Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000364.1 Hibiscus syriacus cultivar Beakdansim tig00000664_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: 61401
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:2710 original size:2 final size:2
Alignment explanation
Indices: 2703--2729 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2693 CTCCTACTCC
2703 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2730 GGAATATTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4093 original size:167 final size:170
Alignment explanation
Indices: 3909--4250 Score: 548
Period size: 175 Copynumber: 2.0 Consensus size: 170
3899 TTCATTCTTA
3909 AAAATTTTAAATTATTATACATTTTAGATTATTTTTATGTA-TTTTTTGTTT-AAA-TTTTTTTT
1 AAAATTTTAAATTATTATACATTTTAGATTATTTTTATGTATTTTTTTGTTTAAAATTTTTTTTT
* *
3971 CTTTTCAAATTTTTTAATTTTACAAGTTTGAGTTAATTTCCGCTTAAATTTTTTAAATTTAAATA
66 CTTTTCAAAATTTTTAATTTTACAAGTTTGAGTTAATTTCCACTTAAATTTTTTAAATTTAAAT-
*
4036 T-ACCTTTTAATATAAGATCTTGCTTCCGTCTTTAGTTAAG
130 TCACCTTTTAATATAAGATCTTGCTTACGTCTTTAGTTAAG
*
4076 AAAATTTTAAATTATTATATATTTTAGATTATTTTTATGTATTTTTTTGTTTAAAATTTGTTTTT
1 AAAATTTTAAATTATTATACATTTTAGATTATTTTTATGTATTTTTTTGTTTAAAA-----TTTT
4141 TTTTTCTTTTCAAAATTTTTAATTTTACAAGTTTGAGTTAATTTCCACTTAAATTTTTTAAATTT
61 TTTTTCTTTTCAAAATTTTTAATTTTACAAGTTTGAGTTAATTTCCACTTAAATTTTTTAAATTT
* *
4206 AAATTCACCTTTTAGTATAAGATCTTGTTTACGTCTTTAGTTAAG
126 AAATTCACCTTTTAATATAAGATCTTGCTTACGTCTTTAGTTAAG
4251 TTAGTGATGG
Statistics
Matches: 160, Mismatches: 6, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
167 40 0.25
168 10 0.06
169 3 0.02
174 1 0.01
175 106 0.66
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (170 bp):
AAAATTTTAAATTATTATACATTTTAGATTATTTTTATGTATTTTTTTGTTTAAAATTTTTTTTT
CTTTTCAAAATTTTTAATTTTACAAGTTTGAGTTAATTTCCACTTAAATTTTTTAAATTTAAATT
CACCTTTTAATATAAGATCTTGCTTACGTCTTTAGTTAAG
Found at i:17230 original size:23 final size:24
Alignment explanation
Indices: 17183--17235 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
17173 AGGATCGTGC
17183 CACAAGAGCATAAAAAAATCATGT
1 CACAAGAGCATAAAAAAATCATGT
* *
17207 CACAAGAGCATAGAAAAAT-GTGT
1 CACAAGAGCATAAAAAAATCATGT
17230 CACAAG
1 CACAAG
17236 GATATAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (24 bp):
CACAAGAGCATAAAAAAATCATGT
Found at i:23844 original size:15 final size:15
Alignment explanation
Indices: 23826--23859 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
23816 GAGGGTATAA
23826 TAGTCCTTCAGGATG
1 TAGTCCTTCAGGATG
*
23841 TAGTCCTTCGGGATG
1 TAGTCCTTCAGGATG
23856 TAGT
1 TAGT
23860 GGTCATACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCAGGATG
Found at i:25793 original size:21 final size:22
Alignment explanation
Indices: 25763--25815 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
25753 AAAAATAATG
* *
25763 TAATTAATATTT-TTTTTTAAA
1 TAATTTATATTTAATTTTTAAA
*
25784 TAATTTATATTTAGATTTTTAAC
1 TAATTTATATTTA-ATTTTTAAA
25807 TAATTTATA
1 TAATTTATA
25816 ATTATACATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
23 16 0.59
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TAATTTATATTTAATTTTTAAA
Found at i:30055 original size:21 final size:20
Alignment explanation
Indices: 30031--30079 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
30021 TGAAGCAAAC
*
30031 GATCCTTTTCCTCGAGGGATT
1 GATCCTTTTCC-CAAGGGATT
* *
30052 GATCATTTTGCCAAGGGATT
1 GATCCTTTTCCCAAGGGATT
30072 GATCCTTT
1 GATCCTTT
30080 GAGCCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
GATCCTTTTCCCAAGGGATT
Found at i:42014 original size:26 final size:25
Alignment explanation
Indices: 41955--42020 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
41945 CGAATAAACC
* *
41955 AAAAAAATTAAATTTTCTAATTTAT
1 AAAAAAATTAAATTTTCTAATTCAA
* *
41980 ATAACAATTGAATATTTT-TAATTCAA
1 AAAAAAATT-AA-ATTTTCTAATTCAA
42006 AAAAAAATTACAATT
1 AAAAAAATTA-AATT
42021 AATTTAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
25 11 0.34
26 16 0.50
27 5 0.16
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAAAAATTAAATTTTCTAATTCAA
Found at i:44478 original size:20 final size:21
Alignment explanation
Indices: 44438--44480 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
44428 TTCATATTGT
44438 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
44459 CCAGGGGGTATC-GATTCCCCC
1 CCAGGGGGTA-CAGATTCCCCC
44480 C
1 C
44481 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:45780 original size:19 final size:20
Alignment explanation
Indices: 45756--45803 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
45746 AACGATTTTC
*
45756 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
45775 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
45795 TTTTGAAAA
1 TTTTGAAAA
45804 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:47223 original size:21 final size:20
Alignment explanation
Indices: 47178--47257 Score: 101
Period size: 19 Copynumber: 4.0 Consensus size: 20
47168 TTCAGATTGT
*
47178 CCAGGGGGTACAGA-TCCCC
1 CCAGGGGGAACAGATTCCCC
*
47197 CCAGGGGGAATAGATTCCCC
1 CCAGGGGGAACAGATTCCCC
* *
47217 CCTAGGGGGTACCGATT-CCC
1 CC-AGGGGGAACAGATTCCCC
47237 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGAACAGATTCCCC
47257 C
1 C
47258 TGTCTAACGG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 24 0.47
20 16 0.31
21 11 0.22
ACGTcount: A:0.21, C:0.35, G:0.30, T:0.14
Consensus pattern (20 bp):
CCAGGGGGAACAGATTCCCC
Found at i:47224 original size:40 final size:40
Alignment explanation
Indices: 47180--47257 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
47170 CAGATTGTCC
*
47180 AGGGGGTACAGATCCCCCCAGGGGGAATAGATTCCCCCCT
1 AGGGGGTACAGATCCCCCCAGGGGGAACAGATTCCCCCCT
* *
47220 AGGGGGTACCGATTCCCCCAGGGGGAACAGATTCCCCC
1 AGGGGGTACAGATCCCCCCAGGGGGAACAGATTCCCCC
47258 TGTCTAACGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.14
Consensus pattern (40 bp):
AGGGGGTACAGATCCCCCCAGGGGGAACAGATTCCCCCCT
Found at i:57295 original size:31 final size:31
Alignment explanation
Indices: 57209--57333 Score: 110
Period size: 32 Copynumber: 4.0 Consensus size: 31
57199 GTCGAGGGTT
57209 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTACGGAACATATGGACAGT-A
* * * *
57240 TTACCTATG-TCTTTCGGGATATATGGATAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* *
57272 TACCTATGTTCTAAGGAACATATGGGCAGTA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * * *
57303 TACCTAGGTTCTTTCGGGACCTATGGACAGT
1 TACCTATGTTC-TACGGAACATATGGACAGT
57334 TGCCCGAGGA
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
31 34 0.47
32 38 0.52
33 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:57328 original size:63 final size:63
Alignment explanation
Indices: 57209--57329 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
57199 GTCGAGGGTT
* * *
57209 TACCTATGTTCTACGGAACATATGGACATAATTACCTATGTCTTTCGGGATATATGGATAGTA
1 TACCTATGTTCTAAGGAACATATGGACATAATTACCTAGGTCTTTCGGGACATATGGATAGTA
* *
57272 TACCTATGTTCTAAGGAACATATGGGCAGT-A-TACCTAGGTTCTTTCGGGACCTATGGA
1 TACCTATGTTCTAAGGAACATATGGACA-TAATTACCTAGG-TCTTTCGGGACATATGGA
57330 CAGTTGCCCG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 7 0.14
63 43 0.84
64 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (63 bp):
TACCTATGTTCTAAGGAACATATGGACATAATTACCTAGGTCTTTCGGGACATATGGATAGTA
Found at i:57371 original size:30 final size:30
Alignment explanation
Indices: 57337--57393 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
57327 GGACAGTTGC
57337 CCGAGGATCTTTATGACCTCTGGATAGTTA
1 CCGAGGATCTTTATGACCTCTGGATAGTTA
57367 CCGAGGATCTTTATGACCTCTGGATAG
1 CCGAGGATCTTTATGACCTCTGGATAG
57394 GTCCTTTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
CCGAGGATCTTTATGACCTCTGGATAGTTA
Found at i:59613 original size:24 final size:24
Alignment explanation
Indices: 59586--59640 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
59576 ATATATTTTC
59586 TTTAAAAAATTTAAATTCATAAAA
1 TTTAAAAAATTTAAATTCATAAAA
* * *** *
59610 TTTATATAATTTTTTTTTATAAAA
1 TTTAAAAAATTTAAATTCATAAAA
59634 TTTAAAA
1 TTTAAAA
59641 TATAAAAAGG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAAAAAATTTAAATTCATAAAA
Found at i:59634 original size:39 final size:36
Alignment explanation
Indices: 59572--59647 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 36
59562 GTTGGAAAAT
*
59572 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTTAAAAT-ATAAA
* *
59609 ATTTATATAATTTTTTTTTATAAAATTTAAAATATAAA
1 ATTTATAT-A-TTTTCTTTAAAAAATTTAAAATATAAA
59647 A
1 A
59648 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 8 0.24
38 7 0.21
39 19 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTTAAAATATAAA
Found at i:61117 original size:17 final size:18
Alignment explanation
Indices: 61083--61117 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61073 AGTCGATATC
*
61083 GAGAAAAATATTATTTTA
1 GAGAAAAATATTAATTTA
61101 GAGAAAAAT-TTAATTTA
1 GAGAAAAATATTAATTTA
61118 TTGAGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (18 bp):
GAGAAAAATATTAATTTA
Found at i:61382 original size:17 final size:17
Alignment explanation
Indices: 61360--61394 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61350 TCTGATTTAC
61360 TTTTTAGATACATATTT
1 TTTTTAGATACATATTT
* *
61377 TTTTTATATATATATTT
1 TTTTTAGATACATATTT
61394 T
1 T
61395 GGTAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTAGATACATATTT
Done.