Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023397.1 Corchorus olitorius cultivar O-4 contig23430, 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: 11201
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39


Found at i:7200 original size:271 final size:273

Alignment explanation


    Indices: 6689--7235  Score: 1062
    Period size: 271  Copynumber: 2.0  Consensus size: 273

       6679 CCATCTTTCT

                                                                             
       6689 ATAGTTTGGTTAGTCAGGTTGCGTTCTTATATGATTTGTCTGTTGAAAAGATAATACCGATTGCC
          1 ATAGTTTGGTTAGTCAGGTTGCGTTCTTATATGATTTGTCTGTTGAAAAGATAATACCGATTGCC

                                                                             
       6754 AAGCTTTGATGTTCTGTTTCTTTGTTCAAGTTATTTGCAGATATGATATCGTGCGGTTAACAACA
         66 AAGCTTTGATGTTCTGTTTCTTTGTTCAAGTTATTTGCAGA-ATGATATCGTGCGGTTAACAACA

                                                                             
       6819 GGTGCGCACCTAATTACCTAGCTCTAAGTATGCATCCTCTTATATTCTTGGGAATTTACAATCGG
        130 GGTGCGCACCTAATTACCTAGCTCTAAGTATGCATCCTCTTATATTCTTGGGAATTTACAATCGG

                                                                             
       6884 TATGCCTATTTGATGTTGGAGTTTACATTGTCTGCTATTCTCATGATCTTGGTGTTGTACAATGG
        195 TATGCCTATTTGATGTTGGAGTTTACATTGTCTGCTATTCTCATGATCTTGGTGTTGTACAATGG

                          
       6949 GAGAATCCTGCTCC
        260 GAGAATCCTGCTCC

                                                                             
       6963 ATAGTTTGGTTAGTCAGGTTGCGTTCTTATATGATTTGTCTGTTGAAAAGATAATACCGATTGCC
          1 ATAGTTTGGTTAGTCAGGTTGCGTTCTTATATGATTTGTCTGTTGAAAAGATAATACCGATTGCC

                                                                             
       7028 AAGCTTTGATGTTCTGTTTCTTTGTTCAAGTTATTTGCAG-ATGATATCGTGCGGTTAACAACAG
         66 AAGCTTTGATGTTCTGTTTCTTTGTTCAAGTTATTTGCAGAATGATATCGTGCGGTTAACAACAG

                                                                         *   
       7092 G-GCGCACCTAATTACCTAGCTCTAAGTATGCATCCTCTTATATTCTTGGGAATTTACAATTGGT
        131 GTGCGCACCTAATTACCTAGCTCTAAGTATGCATCCTCTTATATTCTTGGGAATTTACAATCGGT

                                                                             
       7156 ATGCCTATTTGATGTTGGAGTTTACATTGTCTGCTATTCTCATGATCTTGGTGTTGTACAATGGG
        196 ATGCCTATTTGATGTTGGAGTTTACATTGTCTGCTATTCTCATGATCTTGGTGTTGTACAATGGG

                         
       7221 AGAATCCTGCTCC
        261 AGAATCCTGCTCC

              
       7234 AT
          1 AT

       7236 GGTTGTTTAT


Statistics
Matches: 272,  Mismatches: 1, Indels: 3
        0.99            0.00        0.01

Matches are distributed among these distances:
 271  142  0.52
 272   25  0.09
 274  105  0.39

ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39


Consensus pattern (273 bp):   
ATAGTTTGGTTAGTCAGGTTGCGTTCTTATATGATTTGTCTGTTGAAAAGATAATACCGATTGCC
AAGCTTTGATGTTCTGTTTCTTTGTTCAAGTTATTTGCAGAATGATATCGTGCGGTTAACAACAG
GTGCGCACCTAATTACCTAGCTCTAAGTATGCATCCTCTTATATTCTTGGGAATTTACAATCGGT
ATGCCTATTTGATGTTGGAGTTTACATTGTCTGCTATTCTCATGATCTTGGTGTTGTACAATGGG
AGAATCCTGCTCC

Found at i:7818 original size:2 final size:2

Alignment explanation


    Indices: 7811--7840  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       7801 TAGATTAGGC

                                                        
       7811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7841 GTGTGTGTGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7845 original size:2 final size:2

Alignment explanation


    Indices: 7840--7874  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       7830 TATATATATA

                                                                
       7840 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T

       7875 CATATAGCAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51


Consensus pattern (2 bp):   
TG

Found at i:9619 original size:16 final size:16

Alignment explanation


    Indices: 9595--9627  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9585 TTCTTCACAC

                            
       9595 TTGGACAGATCTTAAT
          1 TTGGACAGATCTTAAT

                *           
       9611 TTGGGCAGATCTTAAT
          1 TTGGACAGATCTTAAT

             
       9627 T
          1 T

       9628 CTGGTACCTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39


Consensus pattern (16 bp):   
TTGGACAGATCTTAAT

Found at i:11182 original size:14 final size:14

Alignment explanation


    Indices: 11163--11190  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      11153 TTTATTTGTT

                          
      11163 CATTTTCCATGTGC
          1 CATTTTCCATGTGC

                          
      11177 CATTTTCCATGTGC
          1 CATTTTCCATGTGC

      11191 ATTCAAGCAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43


Consensus pattern (14 bp):   
CATTTTCCATGTGC
Done.