Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004172.1 Corchorus capsularis cultivar CVL-1 contig04180, 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, 621

Length: 1036
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30


Found at i:827 original size:35 final size:35

Alignment explanation


    Indices: 781--997  Score: 294
    Period size: 35  Copynumber: 5.9  Consensus size: 35

        771 CTCTGTGCGG

                                               
        781 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC

                                                           
        816 TCATTTCAAGAAGTTTTCAGAGAAGTTTTCAGAGGTCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTC-----AG-----AG-G-TCAGAGTTGATC

                                               
        863 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC

                                               
        898 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC

              * *                              
        933 TCGTATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC

                                            
        968 TCATTTCAAGAAGTTTTCAGA-G-CAGAGTTG
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTG

        998 TCAGAGGTCA


Statistics
Matches: 166,  Mismatches: 4, Indels: 26
        0.85            0.02        0.13

Matches are distributed among these distances:
  33    8  0.05
  34    1  0.01
  35  117  0.70
  36    1  0.01
  37    2  0.01
  40    2  0.01
  42    2  0.01
  45    2  0.01
  46    1  0.01
  47   30  0.18

ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34


Consensus pattern (35 bp):   
TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC

Found at i:841 original size:12 final size:12

Alignment explanation


    Indices: 819--849  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

        809 GTTGATCTCA

                        
        819 TTTCA-AGAAGT
          1 TTTCAGAGAAGT

                        
        830 TTTCAGAGAAGT
          1 TTTCAGAGAAGT

                    
        842 TTTCAGAG
          1 TTTCAGAG

        850 GTCAGAGTTG


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11    5  0.26
  12   14  0.74

ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35


Consensus pattern (12 bp):   
TTTCAGAGAAGT

Found at i:918 original size:82 final size:82

Alignment explanation


    Indices: 781--1036  Score: 383
    Period size: 70  Copynumber: 3.2  Consensus size: 82

        771 CTCTGTGCGG

                                                                             
        781 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGAAGTTTTC
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGAAGTTTTC

                             
        846 AGAGGTCAGAGTTGATC
         66 AGAGGTCAGAGTTGATC

                                                                             
        863 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGA--TC---TC----A--TTTCA-AGAAGTTTTC
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGAAGTTTTC

                             
        916 AGAGGTCAGAGTTGATC
         66 AGAGGTCAGAGTTGATC

              * *                                                           *
        933 TCGTATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGCAGAGTTG
          1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAG-A-AGTTT

                               
        998 TCAGAGGTCAGAGTTGATC
         64 TCAGAGGTCAGAGTTGATC

                                
       1017 TCATTTCAAGAAGTTTTCAG
          1 TCATTTCAAGAAGTTTTCAG


Statistics
Matches: 155,  Mismatches: 5, Indels: 26
        0.83            0.03        0.14

Matches are distributed among these distances:
  70   58  0.37
  71    5  0.03
  72    2  0.01
  73    1  0.01
  75    2  0.01
  77    2  0.01
  79    1  0.01
  80    2  0.01
  81    5  0.03
  82   35  0.23
  83    1  0.01
  84   41  0.26

ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34


Consensus pattern (82 bp):   
TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGAAGTTTTC
AGAGGTCAGAGTTGATC
Done.