Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015346.1 Corchorus olitorius cultivar O-4 contig15379, 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: 11607
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33


Found at i:1340 original size:67 final size:67

Alignment explanation


    Indices: 1232--1365  Score: 268
    Period size: 67  Copynumber: 2.0  Consensus size: 67

       1222 TGAAAGGCAA

                                                                             
       1232 CCAACACTTCCTGTGGTGGAGAACGAGCATCCGAGCTTAGAGTTAGAGAGCCTATATGCACTGAA
          1 CCAACACTTCCTGTGGTGGAGAACGAGCATCCGAGCTTAGAGTTAGAGAGCCTATATGCACTGAA

              
       1297 AT
         66 AT

                                                                             
       1299 CCAACACTTCCTGTGGTGGAGAACGAGCATCCGAGCTTAGAGTTAGAGAGCCTATATGCACTGAA
          1 CCAACACTTCCTGTGGTGGAGAACGAGCATCCGAGCTTAGAGTTAGAGAGCCTATATGCACTGAA

              
       1364 AT
         66 AT

       1366 TACCCTCCCT


Statistics
Matches: 67,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  67   67  1.00

ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22


Consensus pattern (67 bp):   
CCAACACTTCCTGTGGTGGAGAACGAGCATCCGAGCTTAGAGTTAGAGAGCCTATATGCACTGAA
AT

Found at i:6272 original size:21 final size:19

Alignment explanation


    Indices: 6224--6281  Score: 71
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       6214 CTGTTTAGCA

                               
       6224 ACTGTACAGATGAGATTAC
          1 ACTGTACAGATGAGATTAC

              *        *        *
       6243 ACGGTACAGATTAGATTAGGT
          1 ACTGTACAGATGAGATTA--C

                              
       6264 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

       6282 TTAGAGTAGC


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  19   16  0.50
  21   16  0.50

ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC

Found at i:7705 original size:17 final size:17

Alignment explanation


    Indices: 7683--7717  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       7673 CATATTAATT

                         *   
       7683 GGTTGGTTGCAATGCCG
          1 GGTTGGTTGCAATACCG

                             
       7700 GGTTGGTTGCAATACCG
          1 GGTTGGTTGCAATACCG

             
       7717 G
          1 G

       7718 TGCCACCTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.14, C:0.17, G:0.40, T:0.29


Consensus pattern (17 bp):   
GGTTGGTTGCAATACCG
Done.