Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019147.1 Corchorus olitorius cultivar O-4 contig19180, 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: 7817
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:5175 original size:30 final size:29

Alignment explanation


    Indices: 5134--5200  Score: 77
    Period size: 30  Copynumber: 2.3  Consensus size: 29

       5124 TCTCTATTGA

                                           
       5134 TTCTT-TTTTTTTTTGGTTTC-ATATATATC
          1 TTCTTATTTTTTTTT-G-TTCGATATATATC

                                           
       5163 TTCTTA-TTTTTTTTGTTCGGAATATATATC
          1 TTCTTATTTTTTTTTGTTC-G-ATATATATC

                    
       5193 TTCTTATT
          1 TTCTTATT

       5201 GAATATGCTG


Statistics
Matches: 33,  Mismatches: 0, Indels: 8
        0.80            0.00        0.20

Matches are distributed among these distances:
  27    3  0.09
  28    1  0.03
  29   13  0.39
  30   15  0.45
  31    1  0.03

ACGTcount: A:0.16, C:0.10, G:0.07, T:0.66


Consensus pattern (29 bp):   
TTCTTATTTTTTTTTGTTCGATATATATC

Found at i:6580 original size:24 final size:25

Alignment explanation


    Indices: 6534--6584  Score: 68
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       6524 ATTGGAGTAT

                           *         
       6534 TTATTTATCTTGTTGCTTAATTTTA
          1 TTATTTATCTTGTTGATTAATTTTA

                          *   *      
       6559 TTATTT-TCTTGTTTATTTATTTTA
          1 TTATTTATCTTGTTGATTAATTTTA

              
       6583 TT
          1 TT

       6585 GTTCACATAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24   17  0.74
  25    6  0.26

ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71


Consensus pattern (25 bp):   
TTATTTATCTTGTTGATTAATTTTA

Found at i:7210 original size:21 final size:22

Alignment explanation


    Indices: 7185--7252  Score: 72
    Period size: 21  Copynumber: 3.2  Consensus size: 22

       7175 TTGAAAGTCA

                                   
       7185 GTTGAAAAC-TAATG-AGAATAT
          1 GTTGAAAACATAA-GAAGAATAT

                  *               
       7206 GTTG-AGACATAAGAAGAATAT
          1 GTTGAAAACATAAGAAGAATAT

                  *    *          
       7227 GTTG-AGACATGAGAAGAATAT
          1 GTTGAAAACATAAGAAGAATAT

                 
       7248 GTTGA
          1 GTTGA

       7253 GACATGAAGG


Statistics
Matches: 42,  Mismatches: 2, Indels: 5
        0.86            0.04        0.10

Matches are distributed among these distances:
  20    4  0.10
  21   38  0.90

ACGTcount: A:0.44, C:0.04, G:0.25, T:0.26


Consensus pattern (22 bp):   
GTTGAAAACATAAGAAGAATAT

Found at i:7253 original size:21 final size:21

Alignment explanation


    Indices: 7199--7259  Score: 113
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       7189 AAAACTAATG

                             *   
       7199 AGAATATGTTGAGACATAAGA
          1 AGAATATGTTGAGACATGAGA

                                 
       7220 AGAATATGTTGAGACATGAGA
          1 AGAATATGTTGAGACATGAGA

                               
       7241 AGAATATGTTGAGACATGA
          1 AGAATATGTTGAGACATGA

       7260 AGGAGAGCTC


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  21   39  1.00

ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25


Consensus pattern (21 bp):   
AGAATATGTTGAGACATGAGA

Found at i:7452 original size:22 final size:22

Alignment explanation


    Indices: 7422--7467  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       7412 AAAATCTCCT

                                   
       7422 AATTCAACC-TCTGGAGAGGTCG
          1 AATTCAACCTTC-GGAGAGGTCG

                *        *        
       7444 AATTTAACCTTCGTAGAGGTCG
          1 AATTCAACCTTCGGAGAGGTCG

              
       7466 AA
          1 AA

       7468 ACAACAACTT


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

Matches are distributed among these distances:
  22   19  0.90
  23    2  0.10

ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26


Consensus pattern (22 bp):   
AATTCAACCTTCGGAGAGGTCG
Done.