Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015079.1 Corchorus olitorius cultivar O-4 contig15112, 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: 8205
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37


Found at i:1769 original size:30 final size:28

Alignment explanation


    Indices: 1733--1806  Score: 107
    Period size: 30  Copynumber: 2.6  Consensus size: 28

       1723 CGAGGCCACA

                                         
       1733 CATCCTCCACTTTCCTTCCTTTTTTTTGG
          1 CATCCTCCACTTTCCTTCCTTTTTTTT-G

                                         
       1762 CCATCCTCCACTTTCCTT-CTTTTTTTTG
          1 -CATCCTCCACTTTCCTTCCTTTTTTTTG

                *             
       1790 CA-CATCCACTTTCCTTC
          1 CATCCTCCACTTTCCTTC

       1807 TTTAGTAAAT


Statistics
Matches: 42,  Mismatches: 1, Indels: 5
        0.88            0.02        0.10

Matches are distributed among these distances:
  26   13  0.31
  27    2  0.05
  28    1  0.02
  29    9  0.21
  30   17  0.40

ACGTcount: A:0.09, C:0.38, G:0.04, T:0.49


Consensus pattern (28 bp):   
CATCCTCCACTTTCCTTCCTTTTTTTTG

Found at i:1797 original size:26 final size:29

Alignment explanation


    Indices: 1733--1809  Score: 106
    Period size: 26  Copynumber: 2.7  Consensus size: 29

       1723 CGAGGCCACA

                *                         
       1733 CATCCTCCACTTTCCTTCCTTTTTTTTGGC
          1 CATCATCCACTTTCCTT-CTTTTTTTTGGC

                *                        
       1763 CATCCTCCACTTTCCTTCTTTTTTTT-G-
          1 CATCATCCACTTTCCTTCTTTTTTTTGGC

                                 
       1790 CA-CATCCACTTTCCTTCTTT
          1 CATCATCCACTTTCCTTCTTT

       1810 AGTAAATCCA


Statistics
Matches: 46,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  26   17  0.37
  27    2  0.04
  28    1  0.02
  29    9  0.20
  30   17  0.37

ACGTcount: A:0.09, C:0.36, G:0.04, T:0.51


Consensus pattern (29 bp):   
CATCATCCACTTTCCTTCTTTTTTTTGGC

Found at i:2985 original size:18 final size:16

Alignment explanation


    Indices: 2954--2987  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       2944 CCAAAAAATG

                            
       2954 GAAAAAAAAAAAGAAA
          1 GAAAAAAAAAAAGAAA

                              
       2970 GAAAAAAAGAAGAAGAAA
          1 GAAAAAAA-AA-AAGAAA

       2988 ATATTGGTGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    8  0.50
  17    2  0.12
  18    6  0.38

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (16 bp):   
GAAAAAAAAAAAGAAA

Found at i:4161 original size:93 final size:91

Alignment explanation


    Indices: 4025--4192  Score: 273
    Period size: 93  Copynumber: 1.8  Consensus size: 91

       4015 TTGTTTAAAT

                         *        *                      *      *            
       4025 TTTTATAGTTTTAGTCAACTAAGCTCTATTTTTATTTAATTAAATTTAATATTCTTATAACTATT
          1 TTTTATAGTTTTACTCAACTAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATT

                                      
       4090 TTATTTTTACCATTTTACGATTTTAC
         66 TTATTTTTACCATTTTACGATTTTAC

                                                                         *   
       4116 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
          1 TTTTATAGTTTTACTCAACT--AAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA

                        
       4181 TTTTATTTTTAC
         64 TTTTATTTTTAC

       4193 GATATTACTA


Statistics
Matches: 70,  Mismatches: 5, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  91   19  0.27
  93   51  0.73

ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54


Consensus pattern (91 bp):   
TTTTATAGTTTTACTCAACTAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATT
TTATTTTTACCATTTTACGATTTTAC

Found at i:4327 original size:28 final size:26

Alignment explanation


    Indices: 4265--4327  Score: 72
    Period size: 28  Copynumber: 2.3  Consensus size: 26

       4255 TAACATTGTT

                            *     *   
       4265 TAAATTTTACAGTTTTTTGCTAGAAA
          1 TAAATTTTACAGTTTTCTGCTAAAAA

                                        
       4291 TAAACTTTTACAGTTATTCTGCTAAAAA
          1 TAAA-TTTTACAGTT-TTCTGCTAAAAA

              *      
       4319 CTCAATTTT
          1 -TAAATTTT

       4328 TATTTAATTA


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
  26    4  0.13
  27   10  0.32
  28   14  0.45
  29    3  0.10

ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44


Consensus pattern (26 bp):   
TAAATTTTACAGTTTTCTGCTAAAAA

Found at i:8201 original size:22 final size:22

Alignment explanation


    Indices: 8133--8201  Score: 95
    Period size: 22  Copynumber: 3.1  Consensus size: 22

       8123 ATAACCTTCG

                                   
       8133 TATGAAACTTTTG-TAACCACAC
          1 TATGAAA-TTTTGATAACCACAC

            *                 * * 
       8155 AATGAAATTTTGATAACCTCTC
          1 TATGAAATTTTGATAACCACAC

                                  
       8177 TATGAAATTTTGATAACCACAC
          1 TATGAAATTTTGATAACCACAC

               
       8199 TAT
          1 TAT

       8202 AAAA


Statistics
Matches: 40,  Mismatches: 6, Indels: 2
        0.83            0.12        0.04

Matches are distributed among these distances:
  21    5  0.12
  22   35  0.88

ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCACAC
Done.