Multiple sequence alignment - TraesCS3B01G454600

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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 TraesCS3B01G454600 chr3B 100.000 3485 0 0 1 3485 696327536 696331020 0.000000e+00 6436
1 TraesCS3B01G454600 chr3A 94.936 3495 153 14 2 3485 661472694 661476175 0.000000e+00 5452
2 TraesCS3B01G454600 chr3D 94.073 3003 124 13 2 2975 526973932 526976909 0.000000e+00 4510
3 TraesCS3B01G454600 chr3D 94.360 461 17 7 3032 3485 526976906 526977364 0.000000e+00 699
4 TraesCS3B01G454600 chr7D 90.458 1048 97 1 964 2011 496314147 496315191 0.000000e+00 1378
5 TraesCS3B01G454600 chr7B 96.094 128 5 0 475 602 312023750 312023623 3.520000e-50 209
6 TraesCS3B01G454600 chr7B 95.312 128 6 0 475 602 311927075 311926948 1.640000e-48 204
7 TraesCS3B01G454600 chr2D 92.381 105 6 2 3382 3485 317593006 317593109 7.790000e-32 148
8 TraesCS3B01G454600 chr2B 90.476 105 8 2 3382 3485 385199438 385199541 1.690000e-28 137
9 TraesCS3B01G454600 chr2A 90.566 106 7 3 3382 3485 416919562 416919458 1.690000e-28 137


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 TraesCS3B01G454600 chr3B 696327536 696331020 3484 False 6436.0 6436 100.0000 1 3485 1 chr3B.!!$F1 3484
1 TraesCS3B01G454600 chr3A 661472694 661476175 3481 False 5452.0 5452 94.9360 2 3485 1 chr3A.!!$F1 3483
2 TraesCS3B01G454600 chr3D 526973932 526977364 3432 False 2604.5 4510 94.2165 2 3485 2 chr3D.!!$F1 3483
3 TraesCS3B01G454600 chr7D 496314147 496315191 1044 False 1378.0 1378 90.4580 964 2011 1 chr7D.!!$F1 1047

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
45 46 0.398318 GGTTCAGCACCTTCACCTCT 59.602 55.0 0.0 0.0 43.29 3.69 F
1826 1860 0.883833 ATGCTTGCTGTGCTTACCAC 59.116 50.0 0.0 0.0 44.90 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1910 0.106708 TCAAAGCTCGCAACAGTCCT 59.893 50.0 0.0 0.0 0.00 3.85 R
2881 2923 0.321122 CTTCTTGGCTGCTCCTTCGT 60.321 55.0 0.0 0.0 35.26 3.85 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
45 46 0.398318 GGTTCAGCACCTTCACCTCT 59.602 55.000 0.00 0.00 43.29 3.69
63 64 2.164865 CTGGCTCCGCAGTCTCTGTT 62.165 60.000 0.00 0.00 33.43 3.16
92 93 3.616956 ACAATTTCAGAGCCGATCAGA 57.383 42.857 0.00 0.00 0.00 3.27
95 96 5.295950 ACAATTTCAGAGCCGATCAGATAG 58.704 41.667 0.00 0.00 0.00 2.08
96 97 5.163364 ACAATTTCAGAGCCGATCAGATAGT 60.163 40.000 0.00 0.00 0.00 2.12
114 115 8.316946 TCAGATAGTTAATTGGCAGATGGATAG 58.683 37.037 0.00 0.00 0.00 2.08
242 244 3.710165 TCAGACTCTCATCATCCTGCATT 59.290 43.478 0.00 0.00 0.00 3.56
245 247 3.806380 ACTCTCATCATCCTGCATTGAC 58.194 45.455 0.00 0.00 0.00 3.18
255 257 3.219281 TCCTGCATTGACCATCATCATG 58.781 45.455 0.00 0.00 0.00 3.07
266 269 5.769162 TGACCATCATCATGAGAAACAAACA 59.231 36.000 0.09 0.00 30.57 2.83
285 291 7.279615 ACAAACAAGGATCATATGGACGAATA 58.720 34.615 2.13 0.00 0.00 1.75
291 297 9.224267 CAAGGATCATATGGACGAATAAATTCT 57.776 33.333 2.13 0.00 34.69 2.40
352 358 6.042437 AGCATTGAAGAAAGTTTCCCAGAATT 59.958 34.615 12.05 0.00 0.00 2.17
378 384 5.183014 AGAATGGAAGGAAACGAACAAAC 57.817 39.130 0.00 0.00 0.00 2.93
410 416 5.443185 AATTAATCACTGATTGATGGGCG 57.557 39.130 13.66 0.00 44.86 6.13
613 619 2.363147 GGCTCCTCCTCCGTCACT 60.363 66.667 0.00 0.00 0.00 3.41
993 1027 1.920835 GGGGAACTCTGAGGCTGGT 60.921 63.158 9.85 0.00 0.00 4.00
994 1028 1.298014 GGGAACTCTGAGGCTGGTG 59.702 63.158 9.85 0.00 0.00 4.17
1318 1352 0.962489 CTCCATATTCCGCTCCTCGT 59.038 55.000 0.00 0.00 36.19 4.18
1496 1530 2.265739 GGAGATGTGTCGCCTGCA 59.734 61.111 0.00 0.00 40.76 4.41
1554 1588 3.578282 TGTCTAATCAGTGTCTTGAGCCA 59.422 43.478 0.00 0.00 0.00 4.75
1620 1654 1.433471 CATGCTCGACGAGGCTACA 59.567 57.895 25.31 15.06 0.00 2.74
1639 1673 1.199327 CACACGTCGTCTACTCCATGT 59.801 52.381 0.00 0.00 0.00 3.21
1794 1828 4.537433 CCAGGCAGTAGGCGCTCC 62.537 72.222 7.64 0.00 46.16 4.70
1826 1860 0.883833 ATGCTTGCTGTGCTTACCAC 59.116 50.000 0.00 0.00 44.90 4.16
1869 1903 2.637025 CGTGCTTTGGTTGTCCGG 59.363 61.111 0.00 0.00 36.30 5.14
1876 1910 4.902258 TGGTTGTCCGGGGTGGGA 62.902 66.667 0.00 0.00 38.76 4.37
1917 1951 9.823647 TTTGAGTCCATTATTCTTGATCTCTAC 57.176 33.333 0.00 0.00 0.00 2.59
1943 1977 1.648467 GGACGGTTGAATGAGGCAGC 61.648 60.000 0.00 0.00 0.00 5.25
1978 2012 0.324614 CATGGGCAAAAAGGGGTTCC 59.675 55.000 0.00 0.00 0.00 3.62
1979 2013 1.191489 ATGGGCAAAAAGGGGTTCCG 61.191 55.000 0.00 0.00 38.33 4.30
2001 2035 3.365832 GCCGACAATATGCATGTTTGAG 58.634 45.455 23.28 17.34 0.00 3.02
2011 2045 2.367894 TGCATGTTTGAGGCCAAAATCA 59.632 40.909 5.01 4.53 43.18 2.57
2046 2080 2.546795 GGAACAGAGGGTAGATGATGCG 60.547 54.545 0.00 0.00 0.00 4.73
2099 2133 1.548719 TGGTATCGTTCCCACTGTGAG 59.451 52.381 9.86 0.00 0.00 3.51
2180 2214 7.603024 CCTCGGATACCTTAAAAAGATGGATAC 59.397 40.741 0.00 0.00 0.00 2.24
2190 2224 0.833287 AGATGGATACGCAGCTTGGT 59.167 50.000 0.00 0.00 42.51 3.67
2208 2242 1.880027 GGTTGTGTTGCTCGAAAGGAT 59.120 47.619 0.00 0.00 0.00 3.24
2309 2343 0.396435 AACCAGCATCGTCCTGACAA 59.604 50.000 0.00 0.00 32.03 3.18
2324 2358 4.278170 TCCTGACAAAAACGAATTCAGCAT 59.722 37.500 6.22 0.00 33.70 3.79
2530 2564 1.027357 CTTGCAGCACACCAAAGACT 58.973 50.000 0.00 0.00 0.00 3.24
2537 2571 1.535462 GCACACCAAAGACTACGCAAT 59.465 47.619 0.00 0.00 0.00 3.56
2562 2596 4.917385 AGTTGCCTGTGATGGTAATAACA 58.083 39.130 0.00 0.00 34.42 2.41
2590 2624 4.943705 AGAGAAAAAGAAAGACAGTGTGCA 59.056 37.500 0.00 0.00 0.00 4.57
2667 2709 4.808414 TTGAGCTAGCTATGTTGTGTCT 57.192 40.909 19.38 0.00 0.00 3.41
2746 2788 1.421268 TGATGAACAGGTGGAAGTGCT 59.579 47.619 0.00 0.00 0.00 4.40
2753 2795 2.573462 ACAGGTGGAAGTGCTATCACAT 59.427 45.455 0.00 0.00 45.49 3.21
2760 2802 6.350445 GGTGGAAGTGCTATCACATTGAAAAT 60.350 38.462 0.00 0.00 45.49 1.82
2796 2838 1.145156 CGTGGTGGTGACAGGTTGA 59.855 57.895 0.00 0.00 44.46 3.18
2880 2922 2.695666 CCACAAGTCCGAGTATGGATCT 59.304 50.000 0.00 0.00 40.91 2.75
2881 2923 3.889538 CCACAAGTCCGAGTATGGATCTA 59.110 47.826 0.00 0.00 40.91 1.98
2975 3017 4.141733 TGTTCTTGAGAGTGAACATGGACA 60.142 41.667 0.00 0.00 44.89 4.02
3142 3185 9.772973 TGCCGATGAGTTGTAATATTAGTATTT 57.227 29.630 0.00 0.00 32.84 1.40
3172 3215 1.553248 ACTGTCGGGCTAAGCATAACA 59.447 47.619 0.00 0.00 0.00 2.41
3185 3228 4.443978 AGCATAACATCATTGTAGGGCT 57.556 40.909 0.00 0.00 34.06 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.659063 CCTGACCATCCTGTCGCCA 61.659 63.158 0.00 0.00 38.11 5.69
63 64 4.074970 GGCTCTGAAATTGTTTGAGGAGA 58.925 43.478 0.00 0.00 0.00 3.71
92 93 7.574021 TCCTATCCATCTGCCAATTAACTAT 57.426 36.000 0.00 0.00 0.00 2.12
95 96 6.064717 ACTTCCTATCCATCTGCCAATTAAC 58.935 40.000 0.00 0.00 0.00 2.01
96 97 6.266131 ACTTCCTATCCATCTGCCAATTAA 57.734 37.500 0.00 0.00 0.00 1.40
114 115 3.679389 TGCTTCCTTGATCTCAACTTCC 58.321 45.455 0.00 0.00 0.00 3.46
242 244 5.769162 TGTTTGTTTCTCATGATGATGGTCA 59.231 36.000 0.00 0.00 0.00 4.02
245 247 6.071784 TCCTTGTTTGTTTCTCATGATGATGG 60.072 38.462 0.00 0.00 0.00 3.51
255 257 7.475840 GTCCATATGATCCTTGTTTGTTTCTC 58.524 38.462 3.65 0.00 0.00 2.87
285 291 7.865706 AATCTGGCGTTGATTAGTAGAATTT 57.134 32.000 0.00 0.00 32.98 1.82
291 297 5.730550 ACTGAAATCTGGCGTTGATTAGTA 58.269 37.500 1.68 0.00 34.19 1.82
301 307 2.223112 CCGATGAAACTGAAATCTGGCG 60.223 50.000 0.00 0.00 0.00 5.69
352 358 8.508875 GTTTGTTCGTTTCCTTCCATTCTATTA 58.491 33.333 0.00 0.00 0.00 0.98
356 362 4.037565 GGTTTGTTCGTTTCCTTCCATTCT 59.962 41.667 0.00 0.00 0.00 2.40
358 364 3.702045 TGGTTTGTTCGTTTCCTTCCATT 59.298 39.130 0.00 0.00 0.00 3.16
410 416 3.550678 CGAGCTCGACAAGGTAATTAACC 59.449 47.826 32.06 0.00 45.24 2.85
993 1027 3.087253 CCCCTCGCCATACCCACA 61.087 66.667 0.00 0.00 0.00 4.17
994 1028 4.564110 GCCCCTCGCCATACCCAC 62.564 72.222 0.00 0.00 0.00 4.61
1554 1588 3.141488 CGGTAGGCGCCTCTGTCT 61.141 66.667 36.73 11.27 0.00 3.41
1594 1628 2.466982 CGTCGAGCATGCCAGCATT 61.467 57.895 15.66 0.00 36.85 3.56
1620 1654 1.531423 ACATGGAGTAGACGACGTGT 58.469 50.000 4.58 3.29 0.00 4.49
1782 1816 2.105128 CGAAGGGAGCGCCTACTG 59.895 66.667 2.29 0.00 0.00 2.74
1794 1828 2.981560 AAGCATTGGCACGCGAAGG 61.982 57.895 15.93 2.40 44.61 3.46
1826 1860 4.241555 CTTCCCGGGCATCCTCGG 62.242 72.222 18.49 0.00 45.29 4.63
1869 1903 2.034221 GCAACAGTCCTCCCACCC 59.966 66.667 0.00 0.00 0.00 4.61
1876 1910 0.106708 TCAAAGCTCGCAACAGTCCT 59.893 50.000 0.00 0.00 0.00 3.85
1917 1951 1.076533 CATTCAACCGTCCCTCGTCG 61.077 60.000 0.00 0.00 37.94 5.12
1943 1977 3.865684 GCCCATGTCCTGAAACAAATTGG 60.866 47.826 0.00 0.00 31.81 3.16
1978 2012 0.662619 AACATGCATATTGTCGGCCG 59.337 50.000 22.12 22.12 0.00 6.13
1979 2013 2.098934 TCAAACATGCATATTGTCGGCC 59.901 45.455 18.62 0.00 0.00 6.13
2001 2035 2.874086 GCATAAGGCAATGATTTTGGCC 59.126 45.455 0.00 0.00 44.88 5.36
2046 2080 1.909302 TCCTCCTCCAACACCTTGATC 59.091 52.381 0.00 0.00 0.00 2.92
2083 2117 2.457366 GTTCTCACAGTGGGAACGAT 57.543 50.000 26.94 0.00 46.44 3.73
2180 2214 1.945662 GCAACACAACCAAGCTGCG 60.946 57.895 0.00 0.00 0.00 5.18
2190 2224 3.734463 TGTATCCTTTCGAGCAACACAA 58.266 40.909 0.00 0.00 0.00 3.33
2208 2242 6.552725 AGCCACTGATCAAGATAGAGAATGTA 59.447 38.462 0.00 0.00 0.00 2.29
2295 2329 1.529438 TCGTTTTTGTCAGGACGATGC 59.471 47.619 0.00 0.00 39.33 3.91
2324 2358 5.995282 ACAGAACATAAACCTTCAATGACGA 59.005 36.000 0.00 0.00 0.00 4.20
2328 2362 5.634859 GCCAACAGAACATAAACCTTCAATG 59.365 40.000 0.00 0.00 0.00 2.82
2504 2538 1.967779 TGGTGTGCTGCAAGAGTACTA 59.032 47.619 2.77 0.00 38.11 1.82
2562 2596 6.881602 ACACTGTCTTTCTTTTTCTCTTCAGT 59.118 34.615 0.00 0.00 33.62 3.41
2590 2624 7.500559 GGCAAGAATTCAGGTTAATCTCTACAT 59.499 37.037 8.44 0.00 0.00 2.29
2667 2709 2.655090 TGAACCTCCTCATGTTTGCA 57.345 45.000 0.00 0.00 0.00 4.08
2742 2784 6.198403 CAGCATGATTTTCAATGTGATAGCAC 59.802 38.462 3.61 3.61 41.93 4.40
2746 2788 6.127563 ACAGCAGCATGATTTTCAATGTGATA 60.128 34.615 0.00 0.00 39.69 2.15
2753 2795 4.052608 CACAACAGCAGCATGATTTTCAA 58.947 39.130 0.00 0.00 39.69 2.69
2760 2802 1.229975 CGTCCACAACAGCAGCATGA 61.230 55.000 0.00 0.00 39.69 3.07
2880 2922 0.973632 TTCTTGGCTGCTCCTTCGTA 59.026 50.000 0.00 0.00 35.26 3.43
2881 2923 0.321122 CTTCTTGGCTGCTCCTTCGT 60.321 55.000 0.00 0.00 35.26 3.85
2970 3012 2.507484 CCTGATCAAAAGCTGTGTCCA 58.493 47.619 0.00 0.00 0.00 4.02
2975 3017 1.202976 AGCACCCTGATCAAAAGCTGT 60.203 47.619 9.86 0.00 0.00 4.40
3052 3094 4.591321 AACATCCCAACACCATGACTAT 57.409 40.909 0.00 0.00 0.00 2.12
3142 3185 2.347630 CCCGACAGTGGGCGATATA 58.652 57.895 8.94 0.00 43.70 0.86
3172 3215 2.283145 GCATCCAGCCCTACAATGAT 57.717 50.000 0.00 0.00 37.23 2.45
3185 3228 1.208776 CTCTCCACATGACAGCATCCA 59.791 52.381 0.00 0.00 30.68 3.41
3315 3360 5.733620 AATCATTCTGCCTTCACACAAAT 57.266 34.783 0.00 0.00 0.00 2.32
3325 3370 1.743772 CGTCCGGAAATCATTCTGCCT 60.744 52.381 5.23 0.00 40.08 4.75


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

AutoCloner maintained by Alex Coulton.