Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008538.1 Corchorus olitorius cultivar O-4 contig08565, 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: 2593
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32


Found at i:985 original size:60 final size:60

Alignment explanation


    Indices: 898--1062  Score: 242
    Period size: 60  Copynumber: 2.8  Consensus size: 60

        888 GTTAATTGCT

                       *   *    *                                        
        898 CAAATAAGGGTTTAATGTTTGTC-AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
          1 CAAATAAGGGTCTAACG-TTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC

                                        *              * *              
        958 CAAATAAGGGTCTAACGTTATCGAAAATACTCAAATAAGGGCCCGGTCTTTTAATTTGGC
          1 CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC

                      *         *                        
       1018 CAAATAAGGGCCTAACGTTACCGAAAATGCTCAAATAAGGGCCTG
          1 CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCCTG

       1063 TCGTCAGTTT


Statistics
Matches: 94,  Mismatches: 10, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  59    4  0.04
  60   90  0.96

ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28


Consensus pattern (60 bp):   
CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC

Found at i:1137 original size:31 final size:31

Alignment explanation


    Indices: 1099--1264  Score: 132
    Period size: 31  Copynumber: 5.5  Consensus size: 31

       1089 TTTTCGACGC

                                           
       1099 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
          1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT

                               **        *   
       1130 TAGGCCCTTATTTG-GCCAAATT---AAAAGAT
          1 TAGGCCCTTATTTGAG-CATTTTGGCAAACG-T

            *  *                           
       1159 CAGACCCTTATTTGAGCATTTTGGCAAACGT
          1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT

                               **  *         
       1190 TAGGCCCTTATTTG-GTCAAATTAG--AA-GAT
          1 TAGGCCCTTATTTGAG-CATTTTGGCAAACG-T

            *                      *     * 
       1219 CAGGCCCTTATTTGAGCATTTTGACAAACAT
          1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT

               *           
       1250 TAGACCCTTATTTGA
          1 TAGGCCCTTATTTGA

       1265 ACAATTAGCC


Statistics
Matches: 102,  Mismatches: 21, Indels: 24
        0.69            0.14        0.16

Matches are distributed among these distances:
  28    5  0.05
  29   37  0.36
  30    4  0.04
  31   52  0.51
  32    4  0.04

ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Consensus pattern (31 bp):   
TAGGCCCTTATTTGAGCATTTTGGCAAACGT

Found at i:1196 original size:60 final size:60

Alignment explanation


    Indices: 1103--1263  Score: 268
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       1093 CGACGCTAGG

                                                                        
       1103 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
          1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA

                                                      *       *        *
       1163 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAGAAGATCAGG
          1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA

                               *     *    *          
       1223 CCCTTATTTGAGCATTTTGACAAACATTAGACCCTTATTTG
          1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG

       1264 AACAATTAGC


Statistics
Matches: 95,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  60   95  1.00

ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34


Consensus pattern (60 bp):   
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA

Found at i:1229 original size:29 final size:28

Alignment explanation


    Indices: 1131--1232  Score: 89
    Period size: 29  Copynumber: 3.5  Consensus size: 28

       1121 GGCAAACGTT

                                  *      
       1131 AGGCCCTTATTTGGCCAAATTAAAAGATC
          1 AGGCCCTTATTTGG-CAAATTAGAAGATC

              *              **  *         *
       1160 AGACCCTTATTTGAGCATTTTGGCAA-ACGTT
          1 AGGCCCTTATTTG-GCAAATTAG-AAGA--TC

                                         
       1191 AGGCCCTTATTTGGTCAAATTAGAAGATC
          1 AGGCCCTTATTTGG-CAAATTAGAAGATC

                         
       1220 AGGCCCTTATTTG
          1 AGGCCCTTATTTG

       1233 AGCATTTTGA


Statistics
Matches: 56,  Mismatches: 11, Indels: 12
        0.71            0.14        0.15

Matches are distributed among these distances:
  29   31  0.55
  30    6  0.11
  31   19  0.34

ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32


Consensus pattern (28 bp):   
AGGCCCTTATTTGGCAAATTAGAAGATC

Found at i:1802 original size:24 final size:24

Alignment explanation


    Indices: 1770--1822  Score: 106
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1760 TGTCTGCACT

                                    
       1770 TGATTTATACACCAATTCAGCAGG
          1 TGATTTATACACCAATTCAGCAGG

                                    
       1794 TGATTTATACACCAATTCAGCAGG
          1 TGATTTATACACCAATTCAGCAGG

                 
       1818 TGATT
          1 TGATT

       1823 AAAAGAAGAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Consensus pattern (24 bp):   
TGATTTATACACCAATTCAGCAGG
Done.