Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011577.1 Corchorus capsularis cultivar CVL-1 contig11598, 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: 36871
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:2347 original size:6 final size:6

Alignment explanation


    Indices: 2332--2361  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       2322 AGGCTTTTTT

                                                
       2332 AAAA-A AAAATA AAAATA AAAATA AAAATA A
          1 AAAATA AAAATA AAAATA AAAATA AAAATA A

       2362 TTAGCTATTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    4  0.17
   6   20  0.83

ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13


Consensus pattern (6 bp):   
AAAATA

Found at i:2495 original size:32 final size:32

Alignment explanation


    Indices: 2459--2531  Score: 85
    Period size: 33  Copynumber: 2.2  Consensus size: 32

       2449 CGCCCCAGGA

                         *        *          
       2459 GGGCGGCAT-GCCCTGGCACAGTCGCTCTCCTG
          1 GGGCGGCATAGCCATGGCA-AGCCGCTCTCCTG

                   *          *              
       2491 GGGCGGCTTGAGCCATGGTAAGCCGCTCTCCTG
          1 GGGCGGCAT-AGCCATGGCAAGCCGCTCTCCTG

                    
       2524 GGGCGGCA
          1 GGGCGGCA

       2532 CGGGTCATCA


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  32    8  0.24
  33   19  0.56
  34    7  0.21

ACGTcount: A:0.11, C:0.33, G:0.38, T:0.18


Consensus pattern (32 bp):   
GGGCGGCATAGCCATGGCAAGCCGCTCTCCTG

Found at i:14765 original size:5 final size:5

Alignment explanation


    Indices: 14755--14795  Score: 50
    Period size: 5  Copynumber: 8.6  Consensus size: 5

      14745 CAAATCTCTC

                                            *      *           
      14755 TTCTT TTCTT TTCTT TTCTT TT-TT TTTTT TTCCT TT-TT TTC
          1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTC

      14796 CCTTGGGGGT


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
   4    7  0.23
   5   24  0.77

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


Consensus pattern (5 bp):   
TTCTT

Found at i:14775 original size:15 final size:14

Alignment explanation


    Indices: 14755--14795  Score: 55
    Period size: 14  Copynumber: 2.9  Consensus size: 14

      14745 CAAATCTCTC

                           
      14755 TTCTTTTCTTTTCTT
          1 TTCTTTT-TTTTCTT

                       *  
      14770 TTCTTTTTTTTTTT
          1 TTCTTTTTTTTCTT

               *        
      14784 TTCCTTTTTTTC
          1 TTCTTTTTTTTC

      14796 CCTTGGGGGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  14   16  0.70
  15    7  0.30

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


Consensus pattern (14 bp):   
TTCTTTTTTTTCTT

Found at i:20065 original size:13 final size:13

Alignment explanation


    Indices: 20047--20076  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      20037 ACGTTTGGCA

                         
      20047 AAAAGAAAAAAAG
          1 AAAAGAAAAAAAG

                         
      20060 AAAAGAAAAAAAG
          1 AAAAGAAAAAAAG

                
      20073 AAAA
          1 AAAA

      20077 CCATGTTTGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (13 bp):   
AAAAGAAAAAAAG

Found at i:29184 original size:82 final size:81

Alignment explanation


    Indices: 29073--29232  Score: 180
    Period size: 82  Copynumber: 2.0  Consensus size: 81

      29063 AATAAGGCAA

                                 *  *             *                      *   
      29073 ATAGTCATCTTTTCTTTTCCATTCTAATTACAAAACAAGTTATTATTAACCTCCCAAATCCTGTC
          1 ATAGTCATCTTTTCTTTTCCACTCCAATTACAAAACAAATTATT-TTAACCTCCCAAATCCCGTC

                             
      29138 GACCTTCAACACTACAT
         65 GACCTTCAACACTACAT

                                            * *               *      *       
      29155 ATAGTCATCTTTT-TTCCTT-CACTCCAATTATATAACAAATTATTTTAATCTCCCATATCCCGT
          1 ATAGTCATCTTTTCTT--TTCCACTCCAATTACAAAACAAATTATTTTAACCTCCCAAATCCCGT

            *  *     *     
      29218 TGATCTTCAGCACTA
         64 CGACCTTCAACACTA

      29233 TATCATTTCT


Statistics
Matches: 65,  Mismatches: 11, Indels: 5
        0.80            0.14        0.06

Matches are distributed among these distances:
  81   30  0.46
  82   33  0.51
  83    2  0.03

ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39


Consensus pattern (81 bp):   
ATAGTCATCTTTTCTTTTCCACTCCAATTACAAAACAAATTATTTTAACCTCCCAAATCCCGTCG
ACCTTCAACACTACAT

Found at i:34335 original size:5 final size:5

Alignment explanation


    Indices: 34325--34352  Score: 56
    Period size: 5  Copynumber: 5.6  Consensus size: 5

      34315 CAAGTACTTC

                                             
      34325 AAATA AAATA AAATA AAATA AAATA AAA
          1 AAATA AAATA AAATA AAATA AAATA AAA

      34353 ATTTATGTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   23  1.00

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


Consensus pattern (5 bp):   
AAATA

Done.