Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009579.1 Corchorus olitorius cultivar O-4 contig09611, 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: 15101
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:1209 original size:12 final size:11

Alignment explanation


    Indices: 1186--1220  Score: 52
    Period size: 12  Copynumber: 3.0  Consensus size: 11

       1176 TACTTCCCTG

                        
       1186 CTTTTTTCTTTT
          1 CTTTTTT-TTTT

                        
       1198 CTTTTCTTTTTT
          1 CTTTT-TTTTTT

                       
       1210 CTTTTTTTTTT
          1 CTTTTTTTTTT

       1221 GAGATTTTCG


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  11    6  0.27
  12   14  0.64
  13    2  0.09

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (11 bp):   
CTTTTTTTTTT

Found at i:1219 original size:17 final size:17

Alignment explanation


    Indices: 1186--1218  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1176 TACTTCCCTG

                             
       1186 CTTTTTTCTTTTCTTTT
          1 CTTTTTTCTTTTCTTTT

                             
       1203 CTTTTTTCTTTT-TTTT
          1 CTTTTTTCTTTTCTTTT

       1219 TTGAGATTTT


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

Matches are distributed among these distances:
  16    4  0.25
  17   12  0.75

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (17 bp):   
CTTTTTTCTTTTCTTTT

Found at i:5072 original size:23 final size:21

Alignment explanation


    Indices: 5042--5087  Score: 56
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       5032 TATCACGTCT

                     *        *   
       5042 AAATAATATTTTGAAATATTGA
          1 AAATAATATCTT-AAATAATGA

                                  
       5064 AAATCAATATCTTAAATAATGA
          1 AAAT-AATATCTTAAATAATGA

              
       5086 AA
          1 AA

       5088 TTATTTCAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  22   14  0.67
  23    7  0.33

ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35


Consensus pattern (21 bp):   
AAATAATATCTTAAATAATGA
Done.