Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018662.1 Corchorus olitorius cultivar O-4 contig18695, 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: 37203
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:6403 original size:15 final size:15

Alignment explanation


    Indices: 6354--6413  Score: 61
    Period size: 15  Copynumber: 4.1  Consensus size: 15

       6344 GGCACATGTG

                 *         
       6354 TAATTTTTAA-TAA-
          1 TAATTATTAATTAAT

                        *  *
       6367 TAATTATTCAATAAAA
          1 TAATTATT-AATTAAT

                     *     
       6383 TAATTATTATTTAAT
          1 TAATTATTAATTAAT

                           
       6398 TAATTATTAATTAAT
          1 TAATTATTAATTAAT

             
       6413 T
          1 T

       6414 TCAGCCCTTG


Statistics
Matches: 38,  Mismatches: 6, Indels: 4
        0.79            0.12        0.08

Matches are distributed among these distances:
  13    7  0.18
  14    2  0.05
  15   21  0.55
  16    8  0.21

ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52


Consensus pattern (15 bp):   
TAATTATTAATTAAT

Found at i:8151 original size:24 final size:24

Alignment explanation


    Indices: 8119--8167  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       8109 TTTACAAAAC

                                    
       8119 TTGCACTTTTATATAAATTATATA
          1 TTGCACTTTTATATAAATTATATA

                                    
       8143 TTGCACTTTTATATAAATTATATA
          1 TTGCACTTTTATATAAATTATATA

             
       8167 T
          1 T

       8168 ATAGTATAGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51


Consensus pattern (24 bp):   
TTGCACTTTTATATAAATTATATA

Found at i:8469 original size:24 final size:24

Alignment explanation


    Indices: 8429--8484  Score: 98
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       8419 AACATCAATC

                                    
       8429 AATTCAAG--TGTGGTTGATTTTT
          1 AATTCAAGTTTGTGGTTGATTTTT

                                    
       8451 AATTCAAGTTTGTGGTTGATTTTT
          1 AATTCAAGTTTGTGGTTGATTTTT

                      
       8475 AATTCAAGTT
          1 AATTCAAGTT

       8485 GGATGAAAAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  22    8  0.25
  24   24  0.75

ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50


Consensus pattern (24 bp):   
AATTCAAGTTTGTGGTTGATTTTT

Found at i:18020 original size:3 final size:3

Alignment explanation


    Indices: 18012--18079  Score: 118
    Period size: 3  Copynumber: 22.7  Consensus size: 3

      18002 TTTGGTGGCT

                                                                           
      18012 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

             *                  *     
      18060 TCA TTA TTA TTA TTA CTA TT
          1 TTA TTA TTA TTA TTA TTA TT

      18080 CATTTCTGTC


Statistics
Matches: 61,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   61  1.00

ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65


Consensus pattern (3 bp):   
TTA

Found at i:34224 original size:63 final size:63

Alignment explanation


    Indices: 34095--34231  Score: 150
    Period size: 63  Copynumber: 2.2  Consensus size: 63

      34085 CTAGTATTAT

                  *               *        *    *    * *         *    *    
      34095 AAGAAGCAGAACCGGAATAACCGTAACCGAAGCCACTGTTGTTTTTACTATAATGTTGGTGAG
          1 AAGAAGAAGAACCGGAATAACCATAACCGAAACCACGGTTGGTGTTACTATAACGTTGCTGAG

                                               *           *  *           * 
      34158 AAGAAGAAGAACCGGAATAACCATAACC-ATAACCCCGGTTGGTGTTGCTGTAACGTTGCTGGG
          1 AAGAAGAAGAACCGGAATAACCATAACCGA-AACCACGGTTGGTGTTACTATAACGTTGCTGAG

                       
      34221 AAGAAGAAGAA
          1 AAGAAGAAGAA

      34232 GAAGAAGAAG


Statistics
Matches: 61,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  62    1  0.02
  63   60  0.98

ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21


Consensus pattern (63 bp):   
AAGAAGAAGAACCGGAATAACCATAACCGAAACCACGGTTGGTGTTACTATAACGTTGCTGAG

Found at i:36640 original size:25 final size:24

Alignment explanation


    Indices: 36612--36673  Score: 81
    Period size: 25  Copynumber: 2.6  Consensus size: 24

      36602 GTGGATTGTA

                        *            
      36612 AAATAAATTGAATAATTAAGACATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
      36637 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     *    
      36661 AAA-AAATTCAAGA
          1 AAATAAATTGAAGA

      36674 CTGACCCAAT


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  23    9  0.26
  24    8  0.24
  25   17  0.50

ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT
Done.