Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011312.1 Corchorus olitorius cultivar O-4 contig11345, 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: 3784
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32


Found at i:133 original size:15 final size:15

Alignment explanation


    Indices: 103--144  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

         93 TTACTTTGCT

                            
        103 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        119 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        134 TTGCTTTCTGT
          1 TTGTTTTCTGT

        145 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:993 original size:33 final size:32

Alignment explanation


    Indices: 948--1045  Score: 97
    Period size: 33  Copynumber: 3.0  Consensus size: 32

        938 TCCCAAACGG

                   *                        
        948 AATTTGTTTCATCACAAACAACACCTAAAACA
          1 AATTTGTATCATCACAAACAACACCTAAAACA

                    *                *    ** 
        980 AATTTAGTGTCATCACAAACAACACTTAAATTA
          1 AATTT-GTATCATCACAAACAACACCTAAAACA

            **              *       *        
       1013 GGTTTGGTATCATCACTAACAACATCTAAAACA
          1 AATTT-GTATCATCACAAACAACACCTAAAACA

       1046 CTCTTTGCAA


Statistics
Matches: 52,  Mismatches: 13, Indels: 1
        0.79            0.20        0.02

Matches are distributed among these distances:
  32    5  0.10
  33   47  0.90

ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28


Consensus pattern (32 bp):   
AATTTGTATCATCACAAACAACACCTAAAACA

Found at i:2012 original size:22 final size:23

Alignment explanation


    Indices: 1973--2015  Score: 79
    Period size: 22  Copynumber: 1.9  Consensus size: 23

       1963 AATCCTAATC

                                   
       1973 CTGGTAGGAATAGTAAAACCTTT
          1 CTGGTAGGAATAGTAAAACCTTT

                                 
       1996 CTGGTAGGAA-AGTAAAACCT
          1 CTGGTAGGAATAGTAAAACCT

       2016 ACTCCTTCTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  22   10  0.50
  23   10  0.50

ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26


Consensus pattern (23 bp):   
CTGGTAGGAATAGTAAAACCTTT
Done.