Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020489.1 Corchorus olitorius cultivar O-4 contig20522, 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: 6979
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:2102 original size:14 final size:15

Alignment explanation


    Indices: 2083--2112  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2073 CAATCAAAGC

                           
       2083 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       2097 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       2112 A
          1 A

       2113 TTAAAAAGAT


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

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:2489 original size:21 final size:21

Alignment explanation


    Indices: 2465--2540  Score: 98
    Period size: 21  Copynumber: 3.6  Consensus size: 21

       2455 GGCTTGGAAT

                           *  *  
       2465 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCTTGACC

                *            *   
       2486 GGTGGTGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCTTGACC

                                 
       2507 GGTGATGGCACGGGCTTGACC
          1 GGTGATGGCACGGGCTTGACC

                * *      
       2528 GGTGGTTGCACGG
          1 GGTGATGGCACGG

       2541 CTTTGGACGG


Statistics
Matches: 47,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   47  1.00

ACGTcount: A:0.13, C:0.22, G:0.46, T:0.18


Consensus pattern (21 bp):   
GGTGATGGCACGGGCTTGACC

Found at i:5043 original size:22 final size:22

Alignment explanation


    Indices: 5018--5072  Score: 58
    Period size: 25  Copynumber: 2.4  Consensus size: 22

       5008 TTTTAGAGAA

                     **           
       5018 ACGCAAAAACTTTTTTTTTATG
          1 ACGCAAAAAAATTTTTTTTATG

                                     
       5040 ACGCAGAAACAAAATTTTTTTTATG
          1 ACGC--AAA-AAAATTTTTTTTATG

                     
       5065 ACG-AAAAA
          1 ACGCAAAAA

       5073 TATATATATT


Statistics
Matches: 28,  Mismatches: 2, Indels: 7
        0.76            0.05        0.19

Matches are distributed among these distances:
  21    2  0.07
  22    7  0.25
  24    3  0.11
  25   16  0.57

ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35


Consensus pattern (22 bp):   
ACGCAAAAAAATTTTTTTTATG

Found at i:5584 original size:16 final size:15

Alignment explanation


    Indices: 5546--5587  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5536 ACATAGATTG

                   *       
       5546 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       5561 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

              *         
       5576 ATTAGAAAACAA
          1 A-CAGAAAACAA

       5588 AACAAAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.