Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007743.1 Corchorus capsularis cultivar CVL-1 contig07764, 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: 14211
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33


Found at i:2109 original size:28 final size:29

Alignment explanation


    Indices: 2051--2125  Score: 98
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       2041 GTAGATTAAG

                         *                
       2051 AATGACCAAAATACCCCCCTAAATGC-AAA
          1 AATGACCAAAAT-GCCCCCTAAATGCAAAA

                                *   **   
       2080 AATGACCAAAATGCCCCCTAGATGTGAAA
          1 AATGACCAAAATGCCCCCTAAATGCAAAA

                             
       2109 AATGACCAAAATGCCCC
          1 AATGACCAAAATGCCCC

       2126 TGGATGACTC


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  28   10  0.24
  29   32  0.76

ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15


Consensus pattern (29 bp):   
AATGACCAAAATGCCCCCTAAATGCAAAA

Found at i:8439 original size:37 final size:37

Alignment explanation


    Indices: 8398--8532  Score: 173
    Period size: 37  Copynumber: 3.6  Consensus size: 37

       8388 GGCTCTCTTA

                                             *   
       8398 TTGATATTTGTTTGGACTTGAGCCCGAGGCTCAGTGG
          1 TTGATATTTGTTTGGACTTGAGCCCGAGGCTCAATGG

                 *                          ** **
       8435 TTGATTTTTGTTTGGACTTGAGCCCGAGGCTCTCTTA
          1 TTGATATTTGTTTGGACTTGAGCCCGAGGCTCAATGG

                    *                            
       8472 TTGATATTGGTTTGGACTTGAGCCCGAGGCTCAATGG
          1 TTGATATTTGTTTGGACTTGAGCCCGAGGCTCAATGG

                       *     *       
       8509 TTGATGA-TTGCTTGGATTTGAGCC
          1 TTGAT-ATTTGTTTGGACTTGAGCC

       8533 TGAGACTCTT


Statistics
Matches: 83,  Mismatches: 14, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
  37   82  0.99
  38    1  0.01

ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38


Consensus pattern (37 bp):   
TTGATATTTGTTTGGACTTGAGCCCGAGGCTCAATGG

Found at i:8504 original size:74 final size:74

Alignment explanation


    Indices: 8383--8541  Score: 246
    Period size: 74  Copynumber: 2.1  Consensus size: 74

       8373 ATTGTAGCAT

                                   *                        *        **   *  
       8383 CCCGAGGCTCTCTTATTGATATTTGTTTGGACTTGAGCCCGAGGCTCAGTGGTTGATTTTTGTTT
          1 CCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAATGGTTGATGATTGCTT

                     
       8448 GGACTTGAG
         66 GGACTTGAG

                                                                             
       8457 CCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAATGGTTGATGATTGCTT
          1 CCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAATGGTTGATGATTGCTT

               *     
       8522 GGATTTGAG
         66 GGACTTGAG

              *   *    
       8531 CCTGAGACTCT
          1 CCCGAGGCTCT

       8542 TTTTGTTGTT


Statistics
Matches: 77,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  74   77  1.00

ACGTcount: A:0.16, C:0.19, G:0.28, T:0.36


Consensus pattern (74 bp):   
CCCGAGGCTCTCTTATTGATATTGGTTTGGACTTGAGCCCGAGGCTCAATGGTTGATGATTGCTT
GGACTTGAG

Found at i:13792 original size:30 final size:31

Alignment explanation


    Indices: 13749--13807  Score: 77
    Period size: 30  Copynumber: 1.9  Consensus size: 31

      13739 TGAGGGACCC

                                     *      
      13749 AATTGATCAATTAAC-TCAACTTCATGGACTT
          1 AATTGATCAATTAACTTC-ACTTCAAGGACTT

                 *                       
      13780 AATTGCTC-ATTAACTTCACTTCAAGGAC
          1 AATTGATCAATTAACTTCACTTCAAGGAC

      13808 CCATTTGCAC


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  30   16  0.64
  31    9  0.36

ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34


Consensus pattern (31 bp):   
AATTGATCAATTAACTTCACTTCAAGGACTT
Done.