Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012548.1 Corchorus olitorius cultivar O-4 contig12581, 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: 14879
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:7195 original size:15 final size:15

Alignment explanation


    Indices: 7159--7187  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       7149 AGACATACTT

                           
       7159 ACAC-AAACACTTAA
          1 ACACAAAACACTTAA

                           
       7173 ACACAAAACACTTAA
          1 ACACAAAACACTTAA

       7188 TCCAAAAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    4  0.29
  15   10  0.71

ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14


Consensus pattern (15 bp):   
ACACAAAACACTTAA

Found at i:8769 original size:19 final size:20

Alignment explanation


    Indices: 8739--8798  Score: 56
    Period size: 17  Copynumber: 3.2  Consensus size: 20

       8729 TAACTTTTAT

                 *              
       8739 ATTGCTTTTAAACAGATAGA
          1 ATTGCATTTAAACAGATAGA

                        **      
       8759 ATTG-ATTTAAATGGAT---
          1 ATTGCATTTAAACAGATAGA

                 *              
       8775 ATTGCTTTTAAACAGATAGA
          1 ATTGCATTTAAACAGATAGA

                
       8795 ATTG
          1 ATTG

       8799 TTCAAATATT


Statistics
Matches: 30,  Mismatches: 6, Indels: 8
        0.68            0.14        0.18

Matches are distributed among these distances:
  16    4  0.13
  17    9  0.30
  19    9  0.30
  20    8  0.27

ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38


Consensus pattern (20 bp):   
ATTGCATTTAAACAGATAGA

Found at i:14353 original size:23 final size:23

Alignment explanation


    Indices: 14303--14363  Score: 72
    Period size: 23  Copynumber: 2.7  Consensus size: 23

      14293 TAAATGTTGC

                                   
      14303 TGATAATTTTCTC-TTTAATCTA
          1 TGATAATTTTCTCATTTAATCTA

             *                      
      14325 TCATAATTTTCTCATTT-ATCTTA
          1 TGATAATTTTCTCATTTAATC-TA

                   *   *    
      14348 TGATAATATTCACATT
          1 TGATAATTTTCTCATT

      14364 AATAATTCCA


Statistics
Matches: 33,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  22   15  0.45
  23   18  0.55

ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52


Consensus pattern (23 bp):   
TGATAATTTTCTCATTTAATCTA

Found at i:14567 original size:76 final size:76

Alignment explanation


    Indices: 14436--14626  Score: 244
    Period size: 76  Copynumber: 2.5  Consensus size: 76

      14426 TTGTACATGC

                       *           *   * *                    *      *       
      14436 ATGGTCAAACCACAAAGTTTGATCGTCCACCCACAAAAAATATCATTGTATATGCATGGTCAAAA
          1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAATATCATTGTACATGCATAGT-AAAA

                         
      14501 -CCC-AAATGATG
         65 TCCCAAAAT-ATG

                                 *                                           
      14512 ATGGTCAAACCCCAAAGTTTGGTAGTCAAACCACAAAAAATATCATTGTACATGCATAGTAAAAT
          1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAATATCATTGTACATGCATAGTAAAAT

                    *  
      14577 CCCAAAATTTG
         66 CCCAAAATATG

              *                **                   
      14588 ATAGTCAAA-CCCAAAGTTCCATAGTCAAACCACAAAAAA
          1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAA

      14627 CATTTTATTG


Statistics
Matches: 101,  Mismatches: 12, Indels: 5
        0.86            0.10        0.04

Matches are distributed among these distances:
  75   31  0.31
  76   66  0.65
  77    4  0.04

ACGTcount: A:0.43, C:0.22, G:0.13, T:0.23


Consensus pattern (76 bp):   
ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAATATCATTGTACATGCATAGTAAAAT
CCCAAAATATG

Found at i:14602 original size:20 final size:20

Alignment explanation


    Indices: 14566--14624  Score: 64
    Period size: 20  Copynumber: 2.9  Consensus size: 20

      14556 ATTGTACATG

                  *             *
      14566 CATAGTAAAATCCCAAAATTT
          1 CATAGTCAAA-CCCAAAATTC

            *               *   
      14587 GATAGTCAAACCCAAAGTTC
          1 CATAGTCAAACCCAAAATTC

                              
      14607 CATAGTCAAACCACAAAA
          1 CATAGTCAAACC-CAAAA

      14625 AACATTTTAT


Statistics
Matches: 31,  Mismatches: 6, Indels: 2
        0.79            0.15        0.05

Matches are distributed among these distances:
  20   19  0.61
  21   12  0.39

ACGTcount: A:0.47, C:0.24, G:0.08, T:0.20


Consensus pattern (20 bp):   
CATAGTCAAACCCAAAATTC
Done.