Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009613.1 Corchorus capsularis cultivar CVL-1 contig09634, 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: 20437
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:362 original size:195 final size:196

Alignment explanation


    Indices: 1--399  Score: 739
    Period size: 195  Copynumber: 2.0  Consensus size: 196

                                                           **                
          1 TATTTTTACTTGATAAATTTCTTTCGGCTTAATGCCCAAAATCCCCCTTGAAGTATCACAAAAAG
          1 TATTTTTACTTGATAAATTTCTTTCGGCTTAATGCCCAAAATCCCCCCAGAAGTATCACAAAAAG

                                                                             
         66 GACACTTTGCCCCCTAATCTTTTTTTTTGTCCAACTTTGCCCCCTGAGGTATGAAATAAGGACAC
         66 GACACTTTGCCCCCTAA--TTTTTTTTTGTCCAACTTTGCCCCCTGAGGTATGAAATAAGGACAC

                                                                             
        131 TTTGCCCCCTGCCGTAACAGAATTCAGTCATGTGCGTGCACATGAATAACGGGTCTGTTAACTCG
        129 TTTGCCCCCTGCCGTAACAGAATTCAGTCATGTGCGTGCACATGAATAACGGGTCTGTTAACTCG

               
        196 AGG
        194 AGG

                                                                             
        199 TATTTTTACTTGATAAATTTCTTTCGGCTTAATGCCCAAAATCCCCCCAGAAGTATCACAAAAAG
          1 TATTTTTACTTGATAAATTTCTTTCGGCTTAATGCCCAAAATCCCCCCAGAAGTATCACAAAAAG

                                                                          *  
        264 GACACTTTGCCCCCTAA-TTTTTTTTGTCCAACTTTGCCCCCTGAGGTATGAAATAAGGACATTT
         66 GACACTTTGCCCCCTAATTTTTTTTTGTCCAACTTTGCCCCCTGAGGTATGAAATAAGGACACTT

                                                                             
        328 TGCCCCCTGCCGTAACAGAATTCAGTCATGTGCGTGCACATGAATAACGGGTCTGTTAACTCGAG
        131 TGCCCCCTGCCGTAACAGAATTCAGTCATGTGCGTGCACATGAATAACGGGTCTGTTAACTCGAG

             
        393 G
        196 G

                   
        394 T-TTTTT
          1 TATTTTT

        400 GCTGATGTGA


Statistics
Matches: 198,  Mismatches: 3, Indels: 4
        0.97            0.01        0.02

Matches are distributed among these distances:
 194    5  0.03
 195  113  0.57
 198   80  0.40

ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32


Consensus pattern (196 bp):   
TATTTTTACTTGATAAATTTCTTTCGGCTTAATGCCCAAAATCCCCCCAGAAGTATCACAAAAAG
GACACTTTGCCCCCTAATTTTTTTTTGTCCAACTTTGCCCCCTGAGGTATGAAATAAGGACACTT
TGCCCCCTGCCGTAACAGAATTCAGTCATGTGCGTGCACATGAATAACGGGTCTGTTAACTCGAG
G

Found at i:3989 original size:26 final size:27

Alignment explanation


    Indices: 3951--4001  Score: 95
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       3941 CTGGATCTGC

                                       
       3951 ATTATTATATTCATATCTAATCTAACT
          1 ATTATTATATTCATATCTAATCTAACT

                                     
       3978 ATTA-TATATTCATATCTAATCTAA
          1 ATTATTATATTCATATCTAATCTAA

       4002 TCTAACTTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  26   20  0.83
  27    4  0.17

ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47


Consensus pattern (27 bp):   
ATTATTATATTCATATCTAATCTAACT

Found at i:7184 original size:15 final size:15

Alignment explanation


    Indices: 7161--7192  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       7151 ACTTGACTTG

                *          
       7161 ATAATAATAATTATT
          1 ATAAAAATAATTATT

                           
       7176 ATAAAAATAATTATT
          1 ATAAAAATAATTATT

              
       7191 AT
          1 AT

       7193 TGGCCCTTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (15 bp):   
ATAAAAATAATTATT

Found at i:14382 original size:17 final size:17

Alignment explanation


    Indices: 14362--14394  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      14352 GCAGCCTATC

                             
      14362 ACCTCATACTACCTAGT
          1 ACCTCATACTACCTAGT

                            
      14379 ACCTCATACTACCTAG
          1 ACCTCATACTACCTAG

      14395 GTACTATGAG


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27


Consensus pattern (17 bp):   
ACCTCATACTACCTAGT
Done.