Multiple sequence alignment - TraesCS3D01G134600

Loading Multiple Alignment...

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 TraesCS3D01G134600 chr3D 100.000 2372 0 0 1 2372 93481723 93484094 0.000000e+00 4381
1 TraesCS3D01G134600 chr3B 92.955 1533 78 19 1 1510 142722148 142720623 0.000000e+00 2206
2 TraesCS3D01G134600 chr3B 95.074 873 24 10 1508 2372 142720509 142719648 0.000000e+00 1356
3 TraesCS3D01G134600 chr3B 88.889 126 14 0 1141 1266 142721018 142720893 3.160000e-34 156
4 TraesCS3D01G134600 chr3B 98.387 62 1 0 256 317 142721806 142721745 2.490000e-20 110
5 TraesCS3D01G134600 chr3A 95.515 1271 49 5 1 1266 546572147 546570880 0.000000e+00 2025
6 TraesCS3D01G134600 chr3A 92.251 942 42 16 1441 2372 546570583 546569663 0.000000e+00 1306
7 TraesCS3D01G134600 chr3A 91.892 333 22 3 1112 1443 546571004 546570676 5.970000e-126 460


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 TraesCS3D01G134600 chr3D 93481723 93484094 2371 False 4381.000000 4381 100.000000 1 2372 1 chr3D.!!$F1 2371
1 TraesCS3D01G134600 chr3B 142719648 142722148 2500 True 957.000000 2206 93.826250 1 2372 4 chr3B.!!$R1 2371
2 TraesCS3D01G134600 chr3A 546569663 546572147 2484 True 1263.666667 2025 93.219333 1 2372 3 chr3A.!!$R1 2371

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
876 902 0.257328 TGCAGTTCCACTGGGTGAAA 59.743 50.0 6.05 0.0 46.01 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2260 0.668535 AAGCTGGCGACTGGAAAAAC 59.331 50.0 0.0 0.0 0.0 2.43 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
341 345 0.458543 TCAGAGAAGCGCGGTTGATC 60.459 55.000 30.19 23.88 0.00 2.92
342 346 0.737367 CAGAGAAGCGCGGTTGATCA 60.737 55.000 30.19 0.00 0.00 2.92
349 353 3.186047 GCGGTTGATCACGACGGG 61.186 66.667 9.68 0.00 33.25 5.28
357 361 1.379443 ATCACGACGGGCTGGACTA 60.379 57.895 0.00 0.00 0.00 2.59
369 373 1.162698 CTGGACTACTCCGACGTGAA 58.837 55.000 0.00 0.00 39.88 3.18
518 525 1.915141 CAGATGAACCCATATGGCCC 58.085 55.000 16.97 7.67 38.11 5.80
524 531 5.738108 AGATGAACCCATATGGCCCTATATT 59.262 40.000 16.97 1.40 37.83 1.28
598 606 2.489938 TGTTTCCCCTCCATCTTTCG 57.510 50.000 0.00 0.00 0.00 3.46
815 841 6.575162 ACATGTTTGGAGAGTTTCATAACC 57.425 37.500 0.00 0.00 34.71 2.85
860 886 1.841302 GACCCTCACCAGGTGATGCA 61.841 60.000 23.21 0.13 41.94 3.96
861 887 1.077930 CCCTCACCAGGTGATGCAG 60.078 63.158 23.21 10.97 41.94 4.41
876 902 0.257328 TGCAGTTCCACTGGGTGAAA 59.743 50.000 6.05 0.00 46.01 2.69
877 903 0.954452 GCAGTTCCACTGGGTGAAAG 59.046 55.000 6.05 0.00 46.01 2.62
880 906 1.215423 AGTTCCACTGGGTGAAAGCTT 59.785 47.619 0.00 0.00 35.23 3.74
987 1014 0.811616 GGCTCAGGCTACGACCATTG 60.812 60.000 0.00 0.00 38.73 2.82
1005 1032 1.980772 GGCAGCTGGGCTCATGTTT 60.981 57.895 17.12 0.00 36.40 2.83
1041 1068 0.991146 TCATTGGGCTCCTGCTGTTA 59.009 50.000 0.00 0.00 39.59 2.41
1110 1137 2.115910 CCCTTGGCAGGTGAAGCA 59.884 61.111 0.00 0.00 38.79 3.91
1128 1155 2.123683 CTCCTCCTAGGGCTGCGA 60.124 66.667 9.46 0.00 35.59 5.10
1193 1220 0.613260 TTCATAGGGCTGCGACTGTT 59.387 50.000 5.84 0.00 0.00 3.16
1254 1311 3.114616 CTTGGGCTGCGACTGTCG 61.115 66.667 24.78 24.78 43.89 4.35
1514 1782 9.461312 TTCAGCAGGTTAGTAAAATGTATGAAT 57.539 29.630 10.77 0.00 0.00 2.57
1643 1911 5.444663 AAGAGGCTTTAGTTTGCAAGAAG 57.555 39.130 0.00 4.61 0.00 2.85
1670 1938 9.593134 AAAGAATGACAGTACTATGATCAGAAC 57.407 33.333 0.09 0.00 0.00 3.01
1674 1942 7.703058 TGACAGTACTATGATCAGAACTCAA 57.297 36.000 0.09 0.00 0.00 3.02
1719 1987 4.166725 AGGGAATCATGCCACAGAATAAGA 59.833 41.667 0.00 0.00 40.09 2.10
1731 1999 4.452455 CACAGAATAAGAAGAAACGGTGCT 59.548 41.667 0.00 0.00 0.00 4.40
1843 2114 1.275573 GGAGTAACTCTTTCCACGCCT 59.724 52.381 0.00 0.00 0.00 5.52
1844 2115 2.338500 GAGTAACTCTTTCCACGCCTG 58.662 52.381 0.00 0.00 0.00 4.85
1859 2130 2.425312 ACGCCTGTGTTTTCATCAACAA 59.575 40.909 0.00 0.00 38.40 2.83
1880 2151 8.506437 CAACAAAACTAAAGTCAGATATGCTCA 58.494 33.333 0.00 0.00 0.00 4.26
1881 2152 8.034058 ACAAAACTAAAGTCAGATATGCTCAC 57.966 34.615 0.00 0.00 0.00 3.51
1882 2153 7.880195 ACAAAACTAAAGTCAGATATGCTCACT 59.120 33.333 0.00 0.00 0.00 3.41
1884 2155 9.944376 AAAACTAAAGTCAGATATGCTCACTTA 57.056 29.630 0.00 0.00 0.00 2.24
1887 2158 8.700051 ACTAAAGTCAGATATGCTCACTTATGT 58.300 33.333 0.00 0.00 0.00 2.29
1888 2159 7.783090 AAAGTCAGATATGCTCACTTATGTG 57.217 36.000 2.36 2.36 45.07 3.21
1906 2177 8.827677 ACTTATGTGTAGAACAGAAAAGACAAC 58.172 33.333 0.00 0.00 43.64 3.32
1943 2215 2.567615 GAGGTTCTTAGGGCTGTTCTGA 59.432 50.000 0.00 0.00 0.00 3.27
1988 2260 1.204704 TCTCCACAACGATAGCACCTG 59.795 52.381 0.00 0.00 42.67 4.00
2015 2287 2.669569 TCGCCAGCTTTGCAGTCC 60.670 61.111 5.87 0.00 0.00 3.85
2054 2326 0.948678 TCCCACAGTTAAAGCAACGC 59.051 50.000 0.00 0.00 42.35 4.84
2159 2431 2.404215 CCACGCGGAACCTATAATGAG 58.596 52.381 12.47 0.00 0.00 2.90
2193 2465 3.745975 GGAAGGGCAAATAACAAAAGCAC 59.254 43.478 0.00 0.00 0.00 4.40
2197 2469 5.189180 AGGGCAAATAACAAAAGCACAAAA 58.811 33.333 0.00 0.00 0.00 2.44
2354 2630 9.566432 AACTCCTGCAATAAGATTTATAGAAGG 57.434 33.333 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 4.492160 TACTTCCTCAGCGCCGCG 62.492 66.667 8.83 8.83 0.00 6.46
341 345 2.181021 GTAGTCCAGCCCGTCGTG 59.819 66.667 0.00 0.00 0.00 4.35
342 346 2.035312 AGTAGTCCAGCCCGTCGT 59.965 61.111 0.00 0.00 0.00 4.34
349 353 1.136984 CACGTCGGAGTAGTCCAGC 59.863 63.158 16.94 7.29 44.18 4.85
357 361 2.143594 GAGGCTGTTCACGTCGGAGT 62.144 60.000 0.00 0.00 0.00 3.85
369 373 2.371841 TCTGTAACCATGTTGAGGCTGT 59.628 45.455 0.00 0.00 0.00 4.40
432 436 3.624861 GTCTGTGAAATCATCATCGGCTT 59.375 43.478 0.00 0.00 40.97 4.35
442 449 2.470983 TGGATGCGTCTGTGAAATCA 57.529 45.000 5.77 0.00 0.00 2.57
598 606 7.481798 CGAAAATGCTTGTAGTATTTGTCCTTC 59.518 37.037 3.99 0.00 39.13 3.46
815 841 6.442952 AGAGATCGATCAAATTCTTCCTACG 58.557 40.000 26.47 0.00 0.00 3.51
833 859 1.028905 CTGGTGAGGGTCGAGAGATC 58.971 60.000 0.00 0.00 45.19 2.75
861 887 1.338020 CAAGCTTTCACCCAGTGGAAC 59.662 52.381 11.95 0.00 33.87 3.62
944 971 2.746277 ACGGCGAAGACAATGGCC 60.746 61.111 16.62 0.00 42.14 5.36
973 1000 1.221840 CTGCCAATGGTCGTAGCCT 59.778 57.895 0.00 0.00 0.00 4.58
987 1014 1.538687 AAAACATGAGCCCAGCTGCC 61.539 55.000 8.66 0.77 39.88 4.85
1110 1137 2.443016 CGCAGCCCTAGGAGGAGT 60.443 66.667 11.48 0.00 37.67 3.85
1128 1155 4.640690 AGGAGCCCCCGTGACAGT 62.641 66.667 0.00 0.00 40.87 3.55
1209 1266 2.262915 CGTGACAGTCTCAGCCCC 59.737 66.667 1.31 0.00 0.00 5.80
1216 1273 2.997897 GAGCCCCCGTGACAGTCT 60.998 66.667 1.31 0.00 0.00 3.24
1254 1311 2.279784 CGATCAAGGAGCCCTCGC 60.280 66.667 0.00 0.00 30.89 5.03
1373 1430 7.316640 TGCTTTTAAACATACTTGTGTTGTGT 58.683 30.769 0.00 0.00 41.22 3.72
1514 1782 2.685106 TTCTGTGGGCATGGGTTTAA 57.315 45.000 0.00 0.00 0.00 1.52
1521 1789 0.666913 GCTGCTATTCTGTGGGCATG 59.333 55.000 0.00 0.00 34.12 4.06
1643 1911 9.809096 TTCTGATCATAGTACTGTCATTCTTTC 57.191 33.333 5.39 0.00 0.00 2.62
1670 1938 6.984474 TGTTCTGGTAGTCTGTTTAGTTTGAG 59.016 38.462 0.00 0.00 0.00 3.02
1674 1942 6.289064 CCTTGTTCTGGTAGTCTGTTTAGTT 58.711 40.000 0.00 0.00 0.00 2.24
1719 1987 5.004922 TGAAAATTTGAGCACCGTTTCTT 57.995 34.783 0.00 0.00 0.00 2.52
1843 2114 9.134734 GACTTTAGTTTTGTTGATGAAAACACA 57.865 29.630 0.00 0.00 43.03 3.72
1844 2115 9.134734 TGACTTTAGTTTTGTTGATGAAAACAC 57.865 29.630 0.00 0.00 43.03 3.32
1880 2151 8.827677 GTTGTCTTTTCTGTTCTACACATAAGT 58.172 33.333 0.00 0.00 33.76 2.24
1881 2152 8.283291 GGTTGTCTTTTCTGTTCTACACATAAG 58.717 37.037 0.00 0.00 33.76 1.73
1882 2153 7.227910 GGGTTGTCTTTTCTGTTCTACACATAA 59.772 37.037 0.00 0.00 33.76 1.90
1884 2155 5.531287 GGGTTGTCTTTTCTGTTCTACACAT 59.469 40.000 0.00 0.00 33.76 3.21
1885 2156 4.879545 GGGTTGTCTTTTCTGTTCTACACA 59.120 41.667 0.00 0.00 0.00 3.72
1887 2158 4.124238 CGGGTTGTCTTTTCTGTTCTACA 58.876 43.478 0.00 0.00 0.00 2.74
1888 2159 3.059120 GCGGGTTGTCTTTTCTGTTCTAC 60.059 47.826 0.00 0.00 0.00 2.59
1943 2215 2.311542 TGGCCACATAGAAAGGGATTGT 59.688 45.455 0.00 0.00 0.00 2.71
1988 2260 0.668535 AAGCTGGCGACTGGAAAAAC 59.331 50.000 0.00 0.00 0.00 2.43
2054 2326 1.229658 ACCTCCTCCTGGTTCTGGG 60.230 63.158 0.00 0.00 33.34 4.45
2109 2381 3.569049 GAGGTGACCGTGACCGTGG 62.569 68.421 1.10 0.00 38.64 4.94
2110 2382 2.049433 GAGGTGACCGTGACCGTG 60.049 66.667 1.10 0.00 38.64 4.94
2111 2383 3.300765 GGAGGTGACCGTGACCGT 61.301 66.667 1.10 0.00 38.64 4.83
2159 2431 8.523658 GTTATTTGCCCTTCCTTATTATGATCC 58.476 37.037 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.