Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009249.1 Corchorus capsularis cultivar CVL-1 contig09270, 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: 10156
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:2310 original size:3 final size:3

Alignment explanation


    Indices: 2302--2333  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       2292 TTCACTATAT

                                                      
       2302 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

       2334 TTCTGCAAGC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:5222 original size:42 final size:43

Alignment explanation


    Indices: 5148--5304  Score: 201
    Period size: 43  Copynumber: 3.7  Consensus size: 43

       5138 CCCGAACAAG

                            * *         *      *        
       5148 GGAGAAC-GACAACATTGTAGATCGGCATAAGTGTTAGAACATA
          1 GGAGAACAGA-AACATCGAAGATCGGCAGAAGTGTCAGAACATA

                         *                             
       5191 GGAGAACAG-AACCTCGAAGATCGGCAGAAGTGTCAGAACATA
          1 GGAGAACAGAAACATCGAAGATCGGCAGAAGTGTCAGAACATA

                             *         *               
       5233 GGAGAACAGAAACATCGCAGATCGGCAAAAGTGTCAGAACATA
          1 GGAGAACAGAAACATCGAAGATCGGCAGAAGTGTCAGAACATA

                * *                *     
       5276 GGAGGATAGAAACATCGAAGATCAGCAGA
          1 GGAGAACAGAAACATCGAAGATCGGCAGA

       5305 TCATATATGG


Statistics
Matches: 99,  Mismatches: 13, Indels: 4
        0.85            0.11        0.03

Matches are distributed among these distances:
  42   37  0.37
  43   61  0.62
  44    1  0.01

ACGTcount: A:0.42, C:0.17, G:0.27, T:0.14


Consensus pattern (43 bp):   
GGAGAACAGAAACATCGAAGATCGGCAGAAGTGTCAGAACATA

Found at i:5444 original size:100 final size:100

Alignment explanation


    Indices: 5321--5504  Score: 307
    Period size: 100  Copynumber: 1.8  Consensus size: 100

       5311 ATGGAGATCA

                                                                   *         
       5321 TTGTGTTGATTACAAACTTGAAAGATTTAATCGCCGCAAGACCCGAA-AGTGGGAGAACGACAAC
          1 TTGTGTTGATTACAAACTTGAAAGATTTAATCGCCGCAAGACCCGAACA-TGGGAAAACGACAAC

                       *                        
       5385 ATTGTAAATCGGCAGAAGTGTCAGACAAGGAAATCC
         65 ATTGTAAATCGACAGAAGTGTCAGACAAGGAAATCC

                            *                   * *                          
       5421 TTGTGTTGATTACAAAGTTGAAAGATTTAATCGCCGTAGGACCCGAACATGGGAAAACGACAACA
          1 TTGTGTTGATTACAAACTTGAAAGATTTAATCGCCGCAAGACCCGAACATGGGAAAACGACAACA

                               
       5486 TTGTAAATCGACAGAAGTG
         66 TTGTAAATCGACAGAAGTG

       5505 GCCGTATGAC


Statistics
Matches: 78,  Mismatches: 5, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
 100   77  0.99
 101    1  0.01

ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22


Consensus pattern (100 bp):   
TTGTGTTGATTACAAACTTGAAAGATTTAATCGCCGCAAGACCCGAACATGGGAAAACGACAACA
TTGTAAATCGACAGAAGTGTCAGACAAGGAAATCC

Found at i:5544 original size:52 final size:52

Alignment explanation


    Indices: 5453--5552  Score: 139
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       5443 AGATTTAATC

                                        *     *                 
       5453 GCCGTAGGACCCGAACATGGGAAAACGACAACATTGTAAATCGACAGAAGTG
          1 GCCGTAGGACCCGAACATGGGAAAACGAAAACATCGTAAATCGACAGAAGTG

                  *               *                     *    
       5505 GCCGTATGACCCGAACATGGGAGAAC-AAATACATCGTAAATCGGCAGA
          1 GCCGTAGGACCCGAACATGGGAAAACGAAA-ACATCGTAAATCGACAGA

       5553 GTGCCAGATA


Statistics
Matches: 42,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  51    2  0.05
  52   40  0.95

ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14


Consensus pattern (52 bp):   
GCCGTAGGACCCGAACATGGGAAAACGAAAACATCGTAAATCGACAGAAGTG

Found at i:8010 original size:24 final size:23

Alignment explanation


    Indices: 7979--8028  Score: 73
    Period size: 24  Copynumber: 2.1  Consensus size: 23

       7969 AGGCATTGCC

                        *          
       7979 CTGATTTTAGGCTTGCTCTATTT
          1 CTGATTTTAGGCATGCTCTATTT

                                *   
       8002 CTGAGTTTTAGGCATGCTCTGTTT
          1 CTGA-TTTTAGGCATGCTCTATTT

               
       8026 CTG
          1 CTG

       8029 TTAAATGTAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  23    4  0.17
  24   20  0.83

ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48


Consensus pattern (23 bp):   
CTGATTTTAGGCATGCTCTATTT

Found at i:10132 original size:2 final size:2

Alignment explanation


    Indices: 10125--10156  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      10115 GAAATATTAC

                                                           
      10125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Done.