Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007941.1 Corchorus capsularis cultivar CVL-1 contig07962, 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: 8196
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Found at i:4144 original size:63 final size:63
Alignment explanation
Indices: 4074--4280 Score: 204
Period size: 63 Copynumber: 3.2 Consensus size: 63
4064 ACACATGATA
* **
4074 CACTGCTGAATAATACCATAAATTCCGAGTATACAATTAAACACATAGTCTGAAAATAGTATC
1 CACTGCTGAATAATACCATAAACTCCGAGTATACAATTAAACACATAGTCTGAAAATACCATC
* * * * *
4137 CACTGCTGAATAATATCATAAACTCTGA--ATACAAGTATTGAATAATAACATAGTCTGGAAACA
1 CACTGCTGAATAATACCATAAACTCCGAGTATAC-A--ATT--A-AA-CACATAGTCTGAAAATA
4200 CCATC
59 CCATC
* * * *
4205 CCCTGCTGAATAATACCATAAACTCCGAGTACATAATTAAACATATAGTCTGAAAATACCA-C
1 CACTGCTGAATAATACCATAAACTCCGAGTATACAATTAAACACATAGTCTGAAAATACCATC
*
4267 CAACTACTGAATAA
1 C-ACTGCTGAATAA
4281 CACATTGTCT
Statistics
Matches: 115, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
61 4 0.03
62 3 0.03
63 51 0.44
64 5 0.04
65 1 0.01
66 1 0.01
67 5 0.04
68 42 0.37
69 1 0.01
70 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.26
Consensus pattern (63 bp):
CACTGCTGAATAATACCATAAACTCCGAGTATACAATTAAACACATAGTCTGAAAATACCATC
Found at i:7895 original size:43 final size:42
Alignment explanation
Indices: 7835--8172 Score: 254
Period size: 43 Copynumber: 7.7 Consensus size: 42
7825 CTGATTATTC
*
7835 TTTA-TTTTGTACTGATTACTATTCTACTCTTGTTGATTACCT
1 TTTACTTTT-TACTGATTACTATTTTACTCTTGTTGATTACCT
* * *
7877 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTTGT--TGATTAC---CT
* * * *
7925 TCTGCTCATTTTTTACTGATTACTCTTTTACT-TTTTACTGATTGCCT
1 T-T--T-ACTTTTTACTGATTACTATTTTACTCTTGT--TGATTACCT
* * * *
7972 TTTGCTTTTTAGTGATTACCT-TTTTACTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTGTTGATTA-CCT
* * * ** *
8016 TTTACTCTTTACTGATCAC-CTTTTACTCTTACTGATTTCCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* * * **
8057 TTTACTTCTTACTTATTACTTTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* *
8098 ATTTACTTTTTACTGACTATTATTTTACTCTTGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
8141 TCTTACTTTTTACTGATTACTATTTTACTCTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTT
8173 TACTAATTAC
Statistics
Matches: 239, Mismatches: 38, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
41 19 0.08
42 61 0.26
43 84 0.35
44 24 0.10
45 9 0.04
46 1 0.00
47 2 0.01
48 4 0.02
50 13 0.05
51 22 0.09
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
Found at i:7908 original size:28 final size:28
Alignment explanation
Indices: 7877--7956 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 28
7867 TTGATTACCT
7877 TCTTACTTTTTACTGATTACCATTTTA-
1 TCTTACTTTTTACTGATTACCATTTTAC
*
7904 -C-T-C-TTTTACTGATTACTATTTT-C
1 TCTTACTTTTTACTGATTACCATTTTAC
* *
7927 TGCTCATTTTTTACTGATTACTC-TTTTAC
1 T-CTTACTTTTTACTGATTAC-CATTTTAC
7956 T
1 T
7957 TTTTACTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
23 18 0.44
24 1 0.02
25 2 0.05
26 1 0.02
28 17 0.41
29 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (28 bp):
TCTTACTTTTTACTGATTACCATTTTAC
Found at i:7919 original size:15 final size:15
Alignment explanation
Indices: 7901--7956 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
7891 GATTACCATT
7901 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
* *
7916 TTACTATTTT-CTGC
1 TTACTCTTTTACTGA
* *
7930 TCA-TTTTTTACTGA
1 TTACTCTTTTACTGA
7944 TTACTCTTTTACT
1 TTACTCTTTTACT
7957 TTTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 17 0.53
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:8110 original size:14 final size:13
Alignment explanation
Indices: 8036--8111 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
8026 ACTGATCACC
*
8036 TTTTACTCTTACT
1 TTTTACTTTTACT
* *
8049 GATTTCCTTTTACT
1 -TTTTACTTTTACT
*
8063 TCTTACTTATTACTT
1 TTTTACTT-TTAC-T
*
8078 TTTTACTCTTACT
1 TTTTACTTTTACT
**
8091 GATTACTATTTACT
1 TTTTACT-TTTACT
8105 TTTTACT
1 TTTTACT
8112 GACTATTATT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
13 11 0.24
14 28 0.61
15 7 0.15
ACGTcount: A:0.18, C:0.20, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTACTTTTACT
Found at i:8187 original size:22 final size:21
Alignment explanation
Indices: 7936--8195 Score: 192
Period size: 22 Copynumber: 12.1 Consensus size: 21
7926 CTGCTCATTT
*
7936 TTTACTGATTACTCTTTTACTT
1 TTTACTGATTAC-CTTTTACTC
* * *
7958 TTTACTGATTGCCTTTTGCTT
1 TTTACTGATTACCTTTTACTC
*
7979 TTTAGTGATTACCTTTTTACT-
1 TTTACTGATTACC-TTTTACTC
* *
8000 TCTTGCTGATTAGCTTTTTACTC
1 T-TTACTGATTA-CCTTTTACTC
*
8023 TTTACTGATCACCTTTTACTC
1 TTTACTGATTACCTTTTACTC
*
8044 -TTACTGATTTCCTTTTACT-
1 TTTACTGATTACCTTTTACTC
* *
8063 TCTTACTTATTACTTTTTTACTC
1 T-TTACTGATTAC-CTTTTACTC
*
8086 -TTACTGATTA-CTATTTACTT
1 TTTACTGATTACCT-TTTACTC
* **
8106 TTTACTGACTATTATTTTACTC
1 TTTACTGATTA-CCTTTTACTC
*
8128 TTGT--TGATTACCTTCTTACTT
1 TT-TACTGATTACCTT-TTACTC
*
8149 TTTACTGATTACTATTTTACTC
1 TTTACTGATTAC-CTTTTACTC
* *
8171 TTTACTAATTACCATTTTACCC
1 TTTACTGATTACC-TTTTACTC
8193 TTT
1 TTT
8196 T
Statistics
Matches: 189, Mismatches: 31, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 26 0.14
21 68 0.36
22 88 0.47
23 6 0.03
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTC
Done.