Multiple sequence alignment - TraesCS4A01G155100

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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 TraesCS4A01G155100 chr4A 100.000 2375 0 0 1 2375 310747587 310749961 0 4386
1 TraesCS4A01G155100 chr6D 95.968 2381 88 4 1 2375 389247276 389244898 0 3858
2 TraesCS4A01G155100 chr3D 95.923 2379 90 5 1 2375 589264977 589262602 0 3849
3 TraesCS4A01G155100 chr7B 95.884 2381 90 4 1 2375 663100879 663098501 0 3847
4 TraesCS4A01G155100 chr7B 95.506 2381 99 4 1 2375 662724950 662727328 0 3797
5 TraesCS4A01G155100 chr5D 95.758 2381 93 4 1 2375 503243818 503246196 0 3831
6 TraesCS4A01G155100 chr3A 95.756 2380 94 4 1 2375 66006586 66004209 0 3829
7 TraesCS4A01G155100 chr3A 95.332 2378 102 6 1 2372 695638934 695641308 0 3768
8 TraesCS4A01G155100 chr2A 95.716 2381 94 4 1 2375 726907909 726905531 0 3825
9 TraesCS4A01G155100 chr3B 95.676 2382 94 4 1 2375 201538067 201540446 0 3819


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 TraesCS4A01G155100 chr4A 310747587 310749961 2374 False 4386 4386 100.000 1 2375 1 chr4A.!!$F1 2374
1 TraesCS4A01G155100 chr6D 389244898 389247276 2378 True 3858 3858 95.968 1 2375 1 chr6D.!!$R1 2374
2 TraesCS4A01G155100 chr3D 589262602 589264977 2375 True 3849 3849 95.923 1 2375 1 chr3D.!!$R1 2374
3 TraesCS4A01G155100 chr7B 663098501 663100879 2378 True 3847 3847 95.884 1 2375 1 chr7B.!!$R1 2374
4 TraesCS4A01G155100 chr7B 662724950 662727328 2378 False 3797 3797 95.506 1 2375 1 chr7B.!!$F1 2374
5 TraesCS4A01G155100 chr5D 503243818 503246196 2378 False 3831 3831 95.758 1 2375 1 chr5D.!!$F1 2374
6 TraesCS4A01G155100 chr3A 66004209 66006586 2377 True 3829 3829 95.756 1 2375 1 chr3A.!!$R1 2374
7 TraesCS4A01G155100 chr3A 695638934 695641308 2374 False 3768 3768 95.332 1 2372 1 chr3A.!!$F1 2371
8 TraesCS4A01G155100 chr2A 726905531 726907909 2378 True 3825 3825 95.716 1 2375 1 chr2A.!!$R1 2374
9 TraesCS4A01G155100 chr3B 201538067 201540446 2379 False 3819 3819 95.676 1 2375 1 chr3B.!!$F1 2374

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
424 426 0.31836 CATCGCCCGTCGCACTATAA 60.318 55.0 0.0 0.0 37.3 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2094 0.689623 GGGATCCCAGATGAGCGAAT 59.31 55.0 26.95 0.0 35.81 3.34 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
72 73 1.909781 AAAGGTGGTGCATGGCTGG 60.910 57.895 0.00 0.00 0.00 4.85
78 79 3.136123 GTGCATGGCTGGCGTCAT 61.136 61.111 0.00 0.00 35.41 3.06
108 109 4.383173 CGTAAGGTGTTGGGTTAAGTCTT 58.617 43.478 0.00 0.00 0.00 3.01
109 110 4.818005 CGTAAGGTGTTGGGTTAAGTCTTT 59.182 41.667 0.00 0.00 0.00 2.52
150 152 5.389516 CGTGTTTAGTGCCACTATGAGTTTC 60.390 44.000 5.21 0.00 29.64 2.78
167 169 1.124780 TTCGAACCCTGAACAGACCA 58.875 50.000 3.19 0.00 0.00 4.02
247 249 1.200839 GCGACACACGTGCTACAAC 59.799 57.895 17.22 0.00 44.60 3.32
276 278 2.558554 AAAGGGTCACGATCTCGCGG 62.559 60.000 6.13 0.00 44.43 6.46
309 311 2.038033 CTCCAAAAACCCGTCCTCAGTA 59.962 50.000 0.00 0.00 0.00 2.74
387 389 1.145156 CCATACGGCGGTGAATCCA 59.855 57.895 13.24 0.00 35.57 3.41
407 409 1.493854 TTCCCGGGCCTTGTACACAT 61.494 55.000 18.49 0.00 0.00 3.21
416 418 1.410737 CTTGTACACATCGCCCGTCG 61.411 60.000 0.00 0.00 40.15 5.12
424 426 0.318360 CATCGCCCGTCGCACTATAA 60.318 55.000 0.00 0.00 37.30 0.98
458 460 7.176690 CCATGTTTGAAGTCATTACCCTTAACT 59.823 37.037 0.00 0.00 0.00 2.24
627 629 1.827344 GCCCAAAAAGAAGGCAGCTAT 59.173 47.619 0.00 0.00 46.34 2.97
663 665 7.020827 ACTTGGATATGGAAGTCTTCTTTCA 57.979 36.000 12.31 2.81 42.55 2.69
826 829 2.223711 GGAGTTTTTCTCGCTTTTGGCA 60.224 45.455 0.00 0.00 43.60 4.92
885 888 2.215942 TAGCTCAGTGGTAGAGTGCA 57.784 50.000 0.00 0.00 35.55 4.57
899 902 2.578021 AGAGTGCACCCCTGATAATTGT 59.422 45.455 14.63 0.00 0.00 2.71
912 915 5.589855 CCTGATAATTGTGTCATTGTGCCTA 59.410 40.000 0.00 0.00 0.00 3.93
960 963 5.121811 GGATAGTTCAATGTGCTCATCAGT 58.878 41.667 1.01 0.00 32.56 3.41
1016 1019 0.106167 AGCATGGCGTACTCCTCCTA 60.106 55.000 3.08 0.00 0.00 2.94
1117 1120 8.057536 AGATCTAACTTTCTATTCACTCGTGT 57.942 34.615 0.00 0.00 0.00 4.49
1180 1192 4.291792 TCGAGAACCCATACATCCCTTAA 58.708 43.478 0.00 0.00 0.00 1.85
1192 1204 5.975988 ACATCCCTTAACAGTGTATGGAT 57.024 39.130 0.00 3.18 0.00 3.41
1298 1310 4.030913 ACGAGATCACCCCTTTCATTCTA 58.969 43.478 0.00 0.00 0.00 2.10
1299 1311 4.141914 ACGAGATCACCCCTTTCATTCTAC 60.142 45.833 0.00 0.00 0.00 2.59
1345 1359 3.305608 CGAGCCTTTTTCATGCTTTTCCT 60.306 43.478 0.00 0.00 34.99 3.36
1437 1451 8.933653 TGAAATTCTTTTTCCTTAAATGGGAGT 58.066 29.630 0.00 0.00 34.06 3.85
1444 1458 5.772393 TTCCTTAAATGGGAGTAGAGCAA 57.228 39.130 0.00 0.00 34.06 3.91
1458 1472 6.378710 AGTAGAGCAAGTTTGAAAAAGGAC 57.621 37.500 0.00 0.00 0.00 3.85
1510 1524 4.320275 GGTCTCTTAACGCCTTCCTTTTTG 60.320 45.833 0.00 0.00 0.00 2.44
1521 1535 0.178975 TCCTTTTTGTGCCCATCGGT 60.179 50.000 0.00 0.00 0.00 4.69
1581 1595 2.576615 GGGAAGAAGCACACTTGAAGT 58.423 47.619 0.00 0.00 35.82 3.01
1682 1696 1.202099 TTGGTTGGATCGTAGGGGCA 61.202 55.000 0.00 0.00 0.00 5.36
1696 1710 4.821805 CGTAGGGGCAATGATTTACTTCAT 59.178 41.667 0.00 0.00 37.96 2.57
1720 1734 1.889829 CGAGGTCTCTGGTTCAAGTCT 59.110 52.381 0.00 0.00 0.00 3.24
1737 1751 2.691996 TAGGATGGCCCAGCTGCA 60.692 61.111 8.66 0.81 37.41 4.41
1739 1753 4.437587 GGATGGCCCAGCTGCACT 62.438 66.667 8.66 0.00 34.14 4.40
1826 1840 6.661805 GGATATAGCTTAGTTGGTAGAGCTCT 59.338 42.308 22.17 22.17 43.86 4.09
1847 1861 1.401539 GCTCTTGCAATTGGGTCGTTC 60.402 52.381 7.72 0.00 39.41 3.95
1848 1862 2.154462 CTCTTGCAATTGGGTCGTTCT 58.846 47.619 7.72 0.00 0.00 3.01
1877 1891 2.488153 GGTTGGCTGTCTAATTGTCCAC 59.512 50.000 0.00 0.00 0.00 4.02
1958 1972 2.107204 AGAGGACTGAAACATGCCACTT 59.893 45.455 0.00 0.00 0.00 3.16
1959 1973 2.227388 GAGGACTGAAACATGCCACTTG 59.773 50.000 0.00 0.00 0.00 3.16
1991 2005 5.140454 ACTAAGACAAAAAGATGGGCTGTT 58.860 37.500 0.00 0.00 0.00 3.16
2013 2027 6.212187 TGTTAAAAAGGTAGAGGAGGTAGGAC 59.788 42.308 0.00 0.00 0.00 3.85
2016 2030 0.842635 GGTAGAGGAGGTAGGACGGA 59.157 60.000 0.00 0.00 0.00 4.69
2080 2094 3.805497 TCGGCGGCTCTCCTAGGA 61.805 66.667 11.98 11.98 0.00 2.94
2084 2098 1.287503 GCGGCTCTCCTAGGATTCG 59.712 63.158 13.12 14.16 0.00 3.34
2125 2139 1.213296 GGAGGATCAAGTTGGCCCTA 58.787 55.000 14.29 0.00 36.25 3.53
2249 2263 1.924731 ACGAGATCACTCCAAGGACA 58.075 50.000 0.00 0.00 39.76 4.02
2289 2303 0.179009 CGGACCGACCATAGACCCTA 60.179 60.000 8.64 0.00 38.90 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.358725 TTTCAAGAGGATTCGCGGCG 61.359 55.000 17.70 17.70 0.00 6.46
55 56 2.283388 CCAGCCATGCACCACCTT 60.283 61.111 0.00 0.00 0.00 3.50
108 109 1.959226 GAGGGTTGCGCTCGTTGAA 60.959 57.895 9.73 0.00 34.01 2.69
109 110 2.357034 GAGGGTTGCGCTCGTTGA 60.357 61.111 9.73 0.00 34.01 3.18
150 152 0.602905 GGTGGTCTGTTCAGGGTTCG 60.603 60.000 0.00 0.00 0.00 3.95
167 169 0.834687 TCCTCCAGCTTAACACCGGT 60.835 55.000 0.00 0.00 0.00 5.28
212 214 3.105928 CCCAGGGCATAAGGGGCT 61.106 66.667 0.00 0.00 38.98 5.19
247 249 2.359975 GACCCTTTGTCCTGCCCG 60.360 66.667 0.00 0.00 38.09 6.13
276 278 2.557056 GTTTTTGGAGTTAGCTCACCCC 59.443 50.000 8.96 0.00 43.37 4.95
387 389 1.301954 GTGTACAAGGCCCGGGAAT 59.698 57.895 29.31 8.77 0.00 3.01
416 418 2.149578 CATGGCCAGCTCTTATAGTGC 58.850 52.381 13.05 0.00 35.13 4.40
424 426 1.202976 ACTTCAAACATGGCCAGCTCT 60.203 47.619 13.05 0.00 0.00 4.09
458 460 0.645496 TAGGCATCCCCCTCCTTACA 59.355 55.000 0.00 0.00 36.41 2.41
627 629 5.425217 TCCATATCCAAGTTTAGCTCAGACA 59.575 40.000 0.00 0.00 0.00 3.41
663 665 5.014228 AGCTTGGTCTTACTTCACCCTAAAT 59.986 40.000 0.00 0.00 0.00 1.40
785 788 4.750941 TCCATCCCTTTCCTTTTGACATT 58.249 39.130 0.00 0.00 0.00 2.71
826 829 1.925888 CCAAAGGGAGGCCTGCTAT 59.074 57.895 24.77 10.52 35.59 2.97
854 857 2.099921 CACTGAGCTAATAGCCTGTCGT 59.900 50.000 8.88 1.12 43.77 4.34
859 862 4.148838 CTCTACCACTGAGCTAATAGCCT 58.851 47.826 8.88 0.00 43.77 4.58
885 888 4.706476 CACAATGACACAATTATCAGGGGT 59.294 41.667 0.00 0.00 0.00 4.95
899 902 0.692476 ACAGCCTAGGCACAATGACA 59.308 50.000 34.70 0.00 44.88 3.58
912 915 1.988956 CTGAGAGCCCTCACAGCCT 60.989 63.158 9.26 0.00 44.01 4.58
960 963 1.296392 CACATCTTCGGGTCAGGCA 59.704 57.895 0.00 0.00 0.00 4.75
1016 1019 5.782893 TGGTTTCAAACTCCGATTCAAAT 57.217 34.783 0.00 0.00 0.00 2.32
1165 1177 4.503714 ACACTGTTAAGGGATGTATGGG 57.496 45.455 0.00 0.00 0.00 4.00
1180 1192 5.645929 CGAGAGATAGCTATCCATACACTGT 59.354 44.000 26.65 8.00 33.17 3.55
1192 1204 2.158740 ACCTGTGCTCGAGAGATAGCTA 60.159 50.000 18.75 0.00 40.84 3.32
1298 1310 2.541547 TACGATCCCTCCGTCACCGT 62.542 60.000 0.00 0.00 40.95 4.83
1299 1311 1.820906 TACGATCCCTCCGTCACCG 60.821 63.158 0.00 0.00 40.95 4.94
1345 1359 2.347490 GCTTTCTCCAGACCGCCA 59.653 61.111 0.00 0.00 0.00 5.69
1409 1423 8.933653 TCCCATTTAAGGAAAAAGAATTTCACT 58.066 29.630 0.00 0.00 37.28 3.41
1437 1451 5.445964 AGGTCCTTTTTCAAACTTGCTCTA 58.554 37.500 0.00 0.00 0.00 2.43
1444 1458 6.424032 ACACTCTAAGGTCCTTTTTCAAACT 58.576 36.000 10.04 0.00 0.00 2.66
1458 1472 2.766828 CCCAACCCTAGACACTCTAAGG 59.233 54.545 0.00 0.00 36.77 2.69
1510 1524 1.404035 GGAAATAACACCGATGGGCAC 59.596 52.381 0.00 0.00 36.48 5.01
1521 1535 4.730966 TGGCAAGTACTTGGGAAATAACA 58.269 39.130 31.42 5.92 40.74 2.41
1581 1595 1.324740 ACTCCCCGTTATACTGCGCA 61.325 55.000 10.98 10.98 0.00 6.09
1590 1604 1.406341 GCAGCATACAACTCCCCGTTA 60.406 52.381 0.00 0.00 33.63 3.18
1644 1658 5.699143 ACCAATTGGGAGAGAATCAATAGG 58.301 41.667 27.89 0.00 41.15 2.57
1682 1696 3.885297 CCTCGCCCATGAAGTAAATCATT 59.115 43.478 0.00 0.00 37.96 2.57
1696 1710 2.203788 AACCAGAGACCTCGCCCA 60.204 61.111 0.00 0.00 34.09 5.36
1720 1734 2.691996 TGCAGCTGGGCCATCCTA 60.692 61.111 17.12 0.00 36.20 2.94
1737 1751 7.259088 TGCTTCTTCTATTCTTTTCCCTAGT 57.741 36.000 0.00 0.00 0.00 2.57
1739 1753 7.989741 CAGATGCTTCTTCTATTCTTTTCCCTA 59.010 37.037 0.00 0.00 0.00 3.53
1801 1815 6.661805 AGAGCTCTACCAACTAAGCTATATCC 59.338 42.308 16.50 0.00 44.77 2.59
1802 1816 7.535139 CAGAGCTCTACCAACTAAGCTATATC 58.465 42.308 17.75 0.00 44.77 1.63
1847 1861 1.066143 AGACAGCCAACCCGTAATCAG 60.066 52.381 0.00 0.00 0.00 2.90
1848 1862 0.981183 AGACAGCCAACCCGTAATCA 59.019 50.000 0.00 0.00 0.00 2.57
1877 1891 5.798934 GGTACAAGATACTATCATTACCGCG 59.201 44.000 0.00 0.00 0.00 6.46
1958 1972 9.698309 CATCTTTTTGTCTTAGTAGAGTCTTCA 57.302 33.333 0.00 0.00 0.00 3.02
1959 1973 9.145865 CCATCTTTTTGTCTTAGTAGAGTCTTC 57.854 37.037 0.00 0.00 0.00 2.87
1991 2005 4.952335 CGTCCTACCTCCTCTACCTTTTTA 59.048 45.833 0.00 0.00 0.00 1.52
2013 2027 2.755655 ACTAGATCTGACCAACTGTCCG 59.244 50.000 5.18 0.00 43.78 4.79
2016 2030 5.519808 TCCATACTAGATCTGACCAACTGT 58.480 41.667 5.18 0.00 0.00 3.55
2080 2094 0.689623 GGGATCCCAGATGAGCGAAT 59.310 55.000 26.95 0.00 35.81 3.34
2084 2098 1.759881 CCAGGGATCCCAGATGAGC 59.240 63.158 32.69 2.64 38.92 4.26
2106 2120 1.141858 CTAGGGCCAACTTGATCCTCC 59.858 57.143 6.18 0.00 0.00 4.30
2125 2139 5.605534 AGATAGTGCATCAAGTTATTCGCT 58.394 37.500 0.00 0.00 35.96 4.93
2289 2303 7.394359 ACAGCTAATGTGTTCCACTTATTGAAT 59.606 33.333 0.00 0.00 41.91 2.57


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

AutoCloner maintained by Alex Coulton.