Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002123.1 Corchorus capsularis cultivar CVL-1 contig02127, 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, 887

Length: 1479
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27


Found at i:1067 original size:6 final size:6

Alignment explanation


    Indices: 1056--1118  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

       1046 GGGATCACTA

                                          *      *                 
       1056 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                   *              
       1100 ACTAAT TCTAAT ACTAAT A
          1 ACTAAT ACTAAT ACTAAT A

       1119 GAATAGAAAA


Statistics
Matches: 50,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
   5   19  0.38
   6   31  0.62

ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33


Consensus pattern (6 bp):   
ACTAAT

Found at i:1073 original size:11 final size:11

Alignment explanation


    Indices: 1052--1117  Score: 62
    Period size: 11  Copynumber: 5.5  Consensus size: 11

       1042 AGCCGGGATC

                       
       1052 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
       1062 ACTAATCTAAT
          1 ACTAATCTAAT

                     *      
       1073 ACTAATAGAATAGAAT
          1 ACTAAT---CT--AAT

                       
       1089 ACTAATCTAAT
          1 ACTAATCTAAT

                        
       1100 ACTAATTCTAAT
          1 ACTAA-TCTAAT

                  
       1112 ACTAAT
          1 ACTAAT

       1118 AGAATAGAAA


Statistics
Matches: 47,  Mismatches: 2, Indels: 13
        0.76            0.03        0.21

Matches are distributed among these distances:
  10    5  0.11
  11   20  0.43
  12   11  0.23
  13    1  0.02
  14    1  0.02
  16    9  0.19

ACGTcount: A:0.48, C:0.15, G:0.03, T:0.33


Consensus pattern (11 bp):   
ACTAATCTAAT

Found at i:1116 original size:39 final size:37

Alignment explanation


    Indices: 1052--1126  Score: 132
    Period size: 39  Copynumber: 2.0  Consensus size: 37

       1042 AGCCGGGATC

                                                 
       1052 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
          1 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

                                                  
       1089 ACTAATCTAATACTAATTCTAATACTAATAGAATAGAA
          1 ACTAA-CTAATACTAA-TCTAATACTAATAGAATAGAA

       1127 AAAATAGAAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  37    5  0.14
  38   10  0.28
  39   21  0.58

ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31


Consensus pattern (37 bp):   
ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

Found at i:1134 original size:14 final size:14

Alignment explanation


    Indices: 1115--1142  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1105 TTCTAATACT

                          
       1115 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

                          
       1129 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

       1143 TACTAATAGA


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATAGAATAGAAAA

Found at i:1152 original size:18 final size:18

Alignment explanation


    Indices: 1109--1159  Score: 74
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       1099 TACTAATTCT

                              
       1109 AATACTAATAGAATAG-A
          1 AATACTAATAGAATAGAA

                              
       1126 AA-A--AATAGAATAGAA
          1 AATACTAATAGAATAGAA

                              
       1141 AATACTAATAGAATAGAA
          1 AATACTAATAGAATAGAA

             
       1159 A
          1 A

       1160 GAAAAGAACT


Statistics
Matches: 30,  Mismatches: 0, Indels: 7
        0.81            0.00        0.19

Matches are distributed among these distances:
  14   10  0.33
  15    3  0.10
  16    2  0.07
  17    2  0.07
  18   13  0.43

ACGTcount: A:0.65, C:0.04, G:0.12, T:0.20


Consensus pattern (18 bp):   
AATACTAATAGAATAGAA
Done.