Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017430.1 Corchorus olitorius cultivar O-4 contig17463, 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: 6074
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Found at i:1311 original size:65 final size:59

Alignment explanation


    Indices: 1188--1300  Score: 172
    Period size: 59  Copynumber: 1.9  Consensus size: 59

       1178 AATTAAAAGA

                              *     *                                  
       1188 CATTAATACTAATTGATTTTAATTTGATCAATATTCAAATCAATCAATCAATTTAATAT
          1 CATTAATACTAATTGATTCTAATTGGATCAATATTCAAATCAATCAATCAATTTAATAT

                 *                                   *            
       1247 CATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAACCAATCAATCAAT
          1 CATTAATACTAATTGATTCTAATTGGATC-A-ATATTCAAATCAATCAATCAAT

       1301 CAATTTAATA


Statistics
Matches: 48,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  59   26  0.54
  60    1  0.02
  61   21  0.44

ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38


Consensus pattern (59 bp):   
CATTAATACTAATTGATTCTAATTGGATCAATATTCAAATCAATCAATCAATTTAATAT

Found at i:2347 original size:12 final size:13

Alignment explanation


    Indices: 2321--2377  Score: 50
    Period size: 12  Copynumber: 4.7  Consensus size: 13

       2311 TTATGCACCC

                     *   
       2321 AAAACATTTGT-T
          1 AAAACATTTATAT

                         
       2333 AAAACATTT-TAT
          1 AAAACATTTATAT

               *         
       2345 AAAGCATTTATAT
          1 AAAACATTTATAT

               *   *     
       2358 AAAGCA-GT-TAT
          1 AAAACATTTATAT

                     
       2369 AAAACATTT
          1 AAAACATTT

       2378 CCTCAACGGG


Statistics
Matches: 38,  Mismatches: 4, Indels: 6
        0.79            0.08        0.12

Matches are distributed among these distances:
  11    9  0.24
  12   20  0.53
  13    9  0.24

ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37


Consensus pattern (13 bp):   
AAAACATTTATAT

Found at i:2360 original size:13 final size:13

Alignment explanation


    Indices: 2332--2377  Score: 53
    Period size: 13  Copynumber: 3.8  Consensus size: 13

       2322 AAACATTTGT

                *        
       2332 TAAAACATTT-TA
          1 TAAAGCATTTATA

                         
       2344 TAAAGCATTTATA
          1 TAAAGCATTTATA

                   *     
       2357 TAAAGCAGTTATA
          1 TAAAGCATTTATA

                      
       2370 -AAA-CATTT
          1 TAAAGCATTT

       2378 CCTCAACGGG


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  11    4  0.13
  12   12  0.40
  13   14  0.47

ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37


Consensus pattern (13 bp):   
TAAAGCATTTATA

Found at i:2545 original size:13 final size:13

Alignment explanation


    Indices: 2517--2555  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       2507 CAAACACAAG

                           
       2517 AAAATCATTAAAATC
          1 AAAATCA-T-AAATC

                         
       2532 AAAATCATAAATC
          1 AAAATCATAAATC

               *       
       2545 AAAGTCATAAA
          1 AAAATCATAAA

       2556 CCAGAGTAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  13   15  0.65
  14    1  0.04
  15    7  0.30

ACGTcount: A:0.62, C:0.13, G:0.03, T:0.23


Consensus pattern (13 bp):   
AAAATCATAAATC

Found at i:3691 original size:42 final size:45

Alignment explanation


    Indices: 3605--3707  Score: 117
    Period size: 42  Copynumber: 2.3  Consensus size: 45

       3595 TTTTATTCCC

                                                          
       3605 TCTTCCTTTATT-TTAAAATTCGGGCCTTAGCCCATCATTTCTTCT
          1 TCTTCCTTT-TTCTTAAAATTCGGGCCTTAGCCCATCATTTCTTCT

                             *                  *         
       3650 T-TTCCTTTTTCTTAAAGTT-GGGCC-TAGCCCAT-TTTTCCTTCT
          1 TCTTCCTTTTTCTTAAAATTCGGGCCTTAGCCCATCATTT-CTTCT

                            
       3692 TCTTCTTCTTTTTCTT
          1 TCTTC--CTTTTTCTT

       3708 TTCTTTTTTT


Statistics
Matches: 51,  Mismatches: 2, Indels: 10
        0.81            0.03        0.16

Matches are distributed among these distances:
  41    3  0.06
  42   14  0.27
  43   10  0.20
  44   14  0.27
  45   10  0.20

ACGTcount: A:0.13, C:0.26, G:0.09, T:0.52


Consensus pattern (45 bp):   
TCTTCCTTTTTCTTAAAATTCGGGCCTTAGCCCATCATTTCTTCT
Done.