Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011354.1 Corchorus olitorius cultivar O-4 contig11387, 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: 18081
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:2015 original size:20 final size:20

Alignment explanation


    Indices: 2000--2045  Score: 92
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       1990 TGCCCGGCCA

                                
       2000 CGGGTACCCCTACCCGCCCC
          1 CGGGTACCCCTACCCGCCCC

                                
       2020 CGGGTACCCCTACCCGCCCC
          1 CGGGTACCCCTACCCGCCCC

                  
       2040 CGGGTA
          1 CGGGTA

       2046 GCCTCAGAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   26  1.00

ACGTcount: A:0.11, C:0.54, G:0.24, T:0.11


Consensus pattern (20 bp):   
CGGGTACCCCTACCCGCCCC

Found at i:7075 original size:19 final size:18

Alignment explanation


    Indices: 7051--7086  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7041 TGAAGACTTA

                               
       7051 TTGAAGAGAATTTGAAGAT
          1 TTGAAGAGAA-TTGAAGAT

                   *         
       7070 TTGAAGATAATTGAAGA
          1 TTGAAGAGAATTGAAGA

       7087 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31


Consensus pattern (18 bp):   
TTGAAGAGAATTGAAGAT

Found at i:8383 original size:22 final size:22

Alignment explanation


    Indices: 8358--8399  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       8348 ATTCACTACT

                         *        
       8358 ATTTTATTAATTGTTTTCTTTA
          1 ATTTTATTAATTGCTTTCTTTA

                 *              
       8380 ATTTTCTTAATTGCTTTCTT
          1 ATTTTATTAATTGCTTTCTT

       8400 AGTTAATTTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67


Consensus pattern (22 bp):   
ATTTTATTAATTGCTTTCTTTA

Found at i:11513 original size:12 final size:12

Alignment explanation


    Indices: 11496--11522  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      11486 ATACTTTCAT

                        
      11496 AATTGTAATTTC
          1 AATTGTAATTTC

                        
      11508 AATTGTAATTTC
          1 AATTGTAATTTC

               
      11520 AAT
          1 AAT

      11523 AAAAATTAAA


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

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48


Consensus pattern (12 bp):   
AATTGTAATTTC

Found at i:15311 original size:40 final size:41

Alignment explanation


    Indices: 15262--15355  Score: 118
    Period size: 40  Copynumber: 2.3  Consensus size: 41

      15252 AGAAAAATAA

                                  * *                
      15262 GGACCAAATTGAATCAAATAGTGACTAGAATCCT-AATCAG
          1 GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG

                *      *        *                 *  
      15302 GGACTAAATTGTATCAAATATTAAATAGAATCCTAAATTAG
          1 GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG

                  *      
      15343 GGACCATATTGAA
          1 GGACCAAATTGAA

      15356 CATGGAAATA


Statistics
Matches: 44,  Mismatches: 9, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  40   29  0.66
  41   15  0.34

ACGTcount: A:0.44, C:0.14, G:0.16, T:0.27


Consensus pattern (41 bp):   
GGACCAAATTGAATCAAATAGTAAATAGAATCCTAAATCAG

Found at i:17667 original size:22 final size:22

Alignment explanation


    Indices: 17642--17691  Score: 91
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      17632 AAAAGGATGG

                                  
      17642 ATGCAAAAGATACCATGCAAAA
          1 ATGCAAAAGATACCATGCAAAA

                       *          
      17664 ATGCAAAAGATGCCATGCAAAA
          1 ATGCAAAAGATACCATGCAAAA

                  
      17686 ATGCAA
          1 ATGCAA

      17692 CTATTAAACT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14


Consensus pattern (22 bp):   
ATGCAAAAGATACCATGCAAAA
Done.