Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006596.1 Corchorus capsularis cultivar CVL-1 contig06617, 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: 3232
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41


Found at i:1402 original size:57 final size:57

Alignment explanation


    Indices: 1333--1443  Score: 197
    Period size: 57  Copynumber: 1.9  Consensus size: 57

       1323 CCATCTACTC

                           *                                          
       1333 TGAGATAAATCATATTGATAATGACCCCTTAACCAGTTTTTCCA-TTCATTCATCCCA
          1 TGAGATAAATCATATCGATAATGACCCCTTAACCAGTTTTTCCATTTC-TTCATCCCA

                                                                  
       1390 TGAGATAAATCATATCGATAATGACCCCTTAACCAGTTTTTCCATTTCTTCATC
          1 TGAGATAAATCATATCGATAATGACCCCTTAACCAGTTTTTCCATTTCTTCATC

       1444 TTCTTCATCC


Statistics
Matches: 52,  Mismatches: 1, Indels: 2
        0.95            0.02        0.04

Matches are distributed among these distances:
  57   49  0.94
  58    3  0.06

ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36


Consensus pattern (57 bp):   
TGAGATAAATCATATCGATAATGACCCCTTAACCAGTTTTTCCATTTCTTCATCCCA

Found at i:1825 original size:18 final size:18

Alignment explanation


    Indices: 1802--1836  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1792 TTTATCAATA

                              
       1802 ATTTTTTTTGTTGATTCC
          1 ATTTTTTTTGTTGATTCC

                             
       1820 ATTTTTTTTGTTGATTC
          1 ATTTTTTTTGTTGATTC

       1837 AAAAAAAAGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.11, C:0.09, G:0.11, T:0.69


Consensus pattern (18 bp):   
ATTTTTTTTGTTGATTCC

Found at i:2119 original size:18 final size:18

Alignment explanation


    Indices: 2096--2134  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2086 TTTTATTTGT

                              
       2096 TTTTCTGTTAATGAATAA
          1 TTTTCTGTTAATGAATAA

                              
       2114 TTTTCTGTTAATGAATAA
          1 TTTTCTGTTAATGAATAA

               
       2132 TTT
          1 TTT

       2135 GTCAAATCAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54


Consensus pattern (18 bp):   
TTTTCTGTTAATGAATAA

Found at i:2474 original size:18 final size:18

Alignment explanation


    Indices: 2451--2486  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       2441 TTTCGTTGGA

                              
       2451 TCTTTATCAGAGGATTGT
          1 TCTTTATCAGAGGATTGT

                              
       2469 TCTTTATCAGAGGATTGT
          1 TCTTTATCAGAGGATTGT

       2487 AGTTTAAATC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44


Consensus pattern (18 bp):   
TCTTTATCAGAGGATTGT

Found at i:2492 original size:18 final size:18

Alignment explanation


    Indices: 2452--2492  Score: 64
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       2442 TTCGTTGGAT

                             *
       2452 CTTTATCAGAGGATTGTT
          1 CTTTATCAGAGGATTGTA

                              
       2470 CTTTATCAGAGGATTGTA
          1 CTTTATCAGAGGATTGTA

            *    
       2488 GTTTA
          1 CTTTA

       2493 AATCTGTGCC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44


Consensus pattern (18 bp):   
CTTTATCAGAGGATTGTA

Found at i:3174 original size:9 final size:9

Alignment explanation


    Indices: 3157--3200  Score: 70
    Period size: 9  Copynumber: 4.9  Consensus size: 9

       3147 TCCCTTAGGC

                *    
       3157 TCATTGGTA
          1 TCATCGGTA

                     
       3166 TCATCGGTA
          1 TCATCGGTA

                    *
       3175 TCATCGGTC
          1 TCATCGGTA

                     
       3184 TCATCGGTA
          1 TCATCGGTA

                    
       3193 TCATCGGT
          1 TCATCGGT

       3201 TTTAGTATAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   32  1.00

ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36


Consensus pattern (9 bp):   
TCATCGGTA

Done.