Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022592.1 Corchorus olitorius cultivar O-4 contig22625, 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: 7964
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:3574 original size:20 final size:19

Alignment explanation


    Indices: 3543--3589  Score: 58
    Period size: 20  Copynumber: 2.4  Consensus size: 19

       3533 ACCAACCAAA

                 *      *      
       3543 AAACACACCCACTAAAGCC
          1 AAACAAACCCACCAAAGCC

                           *    
       3562 AAGACAAACCCACCACAGCC
          1 AA-ACAAACCCACCAAAGCC

                    
       3582 AAACAAAC
          1 AAACAAAC

       3590 GGAAATAAAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  19    8  0.33
  20   16  0.67

ACGTcount: A:0.51, C:0.40, G:0.06, T:0.02


Consensus pattern (19 bp):   
AAACAAACCCACCAAAGCC

Found at i:5091 original size:76 final size:76

Alignment explanation


    Indices: 4995--5140  Score: 256
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       4985 AAACCTCTAT

                      *                                              *       
       4995 AAATTAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGGTTACTAATTTATTGAGTATT
          1 AAATTAATAAGGTTGGGACCATGAAAAATTATTAATTTAGAGAGGTTACTAATTTATCGAGTATT

                       
       5060 AATTTTTATGC
         66 AATTTTTATGC

                  *                                         *                
       5071 AAATTATTAAGGTTGGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
          1 AAATTAATAAGGTTGGGACCATGAAAAATTATTAATTTAGAGAGGTTACTAATTTATCGAGTATT

                 
       5136 AATTT
         66 AATTT

       5141 ATGGAGGTTA


Statistics
Matches: 66,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  76   66  1.00

ACGTcount: A:0.38, C:0.05, G:0.16, T:0.40


Consensus pattern (76 bp):   
AAATTAATAAGGTTGGGACCATGAAAAATTATTAATTTAGAGAGGTTACTAATTTATCGAGTATT
AATTTTTATGC

Found at i:5121 original size:17 final size:16

Alignment explanation


    Indices: 5099--5151  Score: 56
    Period size: 17  Copynumber: 3.2  Consensus size: 16

       5089 CCATGAAAAA

                             
       5099 TTATTAATTTAGAGAGG
          1 TTATTAATTTAG-GAGG

                        *    
       5116 TTATTAATTTATCGA-G
          1 TTATTAATTTA-GGAGG

                             
       5132 -TATTAATTTATGGAGG
          1 TTATTAATTTA-GGAGG

                
       5148 TTAT
          1 TTAT

       5152 ACTGTATTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  15   13  0.42
  16    2  0.06
  17   16  0.52

ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47


Consensus pattern (16 bp):   
TTATTAATTTAGGAGG

Found at i:5372 original size:13 final size:13

Alignment explanation


    Indices: 5354--5379  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       5344 TTTAATGTTC

                         
       5354 TAAATATTATTTA
          1 TAAATATTATTTA

                         
       5367 TAAATATTATTTA
          1 TAAATATTATTTA

       5380 GAATTCTAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (13 bp):   
TAAATATTATTTA
Done.