Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009978.1 Corchorus olitorius cultivar O-4 contig10010, 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: 24277
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:1202 original size:19 final size:19

Alignment explanation


    Indices: 1152--1202  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       1142 CATAAGATTT

                               
       1152 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       1170 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       1189 TTAATAATTAATTA
          1 TTAATAATTAATTA

       1203 ATTTCAGCCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:12617 original size:20 final size:20

Alignment explanation


    Indices: 12589--12626  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      12579 AACCCCTTTC

                      *         
      12589 TCTCAAACCTTGAAATAATT
          1 TCTCAAACCTAGAAATAATT

                *             
      12609 TCTCCAACCTAGAAATAA
          1 TCTCAAACCTAGAAATAA

      12627 CCCACGTTGC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29


Consensus pattern (20 bp):   
TCTCAAACCTAGAAATAATT

Found at i:12674 original size:21 final size:20

Alignment explanation


    Indices: 12650--12688  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      12640 CTTTAGTGAC

                   *             
      12650 AAAATCATAAACAAATTCCTA
          1 AAAATCACAAAC-AATTCCTA

                 *            
      12671 AAAATTACAAACAATTCC
          1 AAAATCACAAACAATTCC

      12689 CATTGTGGCA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    6  0.38
  21   10  0.62

ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23


Consensus pattern (20 bp):   
AAAATCACAAACAATTCCTA

Found at i:13324 original size:24 final size:24

Alignment explanation


    Indices: 13288--13337  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      13278 ACAGCTTCCA

                *   *                
      13288 TCTTTTCTGTCTTCTTCCTTT-CTT
          1 TCTTCTCTATCTT-TTCCTTTCCTT

                                    
      13312 TCTTCTCTATCTTTTCCTTTCCTT
          1 TCTTCTCTATCTTTTCCTTTCCTT

              
      13336 TC
          1 TC

      13338 CCCTCGCGAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  23    7  0.30
  24   16  0.70

ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64


Consensus pattern (24 bp):   
TCTTCTCTATCTTTTCCTTTCCTT

Found at i:23700 original size:39 final size:37

Alignment explanation


    Indices: 23657--23737  Score: 92
    Period size: 39  Copynumber: 2.1  Consensus size: 37

      23647 CTTGAGTCCA

                                                    
      23657 GAGAGAATTTTTTT-GTGTGAGGGTGAGTTTGAGAGAGAT
          1 GAGAGAATTTTTTTGGT-TGAGGGTGA--TTGAGAGAGAT

                 **            * *               
      23696 GAGAGTGTTTTTTTGGTTGCGTGTGATTGAGAGAGAT
          1 GAGAGAATTTTTTTGGTTGAGGGTGATTGAGAGAGAT

                 
      23733 GAGAG
          1 GAGAG

      23738 TGTTTTTGAG


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  37   16  0.43
  39   19  0.51
  40    2  0.05

ACGTcount: A:0.23, C:0.01, G:0.40, T:0.36


Consensus pattern (37 bp):   
GAGAGAATTTTTTTGGTTGAGGGTGATTGAGAGAGAT

Found at i:23707 original size:37 final size:37

Alignment explanation


    Indices: 23666--23745  Score: 101
    Period size: 37  Copynumber: 2.2  Consensus size: 37

      23656 AGAGAGAATT

                                                   
      23666 TTTTTGT-G-TGAGGGTGAGTTTGAGAGAGATGAGAGTG
          1 TTTTTGTGGTTGAGGGTGA--TTGAGAGAGATGAGAGTG

                 *      * *                      
      23703 TTTTTTTGGTTGCGTGTGATTGAGAGAGATGAGAGTG
          1 TTTTTGTGGTTGAGGGTGATTGAGAGAGATGAGAGTG

                  
      23740 TTTTTG
          1 TTTTTG

      23746 AGCGAATGGG


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  37   29  0.78
  38    1  0.03
  39    7  0.19

ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41


Consensus pattern (37 bp):   
TTTTTGTGGTTGAGGGTGATTGAGAGAGATGAGAGTG
Done.