Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004717.1 Corchorus capsularis cultivar CVL-1 contig04733, 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, 659

Length: 1099
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.26


Found at i:245 original size:32 final size:32

Alignment explanation


    Indices: 156--246  Score: 157
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        146 GGACACCCTT

                                     *      
        156 CGTCGGCATTCTCCGATGGCACTTGACCTTGG
          1 CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

                                             
        188 CGTCGGCATTCTCCGATGG-ATCTTGGCCTTGG
          1 CGTCGGCATTCTCCGATGGCA-CTTGGCCTTGG

                                       
        220 CGTCGGCATTCTCCGATGGCACTTGGC
          1 CGTCGGCATTCTCCGATGGCACTTGGC

        247 ATCGGCACTT


Statistics
Matches: 56,  Mismatches: 1, Indels: 4
        0.92            0.02        0.07

Matches are distributed among these distances:
  31    1  0.02
  32   54  0.96
  33    1  0.02

ACGTcount: A:0.11, C:0.31, G:0.30, T:0.29


Consensus pattern (32 bp):   
CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

Found at i:246 original size:26 final size:26

Alignment explanation


    Indices: 234--316  Score: 166
    Period size: 26  Copynumber: 3.2  Consensus size: 26

        224 GGCATTCTCC

                                      
        234 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                                      
        260 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                                      
        286 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                 
        312 GATGG
          1 GATGG

        317 ATGGCACTTG


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   57  1.00

ACGTcount: A:0.16, C:0.25, G:0.33, T:0.27


Consensus pattern (26 bp):   
GATGGCACTTGGCATCGGCACTTGCT

Found at i:253 original size:13 final size:13

Alignment explanation


    Indices: 237--309  Score: 82
    Period size: 13  Copynumber: 5.6  Consensus size: 13

        227 ATTCTCCGAT

                         
        237 GGCACTTGGCATC
          1 GGCACTTGGCATC

                           
        250 GGCACTT-GCTGAT-
          1 GGCACTTGGC--ATC

                         
        263 GGCACTTGGCATC
          1 GGCACTTGGCATC

                           
        276 GGCACTT-GCTGAT-
          1 GGCACTTGGC--ATC

                         
        289 GGCACTTGGCATC
          1 GGCACTTGGCATC

                    
        302 GGCACTTG
          1 GGCACTTG

        310 CTGATGGATG


Statistics
Matches: 52,  Mismatches: 0, Indels: 16
        0.76            0.00        0.24

Matches are distributed among these distances:
  12    8  0.15
  13   36  0.69
  14    8  0.15

ACGTcount: A:0.15, C:0.27, G:0.32, T:0.26


Consensus pattern (13 bp):   
GGCACTTGGCATC

Found at i:278 original size:52 final size:51

Alignment explanation


    Indices: 211--316  Score: 162
    Period size: 52  Copynumber: 2.1  Consensus size: 51

        201 CGATGGATCT

                      *                                          
        211 TGGCCTTGGCGTCGGCA-TT-CTCCGATGGCACTTGGCATCGGCACTTGCTGA
          1 TGGCCTTGGCATCGGCACTTGCT--GATGGCACTTGGCATCGGCACTTGCTGA

                                                                
        262 TGGCACTTGGCATCGGCACTTGCTGATGGCACTTGGCATCGGCACTTGCTGA
          1 TGGC-CTTGGCATCGGCACTTGCTGATGGCACTTGGCATCGGCACTTGCTGA

               
        314 TGG
          1 TGG

        317 ATGGCACTTG


Statistics
Matches: 51,  Mismatches: 1, Indels: 5
        0.89            0.02        0.09

Matches are distributed among these distances:
  51    4  0.08
  52   43  0.84
  53    2  0.04
  54    2  0.04

ACGTcount: A:0.13, C:0.27, G:0.32, T:0.27


Consensus pattern (51 bp):   
TGGCCTTGGCATCGGCACTTGCTGATGGCACTTGGCATCGGCACTTGCTGA
Done.