Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008661.1 Corchorus capsularis cultivar CVL-1 contig08682, 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: 6321
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32


Found at i:6212 original size:22 final size:22

Alignment explanation


    Indices: 6187--6268  Score: 57
    Period size: 22  Copynumber: 3.8  Consensus size: 22

       6177 CTCTTACTGA

                                  
       6187 TTACCTTCTACTGATTATCATT
          1 TTACCTTCTACTGATTATCATT

                        *       *  
       6209 TTACTCTT-TACCGATTA-CCTT
          1 TTAC-CTTCTACTGATTATCATT

                 *  *               
       6230 CTTACTTTTTACTGATTAAT-ATT
          1 -TTACCTTCTACTGATT-ATCATT

                              
       6253 TTA-C-TCTTACTGATTA
          1 TTACCTTC-TACTGATTA

       6269 CCTTCTACTG


Statistics
Matches: 47,  Mismatches: 7, Indels: 14
        0.69            0.10        0.21

Matches are distributed among these distances:
  20    2  0.04
  21   13  0.28
  22   26  0.55
  23    6  0.13

ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51


Consensus pattern (22 bp):   
TTACCTTCTACTGATTATCATT

Found at i:6244 original size:79 final size:79

Alignment explanation


    Indices: 6147--6321  Score: 300
    Period size: 79  Copynumber: 2.2  Consensus size: 79

       6137 ATCACTGACC

                       *           *                                         
       6147 ACCTT-TTACTCTTTACTGATTACTATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTT
          1 ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTT

                           
       6211 ACT-CTTTACCGATT
         66 ACTAC-TTACCGATT

                                                                             
       6225 ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTT
          1 ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTT

                     *    
       6290 ACTACTTACTGATT
         66 ACTACTTACCGATT

                              
       6304 ACCTTCTTACTTTTTACT
          1 ACCTTCTTACTTTTTACT


Statistics
Matches: 92,  Mismatches: 3, Indels: 3
        0.94            0.03        0.03

Matches are distributed among these distances:
  78    5  0.05
  79   86  0.93
  80    1  0.01

ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51


Consensus pattern (79 bp):   
ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTT
ACTACTTACCGATT

Found at i:6305 original size:36 final size:35

Alignment explanation


    Indices: 6239--6310  Score: 119
    Period size: 36  Copynumber: 2.0  Consensus size: 35

       6229 TCTTACTTTT

                                               
       6239 TACTGATTAATATTTTACTCTTACTGATTACCTTC
          1 TACTGATTAATATTTTACTCTTACTGATTACCTTC

                                                 
       6274 TACTGATT-ATCATTTTACTACTTACTGATTACCTTC
          1 TACTGATTAAT-ATTTTACT-CTTACTGATTACCTTC

             
       6310 T
          1 T

       6311 TACTTTTTAC


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  34    2  0.06
  35   16  0.46
  36   17  0.49

ACGTcount: A:0.25, C:0.21, G:0.06, T:0.49


Consensus pattern (35 bp):   
TACTGATTAATATTTTACTCTTACTGATTACCTTC

Found at i:6314 original size:57 final size:57

Alignment explanation


    Indices: 6152--6314  Score: 149
    Period size: 57  Copynumber: 2.8  Consensus size: 57

       6142 TGACCACCTT

                                                                     *
       6152 TTACTCTTTACTGATTACTATTTTACTCTTACTGATTACCTTC-TACTGATTATCATT
          1 TTACTCTTTACTGATTAC-ATTTTACTCTTACTGATTACCTTCTTACTGATTATCATA

                       *      *         *           *   *      *         
       6209 TTACTCTTTACCGATTACCTTCTTACTTTTTACTGATTA-ATATTTTACT-CTTA-C-TGA
          1 TTACTCTTTACTGATTACATT-TTAC-TCTTACTGATTACCT-TCTTACTGATTATCAT-A

                                                              
       6266 TTAC-CTTCTACTGATTATCATTTTACTACTTACTGATTACCTTCTTACT
          1 TTACTCTT-TACTGATTA-CATTTTACT-CTTACTGATTACCTTCTTACT

       6315 TTTTACT


Statistics
Matches: 85,  Mismatches: 12, Indels: 18
        0.74            0.10        0.16

Matches are distributed among these distances:
  56    7  0.08
  57   55  0.65
  58   19  0.22
  59    4  0.05

ACGTcount: A:0.23, C:0.22, G:0.05, T:0.50


Consensus pattern (57 bp):   
TTACTCTTTACTGATTACATTTTACTCTTACTGATTACCTTCTTACTGATTATCATA
Done.