Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000992.1 Corchorus olitorius cultivar O-4 contig00992, 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: 5071
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:320 original size:20 final size:21

Alignment explanation


    Indices: 283--325  Score: 70
    Period size: 20  Copynumber: 2.1  Consensus size: 21

        273 ATCTCACACA

                                 
        283 AAGATTATCAAAAATCATAGG
          1 AAGATTATCAAAAATCATAGG

                         *       
        304 AAGATTA-CAAAATTCATAGG
          1 AAGATTATCAAAAATCATAGG

              
        324 AA
          1 AA

        326 AATTTATTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20   14  0.67
  21    7  0.33

ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23


Consensus pattern (21 bp):   
AAGATTATCAAAAATCATAGG

Found at i:399 original size:21 final size:21

Alignment explanation


    Indices: 373--448  Score: 98
    Period size: 21  Copynumber: 3.6  Consensus size: 21

        363 CTTATGGAGT

                  *     *        
        373 TTATCACAATTTTATAGGTAA
          1 TTATCAAAATTTAATAGGTAA

                        *       **
        394 TTATCAAAATTTCATATGGTGG
          1 TTATCAAAATTTAATA-GGTAA

                                 
        416 TTATCAAAATTTAATAGGTAA
          1 TTATCAAAATTTAATAGGTAA

                        
        437 TTATCAAAATTT
          1 TTATCAAAATTT

        449 CATAAAAAGA


Statistics
Matches: 47,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  21   29  0.62
  22   18  0.38

ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42


Consensus pattern (21 bp):   
TTATCAAAATTTAATAGGTAA

Found at i:412 original size:43 final size:43

Alignment explanation


    Indices: 329--452  Score: 158
    Period size: 43  Copynumber: 2.9  Consensus size: 43

        319 ATAGGAAAAT

                *            *   *        *    *       *
        329 TTATTAAAATTTTATAGTTAGGTTATCAAAGTTTCTTATGGAGT
          1 TTATCAAAATTTTATAGGTA-ATTATCAAAATTTCATATGGAGG

                  *                                 *  
        373 TTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGTGG
          1 TTATCAAAATTTTATAGGTAATTATCAAAATTTCATATGGAGG

                        *                        
        416 TTATCAAAATTTAATAGGTAATTATCAAAATTTCATA
          1 TTATCAAAATTTTATAGGTAATTATCAAAATTTCATA

        453 AAAAGATTCA


Statistics
Matches: 70,  Mismatches: 10, Indels: 1
        0.86            0.12        0.01

Matches are distributed among these distances:
  43   53  0.76
  44   17  0.24

ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44


Consensus pattern (43 bp):   
TTATCAAAATTTTATAGGTAATTATCAAAATTTCATATGGAGG

Found at i:420 original size:22 final size:21

Alignment explanation


    Indices: 285--452  Score: 99
    Period size: 22  Copynumber: 7.9  Consensus size: 21

        275 CTCACACAAA

                        *        *
        285 GATTATCAAAA-ATCATAGGAA
          1 GATTATCAAAATTTCATAGG-T

                                 *
        306 GATTA-CAAAA-TTCATAGGAA
          1 GATTATCAAAATTTCATAGG-T

            *      *       *    * 
        326 AATTTATTAAAATTTTATAGTT
          1 GA-TTATCAAAATTTCATAGGT

              *        *    *     *
        348 AGGTTATCAAAGTTTCTTATGGA
          1 -GATTATCAAAATTTCATA-GGT

             *      *     *      
        371 GTTTATCACAATTTTATAGGT
          1 GATTATCAAAATTTCATAGGT

            *                     
        392 AATTATCAAAATTTCATATGGT
          1 GATTATCAAAATTTCATA-GGT

             *            *      
        414 GGTTATCAAAATTTAATAGGT
          1 GATTATCAAAATTTCATAGGT

            *                 
        435 AATTATCAAAATTTCATA
          1 GATTATCAAAATTTCATA

        453 AAAAGATTCA


Statistics
Matches: 111,  Mismatches: 30, Indels: 12
        0.73            0.20        0.08

Matches are distributed among these distances:
  20   15  0.14
  21   42  0.38
  22   47  0.42
  23    7  0.06

ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39


Consensus pattern (21 bp):   
GATTATCAAAATTTCATAGGT

Found at i:1233 original size:7 final size:7

Alignment explanation


    Indices: 1211--1252  Score: 59
    Period size: 7  Copynumber: 6.1  Consensus size: 7

       1201 ATCCTACTAT

                   
       1211 ATATAAA
          1 ATATAAA

             *     
       1218 ACA-AAA
          1 ATATAAA

                   
       1224 ATATAAA
          1 ATATAAA

                   
       1231 ATATAAA
          1 ATATAAA

               *   
       1238 ATACAAA
          1 ATATAAA

                   
       1245 ATATAAA
          1 ATATAAA

             
       1252 A
          1 A

       1253 ATATTATTAT


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
   6    5  0.17
   7   25  0.83

ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21


Consensus pattern (7 bp):   
ATATAAA

Found at i:1234 original size:22 final size:22

Alignment explanation


    Indices: 1209--1256  Score: 66
    Period size: 21  Copynumber: 2.3  Consensus size: 22

       1199 TCATCCTACT

                                   
       1209 ATATATAAA-ACAAAAATATAAA
          1 ATATATAAATAC-AAAATATAAA

                                  
       1231 ATATA-AAATACAAAATATAAA
          1 ATATATAAATACAAAATATAAA

                  
       1252 A-ATAT
          1 ATATAT

       1257 TATTATATTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  20    3  0.12
  21   14  0.58
  22    7  0.29

ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25


Consensus pattern (22 bp):   
ATATATAAATACAAAATATAAA

Done.