Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019432.1 Corchorus olitorius cultivar O-4 contig19465, 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: 9308
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:5776 original size:27 final size:27

Alignment explanation


    Indices: 5746--5802  Score: 71
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       5736 AAATCAACAT

                                        
       5746 TTTCAACAC-CTAAGGGTAAAATAGTAA
          1 TTTC-ACACGCTAAGGGTAAAATAGTAA

                * *               *    
       5773 TTTCCCGCGCTAAGGGTAAAATGGTAA
          1 TTTCACACGCTAAGGGTAAAATAGTAA

               
       5800 TTT
          1 TTT

       5803 AACTTATATT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  26    2  0.08
  27   24  0.92

ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30


Consensus pattern (27 bp):   
TTTCACACGCTAAGGGTAAAATAGTAA

Found at i:8160 original size:16 final size:15

Alignment explanation


    Indices: 8139--8184  Score: 58
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       8129 TTACTTTGCT

                        *   
       8139 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTATAA

                           
       8155 TTGTTTTCTGTATAA
          1 TTGTTTTCTGTATAA

               *           
       8170 TTGCTTTCTGT-TAA
          1 TTGTTTTCTGTATAA

             
       8184 T
          1 T

       8185 CTCTGTTTTC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  14    4  0.14
  15   15  0.54
  16    9  0.32

ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61


Consensus pattern (15 bp):   
TTGTTTTCTGTATAA

Found at i:9278 original size:2 final size:2

Alignment explanation


    Indices: 9271--9308  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       9261 ACAAGTCCAA

                                                                    
       9271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.