Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024323.1 Corchorus olitorius cultivar O-4 contig24356, 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: 9328
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:4492 original size:2 final size:2

Alignment explanation


    Indices: 4485--4533  Score: 98
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       4475 GGTTGATGGG

                                                                          
       4485 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                      
       4527 TC TC TC T
          1 TC TC TC T

       4534 TTTCCTACTT


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   47  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:5951 original size:27 final size:26

Alignment explanation


    Indices: 5896--5973  Score: 84
    Period size: 27  Copynumber: 2.9  Consensus size: 26

       5886 TCTCTTAGTT

                    *        *         
       5896 GGCATTTTAGTCGTTTGCACGTCCAGG
          1 GGCATTTTGGTCGTTTGTAC-TCCAGG

                                 *     
       5923 GGCATTTTGGTCGTTTGTACTTCAGGG
          1 GGCATTTTGGTCGTTTGTACTCCA-GG

                  *     *   *       
       5950 GGCATTGTGGTCATTTCTACTCCA
          1 GGCATTTTGGTCGTTTGTACTCCA

       5974 TTGCTCAAGT


Statistics
Matches: 43,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  26    3  0.07
  27   40  0.93

ACGTcount: A:0.14, C:0.21, G:0.28, T:0.37


Consensus pattern (26 bp):   
GGCATTTTGGTCGTTTGTACTCCAGG

Found at i:6109 original size:19 final size:20

Alignment explanation


    Indices: 6064--6110  Score: 69
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       6054 TGTTGGGTTC

                       *        
       6064 TTTTGCATATTTATATCACA
          1 TTTTGCATATTAATATCACA

                          *     
       6084 TTTTGCATATTAATCTCACA
          1 TTTTGCATATTAATATCACA

                    
       6104 -TTTGCAT
          1 TTTTGCAT

       6111 CTGCATGATC


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  19    7  0.28
  20   18  0.72

ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49


Consensus pattern (20 bp):   
TTTTGCATATTAATATCACA

Found at i:9216 original size:36 final size:35

Alignment explanation


    Indices: 9170--9300  Score: 158
    Period size: 36  Copynumber: 3.6  Consensus size: 35

       9160 GAAAATGACA

                           *                     
       9170 GGAACTTTCCCTTAAATTAAAAAC-TAAAACTTGATG
          1 GGAACTTTCCC--AATTTAAAAACTTAAAACTTGATG

                                                   
       9206 GGAACTTTCCCAATTTAAAAACTTTGAAAAAC-TGAATG
          1 GGAACTTTCCCAATTTAAAAAC-TT--AAAACTTG-ATG

                                           *    
       9244 GGAACTTTCCCAATTTGAAAAACTTAAAACTGGATG
          1 GGAACTTTCCCAATTT-AAAAACTTAAAACTTGATG

                           *     
       9280 GGAACTTTCCCAATTAAAAAA
          1 GGAACTTTCCCAATTTAAAAA

       9301 AACTTTGAAC


Statistics
Matches: 85,  Mismatches: 3, Indels: 15
        0.83            0.03        0.15

Matches are distributed among these distances:
  34   10  0.12
  35    5  0.06
  36   35  0.41
  37    3  0.04
  38   26  0.31
  39    6  0.07

ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28


Consensus pattern (35 bp):   
GGAACTTTCCCAATTTAAAAACTTAAAACTTGATG

Found at i:9245 original size:38 final size:37

Alignment explanation


    Indices: 9195--9309  Score: 146
    Period size: 38  Copynumber: 3.0  Consensus size: 37

       9185 ATTAAAAACT

                                                  
       9195 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGA
          1 AAAAC-TGATGGGAACTTTCCCAATTTAAAAACTTTGA

                                                   
       9233 AAAACTGAATGGGAACTTTCCCAATTTGAAAAAC-TT--
          1 AAAACTG-ATGGGAACTTTCCCAATTT-AAAAACTTTGA

                                        *           
       9269 AAAACTGGATGGGAACTTTCCCAATTAAAAAAAACTTTGA
          1 AAAACT-GATGGGAACTTTCCCAATT--TAAAAACTTTGA

             
       9309 A
          1 A

       9310 CATGATGAAA


Statistics
Matches: 68,  Mismatches: 1, Indels: 14
        0.82            0.01        0.17

Matches are distributed among these distances:
  36   24  0.35
  37    9  0.13
  38   28  0.41
  39    6  0.09
  40    1  0.01

ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28


Consensus pattern (37 bp):   
AAAACTGATGGGAACTTTCCCAATTTAAAAACTTTGA

Found at i:9280 original size:74 final size:74

Alignment explanation


    Indices: 9170--9309  Score: 203
    Period size: 74  Copynumber: 1.9  Consensus size: 74

       9160 GAAAATGACA

                                           *                    *            
       9170 GGAACTTTCCCTTAAATTAAAAACTAAAACTTGATGGGAACTTTCCCAATT-TAAAAACTTTGAA
          1 GGAACTTTCCC-TAAATTAAAAACTAAAACTGGATGGGAACTTTCCCAATTAAAAAAACTTTGAA

                      
       9234 AAACTGAATG
         65 AAACTGAATG

                          *                                                  
       9244 GGAACTTTCCC-AATTTGAAAAACTTAAAACTGGATGGGAACTTTCCCAATTAAAAAAAACTTTG
          1 GGAACTTTCCCTAAATT-AAAAAC-TAAAACTGGATGGGAACTTTCCCAATT-AAAAAAACTTTG

              
       9308 AA
         63 AA

       9310 CATGATGAAA


Statistics
Matches: 59,  Mismatches: 3, Indels: 6
        0.87            0.04        0.09

Matches are distributed among these distances:
  72    4  0.07
  73    6  0.10
  74   37  0.63
  76   12  0.20

ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29


Consensus pattern (74 bp):   
GGAACTTTCCCTAAATTAAAAACTAAAACTGGATGGGAACTTTCCCAATTAAAAAAACTTTGAAA
AACTGAATG

Done.