Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012087.1 Corchorus olitorius cultivar O-4 contig12120, 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: 24455
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:422 original size:16 final size:16

Alignment explanation


    Indices: 401--443  Score: 68
    Period size: 16  Copynumber: 2.7  Consensus size: 16

        391 TTTCTATAAA

                          * 
        401 TTAATTTCTAATTGTG
          1 TTAATTTCTAATTGAG

                   *        
        417 TTAATTTGTAATTGAG
          1 TTAATTTCTAATTGAG

                       
        433 TTAATTTCTAA
          1 TTAATTTCTAA

        444 ATTATATATA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53


Consensus pattern (16 bp):   
TTAATTTCTAATTGAG

Found at i:3836 original size:109 final size:111

Alignment explanation


    Indices: 3634--3842  Score: 316
    Period size: 109  Copynumber: 1.9  Consensus size: 111

       3624 ATTAAATAAG

                                   *                                         
       3634 TACTCAATTTAGAAATTAATTTTGAAGAGTTATTTTACATTTAAATTAGCAAATCAATTGTAACT
          1 TACTCAATTTAGAAATTAATTTTCAAGAGTTATTTTACATTTAAATTA--AAATCAATTGTAACT

                 *                                          
       3699 AATTGGTAGCATTAAATTACTCAAAAATTACACCATTGATTATTTAAT
         64 AATTGATAGCATTAAATTACTCAAAAATTACACCATTGATTATTTAAT

                          *                     ***                          
       3747 TACTCAA-TTAGAAGTTAATTTTCAAGAGTTATTTTTTGTTTAAATT-AAATCAATTGTAA-TGA
          1 TACTCAATTTAGAAATTAATTTTCAAGAGTTATTTTACATTTAAATTAAAATCAATTGTAACT-A

                                              
       3809 ATTGATAGCATTAAATTACTCAAAAATTACACCA
         65 ATTGATAGCATTAAATTACTCAAAAATTACACCA

       3843 ACTATTTACT


Statistics
Matches: 89,  Mismatches: 6, Indels: 6
        0.88            0.06        0.06

Matches are distributed among these distances:
 108    1  0.01
 109   47  0.53
 112   34  0.38
 113    7  0.08

ACGTcount: A:0.41, C:0.11, G:0.09, T:0.40


Consensus pattern (111 bp):   
TACTCAATTTAGAAATTAATTTTCAAGAGTTATTTTACATTTAAATTAAAATCAATTGTAACTAA
TTGATAGCATTAAATTACTCAAAAATTACACCATTGATTATTTAAT

Found at i:7737 original size:38 final size:36

Alignment explanation


    Indices: 7663--7742  Score: 99
    Period size: 38  Copynumber: 2.2  Consensus size: 36

       7653 CAAGTGCCAA

                                  *    *        
       7663 GCCTGGCCGCTAGGCCTGCGCTGGCCCTCGCACCTG
          1 GCCTGGCCGCTAGGCCTGCGCTAGCCCACGCACCTG

                         *                   *    
       7699 GCCTGGCACGCTTGGGCCTGCGCTAGCCCACGCGCCTG
          1 GCCTGGC-CGC-TAGGCCTGCGCTAGCCCACGCACCTG

                   
       7737 G-CTGGC
          1 GCCTGGC

       7743 GCCTAGGTCG


Statistics
Matches: 38,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  36    7  0.18
  37    8  0.21
  38   23  0.61

ACGTcount: A:0.06, C:0.42, G:0.35, T:0.16


Consensus pattern (36 bp):   
GCCTGGCCGCTAGGCCTGCGCTAGCCCACGCACCTG

Found at i:13955 original size:10 final size:10

Alignment explanation


    Indices: 13942--13966  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

      13932 CAAACATTTT

                      
      13942 AAATCCTCTG
          1 AAATCCTCTG

                      
      13952 AAATCCTCTG
          1 AAATCCTCTG

                 
      13962 AAATC
          1 AAATC

      13967 TTCAAGCTAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28


Consensus pattern (10 bp):   
AAATCCTCTG

Found at i:18869 original size:17 final size:19

Alignment explanation


    Indices: 18847--18887  Score: 59
    Period size: 17  Copynumber: 2.3  Consensus size: 19

      18837 ATCACAAAAT

                     *         
      18847 ATTAACAACTA-T-AATTA
          1 ATTAACAACAATTAAATTA

                               
      18864 ATTAACAACAATTAAATTA
          1 ATTAACAACAATTAAATTA

                 
      18883 ATTAA
          1 ATTAA

      18888 TTAATTATAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17   10  0.48
  18    1  0.05
  19   10  0.48

ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34


Consensus pattern (19 bp):   
ATTAACAACAATTAAATTA

Found at i:23327 original size:16 final size:17

Alignment explanation


    Indices: 23308--23347  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      23298 CTTCTTTTAA

                           * 
      23308 TTTTTCT-GATTTTTTC
          1 TTTTTCTGGATTTTTCC

                 *           
      23324 TTTTTTTGGATTTTTCC
          1 TTTTTCTGGATTTTTCC

                   
      23341 TTTTTCT
          1 TTTTTCT

      23348 ATCTCTAAAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  16    6  0.30
  17   14  0.70

ACGTcount: A:0.05, C:0.12, G:0.07, T:0.75


Consensus pattern (17 bp):   
TTTTTCTGGATTTTTCC
Done.