Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01841.N2

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, 954

Length: 1590
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33


Found at i:324 original size:26 final size:26

Alignment explanation


    Indices: 266--401  Score: 222
    Period size: 26  Copynumber: 5.3  Consensus size: 26

        256 TGATACAAAT

                                      
        266 TGATAATAGGTTAGGTAAAT-TT-CA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
        290 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
        316 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
        342 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
        368 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                    
        394 TGATAATA
          1 TGATAATA

        402 ATTTCATGTC


Statistics
Matches: 107,  Mismatches: 3, Indels: 2
        0.96            0.03        0.02

Matches are distributed among these distances:
  24   20  0.19
  25    2  0.02
  26   85  0.79

ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37


Consensus pattern (26 bp):   
TGATAATAGGTTAGGTAAATGTTCCA

Found at i:1336 original size:18 final size:18

Alignment explanation


    Indices: 1297--1412  Score: 146
    Period size: 18  Copynumber: 6.5  Consensus size: 18

       1287 AATGATATGT

                            * 
       1297 AATCTTAGATATGA-TAC
          1 AATCTTAGATATGATTGC

                   *          
       1314 AATCTTACATATGATTGC
          1 AATCTTAGATATGATTGC

                              
       1332 AATCTTAGATATGATTGC
          1 AATCTTAGATATGATTGC

                       *    * 
       1350 AATCTTAGATACGA-TAC
          1 AATCTTAGATATGATTGC

                   *          
       1367 AATCTTAAATATGATTGC
          1 AATCTTAGATATGATTGC

                *            * 
       1385 AATCCTAGATATGATATAC
          1 AATCTTAGATATGAT-TGC

                     
       1404 AATCTTAGA
          1 AATCTTAGA

       1413 AGATATGATT


Statistics
Matches: 84,  Mismatches: 12, Indels: 4
        0.84            0.12        0.04

Matches are distributed among these distances:
  17   27  0.32
  18   47  0.56
  19   10  0.12

ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35


Consensus pattern (18 bp):   
AATCTTAGATATGATTGC

Found at i:1337 original size:35 final size:37

Alignment explanation


    Indices: 1280--1412  Score: 143
    Period size: 35  Copynumber: 3.8  Consensus size: 37

       1270 ATGGAAATAT

                             **                * 
       1280 AATCTT-CA-ATGATATGTAATCTTAGATATGA-TAC
          1 AATCTTACATATGATATACAATCTTAGATATGATTGC

                             *                   
       1314 AATCTTACATATGAT-TGCAATCTTAGATATGATTGC
          1 AATCTTACATATGATATACAATCTTAGATATGATTGC

                   *   *              *          
       1350 AATCTTAGATACG--ATACAATCTTAAATATGATTGC
          1 AATCTTACATATGATATACAATCTTAGATATGATTGC

                *  *                    
       1385 AATCCTAGATATGATATACAATCTTAGA
          1 AATCTTACATATGATATACAATCTTAGA

       1413 AGATATGATT


Statistics
Matches: 84,  Mismatches: 9, Indels: 9
        0.82            0.09        0.09

Matches are distributed among these distances:
  34    6  0.07
  35   48  0.57
  36   18  0.21
  37   12  0.14

ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36


Consensus pattern (37 bp):   
AATCTTACATATGATATACAATCTTAGATATGATTGC

Found at i:1360 original size:53 final size:54

Alignment explanation


    Indices: 1288--1412  Score: 198
    Period size: 53  Copynumber: 2.3  Consensus size: 54

       1278 ATAATCTTCA

                    *           *            *              *     
       1288 ATGATATGTAATCTTAGATATGATACAATCTTACATATGATTGCAATCTTAGAT
          1 ATGATATGCAATCTTAGATACGATACAATCTTAAATATGATTGCAATCCTAGAT

                                                                  
       1342 ATGAT-TGCAATCTTAGATACGATACAATCTTAAATATGATTGCAATCCTAGAT
          1 ATGATATGCAATCTTAGATACGATACAATCTTAAATATGATTGCAATCCTAGAT

                   *          
       1395 ATGATATACAATCTTAGA
          1 ATGATATGCAATCTTAGA

       1413 AGATATGATT


Statistics
Matches: 65,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  53   49  0.75
  54   16  0.25

ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36


Consensus pattern (54 bp):   
ATGATATGCAATCTTAGATACGATACAATCTTAAATATGATTGCAATCCTAGAT
Done.