Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004146.1 Corchorus capsularis cultivar CVL-1 contig04154, 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, 748

Length: 1247
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37


Found at i:64 original size:22 final size:22

Alignment explanation


    Indices: 39--97  Score: 68
    Period size: 22  Copynumber: 2.7  Consensus size: 22

         29 ATAACCCCCT

                                    
         39 TATGAAATTTTGA-AA-ATTAAAA
          1 TATGAAATTTTGATAACATT--AA

                   *            * 
         61 TATGAAACTTTGATAACATTCA
          1 TATGAAATTTTGATAACATTAA

                           
         83 TATGAAATTTTGATA
          1 TATGAAATTTTGATA

         98 TCCTCCCTGA


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  22   27  0.84
  23    2  0.06
  24    3  0.09

ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39


Consensus pattern (22 bp):   
TATGAAATTTTGATAACATTAA

Found at i:274 original size:22 final size:22

Alignment explanation


    Indices: 223--301  Score: 70
    Period size: 22  Copynumber: 3.6  Consensus size: 22

        213 ATCACATTTC

                *   *         *   
        223 GAAAATTTGATAACCTCTTTAT
          1 GAAATTTTAATAACCTCTCTAT

                                  
        245 GAAATTTTAATAACCTCTCTAT
          1 GAAATTTTAATAACCTCTCTAT

                     ** *   *      
        267 -AAATTTTTGTTGACCCCTCTAT
          1 GAAA-TTTTAATAACCTCTCTAT

                    *    
        289 GAAATTTTGATAA
          1 GAAATTTTAATAA

        302 TGACATTATG


Statistics
Matches: 46,  Mismatches: 9, Indels: 4
        0.78            0.15        0.07

Matches are distributed among these distances:
  21    3  0.07
  22   40  0.87
  23    3  0.07

ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42


Consensus pattern (22 bp):   
GAAATTTTAATAACCTCTCTAT

Found at i:338 original size:22 final size:22

Alignment explanation


    Indices: 198--342  Score: 68
    Period size: 22  Copynumber: 6.6  Consensus size: 22

        188 GAAATACCAC

                        *         
        198 TATGAAATTTTGGTAATCACAT
          1 TATGAAATTTTGATAATCACAT

                    *        * * * 
        220 T-TCGAAAATTTGATAACCTCTT
          1 TAT-GAAATTTTGATAATCACAT

                       *    * *   
        242 TATGAAATTTTAATAACCTC-T
          1 TATGAAATTTTGATAATCACAT

                          * *   * * 
        263 CTAT-AAATTTTTGTTGA-CCCCT
          1 -TATGAAA-TTTTGATAATCACAT

                              *    
        285 CTATGAAATTTTGATAATGACAT
          1 -TATGAAATTTTGATAATCACAT

                *                   
        308 TATGTAATTTTGATAACTTCA-AT
          1 TATGAAATTTTGATAA--TCACAT

                         
        331 T-TGAAATTTTGA
          1 TATGAAATTTTGA

        343 AATTGGACCA


Statistics
Matches: 95,  Mismatches: 19, Indels: 18
        0.72            0.14        0.14

Matches are distributed among these distances:
  21    7  0.07
  22   77  0.81
  23    9  0.09
  24    2  0.02

ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43


Consensus pattern (22 bp):   
TATGAAATTTTGATAATCACAT

Found at i:970 original size:22 final size:22

Alignment explanation


    Indices: 945--1105  Score: 77
    Period size: 22  Copynumber: 7.5  Consensus size: 22

        935 ATGACGTCCT

                                  
        945 TATGAAATTTTGATAACCTTCC
          1 TATGAAATTTTGATAACCTTCC

                     *              
        967 TATGAAATTATGATAA--TTACAC
          1 TATGAAATTTTGATAACCTT-C-C

                       *  *   *   
        989 TAT----TTTTTATGA-CGTCC
          1 TATGAAATTTTGATAACCTTCC

                                   
       1006 TTATGAAATTTTGATAACCTTCC
          1 -TATGAAATTTTGATAACCTTCC

                      **     ** * 
       1029 TATGAAATTTCAATAACGATAC
          1 TATGAAATTTTGATAACCTTCC

                *     *  *      **
       1051 TATGGAATTTCGAGAACCTTTT
          1 TATGAAATTTTGATAACCTTCC

                  *    **        *
       1073 TAT-AATTTTTTTTAACCTTCT
          1 TATGAAATTTTGATAACCTTCC

                        
       1094 TATGAAATTTTG
          1 TATGAAATTTTG

       1106 TTACCAGGGT


Statistics
Matches: 100,  Mismatches: 29, Indels: 20
        0.67            0.19        0.13

Matches are distributed among these distances:
  17    1  0.01
  18   10  0.10
  19    1  0.01
  20    2  0.02
  21   15  0.15
  22   67  0.67
  23    4  0.04

ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTTCC

Found at i:1053 original size:62 final size:62

Alignment explanation


    Indices: 886--1037  Score: 277
    Period size: 62  Copynumber: 2.5  Consensus size: 62

        876 ATATTGATAC

                  *               *                 *                     
        886 GAAATTATGATAACCTTCCTATTAAATTATGATAATTACAGTATTTTTTATGACGTCCTTAT
          1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT

                                                                          
        948 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
          1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT

                                        
       1010 GAAATTTTGATAACCTTCCTATGAAATT
          1 GAAATTTTGATAACCTTCCTATGAAATT

       1038 TCAATAACGA


Statistics
Matches: 87,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  62   87  1.00

ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43


Consensus pattern (62 bp):   
GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
Done.