Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167971.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_23, 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: 19268551
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 68000 characters in sequence are not A, C, G, or T
File 112 of 120
Found at i:16622225 original size:23 final size:23
Alignment explanation
Indices: 16622199--16622320 Score: 77
Period size: 23 Copynumber: 5.0 Consensus size: 23
16622189 CTTATAAGTA
16622199 ATATTATATTAATAAATAATATT
1 ATATTATATTAATAAATAATATT
* *
16622222 ATATTACAATATATGAGTAAACAATATT
1 ATATT---ATAT-T-AATAAATAATATT
* *
16622250 ATATTA-ATAAATAACATACTATT
1 ATATTATATTAATAA-ATAATATT
* *
16622273 AATATAATA-TATTAATAAATAATATT
1 -ATATTATATTAAT-A--AATAATATT
*
16622299 ATAATATATTAATAAATAATAT
1 ATATTATATTAATAAATAATAT
16622321 AAAGAATAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 24
0.67 0.12 0.22
Matches are distributed among these distances:
22 4 0.05
23 19 0.26
24 9 0.12
25 10 0.14
26 14 0.19
27 2 0.03
28 16 0.22
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATATTAATAAATAATATT
Found at i:16622304 original size:46 final size:47
Alignment explanation
Indices: 16622192--16622313 Score: 106
Period size: 49 Copynumber: 2.6 Consensus size: 47
16622182 AATTTTACTT
* *
16622192 ATAAGTAATATTAT-ATTAATAAATAATATTATATTACAATATATGA
1 ATAAATAATATTATAATAAATAAATAATATTATATTACAATATATGA
* * * * *
16622238 GTAAACAATATTATATTAATAAATAACATACTATTA-A-TATAATATATTA
1 ATAAATAATA-T-TA-TAATAAATAA-ATAATATTATATTACAATATATGA
* *
16622287 ATAAATAATATTATAATATATTAATAA
1 ATAAATAATATTATAATAAATAAATAA
16622314 ATAATATAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
45 3 0.05
46 15 0.25
47 3 0.05
48 3 0.05
49 19 0.32
50 8 0.14
51 8 0.14
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (47 bp):
ATAAATAATATTATAATAAATAAATAATATTATATTACAATATATGA
Found at i:16622335 original size:23 final size:24
Alignment explanation
Indices: 16622256--16622335 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 24
16622246 TATTATATTA
*
16622256 ATAAATAACATACTATTAATATAATAT
1 ATAAATAA-ATAATA-TAA-ATAATAT
* *
16622283 ATTAATAAATAATAT-TATAATAT
1 ATAAATAAATAATATAAATAATAT
* *
16622306 ATTAATAAATAATATAAAGAATA-
1 ATAAATAAATAATATAAATAATAT
16622329 ATAAATA
1 ATAAATA
16622336 GTTTTATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
23 28 0.61
24 5 0.11
25 1 0.02
26 5 0.11
27 7 0.15
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (24 bp):
ATAAATAAATAATATAAATAATAT
Found at i:16622390 original size:18 final size:18
Alignment explanation
Indices: 16622344--16622427 Score: 65
Period size: 18 Copynumber: 5.0 Consensus size: 18
16622334 TAGTTTTATT
*
16622344 TTAAGTATT-TTTT-ATA
1 TTAAATATTATTTTAATA
*
16622360 TTAACATAATATTTTAATA
1 TTAA-ATATTATTTTAATA
**
16622379 TTAAATATTATTAAAATA
1 TTAAATATTATTTTAATA
*
16622397 -TAATTATT-TTTTAATA
1 TTAAATATTATTTTAATA
16622413 TT-AATA--ATTTTAATA
1 TTAAATATTATTTTAATA
16622428 AATAAATAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
15 8 0.15
16 13 0.24
17 11 0.20
18 15 0.28
19 7 0.13
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TTAAATATTATTTTAATA
Found at i:16622417 original size:17 final size:17
Alignment explanation
Indices: 16622344--16622423 Score: 56
Period size: 17 Copynumber: 4.6 Consensus size: 17
16622334 TAGTTTTATT
*
16622344 TTAAGTATTTTTT-ATA
1 TTAATTATTTTTTAATA
* *
16622360 TTAACATAATATTTTAATA
1 TT-A-ATTATTTTTTAATA
* * *
16622379 TTAAATA-TTATTAAAA
1 TTAATTATTTTTTAATA
16622395 TATAATTATTTTTTAATA
1 T-TAATTATTTTTTAATA
*
16622413 TTAATAATTTT
1 TTAATTATTTT
16622424 AATAAATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
16 9 0.19
17 17 0.36
18 16 0.34
19 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
TTAATTATTTTTTAATA
Found at i:16624880 original size:29 final size:30
Alignment explanation
Indices: 16624847--16624911 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
16624837 TATTAAGAGT
*
16624847 TTATTTAAATATATATTAAAAAATAAT-AC
1 TTATTTAAATATAAATTAAAAAATAATAAC
* * *
16624876 TTATTTGAATATAAATTAAAGATTAATAAC
1 TTATTTAAATATAAATTAAAAAATAATAAC
16624906 TTATTT
1 TTATTT
16624912 CATGCAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TTATTTAAATATAAATTAAAAAATAATAAC
Found at i:16635125 original size:20 final size:20
Alignment explanation
Indices: 16635100--16635137 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16635090 AGACTGATAT
*
16635100 ATTTTTTATTTTTTTAATTA
1 ATTTTTTATTGTTTTAATTA
16635120 ATTTTTTATTGTTTTAAT
1 ATTTTTTATTGTTTTAAT
16635138 ATACATATAT
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:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
ATTTTTTATTGTTTTAATTA
Found at i:16641366 original size:12 final size:12
Alignment explanation
Indices: 16641349--16641374 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16641339 ATTTATTAAT
16641349 TTAAATTTTTTA
1 TTAAATTTTTTA
16641361 TTAAATTTTTTA
1 TTAAATTTTTTA
16641373 TT
1 TT
16641375 TATTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAAATTTTTTA
Found at i:16644149 original size:18 final size:18
Alignment explanation
Indices: 16644108--16644173 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
16644098 AAATTCGAAA
*
16644108 TTAATA-AAATATTATTT
1 TTAATATAAATATTAATT
*
16644125 TTAAATATAAATTTTAATT
1 TT-AATATAAATATTAATT
**
16644144 TTAATATAAATA-TAAAA
1 TTAATATAAATATTAATT
16644161 TTAA-ATAAATATT
1 TTAATATAAATATT
16644174 TAAATTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
16 7 0.17
17 10 0.24
18 13 0.32
19 11 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATATAAATATTAATT
Found at i:16644167 original size:12 final size:12
Alignment explanation
Indices: 16644124--16644191 Score: 66
Period size: 12 Copynumber: 5.7 Consensus size: 12
16644114 AAATATTATT
16644124 TTTAAATATAAA
1 TTTAAATATAAA
* * *
16644136 TTTTAATTTTAA
1 TTTAAATATAAA
*
16644148 TATAAATATAAA
1 TTTAAATATAAA
*
16644160 ATTAAATA-AATA
1 TTTAAATATAA-A
*
16644172 TTTAAATTTAAA
1 TTTAAATATAAA
16644184 TTTAAATA
1 TTTAAATA
16644192 GATAAATAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAATATAAA
Found at i:16644177 original size:18 final size:18
Alignment explanation
Indices: 16644131--16644184 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
16644121 ATTTTTAAAT
*
16644131 ATAAAT-TTTAATTTTAA
1 ATAAATATTTAAATTTAA
*
16644148 TATAAATA--TAAAATTAA
1 -ATAAATATTTAAATTTAA
16644165 ATAAATATTTAAATTTAA
1 ATAAATATTTAAATTTAA
16644183 AT
1 AT
16644185 TTAAATAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 16 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATATTTAAATTTAA
Found at i:16644201 original size:24 final size:24
Alignment explanation
Indices: 16644149--16644203 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
16644139 TAATTTTAAT
*
16644149 ATAAATATAAAATTAAATAAATAT
1 ATAAATATAAAATTAAATAAATAA
* * * *
16644173 TTAAATTTAAATTTAAATAGATAA
1 ATAAATATAAAATTAAATAAATAA
16644197 ATAAATA
1 ATAAATA
16644204 AATAATAATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAAATATAAAATTAAATAAATAA
Found at i:16644202 original size:36 final size:35
Alignment explanation
Indices: 16644131--16644207 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
16644121 ATTTTTAAAT
* *
16644131 ATAAAT-TTTAATTTTAATATAAATATAAAATTAA
1 ATAAATATTTAATTTAAATATAAATAGAAAATTAA
*
16644165 ATAAATATTTAAATTTAAATTTAAATAGATAAA-TAA
1 ATAAATATTT-AATTTAAATATAAATAGA-AAATTAA
16644201 ATAAATA
1 ATAAATA
16644208 ATAATTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 6 0.16
35 3 0.08
36 25 0.68
37 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (35 bp):
ATAAATATTTAATTTAAATATAAATAGAAAATTAA
Found at i:16644872 original size:23 final size:24
Alignment explanation
Indices: 16644846--16644899 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
16644836 CAAAATTATG
16644846 TCTTTTTTTTTTA-AATCTAAAAT
1 TCTTTTTTTTTTATAATCTAAAAT
** * *
16644869 TCTTACTTTTTTATATTTTAAAAT
1 TCTTTTTTTTTTATAATCTAAAAT
16644893 TACTTTT
1 T-CTTTT
16644900 ATGATTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 11 0.48
24 9 0.39
25 3 0.13
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (24 bp):
TCTTTTTTTTTTATAATCTAAAAT
Found at i:16646883 original size:85 final size:86
Alignment explanation
Indices: 16646720--16646883 Score: 226
Period size: 85 Copynumber: 1.9 Consensus size: 86
16646710 TAAAGCATGT
* * * *
16646720 TATATTATGTTAGGATATTAAACTTTGAATAGAAGTTAATTTACTATATATCACATATACACACT
1 TATATTATGTTAGGATATTAAACTTTGAACAGAAGTTAATTTACAATAAATCACATACACACACT
*
16646785 CTATTTGGATATAAGACGAGC
66 ATATTTGGATATAAGACGAGC
* *
16646806 TATATTATGTTA-GACTATT-AACTTTGAACATAATTTAATTTACCAATAAATCACATACACACA
1 TATATTATGTTAGGA-TATTAAACTTTGAACAGAAGTTAATTTA-CAATAAATCACATACACACA
16646869 -TATATTTGGATATAA
64 CTATATTTGGATATAA
16646884 AACTATATTA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 36 0.52
86 33 0.48
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (86 bp):
TATATTATGTTAGGATATTAAACTTTGAACAGAAGTTAATTTACAATAAATCACATACACACACT
ATATTTGGATATAAGACGAGC
Found at i:16656077 original size:148 final size:148
Alignment explanation
Indices: 16655899--16656193 Score: 590
Period size: 148 Copynumber: 2.0 Consensus size: 148
16655889 AAGAAGAGGG
16655899 AAGAGAAAGAGATTAATAATAAAATGTTGAGTATCAACCAAGATAGTGAACTAACATTGACAAAG
1 AAGAGAAAGAGATTAATAATAAAATGTTGAGTATCAACCAAGATAGTGAACTAACATTGACAAAG
16655964 GAACTAAACACAGCCCTTTTTTGTTTAGCTCTGTGCAATCATTCTTCCCATGATCAAAATTCATT
66 GAACTAAACACAGCCCTTTTTTGTTTAGCTCTGTGCAATCATTCTTCCCATGATCAAAATTCATT
16656029 TTGTTTCCTTCTTCCATT
131 TTGTTTCCTTCTTCCATT
16656047 AAGAGAAAGAGATTAATAATAAAATGTTGAGTATCAACCAAGATAGTGAACTAACATTGACAAAG
1 AAGAGAAAGAGATTAATAATAAAATGTTGAGTATCAACCAAGATAGTGAACTAACATTGACAAAG
16656112 GAACTAAACACAGCCCTTTTTTGTTTAGCTCTGTGCAATCATTCTTCCCATGATCAAAATTCATT
66 GAACTAAACACAGCCCTTTTTTGTTTAGCTCTGTGCAATCATTCTTCCCATGATCAAAATTCATT
16656177 TTGTTTCCTTCTTCCAT
131 TTGTTTCCTTCTTCCAT
16656194 CTGTATCTCT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 147 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (148 bp):
AAGAGAAAGAGATTAATAATAAAATGTTGAGTATCAACCAAGATAGTGAACTAACATTGACAAAG
GAACTAAACACAGCCCTTTTTTGTTTAGCTCTGTGCAATCATTCTTCCCATGATCAAAATTCATT
TTGTTTCCTTCTTCCATT
Found at i:16661316 original size:14 final size:13
Alignment explanation
Indices: 16661285--16661317 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
16661275 AATATACCAT
16661285 GAGAAAAAAAAAA
1 GAGAAAAAAAAAA
16661298 G-GAAATAAAAAAA
1 GAGAAA-AAAAAAA
16661311 GAGAAAA
1 GAGAAAA
16661318 TGTGGATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.22
13 10 0.56
14 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (13 bp):
GAGAAAAAAAAAA
Found at i:16661879 original size:2 final size:2
Alignment explanation
Indices: 16661872--16661896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16661862 GGTTTATCTT
16661872 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16661897 CATCTCCTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16666889 original size:35 final size:31
Alignment explanation
Indices: 16666849--16666922 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 31
16666839 TTTTTATTAA
16666849 AATAAATTTTAAAAATTAATAAATCAAATCAAATT
1 AATAAATTTT--AAATT--TAAATCAAATCAAATT
*
16666884 AATAAA-TTTAAATTTAAATCAAATCAATTT
1 AATAAATTTTAAATTTAAATCAAATCAAATT
16666914 AA-AAATTTT
1 AATAAATTTT
16666923 GATTGAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 3 0.08
30 20 0.54
32 5 0.14
34 3 0.08
35 6 0.16
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (31 bp):
AATAAATTTTAAATTTAAATCAAATCAAATT
Found at i:16666931 original size:29 final size:30
Alignment explanation
Indices: 16666869--16666931 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
16666859 AAAAATTAAT
*
16666869 AAATCAAATCAAATTAATAAATTTAAATTT
1 AAATCAAATCAAATTAATAAATTTAAATTG
* **
16666899 AAATCAAATCAATTTAA-AAATTTTGATTG
1 AAATCAAATCAAATTAATAAATTTAAATTG
16666928 AAAT
1 AAAT
16666932 TTAAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATCAAATCAAATTAATAAATTTAAATTG
Found at i:16667989 original size:9 final size:9
Alignment explanation
Indices: 16667975--16667999 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16667965 ATGAAATTTT
16667975 AATTTTATA
1 AATTTTATA
16667984 AATTTTATA
1 AATTTTATA
16667993 AATTTTA
1 AATTTTA
16668000 ATATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTATA
Found at i:16671150 original size:12 final size:12
Alignment explanation
Indices: 16671133--16671157 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16671123 TTTTCAGAGT
16671133 AAGAAAAGATAA
1 AAGAAAAGATAA
16671145 AAGAAAAGATAA
1 AAGAAAAGATAA
16671157 A
1 A
16671158 TGCCAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAGAAAAGATAA
Found at i:16682827 original size:21 final size:22
Alignment explanation
Indices: 16682799--16682847 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
16682789 ATAGTTAATA
* *
16682799 AAAT-ATTAAATTTTTAAT-TT
1 AAATAATTAAAATTTGAATCTT
16682819 AAATAATTAAAATTTGAATCTT
1 AAATAATTAAAATTTGAATCTT
16682841 -AATAATT
1 AAATAATT
16682848 TTAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATAATTAAAATTTGAATCTT
Found at i:16688475 original size:17 final size:17
Alignment explanation
Indices: 16688455--16688489 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16688445 AATATTGAAG
16688455 AAATAAATAAAACAAAA
1 AAATAAATAAAACAAAA
* *
16688472 AAATATATAATACAAAA
1 AAATAAATAAAACAAAA
16688489 A
1 A
16688490 GTTAATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAATAAAACAAAA
Found at i:16701575 original size:13 final size:13
Alignment explanation
Indices: 16701554--16701609 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
16701544 ATTAGGTATA
16701554 ATAAT-TTAAAAT
1 ATAATATTAAAAT
16701566 ATAATATTAAAAT
1 ATAATATTAAAAT
* **
16701579 ATGATACAAAAAT
1 ATAATATTAAAAT
*
16701592 AAAATA-TAAAA-
1 ATAATATTAAAAT
16701603 ATAATAT
1 ATAATAT
16701610 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 5 0.14
12 9 0.26
13 21 0.60
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (13 bp):
ATAATATTAAAAT
Found at i:16701721 original size:31 final size:31
Alignment explanation
Indices: 16701673--16701749 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
16701663 TACAATTAAT
*
16701673 TATAAA-ATAT-AATTTTTATATAAAATATGA
1 TATAAATATATAAATTTTAATAT-AAATATGA
**
16701703 TATAAATATATAAATTTTAATATTTATATGA
1 TATAAATATATAAATTTTAATATAAATATGA
*
16701734 TATAAATATACAAATT
1 TATAAATATATAAATT
16701750 ATTCAATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 6 0.15
31 25 0.61
32 10 0.24
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (31 bp):
TATAAATATATAAATTTTAATATAAATATGA
Found at i:16702032 original size:14 final size:15
Alignment explanation
Indices: 16702015--16702051 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
16702005 CTACTGCTTC
16702015 AATTTTACTGTTT-T
1 AATTTTACTGTTTGT
16702029 AA-TTTACTGTTTGT
1 AATTTTACTGTTTGT
*
16702043 ATTTTTACT
1 AATTTTACT
16702052 TTAGTCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 10 0.50
14 4 0.20
15 6 0.30
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (15 bp):
AATTTTACTGTTTGT
Found at i:16705011 original size:43 final size:42
Alignment explanation
Indices: 16704950--16705034 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
16704940 AGGCGTCCAC
* *
16704950 GTGAATAAAGTGTCGCTATTTGTTTGATTGATTGACGTGAAAG
1 GTGAATAAAGTGTCGCTATTTGTTCGATCGA-TGACGTGAAAG
16704993 GTGAATAAAGTGTCGCTATTTGTTCGATCGATGACGTGAAAG
1 GTGAATAAAGTGTCGCTATTTGTTCGATCGATGACGTGAAAG
16705035 ATAAGATTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 11 0.28
43 29 0.73
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.34
Consensus pattern (42 bp):
GTGAATAAAGTGTCGCTATTTGTTCGATCGATGACGTGAAAG
Found at i:16713589 original size:16 final size:17
Alignment explanation
Indices: 16713568--16713600 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
16713558 ATGATTGATT
16713568 TTCAATAATA-TATTAA
1 TTCAATAATATTATTAA
16713584 TTCAATAATATTATTAA
1 TTCAATAATATTATTAA
16713601 AATTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCAATAATATTATTAA
Found at i:16714147 original size:13 final size:14
Alignment explanation
Indices: 16714122--16714150 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16714112 TTAATTCAAT
16714122 TAAATTAATCAAAA
1 TAAATTAATCAAAA
16714136 TAAATTAA-CAAAA
1 TAAATTAATCAAAA
16714149 TA
1 TA
16714151 CATATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAATTAATCAAAA
Found at i:16714372 original size:40 final size:41
Alignment explanation
Indices: 16714328--16714407 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
16714318 TTCATAACTT
*
16714328 TTTAAGTATGAATTTAAAATAT-TATT-ATATTAAAAAATTA
1 TTTAAGTATAAATTTAAAATATAT-TTAATATTAAAAAATTA
* * *
16714368 TTTAATTTTAAATTTAAAATATATTTAATATTATAAAATT
1 TTTAAGTATAAATTTAAAATATATTTAATATTAAAAAATT
16714408 TTAACATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 21 0.62
41 13 0.38
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (41 bp):
TTTAAGTATAAATTTAAAATATATTTAATATTAAAAAATTA
Found at i:16715669 original size:15 final size:15
Alignment explanation
Indices: 16715649--16715678 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16715639 ATATGTATAA
16715649 TTAATTATTAAAAAT
1 TTAATTATTAAAAAT
*
16715664 TTAATTTTTAAAAAT
1 TTAATTATTAAAAAT
16715679 AAAAAGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTATTAAAAAT
Found at i:16718986 original size:68 final size:68
Alignment explanation
Indices: 16718877--16719013 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
16718867 AGAAATAGAA
16718877 GTTGTGATGCAAAAAAATTGCCTACTTTTACGGGGCTTTCTTTCGGTTTTGTGTATTAGAGGAAA
1 GTTGTGATGCAAAAAAATTGCCTACTTTTACGGGGCTTTCTTTCGGTTTTGTGTATTAGAGGAAA
16718942 GAG
66 GAG
16718945 GTTGTGATGCAAAAAAATTGCCTACTTTTACGGGGCTTTCTTTCGGTTTTGTGTATTAGAGGAAA
1 GTTGTGATGCAAAAAAATTGCCTACTTTTACGGGGCTTTCTTTCGGTTTTGTGTATTAGAGGAAA
16719010 GAG
66 GAG
16719013 G
1 G
16719014 CTTGAGCCTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (68 bp):
GTTGTGATGCAAAAAAATTGCCTACTTTTACGGGGCTTTCTTTCGGTTTTGTGTATTAGAGGAAA
GAG
Found at i:16721722 original size:18 final size:18
Alignment explanation
Indices: 16721670--16721729 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
16721660 ATATGATAAA
*
16721670 ATATATTAA-TTAATTATT
1 ATAT-TTAATTTAATTTTT
*
16721688 A-ATTTACTCTTAA-TTTT
1 ATATTTAAT-TTAATTTTT
16721705 ATATTTAATTTAATTTTT
1 ATATTTAATTTAATTTTT
*
16721723 TTATTTA
1 ATATTTA
16721730 TTTCGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 21 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTAATTTAATTTTT
Found at i:16721732 original size:17 final size:17
Alignment explanation
Indices: 16721670--16721721 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
16721660 ATATGATAAA
16721670 ATATATTAA-TTAATTATT
1 ATAT-TTAATTTAATT-TT
*
16721688 A-ATTTACTCTTAATTTT
1 ATATTTAAT-TTAATTTT
16721705 ATATTTAATTTAATTTT
1 ATATTTAATTTAATTTT
16721722 TTTATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 3 0.10
17 13 0.45
18 13 0.45
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTAATTTAATTTT
Found at i:16722376 original size:15 final size:14
Alignment explanation
Indices: 16722356--16722395 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
16722346 ATATTTTAAA
16722356 AATATATTAAAAATT
1 AATATATTAAAAA-T
*
16722371 AATATAATAAAAAT
1 AATATATTAAAAAT
16722385 ACATATATTAA
1 A-ATATATTAA
16722396 TTTTTTAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATATTAAAAAT
Found at i:16722776 original size:24 final size:23
Alignment explanation
Indices: 16722749--16722793 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
16722739 ATTTTCATTA
16722749 TATAATAACTATTATAA-AAAATTT
1 TATAATAAC-ATT-TAATAAAATTT
16722773 TATAATAACATTTAATAAAAT
1 TATAATAACATTTAATAAAAT
16722794 ATTAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
TATAATAACATTTAATAAAATTT
Found at i:16726938 original size:9 final size:9
Alignment explanation
Indices: 16726916--16726968 Score: 61
Period size: 10 Copynumber: 5.4 Consensus size: 9
16726906 TCGATAAATA
*
16726916 AAATCTAATC
1 AAAT-TAATT
16726926 AAATTAATT
1 AAATTAATT
16726935 AAATTAATT
1 AAATTAATT
16726944 AAATTTAATT
1 AAA-TTAATT
16726954 AAATTTAAATT
1 AAA-TT-AATT
16726965 AAAT
1 AAAT
16726969 AAAAATTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
9 16 0.40
10 17 0.43
11 7 0.17
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:16726953 original size:10 final size:10
Alignment explanation
Indices: 16726916--16726968 Score: 65
Period size: 9 Copynumber: 5.4 Consensus size: 10
16726906 TCGATAAATA
* *
16726916 AAATCTAATC
1 AAATTTAATT
16726926 AAA-TTAATT
1 AAATTTAATT
16726935 AAA-TTAATT
1 AAATTTAATT
16726944 AAATTTAATT
1 AAATTTAATT
16726954 AAATTTAAATT
1 AAATTT-AATT
16726965 AAAT
1 AAAT
16726969 AAAAATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
9 16 0.41
10 15 0.38
11 8 0.21
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (10 bp):
AAATTTAATT
Found at i:16726971 original size:4 final size:5
Alignment explanation
Indices: 16726926--16726968 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
16726916 AAATCTAATC
*
16726926 AAATT -AATT AAATT -AATT AAATT TAATT AAATTT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAA-TT AAATT AAAT
16726969 AAAAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
AAATT
Found at i:16726985 original size:27 final size:27
Alignment explanation
Indices: 16726944--16726995 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
16726934 TAAATTAATT
*
16726944 AAATTTAATTAAATTTAAATTAAATAA
1 AAATTTAATTAAATTTAAATCAAATAA
*
16726971 AAATTTAA-TATAATTTGAATCAAAT
1 AAATTTAATTA-AATTTAAATCAAAT
16726996 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATTTAATTAAATTTAAATCAAATAA
Found at i:16727964 original size:29 final size:30
Alignment explanation
Indices: 16727913--16727970 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
16727903 AAATTAAAAC
**
16727913 AAAATATTAAAAATTTACTTAATT-TTGAT
1 AAAATATTAAAAATTTAAATAATTATTGAT
16727942 AAAATATTAAAAATTTAAATAATTATTGA
1 AAAATATTAAAAATTTAAATAATTATTGA
16727971 ATTATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATATTAAAAATTTAAATAATTATTGAT
Found at i:16729023 original size:2 final size:2
Alignment explanation
Indices: 16729016--16729042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16729006 AATAAAGTTA
16729016 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16729043 AATTGGTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16732062 original size:89 final size:89
Alignment explanation
Indices: 16731911--16732088 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
16731901 TAACATTTTA
16731911 GGGAGGCATCTGATATTTTGTTTCTAAAGAGAGAAATGGGATATTCGTAGTTGTAGGAACAAGCA
1 GGGAGGCATCTGATATTTTGTTTCTAAAGAGAGAAATGGGATATTCGTAGTTGTAGGAACAAGCA
16731976 ATGCAAGAATGATCAGGTGGGCTT
66 ATGCAAGAATGATCAGGTGGGCTT
16732000 GGGAGGCATCTGATATTTTGTTTCTAAAGAGAGAAATGGGATATTCGTAGTTGTAGGAACAAGCA
1 GGGAGGCATCTGATATTTTGTTTCTAAAGAGAGAAATGGGATATTCGTAGTTGTAGGAACAAGCA
16732065 ATGCAAGAATGATCAGGTGGGCTT
66 ATGCAAGAATGATCAGGTGGGCTT
16732089 CCTGCATGGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.28
Consensus pattern (89 bp):
GGGAGGCATCTGATATTTTGTTTCTAAAGAGAGAAATGGGATATTCGTAGTTGTAGGAACAAGCA
ATGCAAGAATGATCAGGTGGGCTT
Found at i:16734198 original size:2 final size:2
Alignment explanation
Indices: 16734191--16734225 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16734181 TTACACAAAA
16734191 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16734226 TACTCGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16735265 original size:33 final size:33
Alignment explanation
Indices: 16735227--16735324 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
16735217 TTTCTGCGAC
* *
16735227 CGCCATCACTTCCGTCGTCGGAGCTGCCACCAT
1 CGCCATCACTTCCGTGGTCGCAGCTGCCACCAT
* *
16735260 TGCCATTACTTCCGTGGTCGCAGCTGCCACCAT
1 CGCCATCACTTCCGTGGTCGCAGCTGCCACCAT
*
16735293 CGCCATCACTTCCGTGGCCGCAGCTGCCACCA
1 CGCCATCACTTCCGTGGTCGCAGCTGCCACCA
16735325 CCACCGTCGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.15, C:0.42, G:0.21, T:0.21
Consensus pattern (33 bp):
CGCCATCACTTCCGTGGTCGCAGCTGCCACCAT
Found at i:16737026 original size:22 final size:22
Alignment explanation
Indices: 16736981--16737022 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16736971 AAACAAAAAT
16736981 TTAAAATAAAATTTATATTTTA
1 TTAAAATAAAATTTATATTTTA
*
16737003 TTAAATTAAAATTT-TATTTT
1 TTAAAATAAAATTTATATTTT
16737023 TATTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAAATAAAATTTATATTTTA
Found at i:16737103 original size:19 final size:20
Alignment explanation
Indices: 16737081--16737130 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
16737071 TAATATTTTT
*
16737081 TTAAATTTTATTATATA-AA
1 TTAAATTTTATTAAATAGAA
* * *
16737100 TTAAGTTTGA-TAAATAGAT
1 TTAAATTTTATTAAATAGAA
16737119 TTAAATTTTATT
1 TTAAATTTTATT
16737131 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (20 bp):
TTAAATTTTATTAAATAGAA
Found at i:16747323 original size:9 final size:9
Alignment explanation
Indices: 16747309--16747335 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
16747299 TCAAGCAAAT
16747309 GAATGAGAA
1 GAATGAGAA
16747318 GAATGAGAA
1 GAATGAGAA
16747327 GAATGAGAA
1 GAATGAGAA
16747336 AAGTCTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (9 bp):
GAATGAGAA
Found at i:16749073 original size:2 final size:2
Alignment explanation
Indices: 16749066--16749090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16749056 ATGCACGTAT
16749066 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
16749091 TATATATATA
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:16752786 original size:22 final size:23
Alignment explanation
Indices: 16752729--16752786 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
16752719 ATTTTACAAA
* *
16752729 AAATACTT-CATAAATATGAATT
1 AAATATTTACATATATATGAATT
16752751 AAATATTTACATATATAT-AATT
1 AAATATTTACATATATATGAATT
*
16752773 AATTA-TTACA-ATAT
1 AAATATTTACATATAT
16752787 TTTGATATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 5 0.16
22 15 0.47
23 8 0.25
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (23 bp):
AAATATTTACATATATATGAATT
Found at i:16768453 original size:28 final size:28
Alignment explanation
Indices: 16768370--16768440 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
16768360 AGCTGTTCAG
16768370 AAAAAGATCAAACAATTTGGTAAAGAAA
1 AAAAAGATCAAACAATTTGGTAAAGAAA
16768398 AAAAAGATCAAACAATTTGGTAAAGAAA
1 AAAAAGATCAAACAATTTGGTAAAGAAA
16768426 AAAAAGATCAAACAA
1 AAAAAGATCAAACAA
16768441 AGTTGAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.15
Consensus pattern (28 bp):
AAAAAGATCAAACAATTTGGTAAAGAAA
Found at i:16780708 original size:3 final size:3
Alignment explanation
Indices: 16780700--16780724 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16780690 ACATATATTT
16780700 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
16780725 TTGTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:16781569 original size:25 final size:25
Alignment explanation
Indices: 16781514--16781571 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
16781504 CAATAATTAA
*
16781514 CAAAAGAAGCTTTACAAATTTAATGG
1 CAAAA-AAGCTTTACAAAATTAATGG
* *
16781540 GAAAAAAGC-TTACAAAATTATTGG
1 CAAAAAAGCTTTACAAAATTAATGG
16781564 CCAAAAAA
1 -CAAAAAA
16781572 TTATATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 13 0.48
25 10 0.37
26 4 0.15
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (25 bp):
CAAAAAAGCTTTACAAAATTAATGG
Found at i:16782791 original size:2 final size:2
Alignment explanation
Indices: 16782784--16782822 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16782774 TGGATCTAAT
16782784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16782823 GAGAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16783187 original size:29 final size:29
Alignment explanation
Indices: 16783154--16783210 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
16783144 ATATAAATAT
16783154 CTCAAGTGTTTTGCTTTTAATGCTTCTAC
1 CTCAAGTGTTTTGCTTTTAATGCTTCTAC
16783183 CTCAAGTGTTTTGCTTTTAATGCTTCTA
1 CTCAAGTGTTTTGCTTTTAATGCTTCTA
16783211 TCTAATTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (29 bp):
CTCAAGTGTTTTGCTTTTAATGCTTCTAC
Found at i:16790319 original size:14 final size:15
Alignment explanation
Indices: 16790300--16790328 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16790290 AAACTATAAT
16790300 CAAAC-AAATTTAAA
1 CAAACAAAATTTAAA
16790314 CAAACAAAATTTAAA
1 CAAACAAAATTTAAA
16790329 TGAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.21
Consensus pattern (15 bp):
CAAACAAAATTTAAA
Found at i:16790455 original size:11 final size:11
Alignment explanation
Indices: 16790439--16790465 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16790429 TAAACGAACG
16790439 AATTTTAAATA
1 AATTTTAAATA
16790450 AATTTTAAATA
1 AATTTTAAATA
16790461 AATTT
1 AATTT
16790466 ATTCATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTTTAAATA
Found at i:16790790 original size:27 final size:27
Alignment explanation
Indices: 16790760--16790813 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
16790750 TATATTATAA
16790760 ATAAGTTTCATATTA-ATTAATAAATTT
1 ATAAGTTTCATATTACATT-ATAAATTT
* *
16790787 ATAATTTTGATATTACATTATAAATTT
1 ATAAGTTTCATATTACATTATAAATTT
16790814 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (27 bp):
ATAAGTTTCATATTACATTATAAATTT
Found at i:16795306 original size:2 final size:2
Alignment explanation
Indices: 16795290--16795322 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
16795280 AATGTATTTA
*
16795290 AT AT AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16795323 CTAACATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16799474 original size:199 final size:200
Alignment explanation
Indices: 16799049--16799860 Score: 929
Period size: 199 Copynumber: 4.0 Consensus size: 200
16799039 TCACTCGTGC
* * * *
16799049 AAAAGAACTAATCTGTCAATTGAATTTAGGCGTGATTTTGGAGAATTTTCCGTACTTGTGTGGAT
1 AAAAGAACTAATCTGTCAACTGAGTTTAGGCGTGACTTTGGAGAATTTTCTGTACTTGTGTGGAT
* * * * * * *
16799114 GGAATTTGAAGCTAATTTTTTTCAGAATTAAACATTTATGAGTTACGAATCTAACAAAAAAATTT
66 GGAATTTAAAGCTAATTTTTTTCAAAATTAAAGATCTATGAGTTAGGATTCTAA-AAAAAAA-AT
* * * * *
16799179 TGGCTCAAAACAAGCTAAAATTCATCGAGAACTGATCCAAAAACCACAAAGAGGTCAAAATCGTA
129 TGGCTCAAAACAAGTTAGAATTCATCAAGAACTGATCCAAAAACCACAAAGAGATCAAAATCGTG
16799244 AATTTCA
194 AATTTCA
* * * *
16799251 AAAAGAGCTAATCTGTCAACTGAGTTTAGGCTTGACTTTGGAGAATTTTTTATACTTGTGTGGAT
1 AAAAGAACTAATCTGTCAACTGAGTTTAGGCGTGACTTTGGAGAATTTTCTGTACTTGTGTGGAT
* * * *
16799316 GAAATTTGAAGTTAA-TTTTCT-AATAATTAAAGATCTATGAGTTAGGATTCTAATAAAAAAAAT
66 GGAATTTAAAGCTAATTTTTTTCAA-AATTAAAGATCTATGAGTTAGGATTCTAA-AAAAAAAAT
* * *
16799379 TGGCT-AAAATAAGTTAGAATTCATCAATAATTGATCCAAAAACCACAAAGAGATCAAAA-CTGT
129 TGGCTCAAAACAAGTTAGAATTCATCAAGAACTGATCCAAAAACCACAAAGAGATCAAAATC-GT
16799442 GAATTTCA
193 GAATTTCA
* * * *
16799450 AAAAGAATTAATCTGTCAACTGAGTTTAGGCATGACTTT-GAAAATTTTTCTGTACTTGTGTGAA
1 AAAAGAACTAATCTGTCAACTGAGTTTAGGCGTGACTTTGGAGAA-TTTTCTGTACTTGTGTGGA
16799514 TGGAATTTAAAGCTAATTTTTTTTTCAAAATTAAAGATCTATGAGTTAGGATTCTAACAAAAAAA
65 TGGAATTTAAAGCTAA--TTTTTTTCAAAATTAAAGATCTATGAGTTAGGATTCT-A-AAAAAAA
* * *
16799579 AATTTGGCTGAAAACAAATTAGAATTCATCAAGAACTGATCCAAAAACCACAAAGAGATCAAATT
126 AA-TTGGCTCAAAACAAGTTAGAATTCATCAAGAACTGATCCAAAAACCACAAAGAGATCAAAAT
* *
16799644 CGCGAATAT-A
190 CGTGAATTTCA
* * * * * *
16799654 AAAAAAATCCTAATCCGTCAACTAAGTTTGGGCGTGAGTTTGGAGAGTTTTCTGTACTTGTGTGG
1 AAAAGAA--CTAATCTGTCAACTGAGTTTAGGCGTGACTTTGGAGAATTTTCTGTACTTGTGTGG
* * *
16799719 ATGTAATTTAAAGCTAATTTTTTTCAAAATTAAAGATTTATGAGTTAAGAATT-TAGCAAAAAAA
64 ATGGAATTTAAAGCTAATTTTTTTCAAAATTAAAGATCTATGAGTT-AGGATTCTA--AAAAAAA
* * * * ** * *
16799783 AATTGGCTCAAAACATGCTT-GAATTCATTAAGAATTAATCCAAAAATTATAAAGAGGTCAAAAT
126 AATTGGCTCAAAACAAG-TTAGAATTCATCAAGAACTGATCCAAAAACCACAAAGAGATCAAAAT
*
16799847 CATGAATTTCA
190 CGTGAATTTCA
16799858 AAA
1 AAA
16799861 CAAATTTGAA
Statistics
Matches: 520, Mismatches: 71, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
198 5 0.01
199 121 0.23
200 7 0.01
201 37 0.07
202 102 0.20
203 66 0.13
204 59 0.11
205 60 0.12
206 60 0.12
207 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (200 bp):
AAAAGAACTAATCTGTCAACTGAGTTTAGGCGTGACTTTGGAGAATTTTCTGTACTTGTGTGGAT
GGAATTTAAAGCTAATTTTTTTCAAAATTAAAGATCTATGAGTTAGGATTCTAAAAAAAAAATTG
GCTCAAAACAAGTTAGAATTCATCAAGAACTGATCCAAAAACCACAAAGAGATCAAAATCGTGAA
TTTCA
Found at i:16800993 original size:58 final size:55
Alignment explanation
Indices: 16800856--16800994 Score: 165
Period size: 58 Copynumber: 2.5 Consensus size: 55
16800846 ATTTTTTTAT
* *
16800856 GAAGAGATTATTCAATGTATTTTCT-GTAAAATAATCTTTAATAATAAAAAAAATG
1 GAAGAGATTATTCAATGCATTTT-TGGTAAAAAAATCTTTAATAATAAAAAAAATG
* * *
16800911 AAAGGGAATTATTCAA-GACGTTTTTGGGTAAAAAAATCTTTAATAATACAAAAAAATG
1 GAAGAG-ATTATTCAATG-CATTTTT-GGTAAAAAAATCTTTAATAATA-AAAAAAATG
16800969 GAAGAAGATTATTCAATGCATTTTTG
1 GAAG-AGATTATTCAATGCATTTTTG
16800995 ACCAAAAATG
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
55 6 0.09
56 13 0.19
57 21 0.30
58 27 0.39
59 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.34
Consensus pattern (55 bp):
GAAGAGATTATTCAATGCATTTTTGGTAAAAAAATCTTTAATAATAAAAAAAATG
Found at i:16801002 original size:57 final size:53
Alignment explanation
Indices: 16800856--16801015 Score: 151
Period size: 58 Copynumber: 2.8 Consensus size: 53
16800846 ATTTTTTTAT
* *
16800856 GAAGAGATTATTCAATGTATTTTCTGTAAAATAATCTTTAATAATAAAAAAAATG
1 GAAGAGATTATTCAATGCATTTT-TG-AAAAAAATCTTTAATAATAAAAAAAATG
* * *
16800911 AAAGGGAATTATTCAA-GACGTTTTTGGGTAAAAAAATCTTTAATAATACAAAAAAATG
1 GAAGAG-ATTATTCAATG-CATTTTT--G-AAAAAAATCTTTAATAATA-AAAAAAATG
*
16800969 GAAGAAGATTATTCAATGCATTTTTGACCAAAAATGCTTTGAATAAT
1 GAAG-AGATTATTCAATGCATTTTTGA-AAAAAAT-CTTT-AATAAT
16801016 CTTTAAAAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
55 7 0.08
56 20 0.23
57 24 0.28
58 33 0.38
59 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (53 bp):
GAAGAGATTATTCAATGCATTTTTGAAAAAAATCTTTAATAATAAAAAAAATG
Found at i:16801114 original size:61 final size:61
Alignment explanation
Indices: 16801007--16801125 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 61
16800997 CAAAAATGCT
** * * *
16801007 TTGAATAATCTTTAAAAAAAATTGAAGGGGATCAGTGAATGTGTTTTTAGCTAAAAACATC
1 TTGAATAATCCCTAAAAAAAATCGAAGGGGATCAGTGAAGGCGTTTTTAGCTAAAAACATC
* * * * *
16801068 TTGAATAATCCCTAAAAAAAATCGAAGGGGATTATTTAAGGCGTTTTTGGTTAAAAAC
1 TTGAATAATCCCTAAAAAAAATCGAAGGGGATCAGTGAAGGCGTTTTTAGCTAAAAAC
16801126 GCCTTAAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.32
Consensus pattern (61 bp):
TTGAATAATCCCTAAAAAAAATCGAAGGGGATCAGTGAAGGCGTTTTTAGCTAAAAACATC
Found at i:16801292 original size:184 final size:182
Alignment explanation
Indices: 16801059--16801504 Score: 429
Period size: 184 Copynumber: 2.4 Consensus size: 182
16801049 GTTTTTAGCT
* * * * * *
16801059 AAAAACATCTTGAATAATCCCTAAAAAAAATCGAAGGGGATTATTTAAGGCGTTTTTGGTTAAAA
1 AAAAACGTCTTAAATAAT--CTTAAAAAAAT-GAA-GAGATTATTTAAGGCATTTTTGGCTAAAA
* * * * * *
16801124 ACGCCTTAAATAACCTAATTTAATTTTTTGTAAGAGAATATTCAAGGCATTTTCTAG-CCAAAAA
62 ACGCCTTGAATAACCCAATTCAATTTCTTGTAAAAGAATATTCAAGGCATTTT-TAGACAAAAAA
* * * *
16801188 TGTCTTGAATAATCT-CAAAAAAAAGG-AAGAAGATTATTAAAGGTGTTTTTTTTTGTAAA
126 CGCCTTAAATAATCTCCAAAAAAAAGGAAAG-AGATTATTAAAGGTG---TTTTTGGTAAA
* * * *
16801247 AAAATAC-T-TTCAATAATTCTT-AAAAAATGAAGCAGATTATTTAAGGTATTTTTTGCTAGAAA
1 AAAA-ACGTCTTAAATAA-TCTTAAAAAAATGAAG-AGATTATTTAAGGCATTTTTGGCTAAAAA
* * * ** * *
16801309 CGCCTTGAATAACCCGATTCAATTTCTTGTAAAAGATTATTTAAGTTATTTTTTGATAAAAAACG
63 CGCCTTGAATAACCCAATTCAATTTCTTGTAAAAGAATATTCAAGGCATTTTTAGACAAAAAACG
* * *
16801374 CCTTAAATAATCTCCAAAAAAATGGAAAGGGATTATTTAAGGTGTTTTTGGTAAA
128 CCTTAAATAATCTCCAAAAAAAAGGAAAGAGATTATTAAAGGTGTTTTTGGTAAA
*
16801429 AAAAACGTCTTAAATAATCTTAAAAAAAGTTGAAAGAGATTATTGAAGGCATTTTTGGCT-AAAA
1 AAAAACGTCTTAAATAATCTTAAAAAAA--TG-AAGAGATTATTTAAGGCATTTTTGGCTAAAAA
16801493 CGCCTTGAATAA
63 CGCCTTGAATAA
16801505 TAATAAAAAA
Statistics
Matches: 213, Mismatches: 33, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
181 2 0.01
182 19 0.09
183 16 0.08
184 100 0.47
185 53 0.25
186 8 0.04
187 7 0.03
188 6 0.03
189 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (182 bp):
AAAAACGTCTTAAATAATCTTAAAAAAATGAAGAGATTATTTAAGGCATTTTTGGCTAAAAACGC
CTTGAATAACCCAATTCAATTTCTTGTAAAAGAATATTCAAGGCATTTTTAGACAAAAAACGCCT
TAAATAATCTCCAAAAAAAAGGAAAGAGATTATTAAAGGTGTTTTTGGTAAA
Found at i:16801464 original size:62 final size:62
Alignment explanation
Indices: 16801342--16801492 Score: 180
Period size: 62 Copynumber: 2.4 Consensus size: 62
16801332 TTCTTGTAAA
* * *
16801342 AGATTATTTAAGTTATTTTTTG-ATAAAAAACGCCTTAAATAATCTCCAAAAAAATGGAAAG
1 AGATTATTTAAGGTATTTTTGGTAAAAAAAACGCCTTAAATAATCTCCAAAAAAATGGAAAG
* * * * *
16801403 GGATTATTTAAGGTGTTTTTGGTAAAAAAAACGTCTTAAATAATCT-TAAAAAAAGTTGAAAG
1 AGATTATTTAAGGTATTTTTGGTAAAAAAAACGCCTTAAATAATCTCCAAAAAAA-TGGAAAG
* *
16801465 AGATTATTGAAGGCATTTTTGGCTAAAA
1 AGATTATTTAAGGTATTTTTGG-TAAAA
16801493 CGCCTTGAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
61 25 0.33
62 45 0.60
63 5 0.07
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (62 bp):
AGATTATTTAAGGTATTTTTGGTAAAAAAAACGCCTTAAATAATCTCCAAAAAAATGGAAAG
Found at i:16801998 original size:34 final size:34
Alignment explanation
Indices: 16801955--16802024 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
16801945 TTCTTGCATT
*
16801955 TTGGGTCAAATCCCTAAAC-TTCTTGTCTGATTTG
1 TTGGGTCAAATCCCTAAACTTTC-TATCTGATTTG
**
16801989 TTGGGTCAAATCTTTAAACTTTCTATCTGATTTG
1 TTGGGTCAAATCCCTAAACTTTCTATCTGATTTG
16802023 TT
1 TT
16802025 TTGTTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 29 0.91
35 3 0.09
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (34 bp):
TTGGGTCAAATCCCTAAACTTTCTATCTGATTTG
Found at i:16805796 original size:14 final size:14
Alignment explanation
Indices: 16805777--16805832 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
16805767 CTAATGATAC
*
16805777 AAATATTTAATTAT
1 AAATATTAAATTAT
* *
16805791 AAATATAAAAATAT
1 AAATATTAAATTAT
*
16805805 AAAAATATAAATTAT
1 AAATAT-TAAATTAT
16805820 -AATATTATAATTA
1 AAATATTA-AATTA
16805833 ACTATAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
13 2 0.06
14 25 0.76
15 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATTAAATTAT
Found at i:16805802 original size:22 final size:22
Alignment explanation
Indices: 16805760--16805804 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16805750 ATTTTTTATC
* *
16805760 TTTAATTCTAATGATACAAATA
1 TTTAATTATAATGATAAAAATA
16805782 TTTAATTATAAAT-ATAAAAATA
1 TTTAATTAT-AATGATAAAAATA
16805804 T
1 T
16805805 AAAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTAATTATAATGATAAAAATA
Found at i:16805804 original size:8 final size:8
Alignment explanation
Indices: 16805791--16805815 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16805781 ATTTAATTAT
16805791 AAATATAA
1 AAATATAA
16805799 AAATATAA
1 AAATATAA
16805807 AAATATAA
1 AAATATAA
16805815 A
1 A
16805816 TTATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATATAA
Found at i:16807263 original size:2 final size:2
Alignment explanation
Indices: 16807256--16807290 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16807246 TAATAAAATG
16807256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16807291 ACATTTGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16808646 original size:23 final size:23
Alignment explanation
Indices: 16808620--16808669 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
16808610 GATAAGTAAT
16808620 TGAATGTATTTAAATAAAATTTG
1 TGAATGTATTTAAATAAAATTTG
* *
16808643 TGAATTTTTTTAAATAAAATTTG
1 TGAATGTATTTAAATAAAATTTG
16808666 TGAA
1 TGAA
16808670 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (23 bp):
TGAATGTATTTAAATAAAATTTG
Found at i:16808685 original size:23 final size:23
Alignment explanation
Indices: 16808628--16808677 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
16808618 ATTGAATGTA
*
16808628 TTTAAATAAAATTTGTGAATTTT
1 TTTAAATAAAATTTGTGAAATTT
16808651 TTTAAATAAAATTTGTGAAATTT
1 TTTAAATAAAATTTGTGAAATTT
16808674 TTTA
1 TTTA
16808678 TTAAAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (23 bp):
TTTAAATAAAATTTGTGAAATTT
Found at i:16811052 original size:17 final size:15
Alignment explanation
Indices: 16811032--16811065 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
16811022 TTAATTAATC
16811032 AAAATTTATGATTATAT
1 AAAATTTAT-ATT-TAT
16811049 AAAATTTATATTTAT
1 AAAATTTATATTTAT
16811064 AA
1 AA
16811066 GCAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 3 0.18
17 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAAATTTATATTTAT
Found at i:16812957 original size:22 final size:20
Alignment explanation
Indices: 16812932--16812981 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
16812922 AAAAAATTTA
16812932 TTTTAAAAATATATTGATAAAT
1 TTTTAAAAAT-TATTGAT-AAT
* *
16812954 TTTTAAATATTATTTATAAT
1 TTTTAAAAATTATTGATAAT
*
16812974 ATTTAAAA
1 TTTTAAAA
16812982 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.38
21 6 0.25
22 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTAAAAATTATTGATAAT
Found at i:16812963 original size:20 final size:22
Alignment explanation
Indices: 16812932--16812977 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16812922 AAAAAATTTA
*
16812932 TTTTAAAAATATATTGATAA-AT
1 TTTTAAATAT-TATTGATAATAT
*
16812954 TTTTAAATATTATTTATAATAT
1 TTTTAAATATTATTGATAATAT
16812976 TT
1 TT
16812978 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTAAATATTATTGATAATAT
Found at i:16812982 original size:21 final size:20
Alignment explanation
Indices: 16812931--16812982 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
16812921 TAAAAAATTT
16812931 ATTTTAAAAATATATTGATAA
1 ATTTT-AAAATATATTGATAA
* *
16812952 ATTTTTAAATATTATTTAT-A
1 ATTTTAAAATA-TATTGATAA
16812972 ATATTTAAAAT
1 AT-TTTAAAAT
16812983 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTTAAAATATATTGATAA
Found at i:16814156 original size:21 final size:20
Alignment explanation
Indices: 16814131--16814868 Score: 134
Period size: 21 Copynumber: 35.2 Consensus size: 20
16814121 ATACTTTTTG
16814131 TTTTGATAACTTTTGATAAA
1 TTTTGATAACTTTTGATAAA
* **
16814151 TTTTTGGTAACTTTTCCTATAA
1 -TTTTGATAACTTTTGATA-AA
* * * *
16814173 TTTCGGTAAGTTTTTATATAA
1 TTTTGATAACTTTTGATA-AA
* *
16814194 TTTTGATAAGTTTTTACATAATTTTTA
1 TTTTGATAA-CTTTT-GATAA-----A
* * *
16814221 TTTTGACAACCTTTGATATA
1 TTTTGATAACTTTTGATAAA
* * *
16814241 TTTTGGTAACTTTTGTTAGA
1 TTTTGATAACTTTTGATAAA
* *
16814261 TGTTTGATTACCTTTGATAAAA
1 T-TTTGATAACTTTTGAT-AAA
*
16814283 TTTTGATAACTTTTGATATTA
1 TTTTGATAACTTTTGATA-AA
* *
16814304 TTTTGAGAA-TCTTGAATAAAA
1 TTTTGATAACTTTTG-AT-AAA
*
16814325 TTTTGATAA-TCTTTGACAAAA
1 TTTTGATAACT-TTTGA-TAAA
* *
16814346 TTTT-AGTAAC-CTTAATATAA
1 TTTTGA-TAACTTTTGATA-AA
16814366 TTTT-AGTAACTTTT--T--A
1 TTTTGA-TAACTTTTGATAAA
16814382 ---T-ATAA-TTTT-AGT-AA
1 TTTTGATAACTTTTGA-TAAA
* * *
16814396 TTTTAATAACCTTTGATACTA
1 TTTTGATAACTTTTGATA-AA
16814417 TTTTGATAA-TTATTGATACAA
1 TTTTGATAACTT-TTGATA-AA
* * *
16814438 TTTGGATAATTTTTGACAAAA
1 TTTTGATAACTTTTGA-TAAA
*
16814459 TTTT-AGTAAC-CTTGATATAA
1 TTTTGA-TAACTTTTGATA-AA
*
16814479 TTTTGATAACTTTTAATACAA
1 TTTTGATAACTTTTGATA-AA
*
16814500 GTTTT-ATAA-TTTTCTATATAA
1 -TTTTGATAACTTTT-GATA-AA
* * *
16814521 TTTTTGTTTTGATAACCTCT-ATTAGA
1 ------TTTTGATAACTTTTGA-TAAA
16814547 TATTTGATAACTTTTGATAAA
1 T-TTTGATAACTTTTGATAAA
*
16814568 TTTTTGGTAACTTTTGATATAA
1 -TTTTGATAACTTTTGATA-AA
* * *
16814590 TTTTGGTAA-TATTGGAGATAA
1 TTTTGATAACT-TTTGATA-AA
* *
16814611 TTTTGATAAATTTTTACGTAATTTTTA
1 TTTTGATAACTTTTGA--TAA-----A
* *
16814638 TTTTGATAACCTTTGATATA
1 TTTTGATAACTTTTGATAAA
* *
16814658 TTTTGGTAAAC-TTTGTTAAA
1 TTTTGAT-AACTTTTGATAAA
16814678 TGTTT-ATAACTTTTGATAAAA
1 T-TTTGATAACTTTTGAT-AAA
*
16814699 TTTTGATAACTTTTGATATTA
1 TTTTGATAACTTTTGATA-AA
*
16814720 TTTTGATAA-TCATTGATAAAA
1 TTTTGATAACT-TTTGAT-AAA
* * * *
16814741 TTTTGGTAATTTTTAACAAAA
1 TTTTGATAACTTTTGA-TAAA
* * *
16814762 TTTTGGTAA-TCTTTAACAAAA
1 TTTTGATAACT-TTTGA-TAAA
* *
16814783 TTTT-AGTAAC-CTTAATATAA
1 TTTTGA-TAACTTTTGATA-AA
* *
16814803 TTTTAATAACTTTTAATACAA
1 TTTTGATAACTTTTGATA-AA
*
16814824 TTTT-AGTAACTTTTAATACAA
1 TTTTGA-TAACTTTTGATA-AA
*
16814845 -TTTGATAACTTTTTATATAA
1 TTTTGATAACTTTTGATA-AA
16814865 TTTT
1 TTTT
16814869 CGTTTTAATA
Statistics
Matches: 547, Mismatches: 91, Indels: 158
0.69 0.11 0.20
Matches are distributed among these distances:
11 4 0.01
12 3 0.01
13 3 0.01
14 1 0.00
16 1 0.00
17 1 0.00
18 4 0.01
19 11 0.02
20 119 0.22
21 321 0.59
22 29 0.05
23 4 0.01
25 5 0.01
26 10 0.02
27 29 0.05
28 2 0.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTTGATAACTTTTGATAAA
Found at i:16814181 original size:90 final size:89
Alignment explanation
Indices: 16814078--16814254 Score: 237
Period size: 90 Copynumber: 2.0 Consensus size: 89
16814068 GTAACCTTGT
* * * * * *
16814078 TATAATTTTGGTAAGTTTTAATACAAATTTGATAACCTTTTATATACTTTTTGTTTTGATAACTT
1 TATAATTTCGGTAAGTTTTAATACAAATTTGATAACCTTTTACATAATTTTTATTTTGACAACCT
16814143 TTGATAAATTTTTGGTAACTTTTCC
66 TTGATAAA-TTTTGGTAACTTTTCC
* * * **
16814168 TATAATTTCGGTAAGTTTTTATATAATTTTGATAAGTTTTTACATAATTTTTATTTTGACAACCT
1 TATAATTTCGGTAAGTTTTAATACAAATTTGATAACCTTTTACATAATTTTTATTTTGACAACCT
*
16814233 TTGATATATTTTGGTAACTTTT
66 TTGATAAATTTTGGTAACTTTT
16814255 GTTAGATGTT
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 14 0.19
90 61 0.81
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (89 bp):
TATAATTTCGGTAAGTTTTAATACAAATTTGATAACCTTTTACATAATTTTTATTTTGACAACCT
TTGATAAATTTTGGTAACTTTTCC
Found at i:16814369 original size:20 final size:21
Alignment explanation
Indices: 16814344--16814403 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
16814334 TCTTTGACAA
16814344 AATTTTAGTAAC-CTTAATAT
1 AATTTTAGTAACTCTTAATAT
* *
16814364 AATTTTAGTAACTTTTTATAT
1 AATTTTAGTAACTCTTAATAT
*
16814385 AATTTTAGTAA-TTTTAATA
1 AATTTTAGTAACTCTTAATA
16814404 ACCTTTGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
AATTTTAGTAACTCTTAATAT
Found at i:16814427 original size:30 final size:30
Alignment explanation
Indices: 16814362--16814496 Score: 91
Period size: 30 Copynumber: 4.4 Consensus size: 30
16814352 TAACCTTAAT
* * *
16814362 ATAATTTTAGTAACTTTTTATATAATTTT-
1 ATAATTTTAATAACCTTTGATATAATTTTG
16814391 AGTAATTTTAATAACCTTTGATACT-ATTTTG
1 A-TAATTTTAATAACCTTTGATA-TAATTTTG
* * *
16814422 ATAATTATTGAT-ACAATTTGGATA-ATTTTTG
1 ATAATT-TTAATAAC-CTTT-GATATAATTTTG
* *
16814453 ACAAAATTTTAGTAACC-TTGATATAATTTTG
1 --ATAATTTTAATAACCTTTGATATAATTTTG
16814484 ATAACTTTTAATA
1 ATAA-TTTTAATA
16814497 CAAGTTTTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
29 4 0.05
30 41 0.51
31 22 0.27
32 7 0.09
33 7 0.09
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (30 bp):
ATAATTTTAATAACCTTTGATATAATTTTG
Found at i:16814479 original size:113 final size:113
Alignment explanation
Indices: 16814281--16814512 Score: 317
Period size: 113 Copynumber: 2.1 Consensus size: 113
16814271 CCTTTGATAA
* * * * *
16814281 AATTTTGATAACTTTTGATATTATTTTGAGAATCTTGAATAAAATTTTGATAATCTTTGACAAAA
1 AATTTTAATAACCTTTGATACTATTTTGAGAATATTGAATAAAATTTGGATAATCTTTGACAAAA
* *
16814346 TTTTAGTAACCTTAATATAATTTT-AGTAACTTTTTATATAA-TTTTAGT
66 TTTTAGTAACCTTAATATAATTTTGA-TAACTTTTAATACAAGTTTTA-T
* * *
16814394 AATTTTAATAACCTTTGATACTATTTTGATAATTATTG-ATACAATTTGGATAATTTTTGACAAA
1 AATTTTAATAACCTTTGATACTATTTTGAGAA-TATTGAATAAAATTTGGATAATCTTTGACAAA
*
16814458 ATTTTAGTAACCTTGATATAATTTTGATAACTTTTAATACAAGTTTTAT
65 ATTTTAGTAACCTTAATATAATTTTGATAACTTTTAATACAAGTTTTAT
16814507 AATTTT
1 AATTTT
16814513 CTATATAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
113 95 0.90
114 10 0.10
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (113 bp):
AATTTTAATAACCTTTGATACTATTTTGAGAATATTGAATAAAATTTGGATAATCTTTGACAAAA
TTTTAGTAACCTTAATATAATTTTGATAACTTTTAATACAAGTTTTAT
Found at i:16814485 original size:62 final size:63
Alignment explanation
Indices: 16814394--16814512 Score: 156
Period size: 62 Copynumber: 1.9 Consensus size: 63
16814384 TAATTTTAGT
*
16814394 AATTTTAATAACCTTTGATACTATTTTGATAA-TTATTGATACAA-TTTGGATAATTTTTGACAA
1 AATTTTAATAACCTTTGATACTATTTTGATAACTT-TTAATACAAGTTT-GATAATTTTTGACAA
* *
16814457 AATTTTAGTAACC-TTGATA-TAATTTTGATAACTTTTAATACAAGTTTTATAATTTT
1 AATTTTAATAACCTTTGATACT-ATTTTGATAACTTTTAATACAAGTTTGATAATTTT
16814513 CTATATAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
61 1 0.02
62 32 0.64
63 17 0.34
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (63 bp):
AATTTTAATAACCTTTGATACTATTTTGATAACTTTTAATACAAGTTTGATAATTTTTGACAA
Found at i:16814593 original size:11 final size:10
Alignment explanation
Indices: 16814549--16814728 Score: 86
Period size: 10 Copynumber: 17.8 Consensus size: 10
16814539 CTATTAGATA
*
16814549 TTTGATAACT
1 TTTGATAAAT
16814559 TTTGATAAATT
1 TTTGATAAA-T
* *
16814570 TTTGGTAACT
1 TTTGATAAAT
16814580 TTTGATATAAT
1 TTTGATA-AAT
*
16814591 TTTGGT-AAT
1 TTTGATAAAT
* *
16814600 ATTGGAGATAAT
1 -TTTGATA-AAT
16814612 TTTGATAAAT
1 TTTGATAAAT
*
16814622 TTTTACGT-AAT
1 TTTGA--TAAAT
16814633 TTT--T--AT
1 TTTGATAAAT
**
16814639 TTTGATAACC
1 TTTGATAAAT
*
16814649 TTTGATATAT
1 TTTGATAAAT
* *
16814659 TTTGGTAAAC
1 TTTGATAAAT
*
16814669 TTTGTTAAAT
1 TTTGATAAAT
*
16814679 GTTT-ATAACT
1 -TTTGATAAAT
16814689 TTTGATAAAAT
1 TTTGAT-AAAT
*
16814700 TTTGATAACT
1 TTTGATAAAT
*
16814710 TTTGATATTAT
1 TTTGATA-AAT
16814721 TTTGATAA
1 TTTGATAA
16814729 TCATTGATAA
Statistics
Matches: 126, Mismatches: 29, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
6 5 0.04
7 1 0.01
8 1 0.01
9 6 0.05
10 63 0.50
11 46 0.37
12 4 0.03
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (10 bp):
TTTGATAAAT
Found at i:16814818 original size:10 final size:10
Alignment explanation
Indices: 16814799--16814841 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
16814789 TAACCTTAAT
16814799 ATAA-TTTTA
1 ATAACTTTTA
16814808 ATAACTTTTA
1 ATAACTTTTA
*
16814818 ATACAATTTTA
1 ATA-ACTTTTA
*
16814829 GTAACTTTTA
1 ATAACTTTTA
16814839 ATA
1 ATA
16814842 CAATTTGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 4 0.14
10 16 0.57
11 8 0.29
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (10 bp):
ATAACTTTTA
Found at i:16814867 original size:41 final size:41
Alignment explanation
Indices: 16814781--16814868 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
16814771 TCTTTAACAA
*
16814781 AATTTTAGTAACCTTAATATAATTTTAATAACTTTTAATAC
1 AATTTTAGTAACCTTAATACAATTTTAATAACTTTTAATAC
* * * *
16814822 AATTTTAGTAACTTTTAATACAA-TTTGATAACTTTTTATAT
1 AATTTTAGTAAC-CTTAATACAATTTTAATAACTTTTAATAC
16814863 AATTTT
1 AATTTT
16814869 CGTTTTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 33 0.80
42 8 0.20
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (41 bp):
AATTTTAGTAACCTTAATACAATTTTAATAACTTTTAATAC
Found at i:16816954 original size:15 final size:15
Alignment explanation
Indices: 16816934--16816968 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16816924 AAATTTTATC
* *
16816934 AATATTTTTATTAAA
1 AATATTTATATAAAA
16816949 AATATTTATATAAAA
1 AATATTTATATAAAA
16816964 AATAT
1 AATAT
16816969 ATCAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTATATAAAA
Found at i:16816972 original size:38 final size:38
Alignment explanation
Indices: 16816911--16816987 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 38
16816901 AATTTAAATT
* * *
16816911 TATTTATTCATAAAAATTTTATCAATATTTTTATTAAAAA
1 TATTTATTCATAAAAAATATATCAA-A-ATTTATTAAAAA
16816951 TATTTA-T-ATAAAAAATATATCAAAATTTATTAAAAA
1 TATTTATTCATAAAAAATATATCAAAATTTATTAAAAA
16816987 T
1 T
16816988 TTTTCAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 12 0.35
37 1 0.03
38 14 0.41
39 1 0.03
40 6 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (38 bp):
TATTTATTCATAAAAAATATATCAAAATTTATTAAAAA
Found at i:16816987 original size:21 final size:23
Alignment explanation
Indices: 16816952--16817004 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
16816942 TATTAAAAAT
16816952 ATTTATATAAAAAATATATCAAA
1 ATTTATATAAAAAATATATCAAA
* *
16816975 ATTTAT-T-AAAAATTTTTCAAA
1 ATTTATATAAAAAATATATCAAA
*
16816996 TTTTATATA
1 ATTTATATA
16817005 TTTAATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 17 0.68
22 2 0.08
23 6 0.24
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTATATAAAAAATATATCAAA
Found at i:16819402 original size:3 final size:3
Alignment explanation
Indices: 16819389--16819427 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
16819379 GTATAAGTAC
* *
16819389 TAT TGT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16819428 AGCGAATCCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16824755 original size:22 final size:22
Alignment explanation
Indices: 16824711--16824762 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
16824701 AATTTTTTAT
* *
16824711 ATTTTTATTATATCTAAATAAA
1 ATTTTAATTATATCCAAATAAA
16824733 ATTTTAATGTATATCCAAA-AAA
1 ATTTTAAT-TATATCCAAATAAA
*
16824755 ACTTTAAT
1 ATTTTAAT
16824763 ATAAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTTAATTATATCCAAATAAA
Found at i:16831771 original size:7 final size:6
Alignment explanation
Indices: 16831751--16831792 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
16831741 GGCTTAGTTC
*
16831751 AATTTT AGTTTT AATTTTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AATTTT AA-TTTT AATTTT AATTTT AATTTT AATTT
16831793 ATTATTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:16831775 original size:13 final size:13
Alignment explanation
Indices: 16831753--16831792 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
16831743 CTTAGTTCAA
*
16831753 TTTTAGTTTTAAT
1 TTTTAATTTTAAT
16831766 TTTTAATTTTAA-
1 TTTTAATTTTAAT
16831778 TTTTAATTTTAAT
1 TTTTAATTTTAAT
16831791 TT
1 TT
16831793 ATTATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:16831775 original size:19 final size:18
Alignment explanation
Indices: 16831751--16831792 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
16831741 GGCTTAGTTC
*
16831751 AATTTTAGTTTTAATTTTT
1 AATTTTAATTTTAA-TTTT
16831770 AATTTTAATTTTAATTTT
1 AATTTTAATTTTAATTTT
16831788 AATTT
1 AATTT
16831793 ATTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
AATTTTAATTTTAATTTT
Found at i:16831799 original size:3 final size:3
Alignment explanation
Indices: 16831791--16831881 Score: 72
Period size: 3 Copynumber: 32.7 Consensus size: 3
16831781 TAATTTTAAT
* *
16831791 TTA TTA TTA TTA TTA TTA TTA GT- TTA TT- TT- TTA TT- TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
16831835 TT- TTA TTA TT- TTCG TTA TT- TTG TTT TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16831877 TTA TT
1 TTA TT
16831882 TTTTGGTCCA
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
2 15 0.20
3 57 0.77
4 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:16831828 original size:8 final size:8
Alignment explanation
Indices: 16831813--16831885 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
16831803 TTATTATTAG
16831813 TTTA-TTT
1 TTTATTTT
16831820 TTTATTTT
1 TTTATTTT
*
16831828 TTTATTAT
1 TTTATTTT
*
16831836 TTTATTAT
1 TTTATTTT
** *
16831844 TTTCGTTA
1 TTTATTTT
*
16831852 TTT-TGTT
1 TTTATTTT
*
16831859 TTTATTAT
1 TTTATTTT
16831867 TTTATTATT
1 TTTATT-TT
*
16831876 ATTATTTT
1 TTTATTTT
16831884 TT
1 TT
16831886 GGTCCAAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
7 8 0.16
8 36 0.72
9 6 0.12
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:16831866 original size:14 final size:14
Alignment explanation
Indices: 16831790--16831883 Score: 79
Period size: 14 Copynumber: 6.8 Consensus size: 14
16831780 TTAATTTTAA
16831790 TTTATTATTATTATT
1 TTTATTATT-TTATT
* *
16831805 ATTATTAGTTTA-T
1 TTTATTATTTTATT
16831818 TTT-TTATTTT-TT
1 TTTATTATTTTATT
16831830 TATTATT-TTATTATT
1 T-TTATTATT-TTATT
** *
16831845 TTCGTTATTTTGTT
1 TTTATTATTTTATT
16831859 TTTATTATTTTATT
1 TTTATTATTTTATT
*
16831873 ATTATTATTTT
1 TTTATTATTTT
16831884 TTGGTCCAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
12 8 0.13
13 7 0.11
14 35 0.56
15 12 0.19
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTATTATTTTATT
Found at i:16831883 original size:23 final size:23
Alignment explanation
Indices: 16831790--16831884 Score: 90
Period size: 23 Copynumber: 4.1 Consensus size: 23
16831780 TTAATTTTAA
*
16831790 TTTATTATTATTATTATTATTA-G
1 TTTATTATT-TTATTATTATTATT
*
16831813 TTTATT-TTTTATT-TTTTTATTAT
1 TTTATTATTTTATTATTATTA-T-T
* *
16831836 TTTATTATTTTCGTTATT-TTGTT
1 TTTATTATTTT-ATTATTATTATT
16831859 TTTATTATTTTATTATTATTATT
1 TTTATTATTTTATTATTATTATT
16831882 TTT
1 TTT
16831885 TGGTCCAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
20 5 0.08
21 5 0.08
22 7 0.12
23 31 0.53
24 5 0.08
25 4 0.07
26 2 0.03
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.75
Consensus pattern (23 bp):
TTTATTATTTTATTATTATTATT
Found at i:16832673 original size:17 final size:17
Alignment explanation
Indices: 16832653--16832685 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16832643 TTATTTCAGC
16832653 ATTTTA-TTTATTTATTT
1 ATTTTAGTTT-TTTATTT
16832670 ATTTTAGTTTTTTATT
1 ATTTTAGTTTTTTATT
16832686 AAATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
ATTTTAGTTTTTTATTT
Found at i:16832767 original size:26 final size:25
Alignment explanation
Indices: 16832738--16832796 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
16832728 AATAAATATT
16832738 AATTATCTAATGATAGAATTTATA-AA
1 AATT-TCTAATGATA-AATTTATATAA
* * *
16832764 AATTTCAAATGGTAAATTTTTATAA
1 AATTTCTAATGATAAATTTATATAA
16832789 AATTTCTA
1 AATTTCTA
16832797 GGTGAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 7 0.25
25 17 0.61
26 4 0.14
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (25 bp):
AATTTCTAATGATAAATTTATATAA
Found at i:16832900 original size:8 final size:8
Alignment explanation
Indices: 16832887--16832915 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16832877 TTCAAACCAA
16832887 AAAAAATT
1 AAAAAATT
16832895 AAAAAATT
1 AAAAAATT
16832903 -AAAAATT
1 AAAAAATT
16832910 AAAAAA
1 AAAAAA
16832916 AAAACATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:16833234 original size:170 final size:175
Alignment explanation
Indices: 16832955--16833269 Score: 460
Period size: 170 Copynumber: 1.8 Consensus size: 175
16832945 ATTAAATACA
* * * *
16832955 AATTATCCAATGATGAGATTTTTTAGAAATTTCAAATGATAAATTTTCTAAGAACTCTCTAGGTG
1 AATTATCCAAAGATGAGATTTCTTAGAAATTTCAAATGATAAAATTTCTAAGAAATCTCTAGGTG
* * * * *
16833020 ATAAATTTTATTTAAGTTTGGCCCAAATGATGGAATAATTTAGAT-AAAA-TTTCAATAAAAATA
66 AAAAATTTTATCTAAATTTGACCCAAATGATGAAATAATTTAGATGAAAATTTTCAATAAAAATA
16833083 ATT-GTATTATTTTCCAAATAAAATTTAGATTGTAAATATTTGAT
131 ATTAGTATTATTTTCCAAATAAAATTTAGATTGTAAATATTTGAT
*
16833127 AATTATCCAAAGATGAGA-TTCTTAGAAATTTCAAATGGTAAAATTT-TAAGAAATCTCTAGGTG
1 AATTATCCAAAGATGAGATTTCTTAGAAATTTCAAATGATAAAATTTCTAAGAAATCTCTAGGTG
* * * *
16833190 AAAAATTTTCTCTAAATTTGACGCAAATGGTGAAATAGTTTAGATGAAAATTTTCAATAAAAATA
66 AAAAATTTTATCTAAATTTGACCCAAATGATGAAATAATTTAGATGAAAATTTTCAATAAAAATA
*
16833255 ATTATTATTATTTTC
131 ATTAGTATTATTTTC
16833270 TTTCCAAAGT
Statistics
Matches: 125, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
170 52 0.42
171 29 0.23
172 34 0.27
173 10 0.08
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (175 bp):
AATTATCCAAAGATGAGATTTCTTAGAAATTTCAAATGATAAAATTTCTAAGAAATCTCTAGGTG
AAAAATTTTATCTAAATTTGACCCAAATGATGAAATAATTTAGATGAAAATTTTCAATAAAAATA
ATTAGTATTATTTTCCAAATAAAATTTAGATTGTAAATATTTGAT
Found at i:16843837 original size:27 final size:27
Alignment explanation
Indices: 16843807--16843858 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
16843797 TATTATGCTT
*
16843807 TAAAAAAATAGAAA-AAATGAAAAATAA
1 TAAAAAAATA-AAATAAATAAAAAATAA
*
16843834 TAAAATAATAAAATAAATAAAAAAT
1 TAAAAAAATAAAATAAATAAAAAAT
16843859 GAAGACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (27 bp):
TAAAAAAATAAAATAAATAAAAAATAA
Found at i:16845192 original size:3 final size:3
Alignment explanation
Indices: 16845186--16845229 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
16845176 ATAATAATAA
*
16845186 TAT TAT TAT TAT TAT TAT TAT TA- TAT TTT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16845230 TTTACCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:16846165 original size:26 final size:26
Alignment explanation
Indices: 16846136--16846188 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
16846126 AATAATGAAA
*
16846136 TTTATAAAAATTTTAAATGATAAATT
1 TTTATAAAAATTTTAAATGAGAAATT
* *
16846162 TTTATAAAATTTTTAAGTGAGAAATT
1 TTTATAAAAATTTTAAATGAGAAATT
16846188 T
1 T
16846189 ATCTAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTATAAAAATTTTAAATGAGAAATT
Found at i:16846296 original size:16 final size:16
Alignment explanation
Indices: 16846267--16846327 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
16846257 TCAAACCCAA
*
16846267 AAAAATTTAAAAAATT
1 AAAAATTAAAAAAATT
*
16846283 AAAAATTAAAAAAAACATA
1 AAAAATT--AAAAAA-ATT
*
16846302 AAAAATAAAAAAAATT
1 AAAAATTAAAAAAATT
*
16846318 TAAAATTAAA
1 AAAAATTAAA
16846328 TACAAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 17 0.47
17 6 0.17
18 5 0.14
19 8 0.22
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATTAAAAAAATT
Found at i:16846570 original size:170 final size:179
Alignment explanation
Indices: 16846332--16846660 Score: 444
Period size: 171 Copynumber: 1.9 Consensus size: 179
16846322 ATTAAATACA
* * * * * *
16846332 AATTATCCAATGATGAGATTTTTTTAAAAATTTTAAATGGTAAATTTTTTAAGAACTCTTTAGGT
1 AATTATCCAAAGATGAGA-TTTCTTAAAAATTTCAAATGGTAAATATTCTAAGAAATCTTTAGGT
* *
16846397 GAGAAATTTTATTTAAGTTTGG-CCAAATGGT-GAAATAATTTAGA-CAAAA-TTTCAATAAAAA
65 GAGAAATTTTATCTAAATTTGGTCCAAATGGTAG-AATAATTTAGATCAAAATTTTCAATAAAAA
*
16846458 TAATT-TTATT-TTTT-TTT-CAAATAAAATTTGGATTGTAAATATTTGAT
129 TAATTATTATTATTTTCTTTCCAAAGAAAATTTGGATTGTAAATATTTGAT
16846505 AATTATCCAAAGATGAGA-TTCTTAAAAATTTCAAATGGTAAA-ATTCTAAGAAATCTTTAGGTG
1 AATTATCCAAAGATGAGATTTCTTAAAAATTTCAAATGGTAAATATTCTAAGAAATCTTTAGGTG
* * * * *
16846568 AGAAATTTTCTCTAAATTTGGTGCAAATGGTAGAATAGTTTAGATGAAAATTTTCAATAAAAGTA
66 AGAAATTTTATCTAAATTTGGTCCAAATGGTAGAATAATTTAGATCAAAATTTTCAATAAAAATA
16846633 ATTATTATTATTTTCTTTCCAAAGAAAA
131 ATTATTATTATTTTCTTTCCAAAGAAAA
16846661 AAAATTAAAA
Statistics
Matches: 134, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
170 36 0.27
171 40 0.30
172 5 0.04
173 33 0.25
174 5 0.04
175 4 0.03
176 3 0.02
177 8 0.06
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (179 bp):
AATTATCCAAAGATGAGATTTCTTAAAAATTTCAAATGGTAAATATTCTAAGAAATCTTTAGGTG
AGAAATTTTATCTAAATTTGGTCCAAATGGTAGAATAATTTAGATCAAAATTTTCAATAAAAATA
ATTATTATTATTTTCTTTCCAAAGAAAATTTGGATTGTAAATATTTGAT
Found at i:16849883 original size:31 final size:31
Alignment explanation
Indices: 16849848--16849919 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
16849838 ATACATAATT
* * *
16849848 ATTTTTATACTTTTAAATAAAATAATATTTA
1 ATTTTTATAATATCAAATAAAATAATATTTA
* * *
16849879 ATTTTAATAATATCAAATATAATAATCTTTA
1 ATTTTTATAATATCAAATAAAATAATATTTA
16849910 ATTTTTATAA
1 ATTTTTATAA
16849920 CTTAATGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTTTTATAATATCAAATAAAATAATATTTA
Found at i:16849887 original size:16 final size:16
Alignment explanation
Indices: 16849868--16849919 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
16849858 TTTTAAATAA
16849868 AATAATATTTAATTTT
1 AATAATATTTAATTTT
* * *
16849884 AATAATA-TCAAATAT
1 AATAATATTTAATTTT
*
16849899 AATAATCTTTAATTTT
1 AATAATATTTAATTTT
*
16849915 TATAA
1 AATAA
16849920 CTTAATGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAATATTTAATTTT
Found at i:16852544 original size:19 final size:20
Alignment explanation
Indices: 16852522--16852559 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
16852512 TATATAGTAT
16852522 TTTATTTTT-AAATTTTTAA
1 TTTATTTTTAAAATTTTTAA
16852541 TTTATTTTTAAAATTTTTA
1 TTTATTTTTAAAATTTTTA
16852560 TCTAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTTTTAAAATTTTTAA
Found at i:16852549 original size:20 final size:19
Alignment explanation
Indices: 16852522--16852559 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
16852512 TATATAGTAT
*
16852522 TTTATTTTTAAATTTTTAA
1 TTTATTTTAAAATTTTTAA
16852541 TTTATTTTTAAAATTTTTA
1 TTTA-TTTTAAAATTTTTA
16852560 TCTAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTTAAAATTTTTAA
Found at i:16853764 original size:24 final size:23
Alignment explanation
Indices: 16853726--16853779 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
16853716 AACAACTTCA
*
16853726 ATATAAAAATAAATAAAAATTTT
1 ATATAAAAATAAATAAAAATTAT
* * *
16853749 ATTTAAAAATTTAATAATAATTAT
1 ATATAAAAA-TAAATAAAAATTAT
16853773 ATATAAA
1 ATATAAA
16853780 TTTAACAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAAAAATAAATAAAAATTAT
Found at i:16853772 original size:22 final size:21
Alignment explanation
Indices: 16853747--16853792 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
16853737 AATAAAAATT
* *
16853747 TTATTTAAAAATTTAATAATAA
1 TTATATAAAAATTTAACAA-AA
*
16853769 TTATATATAAATTTAACAAAA
1 TTATATAAAAATTTAACAAAA
16853790 TTA
1 TTA
16853793 AAAATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATATAAAAATTTAACAAAA
Found at i:16854405 original size:21 final size:21
Alignment explanation
Indices: 16854354--16854405 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
16854344 TAATTTATAT
*
16854354 AATTTTATATTTATATTAAAAA
1 AATTTTAT-TTTAAATTAAAAA
**
16854376 AATAATATTTTAAATTAAAAA
1 AATTTTATTTTAAATTAAAAA
*
16854397 TATTTTATT
1 AATTTTATT
16854406 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTTATTTTAAATTAAAAA
Found at i:16854476 original size:17 final size:18
Alignment explanation
Indices: 16854442--16854479 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
16854432 TAATTTATAC
16854442 AATATCAAAATAAATTTA
1 AATATCAAAATAAATTTA
16854460 AATAT-AAAA-AAATTTTA
1 AATATCAAAATAAA-TTTA
16854477 AAT
1 AAT
16854480 CGAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 11 0.58
18 5 0.26
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATCAAAATAAATTTA
Found at i:16857949 original size:16 final size:16
Alignment explanation
Indices: 16857930--16857992 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 16
16857920 TTAAATATTT
16857930 TTATATTTAATTTTAA
1 TTATATTTAATTTTAA
16857946 TTAT-TTATAATTTTAA
1 TTATATT-TAATTTTAA
*
16857962 TTAAATTTTTATATTTTAA
1 TT--ATATTTA-ATTTTAA
16857981 -TATATTTTAATT
1 TTATA-TTTAATT
16857993 GATAAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
16 20 0.50
17 4 0.10
18 5 0.12
19 9 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTTAATTTTAA
Found at i:16857954 original size:20 final size:18
Alignment explanation
Indices: 16857926--16857977 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
16857916 GAATTTAAAT
*
16857926 ATTTTTATATTTAATTTTA
1 ATTTTTATATTTAA-TTAA
16857945 ATTATTTATAATTTTAATTAA
1 ATT-TTTAT-A-TTTAATTAA
16857966 ATTTTTATATTT
1 ATTTTTATATTT
16857978 TAATATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.10
19 4 0.14
20 10 0.34
21 7 0.24
22 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTATATTTAATTAA
Found at i:16858014 original size:6 final size:6
Alignment explanation
Indices: 16858003--16858227 Score: 89
Period size: 6 Copynumber: 37.5 Consensus size: 6
16857993 GATAAAATAT
* * ** *
16858003 TTTAAA TTTAAA TTTAAG TATAAA TAATTAAA TTTTTA -TCAAA TTTATGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA TTTAAA TTTA--AA
** * *
16858054 -TTAAA TTTATT TTTATA TATT-AA -TTAAA TTT-AA -TCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
16858098 --T-AA TTTAAT TTTTAT TTTAAA -TTAAA TTTAAA TTATAAAA TTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA
* * * *
16858144 TTT-GA -TCAAA TTTAAA -TTAAA TTTTAAA TATTAAA TTTAAA ATCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA T-TTAAA TTTAAA TTTAAA
16858191 TTTAAA TTTAAA TTTAATA TTATATCAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAA-A TT-TA--AA TTTAAA TTT
16858228 TATCGATTAT
Statistics
Matches: 163, Mismatches: 30, Indels: 52
0.67 0.12 0.21
Matches are distributed among these distances:
3 2 0.01
4 5 0.03
5 23 0.14
6 93 0.57
7 20 0.12
8 16 0.10
9 3 0.02
10 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:16858121 original size:42 final size:45
Alignment explanation
Indices: 16858027--16858128 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 45
16858017 TAAGTATAAA
*
16858027 TAATTAAATTTTTATCAAATTTATGAATTAAATTTATTTTTATATAT
1 TAATTAAA-TTTAATCAAATTTA-GAATTAAATTTATTTTTATATAT
16858074 TAATTAAATTTAATCAAATTTA-AA-T-AATTTAATTTTTAT-T-T
1 TAATTAAATTTAATCAAATTTAGAATTAAATTT-ATTTTTATATAT
16858115 TAAATTAAATTTAA
1 T-AATTAAATTTAA
16858129 ATTATAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
41 2 0.04
42 18 0.35
43 9 0.17
44 2 0.04
46 13 0.25
47 8 0.15
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (45 bp):
TAATTAAATTTAATCAAATTTAGAATTAAATTTATTTTTATATAT
Found at i:16858126 original size:12 final size:12
Alignment explanation
Indices: 16858119--16858205 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 12
16858109 TTATTTTAAA
16858119 TTAAATTTAAATT
1 TTAAA-TTAAATT
* *
16858132 ATAAAATTAAAAT
1 -TTAAATTAAATT
* *
16858145 TT-GATCAAA-T
1 TTAAATTAAATT
16858155 TTAAATTAAATT
1 TTAAATTAAATT
16858167 TTAAATATTAAATT
1 TT-AA-ATTAAATT
* *
16858181 TAAAATCAAA-T
1 TTAAATTAAATT
16858192 TTAAATTTAAATT
1 TTAAA-TTAAATT
16858205 T
1 T
16858206 AATATTATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
10 3 0.05
11 15 0.27
12 13 0.23
13 12 0.21
14 13 0.23
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (12 bp):
TTAAATTAAATT
Done.