Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020713.1 Corchorus olitorius cultivar O-4 contig20746, 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: 11795
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:1220 original size:21 final size:24

Alignment explanation


    Indices: 1191--1241  Score: 72
    Period size: 22  Copynumber: 2.2  Consensus size: 24

       1181 TTTTGAACTC

                                     
       1191 ATTATT-TATTATTTAA-AATATAT
          1 ATTATTAT-TTATTTAATAATATAT

                                    
       1214 -TTATTATTTATTTAATAATATAT
          1 ATTATTATTTATTTAATAATATAT

                 
       1237 ATTAT
          1 ATTAT

       1242 ATCTAAGATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  22   13  0.52
  23    8  0.32
  24    4  0.16

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (24 bp):   
ATTATTATTTATTTAATAATATAT

Found at i:1236 original size:25 final size:25

Alignment explanation


    Indices: 1191--1239  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1181 TTTTGAACTC

                        *            
       1191 ATTATTTATTATTTAAAATATATTT
          1 ATTATTTATTATATAAAATATATTT

                             *       
       1216 ATTATTTATT-TAATAATATATATT
          1 ATTATTTATTAT-ATAAAATATATT

       1240 ATATCTAAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    1  0.05
  25   20  0.95

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (25 bp):   
ATTATTTATTATATAAAATATATTT

Found at i:3672 original size:23 final size:24

Alignment explanation


    Indices: 3638--3685  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       3628 ATTTTGTTAT

                                    
       3638 ATTTTG-TTT-TCTCTTGTTTGGA
          1 ATTTTGTTTTCTCTCTTGTTTGGA

                 *                   
       3660 ATTTTTTTCTTCTCTCTTGTTTGGA
          1 ATTTTGTT-TTCTCTCTTGTTTGGA

             
       3685 A
          1 A

       3686 AAACTAAAGA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  22    5  0.23
  23    1  0.05
  24    2  0.09
  25   14  0.64

ACGTcount: A:0.10, C:0.12, G:0.15, T:0.62


Consensus pattern (24 bp):   
ATTTTGTTTTCTCTCTTGTTTGGA

Found at i:8827 original size:24 final size:23

Alignment explanation


    Indices: 8787--8831  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 23

       8777 TCTTTTTTTT

                                   
       8787 AAAAAAAAAAATTGCATGCTTAG
          1 AAAAAAAAAAATTGCATGCTTAG

                                   
       8810 AAAACAAATAAAA-TGCATGCTT
          1 AAAA-AAA-AAAATTGCATGCTT

       8832 TATGTGTGCA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  23    4  0.20
  24   12  0.60
  25    4  0.20

ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22


Consensus pattern (23 bp):   
AAAAAAAAAAATTGCATGCTTAG

Found at i:11795 original size:6 final size:6

Alignment explanation


    Indices: 11758--11787  Score: 51
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      11748 TTAAACCCAA

                                              
      11758 AAAAAGG AAAAAG AAAAAG AAAAAG AAAAA
          1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAA

      11788 AAAGAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   18  0.78
   7    5  0.22

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (6 bp):   
AAAAAG
Done.