Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010850.1 Corchorus olitorius cultivar O-4 contig10882, 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: 11282
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32


Found at i:296 original size:25 final size:24

Alignment explanation


    Indices: 259--305  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

        249 CTAGAAAATT

                                      
        259 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
        285 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

        306 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:3657 original size:78 final size:78

Alignment explanation


    Indices: 3487--3843  Score: 456
    Period size: 78  Copynumber: 4.6  Consensus size: 78

       3477 CGTTTTTATC

                 *     *               *                   *           * *  *
       3487 TGTGATGAAACGGTCTCAATGGAGACGTTCGTTTCTTTTATTTATTTCTATACGGGGACTCTGAT
          1 TGTGACGAAACAGTCTCAATGGAGACGATCGTTTC----ATTTATTTTTATACGGGGACACCGAG

                           *  
       3552 GCTGGTG-TCTGGCCATT
         62 GCTGGTGTTC-GGCCGTT

                 *                                                           
       3569 TGTGATGAAACAGTCTCAATGGAGACGATCGTTTCATTTATTTTTATACGGGGACACCGAGGCTG
          1 TGTGACGAAACAGTCTCAATGGAGACGATCGTTTCATTTATTTTTATACGGGGACACCGAGGCTG

               *         
       3634 GTGCTCGGCCGTT
         66 GTGTTCGGCCGTT

                                               *                      *      
       3647 TGTGACGAAACAGTCTCAATGGAGACGATCGTTTCGTTTATTTTTATACGGGGACACCAAGGCTG
          1 TGTGACGAAACAGTCTCAATGGAGACGATCGTTTCATTTATTTTTATACGGGGACACCGAGGCTG

                         
       3712 GTGTTCGGCCGTT
         66 GTGTTCGGCCGTT

            *                  *              *                              
       3725 CGTGACG-AA-AGTCTCAAAGGAGACGATCGTTTTATTTTTATTTTTATACGGGGACACCGAGGC
          1 TGTGACGAAACAGTCTCAATGGAGACGATCGTTTCA--TTTATTTTTATACGGGGACACCGAGGC

                           
       3788 TGGTGTTCGGCCGTT
         64 TGGTGTTCGGCCGTT

                               *              *         
       3803 TGTGACG-AA-AGTCTCAAAGGAGACGATCGTTTTATTT-TTTT
          1 TGTGACGAAACAGTCTCAATGGAGACGATCGTTTCATTTATTTT

       3844 CCAAAATTTC


Statistics
Matches: 255,  Mismatches: 17, Indels: 13
        0.89            0.06        0.05

Matches are distributed among these distances:
  75    4  0.02
  76   25  0.10
  77    2  0.01
  78  189  0.74
  79    2  0.01
  82   33  0.13

ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34


Consensus pattern (78 bp):   
TGTGACGAAACAGTCTCAATGGAGACGATCGTTTCATTTATTTTTATACGGGGACACCGAGGCTG
GTGTTCGGCCGTT

Found at i:6772 original size:25 final size:25

Alignment explanation


    Indices: 6738--6792  Score: 101
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       6728 TCGGTTTTCA

                *                    
       6738 ATTACTAGTTTTTCATAATCTTCTT
          1 ATTAATAGTTTTTCATAATCTTCTT

                                     
       6763 ATTAATAGTTTTTCATAATCTTCTT
          1 ATTAATAGTTTTTCATAATCTTCTT

                 
       6788 ATTAA
          1 ATTAA

       6793 GACTTGTTCA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  25   29  1.00

ACGTcount: A:0.29, C:0.13, G:0.04, T:0.55


Consensus pattern (25 bp):   
ATTAATAGTTTTTCATAATCTTCTT

Found at i:6802 original size:25 final size:25

Alignment explanation


    Indices: 6749--6803  Score: 83
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       6739 TTACTAGTTT

                               * *  *
       6749 TTCATAATCTTCTTATTAATAGTTT
          1 TTCATAATCTTCTTATTAAGACTTG

                                     
       6774 TTCATAATCTTCTTATTAAGACTTG
          1 TTCATAATCTTCTTATTAAGACTTG

                 
       6799 TTCAT
          1 TTCAT

       6804 CTTGGTCTTG


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.27, C:0.15, G:0.05, T:0.53


Consensus pattern (25 bp):   
TTCATAATCTTCTTATTAAGACTTG

Found at i:7097 original size:2 final size:2

Alignment explanation


    Indices: 7090--7116  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       7080 TACTAAATAC

                                                    
       7090 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       7117 CTATCTATGC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:8026 original size:16 final size:16

Alignment explanation


    Indices: 7995--8037  Score: 70
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       7985 CATGTATTCA

                      *     
       7995 AGTTATTCA-CTTTGG
          1 AGTTATTCATATTTGG

                            
       8010 AGTTATTCATATTTGG
          1 AGTTATTCATATTTGG

                        
       8026 AGTTATTCATAT
          1 AGTTATTCATAT

       8038 GGATTTTATT


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15    9  0.35
  16   17  0.65

ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49


Consensus pattern (16 bp):   
AGTTATTCATATTTGG
Done.