Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020392.1 Corchorus olitorius cultivar O-4 contig20425, 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: 26943
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:4141 original size:28 final size:28

Alignment explanation


    Indices: 4101--4155  Score: 92
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       4091 TGCTTGATTC

                                        
       4101 GCTCTCTATAACACAAGGATCAGTTATA
          1 GCTCTCTATAACACAAGGATCAGTTATA

                 *       *             
       4129 GCTCTTTATAACAGAAGGATCAGTTAT
          1 GCTCTCTATAACACAAGGATCAGTTAT

       4156 GCATGCACCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Consensus pattern (28 bp):   
GCTCTCTATAACACAAGGATCAGTTATA

Found at i:16639 original size:56 final size:56

Alignment explanation


    Indices: 16550--16656  Score: 171
    Period size: 56  Copynumber: 1.9  Consensus size: 56

      16540 GATGGGATAT

                                        *                            
      16550 TTTATCAGCATAATCAGATTATATAGTTTTTGGAATGTTTAGCCT-TTCATTATTGC
          1 TTTATCAGCATAATCAGATTATATAGTTGTTGGAATGTTTAG-CTGTTCATTATTGC

                  *             *                              
      16606 TTTATCGGCATAATCAGATTCTATAGTTGTTGGAATGTTTAGCTGTTCATT
          1 TTTATCAGCATAATCAGATTATATAGTTGTTGGAATGTTTAGCTGTTCATT

      16657 TTTGAAATCG


Statistics
Matches: 47,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  55    2  0.04
  56   45  0.96

ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46


Consensus pattern (56 bp):   
TTTATCAGCATAATCAGATTATATAGTTGTTGGAATGTTTAGCTGTTCATTATTGC

Found at i:24046 original size:15 final size:16

Alignment explanation


    Indices: 24009--24046  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      23999 AGAAGAACTA

                 *          
      24009 TAAGTGAATTGCTGTT
          1 TAAGTTAATTGCTGTT

            *               
      24025 AAAGTTAATTGCT-TT
          1 TAAGTTAATTGCTGTT

                   
      24040 TAAGTTA
          1 TAAGTTA

      24047 GAAGAACTAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  15    8  0.42
  16   11  0.58

ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45


Consensus pattern (16 bp):   
TAAGTTAATTGCTGTT

Found at i:24593 original size:71 final size:71

Alignment explanation


    Indices: 24477--24611  Score: 243
    Period size: 71  Copynumber: 1.9  Consensus size: 71

      24467 TCCGCACATT

                            *                              *                 
      24477 GATGATCAAAATATGATTTTATTCTTTAAGCAACAGCTTAAATTTTTTGACCATCGACTTGCTTG
          1 GATGATCAAAATATGAATTTATTCTTTAAGCAACAGCTTAAATTTTTCGACCATCGACTTGCTTG

                  
      24542 CCCATG
         66 CCCATG

                                               *                            
      24548 GATGATCAAAATATGAATTTATTCTTTAAGCAACATCTTAAATTTTTCGACCATCGACTTGCTT
          1 GATGATCAAAATATGAATTTATTCTTTAAGCAACAGCTTAAATTTTTCGACCATCGACTTGCTT

      24612 TCCAGACCGT


Statistics
Matches: 61,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  71   61  1.00

ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39


Consensus pattern (71 bp):   
GATGATCAAAATATGAATTTATTCTTTAAGCAACAGCTTAAATTTTTCGACCATCGACTTGCTTG
CCCATG
Done.