Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023435.1 Corchorus olitorius cultivar O-4 contig23468, 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: 7524
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:4367 original size:20 final size:21

Alignment explanation


    Indices: 4342--4382  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4332 CTACCGTAGA

                                 
       4342 CTCCA-TTCCCCACTTTTGCT
          1 CTCCATTTCCCCACTTTTGCT

                     *           
       4362 CTCCATTTCTCCACTTTTGCT
          1 CTCCATTTCCCCACTTTTGCT

       4383 TTCATTTTTG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    5  0.26
  21   14  0.74

ACGTcount: A:0.10, C:0.41, G:0.05, T:0.44


Consensus pattern (21 bp):   
CTCCATTTCCCCACTTTTGCT

Found at i:4532 original size:28 final size:28

Alignment explanation


    Indices: 4501--4583  Score: 96
    Period size: 28  Copynumber: 3.0  Consensus size: 28

       4491 TCTGTTTTAC

                            *        *   
       4501 TTGTTGAATT-GAGATGATGTTGTGTGTT
          1 TTGTTGAATTGGA-ATAATGTTGTGGGTT

                              *         
       4529 TTGTTGAATTGGAATAATTTTGTGGGTT
          1 TTGTTGAATTGGAATAATGTTGTGGGTT

              *               *  *     
       4557 TTATTGAATTGGAATAATTTTTTGGGT
          1 TTGTTGAATTGGAATAATGTTGTGGGT

       4584 GCATTTGATT


Statistics
Matches: 49,  Mismatches: 5, Indels: 2
        0.88            0.09        0.04

Matches are distributed among these distances:
  28   47  0.96
  29    2  0.04

ACGTcount: A:0.22, C:0.00, G:0.28, T:0.51


Consensus pattern (28 bp):   
TTGTTGAATTGGAATAATGTTGTGGGTT

Found at i:4591 original size:28 final size:28

Alignment explanation


    Indices: 4532--4595  Score: 78
    Period size: 28  Copynumber: 2.3  Consensus size: 28

       4522 GTGTGTTTTG

                                    **  
       4532 TTGAATTGGAATAATTTTGTGGGTTTTA
          1 TTGAATTGGAATAATTTTGTGGGTCATA

                              *          
       4560 TTGAATTGGAATAATTTTTTGGGTGCAT-
          1 TTGAATTGGAATAATTTTGTGGGT-CATA

                     
       4588 TTG-ATTGG
          1 TTGAATTGG

       4596 GGGTGGTGAT


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  27    5  0.16
  28   26  0.81
  29    1  0.03

ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48


Consensus pattern (28 bp):   
TTGAATTGGAATAATTTTGTGGGTCATA

Found at i:7127 original size:28 final size:27

Alignment explanation


    Indices: 7032--7132  Score: 89
    Period size: 27  Copynumber: 3.7  Consensus size: 27

       7022 AGGGTCATCT

                           *   *   **   
       7032 AGGGGCATTTTGGTCTTTTTAATATTC-
          1 AGGGGCATTTTGGTCATTTGAA-CGTCA

                       *              *
       7059 AGGGGCATTTTAGTCATTTGAACGTCC
          1 AGGGGCATTTTGGTCATTTGAACGTCA

              *                          
       7086 AGAGGCATTTTGGTCATTTGCACAC-TCA
          1 AGGGGCATTTTGGTCATTTG-A-ACGTCA

                     *         
       7114 AGGGGCATTGTGGTCATTT
          1 AGGGGCATTTTGGTCATTT

       7133 TAAGTTCACA


Statistics
Matches: 61,  Mismatches: 10, Indels: 5
        0.80            0.13        0.07

Matches are distributed among these distances:
  26    2  0.03
  27   37  0.61
  28   20  0.33
  29    2  0.03

ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTGAACGTCA
Done.