Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017724.1 Corchorus olitorius cultivar O-4 contig17757, 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: 7538
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:1178 original size:16 final size:15

Alignment explanation


    Indices: 1157--1189  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 15

       1147 GAATTATGTG

                            
       1157 AACAAGAAAATAAATA
          1 AACAAGAAAAT-AATA

                           
       1173 AACAAGAAAATAATA
          1 AACAAGAAAATAATA

              
       1188 AA
          1 AA

       1190 ATTAAGTAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    6  0.35
  16   11  0.65

ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12


Consensus pattern (15 bp):   
AACAAGAAAATAATA

Found at i:1810 original size:21 final size:19

Alignment explanation


    Indices: 1785--1827  Score: 50
    Period size: 21  Copynumber: 2.2  Consensus size: 19

       1775 GATGAAGACC

                                 
       1785 GAGAACAAGAAAAGTAGAAGA
          1 GAGAACAAGAAAAG-AGAA-A

                 *  *          
       1806 GAGAAGAATAAAAGAGAAA
          1 GAGAACAAGAAAAGAGAAA

               
       1825 GAG
          1 GAG

       1828 TGTGTAGAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  19    4  0.20
  20    4  0.20
  21   12  0.60

ACGTcount: A:0.63, C:0.02, G:0.30, T:0.05


Consensus pattern (19 bp):   
GAGAACAAGAAAAGAGAAA

Found at i:6598 original size:14 final size:13

Alignment explanation


    Indices: 6579--6609  Score: 53
    Period size: 14  Copynumber: 2.3  Consensus size: 13

       6569 GCAGTGTATA

                          
       6579 ATATCTATATATCT
          1 ATATCTATATA-CT

                         
       6593 ATATCTATATACT
          1 ATATCTATATACT

                
       6606 ATAT
          1 ATAT

       6610 AAGTCTAAAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.35
  14   11  0.65

ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48


Consensus pattern (13 bp):   
ATATCTATATACT

Found at i:6924 original size:24 final size:25

Alignment explanation


    Indices: 6897--6943  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       6887 AATACTTATA

                                     
       6897 TTAATT-AAATTCTTAGGTATTTTT
          1 TTAATTCAAATTCTTAGGTATTTTT

                                   
       6921 TTAATTCAAATTCTTAGGTATTT
          1 TTAATTCAAATTCTTAGGTATTT

       6944 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 (25 bp):   
TTAATTCAAATTCTTAGGTATTTTT

Done.