Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005416.1 Hibiscus syriacus cultivar Beakdansim tig00012424_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: 61622
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:4403 original size:16 final size:17
Alignment explanation
Indices: 4378--4411 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4368 CCGAGATGTC
4378 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
4394 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
4411 A
1 A
4412 GAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:5136 original size:21 final size:20
Alignment explanation
Indices: 5112--5181 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
5102 GCACATAGAA
*
5112 ATGTCTCGAAAGACCATATAT
1 ATGTCCCGAAA-ACCATATAT
*
5133 ATGTCCCGAAAAACCAAACATAT
1 ATGTCCCG-AAAACC--ATATAT
* *
5156 ATGCCCCGATAAACCATATAG
1 ATGTCCCGA-AAACCATATAT
5177 ATGTC
1 ATGTC
5182 TCGATGGACC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 18 0.46
22 4 0.10
23 17 0.44
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (20 bp):
ATGTCCCGAAAACCATATAT
Found at i:5259 original size:22 final size:23
Alignment explanation
Indices: 5227--5275 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5217 AAAGGACTAA
* *
5227 ATATGTTTCCC-AAGAACCGTAT
1 ATATGTATCCCGAAGAACCGCAT
5249 ATATGTATCCCGAAGAACCGCAT
1 ATATGTATCCCGAAGAACCGCAT
5272 ATAT
1 ATAT
5276 ATTCCAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (23 bp):
ATATGTATCCCGAAGAACCGCAT
Found at i:6201 original size:21 final size:21
Alignment explanation
Indices: 6175--6228 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
6165 ACTAGACACT
6175 TAGTATCGATACC-C-CTTTAAA
1 TAGTATCGATACCACTCTTT--A
*
6196 TAGTATCGAAACCACTCTTTA
1 TAGTATCGATACCACTCTTTA
6217 T-GTATCGATACC
1 TAGTATCGATACC
6229 TCTTAAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 14 0.48
22 1 0.03
23 4 0.14
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.33
Consensus pattern (21 bp):
TAGTATCGATACCACTCTTTA
Found at i:9519 original size:21 final size:21
Alignment explanation
Indices: 9493--9548 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
9483 CATACATATG
9493 TCCCGAAGGACCACATAAATT
1 TCCCGAAGGACCACATAAATT
*** *
9514 TCCCGAAGGACTGTATAGATT
1 TCCCGAAGGACCACATAAATT
*
9535 CCCCGAAGGACCAC
1 TCCCGAAGGACCAC
9549 TCCTTAATGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (21 bp):
TCCCGAAGGACCACATAAATT
Found at i:9621 original size:42 final size:42
Alignment explanation
Indices: 9565--9644 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
9555 ATGATCACAA
* *
9565 ATATATTCCAAAGGACCAAATATGTGTCCCGAAGAACCGTAT
1 ATATATTCCAAAGGACCAAATATATATCCCGAAGAACCGTAT
* ** *
9607 ATATGTTCCAAAGGATTACATATATATCCCGAAGAACC
1 ATATATTCCAAAGGACCAAATATATATCCCGAAGAACC
9645 ACATAGAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (42 bp):
ATATATTCCAAAGGACCAAATATATATCCCGAAGAACCGTAT
Found at i:16111 original size:23 final size:21
Alignment explanation
Indices: 16056--16117 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
16046 TTTTGGTGCA
16056 GAGGGAACCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
* **
16076 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
16097 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
16118 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:19967 original size:19 final size:20
Alignment explanation
Indices: 19943--19982 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19933 AATTTAATCG
*
19943 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
19962 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
19982 A
1 A
19983 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:23019 original size:20 final size:20
Alignment explanation
Indices: 22994--23051 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
22984 GACCGTTACA
*
22994 TAGGGGGAATTGGTACCCCC
1 TAGGGGGAATCGGTACCCCC
23014 TAGGGGGAATCGGTACCCCC
1 TAGGGGGAATCGGTACCCCC
* *
23034 TGGGGGGAATCGATACCC
1 TAGGGGGAATCGGTACCC
23052 TCTGGACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.26, G:0.36, T:0.17
Consensus pattern (20 bp):
TAGGGGGAATCGGTACCCCC
Found at i:23108 original size:20 final size:20
Alignment explanation
Indices: 23083--23150 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
23073 GAGCCAAAAA
*
23083 CCTGGGGGGAATCGGTACCC
1 CCTGGGGGGAATCAGTACCC
* *
23103 CCTGGGGGGAATCTGT--TC
1 CCTGGGGGGAATCAGTACCC
23121 CC---GGGGAATCAGTACCC
1 CCTGGGGGGAATCAGTACCC
23138 CCTGGGGGGAATC
1 CCTGGGGGGAATC
23151 TGTTCCCTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
15 10 0.26
17 3 0.08
18 3 0.08
20 23 0.59
ACGTcount: A:0.16, C:0.28, G:0.38, T:0.18
Consensus pattern (20 bp):
CCTGGGGGGAATCAGTACCC
Found at i:23136 original size:35 final size:35
Alignment explanation
Indices: 23088--23157 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
23078 AAAAACCTGG
*
23088 GGGGAATCGGTACCCCCTGGGGGGAATCTGTTCCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
23123 GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
23158 TCTTGGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.20
Consensus pattern (35 bp):
GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
Found at i:23374 original size:19 final size:20
Alignment explanation
Indices: 23347--23391 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
23337 CGAATAATTT
* *
23347 AATTGAATATATAAT-TTAA
1 AATTCAATATAAAATCTTAA
23366 AATTCAATATAAAATCTTAA
1 AATTCAATATAAAATCTTAA
23386 AATTCA
1 AATTCA
23392 TTAACACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTCAATATAAAATCTTAA
Found at i:24642 original size:18 final size:18
Alignment explanation
Indices: 24605--24643 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
24595 TCATTTTGAT
* *
24605 TTTCAAAATCAACTTTTC
1 TTTCAAAATCAAATTATC
24623 TTTCAAAATCAAATTATC
1 TTTCAAAATCAAATTATC
24641 TTT
1 TTT
24644 AATTTTGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTCAAAATCAAATTATC
Found at i:26546 original size:20 final size:21
Alignment explanation
Indices: 26521--26562 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26511 CCGTTACACA
26521 GGGGG-AATCGATACCCCCTG
1 GGGGGAAATCGATACCCCCTG
* *
26541 GGGGGAAATCGGTACCCTCTG
1 GGGGGAAATCGATACCCCCTG
26562 G
1 G
26563 ACATTCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.19, C:0.26, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGGAAATCGATACCCCCTG
Found at i:27961 original size:21 final size:22
Alignment explanation
Indices: 27932--27975 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27922 AGCTTAACTC
*
27932 CTAACTCA-TAATTTTATTTTT
1 CTAAATCATTAATTTTATTTTT
*
27953 CTAAATCATTTATTTTTATTTTT
1 CTAAATCA-TTAATTTTATTTTT
27976 GAAAGCTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (22 bp):
CTAAATCATTAATTTTATTTTT
Found at i:29950 original size:20 final size:20
Alignment explanation
Indices: 29925--29966 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
29915 CCATTACATA
29925 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
*
29945 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCCCT
29965 GG
1 GG
29967 ACATTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.43, T:0.17
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:30252 original size:19 final size:20
Alignment explanation
Indices: 30228--30267 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30218 AATTTAATCG
*
30228 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
30247 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
30267 A
1 A
30268 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:33696 original size:19 final size:20
Alignment explanation
Indices: 33672--33711 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
33662 AATTTAATCG
*
33672 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
33691 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
33711 A
1 A
33712 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:37160 original size:19 final size:20
Alignment explanation
Indices: 37133--37175 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
37123 CGAATAATTT
* *
37133 AATTGAATATATAAT-TTAA
1 AATTCAATATAAAATCTTAA
37152 AATTCAATATAAAATCTTAA
1 AATTCAATATAAAATCTTAA
37172 AATT
1 AATT
37176 TATTAACACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
AATTCAATATAAAATCTTAA
Found at i:39366 original size:24 final size:23
Alignment explanation
Indices: 39339--39386 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
39329 ATCTTTTAAA
*
39339 TTTTATAAAAAATTATATATAATT
1 TTTTATAAAAAAGTATATA-AATT
*
39363 TTTTATTAAAAAGTATATAAATT
1 TTTTATAAAAAAGTATATAAATT
39386 T
1 T
39387 AAAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTATAAAAAAGTATATAAATT
Found at i:42672 original size:16 final size:16
Alignment explanation
Indices: 42653--42686 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42643 CAATATACGA
42653 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
42669 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
42685 AT
1 AT
42687 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:42758 original size:16 final size:18
Alignment explanation
Indices: 42726--42759 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
42716 TATTAATGTA
42726 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
42744 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
42760 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:43430 original size:129 final size:130
Alignment explanation
Indices: 43227--43473 Score: 406
Period size: 129 Copynumber: 1.9 Consensus size: 130
43217 AATTTTCTTC
* *
43227 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
43292 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
43357 TAATTAGGTGGT-ACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
43421 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGGCCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
43474 TATATAAATA
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
129 96 0.89
130 12 0.11
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:43919 original size:35 final size:35
Alignment explanation
Indices: 43869--43944 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
43859 AATTGAATTT
* *
43869 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
43904 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
43939 AATTGA
1 AATTGA
43945 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:54548 original size:24 final size:26
Alignment explanation
Indices: 54521--54569 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
54511 AGATATAATT
*
54521 TTAAAAT-AAATGAAAGTT-TAGTTG
1 TTAAAATGAAATAAAAGTTATAGTTG
*
54545 TTAAAATGGAATAAAAGTTATAGTT
1 TTAAAATGAAATAAAAGTTATAGTT
54570 TAGGTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (26 bp):
TTAAAATGAAATAAAAGTTATAGTTG
Found at i:58004 original size:21 final size:22
Alignment explanation
Indices: 57987--58035 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
57977 ACCGAAGTGT
57987 CACATA-TTTGTCCTGAAGGAC
1 CACATATTTTGTCCTGAAGGAC
* *
58008 CACATATTTTGTCCCGAAAGAC
1 CACATATTTTGTCCTGAAGGAC
58030 CACATA
1 CACATA
58036 GAACCCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (22 bp):
CACATATTTTGTCCTGAAGGAC
Found at i:61391 original size:14 final size:14
Alignment explanation
Indices: 61372--61402 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
61362 CAACGATCAC
*
61372 GGTCAAAGTCAATG
1 GGTCAAAGTCAACG
61386 GGTCAAAGTCAACG
1 GGTCAAAGTCAACG
61400 GGT
1 GGT
61403 TGACTCGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19
Consensus pattern (14 bp):
GGTCAAAGTCAACG
Found at i:61418 original size:14 final size:14
Alignment explanation
Indices: 61401--61438 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
61391 AAGTCAACGG
*
61401 GTTGACTCGGACGA
1 GTTGACTCAGACGA
61415 GTTGACTCAGACGA
1 GTTGACTCAGACGA
*
61429 GTTAACTCAG
1 GTTGACTCAG
61439 TCAGGTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGACGA
Done.