Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01465.P4

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: 11120
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41


Found at i:2020 original size:39 final size:39

Alignment explanation


    Indices: 1966--2048  Score: 130
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       1956 CCACTGGCCA

                    *                              
       1966 CCACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGT
          1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

                                     *        **   
       2005 CCACCATCATCGTTCACCAGTCAGGTAGTCACCATTGGT
          1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

                 
       2044 CCACC
          1 CCACC

       2049 CGTCACCACC


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20


Consensus pattern (39 bp):   
CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

Found at i:4371 original size:31 final size:31

Alignment explanation


    Indices: 4335--4397  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       4325 TTCCTTATTT

                                           
       4335 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

                                           
       4366 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

             
       4397 C
          1 C

       4398 TTCTCGTACT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57


Consensus pattern (31 bp):   
CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

Found at i:8339 original size:16 final size:16

Alignment explanation


    Indices: 8318--8370  Score: 65
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       8308 AATTCCGAGG

                            
       8318 ATATCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                    *       
       8334 ATATCCC-ACTTAGG-
          1 ATATCCCGGCTTAGGT

               *       *    
       8348 ATAGCCCGGCTGAGGT
          1 ATATCCCGGCTTAGGT

                   
       8364 ATATCCC
          1 ATATCCC

       8371 ACCTGCGGAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 4
        0.77            0.13        0.10

Matches are distributed among these distances:
  14    6  0.20
  15   11  0.37
  16   13  0.43

ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26


Consensus pattern (16 bp):   
ATATCCCGGCTTAGGT

Found at i:8349 original size:30 final size:31

Alignment explanation


    Indices: 8314--8396  Score: 105
    Period size: 30  Copynumber: 2.7  Consensus size: 31

       8304 GTATAATTCC

                                           
       8314 GAGGATATCCCGGCTTAGGTATATCCCA-CT
          1 GAGGATATCCCGGCTTAGGTATATCCCACCT

            *      *       *               
       8344 TAGGATAGCCCGGCTGAGGTATATCCCACCT
          1 GAGGATATCCCGGCTTAGGTATATCCCACCT

             *           *  *     
       8375 GCGGATATCCCGGTTTCGGTAT
          1 GAGGATATCCCGGCTTAGGTAT

       8397 TAATTTAATT


Statistics
Matches: 43,  Mismatches: 9, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  30   25  0.58
  31   18  0.42

ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27


Consensus pattern (31 bp):   
GAGGATATCCCGGCTTAGGTATATCCCACCT

Found at i:9586 original size:15 final size:16

Alignment explanation


    Indices: 9566--9595  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       9556 ATCCATGATT

                            
       9566 GTTGAAA-TATCCAAG
          1 GTTGAAATTATCCAAG

                           
       9581 GTTGAAATTATCCAA
          1 GTTGAAATTATCCAA

       9596 ATGGACTAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30


Consensus pattern (16 bp):   
GTTGAAATTATCCAAG

Found at i:10141 original size:106 final size:105

Alignment explanation


    Indices: 9949--10160  Score: 415
    Period size: 106  Copynumber: 2.0  Consensus size: 105

       9939 ATATGATTGA

                                                                             
       9949 TATCATGTTATCTTAGTCCTGAGGCTTCAGTCAGAGTACCAGATCTAAGGCTGCAGTCTTTGCCT
          1 TATCATGTTATCTTAGTCCTGAGGCTTCAGTCAGAGTACCAGATCTAAGGCTGCAGTCTTTGCCT

                                                    
      10014 GGCTGCTAATGTTCTGGATCTAACCTATTATCATTTGTTG
         66 GGCTGCTAATGTTCTGGATCTAACCTATTATCATTTGTTG

                                                                             
      10054 TATCATGTTTATCTTAGTCCTGAGGCTTCAGTCAGAGTACCAGATCTAAGGCTGCAGTCTTTGCC
          1 TATCATG-TTATCTTAGTCCTGAGGCTTCAGTCAGAGTACCAGATCTAAGGCTGCAGTCTTTGCC

                                                     
      10119 TGGCTGCTAATGTTCTGGATCTAACCTATTATCATTTGTTG
         65 TGGCTGCTAATGTTCTGGATCTAACCTATTATCATTTGTTG

             
      10160 T
          1 T

      10161 CACATGAACT


Statistics
Matches: 106,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
 105    7  0.07
 106   99  0.93

ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38


Consensus pattern (105 bp):   
TATCATGTTATCTTAGTCCTGAGGCTTCAGTCAGAGTACCAGATCTAAGGCTGCAGTCTTTGCCT
GGCTGCTAATGTTCTGGATCTAACCTATTATCATTTGTTG
Done.