Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001125.1 Corchorus capsularis cultivar CVL-1 contig01125, 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: 2435
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:1756 original size:7 final size:7

Alignment explanation


    Indices: 1746--1772  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

       1736 GAGGTGAGAT

                   
       1746 ATATGTC
          1 ATATGTC

                   
       1753 ATATGTC
          1 ATATGTC

                   
       1760 ATATGTC
          1 ATATGTC

                  
       1767 ATATGT
          1 ATATGT

       1773 GGATGGTTTG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44


Consensus pattern (7 bp):   
ATATGTC

Found at i:1852 original size:49 final size:49

Alignment explanation


    Indices: 1780--1879  Score: 200
    Period size: 49  Copynumber: 2.0  Consensus size: 49

       1770 TGTGGATGGT

                                                             
       1780 TTGCTTTGCCAAATTGCATGGCCATTAATTGCTCTTGCTATTCTAGCTA
          1 TTGCTTTGCCAAATTGCATGGCCATTAATTGCTCTTGCTATTCTAGCTA

                                                             
       1829 TTGCTTTGCCAAATTGCATGGCCATTAATTGCTCTTGCTATTCTAGCTA
          1 TTGCTTTGCCAAATTGCATGGCCATTAATTGCTCTTGCTATTCTAGCTA

              
       1878 TT
          1 TT

       1880 CTAGATGAAG


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   51  1.00

ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42


Consensus pattern (49 bp):   
TTGCTTTGCCAAATTGCATGGCCATTAATTGCTCTTGCTATTCTAGCTA

Found at i:2171 original size:21 final size:22

Alignment explanation


    Indices: 2145--2187  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       2135 ATTAAGGGGA

                                  
       2145 TTACTAAATACCGCCC-CCTTT
          1 TTACTAAATACCGCCCTCCTTT

                  **              
       2166 TTACTAGGTACCGCCCTCCTTT
          1 TTACTAAATACCGCCCTCCTTT

       2188 AGACAATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35


Consensus pattern (22 bp):   
TTACTAAATACCGCCCTCCTTT
Done.