Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016094.1 Corchorus olitorius cultivar O-4 contig16127, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45083
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4162 original size:42 final size:42
Alignment explanation
Indices: 4103--4183 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
4093 GCTAAGTCTT
4103 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* *
4145 GAAAATTCTTTGTAAATTAAGAAATACTCAATTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
4184 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:4332 original size:56 final size:56
Alignment explanation
Indices: 4250--4363 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
4240 TTTATTTTGT
4250 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
* *
4306 AGAATAATTAAGTAGAGATAGTGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
4362 AG
1 AG
4364 GAAACGTATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:23283 original size:49 final size:49
Alignment explanation
Indices: 23211--23305 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
23201 ATAAGGAAAG
*
23211 GAGATAAAAATAGACTAATGAGAGACCTGAATCTGAAAGTGATAATTCA
1 GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAATTCA
23260 GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAAT
1 GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAAT
23306 CCATATGTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21
Consensus pattern (49 bp):
GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAATTCA
Found at i:25300 original size:287 final size:285
Alignment explanation
Indices: 24816--25339 Score: 836
Period size: 287 Copynumber: 1.8 Consensus size: 285
24806 GGGATTAAAT
**
24816 AGCATAAAGCATAAAAGTATAGGAACCATTTGCTAAATATTACAAAAAAAAATTAGTTTATTGAT
1 AGCATAAAGCATAAAAGTATAAAAACCATTTGCTAAATATTACAAAAAAAAATTAGTTTATTGAT
*
24881 AGTGGGTCCACCAATAGTAATTTTTAAGCAAAGTTTCCAAAACGCCCTTGGCTAACAACCTAAAT
66 AGTGGGTCCACCAATAGTAACTTTTAAGCAAAGTTTCCAAAACGCCCTTGGCTAACAACCTAAAT
* * * *
24946 AACGAAAAAATCGAGTATGAAAGTACCAAAATGCCCCTGATAATTTGTTCTTGGATGAATGTGGT
131 AACGAAAAAACCGAGTAAGAAAGTACCAAAATACCCCTGACAATTTGTTCTTGGATGAATGTGGT
* *
25011 GCATCTTATAGCTAGAC-AAACGGTAATTCTATTTTCAACTTAACGCTAAATCGTCCAACTCAAA
196 GCATCTTATAGCTAGACAAAACGATAATTCCATTTTCAACTTAACGCTAAATCGTCCAACTCAAA
25075 ATTTGTGAGGAATTAAATAGCATAA
261 ATTTGTGAGGAATTAAATAGCATAA
*
25100 AGCATAAAAGCATAAAAGTATAAAAATCATTTGCTAAATATTACAAAAAAAAGATTAGTTTATTG
1 AGCAT-AAAGCATAAAAGTATAAAAACCATTTGCTAAATATTACAAAAAAAA-ATTAGTTTATTG
** * * *
25165 ATAGTGGGGTCCATGAATAGTAACTTTTAATCAAAG-TTCTCAAAACGCCCTTGGCTATCAACTT
64 ATAGT-GGGTCCACCAATAGTAACTTTTAAGCAAAGTTTC-CAAAACGCCCTTGGCTAACAACCT
*
25229 AAATAGCGAAAAAACCGAGTAAGAAAGTACCAAAATACCCCTGACAATTTGTTCTTGGATGAATG
127 AAATAACGAAAAAACCGAGTAAGAAAGTACCAAAATACCCCTGACAATTTGTTCTTGGATGAATG
* *
25294 TGGTGCATCTTATAGCTGGACAAAATGATAATTCCATTTTCAACTT
192 TGGTGCATCTTATAGCTAGACAAAACGATAATTCCATTTTCAACTT
25340 TAATATATGT
Statistics
Matches: 217, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
284 5 0.02
285 43 0.20
286 20 0.09
287 128 0.59
288 21 0.10
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (285 bp):
AGCATAAAGCATAAAAGTATAAAAACCATTTGCTAAATATTACAAAAAAAAATTAGTTTATTGAT
AGTGGGTCCACCAATAGTAACTTTTAAGCAAAGTTTCCAAAACGCCCTTGGCTAACAACCTAAAT
AACGAAAAAACCGAGTAAGAAAGTACCAAAATACCCCTGACAATTTGTTCTTGGATGAATGTGGT
GCATCTTATAGCTAGACAAAACGATAATTCCATTTTCAACTTAACGCTAAATCGTCCAACTCAAA
ATTTGTGAGGAATTAAATAGCATAA
Found at i:26780 original size:29 final size:29
Alignment explanation
Indices: 26726--26785 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
26716 CTTAATCATA
*
26726 AATAGAGTTCATGTGAAATCATTTCACAG
1 AATAGAGTTCATGTGAAATCAATTCACAG
* *
26755 AATAGAGTTCATGTGAAATTAATTCATAG
1 AATAGAGTTCATGTGAAATCAATTCACAG
26784 AA
1 AA
26786 ATGTTAGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (29 bp):
AATAGAGTTCATGTGAAATCAATTCACAG
Found at i:26905 original size:260 final size:260
Alignment explanation
Indices: 26491--26989 Score: 953
Period size: 260 Copynumber: 1.9 Consensus size: 260
26481 ATTTTAGGAA
26491 ACAGAATAGAGTTAATGTGAAATCAATTCAGAGAAATGTTAGGGAAGAAGAAACTCACCCAAATA
1 ACAGAATAGAGTTAATGTGAAATCAATTCAGAGAAATGTTAGGGAAGAAGAAACTCACCCAAATA
26556 AAAATGAAGACGAAAGGAAAACAGAACTGGAATATCAATAGTTTACCCATGAATCAACCTTACAG
66 AAAATGAAGACGAAAGGAAAACAGAACTGGAATATCAATAGTTTACCCATGAATCAACCTTACAG
26621 ATACATTTATAACACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATC
131 ATACATTTATAACACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATC
26686 TACACACAATTAATATGTAATTAAAACACACTTAATCATAAATAGAGTTCATGTGAAATCATTTC
196 TACACACAATTAATATGTAATTAAAACACACTTAATCATAAATAGAGTTCATGTGAAATCATTTC
* * * *
26751 ACAGAATAGAGTTCATGTGAAATTAATTCATAGAAATGTTAGGTAAGAAGAAACTCACCCAAATA
1 ACAGAATAGAGTTAATGTGAAATCAATTCAGAGAAATGTTAGGGAAGAAGAAACTCACCCAAATA
*
26816 AAAATGAAGACGAAAGGAAAACAGAACTGGAATGTCAATAGTTTACCCATGAATCAACCTTACAG
66 AAAATGAAGACGAAAGGAAAACAGAACTGGAATATCAATAGTTTACCCATGAATCAACCTTACAG
26881 ATACATTTATAACACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATC
131 ATACATTTATAACACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATC
26946 TACACACAATTAATATGTAATTAAAACACACTTAATCATAAATA
196 TACACACAATTAATATGTAATTAAAACACACTTAATCATAAATA
26990 TAAAAATAGT
Statistics
Matches: 234, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
260 234 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.25
Consensus pattern (260 bp):
ACAGAATAGAGTTAATGTGAAATCAATTCAGAGAAATGTTAGGGAAGAAGAAACTCACCCAAATA
AAAATGAAGACGAAAGGAAAACAGAACTGGAATATCAATAGTTTACCCATGAATCAACCTTACAG
ATACATTTATAACACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATC
TACACACAATTAATATGTAATTAAAACACACTTAATCATAAATAGAGTTCATGTGAAATCATTTC
Found at i:28017 original size:27 final size:28
Alignment explanation
Indices: 27980--28035 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
27970 ATCTATATAT
* *
27980 ATATATATTTATAC-GTTTTTTTGCCGA
1 ATATATATTTATACAATTTTTTGGCCGA
28007 ATATATATTTATACAATTTTTTGGCCGA
1 ATATATATTTATACAATTTTTTGGCCGA
28035 A
1 A
28036 GGCCGTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (28 bp):
ATATATATTTATACAATTTTTTGGCCGA
Found at i:42401 original size:4 final size:4
Alignment explanation
Indices: 42392--42418 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42382 TACATCAGTG
42392 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
42419 GAAACAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:45007 original size:33 final size:33
Alignment explanation
Indices: 44946--45015 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
44936 TCCTCAGGGT
44946 CCAGGGGGCGCCACCCACCGTGGTGTGGCGTCC
1 CCAGGGGGCGCCACCCACCGTGGTGTGGCGTCC
* * *
44979 CCAGGGGGTGTCACACCACGGTGG-GTGGCGTCC
1 CCAGGGGGCGCCAC-CCACCGTGGTGTGGCGTCC
45012 CCAG
1 CCAG
45016 CCTTCGCGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.11, C:0.36, G:0.40, T:0.13
Consensus pattern (33 bp):
CCAGGGGGCGCCACCCACCGTGGTGTGGCGTCC
Done.