Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010519.1 Corchorus olitorius cultivar O-4 contig10551, 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: 10795
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1349 original size:9 final size:9

Alignment explanation


    Indices: 1335--1370  Score: 65
    Period size: 9  Copynumber: 4.1  Consensus size: 9

       1325 TTCTTTTCCC

                     
       1335 TTCTTTTTT
          1 TTCTTTTTT

                     
       1344 TTCTTTTTT
          1 TTCTTTTTT

                     
       1353 TTCTTTTTT
          1 TTCTTTTTT

                     
       1362 TT-TTTTTT
          1 TTCTTTTTT

             
       1370 T
          1 T

       1371 GTATTTGTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   8    7  0.26
   9   20  0.74

ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92


Consensus pattern (9 bp):   
TTCTTTTTT

Found at i:1361 original size:16 final size:15

Alignment explanation


    Indices: 1340--1369  Score: 51
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       1330 TTCCCTTCTT

                            
       1340 TTTTTTCTTTTTTTTC
          1 TTTTTT-TTTTTTTTC

                          
       1356 TTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTT

       1370 TGTATTTGTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93


Consensus pattern (15 bp):   
TTTTTTTTTTTTTTC

Found at i:1361 original size:17 final size:16

Alignment explanation


    Indices: 1339--1370  Score: 55
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1329 TTTCCCTTCT

                             
       1339 TTTTTTTCTTTTTTTTC
          1 TTTTTTT-TTTTTTTTC

                           
       1356 TTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTT

       1371 GTATTTGTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    8  0.53
  17    7  0.47

ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94


Consensus pattern (16 bp):   
TTTTTTTTTTTTTTTC

Found at i:2421 original size:21 final size:20

Alignment explanation


    Indices: 2375--2432  Score: 82
    Period size: 19  Copynumber: 2.9  Consensus size: 20

       2365 CTGTTTAGCA

                                
       2375 ACTGTACAGATGAGATTACG
          1 ACTGTACAGATGAGATTACG

                       *      * 
       2395 -CTGTACAGATTAGATTAGG
          1 ACTGTACAGATGAGATTACG

                               
       2414 TACTGTACAGATGAGATTA
          1 -ACTGTACAGATGAGATTA

       2433 TTAGAGCAGC


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  19   17  0.52
  21   16  0.48

ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29


Consensus pattern (20 bp):   
ACTGTACAGATGAGATTACG

Found at i:3289 original size:13 final size:13

Alignment explanation


    Indices: 3271--3296  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3261 CATTTATGCG

                         
       3271 TATGCGTATGTTT
          1 TATGCGTATGTTT

                         
       3284 TATGCGTATGTTT
          1 TATGCGTATGTTT

       3297 GAAGGGGAGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54


Consensus pattern (13 bp):   
TATGCGTATGTTT

Found at i:5504 original size:21 final size:20

Alignment explanation


    Indices: 5480--5524  Score: 63
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       5470 TAGAAATATT

                  *              
       5480 TAATTAGAAATTAATTTCTAA
          1 TAATTACAAATT-ATTTCTAA

                    *           
       5501 TAATTACATATTATTTCTAA
          1 TAATTACAAATTATTTCTAA

                
       5521 TAAT
          1 TAAT

       5525 ATGTATTGCA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20   12  0.55
  21   10  0.45

ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47


Consensus pattern (20 bp):   
TAATTACAAATTATTTCTAA
Done.