Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021730.1 Corchorus olitorius cultivar O-4 contig21763, 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: 17880
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29


Found at i:1117 original size:9 final size:9

Alignment explanation


    Indices: 1103--1127  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       1093 ATGAATTTTT

                     
       1103 GAATTTTCG
          1 GAATTTTCG

                     
       1112 GAATTTTCG
          1 GAATTTTCG

                   
       1121 GAATTTT
          1 GAATTTT

       1128 TAGATCTAGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48


Consensus pattern (9 bp):   
GAATTTTCG

Found at i:1180 original size:25 final size:24

Alignment explanation


    Indices: 1143--1189  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1133 CTAGAAAATT

                                      
       1143 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       1169 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1190 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:2059 original size:21 final size:21

Alignment explanation


    Indices: 2035--2105  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       2025 CTTAGCCAAT

                         *       
       2035 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       2056 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2077 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       2098 TCCAATGA
          1 TCCAATGA

       2106 TCTCCTAACA


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   45  0.94

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC
Done.