Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1943

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: 47863
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:658 original size:16 final size:17

Alignment explanation


    Indices: 617--660  Score: 56
    Period size: 16  Copynumber: 2.7  Consensus size: 17

        607 AAAATATAAA

                       *     
        617 ATATTATAATTTAATAT
          1 ATATTATAATTAAATAT

                           * 
        634 ATATT-TAATTAAATGT
          1 ATATTATAATTAAATAT

                        
        650 AT-TTATAATTA
          1 ATATTATAATTA

        661 TATTGAAATA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  15    2  0.08
  16   17  0.71
  17    5  0.21

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52


Consensus pattern (17 bp):   
ATATTATAATTAAATAT

Found at i:12965 original size:2 final size:2

Alignment explanation


    Indices: 12958--12988  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      12948 AGTTAAAGCA

                                                          
      12958 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

      12989 ACACACACAC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48


Consensus pattern (2 bp):   
CT

Found at i:30375 original size:30 final size:30

Alignment explanation


    Indices: 30336--30399  Score: 83
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      30326 TCTCTTTTAC

                *                  * *    
      30336 ATAATAAACAAACTTACTTTTATTATTCAT
          1 ATAACAAACAAACTTACTTTTATGACTCAT

                        *   *             
      30366 ATAACAAACAAATTTATTTTTATGACTCAT
          1 ATAACAAACAAACTTACTTTTATGACTCAT

                
      30396 ATAA
          1 ATAA

      30400 AATAATAAAA


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41


Consensus pattern (30 bp):   
ATAACAAACAAACTTACTTTTATGACTCAT

Found at i:34389 original size:15 final size:15

Alignment explanation


    Indices: 34364--34396  Score: 50
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      34354 GGCCCAATTA

                           
      34364 CAACACCCAATA-CC
          1 CAACACCCAATAGCC

                            
      34378 CAACAGCCCAATAGCC
          1 CAACA-CCCAATAGCC

               
      34394 CAA
          1 CAA

      34397 AATCATCAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    5  0.29
  15    7  0.41
  16    5  0.29

ACGTcount: A:0.42, C:0.45, G:0.06, T:0.06


Consensus pattern (15 bp):   
CAACACCCAATAGCC

Found at i:35432 original size:3 final size:3

Alignment explanation


    Indices: 35368--35423  Score: 69
    Period size: 3  Copynumber: 18.7  Consensus size: 3

      35358 TTTGTTAACT

                                                         *           *  
      35368 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA

                    *     
      35413 TTA TTA GTA TT
          1 TTA TTA TTA TT

      35424 GGTATTATTG


Statistics
Matches: 45,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
   2    1  0.02
   3   44  0.98

ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62


Consensus pattern (3 bp):   
TTA

Found at i:35504 original size:22 final size:23

Alignment explanation


    Indices: 35457--35505  Score: 57
    Period size: 24  Copynumber: 2.1  Consensus size: 23

      35447 ATCTCTATTC

                             *      
      35457 ATATATACTTATGTATTTTCAAAT
          1 ATATATACTTATGTATTATC-AAT

                                    
      35481 ATATATATCTTAT-TATTATC-AT
          1 ATATATA-CTTATGTATTATCAAT

               
      35503 ATA
          1 ATA

      35506 AGTGCTTGTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  22    5  0.22
  24   13  0.57
  25    5  0.22

ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51


Consensus pattern (23 bp):   
ATATATACTTATGTATTATCAAT

Found at i:35629 original size:35 final size:36

Alignment explanation


    Indices: 35552--35629  Score: 90
    Period size: 35  Copynumber: 2.2  Consensus size: 36

      35542 AATTTGTTTA

                    *                            
      35552 ATATATACGTATACTCATATTTCTTTTTTATATATAT
          1 ATATATACATATAC-CATATTTCTTTTTTATATATAT

            *                                     
      35589 CTATATACATATA-CATATTT-TATTTTTATA-AGTAT
          1 ATATATACATATACCATATTTCT-TTTTTATATA-TAT

                  
      35624 ATATAT
          1 ATATAT

      35630 TTATATGTAT


Statistics
Matches: 36,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  34    2  0.06
  35   23  0.64
  37   11  0.31

ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53


Consensus pattern (36 bp):   
ATATATACATATACCATATTTCTTTTTTATATATAT
Done.