Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001065.1 Hibiscus syriacus cultivar Beakdansim tig00002105_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: 130476
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1838 original size:18 final size:18
Alignment explanation
Indices: 1811--1899 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
1801 AGGGTCTATA
** *
1811 TGGTCCTTCGACAGATAG
1 TGGTCCTTCGGGACATAG
*
1829 TGGTCTTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
1847 TGGTCTTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
1865 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
1883 TGGTCCTTCGAGACATA
1 TGGTCCTTCGGGACATA
1900 TGTGTTATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:9937 original size:21 final size:21
Alignment explanation
Indices: 9911--9959 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
9901 TAATATGTAT
9911 GATCATGACCAACCTATCCAA
1 GATCATGACCAACCTATCCAA
*
9932 GATCATGACCAACTTATCCAA
1 GATCATGACCAACCTATCCAA
*
9953 GAACATG
1 GATCATG
9960 TAGTGACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (21 bp):
GATCATGACCAACCTATCCAA
Found at i:18235 original size:42 final size:42
Alignment explanation
Indices: 18188--18304 Score: 207
Period size: 42 Copynumber: 2.8 Consensus size: 42
18178 GATGAAAACA
* *
18188 TTTTGTCACTAGTCTTAGTAGGTGATTTGTGACGTTAATTGC
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGC
*
18230 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGG
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGC
18272 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGAC
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGAC
18305 AACAATACTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.46
Consensus pattern (42 bp):
TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGC
Found at i:18301 original size:24 final size:24
Alignment explanation
Indices: 18189--18301 Score: 79
Period size: 24 Copynumber: 5.2 Consensus size: 24
18179 ATGAAAACAT
*
18189 TTTGTCACTAGTCTTAGTAGGTGA
1 TTTGTCACTAGTCTTAGTTGGTGA
* * *
18213 TTTGTGAC--G--TTAATTGCT--
1 TTTGTCACTAGTCTTAGTTGGTGA
18231 TTTGTCACTAGTCTTAGTTGGTGA
1 TTTGTCACTAGTCTTAGTTGGTGA
* * *
18255 TTTGTGAC--G--ATAATTGGT--
1 TTTGTCACTAGTCTTAGTTGGTGA
18273 TTTGTCACTAGTCTTAGTTGGTGA
1 TTTGTCACTAGTCTTAGTTGGTGA
18297 TTTGT
1 TTTGT
18302 GACAACAATA
Statistics
Matches: 64, Mismatches: 13, Indels: 24
0.63 0.13 0.24
Matches are distributed among these distances:
18 14 0.22
20 15 0.23
22 16 0.25
24 19 0.30
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.47
Consensus pattern (24 bp):
TTTGTCACTAGTCTTAGTTGGTGA
Found at i:18640 original size:43 final size:42
Alignment explanation
Indices: 18592--18937 Score: 347
Period size: 43 Copynumber: 8.1 Consensus size: 42
18582 TGAGAACCAA
* * *
18592 AAACGCCGCAATATGCCAAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
** * * *
18635 AAACGCCAAAAAAGGTCGATATTTATAGCGGCG-TTTT-GAAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * *
18676 AAACGCCGCAAAAGGTTGATATTTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
18719 AAACGTCGCAAAAAGATGATATCTATAGCGCCGTTTTTGGAAC
1 AAACGCCGC-AAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* *
18762 AAACGCCGCAATAGGTCAGATCTATAGCGGCATTTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGC--GTTTTTGGAAC
* * *
18806 AAATGTCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGGATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
* * * *
18849 AAACGCCGTAAAAGATCAGATATATAGCGGCGTTTTTTGAAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
**
18892 AAACGCCGCAAAAAATCAGATCTATAGCGGCG-TTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
18934 AAAC
1 AAAC
18938 ACTGCTAATT
Statistics
Matches: 255, Mismatches: 40, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
41 37 0.15
42 32 0.13
43 143 0.56
44 43 0.17
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:22600 original size:42 final size:40
Alignment explanation
Indices: 22551--22682 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 40
22541 TATATCAGTT
22551 TATAGCGGCATTTAAT-ATACAAACGCCACTAAAGTACGAGAA
1 TATAGCGGCATTT-ATCATA-AAA-GCCACTAAAGTACGAGAA
* * * * *
22593 TTTAGCGGCGTTTGTGCTTAAAAGCCACTAAAGTACGAGTA
1 TATAGCGGCATTTAT-CATAAAAGCCACTAAAGTACGAGAA
* * * *
22634 TATAGCGGCATTTGTACTTAAAATGTCACTAAAGTACGAGTA
1 TATAGCGGCATTTAT-CATAAAA-GCCACTAAAGTACGAGAA
22676 TATAGCG
1 TATAGCG
22683 ACGTTTGTAC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 38 0.49
42 38 0.49
43 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (40 bp):
TATAGCGGCATTTATCATAAAAGCCACTAAAGTACGAGAA
Found at i:22622 original size:41 final size:42
Alignment explanation
Indices: 22575--22710 Score: 177
Period size: 42 Copynumber: 3.3 Consensus size: 42
22565 ATATACAAAC
* * *
22575 GCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTAAAA-
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
*
22616 GCCACTAAAGTACGAGTATATAGCGGCATTTGTACTTAAAAT
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
* * * *
22658 GTCACTAAAGTACGAGTATATAGCGACGTTTGTAC-AAGAAAC
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTA-AAAT
22700 GCCACTAAAGT
1 GCCACTAAAGT
22711 TTAGTATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
41 38 0.46
42 45 0.54
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (42 bp):
GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
Found at i:24836 original size:106 final size:103
Alignment explanation
Indices: 24654--24844 Score: 274
Period size: 106 Copynumber: 1.8 Consensus size: 103
24644 GTGACAGAGT
* * *
24654 TATTGTTAATAGTATCACATTTGGTCACTAAAAAAAACTTACTGTGGCAACATTGATGGTCAAAA
1 TATTGATAATAATATCACATTTGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAA
24719 AATATACTTTTAGTATCAAATAAATTTATCACAATTTC
66 AATATACTTTTAGTATCAAATAAATTTATCACAATTTC
* * *
24757 TATTGATAATAATATCAAACATTTGGTCACTAAAAACATACTTAGTGTGACAATATTGATGGTCA
1 TATTGATAATAATATC--ACATTTGGTCACTAAAAA-AAACTTACTGTGACAACATTGATGGTCA
* * *
24822 CAAAATATATTTTTAGTGTCAAA
63 AAAAATATACTTTTAGTATCAAA
24845 AAAGATCATC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
103 14 0.18
105 18 0.24
106 44 0.58
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (103 bp):
TATTGATAATAATATCACATTTGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAA
AATATACTTTTAGTATCAAATAAATTTATCACAATTTC
Found at i:24867 original size:106 final size:103
Alignment explanation
Indices: 24654--24872 Score: 269
Period size: 106 Copynumber: 2.1 Consensus size: 103
24644 GTGACAGAGT
* * *
24654 TATTGTTAATAGTATCACATTTGGTCACTAAAAAAAACTTACTGTGGCAACATTGATGGTCAAAA
1 TATTGATAATAATATCACATTTGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAA
* * * *
24719 AATATACTTTTAGTATCAAATAAATTTATCACAATTTC
66 AATATACTTTTAGTATCAAATAAAATCATCACAAATTA
* * *
24757 TATTGATAATAATATCAAACATTTGGTCACTAAAAACATACTTAGTGTGACAATATTGATGGTCA
1 TATTGATAATAATATC--ACATTTGGTCACTAAAAA-AAACTTACTGTGACAACATTGATGGTCA
* * * *
24822 CAAAATATATTTTTAGTGTCAAA-AAAGATCATCATAAATTA
63 AAAAATATACTTTTAGTATCAAATAAA-ATCATCACAAATTA
24863 TATTGATAAT
1 TATTGATAAT
24873 TGTGTCGAAT
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
103 14 0.14
105 21 0.21
106 63 0.64
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (103 bp):
TATTGATAATAATATCACATTTGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAA
AATATACTTTTAGTATCAAATAAAATCATCACAAATTA
Found at i:24890 original size:106 final size:105
Alignment explanation
Indices: 24675--24899 Score: 247
Period size: 106 Copynumber: 2.1 Consensus size: 105
24665 GTATCACATT
*
24675 TGGTCACTAAAAAAAACTTACTGTGGCAACATTGATGGTCAAAAAATATACTTTTAGTATCAAAT
1 TGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATCAAAT
* * * * **
24740 AAATTTATCACAATTTCTATTGATAATAATATCAAACATT
66 AAAATCATCACAAATTATATTGATAATAATATCAAACAGA
* * * * * *
24780 TGGTCACTAAAAACATACTTAGTGTGACAATATTGATGGTCACAAAATATATTTTTAGTGTCAAA
1 TGGTCACTAAAAA-AAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATCAAA
* ** * * *
24845 -AAAGATCATCATAAATTATATTGATAATTGTGTCGAATAGA
65 TAAA-ATCATCACAAATTATATTGATAATAATATCAAACAGA
24886 TGGTCA-TAAAAAAA
1 TGGTCACTAAAAAAA
24900 TAAACAATTG
Statistics
Matches: 98, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
104 1 0.01
105 22 0.22
106 75 0.77
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (105 bp):
TGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATCAAAT
AAAATCATCACAAATTATATTGATAATAATATCAAACAGA
Found at i:28987 original size:24 final size:21
Alignment explanation
Indices: 28960--29017 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
28950 ATGTGAAATA
28960 ATGAAAGTGATCACATGTGTGTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
28984 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
29006 ATGAAAAGTGAT
1 ATG-AAAGTGAT
29018 GAGAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:29243 original size:22 final size:19
Alignment explanation
Indices: 29215--29310 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 19
29205 GTTCTTAAGG
29215 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGACA-AT
29235 ACAGTGGTCCTTCGGGAC-AT
1 --AGTGGTCCTTCGGGACAAT
* *
29255 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGACAAT
*
29274 CAGTGGTCCTTCGGGA-TAT
1 -AGTGGTCCTTCGGGACAAT
*
29293 AGTGGTCCTTCGAGACAA
1 AGTGGTCCTTCGGGACAA
29311 ATATTCAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 28 0.44
19 5 0.08
20 15 0.23
22 16 0.25
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:29285 original size:38 final size:40
Alignment explanation
Indices: 29215--29304 Score: 139
Period size: 38 Copynumber: 2.3 Consensus size: 40
29205 GTTCTTAAGG
*
29215 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
* *
29255 AGTGGTTCTTCGGAACA-AT-CAGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
29293 AGTGGTCCTTCG
1 AGTGGTCCTTCG
29305 AGACAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 29 0.63
39 2 0.04
40 15 0.33
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (40 bp):
AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
Found at i:34295 original size:21 final size:21
Alignment explanation
Indices: 34254--34296 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34244 CATGCACGAG
*
34254 CGTACCACCATGCATCCTCAA
1 CGTACCACCATGCATACTCAA
* *
34275 CGTACCAGCATGCATATTCAA
1 CGTACCACCATGCATACTCAA
34296 C
1 C
34297 ATACTTCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.37, G:0.12, T:0.21
Consensus pattern (21 bp):
CGTACCACCATGCATACTCAA
Found at i:40868 original size:42 final size:42
Alignment explanation
Indices: 40821--40937 Score: 207
Period size: 42 Copynumber: 2.8 Consensus size: 42
40811 GATGAAAACA
* * *
40821 TTTTGTCACTAGTCTTAGTAGGTGATTTGTGACGTTAATTGT
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGG
40863 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGG
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGG
40905 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGAC
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGAC
40938 AACAATACTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.47
Consensus pattern (42 bp):
TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTGG
Found at i:40934 original size:24 final size:24
Alignment explanation
Indices: 40822--40934 Score: 79
Period size: 24 Copynumber: 5.2 Consensus size: 24
40812 ATGAAAACAT
*
40822 TTTGTCACTAGTCTTAGTAGGTGA
1 TTTGTCACTAGTCTTAGTTGGTGA
* * *
40846 TTTGTGAC--G--TTAATT-GT-T
1 TTTGTCACTAGTCTTAGTTGGTGA
40864 TTTGTCACTAGTCTTAGTTGGTGA
1 TTTGTCACTAGTCTTAGTTGGTGA
* * *
40888 TTTGTGAC--G--ATAATTGGT--
1 TTTGTCACTAGTCTTAGTTGGTGA
40906 TTTGTCACTAGTCTTAGTTGGTGA
1 TTTGTCACTAGTCTTAGTTGGTGA
40930 TTTGT
1 TTTGT
40935 GACAACAATA
Statistics
Matches: 64, Mismatches: 13, Indels: 24
0.63 0.13 0.24
Matches are distributed among these distances:
18 14 0.22
19 2 0.03
20 13 0.20
22 14 0.22
23 2 0.03
24 19 0.30
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.48
Consensus pattern (24 bp):
TTTGTCACTAGTCTTAGTTGGTGA
Found at i:41273 original size:43 final size:42
Alignment explanation
Indices: 41225--41570 Score: 347
Period size: 43 Copynumber: 8.1 Consensus size: 42
41215 TGAGAACCAA
* * *
41225 AAACGCCGCAATATGCCAAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
** * * *
41268 AAACGCCAAAAAAGGTCGATATTTATAGCGGCG-TTTT-GAAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * *
41309 AAACGCCGCAAAAGGTTGATATTTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
41352 AAACGTCGCAAAAAGATGATATCTATAGCGTCGTTTTTGGAAC
1 AAACGCCGC-AAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* *
41395 AAACGCCGCAATAGGTCAGATCTATAGCGGCATTTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGC--GTTTTTGGAAC
* * *
41439 AAATGTCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGGATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
* * * *
41482 AAACGCCGTAAAAGATCAGATATATAGCGGCGTTTTTTGAAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
**
41525 AAACGCCGCAAAAAATCAGATCTATAGCGGCG-TTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
41567 AAAC
1 AAAC
41571 ACTGCTAATT
Statistics
Matches: 255, Mismatches: 40, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
41 37 0.15
42 32 0.13
43 143 0.56
44 43 0.17
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:45211 original size:42 final size:40
Alignment explanation
Indices: 45162--45293 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 40
45152 TATATCAGTT
45162 TATAGCGGCATTTAAT-ATACAAACGCCACTAAAGTACGAGAA
1 TATAGCGGCATTT-ATCATA-AAA-GCCACTAAAGTACGAGAA
* * * * *
45204 TTTAGCGGCGTTTGTGCTTAAAAGCCACTAAAGTACGAGTA
1 TATAGCGGCATTTAT-CATAAAAGCCACTAAAGTACGAGAA
* * * *
45245 TATAGCGGCATTTGTACTTAAAATGTCACTAAAGTACGAGTA
1 TATAGCGGCATTTAT-CATAAAA-GCCACTAAAGTACGAGAA
45287 TATAGCG
1 TATAGCG
45294 ACGTTTGTAC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 38 0.49
42 38 0.49
43 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (40 bp):
TATAGCGGCATTTATCATAAAAGCCACTAAAGTACGAGAA
Found at i:45233 original size:41 final size:42
Alignment explanation
Indices: 45186--45321 Score: 177
Period size: 42 Copynumber: 3.3 Consensus size: 42
45176 ATATACAAAC
* * *
45186 GCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTAAAA-
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
*
45227 GCCACTAAAGTACGAGTATATAGCGGCATTTGTACTTAAAAT
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
* * * *
45269 GTCACTAAAGTACGAGTATATAGCGACGTTTGTAC-AAGAAAC
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTA-AAAT
45311 GCCACTAAAGT
1 GCCACTAAAGT
45322 TTAGTATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
41 38 0.46
42 45 0.54
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (42 bp):
GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
Found at i:46696 original size:19 final size:18
Alignment explanation
Indices: 46672--46720 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
46662 TTCGTATGAG
46672 AAATTATATAA-AATTAACT
1 AAATTATATAACAA-TAA-T
46691 AAATTATCATAACAATAAT
1 AAATTAT-ATAACAATAAT
46710 AATATTATATA
1 AA-ATTATATA
46721 TATATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 13 0.48
20 12 0.44
21 2 0.07
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTATATAACAATAAT
Found at i:47450 original size:106 final size:104
Alignment explanation
Indices: 47254--47455 Score: 271
Period size: 106 Copynumber: 1.9 Consensus size: 104
47244 TTATAGTATC
*
47254 ACATTTGGTCACTAAAAAAACTTACTGTGGCAACATTGATGGTCAAAAAATATACTTTTAGTATC
1 ACATTTGGTCACTAAAAAAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATC
* * * *
47319 AAATAAATTTATCACAATTTCTATTGATAATAATATCAA
66 AAATAAAATCATCACAAATTATATTGATAATAATATCAA
* * * * *
47358 ACATTTGGTCACTAAAAACATACTTAGTGTGACAATATTGATGGTCACAAAATATATTTTTAGTG
1 ACATTTGGTCACTAAAAA-A-ACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTA
*
47423 TCAAA-AAAGATCATCATAAATTATATTGATAAT
64 TCAAATAAA-ATCATCACAAATTATATTGATAAT
47456 TGTGTCGAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
104 18 0.21
105 4 0.05
106 62 0.74
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (104 bp):
ACATTTGGTCACTAAAAAAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATC
AAATAAAATCATCACAAATTATATTGATAATAATATCAA
Found at i:51524 original size:24 final size:21
Alignment explanation
Indices: 51497--51554 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
51487 ATGTGAAATA
51497 ATGAAAGTGATCACATGTGTGTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
51521 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
51543 ATGAAAAGTGAT
1 ATG-AAAGTGAT
51555 GAGAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:51792 original size:18 final size:20
Alignment explanation
Indices: 51747--51836 Score: 107
Period size: 18 Copynumber: 4.6 Consensus size: 20
51737 GTTCTTAAGG
51747 AGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGACA-AT-C
51769 AGTGGTCCTTCGGGAC-AT-
1 AGTGGTCCTTCGGGACAATC
* *
51787 AGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACAATC
*
51807 AGTGGTCCTTCGGGA-TAT-
1 AGTGGTCCTTCGGGACAATC
51825 AGTGGTCCTTCG
1 AGTGGTCCTTCG
51837 ACAAATATTC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
18 26 0.43
19 4 0.07
20 15 0.25
22 16 0.26
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAATC
Found at i:51817 original size:38 final size:40
Alignment explanation
Indices: 51747--51836 Score: 139
Period size: 38 Copynumber: 2.3 Consensus size: 40
51737 GTTCTTAAGG
*
51747 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
* *
51787 AGTGGTTCTTCGGAACA-AT-CAGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
51825 AGTGGTCCTTCG
1 AGTGGTCCTTCG
51837 ACAAATATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 29 0.63
39 2 0.04
40 15 0.33
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (40 bp):
AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
Found at i:56793 original size:21 final size:21
Alignment explanation
Indices: 56763--56807 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56753 TGCACGAGCG
*
56763 TACCACCATGCATCCTCAACA
1 TACCACCATGCATACTCAACA
* *
56784 TACCAGCATGCATATTCAACA
1 TACCACCATGCATACTCAACA
56805 TAC
1 TAC
56808 TTCAACATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.22
Consensus pattern (21 bp):
TACCACCATGCATACTCAACA
Found at i:61378 original size:10 final size:10
Alignment explanation
Indices: 61363--61391 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
61353 CAACATGCAT
61363 CTTCAACATA
1 CTTCAACATA
61373 CTTCAACATA
1 CTTCAACATA
61383 CTTCAACAT
1 CTTCAACAT
61392 TGGCGCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (10 bp):
CTTCAACATA
Found at i:65046 original size:128 final size:128
Alignment explanation
Indices: 64773--65015 Score: 400
Period size: 128 Copynumber: 1.9 Consensus size: 128
64763 GGGTGCACTT
* *
64773 TATATGCAATAATGTAATAATAAGTAAATCTTCGTTTTGAAGCTTCATGTTTTACTTCCTGAAGT
1 TATATGAAACAATGTAATAATAAGTAAATCTTCGTTTTGAAGCTTCATGTTTTACTTCCTGAAGT
* * **
64838 CTTTTCACAATTTGTGGAGTCTCATGCGTGTGTGGCTTGCAGTGTCGCTGTTGGGGTGCACTT
66 CTTTTCACAATTTGTGGAGTCTCATGCGTGTGTGGCTTGCAGTGTCGCTGTTGAGGTGAACGC
* *
64901 TATATGCAATAATGTAATAATAAGTAAATCTTCGTTTTGAAGCTTCATGTTTTACTTCCTGAAGT
1 TATATGAAACAATGTAATAATAAGTAAATCTTCGTTTTGAAGCTTCATGTTTTACTTCCTGAAGT
64966 CTTTTCACAATTTGTGGAGTC-CATGCGTGT-TGGCTTGCAGTGTCGCTGTT
66 CTTTTCACAATTTGTGGAGTCTCATGCGTGTGTGGCTTGCAGTGTCGCTGTT
65016 ATGTAAATAA
Statistics
Matches: 115, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
126 20 0.17
127 9 0.08
128 86 0.75
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (128 bp):
TATATGAAACAATGTAATAATAAGTAAATCTTCGTTTTGAAGCTTCATGTTTTACTTCCTGAAGT
CTTTTCACAATTTGTGGAGTCTCATGCGTGTGTGGCTTGCAGTGTCGCTGTTGAGGTGAACGC
Found at i:66751 original size:82 final size:81
Alignment explanation
Indices: 66646--66809 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 81
66636 AATGGATCAT
66646 TAAAATATTTAAAATAAAATAATTCTTAACCAATAAAATTAAAATAAAATCTCAAATAAATATGA
1 TAAAATATTTAAAATAAAATAATTCTTAACCAATAAAATTAAAATAAAATCTCAAATAAATATGA
66711 TCAATTGAAATTTAGG
66 TCAATTGAAATTTAGG
66727 TAAAATATTTAAAAATAAAATAATTCTTAACCAATAAAATTAAAATAAAATCTCAAATAAATATG
1 TAAAATATTT-AAAATAAAATAATTCTTAACCAATAAAATTAAAATAAAATCTCAAATAAATATG
66792 ATCAATTGAAATTTAGG
65 ATCAATTGAAATTTAGG
66809 T
1 T
66810 CAATCCCTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 10 0.12
82 72 0.88
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.32
Consensus pattern (81 bp):
TAAAATATTTAAAATAAAATAATTCTTAACCAATAAAATTAAAATAAAATCTCAAATAAATATGA
TCAATTGAAATTTAGG
Found at i:81920 original size:46 final size:46
Alignment explanation
Indices: 81820--81911 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
81810 ACAGGAAAGT
*
81820 GCATTCAAGTGAATGCTATAGACGATTGCACCATTGGAGAAGATAA
1 GCATTCAAGTAAATGCTATAGACGATTGCACCATTGGAGAAGATAA
81866 GCATTCAAGTAAATGCTATAGACGATTGCACCATTGGAGAAGATAA
1 GCATTCAAGTAAATGCTATAGACGATTGCACCATTGGAGAAGATAA
81912 TGGTTCAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (46 bp):
GCATTCAAGTAAATGCTATAGACGATTGCACCATTGGAGAAGATAA
Found at i:82633 original size:28 final size:28
Alignment explanation
Indices: 82601--82685 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
82591 GACACGTGGT
* *
82601 ACAATACGTGATATCAGTGATACATGAC
1 ACAATACGTGATACCAGTGACACATGAC
* *
82629 ACAATACGTGGTACCAGTGACACATGGC
1 ACAATACGTGATACCAGTGACACATGAC
* * * *
82657 ACGATACATGATACAAGTGACACGTGAC
1 ACAATACGTGATACCAGTGACACATGAC
82685 A
1 A
82686 TCATTAGATG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (28 bp):
ACAATACGTGATACCAGTGACACATGAC
Found at i:86677 original size:2 final size:2
Alignment explanation
Indices: 86670--86716 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
86660 GTTACTTGAC
*
86670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
86712 AT AT A
1 AT AT A
86717 ATTAAAGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:87075 original size:24 final size:23
Alignment explanation
Indices: 87030--87084 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
87020 AATTATTCTG
* **
87030 TTCATTTATATAAGACCATTTAGT
1 TTCA-TTATATAAAACCATTTAAC
87054 TTCATTATATAAAACCATTTTAAC
1 TTCATTATATAAAACCA-TTTAAC
87078 TTCATTA
1 TTCATTA
87085 GGTTCGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (23 bp):
TTCATTATATAAAACCATTTAAC
Found at i:89308 original size:79 final size:80
Alignment explanation
Indices: 89204--89362 Score: 295
Period size: 79 Copynumber: 2.0 Consensus size: 80
89194 AATGATTTTT
89204 TTTGTTTATATTTTTTATTCGGAACTTGTA-TAAAATATATAAGTAGTAAAGTGTAACACCCCCA
1 TTTGTTTATATTTTTTATTCGGAACTTGTATTAAAATATA-AAGTAGTAAAGTGTAACACCCCCA
89268 GACCGATGTAGGTGAC
65 GACCGATGTAGGTGAC
89284 TTTGTTTATA-TTTTTATTCGGAACTTGTATTAAAATATAAAGTAGTAAAGTGTAACACCCCCAG
1 TTTGTTTATATTTTTTATTCGGAACTTGTATTAAAATATAAAGTAGTAAAGTGTAACACCCCCAG
89348 ACCGATGTAGGTGAC
66 ACCGATGTAGGTGAC
89363 CGATCCGATC
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
79 59 0.76
80 19 0.24
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (80 bp):
TTTGTTTATATTTTTTATTCGGAACTTGTATTAAAATATAAAGTAGTAAAGTGTAACACCCCCAG
ACCGATGTAGGTGAC
Found at i:94000 original size:16 final size:16
Alignment explanation
Indices: 93979--94015 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
93969 GTCTCCAACG
93979 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
93995 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
94011 TTTAT
1 TTTAT
94016 ATCGTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:98420 original size:15 final size:16
Alignment explanation
Indices: 98400--98429 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
98390 TTCCCAGTAA
98400 TATTCCCT-GTAATCC
1 TATTCCCTAGTAATCC
98415 TATTCCCTAGTAATC
1 TATTCCCTAGTAATC
98430 TTTATTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (16 bp):
TATTCCCTAGTAATCC
Found at i:98611 original size:15 final size:16
Alignment explanation
Indices: 98588--98621 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
98578 TACAACACCC
*
98588 AATCTTATTCCCT-GT
1 AATCCTATTCCCTAGT
98603 AATCCTATTCCCTAGT
1 AATCCTATTCCCTAGT
98619 AAT
1 AAT
98622 TTTTATTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (16 bp):
AATCCTATTCCCTAGT
Found at i:100110 original size:29 final size:29
Alignment explanation
Indices: 100052--100226 Score: 198
Period size: 29 Copynumber: 6.1 Consensus size: 29
100042 CCCAATGATA
100052 TTTGGGAATTATTTTGAAAAA-GTGACAT
1 TTTGGGAATTATTTTGAAAAATGTGACAT
100080 TTTGGGAATTATTTTGAAAAATGTGACAT
1 TTTGGGAATTATTTTGAAAAATGTGACAT
*
100109 TTTGGGAATTATTTTG-AAAATGTAACAT
1 TTTGGGAATTATTTTGAAAAATGTGACAT
* *
100137 TTTGGAAATT-TTTTTAAAAATAGTGACAT
1 TTTGGGAATTATTTTGAAAAAT-GTGACAT
* * * *
100166 TCTAGTAATTATTTT-TAAAATGATGACAT
1 TTTGGGAATTATTTTGAAAAATG-TGACAT
* * *
100195 TTTGGG-ATTATTTTTAATAAAGGTGATAT
1 TTTGGGAATTATTTTGAA-AAATGTGACAT
100224 TTT
1 TTT
100227 TATAATTTTC
Statistics
Matches: 126, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
27 4 0.03
28 55 0.44
29 59 0.47
30 8 0.06
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (29 bp):
TTTGGGAATTATTTTGAAAAATGTGACAT
Found at i:100140 original size:57 final size:57
Alignment explanation
Indices: 100052--100226 Score: 219
Period size: 57 Copynumber: 3.1 Consensus size: 57
100042 CCCAATGATA
* *
100052 TTTGGGAATTATTTTGAAAAAGTGACATTTTGGGAATTATTTTGAAAAATGTGACAT
1 TTTGGGAATTATTTTGAAAATGTGACATTTTGGGAATTATTTTTAAAAATGTGACAT
* *
100109 TTTGGGAATTATTTTGAAAATGTAACATTTTGGAAATT-TTTTTAAAAATAGTGACAT
1 TTTGGGAATTATTTTGAAAATGTGACATTTTGGGAATTATTTTTAAAAAT-GTGACAT
* * * * * *
100166 TCTAGTAATTATTTTTAAAATGATGACATTTTGGG-ATTATTTTTAATAAAGGTGATAT
1 TTTGGGAATTATTTTGAAAATG-TGACATTTTGGGAATTATTTTTAA-AAATGTGACAT
100224 TTT
1 TTT
100227 TATAATTTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
56 10 0.10
57 63 0.62
58 25 0.25
59 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (57 bp):
TTTGGGAATTATTTTGAAAATGTGACATTTTGGGAATTATTTTTAAAAATGTGACAT
Found at i:105991 original size:10 final size:10
Alignment explanation
Indices: 105973--106002 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
105963 AATTTAGCTT
*
105973 ATTCGTGTTC
1 ATTCATGTTC
105983 ATTCATGTTC
1 ATTCATGTTC
105993 ATTCATGTTC
1 ATTCATGTTC
106003 GTTCGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (10 bp):
ATTCATGTTC
Found at i:106069 original size:25 final size:24
Alignment explanation
Indices: 106016--106069 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
106006 CGTTTAAATG
* *
106016 ATAAACAAACATAAATGAACGAAC
1 ATAAACAAACAAAAACGAACGAAC
* *
106040 GTAAACAAACAAAAAACGGACGAAC
1 ATAAACAAAC-AAAAACGAACGAAC
106065 ATAAA
1 ATAAA
106070 ATTAATTGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.63, C:0.17, G:0.11, T:0.09
Consensus pattern (24 bp):
ATAAACAAACAAAAACGAACGAAC
Found at i:106274 original size:14 final size:14
Alignment explanation
Indices: 106254--106309 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
106244 CATAAACGAT
106254 CATAAACAAATGAA
1 CATAAACAAATGAA
*
106268 TATAAACAAATGAA
1 CATAAACAAATGAA
*
106282 CATAAATGAAA-GAA
1 CATAAA-CAAATGAA
*
106296 CATAAACGAATGAA
1 CATAAACAAATGAA
106310 TTATCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 2 0.06
14 30 0.86
15 3 0.09
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (14 bp):
CATAAACAAATGAA
Found at i:113469 original size:20 final size:20
Alignment explanation
Indices: 113446--113657 Score: 62
Period size: 20 Copynumber: 10.5 Consensus size: 20
113436 ATAATTTCCG
113446 AATTTGCAACTCGAATTTAT
1 AATTTGCAACTCGAATTTAT
* * ** **
113466 AATTCGCAACAC-ATAAGTCG
1 AATTTGCAACTCGA-ATTTAT
* *
113486 AATTCGCAACTCGAATTTGAC
1 AATTTGCAACTCGAATTT-AT
* *
113507 ATTTTCGCAA-TACGAATTTCT
1 AATTT-GCAACT-CGAATTTAT
* *
113528 -TTTTCGCAACTCG-ATTTTT
1 AATTT-GCAACTCGAATTTAT
* * * *
113547 AAATTCGCAACACGAGTTTCT
1 -AATTTGCAACTCGAATTTAT
*
113568 -CTTTCGCAACTCGAATTTAT
1 AATTT-GCAACTCGAATTTAT
* *
113588 AATTCGCAACACGAATTTCAT
1 AATTTGCAACTCGAATTT-AT
* **
113609 --TTTCGCAACTCGATTTTCG
1 AATTT-GCAACTCGAATTTAT
* *
113628 AATTCGCAACGCGAATTTA-
1 AATTTGCAACTCGAATTTAT
113647 AATTTCGCAAC
1 AATTT-GCAAC
113658 ACAAATATTT
Statistics
Matches: 137, Mismatches: 39, Indels: 32
0.66 0.19 0.15
Matches are distributed among these distances:
19 14 0.10
20 94 0.69
21 18 0.13
22 11 0.08
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (20 bp):
AATTTGCAACTCGAATTTAT
Found at i:113477 original size:60 final size:60
Alignment explanation
Indices: 113385--113663 Score: 152
Period size: 60 Copynumber: 4.7 Consensus size: 60
113375 AAATAACCAA
* * *
113385 CGAATTCGTAACTC-AATTTCA-AATTCTCAACACGAAATCCAATTTCGCAACAT-AATTTC
1 CGAATTTGCAACTCGAATTT-ATAATTCGCAACACGAAATCCAATTTCGCAAC-TCAATTTC
*
113444 CGAATTTGCAACTCGAATTTATAATTCGCAACAC-ATAAGTCGAA-TTCGCAACTCGAATTT-
1 CGAATTTGCAACTCGAATTTATAATTCGCAACACGA-AA-TCCAATTTCGCAACTC-AATTTC
* ** * ** ** * * *
113504 -GACATTTTCGCAA-TACGAATTTCTTTTTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTC
1 CGA-A-TTT-GCAACT-CGAATTTATAATTCGCAACACGAAATCCAATTTCGCAACTC-AATTTC
* * * * *
113567 TC---TTTCGCAACTCGAATTTATAATTCGCAACACGAATTTCATTTTCGCAACTCGATTTT
1 -CGAATTT-GCAACTCGAATTTATAATTCGCAACACGAAATCCAATTTCGCAACTCAATTTC
* *
113626 CGAATTCGCAACGCGAATTTA-AATTTCGCAACAC-AAAT
1 CGAATTTGCAACTCGAATTTATAA-TTCGCAACACGAAAT
113664 ATTTAGGGTA
Statistics
Matches: 171, Mismatches: 29, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
58 1 0.01
59 25 0.15
60 90 0.53
61 19 0.11
62 35 0.20
63 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (60 bp):
CGAATTTGCAACTCGAATTTATAATTCGCAACACGAAATCCAATTTCGCAACTCAATTTC
Found at i:113567 original size:40 final size:40
Alignment explanation
Indices: 113510--113645 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 40
113500 ATTTGACATT
*
113510 TTCGCAATACGAATTTCTTTTTCGCAACTCGATTTTTAAA
1 TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTAAA
* * *
113550 TTCGCAACACGAGTTTCTCTTTCGCAACTCGA-ATTTATAA
1 TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTA-AA
* **
113590 TTCGCAACACGAATTTCATTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTAAA
*
113630 TTCGCAACGCGAATTT
1 TTCGCAACACGAATTT
113646 AAATTTCGCA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 77 0.93
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (40 bp):
TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTAAA
Found at i:113653 original size:40 final size:40
Alignment explanation
Indices: 113428--113657 Score: 180
Period size: 40 Copynumber: 5.7 Consensus size: 40
113418 GAAATCCAAT
* * *
113428 TTCGCAACA-TAATTTCCGAATTT-GCAACTCGAATTTATAA
1 TTCGCAACACGAATTT-C-AATTTCGCAACTCGATTTTAAAA
** * **
113468 TTCGCAACAC-ATAAGTCGAA-TTCGCAACTCGAATTTGACATT
1 TTCGCAACACGA-ATTTC-AATTTCGCAACTCG-ATTTTA-AAA
* ** *
113510 TTCGCAATACGAATTTCTTTTTCGCAACTCGATTTTTAAA
1 TTCGCAACACGAATTTCAATTTCGCAACTCGATTTTAAAA
* ** * *
113550 TTCGCAACACGAGTTTCTCTTTCGCAACTCGAATTTATAA
1 TTCGCAACACGAATTTCAATTTCGCAACTCGATTTTAAAA
* **
113590 TTCGCAACACGAATTTCATTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTCAATTTCGCAACTCGATTTTAAAA
* *
113630 TTCGCAACGCGAATTTAAATTTCGCAAC
1 TTCGCAACACGAATTTCAATTTCGCAAC
113658 ACAAATATTT
Statistics
Matches: 152, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
39 2 0.01
40 116 0.76
41 10 0.07
42 23 0.15
43 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (40 bp):
TTCGCAACACGAATTTCAATTTCGCAACTCGATTTTAAAA
Found at i:115639 original size:2 final size:2
Alignment explanation
Indices: 115632--115656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
115622 TATTGGGCGT
115632 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
115657 TAAACAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:115941 original size:42 final size:42
Alignment explanation
Indices: 115879--116068 Score: 262
Period size: 42 Copynumber: 4.6 Consensus size: 42
115869 CTCATCCTAC
115879 ACCTCGACACCGAGATCCATCACCTCATCGAGCCGATTCTCT
1 ACCTCGACACCGAGATCCATCACCTCATCGAGCCGATTCTCT
*
115921 ACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCTCT
1 ACCTCGACACCGAGATCCATCACCTCATCGAGCCGATTCTCT
** * **
115963 AATTCGACACCGAGATCCATCACCTTATCGAGCCGATTCTAA
1 ACCTCGACACCGAGATCCATCACCTCATCGAGCCGATTCTCT
* * *
116005 ACCTCAACACCGAGATTCATCACCTC-T--AGCCGACTCTAC-
1 ACCTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT-CT
116044 ACCTCGACACCGAGATCCATCACCT
1 ACCTCGACACCGAGATCCATCACCT
116069 ATTCCATCAC
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 32 0.24
41 1 0.01
42 100 0.75
ACGTcount: A:0.27, C:0.38, G:0.13, T:0.22
Consensus pattern (42 bp):
ACCTCGACACCGAGATCCATCACCTCATCGAGCCGATTCTCT
Found at i:115951 original size:24 final size:24
Alignment explanation
Indices: 115882--115951 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 24
115872 ATCCTACACC
115882 TCGACACCGAGATCCATCACCTCA
1 TCGACACCGAGATCCATCACCTCA
* *
115906 TCGA-GCC--GATTC-TCTA-CT--
1 TCGACACCGAGATCCATC-ACCTCA
115924 TCGACACCGAGATCCATCACCTCA
1 TCGACACCGAGATCCATCACCTCA
115948 TCGA
1 TCGA
115952 GCCGATTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 4 0.12
21 10 0.29
22 4 0.12
23 2 0.06
24 8 0.24
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (24 bp):
TCGACACCGAGATCCATCACCTCA
Found at i:116204 original size:21 final size:21
Alignment explanation
Indices: 116168--116337 Score: 173
Period size: 21 Copynumber: 8.1 Consensus size: 21
116158 ACCTCCATGG
*
116168 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* * *
116189 GATAAGGTATGTGCTTTATGT
1 GATGAGGTAGGTGCTTTACGT
* *
116210 GATGAGGTCGGTGCTTTACAT
1 GATGAGGTAGGTGCTTTACGT
** *
116231 GATGA-CAATGATGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
*
116252 GATGAGGCAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
116273 GGTGAGGTAAGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
**
116294 GATGA-CAATGGTGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
*
116315 GATGAGGTAGGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
116336 GA
1 GA
116338 GATTGTTTCA
Statistics
Matches: 118, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.01
21 115 0.97
22 2 0.02
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.34
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:116252 original size:63 final size:63
Alignment explanation
Indices: 116179--116337 Score: 228
Period size: 63 Copynumber: 2.5 Consensus size: 63
116169 ATGAGTTAGG
* * * **
116179 TGCTTTACGTGATAAGGTATGTGCTTTATGTGATGAGGTCGGTGCTTTACATGATGACAATGA
1 TGCTTTACGTGATGAGGTAGGTGCTTTACGTGATGAGGTAAGTGCTTTACATGATGACAATGA
* * * *
116242 TGCTTTACGTGATGAGGCAGGTGCTTTACGTGGTGAGGTAAGTGCTTTACGTGATGACAATGG
1 TGCTTTACGTGATGAGGTAGGTGCTTTACGTGATGAGGTAAGTGCTTTACATGATGACAATGA
*
116305 TGCTTTACGTGATGAGGTAGGTGCTCTACGTGA
1 TGCTTTACGTGATGAGGTAGGTGCTTTACGTGA
116338 GATTGTTTCA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 84 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (63 bp):
TGCTTTACGTGATGAGGTAGGTGCTTTACGTGATGAGGTAAGTGCTTTACATGATGACAATGA
Found at i:116745 original size:20 final size:21
Alignment explanation
Indices: 116709--116783 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 21
116699 ATTCAGGATT
* *
116709 CACCTCTCATAGTTCAAGAGAC
1 CACCTCCCATCGTTCAAGA-AC
*
116731 C-CCT-CCATCGTTCAAGATC
1 CACCTCCCATCGTTCAAGAAC
* *
116750 CACCTCCCATCGTTCAGGATC
1 CACCTCCCATCGTTCAAGAAC
*
116771 CACC-CGCATCGTT
1 CACCTCCCATCGTT
116784 TAGGATCCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 2 0.04
20 22 0.48
21 21 0.46
22 1 0.02
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.24
Consensus pattern (21 bp):
CACCTCCCATCGTTCAAGAAC
Found at i:116788 original size:20 final size:21
Alignment explanation
Indices: 116663--116793 Score: 108
Period size: 21 Copynumber: 6.3 Consensus size: 21
116653 GAAAAAGCCT
* *
116663 GATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* * **
116684 GTTCCACCTCCTATTATTCAG
1 GATCCACCTCCCATCGTTCAG
* * *
116705 GATTCACCTCTCATAGTTCAAG
1 GATCCACCTCCCATCGTTC-AG
*
116727 AGA-CC-CCT-CCATCGTTCAA
1 -GATCCACCTCCCATCGTTCAG
116746 GATCCACCTCCCATCGTTCAG
1 GATCCACCTCCCATCGTTCAG
* *
116767 GATCCACC-CGCATCGTTTAG
1 GATCCACCTCCCATCGTTCAG
116787 GATCCAC
1 GATCCAC
116794 ATTCATACTA
Statistics
Matches: 88, Mismatches: 17, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 27 0.31
21 51 0.58
22 3 0.03
23 2 0.02
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:120210 original size:34 final size:34
Alignment explanation
Indices: 120165--120231 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
120155 AATTGTGAAT
* * *
120165 TCGCAATTCGAAACTCAAATTTGCAACACGAAAA
1 TCGCAACTCGAAAATCAAATTCGCAACACGAAAA
* *
120199 TCGCAACTCGAAAATGAAATTCGCAACTCGAAA
1 TCGCAACTCGAAAATCAAATTCGCAACACGAAA
120232 TGGAGTTGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.19
Consensus pattern (34 bp):
TCGCAACTCGAAAATCAAATTCGCAACACGAAAA
Found at i:120222 original size:20 final size:20
Alignment explanation
Indices: 120194--120231 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
120184 TTTGCAACAC
120194 GAAAATCGCAACTCGAAAAT
1 GAAAATCGCAACTCGAAAAT
*
120214 GAAATTCGCAACTCGAAA
1 GAAAATCGCAACTCGAAA
120232 TGGAGTTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (20 bp):
GAAAATCGCAACTCGAAAAT
Found at i:120279 original size:20 final size:20
Alignment explanation
Indices: 120234--120363 Score: 156
Period size: 20 Copynumber: 6.6 Consensus size: 20
120224 ACTCGAAATG
**
120234 GAGTTGCGAATTC-AAATTC
1 GAGTTGCGAATTCGATTTTC
120253 GAGTTGCGAATTCGATTTTC
1 GAGTTGCGAATTCGATTTTC
*
120273 AAGTTGCGAATTCGATTTTC
1 GAGTTGCGAATTCGATTTTC
* * * *
120293 AAGTTGCGAATTTGAATATC
1 GAGTTGCGAATTCGATTTTC
* *
120313 GAGTTGCGAATTCAATTTTT
1 GAGTTGCGAATTCGATTTTC
*
120333 GAGTTGCGAATTTGATTTTC
1 GAGTTGCGAATTCGATTTTC
120353 GAGTTGC-AATT
1 GAGTTGCGAATT
120364 TGAGTTGCGA
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
19 17 0.18
20 78 0.82
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.39
Consensus pattern (20 bp):
GAGTTGCGAATTCGATTTTC
Found at i:120323 original size:60 final size:59
Alignment explanation
Indices: 120235--120366 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 59
120225 CTCGAAATGG
** *
120235 AGTTGCGAATTCAAATTCGAGTTGCGAATTCGATTTTCAAGTTGCGAATTCGATTTTCA
1 AGTTGCGAATTTGAATTCGAGTTGCGAATTCAATTTTCAAGTTGCGAATTCGATTTTCA
** * *
120294 AGTTGCGAATTTGAATATCGAGTTGCGAATTCAATTTTTGAGTTGCGAATTTGATTTTCG
1 AGTTGCGAATTTGAAT-TCGAGTTGCGAATTCAATTTTCAAGTTGCGAATTCGATTTTCA
120354 AGTTGC-AATTTGA
1 AGTTGCGAATTTGA
120367 GTTGCGAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 21 0.32
60 44 0.68
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (59 bp):
AGTTGCGAATTTGAATTCGAGTTGCGAATTCAATTTTCAAGTTGCGAATTCGATTTTCA
Found at i:123879 original size:16 final size:15
Alignment explanation
Indices: 123857--123895 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
123847 GAAATCATTG
123857 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
123873 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
123888 AAAAATTA
1 AAAAATTA
123896 GAGACGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:124059 original size:20 final size:21
Alignment explanation
Indices: 124033--124102 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 21
124023 AAACATTTGC
*
124033 GTTGCGAAATT-TAAATTCGCA
1 GTTGCGAAATTCTAAAATCG-A
124054 -TTGCG-AATTCTAAAATCGA
1 GTTGCGAAATTCTAAAATCGA
*
124073 GTTGCGAAA--C-AAAATTCGT
1 GTTGCGAAATTCTAAAA-TCGA
124092 GTTGCGAAATT
1 GTTGCGAAATT
124103 GAAACTTGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 17 0.41
21 2 0.05
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (21 bp):
GTTGCGAAATTCTAAAATCGA
Found at i:124160 original size:40 final size:40
Alignment explanation
Indices: 124073--124199 Score: 125
Period size: 40 Copynumber: 3.2 Consensus size: 40
124063 CTAAAATCGA
** * *
124073 GTTGCGAA--ACAAAATTCGTGTTGCGAAATTGAAACTTGC
1 GTTGCGAATTACAAAA-TCGTGTTGCGAAAAAGAAACTCGT
* * * *
124112 GTTACGAATTACAAAATCTTGTTGCGAAAAGGAAACTCAT
1 GTTGCGAATTACAAAATCGTGTTGCGAAAAAGAAACTCGT
* *
124152 GTTGCGAATTTA-AAAATCGAGTTGCGAAAAAGAAATTCGT
1 GTTGCGAA-TTACAAAATCGTGTTGCGAAAAAGAAACTCGT
124192 GTTGCGAA
1 GTTGCGAA
124200 ATTGTCAAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 7 0.10
40 56 0.78
41 9 0.12
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (40 bp):
GTTGCGAATTACAAAATCGTGTTGCGAAAAAGAAACTCGT
Found at i:124195 original size:20 final size:20
Alignment explanation
Indices: 124073--124200 Score: 66
Period size: 20 Copynumber: 6.5 Consensus size: 20
124063 CTAAAATCGA
*
124073 GTTGCGAAACA-AAATTCGT
1 GTTGCGAAAAAGAAATTCGT
** *
124092 GTTGCGAAATTGAAACTT-GC
1 GTTGCGAAAAAGAAA-TTCGT
* ** * * *
124112 GTTACGAATTACAAAATCTT
1 GTTGCGAAAAAGAAATTCGT
* * *
124132 GTTGCGAAAAGGAAACTCAT
1 GTTGCGAAAAAGAAATTCGT
* *
124152 GTTGCGAATTTAA-AAA-TCGA
1 GTTGCGAA--AAAGAAATTCGT
124172 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
124192 GTTGCGAAA
1 GTTGCGAAA
124201 TTGTCAAATT
Statistics
Matches: 79, Mismatches: 23, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
18 2 0.03
19 13 0.16
20 58 0.73
21 5 0.06
22 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (20 bp):
GTTGCGAAAAAGAAATTCGT
Found at i:124230 original size:20 final size:20
Alignment explanation
Indices: 124184--124244 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
124174 TGCGAAAAAG
* *
124184 AAATTCGTGTTGCGAAATTGTC
1 AAATTCGAGTTGC-AAATT-CC
124206 AAATTCGAGTTGCAAATTCC
1 AAATTCGAGTTGCAAATTCC
124226 AAATTCGAGTTGCAAATTC
1 AAATTCGAGTTGCAAATTC
124245 GTAAATTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 20 0.54
21 5 0.14
22 12 0.32
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (20 bp):
AAATTCGAGTTGCAAATTCC
Done.