Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010813.1 Corchorus olitorius cultivar O-4 contig10845, 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: 14301
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:1609 original size:21 final size:21

Alignment explanation


    Indices: 1583--1632  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1573 CGGCCATTCA

                           **    
       1583 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       1604 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    
       1625 CCGTGCCA
          1 CCGTGCCA

       1633 TCGCCATTCC


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:2009 original size:15 final size:14

Alignment explanation


    Indices: 1989--2018  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       1979 ATCTCTTTAA

                           
       1989 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       2004 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       2018 T
          1 T

       2019 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT

Found at i:4910 original size:16 final size:15

Alignment explanation


    Indices: 4889--4930  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4879 TTACTCTGCT

                            
       4889 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                  *        
       4905 TTGTTTACTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       4920 TTGCTTTCTGT
          1 TTGTTTTCTGT

       4931 CAATCTCTGT


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

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:5298 original size:21 final size:23

Alignment explanation


    Indices: 5274--5322  Score: 68
    Period size: 21  Copynumber: 2.3  Consensus size: 23

       5264 TATAAAAAAA

                         *         
       5274 TTTTGATTTTT-TTTTTGCGT-T
          1 TTTTGATTTTTGTGTTTGCGTCT

                                   
       5295 TTTT-ATTTTTGTGTTTGCGTCT
          1 TTTTGATTTTTGTGTTTGCGTCT

                  
       5317 TTTTGA
          1 TTTTGA

       5323 AAAAAAAAAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  20    6  0.25
  21   12  0.50
  22    5  0.21
  23    1  0.04

ACGTcount: A:0.06, C:0.06, G:0.16, T:0.71


Consensus pattern (23 bp):   
TTTTGATTTTTGTGTTTGCGTCT

Found at i:5373 original size:23 final size:24

Alignment explanation


    Indices: 5343--5387  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       5333 TTGTTTTGTG

                                    
       5343 TTTTGCGTC-GAAAAAAAAAGAGT
          1 TTTTGCGTCAGAAAAAAAAAGAGT

                      *           
       5366 TTTTGCGTCATAAAAAAAAAGA
          1 TTTTGCGTCAGAAAAAAAAAGA

       5388 AAAGAAAATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  23    9  0.45
  24   11  0.55

ACGTcount: A:0.47, C:0.09, G:0.18, T:0.27


Consensus pattern (24 bp):   
TTTTGCGTCAGAAAAAAAAAGAGT

Found at i:5501 original size:13 final size:13

Alignment explanation


    Indices: 5479--5511  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       5469 CTACTAACAA

                         
       5479 TTTTTCTTTTGAG
          1 TTTTTCTTTTGAG

                 *       
       5492 TTTTTTTTTTGAG
          1 TTTTTCTTTTGAG

                   
       5505 TTTTTCT
          1 TTTTTCT

       5512 AGGAAGCTGC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76


Consensus pattern (13 bp):   
TTTTTCTTTTGAG

Found at i:12094 original size:72 final size:72

Alignment explanation


    Indices: 11961--12099  Score: 165
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      11951 AAATACCGAT

                               *         *    *         *    * *             
      11961 AATTGATGGTTGAACCCAATCATTCCTTCTGTTCTTGAATAATTTTGAGTGCCACCCGCATTGAA
          1 AATTGATGGTTGAACCCAAACATTCCTTCAGTTCATGAATAATTGTGAGCGACACCCGCATTGAA

                   
      12026 TATAGCC
         66 TATAGCC

                 *     *                                              *      
      12033 AATTGTTGGTTTAACCCAAACATTCCTTCAGTTGCATG-ATAATTGTG-GCGAACACCTGCATTG
          1 AATTGATGGTTGAACCCAAACATTCCTTCAGTT-CATGAATAATTGTGAGCG-ACACCCGCATTG

                
      12096 AATA
         64 AATA

      12100 GAGCAACTGG


Statistics
Matches: 56,  Mismatches: 9, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  71    2  0.04
  72   51  0.91
  73    3  0.05

ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34


Consensus pattern (72 bp):   
AATTGATGGTTGAACCCAAACATTCCTTCAGTTCATGAATAATTGTGAGCGACACCCGCATTGAA
TATAGCC
Done.