Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009993.1 Corchorus olitorius cultivar O-4 contig10025, 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: 3460
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36


Found at i:420 original size:17 final size:17

Alignment explanation


    Indices: 393--443  Score: 68
    Period size: 17  Copynumber: 2.9  Consensus size: 17

        383 ATAATCTTCT

                              
        393 TTTTCTTTTTCTTTTTTC
          1 TTTT-TTTTTCTTTTTTC

                           * 
        411 TTTTTTTTTCTTTTTCC
          1 TTTTTTTTTCTTTTTTC

                             
        428 TTTTTTTCTT-TTTTTT
          1 TTTTTTT-TTCTTTTTT

        444 TATTCACATC


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  17   24  0.80
  18    6  0.20

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (17 bp):   
TTTTTTTTTCTTTTTTC

Found at i:422 original size:23 final size:25

Alignment explanation


    Indices: 392--444  Score: 92
    Period size: 25  Copynumber: 2.2  Consensus size: 25

        382 AATAATCTTC

                                     
        392 TTTTTCTTTTT-C-TTTTTTCTTTT
          1 TTTTTCTTTTTCCTTTTTTTCTTTT

                                     
        415 TTTTTCTTTTTCCTTTTTTTCTTTT
          1 TTTTTCTTTTTCCTTTTTTTCTTTT

                 
        440 TTTTT
          1 TTTTT

        445 ATTCACATCT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  23   11  0.39
  24    1  0.04
  25   16  0.57

ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87


Consensus pattern (25 bp):   
TTTTTCTTTTTCCTTTTTTTCTTTT

Found at i:440 original size:6 final size:6

Alignment explanation


    Indices: 389--432  Score: 56
    Period size: 6  Copynumber: 7.3  Consensus size: 6

        379 AAGAATAATC

                                                                 
        389 TTCTTT TTCTTT TTCTTT TT-TCTT TT-TTT TTCTTT TTCCTTT TT
          1 TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT TTCTTT TT-CTTT TT

        433 TTCTTTTTTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
   5    5  0.14
   6   24  0.69
   7    6  0.17

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (6 bp):   
TTCTTT

Found at i:751 original size:14 final size:13

Alignment explanation


    Indices: 686--750  Score: 87
    Period size: 14  Copynumber: 4.8  Consensus size: 13

        676 ACTTAAAACC

                          
        686 TTTTTGAAAACTCA
          1 TTTTTGAAAA-TCA

                         
        700 TTTTTGAAAATCA
          1 TTTTTGAAAATCA

                          
        713 TTTCTTGAAAA-CA
          1 TTT-TTGAAAATCA

                           
        726 GTTTCTTGAAAATCA
          1 -TTT-TTGAAAATCA

                      
        741 TTTTTGAAAA
          1 TTTTTGAAAA

        751 ACGTCCTTTA


Statistics
Matches: 48,  Mismatches: 0, Indels: 7
        0.87            0.00        0.13

Matches are distributed among these distances:
  13   15  0.31
  14   31  0.65
  15    2  0.04

ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43


Consensus pattern (13 bp):   
TTTTTGAAAATCA

Done.