Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010679.1 Corchorus capsularis cultivar CVL-1 contig10700, 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: 15484
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:3973 original size:3 final size:3

Alignment explanation


    Indices: 3934--3961  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       3924 CTACTCATCG

                                                 
       3934 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T

       3962 CCTCGTTCTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTC

Found at i:6936 original size:37 final size:35

Alignment explanation


    Indices: 6857--6936  Score: 99
    Period size: 40  Copynumber: 2.2  Consensus size: 35

       6847 TCAGCCAGCC

                                               
       6857 AATTACAAACTTAATTCAGAGAAATCATTAAAGAA
          1 AATTACAAACTTAATTCAGAGAAATCATTAAAGAA

                                          *         
       6892 ATTATTACAAACGTAATAATTCAGAGAAATTATTAAAG-A
          1 A--ATTACAAAC-T--TAATTCAGAGAAATCATTAAAGAA

                  
       6931 AATTAC
          1 AATTAC

       6937 TTAATTCAAA


Statistics
Matches: 39,  Mismatches: 1, Indels: 8
        0.81            0.02        0.17

Matches are distributed among these distances:
  35    1  0.03
  37   14  0.36
  38    1  0.03
  39    2  0.05
  40   21  0.54

ACGTcount: A:0.53, C:0.10, G:0.09, T:0.29


Consensus pattern (35 bp):   
AATTACAAACTTAATTCAGAGAAATCATTAAAGAA

Found at i:7980 original size:24 final size:26

Alignment explanation


    Indices: 7922--7983  Score: 92
    Period size: 27  Copynumber: 2.4  Consensus size: 26

       7912 AACCTCACCC

                                       
       7922 CCAACATTTTCAGCCCCACCATCCATA
          1 CCAACATTTTCAGCCCCACCATCCA-A

                      *               
       7949 CCAACATTTTGAGCCCCACCAT-C-A
          1 CCAACATTTTCAGCCCCACCATCCAA

                       
       7973 CCAACATTTTC
          1 CCAACATTTTC

       7984 TCTCTGACCT


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  24   11  0.33
  26    1  0.03
  27   21  0.64

ACGTcount: A:0.29, C:0.42, G:0.05, T:0.24


Consensus pattern (26 bp):   
CCAACATTTTCAGCCCCACCATCCAA

Found at i:8914 original size:2 final size:2

Alignment explanation


    Indices: 8909--8936  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       8899 CACACACATA

                                                     
       8909 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

       8937 TGCACTGTAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:8994 original size:2 final size:2

Alignment explanation


    Indices: 8987--9026  Score: 55
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       8977 TAGGTAATCT

                                                    *                   
       8987 TA TA TA TA TA TA TA TA TA TA TA TA CTA CA TA T- TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA

       9027 ATAATAATAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.91
   3    2  0.06

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:13195 original size:42 final size:42

Alignment explanation


    Indices: 13136--13224  Score: 160
    Period size: 42  Copynumber: 2.1  Consensus size: 42

      13126 CGCTGCCAAA

                                       *   *          
      13136 AATTTGCCTATTCCAAATACTCAAAGCTCGACCACAATTACT
          1 AATTTGCCTATTCCAAATACTCAAAGCCCGAACACAATTACT

                                                      
      13178 AATTTGCCTATTCCAAATACTCAAAGCCCGAACACAATTACT
          1 AATTTGCCTATTCCAAATACTCAAAGCCCGAACACAATTACT

                 
      13220 AATTT
          1 AATTT

      13225 TTCCTTGAAT


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  42   45  1.00

ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29


Consensus pattern (42 bp):   
AATTTGCCTATTCCAAATACTCAAAGCCCGAACACAATTACT

Found at i:14700 original size:6 final size:6

Alignment explanation


    Indices: 14691--14718  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

      14681 CAAATTAAAA

                                            
      14691 TAAATC TAAATC TAAATC TAAATC TAAA
          1 TAAATC TAAATC TAAATC TAAATC TAAA

      14719 GTAAATTAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32


Consensus pattern (6 bp):   
TAAATC

Done.