Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009195.1 Hibiscus syriacus cultivar Beakdansim tig00112777_pilon, 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: 57952
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:16418 original size:20 final size:21
Alignment explanation
Indices: 16384--16424 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
16374 TGCAGAGTTT
16384 TCATCCCCAAACGGCTAGAAA
1 TCATCCCCAAACGGCTAGAAA
16405 TCATCCCC-AACGGCTAGAAA
1 TCATCCCCAAACGGCTAGAAA
16425 CGACCACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.37, C:0.34, G:0.15, T:0.15
Consensus pattern (21 bp):
TCATCCCCAAACGGCTAGAAA
Found at i:23716 original size:38 final size:38
Alignment explanation
Indices: 23662--23735 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
23652 TGGAATGGAC
* *
23662 GACATGTTCTCTTTTGCGGTATGTAAATTTATATGCTT
1 GACATGTTCTCCTTTGCAGTATGTAAATTTATATGCTT
23700 GACATGTTCTCCTTTGCAGTATGTAAATTTATATGC
1 GACATGTTCTCCTTTGCAGTATGTAAATTTATATGC
23736 ATGGTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.45
Consensus pattern (38 bp):
GACATGTTCTCCTTTGCAGTATGTAAATTTATATGCTT
Found at i:30483 original size:32 final size:31
Alignment explanation
Indices: 30455--30531 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
30445 CGGGGCCGTG
*
30455 GGGCCTACCTAAGAATACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAAT-CATCTCAGGGCCGCA
** *
30487 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATCATCTCAGGGCCGCA
*
30518 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
30532 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAATCATCTCAGGGCCGCA
Found at i:30514 original size:63 final size:63
Alignment explanation
Indices: 30408--30531 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
30398 CCCTAAGGGA
* * * ** *
30408 ACATCTTAGGGCCTGAGAGCCTATCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAT
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAT
* *
30471 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
30532 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAT
Found at i:31470 original size:29 final size:29
Alignment explanation
Indices: 31438--31522 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
31428 ACAACACATG
*
31438 TTTAAAAATAATTACCAAAATATCATCTT
1 TTTAAAAATAATTACCAAAATATCACCTT
* * *
31467 TTTAAAAATAATTATCAAAACATCGCCTT
1 TTTAAAAATAATTACCAAAATATCACCTT
* *
31496 TTTCAAAATAATTACTAAAATATCACC
1 TTTAAAAATAATTACCAAAATATCACC
31523 GGGCCGGGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.35
Consensus pattern (29 bp):
TTTAAAAATAATTACCAAAATATCACCTT
Found at i:35765 original size:27 final size:28
Alignment explanation
Indices: 35734--35854 Score: 83
Period size: 27 Copynumber: 4.5 Consensus size: 28
35724 GTGTTGCCAC
35734 AAGTTCTAATGCTTCCAGTGTTGCA-AT
1 AAGTTCTAATGCTTCCAGTGTTGCAGAT
* * * * *
35761 GAGTTCTACTTCTGT-TAGTGTTGCAGCT
1 AAGTTCTAATGCT-TCCAGTGTTGCAGAT
* ***
35789 -GGTT-TGAATGCTGATAGTGTTGCAGA-
1 AAGTTCT-AATGCTTCCAGTGTTGCAGAT
*
35815 AAGTTTTAATGCTTCCAGTGTTGCA-AT
1 AAGTTCTAATGCTTCCAGTGTTGCAGAT
*
35842 AAGTTCTACTGCT
1 AAGTTCTAATGCT
35855 ATTACCGTTA
Statistics
Matches: 71, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
26 2 0.03
27 66 0.93
28 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (28 bp):
AAGTTCTAATGCTTCCAGTGTTGCAGAT
Found at i:35869 original size:81 final size:81
Alignment explanation
Indices: 35716--35873 Score: 219
Period size: 81 Copynumber: 2.0 Consensus size: 81
35706 CAACTATTGG
* * * * * **
35716 TGCTGGTAGTGTTGCCACAAGTTCTAATGCTTCCAGTGTTGCAATGAGTTCTACTTCTGTTAGTG
1 TGCTGATAGTGTTGCCAAAAGTTCTAATGCTTCCAGTGTTGCAATAAGTTCTACTGCTATTACCG
*
35781 TTGCAGCTGGTTTGAA
66 TTACAGCTGGTTTGAA
*
35797 TGCTGATAGTGTTG-CAGAAAGTTTTAATGCTTCCAGTGTTGCAATAAGTTCTACTGCTATTACC
1 TGCTGATAGTGTTGCCA-AAAGTTCTAATGCTTCCAGTGTTGCAATAAGTTCTACTGCTATTACC
35861 GTTACAGCTGGTT
65 GTTACAGCTGGTT
35874 CGATAGCTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
80 2 0.03
81 65 0.97
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (81 bp):
TGCTGATAGTGTTGCCAAAAGTTCTAATGCTTCCAGTGTTGCAATAAGTTCTACTGCTATTACCG
TTACAGCTGGTTTGAA
Found at i:42887 original size:19 final size:16
Alignment explanation
Indices: 42846--42877 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42836 TGGAATCATC
*
42846 ATATATTATTAAAAAA
1 ATATAATATTAAAAAA
42862 ATATAATATTAAAAAA
1 ATATAATATTAAAAAA
42878 TACTCATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAATATTAAAAAA
Found at i:47444 original size:2 final size:2
Alignment explanation
Indices: 47437--47465 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47427 ATATGAGGTA
47437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47466 CATGTACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47589 original size:24 final size:25
Alignment explanation
Indices: 47551--47597 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
47541 TATAATAAAA
*
47551 AATTTAAACAATTTGATTTAACTCG
1 AATTTAAACAATTTGATTCAACTCG
*
47576 AATTTTAA-AATTTGATTCAACT
1 AATTTAAACAATTTGATTCAACT
47598 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (25 bp):
AATTTAAACAATTTGATTCAACTCG
Found at i:51710 original size:39 final size:41
Alignment explanation
Indices: 51667--51743 Score: 131
Period size: 39 Copynumber: 1.9 Consensus size: 41
51657 ATTTTTTTTA
*
51667 GAGTTCATGATCAAA-TTGTCACC-GCCACTACTATATCTT
1 GAGTTAATGATCAAATTTGTCACCGGCCACTACTATATCTT
51706 GAGTTAATGATCAAATTTGTCACCGGCCACTACTATAT
1 GAGTTAATGATCAAATTTGTCACCGGCCACTACTATAT
51744 TGTACTCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 14 0.40
40 8 0.23
41 13 0.37
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (41 bp):
GAGTTAATGATCAAATTTGTCACCGGCCACTACTATATCTT
Done.