Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008969.1 Corchorus capsularis cultivar CVL-1 contig08990, 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: 6520
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30


Found at i:6205 original size:20 final size:21

Alignment explanation


    Indices: 6180--6222  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       6170 GCAAACTGGA

                      *          
       6180 TTACTAAACATCG-CCCCCTT
          1 TTACTAAACACCGTCCCCCTT

                    *            
       6200 TTACTAAATACCGTCCCCCTT
          1 TTACTAAACACCGTCCCCCTT

              
       6221 TT
          1 TT

       6223 TACACTTTTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   11  0.55
  21    9  0.45

ACGTcount: A:0.23, C:0.37, G:0.05, T:0.35


Consensus pattern (21 bp):   
TTACTAAACACCGTCCCCCTT

Found at i:6328 original size:25 final size:24

Alignment explanation


    Indices: 6285--6352  Score: 77
    Period size: 25  Copynumber: 2.9  Consensus size: 24

       6275 TCTCAACTTT

                  *        *        
       6285 CAAATCCT-AAACTTTATTTTTAA
          1 CAAATCTTCAAACTTCATTTTTAA

                *                *   
       6308 CAACTTCTTCAAACTTCATTTCTAA
          1 CAA-ATCTTCAAACTTCATTTTTAA

                                 
       6333 CAAATCTTCAAA-TTCATTTT
          1 CAAATCTTCAAACTTCATTTT

       6353 CCTTCATTTT


Statistics
Matches: 37,  Mismatches: 6, Indels: 4
        0.79            0.13        0.09

Matches are distributed among these distances:
  23   10  0.27
  24   11  0.30
  25   16  0.43

ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43


Consensus pattern (24 bp):   
CAAATCTTCAAACTTCATTTTTAA

Found at i:6353 original size:24 final size:26

Alignment explanation


    Indices: 6293--6353  Score: 76
    Period size: 24  Copynumber: 2.5  Consensus size: 26

       6283 TTCAAATCCT

                  *             *     
       6293 AAACTTTATTTT-TAACAACTTCTTC
          1 AAACTTCATTTTCTAACAACATCTTC

                                      
       6318 AAACTTCA-TTTCTAACAA-ATCTTC
          1 AAACTTCATTTTCTAACAACATCTTC

                         
       6342 AAA-TTCATTTTC
          1 AAACTTCATTTTC

       6354 CTTCATTTTA


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

Matches are distributed among these distances:
  23    4  0.12
  24   15  0.47
  25   13  0.41

ACGTcount: A:0.34, C:0.21, G:0.00, T:0.44


Consensus pattern (26 bp):   
AAACTTCATTTTCTAACAACATCTTC

Found at i:6390 original size:26 final size:26

Alignment explanation


    Indices: 6361--6428  Score: 109
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       6351 TTCCTTCATT

                                      
       6361 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *            *       
       6387 TTAATAATAAACTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
       6413 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

       6429 AAACTAAGTA


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   38  1.00

ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA

Found at i:6452 original size:52 final size:51

Alignment explanation


    Indices: 6361--6478  Score: 122
    Period size: 52  Copynumber: 2.4  Consensus size: 51

       6351 TTCCTTCATT

                *                                         *     
       6361 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
          1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA

                                    *      *    *                
       6413 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
          1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA

                               
       6464 -T---CATAAACTAATTAA
          1 TTAAACATAAACTAATTAA

       6479 TATTAAAAAA


Statistics
Matches: 58,  Mismatches: 5, Indels: 10
        0.79            0.07        0.14

Matches are distributed among these distances:
  47   10  0.17
  48    3  0.05
  50    1  0.02
  51   10  0.17
  52   28  0.48
  53    6  0.10

ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34


Consensus pattern (51 bp):   
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Done.