Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000672.1 Corchorus olitorius cultivar O-4 contig00672, 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, 639

Length: 1066
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37


Found at i:482 original size:2 final size:2

Alignment explanation


    Indices: 475--505  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        465 TTGGAGTTGA

                                                           
        475 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        506 TGAGTATTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

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


Consensus pattern (2 bp):   
AT

Found at i:488 original size:159 final size:159

Alignment explanation


    Indices: 190--486  Score: 433
    Period size: 159  Copynumber: 1.9  Consensus size: 159

        180 ATCTCTGCCG

                *        *                           *                       
        190 CATTGCATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTTTTTCGATTTAATTAGAAATTAAT
          1 CATTACATTTAAGAATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT

                                           *              *           *      
        255 TCAGAAAAAATATGAAAAAACGATATGAAAAGAGTGAAAAGTCCTCTAATCTTTTTGGTGTTAAA
         66 TCAGAAAAAATATGAAAAAACGATATGAAAAAAGTGAAAAGTCCTCCAATCTTTTTGGAGTTAAA

                                         
        320 TTATATATATTTCAAGAGTATTTTAGCCA
        131 TTATATATATTTCAAGAGTATTTTAGCCA

                                             *                        *      
        349 CATTACATTTAAGAATTTGTTTTTACGA-ACATTTGAATCTTGTTTCGA-TTAATTAGGAATTAA
          1 CATTACATTTAAGAATTTGTTTTTACGAGA-ATCTGAATCTTGTTTCGATTTAATTAGAAATTAA

                *                      *                                    *
        412 TTC-TAAAAAATATGAAAAAA-GAT-TTAAAAAACGTGAAAAGTCCTCCAATCTTTTTGGAGTTG
         65 TTCAGAAAAAATATGAAAAAACGATATGAAAAAA-GTGAAAAGTCCTCCAATCTTTTTGGAGTTA

                         
        474 AATATATATATAT
        129 AAT-TATATATAT

        487 ATATAATATA


Statistics
Matches: 124,  Mismatches: 11, Indels: 8
        0.87            0.08        0.06

Matches are distributed among these distances:
 155    6  0.05
 156   33  0.27
 157   25  0.20
 158   18  0.15
 159   42  0.34

ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38


Consensus pattern (159 bp):   
CATTACATTTAAGAATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
TCAGAAAAAATATGAAAAAACGATATGAAAAAAGTGAAAAGTCCTCCAATCTTTTTGGAGTTAAA
TTATATATATTTCAAGAGTATTTTAGCCA

Found at i:497 original size:15 final size:15

Alignment explanation


    Indices: 477--505  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        467 GGAGTTGAAT

                           
        477 ATATATATATATATA
          1 ATATATATATATATA

                          
        492 ATATATATATATAT
          1 ATATATATATATAT

        506 TGAGTATTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

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


Consensus pattern (15 bp):   
ATATATATATATATA
Done.