Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011961.1 Corchorus capsularis cultivar CVL-1 contig11982, 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: 7142
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29


Found at i:1240 original size:9 final size:8

Alignment explanation


    Indices: 1206--1239  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       1196 GAATCAGCTA

                    
       1206 TGAATTTT
          1 TGAATTTT

                    *
       1214 TGAAGTTTC
          1 TGAA-TTTT

                    
       1223 TGAATTTT
          1 TGAATTTT

                    
       1231 TGAATTTT
          1 TGAATTTT

             
       1239 T
          1 T

       1240 TTTTAAGAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:1774 original size:48 final size:48

Alignment explanation


    Indices: 1703--1798  Score: 192
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       1693 GGGGGATGGT

                                                            
       1703 CCCTTTATATAGGGCACGCATAACCCTTCTCCTAAAGCTAAAAGGAAA
          1 CCCTTTATATAGGGCACGCATAACCCTTCTCCTAAAGCTAAAAGGAAA

                                                            
       1751 CCCTTTATATAGGGCACGCATAACCCTTCTCCTAAAGCTAAAAGGAAA
          1 CCCTTTATATAGGGCACGCATAACCCTTCTCCTAAAGCTAAAAGGAAA

       1799 ACATTACATA


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   48  1.00

ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23


Consensus pattern (48 bp):   
CCCTTTATATAGGGCACGCATAACCCTTCTCCTAAAGCTAAAAGGAAA

Found at i:2268 original size:33 final size:33

Alignment explanation


    Indices: 2216--2306  Score: 146
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       2206 TCCGGATGGC

                *         *                  
       2216 CCAATCGATGTCCGATTGTGGCCGGTTGGTGCG
          1 CCAAGCGATGTCCGGTTGTGGCCGGTTGGTGCG

                                             
       2249 CCAAGCGATGTCCGGTTGTGGCCGGTTGGTGCG
          1 CCAAGCGATGTCCGGTTGTGGCCGGTTGGTGCG

               *      *              
       2282 CCATGCGATGGCCGGTTGTGGCCGG
          1 CCAAGCGATGTCCGGTTGTGGCCGG

       2307 ATGCCCCATG


Statistics
Matches: 54,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  33   54  1.00

ACGTcount: A:0.10, C:0.25, G:0.41, T:0.24


Consensus pattern (33 bp):   
CCAAGCGATGTCCGGTTGTGGCCGGTTGGTGCG

Found at i:4798 original size:33 final size:33

Alignment explanation


    Indices: 4741--4848  Score: 121
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       4731 AGCACTTGTG

                                *              
       4741 ACCGGCCACGCGACTTGGA-GATGCCCGGCCATC-
          1 ACCGGCCACGCGACTT-GACCATGCCCGGCCA-CA

                                     *       
       4774 ACCGGCCACGCGACTTGACCATGCCTGGCCACA
          1 ACCGGCCACGCGACTTGACCATGCCCGGCCACA

                 *   **    * *               
       4807 ACCGGTCACATGACTCGGCCATGCCCGGCCACA
          1 ACCGGCCACGCGACTTGACCATGCCCGGCCACA

                     
       4840 ACCGGCCAC
          1 ACCGGCCAC

       4849 ATGATCCTTT


Statistics
Matches: 64,  Mismatches: 9, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  32    3  0.05
  33   61  0.95

ACGTcount: A:0.20, C:0.43, G:0.26, T:0.11


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGACCATGCCCGGCCACA

Found at i:6489 original size:30 final size:31

Alignment explanation


    Indices: 6434--6495  Score: 83
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       6424 GCACTCAACC

                                           
       6434 AAGGAACTGAGGCGCCCAAGGCTTATCATGG
          1 AAGGAACTGAGGCGCCCAAGGCTTATCATGG

                      *                *    
       6465 AAGGAA-TGATGCG-CCAAGGACTTATTATGG
          1 AAGGAACTGAGGCGCCCAAGG-CTTATCATGG

             
       6495 A
          1 A

       6496 CTTGAAGACA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  29    6  0.21
  30   16  0.57
  31    6  0.21

ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19


Consensus pattern (31 bp):   
AAGGAACTGAGGCGCCCAAGGCTTATCATGG
Done.