Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010729.1 Corchorus olitorius cultivar O-4 contig10761, 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: 7559
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32


Found at i:2296 original size:54 final size:54

Alignment explanation


    Indices: 2237--2341  Score: 167
    Period size: 54  Copynumber: 1.9  Consensus size: 54

       2227 AAACTGATCC

                       *  *                                        
       2237 AACCCAGAAATTACTCGAAC-CGATCAACCCGACAAATTAACCCGAAATGACGCA
          1 AACCCA-AAATGACCCGAACACGATCAACCCGACAAATTAACCCGAAATGACGCA

                                              *                
       2291 AACCCAAAATGACCCGAACACGATCAACCCGACAGATTAACCCGAAATGAC
          1 AACCCAAAATGACCCGAACACGATCAACCCGACAAATTAACCCGAAATGAC

       2342 CCGAATTAAA


Statistics
Matches: 47,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  53   11  0.23
  54   36  0.77

ACGTcount: A:0.43, C:0.32, G:0.13, T:0.11


Consensus pattern (54 bp):   
AACCCAAAATGACCCGAACACGATCAACCCGACAAATTAACCCGAAATGACGCA

Found at i:3538 original size:15 final size:15

Alignment explanation


    Indices: 3518--3549  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3508 TATAGTAAAA

                           
       3518 ATTTAATATAAAGTT
          1 ATTTAATATAAAGTT

                           
       3533 ATTTAATATAAAGTT
          1 ATTTAATATAAAGTT

              
       3548 AT
          1 AT

       3550 CAAACAAATG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47


Consensus pattern (15 bp):   
ATTTAATATAAAGTT

Found at i:5534 original size:21 final size:21

Alignment explanation


    Indices: 5488--5534  Score: 51
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       5478 AATTTATTAT

                        *       *
       5488 ATAAGTTAAATATTAAATATG
          1 ATAAGTTAAATAATAAATATA

            *                     
       5509 CTAAGTTAAATAAT-AATAATA
          1 ATAAGTTAAATAATAAAT-ATA

                 
       5530 ATAAG
          1 ATAAG

       5535 CATATATTTA


Statistics
Matches: 21,  Mismatches: 4, Indels: 2
        0.78            0.15        0.07

Matches are distributed among these distances:
  20    3  0.14
  21   18  0.86

ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34


Consensus pattern (21 bp):   
ATAAGTTAAATAATAAATATA

Found at i:7530 original size:2 final size:2

Alignment explanation


    Indices: 7525--7559  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       7515 ATAAGAAAAC

                                                                
       7525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.