Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015581.1 Corchorus olitorius cultivar O-4 contig15614, 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: 9990
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34


Found at i:2420 original size:29 final size:29

Alignment explanation


    Indices: 2378--2444  Score: 134
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       2368 ATCGAAGTAA

                                         
       2378 AACAAAAACGAGGAATAGGAGATAGCAAT
          1 AACAAAAACGAGGAATAGGAGATAGCAAT

                                         
       2407 AACAAAAACGAGGAATAGGAGATAGCAAT
          1 AACAAAAACGAGGAATAGGAGATAGCAAT

                     
       2436 AACAAAAAC
          1 AACAAAAAC

       2445 AACTGCCAGT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   38  1.00

ACGTcount: A:0.58, C:0.12, G:0.21, T:0.09


Consensus pattern (29 bp):   
AACAAAAACGAGGAATAGGAGATAGCAAT

Found at i:5220 original size:25 final size:25

Alignment explanation


    Indices: 5192--5246  Score: 69
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       5182 TCATGCACCC

                        *        *    
       5192 AAAACAAT-TTATTAAAACCATTAAT
          1 AAAACAATATTAATAAAA-CAGTAAT

                                     
       5217 AAAAC-ATATTAATAAAACAGTAAT
          1 AAAACAATATTAATAAAACAGTAAT

                  
       5241 AAAACA
          1 AAAACA

       5247 GTTCCTCAAC


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  24   13  0.50
  25   13  0.50

ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25


Consensus pattern (25 bp):   
AAAACAATATTAATAAAACAGTAAT

Found at i:5227 original size:13 final size:13

Alignment explanation


    Indices: 5211--5235  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5201 TATTAAAACC

                         
       5211 ATTAATAAAACAT
          1 ATTAATAAAACAT

                        
       5224 ATTAATAAAACA
          1 ATTAATAAAACA

       5236 GTAATAAAAC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28


Consensus pattern (13 bp):   
ATTAATAAAACAT

Found at i:6836 original size:18 final size:18

Alignment explanation


    Indices: 6813--6847  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       6803 AAGCGGCCCT

                              
       6813 TTTCTTCTTTTTTTTTTC
          1 TTTCTTCTTTTTTTTTTC

                             
       6831 TTTCTTCTTTTTTTTTT
          1 TTTCTTCTTTTTTTTTT

       6848 TTTTTAAGAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (18 bp):   
TTTCTTCTTTTTTTTTTC

Found at i:7682 original size:17 final size:16

Alignment explanation


    Indices: 7636--7678  Score: 59
    Period size: 17  Copynumber: 2.6  Consensus size: 16

       7626 CCAGATTACT

                             
       7636 AGTGATCTAAGATCACC
          1 AGTGATC-AAGATCACC

                             
       7653 AGTGATGCAAGATCACC
          1 AGTGAT-CAAGATCACC

            *        
       7670 GGTGATCAA
          1 AGTGATCAA

       7679 AGATTACATG


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  16    3  0.12
  17   20  0.83
  18    1  0.04

ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21


Consensus pattern (16 bp):   
AGTGATCAAGATCACC
Done.