Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006936.1 Hibiscus syriacus cultivar Beakdansim tig00017808_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: 2176229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:2154821 original size:45 final size:45
Alignment explanation
Indices: 2154755--2154843 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
2154745 GTCAGACATG
* *
2154755 TGGTAGAGCACACCGAGGAGTATGCAAACTTCTTAGTAGAGCTTT
1 TGGTAGAGCACACCAAAGAGTATGCAAACTTCTTAGTAGAGCTTT
*
2154800 TGGTAGAGCACACCAAAGAGTATGCAAACTTCTTAGTGGAGCTT
1 TGGTAGAGCACACCAAAGAGTATGCAAACTTCTTAGTAGAGCTT
2154844 GCTTCCAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (45 bp):
TGGTAGAGCACACCAAAGAGTATGCAAACTTCTTAGTAGAGCTTT
Found at i:2155066 original size:81 final size:81
Alignment explanation
Indices: 2154932--2155941 Score: 1447
Period size: 81 Copynumber: 12.5 Consensus size: 81
2154922 TATATGTGGT
* * * * * *
2154932 AATTATTCCAGTTATATAAAAGGTT-AATACATTTGAGTAAAACATTAATAGCCTAGTTGTACAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
2154996 TTGACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
** * *
2155012 AATTATGCTTGTTAGATGAAAGGTTAAATACCTTTGAGAAAAAGATTAATAGCCTAGCTGTGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
*
2155077 TTAACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
2155093 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCA-
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
*
2155157 TT-AAAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* * *
2155172 AATTATTCCAGTTAGATGAAAAGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
2155237 TTGACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* * * *
2155253 AATTATGCCAGTTAGAT-AAAAGTTTAATATCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
2155317 TTGACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* * * *
2155333 AATTATG-CATGTTAGATGAAAGTTTAAATACCTTTGAGTAAAAGATTAATAACCTAGCTATGCA
1 AATTATGCCA-GTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCA
*
2155397 TTTGACAGAAATGTGTC
65 TTTGACAGAAAGGTGTC
* *
2155414 AATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATAGCCTAGTTGTTCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
2155479 TTGACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* * * * *
2155495 AATTATGCCAGTTAGATTAAAGGTTAAATATCTTTGAGTAAAAGACT-ATAGTCTAGTTGCGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
* * *
2155559 TTGACTGAAATGTATC
66 TTGACAGAAAGGTGTC
* *
2155575 AATTATGCCAGTTAGATGAAAGCTTAAATACGTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
* *
2155640 TTGAAAGAAATGTGTC
66 TTGACAGAAAGGTGTC
* * * *
2155656 AATTATGCCAGTTAGATGAAAGTTTAAATACCTTTGAGTAAAATATTAATAGCCTAGGTGTGCTT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
*
2155721 TTGACAAAAAGGTGTC
66 TTGACAGAAAGGTGTC
** * *
2155737 AATTATGTTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAGGATTAATAGCCTAATTGTGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
*
2155802 TTGACAGAAAGGTGCC
66 TTGACAGAAAGGTGTC
* * * * *
2155818 AATTATTCTAGTTAGATTAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTATGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
*
2155883 TTGGCAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* * * *
2155899 AATTATGCAAGTTAGATGAAAGGCTAAATGCCTTTGGGTAAAA
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
2155942 AATTTAAGGA
Statistics
Matches: 835, Mismatches: 88, Indels: 13
0.89 0.09 0.01
Matches are distributed among these distances:
79 75 0.09
80 168 0.20
81 590 0.71
82 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (81 bp):
AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
TTGACAGAAAGGTGTC
Found at i:2155561 original size:242 final size:243
Alignment explanation
Indices: 2154932--2155941 Score: 1447
Period size: 242 Copynumber: 4.2 Consensus size: 243
2154922 TATATGTGGT
* * * * * *
2154932 AATTATTCCAGTTATATAAAAGGTT-AATACATTTGAGTAAAACATTAATAGCCTAGTTGTACAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
** *
2154996 TTGACAGAAAGGTGTCAATTATGCTTGTTAGATGAAAGGTTAAATACCTTTGAGAAAAAGATTAA
66 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
*
2155061 TAGCCTAGCTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCT
131 TAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCT
* *
2155126 TTGAGTAAAAGATTAATAGCCTAGTTGTGCA-TT-AAAGAAAGGTGTC
196 TTGAGTAAAAGATTAATAGCCTAGCTATGCATTTGAAAGAAAGGTGTC
* * *
2155172 AATTATTCCAGTTAGATGAAAAGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
* * *
2155237 TTGACAGAAAGGTGTCAATTATGCCAGTTAGAT-AAAAGTTTAATATCTTTGAGTAAAAGATTAA
66 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
*
2155301 TAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-CATGTTAGATGAAAGTTTAAATACC
131 TAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCA-GTTAGATGAAAGGTTAAATACC
* * *
2155365 TTTGAGTAAAAGATTAATAACCTAGCTATGCATTTGACAGAAATGTGTC
195 TTTGAGTAAAAGATTAATAGCCTAGCTATGCATTTGAAAGAAAGGTGTC
* *
2155414 AATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATAGCCTAGTTGTTCAT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
* * *
2155479 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATTAAAGGTTAAATATCTTTGAGTAAAAGACT-A
66 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
* * * * * * * *
2155543 TAGTCTAGTTGCGCATTTGACTGAAATGTATCAATTATGCCAGTTAGATGAAAGCTTAAATACGT
131 TAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCT
* * *
2155608 TTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGAAAGAAATGTGTC
196 TTGAGTAAAAGATTAATAGCCTAGCTATGCATTTGAAAGAAAGGTGTC
* * * *
2155656 AATTATGCCAGTTAGATGAAAGTTTAAATACCTTTGAGTAAAATATTAATAGCCTAGGTGTGCTT
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
* ** *
2155721 TTGACAAAAAGGTGTCAATTATGTTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAGGATTAA
66 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
** * * * *
2155786 TAGCCTAATTGTGCATTTGACAGAAAGGTGCCAATTATTCTAGTTAGATTAAAGGTTAAATACCT
131 TAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCT
**
2155851 TTGAGTAAAAGATTAATAGCCTAGCTATGCATTTGGCAGAAAGGTGTC
196 TTGAGTAAAAGATTAATAGCCTAGCTATGCATTTGAAAGAAAGGTGTC
* * * *
2155899 AATTATGCAAGTTAGATGAAAGGCTAAATGCCTTTGGGTAAAA
1 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
2155942 AATTTAAGGA
Statistics
Matches: 688, Mismatches: 75, Indels: 11
0.89 0.10 0.01
Matches are distributed among these distances:
239 2 0.00
240 137 0.20
241 68 0.10
242 318 0.46
243 163 0.24
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (243 bp):
AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCAT
TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
TAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCT
TTGAGTAAAAGATTAATAGCCTAGCTATGCATTTGAAAGAAAGGTGTC
Found at i:2156092 original size:45 final size:46
Alignment explanation
Indices: 2155992--2156104 Score: 142
Period size: 45 Copynumber: 2.5 Consensus size: 46
2155982 TTAACAGTAT
* * *
2155992 GAAAGGATGTCATATAT-AAAATGTACAACAATGCATAATTAGTTA
1 GAAAGGATGTCATAAATGAAAATGTACAACAATGCATAAGTAGGTA
*
2156037 AAAAGGATGTCATAAATGAAAATGTA-AACAATGCATAAGT-GGTA
1 GAAAGGATGTCATAAATGAAAATGTACAACAATGCATAAGTAGGTA
* *
2156081 CGAAAGAATGTCAGAAATGAAAAT
1 -GAAAGGATGTCATAAATGAAAAT
2156105 AGAAAATGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 3 0.05
45 48 0.81
46 8 0.14
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.24
Consensus pattern (46 bp):
GAAAGGATGTCATAAATGAAAATGTACAACAATGCATAAGTAGGTA
Found at i:2161121 original size:28 final size:28
Alignment explanation
Indices: 2161081--2161142 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
2161071 TGTTAAATTG
2161081 TATTACATTTCACTTAAATGATGAACTA
1 TATTACATTTCACTTAAATGATGAACTA
* *
2161109 TATTACATTTCACTTGAATGTTGAACTA
1 TATTACATTTCACTTAAATGATGAACTA
*
2161137 CATTAC
1 TATTAC
2161143 TTGAATGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (28 bp):
TATTACATTTCACTTAAATGATGAACTA
Found at i:2162021 original size:26 final size:26
Alignment explanation
Indices: 2161986--2162303 Score: 401
Period size: 26 Copynumber: 12.0 Consensus size: 26
2161976 CCTCGAGTCA
2161986 TAAA-CAATTTTAACTCAAATCAATT
1 TAAATCAATTTTAACTCAAATCAATT
2162011 TAAATCAATTTTAACTCAAATCAATT
1 TAAATCAATTTTAACTCAAATCAATT
2162037 TAAATCAATTTTAACTCAAATCAATTT
1 TAAATCAATTTTAACTCAAATCAA-TT
* * * * *
2162064 TAACTCAA-ATCAATTTAAATCAATTT
1 TAAATCAATTTTAACTCAAATCAA-TT
* * * * *
2162090 TAACTCAA-ATCAATTTAAATCAATTT
1 TAAATCAATTTTAACTCAAATCAA-TT
* * *
2162116 TAACTCAA-ATCAACTCAAATCAATTTT
1 TAAATCAATTTTAACTCAAATCAA--TT
2162143 AACTCAAATCAATTTTAACTCAAATCAATT
1 ---T-AAATCAATTTTAACTCAAATCAATT
2162173 TAAATCAATTTTAACTCAAATCAATT
1 TAAATCAATTTTAACTCAAATCAATT
2162199 TAAATCAATTTTAACTCAAATCAATT
1 TAAATCAATTTTAACTCAAATCAATT
*
2162225 TAAATCAATTTAAACTCAAATCAATT
1 TAAATCAATTTTAACTCAAATCAATT
2162251 TAAATCAATTTTAACTCAAATCAATT
1 TAAATCAATTTTAACTCAAATCAATT
2162277 TAAATCAATTTTAACTCAAATCAATT
1 TAAATCAATTTTAACTCAAATCAATT
2162303 T
1 T
2162304 TAACTCAAAT
Statistics
Matches: 273, Mismatches: 12, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
25 4 0.01
26 234 0.86
27 13 0.05
30 3 0.01
31 6 0.02
32 13 0.05
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAATCAATTTTAACTCAAATCAATT
Found at i:2162107 original size:94 final size:94
Alignment explanation
Indices: 2161986--2162411 Score: 606
Period size: 94 Copynumber: 4.4 Consensus size: 94
2161976 CCTCGAGTCA
2161986 TAAA-CAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
2162050 ACTCAAATCAATTTTAACTCAAATCAATT
66 ACTCAAATCAATTTTAACTCAAATCAATT
* *
2162079 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAACTCAAATCAATTTTA
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
2162144 ACTCAAATCAATTTTAACTCAAATCAATT
66 ACTCAAATCAATTTTAACTCAAATCAATT
2162173 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTAA
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTT--
*
2162238 ACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
64 --T--AA-C---TCAAATCAATTTTAACTCAAATCAATT
* * * * * * *
2162277 TAAATCAATTTTAACTCAAATCAATTTTAACTCAA-ATCAATTTAAATCAATTTTAACTCAA-AT
1 TAAATCAATTTTAACTCAAATCAA-TTTAAATCAATTTTAACTCAAATCAA-TTTAAATCAATTT
* * *
2162340 CAATTTAAATCAATTTTAACTCAAATCAATT
64 TAACTCAAATCAATTTTAACTCAAATCAATT
2162371 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAAC
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAAC
2162412 GCTTGAAGTC
Statistics
Matches: 301, Mismatches: 18, Indels: 27
0.87 0.05 0.08
Matches are distributed among these distances:
93 13 0.04
94 202 0.67
98 3 0.01
100 2 0.01
101 1 0.00
104 62 0.21
105 18 0.06
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (94 bp):
TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
ACTCAAATCAATTTTAACTCAAATCAATT
Found at i:2162149 original size:120 final size:120
Alignment explanation
Indices: 2161986--2162411 Score: 757
Period size: 120 Copynumber: 3.6 Consensus size: 120
2161976 CCTCGAGTCA
2161986 TAAA-CAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
2162050 ACTCAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
66 ACTCAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
* * * * *
2162105 TAAATCAATTTTAACTCAAATCAACTCAAATCAATTTTAACTCAAATCAATTTTAACTCAA-ATC
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAA-TTTAAATCAATTTT
* *
2162169 AATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
65 AACTCAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
*
2162225 TAAATCAATTTAAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
2162290 ACTCAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
66 ACTCAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
2162345 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
1 TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
2162410 AC
66 AC
2162412 GCTTGAAGTC
Statistics
Matches: 288, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
119 13 0.05
120 266 0.92
121 9 0.03
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (120 bp):
TAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTA
ACTCAAATCAATTTTAACTCAAATCAATTTAAATCAATTTTAACTCAAATCAATT
Found at i:2162323 original size:26 final size:26
Alignment explanation
Indices: 2162294--2162411 Score: 236
Period size: 26 Copynumber: 4.5 Consensus size: 26
2162284 ATTTTAACTC
2162294 AAATCAATTTTAACTCAAATCAATTT
1 AAATCAATTTTAACTCAAATCAATTT
2162320 AAATCAATTTTAACTCAAATCAATTT
1 AAATCAATTTTAACTCAAATCAATTT
2162346 AAATCAATTTTAACTCAAATCAATTT
1 AAATCAATTTTAACTCAAATCAATTT
2162372 AAATCAATTTTAACTCAAATCAATTT
1 AAATCAATTTTAACTCAAATCAATTT
2162398 AAATCAATTTTAAC
1 AAATCAATTTTAAC
2162412 GCTTGAAGTC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 92 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATCAATTTTAACTCAAATCAATTT
Found at i:2162657 original size:5 final size:5
Alignment explanation
Indices: 2162647--2162702 Score: 58
Period size: 5 Copynumber: 11.2 Consensus size: 5
2162637 AACTTTCACA
* * * * *
2162647 CTCCT CTCCT CTCCT CTCCT GTCCT CTCCT CACCT CACCT CACCT CACCT
1 CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT
*
2162697 CACCT C
1 CTCCT C
2162703 AACCTCACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.09, C:0.59, G:0.02, T:0.30
Consensus pattern (5 bp):
CTCCT
Found at i:2162703 original size:5 final size:5
Alignment explanation
Indices: 2162669--2162710 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
2162659 CCTCTCCTGT
*
2162669 CCTCT CCTCA CCTCA CCTCA CCTCA CCTCA CCTCAA CCTCA C
1 CCTCA CCTCA CCTCA CCTCA CCTCA CCTCA CCTC-A CCTCA C
2162711 AATTGTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.19, C:0.60, G:0.00, T:0.21
Consensus pattern (5 bp):
CCTCA
Found at i:2170711 original size:12 final size:12
Alignment explanation
Indices: 2170680--2170713 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2170670 AGGAGGTGAT
*
2170680 AATGAAGATTTC
1 AATGAAGGTTTC
2170692 AATGAAGGTTTC
1 AATGAAGGTTTC
2170704 AATGAAGGTT
1 AATGAAGGTT
2170714 CATGTTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (12 bp):
AATGAAGGTTTC
Found at i:2170887 original size:37 final size:39
Alignment explanation
Indices: 2170840--2170926 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 39
2170830 CTGCAAAAAA
*
2170840 AATAAAATAATTAAATAAAATACTAA-AACA-ATTAAAT
1 AATAAAATAATTAAATAAAATACTAATAAAATATTAAAT
*
2170877 AATACAATAATTAAATAAAATACTAATAAAATATTAAATAT
1 AATAAAATAATTAAATAAAATACTAATAAAATATT-AA-AT
2170918 AATAAAATA
1 AATAAAATA
2170927 TATCTTATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 25 0.58
38 3 0.07
39 3 0.07
40 2 0.05
41 10 0.23
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (39 bp):
AATAAAATAATTAAATAAAATACTAATAAAATATTAAAT
Found at i:2170903 original size:16 final size:16
Alignment explanation
Indices: 2170847--2170926 Score: 56
Period size: 16 Copynumber: 4.6 Consensus size: 16
2170837 AAAAATAAAA
*
2170847 TAATTAAATAAAATAC
1 TAATAAAATAAAATAC
2170863 TAA-AACAATTAAATAATAC
1 TAATAA-AA-T-AA-AATAC
*
2170882 AATAATTAAATAAAATAC
1 --TAATAAAATAAAATAC
2170900 TAATAAAATATTAAATA-
1 TAATAAAATA--AAATAC
2170917 TAATAAAATA
1 TAATAAAATA
2170927 TATCTTATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
15 1 0.02
16 14 0.27
17 11 0.21
18 12 0.23
19 7 0.13
20 1 0.02
21 5 0.10
22 1 0.02
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATAAAATAAAATAC
Found at i:2170916 original size:23 final size:24
Alignment explanation
Indices: 2170876--2170921 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2170866 AACAATTAAA
*
2170876 TAATACAATAATTAAATAAAATAC
1 TAATAAAATAATTAAATAAAATAC
*
2170900 TAATAAAAT-ATTAAATATAATA
1 TAATAAAATAATTAAATAAAATA
2170922 AAATATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
TAATAAAATAATTAAATAAAATAC
Found at i:2170921 original size:12 final size:12
Alignment explanation
Indices: 2170839--2170921 Score: 57
Period size: 12 Copynumber: 6.8 Consensus size: 12
2170829 ACTGCAAAAA
2170839 AAATAAAATAATT
1 AAATAAAAT-ATT
*
2170852 AAATAAAATACT
1 AAATAAAATATT
*
2170864 -AA-AACA-ATT
1 AAATAAAATATT
2170873 AAATAATACAATAATT
1 AAAT-A-A-AAT-ATT
*
2170889 AAATAAAATACT
1 AAATAAAATATT
2170901 -AATAAAATATT
1 AAATAAAATATT
*
2170912 AAATATAATA
1 AAATAAAATA
2170922 AAATATATCT
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
9 2 0.04
10 5 0.09
11 12 0.22
12 13 0.24
13 13 0.24
14 2 0.04
15 1 0.02
16 7 0.13
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAAATATT
Found at i:2170922 original size:17 final size:18
Alignment explanation
Indices: 2170894--2170927 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2170884 TAATTAAATA
2170894 AAATACTAATAAAATATT
1 AAATACTAATAAAATATT
2170912 AAATA-TAATAAAATAT
1 AAATACTAATAAAATAT
2170928 ATCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATACTAATAAAATATT
Found at i:2173023 original size:8 final size:7
Alignment explanation
Indices: 2173002--2173052 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
2172992 AGATTATTTT
2173002 AATTAAA
1 AATTAAA
2173009 AATTAAA
1 AATTAAA
2173016 ACATT-AA
1 A-ATTAAA
2173023 AATTAAA
1 AATTAAA
2173030 ATATTAAA
1 A-ATTAAA
*
2173038 AA-AATAA
1 AATTA-AA
2173045 AATTAAA
1 AATTAAA
2173052 A
1 A
2173053 TAATCATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 4 0.11
7 22 0.59
8 11 0.30
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (7 bp):
AATTAAA
Found at i:2173023 original size:15 final size:15
Alignment explanation
Indices: 2173003--2173039 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2172993 GATTATTTTA
2173003 ATTAAAAATTAAAAC
1 ATTAAAAATTAAAAC
*
2173018 ATT-AAAATTAAAAT
1 ATTAAAAATTAAAAC
2173032 ATTAAAAA
1 ATTAAAAA
2173040 AATAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAAATTAAAAC
Found at i:2173038 original size:22 final size:22
Alignment explanation
Indices: 2173002--2173054 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2172992 AGATTATTTT
* *
2173002 AATTAAAA-ATTAAAACATTAA
1 AATTAAAATATTAAAAAAATAA
2173023 AATTAAAATATTAAAAAAATAA
1 AATTAAAATATTAAAAAAATAA
2173045 AATTAAAATA
1 AATTAAAATA
2173055 ATCATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATTAAAATATTAAAAAAATAA
Found at i:2174739 original size:31 final size:31
Alignment explanation
Indices: 2174685--2174753 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2174675 TTTTTTGATG
* *
2174685 TGTGATAATTGTACTTCAATAAAATGTCTAA
1 TGTGATAATTGTACTTCAATAAAATATCCAA
* ***
2174716 TGTGATACTTGTACTTTGTTAAAATATCCAA
1 TGTGATAATTGTACTTCAATAAAATATCCAA
2174747 TGTGATA
1 TGTGATA
2174754 TATGCACTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (31 bp):
TGTGATAATTGTACTTCAATAAAATATCCAA
Found at i:2175526 original size:13 final size:12
Alignment explanation
Indices: 2175495--2175529 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2175485 ACATTCTGAT
2175495 AATTTAAAAAAA
1 AATTTAAAAAAA
*
2175507 TATTTAAAATAAA
1 AATTTAAAA-AAA
2175520 AATTTAAAAA
1 AATTTAAAAA
2175530 TATGATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTTAAAAAAA
Done.