Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013127.1 Corchorus olitorius cultivar O-4 contig13160, 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: 10352
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:246 original size:33 final size:33

Alignment explanation


    Indices: 199--266  Score: 127
    Period size: 33  Copynumber: 2.1  Consensus size: 33

        189 ATAGGAATAT

                *                            
        199 GTTCGTAGCCATACGAATAAGCGATCGTAGCTA
          1 GTTCATAGCCATACGAATAAGCGATCGTAGCTA

                                             
        232 GTTCATAGCCATACGAATAAGCGATCGTAGCTA
          1 GTTCATAGCCATACGAATAAGCGATCGTAGCTA

              
        265 GT
          1 GT

        267 CCGTAGCAAT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25


Consensus pattern (33 bp):   
GTTCATAGCCATACGAATAAGCGATCGTAGCTA

Found at i:1783 original size:23 final size:24

Alignment explanation


    Indices: 1752--1797  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       1742 GTACCTTTAT

                                     
       1752 TTAACAAATCAATTTAAG-AATTAC
          1 TTAACAAATCAA-TTAAGTAATTAC

                     *             
       1776 TTAA-AAATTAATTAAGTAATTA
          1 TTAACAAATCAATTAAGTAATTA

       1798 GGGGAAAAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  22    5  0.25
  23   11  0.55
  24    4  0.20

ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37


Consensus pattern (24 bp):   
TTAACAAATCAATTAAGTAATTAC

Found at i:5510 original size:15 final size:15

Alignment explanation


    Indices: 5480--5521  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5470 TTACTTTGTT

                            
       5480 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       5496 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
       5511 TTGTTTTCTGT
          1 TTGTTTTCTGT

       5522 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

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

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:5892 original size:31 final size:29

Alignment explanation


    Indices: 5854--5912  Score: 82
    Period size: 31  Copynumber: 2.0  Consensus size: 29

       5844 GCGTCGTTTT

                      **                   
       5854 GAAAAAAAAATTTCTTTTGTGTTTTTGCGTC
          1 GAAAAAAAAAAATCTTTT-TG-TTTTGCGTC

                                        
       5885 GAAAAAAAAAAATCTTTTTGTTTTGCGT
          1 GAAAAAAAAAAATCTTTTTGTTTTGCGT

       5913 TTTTAATTTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  29    8  0.31
  30    2  0.08
  31   16  0.62

ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42


Consensus pattern (29 bp):   
GAAAAAAAAAAATCTTTTTGTTTTGCGTC

Found at i:5989 original size:23 final size:21

Alignment explanation


    Indices: 5961--6035  Score: 60
    Period size: 23  Copynumber: 3.3  Consensus size: 21

       5951 GAGTTTTGTG

                                   
       5961 TTTTGCATCGAAAAAAAAAATAT
          1 TTTTGCATC-AAAAAAAAAAT-T

                  *             *  
       5984 TTTTGCGTCATAAAAAAAATTTT
          1 TTTTGCATCA-AAAAAAAA-ATT

                   *             * 
       6007 TGTTTGCGTCATAAAAAAAAAGT
          1 T-TTTGCATCA-AAAAAAAAATT

                  
       6030 TTTTGC
          1 TTTTGC

       6036 GTTTTTCTAA


Statistics
Matches: 45,  Mismatches: 4, Indels: 7
        0.80            0.07        0.12

Matches are distributed among these distances:
  22    6  0.13
  23   20  0.44
  24   19  0.42

ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37


Consensus pattern (21 bp):   
TTTTGCATCAAAAAAAAAATT

Found at i:6012 original size:24 final size:23

Alignment explanation


    Indices: 5972--6037  Score: 89
    Period size: 24  Copynumber: 2.9  Consensus size: 23

       5962 TTTGCATCGA

                                   
       5972 AAAAAAAAATATTTTTGCGTCAT
          1 AAAAAAAAATATTTTTGCGTCAT

                    * *             
       5995 AAAAAAAATTTTTGTTTGCGTCAT
          1 AAAAAAAAATATT-TTTGCGTCAT

                      *         
       6019 AAAAAAAAA-GTTTTTGCGT
          1 AAAAAAAAATATTTTTGCGT

       6038 TTTTCTAAAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  22    7  0.18
  23   13  0.34
  24   18  0.47

ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36


Consensus pattern (23 bp):   
AAAAAAAAATATTTTTGCGTCAT

Found at i:6115 original size:24 final size:24

Alignment explanation


    Indices: 6070--6119  Score: 75
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       6060 GAGAGTTTTT

                                     
       6070 TGCGTCATTTAAAAAAAAAAATTTC
          1 TGCGTCA-TTAAAAAAAAAAATTTC

                                     
       6095 TGCGTCA-TAAATAAAAAAAATTTC
          1 TGCGTCATTAAA-AAAAAAAATTTC

             
       6119 T
          1 T

       6120 TGTTCTTGCG


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  23    4  0.17
  24   13  0.54
  25    7  0.29

ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32


Consensus pattern (24 bp):   
TGCGTCATTAAAAAAAAAAATTTC
Done.