Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022735.1 Corchorus olitorius cultivar O-4 contig22768, 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: 16162
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:1967 original size:12 final size:12

Alignment explanation


    Indices: 1950--1975  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1940 ATTCCTAATA

                        
       1950 ATCTCAAAAAAT
          1 ATCTCAAAAAAT

                        
       1962 ATCTCAAAAAAT
          1 ATCTCAAAAAAT

              
       1974 AT
          1 AT

       1976 GAAATGATTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27


Consensus pattern (12 bp):   
ATCTCAAAAAAT

Found at i:2156 original size:35 final size:36

Alignment explanation


    Indices: 2080--2180  Score: 186
    Period size: 36  Copynumber: 2.8  Consensus size: 36

       2070 ATCAAATTAA

                                                
       2080 AAAAAAAAAAAAGAATTTCTCGCATCCCCTGTGGCC
          1 AAAAAAAAAAAAGAATTTCTCGCATCCCCTGTGGCC

                                                
       2116 AAAAAAAAAAAAGAATTTCTCGCATCCCCTGTGGCC
          1 AAAAAAAAAAAAGAATTTCTCGCATCCCCTGTGGCC

                              *           
       2152 -AAAAAAAAAAAGAATTTATCGCATCCCCT
          1 AAAAAAAAAAAAGAATTTCTCGCATCCCCT

       2181 TTTACTTGGA


Statistics
Matches: 64,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  35   28  0.44
  36   36  0.56

ACGTcount: A:0.45, C:0.24, G:0.12, T:0.20


Consensus pattern (36 bp):   
AAAAAAAAAAAAGAATTTCTCGCATCCCCTGTGGCC

Found at i:2865 original size:41 final size:41

Alignment explanation


    Indices: 2818--2953  Score: 193
    Period size: 41  Copynumber: 3.3  Consensus size: 41

       2808 TCATCATAAT

                     *                *              
       2818 ATATCCTTCGAAAATAAATTCTTTAAGAAATAAATTCTTAA
          1 ATATCCTTCAAAAATAAATTCTTTAAAAAATAAATTCTTAA

                                             *      * 
       2859 ATATCCTTCAAAAATAAA-TCTTTTAAAAAATACATTCTTGA
          1 ATATCCTTCAAAAATAAATTC-TTTAAAAAATAAATTCTTAA

                               *                       
       2900 ATATCCTTCAAAAATAAATCCTTTAAAAAATATACATTCTTAA
          1 ATATCCTTCAAAAATAAATTCTTTAAAAAATA-A-ATTCTTAA

                       
       2943 ATATCCTTCAA
          1 ATATCCTTCAA

       2954 CAATGGAGGA


Statistics
Matches: 84,  Mismatches: 7, Indels: 6
        0.87            0.07        0.06

Matches are distributed among these distances:
  40    2  0.02
  41   63  0.75
  42    1  0.01
  43   18  0.21

ACGTcount: A:0.46, C:0.15, G:0.02, T:0.36


Consensus pattern (41 bp):   
ATATCCTTCAAAAATAAATTCTTTAAAAAATAAATTCTTAA

Found at i:5953 original size:43 final size:43

Alignment explanation


    Indices: 5906--5994  Score: 169
    Period size: 43  Copynumber: 2.1  Consensus size: 43

       5896 CATATAACCC

                                                       
       5906 ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG
          1 ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG

                                                  *    
       5949 ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGTATCG
          1 ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG

               
       5992 ATT
          1 ATT

       5995 GAGTAACGCA


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   45  1.00

ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33


Consensus pattern (43 bp):   
ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG

Found at i:11573 original size:2 final size:2

Alignment explanation


    Indices: 11561--11600  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      11551 ATTACTTTTC

                                                                         
      11561 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      11601 CTGGCTATCT


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   36  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:14503 original size:16 final size:15

Alignment explanation


    Indices: 14474--14506  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 15

      14464 GACAGAAAGG

                           
      14474 AATTAAACAGAAAAC
          1 AATTAAACAGAAAAC

                            
      14489 AATTAAACTAGAAAAC
          1 AATTAAAC-AGAAAAC

              
      14505 AA
          1 AA

      14507 AGCAAAGTAA


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

Matches are distributed among these distances:
  15    8  0.47
  16    9  0.53

ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15


Consensus pattern (15 bp):   
AATTAAACAGAAAAC
Done.