Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008288.1 Corchorus capsularis cultivar CVL-1 contig08309, 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: 17968
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30


Found at i:6162 original size:59 final size:59

Alignment explanation


    Indices: 6070--6188  Score: 238
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       6060 CTGCAAATTT

                                                                       
       6070 AAATTATCTATTGGTTTTTTCTACTAACTTAGGATTTTCTTTTTTATCTCAATTCTCAG
          1 AAATTATCTATTGGTTTTTTCTACTAACTTAGGATTTTCTTTTTTATCTCAATTCTCAG

                                                                       
       6129 AAATTATCTATTGGTTTTTTCTACTAACTTAGGATTTTCTTTTTTATCTCAATTCTCAG
          1 AAATTATCTATTGGTTTTTTCTACTAACTTAGGATTTTCTTTTTTATCTCAATTCTCAG

             
       6188 A
          1 A

       6189 TGCAAGGATG


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  59   60  1.00

ACGTcount: A:0.24, C:0.15, G:0.08, T:0.52


Consensus pattern (59 bp):   
AAATTATCTATTGGTTTTTTCTACTAACTTAGGATTTTCTTTTTTATCTCAATTCTCAG

Found at i:10374 original size:2 final size:2

Alignment explanation


    Indices: 10367--10391  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      10357 TCCGTAAGAT

                                                 
      10367 AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC A

      10392 AAAAAAAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:17469 original size:32 final size:31

Alignment explanation


    Indices: 17403--17636  Score: 138
    Period size: 32  Copynumber: 7.6  Consensus size: 31

      17393 TTTAAACCTC

                             *  *  **    *  
      17403 GTGTGCATCTCCCGCACGCTTTAACAATAATT
          1 GTGTGCATCTCCCGCACAC-ATATTAATATTT

                  *                         
      17435 GTGTGCTTCTCCCGCACATCATATTAATATTT
          1 GTGTGCATCTCCCGCACA-CATATTAATATTT

                 * *                    *  *
      17467 GTGTGAACCTCCCGCACACTATATTAATGTTC
          1 GTGTGCATCTCCCGCACAC-ATATTAATATTT

                * *       *                
      17499 GTGTACTTCTCCCGTACAC-TA-TAATATTT
          1 GTGTGCATCTCCCGCACACATATTAATATTT

            *                      *      *
      17528 ATGTGCATCTCCCGCACAC-T-TGAATATTC
          1 GTGTGCATCTCCCGCACACATATTAATATTT

            *     *     *          * *   *  
      17557 ATGTGCGTCTCCTGCACACCATACTGATACTT
          1 GTGTGCATCTCCCGCACA-CATATTAATATTT

                *      *  *         *     *
      17589 GTGTACATCTCTCGTACAC-TA-TCATATTC
          1 GTGTGCATCTCCCGCACACATATTAATATTT

            *                  
      17618 ATGTGCATCTCCCGCACAC
          1 GTGTGCATCTCCCGCACAC

      17637 TTTTTCTATC


Statistics
Matches: 152,  Mismatches: 44, Indels: 15
        0.72            0.21        0.07

Matches are distributed among these distances:
  29   64  0.42
  30    5  0.03
  31    3  0.02
  32   79  0.52
  33    1  0.01

ACGTcount: A:0.24, C:0.29, G:0.14, T:0.34


Consensus pattern (31 bp):   
GTGTGCATCTCCCGCACACATATTAATATTT

Found at i:17539 original size:29 final size:29

Alignment explanation


    Indices: 17436--17637  Score: 127
    Period size: 29  Copynumber: 6.7  Consensus size: 29

      17426 ACAATAATTG

                 *                        **
      17436 TGTGCTTCTCCCGCACATCATATTAATATTTG
          1 TGTGCATCTCCCGCACA-C-TA-TAATATTCA

                * *                    *   *
      17468 TGTGAACCTCCCGCACACTATATTAATGTTCG
          1 TGTGCATCTCCCGCACAC--TA-TAATATTCA

               * *       *             * 
      17500 TGTACTTCTCCCGTACACTATAATATTTA
          1 TGTGCATCTCCCGCACACTATAATATTCA

                                          
      17529 TGTGCATCTCCCGCACACT-TGAATATTCA
          1 TGTGCATCTCCCGCACACTAT-AATATTCA

                 *     *      *   *    * *
      17558 TGTGCGTCTCCTGCACACCATACTGATACT
          1 TGTGCATCTCCCGCACACTATAAT-ATTCA

                        *  *       *       
      17588 TGTGTACATCTCTCGTACACTATCATATTCA
          1 TGTG--CATCTCCCGCACACTATAATATTCA

                               
      17619 TGTGCATCTCCCGCACACT
          1 TGTGCATCTCCCGCACACT

      17638 TTTTCTATCA


Statistics
Matches: 130,  Mismatches: 34, Indels: 15
        0.73            0.19        0.08

Matches are distributed among these distances:
  28    1  0.01
  29   60  0.46
  30   10  0.08
  31    8  0.06
  32   51  0.39

ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35


Consensus pattern (29 bp):   
TGTGCATCTCCCGCACACTATAATATTCA

Found at i:17545 original size:61 final size:64

Alignment explanation


    Indices: 17404--17547  Score: 161
    Period size: 64  Copynumber: 2.3  Consensus size: 64

      17394 TTAAACCTCG

                            *  *               *                           *
      17404 TGTGCATCTCCCGCACGCTTTAACAATAATTGTGTGCTTCTCCCGCACATCATATTAATATTTG
          1 TGTGCATCTCCCGCACACTATAACAATAATTGTGTACTTCTCCCGCACATCATATTAATATTTA

                * *               **    *                 *                  
      17468 TGTGAACCTCCCGCACACTATATTAAT-GTTCGTGTACTTCTCCCGTACA-C-TA-TAATATTTA
          1 TGTGCATCTCCCGCACACTATAACAATAATT-GTGTACTTCTCCCGCACATCATATTAATATTTA

                               
      17529 TGTGCATCTCCCGCACACT
          1 TGTGCATCTCCCGCACACT

      17548 TGAATATTCA


Statistics
Matches: 67,  Mismatches: 12, Indels: 5
        0.80            0.14        0.06

Matches are distributed among these distances:
  61   25  0.37
  62    2  0.03
  63    3  0.04
  64   37  0.55

ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35


Consensus pattern (64 bp):   
TGTGCATCTCCCGCACACTATAACAATAATTGTGTACTTCTCCCGCACATCATATTAATATTTA
Done.