Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023051.1 Corchorus olitorius cultivar O-4 contig23084, 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: 23819
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Found at i:8669 original size:30 final size:30
Alignment explanation
Indices: 8633--8692 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
8623 TAACTCCAAA
8633 TTCAACATATTCCATCTTCAATTCAACAGG
1 TTCAACATATTCCATCTTCAATTCAACAGG
8663 TTCAACATATTCCATCTTCAATTCAACAGG
1 TTCAACATATTCCATCTTCAATTCAACAGG
8693 CAGATGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (30 bp):
TTCAACATATTCCATCTTCAATTCAACAGG
Found at i:8912 original size:26 final size:26
Alignment explanation
Indices: 8876--8937 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
8866 TGTATAGTTC
8876 TAATACTTATCTTATACTTTCAAATG
1 TAATACTTATCTTATACTTTCAAATG
8902 TAATACTTATCTTATACTTTCAAATG
1 TAATACTTATCTTATACTTTCAAATG
8928 TAAT-CTTATC
1 TAATACTTATC
8938 ATATCTTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 6 0.17
26 30 0.83
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (26 bp):
TAATACTTATCTTATACTTTCAAATG
Found at i:22773 original size:16 final size:16
Alignment explanation
Indices: 22752--22810 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
22742 GGTTGGGTAC
22752 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
22768 TTCGGGTTCAGGTATT
1 TTCGGGTTCGGGTATT
22784 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
22800 TTCGGGTTCGG
1 TTCGGGTTCGG
22811 TCTCGGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.07, C:0.14, G:0.37, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:22809 original size:6 final size:6
Alignment explanation
Indices: 22800--22870 Score: 67
Period size: 6 Copynumber: 12.2 Consensus size: 6
22790 TTCGGGTATT
* * *
22800 TTCGGG TTC-GG TCTCGGG TT-TGG TTCGGG CTCGGG CTCGGG -TCGGG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* *
22846 TTCGGG TTCGGG CTCGGG CTCGGG T
1 TTCGGG TTCGGG TTCGGG TTCGGG T
22871 CGAGTACGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
5 12 0.21
6 41 0.73
7 3 0.05
ACGTcount: A:0.00, C:0.23, G:0.48, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:22833 original size:23 final size:23
Alignment explanation
Indices: 22800--22870 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
22790 TTCGGGTATT
* **
22800 TTCGGGTTCGGTCTCGGGTTTGG
1 TTCGGGTTCGGGCTCGGGTCGGG
*
22823 TTCGGGCTCGGGCTCGGGTCGGG
1 TTCGGGTTCGGGCTCGGGTCGGG
22846 TTCGGGTTCGGGCTCGGGCTCGGG
1 TTCGGGTTCGGGCTCGGG-TCGGG
22870 T
1 T
22871 CGAGTACGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 36 0.86
24 6 0.14
ACGTcount: A:0.00, C:0.23, G:0.48, T:0.30
Consensus pattern (23 bp):
TTCGGGTTCGGGCTCGGGTCGGG
Found at i:22853 original size:29 final size:28
Alignment explanation
Indices: 22813--22872 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 28
22803 GGGTTCGGTC
*
22813 TCGGGTTTGGTTCGGGCTCGGGCTCGGG
1 TCGGGTTGGGTTCGGGCTCGGGCTCGGG
22841 TCGGGTTCGGGTTCGGGCTCGGGCTCGGG
1 TCGGGTT-GGGTTCGGGCTCGGGCTCGGG
22870 TCG
1 TCG
22873 AGTACGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.00, C:0.23, G:0.50, T:0.27
Consensus pattern (28 bp):
TCGGGTTGGGTTCGGGCTCGGGCTCGGG
Found at i:22884 original size:29 final size:29
Alignment explanation
Indices: 22821--22878 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
22811 TCTCGGGTTT
* *
22821 GGTTCGGGCTCGGGCTCGGGTCGGGTTCG
1 GGTTCGGGCTCGGGCTCGGGTCGAGTACG
22850 GGTTCGGGCTCGGGCTCGGGTCGAGTACG
1 GGTTCGGGCTCGGGCTCGGGTCGAGTACG
22879 TTTTCGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.03, C:0.24, G:0.50, T:0.22
Consensus pattern (29 bp):
GGTTCGGGCTCGGGCTCGGGTCGAGTACG
Found at i:23094 original size:15 final size:16
Alignment explanation
Indices: 23074--23114 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
23064 TGCATATGAA
23074 AATTATTCTAAA-TCT
1 AATTATTCTAAAGTCT
23089 AATTA-T-TAAAGTCT
1 AATTATTCTAAAGTCT
23103 AATTAATTCTAA
1 AATT-ATTCTAA
23115 TTTCACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 6 0.27
16 1 0.05
17 3 0.14
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (16 bp):
AATTATTCTAAAGTCT
Done.