Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021085.1 Corchorus olitorius cultivar O-4 contig21118, 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: 10389
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:2062 original size:3 final size:3

Alignment explanation


    Indices: 2056--2080  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       2046 CTTCTCTTTC

                                             
       2056 TCA TCA TCA TCA TCA TCA TCA TCA T
          1 TCA TCA TCA TCA TCA TCA TCA TCA T

       2081 TCTTATTTGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36


Consensus pattern (3 bp):   
TCA

Found at i:2265 original size:60 final size:62

Alignment explanation


    Indices: 2201--2328  Score: 179
    Period size: 60  Copynumber: 2.1  Consensus size: 62

       2191 ACTGCTTTTG

                      *    *                       *        *             
       2201 CTTCATTTTCCTTTGCTTGATCACCATCCTTGATCA-T-CTCTTCATGTAATTCTTTCTTTA
          1 CTTCATTTTCATTTGATTGATCACCATCCTTGATCACTGATCTTCATGCAATTCTTTCTTTA

                                       *                       *           
       2261 CTTCATTTTCATTTGATTGATCACCATTCTTGATCACCTGATCTTCATGCATTTCTTTCTTTA
          1 CTTCATTTTCATTTGATTGATCACCATCCTTGATCA-CTGATCTTCATGCAATTCTTTCTTTA

                 
       2324 CTTCA
          1 CTTCA

       2329 CAAACATCAA


Statistics
Matches: 59,  Mismatches: 6, Indels: 3
        0.87            0.09        0.04

Matches are distributed among these distances:
  60   33  0.56
  62    1  0.02
  63   25  0.42

ACGTcount: A:0.18, C:0.26, G:0.07, T:0.49


Consensus pattern (62 bp):   
CTTCATTTTCATTTGATTGATCACCATCCTTGATCACTGATCTTCATGCAATTCTTTCTTTA

Found at i:8040 original size:26 final size:27

Alignment explanation


    Indices: 7990--8041  Score: 70
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       7980 ATTATTAAGA

                                       
       7990 TAAAGAAAAAAAAACAAAAATAATAGC
          1 TAAAGAAAAAAAAACAAAAATAATAGC

                   **      *          
       8017 TAAAGAATTAAAAACGAAAA-AATAG
          1 TAAAGAAAAAAAAACAAAAATAATAG

       8042 AATCAAAACC


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26    5  0.23
  27   17  0.77

ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13


Consensus pattern (27 bp):   
TAAAGAAAAAAAAACAAAAATAATAGC

Found at i:8790 original size:22 final size:20

Alignment explanation


    Indices: 8757--8796  Score: 53
    Period size: 22  Copynumber: 1.9  Consensus size: 20

       8747 GCAGTGTAGA

                         *      
       8757 AAGAAAACAAAAGTGAAACG
          1 AAGAAAACAAAAGAGAAACG

                                
       8777 AAGAAGAAGCAAAAGAGAAA
          1 AAGAA-AA-CAAAAGAGAAA

       8797 TGGCGACTGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    5  0.29
  21    2  0.12
  22   10  0.59

ACGTcount: A:0.68, C:0.07, G:0.23, T:0.03


Consensus pattern (20 bp):   
AAGAAAACAAAAGAGAAACG
Done.