Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010036.1 Corchorus capsularis cultivar CVL-1 contig10057, 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: 3660
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Found at i:997 original size:31 final size:31

Alignment explanation


    Indices: 962--1026  Score: 130
    Period size: 31  Copynumber: 2.1  Consensus size: 31

        952 AACTGAACAA

                                           
        962 ACTCAAACATCCAAGATCTAAAGATCTGGAG
          1 ACTCAAACATCCAAGATCTAAAGATCTGGAG

                                           
        993 ACTCAAACATCCAAGATCTAAAGATCTGGAG
          1 ACTCAAACATCCAAGATCTAAAGATCTGGAG

               
       1024 ACT
          1 ACT

       1027 GATAACCCAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20


Consensus pattern (31 bp):   
ACTCAAACATCCAAGATCTAAAGATCTGGAG

Found at i:1327 original size:10 final size:10

Alignment explanation


    Indices: 1312--1340  Score: 58
    Period size: 10  Copynumber: 2.9  Consensus size: 10

       1302 TTCAGCGAAA

                      
       1312 AAAAAAAAAG
          1 AAAAAAAAAG

                      
       1322 AAAAAAAAAG
          1 AAAAAAAAAG

                     
       1332 AAAAAAAAA
          1 AAAAAAAAA

       1341 AGAAGAGGGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00


Consensus pattern (10 bp):   
AAAAAAAAAG

Found at i:1327 original size:11 final size:11

Alignment explanation


    Indices: 1311--1344  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       1301 TTTCAGCGAA

                       
       1311 AAAAAAAAAAG
          1 AAAAAAAAAAG

                       
       1322 -AAAAAAAAAG
          1 AAAAAAAAAAG

                       
       1332 AAAAAAAAAAG
          1 AAAAAAAAAAG

              
       1343 AA
          1 AA

       1345 GAGGGAAACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  10   10  0.45
  11   12  0.55

ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00


Consensus pattern (11 bp):   
AAAAAAAAAAG

Found at i:1328 original size:14 final size:14

Alignment explanation


    Indices: 1309--1346  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       1299 CTTTTCAGCG

                         *
       1309 AAAAAAAAA-AAAG
          1 AAAAAAAAAGAAAA

                          
       1322 AAAAAAAAAGAAAA
          1 AAAAAAAAAGAAAA

                  *    
       1336 AAAAAAGAAGA
          1 AAAAAAAAAGA

       1347 GGGAAACTAC


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  13    9  0.41
  14   13  0.59

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (14 bp):   
AAAAAAAAAGAAAA

Found at i:3116 original size:18 final size:19

Alignment explanation


    Indices: 3093--3130  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       3083 AATAAATTAA

                  *            
       3093 AAATTGCATT-AAATATAT
          1 AAATTGAATTCAAATATAT

                           *   
       3111 AAATTGAATTCAAATTTAT
          1 AAATTGAATTCAAATATAT

             
       3130 A
          1 A

       3131 CCGTGTCCCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  18    9  0.53
  19    8  0.47

ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39


Consensus pattern (19 bp):   
AAATTGAATTCAAATATAT
Done.