Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008989.1 Corchorus capsularis cultivar CVL-1 contig09010, 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: 11456
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:956 original size:2 final size:2

Alignment explanation


    Indices: 949--982  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

        939 GTTAGGTGAG

                                                              
        949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        983 TGCATTTTAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2954 original size:17 final size:18

Alignment explanation


    Indices: 2927--2961  Score: 63
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       2917 AACCCACACG

                              
       2927 TGCCTTTCTCTGCATTTT
          1 TGCCTTTCTCTGCATTTT

                              
       2945 TGCC-TTCTCTGCATTTT
          1 TGCCTTTCTCTGCATTTT

       2962 GTCAATTCCT


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

Matches are distributed among these distances:
  17   13  0.76
  18    4  0.24

ACGTcount: A:0.06, C:0.29, G:0.11, T:0.54


Consensus pattern (18 bp):   
TGCCTTTCTCTGCATTTT

Found at i:3432 original size:6 final size:6

Alignment explanation


    Indices: 3421--3445  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       3411 AAGAAGGCCC

                                         
       3421 CAAAAG CAAAAG CAAAAG CAAAAG C
          1 CAAAAG CAAAAG CAAAAG CAAAAG C

       3446 TCTCTTTTAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.64, C:0.20, G:0.16, T:0.00


Consensus pattern (6 bp):   
CAAAAG

Found at i:6884 original size:31 final size:32

Alignment explanation


    Indices: 6840--6904  Score: 114
    Period size: 31  Copynumber: 2.1  Consensus size: 32

       6830 GGGGCCATGA

                                  *         
       6840 CCCCCAAAAAAATGGAAAAATTGCATAGTAAT
          1 CCCCCAAAAAAATGGAAAAATTACATAGTAAT

                                            
       6872 CCCCC-AAAAAATGGAAAAATTACATAGTAAT
          1 CCCCCAAAAAAATGGAAAAATTACATAGTAAT

              
       6903 CC
          1 CC

       6905 GTAAATTTAT


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  31   27  0.84
  32    5  0.16

ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18


Consensus pattern (32 bp):   
CCCCCAAAAAAATGGAAAAATTACATAGTAAT

Found at i:8078 original size:30 final size:30

Alignment explanation


    Indices: 8042--8098  Score: 87
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       8032 TCAATCTTGG

                              *           
       8042 ATCCTGCTGTAAACAAACTGTTGACTTTAA
          1 ATCCTGCTGTAAACAAACAGTTGACTTTAA

                         * *           
       8072 ATCCTGCTGTAAATACACAGTTGACTT
          1 ATCCTGCTGTAAACAAACAGTTGACTT

       8099 ATTTCGTCAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33


Consensus pattern (30 bp):   
ATCCTGCTGTAAACAAACAGTTGACTTTAA
Done.