Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023773.1 Corchorus olitorius cultivar O-4 contig23806, 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: 4611
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:201 original size:26 final size:28

Alignment explanation


    Indices: 165--222  Score: 84
    Period size: 27  Copynumber: 2.1  Consensus size: 28

        155 GTATATGTTC

                                        
        165 AAAATACATAATTAAC-TTTTATAAAAA
          1 AAAATACATAATTAACTTTTTATAAAAA

                         *       *      
        192 AAAAT-CATAATTGACTTTTTTTAAAAA
          1 AAAATACATAATTAACTTTTTATAAAAA

                
        219 AAAA
          1 AAAA

        223 CTAAAGAAAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  26    9  0.32
  27   19  0.68

ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34


Consensus pattern (28 bp):   
AAAATACATAATTAACTTTTTATAAAAA

Found at i:1155 original size:21 final size:20

Alignment explanation


    Indices: 1125--1163  Score: 60
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       1115 TTTTATTAGA

                         *      
       1125 TTTTTAAAAAAAATATATGT
          1 TTTTTAAAAAAAAAATATGT

                               
       1145 TTTTTAGAAAAAAAAATAT
          1 TTTTTA-AAAAAAAAATAT

       1164 TATTTATTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41


Consensus pattern (20 bp):   
TTTTTAAAAAAAAAATATGT

Found at i:1523 original size:15 final size:16

Alignment explanation


    Indices: 1490--1530  Score: 59
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       1480 AATTTTTCAA

                            
       1490 ATTTTTTAAAGAAATT
          1 ATTTTTTAAAGAAATT

                             
       1506 ATTTTTTGAAA-AAA-T
          1 ATTTTTT-AAAGAAATT

                      
       1521 ATTTTTTAAA
          1 ATTTTTTAAA

       1531 TAAAAAAAGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  14    3  0.12
  15    8  0.33
  16   10  0.42
  17    3  0.12

ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51


Consensus pattern (16 bp):   
ATTTTTTAAAGAAATT

Found at i:1535 original size:16 final size:15

Alignment explanation


    Indices: 1490--1535  Score: 56
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       1480 AATTTTTCAA

                          * 
       1490 ATTTTTTAAAGAAATT
          1 ATTTTTTAAA-AAAAT

                   *       
       1506 ATTTTTTGAAAAAAT
          1 ATTTTTTAAAAAAAT

                           
       1521 ATTTTTTAAATAAAA
          1 ATTTTTTAAA-AAAA

       1536 AAAGTGATGT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  15   13  0.50
  16   13  0.50

ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48


Consensus pattern (15 bp):   
ATTTTTTAAAAAAAT

Found at i:3170 original size:12 final size:12

Alignment explanation


    Indices: 3153--3185  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       3143 TCCCATTTCC

                    *   
       3153 AGGAAAATTATT
          1 AGGAAAATAATT

                        
       3165 AGGAAAATAATT
          1 AGGAAAATAATT

                     
       3177 AGGAAAATA
          1 AGGAAAATA

       3186 TATCTTGATG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24


Consensus pattern (12 bp):   
AGGAAAATAATT
Done.