Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018782.1 Corchorus olitorius cultivar O-4 contig18815, 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: 21414
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31


Found at i:5803 original size:16 final size:18

Alignment explanation


    Indices: 5777--5809  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       5767 AGTGCAAATT

                              
       5777 AAAATAG-AAAAATAAAG
          1 AAAATAGAAAAAATAAAG

                             
       5794 AAAA-AGAAAAAATAAA
          1 AAAATAGAAAAAATAAA

       5810 ATCGCAATTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    2  0.13
  17   13  0.87

ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09


Consensus pattern (18 bp):   
AAAATAGAAAAAATAAAG

Found at i:6042 original size:12 final size:13

Alignment explanation


    Indices: 6020--6049  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

       6010 ACTAACAATT

                         
       6020 AAAATCAATCAAG
          1 AAAATCAATCAAG

                         
       6033 AAAA-CAATCAAG
          1 AAAATCAATCAAG

                 
       6045 AAAAT
          1 AAAAT

       6050 TAAAGAAAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13


Consensus pattern (13 bp):   
AAAATCAATCAAG

Found at i:8668 original size:21 final size:21

Alignment explanation


    Indices: 8644--8685  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8634 TCTTTCTCTT

                *      *         
       8644 GTCATTGGACCTAATGGCATC
          1 GTCAATGGACCAAATGGCATC

                     *           
       8665 GTCAATGGATCAAATGGCATC
          1 GTCAATGGACCAAATGGCATC

       8686 TTTGGCATCT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26


Consensus pattern (21 bp):   
GTCAATGGACCAAATGGCATC

Found at i:15123 original size:22 final size:21

Alignment explanation


    Indices: 15071--15124  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

      15061 TGCTTCTTGA

                                  
      15071 AATAATTCTTC-AATGATCTTC
          1 AATAA-TCTTCAAATGATCTTC

                          *      
      15092 -A-AATCTTCAAATTATCTTC
          1 AATAATCTTCAAATGATCTTC

                          
      15111 AATAAGTCTTCAAA
          1 AATAA-TCTTCAAA

      15125 CACGAACTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    5  0.18
  19   11  0.39
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39


Consensus pattern (21 bp):   
AATAATCTTCAAATGATCTTC

Found at i:17592 original size:31 final size:30

Alignment explanation


    Indices: 17557--17633  Score: 102
    Period size: 29  Copynumber: 2.6  Consensus size: 30

      17547 ATACCGTACA

                                           
      17557 GGTCCCTCTACTTACAAAAAAGGATCAATTT
          1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT

                          *     **    *   
      17588 GGTCCCTCTAC-TATAAAAACTGTCACTTT
          1 GGTCCCTCTACTTACAAAAAAGGTCAATTT

                             
      17617 GGTCCCTCTACTTACAA
          1 GGTCCCTCTACTTACAA

      17634 TTTAGTATCA


Statistics
Matches: 40,  Mismatches: 5, Indels: 3
        0.83            0.10        0.06

Matches are distributed among these distances:
  29   17  0.43
  30   12  0.30
  31   11  0.28

ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31


Consensus pattern (30 bp):   
GGTCCCTCTACTTACAAAAAAGGTCAATTT

Found at i:20382 original size:6 final size:6

Alignment explanation


    Indices: 20371--20395  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      20361 CAAATCAAAT

                                         
      20371 AGAAAA AGAAAA AGAAAA AGAAAA A
          1 AGAAAA AGAAAA AGAAAA AGAAAA A

      20396 TAATACACAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Done.