Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019892.1 Corchorus olitorius cultivar O-4 contig19925, 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: 11344
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32


Found at i:9082 original size:2 final size:2

Alignment explanation


    Indices: 9075--9115  Score: 55
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       9065 TTTTGGACAT

                                           *        *                   
       9075 TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA TA TA CTA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA

       9116 AGTCTAAACT


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
   2   32  0.94
   3    2  0.06

ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:9428 original size:147 final size:144

Alignment explanation


    Indices: 9221--9485  Score: 433
    Period size: 147  Copynumber: 1.8  Consensus size: 144

       9211 TCCAATCAGA

                                                                             
       9221 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACATTAAACAACTTATTAT
          1 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACATTAAACAACTTATTAT

                                              *                              
       9286 TATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTGAGGA
         66 TATAATTATTAAAATTATTATTAGTTATATATATAATTAGTCATTACGTTTTTTTTTTTTGAGGA

                          
       9351 ATTAGTCATTACGT
        131 ATTAGTCATTACGT

                *           *                 *   *             *            
       9365 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAACTT-TTTTTACGTTAAACAACTTA
          1 TTTTATTTCCATATTAAAAAAGTC-TAAA--ATAATAACAA-TTATTTTTACATTAAACAACTTA

                                                                     
       9429 TTATTATAATTATTAAAATTATTATTAGTTATATATATAATTAGTCATTACGTTTTT
         62 TTATTATAATTATTAAAATTATTATTAGTTATATATATAATTAGTCATTACGTTTTT

       9486 CTTTCCATAT


Statistics
Matches: 111,  Mismatches: 6, Indels: 5
        0.91            0.05        0.04

Matches are distributed among these distances:
 144   22  0.20
 145    4  0.04
 147   83  0.75
 148    2  0.02

ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48


Consensus pattern (144 bp):   
TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACATTAAACAACTTATTAT
TATAATTATTAAAATTATTATTAGTTATATATATAATTAGTCATTACGTTTTTTTTTTTTGAGGA
ATTAGTCATTACGT

Found at i:9570 original size:15 final size:16

Alignment explanation


    Indices: 9547--9594  Score: 53
    Period size: 15  Copynumber: 2.9  Consensus size: 16

       9537 CATCTTCTTA

                *           
       9547 TTATAATTATTA-AAC
          1 TTATTATTATTATAAC

                            
       9562 TTATTATTATTATAAC
          1 TTATTATTATTATAAC

                             
       9578 AATTATTATTAGTTATA
          1 --TTATTATTA-TTATA

       9595 TGATCACTAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  15   11  0.39
  16    3  0.11
  18    9  0.32
  19    5  0.18

ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52


Consensus pattern (16 bp):   
TTATTATTATTATAAC

Found at i:9583 original size:18 final size:17

Alignment explanation


    Indices: 9544--9594  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 17

       9534 AAACATCTTC

                   *         *
       9544 TTATTATAATTATTAAAC
          1 TTATTATTATTA-TAAAA

                              
       9562 TTATTATTATTATAACAA
          1 TTATTATTATTATAA-AA

                           
       9580 TTATTATTAGTTATA
          1 TTATTATTA-TTATA

       9595 TGATCACTAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  17    3  0.10
  18   21  0.72
  19    5  0.17

ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53


Consensus pattern (17 bp):   
TTATTATTATTATAAAA

Found at i:9590 original size:117 final size:117

Alignment explanation


    Indices: 9350--9576  Score: 354
    Period size: 117  Copynumber: 2.0  Consensus size: 117

       9340 TTTTTTGAGG

                                                *        *                   
       9350 AATTAGTCATTACGTTTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAACTTTTTTTA
          1 AATTAGTCATTACGTTTTTCTTTCCATATTACAAAAATCTTAAATAATACTAATAACTTTTTTTA

                                                           *    
       9415 CGTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATAT
         66 CGTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATAAATAT

                                                                   *         
       9467 AATTAGTCATTACGTTTTTCTTTCCATATTACAAAAAT-TTAAAATAATACTAA-CA-TTTTTTT
          1 AATTAGTCATTACGTTTTTCTTTCCATATTACAAAAATCTT-AAATAATACTAATAACTTTTTTT

                      *   *                 *                
       9529 ACGTTAAACATCTTCTTATTATAATTATTAAACTTATTATTA-TTATAA
         65 ACGTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATAA

       9577 CAATTATTAT


Statistics
Matches: 102,  Mismatches: 7, Indels: 5
        0.89            0.06        0.04

Matches are distributed among these distances:
 114    5  0.05
 115   46  0.45
 116    3  0.03
 117   48  0.47

ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47


Consensus pattern (117 bp):   
AATTAGTCATTACGTTTTTCTTTCCATATTACAAAAATCTTAAATAATACTAATAACTTTTTTTA
CGTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATAAATAT
Done.