Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001918.1 Corchorus olitorius cultivar O-4 contig01918, 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: 8975
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:2179 original size:29 final size:29

Alignment explanation


    Indices: 2132--2188  Score: 73
    Period size: 28  Copynumber: 2.0  Consensus size: 29

       2122 GAGGCTTCAA

                                  *       
       2132 ATTGAGAGTTCAAGGGGCAACATGTCCAAG
          1 ATTGAGAGTTCAAGGGGCAA-ACGTCCAAG

                                         
       2162 ATTGA-AGTTC-AGGAGGCAAACGTCCAA
          1 ATTGAGAGTTCAAGG-GGCAAACGTCCAA

       2189 ATACAAATTG


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  28   10  0.40
  29   10  0.40
  30    5  0.20

ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19


Consensus pattern (29 bp):   
ATTGAGAGTTCAAGGGGCAAACGTCCAAG

Found at i:4210 original size:17 final size:16

Alignment explanation


    Indices: 4163--4212  Score: 55
    Period size: 17  Copynumber: 2.9  Consensus size: 16

       4153 ATAAACCCAT

                           * 
       4163 GTAATCTTTGATCACCG
          1 GTAATC-TTGATCACTG

              *              
       4180 GTGATCTTGCATCACTG
          1 GTAATCTTG-ATCACTG

                            
       4197 GTAATCTTAGATCACT
          1 GTAATCTT-GATCACT

       4213 AGTGATCTGG


Statistics
Matches: 28,  Mismatches: 3, Indels: 4
        0.80            0.09        0.11

Matches are distributed among these distances:
  16    3  0.11
  17   24  0.86
  18    1  0.04

ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36


Consensus pattern (16 bp):   
GTAATCTTGATCACTG

Found at i:4220 original size:17 final size:16

Alignment explanation


    Indices: 4170--4220  Score: 57
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       4160 CATGTAATCT

                    *       
       4170 TTGATCACCGGTGATC
          1 TTGATCACTGGTGATC

                         *   
       4186 TTGCATCACTGGTAATC
          1 TTG-ATCACTGGTGATC

                      *      
       4203 TTAGATCACTAGTGATC
          1 TT-GATCACTGGTGATC

             
       4220 T
          1 T

       4221 GGGGGTGATC


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   25  0.86
  18    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35


Consensus pattern (16 bp):   
TTGATCACTGGTGATC

Found at i:4569 original size:21 final size:21

Alignment explanation


    Indices: 4519--4576  Score: 62
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       4509 CCTAATTATG

                                   
       4519 AAATTTTAATAAACCTTCCTATA
          1 AAATTTT-AT-AACCTTCCTATA

                   *            *
       4542 AAATTTTGTAACCTTCCTATG
          1 AAATTTTATAACCTTCCTATA

             **           
       4563 ATTTTTTATAACCT
          1 AAATTTTATAACCT

       4577 CTCTGTGAGA


Statistics
Matches: 30,  Mismatches: 5, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  21   22  0.73
  22    1  0.03
  23    7  0.23

ACGTcount: A:0.34, C:0.17, G:0.03, T:0.45


Consensus pattern (21 bp):   
AAATTTTATAACCTTCCTATA

Found at i:8327 original size:20 final size:20

Alignment explanation


    Indices: 8263--8327  Score: 69
    Period size: 20  Copynumber: 3.2  Consensus size: 20

       8253 GACATCTATG

                                
       8263 GTTTTTCATTATATATTATT
          1 GTTTTTCATTATATATTATT

                *     * *        *
       8283 GTTTCT-AGTAAGATATTTATA
          1 GTTTTTCA-TTATATA-TTATT

                                
       8304 GTTTTTCATTATATATTATT
          1 GTTTTTCATTATATATTATT

                
       8324 GTTT
          1 GTTT

       8328 CTTATAAGAC


Statistics
Matches: 34,  Mismatches: 8, Indels: 6
        0.71            0.17        0.12

Matches are distributed among these distances:
  19    1  0.03
  20   18  0.53
  21   14  0.41
  22    1  0.03

ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60


Consensus pattern (20 bp):   
GTTTTTCATTATATATTATT

Found at i:8545 original size:51 final size:51

Alignment explanation


    Indices: 8469--8566  Score: 187
    Period size: 51  Copynumber: 1.9  Consensus size: 51

       8459 TTCTAGTTCT

                          *                                    
       8469 GCTCTTTGCTATGGTGCGGAAGTCACGACCACCCCACTCATGTTCGATTCC
          1 GCTCTTTGCTATGGCGCGGAAGTCACGACCACCCCACTCATGTTCGATTCC

                                                           
       8520 GCTCTTTGCTATGGCGCGGAAGTCACGACCACCCCACTCATGTTCGA
          1 GCTCTTTGCTATGGCGCGGAAGTCACGACCACCCCACTCATGTTCGA

       8567 CGGCGGTGCT


Statistics
Matches: 46,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   46  1.00

ACGTcount: A:0.18, C:0.34, G:0.22, T:0.26


Consensus pattern (51 bp):   
GCTCTTTGCTATGGCGCGGAAGTCACGACCACCCCACTCATGTTCGATTCC
Done.