Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013482.1 Corchorus olitorius cultivar O-4 contig13515, 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: 24317
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:12692 original size:6 final size:6

Alignment explanation


    Indices: 12681--12710  Score: 51
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      12671 TTAAAAAACA

                                              
      12681 TGGCAT TGGCAT TGGCAT TGGCATT TGGCA
          1 TGGCAT TGGCAT TGGCAT TGGCA-T TGGCA

      12711 ACCCTTTCTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   17  0.74
   7    6  0.26

ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33


Consensus pattern (6 bp):   
TGGCAT

Found at i:15402 original size:29 final size:29

Alignment explanation


    Indices: 15364--15433  Score: 140
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      15354 CTCGATTTGA

                                         
      15364 GGCCAAACGTTTCAATCGTAACAAAATGG
          1 GGCCAAACGTTTCAATCGTAACAAAATGG

                                         
      15393 GGCCAAACGTTTCAATCGTAACAAAATGG
          1 GGCCAAACGTTTCAATCGTAACAAAATGG

                        
      15422 GGCCAAACGTTT
          1 GGCCAAACGTTT

      15434 TCGGGGCTGC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   41  1.00

ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21


Consensus pattern (29 bp):   
GGCCAAACGTTTCAATCGTAACAAAATGG

Found at i:17663 original size:51 final size:52

Alignment explanation


    Indices: 17562--17663  Score: 129
    Period size: 51  Copynumber: 2.0  Consensus size: 52

      17552 GTTCTTCATA

                                                     * **       
      17562 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTT
          1 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT

                                           *                     
      17614 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
          1 TTCTCCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT

      17664 CTTCATTCAG


Statistics
Matches: 44,  Mismatches: 4, Indels: 5
        0.83            0.08        0.09

Matches are distributed among these distances:
  50    2  0.05
  51   37  0.84
  52    5  0.11

ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40


Consensus pattern (52 bp):   
TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT

Found at i:19006 original size:3 final size:3

Alignment explanation


    Indices: 18998--19029  Score: 55
    Period size: 3  Copynumber: 10.7  Consensus size: 3

      18988 TCAGGAAACT

                          *                           
      18998 AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

      19030 ATTGCAGGAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (3 bp):   
AAG

Done.