Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012383.1 Corchorus capsularis cultivar CVL-1 contig12404, 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: 31026
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1313 original size:15 final size:15

Alignment explanation


    Indices: 1295--1333  Score: 60
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       1285 CCTCCGTTGG

                     *     
       1295 CTTCTCGGCGGGCTT
          1 CTTCTCGGCAGGCTT

                           
       1310 CTTCTCGGCAGGCTT
          1 CTTCTCGGCAGGCTT

            *        
       1325 TTTCTCGGC
          1 CTTCTCGGC

       1334 TTTTGGCGCC


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

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.03, C:0.33, G:0.28, T:0.36


Consensus pattern (15 bp):   
CTTCTCGGCAGGCTT

Found at i:10770 original size:20 final size:20

Alignment explanation


    Indices: 10732--10775  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      10722 CTCGTCTTCC

                          **    
      10732 TTTT-CTTTCTTTTTTTTTT
          1 TTTTCCTTTCTTTTAATTTT

                                
      10751 TTTTCCTTTCTTTTAATTTT
          1 TTTTCCTTTCTTTTAATTTT

            *    
      10771 GTTTC
          1 TTTTC

      10776 TCCGTTTGAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  19    4  0.19
  20   17  0.81

ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80


Consensus pattern (20 bp):   
TTTTCCTTTCTTTTAATTTT

Found at i:16595 original size:19 final size:19

Alignment explanation


    Indices: 16571--16608  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      16561 ACTTTCATAT

                         *     
      16571 GATTCTGGTTTCCCTTTTC
          1 GATTCTGGTTTCCATTTTC

                               
      16590 GATTCTGGTTTCCATTTTC
          1 GATTCTGGTTTCCATTTTC

      16609 TTGTTTTTGT


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

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.08, C:0.24, G:0.16, T:0.53


Consensus pattern (19 bp):   
GATTCTGGTTTCCATTTTC

Found at i:20659 original size:18 final size:17

Alignment explanation


    Indices: 20638--20679  Score: 52
    Period size: 15  Copynumber: 2.5  Consensus size: 17

      20628 CTACCGTCGT

                           *  
      20638 CTTCTTCTCCTCTGCTGG
          1 CTTCTTCT-CTCTGCCGG

                             
      20656 CTTCTT-T-TCTGCCGG
          1 CTTCTTCTCTCTGCCGG

                     
      20671 CTTCTTCTC
          1 CTTCTTCTC

      20680 AGCTTTTGGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 5
        0.78            0.04        0.19

Matches are distributed among these distances:
  15   13  0.62
  16    1  0.05
  17    1  0.05
  18    6  0.29

ACGTcount: A:0.00, C:0.38, G:0.14, T:0.48


Consensus pattern (17 bp):   
CTTCTTCTCTCTGCCGG

Found at i:29948 original size:46 final size:46

Alignment explanation


    Indices: 29879--29970  Score: 166
    Period size: 46  Copynumber: 2.0  Consensus size: 46

      29869 GATGTAGGGG

                              *                           
      29879 TTAATTATGTCTGATGCGGATTACCTCTGCACGTTTGTAATTCTGA
          1 TTAATTATGTCTGATGCGAATTACCTCTGCACGTTTGTAATTCTGA

                                         *                
      29925 TTAATTATGTCTGATGCGAATTACCTCTGTACGTTTGTAATTCTGA
          1 TTAATTATGTCTGATGCGAATTACCTCTGCACGTTTGTAATTCTGA

      29971 CTATTGATAT


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  46   44  1.00

ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42


Consensus pattern (46 bp):   
TTAATTATGTCTGATGCGAATTACCTCTGCACGTTTGTAATTCTGA
Done.