Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008148.1 Corchorus capsularis cultivar CVL-1 contig08169, 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: 17339
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35


Found at i:4262 original size:28 final size:28

Alignment explanation


    Indices: 4222--4281  Score: 102
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       4212 TTGGCTTGCT

                    *    *              
       4222 TTTTTTGTTGGCTGTAATTGCATGTTTG
          1 TTTTTTGTCGGCTCTAATTGCATGTTTG

                                        
       4250 TTTTTTGTCGGCTCTAATTGCATGTTTG
          1 TTTTTTGTCGGCTCTAATTGCATGTTTG

                
       4278 TTTT
          1 TTTT

       4282 ACCCTTCTTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.10, C:0.10, G:0.22, T:0.58


Consensus pattern (28 bp):   
TTTTTTGTCGGCTCTAATTGCATGTTTG

Found at i:5071 original size:32 final size:32

Alignment explanation


    Indices: 5035--5108  Score: 114
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       5025 GCCTGAACCT

                                            
       5035 GAACCCGAAAAAGCTCAAACCCGAAAAAATCC
          1 GAACCCGAAAAAGCTCAAACCCGAAAAAATCC

                                   *   *    
       5067 GAACCCGAAAAAGCTCAAACCCGGAAATATCC
          1 GAACCCGAAAAAGCTCAAACCCGAAAAAATCC

               *       
       5099 G-ATCCGAAAA
          1 GAACCCGAAAA

       5109 TTTATGAAAA


Statistics
Matches: 39,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  31    8  0.21
  32   31  0.79

ACGTcount: A:0.47, C:0.30, G:0.15, T:0.08


Consensus pattern (32 bp):   
GAACCCGAAAAAGCTCAAACCCGAAAAAATCC

Found at i:5093 original size:17 final size:16

Alignment explanation


    Indices: 5036--5089  Score: 74
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       5026 CCTGAACCTG

                            
       5036 AACCCGAAAAAGCTCA
          1 AACCCGAAAAAGCTCA

                        *   *
       5052 AACCCGAAAAA-ATCCG
          1 AACCCGAAAAAGCT-CA

                            
       5068 AACCCGAAAAAGCTCA
          1 AACCCGAAAAAGCTCA

                  
       5084 AACCCG
          1 AACCCG

       5090 GAAATATCCG


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  15    1  0.03
  16   30  0.94
  17    1  0.03

ACGTcount: A:0.48, C:0.33, G:0.13, T:0.06


Consensus pattern (16 bp):   
AACCCGAAAAAGCTCA

Found at i:7969 original size:32 final size:32

Alignment explanation


    Indices: 7932--8016  Score: 118
    Period size: 32  Copynumber: 2.7  Consensus size: 32

       7922 GGTTTGAGTC

                                             
       7932 CGGGTTAAATTTGGGTCAGGTCGATTC-GGATT
          1 CGGGTTAAATTTGGGTCAGGTCGATTCAGG-TT

                                            
       7964 CGGGTTAAATTTGGGTCAGGTCGATTCAGGTT
          1 CGGGTTAAATTTGGGTCAGGTCGATTCAGGTT

             * *        * *      
       7996 CAGATTAAATTTAGATCAGGT
          1 CGGGTTAAATTTGGGTCAGGT

       8017 TAATTTGGGT


Statistics
Matches: 48,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  32   46  0.96
  33    2  0.04

ACGTcount: A:0.24, C:0.12, G:0.31, T:0.34


Consensus pattern (32 bp):   
CGGGTTAAATTTGGGTCAGGTCGATTCAGGTT

Found at i:8204 original size:20 final size:20

Alignment explanation


    Indices: 8179--8217  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       8169 CATAAGTGAA

                          *     
       8179 ATTTTCAAAAATTATTATTT
          1 ATTTTCAAAAATTAGTATTT

                     *         
       8199 ATTTTCAAATATTAGTATT
          1 ATTTTCAAAAATTAGTATT

       8218 GAGTTTGGGT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54


Consensus pattern (20 bp):   
ATTTTCAAAAATTAGTATTT

Found at i:8608 original size:2 final size:2

Alignment explanation


    Indices: 8592--8631  Score: 57
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       8582 TGGCTTCTCA

                                                                          
       8592 AT AT AT CAT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
          1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       8632 ATAAGCTTAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   1    2  0.06
   2   31  0.89
   3    2  0.06

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:12953 original size:27 final size:27

Alignment explanation


    Indices: 12923--12990  Score: 77
    Period size: 27  Copynumber: 2.5  Consensus size: 27

      12913 GTCAGAATCT

                 *                       
      12923 CATTCCAAGTTAGTCA-AGACAA-TTCTC
          1 CATTCAAAGTTAGTCAGA-ACAATTTC-C

                     *           *     
      12950 CATTCAAAGCTAGTCAGAACAGTTTCC
          1 CATTCAAAGTTAGTCAGAACAATTTCC

                          
      12977 CATTCAAAGTTAGT
          1 CATTCAAAGTTAGT

      12991 TCCCTAAGAT


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
  27   31  0.89
  28    4  0.11

ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29


Consensus pattern (27 bp):   
CATTCAAAGTTAGTCAGAACAATTTCC
Done.