Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018314.1 Corchorus olitorius cultivar O-4 contig18347, 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: 6692
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:917 original size:25 final size:25

Alignment explanation


    Indices: 839--905  Score: 125
    Period size: 25  Copynumber: 2.7  Consensus size: 25

        829 ACATAAAATT

                                     
        839 ATATTTTAATAATGACATAATTAAA
          1 ATATTTTAATAATGACATAATTAAA

               *                     
        864 ATAATTTAATAATGACATAATTAAA
          1 ATATTTTAATAATGACATAATTAAA

                             
        889 ATATTTTAATAATGACA
          1 ATATTTTAATAATGACA

        906 ATTTAGAAAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  25   40  1.00

ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39


Consensus pattern (25 bp):   
ATATTTTAATAATGACATAATTAAA

Found at i:1105 original size:23 final size:23

Alignment explanation


    Indices: 1079--1152  Score: 98
    Period size: 24  Copynumber: 3.3  Consensus size: 23

       1069 GATAACCTAA

                                   
       1079 CTATGAAATTTTAATAAACCTTC
          1 CTATGAAATTTTAATAAACCTTC

                *                   
       1102 CTATAAAATTTTTAATAAACCTTC
          1 CTATGAAA-TTTTAATAAACCTTC

            *            *         
       1126 TTATGAAATTTT-GT-AACCTTC
          1 CTATGAAATTTTAATAAACCTTC

                  
       1147 CTATGA
          1 CTATGA

       1153 TTTTTGATAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  21   12  0.27
  22    1  0.02
  23   11  0.24
  24   21  0.47

ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42


Consensus pattern (23 bp):   
CTATGAAATTTTAATAAACCTTC

Found at i:1145 original size:21 final size:21

Alignment explanation


    Indices: 1119--1181  Score: 67
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       1109 ATTTTTAATA

                                 
       1119 AACCTTCTTATGAAATTTTGT
          1 AACCTTCTTATGAAATTTTGT

                   *      *       
       1140 AACCTTCCTATG-ATTTTTGAT
          1 AACCTTCTTATGAAATTTTG-T

                          *       
       1161 AACC-TCTCTATGAGATTTTGT
          1 AACCTTCT-TATGAAATTTTGT

       1182 TAATTTCCCT


Statistics
Matches: 34,  Mismatches: 5, Indels: 6
        0.76            0.11        0.13

Matches are distributed among these distances:
  20    8  0.24
  21   21  0.62
  22    5  0.15

ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46


Consensus pattern (21 bp):   
AACCTTCTTATGAAATTTTGT

Found at i:4739 original size:17 final size:15

Alignment explanation


    Indices: 4705--4753  Score: 62
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       4695 ATTTGAAGTG

                           
       4705 AAATATATGTTTTGT
          1 AAATATATGTTTTGT

                             
       4720 AAATATATGCTTTTGAT
          1 AAATATATG-TTTTG-T

                  *    *   
       4737 AAATATTTGTTATGT
          1 AAATATATGTTTTGT

              
       4752 AA
          1 AA

       4754 GTTGAGCAGA


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  15   12  0.40
  16    9  0.30
  17    9  0.30

ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49


Consensus pattern (15 bp):   
AAATATATGTTTTGT

Found at i:5543 original size:16 final size:16

Alignment explanation


    Indices: 5509--5547  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       5499 GTAGATGTTA

                      * *   
       5509 TTTGTTTCTACAGTAG
          1 TTTGTTTCTAAACTAG

                          * 
       5525 TTTGTTTCTAAACTTG
          1 TTTGTTTCTAAACTAG

                   
       5541 TTTGTTT
          1 TTTGTTT

       5548 ATTTTTATTG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59


Consensus pattern (16 bp):   
TTTGTTTCTAAACTAG
Done.