Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 13 of 325
Found at i:4851661 original size:18 final size:18
Alignment explanation
Indices: 4851640--4851830 Score: 167
Period size: 18 Copynumber: 10.6 Consensus size: 18
4851630 TAACTGATTA
*
4851640 TTACTGAATAATTTACTG
1 TTACTGAATAATTGACTG
* *
4851658 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
* *
4851676 TTACTGGAT-ATTAAACTG
1 TTACTGAATAATT-GACTG
* * *
4851694 TTACTAAATAATTGAATA
1 TTACTGAATAATTGACTG
*
4851712 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
*
4851730 TTACTGAATAATTGATTG
1 TTACTGAATAATTGACTG
*
4851748 TCACTGAATGAATT-ACTG
1 TTACTGAAT-AATTGACTG
* *
4851766 TTACTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
*
4851785 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
4851802 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
4851820 TTACTGGATAA
1 TTACTGAATAA
4851831 CCGATCAATT
Statistics
Matches: 143, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
17 20 0.14
18 103 0.72
19 20 0.14
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:4851744 original size:72 final size:73
Alignment explanation
Indices: 4851627--4851829 Score: 204
Period size: 72 Copynumber: 2.8 Consensus size: 73
4851617 TAAAGGTATA
* * * * * * *
4851627 AAATAACTGATTATTACTGAATAATTTA-CTGTTACCGGATAATTGACTGTTACTGGATATTAA-
1 AAATAATTGAATATTACTGAATAATTGATC-ATTACTGAATAATTGACTGTTACTGGATATGAAT
4851690 ACTGTTACT
65 ACTGTTACT
* *
4851699 AAATAATTGAATATTACTGAATAATTGATCATTACTGAATAATTGATTGTCACT-GA-ATGAATT
1 AAATAATTGAATATTACTGAATAATTGATCATTACTGAATAATTGACTGTTACTGGATATGAA-T
4851762 ACTGTTACT
65 ACTGTTACT
* * *
4851771 GAATAACTT-AATTGTTACTGAAT-ATCTGAT-TTTACTGAATAATTGACTGTTACTGGATA
1 AAATAA-TTGAA-TATTACTGAATAAT-TGATCATTACTGAATAATTGACTGTTACTGGATA
4851830 ACCGATCAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
70 4 0.04
71 2 0.02
72 83 0.76
73 19 0.17
74 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (73 bp):
AAATAATTGAATATTACTGAATAATTGATCATTACTGAATAATTGACTGTTACTGGATATGAATA
CTGTTACT
Found at i:4851877 original size:36 final size:36
Alignment explanation
Indices: 4851837--4851910 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
4851827 ATAACCGATC
* **
4851837 AATTGATCGATACTGAATAACTGGTTATTATTGAAT
1 AATTGATCGATACCGAATAACTGACTATTATTGAAT
* * *
4851873 AATTGATTGTTACCGAATAATTGACTATTATTGAAT
1 AATTGATCGATACCGAATAACTGACTATTATTGAAT
4851909 AA
1 AA
4851911 ATAATTGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (36 bp):
AATTGATCGATACCGAATAACTGACTATTATTGAAT
Found at i:4851908 original size:18 final size:18
Alignment explanation
Indices: 4851862--4851910 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
4851852 AATAACTGGT
*
4851862 TATTATTGAATAATTGAT
1 TATTATTGAATAATTGAC
* **
4851880 TGTTACCGAATAATTGAC
1 TATTATTGAATAATTGAC
4851898 TATTATTGAATAA
1 TATTATTGAATAA
4851911 ATAATTGTTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (18 bp):
TATTATTGAATAATTGAC
Found at i:4853469 original size:16 final size:16
Alignment explanation
Indices: 4853448--4853479 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4853438 ATGATTCCAG
*
4853448 ATAAACATGTACGAAA
1 ATAAACAGGTACGAAA
4853464 ATAAACAGGTACGAAA
1 ATAAACAGGTACGAAA
4853480 GCTATAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (16 bp):
ATAAACAGGTACGAAA
Found at i:4862988 original size:5 final size:5
Alignment explanation
Indices: 4862978--4863009 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
4862968 ATAGAATGAT
*
4862978 TTTTA TTTTA TTTTA TTTTA TTTTA TTATA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
4863010 CTAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:4863039 original size:24 final size:23
Alignment explanation
Indices: 4863002--4863047 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
4862992 ATTTTATTTT
*
4863002 ATTATATTCTAAATTTAATTTTAA
1 ATTATATTCTAAA-TAAATTTTAA
4863026 ATTATATATC-AAATAAATTTTA
1 ATTATAT-TCTAAATAAATTTTA
4863048 TAACTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 10 0.50
25 2 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATATTCTAAATAAATTTTAA
Found at i:4866077 original size:30 final size:30
Alignment explanation
Indices: 4866043--4866102 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4866033 ATAATTAGAG
4866043 ATAGTTTAAAATTTTTGAGATTTTTTCTTC
1 ATAGTTTAAAATTTTTGAGATTTTTTCTTC
4866073 ATAGTTTAAAATTTTTGAGATTTTTTCTTC
1 ATAGTTTAAAATTTTTGAGATTTTTTCTTC
4866103 TTTTTTTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.57
Consensus pattern (30 bp):
ATAGTTTAAAATTTTTGAGATTTTTTCTTC
Found at i:4880279 original size:13 final size:13
Alignment explanation
Indices: 4880261--4880286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4880251 TCTTTTTTTC
4880261 CTCGTTTATAGTT
1 CTCGTTTATAGTT
4880274 CTCGTTTATAGTT
1 CTCGTTTATAGTT
4880287 AGACTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
CTCGTTTATAGTT
Found at i:4884935 original size:4 final size:4
Alignment explanation
Indices: 4884920--4884959 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
4884910 TATGTCAAGA
*
4884920 TATG TCATG TATG TATG TATG TATA TATG TATG TATG TAT
1 TATG T-ATG TATG TATG TATG TATG TATG TATG TATG TAT
4884960 AATTTGAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4889687 original size:19 final size:19
Alignment explanation
Indices: 4889663--4889699 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4889653 TTATTATTGT
*
4889663 GTTTGTTTTATAAAAAATA
1 GTTTGTTTAATAAAAAATA
*
4889682 GTTTGTTTAATAGAAAAT
1 GTTTGTTTAATAAAAAAT
4889700 TACTTATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (19 bp):
GTTTGTTTAATAAAAAATA
Found at i:4889904 original size:13 final size:14
Alignment explanation
Indices: 4889888--4889929 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
4889878 TTTTAATTTT
4889888 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
4889901 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
4889916 ATTTTAATTAATAT
1 ATTTTAA-TAATAT
4889930 TCTTTACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:4889920 original size:15 final size:16
Alignment explanation
Indices: 4889893--4889922 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4889883 ATTTTATTTT
4889893 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
4889909 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
4889923 TTAATATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:4889928 original size:16 final size:16
Alignment explanation
Indices: 4889881--4889928 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4889871 TTTAATATTT
*
4889881 TAATTTTATTTTAATAA
1 TAATTTTA-ATTAATAA
*
4889898 TAAATTTTAA-AAATAA
1 T-AATTTTAATTAATAA
4889914 TAATTTTAATTAATA
1 TAATTTTAATTAATA
4889929 TTCTTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 8 0.31
16 10 0.38
17 1 0.04
18 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTTAATTAATAA
Found at i:4889981 original size:15 final size:15
Alignment explanation
Indices: 4889961--4890012 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
4889951 ATTCAATATT
4889961 AATATTTTAATAATA
1 AATATTTTAATAATA
*
4889976 AATATTTATTTCAATTATA
1 AATA--T-TTT-AATAATA
*
4889995 AATATATTAATAATA
1 AATATTTTAATAATA
4890010 AAT
1 AAT
4890013 GTACTCTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 13 0.43
16 2 0.07
17 2 0.07
18 3 0.10
19 10 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:4889995 original size:19 final size:19
Alignment explanation
Indices: 4889963--4889999 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4889953 TCAATATTAA
*
4889963 TATTTTAATAATAAATATT
1 TATTTCAATAATAAATATT
*
4889982 TATTTCAATTATAAATAT
1 TATTTCAATAATAAATAT
4890000 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTCAATAATAAATATT
Found at i:4890048 original size:33 final size:34
Alignment explanation
Indices: 4889952--4890056 Score: 94
Period size: 33 Copynumber: 3.1 Consensus size: 34
4889942 ATTGAAAATA
* * *
4889952 TTCAA-TATTAATATTTTAATAATAAATATTTA-T-
1 TTCAATTATAAATATATTAATAAT-AA-ATGTACTC
4889985 TTCAATTATAAATATATTAATAATAAATGTACTC
1 TTCAATTATAAATATATTAATAATAAATGTACTC
* **
4890019 TTCAATTA-AAATATA-TCATAACTTTATGTACTC
1 TTCAATTATAAATATATTAATAA-TAAATGTACTC
4890052 TTCAA
1 TTCAA
4890057 AAAAATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
32 9 0.15
33 29 0.47
34 24 0.39
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.45
Consensus pattern (34 bp):
TTCAATTATAAATATATTAATAATAAATGTACTC
Found at i:4893673 original size:20 final size:21
Alignment explanation
Indices: 4893648--4893688 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4893638 AATTTAAAAA
*
4893648 TACATAATTAAT-TTATAATT
1 TACATAATAAATGTTATAATT
4893668 TACATAATAAATGTTATAATT
1 TACATAATAAATGTTATAATT
4893689 CATTGGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (21 bp):
TACATAATAAATGTTATAATT
Found at i:4903273 original size:65 final size:65
Alignment explanation
Indices: 4903197--4903326 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
4903187 CATTCGCGCT
4903197 AATGCTAACCATATATAAATAGATTTTTTTGTGATTATACACTAATTGGAATCCACGAAGTCAAA
1 AATGCTAACCATATATAAATAGATTTTTTTGTGATTATACACTAATTGGAATCCACGAAGTCAAA
4903262 AATGCTAACCATATATAAATAGATTTTTTTGTGATTATACACTAATTGGAATCCACGAAGTCAAA
1 AATGCTAACCATATATAAATAGATTTTTTTGTGATTATACACTAATTGGAATCCACGAAGTCAAA
4903327 CTTTATATAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (65 bp):
AATGCTAACCATATATAAATAGATTTTTTTGTGATTATACACTAATTGGAATCCACGAAGTCAAA
Found at i:4925005 original size:20 final size:20
Alignment explanation
Indices: 4924980--4925021 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4924970 AACTAAAAAG
4924980 TTAATTCAAACCATGGTATC
1 TTAATTCAAACCATGGTATC
4925000 TTAATTCAAACCATGGTATC
1 TTAATTCAAACCATGGTATC
4925020 TT
1 TT
4925022 TGAAAATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (20 bp):
TTAATTCAAACCATGGTATC
Found at i:4927919 original size:26 final size:26
Alignment explanation
Indices: 4927890--4927943 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4927880 AATTACAAAT
4927890 AATT-TAATAAATAAAAATAAAAATAA
1 AATTCTAA-AAATAAAAATAAAAATAA
* * *
4927916 AATTCTAAAACTAAAACTAAAACTAA
1 AATTCTAAAAATAAAAATAAAAATAA
4927942 AA
1 AA
4927944 CTAAAGTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (26 bp):
AATTCTAAAAATAAAAATAAAAATAA
Found at i:4927929 original size:6 final size:6
Alignment explanation
Indices: 4927901--4927948 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
4927891 ATTTAATAAA
* *
4927901 TAAAAA TAAAAA TAAAATTC TAAAAC TAAAAC TAAAAC TAAAAC TAAA
1 TAAAAC TAAAAC TAAAA--C TAAAAC TAAAAC TAAAAC TAAAAC TAAA
4927949 GTCTAAAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 34 0.87
8 5 0.13
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (6 bp):
TAAAAC
Found at i:4927943 original size:18 final size:19
Alignment explanation
Indices: 4927901--4927948 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
4927891 ATTTAATAAA
*
4927901 TAAAAATAAAAATAAAATTC
1 TAAAACTAAAAATAAAA-TC
*
4927921 TAAAACTAAAACTAAAA-C
1 TAAAACTAAAAATAAAATC
4927939 TAAAACTAAA
1 TAAAACTAAA
4927949 GTCTAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAACTAAAAATAAAATC
Found at i:4928002 original size:9 final size:9
Alignment explanation
Indices: 4927988--4928063 Score: 116
Period size: 9 Copynumber: 8.4 Consensus size: 9
4927978 GTAGTGATTC
4927988 AATTCGGTT
1 AATTCGGTT
*
4927997 AATTCGGGT
1 AATTCGGTT
4928006 AATTCGGTT
1 AATTCGGTT
*
4928015 AATTCGGGT
1 AATTCGGTT
*
4928024 AATCCGGTT
1 AATTCGGTT
*
4928033 AATTCGGGT
1 AATTCGGTT
4928042 AATTCGGTT
1 AATTCGGTT
4928051 AATTCGGTT
1 AATTCGGTT
4928060 AATT
1 AATT
4928064 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4928011 original size:18 final size:18
Alignment explanation
Indices: 4927988--4928063 Score: 134
Period size: 18 Copynumber: 4.2 Consensus size: 18
4927978 GTAGTGATTC
4927988 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
4928006 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
4928024 AATCCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
4928042 AATTCGGTTAATTCGGTT
1 AATTCGGTTAATTCGGGT
4928060 AATT
1 AATT
4928064 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:4932215 original size:78 final size:78
Alignment explanation
Indices: 4932086--4932238 Score: 306
Period size: 78 Copynumber: 2.0 Consensus size: 78
4932076 CCATGGGGGC
4932086 TTCAATAACTTTAACACTGGTAGAAAAATGAGACTAATGCCTCGGGAGAATGTTTGAAAATCCAA
1 TTCAATAACTTTAACACTGGTAGAAAAATGAGACTAATGCCTCGGGAGAATGTTTGAAAATCCAA
4932151 CTCCAAATATAAT
66 CTCCAAATATAAT
4932164 TTCAATAACTTTAACACTGGTAGAAAAATGAGACTAATGCCTCGGGAGAATGTTTGAAAATCCAA
1 TTCAATAACTTTAACACTGGTAGAAAAATGAGACTAATGCCTCGGGAGAATGTTTGAAAATCCAA
4932229 CTCCAAATAT
66 CTCCAAATAT
4932239 GGTAAACACA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (78 bp):
TTCAATAACTTTAACACTGGTAGAAAAATGAGACTAATGCCTCGGGAGAATGTTTGAAAATCCAA
CTCCAAATATAAT
Found at i:4950890 original size:121 final size:121
Alignment explanation
Indices: 4950676--4950911 Score: 445
Period size: 121 Copynumber: 2.0 Consensus size: 121
4950666 GACGTTCATA
4950676 AGAATTGGATTACCTTGAAATCGCCCTCTTGCGTACTGATTCCTACATGTCAGCTAGGTTTGGCA
1 AGAATTGGATTACCTTGAAATCGCCCTCTTGCGTACTGATTCCTACATGTCAGCTAGGTTTGGCA
4950741 TGACATAGTACTGAGACAAATTAGATTTACCCTGAAATCAGTCCAAATATACCATG
66 TGACATAGTACTGAGACAAATTAGATTTACCCTGAAATCAGTCCAAATATACCATG
* *
4950797 AGAATTGGATTACCTTGAAATCGCCCTCTTGTGTACTGATTCCTACATGTTAGCTAGGTTTGGCA
1 AGAATTGGATTACCTTGAAATCGCCCTCTTGCGTACTGATTCCTACATGTCAGCTAGGTTTGGCA
*
4950862 TGACATAGTACTGTGACAAATTAGATTTACCCTGAAATCAGTCCAAATAT
66 TGACATAGTACTGAGACAAATTAGATTTACCCTGAAATCAGTCCAAATAT
4950912 GTGACGTAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (121 bp):
AGAATTGGATTACCTTGAAATCGCCCTCTTGCGTACTGATTCCTACATGTCAGCTAGGTTTGGCA
TGACATAGTACTGAGACAAATTAGATTTACCCTGAAATCAGTCCAAATATACCATG
Found at i:4957860 original size:51 final size:51
Alignment explanation
Indices: 4957784--4957897 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
4957774 AGTGACAAGC
* * *
4957784 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
*
4957835 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
*
4957886 AACAAGTGATAA
1 GACAAGTGATAA
4957898 ATGTGATCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:4965642 original size:51 final size:51
Alignment explanation
Indices: 4965566--4965679 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
4965556 AGTGACAAGC
* * *
4965566 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
*
4965617 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
4965668 GACAAGTGATAA
1 GACAAGTGATAA
4965680 ATGTGATCAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:4966994 original size:49 final size:49
Alignment explanation
Indices: 4966933--4967196 Score: 200
Period size: 49 Copynumber: 5.6 Consensus size: 49
4966923 ACATTAAAGT
*
4966933 CGATGCCGTGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
* * *
4966982 CGATGCCATGTCCCAGACAGGTCTTACACTG-GTTCTCATCTATCG-GTGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTT-TCATATATCGAG-GC
* * * *
4967031 CGTTGCCATGTCCCAGACAGGTCTTACACTGA--TGC-----GC-AAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
* * * * * * *
4967072 TGACGCCATGTCTCAGATAGGTCTTACACTAAC-TTCTATATCTCAAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTC-ATATATCGAGGC
* * *
4967121 CGATG-CATGTCCCAGACATGTCTTACACTAACTCTT-ATA-AT-GTGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACT-TTCATATATCGAGGC
* *
4967167 CGATG-CATGTCTCAGACATGTCTTACACTG
1 CGATGCCATGTCCCAGACAGGTCTTACACTG
4967197 GCTCACATAC
Statistics
Matches: 173, Mismatches: 28, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
41 27 0.16
42 3 0.02
46 31 0.18
47 2 0.01
48 32 0.18
49 76 0.44
50 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
Found at i:4967183 original size:46 final size:46
Alignment explanation
Indices: 4967078--4967195 Score: 150
Period size: 46 Copynumber: 2.5 Consensus size: 46
4967068 AAGCTGACGC
* *
4967078 CATGTCTCAGATAGGTCTTACACTAACTTCTATATCTCAAGGCCGATG
1 CATGTCTCAGACATGTCTTACACTAACTTCTATATCT--AGGCCGATG
* *
4967126 CATGTCCCAGACATGTCTTACACTAAC-TCTTATAATGT-GGCCGATG
1 CATGTCTCAGACATGTCTTACACTAACTTC-TAT-ATCTAGGCCGATG
4967172 CATGTCTCAGACATGTCTTACACT
1 CATGTCTCAGACATGTCTTACACT
4967196 GGCTCACATA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
46 31 0.49
47 2 0.03
48 27 0.43
49 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (46 bp):
CATGTCTCAGACATGTCTTACACTAACTTCTATATCTAGGCCGATG
Found at i:4977262 original size:12 final size:12
Alignment explanation
Indices: 4977247--4977308 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
4977237 TGTTATCAAT
4977247 TTATTATTATAA
1 TTATTATTATAA
**
4977259 TTATTATTATGG
1 TTATTATTATAA
*
4977271 TTTTTATT-TAA
1 TTATTATTATAA
*
4977282 ATATTATTATTAA
1 TTATTATTA-TAA
4977295 -TATTATTAT-A
1 TTATTATTATAA
4977305 TTAT
1 TTAT
4977309 GAAATAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
10 1 0.03
11 11 0.28
12 25 0.62
13 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TTATTATTATAA
Found at i:4977581 original size:24 final size:23
Alignment explanation
Indices: 4977554--4977610 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
4977544 TATGTATTTG
4977554 TTATTAAATAGATATT-TATTATAA
1 TTATTAAATAG-TATTATATTA-AA
* *
4977578 TTATTATTATAGTTTTATATTAAA
1 TTATTA-AATAGTATTATATTAAA
4977602 TTATTAAAT
1 TTATTAAAT
4977611 TATGATTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.07
24 17 0.61
25 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TTATTAAATAGTATTATATTAAA
Found at i:4977711 original size:5 final size:5
Alignment explanation
Indices: 4977701--4977735 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
4977691 ATATTTATGA
4977701 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
4977736 TATAATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:4977746 original size:10 final size:10
Alignment explanation
Indices: 4977703--4977748 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
4977693 ATTTATGAAT
*
4977703 TATATTATAT
1 TATATTATAA
*
4977713 TATATTATAT
1 TATATTATAA
4977723 TATATTAT-A
1 TATATTATAA
4977732 T-TATTATAA
1 TATATTATAA
*
4977741 TGTATTAT
1 TATATTAT
4977749 TATTATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
8 6 0.18
9 3 0.09
10 24 0.73
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TATATTATAA
Found at i:4978683 original size:70 final size:76
Alignment explanation
Indices: 4978596--4978771 Score: 193
Period size: 70 Copynumber: 2.3 Consensus size: 76
4978586 ATGTGAAGAA
* ** *
4978596 ATTGGAAATTAAAAGTGATTTGAATT-AA-GTAATTGAATT-AT-G-AATTATGTGAATATTTGA
1 ATTGGAAACTAAAAGTGATTTGAATTGAACCAAATTGAATTAATAGAAAATATGTGAATATTTGA
4978656 AA-GTATATTG
66 AATGTATATTG
* *
4978666 ATTGGAAACTAAGAGTGATTTGAATTGAACCAAATTGAATTGAATGAAGAAAATATGTGAGTATT
1 ATTGGAAACTAAAAGTGATTTGAATTGAACCAAATTGAATT-AAT--AGAAAATATGTGAATATT
4978731 TGAAATGTATATTG
63 TGAAATGTATATTG
* * *
4978745 ATTGAAAAGTAATTAGTGATTTGAATT
1 ATTGGAAACTAA-AAGTGATTTGAATT
4978772 TGATTGGAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
70 24 0.28
71 2 0.02
72 9 0.10
74 2 0.02
77 1 0.01
78 18 0.21
79 18 0.21
80 13 0.15
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (76 bp):
ATTGGAAACTAAAAGTGATTTGAATTGAACCAAATTGAATTAATAGAAAATATGTGAATATTTGA
AATGTATATTG
Found at i:4978995 original size:18 final size:18
Alignment explanation
Indices: 4978934--4979009 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
4978924 AGAAAGTGGA
4978934 AAAGTG-AATTTGAATTG
1 AAAGTGAAATTTGAATTG
4978951 -AA-TGAGAA-TTGAATTG
1 AAAGTGA-AATTTGAATTG
*
4978967 AATTGTG-AATTTGAATTG
1 AA-AGTGAAATTTGAATTG
* *
4978985 AAAGTGAAATTGGCATTG
1 AAAGTGAAATTTGAATTG
4979003 AAAGTGA
1 AAAGTGA
4979010 TTTGAAATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
15 2 0.04
16 10 0.21
17 8 0.17
18 26 0.54
19 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33
Consensus pattern (18 bp):
AAAGTGAAATTTGAATTG
Found at i:4979013 original size:34 final size:33
Alignment explanation
Indices: 4978934--4979015 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 33
4978924 AGAAAGTGGA
4978934 AAAGTGAATTTGAATTGAATGAGAATTGAATTG
1 AAAGTGAATTTGAATTGAATGAGAATTGAATTG
* *
4978967 AATTGTGAATTTGAATTGAAAGTGA-AATTGGCATTG
1 AA-AGTGAATTTGAATTG-AA-TGAGAATT-GAATTG
4979003 AAAGTG-ATTTGAA
1 AAAGTGAATTTGAA
4979016 ATGTGAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 2 0.05
34 21 0.50
35 9 0.21
36 10 0.24
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.34
Consensus pattern (33 bp):
AAAGTGAATTTGAATTGAATGAGAATTGAATTG
Found at i:4980943 original size:23 final size:22
Alignment explanation
Indices: 4980894--4980945 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4980884 TAACTTTTAA
* * *
4980894 AATTTTATTATAAATGAGTAAT
1 AATTTTTTTATAAATAAATAAT
4980916 AATTTTTTTATAAATAAATACAT
1 AATTTTTTTATAAATAAATA-AT
*
4980939 TATTTTT
1 AATTTTT
4980946 GTAATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
AATTTTTTTATAAATAAATAAT
Found at i:4994358 original size:45 final size:45
Alignment explanation
Indices: 4994254--4994360 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
4994244 GTAGCAGTAG
* * *
4994254 CAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCTGTAA
1 CAGTAACGGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAA
* *
4994299 CAGTAGCGGTAACAGTATTCGACACACAAAGTG-TCGAATCGGTAA
1 CAGTAACGGTAACAGTATTCAACACACAAAGTGCT-GAATCGGTAA
*
4994344 CAGTAATGGTAACAGTA
1 CAGTAACGGTAACAGTA
4994361 ACAGTAGTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.02
45 53 0.98
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (45 bp):
CAGTAACGGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAA
Found at i:4994364 original size:51 final size:48
Alignment explanation
Indices: 4994255--4994375 Score: 124
Period size: 45 Copynumber: 2.5 Consensus size: 48
4994245 TAGCAGTAGC
* * *
4994255 AGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCTGTAACAGT
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCGGTAACAGT
*
4994303 AG---CGGTAACAGTATTCGACACACAAAGTG-TCGAATCGGTAACAGT
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCT-GAATCGGTAACAGT
* *
4994348 AATGGTAACAGTAACAGTAGTCGGCACA
1 -A--GTAACAGTAACAGTATTCGACACA
4994376 TAAGTGCCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
44 1 0.02
45 37 0.63
46 1 0.02
48 3 0.05
51 17 0.29
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (48 bp):
AGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCGGTAACAGT
Found at i:4999618 original size:16 final size:16
Alignment explanation
Indices: 4999597--4999647 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
4999587 TAAATTATTG
4999597 ATTACAGTTTTATTTC
1 ATTACAGTTTTATTTC
* *
4999613 ATTACAGCTCTA-TTC
1 ATTACAGTTTTATTTC
* *
4999628 AATTACAATCTTATTTC
1 -ATTACAGTTTTATTTC
4999645 ATT
1 ATT
4999648 CGAGTGGACG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (16 bp):
ATTACAGTTTTATTTC
Found at i:5013248 original size:81 final size:81
Alignment explanation
Indices: 5013113--5013274 Score: 297
Period size: 81 Copynumber: 2.0 Consensus size: 81
5013103 CTCTATGATA
* *
5013113 GAGGCATATCTGTTACCCTCTATTACCACTGGTTTTATTTTGTACATTTCTTACCGAACCAATTT
1 GAGGCATATCTGTTACCCTCTATTACCACTAGTTTTATTTTGTACATTTCTTACCAAACCAATTT
5013178 CATGAATGTACAATGC
66 CATGAATGTACAATGC
*
5013194 GAGGCATATCTGTTACCCTCTCTTACCACTAGTTTTATTTTGTACATTTCTTACCAAACCAATTT
1 GAGGCATATCTGTTACCCTCTATTACCACTAGTTTTATTTTGTACATTTCTTACCAAACCAATTT
5013259 CATGAATGTACAATGC
66 CATGAATGTACAATGC
5013275 AGTGTTAAAC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (81 bp):
GAGGCATATCTGTTACCCTCTATTACCACTAGTTTTATTTTGTACATTTCTTACCAAACCAATTT
CATGAATGTACAATGC
Found at i:5019650 original size:77 final size:77
Alignment explanation
Indices: 5019520--5019681 Score: 297
Period size: 77 Copynumber: 2.1 Consensus size: 77
5019510 TTAGTGAAAT
*
5019520 AAAGACACAAAGCTTATATGACTGCAAAGCATATATAATAGCAAATAGCATGCAGCTCCAGCCCA
1 AAAGACACAAAGCTTACATGACTGCAAAGCATATATAATAGCAAATAGCATGCAGCTCCAGCCCA
5019585 TGCAGTTTCAGC
66 TGCAGTTTCAGC
* *
5019597 AAAGACACAAAGCTTACATGACTGCAAAGCATATATAATAGCAAATAGTATGCAGGTCCAGCCCA
1 AAAGACACAAAGCTTACATGACTGCAAAGCATATATAATAGCAAATAGCATGCAGCTCCAGCCCA
5019662 TGCAGTTTCAGC
66 TGCAGTTTCAGC
5019674 AAAGACAC
1 AAAGACAC
5019682 CTGCCGTTCT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (77 bp):
AAAGACACAAAGCTTACATGACTGCAAAGCATATATAATAGCAAATAGCATGCAGCTCCAGCCCA
TGCAGTTTCAGC
Found at i:5024542 original size:61 final size:61
Alignment explanation
Indices: 5024445--5024583 Score: 181
Period size: 61 Copynumber: 2.2 Consensus size: 61
5024435 TGTAAGAATG
* * * *
5024445 TAAATTTTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTCAATAATTT-AGTATTATGTTA
1 TAAATTGTTTTG--TTTTATAATTATTCTAAAATTAATTTATCAATAATTTAAG-ATTATATTA
* *
5024508 TAAATTGTTTTGTTTTGTAATTATTCTAAAATTAATTTATTAATAATTTAAGATTATATTA
1 TAAATTGTTTTGTTTTATAATTATTCTAAAATTAATTTATCAATAATTTAAGATTATATTA
*
5024569 TAAATTGTTGTGTTT
1 TAAATTGTTTTGTTT
5024584 AGTTTAGTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
61 55 0.81
62 2 0.03
63 11 0.16
ACGTcount: A:0.34, C:0.01, G:0.08, T:0.57
Consensus pattern (61 bp):
TAAATTGTTTTGTTTTATAATTATTCTAAAATTAATTTATCAATAATTTAAGATTATATTA
Found at i:5035462 original size:5 final size:5
Alignment explanation
Indices: 5035452--5035478 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5035442 AGTATAAATA
5035452 TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TA
5035479 GTTTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:5035500 original size:9 final size:9
Alignment explanation
Indices: 5035486--5035524 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5035476 TTAGTTTAAT
5035486 AATAAAAGA
1 AATAAAAGA
5035495 AATAAAAGA
1 AATAAAAGA
*
5035504 AATAAAACA
1 AATAAAAGA
*
5035513 ATAGAAAAGA
1 A-ATAAAAGA
5035523 AA
1 AA
5035525 CAGAGAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
AATAAAAGA
Found at i:5035554 original size:17 final size:14
Alignment explanation
Indices: 5035546--5035572 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5035536 AAGAAATAGG
5035546 AAAGAAAAAGAAAT
1 AAAGAAAAAGAAAT
5035560 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
5035573 GGGAGAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAGAAAT
Found at i:5035909 original size:12 final size:12
Alignment explanation
Indices: 5035887--5035925 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5035877 AAGTTGTAAT
5035887 TGAATGAAAATAA
1 TGAA-GAAAATAA
**
5035900 TGAAGAAAATTG
1 TGAAGAAAATAA
5035912 TGAAGAAAATAA
1 TGAAGAAAATAA
5035924 TG
1 TG
5035926 TTAGATTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (12 bp):
TGAAGAAAATAA
Found at i:5038827 original size:47 final size:47
Alignment explanation
Indices: 5038720--5038910 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 47
5038710 AATGTGATTT
* * * * *
5038720 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTTCTT
1 CCGTATAAGACCATATCTGGGATATGGCATC-G-G---TGTGATATGTGCTA
*
5038772 CCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * *
5038819 CTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* ** * *
5038865 CCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
5038911 ACTATGTGCA
Statistics
Matches: 120, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
46 26 0.22
47 54 0.45
48 11 0.09
50 1 0.01
51 1 0.01
52 27 0.22
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:5041702 original size:22 final size:22
Alignment explanation
Indices: 5041660--5041702 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5041650 TAATATAATT
* *
5041660 AAAATATAAAAGTAAATGAAAC
1 AAAATAAAAAAGTAAAAGAAAC
5041682 AAAATAAATAAAG-AAAAGAAA
1 AAAATAAA-AAAGTAAAAGAAA
5041703 AAGAGAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (22 bp):
AAAATAAAAAAGTAAAAGAAAC
Found at i:5042358 original size:51 final size:53
Alignment explanation
Indices: 5042282--5042397 Score: 146
Period size: 51 Copynumber: 2.2 Consensus size: 53
5042272 ATGTGTCGAC
* *
5042282 TACTGTGACCGTTCCGGATTCGTTCCGAAGAGGTAC-TCTGTACC-TGACTGT
1 TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTTCTGTACCGTGACTGT
* * * *
5042333 TACTGTTACTGTTCCGGATTTGTTCCGATGAGGTACTTTGTGTACCGTTACTGT
1 TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTAC-TTCTGTACCGTGACTGT
*
5042387 TACTATTACTG
1 TACTGTTACTG
5042398 ATACAGTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
51 32 0.58
53 7 0.13
54 16 0.29
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (53 bp):
TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTTCTGTACCGTGACTGT
Found at i:5049730 original size:16 final size:16
Alignment explanation
Indices: 5049709--5049742 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5049699 TTGTTGGATA
*
5049709 TGAATGTGTTTAGTAC
1 TGAATGTGCTTAGTAC
5049725 TGAATGTGCTTAGTAC
1 TGAATGTGCTTAGTAC
5049741 TG
1 TG
5049743 TTATCAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (16 bp):
TGAATGTGCTTAGTAC
Found at i:5055255 original size:27 final size:27
Alignment explanation
Indices: 5055225--5055328 Score: 72
Period size: 27 Copynumber: 3.9 Consensus size: 27
5055215 ATTTATAGTA
5055225 TATTAGTTTTGTTATATAAATTTAATT
1 TATTAGTTTTGTTATATAAATTTAATT
* * * *
5055252 TATTTA-TTTAGTTATATCAACTCAATT
1 TA-TTAGTTTTGTTATATAAATTTAATT
* * *
5055279 AATT-GTTTTATT-TAT-AATATTAATA
1 TATTAGTTTTGTTATATAAAT-TTAATT
* * *
5055304 TATTAATTATGTTACATAAATTTAA
1 TATTAGTTTTGTTATATAAATTTAA
5055329 AAAAAAAATT
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
24 2 0.04
25 10 0.18
26 12 0.21
27 26 0.46
28 6 0.11
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (27 bp):
TATTAGTTTTGTTATATAAATTTAATT
Found at i:5059704 original size:46 final size:45
Alignment explanation
Indices: 5059651--5059823 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
5059641 TTGGGCATCT
5059651 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
*** * *
5059697 GAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCC
*
5059744 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
* *
5059789 TGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 -GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5059824 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 63 0.59
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCC
Found at i:5059803 original size:93 final size:93
Alignment explanation
Indices: 5059644--5059816 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
5059634 AGGATATTTG
* *
5059644 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
5059709 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
5059737 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGA
5059801 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
5059817 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:5062330 original size:3 final size:3
Alignment explanation
Indices: 5062322--5062365 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
5062312 AAATAGCCTC
* * * *
5062322 AAT AAT AAT AAT AAT AAT GAT GAT AAT ATT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5062366 GTAGTCTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5062681 original size:3 final size:3
Alignment explanation
Indices: 5062673--5062866 Score: 84
Period size: 3 Copynumber: 65.3 Consensus size: 3
5062663 ATGGTTTTAA
5062673 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAGGT AA- AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT AAT
* * * * * * *
5062718 AAT AA- AA- AAGC ACT ATT ACGT CACT ACT ACT AAT AAT AAT AAT AA-
1 AAT AAT AAT AA-T AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
5062763 AAG AA- AAC AGT AAT -AT TAT ATAG AAT AAT AGT AA- ATGT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT -AAT
* * *
5062808 AAT AAT AAT AAT AGT AAT AA- AAT AAT AAT AAT ACT AAT -AT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5062854 AAT AAT AAA AAT A
1 AAT AAT AAT AAT A
5062867 GCACTCTCCC
Statistics
Matches: 150, Mismatches: 24, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
2 19 0.13
3 118 0.79
4 9 0.06
5 4 0.03
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:5062814 original size:22 final size:23
Alignment explanation
Indices: 5062805--5062867 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
5062795 AAATGTAATA
5062805 AATAATAATAATAATAGTAATAA
1 AATAATAATAATAATAGTAATAA
* *
5062828 AATAATAATAATACTAAT-ATAA
1 AATAATAATAATAATAGTAATAA
* *
5062850 TAACAATAATAAAAATAG
1 -AATAATAATAATAATAG
5062868 CACTCTCCCC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (23 bp):
AATAATAATAATAATAGTAATAA
Found at i:5062866 original size:20 final size:20
Alignment explanation
Indices: 5062673--5062866 Score: 83
Period size: 20 Copynumber: 9.5 Consensus size: 20
5062663 ATGGTTTTAA
5062673 AATAATAATAATAATAATAAT
1 AATAATAAT-ATAATAATAAT
**
5062694 AATAATAAGGTAA-AATAAT
1 AATAATAATATAATAATAAT
* * *
5062713 AATAA-AATA-AAAAAGCACT
1 AATAATAATATAATAA-TAAT
* * * *
5062732 ATTACGTCACTACTACTAATAAT
1 AATA-AT-AATA-TAATAATAAT
* * * *
5062755 AATAATAAAAGAA-AACAGT
1 AATAATAATATAATAATAAT
* * *
5062774 AATATTATATAGAATAATAGT
1 AATAATA-ATATAATAATAAT
5062795 AAATGTAATAA-ATAATAATAAT
1 -AA--TAATAATATAATAATAAT
* *
5062817 AATAGTAATAAAATAATAAT
1 AATAATAATATAATAATAAT
* *
5062837 AATACTAATATAATAACAAT
1 AATAATAATATAATAATAAT
*
5062857 AATAAAAATA
1 AATAATAATA
5062867 GCACTCTCCC
Statistics
Matches: 126, Mismatches: 34, Indels: 27
0.67 0.18 0.14
Matches are distributed among these distances:
17 2 0.02
18 4 0.03
19 31 0.25
20 44 0.35
21 17 0.13
22 15 0.12
23 6 0.05
24 7 0.06
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AATAATAATATAATAATAAT
Found at i:5064416 original size:21 final size:21
Alignment explanation
Indices: 5064385--5064610 Score: 196
Period size: 21 Copynumber: 11.0 Consensus size: 21
5064375 TTTTACTTTA
5064385 TGTTCAGCTCTTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* * *
5064406 TATTCAACTCTTATGAGTTTC
1 TGTTCAGCTCTTATGAGCTTC
* *
5064427 TGTTTAGCTCTTACGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* * * *
5064448 TATTTAGCT-TT-CGAGCTTT
1 TGTTCAGCTCTTATGAGCTTC
* *
5064467 TGTTCAACTCTTATGAGTTTC
1 TGTTCAGCTCTTATGAGCTTC
* * *
5064488 TGTTTAGCTCTTACGAGCTTA
1 TGTTCAGCTCTTATGAGCTTC
5064509 TGTTCAGCT-TT-TGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* * *
5064528 TGTTCAACTCTTATGAGTTTT
1 TGTTCAGCTCTTATGAGCTTC
* *
5064549 TGTTTAGCTATTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* *
5064570 TATTCAG-T-TT-TCGAGTTTC
1 TGTTCAGCTCTTAT-GAGCTTC
*
5064589 TGTTCAGCTCTTACGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
5064610 T
1 T
5064611 ATTGGTGTAT
Statistics
Matches: 159, Mismatches: 38, Indels: 16
0.75 0.18 0.08
Matches are distributed among these distances:
18 1 0.01
19 41 0.26
20 10 0.06
21 107 0.67
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (21 bp):
TGTTCAGCTCTTATGAGCTTC
Found at i:5064494 original size:40 final size:42
Alignment explanation
Indices: 5064382--5064610 Score: 155
Period size: 40 Copynumber: 5.6 Consensus size: 42
5064372 GTGTTTTACT
* * * * * *
5064382 TTATGTTCAGCTCTTATGAGCTTCTATTCAACTCTTATGAGT
1 TTATGTTCAACTCTTATGAGCTTCTGTTTAGCTCTTACGAGC
* * * * *
5064424 TTCTGTTTAGCTCTTACGAGCTTCTATTTAGCT-TT-CGAGC
1 TTATGTTCAACTCTTATGAGCTTCTGTTTAGCTCTTACGAGC
* *
5064464 TTTTGTTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGC
1 TTATGTTCAACTCTTATGAGCTTCTGTTTAGCTCTTACGAGC
* * * * *
5064506 TTATGTTCAGCT-TT-TGAGCTTCTGTTCAACTCTTATGAGT
1 TTATGTTCAACTCTTATGAGCTTCTGTTTAGCTCTTACGAGC
* * * * * * * *
5064546 TTTTGTTTAGCTATTATGAGCTTCTATTCAG-T-TTTCGAGT
1 TTATGTTCAACTCTTATGAGCTTCTGTTTAGCTCTTACGAGC
* * *
5064586 TTCTGTTCAGCTCTTACGAGCTTCT
1 TTATGTTCAACTCTTATGAGCTTCT
5064611 ATTGGTGTAT
Statistics
Matches: 153, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
40 88 0.58
41 9 0.06
42 56 0.37
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (42 bp):
TTATGTTCAACTCTTATGAGCTTCTGTTTAGCTCTTACGAGC
Found at i:5064494 original size:61 final size:61
Alignment explanation
Indices: 5064399--5064610 Score: 298
Period size: 61 Copynumber: 3.5 Consensus size: 61
5064389 CAGCTCTTAT
* *
5064399 GAGCTTCTATTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGCTTCTATTTAGCTTTC
1 GAGCTTCTGTTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
* * * *
5064460 GAGCTTTTGTTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGCTTATGTTCAGCTTTT
1 GAGCTTCTGTTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
* * * *
5064521 GAGCTTCTGTTCAACTCTTATGAGTTTTTGTTTAGCTATTATGAGCTTCTATTCAGTTTTC
1 GAGCTTCTGTTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
* * * *
5064582 GAGTTTCTGTTCAGCTCTTACGAGCTTCT
1 GAGCTTCTGTTCAACTCTTATGAGTTTCT
5064611 ATTGGTGTAT
Statistics
Matches: 132, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 132 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (61 bp):
GAGCTTCTGTTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
Found at i:5067743 original size:4 final size:4
Alignment explanation
Indices: 5067734--5067770 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
5067724 TTTAATAATA
5067734 AAAT AAAT AAAT AAAT GAAAT AAAT AAAT GAAAT AAA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AAA
5067771 AGAAATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5067744 original size:9 final size:9
Alignment explanation
Indices: 5067730--5067781 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
5067720 ATAGTTTAAT
5067730 AATAAAATA
1 AATAAAATA
5067739 AAT-AAATA
1 AATAAAATA
*
5067747 AATGAAATA
1 AATAAAATA
5067756 AAT-AAATGA
1 AATAAAAT-A
*
5067765 AATAAAAGA
1 AATAAAATA
5067774 AATGAAAA
1 AAT-AAAA
5067782 AGAAAAACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 12 0.32
9 19 0.50
10 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:5067748 original size:13 final size:13
Alignment explanation
Indices: 5067734--5067780 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
5067724 TTTAATAATA
5067734 AAAT-AAATAAAT
1 AAATGAAATAAAT
5067746 AAATGAAATAAAT
1 AAATGAAATAAAT
*
5067759 AAATGAAATAAAAG
1 AAATGAAAT-AAAT
5067773 AAATGAAA
1 AAATGAAA
5067781 AAGAAAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 4 0.12
13 17 0.53
14 11 0.34
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (13 bp):
AAATGAAATAAAT
Found at i:5067756 original size:17 final size:18
Alignment explanation
Indices: 5067734--5067767 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5067724 TTTAATAATA
5067734 AAATAAATAAAT-AAATG
1 AAATAAATAAATGAAATG
5067751 AAATAAATAAATGAAAT
1 AAATAAATAAATGAAAT
5067768 AAAAGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (18 bp):
AAATAAATAAATGAAATG
Found at i:5069071 original size:15 final size:15
Alignment explanation
Indices: 5069030--5069076 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5069020 GAATTTATCA
5069030 AATTTATATTGATTG
1 AATTTATATTGATTG
* * *
5069045 AAATCATTTTGATTG
1 AATTTATATTGATTG
*
5069060 AATTTATATTGACTG
1 AATTTATATTGATTG
5069075 AA
1 AA
5069077 ATATATATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (15 bp):
AATTTATATTGATTG
Found at i:5069739 original size:18 final size:19
Alignment explanation
Indices: 5069716--5069756 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5069706 AATGAAATGA
5069716 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5069734 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5069753 GAAA
1 GAAA
5069757 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5075711 original size:20 final size:20
Alignment explanation
Indices: 5075686--5075725 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5075676 CTCACTACTT
5075686 TGACAAAAGGGACGGGGCTA
1 TGACAAAAGGGACGGGGCTA
*
5075706 TGACAAAAGGGATGGGGCTA
1 TGACAAAAGGGACGGGGCTA
5075726 GTAAAAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.40, T:0.12
Consensus pattern (20 bp):
TGACAAAAGGGACGGGGCTA
Found at i:5080419 original size:13 final size:13
Alignment explanation
Indices: 5080401--5080425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5080391 TATACTTCTT
5080401 TAAAAAAGTCCTA
1 TAAAAAAGTCCTA
5080414 TAAAAAAGTCCT
1 TAAAAAAGTCCT
5080426 GTCTATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (13 bp):
TAAAAAAGTCCTA
Found at i:5105156 original size:30 final size:30
Alignment explanation
Indices: 5105120--5105178 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
5105110 CATCTGCAAA
5105120 GATGTTTTAACTCTATAGTTATTCAGGATT
1 GATGTTTTAACTCTATAGTTATTCAGGATT
5105150 GATGTTTTAACTCTATAGTTATTCAGGAT
1 GATGTTTTAACTCTATAGTTATTCAGGAT
5105179 AACCAATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (30 bp):
GATGTTTTAACTCTATAGTTATTCAGGATT
Found at i:5110013 original size:9 final size:9
Alignment explanation
Indices: 5109989--5110035 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
5109979 TGGCTGAAGC
5109989 TCTTCCTCT
1 TCTTCCTCT
* *
5109998 TCATCCTCG
1 TCTTCCTCT
5110007 TCTTCCTCT
1 TCTTCCTCT
*
5110016 TCTTCTTCT
1 TCTTCCTCT
*
5110025 TCCTCCTCT
1 TCTTCCTCT
5110034 TC
1 TC
5110036 CTCACCATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.51
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:5110022 original size:24 final size:24
Alignment explanation
Indices: 5109988--5110038 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5109978 GTGGCTGAAG
*
5109988 CTCTTCCTCTTCATCCTCGTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
* *
5110012 CTCTTCTTCTTCTTCCTCCTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
5110036 CTC
1 CTC
5110039 ACCATCATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (24 bp):
CTCTTCCTCTTCATCCTCCTCTTC
Found at i:5110061 original size:12 final size:12
Alignment explanation
Indices: 5110041--5110083 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5110031 TCTTCCTCAC
*
5110041 CATCATCGTCGT
1 CATCATCGTCAT
*
5110053 CATCGTCGTCAT
1 CATCATCGTCAT
*
5110065 CATCCTCGTCAT
1 CATCATCGTCAT
5110077 CATCATC
1 CATCATC
5110084 CTCGTCTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.19, C:0.37, G:0.12, T:0.33
Consensus pattern (12 bp):
CATCATCGTCAT
Found at i:5110079 original size:15 final size:15
Alignment explanation
Indices: 5110055--5110089 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5110045 ATCGTCGTCA
*
5110055 TCGTCGTCATCATCC
1 TCGTCATCATCATCC
5110070 TCGTCATCATCATCC
1 TCGTCATCATCATCC
5110085 TCGTC
1 TCGTC
5110090 TCCACTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.40, G:0.11, T:0.34
Consensus pattern (15 bp):
TCGTCATCATCATCC
Found at i:5110187 original size:21 final size:21
Alignment explanation
Indices: 5110163--5110202 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5110153 TGCATCCTCC
5110163 TCATCTGCAT-CTTCATCTTGA
1 TCATCT-CATGCTTCATCTTGA
*
5110184 TCATCTCCTGCTTCATCTT
1 TCATCTCATGCTTCATCTT
5110203 TCTCATCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.45
Consensus pattern (21 bp):
TCATCTCATGCTTCATCTTGA
Found at i:5115410 original size:89 final size:90
Alignment explanation
Indices: 5115242--5115423 Score: 312
Period size: 89 Copynumber: 2.0 Consensus size: 90
5115232 AGCTACGTCC
* *
5115242 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATGACGAAATAACT
1 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTA---TTCTTCATATCAATAAAGAAATAACT
5115307 ATTCAATCATAACTAACCTTGATGGTCT
63 ATTCAATCATAACTAACCTTGATGGTCT
5115335 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTA-TCTTCATATCAATAAAGAAATAACTATT
1 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTCTTCATATCAATAAAGAAATAACTATT
5115399 CAATCATAACTAACCTTGATGGTCT
66 CAATCATAACTAACCTTGATGGTCT
5115424 TGTCATCACC
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
89 51 0.59
93 36 0.41
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (90 bp):
CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTCTTCATATCAATAAAGAAATAACTATT
CAATCATAACTAACCTTGATGGTCT
Found at i:5120182 original size:18 final size:17
Alignment explanation
Indices: 5120140--5120188 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
5120130 AAAAAGTTCA
5120140 TAAATATTTTTAAAAATT
1 TAAAT-TTTTTAAAAATT
*
5120158 AATAATTTTTTAAAAATTT
1 TA-AATTTTTTAAAAA-TT
5120177 TAAATTATTTTA
1 TAAATT-TTTTA
5120189 CCATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTTTTAAAAATT
Found at i:5126685 original size:17 final size:17
Alignment explanation
Indices: 5126663--5126695 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5126653 ATTTTTTTAA
5126663 TAAATAATTA-TTAAATT
1 TAAAT-ATTAGTTAAATT
5126680 TAAATATTAGTTAAAT
1 TAAATATTAGTTAAAT
5126696 CAGATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAATATTAGTTAAATT
Found at i:5127963 original size:24 final size:24
Alignment explanation
Indices: 5127931--5127979 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5127921 ATAAAAGAAG
5127931 TTGAAGAGTAAAAAGCTTTACCTA
1 TTGAAGAGTAAAAAGCTTTACCTA
5127955 TTGAAGAGTAAAAAGCTTTACCTA
1 TTGAAGAGTAAAAAGCTTTACCTA
5127979 T
1 T
5127980 CTTAGTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (24 bp):
TTGAAGAGTAAAAAGCTTTACCTA
Found at i:5144718 original size:39 final size:40
Alignment explanation
Indices: 5144675--5144786 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 40
5144665 TCGGATAGTT
*
5144675 CGAAGTAATAGTTGACACCCAGTGTCTCATC-AGCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
** * ** * *
5144714 CGAAGTAA-AGTTGGTACCCGGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
5144753 CGAAGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT--TGACACCCAGTGTCTCATCGA
5144787 CTCGAGGTCG
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
38 17 0.31
39 21 0.38
40 1 0.02
41 16 0.29
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:5149986 original size:19 final size:20
Alignment explanation
Indices: 5149950--5149989 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5149940 AAAATAATAT
*
5149950 AAAATTTTAAAGTATTTATA
1 AAAATTTCAAAGTATTTATA
*
5149970 AAAATTTCAAA-TTTTTATA
1 AAAATTTCAAAGTATTTATA
5149989 A
1 A
5149990 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATTTCAAAGTATTTATA
Found at i:5152596 original size:16 final size:16
Alignment explanation
Indices: 5152577--5152627 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
5152567 AGAGTGAAAT
5152577 AAAATTAGAAAAATAA
1 AAAATTAGAAAAATAA
**
5152593 AAAATT-GAAAGGTTAA
1 AAAATTAGAAA-AATAA
5152609 AAAA-TAGAAAAATAA
1 AAAATTAGAAAAATAA
5152624 AAAA
1 AAAA
5152628 ATTTCATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.18
Consensus pattern (16 bp):
AAAATTAGAAAAATAA
Found at i:5152629 original size:16 final size:15
Alignment explanation
Indices: 5152573--5152627 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
5152563 TGATAGAGTG
*
5152573 AAAT-AAAATTAGAA
1 AAATAAAAAATAGAA
*
5152587 AAATAAAAAATTGAA
1 AAATAAAAAATAGAA
**
5152602 AGGTTAAAAAATAGAA
1 A-AATAAAAAATAGAA
5152618 AAATAAAAAA
1 AAATAAAAAA
5152628 ATTTCATCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 4 0.12
15 16 0.50
16 12 0.38
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
AAATAAAAAATAGAA
Found at i:5165675 original size:20 final size:19
Alignment explanation
Indices: 5165629--5165681 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
5165619 TCATTTCAAA
*
5165629 CCAACTTATACAT-ATATT
1 CCAACATATACATGATATT
*
5165647 CAAATCATATACATGATATT
1 CCAA-CATATACATGATATT
5165667 GCCAACATATA-ATGA
1 -CCAACATATACATGA
5165682 CATACCATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 11 0.38
21 3 0.10
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (19 bp):
CCAACATATACATGATATT
Found at i:5168147 original size:47 final size:47
Alignment explanation
Indices: 5168031--5168149 Score: 114
Period size: 47 Copynumber: 2.5 Consensus size: 47
5168021 TCTTGAGTTA
* ** * *
5168031 ATGAGGCACTATAAGTGTCGTACTGTTACTGTTATTTCGGTTTAATCTG
1 ATGAGGCAC--TAAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGCCG
* * ** *
5168080 ATGAGGTACTGAGTACCGTACTGTTACTATTTACTTCGG-CAAAGCCG
1 ATGAGGCACTAAGTGTCGTACTGTTACT-GTTACTTCGGTCAAAGCCG
5168127 ATGAGGCACTAAGTGTCGTACTG
1 ATGAGGCACTAAGTGTCGTACTG
5168150 GTGTGTTGGT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
47 39 0.71
48 8 0.15
49 8 0.15
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (47 bp):
ATGAGGCACTAAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGCCG
Found at i:5171657 original size:38 final size:39
Alignment explanation
Indices: 5171573--5171707 Score: 107
Period size: 39 Copynumber: 3.4 Consensus size: 39
5171563 ACCAATATGG
*
5171573 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
5171612 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * * *
5171650 TACCCAGTACCTTATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
5171691 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5171708 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
38 18 0.25
39 36 0.49
40 4 0.05
41 15 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:5172833 original size:5 final size:5
Alignment explanation
Indices: 5172823--5172860 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
5172813 TTTATATATA
5172823 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
5172861 CTTAATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:5177475 original size:6 final size:6
Alignment explanation
Indices: 5177466--5177499 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5177456 ATAGTCTTAG
5177466 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTT
5177500 GTCAGTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTTC
Found at i:5188840 original size:50 final size:50
Alignment explanation
Indices: 5188765--5189041 Score: 446
Period size: 50 Copynumber: 5.5 Consensus size: 50
5188755 CCATGGCAAC
* *
5188765 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
5188815 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
5188865 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
5188915 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
5188965 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
5189016 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
5189042 CTGATCAATG
Statistics
Matches: 210, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 187 0.89
51 23 0.11
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:5189059 original size:31 final size:31
Alignment explanation
Indices: 5189021--5189079 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
5189011 ATGGCAAGTA
5189021 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
5189052 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
5189080 TCAGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:5189129 original size:31 final size:31
Alignment explanation
Indices: 5189083--5189149 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
5189073 CTGATCATCA
* * *
5189083 GCTACTTGATTAGTGAAAAATGGTAGCTCCG
1 GCTACCTGATCAGTGAAAAATGATAGCTCCG
* * *
5189114 GCTACCTGATCAGTGAATAGTGATAGCTTCG
1 GCTACCTGATCAGTGAAAAATGATAGCTCCG
5189145 GCTAC
1 GCTAC
5189150 AAGTGACAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (31 bp):
GCTACCTGATCAGTGAAAAATGATAGCTCCG
Found at i:5194036 original size:50 final size:50
Alignment explanation
Indices: 5193961--5194287 Score: 564
Period size: 50 Copynumber: 6.5 Consensus size: 50
5193951 CCATGGCAAC
* *
5193961 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
5194011 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
5194061 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
5194111 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
5194161 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
5194211 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
5194262 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
5194288 CTGATCAATG
Statistics
Matches: 264, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
50 241 0.91
51 23 0.09
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:5194305 original size:31 final size:31
Alignment explanation
Indices: 5194267--5194325 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
5194257 ATGGCAAGTA
5194267 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
5194298 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
5194326 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:5194333 original size:46 final size:46
Alignment explanation
Indices: 5194280--5194371 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
5194270 AGTGGTAGCT
* *
5194280 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* * *
5194326 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
5194372 GTGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:5194375 original size:31 final size:31
Alignment explanation
Indices: 5194327--5194395 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
5194317 ACCTGATCAT
* * *
5194327 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
5194358 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
5194389 CGGCTAC
1 CGGCTAC
5194396 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:5196489 original size:38 final size:39
Alignment explanation
Indices: 5196405--5196498 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
5196395 ACAAATATGG
*
5196405 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
5196444 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* *
5196482 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
5196499 AATCTATCCG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
38 19 0.40
39 25 0.53
40 3 0.06
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:5202910 original size:8 final size:8
Alignment explanation
Indices: 5202897--5202925 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5202887 TATGGTCTTG
5202897 CACATAGT
1 CACATAGT
5202905 CACATAGT
1 CACATAGT
5202913 CACATA-T
1 CACATAGT
5202920 CACATA
1 CACATA
5202926 CCGAGGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (8 bp):
CACATAGT
Found at i:5217381 original size:36 final size:36
Alignment explanation
Indices: 5217341--5217414 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5217331 TCATTACAGT
5217341 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
1 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
5217377 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
1 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
5217413 AG
1 AG
5217415 AAACAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (36 bp):
AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
Found at i:5222719 original size:39 final size:37
Alignment explanation
Indices: 5222652--5222744 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
5222642 ACCAGAATGG
* *
5222652 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
5222691 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
5222728 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
5222745 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:5223108 original size:3 final size:3
Alignment explanation
Indices: 5223100--5223135 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5223090 ATTCCCACTC
* *
5223100 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5223136 CTTACCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5223117 original size:12 final size:12
Alignment explanation
Indices: 5223100--5223135 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5223090 ATTCCCACTC
*
5223100 ATAATAATAATA
1 ATAATACTAATA
5223112 ATAATACTAATA
1 ATAATACTAATA
5223124 ATAATACTAATA
1 ATAATACTAATA
5223136 CTTACCTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:5223803 original size:11 final size:11
Alignment explanation
Indices: 5223789--5223814 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5223779 CTTTTTCTTC
5223789 TTTCTCCCCTG
1 TTTCTCCCCTG
5223800 TTTCTCCCCTG
1 TTTCTCCCCTG
5223811 TTTC
1 TTTC
5223815 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:5224196 original size:21 final size:21
Alignment explanation
Indices: 5224172--5224214 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5224162 AATAATAACT
5224172 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
5224193 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
5224214 A
1 A
5224215 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:5249202 original size:96 final size:96
Alignment explanation
Indices: 5249038--5249230 Score: 305
Period size: 96 Copynumber: 2.0 Consensus size: 96
5249028 TCAAGTTTAG
* * * *
5249038 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATGGTCCAAC
1 TGAAGATGAAAACTTAGCAATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
*
5249103 CTAGTCGACAGGGAAGTTACATTCCTGATAA
66 CTAGGCGACAGGGAAGTTACATTCCTGATAA
* *
5249134 TGAAGATGAAAACTTTGCAATGGAACCATCGGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
1 TGAAGATGAAAACTTAGCAATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
* *
5249199 CTAGGCGACAGGGAAGTTATATTCCTGGTAA
66 CTAGGCGACAGGGAAGTTACATTCCTGATAA
5249230 T
1 T
5249231 CTTGGCTCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (96 bp):
TGAAGATGAAAACTTAGCAATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
CTAGGCGACAGGGAAGTTACATTCCTGATAA
Found at i:5268761 original size:4 final size:4
Alignment explanation
Indices: 5268752--5268777 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5268742 TTGTCAATTG
5268752 CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
5268778 ATCAAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:5272411 original size:12 final size:12
Alignment explanation
Indices: 5272387--5272430 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5272377 GGACGTTTTG
*
5272387 GGAGGAGGAGGA
1 GGAGGAGGCGGA
*
5272399 GGAGGCGGCGGA
1 GGAGGAGGCGGA
*
5272411 GGCGGAGGCGGA
1 GGAGGAGGCGGA
5272423 GGAAGGAG
1 GG-AGGAG
5272431 AACCTTGATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.25, C:0.09, G:0.66, T:0.00
Consensus pattern (12 bp):
GGAGGAGGCGGA
Found at i:5275915 original size:20 final size:21
Alignment explanation
Indices: 5275890--5275929 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5275880 CGTTGAGTTT
*
5275890 GTGGCA-GGGTCTCAAGGATA
1 GTGGCATGGATCTCAAGGATA
5275910 GTGGCATTGGATCTCAAGGA
1 GTGGCA-TGGATCTCAAGGA
5275930 ATCACCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.23
Consensus pattern (21 bp):
GTGGCATGGATCTCAAGGATA
Found at i:5278336 original size:21 final size:19
Alignment explanation
Indices: 5278311--5278349 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
5278301 AAATTATATG
5278311 AATAAAAAATGATCTTTTAAT
1 AATAAAAAATG-T-TTTTAAT
*
5278332 AATAAATAATGTTTTTAA
1 AATAAAAAATGTTTTTAA
5278350 CTATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
AATAAAAAATGTTTTTAAT
Found at i:5278828 original size:59 final size:58
Alignment explanation
Indices: 5278752--5278864 Score: 208
Period size: 59 Copynumber: 1.9 Consensus size: 58
5278742 ATGTTTTTCT
*
5278752 ATAACCAATTAGGAGTAAACAATTATTAAATACCCCGTCAATCATCTTGTTCATAATC
1 ATAACCAATTAGGAGTAAACAATTATTAAATACCCCGTCAATCATCTTCTTCATAATC
5278810 ATAACCAAATTAGGAGTAAACAATTATTAAATACCCCGTCAATCATCTTCTTCAT
1 ATAACC-AATTAGGAGTAAACAATTATTAAATACCCCGTCAATCATCTTCTTCAT
5278865 GTCAATTATG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 6 0.11
59 47 0.89
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (58 bp):
ATAACCAATTAGGAGTAAACAATTATTAAATACCCCGTCAATCATCTTCTTCATAATC
Found at i:5279817 original size:11 final size:11
Alignment explanation
Indices: 5279794--5279826 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
5279784 AACCAGTTCA
5279794 ATTAAATAAATT
1 ATTAAA-AAATT
5279806 ATTAAAAAATT
1 ATTAAAAAATT
5279817 ATTAAAAAAT
1 ATTAAAAAAT
5279827 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:5302930 original size:6 final size:6
Alignment explanation
Indices: 5302919--5302945 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5302909 GGTGCTGCTG
5302919 ATGCAA ATGCAA ATGCAA ATGCAA ATG
1 ATGCAA ATGCAA ATGCAA ATGCAA ATG
5302946 GGTGCTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:5327440 original size:21 final size:21
Alignment explanation
Indices: 5327414--5327457 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5327404 ATAAGAACAA
5327414 AAACTAGTATTTAATTCAAAC
1 AAACTAGTATTTAATTCAAAC
5327435 AAACTAGTATTTAATTCAAAC
1 AAACTAGTATTTAATTCAAAC
5327456 AA
1 AA
5327458 CTGATTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.32
Consensus pattern (21 bp):
AAACTAGTATTTAATTCAAAC
Found at i:5332009 original size:6 final size:6
Alignment explanation
Indices: 5331998--5332027 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5331988 ATGATTAAAT
5331998 TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA
5332028 AACTCTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:5341617 original size:17 final size:18
Alignment explanation
Indices: 5341581--5341618 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5341571 TATCATTCTT
*
5341581 TTATTTTGCTTGAGGGTA
1 TTATTTTGCTTCAGGGTA
*
5341599 TTATTTTG-TTCATGGTA
1 TTATTTTGCTTCAGGGTA
5341616 TTA
1 TTA
5341619 CCTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.55
Consensus pattern (18 bp):
TTATTTTGCTTCAGGGTA
Found at i:5344333 original size:75 final size:75
Alignment explanation
Indices: 5344160--5344335 Score: 235
Period size: 75 Copynumber: 2.3 Consensus size: 75
5344150 AAGCCACGTT
* * * * * *
5344160 AGGGAGTGGCGGAGGAGGAGGGGAAGCTGAAGATGAATTATTTACGGTAGAAAATGGAGATATAG
1 AGGGAGTGGCGGAGGGGGAGGGGGAGCTGAAAACGAATTATTTACAGAAGAAAATGGAGATATAG
5344225 CTGAGAATGG
66 CTGAGAATGG
* * * *
5344235 AGGGAGTGGGGGAGGGGGAGGGGGAGCTGAAAACGAATTCTTTACAGAAGAAGATGGAGATGTAG
1 AGGGAGTGGCGGAGGGGGAGGGGGAGCTGAAAACGAATTATTTACAGAAGAAAATGGAGATATAG
*
5344300 CTGAGGATGG
66 CTGAGAATGG
* *
5344310 AGGGAGTGGTGGTGGGGGAGGGGGAG
1 AGGGAGTGGCGGAGGGGGAGGGGGAG
5344336 ACTGGCACAA
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.30, C:0.05, G:0.48, T:0.16
Consensus pattern (75 bp):
AGGGAGTGGCGGAGGGGGAGGGGGAGCTGAAAACGAATTATTTACAGAAGAAAATGGAGATATAG
CTGAGAATGG
Found at i:5349055 original size:22 final size:22
Alignment explanation
Indices: 5349030--5349083 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5349020 ATTTAAGAAT
5349030 AAATTAAAAATTATAA-TGATTA
1 AAATTAAAAA-TATAATTGATTA
*
5349052 AAATTCAAAATATAATTGATTA
1 AAATTAAAAATATAATTGATTA
*
5349074 AAATTTAAAA
1 AAATTAAAAA
5349084 CATTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATTAAAAATATAATTGATTA
Found at i:5354055 original size:47 final size:47
Alignment explanation
Indices: 5353946--5354056 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
5353936 CCAGGATAAG
*
5353946 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
5353993 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
5354040 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
5354057 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:5354828 original size:4 final size:4
Alignment explanation
Indices: 5354819--5354847 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5354809 CCCTTTTCTA
5354819 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
5354848 CACGTTTGCT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Done.