Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010948.1 Corchorus capsularis cultivar CVL-1 contig10969, 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: 6559
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:82 original size:23 final size:23

Alignment explanation


    Indices: 56--152  Score: 97
    Period size: 23  Copynumber: 4.0  Consensus size: 23

         46 AATTCATTAC

                                   
         56 ACATAATTTTCCATATTAAGCAT
          1 ACATAATTTTCCATATTAAGCAT

                       **  *            
         79 ACATAATTGACAACCTTATTTCAAGCAT
          1 ACATAATT---TTCCATA-TT-AAGCAT

             *                     
        107 ATATAATTTTCCATATTAAGCAT
          1 ACATAATTTTCCATATTAAGCAT

                     *             
        130 ACATAA-TTCCCATATTAAGCAT
          1 ACATAATTTTCCATATTAAGCAT

             
        152 A
          1 A

        153 GCATTTCAAT


Statistics
Matches: 60,  Mismatches: 9, Indels: 11
        0.75            0.11        0.14

Matches are distributed among these distances:
  22   16  0.27
  23   19  0.32
  24    2  0.03
  25    4  0.07
  26    4  0.07
  27    2  0.03
  28   13  0.22

ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36


Consensus pattern (23 bp):   
ACATAATTTTCCATATTAAGCAT

Found at i:3420 original size:8 final size:8

Alignment explanation


    Indices: 3407--3440  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       3397 ACCTTCTTGA

                    
       3407 AAAAATTC
          1 AAAAATTC

                    
       3415 AAAAATTC
          1 AAAAATTC

                 *   
       3423 AGAAACTTC
          1 A-AAAATTC

                    
       3432 AAAAATTC
          1 AAAAATTC

             
       3440 A
          1 A

       3441 TAGCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:3526 original size:10 final size:9

Alignment explanation


    Indices: 3513--3547  Score: 52
    Period size: 10  Copynumber: 3.7  Consensus size: 9

       3503 AGTTATATCG

                      
       3513 AAAAATATAA
          1 AAAAATA-AA

                     
       3523 AAAAATAAA
          1 AAAAATAAA

                      
       3532 ATAAAATAAA
          1 A-AAAATAAA

                  
       3542 AAAAAT
          1 AAAAAT

       3548 TTTCGACCAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
   9    8  0.33
  10   16  0.67

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


Consensus pattern (9 bp):   
AAAAATAAA

Found at i:5171 original size:33 final size:31

Alignment explanation


    Indices: 5127--5240  Score: 131
    Period size: 33  Copynumber: 3.6  Consensus size: 31

       5117 TTAATTGTGA

                                             
       5127 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
          1 TGAAAACAATTCTGTTTTGGTTG-A-ATAGCAT

             *                               
       5160 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
          1 TGAAAACAATTCTGTTTTGGTTGA--ATAGCAT

              *   *   *                    
       5193 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
          1 TGAAAACAATTCTGTTTTGGTTGAATAGCAT

                  *  *        
       5223 TGAAAATAAATCTGTTTT
          1 TGAAAACAATTCTGTTTT

       5241 TGGTGACGAG


Statistics
Matches: 71,  Mismatches: 9, Indels: 5
        0.84            0.11        0.06

Matches are distributed among these distances:
  30   22  0.31
  32    1  0.01
  33   48  0.68

ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40


Consensus pattern (31 bp):   
TGAAAACAATTCTGTTTTGGTTGAATAGCAT

Done.