Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012017.1 Corchorus olitorius cultivar O-4 contig12050, 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: 7199
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:608 original size:17 final size:17

Alignment explanation


    Indices: 580--612  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        570 TCCTATTTTC

                              
        580 AATTTCTATCATCTGATA
          1 AATTTCTATCAT-TGATA

                            
        598 AATTT-TATCATTGAT
          1 AATTTCTATCATTGAT

        613 TTTTATATTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    4  0.27
  17    6  0.40
  18    5  0.33

ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48


Consensus pattern (17 bp):   
AATTTCTATCATTGATA

Found at i:2167 original size:18 final size:20

Alignment explanation


    Indices: 2140--2179  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       2130 TTGAGTAGAC

                        *       
       2140 TTTAACTTTC-TGTTGGGCT
          1 TTTAACTTTCTTATTGGGCT

                                
       2159 TTTAA-TTTCTTATTGGGCT
          1 TTTAACTTTCTTATTGGGCT

              
       2178 TT
          1 TT

       2180 GCTAAGCTAT


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

Matches are distributed among these distances:
  18    4  0.21
  19   15  0.79

ACGTcount: A:0.12, C:0.12, G:0.17, T:0.57


Consensus pattern (20 bp):   
TTTAACTTTCTTATTGGGCT

Found at i:4959 original size:65 final size:65

Alignment explanation


    Indices: 4878--5005  Score: 256
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       4868 TTTTGAAATC

                                                                             
       4878 GAGGCCCAACGAGCATAAAATAAACTTATCGAACCAATCAAGTAACCAAATGCAGATATATAATA
          1 GAGGCCCAACGAGCATAAAATAAACTTATCGAACCAATCAAGTAACCAAATGCAGATATATAATA

                                                                           
       4943 GAGGCCCAACGAGCATAAAATAAACTTATCGAACCAATCAAGTAACCAAATGCAGATATATAA
          1 GAGGCCCAACGAGCATAAAATAAACTTATCGAACCAATCAAGTAACCAAATGCAGATATATAA

       5006 GTGAATAACT


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  65   63  1.00

ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18


Consensus pattern (65 bp):   
GAGGCCCAACGAGCATAAAATAAACTTATCGAACCAATCAAGTAACCAAATGCAGATATATAATA

Found at i:6005 original size:11 final size:12

Alignment explanation


    Indices: 5982--6011  Score: 51
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       5972 CCTTAATCGG

                        
       5982 AAAAATAGAAAA
          1 AAAAATAGAAAA

                        
       5994 AAAAATAGAAAA
          1 AAAAATAGAAAA

                  
       6006 ATAAAA
          1 A-AAAA

       6012 GTCAAAGCGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   13  0.76
  13    4  0.24

ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10


Consensus pattern (12 bp):   
AAAAATAGAAAA

Found at i:7048 original size:125 final size:128

Alignment explanation


    Indices: 6908--7164  Score: 362
    Period size: 125  Copynumber: 2.0  Consensus size: 128

       6898 CATTGTTTAA

                   *                                                         
       6908 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA

                                                                             
       6969 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATTAGAATTTTTTAAATAT
         66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAAC-T-TATATATATTAGAATTTTTTAAATAT

                                   *        *                                
       7033 ACTTTTACAGTTTTACTCAACTACAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C

                 *       *               *  *                           *    
       7098 TATTTTATTTTTATCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTTAATA
         64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA

             
       7163 T
        128 T

             
       7164 A
          1 A

       7165 TTTCTTAAAT


Statistics
Matches: 116,  Mismatches: 8, Indels: 10
        0.87            0.06        0.07

Matches are distributed among these distances:
 125   53  0.46
 126    1  0.01
 127    1  0.01
 128    1  0.01
 131   28  0.24
 132    1  0.01
 133   31  0.27

ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51


Consensus pattern (128 bp):   
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT

Found at i:7112 original size:23 final size:22

Alignment explanation


    Indices: 7086--7130  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7076 TTAAATCTAA

                *                  
       7086 TATCCTTATACCTATTTTATTTT
          1 TATCATTATA-CTATTTTATTTT

                   *              
       7109 TATCATTTTACTATTTTATTTT
          1 TATCATTATACTATTTTATTTT

       7131 AAAAACTTAT


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

Matches are distributed among these distances:
  22   12  0.60
  23    8  0.40

ACGTcount: A:0.22, C:0.13, G:0.00, T:0.64


Consensus pattern (22 bp):   
TATCATTATACTATTTTATTTT
Done.