Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020952.1 Corchorus olitorius cultivar O-4 contig20985, 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: 17233
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33


Found at i:3355 original size:47 final size:47

Alignment explanation


    Indices: 3286--3404  Score: 220
    Period size: 47  Copynumber: 2.5  Consensus size: 47

       3276 CTAGCAAATC

                                                           
       3286 TTTAAGGCTTGACGGCTAATTTATTAGTTAGGAGGAGAAAGGGGTAA
          1 TTTAAGGCTTGACGGCTAATTTATTAGTTAGGAGGAGAAAGGGGTAA

                                                           
       3333 TTTAAGGCTTGACGGCTAATTTATTAGTTAGGAGGAGAAAGGGGTAA
          1 TTTAAGGCTTGACGGCTAATTTATTAGTTAGGAGGAGAAAGGGGTAA

                   *                 
       3380 TTTAAGGTTTGACGGCTAATCTTAT
          1 TTTAAGGCTTGACGGCTAAT-TTAT

       3405 CTAAATAGCA


Statistics
Matches: 70,  Mismatches: 1, Indels: 1
        0.97            0.01        0.01

Matches are distributed among these distances:
  47   66  0.94
  48    4  0.06

ACGTcount: A:0.30, C:0.08, G:0.29, T:0.33


Consensus pattern (47 bp):   
TTTAAGGCTTGACGGCTAATTTATTAGTTAGGAGGAGAAAGGGGTAA

Found at i:6290 original size:27 final size:28

Alignment explanation


    Indices: 6226--6300  Score: 98
    Period size: 27  Copynumber: 2.7  Consensus size: 28

       6216 AGGGTCATCT

                                         
       6226 AGGGGCATTTTGGTCATTTCCAAAAATTC
          1 AGGGGCATTTTGGTCATTTCC-AAAATTC

                               *   **   
       6255 AGGGGCATTTTGGTCATTTGC-ATGTTC
          1 AGGGGCATTTTGGTCATTTCCAAAATTC

                      *        
       6282 AGGGGCATTTAGGTCATTT
          1 AGGGGCATTTTGGTCATTT

       6301 TAGGTTCACT


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  27   22  0.52
  29   20  0.48

ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37


Consensus pattern (28 bp):   
AGGGGCATTTTGGTCATTTCCAAAATTC

Found at i:11031 original size:16 final size:16

Alignment explanation


    Indices: 11006--11038  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      10996 GTGGCCCTTT

                            
      11006 TTTATGTGTGGAATAC
          1 TTTATGTGTGGAATAC

                 *          
      11022 TTTATTTGTGGAATAC
          1 TTTATGTGTGGAATAC

             
      11038 T
          1 T

      11039 CATGTGTGTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48


Consensus pattern (16 bp):   
TTTATGTGTGGAATAC

Found at i:11141 original size:19 final size:18

Alignment explanation


    Indices: 11089--11187  Score: 96
    Period size: 19  Copynumber: 5.4  Consensus size: 18

      11079 TGGAGTACCC

                   *           
      11089 CGTATGTATGTAGAATATT
          1 CGTATGTGTGTA-AATATT

                              
      11108 C--ATGTGTG-AAATATT
          1 CGTATGTGTGTAAATATT

                               
      11123 CGTATGTGTGTAAAGTATT
          1 CGTATGTGTGTAAA-TATT

             *           *     
      11142 CATATGTGTGTGAGATATT
          1 CGTATGTGTGT-AAATATT

            *                  
      11161 TGTATGTGTGTAGAATATT
          1 CGTATGTGTGTA-AATATT

             *      
      11180 CATATGTG
          1 CGTATGTG

      11188 AATGTGTGTG


Statistics
Matches: 66,  Mismatches: 8, Indels: 12
        0.77            0.09        0.14

Matches are distributed among these distances:
  15    7  0.11
  16    1  0.02
  17   13  0.20
  18    4  0.06
  19   39  0.59
  20    2  0.03

ACGTcount: A:0.28, C:0.05, G:0.24, T:0.42


Consensus pattern (18 bp):   
CGTATGTGTGTAAATATT

Found at i:11166 original size:38 final size:38

Alignment explanation


    Indices: 11089--11187  Score: 127
    Period size: 38  Copynumber: 2.7  Consensus size: 38

      11079 TGGAGTACCC

                   *                              
      11089 CGTATGTATGTAGAATATTC--A--TGTGTGAAATATT
          1 CGTATGTGTGTAGAATATTCATATGTGTGTGAAATATT

                                             *     
      11123 CGTATGTGTGTA-AAGTATTCATATGTGTGTGAGATATT
          1 CGTATGTGTGTAGAA-TATTCATATGTGTGTGAAATATT

            *                          
      11161 TGTATGTGTGTAGAATATTCATATGTG
          1 CGTATGTGTGTAGAATATTCATATGTG

      11188 AATGTGTGTG


Statistics
Matches: 56,  Mismatches: 3, Indels: 8
        0.84            0.04        0.12

Matches are distributed among these distances:
  33    2  0.04
  34   16  0.29
  36    1  0.02
  38   35  0.62
  39    2  0.04

ACGTcount: A:0.28, C:0.05, G:0.24, T:0.42


Consensus pattern (38 bp):   
CGTATGTGTGTAGAATATTCATATGTGTGTGAAATATT

Found at i:11218 original size:25 final size:25

Alignment explanation


    Indices: 11156--11220  Score: 76
    Period size: 27  Copynumber: 2.5  Consensus size: 25

      11146 TGTGTGTGAG

                *   *                
      11156 ATATTTGTATGTGTGTAGAATATTC
          1 ATATGTGTGTGTGTGTAGAATATTC

                              *    *   
      11181 ATATGTGAATGTGTGTGTGGAATTTTC
          1 ATATGTG--TGTGTGTGTAGAATATTC

                         
      11208 ATATGTGTGTGTG
          1 ATATGTGTGTGTG

      11221 GTGCAGCTGT


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  25   12  0.35
  27   22  0.65

ACGTcount: A:0.23, C:0.03, G:0.28, T:0.46


Consensus pattern (25 bp):   
ATATGTGTGTGTGTGTAGAATATTC
Done.