Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015325.1 Corchorus olitorius cultivar O-4 contig15358, 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: 6592
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31


Found at i:3186 original size:16 final size:16

Alignment explanation


    Indices: 3161--3202  Score: 57
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       3151 TAAATAAAAT

                *           
       3161 ATTCTCTCTCTCTCAA
          1 ATTCCCTCTCTCTCAA

                 *        * 
       3177 ATTCCTTCTCTCTCCA
          1 ATTCCCTCTCTCTCAA

                      
       3193 ATTCCCTCTC
          1 ATTCCCTCTC

       3203 AACTTTTCTC


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43


Consensus pattern (16 bp):   
ATTCCCTCTCTCTCAA

Found at i:3430 original size:21 final size:21

Alignment explanation


    Indices: 3404--3516  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       3394 TGCTAGAAGT

                                 
       3404 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
       3425 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
       3446 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
       3467 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
       3488 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
       3509 TCATTGGA
          1 TCATTGGA

       3517 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   84  0.99

ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:3658 original size:20 final size:21

Alignment explanation


    Indices: 3630--3672  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3620 CATCTTGAAG

                                 
       3630 ATTTAAAG-CCATCGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

                *        *       
       3650 ATTTGAAGCCCATTGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

              
       3671 AT
          1 AT

       3673 CAACAAAGGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28


Consensus pattern (21 bp):   
ATTTAAAGCCCATCGGAGATC

Found at i:5439 original size:21 final size:21

Alignment explanation


    Indices: 5415--5481  Score: 89
    Period size: 21  Copynumber: 3.1  Consensus size: 21

       5405 GGCTTGGAAT

                *                
       5415 GGTGATGGCACGGGCATGGCC
          1 GGTGGTGGCACGGGCATGGCC

                           *  *  
       5436 GGTGGTGGCACGGGCTTGACC
          1 GGTGGTGGCACGGGCATGGCC

                           *      
       5457 GGTGGTGGCACGGTGAATGGCC
          1 GGTGGTGGCACGG-GCATGGCC

               
       5479 GGT
          1 GGT

       5482 AATGACTTAG


Statistics
Matches: 39,  Mismatches: 6, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  21   31  0.79
  22    8  0.21

ACGTcount: A:0.12, C:0.21, G:0.49, T:0.18


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCATGGCC
Done.