Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023911.1 Corchorus olitorius cultivar O-4 contig23944, 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: 4176
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36


Found at i:1935 original size:39 final size:39

Alignment explanation


    Indices: 1890--1967  Score: 156
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       1880 ATTCATTTAA

                                                   
       1890 AGGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTT
          1 AGGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTT

                                                   
       1929 AGGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTT
          1 AGGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTT

       1968 CAATATGTAA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38


Consensus pattern (39 bp):   
AGGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTT

Found at i:2127 original size:42 final size:40

Alignment explanation


    Indices: 2068--2151  Score: 123
    Period size: 42  Copynumber: 2.0  Consensus size: 40

       2058 TTTAATTCCG

                              *       *             
       2068 ATGTAATATATATAATAATTAAAATATTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                                  *                   
       2108 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA

              
       2150 AT
          1 AT

       2152 TCTTAGGTTT


Statistics
Matches: 39,  Mismatches: 3, Indels: 2
        0.89            0.07        0.05

Matches are distributed among these distances:
  40    7  0.18
  41    3  0.08
  42   29  0.74

ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:3251 original size:36 final size:36

Alignment explanation


    Indices: 3204--3273  Score: 106
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       3194 GAGATTTTGG

                                 *               
       3204 AGAAATATGATAATC-AAAATTACAAAAAATGTAATA
          1 AGAAATATGATAA-CAAAAATCACAAAAAATGTAATA

                                       *      
       3240 AGAAATATGATAACAAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACAAAAATCACAAAAAATGTAA

       3274 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  35    1  0.03
  36   30  0.97

ACGTcount: A:0.61, C:0.07, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACAAAAATCACAAAAAATGTAATA
Done.