Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008699.1 Corchorus capsularis cultivar CVL-1 contig08720, 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: 23311
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:15505 original size:56 final size:57

Alignment explanation


    Indices: 15370--15539  Score: 216
    Period size: 60  Copynumber: 2.9  Consensus size: 57

      15360 CTTTCAAAGG

                               *                                 *      
      15370 CCAAATTGTCCTTTTATTGTAAGTTTGAGGGCATCTAATAATAAGCCATTTTTTCCCCTA
          1 CCAAATTGTCCTTTTATTGCAAGTTTGAGGGCATC---TAATAAGCCATTTTTCCCCCTA

                                    *                                
      15430 CCAAATTGTCCTTTTATTGCAAGTGTGAGGGCATCTAATAAGCC-TTTTTCCCCCTA
          1 CCAAATTGTCCTTTTATTGCAAGTTTGAGGGCATCTAATAAGCCATTTTTCCCCCTA

                    *     *                            *          
      15486 CCAAATTGCCCTTTAATTGCAAACTAGTTTGAGGGCATCTAATCAGCCATTTTT
          1 CCAAATTGTCCTTTTATTGC--A--AGTTTGAGGGCATCTAATAAGCCATTTTT

      15540 TCTCTTTTAA


Statistics
Matches: 98,  Mismatches: 7, Indels: 9
        0.86            0.06        0.08

Matches are distributed among these distances:
  56   29  0.30
  57    9  0.09
  58    1  0.01
  60   54  0.55
  61    5  0.05

ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37


Consensus pattern (57 bp):   
CCAAATTGTCCTTTTATTGCAAGTTTGAGGGCATCTAATAAGCCATTTTTCCCCCTA

Found at i:16367 original size:3 final size:3

Alignment explanation


    Indices: 16345--16396  Score: 79
    Period size: 3  Copynumber: 17.7  Consensus size: 3

      16335 ATTAGAAAAA

                  *       *                                                
      16345 TAT TAC TAT TAC TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                  
      16392 TAT TA
          1 TAT TA

      16397 ATTAATTAAT


Statistics
Matches: 45,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
   2    2  0.04
   3   43  0.96

ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62


Consensus pattern (3 bp):   
TAT

Found at i:17368 original size:31 final size:31

Alignment explanation


    Indices: 17330--17391  Score: 124
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      17320 CGATACATAC

                                           
      17330 ACAATTCTACTATAAGAAAGCTTAAATAGTT
          1 ACAATTCTACTATAAGAAAGCTTAAATAGTT

                                           
      17361 ACAATTCTACTATAAGAAAGCTTAAATAGTT
          1 ACAATTCTACTATAAGAAAGCTTAAATAGTT

      17392 GGCCTTGCAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32


Consensus pattern (31 bp):   
ACAATTCTACTATAAGAAAGCTTAAATAGTT

Found at i:18360 original size:12 final size:12

Alignment explanation


    Indices: 18343--18385  Score: 68
    Period size: 12  Copynumber: 3.5  Consensus size: 12

      18333 TCCCACCCTC

                        
      18343 TCATCTCTTGCA
          1 TCATCTCTTGCA

                   *     
      18355 TCATCTTTTTGCA
          1 TCATC-TCTTGCA

                        
      18368 TCATCTCTTGCA
          1 TCATCTCTTGCA

                  
      18380 TCATCT
          1 TCATCT

      18386 TTGATCTTTC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  12   17  0.61
  13   11  0.39

ACGTcount: A:0.16, C:0.30, G:0.07, T:0.47


Consensus pattern (12 bp):   
TCATCTCTTGCA

Found at i:19791 original size:16 final size:16

Alignment explanation


    Indices: 19770--19801  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      19760 CTAAAATATT

                            
      19770 AAAATCAGACAAATAA
          1 AAAATCAGACAAATAA

                       *    
      19786 AAAATCAGACAGATAA
          1 AAAATCAGACAAATAA

      19802 TTCAAACAAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.66, C:0.12, G:0.09, T:0.12


Consensus pattern (16 bp):   
AAAATCAGACAAATAA
Done.