Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016125.1 Corchorus olitorius cultivar O-4 contig16158, 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: 12370
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:1239 original size:51 final size:50

Alignment explanation


    Indices: 1138--1240  Score: 120
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       1128 GTTCTTCATA

                                          *           *       
       1138 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCTAAACACTCTTTTAGTGT
          1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAACTAAACACTCTATTAGTGT

                                      *                *    *    
       1188 TTTTCTCTTGTTTCA-ATCTTGTCTCTGGACATAC-AAACACTGTATTCGTGT
          1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACA-ACTAAACACTCTATTAGTGT

              
       1239 TT
          1 TT

       1241 CTCTTTCAGA


Statistics
Matches: 45,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  50    4  0.09
  51   39  0.87
  52    2  0.04

ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47


Consensus pattern (50 bp):   
TTTTTCTTGTTTAGATCTTGTCTCAGGACAACTAAACACTCTATTAGTGT

Found at i:9114 original size:122 final size:118

Alignment explanation


    Indices: 8844--9153  Score: 342
    Period size: 122  Copynumber: 2.6  Consensus size: 118

       8834 ATGTAGCTAG

                  *                           *     *                 *      
       8844 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGATAAAACC-AGTCATAAGGAAAAAAG
          1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAGTGGGACAAAACCGA-TCATAAGGGAAAAAG

                                     *   *       *    *        *    
       8907 AGTGCAGCATATTAAGTCCATTTGTCTTCTGGACAAATATTACATGTGCTCTTTAT
         64 AGTGCAGCATATTAAGTCCA-TTGTATTCAGGACAAACATTAAATGTGCTCATTAT

                 *            **                            *  *             
       8963 TGCCTTATTAAAAACCTTGTGTCGGAAAACCCAGTGGGACAAAACCGAACAGAAGGGAAAAAGAG
          1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAGTGGGACAAAACCGATCATAAGGGAAAAAGAG

                                                                      * 
       9028 TGCTAGAGCA-ATTTAAGTCCA-TGTATTCAGGACAATTACATCTAAATGTGCT-ATTGT
         66 TGC---AGCATA-TTAAGTCCATTGTATTCAGGACAA--ACAT-TAAATGTGCTCATTAT

              *                             *                                
       9085 TGTCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG
          1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAGTGGGACAAAACCGATCATAAGGGAAAAAGAG

                
       9150 TGCA
         66 TGCA

       9154 ACGCACTTTA


Statistics
Matches: 160,  Mismatches: 22, Indels: 18
        0.80            0.11        0.09

Matches are distributed among these distances:
 119   56  0.35
 120   14  0.09
 121    1  0.01
 122   80  0.50
 123    9  0.06

ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25


Consensus pattern (118 bp):   
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAGTGGGACAAAACCGATCATAAGGGAAAAAGAG
TGCAGCATATTAAGTCCATTGTATTCAGGACAAACATTAAATGTGCTCATTAT
Done.