Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022954.1 Corchorus olitorius cultivar O-4 contig22987, 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: 6026
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36


Found at i:134 original size:72 final size:72

Alignment explanation


    Indices: 1--135  Score: 216
    Period size: 72  Copynumber: 1.9  Consensus size: 72

                                                                    *        
          1 AATTTTATACTTCCTTATGTTGCATTAAGATTAGTTATAAATTATAACCTTATAACTAAATTTTG
          1 AATTTTATACTTCCTTATGTTGCATTAAGATTAGTTATAAATTATAACCTTATAACGAAATTTTG

                   
         66 TACACCT
         66 TACACCT

                        *                *          *             **       
         73 AATTTTATACTTTCTTATGTTGCATTAAGTTTAGTTATAAGTTATAACCTTATATGGAAATTT
          1 AATTTTATACTTCCTTATGTTGCATTAAGATTAGTTATAAATTATAACCTTATAACGAAATTT

        136 GACTTACAGG


Statistics
Matches: 57,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  72   57  1.00

ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47


Consensus pattern (72 bp):   
AATTTTATACTTCCTTATGTTGCATTAAGATTAGTTATAAATTATAACCTTATAACGAAATTTTG
TACACCT

Found at i:227 original size:36 final size:36

Alignment explanation


    Indices: 180--249  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        170 GAGATTTTGG

                         *      *               
        180 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
        216 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

        250 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:1621 original size:58 final size:58

Alignment explanation


    Indices: 1523--1632  Score: 159
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       1513 ATCATGCCTC

                 *                   *                                
       1523 GGTCCTAAAACGTCTTTTTTAGACATCTAATAGAAAAACATGTCACTCGATAAGACTT
          1 GGTCCGAAAACGTCTTTTTTAGACACCTAATAGAAAAACATGTCACTCGATAAGACTT

                                  *             *           *    
       1581 GGTCCGAAAACGTCTTTTTTTATACACCTAATA-AAGAACATGTCACTTGATA
          1 GGTCCGAAAACGTC-TTTTTTAGACACCTAATAGAAAAACATGTCACTCGATA

       1633 TTTGATTAAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  58   30  0.65
  59   16  0.35

ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32


Consensus pattern (58 bp):   
GGTCCGAAAACGTCTTTTTTAGACACCTAATAGAAAAACATGTCACTCGATAAGACTT
Done.