Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007497.1 Corchorus olitorius cultivar O-4 contig07522, 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: 3641
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40


Found at i:1598 original size:15 final size:15

Alignment explanation


    Indices: 1578--1652  Score: 64
    Period size: 15  Copynumber: 5.0  Consensus size: 15

       1568 TTTTACTTTG

                           
       1578 TATATTATTCAATTA
          1 TATATTATTCAATTA

                     *  *  *
       1593 TATATT-TTTACTTTG
          1 TATATTATTCA-ATTA

                           
       1608 TATATTATTCAATTA
          1 TATATTATTCAATTA

                     *  *  *
       1623 TATATT-TTTACTTTG
          1 TATATTATTCA-ATTA

                           
       1638 TATATTATTCAATTA
          1 TATATTATTCAATTA

       1653 GACAAACTTT


Statistics
Matches: 44,  Mismatches: 12, Indels: 8
        0.69            0.19        0.12

Matches are distributed among these distances:
  14    6  0.14
  15   32  0.73
  16    6  0.14

ACGTcount: A:0.32, C:0.07, G:0.03, T:0.59


Consensus pattern (15 bp):   
TATATTATTCAATTA

Found at i:1603 original size:30 final size:30

Alignment explanation


    Indices: 1567--1652  Score: 172
    Period size: 30  Copynumber: 2.9  Consensus size: 30

       1557 ATTGTGTTTG

                                          
       1567 TTTTTACTTTGTATATTATTCAATTATATA
          1 TTTTTACTTTGTATATTATTCAATTATATA

                                          
       1597 TTTTTACTTTGTATATTATTCAATTATATA
          1 TTTTTACTTTGTATATTATTCAATTATATA

                                      
       1627 TTTTTACTTTGTATATTATTCAATTA
          1 TTTTTACTTTGTATATTATTCAATTA

       1653 GACAAACTTT


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   56  1.00

ACGTcount: A:0.29, C:0.07, G:0.03, T:0.60


Consensus pattern (30 bp):   
TTTTTACTTTGTATATTATTCAATTATATA

Found at i:3364 original size:21 final size:21

Alignment explanation


    Indices: 3340--3426  Score: 56
    Period size: 21  Copynumber: 4.2  Consensus size: 21

       3330 AATTATTATT

                                 
       3340 TAAAAAACTTATCCAAGTTAC
          1 TAAAAAACTTATCCAAGTTAC

                  **       *      
       3361 TAAAAAGTTTA-CACGAG-TA-
          1 TAAAAAACTTATC-CAAGTTAC

              *          *        
       3380 TATAAAACTT-TCTAAGGTTAC
          1 TAAAAAACTTATCCAA-GTTAC

                  *    * *       
       3401 TAAAAATCTTAACAAAGTTAC
          1 TAAAAAACTTATCCAAGTTAC

                 
       3422 TAAAA
          1 TAAAA

       3427 TGCTTACTAA


Statistics
Matches: 48,  Mismatches: 12, Indels: 12
        0.67            0.17        0.17

Matches are distributed among these distances:
  18    1  0.02
  19    9  0.19
  20    5  0.10
  21   30  0.62
  22    3  0.06

ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30


Consensus pattern (21 bp):   
TAAAAAACTTATCCAAGTTAC

Found at i:3438 original size:20 final size:21

Alignment explanation


    Indices: 3391--3440  Score: 59
    Period size: 20  Copynumber: 2.4  Consensus size: 21

       3381 ATAAAACTTT

                                  
       3391 CTAAGGTTACTAAAAATCTTAA
          1 CTAA-GTTACTAAAAATCTTAA

             *                    
       3413 CAAAGTTACT-AAAATGCTT-A
          1 CTAAGTTACTAAAAAT-CTTAA

                    
       3433 CTAAGTTA
          1 CTAAGTTA

       3441 TATATTGAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  20   13  0.52
  21    9  0.36
  22    3  0.12

ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32


Consensus pattern (21 bp):   
CTAAGTTACTAAAAATCTTAA
Done.