Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold8388.1

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: 5187
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36


Found at i:4401 original size:23 final size:23

Alignment explanation


    Indices: 4323--4405  Score: 66
    Period size: 21  Copynumber: 3.8  Consensus size: 23

       4313 ATCAGTATAT

                                  *
       4323 GACACATAAAGTGCCT-AAA-AT
          1 GACACATAAAGTGCCTGAAATAC

                  ** *           * 
       4344 GACACACGAGGTGCCTG--ATTC
          1 GACACATAAAGTGCCTGAAATAC

            *      * *             
       4365 AACACATGAGGTGCCTGAAATAC
          1 GACACATAAAGTGCCTGAAATAC

                              
       4388 GACACATAAAGTGCCTGA
          1 GACACATAAAGTGCCTGA

       4406 TCGGTATAGC


Statistics
Matches: 47,  Mismatches: 11, Indels: 6
        0.73            0.17        0.09

Matches are distributed among these distances:
  20    1  0.02
  21   28  0.60
  23   18  0.38

ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18


Consensus pattern (23 bp):   
GACACATAAAGTGCCTGAAATAC

Found at i:4605 original size:23 final size:24

Alignment explanation


    Indices: 4578--4678  Score: 77
    Period size: 23  Copynumber: 4.2  Consensus size: 24

       4568 AATTCATACA

                                    
       4578 ATTTCATTCAATTCAA-CAAATAT
          1 ATTTCATTCAATTCAATCAAATAT

                               *  *    
       4601 ATTTCAATT--ATTCATATTAATTCAT
          1 ATTTC-ATTCAATTCA-ATCAAAT-AT

                *   *           * *  
       4626 AATTCCATACAATTCAATCATACA-
          1 -ATTTCATTCAATTCAATCAAATAT

                                    
       4650 ATTTCATTCAATTCAA-CAAATAT
          1 ATTTCATTCAATTCAATCAAATAT

                  
       4673 ATTTCA
          1 ATTTCA

       4679 ATTATTCACA


Statistics
Matches: 58,  Mismatches: 12, Indels: 16
        0.67            0.14        0.19

Matches are distributed among these distances:
  22    9  0.16
  23   26  0.45
  24    6  0.10
  25    5  0.09
  26    7  0.12
  27    5  0.09

ACGTcount: A:0.42, C:0.18, G:0.00, T:0.41


Consensus pattern (24 bp):   
ATTTCATTCAATTCAATCAAATAT

Found at i:4647 original size:72 final size:72

Alignment explanation


    Indices: 4571--4715  Score: 263
    Period size: 72  Copynumber: 2.0  Consensus size: 72

       4561 ATTTTCAAAT

                                                        *               *    
       4571 TCATACAATTTCATTCAATTCAACAAATATATTTCAATTATTCATATTAATTCATAATTCCATAC
          1 TCATACAATTTCATTCAATTCAACAAATATATTTCAATTATTCACATTAATTCATAATTCAATAC

                   
       4636 AATTCAA
         66 AATTCAA

                                                                            *
       4643 TCATACAATTTCATTCAATTCAACAAATATATTTCAATTATTCACATTAATTCATAATTCAATAT
          1 TCATACAATTTCATTCAATTCAACAAATATATTTCAATTATTCACATTAATTCATAATTCAATAC

                   
       4708 AATTCAA
         66 AATTCAA

             
       4715 T
          1 T

       4716 TCACTTTTCA


Statistics
Matches: 70,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  72   70  1.00

ACGTcount: A:0.42, C:0.17, G:0.00, T:0.41


Consensus pattern (72 bp):   
TCATACAATTTCATTCAATTCAACAAATATATTTCAATTATTCACATTAATTCATAATTCAATAC
AATTCAA

Found at i:4714 original size:35 final size:34

Alignment explanation


    Indices: 4596--4716  Score: 102
    Period size: 35  Copynumber: 3.4  Consensus size: 34

       4586 CAATTCAACA

                  *                            
       4596 AATATATTTCAATTATTCATATTAATTCATAATTC
          1 AATATAATTCAATTATTCA-ATTAATTCATAATTC

            *   *        *  *      *              
       4631 CATACAATTCAATCATACAATTTCATTC--AATTCAAC
          1 AATATAATTCAATTATTCAA-TTAATTCATAATT---C

                   *                            
       4667 AAATATATTTCAATTATTCACATTAATTCATAATTC
          1 -AATATAATTCAATTATTCA-ATTAATTCATAATTC

                          
       4703 AATATAATTCAATT
          1 AATATAATTCAATT

       4717 CACTTTTCAA


Statistics
Matches: 65,  Mismatches: 13, Indels: 16
        0.69            0.14        0.17

Matches are distributed among these distances:
  33    4  0.06
  34    1  0.02
  35   33  0.51
  36    2  0.03
  37   20  0.31
  38    1  0.02
  39    4  0.06

ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42


Consensus pattern (34 bp):   
AATATAATTCAATTATTCAATTAATTCATAATTC

Done.