Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012531.1 Corchorus olitorius cultivar O-4 contig12564, 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: 45679
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1628 original size:15 final size:15
Alignment explanation
Indices: 1608--1673 Score: 87
Period size: 15 Copynumber: 4.4 Consensus size: 15
1598 TTTTCTTCCA
1608 GTTGGATGCAGCTTG
1 GTTGGATGCAGCTTG
*
1623 GTTGGATGCAGATTG
1 GTTGGATGCAGCTTG
*
1638 GTTAGATGCAGCTTG
1 GTTGGATGCAGCTTG
* **
1653 GTTTGATGTTGCTTG
1 GTTGGATGCAGCTTG
1668 GTTGGA
1 GTTGGA
1674 GGTTGCTTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.15, C:0.09, G:0.38, T:0.38
Consensus pattern (15 bp):
GTTGGATGCAGCTTG
Found at i:1669 original size:30 final size:30
Alignment explanation
Indices: 1612--1691 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
1602 CTTCCAGTTG
* *
1612 GATGCAGCTTGGTTGGATGCAGATTGGTTA
1 GATGCAGCTTGGTTTGATGTAGATTGGTTA
* * *
1642 GATGCAGCTTGGTTTGATGTTGCTTGGTTG
1 GATGCAGCTTGGTTTGATGTAGATTGGTTA
* **
1672 GAGGTTGCTTGGTTTGATGT
1 GATGCAGCTTGGTTTGATGT
1692 GGATGCAGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.14, C:0.09, G:0.38, T:0.40
Consensus pattern (30 bp):
GATGCAGCTTGGTTTGATGTAGATTGGTTA
Found at i:1678 original size:15 final size:15
Alignment explanation
Indices: 1648--1685 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1638 GTTAGATGCA
* *
1648 GCTTGGTTTGATGTT
1 GCTTGGTTGGAGGTT
1663 GCTTGGTTGGAGGTT
1 GCTTGGTTGGAGGTT
1678 GCTTGGTT
1 GCTTGGTT
1686 TGATGTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.08, G:0.39, T:0.47
Consensus pattern (15 bp):
GCTTGGTTGGAGGTT
Found at i:3193 original size:15 final size:14
Alignment explanation
Indices: 3175--3218 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
3165 AATCCACACT
3175 ATCAGAATCCCCATA
1 ATCAG-ATCCCCATA
*
3190 ATCAGGATCCCCATT
1 ATCA-GATCCCCATA
3205 ATCATGATCCCCAT
1 ATCA-GATCCCCAT
3219 CCTCAACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 25 0.96
16 1 0.04
ACGTcount: A:0.32, C:0.34, G:0.09, T:0.25
Consensus pattern (14 bp):
ATCAGATCCCCATA
Found at i:3878 original size:33 final size:34
Alignment explanation
Indices: 3829--3896 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
3819 AGACAAAACA
* *
3829 AAAAGAAATAGTTTATTAAACACATATAA-CAGAC
1 AAAACAAATAGTTTATTAAACAAATA-AACCAGAC
*
3863 AAAACAAATA-TTTATTCAACAAATAAACCAGAC
1 AAAACAAATAGTTTATTAAACAAATAAACCAGAC
3896 A
1 A
3897 TTAAACATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 2 0.07
33 19 0.63
34 9 0.30
ACGTcount: A:0.57, C:0.15, G:0.06, T:0.22
Consensus pattern (34 bp):
AAAACAAATAGTTTATTAAACAAATAAACCAGAC
Found at i:4001 original size:11 final size:11
Alignment explanation
Indices: 3987--4018 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
3977 GCAAAACCCA
3987 TAAAAAACAAT
1 TAAAAAACAAT
3998 TAAAAAACAA-
1 TAAAAAACAAT
4008 TAAAAAACAAT
1 TAAAAAACAAT
4019 AGCCTTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
TAAAAAACAAT
Found at i:4066 original size:14 final size:15
Alignment explanation
Indices: 4047--4082 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4037 TTGCAAAACC
4047 CATAAAAAAC-AATA
1 CATAAAAAACAAATA
*
4061 CATAAAAACCAAATA
1 CATAAAAAACAAATA
4076 CATAAAA
1 CATAAAA
4083 CTTACCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (15 bp):
CATAAAAAACAAATA
Found at i:6195 original size:21 final size:23
Alignment explanation
Indices: 6153--6198 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
6143 CAGAAACAAA
* *
6153 ACAAAAGCAGTAGGACAGAGCAG
1 ACAAAAGCAGTAGAACAAAGCAG
6176 ACAAAA-C-GTAGAACAAAGCAG
1 ACAAAAGCAGTAGAACAAAGCAG
6197 AC
1 AC
6199 CAAGACAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 1 0.05
23 6 0.29
ACGTcount: A:0.52, C:0.20, G:0.24, T:0.04
Consensus pattern (23 bp):
ACAAAAGCAGTAGAACAAAGCAG
Found at i:7419 original size:30 final size:31
Alignment explanation
Indices: 7362--7434 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
7352 CGTCTAATTT
*
7362 TATCCTGAATTGACACAACCCGATAACGTTA
1 TATCCTGAATTGACACAACCAGATAACGTTA
*
7393 TATCCTGAATTGACACAA-GAGATAACGTTA
1 TATCCTGAATTGACACAACCAGATAACGTTA
* *
7423 GAACCTGAATTG
1 TATCCTGAATTG
7435 TAGTTTGCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 20 0.53
31 18 0.47
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (31 bp):
TATCCTGAATTGACACAACCAGATAACGTTA
Found at i:10204 original size:16 final size:18
Alignment explanation
Indices: 10185--10218 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
10175 AACAAAAGGT
10185 TTATGAG-AAAAA-AAAA
1 TTATGAGCAAAAATAAAA
10201 TTATGAGCAAAAATAAAA
1 TTATGAGCAAAAATAAAA
10219 ATAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (18 bp):
TTATGAGCAAAAATAAAA
Found at i:13698 original size:25 final size:25
Alignment explanation
Indices: 13664--13714 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
13654 TTAACTTTTC
13664 TACTACTATGCGAATTGCCAAAAGG
1 TACTACTATGCGAATTGCCAAAAGG
* * *
13689 TACTACTATGTGAATTGTCAAGAGG
1 TACTACTATGCGAATTGCCAAAAGG
13714 T
1 T
13715 GCAGGTGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
TACTACTATGCGAATTGCCAAAAGG
Found at i:30971 original size:28 final size:27
Alignment explanation
Indices: 30939--31007 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
30929 TCAGGCTTCT
30939 TCGGGTTCGGGTTATGTCGGGCTC-GG
1 TCGGGTTCGGGTTATGTCGGGCTCAGG
* *
30965 TCTCGGGTT-GGGCTCGATTTCGGGCTCAGG
1 --TCGGGTTCGGG-T-TATGTCGGGCTCAGG
30995 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
31008 TGATTTCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
27 3 0.09
28 16 0.47
29 13 0.38
30 2 0.06
ACGTcount: A:0.04, C:0.20, G:0.43, T:0.32
Consensus pattern (27 bp):
TCGGGTTCGGGTTATGTCGGGCTCAGG
Found at i:31012 original size:29 final size:28
Alignment explanation
Indices: 30939--31014 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
30929 TCAGGCTTCT
*
30939 TCGGGTTCGGGTT-ATGTCGGGCTCGGTC
1 TCGGGTTCGGGTTGATTTCGGGCTCGG-C
*
30967 TCGGGTT-GGGCTCGATTTCGGGCTCAGG-
1 TCGGGTTCGGG-TTGATTTCGGGCTC-GGC
30995 TCGGGTTCGGGTTTGATTTC
1 TCGGGTTCGGG-TTGATTTC
31015 TATTCGATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.08
28 15 0.38
29 20 0.50
30 2 0.05
ACGTcount: A:0.05, C:0.20, G:0.41, T:0.34
Consensus pattern (28 bp):
TCGGGTTCGGGTTGATTTCGGGCTCGGC
Found at i:38348 original size:27 final size:29
Alignment explanation
Indices: 38311--38385 Score: 109
Period size: 27 Copynumber: 2.7 Consensus size: 29
38301 TGTGAACTTA
38311 AAAAATGACCAAAATGCCCCT-GAA-TGT
1 AAAAATGACCAAAATGCCCCTGGAATTGT
* *
38338 AAAAATAACCAAAATGCCCCTGGAATTTT
1 AAAAATGACCAAAATGCCCCTGGAATTGT
*
38367 GAAAATGACCAAAATGCCC
1 AAAAATGACCAAAATGCCC
38386 ATAGGTGATC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 20 0.48
28 3 0.07
29 19 0.45
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (29 bp):
AAAAATGACCAAAATGCCCCTGGAATTGT
Done.