Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017093.1 Corchorus olitorius cultivar O-4 contig17126, 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: 6314
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35


Found at i:410 original size:18 final size:20

Alignment explanation


    Indices: 362--410  Score: 57
    Period size: 21  Copynumber: 2.5  Consensus size: 20

        352 TTCACATCTA

                     *          
        362 ATAAGATTACTAAAAAAACT
          1 ATAAGATTATTAAAAAAACT

                  *              
        382 ATAGAGGTTATTAAAAAAA-T
          1 ATA-AGATTATTAAAAAAACT

                      
        402 -TAAGATTAT
          1 ATAAGATTAT

        411 AACTTCAACG


Statistics
Matches: 25,  Mismatches: 3, Indels: 4
        0.78            0.09        0.12

Matches are distributed among these distances:
  18    6  0.24
  19    2  0.08
  20    4  0.16
  21   13  0.52

ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31


Consensus pattern (20 bp):   
ATAAGATTATTAAAAAAACT

Found at i:1303 original size:18 final size:17

Alignment explanation


    Indices: 1269--1302  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1259 TATAAAACTA

                             
       1269 AATGTTACCATTTTTTT
          1 AATGTTACCATTTTTTT

                             
       1286 AATGTTACCATTTTTTT
          1 AATGTTACCATTTTTTT

       1303 TTTAGGAGGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59


Consensus pattern (17 bp):   
AATGTTACCATTTTTTT

Found at i:2361 original size:18 final size:18

Alignment explanation


    Indices: 2326--2362  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2316 TAATTAAAAT

                         *    
       2326 TTAAAATTTCCAACTTAA
          1 TTAAAATTTCCAAATTAA

                      *       
       2344 TTAAAATTTCTAAATTAA
          1 TTAAAATTTCCAAATTAA

             
       2362 T
          1 T

       2363 ATAGAGGTGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43


Consensus pattern (18 bp):   
TTAAAATTTCCAAATTAA
Done.