Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005626.1 Corchorus capsularis cultivar CVL-1 contig05644, 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: 3082
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40


Found at i:301 original size:20 final size:20

Alignment explanation


    Indices: 264--305  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        254 ATATTTAGAT

                  *  *          
        264 TTTTTTTAGTATTGTTTTTC
          1 TTTTTTGAGAATTGTTTTTC

                                
        284 TTTTTTGAGAATT-TTTTT-
          1 TTTTTTGAGAATTGTTTTTC

                
        302 TTTT
          1 TTTT

        306 GAGTATTATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  18    4  0.20
  19    5  0.25
  20   11  0.55

ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76


Consensus pattern (20 bp):   
TTTTTTGAGAATTGTTTTTC

Found at i:332 original size:13 final size:13

Alignment explanation


    Indices: 314--340  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        304 TTGAGTATTA

                         
        314 TTATGTTCTGAAC
          1 TTATGTTCTGAAC

                         
        327 TTATGTTCTGAAC
          1 TTATGTTCTGAAC

             
        340 T
          1 T

        341 CATTTCATCT


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

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48


Consensus pattern (13 bp):   
TTATGTTCTGAAC

Found at i:1129 original size:82 final size:82

Alignment explanation


    Indices: 1031--1201  Score: 263
    Period size: 82  Copynumber: 2.1  Consensus size: 82

       1021 GAAAAGAACT

                       *         *         *         *                *      
       1031 TTTCTATTGGTGAAATTTAAAGTAATTATAATTAATTTGCATATTAATTAACTAGATTGA-TATT
          1 TTTCTATTGGTCAAATTTAAACTAATTATAAATAATTTGCACATTAATTAACTAGA-TCACTATT

                              
       1095 CTATCAATAAGCATTGAC
         65 CTATCAATAAGCATTGAC

                                                                             
       1113 TTTCTATTGGTCAAATTTAAACTAATTATAAATAATTTGCACATTAATTAACTAGATCACTATTC
          1 TTTCTATTGGTCAAATTTAAACTAATTATAAATAATTTGCACATTAATTAACTAGATCACTATTC

                     **      
       1178 TATCAATAATTATTGAC
         66 TATCAATAAGCATTGAC

                   
       1195 TTTCTAT
          1 TTTCTAT

       1202 AATTGTATAA


Statistics
Matches: 81,  Mismatches: 7, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  81    2  0.02
  82   79  0.98

ACGTcount: A:0.37, C:0.11, G:0.08, T:0.43


Consensus pattern (82 bp):   
TTTCTATTGGTCAAATTTAAACTAATTATAAATAATTTGCACATTAATTAACTAGATCACTATTC
TATCAATAAGCATTGAC
Done.