Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012907.1 Corchorus olitorius cultivar O-4 contig12940, 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: 10009
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35


Found at i:1063 original size:36 final size:36

Alignment explanation


    Indices: 1016--1085  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1006 GAGATTTTGG

                         *      *               
       1016 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       1052 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       1086 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:2456 original size:58 final size:58

Alignment explanation


    Indices: 2353--2467  Score: 151
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       2343 ATAGCATCAT

                      *                   *                           
       2353 GTCTCGGTCCTAAAACGTCTGTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA
          1 GTCTCGGTCCGAAAACGTCTGTTTTAGACACCTAATAAAAAAACATGTCACTCGATAA

                *                *     *             *           *    
       2411 GTCTTGGTCCGAAAACGTCTTTTTTTATACACCTAAT-AAAGAACATGTCACTTGATA
          1 GTCTCGGTCCGAAAACGTC-TGTTTTAGACACCTAATAAAAAAACATGTCACTCGATA

       2468 TTTGATTAAT


Statistics
Matches: 49,  Mismatches: 7, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  58   35  0.71
  59   14  0.29

ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32


Consensus pattern (58 bp):   
GTCTCGGTCCGAAAACGTCTGTTTTAGACACCTAATAAAAAAACATGTCACTCGATAA

Found at i:5395 original size:2 final size:2

Alignment explanation


    Indices: 5388--5421  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       5378 TGTAACAATT

                                                       *      
       5388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       5422 ATAACTTACT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:7034 original size:131 final size:132

Alignment explanation


    Indices: 6860--7120  Score: 427
    Period size: 132  Copynumber: 2.0  Consensus size: 132

       6850 TAAGAAATAT

                                *                 *                          
       6860 TTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAAGTAGTAAAATGGTAAAAATAAAATAGG
          1 TTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGG

                                                           *                 
       6925 TATAAGG-ATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGACTAAAACTATAAAAGT
         66 TATAAGGAATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTAACTAAAACTATAAAAGT

               
       6989 ATA
        130 ATA

                                                                     *      *
       6992 TTTTAAAAATTCTAATAT-TATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGT
          1 TTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGG

                                                             * *             
       7056 TATAAGGATATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTTAAACTATAAAAGT
         66 TATAAGGA-ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAACTAAAACTATAAAAGT

       7121 TTAAACAATG


Statistics
Matches: 120,  Mismatches: 7, Indels: 4
        0.92            0.05        0.03

Matches are distributed among these distances:
 131   49  0.41
 132   52  0.43
 133   19  0.16

ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39


Consensus pattern (132 bp):   
TTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGG
TATAAGGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAACTAAAACTATAAAAGTA
TA

Found at i:7395 original size:73 final size:73

Alignment explanation


    Indices: 7249--7385  Score: 229
    Period size: 73  Copynumber: 1.9  Consensus size: 73

       7239 AAAAATCTTA

                                                                             
       7249 ATTACTCAATTACTAAAATACCCTTAATATTATAGTATAATAATTTTTAAATAAGTATTCTCTTC
          1 ATTACTCAATTACTAAAATACCCTTAATATTATAGTATAATAATTTTTAAATAAGTATTCTCTTC

                    
       7314 AATCATTC
         66 AATCATTC

                *               ***                           *             
       7322 ATTAGTCAATTACTAAAATATTGTTAATATTATAGTATAATAATTTTTAAGTAAGTATTCTCTT
          1 ATTACTCAATTACTAAAATACCCTTAATATTATAGTATAATAATTTTTAAATAAGTATTCTCTT

       7386 TAGTTATTCA


Statistics
Matches: 59,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  73   59  1.00

ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45


Consensus pattern (73 bp):   
ATTACTCAATTACTAAAATACCCTTAATATTATAGTATAATAATTTTTAAATAAGTATTCTCTTC
AATCATTC

Found at i:8691 original size:45 final size:44

Alignment explanation


    Indices: 8632--8760  Score: 213
    Period size: 45  Copynumber: 2.9  Consensus size: 44

       8622 CTAAATTCTA

                                 *                       
       8632 CTCCATCTCTAGGTAATTCATGAGAATAAAGCTAATATTATACTC
          1 CTCCATCTCTAGGTAATTCATCA-AATAAAGCTAATATTATACTC

              *                                    *     
       8677 CTTCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTC
          1 CTCCATCTCTAGGTAATTCATC-AAATAAAGCTAATATTATACTC

                                                   
       8722 CTCCATCTCTAGGTAATTCATCAAATAAAGCTAATATTA
          1 CTCCATCTCTAGGTAATTCATCAAATAAAGCTAATATTA

       8761 ATTGTTGCTT


Statistics
Matches: 78,  Mismatches: 5, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  44   16  0.21
  45   61  0.78
  46    1  0.01

ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34


Consensus pattern (44 bp):   
CTCCATCTCTAGGTAATTCATCAAATAAAGCTAATATTATACTC
Done.