Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008315.1 Corchorus olitorius cultivar O-4 contig08342, 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, 712

Length: 1188
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36


Found at i:578 original size:13 final size:13

Alignment explanation


    Indices: 556--591  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

        546 TTTCCCTTTT

                         
        556 TTTTTC-TTTTCC
          1 TTTTTCTTTTTCC

                         
        568 TTTTTCTTTTTCC
          1 TTTTTCTTTTTCC

                *      
        581 TTTTCCTTTTT
          1 TTTTTCTTTTT

        592 TTTTCCTCTC


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  12    6  0.27
  13   16  0.73

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (13 bp):   
TTTTTCTTTTTCC

Found at i:589 original size:35 final size:39

Alignment explanation


    Indices: 513--596  Score: 106
    Period size: 41  Copynumber: 2.2  Consensus size: 39

        503 TTTATTTTTA

                                                     
        513 TTTTTTTT-ATTTCCTTTTTCTTCCTTATCCGGTTTTCCCT
          1 TTTTTTTTCATTTCCTTTTTCTT-CTTATCC-GTTTTCCCT

                     *                             
        553 TTTTTTTTCTTTTCCTTTTTCTT-TT-TCC-TTTT-CCT
          1 TTTTTTTTCATTTCCTTTTTCTTCTTATCCGTTTTCCCT

                     
        588 TTTTTTTTC
          1 TTTTTTTTC

        597 CTCTCTTTTC


Statistics
Matches: 42,  Mismatches: 1, Indels: 7
        0.84            0.02        0.14

Matches are distributed among these distances:
  35   12  0.29
  36    4  0.10
  38    3  0.07
  39    2  0.05
  40    8  0.19
  41   13  0.31

ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73


Consensus pattern (39 bp):   
TTTTTTTTCATTTCCTTTTTCTTCTTATCCGTTTTCCCT

Found at i:597 original size:17 final size:17

Alignment explanation


    Indices: 545--598  Score: 74
    Period size: 17  Copynumber: 3.1  Consensus size: 17

        535 CCTTATCCGG

                              
        545 TTTTCCCTTTTTTTTT-C
          1 TTTT-CCTTTTTTTTTCC

                               
        562 TTTTCCTTTTTCTTTTTCC
          1 TTTTCC-TTTT-TTTTTCC

                             
        581 TTTTCCTTTTTTTTTCC
          1 TTTTCCTTTTTTTTTCC

             
        598 T
          1 T

        599 CTCTTTTCCT


Statistics
Matches: 34,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
  16    2  0.06
  17   16  0.47
  18    9  0.26
  19    7  0.21

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (17 bp):   
TTTTCCTTTTTTTTTCC
Done.