Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008847.1 Corchorus capsularis cultivar CVL-1 contig08868, 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: 15559
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:4155 original size:3 final size:3

Alignment explanation


    Indices: 4147--4178  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       4137 AAGGTCCTAT

                                                      
       4147 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT

       4179 TCTGTTTTCA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTC

Found at i:9108 original size:5 final size:6

Alignment explanation


    Indices: 9090--9118  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       9080 TTCAATAGCC

                                             
       9090 TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
          1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTT

       9119 GTGTCTTGTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (6 bp):   
TTCTTT

Found at i:10708 original size:45 final size:45

Alignment explanation


    Indices: 10652--10741  Score: 162
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      10642 GATTACTTCT

                                                         
      10652 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
          1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC

                  *         *                            
      10697 CCAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
          1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC

      10742 TACTCTATTA


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   43  1.00

ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33


Consensus pattern (45 bp):   
CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC

Found at i:15049 original size:6 final size:6

Alignment explanation


    Indices: 15038--15071  Score: 68
    Period size: 6  Copynumber: 5.7  Consensus size: 6

      15028 AAAAGCACTC

                                                   
      15038 GAAGCG GAAGCG GAAGCG GAAGCG GAAGCG GAAG
          1 GAAGCG GAAGCG GAAGCG GAAGCG GAAGCG GAAG

      15072 AGGAGAAACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.35, C:0.15, G:0.50, T:0.00


Consensus pattern (6 bp):   
GAAGCG

Found at i:15461 original size:26 final size:26

Alignment explanation


    Indices: 15432--15497  Score: 105
    Period size: 26  Copynumber: 2.5  Consensus size: 26

      15422 TTCCTTCATT

                                      
      15432 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *            *       
      15458 TTAATAATAAACTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *         
      15484 TTAAACATAAACTA
          1 TTAATCATAAACTA

      15498 TAAACTAAGT


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   36  1.00

ACGTcount: A:0.55, C:0.11, G:0.02, T:0.33


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA
Done.