Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019901.1 Corchorus olitorius cultivar O-4 contig19934, 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: 3179
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:244 original size:20 final size:21
Alignment explanation
Indices: 219--264 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
209 GTGATAGTTA
* *
219 TTTCTAT-TTAAAATATGAAG
1 TTTCTATGTAAAAATATGAAC
239 TTTCTATGTAAAAATATGAAC
1 TTTCTATGTAAAAATATGAAC
260 TTTCT
1 TTTCT
265 CATAGCTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTCTATGTAAAAATATGAAC
Found at i:2690 original size:2 final size:2
Alignment explanation
Indices: 2685--2719 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2675 AGTGTGTATG
2685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2720 GGAATTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2873 original size:41 final size:41
Alignment explanation
Indices: 2828--3144 Score: 284
Period size: 41 Copynumber: 7.7 Consensus size: 41
2818 ATAAGGAGAA
*
2828 ATGCCTCTGTGTTATATATGTGTTT-GACTTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGAC-TTTGTAATAGAG
2869 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTT--GGACTTTGTA-ATAGAG
*
2910 ATGCCTCTGTG-T-TATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTT--GGACTTTGTAATAGAG
* *
2951 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG--ATATAG
1 ATGCCCCTGTGTTATATATGTGTTT--GGACTTTGTAATAGAG
* *
2992 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCCCTGTGTTATATATGTGTTT--GGACTTTGTAATAGAG
** *
3035 GCGCCCCTGTG-T-TATATGTGTTTGGGGAC-TTGGATATAG-G
1 ATGCCCCTGTGTTATATATGTGTTT--GGACTTTGTA-ATAGAG
* *
3075 -TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-
1 ATGCCCCTGTGTTATATATGTGTTT--GGAC-TTTGTAATAGAG
3117 ATTGCCCCTGTGTTATATATGTGTTTGG
1 A-TGCCCCTGTGTTATATATGTGTTTGG
3145 GGACTTTTTG
Statistics
Matches: 236, Mismatches: 21, Indels: 37
0.80 0.07 0.13
Matches are distributed among these distances:
39 31 0.13
40 9 0.04
41 115 0.49
42 10 0.04
43 45 0.19
44 26 0.11
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.42
Consensus pattern (41 bp):
ATGCCCCTGTGTTATATATGTGTTTGGACTTTGTAATAGAG
Found at i:2921 original size:82 final size:82
Alignment explanation
Indices: 2826--3151 Score: 448
Period size: 82 Copynumber: 3.9 Consensus size: 82
2816 CCATAAGGAG
2826 AAATGCCTCTGTGTTATATATGTGTTT-GACTTTTGTAATAGAGATGCCCCTGTGTTATATATGT
1 AAATGCCTCTGTGTTATATATGTGTTTGGAC-TTTGTAATAGAGATGCCCCTGTGTTATATATGT
2890 GTTTGGGGACTTTGATAT
65 GTTTGGGGACTTTGATAT
*
2908 AAATGCCTCTGTG-T-TATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTT--GGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
2971 TGTTTGGGGACTTTGATAT
64 TGTTTGGGGACTTTGATAT
* * **
2990 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGCGCCCCTGTG-T-TATATG
1 AAATGCCTCTGTGTTATATATGTGTTT--GGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
*
3053 TGTTTGGGGACTTGGATAT
64 TGTTTGGGGACTTTGATAT
** *
3072 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-ATTGCCCCTGTGTTATATA
1 AAATGCCTCTGTGTTATATATGTGTTT--GGAC-TTTGTAATAGAGA-TGCCCCTGTGTTATATA
3136 TGTGTTTGGGGACTTT
62 TGTGTTTGGGGACTTT
3152 TTGATTATTG
Statistics
Matches: 223, Mismatches: 12, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
80 11 0.05
81 1 0.00
82 131 0.59
83 23 0.10
84 38 0.17
85 19 0.09
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (82 bp):
AAATGCCTCTGTGTTATATATGTGTTTGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTTGATAT
Found at i:3023 original size:123 final size:122
Alignment explanation
Indices: 2829--3151 Score: 417
Period size: 123 Copynumber: 2.6 Consensus size: 122
2819 TAAGGAGAAA
*
2829 TGCCTCTGTGTTATATATGTGTTT--GACTTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
1 TGCCTCTGTGTTATATATGTGTTTGGGACTTTTG--ATATAGATGCCCCTGTGTTATATATGTGT
* * *
2892 TTGGGGACTTTG-ATATAAA-TGCCTCTGTGTTATATGTGTTTGAGGACTTTG-TAATAGAG
64 TTGGGGACTTTGTA-ATAAAGCGCCCCTGTGTTATATGTGTTTGAGGACTTGGAT-ATAG-G
* *
2951 TTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGATATAGATGCCTCTGTGTTATATATGTGT
1 -TGCCTCTGTGTTATATATGTGTTT-GGGACTTTTGATATAGATGCCCCTGTGTTATATATGTGT
* *
3015 TTGAGGACTTTGTAATAAAGGCGCCCCTGTGTTATATGTGTTTGGGGACTTGGATATAGG
64 TTGGGGACTTTGTAATAAA-GCGCCCCTGTGTTATATGTGTTTGAGGACTTGGATATAGG
3075 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGA-ATAGAATTGCCCCTGTGTTATATATGT
1 TGCCTCTGTGTTATATATGTGTTTG-GGACTTTT-GATATAG-A-TGCCCCTGTGTTATATATGT
3139 GTTTGGGGACTTT
62 GTTTGGGGACTTT
3152 TTGATTATTG
Statistics
Matches: 177, Mismatches: 11, Indels: 21
0.85 0.05 0.10
Matches are distributed among these distances:
122 1 0.01
123 93 0.53
124 9 0.05
125 39 0.22
126 35 0.20
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.42
Consensus pattern (122 bp):
TGCCTCTGTGTTATATATGTGTTTGGGACTTTTGATATAGATGCCCCTGTGTTATATATGTGTTT
GGGGACTTTGTAATAAAGCGCCCCTGTGTTATATGTGTTTGAGGACTTGGATATAGG
Done.