Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011178.1 Corchorus capsularis cultivar CVL-1 contig11199, 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: 2680
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41


Found at i:1085 original size:13 final size:13

Alignment explanation


    Indices: 1064--1105  Score: 68
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       1054 AACTACCAAG

                         
       1064 AAAATTGAAAAAA
          1 AAAATTGAAAAAA

                *        
       1077 AAAAGTG-AAAAA
          1 AAAATTGAAAAAA

                         
       1089 AAAATTGAAAAAA
          1 AAAATTGAAAAAA

                
       1102 AAAA
          1 AAAA

       1106 CACTTGTGCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  12   11  0.42
  13   15  0.58

ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12


Consensus pattern (13 bp):   
AAAATTGAAAAAA

Found at i:1087 original size:12 final size:12

Alignment explanation


    Indices: 1072--1104  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       1062 AGAAAATTGA

                        
       1072 AAAAAAAAAGTG
          1 AAAAAAAAAGTG

                     *  
       1084 AAAAAAAAATTG
          1 AAAAAAAAAGTG

                     
       1096 AAAAAAAAA
          1 AAAAAAAAA

       1105 ACACTTGTGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09


Consensus pattern (12 bp):   
AAAAAAAAAGTG

Found at i:1803 original size:16 final size:17

Alignment explanation


    Indices: 1773--1807  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       1763 TTTAAATTTT

                      *      
       1773 TTTTCAAAAATTTTTGC
          1 TTTTCAAAAACTTTTGC

                             
       1790 TTTTC-AAAACTTTTGC
          1 TTTTCAAAAACTTTTGC

              
       1806 TT
          1 TT

       1808 CTCTAGTGAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16   12  0.71
  17    5  0.29

ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54


Consensus pattern (17 bp):   
TTTTCAAAAACTTTTGC

Found at i:2067 original size:18 final size:17

Alignment explanation


    Indices: 2026--2068  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 17

       2016 ATTTATTTGC

                *            
       2026 TTGTCTTTAGTTTTGTT
          1 TTGTTTTTAGTTTTGTT

              *                
       2043 TAAGTTTTTAGTTTTTGTT
          1 T-TGTTTTTAG-TTTTGTT

                   
       2062 TTGTTTT
          1 TTGTTTT

       2069 CTAGCTTGCT


Statistics
Matches: 21,  Mismatches: 3, Indels: 3
        0.78            0.11        0.11

Matches are distributed among these distances:
  17    1  0.05
  18   12  0.57
  19    8  0.38

ACGTcount: A:0.09, C:0.02, G:0.16, T:0.72


Consensus pattern (17 bp):   
TTGTTTTTAGTTTTGTT
Done.