Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019982.1 Corchorus olitorius cultivar O-4 contig20015, 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: 5262
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33


Found at i:545 original size:21 final size:21

Alignment explanation


    Indices: 519--652  Score: 184
    Period size: 21  Copynumber: 6.4  Consensus size: 21

        509 TGCTAGAAGT

                                  
        519 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
        540 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                *                 
        561 TCATCGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        582 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        603 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
        624 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        645 TCATTGGA
          1 TCATTGGA

        653 ATTGCCTAAG


Statistics
Matches: 106,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  104  0.98

ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:2537 original size:15 final size:15

Alignment explanation


    Indices: 2517--2548  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2507 CCTTGGGGGT

                           
       2517 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

                           
       2532 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

              
       2547 TC
          1 TC

       2549 CACTTAGTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16


Consensus pattern (15 bp):   
TCAAAATCAACAAGC

Found at i:3270 original size:33 final size:33

Alignment explanation


    Indices: 3164--3306  Score: 139
    Period size: 33  Copynumber: 4.3  Consensus size: 33

       3154 CAATGACATG

                         *       *       *   
       3164 AAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AAATCTGTTTTAGGTGTTGTTTGTGATGAAACT

               *  **    *                *   
       3197 AAACCTAATTTAAGTGTTGTTTGTGATGACACT
          1 AAATCTGTTTTAGGTGTTGTTTGTGATGAAACT

                                             
       3230 AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-
          1 AAATCTGTTTTAGGTGTTGTTTGTGATGAAACT

                              * **              
       3262 AAATTCTGTTTT-GGATGCTAATTGTGATGAAAAC-
          1 AAA-TCTGTTTTAGG-TGTTGTTTGTGATG-AAACT

                       
       3296 AAATCTGTTTT
          1 AAATCTGTTTT

       3307 GGTTGATCAT


Statistics
Matches: 92,  Mismatches: 15, Indels: 6
        0.81            0.13        0.05

Matches are distributed among these distances:
  32    5  0.05
  33   80  0.87
  34    7  0.08

ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43


Consensus pattern (33 bp):   
AAATCTGTTTTAGGTGTTGTTTGTGATGAAACT

Found at i:5181 original size:21 final size:21

Alignment explanation


    Indices: 5142--5184  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5132 GGAGTTACCT

                       *  *      
       5142 AAGATGCCATTTGATCCATTG
          1 AAGATGCCATTAGACCCATTG

                         *       
       5163 AAGATGCCATTAGGCCCATTG
          1 AAGATGCCATTAGACCCATTG

             
       5184 A
          1 A

       5185 CAAGGGCAAG


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28


Consensus pattern (21 bp):   
AAGATGCCATTAGACCCATTG
Done.