Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017864.1 Corchorus olitorius cultivar O-4 contig17897, 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: 2890
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:445 original size:23 final size:22

Alignment explanation


    Indices: 419--467  Score: 53
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        409 GAAGTTCTCC

                    * *            
        419 AAAAAAAGGTTAAGAAGAGAAAG
          1 AAAAAAAGATGAA-AAGAGAAAG

                *             *   
        442 AAAATAAGATGAAAAGAGGAAG
          1 AAAAAAAGATGAAAAGAGAAAG

                
        464 AAAA
          1 AAAA

        468 CAACCTTAAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  22   12  0.55
  23   10  0.45

ACGTcount: A:0.67, C:0.00, G:0.24, T:0.08


Consensus pattern (22 bp):   
AAAAAAAGATGAAAAGAGAAAG

Found at i:1199 original size:14 final size:14

Alignment explanation


    Indices: 1180--1207  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1170 GATAATCTTA

                          
       1180 TTCTTATTTTTTGC
          1 TTCTTATTTTTTGC

                          
       1194 TTCTTATTTTTTGC
          1 TTCTTATTTTTTGC

       1208 ATCAGAGATC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.07, C:0.14, G:0.07, T:0.71


Consensus pattern (14 bp):   
TTCTTATTTTTTGC

Found at i:1501 original size:2 final size:2

Alignment explanation


    Indices: 1494--1522  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       1484 CTTTAACTAG

                                                       
       1494 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 T

       1523 TGTTCACTTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2800 original size:2 final size:2

Alignment explanation


    Indices: 2793--2820  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2783 CAAATTTTCA

                                                     
       2793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2821 CTTATCTTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.