Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold5001.1

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: 36676
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.31

Warning! 855 characters in sequence are not A, C, G, or T


Found at i:17479 original size:12 final size:12

Alignment explanation


    Indices: 17457--17488  Score: 55
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      17447 CATAAAAATT

                         
      17457 TAAACTAAGTAAA
          1 TAAA-TAAGTAAA

                        
      17470 TAAATAAGTAAA
          1 TAAATAAGTAAA

                   
      17482 TAAATAA
          1 TAAATAA

      17489 AAATAAAAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12   15  0.79
  13    4  0.21

ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25


Consensus pattern (12 bp):   
TAAATAAGTAAA

Found at i:18522 original size:36 final size:36

Alignment explanation


    Indices: 18481--18552  Score: 135
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      18471 TTTTACACAA

                                                
      18481 GGTAAATCAAGAGAATAACAAATCACACTTCTTTTC
          1 GGTAAATCAAGAGAATAACAAATCACACTTCTTTTC

                                      *         
      18517 GGTAAATCAAGAGAATAACAAATCACGCTTCTTTTC
          1 GGTAAATCAAGAGAATAACAAATCACACTTCTTTTC

      18553 ATAATGACTT


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   35  1.00

ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28


Consensus pattern (36 bp):   
GGTAAATCAAGAGAATAACAAATCACACTTCTTTTC

Found at i:18936 original size:23 final size:22

Alignment explanation


    Indices: 18885--18936  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 22

      18875 CCTCGTCTTT

                   *              
      18885 TTCTTTTGTTTCTTTTTCTAAC
          1 TTCTTTTCTTTCTTTTTCTAAC

                                     
      18907 -TCATTTTCTCTTCTTTCTTC-AAC
          1 TTC-TTTTCT-TTCTTT-TTCTAAC

                   
      18930 TTCTTTT
          1 TTCTTTT

      18937 TCAATTTTCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    2  0.08
  22    5  0.20
  23   13  0.52
  24    5  0.20

ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65


Consensus pattern (22 bp):   
TTCTTTTCTTTCTTTTTCTAAC

Found at i:20481 original size:23 final size:22

Alignment explanation


    Indices: 20430--20481  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 22

      20420 CCTCGTCTTT

                   *              
      20430 TTCTTTTGTTTCTTTTTCTAAC
          1 TTCTTTTCTTTCTTTTTCTAAC

                                     
      20452 -TCATTTTCTCTTCTTTCTTC-AAC
          1 TTC-TTTTCT-TTCTTT-TTCTAAC

                   
      20475 TTCTTTT
          1 TTCTTTT

      20482 TCAATTTTCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    2  0.08
  22    5  0.20
  23   13  0.52
  24    5  0.20

ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65


Consensus pattern (22 bp):   
TTCTTTTCTTTCTTTTTCTAAC

Found at i:23997 original size:41 final size:40

Alignment explanation


    Indices: 23939--24021  Score: 139
    Period size: 41  Copynumber: 2.0  Consensus size: 40

      23929 GCACATTTTA

                  *                        *        
      23939 TTCCCTCCACTAAGACTAACGATGCTTCTTTTGTTGCTTC
          1 TTCCCTACACTAAGACTAACGATGCTTCTTTGGTTGCTTC

                                                     
      23979 TNTCCCTACACTAAGACTAACGATGCTTCTTTGGTTGCTTC
          1 T-TCCCTACACTAAGACTAACGATGCTTCTTTGGTTGCTTC

              
      24020 TT
          1 TT

      24022 TGTTTTTCAG


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  40    2  0.05
  41   38  0.95

ACGTcount: A:0.18, C:0.28, G:0.13, T:0.40


Consensus pattern (40 bp):   
TTCCCTACACTAAGACTAACGATGCTTCTTTGGTTGCTTC

Found at i:35203 original size:23 final size:22

Alignment explanation


    Indices: 35152--35203  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 22

      35142 CCTCGTCTTT

                   *              
      35152 TTCTTTTGTTTCTTTTTCTAAC
          1 TTCTTTTCTTTCTTTTTCTAAC

                                     
      35174 -TCATTTTCTCTTCTTTCTTC-AAC
          1 TTC-TTTTCT-TTCTTT-TTCTAAC

                   
      35197 TTCTTTT
          1 TTCTTTT

      35204 TCAATTTTCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    2  0.08
  22    5  0.20
  23   13  0.52
  24    5  0.20

ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65


Consensus pattern (22 bp):   
TTCTTTTCTTTCTTTTTCTAAC
Done.