Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001950.1 Corchorus capsularis cultivar CVL-1 contig01952, 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, 650

Length: 1084
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34


Found at i:317 original size:14 final size:13

Alignment explanation


    Indices: 289--313  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        279 AAAGTGATAC

                         
        289 AATACAAAAATAG
          1 AATACAAAAATAG

                        
        302 AATACAAAAATA
          1 AATACAAAAATA

        314 AGAACCGAGT


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:0.72, C:0.08, G:0.04, T:0.16


Consensus pattern (13 bp):   
AATACAAAAATAG

Found at i:371 original size:17 final size:17

Alignment explanation


    Indices: 337--371  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        327 TTGTTTTTGT

                         *   
        337 AGTCTATCTAAAAGAAA
          1 AGTCTATCTAAAAAAAA

                             
        354 AGTCTATCTAAAAAAAA
          1 AGTCTATCTAAAAAAAA

             
        371 A
          1 A

        372 ATAGGAGATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23


Consensus pattern (17 bp):   
AGTCTATCTAAAAAAAA

Found at i:987 original size:13 final size:12

Alignment explanation


    Indices: 969--1020  Score: 59
    Period size: 12  Copynumber: 4.1  Consensus size: 12

        959 GCTGACAAAT

                         
        969 TACAATTATACAA
          1 TACAATTATA-AA

                       *
        982 TACAATTATAAG
          1 TACAATTATAAA

                    *     
        994 TACAATTACAATTA
          1 TACAATTATAA--A

                        
       1008 TACAATTATAAA
          1 TACAATTATAAA

             
       1020 T
          1 T

       1021 TATATATAAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 5
        0.79            0.10        0.12

Matches are distributed among these distances:
  12   13  0.39
  13   10  0.30
  14   10  0.30

ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35


Consensus pattern (12 bp):   
TACAATTATAAA

Found at i:999 original size:12 final size:13

Alignment explanation


    Indices: 969--1001  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

        959 GCTGACAAAT

                         
        969 TACAATTATACAA
          1 TACAATTATACAA

                        *
        982 TACAATTATA-AG
          1 TACAATTATACAA

                    
        994 TACAATTA
          1 TACAATTA

       1002 CAATTATACA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  12    9  0.47
  13   10  0.53

ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33


Consensus pattern (13 bp):   
TACAATTATACAA

Found at i:1030 original size:11 final size:11

Alignment explanation


    Indices: 1014--1038  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       1004 ATTATACAAT

                       
       1014 TATAAATTATA
          1 TATAAATTATA

                       
       1025 TATAAATTATA
          1 TATAAATTATA

               
       1036 TAT
          1 TAT

       1039 TTTTTTTATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

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


Consensus pattern (11 bp):   
TATAAATTATA

Found at i:1078 original size:14 final size:12

Alignment explanation


    Indices: 1043--1084  Score: 50
    Period size: 11  Copynumber: 3.4  Consensus size: 12

       1033 ATATATTTTT

                  *     
       1043 TTTATTCTATTA
          1 TTTATTATATTA

                        
       1055 TTTA-TATATTA
          1 TTTATTATATTA

                          
       1066 TTTATTTAGTATTA
          1 TTTA-TTA-TATTA

                 
       1080 TTTAT
          1 TTTAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  11   10  0.38
  12    4  0.15
  13    3  0.12
  14    9  0.35

ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67


Consensus pattern (12 bp):   
TTTATTATATTA
Done.