Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010026.1 Corchorus olitorius cultivar O-4 contig10058, 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: 22702
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:10004 original size:12 final size:13
Alignment explanation
Indices: 9985--10016 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
9975 TTTAATCAAA
9985 ATAATATATTGGG
1 ATAATATATTGGG
9998 A-AATATATTGGG
1 ATAATATATTGGG
10010 ATAATAT
1 ATAATAT
10017 TGAATTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (13 bp):
ATAATATATTGGG
Found at i:15735 original size:20 final size:20
Alignment explanation
Indices: 15710--15751 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
15700 AGCTACTCGG
15710 TACACACA-CATATGTATATA
1 TACACACATCATAT-TATATA
15730 TACACACATCATATTATATA
1 TACACACATCATATTATATA
15750 TA
1 TA
15752 TTTAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (20 bp):
TACACACATCATATTATATA
Found at i:15747 original size:18 final size:18
Alignment explanation
Indices: 15713--15751 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
15703 TACTCGGTAC
*
15713 ACACACATATGTATATAT
1 ACACACATATATATATAT
15731 ACACACATCATATTATATAT
1 ACACACAT-ATA-TATATAT
15751 A
1 A
15752 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (18 bp):
ACACACATATATATATAT
Found at i:19319 original size:69 final size:69
Alignment explanation
Indices: 19208--19357 Score: 266
Period size: 69 Copynumber: 2.2 Consensus size: 69
19198 GGCATGAAAC
* * *
19208 CACTTTGGAATTGCTATCTTTTCTTTTGCTCTGTTTCCTTATGCTTTTCAAGTAATGGGTGTTGT
1 CACTTTGAAATTGCTATCTTTTATGTTGCTCTGTTTCCTTATGCTTTTCAAGTAATGGGTGTTGT
19273 TGTA
66 TGTA
19277 CACTTTGAAATTGCTATCTTTTATGTTGCTCTGTTTCCTTATGCTTTTCAAGTAATGGGTGTTGT
1 CACTTTGAAATTGCTATCTTTTATGTTGCTCTGTTTCCTTATGCTTTTCAAGTAATGGGTGTTGT
19342 TGTA
66 TGTA
19346 CA-TTTGAAATTG
1 CACTTTGAAATTG
19358 AATGGTGAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
68 10 0.13
69 68 0.87
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (69 bp):
CACTTTGAAATTGCTATCTTTTATGTTGCTCTGTTTCCTTATGCTTTTCAAGTAATGGGTGTTGT
TGTA
Found at i:20155 original size:18 final size:18
Alignment explanation
Indices: 20134--20182 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
20124 TATTAATAAA
**
20134 TAAATAATAAATATGTTT
1 TAAATAATAAATATGACT
20152 TAAATAATAAATAATGACT
1 TAAATAATAAAT-ATGACT
20171 TAAA-AATAAATA
1 TAAATAATAAATA
20183 AATAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 19 0.68
19 8 0.29
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (18 bp):
TAAATAATAAATATGACT
Found at i:21213 original size:24 final size:24
Alignment explanation
Indices: 21186--21234 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
21176 CATGATGTGT
21186 TTATATCAAAAATAGGGTAGGAAA
1 TTATATCAAAAATAGGGTAGGAAA
21210 TTATATCAAAAATAGGGTAGGAAA
1 TTATATCAAAAATAGGGTAGGAAA
21234 T
1 T
21235 GAAAATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (24 bp):
TTATATCAAAAATAGGGTAGGAAA
Found at i:21907 original size:27 final size:27
Alignment explanation
Indices: 21855--21908 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
21845 AGCCTAATAC
*
21855 CTTGTCCCTTTTTATATGTCGGTTTTG
1 CTTGTCCCTTTTTATATGTCAGTTTTG
* *
21882 CTTGTCCCTTTTTATCTGTCATTTTTG
1 CTTGTCCCTTTTTATATGTCAGTTTTG
21909 GACATGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.07, C:0.20, G:0.15, T:0.57
Consensus pattern (27 bp):
CTTGTCCCTTTTTATATGTCAGTTTTG
Found at i:22689 original size:16 final size:15
Alignment explanation
Indices: 22644--22691 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
22634 TTTTTTAATT
* *
22644 AAAAAATAATTTTTC
1 AAAAAATATTTTTTG
22659 AAAAAA-ATTTATTTG
1 AAAAAATATTT-TTTG
22674 AAAAAATTATTTTTTG
1 AAAAAA-TATTTTTTG
22690 AA
1 AA
22692 CTAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 3 0.11
15 15 0.54
16 6 0.21
17 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (15 bp):
AAAAAATATTTTTTG
Done.