Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001139.1 Corchorus capsularis cultivar CVL-1 contig01139, 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: 11137
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:1149 original size:2 final size:2

Alignment explanation


    Indices: 1144--1178  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       1134 GTTGTTATGT

                                                                
       1144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1179 TAGAATTACT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:6612 original size:3 final size:3

Alignment explanation


    Indices: 6598--6630  Score: 59
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       6588 AAGTTTTTTC

                                                         
       6598 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

       6631 AGCACATTTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2    2  0.07
   3   27  0.93

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (3 bp):   
TTA

Found at i:10833 original size:30 final size:29

Alignment explanation


    Indices: 10764--10836  Score: 103
    Period size: 29  Copynumber: 2.5  Consensus size: 29

      10754 ATAGCGTTTA

                          *               
      10764 GACGTTTT-CCTCCTCGAACTTCAATTTTG
          1 GACGTTTTGCC-CCCCGAACTTCAATTTTG

               *                          
      10793 GACATTTTGCCCCCCGAACTTCAATTTTGG
          1 GACGTTTTGCCCCCCGAACTTCAATTTT-G

                          
      10823 GACGTTTTGCCCCC
          1 GACGTTTTGCCCCC

      10837 TCAACCTAAC


Statistics
Matches: 39,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  29   23  0.59
  30   16  0.41

ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36


Consensus pattern (29 bp):   
GACGTTTTGCCCCCCGAACTTCAATTTTG
Done.