Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017002.1 Corchorus olitorius cultivar O-4 contig17035, 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: 4588
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30


Found at i:1135 original size:29 final size:29

Alignment explanation


    Indices: 1039--1201  Score: 199
    Period size: 29  Copynumber: 5.7  Consensus size: 29

       1029 TTTTCAAAAA

                                    *    
       1039 AAAAATGACCAAAATG-CCCTGAACGTGC
          1 AAAAATGACCAAAATGCCCCTGAATGTGC

                           *   *     *    
       1067 --AAATGACCAAAATACCCTTGAATATGCC
          1 AAAAATGACCAAAATGCCCCTGAATGTG-C

                                   *     
       1095 AAAAATGACCAAAATGCCCCTGAGTGTGC
          1 AAAAATGACCAAAATGCCCCTGAATGTGC

                              **         
       1124 AAAAATGACCAAAATGCCGTTGAATGTGC
          1 AAAAATGACCAAAATGCCCCTGAATGTGC

             *                       *  *
       1153 AGAAATGACCAAAATGCCCCTGAATAT-A
          1 AAAAATGACCAAAATGCCCCTGAATGTGC

                                 
       1181 AAAAATGACCAAAATGCCCCT
          1 AAAAATGACCAAAATGCCCCT

       1202 AGGTGACCCT


Statistics
Matches: 114,  Mismatches: 17, Indels: 8
        0.82            0.12        0.06

Matches are distributed among these distances:
  26   13  0.11
  27    8  0.07
  28   21  0.18
  29   50  0.44
  30   22  0.19

ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18


Consensus pattern (29 bp):   
AAAAATGACCAAAATGCCCCTGAATGTGC

Found at i:1173 original size:58 final size:59

Alignment explanation


    Indices: 1039--1199  Score: 215
    Period size: 57  Copynumber: 2.8  Consensus size: 59

       1029 TTTTCAAAAA

                                    *                   *              
       1039 AAAAATGACCAAAATG-CCCTGAACGTGC--AAATGACCAAAATACCCTTGAATATGCC
          1 AAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCTTGAATATGCC

                                   *                       *      *    
       1095 AAAAATGACCAAAATGCCCCTGAGTGTGCAAAAATGACCAAAATGCCGTTGAATGTG-C
          1 AAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCTTGAATATGCC

             *                       *  *                   
       1153 AGAAATGACCAAAATGCCCCTGAATAT-AAAAAATGACCAAAATGCCC
          1 AAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCC

       1200 CTAGGTGACC


Statistics
Matches: 92,  Mismatches: 10, Indels: 5
        0.86            0.09        0.05

Matches are distributed among these distances:
  56   16  0.17
  57   28  0.30
  58   25  0.27
  59   23  0.25

ACGTcount: A:0.43, C:0.23, G:0.16, T:0.17


Consensus pattern (59 bp):   
AAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCTTGAATATGCC

Found at i:1200 original size:86 final size:84

Alignment explanation


    Indices: 1039--1201  Score: 238
    Period size: 86  Copynumber: 1.9  Consensus size: 84

       1029 TTTTCAAAAA

                                                         *         *         
       1039 AAAAATGACCAAAATGCCCTGAACGTGCAAATGACCAAAATACCCTTGAATATGCCAAAAATGAC
          1 AAAAATGACCAAAATGCCCTGAACGTGCAAATGACCAAAATACCCCTGAATAT-CAAAAAATGAC

                                
       1104 CAAAATGCCCCTGAGTGTGC
         65 CAAAATGCCCCTGAGTGTGC

                               *    *                   *                    
       1124 AAAAATGACCAAAATGCCGTTGAATGTGCAGAAATGACCAAAATGCCCCTGAATAT-AAAAAATG
          1 AAAAATGACCAAAATGCC-CTGAACGTGC--AAATGACCAAAATACCCCTGAATATCAAAAAATG

                          
       1188 ACCAAAATGCCCCT
         63 ACCAAAATGCCCCT

       1202 AGGTGACCCT


Statistics
Matches: 70,  Mismatches: 5, Indels: 5
        0.88            0.06        0.06

Matches are distributed among these distances:
  85   18  0.26
  86   29  0.41
  88   23  0.33

ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18


Consensus pattern (84 bp):   
AAAAATGACCAAAATGCCCTGAACGTGCAAATGACCAAAATACCCCTGAATATCAAAAAATGACC
AAAATGCCCCTGAGTGTGC
Done.