Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002326.1 Corchorus olitorius cultivar O-4 contig02326, 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: 3606
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:1014 original size:56 final size:57

Alignment explanation


    Indices: 903--1017  Score: 180
    Period size: 57  Copynumber: 2.0  Consensus size: 57

        893 TATCCGTTTC

                                                      *              
        903 CTTTCACACAATAAATGTTATAATAAATTCTATCCCCTCTATTTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATTCTATCCCCTCTATCTCTACTTAATTATT

                                  *            *                      
        960 CTTTCACACAATAAATGTTATAGT-AATTCTTATCTCC-CTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATTC-TATCCCCTCTATCTCTACTTAATTATT

              
       1016 CT
          1 CT

       1018 ACAAAATAAA


Statistics
Matches: 54,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  56   25  0.46
  57   29  0.54

ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44


Consensus pattern (57 bp):   
CTTTCACACAATAAATGTTATAATAAATTCTATCCCCTCTATCTCTACTTAATTATT

Found at i:1030 original size:57 final size:57

Alignment explanation


    Indices: 912--1023  Score: 140
    Period size: 56  Copynumber: 2.0  Consensus size: 57

        902 CCTTTCACAC

                                             *                 *  * *
        912 AATAAATGTTATAATAAATTCTATCCCCTCTATTTCTACTTAATTATTCTTTCACAC
          1 AATAAATGTTATAATAAATTCTATCCCCTCTATCTCTACTTAATTATTCTTACAAAA

                         *            *                               
        969 AATAAATGTTATAGT-AATTCTTATCTCC-CTATCTCTACTTAATTATTC-TACAAAA
          1 AATAAATGTTATAATAAATTC-TATCCCCTCTATCTCTACTTAATTATTCTTACAAAA

       1024 TAAATAATAT


Statistics
Matches: 48,  Mismatches: 6, Indels: 4
        0.83            0.10        0.07

Matches are distributed among these distances:
  55    4  0.08
  56   24  0.50
  57   20  0.42

ACGTcount: A:0.35, C:0.20, G:0.03, T:0.43


Consensus pattern (57 bp):   
AATAAATGTTATAATAAATTCTATCCCCTCTATCTCTACTTAATTATTCTTACAAAA

Found at i:1130 original size:42 final size:42

Alignment explanation


    Indices: 1083--1163  Score: 128
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       1073 TAAGAATCAA

                                                       
       1083 GATTTGAGTTGAA-TATTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTGAGTT-AAGTATTTCTTAATTTACAAAGAATTTTCTAT

                                      *  *         
       1125 GATTTGAGTTAAGTATTTCTTAATTTGCAGAGAATTTTC
          1 GATTTGAGTTAAGTATTTCTTAATTTACAAAGAATTTTC

       1164 AAGACTTAGC


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  41    2  0.06
  42   34  0.94

ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47


Consensus pattern (42 bp):   
GATTTGAGTTAAGTATTTCTTAATTTACAAAGAATTTTCTAT

Found at i:1151 original size:21 final size:21

Alignment explanation


    Indices: 1084--1151  Score: 52
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       1074 AAGAATCAAG

                                  
       1084 ATTTGAGTTGAA-TATTTCTTA
          1 ATTTGAGTT-AAGTATTTCTTA

                   **   *         *
       1105 ATTT-A-CAAAGAATTTTCTATG
          1 ATTTGAGTTAAGTA-TTTCT-TA

                                 
       1126 ATTTGAGTTAAGTATTTCTTA
          1 ATTTGAGTTAAGTATTTCTTA

                 
       1147 ATTTG
          1 ATTTG

       1152 CAGAGAATTT


Statistics
Matches: 34,  Mismatches: 8, Indels: 10
        0.65            0.15        0.19

Matches are distributed among these distances:
  18    2  0.06
  19    1  0.03
  20    6  0.18
  21   15  0.44
  22    6  0.18
  23    4  0.12

ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50


Consensus pattern (21 bp):   
ATTTGAGTTAAGTATTTCTTA
Done.