Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023393.1 Corchorus olitorius cultivar O-4 contig23426, 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: 11713
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30


Found at i:1758 original size:33 final size:33

Alignment explanation


    Indices: 1716--1779  Score: 119
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       1706 AGAATTTGTT

                                             
       1716 TCATCACAAACAACACCTAAAACAGATTTAGTG
          1 TCATCACAAACAACACCTAAAACAGATTTAGTG

                           *               
       1749 TCATCACAAACAACATCTAAAACAGATTTAG
          1 TCATCACAAACAACACCTAAAACAGATTTAG

       1780 AATTACTCTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.47, C:0.23, G:0.08, T:0.22


Consensus pattern (33 bp):   
TCATCACAAACAACACCTAAAACAGATTTAGTG

Found at i:3354 original size:25 final size:24

Alignment explanation


    Indices: 3317--3363  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       3307 CTTGAAAATT

                                      
       3317 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       3343 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       3364 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:4115 original size:20 final size:21

Alignment explanation


    Indices: 4073--4115  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4063 TCCTTTGTAG

                                 
       4073 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGGGCTTCAA

                     *        *  
       4094 ATGATCTCCGAT-GGCTTTAA
          1 ATGATCTCCAATGGGCTTCAA

              
       4114 AT
          1 AT

       4116 TCTTCAAGAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33


Consensus pattern (21 bp):   
ATGATCTCCAATGGGCTTCAA

Found at i:4921 original size:76 final size:76

Alignment explanation


    Indices: 4770--4913  Score: 166
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       4760 ACAAGGACCC

                       *                   *                   * *      *    
       4770 CGACTCCACCTGGGCGCCCACATGGTTGCCTTAAGCACCCATGTGGTTTGCTTGAGAACCCAGAT
          1 CGACTCCACCTAGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTAAGAACCAAGAT

                       
       4835 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                           **      
       4846 CGACTCCAGCTAGGTGCCCACATGGTTTGTCTGAAG-ACCCATGT-GTTTCGCCTAATCACCAAG
          1 CGACTCCACCTAGGCGCCCACATGG-TTGCCTGAAGCACCCATGTGGTTT-GCCTAAGAACCAAG

                 
       4909 ATGGG
         64 ATGGG

       4914 TTGTGTCATA


Statistics
Matches: 56,  Mismatches: 10, Indels: 4
        0.80            0.14        0.06

Matches are distributed among these distances:
  75    4  0.07
  76   44  0.79
  77    8  0.14

ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTAGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTAAGAACCAAGAT
GGGCAGTGTCA

Found at i:10137 original size:29 final size:29

Alignment explanation


    Indices: 10104--10161  Score: 107
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      10094 CTCCAAATCT

                                         
      10104 TCAACAATTCTTCAAAATAAAATCTCTAG
          1 TCAACAATTCTTCAAAATAAAATCTCTAG

                        *                
      10133 TCAACAATTCTTTAAAATAAAATCTCTAG
          1 TCAACAATTCTTCAAAATAAAATCTCTAG

      10162 ATCTACATAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33


Consensus pattern (29 bp):   
TCAACAATTCTTCAAAATAAAATCTCTAG

Found at i:10178 original size:29 final size:29

Alignment explanation


    Indices: 10104--10178  Score: 80
    Period size: 29  Copynumber: 2.6  Consensus size: 29

      10094 CTCCAAATCT

                    * *                  
      10104 TCAACAATTCTTCAAAATAAAATCTCTAG
          1 TCAACAATACATCAAAATAAAATCTCTAG

                    * * *                
      10133 TCAACAATTCTTTAAAATAAAATCTCTAG
          1 TCAACAATACATCAAAATAAAATCTCTAG

               *              
      10162 ATCTAC-ATACATCAAAA
          1 -TCAACAATACATCAAAA

      10179 ACCTAAACCT


Statistics
Matches: 40,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  29   36  0.90
  30    4  0.10

ACGTcount: A:0.47, C:0.20, G:0.03, T:0.31


Consensus pattern (29 bp):   
TCAACAATACATCAAAATAAAATCTCTAG
Done.