Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019993.1 Corchorus olitorius cultivar O-4 contig20026, 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: 12605
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:1172 original size:12 final size:13

Alignment explanation


    Indices: 1155--1183  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       1145 TTTTCTTTAA

                         
       1155 TTTTCTTGATT-G
          1 TTTTCTTGATTGG

                         
       1167 TTTTCTTGATTGG
          1 TTTTCTTGATTGG

                
       1180 TTTT
          1 TTTT

       1184 AATTGTTAGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.69
  13    5  0.31

ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69


Consensus pattern (13 bp):   
TTTTCTTGATTGG

Found at i:3745 original size:21 final size:21

Alignment explanation


    Indices: 3720--3767  Score: 55
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3710 TATCTTAGAT

                                   
       3720 ATAAT-ATATATTAATAAAT-AA
          1 ATAATAATATATT--TAAATAAA

                                  
       3741 ATAATAAATATATTTAAATAAA
          1 ATAAT-AATATATTTAAATAAA

                 
       3763 ATAAT
          1 ATAAT

       3768 GAGTTAAAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  21   10  0.42
  22    7  0.29
  23    7  0.29

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (21 bp):   
ATAATAATATATTTAAATAAA

Found at i:5104 original size:30 final size:31

Alignment explanation


    Indices: 5069--5130  Score: 117
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       5059 ATAGTTAATG

                                           
       5069 AGTCATTAAAATTTGAGGGTATAAGA-GAAA
          1 AGTCATTAAAATTTGAGGGTATAAGAGGAAA

                                           
       5099 AGTCATTAAAATTTGAGGGTATAAGAGGAAA
          1 AGTCATTAAAATTTGAGGGTATAAGAGGAAA

             
       5130 A
          1 A

       5131 TCAAGATAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30   26  0.84
  31    5  0.16

ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26


Consensus pattern (31 bp):   
AGTCATTAAAATTTGAGGGTATAAGAGGAAA

Found at i:8964 original size:13 final size:13

Alignment explanation


    Indices: 8946--8970  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       8936 TTCAATGTTC

                         
       8946 TAAATATTATTTA
          1 TAAATATTATTTA

                        
       8959 TAAATATTATTT
          1 TAAATATTATTT

       8971 GGAATTCGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA

Found at i:10203 original size:31 final size:30

Alignment explanation


    Indices: 10165--10234  Score: 81
    Period size: 29  Copynumber: 2.3  Consensus size: 30

      10155 GAAAAGGTAC

                                *           
      10165 TAAATTGAACCAA-TTTGATGAGGTTTAGTAT
          1 TAAATTGAACCAACTTT-A-AAGGTTTAGTAT

                     **                   
      10196 TAAATTG-AGTAACTTTAAAGGTTTAGTAT
          1 TAAATTGAACCAACTTTAAAGGTTTAGTAT

                      
      10225 TAAATTGAAC
          1 TAAATTGAAC

      10235 ATTTCGTGAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 5
        0.79            0.10        0.12

Matches are distributed among these distances:
  29   18  0.55
  30    5  0.15
  31   10  0.30

ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39


Consensus pattern (30 bp):   
TAAATTGAACCAACTTTAAAGGTTTAGTAT

Found at i:11334 original size:131 final size:133

Alignment explanation


    Indices: 11155--11409  Score: 372
    Period size: 132  Copynumber: 1.9  Consensus size: 133

      11145 TCATTTATTC

                 *        *                 **                               
      11155 AAATTTTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATAAAAA-TAAAT-TAGGTATA
          1 AAATTCTAATATATATAAGTTTTTTAATTAAAAAAGTAAAATGATAAAAATTAAATATAGGTATA

             *              *                         *     *                
      11218 AGGATATAAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAACACTATAAAAGTATATT
         66 AAGATATAAGATTTAAGTAAAT-AAAAATAGAGTTTTTAGTTCAGTAAAACTATAAAAGTATATT

                
      11283 TAAA
        130 TAAA

                                                       *                *    
      11287 AAATTCTAATATATATAAG-TTTTTAATTAAAAAAGTAAAATGGTAAAAATTAAATATAGTTATA
          1 AAATTCTAATATATATAAGTTTTTTAATTAAAAAAGTAAAATGATAAAAATTAAATATAGGTATA

                   *                                         *         
      11351 AAGATATTAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTCAGTAAAATTATAAAAGT
         66 AAGATATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTCAGTAAAACTATAAAAGT

      11410 TTAAACAATG


Statistics
Matches: 109,  Mismatches: 12, Indels: 4
        0.87            0.10        0.03

Matches are distributed among these distances:
 131   27  0.25
 132   56  0.51
 133   26  0.24

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37


Consensus pattern (133 bp):   
AAATTCTAATATATATAAGTTTTTTAATTAAAAAAGTAAAATGATAAAAATTAAATATAGGTATA
AAGATATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTCAGTAAAACTATAAAAGTATATTT
AAA

Done.