Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009048.1 Corchorus olitorius cultivar O-4 contig09076, 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, 744

Length: 1241
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44


Found at i:85 original size:15 final size:15

Alignment explanation


    Indices: 65--95  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

         55 AATTACAATG

                           
         65 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

                           
         80 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

             
         95 A
          1 A

         96 ATGTTAACTA


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

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45


Consensus pattern (15 bp):   
ATCATAGTTAATGTT

Found at i:488 original size:18 final size:18

Alignment explanation


    Indices: 456--500  Score: 72
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        446 AGTGTTTTAA

                      *        
        456 ATTTCTTAAATTTCTTTTC
          1 ATTTC-TAAACTTCTTTTC

                              
        475 ATTTCTAAACTTCTTTTC
          1 ATTTCTAAACTTCTTTTC

                    
        493 ATTTCTAA
          1 ATTTCTAA

        501 GTGTTTTAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  18   20  0.80
  19    5  0.20

ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58


Consensus pattern (18 bp):   
ATTTCTAAACTTCTTTTC

Found at i:510 original size:27 final size:27

Alignment explanation


    Indices: 437--516  Score: 74
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        427 CTTATCCGTC

                                       
        437 TCATTTCTAAGTGTTTTAAATTTC-TT
          1 TCATTTCTAAGTGTTTTAAATTTCTTT

            **       **  *        *      
        463 AAATTTCT-TTTCATTTCTAAACTTCTTT
          1 TCATTTCTAAGT-GTTT-TAAATTTCTTT

                                      
        491 TCATTTCTAAGTGTTTTAAATTTCTT
          1 TCATTTCTAAGTGTTTTAAATTTCTT

        517 AAATTTATTT


Statistics
Matches: 38,  Mismatches: 12, Indels: 7
        0.67            0.21        0.12

Matches are distributed among these distances:
  25    1  0.03
  26    9  0.24
  27   16  0.42
  28   11  0.29
  29    1  0.03

ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57


Consensus pattern (27 bp):   
TCATTTCTAAGTGTTTTAAATTTCTTT

Found at i:1196 original size:59 final size:59

Alignment explanation


    Indices: 1130--1241  Score: 224
    Period size: 59  Copynumber: 1.9  Consensus size: 59

       1120 ATACAATTTA

                                                                       
       1130 ATAGAATTAATTATAGTGATTTCCCCGTGTTGTGTCAAGTCTTTTTCTTTTGAATTAAT
          1 ATAGAATTAATTATAGTGATTTCCCCGTGTTGTGTCAAGTCTTTTTCTTTTGAATTAAT

                                                                 
       1189 ATAGAATTAATTATAGTGATTTCCCCGTGTTGTGTCAAGTCTTTTTCTTTTGA
          1 ATAGAATTAATTATAGTGATTTCCCCGTGTTGTGTCAAGTCTTTTTCTTTTGA


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  59   53  1.00

ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47


Consensus pattern (59 bp):   
ATAGAATTAATTATAGTGATTTCCCCGTGTTGTGTCAAGTCTTTTTCTTTTGAATTAAT
Done.