Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010659.1 Corchorus olitorius cultivar O-4 contig10691, 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: 13571
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:727 original size:2 final size:2

Alignment explanation


    Indices: 722--756  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

        712 AGATGCAAGG

                         * *                                    
        722 TA TA TA TA TG CA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        757 GTAATTAATG


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:3832 original size:74 final size:74

Alignment explanation


    Indices: 3711--3858  Score: 269
    Period size: 74  Copynumber: 2.0  Consensus size: 74

       3701 CAAAGGGAAA

                                                                             
       3711 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAAGAAAATCAACGTTTGATAAGGCTATTGT
          1 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAAGAAAATCAACGTTTGATAAGGCTATTGT

            *        
       3776 GGCATTCTT
         66 AGCATTCTT

                                                *                     *      
       3785 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAGGAAAATCAACGTTTGATAAGGTTATTGT
          1 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAAGAAAATCAACGTTTGATAAGGCTATTGT

                     
       3850 AGCATTCTT
         66 AGCATTCTT

       3859 CAATAGGTAA


Statistics
Matches: 71,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  74   71  1.00

ACGTcount: A:0.32, C:0.11, G:0.27, T:0.29


Consensus pattern (74 bp):   
GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAAGAAAATCAACGTTTGATAAGGCTATTGT
AGCATTCTT

Found at i:6113 original size:3 final size:3

Alignment explanation


    Indices: 6105--6150  Score: 74
    Period size: 3  Copynumber: 15.3  Consensus size: 3

       6095 GATCACAGTA

                                                 *               *       
       6105 ATG ATG ATG ATG ATG ATG ATG ATG ATG AAG ATG ATG ATG AAG ATG A
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A

       6151 GCTATTATGT


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28


Consensus pattern (3 bp):   
ATG

Found at i:13134 original size:30 final size:31

Alignment explanation


    Indices: 13100--13159  Score: 77
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      13090 AAGGGAATGA

                            *      *       
      13100 GAATTAATTCT-AAAAGTACAATGATTTGGG
          1 GAATTAATTCTAAAAACTACAATAATTTGGG

                  *  *                    
      13130 GAATTATTTTTAAAAACTACAATAATTTGG
          1 GAATTAATTCTAAAAACTACAATAATTTGG

      13160 TAAATATTTC


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  30    9  0.36
  31   16  0.64

ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37


Consensus pattern (31 bp):   
GAATTAATTCTAAAAACTACAATAATTTGGG

Found at i:13168 original size:30 final size:31

Alignment explanation


    Indices: 13111--13168  Score: 73
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      13101 AATTAATTCT

                *      *          *        
      13111 AAAAGTACAATGATTTGGGGAATTATTTTTA
          1 AAAACTACAATAATTTGGGGAAATATTTTTA

                               *        
      13142 AAAACTACAATAATTT-GGTAAATATTT
          1 AAAACTACAATAATTTGGGGAAATATTT

      13169 CAAGTTTTAC


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  30    9  0.39
  31   14  0.61

ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38


Consensus pattern (31 bp):   
AAAACTACAATAATTTGGGGAAATATTTTTA
Done.