Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023377.1 Corchorus olitorius cultivar O-4 contig23410, 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: 22047
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32


Found at i:1264 original size:25 final size:24

Alignment explanation


    Indices: 1228--1274  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1218 TCCTTCTATT

                                    
       1228 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
       1251 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

       1275 AATTTTCTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Found at i:5993 original size:13 final size:13

Alignment explanation


    Indices: 5975--5999  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5965 TTTGCCAAAA

                         
       5975 AATAATTTTAAGC
          1 AATAATTTTAAGC

                        
       5988 AATAATTTTAAG
          1 AATAATTTTAAG

       6000 GTGGTAAAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40


Consensus pattern (13 bp):   
AATAATTTTAAGC

Found at i:18309 original size:66 final size:66

Alignment explanation


    Indices: 18130--18319  Score: 292
    Period size: 66  Copynumber: 2.9  Consensus size: 66

      18120 AATTCTGAAC

                                *       *                 * *                
      18130 CTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTT-GAGTGATCTTAGTGATGATACTAA
          1 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAG-GTGTTGTTAGTGATGATACTAA

             *
      18194 AC
         65 AA

                                                      *                      
      18196 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACTAAA
          1 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGGTGTTGTTAGTGATGATACTAAA

             
      18261 A
         66 A

                               *                              *       
      18262 CTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
          1 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGGTGTTGTTAGTGATGA

      18320 AACAAATTCT


Statistics
Matches: 114,  Mismatches: 9, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  66  113  0.99
  67    1  0.01

ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42


Consensus pattern (66 bp):   
CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGGTGTTGTTAGTGATGATACTAAA
A

Found at i:18331 original size:33 final size:32

Alignment explanation


    Indices: 18134--18370  Score: 172
    Period size: 33  Copynumber: 7.2  Consensus size: 32

      18124 CTGAACCTAA

                           **    *  *        
      18134 TTTGAGTGTTGTTTGCAATGACACGAAATCTGT
          1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT

                    * *  *       *      *  **
      18167 TTTGAGTGATCTTAGTGATGATACTAAACCTAA
          1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT

                           *     *           
      18200 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT
          1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT

                 *       *       *      *  **
      18233 TTTAGATGTTGTTAGTGATGATACTAAAACTAA
          1 TTT-GGTGTTGTTTGTGATGAAACTAAATCTGT

                                 *           
      18266 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
          1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT

                                              
      18299 TTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGT
          1 TTT-GGTGTTGTTTGTGATGAAACTAAA-TCTGT

                    * **                      
      18332 TTTGGATGCTAATTGTGATGAAAAC-AAATCTGT
          1 TTTGG-TGTTGTTTGTGATG-AAACTAAATCTGT

                  
      18365 TTTGGT
          1 TTTGGT

      18371 TGATCATAGC


Statistics
Matches: 163,  Mismatches: 35, Indels: 13
        0.77            0.17        0.06

Matches are distributed among these distances:
  32    7  0.04
  33  147  0.90
  34    9  0.06

ACGTcount: A:0.27, C:0.09, G:0.22, T:0.41


Consensus pattern (32 bp):   
TTTGGTGTTGTTTGTGATGAAACTAAATCTGT

Found at i:18348 original size:66 final size:66

Alignment explanation


    Indices: 18151--18367  Score: 199
    Period size: 66  Copynumber: 3.3  Consensus size: 66

      18141 GTTGTTTGCA

                   *                 * *          *      *            * **   
      18151 ATGACACGAAATCTGTTTT-GAGTGATCTTAGTGATGATACTAAACCTAATTTGAGTGTTGTTTG
          1 ATGACACTAAATCTGTTTTAGA-TGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTG

            * 
      18215 CG
         65 TG

                                                 *                   * **    
      18217 ATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGT
          1 ATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTGT

             
      18282 G
         66 G

                                 *       *               *  **               
      18283 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGTTTTG-GATGCTAATT
          1 ATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGAAACTAAA-ACTAATTTGAG-TGCTAATT

               
      18346 GTG
         64 GTG

                 *              
      18349 ATGAAAAC-AAATCTGTTTT
          1 ATG-ACACTAAATCTGTTTT

      18368 GGTTGATCAT


Statistics
Matches: 132,  Mismatches: 15, Indels: 8
        0.85            0.10        0.05

Matches are distributed among these distances:
  65    4  0.03
  66  123  0.93
  67    5  0.04

ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41


Consensus pattern (66 bp):   
ATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTGT
G
Done.