Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006370.1 Hibiscus syriacus cultivar Beakdansim tig00015319_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: 56442
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2350 original size:36 final size:36
Alignment explanation
Indices: 2303--2382 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
2293 AATGTACATC
*
2303 TGTAATCTTAATAATTAAGATTATAATTGAATGACT
1 TGTAATCTTAATAATTAAGATCATAATTGAATGACT
*
2339 TGTAATCTTAATATTTAAGATCATAATTGAATGACT
1 TGTAATCTTAATAATTAAGATCATAATTGAATGACT
2375 TGTAATCT
1 TGTAATCT
2383 CACTATAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.42
Consensus pattern (36 bp):
TGTAATCTTAATAATTAAGATCATAATTGAATGACT
Found at i:3267 original size:13 final size:13
Alignment explanation
Indices: 3249--3275 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3239 CAGGCGACAT
3249 GGGTGACATACGA
1 GGGTGACATACGA
3262 GGGTGACATACGA
1 GGGTGACATACGA
3275 G
1 G
3276 CCATATACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.41, T:0.15
Consensus pattern (13 bp):
GGGTGACATACGA
Found at i:3285 original size:11 final size:11
Alignment explanation
Indices: 3269--3333 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
3259 CGAGGGTGAC
3269 ATACGAGCCAT
1 ATACGAGCCAT
3280 ATACGAGCC--
1 ATACGAGCCAT
3289 ATACGAGCCA-
1 ATACGAGCCAT
*
3299 ATAGGGAG-CAT
1 ATA-CGAGCCAT
3310 GCA-ACGAGCCAT
1 --ATACGAGCCAT
3322 ATACGAGCCAT
1 ATACGAGCCAT
3333 A
1 A
3334 CGAGCCAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 9 0.20
10 6 0.13
11 25 0.56
12 4 0.09
13 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.14
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:3330 original size:42 final size:42
Alignment explanation
Indices: 3271--3354 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
3261 AGGGTGACAT
3271 ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
1 ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
*
3313 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
1 ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
3355 GGAATAGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.26, G:0.27, T:0.12
Consensus pattern (42 bp):
ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
Found at i:3375 original size:28 final size:28
Alignment explanation
Indices: 3335--3393 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
3325 CGAGCCATAC
3335 GAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAGGAATAGA
3363 GAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAGGAATAGA
3391 GAG
1 GAG
3394 GTCGCCATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.41, T:0.10
Consensus pattern (28 bp):
GAGCCAATGGGGAGCATGCAGGAATAGA
Found at i:3442 original size:29 final size:29
Alignment explanation
Indices: 3392--3467 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
3382 AGGAATAGAG
* *
3392 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
3421 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
3450 AGGTTGCCATGTAGTCCC
1 AGGTCGCCATGTAGTCCC
3468 AGCGCCATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 41 0.95
30 2 0.05
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:3578 original size:27 final size:27
Alignment explanation
Indices: 3546--3598 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3536 CCTACAGCTC
3546 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
3573 CCAATGCATGCATGTGAACCATTTGA
1 CCAATGCATGCATGTGAACCATTTGA
3599 TATTGGTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:3763 original size:25 final size:24
Alignment explanation
Indices: 3709--3755 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
3699 AAAAGAAAGA
3709 AAGAAAGGAGAGAAGAGATTGCAG
1 AAGAAAGGAGAGAAGAGATTGCAG
3733 AAGAAAGG-GAGAAGAGATTGCAG
1 AAGAAAGGAGAGAAGAGATTGCAG
3756 CAGAGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.38, T:0.09
Consensus pattern (24 bp):
AAGAAAGGAGAGAAGAGATTGCAG
Found at i:3809 original size:20 final size:19
Alignment explanation
Indices: 3771--3811 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
3761 AAATGGTTGG
3771 AGGGAGAAAGAAAGAAAGA
1 AGGGAGAAAGAAAGAAAGA
*
3790 AGGGAGAAAGGAAAGTAAGA
1 AGGGAGAAA-GAAAGAAAGA
3810 AG
1 AG
3812 AAGAAAGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (19 bp):
AGGGAGAAAGAAAGAAAGA
Found at i:3816 original size:19 final size:20
Alignment explanation
Indices: 3775--3819 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3765 GGTTGGAGGG
*
3775 AGAAA-GAAAGAAAGAAGGG
1 AGAAAGGAAAGAAAGAAGGA
*
3794 AGAAAGGAAAGTAAGAA-GA
1 AGAAAGGAAAGAAAGAAGGA
3813 AGAAAGG
1 AGAAAGG
3820 GAGATAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (20 bp):
AGAAAGGAAAGAAAGAAGGA
Found at i:3989 original size:41 final size:41
Alignment explanation
Indices: 3944--4032 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
3934 TATATGATTG
* *
3944 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
3985 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
4026 TTAGTTT
1 TTAGTTT
4033 GTTTTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:4075 original size:45 final size:45
Alignment explanation
Indices: 3972--4103 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
3962 TACATAAATT
*
3972 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
4014 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
4058 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
4104 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:4177 original size:32 final size:33
Alignment explanation
Indices: 4141--4217 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
4131 TTAGTTAGTA
4141 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
4173 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
4207 ATTTTATTAGT
1 AGTTTATTAGT
4218 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:4294 original size:16 final size:16
Alignment explanation
Indices: 4262--4308 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
4252 TTTAAAAAGT
*
4262 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
4278 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
4294 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
4309 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:4303 original size:15 final size:14
Alignment explanation
Indices: 4283--4313 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4273 GTTTATTAGT
4283 TTATTATATTATAAG
1 TTATTATATTA-AAG
4298 TTATTATATTAAAG
1 TTATTATATTAAAG
4312 TT
1 TT
4314 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:8256 original size:26 final size:24
Alignment explanation
Indices: 8198--8256 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
8188 CTAATAAACC
*
8198 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
8222 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
8250 TAATAAT
1 TAATAAT
8257 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:8563 original size:15 final size:15
Alignment explanation
Indices: 8517--8567 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
8507 ACAATGTAAA
*
8517 TTAAACAAAATATTT
1 TTAAACACAATATTT
8532 TTAAAACAACACTATATTT
1 TT-AAAC-ACA--ATATTT
8551 TTAAACACAATATTT
1 TTAAACACAATATTT
8566 TT
1 TT
8568 TAAAACGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 10 0.32
16 4 0.13
17 5 0.16
18 4 0.13
19 8 0.26
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAACACAATATTT
Found at i:8573 original size:17 final size:17
Alignment explanation
Indices: 8519--8573 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
8509 AATGTAAATT
*
8519 AAACAAAATA-TTTTTA
1 AAACACAATATTTTTTA
*
8535 AAACAACACTATATTTTT-
1 AAAC-ACAATAT-TTTTTA
8553 AAACACAATATTTTTTA
1 AAACACAATATTTTTTA
8570 AAAC
1 AAAC
8574 GGAAATTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 9 0.28
17 14 0.44
18 4 0.12
19 5 0.16
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (17 bp):
AAACACAATATTTTTTA
Found at i:9762 original size:29 final size:29
Alignment explanation
Indices: 9719--9794 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
9709 ACACACAGGA
***
9719 CGCCCGGA-TGCCATGGCGACCTTGGAGGT
1 CGCCCGGATTG-CATGGCGACCTCCAAGGT
9748 CGCCCGGATTGCATGGCGACCTCCAAGGT
1 CGCCCGGATTGCATGGCGACCTCCAAGGT
*
9777 CGCCTGGATTGCATGGCG
1 CGCCCGGATTGCATGGCG
9795 TCCTATGACG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 40 0.95
30 2 0.05
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (29 bp):
CGCCCGGATTGCATGGCGACCTCCAAGGT
Found at i:27167 original size:27 final size:27
Alignment explanation
Indices: 27123--27176 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
27113 TTTTAAGAAG
* *
27123 TTATATTATAAATTTAAAA-ATATAAAA
1 TTATATCATAAATATAAAAGAT-TAAAA
*
27150 TTATATCATTAATATAAAAGATTAAAA
1 TTATATCATAAATATAAAAGATTAAAA
27177 AACTCTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TTATATCATAAATATAAAAGATTAAAA
Found at i:37173 original size:19 final size:19
Alignment explanation
Indices: 37149--37187 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
37139 ATAGAGGGGT
37149 ATTAGTGTAATTATTTCTA
1 ATTAGTGTAATTATTTCTA
37168 ATTAGTGTAATTATTTCTA
1 ATTAGTGTAATTATTTCTA
37187 A
1 A
37188 ATATATAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
ATTAGTGTAATTATTTCTA
Found at i:39781 original size:21 final size:21
Alignment explanation
Indices: 39757--39809 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
39747 GTTTCCAGAT
*
39757 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
39778 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
39799 TCGCAATGCGA
1 TCGCAATGCGA
39810 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:39848 original size:21 final size:21
Alignment explanation
Indices: 39818--39942 Score: 105
Period size: 21 Copynumber: 6.0 Consensus size: 21
39808 GATTTACATA
*
39818 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
39839 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
39860 TTTGCGTTGTGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
39883 TT--CGTTGCGATAGTCTAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
39902 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
39925 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
39943 AATCGCAACG
Statistics
Matches: 83, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
19 15 0.18
21 52 0.63
23 16 0.19
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:39890 original size:42 final size:42
Alignment explanation
Indices: 39843--39939 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
39833 TCCAAGTTCG
* *
39843 CGTTGCGATAGTCGAAGTTTGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
39885 CGTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
39927 CGTTGCGATAGTC
1 CGTTGCGATAGTC
39940 CAAAATCGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Done.