Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000825.1 Corchorus olitorius cultivar O-4 contig00825, 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, 993

Length: 1656
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33


Found at i:561 original size:24 final size:24

Alignment explanation


    Indices: 534--581  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        524 GATTCAAACC

                                    
        534 CGAGACATTACTTAAGAGAACAAA
          1 CGAGACATTACTTAAGAGAACAAA

                                    
        558 CGAGACATTACTTAAGAGAACAAA
          1 CGAGACATTACTTAAGAGAACAAA

        582 TGTCAAACCA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17


Consensus pattern (24 bp):   
CGAGACATTACTTAAGAGAACAAA

Found at i:1259 original size:14 final size:13

Alignment explanation


    Indices: 1240--1278  Score: 53
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       1230 ACTCAACACT

                          
       1240 AACTGACTCGAAAA
          1 AACTGACTC-AAAA

                       * 
       1254 AACTGACTCAACA
          1 AACTGACTCAAAA

                         
       1267 AACTGACT-AAAA
          1 AACTGACTCAAAA

       1279 CCCGACAGAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  12    3  0.13
  13   11  0.48
  14    9  0.39

ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15


Consensus pattern (13 bp):   
AACTGACTCAAAA

Found at i:1271 original size:13 final size:13

Alignment explanation


    Indices: 1229--1274  Score: 56
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       1219 CTCAGACTCA

                           
       1229 GACTCAACACTAACT
          1 GACTCAACA--AACT

                    *     
       1244 GACTCGAAAAAACT
          1 GACTC-AACAAACT

                         
       1258 GACTCAACAAACT
          1 GACTCAACAAACT

                
       1271 GACT
          1 GACT

       1275 AAAACCCGAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  13   11  0.39
  14    9  0.32
  15    5  0.18
  16    3  0.11

ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17


Consensus pattern (13 bp):   
GACTCAACAAACT
Done.