Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017187.1 Corchorus olitorius cultivar O-4 contig17220, 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: 38675
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:11250 original size:45 final size:45
Alignment explanation
Indices: 11182--11279 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
11172 AAGCAACAGT
* *
11182 TAATATTAGCTTTATTTTGATGAATTGCCTAGAGATGAAGG-AGTA
1 TAATATTAGCTTTATTTTAATGAATTACCTAGAGATG-AGGAAGTA
* * *
11227 TAATATTAGTTTTTTTTTAATGAATTACCTTGAGATGAGGAAGTA
1 TAATATTAGCTTTATTTTAATGAATTACCTAGAGATGAGGAAGTA
11272 TAAT-TTAG
1 TAATATTAG
11280 GTAATGCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
44 7 0.15
45 40 0.85
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (45 bp):
TAATATTAGCTTTATTTTAATGAATTACCTAGAGATGAGGAAGTA
Found at i:13048 original size:15 final size:15
Alignment explanation
Indices: 13028--13064 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
13018 AGGTACGTTA
13028 CACTCTCTATCTACT
1 CACTCTCTATCTACT
13043 CACTCTCTATCTACT
1 CACTCTCTATCTACT
13058 CACTCTC
1 CACTCTC
13065 ATTCAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.38
Consensus pattern (15 bp):
CACTCTCTATCTACT
Found at i:22855 original size:75 final size:76
Alignment explanation
Indices: 22668--22966 Score: 426
Period size: 76 Copynumber: 4.0 Consensus size: 76
22658 TAACCATTGG
* * * *
22668 GTGAGCGGCGTCTGCGTGAACG--CTATCTCACTGGTGGACGAACGGGGGCGCCAGTCTAGGCAC
1 GTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCACCAGTCTAGGTAC
22731 TCAGCCGTTGA
66 TCAGCCGTTGA
* *
22742 GTGAGCGGCGTCTGCGTGGACGCTCTGTCTCA-TAGGTGGACGAACGGGGGCACCATTCTAGGTG
1 GTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACT-GGTGGACGAACGGGGGCACCAGTCTAGGTA
22806 CTCAGCCGTT-A
65 CTCAGCCGTTGA
* * *
22817 GTGAGCGGCGTCTGGGTGGACGCTCTGTCTCACTGGTGGGCGAACGGGGGCGCCAGTCTAGGTAC
1 GTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCACCAGTCTAGGTAC
22882 TCAGCCGTTGA
66 TCAGCCGTTGA
* * * * * *
22893 GTGGGCGGCATCTGCGTGGGCTCTCTGTCTCACTGGTGGACGAACGGGGGCACCATTCTAGGTGC
1 GTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCACCAGTCTAGGTAC
22958 TCAGCCGTT
66 TCAGCCGTT
22967 ACTTGAAATG
Statistics
Matches: 200, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
74 21 0.10
75 69 0.34
76 110 0.55
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (76 bp):
GTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCACCAGTCTAGGTAC
TCAGCCGTTGA
Found at i:22901 original size:151 final size:149
Alignment explanation
Indices: 22668--22967 Score: 485
Period size: 151 Copynumber: 2.0 Consensus size: 149
22658 TAACCATTGG
22668 GTGAGCGGCGTCTGCGTGAACGCTATCTCACTGGTGGACGAACGGGGGCGCCAGTCTAGGCACTC
1 GTGAGCGGCGTCTGCGTGAACGCTATCTCACTGGTGGACGAACGGGGGCGCCAGTCTAGGCACTC
*
22733 AGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTGTCTCA-TAGGTGGACGAACGGGGGCACCA
66 AGCCGTTGAGTGAGCGGCATCTGCGTGGACGCTCTGTCTCACT-GGTGGACGAACGGGGGCACCA
22797 TTCTAGGTGCTCAGCCGTTA
130 TTCTAGGTGCTCAGCCGTTA
* * * * *
22817 GTGAGCGGCGTCTGGGTGGACGCTCTGTCTCACTGGTGGGCGAACGGGGGCGCCAGTCTAGGTAC
1 GTGAGCGGCGTCTGCGTGAACG--CTATCTCACTGGTGGACGAACGGGGGCGCCAGTCTAGGCAC
* * *
22882 TCAGCCGTTGAGTGGGCGGCATCTGCGTGGGCTCTCTGTCTCACTGGTGGACGAACGGGGGCACC
64 TCAGCCGTTGAGTGAGCGGCATCTGCGTGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCACC
22947 ATTCTAGGTGCTCAGCCGTTA
129 ATTCTAGGTGCTCAGCCGTTA
22968 CTTGAAATGT
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
149 20 0.14
151 118 0.85
152 1 0.01
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (149 bp):
GTGAGCGGCGTCTGCGTGAACGCTATCTCACTGGTGGACGAACGGGGGCGCCAGTCTAGGCACTC
AGCCGTTGAGTGAGCGGCATCTGCGTGGACGCTCTGTCTCACTGGTGGACGAACGGGGGCACCAT
TCTAGGTGCTCAGCCGTTA
Found at i:30189 original size:75 final size:75
Alignment explanation
Indices: 30087--30234 Score: 251
Period size: 75 Copynumber: 2.0 Consensus size: 75
30077 AATATATGTT
* *
30087 GTTGTTAAAATATTTTTACGCAACAATATTTAGTAATTGCGTAAAATATAATTTTTTTAACAACA
1 GTTGTTAAAATATTTTTACGCAACAATATTGAGTAATTGCGTAAAATATAATTCTTTTAACAACA
30152 ATAAAATGAC
66 ATAAAATGAC
** *
30162 GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATATAATTCTTTTAGCAACA
1 GTTGTTAAAATATTTTTACGCAACAATATTGAGTAATTGCGTAAAATATAATTCTTTTAACAACA
30227 ATAAAATG
66 ATAAAATG
30235 GTGTAATGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (75 bp):
GTTGTTAAAATATTTTTACGCAACAATATTGAGTAATTGCGTAAAATATAATTCTTTTAACAACA
ATAAAATGAC
Found at i:34223 original size:10 final size:10
Alignment explanation
Indices: 34194--34228 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
34184 TGATCTCACA
34194 TAATAGAGCT
1 TAATAGAGCT
*
34204 TAGCTAGAGCT
1 TA-ATAGAGCT
34215 TAATAGAGCT
1 TAATAGAGCT
34225 TAAT
1 TAAT
34229 TCACATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (10 bp):
TAATAGAGCT
Found at i:34485 original size:28 final size:28
Alignment explanation
Indices: 34442--34513 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
34432 TGTTAGTTTA
*
34442 TACTCAATCGCAGAGTCCATGTAGATTT
1 TACTCAATCGCGGAGTCCATGTAGATTT
* *
34470 TACTCAATCGTGGAGTCCATGTAGTTTT
1 TACTCAATCGCGGAGTCCATGTAGATTT
34498 TACTCAATCGCGGAGT
1 TACTCAATCGCGGAGT
34514 GAAATATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (28 bp):
TACTCAATCGCGGAGTCCATGTAGATTT
Found at i:38078 original size:13 final size:12
Alignment explanation
Indices: 38036--38080 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
38026 TCATGCACCC
38036 AAAACAATTTATTT
1 AAAACAATTTA--T
*
38050 AAAACCATTTAT
1 AAAACAATTTAT
38062 AAAACAATTTGAT
1 AAAACAATTT-AT
38075 AAAACA
1 AAAACA
38081 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 8 0.29
14 10 0.36
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (12 bp):
AAAACAATTTAT
Done.