Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021581.1 Corchorus olitorius cultivar O-4 contig21614, 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: 11478
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:7986 original size:22 final size:21

Alignment explanation


    Indices: 7948--8020  Score: 71
    Period size: 22  Copynumber: 3.4  Consensus size: 21

       7938 TAAATCTTTA

                         *         
       7948 TTTCCTTATTTC-CTTCTTCTTT
          1 TTTCCTT-TTTCTTTTCTT-TTT

                               * 
       7970 TTTCCTTTTTCTTTTCTTTCT
          1 TTTCCTTTTTCTTTTCTTTTT

                                   
       7991 TTTCCTTTCTAT-TTTTCTTTTT
          1 TTTCCTTT-T-TCTTTTCTTTTT

                     
       8013 TTT-CTTTT
          1 TTTCCTTTT

       8021 CCCTTTTTGG


Statistics
Matches: 45,  Mismatches: 3, Indels: 8
        0.80            0.05        0.14

Matches are distributed among these distances:
  20    1  0.02
  21   18  0.40
  22   25  0.56
  23    1  0.02

ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75


Consensus pattern (21 bp):   
TTTCCTTTTTCTTTTCTTTTT

Found at i:7989 original size:9 final size:9

Alignment explanation


    Indices: 7977--8021  Score: 56
    Period size: 9  Copynumber: 5.0  Consensus size: 9

       7967 TTTTTTCCTT

                     
       7977 TTTCTTTTC
          1 TTTCTTTTC

                      
       7986 TTTCTTTTCC
          1 TTTCTTTT-C

                 *   
       7996 TTTCTATT-
          1 TTTCTTTTC

                    *
       8004 TTTCTTTTT
          1 TTTCTTTTC

                     
       8013 TTTCTTTTC
          1 TTTCTTTTC

       8022 CCTTTTTGGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
   8    7  0.23
   9   16  0.52
  10    8  0.26

ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78


Consensus pattern (9 bp):   
TTTCTTTTC

Found at i:8027 original size:22 final size:22

Alignment explanation


    Indices: 7981--8028  Score: 60
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       7971 TTCCTTTTTC

                               *  
       7981 TTTTCTTTCTTTTCCTTTCTAT
          1 TTTTCTTTCTTTTCCTTTCCAT

                    *     *     * 
       8003 TTTTCTTTTTTTTCTTTTCCCT
          1 TTTTCTTTCTTTTCCTTTCCAT

                
       8025 TTTT
          1 TTTT

       8029 GGGCCAGCCC


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77


Consensus pattern (22 bp):   
TTTTCTTTCTTTTCCTTTCCAT

Found at i:9619 original size:22 final size:21

Alignment explanation


    Indices: 9575--9621  Score: 58
    Period size: 22  Copynumber: 2.2  Consensus size: 21

       9565 CCAATTTAGG

                     *     *     
       9575 TTTAGATTTCAATTTCTTGTT
          1 TTTAGATTTAAATTTATTGTT

                               *  
       9596 TTTAGATTTAAGATTTATTTTT
          1 TTTAGATTTAA-ATTTATTGTT

                
       9618 TTTA
          1 TTTA

       9622 TGCATCTTAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  21   10  0.45
  22   12  0.55

ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64


Consensus pattern (21 bp):   
TTTAGATTTAAATTTATTGTT

Found at i:10948 original size:15 final size:16

Alignment explanation


    Indices: 10919--10948  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      10909 GTGTGAATTC

                            
      10919 AAATTGATCTTTTGAA
          1 AAATTGATCTTTTGAA

                           
      10935 AAATTGAT-TTTTGA
          1 AAATTGATCTTTTGA

      10949 TAAACTTACA


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

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47


Consensus pattern (16 bp):   
AAATTGATCTTTTGAA
Done.