Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009444.1 Corchorus capsularis cultivar CVL-1 contig09465, 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: 26083
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:5388 original size:45 final size:45

Alignment explanation


    Indices: 5337--5435  Score: 198
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       5327 CTATGAAAAG

                                                         
       5337 GAGACACCAGAAGAGATGGCTTCAAACTTCACCTGTGCAATGTTT
          1 GAGACACCAGAAGAGATGGCTTCAAACTTCACCTGTGCAATGTTT

                                                         
       5382 GAGACACCAGAAGAGATGGCTTCAAACTTCACCTGTGCAATGTTT
          1 GAGACACCAGAAGAGATGGCTTCAAACTTCACCTGTGCAATGTTT

                     
       5427 GAGACACCA
          1 GAGACACCA

       5436 CAAGCTGTCC


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   54  1.00

ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22


Consensus pattern (45 bp):   
GAGACACCAGAAGAGATGGCTTCAAACTTCACCTGTGCAATGTTT

Found at i:17234 original size:2 final size:2

Alignment explanation


    Indices: 17227--17259  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      17217 TCATTTCAGC

                                                              
      17227 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      17260 AGGAACTATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

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


Consensus pattern (2 bp):   
TA

Found at i:22067 original size:31 final size:29

Alignment explanation


    Indices: 21981--22074  Score: 89
    Period size: 31  Copynumber: 3.1  Consensus size: 29

      21971 TTAAATTGCA

                        *                
      21981 TCCCTATACTCAAAAAATTATCAATTTAG
          1 TCCCTATACTCACAAAATTATCAATTTAG

               * *    *    *               
      22010 TCCATCTACTTACAAGATTAAGTCAATTTAG
          1 TCCCTATACTCACAAAATT-A-TCAATTTAG

                           *            *  
      22041 TCCCTATACTCACAATATTGGATCAATTGAG
          1 TCCCTATACTCACAAAATT--ATCAATTTAG

               
      22072 TCC
          1 TCC

      22075 AATCGTTAAA


Statistics
Matches: 51,  Mismatches: 11, Indels: 4
        0.77            0.17        0.06

Matches are distributed among these distances:
  29   14  0.27
  30    1  0.02
  31   35  0.69
  32    1  0.02

ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34


Consensus pattern (29 bp):   
TCCCTATACTCACAAAATTATCAATTTAG

Found at i:23189 original size:2 final size:2

Alignment explanation


    Indices: 23182--23212  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      23172 GTTAATTTAC

                                                          
      23182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      23213 GGTAGGTTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Done.