Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004360.1 Corchorus capsularis cultivar CVL-1 contig04368, 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, 625

Length: 1042
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36


Found at i:191 original size:13 final size:13

Alignment explanation


    Indices: 175--223  Score: 52
    Period size: 13  Copynumber: 4.0  Consensus size: 13

        165 TTACTGTTTA

                         
        175 ATATTATAATTAT
          1 ATATTATAATTAT

                       * 
        188 ATATT-TAA-TCT
          1 ATATTATAATTAT

                         
        199 AT-TTATAATTAT
          1 ATATTATAATTAT

                          
        211 ATA-TATTAATTAT
          1 ATATTA-TAATTAT

        224 TAATTCTATA


Statistics
Matches: 30,  Mismatches: 2, Indels: 8
        0.75            0.05        0.20

Matches are distributed among these distances:
  10    2  0.07
  11    7  0.23
  12    9  0.30
  13   12  0.40

ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55


Consensus pattern (13 bp):   
ATATTATAATTAT

Found at i:207 original size:23 final size:23

Alignment explanation


    Indices: 178--249  Score: 80
    Period size: 23  Copynumber: 3.2  Consensus size: 23

        168 CTGTTTAATA

                                    
        178 TTATAATTATATAT-TTAATCTAT
          1 TTATAATTATATATATTAAT-TAT

                                   
        201 TTATAATTATATATATTAATTA-
          1 TTATAATTATATATATTAATTAT

                    *     *         
        223 -T-TAATTCTATATTTCTAATTAT
          1 TTATAATTATATATAT-TAATTAT

                 
        245 TTATA
          1 TTATA

        250 TATTTCGAAT


Statistics
Matches: 42,  Mismatches: 2, Indels: 9
        0.79            0.04        0.17

Matches are distributed among these distances:
  20   11  0.26
  21    7  0.17
  23   17  0.40
  24    7  0.17

ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57


Consensus pattern (23 bp):   
TTATAATTATATATATTAATTAT

Found at i:233 original size:20 final size:21

Alignment explanation


    Indices: 177--245  Score: 63
    Period size: 20  Copynumber: 3.3  Consensus size: 21

        167 ACTGTTTAAT

                                    
        177 ATTA-TAATTATATATTTAATCTA
          1 ATTATTAATTATATA--T-ATCTA

            *                    
        200 TTTA-TAATTATATATAT-TA
          1 ATTATTAATTATATATATCTA

                      *     *    
        219 ATTATTAATTCTATATTTCTA
          1 ATTATTAATTATATATATCTA

                  
        240 ATTATT
          1 ATTATT

        246 TATATATTTC


Statistics
Matches: 40,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
  19    5  0.12
  20   13  0.32
  21    9  0.22
  23   13  0.32

ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57


Consensus pattern (21 bp):   
ATTATTAATTATATATATCTA

Found at i:476 original size:13 final size:13

Alignment explanation


    Indices: 458--483  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        448 AACCATTATG

                         
        458 ATTAGTTGATAAT
          1 ATTAGTTGATAAT

                         
        471 ATTAGTTGATAAT
          1 ATTAGTTGATAAT

        484 TTTGTGAAAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46


Consensus pattern (13 bp):   
ATTAGTTGATAAT
Done.