Multiple sequence alignment - TraesCS7D01G501900

Loading Multiple Alignment...

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 TraesCS7D01G501900 chr7D 100.000 6842 0 0 1 6842 607565951 607572792 0 12635
1 TraesCS7D01G501900 chr7D 96.366 3550 116 8 3298 6842 54982502 54978961 0 5829
2 TraesCS7D01G501900 chr4D 96.594 3905 117 10 2951 6842 65866350 65870251 0 6460
3 TraesCS7D01G501900 chr4D 95.455 2970 106 25 1 2953 65863425 65866382 0 4710
4 TraesCS7D01G501900 chr3D 96.611 3895 121 7 2951 6841 175412138 175416025 0 6451
5 TraesCS7D01G501900 chr3D 92.587 3912 251 21 2951 6842 610716742 610712850 0 5581
6 TraesCS7D01G501900 chr1D 96.543 3905 116 10 2951 6842 10794165 10798063 0 6445
7 TraesCS7D01G501900 chr1D 96.414 2956 87 17 1 2953 466333237 466336176 0 4854
8 TraesCS7D01G501900 chr1D 96.023 2967 92 24 1 2953 108776439 108779393 0 4802
9 TraesCS7D01G501900 chr1D 95.387 2970 109 25 1 2953 10791239 10794197 0 4700
10 TraesCS7D01G501900 chr5B 95.638 3897 149 10 2951 6842 12566192 12562312 0 6235
11 TraesCS7D01G501900 chrUn 95.128 3900 167 13 2951 6842 52483389 52479505 0 6128
12 TraesCS7D01G501900 chr6A 94.190 3907 199 22 2951 6842 572219024 572222917 0 5932
13 TraesCS7D01G501900 chr7B 94.008 3905 208 15 2951 6842 475376056 475372165 0 5891
14 TraesCS7D01G501900 chr7B 93.878 2973 151 21 1 2953 709379342 709382303 0 4453
15 TraesCS7D01G501900 chr5A 96.049 2961 101 16 1 2953 49879131 49882083 0 4806
16 TraesCS7D01G501900 chr6D 95.198 2957 121 17 1 2953 118583247 118586186 0 4654
17 TraesCS7D01G501900 chr4A 93.206 2973 170 28 1 2953 740386402 740389362 0 4342
18 TraesCS7D01G501900 chr6B 92.898 2971 178 29 1 2953 599665557 599668512 0 4287
19 TraesCS7D01G501900 chr2A 92.253 2672 144 23 2951 5583 58491578 58494225 0 3729


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 TraesCS7D01G501900 chr7D 607565951 607572792 6841 False 12635.0 12635 100.0000 1 6842 1 chr7D.!!$F1 6841
1 TraesCS7D01G501900 chr7D 54978961 54982502 3541 True 5829.0 5829 96.3660 3298 6842 1 chr7D.!!$R1 3544
2 TraesCS7D01G501900 chr4D 65863425 65870251 6826 False 5585.0 6460 96.0245 1 6842 2 chr4D.!!$F1 6841
3 TraesCS7D01G501900 chr3D 175412138 175416025 3887 False 6451.0 6451 96.6110 2951 6841 1 chr3D.!!$F1 3890
4 TraesCS7D01G501900 chr3D 610712850 610716742 3892 True 5581.0 5581 92.5870 2951 6842 1 chr3D.!!$R1 3891
5 TraesCS7D01G501900 chr1D 10791239 10798063 6824 False 5572.5 6445 95.9650 1 6842 2 chr1D.!!$F3 6841
6 TraesCS7D01G501900 chr1D 466333237 466336176 2939 False 4854.0 4854 96.4140 1 2953 1 chr1D.!!$F2 2952
7 TraesCS7D01G501900 chr1D 108776439 108779393 2954 False 4802.0 4802 96.0230 1 2953 1 chr1D.!!$F1 2952
8 TraesCS7D01G501900 chr5B 12562312 12566192 3880 True 6235.0 6235 95.6380 2951 6842 1 chr5B.!!$R1 3891
9 TraesCS7D01G501900 chrUn 52479505 52483389 3884 True 6128.0 6128 95.1280 2951 6842 1 chrUn.!!$R1 3891
10 TraesCS7D01G501900 chr6A 572219024 572222917 3893 False 5932.0 5932 94.1900 2951 6842 1 chr6A.!!$F1 3891
11 TraesCS7D01G501900 chr7B 475372165 475376056 3891 True 5891.0 5891 94.0080 2951 6842 1 chr7B.!!$R1 3891
12 TraesCS7D01G501900 chr7B 709379342 709382303 2961 False 4453.0 4453 93.8780 1 2953 1 chr7B.!!$F1 2952
13 TraesCS7D01G501900 chr5A 49879131 49882083 2952 False 4806.0 4806 96.0490 1 2953 1 chr5A.!!$F1 2952
14 TraesCS7D01G501900 chr6D 118583247 118586186 2939 False 4654.0 4654 95.1980 1 2953 1 chr6D.!!$F1 2952
15 TraesCS7D01G501900 chr4A 740386402 740389362 2960 False 4342.0 4342 93.2060 1 2953 1 chr4A.!!$F1 2952
16 TraesCS7D01G501900 chr6B 599665557 599668512 2955 False 4287.0 4287 92.8980 1 2953 1 chr6B.!!$F1 2952
17 TraesCS7D01G501900 chr2A 58491578 58494225 2647 False 3729.0 3729 92.2530 2951 5583 1 chr2A.!!$F1 2632

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
35 36 0.038067 TGTGTGCAATGCATTGGCTC 60.038 50.000 34.23 25.93 41.91 4.70 F
336 355 1.555075 GTGTGCATCCAGGGACTCTTA 59.445 52.381 0.00 0.00 34.60 2.10 F
1872 1937 0.947244 GTTGCACACTGGGAGTCTTG 59.053 55.000 0.00 0.00 0.00 3.02 F
2581 2655 0.183492 TGAAGCTCAGCCCAAAGTGT 59.817 50.000 0.00 0.00 0.00 3.55 F
3470 3565 1.475034 GGAGCAGACACCACTGTTTGA 60.475 52.381 0.00 0.00 34.99 2.69 F
4385 4551 1.230281 TGAGGCCAAAGAGGGGGAT 60.230 57.895 5.01 0.00 38.09 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1204 1.289066 CAGGACGCTTCGAGTTCCA 59.711 57.895 6.49 0.00 0.00 3.53 R
2058 2129 0.393077 CACCTCAACTCCTTCACCGT 59.607 55.000 0.00 0.00 0.00 4.83 R
2972 3051 0.394488 TTTGCCGAACACACCAGGAA 60.394 50.000 0.00 0.00 0.00 3.36 R
4385 4551 0.251297 CTGATGCACCTTTGTCCCCA 60.251 55.000 0.00 0.00 0.00 4.96 R
4528 4694 0.386838 ATCATCATCGCAGCTGTCGA 59.613 50.000 27.06 27.06 40.45 4.20 R
6067 6248 0.108898 CCTCCTCTGTCTTCGTGCAG 60.109 60.000 0.00 0.00 0.00 4.41 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
35 36 0.038067 TGTGTGCAATGCATTGGCTC 60.038 50.000 34.23 25.93 41.91 4.70
116 128 3.005472 GGCTGCGTCCATATAGTACTTGA 59.995 47.826 0.00 0.00 0.00 3.02
254 268 6.515035 GCATCACTTTTACTAGTTGGCTGTTT 60.515 38.462 0.00 0.00 0.00 2.83
336 355 1.555075 GTGTGCATCCAGGGACTCTTA 59.445 52.381 0.00 0.00 34.60 2.10
544 566 3.112580 GTTGTGGATGTGGTTGTTTTCG 58.887 45.455 0.00 0.00 0.00 3.46
563 587 1.813862 CGTGTGTTTCCCCTCATGTGT 60.814 52.381 0.00 0.00 0.00 3.72
564 588 1.608590 GTGTGTTTCCCCTCATGTGTG 59.391 52.381 0.00 0.00 0.00 3.82
700 729 6.936900 AGTTTGCACAAGTTATCATACTGAGT 59.063 34.615 0.00 0.00 0.00 3.41
1084 1119 8.600449 TTCTGTGTTTTTGAGTTGTTTTCAAT 57.400 26.923 0.00 0.00 42.08 2.57
1165 1204 1.080434 GGAAGTCAGTCGCTTCGCT 60.080 57.895 0.00 0.00 42.23 4.93
1411 1456 2.244486 AGGGAGCTGAGTCATCTTCA 57.756 50.000 4.69 0.00 0.00 3.02
1426 1472 9.886132 GAGTCATCTTCAAGGGTAAGTAAATTA 57.114 33.333 0.00 0.00 0.00 1.40
1625 1675 8.408601 GTTGGCATCTTTTATAGTTGACATCAT 58.591 33.333 0.00 0.00 40.45 2.45
1702 1752 1.813092 GCAGATGCTGAGGTATGTGGG 60.813 57.143 0.00 0.00 38.21 4.61
1708 1762 4.374689 TGCTGAGGTATGTGGGTTTTTA 57.625 40.909 0.00 0.00 0.00 1.52
1738 1793 9.162764 GTTTATGAGCTATTGAACAGTTCCTTA 57.837 33.333 10.93 2.03 0.00 2.69
1777 1835 8.574251 AGTTGGTGTTATCTTGTTGCAATATA 57.426 30.769 0.59 0.00 0.00 0.86
1865 1929 1.110442 TTTGAAGGTTGCACACTGGG 58.890 50.000 0.00 0.00 0.00 4.45
1872 1937 0.947244 GTTGCACACTGGGAGTCTTG 59.053 55.000 0.00 0.00 0.00 3.02
1881 1946 1.071385 CTGGGAGTCTTGCAGTTGTCT 59.929 52.381 0.00 0.00 0.00 3.41
2058 2129 8.686334 GTTTTTATCTTCTCATCAATAGGCCAA 58.314 33.333 5.01 0.00 0.00 4.52
2247 2320 1.079543 CACTTCCAGCGGACCTCAG 60.080 63.158 0.00 0.00 0.00 3.35
2377 2450 2.364972 ACAGGGGTCAAAAAGTCAGG 57.635 50.000 0.00 0.00 0.00 3.86
2554 2628 1.873591 AGCACTTTTCTAGCACCAACG 59.126 47.619 0.00 0.00 0.00 4.10
2559 2633 0.390124 TTTCTAGCACCAACGACGGT 59.610 50.000 0.00 0.00 41.07 4.83
2581 2655 0.183492 TGAAGCTCAGCCCAAAGTGT 59.817 50.000 0.00 0.00 0.00 3.55
2628 2702 6.882610 AATGCTCAAGAACACAAACATCTA 57.117 33.333 0.00 0.00 0.00 1.98
2741 2815 4.345859 AGTGAAAACGACCACTTCCATA 57.654 40.909 0.00 0.00 40.40 2.74
2847 2926 5.279708 GGTGCAGATACTATACCTTGATGCT 60.280 44.000 0.00 0.00 32.53 3.79
3007 3086 5.543714 TCGGCAAATTACAAGTGAGTTCTA 58.456 37.500 0.00 0.00 0.00 2.10
3147 3233 6.265422 ACTTGTAGCTTTAAGTTTGGCATCTT 59.735 34.615 8.90 9.66 33.59 2.40
3405 3499 8.194769 TCTGTTTTGATAACCTTGTTCTTTTCC 58.805 33.333 0.00 0.00 0.00 3.13
3470 3565 1.475034 GGAGCAGACACCACTGTTTGA 60.475 52.381 0.00 0.00 34.99 2.69
3480 3575 6.549364 AGACACCACTGTTTGATGGAATTTTA 59.451 34.615 0.00 0.00 39.46 1.52
3690 3790 8.258007 AGTTGCACATATAAGCTTCTGTAGTTA 58.742 33.333 0.00 0.00 0.00 2.24
3837 3941 3.982058 CAGAAAGTGTGTCTTAGTCGGTC 59.018 47.826 0.00 0.00 35.02 4.79
4117 4229 2.271944 AAAAGAAAGAGACGGGGGTG 57.728 50.000 0.00 0.00 0.00 4.61
4385 4551 1.230281 TGAGGCCAAAGAGGGGGAT 60.230 57.895 5.01 0.00 38.09 3.85
4528 4694 1.733387 GGGGGATCCAATGGAGGCAT 61.733 60.000 15.23 0.00 34.05 4.40
4831 5003 2.315925 AGCGACCAAGATATGTGTGG 57.684 50.000 0.00 0.00 38.46 4.17
4911 5084 4.346730 TCAAATTGACATGGAGGAAGCAT 58.653 39.130 0.00 0.00 0.00 3.79
4939 5112 4.082125 GGTCTTGACTGGGTTCATTCAAT 58.918 43.478 0.61 0.00 40.27 2.57
4941 5114 4.761739 GTCTTGACTGGGTTCATTCAATGA 59.238 41.667 0.00 0.00 40.27 2.57
5209 5382 4.104738 AGTTCAACAGATCAAGGGGAAGAA 59.895 41.667 0.00 0.00 0.00 2.52
5325 5499 3.020984 GGGTTCAGAGACGAGAGAGAAT 58.979 50.000 0.00 0.00 0.00 2.40
5369 5543 0.324943 GGGTGCCAAGTTCTGCTAGA 59.675 55.000 0.00 0.00 0.00 2.43
5572 5746 1.547372 TCCTACTACCAAAGTGCCGTC 59.453 52.381 0.00 0.00 39.39 4.79
5589 5764 0.543749 GTCCCCAAGAGCTAGCACAT 59.456 55.000 18.83 0.00 0.00 3.21
5698 5873 1.002624 CTCCAAGGCCGCCAACTAA 60.003 57.895 13.15 0.00 0.00 2.24
6067 6248 1.192803 AGTTCTTCGGGACCACCTCC 61.193 60.000 0.00 0.00 38.55 4.30
6151 6332 6.103997 ACTACAACAAGAAGAAGACGTTCAA 58.896 36.000 0.00 0.00 34.82 2.69
6279 6461 9.686683 AGCCTACATACATATCTTTTTCAGTTT 57.313 29.630 0.00 0.00 0.00 2.66
6400 6585 1.301716 GCTGCTGTGACCCTTCGAA 60.302 57.895 0.00 0.00 0.00 3.71
6408 6593 4.377897 CTGTGACCCTTCGAACTAACTTT 58.622 43.478 0.00 0.00 0.00 2.66
6536 6726 7.495901 TGGCTGTCAAAAATTGTTATTGAGAA 58.504 30.769 0.00 0.00 34.02 2.87
6611 6801 3.892284 TGCCACTGAGGTTTTCTGTAAA 58.108 40.909 0.00 0.00 40.61 2.01
6747 6940 5.163478 GCAGATGAATTTACAGCAAGGGATT 60.163 40.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.202663 AGCCAATGCATTGCACACAAA 60.203 42.857 30.15 0.00 43.04 2.83
35 36 6.618287 TCTCTGAACACCAACTACAAAATG 57.382 37.500 0.00 0.00 0.00 2.32
116 128 3.572632 ACTGCAGAGCATATGGACAAT 57.427 42.857 23.35 0.00 38.13 2.71
254 268 7.115805 GCAACTAGCGCAAGTGTATAACATATA 59.884 37.037 11.47 0.00 41.68 0.86
323 341 6.636454 ATTACACAAATAAGAGTCCCTGGA 57.364 37.500 0.00 0.00 0.00 3.86
325 343 8.398665 GCTAAATTACACAAATAAGAGTCCCTG 58.601 37.037 0.00 0.00 0.00 4.45
544 566 1.608590 CACACATGAGGGGAAACACAC 59.391 52.381 0.00 0.00 34.58 3.82
563 587 3.343941 AAATAAGCGTCCCTAGTTGCA 57.656 42.857 0.00 0.00 0.00 4.08
564 588 4.696899 AAAAATAAGCGTCCCTAGTTGC 57.303 40.909 0.00 0.00 0.00 4.17
1165 1204 1.289066 CAGGACGCTTCGAGTTCCA 59.711 57.895 6.49 0.00 0.00 3.53
1201 1240 1.300931 GCTCAACACTCCGTGCAGA 60.301 57.895 0.00 0.00 36.98 4.26
1349 1394 2.572173 CGCTTTACAACACGGAACTC 57.428 50.000 0.00 0.00 0.00 3.01
1565 1615 2.756760 AGATGCCAACTAATGCCAACTG 59.243 45.455 0.00 0.00 0.00 3.16
1708 1762 7.928307 ACTGTTCAATAGCTCATAAACACAT 57.072 32.000 0.00 0.00 0.00 3.21
1798 1856 4.884744 TGGCAACTACAAAAAGTTCTAGCA 59.115 37.500 0.00 0.00 37.61 3.49
1865 1929 4.060900 TCATGAAGACAACTGCAAGACTC 58.939 43.478 0.00 0.00 35.05 3.36
1872 1937 3.911661 AAAGCTCATGAAGACAACTGC 57.088 42.857 0.00 0.00 0.00 4.40
1881 1946 6.816134 TGTGCAACTAATAAAGCTCATGAA 57.184 33.333 0.00 0.00 38.04 2.57
2058 2129 0.393077 CACCTCAACTCCTTCACCGT 59.607 55.000 0.00 0.00 0.00 4.83
2247 2320 1.348036 AGGACTGCACCAGGAACTTAC 59.652 52.381 0.00 0.00 34.60 2.34
2377 2450 5.648092 AGTGGCATCCTTGTCAACTAAATAC 59.352 40.000 0.00 0.00 39.65 1.89
2554 2628 1.016653 GGCTGAGCTTCAAGACCGTC 61.017 60.000 3.72 0.00 0.00 4.79
2559 2633 1.143684 ACTTTGGGCTGAGCTTCAAGA 59.856 47.619 3.72 1.29 0.00 3.02
2581 2655 4.401202 TGATGATCTAGCACAAGTCCGTAA 59.599 41.667 0.00 0.00 0.00 3.18
2628 2702 3.838244 TGTGTTCTGCTACAAAGAGGT 57.162 42.857 0.00 0.00 0.00 3.85
2741 2815 5.329035 ACTGCACAAAAGAACAAGAACAT 57.671 34.783 0.00 0.00 0.00 2.71
2847 2926 2.735151 ACTGGGATGTCATGTACGAGA 58.265 47.619 0.00 0.00 0.00 4.04
2972 3051 0.394488 TTTGCCGAACACACCAGGAA 60.394 50.000 0.00 0.00 0.00 3.36
3147 3233 6.988580 TGCCAATTTAAAATGAACATGTGTGA 59.011 30.769 0.00 0.00 0.00 3.58
3470 3565 5.726980 TGCTTCAGCTTGTAAAATTCCAT 57.273 34.783 0.00 0.00 42.66 3.41
3480 3575 0.877071 CCACGAATGCTTCAGCTTGT 59.123 50.000 0.00 0.00 42.66 3.16
3690 3790 4.269183 TGACTGTCCAAAAGAACATGTGT 58.731 39.130 0.00 0.00 0.00 3.72
3837 3941 5.356190 ACTGACCATGATGTGATAAGCAAAG 59.644 40.000 0.00 0.00 0.00 2.77
4385 4551 0.251297 CTGATGCACCTTTGTCCCCA 60.251 55.000 0.00 0.00 0.00 4.96
4528 4694 0.386838 ATCATCATCGCAGCTGTCGA 59.613 50.000 27.06 27.06 40.45 4.20
4628 4800 4.516323 TGCTACTCAATGAATTGCTGCTA 58.484 39.130 0.00 0.00 37.68 3.49
4831 5003 4.022068 TGTCAATGGCAAAGTTGATCTTCC 60.022 41.667 5.40 0.00 36.79 3.46
4911 5084 1.518367 ACCCAGTCAAGACCCTTTCA 58.482 50.000 0.00 0.00 0.00 2.69
5043 5216 7.463961 ACTGCAGATTCTTCTTCATTGAAAT 57.536 32.000 23.35 0.00 0.00 2.17
5209 5382 1.075536 GTGGGACTGTTGAAAGGGGAT 59.924 52.381 0.00 0.00 0.00 3.85
5369 5543 1.531423 CAGTCTGAGTTGGCAGCAAT 58.469 50.000 3.63 0.00 35.86 3.56
5572 5746 2.540265 CTATGTGCTAGCTCTTGGGG 57.460 55.000 17.23 2.75 0.00 4.96
5589 5764 2.759114 AGGCTTGCTTGGCTGCTA 59.241 55.556 0.00 0.00 41.44 3.49
5698 5873 3.880490 TGACTTGGTTCGCAATAGTGTTT 59.120 39.130 0.00 0.00 0.00 2.83
5760 5935 2.193127 TCGTATGGGTTCAAGGACCAT 58.807 47.619 0.00 0.00 46.21 3.55
6067 6248 0.108898 CCTCCTCTGTCTTCGTGCAG 60.109 60.000 0.00 0.00 0.00 4.41
6151 6332 1.421268 TGTTCACTGCCTCATTGGAGT 59.579 47.619 0.00 0.00 39.64 3.85
6186 6367 2.380064 TGCCTGACCCAAAACAAGAT 57.620 45.000 0.00 0.00 0.00 2.40
6193 6374 4.841441 GGTGATGCCTGACCCAAA 57.159 55.556 0.00 0.00 0.00 3.28
6279 6461 0.976641 CTAAGTGGCTGGTCCTGTGA 59.023 55.000 0.00 0.00 35.26 3.58
6536 6726 8.443176 AGTTATCCATGATGTGTAAGATTCCAT 58.557 33.333 0.00 0.00 0.00 3.41
6611 6801 7.126573 TGAGGGTAAAGAAGGTTTTGGAAAAAT 59.873 33.333 0.00 0.00 0.00 1.82
6747 6940 6.704050 TCTTGTTTATCTCATTCACGTTGTGA 59.296 34.615 0.00 0.00 41.09 3.58


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

AutoCloner maintained by Alex Coulton.