Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010934.1 Corchorus capsularis cultivar CVL-1 contig10955, 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: 1706
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1403 original size:13 final size:13

Alignment explanation


    Indices: 1385--1431  Score: 62
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       1375 CATCCATCAG

                         
       1385 CAAGTGCCGATGC
          1 CAAGTGCCGATGC

                         
       1398 CAAGTGCC-AT-C
          1 CAAGTGCCGATGC

                           
       1409 AGCAAGTGCCGATGC
          1 --CAAGTGCCGATGC

                    
       1424 CAAGTGCC
          1 CAAGTGCC

       1432 ATCGGAGAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 8
        0.79            0.00        0.21

Matches are distributed among these distances:
  11    1  0.03
  12    2  0.07
  13   24  0.80
  14    2  0.07
  15    1  0.03

ACGTcount: A:0.26, C:0.32, G:0.28, T:0.15


Consensus pattern (13 bp):   
CAAGTGCCGATGC

Found at i:1446 original size:26 final size:26

Alignment explanation


    Indices: 1378--1434  Score: 114
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       1368 CAAGTGCCAT

                                      
       1378 CCATCAGCAAGTGCCGATGCCAAGTG
          1 CCATCAGCAAGTGCCGATGCCAAGTG

                                      
       1404 CCATCAGCAAGTGCCGATGCCAAGTG
          1 CCATCAGCAAGTGCCGATGCCAAGTG

                 
       1430 CCATC
          1 CCATC

       1435 GGAGAATGCC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   31  1.00

ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16


Consensus pattern (26 bp):   
CCATCAGCAAGTGCCGATGCCAAGTG

Found at i:1451 original size:26 final size:26

Alignment explanation


    Indices: 1389--1489  Score: 82
    Period size: 26  Copynumber: 3.7  Consensus size: 26

       1379 CATCAGCAAG

                  *                    
       1389 TGCCGATGCCAAGTGCCATC--AGCAA
          1 TGCCGACGCCAAGTGCCATCGGAG-AA

                   *                   
       1414 GTGCCGATGCCAAGTGCCATCGGAGAA
          1 -TGCCGACGCCAAGTGCCATCGGAGAA

                             *              
       1441 TGCCGACGCCAAGGCCAAGATCCATCGGAGAA
          1 TGCCGACGCCAA-G---TG--CCATCGGAGAA

                              
       1473 TGCCGACGCCAAG-GCCA
          1 TGCCGACGCCAAGTGCCA

       1490 AGTGTCATCA


Statistics
Matches: 65,  Mismatches: 2, Indels: 17
        0.77            0.02        0.20

Matches are distributed among these distances:
  25    3  0.05
  26   31  0.48
  27    4  0.06
  28    2  0.03
  30    1  0.02
  31    1  0.02
  32   23  0.35

ACGTcount: A:0.28, C:0.32, G:0.29, T:0.12


Consensus pattern (26 bp):   
TGCCGACGCCAAGTGCCATCGGAGAA

Found at i:1458 original size:32 final size:32

Alignment explanation


    Indices: 1422--1498  Score: 129
    Period size: 32  Copynumber: 2.4  Consensus size: 32

       1412 AAGTGCCGAT

                                            
       1422 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
          1 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG

                                             
       1454 GCCAAGAT-CCATCGGAGAATGCCGACGCCAAG
          1 GCCAAG-TGCCATCGGAGAATGCCGACGCCAAG

                    *    
       1486 GCCAAGTGTCATC
          1 GCCAAGTGCCATC

       1499 AACAAGTGCC


Statistics
Matches: 42,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
  31    1  0.02
  32   40  0.95
  33    1  0.02

ACGTcount: A:0.29, C:0.31, G:0.29, T:0.12


Consensus pattern (32 bp):   
GCCAAGTGCCATCGGAGAATGCCGACGCCAAG

Found at i:1509 original size:32 final size:32

Alignment explanation


    Indices: 1422--1512  Score: 89
    Period size: 32  Copynumber: 2.8  Consensus size: 32

       1412 AAGTGCCGAT

                           * *               
       1422 GCCAAG-TGCCATCGGAGAATGCCGACGCCAAG
          1 GCCAAGAT-CCATCGAACAATGCCGACGCCAAG

                          * *               
       1454 GCCAAGATCCATCGGAGAATGCCGACGCCAAG
          1 GCCAAGATCCATCGAACAATGCCGACGCCAAG

                     *                   
       1486 GCCAAG-TGTCATC-AACAAGTGCCGACG
          1 GCCAAGAT-CCATCGAACAA-TGCCGACG

       1513 AAGGGTGTCC


Statistics
Matches: 53,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  31    4  0.08
  32   48  0.91
  33    1  0.02

ACGTcount: A:0.30, C:0.31, G:0.29, T:0.11


Consensus pattern (32 bp):   
GCCAAGATCCATCGAACAATGCCGACGCCAAG
Done.