Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009154.1 Corchorus capsularis cultivar CVL-1 contig09175, 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: 31872
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:1270 original size:12 final size:12

Alignment explanation


    Indices: 1253--1277  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       1243 GGTTAAATGG

                        
       1253 CACCAAGTTGGA
          1 CACCAAGTTGGA

                        
       1265 CACCAAGTTGGA
          1 CACCAAGTTGGA

             
       1277 C
          1 C

       1278 TGTTGGAGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16


Consensus pattern (12 bp):   
CACCAAGTTGGA

Found at i:1385 original size:19 final size:20

Alignment explanation


    Indices: 1347--1385  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1337 CAACCTATTA

                   *            
       1347 AATGTTTTTGAATATTATGT
          1 AATGTTTATGAATATTATGT

                                
       1367 AATGTTTATGAAT-TTATGT
          1 AATGTTTATGAATATTATGT

       1386 TGTTGAAGAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19    6  0.33
  20   12  0.67

ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54


Consensus pattern (20 bp):   
AATGTTTATGAATATTATGT

Found at i:12664 original size:30 final size:30

Alignment explanation


    Indices: 12624--12687  Score: 110
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      12614 CCATATATGT

                                          
      12624 TGAAGCCTCTCCAGAGGTTAAAGATGAAGA
          1 TGAAGCCTCTCCAGAGGTTAAAGATGAAGA

                 *                    *   
      12654 TGAAGTCTCTCCAGAGGTTAAAGATGCAGA
          1 TGAAGCCTCTCCAGAGGTTAAAGATGAAGA

                
      12684 TGAA
          1 TGAA

      12688 CTCTGATGCT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   32  1.00

ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22


Consensus pattern (30 bp):   
TGAAGCCTCTCCAGAGGTTAAAGATGAAGA

Found at i:18390 original size:35 final size:35

Alignment explanation


    Indices: 18349--18416  Score: 118
    Period size: 35  Copynumber: 1.9  Consensus size: 35

      18339 ACAAGACTTG

                      *                        
      18349 TAAACCAAACTGAGACGCAAGATGCAGCTATTGTA
          1 TAAACCAAACCGAGACGCAAGATGCAGCTATTGTA

                                    *        
      18384 TAAACCAAACCGAGACGCAAGATGTAGCTATTG
          1 TAAACCAAACCGAGACGCAAGATGCAGCTATTG

      18417 GGATGCAGGA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   31  1.00

ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19


Consensus pattern (35 bp):   
TAAACCAAACCGAGACGCAAGATGCAGCTATTGTA

Found at i:20067 original size:18 final size:18

Alignment explanation


    Indices: 20044--20078  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      20034 ATAATTTGTC

                               
      20044 TATAT-ATATATATAATAT
          1 TATATAATA-ATATAATAT

                             
      20062 TATATAATAATATAATA
          1 TATATAATAATATAATA

      20079 ATAATAGGGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   13  0.81
  19    3  0.19

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (18 bp):   
TATATAATAATATAATAT

Found at i:31846 original size:2 final size:2

Alignment explanation


    Indices: 31835--31868  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      31825 TTTTACGATG

                                                                
      31835 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      31869 CACA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.