Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014912.1 Corchorus olitorius cultivar O-4 contig14945, 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: 10119
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:4343 original size:16 final size:16

Alignment explanation


    Indices: 4300--4343  Score: 63
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       4290 TATACAATGC

                       *    
       4300 AAAAA-GAAAAAAAAG
          1 AAAAAGGAAAAGAAAG

                            
       4315 AAAAAGGAAAAGAAAG
          1 AAAAAGGAAAAGAAAG

                    *    
       4331 AAAAAGGAGAAGA
          1 AAAAAGGAAAAGA

       4344 GAAGTGAAGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  15    5  0.19
  16   21  0.81

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (16 bp):   
AAAAAGGAAAAGAAAG

Found at i:4493 original size:10 final size:10

Alignment explanation


    Indices: 4456--4511  Score: 69
    Period size: 10  Copynumber: 5.6  Consensus size: 10

       4446 TCTTTTTTTA

                   *  
       4456 TTCTTTCCCT
          1 TTCTTTCTCT

                   *  
       4466 TTCTTTCCCT
          1 TTCTTTCTCT

                      
       4476 TTCTTTCTCT
          1 TTCTTTCTCT

                     * 
       4486 TTCTTTCTTTT
          1 TTCTTTC-TCT

                      
       4497 TTCTTTCTC-
          1 TTCTTTCTCT

                  
       4506 TTCTTT
          1 TTCTTT

       4512 TATTGCTGGT


Statistics
Matches: 42,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
   9    6  0.14
  10   27  0.64
  11    9  0.21

ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70


Consensus pattern (10 bp):   
TTCTTTCTCT

Found at i:5567 original size:60 final size:60

Alignment explanation


    Indices: 5493--5606  Score: 142
    Period size: 60  Copynumber: 1.9  Consensus size: 60

       5483 TGAACGTATT

                               **    *       *                           
       5493 CGAAAATGATCAAATAAGGGCGCATTCTTTTAATTTAGTCAAATA-GGACCCTAATATATG
          1 CGAAAATGATCAAATAAGGAAGCATGCTTTTAAGTTAGTCAAATACGG-CCCTAATATATG

                                  *              *                 
       5553 CGAAAAT-ACTCAAATAAGGAATCATGCTTTTAAGTTGGTCAAATACGGCCCTAA
          1 CGAAAATGA-TCAAATAAGGAAGCATGCTTTTAAGTTAGTCAAATACGGCCCTAA

       5607 GGTTACCTTA


Statistics
Matches: 46,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  59    1  0.02
  60   43  0.93
  61    2  0.04

ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28


Consensus pattern (60 bp):   
CGAAAATGATCAAATAAGGAAGCATGCTTTTAAGTTAGTCAAATACGGCCCTAATATATG

Found at i:9174 original size:137 final size:139

Alignment explanation


    Indices: 9004--9255  Score: 429
    Period size: 140  Copynumber: 1.8  Consensus size: 139

       8994 TTACTTATGA

                    *                            *                           
       9004 ATTACAATTTAAAGTTTTGATCTTTAGCACAAAAACTTTTGCTTTTATAGGTT-T-TGATATCAA
          1 ATTACAATCTAAAGTTTTGATCTTTAGCACAAAAACTCTTGCTTTTATAGGTTATCTGATATCAA

                                                                             
       9067 -TCTGGGTCTTTTGTTTGGTTGATTTATTTATTTAAATCAAACTCTTTTTCTCTCTTCTTTTACT
         66 TTC-GGGTCTTTTGTTTGGTTGATTTATTTATTTAAATCAAACTCTTTTTCTCTCTTCTTTTACT

                      
       9131 TCTTATATCG
        130 TCTTATATCG

                 *                                                           
       9141 ATTACCATCTAAAGTTTTGATCTTTAGCACAAAAACTCTTGCTTTTATAGGTTATCGTGATATCA
          1 ATTACAATCTAAAGTTTTGATCTTTAGCACAAAAACTCTTGCTTTTATAGGTTATC-TGATATCA

                                                        *     
       9206 ATTCGGGTCTTTTGTTTGGTTGATTTATTTATTTAAATCAAACTTTTTTT
         65 ATTCGGGTCTTTTGTTTGGTTGATTTATTTATTTAAATCAAACTCTTTTT

       9256 TCTGGATTAT


Statistics
Matches: 107,  Mismatches: 4, Indels: 5
        0.92            0.03        0.04

Matches are distributed among these distances:
 137   50  0.47
 138    1  0.01
 140   54  0.50
 141    2  0.02

ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50


Consensus pattern (139 bp):   
ATTACAATCTAAAGTTTTGATCTTTAGCACAAAAACTCTTGCTTTTATAGGTTATCTGATATCAA
TTCGGGTCTTTTGTTTGGTTGATTTATTTATTTAAATCAAACTCTTTTTCTCTCTTCTTTTACTT
CTTATATCG

Done.