Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015628.1 Corchorus capsularis cultivar CVL-1 contig15649, 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: 6925
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34


Found at i:428 original size:47 final size:47

Alignment explanation


    Indices: 359--453  Score: 181
    Period size: 47  Copynumber: 2.0  Consensus size: 47

        349 GGCGGTATTT

                                                           
        359 AGTAATTCACTTTATTTATTCATGAACGAAATTTGATGCAAGTTTCC
          1 AGTAATTCACTTTATTTATTCATGAACGAAATTTGATGCAAGTTTCC

                                      *                    
        406 AGTAATTCACTTTATTTATTCATGAATGAAATTTGATGCAAGTTTCC
          1 AGTAATTCACTTTATTTATTCATGAACGAAATTTGATGCAAGTTTCC

             
        453 A
          1 A

        454 ACTAAATTAA


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  47   47  1.00

ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41


Consensus pattern (47 bp):   
AGTAATTCACTTTATTTATTCATGAACGAAATTTGATGCAAGTTTCC

Found at i:1172 original size:43 final size:44

Alignment explanation


    Indices: 1111--1197  Score: 167
    Period size: 43  Copynumber: 2.0  Consensus size: 44

       1101 AATGACTGTG

                                                        
       1111 TATCAAATAATTACCCTATATCATTAG-TTTTTTTTTGGTCAAA
          1 TATCAAATAATTACCCTATATCATTAGTTTTTTTTTTGGTCAAA

                                                        
       1154 TATCAAATAATTACCCTATATCATTAGTTTTTTTTTTGGTCAAA
          1 TATCAAATAATTACCCTATATCATTAGTTTTTTTTTTGGTCAAA

       1198 ATTATATCAT


Statistics
Matches: 43,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  43   27  0.63
  44   16  0.37

ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47


Consensus pattern (44 bp):   
TATCAAATAATTACCCTATATCATTAGTTTTTTTTTTGGTCAAA

Found at i:1712 original size:43 final size:44

Alignment explanation


    Indices: 1644--1731  Score: 151
    Period size: 43  Copynumber: 2.0  Consensus size: 44

       1634 AATTTTTTAA

                *                                       
       1644 TAAATAAAAGCAATTTAATTAACATTAATA-AAAAAAAACTCAC
          1 TAAACAAAAGCAATTTAATTAACATTAATAGAAAAAAAACTCAC

                                *                       
       1687 TAAACAAAAGCAATTTAATTCACATTAATAGAAAAAAAACTCAC
          1 TAAACAAAAGCAATTTAATTAACATTAATAGAAAAAAAACTCAC

             
       1731 T
          1 T

       1732 TTAACGCAGG


Statistics
Matches: 42,  Mismatches: 2, Indels: 1
        0.93            0.04        0.02

Matches are distributed among these distances:
  43   28  0.67
  44   14  0.33

ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25


Consensus pattern (44 bp):   
TAAACAAAAGCAATTTAATTAACATTAATAGAAAAAAAACTCAC

Found at i:2456 original size:48 final size:48

Alignment explanation


    Indices: 2385--2510  Score: 198
    Period size: 48  Copynumber: 2.6  Consensus size: 48

       2375 AAACTCACTT

                       *     *      *     *                 
       2385 TTCGAGGGGCAAAATTATAGGCGGTGGAGGCAGATGATGAATTGGAGG
          1 TTCGAGGGGCAGAATTAGAGGCGGCGGAGGAAGATGATGAATTGGAGG

                                                *           
       2433 TTCGAGGGGCAGAATTAGAGGCGGCGGAGGAAGATGTTGAATTGGAGG
          1 TTCGAGGGGCAGAATTAGAGGCGGCGGAGGAAGATGATGAATTGGAGG

                                 *        
       2481 TTCGAGGGGCAGAATTAGAGGTGGCGGAGG
          1 TTCGAGGGGCAGAATTAGAGGCGGCGGAGG

       2511 TAGAAAGGTT


Statistics
Matches: 72,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  48   72  1.00

ACGTcount: A:0.27, C:0.09, G:0.45, T:0.19


Consensus pattern (48 bp):   
TTCGAGGGGCAGAATTAGAGGCGGCGGAGGAAGATGATGAATTGGAGG

Found at i:3435 original size:34 final size:34

Alignment explanation


    Indices: 3397--3464  Score: 136
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       3387 CAGAGAAAGA

                                              
       3397 CTCAAATCAGAATTGACCCGACATTTGAGCGATC
          1 CTCAAATCAGAATTGACCCGACATTTGAGCGATC

                                              
       3431 CTCAAATCAGAATTGACCCGACATTTGAGCGATC
          1 CTCAAATCAGAATTGACCCGACATTTGAGCGATC

       3465 AGAACATAAC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24


Consensus pattern (34 bp):   
CTCAAATCAGAATTGACCCGACATTTGAGCGATC
Done.