Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019226.1 Corchorus olitorius cultivar O-4 contig19259, 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: 10225
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:1964 original size:19 final size:19

Alignment explanation


    Indices: 1937--1975  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1927 ACAGGAAGAT

                *    *         
       1937 TGTGGTTATTAAAATTTAA
          1 TGTGATTATCAAAATTTAA

                               
       1956 TGTGATTATCAAAATTTAA
          1 TGTGATTATCAAAATTTAA

             
       1975 T
          1 T

       1976 AGGGGTTATC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46


Consensus pattern (19 bp):   
TGTGATTATCAAAATTTAA

Found at i:2014 original size:22 final size:22

Alignment explanation


    Indices: 1937--2028  Score: 104
    Period size: 22  Copynumber: 4.4  Consensus size: 22

       1927 ACAGGAAGAT

                     *            
       1937 TGTGGTTATTAAAATTT-A-A-
          1 TGTGGTTATCAAAATTTCATAG

                *            *    
       1956 TGTGATTATCAAAATTTAATAG
          1 TGTGGTTATCAAAATTTCATAG

                        *         
       1978 -G-GGTTATCAACATTTCATAG
          1 TGTGGTTATCAAAATTTCATAG

                    *             
       1998 TGTGGTTACCAAAATTTCATAG
          1 TGTGGTTATCAAAATTTCATAG

                     
       2020 TGTGGTTAT
          1 TGTGGTTAT

       2029 GGGGTTATCA


Statistics
Matches: 60,  Mismatches: 8, Indels: 7
        0.80            0.11        0.09

Matches are distributed among these distances:
  19   15  0.25
  20   17  0.28
  21    3  0.05
  22   25  0.42

ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41


Consensus pattern (22 bp):   
TGTGGTTATCAAAATTTCATAG

Found at i:3128 original size:43 final size:43

Alignment explanation


    Indices: 3067--3149  Score: 157
    Period size: 43  Copynumber: 1.9  Consensus size: 43

       3057 GAATTCTTCG

                                                       
       3067 CAAAAAGTAGTACTAGCAACAACTTAGAGAATTCATGCAATAT
          1 CAAAAAGTAGTACTAGCAACAACTTAGAGAATTCATGCAATAT

                                 *                  
       3110 CAAAAAGTAGTACTAGCAACAGCTTAGAGAATTCATGCAA
          1 CAAAAAGTAGTACTAGCAACAACTTAGAGAATTCATGCAA

       3150 ACTCAATTTA


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  43   39  1.00

ACGTcount: A:0.46, C:0.17, G:0.16, T:0.22


Consensus pattern (43 bp):   
CAAAAAGTAGTACTAGCAACAACTTAGAGAATTCATGCAATAT

Found at i:4475 original size:32 final size:32

Alignment explanation


    Indices: 4428--4492  Score: 103
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       4418 TACCCCTGAT

                     *                      
       4428 ATTTGTTTCTTTCAGTTAAAATATACATGTCA
          1 ATTTGTTTCCTTCAGTTAAAATATACATGTCA

                *                 *         
       4460 ATTTTTTTCCTTCAGTTAAAATCTACATGTCA
          1 ATTTGTTTCCTTCAGTTAAAATATACATGTCA

             
       4492 A
          1 A

       4493 AAATTTAGAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46


Consensus pattern (32 bp):   
ATTTGTTTCCTTCAGTTAAAATATACATGTCA

Found at i:9437 original size:19 final size:20

Alignment explanation


    Indices: 9390--9437  Score: 59
    Period size: 17  Copynumber: 2.6  Consensus size: 20

       9380 TTTAATGTGG

                                
       9390 GTATACTTGTTTATACATGT
          1 GTATACTTGTTTATACATGT

                          *     
       9410 -TAT--TTGTTT-TGCATGT
          1 GTATACTTGTTTATACATGT

                        
       9426 GTATACTTGTTT
          1 GTATACTTGTTT

       9438 CCACACCTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 7
        0.75            0.03        0.22

Matches are distributed among these distances:
  16    6  0.25
  17    9  0.38
  19    9  0.38

ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56


Consensus pattern (20 bp):   
GTATACTTGTTTATACATGT
Done.