Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024259.1 Corchorus olitorius cultivar O-4 contig24292, 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: 22544
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30


Found at i:27 original size:21 final size:21

Alignment explanation


    Indices: 1--70  Score: 115
    Period size: 21  Copynumber: 3.3  Consensus size: 21

                                  
          1 CATTGGAGCAA-GTTCCAAGCT
          1 CATTGGAG-AAGGTTCCAAGCT

                                 
         22 CATTGGAGAAGGTTCCAAGCT
          1 CATTGGAGAAGGTTCCAAGCT

                          *      
         43 CATTGGAGAAGGTTTCAAGCT
          1 CATTGGAGAAGGTTCCAAGCT

                   
         64 CATTGGA
          1 CATTGGA

         71 ATTGCCTAAG


Statistics
Matches: 47,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    2  0.04
  21   45  0.96

ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26


Consensus pattern (21 bp):   
CATTGGAGAAGGTTCCAAGCT

Found at i:2968 original size:20 final size:21

Alignment explanation


    Indices: 2943--2984  Score: 68
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       2933 TAAGAGATAT

                   *             
       2943 TTGATGATGAAAAT-CCAAGC
          1 TTGATGAAGAAAATCCCAAGC

                                 
       2963 TTGATGAAGAAAATCCCAAGC
          1 TTGATGAAGAAAATCCCAAGC

             
       2984 T
          1 T

       2985 CCATGAGAGG


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  20   13  0.65
  21    7  0.35

ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24


Consensus pattern (21 bp):   
TTGATGAAGAAAATCCCAAGC

Found at i:2990 original size:21 final size:20

Alignment explanation


    Indices: 2946--2990  Score: 54
    Period size: 21  Copynumber: 2.2  Consensus size: 20

       2936 GAGATATTTG

                *             **
       2946 ATGATGAAAATCCAAGCTTG
          1 ATGAAGAAAATCCAAGCTCC

                                 
       2966 ATGAAGAAAATCCCAAGCTCC
          1 ATGAAGAAAAT-CCAAGCTCC

                
       2987 ATGA
          1 ATGA

       2991 GAGGTCTCCA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  20   10  0.48
  21   11  0.52

ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20


Consensus pattern (20 bp):   
ATGAAGAAAATCCAAGCTCC

Found at i:12219 original size:21 final size:22

Alignment explanation


    Indices: 12186--12234  Score: 57
    Period size: 21  Copynumber: 2.3  Consensus size: 22

      12176 GTCCACCTGG

                                * 
      12186 GCACCCACATGG-TTGCCTTGA
          1 GCACCCACATGGTTTGCCTTAA

                   **             
      12207 GCACCCATGTGGTTTGCCTTAA
          1 GCACCCACATGGTTTGCCTTAA

                   
      12229 G-ACCCA
          1 GCACCCA

      12235 GCTGGGCAGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  21   15  0.62
  22    9  0.38

ACGTcount: A:0.20, C:0.33, G:0.22, T:0.24


Consensus pattern (22 bp):   
GCACCCACATGGTTTGCCTTAA

Found at i:20072 original size:2 final size:2

Alignment explanation


    Indices: 20065--20093  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      20055 ATTATTTTTC

                                                       
      20065 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 T

      20094 CTTGCTACCT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.