Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001828.1 Corchorus capsularis cultivar CVL-1 contig01829, 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: 2704
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29


Found at i:157 original size:46 final size:44

Alignment explanation


    Indices: 78--163  Score: 136
    Period size: 46  Copynumber: 1.9  Consensus size: 44

         68 GGGTTTGTAG

                            **                          
         78 AGTCTTGGGGGCTGGTTTGGATGCCAAAGAGCATGTGATGCCAA
          1 AGTCTTGGGGGCTGGTGGGGATGCCAAAGAGCATGTGATGCCAA

                                                      
        122 AGTCTTGGGGGCTGGTCAGGGGATGCCAAAGAGCATGTGATG
          1 AGTCTTGGGGGCTGGT--GGGGATGCCAAAGAGCATGTGATG

        164 AGGTTTCTGG


Statistics
Matches: 38,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  44   16  0.42
  46   22  0.58

ACGTcount: A:0.22, C:0.15, G:0.40, T:0.23


Consensus pattern (44 bp):   
AGTCTTGGGGGCTGGTGGGGATGCCAAAGAGCATGTGATGCCAA

Found at i:251 original size:33 final size:33

Alignment explanation


    Indices: 209--276  Score: 136
    Period size: 33  Copynumber: 2.1  Consensus size: 33

        199 TGATGATTTG

                                             
        209 ACAGGGAAAGCTTACACATGGTATGTCAATCTT
          1 ACAGGGAAAGCTTACACATGGTATGTCAATCTT

                                             
        242 ACAGGGAAAGCTTACACATGGTATGTCAATCTT
          1 ACAGGGAAAGCTTACACATGGTATGTCAATCTT

              
        275 AC
          1 AC

        277 TCCAGGGTTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26


Consensus pattern (33 bp):   
ACAGGGAAAGCTTACACATGGTATGTCAATCTT

Found at i:1302 original size:36 final size:36

Alignment explanation


    Indices: 1262--1425  Score: 159
    Period size: 36  Copynumber: 4.6  Consensus size: 36

       1252 GTAATGTTGC

                   *   *            *     *     
       1262 TGGCCTTGGTCTCCCAATACTTAGTTATAATGCCGA
          1 TGGCCTTAGTCGCCCAATACTTAGCTATAACGCCGA

                              *   *            *
       1298 TGGCCTTAGTCGCCCAATGCTTGGCTATAACGCCGC
          1 TGGCCTTAGTCGCCCAATACTTAGCTATAACGCCGA

                    *         **  *            *
       1334 TGGCCTTATTCGCCCAATGTTTGGCTATAACGCCGC
          1 TGGCCTTAGTCGCCCAATACTTAGCTATAACGCCGA

                              **  *             
       1370 TGGCCTTAGTCGCCCAATGTTTGGCTATAACGCC-A
          1 TGGCCTTAGTCGCCCAATACTTAGCTATAACGCCGA

                   *       *     
       1405 CTGGCCTAAGTCGCCTAATAC
          1 -TGGCCTTAGTCGCCCAATAC

       1426 ATAATTGGCT


Statistics
Matches: 112,  Mismatches: 15, Indels: 2
        0.87            0.12        0.02

Matches are distributed among these distances:
  36  112  1.00

ACGTcount: A:0.20, C:0.30, G:0.22, T:0.29


Consensus pattern (36 bp):   
TGGCCTTAGTCGCCCAATACTTAGCTATAACGCCGA

Found at i:2478 original size:2 final size:2

Alignment explanation


    Indices: 2471--2498  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2461 TCTTTGAAAA

                                                     
       2471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2499 TTGAATTGCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2690 original size:20 final size:22

Alignment explanation


    Indices: 2665--2704  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2655 ATATTGTTAT

                                  
       2665 TATA-TTACT-TTTAAAAAATA
          1 TATATTTACTGTTTAAAAAATA

                    *           
       2685 TATATTTATTGTTTAAAAAA
          1 TATATTTACTGTTTAAAAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    4  0.24
  22    9  0.53

ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47


Consensus pattern (22 bp):   
TATATTTACTGTTTAAAAAATA
Done.