Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006828.1 Corchorus olitorius cultivar O-4 contig06853, 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: 1744
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34


Found at i:469 original size:12 final size:12

Alignment explanation


    Indices: 454--499  Score: 53
    Period size: 12  Copynumber: 4.0  Consensus size: 12

        444 AATTATTCTA

                        
        454 ATATAATATATT
          1 ATATAATATATT

                        
        466 ATATAATA-A-T
          1 ATATAATATATT

                      *  
        476 A-ATAATAATCTT
          1 ATATAAT-ATATT

                        
        488 ATATAATATATT
          1 ATATAATATATT

        500 GTCTTGATAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 8
        0.74            0.05        0.21

Matches are distributed among these distances:
   9    5  0.18
  10    3  0.11
  11    1  0.04
  12   14  0.50
  13    5  0.18

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46


Consensus pattern (12 bp):   
ATATAATATATT

Found at i:484 original size:29 final size:30

Alignment explanation


    Indices: 421--498  Score: 72
    Period size: 29  Copynumber: 2.7  Consensus size: 30

        411 ATAATTATTC

                           *            * 
        421 TAAT-ATATAATATAGTAT-TAAATAATTA
          1 TAATAATATAATATAATATATAAATAATAA

             **            *              
        449 TTCTAATATAATATATTATAT-AATAATAA
          1 TAATAATATAATATAATATATAAATAATAA

                   * *           
        478 TAATAATCTTATATAATATAT
          1 TAATAATATAATATAATATAT

        499 TGTCTTGATA


Statistics
Matches: 39,  Mismatches: 9, Indels: 3
        0.76            0.18        0.06

Matches are distributed among these distances:
  28    2  0.05
  29   36  0.92
  30    1  0.03

ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45


Consensus pattern (30 bp):   
TAATAATATAATATAATATATAAATAATAA

Found at i:492 original size:22 final size:20

Alignment explanation


    Indices: 452--495  Score: 61
    Period size: 22  Copynumber: 2.1  Consensus size: 20

        442 ATAATTATTC

                                
        452 TAATATAATATATTATATAA
          1 TAATATAATATATTATATAA

                         *        
        472 TAATAATAATAATCTTATATAA
          1 TAAT-ATAAT-ATATTATATAA

              
        494 TA
          1 TA

        496 TATTGTCTTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    4  0.19
  21    5  0.24
  22   12  0.57

ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43


Consensus pattern (20 bp):   
TAATATAATATATTATATAA

Found at i:492 original size:34 final size:36

Alignment explanation


    Indices: 421--499  Score: 99
    Period size: 34  Copynumber: 2.2  Consensus size: 36

        411 ATAATTATTC

                    *     *  *          *       
        421 TAATATATAATATAGTATTAAATAATTATTCTAATA
          1 TAATATATTATATAATAATAAATAATTAATCTAATA

                                            *   
        457 TAATATATTATATAATAAT-AATAA-TAATCTTATA
          1 TAATATATTATATAATAATAAATAATTAATCTAATA

                     
        491 TAATATATT
          1 TAATATATT

        500 GTCTTGATAA


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  34   17  0.45
  35    5  0.13
  36   16  0.42

ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46


Consensus pattern (36 bp):   
TAATATATTATATAATAATAAATAATTAATCTAATA
Done.