Multiple sequence alignment - TraesCS5B01G110800

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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 TraesCS5B01G110800 chr5B 100.000 4958 0 0 801 5758 162775892 162770935 0.000000e+00 9156
1 TraesCS5B01G110800 chr5B 100.000 410 0 0 1 410 162776692 162776283 0.000000e+00 758
2 TraesCS5B01G110800 chr5D 96.305 4871 113 35 808 5649 170381257 170376425 0.000000e+00 7936
3 TraesCS5B01G110800 chr5D 97.500 360 9 0 1 360 170381699 170381340 2.950000e-172 616
4 TraesCS5B01G110800 chr5D 95.556 90 4 0 3832 3921 509426471 509426560 1.670000e-30 145
5 TraesCS5B01G110800 chr5D 94.521 73 3 1 5687 5758 170376425 170376353 1.700000e-20 111
6 TraesCS5B01G110800 chr5A 96.704 3064 52 10 812 3833 175832413 175835469 0.000000e+00 5053
7 TraesCS5B01G110800 chr5A 95.043 1513 37 13 3915 5408 175835468 175836961 0.000000e+00 2344
8 TraesCS5B01G110800 chr5A 96.620 355 10 2 9 362 175832014 175832367 6.430000e-164 588
9 TraesCS5B01G110800 chr5A 95.950 321 11 1 5440 5758 175836960 175837280 2.380000e-143 520
10 TraesCS5B01G110800 chr5A 81.343 134 23 2 5477 5608 494224356 494224223 2.190000e-19 108
11 TraesCS5B01G110800 chr6B 97.727 88 2 0 3829 3916 713960523 713960610 9.990000e-33 152
12 TraesCS5B01G110800 chr3A 96.703 91 3 0 3830 3920 642160657 642160747 9.990000e-33 152
13 TraesCS5B01G110800 chr3A 92.929 99 4 2 3818 3916 710277979 710277884 2.160000e-29 141
14 TraesCS5B01G110800 chr2B 94.792 96 5 0 3830 3925 28631534 28631629 3.590000e-32 150
15 TraesCS5B01G110800 chr2B 94.667 75 4 0 3915 3989 446046915 446046989 3.650000e-22 117
16 TraesCS5B01G110800 chr3D 95.604 91 4 0 3829 3919 497908041 497907951 4.650000e-31 147
17 TraesCS5B01G110800 chr3B 95.604 91 4 0 3832 3922 551513972 551513882 4.650000e-31 147
18 TraesCS5B01G110800 chr4B 90.566 106 8 2 3815 3919 423051097 423050993 7.780000e-29 139
19 TraesCS5B01G110800 chr1A 98.571 70 1 0 3917 3986 469589921 469589990 2.180000e-24 124
20 TraesCS5B01G110800 chr1D 98.551 69 1 0 3915 3983 233084864 233084796 7.840000e-24 122
21 TraesCS5B01G110800 chr1D 94.737 76 3 1 3915 3989 74276328 74276253 3.650000e-22 117
22 TraesCS5B01G110800 chr7D 97.183 71 2 0 3915 3985 620699455 620699525 2.820000e-23 121
23 TraesCS5B01G110800 chr4D 91.463 82 7 0 3900 3981 49514676 49514757 4.720000e-21 113
24 TraesCS5B01G110800 chr2D 94.366 71 4 0 3915 3985 461087353 461087283 6.100000e-20 110
25 TraesCS5B01G110800 chr6A 80.741 135 22 4 5477 5608 613628513 613628380 1.020000e-17 102


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 TraesCS5B01G110800 chr5B 162770935 162776692 5757 True 4957.000000 9156 100.000000 1 5758 2 chr5B.!!$R1 5757
1 TraesCS5B01G110800 chr5D 170376353 170381699 5346 True 2887.666667 7936 96.108667 1 5758 3 chr5D.!!$R1 5757
2 TraesCS5B01G110800 chr5A 175832014 175837280 5266 False 2126.250000 5053 96.079250 9 5758 4 chr5A.!!$F1 5749

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
208 209 2.671396 CTCGTTTTGATCCGGTTACCTG 59.329 50.0 0.00 0.0 0.00 4.00 F
1017 1027 0.469494 TCATGGACATGGTGGGATCG 59.531 55.0 11.98 0.0 39.24 3.69 F
1311 1321 0.472925 TGCCTCAGGGTGTAGGTTCA 60.473 55.0 0.00 0.0 35.16 3.18 F
2039 2049 1.237285 ATCAACGGCAAGAGTGGTGC 61.237 55.0 0.00 0.0 41.45 5.01 F
3599 3636 0.256752 CATGGATTCAGCCACCTGGA 59.743 55.0 0.00 0.0 41.56 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1231 1241 1.071471 CACCACGGAAGCAGTCCTT 59.929 57.895 5.06 0.0 45.36 3.36 R
2691 2701 2.104967 ACCTTGGCATCACATCCAATG 58.895 47.619 0.00 0.0 41.10 2.82 R
3227 3240 2.236146 CAACACCACCCATGTAGCTAGA 59.764 50.000 0.00 0.0 0.00 2.43 R
3985 4032 0.037232 GCTAAGACAAGCCACCGAGT 60.037 55.000 0.00 0.0 36.45 4.18 R
5073 5134 2.624838 CCCAAAGCTATGCCTATTGTGG 59.375 50.000 0.00 0.0 0.00 4.17 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
208 209 2.671396 CTCGTTTTGATCCGGTTACCTG 59.329 50.000 0.00 0.00 0.00 4.00
283 285 5.888161 GGTGAATCCAAGGTGATCAATTAGT 59.112 40.000 0.00 0.00 35.97 2.24
311 313 2.938756 GCCAGAGAGGAGACCACAATTG 60.939 54.545 3.24 3.24 41.22 2.32
365 367 9.699106 TTTTTCTCCCCTTATATATTACTCCCT 57.301 33.333 0.00 0.00 0.00 4.20
367 369 7.865347 TCTCCCCTTATATATTACTCCCTCT 57.135 40.000 0.00 0.00 0.00 3.69
369 371 7.244239 TCTCCCCTTATATATTACTCCCTCTGT 59.756 40.741 0.00 0.00 0.00 3.41
370 372 8.486556 TCCCCTTATATATTACTCCCTCTGTA 57.513 38.462 0.00 0.00 0.00 2.74
371 373 8.918601 TCCCCTTATATATTACTCCCTCTGTAA 58.081 37.037 0.00 0.00 34.87 2.41
372 374 9.556772 CCCCTTATATATTACTCCCTCTGTAAA 57.443 37.037 0.00 0.00 34.20 2.01
377 379 4.820894 ATTACTCCCTCTGTAAAAGCGT 57.179 40.909 0.00 0.00 34.20 5.07
379 381 3.487120 ACTCCCTCTGTAAAAGCGTTT 57.513 42.857 2.53 2.53 0.00 3.60
380 382 4.612264 ACTCCCTCTGTAAAAGCGTTTA 57.388 40.909 0.33 0.33 0.00 2.01
381 383 4.566987 ACTCCCTCTGTAAAAGCGTTTAG 58.433 43.478 5.01 0.00 29.74 1.85
382 384 4.040095 ACTCCCTCTGTAAAAGCGTTTAGT 59.960 41.667 5.01 0.00 29.74 2.24
383 385 4.964593 TCCCTCTGTAAAAGCGTTTAGTT 58.035 39.130 5.01 0.00 29.74 2.24
385 387 6.523840 TCCCTCTGTAAAAGCGTTTAGTTAA 58.476 36.000 5.01 0.00 29.74 2.01
386 388 7.163441 TCCCTCTGTAAAAGCGTTTAGTTAAT 58.837 34.615 5.01 0.00 29.74 1.40
387 389 7.332678 TCCCTCTGTAAAAGCGTTTAGTTAATC 59.667 37.037 5.01 0.00 29.74 1.75
388 390 7.333672 CCCTCTGTAAAAGCGTTTAGTTAATCT 59.666 37.037 5.01 0.00 29.74 2.40
843 845 5.640732 ACTGATGTCCGAAAATTATTGTGC 58.359 37.500 0.00 0.00 0.00 4.57
847 849 4.804108 TGTCCGAAAATTATTGTGCAAGG 58.196 39.130 0.00 0.00 0.00 3.61
1006 1016 4.819783 GGCCAACTGTCATGGACA 57.180 55.556 0.00 0.00 45.90 4.02
1017 1027 0.469494 TCATGGACATGGTGGGATCG 59.531 55.000 11.98 0.00 39.24 3.69
1231 1241 0.911769 CTCAAGCCATACCTGGACCA 59.088 55.000 0.00 0.00 46.37 4.02
1308 1318 1.201429 CCTTGCCTCAGGGTGTAGGT 61.201 60.000 0.00 0.00 35.16 3.08
1311 1321 0.472925 TGCCTCAGGGTGTAGGTTCA 60.473 55.000 0.00 0.00 35.16 3.18
1687 1697 3.283751 TCGGTGAAACAAGTTGGTCAAT 58.716 40.909 7.96 0.00 39.98 2.57
1815 1825 2.813754 GTCTGGCATTAAGACAACTGCA 59.186 45.455 0.21 0.00 42.98 4.41
1875 1885 4.500499 AGGATTTGCTAGACTGCAGAAT 57.500 40.909 23.35 10.77 44.27 2.40
1958 1968 6.484643 ACATGTGGATCTGACATTACTAATGC 59.515 38.462 0.00 3.35 42.69 3.56
2039 2049 1.237285 ATCAACGGCAAGAGTGGTGC 61.237 55.000 0.00 0.00 41.45 5.01
2155 2165 6.194235 ACACCTTATATTTTGCAATGGAGGA 58.806 36.000 0.00 0.00 0.00 3.71
2609 2619 3.519913 AGACTATCCTTCAACTTCCACCC 59.480 47.826 0.00 0.00 0.00 4.61
2691 2701 9.162764 TGATTTAGTTTCTATTGACTTGTAGGC 57.837 33.333 0.00 0.00 0.00 3.93
2772 2782 6.203723 CAGATAAATTTAGCAGTCAGGTAGGC 59.796 42.308 15.37 0.00 0.00 3.93
2822 2835 7.925483 ACAGCTTAAATCTATCTTACTGCAGAG 59.075 37.037 23.35 8.59 0.00 3.35
2893 2906 7.032377 AGAACAGTTTCTTGTGAAATTCCTC 57.968 36.000 0.00 0.00 43.14 3.71
3227 3240 8.032045 AGAAGGTGTGATCATTCTGAATATCT 57.968 34.615 8.21 0.40 37.14 1.98
3432 3469 7.340122 TCGCTTCTATATAATGCTATCAGCT 57.660 36.000 0.00 0.00 42.97 4.24
3599 3636 0.256752 CATGGATTCAGCCACCTGGA 59.743 55.000 0.00 0.00 41.56 3.86
3639 3676 3.257624 CCGTGGACAGGTACTTTACTTCT 59.742 47.826 0.00 0.00 34.60 2.85
3793 3837 1.664649 CTTCGAACTCCACGCAGCA 60.665 57.895 0.00 0.00 0.00 4.41
3812 3856 2.359900 CAAAGGGATTCCGTTCTCCAG 58.640 52.381 10.89 0.00 38.33 3.86
3952 3996 1.880271 CATCGATTGATGCAGAGGCT 58.120 50.000 10.05 0.00 45.06 4.58
4589 4647 1.205064 CGTTTCTGACGCTGCCTTG 59.795 57.895 0.00 0.00 45.86 3.61
4590 4648 1.081840 GTTTCTGACGCTGCCTTGC 60.082 57.895 0.00 0.00 0.00 4.01
4591 4649 1.227943 TTTCTGACGCTGCCTTGCT 60.228 52.632 0.00 0.00 0.00 3.91
4592 4650 1.509644 TTTCTGACGCTGCCTTGCTG 61.510 55.000 0.00 0.00 0.00 4.41
4771 4829 3.528078 TCCTCCTGACAGTCCATACTACT 59.472 47.826 0.93 0.00 33.48 2.57
5066 5127 6.671614 TTTTGTAACTGGAGTGTGTGTTAG 57.328 37.500 0.00 0.00 0.00 2.34
5067 5128 5.347620 TTGTAACTGGAGTGTGTGTTAGT 57.652 39.130 0.00 0.00 0.00 2.24
5068 5129 4.689071 TGTAACTGGAGTGTGTGTTAGTG 58.311 43.478 0.00 0.00 0.00 2.74
5069 5130 3.906720 AACTGGAGTGTGTGTTAGTGT 57.093 42.857 0.00 0.00 0.00 3.55
5070 5131 3.454371 ACTGGAGTGTGTGTTAGTGTC 57.546 47.619 0.00 0.00 0.00 3.67
5071 5132 3.031736 ACTGGAGTGTGTGTTAGTGTCT 58.968 45.455 0.00 0.00 0.00 3.41
5072 5133 3.451178 ACTGGAGTGTGTGTTAGTGTCTT 59.549 43.478 0.00 0.00 0.00 3.01
5073 5134 4.051922 CTGGAGTGTGTGTTAGTGTCTTC 58.948 47.826 0.00 0.00 0.00 2.87
5074 5135 3.181469 TGGAGTGTGTGTTAGTGTCTTCC 60.181 47.826 0.00 0.00 0.00 3.46
5075 5136 3.181469 GGAGTGTGTGTTAGTGTCTTCCA 60.181 47.826 0.00 0.00 0.00 3.53
5183 5244 4.454678 TCTTGATGTATGTCTGCAATCCC 58.545 43.478 0.00 0.00 0.00 3.85
5288 5350 7.062848 CACGAAATGAAAATAAAACAAGGTGC 58.937 34.615 0.00 0.00 0.00 5.01
5363 5426 6.238759 GGTCTTCATTCATATAGCCACAAACC 60.239 42.308 0.00 0.00 0.00 3.27
5452 5515 6.700352 TCATTCCCCACAATTTTCATTCTTC 58.300 36.000 0.00 0.00 0.00 2.87
5577 5641 6.867662 ACTATGGTGAAACAGAAGAACAAG 57.132 37.500 0.00 0.00 39.98 3.16
5620 5684 4.559862 AACCCTCTCAACCTTCATACAG 57.440 45.455 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 2.036862 AGACAAGGAAACCGGAGTACAC 59.963 50.000 9.46 0.00 0.00 2.90
171 172 0.317479 CGAGACAAGGAAACCGGAGT 59.683 55.000 9.46 0.00 0.00 3.85
208 209 2.679996 AACCAAATCGGGGCCAGC 60.680 61.111 4.39 0.00 40.22 4.85
311 313 6.483640 ACAGCATATAGGAAAATTCTCGTTCC 59.516 38.462 0.00 0.00 43.17 3.62
363 365 8.252964 AGATTAACTAAACGCTTTTACAGAGG 57.747 34.615 0.00 0.00 0.00 3.69
804 806 9.040939 CGGACATCAGTATATTATTCACAACAA 57.959 33.333 0.00 0.00 0.00 2.83
805 807 8.417884 TCGGACATCAGTATATTATTCACAACA 58.582 33.333 0.00 0.00 0.00 3.33
806 808 8.812147 TCGGACATCAGTATATTATTCACAAC 57.188 34.615 0.00 0.00 0.00 3.32
807 809 9.825109 TTTCGGACATCAGTATATTATTCACAA 57.175 29.630 0.00 0.00 0.00 3.33
808 810 9.825109 TTTTCGGACATCAGTATATTATTCACA 57.175 29.630 0.00 0.00 0.00 3.58
843 845 3.181479 TGGCGCTACTGTATCTTACCTTG 60.181 47.826 7.64 0.00 0.00 3.61
847 849 3.431922 TGTGGCGCTACTGTATCTTAC 57.568 47.619 24.82 0.00 0.00 2.34
987 997 0.184692 TGTCCATGACAGTTGGCCAA 59.815 50.000 16.05 16.05 37.67 4.52
1006 1016 1.703014 ATCAGCAGCGATCCCACCAT 61.703 55.000 0.00 0.00 0.00 3.55
1017 1027 1.331756 CGGGTCATGTTTATCAGCAGC 59.668 52.381 0.00 0.00 0.00 5.25
1231 1241 1.071471 CACCACGGAAGCAGTCCTT 59.929 57.895 5.06 0.00 45.36 3.36
1311 1321 2.606587 ATCAGCGTCAAGGGCCCTT 61.607 57.895 32.48 32.48 36.60 3.95
1368 1378 2.185350 CCCTGCGAGCAGTACCAG 59.815 66.667 21.73 7.65 42.15 4.00
1687 1697 3.164977 TCCACTGGTTGCCGGACA 61.165 61.111 5.05 0.00 33.36 4.02
1815 1825 4.520492 AGAATTGAACTGTCTGCGGAAATT 59.480 37.500 0.00 0.00 0.00 1.82
1875 1885 5.425217 TGCCAGAGTATACTTTCCATTCAGA 59.575 40.000 6.88 0.00 0.00 3.27
1958 1968 5.936956 ACAAGCTCATACTTCTTTTCCTCTG 59.063 40.000 0.00 0.00 0.00 3.35
2155 2165 7.398024 AGGTTAGAGCATCAAATCTGTTACTT 58.602 34.615 0.00 0.00 37.82 2.24
2609 2619 9.229784 GCAATACATCAAATGTTGACTAAGATG 57.770 33.333 0.00 0.00 43.48 2.90
2691 2701 2.104967 ACCTTGGCATCACATCCAATG 58.895 47.619 0.00 0.00 41.10 2.82
2796 2809 7.786030 TCTGCAGTAAGATAGATTTAAGCTGT 58.214 34.615 14.67 0.00 0.00 4.40
2843 2856 9.810870 TCATGTGGGAATATGATAAATTCATGA 57.189 29.630 0.00 0.00 44.90 3.07
2893 2906 9.763465 GCATTGTCTGAAATGGAAAAATTATTG 57.237 29.630 11.68 0.00 37.89 1.90
2902 2915 6.647334 TGTTTAGCATTGTCTGAAATGGAA 57.353 33.333 11.68 0.00 37.89 3.53
3227 3240 2.236146 CAACACCACCCATGTAGCTAGA 59.764 50.000 0.00 0.00 0.00 2.43
3432 3469 9.953697 AGTTAACGCTAACATTATTGTTGAAAA 57.046 25.926 11.07 0.00 45.56 2.29
3658 3695 6.484818 TGTGTGTGTGTGAATTCTATCATG 57.515 37.500 7.05 0.00 0.00 3.07
3793 3837 1.282157 CCTGGAGAACGGAATCCCTTT 59.718 52.381 0.00 0.00 34.47 3.11
3853 3897 9.088512 CACTAAAGTATTGATCTAAACGCTCTT 57.911 33.333 0.00 0.00 0.00 2.85
3856 3900 9.250624 GATCACTAAAGTATTGATCTAAACGCT 57.749 33.333 7.85 0.00 40.02 5.07
3903 3947 4.282703 GCCATCTTTATTACTCCCTCCGTA 59.717 45.833 0.00 0.00 0.00 4.02
3904 3948 3.071167 GCCATCTTTATTACTCCCTCCGT 59.929 47.826 0.00 0.00 0.00 4.69
3905 3949 3.325135 AGCCATCTTTATTACTCCCTCCG 59.675 47.826 0.00 0.00 0.00 4.63
3906 3950 4.646572 CAGCCATCTTTATTACTCCCTCC 58.353 47.826 0.00 0.00 0.00 4.30
3952 3996 2.518834 TGAAAAGGAGGTTAAACCCCCA 59.481 45.455 0.00 0.00 39.75 4.96
3985 4032 0.037232 GCTAAGACAAGCCACCGAGT 60.037 55.000 0.00 0.00 36.45 4.18
4037 4084 2.288961 TAACGATTCGCTCCCTGTTC 57.711 50.000 5.86 0.00 0.00 3.18
4086 4133 1.070175 CGTTCATGACCACCAAACGTC 60.070 52.381 0.00 0.00 38.24 4.34
4202 4249 2.363680 GAGCTGAGCCAGAGCATAGTAA 59.636 50.000 0.00 0.00 43.56 2.24
4203 4250 1.959985 GAGCTGAGCCAGAGCATAGTA 59.040 52.381 0.00 0.00 43.56 1.82
4208 4255 3.767806 CGGAGCTGAGCCAGAGCA 61.768 66.667 0.00 0.00 43.56 4.26
4549 4607 5.133264 CGATTTCGCTATGTATTTGCACTC 58.867 41.667 0.00 0.00 0.00 3.51
4771 4829 4.281182 GTGTTAGGTTTCTGAGTGGAGAGA 59.719 45.833 0.00 0.00 0.00 3.10
5042 5103 5.968528 AACACACACTCCAGTTACAAAAA 57.031 34.783 0.00 0.00 0.00 1.94
5067 5128 3.455910 AGCTATGCCTATTGTGGAAGACA 59.544 43.478 0.00 0.00 0.00 3.41
5068 5129 4.078639 AGCTATGCCTATTGTGGAAGAC 57.921 45.455 0.00 0.00 0.00 3.01
5069 5130 4.778213 AAGCTATGCCTATTGTGGAAGA 57.222 40.909 0.00 0.00 0.00 2.87
5070 5131 4.037208 CCAAAGCTATGCCTATTGTGGAAG 59.963 45.833 0.00 0.00 0.00 3.46
5071 5132 3.953612 CCAAAGCTATGCCTATTGTGGAA 59.046 43.478 0.00 0.00 0.00 3.53
5072 5133 3.554934 CCAAAGCTATGCCTATTGTGGA 58.445 45.455 0.00 0.00 0.00 4.02
5073 5134 2.624838 CCCAAAGCTATGCCTATTGTGG 59.375 50.000 0.00 0.00 0.00 4.17
5074 5135 2.624838 CCCCAAAGCTATGCCTATTGTG 59.375 50.000 0.00 0.00 0.00 3.33
5075 5136 2.949447 CCCCAAAGCTATGCCTATTGT 58.051 47.619 0.00 0.00 0.00 2.71
5183 5244 4.853196 CACACAAATTTTCAGCACGGATAG 59.147 41.667 0.00 0.00 0.00 2.08
5237 5299 5.816777 CACACAATTTTCCAGTTTTCACCAT 59.183 36.000 0.00 0.00 0.00 3.55
5332 5395 7.661437 GTGGCTATATGAATGAAGACCACAATA 59.339 37.037 0.00 0.00 43.52 1.90
5589 5653 5.953571 AGGTTGAGAGGGTTATTTTTCAGT 58.046 37.500 0.00 0.00 0.00 3.41
5620 5684 0.469144 TCCTTTGGCTTTGGGACCAC 60.469 55.000 0.00 0.00 35.10 4.16
5675 5741 3.127548 ACGCAGCCTGAAGTTCAAATATG 59.872 43.478 7.06 5.07 0.00 1.78
5682 5748 1.347817 CGAGACGCAGCCTGAAGTTC 61.348 60.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.