Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011804.1 Corchorus capsularis cultivar CVL-1 contig11825, 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: 26093
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:2025 original size:1 final size:1

Alignment explanation


    Indices: 2021--2045  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

       2011 AAAAGAGAAG

                                     
       2021 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

       2046 GACTGCCGGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:4089 original size:19 final size:19

Alignment explanation


    Indices: 4046--4092  Score: 60
    Period size: 20  Copynumber: 2.4  Consensus size: 19

       4036 TTTTCCAGAA

                *              
       4046 AACAATTTTTAGAAAATAG
          1 AACATTTTTTAGAAAATAG

                                 
       4065 ATACATTTTTTAGAAAATATG
          1 A-ACATTTTTTAGAAAATA-G

                    
       4086 -ACATTTT
          1 AACATTTT

       4093 CTGTTGTTTG


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

Matches are distributed among these distances:
  19    8  0.32
  20   16  0.64
  21    1  0.04

ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40


Consensus pattern (19 bp):   
AACATTTTTTAGAAAATAG

Found at i:13775 original size:12 final size:13

Alignment explanation


    Indices: 13753--13781  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

      13743 AAAGAAGAGG

                         
      13753 AGAAATAAGAATA
          1 AGAAATAAGAATA

                         
      13766 AGAAAT-AGAATA
          1 AGAAATAAGAATA

                
      13778 AGAA
          1 AGAA

      13782 TCCTCCAACT


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

Matches are distributed among these distances:
  12   10  0.62
  13    6  0.38

ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14


Consensus pattern (13 bp):   
AGAAATAAGAATA

Found at i:17901 original size:40 final size:42

Alignment explanation


    Indices: 17846--17930  Score: 156
    Period size: 42  Copynumber: 2.1  Consensus size: 42

      17836 TTTCGACAAC

                                                      
      17846 TTATCATTGAT-A-ATATATTCATGCTATAGTAAGCGCCTGA
          1 TTATCATTGATAATATATATTCATGCTATAGTAAGCGCCTGA

                                                      
      17886 TTATCATTGATAATATATATTCATGCTATAGTAAGCGCCTGA
          1 TTATCATTGATAATATATATTCATGCTATAGTAAGCGCCTGA

               
      17928 TTA
          1 TTA

      17931 GGAACATGGG


Statistics
Matches: 43,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  40   11  0.26
  41    1  0.02
  42   31  0.72

ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39


Consensus pattern (42 bp):   
TTATCATTGATAATATATATTCATGCTATAGTAAGCGCCTGA

Found at i:18390 original size:23 final size:23

Alignment explanation


    Indices: 18360--18405  Score: 83
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      18350 CCTTATCATC

                                   
      18360 CTCATCACACCCATTACTTTGTT
          1 CTCATCACACCCATTACTTTGTT

                     *             
      18383 CTCATCACAGCCATTACTTTGTT
          1 CTCATCACACCCATTACTTTGTT

      18406 TAACATAGTC


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.22, C:0.33, G:0.07, T:0.39


Consensus pattern (23 bp):   
CTCATCACACCCATTACTTTGTT

Found at i:18453 original size:16 final size:16

Alignment explanation


    Indices: 18432--18463  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      18422 AGTTGCTCCA

                            
      18432 CCATAAATTGTTTCCT
          1 CCATAAATTGTTTCCT

                            
      18448 CCATAAATTGTTTCCT
          1 CCATAAATTGTTTCCT

      18464 TGTAGCTTAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44


Consensus pattern (16 bp):   
CCATAAATTGTTTCCT
Done.