Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000990.1 Corchorus capsularis cultivar CVL-1 contig00990, 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: 9781
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:370 original size:15 final size:17

Alignment explanation


    Indices: 338--377  Score: 50
    Period size: 15  Copynumber: 2.5  Consensus size: 17

        328 AACTACTTCA

                         *   
        338 AATATATATATTATTAT
          1 AATATATATATTAATAT

                             
        355 AATATA-ATA-TAATAT
          1 AATATATATATTAATAT

                     
        370 AATA-ATAT
          1 AATATATAT

        378 GGAAAAAACG


Statistics
Matches: 21,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  14    1  0.05
  15   11  0.52
  16    3  0.14
  17    6  0.29

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (17 bp):   
AATATATATATTAATAT

Found at i:3670 original size:14 final size:14

Alignment explanation


    Indices: 3651--3695  Score: 65
    Period size: 14  Copynumber: 3.3  Consensus size: 14

       3641 AGCTGGTTAG

                   *      
       3651 TCTCTTTTTTTCTT
          1 TCTCTTTCTTTCTT

                          
       3665 TCTC-TTCTTTCTT
          1 TCTCTTTCTTTCTT

                         *
       3678 TCTCTTTCTTTCTC
          1 TCTCTTTCTTTCTT

                
       3692 TCTC
          1 TCTC

       3696 AAATCTGAAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  13   12  0.43
  14   16  0.57

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (14 bp):   
TCTCTTTCTTTCTT

Found at i:7545 original size:13 final size:13

Alignment explanation


    Indices: 7527--7551  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7517 AAAGATTTTA

                         
       7527 AGGTCATAATTAT
          1 AGGTCATAATTAT

                        
       7540 AGGTCATAATTA
          1 AGGTCATAATTA

       7552 ATTATATGGT


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:0.40, C:0.08, G:0.16, T:0.36


Consensus pattern (13 bp):   
AGGTCATAATTAT

Found at i:9749 original size:25 final size:27

Alignment explanation


    Indices: 9697--9749  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       9687 TTACTCAACT

                                **     
       9697 AAAAACTCTATTTTTATTTTTCTGTAA
          1 AAAAACTCTATTTTTATTTTAATGTAA

                                       
       9724 AAAAACTCTATTTTTA-TTTAAT-TAA
          1 AAAAACTCTATTTTTATTTTAATGTAA

             
       9749 A
          1 A

       9750 TCTAATATCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  25    4  0.17
  26    4  0.17
  27   16  0.67

ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49


Consensus pattern (27 bp):   
AAAAACTCTATTTTTATTTTAATGTAA
Done.