Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014625.1 Corchorus olitorius cultivar O-4 contig14658, 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: 23648
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1229 original size:17 final size:15

Alignment explanation


    Indices: 1210--1241  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       1200 AGCTTATTAT

                           
       1210 TATTAT-TATATATA
          1 TATTATATATATATA

                           
       1224 TATTATATATATATA
          1 TATTATATATATATA

               
       1239 TAT
          1 TAT

       1242 AGTAATAGAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.35
  15   11  0.65

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (15 bp):   
TATTATATATATATA

Found at i:5163 original size:12 final size:12

Alignment explanation


    Indices: 5146--5188  Score: 59
    Period size: 12  Copynumber: 3.6  Consensus size: 12

       5136 GGAGGAAGAG

                        
       5146 GATGATGATGAC
          1 GATGATGATGAC

                       *
       5158 GATGATGATGAG
          1 GATGATGATGAC

                    *   
       5170 GATGATGAGGAC
          1 GATGATGATGAC

              *    
       5182 GAGGATG
          1 GATGATG

       5189 GTGGAGAAGA


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  12   27  1.00

ACGTcount: A:0.33, C:0.05, G:0.42, T:0.21


Consensus pattern (12 bp):   
GATGATGATGAC

Found at i:5176 original size:15 final size:15

Alignment explanation


    Indices: 5146--5212  Score: 55
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       5136 GGAGGAAGAG

                    *  *   
       5146 GATGATGATGACGAT
          1 GATGATGAGGATGAT

                           
       5161 GATGATGAGGATGAT
          1 GATGATGAGGATGAT

              *  *       * 
       5176 GAGGACGAGGATGGT
          1 GATGATGAGGATGAT

                  *        *
       5191 GGA-GAAGAGGATGAG
          1 -GATGATGAGGATGAT

                   
       5206 GATGATG
          1 GATGATG

       5213 TTGAAGGGGT


Statistics
Matches: 41,  Mismatches: 9, Indels: 4
        0.76            0.17        0.07

Matches are distributed among these distances:
  14    2  0.05
  15   37  0.90
  16    2  0.05

ACGTcount: A:0.33, C:0.03, G:0.45, T:0.19


Consensus pattern (15 bp):   
GATGATGAGGATGAT

Found at i:5248 original size:15 final size:15

Alignment explanation


    Indices: 5230--5263  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       5220 GGTAGAAAAT

                    *  *   
       5230 GAAGATGAGGATGAG
          1 GAAGATGAAGACGAG

                           
       5245 GAAGATGAAGACGAG
          1 GAAGATGAAGACGAG

                
       5260 GAAG
          1 GAAG

       5264 CCCTCCAGCC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.44, C:0.03, G:0.44, T:0.09


Consensus pattern (15 bp):   
GAAGATGAAGACGAG

Found at i:23563 original size:3 final size:3

Alignment explanation


    Indices: 23557--23648  Score: 184
    Period size: 3  Copynumber: 30.7  Consensus size: 3

      23547 CTCCATTATT

                                                                           
      23557 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                                                                      
      23605 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT


Statistics
Matches: 89,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   89  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Done.