Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011459.1 Corchorus olitorius cultivar O-4 contig11492, 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: 6556
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1115 original size:22 final size:22

Alignment explanation


    Indices: 1069--1256  Score: 68
    Period size: 22  Copynumber: 8.5  Consensus size: 22

       1059 TGAATGTTTT

                            **    
       1069 TATGAAATTTTGATAATTATCC
          1 TATGAAATTTTGATAAACATCC

               *                   
       1091 TATTAAATTTTGATAAACA-CGC
          1 TATGAAATTTTGATAAACATC-C

                    *         *    
       1113 TATGAAATATTGAT-AA-TTGCC
          1 TATGAAATTTTGATAAACAT-CC

                    **        *     
       1134 TATGAAATCGTGATAATAAACTCC
          1 TATGAAATTTTGATAA-ACA-TCC

                    *          *  **
       1158 ATATG-AACTTTGAT-AACCTAAA
          1 -TATGAAATTTTGATAAACAT-CC

                       *           
       1180 TATGAAATTTTAATAAACCATCC
          1 TATGAAATTTTGATAAA-CATCC

               *            * *  *
       1203 TATAAAATTTTG-TAACCTTCT
          1 TATGAAATTTTGATAAACATCC

                 *          *      
       1224 TATGATA-TTTGATAATC-TCCC
          1 TATGAAATTTTGATAAACAT-CC

                 *      
       1245 TATGAGATTTTG
          1 TATGAAATTTTG

       1257 TTAATCTCCC


Statistics
Matches: 120,  Mismatches: 31, Indels: 30
        0.66            0.17        0.17

Matches are distributed among these distances:
  20    5  0.04
  21   40  0.33
  22   46  0.38
  23   14  0.12
  24   10  0.08
  25    5  0.04

ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39


Consensus pattern (22 bp):   
TATGAAATTTTGATAAACATCC

Found at i:1138 original size:21 final size:21

Alignment explanation


    Indices: 1069--1150  Score: 83
    Period size: 22  Copynumber: 3.8  Consensus size: 21

       1059 TGAATGTTTT

                                  
       1069 TATGAAATTTTGATAATTATCC
          1 TATGAAATTTTGATAATTA-CC

               *            **    
       1091 TATTAAATTTTGATAAACACGC
          1 TATGAAATTTTGATAATTAC-C

                    *         *  
       1113 TATGAAATATTGATAATTGCC
          1 TATGAAATTTTGATAATTACC

                    **       
       1134 TATGAAATCGTGATAAT
          1 TATGAAATTTTGATAAT

       1151 AAACTCCATA


Statistics
Matches: 49,  Mismatches: 10, Indels: 3
        0.79            0.16        0.05

Matches are distributed among these distances:
  21   17  0.35
  22   32  0.65

ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39


Consensus pattern (21 bp):   
TATGAAATTTTGATAATTACC

Found at i:3697 original size:14 final size:15

Alignment explanation


    Indices: 3658--3699  Score: 59
    Period size: 16  Copynumber: 2.8  Consensus size: 15

       3648 TTACTTTGCT

                        *   
       3658 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTCTAA

                           
       3674 TTGTTTTCTGTCTAA
          1 TTGTTTTCTGTCTAA

                        
       3689 TTG-TTTCTGTC
          1 TTGTTTTCTGTC

       3700 AACCTCTGTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  14    8  0.32
  15    8  0.32
  16    9  0.36

ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62


Consensus pattern (15 bp):   
TTGTTTTCTGTCTAA

Found at i:4127 original size:27 final size:28

Alignment explanation


    Indices: 4077--4130  Score: 76
    Period size: 27  Copynumber: 2.0  Consensus size: 28

       4067 TAAAAAAAAC

                                        
       4077 AAAAAAATTTTGCGTTTTTACGTTTTTG
          1 AAAAAAATTTTGCGTTTTTACGTTTTTG

                                *       
       4105 AAAAAAA-TTTG-GTTTTGTCCGTTTTT
          1 AAAAAAATTTTGCGTTTT-TACGTTTTT

       4131 AATTTTGTGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  26    5  0.21
  27   12  0.50
  28    7  0.29

ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50


Consensus pattern (28 bp):   
AAAAAAATTTTGCGTTTTTACGTTTTTG
Done.