Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012904.1 Corchorus olitorius cultivar O-4 contig12937, 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: 8603
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1401 original size:75 final size:75

Alignment explanation


    Indices: 1262--1401  Score: 230
    Period size: 75  Copynumber: 1.9  Consensus size: 75

       1252 TGAAAAGTCT

                                               *                       *     
       1262 ATAAGAACAAAATAAATACTACTTTCAAGAAATATTAATAAATAGTTTCATTCCCCATCCAAAAA
          1 ATAAGAACAAAATAAATACTACTTTCAAGAAATATAAATAAATAGTTTCATTCCCCATCAAAAAA

                      
       1327 GTCTTACCAA
         66 GTCTTACCAA

                                                                             
       1337 ATAAGAACAAAATAAATACTACAATTTCAAGAAATATAAATAAATAGTTTCATT-CCC-TCAAAA
          1 ATAAGAACAAAATAAATACTAC--TTTCAAGAAATATAAATAAATAGTTTCATTCCCCATCAAAA

              
       1400 AA
         64 AA

       1402 ATAATTCATT


Statistics
Matches: 61,  Mismatches: 2, Indels: 4
        0.91            0.03        0.06

Matches are distributed among these distances:
  75   29  0.48
  76    3  0.05
  77   29  0.48

ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27


Consensus pattern (75 bp):   
ATAAGAACAAAATAAATACTACTTTCAAGAAATATAAATAAATAGTTTCATTCCCCATCAAAAAA
GTCTTACCAA

Found at i:2489 original size:23 final size:24

Alignment explanation


    Indices: 2463--2508  Score: 76
    Period size: 23  Copynumber: 1.9  Consensus size: 24

       2453 AAAAATAGTT

                                    
       2463 TAATCAATGTAT-ATGTATATAGA
          1 TAATCAATGTATAATGTATATAGA

                                   
       2486 TAATCAATGTATAGATGTATATA
          1 TAATCAATGTATA-ATGTATATA

       2509 TGTACGTATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  23   12  0.57
  25    9  0.43

ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39


Consensus pattern (24 bp):   
TAATCAATGTATAATGTATATAGA

Found at i:2532 original size:2 final size:2

Alignment explanation


    Indices: 2527--2554  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2517 TAGATGTGTG

                                                     
       2527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2555 ATTCGTGACT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4603 original size:51 final size:47

Alignment explanation


    Indices: 4530--4671  Score: 142
    Period size: 51  Copynumber: 2.9  Consensus size: 47

       4520 AAAGCAATCT

                 *                                         *
       4530 TTTACATTTCCT-GCACTTTTTCTCAATTTTTACTACAAAATTGAACC
          1 TTTACTTTTCCTCGCACTTTTTCTCAATTTTTA-TACAAAATTGAACA

                *                              * * *        *  
       4577 TTTATTTTTCCTCGCACATTTTTTTCTCAATTTTCAAGATAAAATTGATCA
          1 TTTACTTTTCCTCGCAC---TTTTTCTCAATTTT-TATACAAAATTGAACA

                      * *         *                     
       4628 TTTACTTTTCTTTGCACTTTTTATCAATTTTTATACAAAATTGA
          1 TTTACTTTTCCTCGCACTTTTTCTCAATTTTTATACAAAATTGA

       4672 TTGGTACGCT


Statistics
Matches: 76,  Mismatches: 14, Indels: 10
        0.76            0.14        0.10

Matches are distributed among these distances:
  47   20  0.26
  48   17  0.22
  51   38  0.50
  52    1  0.01

ACGTcount: A:0.27, C:0.18, G:0.05, T:0.49


Consensus pattern (47 bp):   
TTTACTTTTCCTCGCACTTTTTCTCAATTTTTATACAAAATTGAACA

Found at i:7482 original size:17 final size:17

Alignment explanation


    Indices: 7462--7494  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       7452 ACCTTTTCAT

                              
       7462 TTCTTTCATTTT-TTTTA
          1 TTCTTTC-TTTTCTTTTA

                            
       7479 TTCTTTCTTTTCTTTT
          1 TTCTTTCTTTTCTTTT

       7495 TTATTTGTAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    4  0.27
  17   11  0.73

ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79


Consensus pattern (17 bp):   
TTCTTTCTTTTCTTTTA
Done.