Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024204.1 Corchorus olitorius cultivar O-4 contig24237, 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: 23816
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:6403 original size:15 final size:16

Alignment explanation


    Indices: 6370--6409  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       6360 TTACTTTGCT

                            
       6370 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       6386 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
       6401 TTGCTTTCT
          1 TTGTTTTCT

       6410 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:9147 original size:36 final size:36

Alignment explanation


    Indices: 9107--9178  Score: 144
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       9097 AGATGTGTAA

                                                
       9107 GCAATTATATGTAAATAATCAATGGTAGATAGAGAT
          1 GCAATTATATGTAAATAATCAATGGTAGATAGAGAT

                                                
       9143 GCAATTATATGTAAATAATCAATGGTAGATAGAGAT
          1 GCAATTATATGTAAATAATCAATGGTAGATAGAGAT

       9179 ATGAAAATAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31


Consensus pattern (36 bp):   
GCAATTATATGTAAATAATCAATGGTAGATAGAGAT

Found at i:10368 original size:35 final size:35

Alignment explanation


    Indices: 10328--10400  Score: 137
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      10318 AGACCCACTC

                                               
      10328 CAACCAATAAAATCTTTGGAAGTTACCATTACTTG
          1 CAACCAATAAAATCTTTGGAAGTTACCATTACTTG

                                          *    
      10363 CAACCAATAAAATCTTTGGAAGTTACCATTGCTTG
          1 CAACCAATAAAATCTTTGGAAGTTACCATTACTTG

               
      10398 CAA
          1 CAA

      10401 ATCACACTTA


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   37  1.00

ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30


Consensus pattern (35 bp):   
CAACCAATAAAATCTTTGGAAGTTACCATTACTTG

Found at i:23233 original size:21 final size:21

Alignment explanation


    Indices: 23194--23242  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      23184 TCAATGCTTT

                         **       
      23194 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
      23216 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
      23237 A-GAAGC
          1 AGGAAGC

      23243 TACAATTCTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA
Done.