Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018449.1 Corchorus olitorius cultivar O-4 contig18482, 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: 57898
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2004 original size:60 final size:60
Alignment explanation
Indices: 1940--2055 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
1930 AAACGCCAGG
* **
1940 CCCTTATTTGAGCATTTTTGATAATGTTAGGCCATTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTCGATAACATTAGGCCATTATTTGGCCAAATTAAAAGATCAGA
* *
2000 CCCTTATTTGAGCATTTTCGGTAACATTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CCCTTATTTGAGCATTTTCGATAACATTAGGCCATTATTTGGCCAAATTAAAAGAT
2056 TGGGTCCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACATTAGGCCATTATTTGGCCAAATTAAAAGATCAGA
Found at i:2065 original size:60 final size:58
Alignment explanation
Indices: 1940--2097 Score: 183
Period size: 60 Copynumber: 2.7 Consensus size: 58
1930 AAACGCCAGG
* * *
1940 CCCTTATTTGAGCATTTTTGATAATGTTAGGCCATTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCA-TTTTGGTAA-ATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
** *
2000 CCCTTATTTGAGCATTTTCGGTAACATTAGGCCCTTATTTGGCCAAATTAAAAGATTGGG
1 CCCTTATTTGAGCATTTT-GGTAA-ATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * * *
2060 TCCTTATTTGAACATTTTGG-CAATTAGGTCCTTATTTG
1 CCCTTATTTGAGCATTTTGGTAAATTAGGCCCTTATTTG
2098 AGCAATTAGC
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 15 0.17
58 1 0.01
59 6 0.07
60 64 0.74
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (58 bp):
CCCTTATTTGAGCATTTTGGTAAATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:6933 original size:31 final size:30
Alignment explanation
Indices: 6900--6959 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
6890 GACGTAAGTA
6900 TTTCCAAATTTCCATTTTTTTTATTTCCTTAT
1 TTTCC-AATTT-CATTTTTTTTATTTCCTTAT
* *
6932 TTTCCTATTTCATTTTTTTTCTTTCCTT
1 TTTCCAATTTCATTTTTTTTATTTCCTT
6960 TTCCTTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 17 0.65
31 4 0.15
32 5 0.19
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTCCAATTTCATTTTTTTTATTTCCTTAT
Found at i:27213 original size:11 final size:11
Alignment explanation
Indices: 27197--27242 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
27187 TCCTCCTTGA
27197 AATAATTCTTC
1 AATAATTCTTC
27208 AATAA-TCTTC
1 AATAATTCTTC
*
27218 AA-ATTATCTTC
1 AATAAT-TCTTC
*
27229 AATAAGTCTTC
1 AATAATTCTTC
27240 AAT
1 AAT
27243 CACGAATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 1 0.03
10 7 0.24
11 20 0.69
12 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (11 bp):
AATAATTCTTC
Found at i:27688 original size:22 final size:22
Alignment explanation
Indices: 27663--27709 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
27653 TTTATATGCA
27663 TATATATATATATAATAATCTT
1 TATATATATATATAATAATCTT
* *
27685 TATATATATATGTAATACTCTT
1 TATATATATATATAATAATCTT
27707 TAT
1 TAT
27710 TGAAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATATATATATAATAATCTT
Found at i:29743 original size:11 final size:11
Alignment explanation
Indices: 29729--29761 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29719 ATTCATAACA
29729 AATTTATAATT
1 AATTTATAATT
29740 AATTTATAATT
1 AATTTATAATT
29751 -ATTTGATAATT
1 AATTT-ATAATT
29762 TATGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:31448 original size:127 final size:127
Alignment explanation
Indices: 31306--31538 Score: 389
Period size: 127 Copynumber: 1.8 Consensus size: 127
31296 TTATTTATTT
* *
31306 ATCTATACCTTACTATTAAAGTTATC-CACAAACTGCTGTAGGCTTAGTATTTGGTTCTTCTCTT
1 ATCTATACCTGACTATTAAAGTTATCTC-CAAACTGCTGTAGGCTCAGTATTTGGTTCTTCTCTT
31370 GTTGACATTTGTTCAAAGTTGATTGGCTG-GCAGAAAATCATATTGTATTATTATATATTTGAA
65 GTTGACATTTGTTCAAAGTTGATTGGCTGAG-AGAAAATCATATTGTATTATTATATATTTGAA
* *
31433 ATCTATACCTGACTATTAAAGTTATCTCCAAACTGGTGTATGCTCAGTATTTGGTTCTTCTCTTG
1 ATCTATACCTGACTATTAAAGTTATCTCCAAACTGCTGTAGGCTCAGTATTTGGTTCTTCTCTTG
*
31498 TTGACATTTGTTCAAAGTTGATTGGTTGAGAGAAAATCATA
66 TTGACATTTGTTCAAAGTTGATTGGCTGAGAGAAAATCATA
31539 ATATATTTAT
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
127 97 0.98
128 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (127 bp):
ATCTATACCTGACTATTAAAGTTATCTCCAAACTGCTGTAGGCTCAGTATTTGGTTCTTCTCTTG
TTGACATTTGTTCAAAGTTGATTGGCTGAGAGAAAATCATATTGTATTATTATATATTTGAA
Found at i:31953 original size:20 final size:20
Alignment explanation
Indices: 31928--31966 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31918 CATATAAAAT
* *
31928 AATAATAATTAATTTTTAAA
1 AATAATAACTAATTATTAAA
31948 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
31967 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:32287 original size:17 final size:18
Alignment explanation
Indices: 32262--32308 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
32252 ATTGAGGTTT
*
32262 GAAAGTTTGAA-AATTGA
1 GAAAATTTGAAGAATTGA
32279 GAAAATTTGAGAGAATTGA
1 GAAAATTTGA-AGAATTGA
*
32298 -AAATTTTGAAG
1 GAAAATTTGAAG
32309 TTTGAACGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAAATTTGAAGAATTGA
Found at i:37148 original size:6 final size:6
Alignment explanation
Indices: 37137--37189 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
37127 TTGATAGCGC
* *
37137 AACAAA AAC-AA AACGAA AAC-GA AACAAA AACAAA AACAGAAA AACAAA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AAC--AAA AACAAA
37185 AACAA
1 AACAA
37190 TACCAAACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 9 0.22
6 26 0.63
8 6 0.15
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:37161 original size:11 final size:11
Alignment explanation
Indices: 37137--37189 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
37127 TTGATAGCGC
37137 AACAAAAACAA
1 AACAAAAACAA
* *
37148 AACGAAAACGA
1 AACAAAAACAA
37159 AACAAAAACAA
1 AACAAAAACAA
* *
37170 AA-ACAGA-AA
1 AACAAAAACAA
37179 AACAAAAACAA
1 AACAAAAACAA
37190 TACCAAACGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 4 0.12
10 6 0.19
11 22 0.69
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:37181 original size:14 final size:14
Alignment explanation
Indices: 37162--37188 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37152 AAAACGAAAC
37162 AAAAACAAAAACAG
1 AAAAACAAAAACAG
37176 AAAAACAAAAACA
1 AAAAACAAAAACA
37189 ATACCAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.15, G:0.04, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAACAG
Found at i:44197 original size:15 final size:15
Alignment explanation
Indices: 44179--44217 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
44169 AATGATATTT
*
44179 AAAAAAATTATATAA
1 AAAAAAATTATAGAA
**
44194 AAAAAAACAATAGAA
1 AAAAAAATTATAGAA
44209 AAAAAAATT
1 AAAAAAATT
44218 CCGAGCATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAAAATTATAGAA
Found at i:48362 original size:15 final size:16
Alignment explanation
Indices: 48332--48364 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48322 TCATGCACCC
48332 AAAAATAATTTAATAA
1 AAAAATAATTTAATAA
*
48348 AAAAATCATTT-ATAA
1 AAAAATAATTTAATAA
48363 AA
1 AA
48365 CACGTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATAATTTAATAA
Found at i:55216 original size:28 final size:29
Alignment explanation
Indices: 55168--55227 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
55158 TCAATGACGT
* *
55168 TTTGTCTCCTGAATTTTAAA-TCAGGATA
1 TTTGTCTCCTGAATTTCAAATTCAGGACA
*
55196 TTTGTC-CTTGAACTTTCAAATTCAGGACA
1 TTTGTCTCCTGAA-TTTCAAATTCAGGACA
55225 TTT
1 TTT
55228 AGCCCCCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 12 0.44
29 10 0.37
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTGTCTCCTGAATTTCAAATTCAGGACA
Found at i:57733 original size:2 final size:2
Alignment explanation
Indices: 57726--57765 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
57716 ACCAACAAGA
*
57726 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
57766 AGTCTAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.