Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018025.1 Corchorus olitorius cultivar O-4 contig18058, 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: 13477
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29


Found at i:1124 original size:3 final size:3

Alignment explanation


    Indices: 1116--1144  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

       1106 TGCAGGTGTT

                                                  
       1116 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       1145 TAGTGGGGGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:1722 original size:62 final size:62

Alignment explanation


    Indices: 1625--1748  Score: 248
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       1615 CCGAGTATCA

                                                                          
       1625 CCAGAGTACACAACTTTCCAACCTGGTATCACTTTTCCAAAACTGTTTATTCTATCTGCTGC
          1 CCAGAGTACACAACTTTCCAACCTGGTATCACTTTTCCAAAACTGTTTATTCTATCTGCTGC

                                                                          
       1687 CCAGAGTACACAACTTTCCAACCTGGTATCACTTTTCCAAAACTGTTTATTCTATCTGCTGC
          1 CCAGAGTACACAACTTTCCAACCTGGTATCACTTTTCCAAAACTGTTTATTCTATCTGCTGC

       1749 TTTTAAGATG


Statistics
Matches: 62,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  62   62  1.00

ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34


Consensus pattern (62 bp):   
CCAGAGTACACAACTTTCCAACCTGGTATCACTTTTCCAAAACTGTTTATTCTATCTGCTGC

Found at i:2536 original size:21 final size:21

Alignment explanation


    Indices: 2493--2537  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2483 GTCTGATGCC

                       *      *  
       2493 GCCATCACCGAGGCCATACAT
          1 GCCATCACCGAAGCCATAAAT

                        *  *     
       2514 GCCATCACCGAATCCTTAAAT
          1 GCCATCACCGAAGCCATAAAT

               
       2535 GCC
          1 GCC

       2538 CAACTTCAAG


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.29, C:0.38, G:0.16, T:0.18


Consensus pattern (21 bp):   
GCCATCACCGAAGCCATAAAT

Found at i:7304 original size:20 final size:20

Alignment explanation


    Indices: 7277--7317  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       7267 TATTCTCTCT

                     *          
       7277 TTCCTCCCTGTTTCT-CTTC
          1 TTCCTCCCTCTTTCTGCTTC

                                 
       7296 TTCCTTCCCTCTTTCTGCTTC
          1 TTCC-TCCCTCTTTCTGCTTC

             
       7317 T
          1 T

       7318 CTTATCTCTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19    4  0.21
  20   10  0.53
  21    5  0.26

ACGTcount: A:0.00, C:0.41, G:0.05, T:0.54


Consensus pattern (20 bp):   
TTCCTCCCTCTTTCTGCTTC
Done.