Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018792.1 Corchorus olitorius cultivar O-4 contig18825, 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: 5793
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:4072 original size:29 final size:29

Alignment explanation


    Indices: 3995--4143  Score: 165
    Period size: 29  Copynumber: 5.1  Consensus size: 29

       3985 CCAAAGAGAA

                              *      *    
       3995 CCTAGAGTATGCAAAAATAACCAAACTGCC
          1 CCTAGA-TATGCAAAAATGACCAAAATGCC

                    *  *   *      *       
       4025 CC-AGAATGTGTAAAGATGACCGAAATGCC
          1 CCTAG-ATATGCAAAAATGACCAAAATGCC

               *        *               *
       4054 CCTGGATATGCAGAAATGACCAAAATGCT
          1 CCTAGATATGCAAAAATGACCAAAATGCC

                                         
       4083 CCTAGATATGCAAAAATGACCAAAATGCC
          1 CCTAGATATGCAAAAATGACCAAAATGCC

              * *                     *  
       4112 CCCATATATGCAAAAATGACCAAAATTCC
          1 CCTAGATATGCAAAAATGACCAAAATGCC

               
       4141 CCT
          1 CCT

       4144 GAGCGTGCGA


Statistics
Matches: 97,  Mismatches: 20, Indels: 5
        0.80            0.16        0.04

Matches are distributed among these distances:
  29   93  0.96
  30    4  0.04

ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19


Consensus pattern (29 bp):   
CCTAGATATGCAAAAATGACCAAAATGCC

Found at i:4633 original size:59 final size:59

Alignment explanation


    Indices: 4385--4777  Score: 582
    Period size: 59  Copynumber: 6.8  Consensus size: 59

       4375 TGAAATATAG

                  *              *     *           *    *              
       4385 ACTCTCAAACAGAGACCTCGACCAGGAGTTT-AAAACAAAATAAAATTTTGAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA

                                    *     *                            
       4443 ACTCTCTAACAGAGACCTCGAACAAGA--TCAAAAACAAGATAAGATTTTGAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA

                                                 *    *        **      
       4500 ACTCTCTAACAGAGACCTCGAACAGGATTTT--AAACGAGATGAGATTTTGTTTTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA

                                            *  *    * *                
       4557 ACTCTCTAACAGAGACCTCGAACAGGATTTTAGAAGCAAGGTTAGATTTTGAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA

                                                                       
       4616 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA

                     *                                                 
       4675 ACTCTCTAATAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA

                  *                              *       
       4734 ACTCTCCAACAGAGACCTCGAACAGGATTTT-AAAACGAGATAAG
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAG

       4778 GGAATTTTGA


Statistics
Matches: 304,  Mismatches: 26, Indels: 10
        0.89            0.08        0.03

Matches are distributed among these distances:
  56    1  0.00
  57  104  0.34
  58   36  0.12
  59  163  0.54

ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25


Consensus pattern (59 bp):   
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA

Found at i:5644 original size:18 final size:18

Alignment explanation


    Indices: 5615--5670  Score: 58
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       5605 GTTTTTATGA

                 *            
       5615 CCTCTCTCTGTTTTAGGC
          1 CCTCTTTCTGTTTTAGGC

               *   *      ** *
       5633 CCTGTTTTTGTTTTTCGA
          1 CCTCTTTCTGTTTTAGGC

                              
       5651 CCTCTTTCTGTTTTAGGC
          1 CCTCTTTCTGTTTTAGGC

              
       5669 CC
          1 CC

       5671 AGCTTTTTTT


Statistics
Matches: 27,  Mismatches: 11, Indels: 0
        0.71            0.29        0.00

Matches are distributed among these distances:
  18   27  1.00

ACGTcount: A:0.05, C:0.29, G:0.16, T:0.50


Consensus pattern (18 bp):   
CCTCTTTCTGTTTTAGGC

Found at i:5654 original size:36 final size:37

Alignment explanation


    Indices: 5598--5684  Score: 115
    Period size: 36  Copynumber: 2.4  Consensus size: 37

       5588 TGAACCCCTC

                          *                      * 
       5598 CTTTTTAGTTTTTATGACCTCTCTCTGTTTTAGGCCCTG
          1 CTTTTT-GTTTTT-CGACCTCTCTCTGTTTTAGGCCCAG

                                *                
       5637 -TTTTTGTTTTTCGACCTCTTTCTGTTTTAGGCCCAG
          1 CTTTTTGTTTTTCGACCTCTCTCTGTTTTAGGCCCAG

                         
       5673 CTTTTT-TTTTTC
          1 CTTTTTGTTTTTC

       5685 AGCTTCTTTT


Statistics
Matches: 44,  Mismatches: 3, Indels: 5
        0.85            0.06        0.10

Matches are distributed among these distances:
  36   28  0.64
  37   11  0.25
  38    5  0.11

ACGTcount: A:0.08, C:0.22, G:0.14, T:0.56


Consensus pattern (37 bp):   
CTTTTTGTTTTTCGACCTCTCTCTGTTTTAGGCCCAG

Done.