Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002782.1 Hibiscus syriacus cultivar Beakdansim tig00005736_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: 73840
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7047 original size:32 final size:32
Alignment explanation
Indices: 6993--7070 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
6983 TAAAGTGCCC
6993 CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
1 CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
* * *
7025 CTTGAGTAAGCTCTGAGGACCCGATAAACTTT
1 CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
7057 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
7071 CAGGCCCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (32 bp):
CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
Found at i:7343 original size:31 final size:31
Alignment explanation
Indices: 7305--7383 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
7295 TAAGGTGACC
*
7305 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCGAGGCCCCAAGATCTTT
* *
7336 CTTGGGTAGGCCATAC-A-GCCCTAAGATCTTT
1 CTTGGGTAGG-C-TCCGAGGCCCCAAGATCTTT
*
7367 CTTGGGTAGGCCCCGAG
1 CTTGGGTAGGCTCCGAG
7384 TAACCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
29 1 0.03
30 2 0.05
31 32 0.82
32 2 0.05
33 2 0.05
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.25
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGAGGCCCCAAGATCTTT
Found at i:12502 original size:31 final size:31
Alignment explanation
Indices: 12467--12536 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
12457 TTACCCTCGA
*
12467 GTAGGCTCC-ATGGCCCCGAGATCTTTCTTGG
1 GTAGGC-CCTATGGCCCCGAGATCTCTCTTGG
* *
12498 GTAGGCCCTATGGCCCTGAGATCTCTCTTAG
1 GTAGGCCCTATGGCCCCGAGATCTCTCTTGG
*
12529 ATAGGCCC
1 GTAGGCCC
12537 CGTAGCCCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (31 bp):
GTAGGCCCTATGGCCCCGAGATCTCTCTTGG
Found at i:14641 original size:35 final size:35
Alignment explanation
Indices: 14517--14644 Score: 129
Period size: 35 Copynumber: 3.6 Consensus size: 35
14507 GGTCAGTTCT
*
14517 GGTCAAGCTGGTAATTCCTTATATAGGTTCAACACC
1 GGTCAAGCTGGTAATTCCTTATATAGGTTC-AGACC
* * *
14553 GATC-AG-TTGTAATTCCTTAT-TGCAGGTTCAG-CTTT
1 GGTCAAGCTGGTAATTCCTTATAT--AGGTTCAGAC--C
*
14588 GGTCAAACTGGTAATTCCTTATATAGGTTCAGACC
1 GGTCAAGCTGGTAATTCCTTATATAGGTTCAGACC
*
14623 GGTCGAGCTGGTAATTCCTTAT
1 GGTCAAGCTGGTAATTCCTTAT
14645 GGACCTAAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
33 2 0.03
34 14 0.19
35 31 0.42
36 12 0.16
37 14 0.19
38 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (35 bp):
GGTCAAGCTGGTAATTCCTTATATAGGTTCAGACC
Found at i:19157 original size:30 final size:30
Alignment explanation
Indices: 19123--19180 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
19113 ATTTTAATAG
19123 AAGA-TAATACAATGGTATTTGGTAATTTTC
1 AAGATTAAT-CAATGGTATTTGGTAATTTTC
* * *
19153 AAGATTCATTAATGGTATTTTGTAATTT
1 AAGATTAATCAATGGTATTTGGTAATTT
19181 CTCATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (30 bp):
AAGATTAATCAATGGTATTTGGTAATTTTC
Found at i:22562 original size:2 final size:2
Alignment explanation
Indices: 22555--22584 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22545 TTTAAAATTA
*
22555 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22585 TTTTCCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22615 original size:127 final size:123
Alignment explanation
Indices: 22385--22617 Score: 308
Period size: 127 Copynumber: 1.8 Consensus size: 123
22375 TGTATGAATA
22385 GAGCTATCTCAATAGTTAAATTAATAAATTATTTTTAAAATTAATATATATATATATATAACATT
1 GAGCTATCTCAATAGTTAAATTAATAAATTATTTTTAAAATTAATATATATATATATATAACATT
*
22450 TTTCTGTCCCATTAAATTTATCTTTTTAGATTTTAAAATTATCTTATTTAAAATATTTTATT
66 TTTCTGTCCCATTAAATTTAGCTTTTTAG----TAAAATTATCTTATTTAAAATATTTTATT
* * * *
22512 GAGCTATCTTAATAGTTAAATTAATATATTGTTTTTAAAATTAATATATATATATATATATGTAT
1 GAGCTATCTCAATAGTTAAATTAATAAATTATTTTTAAAATTAATATATATATATATATA---AC
*
22577 ATATATATT-TTTCCCATTAAATTTAGCTTTTTAG-AAAATTA
63 AT-T-T-TTCTGTCCCATTAAATTTAGCTTTTTAGTAAAATTA
22618 ATATATTTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
127 64 0.68
130 3 0.03
131 1 0.01
132 24 0.26
133 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (123 bp):
GAGCTATCTCAATAGTTAAATTAATAAATTATTTTTAAAATTAATATATATATATATATAACATT
TTTCTGTCCCATTAAATTTAGCTTTTTAGTAAAATTATCTTATTTAAAATATTTTATT
Found at i:27826 original size:21 final size:22
Alignment explanation
Indices: 27800--27840 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
27790 TCAGGATAGG
27800 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCGGTACTTCCTTTAAT
*
27821 GAGTATTGGTACTTCCTTTA
1 GAGTATCGGTACTTCCTTTA
27841 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (22 bp):
GAGTATCGGTACTTCCTTTAAT
Found at i:37172 original size:3 final size:3
Alignment explanation
Indices: 37156--37228 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
37146 TGTAATATTA
* * * * *
37156 AAT AAT -AT ATAT AAT AAT AAT AAT TAT TAT TAT TAT AAT TAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
37201 AAT AAT AAT TAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
37229 TAAATAACAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:37498 original size:17 final size:17
Alignment explanation
Indices: 37476--37531 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
37466 TTGAATAAGC
37476 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
*
37493 TCTTCTTC-TCCTGATG-AGT
1 TCTTC-TCAT--T-ATGAACT
37512 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
37529 TCT
1 TCT
37532 CTGGAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 4 0.13
19 9 0.29
20 3 0.10
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:37679 original size:113 final size:112
Alignment explanation
Indices: 37459--38321 Score: 1369
Period size: 113 Copynumber: 7.8 Consensus size: 112
37449 TAGAGTCATT
* ** *
37459 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTC-TC--CTGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
* * * *
37521 TATGAACTTC--TCTGGAAAA-ACTGACCCATCAAGTGATGGATTTGAG
66 TATGAAC-TCGAACTGGAAAAGA-TAATCCATCAAGTGATAGATTTGAG
* * * *
37567 CAAAAAGCTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTTAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCA
* *
37632 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
65 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
37680 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
37745 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
65 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
37793 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCA
*
37858 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTTAG
65 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
37906 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCA
*
37971 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATATATTTGAG
65 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
38019 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATACTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCA
38084 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
65 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
38132 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATACTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCA
38197 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
65 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
38245 CAAAAGGTTGAACAAATTCTTCTCATTATGAA---------CTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
38301 TATGAACTCGAACTGGAAAAG
66 TATGAACTCGAACTGGAAAAG
38322 TTGATCCGTC
Statistics
Matches: 722, Mismatches: 24, Indels: 23
0.94 0.03 0.03
Matches are distributed among these distances:
103 45 0.06
108 37 0.05
110 2 0.00
111 2 0.00
112 22 0.03
113 612 0.85
114 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
Found at i:40334 original size:19 final size:17
Alignment explanation
Indices: 40310--40355 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
40300 TTCATAGAAG
*
40310 AATAAATTGAAATTTCGAA
1 AATAAATTGAAATCTC--A
40329 AATAAATTG-AATCTCA
1 AATAAATTGAAATCTCA
40345 AATAAATTGAA
1 AATAAATTGAA
40356 CTTGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 10 0.40
17 1 0.04
18 5 0.20
19 9 0.36
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (17 bp):
AATAAATTGAAATCTCA
Found at i:51321 original size:11 final size:11
Alignment explanation
Indices: 51302--51331 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
51292 ATGAAATATT
51302 AATAATATAAA
1 AATAATATAAA
*
51313 AATACTATAAA
1 AATAATATAAA
51324 AATAATAT
1 AATAATAT
51332 GTATATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAATATAAA
Found at i:53462 original size:3 final size:3
Alignment explanation
Indices: 53444--53522 Score: 72
Period size: 3 Copynumber: 26.7 Consensus size: 3
53434 TGTAATATTA
* * * * * * *
53444 AAT AAT ATAT ATT AAT AAT AAT AAT TAT TAT TAT TAT TAT AAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53490 AAT AAT AAT AAT AAT AAT AAT AAT -AT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53523 CATTAAAATG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 60 0.90
4 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:60874 original size:43 final size:44
Alignment explanation
Indices: 60815--60910 Score: 149
Period size: 43 Copynumber: 2.2 Consensus size: 44
60805 CTATGTGACT
*
60815 ATATGAAATGATATATGAATATGCAATACGTGATACA-TGATATG
1 ATATG-AATGACATATGAATATGCAATACGTGATACAGTGATATG
*
60859 ATATGAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAATGACATATGAATATGCAATACGTGATACA-GTGATATG
60904 ATATGAA
1 ATATGAA
60911 ATACATGGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
43 29 0.60
44 5 0.10
45 14 0.29
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (44 bp):
ATATGAATGACATATGAATATGCAATACGTGATACAGTGATATG
Found at i:61116 original size:17 final size:17
Alignment explanation
Indices: 61094--61158 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
61084 ACAGATTACA
61094 TCCTTCGGGATGACAGG
1 TCCTTCGGGATGACAGG
*
61111 TCCTTCGGGA-CACAGATG
1 TCCTTCGGGATGACAG--G
*
61129 ACATCCTTCGGGATGATAGG
1 ---TCCTTCGGGATGACAGG
61149 TCCTTCGGGA
1 TCCTTCGGGA
61159 CATTTGTACG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.10
17 20 0.51
18 1 0.03
20 1 0.03
21 10 0.26
22 3 0.08
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Found at i:61121 original size:38 final size:38
Alignment explanation
Indices: 61065--61160 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
61055 TATAAGACAT
* *
61065 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
61103 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
61141 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
61161 TTTGTACGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:61137 original size:21 final size:21
Alignment explanation
Indices: 61073--61141 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
61063 ATATGATAGG
* *
61073 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
61094 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
61111 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
61132 TCCTTCGGGA
1 TCCTTCGGGA
61142 TGATAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Done.