Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009907.1 Corchorus olitorius cultivar O-4 contig09939, 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: 1984
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:1228 original size:14 final size:16

Alignment explanation


    Indices: 1204--1236  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       1194 TTAGACCATA

                            
       1204 AAAATGAAAATG-AAT
          1 AAAATGAAAATGAAAT

                            
       1219 AAAA-GAAAATGAAAT
          1 AAAATGAAAATGAAAT

               
       1234 AAA
          1 AAA

       1237 GGGAAGGTGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    7  0.41
  15   10  0.59

ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15


Consensus pattern (16 bp):   
AAAATGAAAATGAAAT

Found at i:1309 original size:24 final size:24

Alignment explanation


    Indices: 1281--1332  Score: 95
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1271 ATGATATGCT

                                    
       1281 AAATGCAACATTAAAATGAACTAA
          1 AAATGCAACATTAAAATGAACTAA

                              *     
       1305 AAATGCAACATTAAAATGCACTAA
          1 AAATGCAACATTAAAATGAACTAA

                
       1329 AAAT
          1 AAAT

       1333 TTATGCATGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21


Consensus pattern (24 bp):   
AAATGCAACATTAAAATGAACTAA

Found at i:1322 original size:13 final size:13

Alignment explanation


    Indices: 1281--1324  Score: 65
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       1271 ATGATATGCT

                         
       1281 AAATGCAACATTA
          1 AAATGCAACATTA

                       * 
       1294 AAATG-AAC-TAA
          1 AAATGCAACATTA

                         
       1305 AAATGCAACATTA
          1 AAATGCAACATTA

                   
       1318 AAATGCA
          1 AAATGCA

       1325 CTAAAAATTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  11    7  0.26
  12    6  0.22
  13   14  0.52

ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20


Consensus pattern (13 bp):   
AAATGCAACATTA
Done.