Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006105.1 Kokia drynarioides strain JFW-HI SEQ_120611, 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: 3462
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:1128 original size:18 final size:18

Alignment explanation


    Indices: 1107--1152  Score: 51
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       1097 AATCTATCCC

                              
       1107 ATATATTAAATAAATTAT
          1 ATATATTAAATAAATTAT

                  * *   *     
       1125 ATATATCACATATATTAT
          1 ATATATTAAATAAATTAT

                        
       1143 AT-TA-TAAATA
          1 ATATATTAAATA

       1153 TATATAAGTT


Statistics
Matches: 23,  Mismatches: 5, Indels: 2
        0.77            0.17        0.07

Matches are distributed among these distances:
  16    4  0.17
  17    2  0.09
  18   17  0.74

ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43


Consensus pattern (18 bp):   
ATATATTAAATAAATTAT

Found at i:1131 original size:27 final size:28

Alignment explanation


    Indices: 1101--1158  Score: 75
    Period size: 27  Copynumber: 2.1  Consensus size: 28

       1091 ACAAGAAATC

                *                        
       1101 TATCCCATATATTA-A-ATAAATTATATA
          1 TATCACATATATTATATATAAA-TATATA

                                         
       1128 TATCACATATATTATATTATAAATATATA
          1 TATCACATATATTATA-TATAAATATATA

              
       1157 TA
          1 TA

       1159 AGTTAATTTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  27   13  0.48
  28    1  0.04
  29    8  0.30
  30    5  0.19

ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43


Consensus pattern (28 bp):   
TATCACATATATTATATATAAATATATA

Found at i:1435 original size:51 final size:51

Alignment explanation


    Indices: 1374--1477  Score: 181
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       1364 ATTATACCAA

                                                               
       1374 CAGTCACTCAATTTTGATAAAGGGAAACAAATAGTCACTTGATTTACATTT
          1 CAGTCACTCAATTTTGATAAAGGGAAACAAATAGTCACTTGATTTACATTT

                *               *                    *         
       1425 CAGTTACTCAATTTTGATAAGGGGAAACAAATAGTCACTTGGTTTACATTT
          1 CAGTCACTCAATTTTGATAAAGGGAAACAAATAGTCACTTGATTTACATTT

              
       1476 CA
          1 CA

       1478 ATCATTTTTT


Statistics
Matches: 50,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  51   50  1.00

ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Consensus pattern (51 bp):   
CAGTCACTCAATTTTGATAAAGGGAAACAAATAGTCACTTGATTTACATTT

Found at i:1866 original size:47 final size:46

Alignment explanation


    Indices: 1733--1866  Score: 110
    Period size: 47  Copynumber: 2.8  Consensus size: 46

       1723 TGTGAATAAC

                            **         *               **     
       1733 AAATCAAA-CAAAAATTTAAATAACCCAAAATCCAAAATAGTAGCAATCA
          1 AAATCAAATC-AAAATCGAAATAACCCTAAAT-CAAAA-A-TAAAAATCA

                 *   *               *      *             
       1782 AAATCCAATTAAAATCGAAATAACCTTAAATCGAAAATAAAAATCA
          1 AAATCAAATCAAAATCGAAATAACCCTAAATCAAAAATAAAAATCA

                                           *        
       1828 AAATTCAAATCAAAATCG-AATAAACCCTAAGTCAAAAAT
          1 AAA-TCAAATCAAAATCGAAAT-AACCCTAAATCAAAAAT

       1867 CACAATAAAT


Statistics
Matches: 68,  Mismatches: 14, Indels: 8
        0.76            0.16        0.09

Matches are distributed among these distances:
  46   13  0.19
  47   27  0.40
  48    4  0.06
  49   24  0.35

ACGTcount: A:0.58, C:0.17, G:0.04, T:0.20


Consensus pattern (46 bp):   
AAATCAAATCAAAATCGAAATAACCCTAAATCAAAAATAAAAATCA
Done.