Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018484.1 Corchorus olitorius cultivar O-4 contig18517, 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: 5805
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35


Found at i:744 original size:2 final size:2

Alignment explanation


    Indices: 737--772  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

        727 CCACACTAGA

                                                                 
        737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        773 TCATGCATAA


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

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1420 original size:13 final size:13

Alignment explanation


    Indices: 1402--1426  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1392 TATTTAATTA

                         
       1402 TTTTGTATTTTTG
          1 TTTTGTATTTTTG

                        
       1415 TTTTGTATTTTT
          1 TTTTGTATTTTT

       1427 TCTTTAAGTT


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:0.08, C:0.00, G:0.12, T:0.80


Consensus pattern (13 bp):   
TTTTGTATTTTTG

Found at i:1584 original size:31 final size:30

Alignment explanation


    Indices: 1546--1650  Score: 97
    Period size: 31  Copynumber: 3.5  Consensus size: 30

       1536 ACGGAGTGGA

                               *           
       1546 CTTATTTGAGATTTTTCGCGAAGTTGGGGCC
          1 CTTATTTGAGATTTTT-GCAAAGTTGGGGCC

                     **             *     
       1577 CTTATTTGACCTTTTT-CAAAGTTCGGGCC
          1 CTTATTTGAGATTTTTGCAAAGTTGGGGCC

                     *      *          *   *
       1606 CTTATTTGATATTTATGGCAAAGTTCGAGG-A
          1 CTTATTTGAGATTT-TTGCAAAGTT-GGGGCC

                          
       1637 CTTATTTGAGATTT
          1 CTTATTTGAGATTT

       1651 CAGCCGAAGT


Statistics
Matches: 60,  Mismatches: 11, Indels: 6
        0.78            0.14        0.08

Matches are distributed among these distances:
  29   23  0.38
  30    1  0.02
  31   34  0.57
  32    2  0.03

ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42


Consensus pattern (30 bp):   
CTTATTTGAGATTTTTGCAAAGTTGGGGCC

Found at i:5654 original size:80 final size:80

Alignment explanation


    Indices: 5542--5694  Score: 211
    Period size: 80  Copynumber: 1.9  Consensus size: 80

       5532 CACATCAAAT

                               *               *                             
       5542 CAATTTTAGTTCAAGTTTAGGGTTTTAGAAAATATTAAG-ATATCATTAG-AATAAGCTTTTAAA
          1 CAATTTTAGTTCAAGTTTAAGGTTTTAGAAAATATCAAGAATATCATTAGAAATAAGCTTTTAAA

                           
       5605 AATATGATTTAGGCA
         66 AATATGATTTAGGCA

                                        *                        *           
       5620 CAATTTTAGTTCAAGTATTTAAGGTTTTTGAAAATATCAAGATATATATCATTCGAAATAAGCTT
          1 CAATTTTAGTTCAAG--TTTAAGGTTTTAGAAAATATCAAG--A-ATATCATTAGAAATAAGCTT

                      
       5685 TTAAAAATAT
         61 TTAAAAATAT

       5695 TTTTTGAATT


Statistics
Matches: 64,  Mismatches: 4, Indels: 7
        0.85            0.05        0.09

Matches are distributed among these distances:
  78   15  0.23
  80   21  0.33
  84    9  0.14
  85   19  0.30

ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39


Consensus pattern (80 bp):   
CAATTTTAGTTCAAGTTTAAGGTTTTAGAAAATATCAAGAATATCATTAGAAATAAGCTTTTAAA
AATATGATTTAGGCA

Done.