Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010166.1 Corchorus olitorius cultivar O-4 contig10198, 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: 7075
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:564 original size:2 final size:2

Alignment explanation


    Indices: 557--587  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        547 CTTTAACTAG

                                                          
        557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        588 TATCTTATCA


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

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:644 original size:66 final size:66

Alignment explanation


    Indices: 574--712  Score: 269
    Period size: 66  Copynumber: 2.1  Consensus size: 66

        564 ATATATATAT

                                                                             
        574 ATATATATATATATTATCTTATCACTAATAATAATAATTAACAATACTCAATTTCATGTTAGGGA
          1 ATATATATATATATTATCTTATCACTAATAATAATAATTAACAATACTCAATTTCATGTTAGGGA

             
        639 C
         66 C

                                                     *                       
        640 ATATATATATATATTATCTTATCACTAATAATAATAATTAAGAATACTCAATTTCATGTTAGGGA
          1 ATATATATATATATTATCTTATCACTAATAATAATAATTAACAATACTCAATTTCATGTTAGGGA

             
        705 C
         66 C

                   
        706 ATATATA
          1 ATATATA

        713 GAGAGAGTTA


Statistics
Matches: 72,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  66   72  1.00

ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40


Consensus pattern (66 bp):   
ATATATATATATATTATCTTATCACTAATAATAATAATTAACAATACTCAATTTCATGTTAGGGA
C

Found at i:4585 original size:113 final size:112

Alignment explanation


    Indices: 4315--4638  Score: 444
    Period size: 113  Copynumber: 3.0  Consensus size: 112

       4305 ATATTTATAA

                            *           *        *                           
       4315 AGAATTTGGCATTTCCTCCCAT-TTTCCTTTTTTTCCATTTCTCTAATCAAACAAAACTCCCTTG
          1 AGAATTTGGCATTTCCCCCCATATTTCCCTTTTTTCCTTTTCTCTAATCAAACAAAACTCCCTTG

                                           *                
       4379 AGAAGAAATGGCAAATCTAT----AGAT-GAATCATATGTATTCAAAT
         66 AGAAGAAATGGC-AATCTATACGAAGATGGATTCATATGTATTCAAAT

                                                 *                           
       4422 AGAATTTGG-------CCCC--ATTTCCCTTTTTTCATTTTTCTCTAATCAAACAAAACTCCCTT
          1 AGAATTTGGCATTTCCCCCCATATTTCCCTTTTTTC-CTTTTCTCTAATCAAACAAAACTCCCTT

                                                            
       4478 GAGAAGAAATGGCAATCTATACGAAGATGGATTCATATGTATTCAAAT
         65 GAGAAGAAATGGCAATCTATACGAAGATGGATTCATATGTATTCAAAT

                                                                         *   
       4526 AGAATTTGGCATTTCCCCCCATAATTTCCCTTTTTTCCTTTTCTCTAATCAAACAAAACTCACTT
          1 AGAATTTGGCATTTCCCCCCAT-ATTTCCCTTTTTTCCTTTTCTCTAATCAAACAAAACTCCCTT

                    *                             *         
       4591 GAGAAGAAGTGGCAATCTATACGAAGATGGATTCATATATATTCAAAT
         65 GAGAAGAAATGGCAATCTATACGAAGATGGATTCATATGTATTCAAAT

       4639 GGACATGTCC


Statistics
Matches: 191,  Mismatches: 9, Indels: 28
        0.84            0.04        0.12

Matches are distributed among these distances:
  99   19  0.10
 100   42  0.22
 103    4  0.02
 104   27  0.14
 107    9  0.05
 111    4  0.02
 113   72  0.38
 114   14  0.07

ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35


Consensus pattern (112 bp):   
AGAATTTGGCATTTCCCCCCATATTTCCCTTTTTTCCTTTTCTCTAATCAAACAAAACTCCCTTG
AGAAGAAATGGCAATCTATACGAAGATGGATTCATATGTATTCAAAT

Found at i:5857 original size:29 final size:30

Alignment explanation


    Indices: 5808--5907  Score: 112
    Period size: 29  Copynumber: 3.3  Consensus size: 30

       5798 AAGTACCTAA

                     *                    
       5808 TTAGTCCCTGTACTATTGAAAAAAATCAAT
          1 TTAGTCCCTCTACTATTGAAAAAAATCAAT

                        *        ***  *   
       5838 TTAGTCCCTCTATTA-TGAAATCTATTAAT
          1 TTAGTCCCTCTACTATTGAAAAAAATCAAT

                      *             *      
       5867 TTAGTCCCTCCACTATTGAAAAGAGATCAAT
          1 TTAGTCCCTCTACTATTGAAAA-AAATCAAT

                      
       5898 TTAGTCCCTC
          1 TTAGTCCCTC

       5908 CGTTAAATTG


Statistics
Matches: 56,  Mismatches: 12, Indels: 3
        0.79            0.17        0.04

Matches are distributed among these distances:
  29   23  0.41
  30   18  0.32
  31   15  0.27

ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36


Consensus pattern (30 bp):   
TTAGTCCCTCTACTATTGAAAAAAATCAAT
Done.