Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002280.1 Corchorus capsularis cultivar CVL-1 contig02286, 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, 887

Length: 1479
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31


Found at i:1258 original size:27 final size:27

Alignment explanation


    Indices: 1220--1479  Score: 376
    Period size: 27  Copynumber: 9.2  Consensus size: 27

       1210 TCTGCAAGAA

                                       
       1220 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
       1247 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
       1274 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *           
       1301 CTCCGAATCATAAATGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                       
       1334 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
       1361 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                            *    *           
       1388 CTCCGAATCATAAATGATCCGCTGAAGCTCATC
          1 CTCCGAATCAT---T-CT-C-TTGAAGCTCATC

                                       
       1421 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                                       
       1448 CTCCGAATCATTCTCTTGAAGCTCATC
          1 CTCCGAATCATTCTCTTGAAGCTCATC

                 
       1475 CTCCG
          1 CTCCG


Statistics
Matches: 213,  Mismatches: 8, Indels: 24
        0.87            0.03        0.10

Matches are distributed among these distances:
  27  157  0.74
  28    2  0.01
  29    2  0.01
  30    4  0.02
  31    2  0.01
  32    2  0.01
  33   44  0.21

ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31


Consensus pattern (27 bp):   
CTCCGAATCATTCTCTTGAAGCTCATC

Found at i:1360 original size:87 final size:87

Alignment explanation


    Indices: 1236--1479  Score: 488
    Period size: 87  Copynumber: 2.8  Consensus size: 87

       1226 ATCATTCTCT

                                                                             
       1236 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
       1301 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                             
       1323 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                                  
       1388 CTCCGAATCATAAATGATCCGC
         66 CTCCGAATCATAAATGATCCGC

                                                                             
       1410 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
          1 TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC

                 
       1475 CTCCG
         66 CTCCG


Statistics
Matches: 157,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  87  157  1.00

ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30


Consensus pattern (87 bp):   
TGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATC
CTCCGAATCATAAATGATCCGC

Found at i:1441 original size:114 final size:112

Alignment explanation


    Indices: 1220--1479  Score: 384
    Period size: 114  Copynumber: 2.3  Consensus size: 112

       1210 TCTGCAAGAA

                                                                             
       1220 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT

             *  *                                            
       1285 TCTCTTGAAGCTCATCCTCCGAATCATAAATGATCCGCTGAAGCTCATC
         66 TATCCTGAAGCTCATCCTCCGAATCAT--ATGATCCGCTGAAGCTCATC

                                                                             
       1334 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT

                                                *    *           
       1399 AAATGATCCGCTGAAGCTCATCCTCCGAATCAT-T-CT-C-TTGAAGCTCATC
         66 ---T-AT-C-CTGAAGCTCATCCTCCGAATCATATGATCCGCTGAAGCTCATC

                                            
       1448 CTCCGAATCATTCTCTTGAAGCTCATCCTCCG
          1 CTCCGAATCATTCTCTTGAAGCTCATCCTCCG


Statistics
Matches: 136,  Mismatches: 4, Indels: 12
        0.89            0.03        0.08

Matches are distributed among these distances:
 114  108  0.79
 115    1  0.01
 116    1  0.01
 117    2  0.01
 118    1  0.01
 119    1  0.01
 120   22  0.16

ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31


Consensus pattern (112 bp):   
CTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCATTCTCTTGAAGCTCATCCTCCGAATCAT
TATCCTGAAGCTCATCCTCCGAATCATATGATCCGCTGAAGCTCATC
Done.