Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023457.1 Corchorus olitorius cultivar O-4 contig23490, 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: 2898
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39


Found at i:75 original size:32 final size:28

Alignment explanation


    Indices: 6--89  Score: 107
    Period size: 32  Copynumber: 2.8  Consensus size: 28

          1 TTTGG

                                        
          6 TATGACAACTTCTGGTGTC-AATAATTT
          1 TATGACAACTTCTGGTGTCAAATAATTT

                                            
         33 TCATGAACAACTTCTGGATGTCAAGATAATTT
          1 T-ATG-ACAACTTCTGG-TGTCAA-ATAATTT

                                     
         65 AATATGACAACTTCTGGTGTCAAAT
          1 --TATGACAACTTCTGGTGTCAAAT

         90 TAAAATTTAA


Statistics
Matches: 50,  Mismatches: 0, Indels: 11
        0.82            0.00        0.18

Matches are distributed among these distances:
  27    1  0.02
  28    3  0.06
  29   11  0.22
  30    6  0.12
  31    7  0.14
  32   18  0.36
  33    3  0.06
  34    1  0.02

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36


Consensus pattern (28 bp):   
TATGACAACTTCTGGTGTCAAATAATTT

Found at i:888 original size:147 final size:144

Alignment explanation


    Indices: 668--932  Score: 449
    Period size: 147  Copynumber: 1.8  Consensus size: 144

        658 TCCAATCAGA

                                                                             
        668 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAAAAATTATTTTTACATTAAACAACTTATTAT
          1 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAAAAATTATTTTTACATTAAACAACTTATTAT

                                                                             
        733 TATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTGAGGA
         66 TATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTGAGGA

                          
        798 ATTAGTCATTACGT
        131 ATTAGTCATTACGT

                *           *                 *   *    *       *             
        812 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTTACGTTAAACAACTTAT
          1 TTTTATTTCCATATTAAAAAAGTC-TAAA--ATAATAAAAATTATTTTTACATTAAACAACTTAT

                                                                    
        877 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTT
         63 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTT

        933 CTTTCCATAT


Statistics
Matches: 112,  Mismatches: 6, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
 144   22  0.20
 145    4  0.04
 147   86  0.77

ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49


Consensus pattern (144 bp):   
TTTTATTTCCATATTAAAAAAGTCTAAAATAATAAAAATTATTTTTACATTAAACAACTTATTAT
TATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTGAGGA
ATTAGTCATTACGT

Found at i:1017 original size:15 final size:16

Alignment explanation


    Indices: 994--1041  Score: 53
    Period size: 15  Copynumber: 2.9  Consensus size: 16

        984 CATCTTCTTA

                *           
        994 TTATAATTATTA-AAC
          1 TTATTATTATTATAAC

                            
       1009 TTATTATTATTATAAC
          1 TTATTATTATTATAAC

                             
       1025 AATTATTATTAGTTATA
          1 --TTATTATTA-TTATA

       1042 TGATCACTAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  15   11  0.39
  16    3  0.11
  18    9  0.32
  19    5  0.18

ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52


Consensus pattern (16 bp):   
TTATTATTATTATAAC

Found at i:1030 original size:18 final size:17

Alignment explanation


    Indices: 991--1041  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 17

        981 AAACATCTTC

                   *         *
        991 TTATTATAATTATTAAAC
          1 TTATTATTATTA-TAAAA

                              
       1009 TTATTATTATTATAACAA
          1 TTATTATTATTATAA-AA

                           
       1027 TTATTATTAGTTATA
          1 TTATTATTA-TTATA

       1042 TGATCACTAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  17    3  0.10
  18   21  0.72
  19    5  0.17

ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53


Consensus pattern (17 bp):   
TTATTATTATTATAAAA

Found at i:1037 original size:117 final size:117

Alignment explanation


    Indices: 798--1023  Score: 361
    Period size: 117  Copynumber: 2.0  Consensus size: 117

        788 TTTTTGAGGA

                                                        *                    
        798 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTTAC
          1 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAGTCTTAAATAATACTAATAATTTTTTTTAC

                                                          *     
        863 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATATC
         66 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATAAATATC

                                                                  *          
        915 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAGT-TTAAAATAATACTAA-CA-TTTTTTTA
          1 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAGTCTT-AAATAATACTAATAATTTTTTTTA

                     *   *                 *                
        977 CGTTAAACATCTTCTTATTATAATTATTAAACTTATTATTA-TTATAA
         65 CGTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATAA

       1024 CAATTATTAT


Statistics
Matches: 102,  Mismatches: 6, Indels: 5
        0.90            0.05        0.04

Matches are distributed among these distances:
 114    5  0.05
 115   46  0.45
 116    3  0.03
 117   48  0.47

ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48


Consensus pattern (117 bp):   
ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAGTCTTAAATAATACTAATAATTTTTTTTAC
GTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATAAATATC
Done.