Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000616.1 Corchorus olitorius cultivar O-4 contig00616, 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, 834

Length: 1390
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:156 original size:29 final size:29

Alignment explanation


    Indices: 122--199  Score: 102
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        112 AAATGAACTT

                   *                   * 
        122 AAAATGATCAAAATGCCCCTGAATATGCA
          1 AAAATGACCAAAATGCCCCTGAATATGAA

            *         *             *    
        151 GAAATGACCATAATGCCCCTGAATGTGAA
          1 AAAATGACCAAAATGCCCCTGAATATGAA

                 *              
        180 AAAATTACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

        200 AGGTGATCCT


Statistics
Matches: 41,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  29   41  1.00

ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGAATATGAA

Found at i:243 original size:14 final size:14

Alignment explanation


    Indices: 224--253  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

        214 CAAATTAAGC

                          
        224 AACAAATTGATTTA
          1 AACAAATTGATTTA

                          
        238 AACAAATTGATTTA
          1 AACAAATTGATTTA

              
        252 AA
          1 AA

        254 TAAAGGATAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33


Consensus pattern (14 bp):   
AACAAATTGATTTA

Found at i:955 original size:35 final size:35

Alignment explanation


    Indices: 474--954  Score: 686
    Period size: 35  Copynumber: 13.7  Consensus size: 35

        464 TGAGTCTATA

                                    * *     *  
        474 TTGAAGATGCTACACCGAGTCATCCGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

                  *                            
        509 TTGAAGGTGCTACACCGAGTCATCTGGATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

                                                
        544 TTGAAGATGCTACACCGAGTCATCT-GAGTTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCAACT

                     *        *       *   *     
        579 TTGAAGATGTTACACCGAATCATCTGAATTGATA-T
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCA-ACT

                                *              
        614 TTGAAGATGCTACACCGAGTTATCTGGATTCAA-T
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

                                    *         * 
        648 TTCGAAGATGCTACACCGAGTCATTTGGATT-AAAT
          1 TT-GAAGATGCTACACCGAGTCATCTGGATTCAACT

                                              * 
        683 TTCGAAGATGCTACACCGAGTCATCTGGATTCAATT
          1 TT-GAAGATGCTACACCGAGTCATCTGGATTCAACT

                                             * 
        719 TTGAAGATGCTACACCGAGTCATCTGGATTCAATT
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

                 *                 *         * 
        754 TTGAAAATGCTACACCGAGTCATTTGGATTCAATT
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

                                             * 
        789 TTGAAGATGCTACACCGAGTCATCTGGATTCAATT
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

                                             * 
        824 TTGAAGATGCTACACCGAGTCATCTGGATTCAATT
          1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

                 *                              
        859 TTGAAAATGCTACACCGAGTCATCT-GAGTTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCAACT

                                      *         
        894 TTGAAGATGCTACACCGAGTCATCTGAATAT-AACT
          1 TTGAAGATGCTACACCGAGTCATCTGGAT-TCAACT

                                      
        929 TTGAAGATGCTACACCGAGTCATCTG
          1 TTGAAGATGCTACACCGAGTCATCTG

        955 AGAAGATGGT


Statistics
Matches: 411,  Mismatches: 26, Indels: 18
        0.90            0.06        0.04

Matches are distributed among these distances:
  34   10  0.02
  35  392  0.95
  36    9  0.02

ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGGATTCAACT

Found at i:1053 original size:50 final size:50

Alignment explanation


    Indices: 971--1100  Score: 206
    Period size: 50  Copynumber: 2.6  Consensus size: 50

        961 TGGTAATGTA

                           * *      *                          
        971 TCGTATGGAAACGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTGAC
          1 TCGTATGGAAACG-AGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC

                                              *               
       1022 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
          1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC

                       *                 
       1072 TCGTATGGAAAAGAGTTTGGCTTGTGGAA
          1 TCGTATGGAAACGAGTTTGGCTTGTGGAA

       1101 TGTTTCACTT


Statistics
Matches: 74,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  50   61  0.82
  51   13  0.18

ACGTcount: A:0.29, C:0.12, G:0.28, T:0.30


Consensus pattern (50 bp):   
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC

Found at i:1229 original size:50 final size:49

Alignment explanation


    Indices: 1150--1275  Score: 173
    Period size: 50  Copynumber: 2.5  Consensus size: 49

       1140 CGATCAATTT

                   *                 *          *              
       1150 CTTTGAATTGTTCTCCAA-TCTAATATTAAAAGGACTGTCTTCCGCTTATC
          1 CTTTGAACTG-TCTCCAATTC-AATCTTAAAAGGACCGTCTTCCGCTTATC

                                             *                
       1200 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGGCCGTCTTCCGCTTATC
          1 CTTTGAACTGTCT-CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                      
       1250 CTTTGAACTGTCTTCCAATTCAATCT
          1 CTTTGAACTGTC-TCCAATTCAATCT

       1276 CGAGAAAACC


Statistics
Matches: 69,  Mismatches: 4, Indels: 6
        0.87            0.05        0.08

Matches are distributed among these distances:
  49    3  0.04
  50   63  0.91
  51    3  0.04

ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38


Consensus pattern (49 bp):   
CTTTGAACTGTCTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Done.