Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018704.1 Corchorus olitorius cultivar O-4 contig18737, 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: 4997
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32


Found at i:3565 original size:15 final size:15

Alignment explanation


    Indices: 3545--3581  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       3535 TTATTGTTCA

                           
       3545 CACCATTGTTATTCG
          1 CACCATTGTTATTCG

                      *  * 
       3560 CACCATTGTTGTTTG
          1 CACCATTGTTATTCG

                   
       3575 CACCATT
          1 CACCATT

       3582 CACCCTAGCA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41


Consensus pattern (15 bp):   
CACCATTGTTATTCG

Found at i:3792 original size:24 final size:24

Alignment explanation


    Indices: 3760--3847  Score: 113
    Period size: 24  Copynumber: 3.5  Consensus size: 24

       3750 AGGATTTTGG

                *                   
       3760 TTATCCACACCATTGTTGATGGCA
          1 TTATTCACACCATTGTTGATGGCA

                                    
       3784 TTATTCACACCATTGTTGATGGCA
          1 TTATTCACACCATTGTTGATGGCA

                      *     *      *   
       3808 TTATTCACACAATTCACTTGATTTGCA
          1 TTATTCACACCATT--GTTGA-TGGCA

                         
       3835 TTATTCACACCAT
          1 TTATTCACACCAT

       3848 GATGGAGAGG


Statistics
Matches: 56,  Mismatches: 5, Indels: 3
        0.88            0.08        0.05

Matches are distributed among these distances:
  24   36  0.64
  26    4  0.07
  27   16  0.29

ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38


Consensus pattern (24 bp):   
TTATTCACACCATTGTTGATGGCA

Found at i:4665 original size:8 final size:9

Alignment explanation


    Indices: 4639--4667  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

       4629 CCTAAATTAC

                     
       4639 TTATGGAAA
          1 TTATGGAAA

                     
       4648 TTATGGAAA
          1 TTATGGAAA

                     
       4657 TTA-GGAAA
          1 TTATGGAAA

               
       4665 TTA
          1 TTA

       4668 AAGAAATTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   8    8  0.40
   9   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34


Consensus pattern (9 bp):   
TTATGGAAA

Found at i:4673 original size:17 final size:17

Alignment explanation


    Indices: 4643--4676  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       4633 AATTACTTAT

                    **       
       4643 GGAAATTATGGAAATTA
          1 GGAAATTAAAGAAATTA

                             
       4660 GGAAATTAAAGAAATTA
          1 GGAAATTAAAGAAATTA

       4677 AATGTTTTTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26


Consensus pattern (17 bp):   
GGAAATTAAAGAAATTA
Done.