Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005162.1 Hibiscus syriacus cultivar Beakdansim tig00011645_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: 27782
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1514 original size:30 final size:31
Alignment explanation
Indices: 1480--1552 Score: 112
Period size: 33 Copynumber: 2.3 Consensus size: 31
1470 GACAGCCCAA
*
1480 GTGATGCTCCCATGT-GCTCTCCACCAACGT
1 GTGATGCTCCCATGTGGCTCTCCACCAACGC
1510 GTGATGCTCCCATGTGCGGCTCTCCACCAACGC
1 GTGATGCTCCCATGT--GGCTCTCCACCAACGC
1543 GTGATGCTCC
1 GTGATGCTCC
1553 ATCAGATTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 15 0.38
33 24 0.62
ACGTcount: A:0.15, C:0.37, G:0.23, T:0.25
Consensus pattern (31 bp):
GTGATGCTCCCATGTGGCTCTCCACCAACGC
Found at i:5196 original size:85 final size:85
Alignment explanation
Indices: 5053--5218 Score: 278
Period size: 85 Copynumber: 2.0 Consensus size: 85
5043 ATCAACTCAT
* * *
5053 ATAGTCATATTAATTTCAATAATCAATAAATATAATTAAGTTCAAGATTTGTTTTAATAAAATGG
1 ATAGTCATATAAATTTCAATAATCAATAAATATAATTAAGTTCAAGATTTATTTTAATAAAATAG
*
5118 GCAAAATTTCATTTATCTAA
66 ACAAAATTTCATTTATCTAA
*
5138 ATAGTCATATAAATTTCAATAATCAATAAATATAATTAAGTTCAAGATTTATTTTAATAAAATAT
1 ATAGTCATATAAATTTCAATAATCAATAAATATAATTAAGTTCAAGATTTATTTTAATAAAATAG
*
5203 ACAAATTTTCATTTAT
66 ACAAAATTTCATTTAT
5219 GTAATAAGTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (85 bp):
ATAGTCATATAAATTTCAATAATCAATAAATATAATTAAGTTCAAGATTTATTTTAATAAAATAG
ACAAAATTTCATTTATCTAA
Found at i:7173 original size:16 final size:17
Alignment explanation
Indices: 7154--7196 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
7144 AATAATTAAT
*
7154 ATATTAAATATTAAA-A
1 ATATTAAATATAAAATA
*
7170 ATATAAAATATAAAATA
1 ATATTAAATATAAAATA
*
7187 ATTTTAAATA
1 ATATTAAATA
7197 CTCAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATTAAATATAAAATA
Found at i:7730 original size:5 final size:5
Alignment explanation
Indices: 7716--7750 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
7706 CATAAGTATC
7716 ATAT- ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
7751 AAAATAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:7986 original size:3 final size:3
Alignment explanation
Indices: 7978--8021 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
7968 ACTCTTTGTA
7978 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8022 AGTTTATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9798 original size:20 final size:18
Alignment explanation
Indices: 9766--9812 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
9756 TTTGAATTTA
9766 ATAA-ATTTATTTATTTGGTT
1 ATAATATTT-TTTATTT--TT
9786 ATAATATTTTTTATTTTT
1 ATAATATTTTTTATTTTT
9804 A-AATATTTT
1 ATAATATTTT
9813 AGATGGCGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
20 11 0.42
21 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
ATAATATTTTTTATTTTT
Found at i:13259 original size:3 final size:3
Alignment explanation
Indices: 13251--13326 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
13241 TTTTTATCCA
* *
13251 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13299 TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
13327 AATAATAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:13825 original size:19 final size:18
Alignment explanation
Indices: 13788--13822 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13778 GACAGAACCG
13788 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
13806 AGAGAAAGAAAAAAAAA
1 AGAGAAAGAAAAAAAAA
13823 ACAACAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAAAAAAAC
Found at i:14655 original size:20 final size:21
Alignment explanation
Indices: 14616--14656 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
14606 TAGGAATTAG
14616 ATTTAGTTTATTTTTATTATA
1 ATTTAGTTTATTTTTATTATA
14637 ATTTAG-TTATTTATT-TTATA
1 ATTTAGTTTATTT-TTATTATA
14657 TGTTTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
ATTTAGTTTATTTTTATTATA
Found at i:14741 original size:20 final size:21
Alignment explanation
Indices: 14704--14744 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
14694 GATATTTTTA
**
14704 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
14725 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
14745 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:25854 original size:1 final size:1
Alignment explanation
Indices: 25848--25898 Score: 66
Period size: 1 Copynumber: 51.0 Consensus size: 1
25838 ATGCTTGAAG
* * * *
25848 AAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25899 GGGGGGTCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:25868 original size:15 final size:15
Alignment explanation
Indices: 25848--25899 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
25838 ATGCTTGAAG
25848 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
25863 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
*
25878 AAAAAAA-AAAAGAA
1 AAAAAAAGAAAAAAA
*
25892 AGAAAAAG
1 AAAAAAAG
25900 GGGGGTCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.35
15 22 0.65
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Found at i:25872 original size:23 final size:23
Alignment explanation
Indices: 25845--25898 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
25835 ATTATGCTTG
25845 AAGAAAAAAAGAAAAAAAAAAA-A
1 AAGAAAAAAA-AAAAAAAAAAAGA
25868 AAGAAAAAAAAAAAAAAAAAAGA
1 AAGAAAAAAAAAAAAAAAAAAGA
25891 AAGAAAAA
1 AAGAAAAA
25899 GGGGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (23 bp):
AAGAAAAAAAAAAAAAAAAAAGA
Found at i:25880 original size:19 final size:19
Alignment explanation
Indices: 25851--25898 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 19
25841 CTTGAAGAAA
25851 AAAAGAAAAAAAAAAAAAAG
1 AAAA-AAAAAAAAAAAAAAG
25871 AAAAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAG
25890 AAAGAAAAA
1 AAA-AAAAA
25899 GGGGGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAG
Found at i:27089 original size:78 final size:80
Alignment explanation
Indices: 26915--27668 Score: 1029
Period size: 78 Copynumber: 9.5 Consensus size: 80
26905 TAAATGAACA
26915 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAA
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAACAA
26980 TCATTGAA-TTGGAAG
65 TCATTGAATTTGGAAG
*
26995 A--AATTTGTTAAT-GCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-ACAGAACAA
1 ATGAATTTG-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGACAGAACAA
27056 TCATTGAATTTGGAAG
65 TCATTGAATTTGGAAG
27072 ATGAA-TTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACA
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TT-GACAGAACA
27136 ATCATTGAATTTGGAAG
64 ATCATTGAATTTGGAAG
* * *
27153 AAGAATGTT-TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGACA-AACA
1 ATGAAT-TTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAACA
27216 ATCATTGAATTT-GAAG
64 ATCATTGAATTTGGAAG
27232 AT-AATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAA-CA
27296 ATCATTGAATTTGGAAG
64 ATCATTGAATTTGGAAG
* * *
27313 AAGAATGTGTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC-GAATC-
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAA-CA
*
27376 ATCATTGAA-TT--AGG
64 ATCATTGAATTTGGAAG
* *
27390 ATGAATTTGCCATAGCATCTTC-GG-AGTGTTCTTTGAGTTATCTGATCT-GTGGACAGAATCAA
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGACAGAA-CAA
27452 TCATTGAATTTGGAAG
65 TCATTGAATTTGGAAG
*
27468 ATG-ATGTT--TATAGCATCTTCTGGAAGTGTTCTTTGAG-TATCTGATCTGGTTGGACA-AACA
1 ATGAAT-TTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAACA
*
27528 ATCATTGAATTTGAAAG
64 ATCATTGAATTTGGAAG
*
27545 ATAAATTTGCCAATAGCATCTTCTGG-AGTGTTC-TTGAGTTATCTGATCTGGTTGGACAGAATC
1 ATGAATTTG-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAA--
27608 CAATCATTGAATTTGGAAG
62 CAATCATTGAATTTGGAAG
* **
27627 ATG-ATGTGTTATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
27669 GATCTGTTTG
Statistics
Matches: 611, Mismatches: 28, Indels: 68
0.86 0.04 0.10
Matches are distributed among these distances:
73 3 0.00
74 7 0.01
75 33 0.05
76 32 0.05
77 69 0.11
78 169 0.28
79 46 0.08
80 70 0.11
81 57 0.09
82 123 0.20
83 2 0.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (80 bp):
ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGACAGAACAAT
CATTGAATTTGGAAG
Found at i:27247 original size:160 final size:161
Alignment explanation
Indices: 26915--27668 Score: 1178
Period size: 160 Copynumber: 4.8 Consensus size: 161
26905 TAAATGAACA
26915 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CA
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
*
26979 ATCATTGAA-TTGGAAG-A-AATTTGTTAAT-GCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
66 ATCATTGAATTTGGAAGAAGAATGT-TTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
27040 TCTGGTT--ACAGAACAATCATTGAATTTGGAAG
130 TCTGGTTGGACA-AACAATCATTGAATTT-GAAG
27072 ATGAA-TTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAA-C
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAATC
27135 AATCATTGAATTTGGAAGAAGAATGTTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
65 AATCATTGAATTTGGAAGAAGAATGTTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
*
27200 TCTGTTTGGACAAACAATCATTGAATTTGAAG
130 TCTGGTTGGACAAACAATCATTGAATTTGAAG
27232 AT-AATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
*
27296 ATCATTGAATTTGGAAGAAGAATGTGTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
66 ATCATTGAATTTGGAAGAAGAATGTTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
* *
27361 CTGGTTGGACGAATC-ATCATTGAA-TT-AGG
131 CTGGTTGGAC-AAACAATCATTGAATTTGAAG
*
27390 ATGAATTTGCCATAGCATCTTC-GG-AGTGTTCTTTGAGTTATCTGATCT-G-TGGACAGAATCA
1 ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
*
27451 ATCATTGAATTTGGAAGATG-ATGTTT-ATAGCATCTTCTGGAAGTGTTCTTTGAG-TATCTGAT
66 ATCATTGAATTTGGAAGAAGAATGTTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
27513 CTGGTTGGACAAACAATCATTGAATTTGAAAG
131 CTGGTTGGACAAACAATCATTGAATTTG-AAG
*
27545 ATAAATTTGCCAATAGCATCTTCTGG-AGTGTTC-TTGAGTTATCTGATCTGGTTGGACAGAATC
1 ATGAATTTG-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT-
*
27608 CAATCATTGAATTTGGAAGATG-ATGTGTT-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
64 CAATCATTGAATTTGGAAGAAGAATGT-TTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
27669 GATCTGTTTG
Statistics
Matches: 562, Mismatches: 13, Indels: 40
0.91 0.02 0.07
Matches are distributed among these distances:
151 3 0.01
152 27 0.05
153 30 0.05
154 5 0.01
155 41 0.07
156 75 0.13
157 60 0.11
158 23 0.04
159 64 0.11
160 209 0.37
161 22 0.04
162 3 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (161 bp):
ATGAATTTGCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
ATCATTGAATTTGGAAGAAGAATGTTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
CTGGTTGGACAAACAATCATTGAATTTGAAG
Done.