Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000960.1 Corchorus olitorius cultivar O-4 contig00960, 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, 676

Length: 1128
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34


Found at i:266 original size:28 final size:28

Alignment explanation


    Indices: 235--291  Score: 69
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        225 ATTCTAAAAA

                *             **        
        235 TTACTCATCAAAGGGTAATTTAGTAATT
          1 TTACCCATCAAAGGGTAAAATAGTAATT

                  *  *                  
        263 TTACCCCTCCAAGGGTAAAATAGTAATT
          1 TTACCCATCAAAGGGTAAAATAGTAATT

             
        291 T
          1 T

        292 CACTTTCCAA


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Consensus pattern (28 bp):   
TTACCCATCAAAGGGTAAAATAGTAATT

Found at i:386 original size:17 final size:16

Alignment explanation


    Indices: 366--417  Score: 70
    Period size: 17  Copynumber: 3.2  Consensus size: 16

        356 TTATTTTTAT

                             
        366 TTTTCCTTTTCTTTTCC
          1 TTTTCCTTTTCTTTT-C

                            
        383 TTTTCCTTTTCTTTTC
          1 TTTTCCTTTTCTTTTC

                *            
        399 TTTTTC-TTTCTCTTTC
          1 TTTTCCTTTTCT-TTTC

               
        415 TTT
          1 TTT

        418 CTTTCTTTTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  15    5  0.15
  16   13  0.39
  17   15  0.45

ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75


Consensus pattern (16 bp):   
TTTTCCTTTTCTTTTC

Found at i:405 original size:6 final size:6

Alignment explanation


    Indices: 359--432  Score: 57
    Period size: 6  Copynumber: 12.8  Consensus size: 6

        349 TTCCTATTTA

                 *        *             *      *                   
        359 TTTTTA TTTTTC CTTTTC -TTTTC CTTTTC CTTTTC -TTTTC TTTTTC
          1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC

               *            *                 
        405 TTTCTC TTTCTT- TCTTTC TTTTT- TTTTT
          1 TTTTTC TTT-TTC TTTTTC TTTTTC TTTTT

        433 TTGACTTGGG


Statistics
Matches: 58,  Mismatches: 6, Indels: 9
        0.79            0.08        0.12

Matches are distributed among these distances:
   5   17  0.29
   6   40  0.69
   7    1  0.02

ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78


Consensus pattern (6 bp):   
TTTTTC

Found at i:408 original size:10 final size:11

Alignment explanation


    Indices: 360--431  Score: 67
    Period size: 11  Copynumber: 6.4  Consensus size: 11

        350 TCCTATTTAT

                *       
        360 TTTTATTTTTCC
          1 TTTTCTTTTT-C

                     * 
        372 TTTTCTTTTCC
          1 TTTTCTTTTTC

                 *     
        383 TTTTCCTTTTC
          1 TTTTCTTTTTC

                       
        394 TTTTCTTTTTC
          1 TTTTCTTTTTC

                         
        405 TTTCTCTTTCTT-
          1 TTT-TCTTT-TTC

                        
        417 TCTTTCTTTTT-
          1 T-TTTCTTTTTC

                
        428 TTTT
          1 TTTT

        432 TTTGACTTGG


Statistics
Matches: 52,  Mismatches: 5, Indels: 8
        0.80            0.08        0.12

Matches are distributed among these distances:
  10    3  0.06
  11   26  0.50
  12   19  0.37
  13    4  0.08

ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78


Consensus pattern (11 bp):   
TTTTCTTTTTC
Done.