Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019983.1 Corchorus olitorius cultivar O-4 contig20016, 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: 8942
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30


Found at i:3351 original size:29 final size:29

Alignment explanation


    Indices: 3318--3553  Score: 219
    Period size: 29  Copynumber: 8.1  Consensus size: 29

       3308 TCGCACGCTC

                 *                  *    
       3318 AGGGGAATTTTGGTCATTTTTGCATATCT
          1 AGGGGCATTTTGGTCATTTTTGCACATCT

                                *        
       3347 AGGGGCATTTTGGTCATTTTCGCACAT-T
          1 AGGGGCATTTTGGTCATTTTTGCACATCT

                  * *                      
       3375 CAGGGGAACTTTGGTCATTTTTGCACATAC-
          1 -AGGGGCATTTTGGTCATTTTTGCACAT-CT

              *                     *     
       3405 AGTGGCATTTTGGTCATTTTTGCATATAC-
          1 AGGGGCATTTTGGTCATTTTTGCACAT-CT

            *                    *      *
       3434 GGGGGCATTTTGGTCATTTTTACACATCC
          1 AGGGGCATTTTGGTCATTTTTGCACATCT

             *        *          *      *
       3463 AAGGGCATTTCGGTCATTTTTACACATCC
          1 AGGGGCATTTTGGTCATTTTTGCACATCT

             *        *      *   *        
       3492 AAGGGCATTTCGGTCATCTTTACACATTCT
          1 AGGGGCATTTTGGTCATTTTTGCACA-TCT

                   *                *     
       3522 -GGGGCAGTTTGGTCATTTTTGCATACTCT
          1 AGGGGCATTTTGGTCATTTTTGCACA-TCT

               
       3551 AGG
          1 AGG

       3554 TTCTCCTTGG


Statistics
Matches: 175,  Mismatches: 26, Indels: 11
        0.83            0.12        0.05

Matches are distributed among these distances:
  28    2  0.01
  29  169  0.97
  30    4  0.02

ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39


Consensus pattern (29 bp):   
AGGGGCATTTTGGTCATTTTTGCACATCT

Found at i:3478 original size:87 final size:86

Alignment explanation


    Indices: 3324--3541  Score: 251
    Period size: 87  Copynumber: 2.5  Consensus size: 86

       3314 GCTCAGGGGA

                                                       **     *  *           
       3324 ATTTTGGTCATTTTTGCATATCTAGGGGCATTTTGGTCATTTTCGCACATTCAGGGGAACTTTGG
          1 ATTTTGGTCATTTTTGCATATC-AGGGGCATTTTGGTCATTTTTACACATCCAAGGGAACTTTGG

                    *              
       3389 TCATTTTTGCACATAC-AGTGGC
         65 TCATTTTTACACATACAAG-GGC

                                   *                                 *       
       3411 ATTTTGGTCATTTTTGCATATACGGGGGCATTTTGGTCATTTTTACACATCCAAGGGCA-TTTCG
          1 ATTTTGGTCATTTTTGCATAT-CAGGGGCATTTTGGTCATTTTTACACATCCAAGGGAACTTT-G

                           *       
       3475 GTCATTTTTACACATCCAAGGGC
         64 GTCATTTTTACACATACAAGGGC

                *      *   *  *    *      *             
       3498 ATTTCGGTCATCTTTACACATTCTGGGGCAGTTTGGTCATTTTT
          1 ATTTTGGTCATTTTTGCATA-TCAGGGGCATTTTGGTCATTTTT

       3542 GCATACTCTA


Statistics
Matches: 113,  Mismatches: 14, Indels: 8
        0.84            0.10        0.06

Matches are distributed among these distances:
  86    3  0.03
  87  106  0.94
  88    4  0.04

ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40


Consensus pattern (86 bp):   
ATTTTGGTCATTTTTGCATATCAGGGGCATTTTGGTCATTTTTACACATCCAAGGGAACTTTGGT
CATTTTTACACATACAAGGGC

Found at i:5223 original size:15 final size:15

Alignment explanation


    Indices: 5203--5234  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5193 GTTGGGTAAA

                           
       5203 AAAAATCAATCAATC
          1 AAAAATCAATCAATC

                   *       
       5218 AAAAATCCATCAATC
          1 AAAAATCAATCAATC

              
       5233 AA
          1 AA

       5235 CACGTGCCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19


Consensus pattern (15 bp):   
AAAAATCAATCAATC

Found at i:8833 original size:15 final size:15

Alignment explanation


    Indices: 8813--8844  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       8803 TTGGGTAAAA

                           
       8813 AAAAATCAATCAATC
          1 AAAAATCAATCAATC

                   *       
       8828 AAAAATCCATCAATC
          1 AAAAATCAATCAATC

              
       8843 AA
          1 AA

       8845 CACGTGCCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19


Consensus pattern (15 bp):   
AAAAATCAATCAATC
Done.