Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005991.1 Corchorus capsularis cultivar CVL-1 contig06009, 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: 5862
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32


Found at i:1734 original size:17 final size:17

Alignment explanation


    Indices: 1712--1746  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1702 TGAAGAATGA

                    *   *    
       1712 TATGGGTACTTATATGC
          1 TATGGGTAATTAGATGC

                             
       1729 TATGGGTAATTAGATGC
          1 TATGGGTAATTAGATGC

             
       1746 T
          1 T

       1747 TCTAATTTGG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40


Consensus pattern (17 bp):   
TATGGGTAATTAGATGC

Found at i:2143 original size:32 final size:32

Alignment explanation


    Indices: 2107--2204  Score: 78
    Period size: 32  Copynumber: 3.2  Consensus size: 32

       2097 ATTAACGAAA

                                            
       2107 TCCAATTATAAAAAAACATAATACTTCCCATC
          1 TCCAATTATAAAAAAACATAATACTTCCCATC

                    * *   * *   *      * * **
       2139 TCCAA--ACATAAAGATAT-TTA-TTAACGAAA
          1 TCCAATTATAAAAAAACATAATACTT-CCCATC

                                            
       2168 TCCAATTATAAAAAAACATAATACTTCCCATC
          1 TCCAATTATAAAAAAACATAATACTTCCCATC

                 
       2200 TCCAA
          1 TCCAA

       2205 ACATACAGAA


Statistics
Matches: 43,  Mismatches: 18, Indels: 10
        0.61            0.25        0.14

Matches are distributed among these distances:
  28    2  0.05
  29    9  0.21
  30    8  0.19
  31    8  0.19
  32   14  0.33
  33    2  0.05

ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28


Consensus pattern (32 bp):   
TCCAATTATAAAAAAACATAATACTTCCCATC

Found at i:2166 original size:61 final size:61

Alignment explanation


    Indices: 2091--2209  Score: 238
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       2081 CAACAACTAA

                                                                         
       2091 ATATTTATTAACGAAATCCAATTATAAAAAAACATAATACTTCCCATCTCCAAACATAAAG
          1 ATATTTATTAACGAAATCCAATTATAAAAAAACATAATACTTCCCATCTCCAAACATAAAG

                                                                      
       2152 ATATTTATTAACGAAATCCAATTATAAAAAAACATAATACTTCCCATCTCCAAACATA
          1 ATATTTATTAACGAAATCCAATTATAAAAAAACATAATACTTCCCATCTCCAAACATA

       2210 CAGAACCAAG


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  61   58  1.00

ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29


Consensus pattern (61 bp):   
ATATTTATTAACGAAATCCAATTATAAAAAAACATAATACTTCCCATCTCCAAACATAAAG

Found at i:5401 original size:27 final size:27

Alignment explanation


    Indices: 5371--5428  Score: 71
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       5361 TACTCATTCC

                        *     *        
       5371 ATTCACCTCTGCTTCCTCTATAACTAT
          1 ATTCACCTCTGCATCCTCCATAACTAT

                *   * *                
       5398 ATTCCCCTGTTCATCCTCCATAACTAT
          1 ATTCACCTCTGCATCCTCCATAACTAT

                
       5425 ATTC
          1 ATTC

       5429 CCCTGTTCAC


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.22, C:0.34, G:0.03, T:0.40


Consensus pattern (27 bp):   
ATTCACCTCTGCATCCTCCATAACTAT

Found at i:5429 original size:27 final size:27

Alignment explanation


    Indices: 5384--5437  Score: 99
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       5374 CACCTCTGCT

                 *                     
       5384 TCCTCTATAACTATATTCCCCTGTTCA
          1 TCCTCCATAACTATATTCCCCTGTTCA

                                       
       5411 TCCTCCATAACTATATTCCCCTGTTCA
          1 TCCTCCATAACTATATTCCCCTGTTCA

       5438 CATTCAATAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.22, C:0.35, G:0.04, T:0.39


Consensus pattern (27 bp):   
TCCTCCATAACTATATTCCCCTGTTCA

Done.