Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010671.1 Corchorus olitorius cultivar O-4 contig10703, 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: 11595
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:3244 original size:23 final size:24

Alignment explanation


    Indices: 3187--3247  Score: 70
    Period size: 23  Copynumber: 2.5  Consensus size: 24

       3177 AAGAAAGTAA

                                 **  
       3187 AAAAATAATAAAAAAATCAAATCAG
          1 AAAAATAA-AAAAAAATCAAAAAAG

                 *                  
       3212 AAAAAGAAAAAAAAA-CAAAAAAG
          1 AAAAATAAAAAAAAATCAAAAAAG

             *           
       3235 ACAAATAAAAAAA
          1 AAAAATAAAAAAA

       3248 TTGATTAAAA


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  23   17  0.55
  24    7  0.23
  25    7  0.23

ACGTcount: A:0.80, C:0.07, G:0.05, T:0.08


Consensus pattern (24 bp):   
AAAAATAAAAAAAAATCAAAAAAG

Found at i:8479 original size:22 final size:23

Alignment explanation


    Indices: 8451--8498  Score: 71
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       8441 TTCCCATAAA

                                 * 
       8451 AAAAGAA-GAAAAAAAGAAAGTG
          1 AAAAGAATGAAAAAAAGAAAGAG

                           *       
       8473 AAAAGAATGAAAAAAGGAAAGAG
          1 AAAAGAATGAAAAAAAGAAAGAG

               
       8496 AAA
          1 AAA

       8499 TCAAGTTGCA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  22    7  0.30
  23   16  0.70

ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04


Consensus pattern (23 bp):   
AAAAGAATGAAAAAAAGAAAGAG

Found at i:9251 original size:20 final size:22

Alignment explanation


    Indices: 9213--9253  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       9203 AAAGACCTAC

                                  
       9213 CAAAAAGAAGAAAATTGTTTTG
          1 CAAAAAGAAGAAAATTGTTTTG

                 *               
       9235 CAAAAGGAA-AAAA-TGTTTT
          1 CAAAAAGAAGAAAATTGTTTT

       9254 TCTCAAAAGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    6  0.33
  21    4  0.22
  22    8  0.44

ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27


Consensus pattern (22 bp):   
CAAAAAGAAGAAAATTGTTTTG

Found at i:9254 original size:21 final size:23

Alignment explanation


    Indices: 9213--9263  Score: 54
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       9203 AAAGACCTAC

                 *                 
       9213 CAAAAAGAAGAAAATTGTTTT-G
          1 CAAAAGGAAGAAAATTGTTTTCG

                                   *
       9235 CAAAAGGAA-AAAA-TGTTTTTCT
          1 CAAAAGGAAGAAAATTG-TTTTCG

                   
       9257 CAAAAGG
          1 CAAAAGG

       9264 GGTTTTTAGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  20    2  0.08
  21    8  0.32
  22   15  0.60

ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25


Consensus pattern (23 bp):   
CAAAAGGAAGAAAATTGTTTTCG

Found at i:10398 original size:22 final size:22

Alignment explanation


    Indices: 10373--10449  Score: 118
    Period size: 22  Copynumber: 3.5  Consensus size: 22

      10363 CGATTCTGAC

                         *        
      10373 AGCCTCCGGGCACGAAATTAGA
          1 AGCCTCCGGGCACAAAATTAGA

                  *               
      10395 AGCCTCTGGGCACAAAATTAGA
          1 AGCCTCCGGGCACAAAATTAGA

                  *           *   
      10417 AGCCTCTGGGCACAAAATCAGA
          1 AGCCTCCGGGCACAAAATTAGA

                       
      10439 AGCCTCCGGGC
          1 AGCCTCCGGGC

      10450 CGCAATTCTG


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  22   51  1.00

ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14


Consensus pattern (22 bp):   
AGCCTCCGGGCACAAAATTAGA
Done.