Multiple sequence alignment - TraesCS4D01G173100

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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 TraesCS4D01G173100 chr4D 100.000 4673 0 0 1 4673 301009999 301005327 0.000000e+00 8630.0
1 TraesCS4D01G173100 chr4B 96.287 4067 104 16 43 4082 374630794 374626748 0.000000e+00 6630.0
2 TraesCS4D01G173100 chr4B 91.260 492 27 10 4081 4570 374626700 374626223 0.000000e+00 656.0
3 TraesCS4D01G173100 chr4B 96.774 62 2 0 4597 4658 374626223 374626162 2.300000e-18 104.0
4 TraesCS4D01G173100 chr4B 87.302 63 4 3 1 61 374707805 374707745 8.390000e-08 69.4
5 TraesCS4D01G173100 chr4A 96.526 3771 94 16 337 4082 181707259 181711017 0.000000e+00 6204.0
6 TraesCS4D01G173100 chr4A 89.775 489 18 8 4201 4673 181711072 181711544 8.650000e-167 597.0
7 TraesCS4D01G173100 chr4A 92.574 202 9 4 122 323 181706808 181707003 7.650000e-73 285.0
8 TraesCS4D01G173100 chr4A 90.152 132 10 2 1 131 181706556 181706685 8.040000e-38 169.0
9 TraesCS4D01G173100 chr4A 100.000 39 0 0 4095 4133 90592946 90592984 6.490000e-09 73.1
10 TraesCS4D01G173100 chr4A 90.476 42 4 0 4095 4136 505796611 505796570 6.530000e-04 56.5
11 TraesCS4D01G173100 chr1D 89.050 3315 258 60 759 4015 316856463 316859730 0.000000e+00 4013.0
12 TraesCS4D01G173100 chr1A 89.550 3225 253 41 833 4015 398050442 398053624 0.000000e+00 4012.0
13 TraesCS4D01G173100 chr1B 90.019 3126 236 45 759 3843 429001921 429005011 0.000000e+00 3975.0
14 TraesCS4D01G173100 chr1B 95.122 41 2 0 4095 4135 513163295 513163335 1.090000e-06 65.8
15 TraesCS4D01G173100 chrUn 97.852 419 9 0 2213 2631 476932637 476932219 0.000000e+00 725.0
16 TraesCS4D01G173100 chr6D 94.231 52 3 0 4083 4134 472932539 472932488 3.880000e-11 80.5
17 TraesCS4D01G173100 chr2D 100.000 38 0 0 4096 4133 467971389 467971426 2.330000e-08 71.3
18 TraesCS4D01G173100 chr2A 100.000 37 0 0 4098 4134 39177836 39177872 8.390000e-08 69.4
19 TraesCS4D01G173100 chr6B 97.436 39 1 0 4095 4133 560192875 560192913 3.020000e-07 67.6
20 TraesCS4D01G173100 chr3A 97.436 39 1 0 4095 4133 556457678 556457640 3.020000e-07 67.6


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 TraesCS4D01G173100 chr4D 301005327 301009999 4672 True 8630.000000 8630 100.000000 1 4673 1 chr4D.!!$R1 4672
1 TraesCS4D01G173100 chr4B 374626162 374630794 4632 True 2463.333333 6630 94.773667 43 4658 3 chr4B.!!$R2 4615
2 TraesCS4D01G173100 chr4A 181706556 181711544 4988 False 1813.750000 6204 92.256750 1 4673 4 chr4A.!!$F2 4672
3 TraesCS4D01G173100 chr1D 316856463 316859730 3267 False 4013.000000 4013 89.050000 759 4015 1 chr1D.!!$F1 3256
4 TraesCS4D01G173100 chr1A 398050442 398053624 3182 False 4012.000000 4012 89.550000 833 4015 1 chr1A.!!$F1 3182
5 TraesCS4D01G173100 chr1B 429001921 429005011 3090 False 3975.000000 3975 90.019000 759 3843 1 chr1B.!!$F1 3084

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
230 364 0.678684 CCGTGGCTTATTCCGGGTTT 60.679 55.0 0.0 0.0 36.84 3.27 F
800 1192 0.903454 GTCCCGAAACCTCTCTCCCA 60.903 60.0 0.0 0.0 0.00 4.37 F
2068 2511 0.038892 CAACAACCAGACTGCCATGC 60.039 55.0 0.0 0.0 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 2269 0.249398 AGGGTAGGTGATTGCGACAC 59.751 55.000 0.0 0.00 37.51 3.67 R
2338 2781 1.066716 ACCAACAATAGGCGCGACTAA 60.067 47.619 28.1 9.87 0.00 2.24 R
3749 4200 0.940126 AGACAGCAAGAGCACAAACG 59.060 50.000 0.0 0.00 45.49 3.60 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
67 69 7.010460 GGCTTATTTGGTGATTTGAATACAAGC 59.990 37.037 0.00 0.00 37.32 4.01
74 76 9.941325 TTGGTGATTTGAATACAAGCATATTTT 57.059 25.926 0.00 0.00 37.32 1.82
230 364 0.678684 CCGTGGCTTATTCCGGGTTT 60.679 55.000 0.00 0.00 36.84 3.27
280 414 2.707849 GGCCGCGGTCTCTGACTAA 61.708 63.158 28.70 0.00 32.47 2.24
288 422 1.409427 GGTCTCTGACTAATGGGACCG 59.591 57.143 0.00 0.00 34.79 4.79
289 423 1.112113 TCTCTGACTAATGGGACCGC 58.888 55.000 0.00 0.00 0.00 5.68
501 881 3.066380 GACGGTACCGAAAAGGCTTTTA 58.934 45.455 39.52 7.00 46.52 1.52
646 1026 3.052082 CCAGCGGAACACAGCAGG 61.052 66.667 0.00 0.00 33.84 4.85
800 1192 0.903454 GTCCCGAAACCTCTCTCCCA 60.903 60.000 0.00 0.00 0.00 4.37
987 1403 1.414897 CGACGAAACGCAAGCTACC 59.585 57.895 0.00 0.00 45.62 3.18
1381 1824 1.302192 GCCAACTACTCCAACCGCA 60.302 57.895 0.00 0.00 0.00 5.69
1826 2269 1.100510 TCGTACCAGAACGATCCCAG 58.899 55.000 0.00 0.00 46.29 4.45
1831 2274 0.458543 CCAGAACGATCCCAGTGTCG 60.459 60.000 0.00 0.48 43.13 4.35
2012 2455 6.823286 TTTCTGTGAGATACAATCCCCATA 57.177 37.500 0.00 0.00 39.20 2.74
2013 2456 5.808366 TCTGTGAGATACAATCCCCATAC 57.192 43.478 0.00 0.00 39.20 2.39
2068 2511 0.038892 CAACAACCAGACTGCCATGC 60.039 55.000 0.00 0.00 0.00 4.06
2196 2639 2.103771 GGCTCTACATCCAGATGCAGAA 59.896 50.000 10.91 0.00 39.84 3.02
2338 2781 3.369892 CGGGTCAGGAGACAAGAAATCAT 60.370 47.826 0.00 0.00 46.80 2.45
2601 3044 0.674581 CAGAGATCAAGGCCGCAACA 60.675 55.000 0.00 0.00 0.00 3.33
2685 3128 0.183014 TTGACGGGGGCACAACTAAA 59.817 50.000 0.00 0.00 0.00 1.85
2955 3398 1.348036 GGGCTTCACTACCTTCACACT 59.652 52.381 0.00 0.00 0.00 3.55
3919 4395 3.503363 CACCACTGCTATGTGTTGTTGAT 59.497 43.478 0.00 0.00 36.30 2.57
4106 4646 3.513517 ACTACTAGTAACTGCCCCAACA 58.486 45.455 3.76 0.00 0.00 3.33
4125 4665 8.170061 CCCCAACATCTTATATTTAGGAATGGA 58.830 37.037 0.00 0.00 0.00 3.41
4324 4870 5.174398 CAGACAACATCAATTGTTTGTGAGC 59.826 40.000 20.17 10.88 46.51 4.26
4338 4894 6.980593 TGTTTGTGAGCTGTATTTAATTGCT 58.019 32.000 0.00 0.00 36.63 3.91
4390 4946 2.611292 GCAGCTGTCTAGGCATGTTTAG 59.389 50.000 16.64 0.00 0.00 1.85
4437 4993 5.130145 CCACTCTCCCTCTGTTATCTTGATT 59.870 44.000 0.00 0.00 0.00 2.57
4498 5054 2.736347 ACTAGGACGTTGTGAGGCTAT 58.264 47.619 0.00 0.00 0.00 2.97
4512 5068 1.001406 AGGCTATGCTTGATCGCTACC 59.999 52.381 0.00 0.00 0.00 3.18
4570 5126 5.639931 GGAATCGAATAAATCTAGCTCCCAC 59.360 44.000 0.00 0.00 0.00 4.61
4571 5127 6.426646 AATCGAATAAATCTAGCTCCCACT 57.573 37.500 0.00 0.00 0.00 4.00
4572 5128 5.455056 TCGAATAAATCTAGCTCCCACTC 57.545 43.478 0.00 0.00 0.00 3.51
4573 5129 4.281182 TCGAATAAATCTAGCTCCCACTCC 59.719 45.833 0.00 0.00 0.00 3.85
4574 5130 4.561734 CGAATAAATCTAGCTCCCACTCCC 60.562 50.000 0.00 0.00 0.00 4.30
4575 5131 2.270434 AAATCTAGCTCCCACTCCCA 57.730 50.000 0.00 0.00 0.00 4.37
4576 5132 1.799933 AATCTAGCTCCCACTCCCAG 58.200 55.000 0.00 0.00 0.00 4.45
4577 5133 0.762461 ATCTAGCTCCCACTCCCAGC 60.762 60.000 0.00 0.00 0.00 4.85
4578 5134 1.382420 CTAGCTCCCACTCCCAGCT 60.382 63.158 0.00 0.00 45.59 4.24
4579 5135 1.684386 CTAGCTCCCACTCCCAGCTG 61.684 65.000 6.78 6.78 43.49 4.24
4580 5136 2.461986 TAGCTCCCACTCCCAGCTGT 62.462 60.000 13.81 0.00 43.49 4.40
4581 5137 2.900106 GCTCCCACTCCCAGCTGTT 61.900 63.158 13.81 0.00 0.00 3.16
4582 5138 1.298014 CTCCCACTCCCAGCTGTTC 59.702 63.158 13.81 0.00 0.00 3.18
4583 5139 2.190488 CTCCCACTCCCAGCTGTTCC 62.190 65.000 13.81 0.00 0.00 3.62
4584 5140 2.046892 CCACTCCCAGCTGTTCCG 60.047 66.667 13.81 0.00 0.00 4.30
4585 5141 2.743928 CACTCCCAGCTGTTCCGC 60.744 66.667 13.81 0.00 0.00 5.54
4586 5142 4.021925 ACTCCCAGCTGTTCCGCC 62.022 66.667 13.81 0.00 0.00 6.13
4590 5146 4.069232 CCAGCTGTTCCGCCGAGA 62.069 66.667 13.81 0.00 0.00 4.04
4591 5147 2.507992 CAGCTGTTCCGCCGAGAG 60.508 66.667 5.25 0.00 0.00 3.20
4592 5148 2.676822 AGCTGTTCCGCCGAGAGA 60.677 61.111 0.00 0.00 0.00 3.10
4593 5149 2.261671 GCTGTTCCGCCGAGAGAA 59.738 61.111 0.00 0.00 0.00 2.87
4594 5150 1.153549 GCTGTTCCGCCGAGAGAAT 60.154 57.895 0.00 0.00 0.00 2.40
4595 5151 0.741221 GCTGTTCCGCCGAGAGAATT 60.741 55.000 0.00 0.00 0.00 2.17
4596 5152 1.470979 GCTGTTCCGCCGAGAGAATTA 60.471 52.381 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.156165 TCAAATCACCAAATAAGCCTCAAAATT 58.844 29.630 0.00 0.00 0.00 1.82
34 35 7.678837 TCAAATCACCAAATAAGCCTCAAAAT 58.321 30.769 0.00 0.00 0.00 1.82
39 40 7.771183 TGTATTCAAATCACCAAATAAGCCTC 58.229 34.615 0.00 0.00 0.00 4.70
81 83 0.108585 GCAGCGGGATCAGGGATAAA 59.891 55.000 0.00 0.00 0.00 1.40
82 84 1.053835 TGCAGCGGGATCAGGGATAA 61.054 55.000 0.00 0.00 0.00 1.75
83 85 0.837691 ATGCAGCGGGATCAGGGATA 60.838 55.000 0.00 0.00 0.00 2.59
280 414 3.319198 ACCAGAACGCGGTCCCAT 61.319 61.111 22.82 2.62 27.30 4.00
288 422 0.941542 TGTTGTTAGCACCAGAACGC 59.058 50.000 0.00 0.00 0.00 4.84
289 423 1.070843 CGTGTTGTTAGCACCAGAACG 60.071 52.381 0.00 0.00 33.61 3.95
479 859 0.668401 AAGCCTTTTCGGTACCGTCG 60.668 55.000 32.16 18.29 40.74 5.12
646 1026 2.016704 CGTGTGTCACTCTCGTGGC 61.017 63.158 4.27 0.00 45.85 5.01
800 1192 2.237392 CGTCAAGGAGGAAGAAGGGAAT 59.763 50.000 0.00 0.00 0.00 3.01
886 1300 3.849951 GGAGAATCGGCGGGCAGA 61.850 66.667 7.21 0.00 34.37 4.26
987 1403 1.079612 TCTCATGGTGCGAGCTGTG 60.080 57.895 0.00 0.00 0.00 3.66
1419 1862 3.240134 GAGGAGCGTGACCTTGGCA 62.240 63.158 0.00 0.00 37.93 4.92
1826 2269 0.249398 AGGGTAGGTGATTGCGACAC 59.751 55.000 0.00 0.00 37.51 3.67
1831 2274 2.489938 TTGTCAGGGTAGGTGATTGC 57.510 50.000 0.00 0.00 0.00 3.56
2012 2455 1.613255 CCCGCTGATTGGGTTTAGTGT 60.613 52.381 0.00 0.00 42.07 3.55
2013 2456 1.094785 CCCGCTGATTGGGTTTAGTG 58.905 55.000 0.00 0.00 42.07 2.74
2068 2511 2.014857 CTGGATCACATCAGCACCTTG 58.985 52.381 0.00 0.00 0.00 3.61
2196 2639 4.517285 CATCATAGTACTGTGGCTTGGTT 58.483 43.478 18.32 0.00 0.00 3.67
2338 2781 1.066716 ACCAACAATAGGCGCGACTAA 60.067 47.619 28.10 9.87 0.00 2.24
2418 2861 2.034066 TTGGCAGCTTTCCTCCGG 59.966 61.111 0.00 0.00 0.00 5.14
2685 3128 1.450312 GCCACGCTTGATAGCCACT 60.450 57.895 0.00 0.00 44.86 4.00
3015 3458 3.309296 TGAAACCTTGGCAACCCATTTA 58.691 40.909 0.00 0.00 41.78 1.40
3749 4200 0.940126 AGACAGCAAGAGCACAAACG 59.060 50.000 0.00 0.00 45.49 3.60
3919 4395 9.952030 TTTTCTCATACAGTATTACATGTTGGA 57.048 29.630 2.30 0.00 0.00 3.53
4075 4565 8.858094 GGGCAGTTACTAGTAGTACATATTTCT 58.142 37.037 9.62 0.00 28.93 2.52
4076 4566 8.087136 GGGGCAGTTACTAGTAGTACATATTTC 58.913 40.741 9.62 0.00 28.93 2.17
4079 4569 6.617538 TGGGGCAGTTACTAGTAGTACATAT 58.382 40.000 9.62 0.00 28.93 1.78
4096 4634 6.542821 TCCTAAATATAAGATGTTGGGGCAG 58.457 40.000 0.00 0.00 0.00 4.85
4097 4635 6.523035 TCCTAAATATAAGATGTTGGGGCA 57.477 37.500 0.00 0.00 0.00 5.36
4098 4636 7.093771 CCATTCCTAAATATAAGATGTTGGGGC 60.094 40.741 0.00 0.00 0.00 5.80
4125 4665 6.707290 TCAATAACACAAGCACATACTACCT 58.293 36.000 0.00 0.00 0.00 3.08
4366 4922 1.271543 ACATGCCTAGACAGCTGCAAA 60.272 47.619 15.27 0.00 37.27 3.68
4390 4946 5.153950 ACACTACTCTGGATCAAGAAACC 57.846 43.478 0.40 0.00 0.00 3.27
4437 4993 7.011109 GCTCTAGGTAAAGCAATCAAATAACGA 59.989 37.037 0.00 0.00 38.42 3.85
4498 5054 1.202417 GCTGTAGGTAGCGATCAAGCA 60.202 52.381 0.00 0.00 40.15 3.91
4512 5068 4.509756 AGATGCGCACAGCTGTAG 57.490 55.556 21.20 17.47 42.10 2.74
4573 5129 3.997064 CTCTCGGCGGAACAGCTGG 62.997 68.421 19.93 0.31 43.39 4.85
4574 5130 2.492449 TTCTCTCGGCGGAACAGCTG 62.492 60.000 13.48 13.48 44.50 4.24
4575 5131 1.608717 ATTCTCTCGGCGGAACAGCT 61.609 55.000 7.21 0.00 37.29 4.24
4576 5132 0.741221 AATTCTCTCGGCGGAACAGC 60.741 55.000 7.21 0.00 0.00 4.40
4577 5133 2.464865 CTAATTCTCTCGGCGGAACAG 58.535 52.381 7.21 0.00 0.00 3.16
4578 5134 1.470979 GCTAATTCTCTCGGCGGAACA 60.471 52.381 7.21 0.00 0.00 3.18
4579 5135 1.202428 AGCTAATTCTCTCGGCGGAAC 60.202 52.381 7.21 0.00 0.00 3.62
4580 5136 1.112113 AGCTAATTCTCTCGGCGGAA 58.888 50.000 7.21 2.87 0.00 4.30
4581 5137 1.067212 GAAGCTAATTCTCTCGGCGGA 59.933 52.381 7.21 2.06 34.86 5.54
4582 5138 1.492720 GAAGCTAATTCTCTCGGCGG 58.507 55.000 7.21 0.00 34.86 6.13
4583 5139 1.067821 AGGAAGCTAATTCTCTCGGCG 59.932 52.381 0.00 0.00 38.07 6.46
4584 5140 2.159028 ACAGGAAGCTAATTCTCTCGGC 60.159 50.000 0.00 0.00 38.07 5.54
4585 5141 3.118956 ACACAGGAAGCTAATTCTCTCGG 60.119 47.826 0.00 0.00 38.07 4.63
4586 5142 4.109050 GACACAGGAAGCTAATTCTCTCG 58.891 47.826 0.00 0.00 38.07 4.04
4587 5143 4.081420 TGGACACAGGAAGCTAATTCTCTC 60.081 45.833 0.00 0.00 38.07 3.20
4588 5144 3.840666 TGGACACAGGAAGCTAATTCTCT 59.159 43.478 0.00 0.00 38.07 3.10
4589 5145 4.187694 CTGGACACAGGAAGCTAATTCTC 58.812 47.826 0.00 0.00 41.13 2.87
4590 5146 4.213564 CTGGACACAGGAAGCTAATTCT 57.786 45.455 0.00 0.00 41.13 2.40


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

AutoCloner maintained by Alex Coulton.