Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018065.1 Corchorus olitorius cultivar O-4 contig18098, 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: 26082
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:52 original size:6 final size:6
Alignment explanation
Indices: 29--64 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
19 CCTAATGGAA
* *
29 GATTCC GGTTCT GATTCC GATTCC GATTCC GATTCC
1 GATTCC GATTCC GATTCC GATTCC GATTCC GATTCC
65 AAGGGGATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.36
Consensus pattern (6 bp):
GATTCC
Found at i:1730 original size:41 final size:41
Alignment explanation
Indices: 1628--1955 Score: 351
Period size: 41 Copynumber: 7.8 Consensus size: 41
1618 CAATAACCAA
* *
1628 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-CCTATAT-C
*
1671 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
* * * *
1713 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATA-T-C
* * *
1754 AAAGTCCTCAAACACATATATAACACAGAAGCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
*
1795 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-AC-CTATAT-C
* * **
1838 AAAGTCCTCAAACACATATATAACACAGAGACATTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
*
1879 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA-C-CTATAT-C
*
1922 AAAAGTCCTCAAACACATATATAACACAGAGGCA
1 -AAAGTCCCCAAACACATATATAACACAGAGGCA
1956 TTTCTCCTTA
Statistics
Matches: 240, Mismatches: 31, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
39 19 0.08
40 1 0.00
41 91 0.38
42 11 0.05
43 57 0.24
44 61 0.25
ACGTcount: A:0.43, C:0.27, G:0.11, T:0.20
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
Found at i:1842 original size:84 final size:85
Alignment explanation
Indices: 1628--1956 Score: 515
Period size: 84 Copynumber: 3.9 Consensus size: 85
1618 CAATAACCAA
* *
1628 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
* *
1693 AACACAGAGGCACCTATATC
66 AACACAGAAGCATCTATATC
* ** *
1713 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
1775 AACACAGAAGCATCTATATC
66 AACACAGAAGCATCTATATC
1795 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
1859 AACACAG-AGACATTTATATC
66 AACACAGAAG-CATCTATATC
*
1879 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
1944 AACACAGAGGCAT
66 AACACAGAAGCAT
1957 TTCTCCTTAT
Statistics
Matches: 224, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
82 53 0.24
83 23 0.10
84 102 0.46
85 45 0.20
86 1 0.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAAGCATCTATATC
Found at i:7161 original size:7 final size:7
Alignment explanation
Indices: 7149--7175 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
7139 TGATCTTGCC
7149 TGTTGAT
1 TGTTGAT
7156 TGTTGAT
1 TGTTGAT
7163 TGTTGAT
1 TGTTGAT
7170 TGTTGA
1 TGTTGA
7176 AACTATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (7 bp):
TGTTGAT
Found at i:9050 original size:49 final size:47
Alignment explanation
Indices: 8949--9090 Score: 169
Period size: 49 Copynumber: 3.0 Consensus size: 47
8939 GAGCGTGCCA
* * * *
8949 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
8996 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
9045 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
9091 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.34
49 42 0.51
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:13571 original size:21 final size:21
Alignment explanation
Indices: 13547--13630 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
13537 CCCGACTACT
* *
13547 ACTCCGACGACACCTACCACA
1 ACTCCGACAACACCAACCACA
*
13568 ACTCCGACAACACCAACCATA
1 ACTCCGACAACACCAACCACA
* *
13589 ACTCCGACAACCCCAACGACA
1 ACTCCGACAACACCAACCACA
* *
13610 ACTCCAACAACCCCAACCACA
1 ACTCCGACAACACCAACCACA
13631 GGAGGTACCT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.39, C:0.48, G:0.06, T:0.07
Consensus pattern (21 bp):
ACTCCGACAACACCAACCACA
Found at i:14154 original size:21 final size:18
Alignment explanation
Indices: 14096--14148 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
14086 CAGTGTACCT
* *
14096 CCACCGGCCACCATAACA
1 CCACCAGCCACCATAACG
14114 CCACCAGCCACCATAACG
1 CCACCAGCCACCATAACG
14132 CCACCAGCCACCATAAC
1 CCACCAGCCACCATAAC
14149 CCCGCCTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.34, C:0.51, G:0.09, T:0.06
Consensus pattern (18 bp):
CCACCAGCCACCATAACG
Done.