Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020223.1 Corchorus olitorius cultivar O-4 contig20256, 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: 23186
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32


Found at i:1336 original size:88 final size:89

Alignment explanation


    Indices: 1217--1387  Score: 274
    Period size: 88  Copynumber: 1.9  Consensus size: 89

       1207 TGGTTTGTGG

                             *                               *               
       1217 GGTTAAAAAAATGATGTTTTACTCATGTCATGAATTCATATAACAATTATGTACTAAGTCAAATC
          1 GGTTAAAAAAA-GATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATC

              *                      
       1282 T-TCAATCTTTAAGAAAAAGTTATC
         65 TCCCAATCTTTAAGAAAAAGTTATC

                                                                             
       1306 GGTTAAAAGAAA-ATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATC
          1 GGTTAAAA-AAAGATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATC

                   *          
       1370 TCCCAATTTTTAAGAAAA
         65 TCCCAATCTTTAAGAAAA

       1388 TCCAAGCATG


Statistics
Matches: 76,  Mismatches: 4, Indels: 4
        0.90            0.05        0.05

Matches are distributed among these distances:
  88   51  0.67
  89   22  0.29
  90    3  0.04

ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34


Consensus pattern (89 bp):   
GGTTAAAAAAAGATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCT
CCCAATCTTTAAGAAAAAGTTATC

Found at i:2420 original size:21 final size:22

Alignment explanation


    Indices: 2264--2462  Score: 122
    Period size: 22  Copynumber: 9.1  Consensus size: 22

       2254 TGAATATTTT

                                *  
       2264 TATGAAATTTTGATAA-CTACCC
          1 TATGAAATTTTGATAATCT-TCC

               *              **  
       2286 TATTAAATTTTGATAATCAGCC
          1 TATGAAATTTTGATAATCTTCC

                                   
       2308 TATGAAATTTTGATAAT-TAT-C
          1 TATGAAATTTTGATAATCT-TCC

                    **         *  *
       2329 TATGAAATCGTGATAAAT-GTCA
          1 TATGAAATTTTGAT-AATCTTCC

                   *        *  ** 
       2351 TATGAAACTTTGATAACCTAAC
          1 TATGAAATTTTGATAATCTTCC

                      **     *     
       2373 TATGAAATTTAAATAAACCTTCC
          1 TATGAAATTTTGAT-AATCTTCC

                                 *
       2396 TATGAAATTTTG-TAATCTTCT
          1 TATGAAATTTTGATAATCTTCC

                  *         *  *  
       2417 TATG-ATTTTTGATAACCTCCC
          1 TATGAAATTTTGATAATCTTCC

                 *      *      *  
       2438 TATGAGATTTTGTTAATCTCCC
          1 TATGAAATTTTGATAATCTTCC

               
       2460 TAT
          1 TAT

       2463 AATTTTTTCA


Statistics
Matches: 134,  Mismatches: 35, Indels: 16
        0.72            0.19        0.09

Matches are distributed among these distances:
  20    6  0.04
  21   36  0.27
  22   75  0.56
  23   17  0.13

ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41


Consensus pattern (22 bp):   
TATGAAATTTTGATAATCTTCC

Found at i:2447 original size:23 final size:22

Alignment explanation


    Indices: 2420--2469  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       2410 ATCTTCTTAT

                                   
       2420 GATTTTTGATAACCTCCCTATGA
          1 GATTTTTGATAACCTCCCTAT-A

                    *   *         
       2443 GA-TTTTGTTAATCTCCCTATA
          1 GATTTTTGATAACCTCCCTATA

                   
       2464 -ATTTTT
          1 GATTTTT

       2470 TCATACTATG


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  20    1  0.04
  21    5  0.21
  22   16  0.67
  23    2  0.08

ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48


Consensus pattern (22 bp):   
GATTTTTGATAACCTCCCTATA

Found at i:18671 original size:51 final size:51

Alignment explanation


    Indices: 18595--18691  Score: 176
    Period size: 51  Copynumber: 1.9  Consensus size: 51

      18585 GACCGAAAAA

                   *                                           
      18595 ATTGAAGTGGTAAGGCAAGAAGAATATTGTCCCAAAACTGGATTTGAAGAG
          1 ATTGAAGAGGTAAGGCAAGAAGAATATTGTCCCAAAACTGGATTTGAAGAG

                                                 *        
      18646 ATTGAAGAGGTAAGGCAAGAAGAATATTGTCCCAAAATTGGATTTG
          1 ATTGAAGAGGTAAGGCAAGAAGAATATTGTCCCAAAACTGGATTTG

      18692 GAAAGTGGGG


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  51   44  1.00

ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25


Consensus pattern (51 bp):   
ATTGAAGAGGTAAGGCAAGAAGAATATTGTCCCAAAACTGGATTTGAAGAG

Found at i:22027 original size:24 final size:25

Alignment explanation


    Indices: 21994--22050  Score: 82
    Period size: 25  Copynumber: 2.4  Consensus size: 25

      21984 GTCAGCCTTG

                                 *   
      21994 AATTT-TTTAATGT-TTAATTCTTA
          1 AATTTATTTAATGTCTTAATTATTA

                                    *
      22017 AATTTATTTAATGTCTTAATTATTC
          1 AATTTATTTAATGTCTTAATTATTA

                     
      22042 AATTTATTT
          1 AATTTATTT

      22051 TACAATCCAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60


Consensus pattern (25 bp):   
AATTTATTTAATGTCTTAATTATTA

Done.