Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006829.1 Corchorus capsularis cultivar CVL-1 contig06850, 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: 27764
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Found at i:1322 original size:16 final size:16

Alignment explanation


    Indices: 1293--1367  Score: 98
    Period size: 16  Copynumber: 4.8  Consensus size: 16

       1283 GTCGGGTTGA

                     *      
       1293 TCGGGTTCGAGTCATT
          1 TCGGGTTCGGGTCATT

             *     *        
       1309 TTGGGTTTGGGTCATT
          1 TCGGGTTCGGGTCATT

                         *  
       1325 TCGGGTTCGGGTCGTT
          1 TCGGGTTCGGGTCATT

                *           
       1341 T-GGATTCGGGTCATT
          1 TCGGGTTCGGGTCATT

                        
       1356 TCGGGTTCGGGT
          1 TCGGGTTCGGGT

       1368 ACCCAAAAAT


Statistics
Matches: 49,  Mismatches: 9, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  15   13  0.27
  16   36  0.73

ACGTcount: A:0.07, C:0.15, G:0.39, T:0.40


Consensus pattern (16 bp):   
TCGGGTTCGGGTCATT

Found at i:1352 original size:31 final size:32

Alignment explanation


    Indices: 1293--1367  Score: 107
    Period size: 31  Copynumber: 2.4  Consensus size: 32

       1283 GTCGGGTTGA

                     *    *     *  *        
       1293 TCGGGTTCGAGTCATTTTGGGTTTGGGTCATT
          1 TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT

                                            
       1325 TCGGGTTCGGGTC-GTTTGGATTCGGGTCATT
          1 TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT

                        
       1356 TCGGGTTCGGGT
          1 TCGGGTTCGGGT

       1368 ACCCAAAAAT


Statistics
Matches: 39,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  31   27  0.69
  32   12  0.31

ACGTcount: A:0.07, C:0.15, G:0.39, T:0.40


Consensus pattern (32 bp):   
TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT

Found at i:7038 original size:21 final size:21

Alignment explanation


    Indices: 7014--7060  Score: 85
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       7004 GTCAAGATAT

                         *       
       7014 CAAAGTTATCAAGTAAAAGGC
          1 CAAAGTTATCAAGAAAAAGGC

                                 
       7035 CAAAGTTATCAAGAAAAAGGC
          1 CAAAGTTATCAAGAAAAAGGC

                 
       7056 CAAAG
          1 CAAAG

       7061 ATAATGTAAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.51, C:0.15, G:0.19, T:0.15


Consensus pattern (21 bp):   
CAAAGTTATCAAGAAAAAGGC

Found at i:8601 original size:65 final size:65

Alignment explanation


    Indices: 8497--8630  Score: 268
    Period size: 65  Copynumber: 2.1  Consensus size: 65

       8487 ATTACTCGAG

                                                                             
       8497 AAATTATTAGGTGGGACGGACCTCCACGTTATCTATAGGACTAACAAATAGAATTTTGTCATGTT
          1 AAATTATTAGGTGGGACGGACCTCCACGTTATCTATAGGACTAACAAATAGAATTTTGTCATGTT

                                                                             
       8562 AAATTATTAGGTGGGACGGACCTCCACGTTATCTATAGGACTAACAAATAGAATTTTGTCATGTT
          1 AAATTATTAGGTGGGACGGACCTCCACGTTATCTATAGGACTAACAAATAGAATTTTGTCATGTT

                
       8627 AAAT
          1 AAAT

       8631 AAACTCCTTA


Statistics
Matches: 69,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  65   69  1.00

ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32


Consensus pattern (65 bp):   
AAATTATTAGGTGGGACGGACCTCCACGTTATCTATAGGACTAACAAATAGAATTTTGTCATGTT

Found at i:20289 original size:35 final size:35

Alignment explanation


    Indices: 20238--20307  Score: 104
    Period size: 35  Copynumber: 2.0  Consensus size: 35

      20228 TCATCTTTCC

                       *      *                
      20238 CCATTTGTTCTTACAGTTTTAGTAACCTCAAAGGA
          1 CCATTTGTTCTCACAGTTCTAGTAACCTCAAAGGA

                                    *     *    
      20273 CCATTTGTTCTCACAGTTCTAGTACCCTCACAGGA
          1 CCATTTGTTCTCACAGTTCTAGTAACCTCAAAGGA

      20308 ACTGTATCAG


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  35   31  1.00

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


Consensus pattern (35 bp):   
CCATTTGTTCTCACAGTTCTAGTAACCTCAAAGGA

Found at i:23652 original size:18 final size:17

Alignment explanation


    Indices: 23624--23660  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 17

      23614 GAAATCCGAA

                             
      23624 ATTAAAAAAGCAAAAAT
          1 ATTAAAAAAGCAAAAAT

                           *  
      23641 ATTAACAAAAGCAAATAT
          1 ATTAA-AAAAGCAAAAAT

              
      23659 AT
          1 AT

      23661 ATATATATAT


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

Matches are distributed among these distances:
  17    5  0.28
  18   13  0.72

ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22


Consensus pattern (17 bp):   
ATTAAAAAAGCAAAAAT

Found at i:24252 original size:18 final size:18

Alignment explanation


    Indices: 24229--24264  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      24219 GAAAAAGACC

                              
      24229 ATTGGTGTAATGGTTTTA
          1 ATTGGTGTAATGGTTTTA

                              
      24247 ATTGGTGTAATGGTTTTA
          1 ATTGGTGTAATGGTTTTA

      24265 GATTATCCCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50


Consensus pattern (18 bp):   
ATTGGTGTAATGGTTTTA
Done.