Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001984.1 Corchorus olitorius cultivar O-4 contig01984, 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: 2153
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35


Found at i:32 original size:16 final size:16

Alignment explanation


    Indices: 11--44  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

          1 AAAAATCTGA

                   *        
         11 AACCCGATAAAACCCG
          1 AACCCGAAAAAACCCG

                            
         27 AACCCGAAAAAACCCG
          1 AACCCGAAAAAACCCG

              
         43 AA
          1 AA

         45 TTCAATACTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.50, C:0.35, G:0.12, T:0.03


Consensus pattern (16 bp):   
AACCCGAAAAAACCCG

Found at i:311 original size:31 final size:32

Alignment explanation


    Indices: 220--337  Score: 132
    Period size: 32  Copynumber: 3.7  Consensus size: 32

        210 GCCAAAACCC

                    *      *    *        *  
        220 AACCCGAATCTGAATTAACCTGACCCAAAATT
          1 AACCCGAACCTGAATCAACCCGACCCAAATTT

            *        *          *           
        252 GACCCGAACTTGAATCAACCTGACCCAAATTT
          1 AACCCGAACCTGAATCAACCCGACCCAAATTT

                      *                     
        284 AACCCGAACCCGAATCAACCCGA-CCAAATTT
          1 AACCCGAACCTGAATCAACCCGACCCAAATTT

                         *          
        315 AACCC-AACCTGACTCAAACCCGA
          1 AACCCGAACCTGAATC-AACCCGA

        338 ACCTGAAAAT


Statistics
Matches: 74,  Mismatches: 11, Indels: 3
        0.84            0.12        0.03

Matches are distributed among these distances:
  30    8  0.11
  31   20  0.27
  32   46  0.62

ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17


Consensus pattern (32 bp):   
AACCCGAACCTGAATCAACCCGACCCAAATTT

Found at i:1703 original size:26 final size:29

Alignment explanation


    Indices: 1647--1709  Score: 69
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       1637 CTATGAAAAA

                                      *    
       1647 TTATTTTATTATTAGGAAAGAATTTTTATTT
          1 TTATTTTATTATTAGGAAAGAA--TTCATTT

                                         
       1678 TTATTTT-TT-TTAGGAAAGAA-TCATTT
          1 TTATTTTATTATTAGGAAAGAATTCATTT

             *    
       1704 TCATTT
          1 TTATTT

       1710 CCTGGTTTAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
  26   10  0.33
  29   11  0.37
  30    2  0.07
  31    7  0.23

ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57


Consensus pattern (29 bp):   
TTATTTTATTATTAGGAAAGAATTCATTT

Found at i:1915 original size:15 final size:16

Alignment explanation


    Indices: 1887--1920  Score: 61
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       1877 CTACCTATCT

                            
       1887 AACAAATGTACAAACA
          1 AACAAATGTACAAACA

                            
       1903 AACAAAT-TACAAACA
          1 AACAAATGTACAAACA

               
       1918 AAC
          1 AAC

       1921 TCACAGTCCG


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   11  0.61
  16    7  0.39

ACGTcount: A:0.65, C:0.21, G:0.03, T:0.12


Consensus pattern (16 bp):   
AACAAATGTACAAACA

Found at i:2046 original size:2 final size:2

Alignment explanation


    Indices: 2035--2064  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2025 TAATAGTATC

                                                          
       2035 AT AT -T 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 AT AT AT A

       2065 AATAATTAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.