Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000414.1 Corchorus capsularis cultivar CVL-1 contig00414, 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: 14540
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:5793 original size:3 final size:3

Alignment explanation


    Indices: 5785--5812  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       5775 CTTTTAGGTC

                                                 
       5785 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A

       5813 GATGATGCCC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (3 bp):   
ATT

Found at i:7609 original size:6 final size:6

Alignment explanation


    Indices: 7598--7628  Score: 62
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       7588 AAATATTATA

                                                
       7598 AGCAAG AGCAAG AGCAAG AGCAAG AGCAAG A
          1 AGCAAG AGCAAG AGCAAG AGCAAG AGCAAG A

       7629 TGTAAACCGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.52, C:0.16, G:0.32, T:0.00


Consensus pattern (6 bp):   
AGCAAG

Found at i:13249 original size:17 final size:17

Alignment explanation


    Indices: 13227--13264  Score: 76
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      13217 CCATTCTCTG

                             
      13227 TTTAACATTCACCATCC
          1 TTTAACATTCACCATCC

                             
      13244 TTTAACATTCACCATCC
          1 TTTAACATTCACCATCC

                
      13261 TTTA
          1 TTTA

      13265 GGAATCCCAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39


Consensus pattern (17 bp):   
TTTAACATTCACCATCC

Found at i:13643 original size:21 final size:21

Alignment explanation


    Indices: 13617--13659  Score: 86
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      13607 ACAGTTGGCA

                                 
      13617 GGTCTCGGCATCCTCAACGAT
          1 GGTCTCGGCATCCTCAACGAT

                                 
      13638 GGTCTCGGCATCCTCAACGAT
          1 GGTCTCGGCATCCTCAACGAT

             
      13659 G
          1 G

      13660 CTTGCCAACA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.19, C:0.33, G:0.26, T:0.23


Consensus pattern (21 bp):   
GGTCTCGGCATCCTCAACGAT
Done.