Multiple sequence alignment - TraesCS5D01G077500

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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 TraesCS5D01G077500 chr5D 100.000 2372 0 0 1 2372 77199606 77197235 0 4381
1 TraesCS5D01G077500 chr5D 97.175 991 24 4 902 1889 483803401 483804390 0 1672
2 TraesCS5D01G077500 chr5D 88.209 899 106 0 2 900 341795558 341796456 0 1074
3 TraesCS5D01G077500 chr2D 97.376 991 22 4 902 1889 359630519 359631508 0 1683
4 TraesCS5D01G077500 chr2D 97.273 990 23 4 902 1889 643857716 643856729 0 1676
5 TraesCS5D01G077500 chr2D 96.875 992 26 5 902 1889 628292134 628293124 0 1655
6 TraesCS5D01G077500 chr2D 88.222 900 105 1 1 900 49542713 49543611 0 1074
7 TraesCS5D01G077500 chr2D 93.542 480 30 1 1894 2372 49543618 49544097 0 713
8 TraesCS5D01G077500 chr2B 96.266 991 33 4 902 1889 474939226 474938237 0 1622
9 TraesCS5D01G077500 chr3B 96.429 980 32 3 902 1879 201497377 201496399 0 1613
10 TraesCS5D01G077500 chr3B 88.568 901 98 4 1 899 243842575 243841678 0 1088
11 TraesCS5D01G077500 chr1D 96.069 992 31 7 902 1889 254481353 254480366 0 1609
12 TraesCS5D01G077500 chr1D 93.333 480 31 1 1894 2372 76309067 76308588 0 708
13 TraesCS5D01G077500 chr4A 94.758 992 46 6 902 1889 309271654 309272643 0 1539
14 TraesCS5D01G077500 chr3D 94.848 990 41 5 902 1889 451862884 451863865 0 1537
15 TraesCS5D01G077500 chr3D 91.753 485 38 2 1889 2372 546035887 546036370 0 673
16 TraesCS5D01G077500 chr7B 90.817 893 82 0 2 894 625419784 625420676 0 1195
17 TraesCS5D01G077500 chr7D 89.655 899 93 0 2 900 161315577 161316475 0 1146
18 TraesCS5D01G077500 chr7D 92.500 480 35 1 1894 2372 271669069 271668590 0 686
19 TraesCS5D01G077500 chr7D 92.500 480 35 1 1894 2372 526562308 526562787 0 686
20 TraesCS5D01G077500 chr7D 92.292 480 36 1 1894 2372 488750954 488750475 0 680
21 TraesCS5D01G077500 chr4B 89.000 900 97 2 2 900 235587807 235586909 0 1112
22 TraesCS5D01G077500 chr4B 88.939 895 96 3 2 894 189873805 189874698 0 1101
23 TraesCS5D01G077500 chr6D 88.778 900 101 0 1 900 348696158 348695259 0 1103
24 TraesCS5D01G077500 chr6D 92.708 480 34 1 1894 2372 280933434 280933913 0 691
25 TraesCS5D01G077500 chr5B 88.235 901 104 2 1 900 212713403 212714302 0 1075
26 TraesCS5D01G077500 chr4D 92.708 480 33 2 1894 2372 106751147 106751625 0 691
27 TraesCS5D01G077500 chr4D 92.292 480 36 1 1894 2372 289664056 289663577 0 680


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 TraesCS5D01G077500 chr5D 77197235 77199606 2371 True 4381.0 4381 100.000 1 2372 1 chr5D.!!$R1 2371
1 TraesCS5D01G077500 chr5D 483803401 483804390 989 False 1672.0 1672 97.175 902 1889 1 chr5D.!!$F2 987
2 TraesCS5D01G077500 chr5D 341795558 341796456 898 False 1074.0 1074 88.209 2 900 1 chr5D.!!$F1 898
3 TraesCS5D01G077500 chr2D 359630519 359631508 989 False 1683.0 1683 97.376 902 1889 1 chr2D.!!$F1 987
4 TraesCS5D01G077500 chr2D 643856729 643857716 987 True 1676.0 1676 97.273 902 1889 1 chr2D.!!$R1 987
5 TraesCS5D01G077500 chr2D 628292134 628293124 990 False 1655.0 1655 96.875 902 1889 1 chr2D.!!$F2 987
6 TraesCS5D01G077500 chr2D 49542713 49544097 1384 False 893.5 1074 90.882 1 2372 2 chr2D.!!$F3 2371
7 TraesCS5D01G077500 chr2B 474938237 474939226 989 True 1622.0 1622 96.266 902 1889 1 chr2B.!!$R1 987
8 TraesCS5D01G077500 chr3B 201496399 201497377 978 True 1613.0 1613 96.429 902 1879 1 chr3B.!!$R1 977
9 TraesCS5D01G077500 chr3B 243841678 243842575 897 True 1088.0 1088 88.568 1 899 1 chr3B.!!$R2 898
10 TraesCS5D01G077500 chr1D 254480366 254481353 987 True 1609.0 1609 96.069 902 1889 1 chr1D.!!$R2 987
11 TraesCS5D01G077500 chr4A 309271654 309272643 989 False 1539.0 1539 94.758 902 1889 1 chr4A.!!$F1 987
12 TraesCS5D01G077500 chr3D 451862884 451863865 981 False 1537.0 1537 94.848 902 1889 1 chr3D.!!$F1 987
13 TraesCS5D01G077500 chr7B 625419784 625420676 892 False 1195.0 1195 90.817 2 894 1 chr7B.!!$F1 892
14 TraesCS5D01G077500 chr7D 161315577 161316475 898 False 1146.0 1146 89.655 2 900 1 chr7D.!!$F1 898
15 TraesCS5D01G077500 chr4B 235586909 235587807 898 True 1112.0 1112 89.000 2 900 1 chr4B.!!$R1 898
16 TraesCS5D01G077500 chr4B 189873805 189874698 893 False 1101.0 1101 88.939 2 894 1 chr4B.!!$F1 892
17 TraesCS5D01G077500 chr6D 348695259 348696158 899 True 1103.0 1103 88.778 1 900 1 chr6D.!!$R1 899
18 TraesCS5D01G077500 chr5B 212713403 212714302 899 False 1075.0 1075 88.235 1 900 1 chr5B.!!$F1 899

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
204 206 0.033366 GTGGCGGCTCAAATTTTGGT 59.967 50.0 11.43 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2101 0.042967 GAGCGCGCTTTCCTATTTCG 60.043 55.0 36.87 0.0 0.0 3.46 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
95 96 7.500227 TCATCTATGGAAGGATTGTTTCATCAC 59.500 37.037 0.00 0.00 0.00 3.06
108 109 4.954202 TGTTTCATCACGAGGGAGTATAGT 59.046 41.667 0.00 0.00 0.00 2.12
200 202 1.250840 GGAGGTGGCGGCTCAAATTT 61.251 55.000 11.43 0.00 0.00 1.82
204 206 0.033366 GTGGCGGCTCAAATTTTGGT 59.967 50.000 11.43 0.00 0.00 3.67
342 345 3.181505 TGTTTACCACGAGTTTGTGCAAG 60.182 43.478 0.00 0.00 38.55 4.01
377 380 1.139256 TCATAAGCGGGCGGTGAATTA 59.861 47.619 0.00 0.00 0.00 1.40
426 429 2.548920 GCGATGGTCTAAGCAGCCTATT 60.549 50.000 0.00 0.00 0.00 1.73
434 437 5.454755 GGTCTAAGCAGCCTATTGTATGGAA 60.455 44.000 0.00 0.00 0.00 3.53
442 445 3.181469 GCCTATTGTATGGAACCGTGAGA 60.181 47.826 0.00 0.00 0.00 3.27
483 486 0.988832 ATCCGGGTCAGTTGGCTTTA 59.011 50.000 0.00 0.00 0.00 1.85
484 487 0.988832 TCCGGGTCAGTTGGCTTTAT 59.011 50.000 0.00 0.00 0.00 1.40
492 495 2.030363 TCAGTTGGCTTTATTGGTTGCG 60.030 45.455 0.00 0.00 0.00 4.85
543 546 0.179009 TGCTTATGGATGGAGGCAGC 60.179 55.000 0.00 0.00 0.00 5.25
617 620 8.740906 TGACAAAGATCTTAAGTCGTCTTCTAT 58.259 33.333 24.42 8.42 35.36 1.98
650 653 0.396811 GTGGTGCCTGGTAAGTCAGT 59.603 55.000 0.00 0.00 33.14 3.41
700 703 1.643832 GCTTTCGGCGATGACCATC 59.356 57.895 11.76 0.04 34.56 3.51
804 807 2.923020 CAAATTTATGGCACGACCTTGC 59.077 45.455 0.00 0.00 42.18 4.01
879 882 5.475220 GCACAGTGATAGGAAGATAGCTCTA 59.525 44.000 4.15 0.00 0.00 2.43
1014 1022 8.463930 TTGTGATAATTATGAGAACCAATCCC 57.536 34.615 1.78 0.00 0.00 3.85
1086 1094 6.645415 GTCGTATCGATCAAATTATTGGACCT 59.355 38.462 0.00 0.00 38.42 3.85
1162 1170 4.781621 TGGTAGTCCAGAGTAGAGACACTA 59.218 45.833 0.00 0.00 39.03 2.74
1180 1188 8.732746 AGACACTACCGATAAGCAAATTAATT 57.267 30.769 0.00 0.00 0.00 1.40
1264 1272 1.134965 CAGACGGGTTGATGAGAGGAC 60.135 57.143 0.00 0.00 0.00 3.85
1306 1314 0.178973 TCCTCTCAGTGTTCCGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
1311 1319 1.046472 TCAGTGTTCCGGTCAGTGGT 61.046 55.000 24.93 3.82 37.01 4.16
1338 1347 3.060138 TCTCGGACGAATTTTCAACGTTG 60.060 43.478 22.35 22.35 40.29 4.10
1483 1493 4.734370 GTCGTCGATCTTTTAGCTCCTTAC 59.266 45.833 0.00 0.00 0.00 2.34
1614 1625 1.328430 GGTGGAGTAGGGGAACGGAG 61.328 65.000 0.00 0.00 0.00 4.63
1670 1681 8.050325 TGAAGGAATCCGGAGTAATTAATGAAA 58.950 33.333 11.34 0.00 0.00 2.69
1856 1867 3.921104 TCAAGCAGGATCAGAGGTATCT 58.079 45.455 0.00 0.00 35.63 1.98
1912 1923 1.401552 GTGCTGAGTCTGTTTGTGCAA 59.598 47.619 0.00 0.00 0.00 4.08
1957 1969 2.332063 AATGTTGACCCGGCAGATAG 57.668 50.000 0.00 0.00 0.00 2.08
1962 1974 0.616395 TGACCCGGCAGATAGGACAA 60.616 55.000 0.00 0.00 0.00 3.18
1970 1982 3.372206 CGGCAGATAGGACAACTTTGAAG 59.628 47.826 0.00 0.00 0.00 3.02
1973 1985 5.123027 GGCAGATAGGACAACTTTGAAGAAG 59.877 44.000 0.00 0.00 0.00 2.85
1988 2000 2.758736 AGAAGCCAACTACAGAGCAG 57.241 50.000 0.00 0.00 0.00 4.24
2003 2015 0.111253 AGCAGGACCCCTTGTTGAAG 59.889 55.000 0.00 0.00 0.00 3.02
2021 2033 4.832248 TGAAGTTTAAGTCGGCAGATGAT 58.168 39.130 0.00 0.00 0.00 2.45
2030 2042 3.005261 AGTCGGCAGATGATACTAAGCTG 59.995 47.826 0.00 0.00 0.00 4.24
2031 2043 2.959030 TCGGCAGATGATACTAAGCTGT 59.041 45.455 0.00 0.00 0.00 4.40
2040 2052 8.173775 CAGATGATACTAAGCTGTTTGACTTTG 58.826 37.037 0.00 0.00 0.00 2.77
2048 2060 2.799562 GCTGTTTGACTTTGTTCCTGGC 60.800 50.000 0.00 0.00 0.00 4.85
2061 2073 0.464373 TCCTGGCGATTCATCCAAGC 60.464 55.000 0.00 0.00 30.98 4.01
2072 2084 2.799017 TCATCCAAGCAGTTCAGCATT 58.201 42.857 0.00 0.00 36.85 3.56
2129 2141 3.381590 TCATCGAGTTCATCCGTGAGAAT 59.618 43.478 0.00 0.00 35.39 2.40
2131 2143 4.976224 TCGAGTTCATCCGTGAGAATTA 57.024 40.909 0.00 0.00 35.39 1.40
2157 2169 4.021719 ACATCTTTGCATGGAAACCTTCTG 60.022 41.667 8.47 4.85 0.00 3.02
2212 2224 7.828717 TGAGCATACTCTTAATGTTGATCCAAA 59.171 33.333 0.00 0.00 43.85 3.28
2213 2225 8.579850 AGCATACTCTTAATGTTGATCCAAAA 57.420 30.769 0.00 0.00 0.00 2.44
2240 2252 2.224523 ACCAGTCAAGCAATTCCTTCGA 60.225 45.455 0.00 0.00 0.00 3.71
2248 2260 5.007823 TCAAGCAATTCCTTCGACGTTTTAA 59.992 36.000 0.00 0.00 0.00 1.52
2310 2322 0.179020 CTTGGCGGCTGGGATTATCA 60.179 55.000 11.43 0.00 0.00 2.15
2342 2354 2.846206 TCATCCTGAGTGGTTGGCTAAT 59.154 45.455 0.00 0.00 36.44 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.739067 GGCTTCTCTTACGTGCCATT 58.261 50.000 0.00 0.00 42.79 3.16
48 49 1.810030 GGCCGGCTTCTCTTACGTG 60.810 63.158 28.56 0.00 0.00 4.49
95 96 8.904099 AAAATTGGAATTACTATACTCCCTCG 57.096 34.615 0.00 0.00 0.00 4.63
200 202 1.406860 GCCTTGGCCCTGAAAACCAA 61.407 55.000 0.00 0.00 41.08 3.67
204 206 0.975887 GATTGCCTTGGCCCTGAAAA 59.024 50.000 9.35 0.00 0.00 2.29
342 345 4.317698 CGCTTATGAACTTTCTGATCTCGC 60.318 45.833 0.00 0.00 0.00 5.03
426 429 3.857052 GTGATTCTCACGGTTCCATACA 58.143 45.455 0.00 0.00 37.67 2.29
483 486 1.973281 CACCTGAGGCGCAACCAAT 60.973 57.895 10.83 0.00 43.14 3.16
484 487 2.594303 CACCTGAGGCGCAACCAA 60.594 61.111 10.83 0.00 43.14 3.67
617 620 1.139853 GCACCACCCCATGAAAAACAA 59.860 47.619 0.00 0.00 0.00 2.83
650 653 4.295775 AGGTTATCCTACCCACCGGATATA 59.704 45.833 9.46 0.00 43.12 0.86
700 703 4.156739 GGTCAATTTTTCAGCCCTAGAGTG 59.843 45.833 0.00 0.00 0.00 3.51
859 862 8.170061 ACAATCTAGAGCTATCTTCCTATCACT 58.830 37.037 0.00 0.00 36.96 3.41
879 882 2.494870 GGCATTGCCTTCTTCACAATCT 59.505 45.455 20.66 0.00 46.69 2.40
989 997 8.058235 TGGGATTGGTTCTCATAATTATCACAA 58.942 33.333 0.00 0.00 26.46 3.33
1086 1094 2.229792 GGAAAAGTGACATCCAGCACA 58.770 47.619 0.00 0.00 37.48 4.57
1162 1170 8.303876 ACAAGTCAAATTAATTTGCTTATCGGT 58.696 29.630 29.37 24.04 45.06 4.69
1245 1253 1.187087 GTCCTCTCATCAACCCGTCT 58.813 55.000 0.00 0.00 0.00 4.18
1264 1272 3.332919 CTCCTGTGTCAATCACTTCCAG 58.667 50.000 0.00 0.00 46.27 3.86
1306 1314 0.612229 TCGTCCGAGAGTAGACCACT 59.388 55.000 0.00 0.00 41.47 4.00
1311 1319 5.159209 GTTGAAAATTCGTCCGAGAGTAGA 58.841 41.667 0.00 0.00 0.00 2.59
1338 1347 0.467290 TTGTCAACAGGCTCCCCAAC 60.467 55.000 0.00 0.00 0.00 3.77
1483 1493 3.877508 GTCCTATTTTTCCTCCATGTCGG 59.122 47.826 0.00 0.00 0.00 4.79
1614 1625 8.499162 CCATATAAAGATCATTTCCTTCACGAC 58.501 37.037 0.00 0.00 0.00 4.34
1856 1867 3.832527 GGGCATTCTCCCTAATAAAGCA 58.167 45.455 0.00 0.00 43.13 3.91
1889 1900 2.603892 GCACAAACAGACTCAGCACATG 60.604 50.000 0.00 0.00 0.00 3.21
1890 1901 1.605710 GCACAAACAGACTCAGCACAT 59.394 47.619 0.00 0.00 0.00 3.21
1891 1902 1.016627 GCACAAACAGACTCAGCACA 58.983 50.000 0.00 0.00 0.00 4.57
1892 1903 1.016627 TGCACAAACAGACTCAGCAC 58.983 50.000 0.00 0.00 0.00 4.40
1912 1923 8.753497 ATCTTTTAAAACTTCAACTCCTCTGT 57.247 30.769 0.00 0.00 0.00 3.41
1928 1939 5.477291 TGCCGGGTCAACATTATCTTTTAAA 59.523 36.000 2.18 0.00 0.00 1.52
1957 1969 3.381590 AGTTGGCTTCTTCAAAGTTGTCC 59.618 43.478 0.00 0.00 0.00 4.02
1962 1974 5.036117 TCTGTAGTTGGCTTCTTCAAAGT 57.964 39.130 0.00 0.00 0.00 2.66
1970 1982 1.276421 TCCTGCTCTGTAGTTGGCTTC 59.724 52.381 0.00 0.00 0.00 3.86
1973 1985 0.391793 GGTCCTGCTCTGTAGTTGGC 60.392 60.000 0.00 0.00 0.00 4.52
1988 2000 4.212716 ACTTAAACTTCAACAAGGGGTCC 58.787 43.478 0.00 0.00 33.37 4.46
2003 2015 6.074249 GCTTAGTATCATCTGCCGACTTAAAC 60.074 42.308 0.00 0.00 0.00 2.01
2021 2033 6.260050 CAGGAACAAAGTCAAACAGCTTAGTA 59.740 38.462 0.00 0.00 0.00 1.82
2030 2042 1.673920 TCGCCAGGAACAAAGTCAAAC 59.326 47.619 0.00 0.00 0.00 2.93
2031 2043 2.045561 TCGCCAGGAACAAAGTCAAA 57.954 45.000 0.00 0.00 0.00 2.69
2040 2052 1.672881 CTTGGATGAATCGCCAGGAAC 59.327 52.381 0.00 0.00 33.47 3.62
2048 2060 2.223203 GCTGAACTGCTTGGATGAATCG 60.223 50.000 0.00 0.00 0.00 3.34
2072 2084 9.031537 TCCTATTTCGGATTCATATTAGCACTA 57.968 33.333 0.00 0.00 0.00 2.74
2085 2097 1.597663 CGCGCTTTCCTATTTCGGATT 59.402 47.619 5.56 0.00 32.02 3.01
2089 2101 0.042967 GAGCGCGCTTTCCTATTTCG 60.043 55.000 36.87 0.00 0.00 3.46
2129 2141 4.462483 GGTTTCCATGCAAAGATGTCCTAA 59.538 41.667 0.00 0.00 0.00 2.69
2131 2143 2.827921 GGTTTCCATGCAAAGATGTCCT 59.172 45.455 0.00 0.00 0.00 3.85
2157 2169 0.460284 CTCGGTACACCTGGCATGTC 60.460 60.000 0.00 0.00 0.00 3.06
2212 2224 7.066307 AGGAATTGCTTGACTGGTTTAAATT 57.934 32.000 0.00 0.00 0.00 1.82
2213 2225 6.670695 AGGAATTGCTTGACTGGTTTAAAT 57.329 33.333 0.00 0.00 0.00 1.40
2222 2234 2.069273 CGTCGAAGGAATTGCTTGACT 58.931 47.619 24.84 5.08 0.00 3.41
2240 2252 2.415512 GCGCCTCTCTTCATTAAAACGT 59.584 45.455 0.00 0.00 0.00 3.99
2248 2260 1.451028 GCCTTGCGCCTCTCTTCAT 60.451 57.895 4.18 0.00 0.00 2.57
2266 2278 0.890683 GGCCACTTCTTCACCAATGG 59.109 55.000 0.00 0.00 0.00 3.16
2342 2354 1.927487 TCTTAAGTACCAGCACCGGA 58.073 50.000 9.46 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.