Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012178.1 Corchorus capsularis cultivar CVL-1 contig12199, 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: 14384
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:1182 original size:18 final size:18

Alignment explanation


    Indices: 1159--1206  Score: 53
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       1149 AGCGTGGCAT

                              
       1159 ATCGTGTGCTCTTATGGC
          1 ATCGTGTGCTCTTATGGC

                  *            
       1177 ATCGTGCGC-CTTTATGGC
          1 ATCGTGTGCTC-TTATGGC

            *  *        
       1195 GTCTTGTGCTCT
          1 ATCGTGTGCTCT

       1207 CCGCTTTTTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 4
        0.75            0.12        0.12

Matches are distributed among these distances:
  17    1  0.04
  18   22  0.92
  19    1  0.04

ACGTcount: A:0.08, C:0.25, G:0.27, T:0.40


Consensus pattern (18 bp):   
ATCGTGTGCTCTTATGGC

Found at i:1929 original size:90 final size:90

Alignment explanation


    Indices: 1773--1995  Score: 304
    Period size: 90  Copynumber: 2.5  Consensus size: 90

       1763 GTATATACCA

                     *      *       *    *  *                         **     
       1773 CCATCAAAATATGATATAACATGTAAGT-GTGTTTAAACGATGCTCTTGCATGATCATTTTAACT
          1 CCATCAAAAAATGATAAAACATGTTA-TCATGCTTAAACGATGCTCTTGCATGATCATAATAACT

                           *    *     
       1837 CAATTTATGCATATAGGCATGTACTT
         65 CAATTTATGCATATAAGCATATACTT

                                                                         *   
       1863 CCATCAAAAAATGATAAAACATGTTATCATGCTTAAACGATGCTCTTGCATGATCATAATATCTC
          1 CCATCAAAAAATGATAAAACATGTTATCATGCTTAAACGATGCTCTTGCATGATCATAATAACTC

                                     
       1928 AATTTATGCATATAAGCATATACTT
         66 AATTTATGCATATAAGCATATACTT

             * *                                       
       1953 CTACCAAAAAATGATAAAAGGCATGTTATCATGCTTAAACGAT
          1 CCATCAAAAAATGATAAAA--CATGTTATCATGCTTAAACGAT

       1996 CATATTAACT


Statistics
Matches: 118,  Mismatches: 12, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
  89    1  0.01
  90   95  0.81
  92   22  0.19

ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33


Consensus pattern (90 bp):   
CCATCAAAAAATGATAAAACATGTTATCATGCTTAAACGATGCTCTTGCATGATCATAATAACTC
AATTTATGCATATAAGCATATACTT

Found at i:5763 original size:20 final size:21

Alignment explanation


    Indices: 5732--5773  Score: 77
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       5722 AATTTCATTG

                                 
       5732 AGCAATGCATTGCAGCCAGTA
          1 AGCAATGCATTGCAGCCAGTA

                                 
       5753 AGCAA-GCATTGCAGCCAGTA
          1 AGCAATGCATTGCAGCCAGTA

             
       5773 A
          1 A

       5774 ATATCAGTTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20   16  0.76
  21    5  0.24

ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17


Consensus pattern (21 bp):   
AGCAATGCATTGCAGCCAGTA

Found at i:10623 original size:3 final size:3

Alignment explanation


    Indices: 10617--10644  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

      10607 GAGAGGAGGT

                                                 
      10617 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G

      10645 TCACTCAACC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:11045 original size:17 final size:17

Alignment explanation


    Indices: 11025--11058  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      11015 ACAGACAAGG

                              
      11025 GAATAAA-CTTATTCCAA
          1 GAATAAATCTT-TTCCAA

                             
      11042 GAATAAATCTTTTCCAA
          1 GAATAAATCTTTTCCAA

      11059 AAATTACTTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17   13  0.81
  18    3  0.19

ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32


Consensus pattern (17 bp):   
GAATAAATCTTTTCCAA
Done.