Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015889.1 Corchorus capsularis cultivar CVL-1 contig15910, 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: 18376
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:3731 original size:23 final size:23

Alignment explanation


    Indices: 3705--3750  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3695 CTTCCTATCG

                                   
       3705 ACGCACTCCTAAGAGAATTAGAT
          1 ACGCACTCCTAAGAGAATTAGAT

                                   
       3728 ACGCACTCCTAAGAGAATTAGAT
          1 ACGCACTCCTAAGAGAATTAGAT

       3751 CTAGGTTATG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22


Consensus pattern (23 bp):   
ACGCACTCCTAAGAGAATTAGAT

Found at i:16263 original size:204 final size:202

Alignment explanation


    Indices: 15897--16310  Score: 620
    Period size: 204  Copynumber: 2.1  Consensus size: 202

      15887 ACTTTTTTAA

                                         **                                  
      15897 TATTAATA--TGGGTTTATATATAATACATTGTCAGTGGAGTTTAACAGACTGCACAAACGGATC
          1 TATTAATATTTGGGTTTATATATAATACACCGTCAGTGGAGTTTAACAGACTGCACAAACGGATC

                                                              *      *       
      15960 TTGAAGGGTGACATGTGTCCCCTAGGGAATAGATTGAAATATTTAAAATTTAATTAATTCAGAAA
         66 TTGAAGGGTGACATGTGTCCCCTAGGGAATAGATTGAAATATTTAAAATTAAATTAACTCAGAAA

                 *                   * *                                     
      16025 AAGGATATGTGTCAACTCCACAACCTGTTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAA
        131 AAGGACATGTGTCAACTCCACAACCCGCTTGTGGAGT-CAAAATTTACACCGCCGGTGTATCAAA

                     
      16090 TAATTACCC
        195 TAATTA-CC

                                   *          *          *    *  *    *      
      16099 TATTAATATTTGGGTTTATATATGATACACCGTCGGTGGAGTTTAGCAGATTGTACAAGCAGG-T
          1 TATTAATATTTGGGTTTATATATAATACACCGTCAGTGGAGTTTAACAGACTGCACAAAC-GGAT

                                  *      *                                   
      16163 CTTGAAGGGTGACATGTGTCCCTTAGGGATTAGATTGAAATATTTAAAATTAAATTAACTCAGAA
         65 CTTGAAGGGTGACATGTGTCCCCTAGGGAATAGATTGAAATATTTAAAATTAAATTAACTCAGAA

              *                                                 *            
      16228 AATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCAAAATTTACACCGTCGGTGTATCAAA
        130 AAAGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCAAAATTTACACCGCCGGTGTATCAAA

                    
      16293 TAATTACC
        195 TAATTACC

                       
      16301 T-TTAATATTT
          1 TATTAATATTT

      16311 AGTTAATTAA


Statistics
Matches: 192,  Mismatches: 17, Indels: 7
        0.89            0.08        0.03

Matches are distributed among these distances:
 201    9  0.05
 202   11  0.06
 203   32  0.17
 204  138  0.72
 205    2  0.01

ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32


Consensus pattern (202 bp):   
TATTAATATTTGGGTTTATATATAATACACCGTCAGTGGAGTTTAACAGACTGCACAAACGGATC
TTGAAGGGTGACATGTGTCCCCTAGGGAATAGATTGAAATATTTAAAATTAAATTAACTCAGAAA
AAGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCAAAATTTACACCGCCGGTGTATCAAAT
AATTACC

Found at i:17735 original size:60 final size:59

Alignment explanation


    Indices: 17596--17735  Score: 172
    Period size: 60  Copynumber: 2.3  Consensus size: 59

      17586 ACTGACATCA

                               *      *     *           *          *   
      17596 GGCCCTTATTTGAGCATTTGCGATAATGTTAGTCCCTTATTTGGTCAAATTAAAAGATC
          1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAAATC

                           *     *                                     *
      17655 GGACCCTTATTTGAGTATTTTTGATAACGTTAGACCCTTATTTGGCCAAATTAAAAAATT
          1 GG-CCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAAATC

                        * *      
      17715 GTGCCCTTATTTAAACATTTT
          1 G-GCCCTTATTTGAGCATTTT

      17736 AACAAACGTT


Statistics
Matches: 68,  Mismatches: 11, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  59    2  0.03
  60   65  0.96
  61    1  0.01

ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39


Consensus pattern (59 bp):   
GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAAATC

Found at i:17744 original size:60 final size:60

Alignment explanation


    Indices: 17623--17758  Score: 141
    Period size: 60  Copynumber: 2.3  Consensus size: 60

      17613 TTGCGATAAT

                 *           *          *               * **      * *   
      17623 GTTAGTCCCTTATTTGGTCAAATTAAAAGATCGGACCCTTATTTGAGTATTTTTGATAAC
          1 GTTAGACCCTTATTTGGCCAAATTAAAAAATCGGACCCTTATTTAAACATTTTTAAAAAC

                                           *                              
      17683 GTTAGACCCTTATTTGGCCAAATTAAAAAATTGTG-CCCTTATTTAAACA-TTTTAACAAAC
          1 GTTAGACCCTTATTTGGCCAAATTAAAAAATCG-GACCCTTATTTAAACATTTTTAA-AAAC

                 **         
      17743 GTTAGGTCCTTATTTG
          1 GTTAGACCCTTATTTG

      17759 AACAATTAAC


Statistics
Matches: 63,  Mismatches: 11, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  59    5  0.08
  60   57  0.90
  61    1  0.02

ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39


Consensus pattern (60 bp):   
GTTAGACCCTTATTTGGCCAAATTAAAAAATCGGACCCTTATTTAAACATTTTTAAAAAC
Done.