Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007690.1 Corchorus olitorius cultivar O-4 contig07716, 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, 975

Length: 1625
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37


Found at i:274 original size:11 final size:11

Alignment explanation


    Indices: 258--295  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        248 ATTCGTAACA

                       
        258 AATTTATAATT
          1 AATTTATAATT

                       
        269 AATTTATAATT
          1 AATTTATAATT

                        
        280 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
        291 TATTT
          1 AATTT

        296 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:1299 original size:2 final size:2

Alignment explanation


    Indices: 1277--1314  Score: 51
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       1267 TTTTTTGTAA

                  *        *                                          
       1277 AT AT CT AT AT CT AT A- AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1315 ATACTTTTTA


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:1374 original size:83 final size:82

Alignment explanation


    Indices: 1236--1625  Score: 313
    Period size: 83  Copynumber: 4.8  Consensus size: 82

       1226 CCACCTCCAC

                                                                             
       1236 CTTTTTATTTCTCCAATGTTTTTTATCAAGTTTTTTTGTAAATATCTATATCTATAATATATATA
          1 CTTTTTATTTCTCCAATGTTTTTTATCAAGTTTTTTTGTAAATATCTATATCTATAATATATATA

                             
       1301 TATATATATATATAATA
         66 TATATATATATATAATA

                                                  *                          
       1318 CTTTTTATTTCTCCAATGTTTTTTATTCAAGTTTTTTTTTAAATATCTATATCTAT-A-ATATAT
          1 CTTTTTATTTCTCCAATGTTTTTTA-TCAAGTTTTTTTGTAAATATCTATATCTATAATATATAT

                       ** *   
       1381 ATATA-ATA-AGGTGA-A
         65 ATATATATATATATAATA

                       *                    *    * * *   *       *           
       1396 -TTTTTATGTTTTCCAATTGTACGTTTTTTTTTTCAAATATATTTCTAAAT-TGTCATTAT-TA-
          1 CTTTTTAT-TTCTCCAA---T--G--TTTTTTATCAAGTTTTTTTGTAAATATCT-A-TATCTAT

                       *                *       
       1457 AATA-ATAT-TTTAATTATTCAATTATTGTAATGAA
         56 AATATATATATAT-A-TA-T--A-TA-TATAAT--A

                                                                             
       1491 CTTTTTATTTCTCCAATG-TTTTTATCAAG-TTTTTTGTAAATATCTATATC--T-ATA-ATATA
          1 CTTTTTATTTCTCCAATGTTTTTTATCAAGTTTTTTTGTAAATATCTATATCTATAATATATATA

                             
       1550 TATATATATA-A-AATA
         66 TATATATATATATAATA

                                                                             
       1565 C-TTTTA-TTCTCCAATG-TTTTTATCAAGTTTTTTT-TCAAATATCTATATCTATAATATATAT
          1 CTTTTTATTTCTCCAATGTTTTTTATCAAGTTTTTTTGT-AAATATCTATATCTATAATATATAT


Statistics
Matches: 249,  Mismatches: 23, Indels: 77
        0.71            0.07        0.22

Matches are distributed among these distances:
  72   22  0.09
  73   24  0.10
  74    2  0.01
  75    1  0.00
  76    6  0.02
  77   11  0.04
  78    8  0.03
  79    5  0.02
  80    4  0.02
  81   12  0.05
  82   27  0.11
  83   36  0.14
  84   31  0.12
  85   15  0.06
  86   11  0.04
  87   12  0.05
  89    1  0.00
  90    1  0.00
  91    1  0.00
  92    4  0.02
  95    8  0.03
  96    7  0.03

ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53


Consensus pattern (82 bp):   
CTTTTTATTTCTCCAATGTTTTTTATCAAGTTTTTTTGTAAATATCTATATCTATAATATATATA
TATATATATATATAATA
Done.