Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014707.1 Corchorus capsularis cultivar CVL-1 contig14728, 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: 11292
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37


Found at i:2468 original size:2 final size:2

Alignment explanation


    Indices: 2455--2491  Score: 65
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       2445 GTTAAAAATA

                                                                  
       2455 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2492 GCAATAAGGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   32  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:4616 original size:6 final size:6

Alignment explanation


    Indices: 4605--4637  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       4595 ATTATAGAGT

                                           *      
       4605 ATAAAG ATAAAG ATAAAG ATAAAG ATACAG ATA
          1 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATA

       4638 TATATATTAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.64, C:0.03, G:0.15, T:0.18


Consensus pattern (6 bp):   
ATAAAG

Found at i:8835 original size:21 final size:20

Alignment explanation


    Indices: 8802--8845  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       8792 GTGGAAAGAA

                 *               
       8802 TTATAGCTATTTTAATAACTT
          1 TTATAACTATTTTAATAA-TT

                    *     *     
       8823 TTATAACTTTTTTAGTAATT
          1 TTATAACTATTTTAATAATT

               
       8843 TTA
          1 TTA

       8846 GATTACAAGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    5  0.25
  21   15  0.75

ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57


Consensus pattern (20 bp):   
TTATAACTATTTTAATAATT

Found at i:8954 original size:2 final size:2

Alignment explanation


    Indices: 8941--8976  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       8931 ACTATAGCTT

                      *                                          
       8941 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       8977 ATCTTCACAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:9169 original size:21 final size:21

Alignment explanation


    Indices: 9131--9171  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       9121 TTATAATACT

                         *       
       9131 ATAACATTTTTTATAACCTTC
          1 ATAACATTTTTTACAACCTTC

                                 
       9152 ATAAC-TTTTTTAGCAACCTT
          1 ATAACATTTTTTA-CAACCTT

       9172 AAAGAAGAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    7  0.39
  21   11  0.61

ACGTcount: A:0.32, C:0.20, G:0.02, T:0.46


Consensus pattern (21 bp):   
ATAACATTTTTTACAACCTTC
Done.