Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011846.1 Corchorus olitorius cultivar O-4 contig11879, 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: 21365
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:3333 original size:22 final size:22
Alignment explanation
Indices: 3301--3342 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3291 CTTTTAATAT
* *
3301 ACACTTGAATAATCTAAATCAG
1 ACACTTAAATAACCTAAATCAG
3323 ACACTTAAATAACCTAAATC
1 ACACTTAAATAACCTAAATC
3343 GGATATCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (22 bp):
ACACTTAAATAACCTAAATCAG
Found at i:8881 original size:29 final size:30
Alignment explanation
Indices: 8848--8908 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
8838 TATAAATAAT
*
8848 ATAATATAATCAAATAA-TTATATTTATAC
1 ATAATAAAATCAAATAATTTATATTTATAC
** *
8877 ATAATAAAATTGAATAATTTATCTTTATAC
1 ATAATAAAATCAAATAATTTATATTTATAC
8907 AT
1 AT
8909 TAATTAGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (30 bp):
ATAATAAAATCAAATAATTTATATTTATAC
Found at i:9061 original size:24 final size:25
Alignment explanation
Indices: 9005--9061 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
8995 TTTTAATGTT
* *
9005 TAAATTTTATTTTTTATTAAAAATT
1 TAAATATTATTTTTTATTAAAAATA
*
9030 TAATTATTATTTTATT-TTAAAAA-A
1 TAAATATTATTTT-TTATTAAAAATA
9054 TAAATATT
1 TAAATATT
9062 GGCAAGCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.26
25 18 0.67
26 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAAATATTATTTTTTATTAAAAATA
Found at i:9167 original size:41 final size:41
Alignment explanation
Indices: 9105--9200 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
9095 AAAATATGGA
9105 CGGGTCTTGGACAAAAATTGAGGCCCGTTTTTCGGGCCGAAC
1 CGGG-CTTGGACAAAAATTGAGGCCCGTTTTTCGGGCCGAAC
9147 CGGGCTTGGACAAAAATTGAGGCCCGTTTTTCGGGCCGAAC
1 CGGGCTTGGACAAAAATTGAGGCCCGTTTTTCGGGCCGAAC
9188 CGGGCTTGGACAA
1 CGGGCTTGGACAA
9201 GCATATATTG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 50 0.93
42 4 0.07
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.22
Consensus pattern (41 bp):
CGGGCTTGGACAAAAATTGAGGCCCGTTTTTCGGGCCGAAC
Found at i:9816 original size:178 final size:178
Alignment explanation
Indices: 9514--9946 Score: 547
Period size: 178 Copynumber: 2.4 Consensus size: 178
9504 TATAATCATT
* * *
9514 GACACTTGAATCAGCTCAATCGGACAT-TTAGAGCAAAAATTATGTTATATTAAGTTGA-C-TGT
1 GACACTTAAATCACCTCAATCGGACATCTGA-AGCAAAAATTATGTTATATTAAGTTGACCAT-T
* * *
9576 CAATTCCCGCTAACCGAAATAATAAATTTTTCGGAAGCATTTTTAATACCTAAAATATCAAATTT
64 C-ATT-CCGCTAACCGAAACAATAAATTTTTCAGAAGCATTTTTAATACCTAAAACATCAAATTT
** *
9641 AGCTTTCGAG-TCATTCATGAAAGTTGTAGATCAAGTAAGAACC-TTTTAATA
127 AAATTTCGAGTTC-TTCATGAAAGTTGTAGATCAAGTAACAACCTTTTTAATA
* *
9692 GACACTTAAATCACCTCAATCGGACATCTGAAGCCAAAATTATGTTATATTAAGTTAACCATTCA
1 GACACTTAAATCACCTCAATCGGACATCTGAAGCAAAAATTATGTTATATTAAGTTGACCATTCA
* * * *
9757 TTCCTGCTAATCGAAACAACT-AATTTTTCAGAAGTATTTTTAGTGCCTAAAACATCAAATTTAA
66 TTCC-GCTAACCGAAACAA-TAAATTTTTCAGAAGCATTTTTAATACCTAAAACATCAAATTTAA
*
9821 ATTTCGAGTTCTTCATGAAAGTTGTAGATTAAGTAACAACCTTTTTAATA
129 ATTTCGAGTTCTTCATGAAAGTTGTAGATCAAGTAACAACCTTTTTAATA
* * * * * *
9871 GACGCTTAAATCATCTCAATCGGACATCTGTAA-CAAAAACTATATAATATTAAGTTGACCATCC
1 GACACTTAAATCACCTCAATCGGACATCTG-AAGCAAAAATTATGTTATATTAAGTTGACCATTC
9935 ATTCCGCTAACC
65 ATTCCGCTAACC
9947 AAAATTTGGA
Statistics
Matches: 222, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
177 2 0.01
178 143 0.64
179 74 0.33
180 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (178 bp):
GACACTTAAATCACCTCAATCGGACATCTGAAGCAAAAATTATGTTATATTAAGTTGACCATTCA
TTCCGCTAACCGAAACAATAAATTTTTCAGAAGCATTTTTAATACCTAAAACATCAAATTTAAAT
TTCGAGTTCTTCATGAAAGTTGTAGATCAAGTAACAACCTTTTTAATA
Found at i:12377 original size:41 final size:40
Alignment explanation
Indices: 12332--12418 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
12322 ATAATCAAAG
* *
12332 CAATGCTTAAGTTCAATCATACTTGTCTACTCCCTTTTTAT
1 CAATG-TTAACTTCAATCATACATGTCTACTCCCTTTTTAT
* * * *
12373 CAATGTTAACTTCAATGATTCATGTCTACTTCC-TTTTCT
1 CAATGTTAACTTCAATCATACATGTCTACTCCCTTTTTAT
12412 CAATGTT
1 CAATGTT
12419 GGCCCTAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
39 12 0.30
40 23 0.57
41 5 0.12
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (40 bp):
CAATGTTAACTTCAATCATACATGTCTACTCCCTTTTTAT
Done.