Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010652.1 Corchorus capsularis cultivar CVL-1 contig10673, 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: 30565
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:1606 original size:13 final size:12

Alignment explanation


    Indices: 1583--1613  Score: 53
    Period size: 13  Copynumber: 2.5  Consensus size: 12

       1573 CTAGTCGAAA

                        
       1583 ATTTTTTTTTTT
          1 ATTTTTTTTTTT

                         
       1595 ATTTTTTATTTTT
          1 ATTTTTT-TTTTT

                  
       1608 ATTTTT
          1 ATTTTT

       1614 CGATATAACT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    7  0.39
  13   11  0.61

ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87


Consensus pattern (12 bp):   
ATTTTTTTTTTT

Found at i:2795 original size:8 final size:8

Alignment explanation


    Indices: 2767--2800  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       2757 GAATCGGCTA

                    
       2767 TGAATTTT
          1 TGAATTTT

                    *
       2775 TGAAGTTTC
          1 TGAA-TTTT

                    
       2784 TGAATTTT
          1 TGAATTTT

                    
       2792 TGAATTTT
          1 TGAATTTT

             
       2800 T
          1 T

       2801 CAAGAAGGTG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:6779 original size:13 final size:14

Alignment explanation


    Indices: 6761--6789  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       6751 ATAATCGGAC

                          
       6761 TTTGCATTCAT-CA
          1 TTTGCATTCATGCA

                          
       6774 TTTGCATTCATGCA
          1 TTTGCATTCATGCA

              
       6788 TT
          1 TT

       6790 GAGTAGAAGT


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

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48


Consensus pattern (14 bp):   
TTTGCATTCATGCA

Found at i:7316 original size:21 final size:22

Alignment explanation


    Indices: 7290--7334  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       7280 GATAACTGAA

                             *    
       7290 TTGCTAAACACCG-CCCCCTTT
          1 TTGCTAAACACCGTCCCACTTT

                  **              
       7311 TTGCTATTCACCGTCCCACTTT
          1 TTGCTAAACACCGTCCCACTTT

              
       7333 TT
          1 TT

       7335 ACACTTTTGC


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

Matches are distributed among these distances:
  21   11  0.55
  22    9  0.45

ACGTcount: A:0.16, C:0.38, G:0.09, T:0.38


Consensus pattern (22 bp):   
TTGCTAAACACCGTCCCACTTT

Found at i:14364 original size:31 final size:31

Alignment explanation


    Indices: 14259--14421  Score: 186
    Period size: 31  Copynumber: 5.1  Consensus size: 31

      14249 GGTTTTTTCT

                      *                     
      14259 TTTTTTTTTTTGC-CAGAAGAGGTTTATAGGG
          1 TTTTTTTTTTGGCACA-AAGAGGTTTATAGGG

                        *  *                    
      14290 TTTTTTTGTTGTTGCCCAAAGAGGTTGTTTATAGGG
          1 TTTTTTT-TT-TGGCACAAAGA-G--GTTTATAGGG

                          *                
      14326 -TTTTTTTTTGGCAGAAAGAGGTTTATAGGG
          1 TTTTTTTTTTGGCACAAAGAGGTTTATAGGG

                            *               
      14356 TTTTTTTTTTGGGCACCAAGAGGTTTATAGGG
          1 TTTTTTTTTT-GGCACAAAGAGGTTTATAGGG

                     *     *               
      14388 TTTTTTTTTGGGCACCAAGAGGTTTATAGGG
          1 TTTTTTTTTTGGCACAAAGAGGTTTATAGGG

               
      14419 TTT
          1 TTT

      14422 AAGAATTAAG


Statistics
Matches: 118,  Mismatches: 6, Indels: 16
        0.84            0.04        0.11

Matches are distributed among these distances:
  30   10  0.08
  31   40  0.34
  32   31  0.26
  33   16  0.14
  34    5  0.04
  35    6  0.05
  36   10  0.08

ACGTcount: A:0.19, C:0.07, G:0.28, T:0.46


Consensus pattern (31 bp):   
TTTTTTTTTTGGCACAAAGAGGTTTATAGGG

Found at i:19303 original size:21 final size:21

Alignment explanation


    Indices: 19277--19320  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      19267 TATTTTTATG

                      *           
      19277 TATCAACAATGCATACG-ATAA
          1 TATCAACAATACATA-GAATAA

                                 
      19298 TATCAACAATACATAGAATAA
          1 TATCAACAATACATAGAATAA

              
      19319 TA
          1 TA

      19321 ATATCAAGCC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    1  0.05
  21   20  0.95

ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25


Consensus pattern (21 bp):   
TATCAACAATACATAGAATAA

Found at i:28359 original size:12 final size:12

Alignment explanation


    Indices: 28342--28368  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      28332 TTTGGTGGTG

                        
      28342 TTTATTTTATTT
          1 TTTATTTTATTT

                        
      28354 TTTATTTTATTT
          1 TTTATTTTATTT

               
      28366 TTT
          1 TTT

      28369 TCTGCATGGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (12 bp):   
TTTATTTTATTT
Done.