Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014184.1 Corchorus capsularis cultivar CVL-1 contig14205, 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: 9187
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:49 original size:22 final size:22

Alignment explanation


    Indices: 21--66  Score: 74
    Period size: 22  Copynumber: 2.1  Consensus size: 22

         11 CAAGCAATGG

                     *            
         21 CCGGTCACAGGTGCTTCCATCT
          1 CCGGTCACAAGTGCTTCCATCT

                         *        
         43 CCGGTCACAAGTGTTTCCATCT
          1 CCGGTCACAAGTGCTTCCATCT

              
         65 CC
          1 CC

         67 ATGCTTCTCC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.15, C:0.37, G:0.20, T:0.28


Consensus pattern (22 bp):   
CCGGTCACAAGTGCTTCCATCT

Found at i:2288 original size:4 final size:4

Alignment explanation


    Indices: 2279--2304  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

       2269 GGTCGAAATT

                                            
       2279 TTTA TTTA TTTA TTTA TTTA TTTA TT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TT

       2305 GATATTTTTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTTA

Found at i:3363 original size:33 final size:33

Alignment explanation


    Indices: 3308--3387  Score: 106
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       3298 AGTTAAAGGA

                         *            *   *  
       3308 TCATGTGGTCGGTTGTGGCCGGGCATGGCCGAG
          1 TCATGTGGTCGGTGGTGGCCGGGCATCGCCAAG

                    *        *         *     
       3341 TCATGTGGCCGGTGGTGTCCGGGCATCTCCAAG
          1 TCATGTGGTCGGTGGTGGCCGGGCATCGCCAAG

                          
       3374 TCATGTGGTCGGTG
          1 TCATGTGGTCGGTG

       3388 TTGCGTGGCG


Statistics
Matches: 40,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  33   40  1.00

ACGTcount: A:0.10, C:0.23, G:0.41, T:0.26


Consensus pattern (33 bp):   
TCATGTGGTCGGTGGTGGCCGGGCATCGCCAAG

Found at i:3560 original size:22 final size:22

Alignment explanation


    Indices: 3529--3579  Score: 75
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       3519 GCGCATCAGC

                       *    *     
       3529 TTCTTCCTCTTTCTTCTCTCCA
          1 TTCTTCCTCTTCCTTCCCTCCA

                 *                
       3551 TTCTTTCTCTTCCTTCCCTCCA
          1 TTCTTCCTCTTCCTTCCCTCCA

                   
       3573 TTCTTCC
          1 TTCTTCC

       3580 ATAACATTTT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53


Consensus pattern (22 bp):   
TTCTTCCTCTTCCTTCCCTCCA

Found at i:3612 original size:20 final size:20

Alignment explanation


    Indices: 3589--3627  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3579 CATAACATTT

                                 
       3589 TCTTTCC-TTCTTCCTCTTCC
          1 TCTTTCCATT-TTCCTCTTCC

                               
       3609 TCTTTCCATTTTCCTCTTC
          1 TCTTTCCATTTTCCTCTTC

       3628 TTTCAAATCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20   16  0.89
  21    2  0.11

ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56


Consensus pattern (20 bp):   
TCTTTCCATTTTCCTCTTCC

Found at i:8341 original size:50 final size:51

Alignment explanation


    Indices: 8266--8400  Score: 245
    Period size: 51  Copynumber: 2.7  Consensus size: 51

       8256 GTGTTCGCTC

                             *                                 
       8266 ACTGTGTGGCTTGAATATGCCCCCTGTTATCTCAGTGGC-TGGATGACCTG
          1 ACTGTGTGGCTTGAATACGCCCCCTGTTATCTCAGTGGCTTGGATGACCTG

                          *                                    
       8316 ACTGTGTGGCTTGACTACGCCCCCTGTTATCTCAGTGGCTTGGATGACCTG
          1 ACTGTGTGGCTTGAATACGCCCCCTGTTATCTCAGTGGCTTGGATGACCTG

                                              
       8367 ACTGTGTGGCTTGAATACGCCCCCTGTTATCTCA
          1 ACTGTGTGGCTTGAATACGCCCCCTGTTATCTCA

       8401 ATGCTTCTAA


Statistics
Matches: 81,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  50   37  0.46
  51   44  0.54

ACGTcount: A:0.16, C:0.27, G:0.26, T:0.32


Consensus pattern (51 bp):   
ACTGTGTGGCTTGAATACGCCCCCTGTTATCTCAGTGGCTTGGATGACCTG

Done.