Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015421.1 Corchorus olitorius cultivar O-4 contig15454, 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: 4487
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--34  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

                                                              
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         35 ATGGTAATTC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:615 original size:217 final size:217

Alignment explanation


    Indices: 240--674  Score: 870
    Period size: 217  Copynumber: 2.0  Consensus size: 217

        230 GCCAGTCTGT

                                                                             
        240 TCCCTCTCTATAGGCTATAGCATTGAGAGATCTTCAGATTCCTGAGGCTGCTCATCAGATTCCTG
          1 TCCCTCTCTATAGGCTATAGCATTGAGAGATCTTCAGATTCCTGAGGCTGCTCATCAGATTCCTG

                                                                             
        305 CAGTAAAAGATCATATTCCCTAGTGGATGAATTTCAGCATTAGCCTCGTGGATAAGATGTAAAAC
         66 CAGTAAAAGATCATATTCCCTAGTGGATGAATTTCAGCATTAGCCTCGTGGATAAGATGTAAAAC

                                                                             
        370 AACTTGAGCATTAATAGAGATTTCCAGATTATCAATGCCCTTGCCAAGAGCAAGCTTCAATCCAT
        131 AACTTGAGCATTAATAGAGATTTCCAGATTATCAATGCCCTTGCCAAGAGCAAGCTTCAATCCAT

                                  
        435 CCCTCAATCCCCATAGCTCAGC
        196 CCCTCAATCCCCATAGCTCAGC

                                                                             
        457 TCCCTCTCTATAGGCTATAGCATTGAGAGATCTTCAGATTCCTGAGGCTGCTCATCAGATTCCTG
          1 TCCCTCTCTATAGGCTATAGCATTGAGAGATCTTCAGATTCCTGAGGCTGCTCATCAGATTCCTG

                                                                             
        522 CAGTAAAAGATCATATTCCCTAGTGGATGAATTTCAGCATTAGCCTCGTGGATAAGATGTAAAAC
         66 CAGTAAAAGATCATATTCCCTAGTGGATGAATTTCAGCATTAGCCTCGTGGATAAGATGTAAAAC

                                                                             
        587 AACTTGAGCATTAATAGAGATTTCCAGATTATCAATGCCCTTGCCAAGAGCAAGCTTCAATCCAT
        131 AACTTGAGCATTAATAGAGATTTCCAGATTATCAATGCCCTTGCCAAGAGCAAGCTTCAATCCAT

                                  
        652 CCCTCAATCCCCATAGCTCAGC
        196 CCCTCAATCCCCATAGCTCAGC

             
        674 T
          1 T

        675 GGGAGTCTAT


Statistics
Matches: 218,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 217  218  1.00

ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28


Consensus pattern (217 bp):   
TCCCTCTCTATAGGCTATAGCATTGAGAGATCTTCAGATTCCTGAGGCTGCTCATCAGATTCCTG
CAGTAAAAGATCATATTCCCTAGTGGATGAATTTCAGCATTAGCCTCGTGGATAAGATGTAAAAC
AACTTGAGCATTAATAGAGATTTCCAGATTATCAATGCCCTTGCCAAGAGCAAGCTTCAATCCAT
CCCTCAATCCCCATAGCTCAGC

Found at i:2426 original size:3 final size:3

Alignment explanation


    Indices: 2418--2445  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       2408 TTCAGGTATT

                                                 
       2418 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG C

       2446 GACAATATAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00


Consensus pattern (3 bp):   
CAG

Found at i:3441 original size:45 final size:45

Alignment explanation


    Indices: 3386--3482  Score: 142
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       3376 AGTGCATCAC

                                      *                  
       3386 CTAA-ATTCTACTCCTCCATCTCTAGGTAATTCATCAAAATAAAA
          1 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA

               *         *           *                  *
       3430 CTAGTATTCTACTTCTCCATCTCTATATAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA

                    
       3475 CTAATATT
          1 CTAATATT

       3483 AATTGTTGTT


Statistics
Matches: 46,  Mismatches: 6, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  44    3  0.07
  45   43  0.93

ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36


Consensus pattern (45 bp):   
CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA

Found at i:4125 original size:7 final size:7

Alignment explanation


    Indices: 4112--4145  Score: 52
    Period size: 7  Copynumber: 5.0  Consensus size: 7

       4102 GAATTAAAAG

                   
       4112 TTATTTT
          1 TTATTTT

            *      
       4119 GTA-TTT
          1 TTATTTT

                   
       4125 TTATTTT
          1 TTATTTT

                   
       4132 TTATTTT
          1 TTATTTT

                   
       4139 TTATTTT
          1 TTATTTT

       4146 ATGTTAGTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
   6    5  0.21
   7   19  0.79

ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82


Consensus pattern (7 bp):   
TTATTTT

Done.