Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020402.1 Corchorus olitorius cultivar O-4 contig20435, 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: 6180
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35


Found at i:1185 original size:3 final size:3

Alignment explanation


    Indices: 1177--1249  Score: 146
    Period size: 3  Copynumber: 24.3  Consensus size: 3

       1167 GCACAACCTA

                                                                           
       1177 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                                             
       1225 TAT TAT TAT TAT TAT TAT TAT TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT T

       1250 TAATACTAAT


Statistics
Matches: 70,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   70  1.00

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


Consensus pattern (3 bp):   
TAT

Found at i:1383 original size:25 final size:25

Alignment explanation


    Indices: 1341--1388  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       1331 CAATTTCAAC

                      **             
       1341 TTTGATCATTGGTCAAAAGAAAATT
          1 TTTGATCATTAATCAAAAGAAAATT

                         *         
       1366 TTTGATCATTAATTAAAAGAAAA
          1 TTTGATCATTAATCAAAAGAAAA

       1389 ATATGTAGAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  25   20  1.00

ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35


Consensus pattern (25 bp):   
TTTGATCATTAATCAAAAGAAAATT

Found at i:3349 original size:55 final size:55

Alignment explanation


    Indices: 3283--3388  Score: 187
    Period size: 55  Copynumber: 1.9  Consensus size: 55

       3273 GAATATACTT

                                     *                              
       3283 CACTTGAAGCAACCCCTGA-ATTATTAGCAAAGATAAGATAAATCAACAAACACTC
          1 CACTTGAAGCAACCCCT-ATATTATCAGCAAAGATAAGATAAATCAACAAACACTC

                                                               
       3338 CACTTGAAGCAACCCCTATATTATCAGCAAAGATAAGATAAATCAACAAAC
          1 CACTTGAAGCAACCCCTATATTATCAGCAAAGATAAGATAAATCAACAAAC

       3389 TAGGCTATGA


Statistics
Matches: 49,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  54    1  0.02
  55   48  0.98

ACGTcount: A:0.46, C:0.24, G:0.10, T:0.20


Consensus pattern (55 bp):   
CACTTGAAGCAACCCCTATATTATCAGCAAAGATAAGATAAATCAACAAACACTC

Found at i:6159 original size:2 final size:2

Alignment explanation


    Indices: 6152--6180  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       6142 ATCTCATTGG

                                                       
       6152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


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


Consensus pattern (2 bp):   
AT

Done.