Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020043.1 Corchorus olitorius cultivar O-4 contig20076, 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: 12081
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:2722 original size:22 final size:21

Alignment explanation


    Indices: 2675--2756  Score: 85
    Period size: 22  Copynumber: 3.8  Consensus size: 21

       2665 CTTATGGAGT

                  *     *         
       2675 TTATCACAATTTTAT-AGGTAA
          1 TTATCAAAATTTCATAAGGT-A

                            * *   
       2696 TTATCAAAATTTCATATGTTGA
          1 TTATCAAAATTTCATAAGGT-A

                        *        
       2718 TTATCAAAATTTAATAAGGTA
          1 TTATCAAAATTTCATAAGGTA

                              
       2739 GTTATCAAAATTTCATAA
          1 -TTATCAAAATTTCATAA

       2757 AAATGTTCAA


Statistics
Matches: 50,  Mismatches: 9, Indels: 3
        0.81            0.15        0.05

Matches are distributed among these distances:
  21   14  0.28
  22   36  0.72

ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41


Consensus pattern (21 bp):   
TTATCAAAATTTCATAAGGTA

Found at i:4419 original size:19 final size:16

Alignment explanation


    Indices: 4381--4412  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       4371 GAAAAAAATT

                      *     
       4381 TATTATACTATCATGC
          1 TATTATACTAACATGC

                            
       4397 TATTATACTAACATGC
          1 TATTATACTAACATGC

       4413 GGGTATTTAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41


Consensus pattern (16 bp):   
TATTATACTAACATGC

Found at i:4478 original size:5 final size:5

Alignment explanation


    Indices: 4468--4508  Score: 55
    Period size: 5  Copynumber: 8.2  Consensus size: 5

       4458 TTATATAAAG

                          *          *     *                 
       4468 TAAGA TAAGA TACGA TAAGA TGAGA TGAGA TAAGA TAAGA T
          1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T

       4509 TAGACTTGGT


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   5   32  1.00

ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22


Consensus pattern (5 bp):   
TAAGA

Found at i:4548 original size:2 final size:2

Alignment explanation


    Indices: 4541--4592  Score: 54
    Period size: 2  Copynumber: 26.5  Consensus size: 2

       4531 AATCACAACC

                                                          *     **         
       4541 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TCA CA -A CC TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA

                            
       4582 TA TA TA TA TA T
          1 TA TA TA TA TA T

       4593 TCTACCAATA


Statistics
Matches: 43,  Mismatches: 4, Indels: 6
        0.81            0.08        0.11

Matches are distributed among these distances:
   1    2  0.05
   2   40  0.93
   3    1  0.02

ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44


Consensus pattern (2 bp):   
TA

Found at i:7576 original size:47 final size:47

Alignment explanation


    Indices: 7509--7651  Score: 232
    Period size: 47  Copynumber: 3.0  Consensus size: 47

       7499 GACTTCTTAT

                 *    *    *                               
       7509 GAGAAATCCCCGGTTCGAATCTTGAGATGGGCGGAGTGGGATTATGG
          1 GAGAAGTCCCTGGTTTGAATCTTGAGATGGGCGGAGTGGGATTATGG

                                         *                 
       7556 GAGAAGTCCCTGGTTTGAATCTTGAGATGAGCGGAGTGGGATTATGG
          1 GAGAAGTCCCTGGTTTGAATCTTGAGATGGGCGGAGTGGGATTATGG

                        *                         *        
       7603 GAGAAGTCCCTGATTTGAATCTTGAGATGGGCGGAGTGAGATTATGG
          1 GAGAAGTCCCTGGTTTGAATCTTGAGATGGGCGGAGTGGGATTATGG

              
       7650 GA
          1 GA

       7652 AAGGAGAGGG


Statistics
Matches: 89,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  47   89  1.00

ACGTcount: A:0.24, C:0.12, G:0.38, T:0.26


Consensus pattern (47 bp):   
GAGAAGTCCCTGGTTTGAATCTTGAGATGGGCGGAGTGGGATTATGG

Found at i:7740 original size:4 final size:4

Alignment explanation


    Indices: 7731--7760  Score: 60
    Period size: 4  Copynumber: 7.5  Consensus size: 4

       7721 TAATAATAAT

                                                 
       7731 AATA AATA AATA AATA AATA AATA AATA AA
          1 AATA AATA AATA AATA AATA AATA AATA AA

       7761 ACACTTGAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   26  1.00

ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23


Consensus pattern (4 bp):   
AATA

Done.