Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009710.1 Corchorus capsularis cultivar CVL-1 contig09731, 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: 17863
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:2272 original size:1 final size:1

Alignment explanation


    Indices: 2266--2309  Score: 79
    Period size: 1  Copynumber: 44.0  Consensus size: 1

       2256 AAGGAAGAAG

                                           *            
       2266 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       2310 CTAAACAGGA


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   1   41  1.00

ACGTcount: A:0.98, C:0.00, G:0.00, T:0.02


Consensus pattern (1 bp):   
A

Found at i:2314 original size:14 final size:14

Alignment explanation


    Indices: 2266--2314  Score: 75
    Period size: 13  Copynumber: 3.6  Consensus size: 14

       2256 AAGGAAGAAG

                          
       2266 AAAAA-AAAAAAAA
          1 AAAAATAAAAAAAA

                          
       2279 AAAAA-AAAAAAAA
          1 AAAAATAAAAAAAA

                          
       2292 AAAAATAAAAAAAA
          1 AAAAATAAAAAAAA

                *    
       2306 AAAACTAAA
          1 AAAAATAAA

       2315 CAGGAGGAAC


Statistics
Matches: 34,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  13   18  0.53
  14   16  0.47

ACGTcount: A:0.94, C:0.02, G:0.00, T:0.04


Consensus pattern (14 bp):   
AAAAATAAAAAAAA

Found at i:2604 original size:19 final size:20

Alignment explanation


    Indices: 2577--2614  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       2567 CTTCAAAACA

                                
       2577 AAATAAAAACTACCAATTTT
          1 AAATAAAAACTACCAATTTT

                          *    
       2597 AAAT-AAAACTACCCATTT
          1 AAATAAAAACTACCAATTT

       2615 AAAGGATAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   13  0.76
  20    4  0.24

ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29


Consensus pattern (20 bp):   
AAATAAAAACTACCAATTTT

Found at i:7880 original size:31 final size:31

Alignment explanation


    Indices: 7830--7908  Score: 79
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       7820 ATACATGACA

                         *                  
       7830 TGTCACTTTTTG-GCACACGTGACATGCCACG
          1 TGTCACTTTTTGATC-CACGTGACATGCCACG

                                 ***     * 
       7861 TGTCACTTTTTGATCCACGTGGTGTGCCATG
          1 TGTCACTTTTTGATCCACGTGACATGCCACG

               *       *     
       7892 TGTTACTTTTTTATCCA
          1 TGTCACTTTTTGATCCA

       7909 TGTGGCATAT


Statistics
Matches: 40,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  31   39  0.98
  32    1  0.03

ACGTcount: A:0.16, C:0.24, G:0.20, T:0.39


Consensus pattern (31 bp):   
TGTCACTTTTTGATCCACGTGACATGCCACG
Done.