Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002083.1 Corchorus capsularis cultivar CVL-1 contig02087, 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, 834

Length: 1390
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40


Found at i:1105 original size:22 final size:22

Alignment explanation


    Indices: 1060--1104  Score: 65
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1050 ACTAACTGGA

                                  
       1060 TTGCTAAACACCGCCTCCCCTT
          1 TTGCTAAACACCGCCTCCCCTT

                    *    *        
       1082 TTGCTAAATACCGTC-CCCCTT
          1 TTGCTAAACACCGCCTCCCCTT

              
       1103 TT
          1 TT

       1105 TACACTTTTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    8  0.38
  22   13  0.62

ACGTcount: A:0.18, C:0.40, G:0.09, T:0.33


Consensus pattern (22 bp):   
TTGCTAAACACCGCCTCCCCTT

Found at i:1235 original size:24 final size:25

Alignment explanation


    Indices: 1175--1233  Score: 95
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       1165 TTCAAACCCT

                               *     
       1175 AAACTTCATTTCTAACAACTTCTTC
          1 AAACTTCATTTCTAACAACATCTTC

                                     
       1200 AAACTTCATTTCTAACAA-ATCTTC
          1 AAACTTCATTTCTAACAACATCTTC

                       
       1224 AAA-TTCATTT
          1 AAACTTCATTT

       1234 TCCTTCATTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  23    7  0.21
  24    8  0.24
  25   18  0.55

ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41


Consensus pattern (25 bp):   
AAACTTCATTTCTAACAACATCTTC

Found at i:1272 original size:26 final size:26

Alignment explanation


    Indices: 1243--1310  Score: 127
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       1233 TTCCTTCATT

                                      
       1243 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                                      
       1269 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
       1295 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

       1311 AAACTAAGTA


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  26   41  1.00

ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA

Found at i:1310 original size:15 final size:15

Alignment explanation


    Indices: 1243--1314  Score: 63
    Period size: 11  Copynumber: 5.4  Consensus size: 15

       1233 TTCCTTCATT

                *          
       1243 TTAATCATAAACTAA
          1 TTAAACATAAACTAA

                           
       1258 TT-AA-AT--ACTAA
          1 TTAAACATAAACTAA

                *          
       1269 TTAATCATAAACTAA
          1 TTAAACATAAACTAA

                           
       1284 TT-AA-AT--ACTAA
          1 TTAAACATAAACTAA

                           
       1295 TTAAACATAAACTAA
          1 TTAAACATAAACTAA

                  
       1310 -TAAAC
          1 TTAAAC

       1315 TAAGTAATTT


Statistics
Matches: 46,  Mismatches: 3, Indels: 17
        0.70            0.05        0.26

Matches are distributed among these distances:
  11   14  0.30
  12    3  0.07
  13    8  0.17
  14    7  0.15
  15   14  0.30

ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32


Consensus pattern (15 bp):   
TTAAACATAAACTAA
Done.