Multiple sequence alignment - TraesCS7B01G253400

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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 TraesCS7B01G253400 chr7B 100.000 2429 0 0 1 2429 467424835 467422407 0.000000e+00 4486
1 TraesCS7B01G253400 chr7B 91.689 373 17 4 442 801 685614494 685614865 2.790000e-139 505
2 TraesCS7B01G253400 chr7D 92.706 1933 78 20 1 1882 449457925 449456005 0.000000e+00 2730
3 TraesCS7B01G253400 chr7D 96.250 240 7 1 2190 2429 449455735 449455498 2.260000e-105 392
4 TraesCS7B01G253400 chr7D 93.548 248 15 1 1944 2190 449456007 449455760 3.820000e-98 368
5 TraesCS7B01G253400 chr7A 87.605 1428 112 30 435 1823 546634935 546636336 0.000000e+00 1596
6 TraesCS7B01G253400 chr7A 85.762 302 29 7 126 416 546634664 546634962 8.440000e-80 307
7 TraesCS7B01G253400 chr7A 84.691 307 25 13 2133 2429 546636623 546636917 1.100000e-73 287
8 TraesCS7B01G253400 chr6D 96.226 530 8 3 439 959 322696623 322697149 0.000000e+00 857
9 TraesCS7B01G253400 chr6D 95.446 527 12 3 442 959 384197593 384197070 0.000000e+00 830
10 TraesCS7B01G253400 chr3D 95.472 530 12 3 439 959 596627359 596627885 0.000000e+00 835
11 TraesCS7B01G253400 chrUn 95.256 527 13 3 442 959 102601227 102600704 0.000000e+00 824
12 TraesCS7B01G253400 chrUn 95.043 464 9 4 439 893 162675393 162675851 0.000000e+00 717
13 TraesCS7B01G253400 chrUn 98.571 70 1 0 890 959 162681515 162681584 9.120000e-25 124
14 TraesCS7B01G253400 chr1D 91.587 523 18 7 437 959 353179744 353180240 0.000000e+00 699
15 TraesCS7B01G253400 chr4B 90.960 531 15 8 442 959 608368229 608367719 0.000000e+00 684
16 TraesCS7B01G253400 chr2B 92.819 376 13 4 442 804 50582124 50581750 1.280000e-147 532
17 TraesCS7B01G253400 chr2B 91.223 376 12 7 446 801 795857029 795857403 2.170000e-135 492


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 TraesCS7B01G253400 chr7B 467422407 467424835 2428 True 4486.000000 4486 100.000000 1 2429 1 chr7B.!!$R1 2428
1 TraesCS7B01G253400 chr7D 449455498 449457925 2427 True 1163.333333 2730 94.168000 1 2429 3 chr7D.!!$R1 2428
2 TraesCS7B01G253400 chr7A 546634664 546636917 2253 False 730.000000 1596 86.019333 126 2429 3 chr7A.!!$F1 2303
3 TraesCS7B01G253400 chr6D 322696623 322697149 526 False 857.000000 857 96.226000 439 959 1 chr6D.!!$F1 520
4 TraesCS7B01G253400 chr6D 384197070 384197593 523 True 830.000000 830 95.446000 442 959 1 chr6D.!!$R1 517
5 TraesCS7B01G253400 chr3D 596627359 596627885 526 False 835.000000 835 95.472000 439 959 1 chr3D.!!$F1 520
6 TraesCS7B01G253400 chrUn 102600704 102601227 523 True 824.000000 824 95.256000 442 959 1 chrUn.!!$R1 517
7 TraesCS7B01G253400 chr4B 608367719 608368229 510 True 684.000000 684 90.960000 442 959 1 chr4B.!!$R1 517

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
44 45 0.460987 CCAGGGAGAACGACATGAGC 60.461 60.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2316 0.098376 AGAACTACGCTCGGCTAACG 59.902 55.0 0.0 0.0 46.11 3.18 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
36 37 2.093447 AGAAATGCTACCAGGGAGAACG 60.093 50.000 1.25 0.00 0.00 3.95
44 45 0.460987 CCAGGGAGAACGACATGAGC 60.461 60.000 0.00 0.00 0.00 4.26
53 54 4.072839 AGAACGACATGAGCGGATATAGA 58.927 43.478 14.96 0.00 0.00 1.98
56 57 3.010420 CGACATGAGCGGATATAGAGGA 58.990 50.000 0.00 0.00 0.00 3.71
65 77 5.337788 AGCGGATATAGAGGAGGAAGAAAT 58.662 41.667 0.00 0.00 0.00 2.17
67 79 7.129425 AGCGGATATAGAGGAGGAAGAAATAT 58.871 38.462 0.00 0.00 0.00 1.28
91 107 5.769662 TGTTGGCAGTCTGTATCATTTTCTT 59.230 36.000 0.93 0.00 0.00 2.52
92 108 6.265196 TGTTGGCAGTCTGTATCATTTTCTTT 59.735 34.615 0.93 0.00 0.00 2.52
187 203 1.645710 CACCTTCCACCACTCTACCT 58.354 55.000 0.00 0.00 0.00 3.08
243 259 1.670811 CGGAGCCGAAATACAATTGCT 59.329 47.619 5.05 0.00 42.83 3.91
320 341 5.121768 ACTGTTTCTCCATTAACCGAATTCG 59.878 40.000 20.92 20.92 39.44 3.34
357 381 6.299141 TCATATGAAAGGTAAGATTCCTGCC 58.701 40.000 1.98 0.00 35.27 4.85
371 395 0.597568 CCTGCCGCACAATTTTCTCA 59.402 50.000 0.00 0.00 0.00 3.27
372 396 1.666888 CCTGCCGCACAATTTTCTCAC 60.667 52.381 0.00 0.00 0.00 3.51
418 442 5.060940 CGACGCATATCATACATACACCTTG 59.939 44.000 0.00 0.00 0.00 3.61
422 446 6.534793 CGCATATCATACATACACCTTGCATA 59.465 38.462 0.00 0.00 0.00 3.14
1131 1196 2.361104 GGCACCGATGAAGCCCAA 60.361 61.111 0.00 0.00 42.58 4.12
1177 1242 4.891727 GCGGCGTCGGGATGATGT 62.892 66.667 13.05 0.00 35.92 3.06
1185 1250 4.256090 GGGATGATGTTGCGCCGC 62.256 66.667 4.18 0.00 0.00 6.53
1201 1272 4.750460 GCGGTGGCGATGATAAGA 57.250 55.556 0.00 0.00 0.00 2.10
1338 1415 2.685017 TCCGGCTGCATCCTCTGT 60.685 61.111 4.84 0.00 0.00 3.41
1357 1434 4.161295 CCATCTTCGGCGGCTCCA 62.161 66.667 7.21 0.00 34.01 3.86
1431 1514 2.812178 CGGTCGGCGGTGTAAAGG 60.812 66.667 7.21 0.00 0.00 3.11
1651 1746 8.102047 AGATCTGTGATGTTCTTTCTTGATCTT 58.898 33.333 0.00 0.00 35.00 2.40
1660 1755 3.752747 TCTTTCTTGATCTTGCGCATGAA 59.247 39.130 27.09 11.38 0.00 2.57
1744 1858 0.464373 AGTGTGAGGTGTTGGCACTG 60.464 55.000 0.00 0.00 44.65 3.66
1745 1859 0.748005 GTGTGAGGTGTTGGCACTGT 60.748 55.000 0.00 0.00 44.65 3.55
1746 1860 0.034574 TGTGAGGTGTTGGCACTGTT 60.035 50.000 0.00 0.00 44.65 3.16
1747 1861 0.381801 GTGAGGTGTTGGCACTGTTG 59.618 55.000 0.00 0.00 44.65 3.33
1823 1937 2.828095 GGCATGGCCGCATGTGTA 60.828 61.111 8.35 0.00 39.62 2.90
1824 1938 2.717485 GCATGGCCGCATGTGTAG 59.283 61.111 5.38 0.00 35.16 2.74
1825 1939 2.837883 GCATGGCCGCATGTGTAGG 61.838 63.158 5.38 0.09 35.16 3.18
1826 1940 1.451927 CATGGCCGCATGTGTAGGT 60.452 57.895 5.38 0.00 0.00 3.08
1827 1941 1.451927 ATGGCCGCATGTGTAGGTG 60.452 57.895 5.38 0.00 0.00 4.00
1836 1950 3.423154 GTGTAGGTGTGCTGCCGC 61.423 66.667 0.00 0.00 0.00 6.53
1855 1969 4.030452 GCGTGTGCTGTTCTGGCC 62.030 66.667 0.00 0.00 38.39 5.36
1857 1971 2.203337 GTGTGCTGTTCTGGCCCA 60.203 61.111 0.00 0.00 0.00 5.36
1883 1997 1.227263 GTGCCGACGCTATGGTGAT 60.227 57.895 0.00 0.00 35.36 3.06
1887 2001 1.400494 GCCGACGCTATGGTGATTTTT 59.600 47.619 0.00 0.00 0.00 1.94
1920 2193 7.493971 TGAAACAAGTTATGGTGAAATTTGTGG 59.506 33.333 0.00 0.00 37.02 4.17
1942 2215 4.873259 GGCTCACCAGAAGTAAATCTCTTC 59.127 45.833 0.00 0.00 40.83 2.87
1943 2216 4.564769 GCTCACCAGAAGTAAATCTCTTCG 59.435 45.833 0.00 0.00 43.93 3.79
1945 2218 5.470368 TCACCAGAAGTAAATCTCTTCGTG 58.530 41.667 0.00 0.00 43.93 4.35
1946 2219 4.092091 CACCAGAAGTAAATCTCTTCGTGC 59.908 45.833 0.00 0.00 43.93 5.34
1953 2231 7.656137 AGAAGTAAATCTCTTCGTGCAAGTTTA 59.344 33.333 0.00 0.00 43.93 2.01
1996 2274 7.588497 AAAGAGTTACAAATTTCTCTGCCTT 57.412 32.000 7.65 0.00 37.35 4.35
2003 2281 2.283145 ATTTCTCTGCCTTGCACACT 57.717 45.000 0.00 0.00 33.79 3.55
2038 2316 4.022068 TGAAATTCATGTGCTCCAAACTCC 60.022 41.667 0.00 0.00 0.00 3.85
2060 2338 3.553532 GTTAGCCGAGCGTAGTTCTATC 58.446 50.000 0.00 0.00 34.89 2.08
2087 2365 3.487202 CGGTCACCGGAACATGCG 61.487 66.667 8.94 1.45 44.15 4.73
2106 2384 1.956802 CCGGTTGGCTCAAGAAACC 59.043 57.895 0.00 5.43 40.02 3.27
2243 2549 5.237815 TCCTAGCACACACAAAGTAGAATG 58.762 41.667 0.00 0.00 0.00 2.67
2314 2621 3.659786 CACATGAAGGTCCGAGTAACAA 58.340 45.455 0.00 0.00 0.00 2.83
2366 2673 1.419012 GCCACATGATGATCTCCTCCA 59.581 52.381 0.00 0.00 0.00 3.86
2373 2680 7.166167 CACATGATGATCTCCTCCATTTCATA 58.834 38.462 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.380004 CCTCCTCTATATCCGCTCATGTC 59.620 52.174 0.00 0.00 0.00 3.06
44 45 8.299990 ACATATTTCTTCCTCCTCTATATCCG 57.700 38.462 0.00 0.00 0.00 4.18
53 54 4.018050 ACTGCCAACATATTTCTTCCTCCT 60.018 41.667 0.00 0.00 0.00 3.69
56 57 4.946157 CAGACTGCCAACATATTTCTTCCT 59.054 41.667 0.00 0.00 0.00 3.36
65 77 7.112122 AGAAAATGATACAGACTGCCAACATA 58.888 34.615 1.25 0.00 0.00 2.29
67 79 5.316167 AGAAAATGATACAGACTGCCAACA 58.684 37.500 1.25 0.00 0.00 3.33
108 124 8.972127 TCCACTAGCTGAAGGATATGTATAATC 58.028 37.037 0.00 0.00 0.00 1.75
112 128 7.236432 ACAATCCACTAGCTGAAGGATATGTAT 59.764 37.037 13.81 0.00 34.80 2.29
115 131 5.862845 ACAATCCACTAGCTGAAGGATATG 58.137 41.667 13.81 14.73 34.80 1.78
124 140 5.016051 AGATGTGTACAATCCACTAGCTG 57.984 43.478 0.00 0.00 33.92 4.24
187 203 5.163903 CGAACAACCAATCATCATTACACGA 60.164 40.000 0.00 0.00 0.00 4.35
243 259 6.594788 AGAGAAATGAAGCAAAGGCAAATA 57.405 33.333 0.00 0.00 44.61 1.40
320 341 1.134521 TCATATGAACAGTCGCCACCC 60.135 52.381 1.98 0.00 0.00 4.61
329 350 8.834465 CAGGAATCTTACCTTTCATATGAACAG 58.166 37.037 17.76 16.19 35.35 3.16
357 381 4.685169 ACATAGGTGAGAAAATTGTGCG 57.315 40.909 0.00 0.00 0.00 5.34
371 395 7.387948 GTCGGCATAAAGATGATAAACATAGGT 59.612 37.037 0.00 0.00 39.56 3.08
372 396 7.411912 CGTCGGCATAAAGATGATAAACATAGG 60.412 40.741 0.00 0.00 39.56 2.57
418 442 6.446318 TCGGCATAAAGATGGAAAAATATGC 58.554 36.000 6.95 6.95 42.89 3.14
422 446 5.291971 GCATCGGCATAAAGATGGAAAAAT 58.708 37.500 7.43 0.00 43.14 1.82
507 545 0.534877 TTGGCGCTGATGTGAACTGT 60.535 50.000 7.64 0.00 0.00 3.55
1185 1250 0.861837 GCTTCTTATCATCGCCACCG 59.138 55.000 0.00 0.00 0.00 4.94
1188 1253 1.134431 TGCTGCTTCTTATCATCGCCA 60.134 47.619 0.00 0.00 0.00 5.69
1194 1259 1.339342 TGCTGCTGCTGCTTCTTATCA 60.339 47.619 27.67 6.46 40.48 2.15
1197 1262 0.322648 TCTGCTGCTGCTGCTTCTTA 59.677 50.000 27.67 10.07 40.48 2.10
1201 1272 0.748450 TTTTTCTGCTGCTGCTGCTT 59.252 45.000 27.67 0.00 40.48 3.91
1424 1507 0.693622 TGGCCCGATCAACCTTTACA 59.306 50.000 0.00 0.00 0.00 2.41
1431 1514 2.120909 CCACCATGGCCCGATCAAC 61.121 63.158 13.04 0.00 0.00 3.18
1666 1761 1.056660 AGCTCAAGAAAAGGACGGGA 58.943 50.000 0.00 0.00 0.00 5.14
1696 1791 4.514585 AACCAACACCCAGCGGCA 62.515 61.111 1.45 0.00 0.00 5.69
1747 1861 1.027357 CTCCATACATGCAACCCAGC 58.973 55.000 0.00 0.00 0.00 4.85
1748 1862 2.424601 CAACTCCATACATGCAACCCAG 59.575 50.000 0.00 0.00 0.00 4.45
1749 1863 2.445427 CAACTCCATACATGCAACCCA 58.555 47.619 0.00 0.00 0.00 4.51
1750 1864 1.134946 GCAACTCCATACATGCAACCC 59.865 52.381 0.00 0.00 38.63 4.11
1751 1865 1.818060 TGCAACTCCATACATGCAACC 59.182 47.619 0.00 0.00 45.04 3.77
1836 1950 2.941333 CCAGAACAGCACACGCAG 59.059 61.111 0.00 0.00 42.27 5.18
1844 1958 1.751927 CCTCATGGGCCAGAACAGC 60.752 63.158 13.78 0.00 0.00 4.40
1893 2007 8.877779 CACAAATTTCACCATAACTTGTTTCAA 58.122 29.630 0.00 0.00 0.00 2.69
1894 2008 7.493971 CCACAAATTTCACCATAACTTGTTTCA 59.506 33.333 0.00 0.00 0.00 2.69
1895 2009 7.518211 GCCACAAATTTCACCATAACTTGTTTC 60.518 37.037 0.00 0.00 0.00 2.78
1896 2010 6.259829 GCCACAAATTTCACCATAACTTGTTT 59.740 34.615 0.00 0.00 0.00 2.83
1897 2011 5.757808 GCCACAAATTTCACCATAACTTGTT 59.242 36.000 0.00 0.00 0.00 2.83
1898 2012 5.070313 AGCCACAAATTTCACCATAACTTGT 59.930 36.000 0.00 0.00 0.00 3.16
1899 2013 5.540911 AGCCACAAATTTCACCATAACTTG 58.459 37.500 0.00 0.00 0.00 3.16
1900 2014 5.304101 TGAGCCACAAATTTCACCATAACTT 59.696 36.000 0.00 0.00 0.00 2.66
1901 2015 4.832266 TGAGCCACAAATTTCACCATAACT 59.168 37.500 0.00 0.00 0.00 2.24
1903 2017 5.132897 GTGAGCCACAAATTTCACCATAA 57.867 39.130 0.00 0.00 35.15 1.90
1904 2018 4.782019 GTGAGCCACAAATTTCACCATA 57.218 40.909 0.00 0.00 35.15 2.74
1909 2182 2.942804 TCTGGTGAGCCACAAATTTCA 58.057 42.857 7.49 0.00 40.46 2.69
1913 2186 2.664402 ACTTCTGGTGAGCCACAAAT 57.336 45.000 7.49 0.00 40.46 2.32
1917 2190 3.935828 GAGATTTACTTCTGGTGAGCCAC 59.064 47.826 0.00 0.00 40.46 5.01
1920 2193 4.564769 CGAAGAGATTTACTTCTGGTGAGC 59.435 45.833 0.00 0.00 40.78 4.26
1936 2209 7.724305 AAGTAAATAAACTTGCACGAAGAGA 57.276 32.000 0.00 0.00 38.28 3.10
1937 2210 7.149128 GCAAAGTAAATAAACTTGCACGAAGAG 60.149 37.037 0.00 0.00 39.62 2.85
1942 2215 6.523201 CCTAGCAAAGTAAATAAACTTGCACG 59.477 38.462 7.72 0.00 39.62 5.34
1943 2216 6.308041 GCCTAGCAAAGTAAATAAACTTGCAC 59.692 38.462 7.72 0.00 39.62 4.57
1945 2218 6.386654 TGCCTAGCAAAGTAAATAAACTTGC 58.613 36.000 0.00 0.00 39.62 4.01
1981 2259 3.054878 GTGTGCAAGGCAGAGAAATTTG 58.945 45.455 0.00 0.00 40.08 2.32
2003 2281 4.704540 ACATGAATTTCATAAGAACGGGCA 59.295 37.500 11.44 0.00 34.28 5.36
2038 2316 0.098376 AGAACTACGCTCGGCTAACG 59.902 55.000 0.00 0.00 46.11 3.18
2093 2371 0.035439 GGGATCGGTTTCTTGAGCCA 60.035 55.000 0.00 0.00 42.41 4.75
2229 2535 6.591834 CGATCCTTCTTCATTCTACTTTGTGT 59.408 38.462 0.00 0.00 0.00 3.72
2230 2536 6.813649 TCGATCCTTCTTCATTCTACTTTGTG 59.186 38.462 0.00 0.00 0.00 3.33
2243 2549 2.100916 TGAACGGGATCGATCCTTCTTC 59.899 50.000 36.72 30.47 46.35 2.87
2284 2590 2.027192 GGACCTTCATGTGCCTGTCTTA 60.027 50.000 0.00 0.00 0.00 2.10
2314 2621 4.278419 GTGGTGTTTCTATTTTCTGCTGGT 59.722 41.667 0.00 0.00 0.00 4.00
2366 2673 2.550978 CCGGCGACAGAGTTATGAAAT 58.449 47.619 9.30 0.00 0.00 2.17
2373 2680 3.692406 GGACCCGGCGACAGAGTT 61.692 66.667 9.30 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.