Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011137.1 Kokia drynarioides strain JFW-HI SEQ_126110, 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: 8161
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:338 original size:111 final size:108

Alignment explanation


    Indices: 105--347  Score: 263
    Period size: 111  Copynumber: 2.2  Consensus size: 108

         95 TATTGTGCTG

                            *   *          *                           *  *  
        105 ATTTTTTTCTTTTTTTCTTTAAGAATATGTTGGACCTTTTAACGCGAAATGAAATGACATCCTAG
          1 ATTTTTTTCTTTTTTTTTTTTAGAATATGTTAGACCTTTTAACGCGAAATGAAATGACAACCAAG

                               *        **              
        170 CACTCCATCCCGATTACTTTGCCCAACATGCTCTCAATCATTTT
         66 CACTCCATCCCGATTACTTAGCCCAACACACTCTCAATCA-TTT

            *                           *      *      *   *                  
        214 TTTCTTTTTCTTTTTCTTTTTTTAGAATGTGTTAGCCCTTTTGACGTGAAATGAAATGACAACCA
          1 ATT-TTTTTCTTTTT-TTTTTTTAGAATATGTTAGACCTTTTAACGCGAAATGAAATGACAACCA

                          *          *                *    
        279 AGCACTCCATCCCGGTTACTTAGCCTAACACACTC-CGAATTTATTT
         64 AGCACTCCATCCCGATTACTTAGCCCAACACACTCTC-AA-TCATTT

                    *              
        325 ATTTATTTCCTTTTTTTCTTTTT
          1 ATTT-TTTTCTTTTTTT-TTTTT

        348 TCCCAATTAG


Statistics
Matches: 110,  Mismatches: 18, Indels: 10
        0.80            0.13        0.07

Matches are distributed among these distances:
 109    2  0.02
 110   15  0.14
 111   91  0.83
 112    2  0.02

ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44


Consensus pattern (108 bp):   
ATTTTTTTCTTTTTTTTTTTTAGAATATGTTAGACCTTTTAACGCGAAATGAAATGACAACCAAG
CACTCCATCCCGATTACTTAGCCCAACACACTCTCAATCATTT

Found at i:3533 original size:114 final size:111

Alignment explanation


    Indices: 3395--3615  Score: 379
    Period size: 114  Copynumber: 2.0  Consensus size: 111

       3385 ACACAATATG

                        *                          *                         
       3395 ATAAAATTAGAGTTTTTTATTGAACTAGGGTTTTGGAGATATGGAGGATTTTTTCAATGAATGGA
          1 ATAAAATTAGAGCTTTTTATTGAACTAGGGTTTTGGAGAGATGGAGGATTTTTTCAATGAATGGA

                                                             
       3460 AGTGAATAATTCAATCACTCCACCTCCTATTTATAGTAAATAATAGATA
         66 AGTG---AATTCAATCACTCCACCTCCTATTTATAGTAAATAATAGATA

                                                         *              *    
       3509 ATAAAATTAGAGCTTTTTATTGAACTAGGGTTTTGGAGAGATGGATGATTTTTTCAATGACTGGA
          1 ATAAAATTAGAGCTTTTTATTGAACTAGGGTTTTGGAGAGATGGAGGATTTTTTCAATGAATGGA

                                                      
       3574 AGTGAATTCAATCACTCCACCTCCTATTTATAGTAAATAATA
         66 AGTGAATTCAATCACTCCACCTCCTATTTATAGTAAATAATA

       3616 CTCCTAGTTG


Statistics
Matches: 103,  Mismatches: 4, Indels: 3
        0.94            0.04        0.03

Matches are distributed among these distances:
 111   38  0.37
 114   65  0.63

ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37


Consensus pattern (111 bp):   
ATAAAATTAGAGCTTTTTATTGAACTAGGGTTTTGGAGAGATGGAGGATTTTTTCAATGAATGGA
AGTGAATTCAATCACTCCACCTCCTATTTATAGTAAATAATAGATA

Found at i:4576 original size:111 final size:109

Alignment explanation


    Indices: 4334--4576  Score: 263
    Period size: 111  Copynumber: 2.2  Consensus size: 109

       4324 TATTGTGCTG

                *     *          *          *                           *  * 
       4334 ATTTTTTTCTTTTTTTC-TTTAAGAATATGTTGGACCTTTTAACGCGAAATGAAATGACATCCTA
          1 ATTTATTTCTCTTTTTCTTTTTAGAATATGTTAGACCTTTTAACGCGAAATGAAATGACAACCAA

                                *        **             
       4398 GCACTCCATCCCGATTACTTTGCCCAACATGCTCTCAATCATTT
         66 GCACTCCATCCCGATTACTTAGCCCAACACACTCTCAATCATTT

            *   *   *                    *      *      *   *                 
       4442 TTTTCTTTTTCTTTTTCTTTTTTTAGAATGTGTTAGCCCTTTTGACGTGAAATGAAATGACAACC
          1 ATTTATTTCTCTTTTTC--TTTTTAGAATATGTTAGACCTTTTAACGCGAAATGAAATGACAACC

                           *          *          *    *    
       4507 AAGCACTCCATCCCGGTTACTTAGCCTAACACACTCTGAATTTATTT
         64 AAGCACTCCATCCCGATTACTTAGCCCAACACACTCTCAA-TCATTT

                                   
       4554 ATTTATTTCCTCTTTTTCTTTTT
          1 ATTTATTT-CTCTTTTTCTTTTT

       4577 TCCCAATTAG


Statistics
Matches: 108,  Mismatches: 22, Indels: 7
        0.79            0.16        0.05

Matches are distributed among these distances:
 108   13  0.12
 111   76  0.70
 112   11  0.10
 113    8  0.07

ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44


Consensus pattern (109 bp):   
ATTTATTTCTCTTTTTCTTTTTAGAATATGTTAGACCTTTTAACGCGAAATGAAATGACAACCAA
GCACTCCATCCCGATTACTTAGCCCAACACACTCTCAATCATTT

Found at i:5325 original size:21 final size:21

Alignment explanation


    Indices: 5300--5346  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5290 TTTTATAGAC

                            *     
       5300 AAATAAG-AAAATAAATATATA
          1 AAATAAGAAAAATAAAAATA-A

                                 
       5321 AAAT-AGAAAAATAAAAATAA
          1 AAATAAGAAAAATAAAAATAA

                  
       5341 AAATAA
          1 AAATAA

       5347 AATAATTAGG


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

Matches are distributed among these distances:
  20    7  0.30
  21   16  0.70

ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19


Consensus pattern (21 bp):   
AAATAAGAAAAATAAAAATAA
Done.