Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010679.1 Corchorus olitorius cultivar O-4 contig10711, 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: 3866
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Found at i:113 original size:21 final size:21

Alignment explanation


    Indices: 89--159  Score: 72
    Period size: 21  Copynumber: 3.3  Consensus size: 21

         79 TAAAATCCAC

                             *   
         89 AATAAGATTACTAAAAATCTT
          1 AATAAGATTACTAAAAAACTT

                        *           
        110 AATAA-AGTTAGGTAAAAACACTT
          1 AATAAGA-TTA-CTAAAAA-ACTT

                    *            
        133 AATAAGATGACTAAAAAACTT
          1 AATAAGATTACTAAAAAACTT

            *     
        154 TATAAG
          1 AATAAG

        160 GCCAAACAAG


Statistics
Matches: 41,  Mismatches: 5, Indels: 8
        0.76            0.09        0.15

Matches are distributed among these distances:
  20    1  0.02
  21   17  0.41
  22   12  0.29
  23   10  0.24
  24    1  0.02

ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28


Consensus pattern (21 bp):   
AATAAGATTACTAAAAAACTT

Found at i:1714 original size:23 final size:25

Alignment explanation


    Indices: 1682--1729  Score: 73
    Period size: 23  Copynumber: 2.0  Consensus size: 25

       1672 GTTGCCCACC

                                     
       1682 ACTTTAATCTTTTT-TTTT-TTTTT
          1 ACTTTAATCTTTTTCTTTTCTTTTT

                 *                   
       1705 ACTTTCATCTTTTTCTTTTCTTTTT
          1 ACTTTAATCTTTTTCTTTTCTTTTT

       1730 TTTTTCCTTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23   13  0.59
  24    4  0.18
  25    5  0.23

ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75


Consensus pattern (25 bp):   
ACTTTAATCTTTTTCTTTTCTTTTT

Found at i:2077 original size:18 final size:18

Alignment explanation


    Indices: 2047--2091  Score: 58
    Period size: 17  Copynumber: 2.6  Consensus size: 18

       2037 ATTTTACTGA

                               
       2047 AGAAAATTAATTATATAAC
          1 AGAAAATTAATTA-ATAAC

                              
       2066 AGAAAA-TAATTAATAA-
          1 AGAAAATTAATTAATAAC

            *         
       2082 TGAAAATTAA
          1 AGAAAATTAA

       2092 ATTACATAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  16    5  0.21
  17    7  0.29
  18    6  0.25
  19    6  0.25

ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29


Consensus pattern (18 bp):   
AGAAAATTAATTAATAAC

Found at i:2094 original size:18 final size:19

Alignment explanation


    Indices: 2047--2100  Score: 60
    Period size: 18  Copynumber: 2.9  Consensus size: 19

       2037 ATTTTACTGA

                         *     
       2047 AGAAAATTAATTATATAAC
          1 AGAAAATTAATTACATAAC

                               
       2066 AGAAAA-TAATTA-ATAA-
          1 AGAAAATTAATTACATAAC

            *                  
       2082 TGAAAATTAAATTACATAA
          1 AGAAAATT-AATTACATAA

       2101 AGATTTGATT


Statistics
Matches: 31,  Mismatches: 1, Indels: 6
        0.82            0.03        0.16

Matches are distributed among these distances:
  16    5  0.16
  17    5  0.16
  18   11  0.35
  19   10  0.32

ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30


Consensus pattern (19 bp):   
AGAAAATTAATTACATAAC

Found at i:3636 original size:21 final size:22

Alignment explanation


    Indices: 3610--3650  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       3600 GCAGAATGAA

                     *            
       3610 TTCTTCAAGTTC-GCAAGGTTC
          1 TTCTTCAAGATCTGCAAGGTTC

                  *             
       3631 TTCTTCCAGATCTGCAAGGT
          1 TTCTTCAAGATCTGCAAGGT

       3651 CGGCTTCAAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37


Consensus pattern (22 bp):   
TTCTTCAAGATCTGCAAGGTTC
Done.