Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012871.1 Corchorus capsularis cultivar CVL-1 contig12892, 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: 24876
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:1001 original size:17 final size:17

Alignment explanation


    Indices: 979--1013  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        969 GGTTACTAAC

                             
        979 GTTTACCTTTAAACTAT
          1 GTTTACCTTTAAACTAT

                             
        996 GTTTACCTTTAAACTAT
          1 GTTTACCTTTAAACTAT

             
       1013 G
          1 G

       1014 CCTAACGTTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46


Consensus pattern (17 bp):   
GTTTACCTTTAAACTAT

Found at i:1860 original size:27 final size:27

Alignment explanation


    Indices: 1809--1860  Score: 63
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       1799 TAACTATGAA

                                *      
       1809 AAATGACTGATGAATGTCGCTATATTG
          1 AAATGACTGATGAATGTCGCGATATTG

                                       
       1836 AAATGA-TGAATGAATG-CTGCGATAT
          1 AAATGACTG-ATGAATGTC-GCGATAT

       1861 GTTGTGCCTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  26    3  0.14
  27   19  0.86

ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31


Consensus pattern (27 bp):   
AAATGACTGATGAATGTCGCGATATTG

Found at i:2964 original size:59 final size:59

Alignment explanation


    Indices: 2892--3011  Score: 222
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       2882 AAGGACTTAA

                                                                       
       2892 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCAATAT
          1 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCAATAT

                                               *            *          
       2951 GCTCTATGATTAAAATGCAACACTACTAAATTACTTAATGAAAAGAAATCATGCAATAT
          1 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCAATAT

              
       3010 GC
          1 GC

       3012 GAAAATGCTA


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  59   59  1.00

ACGTcount: A:0.46, C:0.17, G:0.11, T:0.27


Consensus pattern (59 bp):   
GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCATGCAATAT

Found at i:3143 original size:28 final size:28

Alignment explanation


    Indices: 3111--3183  Score: 92
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       3101 GTAGATTAAG

                                        
       3111 AATGACCAAAATACCCCCTAAATACAAA
          1 AATGACCAAAATACCCCCTAAATACAAA

                        *       *  ***  
       3139 AATGACCAAAATTCCCCCTAGATGTGAA
          1 AATGACCAAAATACCCCCTAAATACAAA

                        *    
       3167 AATGACCAAAATGCCCC
          1 AATGACCAAAATACCCC

       3184 TGGATGACCC


Statistics
Matches: 39,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  28   39  1.00

ACGTcount: A:0.45, C:0.29, G:0.10, T:0.16


Consensus pattern (28 bp):   
AATGACCAAAATACCCCCTAAATACAAA

Found at i:6203 original size:15 final size:16

Alignment explanation


    Indices: 6174--6207  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       6164 AGCCCCATCC

                      *     
       6174 AAGCAAAAGCCAGATG
          1 AAGCAAAAGCAAGATG

                            
       6190 AAGC-AAAGCAAGATG
          1 AAGCAAAAGCAAGATG

               
       6205 AAG
          1 AAG

       6208 GCTCAGCATA


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

Matches are distributed among these distances:
  15   13  0.76
  16    4  0.24

ACGTcount: A:0.53, C:0.15, G:0.26, T:0.06


Consensus pattern (16 bp):   
AAGCAAAAGCAAGATG

Found at i:8286 original size:10 final size:11

Alignment explanation


    Indices: 8259--8285  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       8249 AAATTAAAGG

                       
       8259 TTTTTTATTTT
          1 TTTTTTATTTT

                       
       8270 TTTTTTATTTT
          1 TTTTTTATTTT

                 
       8281 TTTTT
          1 TTTTT

       8286 AATAAAAAAA


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

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93


Consensus pattern (11 bp):   
TTTTTTATTTT

Found at i:13060 original size:2 final size:2

Alignment explanation


    Indices: 13053--13101  Score: 98
    Period size: 2  Copynumber: 24.5  Consensus size: 2

      13043 TTCCTAAAGT

                                                                          
      13053 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC

                      
      13095 AC AC AC A
          1 AC AC AC A

      13102 TATATATATA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   47  1.00

ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Done.