Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011607.1 Corchorus capsularis cultivar CVL-1 contig11628, 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: 4158
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37


Found at i:1944 original size:31 final size:29

Alignment explanation


    Indices: 1909--1978  Score: 88
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       1899 CTAAAGTAGA

                                       *   
       1909 ACCAAATTGAGCCGATTTTGAAAGGTTTGGT
          1 ACCAAATTGAGCCGA-TTTG-AAGGTTGGGT

                         *                
       1940 ACC-AATATGAGCTGATTTGAAGGTTGGGT
          1 ACCAAAT-TGAGCCGATTTGAAGGTTGGGT

                      
       1969 ACCAAATTGA
          1 ACCAAATTGA

       1979 TATTTTTCAC


Statistics
Matches: 35,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  29   15  0.43
  30   10  0.29
  31   10  0.29

ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30


Consensus pattern (29 bp):   
ACCAAATTGAGCCGATTTGAAGGTTGGGT

Found at i:2142 original size:2 final size:2

Alignment explanation


    Indices: 2135--2164  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2125 CTTTAGTAGC

                                                          
       2135 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2165 ATAGACCTAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:3162 original size:34 final size:33

Alignment explanation


    Indices: 3106--3189  Score: 96
    Period size: 34  Copynumber: 2.5  Consensus size: 33

       3096 TCTTTTTTGT

                             *            *   
       3106 AGAAAAGATGGTTTCTTTTGCAAATTATTATTGA
          1 AGAAAAGATGGTTT-TTCTGCAAATTATTAATGA

                                      *      *
       3140 AGAAAAGATGGTTTTTCCTGCAAATTGTTAATGG
          1 AGAAAAGATGGTTTTT-CTGCAAATTATTAATGA

                *     *     
       3174 AGAAGAGATGTTTTTT
          1 AGAAAAGATGGTTTTT

       3190 TATGAACATC


Statistics
Matches: 43,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  33    2  0.05
  34   41  0.95

ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39


Consensus pattern (33 bp):   
AGAAAAGATGGTTTTTCTGCAAATTATTAATGA

Found at i:3493 original size:2 final size:2

Alignment explanation


    Indices: 3488--3526  Score: 57
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       3478 TGTGTGTGTC

                                                                          
       3488 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA -A TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3527 AACATAAATA


Statistics
Matches: 34,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   1    3  0.09
   2   31  0.91

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Done.