Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010703.1 Corchorus capsularis cultivar CVL-1 contig10724, 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: 8591
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1688 original size:22 final size:22

Alignment explanation


    Indices: 1663--1704  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1653 ACTAAAGATT

                  *               
       1663 GTGGCCGTGAGATTCGGCCATA
          1 GTGGCCATGAGATTCGGCCATA

                *               
       1685 GTGGTCATGAGATTCGGCCA
          1 GTGGCCATGAGATTCGGCCA

       1705 CATGATGGTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24


Consensus pattern (22 bp):   
GTGGCCATGAGATTCGGCCATA

Found at i:3044 original size:350 final size:350

Alignment explanation


    Indices: 2403--3077  Score: 1305
    Period size: 350  Copynumber: 1.9  Consensus size: 350

       2393 TTTTCTTTTG

                            *                                                
       2403 GACTCTTGTCTACTTATCTGAGACTCTTGTCTCCATCATTCCTCTCAATCTCTTGATTAAGCTTA
          1 GACTCTTGTCTACTTACCTGAGACTCTTGTCTCCATCATTCCTCTCAATCTCTTGATTAAGCTTA

                                                                             
       2468 CTCTTGTAATTTTCCTTTTTGCAATAATAACAATACGTTGTTATTTTGTCCACAAACTTGTTTGA
         66 CTCTTGTAATTTTCCTTTTTGCAATAATAACAATACGTTGTTATTTTGTCCACAAACTTGTTTGA

                                                                            *
       2533 AACCTGATTATACTCTGCAAGAAGTCTGGGTTGCATGTATTAAACACTTCGGTGTGACTTACAAT
        131 AACCTGATTATACTCTGCAAGAAGTCTGGGTTGCATGTATTAAACACTTCGGTGTGACTTACAAC

                                                                             
       2598 CAGATCTCACAAATCGTCTGATTCAATCGTATTTCAAGCTCTCTGAGCTCGCATTAATTCCTTTG
        196 CAGATCTCACAAATCGTCTGATTCAATCGTATTTCAAGCTCTCTGAGCTCGCATTAATTCCTTTG

                                                                             
       2663 TCAATTTGTGCAAATTGACTGGCACGCCCCTCTCCACGATCAGAGCGTGCGCCCAGGGAGATTTT
        261 TCAATTTGTGCAAATTGACTGGCACGCCCCTCTCCACGATCAGAGCGTGCGCCCAGGGAGATTTT

                                     
       2728 TTCTTTTGGACTCTTGTCTACTTGA
        326 TTCTTTTGGACTCTTGTCTACTTGA

                                                                      *  *   
       2753 GACTCTTGTCTACTTACCTGAGACTCTTGTCTCCATCATTCCTCTCAATCTCTTGATTGAGTTTA
          1 GACTCTTGTCTACTTACCTGAGACTCTTGTCTCCATCATTCCTCTCAATCTCTTGATTAAGCTTA

                                                *                            
       2818 CTCTTGTAATTTTCCTTTTTGCAATAATAACAATACTTTGTTATTTTGTCCACAAACTTGTTTGA
         66 CTCTTGTAATTTTCCTTTTTGCAATAATAACAATACGTTGTTATTTTGTCCACAAACTTGTTTGA

                                                                             
       2883 AACCTGATTATACTCTGCAAGAAGTCTGGGTTGCATGTATTAAACACTTCGGTGTGACTTACAAC
        131 AACCTGATTATACTCTGCAAGAAGTCTGGGTTGCATGTATTAAACACTTCGGTGTGACTTACAAC

                                                                             
       2948 CAGATCTCACAAATCGTCTGATTCAATCGTATTTCAAGCTCTCTGAGCTCGCATTAATTCCTTTG
        196 CAGATCTCACAAATCGTCTGATTCAATCGTATTTCAAGCTCTCTGAGCTCGCATTAATTCCTTTG

                                                                             
       3013 TCAATTTGTGCAAATTGACTGGCACGCCCCTCTCCACGATCAGAGCGTGCGCCCAGGGAGATTTT
        261 TCAATTTGTGCAAATTGACTGGCACGCCCCTCTCCACGATCAGAGCGTGCGCCCAGGGAGATTTT

       3078 GGCGCAGCAC


Statistics
Matches: 320,  Mismatches: 5, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 350  320  1.00

ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37


Consensus pattern (350 bp):   
GACTCTTGTCTACTTACCTGAGACTCTTGTCTCCATCATTCCTCTCAATCTCTTGATTAAGCTTA
CTCTTGTAATTTTCCTTTTTGCAATAATAACAATACGTTGTTATTTTGTCCACAAACTTGTTTGA
AACCTGATTATACTCTGCAAGAAGTCTGGGTTGCATGTATTAAACACTTCGGTGTGACTTACAAC
CAGATCTCACAAATCGTCTGATTCAATCGTATTTCAAGCTCTCTGAGCTCGCATTAATTCCTTTG
TCAATTTGTGCAAATTGACTGGCACGCCCCTCTCCACGATCAGAGCGTGCGCCCAGGGAGATTTT
TTCTTTTGGACTCTTGTCTACTTGA

Found at i:3818 original size:2 final size:2

Alignment explanation


    Indices: 3811--3836  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       3801 TAAAAACATC

                                                  
       3811 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       3837 CACACACACA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.