Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023072.1 Corchorus olitorius cultivar O-4 contig23105, 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: 8457
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:4773 original size:13 final size:13

Alignment explanation


    Indices: 4755--4780  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4745 ATATATATAA

                         
       4755 AAAAAATTATATT
          1 AAAAAATTATATT

                         
       4768 AAAAAATTATATT
          1 AAAAAATTATATT

       4781 TTTATATTGG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (13 bp):   
AAAAAATTATATT

Found at i:5281 original size:23 final size:22

Alignment explanation


    Indices: 5255--5300  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5245 TCTCAACCTT

                                   
       5255 AATCAATCAAAACAACATCAAAA
          1 AATCAA-CAAAACAACATCAAAA

                   **         *   
       5278 AATCAACCCAACAACATCTAAA
          1 AATCAACAAAACAACATCAAAA

             
       5300 A
          1 A

       5301 TCATGGAGGG


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  22   14  0.70
  23    6  0.30

ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13


Consensus pattern (22 bp):   
AATCAACAAAACAACATCAAAA

Found at i:5686 original size:3 final size:3

Alignment explanation


    Indices: 5678--5772  Score: 104
    Period size: 3  Copynumber: 31.3  Consensus size: 3

       5668 TATTTAGGTT

                                                                           
       5678 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                 *            *   * *                           *         
       5726 TT- TAA TTA TGTAA GTA ATG TTA TTA TTA TTA TTAA TTA -AA TTA TTA
          1 TTA TTA TTA T-T-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA

             
       5772 T
          1 T

       5773 GAAAATAGTT


Statistics
Matches: 78,  Mismatches: 9, Indels: 10
        0.80            0.09        0.10

Matches are distributed among these distances:
   2    2  0.03
   3   70  0.90
   4    5  0.06
   5    1  0.01

ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61


Consensus pattern (3 bp):   
TTA

Found at i:5874 original size:20 final size:22

Alignment explanation


    Indices: 5849--5897  Score: 66
    Period size: 20  Copynumber: 2.3  Consensus size: 22

       5839 AGAATTAGGA

                               *  
       5849 TTATTAAGTATTAA-TA-TGTT
          1 TTATTAAGTATTAATTATTATT

                   *              
       5869 TTATTAATTATTAATTATTATT
          1 TTATTAAGTATTAATTATTATT

                   
       5891 TTATTAA
          1 TTATTAA

       5898 AATATGAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20   13  0.52
  21    2  0.08
  22   10  0.40

ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59


Consensus pattern (22 bp):   
TTATTAAGTATTAATTATTATT

Found at i:7661 original size:3 final size:3

Alignment explanation


    Indices: 7653--7679  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       7643 AGACATTGCT

                                               
       7653 TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA

       7680 ATTATATCAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
TAA

Done.