Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013533.1 Corchorus capsularis cultivar CVL-1 contig13554, 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: 24316
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--43  Score: 77
    Period size: 2  Copynumber: 21.0  Consensus size: 2

                                                                           
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

         44 TATTTTTGTC


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   38  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:198 original size:11 final size:11

Alignment explanation


    Indices: 182--224  Score: 68
    Period size: 11  Copynumber: 3.9  Consensus size: 11

        172 TATACTATAT

                       
        182 CTAATTAATAG
          1 CTAATTAATAG

                      *
        193 CTAATTAATAT
          1 CTAATTAATAG

                       
        204 CTAATTAATAG
          1 CTAATTAATAG

            *         
        215 TTAATTAATA
          1 CTAATTAATA

        225 ATGAATAAAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  11   29  1.00

ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42


Consensus pattern (11 bp):   
CTAATTAATAG

Found at i:206 original size:22 final size:22

Alignment explanation


    Indices: 178--224  Score: 85
    Period size: 22  Copynumber: 2.1  Consensus size: 22

        168 CCATTATACT

                                  
        178 ATATCTAATTAATAGCTAATTA
          1 ATATCTAATTAATAGCTAATTA

                           *      
        200 ATATCTAATTAATAGTTAATTA
          1 ATATCTAATTAATAGCTAATTA

               
        222 ATA
          1 ATA

        225 ATGAATAAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43


Consensus pattern (22 bp):   
ATATCTAATTAATAGCTAATTA

Found at i:2915 original size:30 final size:30

Alignment explanation


    Indices: 2872--2974  Score: 147
    Period size: 30  Copynumber: 3.5  Consensus size: 30

       2862 GTTTTGCCCT

                                          
       2872 ATGAACT-TTAATTTTAGACATTTTGTCTC
          1 ATGAACTCTTAATTTTAGACATTTTGTCTC

            *               *             
       2901 TTGAACTCTTAATTTTGGACATTTTGTCTC
          1 ATGAACTCTTAATTTTAGACATTTTGTCTC

            *    *   *                    
       2931 CTGAATTCTCAATTTTAGACATTTTGTC-C
          1 ATGAACTCTTAATTTTAGACATTTTGTCTC

                           
       2960 ATGAACTCTTAATTT
          1 ATGAACTCTTAATTT

       2975 GAGCCTCTGT


Statistics
Matches: 64,  Mismatches: 9, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  29   19  0.30
  30   45  0.70

ACGTcount: A:0.25, C:0.17, G:0.11, T:0.48


Consensus pattern (30 bp):   
ATGAACTCTTAATTTTAGACATTTTGTCTC

Found at i:3214 original size:29 final size:30

Alignment explanation


    Indices: 3163--3220  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       3153 CCAAGGCTCC

                            * *    *      
       3163 AATTGTAAGTTCAAGGGATAAAATGTCCAA
          1 AATTGTAAGTTCAAGGAACAAAACGTCCAA

                         *               
       3193 AATTG-AAGTTCATGGAACAAAACGTCCA
          1 AATTGTAAGTTCAAGGAACAAAACGTCCA

       3221 TACGCTACAA


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

Matches are distributed among these distances:
  29   19  0.79
  30    5  0.21

ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24


Consensus pattern (30 bp):   
AATTGTAAGTTCAAGGAACAAAACGTCCAA

Found at i:5596 original size:11 final size:11

Alignment explanation


    Indices: 5553--5590  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       5543 TTCCTATATA

                *      
       5553 AAATAAATTAT
          1 AAATTAATTAT

                        
       5564 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       5575 AAATTAATTAT
          1 AAATTAATTAT

                 
       5586 AAATT
          1 AAATT

       5591 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:23262 original size:2 final size:2

Alignment explanation


    Indices: 23255--23292  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      23245 CAAGTACCTT

                                                                    
      23255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      23293 AAGGACACGA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.