Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001666.1 Corchorus olitorius cultivar O-4 contig01666, 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, 865

Length: 1442
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35


Found at i:131 original size:11 final size:11

Alignment explanation


    Indices: 117--154  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        107 ATTCATAACA

                       
        117 AATTTATAATT
          1 AATTTATAATT

                       
        128 AATTTATAATT
          1 AATTTATAATT

                        
        139 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
        150 TATTT
          1 AATTT

        155 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:488 original size:15 final size:15

Alignment explanation


    Indices: 448--534  Score: 54
    Period size: 15  Copynumber: 5.8  Consensus size: 15

        438 GTTAATTTAG

                        *   
        448 ACTTATTATTATTATA
          1 ACTTATTATTATGA-A

               *  *        
        464 A-TAATAATTATGAA
          1 ACTTATTATTATGAA

                          **
        478 ACTTATTATTAGTGGT
          1 ACTTATTATTA-TGAA

                  *     *  
        494 A-TTATAATTATTAA
          1 ACTTATTATTATGAA

                           
        508 ACTTATTATTAT-AA
          1 ACTTATTATTATGAA

              *          
        522 TAATTATTATTAT
          1 -ACTTATTATTAT

        535 TAGTGGTATG


Statistics
Matches: 54,  Mismatches: 13, Indels: 9
        0.71            0.17        0.12

Matches are distributed among these distances:
  14    6  0.11
  15   44  0.81
  16    4  0.07

ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51


Consensus pattern (15 bp):   
ACTTATTATTATGAA

Found at i:535 original size:30 final size:30

Alignment explanation


    Indices: 448--536  Score: 108
    Period size: 30  Copynumber: 3.0  Consensus size: 30

        438 GTTAATTTAG

                        *     *        *  
        448 ACTTATTATTATTATAATAATAATTATGAA
          1 ACTTATTATTATAATAATTATAATTATTAA

                         **                
        478 ACTTATTATTAGTGGT-ATTATAATTATTAA
          1 ACTTATTATTA-TAATAATTATAATTATTAA

                                 *       
        508 ACTTATTATTATAATAATTATTATTATTA
          1 ACTTATTATTATAATAATTATAATTATTA

        537 GTGGTATGTA


Statistics
Matches: 50,  Mismatches: 7, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  29    2  0.04
  30   46  0.92
  31    2  0.04

ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51


Consensus pattern (30 bp):   
ACTTATTATTATAATAATTATAATTATTAA
Done.