Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021746.1 Corchorus olitorius cultivar O-4 contig21779, 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: 9494
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Found at i:4474 original size:151 final size:151

Alignment explanation


    Indices: 4200--4535  Score: 627
    Period size: 151  Copynumber: 2.2  Consensus size: 151

       4190 ATTTTTGGCG

                                   *                                         
       4200 CAACATCTCTTTTTGGCACGCCCAGTGGGACACAGCAAGATCCTGTCTTCTCAACTCGGCGTCTC
          1 CAACATCTCTTTTTGGCACGCCCGGTGGGACACAGCAAGATCCTGTCTTCTCAACTCGGCGTCTC

                                       *                                    *
       4265 CATAAGCTTTCTCTCTCTCAAAGTCGGTGATCCCCGACTCTCTTCTCAACTTTCTGTGCTACGTT
         66 CATAAGCTTTCTCTCTCTCAAAGTCGGCGATCCCCGACTCTCTTCTCAACTTTCTGTGCTACGTC

                                 
       4330 GGACTGCCCACTCGGCCGCAC
        131 GGACTGCCCACTCGGCCGCAC

                                  *                                          
       4351 CAACATCTCTTTTTGGCACGCCTGGTGGGACACAGCAAGATCCTGTCTTCTCAACTCGGCGTCTC
          1 CAACATCTCTTTTTGGCACGCCCGGTGGGACACAGCAAGATCCTGTCTTCTCAACTCGGCGTCTC

                                                                             
       4416 CATAAGCTTTCTCTCTCTCAAAGTCGGCGATCCCCGACTCTCTTCTCAACTTTCTGTGCTACGTC
         66 CATAAGCTTTCTCTCTCTCAAAGTCGGCGATCCCCGACTCTCTTCTCAACTTTCTGTGCTACGTC

                           *     
       4481 GGACTGCCCACTCGGTCGCAC
        131 GGACTGCCCACTCGGCCGCAC

                                              
       4502 CAACATCTCTTTTTGGCACGCCCGGTGGGACACA
          1 CAACATCTCTTTTTGGCACGCCCGGTGGGACACA

       4536 ACAAACAGTT


Statistics
Matches: 179,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 151  179  1.00

ACGTcount: A:0.18, C:0.35, G:0.19, T:0.28


Consensus pattern (151 bp):   
CAACATCTCTTTTTGGCACGCCCGGTGGGACACAGCAAGATCCTGTCTTCTCAACTCGGCGTCTC
CATAAGCTTTCTCTCTCTCAAAGTCGGCGATCCCCGACTCTCTTCTCAACTTTCTGTGCTACGTC
GGACTGCCCACTCGGCCGCAC

Found at i:7561 original size:19 final size:18

Alignment explanation


    Indices: 7537--7572  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7527 TGAAGACTTA

                               
       7537 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       7556 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       7573 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:7579 original size:30 final size:30

Alignment explanation


    Indices: 7525--7584  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       7515 GAAGTTCGTG

                      *              *    
       7525 TTTGAAGACTTATTGAAGACAATTTGAAGA
          1 TTTGAAGACTCATTGAAGACAATTTCAAGA

                                *          
       7555 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA

       7585 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTTGAAGACTCATTGAAGACAATTTCAAGA

Found at i:9124 original size:5 final size:6

Alignment explanation


    Indices: 9109--9133  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       9099 TTGTGTATTA

                                         
       9109 TTTTTC TTTTTC TTTTTC TTTTTC T
          1 TTTTTC TTTTTC TTTTTC TTTTTC T

       9134 ATTTGATTTG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (6 bp):   
TTTTTC

Done.