Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024085.1 Corchorus olitorius cultivar O-4 contig24118, 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: 4991
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34


Found at i:1455 original size:25 final size:25

Alignment explanation


    Indices: 1427--1478  Score: 95
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1417 AAAAATGCCA

                  *                  
       1427 ATAAACTAATGGATGGTGATTGAGG
          1 ATAAACCAATGGATGGTGATTGAGG

                                     
       1452 ATAAACCAATGGATGGTGATTGAGG
          1 ATAAACCAATGGATGGTGATTGAGG

              
       1477 AT
          1 AT

       1479 CGAAAACTGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.37, C:0.06, G:0.31, T:0.27


Consensus pattern (25 bp):   
ATAAACCAATGGATGGTGATTGAGG

Found at i:2317 original size:3 final size:3

Alignment explanation


    Indices: 2309--2337  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       2299 TATATTATAT

                                                   
       2309 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

       2338 CTAAATGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   23  0.92

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


Consensus pattern (3 bp):   
ATA

Found at i:4305 original size:183 final size:182

Alignment explanation


    Indices: 3990--4473  Score: 637
    Period size: 183  Copynumber: 2.6  Consensus size: 182

       3980 CCCACAATAC

                      *               *                  *        *       *  
       3990 CTTCTCTCTCAAGTTCAGATACTCCTCCAGGTTCTCTCATAGTCTTAATAGGAATTAGGATTTTC
          1 CTTCTCTCTCCAGTTCAGATACTCCTTCAGGTTCTCTCATAGTCTCAATAGGAACTAGGA-TATC

                               *                                             
       4055 TTCCTTCTTTTTATGATCATCGGCTTTTGACATTTTTGGTAAATAAACTCTTCCACTATTGGTCA
         65 TT-CTTCTTTTTATGATCAACGGCTTTTGACATTTTTGGTAAATAAACTCTTCCACTATTGGTCA

                                   * *      *                      
       4120 TCCT-TTCGTAACGCGCAGGTCCCGGAATCCTTTCGTTCCGATCAATAAAAACAA
        129 TCCTATT-GTAACGCGCAGGTCCAGAAATCCTATCGTTCCGATCAATAAAAACAA

                   *       *                                *   *            
       4174 CTTCTCTTTCCAGTTTAGATACTCCTTCAGGTTCTCTCATAGTCTCAACAGGCACTAGGATATCT
          1 CTTCTCTCTCCAGTTCAGATACTCCTTCAGGTTCTCTCATAGTCTCAATAGGAACTAGGATATCT

                       *         *                 *     *  *    *  *        
       4239 TCATTCTTTTTGTGATCAACGACTTTTGACATTTTTGGTTAATAACCTTTTCCTCTCTTGGTCAT
         66 TC-TTCTTTTTATGATCAACGGCTTTTGACATTTTTGGTAAATAAACTCTTCCACTATTGGTCAT

                               *                *        *      *
       4304 CCTATTGTAACGCGCAGGTTCAGAAATCCTATCGTTTCGATCAATTAAAACAG
        130 CCTATTGTAACGCGCAGGTCCAGAAATCCTATCGTTCCGATCAATAAAAACAA

                        *                      *     *     *       *         
       4357 CTTCTCTCTCCAATTCAGATACTCCTTCAGGTTCTTTCATACTCTCATTAGGAACGAGGATATCT
          1 CTTCTCTCTCCAGTTCAGATACTCCTTCAGGTTCTCTCATAGTCTCAATAGGAACTAGGATATC-

                       *                            *           
       4422 TTCTTCTTTTTCTGATCAACGGCTTTTGACATTTTTGGTACATAAACTCTTC
         65 TTCTTCTTTTTATGATCAACGGCTTTTGACATTTTTGGTAAATAAACTCTTC

       4474 GATCAGCGGC


Statistics
Matches: 258,  Mismatches: 39, Indels: 7
        0.85            0.13        0.02

Matches are distributed among these distances:
 182    1  0.00
 183  200  0.78
 184   57  0.22

ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39


Consensus pattern (182 bp):   
CTTCTCTCTCCAGTTCAGATACTCCTTCAGGTTCTCTCATAGTCTCAATAGGAACTAGGATATCT
TCTTCTTTTTATGATCAACGGCTTTTGACATTTTTGGTAAATAAACTCTTCCACTATTGGTCATC
CTATTGTAACGCGCAGGTCCAGAAATCCTATCGTTCCGATCAATAAAAACAA

Found at i:4489 original size:39 final size:39

Alignment explanation


    Indices: 4435--4512  Score: 129
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       4425 TTCTTTTTCT

                              *        *           
       4435 GATCAACGGCTTTTGACATTTTTGGTACATAAACTCTTC
          1 GATCAACGGCTTTTGACAGTTTTGGTAAATAAACTCTTC

                 *                                 
       4474 GATCAGCGGCTTTTGACAGTTTTGGTAAATAAACTCTTC
          1 GATCAACGGCTTTTGACAGTTTTGGTAAATAAACTCTTC

       4513 CACTCTTGGT


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  39   36  1.00

ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37


Consensus pattern (39 bp):   
GATCAACGGCTTTTGACAGTTTTGGTAAATAAACTCTTC
Done.