Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003681.1 Corchorus capsularis cultivar CVL-1 contig03689, 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: 9904
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37


Found at i:3789 original size:38 final size:39

Alignment explanation


    Indices: 3722--3796  Score: 116
    Period size: 38  Copynumber: 1.9  Consensus size: 39

       3712 AGATCCGAAC

                           *                       
       3722 TGATTTGGGTAAAGTTACATTGCATCTTAAATGGAGATT
          1 TGATTTGGGTAAAGTCACATTGCATCTTAAATGGAGATT

                            *     *              
       3761 TGATTTGGGT-AAGTCGCATTGGATCTTAAATGGAGA
          1 TGATTTGGGTAAAGTCACATTGCATCTTAAATGGAGA

       3797 AAATCTCTCC


Statistics
Matches: 33,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  38   23  0.70
  39   10  0.30

ACGTcount: A:0.29, C:0.08, G:0.27, T:0.36


Consensus pattern (39 bp):   
TGATTTGGGTAAAGTCACATTGCATCTTAAATGGAGATT

Found at i:6970 original size:6 final size:6

Alignment explanation


    Indices: 6959--6990  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       6949 TAATGAATCC

                                                  
       6959 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T TTT
          1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT

       6991 CAGGGCATTA


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

Matches are distributed among these distances:
   5    4  0.15
   6   22  0.85

ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88


Consensus pattern (6 bp):   
TTTTCT

Found at i:9407 original size:12 final size:11

Alignment explanation


    Indices: 9384--9442  Score: 55
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       9374 TCTTCCCCAA

                       
       9384 TTTCTTAATTT
          1 TTTCTTAATTT

                        
       9395 TTTCTTAAGTTT
          1 TTTCTTAA-TTT

                             
       9407 TTATACATTGTATATTT
          1 TT-T-C--T-TA-ATTT

                       
       9424 TTTCTTAATTT
          1 TTTCTTAATTT

                    
       9435 TTTCTTAA
          1 TTTCTTAA

       9443 ATTTATTTTC


Statistics
Matches: 41,  Mismatches: 0, Indels: 14
        0.75            0.00        0.25

Matches are distributed among these distances:
  11   20  0.49
  12    7  0.17
  13    2  0.05
  14    1  0.02
  15    1  0.02
  16    2  0.05
  17    7  0.17
  18    1  0.02

ACGTcount: A:0.22, C:0.08, G:0.03, T:0.66


Consensus pattern (11 bp):   
TTTCTTAATTT

Found at i:9830 original size:24 final size:23

Alignment explanation


    Indices: 9786--9830  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       9776 TCTAAAGAAT

                     *  * *        
       9786 TTGGGGATGGTGCATAAGATTAA
          1 TTGGGGATGATGAAAAAGATTAA

                                  
       9809 TTGGGGATGATGAAAAATGATT
          1 TTGGGGATGATGAAAAA-GATT

       9831 TGGGTATAAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  23   14  0.78
  24    4  0.22

ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31


Consensus pattern (23 bp):   
TTGGGGATGATGAAAAAGATTAA

Found at i:9876 original size:222 final size:221

Alignment explanation


    Indices: 9457--9904  Score: 754
    Period size: 222  Copynumber: 2.0  Consensus size: 221

       9447 ATTTTCCACC

                                                                             
       9457 ATCATATAGACGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTTTTTAAA
          1 ATCATATAGACGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTTTTTAAA

                            *  *           *                          *     *
       9522 GTCAAATTTGTGTATATGAGAAAATAGCAATTTCTAAAGAAATTGGGAATGGTGCATATGATTAT
         66 GTCAAATTTGTGTATACGAAAAAATAGCAATCTCTAAAGAAATTGGGAATGGTGCATAAGATTAA

                     *   *                  *                                
       9587 TTGGGGATGGTGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATT
        131 TTGGGGATGATGAAAAATGATTTGGGTATAAACTATATCAGTTTGGGGATACTGAATTTTGCATT

                                      
       9652 TTGTTTAATTATGAGACGGCGCTAAA
        196 TTGTTTAATTATGAGACGGCGCTAAA

                              *                                              
       9678 ATCATATAGACGTGGTTTGTTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTTTTTAAA
          1 ATCATATAGACGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTTTTTAAA

                                                       *     *               
       9743 GTCAAATTTGTGTATACGAAAAAA-ATGTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATT
         66 GTCAAATTTGTGTATACGAAAAAATA-G-CAATCTCTAAAGAAATTGGGAATGGTGCATAAGATT

                                                      *                      
       9807 AATTGGGGATGATGAAAAATGATTTGGGTATAAACTATATCATTTTGGGGATACTGAATTTTGCA
        129 AATTGGGGATGATGAAAAATGATTTGGGTATAAACTATATCAGTTTGGGGATACTGAATTTTGCA

                              *         
       9872 TTTTGTTTAATTATGAGATGGCGCTAAA
        194 TTTTGTTTAATTATGAGACGGCGCTAAA

                 
       9900 ATCAT
          1 ATCAT


Statistics
Matches: 212,  Mismatches: 13, Indels: 3
        0.93            0.06        0.01

Matches are distributed among these distances:
 220    1  0.00
 221   87  0.41
 222  124  0.58

ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36


Consensus pattern (221 bp):   
ATCATATAGACGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTTTTTAAA
GTCAAATTTGTGTATACGAAAAAATAGCAATCTCTAAAGAAATTGGGAATGGTGCATAAGATTAA
TTGGGGATGATGAAAAATGATTTGGGTATAAACTATATCAGTTTGGGGATACTGAATTTTGCATT
TTGTTTAATTATGAGACGGCGCTAAA
Done.