Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006139.1 Corchorus capsularis cultivar CVL-1 contig06157, 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: 12961
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Found at i:8593 original size:14 final size:14

Alignment explanation


    Indices: 8574--8615  Score: 50
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       8564 GACTGGTAGC

                           
       8574 GAGTTGGG-GAGTTG
          1 GAGTTGGGAGAG-TG

                          
       8588 GAGTTGGGAGAGTG
          1 GAGTTGGGAGAGTG

                          
       8602 GAGTGTGTGGAGAG
          1 GAGT-TG-GGAGAG

       8616 AGGGGCGAGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  14   14  0.56
  15    5  0.20
  16    6  0.24

ACGTcount: A:0.19, C:0.00, G:0.57, T:0.24


Consensus pattern (14 bp):   
GAGTTGGGAGAGTG

Found at i:10193 original size:112 final size:112

Alignment explanation


    Indices: 9996--10221  Score: 443
    Period size: 112  Copynumber: 2.0  Consensus size: 112

       9986 CTTTTTTCTC

                                                                             
       9996 TTTTTATACTTAGACGAGAAATTATTAGATGAATCAGTTCCATCACGTCATCCATAGTTTCAACC
          1 TTTTTATACTTAGACGAGAAATTATTAGATGAATCAGTTCCATCACGTCATCCATAGTTTCAACC

                                                           
      10061 AATAAGATTGTAACAATTCAGAATTATTCATAAGATTTAAATACAAA
         66 AATAAGATTGTAACAATTCAGAATTATTCATAAGATTTAAATACAAA

                                                   *                         
      10108 TTTTTATACTTAGACGAGAAATTATTAGATGAATCAGTTTCATCACGTCATCCATAGTTTCAACC
          1 TTTTTATACTTAGACGAGAAATTATTAGATGAATCAGTTCCATCACGTCATCCATAGTTTCAACC

                                                           
      10173 AATAAGATTGTAACAATTCAGAATTATTCATAAGATTTAAATACAAA
         66 AATAAGATTGTAACAATTCAGAATTATTCATAAGATTTAAATACAAA

              
      10220 TT
          1 TT

      10222 AAGTACCAGA


Statistics
Matches: 113,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 112  113  1.00

ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35


Consensus pattern (112 bp):   
TTTTTATACTTAGACGAGAAATTATTAGATGAATCAGTTCCATCACGTCATCCATAGTTTCAACC
AATAAGATTGTAACAATTCAGAATTATTCATAAGATTTAAATACAAA

Found at i:10486 original size:27 final size:27

Alignment explanation


    Indices: 10448--10500  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      10438 AAGAGTTTAG

                                       
      10448 TACTCTTTCTTATCATCAGATAATGTA
          1 TACTCTTTCTTATCATCAGATAATGTA

                                      
      10475 TACTCTTTCTTATCATCAGATAATGT
          1 TACTCTTTCTTATCATCAGATAATGT

      10501 GACGGATGAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45


Consensus pattern (27 bp):   
TACTCTTTCTTATCATCAGATAATGTA

Found at i:12909 original size:2 final size:2

Alignment explanation


    Indices: 12902--12961  Score: 120
    Period size: 2  Copynumber: 30.0  Consensus size: 2

      12892 TTTAAAACAC

                                                                          
      12902 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                      
      12944 AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG


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

Matches are distributed among these distances:
   2   58  1.00

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


Consensus pattern (2 bp):   
AG

Done.