Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000929.1 Corchorus olitorius cultivar O-4 contig00929, 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: 4013
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36


Found at i:486 original size:14 final size:14

Alignment explanation


    Indices: 467--500  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

        457 ACAGCTCTAC

                      *   
        467 CTGGAACCTAGGAT
          1 CTGGAACCTAAGAT

                          
        481 CTGGAACCTAAGAT
          1 CTGGAACCTAAGAT

            *     
        495 ATGGAA
          1 CTGGAA

        501 AGTTAATGAC


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

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21


Consensus pattern (14 bp):   
CTGGAACCTAAGAT

Found at i:2220 original size:5 final size:5

Alignment explanation


    Indices: 2210--2280  Score: 124
    Period size: 5  Copynumber: 14.2  Consensus size: 5

       2200 AGAAATAAGA

                                    *     *                            
       2210 AATAT AATAT AATAT AATAT TATAT TATAT AATAT AATAT AATAT AATAT
          1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT

                                     
       2260 AATAT AATAT AATAT AATAT A
          1 AATAT AATAT AATAT AATAT A

       2281 CATACATAGT


Statistics
Matches: 64,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   5   64  1.00

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (5 bp):   
AATAT

Found at i:3617 original size:13 final size:13

Alignment explanation


    Indices: 3599--3623  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3589 TTCAATGTTC

                         
       3599 TAAATATTATTTA
          1 TAAATATTATTTA

                        
       3612 TAAATATTATTT
          1 TAAATATTATTT

       3624 GGAATTCCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA

Found at i:3649 original size:2 final size:2

Alignment explanation


    Indices: 3634--3665  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       3624 GGAATTCCAA

                                                              
       3634 AT AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3666 TAGTTTTCTC


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   26  0.93

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.