Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013123.1 Corchorus olitorius cultivar O-4 contig13156, 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: 19365
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:1601 original size:19 final size:19

Alignment explanation


    Indices: 1550--1601  Score: 50
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       1540 AAATAAATGG

                                 
       1550 AACAGAACATAACAGAACAAC
          1 AACAGAAC--AACAGAACAAC

              *  ***           
       1571 AATAGTGGAACAGAACAAC
          1 AACAGAACAACAGAACAAC

                        
       1590 AACAGAACAACA
          1 AACAGAACAACA

       1602 TTCTTTTAAT


Statistics
Matches: 23,  Mismatches: 8, Indels: 2
        0.70            0.24        0.06

Matches are distributed among these distances:
  19   19  0.83
  21    4  0.17

ACGTcount: A:0.60, C:0.21, G:0.13, T:0.06


Consensus pattern (19 bp):   
AACAGAACAACAGAACAAC

Found at i:7312 original size:18 final size:18

Alignment explanation


    Indices: 7289--7328  Score: 80
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       7279 CATAGGAAGA

                              
       7289 ACAAATTTGATACAATTC
          1 ACAAATTTGATACAATTC

                              
       7307 ACAAATTTGATACAATTC
          1 ACAAATTTGATACAATTC

                
       7325 ACAA
          1 ACAA

       7329 CGCTATATTA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30


Consensus pattern (18 bp):   
ACAAATTTGATACAATTC

Found at i:11595 original size:15 final size:15

Alignment explanation


    Indices: 11575--11606  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      11565 GCATCTTTTG

                           
      11575 CCTACTAGGGTTCAA
          1 CCTACTAGGGTTCAA

                        *  
      11590 CCTACTAGGGTTGAA
          1 CCTACTAGGGTTCAA

              
      11605 CC
          1 CC

      11607 AAGATGGGTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25


Consensus pattern (15 bp):   
CCTACTAGGGTTCAA

Found at i:12564 original size:7 final size:7

Alignment explanation


    Indices: 12552--12594  Score: 50
    Period size: 7  Copynumber: 5.9  Consensus size: 7

      12542 ACGTTGGTTA

                   
      12552 AAAAAAT
          1 AAAAAAT

                    
      12559 AAAAAATT
          1 AAAAAA-T

                    
      12567 AAAAAAAT
          1 -AAAAAAT

                ** 
      12575 AAAATGT
          1 AAAAAAT

                   
      12582 AAAAAAT
          1 AAAAAAT

                  
      12589 AAAAAA
          1 AAAAAA

      12595 GCAACTGACT


Statistics
Matches: 30,  Mismatches: 4, Indels: 4
        0.79            0.11        0.11

Matches are distributed among these distances:
   7   22  0.73
   8    2  0.07
   9    6  0.20

ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16


Consensus pattern (7 bp):   
AAAAAAT

Found at i:12568 original size:16 final size:16

Alignment explanation


    Indices: 12549--12594  Score: 62
    Period size: 16  Copynumber: 3.0  Consensus size: 16

      12539 GCCACGTTGG

                            
      12549 TTAAAAAAATAAAAAA
          1 TTAAAAAAATAAAAAA

                            
      12565 TTAAAAAAAT--AAAA
          1 TTAAAAAAATAAAAAA

                             
      12579 TGT-AAAAAATAAAAAA
          1 T-TAAAAAAATAAAAAA

      12595 GCAACTGACT


Statistics
Matches: 27,  Mismatches: 0, Indels: 6
        0.82            0.00        0.18

Matches are distributed among these distances:
  14   12  0.44
  15    1  0.04
  16   14  0.52

ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20


Consensus pattern (16 bp):   
TTAAAAAAATAAAAAA

Found at i:18753 original size:58 final size:57

Alignment explanation


    Indices: 18658--18771  Score: 165
    Period size: 58  Copynumber: 2.0  Consensus size: 57

      18648 ATAGCATCAT

                      *                                               
      18658 GCCTCGGTCCTAAAACATCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
          1 GCCTCGGTCCGAAAACATCTTTTTTAGGCATCTAAT-AAAAAACATGTCACTCGATAA

                *           *         *            *           *    
      18716 GCCTTGGTCCGAAAACGTCTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
          1 GCCTCGGTCCGAAAACATCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA

      18772 TTTGATTAAT


Statistics
Matches: 50,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  57   18  0.36
  58   32  0.64

ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32


Consensus pattern (57 bp):   
GCCTCGGTCCGAAAACATCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
Done.