Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003833.1 Hibiscus syriacus cultivar Beakdansim tig00008219_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: 72426
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:4696 original size:18 final size:18
Alignment explanation
Indices: 4669--4703 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4659 TAATTTAAAA
4669 TTTTAATAATAAAAATAT
1 TTTTAATAATAAAAATAT
* *
4687 TTTTATTAATCAAAATA
1 TTTTAATAATAAAAATA
4704 AAATATAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAATAATAAAAATAT
Found at i:5661 original size:28 final size:28
Alignment explanation
Indices: 5609--5663 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5599 GTTAACCAAA
* *
5609 TATCAATAAGACAGTATAACCGACCATT
1 TATCAATAAGACAGCAGAACCGACCATT
* *
5637 TATCAATTAGACAGCAGAACTGACCAT
1 TATCAATAAGACAGCAGAACCGACCAT
5664 ATAATAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.24
Consensus pattern (28 bp):
TATCAATAAGACAGCAGAACCGACCATT
Found at i:6124 original size:2 final size:2
Alignment explanation
Indices: 6117--6178 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
6107 CATGCTTGTC
6117 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6158 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
6179 GTTTGTATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6432 original size:2 final size:2
Alignment explanation
Indices: 6290--6412 Score: 181
Period size: 2 Copynumber: 65.5 Consensus size: 2
6280 CGGTGTATCC
6290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6373 AT AT -T AT AT AT AT -T AT -T A- AT -T AT -T AT -T AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6408 AT AT A
1 AT AT A
6413 AGTGGTTATA
Statistics
Matches: 111, Mismatches: 2, Indels: 16
0.86 0.02 0.12
Matches are distributed among these distances:
1 8 0.07
2 103 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7416 original size:2 final size:2
Alignment explanation
Indices: 7409--7445 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
7399 ATGCTAAACT
7409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7446 GTCAAAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12420 original size:3 final size:3
Alignment explanation
Indices: 12412--12487 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
12402 CTGCATTAAA
* * *
12412 AAT AAT AAT ATT AAT AAT ATT AAT AAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12460 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12488 GCAGGACGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:14146 original size:32 final size:26
Alignment explanation
Indices: 14062--14126 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
14052 ATTATTTTTA
14062 ATGTATTTTTATTAAATATTATAAAT
1 ATGTATTTTTATTAAATATTATAAAT
14088 ATGTATTTTTATTAAATATTATAAAT
1 ATGTATTTTTATTAAATATTATAAAT
14114 ATGTATTTTTATT
1 ATGTATTTTTATT
14127 TAGTTAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (26 bp):
ATGTATTTTTATTAAATATTATAAAT
Found at i:19637 original size:17 final size:17
Alignment explanation
Indices: 19615--19649 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19605 TAGTAACCCG
19615 TTTATTA-ATATTATATT
1 TTTATTATA-ATTATATT
19632 TTTATTATAATTATATT
1 TTTATTATAATTATATT
19649 T
1 T
19650 GAAGTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTATAATTATATT
Found at i:19827 original size:19 final size:19
Alignment explanation
Indices: 19805--19867 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
19795 CTTATTTCCA
19805 TTTGAAAGTTCAATTTTCT
1 TTTGAAAGTTCAATTTTCT
* * * *
19824 TTTGACA-TCTCTTATTTCCA
1 TTTGAAAGT-TC-AATTTTCT
19844 TTTGAAAGTTCAATTTTCT
1 TTTGAAAGTTCAATTTTCT
19863 TTTGA
1 TTTGA
19868 CCAGATGGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 18 0.55
20 13 0.39
21 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (19 bp):
TTTGAAAGTTCAATTTTCT
Found at i:19861 original size:20 final size:20
Alignment explanation
Indices: 19799--19861 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
19789 TTTTTCCTTA
19799 TTTCCATTTGAAAGTTCAAT
1 TTTCCATTTGAAAGTTCAAT
* * *
19819 TTT-CTTTTGACA-TCTC-TT
1 TTTCCATTTGAAAGT-TCAAT
19837 ATTTCCATTTGAAAGTTCAAT
1 -TTTCCATTTGAAAGTTCAAT
19858 TTTC
1 TTTC
19862 TTTTGACCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
18 2 0.06
19 12 0.38
20 16 0.50
21 2 0.06
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTCCATTTGAAAGTTCAAT
Found at i:22203 original size:26 final size:23
Alignment explanation
Indices: 22157--22207 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
22147 ATTTATTTTA
*
22157 TTATTTATGTCTATTCTAAAATT
1 TTATTTATGTCTATTATAAAATT
22180 TTATTTATGTCTACTCTATAAAAATT
1 TTATTTATGTCTA-T-TAT-AAAATT
22206 TT
1 TT
22208 GTATGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 13 0.54
24 1 0.04
25 2 0.08
26 8 0.33
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (23 bp):
TTATTTATGTCTATTATAAAATT
Found at i:23102 original size:10 final size:10
Alignment explanation
Indices: 23060--23111 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
23050 GTTGGAAACT
23060 GGTTTTGACC
1 GGTTTTGACC
*
23070 GG-TTTAACC
1 GGTTTTGACC
23079 GGTTTTGAACC
1 GGTTTTG-ACC
23090 GGTTTTGACC
1 GGTTTTGACC
23100 GG-TTTGACC
1 GGTTTTGACC
23109 GGT
1 GGT
23112 CACGACCCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 17 0.46
10 10 0.27
11 10 0.27
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (10 bp):
GGTTTTGACC
Found at i:23151 original size:18 final size:18
Alignment explanation
Indices: 23128--23175 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
23118 CCGTTTACCC
23128 GTTTACCCGACCCGACCA
1 GTTTACCCGACCCGACCA
*
23146 GTTTACCCGACCCGACCC
1 GTTTACCCGACCCGACCA
23164 GTTTACCCGACC
1 GTTTACCCGACC
23176 GTTGACCCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.46, G:0.17, T:0.19
Consensus pattern (18 bp):
GTTTACCCGACCCGACCA
Found at i:23171 original size:13 final size:13
Alignment explanation
Indices: 23154--23195 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
23144 CAGTTTACCC
23154 GACCCGACCCGTT
1 GACCCGACCCGTT
*
23167 TACCCGA-CCGTT
1 GACCCGACCCGTT
23179 GACCCGACCCGTT
1 GACCCGACCCGTT
23192 GACC
1 GACC
23196 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:23271 original size:29 final size:29
Alignment explanation
Indices: 23210--23276 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
23200 ACCGTTGACC
* *** *
23210 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGAGAATTAATTCGAAATG
*
23239 GGTGCTATTCTGAGAATTAATTTGAAATG
1 GGTGCTATTCTGAGAATTAATTCGAAATG
23268 GGTGCTATT
1 GGTGCTATT
23277 TTAGTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGAGAATTAATTCGAAATG
Found at i:23334 original size:29 final size:29
Alignment explanation
Indices: 23210--23335 Score: 69
Period size: 29 Copynumber: 4.3 Consensus size: 29
23200 ACCGTTGACC
* * ****
23210 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTTTGGGAATTAATTTGAAAAT
* *
23239 GGTGCTATTCTGAGAATTAATTTG-AAAT
1 GGTGCTATTTTGGGAATTAATTTGAAAAT
* * *
23267 GGGTGCTATTTTAGTAATT--TTTCGAAAAAA
1 -GGTGCTATTTTGGGAATTAATTT-G-AAAAT
** **
23297 AATAATATTTTGGGAATTAATTTGAAAAT
1 GGTGCTATTTTGGGAATTAATTTGAAAAT
23326 GGTGCTATTT
1 GGTGCTATTT
23336 GTGTAAAATG
Statistics
Matches: 70, Mismatches: 21, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
27 3 0.04
28 2 0.03
29 58 0.83
30 4 0.06
31 3 0.04
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTTGAAAAT
Found at i:30455 original size:18 final size:18
Alignment explanation
Indices: 30450--30501 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
30440 CGACCCGTTT
30450 ACCCGTTTACCCGACCCG
1 ACCCGTTTACCCGACCCG
*
30468 ACCAGTTTACCCGACCCG
1 ACCCGTTTACCCGACCCG
30486 ACCCGTTTACCCGACC
1 ACCCGTTTACCCGACC
30502 GTTGACCCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.48, G:0.15, T:0.17
Consensus pattern (18 bp):
ACCCGTTTACCCGACCCG
Found at i:30497 original size:13 final size:13
Alignment explanation
Indices: 30480--30521 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
30470 CAGTTTACCC
30480 GACCCGACCCGTT
1 GACCCGACCCGTT
*
30493 TACCCGA-CCGTT
1 GACCCGACCCGTT
30505 GACCCGACCCGTT
1 GACCCGACCCGTT
30518 GACC
1 GACC
30522 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:30597 original size:29 final size:29
Alignment explanation
Indices: 30536--30602 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
30526 ACCGTTGACC
* *** *
30536 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGAGAATTAATTCGAAATG
30565 GGTGCTATTCTGAGAATTAATTCGAAATG
1 GGTGCTATTCTGAGAATTAATTCGAAATG
30594 GGTGCTATT
1 GGTGCTATT
30603 TTAGTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGAGAATTAATTCGAAATG
Found at i:30611 original size:29 final size:28
Alignment explanation
Indices: 30536--30619 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
30526 ACCGTTGACC
* *** *
30536 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGAGAATT-ATTCGAAATG
30565 GGTGCTATTCTGAGAATTAATTCGAAATG
1 GGTGCTATTCTGAGAATT-ATTCGAAATG
* *
30594 GGTGCTATT-TTAGTAATTTTTCGAAA
1 GGTGCTATTCTGAG-AATTATTCGAAA
30620 AAAATAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
28 10 0.21
29 37 0.79
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.42
Consensus pattern (28 bp):
GGTGCTATTCTGAGAATTATTCGAAATG
Found at i:32005 original size:1 final size:1
Alignment explanation
Indices: 31999--32025 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
31989 ATTGTAAGAT
31999 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
32026 CCTCTGAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32173 original size:24 final size:24
Alignment explanation
Indices: 32141--32186 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
32131 GTGGTCAAAA
*
32141 ATGATTTTTTAATTTTAAATACGT
1 ATGATTTTTTAATTTGAAATACGT
32165 ATGATTTTTTAATTTGAAATAC
1 ATGATTTTTTAATTTGAAATAC
32187 CTATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (24 bp):
ATGATTTTTTAATTTGAAATACGT
Found at i:32708 original size:40 final size:40
Alignment explanation
Indices: 32652--32734 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
32642 ATTGATGTTA
* * * *
32652 TTTTAGATTGCGACATGGAATGTTACTAAACATATAACAT
1 TTTTAGATTGCAACATGAAATGATACCAAACATATAACAT
*
32692 TTTTAGTTTGCAACATGAAATGATACCAAACATATAACAT
1 TTTTAGATTGCAACATGAAATGATACCAAACATATAACAT
32732 TTT
1 TTT
32735 AGGTTGATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (40 bp):
TTTTAGATTGCAACATGAAATGATACCAAACATATAACAT
Found at i:32973 original size:2 final size:2
Alignment explanation
Indices: 32962--33024 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
32952 TCAACCTAAA
32962 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33003 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
33025 TGGTAACATT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:36169 original size:3 final size:3
Alignment explanation
Indices: 36161--36234 Score: 112
Period size: 3 Copynumber: 24.3 Consensus size: 3
36151 CTGCATTAAA
* * *
36161 AAT AAT AAT ATT AAT AAT ATT AAT ACT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
36210 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
36235 GCAGGACGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:37883 original size:30 final size:26
Alignment explanation
Indices: 37803--37866 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
37793 ATTATTTTTA
37803 ATGTA-TTTTATT-AATATTATAAAT
1 ATGTATTTTTATTAAATATTATAAAT
37827 ATGTATTTTTATTAAATATTATAAAT
1 ATGTATTTTTATTAAATATTATAAAT
37853 ATGTATTTTTATTA
1 ATGTATTTTTATTA
37867 GTTAAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 5 0.13
25 7 0.18
26 26 0.68
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (26 bp):
ATGTATTTTTATTAAATATTATAAAT
Found at i:37943 original size:65 final size:65
Alignment explanation
Indices: 37744--37945 Score: 187
Period size: 65 Copynumber: 3.1 Consensus size: 65
37734 TTTAGTTAAA
37744 TATTAAAATAATGTGTATGTGGTCCTAAATTTAATAATTTAAAATATAAATTATTTTTAATGTAT
1 TATTAAAATAATGTGTATGTGGTCCTAAATTTAATAATTT-AAATATAAATTA-TTTTAATGTAT
37809 TT
64 TT
* * *** * * ** * ** * * *
37811 TATTAATATTATAAATATGT-AT-TTTTATTAAAT-ATTATAAATATGTATTTTTATTAGT-TAA
1 TATTAAAATAATGTGTATGTGGTCCTAAATTTAATAATT-TAAATATAAATTATT-TTAATGTAT
**
37872 AA
64 TT
37874 TATTAAAATAATGTGTATGTGGTCCTAAATTTAATAATTTAAATATAAATTATTTTAATGTATTT
1 TATTAAAATAATGTGTATGTGGTCCTAAATTTAATAATTTAAATATAAATTATTTTAATGTATTT
37939 TATTAAA
1 TATTAAA
37946 TTTTAATTAA
Statistics
Matches: 95, Mismatches: 34, Indels: 14
0.66 0.24 0.10
Matches are distributed among these distances:
63 19 0.20
64 21 0.22
65 36 0.38
66 4 0.04
67 15 0.16
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (65 bp):
TATTAAAATAATGTGTATGTGGTCCTAAATTTAATAATTTAAATATAAATTATTTTAATGTATTT
Found at i:43345 original size:17 final size:17
Alignment explanation
Indices: 43323--43357 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
43313 TAGTAACCCG
43323 TTTATTA-ATATTATATT
1 TTTATTATA-ATTATATT
43340 TTTATTATAATTATATT
1 TTTATTATAATTATATT
43357 T
1 T
43358 GAAGTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTATAATTATATT
Found at i:43535 original size:19 final size:19
Alignment explanation
Indices: 43506--43568 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
43496 TTTTTTCCTT
*
43506 ATTTCCATTTGAAAGTTCA
1 ATTTTCATTTGAAAGTTCA
* * *
43525 ATTTTCTTTTGACA-TCTCTT
1 ATTTTCATTTGAAAGT-TC-A
*
43545 ATTTCCATTTGAAAGTTCA
1 ATTTTCATTTGAAAGTTCA
43564 ATTTT
1 ATTTT
43569 TTTGACCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 13 0.41
21 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (19 bp):
ATTTTCATTTGAAAGTTCA
Found at i:45903 original size:26 final size:23
Alignment explanation
Indices: 45857--45907 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
45847 ATTTATTTTA
*
45857 TTATTTATGTCTATTCTAAAATT
1 TTATTTATGTCTATTATAAAATT
45880 TTATTTATGTCTACTCTATAAAAATT
1 TTATTTATGTCTA-T-TAT-AAAATT
45906 TT
1 TT
45908 GTATGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 13 0.54
24 1 0.04
25 2 0.08
26 8 0.33
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (23 bp):
TTATTTATGTCTATTATAAAATT
Found at i:46045 original size:46 final size:46
Alignment explanation
Indices: 45958--46050 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
45948 AATCTGTTAA
45958 TGTTTAAAGCATAAAAATAAGGATGACGTGTTAAACTTTGAAGTGG
1 TGTTTAAAGCATAAAAATAAGGATGACGTGTTAAACTTTGAAGTGG
*
46004 TGTTTAAAGCATAAAAAATACGGATGACGTGTTAAAC-TTGAAGTGG
1 TGTTTAAAGCAT-AAAAATAAGGATGACGTGTTAAACTTTGAAGTGG
46050 T
1 T
46051 CAAAAATGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 22 0.49
47 23 0.51
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.30
Consensus pattern (46 bp):
TGTTTAAAGCATAAAAATAAGGATGACGTGTTAAACTTTGAAGTGG
Found at i:46088 original size:24 final size:24
Alignment explanation
Indices: 46056--46101 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
46046 GTGGTCAAAA
*
46056 ATGATTTTTTAATTTTAAATACGT
1 ATGATTTTTTAATTTGAAATACGT
46080 ATGATTTTTTAATTTGAAATAC
1 ATGATTTTTTAATTTGAAATAC
46102 CTATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (24 bp):
ATGATTTTTTAATTTGAAATACGT
Found at i:46414 original size:16 final size:18
Alignment explanation
Indices: 46382--46415 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
46372 CAATCGGAAA
46382 TTTTATTAAATATAGTAC
1 TTTTATTAAATATAGTAC
46400 TTTT-TTAAA-ATAGTAC
1 TTTTATTAAATATAGTAC
46416 AATCAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTATTAAATATAGTAC
Found at i:46643 original size:40 final size:40
Alignment explanation
Indices: 46587--46669 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
46577 ATTGATGTTA
* * *
46587 TTTTAGATTGCGACATGGAATGTTACTAAACATATAACAT
1 TTTTAGATTGCAACATGAAATGTTACCAAACATATAACAT
*
46627 TTTTAGTTTGCAACATGAAATGTTACCAAACATATAACAT
1 TTTTAGATTGCAACATGAAATGTTACCAAACATATAACAT
46667 TTT
1 TTT
46670 AGGTTGATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (40 bp):
TTTTAGATTGCAACATGAAATGTTACCAAACATATAACAT
Found at i:46903 original size:2 final size:2
Alignment explanation
Indices: 46896--46957 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
46886 TCAACCTAAA
46896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46938 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
46958 GGTAACATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51037 original size:20 final size:21
Alignment explanation
Indices: 50992--51037 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
50982 TAACATAATT
*
50992 TCTTTTATTGGTATTTTTTCA
1 TCTTTTAATGGTATTTTTTCA
51013 T-TTTTAATGGT-TTTTTT-A
1 TCTTTTAATGGTATTTTTTCA
51031 CTCTTTT
1 -TCTTTT
51038 TTATCTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 1 0.05
19 7 0.32
20 13 0.59
21 1 0.05
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.70
Consensus pattern (21 bp):
TCTTTTAATGGTATTTTTTCA
Found at i:56384 original size:54 final size:54
Alignment explanation
Indices: 56319--56423 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
56309 TTACGCCAGG
*
56319 CATGTCGGACTTCTACAACCCAACCTTCCTCCAGGATATTTATGCAATCTTAAT
1 CATGTCAGACTTCTACAACCCAACCTTCCTCCAGGATATTTATGCAATCTTAAT
* * *
56373 CATGTCAGACTTTTACATCCCAACCTTCCTCCAGGATATTTATGCAGTCTT
1 CATGTCAGACTTCTACAACCCAACCTTCCTCCAGGATATTTATGCAATCTT
56424 TAACCAGCTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (54 bp):
CATGTCAGACTTCTACAACCCAACCTTCCTCCAGGATATTTATGCAATCTTAAT
Found at i:63080 original size:12 final size:12
Alignment explanation
Indices: 63063--63087 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63053 GAGCTTAAAT
63063 TTTTTTTATTTA
1 TTTTTTTATTTA
63075 TTTTTTTATTTA
1 TTTTTTTATTTA
63087 T
1 T
63088 ATAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:63193 original size:18 final size:19
Alignment explanation
Indices: 63144--63195 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
63134 TAGTTTGAAG
*
63144 ATTAATAAATTAAAAATAGT
1 ATTAA-AAATTATAAATAGT
* * *
63164 ATTATAATTTATATATA-T
1 ATTAAAAATTATAAATAGT
63182 ATTAAAAATTATAA
1 ATTAAAAATTATAA
63196 TTAATATTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
18 12 0.48
19 9 0.36
20 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAAAATTATAAATAGT
Found at i:63232 original size:15 final size:16
Alignment explanation
Indices: 63212--63244 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
63202 TTATATGCAT
63212 AATAAAAA-AGTATAA
1 AATAAAAATAGTATAA
*
63227 AATAAAAATATTATAA
1 AATAAAAATAGTATAA
63243 AA
1 AA
63245 AAAGTTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AATAAAAATAGTATAA
Found at i:64143 original size:17 final size:17
Alignment explanation
Indices: 64121--64160 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
64111 CCGTGTCCCG
64121 ACCCGGATGTTACGGGT
1 ACCCGGATGTTACGGGT
* *
64138 ACCCGGATTTTGCGGGT
1 ACCCGGATGTTACGGGT
64155 ACCCGG
1 ACCCGG
64161 TAATCGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.23
Consensus pattern (17 bp):
ACCCGGATGTTACGGGT
Done.