Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009636.1 Corchorus olitorius cultivar O-4 contig09668, 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: 7435
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32


Found at i:321 original size:2 final size:2

Alignment explanation


    Indices: 314--348  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

        304 GTTCCACTTG

                                                                
        314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        349 ATAAAACATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:6452 original size:11 final size:11

Alignment explanation


    Indices: 6436--6460  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       6426 GGAAATAATT

                       
       6436 TATTGTATTGC
          1 TATTGTATTGC

                       
       6447 TATTGTATTGC
          1 TATTGTATTGC

               
       6458 TAT
          1 TAT

       6461 ATATCTATGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56


Consensus pattern (11 bp):   
TATTGTATTGC

Found at i:6577 original size:27 final size:27

Alignment explanation


    Indices: 6547--6619  Score: 73
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       6537 ACTATAGTAC

                                        
       6547 TATACTATTATTATATAATAATA-ATAT
          1 TATACTATTATTATAT-ATAATATATAT

                      *                
       6574 TATACTA-TACTAT-TATAATATATAT
          1 TATACTATTATTATATATAATATATAT

                    *  *          
       6599 TATA-TATAATAATATTATAAT
          1 TATACTATTATTATA-TATAAT

       6620 TGGCTGCCAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  24    8  0.21
  25   12  0.32
  26    5  0.13
  27   13  0.34

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (27 bp):   
TATACTATTATTATATATAATATATAT

Found at i:6608 original size:40 final size:40

Alignment explanation


    Indices: 6531--6617  Score: 122
    Period size: 40  Copynumber: 2.2  Consensus size: 40

       6521 TGGAAATCCT

                 *      *       *                   
       6531 TATTAAACTATAGTACTATACTATTATTATATAATAATAA
          1 TATTATACTATACTACTATAATATTATTATATAATAATAA

                           *                         
       6571 TATTATACTATACTATTATAATATATATTATAT-ATAATAA
          1 TATTATACTATACTACTATAATAT-TATTATATAATAATAA

                   
       6611 TATTATA
          1 TATTATA

       6618 ATTGGCTGCC


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  40   34  0.81
  41    8  0.19

ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46


Consensus pattern (40 bp):   
TATTATACTATACTACTATAATATTATTATATAATAATAA
Done.