Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014902.1 Corchorus capsularis cultivar CVL-1 contig14923, 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: 24301
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:2912 original size:143 final size:143

Alignment explanation


    Indices: 2703--2993  Score: 458
    Period size: 143  Copynumber: 2.0  Consensus size: 143

       2693 ACCACCCATA

                      *                                *                     
       2703 AACT-CTTTTTTTTTTCAACTTTCAAAAAATGTTGACTTTGGTCAAAAATCCAGGTCAACCAATC
          1 AACTCCTTTTCTTTTTCAACTTTCAAAAAATGTTGACTTTGGTAAAAAATCCAGGTCAACCAATC

                    *            *                            *              
       2767 CACTTTTCGATTCAAACACAATTTGAACCGAGTCAATGTCGGACCGTTGATCAAACAGTTAACAT
         66 CACTTTTCAATTCAAACACAAGTTGAACCGAGTCAATGTCGGACCGTTGACCAAACAGTTAACAT

                    *    
       2832 TCGGACCGTTCTG
        131 TCGGACCGGTCTG

                                                                 *     * **  
       2845 AACTCCTTTTCTTTTTCAACTTTCAAAAAATGTTGACTTTGGTAAAAAATCCATGTCAATCGGTC
          1 AACTCCTTTTCTTTTTCAACTTTCAAAAAATGTTGACTTTGGTAAAAAATCCAGGTCAACCAATC

                                          *             *                *   
       2910 CACTTTTCAATTCAAACACAAGTTGAACCGGGTCAATGTCGGACTGTTGACCAAACAGTTAGCAT
         66 CACTTTTCAATTCAAACACAAGTTGAACCGAGTCAATGTCGGACCGTTGACCAAACAGTTAACAT

                         
       2975 TCGGACCGGTCTG
        131 TCGGACCGGTCTG

                  
       2988 AACTCC
          1 AACTCC

       2994 AGTTTCCAGT


Statistics
Matches: 135,  Mismatches: 13, Indels: 1
        0.91            0.09        0.01

Matches are distributed among these distances:
 142    4  0.03
 143  131  0.97

ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32


Consensus pattern (143 bp):   
AACTCCTTTTCTTTTTCAACTTTCAAAAAATGTTGACTTTGGTAAAAAATCCAGGTCAACCAATC
CACTTTTCAATTCAAACACAAGTTGAACCGAGTCAATGTCGGACCGTTGACCAAACAGTTAACAT
TCGGACCGGTCTG

Found at i:5942 original size:33 final size:33

Alignment explanation


    Indices: 5890--5966  Score: 120
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       5880 ATTTATCAAA

                    *      *                 
       5890 TAATCC-TCACACTTTTTATGCTTTATGCTATT
          1 TAATCCTTTACACTTCTTATGCTTTATGCTATT

                                             
       5922 TAATCCTTTACACTTCTTATGCTTTATGCTATT
          1 TAATCCTTTACACTTCTTATGCTTTATGCTATT

              *         
       5955 TAGTCCTTTACA
          1 TAATCCTTTACA

       5967 ATTATGGGTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  32    6  0.15
  33   35  0.85

ACGTcount: A:0.22, C:0.22, G:0.06, T:0.49


Consensus pattern (33 bp):   
TAATCCTTTACACTTCTTATGCTTTATGCTATT

Found at i:7316 original size:2 final size:2

Alignment explanation


    Indices: 7309--7353  Score: 54
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       7299 CAAATTAAGA

                                                *   *   *                  
       7309 AT AT AT AT AT AT AT AT AT AT AT AT CT AA ACC AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT

              
       7352 AT
          1 AT

       7354 CATGTAATGT


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   2   36  0.97
   3    1  0.03

ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44


Consensus pattern (2 bp):   
AT

Found at i:7994 original size:1 final size:1

Alignment explanation


    Indices: 7988--8014  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

       7978 CTCTCTTATC

                                       
       7988 TTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTT

       8015 CTATTTTCGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:12110 original size:15 final size:16

Alignment explanation


    Indices: 12090--12119  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      12080 TGTGTTTCTT

                            
      12090 TTGACAA-GAAAAAAG
          1 TTGACAAGGAAAAAAG

                           
      12105 TTGACAAGGAAAAAA
          1 TTGACAAGGAAAAAA

      12120 TCGTTTTTCC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.60, C:0.07, G:0.20, T:0.13


Consensus pattern (16 bp):   
TTGACAAGGAAAAAAG

Done.