Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011964.1 Corchorus capsularis cultivar CVL-1 contig11985, 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: 7893
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36


Found at i:4953 original size:21 final size:23

Alignment explanation


    Indices: 4929--4970  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       4919 ATAATCATCA

                          *        
       4929 TATAT-GA-TATATTTATATATT
          1 TATATGGAGTATATATATATATT

                                 
       4950 TATATGGAGTATATATATATA
          1 TATATGGAGTATATATATATA

       4971 CATATATATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    5  0.28
  22    2  0.11
  23   11  0.61

ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50


Consensus pattern (23 bp):   
TATATGGAGTATATATATATATT

Found at i:4976 original size:23 final size:21

Alignment explanation


    Indices: 4927--4982  Score: 60
    Period size: 23  Copynumber: 2.6  Consensus size: 21

       4917 TAATAATCAT

                          *      
       4927 CATATATGATATATTTATATA
          1 CATATATGATATATATATATA

            **                     
       4948 TTTATATGGAGTATATATATATA
          1 CATATAT-GA-TATATATATATA

                         
       4971 CATATAT-ATATA
          1 CATATATGATATA

       4983 CTAATAATTC


Statistics
Matches: 28,  Mismatches: 5, Indels: 5
        0.74            0.13        0.13

Matches are distributed among these distances:
  20    4  0.14
  21    6  0.21
  22    2  0.07
  23   16  0.57

ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46


Consensus pattern (21 bp):   
CATATATGATATATATATATA

Found at i:7220 original size:2 final size:2

Alignment explanation


    Indices: 7213--7244  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       7203 AAGTCTGAAC

                                                           
       7213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7245 TTTACATCAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.