Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006176.1 Kokia drynarioides strain JFW-HI SEQ_120741, 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: 11515
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:6371 original size:23 final size:23

Alignment explanation


    Indices: 6322--6377  Score: 67
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       6312 ACTCGAACTT

                                  *
       6322 GATCGTTGACTATGATCGAAACG
          1 GATCGTTGACTATGATCGAAACA

                       *    *   *  
       6345 GATCGTTGACTTTGATTGAATCA
          1 GATCGTTGACTATGATCGAAACA

                *     
       6368 GATCATTGAC
          1 GATCGTTGAC

       6378 AGTTGACAGT


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32


Consensus pattern (23 bp):   
GATCGTTGACTATGATCGAAACA

Found at i:6409 original size:7 final size:7

Alignment explanation


    Indices: 6373--6461  Score: 70
    Period size: 7  Copynumber: 12.7  Consensus size: 7

       6363 AATCAGATCA

                 * 
       6373 TTGACAG
          1 TTGACCG

                 * 
       6380 TTGACAG
          1 TTGACCG

                   
       6387 TTGACCG
          1 TTGACCG

              *    
       6394 TTAACCG
          1 TTGACCG

                *  
       6401 TTGATCG
          1 TTGACCG

                * *
       6408 TTGATCA
          1 TTGACCG

                  *
       6415 TTGACCT
          1 TTGACCG

                  *
       6422 TTGACCA
          1 TTGACCG

                  *
       6429 TTGACCA
          1 TTGACCG

                   
       6436 TTGACCG
          1 TTGACCG

                ** 
       6443 TTGATTG
          1 TTGACCG

                *  
       6450 TTGATCG
          1 TTGACCG

                 
       6457 TTGAC
          1 TTGAC

       6462 TTTTTCGTTG


Statistics
Matches: 69,  Mismatches: 13, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   7   69  1.00

ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36


Consensus pattern (7 bp):   
TTGACCG

Found at i:6410 original size:21 final size:21

Alignment explanation


    Indices: 6371--6453  Score: 78
    Period size: 21  Copynumber: 4.0  Consensus size: 21

       6361 TGAATCAGAT

                   *              
       6371 CATTGACAGTTGA-CAGTTGAC
          1 CATTGACCGTTGATC-GTTGAC

             *  *               *
       6392 CGTTAACCGTTGATCGTTGAT
          1 CATTGACCGTTGATCGTTGAC

                    *    * *     
       6413 CATTGACCTTTGACCATTGAC
          1 CATTGACCGTTGATCGTTGAC

                          *     
       6434 CATTGACCGTTGATTGTTGA
          1 CATTGACCGTTGATCGTTGA

       6454 TCGTTGACTT


Statistics
Matches: 47,  Mismatches: 14, Indels: 2
        0.75            0.22        0.03

Matches are distributed among these distances:
  21   46  0.98
  22    1  0.02

ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35


Consensus pattern (21 bp):   
CATTGACCGTTGATCGTTGAC

Found at i:6414 original size:42 final size:42

Alignment explanation


    Indices: 6368--6461  Score: 118
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       6358 GATTGAATCA

                                      *                
       6368 GATCATTGACAGTTGA-CAGTTGACCGTTAACCGTTGATCGTT
          1 GATCATTGACAGTTGACCA-TTGACCATTAACCGTTGATCGTT

                      **                *         *   
       6410 GATCATTGACCTTTGACCATTGACCATTGACCGTTGATTGTT
          1 GATCATTGACAGTTGACCATTGACCATTAACCGTTGATCGTT

                *     
       6452 GATCGTTGAC
          1 GATCATTGAC

       6462 TTTTTCGTTG


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  42   43  0.96
  43    2  0.04

ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35


Consensus pattern (42 bp):   
GATCATTGACAGTTGACCATTGACCATTAACCGTTGATCGTT

Found at i:7540 original size:18 final size:19

Alignment explanation


    Indices: 7519--7569  Score: 50
    Period size: 18  Copynumber: 2.7  Consensus size: 19

       7509 TTTATTTCAT

                             * 
       7519 ATTTTATTTTATTTTG-GG
          1 ATTTTATTTTATTTTGTCG

                **  *          
       7537 ATTTCGTTATATTTTGTCG
          1 ATTTTATTTTATTTTGTCG

                          
       7556 ATTATTATTTTATT
          1 ATT-TTATTTTATT

       7570 GGGATTGTAA


Statistics
Matches: 24,  Mismatches: 7, Indels: 2
        0.73            0.21        0.06

Matches are distributed among these distances:
  18   13  0.54
  19    4  0.17
  20    7  0.29

ACGTcount: A:0.20, C:0.04, G:0.12, T:0.65


Consensus pattern (19 bp):   
ATTTTATTTTATTTTGTCG
Done.