Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003311.1 Corchorus capsularis cultivar CVL-1 contig03319, 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: 1904
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31


Found at i:32 original size:16 final size:17

Alignment explanation


    Indices: 11--42  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

          1 AACATCTACA

                             
         11 ATCAT-GGAGGGGCAAC
          1 ATCATGGGAGGGGCAAC

                            
         27 ATCATGGGAGGGGCAA
          1 ATCATGGGAGGGGCAA

         43 AGGATTTCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.31, C:0.16, G:0.41, T:0.12


Consensus pattern (17 bp):   
ATCATGGGAGGGGCAAC

Found at i:210 original size:39 final size:39

Alignment explanation


    Indices: 167--286  Score: 101
    Period size: 39  Copynumber: 3.1  Consensus size: 39

        157 CTAGGCCGCG

                                                   
        167 CGCGACCCAGGGTCGGACGCGACCCAGCCGACGGTAAGT
          1 CGCGACCCAGGGTCGGACGCGACCCAGCCGACGGTAAGT

                  *   *                       *        *
        206 CGCGA-TCA-AGTCGTGAC-CGA-CC-GCCG--GCTAGATCGCG
          1 CGCGACCCAGGGTCG-GACGCGACCCAGCCGACGGTA-A--G-T

                                    *              
        243 CGCGACCCAGGGTCGGACGCGACCTAGCCGACGGTAAGT
          1 CGCGACCCAGGGTCGGACGCGACCCAGCCGACGGTAAGT

                 
        282 CGCGA
          1 CGCGA

        287 TCAAGTCGCG


Statistics
Matches: 60,  Mismatches: 9, Indels: 24
        0.65            0.10        0.26

Matches are distributed among these distances:
  33    3  0.05
  34    1  0.02
  35    4  0.07
  36    3  0.05
  37   12  0.20
  38   10  0.17
  39   17  0.28
  40    2  0.03
  41    4  0.07
  42    1  0.02
  43    3  0.05

ACGTcount: A:0.20, C:0.35, G:0.35, T:0.10


Consensus pattern (39 bp):   
CGCGACCCAGGGTCGGACGCGACCCAGCCGACGGTAAGT

Found at i:277 original size:76 final size:75

Alignment explanation


    Indices: 139--344  Score: 286
    Period size: 76  Copynumber: 2.7  Consensus size: 75

        129 AATCCCGGCG

                       *           *                            *            
        139 GTCGCGACCCATCGCCGGCTAGGCCGCGCGCGACCCAGGGTCGGACGCGACCCAGCCGACGGTAA
          1 GTCGCGACCCACCGCCGGCTA-GTCGCGCGCGACCCAGGGTCGGACGCGACCTAGCCGACGGTAA

                       
        204 GTCGCGATCAA
         65 GTCGCGATCAA

                *    *                                                       
        215 GTCGTGACCGACCGCCGGCTAGATCGCGCGCGACCCAGGGTCGGACGCGACCTAGCCGACGGTAA
          1 GTCGCGACCCACCGCCGGCTAG-TCGCGCGCGACCCAGGGTCGGACGCGACCTAGCCGACGGTAA

                       
        280 GTCGCGATCAA
         65 GTCGCGATCAA

                  *             *  *  *         *       *         
        291 GTCGCGCCCCACCGCCGGCTCGTTGCTCGCGACCCCGGGGTCGGTCGCGACCTA
          1 GTCGCGACCCACCGCCGGCTAGTCGCGCGCGA-CCCAGGGTCGGACGCGACCTA

        345 AACCTCGGTG


Statistics
Matches: 115,  Mismatches: 13, Indels: 4
        0.87            0.10        0.03

Matches are distributed among these distances:
  75    9  0.08
  76  106  0.92

ACGTcount: A:0.16, C:0.38, G:0.34, T:0.12


Consensus pattern (75 bp):   
GTCGCGACCCACCGCCGGCTAGTCGCGCGCGACCCAGGGTCGGACGCGACCTAGCCGACGGTAAG
TCGCGATCAA

Done.