Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023291.1 Corchorus olitorius cultivar O-4 contig23324, 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: 6813
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30


Found at i:637 original size:15 final size:15

Alignment explanation


    Indices: 617--648  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        607 TTGTTTTTTA

                           
        617 GTTTAATTGCTTTCT
          1 GTTTAATTGCTTTCT

                     *     
        632 GTTTAATTGTTTTCT
          1 GTTTAATTGCTTTCT

              
        647 GT
          1 GT

        649 CAACCTCTGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.12, C:0.09, G:0.16, T:0.62


Consensus pattern (15 bp):   
GTTTAATTGCTTTCT

Found at i:1059 original size:33 final size:31

Alignment explanation


    Indices: 1011--1071  Score: 79
    Period size: 30  Copynumber: 1.9  Consensus size: 31

       1001 GCGTTATTAA

                *                             
       1011 TTTTTTGTTGTTGCGTCTTTGAAAAAAAAAATTG
          1 TTTTGTGTTGTTGCGTC---GAAAAAAAAAATTG

                                        
       1045 TTTTGTGTT-TTGCGTCGAAAAAAAAAA
          1 TTTTGTGTTGTTGCGTCGAAAAAAAAAA

       1072 ATTTCCTGCG


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  30   11  0.42
  33    7  0.27
  34    8  0.31

ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43


Consensus pattern (31 bp):   
TTTTGTGTTGTTGCGTCGAAAAAAAAAATTG

Found at i:1083 original size:23 final size:24

Alignment explanation


    Indices: 1055--1099  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       1045 TTTTGTGTTT

                                    
       1055 TGCGTC-GAAAAAAAAAAATTTCC
          1 TGCGTCAGAAAAAAAAAAATTTCC

                   *              
       1078 TGCGTCATAAAAAAAAAAATTT
          1 TGCGTCAGAAAAAAAAAAATTT

       1100 TTTTGTGTCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  23    6  0.30
  24   14  0.70

ACGTcount: A:0.51, C:0.13, G:0.11, T:0.24


Consensus pattern (24 bp):   
TGCGTCAGAAAAAAAAAAATTTCC

Found at i:6116 original size:15 final size:15

Alignment explanation


    Indices: 6096--6137  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6086 ACAGAGGTTG

                           
       6096 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                   *       
       6111 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                        
       6126 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6138 AACAGAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.