Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015062.1 Corchorus capsularis cultivar CVL-1 contig15083, 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: 28253
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:883 original size:9 final size:9
Alignment explanation
Indices: 863--893 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
853 GATCATCGCT
863 TATATA-TA
1 TATATACTA
871 TATATACTA
1 TATATACTA
880 TATATACTA
1 TATATACTA
889 TATAT
1 TATAT
894 TATTTGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (9 bp):
TATATACTA
Found at i:1876 original size:14 final size:14
Alignment explanation
Indices: 1859--1885 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1849 CATTAATTTA
1859 ATATAAAAAATTAC
1 ATATAAAAAATTAC
1873 ATATAAAAAATTA
1 ATATAAAAAATTA
1886 GGAAGTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATAAAAAATTAC
Found at i:13300 original size:21 final size:21
Alignment explanation
Indices: 13275--13320 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
13265 TGGCTGTGCG
* *
13275 CCCAGGCGCTTTGCCTGCGCA
1 CCCAGCCGCTTGGCCTGCGCA
* *
13296 CCCAGCCGGTTGGCCTGGGCA
1 CCCAGCCGCTTGGCCTGCGCA
13317 CCCA
1 CCCA
13321 TGTGCCCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.43, G:0.30, T:0.15
Consensus pattern (21 bp):
CCCAGCCGCTTGGCCTGCGCA
Found at i:21446 original size:21 final size:21
Alignment explanation
Indices: 21422--21475 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
21412 TCGGGTCATG
21422 TGGCCGGGCATGCGATGGTGA
1 TGGCCGGGCATGCGATGGTGA
* *
21443 TGGCCAGTCATGCGATGGTGA
1 TGGCCGGGCATGCGATGGTGA
21464 TGGCCGGGCATG
1 TGGCCGGGCATG
21476 TGGCCGGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.20
Consensus pattern (21 bp):
TGGCCGGGCATGCGATGGTGA
Found at i:23868 original size:10 final size:10
Alignment explanation
Indices: 23853--23877 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23843 GTTGCTGCAC
23853 AATTCCAGAA
1 AATTCCAGAA
23863 AATTCCAGAA
1 AATTCCAGAA
23873 AATTC
1 AATTC
23878 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:24812 original size:12 final size:13
Alignment explanation
Indices: 24787--24820 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
24777 TTAATTATTG
24787 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
24800 TTTGTTTTA-TAA
1 TTTGCTTTATTAA
24812 TTTGCTTTA
1 TTTGCTTTA
24821 GATTTAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:24828 original size:6 final size:6
Alignment explanation
Indices: 24817--24843 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24807 TATAATTTGC
24817 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
24844 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:25226 original size:34 final size:35
Alignment explanation
Indices: 25160--25232 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
25150 AAAAAAATTA
* *
25160 TTTTTACGAAAAAAAAAAATTTTTAGGGTTTCCGAT
1 TTTTTACGAAAAAAAAAAAGTTTTACGGTTTCCG-T
**
25196 TTTTTA-GAAAAAAAAAAAGTTTT-CTTTTTCCGT
1 TTTTTACGAAAAAAAAAAAGTTTTACGGTTTCCGT
25229 TTTT
1 TTTT
25233 CCTTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 5 0.15
34 6 0.18
35 16 0.48
36 6 0.18
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (35 bp):
TTTTTACGAAAAAAAAAAAGTTTTACGGTTTCCGT
Found at i:25683 original size:50 final size:50
Alignment explanation
Indices: 25625--25728 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
25615 TTGAAATTAA
25625 ATCCGGATTTATTCAGATTTTACCCAAATTTCACGGTTTGCCTGGAGAAG
1 ATCCGGATTTATTCAGATTTTACCCAAATTTCACGGTTTGCCTGGAGAAG
25675 ATCCGGATTTATTCAGATTTTACCCAAATTTCACGGTTTGCCTGGAGAAG
1 ATCCGGATTTATTCAGATTTTACCCAAATTTCACGGTTTGCCTGGAGAAG
25725 ATCC
1 ATCC
25729 TCACCGACAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (50 bp):
ATCCGGATTTATTCAGATTTTACCCAAATTTCACGGTTTGCCTGGAGAAG
Found at i:28010 original size:27 final size:27
Alignment explanation
Indices: 27973--28032 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
27963 TTCATAAAAT
27973 TTCAT-TTAATTACAAAAGAAATTACA
1 TTCATATTAATTACAAAAGAAATTACA
27999 TTCATATTAATTACAAAAGAAATTACA
1 TTCATATTAATTACAAAAGAAATTACA
28026 TTCATAT
1 TTCATAT
28033 GAGATATACG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (27 bp):
TTCATATTAATTACAAAAGAAATTACA
Done.