Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009630.1 Corchorus olitorius cultivar O-4 contig09662, 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: 3182
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:1302 original size:15 final size:16

Alignment explanation


    Indices: 1278--1309  Score: 57
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       1268 CCCTAAAACA

                            
       1278 AAAAAGGCTCTCAATC
          1 AAAAAGGCTCTCAATC

                            
       1294 AAAAA-GCTCTCAATC
          1 AAAAAGGCTCTCAATC

             
       1309 A
          1 A

       1310 CTCTGTAAAT


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

Matches are distributed among these distances:
  15   11  0.69
  16    5  0.31

ACGTcount: A:0.47, C:0.25, G:0.09, T:0.19


Consensus pattern (16 bp):   
AAAAAGGCTCTCAATC

Found at i:3122 original size:16 final size:16

Alignment explanation


    Indices: 3101--3131  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       3091 TCAAGGCTAG

                      *     
       3101 ACCCGGCCCGGCCCGA
          1 ACCCGGCCCGACCCGA

                           
       3117 ACCCGGCCCGACCCG
          1 ACCCGGCCCGACCCG

       3132 GCCCATGAAC


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.13, C:0.58, G:0.29, T:0.00


Consensus pattern (16 bp):   
ACCCGGCCCGACCCGA

Found at i:3130 original size:10 final size:10

Alignment explanation


    Indices: 3102--3135  Score: 50
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       3092 CAAGGCTAGA

                *     
       3102 CCCGGCCCGG
          1 CCCGACCCGG

                       
       3112 CCCGAACCCGG
          1 CCCG-ACCCGG

                      
       3123 CCCGACCCGG
          1 CCCGACCCGG

               
       3133 CCC
          1 CCC

       3136 ATGAACAGGT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  10   13  0.59
  11    9  0.41

ACGTcount: A:0.09, C:0.62, G:0.29, T:0.00


Consensus pattern (10 bp):   
CCCGACCCGG
Done.