Multiple sequence alignment - TraesCS7D01G054100

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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 TraesCS7D01G054100 chr7D 100.000 2548 0 0 1 2548 28674016 28676563 0.000000e+00 4706
1 TraesCS7D01G054100 chr7D 87.093 2394 246 37 1 2359 28695993 28698358 0.000000e+00 2651
2 TraesCS7D01G054100 chr4A 88.516 2203 201 26 292 2466 702398791 702400969 0.000000e+00 2619
3 TraesCS7D01G054100 chr4A 86.174 2394 263 39 74 2428 701313074 701310710 0.000000e+00 2525
4 TraesCS7D01G054100 chr4A 91.673 1369 74 19 795 2142 702380993 702382342 0.000000e+00 1860
5 TraesCS7D01G054100 chr4A 93.293 820 45 6 1 819 702380163 702380973 0.000000e+00 1201
6 TraesCS7D01G054100 chr4A 85.753 1116 131 16 853 1949 702339892 702340998 0.000000e+00 1155
7 TraesCS7D01G054100 chr4A 85.884 843 99 6 853 1678 702505160 702505999 0.000000e+00 880
8 TraesCS7D01G054100 chr4A 83.079 656 98 11 1 652 702504403 702505049 3.650000e-163 584
9 TraesCS7D01G054100 chr4A 94.595 333 16 2 2217 2548 702382348 702382679 4.860000e-142 514
10 TraesCS7D01G054100 chr7A 86.683 2403 249 38 1 2374 29109736 29112096 0.000000e+00 2599
11 TraesCS7D01G054100 chr7A 90.350 1627 128 18 1 1611 29032424 29034037 0.000000e+00 2108


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 TraesCS7D01G054100 chr7D 28674016 28676563 2547 False 4706.000000 4706 100.0000 1 2548 1 chr7D.!!$F1 2547
1 TraesCS7D01G054100 chr7D 28695993 28698358 2365 False 2651.000000 2651 87.0930 1 2359 1 chr7D.!!$F2 2358
2 TraesCS7D01G054100 chr4A 702398791 702400969 2178 False 2619.000000 2619 88.5160 292 2466 1 chr4A.!!$F2 2174
3 TraesCS7D01G054100 chr4A 701310710 701313074 2364 True 2525.000000 2525 86.1740 74 2428 1 chr4A.!!$R1 2354
4 TraesCS7D01G054100 chr4A 702380163 702382679 2516 False 1191.666667 1860 93.1870 1 2548 3 chr4A.!!$F3 2547
5 TraesCS7D01G054100 chr4A 702339892 702340998 1106 False 1155.000000 1155 85.7530 853 1949 1 chr4A.!!$F1 1096
6 TraesCS7D01G054100 chr4A 702504403 702505999 1596 False 732.000000 880 84.4815 1 1678 2 chr4A.!!$F4 1677
7 TraesCS7D01G054100 chr7A 29109736 29112096 2360 False 2599.000000 2599 86.6830 1 2374 1 chr7A.!!$F2 2373
8 TraesCS7D01G054100 chr7A 29032424 29034037 1613 False 2108.000000 2108 90.3500 1 1611 1 chr7A.!!$F1 1610

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
145 147 0.539986 TGGGCTATTGGACGAGAACC 59.46 55.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2113 1.144708 TGACTGGTGCCTTCCAATGAA 59.855 47.619 0.0 0.0 37.01 2.57 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
82 84 4.899502 AGAAGTAGACAAGGGTGTGAATG 58.100 43.478 0.00 0.00 38.41 2.67
99 101 6.801862 GTGTGAATGTATTTAGTTGGCAGTTC 59.198 38.462 0.00 0.00 0.00 3.01
139 141 5.147330 TGAATAGTATGGGCTATTGGACG 57.853 43.478 3.43 0.00 40.55 4.79
145 147 0.539986 TGGGCTATTGGACGAGAACC 59.460 55.000 0.00 0.00 0.00 3.62
323 329 7.765307 AGATATGTGCAAAACCATACAGAAAG 58.235 34.615 0.00 0.00 0.00 2.62
325 331 5.590530 TGTGCAAAACCATACAGAAAGTT 57.409 34.783 0.00 0.00 0.00 2.66
582 590 9.745880 CAAACTAAGGTCGTATCTATGTAATGT 57.254 33.333 0.00 0.00 0.00 2.71
652 660 4.217767 TCGTAATTCGTATGGAGGAGATGG 59.782 45.833 0.00 0.00 40.80 3.51
789 819 0.801574 AACTAACCCCTCCACCCCTA 59.198 55.000 0.00 0.00 0.00 3.53
794 824 2.338377 CCCCTCCACCCCTACCCTA 61.338 68.421 0.00 0.00 0.00 3.53
811 887 1.003108 CTACACACACACACACGCAA 58.997 50.000 0.00 0.00 0.00 4.85
899 979 0.547075 TCCTCCTCCTCCTCTACACG 59.453 60.000 0.00 0.00 0.00 4.49
916 997 4.198028 ACACGTAGGGTAGTTGAATTCC 57.802 45.455 2.27 0.00 0.00 3.01
917 998 3.579586 ACACGTAGGGTAGTTGAATTCCA 59.420 43.478 2.27 0.00 0.00 3.53
931 1012 8.463930 AGTTGAATTCCATCAAAGACAAACTA 57.536 30.769 2.27 0.00 40.76 2.24
970 1051 1.078497 CCTGACCGTGCCTGCAATA 60.078 57.895 0.00 0.00 0.00 1.90
1092 1186 1.138036 CGGCGTCGGTATTGTCTCA 59.862 57.895 0.00 0.00 0.00 3.27
1114 1208 3.389983 AGCTATTATGGAACCAACCGCTA 59.610 43.478 0.00 0.00 0.00 4.26
1132 1226 2.287457 TACACGCCTACGCATGGTCC 62.287 60.000 0.00 0.00 45.53 4.46
1414 1513 6.486993 GGATTTTGTAAACAGGAGTGTCTCTT 59.513 38.462 0.00 0.00 35.08 2.85
1530 1632 2.094854 CAGAGCTGCATTTTCTTCACCC 60.095 50.000 1.02 0.00 0.00 4.61
1581 1696 7.674120 CATCTATGTTTGAGAGATGTATGGGA 58.326 38.462 3.46 0.00 42.99 4.37
1729 1851 0.032952 TAACGAGGGATGCATACGCC 59.967 55.000 1.96 0.00 37.32 5.68
1770 1895 7.805071 CCTTTTTGCATGCTAGCTATATAACAC 59.195 37.037 20.33 0.00 34.99 3.32
1771 1896 8.450578 TTTTTGCATGCTAGCTATATAACACT 57.549 30.769 20.33 0.00 34.99 3.55
1840 1967 9.449719 ACTGCTTTATACTTTTGCTAACTATGT 57.550 29.630 0.00 0.00 0.00 2.29
1935 2062 5.746065 GCATGGTCCCAGCTGTATATTAACT 60.746 44.000 13.81 0.00 0.00 2.24
1970 2097 7.765695 ATGATTGGGTGTAATCCATATGTTC 57.234 36.000 1.24 0.00 36.46 3.18
1982 2109 6.808008 ATCCATATGTTCGGCTAAGATTTG 57.192 37.500 1.24 0.00 0.00 2.32
1986 2113 1.004277 TGTTCGGCTAAGATTTGCCCT 59.996 47.619 11.58 0.00 44.58 5.19
2005 2132 1.815003 CTTCATTGGAAGGCACCAGTC 59.185 52.381 3.88 0.00 45.52 3.51
2200 2334 4.299155 AGTGTGTGTGTTCTCAGTATTCG 58.701 43.478 0.00 0.00 0.00 3.34
2299 2433 8.610035 GTGCCACAAGTTACCTATAATAAGTTC 58.390 37.037 0.00 0.00 0.00 3.01
2369 2507 1.806542 CAGTGTGACACAAGTATGGCC 59.193 52.381 18.95 0.00 36.74 5.36
2454 2593 1.134530 CGCGCAACCGTTGTTTTTCA 61.135 50.000 8.75 0.00 36.67 2.69
2472 2612 2.588989 GGCTCAAGAGGCCCAGAG 59.411 66.667 12.19 2.75 46.99 3.35
2524 2664 1.375908 GCACGATTGTCAGCCCTCA 60.376 57.895 0.00 0.00 0.00 3.86
2525 2665 0.955428 GCACGATTGTCAGCCCTCAA 60.955 55.000 0.00 0.00 0.00 3.02
2527 2667 0.687354 ACGATTGTCAGCCCTCAAGT 59.313 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 5.857822 AACTCGAACTGCCAACTAAATAC 57.142 39.130 0.00 0.00 0.00 1.89
99 101 8.425577 ACTATTCATTTGACCTCATTAACTCG 57.574 34.615 0.00 0.00 0.00 4.18
128 130 1.207329 AGTGGTTCTCGTCCAATAGCC 59.793 52.381 0.00 0.00 36.68 3.93
139 141 3.686016 TGGCCTATTTTCAGTGGTTCTC 58.314 45.455 3.32 0.00 0.00 2.87
220 222 7.822161 TTAGGCGTACCAATATGTAGTTCTA 57.178 36.000 0.00 0.00 39.06 2.10
323 329 4.957759 ACCATGTAAATGCGGAGTAAAC 57.042 40.909 0.00 0.00 0.00 2.01
325 331 7.051623 AGAATTACCATGTAAATGCGGAGTAA 58.948 34.615 0.00 0.00 0.00 2.24
394 401 9.151471 GTAGTACAGCTAAATTGTTTCATGAGA 57.849 33.333 0.00 0.00 0.00 3.27
582 590 6.994496 CCTCTCAAATTCCAGTGATATTGCTA 59.006 38.462 0.00 0.00 0.00 3.49
652 660 2.709475 CCAATAGGTCGCAAGCGC 59.291 61.111 9.97 0.00 39.59 5.92
687 717 9.478768 GAAGCATTTATCCTAGTTAGTACCTTC 57.521 37.037 0.00 0.00 0.00 3.46
709 739 3.435275 AGGATTTCTCTTTTGGGGAAGC 58.565 45.455 0.00 0.00 0.00 3.86
789 819 0.179094 CGTGTGTGTGTGTGTAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
794 824 0.109964 GTTTGCGTGTGTGTGTGTGT 60.110 50.000 0.00 0.00 0.00 3.72
811 887 9.719355 AAAACCTTTTTAATCTCTTTGTGTGTT 57.281 25.926 0.00 0.00 0.00 3.32
899 979 7.065923 GTCTTTGATGGAATTCAACTACCCTAC 59.934 40.741 7.93 0.00 35.42 3.18
916 997 7.029563 GGTGCCTAATTAGTTTGTCTTTGATG 58.970 38.462 11.50 0.00 0.00 3.07
917 998 6.719370 TGGTGCCTAATTAGTTTGTCTTTGAT 59.281 34.615 11.50 0.00 0.00 2.57
970 1051 2.107901 GAGATGATGCCCCTGGAATTCT 59.892 50.000 5.23 0.00 0.00 2.40
1092 1186 2.172717 AGCGGTTGGTTCCATAATAGCT 59.827 45.455 0.00 0.00 0.00 3.32
1132 1226 2.184020 TTGGTGTGGATGAGAGGCCG 62.184 60.000 0.00 0.00 0.00 6.13
1530 1632 4.897357 TCATAGGCTGCCAGCGCG 62.897 66.667 22.65 0.00 43.62 6.86
1581 1696 8.390921 TGAAAAATAGGTTCCAGTCCTTCTAAT 58.609 33.333 0.00 0.00 36.60 1.73
1729 1851 4.378459 GCAAAAAGGTGAACACTATCTCGG 60.378 45.833 4.96 0.00 0.00 4.63
1770 1895 6.556212 AGTTGTGACAATCTATACGTGAGAG 58.444 40.000 0.00 0.00 0.00 3.20
1771 1896 6.510879 AGTTGTGACAATCTATACGTGAGA 57.489 37.500 0.00 0.60 0.00 3.27
1953 2080 3.740115 AGCCGAACATATGGATTACACC 58.260 45.455 7.80 0.00 0.00 4.16
1986 2113 1.144708 TGACTGGTGCCTTCCAATGAA 59.855 47.619 0.00 0.00 37.01 2.57
2003 2130 3.181500 GGAAGGCATACACGGAAATTGAC 60.181 47.826 0.00 0.00 0.00 3.18
2005 2132 2.099098 GGGAAGGCATACACGGAAATTG 59.901 50.000 0.00 0.00 0.00 2.32
2120 2252 2.886134 TTGCCTACGGGTCACCACC 61.886 63.158 0.00 0.00 42.90 4.61
2135 2267 9.740239 ATTAGATATTGTCAAATCATGTGTTGC 57.260 29.630 0.00 0.00 0.00 4.17
2163 2295 4.263994 ACACACACTCTACTAGGTCTGGAT 60.264 45.833 0.00 0.00 0.00 3.41
2200 2334 3.711086 TCTTATGCTTCTCGAGACATGC 58.289 45.455 22.33 21.47 0.00 4.06
2299 2433 0.389296 TTCCGCGGTACACACATGAG 60.389 55.000 27.15 0.00 0.00 2.90
2447 2586 2.713895 GCCTCTTGAGCCTGAAAAAC 57.286 50.000 0.00 0.00 0.00 2.43
2472 2612 4.724602 TGCTCGCGTGAGTGCTCC 62.725 66.667 25.72 10.34 44.48 4.70
2482 2622 3.234368 AAAAACTGTTGTGCTCGCG 57.766 47.368 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.