Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000298.1 Corchorus olitorius cultivar O-4 contig00298, 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: 1897
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1208 original size:20 final size:21

Alignment explanation


    Indices: 1164--1234  Score: 108
    Period size: 20  Copynumber: 3.4  Consensus size: 21

       1154 AGATTCAGTT

                *         *       
       1164 TTAGAGTTCATTGAATTCAAAA
          1 TTAGGGTTC-TTGAGTTCAAAA

                                 
       1186 TTAGGGTTCTTGAGTTC-AAA
          1 TTAGGGTTCTTGAGTTCAAAA

                                 
       1206 TTAGGGTTCTTGAGTTCAAAA
          1 TTAGGGTTCTTGAGTTCAAAA

                    
       1227 TTAGGGTT
          1 TTAGGGTT

       1235 ATTGGTTGAT


Statistics
Matches: 46,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  20   20  0.43
  21   18  0.39
  22    8  0.17

ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39


Consensus pattern (21 bp):   
TTAGGGTTCTTGAGTTCAAAA

Found at i:1566 original size:27 final size:29

Alignment explanation


    Indices: 1493--1569  Score: 95
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       1483 TTAGGATCAC

                                 *       
       1493 CTAGGGGCATTTTGGTCATTTTCAAAAAT
          1 CTAGGGGCATTTTGGTCATTTGCAAAAAT

                         *           * * 
       1522 CTAGGGGCATTTTAGTCATTTGC-ATATT
          1 CTAGGGGCATTTTGGTCATTTGCAAAAAT

               *                 
       1550 C-ATGGGCATTTTGGTCATTT
          1 CTAGGGGCATTTTGGTCATTT

       1570 TAAGGCCACG


Statistics
Matches: 42,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  27   17  0.40
  28    4  0.10
  29   21  0.50

ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42


Consensus pattern (29 bp):   
CTAGGGGCATTTTGGTCATTTGCAAAAAT

Found at i:1726 original size:22 final size:22

Alignment explanation


    Indices: 1692--1746  Score: 92
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       1682 TGATTTAGCT

                *   *             
       1692 TCATTTAGTTTTTGCACTTTGA
          1 TCATATAGCTTTTGCACTTTGA

                                  
       1714 TCATATAGCTTTTGCACTTTGA
          1 TCATATAGCTTTTGCACTTTGA

                       
       1736 TCATATAGCTT
          1 TCATATAGCTT

       1747 AAGCCCTTGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  22   31  1.00

ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49


Consensus pattern (22 bp):   
TCATATAGCTTTTGCACTTTGA
Done.