Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010195.1 Corchorus olitorius cultivar O-4 contig10227, 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: 19792
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:3268 original size:19 final size:17

Alignment explanation


    Indices: 3225--3259  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

       3215 ACTAGAGAAG

                 *           
       3225 CAAAAGTTTTGAAAAAT
          1 CAAAATTTTTGAAAAAT

                              
       3242 CGAAAATTTTTGAAAAAT
          1 C-AAAATTTTTGAAAAAT

       3260 TTCAAAATTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    1  0.06
  18   15  0.94

ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31


Consensus pattern (17 bp):   
CAAAATTTTTGAAAAAT

Found at i:3962 original size:20 final size:18

Alignment explanation


    Indices: 3930--3967  Score: 58
    Period size: 20  Copynumber: 2.0  Consensus size: 18

       3920 CACAAGTGTC

                              
       3930 TTTTTTTTTAATTTTCTT
          1 TTTTTTTTTAATTTTCTT

                                
       3948 TTTTTCTTTTAAATTTTCTT
          1 TTTTT-TTTT-AATTTTCTT

       3968 GGTGGTTGCA


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

Matches are distributed among these distances:
  18    5  0.28
  19    4  0.22
  20    9  0.50

ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79


Consensus pattern (18 bp):   
TTTTTTTTTAATTTTCTT

Found at i:7567 original size:18 final size:20

Alignment explanation


    Indices: 7540--7587  Score: 64
    Period size: 18  Copynumber: 2.5  Consensus size: 20

       7530 GAAACAGGAA

                                
       7540 AATTTACTT-CTTTG-CTCC
          1 AATTTACTTCCTTTGTCTCC

                 *              
       7558 AATTTGCTTCCTTTGTCTCC
          1 AATTTACTTCCTTTGTCTCC

                      
       7578 AATTCTACTT
          1 AATT-TACTT

       7588 TTAAGTACCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  18    8  0.32
  19    5  0.20
  20    8  0.32
  21    4  0.16

ACGTcount: A:0.17, C:0.27, G:0.06, T:0.50


Consensus pattern (20 bp):   
AATTTACTTCCTTTGTCTCC

Found at i:10558 original size:57 final size:58

Alignment explanation


    Indices: 10476--10587  Score: 190
    Period size: 57  Copynumber: 1.9  Consensus size: 58

      10466 TTTTCAAGCA

                                                                      
      10476 TTTCTAATTTTTCTCCCTTTGAGTCAACATGATAGCTTTCCTCTTCTAATCAAGTATT
          1 TTTCTAATTTTTCTCCCTTTGAGTCAACATGATAGCTTTCCTCTTCTAATCAAGTATT

                          *     *      *                           
      10534 TTTCTAA-TTTTCTTCCTTTTAGTCAATATGATAGCTTTCCTCTTCTAATCAAGT
          1 TTTCTAATTTTTCTCCCTTTGAGTCAACATGATAGCTTTCCTCTTCTAATCAAGT

      10588 TATTGAGTGA


Statistics
Matches: 51,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  57   44  0.86
  58    7  0.14

ACGTcount: A:0.22, C:0.21, G:0.08, T:0.48


Consensus pattern (58 bp):   
TTTCTAATTTTTCTCCCTTTGAGTCAACATGATAGCTTTCCTCTTCTAATCAAGTATT

Found at i:13765 original size:23 final size:22

Alignment explanation


    Indices: 13733--13778  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 22

      13723 AAAGTTCCCA

                                  
      13733 TCAAGTTTTCAAAATATTCAAT
          1 TCAAGTTTTCAAAATATTCAAT

                          * *      
      13755 TCAAGCTTTTCAAAGTTTTCAAT
          1 TCAAG-TTTTCAAAATATTCAAT

             
      13778 T
          1 T

      13779 TAGGGAAAGT


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

Matches are distributed among these distances:
  22    5  0.24
  23   16  0.76

ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43


Consensus pattern (22 bp):   
TCAAGTTTTCAAAATATTCAAT

Found at i:13868 original size:61 final size:62

Alignment explanation


    Indices: 13700--13868  Score: 272
    Period size: 61  Copynumber: 2.8  Consensus size: 62

      13690 AAAGAAGTTT

                                                           *   *          
      13700 TTTTC-AAGGTTTTCAATTTAGGGAAAGTTCCCATCAAGTTTTCAAAATATTCAATTCAAGC
          1 TTTTCAAAGGTTTTCAATTTAGGGAAAGTTCCCATCAAGTTTTCAAAGTATACAATTCAAGC

                                            *                             
      13761 TTTTCAAA-GTTTTCAATTTAGGGAAAGTTCCTATCAAGTTTTCAAAGTATACAATTCAAG-
          1 TTTTCAAAGGTTTTCAATTTAGGGAAAGTTCCCATCAAGTTTTCAAAGTATACAATTCAAGC

                              *     *                       
      13821 TTTTCAAAGGTTTTCAATCTAGGGTAAGTTCCCATCAAGTTTTCAAAG
          1 TTTTCAAAGGTTTTCAATTTAGGGAAAGTTCCCATCAAGTTTTCAAAG

      13869 CATTCCTATA


Statistics
Matches: 100,  Mismatches: 6, Indels: 4
        0.91            0.05        0.04

Matches are distributed among these distances:
  60    8  0.08
  61   90  0.90
  62    2  0.02

ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38


Consensus pattern (62 bp):   
TTTTCAAAGGTTTTCAATTTAGGGAAAGTTCCCATCAAGTTTTCAAAGTATACAATTCAAGC

Found at i:16601 original size:2 final size:2

Alignment explanation


    Indices: 16594--16618  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      16584 AATTAGTATC

                                                 
      16594 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      16619 ATTGATATAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Done.