Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015624.1 Corchorus olitorius cultivar O-4 contig15657, 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: 13174
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34


Found at i:1539 original size:17 final size:19

Alignment explanation


    Indices: 1505--1539  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       1495 TCAATTCAAC

                               
       1505 ATCAAAACCAGTATCAAAT
          1 ATCAAAACCAGTATCAAAT

                              
       1524 ATCAAAA-CAG-ATCAAA
          1 ATCAAAACCAGTATCAAA

       1540 CCATGCAACA


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

Matches are distributed among these distances:
  17    6  0.38
  18    3  0.19
  19    7  0.44

ACGTcount: A:0.57, C:0.20, G:0.06, T:0.17


Consensus pattern (19 bp):   
ATCAAAACCAGTATCAAAT

Found at i:5100 original size:107 final size:105

Alignment explanation


    Indices: 4868--5130  Score: 429
    Period size: 107  Copynumber: 2.5  Consensus size: 105

       4858 AATTTTTCTA

                           * **                                              
       4868 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGGCTAAACTTAGTG-AATTAGTTATATATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                                              *     
       4932 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
         66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT

                                                   *               * *       
       4972 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAAGTTAGTGAAATTAGTTTTGTATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                                             *        
       5037 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
         66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT

                                                                
       5079 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA

       5131 AGGCTAAACT


Statistics
Matches: 147,  Mismatches: 9, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
 104   42  0.29
 105   37  0.25
 107   68  0.46

ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40


Consensus pattern (105 bp):   
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT

Found at i:5718 original size:196 final size:189

Alignment explanation


    Indices: 5370--5739  Score: 577
    Period size: 196  Copynumber: 1.9  Consensus size: 189

       5360 AATTTTCCAT

                                                                 *           
       5370 ATATGATAATAATGTTCTTTTTAGTCATGAAACCTTTTTTCTTATTATGGAAAGATATTATAAAT
          1 ATATGATAATAATGTTCTTTTTAGTCATGAAACCTTTTTTCTTATTATGGAAAAATATTATAAAT

                                                                             
       5435 CCATTAAAATTGTAATATCTTCCCATGTTAAATACTTTTTGTTAAAATTTATAATTATTTAATTC
         66 CCATTAAAATTGTAATATCTTCCCATGTTAAATACTTTTTGTTAAAATTTATAATTATTTAATTC

                           *           *                               
       5500 GTTGGTGGCTATATATATGGAAAAAATTTGATGAAATCACCAATAATTTTCCATATAAA
        131 GTTGGTGGCTATATACATGGAAAAAATATGATGAAATCACCAATAATTTTCCATATAAA

                                                                             
       5559 ATATGATAATAATGTTCTTTTTAGTCATGAAACC-TTTTTCTTA-T-TGGAAAAATATTATAAAT
          1 ATATGATAATAATGTTCTTTTTAGTCATGAAACCTTTTTTCTTATTATGGAAAAATATTATAAAT

                                               *                             
       5621 CCATTAAAATTGTAATACTTCTCTTCCCATAATTATTTGAAATACTTTTTGTTTAAAATTTATAA
         66 CCATTAAAATTGTAATA----TCTTCCC---A-T-GTT-AAATACTTTTTG-TTAAAATTTATAA

                                                                   
       5686 TT-TTTAATTCGTTGGTGGCTATATACATGGAAAAAATATGATGAAATCACCAAT
        120 TTATTTAATTCGTTGGTGGCTATATACATGGAAAAAATATGATGAAATCACCAAT

       5740 TTATTAAACC


Statistics
Matches: 166,  Mismatches: 4, Indels: 15
        0.90            0.02        0.08

Matches are distributed among these distances:
 186   34  0.20
 187    1  0.01
 188    9  0.05
 189   34  0.20
 190    7  0.04
 193    1  0.01
 194    1  0.01
 195    2  0.01
 196   62  0.37
 197   15  0.09

ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43


Consensus pattern (189 bp):   
ATATGATAATAATGTTCTTTTTAGTCATGAAACCTTTTTTCTTATTATGGAAAAATATTATAAAT
CCATTAAAATTGTAATATCTTCCCATGTTAAATACTTTTTGTTAAAATTTATAATTATTTAATTC
GTTGGTGGCTATATACATGGAAAAAATATGATGAAATCACCAATAATTTTCCATATAAA

Found at i:11195 original size:19 final size:20

Alignment explanation


    Indices: 11148--11195  Score: 57
    Period size: 19  Copynumber: 2.5  Consensus size: 20

      11138 GGGATTTTTG

                                
      11148 ATAA-TAATTATTCAATAAA
          1 ATAATTAATTATTCAATAAA

                         *    * 
      11167 ATAATT-ATTATTTAAT-TA
          1 ATAATTAATTATTCAATAAA

                       
      11185 ATAATTAATTA
          1 ATAATTAATTA

      11196 ATTTCAGTCC


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

Matches are distributed among these distances:
  18    7  0.28
  19   17  0.68
  20    1  0.04

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46


Consensus pattern (20 bp):   
ATAATTAATTATTCAATAAA

Found at i:11830 original size:6 final size:6

Alignment explanation


    Indices: 11793--11819  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      11783 TCTGATGCAA

                                           
      11793 AAAAAT AAAAAT AAAAAT AAAAAT AAA
          1 AAAAAT AAAAAT AAAAAT AAAAAT AAA

      11820 TAAGAATAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (6 bp):   
AAAAAT
Done.