Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004856.1 Corchorus capsularis cultivar CVL-1 contig04874, 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: 6781
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37


Found at i:549 original size:40 final size:40

Alignment explanation


    Indices: 494--584  Score: 155
    Period size: 40  Copynumber: 2.3  Consensus size: 40

        484 GAAAGCAGGA

                   *              *                 
        494 CTTCTTTATATACAACATTTTTTGTATATGTTCCCTTTTG
          1 CTTCTTTGTATACAACATTTTTGGTATATGTTCCCTTTTG

                                                    
        534 CTTCTTTGTATACAACATTTTTGGTATATGTTCCCTTTTG
          1 CTTCTTTGTATACAACATTTTTGGTATATGTTCCCTTTTG

                  *    
        574 CTTCTTCGTAT
          1 CTTCTTTGTAT

        585 TTTCCGACTT


Statistics
Matches: 48,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  40   48  1.00

ACGTcount: A:0.18, C:0.19, G:0.10, T:0.54


Consensus pattern (40 bp):   
CTTCTTTGTATACAACATTTTTGGTATATGTTCCCTTTTG

Found at i:1862 original size:2 final size:2

Alignment explanation


    Indices: 1855--1894  Score: 62
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       1845 CATTGATGGA

                         *              *                              
       1855 AT AT AT AT AA AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1895 GAATTTAAAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:1894 original size:10 final size:10

Alignment explanation


    Indices: 1854--1893  Score: 71
    Period size: 10  Copynumber: 4.0  Consensus size: 10

       1844 TCATTGATGG

                      
       1854 AATATATATA
          1 AATATATATA

                      
       1864 AATATATATA
          1 AATATATATA

                      
       1874 AATATATATA
          1 AATATATATA

            *         
       1884 TATATATATA
          1 AATATATATA

       1894 TGAATTTAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  10   29  1.00

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42


Consensus pattern (10 bp):   
AATATATATA

Found at i:5420 original size:18 final size:18

Alignment explanation


    Indices: 5394--5435  Score: 66
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       5384 GTTAAAAAAT

                *             
       5394 TTCTTAATTTTGGTTGGA
          1 TTCTCAATTTTGGTTGGA

                              
       5412 TTCTCAATTTTGGTTGGA
          1 TTCTCAATTTTGGTTGGA

            *     
       5430 CTCTCA
          1 TTCTCA

       5436 TTTAAATAAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50


Consensus pattern (18 bp):   
TTCTCAATTTTGGTTGGA

Found at i:6159 original size:3 final size:3

Alignment explanation


    Indices: 6153--6179  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       6143 AATAATAATT

                                               
       6153 TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA

       6180 ATGTTTCAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:6635 original size:21 final size:21

Alignment explanation


    Indices: 6590--6635  Score: 76
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       6580 CTTCATGATA

                       *         
       6590 ACTTTGCAGACCATTATTTTT
          1 ACTTTGCAGACAATTATTTTT

                                 
       6611 -CTTTGCAGACAATTATTTTT
          1 ACTTTGCAGACAATTATTTTT

                 
       6631 ACTTT
          1 ACTTT

       6636 TTTTTTTTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20   19  0.83
  21    4  0.17

ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50


Consensus pattern (21 bp):   
ACTTTGCAGACAATTATTTTT
Done.