Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011361.1 Corchorus olitorius cultivar O-4 contig11394, 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: 4713
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:3253 original size:21 final size:21

Alignment explanation


    Indices: 3186--3263  Score: 77
    Period size: 22  Copynumber: 3.6  Consensus size: 21

       3176 TTTTGATAGT

                                *  
       3186 TATGAAATTTT-ATTAACCTACC
          1 TATGAAATTTTGATT-ACC-CCC

              *               * * 
       3208 TAAGAAATTTTGATTTACACAC
          1 TATGAAATTTTGA-TTACCCCC

                                 
       3230 TATGAAATTTTGATTACCCCC
          1 TATGAAATTTTGATTACCCCC

                   *     
       3251 TATGAAAATTTGA
          1 TATGAAATTTTGA

       3264 AAACTAAACT


Statistics
Matches: 46,  Mismatches: 8, Indels: 5
        0.78            0.14        0.08

Matches are distributed among these distances:
  21   18  0.39
  22   23  0.50
  23    3  0.07
  24    2  0.04

ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38


Consensus pattern (21 bp):   
TATGAAATTTTGATTACCCCC

Found at i:3260 original size:44 final size:45

Alignment explanation


    Indices: 3186--3311  Score: 118
    Period size: 43  Copynumber: 2.8  Consensus size: 45

       3176 TTTTGATAGT

                                     *            **    *  
       3186 TATGAAATTTT-ATTAACCTACCTAAG-AAATTTTGATTTAC-ACAC
          1 TATGAAATTTTGATT-ACC-ACCTATGAAAATTTTGATAAACTAAAC

                              *                          
       3230 TATGAAATTTTGATTACCCCCTATGAAAA-TTTGA-AAACTAAAC
          1 TATGAAATTTTGATTACCACCTATGAAAATTTTGATAAACTAAAC

                *          *  *                    
       3273 TATGGAATTTTGATTTCCTCCTCATGAAAATTTTGATAA
          1 TATGAAATTTTGATTACCACCT-ATGAAAATTTTGATAA

       3312 TGTTTATAGA


Statistics
Matches: 68,  Mismatches: 8, Indels: 10
        0.79            0.09        0.12

Matches are distributed among these distances:
  42    2  0.03
  43   32  0.47
  44   24  0.35
  45    8  0.12
  46    2  0.03

ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38


Consensus pattern (45 bp):   
TATGAAATTTTGATTACCACCTATGAAAATTTTGATAAACTAAAC

Found at i:4134 original size:21 final size:21

Alignment explanation


    Indices: 4086--4134  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       4076 GTGAACAATA

                           *     
       4086 AAATAAA-TAAACAAGAAAAT
          1 AAATAAATTAAACAACAAAAT

                        *         
       4106 -AATAAAATTAAGCAACAAAAT
          1 AAAT-AAATTAAACAACAAAAT

                    
       4127 AAATAAAT
          1 AAATAAAT

       4135 ACTCCAATCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  19    3  0.12
  20    3  0.12
  21   15  0.62
  22    3  0.12

ACGTcount: A:0.71, C:0.06, G:0.04, T:0.18


Consensus pattern (21 bp):   
AAATAAATTAAACAACAAAAT
Done.