Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022917.1 Corchorus olitorius cultivar O-4 contig22950, 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: 8679
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:622 original size:22 final size:22

Alignment explanation


    Indices: 594--639  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

        584 AAAATCTCCT

                                   
        594 AATTCAACC-TCTGGAGAGGTCG
          1 AATTCAACCTTC-GGAGAGGTCG

                         *        
        616 AATTCAACCTTCGTAGAGGTCG
          1 AATTCAACCTTCGGAGAGGTCG

              
        638 AA
          1 AA

        640 ACAACAACTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   20  0.91
  23    2  0.09

ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24


Consensus pattern (22 bp):   
AATTCAACCTTCGGAGAGGTCG

Found at i:1479 original size:16 final size:15

Alignment explanation


    Indices: 1441--1482  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1431 ACAGAGATTG

                   *       
       1441 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1456 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1471 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1483 AGCAGAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3496 original size:14 final size:15

Alignment explanation


    Indices: 3477--3506  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3467 CAATCAAAGC

                           
       3477 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       3491 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       3506 A
          1 A

       3507 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:3901 original size:21 final size:21

Alignment explanation


    Indices: 3875--3936  Score: 70
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       3865 GGAATGCCTA

                                 
       3875 TGGCACGGGCATGGCCGGTGG
          1 TGGCACGGGCATGGCCGGTGG

                      * **  *    
       3896 TGGCACGGGCTTAACCAGTGG
          1 TGGCACGGGCATGGCCGGTGG

                      *         
       3917 TGGCACGGTGAATGGCCGGT
          1 TGGCACGG-GCATGGCCGGT

       3937 AATGGCTTGG


Statistics
Matches: 31,  Mismatches: 9, Indels: 1
        0.76            0.22        0.02

Matches are distributed among these distances:
  21   25  0.81
  22    6  0.19

ACGTcount: A:0.15, C:0.23, G:0.45, T:0.18


Consensus pattern (21 bp):   
TGGCACGGGCATGGCCGGTGG

Found at i:6541 original size:27 final size:25

Alignment explanation


    Indices: 6511--6567  Score: 78
    Period size: 27  Copynumber: 2.2  Consensus size: 25

       6501 GCAAAAAAAA

                                       
       6511 TTTTTTATGACGCAGAAACAAATTTTT
          1 TTTTTTATGACGCA-AAA-AAATTTTT

                *             *      
       6538 TTTTATATGACGCAAAAATATTTTT
          1 TTTTTTATGACGCAAAAAAATTTTT

                 
       6563 TTTTT
          1 TTTTT

       6568 CGACGCAAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  25   11  0.41
  26    3  0.11
  27   13  0.48

ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51


Consensus pattern (25 bp):   
TTTTTTATGACGCAAAAAAATTTTT

Found at i:6556 original size:23 final size:23

Alignment explanation


    Indices: 6532--6577  Score: 65
    Period size: 25  Copynumber: 1.9  Consensus size: 23

       6522 GCAGAAACAA

                         *           
       6532 ATTTTTTTTTATATGACGCAAAAAT
          1 ATTTTTTTTT-T-CGACGCAAAAAT

                                 
       6557 ATTTTTTTTTTCGACGCAAAA
          1 ATTTTTTTTTTCGACGCAAAA

       6578 CACAAAACAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23    9  0.45
  24    1  0.05
  25   10  0.50

ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48


Consensus pattern (23 bp):   
ATTTTTTTTTTCGACGCAAAAAT

Found at i:8259 original size:22 final size:23

Alignment explanation


    Indices: 8213--8272  Score: 63
    Period size: 22  Copynumber: 2.7  Consensus size: 23

       8203 AATATTAATA

                       *  *        
       8213 AAATA-GCATATAATTA-AGCAT
          1 AAATAGGCATAAAAATATAGCAT

                *   *              
       8234 AAATGGGCCTAAAAATATAGCA-
          1 AAATAGGCATAAAAATATAGCAT

                             
       8256 AAATAGGCATAAAAATA
          1 AAATAGGCATAAAAATA

       8273 GGGTCAATTT


Statistics
Matches: 31,  Mismatches: 6, Indels: 3
        0.77            0.15        0.08

Matches are distributed among these distances:
  21    4  0.13
  22   23  0.74
  23    4  0.13

ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22


Consensus pattern (23 bp):   
AAATAGGCATAAAAATATAGCAT
Done.