Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006380.1 Corchorus capsularis cultivar CVL-1 contig06401, 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: 17745
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33


Found at i:1789 original size:3 final size:3

Alignment explanation


    Indices: 1775--1829  Score: 101
    Period size: 3  Copynumber: 18.3  Consensus size: 3

       1765 TCAACAAATT

                  *                                                        
       1775 TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                     
       1823 TTA TTA T
          1 TTA TTA T

       1830 ATTTTGATAT


Statistics
Matches: 50,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   50  1.00

ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:2131 original size:21 final size:21

Alignment explanation


    Indices: 2107--2152  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2097 CTCTACCAAA

                         *       
       2107 CTAATGAATGATCTATGTGAT
          1 CTAATGAATGATCAATGTGAT

                                 
       2128 CTAATGAATGATCAATGTGAT
          1 CTAATGAATGATCAATGTGAT

                
       2149 CTAA
          1 CTAA

       2153 AATAACATAG


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

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35


Consensus pattern (21 bp):   
CTAATGAATGATCAATGTGAT

Found at i:9982 original size:15 final size:15

Alignment explanation


    Indices: 9962--9995  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       9952 CTGGTGACCT

                   *     * 
       9962 AGCACTGGCTTCCTC
          1 AGCACTGACTTCCCC

                           
       9977 AGCACTGACTTCCCC
          1 AGCACTGACTTCCCC

                
       9992 AGCA
          1 AGCA

       9996 GCCATCGATG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.21, C:0.41, G:0.18, T:0.21


Consensus pattern (15 bp):   
AGCACTGACTTCCCC

Found at i:12128 original size:17 final size:17

Alignment explanation


    Indices: 12106--12141  Score: 72
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      12096 ATAGTCAACA

                             
      12106 CTTAAGATGTACTCCCT
          1 CTTAAGATGTACTCCCT

                             
      12123 CTTAAGATGTACTCCCT
          1 CTTAAGATGTACTCCCT

              
      12140 CT
          1 CT

      12142 GTCCCATAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36


Consensus pattern (17 bp):   
CTTAAGATGTACTCCCT

Found at i:13724 original size:27 final size:27

Alignment explanation


    Indices: 13686--13740  Score: 92
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      13676 TTCTCCTCTG

                                       
      13686 CTTACTACCTTGAGCTTTAGTAATGAA
          1 CTTACTACCTTGAGCTTTAGTAATGAA

                              *  *     
      13713 CTTACTACCTTGAGCTTTGGTCATGAA
          1 CTTACTACCTTGAGCTTTAGTAATGAA

             
      13740 C
          1 C

      13741 CTGCAAATAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36


Consensus pattern (27 bp):   
CTTACTACCTTGAGCTTTAGTAATGAA

Found at i:17587 original size:25 final size:23

Alignment explanation


    Indices: 17551--17606  Score: 76
    Period size: 25  Copynumber: 2.3  Consensus size: 23

      17541 AAGCCTAAAT

                   *       *        
      17551 TTCATTTCTAACAACTTCTTCAAA
          1 TTCATTTTTAACAA-ATCTTCAAA

                                    
      17575 CTTCATTTTTAACAAATCTTCAAA
          1 -TTCATTTTTAACAAATCTTCAAA

                    
      17599 TTCATTTT
          1 TTCATTTT

      17607 CCTTCATTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    8  0.28
  24    8  0.28
  25   13  0.45

ACGTcount: A:0.32, C:0.21, G:0.00, T:0.46


Consensus pattern (23 bp):   
TTCATTTTTAACAAATCTTCAAA

Found at i:17644 original size:26 final size:26

Alignment explanation


    Indices: 17615--17682  Score: 109
    Period size: 26  Copynumber: 2.6  Consensus size: 26

      17605 TTCCTTCATT

                                      
      17615 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *                *   
      17641 TTAATAATAAACTAATTAAATATTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
      17667 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

      17683 AAACTAAGTA


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   38  1.00

ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA
Done.