Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017856.1 Corchorus olitorius cultivar O-4 contig17889, 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: 17043
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:2084 original size:6 final size:7
Alignment explanation
Indices: 2055--2384 Score: 305
Period size: 7 Copynumber: 50.3 Consensus size: 7
2045 TAAGCAAGCT
2055 CCTAAAC
1 CCTAAAC
*
2062 CCTAAGC
1 CCTAAAC
2069 CCTAAAC
1 CCTAAAC
2076 CCT-AAC
1 CCTAAAC
*
2082 CCTAAAT
1 CCTAAAC
*
2089 ACT-AAC
1 CCTAAAC
2095 CCTAAA-
1 CCTAAAC
*
2101 CC-ATA-
1 CCTAAAC
2106 CCTAAAC
1 CCTAAAC
2113 CCT-AAC
1 CCTAAAC
2119 CCTAAACC
1 CCTAAA-C
2127 CCTAAA-
1 CCTAAAC
2133 -CTAAAC
1 CCTAAAC
*
2139 CCTAACC
1 CCTAAAC
2146 CCTAAAC
1 CCTAAAC
2153 CCT-AAC
1 CCTAAAC
2159 CCTAAAC
1 CCTAAAC
*
2166 TCGTAAAC
1 -CCTAAAC
2174 CCTAAA-
1 CCTAAAC
2180 CCTAAAC
1 CCTAAAC
*
2187 CATAAAC
1 CCTAAAC
2194 CCT-AAC
1 CCTAAAC
2200 CCT--AC
1 CCTAAAC
*
2205 CATAAAC
1 CCTAAAC
2212 CCTAAAC
1 CCTAAAC
2219 CCT-AAC
1 CCTAAAC
2225 CCTAAA-
1 CCTAAAC
*
2231 CATAAAC
1 CCTAAAC
2238 CCT-AAC
1 CCTAAAC
2244 CCTAAAC
1 CCTAAAC
*
2251 CCTAAAAA
1 CCT-AAAC
*
2259 CATAAAC
1 CCTAAAC
*
2266 CCTCAAC
1 CCTAAAC
*
2273 CATAAAC
1 CCTAAAC
2280 CCTAAA-
1 CCTAAAC
2286 -CTAAAC
1 CCTAAAC
2292 CCTAAAC
1 CCTAAAC
2299 CCT-AAC
1 CCTAAAC
*
2305 CAT-AAC
1 CCTAAAC
2311 CCTAAAC
1 CCTAAAC
*
2318 CATAAAC
1 CCTAAAC
2325 CCTAAA-
1 CCTAAAC
2331 -CTAAAC
1 CCTAAAC
2337 CCT-AAC
1 CCTAAAC
*
2343 CCT-ACC
1 CCTAAAC
2349 CCTAAAC
1 CCTAAAC
2356 CCT-AAC
1 CCTAAAC
2362 CCTAAAC
1 CCTAAAC
*
2369 CTTAAAC
1 CCTAAAC
2376 CCTAAAC
1 CCTAAAC
2383 CC
1 CC
2385 CTTTTAAGTC
Statistics
Matches: 265, Mismatches: 34, Indels: 48
0.76 0.10 0.14
Matches are distributed among these distances:
5 23 0.09
6 82 0.31
7 142 0.54
8 18 0.07
ACGTcount: A:0.43, C:0.41, G:0.01, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:2086 original size:13 final size:13
Alignment explanation
Indices: 2055--2384 Score: 278
Period size: 13 Copynumber: 25.7 Consensus size: 13
2045 TAAGCAAGCT
2055 CCTAAACCCTAAGC
1 CCTAAACCCTAA-C
2069 CCTAAACCCTAAC
1 CCTAAACCCTAAC
**
2082 CCTAAATACTAAC
1 CCTAAACCCTAAC
*
2095 CCTAAACCAT-A-
1 CCTAAACCCTAAC
2106 CCTAAACCCTAAC
1 CCTAAACCCTAAC
2119 CCTAAACCCCTAA-
1 CCTAAA-CCCTAAC
*
2132 ACTAAACCCTAACC
1 CCTAAACCCTAA-C
2146 CCTAAACCCTAAC
1 CCTAAACCCTAAC
2159 CCTAAA--CT---
1 CCTAAACCCTAAC
* *
2167 CGTAAACCCTAAA
1 CCTAAACCCTAAC
*
2180 CCTAAACCATAAAC
1 CCTAAACCCT-AAC
2194 CCT-AACCCT-AC
1 CCTAAACCCTAAC
*
2205 CATAAACCCTAAAC
1 CCTAAACCCT-AAC
*
2219 CCT-AACCCTAAA
1 CCTAAACCCTAAC
*
2231 CATAAACCCTAAC
1 CCTAAACCCTAAC
*
2244 CCTAAACCCTAAAAA
1 CCTAAACCCT--AAC
*
2259 CATAAACCCTCAAC
1 CCTAAACCCT-AAC
*
2273 CATAAACCCTAA-
1 CCTAAACCCTAAC
*
2285 ACTAAACCCTAAAC
1 CCTAAACCCT-AAC
*
2299 CCT-AACCATAAC
1 CCTAAACCCTAAC
*
2311 CCTAAACCATAAAC
1 CCTAAACCCT-AAC
2325 CCTAAA--CTAAAC
1 CCTAAACCCT-AAC
*
2337 CCT-AACCCTACC
1 CCTAAACCCTAAC
2349 CCTAAACCCTAAC
1 CCTAAACCCTAAC
*
2362 CCTAAACCTTAAAC
1 CCTAAACCCT-AAC
2376 CCTAAACCC
1 CCTAAACCC
2385 CTTTTAAGTC
Statistics
Matches: 259, Mismatches: 32, Indels: 50
0.76 0.09 0.15
Matches are distributed among these distances:
8 5 0.02
10 2 0.01
11 17 0.07
12 45 0.17
13 107 0.41
14 72 0.28
15 11 0.04
ACGTcount: A:0.43, C:0.41, G:0.01, T:0.16
Consensus pattern (13 bp):
CCTAAACCCTAAC
Found at i:7632 original size:17 final size:17
Alignment explanation
Indices: 7610--7643 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
7600 AACTAAGACC
7610 CCATGCAATTCCATTTT
1 CCATGCAATTCCATTTT
7627 CCATGCAATTCCATTTT
1 CCATGCAATTCCATTTT
7644 TCAAACTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (17 bp):
CCATGCAATTCCATTTT
Found at i:11698 original size:24 final size:24
Alignment explanation
Indices: 11666--11711 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
11656 GATGATGATG
11666 TGATCCATATAATAAGAGTATTGC
1 TGATCCATATAATAAGAGTATTGC
*
11690 TGATCCATATAATAAGATTATT
1 TGATCCATATAATAAGAGTATT
11712 AAATACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (24 bp):
TGATCCATATAATAAGAGTATTGC
Found at i:16413 original size:18 final size:18
Alignment explanation
Indices: 16386--16420 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16376 ATATACGGTG
16386 TTAATTAATTTT-AATTA
1 TTAATTAATTTTCAATTA
16403 TTAATTTAATTTTCAATT
1 TTAA-TTAATTTTCAATT
16421 TATTTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTAATTTTCAATTA
Done.