Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018528.1 Corchorus olitorius cultivar O-4 contig18561, 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: 10453
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:2120 original size:16 final size:17

Alignment explanation


    Indices: 2095--2132  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       2085 TACCCTTATC

                             
       2095 TTTTTATTTTTC-ATTA
          1 TTTTTATTTTTCTATTA

                 *       *   
       2111 TTTTTCTTTTTCTTTTA
          1 TTTTTATTTTTCTATTA

                 
       2128 TTTTT
          1 TTTTT

       2133 GTTTATTTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  16   11  0.58
  17    8  0.42

ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82


Consensus pattern (17 bp):   
TTTTTATTTTTCTATTA

Found at i:3310 original size:21 final size:21

Alignment explanation


    Indices: 3271--3319  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3261 TCAATGCTTT

                         **       
       3271 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
       3293 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
       3314 A-GAAGC
          1 AGGAAGC

       3320 TACAATTCTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA

Found at i:8056 original size:26 final size:25

Alignment explanation


    Indices: 8014--8062  Score: 71
    Period size: 26  Copynumber: 1.9  Consensus size: 25

       8004 TGTCCCTCTG

                        *            
       8014 AAAAAAAAAGAGCGTTAGTAACCTC
          1 AAAAAAAAAGAGAGTTAGTAACCTC

                       *            
       8039 AAAAGAAAAAGGGAGTTAGTAACC
          1 AAAA-AAAAAGAGAGTTAGTAACC

       8063 CCTAAATCGT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25    4  0.19
  26   17  0.81

ACGTcount: A:0.53, C:0.12, G:0.20, T:0.14


Consensus pattern (25 bp):   
AAAAAAAAAGAGAGTTAGTAACCTC
Done.