Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008437.1 Kokia drynarioides strain JFW-HI SEQ_123109, 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: 3596
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Found at i:263 original size:14 final size:13

Alignment explanation


    Indices: 222--269  Score: 53
    Period size: 13  Copynumber: 3.6  Consensus size: 13

        212 ATACAATTTT

                        *
        222 TTTTTCTTTTC-T
          1 TTTTTCTTTTCAA

                  *       
        234 TTTCTTTTTTTCAA
          1 TTT-TTCTTTTCAA

                          
        248 TTTTTCTTTTCGAA
          1 TTTTTCTTTTC-AA

                    
        262 TTTTTCTT
          1 TTTTTCTT

        270 CTTCTTCTTT


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  12    3  0.10
  13   14  0.47
  14   13  0.43

ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75


Consensus pattern (13 bp):   
TTTTTCTTTTCAA

Found at i:1225 original size:12 final size:13

Alignment explanation


    Indices: 1203--1308  Score: 134
    Period size: 12  Copynumber: 8.4  Consensus size: 13

       1193 AGTGCATAAT

                         
       1203 AAAAT-AAAAAT-
          1 AAAATGAAAAATG

                         
       1214 AAAATGAAAAAT-
          1 AAAATGAAAAATG

                         
       1226 AAAATGAAAAATG
          1 AAAATGAAAAATG

                          
       1239 AAAAATGAAAAATG
          1 -AAAATGAAAAATG

                          
       1253 AAAAATGAAAAATG
          1 -AAAATGAAAAATG

                          
       1267 AAAAATG-AAAATG
          1 -AAAATGAAAAATG

                         
       1280 AAAATG-AAAATG
          1 AAAATGAAAAATG

                        *
       1292 AAAAT-AAAAATA
          1 AAAATGAAAAATG

                 
       1304 AAAAT
          1 AAAAT

       1309 AAATGTACTA


Statistics
Matches: 90,  Mismatches: 1, Indels: 7
        0.92            0.01        0.07

Matches are distributed among these distances:
  11    5  0.06
  12   45  0.50
  13    6  0.07
  14   34  0.38

ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16


Consensus pattern (13 bp):   
AAAATGAAAAATG

Found at i:1236 original size:7 final size:7

Alignment explanation


    Indices: 1203--1308  Score: 135
    Period size: 7  Copynumber: 16.7  Consensus size: 7

       1193 AGTGCATAAT

                   
       1203 AAAAT-A
          1 AAAATGA

                   
       1209 AAAAT--
          1 AAAATGA

                   
       1214 AAAATGA
          1 AAAATGA

                   
       1221 AAAAT--
          1 AAAATGA

                   
       1226 AAAATGA
          1 AAAATGA

                   
       1233 AAAATGA
          1 AAAATGA

                   
       1240 AAAATGA
          1 AAAATGA

                   
       1247 AAAATGA
          1 AAAATGA

                   
       1254 AAAATGA
          1 AAAATGA

                   
       1261 AAAATGA
          1 AAAATGA

                   
       1268 AAAATG-
          1 AAAATGA

                   
       1274 AAAATG-
          1 AAAATGA

                   
       1280 AAAATG-
          1 AAAATGA

                   
       1286 AAAATG-
          1 AAAATGA

                   
       1292 AAAAT-A
          1 AAAATGA

                   
       1298 AAAAT-A
          1 AAAATGA

                 
       1304 AAAAT
          1 AAAAT

       1309 AAATGTACTA


Statistics
Matches: 95,  Mismatches: 0, Indels: 10
        0.90            0.00        0.10

Matches are distributed among these distances:
   5   10  0.11
   6   39  0.41
   7   46  0.48

ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16


Consensus pattern (7 bp):   
AAAATGA

Done.