Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 20
Found at i:1346032 original size:13 final size:13
Alignment explanation
Indices: 1346014--1346056 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1346004 CTATGTAGTT
1346014 TATATATAAATTA
1 TATATATAAATTA
1346027 TATATAT--ATTA
1 TATATATAAATTA
* *
1346038 AATATATAAACTA
1 TATATATAAATTA
1346051 TATATA
1 TATATA
1346057 ATTATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 10 0.40
13 15 0.60
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATAAATTA
Found at i:1346042 original size:7 final size:8
Alignment explanation
Indices: 1346015--1346083 Score: 50
Period size: 9 Copynumber: 7.9 Consensus size: 8
1346005 TATGTAGTTT
1346015 ATATATAA
1 ATATATAA
*
1346023 AT-TATAT
1 ATATATAA
1346030 ATATATTAA
1 ATATA-TAA
1346039 ATATATAA
1 ATATATAA
1346047 ACTATATATA
1 A-TATATA-A
*
1346057 ATTATATTA
1 A-TATATAA
1346066 ATACGTATAA
1 ATA--TATAA
1346076 ACTATATA
1 A-TATATA
1346084 GTTTATACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
7 6 0.12
8 10 0.20
9 19 0.39
10 12 0.24
11 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (8 bp):
ATATATAA
Found at i:1346047 original size:24 final size:23
Alignment explanation
Indices: 1346015--1346060 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1346005 TATGTAGTTT
*
1346015 ATATATAAATTATATATATATTAA
1 ATATATAAACTATATATA-ATTAA
1346039 ATATATAAACTATATATAATTA
1 ATATATAAACTATATATAATTA
1346061 TATTAATACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATAAACTATATATAATTAA
Found at i:1346113 original size:11 final size:11
Alignment explanation
Indices: 1346099--1346323 Score: 96
Period size: 11 Copynumber: 21.9 Consensus size: 11
1346089 TACATAGTAG
1346099 TATATAAACTA
1 TATATAAACTA
*
1346110 TATATAAACCA
1 TATATAAACTA
1346121 TATAT--ACTA
1 TATATAAACTA
1346130 TATATAAACTATA
1 TATATAAAC--TA
1346143 TATATAAACTA
1 TATATAAACTA
*
1346154 -A-ATAAATTA
1 TATATAAACTA
**
1346163 TATAGTTTA-TA
1 TATA-TAAACTA
1346174 TATATAAAC--
1 TATATAAACTA
1346183 TA-ATAAA-T-
1 TATATAAACTA
1346191 TATATAAACTA
1 TATATAAACTA
*
1346202 TATATAAACTG
1 TATATAAACTA
**
1346213 TATAGTTTA-TA
1 TATA-TAAACTA
* *
1346224 TTTATATACTA
1 TATATAAACTA
1346235 TATAT--A--A
1 TATATAAACTA
1346242 T-TATAAA-T-
1 TATATAAACTA
*
1346250 TATATATACTA
1 TATATAAACTA
* * *
1346261 TGTATAGATTA
1 TATATAAACTA
** *
1346272 TATAGTTTATTA
1 TATA-TAAACTA
1346284 -ATATAAACTA
1 TATATAAACTA
*
1346294 TATATAAACCA
1 TATATAAACTA
1346305 TATAT--ACTA
1 TATATAAACTA
*
1346314 TATGTAAACT
1 TATATAAACT
1346324 GTAAGGTATG
Statistics
Matches: 163, Mismatches: 27, Indels: 48
0.68 0.11 0.20
Matches are distributed among these distances:
6 3 0.02
7 2 0.01
8 9 0.06
9 35 0.21
10 13 0.08
11 81 0.50
12 9 0.06
13 11 0.07
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (11 bp):
TATATAAACTA
Found at i:1346174 original size:92 final size:93
Alignment explanation
Indices: 1346078--1346323 Score: 224
Period size: 92 Copynumber: 2.7 Consensus size: 93
1346068 ACGTATAAAC
*
1346078 TATATAGTTTATACATAGTAGTATATAAACTATATATAAACCATATATACTATATATAAACTATA
1 TATATAGTTTATACATAGTATTATATAAACTATATATAAACCATATATACTATATATAAACTATA
*
1346143 -TATATA-AACTAAATAAATTATATAGTTTA
66 CTATATATAA-T-AATAAATTATATA-TATA
** * * * * **
1346172 TATATA-TAAACTA-ATA-AATTATATAAACTATATATAAA-C-TGTATAGTTTATATTTA-TAT
1 TATATAGTTTA-TACATAGTATTATATAAACTATATATAAACCATATATACTATATATAAACTAT
*
1346231 ACTATATATAATTATAAATTATATATACTA
65 ACTATATATAATAATAAATTATATATA-TA
* * *
1346261 TGTATAGATTAT--ATAGTTTATTAATATAAACTATATATAAACCATATATACTATATGTAAACT
1 TATATAGTTTATACATAG--TATT-ATATAAACTATATATAAACCATATATACTATATATAAACT
1346324 GTAAGGTATG
Statistics
Matches: 118, Mismatches: 22, Indels: 23
0.72 0.13 0.14
Matches are distributed among these distances:
88 4 0.03
89 24 0.20
90 20 0.17
91 6 0.05
92 38 0.32
93 6 0.05
94 19 0.16
95 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (93 bp):
TATATAGTTTATACATAGTATTATATAAACTATATATAAACCATATATACTATATATAAACTATA
CTATATATAATAATAAATTATATATATA
Found at i:1346223 original size:59 final size:59
Alignment explanation
Indices: 1346130--1346300 Score: 161
Period size: 59 Copynumber: 2.9 Consensus size: 59
1346120 ATATATACTA
* * *
1346130 TATATAAACTATATATATAAACTAAATAAATTATATAGTTTATATA-TATA-A-ACTAATAAAT
1 TATATAAAC--TATATATAAACTATAT-AGTT-TATA-TTTATATACTATATATAATAATAAAT
* *
1346191 TATATAAACTATATATAAACTGTATAGTTTATATTTATATACTATATATAATTATAAAT
1 TATATAAACTATATATAAACTATATAGTTTATATTTATATACTATATATAATAATAAAT
* * * * * *
1346250 TATATATACTATGTATAGATTATATAGTTTAT-TAATATAAACTATATATAA
1 TATATAAACTATATATAAACTATATAGTTTATAT-TTATATACTATATATAA
1346301 ACCATATATA
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
56 8 0.09
57 8 0.09
58 5 0.05
59 64 0.68
61 9 0.10
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (59 bp):
TATATAAACTATATATAAACTATATAGTTTATATTTATATACTATATATAATAATAAAT
Found at i:1346288 original size:50 final size:49
Alignment explanation
Indices: 1346101--1346274 Score: 118
Period size: 50 Copynumber: 3.7 Consensus size: 49
1346091 CATAGTAGTA
* * * *
1346101 TATAAACTATATATAAAC--CATA-TATACTATATATAAAC-TATAT-A-
1 TATAAACTATATATAAACTGTATAGTTTA-TATTTATATACATATATAAT
* * * *
1346145 TATAAACTA-A-ATAAATTATATAGTTTATATATATAAAC-TA-ATAAATT
1 TATAAACTATATATAAACTGTATAGTTTATATTTATATACATATAT-AA-T
1346192 ATATAAACTATATATAAACTGTATAGTTTATATTTATATACTATATATAAT
1 -TATAAACTATATATAAACTGTATAGTTTATATTTATATAC-ATATATAAT
* * *
1346243 TATAAATTATATATACTA-TGTATAGATTATAT
1 TATAAACTATATATA-AACTGTATAGTTTATAT
1346275 AGTTTATTAA
Statistics
Matches: 106, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 5 0.05
43 3 0.03
44 25 0.24
45 4 0.04
48 9 0.08
49 1 0.01
50 51 0.48
51 2 0.02
52 4 0.04
53 2 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (49 bp):
TATAAACTATATATAAACTGTATAGTTTATATTTATATACATATATAAT
Found at i:1346307 original size:20 final size:20
Alignment explanation
Indices: 1346284--1346322 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1346274 TAGTTTATTA
1346284 ATATAAACTATATATAAACC
1 ATATAAACTATATATAAACC
* *
1346304 ATATATACTATATGTAAAC
1 ATATAAACTATATATAAAC
1346323 TGTAAGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (20 bp):
ATATAAACTATATATAAACC
Found at i:1350834 original size:17 final size:18
Alignment explanation
Indices: 1350805--1350843 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1350795 ATATGAATTA
*
1350805 TATATATAAACTATATTT
1 TATATATAAACTATATAT
1350823 TATATA-AAACTATATAT
1 TATATATAAACTATATAT
1350840 TATA
1 TATA
1350844 GTTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATATAAACTATATAT
Found at i:1350863 original size:2 final size:2
Alignment explanation
Indices: 1350858--1350923 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
1350848 TTTATATAAG
* * * *
1350858 AT AT AT TT AT AT TT AT AT AT -T TT AT A- AT AT AGT TT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
1350898 AT AT A- AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1350924 ATAAGTATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
1 4 0.08
2 45 0.90
3 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1350877 original size:14 final size:13
Alignment explanation
Indices: 1350858--1350914 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
1350848 TTTATATAAG
1350858 ATATATTTATATTT
1 ATATATTTATA-TT
*
1350872 ATATATTT-TATA
1 ATATATTTATATT
1350884 ATATAGTTTATATT
1 ATATA-TTTATATT
*
1350898 ATATA-ATATA-T
1 ATATATTTATATT
1350909 ATATAT
1 ATATAT
1350915 ACATATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 6 0.16
12 10 0.27
13 5 0.14
14 16 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
ATATATTTATATT
Found at i:1350908 original size:21 final size:21
Alignment explanation
Indices: 1350897--1351120 Score: 76
Period size: 21 Copynumber: 10.5 Consensus size: 21
1350887 TAGTTTATAT
1350897 TATATAATATATATATATACA
1 TATATAATATATATATATACA
*
1350918 TATATAATAAGTATAACTCTATAC-
1 TATATAAT-A-TAT-A-TATATACA
1350942 T-TATAAGTATATA-ATATA-A
1 TATATAA-TATATATATATACA
* *
1350961 GTATATAAGTATACATATA-A-G
1 -TATATAA-TATATATATATACA
* * *
1350982 TATAT-AT-TTTAAATGTACA
1 TATATAATATATATATATACA
* ** * * *
1351001 TGTATTGTACATATATGTAAA
1 TATATAATATATATATATACA
**
1351022 CT-TATATATACTTATATATATATG
1 -TATATA-ATA--TATATATATACA
*
1351046 TATATAATATA-AGTATATATA
1 TATATAATATATA-TATATACA
*
1351067 TATATAAGTATATA-ACAATACA
1 TATATAA-TATATATA-TATACA
*
1351089 T-TATAAGTATAAATATATACA
1 TATATAA-TATATATATATACA
1351110 TATATAATATA
1 TATATAATATA
1351121 AGTAACATTA
Statistics
Matches: 153, Mismatches: 26, Indels: 48
0.67 0.11 0.21
Matches are distributed among these distances:
17 4 0.03
18 2 0.01
19 9 0.06
20 8 0.05
21 70 0.46
22 25 0.16
23 14 0.09
24 15 0.10
25 6 0.04
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (21 bp):
TATATAATATATATATATACA
Found at i:1350920 original size:14 final size:13
Alignment explanation
Indices: 1350865--1351121 Score: 55
Period size: 12 Copynumber: 20.0 Consensus size: 13
1350855 AAGATATATT
* *
1350865 TATATTTATATAT
1 TATATATATATAA
* *
1350878 TTTATA-ATATAG
1 TATATATATATAA
*
1350890 TTTATATTATATAA
1 TATATA-TATATAA
1350904 TATATATATATACA
1 TATATATATATA-A
*
1350918 TATATA-ATA-AG
1 TATATATATATAA
* *
1350929 TATA-ACTCTATAC
1 TATATA-TATATAA
1350942 T-TATAAGTATATAA
1 TATAT-A-TATATAA
1350956 TATA-AGTATATAA
1 TATATA-TATATAA
* *
1350969 GTATACATATA-AG
1 -TATATATATATAA
*
1350982 TATATAT-TTTAAA
1 TATATATATAT-AA
* * * **
1350995 TGTACATGTATTG
1 TATATATATATAA
* *
1351008 TACATATATGTAA
1 TATATATATATAA
*
1351021 -ACT-TATATATAC
1 TA-TATATATATAA
1351033 T-TATATATAT-A
1 TATATATATATAA
*
1351044 TGTATATAATATAA
1 TATATAT-ATATAA
1351058 GTATATATATAT-A
1 -TATATATATATAA
1351071 TA-AGTATATA-ACA
1 TATA-TATATATA-A
*
1351084 -ATACAT-TATAA
1 TATATATATATAA
*
1351095 GTATAAATATATACA
1 -TATATATATATA-A
1351110 TATATA-ATATAA
1 TATATATATATAA
1351122 GTAACATTAT
Statistics
Matches: 179, Mismatches: 35, Indels: 61
0.65 0.13 0.22
Matches are distributed among these distances:
10 1 0.01
11 11 0.06
12 55 0.31
13 54 0.30
14 48 0.27
15 10 0.06
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (13 bp):
TATATATATATAA
Found at i:1350921 original size:45 final size:45
Alignment explanation
Indices: 1350835--1350922 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
1350825 TATAAAACTA
* * **
1350835 TATATTATAGTTTTTTATATAAGATATATTTATATTTATATATTT
1 TATAATATAGTTTTTTATATAAGATATATATATATACATATATTT
1350880 TATAATATAGTTTATATTATAT-A-ATATATATATATACATATAT
1 TATAATATAGTTT-T-TTATATAAGATATATATATATACATATAT
1350923 AATAAGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 29 0.78
46 2 0.05
47 6 0.16
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (45 bp):
TATAATATAGTTTTTTATATAAGATATATATATATACATATATTT
Found at i:1350922 original size:47 final size:45
Alignment explanation
Indices: 1350835--1350923 Score: 115
Period size: 47 Copynumber: 1.9 Consensus size: 45
1350825 TATAAAACTA
* * **
1350835 TATATTATAGTTTTTTATATAAGATATATTTATATTTATATATTT
1 TATAATATAGTTTTTTATATAAGATATATATATACATATATATTT
*
1350880 TATAATATAGTTTATATTATATAATATATATATATACATATATA
1 TATAATATAGTTT-T-TTATATAAGATATATATATACATATATA
1350924 ATAAGTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 12 0.32
46 1 0.03
47 24 0.65
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (45 bp):
TATAATATAGTTTTTTATATAAGATATATATATACATATATATTT
Found at i:1351063 original size:33 final size:32
Alignment explanation
Indices: 1351026--1351150 Score: 93
Period size: 29 Copynumber: 3.9 Consensus size: 32
1351016 TGTAAACTTA
*
1351026 TATATACTTATATATATATGTATATAATATAAG
1 TATATA-TTATATATATAAGTATATAATATAAG
* *
1351059 --TATA-TATATATATAAGTATATAACAATACAT
1 TATATATTATATATATAAGTATATAA-TATA-AG
*
1351090 TATA-AGTATAAATATATACA-TATATAATATAAG
1 TATATA-T-TATATATATA-AGTATATAATATAAG
* *
1351123 TA-ACATTATCT-TATAAGTATATAATATA
1 TATATATTATATATATAAGTATATAATATA
1351151 TAAGTATAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
29 19 0.26
30 18 0.24
31 8 0.11
32 3 0.04
33 6 0.08
34 3 0.04
35 16 0.22
36 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (32 bp):
TATATATTATATATATAAGTATATAATATAAG
Found at i:1351080 original size:2 final size:2
Alignment explanation
Indices: 1351024--1351072 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
1351014 TATGTAAACT
*
1351024 TA TA TA TA CT- TA TA TA TA TA TG TA TA TA -A TA TA -A GTA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
1351065 TA TA TA TA
1 TA TA TA TA
1351073 AGTATATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 3 0.08
2 35 0.88
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1351112 original size:8 final size:7
Alignment explanation
Indices: 1351025--1351120 Score: 60
Period size: 8 Copynumber: 13.7 Consensus size: 7
1351015 ATGTAAACTT
1351025 ATATATA
1 ATATATA
*
1351032 CT-TAT-
1 ATATATA
1351037 ATATATA
1 ATATATA
*
1351044 TGTATATA
1 -ATATATA
1351052 ATATA-A
1 ATATATA
*
1351058 GTATATA
1 ATATATA
1351065 TATATATA
1 -ATATATA
1351073 AGTATATA
1 A-TATATA
*
1351081 ACA-ATA
1 ATATATA
1351087 CAT-TATA
1 -ATATATA
1351094 AGTATA-A
1 A-TATATA
1351101 ATATATA
1 ATATATA
1351108 CATATATA
1 -ATATATA
1351116 ATATA
1 ATATA
1351121 AGTAACATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
5 1 0.01
6 19 0.28
7 21 0.30
8 28 0.41
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:1351120 original size:27 final size:26
Alignment explanation
Indices: 1351025--1351124 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 26
1351015 ATGTAAACTT
* *
1351025 ATATATACTTATATATATATGTATATA
1 ATATATACATATATATATAAGTATA-A
*
1351052 ATATA-A-GTATATATAT-A-TATAA
1 ATATATACATATATATATAAGTATAA
* *
1351074 GTATATAACA-ATACATTATAAGTATAA
1 ATATAT-ACATATATA-TATAAGTATAA
1351101 ATATATACATATATAATATAAGTA
1 ATATATACATATAT-ATATAAGTA
1351125 ACATTATCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
22 5 0.09
23 4 0.07
24 5 0.09
25 12 0.21
26 5 0.09
27 26 0.45
28 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (26 bp):
ATATATACATATATATATAAGTATAA
Found at i:1351121 original size:21 final size:22
Alignment explanation
Indices: 1351037--1351121 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 22
1351027 ATATACTTAT
**
1351037 ATATATATGTATATAA-TATAA
1 ATATATACATATATAAGTATAA
* *
1351058 GTATATATATATATAAGTATATA
1 ATATATACATATATAAGTATA-A
*
1351081 ACA-ATACAT-TATAAGTATAA
1 ATATATACATATATAAGTATAA
1351101 ATATATACATATATAA-TATAA
1 ATATATACATATATAAGTATAA
1351122 GTAACATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.06
21 35 0.65
22 14 0.26
23 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (22 bp):
ATATATACATATATAAGTATAA
Found at i:1352334 original size:12 final size:13
Alignment explanation
Indices: 1352317--1352400 Score: 64
Period size: 14 Copynumber: 6.2 Consensus size: 13
1352307 TAAAATCTTC
1352317 TTTTTGTTTTT-T
1 TTTTTGTTTTTAT
1352329 TTTTTGTTTTTAT
1 TTTTTGTTTTTAT
*
1352342 ATTTTGTTTTGTAT
1 TTTTTGTTTT-TAT
*
1352356 TTGTTT-TTGTTATT
1 TT-TTTGTTTTTA-T
*
1352370 TGTTTTATGTTTTAT
1 T-TTTTGT-TTTTAT
*
1352385 TATTTGTTTTTTAT
1 TTTTTG-TTTTTAT
1352399 TT
1 TT
1352401 CTTTTCGTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
12 11 0.19
13 12 0.21
14 22 0.39
15 8 0.14
16 4 0.07
ACGTcount: A:0.10, C:0.00, G:0.11, T:0.80
Consensus pattern (13 bp):
TTTTTGTTTTTAT
Found at i:1352346 original size:19 final size:19
Alignment explanation
Indices: 1352324--1352405 Score: 55
Period size: 19 Copynumber: 4.4 Consensus size: 19
1352314 TTCTTTTTGT
1352324 TTTTTTTTTTGTTTTTATA
1 TTTTTTTTTTGTTTTTATA
* * *
1352343 -TTTTGTTTTGTATTTGT-
1 TTTTTTTTTTGTTTTTATA
* *
1352360 TTTTGTTATTTG-TTTTATG
1 TTTT-TTTTTTGTTTTTATA
*
1352379 TTTTATTATTTGTTTTT-TA
1 TTTT-TTTTTTGTTTTTATA
1352398 TTTCTTTT
1 TTT-TTTT
1352406 CGTTTTCTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
18 21 0.44
19 22 0.46
20 5 0.10
ACGTcount: A:0.10, C:0.01, G:0.10, T:0.79
Consensus pattern (19 bp):
TTTTTTTTTTGTTTTTATA
Found at i:1352380 original size:7 final size:6
Alignment explanation
Indices: 1352317--1352419 Score: 77
Period size: 6 Copynumber: 16.8 Consensus size: 6
1352307 TAAAATCTTC
* * *
1352317 TTTTTG TTTTTT TTTTTG TTTTTA TATTTTG -TTTTG TATTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTTTG
* * * *
1352365 TTATTTG TTTTATG TTTTAT- TATTTG TTTTT- TATTTC TTTTCG TTTTCTG
1 TT-TTTG TTTT-TG TTTT-TG TTTTTG TTTTTG TTTTTG TTTTTG TTTT-TG
1352415 TTTTT
1 TTTTT
1352420 TAGTAGTATC
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
5 10 0.13
6 44 0.57
7 23 0.30
ACGTcount: A:0.08, C:0.03, G:0.11, T:0.79
Consensus pattern (6 bp):
TTTTTG
Found at i:1352391 original size:43 final size:43
Alignment explanation
Indices: 1352314--1352418 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 43
1352304 TATTAAAATC
*
1352314 TTCTTTTTGTTTTT-TTTTTTGTTTTTATATTTTGTTTTGTAT
1 TTCTTTTTGTTTTTGTTTTATGTTTTTATATTTTGTTTTGTAT
* *
1352356 TTGTTTTTGTTATTTGTTTTATG-TTTTAT-TATTTGTTTTTTAT
1 TTCTTTTTGTT-TTTGTTTTATGTTTTTATAT-TTTGTTTTGTAT
*
1352399 TTCTTTTCGTTTTCTGTTTT
1 TTCTTTTTGTTTT-TGTTTT
1352419 TTAGTAGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
42 13 0.24
43 35 0.65
44 6 0.11
ACGTcount: A:0.08, C:0.04, G:0.10, T:0.78
Consensus pattern (43 bp):
TTCTTTTTGTTTTTGTTTTATGTTTTTATATTTTGTTTTGTAT
Found at i:1353040 original size:11 final size:11
Alignment explanation
Indices: 1353011--1353040 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1353001 TAAAAAATGA
*
1353011 TCTTTTTATTT
1 TCTTTTTTTTT
1353022 TCTTTTTTTTT
1 TCTTTTTTTTT
1353033 TCTTTTTT
1 TCTTTTTT
1353041 ATATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:1353633 original size:82 final size:82
Alignment explanation
Indices: 1353532--1353699 Score: 230
Period size: 82 Copynumber: 2.0 Consensus size: 82
1353522 TATTAGCTGA
** *
1353532 TTATATTGTTTTATGTTTTTATTAGTTGATGTGAAGGATATCAGTTAATTCTT-ATGTTAATGTG
1 TTATATTGTTTTATGTTTTTATTAGTT-ATGTGAAGGATATCAACTAATTATTAATGTTAATGTG
1353596 AAGGATATTAGCTTATTC
65 AAGGATATTAGCTTATTC
* * * * * *
1353614 TTATATTTTTTTCTGTTTTTATTTGTTATGTGGAGGATATTAACTGATTATTAATGTTAATGTGA
1 TTATATTGTTTTATGTTTTTATTAGTTATGTGAAGGATATCAACTAATTATTAATGTTAATGTGA
*
1353679 AGGCTATTAGCTTATTC
66 AGGATATTAGCTTATTC
1353696 TTAT
1 TTAT
1353700 GTTAATGTGA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
81 19 0.25
82 56 0.75
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (82 bp):
TTATATTGTTTTATGTTTTTATTAGTTATGTGAAGGATATCAACTAATTATTAATGTTAATGTGA
AGGATATTAGCTTATTC
Found at i:1353677 original size:32 final size:31
Alignment explanation
Indices: 1353632--1353713 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 31
1353622 TTTTCTGTTT
*
1353632 TTATT-TGTT-ATGTGGAGGATATTAACTGA
1 TTATTATGTTAATGTGAAGGATATTAACTGA
* * *
1353661 TTATTAATGTTAATGTGAAGGCTATTAGCTTA
1 TTATT-ATGTTAATGTGAAGGATATTAACTGA
*
1353693 TTCTTATGTTAATGTGAAGGA
1 TTATTATGTTAATGTGAAGGA
1353714 CTTTTGAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 5 0.11
31 19 0.43
32 20 0.45
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (31 bp):
TTATTATGTTAATGTGAAGGATATTAACTGA
Found at i:1353753 original size:7 final size:7
Alignment explanation
Indices: 1353741--1353847 Score: 76
Period size: 7 Copynumber: 14.9 Consensus size: 7
1353731 CTTATATTGT
1353741 TTTTTTA
1 TTTTTTA
1353748 TTTTTTA
1 TTTTTTA
*
1353755 TTTGTTTT
1 TTT-TTTA
1353763 TTATTTTA
1 TT-TTTTA
1353771 TGTTTTTTA
1 --TTTTTTA
*
1353780 TTTATGTA
1 TTT-TTTA
1353788 -TTTTTA
1 TTTTTTA
*
1353794 TTATTTA
1 TTTTTTA
* *
1353801 GTTTCTA
1 TTTTTTA
1353808 -TTTTTA
1 TTTTTTA
*
1353814 TTTGTT-
1 TTTTTTA
*
1353820 TTTGTTA
1 TTTTTTA
1353827 TTTATTTA
1 TTT-TTTA
1353835 TTTTTTA
1 TTTTTTA
1353842 TTTTTT
1 TTTTTT
1353848 GATATTTATT
Statistics
Matches: 80, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
6 14 0.17
7 41 0.51
8 17 0.21
9 6 0.08
10 2 0.03
ACGTcount: A:0.15, C:0.01, G:0.06, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:1353769 original size:17 final size:17
Alignment explanation
Indices: 1353741--1353879 Score: 69
Period size: 18 Copynumber: 8.2 Consensus size: 17
1353731 CTTATATTGT
1353741 TTTTTTATTTTTTATTTG
1 TTTTTTA-TTTTTATTTG
1353759 TTTTTTA-TTTTA--TG
1 TTTTTTATTTTTATTTG
1353773 TTTTTTA--TTTA--TG
1 TTTTTTATTTTTATTTG
*
1353786 TATTTTTATTATTTAGTTTC
1 T-TTTTTATT-TTTA-TTTG
1353806 TATTTTTATTTGTT-TTTG
1 T-TTTTTATTT-TTATTTG
* * *
1353824 TTATTTATTTATTTTTTA
1 TTTTTTATTT-TTATTTG
* *
1353842 TTTTTTGATATTTATTTA
1 TTTTTT-ATTTTTATTTG
* * *
1353860 TTTGTTGTTTTTTTTTG
1 TTTTTTATTTTTATTTG
1353877 TTT
1 TTT
1353880 AGATTTATTG
Statistics
Matches: 98, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
13 7 0.07
14 15 0.15
16 5 0.05
17 24 0.24
18 30 0.31
19 4 0.04
20 13 0.13
ACGTcount: A:0.14, C:0.01, G:0.07, T:0.78
Consensus pattern (17 bp):
TTTTTTATTTTTATTTG
Found at i:1353831 original size:47 final size:46
Alignment explanation
Indices: 1353742--1353839 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 46
1353732 TTATATTGTT
* * *
1353742 TTTTTATTTTTTATTTGTTTTTTATTTTATGTTTTTTATTTATGTA
1 TTTTTATTATTTATTTCTTTTTTATTTTATGTTTGTTATTTATGTA
*
1353788 TTTTTATTATTTAGTTTCTATTTTTATTTGT-T-TTTGTTATTTATTTA
1 TTTTTATTATTTA-TTTCT-TTTTTATTT-TATGTTTGTTATTTATGTA
1353835 TTTTT
1 TTTTT
1353840 TATTTTTTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
46 12 0.27
47 22 0.49
48 10 0.22
49 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.06, T:0.78
Consensus pattern (46 bp):
TTTTTATTATTTATTTCTTTTTTATTTTATGTTTGTTATTTATGTA
Found at i:1353833 original size:4 final size:4
Alignment explanation
Indices: 1353744--1353862 Score: 66
Period size: 4 Copynumber: 28.8 Consensus size: 4
1353734 ATATTGTTTT
* * * *
1353744 TTTA TTT- TTTA TTTG TTT- TTTA TTTTA TGTTT TTTA TTTA TGTA TTTT
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA T-TTA TTTA TTTA TTTA TTTA
* * *
1353792 TATTA TTTA GTTTC TATT- TTTA TTTG TTTT TGTTA TTTA TTTA TTT-
1 T-TTA TTTA -TTTA T-TTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
*
1353838 TTTA TTTT TTGATA TTTA TTTA TTT
1 TTTA TTTA TT--TA TTTA TTTA TTT
1353863 GTTGTTTTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
3 11 0.12
4 58 0.64
5 18 0.20
6 3 0.03
ACGTcount: A:0.17, C:0.01, G:0.06, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1353835 original size:21 final size:21
Alignment explanation
Indices: 1353810--1353865 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 21
1353800 AGTTTCTATT
*
1353810 TTTATTTGTTTTTGTTATTTA
1 TTTATTTGTTTTTGATATTTA
*
1353831 TTTATTTTTTATTTTTTGATATTTA
1 TTTA---TTT-GTTTTTGATATTTA
1353856 TTTATTTGTT
1 TTTATTTGTT
1353866 GTTTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
21 6 0.21
22 3 0.11
24 3 0.11
25 16 0.57
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (21 bp):
TTTATTTGTTTTTGATATTTA
Found at i:1356340 original size:22 final size:22
Alignment explanation
Indices: 1356315--1356390 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
1356305 TGGATTAGTA
*
1356315 TGAATGCTGACTGGACTT-GATC
1 TGAATGCTGACTGGAATTCG-TC
*
1356337 TGAATGCTGATTGGAATTCGTC
1 TGAATGCTGACTGGAATTCGTC
* * * *
1356359 TGAATGCTGATTAGAAATCGTT
1 TGAATGCTGACTGGAATTCGTC
1356381 TGAATGCTGA
1 TGAATGCTGA
1356391 TTAGTTTTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 47 0.98
23 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (22 bp):
TGAATGCTGACTGGAATTCGTC
Found at i:1356391 original size:22 final size:22
Alignment explanation
Indices: 1356335--1356394 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1356325 CTGGACTTGA
* *
1356335 TCTGAATGCTGATTGGAATTCG
1 TCTGAATGCTGATTAGAAATCG
1356357 TCTGAATGCTGATTAGAAATCG
1 TCTGAATGCTGATTAGAAATCG
*
1356379 TTTGAATGCTGATTAG
1 TCTGAATGCTGATTAG
1356395 TTTTGGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (22 bp):
TCTGAATGCTGATTAGAAATCG
Found at i:1357296 original size:16 final size:16
Alignment explanation
Indices: 1357275--1357309 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1357265 TAAGTTACAA
* *
1357275 ATCAGGTTTATAATAG
1 ATCAGGTTGATAACAG
1357291 ATCAGGTTGATAACAG
1 ATCAGGTTGATAACAG
1357307 ATC
1 ATC
1357310 GGATAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (16 bp):
ATCAGGTTGATAACAG
Found at i:1359815 original size:33 final size:33
Alignment explanation
Indices: 1359772--1359837 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1359762 ATGCCTTTAA
*
1359772 CTCTCTTTTAAGCTTCAAGTTATATGGAAAAGC
1 CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
1359805 CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
1 CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
1359838 TAGCCCTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (33 bp):
CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
Found at i:1364410 original size:2 final size:2
Alignment explanation
Indices: 1364403--1364637 Score: 100
Period size: 2 Copynumber: 125.5 Consensus size: 2
1364393 AAAATGATAA
* * *
1364403 AT AT AT AT AT AT GT AT AT GT AT A- AT A- AA AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1364441 AT A- AT AT AT A- AT AA AT A- AT AC AT AT AA AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1364479 AT GAT A- AT AT AT AT AT AT AT AT AT -T AT A- AT AT AA AT AT ACT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * *
1364520 AT AT A- ACG AC AT A- AT AT AT AC AC ACT AT AT A- AT AT AGT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * * *
1364560 AT AA AC AT AT A- AT AT A- AT AT GT AT AT ACT AT AT A- AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
1364600 AT AT AC A- AA AT AT AT A- AT A- AC AT A- AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364637 A
1 A
1364638 CAATATAAAT
Statistics
Matches: 178, Mismatches: 27, Indels: 56
0.68 0.10 0.21
Matches are distributed among these distances:
1 22 0.12
2 146 0.82
3 10 0.06
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (2 bp):
AT
Found at i:1364437 original size:27 final size:28
Alignment explanation
Indices: 1364401--1364655 Score: 139
Period size: 29 Copynumber: 9.2 Consensus size: 28
1364391 GAAAAATGAT
* *
1364401 AAATATATATATATGTATATGTATAATA
1 AAATATATATATATATATATATATAATA
1364429 AAATA-ATATATA-ATA-ATATATAAT-
1 AAATATATATATATATATATATATAATA
* *
1364453 AAATAATACATATAAATATATATATAATGA
1 AAAT-ATATATATATATATATATATAAT-A
*
1364483 TAATATATATATATATATAT-TATAATA
1 AAATATATATATATATATATATATAATA
* *
1364510 TAAATATACTATATA-ACGACATA-ATATATA
1 -AAATATA-TATATATA-TATATATATA-ATA
*
1364540 CACACTATATA-ATATAGTATATA-A-ACATA
1 -A-AATATATATATATA-TATATATATA-ATA
* *
1364569 TAATATA-ATATGTATATACTATATAATA
1 AAATATATATATATATATA-TATATAATA
* *
1364597 TAAATATACA-A-A-ATATATA-ATAACA
1 -AAATATATATATATATATATATATAATA
* *
1364622 TAATATATATA-ATATACA-ATATAAATA
1 AAATATATATATATATATATATAT-AATA
*
1364649 AACTATA
1 AAATATA
1364656 CAACATAATA
Statistics
Matches: 177, Mismatches: 27, Indels: 47
0.71 0.11 0.19
Matches are distributed among these distances:
24 11 0.06
25 17 0.10
26 21 0.12
27 35 0.20
28 31 0.18
29 41 0.23
30 16 0.09
31 5 0.03
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (28 bp):
AAATATATATATATATATATATATAATA
Found at i:1364515 original size:82 final size:83
Alignment explanation
Indices: 1364393--1364637 Score: 233
Period size: 82 Copynumber: 3.0 Consensus size: 83
1364383 TAAAACAAGA
* *
1364393 AAAATGATAAATATATATATATGTATATGTATAATA-AAATAATATATAATAATATATAATAAAT
1 AAAATGAT-AATATATATATATATATATATATAATATAAATAATATATAATAATATATAATAAAT
1364457 AATACATATAAATATATAT
65 AATACATATAAATATATAT
* * * *
1364476 ATAATGATAATATATATATATATATAT-TATAATATAAAT-ATACTAT-ATAACGACATAATATA
1 AAAATGATAATATATATATATATATATATATAATATAAATAATA-TATAATAA-TATATAATAAA
*
1364538 TACACACTATATAATATAGTATAT
64 TA-ATAC-ATATAA-ATA-TATAT
* *
1364562 AAACAT-ATAATATA-ATATGTATATACTATATAATAT--A-AATATACAA-AATATATAATAAC
1 AAA-ATGATAATATATATATATATATA-TATATAATATAAATAATATATAATAATATATAATAA-
*
1364621 ATAATATATAT-AATATA
63 ATAATACATATAAATATA
1364638 CAATATAAAT
Statistics
Matches: 135, Mismatches: 14, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
79 2 0.01
80 3 0.02
81 15 0.11
82 39 0.29
83 19 0.14
84 13 0.10
85 18 0.13
86 16 0.12
87 10 0.07
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (83 bp):
AAAATGATAATATATATATATATATATATATAATATAAATAATATATAATAATATATAATAAATA
ATACATATAAATATATAT
Found at i:1364656 original size:69 final size:68
Alignment explanation
Indices: 1364472--1364755 Score: 150
Period size: 68 Copynumber: 4.2 Consensus size: 68
1364462 ATATAAATAT
* *
1364472 ATATATAATGATAAT-ATATATATATATATATTATA-ATATA--AATATACTATATAACGACATA
1 ATATATAAT-A-AATAATATATATA-ATATATAATATA-ATATAAATATACTATAT-A--ATATA
*
1364533 ATATATACACA
59 A-ATATACAAA
* * * **
1364544 CTATATAAT--ATAGTATATA-AACATATAATATAATATGTATATACTATATAATATAAATATAC
1 ATATATAATAAATAATATATATAATATATAATATAATATAAATATACTATATAATATAAATATAC
1364606 AAA
66 AAA
* * *
1364609 ATATATAATAACATAATATATATAATATACAATATAA-ATAAACTATACAACATAATA-AAATAT
1 ATATATAATAA-ATAATATATATAATATATAATATAATATAAA-TATACTATATAATATAAATAT
*
1364672 --ATA
64 ACAAA
* * * * *
1364675 GTCATATAATACATTTATACTACATAATATA-AATATACTATAAGATATA-TA-AT-ATATAAAT
1 AT-ATATAATA-AATAATA-TATATAATATATAATATAATATAA-ATATACTATATAATATAAAT
*
1364736 ATA-ATA
62 ATACAAA
1364742 ATATACTATATAAA
1 ATATA-TA-ATAAA
1364756 CAAGGTTGAA
Statistics
Matches: 170, Mismatches: 24, Indels: 41
0.72 0.10 0.17
Matches are distributed among these distances:
65 19 0.11
66 19 0.11
67 37 0.22
68 45 0.26
69 42 0.25
72 8 0.05
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (68 bp):
ATATATAATAAATAATATATATAATATATAATATAATATAAATATACTATATAATATAAATATAC
AAA
Found at i:1364657 original size:18 final size:17
Alignment explanation
Indices: 1364591--1364672 Score: 62
Period size: 17 Copynumber: 4.8 Consensus size: 17
1364581 TATATACTAT
*
1364591 ATAATATAAATATACAAA
1 ATAATA-AAATATACAAC
*
1364609 AT-ATATAATA-ACATA-
1 ATAATAAAATATACA-AC
* *
1364624 ATATATATAATATACAAT
1 ATA-ATAAAATATACAAC
*
1364642 ATAAATAAACTATACAAC
1 AT-AATAAAATATACAAC
1364660 ATAATAAAATATA
1 ATAATAAAATATA
1364673 TAGTCATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
15 5 0.09
16 5 0.09
17 22 0.42
18 20 0.38
19 1 0.02
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAAAATATACAAC
Found at i:1364661 original size:39 final size:39
Alignment explanation
Indices: 1364588--1364665 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 39
1364578 ATGTATATAC
*
1364588 TATATAATATAAATATACAAAATATATAATAACATAATA
1 TATATAATATAAATATACAAAATATATAACAACATAATA
1364627 TATATAATATACAATATA-AATAA-ACTAT-ACAACATAATA
1 TATATAATATA-AATATACAA-AATA-TATAACAACATAATA
1364666 AAATATATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
39 24 0.69
40 11 0.31
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (39 bp):
TATATAATATAAATATACAAAATATATAACAACATAATA
Found at i:1364680 original size:18 final size:19
Alignment explanation
Indices: 1364652--1364711 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
1364642 ATAAATAAAC
*
1364652 TATACAACATAATAAAATA
1 TATACTACATAATAAAATA
* *
1364671 TATAGT-CAT-ATAATACATT
1 TATACTACATAATAA-A-ATA
1364690 TATACTACATAATATAAATA
1 TATACTACATAATA-AAATA
1364710 TA
1 TA
1364712 CTATAAGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
17 4 0.13
18 4 0.13
19 11 0.35
20 7 0.23
21 4 0.13
22 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (19 bp):
TATACTACATAATAAAATA
Found at i:1364712 original size:18 final size:18
Alignment explanation
Indices: 1364431--1364754 Score: 118
Period size: 18 Copynumber: 18.2 Consensus size: 18
1364421 GTATAATAAA
1364431 ATAATATATAATA-A-TAT
1 ATAATATA-AATATACTAT
1364448 AT-A-ATAAATAATAC-AT
1 ATAATATAAAT-ATACTAT
* *
1364464 ATAAATATATATATAATGAT
1 AT-AATATAAATATACT-AT
*
1364484 AATATATATATATATA-TATT
1 -ATA-ATATAAATATACTA-T
1364504 ATAATATAAATATACTAT
1 ATAATATAAATATACTAT
* * *
1364522 ATAACGACATAATATA-TAC
1 ATAA-TATA-AATATACTAT
* * *
1364541 ACACTATATAATATAGTAT
1 ATAATATA-AATATACTAT
*
1364560 AT-A-A-ACATATA--AT
1 ATAATATAAATATACTAT
**
1364573 ATAATATGTATATACTAT
1 ATAATATAAATATACTAT
1364591 ATAATATAAATATAC-A-
1 ATAATATAAATATACTAT
1364607 A-AATATATAATA-AC-AT
1 ATAATATA-AATATACTAT
*
1364623 A-ATATATATAATATACAAT
1 ATA-ATATA-AATATACTAT
* *
1364642 ATAA-ATAAACTATACAAC
1 ATAATATAAA-TATACTAT
* *
1364660 ATAATAAAATATATAGTCAT
1 ATAATATAA-ATATACT-AT
* ** *
1364680 ATAATACATTTATACTAC
1 ATAATATAAATATACTAT
1364698 ATAATATAAATATACTAT
1 ATAATATAAATATACTAT
*
1364716 A-AGATATATA-ATA-TAT
1 ATA-ATATAAATATACTAT
1364732 A-AATATAATAATATACTAT
1 ATAATAT-A-AATATACTAT
1364751 ATAA
1 ATAA
1364755 ACAAGGTTGA
Statistics
Matches: 237, Mismatches: 34, Indels: 69
0.70 0.10 0.20
Matches are distributed among these distances:
13 4 0.02
14 4 0.02
15 23 0.10
16 25 0.11
17 21 0.09
18 84 0.35
19 40 0.17
20 23 0.10
21 13 0.05
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAATATAAATATACTAT
Found at i:1364732 original size:16 final size:16
Alignment explanation
Indices: 1364700--1364746 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1364690 TATACTACAT
1364700 AATATAA-ATATACTATA
1 AATATAATA-ATA-TATA
1364717 AGATAT-ATAATATATA
1 A-ATATAATAATATATA
1364733 AATATAATAATATA
1 AATATAATAATATA
1364747 CTATATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 5 0.19
18 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
AATATAATAATATATA
Found at i:1364744 original size:8 final size:7
Alignment explanation
Indices: 1364402--1364754 Score: 124
Period size: 7 Copynumber: 50.3 Consensus size: 7
1364392 AAAAATGATA
1364402 AATATAT
1 AATATAT
*
1364409 ATATATGT
1 A-ATATAT
*
1364417 ATATGTAT
1 A-ATATAT
1364425 AATA-A-
1 AATATAT
1364430 AATA-AT
1 AATATAT
1364436 -ATATAAT
1 AATAT-AT
1364443 AATATAT
1 AATATAT
*
1364450 AATAAAT
1 AATATAT
1364457 AATACATAT
1 AAT--ATAT
1364466 AA-ATAT
1 AATATAT
1364472 -ATATAT
1 AATATAT
*
1364478 AAT-GAT
1 AATATAT
1364484 AATATAT
1 AATATAT
1364491 -ATATAT
1 AATATAT
1364497 -ATATAT
1 AATATAT
*
1364503 TATAATAT
1 AAT-ATAT
1364511 AA-ATAT
1 AATATAT
*
1364517 ACTATAT
1 AATATAT
* *
1364524 AACGACAT
1 AA-TATAT
1364532 AATATAT
1 AATATAT
1364539 ACACACTATAT
1 --A-A-TATAT
1364550 AATATAGT
1 AATATA-T
1364558 -ATATA-
1 AATATAT
*
1364563 AACATAT
1 AATATAT
1364570 AATATAAT
1 AATAT-AT
*
1364578 ATGTATAT
1 A-ATATAT
*
1364586 ACTATAT
1 AATATAT
1364593 AATATA-
1 AATATAT
*
1364599 AATATAC
1 AATATAT
*
1364606 AAAATAT
1 AATATAT
1364613 -ATA-AT
1 AATATAT
*
1364618 AACATA-
1 AATATAT
1364624 ATATATAT
1 A-ATATAT
*
1364632 AATATAC
1 AATATAT
1364639 AATATA-
1 AATATAT
1364645 AATAAACTAT
1 AAT--A-TAT
*
1364655 ACA-ACAT
1 A-ATATAT
1364662 AATA-A-
1 AATATAT
1364667 AATATAT
1 AATATAT
*
1364674 AGTCATAT
1 AAT-ATAT
*
1364682 AATACAT
1 AATATAT
*
1364689 -TTATACT
1 AATATA-T
1364696 ACATAATAT
1 A-AT-ATAT
1364705 AA-ATAT
1 AATATAT
*
1364711 ACTATA-
1 AATATAT
1364717 AGATATAT
1 A-ATATAT
1364725 AATATAT
1 AATATAT
1364732 AA-ATAT
1 AATATAT
1364738 AATAATAT
1 AAT-ATAT
*
1364746 ACTATAT
1 AATATAT
1364753 AA
1 AA
1364755 ACAAGGTTGA
Statistics
Matches: 263, Mismatches: 37, Indels: 92
0.67 0.09 0.23
Matches are distributed among these distances:
5 15 0.06
6 67 0.25
7 104 0.40
8 51 0.19
9 15 0.06
10 5 0.02
11 6 0.02
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (7 bp):
AATATAT
Found at i:1365387 original size:32 final size:32
Alignment explanation
Indices: 1365351--1365457 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
1365341 GGGTACGATA
1365351 TCCTTCGTTGTGAAGTTGAAATCATGGGTGAC
1 TCCTTCGTTGTGAAGTTGAAATCATGGGTGAC
* * * * *
1365383 TCCTTCGTCGTGAAATT-AAGTCTTTGGGTACGAAG
1 TCCTTCGTTGTGAAGTTGAAATC-ATGGGT--G-AC
* *
1365418 TCCTTCATTGTGAAGTTGAAATCGTGGGTGAC
1 TCCTTCGTTGTGAAGTTGAAATCATGGGTGAC
*
1365450 TCATTCGT
1 TCCTTCGT
1365458 CATGAAATTA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
31 4 0.07
32 27 0.47
33 1 0.02
34 1 0.02
35 20 0.35
36 4 0.07
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (32 bp):
TCCTTCGTTGTGAAGTTGAAATCATGGGTGAC
Found at i:1365446 original size:35 final size:34
Alignment explanation
Indices: 1365340--1365446 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 34
1365330 GTCGATCTTT
1365340 TGGGTACGATATCCTTCGTTGTGAAGTTGAAATCA
1 TGGGTACGA-ATCCTTCGTTGTGAAGTTGAAATCA
* * * * *
1365375 TGGGT--GACTCCTTCGTCGTGAAATT-AAGTCTT
1 TGGGTACGAATCCTTCGTTGTGAAGTTGAAATC-A
* *
1365407 TGGGTACGAAGTCCTTCATTGTGAAGTTGAAATCG
1 TGGGTACGAA-TCCTTCGTTGTGAAGTTGAAATCA
1365442 TGGGT
1 TGGGT
1365447 GACTCATTCG
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
31 4 0.07
32 20 0.36
33 2 0.04
34 2 0.04
35 24 0.43
36 4 0.07
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (34 bp):
TGGGTACGAATCCTTCGTTGTGAAGTTGAAATCA
Found at i:1365511 original size:73 final size:68
Alignment explanation
Indices: 1365335--1365512 Score: 241
Period size: 67 Copynumber: 2.6 Consensus size: 68
1365325 GTTGGGTCGA
* * *
1365335 TCTTTTGGGTACGATATCCTTCGTTGTGAAGTTGAAATCATGGGTGACTCCTTCGTCGTGAAATT
1 TCTTTTGGGTACGATGTCCTTCGTTGTGAAGTTGAAATCATGGGTGACTCATTCGTCATGAAATT
1365400 AAG
66 AAG
* * *
1365403 TC-TTTGGGTACGAAGTCCTTCATTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCATGAAATT
1 TCTTTTGGGTACGATGTCCTTCGTTGTGAAGTTGAAATCATGGGTGACTCATTCGTCATGAAATT
1365467 AAG
66 AAG
*
1365470 TCGAAACTTTTGGGTACGATGTCCTTCGTTGTGAAGCTGAAAT
1 T-----CTTTTGGGTACGATGTCCTTCGTTGTGAAGTTGAAAT
1365513 TCAACTTGGA
Statistics
Matches: 95, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
67 60 0.63
68 2 0.02
72 1 0.01
73 32 0.34
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (68 bp):
TCTTTTGGGTACGATGTCCTTCGTTGTGAAGTTGAAATCATGGGTGACTCATTCGTCATGAAATT
AAG
Found at i:1373789 original size:55 final size:55
Alignment explanation
Indices: 1373727--1373996 Score: 366
Period size: 55 Copynumber: 4.9 Consensus size: 55
1373717 TTATACAGTA
* * *
1373727 ATTCATCAACTCATGATGAATTCTGTGGTTTTACACACAAAGTGCATGTATGATG
1 ATTCATCAACTCATGATGAATTCTGTGGATTTACACACAAAGTGCATGTACGGTG
*
1373782 AATCATCAACTCATGATGAATT-TCGTGGATTTACACACAAAGTGTC-TGTACGGTG
1 ATTCATCAACTCATGATGAATTCT-GTGGATTTACACACAAAGTG-CATGTACGGTG
* *
1373837 ATTCATCAACTCATGATGAATTTTGTGGATTTACACACAAAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCTGTGGATTTACACACAAAGTGCATGTACGGTG
* * *
1373892 ATTCATCAACTCATGATGAATTCCGTTGATTTGCACACAAAGTG-ACTGTACGGTG
1 ATTCATCAACTCATGATGAATTCTGTGGATTTACACACAAAGTGCA-TGTACGGTG
* * * * *
1373947 ATTCATCAACTCATGATGAATTTTGTGGATTTGCATAAAAAATGCATGTA
1 ATTCATCAACTCATGATGAATTCTGTGGATTTACACACAAAGTGCATGTA
1373997 GTACACTTAG
Statistics
Matches: 193, Mismatches: 16, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
54 2 0.01
55 188 0.97
56 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCTGTGGATTTACACACAAAGTGCATGTACGGTG
Found at i:1373864 original size:110 final size:110
Alignment explanation
Indices: 1373727--1373996 Score: 414
Period size: 110 Copynumber: 2.5 Consensus size: 110
1373717 TTATACAGTA
* * *
1373727 ATTCATCAACTCATGATGAATTCTGTGGTTTTACACACAAAGTGCATGTATGATGAATCATCAAC
1 ATTCATCAACTCATGATGAATTTTGTGGATTTACACACAAAGTGCATGTACGATGAATCATCAAC
* *
1373792 TCATGATGAATTTCGTGGATTTACACACAAAGTGTCTGTACGGTG
66 TCATGATGAATTCCGTGGATTTACACACAAAGTGACTGTACGGTG
* * *
1373837 ATTCATCAACTCATGATGAATTTTGTGGATTTACACACAAAGTGCCTGTACGGTGATTCATCAAC
1 ATTCATCAACTCATGATGAATTTTGTGGATTTACACACAAAGTGCATGTACGATGAATCATCAAC
* *
1373902 TCATGATGAATTCCGTTGATTTGCACACAAAGTGACTGTACGGTG
66 TCATGATGAATTCCGTGGATTTACACACAAAGTGACTGTACGGTG
* * * *
1373947 ATTCATCAACTCATGATGAATTTTGTGGATTTGCATAAAAAATGCATGTA
1 ATTCATCAACTCATGATGAATTTTGTGGATTTACACACAAAGTGCATGTA
1373997 GTACACTTAG
Statistics
Matches: 145, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 145 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (110 bp):
ATTCATCAACTCATGATGAATTTTGTGGATTTACACACAAAGTGCATGTACGATGAATCATCAAC
TCATGATGAATTCCGTGGATTTACACACAAAGTGACTGTACGGTG
Found at i:1374482 original size:21 final size:21
Alignment explanation
Indices: 1374456--1374508 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1374446 CACCCTATCG
1374456 GTATCGATACTTCTTGAAGCA
1 GTATCGATACTTCTTGAAGCA
1374477 GTATCGATACTTCTTGAAGCA
1 GTATCGATACTTCTTGAAGCA
1374498 GTATCGATACT
1 GTATCGATACT
1374509 ATCCAACTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
GTATCGATACTTCTTGAAGCA
Found at i:1394605 original size:50 final size:50
Alignment explanation
Indices: 1394530--1394628 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
1394520 GGTTAGACAA
* *
1394530 TTGATTTGTTTTGCTACTAGAGATGAAGTACTTTCATAACATGTTTCATT
1 TTGATTTGTGTTGCTACTAGAGATGAAGTACTTCCATAACATGTTTCATT
1394580 TTGATTTGTGTTGCTACTAGAGATGAAGTACTTCCATAACATGTTTCAT
1 TTGATTTGTGTTGCTACTAGAGATGAAGTACTTCCATAACATGTTTCAT
1394629 ATTTTGATGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (50 bp):
TTGATTTGTGTTGCTACTAGAGATGAAGTACTTCCATAACATGTTTCATT
Found at i:1395072 original size:24 final size:23
Alignment explanation
Indices: 1395045--1395089 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1395035 ATCCTTAAAT
*
1395045 TAGTTTTTTAATAATTTAATTTCG
1 TAGTATTTTAAT-ATTTAATTTCG
*
1395069 TAGTATTTTCATATTTAATTT
1 TAGTATTTTAATATTTAATTT
1395090 ATTGAATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (23 bp):
TAGTATTTTAATATTTAATTTCG
Found at i:1395467 original size:21 final size:21
Alignment explanation
Indices: 1395398--1395468 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
1395388 TTCCAGATTT
* * *
1395398 GCAATGCGATTATCACTA-TC
1 GCAATGCGATTTTCCCAATTC
1395418 GCAATGCGATTTT-CCAATTTC
1 GCAATGCGATTTTCCCAA-TTC
**
1395439 GCGTTGCGATTTTCCCAATTC
1 GCAATGCGATTTTCCCAATTC
1395460 GCAATGCGA
1 GCAATGCGA
1395469 ATAAGTAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 23 0.56
22 4 0.10
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
GCAATGCGATTTTCCCAATTC
Found at i:1395483 original size:20 final size:21
Alignment explanation
Indices: 1395458--1395509 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1395448 TTTTCCCAAT
*
1395458 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1395478 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1395499 TCGCAATGCGA
1 TCGCAATGCGA
1395510 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1395522 original size:41 final size:41
Alignment explanation
Indices: 1395495--1395572 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1395485 GCGAATTGGG
1395495 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* * *
1395536 AAAATCGCAATGTGATATTGACTTTCGCAACGCGATA
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATA
1395573 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1395523 original size:20 final size:20
Alignment explanation
Indices: 1395498--1395612 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
1395488 AATTGGGAAA
* *
1395498 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
1395518 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
* * *
1395539 ATCGCAATGTGATATTGACT
1 ATCGCAACGCGATAATGACT
* *
1395559 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
1395579 TTCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
1395599 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
1395613 TTTCAAAGCG
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.05
20 45 0.61
21 23 0.31
22 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:1395807 original size:22 final size:22
Alignment explanation
Indices: 1395779--1395822 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1395769 CCCTCTCTCA
1395779 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1395801 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1395823 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1396124 original size:20 final size:20
Alignment explanation
Indices: 1396085--1396143 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1396075 TTTATTCTCT
* **
1396085 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1396105 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* * *
1396125 TGTTGTGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1396144 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1396334 original size:25 final size:24
Alignment explanation
Indices: 1396280--1396334 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1396270 TGTTTATTAT
* *
1396280 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1396304 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1396330 TGTTT
1 TGTTT
1396335 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1397483 original size:18 final size:18
Alignment explanation
Indices: 1397462--1397509 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1397452 TCCACTTCGG
1397462 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1397480 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1397498 GAGCCATCACCT
1 GAGCCATCACCT
1397510 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1398066 original size:19 final size:20
Alignment explanation
Indices: 1398012--1398078 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1398002 TAGTTTACTT
* *
1398012 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1398032 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1398052 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1398071 TCGCAACG
1 TCGCAACG
1398079 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1398105 original size:19 final size:19
Alignment explanation
Indices: 1398012--1398114 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
1398002 TAGTTTACTT
* **
1398012 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1398032 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1398052 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1398071 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1398085 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1398104 TCGCAATGCGA
1 TCGCAACGCGA
1398115 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.40
20 24 0.35
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1398145 original size:14 final size:14
Alignment explanation
Indices: 1398126--1398184 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1398116 TTGTGTTTCG
1398126 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1398140 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
1398157 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
1398173 CGTTGCGATTTT
1 CGTTGCGATTTT
1398185 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.53
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 7 0.19
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1398165 original size:33 final size:33
Alignment explanation
Indices: 1398128--1398203 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
1398118 GTGTTTCGCG
1398128 TTGCGATTTTGTCGTTGCGATTTTCATTTCACA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCACA
*
1398161 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCACA
*
1398194 TTGTGATTTT
1 TTGCGATTTT
1398204 CATTTCGCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.16, G:0.20, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCACA
Found at i:1398166 original size:19 final size:19
Alignment explanation
Indices: 1398142--1398219 Score: 85
Period size: 19 Copynumber: 4.4 Consensus size: 19
1398132 GATTTTGTCG
*
1398142 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
*
1398161 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
1398175 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1398194 TTGTGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1398213 TTGCGAT
1 TTGCGAT
1398220 AGCCATTTCC
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 3 0.06
17 4 0.08
18 3 0.06
19 29 0.60
ACGTcount: A:0.14, C:0.18, G:0.19, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1398234 original size:20 final size:19
Alignment explanation
Indices: 1398204--1398258 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1398194 TTGTGATTTT
*
1398204 CATTTCGCGTTGCGATAGC
1 CATTTCGCGTTGCGATAAC
* *
1398223 CATTTCCGCGTTACGATAAT
1 CATTT-CGCGTTGCGATAAC
1398243 CATTTTCGCGTTGCGA
1 CA-TTTCGCGTTGCGA
1398259 AAGTAAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAAC
Found at i:1398269 original size:20 final size:20
Alignment explanation
Indices: 1398246--1398284 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1398236 CGATAATCAT
1398246 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
1398266 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
1398285 ACTATTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:1398660 original size:21 final size:21
Alignment explanation
Indices: 1398627--1398687 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1398617 GACTCACCTG
1398627 TCATCCCTCAAGAGTCCCCT-
1 TCATCCCTCAAGAGTCCCCTA
** *
1398647 TCAATCTTTCAAGAGGCCCCTA
1 TC-ATCCCTCAAGAGTCCCCTA
1398669 TCATCCCTCAAGAGTCCCC
1 TCATCCCTCAAGAGTCCCC
1398688 CCACCGTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.23, C:0.41, G:0.11, T:0.25
Consensus pattern (21 bp):
TCATCCCTCAAGAGTCCCCTA
Found at i:1398713 original size:40 final size:41
Alignment explanation
Indices: 1398624--1398713 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 41
1398614 CCCGACTCAC
* * **
1398624 CTGTCATCCCTCAAGAGTCCCCTTCAATCTTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCC-TCAACCGTTCAAGAGGCAA
* *
1398666 CTATCATCCCTCAAGAGTCCCC-CCACCGTTCAAGAGGCAA
1 CTGTCATCCCTCAAGAGTCCCCTCAACCGTTCAAGAGGCAA
1398706 CTGTCATC
1 CTGTCATC
1398714 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 20 0.49
42 21 0.51
ACGTcount: A:0.23, C:0.39, G:0.14, T:0.23
Consensus pattern (41 bp):
CTGTCATCCCTCAAGAGTCCCCTCAACCGTTCAAGAGGCAA
Found at i:1400156 original size:14 final size:14
Alignment explanation
Indices: 1400122--1400160 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1400112 TTGATTGTTT
1400122 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1400136 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1400150 TGTTGATTTGT
1 AATTGATTTGT
1400161 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1400322 original size:19 final size:19
Alignment explanation
Indices: 1400300--1400342 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1400290 GCAATGAGAG
1400300 AATCGCAATGCAAAATGAA
1 AATCGCAATGCAAAATGAA
* *
1400319 AATCACAATGCGAAATGAA
1 AATCGCAATGCAAAATGAA
1400338 AATCG
1 AATCG
1400343 TAACGAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCAAAATGAA
Found at i:1400408 original size:20 final size:20
Alignment explanation
Indices: 1400383--1400478 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
1400373 TCGCATTGCG
*
1400383 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1400403 ATTTTCGCTTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1400423 ATTTTCGCTTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1400443 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
1400463 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
1400479 TGCGATAGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1401122 original size:20 final size:20
Alignment explanation
Indices: 1401016--1401130 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
1401006 GATTCTGTAT
*
1401016 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
1401036 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1401056 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
1401076 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
1401097 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1401117 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
1401131 TTTCCAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 13 0.16
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1401132 original size:41 final size:41
Alignment explanation
Indices: 1400996--1401133 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
1400986 AACTTTGAAA
* * *
1400996 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
* * ** ** *
1401037 ATCTCGTTGCGA--AAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGT
1401077 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1401118 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1401134 CCAAATTCGC
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 28 0.36
41 46 0.59
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
Found at i:1401149 original size:41 final size:41
Alignment explanation
Indices: 1400996--1401151 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
1400986 AACTTTGAAA
* ** * * *
1400996 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* * *** * *
1401037 ATCTCGTTGCGAAAGTCAGA-ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
** *
1401077 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
*
1401118 ATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 ATCGCATTGCGATTTT-CAAATATCGCGTTGCGAT
1401152 TTACTTATTC
Statistics
Matches: 87, Mismatches: 26, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
40 28 0.32
41 57 0.66
42 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
Found at i:1401163 original size:20 final size:21
Alignment explanation
Indices: 1401119--1401170 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1401109 ATAGTCAGTA
*
1401119 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1401140 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1401160 TCGCATTGCGA
1 TCGCATTGCGA
1401171 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1404807 original size:17 final size:17
Alignment explanation
Indices: 1404768--1404809 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1404758 AATAAATAAA
*
1404768 CAAGAAATGAAGAGAAG
1 CAAGAAATGAAGAGAAC
*
1404785 CGAGAAATGAAGAGAAC
1 CAAGAAATGAAGAGAAC
1404802 CAAGAAAT
1 CAAGAAAT
1404810 ATATCGATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.57, C:0.10, G:0.26, T:0.07
Consensus pattern (17 bp):
CAAGAAATGAAGAGAAC
Found at i:1405183 original size:13 final size:13
Alignment explanation
Indices: 1405161--1405196 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1405151 TCTATTTATA
1405161 TTTTTCCCTTTGT
1 TTTTTCCCTTTGT
*
1405174 TTTTTTCCTTTGT
1 TTTTTCCCTTTGT
1405187 TTTTTCCCTT
1 TTTTTCCCTT
1405197 ACTACCCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.22, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTCCCTTTGT
Found at i:1405759 original size:17 final size:15
Alignment explanation
Indices: 1405720--1405761 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1405710 TTAAAGTTAT
1405720 ATATTATTTTAAATA
1 ATATTATTTTAAATA
1405735 AT-TATATTTGTACAATA
1 ATAT-TATTT-TA-AATA
1405752 ATATTATTTT
1 ATATTATTTT
1405762 TTTCACATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 7 0.30
16 3 0.13
17 11 0.48
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTATTTTAAATA
Found at i:1407542 original size:145 final size:145
Alignment explanation
Indices: 1407279--1407569 Score: 582
Period size: 145 Copynumber: 2.0 Consensus size: 145
1407269 ACATATAAGG
1407279 ATAAAAGCAAATTAATCAAATTTATATAATCAGATTTATAAAGTAAATATATTTTTAATGTCATA
1 ATAAAAGCAAATTAATCAAATTTATATAATCAGATTTATAAAGTAAATATATTTTTAATGTCATA
1407344 TACATATCAATCATCACTAAAGATATCATACAATTTTATATCATATATGTATGTATACTAAACAT
66 TACATATCAATCATCACTAAAGATATCATACAATTTTATATCATATATGTATGTATACTAAACAT
1407409 GATTTCATTATCATA
131 GATTTCATTATCATA
1407424 ATAAAAGCAAATTAATCAAATTTATATAATCAGATTTATAAAGTAAATATATTTTTAATGTCATA
1 ATAAAAGCAAATTAATCAAATTTATATAATCAGATTTATAAAGTAAATATATTTTTAATGTCATA
1407489 TACATATCAATCATCACTAAAGATATCATACAATTTTATATCATATATGTATGTATACTAAACAT
66 TACATATCAATCATCACTAAAGATATCATACAATTTTATATCATATATGTATGTATACTAAACAT
1407554 GATTTCATTATCATA
131 GATTTCATTATCATA
1407569 A
1 A
1407570 AATTATATCA
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.38
Consensus pattern (145 bp):
ATAAAAGCAAATTAATCAAATTTATATAATCAGATTTATAAAGTAAATATATTTTTAATGTCATA
TACATATCAATCATCACTAAAGATATCATACAATTTTATATCATATATGTATGTATACTAAACAT
GATTTCATTATCATA
Found at i:1409671 original size:75 final size:75
Alignment explanation
Indices: 1409578--1409771 Score: 230
Period size: 75 Copynumber: 2.6 Consensus size: 75
1409568 ATAAATAAAA
* * * * * *
1409578 TCAAATATCAATACTCAAACCACAATATTAAGTTTAGAACAATAAAATCTATAAACAAA-TCACA
1 TCAAATCTCAAGACTCAAACCATAATATTAAGTATAGAAAAATAAAATCCATAAACAAACT-ACA
1409642 ATATTAAAATG
65 ATATTAAAATG
* * * * *
1409653 TCAAATCTCAAGATTCAAACCATAATATTAACTCTA-AAATAATAAAATCCATAATCAAACTATA
1 TCAAATCTCAAGACTCAAACCATAATATTAAGTATAGAAA-AATAAAATCCATAAACAAACTACA
*
1409717 ATATTAAAGTG
65 ATATTAAAATG
* *
1409728 TCAAATCTTAAGACTGAAACCATAATATTAAGTATAGAAAAATA
1 TCAAATCTCAAGACTCAAACCATAATATTAAGTATAGAAAAATA
1409772 TTACATGTCG
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
74 2 0.02
75 94 0.94
76 4 0.04
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.28
Consensus pattern (75 bp):
TCAAATCTCAAGACTCAAACCATAATATTAAGTATAGAAAAATAAAATCCATAAACAAACTACAA
TATTAAAATG
Found at i:1409909 original size:16 final size:16
Alignment explanation
Indices: 1409874--1409914 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1409864 GTTTACTTCA
*
1409874 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
*
1409889 GAATGATTCAAATGTT
1 GAATGATTCAAATGCT
1409905 GAATGATTCA
1 GAATGATTCA
1409915 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:1410024 original size:27 final size:23
Alignment explanation
Indices: 1409966--1410029 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
1409956 AATAACGGCT
*
1409966 CTGAATCAGTTAGCACTGTTTTG
1 CTGAATCAGTCAGCACTGTTTTG
1409989 CTGAATCAGTCAGCACTGTTTTG
1 CTGAATCAGTCAGCACTGTTTTG
1410012 CTGAATCAGTCAGCACTG
1 CTGAATCAGTCAGCACTG
1410030 AATCATTCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (23 bp):
CTGAATCAGTCAGCACTGTTTTG
Found at i:1410452 original size:2 final size:2
Alignment explanation
Indices: 1410441--1410507 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
1410431 TCGTTTGAGA
**
1410441 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1410482 AT -T 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
1410508 CAGGACAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1412373 original size:20 final size:20
Alignment explanation
Indices: 1412348--1412393 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1412338 TATATATATG
*
1412348 AAATAT-TTTTGAGTTAATTA
1 AAATATGTTTTAAGTT-ATTA
*
1412368 AAATATGTTTTAAGTTTTTA
1 AAATATGTTTTAAGTTATTA
1412388 AAATAT
1 AAATAT
1412394 AAAAAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (20 bp):
AAATATGTTTTAAGTTATTA
Found at i:1414460 original size:18 final size:18
Alignment explanation
Indices: 1414416--1414465 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1414406 GCTAAGCCTC
*
1414416 CGTTGACCCGTTGACTGT
1 CGTTGACCTGTTGACTGT
1414434 CGTTGACCTGTTGACTGT
1 CGTTGACCTGTTGACTGT
*
1414452 CGTTGACCTATTGA
1 CGTTGACCTGTTGA
1414466 TTATTATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (18 bp):
CGTTGACCTGTTGACTGT
Found at i:1416332 original size:39 final size:39
Alignment explanation
Indices: 1416287--1416397 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
1416277 ATACCAAAAG
* * *
1416287 CTCCTATTCTTTGTACATAGGGTAAATTCTTACCATAGA
1 CTCCTATACTTTGTACACAGGGTAAATCCTTACCATAGA
** **
1416326 CTCCTATACTTTGTGTACAGGGTAGGTCCTTACCATAGA
1 CTCCTATACTTTGTACACAGGGTAAATCCTTACCATAGA
* * ** *
1416365 CTCCTCTACTTTTTGTACAGGGTAAGTCCTTAC
1 CTCCTATACTTTGTACACAGGGTAAATCCTTAC
1416398 TACAGCTCCT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (39 bp):
CTCCTATACTTTGTACACAGGGTAAATCCTTACCATAGA
Found at i:1417288 original size:19 final size:20
Alignment explanation
Indices: 1417251--1417289 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1417241 AGTGTTAATG
*
1417251 AATTTTAAGATTTTATATTC
1 AATTTTAAGATTATATATTC
1417271 AATTTTAA-ATTATATATTC
1 AATTTTAAGATTATATATTC
1417290 GATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTTAAGATTATATATTC
Found at i:1429503 original size:14 final size:14
Alignment explanation
Indices: 1429463--1429499 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1429453 GAAGTGTGTT
1429463 TAAGTGTGTTTAAG
1 TAAGTGTGTTTAAG
1429477 TAAGTGTGTTTAAG
1 TAAGTGTGTTTAAG
1429491 T--GTGTGTTT
1 TAAGTGTGTTT
1429500 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.35
14 15 0.65
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (14 bp):
TAAGTGTGTTTAAG
Found at i:1430837 original size:12 final size:12
Alignment explanation
Indices: 1430820--1430844 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1430810 TCACAAATAC
1430820 ACATGACGTTGG
1 ACATGACGTTGG
1430832 ACATGACGTTGG
1 ACATGACGTTGG
1430844 A
1 A
1430845 GAACAATCAT
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:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:1432487 original size:198 final size:198
Alignment explanation
Indices: 1432148--1432546 Score: 696
Period size: 198 Copynumber: 2.0 Consensus size: 198
1432138 TAGATAGGAA
1432148 AAGAATCTCTGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAATAAA
1 AAGAATCTCTGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAATAAA
1432213 ATAATATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
66 ATAATATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
1432278 TTATGGATGAAACAACAACTTTTAG-A-AAATTGAAGTTGGTACCATACCTATCAAGTGTGACAA
131 TTATGGATG--A-AACAACTTTTAGAAGAAATTGAAGTTGGTACCATACCTATCAAGTGTGACAA
1432341 TACTAG
193 TACTAG
* *
1432347 AAGAATCTCTGATACTTGTTAATTCATAGGAAATATGTTGATTTCTTGGTTTTCAAAGAAA-CAA
1 AAGAATCTCTGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAATAAA
*
1432411 ATAGTATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
66 ATAATATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
1432476 TTATGGATGAAACAACTTTTAGACTATGAAATTGAAGTTGGTACCATACCTATCAAGTGTGACAA
131 TTATGGATGAAACAACTTTTAGA--A-GAAATTGAAGTTGGTACCATACCTATCAAGTGTGACAA
1432541 TACTAG
193 TACTAG
1432547 TACTATTTGT
Statistics
Matches: 192, Mismatches: 3, Indels: 9
0.94 0.01 0.04
Matches are distributed among these distances:
195 12 0.06
196 1 0.01
198 76 0.40
199 60 0.31
200 43 0.22
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (198 bp):
AAGAATCTCTGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAATAAA
ATAATATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
TTATGGATGAAACAACTTTTAGAAGAAATTGAAGTTGGTACCATACCTATCAAGTGTGACAATAC
TAG
Found at i:1435008 original size:21 final size:21
Alignment explanation
Indices: 1434984--1435026 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1434974 TGGGGAGTAA
1434984 TTTATTTTCAAAGTATTAGAG
1 TTTATTTTCAAAGTATTAGAG
1435005 TTTATTTTCAAAGTATTAGAG
1 TTTATTTTCAAAGTATTAGAG
1435026 T
1 T
1435027 AAGGGGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTTATTTTCAAAGTATTAGAG
Found at i:1435457 original size:21 final size:21
Alignment explanation
Indices: 1435433--1435485 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 21
1435423 TTGCTCGGAG
1435433 GGTACCGATACCCCCCCAAGA
1 GGTACCGATACCCCCCCAAGA
*
1435454 GGTACCGATA-CCCCCCAGGA
1 GGTACCGATACCCCCCCAAGA
1435474 GGTACCGATACC
1 GGTACCGATACC
1435486 TCTGTCTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.26, C:0.40, G:0.23, T:0.11
Consensus pattern (21 bp):
GGTACCGATACCCCCCCAAGA
Found at i:1437681 original size:30 final size:30
Alignment explanation
Indices: 1437623--1437681 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1437613 TTTATCCACA
* *
1437623 TAGAACACATTCACATAGAATATTTTCACG
1 TAGAACACATTCACATAGAACATATTCACG
*
1437653 TAGAACACATTCACATATAACATATTCAC
1 TAGAACACATTCACATAGAACATATTCAC
1437682 ATATTGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (30 bp):
TAGAACACATTCACATAGAACATATTCACG
Found at i:1437685 original size:15 final size:15
Alignment explanation
Indices: 1437619--1437684 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 15
1437609 ATCTTTTATC
1437619 CACATAGAACACATT
1 CACATAGAACACATT
* **
1437634 CACATAGAATATTTT
1 CACATAGAACACATT
*
1437649 CACGTAGAACACATT
1 CACATAGAACACATT
* *
1437664 CACATATAACATATT
1 CACATAGAACACATT
1437679 CACATA
1 CACATA
1437685 TTGATAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (15 bp):
CACATAGAACACATT
Found at i:1438169 original size:45 final size:45
Alignment explanation
Indices: 1438105--1438202 Score: 178
Period size: 45 Copynumber: 2.2 Consensus size: 45
1438095 CTACTTCAGG
* *
1438105 ATCGATACCATTTTGGCATTTTGGAATTTCATCTTTAATTACAGT
1 ATCGATACCATTTTGGCATTTTGAAATTTCATCTTTAATTAAAGT
1438150 ATCGATACCATTTTGGCATTTTGAAATTTCATCTTTAATTAAAGT
1 ATCGATACCATTTTGGCATTTTGAAATTTCATCTTTAATTAAAGT
1438195 ATCGATAC
1 ATCGATAC
1438203 TTTACCCTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (45 bp):
ATCGATACCATTTTGGCATTTTGAAATTTCATCTTTAATTAAAGT
Found at i:1440515 original size:5 final size:5
Alignment explanation
Indices: 1440505--1440547 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
1440495 ACCGGTCATA
1440505 ACCCG ACCCG ACCCG ACCCG ACCCGTTG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCC---G ACCCG ACCCG ACCCG
1440548 TTGACCGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 30 0.86
8 5 0.14
ACGTcount: A:0.19, C:0.56, G:0.21, T:0.05
Consensus pattern (5 bp):
ACCCG
Found at i:1440537 original size:18 final size:18
Alignment explanation
Indices: 1440514--1440553 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1440504 AACCCGACCC
1440514 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
1440532 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
1440550 GACC
1 GACC
1440554 GTTGACCCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.50, G:0.23, T:0.10
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:1443055 original size:24 final size:24
Alignment explanation
Indices: 1443028--1443106 Score: 124
Period size: 24 Copynumber: 3.3 Consensus size: 24
1443018 TCAAATTTGA
1443028 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACATGACCTGG
* * *
1443052 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATCTGATACATGACCTGG
1443075 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACATGACCTGG
1443099 ATTCTGAT
1 ATTCTGAT
1443107 ATAATACTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACATGACCTGG
Found at i:1443081 original size:47 final size:48
Alignment explanation
Indices: 1443028--1443118 Score: 166
Period size: 47 Copynumber: 1.9 Consensus size: 48
1443018 TCAAATTTGA
*
1443028 ATTCTGATCTGATACATGACCTGGATTCTGATATGATA-TTGACATGG
1 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGACATGG
1443075 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGAC
1 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGAC
1443119 TTGAATTATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
47 37 0.88
48 5 0.12
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (48 bp):
ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGACATGG
Found at i:1443113 original size:24 final size:24
Alignment explanation
Indices: 1443028--1443118 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
1443018 TCAAATTTGA
*
1443028 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
1443052 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGG
*
1443075 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
1443099 ATTCTGATATAATACTTGAC
1 ATTCTGATATGATACATGAC
1443119 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:1443243 original size:35 final size:35
Alignment explanation
Indices: 1443196--1443270 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
1443186 TGGAGGAAGA
*
1443196 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1443231 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1443266 TTACT
1 TTACT
1443271 GTTCGTGACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.09, C:0.29, G:0.28, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:1448099 original size:20 final size:20
Alignment explanation
Indices: 1448070--1448107 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1448060 CAGAACCCCA
*
1448070 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
1448090 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1448108 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:1448142 original size:20 final size:21
Alignment explanation
Indices: 1448089--1448150 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
1448079 GATTCCCCTG
1448089 TGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGAATCGGTT-CCC-TCAA
*
1448112 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGAATCGGTTCCCTCAA
* *
1448132 TGGGGGGATCGATTCCCTC
1 TGGGGGAATCGGTTCCCTC
1448151 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (21 bp):
TGGGGGAATCGGTTCCCTCAA
Found at i:1451977 original size:22 final size:21
Alignment explanation
Indices: 1451935--1451974 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1451925 GAGTTTGTTT
*
1451935 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1451956 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1451975 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1458150 original size:23 final size:24
Alignment explanation
Indices: 1458081--1458151 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 24
1458071 GTCACATAGG
* *
1458081 TTTATCTTGAAGGACCGCGTAGAA
1 TTTATCCTGAACGACCGCGTAGAA
* ** * * *
1458105 TTTGTCCCAAATGACCACATAGAA
1 TTTATCCTGAACGACCGCGTAGAA
1458129 -TTATCCTGAACGACCGCGTAGAA
1 TTTATCCTGAACGACCGCGTAGAA
1458152 CCCTCGACTC
Statistics
Matches: 34, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (24 bp):
TTTATCCTGAACGACCGCGTAGAA
Found at i:1462270 original size:2 final size:2
Alignment explanation
Indices: 1462252--1462301 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
1462242 ACCCAACAAA
* *
1462252 AT AT AT TT A- AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1462294 A- AT AT AT A
1 AT AT AT AT A
1462302 AATAAATACT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1462753 original size:20 final size:19
Alignment explanation
Indices: 1462717--1462755 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1462707 ATGCAATACG
*
1462717 TAAAATATAAGAAATAAAT
1 TAAAATATAACAAATAAAT
*
1462736 TAAAATCATAACATATAAAT
1 TAAAAT-ATAACAAATAAAT
1462756 ATATACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAAATATAACAAATAAAT
Found at i:1467768 original size:43 final size:43
Alignment explanation
Indices: 1467720--1467904 Score: 289
Period size: 43 Copynumber: 4.3 Consensus size: 43
1467710 CGGCGCTATG
*
1467720 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
* *
1467763 ACAAACGTCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCA
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
* * *
1467806 ACAAACGCCGCAATAGGTGTTGAAATTTAGTGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
* *
1467849 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGTCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
*
1467892 ACAAACACCGCAA
1 ACAAACGCCGCAA
1467905 AAGATCTGGT
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 130 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
Found at i:1467931 original size:86 final size:86
Alignment explanation
Indices: 1467744--1467930 Score: 225
Period size: 86 Copynumber: 2.2 Consensus size: 86
1467734 AGGTGTTGAT
* *
1467744 ATTTAGCGGCGTTTTTCCAACAAACGTCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCAACA
1 ATTTAGCGACGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCAACA
* * * * *
1467809 AACGCCGCAATAGGTGTTGAA
66 AACACCGCAAAAGATCTGGAA
* * * ** *
1467830 ATTTAGTGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGTCGTTTTTCCCACA
1 ATTTAGCGACGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCAACA
*
1467895 AACACCGCAAAAGATCTGG-T
66 AACACCGCAAAAGATCTGGAA
1467915 ATATT-GCGACGTTTTT
1 AT-TTAGCGACGTTTTT
1467931 TTAGAACGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 11 0.13
86 75 0.87
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (86 bp):
ATTTAGCGACGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCAACA
AACACCGCAAAAGATCTGGAA
Found at i:1468125 original size:21 final size:21
Alignment explanation
Indices: 1468096--1468159 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1468086 GTAGCATTTT
* *
1468096 ACAATAAACTTGACATCCATA
1 ACAACAAACTTGAAATCCATA
*
1468117 ACAACAAACTTAAAATCCATA
1 ACAACAAACTTGAAATCCATA
* **
1468138 ACAAGAAAAATGAAATCCATA
1 ACAACAAACTTGAAATCCATA
1468159 A
1 A
1468160 TAATAAATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
ACAACAAACTTGAAATCCATA
Found at i:1472402 original size:25 final size:25
Alignment explanation
Indices: 1472343--1472403 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
1472333 TGGGCAAGAG
*
1472343 GAAAAAGGGAATCGTGGGAACAGAT
1 GAAAAAGGGGATCGTGGGAACAGAT
1472368 GAAAAAGGGGATCGTGGGAACAGAT
1 GAAAAAGGGGATCGTGGGAACAGAT
*
1472393 GGAAAAGGGGA
1 GAAAAAGGGGA
1472404 ATGGGATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.41, T:0.10
Consensus pattern (25 bp):
GAAAAAGGGGATCGTGGGAACAGAT
Found at i:1472711 original size:81 final size:82
Alignment explanation
Indices: 1472521--1472716 Score: 216
Period size: 84 Copynumber: 2.4 Consensus size: 82
1472511 TGTTTTTGCA
* * * * *
1472521 GCGTTTGTGTAAAAATGCCGCTACAGTTCTAATATTTTGCGGCGTTTGTTGGAAAAATGCCACTA
1 GCGTTTGTATAAAAATGCCGCTAAAGTACTAATATGTTGCGGCGTTTGTT-GAAAAACGCCACTA
* **
1472586 TAGGTGAACCCTATTGTG
65 TAGATGAACCCTATTACG
* * * * *
1472604 GCATTTTTTATAAAAATGCCGCTAAAGTACTAATCTGTTGTGGCGTTTGTCT-ATAAACGCCACT
1 GC-GTTTGTATAAAAATGCCGCTAAAGTACTAATATGTTGCGGCGTTTGT-TGAAAAACGCCACT
*
1472668 ATAGATGGA-CCTATTACG
64 ATAGATGAACCCTATTACG
*
1472686 GCGTTTGTATAAAAACGCCGCTAAAGTACTA
1 GCGTTTGTATAAAAATGCCGCTAAAGTACTA
1472717 CTCTATTACG
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
81 26 0.28
82 9 0.10
83 19 0.20
84 39 0.41
85 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (82 bp):
GCGTTTGTATAAAAATGCCGCTAAAGTACTAATATGTTGCGGCGTTTGTTGAAAAACGCCACTAT
AGATGAACCCTATTACG
Found at i:1472782 original size:41 final size:41
Alignment explanation
Indices: 1472596--1472796 Score: 174
Period size: 41 Copynumber: 4.9 Consensus size: 41
1472586 TAGGTGAACC
* * * *
1472596 CTATTGTGGCATTTTTTATAAAAATGCCGCTAAAGTACTAAT
1 CTATTGTGGC-GTTTGTATAAAAACGCCGCTAAAGTACTACT
* * * * *
1472638 CTGTTGTGGCGTTTGTCTATAAACGCCACTATAG-A-TGGAC-
1 CTATTGTGGCGTTTGTATAAAAACGCCGCTAAAGTACT--ACT
**
1472678 CTATTACGGCGTTTGTATAAAAACGCCGCTAAAGTACTACT
1 CTATTGTGGCGTTTGTATAAAAACGCCGCTAAAGTACTACT
** * * *
1472719 CTATTACGACGTTTATACAAAAACGCCGCTAAAGTACTACT
1 CTATTGTGGCGTTTGTATAAAAACGCCGCTAAAGTACTACT
* * *
1472760 CTATTGTGGCATTTGTTTAAAAAACGACGCTAAAGTA
1 CTATTGTGGCGTTTGTAT-AAAAACGCCGCTAAAGTA
1472797 TCATTTTGTG
Statistics
Matches: 126, Mismatches: 27, Indels: 12
0.76 0.16 0.07
Matches are distributed among these distances:
39 1 0.01
40 30 0.24
41 68 0.54
42 27 0.21
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (41 bp):
CTATTGTGGCGTTTGTATAAAAACGCCGCTAAAGTACTACT
Found at i:1473464 original size:17 final size:18
Alignment explanation
Indices: 1473431--1473466 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1473421 AATTCCAAGA
1473431 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
1473449 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
1473466 A
1 A
1473467 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:1473470 original size:25 final size:27
Alignment explanation
Indices: 1473441--1473492 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
1473431 AAATATATTA
*
1473441 ATTTTTATAAAT-ATATATTT-TTTAT
1 ATTTTTATAAATAAGATATTTATTTAT
1473466 ATTTTTATAAATAAGATATTTATTTAT
1 ATTTTTATAAATAAGATATTTATTTAT
1473493 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.50
26 7 0.29
27 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTTTTATAAATAAGATATTTATTTAT
Found at i:1473493 original size:25 final size:24
Alignment explanation
Indices: 1473436--1473494 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
1473426 CAAGAAAATA
* *
1473436 TATTAATTTTTATAAATATATATT
1 TATTTATTTTTATAAATAGATATT
*
1473460 TTTTATATTTTTATAAATAAGATATT
1 TATT-TATTTTTATAAAT-AGATATT
1473486 TATTTATTT
1 TATTTATTT
1473495 AGAAATATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 17 0.59
26 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTTATTTTTATAAATAGATATT
Found at i:1473758 original size:2 final size:2
Alignment explanation
Indices: 1473751--1473812 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
1473741 AATGAAGTAA
1473751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1473793 AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT
1473813 TTATTTATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.