Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001160.1 Corchorus capsularis cultivar CVL-1 contig01160, 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: 12139
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:1615 original size:16 final size:16

Alignment explanation


    Indices: 1574--1618  Score: 56
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       1564 TTTTATTCGA

                            
       1574 GTATTTTCGGGTTTAG
          1 GTATTTTCGGGTTTAG

                 **          
       1590 GT-TAAGTCGGGTTTAG
          1 GTAT-TTTCGGGTTTAG

                         
       1606 GTATTTTCGGGTT
          1 GTATTTTCGGGTT

       1619 CGGTCTCTGG


Statistics
Matches: 23,  Mismatches: 4, Indels: 4
        0.74            0.13        0.13

Matches are distributed among these distances:
  15    1  0.04
  16   21  0.91
  17    1  0.04

ACGTcount: A:0.13, C:0.07, G:0.33, T:0.47


Consensus pattern (16 bp):   
GTATTTTCGGGTTTAG

Found at i:2117 original size:31 final size:31

Alignment explanation


    Indices: 2082--2153  Score: 78
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2072 TAAATTATTG

                            *                
       2082 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
          1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA

                     *                      
       2113 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
          1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA

                      
       2144 CAAATTAAAA
          1 CAAATTAAAA

       2154 GCTGATAGAC


Statistics
Matches: 34,  Mismatches: 3, Indels: 8
        0.76            0.07        0.18

Matches are distributed among these distances:
  30    7  0.21
  31   23  0.68
  32    4  0.12

ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26


Consensus pattern (31 bp):   
CAAATTAAAAAAATGAAAGTCTTAAATTAAA

Found at i:3117 original size:21 final size:21

Alignment explanation


    Indices: 3074--3117  Score: 54
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       3064 CAGGGTTTAG

                            * *  
       3074 AAACAATTAATTAAAAGCGTT
          1 AAACAATTAATTAAAAACATT

                                  
       3095 AAAC-ATTAATTAAAAACAATT
          1 AAACAATTAATTAAAAAC-ATT

              
       3116 AA
          1 AA

       3118 GGAAGGGAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20   12  0.60
  21    8  0.40

ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27


Consensus pattern (21 bp):   
AAACAATTAATTAAAAACATT

Found at i:4053 original size:6 final size:6

Alignment explanation


    Indices: 4044--4083  Score: 57
    Period size: 6  Copynumber: 7.0  Consensus size: 6

       4034 GATGATTCTG

                                        *                   
       4044 ATGATT ATGATT ATGATT ATGATT TTGATT A--ATT ATGATT
          1 ATGATT ATGATT ATGATT ATGATT ATGATT ATGATT ATGATT

       4084 TTTATTGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   4    4  0.13
   6   26  0.87

ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53


Consensus pattern (6 bp):   
ATGATT

Found at i:5178 original size:156 final size:156

Alignment explanation


    Indices: 4894--5198  Score: 547
    Period size: 156  Copynumber: 2.0  Consensus size: 156

       4884 TTTCCAGGTT

                                                       * *           *       
       4894 TTTATTCAGCCTTTCAAGTTACAGTCACAAACTCACAATTGTATAGTTTATGTAAACGATTGAAA
          1 TTTATTCAGCCTTTCAAGTTACAGTCACAAACTCACAATTGTACAATTTATGTAAACAATTGAAA

                                                         *                   
       4959 TCAAGTAGATAAGGACATAGGGTTTGGTCCCTTAAGCTTGAAATTTAGAGAACTATTTAGGATGT
         66 TCAAGTAGATAAGGACATAGGGTTTGGTCCCTTAAGCTTGAAATTCAGAGAACTATTTAGGATGT

                                      
       5024 GAAATTGTTACTGAAATGCGACCCAA
        131 GAAATTGTTACTGAAATGCGACCCAA

                      *      *                                               
       5050 TTTATTCAGCGTTTCAATTTACAGTCACAAACTCACAATTGTACAATTTATGTAAACAATTGAAA
          1 TTTATTCAGCCTTTCAAGTTACAGTCACAAACTCACAATTGTACAATTTATGTAAACAATTGAAA

                          *                                                  
       5115 TCAAGTAGATAAGGGCATAGGGTTTGGTCCCTTAAGCTTGAAATTCAGAGAACTATTTAGGATGT
         66 TCAAGTAGATAAGGACATAGGGTTTGGTCCCTTAAGCTTGAAATTCAGAGAACTATTTAGGATGT

                               
       5180 GAAATTGTTACTGAAATGC
        131 GAAATTGTTACTGAAATGC

       5199 AACCTGATTT


Statistics
Matches: 142,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 156  142  1.00

ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32


Consensus pattern (156 bp):   
TTTATTCAGCCTTTCAAGTTACAGTCACAAACTCACAATTGTACAATTTATGTAAACAATTGAAA
TCAAGTAGATAAGGACATAGGGTTTGGTCCCTTAAGCTTGAAATTCAGAGAACTATTTAGGATGT
GAAATTGTTACTGAAATGCGACCCAA

Found at i:9199 original size:2 final size:2

Alignment explanation


    Indices: 9192--9220  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       9182 GTCATTTCAC

                                                       
       9192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       9221 TAAAGGTTGG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.