Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013709.1 Corchorus olitorius cultivar O-4 contig13742, 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: 3471
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32


Found at i:1982 original size:15 final size:15

Alignment explanation


    Indices: 1962--1993  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1952 CCTTGGGGGT

                           
       1962 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

                    *      
       1977 TCAAAATCGACAAGC
          1 TCAAAATCAACAAGC

              
       1992 TC
          1 TC

       1994 CACTTAGTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16


Consensus pattern (15 bp):   
TCAAAATCAACAAGC

Found at i:2686 original size:66 final size:66

Alignment explanation


    Indices: 2579--2705  Score: 175
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       2569 AGTAATTCTG

                 *    *                                                      
       2579 AACCTGATTTGAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT

             
       2644 A
         66 A

                                  **             *        *       *       
       2645 AACCTAATTTAAGTGTTGTTTGTGATGACACT-AAATTTGTTTTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTAAGTGTTGTTTGCAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGA

       2706 AACAAATTCT


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  66   52  0.98
  67    1  0.02

ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43


Consensus pattern (66 bp):   
AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A

Found at i:2694 original size:33 final size:33

Alignment explanation


    Indices: 2591--2720  Score: 129
    Period size: 33  Copynumber: 3.9  Consensus size: 33

       2581 CCTGATTTGA

                      **                      
       2591 GTGTTGTTTGCAATGACA-TGAAATCTGTTTTAG
          1 GTGTTGTTTGTGATGACACT-AAATCTGTTTTAG

            *       *       *      *  **    *
       2624 ATGTTGTTAGTGATGATACTAAACCTAATTTAA
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                                    *        
       2657 GTGTTGTTTGTGATGACACTAAATTTGTTTTAG
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                            *               
       2690 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTT
          1 GTGTTGTTTGTGATGACACTAAA-TCTGTTTT

       2721 GGATGCTAAT


Statistics
Matches: 76,  Mismatches: 19, Indels: 4
        0.77            0.19        0.04

Matches are distributed among these distances:
  32    3  0.04
  33   72  0.95
  34    1  0.01

ACGTcount: A:0.26, C:0.08, G:0.22, T:0.45


Consensus pattern (33 bp):   
GTGTTGTTTGTGATGACACTAAATCTGTTTTAG
Done.