Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009822.1 Corchorus olitorius cultivar O-4 contig09854, 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: 1760
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31


Found at i:349 original size:15 final size:15

Alignment explanation


    Indices: 316--358  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

        306 TACATACCAC

                      *    
        316 TAATAATAATTATTA
          1 TAATAATAATAATTA

                            
        331 TAATAATAATAAGTT-
          1 TAATAATAATAA-TTA

                   *     
        346 TAATAATTATAAT
          1 TAATAATAATAAT

        359 ATTAAGATGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    1  0.04
  15   22  0.88
  16    2  0.08

ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44


Consensus pattern (15 bp):   
TAATAATAATAATTA

Found at i:358 original size:9 final size:9

Alignment explanation


    Indices: 318--359  Score: 50
    Period size: 9  Copynumber: 4.7  Consensus size: 9

        308 CATACCACTA

                     
        318 ATAATAATT
          1 ATAATAATT

              *     *
        327 ATTATAATA
          1 ATAATAATT

                      
        336 ATAATAAGTT
          1 ATAATAA-TT

                     
        346 -TAATAATT
          1 ATAATAATT

                  
        354 ATAATA
          1 ATAATA

        360 TTAAGATGTT


Statistics
Matches: 27,  Mismatches: 4, Indels: 4
        0.77            0.11        0.11

Matches are distributed among these distances:
   8    2  0.07
   9   24  0.89
  10    1  0.04

ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43


Consensus pattern (9 bp):   
ATAATAATT

Found at i:370 original size:24 final size:24

Alignment explanation


    Indices: 322--372  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        312 CCACTAATAA

                *             *     
        322 TAATTATTATAATAATAATAAGTT
          1 TAATAATTATAATAATAAGAAGTT

                          *     *   
        346 TAATAATTATAATATTAAGATGTT
          1 TAATAATTATAATAATAAGAAGTT

               
        370 TAA
          1 TAA

        373 CGTAAAAAAG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45


Consensus pattern (24 bp):   
TAATAATTATAATAATAAGAAGTT
Done.