Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002251.1 Corchorus olitorius cultivar O-4 contig02251, 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, 728

Length: 1214
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36


Found at i:334 original size:15 final size:17

Alignment explanation


    Indices: 309--341  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

        299 TAAAAAGTGA

                             
        309 TTTAAATAAAA-TATTT
          1 TTTAAATAAAATTATTT

                             
        325 TTTAAA-AAAATTATTT
          1 TTTAAATAAAATTATTT

             
        341 T
          1 T

        342 CTTCTGAATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    4  0.25
  16   12  0.75

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


Consensus pattern (17 bp):   
TTTAAATAAAATTATTT

Found at i:468 original size:60 final size:60

Alignment explanation


    Indices: 372--485  Score: 156
    Period size: 60  Copynumber: 1.9  Consensus size: 60

        362 AGATGATAAG

                     *                 *                                
        372 CAAGCAATTTAGGATATAACGTTTTCTGCCGCAAGCAATTAAGGATATAACGTTACAAAA
          1 CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTTACAAAA

                                     *  ****                *     
        432 CAAGCAATTAAGGATATAACGTTTTTTATTTTAAGCAATTAAGGATATGACGTT
          1 CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTT

        486 TTTGATTTCA


Statistics
Matches: 46,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  60   46  1.00

ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32


Consensus pattern (60 bp):   
CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTTACAAAA

Found at i:471 original size:31 final size:31

Alignment explanation


    Indices: 372--512  Score: 144
    Period size: 31  Copynumber: 4.6  Consensus size: 31

        362 AGATGATAAG

                     *                   ***
        372 CAAGCAATTTAGGATATAACGTTTTCTG-CCG
          1 CAAGCAATTAAGGATATAACGTTTT-TGATTT

                                     ** ***
        403 CAAGCAATTAAGGATATAACG--TTACAAAA
          1 CAAGCAATTAAGGATATAACGTTTTTGATTT

                                      *    
        432 CAAGCAATTAAGGATATAACGTTTTTTATTT
          1 CAAGCAATTAAGGATATAACGTTTTTGATTT

            *                *             
        463 TAAGCAATTAAGGATATGACGTTTTTGATTT
          1 CAAGCAATTAAGGATATAACGTTTTTGATTT

                               
        494 CAAGCAATTAAGGATATAA
          1 CAAGCAATTAAGGATATAA

        513 TCAGTAAGGG


Statistics
Matches: 91,  Mismatches: 16, Indels: 6
        0.81            0.14        0.05

Matches are distributed among these distances:
  29   23  0.25
  31   68  0.75

ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33


Consensus pattern (31 bp):   
CAAGCAATTAAGGATATAACGTTTTTGATTT

Found at i:708 original size:29 final size:31

Alignment explanation


    Indices: 642--708  Score: 102
    Period size: 31  Copynumber: 2.2  Consensus size: 31

        632 CCTAACGGAC

                                           
        642 TATATCCTTAATTGCTCGTTTTTCGTAACGT
          1 TATATCCTTAATTGCTCGTTTTTCGTAACGT

                          * *              
        673 TATATCCTTAATTGTTTG-TTTT-GTAACGT
          1 TATATCCTTAATTGCTCGTTTTTCGTAACGT

                   
        702 TATATCC
          1 TATATCC

        709 CAAATTGCAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  29   14  0.41
  30    4  0.12
  31   16  0.47

ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51


Consensus pattern (31 bp):   
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Done.