Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014806.1 Corchorus olitorius cultivar O-4 contig14839, 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: 17718
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:126 original size:2 final size:2

Alignment explanation


    Indices: 119--150  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        109 TTAATTAGTG

                                                           
        119 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

        151 AGTATAATTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:846 original size:29 final size:30

Alignment explanation


    Indices: 788--848  Score: 88
    Period size: 29  Copynumber: 2.1  Consensus size: 30

        778 GTTCTAATTA

                   *                 *    
        788 ATGTATACATATAAATTATTCAATTTTATT
          1 ATGTATAAATATAAATTATTCAATTATATT

                                *         
        818 ATGTATAAATAT-AATTATTTAATTATATT
          1 ATGTATAAATATAAATTATTCAATTATATT

              
        847 AT
          1 AT

        849 ATTATTTATA


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29   17  0.61
  30   11  0.39

ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51


Consensus pattern (30 bp):   
ATGTATAAATATAAATTATTCAATTATATT

Found at i:3433 original size:16 final size:16

Alignment explanation


    Indices: 3390--3434  Score: 65
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       3380 TAATTTAGAG

                       *    
       3390 GGAATTGAATTGAGAA
          1 GGAATTGAATTAAGAA

                            
       3406 GGAATTGAATTAAGAA
          1 GGAATTGAATTAAGAA

                          
       3422 -GAATTTGAATTAA
          1 GGAA-TTGAATTAA

       3435 CAATTACATA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  15    3  0.11
  16   24  0.89

ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29


Consensus pattern (16 bp):   
GGAATTGAATTAAGAA

Found at i:6291 original size:27 final size:24

Alignment explanation


    Indices: 6238--6297  Score: 84
    Period size: 27  Copynumber: 2.4  Consensus size: 24

       6228 TTGGTGAAAA

                                 *  
       6238 TTCTTAATTGATTTCAAAATATAT
          1 TTCTTAATTGATTTCAAAATACAT

                                       
       6262 TTCTTAATTGATTTCAAAAAAATACAT
          1 TTCTTAATTGATTTC---AAAATACAT

                     
       6289 TTCTTAATT
          1 TTCTTAATT

       6298 TGTTTGAGGA


Statistics
Matches: 32,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  24   15  0.47
  27   17  0.53

ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48


Consensus pattern (24 bp):   
TTCTTAATTGATTTCAAAATACAT

Found at i:6601 original size:3 final size:3

Alignment explanation


    Indices: 6585--6665  Score: 59
    Period size: 3  Copynumber: 28.3  Consensus size: 3

       6575 CTAATATATC

                                                          *   *        *
       6585 TAA T-A TAA -AA TAA TAA TAA TAA TAA TAA TAA TAT TAG TATA TAG
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA

                                                                   
       6629 TATA TAA -ATA TAA -AA TAA TAA -AA TAA -AA TAA -AA TAA T
          1 TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T

       6666 CGATTGAAAT


Statistics
Matches: 63,  Mismatches: 5, Indels: 20
        0.72            0.06        0.23

Matches are distributed among these distances:
   2   13  0.21
   3   45  0.71
   4    5  0.08

ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:17389 original size:27 final size:24

Alignment explanation


    Indices: 17349--17413  Score: 94
    Period size: 27  Copynumber: 2.6  Consensus size: 24

      17339 TCAAAAGATA

                                *   
      17349 AGCCTCTCTCTCCCTCTGAATCTG
          1 AGCCTCTCTCTCCCTCTGAAACTG

                                       
      17373 AGCAACCTCTCTCTCCCTCTGAAACTG
          1 AG---CCTCTCTCTCCCTCTGAAACTG

                          
      17400 AGCCTCTCTCTCCC
          1 AGCCTCTCTCTCCC

      17414 AGCAGACGGA


Statistics
Matches: 37,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
  24   14  0.38
  27   23  0.62

ACGTcount: A:0.15, C:0.45, G:0.11, T:0.29


Consensus pattern (24 bp):   
AGCCTCTCTCTCCCTCTGAAACTG

Found at i:17566 original size:18 final size:18

Alignment explanation


    Indices: 17528--17566  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      17518 ATTAATTGTA

                            * 
      17528 AATAAACTAATTAACACT
          1 AATAAACTAATTAACAAT

                          *   
      17546 AATAAACTAATTAATAAT
          1 AATAAACTAATTAACAAT

               
      17564 AAT
          1 AAT

      17567 TAAATTTCAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31


Consensus pattern (18 bp):   
AATAAACTAATTAACAAT
Done.