Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022986.1 Corchorus olitorius cultivar O-4 contig23019, 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: 32299
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:3301 original size:11 final size:11
Alignment explanation
Indices: 3285--3310 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3275 TATTAAGCTC
3285 TTTTTTATTTT
1 TTTTTTATTTT
3296 TTTTTTATTTT
1 TTTTTTATTTT
3307 TTTT
1 TTTT
3311 ACAAATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:13292 original size:15 final size:16
Alignment explanation
Indices: 13272--13304 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13262 AAAAAGAGAA
*
13272 TACTTA-CTACAAAAT
1 TACTTATCTAAAAAAT
13287 TACTTATCTAAAAAAT
1 TACTTATCTAAAAAAT
13303 TA
1 TA
13305 AATTAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (16 bp):
TACTTATCTAAAAAAT
Found at i:23962 original size:15 final size:15
Alignment explanation
Indices: 23942--23973 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23932 CAAGTGTCTT
23942 TATATAT-TA-ATAA
1 TATATATATATATAA
23955 TATATATATATATAA
1 TATATATATATATAA
23970 TATA
1 TATA
23974 CTTCCGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:27061 original size:21 final size:24
Alignment explanation
Indices: 27032--27082 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
27022 TTTTGAACTC
27032 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
27055 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
27078 ATTAT
1 ATTAT
27083 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:27077 original size:25 final size:25
Alignment explanation
Indices: 27032--27080 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
27022 TTTTGAACTC
*
27032 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
27057 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
27081 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:30190 original size:22 final size:22
Alignment explanation
Indices: 30135--30178 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30125 TTTAATAAAT
30135 TAACCTT-CCTATGAAATTTTG
1 TAACCTTCCCTATGAAATTTTG
*
30156 TAACCTTCCCTATGAGATTTTG
1 TAACCTTCCCTATGAAATTTTG
30178 T
1 T
30179 TAATCTCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.43
Consensus pattern (22 bp):
TAACCTTCCCTATGAAATTTTG
Found at i:31643 original size:27 final size:26
Alignment explanation
Indices: 31589--31649 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
31579 CTAATTTTCC
31589 ATTATTTTAATAATGAAATAATTAAAAT
1 ATTA-TTTAATAATGAAAT-ATTAAAAT
31617 ATTATTTAATAATGACAAT-TTAGAAAT
1 ATTATTTAATAATGA-AATATTA-AAAT
31644 A-TATTT
1 ATTATTT
31650 GAAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGAAATATTAAAAT
Done.