Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012043.1 Corchorus olitorius cultivar O-4 contig12076, 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: 22120
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:14472 original size:25 final size:25

Alignment explanation


    Indices: 14425--14473  Score: 62
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      14415 CAAGTCACTT

                     *    * * *      
      14425 GAAACATAATCAATGGGAGATGGCC
          1 GAAACATAAGCAATCGAAAATGGCC

                                    
      14450 GAAACATAAGCAATCGAAAATGGC
          1 GAAACATAAGCAATCGAAAATGGC

      14474 TCGGCTTGTT


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  25   20  1.00

ACGTcount: A:0.45, C:0.16, G:0.24, T:0.14


Consensus pattern (25 bp):   
GAAACATAAGCAATCGAAAATGGCC

Found at i:16504 original size:17 final size:17

Alignment explanation


    Indices: 16482--16517  Score: 72
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      16472 TAGGTTAGAG

                             
      16482 ATAATATAAAGACTTTA
          1 ATAATATAAAGACTTTA

                             
      16499 ATAATATAAAGACTTTA
          1 ATAATATAAAGACTTTA

              
      16516 AT
          1 AT

      16518 TTATAGTAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36


Consensus pattern (17 bp):   
ATAATATAAAGACTTTA

Found at i:19215 original size:30 final size:31

Alignment explanation


    Indices: 19174--19231  Score: 91
    Period size: 30  Copynumber: 1.9  Consensus size: 31

      19164 TCATTCAGTC

                              *   *        
      19174 AAAAAGGCAAGAATTTTTGGTAGAAAAAAAT
          1 AAAAAGGCAAGAATTTTTAGTACAAAAAAAT

                                        
      19205 AAAAA-GCAAGAATTTTTAGTACAAAAA
          1 AAAAAGGCAAGAATTTTTAGTACAAAAA

      19232 GAAAAACAGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  30   20  0.80
  31    5  0.20

ACGTcount: A:0.57, C:0.05, G:0.16, T:0.22


Consensus pattern (31 bp):   
AAAAAGGCAAGAATTTTTAGTACAAAAAAAT

Found at i:19417 original size:2 final size:2

Alignment explanation


    Indices: 19410--19457  Score: 78
    Period size: 2  Copynumber: 24.0  Consensus size: 2

      19400 TTATTAGTTA

                            *                          *                  
      19410 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
      19452 AT AT AT
          1 AT AT AT

      19458 TCATAAAAGT


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:19433 original size:18 final size:18

Alignment explanation


    Indices: 19410--19456  Score: 94
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      19400 TTATTAGTTA

                              
      19410 ATATATATATACATATAT
          1 ATATATATATACATATAT

                              
      19428 ATATATATATACATATAT
          1 ATATATATATACATATAT

                       
      19446 ATATATATATA
          1 ATATATATATA

      19457 TTCATAAAAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   29  1.00

ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45


Consensus pattern (18 bp):   
ATATATATATACATATAT

Done.