Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016736.1 Corchorus olitorius cultivar O-4 contig16769, 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: 6469
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Found at i:431 original size:8 final size:8
Alignment explanation
Indices: 418--446 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
408 ATAATTTATT
418 CAATTAGA
1 CAATTAGA
426 CAATTAGA
1 CAATTAGA
434 CAATTAGA
1 CAATTAGA
442 CAATT
1 CAATT
447 GTTGAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (8 bp):
CAATTAGA
Found at i:1871 original size:13 final size:13
Alignment explanation
Indices: 1853--1879 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1843 TTAGTAACCT
1853 TGATAATTTGTAG
1 TGATAATTTGTAG
1866 TGATAATTTGTAG
1 TGATAATTTGTAG
1879 T
1 T
1880 AATGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGATAATTTGTAG
Found at i:2112 original size:21 final size:20
Alignment explanation
Indices: 2086--2146 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
2076 CTTAATCTTA
2086 TTAAGTATTTTAGTGACCTCG
1 TTAAGT-TTTTAGTGACCTCG
* * *
2107 TTAAGTTTTATAGTAACTTCT
1 TTAAGTTTT-TAGTGACCTCG
2128 TTAAGGTTTTTAGTGACCT
1 TTAA-GTTTTTAGTGACCT
2147 TATTAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
21 25 0.76
22 5 0.15
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (20 bp):
TTAAGTTTTTAGTGACCTCG
Found at i:2152 original size:21 final size:20
Alignment explanation
Indices: 2082--2152 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
2072 AAATCTTAAT
2082 CTTATTAAGTATTTTAGTGAC
1 CTTATTAAGT-TTTTAGTGAC
** *
2103 CTCGTTAAGTTTTATAGT-AA
1 CTTATTAAGTTTT-TAGTGAC
*
2123 CTTCTTTAAGGTTTTTAGTGAC
1 CTT-ATTAA-GTTTTTAGTGAC
2145 CTTATTAA
1 CTTATTAA
2153 TATTGTTAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.15
21 24 0.62
22 9 0.23
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (20 bp):
CTTATTAAGTTTTTAGTGAC
Found at i:3088 original size:18 final size:18
Alignment explanation
Indices: 3062--3098 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3052 TTATTAAACT
3062 TATTATAGTAACTTATTA
1 TATTATAGTAACTTATTA
*
3080 TATTTTAGTAACTTATTA
1 TATTATAGTAACTTATTA
3098 T
1 T
3099 TAAAATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
TATTATAGTAACTTATTA
Found at i:4144 original size:201 final size:201
Alignment explanation
Indices: 3573--4902 Score: 1813
Period size: 201 Copynumber: 6.7 Consensus size: 201
3563 CCCTAAACCC
* * * ** *
3573 TAATATTCAAAAC-TATTC-CCTAAGGGGAAACATGTCAACCCTTAAACCTCGTGCATGCAGTCT
1 TAATATT-AATACATATTCTCCTAA-GGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCT
* * * *
3636 GCTAAACTCCACTGATGGTGTATTGTAT--TTTTT-TTTTAGGATTATTATACAATATATTGTCA
64 GCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCA
* * *
3698 ATGTAAATTTTGAACTCCATAACCGAGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTA
129 GTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTA
3763 AATATATT
194 AATATATT
* *
3771 TAATATTAATACATATTCCCCTAAGGGACACATGTCGACCCTT-AA------ACGTGCAGTCTGC
1 TAATATTAATACATATTCTCCTAAGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
* * * * *
3829 TAAATTCCAGTGACGGTGTATTGTATAATTTTTCTTATAGGATTATCATACAATACATTGTCCGT
66 TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGT
* * *
3894 GTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACACATACCCCATTTCATAATAAATTAAA
131 GTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAA
3959 TATATT
196 TATATT
* ** * * * *
3965 CAATATTAATACATATTCTCCTAAGGGACACATGTTGACCCTTAAACCCCGCATGTACAATATGC
1 TAATATTAATACATATTCTCCTAAGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
* ** * *
4030 AAAACTCCGGTGACAGTGTATTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGT
66 TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGT
**
4095 GTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAGAAAA
131 GTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAA
4160 TATATT
196 TATATT
*
4166 TAATATTAATACATATTC-CCTAAGAGGACACATGTCAACCCTTAAACCCCGCACGTGCAATCTG
1 TAATATTAATACATATTCTCCTAAG-GGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTG
* *
4230 CTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAA
65 CTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAG
* * *
4295 TGTAAATTTTGGACTCCATAAGCGGGGTAAGAAGTTGGCACATACCCCATTTCATAATTAATTAA
130 TGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAA
4360 ATATATT
195 ATATATT
* * * *
4367 TAATATTAATACATATTC-CTCT-AGTGGACACATGCCAACCCTTAAACCCCACACGTGTAGTAT
1 TAATATTAATACATATTCTC-CTAAG-GGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCT
**
4430 GCTAAACTCCACTGACATTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCA
64 GCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCA
* * *
4495 GTGTAAATTTTGGACTCCATAAGCGGGTT-AGAAGTTGACACATA-CCCATTTCATAAATAAGTA
129 GTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTA
4558 AATATATT
194 AATATATT
* * * *
4566 AAATATTAATACATATTCT-CTAAGGGGA-TCATGTCAATCCTTAAACCCCGCACGTGCAGTCTA
1 TAATATTAATACATATTCTCCTAA-GGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTG
* * * *
4629 CTAACCCCCACTGGCGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATTCACTGTCAG
65 CTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAG
* * *
4694 TGTAAATTTTAAACTCCATAAGCGGGTTAAGAGGTTGACACATGCCCCATTTCATAATTAATT-A
130 TGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAA
4758 A-ATATT
195 ATATATT
* * *
4764 TAATATTAATACATATT-TCCTAAGGTGTCACTTGTCAACCCTTAAACCCCGCACGTTGCGGTCT
1 TAATATTAATACATATTCTCCTAAGG-GACACATGTCAACCCTTAAACCCCGCACG-TGCAGTCT
** *
4828 GCTAAACTATACTGACGGTGTATGGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCA
64 GCTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCA
4893 GTGTAAATTT
129 GTGTAAATTT
4903 CGGTCTTCTT
Statistics
Matches: 1007, Mismatches: 102, Indels: 44
0.87 0.09 0.04
Matches are distributed among these distances:
191 34 0.03
193 5 0.00
194 133 0.13
195 2 0.00
197 9 0.01
198 170 0.17
199 89 0.09
200 111 0.11
201 452 0.45
202 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (201 bp):
TAATATTAATACATATTCTCCTAAGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGT
GTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAA
TATATT
Found at i:5296 original size:7 final size:7
Alignment explanation
Indices: 5278--5306 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5268 ACCAAATTTG
5278 ATTATT-
1 ATTATTA
5284 ATTATTA
1 ATTATTA
5291 ATTATTA
1 ATTATTA
5298 ATTATTA
1 ATTATTA
5305 AT
1 AT
5307 ATAATAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTATTA
Done.