Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003346.1 Corchorus capsularis cultivar CVL-1 contig03354, 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: 6128
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Found at i:3067 original size:23 final size:21
Alignment explanation
Indices: 3008--3097 Score: 63
Period size: 23 Copynumber: 3.9 Consensus size: 21
2998 AAATAGCTAT
*
3008 TGTTTTTATTGCTGTTTTTTGTGGC
1 TGTTTATATTGCTG--TTTT-T-GC
* * *
3033 TGTTTTTGTTGCTGTTTTTGT
1 TGTTTATATTGCTGTTTTTGC
3054 TGTTGTAATATTGCTGTTATATTGC
1 TGTT-T-ATATTGCTGTT-T-TTGC
*
3079 TGTTTTTATTGCTGTTTTT
1 TGTTTATATTGCTGTTTTT
3098 TTTCCTGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
21 7 0.13
22 3 0.05
23 23 0.42
24 2 0.04
25 20 0.36
ACGTcount: A:0.08, C:0.07, G:0.21, T:0.64
Consensus pattern (21 bp):
TGTTTATATTGCTGTTTTTGC
Found at i:3096 original size:11 final size:11
Alignment explanation
Indices: 3011--3096 Score: 64
Period size: 11 Copynumber: 7.4 Consensus size: 11
3001 TAGCTATTGT
3011 TTTTATTGCTG
1 TTTTATTGCTG
*
3022 TTTTTTGTGGCTG
1 TTTTAT-T-GCTG
*
3035 TTTTTGTTGCTG
1 -TTTTATTGCTG
* *
3047 TTTTTGTTGTTG
1 -TTTTATTGCTG
**
3059 TAATATTGCTG
1 TTTTATTGCTG
*
3070 TTATATTGCTG
1 TTTTATTGCTG
3081 TTTTTATTGCTG
1 -TTTTATTGCTG
3093 TTTT
1 TTTT
3097 TTTTCCTGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
11 26 0.42
12 26 0.42
13 5 0.08
14 5 0.08
ACGTcount: A:0.08, C:0.07, G:0.21, T:0.64
Consensus pattern (11 bp):
TTTTATTGCTG
Found at i:3128 original size:59 final size:59
Alignment explanation
Indices: 3082--3216 Score: 227
Period size: 59 Copynumber: 2.3 Consensus size: 59
3072 ATATTGCTGT
* *
3082 TTTTATTGCTGTTTTTTTTCCTGTTTTGTGTGAAGATATTGCTGCTGTTTTTTTGATGA
1 TTTTGTTGCTGTTTTTTTTCATGTTTTGTGTGAAGATATTGCTGCTGTTTTTTTGATGA
* *
3141 TTTTGTTGCTGTTTTTTTTTATGTTTTGTGTGAAGATATTGTTGCTGTTTTTTTGATGA
1 TTTTGTTGCTGTTTTTTTTCATGTTTTGTGTGAAGATATTGCTGCTGTTTTTTTGATGA
3200 TTTTGTTGCT-TTTTTTT
1 TTTTGTTGCTGTTTTTTT
3217 ATGATTTTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
58 7 0.10
59 65 0.90
ACGTcount: A:0.10, C:0.06, G:0.20, T:0.64
Consensus pattern (59 bp):
TTTTGTTGCTGTTTTTTTTCATGTTTTGTGTGAAGATATTGCTGCTGTTTTTTTGATGA
Found at i:3145 original size:36 final size:34
Alignment explanation
Indices: 3085--3205 Score: 86
Period size: 35 Copynumber: 3.8 Consensus size: 34
3075 TTGCTGTTTT
**
3085 TATTGCTGTTTTTTTTCCTG-TTTTGTGTGAAGA
1 TATTGCTGTTTTTTTTGATGATTTTGTGTGAAGA
3118 TATTGCTGCTGTTTTTTTGATGA--TT-T-T---G-
1 TATTGCTG-T-TTTTTTTGATGATTTTGTGTGAAGA
*
3146 --TTGCTGTTTTTTTTTATG-TTTTGTGTGAAGA
1 TATTGCTGTTTTTTTTGATGATTTTGTGTGAAGA
*
3177 TATTGTTGCTGTTTTTTTGATGATTTTGT
1 TATTGCTG-T-TTTTTTTGATGATTTTGT
3206 TGCTTTTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 29
0.66 0.05 0.29
Matches are distributed among these distances:
24 10 0.15
25 3 0.04
26 7 0.10
27 1 0.01
29 1 0.01
30 1 0.01
32 1 0.01
33 14 0.21
34 4 0.06
35 19 0.28
36 6 0.09
ACGTcount: A:0.12, C:0.06, G:0.21, T:0.61
Consensus pattern (34 bp):
TATTGCTGTTTTTTTTGATGATTTTGTGTGAAGA
Found at i:3156 original size:12 final size:12
Alignment explanation
Indices: 3008--3214 Score: 95
Period size: 12 Copynumber: 17.6 Consensus size: 12
2998 AAATAGCTAT
*
3008 TGTTTTTATTGC
1 TGTTTTTGTTGC
*
3020 TGTTTTTTGTGGC
1 TG-TTTTTGTTGC
3033 TGTTTTTGTTGC
1 TGTTTTTGTTGC
*
3045 TGTTTTTGTTGT
1 TGTTTTTGTTGC
** *
3057 TG-TAATATTGC
1 TGTTTTTGTTGC
* *
3068 TG-TTATATTGC
1 TGTTTTTGTTGC
*
3079 TGTTTTTATTGC
1 TGTTTTTGTTGC
* *
3091 TGTTTTTTTTCC
1 TGTTTTTGTTGC
*
3103 TG-TTTTGTGTGA
1 TGTTTTTGT-TGC
* * * *
3115 AGATATTGCTGC
1 TGTTTTTGTTGC
*
3127 TGTTTTT-TTGA
1 TGTTTTTGTTGC
*
3138 TGATTTTGTTGC
1 TGTTTTTGTTGC
* **
3150 TGTTTTTTTTTA
1 TGTTTTTGTTGC
*
3162 TG-TTTTGTGTGA
1 TGTTTTTGT-TGC
* * *
3174 AGATATTGTTGC
1 TGTTTTTGTTGC
*
3186 TGTTTTT-TTGA
1 TGTTTTTGTTGC
*
3197 TGATTTTGTTGC
1 TGTTTTTGTTGC
3209 T-TTTTT
1 TGTTTTT
3215 TTATGATTTT
Statistics
Matches: 145, Mismatches: 42, Indels: 17
0.71 0.21 0.08
Matches are distributed among these distances:
11 48 0.33
12 78 0.54
13 19 0.13
ACGTcount: A:0.10, C:0.06, G:0.21, T:0.63
Consensus pattern (12 bp):
TGTTTTTGTTGC
Found at i:3214 original size:11 final size:11
Alignment explanation
Indices: 3200--3268 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
3190 TTTTTGATGA
*
3200 TTTTGTTGCTT
1 TTTTGTTGATT
*
3211 TTTTTTATGATT
1 TTTTGT-TGATT
*
3223 TTTTGATGATT
1 TTTTGTTGATT
*
3234 TTTTGATGATT
1 TTTTGTTGATT
*
3245 TTGTTGCT-ATT
1 TT-TTGTTGATT
*
3256 TTTTGATGATT
1 TTTTGTTGATT
3267 TT
1 TT
3269 GTAGGCTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 4 0.08
11 33 0.67
12 12 0.24
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTTGTTGATT
Found at i:3216 original size:22 final size:23
Alignment explanation
Indices: 3179--3270 Score: 129
Period size: 22 Copynumber: 4.2 Consensus size: 23
3169 TGTGAAGATA
*
3179 TTGTTGCTGTTTTTTTGATGATT
1 TTGTTGCTGATTTTTTGATGATT
*
3202 TTGTTGCT--TTTTTTTATGATT
1 TTGTTGCTGATTTTTTGATGATT
*
3223 TT-TTGATGATTTTTTGATGATT
1 TTGTTGCTGATTTTTTGATGATT
3245 TTGTTGCT-ATTTTTTGATGATT
1 TTGTTGCTGATTTTTTGATGATT
3267 TTGT
1 TTGT
3271 AGGCTTGCCT
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.06
21 14 0.23
22 32 0.52
23 12 0.19
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.66
Consensus pattern (23 bp):
TTGTTGCTGATTTTTTGATGATT
Found at i:4551 original size:10 final size:10
Alignment explanation
Indices: 4536--4560 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4526 ACTCACTGCT
4536 ATTTGCAACC
1 ATTTGCAACC
4546 ATTTGCAACC
1 ATTTGCAACC
4556 ATTTG
1 ATTTG
4561 GTAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (10 bp):
ATTTGCAACC
Found at i:5666 original size:29 final size:30
Alignment explanation
Indices: 5583--5668 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
5573 TTGTTAAAAT
* *
5583 AAAACTGCATATTACATATCTATATCTAAC
1 AAAATTGCATGTTACATATCTATATCTAAC
* * * *
5613 TAATTTGTCAACG--ACATTTCTATATCTAA-
1 AAAATTG-C-ATGTTACATATCTATATCTAAC
5642 AAAATTGCATGTTACATATCTATATCT
1 AAAATTGCATGTTACATATCTATATCT
5669 GATTTGCATA
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
27 2 0.05
28 1 0.02
29 18 0.43
30 19 0.45
31 1 0.02
32 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (30 bp):
AAAATTGCATGTTACATATCTATATCTAAC
Done.