Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015423.1 Corchorus olitorius cultivar O-4 contig15456, 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: 40095
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:4828 original size:43 final size:41

Alignment explanation


    Indices: 4764--4859  Score: 106
    Period size: 40  Copynumber: 2.3  Consensus size: 41

       4754 TTTTAAGATG

                            **                         *
       4764 GTATAAGATA-TATATTTATTTTTTATAAAATAAAAAGGAATCT
          1 GTATAAGATAGTATATACA-TTTTTAT--AATAAAAAGGAATCA

                                       *     *       
       4807 GTATAAGATAGTAT-TACATTTTTATATTAAAAGGGAATCA
          1 GTATAAGATAGTATATACATTTTTATAATAAAAAGGAATCA

                         
       4847 GTATAAGATAGTA
          1 GTATAAGATAGTA

       4860 GTACTATGGT


Statistics
Matches: 47,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  40   25  0.53
  42    7  0.15
  43   12  0.26
  44    3  0.06

ACGTcount: A:0.45, C:0.03, G:0.14, T:0.39


Consensus pattern (41 bp):   
GTATAAGATAGTATATACATTTTTATAATAAAAAGGAATCA

Found at i:6280 original size:6 final size:6

Alignment explanation


    Indices: 6269--6296  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

       6259 AGTACTATAT

                                            
       6269 TCTAAA TCTAAA TCTAAA TCTAAA TCTA
          1 TCTAAA TCTAAA TCTAAA TCTAAA TCTA

       6297 GCTACAGTAC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36


Consensus pattern (6 bp):   
TCTAAA

Found at i:10869 original size:3 final size:3

Alignment explanation


    Indices: 10861--10888  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

      10851 TCATACAATT

                                                 
      10861 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      10889 GCAGATTAAT


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

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:22139 original size:13 final size:14

Alignment explanation


    Indices: 22110--22142  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

      22100 TCATTGTCTT

                          
      22110 AAGGAAAACAAAAA
          1 AAGGAAAACAAAAA

                      *   
      22124 AAGGAAAA-AGAAA
          1 AAGGAAAACAAAAA

                  
      22137 AAGGAA
          1 AAGGAA

      22143 TTCACCAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  13   10  0.56
  14    8  0.44

ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00


Consensus pattern (14 bp):   
AAGGAAAACAAAAA

Found at i:38495 original size:5 final size:5

Alignment explanation


    Indices: 38485--38510  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

      38475 ACAATCTAGG

                                           
      38485 ATTAA ATTAA ATTAA ATTAA ATTAA A
          1 ATTAA ATTAA ATTAA ATTAA ATTAA A

      38511 GACATTGATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (5 bp):   
ATTAA

Done.