Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008034.1 Hibiscus syriacus cultivar Beakdansim tig00110519_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: 88732
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2511 original size:22 final size:21
Alignment explanation
Indices: 2485--2526 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2475 GGCTGCGGAA
2485 ATGATGGTCTTGATGGATGAAG
1 ATGATGGTCTTGAT-GATGAAG
* *
2507 ATGATGTTGTTGATGATGAA
1 ATGATGGTCTTGATGATGAA
2527 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (21 bp):
ATGATGGTCTTGATGATGAAG
Found at i:6565 original size:21 final size:21
Alignment explanation
Indices: 6526--6565 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6516 AAGGAAGATT
*
6526 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
6547 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
6566 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:25675 original size:11 final size:11
Alignment explanation
Indices: 25659--25720 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
25649 TGCAAAGAAA
25659 AAAAAGAAAAG
1 AAAAAGAAAAG
25670 AAAAAGACAAA-
1 AAAAAGA-AAAG
*
25681 AAGAAGAAAA-
1 AAAAAGAAAAG
*
25691 AAATCAGGAAAAG
1 AAA--AAGAAAAG
25704 -AAAAGAAAAG
1 AAAAAGAAAAG
25714 AAAAAGA
1 AAAAAGA
25721 GAAGTTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 12 0.29
11 19 0.45
12 11 0.26
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:25739 original size:6 final size:5
Alignment explanation
Indices: 25652--25717 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
25642 ATTGGCGTGC
25652 AAAGA AAA-A AAAGA AAAGAA AAAGA CAAA-A AGAAGA AAA-A AATCAGGA
1 AAAGA AAAGA AAAGA AAAG-A AAAGA -AAAGA A-AAGA AAAGA AA--A-GA
25700 AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAA
25718 AGAGAAGTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
4 8 0.15
5 29 0.56
6 12 0.23
8 3 0.06
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:25924 original size:41 final size:41
Alignment explanation
Indices: 25873--25966 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
25863 ACCTCTTTCT
*
25873 TTTTTATACCTTCATTGTCCTTGTCTTCAACCATTTCTATC
1 TTTTAATACCTTCATTGTCCTTGTCTTCAACCATTTCTATC
25914 TTTTAATACCTTCATTGTCCTTGTCTTCAACCATTTCTATC
1 TTTTAATACCTTCATTGTCCTTGTCTTCAACCATTTCTATC
25955 TTTTAATACCTT
1 TTTTAATACCTT
25967 TAAATCATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.19, C:0.26, G:0.04, T:0.51
Consensus pattern (41 bp):
TTTTAATACCTTCATTGTCCTTGTCTTCAACCATTTCTATC
Found at i:30630 original size:8 final size:8
Alignment explanation
Indices: 30617--30643 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
30607 TGAACCACAT
30617 ATTTATAC
1 ATTTATAC
30625 ATTTATAC
1 ATTTATAC
30633 ATTTATAC
1 ATTTATAC
30641 ATT
1 ATT
30644 ATATTACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTATAC
Found at i:31210 original size:12 final size:12
Alignment explanation
Indices: 31193--31221 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31183 CACCAAGAAG
31193 AAGCCACACCAT
1 AAGCCACACCAT
31205 AAGCCACACCAT
1 AAGCCACACCAT
31217 AAGCC
1 AAGCC
31222 CCTATGCCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.41, G:0.10, T:0.07
Consensus pattern (12 bp):
AAGCCACACCAT
Found at i:32837 original size:13 final size:11
Alignment explanation
Indices: 32796--32880 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
32786 ACAATCTGTC
32796 CATCACCATTAT
1 CATCACCA-TAT
*
32808 CA-CGCCTATAT
1 CATCACC-ATAT
32819 CATCACCATAGT
1 CATCACCATA-T
32831 CCATCACCATTAT
1 -CATCACCA-TAT
*
32844 CA-CGCCTATAT
1 CATCACC-ATAT
32855 CATCACCATATT
1 CATCACCATA-T
32867 CCATCACCATAT
1 -CATCACCATAT
32879 CA
1 CA
32881 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:32840 original size:36 final size:36
Alignment explanation
Indices: 32793--32897 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
32783 GATACAATCT
32793 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
32829 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
32865 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
32898 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:33540 original size:16 final size:15
Alignment explanation
Indices: 33507--33558 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
33497 TTAAGTTATC
33507 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
33522 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
33538 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
33553 TTCATT
1 TTCATT
33559 ACCATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:36702 original size:13 final size:11
Alignment explanation
Indices: 36661--36745 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
36651 AGAATCTGTC
36661 CATCACCATTAT
1 CATCACCA-TAT
*
36673 CA-CGCCTATAT
1 CATCACC-ATAT
36684 CATCACCATAGT
1 CATCACCATA-T
36696 CCATCACCATTAT
1 -CATCACCA-TAT
*
36709 CA-CGCCTATAT
1 CATCACC-ATAT
36720 CATCACCATATT
1 CATCACCATA-T
36732 CCATCACCATAT
1 -CATCACCATAT
36744 CA
1 CA
36746 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:36705 original size:36 final size:36
Alignment explanation
Indices: 36658--36762 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
36648 GATAGAATCT
36658 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
36694 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
36730 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
36763 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:37654 original size:35 final size:36
Alignment explanation
Indices: 37595--37662 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
37585 ATACAATCTG
* *
37595 TCCATCGCCATTATCACGCTTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
37631 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
37663 ACTTCTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 20 0.69
36 9 0.31
ACGTcount: A:0.29, C:0.35, G:0.04, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:42863 original size:36 final size:36
Alignment explanation
Indices: 42790--42894 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
42780 ATTTATAAGT
* * *
42790 TGGTGATAATATAGGCGTGAT-ATGATGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
42825 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
42861 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
42895 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:43279 original size:19 final size:20
Alignment explanation
Indices: 43232--43282 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
43222 GAAACCCCTT
**
43232 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
43252 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
43271 TGAAGATACATG
1 TGAAAATACATG
43283 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:45249 original size:35 final size:36
Alignment explanation
Indices: 45193--45260 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
45183 ATACAATCTG
45193 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
45229 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
45261 ACTTCTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:49933 original size:19 final size:18
Alignment explanation
Indices: 49911--49957 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
49901 AGTGAATAAT
49911 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
49930 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
49949 AATA-AAGAA
1 AATATAAGAA
49958 AGGGATAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:55206 original size:13 final size:12
Alignment explanation
Indices: 55182--55240 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
55172 CTTTTTGAAT
55182 TTTTC-TTTTTC
1 TTTTCTTTTTTC
55193 TTTTCTTTTATTC
1 TTTTCTTTT-TTC
55206 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
*
55220 TCTTT-TTTTCTC
1 T-TTTCTTTTTTC
55232 TTTTTCTTT
1 -TTTTCTTT
55241 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
11 5 0.12
12 11 0.28
13 13 0.32
14 5 0.12
15 6 0.15
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:55207 original size:33 final size:32
Alignment explanation
Indices: 55169--55240 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
55159 CTTGGCTTGC
*
55169 TTTCTTTT-TGAATTTTTCTTTTTCTTTTCT-TT
1 TTTCTTTTCTG-ATTTTTCTCTTT-TTTTCTCTT
55201 TATTCTTTTCTGATTTTTCTCTTTTTTTCTCTT
1 T-TTCTTTTCTGATTTTTCTCTTTTTTTCTCTT
55234 TTTCTTT
1 TTTCTTT
55241 CTTTTTGCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
32 13 0.36
33 21 0.58
34 2 0.06
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (32 bp):
TTTCTTTTCTGATTTTTCTCTTTTTTTCTCTT
Found at i:55229 original size:10 final size:10
Alignment explanation
Indices: 55214--55246 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
55204 TCTTTTCTGA
55214 TTTTTCTCTT
1 TTTTTCTCTT
55224 TTTTTCTCTT
1 TTTTTCTCTT
55234 TTTCTT-TCTT
1 TTT-TTCTCTT
55244 TTT
1 TTT
55247 GCACTCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 20 0.91
11 2 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:55530 original size:19 final size:18
Alignment explanation
Indices: 55508--55554 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
55498 AGTGAATAAT
55508 AATATAAGTAATGAAACGA
1 AATATAAG-AATGAAACGA
*
55527 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAACGA
55546 AATA-AAGAA
1 AATATAAGAA
55555 AGGGATAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAACGA
Found at i:62625 original size:15 final size:15
Alignment explanation
Indices: 62589--62618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62579 GTGCTTCAAC
62589 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
62603 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
62618 T
1 T
62619 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:76661 original size:15 final size:15
Alignment explanation
Indices: 76641--76676 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
76631 ATTATTAGCT
*
76641 TTATAATATATGTTA
1 TTATAATATATATTA
76656 TTATAATATATATTA
1 TTATAATATATATTA
*
76671 TGATAA
1 TTATAA
76677 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:80931 original size:15 final size:15
Alignment explanation
Indices: 80911--80946 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
80901 ATTATTAGCT
*
80911 TTATAATATATGTTA
1 TTATAATATATATTA
80926 TTATAATATATATTA
1 TTATAATATATATTA
*
80941 TGATAA
1 TTATAA
80947 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Done.