Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024713.1 Corchorus olitorius cultivar O-4 contig24746, 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: 24988
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32


Found at i:2260 original size:29 final size:29

Alignment explanation


    Indices: 2214--2271  Score: 98
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2204 TACTAATGGG

                     *   *               
       2214 CCTAGTTAATAGACTAATTTTATTAGTCA
          1 CCTAGTTAACAGAATAATTTTATTAGTCA

                                         
       2243 CCTAGTTAACAGAATAATTTTATTAGTCA
          1 CCTAGTTAACAGAATAATTTTATTAGTCA

       2272 AACGATGGGC


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   27  1.00

ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40


Consensus pattern (29 bp):   
CCTAGTTAACAGAATAATTTTATTAGTCA

Found at i:7684 original size:40 final size:41

Alignment explanation


    Indices: 7638--7723  Score: 120
    Period size: 43  Copynumber: 2.1  Consensus size: 41

       7628 GCATTACCTA

                                *           *        
       7638 AATTCTA-CTCCATCTCTAGCTAATTCATCAATATAAAGCT
          1 AATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCT

                                                     * 
       7678 AATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGTT
          1 AATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCT

               
       7721 AAT
          1 AAT

       7724 ATTAATTGTT


Statistics
Matches: 40,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  40    7  0.17
  43   33  0.82

ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35


Consensus pattern (41 bp):   
AATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCT

Found at i:9960 original size:18 final size:18

Alignment explanation


    Indices: 9937--9974  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       9927 CTACTCTATC

                     *        
       9937 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
       9955 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

              
       9973 AT
          1 AT

       9975 TACCATTTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:11638 original size:21 final size:22

Alignment explanation


    Indices: 11612--11656  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 22

      11602 CTTTTCTTAG

                                  
      11612 CTACTT-GTCGACAATTTGCTT
          1 CTACTTAGTCGACAATTTGCTT

                         *         
      11633 CTACTTGAGTCGATAATTTGCTT
          1 CTACTT-AGTCGACAATTTGCTT

             
      11656 C
          1 C

      11657 CTTTGATTGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    6  0.29
  23   15  0.71

ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42


Consensus pattern (22 bp):   
CTACTTAGTCGACAATTTGCTT

Found at i:11701 original size:15 final size:15

Alignment explanation


    Indices: 11683--11726  Score: 52
    Period size: 16  Copynumber: 2.8  Consensus size: 15

      11673 CCTAGTCGAC

                           
      11683 ACTTGCTCTTTATCG
          1 ACTTGCTCTTTATCG

                  *  *      
      11698 ACTTTGATCCTTATCG
          1 AC-TTGCTCTTTATCG

                         
      11714 ACTTGCTCCTTTA
          1 ACTTGCT-CTTTA

      11727 AGTCGACAAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  15    6  0.26
  16   17  0.74

ACGTcount: A:0.16, C:0.27, G:0.11, T:0.45


Consensus pattern (15 bp):   
ACTTGCTCTTTATCG

Found at i:22146 original size:22 final size:22

Alignment explanation


    Indices: 22095--22148  Score: 56
    Period size: 22  Copynumber: 2.5  Consensus size: 22

      22085 ATAACCTTTT

                       *         *
      22095 TATAAAATTTTGATAATCACAT
          1 TATAAAATTTTCATAATCACAC

               *                *  
      22117 TATTAAATTTTCATAA-CGATAC
          1 TATAAAATTTTCATAATC-ACAC

                      
      22139 TATAAAATTT
          1 TATAAAATTT

      22149 CGAGAACCTT


Statistics
Matches: 26,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  21    1  0.04
  22   25  0.96

ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43


Consensus pattern (22 bp):   
TATAAAATTTTCATAATCACAC

Found at i:22185 original size:22 final size:22

Alignment explanation


    Indices: 22160--22207  Score: 71
    Period size: 22  Copynumber: 2.2  Consensus size: 22

      22150 GAGAACCTTT

                         *         
      22160 CTATAAAATTTTGTTA-TATTCC
          1 CTATAAAATTTTGATAGTA-TCC

                                  
      22182 CTATAAAATTTTGATAGTATCC
          1 CTATAAAATTTTGATAGTATCC

                
      22204 CTAT
          1 CTAT

      22208 GATTTTTTTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  22   22  0.92
  23    2  0.08

ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46


Consensus pattern (22 bp):   
CTATAAAATTTTGATAGTATCC
Done.