Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016120.1 Corchorus olitorius cultivar O-4 contig16153, 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: 6297
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:752 original size:31 final size:30

Alignment explanation


    Indices: 714--784  Score: 92
    Period size: 29  Copynumber: 2.4  Consensus size: 30

        704 AGTGGATGGA

                                      *     
        714 CTTATTTGAGACTTTCTGAT-AAGTTGGGGCC
          1 CTTATTTGAGACTTT-T-ATAAAGTTCGGGCC

                      *                   
        745 CTTATTTGA-CCTTTTATAAAGTTCGGGCC
          1 CTTATTTGAGACTTTTATAAAGTTCGGGCC

                       
        774 CTTATTTGAGA
          1 CTTATTTGAGA

        785 TTTATGGCAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  28    2  0.06
  29   20  0.57
  30    4  0.11
  31    9  0.26

ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41


Consensus pattern (30 bp):   
CTTATTTGAGACTTTTATAAAGTTCGGGCC

Found at i:1999 original size:30 final size:30

Alignment explanation


    Indices: 1965--2022  Score: 82
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1955 AATTCTTGCT

                                 *         
       1965 TCTTGAAATAATTCTTCAAT-GATCTTCATA
          1 TCTTGAAATAA-TCTTCAATAAATCTTCATA

                     *                  
       1995 TCTTGAAATTATCTTCAATAAATCTTCA
          1 TCTTGAAATAATCTTCAATAAATCTTCA

       2023 ATAACGAACT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29    8  0.32
  30   17  0.68

ACGTcount: A:0.34, C:0.17, G:0.05, T:0.43


Consensus pattern (30 bp):   
TCTTGAAATAATCTTCAATAAATCTTCATA

Found at i:3566 original size:21 final size:21

Alignment explanation


    Indices: 3540--3581  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3530 AGTGTCGACC

                                  
       3540 CAATCA-AGCAATTCAAAGCAT
          1 CAATCATAGC-ATTCAAAGCAT

                           *     
       3561 CAATCATAGCATTCATAGCAT
          1 CAATCATAGCATTCAAAGCAT

       3582 ATAAGTCATA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21   16  0.84
  22    3  0.16

ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24


Consensus pattern (21 bp):   
CAATCATAGCATTCAAAGCAT
Done.