Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 102 of 121
Found at i:17328957 original size:44 final size:43
Alignment explanation
Indices: 17328680--17329021 Score: 201
Period size: 45 Copynumber: 8.0 Consensus size: 43
17328670 GCTCAACAAT
* * * * *
17328680 AGAGACTCAACAAC-TTTGAGAAAATAAACAAAGACTCTTCTAAGC
1 AGAGGCTCAACAACTTTTGAAAAAAT-AA-ATAG-CTCCTCTAAAC
* * * *
17328725 GGAGGCTCAACGAC-TTTGAAAAAATAAATTGCTCTTCTAAAC
1 AGAGGCTCAACAACTTTTGAAAAAATAAATAGCTCCTCTAAAC
*** * *
17328767 AGAGGCTCAACAACTTAAAAAAAAATAAACAAAGCTCCTATAAAC
1 AGAGGCTCAACAACTTTTGAAAAAAT-AA-ATAGCTCCTCTAAAC
* *
17328812 AGAGGCTCAACGAC-TTTG-AAAAATAAAT-GACTCCTCTAATC
1 AGAGGCTCAACAACTTTTGAAAAAATAAATAG-CTCCTCTAAAC
* * * * *
17328853 AGAAGCATC-ACAA-TGACTTTG-GAAAATAAATGGCTACTCTAATC
1 AGAGGC-TCAACAACT---TTTGAAAAAATAAATAGCTCCTCTAAAC
*
17328897 AGAGGCTCAACGACTTTTGAAAAAATAAATAAAGCTCCT-TAAAC
1 AGAGGCTCAACAACTTTTGAAAAAATAAAT--AGCTCCTCTAAAC
* * * * *
17328941 AGAGGCACCACAAC-TTTG-AAAATTAAATTGCTTCTCTAAAC
1 AGAGGCTCAACAACTTTTGAAAAAATAAATAGCTCCTCTAAAC
*
17328982 AGA-G--CAACTTAACTTTT-AAAAAATAAATGGCTCCTCTAAA
1 AGAGGCTCAAC--AACTTTTGAAAAAATAAATAGCTCCTCTAAA
17329022 TATAGGCAAC
Statistics
Matches: 234, Mismatches: 43, Indels: 44
0.73 0.13 0.14
Matches are distributed among these distances:
38 3 0.01
40 10 0.04
41 48 0.21
42 39 0.17
43 31 0.13
44 51 0.22
45 52 0.22
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (43 bp):
AGAGGCTCAACAACTTTTGAAAAAATAAATAGCTCCTCTAAAC
Found at i:17328957 original size:85 final size:84
Alignment explanation
Indices: 17328807--17328985 Score: 213
Period size: 85 Copynumber: 2.1 Consensus size: 84
17328797 AAAGCTCCTA
* * *
17328807 TAAACAGAGGCTCAACGACTTTGAAAAATAAATGACTCCTCTAATCAGAAGCATCACAATGACTT
1 TAAACAGAGGCTCAACGACTTTGAAAAATAAATAACTCCTCTAAACAGAAGCACCACAA-GACTT
17328872 TGGAAAA-TAAATGGCTACTC
65 T-GAAAATTAAATGGCTACTC
* *
17328892 TAATCAGAGGCTCAACGACTTTTGAAAAAATAAATAAAGCTCCT-TAAACAGAGGCACCAC-A-A
1 TAAACAGAGGCTCAACGAC-TTTG-AAAAATAAAT-AA-CTCCTCTAAACAGAAGCACCACAAGA
* *
17328954 CTTTGAAAATTAAATTGCTTCTC
62 CTTTGAAAATTAAATGGCTACTC
17328977 TAAACAGAG
1 TAAACAGAG
17328986 CAACTTAACT
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
84 5 0.06
85 42 0.52
86 4 0.05
87 11 0.14
88 14 0.17
89 5 0.06
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (84 bp):
TAAACAGAGGCTCAACGACTTTGAAAAATAAATAACTCCTCTAAACAGAAGCACCACAAGACTTT
GAAAATTAAATGGCTACTC
Found at i:17329038 original size:42 final size:42
Alignment explanation
Indices: 17328737--17329040 Score: 137
Period size: 41 Copynumber: 7.1 Consensus size: 42
17328727 AGGCTCAACG
* * *
17328737 ACTTTGAAAAAATAAATTGCTCTTCTAAACAGAGGCTCAAC--A
1 ACTTTTAAAAAATAAATGGCTCCTCTAAACAGAGG--CAACAGA
** ** *
17328779 ACTTAAAAAAAAATAAACAAAGCTCCTATAAACAGAGGCTCAAC-G-
1 ACTT-TTAAAAAAT-AA-ATGGCTCCTCTAAACAGAGG--CAACAGA
* * * *
17328824 AC-TTTGAAAAATAAATGACTCCTCTAATCAGAAGCATCACA-A
1 ACTTTTAAAAAATAAATGGCTCCTCTAAACAGAGGCA--ACAGA
** * *
17328866 TGAC-TTTGGAAAATAAATGGCTACTCTAATCAGAGGCTCAAC-G-
1 --ACTTTTAAAAAATAAATGGCTCCTCTAAACAGAGG--CAACAGA
* * *
17328909 ACTTTTGAAAAAATAAATAAAGCTCCT-TAAACAGAGGCACCACA
1 ACTTTT-AAAAAATAAAT--GGCTCCTCTAAACAGAGGCAACAGA
* * * * **
17328953 AC-TTTGAAAATTAAATTGCTTCTCTAAACAGA-GCAACTTA
1 ACTTTTAAAAAATAAATGGCTCCTCTAAACAGAGGCAACAGA
* *
17328993 ACTTTTAAAAAATAAATGGCTCCTCTAAATATAGGCAACAGA
1 ACTTTTAAAAAATAAATGGCTCCTCTAAACAGAGGCAACAGA
17329035 ACTTTT
1 ACTTTT
17329041 GGGAAATTAA
Statistics
Matches: 199, Mismatches: 41, Indels: 44
0.70 0.14 0.15
Matches are distributed among these distances:
39 2 0.01
40 12 0.06
41 50 0.25
42 33 0.17
43 25 0.13
44 46 0.23
45 29 0.15
46 2 0.01
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (42 bp):
ACTTTTAAAAAATAAATGGCTCCTCTAAACAGAGGCAACAGA
Found at i:17329431 original size:21 final size:21
Alignment explanation
Indices: 17329407--17329460 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
17329397 TTAAAGCTCC
*
17329407 AAGATTTTTTTTTGAAATTCA
1 AAGATTTTTATTTGAAATTCA
* *
17329428 AAGATTCTCATTTGAAATTCA
1 AAGATTTTTATTTGAAATTCA
*
17329449 AATATTTTTATT
1 AAGATTTTTATT
17329461 AAAAGGTTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
AAGATTTTTATTTGAAATTCA
Found at i:17330231 original size:63 final size:63
Alignment explanation
Indices: 17330132--17330306 Score: 260
Period size: 63 Copynumber: 2.8 Consensus size: 63
17330122 GCACTAACCA
* * *
17330132 AAAATAAATTTCATCCTCTGTCACTTGGTCATCATTCATAAGCTTTTCAATACTAGCCATTTT
1 AAAATAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTTTTCAAAACTAGCCATTTC
* * *
17330195 AAAATAAATTTCAGCATCTGTCACTTGATCATCATTCATAAGCTTCTCAAAACTAGCCATTTC
1 AAAATAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTTTTCAAAACTAGCCATTTC
* * * *
17330258 AAAACAGATTTCATCATCTGTCACTTGGTCATCGTTCATAAACTTTTCA
1 AAAATAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTTTTCA
17330307 GCACCAATTT
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 99 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.37
Consensus pattern (63 bp):
AAAATAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTTTTCAAAACTAGCCATTTC
Found at i:17330976 original size:8 final size:8
Alignment explanation
Indices: 17330965--17331025 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 8
17330955 TTGAATATTT
17330965 TTTTTTCA
1 TTTTTTCA
*
17330973 TTTTCTCA
1 TTTTTTCA
17330981 TTTTTTC-
1 TTTTTTCA
17330988 TTTTTT--
1 TTTTTTCA
**
17330994 TTTCCTCTA
1 TTTTTTC-A
17331003 TTTTTTCA
1 TTTTTTCA
17331011 -TTTTTC-
1 TTTTTTCA
17331017 TTTTTTCA
1 TTTTTTCA
17331025 T
1 T
17331026 CATCTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
6 4 0.10
7 18 0.43
8 15 0.36
9 5 0.12
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTCA
Found at i:17331033 original size:25 final size:24
Alignment explanation
Indices: 17330981--17331051 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 24
17330971 CATTTTCTCA
* *
17330981 TTTTTTCTTT-TTTTTTCCTCTATT
1 TTTTTT-TTTCTTTTTTCATCTATC
17331005 TTTTCATTTTTCTTTTTTCATC-ATC
1 TTTT--TTTTTCTTTTTTCATCTATC
17331030 TTTTTTTTTCTCATTTTTCATC
1 TTTTTTTTTCT--TTTTTCATC
17331052 CATTGTTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 7 0.17
24 4 0.10
25 18 0.45
26 11 0.28
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTTTTTCTTTTTTCATCTATC
Found at i:17331035 original size:29 final size:30
Alignment explanation
Indices: 17330972--17331037 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
17330962 TTTTTTTTTC
* ** *
17330972 ATTTTCTCATTTTTTCTTTTTTTTTCCTCT
1 ATTTTTTCATTTTTTCTTTTTTCATCATCT
17331002 ATTTTTTCA-TTTTTCTTTTTTCATCATCT
1 ATTTTTTCATTTTTTCTTTTTTCATCATCT
*
17331031 TTTTTTT
1 ATTTTTT
17331038 TCTCATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (30 bp):
ATTTTTTCATTTTTTCTTTTTTCATCATCT
Found at i:17331349 original size:12 final size:12
Alignment explanation
Indices: 17331332--17331362 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17331322 ATGTGTGACA
17331332 TTTATTTTTTCT
1 TTTATTTTTTCT
17331344 TTTATTTTTTCT
1 TTTATTTTTTCT
17331356 TTTATTT
1 TTTATTT
17331363 CCATCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTTTCT
Found at i:17333876 original size:12 final size:12
Alignment explanation
Indices: 17333856--17333943 Score: 58
Period size: 12 Copynumber: 7.2 Consensus size: 12
17333846 CTTTTGTATT
*
17333856 TTATGTATTGTA
1 TTATTTATTGTA
*
17333868 TTATTTATTATTA
1 TTATTTATT-GTA
17333881 TTA-TTA-TGTA
1 TTATTTATTGTA
*
17333891 TTA-ATATATGTA
1 TTATTTAT-TGTA
17333903 TATATTTATT-TA
1 T-TATTTATTGTA
17333915 TTTATTTATTGTTA
1 -TTATTTATTG-TA
*
17333929 ATATTTATGTGTA
1 TTATTTAT-TGTA
17333942 TT
1 TT
17333944 TTATTATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
10 7 0.12
11 1 0.02
12 26 0.43
13 19 0.32
14 7 0.12
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTATTTATTGTA
Found at i:17333924 original size:16 final size:15
Alignment explanation
Indices: 17333855--17333958 Score: 70
Period size: 16 Copynumber: 6.6 Consensus size: 15
17333845 TCTTTTGTAT
17333855 TTTATGTATTGTATTA
1 TTTATGTATT-TATTA
17333871 TTTAT-TA-TTATTA
1 TTTATGTATTTATTA
*
17333884 -TTATGTATTAATATA
1 TTTATGTATTTAT-TA
* *
17333899 TGTATATATTTATTTA
1 TTTATGTATTTA-TTA
* *
17333915 TTTATTTATTGTTAATA
1 TTTATGTA-T-TTATTA
17333932 TTTATGTGTATTTTATTA
1 TTTA--TGTA-TTTATTA
17333950 TTTATGTAT
1 TTTATGTAT
17333959 ATATATATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
12 4 0.06
13 7 0.10
14 4 0.06
15 5 0.07
16 25 0.36
17 8 0.11
18 12 0.17
19 5 0.07
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (15 bp):
TTTATGTATTTATTA
Found at i:17333935 original size:61 final size:58
Alignment explanation
Indices: 17333855--17333985 Score: 133
Period size: 61 Copynumber: 2.2 Consensus size: 58
17333845 TCTTTTGTAT
* *
17333855 TTTATGTATTGTATTATTTA-T-TATTATTATTATGTAT-TAATATATGTATATATTTATTTA
1 TTTATTTATTGTAATATTTAGTGTATT-TTATTATGTATGT-ATATA--TATATATTT-TTTA
*
17333915 TTTATTTATTGTTAATATTTATGTGTATTTTATTATTTATGTATATATATATATTTTTTA
1 TTTATTTATTG-TAATATTTA-GTGTATTTTATTATGTATGTATATATATATATTTTTTA
*
17333975 TCTTTTTTATT
1 T-TTATTTATT
17333986 TTATTCATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
60 15 0.25
61 25 0.41
63 16 0.26
64 5 0.08
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (58 bp):
TTTATTTATTGTAATATTTAGTGTATTTTATTATGTATGTATATATATATATTTTTTA
Found at i:17333969 original size:18 final size:17
Alignment explanation
Indices: 17333876--17333970 Score: 56
Period size: 16 Copynumber: 5.7 Consensus size: 17
17333866 TATTATTTAT
17333876 TATTAT-TA-TTATGTA
1 TATTATATATTTATGTA
* * *
17333891 T-TAATATATGTATATA
1 TATTATATATTTATGTA
* *
17333907 T-TTATTTATTTATTTA
1 TATTATATATTTATGTA
* *
17333923 TTGTTA-ATATTTATGTG
1 -TATTATATATTTATGTA
*
17333940 TATTTTATTATTTATGTA
1 TATTATA-TATTTATGTA
17333958 TATATATATATTT
1 TAT-TATATATTT
17333971 TTTATCTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 20 0.34
17 10 0.17
18 20 0.34
19 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TATTATATATTTATGTA
Found at i:17334021 original size:61 final size:60
Alignment explanation
Indices: 17333879--17334042 Score: 144
Period size: 61 Copynumber: 2.7 Consensus size: 60
17333869 TATTTATTAT
*
17333879 TATTATTATGTATTAA--TATATGTATATATTTATTTATTTATTTATTGTTAATATTTATGTG
1 TATT-TTAT-TATTAATGTATATATATATATTT-TTTATTTATTTATTGTTAATATTTATGTG
* * *
17333940 TATTTTATTATTTATGTATATATATATATTTTTTATCTTTTTTATT-TTATTCATTT-T-TG
1 TATTTTATTATTAATGTATATATATATATTTTTTAT-TTATTTATTGTTAAT-ATTTATGTG
*
17333999 TATTTTTACTTATCTAAT-TATATATCTGATATATTTTT-TTTATT
1 TA-TTTTA-TTAT-TAATGTATATATAT-ATAT-TTTTTATTTATT
17334043 ATTATTTATC
Statistics
Matches: 87, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
59 9 0.10
60 19 0.22
61 46 0.53
62 8 0.09
63 5 0.06
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (60 bp):
TATTTTATTATTAATGTATATATATATATTTTTTATTTATTTATTGTTAATATTTATGTG
Found at i:17334425 original size:25 final size:25
Alignment explanation
Indices: 17334373--17334425 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
17334363 GGGAGTGAGA
* *
17334373 AAAAATTTTTTAGAGATTTTTGGCG
1 AAAAATTTTTTAGAAATTTCTGGCG
*
17334398 AAAAATTTTTCTGGAAATTTCTGG-G
1 AAAAATTTTT-TAGAAATTTCTGGCG
17334423 AAA
1 AAA
17334426 TTTCCAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (25 bp):
AAAAATTTTTTAGAAATTTCTGGCG
Found at i:17334602 original size:20 final size:20
Alignment explanation
Indices: 17334565--17334602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17334555 ACTTTCGATG
* *
17334565 AAATTTCCAGATTTCGACGA
1 AAATTTCCAGAATCCGACGA
17334585 AAATTTCCAGAATCCGAC
1 AAATTTCCAGAATCCGAC
17334603 ACCGGTGTTC
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:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (20 bp):
AAATTTCCAGAATCCGACGA
Found at i:17335184 original size:120 final size:121
Alignment explanation
Indices: 17335014--17335440 Score: 534
Period size: 120 Copynumber: 3.6 Consensus size: 121
17335004 TTATTTTTTA
* * *
17335014 TTTTCTTTAAATAAAAATAAAAAATTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCA
1 TTTTCTTAAAAGAAAAAT--AAATTTCC-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCA
*
17335079 ATTTTCCTTAAAAATAAATTTCCAAAAAATA-TTTTAGGGAAAAGTTGAAAGTATCAAT
63 ATTTTCCTTAAAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
17335137 TTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATT
1 TTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATT
* * * *
17335202 TTCTTTAGAAATAAATTTTCAAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAA-
66 TTCCTTAAAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
* * *
17335257 TTTTCCT--CAG--AAATAAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAGAAAAATAAATTTC-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAAT
* * *
17335317 TTTCCTTCAAAATCAAAATTTCAAAAAAATATTTTTTGGGGCAAAGTTGAAAGTATCAAT
65 TTTCCTTAAAAAT--AAATTTCCAAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAAT
* ** * *
17335377 TTTCCTTGAAAATCAAAAT---TTTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
1 TTTTCTT-AAAAGAAAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAAT
17335438 TTT
65 TTT
17335441 TCCTACAAAA
Statistics
Matches: 267, Mismatches: 25, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
116 21 0.08
117 37 0.14
118 16 0.06
119 25 0.09
120 110 0.41
121 34 0.13
122 3 0.01
123 17 0.06
125 4 0.01
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (121 bp):
TTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATT
TTCCTTAAAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
Found at i:17338907 original size:9 final size:9
Alignment explanation
Indices: 17338893--17338934 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
17338883 AAAAGGTCTC
17338893 AAAAATAAA
1 AAAAATAAA
17338902 AAAAATAAA
1 AAAAATAAA
17338911 AAAAATAAA
1 AAAAATAAA
*
17338920 AAAAA-AGA
1 AAAAATAAA
17338928 AAAAATA
1 AAAAATA
17338935 CCACACATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:17338913 original size:17 final size:18
Alignment explanation
Indices: 17338893--17338934 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
17338883 AAAAGGTCTC
17338893 AAAAATAAAAAAAATAA-A
1 AAAAATAAAAAAAA-AAGA
17338911 AAAAAT-AAAAAAAAAGA
1 AAAAATAAAAAAAAAAGA
17338928 AAAAATA
1 AAAAATA
17338935 CCACACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 14 0.64
18 6 0.27
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (18 bp):
AAAAATAAAAAAAAAAGA
Found at i:17339278 original size:9 final size:9
Alignment explanation
Indices: 17339266--17339310 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
17339256 AAAAAATGAT
17339266 GAAAAAAAA
1 GAAAAAAAA
17339275 GAAAAAAAA
1 GAAAAAAAA
17339284 GAAAAAAAAA
1 G-AAAAAAAA
**
17339294 GAAAAATGA
1 GAAAAAAAA
17339303 GAAAAAAA
1 GAAAAAAA
17339311 GAAGGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 22 0.71
10 9 0.29
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:17339281 original size:22 final size:21
Alignment explanation
Indices: 17339254--17339329 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
17339244 CAATGGATGA
17339254 AAAAAAAATGATGAAAAAAAAG
1 AAAAAAAATGA-GAAAAAAAAG
17339276 AAAAAAAA-GA-AAAAAAAAG
1 AAAAAAAATGAGAAAAAAAAG
17339295 ---AAAAATGAG-AAAAAAAG
1 AAAAAAAATGAGAAAAAAAAG
17339312 AAGGAAAAAATGAGAAAA
1 AA--AAAAAATGAGAAAA
17339330 TGAAAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
16 5 0.11
17 10 0.22
19 9 0.20
21 2 0.04
22 17 0.37
23 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAAAAAATGAGAAAAAAAAG
Found at i:17339289 original size:19 final size:19
Alignment explanation
Indices: 17339267--17339321 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
17339257 AAAAATGATG
17339267 AAAAAAAAGAAAAAAAAGA
1 AAAAAAAAGAAAAAAAAGA
**
17339286 AAAAAAAAGAAAAATGAGA
1 AAAAAAAAGAAAAAAAAGA
17339305 AAAAAAGAAGGAAAAAA
1 AAAAAA-AA-GAAAAAA
17339322 TGAGAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 23 0.74
20 2 0.06
21 6 0.19
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAGA
Found at i:17339328 original size:10 final size:10
Alignment explanation
Indices: 17339256--17339329 Score: 55
Period size: 9 Copynumber: 7.4 Consensus size: 10
17339246 ATGGATGAAA
17339256 AAAAAATGATG
1 AAAAAATGA-G
*
17339267 AAAAAA-AAG
1 AAAAAATGAG
*
17339276 AAAAAA-AAG
1 AAAAAATGAG
**
17339285 AAAAAAAAAG
1 AAAAAATGAG
17339295 -AAAAATGAG
1 AAAAAATGAG
*
17339304 AAAAAAAGAAGG
1 AAAAAATG-A-G
17339316 AAAAAATGAG
1 AAAAAATGAG
17339326 AAAA
1 AAAA
17339330 TGAAAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
9 23 0.43
10 15 0.28
11 8 0.15
12 8 0.15
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (10 bp):
AAAAAATGAG
Found at i:17339338 original size:19 final size:18
Alignment explanation
Indices: 17339252--17339340 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 18
17339242 AACAATGGAT
17339252 GAAAAAAAAATGATGAAAA
1 GAAAAAAAAATGA-GAAAA
**
17339271 -AAAAGAAAAAAAAGAAAA
1 GAAAA-AAAAATGAGAAAA
*
17339289 AAAAAGAAAAATGAGAAAAAAA
1 GAAAA-AAAAATGAG---AAAA
*
17339311 GAAGGAAAAAATGAGAAAA
1 GAA-AAAAAAATGAGAAAA
17339330 TGAAAAAAAAA
1 -GAAAAAAAAA
17339341 GATTCAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
18 9 0.16
19 28 0.50
20 3 0.05
22 15 0.27
23 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.06
Consensus pattern (18 bp):
GAAAAAAAAATGAGAAAA
Found at i:17339339 original size:10 final size:10
Alignment explanation
Indices: 17339254--17339339 Score: 51
Period size: 8 Copynumber: 8.8 Consensus size: 10
17339244 CAATGGATGA
17339254 AAAAAAAATG
1 AAAAAAAATG
*
17339264 ATGAAAAAAAAG
1 A--AAAAAAATG
17339276 AAAAAAAA-G
1 AAAAAAAATG
17339285 -AAAAAAA--
1 AAAAAAAATG
*
17339292 AAGAAAAATG
1 AAAAAAAATG
17339302 AGAAAAAAA-G
1 A-AAAAAAATG
17339312 AAGGAAAAAATG
1 AA--AAAAAATG
*
17339324 --AGAAAATG
1 AAAAAAAATG
17339332 AAAAAAAA
1 AAAAAAAA
17339340 AGATTCAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
8 20 0.33
9 2 0.03
10 16 0.27
11 12 0.20
12 10 0.17
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:17340609 original size:40 final size:40
Alignment explanation
Indices: 17340558--17340924 Score: 501
Period size: 40 Copynumber: 9.0 Consensus size: 40
17340548 GTCTAGGAGT
17340558 ATTTACTTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
17340599 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* *
17340640 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
17340682 ATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
* *
17340722 ATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
17340763 ATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
* *
17340803 ATTTACTTTTCCAAGTTCGT-TGCCTCTGTTTAGAGGAGTA
1 ATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
* *
17340843 ATTTA-TTTTCCAAAGTCGTGGTACCTCTGTTTAGAAGAGCA
1 ATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
17340884 ATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1 ATTTACTTTTC-AAAGTCGT-GTGCCTCTGTTTAGAGGAGC
17340925 TTTGGTAAAA
Statistics
Matches: 297, Mismatches: 17, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
39 16 0.05
40 108 0.36
41 96 0.32
42 77 0.26
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (40 bp):
ATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:17340761 original size:81 final size:81
Alignment explanation
Indices: 17340581--17340924 Score: 511
Period size: 81 Copynumber: 4.2 Consensus size: 81
17340571 AAGTTCGTTG
17340581 CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAT
1 CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTA-
*
17340646 TTTTCCAAAGTCGTGGTA
64 CTTTCCAAAGTCGTGGTA
17340664 CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCAATTTAC
1 CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCAATTTAC
17340728 TTTCCAAAGTCGTGGTA
65 TTTCCAAAGTCGTGGTA
17340745 CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCAATTTAC
1 CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCAATTTAC
*
17340809 TTTTCC-AAGTTCGT--TG
65 -TTTCCAAAG-TCGTGGTA
* * *
17340825 CCTCTGTTTAGAGGAGTAATTTA-TTTTCCAAAGTCGTGGTACCTCTGTTTAGAAGAGCAATTTA
1 CCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTA
*
17340889 CTTTCCAAAAGTCGTGGTG
64 CTTTCC-AAAGTCGTGGTA
17340908 CCTCTGTTTAGAGGAGC
1 CCTCTGTTTAGAGGAGC
17340925 TTTGGTAAAA
Statistics
Matches: 245, Mismatches: 6, Indels: 20
0.90 0.02 0.07
Matches are distributed among these distances:
79 8 0.03
80 33 0.13
81 112 0.46
82 37 0.15
83 51 0.21
84 4 0.02
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (81 bp):
CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCAATTTACT
TTCCAAAGTCGTGGTA
Found at i:17340853 original size:121 final size:121
Alignment explanation
Indices: 17340558--17340924 Score: 585
Period size: 121 Copynumber: 3.0 Consensus size: 121
17340548 GTCTAGGAGT
*
17340558 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTG
1 ATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCCAAAGTCGTGGTA
* *
17340622 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
64 CCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
17340682 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTACC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTACC
17340747 TCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
66 TCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
* *
17340803 ATTTACTTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGTAATTTATTTTCCAAAGTCGTGGTACC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTACC
* *
17340868 TCTGTTTAGAAGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
66 TCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGT-GTGCCTCTGTTTAGAGGAGC
17340925 TTTGGTAAAA
Statistics
Matches: 229, Mismatches: 9, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
121 110 0.48
122 12 0.05
123 101 0.44
124 6 0.03
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (121 bp):
ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTACC
TCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:17340948 original size:8 final size:8
Alignment explanation
Indices: 17340931--17341004 Score: 86
Period size: 7 Copynumber: 9.9 Consensus size: 8
17340921 GAGCTTTGGT
17340931 AAAAAAA-
1 AAAAAAAC
*
17340938 AAAACAA-
1 AAAAAAAC
17340945 AAAAAAAC
1 AAAAAAAC
17340953 AAAAAAAC
1 AAAAAAAC
17340961 -AAAAAAC
1 AAAAAAAC
17340968 AAAAAAA-
1 AAAAAAAC
*
17340975 AAAAACA-
1 AAAAAAAC
17340982 AAAAAAAC
1 AAAAAAAC
17340990 AAAAAAAC
1 AAAAAAAC
*
17340998 CAAAAAA
1 AAAAAAA
17341005 TGTTGAGTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
7 31 0.53
8 28 0.47
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:17340948 original size:9 final size:9
Alignment explanation
Indices: 17340934--17341004 Score: 90
Period size: 9 Copynumber: 7.7 Consensus size: 9
17340924 CTTTGGTAAA
17340934 AAAAAAAAC
1 AAAAAAAAC
17340943 AAAAAAAA-
1 AAAAAAAAC
17340951 ACAAAAAAAC
1 A-AAAAAAAC
*
17340961 AAAAAACAAAA
1 -AAAAA-AAAC
17340972 AAAAAAAAC
1 AAAAAAAAC
17340981 AAAAAAAAC
1 AAAAAAAAC
*
17340990 AAAAAAACC
1 AAAAAAAAC
17340999 AAAAAA
1 AAAAAA
17341005 TGTTGAGTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
8 1 0.02
9 41 0.75
10 9 0.16
11 4 0.07
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:17340985 original size:37 final size:39
Alignment explanation
Indices: 17340931--17341004 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
17340921 GAGCTTTGGT
17340931 AAAAAAAAAAACAAAAAAAAACAAAAAAA-CAAAAAACA
1 AAAAAAAAAAACAAAAAAAAACAAAAAAACCAAAAAACA
17340969 AAAAAAAAAAAC-AAAAAAAACAAAAAAACCAAAAAA
1 AAAAAAAAAAACAAAAAAAAACAAAAAAACCAAAAAA
17341005 TGTTGAGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 16 0.46
38 19 0.54
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (39 bp):
AAAAAAAAAAACAAAAAAAAACAAAAAAACCAAAAAACA
Found at i:17341004 original size:1 final size:1
Alignment explanation
Indices: 17340931--17340996 Score: 78
Period size: 1 Copynumber: 66.0 Consensus size: 1
17340921 GAGCTTTGGT
* * * * * *
17340931 AAAAAAAAAAACAAAAAAAAACAAAAAAACAAAAAACAAAAAAAAAAAACAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17340996 A
1 A
17340997 CCAAAAAATG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17341214 original size:12 final size:12
Alignment explanation
Indices: 17341194--17341281 Score: 58
Period size: 12 Copynumber: 7.2 Consensus size: 12
17341184 CTTTTGTATT
*
17341194 TTATGTATTGTA
1 TTATTTATTGTA
*
17341206 TTATTTATTATTA
1 TTATTTATT-GTA
17341219 TTA-TTA-TGTA
1 TTATTTATTGTA
*
17341229 TTA-ATATATGTA
1 TTATTTAT-TGTA
17341241 TATATTTATT-TA
1 T-TATTTATTGTA
17341253 TTTATTTATTGTTA
1 -TTATTTATTG-TA
*
17341267 ATATTTATGTGTA
1 TTATTTAT-TGTA
17341280 TT
1 TT
17341282 TTATTATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
10 7 0.12
11 1 0.02
12 26 0.43
13 19 0.32
14 7 0.12
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTATTTATTGTA
Found at i:17341255 original size:61 final size:58
Alignment explanation
Indices: 17341185--17341388 Score: 164
Period size: 61 Copynumber: 3.3 Consensus size: 58
17341175 TTTCTTCTTC
* * *
17341185 TTTTGTATTTTATGTATTGTATTATTTAT-TATTATTATTATGTATTAATATATGTATATA
1 TTTTTTATTTTATTTATTGTATTATTTATGTATT-TTATTATCTATT-ATATAT-TATATA
* *
17341245 TTTATTTA-TTTATTTATTGTTAATATTTATGTGTATTTTATTATTTATGTATATA-TATATA
1 TTT-TTTATTTTATTTATTG-TATTATTTA--TGTATTTTATTATCTAT-TATATATTATATA
* *
17341306 TTTTTTATCTTT-TTTATTTTATTCATTTTTGTATTTTTACTTATCTAATTATATATCTGATATA
1 TTTTTTAT-TTTATTTATTGTATT-ATTTATGTA-TTTTA-TTATCT-ATTATATAT-T-ATATA
17341370 TTTTTTTATTATTATTTAT
1 -TTTTTTATT-TTATTTAT
17341389 CCTATAATAT
Statistics
Matches: 118, Mismatches: 8, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
59 4 0.03
60 25 0.21
61 41 0.35
62 5 0.04
63 17 0.14
64 11 0.09
65 10 0.08
66 5 0.04
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (58 bp):
TTTTTTATTTTATTTATTGTATTATTTATGTATTTTATTATCTATTATATATTATATA
Found at i:17341262 original size:16 final size:15
Alignment explanation
Indices: 17341193--17341296 Score: 70
Period size: 16 Copynumber: 6.6 Consensus size: 15
17341183 TCTTTTGTAT
17341193 TTTATGTATTGTATTA
1 TTTATGTATT-TATTA
17341209 TTTAT-TA-TTATTA
1 TTTATGTATTTATTA
*
17341222 -TTATGTATTAATATA
1 TTTATGTATTTAT-TA
* *
17341237 TGTATATATTTATTTA
1 TTTATGTATTTA-TTA
* *
17341253 TTTATTTATTGTTAATA
1 TTTATGTA-T-TTATTA
17341270 TTTATGTGTATTTTATTA
1 TTTA--TGTA-TTTATTA
17341288 TTTATGTAT
1 TTTATGTAT
17341297 ATATATATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
12 4 0.06
13 7 0.10
14 4 0.06
15 5 0.07
16 25 0.36
17 8 0.11
18 12 0.17
19 5 0.07
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (15 bp):
TTTATGTATTTATTA
Found at i:17341307 original size:18 final size:17
Alignment explanation
Indices: 17341214--17341308 Score: 56
Period size: 16 Copynumber: 5.7 Consensus size: 17
17341204 TATTATTTAT
17341214 TATTAT-TA-TTATGTA
1 TATTATATATTTATGTA
* * *
17341229 T-TAATATATGTATATA
1 TATTATATATTTATGTA
* *
17341245 T-TTATTTATTTATTTA
1 TATTATATATTTATGTA
* *
17341261 TTGTTA-ATATTTATGTG
1 -TATTATATATTTATGTA
*
17341278 TATTTTATTATTTATGTA
1 TATTATA-TATTTATGTA
17341296 TATATATATATTT
1 TAT-TATATATTT
17341309 TTTATCTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 20 0.34
17 10 0.17
18 20 0.34
19 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TATTATATATTTATGTA
Found at i:17341761 original size:25 final size:25
Alignment explanation
Indices: 17341709--17341761 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
17341699 GGGAGTGAGA
* *
17341709 AAAAATTTTTTAGAGATTTTTGGCG
1 AAAAATTTTTTAGAAATTTCTGGCG
*
17341734 AAAAATTTTTCTGGAAATTTCTGG-G
1 AAAAATTTTT-TAGAAATTTCTGGCG
17341759 AAA
1 AAA
17341762 TTTCCAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (25 bp):
AAAAATTTTTTAGAAATTTCTGGCG
Found at i:17341805 original size:31 final size:32
Alignment explanation
Indices: 17341770--17341840 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
17341760 AATTTCCAGA
*
17341770 TTCCGGCGAA-AATTCCGACGAA-ATTTGAATT
1 TTCCGGCGAACAATTCCGACGAACA-TTGAAGT
*
17341801 TTCCGGC-AACAATTCCGGCGAACATTGAAGT
1 TTCCGGCGAACAATTCCGACGAACATTGAAGT
17341832 TTCCGGCGA
1 TTCCGGCGA
17341841 CCAGCCCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 31 0.89
32 2 0.06
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (32 bp):
TTCCGGCGAACAATTCCGACGAACATTGAAGT
Found at i:17342173 original size:5 final size:5
Alignment explanation
Indices: 17342159--17342191 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
17342149 CCAGCCCCCT
*
17342159 CCGAG TCGAG CCGAG CCGAG CCGAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCG
17342192 CTCCCCCCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.18, C:0.39, G:0.39, T:0.03
Consensus pattern (5 bp):
CCGAG
Found at i:17342647 original size:60 final size:58
Alignment explanation
Indices: 17342375--17342771 Score: 486
Period size: 60 Copynumber: 6.7 Consensus size: 58
17342365 AAAAATTCCA
* *
17342375 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
* *
17342433 -CAAAAAATA-TTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-T--CAG--AAATAAATTT-C
* *
17342495 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTTTAGAAATAAATTTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTC
* *
17342554 --AAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
17342610 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTCCTTCA-AAATCAAAATTTC
1 --AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TCAGAAAT--AAATTTC
* *
17342671 -AAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAATCGAAATTTC
1 AAAAAAAATA-TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT--AAATTTC
* *
17342731 CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
17342772 TCCTACAAAA
Statistics
Matches: 303, Mismatches: 15, Indels: 40
0.85 0.04 0.11
Matches are distributed among these distances:
56 36 0.12
57 57 0.19
58 9 0.03
59 45 0.15
60 87 0.29
61 28 0.09
62 1 0.00
63 9 0.03
64 31 0.10
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.34
Consensus pattern (58 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
Found at i:17342736 original size:119 final size:114
Alignment explanation
Indices: 17342376--17342770 Score: 535
Period size: 119 Copynumber: 3.3 Consensus size: 114
17342366 AAAATTCCAA
17342376 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTCCAAAAAA
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTCCTTAAAAATAAAATTT-CAAAAAA
*
17342440 TA-TTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
64 TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT----G-AAAATAAATTTCC
* * *
17342495 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTTTAGAAATAAATTTTCAAAAAA
1 -AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTCCTTAAAAATAAAATTTCAAAAAA
* * *
17342560 TATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCC-TCAGAAATAAATTTCAAA
64 TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAATTTC--C
*
17342613 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTCAAAATCAAAATTTCAAAAAAA
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAAAAAT-AAAATTTC-AAAAAA
17342678 TATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTCC
64 TA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAATTTCC
*
17342732 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTT
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTT
17342771 TTCCTACAAA
Statistics
Matches: 249, Mismatches: 15, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
115 1 0.00
116 21 0.08
117 43 0.17
118 8 0.03
119 74 0.30
120 60 0.24
121 42 0.17
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.34
Consensus pattern (114 bp):
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAAAAATAAAATTTCAAAAAATA
TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTCC
Found at i:17344626 original size:58 final size:58
Alignment explanation
Indices: 17344542--17344788 Score: 194
Period size: 57 Copynumber: 4.1 Consensus size: 58
17344532 CATTTGGAAG
* * * *
17344542 TTTTT-ATTTTAACA-AAAATTTATACTTTCAACTTTTCTTTAAAATATTTTTTTTTAT
1 TTTTTAATTTTAA-AGAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTGAA
* * * * *
17344599 TTTTTAATTTTAAAGAAAATTGGTACTTCCAATTTTTCCCTAAAATA-TTTTTCTGAA
1 TTTTTAATTTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTGAA
* ** * **
17344656 ATTTTAATTTCGAAGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTAAAAA
1 TTTTTAATTTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTT-TGAA
* * * *
17344715 TTTTAGAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAACTTTTTTTTG
1 TTTT--TAATTTTA-----AAG-AAAATTGATACTTTCAACTTTTCCTTAAAATA-TTTTTTTTG
17344780 AA
57 AA
17344782 GTTTTTA
1 -TTTTTA
17344789 TTTAATATAT
Statistics
Matches: 147, Mismatches: 29, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
57 52 0.35
58 38 0.26
59 5 0.03
61 5 0.03
66 4 0.03
67 32 0.22
68 11 0.07
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (58 bp):
TTTTTAATTTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTGAA
Found at i:17345212 original size:12 final size:12
Alignment explanation
Indices: 17345195--17345234 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
17345185 TATAAAAAAT
17345195 TTATTTTTTTAA
1 TTATTTTTTTAA
17345207 TTATTTTTTTAA
1 TTATTTTTTTAA
*
17345219 TT-TTATATTTAA
1 TTATT-TTTTTAA
17345231 TTAT
1 TTAT
17345235 ATATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 2 0.08
12 22 0.88
13 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTTTTTAA
Found at i:17345237 original size:12 final size:12
Alignment explanation
Indices: 17345202--17345268 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
17345192 AATTTATTTT
* *
17345202 TTTAATTATTTT
1 TTTAATTATATA
*
17345214 TTTAATTTTATA
1 TTTAATTATATA
17345226 TTTAATTATATATA
1 TTTAA-T-TATATA
**
17345240 TTTTTTATATATA
1 TTTAAT-TATATA
*
17345253 TTTAATTTTATA
1 TTTAATTATATA
17345265 TTTA
1 TTTA
17345269 TATTTAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 23 0.52
13 13 0.30
14 8 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTAATTATATA
Found at i:17345249 original size:13 final size:13
Alignment explanation
Indices: 17345231--17345255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17345221 TTATATTTAA
17345231 TTATATATATTTT
1 TTATATATATTTT
17345244 TTATATATATTT
1 TTATATATATTT
17345256 AATTTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATATATTTT
Found at i:17347637 original size:59 final size:60
Alignment explanation
Indices: 17347476--17347637 Score: 145
Period size: 59 Copynumber: 2.7 Consensus size: 60
17347466 TTCAATAATT
* * * *
17347476 AAAAAAAT-GAAAGGAGATTATTCAAGACATTTTTGGCCAAAAAGGCCTCAAATAATCTTTA
1 AAAAAAATAGAAAGG-GATTATTAAAGACGTTTTTTGCC-AAAACGCCTCAAATAATCTTTA
* * * ** *
17347537 AAAAAAATTAG-AGGGGATTATTTAAG--GTATTTTTAGACAAAACGCCTTGAATAAT-TTTC
1 AAAAAAA-TAGAAAGGGATTATTAAAGACGT-TTTTT-GCCAAAACGCCTCAAATAATCTTTA
*
17347596 AAAAATATAGAAAGGGATTATTAAAGACGTTTTTTGCCAAAA
1 AAAAAAATAGAAAGGGATTATTAAAGACGTTTTTTGCCAAAA
17347638 ACATCTCGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
58 3 0.04
59 29 0.36
60 23 0.28
61 21 0.26
62 4 0.05
63 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (60 bp):
AAAAAAATAGAAAGGGATTATTAAAGACGTTTTTTGCCAAAACGCCTCAAATAATCTTTA
Found at i:17347639 original size:60 final size:61
Alignment explanation
Indices: 17347476--17347639 Score: 151
Period size: 60 Copynumber: 2.7 Consensus size: 61
17347466 TTCAATAATT
* * * *
17347476 AAAAAAAT-GAAAGGAGATTATTCAAGACATTTTTGGCCAAAAAGGCCTCAAATAATCTTTA
1 AAAAAAATAGAAAGG-GATTATTAAAGACGTTTTTTGCCAAAAACGCCTCAAATAATCTTTA
* * * ** *
17347537 AAAAAAATTAG-AGGGGATTATTTAAG--GTATTTTTAGAC-AAAACGCCTTGAATAAT-TTTC
1 AAAAAAA-TAGAAAGGGATTATTAAAGACGT-TTTTT-GCCAAAAACGCCTCAAATAATCTTTA
*
17347596 AAAAATATAGAAAGGGATTATTAAAGACGTTTTTTGCCAAAAAC
1 AAAAAAATAGAAAGGGATTATTAAAGACGTTTTTTGCCAAAAAC
17347640 ATCTCGAATA
Statistics
Matches: 82, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
58 3 0.04
59 25 0.30
60 28 0.34
61 21 0.26
62 4 0.05
63 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (61 bp):
AAAAAAATAGAAAGGGATTATTAAAGACGTTTTTTGCCAAAAACGCCTCAAATAATCTTTA
Found at i:17347692 original size:102 final size:102
Alignment explanation
Indices: 17347575--17347831 Score: 256
Period size: 101 Copynumber: 2.5 Consensus size: 102
17347565 ATTTTTAGAC
* * *
17347575 AAAACGCCTTGAATAATTTTCAAAAATATAGAAAGGGATTATTAAAGACGTTTTTTGCCA-AAAA
1 AAAACACCTTGAATAATTTT-AAAAAAATAGAAAGGGATTATTAAAGACGTTTTTTACCAGAAAA
*
17347639 CATCTCGAATAAACGT-ATTCAAATCTTTGTAAGGG-TAA
65 -ATCTCGAATAAAC-TCATTCAAATCTTTGTAAGGGCCAA
* ** * *
17347677 AAAACACCTTGAATAATTCTAAAAAAATAG-AAGAAAATTATTGAAGGCGTTTTTTACCAGAAAA
1 AAAACACCTTGAATAATTTTAAAAAAATAGAAAG-GGATTATTAAAGACGTTTTTTACCAGAAAA
* * * * *
17347741 GTTTTGAATAAACTCATTCAATTTTTTGTAAGGGCCAA
65 ATCTCGAATAAACTCATTCAAATCTTTGTAAGGGCCAA
* * * *
17347779 AAAATACCTTAAATACTCTTTAAAAAAAT-GAAAGGGGATTA-TAAAGACATTTT
1 AAAACACCTTGAATAAT-TTTAAAAAAATAGAAA-GGGATTATTAAAGACGTTTT
17347832 GGCTAGAAAC
Statistics
Matches: 125, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
100 4 0.03
101 56 0.45
102 48 0.38
103 16 0.13
104 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (102 bp):
AAAACACCTTGAATAATTTTAAAAAAATAGAAAGGGATTATTAAAGACGTTTTTTACCAGAAAAA
TCTCGAATAAACTCATTCAAATCTTTGTAAGGGCCAA
Found at i:17352262 original size:58 final size:58
Alignment explanation
Indices: 17352156--17352300 Score: 136
Period size: 58 Copynumber: 2.5 Consensus size: 58
17352146 AAATTTGTTT
* **
17352156 ATTAAATTTAATTTATATAATAAAAAATTAATAATTTAATTTAATTTAATTTAATAAG
1 ATTAAATTTAATATATATAATAAAAAATTAATAACATAATTTAATTTAATTTAATAAG
* * * **
17352214 ATTATATTTAATATATATAAT-TAAAATTATATAAACATAATTT-TTTTAATTTATATATC
1 ATTAAATTTAATATATATAATAAAAAATTA-AT-AACATAATTTAATTTAATTTA-ATAAG
* *
17352273 ATTTAAATAT-ATATATA-AATAAATAATT
1 A-TTAAATTTAATATATATAATAAAAAATT
17352301 CATATATATA
Statistics
Matches: 70, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
57 7 0.10
58 33 0.47
59 24 0.34
60 6 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (58 bp):
ATTAAATTTAATATATATAATAAAAAATTAATAACATAATTTAATTTAATTTAATAAG
Found at i:17353321 original size:20 final size:20
Alignment explanation
Indices: 17353296--17353360 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
17353286 GATATATAAA
17353296 TAATTTTTTAATTATTTATT
1 TAATTTTTTAATTATTTATT
* *
17353316 TAATTTTATAATTATTTATA
1 TAATTTTTTAATTATTTATT
*
17353336 T-ATATTTTT-A-TATATATT
1 TAAT-TTTTTAATTATTTATT
17353354 TAATTTT
1 TAATTTT
17353361 ATATTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 10 0.26
19 5 0.13
20 23 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TAATTTTTTAATTATTTATT
Found at i:17353337 original size:12 final size:13
Alignment explanation
Indices: 17353318--17353353 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
17353308 TATTTATTTA
17353318 ATTT-TATA-ATT
1 ATTTATATATATT
17353329 ATTTATATATATT
1 ATTTATATATATT
17353342 -TTTATATATATT
1 ATTTATATATATT
17353354 TAATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 16 0.70
13 3 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTATATATATT
Found at i:17353346 original size:16 final size:17
Alignment explanation
Indices: 17353327--17353370 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
17353317 AATTTTATAA
17353327 TTATTTATATAT-ATTT
1 TTATTTATATATAATTT
* *
17353343 TTATATATATTTAATTT
1 TTATTTATATATAATTT
17353360 TATATTTATAT
1 T-TATTTATAT
17353371 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTTATATATAATTT
Found at i:17355375 original size:23 final size:23
Alignment explanation
Indices: 17355347--17355397 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
17355337 AAAAAATAAT
* **
17355347 AAAAATTATTATAGTTATGATTA
1 AAAAATTATTATAATTACAATTA
17355370 AAAAATTATTATAATTACAATTA
1 AAAAATTATTATAATTACAATTA
17355393 AAAAA
1 AAAAA
17355398 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
AAAAATTATTATAATTACAATTA
Found at i:17355405 original size:21 final size:22
Alignment explanation
Indices: 17355346--17355407 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
17355336 TAAAAAATAA
* * **
17355346 TAAAAATTATTATAGTTATGAT
1 TAAAAAATATTATAATTACAAT
17355368 TAAAAAATTATTATAATTACAAT
1 TAAAAAA-TATTATAATTACAAT
*
17355391 TAAAAAA-ATTTTAATTA
1 TAAAAAATATTATAATTA
17355408 ACATTTTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 9 0.26
22 6 0.18
23 19 0.56
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (22 bp):
TAAAAAATATTATAATTACAAT
Found at i:17355456 original size:17 final size:18
Alignment explanation
Indices: 17355436--17355482 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
17355426 ATTTTATTAA
17355436 AATTAATATT-TAAATTT
1 AATTAATATTATAAATTT
17355453 AATTAATGATATAATAAATTT
1 AATTAAT-AT-T-ATAAATTT
17355474 AATT-ATATT
1 AATTAATATT
17355483 GCACTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.27
18 3 0.12
19 3 0.12
20 2 0.08
21 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTAATATTATAAATTT
Found at i:17363894 original size:2 final size:2
Alignment explanation
Indices: 17363887--17363918 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17363877 ATATCGGATT
*
17363887 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17363919 AATGGATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17366943 original size:19 final size:20
Alignment explanation
Indices: 17366906--17366943 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17366896 AAAAATTTAA
*
17366906 TAAATTAATATGATAATAAC
1 TAAATAAATATGATAATAAC
17366926 TAAATAAATATG-TAATAA
1 TAAATAAATATGATAATAA
17366944 TATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAATAAATATGATAATAAC
Found at i:17367090 original size:20 final size:21
Alignment explanation
Indices: 17367046--17367102 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 21
17367036 TAGTAAAATT
17367046 TAAAAAATT-TTCTTATAATATA
1 TAAAAAATTATT-TT-TAATATA
17367068 TAAAATAA-TATTTTTAATA-A
1 TAAAA-AATTATTTTTAATATA
17367088 TAAAAAATTATTTTT
1 TAAAAAATTATTTTT
17367103 TACATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.06
20 13 0.41
21 5 0.16
22 8 0.25
23 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAAAATTATTTTTAATATA
Found at i:17367103 original size:21 final size:22
Alignment explanation
Indices: 17367046--17367104 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
17367036 TAGTAAAATT
*
17367046 TAAAAAATT-TTCTTATAATATA
1 TAAAAAATTATT-TTTTAATATA
17367068 TAAAATAA-TA-TTTTTAATA-A
1 TAAAA-AATTATTTTTTAATATA
17367088 TAAAAAATTATTTTTTA
1 TAAAAAATTATTTTTTA
17367105 CATTTTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
19 2 0.06
20 8 0.25
21 13 0.41
22 7 0.22
23 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAAAATTATTTTTTAATATA
Found at i:17367103 original size:22 final size:21
Alignment explanation
Indices: 17367046--17367103 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 21
17367036 TAGTAAAATT
* *
17367046 TAAAAAATT-TTCTTATAATA
1 TAAAAAATTATTTTTTTAATA
* * *
17367066 TATAAAATAATATTTTTAATAA
1 TAAAAAATTATTTTTTTAAT-A
17367088 TAAAAAATTATTTTTT
1 TAAAAAATTATTTTTT
17367104 ACATTTTAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 7 0.25
21 7 0.25
22 14 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAAAATTATTTTTTTAATA
Found at i:17368218 original size:3 final size:3
Alignment explanation
Indices: 17368210--17368260 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
17368200 CCATGATCTT
17368210 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17368257 TTA T
1 TTA T
17368261 CAAATTACCT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17368991 original size:6 final size:6
Alignment explanation
Indices: 17368982--17369018 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
17368972 AATATGGAAA
*
17368982 GCAAAG GCAAAG GCAAAG GCAAAC GCATAAG GCAAAG
1 GCAAAG GCAAAG GCAAAG GCAAAG GCA-AAG GCAAAG
17369019 CTTCCAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.49, C:0.19, G:0.30, T:0.03
Consensus pattern (6 bp):
GCAAAG
Found at i:17369015 original size:19 final size:18
Alignment explanation
Indices: 17368982--17369018 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17368972 AATATGGAAA
*
17368982 GCAAAGGCAAAGGCAAAG
1 GCAAACGCAAAGGCAAAG
17369000 GCAAACGCATAAGGCAAAG
1 GCAAACGCA-AAGGCAAAG
17369019 CTTCCAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.49, C:0.19, G:0.30, T:0.03
Consensus pattern (18 bp):
GCAAACGCAAAGGCAAAG
Found at i:17378490 original size:33 final size:35
Alignment explanation
Indices: 17378448--17378518 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 35
17378438 TACAATAATA
*
17378448 TTGCAAT-A-ATGACATTTAGTCACTATTAAATGT
1 TTGCAATAACATGACATTTAGTCACTACTAAATGT
*
17378481 TTGCAATAATCCATTACATTTAGTCACTACTAAATGT
1 TTGCAATAA--CATGACATTTAGTCACTACTAAATGT
17378518 T
1 T
17378519 AACATACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 7 0.22
34 1 0.03
37 24 0.75
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (35 bp):
TTGCAATAACATGACATTTAGTCACTACTAAATGT
Found at i:17386418 original size:18 final size:17
Alignment explanation
Indices: 17386397--17386430 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
17386387 CAGTGGCAAA
17386397 GAAAAAAATAAGAAAAAG
1 GAAAAAAATAA-AAAAAG
17386415 GAAAAAAATAAAAAAA
1 GAAAAAAATAAAAAAA
17386431 CTAATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
GAAAAAAATAAAAAAAG
Found at i:17391339 original size:6 final size:6
Alignment explanation
Indices: 17391328--17391352 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17391318 CCAAGTCTGA
17391328 TTTGCT TTTGCT TTTGCT TTTGCT T
1 TTTGCT TTTGCT TTTGCT TTTGCT T
17391353 GTAAGTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTGCT
Found at i:17393231 original size:8 final size:8
Alignment explanation
Indices: 17393206--17393248 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
17393196 TTTAATTAAT
*
17393206 TAATTATT
1 TAATTATA
*
17393214 TATTTATA
1 TAATTATA
17393222 TATATTTATA
1 TA-A-TTATA
17393232 TAATTATA
1 TAATTATA
17393240 TAATTATA
1 TAATTATA
17393248 T
1 T
17393249 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 22 0.73
9 1 0.03
10 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TAATTATA
Found at i:17395250 original size:2 final size:2
Alignment explanation
Indices: 17395243--17395271 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17395233 TCTATCCAAG
17395243 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 T
17395272 CCTCTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17399553 original size:106 final size:106
Alignment explanation
Indices: 17399396--17399597 Score: 271
Period size: 106 Copynumber: 1.9 Consensus size: 106
17399386 GTTTGTGTTA
* *
17399396 ACACGAAAACATAAAAAAAAATTTTAATTTTATTAAACTTATTTATGATTTTTTTAAAATTTTAA
1 ACACGAAAACATAAAAAAAAATTTTAATTTTATTAAACTTATTTATAATTTTTCTAAAATTTTAA
** *
17399461 GTGTTATTATTTT-ATATTTTTTATTCATATTGTATCATCG
66 GTAATATTATTTTCATATCTTTTATTCATATTGTATCATCG
* * * * * *
17399501 ACACGAAAATATAAAATATAATTTTTTATTTTATTAAATTTATTTATAATTTTTCTCAAATTTTA
1 ACACGAAAACATAAAA-AAAAATTTTAATTTTATTAAACTTATTTATAATTTTTCTAAAATTTTA
* *
17399566 AGTAATGTTATTTTCGTATCTTTTATTCATAT
65 AGTAATATTATTTTCATATCTTTTATTCATAT
17399598 CGTTTGCGTA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 15 0.18
106 52 0.63
107 15 0.18
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (106 bp):
ACACGAAAACATAAAAAAAAATTTTAATTTTATTAAACTTATTTATAATTTTTCTAAAATTTTAA
GTAATATTATTTTCATATCTTTTATTCATATTGTATCATCG
Found at i:17400266 original size:21 final size:22
Alignment explanation
Indices: 17400236--17400279 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 22
17400226 TTTCTTTTTA
17400236 TTTTTTTAATTA-GTA-TACTT
1 TTTTTTTAATTATGTATTACTT
17400256 TTTTTTATAATTATGTATTACTT
1 TTTTTT-TAATTATGTATTACTT
17400279 T
1 T
17400280 ACAATCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 3 0.14
23 6 0.29
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTTTTAATTATGTATTACTT
Found at i:17402678 original size:13 final size:13
Alignment explanation
Indices: 17402662--17402695 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
17402652 ATTGAAGTAA
17402662 AAAATTATTTTTG
1 AAAATTATTTTTG
17402675 AAAATGTATTTTTG
1 AAAAT-TATTTTTG
17402689 AATAATT
1 AA-AATT
17402696 GCTATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 11 0.58
15 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (13 bp):
AAAATTATTTTTG
Found at i:17402746 original size:34 final size:32
Alignment explanation
Indices: 17402707--17402805 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 32
17402697 CTATACTTTG
* **
17402707 TGAAAATACATTTTTGGATA-ATTGTAATGTTTT
1 TGAAAATACATTTTT-GATATAGT-TAAAATTTT
*
17402740 TCGAAAATAAATTTTTGATATAGTTAAAATTTT
1 T-GAAAATACATTTTTGATATAGTTAAAATTTT
* *
17402773 TGAAAATACATTTATGATACA-TTGAAAATTTT
1 TGAAAATACATTTTTGATATAGTT-AAAATTTT
17402805 T
1 T
17402806 TTGAAAATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
31 2 0.04
32 26 0.46
33 13 0.23
34 15 0.27
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.45
Consensus pattern (32 bp):
TGAAAATACATTTTTGATATAGTTAAAATTTT
Found at i:17402812 original size:34 final size:33
Alignment explanation
Indices: 17402662--17402818 Score: 108
Period size: 34 Copynumber: 4.7 Consensus size: 33
17402652 ATTGAAGTAA
**
17402662 AAAATTATTTTTGAAAATGTATTTTTGAATAATTG
1 AAAATT-TTTTTGAAAATACATTTTTG-ATAATTG
** * *
17402697 -CTATACTTTGTGAAAATACATTTTTGGATAATTG
1 AAAAT-TTTTTTGAAAATACATTTTT-GATAATTG
* * *
17402731 -TAATGTTTTTCGAAAATAAATTTTTGATATAGTT-
1 AAAAT-TTTTTTGAAAATACATTTTTGATA-A-TTG
*
17402765 AAAA--TTTTTGAAAATACATTTATGATACATTG
1 AAAATTTTTTTGAAAATACATTTTTGATA-ATTG
*
17402797 AAAATTTTTTTGAAAATTCATT
1 AAAATTTTTTTGAAAATACATT
17402819 CCTAATAACT
Statistics
Matches: 95, Mismatches: 19, Indels: 17
0.73 0.15 0.13
Matches are distributed among these distances:
31 2 0.02
32 25 0.26
33 4 0.04
34 59 0.62
35 5 0.05
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.46
Consensus pattern (33 bp):
AAAATTTTTTTGAAAATACATTTTTGATAATTG
Found at i:17411266 original size:43 final size:43
Alignment explanation
Indices: 17411205--17411293 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
17411195 TTTCTCATTC
17411205 CTTGTGCACTTTGATGGATAGTGAGATACAAATGCATGACTAT
1 CTTGTGCACTTTGATGGATAGTGAGATACAAATGCATGACTAT
17411248 CTTGTGCACTTTGATGGATAGTGAGATACAAATGCATGACTAT
1 CTTGTGCACTTTGATGGATAGTGAGATACAAATGCATGACTAT
17411291 CTT
1 CTT
17411294 CGGATCTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (43 bp):
CTTGTGCACTTTGATGGATAGTGAGATACAAATGCATGACTAT
Found at i:17418586 original size:18 final size:18
Alignment explanation
Indices: 17418531--17418592 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
17418521 TCTATCAATT
*
17418531 TAAAATATAATACAAATTA
1 TAAAATATAATATAAA-TA
* * **
17418550 TAATATATAATTTTCATA
1 TAAAATATAATATAAATA
17418568 TAAAATATAATATAAATA
1 TAAAATATAATATAAATA
17418586 TATAAAT
1 TA-AAAT
17418593 TATTAATATT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATATAATATAAATA
Found at i:17418611 original size:37 final size:34
Alignment explanation
Indices: 17418529--17418611 Score: 80
Period size: 37 Copynumber: 2.3 Consensus size: 34
17418519 AGTCTATCAA
17418529 TTTA-AAATATAATACAAATTATAATATATAATT
1 TTTATAAATATAATACAAATTATAATATATAATT
*
17418562 TTCATATAAAATATAATATAAATATATAA-ATTATTAATAT
1 TT--TAT-AAATATAATACAAAT-TATAATA-TA-TAAT-T
17418602 TTTATAAATA
1 TTTATAAATA
17418612 CGAATTCCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
33 2 0.05
35 2 0.05
37 20 0.49
38 10 0.24
39 4 0.10
40 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (34 bp):
TTTATAAATATAATACAAATTATAATATATAATT
Found at i:17443045 original size:1 final size:1
Alignment explanation
Indices: 17443039--17443097 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
17443029 TAATTTCATG
* * * * * * *
17443039 AAAAAAAAAAAAGAAAAAAAAGACAAAATAAAAAAAACAAAAACAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17443098 CCCCTCATAA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.88, C:0.07, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:17443066 original size:22 final size:20
Alignment explanation
Indices: 17443041--17443097 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
17443031 ATTTCATGAA
17443041 AAAAAAAAAAGAAAAAAAAGAC
1 AAAAAAAAAA-AAAAAAAA-AC
* *
17443063 AAAATAAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAAAC
17443083 AAAAAACAAAAAAAA
1 AAAAAA-AAAAAAAA
17443098 CCCCTCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 7 0.23
21 14 0.47
22 9 0.30
ACGTcount: A:0.88, C:0.07, G:0.04, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAAAC
Found at i:17443677 original size:22 final size:23
Alignment explanation
Indices: 17443630--17443686 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
17443620 AAAAATTGGT
*
17443630 AAAAAGAGAAAACAATAAAGCGA
1 AAAAAGAGAAAACAATAAAGCAA
*
17443653 AAAAAGA-AAAATAATCAAAG-AA
1 AAAAAGAGAAAACAAT-AAAGCAA
*
17443675 AAAGAGAGAAAA
1 AAAAAGAGAAAA
17443687 GAAAAAAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (23 bp):
AAAAAGAGAAAACAATAAAGCAA
Found at i:17443694 original size:16 final size:15
Alignment explanation
Indices: 17443630--17443699 Score: 54
Period size: 16 Copynumber: 4.7 Consensus size: 15
17443620 AAAAATTGGT
*
17443630 AAAA-AGAGAAAACA
1 AAAAGAGAGAAAAGA
* *
17443644 ATAAAGCGAAAAAAGA
1 A-AAAGAGAGAAAAGA
* **
17443660 AAAATA-ATCAAAGA
1 AAAAGAGAGAAAAGA
17443674 AAAAGAGAGAAAAGAA
1 AAAAGAGAGAAAAG-A
17443690 AAAAGAGAGA
1 AAAAGAGAGA
17443700 TCATTGGAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 12 0.29
15 11 0.26
16 19 0.45
ACGTcount: A:0.73, C:0.04, G:0.19, T:0.04
Consensus pattern (15 bp):
AAAAGAGAGAAAAGA
Found at i:17447417 original size:17 final size:18
Alignment explanation
Indices: 17447391--17447442 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
17447381 TGAATTAATG
17447391 TATT-AAATAATAATTT-
1 TATTAAAATAATAATTTA
17447407 TATTAAAATAATACATTTA
1 TATTAAAATAATA-ATTTA
17447426 TAATTAAAATAAATAAT
1 T-ATTAAAAT-AATAAT
17447443 AAAATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.13
17 8 0.26
18 4 0.13
19 1 0.03
20 10 0.32
21 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTAAAATAATAATTTA
Found at i:17456788 original size:13 final size:12
Alignment explanation
Indices: 17456766--17456800 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
17456756 AAATTTGAGA
17456766 AAAATAAATAAC
1 AAAATAAATAAC
17456778 AAAATATAATAAC
1 AAAATA-AATAAC
*
17456791 AAAAAAAATA
1 AAAATAAATA
17456801 TAAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAATAAATAAC
Found at i:17456811 original size:17 final size:17
Alignment explanation
Indices: 17456778--17456811 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17456768 AATAAATAAC
*
17456778 AAAATATAATAACAAAA
1 AAAATATAAAAACAAAA
*
17456795 AAAATATAAAAAGAAAA
1 AAAATATAAAAACAAAA
17456812 GGGTTGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATATAAAAACAAAA
Found at i:17457397 original size:21 final size:22
Alignment explanation
Indices: 17457373--17457420 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
17457363 ATTTTAGTCT
*
17457373 TATTATTATCGTAACTAAT-TA
1 TATTATTATAGTAACTAATCTA
17457394 TATTATTATAGTAACTAATCTA
1 TATTATTATAGTAACTAATCTA
17457416 -ATTAT
1 TATTAT
17457421 CACCTCTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (22 bp):
TATTATTATAGTAACTAATCTA
Found at i:17458108 original size:18 final size:19
Alignment explanation
Indices: 17458085--17458128 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
17458075 GATATGCATT
*
17458085 TTTTAAAA-AT-TTTTAAA
1 TTTTAAAATATATATTAAA
17458102 CTTTTAAAATATATATTAAA
1 -TTTTAAAATATATATTAAA
17458122 TTTTAAA
1 TTTTAAA
17458129 GGCTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAAAATATATATTAAA
Found at i:17462950 original size:11 final size:11
Alignment explanation
Indices: 17462934--17462958 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17462924 TATTAATAAC
17462934 TAAATAAAAAT
1 TAAATAAAAAT
17462945 TAAATAAAAAT
1 TAAATAAAAAT
17462956 TAA
1 TAA
17462959 TTTATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAATAAAAAT
Found at i:17463002 original size:29 final size:29
Alignment explanation
Indices: 17462957--17463014 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
17462947 AATAAAAATT
* *
17462957 AATTTATTTATTTATTTATTATATTATAA
1 AATTTATTTATTAATTTATTATATAATAA
*
17462986 AATTTATTTGTTAATTTATTATATAATAA
1 AATTTATTTATTAATTTATTATATAATAA
17463015 TAATAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
AATTTATTTATTAATTTATTATATAATAA
Found at i:17463362 original size:19 final size:18
Alignment explanation
Indices: 17463324--17463383 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
17463314 TAATATTTAA
* *
17463324 TTTAATGAAATTTTTATAT
1 TTTAATAAAATTTAT-TAT
*
17463343 TTTAATATATATTTATTAT
1 TTTAATA-AAATTTATTAT
* *
17463362 TTTATTAAAAATTATTAT
1 TTTAATAAAATTTATTAT
17463380 TTTA
1 TTTA
17463384 TCTTCATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 13 0.38
19 15 0.44
20 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTAATAAAATTTATTAT
Found at i:17463450 original size:20 final size:22
Alignment explanation
Indices: 17463411--17463451 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17463401 ATTTGAGTTT
17463411 GAATATAAATGAATTTAAATTC
1 GAATATAAATGAATTTAAATTC
17463433 GAATATAAAT-AA-TTAAATT
1 GAATATAAATGAATTTAAATT
17463452 TGAAGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (22 bp):
GAATATAAATGAATTTAAATTC
Found at i:17463578 original size:16 final size:16
Alignment explanation
Indices: 17463539--17463582 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
17463529 TTTATCTCAT
*
17463539 ATTAAATTCAAACTTTA
1 ATTAAATTTAAA-TTTA
17463556 A--AAATTTAAATTTA
1 ATTAAATTTAAATTTA
17463570 ATTAAATTTAAAT
1 ATTAAATTTAAAT
17463583 AAAATTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
16 10 0.42
17 1 0.04
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAAATTTAAATTTA
Found at i:17464367 original size:24 final size:23
Alignment explanation
Indices: 17464315--17464374 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
17464305 TGAGTTGCAC
* * *
17464315 TTAAAATATTTTTTTAATTAATT
1 TTAATATATTTATTTAATCAATT
*
17464338 TAAATATATTTATTTACATCAATT
1 TTAATATATTTATTTA-ATCAATT
*
17464362 TTAATAAATTTAT
1 TTAATATATTTAT
17464375 GAAAAATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATATATTTATTTAATCAATT
Found at i:17467708 original size:27 final size:27
Alignment explanation
Indices: 17467649--17467734 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 27
17467639 TGTAGCTAAA
17467649 ATAATAAAAAA-TTCATAAATTTTATTATT
1 ATAATAAAAAATTTCAT-AA-TTT-TTATT
* *
17467678 TTATTTAAATAAA-TTCATATATTTTTATT
1 ATA-ATAAA-AAATTTCATA-ATTTTTATT
17467707 ATAATAAAAAATTTTCATAATTTTTATT
1 ATAATAAAAAA-TTTCATAATTTTTATT
17467735 TATATCCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
27 3 0.06
28 13 0.27
29 15 0.31
30 8 0.17
31 9 0.19
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAATAAAAAATTTCATAATTTTTATT
Found at i:17467788 original size:29 final size:28
Alignment explanation
Indices: 17467673--17467788 Score: 78
Period size: 29 Copynumber: 4.0 Consensus size: 28
17467663 ATAAATTTTA
* *
17467673 TTATTTTATTTAAATAAATTCATATATTT
1 TTATTTAATTTAAATAAATTCTTA-ATTT
*
17467702 TTATTATAA--TAAA-AAATTTTCATAATTT
1 TTATT-TAATTTAAATAAA--TTCTTAATTT
** * *
17467730 TTATTTATATCCAAATAAA-CCTTTAGTTT
1 TTATTTA-ATTTAAATAAATTC-TTAATTT
17467759 TTAATTTAATTTAAATAAATTCTTAATTT
1 TT-ATTTAATTTAAATAAATTCTTAATTT
17467788 T
1 T
17467789 GAATTTGTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
27 5 0.07
28 15 0.22
29 34 0.50
30 11 0.16
31 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (28 bp):
TTATTTAATTTAAATAAATTCTTAATTT
Found at i:17468659 original size:21 final size:22
Alignment explanation
Indices: 17468635--17468678 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
17468625 AATCTTATCC
17468635 TTATAATAATCAATCTCA-CTG
1 TTATAATAATCAATCTCATCTG
*
17468656 TTATAATAATTAATCTCATCTG
1 TTATAATAATCAATCTCATCTG
17468678 T
1 T
17468679 ACTACTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (22 bp):
TTATAATAATCAATCTCATCTG
Found at i:17471173 original size:37 final size:38
Alignment explanation
Indices: 17471106--17471191 Score: 88
Period size: 37 Copynumber: 2.3 Consensus size: 38
17471096 TGTTATCATT
* *
17471106 AATAGAAAAATTCAAAAAATTTTAACAAAATTCA-AAAA
1 AATAAAAAAATTCAAAAAATTTGAACAAAATT-ATAAAA
* *
17471144 AATAAAAAAA-TCTAAAATATTTGAA-AAAATTATACAA
1 AATAAAAAAATTC-AAAAAATTTGAACAAAATTATAAAA
*
17471181 AATTAAAAAAT
1 AATAAAAAAAT
17471192 GAAATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
36 1 0.03
37 20 0.50
38 19 0.47
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (38 bp):
AATAAAAAAATTCAAAAAATTTGAACAAAATTATAAAA
Found at i:17471225 original size:17 final size:17
Alignment explanation
Indices: 17471205--17471275 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
17471195 ATATTTTTAG
17471205 AAATAATAAAAATTAAA
1 AAATAATAAAAATTAAA
* *
17471222 AAATTAGAAAAATCTTAAA
1 AAATAATAAAAA--TTAAA
** *
17471241 ATTTAATAAAAATTAAC
1 AAATAATAAAAATTAAA
*
17471258 AAA-AATCTAAAATTAAA
1 AAATAAT-AAAAATTAAA
17471275 A
1 A
17471276 TGAAAATTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
16 3 0.08
17 24 0.60
19 13 0.32
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (17 bp):
AAATAATAAAAATTAAA
Found at i:17471251 original size:19 final size:18
Alignment explanation
Indices: 17471127--17471261 Score: 57
Period size: 18 Copynumber: 7.4 Consensus size: 18
17471117 TCAAAAAATT
17471127 TTAACAAAATTCAA-AAAAA
1 TTAA-AAAATT-AATAAAAA
* * *
17471146 TAAAAAAATCTAA-AATAT
1 TTAAAAAAT-TAATAAAAA
17471164 TTGAAAAAATT-ATACAAAA
1 TT-AAAAAATTAATA-AAAA
* * **
17471183 TTAAAAAATGAA-ATATT
1 TTAAAAAATTAATAAAAA
* *
17471200 TTTAGAAA-TAATAAAAA
1 TTAAAAAATTAATAAAAA
*
17471217 TTAAAAAATT-AGAAAAA
1 TTAAAAAATTAATAAAAA
* *
17471234 TCTTAAAATTTAATAAAAA
1 T-TAAAAAATTAATAAAAA
17471253 TTAACAAAA
1 TTAA-AAAA
17471262 ATCTAAAATT
Statistics
Matches: 82, Mismatches: 24, Indels: 20
0.65 0.19 0.16
Matches are distributed among these distances:
16 2 0.02
17 23 0.28
18 31 0.38
19 26 0.32
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAATTAATAAAAA
Found at i:17471281 original size:29 final size:28
Alignment explanation
Indices: 17471220--17471283 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
17471210 ATAAAAATTA
* *
17471220 AAAAATTAGAAAAATCTTAAAATTTAAT
1 AAAAATTACAAAAATCTTAAAATTAAAT
17471248 AAAAATTAACAAAAATC-TAAAATTAAAAT
1 AAAAATT-ACAAAAATCTTAAAATT-AAAT
*
17471277 GAAAATT
1 AAAAATT
17471284 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (28 bp):
AAAAATTACAAAAATCTTAAAATTAAAT
Found at i:17471307 original size:16 final size:17
Alignment explanation
Indices: 17471269--17471309 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
17471259 AAAATCTAAA
17471269 ATTAAAATGAAAATTTT
1 ATTAAAATGAAAATTTT
*
17471286 AATAAAAT-AAAATTTT
1 ATTAAAATGAAAATTTT
*
17471302 CTTAAAAT
1 ATTAAAAT
17471310 TTAGAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTAAAATGAAAATTTT
Found at i:17474165 original size:42 final size:43
Alignment explanation
Indices: 17474081--17474165 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
17474071 AACCTATTGA
* * *
17474081 TATCTATAAATTAGTAATTTAATATTTATACTTATTTCATCTT
1 TATCTATAAATTAGTAATTTAATATATATAATTAATTCATCTT
17474124 TATC-ATAAATTTA-TAATTTAATATATATAATTGAATT-ATCTT
1 TATCTATAAA-TTAGTAATTTAATATATATAATT-AATTCATCTT
17474166 ACTTTTTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 27 0.73
43 10 0.27
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (43 bp):
TATCTATAAATTAGTAATTTAATATATATAATTAATTCATCTT
Found at i:17476381 original size:18 final size:17
Alignment explanation
Indices: 17476360--17476401 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
17476350 ATTTAGTTTT
17476360 TTTAATTATTAAAACACA
1 TTTAATTA-TAAAACACA
*
17476378 TTT-ATTATAGAACACA
1 TTTAATTATAAAACACA
17476394 TATTAATT
1 T-TTAATT
17476402 TTGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 6 0.29
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAATTATAAAACACA
Found at i:17478450 original size:15 final size:14
Alignment explanation
Indices: 17478429--17478471 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
17478419 TAAAGTTAAA
17478429 AATAAAAATTATAT
1 AATAAAAATTATAT
17478443 ACATAAAAATTA-A-
1 A-ATAAAAATTATAT
17478456 AATAAAAAATTATAT
1 AAT-AAAAATTATAT
17478471 A
1 A
17478472 TATTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.08
13 9 0.36
14 3 0.12
15 11 0.44
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAAAATTATAT
Found at i:17478456 original size:28 final size:27
Alignment explanation
Indices: 17478407--17478471 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
17478397 GATTATATTT
* *
17478407 AATTCATATATATAAAGTTAAAA-ATAAA
1 AATT-ATATACATAAAATTAAAATA-AAA
17478435 AATTATATACATAAAAATTAAAATAAAA
1 AATTATATACAT-AAAATTAAAATAAAA
17478463 AATTATATA
1 AATTATATA
17478472 TATTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 7 0.21
28 25 0.76
29 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (27 bp):
AATTATATACATAAAATTAAAATAAAA
Found at i:17480126 original size:23 final size:22
Alignment explanation
Indices: 17480084--17480131 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
17480074 TTTTAGTTAT
17480084 AAATATAAATTTTAATTATAATC
1 AAATATAAATTTTAATTATAA-C
17480107 AAATATTAAA-TTT-ATATATAAC
1 AAATA-TAAATTTTAAT-TATAAC
17480129 AAA
1 AAA
17480132 ATCACTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATAAATTTTAATTATAAC
Found at i:17481270 original size:17 final size:17
Alignment explanation
Indices: 17481248--17481280 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17481238 CATTCCAGAT
*
17481248 TTTTTTAATAAGATTAA
1 TTTTTTAATAAAATTAA
17481265 TTTTTTAATAAAATTA
1 TTTTTTAATAAAATTA
17481281 TATTCATTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTTTAATAAAATTAA
Found at i:17481290 original size:47 final size:48
Alignment explanation
Indices: 17481202--17481293 Score: 150
Period size: 47 Copynumber: 1.9 Consensus size: 48
17481192 TTACTTTTAA
***
17481202 TTTTAATAAGATTAATTTTATTAATCTTATTATATTCATTCCAGATTT
1 TTTTAATAAGATTAATTTTATTAATAAAATTATATTCATTCCAGATTT
17481250 TTTTAATAAGATTAATTTT-TTAATAAAATTATATTCATTCCAGA
1 TTTTAATAAGATTAATTTTATTAATAAAATTATATTCATTCCAGA
17481294 AACATAGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 22 0.54
48 19 0.46
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (48 bp):
TTTTAATAAGATTAATTTTATTAATAAAATTATATTCATTCCAGATTT
Found at i:17481373 original size:15 final size:15
Alignment explanation
Indices: 17481353--17481381 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17481343 CAGAAATCTT
17481353 ATTAATTTTAATAAG
1 ATTAATTTTAATAAG
17481368 ATTAATTTTAATAA
1 ATTAATTTTAATAA
17481382 CATATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTAATTTTAATAAG
Found at i:17482894 original size:38 final size:39
Alignment explanation
Indices: 17482792--17482894 Score: 99
Period size: 41 Copynumber: 2.7 Consensus size: 39
17482782 TTAATATTTC
*
17482792 AATAATAA-ATA-AT-ATTATATTATTATGTTAATAATA
1 AATAATAACATATATAATAATATTATTATGTTAATAATA
* *
17482828 AATAATAACATATATAATAATATTTTATTATTTTAATAATT
1 AATAATAACATATATAATAATA--TTATTATGTTAATAATA
**
17482869 AATGTTAA-ATAGTATAATAA-ATTATT
1 AATAATAACATA-TATAATAATATTATT
17482895 TTCTTGATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
36 8 0.14
37 3 0.05
38 7 0.12
39 5 0.09
40 4 0.07
41 29 0.52
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (39 bp):
AATAATAACATATATAATAATATTATTATGTTAATAATA
Found at i:17483067 original size:21 final size:21
Alignment explanation
Indices: 17483043--17483107 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
17483033 AGCTACTTTC
17483043 AATATAAAATATAAATATTTT
1 AATATAAAATATAAATATTTT
* * *
17483064 AATA-ATAAATATTATTATTGT
1 AATATA-AAATATAAATATTTT
17483085 AATATTAATAA-A-AAATATTTT
1 AATA-TAA-AATATAAATATTTT
17483106 AA
1 AA
17483108 GAATAGTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.03
21 28 0.82
22 2 0.06
23 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATAAAATATAAATATTTT
Found at i:17483112 original size:24 final size:27
Alignment explanation
Indices: 17483062--17483118 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
17483052 TATAAATATT
* *
17483062 TTAATAATAAATATTATTATTGTAATA
1 TTAATAAAAAATATTATTATAGTAATA
17483089 TTAATAAAAAATATT-TTA-AG-AATA
1 TTAATAAAAAATATTATTATAGTAATA
*
17483113 GTAATA
1 TTAATA
17483119 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.33
25 1 0.04
26 3 0.11
27 14 0.52
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (27 bp):
TTAATAAAAAATATTATTATAGTAATA
Found at i:17484413 original size:14 final size:14
Alignment explanation
Indices: 17484390--17484419 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17484380 ACAAAAAATG
17484390 AAAATAAAATCAAA
1 AAAATAAAATCAAA
*
17484404 AAAATAAAATGAAA
1 AAAATAAAATCAAA
17484418 AA
1 AA
17484420 GAAAAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAATAAAATCAAA
Found at i:17484424 original size:20 final size:20
Alignment explanation
Indices: 17484373--17484425 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
17484363 ATCATAAAAT
17484373 AAAT-AAAAC-AAAAAATGA
1 AAATAAAAACAAAAAAATGA
*
17484391 AAATAAAATCAAAAAAAT-A
1 AAATAAAAACAAAAAAATGA
*
17484410 AAATGAAAAAGAAAAA
1 AAAT-AAAAACAAAAA
17484426 GGAAAACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 16 0.55
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (20 bp):
AAATAAAAACAAAAAAATGA
Found at i:17485744 original size:34 final size:34
Alignment explanation
Indices: 17485706--17485810 Score: 124
Period size: 34 Copynumber: 3.1 Consensus size: 34
17485696 AACTGTAAAA
17485706 TTAAAAGGCTCATTTGACTAAAGGTTATGAAACT
1 TTAAAAGGCTCATTTGACTAAAGGTTATGAAACT
* *
17485740 TTAAATGGCTCATTTGACCAGAA-GTTATGAAACT
1 TTAAAAGGCTCATTTGACTA-AAGGTTATGAAACT
* * **
17485774 TTAAATA-GCTCATTTGATTAGAGGCAATGAAACT
1 TTAAA-AGGCTCATTTGACTAAAGGTTATGAAACT
17485808 TTA
1 TTA
17485811 GAATTTAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 1 0.02
34 57 0.95
35 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (34 bp):
TTAAAAGGCTCATTTGACTAAAGGTTATGAAACT
Found at i:17491604 original size:24 final size:26
Alignment explanation
Indices: 17491577--17491632 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
17491567 AATAAAAGAA
*
17491577 ATTTAAGAAATT-TAATATT-TTATT
1 ATTTAAAAAATTCTAATATTATTATT
*
17491601 ATTTTAAAAAATTCTAATCTTATTATT
1 A-TTTAAAAAATTCTAATATTATTATT
*
17491628 TTTTA
1 ATTTA
17491633 TACTTAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.04
25 10 0.38
26 10 0.38
27 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTAAAAAATTCTAATATTATTATT
Found at i:17491606 original size:25 final size:26
Alignment explanation
Indices: 17491578--17491632 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
17491568 ATAAAAGAAA
*
17491578 TTTAAGAAATT-TAATATT-TTATTAT
1 TTTAAAAAATTCTAATATTATTATT-T
*
17491603 TTTAAAAAATTCTAATCTTATTATTT
1 TTTAAAAAATTCTAATATTATTATTT
17491629 TTTA
1 TTTA
17491633 TACTTAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 11 0.42
27 5 0.19
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTAAAAAATTCTAATATTATTATTT
Found at i:17492822 original size:25 final size:26
Alignment explanation
Indices: 17492789--17492838 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
17492779 CTAAATATTA
17492789 ATAATTTTA-ATATATTTTAATAATAC
1 ATAATTTTATA-ATATTTTAATAATAC
17492815 ATAA-TTTATAATATTTTAATAATA
1 ATAATTTTATAATATTTTAATAATA
17492839 ATTAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
ATAATTTTATAATATTTTAATAATAC
Found at i:17492850 original size:21 final size:22
Alignment explanation
Indices: 17492809--17492851 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
17492799 TATATTTTAA
*
17492809 TAATACATAATTTATAATATTT
1 TAATACATAATTTAAAATATTT
17492831 TAATA-ATAA-TTAAAATTATTT
1 TAATACATAATTTAAAA-TATTT
17492852 AAAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATACATAATTTAAAATATTT
Found at i:17505915 original size:27 final size:25
Alignment explanation
Indices: 17505863--17505911 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
17505853 ATTTTGAAAC
* **
17505863 TAAAATTTTATTAAAAAGGATTCAA
1 TAAAATTTTAATAAAAAAAATTCAA
17505888 TAAAATTATTAATAAAAAAAATTC
1 TAAAATT-TTAATAAAAAAAATTC
17505912 CAATTCAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAAATTTTAATAAAAAAAATTCAA
Found at i:17512284 original size:29 final size:30
Alignment explanation
Indices: 17512221--17512325 Score: 94
Period size: 29 Copynumber: 3.6 Consensus size: 30
17512211 AAGGTTCGGA
* * *
17512221 TTTTAAGGGTTTGGATTT-AAGTTTTGAGGG
1 TTTT-AGGGTTTGGATTTAAAGTATGGAAGG
*
17512251 TTTTAGGGTTTGGTTTTAAAGTATGGAAGG
1 TTTTAGGGTTTGGATTTAAAGTATGGAAGG
* *
17512281 -TTTAGGGTTTTGATTTAAAGGTTTGG-A--
1 TTTTAGGGTTTGGATTTAAA-GTATGGAAGG
17512308 TTTTAGAGGTTTGGATTT
1 TTTTAG-GGTTTGGATTT
17512326 TAGAGATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
28 5 0.08
29 40 0.63
30 18 0.29
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (30 bp):
TTTTAGGGTTTGGATTTAAAGTATGGAAGG
Found at i:17512317 original size:15 final size:15
Alignment explanation
Indices: 17512281--17512461 Score: 93
Period size: 16 Copynumber: 11.7 Consensus size: 15
17512271 GTATGGAAGG
*
17512281 TTTAG-GGTTTTGA-
1 TTTAGAGGTTTGGAT
*
17512294 TTTAAAGGTTTGGAT
1 TTTAGAGGTTTGGAT
17512309 TTTAGAGGTTTGGAT
1 TTTAGAGGTTTGGAT
* * *
17512324 TTTAGAGATTAAGGGT
1 TTTAGAGGTT-TGGAT
** *
17512340 TTGGGA-TTTTGGAT
1 TTTAGAGGTTTGGAT
*
17512354 TTTAGGGGGTTTTGGAT
1 TTTA-GAGG-TTTGGAT
* *
17512371 TTTAGGGGTTTTCGAT
1 TTTAGAGG-TTTGGAT
17512387 TTTAG-GGATTTTGGAT
1 TTTAGAGG--TTTGGAT
*
17512403 TTTAGGGGTTTCGGAT
1 TTTAGAGGTTT-GGAT
* *
17512419 CTTAG-GATTTTGGAT
1 TTTAGAG-GTTTGGAT
*
17512434 TTTAGAGGGTTTTAGAT
1 TTTAGA-GG-TTTGGAT
*
17512451 TTTAGGGGTTT
1 TTTAGAGGTTT
17512462 TAGAAACCTA
Statistics
Matches: 132, Mismatches: 23, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.03
14 12 0.09
15 43 0.33
16 48 0.36
17 25 0.19
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.48
Consensus pattern (15 bp):
TTTAGAGGTTTGGAT
Done.