Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022691.1 Corchorus olitorius cultivar O-4 contig22724, 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: 12752
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30


Found at i:1029 original size:12 final size:12

Alignment explanation


    Indices: 995--1037  Score: 50
    Period size: 12  Copynumber: 3.3  Consensus size: 12

        985 GTTTAGACTT

                         
        995 ATATAGTATATAA
          1 ATATAG-ATATAA

                         *
       1008 ATAGATAGATATAG
          1 AT--ATAGATATAA

                        
       1022 ATATAGATATAA
          1 ATATAGATATAA

                
       1034 ATAT
          1 ATAT

       1038 TCATTCAAGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  12   13  0.50
  13    2  0.08
  14    7  0.27
  15    4  0.15

ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35


Consensus pattern (12 bp):   
ATATAGATATAA

Found at i:7302 original size:42 final size:42

Alignment explanation


    Indices: 7247--7371  Score: 155
    Period size: 42  Copynumber: 3.0  Consensus size: 42

       7237 TCCCATACAC

                *   *                                 
       7247 CACCCTTATCCCAAAATGTGACATCTTTACACCCAAACATGT
          1 CACCTTTACCCCAAAATGTGACATCTTTACACCCAAACATGT

                                 *       *         *    
       7289 C-CCATTTACCCCAAAATGTGGCATCTTTGC-CACCAAATATGT
          1 CACC-TTTACCCCAAAATGTGACATCTTTACAC-CCAAACATGT

                        *                    *       
       7331 CACCTTTACCCCCAAATGTGACATCTTTACACCAAAACATG
          1 CACCTTTACCCCAAAATGTGACATCTTTACACCCAAACATG

       7372 AATCCTCTGC


Statistics
Matches: 69,  Mismatches: 10, Indels: 8
        0.79            0.11        0.09

Matches are distributed among these distances:
  41    3  0.04
  42   63  0.91
  43    3  0.04

ACGTcount: A:0.32, C:0.33, G:0.09, T:0.26


Consensus pattern (42 bp):   
CACCTTTACCCCAAAATGTGACATCTTTACACCCAAACATGT

Found at i:7358 original size:21 final size:21

Alignment explanation


    Indices: 7256--7367  Score: 97
    Period size: 21  Copynumber: 5.3  Consensus size: 21

       7246 CCACCCTTAT

                                 
       7256 CCCAAAATGTGACATCTTTAC
          1 CCCAAAATGTGACATCTTTAC

                        **         
       7277 ACCCAAACATGTCCCA--TTTAC
          1 -CCCAAA-ATGTGACATCTTTAC

                       *       * 
       7298 CCCAAAATGTGGCATCTTTGC
          1 CCCAAAATGTGACATCTTTAC

                            *      
       7319 CACCAAATATGT--CACCTTTAC
          1 C-CCAAA-ATGTGACATCTTTAC

               *                 
       7340 CCCCAAATGTGACATCTTTAC
          1 CCCAAAATGTGACATCTTTAC

            *      
       7361 ACCAAAA
          1 CCCAAAA

       7368 CATGAATCCT


Statistics
Matches: 72,  Mismatches: 11, Indels: 15
        0.73            0.11        0.15

Matches are distributed among these distances:
  19   10  0.14
  20   10  0.14
  21   31  0.43
  22   11  0.15
  23   10  0.14

ACGTcount: A:0.33, C:0.32, G:0.09, T:0.26


Consensus pattern (21 bp):   
CCCAAAATGTGACATCTTTAC

Found at i:12590 original size:27 final size:27

Alignment explanation


    Indices: 12553--12612  Score: 113
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      12543 TTCATAAAAT

                                       
      12553 TTCAT-TTAATTACAAAAGAAATTACA
          1 TTCATATTAATTACAAAAGAAATTACA

                                       
      12579 TTCATATTAATTACAAAAGAAATTACA
          1 TTCATATTAATTACAAAAGAAATTACA

                   
      12606 TTCATAT
          1 TTCATAT

      12613 GAAATATACG


Statistics
Matches: 33,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  26    5  0.15
  27   28  0.85

ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37


Consensus pattern (27 bp):   
TTCATATTAATTACAAAAGAAATTACA
Done.