Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021490.1 Corchorus olitorius cultivar O-4 contig21523, 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: 7813
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:1918 original size:33 final size:33

Alignment explanation


    Indices: 1881--1965  Score: 84
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       1871 TTGTGAATCG

                                 *             
       1881 TTCCCAAATACCCAA-TTC-TTTCGAAAACCTAAA
          1 TTCCCAAATACCCAATTTCATATCGAAAA-C-AAA

                   * *                      *
       1914 TTCCCAATTTCCCAATTTCATATCGAAAACAAT
          1 TTCCCAAATACCCAATTTCATATCGAAAACAAA

                     *    *    
       1947 TTCCCAAATCCCCATTTTC
          1 TTCCCAAATACCCAATTTC

       1966 TGTTGAACCC


Statistics
Matches: 43,  Mismatches: 7, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  33   31  0.72
  34    4  0.09
  35    8  0.19

ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32


Consensus pattern (33 bp):   
TTCCCAAATACCCAATTTCATATCGAAAACAAA

Found at i:2145 original size:27 final size:27

Alignment explanation


    Indices: 2110--2183  Score: 123
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       2100 CAAACTTCAA

                *                      
       2110 CAGAGTTCGCAATGCTCAAAAACTTTC
          1 CAGATTTCGCAATGCTCAAAAACTTTC

                                       
       2137 CAGATTTCGCAATGCTCAAAAACTTTC
          1 CAGATTTCGCAATGCTCAAAAACTTTC

                                 
       2164 CAGATTTCGCAA-GCTTCAAA
          1 CAGATTTCGCAATGC-TCAAA

       2184 CTCAATTCCA


Statistics
Matches: 45,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  26    2  0.04
  27   43  0.96

ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27


Consensus pattern (27 bp):   
CAGATTTCGCAATGCTCAAAAACTTTC

Found at i:2523 original size:31 final size:31

Alignment explanation


    Indices: 2485--2589  Score: 99
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       2475 ACAAAATGGA

                               *           
       2485 CTTATTTGAGATTTTTCGCGAAGTTGGGGCC
          1 CTTATTTGAGATTTTTCGCAAAGTTGGGGCC

                      **             **    
       2516 CTTATTTGA-CCTTTTC-CAAAGTTTAGGCC
          1 CTTATTTGAGATTTTTCGCAAAGTTGGGGCC

                          * *     *       * 
       2545 CTTATTTGAGATTTATGGCAAAATTCGGGGAC
          1 CTTATTTGAGATTTTTCGCAAAGTT-GGGGCC

                          
       2577 C-TATTTGAGATTT
          1 CTTATTTGAGATTT

       2590 CAGCCTAATT


Statistics
Matches: 58,  Mismatches: 13, Indels: 6
        0.75            0.17        0.08

Matches are distributed among these distances:
  29   19  0.33
  30    8  0.14
  31   27  0.47
  32    4  0.07

ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40


Consensus pattern (31 bp):   
CTTATTTGAGATTTTTCGCAAAGTTGGGGCC

Found at i:5943 original size:20 final size:20

Alignment explanation


    Indices: 5918--5957  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5908 TTAGGTTCAA

                                
       5918 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

                                
       5938 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

       5958 GTTTGTAATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35


Consensus pattern (20 bp):   
CTCTCACGGAATGTGAGTTT

Found at i:7593 original size:165 final size:165

Alignment explanation


    Indices: 7217--7688  Score: 705
    Period size: 165  Copynumber: 2.8  Consensus size: 165

       7207 TGATTGATTT

                                           *   *          *     *        *   
       7217 ATTTATGGTAAAATTAAATAATCATCAATCAGTTATAACTTTGATTGGCAAAGTTAACTAATGAC
          1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC

                                       *                 *                 * 
       7282 TAACTTGATTCATTT-TGTCTATTTTATCATGTTCAATAATTAATTTTTTTTGGTAACATAATCA
         66 TAACTTGATTCATTTAT-T-TA-TTTACCATGTTCAATAATT--TATTTTTTGGTAACATAATTA

                                                    
       7346 CTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCA
        126 CTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCA

                                  *                        *                 
       7386 ATTTATGGTAAAATTAAATAATTATCAATCAATTAAAACTTTGATTCACAAAATTAACTAACGAC
          1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC

                                                                             
       7451 TAACTTGGATTCATTTATTTATTTACCATGTTCAATAATTTATTTTTTGGTAACATAATTACTAA
         66 TAACTT-GATTCATTTATTTATTTACCATGTTCAATAATTTATTTTTTGGTAACATAATTACTAA

                                               *
       7516 TTGATTTATTTATTTATGGTAA-TTTTTTGGTAGCG
        130 TTGATTTATTTATTTATGGTAATTTTTTTGGTAGCA

                                               *          *                  
       7551 ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTTGCAAAATTAACTAACGAC
          1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC

                                    * *                        *             
       7616 TAACTTGATTCATTTATTTATTTAGCTTGTTCAATCAATTTTATTTTTTTGCTAACATAATTACT
         66 TAACTTGATTCATTTATTTATTTACCATGTTCAAT-AA-TTTA-TTTTTTGGTAACATAATTACT

                    
       7681 AATTGATT
        128 AATTGATT

       7689 CGTTTATTCA


Statistics
Matches: 280,  Mismatches: 18, Indels: 12
        0.90            0.06        0.04

Matches are distributed among these distances:
 164   27  0.10
 165   81  0.29
 166   49  0.17
 167   28  0.10
 168   18  0.06
 169   66  0.24
 170   10  0.04
 171    1  0.00

ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45


Consensus pattern (165 bp):   
ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC
TAACTTGATTCATTTATTTATTTACCATGTTCAATAATTTATTTTTTGGTAACATAATTACTAAT
TGATTTATTTATTTATGGTAATTTTTTTGGTAGCA
Done.