Multiple sequence alignment - TraesCS1D01G197800

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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 TraesCS1D01G197800 chr1D 100.000 1912 0 0 1 1912 279099959 279098048 0.000000e+00 3531.0
1 TraesCS1D01G197800 chr1D 100.000 41 0 0 2517 2557 279097443 279097403 2.730000e-10 76.8
2 TraesCS1D01G197800 chr1A 90.491 1651 78 29 272 1861 351345711 351344079 0.000000e+00 2106.0
3 TraesCS1D01G197800 chr1A 92.000 275 10 5 1 270 351346018 351345751 2.400000e-100 375.0
4 TraesCS1D01G197800 chr1B 92.414 1450 60 22 1 1412 378834443 378833006 0.000000e+00 2023.0
5 TraesCS1D01G197800 chr1B 85.682 440 31 11 1443 1861 378832944 378832516 3.910000e-118 435.0
6 TraesCS1D01G197800 chr2D 100.000 41 0 0 2517 2557 643465423 643465383 2.730000e-10 76.8
7 TraesCS1D01G197800 chr7D 97.561 41 1 0 2517 2557 32697746 32697786 1.270000e-08 71.3
8 TraesCS1D01G197800 chr7B 97.561 41 1 0 2517 2557 7724703 7724743 1.270000e-08 71.3
9 TraesCS1D01G197800 chr5B 97.561 41 1 0 2517 2557 508871885 508871925 1.270000e-08 71.3
10 TraesCS1D01G197800 chr5B 97.561 41 1 0 2517 2557 680095086 680095126 1.270000e-08 71.3
11 TraesCS1D01G197800 chr4B 97.561 41 1 0 2517 2557 570126318 570126278 1.270000e-08 71.3
12 TraesCS1D01G197800 chr4B 97.561 41 1 0 2517 2557 613713972 613713932 1.270000e-08 71.3
13 TraesCS1D01G197800 chr4A 97.561 41 1 0 2517 2557 690664846 690664806 1.270000e-08 71.3
14 TraesCS1D01G197800 chr3D 97.619 42 0 1 2517 2557 56316546 56316587 1.270000e-08 71.3


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 TraesCS1D01G197800 chr1D 279097403 279099959 2556 True 1803.9 3531 100.0000 1 2557 2 chr1D.!!$R1 2556
1 TraesCS1D01G197800 chr1A 351344079 351346018 1939 True 1240.5 2106 91.2455 1 1861 2 chr1A.!!$R1 1860
2 TraesCS1D01G197800 chr1B 378832516 378834443 1927 True 1229.0 2023 89.0480 1 1861 2 chr1B.!!$R1 1860

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
937 1009 0.036671 GGCGGGGTCCTATAATTCCG 60.037 60.0 0.0 0.0 40.33 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 2032 1.381463 GGAGGAACCCTAGTCGCCT 60.381 63.158 0.0 0.0 31.76 5.52 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
51 53 0.778083 AGTTCAAACCCCTTCCTCCC 59.222 55.000 0.00 0.00 0.00 4.30
132 142 3.068024 ACCAGTGCTAATGTTTGGTGTTG 59.932 43.478 0.00 0.00 40.47 3.33
139 152 5.470777 TGCTAATGTTTGGTGTTGTACTACC 59.529 40.000 4.98 6.33 37.48 3.18
249 263 4.309099 ACAAATCATGTGCATTTCACCAC 58.691 39.130 0.00 0.00 45.03 4.16
281 333 7.564128 CATCGTGCGTACATAATAACAAGAAT 58.436 34.615 4.09 0.00 0.00 2.40
307 359 2.776536 CTGACCTCTCCATTCCAGGAAT 59.223 50.000 9.12 9.12 37.20 3.01
379 431 3.403057 CGCGACACCAGTCAACCG 61.403 66.667 0.00 0.00 45.23 4.44
441 493 0.831307 GGCAGAGTTAGGATTCGGGT 59.169 55.000 0.00 0.00 0.00 5.28
801 856 2.044492 TCCCTTCTCTTCTTGGCCTCTA 59.956 50.000 3.32 0.00 0.00 2.43
831 886 0.686441 ATCTCGTCGTGGGGATTGGA 60.686 55.000 0.00 0.00 0.00 3.53
849 904 1.343478 GGAGAATGGGGGAGAGAGACA 60.343 57.143 0.00 0.00 0.00 3.41
857 912 1.137282 GGGGAGAGAGACAAACGGATC 59.863 57.143 0.00 0.00 0.00 3.36
860 915 1.133407 GAGAGAGACAAACGGATCGCT 59.867 52.381 0.00 0.00 0.00 4.93
861 916 1.546476 AGAGAGACAAACGGATCGCTT 59.454 47.619 0.00 0.00 0.00 4.68
862 917 1.921230 GAGAGACAAACGGATCGCTTC 59.079 52.381 0.00 0.00 0.00 3.86
863 918 1.000145 GAGACAAACGGATCGCTTCC 59.000 55.000 0.00 0.00 41.59 3.46
864 919 0.391263 AGACAAACGGATCGCTTCCC 60.391 55.000 0.00 0.00 42.06 3.97
865 920 0.672401 GACAAACGGATCGCTTCCCA 60.672 55.000 0.00 0.00 42.06 4.37
866 921 0.673644 ACAAACGGATCGCTTCCCAG 60.674 55.000 0.00 0.00 42.06 4.45
936 1008 1.061546 TGGCGGGGTCCTATAATTCC 58.938 55.000 0.00 0.00 0.00 3.01
937 1009 0.036671 GGCGGGGTCCTATAATTCCG 60.037 60.000 0.00 0.00 40.33 4.30
939 1011 1.071228 GCGGGGTCCTATAATTCCGTT 59.929 52.381 0.00 0.00 39.64 4.44
1135 1211 0.874390 CATGGCCGGTAAATCCATCG 59.126 55.000 7.51 1.57 38.46 3.84
1138 1214 1.525077 GCCGGTAAATCCATCGCCA 60.525 57.895 1.90 0.00 35.57 5.69
1153 1229 3.499737 CCATCGGCACCTCGCAAC 61.500 66.667 0.00 0.00 45.17 4.17
1160 1237 1.448013 GCACCTCGCAACCCTAGTC 60.448 63.158 0.00 0.00 41.79 2.59
1164 1241 1.686110 CTCGCAACCCTAGTCCCCT 60.686 63.158 0.00 0.00 0.00 4.79
1168 1245 1.205460 GCAACCCTAGTCCCCTTCCA 61.205 60.000 0.00 0.00 0.00 3.53
1169 1246 0.618981 CAACCCTAGTCCCCTTCCAC 59.381 60.000 0.00 0.00 0.00 4.02
1171 1248 0.496841 ACCCTAGTCCCCTTCCACTT 59.503 55.000 0.00 0.00 0.00 3.16
1172 1249 1.132168 ACCCTAGTCCCCTTCCACTTT 60.132 52.381 0.00 0.00 0.00 2.66
1174 1251 2.026169 CCCTAGTCCCCTTCCACTTTTC 60.026 54.545 0.00 0.00 0.00 2.29
1181 1258 1.339151 CCCTTCCACTTTTCTCCTCCG 60.339 57.143 0.00 0.00 0.00 4.63
1184 1261 1.741770 CCACTTTTCTCCTCCGCCG 60.742 63.158 0.00 0.00 0.00 6.46
1188 1265 3.642778 TTTTCTCCTCCGCCGCTCG 62.643 63.158 0.00 0.00 38.08 5.03
1211 1288 1.813513 AAGCAGTCGAATTGGTCTGG 58.186 50.000 14.43 0.30 0.00 3.86
1217 1294 0.036388 TCGAATTGGTCTGGCTGGTC 60.036 55.000 0.00 0.00 0.00 4.02
1218 1295 0.036010 CGAATTGGTCTGGCTGGTCT 60.036 55.000 0.00 0.00 0.00 3.85
1219 1296 1.611673 CGAATTGGTCTGGCTGGTCTT 60.612 52.381 0.00 0.00 0.00 3.01
1220 1297 2.087646 GAATTGGTCTGGCTGGTCTTC 58.912 52.381 0.00 0.00 0.00 2.87
1328 1405 2.268920 GCTCCCGCATCAACCTCA 59.731 61.111 0.00 0.00 35.78 3.86
1369 1456 8.181904 ACAACACCATAAATCTCACTCAAATT 57.818 30.769 0.00 0.00 0.00 1.82
1386 1473 9.414295 CACTCAAATTCAAAATGAGCATAAGAA 57.586 29.630 4.36 0.00 43.41 2.52
1427 1522 8.788806 TGGTTTATTGTTCGAATTGATACTGTT 58.211 29.630 0.00 0.00 0.00 3.16
1430 1526 8.667987 TTATTGTTCGAATTGATACTGTTTGC 57.332 30.769 0.00 0.00 0.00 3.68
1588 1708 1.203441 TTCCATCCAGGCTGTGCTCT 61.203 55.000 14.43 0.00 37.29 4.09
1604 1738 2.050918 GCTCTTAGGGGCTATCACCTT 58.949 52.381 0.00 0.00 38.30 3.50
1661 1810 7.149202 TGCTAGGATATTTAAGTGACCCAAT 57.851 36.000 0.00 0.00 0.00 3.16
1688 1837 2.485426 TGCTGCTGCTCATAACTTGTTC 59.515 45.455 17.00 0.00 40.48 3.18
1695 1844 5.798934 GCTGCTCATAACTTGTTCAAATCAG 59.201 40.000 0.00 0.00 0.00 2.90
1710 1859 4.458989 TCAAATCAGTTTCAGGTACATGCC 59.541 41.667 1.79 0.00 0.00 4.40
1750 1899 8.442632 AGTAATCCAAGTGTTATGATGATGTG 57.557 34.615 0.00 0.00 0.00 3.21
1751 1900 8.267183 AGTAATCCAAGTGTTATGATGATGTGA 58.733 33.333 0.00 0.00 0.00 3.58
1752 1901 7.563888 AATCCAAGTGTTATGATGATGTGAG 57.436 36.000 0.00 0.00 0.00 3.51
1794 1948 6.806388 AATCCTTGCAAATTGATCCAAAAC 57.194 33.333 0.00 0.00 0.00 2.43
1819 1973 9.381033 ACAAATTCTCAGATAAGTCTTGAGATG 57.619 33.333 4.46 3.55 37.90 2.90
1829 1983 2.366590 AGTCTTGAGATGCAGTGTGTCA 59.633 45.455 0.00 0.00 0.00 3.58
1830 1984 2.478134 GTCTTGAGATGCAGTGTGTCAC 59.522 50.000 0.00 0.00 34.10 3.67
1843 1997 2.217750 TGTGTCACACATTGTAGGTGC 58.782 47.619 6.50 0.70 39.62 5.01
1861 2015 9.800433 TGTAGGTGCAAATGTAAAATATTGATG 57.200 29.630 0.00 0.00 0.00 3.07
1863 2017 8.931385 AGGTGCAAATGTAAAATATTGATGAC 57.069 30.769 0.00 0.00 0.00 3.06
1864 2018 7.981225 AGGTGCAAATGTAAAATATTGATGACC 59.019 33.333 0.00 0.00 0.00 4.02
1865 2019 7.224557 GGTGCAAATGTAAAATATTGATGACCC 59.775 37.037 0.00 0.00 0.00 4.46
1866 2020 7.224557 GTGCAAATGTAAAATATTGATGACCCC 59.775 37.037 0.00 0.00 0.00 4.95
1867 2021 6.705825 GCAAATGTAAAATATTGATGACCCCC 59.294 38.462 0.00 0.00 0.00 5.40
1886 2040 4.475444 CCCTCCCCCAGGCGACTA 62.475 72.222 0.00 0.00 41.80 2.59
1887 2041 2.840102 CCTCCCCCAGGCGACTAG 60.840 72.222 0.00 0.00 40.21 2.57
1888 2042 2.840102 CTCCCCCAGGCGACTAGG 60.840 72.222 0.00 0.00 40.21 3.02
1892 2046 2.901042 CCCAGGCGACTAGGGTTC 59.099 66.667 15.55 0.00 41.31 3.62
1893 2047 2.732619 CCCAGGCGACTAGGGTTCC 61.733 68.421 15.55 0.00 41.31 3.62
1894 2048 1.686110 CCAGGCGACTAGGGTTCCT 60.686 63.158 0.00 0.00 40.21 3.36
1895 2049 1.677637 CCAGGCGACTAGGGTTCCTC 61.678 65.000 0.00 0.00 40.21 3.71
1896 2050 1.381463 AGGCGACTAGGGTTCCTCC 60.381 63.158 0.00 0.00 40.61 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 2.256117 AGGTTTTGTCGAGGAGTTGG 57.744 50.000 0.00 0.00 0.00 3.77
76 85 4.885907 GGTTTATAGGGGGTTTGAACTAGC 59.114 45.833 0.00 0.00 0.00 3.42
132 142 3.532542 GAGCTTGGGAATGTGGTAGTAC 58.467 50.000 0.00 0.00 0.00 2.73
139 152 0.890683 GTTGGGAGCTTGGGAATGTG 59.109 55.000 0.00 0.00 0.00 3.21
249 263 0.510790 TGTACGCACGATGCAGTTTG 59.489 50.000 9.95 0.00 45.36 2.93
281 333 1.573108 GAATGGAGAGGTCAGGGTGA 58.427 55.000 0.00 0.00 0.00 4.02
372 424 1.940613 GGCTGATATGGTTCGGTTGAC 59.059 52.381 0.00 0.00 0.00 3.18
373 425 1.557371 TGGCTGATATGGTTCGGTTGA 59.443 47.619 0.00 0.00 0.00 3.18
379 431 4.009675 TGTTTCACTGGCTGATATGGTTC 58.990 43.478 0.00 0.00 0.00 3.62
721 773 2.514824 GAGATGGTGCGGAAGGCC 60.515 66.667 0.00 0.00 42.61 5.19
801 856 1.109920 CGACGAGATCCATCCACCCT 61.110 60.000 0.00 0.00 0.00 4.34
831 886 2.573915 GTTTGTCTCTCTCCCCCATTCT 59.426 50.000 0.00 0.00 0.00 2.40
857 912 0.323629 TAAGTGGGAACTGGGAAGCG 59.676 55.000 0.00 0.00 0.00 4.68
860 915 2.637872 CTCTGTAAGTGGGAACTGGGAA 59.362 50.000 0.00 0.00 33.76 3.97
861 916 2.257207 CTCTGTAAGTGGGAACTGGGA 58.743 52.381 0.00 0.00 33.76 4.37
862 917 1.978580 ACTCTGTAAGTGGGAACTGGG 59.021 52.381 0.00 0.00 36.65 4.45
936 1008 0.104120 TGGTCACTGGTCAGACAACG 59.896 55.000 2.17 0.00 36.50 4.10
937 1009 1.583054 GTGGTCACTGGTCAGACAAC 58.417 55.000 2.17 0.00 36.50 3.32
939 1011 1.407656 GGGTGGTCACTGGTCAGACA 61.408 60.000 2.17 0.00 36.50 3.41
1138 1214 4.778143 GGGTTGCGAGGTGCCGAT 62.778 66.667 0.00 0.00 45.60 4.18
1153 1229 1.670059 AAAGTGGAAGGGGACTAGGG 58.330 55.000 0.00 0.00 42.68 3.53
1160 1237 1.004862 GGAGGAGAAAAGTGGAAGGGG 59.995 57.143 0.00 0.00 0.00 4.79
1164 1241 0.036306 GGCGGAGGAGAAAAGTGGAA 59.964 55.000 0.00 0.00 0.00 3.53
1168 1245 2.047179 GCGGCGGAGGAGAAAAGT 60.047 61.111 9.78 0.00 0.00 2.66
1169 1246 1.811679 GAGCGGCGGAGGAGAAAAG 60.812 63.158 9.78 0.00 0.00 2.27
1171 1248 4.129737 CGAGCGGCGGAGGAGAAA 62.130 66.667 9.78 0.00 36.03 2.52
1184 1261 1.641577 ATTCGACTGCTTAACCGAGC 58.358 50.000 0.00 0.00 43.00 5.03
1188 1265 3.125316 CAGACCAATTCGACTGCTTAACC 59.875 47.826 0.00 0.00 0.00 2.85
1328 1405 1.282157 GTTGTTACCTGGCCTGGAGAT 59.718 52.381 33.43 15.03 0.00 2.75
1369 1456 8.593945 ACCCTAAATTCTTATGCTCATTTTGA 57.406 30.769 0.00 0.00 0.00 2.69
1391 1478 7.090953 TCGAACAATAAACCATAATCAACCC 57.909 36.000 0.00 0.00 0.00 4.11
1421 1516 5.929415 TCTTGTGATCGTATTGCAAACAGTA 59.071 36.000 1.71 0.00 0.00 2.74
1423 1518 5.106948 ACTCTTGTGATCGTATTGCAAACAG 60.107 40.000 1.71 0.00 0.00 3.16
1427 1522 5.940192 AAACTCTTGTGATCGTATTGCAA 57.060 34.783 0.00 0.00 0.00 4.08
1430 1526 9.265938 CAAACATAAACTCTTGTGATCGTATTG 57.734 33.333 0.00 0.00 0.00 1.90
1588 1708 5.034200 TGAACTAAAGGTGATAGCCCCTAA 58.966 41.667 0.00 0.00 0.00 2.69
1604 1738 9.241919 TGGAAATGATTTAGCAGAATGAACTAA 57.758 29.630 0.00 0.00 39.69 2.24
1661 1810 2.406596 TATGAGCAGCAGCATCACAA 57.593 45.000 3.17 0.00 45.49 3.33
1688 1837 4.218200 TGGCATGTACCTGAAACTGATTTG 59.782 41.667 1.92 0.00 0.00 2.32
1695 1844 4.989279 AATCATGGCATGTACCTGAAAC 57.011 40.909 25.62 0.00 0.00 2.78
1794 1948 8.336806 GCATCTCAAGACTTATCTGAGAATTTG 58.663 37.037 8.32 4.77 39.95 2.32
1809 1963 2.478134 GTGACACACTGCATCTCAAGAC 59.522 50.000 0.00 0.00 0.00 3.01
1829 1983 6.398234 TTTACATTTGCACCTACAATGTGT 57.602 33.333 19.30 2.72 36.11 3.72
1830 1984 7.887996 ATTTTACATTTGCACCTACAATGTG 57.112 32.000 19.30 0.00 36.79 3.21
1869 2023 4.475444 TAGTCGCCTGGGGGAGGG 62.475 72.222 11.17 0.00 43.07 4.30
1870 2024 2.840102 CTAGTCGCCTGGGGGAGG 60.840 72.222 11.17 0.00 46.13 4.30
1871 2025 2.840102 CCTAGTCGCCTGGGGGAG 60.840 72.222 11.17 6.15 35.74 4.30
1875 2029 2.732619 GGAACCCTAGTCGCCTGGG 61.733 68.421 0.00 0.00 46.07 4.45
1876 2030 1.677637 GAGGAACCCTAGTCGCCTGG 61.678 65.000 0.00 0.00 31.76 4.45
1877 2031 1.677637 GGAGGAACCCTAGTCGCCTG 61.678 65.000 0.00 0.00 31.76 4.85
1878 2032 1.381463 GGAGGAACCCTAGTCGCCT 60.381 63.158 0.00 0.00 31.76 5.52
1879 2033 3.218227 GGAGGAACCCTAGTCGCC 58.782 66.667 0.00 0.00 31.76 5.54


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

AutoCloner maintained by Alex Coulton.