Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014837.1 Corchorus capsularis cultivar CVL-1 contig14858, 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: 12017
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:7596 original size:13 final size:12

Alignment explanation


    Indices: 7567--7595  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       7557 ACCCTCATTT

                        
       7567 AAAAAGTCAACA
          1 AAAAAGTCAACA

                        
       7579 AAAAAGTCAACA
          1 AAAAAGTCAACA

                 
       7591 AAAAA
          1 AAAAA

       7596 ATTATTTTTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.72, C:0.14, G:0.07, T:0.07


Consensus pattern (12 bp):   
AAAAAGTCAACA

Found at i:7687 original size:38 final size:38

Alignment explanation


    Indices: 7633--7706  Score: 105
    Period size: 38  Copynumber: 1.9  Consensus size: 38

       7623 GGTGATGCGG

                       *         *                 
       7633 TGATCTTGGCTGGTAATCTCATATCACCCTC-TTTGGCT
          1 TGATCTTGGCTAGTAATCTCAGATCA-CCTCGTTTGGCT

                     *                          
       7671 TGATCTTGGGTAGTAATCTCAGATCACCTCGTTTGG
          1 TGATCTTGGCTAGTAATCTCAGATCACCTCGTTTGG

       7707 TTGCGTTTTT


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  37    4  0.12
  38   28  0.88

ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38


Consensus pattern (38 bp):   
TGATCTTGGCTAGTAATCTCAGATCACCTCGTTTGGCT

Found at i:7800 original size:17 final size:17

Alignment explanation


    Indices: 7778--7811  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       7768 AATCTAGGAG

                   *         
       7778 GTAATCTCACATCACCA
          1 GTAATCTAACATCACCA

                     *       
       7795 GTAATCTAAGATCACCA
          1 GTAATCTAACATCACCA

       7812 ATCATCTGAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24


Consensus pattern (17 bp):   
GTAATCTAACATCACCA

Found at i:8123 original size:17 final size:17

Alignment explanation


    Indices: 8103--8143  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       8093 GTGATCTAAG

                             
       8103 ATCACCAGTAATCTTAC
          1 ATCACCAGTAATCTTAC

                 **  *       
       8120 ATCACTGGTGATCTTAC
          1 ATCACCAGTAATCTTAC

                   
       8137 ATCACCA
          1 ATCACCA

       8144 ATGATATGAG


Statistics
Matches: 19,  Mismatches: 5, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29


Consensus pattern (17 bp):   
ATCACCAGTAATCTTAC

Found at i:11286 original size:34 final size:34

Alignment explanation


    Indices: 11224--11326  Score: 167
    Period size: 34  Copynumber: 3.1  Consensus size: 34

      11214 GTTTCATCGG

                                      *       
      11224 CCCTGCCCAGTGGG-T-T-ATAATAATTGGAAGA
          1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA

                                *             
      11255 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
          1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA

                                              
      11289 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
          1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA

                
      11323 CCCT
          1 CCCT

      11327 ACTAACGGGT


Statistics
Matches: 66,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  31   14  0.21
  32    1  0.02
  33    1  0.02
  34   50  0.76

ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23


Consensus pattern (34 bp):   
CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
Done.