Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 186 of 214
Found at i:54658493 original size:41 final size:38
Alignment explanation
Indices: 54658429--54658568 Score: 113
Period size: 40 Copynumber: 3.6 Consensus size: 38
54658419 TGACTTTGAG
*
54658429 TCGATGAGACACTAGGTGTCAATTTATTACTTCGGATTAA
1 TCGATGAGACACTAGGTGCCAA-TTATTACTTCGGATT-A
* * *
54658469 TTCGATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTA
1 -TCGATGAGACACTAGGTGCCAATTATTACTTCGGATTA
* * * * *
54658506 GCCGATGAAACACTGGGTGTCAAATTATTACTTCGAATTA
1 -TCGATGAGACACTAGGTG-CCAATTATTACTTCGGATTA
* *
54658546 TCTGATGAGGCACTAGGTACCAA
1 TC-GATGAGACACTAGGTGCCAA
54658569 ACTAGTGTGT
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
37 16 0.21
38 14 0.18
39 6 0.08
40 23 0.29
41 19 0.24
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (38 bp):
TCGATGAGACACTAGGTGCCAATTATTACTTCGGATTA
Found at i:54658869 original size:9 final size:9
Alignment explanation
Indices: 54658855--54658885 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54658845 GTTAAACGAA
54658855 TCGAGTTAT
1 TCGAGTTAT
*
54658864 TCGAGTTAA
1 TCGAGTTAT
54658873 TCGAGTTAT
1 TCGAGTTAT
54658882 TCGA
1 TCGA
54658886 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:54658956 original size:9 final size:9
Alignment explanation
Indices: 54658939--54658975 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54658929 TGAGTTTTCG
54658939 AATTCGAAT
1 AATTCGAAT
*
54658948 AACTCGAAT
1 AATTCGAAT
54658957 AATTCGAAT
1 AATTCGAAT
54658966 AATTCGAAT
1 AATTCGAAT
54658975 A
1 A
54658976 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54659052 original size:21 final size:21
Alignment explanation
Indices: 54659011--54659053 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
54659001 ACCCCAAACT
* *
54659011 CTCAAACATTTTTACTTTTCC
1 CTCAAACACTTTTACTATTCC
54659032 CTCAAA-ACTTTTACTCATTCC
1 CTCAAACACTTTTACT-ATTCC
54659053 C
1 C
54659054 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAACACTTTTACTATTCC
Found at i:54661349 original size:25 final size:27
Alignment explanation
Indices: 54661320--54661373 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
54661310 TTTTTGAAAT
54661320 ATTAAATA-TTA-AATTTTAGTCACTC
1 ATTAAATATTTATAATTTTAGTCACTC
54661345 ATTAAATATTTTATAATTTTAGTCACTC
1 ATTAAATA-TTTATAATTTTAGTCACTC
54661373 A
1 A
54661374 ACTATCCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 8 0.31
27 3 0.12
28 15 0.58
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (27 bp):
ATTAAATATTTATAATTTTAGTCACTC
Found at i:54663349 original size:3 final size:3
Alignment explanation
Indices: 54663341--54663374 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
54663331 TACTAGAATA
*
54663341 TAT TAT TAT TAT TAT TCT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54663375 TTGCTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54668198 original size:15 final size:15
Alignment explanation
Indices: 54668178--54668207 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54668168 TTAGATGAGA
54668178 TTTTTCTTCTACTTC
1 TTTTTCTTCTACTTC
*
54668193 TTTTTCTTCTTCTTC
1 TTTTTCTTCTACTTC
54668208 AAATTCTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTCTTCTACTTC
Found at i:54679514 original size:126 final size:125
Alignment explanation
Indices: 54679289--54679633 Score: 469
Period size: 126 Copynumber: 2.8 Consensus size: 125
54679279 CGAGTTGATG
** * *
54679289 TTTCTGATAAAATAATATAAAATCGCTTCTAGCAGGATGATATTCGAGAAGAATTTGTGAAATCG
1 TTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
* * * *
54679354 TGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACA
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAA-AATTTTTTTAACA
* *
54679415 TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTG
1 TTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
* * * *
54679480 CGGCCTCGT-CAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAAAATTTTTTTAACG
66 CGGCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAAAATTTTTTTAACA
* * * * *
54679540 TTTTTGAGCAAATAATATAAAATCGTTTATACCAGGATGCTATCTGAGAAGAATTTGTGAAATCG
1 TTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
* *
54679605 C-GCCCCGTGGACGCGATTTTGCTACAGTA
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTA
54679634 ACATGTTTGG
Statistics
Matches: 193, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
124 23 0.12
125 71 0.37
126 99 0.51
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (125 bp):
TTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAAAATTTTTTTAACA
Found at i:54682867 original size:116 final size:116
Alignment explanation
Indices: 54682663--54682880 Score: 357
Period size: 116 Copynumber: 1.9 Consensus size: 116
54682653 TGATAAATTG
* * *
54682663 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATAGACAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAATAGAAAATTATTAATTGA
54682728 TAGTACCACTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCACTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
*
54682779 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAAT-GTAAAATTATTATTTG
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAATAG-AAAATTATTAATTG
* * *
54682843 ATAGTACCAGTCAAAATATTTTTCCAAATCTACCATTA
65 ATAGTACCACTCAAAACATTTTTCCAAATCTAACATTA
54682881 CGTTAAGGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
115 1 0.01
116 93 0.99
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAATAGAAAATTATTAATTGA
TAGTACCACTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:54683027 original size:45 final size:45
Alignment explanation
Indices: 54682962--54683132 Score: 220
Period size: 45 Copynumber: 3.7 Consensus size: 45
54682952 TTAAATTAGG
*
54682962 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGGGT
1 TTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGGGT
54683007 TTAGAGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAGGGT
1 TTAGAGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTTAAGGGT
* *
54683057 TTA-AGGCTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAAGGGT
1 TTAGA-GTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGGGT
* *
54683102 TTAGGGTTTTTAATTGAATTAGGTTAGGGTT
1 TTAGAGTTTTTAATTAAATTAGGTTAGGGTT
54683133 AGTGATACGA
Statistics
Matches: 110, Mismatches: 7, Indels: 18
0.81 0.05 0.13
Matches are distributed among these distances:
44 14 0.13
45 51 0.46
46 2 0.02
47 1 0.01
48 1 0.01
49 3 0.03
50 23 0.21
51 15 0.14
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (45 bp):
TTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGGGT
Found at i:54683032 original size:118 final size:117
Alignment explanation
Indices: 54682889--54683116 Score: 377
Period size: 118 Copynumber: 1.9 Consensus size: 117
54682879 TACGTTAAGG
* * *
54682889 TTAGGGTTTTTAATTGAATTGGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATT
1 TTAGAGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAAGGCTTTTAATT
*
54682954 AAATTAGGTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTTAAGGGT
66 AAATTAGGTTAGAGTTTTTAATTAAA--AGGTTTAGGGTTTTTAATTTAAGGGT
54683007 TTAGAGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAAGGCTTTTAATT
1 TTAGAGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAAGGCTTTTAATT
* *
54683072 AAATTAGGTTAGAGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT
66 AAATTAGGTTAGAGTTTTTAATTAAAAGGTTTAGGGTTTTTAATT
54683117 GAATTAGGTT
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
116 2 0.02
117 15 0.15
118 86 0.83
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.47
Consensus pattern (117 bp):
TTAGAGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAAGGCTTTTAATT
AAATTAGGTTAGAGTTTTTAATTAAAAGGTTTAGGGTTTTTAATTTAAGGGT
Found at i:54684203 original size:45 final size:45
Alignment explanation
Indices: 54684116--54684507 Score: 484
Period size: 45 Copynumber: 8.4 Consensus size: 45
54684106 CCCCGTATCA
* *
54684116 GTTAGGGTTTTTAA-TTAAGGGTTTAAGGCTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAG
*
54684160 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTGATTGAATTAGGTTAGG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT-AA--A--TTA-G
*
54684211 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTGATTGAATTAGGTTAGG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT-AA--A--TTA-G
* *
54684262 GTTAGGGCTTTTAA-TTAAGGGTTTAGGGCTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAG
*
54684306 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTGATTGAATTAGGTTAGG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT-AA--A--TTA-G
*
54684357 GTTAGGGTTTTTAATTTTAA-GGTTTAGGGCTTTTAATTAAATTAG
1 GTTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAATTAAATTAG
54684402 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAG
* * *
54684447 GTTAGAGTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAG
*
54684492 GCTAGGGTTTTTAATT
1 GTTAGGGTTTTTAATT
54684508 AAATTAGGCT
Statistics
Matches: 314, Mismatches: 18, Indels: 31
0.87 0.05 0.09
Matches are distributed among these distances:
44 33 0.11
45 138 0.44
46 7 0.02
47 1 0.00
48 3 0.01
49 2 0.01
50 29 0.09
51 96 0.31
52 5 0.02
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (45 bp):
GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAG
Found at i:54684217 original size:29 final size:30
Alignment explanation
Indices: 54684178--54684273 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 30
54684168 TTTTAATTTA
54684178 AGGGTTTAGGGTTTTTGATTGAATTAGGTT
1 AGGGTTTAGGGTTTTTGATTGAATTAGGTT
*
54684208 AGGG-TTAGGG--TTT--TT-AATT---TA
1 AGGGTTTAGGGTTTTTGATTGAATTAGGTT
54684229 AGGGTTTAGGGTTTTTGATTGAATTAGGTT
1 AGGGTTTAGGGTTTTTGATTGAATTAGGTT
*
54684259 AGGG-TTAGGGCTTTT
1 AGGGTTTAGGGTTTTT
54684274 AATTAAGGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
21 5 0.09
22 6 0.11
24 7 0.13
25 2 0.04
26 2 0.04
27 7 0.13
29 16 0.30
30 9 0.17
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (30 bp):
AGGGTTTAGGGTTTTTGATTGAATTAGGTT
Found at i:54684299 original size:96 final size:90
Alignment explanation
Indices: 54684116--54684507 Score: 484
Period size: 96 Copynumber: 4.2 Consensus size: 90
54684106 CCCCGTATCA
* *
54684116 GTTAGGGTTTTTAA-TTAAGGGTTTAAGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAG
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAG
* *
54684180 GGTTTAGGGTTTTTGATTGAATTAGGTTAGG
66 GGTTTAGGGCTTTTAATT-AA--A--TTA-G
* *
54684211 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTGATTGAATTAGGTTAGGGTTAGGGCTTTTAA
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAA
54684276 -TTAAGGGTTTAGGGCTTTTAATTAAATTAG
60 TTTAAGGGTTTAGGGCTTTTAATTAAATTAG
*
54684306 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTGATTGAATTAGGTTAGGGTTAGGGTTTTTAA
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAA
54684371 TTTTAA-GGTTTAGGGCTTTTAATTAAATTAG
60 -TTTAAGGGTTTAGGGCTTTTAATTAAATTAG
* * *
54684402 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAA
1 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAG
*
54684467 GGTTTAGGGTTTTTAATTAAATTAG
66 GGTTTAGGGCTTTTAATTAAATTAG
*
54684492 GCTAGGGTTTTTAATT
1 GTTAGGGTTTTTAATT
54684508 AAATTAGGCT
Statistics
Matches: 275, Mismatches: 12, Indels: 25
0.88 0.04 0.08
Matches are distributed among these distances:
89 4 0.01
90 53 0.19
91 3 0.01
93 1 0.00
95 81 0.29
96 85 0.31
97 6 0.02
98 1 0.00
99 1 0.00
100 2 0.01
101 24 0.09
102 14 0.05
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (90 bp):
GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAG
GGTTTAGGGCTTTTAATTAAATTAG
Found at i:54684299 original size:146 final size:140
Alignment explanation
Indices: 54684116--54684500 Score: 592
Period size: 146 Copynumber: 2.7 Consensus size: 140
54684106 CCCCGTATCA
*
54684116 GTTAGGGTTTTTAATTAAGGGTTTAAGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGG
1 GTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGG
*
54684181 GTTTAGGGTTTTTGATTGAATTAGGTTAGGGTTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTT
66 GTTTAGGGTTTTTGATTGAATTAGGTTAGGGTTAGGGTTTTTAATTTTAA-GGTTTAGGGCTTTT
*
54684245 GATTGAATTAGGTTAGG
130 AATT-AA--A--TTA-G
*
54684262 GTTAGGGCTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGG
1 GTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGG
54684327 GTTTAGGGTTTTTGATTGAATTAGGTTAGGGTTAGGGTTTTTAATTTTAAGGTTTAGGGCTTTTA
66 GTTTAGGGTTTTTGATTGAATTAGGTTAGGGTTAGGGTTTTTAATTTTAAGGTTTAGGGCTTTTA
54684392 ATTAAATTAG
131 ATTAAATTAG
* * * *
54684402 GTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAA
1 GTTAGGGTTTTTAA-TTAAGGGTTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAG
* * *
54684467 GGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTT
65 GGTTTAGGGTTTTTGATTGAATTAGGTTAGGGTT
54684501 TTTAATTAAA
Statistics
Matches: 225, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
140 14 0.06
141 80 0.36
143 1 0.00
145 2 0.01
146 123 0.55
147 5 0.02
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.46
Consensus pattern (140 bp):
GTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGG
GTTTAGGGTTTTTGATTGAATTAGGTTAGGGTTAGGGTTTTTAATTTTAAGGTTTAGGGCTTTTA
ATTAAATTAG
Found at i:54685060 original size:18 final size:18
Alignment explanation
Indices: 54685037--54685076 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
54685027 GACTCGAAAA
54685037 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGTT
54685055 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGTT
54685073 AGGA
1 AGGA
54685077 AACGCACCTG
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:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAGGGTT
Found at i:54685738 original size:7 final size:7
Alignment explanation
Indices: 54685728--54685752 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54685718 ATACATACAT
54685728 AATACTA
1 AATACTA
54685735 AATACTA
1 AATACTA
54685742 AATACTA
1 AATACTA
54685749 AATA
1 AATA
54685753 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:54686955 original size:40 final size:40
Alignment explanation
Indices: 54686911--54686998 Score: 158
Period size: 40 Copynumber: 2.2 Consensus size: 40
54686901 AAATTGAGAA
* *
54686911 GAAATTGAAATTAAATATGGATTTGAGAGAATTTTTGAAG
1 GAAATTGAAATTAAATATAGATTTGAGAGAATTTTGGAAG
54686951 GAAATTGAAATTAAATATAGATTTGAGAGAATTTTGGAAG
1 GAAATTGAAATTAAATATAGATTTGAGAGAATTTTGGAAG
54686991 GAAATTGA
1 GAAATTGA
54686999 GAGAATTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (40 bp):
GAAATTGAAATTAAATATAGATTTGAGAGAATTTTGGAAG
Found at i:54686998 original size:22 final size:22
Alignment explanation
Indices: 54686973--54687028 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
54686963 AAATATAGAT
54686973 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
54686995 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
54687017 TTGAGAGGAATT
1 TTGAGA-GAATT
54687029 GAGAGGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:54687045 original size:12 final size:11
Alignment explanation
Indices: 54686989--54687045 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
54686979 GAATTTTGGA
54686989 AGGAAATTGAG
1 AGGAAATTGAG
*
54687000 A-GAATTTTG-G
1 AGGAA-ATTGAG
54687010 AAGGAAATTGAG
1 -AGGAAATTGAG
54687022 AGG-AATTGAG
1 AGGAAATTGAG
54687032 AGGAAATATGAG
1 AGGAAAT-TGAG
54687044 AG
1 AG
54687046 AGGATTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:54687566 original size:8 final size:9
Alignment explanation
Indices: 54687452--54687798 Score: 65
Period size: 9 Copynumber: 37.3 Consensus size: 9
54687442 TTTTATAAAC
54687452 TATAATTTT
1 TATAATTTT
54687461 T-TATATTTAT
1 TATA-ATTT-T
*
54687471 TA-ATTTTT
1 TATAATTTT
54687479 TATGAATTTT
1 TAT-AATTTT
54687489 TATAAGTTTT
1 TATAA-TTTT
* *
54687499 TATAAAATAT
1 TAT-AATTTT
*
54687509 TA-AATGTTC
1 TATAAT-TTT
54687518 TA-AATTTTTT
1 TATAA--TTTT
*
54687528 TTTAATTTT
1 TATAATTTT
*
54687537 TATAATAATT
1 TATAAT-TTT
54687547 TATTATATTTT
1 TA-TA-ATTTT
54687558 TATAATTTT
1 TATAATTTT
**
54687567 TATAAGTTAA
1 TATAA-TTTT
54687577 TATCAATTTT
1 TAT-AATTTT
* *
54687587 AATACTTTT
1 TATAATTTT
54687596 TAGT-A-TTT
1 TA-TAATTTT
* *
54687604 AATAATCTT
1 TATAATTTT
*
54687613 TATGATTTT
1 TATAATTTT
* *
54687622 TACACGTTTT
1 TATA-ATTTT
*
54687632 TATATAATTT
1 TATA-ATTTT
*
54687642 TA-AATATT
1 TATAATTTT
*
54687650 TAAATATGTTT
1 TATA-AT-TTT
54687661 TATTAA-TTT
1 TA-TAATTTT
***
54687670 TATAA-AAA
1 TATAATTTT
*
54687678 TAGAATTTAT
1 TATAATTT-T
*
54687688 TAGAATTTAT
1 TATAATTT-T
*
54687698 TA-AAATTT
1 TATAATTTT
54687706 TA-AATGTTT
1 TATAAT-TTT
*
54687715 TA-AATATT
1 TATAATTTT
54687723 TATAAGTTTT
1 TATAA-TTTT
* *
54687733 TATTATTTG
1 TATAATTTT
*
54687742 TATAAGTTTA
1 TATAA-TTTT
54687752 TATCAATTTT
1 TAT-AATTTT
*
54687762 AAT-ATTTT
1 TATAATTTT
* * *
54687770 AAAAATATT
1 TATAATTTT
54687779 T-TAATTTT
1 TATAATTTT
* *
54687787 AATATTTTT
1 TATAATTTT
54687796 TAT
1 TAT
54687799 TTTTCTCTAA
Statistics
Matches: 244, Mismatches: 61, Indels: 66
0.66 0.16 0.18
Matches are distributed among these distances:
7 1 0.00
8 45 0.18
9 90 0.37
10 85 0.35
11 20 0.08
12 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (9 bp):
TATAATTTT
Found at i:54687885 original size:16 final size:17
Alignment explanation
Indices: 54687864--54687896 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54687854 TCAGAAATAA
54687864 ATAAAT-AAACAAAAAT
1 ATAAATAAAACAAAAAT
54687880 ATAAATGAAAACAAAAA
1 ATAAAT-AAAACAAAAA
54687897 ATTTTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
ATAAATAAAACAAAAAT
Found at i:54693152 original size:15 final size:15
Alignment explanation
Indices: 54693132--54693161 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54693122 TTTTTTTGGC
*
54693132 CGATTTGCTTTCTGT
1 CGATTTGCTCTCTGT
54693147 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
54693162 TTTACCCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (15 bp):
CGATTTGCTCTCTGT
Found at i:54694215 original size:19 final size:19
Alignment explanation
Indices: 54694191--54694227 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54694181 GCATGACCTC
54694191 TATATGCACCTGAACGATG
1 TATATGCACCTGAACGATG
*
54694210 TATATGTACCTGAACGAT
1 TATATGCACCTGAACGAT
54694228 AATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TATATGCACCTGAACGATG
Found at i:54696179 original size:26 final size:25
Alignment explanation
Indices: 54696150--54696199 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
54696140 ATATATTTTA
54696150 TTAAATTATATTTAATAATAATTATG
1 TTAAATTATATTTAATAAT-ATTATG
*
54696176 TTAAATTATATTTCATAATATTAT
1 TTAAATTATATTTAATAATATTAT
54696200 ATATTATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAAATTATATTTAATAATATTATG
Found at i:54696272 original size:18 final size:17
Alignment explanation
Indices: 54696246--54696280 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54696236 AATATTAAGA
*
54696246 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54696263 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54696281 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54696292 original size:120 final size:120
Alignment explanation
Indices: 54696139--54696422 Score: 437
Period size: 120 Copynumber: 2.4 Consensus size: 120
54696129 TAATTGAAAA
* * *
54696139 TATATATTTT-ATTAAATTATATTTAATAATAATTATGTTAAATTATATTTCATAATATTATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAATATCATATA
* *
54696203 TTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAAT
* * * *
54696258 TATATATTTTAATTAAAATATATTTAATAGTAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAATATCATATA
*
54696323 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
*
54696378 TATATATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAAT
1 TATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
54696423 ATGATTAAAT
Statistics
Matches: 149, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
119 14 0.09
120 130 0.87
121 5 0.03
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAATATCATATA
TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:54696394 original size:18 final size:17
Alignment explanation
Indices: 54696366--54696400 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54696356 ATTATTAAGA
*
54696366 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54696383 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54696401 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54696400 original size:16 final size:16
Alignment explanation
Indices: 54696366--54696420 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
54696356 ATTATTAAGA
54696366 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
54696383 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
54696399 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
54696413 ATGTTTAA
1 AT-TTTAA
54696421 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:54696657 original size:16 final size:16
Alignment explanation
Indices: 54696636--54696687 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
54696626 GATTTGCTAT
54696636 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
54696652 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
54696668 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54696684 TACA
1 TACA
54696688 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:54697054 original size:22 final size:22
Alignment explanation
Indices: 54697024--54697067 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54697014 ATACAATAAA
*
54697024 TAATAAATATATA-ATTTAAAAT
1 TAATAAATA-ATACATATAAAAT
*
54697046 TAATTAATAATACATATAAAAT
1 TAATAAATAATACATATAAAAT
54697068 ATATACATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATAAATAATACATATAAAAT
Found at i:54698424 original size:7 final size:7
Alignment explanation
Indices: 54698412--54698443 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
54698402 ATGCGGAATG
54698412 ATTTTAA
1 ATTTTAA
54698419 ATTTTAA
1 ATTTTAA
54698426 ATTTTAA
1 ATTTTAA
54698433 ATTTTAA
1 ATTTTAA
54698440 ATTT
1 ATTT
54698444 AATAAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTAA
Found at i:54702035 original size:43 final size:42
Alignment explanation
Indices: 54701935--54702071 Score: 134
Period size: 43 Copynumber: 3.2 Consensus size: 42
54701925 GCGTTTACAG
*
54701935 AAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
54701976 AAAAAATGACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTCA
1 AAAAAA--ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTT-A
** * * * * *
54702021 TCACAAACGTCGCTAAA-AGTAATATTCTTTAGCGGCACTTTTA
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGC-TTTA
*
54702064 TAAAAAAC
1 AAAAAAAC
54702072 ACCACTAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
41 6 0.08
42 1 0.01
43 64 0.80
44 5 0.06
45 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
Found at i:54702742 original size:9 final size:9
Alignment explanation
Indices: 54702713--54702757 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
54702703 AAGTTATATA
*
54702713 TATAAATAT
1 TATAATTAT
54702722 TAT-ATGTA-
1 TATAAT-TAT
54702730 TATAATTAT
1 TATAATTAT
54702739 TATAATTAT
1 TATAATTAT
54702748 TATAATTAT
1 TATAATTAT
54702757 T
1 T
54702758 TATTTAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (9 bp):
TATAATTAT
Found at i:54703120 original size:15 final size:17
Alignment explanation
Indices: 54703102--54703133 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54703092 CAAAATAGAA
54703102 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
54703117 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
54703134 GGGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:54704205 original size:39 final size:39
Alignment explanation
Indices: 54704125--54704297 Score: 125
Period size: 45 Copynumber: 4.2 Consensus size: 39
54704115 ATTTTCCGGC
* * *
54704125 TTACTGA-TCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGACTC-GGCACTTTGTGTGTCGAATACTGTTACTG
* *
54704163 TTACTGATTCGGCACTTTGTGTGTCTAATACTGTTACTG
1 TTACTGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
54704202 TTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACCG
1 TTAC---T---GACTCGGCACTTTGTGTGTCGAATACTGTTACTG
* * * *
54704247 TTACTGTTACAGGTTCAGCACTTTGTGCGTTGAATACTGTTCCTG
1 TTACTG--AC----TCGGCACTTTGTGTGTCGAATACTGTTACTG
54704292 TTACTG
1 TTACTG
54704298 CTACTGTTAT
Statistics
Matches: 109, Mismatches: 12, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
38 12 0.11
39 26 0.24
41 2 0.02
42 2 0.02
45 67 0.61
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (39 bp):
TTACTGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:54704220 original size:45 final size:45
Alignment explanation
Indices: 54704152--54704297 Score: 195
Period size: 45 Copynumber: 3.2 Consensus size: 45
54704142 ATGTGCCGAC
*
54704152 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCTAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCTAATACTGT
* * *
54704197 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCTAATACTGT
* * * *
54704242 TACCGTTACTGTTACAGGTTCAGCACTTTGTGCGT-TGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCT-AATACTGT
*
54704287 TCCTGTTACTG
1 TACTGTTACTG
54704298 CTACTGTTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCTAATACTGT
Found at i:54705612 original size:10 final size:10
Alignment explanation
Indices: 54705583--54705614 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
54705573 ATATTATTCA
*
54705583 TATAAAAAGC
1 TATAAAAAGT
54705593 TATAAAAAGT
1 TATAAAAAGT
54705603 TATAAAAAGT
1 TATAAAAAGT
54705613 TA
1 TA
54705615 AGTGGATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.28
Consensus pattern (10 bp):
TATAAAAAGT
Found at i:54707013 original size:30 final size:30
Alignment explanation
Indices: 54706979--54707039 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
54706969 CTAACTTTTT
54706979 TTGAAATTATATTTCAACCGCTAAAATTTC
1 TTGAAATTATATTTCAACCGCTAAAATTTC
* * *
54707009 TTGAAATTATATTTTAACCTCTAAACTTTC
1 TTGAAATTATATTTCAACCGCTAAAATTTC
54707039 T
1 T
54707040 CAAAATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.44
Consensus pattern (30 bp):
TTGAAATTATATTTCAACCGCTAAAATTTC
Found at i:54707046 original size:30 final size:30
Alignment explanation
Indices: 54706982--54707047 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
54706972 ACTTTTTTTG
**
54706982 AAATTATATTTCAACCGCTAAAATTTCTTG
1 AAATTATATTTCAACCGCTAAAATTTCTCA
* * *
54707012 AAATTATATTTTAACCTCTAAACTTTCTCA
1 AAATTATATTTCAACCGCTAAAATTTCTCA
54707042 AAATTA
1 AAATTA
54707048 AGTTTTGGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (30 bp):
AAATTATATTTCAACCGCTAAAATTTCTCA
Found at i:54707558 original size:19 final size:19
Alignment explanation
Indices: 54707529--54707608 Score: 74
Period size: 19 Copynumber: 4.1 Consensus size: 19
54707519 GGCTATTGCC
54707529 GAAGG-AGAAGAAAAAAAA
1 GAAGGAAGAAGAAAAAAAA
54707547 GAAGGAAGAAGAAAGAAAAA
1 GAAGGAAGAAGAAA-AAAAA
* **
54707567 AAAGGGGGAAAGAAAAAAAA
1 GAAGGAAG-AAGAAAAAAAA
*
54707587 -AAGAGAAAAAGAAAAAGAAA
1 GAAG-GAAGAAGAAAAA-AAA
54707607 GA
1 GA
54707609 TTTTTTTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.10
19 19 0.38
20 19 0.38
21 7 0.14
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (19 bp):
GAAGGAAGAAGAAAAAAAA
Found at i:54707559 original size:22 final size:22
Alignment explanation
Indices: 54707529--54707590 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
54707519 GGCTATTGCC
*
54707529 GAAGGAGAAGAAAAAAAAGAAG
1 GAAGAAGAAGAAAAAAAAGAAG
*
54707551 GAAGAAGAAAGAAAAAAAAG-GG
1 GAAGAAG-AAGAAAAAAAAGAAG
*
54707573 GGA-AAGAA-AAAAAAAAGA
1 GAAGAAGAAGAAAAAAAAGA
54707591 GAAAAAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 3 0.09
22 9 0.26
23 12 0.34
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
GAAGAAGAAGAAAAAAAAGAAG
Found at i:54707566 original size:23 final size:23
Alignment explanation
Indices: 54707536--54707606 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 23
54707526 GCCGAAGGAG
54707536 AAGAAAAAAAAGAAGGAAGAAGA
1 AAGAAAAAAAAGAAGGAAGAAGA
* *
54707559 AAGAAAAAAAAG-GGGGA-AAGA
1 AAGAAAAAAAAGAAGGAAGAAGA
*
54707580 AA-AAAAAAAGAGAA-AAAGAA-A
1 AAGAAAAAAA-AGAAGGAAGAAGA
54707601 AAGAAA
1 AAGAAA
54707607 GATTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 7 0.18
21 12 0.31
22 8 0.21
23 12 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (23 bp):
AAGAAAAAAAAGAAGGAAGAAGA
Found at i:54707594 original size:17 final size:17
Alignment explanation
Indices: 54707556--54707608 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
54707546 AGAAGGAAGA
**
54707556 AGAAAGAAAAAAAAGGG
1 AGAAAGAAAAAAAAAAG
*
54707573 GGAAAGAAAAAAAAAAG
1 AGAAAGAAAAAAAAAAG
54707590 AGAAA-AAGAAAAAGAAAG
1 AGAAAGAA-AAAAA-AAAG
54707608 A
1 A
54707609 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 2 0.07
17 23 0.77
18 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAAAAAAG
Found at i:54707812 original size:12 final size:11
Alignment explanation
Indices: 54707765--54707814 Score: 75
Period size: 12 Copynumber: 4.5 Consensus size: 11
54707755 CCCAGCAGAG
54707765 AAGAA-AAAAA
1 AAGAAGAAAAA
54707775 AAGAAGAAAAAA
1 AAGAAG-AAAAA
54707787 AAGAAGAAAAA
1 AAGAAGAAAAA
54707798 AAGAACGAAAAA
1 AAGAA-GAAAAA
54707810 AAGAA
1 AAGAA
54707815 AAGGGTTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.14
11 10 0.27
12 22 0.59
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:54707812 original size:23 final size:22
Alignment explanation
Indices: 54707765--54707816 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
54707755 CCCAGCAGAG
54707765 AAGAAAAAAAAAGAAGAAAAAA
1 AAGAAAAAAAAAGAAGAAAAAA
54707787 AAGAAGAAAAAAAGAACG-AAAAA
1 AAGAA-AAAAAAAGAA-GAAAAAA
54707810 AAGAAAA
1 AAGAAAA
54707817 GGGTTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.25
23 20 0.71
24 1 0.04
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAAAGAAGAAAAAA
Found at i:54708163 original size:19 final size:18
Alignment explanation
Indices: 54708140--54708214 Score: 71
Period size: 19 Copynumber: 4.0 Consensus size: 18
54708130 TAAAAGTTTT
54708140 CGTGTTTCAAAAAAATTC
1 CGTGTTTCAAAAAAATTC
*
54708158 CAGTGTTTC-AAAAATTTC
1 C-GTGTTTCAAAAAAATTC
***
54708176 CGTGTCTTCAAAATTTTTC
1 CGTGT-TTCAAAAAAATTC
54708195 TCGTGTTTCAAAAAATATTC
1 -CGTGTTTCAAAAAA-ATTC
54708215 TTGTTTTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.09
18 13 0.28
19 21 0.46
20 8 0.17
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (18 bp):
CGTGTTTCAAAAAAATTC
Found at i:54708170 original size:18 final size:17
Alignment explanation
Indices: 54708140--54708210 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
54708130 TAAAAGTTTT
54708140 CGTGTTTCAAAAAAATTC
1 CGTGTTTC-AAAAAATTC
*
54708158 CAGTGTTTCAAAAATTTC
1 C-GTGTTTCAAAAAATTC
**
54708176 CGTGTCTTCAAAATTTTTC
1 CGTGT-TTCAAAA-AATTC
54708195 TCGTGTTTCAAAAAAT
1 -CGTGTTTCAAAAAAT
54708211 ATTCTTGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.09
18 18 0.40
19 18 0.40
20 5 0.11
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (17 bp):
CGTGTTTCAAAAAATTC
Found at i:54708433 original size:18 final size:18
Alignment explanation
Indices: 54708412--54708650 Score: 58
Period size: 18 Copynumber: 13.3 Consensus size: 18
54708402 AAAAGAATCC
54708412 GTTTTTCAAAATTCTCGT
1 GTTTTTCAAAATTCTCGT
* *
54708430 GTTTTTAAAAAAACTCCATTCCGT
1 GTTTTT--CAAAA-TTC--T-CGT
*
54708454 G-TTTTCAAAAATT-T-TT
1 GTTTTTC-AAAATTCTCGT
*
54708470 GTATTTTCAAAAATTTTCGT
1 GT-TTTTC-AAAATTCTCGT
* * *
54708490 G-TTTTAAAAATTTTTGT
1 GTTTTTCAAAATTCTCGT
* ** *
54708507 ATTTTAAAAAATTCTTGT
1 GTTTTTCAAAATTCTCGT
***
54708525 GTTTCAAAAAATT-TCGT
1 GTTTTTCAAAATTCTCGT
*
54708542 -ATT-TCAAAAATTC-CGT
1 GTTTTTCAA-AATTCTCGT
*
54708558 G-TTTTCAAAAATCTTCGT
1 GTTTTTCAAAATTC-TCGT
54708576 G-TTTTCAAGAATTCTCGT
1 GTTTTTCAA-AATTCTCGT
54708594 G--TTTCAAAAACTT-TCGT
1 GTTTTTC-AAAA-TTCTCGT
* ***
54708611 GTTTTTAAAAAAAAT--T
1 GTTTTTCAAAATTCTCGT
*
54708627 GTGTTTCAAAATTCTCGT
1 GTTTTTCAAAATTCTCGT
54708645 GTTTTT
1 GTTTTT
54708651 TTTTAAATTC
Statistics
Matches: 167, Mismatches: 28, Indels: 52
0.68 0.11 0.21
Matches are distributed among these distances:
15 2 0.01
16 28 0.17
17 28 0.17
18 79 0.47
19 8 0.05
20 6 0.04
21 3 0.02
22 4 0.02
23 5 0.03
24 4 0.02
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (18 bp):
GTTTTTCAAAATTCTCGT
Found at i:54708502 original size:35 final size:35
Alignment explanation
Indices: 54708451--54708621 Score: 168
Period size: 35 Copynumber: 4.9 Consensus size: 35
54708441 AACTCCATTC
*
54708451 CGTGTTTTCAAAAATTTTTGTATTTTCAAAAATTTT
1 CGTGTTTT-AAAAATTTTCGTATTTTCAAAAATTTT
* *
54708487 CGTGTTTTAAAAATTTTTGTATTTTAAAAAATTCTT
1 CGTGTTTTAAAAATTTTCGTATTTTCAAAAATT-TT
* * *
54708523 -GTGTTTCAAAAAATTTCGTA-TTTCAAAAA-TTC
1 CGTGTTTTAAAAATTTTCGTATTTTCAAAAATTTT
* * * *
54708555 CGTGTTTTCAAAAATCTTCGTGTTTTCAAGAATTCT
1 CGTGTTTT-AAAAATTTTCGTATTTTCAAAAATTTT
* * * *
54708591 CGTGTTTCAAAAACTTTCGTGTTTTTAAAAA
1 CGTGTTTTAAAAATTTTCGTATTTTCAAAAA
54708622 AAATTGTGTT
Statistics
Matches: 112, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
32 1 0.01
33 7 0.06
34 18 0.16
35 68 0.61
36 18 0.16
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (35 bp):
CGTGTTTTAAAAATTTTCGTATTTTCAAAAATTTT
Found at i:54708600 original size:17 final size:17
Alignment explanation
Indices: 54708447--54708648 Score: 128
Period size: 18 Copynumber: 11.7 Consensus size: 17
54708437 AAAAAACTCC
54708447 ATTC-CGTGTTTTCAAAA
1 ATTCTCGTG-TTTCAAAA
* * *
54708464 ATTTTTGTATTTTCAAAA
1 ATTCTCGT-GTTTCAAAA
* *
54708482 ATTTTCGTGTTTTAAAA
1 ATTCTCGTGTTTCAAAA
* * * *
54708499 ATTTTTGTATTTTAAAAA
1 ATTCTCGT-GTTTCAAAA
*
54708517 ATTCTTGTGTTTCAAAAA
1 ATTCTCGTGTTTC-AAAA
*
54708535 ATT-TCGTATTTCAAAA
1 ATTCTCGTGTTTCAAAA
54708551 ATTC-CGTGTTTTCAAAA
1 ATTCTCGTG-TTTCAAAA
*
54708568 A-TCTTCGTGTTTTCAAGA
1 ATTC-TCGTG-TTTCAAAA
54708586 ATTCTCGTGTTTCAAAA
1 ATTCTCGTGTTTCAAAA
*
54708603 ACTT-TCGTGTTTTTAAAA
1 A-TTCTCGTG-TTTCAAAA
*** *
54708621 AAAATTGTGTTTC-AAA
1 ATTCTCGTGTTTCAAAA
54708637 ATTCTCGTGTTT
1 ATTCTCGTGTTT
54708649 TTTTTTAAAT
Statistics
Matches: 147, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
16 23 0.16
17 52 0.35
18 70 0.48
19 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (17 bp):
ATTCTCGTGTTTCAAAA
Found at i:54708773 original size:27 final size:27
Alignment explanation
Indices: 54708735--54708788 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
54708725 AACATGCGTT
*
54708735 TAACGAGATACCAATTTTGGTCGTCGC
1 TAACGAGATACCAATTTTGGTCATCGC
54708762 TAACGAGATACCAATTTTGGTCATCGC
1 TAACGAGATACCAATTTTGGTCATCGC
54708789 AAGGGTGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (27 bp):
TAACGAGATACCAATTTTGGTCATCGC
Found at i:54710589 original size:38 final size:37
Alignment explanation
Indices: 54710392--54710803 Score: 195
Period size: 38 Copynumber: 11.2 Consensus size: 37
54710382 GAAAACACGG
* *
54710392 TTTTTTT-AAAATACGAGAATTT-TAGAAACACG-AAT
1 TTTTTTTGAAAACACGAAAATTTAT-GAAACACGAAAT
** **
54710427 TGTTTTTAAAAAAACACGAAAATTT-TGAAACACGGGAT
1 T-TTTTT-TGAAAACACGAAAATTTATGAAACACGAAAT
*
54710465 TTTTTTTG-AAACACGAAACTTTATGAAACACGATCAA-
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGA--AAT
* * *
54710502 -TTTTTT-AAAACACGAAAAATTTTTGAAAAACAAGAATT
1 TTTTTTTGAAAACACG-AAAATTTATG--AAACACGAAAT
* *
54710540 TTTTTTTGAAAACACGGAAATTTATGAAACATGAAATT
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGAAA-T
* * * *
54710578 TTTTTTTGAAAACAAGAAAATTT-TCGATATACGGGAA-
1 TTTTTTTGAAAACACGAAAATTTAT-GAAACAC-GAAAT
* * *
54710615 --TTTTTAAAAACACGGGAAATTTTTTTGAAAACAC-AAA-
1 TTTTTTTGAAAACAC--GAAA-ATTTATG-AAACACGAAAT
** * * *
54710652 AATTTTTG-AAACACTG-GAATTTTTAAAACACGAAGA-
1 TTTTTTTGAAAACAC-GAAAATTTATGAAACACGAA-AT
* * *
54710688 --GTTTTG-AAACAAGAAAATTTTTGAAAACACGAAAAT
1 TTTTTTTGAAAACACGAAAATTTATG-AAACACG-AAAT
*
54710724 TTTTTTT-AAAACACGAAAATTTTTGAAACACGAGAAAT
1 TTTTTTTGAAAACACGAAAATTTATGAAACAC--GAAAT
* * *
54710762 TTTTTTTGAAAACATGAAAATTTTTGAAACCCG--AT
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGAAAT
54710797 TTTTTTT
1 TTTTTTT
54710804 AAGAAGTACC
Statistics
Matches: 299, Mismatches: 42, Indels: 72
0.72 0.10 0.17
Matches are distributed among these distances:
33 1 0.00
34 23 0.08
35 49 0.16
36 31 0.10
37 45 0.15
38 85 0.28
39 57 0.19
40 8 0.03
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (37 bp):
TTTTTTTGAAAACACGAAAATTTATGAAACACGAAAT
Found at i:54710591 original size:21 final size:21
Alignment explanation
Indices: 54710521--54710601 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
54710511 ACACGAAAAA
54710521 TTTTTGAAAAACAAG-AATTTT
1 TTTTTG-AAAACAAGAAATTTT
*
54710542 TTTTTGAAAACACGGAAA----
1 TTTTTGAAAACA-AGAAATTTT
* *
54710560 TTTATG-AAACATGAAATTTT
1 TTTTTGAAAACAAGAAATTTT
*
54710580 TTTTTGAAAACAAGAAAATTT
1 TTTTTGAAAACAAGAAATTTT
54710601 T
1 T
54710602 CGATATACGG
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
16 4 0.09
17 5 0.11
18 5 0.11
20 11 0.23
21 20 0.43
22 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (21 bp):
TTTTTGAAAACAAGAAATTTT
Found at i:54710654 original size:56 final size:55
Alignment explanation
Indices: 54710578--54710683 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 55
54710568 ACATGAAATT
* *
54710578 TTTTTTTGAAAACAAGAAAATTTTCGATATACGGGAATTTTTAAAAACACGGGAAA
1 TTTTTTTGAAAACAAGAAAATTTTCGAAACACGGGAATTTTT-AAAACACGGGAAA
* *
54710634 TTTTTTTGAAAACACA-AAAATTTTTGAAACACTGGAATTTTTAAAACACG
1 TTTTTTTGAAAACA-AGAAAATTTTCGAAACACGGGAATTTTTAAAACACG
54710684 AAGAGTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
55 8 0.18
56 36 0.80
57 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (55 bp):
TTTTTTTGAAAACAAGAAAATTTTCGAAACACGGGAATTTTTAAAACACGGGAAA
Found at i:54710787 original size:18 final size:18
Alignment explanation
Indices: 54710437--54710790 Score: 190
Period size: 17 Copynumber: 19.2 Consensus size: 18
54710427 TGTTTTTAAA
54710437 AAAACACGAAAA-TTTTG
1 AAAACACGAAAATTTTTG
***
54710454 -AAACACGGGATTTTTTTTG
1 AAAACAC--GAAAATTTTTG
* *
54710473 -AAACACGAAACTTTATG
1 AAAACACGAAAATTTTTG
* *
54710490 -AAACACGATCAATTTTTT
1 AAAACACGA-AAATTTTTG
54710508 AAAACACGAAAAATTTTTG
1 AAAACACG-AAAATTTTTG
* **
54710527 AAAAACAAGAATTTTTTTTTG
1 -AAAACACGAA--AATTTTTG
* *
54710548 AAAACACGGAAATTTATG
1 AAAACACGAAAATTTTTG
* *
54710566 -AAACATGAAATTTTTTTTTG
1 AAAACACGAAA---ATTTTTG
* *
54710586 AAAACAAGAAAATTTTCG
1 AAAACACGAAAATTTTTG
* * ** *
54710604 -ATATACGGGAATTTTTA
1 AAAACACGAAAATTTTTG
*
54710621 AAAACACGGGAAATTTTTTTG
1 AAAACAC--GAAA-ATTTTTG
*
54710642 AAAACACAAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
54710660 -AAACACTG-GAATTTTT-
1 AAAACAC-GAAAATTTTTG
* *
54710676 AAAACACGAAGAGTTTTG
1 AAAACACGAAAATTTTTG
*
54710694 -AAACAAGAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
54710711 AAAACACGAAAATTTTTTTT
1 AAAACACGAAAA--TTTTTG
54710731 AAAACACGAAAATTTTTG
1 AAAACACGAAAATTTTTG
54710749 -AAACACGAGAAATTTTTTTTG
1 AAAACACGA-AAA---TTTTTG
*
54710770 AAAACATGAAAATTTTTG
1 AAAACACGAAAATTTTTG
54710788 AAA
1 AAA
54710791 CCCGATTTTT
Statistics
Matches: 253, Mismatches: 55, Indels: 57
0.69 0.15 0.16
Matches are distributed among these distances:
16 7 0.03
17 79 0.31
18 54 0.21
19 30 0.12
20 40 0.16
21 36 0.14
22 7 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
AAAACACGAAAATTTTTG
Found at i:54711285 original size:9 final size:9
Alignment explanation
Indices: 54711267--54711317 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
54711257 AATTAAACCA
*
54711267 TTTTTCCTT
1 TTTTTTCTT
54711276 TTTTTTC--
1 TTTTTTCTT
54711283 TTTTTTCTT
1 TTTTTTCTT
54711292 TTTTTTCTT
1 TTTTTTCTT
54711301 TTTTTCTCTT
1 TTTTT-TCTT
54711311 CTTTTTT
1 -TTTTTT
54711318 TTTGGCCTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 7 0.19
9 20 0.54
10 5 0.14
11 5 0.14
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:54711303 original size:26 final size:25
Alignment explanation
Indices: 54711267--54711320 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
54711257 AATTAAACCA
* *
54711267 TTTTTCCTTTTTTTTCTTTTTTCTTT
1 TTTTTCCTTTTTTCTCTTCTTT-TTT
*
54711293 TTTTTCTTTTTTTCTCTTCTTTTTT
1 TTTTTCCTTTTTTCTCTTCTTTTTT
54711318 TTT
1 TTT
54711321 GGCCTGCTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTTCCTTTTTTCTCTTCTTTTTT
Found at i:54711305 original size:17 final size:17
Alignment explanation
Indices: 54711267--54711320 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
54711257 AATTAAACCA
*
54711267 TTTTTCCTTTTTTTTC-
1 TTTTTTCTTTTTTTTCT
54711283 TTTTTTCTTTTTTTTCT
1 TTTTTTCTTTTTTTTCT
54711300 TTTTTTCTCTTCTTTTT-T
1 TTTTTTCT-TT-TTTTTCT
54711318 TTT
1 TTT
54711321 GGCCTGCTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 15 0.44
17 8 0.24
18 6 0.18
19 5 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTCT
Found at i:54711318 original size:16 final size:16
Alignment explanation
Indices: 54711278--54711320 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
54711268 TTTTCCTTTT
* *
54711278 TTTTCTTTTTTCTTTTT
1 TTTT-TTTTTTCTCTTC
54711295 TTTCTTTTTTTCTCTTC
1 TTT-TTTTTTTCTCTTC
54711312 TTTTTTTTT
1 TTTTTTTTT
54711321 GGCCTGCTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 16 0.70
18 1 0.04
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTCTCTTC
Found at i:54711588 original size:13 final size:13
Alignment explanation
Indices: 54711566--54711600 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
54711556 AAAATATTTT
*
54711566 TTCTTTTTCTTCC
1 TTCTTCTTCTTCC
54711579 TTCTTCTTCTTCC
1 TTCTTCTTCTTCC
54711592 TTCCTTCTT
1 TT-CTTCTT
54711601 TCTCTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTCTTCTTCC
Found at i:54711630 original size:19 final size:18
Alignment explanation
Indices: 54711566--54711633 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
54711556 AAAATATTTT
* *
54711566 TTCTTTTTCTTCCTTCTTC
1 TTCTTCTTCTTCTTTC-TC
54711585 TTCTTCCTTCCTTCTTTCTC
1 TTCTT-CTT-CTTCTTTCTC
* *
54711605 TTTTTCTTCTTTTTTCTC
1 TTCTTCTTCTTCTTTCTC
54711623 ATTCTTCTTCT
1 -TTCTTCTTCT
54711634 CCGTTCGGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 9 0.22
19 17 0.41
20 8 0.20
21 7 0.17
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCTTCTTCTTCTTTCTC
Found at i:54712169 original size:30 final size:30
Alignment explanation
Indices: 54712128--54712252 Score: 144
Period size: 30 Copynumber: 4.2 Consensus size: 30
54712118 GGCTGAAACA
* * *
54712128 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTCGAAAAAATTTAGGGGTCAAAATG
*
54712158 TAATTTCGAGAAAATTTAGGGGTCAAAATG
1 TAATTTCGAAAAAATTTAGGGGTCAAAATG
* * * *
54712188 TAGTTTC-AAAAAGTTTAGGGGTAAAAATA
1 TAATTTCGAAAAAATTTAGGGGTCAAAATG
* *
54712217 TAGTTTTGAAAAAATTTAGGGGTCAAAATG
1 TAATTTCGAAAAAATTTAGGGGTCAAAATG
*
54712247 CAATTT
1 TAATTT
54712253 TTTTTAAAAC
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 24 0.30
30 57 0.70
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (30 bp):
TAATTTCGAAAAAATTTAGGGGTCAAAATG
Found at i:54712683 original size:76 final size:75
Alignment explanation
Indices: 54712431--54713358 Score: 1187
Period size: 76 Copynumber: 11.8 Consensus size: 75
54712421 GTGTGGCCCA
* * *
54712431 AGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTTGAAAAA-CAGAAATTGAAAAATACCTC
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAGCAGAAATTTAAAAATACCTC
54712494 AGCGTGACCCG
65 AGCGTGACCCG
* * *
54712505 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAACAGAAATTTTAAAAAAAT
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTTG-AAAAAGCAGAAA-TTT--AAAAAT
54712570 ACCTCAGCGTGACCCG
60 ACCTCAGCGTGACCCG
54712586 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAGAAAGCAGAAATTTAAAAATACCTC
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAA-AAAGCAGAAATTTAAAAATACCTC
54712651 AGCGTGACCCG
65 AGCGTGACCCG
* *
54712662 AGGCTCAACTCACCTCAGTATTATGAGTTGATTTTTTTGAAAAAACAGAAATTAGATTAGAAAAA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTTGAAAAAGCAGAAA-T---TT--AAAAA
*
54712727 TACCTCAGCATGACCCG
59 TACCTCAGCGTGACCCG
*
54712744 AGGCTCAACTAACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAATTTAAAAAGTACCT
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAGCAGAAATTTAAAAA-TACCT
54712809 CAGCGTGACCCG
64 CAGCGTGACCCG
54712821 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAATGCAGAAATTTGAAAAAATACC
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA-GCAGAAATTT--AAAAATACC
54712886 TCAGCGTGACCCGAGGGACCCG
63 TCAGCGT---------GACCCG
** * *
54712908 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAATAGAAATTAAAAAAATACCTT
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAGCAGAAATT-TAAAAATACCTC
54712973 AGCGTGACCCG
65 AGCGTGACCCG
* **** *
54712984 AGGCTCAACTCACCTCTGTATTATGAGTTTATTTGAAAAAAAAAGACATAAA-TTAAAAATACCT
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTT-TTTGAAAAAG-CAGAAATTTAAAAATACCT
*
54713048 CAGCGTGACCTG
64 CAGCGTGACCCG
*
54713060 AGGCTCAACTCACCTCTGTATTATGAGTTGACTTTTTGAAAAAAAGCAGAAATTTTAAAAAATAC
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG--AAAAAGCAGAAA-TTT-AAAAATAC
54713125 CTCAGCGTGACCCG
62 CTCAGCGTGACCCG
*
54713139 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAATTAAAAAAAATACC
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAGCAGAAATT--TAAAAATACC
54713204 TCAGCGTGACCCG
63 TCAGCGTGACCCG
*
54713217 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATTAAAAAAAA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAGCAGAAA-T---TT---AAAAA
54713282 TACCTCAGCGTGACCCG
59 TACCTCAGCGTGACCCG
* *
54713299 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAATTTTAAAAATA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAGCAGAAATTTAAAAATA
54713359 TTTCTTGAAA
Statistics
Matches: 767, Mismatches: 41, Indels: 91
0.85 0.05 0.10
Matches are distributed among these distances:
74 31 0.04
75 7 0.01
76 173 0.23
77 103 0.13
78 106 0.14
79 81 0.11
80 14 0.02
81 49 0.06
82 132 0.17
85 15 0.02
86 7 0.01
87 49 0.06
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAGCAGAAATTTAAAAATACCTCA
GCGTGACCCG
Found at i:54713283 original size:239 final size:231
Alignment explanation
Indices: 54712431--54713356 Score: 1305
Period size: 239 Copynumber: 3.9 Consensus size: 231
54712421 GTGTGGCCCA
* * *
54712431 AGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTTG-AAAAACAGAAATT-GAAAAATACCT
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAAAATACCT
* *
54712493 CAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAACAGAAA
65 CAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTTGAAAAAAACAGAAA
54712558 TTTTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTT
128 -TTT-AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTT
*
54712623 GAAGAAAGCAGAAA-TTT-AAAAATACCTCAGCGTGACCCG
191 GAAAAAAGCAGAAATTTTAAAAAATACCTCAGCGTGACCCG
*
54712662 AGGCTCAACTCACCTCAGTATTATGAGTTGATTTTTTTGAAAAAACAGAAATTAGATTAGAAAAA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTTGAAAAAACAGAAATT--A--A-AAAAA
* * *
54712727 TACCTCAGCATGACCCGAGGCTCAACTAACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAG
60 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAG
*
54712792 AAATTTAAAAAGTACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
125 AAATTTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
* *
54712857 TGAAAAATGCAGAAATTTGAAAAAATACCTCAGCGTGACCCGAGGGACCCG
190 TGAAAAAAGCAGAAATTTTAAAAAATACCTCAGCGT---------GACCCG
* *
54712908 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAATAGAAATTAAAAAAATACCTT
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAAAATACCTC
* **** *
54712973 AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTTATTTGAAAAAAAAAGACATAAA-T
66 AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-ACAGAAATT
* *
54713037 T-AAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTGTATTATGAGTTGACTTTTTGAAA
130 TAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AA
54713101 AAAAGCAGAAATTTTAAAAAATACCTCAGCGTGACCCG
194 AAAAGCAGAAATTTTAAAAAATACCTCAGCGTGACCCG
54713139 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAATTAAAAAAAATACC
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-CAGAAATT-AAAAAAATACC
54713204 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAACAGAAAT
64 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAA-
54713268 TAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT
128 T---TT--AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT
54713333 TTTGAAAAAA-CAG-AATTTTAAAAA
188 TTTGAAAAAAGCAGAAATTTTAAAAA
54713357 TATTTCTTGA
Statistics
Matches: 623, Mismatches: 40, Indels: 59
0.86 0.06 0.08
Matches are distributed among these distances:
230 12 0.02
231 72 0.12
232 18 0.03
233 69 0.11
235 71 0.11
236 18 0.03
237 38 0.06
238 18 0.03
239 152 0.24
240 92 0.15
241 6 0.01
243 1 0.00
245 20 0.03
246 36 0.06
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (231 bp):
AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAAAATACCTC
AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAATTT
AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAA
AAGCAGAAATTTTAAAAAATACCTCAGCGTGACCCG
Found at i:54713386 original size:30 final size:29
Alignment explanation
Indices: 54713329--54713386 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
54713319 TTATGAGTTG
* *
54713329 ATTTTTTGAAAAAACAGAATTTTAAAAAT
1 ATTTCTTGAAAAAACAGAATTTCAAAAAT
**
54713358 ATTTCTTGAAAGAAACAGGGTTTCAAAAA
1 ATTTCTTGAAA-AAACAGAATTTCAAAAA
54713387 CATCTAGTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (29 bp):
ATTTCTTGAAAAAACAGAATTTCAAAAAT
Found at i:54714217 original size:1 final size:1
Alignment explanation
Indices: 54714211--54714330 Score: 51
Period size: 1 Copynumber: 120.0 Consensus size: 1
54714201 TTCATCTTGA
* * * * * * * * * * *
54714211 TTTTTTTTCTTTTTTTTTATTTTTTGTTTTGTCTGTTTTTTCTGTTTTTTTCTTTTTGTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * *
54714276 TTTTGTCTGTTTTTTTCTGTTTTTTCTTTTCTTTTTCTATTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54714331 AAGCATAATA
Statistics
Matches: 77, Mismatches: 42, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.02, C:0.07, G:0.08, T:0.82
Consensus pattern (1 bp):
T
Found at i:54714225 original size:9 final size:9
Alignment explanation
Indices: 54714211--54714330 Score: 79
Period size: 9 Copynumber: 12.9 Consensus size: 9
54714201 TTCATCTTGA
54714211 TTTTTTTTC
1 TTTTTTTTC
54714220 -TTTTTTT-
1 TTTTTTTTC
*
54714227 TTATTTTT-
1 TTTTTTTTC
* *
54714235 TGTTTTGTC
1 TTTTTTTTC
*
54714244 TGTTTTTTC
1 TTTTTTTTC
54714253 TGTTTTTTTC
1 T-TTTTTTTC
54714263 TTTTTGTTT-
1 TTTTT-TTTC
54714272 TTTGTTTTGTC
1 TTT-TTTT-TC
54714283 TGTTTTTTTC
1 T-TTTTTTTC
*
54714293 TGTTTTTTC
1 TTTTTTTTC
54714302 TTTTCTTTTTC
1 -TTT-TTTTTC
54714313 TATTTTTTT-
1 T-TTTTTTTC
54714322 TGTTTTTTT
1 T-TTTTTTT
54714331 AAGCATAATA
Statistics
Matches: 91, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
8 18 0.20
9 33 0.36
10 25 0.27
11 13 0.14
12 2 0.02
ACGTcount: A:0.02, C:0.07, G:0.08, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:54714267 original size:39 final size:39
Alignment explanation
Indices: 54714220--54714305 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
54714210 ATTTTTTTTC
54714220 TTTT-TTTTTATTTTTTGTTTTGTCTG-TTTTTTCTGTTT
1 TTTTCTTTTTATTTTTTGTTTTGTCTGTTTTTTTCTG-TT
*
54714258 TTTTCTTTTTGTTTTTTGTTTTGTCTGTTTTTTTCTGTT
1 TTTTCTTTTTATTTTTTGTTTTGTCTGTTTTTTTCTGTT
54714297 TTTTCTTTT
1 TTTTCTTTT
54714306 CTTTTTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
38 4 0.09
39 32 0.71
40 9 0.20
ACGTcount: A:0.01, C:0.07, G:0.10, T:0.81
Consensus pattern (39 bp):
TTTTCTTTTTATTTTTTGTTTTGTCTGTTTTTTTCTGTT
Found at i:54714326 original size:39 final size:40
Alignment explanation
Indices: 54714220--54714330 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 40
54714210 ATTTTTTTTC
* * *
54714220 TTTT-TTTTTATTTTTTGTTTTGTCTG-TTTTTTCTGTTT
1 TTTTCTTTTTGTTTTCTATTTTGTCTGTTTTTTTCTGTTT
* *
54714258 TTTTCTTTTTGTTTTTTGTTTTGTCTGTTTTTTTCTG-TT
1 TTTTCTTTTTGTTTTCTATTTTGTCTGTTTTTTTCTGTTT
* *
54714297 TTTTCTTTTCT-TTTTCTATTTTTTTTGTTTTTTT
1 TTTTCTTTT-TGTTTTCTATTTTGTCTGTTTTTTT
54714331 AAGCATAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
38 4 0.06
39 51 0.78
40 10 0.15
ACGTcount: A:0.02, C:0.07, G:0.09, T:0.82
Consensus pattern (40 bp):
TTTTCTTTTTGTTTTCTATTTTGTCTGTTTTTTTCTGTTT
Found at i:54717950 original size:4 final size:4
Alignment explanation
Indices: 54717912--54717940 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
54717902 ATGTACATGC
54717912 AATG AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG A
54717941 CCAATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:54719662 original size:18 final size:18
Alignment explanation
Indices: 54719639--54719673 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54719629 CAACTTTTTC
54719639 TTTTTTTGAAAACACGAT
1 TTTTTTTGAAAACACGAT
* *
54719657 TTTTTTTTAAAATACGA
1 TTTTTTTGAAAACACGA
54719674 GAATTTTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTTTTTGAAAACACGAT
Found at i:54719699 original size:19 final size:19
Alignment explanation
Indices: 54719677--54719725 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 19
54719667 AATACGAGAA
*
54719677 TTTTAGAAACACGAATTGT
1 TTTTAAAAACACGAATTGT
54719696 TTTTAAAAAAACACGAATTGT
1 TTTT--AAAAACACGAATTGT
54719717 TTTTAAAAA
1 TTTTAAAAA
54719726 AACACGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
21 18 0.67
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (19 bp):
TTTTAAAAACACGAATTGT
Found at i:54719708 original size:21 final size:21
Alignment explanation
Indices: 54719683--54719733 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
54719673 AGAATTTTAG
54719683 AAACACGAATTGTTTTTAAAA
1 AAACACGAATTGTTTTTAAAA
54719704 AAACACGAATTGTTTTTAAAA
1 AAACACGAATTGTTTTTAAAA
54719725 AAACACGAA
1 AAACACGAA
54719734 AATTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (21 bp):
AAACACGAATTGTTTTTAAAA
Found at i:54719746 original size:16 final size:17
Alignment explanation
Indices: 54719725--54719763 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
54719715 GTTTTTAAAA
54719725 AAACACGAAAATTT-TG
1 AAACACGAAAATTTATG
54719741 AAACACGAAAATTTATG
1 AAACACGAAAATTTATG
54719758 AAACAC
1 AAACAC
54719764 TATCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (17 bp):
AAACACGAAAATTTATG
Found at i:54719823 original size:21 final size:20
Alignment explanation
Indices: 54719789--54719829 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54719779 ACACGAAAAA
*
54719789 TTTTTGAAAAACGGGAATTT
1 TTTTTGAAAAACGGAAATTT
54719809 TTTTTGAAAACACGGAAATTT
1 TTTTTGAAAA-ACGGAAATTT
54719830 ATGAAACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (20 bp):
TTTTTGAAAAACGGAAATTT
Found at i:54719893 original size:56 final size:55
Alignment explanation
Indices: 54719816--54719959 Score: 150
Period size: 56 Copynumber: 2.6 Consensus size: 55
54719806 TTTTTTTTGA
* * * *
54719816 AAACACGGAAATTTATGAAACATGAAATTTTTTTTTGAAAACAAAAAAATTTTCG
1 AAACACTGAAATTTTTAAAACACGAAATTTTTTTTTGAAAACAAAAAAATTTTCG
* * * *
54719871 ATATAC-GAGAATTTTTAAAAACACGGGAAA--TTTTTTTGAAAACACAAAAATTTTTG
1 AAACACTGA-AATTTTT-AAAACAC--GAAATTTTTTTTTGAAAACAAAAAAATTTTCG
54719927 AAACACTGAAATTTTTAAAACACGAAGATTTTT
1 AAACACTGAAATTTTTAAAACACGAA-ATTTTT
54719960 GAAACATGAA
Statistics
Matches: 72, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
53 3 0.04
54 3 0.04
55 17 0.24
56 43 0.60
57 2 0.03
58 4 0.06
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (55 bp):
AAACACTGAAATTTTTAAAACACGAAATTTTTTTTTGAAAACAAAAAAATTTTCG
Found at i:54719926 original size:18 final size:18
Alignment explanation
Indices: 54719724--54720056 Score: 193
Period size: 17 Copynumber: 18.2 Consensus size: 18
54719714 TGTTTTTAAA
54719724 AAAACACGAAAA-TTTTG
1 AAAACACGAAAATTTTTG
*
54719741 -AAACACGAAAATTTATG
1 AAAACACGAAAATTTTTG
* * *
54719758 -AAACACTATCAATTTTTT
1 AAAACACGA-AAATTTTTG
54719776 AAAACACGAAAAATTTTTG
1 AAAACACG-AAAATTTTTG
**
54719795 AAAA-ACGGGAATTTTTTTTG
1 AAAACAC--GAA-AATTTTTG
* *
54719815 AAAACACGGAAATTTATG
1 AAAACACGAAAATTTTTG
* *
54719833 -AAACATGAAATTTTTTTTTG
1 AAAACACGAAA---ATTTTTG
** *
54719853 AAAACAAAAAAATTTTCG
1 AAAACACGAAAATTTTTG
* * * *
54719871 -ATATACGAGAATTTTTA
1 AAAACACGAAAATTTTTG
*
54719888 AAAACACGGGAAATTTTTTTG
1 AAAACAC--GAAA-ATTTTTG
*
54719909 AAAACACAAAAATTTTTG
1 AAAACACGAAAATTTTTG
54719927 -AAACACTG-AAATTTTT-
1 AAAACAC-GAAAATTTTTG
*
54719943 AAAACACGAAGATTTTTG
1 AAAACACGAAAATTTTTG
*
54719961 -AAACATGAAAATTTTTG
1 AAAACACGAAAATTTTTG
* * * *
54719978 AGAACAAGAAATTTTTTTTT
1 AAAACACGAAA--ATTTTTG
*
54719998 AAAACACGGAAATTTTTG
1 AAAACACGAAAATTTTTG
54720016 -AAACACGAGAAATTTTTTTG
1 AAAACACGA-AAA--TTTTTG
*
54720036 AAAACATGAAAATTTTTG
1 AAAACACGAAAATTTTTG
54720054 AAA
1 AAA
54720057 CCCTATTTTT
Statistics
Matches: 238, Mismatches: 51, Indels: 53
0.70 0.15 0.15
Matches are distributed among these distances:
16 12 0.05
17 78 0.33
18 53 0.22
19 24 0.10
20 42 0.18
21 29 0.12
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (18 bp):
AAAACACGAAAATTTTTG
Found at i:54720057 original size:38 final size:37
Alignment explanation
Indices: 54719725--54720057 Score: 205
Period size: 38 Copynumber: 9.1 Consensus size: 37
54719715 GTTTTTAAAA
*
54719725 AAACACGA-AAA--TTTTG-AAACACGAAAATTTATG
1 AAACACGAGAAATTTTTTGAAAACACGAAAATTTTTG
* **
54719758 AAACACTATCAATTTTTT-AAAACACGAAAAATTTTTG
1 AAACACGAGAAATTTTTTGAAAACACG-AAAATTTTTG
* * * * *
54719795 AAAAACGGGAATTTTTTTTGAAAACACGGAAATTTATG
1 AAACACGAGAA-ATTTTTTGAAAACACGAAAATTTTTG
* * ** *
54719833 AAACATGA-AATTTTTTTTTGAAAACAAAAAAATTTTCG
1 AAACACGAGAA--ATTTTTTGAAAACACGAAAATTTTTG
* * * *
54719871 ATATACGAG-AA-TTTTTAAAAACACGGGAAATTTTTTTG
1 AAACACGAGAAATTTTTTGAAAACAC--GAAA-ATTTTTG
* *
54719909 AAAACAC-A-AAAATTTTTG-AAACACTG-AAATTTTTA
1 -AAACACGAGAAATTTTTTGAAAACAC-GAAAATTTTTG
* *
54719944 AAACACGA-AGA-TTTTTG-AAACATGAAAATTTTTG
1 AAACACGAGAAATTTTTTGAAAACACGAAAATTTTTG
* *
54719978 AGAACA--AGAAATTTTTTTTTAAAACACGGAAATTTTTG
1 A-AACACGAGAAA--TTTTTTGAAAACACGAAAATTTTTG
*
54720016 AAACACGAGAAATTTTTTTGAAAACATGAAAATTTTTG
1 AAACACGAGAAA-TTTTTTGAAAACACGAAAATTTTTG
54720054 AAAC
1 AAAC
54720058 CCTATTTTTT
Statistics
Matches: 231, Mismatches: 44, Indels: 45
0.72 0.14 0.14
Matches are distributed among these distances:
33 9 0.04
34 30 0.13
35 23 0.10
36 13 0.06
37 30 0.13
38 104 0.45
39 22 0.10
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (37 bp):
AAACACGAGAAATTTTTTGAAAACACGAAAATTTTTG
Found at i:54720561 original size:7 final size:7
Alignment explanation
Indices: 54720541--54720610 Score: 97
Period size: 7 Copynumber: 9.9 Consensus size: 7
54720531 CATTTTTCCT
54720541 TTTTTTC
1 TTTTTTC
54720548 TTCTTTTTC
1 -T-TTTTTC
54720557 TTTTTTC
1 TTTTTTC
54720564 TTTTTTC
1 TTTTTTC
54720571 TTTTTTC
1 TTTTTTC
54720578 TTTTTTC
1 TTTTTTC
54720585 TTTTTTC
1 TTTTTTC
54720592 TTTTTT-
1 TTTTTTC
* *
54720598 TCTCTTC
1 TTTTTTC
54720605 TTTTTT
1 TTTTTT
54720611 TTGGCCTGCT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
6 4 0.07
7 44 0.79
8 2 0.04
9 6 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:54720653 original size:15 final size:15
Alignment explanation
Indices: 54720613--54720653 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
54720603 TCTTTTTTTT
54720613 GGCCTGCTGCCTTTGG
1 GGCCTGCTG-CTTTGG
54720629 GGCCTG-TGCTATT-G
1 GGCCTGCTGCT-TTGG
54720643 GGCCTGCTGCT
1 GGCCTGCTGCT
54720654 GGTGTTGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.39
15 8 0.35
16 6 0.26
ACGTcount: A:0.02, C:0.29, G:0.37, T:0.32
Consensus pattern (15 bp):
GGCCTGCTGCTTTGG
Found at i:54720746 original size:18 final size:19
Alignment explanation
Indices: 54720705--54720747 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
54720695 GCGCTTGGGC
*
54720705 TGTTTTTGGCCTGTTTCTT
1 TGTTTTTGGCCTCTTTCTT
*
54720724 T-TTTTT-GCCTCTTTTTT
1 TGTTTTTGGCCTCTTTCTT
54720741 TGTTTTT
1 TGTTTTT
54720748 TCTTTGGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 10 0.48
19 1 0.05
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72
Consensus pattern (19 bp):
TGTTTTTGGCCTCTTTCTT
Found at i:54721440 original size:30 final size:30
Alignment explanation
Indices: 54721404--54721528 Score: 137
Period size: 30 Copynumber: 4.2 Consensus size: 30
54721394 GGCTGAAACA
* *
54721404 TAATTTCGAGGAAGTTTAGGTGTCAAAATG
1 TAATTTCGAGAAAGTTTAGGGGTCAAAATG
54721434 TAATTTCGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTCGAGAAAGTTTAGGGGTCAAAATG
* *
54721464 TAGTTTC-AAAAAGTTTAGGGGT-AGAAATG
1 TAATTTCGAGAAAGTTTAGGGGTCA-AAATG
* ** * *
54721493 TAGTTTTAAAAAAATTTAGGGGTCAAAATG
1 TAATTTCGAGAAAGTTTAGGGGTCAAAATG
*
54721523 CAATTT
1 TAATTT
54721529 TTTTAAACAC
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.01
29 25 0.30
30 57 0.68
31 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (30 bp):
TAATTTCGAGAAAGTTTAGGGGTCAAAATG
Found at i:54725432 original size:18 final size:17
Alignment explanation
Indices: 54725412--54725681 Score: 147
Period size: 18 Copynumber: 15.2 Consensus size: 17
54725402 AAGAATCTAT
54725412 TTTTCAAAATTCTCGTG
1 TTTTCAAAATTCTCGTG
*
54725429 TTTTTAAAAAAATTACATTCTGTG
1 -TTTT--CAAAATT-C--TC-GTG
* *
54725453 TTTTCAAAAATTTTCGTA
1 TTTTC-AAAATTCTCGTG
* *
54725471 TTTTCAAAAATTTTCATG
1 TTTTC-AAAATTCTCGTG
54725489 TTTTCAACAATTCTCGTG
1 TTTTCAA-AATTCTCGTG
*
54725507 -TTTCACAAATTTTCGTG
1 TTTTCA-AAATTCTCGTG
* * ** *
54725524 TTTTAAAAATTTTTTTA
1 TTTTCAAAATTCTCGTG
* *
54725541 TTTTAAAAAATTCTCGTC
1 TTTT-CAAAATTCTCGTG
* *
54725559 TTTTAAAAATTGTCGTG
1 TTTTCAAAATTCTCGTG
*
54725576 -TTTCAAAAATTC-CATG
1 TTTTC-AAAATTCTCGTG
*
54725592 TTTTCAAAAATCTTCGTG
1 TTTTCAAAATTC-TCGTG
54725610 TTTTCAAGAATTCTCGTG
1 TTTTCAA-AATTCTCGTG
54725628 -TTTCAAAAACTT-TCGTG
1 TTTTC-AAAA-TTCTCGTG
* *** *
54725645 TTTTTAAAAAAATCATG
1 TTTTCAAAATTCTCGTG
54725662 -TTTCAAAATTCTCGTG
1 TTTTCAAAATTCTCGTG
54725678 TTTT
1 TTTT
54725682 TTTAATTCTT
Statistics
Matches: 197, Mismatches: 34, Indels: 43
0.72 0.12 0.16
Matches are distributed among these distances:
16 23 0.12
17 71 0.36
18 75 0.38
19 6 0.03
20 6 0.03
21 1 0.01
22 6 0.03
23 6 0.03
24 3 0.02
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (17 bp):
TTTTCAAAATTCTCGTG
Found at i:54725552 original size:35 final size:36
Alignment explanation
Indices: 54725450--54725654 Score: 179
Period size: 35 Copynumber: 5.9 Consensus size: 36
54725440 ATTACATTCT
54725450 GTGTTTTCAAAAATTTTCGTATTTTCAAAAATTTTC
1 GTGTTTTCAAAAATTTTCGTATTTTCAAAAATTTTC
* * * * *
54725486 ATGTTTTCAACAATTCTCGT-GTTTCACAAATTTTC
1 GTGTTTTCAAAAATTTTCGTATTTTCAAAAATTTTC
** * *
54725521 GTGTTTT-AAAAATTTTTTTATTTTAAAAAATTCTC
1 GTGTTTTCAAAAATTTTCGTATTTTCAAAAATTTTC
* * * *
54725556 GTCTTTT-AAAAATTGTCGT-GTTTCAAAAA-TTCC
1 GTGTTTTCAAAAATTTTCGTATTTTCAAAAATTTTC
* * * * *
54725589 ATGTTTTCAAAAATCTTCGTGTTTTCAAGAATTCTC
1 GTGTTTTCAAAAATTTTCGTATTTTCAAAAATTTTC
* * *
54725625 GTG-TTTCAAAAACTTTCGTGTTTTTAAAAA
1 GTGTTTTCAAAAATTTTCGTATTTTCAAAAA
54725655 AATCATGTTT
Statistics
Matches: 130, Mismatches: 35, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
33 7 0.05
34 26 0.20
35 76 0.58
36 21 0.16
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (36 bp):
GTGTTTTCAAAAATTTTCGTATTTTCAAAAATTTTC
Found at i:54725664 original size:52 final size:50
Alignment explanation
Indices: 54725564--54725680 Score: 137
Period size: 52 Copynumber: 2.3 Consensus size: 50
54725554 TCGTCTTTTA
* ** *
54725564 AAAATTGTCGTGTTTCAAAAATTCCATGTTTTCAAAAATCTTCGTGTTTTC
1 AAAATTCTCGTGTTTCAAAAATTCCATGTTTTCAAAAATAATCATG-TTTC
* * *
54725615 AAGAATTCTCGTGTTTCAAAAACTTTCGTGTTTTTAAAAA-AATCATGTTTC
1 AA-AATTCTCGTGTTTCAAAAA-TTCCATGTTTTCAAAAATAATCATGTTTC
54725666 AAAATTCTCGTGTTT
1 AAAATTCTCGTGTTT
54725681 TTTTAATTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 13 0.23
51 8 0.14
52 22 0.39
53 14 0.25
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (50 bp):
AAAATTCTCGTGTTTCAAAAATTCCATGTTTTCAAAAATAATCATGTTTC
Found at i:54725666 original size:69 final size:68
Alignment explanation
Indices: 54725549--54725681 Score: 164
Period size: 69 Copynumber: 1.9 Consensus size: 68
54725539 TATTTTAAAA
* * *
54725549 AATTCTCGTCTTTTAAAAATTGTCGTGTTTCAAAAATTCCATGTTTTCAAAAATCTTCGTGTTTT
1 AATTCTCGTCTTTCAAAAATTGTCGTGTTTAAAAAAATCCATGTTTTCAAAAATC-TCGTGTTTT
54725614 CAAG
65 CAAG
* *
54725618 AATTCTCGTGTTTCAAAAACTT-TCGTGTTTTTAAAAAAAT-CATG-TTTCAAAATTCTCGTGTT
1 AATTCTCGTCTTTCAAAAA-TTGTCGTG--TTTAAAAAAATCCATGTTTTCAAAAATCTCGTGTT
54725680 TT
63 TT
54725682 TTTAATTCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
68 9 0.16
69 32 0.57
70 6 0.11
71 9 0.16
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (68 bp):
AATTCTCGTCTTTCAAAAATTGTCGTGTTTAAAAAAATCCATGTTTTCAAAAATCTCGTGTTTTC
AAG
Found at i:54729754 original size:16 final size:18
Alignment explanation
Indices: 54729717--54729754 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
54729707 AGGAAGAAGA
*
54729717 AAGAAATAAAGAAAGGAG
1 AAGAAATAAAGAAAGGAC
54729735 AAGAAA-AAAG-AAGGAC
1 AAGAAATAAAGAAAGGAC
54729751 AAGA
1 AAGA
54729755 TATTTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.68, C:0.03, G:0.26, T:0.03
Consensus pattern (18 bp):
AAGAAATAAAGAAAGGAC
Found at i:54733159 original size:19 final size:19
Alignment explanation
Indices: 54733118--54733156 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54733108 AGCAGAAGAG
*
54733118 AAGAAAGAAGAAAGAAATA
1 AAGAAAGAAGAAAGAAAAA
*
54733137 AAGAAAGGAG-AAGAAAAA
1 AAGAAAGAAGAAAGAAAAA
54733155 AA
1 AA
54733157 AGATAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (19 bp):
AAGAAAGAAGAAAGAAAAA
Found at i:54733386 original size:105 final size:108
Alignment explanation
Indices: 54733258--54733507 Score: 362
Period size: 115 Copynumber: 2.3 Consensus size: 108
54733248 TTTTATGTTG
*
54733258 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAA-CT-ATTATA-AATTGTTTGATTAGTTTAAT
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATCTGATTATAGAATTATTTGATTAGTTTAAT
*
54733320 GTTGATTGTGATTTGTTAGGGTATGAATGTAATCTTTTATTAT
66 ATTGATTGTGATTTGTTAGGGTATGAATGTAATCTTTTATTAT
* * *
54733363 TTTTTAATTTATCTTAAAGTTATTTTGTTAGTAATTTTTGTGATTATAGGTTAATTATTTGTTTA
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAA----TCTGATTATA-G--AATTATTTGATTA
54733428 GTTTAATATTGATTGTGATTTGTTAGGGTATGAATGTAATCTTTTATTAT
59 GTTTAATATTGATTGTGATTTGTTAGGGTATGAATGTAATCTTTTATTAT
*
54733478 TTTTTAATTTATTTTAAAATTATTTTGTTA
1 TTTTTAATTTATTTTAAAGTTATTTTGTTA
54733508 ATCACTTGAT
Statistics
Matches: 128, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
105 33 0.26
110 1 0.01
111 6 0.05
115 88 0.69
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (108 bp):
TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATCTGATTATAGAATTATTTGATTAGTTTAAT
ATTGATTGTGATTTGTTAGGGTATGAATGTAATCTTTTATTAT
Found at i:54735193 original size:13 final size:13
Alignment explanation
Indices: 54735165--54735203 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
54735155 AAAACAAGCC
54735165 TTATTTTATCTAAAT
1 TTATTTT-T-TAAAT
54735180 TTATTTTTTAAAT
1 TTATTTTTTAAAT
54735193 TTATATTTTTA
1 TTAT-TTTTTA
54735204 CTCATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.39
14 7 0.30
15 7 0.30
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTTTTTAAAT
Found at i:54737316 original size:3 final size:3
Alignment explanation
Indices: 54737308--54737338 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
54737298 TATTTTAGTG
54737308 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
54737339 GTTTCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54737329 original size:13 final size:13
Alignment explanation
Indices: 54737311--54737337 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54737301 TTTAGTGTTA
54737311 TTATTATTATTAT
1 TTATTATTATTAT
54737324 TTATTATTATTAT
1 TTATTATTATTAT
54737337 T
1 T
54737338 AGTTTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:54737329 original size:16 final size:16
Alignment explanation
Indices: 54737308--54737338 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54737298 TATTTTAGTG
54737308 TTATTATTATTATTAT
1 TTATTATTATTATTAT
54737324 TTATTATTATTATTA
1 TTATTATTATTATTA
54737339 GTTTCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:54741715 original size:17 final size:17
Alignment explanation
Indices: 54741693--54741731 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
54741683 TTTGTTTAAG
54741693 TTATATATATATAAATA
1 TTATATATATATAAATA
* *
54741710 TTATATGTATATAATTA
1 TTATATATATATAAATA
54741727 TTATA
1 TTATA
54741732 ATTATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATATATATATAAATA
Found at i:54741731 original size:9 final size:9
Alignment explanation
Indices: 54741702--54741746 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
54741692 GTTATATATA
*
54741702 TATAAATAT
1 TATAATTAT
54741711 TAT-ATGTA-
1 TATAAT-TAT
54741719 TATAATTAT
1 TATAATTAT
54741728 TATAATTAT
1 TATAATTAT
54741737 TATAATTAT
1 TATAATTAT
54741746 T
1 T
54741747 TATTTAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (9 bp):
TATAATTAT
Found at i:54742111 original size:15 final size:17
Alignment explanation
Indices: 54742093--54742124 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54742083 CAGAATAGAA
54742093 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
54742108 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
54742125 GGGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:54743200 original size:45 final size:45
Alignment explanation
Indices: 54743134--54743277 Score: 166
Period size: 45 Copynumber: 3.2 Consensus size: 45
54743124 ATGTGCCGAC
* * * *
54743134 TACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTATTACTGT
1 TACTGTTACAGACTCGACACTTTGTGTGTCGAATACTGTTACTGT
* *
54743179 TACTGTTACCGACTCGACACTTTGTGTGTCGAATACTGTTACCGT
1 TACTGTTACAGACTCGACACTTTGTGTGTCGAATACTGTTACTGT
* ** *
54743224 TACTGTTACAG-GTTTAGCACTTTGTGTGTTG-ATACTGTTACTGT
1 TACTGTTACAGACTCGA-CACTTTGTGTGTCGAATACTGTTACTGT
54743268 TACTGATTAC
1 TACTG-TTAC
54743278 TGTATACTAG
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 19 0.22
45 67 0.78
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACAGACTCGACACTTTGTGTGTCGAATACTGTTACTGT
Found at i:54743886 original size:9 final size:9
Alignment explanation
Indices: 54743872--54743900 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
54743862 GAATGTGAAA
54743872 TGAATTGGT
1 TGAATTGGT
54743881 TGAATTGGT
1 TGAATTGGT
54743890 TGAATTGGT
1 TGAATTGGT
54743899 TG
1 TG
54743901 TGATTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (9 bp):
TGAATTGGT
Found at i:54754359 original size:27 final size:28
Alignment explanation
Indices: 54754323--54754385 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
54754313 CATTTTCATA
54754323 TATTTGATTTTG-ATACTCACTCAATTTTT
1 TATTT-ATTTTGAATACTCACT-AATTTTT
* *
54754352 T-TTTATTTTGAATATTTACTAATTTTT
1 TATTTATTTTGAATACTCACTAATTTTT
54754379 TATTTAT
1 TATTTAT
54754386 AAAAAATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 14 0.47
28 15 0.50
29 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (28 bp):
TATTTATTTTGAATACTCACTAATTTTT
Found at i:54754611 original size:28 final size:28
Alignment explanation
Indices: 54754547--54754612 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
54754537 TCAATACAAA
54754547 TCCATATTATTCAGGTAAATAAATTTTG
1 TCCATATTATTCAGGTAAATAAATTTTG
* * * *
54754575 T--ATGTTATTTAGGTAAATATATTTTT
1 TCCATATTATTCAGGTAAATAAATTTTG
54754601 TCCATATTATTC
1 TCCATATTATTC
54754613 CATAAAAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
26 22 0.73
28 8 0.27
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (28 bp):
TCCATATTATTCAGGTAAATAAATTTTG
Found at i:54756485 original size:79 final size:79
Alignment explanation
Indices: 54756354--54756513 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
54756344 CTGAGAACAT
54756354 ATAAAACCAAGCTTAAACATAAAGATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAAAT
1 ATAAAACCAAGCTTAAACATAAAGATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAAAT
54756419 TAGGCCATTTTCGC
66 TAGGCCATTTTCGC
54756433 ATAAAACCAAGCTTAAACATAAAGATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAAAT
1 ATAAAACCAAGCTTAAACATAAAGATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAAAT
54756498 TAGGCCATTTTCGC
66 TAGGCCATTTTCGC
54756512 AT
1 AT
54756514 GGCCATATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (79 bp):
ATAAAACCAAGCTTAAACATAAAGATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAAAT
TAGGCCATTTTCGC
Found at i:54756508 original size:39 final size:39
Alignment explanation
Indices: 54756378--54756508 Score: 131
Period size: 39 Copynumber: 3.3 Consensus size: 39
54756368 AAACATAAAG
54756378 ATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAA
1 ATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAA
* ** *** * * *
54756417 ATTAGGCCATTTTCGCATAAAACC-AAGCTTAAACAT-AAA
1 ATTAAGCCATTTT-TAACCCAACCGAA-TTTAAGCATGGAA
54756456 GATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAA
1 -ATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAA
*
54756496 ATTAGGCCATTTT
1 ATTAAGCCATTTT
54756509 CGCATGGCCA
Statistics
Matches: 68, Mismatches: 19, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
39 40 0.59
40 28 0.41
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (39 bp):
ATTAAGCCATTTTTAACCCAACCGAATTTAAGCATGGAA
Found at i:54757238 original size:42 final size:42
Alignment explanation
Indices: 54757148--54757275 Score: 138
Period size: 42 Copynumber: 3.0 Consensus size: 42
54757138 AGTCCGTACA
*
54757148 ATGCCAACA-TCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCC-ACAGTCCCAGACGTGGTCTTACACG-AATCACATATCG
*
54757191 ATGCCACAGTCCCAGACAG-GGTCTTAAACGAATCACA-AGTCG
1 ATGCCACAGTCCCAGAC-GTGGTCTTACACGAATCACATA-TCG
* *
54757233 ATGCCA-ATGTCCTAGACGTGGTCTTACACGAAAACACATATCG
1 ATGCCACA-GTCCCAGACGTGGTCTTACACG-AATCACATATCG
54757276 GAATCCTATG
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
41 3 0.04
42 37 0.51
43 31 0.42
44 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (42 bp):
ATGCCACAGTCCCAGACGTGGTCTTACACGAATCACATATCG
Found at i:54758172 original size:23 final size:23
Alignment explanation
Indices: 54758145--54758190 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
54758135 TAATTTTTTA
54758145 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
54758168 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
54758191 TACTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:54758182 original size:25 final size:22
Alignment explanation
Indices: 54758153--54758205 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
54758143 TATATTAAAC
*
54758153 ATATATTAACCTTATTATTAATTT
1 ATATATTAACC-T-TTACTAATTT
54758177 ACTATATTAACCTTTACTAATTT
1 A-TATATTAACCTTTACTAATTT
54758200 ATATAT
1 ATATAT
54758206 AACATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 5 0.19
23 10 0.37
24 2 0.07
25 10 0.37
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATTAACCTTTACTAATTT
Found at i:54761026 original size:21 final size:21
Alignment explanation
Indices: 54760979--54761028 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
54760969 TTGTCTCTTT
* **
54760979 AATTTCCTCACTTTTTCTACC
1 AATTTCTTCACTTTCACTACC
* *
54761000 ATTTTCTTCACTTTCACTTCC
1 AATTTCTTCACTTTCACTACC
54761021 AATTTCTT
1 AATTTCTT
54761029 TCTTCCAAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.30, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTCTTCACTTTCACTACC
Found at i:54762864 original size:21 final size:21
Alignment explanation
Indices: 54762806--54762892 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
54762796 CCTAATCAGT
54762806 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* ** *
54762826 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
54762847 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
*
54762868 ATGTATGACACATAAAGTGCCTG
1 A--TACGACACATAAAGTGCCTG
54762891 AT
1 AT
54762893 CGGCAAGGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.16
21 27 0.48
23 20 0.36
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:54762890 original size:44 final size:41
Alignment explanation
Indices: 54762806--54762892 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 41
54762796 CCTAATCAGT
* *
54762806 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
* * *
54762847 ATACGACACATAAAGTGCCTGATGTATGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA--AACGACACACAAAGTGCCTG
54762891 AT
1 AT
54762893 CGGCAAGGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
44 17 0.45
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.20
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:54763098 original size:18 final size:18
Alignment explanation
Indices: 54763075--54763136 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
54763065 ACACATACTT
54763075 TTCAAATTCACATTTCAA
1 TTCAAATTCACATTTCAA
* *
54763093 TTCAAATTCACTTTTTCATT
1 TTCAAATTCAC-ATTTCA-A
*
54763113 TTC-AA-TCACAATTCAA
1 TTCAAATTCACATTTCAA
54763129 TTCAAATT
1 TTCAAATT
54763137 TACTTTTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 6 0.17
18 16 0.46
19 7 0.20
20 3 0.09
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
TTCAAATTCACATTTCAA
Found at i:54763128 original size:36 final size:37
Alignment explanation
Indices: 54763073--54763170 Score: 119
Period size: 36 Copynumber: 2.6 Consensus size: 37
54763063 CAACACATAC
* * *
54763073 TTTTCAAATTCACATTTCAATTCAAATTCACTTTTTCA
1 TTTTC-AAGTCACAATTCAATTCAAATTCACTTTTCCA
*
54763111 TTTTCAA-TCACAATTCAATTCAAATTTACTTTTCCA
1 TTTTCAAGTCACAATTCAATTCAAATTCACTTTTCCA
*
54763147 TTTTCAAGTCA-ATATTCATTTCAA
1 TTTTCAAGTCACA-ATTCAATTCAA
54763171 TTCCACACAT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
36 34 0.63
37 15 0.28
38 5 0.09
ACGTcount: A:0.33, C:0.20, G:0.01, T:0.46
Consensus pattern (37 bp):
TTTTCAAGTCACAATTCAATTCAAATTCACTTTTCCA
Found at i:54763244 original size:16 final size:16
Alignment explanation
Indices: 54763222--54763261 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
54763212 TTAATAATAA
54763222 TACTTACCTTA-TATT
1 TACTTACCTTATTATT
54763237 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
54763254 TACTTACC
1 TACTTACC
54763262 ATACACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.04
16 17 0.74
17 5 0.22
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:54764120 original size:14 final size:17
Alignment explanation
Indices: 54764101--54764138 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
54764091 ATTTATTTCT
54764101 TAATATAA-T-ATTT-A
1 TAATATAACTAATTTAA
54764115 TAATATAACTAATTTAA
1 TAATATAACTAATTTAA
54764132 TAATATA
1 TAATATA
54764139 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATAACTAATTTAA
Found at i:54764178 original size:21 final size:20
Alignment explanation
Indices: 54764130--54764179 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
54764120 TAACTAATTT
*
54764130 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* * *
54764150 ATTTATATATTTATATAAATA
1 AATAATATACTT-TATAAATA
54764171 AATAATATA
1 AATAATATA
54764180 AAAATCTAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:54800018 original size:23 final size:23
Alignment explanation
Indices: 54799992--54800042 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
54799982 TGTTATTGAT
54799992 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
54800015 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
54800038 CAGTG
1 CAGTG
54800043 TTGCACTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:54802218 original size:18 final size:18
Alignment explanation
Indices: 54802195--54802232 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54802185 TGCCAGGTGC
* *
54802195 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
54802213 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
54802231 GT
1 GT
54802233 TTCATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:54802691 original size:34 final size:33
Alignment explanation
Indices: 54802651--54802746 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 33
54802641 GAATATTTTG
54802651 ATATTATTTGATGTAATAAAATAGAAATTCTTCT
1 ATATTATTT-ATGTAATAAAATAGAAATTCTTCT
* *
54802685 ATATTATTTCATGTACTAAAATAGAAATT-TACT
1 ATATTATTT-ATGTAATAAAATAGAAATTCTTCT
*
54802718 -TATATATTT-T-TAATATAATAGAAATTCTT
1 ATAT-TATTTATGTAATAAAATAGAAATTCTT
54802747 TTAAATAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
30 14 0.26
31 2 0.04
32 3 0.06
33 8 0.15
34 27 0.50
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (33 bp):
ATATTATTTATGTAATAAAATAGAAATTCTTCT
Found at i:54802914 original size:116 final size:117
Alignment explanation
Indices: 54802710--54802919 Score: 277
Period size: 116 Copynumber: 1.8 Consensus size: 117
54802700 CTAAAATAGA
*
54802710 AATTTACTTATATATTTTTAATATAATAGAAATTCTTTTAAATAAGGCAATATGTTGAATATTTC
1 AATTTACTTATATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATGTTGAATATTTC
* *
54802775 TATATTATTTCATTTAATAAAATA-AAATGTTGTTTTGAATAAAGTAATTGT
66 TAAATTATTTAATTTAATAAAATATAAATGTTGTTTTGAATAAAGTAATTGT
** **
54802826 AATTTACTT-TAATATTTTTAATAAAATAGATTTTCTTTTAAATAAGTTAATAT-TCTGAATATT
1 AATTTACTTAT-ATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATGT-TGAATATT
*
54802889 TGTACCAATT-TTTAATTTAA-AAAATATAAAT
64 TCTA--AATTATTTAATTTAATAAAATATAAAT
54802920 AATACAAAGT
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
115 2 0.02
116 63 0.78
117 13 0.16
118 3 0.04
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (117 bp):
AATTTACTTATATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATGTTGAATATTTC
TAAATTATTTAATTTAATAAAATATAAATGTTGTTTTGAATAAAGTAATTGT
Found at i:54806127 original size:126 final size:126
Alignment explanation
Indices: 54805902--54806318 Score: 728
Period size: 126 Copynumber: 3.3 Consensus size: 126
54805892 CCAGACATGC
*
54805902 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTATTTCTGCTGATAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGATAAAGCATCCT
*
54805967 GCTTAAAGCGTTTTTGACACTATTTGCTTAGAAACGTCTACTCGAAAATATTTTTTCAAGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAAATATTTTTTCAAGA
*
54806028 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTTAGTACTTCTGCTGATAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGATAAAGCATCCT
*
54806093 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAAATATTTTTTCAAGA
* * *
54806154 GCTACTGTAGCAAAAGCGCGTCAACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGATAAAGCATCCT
54806219 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTC-AAAATTATTTTTTCAAGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAAA-TATTTTTTCAAGA
* * *
54806280 GCTACTGCAGCAAAAGTGCATCCACGTGGGAGCTTCTTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
54806319 AAATTAACAA
Statistics
Matches: 277, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
125 3 0.01
126 274 0.99
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGATAAAGCATCCT
GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAAATATTTTTTCAAGA
Found at i:54806484 original size:97 final size:94
Alignment explanation
Indices: 54806351--54806628 Score: 301
Period size: 97 Copynumber: 2.9 Consensus size: 94
54806341 CGTAACCCTA
* * * *
54806351 AACCCCAAACCCTAATTTATTTAAGTTCTTACTTAAAAACCTTAAACACTAAACCCTAATCTAAC
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTCTTAAAAACCTTAAACACTAAACCCTAATCTAA-
54806416 TTTATAAAAATTTATAATTAATTTACTAAAGT
64 TTT-TAAAAATTTATAATTAATTTACTAAAGT
* * * * *
54806448 AACCCTGAACCCTATTTTATTTGATTTTTTTCTTAAAAACCTTTAACTCTAAACCTTAATC-AGA
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTCTTAAAAACCTTAAACACTAAACCCTAATCTA-A
* * * * *
54806512 TTTTTAAATTTTTTAATTAAATTACTCAAGT
64 TTTTAAAAATTTATAATTAATTTACTAAAGT
* * *** *
54806543 AACCCTAAACCTTAATTTAATTGATTTTTTC-TAAAAAAAATAAACACGAAA-CCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCTTAAACACTAAACCCTAATCTAATT
54806606 TTGAAAAATTTATAATTAATTTA
66 TT-AAAAATTTATAATTAATTTA
54806629 ATTGACAAAT
Statistics
Matches: 148, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
92 11 0.07
93 31 0.21
94 7 0.05
95 43 0.29
96 4 0.03
97 52 0.35
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (94 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCTTAAACACTAAACCCTAATCTAATT
TTAAAAATTTATAATTAATTTACTAAAGT
Done.