Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005706.1 Corchorus capsularis cultivar CVL-1 contig05724, 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: 5207
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37


Found at i:3453 original size:116 final size:116

Alignment explanation


    Indices: 3302--3532  Score: 417
    Period size: 116  Copynumber: 2.0  Consensus size: 116

       3292 ACACAAAAAG

                                                 * *   *                     
       3302 TGCATTTTTTAGTCAATTTGGCTACTTATCCTTACGACTCTTAGTAACTTTCTTGTATACTAAAT
          1 TGCATTTTTTAGTCAATTTGGCTACTTATCCTTACGAATATTAATAACTTTCTTGTATACTAAAT

                                                               
       3367 ATTATCAATCTTGTAATCTTAAATTACTACTCCCTCCATTCCTTATTATTT
         66 ATTATCAATCTTGTAATCTTAAATTACTACTCCCTCCATTCCTTATTATTT

                                                                          *  
       3418 TGCATTTTTTAGTCAATTTGGCTACTTATCCTTACGAATATTAATAACTTTCTTGTATACTAGAT
          1 TGCATTTTTTAGTCAATTTGGCTACTTATCCTTACGAATATTAATAACTTTCTTGTATACTAAAT

                                                     *        
       3483 ATTATCAATCTTGTAATCTTAAATTACTACTCCCTCCATTCGTTATTATT
         66 ATTATCAATCTTGTAATCTTAAATTACTACTCCCTCCATTCCTTATTATT

       3533 ATAAGTCATA


Statistics
Matches: 110,  Mismatches: 5, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 116  110  1.00

ACGTcount: A:0.27, C:0.19, G:0.07, T:0.46


Consensus pattern (116 bp):   
TGCATTTTTTAGTCAATTTGGCTACTTATCCTTACGAATATTAATAACTTTCTTGTATACTAAAT
ATTATCAATCTTGTAATCTTAAATTACTACTCCCTCCATTCCTTATTATTT

Found at i:4019 original size:20 final size:19

Alignment explanation


    Indices: 3974--4036  Score: 58
    Period size: 20  Copynumber: 3.3  Consensus size: 19

       3964 AATGTCACCG

                               
       3974 GATATCCGTCGATATATTC
          1 GATATCCGTCGATATATTC

              *             *    
       3993 GTGTATCCGTCGATATTTATC
          1 G-ATATCCGTCGATATAT-TC

                          *     
       4014 GATAT-C-TCGATAAATCTC
          1 GATATCCGTCGATATAT-TC

                 
       4032 GATAT
          1 GATAT

       4037 ATCCGTAAAT


Statistics
Matches: 36,  Mismatches: 6, Indels: 5
        0.77            0.13        0.11

Matches are distributed among these distances:
  18   14  0.39
  19    2  0.06
  20   17  0.47
  21    3  0.08

ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38


Consensus pattern (19 bp):   
GATATCCGTCGATATATTC

Found at i:4048 original size:10 final size:10

Alignment explanation


    Indices: 4035--4060  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       4025 AAATCTCGAT

                      
       4035 ATATCCGTAA
          1 ATATCCGTAA

                      
       4045 ATATCCGTAA
          1 ATATCCGTAA

                  
       4055 ATATCC
          1 ATATCC

       4061 ATATCAAATT


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

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31


Consensus pattern (10 bp):   
ATATCCGTAA

Found at i:4662 original size:3 final size:3

Alignment explanation


    Indices: 4654--4690  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       4644 TTAAATATAT

                                                             
       4654 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

       4691 CTATTTTGAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATA

Done.