Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005665.1 Corchorus capsularis cultivar CVL-1 contig05683, 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: 13337
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:3540 original size:10 final size:10

Alignment explanation


    Indices: 3525--3552  Score: 56
    Period size: 10  Copynumber: 2.8  Consensus size: 10

       3515 GCTGGAATTT

                      
       3525 AGTCTGTCAC
          1 AGTCTGTCAC

                      
       3535 AGTCTGTCAC
          1 AGTCTGTCAC

                    
       3545 AGTCTGTC
          1 AGTCTGTC

       3553 TGTACAGTCA


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

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.18, C:0.29, G:0.21, T:0.32


Consensus pattern (10 bp):   
AGTCTGTCAC

Found at i:5817 original size:3 final size:3

Alignment explanation


    Indices: 5804--5895  Score: 166
    Period size: 3  Copynumber: 30.7  Consensus size: 3

       5794 TATATATATG

                 *                                                        *
       5804 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                                                                      
       5852 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

       5896 TGATTAATTA


Statistics
Matches: 85,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   85  1.00

ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:9182 original size:30 final size:31

Alignment explanation


    Indices: 9146--9212  Score: 100
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       9136 GCTGACATCA

                            *               
       9146 ATTTTTTTCAAAGAG-GTTGATAAGTAAATTT
          1 ATTTTTTTCAAAGAGAATT-ATAAGTAAATTT

                                           
       9177 ATTTTTTTCAAAGAGAATTATAAGTAAATTT
          1 ATTTTTTTCAAAGAGAATTATAAGTAAATTT

            *    
       9208 CTTTT
          1 ATTTT

       9213 GTCAGAATGA


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  31   31  0.94
  32    2  0.06

ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48


Consensus pattern (31 bp):   
ATTTTTTTCAAAGAGAATTATAAGTAAATTT

Found at i:9931 original size:8 final size:8

Alignment explanation


    Indices: 9918--9942  Score: 50
    Period size: 8  Copynumber: 3.1  Consensus size: 8

       9908 AAAAATTATA

                    
       9918 ATAATAAT
          1 ATAATAAT

                    
       9926 ATAATAAT
          1 ATAATAAT

                    
       9934 ATAATAAT
          1 ATAATAAT

             
       9942 A
          1 A

       9943 ATGCAATAAT


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

Matches are distributed among these distances:
   8   17  1.00

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (8 bp):   
ATAATAAT

Found at i:10110 original size:16 final size:17

Alignment explanation


    Indices: 10091--10128  Score: 60
    Period size: 16  Copynumber: 2.3  Consensus size: 17

      10081 AATTGTAGCG

                        *    
      10091 AAAAAAATTTGTGCC-A
          1 AAAAAAATTTGTACCGA

                             
      10107 AAAAAAATTTGTACCGA
          1 AAAAAAATTTGTACCGA

                 
      10124 AAAAA
          1 AAAAA

      10129 TTGCACTTGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  16   14  0.70
  17    6  0.30

ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21


Consensus pattern (17 bp):   
AAAAAAATTTGTACCGA

Found at i:13257 original size:33 final size:32

Alignment explanation


    Indices: 13220--13326  Score: 117
    Period size: 33  Copynumber: 3.2  Consensus size: 32

      13210 CGCCTAACGA

                         *        *           
      13220 TGGCCGGT-TGTGACCGGACATGTCCATGTCGCG
          1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG

                             *            *  
      13253 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
          1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG

                               *            *
      13286 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
          1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG

                    
      13319 TGGCCGGT
          1 TGGCCGGT

      13327 CACTAGTGCT


Statistics
Matches: 63,  Mismatches: 9, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  33   61  0.97
  34    2  0.03

ACGTcount: A:0.10, C:0.29, G:0.37, T:0.23


Consensus pattern (32 bp):   
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Done.