Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020740.1 Corchorus olitorius cultivar O-4 contig20773, 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: 11759
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38


Found at i:2692 original size:27 final size:27

Alignment explanation


    Indices: 2617--2699  Score: 121
    Period size: 30  Copynumber: 3.0  Consensus size: 27

       2607 ATACCACTAA

                         *             
       2617 TAATAATTATTATTATAATAATAAGTT
          1 TAATAATTATTATAATAATAATAAGTT

                      *                   
       2644 TAATAATTATAATACCACTAATAATAAGTT
          1 TAATAATTATTATA--A-TAATAATAAGTT

                                      
       2674 TAATAATTATTATAATAATAATAAGT
          1 TAATAATTATTATAATAATAATAAGT

       2700 CTAAATTAAC


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

Matches are distributed among these distances:
  27   23  0.46
  28    1  0.02
  29    1  0.02
  30   25  0.50

ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42


Consensus pattern (27 bp):   
TAATAATTATTATAATAATAATAAGTT

Found at i:3107 original size:54 final size:54

Alignment explanation


    Indices: 3016--3140  Score: 175
    Period size: 54  Copynumber: 2.3  Consensus size: 54

       3006 GCACGTGTGT

                            *              **                      
       3016 TCATAATTCATAAAAACAAACAAATAAATATGCTAAATCACATATTAAATTGTAA
          1 TCATAATT-ATAAAAATAAACAAATAAATATAATAAATCACATATTAAATTGTAA

                                                            *      
       3071 TCATAAATTATAAAAATAAA-AAATAAATATAATAAATCACATATTAATTTGTAA
          1 TCAT-AATTATAAAAATAAACAAATAAATATAATAAATCACATATTAAATTGTAA

                              
       3125 T-ATAA-TATAAAAATAA
          1 TCATAATTATAAAAATAA

       3141 TATAATCAAC


Statistics
Matches: 65,  Mismatches: 4, Indels: 6
        0.87            0.05        0.08

Matches are distributed among these distances:
  51   11  0.17
  52    2  0.03
  53    2  0.03
  54   32  0.49
  55   14  0.22
  56    4  0.06

ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31


Consensus pattern (54 bp):   
TCATAATTATAAAAATAAACAAATAAATATAATAAATCACATATTAAATTGTAA

Found at i:7085 original size:48 final size:48

Alignment explanation


    Indices: 7033--7130  Score: 151
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       7023 ACGTTAATTT

                 *                              * * *       
       7033 AATACCAAAATATTATGAGAGTAGAGCAAATCATAATATTTATGAATC
          1 AATACAAAAATATTATGAGAGTAGAGCAAATCATAACACTCATGAATC

                                *                           
       7081 AATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAATC
          1 AATACAAAAATATTATGAGAGTAGAGCAAATCATAACACTCATGAATC

              
       7129 AA
          1 AA

       7131 AATAGTTTTT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  48   45  1.00

ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27


Consensus pattern (48 bp):   
AATACAAAAATATTATGAGAGTAGAGCAAATCATAACACTCATGAATC

Found at i:11185 original size:17 final size:19

Alignment explanation


    Indices: 11156--11191  Score: 58
    Period size: 18  Copynumber: 2.0  Consensus size: 19

      11146 GTAGTTTTTG

                               
      11156 GCAGTTCTTTTTA-AATGA
          1 GCAGTTCTTTTTAGAATGA

                               
      11174 GCAGTT-TTTTTAGAATGA
          1 GCAGTTCTTTTTAGAATGA

      11192 TATAAATACA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.28, C:0.08, G:0.19, T:0.44


Consensus pattern (19 bp):   
GCAGTTCTTTTTAGAATGA

Found at i:11248 original size:19 final size:20

Alignment explanation


    Indices: 11218--11264  Score: 69
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      11208 ATACTTTATA

                           *     
      11218 TTTATCTTAAAATGGGTAG-T
          1 TTTAT-TTAAAATGGATAGTT

                                
      11238 TTTATTTAAAATGGATAGTT
          1 TTTATTTAAAATGGATAGTT

                   
      11258 TTTATTT
          1 TTTATTT

      11265 TGTTTTGAAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  19   12  0.48
  20   13  0.52

ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53


Consensus pattern (20 bp):   
TTTATTTAAAATGGATAGTT

Found at i:11598 original size:33 final size:33

Alignment explanation


    Indices: 11561--11627  Score: 134
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      11551 CGCCATGATC

                                             
      11561 TGCTTGAAAATTTGAGGTTTTTAGTTTGAAGGT
          1 TGCTTGAAAATTTGAGGTTTTTAGTTTGAAGGT

                                             
      11594 TGCTTGAAAATTTGAGGTTTTTAGTTTGAAGGT
          1 TGCTTGAAAATTTGAGGTTTTTAGTTTGAAGGT

             
      11627 T
          1 T

      11628 TCAGAGGATT


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

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46


Consensus pattern (33 bp):   
TGCTTGAAAATTTGAGGTTTTTAGTTTGAAGGT
Done.