Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016704.1 Corchorus olitorius cultivar O-4 contig16737, 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: 12572
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29


Found at i:4067 original size:17 final size:17

Alignment explanation


    Indices: 4045--4089  Score: 81
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       4035 AAAACAGAAC

                      *      
       4045 ACAGAAAACAGAGGTTG
          1 ACAGAAAACAAAGGTTG

                             
       4062 ACAGAAAACAAAGGTTG
          1 ACAGAAAACAAAGGTTG

                       
       4079 ACAGAAAACAA
          1 ACAGAAAACAA

       4090 TTAAACTAGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   27  1.00

ACGTcount: A:0.56, C:0.13, G:0.22, T:0.09


Consensus pattern (17 bp):   
ACAGAAAACAAAGGTTG

Found at i:6986 original size:14 final size:15

Alignment explanation


    Indices: 6967--6996  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6957 CAATCAAAGC

                           
       6967 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       6981 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       6996 A
          1 A

       6997 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:7395 original size:22 final size:21

Alignment explanation


    Indices: 7353--7395  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7343 TTGGAATGGC

                       *         
       7353 GATGGCACGGGCATGGCCGGT
          1 GATGGCACGGGAATGGCCGGT

                             *    
       7374 GATGGCACGGTGAATGGGCGGT
          1 GATGGCACGG-GAATGGCCGGT

       7396 AATGACTTGG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   10  0.53
  22    9  0.47

ACGTcount: A:0.16, C:0.19, G:0.49, T:0.16


Consensus pattern (21 bp):   
GATGGCACGGGAATGGCCGGT

Found at i:10671 original size:20 final size:20

Alignment explanation


    Indices: 10646--10683  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

      10636 AAACAAAAAA

                    *           
      10646 TTTTTTTTAT-GACGCAAAT
          1 TTTTTTTTTTCGACGCAAAT

                               
      10665 TTTTTTTTTTCGACGCAAA
          1 TTTTTTTTTTCGACGCAAA

      10684 ACACAAAACA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53


Consensus pattern (20 bp):   
TTTTTTTTTTCGACGCAAAT

Found at i:11075 original size:16 final size:15

Alignment explanation


    Indices: 11037--11078  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      11027 ACAGAGGTTG

                           
      11037 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
      11052 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      11067 ACTAGAAAACAA
          1 AC-AGAAAACAA

      11079 AACAAAATAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.