Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008264.1 Corchorus capsularis cultivar CVL-1 contig08285, 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: 45844
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:1974 original size:40 final size:40

Alignment explanation


    Indices: 1914--1992  Score: 131
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       1904 TTGACTCTCG

                           *                        
       1914 TAATAATTAAGAAAATAAATTAAATTCAGGTTTAGCCCCC
          1 TAATAATTAAGAAAAGAAATTAAATTCAGGTTTAGCCCCC

                       **                          
       1954 TAATAATTAAGGCAAGAAATTAAATTCAGGTTTAGCCCC
          1 TAATAATTAAGAAAAGAAATTAAATTCAGGTTTAGCCCC

       1993 TAGTTATAAA


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  40   36  1.00

ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29


Consensus pattern (40 bp):   
TAATAATTAAGAAAAGAAATTAAATTCAGGTTTAGCCCCC

Found at i:7191 original size:5 final size:5

Alignment explanation


    Indices: 7181--7214  Score: 68
    Period size: 5  Copynumber: 6.8  Consensus size: 5

       7171 TGACCCAATA

                                                    
       7181 AATTC AATTC AATTC AATTC AATTC AATTC AATT
          1 AATTC AATTC AATTC AATTC AATTC AATTC AATT

       7215 AAAAGAGTAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   29  1.00

ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41


Consensus pattern (5 bp):   
AATTC

Found at i:9555 original size:15 final size:16

Alignment explanation


    Indices: 9535--9568  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       9525 ATCTCTCAAT

                            
       9535 TTTGTTTCTGT-TTTG
          1 TTTGTTTCTGTGTTTG

                     *      
       9550 TTTGTTTCTTTGTTTG
          1 TTTGTTTCTGTGTTTG

               
       9566 TTT
          1 TTT

       9569 CCCCCTATAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15   10  0.59
  16    7  0.41

ACGTcount: A:0.00, C:0.06, G:0.18, T:0.76


Consensus pattern (16 bp):   
TTTGTTTCTGTGTTTG

Found at i:23479 original size:3 final size:3

Alignment explanation


    Indices: 23471--23497  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      23461 TTGATTACGA

                                               
      23471 AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT

      23498 GCAATGTATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:25493 original size:2 final size:2

Alignment explanation


    Indices: 25486--25518  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      25476 ATAATGGTTA

                                                             
      25486 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 A

      25519 GTGATATAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:25677 original size:3 final size:3

Alignment explanation


    Indices: 25669--25704  Score: 65
    Period size: 3  Copynumber: 12.3  Consensus size: 3

      25659 ATATGTGCTG

                                                             
      25669 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      25705 ATTTTGTAAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2    2  0.06
   3   30  0.94

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:31548 original size:16 final size:16

Alignment explanation


    Indices: 31529--31560  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      31519 ATTTTCATTC

                            
      31529 TCTGAAATTTTAAAGA
          1 TCTGAAATTTTAAAGA

                            
      31545 TCTGAAATTTTAAAGA
          1 TCTGAAATTTTAAAGA

      31561 AATCAAGTGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38


Consensus pattern (16 bp):   
TCTGAAATTTTAAAGA

Found at i:44509 original size:29 final size:30

Alignment explanation


    Indices: 44474--44534  Score: 90
    Period size: 29  Copynumber: 2.1  Consensus size: 30

      44464 ACTTATAGCG

                   *                       
      44474 TTTGGACGTTTTACC-CACTGAACT-TCAAT
          1 TTTGGACATTTTACCTC-CTGAACTCTCAAT

                                          
      44503 TTTGGACATTTTACCTCCTGAACTCTCAAT
          1 TTTGGACATTTTACCTCCTGAACTCTCAAT

              
      44533 TT
          1 TT

      44535 GAGCCTCCGT


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  29   21  0.72
  30    8  0.28

ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41


Consensus pattern (30 bp):   
TTTGGACATTTTACCTCCTGAACTCTCAAT

Done.