Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006592.1 Corchorus capsularis cultivar CVL-1 contig06613, 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: 3256
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31


Found at i:840 original size:60 final size:60

Alignment explanation


    Indices: 773--892  Score: 222
    Period size: 60  Copynumber: 2.0  Consensus size: 60

        763 TGTAAGATCG

                                      *                                 
        773 AAGAGAGTCGCATAGCCTTGATGAGGTTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
          1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

                                                                *       
        833 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
          1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

        893 GTTGAAATCG


Statistics
Matches: 58,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  60   58  1.00

ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37


Consensus pattern (60 bp):   
AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

Found at i:1950 original size:60 final size:60

Alignment explanation


    Indices: 1883--2002  Score: 231
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       1873 TGTAAGATCG

                                                                        
       1883 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
          1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

                                                                *       
       1943 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
          1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

       2003 GTTGAAATCG


Statistics
Matches: 59,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  60   59  1.00

ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36


Consensus pattern (60 bp):   
AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

Found at i:3062 original size:60 final size:60

Alignment explanation


    Indices: 2995--3114  Score: 213
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       2985 TGTAAGATCG

                                      *                                 
       2995 AAGAGAGTCGCATAGCCTTGATGAGGTTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
          1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

                    *                                           *       
       3055 AAGAGAGTTGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
          1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT

       3115 GTTGAAATCG


Statistics
Matches: 57,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  60   57  1.00

ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38


Consensus pattern (60 bp):   
AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
Done.