Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001034.1 Corchorus olitorius cultivar O-4 contig01034, 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: 2577
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:1329 original size:15 final size:15

Alignment explanation


    Indices: 1309--1339  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1299 TTTATCTTTA

                           
       1309 TTATCTTCTTATATT
          1 TTATCTTCTTATATT

                           
       1324 TTATCTTCTTATATT
          1 TTATCTTCTTATATT

             
       1339 T
          1 T

       1340 ACAGTTTACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68


Consensus pattern (15 bp):   
TTATCTTCTTATATT

Found at i:1693 original size:45 final size:45

Alignment explanation


    Indices: 1644--1780  Score: 115
    Period size: 45  Copynumber: 3.1  Consensus size: 45

       1634 TCTTTATGTA

                                                         
       1644 TTCTTTCTATATATTTTATTTAACTGATTTGAAATCATTTTGTTT
          1 TTCTTTCTATATATTTTATTTAACTGATTTGAAATCATTTTGTTT

                  * *     ** **            * **       *   
       1689 TTCTTTATCTGA-AAATCCTTT---TG-TTTTAGTTC-TTTTTTTT
          1 TTCTTTCTAT-ATATTTTATTTAACTGATTTGAAATCATTTTGTTT

                                      *                   
       1729 TGTCTTTCTATATATTTTATTTAACTAATTTGAAATCATTTTGTTT
          1 T-TCTTTCTATATATTTTATTTAACTGATTTGAAATCATTTTGTTT

                  
       1775 TTCTTT
          1 TTCTTT

       1781 ATCTTAAAAT


Statistics
Matches: 63,  Mismatches: 21, Indels: 16
        0.63            0.21        0.16

Matches are distributed among these distances:
  40    9  0.14
  41   18  0.29
  42    2  0.03
  44    1  0.02
  45   24  0.38
  46    9  0.14

ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62


Consensus pattern (45 bp):   
TTCTTTCTATATATTTTATTTAACTGATTTGAAATCATTTTGTTT

Found at i:1750 original size:86 final size:86

Alignment explanation


    Indices: 1645--1813  Score: 320
    Period size: 86  Copynumber: 2.0  Consensus size: 86

       1635 CTTTATGTAT

                                    *                                        
       1645 TCTTTCTATATATTTTATTTAACTGATTTGAAATCATTTTGTTTTTCTTTATCTGAAAATCCTTT
          1 TCTTTCTATATATTTTATTTAACTAATTTGAAATCATTTTGTTTTTCTTTATCTGAAAATCCTTT

                                 
       1710 TGTTTTAGTTCTTTTTTTTTG
         66 TGTTTTAGTTCTTTTTTTTTG

                                                                  *          
       1731 TCTTTCTATATATTTTATTTAACTAATTTGAAATCATTTTGTTTTTCTTTATCTTAAAATCCTTT
          1 TCTTTCTATATATTTTATTTAACTAATTTGAAATCATTTTGTTTTTCTTTATCTGAAAATCCTTT

                              
       1796 TGTTTTAGTTCTTTTTTT
         66 TGTTTTAGTTCTTTTTTT

       1814 CTTTACTAAT


Statistics
Matches: 81,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  86   81  1.00

ACGTcount: A:0.21, C:0.11, G:0.07, T:0.62


Consensus pattern (86 bp):   
TCTTTCTATATATTTTATTTAACTAATTTGAAATCATTTTGTTTTTCTTTATCTGAAAATCCTTT
TGTTTTAGTTCTTTTTTTTTG
Done.