Multiple sequence alignment - TraesCS3D01G164500

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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 TraesCS3D01G164500 chr3D 100.000 3412 0 0 1 3412 136043236 136039825 0 6301
1 TraesCS3D01G164500 chr3A 91.695 2962 132 36 3 2895 153079069 153076153 0 4002
2 TraesCS3D01G164500 chr3A 93.726 526 21 9 2893 3410 153076117 153075596 0 778
3 TraesCS3D01G164500 chr3B 92.248 1922 105 20 1 1884 194328409 194326494 0 2684
4 TraesCS3D01G164500 chr3B 95.017 1505 51 9 1916 3410 194326492 194325002 0 2342


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 TraesCS3D01G164500 chr3D 136039825 136043236 3411 True 6301 6301 100.0000 1 3412 1 chr3D.!!$R1 3411
1 TraesCS3D01G164500 chr3A 153075596 153079069 3473 True 2390 4002 92.7105 3 3410 2 chr3A.!!$R1 3407
2 TraesCS3D01G164500 chr3B 194325002 194328409 3407 True 2513 2684 93.6325 1 3410 2 chr3B.!!$R1 3409

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
423 443 1.280133 CTTGACAGCTCTCCCATCCAA 59.720 52.381 0.0 0.0 0.00 3.53 F
1129 1175 1.374758 CGAGTTCCGGCTTCTTGCT 60.375 57.895 0.0 0.0 42.39 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 1988 0.681564 AGAGCCGAGTCTACCTGTGG 60.682 60.0 0.0 0.0 0.0 4.17 R
3091 3219 0.321996 GAGCTCACGTCCCTTTCCTT 59.678 55.0 9.4 0.0 0.0 3.36 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
44 45 6.435430 TGAGCATGGTTTGTTATGTGTATC 57.565 37.500 0.00 0.00 0.00 2.24
63 64 6.035005 GTGTATCCGTATCATCAAATGATCGG 59.965 42.308 21.64 21.64 46.62 4.18
72 73 1.597195 TCAAATGATCGGCGTGTATGC 59.403 47.619 6.85 0.00 0.00 3.14
137 146 3.118531 ACATTTGAGGGGAGCTATCTGT 58.881 45.455 0.00 0.00 0.00 3.41
223 240 9.937175 GTTGGAAGAGAACAAGTATATATTTGC 57.063 33.333 15.70 3.48 0.00 3.68
247 264 6.498304 CACTCCAACATGCATAGGTAAATTC 58.502 40.000 0.00 0.00 0.00 2.17
259 279 8.980596 TGCATAGGTAAATTCCATTTTGAGAAT 58.019 29.630 0.00 0.00 34.18 2.40
338 358 2.684881 GCGAGGATCCATTTCACAACAT 59.315 45.455 15.82 0.00 0.00 2.71
386 406 5.734720 TCCAAGTACAACAAATTTTTGCCA 58.265 33.333 3.00 1.17 41.79 4.92
393 413 4.102996 ACAACAAATTTTTGCCAGGAGGAT 59.897 37.500 3.00 0.00 41.79 3.24
423 443 1.280133 CTTGACAGCTCTCCCATCCAA 59.720 52.381 0.00 0.00 0.00 3.53
432 454 6.547510 ACAGCTCTCCCATCCAATTATAAAAC 59.452 38.462 0.00 0.00 0.00 2.43
657 680 3.771577 ACCTTCTCCTCATTTGACGTT 57.228 42.857 0.00 0.00 0.00 3.99
1115 1161 2.288030 CCTTCAACAAGGTACGTCGAGT 60.288 50.000 0.00 0.00 44.11 4.18
1121 1167 2.202531 GGTACGTCGAGTTCCGGC 60.203 66.667 0.00 0.00 39.99 6.13
1129 1175 1.374758 CGAGTTCCGGCTTCTTGCT 60.375 57.895 0.00 0.00 42.39 3.91
1154 1200 5.694674 TTTCTTGTGAAATTTGTGCGTTC 57.305 34.783 0.00 0.00 37.27 3.95
1155 1201 4.630894 TCTTGTGAAATTTGTGCGTTCT 57.369 36.364 0.00 0.00 0.00 3.01
1256 1306 4.450053 GAGGAGATTGACAAGGAGATTGG 58.550 47.826 0.00 0.00 43.68 3.16
1285 1335 1.552792 AGACAGAACTAGAGCCCAAGC 59.447 52.381 0.00 0.00 40.32 4.01
1414 1474 7.840716 TGTAGGAAGTAGCCACCTTAATTAGTA 59.159 37.037 0.00 0.00 35.52 1.82
1443 1503 7.727578 TCATACTGTTATCTTGTTGTAGGGA 57.272 36.000 0.00 0.00 0.00 4.20
1485 1545 5.174395 ACATCCAAGATCAAGAAGAACTCG 58.826 41.667 0.00 0.00 0.00 4.18
1704 1772 7.781693 ACCTTCATTATCCTGCTTTCACATAAT 59.218 33.333 0.00 0.00 0.00 1.28
1848 1921 4.919168 CAGACAAAACCATAACATGTGCAG 59.081 41.667 0.00 0.00 0.00 4.41
1896 1969 9.573133 AACAGTAATTAATTAAGCAGCACAATC 57.427 29.630 9.48 0.00 0.00 2.67
1912 1985 4.370049 CACAATCTTTCATTGTTGCCACA 58.630 39.130 0.00 0.00 39.94 4.17
1913 1986 4.446385 CACAATCTTTCATTGTTGCCACAG 59.554 41.667 0.00 0.00 39.94 3.66
1914 1987 2.798976 TCTTTCATTGTTGCCACAGC 57.201 45.000 0.00 0.00 40.48 4.40
1915 1988 1.340889 TCTTTCATTGTTGCCACAGCC 59.659 47.619 0.00 0.00 38.69 4.85
1916 1989 0.392336 TTTCATTGTTGCCACAGCCC 59.608 50.000 0.00 0.00 38.69 5.19
1917 1990 0.758310 TTCATTGTTGCCACAGCCCA 60.758 50.000 0.00 0.00 38.69 5.36
1918 1991 1.005867 CATTGTTGCCACAGCCCAC 60.006 57.895 0.00 0.00 38.69 4.61
1924 1997 2.045926 GCCACAGCCCACAGGTAG 60.046 66.667 0.00 0.00 34.57 3.18
1929 2002 1.251527 ACAGCCCACAGGTAGACTCG 61.252 60.000 0.00 0.00 34.57 4.18
2078 2153 4.142038 GTTAATATGCAGATTTCCCCGGT 58.858 43.478 12.49 0.00 0.00 5.28
2262 2346 3.068691 TCGCCGTGGAGGAGAAGG 61.069 66.667 0.00 0.00 46.04 3.46
2448 2535 1.478654 GGAGTCCAAGAGCAACCCAAA 60.479 52.381 3.60 0.00 0.00 3.28
2900 3025 2.279517 GCATACGCCTCCGGTCAG 60.280 66.667 0.00 0.00 39.22 3.51
2916 3043 3.432252 CGGTCAGGTTTCACAAGATGTAC 59.568 47.826 0.00 0.00 0.00 2.90
2951 3078 1.207329 AGTCGGTAGGAAACTGATGGC 59.793 52.381 0.00 0.00 45.27 4.40
3020 3147 9.910912 ATGGAGATAGATAGCTTTGGGATATAT 57.089 33.333 0.00 0.00 0.00 0.86
3149 3277 4.803426 GACACGCCTCTCGCCCAG 62.803 72.222 0.00 0.00 43.23 4.45
3315 3455 3.447918 AGGAGACGTTTCAGTCGAAAA 57.552 42.857 8.50 0.00 42.66 2.29
3336 3476 3.721087 AAAAGGGGTTGATCGTGATCT 57.279 42.857 10.91 0.00 38.60 2.75
3347 3487 5.414789 TGATCGTGATCTTTTCTGGGTTA 57.585 39.130 10.91 0.00 38.60 2.85
3410 3550 1.032014 GGTGCCTTCTGCTTTTGTCA 58.968 50.000 0.00 0.00 42.00 3.58
3411 3551 1.000938 GGTGCCTTCTGCTTTTGTCAG 60.001 52.381 0.00 0.00 42.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.276658 TGATACGGATACACATAACAAACCAT 58.723 34.615 0.00 0.00 0.00 3.55
28 29 7.439955 TGATGATACGGATACACATAACAAACC 59.560 37.037 0.00 0.00 0.00 3.27
72 73 4.730042 CGAAATCTCAAATACATGCAACCG 59.270 41.667 0.00 0.00 0.00 4.44
137 146 2.168326 ATATGTTCGCGGATGCATCA 57.832 45.000 27.25 6.74 42.97 3.07
223 240 6.455360 AATTTACCTATGCATGTTGGAGTG 57.545 37.500 10.16 0.00 0.00 3.51
247 264 9.709495 TTCACCTCAAAAATATTCTCAAAATGG 57.291 29.630 0.00 0.00 0.00 3.16
359 379 7.065204 GGCAAAAATTTGTTGTACTTGGAGAAA 59.935 33.333 7.64 0.00 40.24 2.52
365 385 5.814705 TCCTGGCAAAAATTTGTTGTACTTG 59.185 36.000 7.64 4.37 40.24 3.16
368 388 4.749598 CCTCCTGGCAAAAATTTGTTGTAC 59.250 41.667 7.64 0.00 40.24 2.90
373 393 4.980339 AATCCTCCTGGCAAAAATTTGT 57.020 36.364 7.64 0.00 40.24 2.83
441 463 7.304735 CACAAATGATTTGAGACGGTTAATGA 58.695 34.615 23.37 0.00 43.26 2.57
442 464 6.033831 GCACAAATGATTTGAGACGGTTAATG 59.966 38.462 23.37 8.77 43.26 1.90
481 503 6.537301 TGCTATGACTTTGGTAATCGGTTAAG 59.463 38.462 0.00 0.00 0.00 1.85
888 925 1.836802 AGCAAGGGAAGCTAGAAGGAG 59.163 52.381 0.00 0.00 41.32 3.69
1029 1075 0.909610 AGATCTTGTTGAGCCCGGGA 60.910 55.000 29.31 0.00 0.00 5.14
1154 1200 9.865321 ACATCATCTACCATTTCAAAATTTCAG 57.135 29.630 0.00 0.00 0.00 3.02
1184 1234 9.429359 ACAATCAAGAAACAAACAAAACACATA 57.571 25.926 0.00 0.00 0.00 2.29
1199 1249 1.336440 CACGCCCACACAATCAAGAAA 59.664 47.619 0.00 0.00 0.00 2.52
1202 1252 1.081242 GCACGCCCACACAATCAAG 60.081 57.895 0.00 0.00 0.00 3.02
1256 1306 4.619628 GCTCTAGTTCTGTCTTCTTGTCCC 60.620 50.000 0.00 0.00 0.00 4.46
1285 1335 6.922957 GGAGATGCTTCAATAGTCTCTACAAG 59.077 42.308 2.07 0.00 36.45 3.16
1290 1340 4.588528 GGAGGAGATGCTTCAATAGTCTCT 59.411 45.833 2.07 0.00 36.45 3.10
1296 1346 5.698741 TTTCTGGAGGAGATGCTTCAATA 57.301 39.130 2.07 0.00 0.00 1.90
1387 1439 6.382919 AATTAAGGTGGCTACTTCCTACAA 57.617 37.500 0.00 0.00 0.00 2.41
1388 1440 6.670902 ACTAATTAAGGTGGCTACTTCCTACA 59.329 38.462 0.00 0.00 0.00 2.74
1485 1545 1.652563 GAACTTGGTGACGGCAACC 59.347 57.895 2.41 2.89 0.00 3.77
1888 1961 3.656559 GGCAACAATGAAAGATTGTGCT 58.343 40.909 15.23 0.00 40.94 4.40
1912 1985 1.682684 CCGAGTCTACCTGTGGGCT 60.683 63.158 0.00 0.00 35.63 5.19
1913 1986 2.893398 CCGAGTCTACCTGTGGGC 59.107 66.667 0.00 0.00 35.63 5.36
1914 1987 1.668101 GAGCCGAGTCTACCTGTGGG 61.668 65.000 0.00 0.00 38.88 4.61
1915 1988 0.681564 AGAGCCGAGTCTACCTGTGG 60.682 60.000 0.00 0.00 0.00 4.17
1916 1989 0.736053 GAGAGCCGAGTCTACCTGTG 59.264 60.000 0.00 0.00 0.00 3.66
1917 1990 0.745128 CGAGAGCCGAGTCTACCTGT 60.745 60.000 0.00 0.00 41.76 4.00
1918 1991 1.440938 CCGAGAGCCGAGTCTACCTG 61.441 65.000 0.00 0.00 41.76 4.00
1924 1997 2.194212 TATGCCCGAGAGCCGAGTC 61.194 63.158 0.00 0.00 41.76 3.36
2078 2153 3.939939 TCGCTCACCAGCTTGGCA 61.940 61.111 2.50 0.00 44.40 4.92
2324 2411 1.260538 CCTCCACTACCTCAGCAGCA 61.261 60.000 0.00 0.00 0.00 4.41
2512 2599 1.581954 CTTGACACGGAGAGCGACT 59.418 57.895 0.00 0.00 0.00 4.18
2562 2649 2.035421 CATGGCAAGTGCAGTGTGT 58.965 52.632 5.52 0.00 44.36 3.72
2563 2650 1.372499 GCATGGCAAGTGCAGTGTG 60.372 57.895 8.15 0.00 44.36 3.82
2900 3025 6.314784 GTGCTTATGTACATCTTGTGAAACC 58.685 40.000 12.68 0.00 34.36 3.27
2916 3043 1.560923 CGACTTCCCTCGTGCTTATG 58.439 55.000 0.00 0.00 0.00 1.90
3091 3219 0.321996 GAGCTCACGTCCCTTTCCTT 59.678 55.000 9.40 0.00 0.00 3.36
3092 3220 0.832135 TGAGCTCACGTCCCTTTCCT 60.832 55.000 13.74 0.00 0.00 3.36
3143 3271 4.172512 ATCTCAGGCTGCTGGGCG 62.173 66.667 10.34 0.00 45.89 6.13
3146 3274 1.067749 CGAGATCTCAGGCTGCTGG 59.932 63.158 22.31 2.61 0.00 4.85
3149 3277 0.961019 AGATCGAGATCTCAGGCTGC 59.039 55.000 22.31 5.40 44.37 5.25
3315 3455 4.034285 AGATCACGATCAACCCCTTTTT 57.966 40.909 9.60 0.00 40.22 1.94
3336 3476 3.564053 ACGGAACACTAACCCAGAAAA 57.436 42.857 0.00 0.00 0.00 2.29
3347 3487 0.031721 GACGGACAGAACGGAACACT 59.968 55.000 0.00 0.00 35.23 3.55


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

AutoCloner maintained by Alex Coulton.