Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018724.1 Corchorus olitorius cultivar O-4 contig18757, 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: 11863
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:2881 original size:20 final size:19

Alignment explanation


    Indices: 2858--2921  Score: 53
    Period size: 20  Copynumber: 3.3  Consensus size: 19

       2848 TAATAAAAAA

                                
       2858 ACATATACAAAAAGAAAATC
          1 ACATAT-CAAAAAGAAAATC

                *                 
       2878 ACATTTGGCAAAACA-AAAA-C
          1 ACATAT--CAAAA-AGAAAATC

                   *           
       2898 ACATAT-GAAAAGAAAATC
          1 ACATATCAAAAAGAAAATC

                  
       2916 ACATAT
          1 ACATAT

       2922 GTGCTATGGT


Statistics
Matches: 36,  Mismatches: 4, Indels: 10
        0.72            0.08        0.20

Matches are distributed among these distances:
  16    1  0.03
  17    7  0.19
  18    7  0.19
  20   11  0.31
  21    9  0.25
  22    1  0.03

ACGTcount: A:0.59, C:0.16, G:0.08, T:0.17


Consensus pattern (19 bp):   
ACATATCAAAAAGAAAATC

Found at i:2913 original size:18 final size:19

Alignment explanation


    Indices: 2867--2922  Score: 69
    Period size: 18  Copynumber: 2.9  Consensus size: 19

       2857 AACATATACA

                           *    
       2867 AAAAGAAAATCACATTTGGC
          1 AAAAGAAAATCACATAT-GC

                *    *         
       2887 AAAACAAAAACACATATG-
          1 AAAAGAAAATCACATATGC

                              
       2905 AAAAGAAAATCACATATG
          1 AAAAGAAAATCACATATG

       2923 TGCTATGGTT


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  18   16  0.52
  19    1  0.03
  20   14  0.45

ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16


Consensus pattern (19 bp):   
AAAAGAAAATCACATATGC

Found at i:3079 original size:19 final size:18

Alignment explanation


    Indices: 3055--3097  Score: 50
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       3045 CGACCACATC

                    *          
       3055 ATGCTTCTGACTAAAAACA
          1 ATGCTTCTCA-TAAAAACA

                  *        *  
       3074 ATGCTTGTCATAAAATCA
          1 ATGCTTCTCATAAAAACA

                  
       3092 ATGCTT
          1 ATGCTT

       3098 TCCTTCCTCC


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  18   13  0.62
  19    8  0.38

ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33


Consensus pattern (18 bp):   
ATGCTTCTCATAAAAACA

Found at i:6585 original size:24 final size:24

Alignment explanation


    Indices: 6558--6615  Score: 75
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       6548 AAAAATACCC

                              *     
       6558 TTCATCAATTATTAATTCTAATAA
          1 TTCATCAATTATTAATTCCAATAA

                      *              
       6582 TTCATTC-ATAATTAATTCCAATAA
          1 TTCA-TCAATTATTAATTCCAATAA

                       
       6606 TTCAT-AATTA
          1 TTCATCAATTA

       6616 GAATGCATGA


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

Matches are distributed among these distances:
  23    4  0.14
  24   23  0.79
  25    2  0.07

ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45


Consensus pattern (24 bp):   
TTCATCAATTATTAATTCCAATAA
Done.