Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011881.1 Corchorus olitorius cultivar O-4 contig11914, 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: 12983
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:2876 original size:35 final size:35

Alignment explanation


    Indices: 2836--2908  Score: 137
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       2826 TTCGTTTATA

                                               
       2836 TTCACGAACAGACTCGTTTATTGTTCATTTAAGTG
          1 TTCACGAACAGACTCGTTTATTGTTCATTTAAGTG

                   *                           
       2871 TTCACGAGCAGACTCGTTTATTGTTCATTTAAGTG
          1 TTCACGAACAGACTCGTTTATTGTTCATTTAAGTG

               
       2906 TTC
          1 TTC

       2909 GTTTATATAA


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   37  1.00

ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41


Consensus pattern (35 bp):   
TTCACGAACAGACTCGTTTATTGTTCATTTAAGTG

Found at i:2971 original size:16 final size:16

Alignment explanation


    Indices: 2950--2981  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       2940 TATAATTATT

                            
       2950 TATATATTAATAATAA
          1 TATATATTAATAATAA

                     *      
       2966 TATATATTATTAATAA
          1 TATATATTAATAATAA

       2982 AAATTATAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (16 bp):   
TATATATTAATAATAA

Found at i:2976 original size:19 final size:19

Alignment explanation


    Indices: 2934--2981  Score: 62
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       2924 AAACGTTCAT

                        *  *    
       2934 TTATTATATAATTATTTATA
          1 TTATTA-ATAATAATATATA

                               
       2954 -TATTAATAATAATATATA
          1 TTATTAATAATAATATATA

                      
       2972 TTATTAATAA
          1 TTATTAATAA

       2982 AAATTATAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  18   11  0.44
  19   14  0.56

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (19 bp):   
TTATTAATAATAATATATA

Found at i:3072 original size:13 final size:14

Alignment explanation


    Indices: 3033--3072  Score: 59
    Period size: 13  Copynumber: 3.1  Consensus size: 14

       3023 AATTAAAATT

                          
       3033 TAATTAT-TATATA
          1 TAATTATATATATA

                          
       3046 TAA-TATATATATA
          1 TAATTATATATATA

                          
       3059 TAATTATATA-ATA
          1 TAATTATATATATA

             
       3072 T
          1 T

       3073 TTTGTTCGTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  12    3  0.12
  13   16  0.64
  14    6  0.24

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


Consensus pattern (14 bp):   
TAATTATATATATA

Found at i:3138 original size:18 final size:18

Alignment explanation


    Indices: 3111--3145  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3101 AATTATTACA

                              
       3111 TTGTTCATGAACAATTTT
          1 TTGTTCATGAACAATTTT

                 *           
       3129 TTGTTTATGAACAATTT
          1 TTGTTCATGAACAATTT

       3146 CAATTTTTGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51


Consensus pattern (18 bp):   
TTGTTCATGAACAATTTT

Found at i:5430 original size:21 final size:21

Alignment explanation


    Indices: 5404--5443  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       5394 AAAAAAAATT

                                  
       5404 AAATTAGGTTA-GAAAGAAAAA
          1 AAATTAGG-TAGGAAAGAAAAA

                               
       5425 AAATTAGGTAGGAAAGAAA
          1 AAATTAGGTAGGAAAGAAA

       5444 GGGAAGAAAA


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

Matches are distributed among these distances:
  20    2  0.11
  21   16  0.89

ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17


Consensus pattern (21 bp):   
AAATTAGGTAGGAAAGAAAAA
Done.