Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024033.1 Corchorus olitorius cultivar O-4 contig24066, 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: 6737
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:5319 original size:30 final size:32

Alignment explanation


    Indices: 5269--5340  Score: 85
    Period size: 31  Copynumber: 2.3  Consensus size: 32

       5259 AAAAATATTT

                                 *    *  *   
       5269 TTTTTCTTTTCTAAAAACGCAGGA-ACAAGAAA
          1 TTTTT-TTTTCTAAAAACGCAAGACAAAACAAA

                         *                  
       5301 TTTTTTTTTC-AATAACGCAAGACAAAACAAA
          1 TTTTTTTTTCTAAAAACGCAAGACAAAACAAA

                     
       5332 TTTTTTTTT
          1 TTTTTTTTT

       5341 TCAACGCAAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  30   10  0.29
  31   20  0.57
  32    5  0.14

ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40


Consensus pattern (32 bp):   
TTTTTTTTTCTAAAAACGCAAGACAAAACAAA

Found at i:5346 original size:29 final size:28

Alignment explanation


    Indices: 5325--5395  Score: 76
    Period size: 27  Copynumber: 2.5  Consensus size: 28

       5315 ACGCAAGACA

                                         
       5325 AAACAAATTTTTTTTTTCAACGCAAAAAC
          1 AAAC-AATTTTTTTTTTCAACGCAAAAAC

                 *             *          
       5354 AAACAGTTTTTTTTTTCTTGACGC-AAAAC
          1 AAACAATTTTTTTTTTC--AACGCAAAAAC

                           
       5383 --ACAATTTTTTTTT
          1 AAACAATTTTTTTTT

       5396 CAAAAACGCA


Statistics
Matches: 37,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  27   12  0.32
  28   12  0.32
  29    9  0.24
  30    4  0.11

ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44


Consensus pattern (28 bp):   
AAACAATTTTTTTTTTCAACGCAAAAAC

Found at i:5354 original size:25 final size:25

Alignment explanation


    Indices: 5323--5395  Score: 76
    Period size: 28  Copynumber: 2.7  Consensus size: 25

       5313 TAACGCAAGA

                                     
       5323 CAAAACAAATTTTTTTTTTC-AACG
          1 CAAAACAAATTTTTTTTTTCTAACG

                                      *   
       5347 CAAAAACAAACAGTTTTTTTTTTCTTGACG
          1 C-AAAAC-AA-A-TTTTTTTTTTC-TAACG

                               
       5377 CAAAACACAATTTTTTTTT
          1 CAAAACA-AATTTTTTTTT

       5396 CAAAAACGCA


Statistics
Matches: 41,  Mismatches: 1, Indels: 11
        0.77            0.02        0.21

Matches are distributed among these distances:
  24    1  0.02
  25    5  0.12
  26    2  0.05
  27   10  0.24
  28   13  0.32
  29    6  0.15
  30    4  0.10

ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42


Consensus pattern (25 bp):   
CAAAACAAATTTTTTTTTTCTAACG

Found at i:5849 original size:15 final size:16

Alignment explanation


    Indices: 5825--5864  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       5815 AGAGGTTGAA

                 *          
       5825 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       5840 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       5856 AGAAAACAA
          1 AGAAAACAA

       5865 AACAAAGCAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Done.