Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014649.1 Corchorus capsularis cultivar CVL-1 contig14670, 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: 7544
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:2363 original size:135 final size:135

Alignment explanation


    Indices: 2118--2427  Score: 406
    Period size: 135  Copynumber: 2.3  Consensus size: 135

       2108 GTACGCCTGG

                         *     *  *                                          
       2118 GAAACAAATATAAACCTGGCTATGGAGTGGATGAAGCAGAGGGAAAAAGTTCTTCGTCAGCCTAC
          1 GAAACAAATATAAGCCTGGTTACGGAGTGGATGAAGCAGA--GAAAAAGTTCTTCGTCAGCCTAC

                               *         *      *                         *  
       2183 ATCACAAAGTTGGAAAGCAGATACAAACCTGATTATGGAGTGCTTGAAGATGAGGAGAAGATTGC
         64 ATCACAAAGTTGGAAAGCAAATACAAACCAGATTATAGAGTGCTTGAAGATGAGGAGAAGATGGC

            * **   
       2248 TCGTCTT
        129 ACACCTT

                                                  *      *        *  *  *    
       2255 GAAAGCAAATATAAGCCTGGTTACGGAGTGGATGAAGCTGA-AAAGAGTTCTTCTTCTGCTTACA
          1 GAAA-CAAATATAAGCCTGGTTACGGAGTGGATGAAGCAGAGAAAAAGTTCTTCGTCAGCCTACA

                                     *    *     *         *                  
       2319 TCACAAAGTTGGAAAGCAAATACAAGCCAGGTTATATAGTGCTTGAGGATGAGGAGAAGATGGCA
         65 TCACAAAGTTGGAAAGCAAATACAAACCAGATTATAGAGTGCTTGAAGATGAGGAGAAGATGGCA

                  
       2384 CACCTT
        130 CACCTT

                                                  
       2390 GAAAACAAATATAAGCCTGGTTACGGAGTGGATGAAGC
          1 G-AAACAAATATAAGCCTGGTTACGGAGTGGATGAAGC

       2428 CGAGGAGAAG


Statistics
Matches: 152,  Mismatches: 19, Indels: 6
        0.86            0.11        0.03

Matches are distributed among these distances:
 135  113  0.74
 136    3  0.02
 137    4  0.03
 138   32  0.21

ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23


Consensus pattern (135 bp):   
GAAACAAATATAAGCCTGGTTACGGAGTGGATGAAGCAGAGAAAAAGTTCTTCGTCAGCCTACAT
CACAAAGTTGGAAAGCAAATACAAACCAGATTATAGAGTGCTTGAAGATGAGGAGAAGATGGCAC
ACCTT

Found at i:2572 original size:187 final size:184

Alignment explanation


    Indices: 2260--2620  Score: 578
    Period size: 187  Copynumber: 1.9  Consensus size: 184

       2250 GTCTTGAAAG

                     *                                                       
       2260 CAAATATAAGCCTGGTTACGGAGTGGATGAAGCTGAAAAGAGTTCTTCTTCTGCTTACATCACAA
          1 CAAATATAAACCTGGTTACGGAGTGGATGAAGCTGAAAAGAGTTCTTCTTCTGCTTACATCACAA

                               **  *                *                       *
       2325 AGTTGGAAAGCAAATACAAGCCAGGTTATATAGTGCTTGAGGATGAGGAGAAGATGGCACACCTT
         66 AGTTGGAAAGCAAATACAAAACAAGTTATATAGTGCTTGAAGATGAGGAGAAGATGGCACACCTC

                       *  *    *                                  
       2390 GAAAACAAATATAAGCCTGGTTACGGAGTGGATGAAGCCGAGGAGAAGATGGCA
        131 GAAAACAAATACAAACCTGATTACGGAGTGGATGAAGCCGAGGAGAAGATGGCA

                                                                            *
       2444 CAAATATAAACCTGGTTACGGAGTGGATGAAGCTGAAGGAAAGAGTTCTTCTTCTGCTTACATCG
          1 CAAATATAAACCTGGTTACGGAGTGGATGAAGCTG-A--AAAGAGTTCTTCTTCTGCTTACATCA

                          *                                  *               
       2509 CAAAGTTGGAAAGCCAATACAAAACAAGTTATATAGTGCTTGAAGATGATGAGAAGATGGCACAC
         63 CAAAGTTGGAAAGCAAATACAAAACAAGTTATATAGTGCTTGAAGATGAGGAGAAGATGGCACAC

                                                     *     
       2574 CTCGAAAACAAATACAAACCTGATTACGGAGTGGATGAAGCTGAGGA
        128 CTCGAAAACAAATACAAACCTGATTACGGAGTGGATGAAGCCGAGGA

       2621 AAAAATCGAG


Statistics
Matches: 161,  Mismatches: 13, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
 184   34  0.21
 185    1  0.01
 187  126  0.78

ACGTcount: A:0.37, C:0.16, G:0.26, T:0.22


Consensus pattern (184 bp):   
CAAATATAAACCTGGTTACGGAGTGGATGAAGCTGAAAAGAGTTCTTCTTCTGCTTACATCACAA
AGTTGGAAAGCAAATACAAAACAAGTTATATAGTGCTTGAAGATGAGGAGAAGATGGCACACCTC
GAAAACAAATACAAACCTGATTACGGAGTGGATGAAGCCGAGGAGAAGATGGCA

Found at i:3894 original size:23 final size:23

Alignment explanation


    Indices: 3851--3899  Score: 55
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       3841 GTGATGTGGC

                       *         * 
       3851 ATTTTCTACCATGTTGACATGTT
          1 ATTTTCTACCACGTTGACATGCT

                             *      
       3874 ATTTTCTAACCACG-TGGCATGCT
          1 ATTTTCT-ACCACGTTGACATGCT

               
       3897 ATT
          1 ATT

       3900 GTGGCATTTC


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  23   17  0.77
  24    5  0.23

ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43


Consensus pattern (23 bp):   
ATTTTCTACCACGTTGACATGCT

Found at i:4828 original size:13 final size:13

Alignment explanation


    Indices: 4810--4835  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4800 ACATAAGCAA

                         
       4810 TCTTAAAAGACAC
          1 TCTTAAAAGACAC

                         
       4823 TCTTAAAAGACAC
          1 TCTTAAAAGACAC

       4836 AGAAAGGATA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23


Consensus pattern (13 bp):   
TCTTAAAAGACAC
Done.