Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005763.1 Corchorus capsularis cultivar CVL-1 contig05781, 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: 5571
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3180 original size:6 final size:6

Alignment explanation


    Indices: 3139--3204  Score: 50
    Period size: 6  Copynumber: 11.2  Consensus size: 6

       3129 GACGTGGCTT

                           *           *                             
       3139 TTTTTC TTTTTTC ATTTTC ATTTTCC TTTTTC ---TTC TTTTTC TTTTTC
          1 TTTTTC -TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC

                           *       
       3186 TTTTT- TTTCTTC CTTTTC T
          1 TTTTTC TTT-TTC TTTTTC T

       3205 CCTTCTTTCT


Statistics
Matches: 47,  Mismatches: 6, Indels: 13
        0.71            0.09        0.20

Matches are distributed among these distances:
   3    3  0.06
   5    3  0.06
   6   29  0.62
   7   12  0.26

ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77


Consensus pattern (6 bp):   
TTTTTC

Found at i:3182 original size:15 final size:15

Alignment explanation


    Indices: 3159--3196  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       3149 TTCATTTTCA

                *          
       3159 TTTTCCTTTTTCTTC
          1 TTTTTCTTTTTCTTC

                          *
       3174 TTTTTCTTTTTCTTT
          1 TTTTTCTTTTTCTTC

                    
       3189 TTTTTCTT
          1 TTTTTCTT

       3197 CCTTTTCTCC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (15 bp):   
TTTTTCTTTTTCTTC

Found at i:3195 original size:21 final size:21

Alignment explanation


    Indices: 3136--3196  Score: 70
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       3126 TATGACGTGG

                             *    
       3136 CTTTTT-TTCTTTTTTCATTTT
          1 CTTTTTCTT-TTTTTTCTTTTT

                  *      *        
       3157 CATTTTCCTTTTTCTTCTTTTT
          1 C-TTTTTCTTTTTTTTCTTTTT

                              
       3179 CTTTTTCTTTTTTTTCTT
          1 CTTTTTCTTTTTTTTCTT

       3197 CCTTTTCTCC


Statistics
Matches: 33,  Mismatches: 5, Indels: 4
        0.79            0.12        0.10

Matches are distributed among these distances:
  21   16  0.48
  22   15  0.45
  23    2  0.06

ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79


Consensus pattern (21 bp):   
CTTTTTCTTTTTTTTCTTTTT

Found at i:3197 original size:24 final size:25

Alignment explanation


    Indices: 3164--3223  Score: 77
    Period size: 24  Copynumber: 2.4  Consensus size: 25

       3154 TTTCATTTTC

                      *      **      
       3164 CTTTTTCTTCTTTTTCTTTTTCTTT
          1 CTTTTTCTTCCTTTTCTCCTTCTTT

                                     
       3189 -TTTTTCTTCCTTTTCTCCTTCTTT
          1 CTTTTTCTTCCTTTTCTCCTTCTTT

                       
       3213 CTTTCTTCTTC
          1 CTTT-TTCTTC

       3224 ACTTCAAACT


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  24   21  0.70
  25    3  0.10
  26    6  0.20

ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73


Consensus pattern (25 bp):   
CTTTTTCTTCCTTTTCTCCTTCTTT

Found at i:3199 original size:34 final size:32

Alignment explanation


    Indices: 3139--3222  Score: 87
    Period size: 34  Copynumber: 2.4  Consensus size: 32

       3129 GACGTGGCTT

                                             * 
       3139 TTTTTCTTTTTTCATTTTCATTTTCCTTTTTCTTC
          1 TTTTTC-TTTTTC-TTTTCATTTTCC-TTTTCTCC

                            **               
       3174 TTTTTCTTTTTCTTTTTTTTCTTCCTTTTCTCC
          1 TTTTTCTTTTTCTTTTCATT-TTCCTTTTCTCC

                            
       3207 TTCTTTCTTTCTTCTT
          1 TT-TTTCTTT-TTCTT

       3223 CACTTCAAAC


Statistics
Matches: 43,  Mismatches: 3, Indels: 6
        0.83            0.06        0.12

Matches are distributed among these distances:
  33   15  0.35
  34   17  0.40
  35   11  0.26

ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75


Consensus pattern (32 bp):   
TTTTTCTTTTTCTTTTCATTTTCCTTTTCTCC
Done.