Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 19
Found at i:3893196 original size:13 final size:13
Alignment explanation
Indices: 3893178--3893205 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3893168 TGATATAAGC
3893178 AATGGTTGCGATT
1 AATGGTTGCGATT
3893191 AATGGTTGCGATT
1 AATGGTTGCGATT
3893204 AA
1 AA
3893206 GATGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (13 bp):
AATGGTTGCGATT
Found at i:3893522 original size:2 final size:2
Alignment explanation
Indices: 3893515--3893580 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3893505 GGTGTTGTAA
3893515 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
3893557 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
3893581 GCGATTGCAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3894069 original size:2 final size:2
Alignment explanation
Indices: 3894062--3894088 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3894052 TAAGAGCTAA
3894062 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 A
3894089 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3894139 original size:9 final size:8
Alignment explanation
Indices: 3894088--3894185 Score: 59
Period size: 7 Copynumber: 12.6 Consensus size: 8
3894078 ATATATATAT
3894088 AAAAA-AA
1 AAAAAGAA
3894095 AAAAA-AA
1 AAAAAGAA
3894102 AAAAAG-A
1 AAAAAGAA
3894109 AAAAAG-A
1 AAAAAGAA
*
3894116 AAATAG--
1 AAAAAGAA
3894122 AAAAAGAA
1 AAAAAGAA
3894130 AAAAATGAA
1 AAAAA-GAA
*
3894139 AGAATAAAAA
1 A-AA-AAGAA
3894149 GAAAAAGAA
1 -AAAAAGAA
*
3894158 AACGAAGAA
1 AA-AAAGAA
*
3894167 AAATAG--
1 AAAAAGAA
3894173 AAAAAGAA
1 AAAAAGAA
3894181 AAAAA
1 AAAAA
3894186 ATGAGAGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
6 10 0.14
7 25 0.34
8 14 0.19
9 15 0.21
10 6 0.08
11 3 0.04
ACGTcount: A:0.83, C:0.01, G:0.12, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3894139 original size:29 final size:27
Alignment explanation
Indices: 3894088--3894183 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 27
3894078 ATATATATAT
* *
3894088 AAAAAAAAAAAAAAAAAAAGAAAAAAG
1 AAAAAGAAAAAGAAAAAAAGAAAAAAG
* *
3894115 AAAATAGAAAAAGAAAAAAATGAAAGAAT
1 AAAA-AGAAAAAGAAAAAAA-GAAAAAAG
*
3894144 AAAAAGAAAAAGAAAACGAAGAAAAATAG
1 AAAAAGAAAAAGAAAA-AAAGAAAAA-AG
3894173 AAAAAGAAAAA
1 AAAAAGAAAAA
3894184 AAATGAGAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.07
28 30 0.52
29 24 0.41
ACGTcount: A:0.82, C:0.01, G:0.12, T:0.04
Consensus pattern (27 bp):
AAAAAGAAAAAGAAAAAAAGAAAAAAG
Found at i:3894148 original size:35 final size:35
Alignment explanation
Indices: 3894102--3894183 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
3894092 AAAAAAAAAA
3894102 AAAAAGAAAAAAGAAAATAGAAAAAGAA-AAAAAT-G
1 AAAAAG-AAAAAGAAAA-AGAAAAAGAAGAAAAATAG
* *
3894137 AAAGAATAAAAAGAAAAAGAAAACGAAGAAAAATAG
1 AAA-AAGAAAAAGAAAAAGAAAAAGAAGAAAAATAG
3894173 AAAAAGAAAAA
1 AAAAAGAAAAA
3894184 AAATGAGAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 9 0.22
35 26 0.63
36 6 0.15
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (35 bp):
AAAAAGAAAAAGAAAAAGAAAAAGAAGAAAAATAG
Found at i:3894155 original size:6 final size:6
Alignment explanation
Indices: 3894088--3894183 Score: 74
Period size: 6 Copynumber: 15.7 Consensus size: 6
3894078 ATATATATAT
3894088 AAAA-A AAAA-A AAAA-A AAAAGAA AAAAGA AAATAGA AAAAGAAA AAAATGA
1 AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA AAA-AGA AAAAG--A AAAA-GA
* * * *
3894138 AAGAATA AAAAGA AAAAGA AAACGA AGAA-A AATAGA AAAAGA AAAA
1 AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
3894184 AAATGAGAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
5 17 0.23
6 32 0.43
7 18 0.24
8 7 0.09
9 1 0.01
ACGTcount: A:0.82, C:0.01, G:0.12, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:3894170 original size:51 final size:52
Alignment explanation
Indices: 3894096--3894204 Score: 154
Period size: 48 Copynumber: 2.1 Consensus size: 52
3894086 ATAAAAAAAA
3894096 AAAAAAAAAAAGAAAAAAGAAAATAGAAAAAG-AAAAAAATGA-A-A-GAAT
1 AAAAAAAAAAAGAAAAAAGAAAATAGAAAAAGAAAAAAAATGAGAGATGAAT
*
3894144 AAAAAGAAAAAGAAAACGAAGAAAAATAGAAAAAGAAAAAAAATGAGAGATGAAT
1 AAAAAAAAAAAGAAAA--AAG-AAAATAGAAAAAGAAAAAAAATGAGAGATGAAT
3894199 AAAAAA
1 AAAAAA
3894205 GGAGAAAGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
48 15 0.29
50 3 0.06
51 13 0.25
52 10 0.19
53 1 0.02
54 1 0.02
55 9 0.17
ACGTcount: A:0.78, C:0.01, G:0.15, T:0.06
Consensus pattern (52 bp):
AAAAAAAAAAAGAAAAAAGAAAATAGAAAAAGAAAAAAAATGAGAGATGAAT
Found at i:3894199 original size:28 final size:25
Alignment explanation
Indices: 3894094--3894205 Score: 77
Period size: 27 Copynumber: 4.3 Consensus size: 25
3894084 ATATAAAAAA
* ** *
3894094 AAAAAAAAAAAAAGAAAAAAGAAAAT
1 AAAAAAGAAAAAA-AATGAAGAGAAT
3894120 AGAAAAAG-AAAAAAATGAA-AGAAT
1 A-AAAAAGAAAAAAAATGAAGAGAAT
* *
3894144 -AAAAAGAAAAAGAAAACGAAGAAAAAT
1 AAAAAAG-AAAA-AAAATGAAG-AGAAT
3894171 AGAAAAAGAAAAAAAATGAGAGATGAAT
1 A-AAAAAGAAAAAAAATGA-AGA-GAAT
3894199 AAAAAAG
1 AAAAAAG
3894206 GAGAAAGGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
22 6 0.09
24 7 0.10
25 11 0.16
26 6 0.09
27 22 0.32
28 10 0.15
29 6 0.09
ACGTcount: A:0.78, C:0.01, G:0.15, T:0.06
Consensus pattern (25 bp):
AAAAAAGAAAAAAAATGAAGAGAAT
Found at i:3897972 original size:40 final size:40
Alignment explanation
Indices: 3897865--3898024 Score: 270
Period size: 40 Copynumber: 4.0 Consensus size: 40
3897855 TGCAAGTTTA
3897865 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3897905 TAATACACTTC-G-GTATATGGTGGGCACGACCTTATTTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3897943 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
3897983 TAATACACTTCGGTGTATATGGTGGACACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
3898023 TA
1 TA
3898025 GCACTACGGT
Statistics
Matches: 112, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
38 35 0.31
39 2 0.02
40 75 0.67
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:3897994 original size:78 final size:80
Alignment explanation
Indices: 3897865--3898024 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 80
3897855 TGCAAGTTTA
3897865 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTC-G-GTATATGGTGG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGG
* *
3897928 GCACGACCTTATTTG
66 ACACGACCTTATATG
*
3897943 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGG
3898008 ACACGACCTTATATG
66 ACACGACCTTATATG
3898023 TA
1 TA
3898025 GCACTACGGT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 50 0.65
79 1 0.01
80 26 0.34
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (80 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGG
ACACGACCTTATATG
Found at i:3898191 original size:45 final size:44
Alignment explanation
Indices: 3898131--3898238 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 44
3898121 AGCATGCAAG
* *
3898131 TAAGC-TACGAGCTTATGGA-ATATTGGCAAGTATATGGGTAAAAA
1 TAAGCTTACGAGCTTATGGACA-AATGACAAGTATATGGGT-AAAA
* * *
3898175 TAAGCTTACGAGCTTATGGGACAAATGATAAGTATTTTGGTAAAA
1 TAAGCTTACGAGCTTAT-GGACAAATGACAAGTATATGGGTAAAA
3898220 TAAGCTTACGAGCTTATGG
1 TAAGCTTACGAGCTTATGG
3898239 TTAATAAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
44 7 0.12
45 32 0.57
46 16 0.29
47 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (44 bp):
TAAGCTTACGAGCTTATGGACAAATGACAAGTATATGGGTAAAA
Found at i:3898602 original size:18 final size:18
Alignment explanation
Indices: 3898579--3898617 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3898569 TTATGATTTT
3898579 TGTAGCGCGTCGATGGAC
1 TGTAGCGCGTCGATGGAC
* *
3898597 TGTAGCGCGTTGATGTAC
1 TGTAGCGCGTCGATGGAC
3898615 TGT
1 TGT
3898618 TGCAGTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.36, T:0.31
Consensus pattern (18 bp):
TGTAGCGCGTCGATGGAC
Found at i:3898976 original size:36 final size:36
Alignment explanation
Indices: 3898936--3899039 Score: 110
Period size: 39 Copynumber: 2.9 Consensus size: 36
3898926 GGTGTTAAAC
3898936 TAACATTCTAAATTAATTTCTTAAAATT-TTTCACCA-
1 TAACATTCTAAATTAATTT-TTAAAATTATTTCA-CAT
3898972 TAACATTCTAAATTCTTAATTTGTT-AAATTATTTCACAT
1 TAACATTCTAAA---TTAATTT-TTAAAATTATTTCACAT
*
3899011 TAACATTATAAATT-ATTTTTAAAA-TATTT
1 TAACATTCTAAATTAATTTTTAAAATTATTT
3899040 ATTTTAACTT
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
34 7 0.12
35 7 0.12
36 14 0.23
38 7 0.12
39 25 0.42
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (36 bp):
TAACATTCTAAATTAATTTTTAAAATTATTTCACAT
Done.