Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001957.1 Hibiscus syriacus cultivar Beakdansim tig00003961_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: 105484
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5933 original size:31 final size:31
Alignment explanation
Indices: 5891--5949 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5881 AATTTAAAAG
* *
5891 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
5922 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
5950 CTATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:6000 original size:22 final size:22
Alignment explanation
Indices: 5974--6016 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5964 TAATAAATTA
5974 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
5996 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
6017 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:6025 original size:22 final size:22
Alignment explanation
Indices: 5976--6024 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
5966 ATAAATTATT
**
5976 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
5998 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
6021 TAAA
1 TAAA
6025 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:6028 original size:54 final size:54
Alignment explanation
Indices: 5964--6259 Score: 377
Period size: 54 Copynumber: 5.4 Consensus size: 54
5954 ACAACTACAA
5964 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
6018 TAATAAATTATTTAAAATAAATCAATCCATAAAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * * * *
6078 TAAAATAAATCAATCT-ATACAAATAAAT---TA-TTTAAAATAAATCAGTCTATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
6130 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
6184 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
6238 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
6260 TATTTTAAAA
Statistics
Matches: 207, Mismatches: 21, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
49 3 0.01
50 16 0.08
52 1 0.00
53 2 0.01
54 140 0.68
55 3 0.01
56 1 0.00
57 4 0.02
58 16 0.08
59 1 0.00
60 1 0.00
62 16 0.08
63 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:6034 original size:32 final size:32
Alignment explanation
Indices: 5996--6259 Score: 206
Period size: 32 Copynumber: 9.4 Consensus size: 32
5986 CAATCCATAT
5996 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
6028 TTTAAAATAAATCAATCC--A-T-A-AAACTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
6055 --CAATAATAAATCAATCC--A-T-AT------
1 TTTAA-AATAAATCAATCCATACTAATAAATTA
* *
6076 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
6108 TTTAAAATAAATCAGTCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6140 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6162 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6194 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6216 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6248 TTTAAAATAAAT
1 TTTAAAATAAAT
6260 TATTTTAAAA
Statistics
Matches: 189, Mismatches: 9, Indels: 68
0.71 0.03 0.26
Matches are distributed among these distances:
22 44 0.23
23 6 0.03
24 3 0.02
25 2 0.01
26 24 0.13
27 5 0.03
28 7 0.04
29 1 0.01
30 3 0.02
31 3 0.02
32 91 0.48
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:6115 original size:14 final size:14
Alignment explanation
Indices: 6098--6151 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
6088 CAATCTATAC
6098 AAATAAATTATTTA
1 AAATAAATTATTTA
*
6112 AAATAAATCAGTCTATA
1 AAATAAATTA-T-T-TA
*
6129 CTAATAAATTATTTA
1 -AAATAAATTATTTA
6144 AAATAAAT
1 AAATAAAT
6152 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 16 0.50
15 3 0.09
16 2 0.06
17 3 0.09
18 8 0.25
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:6166 original size:22 final size:22
Alignment explanation
Indices: 6140--6182 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
6130 TAATAAATTA
6140 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
6162 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
6183 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:6191 original size:22 final size:22
Alignment explanation
Indices: 6142--6190 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
6132 ATAAATTATT
**
6142 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
6164 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
6187 TAAA
1 TAAA
6191 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:6220 original size:22 final size:22
Alignment explanation
Indices: 6194--6294 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
6184 TAATAAATTA
6194 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
6216 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
6239 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
6263 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
6285 TTTATAATAA
1 TTTAAAATAA
6295 TTTATTTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:6259 original size:86 final size:81
Alignment explanation
Indices: 5979--6227 Score: 342
Period size: 80 Copynumber: 3.0 Consensus size: 81
5969 AATTATTTAA
5979 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
6044 CCATA--AAACTACAAT
66 CCATATTAAAATA-AAT
* * *
6059 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAGT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
6124 CTATACTAATAAATTATTTAA-
66 CCATA-T--TAAA--A-TAAAT
6145 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
6210 CCATATTTTAAAATAAAT
66 CCATA--TTAAAATAAAT
6228 CAATCCATAC
Statistics
Matches: 147, Mismatches: 12, Indels: 17
0.84 0.07 0.10
Matches are distributed among these distances:
80 66 0.45
82 3 0.02
83 1 0.01
85 7 0.05
86 66 0.45
87 3 0.02
88 1 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (81 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTAAAATAAAT
Found at i:6268 original size:15 final size:15
Alignment explanation
Indices: 6239--6380 Score: 136
Period size: 15 Copynumber: 9.5 Consensus size: 15
6229 AATCCATACT
6239 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
6253 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
6268 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
6290 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
6305 AATAATTTATTTTAA
1 AATAAATTATTTTAA
6320 AAT--A--A--TTAA
1 AATAAATTATTTTAA
*
6329 AATAAATTATTTTAT
1 AATAAATTATTTTAA
6344 AATAAATTATTTTAA
1 AATAAATTATTTTAA
6359 AATAAATTATTTTAA
1 AATAAATTATTTTAA
6374 AATAAAT
1 AATAAAT
6381 AACCTTATTA
Statistics
Matches: 108, Mismatches: 6, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
9 7 0.06
11 2 0.02
13 1 0.01
14 9 0.08
15 72 0.67
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:6329 original size:108 final size:101
Alignment explanation
Indices: 6109--6403 Score: 273
Period size: 108 Copynumber: 2.9 Consensus size: 101
6099 AATAAATTAT
*
6109 TTAAAATAAATCAGTCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
1 TTAAAATAAATCAATCTATACTAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAAAT
* * * *
6174 CAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATT
59 CAATCCATAATAATAAATTATTTAAAATAAATCAATCAAAATA
*
6217 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCCA
1 TTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCCA
* * * * *
6282 TATTTTATAATAATTTATTTTAAAATAATTTATTTTAAAATAA
66 TA----ATAATAAATTA-TTTAAAATAAATCA-ATCAAAAT-A
* *
6325 TTAAAATAAAT-TAT-TTTA-TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT-AA-CC
1 TTAAAATAAATCAATCTATACTAATAAATTA-TTTAAAATAAATTATTTTAAAATAAATCAATCC
*
6385 -T--TATTAAATTATTTAAAAT
65 ATAATAATAAATTATTTAAAAT
6404 TATTTTAATA
Statistics
Matches: 163, Mismatches: 16, Indels: 28
0.79 0.08 0.14
Matches are distributed among these distances:
96 8 0.05
97 8 0.05
101 24 0.15
103 1 0.01
104 5 0.03
105 21 0.13
106 42 0.26
107 6 0.04
108 48 0.29
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (101 bp):
TTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCCA
TAATAATAAATTATTTAAAATAAATCAATCAAAATA
Found at i:6360 original size:54 final size:52
Alignment explanation
Indices: 6238--6382 Score: 211
Period size: 54 Copynumber: 2.8 Consensus size: 52
6228 CAATCCATAC
* **
6238 TAATAAATTA-TTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAAATAAATATTTTA
* * *
6289 TAATAATTTATTTTAAAATAATTTATTTTAAAATAATTAAAATAAATTATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT-AAATAAA-TATTTTA
6343 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAA
6383 CCTTATTAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 9 0.11
52 25 0.30
53 6 0.07
54 42 0.51
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (52 bp):
TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAAATAAATATTTTA
Found at i:8375 original size:39 final size:39
Alignment explanation
Indices: 8326--8442 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 39
8316 TTTAAAAAGT
8326 AATTTAGAATGTTAATGTGAAATAATTTAAAATATTAAG-
1 AATTTAGAATGTTAATGTGAAATAATTTAAAATA-TAAGA
*
8365 AATTTAGAATGTT-ATGGTGACAA-AATTTAAGAA-ATCAGA
1 AATTTAGAATGTTAAT-GTGA-AATAATTTAA-AATATAAGA
8404 AATTTAGAATGTTAGA-GTGAAATAATTTGAAAATTATAA
1 AATTTAGAATGTTA-ATGTGAAATAATTT-AAAA-TATAA
8443 ATAAAAATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
38 7 0.11
39 49 0.74
40 6 0.09
41 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAAATATAAGA
Found at i:18130 original size:16 final size:17
Alignment explanation
Indices: 18109--18143 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
18099 CTGTTCACTC
18109 GAATAGT-AAATTTTGT
1 GAATAGTGAAATTTTGT
18125 GAATAGTGAAATTTTGT
1 GAATAGTGAAATTTTGT
18142 GA
1 GA
18144 GTGATACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (17 bp):
GAATAGTGAAATTTTGT
Found at i:33716 original size:4 final size:4
Alignment explanation
Indices: 33707--33825 Score: 51
Period size: 4 Copynumber: 27.8 Consensus size: 4
33697 GGAGGTAATT
* * * *
33707 TTTA TTTA TTTA TATA TTTTGA ATAA TTTA TTTA TTTA TTTCAAA ATT-
1 TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTT---A TTTA
** * * *
33755 TTTA TTTA TGCA TATA TTTA TTTTGA ATAA TTTA TTTA TTTA TGTTGA
1 TTTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA T-TT-A
* *
33803 ATAA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
33826 GAAGGGATAT
Statistics
Matches: 84, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
3 2 0.02
4 66 0.79
5 10 0.12
6 3 0.04
7 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (4 bp):
TTTA
Found at i:33790 original size:18 final size:18
Alignment explanation
Indices: 33714--33817 Score: 67
Period size: 18 Copynumber: 5.7 Consensus size: 18
33704 ATTTTTATTT
*
33714 ATTTATATATTTTGAATA
1 ATTTATTTATTTTGAATA
*
33732 ATTTATTTATTTATTTCAA-A
1 ATTTATTTA--T-TTTGAATA
*
33752 A-TT-TTTATTTATGCAT-
1 ATTTATTTATTT-TGAATA
33768 A--TATTTATTTTGAATA
1 ATTTATTTATTTTGAATA
33784 ATTTATTTATTTATGTTGAATA
1 ATTTATTTA--T-T-TTGAATA
33806 ATTTATTTATTT
1 ATTTATTTATTT
33818 ATTTATTTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 26
0.69 0.05 0.26
Matches are distributed among these distances:
15 7 0.10
16 12 0.18
18 19 0.28
19 3 0.04
20 5 0.07
21 6 0.09
22 16 0.24
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTTATTTATTTTGAATA
Found at i:33794 original size:22 final size:22
Alignment explanation
Indices: 33769--33821 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
33759 TTTATGCATA
33769 TATTTATTTTGAATAATTTATT
1 TATTTATTTTGAATAATTTATT
*
33791 TATTTATGTTGAATAATTTATT
1 TATTTATTTTGAATAATTTATT
33813 TATTTATTT
1 TATTTATTT
33822 ATTTGAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (22 bp):
TATTTATTTTGAATAATTTATT
Found at i:33825 original size:52 final size:51
Alignment explanation
Indices: 33707--33825 Score: 159
Period size: 52 Copynumber: 2.3 Consensus size: 51
33697 GGAGGTAATT
*
33707 TTTATTTATTTATATATTTTGAATAATTTATTTATTTATTTCAAAATTTTTA
1 TTTATTTATTTATTTATTTTGAATAATTTATTTATTTATTTCAAAA-TTTTA
** * *
33759 TTTATGCATATATTTATTTTGAATAATTTATTTATTTATGTTGAATAA-TTTA
1 TTTATTTATTTATTTATTTTGAATAATTTATTTATTTAT-TTCAA-AATTTTA
33811 TTTATTTATTTATTT
1 TTTATTTATTTATTT
33826 GAAGGGATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
52 51 0.89
53 4 0.07
54 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (51 bp):
TTTATTTATTTATTTATTTTGAATAATTTATTTATTTATTTCAAAATTTTA
Found at i:35781 original size:6 final size:6
Alignment explanation
Indices: 35763--35833 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
35753 ATGACAATGA
* * * * *
35763 TGATGG TAATGG TGGTGG TGATGG TGATGA TGTTGA TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
* * *
35811 TGATGA TGATGA TGATGC TGATG
1 TGATGG TGATGG TGATGG TGATG
35834 AAGATATATT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.21, C:0.01, G:0.42, T:0.35
Consensus pattern (6 bp):
TGATGG
Found at i:35787 original size:9 final size:9
Alignment explanation
Indices: 35760--35834 Score: 75
Period size: 9 Copynumber: 8.7 Consensus size: 9
35750 TAGATGACAA
35760 TGATGATGG
1 TGATGATGG
* *
35769 TAATGGTGG
1 TGATGATGG
*
35778 TGGTGATGG
1 TGATGATGG
*
35787 TGATGATGT
1 TGATGATGG
35796 TGATGAT-G
1 TGATGATGG
35804 -G-TGATGG
1 TGATGATGG
*
35811 TGATGATGA
1 TGATGATGG
*
35820 TGATGATGC
1 TGATGATGG
35829 TGATGA
1 TGATGA
35835 AGATATATTG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
8 1 0.02
9 46 0.87
ACGTcount: A:0.23, C:0.01, G:0.41, T:0.35
Consensus pattern (9 bp):
TGATGATGG
Found at i:35793 original size:3 final size:3
Alignment explanation
Indices: 35781--35834 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
35771 ATGGTGGTGG
* * * * *
35781 TGA TGG TGA TGA TGT TGA TGA TGG TGA TGG TGA TGA TGA TGA TGA TGC
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
35829 TGA TGA
1 TGA TGA
35835 AGATATATTG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:35816 original size:24 final size:24
Alignment explanation
Indices: 35778--35833 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
35768 GTAATGGTGG
*
35778 TGGTGATGGTGATGATGTTGATGA
1 TGGTGATGGTGATGATGATGATGA
35802 TGGTGATGGTGATGATGATGATGA
1 TGGTGATGGTGATGATGATGATGA
*
35826 TGCTGATG
1 TGGTGATG
35834 AAGATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.02, G:0.41, T:0.36
Consensus pattern (24 bp):
TGGTGATGGTGATGATGATGATGA
Found at i:43426 original size:32 final size:32
Alignment explanation
Indices: 43362--43423 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
43352 TTTTTCTGAT
43362 TAATTATGTATTTAGTCATCTAACTATTTTTA
1 TAATTATGTATTTAGTCATCTAACTATTTTTA
* *
43394 TAATTCTGT-TTTGGTCATCTAACTATTTTT
1 TAATTATGTATTTAGTCATCTAACTATTTTT
43424 TATTAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (32 bp):
TAATTATGTATTTAGTCATCTAACTATTTTTA
Found at i:43836 original size:4 final size:4
Alignment explanation
Indices: 43827--43865 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
43817 TTATAAACAA
* * *
43827 ATGT ATGT ATGT ATGT ATGC ATGC ATGC ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
43866 ATGACATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (4 bp):
ATGT
Found at i:46359 original size:111 final size:111
Alignment explanation
Indices: 46165--46386 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
46155 TGGAAATCAT
* *
46165 ATATCTCTACACTTTGCTAATACAATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTAATACAATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
46230 TATTTAGTTGATTGATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGATGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
* **
46276 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTAATACAATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
46341 TAATTAGATGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGATGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
46387 TTTTTGTAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTACTAATACAATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGATGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:47890 original size:18 final size:18
Alignment explanation
Indices: 47867--47901 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
47857 CAGCTACCGT
47867 AGCCATATATGATGCCGC
1 AGCCATATATGATGCCGC
47885 AGCCATATATGATGCCG
1 AGCCATATATGATGCCG
47902 TCATCACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (18 bp):
AGCCATATATGATGCCGC
Found at i:48264 original size:9 final size:9
Alignment explanation
Indices: 48252--48301 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
48242 CGACGATGAC
48252 GATGACGAT
1 GATGACGAT
48261 GATGACGAT
1 GATGACGAT
* *
48270 GATGATGGT
1 GATGACGAT
*
48279 GATGACGAC
1 GATGACGAT
48288 GATGACGAT
1 GATGACGAT
*
48297 AATGA
1 GATGA
48302 TGACAGCGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.34, T:0.22
Consensus pattern (9 bp):
GATGACGAT
Found at i:48269 original size:21 final size:21
Alignment explanation
Indices: 48240--48305 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
48230 TGCTCAGGAC
48240 GACGACGATGACGATGACGAT
1 GACGACGATGACGATGACGAT
* * **
48261 GATGACGATGATGATGGTGAT
1 GACGACGATGACGATGACGAT
* *
48282 GACGACGATGACGATAATGAT
1 GACGACGATGACGATGACGAT
48303 GAC
1 GAC
48306 AGCGAGGAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (21 bp):
GACGACGATGACGATGACGAT
Found at i:59521 original size:21 final size:21
Alignment explanation
Indices: 59497--59549 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
59487 CACCGCGGTT
*
59497 ATTTCCGATGCAACCACAACC
1 ATTTCAGATGCAACCACAACC
59518 ATTTCAGATGCAACCACAACC
1 ATTTCAGATGCAACCACAACC
59539 ATTTCAGATGC
1 ATTTCAGATGC
59550 CACCGTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.23
Consensus pattern (21 bp):
ATTTCAGATGCAACCACAACC
Found at i:60045 original size:20 final size:20
Alignment explanation
Indices: 60022--60096 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
60012 TTTCTTAATG
60022 TTTTTATTTAATTATGGAAT
1 TTTTTATTTAATTATGGAAT
* **
60042 TTTTTATTTATTTTAATTCTTAAT
1 TTTTTATTTA-ATT-A-T-GGAAT
60066 GTTTTTATTTAATTATGGAAT
1 -TTTTTATTTAATTATGGAAT
60087 TTTTTATTTA
1 TTTTTATTTA
60097 TTTTATTTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 20 0.45
21 5 0.11
22 2 0.05
23 2 0.05
24 5 0.11
25 10 0.23
ACGTcount: A:0.27, C:0.01, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTTATTTAATTATGGAAT
Found at i:60062 original size:45 final size:45
Alignment explanation
Indices: 59951--60165 Score: 317
Period size: 45 Copynumber: 4.7 Consensus size: 45
59941 GATAAACTTG
* * *
59951 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATTGACTT
1 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGA-AT
59997 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGAAT
1 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGAAT
*
60042 TTTTTATTTATTTTAATTCTTAATGTTTTTATTTAATTATGGAAT
1 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGAAT
*
60087 TTTTTATTTATTTTATTTCTTAATGTTTTTATTATTTACTTATGG-A-
1 TTTTTATTTATTTTATTTCTTAATG--TTT-TTATTTAATTATGGAAT
* *
60133 CTTTTATTTATTTTGTTTCTTAATGTTTTTATT
1 TTTTTATTTATTTTATTTCTTAATGTTTTTATT
60166 ATTTAATTAT
Statistics
Matches: 158, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
43 5 0.03
44 3 0.02
45 69 0.44
46 64 0.41
47 4 0.03
48 13 0.08
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.68
Consensus pattern (45 bp):
TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGAAT
Found at i:60138 original size:91 final size:91
Alignment explanation
Indices: 59952--60165 Score: 326
Period size: 91 Copynumber: 2.4 Consensus size: 91
59942 ATAAACTTGT
* *
59952 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATTGACTTTTTTTATTTATTTTATTTCT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACATTTTTTATTTATTTTATTTCT
*
60017 TAATGTTTTTATTTAATTATGGAATT
66 TAATGTTTTTATTTAATTATGGAATC
**
60043 TTTTATTTATTTTAATTCTTAATGTTTTTATTTAATTATGGA-ATTTTTTATTTATTTTATTTCT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACATTTTTTATTTATTTTATTTCT
*
60107 TAATGTTTTTATTATTTACTTATGG-A-C
66 TAATG--TTT-TTATTTAATTATGGAATC
60134 TTTTATTTATTTTGTTTCTTAATGTTTTTATT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATT
60166 ATTTAATTAT
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
90 26 0.23
91 69 0.62
92 4 0.04
93 13 0.12
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.68
Consensus pattern (91 bp):
TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACATTTTTTATTTATTTTATTTCT
TAATGTTTTTATTTAATTATGGAATC
Found at i:60231 original size:20 final size:20
Alignment explanation
Indices: 60195--60256 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
60185 AACGTTTGTA
*
60195 TTTAATGTTTCTATTTAATT
1 TTTAATGTTTTTATTTAATT
* *
60215 TTTTAT-TTTTATATTTAGTT
1 TTTAATGTTTT-TATTTAATT
*
60235 TGTAATGTTTTTATTTAATT
1 TTTAATGTTTTTATTTAATT
60255 TT
1 TT
60257 CACTTGAGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.79
21 4 0.12
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (20 bp):
TTTAATGTTTTTATTTAATT
Found at i:64667 original size:2 final size:2
Alignment explanation
Indices: 64660--64690 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
64650 TTAATAGTTT
64660 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64691 AATCGAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:73397 original size:23 final size:23
Alignment explanation
Indices: 73364--73414 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
73354 ATAGAATGTT
*
73364 GGAGTTCCTATGTGGACCTAGAG
1 GGAGTTACTATGTGGACCTAGAG
73387 GGAGTTACTATGTGGACCTAGAG
1 GGAGTTACTATGTGGACCTAGAG
73410 GGAGT
1 GGAGT
73415 CCCAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.37, T:0.25
Consensus pattern (23 bp):
GGAGTTACTATGTGGACCTAGAG
Found at i:74472 original size:88 final size:88
Alignment explanation
Indices: 74323--74499 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
74313 TTACTGTCAC
74323 AAGAGTTCACAACATCCCAAACTTCCTCCTCAAAAAATTCCTGCTCTAAGAACTGATTCTGCTCC
1 AAGAGTTCACAACATCCCAAACTTCCTCCTCAAAAAATTCCTGCTCTAAGAACTGATTCTGCTCC
74388 AAATAAATTCTGGGAAAATCCAG
66 AAATAAATTCTGGGAAAATCCAG
74411 AAGAGTTCACAACATCCCAAACTTCCTCCTCAAAAAATTCCTGCTCTAAGAACTGATTCTGCTCC
1 AAGAGTTCACAACATCCCAAACTTCCTCCTCAAAAAATTCCTGCTCTAAGAACTGATTCTGCTCC
74476 AAATAAATTCTGGGAAAATCCAG
66 AAATAAATTCTGGGAAAATCCAG
74499 A
1 A
74500 TTCAAATCAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (88 bp):
AAGAGTTCACAACATCCCAAACTTCCTCCTCAAAAAATTCCTGCTCTAAGAACTGATTCTGCTCC
AAATAAATTCTGGGAAAATCCAG
Found at i:84852 original size:19 final size:19
Alignment explanation
Indices: 84824--84863 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
84814 CATTTTAGGT
84824 ATTTTTTTTAT-AAGTAAG
1 ATTTTTTTTATCAAGTAAG
84842 ATTTTTATTTATCCAAGTAAG
1 ATTTTT-TTTAT-CAAGTAAG
84863 A
1 A
84864 AAATACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 5 0.26
21 8 0.42
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTTTTTTTATCAAGTAAG
Found at i:91193 original size:16 final size:16
Alignment explanation
Indices: 91143--91193 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
91133 ACACAATAAC
91143 ATTTTATTATATAA-AT
1 ATTTTATTA-ATAATAT
*
91159 AATTTATTCAATTTAATAT
1 ATTTTATT-AA--TAATAT
91178 ATTTTATTAATAATAT
1 ATTTTATTAATAATAT
91194 TAAACTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
18 5 0.17
19 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATTAATAATAT
Found at i:102112 original size:17 final size:15
Alignment explanation
Indices: 102085--102125 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
102075 AGGTATTTAC
102085 ATTTATTA-AAATAAT
1 ATTTATTATAAA-AAT
102100 -TTTATTATAAAAAT
1 ATTTATTATAAAAAT
102114 ATTTATT-TAAAA
1 ATTTATTATAAAA
102126 TGACTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTATAAAAAT
Found at i:103724 original size:16 final size:17
Alignment explanation
Indices: 103667--103725 Score: 77
Period size: 16 Copynumber: 3.6 Consensus size: 17
103657 TTTTTTAATC
**
103667 TTATCATTTGTGTTCAA
1 TTATCATTTAAGTTCAA
*
103684 TT-TCATTCAAGTTCAA
1 TTATCATTTAAGTTCAA
103700 TTATCATTTAA-TTCAA
1 TTATCATTTAAGTTCAA
103716 TTATCATTTA
1 TTATCATTTA
103726 GGAATTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 28 0.76
17 9 0.24
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.51
Consensus pattern (17 bp):
TTATCATTTAAGTTCAA
Found at i:104099 original size:25 final size:27
Alignment explanation
Indices: 104071--104120 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
104061 TTGTGTAATA
104071 TAAA-AAAGTTATTTT-ATAT-TAAATT
1 TAAATAAAG-TATTTTCATATATAAATT
104096 TAAATAAAGTATTTTCATATATAAA
1 TAAATAAAGTATTTTCATATATAAA
104121 AGGAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 8 0.36
27 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
TAAATAAAGTATTTTCATATATAAATT
Done.