440312325 0 3736
8 TraesCS1A01G267500 chr3B 96.100 718 24 3 2022 2736 661409512 661408796 0 1168
9 TraesCS1A01G267500 chr7A 95.426 2055 71 10 1 2036 689992589 689994639 0 3253
10 TraesCS1A01G267500 chr2D 95.091 2037 73 13 11 2036 435216323 435214303 0 3182
11 TraesCS1A01G267500 chr2D 94.020 2057 86 20 1 2036 16069227 16067187 0 3083
12 TraesCS1A01G267500 chr2D 93.771 2055 93 18 4 2036 636785165 636787206 0 3053
13 TraesCS1A01G267500 chr1B 93.191 2056 103 22 1 2036 402026301 402024263 0 2987
14 TraesCS1A01G267500 chr6A 96.379 718 22 3 2022 2736 57902857 57902141 0 1179
15 TraesCS1A01G267500 chr6A 96.133 724 25 2 2016 2736 617221149 617221872 0 1179
16 TraesCS1A01G267500 chr3A 95.989 723 26 3 2016 2736 617402741 617402020 0 1171
17 TraesCS1A01G267500 chr4B 95.851 723 28 1 2016 2736 407107111 407107833 0 1168
18 TraesCS1A01G267500 chrUn 95.845 722 28 2 2016 2736 353552094 353552814 0 1166


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 TraesCS1A01G267500 chr1A 462530529 462533264 2735 True 5053.0 5053 100.000 1 2736 1 chr1A.!!$R2 2735
1 TraesCS1A01G267500 chr1A 547457950 547459992 2042 True 3223.0 3223 95.210 1 2036 1 chr1A.!!$R3 2035
2 TraesCS1A01G267500 chr1A 38374069 38376105 2036 True 3145.0 3145 94.580 1 2036 1 chr1A.!!$R1 2035
3 TraesCS1A01G267500 chr1A 531496244 531499008 2764 False 2184.5 3199 95.521 1 2736 2 chr1A.!!$F1 2735
4 TraesCS1A01G267500 chr2A 613867455 613870164 2709 True 3938.0 3938 92.847 1 2736 1 chr2A.!!$R2 2735
5 TraesCS1A01G267500 chr2A 374682370 374683090 720 True 1171.0 1171 95.983 2016 2736 1 chr2A.!!$R1 720
6 TraesCS1A01G267500 chr3B 440312325 440315075 2750 True 3736.0 3736 91.367 1 2736 1 chr3B.!!$R1 2735
7 TraesCS1A01G267500 chr3B 661408796 661409512 716 True 1168.0 1168 96.100 2022 2736 1 chr3B.!!$R2 714
8 TraesCS1A01G267500 chr7A 689992589 689994639 2050 False 3253.0 3253 95.426 1 2036 1 chr7A.!!$F1 2035
9 TraesCS1A01G267500 chr2D 435214303 435216323 2020 True 3182.0 3182 95.091 11 2036 1 chr2D.!!$R2 2025
10 TraesCS1A01G267500 chr2D 16067187 16069227 2040 True 3083.0 3083 94.020 1 2036 1 chr2D.!!$R1 2035
11 TraesCS1A01G267500 chr2D 636785165 636787206 2041 False 3053.0 3053 93.771 4 2036 1 chr2D.!!$F1 2032
12 TraesCS1A01G267500 chr1B 402024263 402026301 2038 True 2987.0 2987 93.191 1 2036 1 chr1B.!!$R1 2035
13 TraesCS1A01G267500 chr6A 57902141 57902857 716 True 1179.0 1179 96.379 2022 2736 1 chr6A.!!$R1 714
14 TraesCS1A01G267500 chr6A 617221149 617221872 723 False 1179.0 1179 96.133 2016 2736 1 chr6A.!!$F1 720
15 TraesCS1A01G267500 chr3A 617402020 617402741 721 True 1171.0 1171 95.989 2016 2736 1 chr3A.!!$R1 720
16 TraesCS1A01G267500 chr4B 407107111 407107833 722 False 1168.0 1168 95.851 2016 2736 1 chr4B.!!$F1 720
17 TraesCS1A01G267500 chrUn 353552094 353552814 720 False 1166.0 1166 95.845 2016 2736 1 chrUn.!!$F1 720

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
611 624 1.066430 GTTGGGCCGTCTCATTGTCTA 60.066 52.381 0.00 0.0 0.00 2.59 F
1131 1202 1.597302 CATGCCAGAGCTGCGCTAT 60.597 57.895 9.73 0.0 39.88 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1685 0.101579 ACATGACACGACACGACACA 59.898 50.0 0.0 0.0 0.0 3.72 R
2101 2237 0.594110 CGCGGGTTTGTGGTGTTTAT 59.406 50.0 0.0 0.0 0.0 1.40 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
61 65 9.918630 CTCATTTGAATTCTGGTCAAACTTAAT 57.081 29.630 7.05 0.00 45.19 1.40
205 210 8.397906 CAAAACACTTCTCTTCACTTCATACAA 58.602 33.333 0.00 0.00 0.00 2.41
206 211 7.721286 AACACTTCTCTTCACTTCATACAAG 57.279 36.000 0.00 0.00 0.00 3.16
494 503 3.003171 GGTCGTCGATCTAACCCTTCTAC 59.997 52.174 0.00 0.00 0.00 2.59
604 617 3.998672 GACCGTTGGGCCGTCTCA 61.999 66.667 0.00 0.00 36.48 3.27
611 624 1.066430 GTTGGGCCGTCTCATTGTCTA 60.066 52.381 0.00 0.00 0.00 2.59
677 691 4.260609 ATGCATGGAGGCGGCGAT 62.261 61.111 12.98 0.00 36.28 4.58
831 886 5.118990 GGTCAAAGAGCTATGCAGTGATTA 58.881 41.667 0.00 0.00 0.00 1.75
881 938 5.388288 CGTTTTCGTGCAAAAATTTAAGTGC 59.612 36.000 12.26 12.26 35.68 4.40
1009 1066 1.852157 TCTCCCACCCACAAGCCAT 60.852 57.895 0.00 0.00 0.00 4.40
1110 1181 4.324991 ACCTTCAACCGTCCGCCC 62.325 66.667 0.00 0.00 0.00 6.13
1131 1202 1.597302 CATGCCAGAGCTGCGCTAT 60.597 57.895 9.73 0.00 39.88 2.97
1203 1274 1.670015 GAGGGGTTCCGTCGAACTT 59.330 57.895 0.00 0.00 46.46 2.66
1212 1283 3.539107 GTCGAACTTACCCGCGCG 61.539 66.667 25.67 25.67 0.00 6.86
1305 1376 1.789523 GTGGTGGCATCCTCCTACTA 58.210 55.000 0.00 0.00 37.97 1.82
1323 1394 1.611977 CTACTCACGGTCACCTTCACA 59.388 52.381 0.00 0.00 0.00 3.58
1416 1487 6.405508 CCGTCTACAACATCTACACCAACTAT 60.406 42.308 0.00 0.00 0.00 2.12
1766 1866 7.391554 TCATTTCTTCCCTAAACAAGTCATGAG 59.608 37.037 0.00 0.00 0.00 2.90
2030 2166 2.020720 TGTGCAAACATTCACGGTCTT 58.979 42.857 0.00 0.00 36.06 3.01
2101 2237 2.666862 CGGTTACCAGCGCAACCA 60.667 61.111 22.63 0.00 43.70 3.67
2118 2254 1.957877 ACCATAAACACCACAAACCCG 59.042 47.619 0.00 0.00 0.00 5.28
2218 2355 6.222389 TGTTTTTCTCAATGTAATGCCCTTG 58.778 36.000 0.00 0.00 0.00 3.61
2226 2363 6.171921 TCAATGTAATGCCCTTGAAAAATGG 58.828 36.000 0.00 0.00 0.00 3.16
2296 2433 7.377398 CACATTTTCCATGACATTTTGGTCTA 58.623 34.615 0.00 0.00 38.61 2.59
2326 2463 2.623535 TCACGGTGTATTCGAATTGGG 58.376 47.619 17.19 3.20 0.00 4.12
2376 2532 2.017049 CCTAATTGTTTGGCTCCGGAG 58.983 52.381 27.83 27.83 0.00 4.63
2497 2653 2.378038 GGCCTAATTGGATGCAGTTGA 58.622 47.619 5.19 0.00 38.35 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 210 8.154203 TGATATCTCGAGTATCTCAAACTCTCT 58.846 37.037 23.45 0.00 41.02 3.10
206 211 8.317891 TGATATCTCGAGTATCTCAAACTCTC 57.682 38.462 23.45 7.03 41.02 3.20
363 372 3.391965 TGTTTGACCAGATTGCAAATGC 58.608 40.909 1.71 0.00 42.50 3.56
370 379 6.258230 TCAAAGCTATGTTTGACCAGATTG 57.742 37.500 0.00 0.00 40.68 2.67
494 503 1.689273 CTCCTCCCCGTAGATTCCTTG 59.311 57.143 0.00 0.00 0.00 3.61
526 535 3.562973 CAGCCAATTAGATTGCATCTCGT 59.437 43.478 2.47 0.00 40.76 4.18
604 617 1.115467 CGGTCTCAGGCCTAGACAAT 58.885 55.000 28.48 0.00 44.25 2.71
611 624 1.192146 TTTACTGCGGTCTCAGGCCT 61.192 55.000 0.00 0.00 38.36 5.19
677 691 4.340019 CGCGCATGCAAACCCACA 62.340 61.111 19.57 0.00 42.97 4.17
747 799 4.577246 CACCTAGCTCGCCTCGCC 62.577 72.222 0.00 0.00 0.00 5.54
1009 1066 3.910989 TGAAGTTGGAGAGGATCGGATA 58.089 45.455 0.00 0.00 42.67 2.59
1050 1116 1.535444 TTGGTCTCGCTTGGGGAGA 60.535 57.895 9.66 9.66 46.65 3.71
1110 1181 3.561213 CGCAGCTCTGGCATGACG 61.561 66.667 0.00 0.00 41.70 4.35
1203 1274 4.124351 CTGAGGAACGCGCGGGTA 62.124 66.667 35.22 12.41 0.00 3.69
1212 1283 0.249657 CATAGCCGGCTCTGAGGAAC 60.250 60.000 36.73 0.00 0.00 3.62
1287 1358 1.291033 AGTAGTAGGAGGATGCCACCA 59.709 52.381 2.82 0.00 36.71 4.17
1290 1361 2.667470 GTGAGTAGTAGGAGGATGCCA 58.333 52.381 0.00 0.00 0.00 4.92
1305 1376 0.828022 TTGTGAAGGTGACCGTGAGT 59.172 50.000 0.00 0.00 0.00 3.41
1343 1414 1.768684 AAAGACTTGGCCGAGGAGCA 61.769 55.000 24.40 0.00 0.00 4.26
1416 1487 4.838152 GCGGGGAAGATGCGCTCA 62.838 66.667 9.73 0.00 0.00 4.26
1606 1685 0.101579 ACATGACACGACACGACACA 59.898 50.000 0.00 0.00 0.00 3.72
1766 1866 3.375922 TGAAAACCACAAGTTCTCGAACC 59.624 43.478 6.20 0.00 42.06 3.62
2030 2166 7.473593 GGTAGGGAAGGAAGGTATACATAGTA 58.526 42.308 5.01 0.00 0.00 1.82
2098 2234 1.957877 CGGGTTTGTGGTGTTTATGGT 59.042 47.619 0.00 0.00 0.00 3.55
2101 2237 0.594110 CGCGGGTTTGTGGTGTTTAT 59.406 50.000 0.00 0.00 0.00 1.40
2218 2355 7.174772 AGGTGCCAAAATAAATGACCATTTTTC 59.825 33.333 12.51 0.00 40.99 2.29
2226 2363 3.261580 GCCAGGTGCCAAAATAAATGAC 58.738 45.455 0.00 0.00 0.00 3.06
2296 2433 7.780008 TCGAATACACCGTGATTTAAATCAT 57.220 32.000 28.66 17.29 46.17 2.45
2318 2455 6.616947 TGAAGCTGTTAATTAACCCAATTCG 58.383 36.000 22.47 6.37 37.93 3.34
2376 2532 9.476202 ACTTTTTGTGGAAGCTAATTGAATTAC 57.524 29.630 0.00 0.00 0.00 1.89
2439 2595 8.280497 TCTCTTGCGTATTTTTCTGTTTTCTAC 58.720 33.333 0.00 0.00 0.00 2.59
2497 2653 1.486726 GTGCAGGCTAGACTAATGGGT 59.513 52.381 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.