Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007955.1 Corchorus olitorius cultivar O-4 contig07982, 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, 680

Length: 1134
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31


Found at i:82 original size:9 final size:9

Alignment explanation


    Indices: 68--92  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

         58 AATTTCTTTC

                     
         68 TTATTTTAA
          1 TTATTTTAA

                     
         77 TTATTTTAA
          1 TTATTTTAA

                   
         86 TTATTTT
          1 TTATTTT

         93 TGGGTTCATG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (9 bp):   
TTATTTTAA

Found at i:313 original size:3 final size:3

Alignment explanation


    Indices: 305--341  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

        295 TTGCTTTCTC

                                                             
        305 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

        342 AAAATCGGAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:753 original size:17 final size:17

Alignment explanation


    Indices: 705--754  Score: 50
    Period size: 17  Copynumber: 3.1  Consensus size: 17

        695 TGCAAATTGA

                            *
        705 ACAAAAAACCAACAAGG
          1 ACAAAAAACCAACAAGC

            *  *      *      
        722 GCAGAAAA--TACAAGC
          1 ACAAAAAACCAACAAGC

                             
        737 ACAAAAAACCAACAAGC
          1 ACAAAAAACCAACAAGC

             
        754 A
          1 A

        755 TTGCATTGGA


Statistics
Matches: 24,  Mismatches: 7, Indels: 4
        0.69            0.20        0.11

Matches are distributed among these distances:
  15   11  0.46
  17   13  0.54

ACGTcount: A:0.62, C:0.24, G:0.12, T:0.02


Consensus pattern (17 bp):   
ACAAAAAACCAACAAGC
Done.