Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009260.1 Corchorus capsularis cultivar CVL-1 contig09281, 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: 18146
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:3303 original size:4 final size:4

Alignment explanation


    Indices: 3294--3324  Score: 53
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       3284 TCCTCTGTCT

                                   *              
       3294 TTTC TTTC TTTC TTTC TTTA TTTC TTTC TTT
          1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT

       3325 TTCTTCTTCT


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

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTTC

Found at i:11065 original size:13 final size:13

Alignment explanation


    Indices: 11042--11075  Score: 50
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      11032 TACTATATAT

                          
      11042 ATAATTAAAATAAA
          1 ATAA-TAAAATAAA

                       * 
      11056 ATAATAAAATATA
          1 ATAATAAAATAAA

                   
      11069 ATAATAA
          1 ATAATAA

      11076 GATTACATAA


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

Matches are distributed among these distances:
  13   15  0.79
  14    4  0.21

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (13 bp):   
ATAATAAAATAAA

Found at i:15065 original size:19 final size:20

Alignment explanation


    Indices: 15031--15068  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

      15021 GGTGAGAAAA

                                
      15031 CACAGACCACACTAAGGACC
          1 CACAGACCACACTAAGGACC

                   *           
      15051 CACAGACTA-ACTAAGGAC
          1 CACAGACCACACTAAGGAC

      15069 ACCATAACAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.42, C:0.34, G:0.16, T:0.08


Consensus pattern (20 bp):   
CACAGACCACACTAAGGACC

Found at i:15590 original size:2 final size:2

Alignment explanation


    Indices: 15585--15618  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      15575 GATGTTAGTC

                                                              
      15585 AT AT AT AT AT AT AT 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

      15619 GGTAAAATTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:17882 original size:21 final size:21

Alignment explanation


    Indices: 17858--17901  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      17848 AAAAACTGGA

                                  
      17858 TTGCTAAAT-ACCGCCACATTT
          1 TTGCT-AATCACCGCCACATTT

                  *        *     
      17879 TTGCTATTCACCGCCCCATTT
          1 TTGCTAATCACCGCCACATTT

              
      17900 TT
          1 TT

      17902 TACGTTTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    2  0.10
  21   18  0.90

ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39


Consensus pattern (21 bp):   
TTGCTAATCACCGCCACATTT
Done.