Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008775.1 Corchorus olitorius cultivar O-4 contig08802, 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, 826

Length: 1377
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29


Found at i:251 original size:13 final size:13

Alignment explanation


    Indices: 229--271  Score: 59
    Period size: 13  Copynumber: 3.3  Consensus size: 13

        219 TAATGCACCC

                 *       
        229 AAAATCATTTAAT
          1 AAAATAATTTAAT

                 *      *
        242 AAAATTATTTAAA
          1 AAAATAATTTAAT

                         
        255 AAAATAATTTAAT
          1 AAAATAATTTAAT

                
        268 AAAA
          1 AAAA

        272 CAGTAATAAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  13   26  1.00

ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35


Consensus pattern (13 bp):   
AAAATAATTTAAT

Found at i:1335 original size:26 final size:24

Alignment explanation


    Indices: 1288--1360  Score: 78
    Period size: 26  Copynumber: 3.0  Consensus size: 24

       1278 ATGACCCATG

                           * *       
       1288 CATGTCTCAATAACACACATATATA
          1 CATGTCTCAAT-ACATATATATATA

                                      
       1313 CCATGTCTCAATAGCATATATATAT-
          1 -CATGTCTCAATA-CATATATATATA

                        *           
       1338 CAT-TCTCAATATATATATATATA
          1 CATGTCTCAATACATATATATATA

       1361 TATATATATA


Statistics
Matches: 42,  Mismatches: 3, Indels: 7
        0.81            0.06        0.13

Matches are distributed among these distances:
  22   10  0.24
  23    8  0.19
  24    3  0.07
  25    1  0.02
  26   20  0.48

ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36


Consensus pattern (24 bp):   
CATGTCTCAATACATATATATATA

Found at i:1351 original size:2 final size:2

Alignment explanation


    Indices: 1346--1373  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       1336 ATCATTCTCA

                                                     
       1346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1374 CATT


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):   
AT

Found at i:1355 original size:24 final size:24

Alignment explanation


    Indices: 1288--1361  Score: 78
    Period size: 24  Copynumber: 3.0  Consensus size: 24

       1278 ATGACCCATG

                             *       *
       1288 CATGTCTCAATAACACACATATATAC
          1 CATGTCTCAAT-A-ACATATATATAT

                        *           
       1314 CATGTCTCAATAGCATATATATAT
          1 CATGTCTCAATAACATATATATAT

                          *          
       1338 CAT-TCTCAATATATATATATATAT
          1 CATGTCTCAATA-ACATATATATAT

       1362 ATATATATAT


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  23    8  0.19
  24   22  0.52
  25    1  0.02
  26   11  0.26

ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36


Consensus pattern (24 bp):   
CATGTCTCAATAACATATATATAT
Done.