Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023218.1 Corchorus olitorius cultivar O-4 contig23251, 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: 4865
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33


Found at i:351 original size:42 final size:43

Alignment explanation


    Indices: 304--392  Score: 126
    Period size: 45  Copynumber: 2.0  Consensus size: 43

        294 ATTACCTAAG

                              *                        
        304 TTCTA-CTACATCTCTAGGTAATTCATCAAAATAAAGCTAATA
          1 TTCTACCTACATCTCTAGATAATTCATCAAAATAAAGCTAATA

                      *                            *     
        346 TTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAGTTAATA
          1 TTCTA--CCTACATCTCTAGATAATTCATCAAAATAAAGCTAATA

              
        391 TT
          1 TT

        393 AATTGTTGTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  42    5  0.12
  45   36  0.88

ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37


Consensus pattern (43 bp):   
TTCTACCTACATCTCTAGATAATTCATCAAAATAAAGCTAATA

Found at i:2181 original size:3 final size:3

Alignment explanation


    Indices: 2168--2208  Score: 73
    Period size: 3  Copynumber: 13.3  Consensus size: 3

       2158 TGGAATTCCA

                                                                  
       2168 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
          1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A

       2209 TATTGGTTTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   3   34  0.92
   4    3  0.08

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
AAT

Found at i:2325 original size:12 final size:11

Alignment explanation


    Indices: 2298--2323  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       2288 GGATAACTTT

                       
       2298 AAAATTAAAAA
          1 AAAATTAAAAA

                       
       2309 AAAATTAAAAA
          1 AAAATTAAAAA

                
       2320 AAAA
          1 AAAA

       2324 ATCAATAATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (11 bp):   
AAAATTAAAAA

Found at i:3795 original size:2 final size:2

Alignment explanation


    Indices: 3788--3820  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       3778 TCTTTTGAGC

                                                             
       3788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3821 GCCAAACTCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:4691 original size:2 final size:2

Alignment explanation


    Indices: 4684--4739  Score: 73
    Period size: 2  Copynumber: 29.5  Consensus size: 2

       4674 TAATATGTAG

                                 *           *                            
       4684 TA TA TA TA TA TA TA AA TA -A TA AA TA TA TA TA TA TA TA TA -A
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                     
       4724 TA TA TA T- TA TA TA TA T
          1 TA TA TA TA TA TA TA TA T

       4740 CAACGTACGA


Statistics
Matches: 47,  Mismatches: 4, Indels: 6
        0.82            0.07        0.11

Matches are distributed among these distances:
   1    3  0.06
   2   44  0.94

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:4709 original size:17 final size:17

Alignment explanation


    Indices: 4684--4730  Score: 62
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       4674 TAATATGTAG

                             
       4684 TATAT-ATATATATAAA
          1 TATATAATATATATAAA

                            * 
       4700 TA-ATAAATATATATATA
          1 TATAT-AATATATATAAA

                          
       4717 TATATAATATATAT
          1 TATATAATATATAT

       4731 TATATATATC


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  15    2  0.07
  16    2  0.07
  17   21  0.78
  18    2  0.07

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (17 bp):   
TATATAATATATATAAA

Found at i:4709 original size:21 final size:21

Alignment explanation


    Indices: 4685--4739  Score: 83
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       4675 AATATGTAGT

                                 
       4685 ATATATATATATAAATAATAA
          1 ATATATATATATAAATAATAA

                         *      *
       4706 ATATATATATATATATAATAT
          1 ATATATATATATAAATAATAA

                         
       4727 ATATTATATATAT
          1 ATA-TATATATAT

       4740 CAACGTACGA


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  21   22  0.71
  22    9  0.29

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (21 bp):   
ATATATATATATAAATAATAA
Done.