Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015699.1 Corchorus capsularis cultivar CVL-1 contig15720, 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: 17505
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:995 original size:202 final size:201

Alignment explanation


    Indices: 607--1205  Score: 1020
    Period size: 202  Copynumber: 3.0  Consensus size: 201

        597 ATGTTTCCAT

                      *          *                   *     *                 
        607 AAAATTTATATAATACACCGTCAGTGGAGTTTAGCAGACTGTACGTGTGGGGTTTAACTTTAAGG
          1 AAAATTTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG

                    *                                                        
        672 GTTGACATATGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
         66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG

                                                                             
        737 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTAGTATTGTATAATAATC
        131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTA-TATTGTATAATAATC

                   
        802 CTATAAG
        195 CTATAAG

                                                                             
        809 AAAATTTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
          1 AAAATTTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG

                                   *                                         
        874 GTTGACATGTGTACCCTTAGGGAGTATGTATTAAGTATTAAATATTTAATTATGAAATGGGGTAT
         66 GTTGACATGTGTACCCTTAGGGAATATGTATTAA-TATTAAATATTTAATTATGAAATGGGGTAT

                                         *                                   
        939 GTGTTAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACACTGACAGTATATTGTATAATAATC
        130 GTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATC

                   
       1004 CTATAAG
        195 CTATAAG

                             *                                               
       1011 AAAATTTATACAATACAACG-TAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
          1 AAAATTTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG

                         *    *                                      * *     
       1075 GTTGACATGTGTATCCTTTGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGTGTATG
         66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG

                     *    *                         *     * *                
       1140 TGTTAACTTTTTAATCCGCTTATGGAGTCCAAAATTTACATTGACATTGTATTGTATAATAATCC
        131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATCC

             
       1205 T
        196 T

       1206 TATTATAAAG


Statistics
Matches: 377,  Mismatches: 19, Indels: 4
        0.94            0.05        0.01

Matches are distributed among these distances:
 200   89  0.24
 201   75  0.20
 202  134  0.36
 203   79  0.21

ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36


Consensus pattern (201 bp):   
AAAATTTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGG
GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATG
TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATCC
TATAAG

Found at i:5600 original size:18 final size:18

Alignment explanation


    Indices: 5577--5620  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       5567 CTCCCAATAT

                      *       
       5577 TTCGAGTCGGGTCATCAA
          1 TTCGAGTCGGATCATCAA

                  *        *  
       5595 TTCGAGCCGGATCATTAA
          1 TTCGAGTCGGATCATCAA

               *    
       5613 TTCAAGTC
          1 TTCGAGTC

       5621 ACTTTAACAA


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30


Consensus pattern (18 bp):   
TTCGAGTCGGATCATCAA

Found at i:6717 original size:30 final size:32

Alignment explanation


    Indices: 6656--6732  Score: 104
    Period size: 31  Copynumber: 2.5  Consensus size: 32

       6646 ATTATTGTCT

                 *            *             
       6656 AATTGTTCAAATAAGGGTTCAACGTTTGTGAA
          1 AATTGCTCAAATAAGGGTCCAACGTTTGTGAA

                        *         *         
       6688 AA-TGCTCAAATCAGGGTCCAATG-TTGTGAA
          1 AATTGCTCAAATAAGGGTCCAACGTTTGTGAA

                           
       6718 AATTGCTCAAATAAG
          1 AATTGCTCAAATAAG

       6733 ACCCTGCCAT


Statistics
Matches: 39,  Mismatches: 5, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  30    9  0.23
  31   28  0.72
  32    2  0.05

ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30


Consensus pattern (32 bp):   
AATTGCTCAAATAAGGGTCCAACGTTTGTGAA

Found at i:14569 original size:24 final size:23

Alignment explanation


    Indices: 14537--14586  Score: 64
    Period size: 24  Copynumber: 2.1  Consensus size: 23

      14527 CATTGGTTAC

                *                   
      14537 ATTTGAATTTAAACTAATAACAAG
          1 ATTTAAATTTAAACTAATAAC-AG

                      *     *      
      14561 ATTTAAATTTGAACTAGTAACAG
          1 ATTTAAATTTAAACTAATAACAG

               
      14584 ATT
          1 ATT

      14587 GTGATAAGGC


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  23    5  0.22
  24   18  0.78

ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36


Consensus pattern (23 bp):   
ATTTAAATTTAAACTAATAACAG
Done.