Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018690.1 Corchorus olitorius cultivar O-4 contig18723, 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: 25038
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:5979 original size:2 final size:2

Alignment explanation


    Indices: 5972--6011  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       5962 ATAAACATTC

                                                                       
       5972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       6012 CTTAATATTT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:8149 original size:7 final size:7

Alignment explanation


    Indices: 8113--8147  Score: 61
    Period size: 7  Copynumber: 5.0  Consensus size: 7

       8103 CGTGATTCCA

                   
       8113 TCTCAAG
          1 TCTCAAG

                   
       8120 TCTCAAG
          1 TCTCAAG

                   
       8127 TCTCAAG
          1 TCTCAAG

                   
       8134 TCTCAAG
          1 TCTCAAG

            *      
       8141 CCTCAAG
          1 TCTCAAG

       8148 CCAATAGGGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   7   27  1.00

ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26


Consensus pattern (7 bp):   
TCTCAAG

Found at i:17248 original size:3 final size:3

Alignment explanation


    Indices: 17242--17267  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

      17232 TAGTTGTTGT

                                              
      17242 TGC TGC TGC TGC TGC TGC TGC TGC TG
          1 TGC TGC TGC TGC TGC TGC TGC TGC TG

      17268 TGTGGTCTGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35


Consensus pattern (3 bp):   
TGC

Found at i:18362 original size:98 final size:99

Alignment explanation


    Indices: 18192--18369  Score: 270
    Period size: 98  Copynumber: 1.8  Consensus size: 99

      18182 AAAAAGGCAA

                                      *         *                         *  
      18192 AACGCCAATTAACGAAAGGAGACCAATCAACAAACCGAACATCAAACCATCAATCAACAATTTAG
          1 AACGCCAATTAACGAAAGGAGACCAACCAACAAACCAAACATCAAACCATCAATCAACAATTAAG

                      *                       
      18257 ACACATACAAGAGTATTGCCAAATAGGAACATAT
         66 ACACATACAAAAGTATTGCCAAATAGGAACATAT

                          *                *                         *       
      18291 AACGCCAATTAACGCAAGGAGACC-ACCAACGAACCAAACATCAAACCATCAATCAATAGA-TAA
          1 AACGCCAATTAACGAAAGGAGACCAACCAACAAACCAAACATCAAACCATCAATCAACA-ATTAA

                            
      18354 GACACATACAAAAGTA
         65 GACACATACAAAAGTA

      18370 CTGCTATCAA


Statistics
Matches: 71,  Mismatches: 7, Indels: 3
        0.88            0.09        0.04

Matches are distributed among these distances:
  98   47  0.66
  99   24  0.34

ACGTcount: A:0.49, C:0.25, G:0.12, T:0.14


Consensus pattern (99 bp):   
AACGCCAATTAACGAAAGGAGACCAACCAACAAACCAAACATCAAACCATCAATCAACAATTAAG
ACACATACAAAAGTATTGCCAAATAGGAACATAT
Done.