Multiple sequence alignment - TraesCS4D01G219900

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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 TraesCS4D01G219900 chr4D 100.000 1890 0 0 387 2276 375123935 375122046 0.000000e+00 3491
1 TraesCS4D01G219900 chr4D 100.000 202 0 0 1 202 375124321 375124120 7.680000e-100 374
2 TraesCS4D01G219900 chr4B 93.145 1911 91 15 387 2276 462216588 462214697 0.000000e+00 2767
3 TraesCS4D01G219900 chr4B 92.611 203 14 1 1 202 462216810 462216608 7.950000e-75 291
4 TraesCS4D01G219900 chr4A 92.946 1616 88 12 387 1994 89444078 89445675 0.000000e+00 2329
5 TraesCS4D01G219900 chr4A 89.347 291 10 5 1987 2276 89445867 89446137 1.670000e-91 346
6 TraesCS4D01G219900 chr4A 91.089 202 16 2 1 202 89443859 89444058 2.880000e-69 272
7 TraesCS4D01G219900 chr5B 82.863 461 40 30 1824 2276 74990693 74991122 5.930000e-101 377
8 TraesCS4D01G219900 chr5A 82.505 463 41 27 1824 2276 59702715 59703147 9.930000e-99 370
9 TraesCS4D01G219900 chr5D 82.430 461 43 26 1824 2276 69098223 69098653 3.570000e-98 368


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 TraesCS4D01G219900 chr4D 375122046 375124321 2275 True 1932.500000 3491 100.000000 1 2276 2 chr4D.!!$R1 2275
1 TraesCS4D01G219900 chr4B 462214697 462216810 2113 True 1529.000000 2767 92.878000 1 2276 2 chr4B.!!$R1 2275
2 TraesCS4D01G219900 chr4A 89443859 89446137 2278 False 982.333333 2329 91.127333 1 2276 3 chr4A.!!$F1 2275

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
950 967 0.114364 AAATCCCCAAAGCCCTCGTT 59.886 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2400 0.324091 CTTCCCAAGCTGGCATCCTT 60.324 55.0 0.0 0.0 35.79 3.36 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
93 95 7.570132 TGTAACAGGTTATGGCATATTACACT 58.430 34.615 19.30 9.20 0.00 3.55
117 119 5.128663 TGCACTGGAATACTGTTATGCTAGA 59.871 40.000 0.00 0.00 28.35 2.43
141 143 7.548780 AGAAATCTAGCAGAACTCAGAATTCAC 59.451 37.037 8.44 0.00 32.00 3.18
155 157 8.713271 ACTCAGAATTCACTTCGAAATAAAGAC 58.287 33.333 8.44 0.00 38.98 3.01
418 421 3.091203 CAAACGATTGAAGCGAGATGCG 61.091 50.000 10.69 0.00 43.57 4.73
502 505 2.599677 AGAAGGGTGAACGAAGAGAGT 58.400 47.619 0.00 0.00 0.00 3.24
615 618 1.227089 CGACGCCCTCCATCTTCTG 60.227 63.158 0.00 0.00 0.00 3.02
715 718 0.616111 AGTCCGACAGAGAGCCCATT 60.616 55.000 0.40 0.00 0.00 3.16
730 733 2.593148 ATTGTTCACACCGCGCCA 60.593 55.556 0.00 0.00 0.00 5.69
757 760 4.281947 GTACGCCGCCTAGGAGCC 62.282 72.222 14.75 0.00 44.30 4.70
768 771 1.613255 CCTAGGAGCCAAAGCGGAAAA 60.613 52.381 1.05 0.00 46.67 2.29
773 776 2.492088 GGAGCCAAAGCGGAAAATAACT 59.508 45.455 0.00 0.00 46.67 2.24
781 784 6.089417 CCAAAGCGGAAAATAACTGATGTTTC 59.911 38.462 0.00 0.00 35.66 2.78
795 798 0.402504 TGTTTCGCACATAACCCCCT 59.597 50.000 0.00 0.00 0.00 4.79
806 809 0.413037 TAACCCCCTCCAACCGTAGA 59.587 55.000 0.00 0.00 0.00 2.59
849 855 3.649502 GCTTTACTGGGCTAAGGGGTATA 59.350 47.826 0.00 0.00 0.00 1.47
852 858 5.684853 TTACTGGGCTAAGGGGTATAGTA 57.315 43.478 0.00 0.00 0.00 1.82
950 967 0.114364 AAATCCCCAAAGCCCTCGTT 59.886 50.000 0.00 0.00 0.00 3.85
980 997 3.694926 CCAGATTTCTTCTCCAGCCTTT 58.305 45.455 0.00 0.00 29.93 3.11
991 1008 1.298157 CCAGCCTTTCATCGCACGAA 61.298 55.000 0.00 0.00 0.00 3.85
999 1019 0.390998 TCATCGCACGAAAGGCATCA 60.391 50.000 0.00 0.00 0.00 3.07
1207 1227 4.357279 AGCTGGAGGTGGCCAAGC 62.357 66.667 17.05 17.05 37.52 4.01
1370 1392 9.664777 ATGTACTGTTAGTAGGGTTATTATGGA 57.335 33.333 0.00 0.00 30.12 3.41
1481 1503 9.218359 CGCAAATTAATGATCATGATACTATGC 57.782 33.333 9.46 12.65 0.00 3.14
1532 1558 5.246307 ACTACCTGATTGTGGCTTTAGAAC 58.754 41.667 0.00 0.00 0.00 3.01
1567 1593 1.893808 CCTGGTGTTCTTGCAGCGT 60.894 57.895 0.00 0.00 39.49 5.07
1632 1658 1.066858 ACTCCATACTTGTCGTGCTGG 60.067 52.381 0.00 0.00 33.42 4.85
1656 1682 5.567224 GCCATGATCAAATGTGTGGAAGAAA 60.567 40.000 13.76 0.00 0.00 2.52
1676 1702 9.952188 GAAGAAATATTAAGGGTGTATTGAAGC 57.048 33.333 0.00 0.00 0.00 3.86
1763 1789 2.363306 ACCAGATCAGGTTTTGCACA 57.637 45.000 3.50 0.00 39.34 4.57
1843 1869 3.802948 ATGTCCTGATCCGTACAAGAC 57.197 47.619 0.00 0.00 31.70 3.01
1949 1975 8.782533 GCAAATAGCCATTAATACAACTACAC 57.217 34.615 0.00 0.00 37.23 2.90
2063 2289 3.110358 CACAATATGGTGAAGCATTGCG 58.890 45.455 3.96 0.00 41.32 4.85
2064 2290 2.121786 CAATATGGTGAAGCATTGCGC 58.878 47.619 0.00 0.00 42.91 6.09
2070 2296 1.446445 TGAAGCATTGCGCCATTGC 60.446 52.632 15.89 15.89 44.04 3.56
2071 2297 2.125431 AAGCATTGCGCCATTGCC 60.125 55.556 18.87 5.53 44.04 4.52
2074 2300 2.261981 CATTGCGCCATTGCCACA 59.738 55.556 4.18 0.00 0.00 4.17
2075 2301 2.095847 CATTGCGCCATTGCCACAC 61.096 57.895 4.18 0.00 0.00 3.82
2077 2303 2.495366 ATTGCGCCATTGCCACACTG 62.495 55.000 4.18 0.00 0.00 3.66
2078 2304 3.364441 GCGCCATTGCCACACTGA 61.364 61.111 0.00 0.00 0.00 3.41
2079 2305 2.872557 CGCCATTGCCACACTGAG 59.127 61.111 0.00 0.00 0.00 3.35
2080 2306 1.672030 CGCCATTGCCACACTGAGA 60.672 57.895 0.00 0.00 0.00 3.27
2081 2307 1.878775 GCCATTGCCACACTGAGAC 59.121 57.895 0.00 0.00 0.00 3.36
2082 2308 0.607489 GCCATTGCCACACTGAGACT 60.607 55.000 0.00 0.00 0.00 3.24
2083 2309 1.339055 GCCATTGCCACACTGAGACTA 60.339 52.381 0.00 0.00 0.00 2.59
2084 2310 2.681976 GCCATTGCCACACTGAGACTAT 60.682 50.000 0.00 0.00 0.00 2.12
2085 2311 3.432186 GCCATTGCCACACTGAGACTATA 60.432 47.826 0.00 0.00 0.00 1.31
2086 2312 4.122776 CCATTGCCACACTGAGACTATAC 58.877 47.826 0.00 0.00 0.00 1.47
2174 2400 1.468520 GTTGCTTCTTGCTTGCCGATA 59.531 47.619 0.00 0.00 43.37 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 95 4.220693 AGCATAACAGTATTCCAGTGCA 57.779 40.909 0.00 0.00 34.01 4.57
117 119 7.393216 AGTGAATTCTGAGTTCTGCTAGATTT 58.607 34.615 13.11 0.00 0.00 2.17
134 136 9.665264 AGTTTGTCTTTATTTCGAAGTGAATTC 57.335 29.630 3.04 0.00 36.22 2.17
141 143 9.582223 GTGTAGAAGTTTGTCTTTATTTCGAAG 57.418 33.333 0.00 0.00 36.40 3.79
155 157 8.842358 TTAGGGTTTATCTGTGTAGAAGTTTG 57.158 34.615 0.00 0.00 36.32 2.93
418 421 4.284550 TGTGGCTGGGCTCCAACC 62.285 66.667 6.69 6.69 39.99 3.77
615 618 1.909287 GAGGAGGGAGATACCGGCC 60.909 68.421 0.00 0.00 40.11 6.13
715 718 2.824489 TTTGGCGCGGTGTGAACA 60.824 55.556 8.83 0.00 0.00 3.18
737 740 2.517875 TCCTAGGCGGCGTACTCC 60.518 66.667 9.37 0.00 0.00 3.85
757 760 6.183359 CGAAACATCAGTTATTTTCCGCTTTG 60.183 38.462 0.00 0.00 36.84 2.77
781 784 1.029947 GTTGGAGGGGGTTATGTGCG 61.030 60.000 0.00 0.00 0.00 5.34
795 798 2.827322 TCCGAAGAAATCTACGGTTGGA 59.173 45.455 0.00 0.00 44.72 3.53
849 855 7.770897 CCCTTTCTATGAAGCTTATTGTGTACT 59.229 37.037 0.00 0.00 0.00 2.73
852 858 5.888161 CCCCTTTCTATGAAGCTTATTGTGT 59.112 40.000 0.00 0.00 0.00 3.72
870 876 6.726764 TGGTAAATTAGCAAATACACCCCTTT 59.273 34.615 2.04 0.00 32.06 3.11
873 879 6.724893 ATGGTAAATTAGCAAATACACCCC 57.275 37.500 9.04 0.00 39.89 4.95
950 967 2.379907 AGAAGAAATCTGGCTTTGGGGA 59.620 45.455 0.00 0.00 36.88 4.81
980 997 0.390998 TGATGCCTTTCGTGCGATGA 60.391 50.000 0.00 0.00 0.00 2.92
991 1008 3.520862 CGCCGCCATTGATGCCTT 61.521 61.111 0.00 0.00 0.00 4.35
1170 1190 4.302509 TGCTTCCCGTCCGCGAAA 62.303 61.111 8.23 0.00 41.33 3.46
1207 1227 1.291877 GAGTACACCAGCACTTGCCG 61.292 60.000 0.00 0.00 43.38 5.69
1286 1306 2.434359 CGGGCGTGAAACCTCTCC 60.434 66.667 0.00 0.00 0.00 3.71
1335 1355 6.985059 CCCTACTAACAGTACATAAAAGAGCC 59.015 42.308 0.00 0.00 0.00 4.70
1365 1387 4.911390 TCTATCAGCGTCAGATCTCCATA 58.089 43.478 0.00 0.00 0.00 2.74
1366 1388 3.760738 TCTATCAGCGTCAGATCTCCAT 58.239 45.455 0.00 0.00 0.00 3.41
1367 1389 3.214696 TCTATCAGCGTCAGATCTCCA 57.785 47.619 0.00 0.00 0.00 3.86
1368 1390 4.576216 TTTCTATCAGCGTCAGATCTCC 57.424 45.455 0.00 0.00 0.00 3.71
1369 1391 6.363088 CAGAATTTCTATCAGCGTCAGATCTC 59.637 42.308 0.00 0.00 0.00 2.75
1370 1392 6.215121 CAGAATTTCTATCAGCGTCAGATCT 58.785 40.000 0.00 0.00 0.00 2.75
1489 1511 5.678132 AGTTTCACATGTAAAACCGGTAC 57.322 39.130 19.03 2.48 36.29 3.34
1495 1517 8.349983 ACAATCAGGTAGTTTCACATGTAAAAC 58.650 33.333 15.64 15.64 35.97 2.43
1532 1558 2.093973 CCAGGGCAAGGCTATACGATAG 60.094 54.545 0.00 0.00 46.19 2.08
1567 1593 7.878127 GGATGTAGTAATAGCCAAAGATAGCAA 59.122 37.037 0.00 0.00 0.00 3.91
1573 1599 5.665812 AGTGGGATGTAGTAATAGCCAAAGA 59.334 40.000 0.00 0.00 0.00 2.52
1632 1658 3.444742 TCTTCCACACATTTGATCATGGC 59.555 43.478 5.98 0.00 0.00 4.40
1656 1682 7.174946 CGATTGGCTTCAATACACCCTTAATAT 59.825 37.037 0.00 0.00 40.83 1.28
1676 1702 3.126858 CAGTTGATGGGTAACACGATTGG 59.873 47.826 0.00 0.00 39.74 3.16
1843 1869 4.154015 TCGTGTCTTGCATTGTTATCCTTG 59.846 41.667 0.00 0.00 0.00 3.61
1897 1923 4.002982 TGCAGCTTGTGTTATTGACCTAG 58.997 43.478 0.00 0.00 0.00 3.02
1899 1925 2.862541 TGCAGCTTGTGTTATTGACCT 58.137 42.857 0.00 0.00 0.00 3.85
1900 1926 3.855689 ATGCAGCTTGTGTTATTGACC 57.144 42.857 0.00 0.00 0.00 4.02
1901 1927 5.276270 CCATATGCAGCTTGTGTTATTGAC 58.724 41.667 0.00 0.00 0.00 3.18
1941 1967 8.517878 AGATCCATGATTTTTCTTGTGTAGTTG 58.482 33.333 0.00 0.00 0.00 3.16
1949 1975 9.745880 CCAAGAATAGATCCATGATTTTTCTTG 57.254 33.333 18.55 18.55 39.24 3.02
2063 2289 0.607489 AGTCTCAGTGTGGCAATGGC 60.607 55.000 0.00 0.00 40.13 4.40
2064 2290 2.768253 TAGTCTCAGTGTGGCAATGG 57.232 50.000 0.00 0.00 29.97 3.16
2070 2296 1.681793 CCCCGTATAGTCTCAGTGTGG 59.318 57.143 0.00 0.00 0.00 4.17
2071 2297 2.376109 ACCCCGTATAGTCTCAGTGTG 58.624 52.381 0.00 0.00 0.00 3.82
2074 2300 7.236529 TCATATTTACCCCGTATAGTCTCAGT 58.763 38.462 0.00 0.00 0.00 3.41
2075 2301 7.698506 TCATATTTACCCCGTATAGTCTCAG 57.301 40.000 0.00 0.00 0.00 3.35
2077 2303 8.968969 AGATTCATATTTACCCCGTATAGTCTC 58.031 37.037 0.00 0.00 0.00 3.36
2078 2304 8.896722 AGATTCATATTTACCCCGTATAGTCT 57.103 34.615 0.00 0.00 0.00 3.24
2085 2311 9.151177 TCTTAGTAAGATTCATATTTACCCCGT 57.849 33.333 8.59 0.00 31.20 5.28
2086 2312 9.991906 TTCTTAGTAAGATTCATATTTACCCCG 57.008 33.333 13.34 0.00 37.38 5.73
2174 2400 0.324091 CTTCCCAAGCTGGCATCCTT 60.324 55.000 0.00 0.00 35.79 3.36


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

AutoCloner maintained by Alex Coulton.