Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006335.1 Corchorus capsularis cultivar CVL-1 contig06356, 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: 20939
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--49 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1 TC TC TC TC TC -C TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41 TC TC TC TC T
1 TC TC TC TC T
50 ATAGTCGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3920 original size:17 final size:17
Alignment explanation
Indices: 3900--3932 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3890 GCAGCCTATC
3900 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
3917 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
3933 GTACTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:5979 original size:16 final size:18
Alignment explanation
Indices: 5954--5993 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
5944 TAACTTGGAT
5954 TATA-TACTATAG-TACA
1 TATAGTACTATAGTTACA
5970 T-TAGTACTATAGTTACA
1 TATAGTACTATAGTTACA
5987 TATAGTA
1 TATAGTA
5994 ATTAGTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 9 0.43
17 5 0.24
18 5 0.24
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (18 bp):
TATAGTACTATAGTTACA
Found at i:6011 original size:25 final size:26
Alignment explanation
Indices: 5957--6011 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
5947 CTTGGATTAT
5957 ATAC-TATAGTACATTAGTACTATAG
1 ATACATATAGTACATTAGTACTATAG
*
5982 TTACATATAGTA-ATTAGTAACTAT-G
1 ATACATATAGTACATTAGT-ACTATAG
6007 ATACA
1 ATACA
6012 AATATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (26 bp):
ATACATATAGTACATTAGTACTATAG
Found at i:6298 original size:16 final size:16
Alignment explanation
Indices: 6277--6308 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6267 GAGCATTAAA
6277 AACACTTATTGGACTT
1 AACACTTATTGGACTT
6293 AACACTTATTGGACTT
1 AACACTTATTGGACTT
6309 GATATTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
AACACTTATTGGACTT
Found at i:8155 original size:70 final size:70
Alignment explanation
Indices: 8068--8276 Score: 390
Period size: 70 Copynumber: 3.0 Consensus size: 70
8058 AGTGGACATC
8068 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAT
1 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAT
8133 GTAAA
66 GTAAA
8138 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACAT-A--AT
1 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAT
8200 -TAAA
66 GTAAA
8204 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAT
1 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAT
8269 GTAAA
66 GTAAA
8274 TAA
1 TAA
8277 GACATAACAT
Statistics
Matches: 135, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
66 63 0.47
67 3 0.02
69 3 0.02
70 66 0.49
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (70 bp):
TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAT
GTAAA
Found at i:8216 original size:66 final size:66
Alignment explanation
Indices: 8068--8267 Score: 364
Period size: 66 Copynumber: 3.0 Consensus size: 66
8058 AGTGGACATC
8068 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAT
1 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACAT-A--AT
8133 GTAAA
63 -TAAA
8138 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAA
1 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAA
8203 A
66 A
8204 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTA
1 TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTA
8268 TGTAAATAAG
Statistics
Matches: 130, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
66 68 0.52
67 2 0.02
69 1 0.01
70 59 0.45
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (66 bp):
TAATTAGGGACCGAGAGAGTAGTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAA
A
Found at i:8296 original size:66 final size:64
Alignment explanation
Indices: 8089--8288 Score: 215
Period size: 66 Copynumber: 3.0 Consensus size: 64
8079 CGAGAGAGTA
*
8089 GTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTATGTAAATAATTAGGGACCGAGA
1 GTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTATGTAAAT-A--A--GACAGA-A
*
8154 GAGTA-
60 CA-TAT
** * * * *
8159 GTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTAAATAATTAGGGACCGAGAGAGT
1 GTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTATGTAAATA-AGACAGA-ACA-T
8224 A-
63 AT
*
8225 GTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTATGTAAATAAGACATAACATAT
1 GTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTATGTAAATAAGACAGAACATAT
8289 CTCTTAGTCA
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 2 0.02
65 4 0.03
66 61 0.52
69 1 0.01
70 47 0.40
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (64 bp):
GTTAGTTTATAGACATACATGAGAAAGTCGATAGACATAATTATGTAAATAAGACAGAACATAT
Done.