Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024293.1 Corchorus olitorius cultivar O-4 contig24326, 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: 14948
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34


Found at i:11 original size:6 final size:6

Alignment explanation


    Indices: 1--99  Score: 180
    Period size: 6  Copynumber: 16.3  Consensus size: 6

                                                                   
          1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
          1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA

                                                        *           
         49 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTGAAA TTATAAA
          1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTA-AAA

              
         98 TT
          1 TT

        100 GTAGCTAACC


Statistics
Matches: 90,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
   6   85  0.94
   7    5  0.06

ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35


Consensus pattern (6 bp):   
TTAAAA

Found at i:766 original size:29 final size:27

Alignment explanation


    Indices: 703--756  Score: 72
    Period size: 28  Copynumber: 2.0  Consensus size: 27

        693 ATAGTGGTAA

                *             *        
        703 GTATAAAAATTAAGAATATTTATTGTG
          1 GTATTAAAATTAAGAATACTTATTGTG

                           *           
        730 GTAATTAAAATTAAGGATACTTATTGT
          1 GT-ATTAAAATTAAGAATACTTATTGT

        757 ATTGTATTAA


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

Matches are distributed among these distances:
  27    2  0.09
  28   21  0.91

ACGTcount: A:0.43, C:0.02, G:0.15, T:0.41


Consensus pattern (27 bp):   
GTATTAAAATTAAGAATACTTATTGTG

Found at i:4736 original size:49 final size:48

Alignment explanation


    Indices: 4672--4788  Score: 130
    Period size: 49  Copynumber: 2.4  Consensus size: 48

       4662 CACATTTTCA

                      *                        *            * 
       4672 CAATTTTTACAACAAAATTGAATC-TTTAATTTTCGTTGCACCTTCTTCT
          1 CAATTTTTA-TACAAAATTGAATCATTTAATTTTCATTGCA-CTTCTTAT

                                         *    *         *    
       4721 CAATTTTTATGACAAAATTG-ATCATTTACTTTTTATTGCACTTTTTAT
          1 CAATTTTTAT-ACAAAATTGAATCATTTAATTTTCATTGCACTTCTTAT

               *                
       4769 CAACTTTTATACAAAATTGA
          1 CAATTTTTATACAAAATTGA

       4789 TTGGCACGCT


Statistics
Matches: 58,  Mismatches: 7, Indels: 7
        0.81            0.10        0.10

Matches are distributed among these distances:
  47    9  0.16
  48   18  0.31
  49   31  0.53

ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46


Consensus pattern (48 bp):   
CAATTTTTATACAAAATTGAATCATTTAATTTTCATTGCACTTCTTAT

Found at i:4929 original size:25 final size:25

Alignment explanation


    Indices: 4879--4934  Score: 69
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       4869 CGTAATTTAA

                              *  *   
       4879 TTAGAAACAATTTAGATATTATTAT
          1 TTAGAAACAATTTAGATAATACTAT

                                      
       4904 TTAGAAA-AATTTTAGATAATACTAT
          1 TTAGAAACAA-TTTAGATAATACTAT

             *    
       4929 TAAGAA
          1 TTAGAA

       4935 TTTTTTGCTA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  24    2  0.07
  25   25  0.93

ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39


Consensus pattern (25 bp):   
TTAGAAACAATTTAGATAATACTAT

Found at i:12499 original size:33 final size:33

Alignment explanation


    Indices: 12429--12530  Score: 109
    Period size: 33  Copynumber: 3.1  Consensus size: 33

      12419 ATGATCAACC

                                     ** *      
      12429 AAAACAG-ATTTGTTTTCATCACAATTAGCATCC-
          1 AAAACAGAATTT-TTTTCATCACAAACAACA-CCT

                                             
      12462 AAAACAGAATTTTTTTCATCACAAACAACACCT
          1 AAAACAGAATTTTTTTCATCACAAACAACACCT

                       ** *                * 
      12495 AAAACAGAATTAGTGTCATCACAAACAACACTT
          1 AAAACAGAATTTTTTTCATCACAAACAACACCT

               
      12528 AAA
          1 AAA

      12531 TTAGGTTTAG


Statistics
Matches: 60,  Mismatches: 7, Indels: 4
        0.85            0.10        0.06

Matches are distributed among these distances:
  32    2  0.03
  33   54  0.90
  34    4  0.07

ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26


Consensus pattern (33 bp):   
AAAACAGAATTTTTTTCATCACAAACAACACCT

Found at i:12547 original size:33 final size:33

Alignment explanation


    Indices: 12477--12566  Score: 99
    Period size: 33  Copynumber: 2.7  Consensus size: 33

      12467 AGAATTTTTT

                                           **
      12477 TCATCACAAACAACACCTAAAACAGAATTAGTG
          1 TCATCACAAACAACACCTAAAACAGAATTAGCA

                            *    **  **      
      12510 TCATCACAAACAACACTTAAATTAGGTTTAGCA
          1 TCATCACAAACAACACCTAAAACAGAATTAGCA

                   *       *        
      12543 TCATCACTAACAACATCTAAAACA
          1 TCATCACAAACAACACCTAAAACA

      12567 CTCTTTGCAA


Statistics
Matches: 45,  Mismatches: 12, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  33   45  1.00

ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22


Consensus pattern (33 bp):   
TCATCACAAACAACACCTAAAACAGAATTAGCA
Done.