Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006115.1 Corchorus olitorius cultivar O-4 contig06140, 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, 898

Length: 1497
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33


Found at i:155 original size:13 final size:12

Alignment explanation


    Indices: 119--165  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

        109 TAAATCTTTA

                        *
        119 TATATATTGATAA
          1 TATATATT-ATAT

                 *      
        132 TA-ATGTTATAT
          1 TATATATTATAT

                         
        143 TATATTATTATAT
          1 TATA-TATTATAT

                      
        156 TATATATTAT
          1 TATATATTAT

        166 CAATAAACTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  11    5  0.17
  12   11  0.38
  13   13  0.45

ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55


Consensus pattern (12 bp):   
TATATATTATAT

Found at i:351 original size:16 final size:16

Alignment explanation


    Indices: 330--446  Score: 107
    Period size: 16  Copynumber: 7.4  Consensus size: 16

        320 ACCCGAGACT

                            
        330 GAACCCGAAAATACCC
          1 GAACCCGAAAATACCC

                     *    *  
        346 GAACCC-AACATAATCC
          1 GAACCCGAAAAT-ACCC

                            
        362 GAACCCGAAAATACCC
          1 GAACCCGAAAATACCC

                *    **      
        378 GAACTCG-ACTTAACCC
          1 GAACCCGAAAAT-ACCC

                 *         *
        394 GAACCAGAAAATACCT
          1 GAACCCGAAAATACCC

                            
        410 GAACCCGAAAA-ACCC
          1 GAACCCGAAAATACCC

                      *  *  
        425 GAACCCG-AAGTATCC
          1 GAACCCGAAAATACCC

                   
        440 GAACCCG
          1 GAACCCG

        447 TCCGAGTCTG


Statistics
Matches: 80,  Mismatches: 16, Indels: 11
        0.75            0.15        0.10

Matches are distributed among these distances:
  14    2  0.03
  15   26  0.32
  16   46  0.57
  17    6  0.08

ACGTcount: A:0.41, C:0.36, G:0.14, T:0.09


Consensus pattern (16 bp):   
GAACCCGAAAATACCC

Found at i:368 original size:32 final size:32

Alignment explanation


    Indices: 330--433  Score: 131
    Period size: 32  Copynumber: 3.3  Consensus size: 32

        320 ACCCGAGACT

                                         *  
        330 GAACCCGAAAATACCCGAACCCAACATAATCC
          1 GAACCCGAAAATACCCGAACCCAACATAACCC

                                * *  *      
        362 GAACCCGAAAATACCCGAACTCGACTTAACCC
          1 GAACCCGAAAATACCCGAACCCAACATAACCC

                 *         *                 
        394 GAACCAGAAAATACCTGAACCCGAA-A-AACCC
          1 GAACCCGAAAATACCCGAACCC-AACATAACCC

                     
        425 GAACCCGAA
          1 GAACCCGAA

        434 GTATCCGAAC


Statistics
Matches: 61,  Mismatches: 10, Indels: 3
        0.82            0.14        0.04

Matches are distributed among these distances:
  31   13  0.21
  32   47  0.77
  33    1  0.02

ACGTcount: A:0.43, C:0.36, G:0.12, T:0.09


Consensus pattern (32 bp):   
GAACCCGAAAATACCCGAACCCAACATAACCC
Done.