Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023850.1 Corchorus olitorius cultivar O-4 contig23883, 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: 29048
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:2227 original size:21 final size:21

Alignment explanation


    Indices: 2201--2241  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2191 ATCCCTACTA

                        *        
       2201 AGCATATTTACTTAACAAAAT
          1 AGCATATTTACTCAACAAAAT

                                
       2222 AGCATATTTACTCAACAAAA
          1 AGCATATTTACTCAACAAAA

       2242 GGAACTGAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29


Consensus pattern (21 bp):   
AGCATATTTACTCAACAAAAT

Found at i:11042 original size:42 final size:42

Alignment explanation


    Indices: 10995--11074  Score: 142
    Period size: 42  Copynumber: 1.9  Consensus size: 42

      10985 TTCACTGCTG

                               *                      
      10995 TCAATCATCCTACTTAATAGTAGAGTTCATCACTTACTGATA
          1 TCAATCATCCTACTTAATAATAGAGTTCATCACTTACTGATA

                                            *     
      11037 TCAATCATCCTACTTAATAATAGAGTTCATCATTTACT
          1 TCAATCATCCTACTTAATAATAGAGTTCATCACTTACT

      11075 AAAGTCAGGA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38


Consensus pattern (42 bp):   
TCAATCATCCTACTTAATAATAGAGTTCATCACTTACTGATA

Found at i:11066 original size:22 final size:22

Alignment explanation


    Indices: 10999--11067  Score: 63
    Period size: 22  Copynumber: 3.2  Consensus size: 22

      10989 CTGCTGTCAA

                           *      
      10999 TCATCCTACTTAATAGTAGAGT
          1 TCATCCTACTTAATAATAGAGT

                        * *    *  *
      11021 TCAT-C-ACTTACTGATATCA-A
          1 TCATCCTACTTAATAATA-GAGT

                                  
      11041 TCATCCTACTTAATAATAGAGT
          1 TCATCCTACTTAATAATAGAGT

                 
      11063 TCATC
          1 TCATC

      11068 ATTTACTAAA


Statistics
Matches: 34,  Mismatches: 9, Indels: 8
        0.67            0.18        0.16

Matches are distributed among these distances:
  20   12  0.35
  21    4  0.12
  22   18  0.53

ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36


Consensus pattern (22 bp):   
TCATCCTACTTAATAATAGAGT

Found at i:21798 original size:27 final size:27

Alignment explanation


    Indices: 21768--21821  Score: 81
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      21758 CATGTTTTCA

                                       
      21768 AGCTGAACATAATGAGATCAGAACCAG
          1 AGCTGAACATAATGAGATCAGAACCAG

                  *   *       *        
      21795 AGCTGAGCATGATGAGATTAGAACCAG
          1 AGCTGAACATAATGAGATCAGAACCAG

      21822 TACAAAGTTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.41, C:0.17, G:0.26, T:0.17


Consensus pattern (27 bp):   
AGCTGAACATAATGAGATCAGAACCAG

Found at i:26048 original size:127 final size:127

Alignment explanation


    Indices: 25829--26084  Score: 367
    Period size: 127  Copynumber: 2.0  Consensus size: 127

      25819 AAATGCTAAA

                                                                             
      25829 ATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAATAG
          1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAAT---ATA-

                                                                    *        
      25894 GTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTGTAAAAGTA
         62 GTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAGTA

             
      25959 T
        127 T

                                                  *                          
      25960 ATTTAAAAAATTCTAATATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA
          1 ATTTAAAAAATTC---TA-ATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATATA

                                           *              *      *          
      26024 -TA-AAG-ATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAACCTATAAAAGT
         62 GTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAGT

      26085 TTATACAATG


Statistics
Matches: 116,  Mismatches: 5, Indels: 12
        0.87            0.04        0.09

Matches are distributed among these distances:
 127   52  0.45
 128    3  0.03
 129    2  0.02
 131   15  0.13
 134    2  0.02
 135   42  0.36

ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38


Consensus pattern (127 bp):   
ATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATATAGTAT
AAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAGTAT

Found at i:26278 original size:26 final size:26

Alignment explanation


    Indices: 26248--26300  Score: 106
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      26238 ATGACGTTGA

                                      
      26248 AAAACAAAACAATTAACCGAACTAGC
          1 AAAACAAAACAATTAACCGAACTAGC

                                      
      26274 AAAACAAAACAATTAACCGAACTAGC
          1 AAAACAAAACAATTAACCGAACTAGC

             
      26300 A
          1 A

      26301 TATAGATAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.58, C:0.23, G:0.08, T:0.11


Consensus pattern (26 bp):   
AAAACAAAACAATTAACCGAACTAGC
Done.