Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010344.1 Corchorus olitorius cultivar O-4 contig10376, 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: 2154
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42


Found at i:265 original size:11 final size:11

Alignment explanation


    Indices: 222--259  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        212 TTCCTATATA

                *      
        222 AAATAAATTAT
          1 AAATTAATTAT

                        
        233 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
        244 AAATTAATTAT
          1 AAATTAATTAT

                 
        255 AAATT
          1 AAATT

        260 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:945 original size:16 final size:16

Alignment explanation


    Indices: 924--958  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        914 TTAGAATTGA

                            
        924 AGATCTTATTATATGG
          1 AGATCTTATTATATGG

                            
        940 AGATCTTATTATATGG
          1 AGATCTTATTATATGG

               
        956 AGA
          1 AGA

        959 CTTCGATTTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40


Consensus pattern (16 bp):   
AGATCTTATTATATGG

Found at i:1229 original size:15 final size:15

Alignment explanation


    Indices: 1209--1258  Score: 63
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       1199 CATACCACTA

                           
       1209 ATAATAATTATTATT
          1 ATAATAATTATTATT

                            
       1224 ATAATAA-TA--AGTT
          1 ATAATAATTATTA-TT

                           
       1237 -TAATAATTATTATT
          1 ATAATAATTATTATT

                    
       1251 ATAATAAT
          1 ATAATAAT

       1259 AATAAGTCTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 10
        0.75            0.00        0.25

Matches are distributed among these distances:
  12    7  0.23
  13    4  0.13
  14    4  0.13
  15   15  0.50

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (15 bp):   
ATAATAATTATTATT

Found at i:1243 original size:30 final size:30

Alignment explanation


    Indices: 1207--1265  Score: 100
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1197 TACATACCAC

                            *             
       1207 TAATAATAATTATTATTATAATAATAAGTT
          1 TAATAATAATTATTATAATAATAATAAGTT

                   *                     
       1237 TAATAATTATTATTATAATAATAATAAGT
          1 TAATAATAATTATTATAATAATAATAAGT

       1266 CTAAATTAAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (30 bp):   
TAATAATAATTATTATAATAATAATAAGTT

Found at i:1826 original size:39 final size:40

Alignment explanation


    Indices: 1770--1850  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       1760 TTCAATTCCT

                                                    
       1770 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *                   
       1810 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
       1849 AT
          1 AT

       1851 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:1877 original size:25 final size:24

Alignment explanation


    Indices: 1841--1887  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       1831 AATACTTACA

                                    
       1841 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
       1865 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

       1888 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT
Done.