Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002127.1 Corchorus olitorius cultivar O-4 contig02127, 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, 769

Length: 1282
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26


Found at i:339 original size:3 final size:3

Alignment explanation


    Indices: 331--366  Score: 72
    Period size: 3  Copynumber: 12.0  Consensus size: 3

        321 AATTTTACAT

                                                           
        331 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

        367 CACTAATTTC


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

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:1141 original size:16 final size:16

Alignment explanation


    Indices: 1105--1148  Score: 54
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       1095 GCCAAATCGC

                       *    
       1105 CGATAAGG-AGCAAGA
          1 CGATAAGGAAGAAAGA

                           *
       1120 CGATAAGGAAGAAAGT
          1 CGATAAGGAAGAAAGA

                  *      
       1136 CGATAAAGAAGAA
          1 CGATAAGGAAGAA

       1149 GCCAAAATTC


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  15    8  0.32
  16   17  0.68

ACGTcount: A:0.52, C:0.09, G:0.30, T:0.09


Consensus pattern (16 bp):   
CGATAAGGAAGAAAGA

Found at i:1270 original size:23 final size:23

Alignment explanation


    Indices: 1236--1281  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1226 ACTTCAAGAG

                                   
       1236 AAGCAAGTGTCGACTAAAGAGGA
          1 AAGCAAGTGTCGACTAAAGAGGA

                              *     
       1259 AAGCAA-TAGTCGACTAAGGAGGA
          1 AAGCAAGT-GTCGACTAAAGAGGA

       1282 C


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22    1  0.05
  23   20  0.95

ACGTcount: A:0.43, C:0.13, G:0.30, T:0.13


Consensus pattern (23 bp):   
AAGCAAGTGTCGACTAAAGAGGA
Done.