Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021319.1 Corchorus olitorius cultivar O-4 contig21352, 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: 13066
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32


Found at i:676 original size:11 final size:11

Alignment explanation


    Indices: 660--685  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

        650 AGATAATTTC

                       
        660 TTTTCTTCTAG
          1 TTTTCTTCTAG

                       
        671 TTTTCTTCTAG
          1 TTTTCTTCTAG

                
        682 TTTT
          1 TTTT

        686 TAGGCAAAGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69


Consensus pattern (11 bp):   
TTTTCTTCTAG

Found at i:1467 original size:15 final size:15

Alignment explanation


    Indices: 1437--1478  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1427 TTACTCTGCT

                            
       1437 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       1453 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       1468 TTGCTTTCTGT
          1 TTGTTTTCTGT

       1479 CGATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

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


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2726 original size:22 final size:22

Alignment explanation


    Indices: 2677--2727  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       2667 AAATATTACC

                         *   **   
       2677 ATAATTATTTTTGGCAGCCATA
          1 ATAATTATTTTTGCCAGAAATA

                                   
       2699 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGCC-AGAAATA

                   
       2722 A-AATTA
          1 ATAATTA

       2728 GGGAATAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22   19  0.76
  23    6  0.24

ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGCCAGAAATA
Done.