Multiple sequence alignment - TraesCS7A01G291200

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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 TraesCS7A01G291200 chr7A 100.000 2360 0 0 1 2360 353933189 353930830 0 4359
1 TraesCS7A01G291200 chr3B 84.320 2366 338 20 1 2360 158522435 158524773 0 2283
2 TraesCS7A01G291200 chr3B 84.659 2138 285 27 1 2122 564256297 564258407 0 2091
3 TraesCS7A01G291200 chr5B 84.168 2375 335 17 1 2360 34854001 34856349 0 2265
4 TraesCS7A01G291200 chr7D 84.052 2389 334 27 3 2359 170456590 170454217 0 2257
5 TraesCS7A01G291200 chr2A 81.791 2378 363 38 1 2359 603541234 603538908 0 1929
6 TraesCS7A01G291200 chr6A 81.329 2378 373 38 1 2359 391048597 391046272 0 1866
7 TraesCS7A01G291200 chr2D 81.231 2355 361 43 28 2356 285899748 285897449 0 1825
8 TraesCS7A01G291200 chr6D 83.812 1915 285 14 461 2359 50568169 50570074 0 1796
9 TraesCS7A01G291200 chr6B 80.632 2375 380 46 9 2359 648800361 648798043 0 1764
10 TraesCS7A01G291200 chr4B 80.143 2372 385 51 9 2359 472243186 472240880 0 1692


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 TraesCS7A01G291200 chr7A 353930830 353933189 2359 True 4359 4359 100.000 1 2360 1 chr7A.!!$R1 2359
1 TraesCS7A01G291200 chr3B 158522435 158524773 2338 False 2283 2283 84.320 1 2360 1 chr3B.!!$F1 2359
2 TraesCS7A01G291200 chr3B 564256297 564258407 2110 False 2091 2091 84.659 1 2122 1 chr3B.!!$F2 2121
3 TraesCS7A01G291200 chr5B 34854001 34856349 2348 False 2265 2265 84.168 1 2360 1 chr5B.!!$F1 2359
4 TraesCS7A01G291200 chr7D 170454217 170456590 2373 True 2257 2257 84.052 3 2359 1 chr7D.!!$R1 2356
5 TraesCS7A01G291200 chr2A 603538908 603541234 2326 True 1929 1929 81.791 1 2359 1 chr2A.!!$R1 2358
6 TraesCS7A01G291200 chr6A 391046272 391048597 2325 True 1866 1866 81.329 1 2359 1 chr6A.!!$R1 2358
7 TraesCS7A01G291200 chr2D 285897449 285899748 2299 True 1825 1825 81.231 28 2356 1 chr2D.!!$R1 2328
8 TraesCS7A01G291200 chr6D 50568169 50570074 1905 False 1796 1796 83.812 461 2359 1 chr6D.!!$F1 1898
9 TraesCS7A01G291200 chr6B 648798043 648800361 2318 True 1764 1764 80.632 9 2359 1 chr6B.!!$R1 2350
10 TraesCS7A01G291200 chr4B 472240880 472243186 2306 True 1692 1692 80.143 9 2359 1 chr4B.!!$R1 2350

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
953 985 0.677731 CGGGGAAGCTCATTGAAGCA 60.678 55.0 9.67 0.0 45.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 1825 0.032615 CCTAGGCCTCAGAGACCACT 60.033 60.0 9.68 0.0 0.0 4.0 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
133 134 2.819984 AATCGGCCAACCAGCGTCAT 62.820 55.000 2.24 0.00 34.57 3.06
175 176 3.877450 GCCATCCCAGGCGATCCA 61.877 66.667 0.00 0.00 46.12 3.41
299 300 2.609299 TTGGTGGCATCCCGAGGA 60.609 61.111 0.00 0.00 35.55 3.71
353 360 4.496336 GGAGCCAATCCTGCGCCT 62.496 66.667 4.18 0.00 45.64 5.52
376 383 1.925455 CCCCTGTCCCCACACAGAT 60.925 63.158 2.08 0.00 45.92 2.90
379 386 1.257750 CCTGTCCCCACACAGATCGA 61.258 60.000 2.08 0.00 45.92 3.59
471 478 1.819632 GCCGAATCGCTTGGACCAT 60.820 57.895 0.00 0.00 0.00 3.55
482 489 3.861797 GGACCATGCCGATCCCGT 61.862 66.667 0.00 0.00 0.00 5.28
506 513 3.942439 GGCGGGCCCATCCTACTC 61.942 72.222 24.92 0.00 34.39 2.59
507 514 3.161450 GCGGGCCCATCCTACTCA 61.161 66.667 24.92 0.00 34.39 3.41
654 685 2.659610 GCGTCCTCACTGCTTCCT 59.340 61.111 0.00 0.00 0.00 3.36
738 769 3.693382 TATCGTGCGTGCGGACCAG 62.693 63.158 10.39 0.00 32.67 4.00
801 832 0.820871 GTCTCGGCCTCATCTCAAGT 59.179 55.000 0.00 0.00 0.00 3.16
856 887 4.197750 CAAATATGCTCTGCTCCTTGAGT 58.802 43.478 0.00 0.00 33.22 3.41
939 971 3.995809 CTGCCTTCTACCCCGGGGA 62.996 68.421 46.68 27.27 38.96 4.81
953 985 0.677731 CGGGGAAGCTCATTGAAGCA 60.678 55.000 9.67 0.00 45.00 3.91
1021 1056 9.627123 TTCCTATGGATTATAACCTCAAAACAG 57.373 33.333 0.00 0.00 0.00 3.16
1086 1121 1.067084 CGTCCGCAGCATGATCTCT 59.933 57.895 0.00 0.00 39.69 3.10
1113 1148 0.108804 CGCCTACCATCGTGTGTCTT 60.109 55.000 0.00 0.00 0.00 3.01
1158 1193 1.361668 CCGACGCCATTGTCTTGGAG 61.362 60.000 0.00 0.00 41.79 3.86
1233 1273 0.610232 GTGGCATCCTCCTTGCTTGT 60.610 55.000 0.00 0.00 40.03 3.16
1252 1292 2.423892 TGTCAACGCTCTACCATCTCTC 59.576 50.000 0.00 0.00 0.00 3.20
1253 1293 2.685897 GTCAACGCTCTACCATCTCTCT 59.314 50.000 0.00 0.00 0.00 3.10
1254 1294 2.946329 TCAACGCTCTACCATCTCTCTC 59.054 50.000 0.00 0.00 0.00 3.20
1255 1295 2.948979 CAACGCTCTACCATCTCTCTCT 59.051 50.000 0.00 0.00 0.00 3.10
1410 1451 2.431771 CGACGTGCGTGAATCCCA 60.432 61.111 0.67 0.00 34.64 4.37
1455 1496 7.451255 TGGTGGAGATTTTAACATGATCACTTT 59.549 33.333 0.00 0.00 0.00 2.66
1463 1504 1.278985 ACATGATCACTTTGGCCTCGA 59.721 47.619 3.32 0.00 0.00 4.04
1536 1577 1.960040 ATCGCCGACATGGAGCTTCA 61.960 55.000 0.00 0.00 42.00 3.02
1600 1641 2.657620 GACGCCCCGACGCTTATC 60.658 66.667 0.00 0.00 36.19 1.75
1630 1671 3.963733 CATCCTTTGCACCTCTGGA 57.036 52.632 0.00 0.00 0.00 3.86
1651 1692 2.746375 GGAGATCGCCCACCCACAT 61.746 63.158 3.71 0.00 0.00 3.21
1696 1737 3.640407 GCCTCTGACCACTGCCCA 61.640 66.667 0.00 0.00 0.00 5.36
1700 1741 1.152247 TCTGACCACTGCCCACTCT 60.152 57.895 0.00 0.00 0.00 3.24
1702 1743 0.976641 CTGACCACTGCCCACTCTTA 59.023 55.000 0.00 0.00 0.00 2.10
1710 1751 3.258372 CACTGCCCACTCTTAGTTGACTA 59.742 47.826 0.00 0.00 0.00 2.59
1721 1762 1.078426 GTTGACTACATGGCCCGCT 60.078 57.895 0.00 0.00 0.00 5.52
1800 1842 1.561643 CAAGTGGTCTCTGAGGCCTA 58.438 55.000 27.16 12.34 41.63 3.93
1831 1873 2.107141 CCTGACGCCGATCCCTTC 59.893 66.667 0.00 0.00 0.00 3.46
1859 1901 0.999406 CATGACACGTCTTAAGGCGG 59.001 55.000 30.90 21.78 0.00 6.13
1873 1915 2.985847 GCGGCTGCCAGGAAGTTT 60.986 61.111 20.29 0.00 33.98 2.66
1886 1929 4.137543 CAGGAAGTTTAAAGCTGGAGTGT 58.862 43.478 0.00 0.00 0.00 3.55
1896 1939 1.446792 CTGGAGTGTGCGCTCGATT 60.447 57.895 9.73 0.00 36.41 3.34
1900 1943 1.687494 GAGTGTGCGCTCGATTGACC 61.687 60.000 9.73 0.00 0.00 4.02
1911 1954 1.887854 TCGATTGACCACGTGTCCTTA 59.112 47.619 15.65 0.00 43.78 2.69
1951 1994 2.810274 GAGCTCATTGCAAGACTTGACA 59.190 45.455 19.51 12.89 45.94 3.58
1998 2043 1.133915 TCCTCGAAACCTGGCTTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
2040 2085 3.394836 GCCTTGCCTCCCTCGAGT 61.395 66.667 12.31 0.00 33.93 4.18
2051 2096 0.167033 CCCTCGAGTGATCTATCGCG 59.833 60.000 12.31 0.00 41.94 5.87
2060 2105 1.004277 GATCTATCGCGAGGCAACGG 61.004 60.000 16.66 0.00 46.39 4.44
2204 2250 1.738346 CGATGAGATGACCGAGGCCA 61.738 60.000 5.01 0.00 0.00 5.36
2243 2289 1.228245 GTCCTTGGCAGCACTTCCA 60.228 57.895 0.00 0.00 0.00 3.53
2296 2342 1.302192 GGTGCCGCAGTTTGACCTA 60.302 57.895 0.00 0.00 0.00 3.08
2300 2346 0.320421 GCCGCAGTTTGACCTACTCA 60.320 55.000 0.00 0.00 0.00 3.41
2301 2347 1.676014 GCCGCAGTTTGACCTACTCAT 60.676 52.381 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 1.201429 GGGACTTGGAGAGGAAGGCA 61.201 60.000 0.00 0.00 29.01 4.75
175 176 0.908198 GACTCCTGGTTGGCTGATCT 59.092 55.000 0.00 0.00 35.26 2.75
239 240 1.995626 CCCCTCCGTGTCTCCCAAT 60.996 63.158 0.00 0.00 0.00 3.16
299 300 1.893137 TCAGTCGCATCAACAGGTAGT 59.107 47.619 0.00 0.00 0.00 2.73
353 360 4.348495 GTGGGGACAGGGGGAGGA 62.348 72.222 0.00 0.00 44.46 3.71
376 383 3.849951 GGCAGGCTCGGGATTCGA 61.850 66.667 0.00 0.00 46.77 3.71
379 386 4.473520 CACGGCAGGCTCGGGATT 62.474 66.667 0.55 0.00 31.91 3.01
471 478 1.227527 CATAAGCACGGGATCGGCA 60.228 57.895 0.00 0.00 41.39 5.69
482 489 3.790416 GATGGGCCCGCCATAAGCA 62.790 63.158 19.37 0.00 44.04 3.91
506 513 2.473609 GCAACATGCAACACAATGTCTG 59.526 45.455 0.00 0.00 44.26 3.51
507 514 2.746269 GCAACATGCAACACAATGTCT 58.254 42.857 0.00 0.00 44.26 3.41
645 676 2.203337 TTTGGCGCAGGAAGCAGT 60.203 55.556 10.83 0.00 46.13 4.40
674 705 3.031417 GCCGGCAGCTCCTTCCTAA 62.031 63.158 24.80 0.00 38.99 2.69
738 769 2.762535 TCATTTCGGAGTTGAGTCCC 57.237 50.000 0.00 0.00 32.26 4.46
801 832 0.460109 CGGAGATTGGTGCATCGTCA 60.460 55.000 5.15 0.00 0.00 4.35
843 874 0.967887 AGCGCTACTCAAGGAGCAGA 60.968 55.000 8.99 0.00 38.69 4.26
846 877 1.520342 CCAGCGCTACTCAAGGAGC 60.520 63.158 10.99 4.01 32.04 4.70
873 905 4.530710 AATCAGTGAATGCTTGCAACAT 57.469 36.364 0.00 1.66 0.00 2.71
876 908 4.859304 AGAAATCAGTGAATGCTTGCAA 57.141 36.364 0.00 0.00 0.00 4.08
939 971 3.129988 GCCAACTATGCTTCAATGAGCTT 59.870 43.478 0.00 3.41 43.11 3.74
953 985 0.322456 TCGCAAAGGCAGCCAACTAT 60.322 50.000 15.80 0.00 41.24 2.12
990 1025 5.108752 AGGTTATAATCCATAGGAAGGGGG 58.891 45.833 0.00 0.00 34.34 5.40
993 1028 9.067986 GTTTTGAGGTTATAATCCATAGGAAGG 57.932 37.037 0.00 0.00 34.34 3.46
1078 1113 1.591059 GCGCGACAGCAGAGATCAT 60.591 57.895 12.10 0.00 45.49 2.45
1086 1121 3.716539 GATGGTAGGCGCGACAGCA 62.717 63.158 17.71 16.90 45.49 4.41
1091 1126 3.445687 ACACGATGGTAGGCGCGA 61.446 61.111 12.10 0.00 0.00 5.87
1113 1148 1.341209 TGAGCGAGCTTTGTCTCTTGA 59.659 47.619 0.00 0.00 0.00 3.02
1158 1193 1.227002 GAAGGACGGACCGAGCATC 60.227 63.158 23.38 7.34 44.74 3.91
1185 1220 2.124942 GCTGCGGGGAGGAAGAAG 60.125 66.667 0.00 0.00 0.00 2.85
1233 1273 2.946329 GAGAGAGATGGTAGAGCGTTGA 59.054 50.000 0.00 0.00 0.00 3.18
1252 1292 2.468301 TGAGGGGATTGGAGAGAGAG 57.532 55.000 0.00 0.00 0.00 3.20
1253 1293 2.754526 CGATGAGGGGATTGGAGAGAGA 60.755 54.545 0.00 0.00 0.00 3.10
1254 1294 1.617850 CGATGAGGGGATTGGAGAGAG 59.382 57.143 0.00 0.00 0.00 3.20
1255 1295 1.709578 CGATGAGGGGATTGGAGAGA 58.290 55.000 0.00 0.00 0.00 3.10
1410 1451 2.575532 CAATAAGCCATGGACCGATGT 58.424 47.619 18.40 0.00 0.00 3.06
1455 1496 1.416401 AGTTGTTCTTCTTCGAGGCCA 59.584 47.619 5.01 0.00 0.00 5.36
1463 1504 5.007724 GGTTGATGTTCGAGTTGTTCTTCTT 59.992 40.000 0.00 0.00 0.00 2.52
1527 1568 5.482878 TGCATATAGAGATCATGAAGCTCCA 59.517 40.000 19.57 10.94 0.00 3.86
1536 1577 2.159184 CGGCCGTGCATATAGAGATCAT 60.159 50.000 19.50 0.00 0.00 2.45
1598 1639 2.890474 GATGCGGTCGTTGCGGAT 60.890 61.111 0.00 0.00 34.24 4.18
1651 1692 1.210478 GAGAGGCAATGGAGTAGGCAA 59.790 52.381 0.00 0.00 0.00 4.52
1684 1725 0.976641 CTAAGAGTGGGCAGTGGTCA 59.023 55.000 0.00 0.00 0.00 4.02
1696 1737 3.197983 GGGCCATGTAGTCAACTAAGAGT 59.802 47.826 4.39 0.00 0.00 3.24
1700 1741 1.406341 GCGGGCCATGTAGTCAACTAA 60.406 52.381 4.39 0.00 0.00 2.24
1702 1743 1.078426 GCGGGCCATGTAGTCAACT 60.078 57.895 4.39 0.00 0.00 3.16
1710 1751 3.790437 CCAGAGAGCGGGCCATGT 61.790 66.667 4.39 0.00 0.00 3.21
1735 1776 1.997669 ATCTCTCGAAGTGGAAACGC 58.002 50.000 0.00 0.00 42.66 4.84
1783 1825 0.032615 CCTAGGCCTCAGAGACCACT 60.033 60.000 9.68 0.00 0.00 4.00
1800 1842 0.394625 GTCAGGCGGAGTAGAGACCT 60.395 60.000 0.00 0.00 0.00 3.85
1831 1873 0.866061 GACGTGTCATGATCCGTCGG 60.866 60.000 24.71 4.39 40.04 4.79
1859 1901 1.889170 AGCTTTAAACTTCCTGGCAGC 59.111 47.619 9.56 0.00 0.00 5.25
1871 1913 0.591170 GCGCACACTCCAGCTTTAAA 59.409 50.000 0.30 0.00 0.00 1.52
1873 1915 0.670546 GAGCGCACACTCCAGCTTTA 60.671 55.000 11.47 0.00 40.39 1.85
1900 1943 2.993899 CCTTAAGCTGTAAGGACACGTG 59.006 50.000 21.05 15.48 45.24 4.49
1911 1954 1.003718 GCGGGACACCTTAAGCTGT 60.004 57.895 3.00 3.00 33.28 4.40
1951 1994 2.042831 GGCCGCAATCTTGAGCAGT 61.043 57.895 0.00 0.00 32.61 4.40
1998 2043 2.700897 GGTAGGATGCCTTGAGCTTCTA 59.299 50.000 0.00 0.00 43.49 2.10
2040 2085 0.317854 CGTTGCCTCGCGATAGATCA 60.318 55.000 10.36 0.17 39.76 2.92
2204 2250 1.070289 GTCGGAGAAGTGGACAAAGGT 59.930 52.381 0.00 0.00 39.69 3.50
2296 2342 0.321919 ATGGCGTGTCAAGCATGAGT 60.322 50.000 12.89 0.00 35.88 3.41
2300 2346 0.523072 GTGAATGGCGTGTCAAGCAT 59.477 50.000 12.89 2.06 36.08 3.79
2301 2347 1.514678 GGTGAATGGCGTGTCAAGCA 61.515 55.000 12.89 0.00 36.08 3.91


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

AutoCloner maintained by Alex Coulton.