Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1490

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, 991

Length: 1653
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Found at i:224 original size:11 final size:11

Alignment explanation


    Indices: 208--247  Score: 59
    Period size: 10  Copynumber: 3.9  Consensus size: 11

        198 ATAATAATAA

                       
        208 GATTTTTTTTC
          1 GATTTTTTTTC

                       
        219 GA-TTTTTTTC
          1 GATTTTTTTTC

                       
        229 GATTTTTTTT-
          1 GATTTTTTTTC

                      
        239 -ATTTTTTTT
          1 GATTTTTTTT

        248 ACAATCTCGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   9    9  0.32
  10   10  0.36
  11    9  0.32

ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78


Consensus pattern (11 bp):   
GATTTTTTTTC

Found at i:247 original size:10 final size:10

Alignment explanation


    Indices: 208--247  Score: 55
    Period size: 9  Copynumber: 4.0  Consensus size: 10

        198 ATAATAATAA

                      
        208 GATTTTTTTT
          1 GATTTTTTTT

                      *
        218 CGATTTTTTTC
          1 -GATTTTTTTT

                      
        229 GATTTTTTTT
          1 GATTTTTTTT

                      
        239 -ATTTTTTTT
          1 GATTTTTTTT

        248 ACAATCTCGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   9    9  0.33
  10    9  0.33
  11    9  0.33

ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78


Consensus pattern (10 bp):   
GATTTTTTTT

Found at i:1086 original size:23 final size:24

Alignment explanation


    Indices: 1046--1092  Score: 69
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       1036 AAACCTATAC

                       * *          
       1046 CATTTCGTACCTATACCAA-ACCA
          1 CATTTCGTACCAAAACCAATACCA

                                    
       1069 CATTTCGTACCAAAACCAATACCA
          1 CATTTCGTACCAAAACCAATACCA

       1093 TTCCCTAACT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  23   17  0.81
  24    4  0.19

ACGTcount: A:0.38, C:0.34, G:0.04, T:0.23


Consensus pattern (24 bp):   
CATTTCGTACCAAAACCAATACCA

Found at i:1342 original size:10 final size:11

Alignment explanation


    Indices: 1297--1327  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       1287 TAGGTACGTG

                       
       1297 AAAAAAAA-TC
          1 AAAAAAAATTC

                       
       1307 AAAAAAAATTC
          1 AAAAAAAATTC

                      
       1318 AAAAAAAATT
          1 AAAAAAAATT

       1328 GAAATTAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10    8  0.40
  11   12  0.60

ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16


Consensus pattern (11 bp):   
AAAAAAAATTC

Found at i:1351 original size:20 final size:17

Alignment explanation


    Indices: 1312--1355  Score: 52
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       1302 AAATCAAAAA

                 *           
       1312 AAATTCAAAAAAAATTG
          1 AAATTAAAAAAAAATTG

                                
       1329 AAATTAAAAAAAATATTACG
          1 AAATTAAAAAAAA-ATT--G

                   
       1349 AAATTAA
          1 AAATTAA

       1356 TTAGAAAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  17   12  0.52
  18    3  0.13
  20    8  0.35

ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25


Consensus pattern (17 bp):   
AAATTAAAAAAAAATTG
Done.