Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010920.1 Corchorus olitorius cultivar O-4 contig10952, 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: 62829
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:5522 original size:2 final size:2

Alignment explanation


    Indices: 5515--5550  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       5505 AGATAAAATA

                                                                 
       5515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5551 TAAAAATTAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:11099 original size:14 final size:14

Alignment explanation


    Indices: 11080--11116  Score: 56
    Period size: 14  Copynumber: 2.6  Consensus size: 14

      11070 ATCGTTTCTG

                          
      11080 TTTTCTGTTGCAAA
          1 TTTTCTGTTGCAAA

                       *  
      11094 TTTTCTGTTGCCAA
          1 TTTTCTGTTGCAAA

                *    
      11108 TTTTTTGTT
          1 TTTTCTGTT

      11117 TTTTAAAACA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  14   21  1.00

ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59


Consensus pattern (14 bp):   
TTTTCTGTTGCAAA

Found at i:11401 original size:11 final size:11

Alignment explanation


    Indices: 11381--11415  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      11371 TGACCAGCAC

                       
      11381 AACAAAAACAA
          1 AACAAAAACAA

               *       
      11392 AACGAAAACAA
          1 AACAAAAACAA

                       
      11403 AACAAAAACAA
          1 AACAAAAACAA

              
      11414 AA
          1 AA

      11416 AACAGAAAAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:15426 original size:17 final size:17

Alignment explanation


    Indices: 15404--15439  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      15394 TGATTTGTAA

                             
      15404 AGTTTGTTACACCAGAT
          1 AGTTTGTTACACCAGAT

                     *  *    
      15421 AGTTTGTTATACTAGAT
          1 AGTTTGTTACACCAGAT

              
      15438 AG
          1 AG

      15440 CTCTTTGTAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39


Consensus pattern (17 bp):   
AGTTTGTTACACCAGAT

Found at i:16203 original size:2 final size:2

Alignment explanation


    Indices: 16196--16239  Score: 54
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      16186 CAATGCATAC

                                      *                                     
      16196 AT AT AT AT ACT AGT AT -T TT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
      16239 A
          1 A

      16240 AGTTGCTATG


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.87
   3    4  0.11

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:38714 original size:31 final size:31

Alignment explanation


    Indices: 38679--38833  Score: 310
    Period size: 31  Copynumber: 5.0  Consensus size: 31

      38669 AGGATACTGG

                                           
      38679 TTATTGTGATGCACTTCATTTTTATGCATGC
          1 TTATTGTGATGCACTTCATTTTTATGCATGC

                                           
      38710 TTATTGTGATGCACTTCATTTTTATGCATGC
          1 TTATTGTGATGCACTTCATTTTTATGCATGC

                                           
      38741 TTATTGTGATGCACTTCATTTTTATGCATGC
          1 TTATTGTGATGCACTTCATTTTTATGCATGC

                                           
      38772 TTATTGTGATGCACTTCATTTTTATGCATGC
          1 TTATTGTGATGCACTTCATTTTTATGCATGC

                                           
      38803 TTATTGTGATGCACTTCATTTTTATGCATGC
          1 TTATTGTGATGCACTTCATTTTTATGCATGC

      38834 ACTACATGGT


Statistics
Matches: 124,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31  124  1.00

ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48


Consensus pattern (31 bp):   
TTATTGTGATGCACTTCATTTTTATGCATGC

Found at i:47526 original size:21 final size:21

Alignment explanation


    Indices: 47500--47541  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      47490 ACCTTGACAA

                                  
      47500 AACCAATTAGCAGCATA-AAGT
          1 AACCAATTAGCAG-ATACAAGT

                                 
      47521 AACCAATTAGCAGATACAAGT
          1 AACCAATTAGCAGATACAAGT

      47542 GCAAAATAGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20    3  0.15
  21   17  0.85

ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19


Consensus pattern (21 bp):   
AACCAATTAGCAGATACAAGT
Done.