Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012165.1 Corchorus olitorius cultivar O-4 contig12198, 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: 1833
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:1021 original size:6 final size:6

Alignment explanation


    Indices: 1006--1076  Score: 51
    Period size: 6  Copynumber: 12.0  Consensus size: 6

        996 CTATTTCCCT

                             *                                  *    
       1006 TTCTTT TT-TTT CTTTTTT TTCCTTT TTC-TT TTC-TT TTCTTT TCCTTT
          1 TTCTTT TTCTTT -TTCTTT TT-CTTT TTCTTT TTCTTT TTCTTT TTCTTT

              *      *                  
       1053 TCCCTTT TCCTTT TT-TTT TTCTTT
          1 T-TCTTT TTCTTT TTCTTT TTCTTT

       1077 CCTTCCTTCC


Statistics
Matches: 56,  Mismatches: 3, Indels: 12
        0.79            0.04        0.17

Matches are distributed among these distances:
   5   18  0.32
   6   24  0.43
   7   14  0.25

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (6 bp):   
TTCTTT

Found at i:1033 original size:16 final size:17

Alignment explanation


    Indices: 1012--1080  Score: 81
    Period size: 16  Copynumber: 4.1  Consensus size: 17

       1002 CCCTTTCTTT

                             
       1012 TTTTTCTTTT-TTTTCC
          1 TTTTTCTTTTCTTTTCC

                             
       1028 TTTTTCTTTTCTTTT-C
          1 TTTTTCTTTTCTTTTCC

                *              
       1044 TTTTCCTTTTCCCTTTTCC
          1 TTTTTCTTTT--CTTTTCC

                 *           
       1063 TTTTTTTTTTC-TTTCC
          1 TTTTTCTTTTCTTTTCC

              
       1079 TT
          1 TT

       1081 CCTTCCTTCC


Statistics
Matches: 46,  Mismatches: 3, Indels: 8
        0.81            0.05        0.14

Matches are distributed among these distances:
  16   27  0.59
  17    5  0.11
  18    5  0.11
  19    9  0.20

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (17 bp):   
TTTTTCTTTTCTTTTCC

Found at i:1037 original size:5 final size:5

Alignment explanation


    Indices: 1005--1054  Score: 59
    Period size: 5  Copynumber: 9.8  Consensus size: 5

        995 CCTATTTCCC

                                                                    
       1005 TTTCT TTT-T TTTCT TTT-T TTTCCTT TTTCT TTTCT TTTCT TTTCCT
          1 TTTCT TTTCT TTTCT TTTCT TTT-C-T TTTCT TTTCT TTTCT TTT-CT

                
       1051 TTTC
          1 TTTC

       1055 CCTTTTCCTT


Statistics
Matches: 40,  Mismatches: 0, Indels: 10
        0.80            0.00        0.20

Matches are distributed among these distances:
   4    8  0.20
   5   22  0.55
   6    6  0.15
   7    4  0.10

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (5 bp):   
TTTCT
Done.