Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013540.1 Corchorus olitorius cultivar O-4 contig13573, 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: 25364
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:140 original size:34 final size:34

Alignment explanation


    Indices: 97--188  Score: 114
    Period size: 34  Copynumber: 2.6  Consensus size: 34

         87 TTCTTCTATG

                                       *       
         97 ATTAAAATATGACTAGTTGGTATCCTCCAAAAAA-
          1 ATTAAAATATGACTAGTTGGTATCCT-AAAAAAAT

                           *                  
        131 ATTAAAATATGACTAATTGGTATCCTAAAAAAAT
          1 ATTAAAATATGACTAGTTGGTATCCTAAAAAAAT

                                    
        165 ATATATATATATATGACTAGTTGG
          1 AT-TA-A-A-ATATGACTAGTTGG

        189 GGGAGGTCAT


Statistics
Matches: 50,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  33    6  0.12
  34   27  0.54
  35    2  0.04
  36    1  0.02
  37    1  0.02
  38   13  0.26

ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34


Consensus pattern (34 bp):   
ATTAAAATATGACTAGTTGGTATCCTAAAAAAAT

Found at i:12501 original size:3 final size:3

Alignment explanation


    Indices: 12495--12531  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

      12485 TAGTTTTTTT

                                                             
      12495 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T

      12532 TTTAAAAAAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:13007 original size:14 final size:15

Alignment explanation


    Indices: 12982--13010  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

      12972 TTAGTCAAGT

                           
      12982 TAAAATTAAAATAAA
          1 TAAAATTAAAATAAA

                           
      12997 TAAAA-TAAAATAAA
          1 TAAAATTAAAATAAA

      13011 AAAGCAGAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (15 bp):   
TAAAATTAAAATAAA

Found at i:20520 original size:18 final size:19

Alignment explanation


    Indices: 20497--20535  Score: 55
    Period size: 18  Copynumber: 2.1  Consensus size: 19

      20487 TGTCCGAGAA

                                
      20497 GAAATAGT-CT-CTCGTTTG
          1 GAAATAGTACTACTC-TTTG

                               
      20515 GAAATAGTACTACTCTTTG
          1 GAAATAGTACTACTCTTTG

              
      20534 GA
          1 GA

      20536 GTTTGGGGTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    8  0.42
  19    8  0.42
  20    3  0.16

ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36


Consensus pattern (19 bp):   
GAAATAGTACTACTCTTTG

Found at i:24051 original size:14 final size:14

Alignment explanation


    Indices: 24032--24083  Score: 63
    Period size: 12  Copynumber: 3.6  Consensus size: 14

      24022 ATATTTTTTA

                          
      24032 TTAAAAAAATATTT
          1 TTAAAAAAATATTT

                          
      24046 TT--AAAAATATTT
          1 TTAAAAAAATATTT

                             
      24058 TTAAAAAAATACATTTT
          1 TTAAAAAAAT--A-TTT

                     
      24075 TTAAAAAAA
          1 TTAAAAAAA

      24084 AATGAGTCAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 7
        0.82            0.00        0.17

Matches are distributed among these distances:
  12   12  0.36
  14    8  0.24
  16    1  0.03
  17   12  0.36

ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40


Consensus pattern (14 bp):   
TTAAAAAAATATTT

Done.