Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020581.1 Corchorus olitorius cultivar O-4 contig20614, 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: 23612
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:3260 original size:30 final size:31

Alignment explanation


    Indices: 3224--3292  Score: 95
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       3214 GTGCAAATGG

                                           
       3224 GTCCCTGAAGTGAACAT-AGTGAGCAATTGA
          1 GTCCCTGAAGTGAACATAAGTGAGCAATTGA

                          **   *          *
       3254 GTCCCTGAAGTGAAGTTAATTGAGCAATTGG
          1 GTCCCTGAAGTGAACATAAGTGAGCAATTGA

                    
       3285 GTCCCTGA
          1 GTCCCTGA

       3293 CTATTTTTTT


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  30   15  0.44
  31   19  0.56

ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26


Consensus pattern (31 bp):   
GTCCCTGAAGTGAACATAAGTGAGCAATTGA

Found at i:5859 original size:32 final size:32

Alignment explanation


    Indices: 5818--5887  Score: 131
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       5808 AAAATAATCA

                               *            
       5818 AATTTAGTTGTTTCTAATCGTTTAAGAAATTC
          1 AATTTAGTTGTTTCTAATCATTTAAGAAATTC

                                            
       5850 AATTTAGTTGTTTCTAATCATTTAAGAAATTC
          1 AATTTAGTTGTTTCTAATCATTTAAGAAATTC

                  
       5882 AATTTA
          1 AATTTA

       5888 AAATTACCAA


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47


Consensus pattern (32 bp):   
AATTTAGTTGTTTCTAATCATTTAAGAAATTC

Found at i:22460 original size:3 final size:3

Alignment explanation


    Indices: 22454--22514  Score: 122
    Period size: 3  Copynumber: 20.3  Consensus size: 3

      22444 GTTTTAATAT

                                                                           
      22454 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                             
      22502 TTA TTA TTA TTA T
          1 TTA TTA TTA TTA T

      22515 AATATAGTTC


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   58  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:23580 original size:2 final size:2

Alignment explanation


    Indices: 23573--23612  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      23563 TGGGTAAGAT

                                                                       
      23573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
TA

Done.