Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021475.1 Corchorus olitorius cultivar O-4 contig21508, 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: 8186
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:96 original size:31 final size:31
Alignment explanation
Indices: 58--116 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
48 AGTTATAGAG
58 TTTTTTTTTCTCGGTTCTTATGATATATAGT
1 TTTTTTTTTCTCGGTTCTTATGATATATAGT
89 TTTTTTTTTCTCGGTTCTTATGATATAT
1 TTTTTTTTTCTCGGTTCTTATGATATAT
117 GTGAGTAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.63
Consensus pattern (31 bp):
TTTTTTTTTCTCGGTTCTTATGATATATAGT
Found at i:943 original size:7 final size:7
Alignment explanation
Indices: 931--955 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
921 CAAATAATAT
931 GTATGTA
1 GTATGTA
938 GTATGTA
1 GTATGTA
945 GTATGTA
1 GTATGTA
952 GTAT
1 GTAT
956 ATGTAGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (7 bp):
GTATGTA
Found at i:2553 original size:30 final size:30
Alignment explanation
Indices: 2518--2575 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2508 TTCGTTGAAC
2518 TTTTTCTTTTTAACTCCTTAAAATAATTCT
1 TTTTTCTTTTTAACTCCTTAAAATAATTCT
* *
2548 TTTTTCTTTTTAGCTTCTTAAAATAATT
1 TTTTTCTTTTTAACTCCTTAAAATAATT
2576 TATCTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.59
Consensus pattern (30 bp):
TTTTTCTTTTTAACTCCTTAAAATAATTCT
Found at i:5255 original size:26 final size:26
Alignment explanation
Indices: 5215--5265 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
5205 TGACAGTTCC
*
5215 TGTGGCAAGACCCTATGGAAATACCA
1 TGTGGCAACACCCTATGGAAATACCA
*
5241 TGTGGCAACATCCTATGGAAATACC
1 TGTGGCAACACCCTATGGAAATACC
5266 TTATGCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (26 bp):
TGTGGCAACACCCTATGGAAATACCA
Found at i:5490 original size:27 final size:27
Alignment explanation
Indices: 5449--5522 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
5439 ATATATCTTA
*
5449 TGGCAATTACACTCTTGCAAAACCATG
1 TGGCAATTACCCTCTTGCAAAACCATG
* * *
5476 TGGCAATTACCCTCTTGCAATATCTTG
1 TGGCAATTACCCTCTTGCAAAACCATG
* * *
5503 TGCCAATTACCTTCTGGCAA
1 TGGCAATTACCCTCTTGCAA
5523 TAACAATACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (27 bp):
TGGCAATTACCCTCTTGCAAAACCATG
Found at i:7992 original size:16 final size:16
Alignment explanation
Indices: 7971--8004 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
7961 AACACTTAAA
7971 TTTCTAT-TTTTAATTT
1 TTTCTATCTTTT-ATTT
7987 TTTCTATCTTTTATTT
1 TTTCTATCTTTTATTT
8003 TT
1 TT
8005 ATTTCGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTATCTTTTATTT
Done.