Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000130.1 Corchorus capsularis cultivar CVL-1 contig00130, 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: 21427
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1254 original size:5 final size:6

Alignment explanation


    Indices: 1239--1263  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       1229 GGAGGTGGCA

                                         
       1239 TTTTTC TTTTTC TTTTTC TTTTTC T
          1 TTTTTC TTTTTC TTTTTC TTTTTC T

       1264 AGGGAGGTGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (6 bp):   
TTTTTC

Found at i:5820 original size:2 final size:2

Alignment explanation


    Indices: 5809--5849  Score: 66
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       5799 ACAGAGCAAG

                               *                                          
       5809 TA TA TA -A TA TA TG TA 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 TA TA TA TA TA TA TA TA

       5850 ACATACATAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   35  0.97

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:7043 original size:19 final size:19

Alignment explanation


    Indices: 7019--7058  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       7009 ATGATATGAA

                               
       7019 TAATCTTGAAAATGCATAC
          1 TAATCTTGAAAATGCATAC

                               
       7038 TAATCTTGAAAATGCATAC
          1 TAATCTTGAAAATGCATAC

              
       7057 TA
          1 TA

       7059 CTCCCTCTCA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33


Consensus pattern (19 bp):   
TAATCTTGAAAATGCATAC

Found at i:9489 original size:23 final size:22

Alignment explanation


    Indices: 9458--9501  Score: 70
    Period size: 23  Copynumber: 2.0  Consensus size: 22

       9448 AATAATTAAC

                                  
       9458 GAAGAGGGCAGATTTGTCCAGA
          1 GAAGAGGGCAGATTTGTCCAGA

                       *          
       9480 GAAGAAGGGCATATTTGTCCAG
          1 GAAG-AGGGCAGATTTGTCCAG

       9502 CTGAGTAATT


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

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20


Consensus pattern (22 bp):   
GAAGAGGGCAGATTTGTCCAGA

Found at i:21089 original size:19 final size:19

Alignment explanation


    Indices: 21065--21104  Score: 55
    Period size: 20  Copynumber: 2.1  Consensus size: 19

      21055 TCTATTAGTC

                                
      21065 ACCTTATAAA-TTTTTAATA
          1 ACCTTA-AAACTTTTTAATA

                                
      21084 ACCTTAAAACCTTTTTAATA
          1 ACCTTAAAA-CTTTTTAATA

             
      21104 A
          1 A

      21105 GCAAGATTTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    3  0.16
  19    6  0.32
  20   10  0.53

ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42


Consensus pattern (19 bp):   
ACCTTAAAACTTTTTAATA

Found at i:21285 original size:21 final size:21

Alignment explanation


    Indices: 21225--21287  Score: 72
    Period size: 22  Copynumber: 2.9  Consensus size: 21

      21215 GCCTTATATT

                      *      *   
      21225 GTTTTTTAGTCACCTTATTAA
          1 GTTTTTTAGTAACCTTACTAA

                      *            
      21246 GTATTTTTACCTAACCTTACTAA
          1 GT-TTTTTA-GTAACCTTACTAA

                        *      
      21269 GTTTTTTAGTAATCTTACT
          1 GTTTTTTAGTAACCTTACT

      21288 GTGGATTTTA


Statistics
Matches: 35,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  21   11  0.31
  22   12  0.34
  23   12  0.34

ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51


Consensus pattern (21 bp):   
GTTTTTTAGTAACCTTACTAA
Done.