Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016013.1 Corchorus capsularis cultivar CVL-1 contig16034, 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: 23353
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


Found at i:4148 original size:28 final size:29

Alignment explanation


    Indices: 4116--4190  Score: 89
    Period size: 30  Copynumber: 2.6  Consensus size: 29

       4106 ATTTGTAGCA

                                   *   * 
       4116 TTTGGATGTTTTGCCCCTGAA-CTTCACT
          1 TTTGGATGTTTTGCCCCTGAACCATCAAT

                   *         *            
       4144 TTTGGATATTTTGCGCCTTGAACCATCAAT
          1 TTTGGATGTTTTGC-CCCTGAACCATCAAT

                  *          
       4174 TTTGGACGTTTTGCCCC
          1 TTTGGATGTTTTGCCCC

       4191 ATTTCAAGCG


Statistics
Matches: 38,  Mismatches: 7, Indels: 3
        0.79            0.15        0.06

Matches are distributed among these distances:
  28   13  0.34
  29    8  0.21
  30   17  0.45

ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41


Consensus pattern (29 bp):   
TTTGGATGTTTTGCCCCTGAACCATCAAT

Found at i:18117 original size:2 final size:2

Alignment explanation


    Indices: 18110--18136  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      18100 ATTAATTTAC

                                                    
      18110 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 T

      18137 CCTTACTGAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:20054 original size:21 final size:20

Alignment explanation


    Indices: 20017--20055  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      20007 TTTAGAAGCA

                       *        
      20017 ATTAATTAAAAGCATTAAAC
          1 ATTAATTAAAAACATTAAAC

                               
      20037 ATTAATTAAAAACAATTAA
          1 ATTAATTAAAAAC-ATTAA

      20056 GGAAGGGAGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31


Consensus pattern (20 bp):   
ATTAATTAAAAACATTAAAC

Found at i:20700 original size:16 final size:15

Alignment explanation


    Indices: 20670--20708  Score: 69
    Period size: 16  Copynumber: 2.5  Consensus size: 15

      20660 GTGGTGGTAA

                           
      20670 ATTATCATTATTATC
          1 ATTATCATTATTATC

                            
      20685 ATTATCATTAATTATC
          1 ATTATCATT-ATTATC

                    
      20701 ATTATCAT
          1 ATTATCAT

      20709 AATGACAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15    9  0.39
  16   14  0.61

ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51


Consensus pattern (15 bp):   
ATTATCATTATTATC
Done.