Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014205.1 Corchorus olitorius cultivar O-4 contig14238, 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: 25094
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:3537 original size:19 final size:19

Alignment explanation


    Indices: 3487--3537  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       3477 TGTGGGATTT

                               
       3487 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       3505 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       3524 TTAATAATTAATTA
          1 TTAATAATTAATTA

       3538 ATTTCAGCCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:6315 original size:30 final size:31

Alignment explanation


    Indices: 6238--6315  Score: 92
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       6228 TACCGTACAA

                                             
       6238 GTCCCTCTATACTTACAAAAAGCGATCAATTTG
          1 GTCCCTC--TACTTACAAAAAGCGATCAATTTG

                                             
       6271 GT-CCTCCTAC-TACAAAAA-CTG-TCAATTTG
          1 GTCCCT-CTACTTACAAAAAGC-GATCAATTTG

                            
       6300 GTCCCTCTACTTACAA
          1 GTCCCTCTACTTACAA

       6316 TTTTGTGTCA


Statistics
Matches: 41,  Mismatches: 0, Indels: 11
        0.79            0.00        0.21

Matches are distributed among these distances:
  29   15  0.37
  30   17  0.41
  31    3  0.07
  32    3  0.07
  33    3  0.07

ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31


Consensus pattern (31 bp):   
GTCCCTCTACTTACAAAAAGCGATCAATTTG

Found at i:16027 original size:10 final size:10

Alignment explanation


    Indices: 16012--16045  Score: 52
    Period size: 10  Copynumber: 3.5  Consensus size: 10

      16002 AATTCTTAAA

                      
      16012 GTTAATTTAT
          1 GTTAATTTAT

                      
      16022 GTTAATTTAT
          1 GTTAATTTAT

                  *   
      16032 GTT-ATATAT
          1 GTTAATTTAT

                 
      16041 GTTAA
          1 GTTAA

      16046 CTTTGACCAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
   9    8  0.36
  10   14  0.64

ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56


Consensus pattern (10 bp):   
GTTAATTTAT

Found at i:21099 original size:128 final size:119

Alignment explanation


    Indices: 20826--21141  Score: 352
    Period size: 128  Copynumber: 2.6  Consensus size: 119

      20816 ATGTAGCTAG

                                                                      *      
      20826 TGCCTCATTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG
          1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAATGGGACAAAACCGA-TCATAAGGGAAAAAG

                                         **      *    *        *    
      20889 AGTGCAGCATATCAAGTCCATTTGTCTTCTGGACAAATATTACATGTGCTCTTTAT
         64 AGTGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT

                              **                            *  *             
      20945 TGCCTCATTAAAAACCTTGTGTCGGAAAACCCAATGGGACAAAACCGAACAGAAGGGAAAAAGAG
          1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG

                          *                                                * 
      21010 TGCTAGAGCA-ATTTAAGTCCATGTAAATGTCTTCAAGACAATTACATCTAAATGTGCT-ATTGT
         66 TGC---AGCATA-TCAAGTCCAT-T---TGTCTTCAAGACAA--ACAT-TAAATGTGCTCATTAT

                          *                 **                               
      21073 TGCCTCATTAAAAAGCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG
          1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG

                
      21138 TGCA
         66 TGCA

      21142 ACGCACTTTA


Statistics
Matches: 165,  Mismatches: 19, Indels: 20
        0.81            0.09        0.10

Matches are distributed among these distances:
 119   59  0.36
 120    2  0.01
 121    1  0.01
 122   13  0.08
 123    1  0.01
 125    1  0.01
 126   12  0.07
 128   67  0.41
 129    9  0.05

ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23


Consensus pattern (119 bp):   
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
TGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT

Found at i:24984 original size:30 final size:30

Alignment explanation


    Indices: 24912--25094  Score: 276
    Period size: 30  Copynumber: 6.0  Consensus size: 30

      24902 TTTGAAAGGT

                                           *
      24912 AAAATCATGACAACTTCTGGTGTCAATTGAAT
          1 AAAATCATGACAACTTCTGGTGTCAATTG--C

                 *      *    **           
      24944 AAAATTATGACATCTTCAAGTGTCAATTGC
          1 AAAATCATGACAACTTCTGGTGTCAATTGC

                                          
      24974 AAAATCATGACAACTTCTGGTGTCAATTGC
          1 AAAATCATGACAACTTCTGGTGTCAATTGC

                                          
      25004 AAAATCATGACAACTTCTGGTGTCAATTGC
          1 AAAATCATGACAACTTCTGGTGTCAATTGC

              *  *                        
      25034 AAGATTATGACAACTTCTGGTGTCAATTGC
          1 AAAATCATGACAACTTCTGGTGTCAATTGC

                                           
      25064 AAAATCATGACAACTTCTGGTGTACAATTGC
          1 AAAATCATGACAACTTCTGGTGT-CAATTGC


Statistics
Matches: 137,  Mismatches: 13, Indels: 3
        0.90            0.08        0.02

Matches are distributed among these distances:
  30  105  0.77
  31    7  0.05
  32   25  0.18

ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31


Consensus pattern (30 bp):   
AAAATCATGACAACTTCTGGTGTCAATTGC

Done.