Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020122.1 Corchorus olitorius cultivar O-4 contig20155, 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: 8563
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:1300 original size:5 final size:5

Alignment explanation


    Indices: 1290--1328  Score: 50
    Period size: 5  Copynumber: 8.6  Consensus size: 5

       1280 AGTGTGATTA

                                                               
       1290 TTATC TTATC TTATC TTA-C -TATC TTA-C -TATC TTATC TTA
          1 TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTA

       1329 CTATATTATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 8
        0.79            0.00        0.21

Matches are distributed among these distances:
   3    4  0.13
   4    4  0.13
   5   22  0.73

ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56


Consensus pattern (5 bp):   
TTATC

Found at i:1312 original size:13 final size:13

Alignment explanation


    Indices: 1291--1337  Score: 53
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       1281 GTGTGATTAT

                          
       1291 TATCTTATCTTATC
          1 TATCTTATCTTA-C

                          
       1305 T-TAC-TATCTTAC
          1 TAT-CTTATCTTAC

                         
       1317 TATCTTATCTTAC
          1 TATCTTATCTTAC

               *    
       1330 TATATTAT
          1 TATCTTAT

       1338 ATATTATATA


Statistics
Matches: 29,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  12    3  0.10
  13   24  0.83
  14    2  0.07

ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55


Consensus pattern (13 bp):   
TATCTTATCTTAC

Found at i:1342 original size:7 final size:7

Alignment explanation


    Indices: 1330--1357  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

       1320 CTTATCTTAC

                   
       1330 TATATTA
          1 TATATTA

                   
       1337 TATATTA
          1 TATATTA

                   
       1344 TATATTA
          1 TATATTA

                   
       1351 TATATTA
          1 TATATTA

       1358 CTAGTACTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (7 bp):   
TATATTA

Found at i:1817 original size:130 final size:131

Alignment explanation


    Indices: 1583--1821  Score: 444
    Period size: 130  Copynumber: 1.8  Consensus size: 131

       1573 GTGAGATTGA

                                                                             
       1583 AGTTTGATGAAAACTGATTTTAAATTACATCTTGTGTAATTATAAATTTTTTGTTAATCTATACC
          1 AGTTTGATGAAAACTGATTTTAAATTACATCTTGTGTAATTATAAATTTTTTGTTAATCTATACC

                                                                             
       1648 TTACTATTAAAGTTATCCTCAAACTGTTGTATACTCAACATTTGGCATTTCTCTTGTTGTATGCT
         66 TTACTATTAAAGTTATCCTCAAACTGTTGTATACTCAACATTTGGCATTTCTCTTGTTGTATGCT

             
       1713 C
        131 C

                                                 *       *                   
       1714 AGTTTGATGAAAACTGATTTTAAATTACATCTTGTGTGA-TATAATTTTTTTGTTAATCTATACC
          1 AGTTTGATGAAAACTGATTTTAAATTACATCTTGTGTAATTATAAATTTTTTGTTAATCTATACC

                                            *           
       1778 TTACTATTAAAGTTATCCTCAAACTGTTGTATGCTCAACATTTG
         66 TTACTATTAAAGTTATCCTCAAACTGTTGTATACTCAACATTTG

       1822 ACTTTTTCCT


Statistics
Matches: 105,  Mismatches: 3, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
 130   67  0.64
 131   38  0.36

ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45


Consensus pattern (131 bp):   
AGTTTGATGAAAACTGATTTTAAATTACATCTTGTGTAATTATAAATTTTTTGTTAATCTATACC
TTACTATTAAAGTTATCCTCAAACTGTTGTATACTCAACATTTGGCATTTCTCTTGTTGTATGCT
C

Found at i:5587 original size:21 final size:21

Alignment explanation


    Indices: 5548--5596  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5538 TCAATGCTTT

                         **       
       5548 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
       5570 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
       5591 A-GAAGC
          1 AGGAAGC

       5597 TACAATTCTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA
Done.