Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00699.M4

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: 4309
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33


Found at i:1259 original size:19 final size:19

Alignment explanation


    Indices: 1235--1274  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1225 TTCTTTGTGG

                               
       1235 CTGGAAAACTATTATGTTT
          1 CTGGAAAACTATTATGTTT

                               
       1254 CTGGAAAACTATTATGTTT
          1 CTGGAAAACTATTATGTTT

              
       1273 CT
          1 CT

       1275 TTGTGGCTGG


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

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42


Consensus pattern (19 bp):   
CTGGAAAACTATTATGTTT

Found at i:1278 original size:46 final size:49

Alignment explanation


    Indices: 1222--1346  Score: 175
    Period size: 54  Copynumber: 2.5  Consensus size: 49

       1212 CAAGGAAGTT

                                                             
       1222 TGTTTCTTTGTGGCTGGAAAACTATTATG-TT-T-CTGGAAAACTATTA
          1 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTGTGCTGGAAAACTATTA

                                                            *     
       1268 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTCTTTGTGGCTGGAAAATTATTA
          1 TGTTTCTTTGTGGCTGGAAAACTATTATG----TTTGT-GCTGGAAAACTATTA

                                     
       1322 TGTTTCTTTGTGGCTGGAAAACTAT
          1 TGTTTCTTTGTGGCTGGAAAACTAT

       1347 GTTTCTTTTG


Statistics
Matches: 70,  Mismatches: 1, Indels: 8
        0.89            0.01        0.10

Matches are distributed among these distances:
  46   29  0.41
  51    2  0.03
  52    1  0.01
  54   38  0.54

ACGTcount: A:0.23, C:0.10, G:0.22, T:0.45


Consensus pattern (49 bp):   
TGTTTCTTTGTGGCTGGAAAACTATTATGTTTGTGCTGGAAAACTATTA

Found at i:1292 original size:27 final size:27

Alignment explanation


    Indices: 1254--1346  Score: 177
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       1244 TATTATGTTT

                                       
       1254 CTGGAAAACTATTATGTTTCTTTGTGG
          1 CTGGAAAACTATTATGTTTCTTTGTGG

                                       
       1281 CTGGAAAACTATTATGTTTCTTTGTGG
          1 CTGGAAAACTATTATGTTTCTTTGTGG

                    *                  
       1308 CTGGAAAATTATTATGTTTCTTTGTGG
          1 CTGGAAAACTATTATGTTTCTTTGTGG

                        
       1335 CTGGAAAACTAT
          1 CTGGAAAACTAT

       1347 GTTTCTTTTG


Statistics
Matches: 64,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   64  1.00

ACGTcount: A:0.25, C:0.11, G:0.22, T:0.43


Consensus pattern (27 bp):   
CTGGAAAACTATTATGTTTCTTTGTGG

Found at i:2363 original size:126 final size:126

Alignment explanation


    Indices: 2138--2387  Score: 396
    Period size: 126  Copynumber: 2.0  Consensus size: 126

       2128 GGGCCCGAAG

                       *                                                     
       2138 AATCACCAATCGAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
          1 AATCACCAATCAAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT

                                  *                                      
       2203 TATTTGTTGAAGACCCCGTAGCGTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
         66 TATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA

                                                              *    *  *      
       2264 AATCACCAATCAAGTATGAGAAAG-ATCTCTAAGTTTGTTTTGAATTAAGTTTTTTAGTAAATGT
          1 AATCACCAATCAAGTATGAG--AGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGT

                             *                          *    *           
       2328 A-TATTTGTTGAAGACCTCGTAGCCTTGTGTGGCTTAATTTGTAGTTTTGCAGTCATATAG
         64 ATTATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAG

       2388 GAAACTTCTG


Statistics
Matches: 114,  Mismatches: 8, Indels: 4
        0.90            0.06        0.03

Matches are distributed among these distances:
 126   74  0.65
 127   38  0.33
 128    2  0.02

ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39


Consensus pattern (126 bp):   
AATCACCAATCAAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
TATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
Done.