Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019075.1 Corchorus olitorius cultivar O-4 contig19108, 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: 18468
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:3109 original size:33 final size:33

Alignment explanation


    Indices: 3053--3129  Score: 93
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       3043 AATTCCTTCA

                *       **    *      *       
       3053 GCTGGCTTGGATTGATCATCTCACTGACATTTT
          1 GCTGACTTGGATCAATCAACTCACTAACATTTT

                                        *    
       3086 GCTGACTTGGATCAATCAACTCACTAACCTTTT
          1 GCTGACTTGGATCAATCAACTCACTAACATTTT

                        
       3119 GCTGA-TTGGAT
          1 GCTGACTTGGAT

       3130 GCTGTGATAA


Statistics
Matches: 38,  Mismatches: 6, Indels: 1
        0.84            0.13        0.02

Matches are distributed among these distances:
  32    6  0.16
  33   32  0.84

ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36


Consensus pattern (33 bp):   
GCTGACTTGGATCAATCAACTCACTAACATTTT

Found at i:6858 original size:13 final size:13

Alignment explanation


    Indices: 6816--6860  Score: 56
    Period size: 12  Copynumber: 3.5  Consensus size: 13

       6806 TCATGCACCC

                        * 
       6816 AAAACAATTTATTT
          1 AAAACAATTTA-AT

                 *       
       6830 AAAACCATTT-AT
          1 AAAACAATTTAAT

                         
       6842 AAAACAATTTAAT
          1 AAAACAATTTAAT

                  
       6855 AAAACA
          1 AAAACA

       6861 GTAATAAAAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  12   10  0.37
  13    8  0.30
  14    9  0.33

ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31


Consensus pattern (13 bp):   
AAAACAATTTAAT

Found at i:13307 original size:42 final size:40

Alignment explanation


    Indices: 13248--13331  Score: 123
    Period size: 42  Copynumber: 2.0  Consensus size: 40

      13238 TTTAATTCCT

                                      *             
      13248 ATGTAATATATATAATAACTAAAATAGTTACATCAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA

                                  *            *      
      13288 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATCAATTAA

              
      13330 AT
          1 AT

      13332 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 3, Indels: 2
        0.89            0.07        0.05

Matches are distributed among these distances:
  40    7  0.18
  41    3  0.08
  42   29  0.74

ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATCAATTAA

Found at i:13358 original size:25 final size:24

Alignment explanation


    Indices: 13322--13368  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

      13312 AATACTTACA

                                    
      13322 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
      13346 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

      13369 GTGCAAATGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT

Found at i:18447 original size:15 final size:15

Alignment explanation


    Indices: 18429--18460  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      18419 ATCTAAAATG

                           
      18429 AAAAAAAAACACAGA
          1 AAAAAAAAACACAGA

                      *    
      18444 AAAAAAAAACCCAGA
          1 AAAAAAAAACACAGA

              
      18459 AA
          1 AA

      18461 CAGCGGGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00


Consensus pattern (15 bp):   
AAAAAAAAACACAGA
Done.