Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002928.1 Corchorus capsularis cultivar CVL-1 contig02936, 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, 638

Length: 1064
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35


Found at i:592 original size:16 final size:16

Alignment explanation


    Indices: 571--617  Score: 85
    Period size: 16  Copynumber: 2.9  Consensus size: 16

        561 GTGAATATCT

                  *         
        571 CACCAGATGAGTATTA
          1 CACCAGGTGAGTATTA

                            
        587 CACCAGGTGAGTATTA
          1 CACCAGGTGAGTATTA

                           
        603 CACCAGGTGAGTATT
          1 CACCAGGTGAGTATT

        618 GTACTGGGTG


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  16   30  1.00

ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26


Consensus pattern (16 bp):   
CACCAGGTGAGTATTA

Found at i:669 original size:15 final size:15

Alignment explanation


    Indices: 646--675  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        636 TAAGTATCTC

                *          
        646 ACCAGGTGAGTATTT
          1 ACCAAGTGAGTATTT

                           
        661 ACCAAGTGAGTATTT
          1 ACCAAGTGAGTATTT

        676 GTATTGGATG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33


Consensus pattern (15 bp):   
ACCAAGTGAGTATTT

Found at i:689 original size:74 final size:74

Alignment explanation


    Indices: 529--674  Score: 224
    Period size: 74  Copynumber: 2.0  Consensus size: 74

        519 AGCATGGCCT

                                            *                              * 
        529 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGGTGAATATCTCACCAGATGAGTATTACACCAGG
          1 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGATGAATATCTCACCAGATGAGTATTACACCAAG

                     
        594 TGAGTATTA
         66 TGAGTATTA

                                   *                         *         *     
        603 CACCAGGTGAGTATTGTACTGGGTGAGTGTGGAT-AAGTATCTCACCAGGTGAGTATT-TACCAA
          1 CACCAGGTGAGTATTGTACTGGGAGAGTGTGGATGAA-TATCTCACCAGATGAGTATTACACCAA

                     
        666 GTGAGTATT
         65 GTGAGTATT

        675 TGTATTGGAT


Statistics
Matches: 66,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  73   15  0.23
  74   51  0.77

ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29


Consensus pattern (74 bp):   
CACCAGGTGAGTATTGTACTGGGAGAGTGTGGATGAATATCTCACCAGATGAGTATTACACCAAG
TGAGTATTA

Found at i:843 original size:3 final size:3

Alignment explanation


    Indices: 835--890  Score: 94
    Period size: 3  Copynumber: 18.3  Consensus size: 3

        825 AGTCTAACCC

                                                                        
        835 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA

             *           
        881 TGA TTA TTA T
          1 TTA TTA TTA T

        891 ATGATTAAAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
   3   47  0.94
   4    3  0.06

ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64


Consensus pattern (3 bp):   
TTA

Done.