Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009936.1 Corchorus capsularis cultivar CVL-1 contig09957, 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: 30652
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1710 original size:2 final size:2

Alignment explanation


    Indices: 1703--1733  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       1693 TCCCTTATTT

                                                           
       1703 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1734 AGTACTCTAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:4569 original size:13 final size:13

Alignment explanation


    Indices: 4551--4575  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       4541 TGACATATCA

                         
       4551 ACTTTTTTTTTTC
          1 ACTTTTTTTTTTC

                        
       4564 ACTTTTTTTTTT
          1 ACTTTTTTTTTT

       4576 GTCATTGTTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80


Consensus pattern (13 bp):   
ACTTTTTTTTTTC

Found at i:7416 original size:31 final size:31

Alignment explanation


    Indices: 7356--7450  Score: 91
    Period size: 31  Copynumber: 3.1  Consensus size: 31

       7346 TCGTGCCATA

                 *               ** *      
       7356 TGTACAAAAAAGTGACACATGTTACGCCACG
          1 TGTACCAAAAAGTGACACATGACATGCCACG

                                          *
       7387 TGTACCAAAAAGTGACACATGACATGCCACA
          1 TGTACCAAAAAGTGACACATGACATGCCACG

               **      *  *   *  *         
       7418 TGTTTCAAAAAATGGCACGTGGCATGCCACG
          1 TGTACCAAAAAGTGACACATGACATGCCACG

              
       7449 TG
          1 TG

       7451 CACAAAAGGA


Statistics
Matches: 52,  Mismatches: 12, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  31   52  1.00

ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20


Consensus pattern (31 bp):   
TGTACCAAAAAGTGACACATGACATGCCACG

Found at i:15960 original size:39 final size:39

Alignment explanation


    Indices: 15906--15986  Score: 162
    Period size: 39  Copynumber: 2.1  Consensus size: 39

      15896 ACTTCCAGGT

                                                   
      15906 GAAGCATGAACTTGGTGGGTAATTAGAGCTGAATGTTTG
          1 GAAGCATGAACTTGGTGGGTAATTAGAGCTGAATGTTTG

                                                   
      15945 GAAGCATGAACTTGGTGGGTAATTAGAGCTGAATGTTTG
          1 GAAGCATGAACTTGGTGGGTAATTAGAGCTGAATGTTTG

               
      15984 GAA
          1 GAA

      15987 TTCTTACAGA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   42  1.00

ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30


Consensus pattern (39 bp):   
GAAGCATGAACTTGGTGGGTAATTAGAGCTGAATGTTTG

Found at i:20309 original size:30 final size:30

Alignment explanation


    Indices: 20249--20342  Score: 93
    Period size: 30  Copynumber: 3.0  Consensus size: 30

      20239 GATCAATTTA

                *                            
      20249 ATCCTTGTACTTACAAGATATTGGGTCAATTGG
          1 ATCCATGTACTTACAAG--ATTGGGTCAATT-G

                                 *        
      20282 ATCCATGTAC-TACAAGATTGTGTCAATTG
          1 ATCCATGTACTTACAAGATTGGGTCAATTG

                *        *                  
      20311 ACTCTATGTACTTTCAAGATTGGG-CTAATTG
          1 A-TCCATGTACTTACAAGATTGGGTC-AATTG

             
      20342 A
          1 A

      20343 GTCCTTATTG


Statistics
Matches: 53,  Mismatches: 5, Indels: 8
        0.80            0.08        0.12

Matches are distributed among these distances:
  29    2  0.04
  30   20  0.38
  31   16  0.30
  32    6  0.11
  33    9  0.17

ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Consensus pattern (30 bp):   
ATCCATGTACTTACAAGATTGGGTCAATTG

Found at i:28015 original size:2 final size:2

Alignment explanation


    Indices: 28008--28035  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      27998 GAATTCATTC

                                                     
      28008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      28036 TTCCAATTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.