Multiple sequence alignment - TraesCS1D01G189300

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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 TraesCS1D01G189300 chr1D 100.000 6241 0 0 699 6939 261742161 261735921 0.000000e+00 11526
1 TraesCS1D01G189300 chr1D 100.000 382 0 0 1 382 261742859 261742478 0.000000e+00 706
2 TraesCS1D01G189300 chr1D 79.393 922 161 14 995 1891 449274910 449275827 2.130000e-174 623
3 TraesCS1D01G189300 chr1D 77.822 762 126 35 3890 4621 449278301 449279049 1.380000e-116 431
4 TraesCS1D01G189300 chr1D 86.301 365 38 7 5637 5990 449279855 449280218 3.040000e-103 387
5 TraesCS1D01G189300 chr1D 83.014 418 65 5 2978 3391 449276788 449277203 2.360000e-99 374
6 TraesCS1D01G189300 chr1D 85.849 318 37 4 3469 3778 449277306 449277623 1.440000e-86 331
7 TraesCS1D01G189300 chr1D 89.394 132 14 0 2228 2359 449275986 449276117 4.310000e-37 167
8 TraesCS1D01G189300 chr1A 97.045 6261 111 27 699 6939 338582913 338589119 0.000000e+00 10469
9 TraesCS1D01G189300 chr1A 96.364 385 11 1 1 382 338581920 338582304 1.270000e-176 630
10 TraesCS1D01G189300 chr1A 87.088 364 35 7 5637 5989 544474779 544475141 1.080000e-107 401
11 TraesCS1D01G189300 chr1A 80.185 540 86 15 3903 4429 544468246 544468777 1.090000e-102 385
12 TraesCS1D01G189300 chr1A 81.818 440 73 6 2965 3399 544467394 544467831 5.120000e-96 363
13 TraesCS1D01G189300 chr1A 84.615 338 41 10 3444 3771 544467900 544468236 6.710000e-85 326
14 TraesCS1D01G189300 chr1A 85.357 280 32 2 4960 5230 544474252 544474531 1.470000e-71 281
15 TraesCS1D01G189300 chr1A 89.062 128 14 0 2228 2355 544466598 544466725 7.200000e-35 159
16 TraesCS1D01G189300 chr1B 96.876 4353 97 15 2610 6939 350393340 350397676 0.000000e+00 7249
17 TraesCS1D01G189300 chr1B 96.712 1916 61 2 699 2613 350391346 350393260 0.000000e+00 3188
18 TraesCS1D01G189300 chr1B 98.429 382 6 0 1 382 350390300 350390681 0.000000e+00 673
19 TraesCS1D01G189300 chr1B 80.234 855 146 11 995 1827 614789035 614789888 7.640000e-174 621
20 TraesCS1D01G189300 chr1B 88.000 325 32 3 5637 5955 614794129 614794452 1.830000e-100 377
21 TraesCS1D01G189300 chr1B 81.773 406 70 3 2989 3391 614791152 614791556 3.100000e-88 337
22 TraesCS1D01G189300 chr1B 83.158 380 49 11 3469 3837 614791659 614792034 4.010000e-87 333
23 TraesCS1D01G189300 chr1B 85.926 270 30 1 4975 5236 614793628 614793897 1.470000e-71 281
24 TraesCS1D01G189300 chr1B 88.636 132 15 0 2228 2359 614790349 614790480 2.000000e-35 161
25 TraesCS1D01G189300 chr5A 86.928 153 20 0 6787 6939 683231731 683231883 9.250000e-39 172
26 TraesCS1D01G189300 chr4D 86.275 153 21 0 6787 6939 500849981 500850133 4.310000e-37 167
27 TraesCS1D01G189300 chr4B 86.275 153 21 0 6787 6939 644826475 644826627 4.310000e-37 167
28 TraesCS1D01G189300 chr6B 81.290 155 27 2 6786 6939 481396010 481396163 2.630000e-24 124
29 TraesCS1D01G189300 chr6A 81.290 155 27 2 6786 6939 479637485 479637332 2.630000e-24 124
30 TraesCS1D01G189300 chr6D 80.645 155 28 2 6786 6939 338934778 338934625 1.220000e-22 119


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 TraesCS1D01G189300 chr1D 261735921 261742859 6938 True 6116.000000 11526 100.000000 1 6939 2 chr1D.!!$R1 6938
1 TraesCS1D01G189300 chr1D 449274910 449280218 5308 False 385.500000 623 83.628833 995 5990 6 chr1D.!!$F1 4995
2 TraesCS1D01G189300 chr1A 338581920 338589119 7199 False 5549.500000 10469 96.704500 1 6939 2 chr1A.!!$F1 6938
3 TraesCS1D01G189300 chr1A 544474252 544475141 889 False 341.000000 401 86.222500 4960 5989 2 chr1A.!!$F3 1029
4 TraesCS1D01G189300 chr1A 544466598 544468777 2179 False 308.250000 385 83.920000 2228 4429 4 chr1A.!!$F2 2201
5 TraesCS1D01G189300 chr1B 350390300 350397676 7376 False 3703.333333 7249 97.339000 1 6939 3 chr1B.!!$F1 6938
6 TraesCS1D01G189300 chr1B 614789035 614794452 5417 False 351.666667 621 84.621167 995 5955 6 chr1B.!!$F2 4960

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
790 1142 0.466922 CTTCCACCATCAGCCCCATC 60.467 60.000 0.00 0.0 0.0 3.51 F
1726 2099 1.674441 TCCACACGATCGACCTCATAC 59.326 52.381 24.34 0.0 0.0 2.39 F
2767 3450 1.464997 GTCGGAGGTCTTGATTTGTGC 59.535 52.381 0.00 0.0 0.0 4.57 F
3432 4161 2.031682 CCTTCTTGTTTTGACTCAGGCG 60.032 50.000 0.00 0.0 0.0 5.52 F
4785 6291 2.689983 ACAACTGAGTTTTTCTGCCAGG 59.310 45.455 0.00 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2767 3450 0.944311 GTGTATCATAGCGCCCACCG 60.944 60.000 2.29 0.00 40.75 4.94 R
3178 3872 1.561076 ACATCATAAGCTGCTGGACCA 59.439 47.619 1.35 0.00 0.00 4.02 R
4160 5494 0.107654 GACTGGGTATGCTCCACCAC 60.108 60.000 4.67 0.00 37.84 4.16 R
5248 6762 4.696899 TCTCAAAATGCAAGCTCATGAG 57.303 40.909 18.84 18.84 0.00 2.90 R
6330 7874 1.070445 CAAGGCCCAACATTGCTTCAA 59.930 47.619 0.00 0.00 0.00 2.69 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
790 1142 0.466922 CTTCCACCATCAGCCCCATC 60.467 60.000 0.00 0.00 0.00 3.51
1224 1597 2.677037 CGTTTCCAATAGCGAGAACCCT 60.677 50.000 0.00 0.00 0.00 4.34
1533 1906 2.103601 GCCCAATACTTACTTCCCGCTA 59.896 50.000 0.00 0.00 0.00 4.26
1726 2099 1.674441 TCCACACGATCGACCTCATAC 59.326 52.381 24.34 0.00 0.00 2.39
1907 2287 5.354513 TCTCGAGGTCTTTACACTACATGAG 59.645 44.000 13.56 0.00 0.00 2.90
2767 3450 1.464997 GTCGGAGGTCTTGATTTGTGC 59.535 52.381 0.00 0.00 0.00 4.57
3178 3872 2.171237 TGACTTGCATTCCAGGATCGAT 59.829 45.455 0.00 0.00 0.00 3.59
3432 4161 2.031682 CCTTCTTGTTTTGACTCAGGCG 60.032 50.000 0.00 0.00 0.00 5.52
3451 4180 3.503891 GCGTTCAACTCTCTTAGTCTCC 58.496 50.000 0.00 0.00 37.50 3.71
3772 4511 9.265862 TGGGATTCAAACAAAGATATTGGTAAT 57.734 29.630 0.00 0.00 0.00 1.89
4160 5494 6.215845 CACCCTGTTTCTTCCTAATTTGTTG 58.784 40.000 0.00 0.00 0.00 3.33
4294 5630 7.733773 TGAAAGAAGTAGGTCTGGATGATAA 57.266 36.000 0.00 0.00 0.00 1.75
4785 6291 2.689983 ACAACTGAGTTTTTCTGCCAGG 59.310 45.455 0.00 0.00 0.00 4.45
5345 6859 4.685628 CCGCTGCTTCATTACAATTGTTTT 59.314 37.500 17.78 1.53 0.00 2.43
5390 6908 0.977395 GACTGCCTCCAACTACACCT 59.023 55.000 0.00 0.00 0.00 4.00
5405 6923 8.680001 CCAACTACACCTATTTAACATTTACCC 58.320 37.037 0.00 0.00 0.00 3.69
5471 6992 7.542890 CACATAAATACTGTTGGTGGCAATTA 58.457 34.615 0.00 0.00 0.00 1.40
5484 7005 6.242396 TGGTGGCAATTATACAAGTACAGTT 58.758 36.000 0.00 0.00 0.00 3.16
5485 7006 6.373216 TGGTGGCAATTATACAAGTACAGTTC 59.627 38.462 0.00 0.00 0.00 3.01
5486 7007 6.598064 GGTGGCAATTATACAAGTACAGTTCT 59.402 38.462 0.00 0.00 0.00 3.01
5567 7090 7.504238 GTCGGGGTATATCATCTCATCTCTTAT 59.496 40.741 0.00 0.00 0.00 1.73
5568 7091 8.724310 TCGGGGTATATCATCTCATCTCTTATA 58.276 37.037 0.00 0.00 0.00 0.98
6136 7680 0.031994 CTGCCTTTTGGTTGTTCCCG 59.968 55.000 0.00 0.00 42.99 5.14
6393 7937 2.256306 GGAAATTGGTGGGTGGATGTT 58.744 47.619 0.00 0.00 0.00 2.71
6467 8014 5.275067 TGCCTTTGCAACATAAGTTTTCT 57.725 34.783 0.00 0.00 46.66 2.52
6522 8069 4.510167 AAGGGATGTCTGGGTTTCATAG 57.490 45.455 0.00 0.00 0.00 2.23
6623 8171 5.777732 TCCCCCAAATACAATATTATGCCAC 59.222 40.000 0.00 0.00 0.00 5.01
6707 8255 6.605471 TTATGCCCATATACCTGTACAGAG 57.395 41.667 24.68 15.90 0.00 3.35
6771 8324 3.074412 CAGTATAATTGCGGGGGTCATC 58.926 50.000 0.00 0.00 0.00 2.92
6814 8367 1.078214 CATCATGACGGTGGCCTGT 60.078 57.895 3.32 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
824 1176 1.000274 CATCGACGATGGGATAGTGCA 60.000 52.381 26.65 0.00 36.51 4.57
1224 1597 1.452145 GGAAGTTCTGCGCCCAAACA 61.452 55.000 4.18 0.00 0.00 2.83
1726 2099 1.445095 CCTTCTCAGCTCCATCCCG 59.555 63.158 0.00 0.00 0.00 5.14
2767 3450 0.944311 GTGTATCATAGCGCCCACCG 60.944 60.000 2.29 0.00 40.75 4.94
3178 3872 1.561076 ACATCATAAGCTGCTGGACCA 59.439 47.619 1.35 0.00 0.00 4.02
3432 4161 8.361889 AGTAAAAGGAGACTAAGAGAGTTGAAC 58.638 37.037 0.00 0.00 42.68 3.18
3772 4511 7.531857 AGAAACAGAGAACTCTAGAACATGA 57.468 36.000 0.00 0.00 37.98 3.07
4160 5494 0.107654 GACTGGGTATGCTCCACCAC 60.108 60.000 4.67 0.00 37.84 4.16
4294 5630 8.223330 AGTTCAAATAATCCTGAGGCTCATATT 58.777 33.333 19.11 20.77 0.00 1.28
5248 6762 4.696899 TCTCAAAATGCAAGCTCATGAG 57.303 40.909 18.84 18.84 0.00 2.90
5445 6965 3.192422 TGCCACCAACAGTATTTATGTGC 59.808 43.478 0.00 0.00 0.00 4.57
5567 7090 8.640063 TGCGTCATAACTAGATTATTACCCTA 57.360 34.615 0.00 0.00 30.54 3.53
5568 7091 7.534723 TGCGTCATAACTAGATTATTACCCT 57.465 36.000 0.00 0.00 30.54 4.34
6327 7871 2.172293 AGGCCCAACATTGCTTCAAAAA 59.828 40.909 0.00 0.00 0.00 1.94
6330 7874 1.070445 CAAGGCCCAACATTGCTTCAA 59.930 47.619 0.00 0.00 0.00 2.69
6393 7937 2.990066 AAAAATGGAAACCGGTTGCA 57.010 40.000 26.79 18.60 42.34 4.08
6467 8014 8.714179 CATTTCTCTGCATTGCAAAATAAGAAA 58.286 29.630 21.68 21.68 38.41 2.52
6522 8069 7.378728 GTCTTTTAGTGCCTGTTTGTTGATTAC 59.621 37.037 0.00 0.00 0.00 1.89
6623 8171 4.268405 GGAGCCAAATTTGCATGTAATTCG 59.732 41.667 12.92 0.00 0.00 3.34
6727 8275 8.047911 ACTGATCTGAATGAATGAATCAACTCT 58.952 33.333 6.60 0.00 42.54 3.24


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

AutoCloner maintained by Alex Coulton.