Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008548.1 Kokia drynarioides strain JFW-HI SEQ_123225, 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: 1980
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38


Found at i:1116 original size:92 final size:94

Alignment explanation


    Indices: 968--1155  Score: 256
    Period size: 92  Copynumber: 2.0  Consensus size: 94

        958 GACACCCCTA

                                                              *       **     
        968 TTTATCAGATAAAAAAATTTAAAAATTTTCTGATGTTGGCCATTGCATAGTCGACACCTTTTTTT
          1 TTTATCAGATAAAAAAATTTAAAAATTTTCTGATGTTGGCCATTGCATAGCCGACACCCCTTTTT

                           *             
       1033 ATCTGAATAAAAAATTAAATTTTTGGGTG
         66 ATCTGAATAAAAAATCAAATTTTTGGGTG

                 *               *         ** *                              
       1062 TTTATTAGATAAAAAAATTT-CAAATTTT-TTTTTTTGGCCATTGCAT-GACCGACACCCCTTTT
          1 TTTATCAGATAAAAAAATTTAAAAATTTTCTGATGTTGGCCATTGCATAG-CCGACACCCCTTTT

               *                          
       1124 TATTTGAATAAAAAATCAAATTTTTGGGTG
         65 TATCTGAATAAAAAATCAAATTTTTGGGTG

              
       1154 TT
          1 TT

       1156 GGCCATAACT


Statistics
Matches: 83,  Mismatches: 10, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
  91    1  0.01
  92   56  0.67
  93    7  0.08
  94   19  0.23

ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42


Consensus pattern (94 bp):   
TTTATCAGATAAAAAAATTTAAAAATTTTCTGATGTTGGCCATTGCATAGCCGACACCCCTTTTT
ATCTGAATAAAAAATCAAATTTTTGGGTG

Found at i:1244 original size:105 final size:103

Alignment explanation


    Indices: 1062--1263  Score: 241
    Period size: 105  Copynumber: 1.9  Consensus size: 103

       1052 TTTTTGGGTG

                 *                          *                                
       1062 TTTATTAGATAAAAAAATTTCAAATTTTTTTTTTTGGCCATTGCATGACCGACACCCCTTTTTAT
          1 TTTATCAGATAAAAAAATTTCAAATTTTTTTTGTTGGCCATTGCATGACCGACACCCCTTTTTAT

                                                    
       1127 TTGAATAAAAAATCAAATTTTTGGGTGTTGGCCATAACTA
         66 TTGAATAAAAAAT-AAATTTTT-GGTGTTGGCCATAACTA

                            *                     *          *               
       1167 TTTATCAGAT-AAAAATTTTCAAATTTTTTGTTGTTGGTCA-TGCAATGGCCGACACCCCTTTTT
          1 TTTATCAGATAAAAAAATTTCAAATTTTTT-TTGTTGGCCATTGC-ATGACCGACACCCCTTTTT

                  * *        *       *          
       1230 -TTATCTAGT-AAAAATTAATTTTTTGTGTTGGCCA
         64 ATT-T-GAATAAAAAATAAATTTTTGGTGTTGGCCA

       1264 AGCAATGACC


Statistics
Matches: 84,  Mismatches: 9, Indels: 10
        0.82            0.09        0.10

Matches are distributed among these distances:
 103   10  0.12
 104   30  0.36
 105   42  0.50
 106    2  0.02

ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43


Consensus pattern (103 bp):   
TTTATCAGATAAAAAAATTTCAAATTTTTTTTGTTGGCCATTGCATGACCGACACCCCTTTTTAT
TTGAATAAAAAATAAATTTTTGGTGTTGGCCATAACTA

Found at i:1245 original size:259 final size:260

Alignment explanation


    Indices: 739--1225  Score: 577
    Period size: 259  Copynumber: 1.9  Consensus size: 260

        729 AAAATTTTGC

                           *                       *                         
        739 TGTTGGCCATTGCATGGCCGACACTCCCTTTTAATCTGATTAAAAAATAAAATTTTTGGGTGTCT
          1 TGTTGGCCATTGCATAGCCGACACTCCCTTTTAATCTGAATAAAAAATAAAATTTTTGGGTGTCT

                                                    *         *              
        804 GTCATTTGTCAGATAAAAAAATTAATTTTTTTTGTGTTGATCATGTCATGGCCGACACCCCTATT
         66 GTCA-TTGTCAGATAAAAAAATTAATTTTTTTTGTGTTGACCATGTCATGACCGACACCCCTATT

                                                   *   *                 *   
        869 TATTGATAAAAAAATCAAATTTTGGGTGTTGGCACTCTTTTTTGTCAGATAAAAAGTCTAATTTT
        130 TATTGATAAAAAAATCAAATTTTGGGTGTTGGCACTCTTATTTATCAGATAAAAAGTCTAAATTT

                             *     *                                         
        934 TTTGGTATTAGTCATGCCATGGCTGACACCCCTATTTATCAGATAAAAAAATTTAAAAATTTTCT
        195 TTTGGTATTAGTCATGCAATGGCCGACACCCCTATTTATCAGAT-AAAAAATTTAAAAATTTTCT

              
        999 GA
        259 GA

                             *        **    *               *                
       1001 TGTTGGCCATTGCATAGTCGACAC-CTTTTTTTATCTGAATAAAAAATTAAATTTTTGGGTGT-T
          1 TGTTGGCCATTGCATAGCCGACACTCCCTTTTAATCTGAATAAAAAATAAAATTTTTGGGTGTCT

                                                     *                       
       1064 -T-A-T-T-AGATAAAAAAATTTCAAATTTTTTTT-T-TTGGCCAT-TGCATGACCGACACCCCT
         66 GTCATTGTCAGATAAAAAAA-TT--AATTTTTTTTGTGTTGACCATGT-CATGACCGACACCCCT

            *                                                               *
       1121 TTTTATTTGA-ATAAAAAATCAAATTTTTGGGTGTTGGC-CATAAC-TATTTATCAGATAAAAAT
        127 ATTTA-TTGATA-AAAAAATCAAA-TTTTGGGTGTTGGCAC-T--CTTATTTATCAGATAAAAAG

             *            * *  *                       
       1183 TTTCAAATTTTTTGTTGTTGGTCATGCAATGGCCGACACCCCT
        186 TCT-AAATTTTTTGGTATTAGTCATGCAATGGCCGACACCCCT

       1226 TTTTTTATCT


Statistics
Matches: 193,  Mismatches: 21, Indels: 25
        0.81            0.09        0.10

Matches are distributed among these distances:
 254   12  0.06
 255   29  0.15
 256   18  0.09
 257   25  0.13
 258   18  0.09
 259   35  0.18
 260    1  0.01
 261   33  0.17
 262   22  0.11

ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39


Consensus pattern (260 bp):   
TGTTGGCCATTGCATAGCCGACACTCCCTTTTAATCTGAATAAAAAATAAAATTTTTGGGTGTCT
GTCATTGTCAGATAAAAAAATTAATTTTTTTTGTGTTGACCATGTCATGACCGACACCCCTATTT
ATTGATAAAAAAATCAAATTTTGGGTGTTGGCACTCTTATTTATCAGATAAAAAGTCTAAATTTT
TTGGTATTAGTCATGCAATGGCCGACACCCCTATTTATCAGATAAAAAATTTAAAAATTTTCTGA
Done.