Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005107.1 Corchorus capsularis cultivar CVL-1 contig05125, 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: 14495
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32


Found at i:1024 original size:2 final size:2

Alignment explanation


    Indices: 1017--1061  Score: 74
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       1007 GTCAAGTACG

                                          *                               
       1017 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT -T AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 
       1058 AT AT
          1 AT AT

       1062 TTCATGTATA


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   39  0.98

ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Found at i:8107 original size:21 final size:19

Alignment explanation


    Indices: 8081--8120  Score: 53
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       8071 CTGCCTTTGT

                                 
       8081 TTGATTTAACAATTAAAAAGA
          1 TTGA-TTAA-AATTAAAAAGA

                  *            
       8102 TTGATTCAAATTAAAAAGA
          1 TTGATTAAAATTAAAAAGA

       8121 AAGGTTGTTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19   11  0.61
  20    3  0.17
  21    4  0.22

ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33


Consensus pattern (19 bp):   
TTGATTAAAATTAAAAAGA

Found at i:13330 original size:52 final size:52

Alignment explanation


    Indices: 13268--13367  Score: 191
    Period size: 52  Copynumber: 1.9  Consensus size: 52

      13258 ACTGGACAAT

                                                                
      13268 TTCCCAGTACATTAGCTAGATTTTCCTCTTTGAACACCCTCCTTGATCCAAC
          1 TTCCCAGTACATTAGCTAGATTTTCCTCTTTGAACACCCTCCTTGATCCAAC

                *                                           
      13320 TTCCTAGTACATTAGCTAGATTTTCCTCTTTGAACACCCTCCTTGATC
          1 TTCCCAGTACATTAGCTAGATTTTCCTCTTTGAACACCCTCCTTGATC

      13368 TGTCCAGAAA


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  52   47  1.00

ACGTcount: A:0.22, C:0.31, G:0.10, T:0.37


Consensus pattern (52 bp):   
TTCCCAGTACATTAGCTAGATTTTCCTCTTTGAACACCCTCCTTGATCCAAC
Done.