Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022800.1 Corchorus olitorius cultivar O-4 contig22833, 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: 4631
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38


Found at i:1225 original size:58 final size:58

Alignment explanation


    Indices: 1126--1240  Score: 151
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       1116 ATTAATCAAA

                                       *                  *           
       1126 TATCAAGTAACATGTTCTTTATTAGATGCATACAAAAAGACGTTTTCGGACCAAGGCT
          1 TATCAAGTAACATGTTCTTTATTAGATACATACAAAAAGACGTTTTAGGACCAAGGCT

                *   *        *            *                      *    
       1184 TATCGAGTGACATGTTTTTTTATTAGATACTTA-AAAAAGACGTTTTAGGACCGAGGC
          1 TATCAAGTAACATG-TTCTTTATTAGATACATACAAAAAGACGTTTTAGGACCAAGGC

       1241 ATGATGCTAT


Statistics
Matches: 49,  Mismatches: 7, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  58   34  0.69
  59   15  0.31

ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Consensus pattern (58 bp):   
TATCAAGTAACATGTTCTTTATTAGATACATACAAAAAGACGTTTTAGGACCAAGGCT

Found at i:2539 original size:36 final size:36

Alignment explanation


    Indices: 2492--2561  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       2482 ACCAATAACC

                         *      *               
       2492 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
       2528 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

       2562 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:3447 original size:204 final size:201

Alignment explanation


    Indices: 3073--3482  Score: 757
    Period size: 204  Copynumber: 2.0  Consensus size: 201

       3063 GCTTAATAAC

                                                                             
       3073 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                          *                                                  
       3138 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
         66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG

                             *                                               
       3203 ATTTATTAAATTAAATTTGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
        131 ATTTATTAAATTAAATTGGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC

                   
       3268 CGATTTA
        195 CGATTTA

                                                                             
       3275 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                     *                                    *                  
       3340 GATACAACATATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
         66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT

                                                                             
       3405 TGATTTATTAAATTAAATTGGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
        129 TGATTTATTAAATTAAATTGGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT

                    
       3470 CCGATTTA
        194 CCGATTTA

                 
       3478 TTTAT
          1 TTTAT

       3483 TATTAAGGAA


Statistics
Matches: 202,  Mismatches: 4, Indels: 3
        0.97            0.02        0.01

Matches are distributed among these distances:
 202   89  0.44
 203   19  0.09
 204   94  0.47

ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37


Consensus pattern (201 bp):   
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTGGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA

Found at i:3645 original size:39 final size:40

Alignment explanation


    Indices: 3591--3671  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       3581 ATACCTAAGA

                                             *      
       3591 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
       3630 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
       3670 AT
          1 AT

       3672 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:3906 original size:6 final size:6

Alignment explanation


    Indices: 3888--3965  Score: 138
    Period size: 6  Copynumber: 12.8  Consensus size: 6

       3878 GTTTAGACTT

                                                                    
       3888 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
          1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG

                        *                    
       3937 ATATAG ATATAA ATATAG ATATAG ATATA
          1 ATATAG ATATAG ATATAG ATATAG ATATA

       3966 ATGATTTGCA


Statistics
Matches: 69,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
   6   63  0.91
   7    6  0.09

ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35


Consensus pattern (6 bp):   
ATATAG

Done.