Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004150.1 Corchorus capsularis cultivar CVL-1 contig04158, 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, 875

Length: 1459
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31


Found at i:491 original size:30 final size:30

Alignment explanation


    Indices: 451--509  Score: 84
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        441 TGTCTTCAAG

                               *           
        451 TCCATAATAAGTCCTT-GGTGCATCATTCCT
          1 TCCATAATAAG-CCTTGGGCGCATCATTCCT

                 *                       
        481 TCCATGATAAGCCTTGGGCGCATCATTCC
          1 TCCATAATAAGCCTTGGGCGCATCATTCC

        510 CTCCCCCTTG


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  29    4  0.15
  30   22  0.85

ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32


Consensus pattern (30 bp):   
TCCATAATAAGCCTTGGGCGCATCATTCCT

Found at i:956 original size:33 final size:33

Alignment explanation


    Indices: 914--1023  Score: 193
    Period size: 33  Copynumber: 3.3  Consensus size: 33

        904 TTTCAATGCC

                          *                  
        914 ATCAACCAAAACAGGATTATTTGCAATGCTATG
          1 ATCAACCAAAACAGAATTATTTGCAATGCTATG

                         *                   
        947 ATCAACCAAAACAAAATTATTTGCAATGCTATG
          1 ATCAACCAAAACAGAATTATTTGCAATGCTATG

                                             
        980 ATCAACCAAAACAGAATTATTTGCAATGCTATG
          1 ATCAACCAAAACAGAATTATTTGCAATGCTATG

              *        
       1013 ATAAACCAAAA
          1 ATCAACCAAAA

       1024 AAGATTTGTT


Statistics
Matches: 73,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33   73  1.00

ACGTcount: A:0.45, C:0.18, G:0.11, T:0.25


Consensus pattern (33 bp):   
ATCAACCAAAACAGAATTATTTGCAATGCTATG

Found at i:1090 original size:33 final size:33

Alignment explanation


    Indices: 1053--1157  Score: 115
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       1043 ATTAGCATCC

                                             
       1053 AAAACAGATTTAGTATCATCACAAACAACACTT
          1 AAAACAGATTTAGTATCATCACAAACAACACTT

                          *     *            *
       1086 AAAACAGATTTAGTGTCATTGA-AAACAACACTC
          1 AAAACAGATTTAGTATCA-TCACAAACAACACTT

               **  *            *             
       1119 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
          1 AAAACAGATTTAGTATCATCACAAACAACACT-T

                  
       1152 AAAACA
          1 AAAACA

       1158 CTCTTTGCAA


Statistics
Matches: 57,  Mismatches: 12, Indels: 6
        0.76            0.16        0.08

Matches are distributed among these distances:
  32    2  0.04
  33   53  0.93
  34    2  0.04

ACGTcount: A:0.47, C:0.19, G:0.10, T:0.25


Consensus pattern (33 bp):   
AAAACAGATTTAGTATCATCACAAACAACACTT
Done.