Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019035.1 Corchorus olitorius cultivar O-4 contig19068, 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: 12013
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:1668 original size:58 final size:58

Alignment explanation


    Indices: 1570--1679  Score: 159
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       1560 ATCATACCTC

                 *                                                    
       1570 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCCTT
          1 GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCCTT

                      *           *             *           *    
       1628 GGTCCGAAAATGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
          1 GGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA

       1680 TTTGATTAAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  58   30  0.65
  59   16  0.35

ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34


Consensus pattern (58 bp):   
GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCCTT

Found at i:7555 original size:45 final size:45

Alignment explanation


    Indices: 7501--7592  Score: 184
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       7491 AGTTACGGAA

                                                         
       7501 GAGGAGAGGAGTAGAGGACAGAGAAATTTAAAACGACCATCGCAG
          1 GAGGAGAGGAGTAGAGGACAGAGAAATTTAAAACGACCATCGCAG

                                                         
       7546 GAGGAGAGGAGTAGAGGACAGAGAAATTTAAAACGACCATCGCAG
          1 GAGGAGAGGAGTAGAGGACAGAGAAATTTAAAACGACCATCGCAG

              
       7591 GA
          1 GA

       7593 ACAAGAAGAA


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

Matches are distributed among these distances:
  45   47  1.00

ACGTcount: A:0.42, C:0.13, G:0.34, T:0.11


Consensus pattern (45 bp):   
GAGGAGAGGAGTAGAGGACAGAGAAATTTAAAACGACCATCGCAG

Found at i:10164 original size:13 final size:13

Alignment explanation


    Indices: 10146--10170  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      10136 GTTATCAAAT

                         
      10146 TTACAGTAATTAG
          1 TTACAGTAATTAG

                        
      10159 TTACAGTAATTA
          1 TTACAGTAATTA

      10171 CTGAAAAAAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40


Consensus pattern (13 bp):   
TTACAGTAATTAG

Found at i:11319 original size:22 final size:23

Alignment explanation


    Indices: 11270--11319  Score: 57
    Period size: 22  Copynumber: 2.2  Consensus size: 23

      11260 TAACAGAAAC

                        **       * 
      11270 TTTATATTAAAATGAATAAAGTA
          1 TTTATATTAAAACAAATAAAGAA

            *                      
      11293 GTTATA-TAAAACAAATAAAGAA
          1 TTTATATTAAAACAAATAAAGAA

                 
      11315 TTTAT
          1 TTTAT

      11320 TTATAGCATT


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  22   17  0.77
  23    5  0.23

ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36


Consensus pattern (23 bp):   
TTTATATTAAAACAAATAAAGAA

Found at i:11777 original size:15 final size:15

Alignment explanation


    Indices: 11757--11787  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      11747 TCAATGATAT

                           
      11757 ACTTCTCCTGAATTG
          1 ACTTCTCCTGAATTG

                           
      11772 ACTTCTCCTGAATTG
          1 ACTTCTCCTGAATTG

             
      11787 A
          1 A

      11788 AGAAAAGAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39


Consensus pattern (15 bp):   
ACTTCTCCTGAATTG
Done.