Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001853.1 Corchorus capsularis cultivar CVL-1 contig01854, 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: 3533
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31


Found at i:1952 original size:57 final size:57

Alignment explanation


    Indices: 1873--1987  Score: 194
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       1863 ATTAATATTA

                             *           *     *  *                  
       1873 ATGGTTTTGTAACTCCATAATTTAATTTTTAATAACAATTATTTTAATTTTAATAAC
          1 ATGGTTTTGTAACTCCACAATTTAATTTTCAATAAAAACTATTTTAATTTTAATAAC

                                                                     
       1930 ATGGTTTTGTAACTCCACAATTTAATTTTCAATAAAAACTATTTTAATTTTAATAAC
          1 ATGGTTTTGTAACTCCACAATTTAATTTTCAATAAAAACTATTTTAATTTTAATAAC

             
       1987 A
          1 A

       1988 ACTAGGTAAA


Statistics
Matches: 54,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  57   54  1.00

ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46


Consensus pattern (57 bp):   
ATGGTTTTGTAACTCCACAATTTAATTTTCAATAAAAACTATTTTAATTTTAATAAC

Found at i:1978 original size:22 final size:21

Alignment explanation


    Indices: 1950--1991  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1940 AACTCCACAA

                                  
       1950 TTTAATTTTCAATAAAAACTAT
          1 TTTAATTTT-AATAAAAACTAT

                          *     
       1972 TTTAATTTTAATAACAACTA
          1 TTTAATTTTAATAAAAACTA

       1992 GGTAAAGTCC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   10  0.53
  22    9  0.47

ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45


Consensus pattern (21 bp):   
TTTAATTTTAATAAAAACTAT

Found at i:3324 original size:23 final size:23

Alignment explanation


    Indices: 3245--3289  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3235 AACCCTAAAC

                                   
       3245 ATAACGTTAAGAATTTAATATAT
          1 ATAACGTTAAGAATTTAATATAT

                 *         *      
       3268 ATAACCTTAAGAATTAAATATA
          1 ATAACGTTAAGAATTTAATATA

       3290 ACGTTATATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36


Consensus pattern (23 bp):   
ATAACGTTAAGAATTTAATATAT

Found at i:3350 original size:15 final size:14

Alignment explanation


    Indices: 3330--3382  Score: 54
    Period size: 15  Copynumber: 3.7  Consensus size: 14

       3320 ATAACGTTAG

                           
       3330 AATAACGTTAAAATA
          1 AATAACGTT-AAATA

                   *       
       3345 AATAACAATTAAATA
          1 AATAAC-GTTAAATA

            *             
       3360 TATAACGTT-AATA
          1 AATAACGTTAAATA

            *         
       3373 TATAACGTTA
          1 AATAACGTTA

       3383 GAATTTAATT


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  13   13  0.39
  14    2  0.06
  15   16  0.48
  16    2  0.06

ACGTcount: A:0.55, C:0.08, G:0.06, T:0.32


Consensus pattern (14 bp):   
AATAACGTTAAATA

Found at i:3378 original size:43 final size:46

Alignment explanation


    Indices: 3281--3382  Score: 126
    Period size: 43  Copynumber: 2.3  Consensus size: 46

       3271 ACCTTAAGAA

                            *          *                  
       3281 TTAAATATAACGTT-ATATAACATTAAGAATTTAATATATATAACG
          1 TTAAATATAACGTTAAAATAACATTAACAATTTAATATATATAACG

               *                                          
       3326 TTAGA-ATAACGTTAAAATAA-A-TAACAA-TTAA-ATATATAACG
          1 TTAAATATAACGTTAAAATAACATTAACAATTTAATATATATAACG

                            
       3367 TTAATATATAACGTTA
          1 TTAA-ATATAACGTTA

       3383 GAATTTAATT


Statistics
Matches: 50,  Mismatches: 4, Indels: 8
        0.81            0.06        0.13

Matches are distributed among these distances:
  41   13  0.26
  42    5  0.10
  43   14  0.28
  44    9  0.18
  45    9  0.18

ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35


Consensus pattern (46 bp):   
TTAAATATAACGTTAAAATAACATTAACAATTTAATATATATAACG
Done.