Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020660.1 Corchorus olitorius cultivar O-4 contig20693, 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: 8280
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:236 original size:2 final size:2
Alignment explanation
Indices: 231--265 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
221 TATATGTACG
231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
266 CATTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1026 original size:31 final size:31
Alignment explanation
Indices: 919--1105 Score: 180
Period size: 31 Copynumber: 6.1 Consensus size: 31
909 TGACACCAGA
* * *
919 CACATATC-CTTTTT-GTGCACGTGGCATGC
1 CACATGTCACTTTTTGGTACACGTGGCGTGC
* ** * *
948 CACGTGTCACTTTTTGAAACACATGGCATGC
1 CACATGTCACTTTTTGGTACACGTGGCGTGC
* * *
979 AACGTGTCACTTTTTGGTACACGTGACGTGC
1 CACATGTCACTTTTTGGTACACGTGGCGTGC
** *
1010 CACATGTCACTTTTTGGTACACGTGATGTGT
1 CACATGTCACTTTTTGGTACACGTGGCGTGC
* *
1041 CACATGTCGCTTTTTGGTACACATGGCGTGC
1 CACATGTCACTTTTTGGTACACGTGGCGTGC
* * * *
1072 CACATGTCGCTTTTTGGTATATGTGGCATGC
1 CACATGTCACTTTTTGGTACACGTGGCGTGC
1103 CAC
1 CAC
1106 GTCGGACACC
Statistics
Matches: 131, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
29 6 0.05
30 6 0.05
31 119 0.91
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (31 bp):
CACATGTCACTTTTTGGTACACGTGGCGTGC
Found at i:2419 original size:81 final size:82
Alignment explanation
Indices: 2278--2517 Score: 247
Period size: 81 Copynumber: 3.0 Consensus size: 82
2268 AGTTGAATTA
* * *
2278 GCTCCAACTCTCAAACATAGATTAAAATTTTTTTTCCCACTTGGTATCCAGCTCTGACTAAT-CT
1 GCTCCAACTCTCAAACATAGATTAAAATTTTTTTTCCCACTAGGTATCCAGCTCTAACTAATCCA
*
2342 GATTCGACCCGGGTCGC
66 GATTCGACCCGGGTCAC
*** *
2359 GCTCCAACTCTCAAACATAGATT-TTTTTTTTGTTTCCCACTAGGTATCCAGTTCTAACTAATCC
1 GCTCCAACTCTCAAACATAGATTAAAATTTTT-TTTCCCACTAGGTATCCAGCTCTAACTAATCC
**
2423 AGATTCGACTTGGGTCAC
65 AGATTCGACCCGGGTCAC
* * * ** * * * *
2441 GCTCCAACTTTCAAA-ATAGATT-ACA-TTTTTCTCCCACCCGGTATCTAGCTCTGACTAATTCG
1 GCTCCAACTCTCAAACATAGATTAAAATTTTTTTTCCCACTAGGTATCCAGCTCTAACTAATCCA
**
2503 GATTTTACCCGGGTC
66 GATTCGACCCGGGTC
2518 GTGCATCTGG
Statistics
Matches: 131, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
79 36 0.27
80 9 0.07
81 57 0.44
82 29 0.22
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (82 bp):
GCTCCAACTCTCAAACATAGATTAAAATTTTTTTTCCCACTAGGTATCCAGCTCTAACTAATCCA
GATTCGACCCGGGTCAC
Found at i:4254 original size:17 final size:16
Alignment explanation
Indices: 4208--4250 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
4198 CCAGATTACT
4208 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
*
4225 AGTAATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
4242 GGTGATCAA
1 AGTGATCAA
4251 AGATTACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 18 0.82
18 1 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:4808 original size:131 final size:131
Alignment explanation
Indices: 4629--4889 Score: 423
Period size: 131 Copynumber: 2.0 Consensus size: 131
4619 TTGTTTAAAT
*
4629 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAGTTAAATCTAATATCCTTAAAAATA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAAAAATA
* * *
4694 TTTAATTTTTACCATTATACTATTTTAATTAAAAAACTAATATATATTAGAATTTTTTAAATATA
66 TTTAATTTTTACCATTATACTAATTTAATTAAAAAACTAAGATATATTAGAATTTTTAAAATATA
4759 C
131 C
* **
4760 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAAAAATA
* * * *
4825 TTTTATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATA
66 TTTAATTTTTACCATTATACTAATTTAATTAAAAAACTAAGATATATTAGAATTTTTAAAATATA
4890 TTTCTTAAAT
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 119 1.00
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.48
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAAAAATA
TTTAATTTTTACCATTATACTAATTTAATTAAAAAACTAAGATATATTAGAATTTTTAAAATATA
C
Found at i:6100 original size:45 final size:44
Alignment explanation
Indices: 6042--6172 Score: 212
Period size: 42 Copynumber: 3.0 Consensus size: 44
6032 TTACCTAAAT
*
6042 TCTACTTCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
1 TCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
*
6086 TACTCCTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATA-T-
1 T-CTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
*
6129 TCTACTCCATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
1 TCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
6173 ATTGTTGCTT
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
42 38 0.47
43 2 0.03
44 2 0.03
45 38 0.47
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.34
Consensus pattern (44 bp):
TCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
Found at i:7772 original size:13 final size:13
Alignment explanation
Indices: 7754--7778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7744 GGGTGAGAGT
7754 TGGAGTTTTGTGA
1 TGGAGTTTTGTGA
7767 TGGAGTTTTGTG
1 TGGAGTTTTGTG
7779 TTGAACCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (13 bp):
TGGAGTTTTGTGA
Done.