Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009130.1 Corchorus capsularis cultivar CVL-1 contig09151, 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: 8014
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:2584 original size:156 final size:156

Alignment explanation


    Indices: 2424--2778  Score: 484
    Period size: 156  Copynumber: 2.3  Consensus size: 156

       2414 AGCCTTGTTG

                   *                                                   *     
       2424 GACTTAGTATAAAAAACTTATGCTAGTTTTTCATTTAAGGACAACT-CAGGGAGAG-AATCCTAG
          1 GACTTAGAATAAAAAACTTATGCTAGTTTTTCATTTAAGGACAA-TACAGGGAG-GCAAACCTAG

                   *    *      *      **                   *                 
       2487 TTCACCATCAAGGGGAGCTTGGTTTTTGTTAGAA-TTTTTTGAATAGTCTTATG-GAGATATTCT
         64 TTCACCACCAAGAGGAGCTCGGTTTTACTTA-AATTTTTTTGAATAGCCTTATGTG-GATATTCT

                       *  **            * 
       2550 AAGTACCTTGGTAATGTTTCAGCTCATTTA
        127 AAGTACCTTGGAAAAATTTCAGCTCATTCA

                            *                                                
       2580 GACTTAGAATAAAAAAGTTATGCTAGTTTTTCATTTAAGGACAATACAGGGAGGCAAACCTAGTT
          1 GACTTAGAATAAAAAACTTATGCTAGTTTTTCATTTAAGGACAATACAGGGAGGCAAACCTAGTT

                                                  **              *          
       2645 CACCACCAAGAGGAGCTCGGTTTTACTTAAATTTTTTTTCATAGCCTTATGTGGGTATTCTAAGT
         66 CACCACCAAGAGGAGCTCGGTTTTACTTAAATTTTTTTGAATAGCCTTATGTGGATATTCTAAGT

            *                         
       2710 CCCTTGGAAAAATTTCAGCTCATTCA
        131 ACCTTGGAAAAATTTCAGCTCATTCA

                      *                                
       2736 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
          1 GACTTAGAATAAAAAACTTATGCTAGTTTTTCATTTAAGGACA

       2779 GTTTGAGGTG


Statistics
Matches: 176,  Mismatches: 19, Indels: 8
        0.87            0.09        0.04

Matches are distributed among these distances:
 155    4  0.02
 156  171  0.97
 157    1  0.01

ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35


Consensus pattern (156 bp):   
GACTTAGAATAAAAAACTTATGCTAGTTTTTCATTTAAGGACAATACAGGGAGGCAAACCTAGTT
CACCACCAAGAGGAGCTCGGTTTTACTTAAATTTTTTTGAATAGCCTTATGTGGATATTCTAAGT
ACCTTGGAAAAATTTCAGCTCATTCA

Found at i:3160 original size:17 final size:17

Alignment explanation


    Indices: 3138--3170  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       3128 GCAGTCTATC

                             
       3138 ACCTCATACTACCTAGT
          1 ACCTCATACTACCTAGT

                            
       3155 ACCTCATACTACCTAG
          1 ACCTCATACTACCTAG

       3171 GTACTATGGG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27


Consensus pattern (17 bp):   
ACCTCATACTACCTAGT

Found at i:7235 original size:33 final size:33

Alignment explanation


    Indices: 7182--7268  Score: 104
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       7172 CAAAGAATGT

                 *         *     *           
       7182 TTTAGATGTTGTTTGCGATGATACTAAACCTAA
          1 TTTAGGTGTTGTTTGTGATGACACTAAACCTAA

                                         *  * 
       7215 TTT-GAGTGTTGTTTGTGATGACACTAAATCTGA
          1 TTTAG-GTGTTGTTTGTGATGACACTAAACCTAA

                          *      
       7248 TTTAGGTGTTGTTTATGATGA
          1 TTTAGGTGTTGTTTGTGATGA

       7269 ATACAAATCT


Statistics
Matches: 46,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  32    1  0.02
  33   44  0.96
  34    1  0.02

ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44


Consensus pattern (33 bp):   
TTTAGGTGTTGTTTGTGATGACACTAAACCTAA

Found at i:7313 original size:33 final size:33

Alignment explanation


    Indices: 7276--7415  Score: 244
    Period size: 33  Copynumber: 4.2  Consensus size: 33

       7266 TGAATACAAA

                                   *         
       7276 TCTGTTTTGGTTGATCATAGCATAGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                         *                  *
       7309 TCTGTTTTGGTTGGTCATAGCATTGCAAATAAA
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                    *                        
       7342 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                                             
       7375 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                    
       7408 TCTGTTTT
          1 TCTGTTTT

       7416 TGGGTGAAAA


Statistics
Matches: 100,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  33  100  1.00

ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43


Consensus pattern (33 bp):   
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

Found at i:7760 original size:30 final size:30

Alignment explanation


    Indices: 7724--7780  Score: 98
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       7714 TCTTCAAGGG

                                           
       7724 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
          1 GGAGGGAATGATGC-CCCAAGGACTTATCAT

                                       
       7754 GGAGGGAATGATGCCCCAAGGACTTAT
          1 GGAGGGAATGATGCCCCAAGGACTTAT

       7781 TATAGACTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.28, C:0.19, G:0.33, T:0.19


Consensus pattern (30 bp):   
GGAGGGAATGATGCCCCAAGGACTTATCAT
Done.