Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009893.1 Corchorus olitorius cultivar O-4 contig09925, 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: 4719
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:455 original size:7 final size:7

Alignment explanation


    Indices: 428--491  Score: 64
    Period size: 7  Copynumber: 9.4  Consensus size: 7

        418 TAATATCTAG

                   
        428 TATATA-
          1 TATATAT

                   
        434 TATATAT
          1 TATATAT

                     
        441 ATATTATAT
          1 -TA-TATAT

                   
        450 TATATAT
          1 TATATAT

                   
        457 TATATAT
          1 TATATAT

                   
        464 TATATA-
          1 TATATAT

                   
        470 TAT-T-T
          1 TATATAT

               * * 
        475 TATTTTT
          1 TATATAT

                   
        482 TATATAT
          1 TATATAT

               
        489 TAT
          1 TAT

        492 TTGAAACACC


Statistics
Matches: 50,  Mismatches: 2, Indels: 11
        0.79            0.03        0.17

Matches are distributed among these distances:
   5    4  0.08
   6   10  0.20
   7   27  0.54
   8    4  0.08
   9    5  0.10

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (7 bp):   
TATATAT

Found at i:488 original size:2 final size:2

Alignment explanation


    Indices: 428--472  Score: 62
    Period size: 2  Copynumber: 24.5  Consensus size: 2

        418 TAATATCTAG

                                                                          
        428 TA TA TA TA TA TA TA TA T- TA TA T- TA TA TA T- TA TA TA T- TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                      
        466 TA TA TA T
          1 TA TA TA T

        473 TTTATTTTTT


Statistics
Matches: 39,  Mismatches: 0, Indels: 8
        0.83            0.00        0.17

Matches are distributed among these distances:
   1    4  0.10
   2   35  0.90

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (2 bp):   
TA

Found at i:1416 original size:34 final size:34

Alignment explanation


    Indices: 1377--1474  Score: 110
    Period size: 34  Copynumber: 2.9  Consensus size: 34

       1367 ATATTATTAT

                       *                  *     
       1377 ATATTTAGAA-TTTCAAATATA-ATATCTACAAATA
          1 ATATTTAGAACATTCAAATATATA-ATC-AAAAATA

                          *  *                
       1411 ATATTTAGAACATTGAATTATATAATCAAAAATA
          1 ATATTTAGAACATTCAAATATATAATCAAAAATA

                          *  *            
       1445 ATATTTAGAACATTGAATTATATAATCAAA
          1 ATATTTAGAACATTCAAATATATAATCAAA

       1475 GTAAAACTCC


Statistics
Matches: 58,  Mismatches: 4, Indels: 4
        0.88            0.06        0.06

Matches are distributed among these distances:
  34   46  0.79
  35   11  0.19
  36    1  0.02

ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37


Consensus pattern (34 bp):   
ATATTTAGAACATTCAAATATATAATCAAAAATA
Done.