Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015838.1 Corchorus olitorius cultivar O-4 contig15871, 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: 19489
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:7584 original size:5 final size:6

Alignment explanation


    Indices: 7563--7613  Score: 50
    Period size: 6  Copynumber: 8.2  Consensus size: 6

       7553 TAACAAAAAT

                                      *       *                       
       7563 AAAACG AAAACG AAAACG -AAACA AAAACAA AAAACAG AAAAACG AAAACG
          1 AAAACG AAAACG AAAACG AAAACG AAAAC-G AAAAC-G -AAAACG AAAACG

             
       7613 A
          1 A

       7614 TACCAAACGA


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
   5    4  0.10
   6   23  0.57
   7    8  0.20
   8    5  0.12

ACGTcount: A:0.73, C:0.16, G:0.12, T:0.00


Consensus pattern (6 bp):   
AAAACG

Found at i:14415 original size:19 final size:19

Alignment explanation


    Indices: 14391--14427  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      14381 TTAGTTATGG

                               
      14391 TTTTCTAATTCTAATGTTT
          1 TTTTCTAATTCTAATGTTT

                              
      14410 TTTTCTAATTCTAATGTT
          1 TTTTCTAATTCTAATGTT

      14428 GAATATTTAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62


Consensus pattern (19 bp):   
TTTTCTAATTCTAATGTTT

Found at i:16801 original size:6 final size:6

Alignment explanation


    Indices: 16790--16820  Score: 53
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      16780 TTTGGATAAA

                                               
      16790 CTATAT CTATAT CTATAT CTATAT ACTATAT
          1 CTATAT CTATAT CTATAT CTATAT -CTATAT

      16821 AAGTCTAAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   18  0.75
   7    6  0.25

ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48


Consensus pattern (6 bp):   
CTATAT

Done.