Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023069.1 Corchorus olitorius cultivar O-4 contig23102, 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: 10370
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:3881 original size:60 final size:60

Alignment explanation


    Indices: 3817--3979  Score: 236
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       3807 ACTAATTGCT

                          **     *                   * **   *           
       3817 CAAATAAGGGTCTACCGTTTGTCAAAATGCTCAAATAAGGGGCTGATCTTTTAATTTGGC
          1 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCAATCATTTAATTTGGC

                                                   *                    
       3877 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGAGCCCAATCATTTAATTTGGC
          1 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCAATCATTTAATTTGGC

            *         *                                
       3937 AAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCC
          1 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGCC

       3980 TGGCGTCGAA


Statistics
Matches: 92,  Mismatches: 11, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  60   92  1.00

ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28


Consensus pattern (60 bp):   
CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCAATCATTTAATTTGGC

Found at i:3976 original size:31 final size:30

Alignment explanation


    Indices: 3813--3980  Score: 103
    Period size: 31  Copynumber: 5.6  Consensus size: 30

       3803 TTTGACTAAT

                          *   **           
       3813 TGCTCAAATAAGGGTCTACCGTTTGTCAAAA
          1 TGCTCAAATAAGGGCCTAATGTTTG-CAAAA

                          *  *  *    *  **
       3844 TGCTCAAATAAGGGGCTGATCTTT-TAATT
          1 TGCTCAAATAAGGGCCTAATGTTTGCAAAA

                           *                
       3873 TGGC-CAAATAAGGGTCTAATGTTTGCCAAAA
          1 T-GCTCAAATAAGGGCCTAATGTTTG-CAAAA

                        *   *    *       **
       3904 TGCTCAAATAAGAGCCCAATCATTT--AATT
          1 TGCTCAAATAAGGGCCTAAT-GTTTGCAAAA

                 *                          
       3933 TGGC-AAAATAAGGGCCTAATGTTTGCCAAAA
          1 T-GCTCAAATAAGGGCCTAATGTTTG-CAAAA

                             
       3964 TGCTCAAATAAGGGCCT
          1 TGCTCAAATAAGGGCCT

       3981 GGCGTCGAAA


Statistics
Matches: 100,  Mismatches: 27, Indels: 20
        0.68            0.18        0.14

Matches are distributed among these distances:
  28    3  0.03
  29   36  0.36
  30    8  0.08
  31   50  0.50
  32    3  0.03

ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29


Consensus pattern (30 bp):   
TGCTCAAATAAGGGCCTAATGTTTGCAAAA

Found at i:4055 original size:31 final size:29

Alignment explanation


    Indices: 4017--4184  Score: 119
    Period size: 31  Copynumber: 5.6  Consensus size: 29

       4007 CAAACTGATC

                                           
       4017 AGGCCCTTATTTGAGCATTTTCAATAACGTT
          1 AGGCCCTTATTTGAGCATTTT-AA-AACGTT

                              ***      *  
       4048 AGGCCCTTATTTG-GTCAAAATAAAACATT
          1 AGGCCCTTATTTGAG-CATTTTAAAACGTT

                                     *      
       4077 -GAGCCCTTATTTGAGCATTTTCGATAACGTT
          1 AG-GCCCTTATTTGAGCATTTT--AAAACGTT

                 *            **          *
       4108 AGGCCTTTATTTG-GCCAAATTAAAA-GATC
          1 AGGCCCTTATTTGAG-CATTTTAAAACG-TT

            *                              
       4137 GGGCCCTTATTTGAGCATTTTGGAAAACGTT
          1 AGGCCCTTATTTGAGCATTTT--AAAACGTT

                   *         
       4168 AGGCCCTAATTTGAGCA
          1 AGGCCCTTATTTGAGCA

       4185 ATTAGCCGTA


Statistics
Matches: 104,  Mismatches: 21, Indels: 24
        0.70            0.14        0.16

Matches are distributed among these distances:
  28    2  0.02
  29   38  0.37
  30    6  0.06
  31   56  0.54
  32    2  0.02

ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Consensus pattern (29 bp):   
AGGCCCTTATTTGAGCATTTTAAAACGTT

Found at i:4112 original size:60 final size:60

Alignment explanation


    Indices: 4019--4180  Score: 234
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       4009 AACTGATCAG

                                *                      *             *  
       4019 GCCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGTCAAAATAAAACATTGA
          1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAAATAAAACATCGA

                                              *             *     *    *
       4079 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCTTTATTTGGCCAAATTAAAAGATCGG
          1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAAATAAAACATCGA

                               *  *             *     
       4139 GCCCTTATTTGAGCATTTTGGAAAACGTTAGGCCCTAATTTG
          1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTG

       4181 AGCAATTAGC


Statistics
Matches: 91,  Mismatches: 11, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  60   91  1.00

ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35


Consensus pattern (60 bp):   
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAAATAAAACATCGA
Done.