Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011113.1 Corchorus olitorius cultivar O-4 contig11146, 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, 817
Length: 1362
ACGTcount: A:0.21, C:0.28, G:0.27, T:0.24
Found at i:26 original size:20 final size:20
Alignment explanation
Indices: 1--318 Score: 247
Period size: 20 Copynumber: 17.6 Consensus size: 20
*
1 CGATGGCACTCGAGACTTGC
1 CGATGGCACTCGGGACTTGC
21 CGATGGCACTC--G----GC
1 CGATGGCACTCGGGACTTGC
*
35 C-TTGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGC
54 CGATGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGC
**
74 CGATGGCACTCGACACTTGC
1 CGATGGCACTCGGGACTTGC
94 CGATGGCACTC--G----GC
1 CGATGGCACTCGGGACTTGC
*
108 C-TTGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGC
*
127 TGATGGCACTC--G----GC
1 CGATGGCACTCGGGACTTGC
*
141 C-TTGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGC
160 CGATGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGC
**
180 CGATGGCACTCGACACTTGC
1 CGATGGCACTCGGGACTTGC
*
200 CGATGGCACTCGGCACTTGC
1 CGATGGCACTCGGGACTTGC
*
220 CGATGGCACT----A--GGC
1 CGATGGCACTCGGGACTTGC
* *
234 C-TTGGCACTCGGCACTTGC
1 CGATGGCACTCGGGACTTGC
*
253 CGATGGCACT----A--GGC
1 CGATGGCACTCGGGACTTGC
* *
267 C-TTGGCACTCGGGAGTTGC
1 CGATGGCACTCGGGACTTGC
286 CGATGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGC
306 CGATGGCACTCGG
1 CGATGGCACTCGG
319 CCTTGACACT
Statistics
Matches: 240, Mismatches: 23, Indels: 70
0.72 0.07 0.21
Matches are distributed among these distances:
13 38 0.16
14 14 0.06
15 3 0.01
16 2 0.01
17 2 0.01
18 2 0.01
19 14 0.06
20 165 0.69
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (20 bp):
CGATGGCACTCGGGACTTGC
Found at i:51 original size:33 final size:33
Alignment explanation
Indices: 4--345 Score: 237
Period size: 33 Copynumber: 9.7 Consensus size: 33
1 CGA
*
4 TGGCACTCGAGACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
*
37 TGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTC--G----GCC-T
**
77 TGGCACTCGACACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
*
110 TGGCACTCGGGACTTGCTGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
*
143 TGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTC--G----GCC-T
**
183 TGGCACTCGACACTTGCCGATGGCACTCGGCACT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGC-CT
* * * *
217 TGCCGA-T-GGCACTAGGCC-TTGGCACTCGGCACT
1 TGGC-ACTCGGGACT-TGCCGATGGCACTCGGC-CT
* * * * *
250 TGCCGA-T-GGCACTAGGCC-TTGGCACTCGGGAGTTGCCGA
1 TGGC-ACTCGGGACT-TGCCGATGGCACTC----G--GCC-T
289 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
*
322 TGACACTCGGGACTTGCCGATGGC
1 TGGCACTCGGGACTTGCCGATGGC
346 GCTTGGCAAC
Statistics
Matches: 258, Mismatches: 24, Indels: 54
0.77 0.07 0.16
Matches are distributed among these distances:
33 153 0.59
34 15 0.06
35 4 0.02
36 1 0.00
37 1 0.00
38 4 0.02
39 15 0.06
40 65 0.25
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (33 bp):
TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
Found at i:81 original size:53 final size:53
Alignment explanation
Indices: 1--191 Score: 271
Period size: 53 Copynumber: 3.6 Consensus size: 53
*
1 CGATGGCACTCGAGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGC
* * * *
54 CGATGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGA-T-GGCACTCGGC
1 CGATGGCACTCGGGACTTGCCGATGGCACTCGGC-CTTGGC-ACTCGGGACT-TGC
* *
108 C-TTGGCACTCGGGACTTGCTGATGGCACTCGGCCTTGGCACTCGGGACTTGC
1 CGATGGCACTCGGGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGC
160 CGATGGCACTCGGGACTTGCCGATGGCACTCG
1 CGATGGCACTCGGGACTTGCCGATGGCACTCG
192 ACACTTGCCG
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
51 1 0.01
52 9 0.08
53 99 0.83
54 9 0.08
55 1 0.01
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (53 bp):
CGATGGCACTCGGGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGC
Found at i:189 original size:106 final size:106
Alignment explanation
Indices: 4--345 Score: 462
Period size: 106 Copynumber: 3.2 Consensus size: 106
1 CGA
*
4 TGGCACTCGAGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGA
69 CTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCCT
66 CTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCCT
*
110 TGGCACTCGGGACTTGCTGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGA
175 CTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCACT
66 CTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGC-CT
* * * * * * * *
217 TGCCGA-T-GGCACTAGGCC-TTGGCACTCGGCACTTGCCGA-T-GGCACTAGGCC-TTGGCACT
1 TGGC-ACTCGGGACT-TGCCGATGGCACTCGGC-CTTGGC-ACTCGGGACT-TGCCGATGGCACT
* **
276 CGGGAGTTGCCGATGGCACTCGGGACTTGCCGATGGCACTCGGCCT
61 CGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCCT
*
322 TGACACTCGGGACTTGCCGATGGC
1 TGGCACTCGGGACTTGCCGATGGC
346 GCTTGGCAAC
Statistics
Matches: 209, Mismatches: 18, Indels: 18
0.85 0.07 0.07
Matches are distributed among these distances:
104 1 0.00
105 9 0.04
106 180 0.86
107 17 0.08
108 2 0.01
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (106 bp):
TGGCACTCGGGACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGA
CTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCCT
Found at i:227 original size:126 final size:126
Alignment explanation
Indices: 37--317 Score: 490
Period size: 126 Copynumber: 2.2 Consensus size: 126
27 CACTCGGCCT
**
37 TGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCA
1 TGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGACACTTGCCGATGGCA
* * * *
102 CTCGGCCTTGGCACTCGGGACTTGCTGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGA
66 CTAGGCCTTGGCACTCGGCACTTGCCGATGGCACTAGGCCTTGGCACTCGGGACTTGCCGA
*
163 TGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCACTTGCCGATGGCA
1 TGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGACACTTGCCGATGGCA
*
228 CTAGGCCTTGGCACTCGGCACTTGCCGATGGCACTAGGCCTTGGCACTCGGGAGTTGCCGA
66 CTAGGCCTTGGCACTCGGCACTTGCCGATGGCACTAGGCCTTGGCACTCGGGACTTGCCGA
289 TGGCACTCGGGACTTGCCGATGGCACTCG
1 TGGCACTCGGGACTTGCCGATGGCACTCG
318 GCCTTGACAC
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 147 1.00
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (126 bp):
TGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGACACTTGCCGATGGCA
CTAGGCCTTGGCACTCGGCACTTGCCGATGGCACTAGGCCTTGGCACTCGGGACTTGCCGA
Done.