Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018882.1 Corchorus olitorius cultivar O-4 contig18915, 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: 15116
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2748 original size:19 final size:18
Alignment explanation
Indices: 2724--2763 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2714 TTGTAGATTT
*
2724 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
2743 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
2761 ATT
1 ATT
2764 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:4112 original size:20 final size:21
Alignment explanation
Indices: 4069--4117 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4059 ATAGTTTAGA
4069 TTTAATTTAATTTGCTTTATT
1 TTTAATTTAATTTGCTTTATT
* *
4090 TTTAGTTTAA-TTGCTTTTCTT
1 TTTAATTTAATTTGC-TTTATT
4111 TTTAATT
1 TTTAATT
4118 GTTATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTAATTTAATTTGCTTTATT
Found at i:5800 original size:35 final size:33
Alignment explanation
Indices: 5753--5854 Score: 141
Period size: 33 Copynumber: 3.0 Consensus size: 33
5743 AGAACTTTGA
*
5753 AAAACCGAATGGGAACTTTCCCGATTTGAAAACTT
1 AAAACCG-ATGGGAACTTTCCCAATTT-AAAACTT
*
5788 AAAAGCCGATGGGAACTTTCGCAATTTAAAACTT
1 AAAA-CCGATGGGAACTTTCCCAATTTAAAACTT
* *
5822 AAAACTGGTGGGAACTTTCCCAATTTAAAACTT
1 AAAACCGATGGGAACTTTCCCAATTTAAAACTT
5855 GATGAAATTC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
33 26 0.43
34 11 0.18
35 21 0.34
36 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (33 bp):
AAAACCGATGGGAACTTTCCCAATTTAAAACTT
Found at i:14069 original size:35 final size:36
Alignment explanation
Indices: 14003--14074 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
13993 TAAAACTTTG
*
14003 TCCTTTTATTAGAGTTGGACCACAACCCTTTAAAGA
1 TCCTTTTATTAGAGTTAGACCACAACCCTTTAAAGA
14039 TCCTTTTATTAGAGTTAGA-CACAACCCTTTAAAGA
1 TCCTTTTATTAGAGTTAGACCACAACCCTTTAAAGA
14074 T
1 T
14075 AAAAATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (36 bp):
TCCTTTTATTAGAGTTAGACCACAACCCTTTAAAGA
Found at i:14109 original size:2 final size:2
Alignment explanation
Indices: 14102--14166 Score: 59
Period size: 2 Copynumber: 34.0 Consensus size: 2
14092 GGGGCCAACT
* *
14102 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A CTA -A TA AA GGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
14143 TA TA TA TA TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
14167 AAATAATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
1 5 0.09
2 46 0.87
3 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (2 bp):
TA
Found at i:14167 original size:10 final size:10
Alignment explanation
Indices: 14103--14177 Score: 55
Period size: 10 Copynumber: 7.1 Consensus size: 10
14093 GGGCCAACTT
14103 ATATATATATA
1 ATATA-ATATA
14114 TATATATATATA
1 -ATATA-ATATA
*
14126 ATATAA-CTA
1 ATATAATATA
*
14135 ATA-AAGGATA
1 ATATAA-TATA
14145 TATATATATATA
1 -ATATA-ATATA
14157 ATATAATATA
1 ATATAATATA
*
14167 AAATAATATA
1 ATATAATATA
14177 A
1 A
14178 CTAATAAAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
8 2 0.04
9 5 0.09
10 18 0.33
11 13 0.24
12 15 0.28
13 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (10 bp):
ATATAATATA
Found at i:14178 original size:46 final size:43
Alignment explanation
Indices: 14102--14188 Score: 138
Period size: 46 Copynumber: 2.0 Consensus size: 43
14092 GGGGCCAACT
*
14102 TATATATATATATATATATATATAATATAACTAATAAAGGATA
1 TATATATATATATATATATAAATAATATAACTAATAAAGGATA
14145 TATATATATATAATATAATATAAAATAATATAACTAATAAAGGA
1 TATATATATAT-ATAT-ATAT-AAATAATATAACTAATAAAGGA
14189 CCCAAAATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 11 0.28
44 4 0.10
45 4 0.10
46 21 0.52
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (43 bp):
TATATATATATATATATATAAATAATATAACTAATAAAGGATA
Done.