Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016090.1 Corchorus olitorius cultivar O-4 contig16123, 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: 5221
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37


Found at i:1176 original size:36 final size:36

Alignment explanation


    Indices: 1129--1198  Score: 106
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1119 TTCAATAACC

                                 *               
       1129 TTACATCTTTTG-AGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTA-ATTTTGATTATCATATTTCTTA

                  *                           
       1165 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

       1199 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  36   30  0.97
  37    1  0.03

ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:2745 original size:21 final size:20

Alignment explanation


    Indices: 2721--2784  Score: 53
    Period size: 17  Copynumber: 3.2  Consensus size: 20

       2711 TATGAATTTA

                                 
       2721 ATTAATGTAAGTATTTTAGTT
          1 ATTAAT-TAAGTATTTTAGTT

                          ** *  
       2742 ATT-A-T-AGTATTACATTT
          1 ATTAATTAAGTATTTTAGTT

                                  
       2759 AATTAATATAAGTATTTTAGTT
          1 -ATTAAT-TAAGTATTTTAGTT

                
       2781 ATTA
          1 ATTA

       2785 GATATATTAC


Statistics
Matches: 32,  Mismatches: 6, Indels: 10
        0.67            0.12        0.21

Matches are distributed among these distances:
  17    9  0.28
  18    4  0.12
  19    1  0.03
  20    1  0.03
  21    8  0.25
  22    9  0.28

ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52


Consensus pattern (20 bp):   
ATTAATTAAGTATTTTAGTT

Found at i:4856 original size:15 final size:15

Alignment explanation


    Indices: 4836--4869  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       4826 TATCTATATC

                           
       4836 TATATCCATATACTA
          1 TATATCCATATACTA

                           
       4851 TATATCCATATACTA
          1 TATATCCATATACTA

                
       4866 TATA
          1 TATA

       4870 AGTCTAAACT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41


Consensus pattern (15 bp):   
TATATCCATATACTA

Found at i:5141 original size:39 final size:40

Alignment explanation


    Indices: 5085--5165  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       5075 TTTAATTCCT

                                                    
       5085 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

                     *          *         *         
       5125 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

              
       5164 AT
          1 AT

       5166 TTTTAGGTAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

Found at i:5196 original size:25 final size:24

Alignment explanation


    Indices: 5156--5202  Score: 76
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       5146 AATACTTACA

                       *            
       5156 TTAATTAAATTTTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
       5180 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

       5203 GTGCAAACGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  24    6  0.29
  25   15  0.71

ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT
Done.