Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011852.1 Corchorus olitorius cultivar O-4 contig11885, 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: 36719
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:1456 original size:21 final size:21

Alignment explanation


    Indices: 1423--1471  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       1413 GAGAATTGTA

                          **     
       1423 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       1443 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       1464 GCATTCCT
          1 GC-TTCCT

       1472 AAAGCTTTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT

Found at i:20688 original size:17 final size:17

Alignment explanation


    Indices: 20666--20698  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      20656 ATTTGTAAAG

                             
      20666 TTGTTACACCAGATAGT
          1 TTGTTACACCAGATAGT

                     *      
      20683 TTGTTACACTAGATAG
          1 TTGTTACACCAGATAG

      20699 CTCTACGTAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36


Consensus pattern (17 bp):   
TTGTTACACCAGATAGT

Found at i:24402 original size:19 final size:18

Alignment explanation


    Indices: 24369--24404  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      24359 TTGAAATTAT

                              
      24369 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
      24387 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

      24405 TAAATCTTCA


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

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

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


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:26995 original size:22 final size:22

Alignment explanation


    Indices: 26970--27024  Score: 76
    Period size: 22  Copynumber: 2.5  Consensus size: 22

      26960 TCCTCCTTTT

                          *        
      26970 AGTCGACT-ATTGCTCTCCTTGA
          1 AGTCGA-TAATTGCACTCCTTGA

                       *          
      26992 AGTCGATAATTTCACTCCTTGA
          1 AGTCGATAATTGCACTCCTTGA

                       
      27014 AGTCGATAATT
          1 AGTCGATAATT

      27025 CTTAGTCGAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  21    1  0.03
  22   29  0.97

ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36


Consensus pattern (22 bp):   
AGTCGATAATTGCACTCCTTGA

Found at i:36006 original size:13 final size:13

Alignment explanation


    Indices: 35988--36013  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      35978 AGATCTCAAC

                         
      35988 AAAAATCATCACT
          1 AAAAATCATCACT

                         
      36001 AAAAATCATCACT
          1 AAAAATCATCACT

      36014 CGTGCCAAGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23


Consensus pattern (13 bp):   
AAAAATCATCACT
Done.