Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008626.1 Corchorus capsularis cultivar CVL-1 contig08647, 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: 7188
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33


Found at i:3339 original size:36 final size:36

Alignment explanation


    Indices: 3262--3460  Score: 140
    Period size: 36  Copynumber: 5.6  Consensus size: 36

       3252 CTAAAATAAG

                                                
       3262 TAACTGAAGAAAGACCACCCTAGATCATTCCAAACC
          1 TAACTGAAGAAAGACCACCCTAGATCATTCCAAACC

            *     *                        * ** 
       3298 GAACTGGAGAAAGACCACCCTAGATCATTCCGATGC
          1 TAACTGAAGAAAGACCACCCTAGATCATTCCAAACC

                     *        *          * *    *
       3334 TAACTGAAGGAAGACCACTCT-GAGTCA-ACTAAA-A
          1 TAACTGAAGAAAGACCACCCTAGA-TCATTCCAAACC

                        *         *         **   
       3368 TAAACTGAAGAACGACCACCCTCGATCATTCCGGA-C
          1 T-AACTGAAGAAAGACCACCCTAGATCATTCCAAACC

                                   *         **    
       3404 TAAACTGAAGAATA-ACCACCCTCGATCATT-CTGACTC
          1 T-AACTGAAGAA-AGACCACCCTAGATCATTCCAAAC-C

            *  *                
       3441 GAATTGAAGAAAGACCACCC
          1 TAACTGAAGAAAGACCACCC

       3461 CGGGTCAACT


Statistics
Matches: 129,  Mismatches: 26, Indels: 16
        0.75            0.15        0.09

Matches are distributed among these distances:
  34    1  0.01
  35   28  0.22
  36   99  0.77
  37    1  0.01

ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18


Consensus pattern (36 bp):   
TAACTGAAGAAAGACCACCCTAGATCATTCCAAACC

Found at i:3395 original size:107 final size:107

Alignment explanation


    Indices: 3263--3516  Score: 323
    Period size: 107  Copynumber: 2.4  Consensus size: 107

       3253 TAAAATAAGT

                      *         *         *   *      *                       
       3263 AACTGAAGAAAGACCACCCTAGATCATTCCAAACCGAACTGGAGAA-AGACCACCCTAGATCATT
          1 AACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAATA-ACCACCCTAGATCATT

                    *        *        * *               
       3327 CCGA-TGCTAACTGAAGGAAGACCACTCTGAGTCAACTAAAATA
         65 CCGACT-CGAACTGAAGAAAGACCACCCCGAGTCAACTAAAATA

                                           *   *                    *        
       3370 AACTGAAGAACGACCACCCTCGATCATTCCGGACTAAACTGAAGAATAACCACCCTCGATCATTC
          1 AACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAATAACCACCCTAGATCATTC

            *        *                  *       *     
       3435 TGACTCGAATTGAAGAAAGACCACCCCGGGTCAACTGAAATA
         66 CGACTCGAACTGAAGAAAGACCACCCCGAGTCAACTAAAATA

                  *                                 
       3477 AACTGAGGAACGACCACCCTCGATCATTCCGAACTGAACT
          1 AACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACT

       3517 TAAAAGCAAC


Statistics
Matches: 126,  Mismatches: 19, Indels: 4
        0.85            0.13        0.03

Matches are distributed among these distances:
 107  124  0.98
 108    2  0.02

ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17


Consensus pattern (107 bp):   
AACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAATAACCACCCTAGATCATTC
CGACTCGAACTGAAGAAAGACCACCCCGAGTCAACTAAAATA

Found at i:4601 original size:16 final size:16

Alignment explanation


    Indices: 4577--4628  Score: 58
    Period size: 15  Copynumber: 3.4  Consensus size: 16

       4567 CACCCTAGAG

                *           
       4577 CTTTATCTCTTTTCTT
          1 CTTTTTCTCTTTTCTT

                            
       4593 CTTTTTCTC-TTTCTT
          1 CTTTTTCTCTTTTCTT

                             
       4608 -TTTTTCT-TTCTT-TT
          1 CTTTTTCTCTT-TTCTT

                   
       4622 CTTTTTC
          1 CTTTTTC

       4629 GATTGCTTCA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
  14   10  0.31
  15   14  0.44
  16    8  0.25

ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75


Consensus pattern (16 bp):   
CTTTTTCTCTTTTCTT

Found at i:4608 original size:12 final size:12

Alignment explanation


    Indices: 4591--4621  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       4581 ATCTCTTTTC

                        
       4591 TTCTTTTTCTCT
          1 TTCTTTTTCTCT

                    *   
       4603 TTCTTTTTTTCT
          1 TTCTTTTTCTCT

                   
       4615 TTCTTTT
          1 TTCTTTT

       4622 CTTTTTCGAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (12 bp):   
TTCTTTTTCTCT
Done.