Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013567.1 Corchorus olitorius cultivar O-4 contig13600, 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: 25377
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5239 original size:17 final size:17
Alignment explanation
Indices: 5217--5250 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5207 TGAATCTCGG
*
5217 GTTTTCGGGTTCGGGTC
1 GTTTTCGAGTTCGGGTC
*
5234 GTTTTCGATTTCGGGTC
1 GTTTTCGAGTTCGGGTC
5251 ATGCGGTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.18, G:0.35, T:0.44
Consensus pattern (17 bp):
GTTTTCGAGTTCGGGTC
Found at i:5240 original size:68 final size:68
Alignment explanation
Indices: 5152--5304 Score: 229
Period size: 68 Copynumber: 2.3 Consensus size: 68
5142 TTCGGGTCAA
* * *
5152 TTTT-GGG-TCGGGTCGCTTTCGGTTTCGGGTCATACGATTCGGATAATTTCGGGTTTGAATCTC
1 TTTTCGGGTTCGGGTCGTTTTCGATTTCGGGTCATACGATTCGGATAATTTCGGGTTTGAACCTC
5215 GGG
66 GGG
* * *
5218 TTTTCGGGTTCGGGTCGTTTTCGATTTCGGGTCATGCGGTTCGGATAATTTCGGGTTTGAACCTT
1 TTTTCGGGTTCGGGTCGTTTTCGATTTCGGGTCATACGATTCGGATAATTTCGGGTTTGAACCTC
5283 GGG
66 GGG
*
5286 TTTTCGGATTCGGGTCGTT
1 TTTTCGGGTTCGGGTCGTT
5305 ACAGTTCATT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 4 0.05
67 3 0.04
68 71 0.91
ACGTcount: A:0.10, C:0.16, G:0.33, T:0.40
Consensus pattern (68 bp):
TTTTCGGGTTCGGGTCGTTTTCGATTTCGGGTCATACGATTCGGATAATTTCGGGTTTGAACCTC
GGG
Found at i:8543 original size:13 final size:13
Alignment explanation
Indices: 8525--8567 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
8515 TAATGAATAA
8525 AATAAAATAAAAT
1 AATAAAATAAAAT
8538 AATAAAATAAATAT
1 AATAAAATAAA-AT
* *
8552 AATAATATAATAT
1 AATAAAATAAAAT
8565 AAT
1 AAT
8568 TTTTATATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:8555 original size:17 final size:17
Alignment explanation
Indices: 8515--8563 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
8505 ATACTATCCT
8515 TAATGAATAAAATAAAATA
1 TAAT-AATAAAAT-AAATA
*
8534 AAATAATAAAATAAATA
1 TAATAATAAAATAAATA
*
8551 TAATAATATAATA
1 TAATAATAAAATA
8564 TAATTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 16 0.59
18 8 0.30
19 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
TAATAATAAAATAAATA
Found at i:9137 original size:10 final size:10
Alignment explanation
Indices: 9119--9152 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
9109 CCAAACTCTC
*
9119 CCCCTCCCTA
1 CCCCACCCTA
*
9129 CCCCACCCTT
1 CCCCACCCTA
9139 CCCCACCCTA
1 CCCCACCCTA
9149 CCCC
1 CCCC
9153 TCCTCATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.12, C:0.74, G:0.00, T:0.15
Consensus pattern (10 bp):
CCCCACCCTA
Found at i:15114 original size:29 final size:29
Alignment explanation
Indices: 15049--15137 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
15039 CAAAGCTTTG
* *
15049 ACACGAGTGCA-AACCCCACACTCAAAACAA
1 ACACAAGTGCACAA-CCCACACT-TAAACAA
* * * *
15079 TCCCAAGTGTACAACCCACACTTGAACAA
1 ACACAAGTGCACAACCCACACTTAAACAA
*
15108 ACACAAGTGCACAACCCGCACTTAAACAA
1 ACACAAGTGCACAACCCACACTTAAACAA
15137 A
1 A
15138 ATCCGAAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 30 0.64
30 15 0.32
31 2 0.04
ACGTcount: A:0.44, C:0.35, G:0.10, T:0.11
Consensus pattern (29 bp):
ACACAAGTGCACAACCCACACTTAAACAA
Found at i:20410 original size:15 final size:15
Alignment explanation
Indices: 20390--20419 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20380 TCATGGATTT
*
20390 AGGAAAATCTATGAG
1 AGGAAAATCCATGAG
20405 AGGAAAATCCATGAG
1 AGGAAAATCCATGAG
20420 TAGCTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.27, T:0.17
Consensus pattern (15 bp):
AGGAAAATCCATGAG
Found at i:24949 original size:11 final size:11
Alignment explanation
Indices: 24933--24958 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
24923 AGATAATTTC
24933 TTTTCTTCTAG
1 TTTTCTTCTAG
24944 TTTTCTTCTAG
1 TTTTCTTCTAG
24955 TTTT
1 TTTT
24959 TAGGCAAAGG
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:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Done.