Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009013.1 Corchorus capsularis cultivar CVL-1 contig09034, 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: 4769
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39


Found at i:1688 original size:28 final size:25

Alignment explanation


    Indices: 1655--1727  Score: 78
    Period size: 24  Copynumber: 2.9  Consensus size: 25

       1645 AGCAATTACT

                           *            
       1655 TATTAATTAATGAATTTTCACTCTTATA
          1 TATTAATTAATGAA-CTTCA-T-TTATA

                             *       
       1683 TATTAATTAATG-ACTTGATTTATA
          1 TATTAATTAATGAACTTCATTTATA

                             *    
       1707 TATTAATTAATG-ACTTGATTT
          1 TATTAATTAATGAACTTCATTT

       1728 GATTTGAATA


Statistics
Matches: 43,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   26  0.60
  25    1  0.02
  26    3  0.07
  27    1  0.02
  28   12  0.28

ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51


Consensus pattern (25 bp):   
TATTAATTAATGAACTTCATTTATA

Found at i:1739 original size:29 final size:24

Alignment explanation


    Indices: 1678--1727  Score: 100
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       1668 ATTTTCACTC

                                    
       1678 TTATATATTAATTAATGACTTGAT
          1 TTATATATTAATTAATGACTTGAT

                                    
       1702 TTATATATTAATTAATGACTTGAT
          1 TTATATATTAATTAATGACTTGAT

              
       1726 TT
          1 TT

       1728 GATTTGAATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52


Consensus pattern (24 bp):   
TTATATATTAATTAATGACTTGAT

Found at i:2847 original size:43 final size:45

Alignment explanation


    Indices: 2799--2886  Score: 117
    Period size: 47  Copynumber: 2.0  Consensus size: 45

       2789 TTAAATTCCA

                                       *         *       
       2799 ATGTAA-TTTTATT-ATATATCCTCAATTTTGGCAATTAGTATTG
          1 ATGTAATTTTTATTAATATATCCTCAAATTTGGCAATAAGTATTG

                                   *                     
       2842 ATGTAATTTTTTATTACATATATTCTCAAATTTGGCAATAAGTAT
          1 ATGTAA-TTTTTATTA-ATATATCCTCAAATTTGGCAATAAGTAT

       2887 CAATATTGTA


Statistics
Matches: 38,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  43    6  0.16
  45    7  0.18
  47   25  0.66

ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48


Consensus pattern (45 bp):   
ATGTAATTTTTATTAATATATCCTCAAATTTGGCAATAAGTATTG

Found at i:4220 original size:26 final size:26

Alignment explanation


    Indices: 4165--4223  Score: 66
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       4155 GAAACATTAC

                *       *           **
       4165 TAAAATTTCTAACAATGTAGTGTTTC
          1 TAAATTTTCTAAAAATGTAGTGTTAA

                                       
       4191 TAAATTTTCTAAAAATGTGAG-GTTAA
          1 TAAATTTTCTAAAAATGT-AGTGTTAA

                   
       4217 TAAATTT
          1 TAAATTT

       4224 ATGTAGAAAC


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  26   26  0.93
  27    2  0.07

ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42


Consensus pattern (26 bp):   
TAAATTTTCTAAAAATGTAGTGTTAA
Done.