Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022383.1 Corchorus olitorius cultivar O-4 contig22416, 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: 10269
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:7490 original size:97 final size:97

Alignment explanation


    Indices: 7361--7609  Score: 392
    Period size: 97  Copynumber: 2.5  Consensus size: 97

       7351 CACTATCTTA

                      *           *                           *              
       7361 TATAAATTAATTTTCTATTTCACTTGGAAACGGAATTTAACACGGAAACTGCATATCCGTGTCTA
          1 TATAAA-TAAATTT-TATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTA

                                              
       7426 AATCCGATTCAAATTGATAATAATAAAATAATTC
         64 AATCCGATTCAAATTGATAATAATAAAATAATTC

                                                    *                        
       7460 TATAAATAAATTTTATTTCATTTGGAAACGGAATTTAACATGGAAACTACATATCCGTGTCTAAA
          1 TATAAATAAATTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTAAA

                *   *                  *   *
       7525 TCCGCTTCTAATTGATAATAATAAAATTATTT
         66 TCCGATTCAAATTGATAATAATAAAATAATTC

                                                                  
       7557 TATAAATAAATTTTTATTTCATTT-GAAACGGAATTTAACACGGAAACTACATA
          1 TATAAATAAA-TTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATA

       7610 AACGGAAACT


Statistics
Matches: 140,  Mismatches: 9, Indels: 4
        0.92            0.06        0.03

Matches are distributed among these distances:
  97  115  0.82
  98   19  0.14
  99    6  0.04

ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36


Consensus pattern (97 bp):   
TATAAATAAATTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTAAA
TCCGATTCAAATTGATAATAATAAAATAATTC

Found at i:7616 original size:15 final size:15

Alignment explanation


    Indices: 7596--7625  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       7586 GGAATTTAAC

                           
       7596 ACGGAAACTACATAA
          1 ACGGAAACTACATAA

                           
       7611 ACGGAAACTACATAA
          1 ACGGAAACTACATAA

       7626 CAAGACATAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.53, C:0.20, G:0.13, T:0.13


Consensus pattern (15 bp):   
ACGGAAACTACATAA

Found at i:7720 original size:31 final size:31

Alignment explanation


    Indices: 7667--7730  Score: 94
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       7657 AACAGCCAAT

                       *                   
       7667 AAAGCCCAATACTAACTAAAATAAGAAAATA
          1 AAAGCCCAATAATAACTAAAATAAGAAAATA

                  *                         
       7698 AAAGCCTAATAATAATCT-AAATAAGAAAATA
          1 AAAGCCCAATAATAA-CTAAAATAAGAAAATA

              
       7729 AA
          1 AA

       7731 GACAAACTCT


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  31   28  0.93
  32    2  0.07

ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19


Consensus pattern (31 bp):   
AAAGCCCAATAATAACTAAAATAAGAAAATA

Found at i:8528 original size:17 final size:17

Alignment explanation


    Indices: 8506--8538  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       8496 ACTGCCTTCC

                              
       8506 TCTTCTTTCTT-TTCTTT
          1 TCTTC-TTCTTCTTCTTT

                            
       8523 TCTTCTTCTTCTTCTT
          1 TCTTCTTCTTCTTCTT

       8539 CTTCGCAATG


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

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73


Consensus pattern (17 bp):   
TCTTCTTCTTCTTCTTT

Found at i:8560 original size:3 final size:3

Alignment explanation


    Indices: 8501--8542  Score: 52
    Period size: 3  Copynumber: 14.3  Consensus size: 3

       8491 TTATCACTGC

                 *                                                    
       8501 CTT CCT CTT CTTT CTT -TT CTT -TT CTT CTT CTT CTT CTT CTT C
          1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C

       8543 GCAATGCTCC


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
   2    4  0.12
   3   27  0.79
   4    3  0.09

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (3 bp):   
CTT
Done.