Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004589.1 Corchorus capsularis cultivar CVL-1 contig04600, 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: 3797
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34


Found at i:96 original size:29 final size:29

Alignment explanation


    Indices: 63--120  Score: 116
    Period size: 29  Copynumber: 2.0  Consensus size: 29

         53 CCCTCGCGGA

                                         
         63 GAATCTCGCCTTCAATATGCCCGAGGATG
          1 GAATCTCGCCTTCAATATGCCCGAGGATG

                                         
         92 GAATCTCGCCTTCAATATGCCCGAGGATG
          1 GAATCTCGCCTTCAATATGCCCGAGGATG

        121 AAAAGGGAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24


Consensus pattern (29 bp):   
GAATCTCGCCTTCAATATGCCCGAGGATG

Found at i:947 original size:24 final size:24

Alignment explanation


    Indices: 902--947  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

        892 AGGAAAAATC

                          *         
        902 AGTAAAACCAAGATCATAAATCAT
          1 AGTAAAACCAAGATAATAAATCAT

                   *         *    
        926 AGTAAAATCAAGATAATCAATC
          1 AGTAAAACCAAGATAATAAATC

        948 CAAAACCAAG


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22


Consensus pattern (24 bp):   
AGTAAAACCAAGATAATAAATCAT

Found at i:1720 original size:17 final size:18

Alignment explanation


    Indices: 1698--1736  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1688 TTTTTCCTTT

                     *        
       1698 TTCCC-TTTGTTTTTCTC
          1 TTCCCTTTTCTTTTTCTC

                             *
       1715 TTCCCTTTTCTTTTTCTT
          1 TTCCCTTTTCTTTTTCTC

                
       1733 TTCC
          1 TTCC

       1737 TTCAAATTGG


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

Matches are distributed among these distances:
  17    5  0.26
  18   14  0.74

ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67


Consensus pattern (18 bp):   
TTCCCTTTTCTTTTTCTC

Found at i:1935 original size:5 final size:5

Alignment explanation


    Indices: 1891--1933  Score: 79
    Period size: 5  Copynumber: 8.8  Consensus size: 5

       1881 AAATGGCCCT

                                                                
       1891 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTTT
          1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT

       1934 TTGGGCTGTT


Statistics
Matches: 38,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   4    4  0.11
   5   34  0.89

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (5 bp):   
TTTTC

Found at i:2937 original size:5 final size:6

Alignment explanation


    Indices: 2889--2944  Score: 58
    Period size: 6  Copynumber: 8.7  Consensus size: 6

       2879 GCGAAACTTT

                                              *        *               
       2889 AAAATA AAAATA AAAATAGA AAACATA AATGATA AAAAGA AAAATA AAAATA
          1 AAAATA AAAATA AAAAT--A AAA-ATA AA-AATA AAAATA AAAATA AAAATA

                
       2941 AAAA
          1 AAAA

       2945 AGCGATCTCA


Statistics
Matches: 42,  Mismatches: 4, Indels: 8
        0.78            0.07        0.15

Matches are distributed among these distances:
   6   28  0.67
   7    8  0.19
   8    4  0.10
   9    2  0.05

ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14


Consensus pattern (6 bp):   
AAAATA
Done.