Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006422.1 Corchorus capsularis cultivar CVL-1 contig06443, 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: 13333
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32


Found at i:1011 original size:23 final size:23

Alignment explanation


    Indices: 962--1024  Score: 67
    Period size: 23  Copynumber: 2.7  Consensus size: 23

        952 AAAGGATCAT

                                  *
        962 GTGGCCGGGCATGGCCGAGTCAT
          1 GTGGCCGGGCATGGCCGAGTCAC

                          *       * 
        985 GTGGCCGGGCATGGTC-ATGTCGC
          1 GTGGCCGGGCATGGCCGA-GTCAC

                              
       1008 GTGGCCGGTG-ATGGCCG
          1 GTGGCCGG-GCATGGCCG

       1025 GGCATCTCCA


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

Matches are distributed among these distances:
  22    1  0.03
  23   31  0.94
  24    1  0.03

ACGTcount: A:0.10, C:0.25, G:0.46, T:0.19


Consensus pattern (23 bp):   
GTGGCCGGGCATGGCCGAGTCAC

Found at i:1024 original size:33 final size:33

Alignment explanation


    Indices: 986--1082  Score: 142
    Period size: 33  Copynumber: 2.9  Consensus size: 33

        976 CCGAGTCATG

                        *    *                
        986 TGGCCGGGCATGGT-CATGTCGCGTGGCCGGTGA
          1 TGGCCGGGCAT-CTCCAAGTCGCGTGGCCGGTGA

                                             
       1019 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGA
          1 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGA

               *                  *        
       1052 TGGTCGGGCATCTCCAAGTCGCATGGCCGGT
          1 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGT

       1083 CACAAGTGCT


Statistics
Matches: 59,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   58  0.98

ACGTcount: A:0.11, C:0.28, G:0.40, T:0.21


Consensus pattern (33 bp):   
TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGA

Found at i:4702 original size:6 final size:6

Alignment explanation


    Indices: 4691--4720  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       4681 ACGAGCATGC

                                              
       4691 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
          1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT

       4721 TCTATTTGGA


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

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67


Consensus pattern (6 bp):   
ATTTGT

Found at i:7076 original size:33 final size:33

Alignment explanation


    Indices: 7025--7131  Score: 119
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       7015 ACCTAAAGAT

                        **                    
       7025 CCGGCCACGCGATTTGGAGATGCCC-GCGCAACA
          1 CCGGCCACGCGACATGGAGATGCCCGGC-CAACA

                   *                      *  
       7058 CCGGCCATGCGACATGGAGATGCCCGGCCATCA
          1 CCGGCCACGCGACATGGAGATGCCCGGCCAACA

                             ** *            
       7091 CCGGCCACGCGACATGGCCAAGCCCGGCC-ACA
          1 CCGGCCACGCGACATGGAGATGCCCGGCCAACA

                     
       7123 CCCGGCCAC
          1 -CCGGCCAC

       7132 ATGACTCGGC


Statistics
Matches: 63,  Mismatches: 9, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   59  0.94
  34    2  0.03

ACGTcount: A:0.21, C:0.42, G:0.29, T:0.08


Consensus pattern (33 bp):   
CCGGCCACGCGACATGGAGATGCCCGGCCAACA

Found at i:7143 original size:33 final size:32

Alignment explanation


    Indices: 7046--7155  Score: 87
    Period size: 33  Copynumber: 3.3  Consensus size: 32

       7036 ATTTGGAGAT

                    *          **        ** *
       7046 GCCCGCGCAACACCGGCCATGCGACATGGAGAT
          1 GCCCG-GCCACACCGGCCACACGACATGGCCAA

                                *            
       7079 GCCCGGCCATCACCGGCCACGCGACATGGCCAA
          1 GCCCGGCCA-CACCGGCCACACGACATGGCCAA

                                 *           *
       7112 GCCCGGCCACACCCGGCCACATGAC-TCGGCCAT
          1 GCCCGGCCACA-CCGGCCACACGACAT-GGCCAA

            *          
       7145 TCCCGGCCACA
          1 GCCCGGCCACA

       7156 ACCAGCCATA


Statistics
Matches: 65,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  32    6  0.09
  33   59  0.91

ACGTcount: A:0.21, C:0.45, G:0.26, T:0.08


Consensus pattern (32 bp):   
GCCCGGCCACACCGGCCACACGACATGGCCAA

Found at i:11521 original size:21 final size:20

Alignment explanation


    Indices: 11495--11536  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 20

      11485 TCTTGAAGGT

                  *              
      11495 TTGAAGTCCATTGAAGATCAA
          1 TTGAAGACCATTGAAGA-CAA

                   *            
      11516 TTGAAGAGCATTGAAGACAA
          1 TTGAAGACCATTGAAGACAA

             
      11536 T
          1 T

      11537 AAGCAAAGGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20    4  0.21
  21   15  0.79

ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26


Consensus pattern (20 bp):   
TTGAAGACCATTGAAGACAA
Done.