Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006053.1 Corchorus capsularis cultivar CVL-1 contig06071, 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: 9224
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30


Found at i:1963 original size:17 final size:17

Alignment explanation


    Indices: 1939--1973  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1929 TGGTCGAAAA

                       *      
       1939 ATTTTTTTATTTTATTTT
          1 ATTTTTTT-TTATATTTT

                             
       1957 ATTTTTTTTTATATTTT
          1 ATTTTTTTTTATATTTT

       1974 TCGATATAAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    8  0.50
  18    8  0.50

ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83


Consensus pattern (17 bp):   
ATTTTTTTTTATATTTT

Found at i:2729 original size:17 final size:19

Alignment explanation


    Indices: 2707--2742  Score: 58
    Period size: 17  Copynumber: 2.0  Consensus size: 19

       2697 CCAATGTCTT

                               
       2707 CTAAACTAA-ATA-AATAA
          1 CTAAACTAAGATAGAATAA

                               
       2724 CTAAACTAAGATAGAATAA
          1 CTAAACTAAGATAGAATAA

       2743 AGGCCCAATG


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    9  0.53
  18    3  0.18
  19    5  0.29

ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22


Consensus pattern (19 bp):   
CTAAACTAAGATAGAATAA

Found at i:3075 original size:33 final size:32

Alignment explanation


    Indices: 2978--3117  Score: 138
    Period size: 33  Copynumber: 4.2  Consensus size: 32

       2968 AAAGGATCAT

                                  **        **
       2978 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCAA
          1 GTGGCCGG-TGTGGCCGGGCATCTCC-ATGTCGC

                                  **         
       3011 GTGGCCGGGTGTGGCCGGGCATGGCCATGTCGC
          1 GTGGCC-GGTGTGGCCGGGCATCTCCATGTCGC

                                             
       3044 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
          1 GTGGCCGGTG-TGGCCGGGCATCTCCATGTCGC

            *      *   *               *     
       3077 ATGGCCGATGTTGCGCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTGTGGC-CGGGCATCTCCATGTCGC

                    
       3110 GTGGCCGG
          1 GTGGCCGG

       3118 CTCTCCAAGT


Statistics
Matches: 93,  Mismatches: 10, Indels: 8
        0.84            0.09        0.07

Matches are distributed among these distances:
  32    8  0.09
  33   83  0.89
  34    2  0.02

ACGTcount: A:0.10, C:0.28, G:0.43, T:0.19


Consensus pattern (32 bp):   
GTGGCCGGTGTGGCCGGGCATCTCCATGTCGC

Found at i:3124 original size:21 final size:21

Alignment explanation


    Indices: 3098--3138  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3088 TGCGCGGGCA

                        *        
       3098 TCTCCAAGTCGCGTGGCCGGC
          1 TCTCCAAGTCGCATGGCCGGC

                                
       3119 TCTCCAAGTCGCATGGCCGG
          1 TCTCCAAGTCGCATGGCCGG

       3139 TCACTTGTGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.12, C:0.37, G:0.32, T:0.20


Consensus pattern (21 bp):   
TCTCCAAGTCGCATGGCCGGC
Done.