Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 163 of 343
Found at i:53897834 original size:48 final size:48
Alignment explanation
Indices: 53897763--53897940 Score: 174
Period size: 48 Copynumber: 3.8 Consensus size: 48
53897753 ACCACAGTTA
53897763 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGAT
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGAT
* **
53897811 ATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCACCGTTGAT
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGAT
* * * * * *
53897859 ACGTA-TGCTACTGTAAGACCATTTCTGGG--AT---AT-GGCATTGAT
1 ATG-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGAT
* **
53897901 ATGAAATATC-GTGTAAGACCATGTCTGGGACATGGCATCG
1 ATGAGA-GCCAGTGTAAGACCATGTCTGGGACATGGCATCG
53897941 ATGTGAGGCC
Statistics
Matches: 102, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
41 1 0.01
42 25 0.25
43 2 0.02
44 2 0.02
46 2 0.02
47 2 0.02
48 67 0.66
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (48 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGAT
Found at i:53898050 original size:90 final size:89
Alignment explanation
Indices: 53897901--53898068 Score: 205
Period size: 90 Copynumber: 1.9 Consensus size: 89
53897891 TGGCATTGAT
* * * * *
53897901 ATGAAATATCGTGTAAGACCATGTCTGGGACATGGCATCGATGTGAGGCCCCGTATAAGAACATG
1 ATGAAATATCGTGTAAGACCATATATGGGACATGGCATCGATGT-AGGACCCATATAAGAACACG
*
53897966 TCTGGGACATGGCATCGGCGCCGAC
65 TCAGGGACATGGCATCGGCGCCGAC
* * *
53897991 ATGAAACT-TCGTGTAAGACCATATATGGGATATGGCATCGGCATGT-GGACCCATGTAAGACCA
1 ATGAAA-TATCGTGTAAGACCATATATGGGACATGGCATC-G-ATGTAGGACCCATATAAGAACA
53898054 CGTCAGGGACATGGC
63 CGTCAGGGACATGGC
53898069 TTTGGCATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
90 60 0.91
91 2 0.03
92 4 0.06
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (89 bp):
ATGAAATATCGTGTAAGACCATATATGGGACATGGCATCGATGTAGGACCCATATAAGAACACGT
CAGGGACATGGCATCGGCGCCGAC
Found at i:53899988 original size:47 final size:47
Alignment explanation
Indices: 53899925--53900029 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
53899915 CCCTTCGGGA
* *
53899925 CTTATCACATTTATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
53899972 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
*
53900019 CTTACCACATA
1 CTTATCACATA
53900030 ATTAATACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:53909789 original size:29 final size:29
Alignment explanation
Indices: 53909750--53909809 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
53909740 ACTCACTATA
53909750 TATATATGATTTAAATAATAGTGATGAGT
1 TATATATGATTTAAATAATAGTGATGAGT
53909779 TATATATGATTTAAATAATAGTGATGAGT
1 TATATATGATTTAAATAATAGTGATGAGT
53909808 TA
1 TA
53909810 ATAGGTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (29 bp):
TATATATGATTTAAATAATAGTGATGAGT
Found at i:53909810 original size:18 final size:18
Alignment explanation
Indices: 53909755--53909810 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
53909745 CTATATATAT
*
53909755 ATGATTTAAATAATAGTG
1 ATGAGTTAAATAATAGTG
53909773 ATGAGTT--AT-ATA-TG
1 ATGAGTTAAATAATAGTG
53909787 AT---TTAAATAATAGTG
1 ATGAGTTAAATAATAGTG
53909802 ATGAGTTAA
1 ATGAGTTAA
53909811 TAGGTTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 14
0.67 0.02 0.31
Matches are distributed among these distances:
11 2 0.07
13 2 0.07
14 7 0.23
15 7 0.23
16 2 0.07
18 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (18 bp):
ATGAGTTAAATAATAGTG
Found at i:53909908 original size:35 final size:35
Alignment explanation
Indices: 53909862--53909934 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
53909852 AACGCACTCA
*
53909862 AATAGACATTTAAGCTTAAATTACACTACTACATT
1 AATAGACATTTAAGCTTAAATTACACTACTAAATT
53909897 AATAGACATTTAAGCTTAAATTACACTACTAAATT
1 AATAGACATTTAAGCTTAAATTACACTACTAAATT
53909932 AAT
1 AAT
53909935 TGAATTCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.34
Consensus pattern (35 bp):
AATAGACATTTAAGCTTAAATTACACTACTAAATT
Found at i:53909951 original size:35 final size:35
Alignment explanation
Indices: 53909862--53909943 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
53909852 AACGCACTCA
* *
53909862 AATAGACATTTAAGCTTAAATTACACTACTACATT
1 AATAGACATTCAAGCTTAAATTACACTACTAAATT
*
53909897 AATAGACATTTAAGCTTAAATTACACTACTAAATT
1 AATAGACATTCAAGCTTAAATTACACTACTAAATT
*
53909932 AATTGA-ATTCAA
1 AATAGACATTCAA
53909944 TTTTTAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 5 0.11
35 39 0.89
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (35 bp):
AATAGACATTCAAGCTTAAATTACACTACTAAATT
Found at i:53911673 original size:12 final size:11
Alignment explanation
Indices: 53911654--53911684 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
53911644 TGTATAAAAT
53911654 TTATTTTATTA
1 TTATTTTATTA
53911665 TTAATTTTATTA
1 TT-ATTTTATTA
53911677 TTATTTTA
1 TTATTTTA
53911685 AAGGCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:53911700 original size:30 final size:30
Alignment explanation
Indices: 53911665--53911724 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53911655 TATTTTATTA
53911665 TTAATTTTATTATTATTTTAAAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* * *
53911695 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
53911725 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Found at i:53912027 original size:32 final size:32
Alignment explanation
Indices: 53911986--53912050 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
53911976 TTCAGTTCAT
53911986 GCAGGTTTTTTTTTTAATTTAAAAAATATGGA
1 GCAGGTTTTTTTTTTAATTTAAAAAATATGGA
53912018 GCAGGTTTTTTTTTTAATTTAAAAAATATGGA
1 GCAGGTTTTTTTTTTAATTTAAAAAATATGGA
53912050 G
1 G
53912051 AGAGAGGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (32 bp):
GCAGGTTTTTTTTTTAATTTAAAAAATATGGA
Found at i:53913555 original size:19 final size:21
Alignment explanation
Indices: 53913514--53913557 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
53913504 GAAGAAAATA
*
53913514 AAATAGTAACTTTTAAATTGG
1 AAATAGTAACTTTTAAATGGG
*
53913535 AAATA-TAATTTTTAAA-GGG
1 AAATAGTAACTTTTAAATGGG
53913554 AAAT
1 AAAT
53913558 TTATTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (21 bp):
AAATAGTAACTTTTAAATGGG
Found at i:53914121 original size:30 final size:30
Alignment explanation
Indices: 53914085--53914142 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
53914075 CATAAGTATA
* *
53914085 ATATATCTGTTTGTTATGGGTCACTCTACG
1 ATATATCTATCTGTTATGGGTCACTCTACG
53914115 ATATATCTATCTGTTATGGGTCACTCTA
1 ATATATCTATCTGTTATGGGTCACTCTA
53914143 ACCTCCAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (30 bp):
ATATATCTATCTGTTATGGGTCACTCTACG
Found at i:53916708 original size:25 final size:25
Alignment explanation
Indices: 53916680--53916762 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
53916670 TACTGATCAG
53916680 GATGCTCGTAGGAACTATATAACAT
1 GATGCTCGTAGGAACTATATAACAT
* * *
53916705 GATGCTTGCAGGAACTATATAACAG
1 GATGCTCGTAGGAACTATATAACAT
*
53916730 GATGCTCG-AGAGAGCT-TATAACAT
1 GATGCTCGTAG-GAACTATATAACAT
*
53916754 GTTGCTCGT
1 GATGCTCGT
53916763 CCGAGCTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
24 16 0.33
25 33 0.67
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (25 bp):
GATGCTCGTAGGAACTATATAACAT
Found at i:53920800 original size:9 final size:9
Alignment explanation
Indices: 53920786--53920811 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
53920776 AAGTTTAGTA
53920786 AAAATATGT
1 AAAATATGT
53920795 AAAATATGT
1 AAAATATGT
53920804 AAAATATG
1 AAAATATG
53920812 GGTCACACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (9 bp):
AAAATATGT
Found at i:53927414 original size:14 final size:14
Alignment explanation
Indices: 53927395--53927429 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
53927385 GACATTTTTT
*
53927395 TTCTAATGATACTA
1 TTCTAACGATACTA
53927409 TTCTAACGATACTA
1 TTCTAACGATACTA
53927423 TTCTAAC
1 TTCTAAC
53927430 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:53928304 original size:6 final size:6
Alignment explanation
Indices: 53928074--53928301 Score: 366
Period size: 6 Copynumber: 38.0 Consensus size: 6
53928064 AGGCAGAACT
* * ** *
53928074 TGAGCC TGAGCC TGAGCC CGAGCC CGAGCC TGAGCC CAAGCC CGAGCC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
* * * *
53928122 CGAGCC TGACCC TGACCC TGACCC TGAGCC TGAGCC TGAGCC TGAGCC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
53928170 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
53928218 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
*
53928266 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC CGAGCC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
53928302 CGAACGGTCG
Statistics
Matches: 213, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 213 1.00
ACGTcount: A:0.17, C:0.37, G:0.32, T:0.14
Consensus pattern (6 bp):
TGAGCC
Found at i:53928955 original size:14 final size:14
Alignment explanation
Indices: 53928932--53928966 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53928922 AAAAATTGGA
*
53928932 ATAAACTTTGTAAT
1 ATAAATTTTGTAAT
*
53928946 ATAAATTTTGTTAT
1 ATAAATTTTGTAAT
53928960 ATAAATT
1 ATAAATT
53928967 AAATACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (14 bp):
ATAAATTTTGTAAT
Found at i:53928969 original size:62 final size:62
Alignment explanation
Indices: 53928844--53929186 Score: 244
Period size: 62 Copynumber: 5.7 Consensus size: 62
53928834 CAACATTACA
* * * * *
53928844 ACATTAAAACACTAAAACTT-TAACAAATTTTGTAATATAAATTTTATTTGTAATATAAATTAAA
1 ACATTACAACACTAAAAATTGGAATAAACTTTGTAATATAAA---T-TTTGTAATATAAATTAAA
53928908 T
62 T
*
53928909 ACATTACAACACTAAAAATTGGAATAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAATAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* * *
53928971 ACATTACAACATTAAAAATTGGAATAAACTTTGTAATATAAA---T-TAA-ATACATTACA-
1 ACATTACAACACTAAAAATTGGAATAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* * * * * * *
53929027 ACCTTA-AAAATTGGAATAAACTTCGTAATATAAATTTTGTTATATAAA---T-TAA-ATACATT
1 ACATTACAACACT--AA-AAA-TT-G-GA-ATAAACTTTGTAATATAAATTTTGTAATATAAATT
*
53929086 ACA-
59 AAAT
* *
53929089 ACATT-----A---AAAATTAGAATAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAATAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* *
53929143 ACATTACAATATTAAAAATTGGAATAAACTTTGTAATATAAATT
1 ACATTACAACACTAAAAATTGGAATAAACTTTGTAATATAAATT
53929187 AAGTACATTG
Statistics
Matches: 232, Mismatches: 24, Indels: 47
0.77 0.08 0.16
Matches are distributed among these distances:
48 17 0.07
49 1 0.00
51 3 0.01
52 5 0.02
53 9 0.04
54 5 0.02
55 5 0.02
56 5 0.02
57 10 0.04
58 6 0.03
59 4 0.02
60 1 0.00
61 1 0.00
62 123 0.53
63 1 0.00
65 18 0.08
66 18 0.08
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (62 bp):
ACATTACAACACTAAAAATTGGAATAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
Found at i:53928989 original size:24 final size:24
Alignment explanation
Indices: 53928962--53929038 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
53928952 TTTGTTATAT
53928962 AAATTAAATACATTACAACATTAA
1 AAATTAAATACATTACAACATTAA
* * *** *
53928986 AAATTGGAATAAACTTTGTA-A-TAT
1 AAATT-AAATACA-TTACAACATTAA
*
53929010 AAATTAAATACATTACAACCTTAA
1 AAATTAAATACATTACAACATTAA
53929034 AAATT
1 AAATT
53929039 GGAATAAACT
Statistics
Matches: 36, Mismatches: 13, Indels: 8
0.63 0.23 0.14
Matches are distributed among these distances:
22 3 0.08
23 5 0.14
24 19 0.53
25 6 0.17
26 3 0.08
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATTAAATACATTACAACATTAA
Found at i:53928998 original size:48 final size:48
Alignment explanation
Indices: 53928946--53929062 Score: 198
Period size: 48 Copynumber: 2.4 Consensus size: 48
53928936 ACTTTGTAAT
* *
53928946 ATAAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGA
1 ATAAACTTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGA
*
53928994 ATAAACTTTGTAATATAAATTAAATACATTACAACCTTAAAAATTGGA
1 ATAAACTTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGA
*
53929042 ATAAACTTCGTAATATAAATT
1 ATAAACTTTGTAATATAAATT
53929063 TTGTTATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.36
Consensus pattern (48 bp):
ATAAACTTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGA
Found at i:53929028 original size:110 final size:110
Alignment explanation
Indices: 53928890--53929124 Score: 436
Period size: 110 Copynumber: 2.1 Consensus size: 110
53928880 ATAAATTTTA
*
53928890 TTTGTAATATAAATTAAATACATTACAACAC-TAAAAATTGGAATAAACTTTGTAATATAAATTT
1 TTTGTAATATAAATTAAATACATTACAAC-CTTAAAAATTGGAATAAACTTCGTAATATAAATTT
*
53928954 TGTTATATAAATTAAATACATTACAACATTAAAAATTGGAATAAAC
65 TGTTATATAAATTAAATACATTACAACATTAAAAATTAGAATAAAC
53929000 TTTGTAATATAAATTAAATACATTACAACCTTAAAAATTGGAATAAACTTCGTAATATAAATTTT
1 TTTGTAATATAAATTAAATACATTACAACCTTAAAAATTGGAATAAACTTCGTAATATAAATTTT
53929065 GTTATATAAATTAAATACATTACAACATTAAAAATTAGAATAAAC
66 GTTATATAAATTAAATACATTACAACATTAAAAATTAGAATAAAC
53929110 TTTGTAATATAAATT
1 TTTGTAATATAAATT
53929125 TTGTTATATA
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
109 1 0.01
110 121 0.99
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (110 bp):
TTTGTAATATAAATTAAATACATTACAACCTTAAAAATTGGAATAAACTTCGTAATATAAATTTT
GTTATATAAATTAAATACATTACAACATTAAAAATTAGAATAAAC
Found at i:53929127 original size:14 final size:14
Alignment explanation
Indices: 53929104--53929138 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53929094 AAAAATTAGA
*
53929104 ATAAACTTTGTAAT
1 ATAAATTTTGTAAT
*
53929118 ATAAATTTTGTTAT
1 ATAAATTTTGTAAT
53929132 ATAAATT
1 ATAAATT
53929139 AAATACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (14 bp):
ATAAATTTTGTAAT
Found at i:53932308 original size:14 final size:14
Alignment explanation
Indices: 53932285--53932328 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
53932275 ATAATAATAC
*
53932285 CTTTTATTTCTTCT
1 CTTTTCTTTCTTCT
*
53932299 CTTTTCTTTCCTCT
1 CTTTTCTTTCTTCT
53932313 CTTTTCTTTCTT-T
1 CTTTTCTTTCTTCT
53932326 CTT
1 CTT
53932329 CTCCTCTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTTCTTTCTTCT
Found at i:53932333 original size:23 final size:24
Alignment explanation
Indices: 53932291--53932336 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
53932281 ATACCTTTTA
53932291 TTTCTTCTCTTTTCTTTCCTCTCT
1 TTTCTTCTCTTTTCTTTCCTCTCT
53932315 TTTCTT-TC-TTTCTTCTCCTCTC
1 TTTCTTCTCTTTTCTT-TCCTCTC
53932337 CCTCTCTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTCTTCTCTTTTCTTTCCTCTCT
Found at i:53941847 original size:39 final size:39
Alignment explanation
Indices: 53941800--53942062 Score: 384
Period size: 39 Copynumber: 6.7 Consensus size: 39
53941790 TGTGTGAGAT
*
53941800 TTATATCCGGGCTAAGTCCCGAAGGCATTCATGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
53941839 TTATATCCGGGCTAAGT-CCGAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCG-AAGGCATTCGTGCTGGTG
* * *
53941878 TTATGTCCGGGCTAAGTCCGGAAGGCATTCATGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
53941917 TTATATCCGGGCTCAGTCCCGAAGGTATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
53941956 TTATATCTGGGCTAAGTCCTGAAGGTATTCGTACTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
53941995 TTATATCCGGGCTAAGTCCCGAAGGTATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
53942034 TTATATCCGGGCTCAGTCCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
53942063 TGTGTTGGAA
Statistics
Matches: 201, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 3 0.01
39 196 0.98
40 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:53950029 original size:40 final size:40
Alignment explanation
Indices: 53949945--53950128 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
53949935 TTGAATGCTG
* * * *
53949945 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
53949984 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
53950025 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
53950065 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
53950105 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
53950129 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:53950082 original size:80 final size:81
Alignment explanation
Indices: 53949945--53950125 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
53949935 TTGAATGCTG
* * *
53949945 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
53950009 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
53950025 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
53950086 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
53950105 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
53950126 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:53950149 original size:39 final size:38
Alignment explanation
Indices: 53950026--53950175 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
53950016 GTTATTAATT
* ** * *
53950026 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
53950066 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
53950105 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
53950145 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
53950176 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:53957243 original size:40 final size:40
Alignment explanation
Indices: 53957159--53957342 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
53957149 TTGAATGCTG
* * * *
53957159 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
53957198 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
53957239 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
53957279 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
53957319 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
53957343 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:53957296 original size:80 final size:81
Alignment explanation
Indices: 53957159--53957339 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
53957149 TTGAATGCTG
* * *
53957159 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
53957223 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
53957239 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
53957300 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
53957319 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
53957340 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:53957363 original size:39 final size:38
Alignment explanation
Indices: 53957240--53957389 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
53957230 GTTATTAATT
* ** * *
53957240 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
53957280 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
53957319 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
53957359 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
53957390 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:53959568 original size:39 final size:39
Alignment explanation
Indices: 53959523--53959746 Score: 331
Period size: 39 Copynumber: 5.7 Consensus size: 39
53959513 TGTGTGAGAT
53959523 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
53959562 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * **
53959601 TTATGTCCGAGCTAAGTTTCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
53959640 TTATATCCAGGCTAAATCCCGAAGGTATGCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * * *
53959679 TTATATCCCGGCTATGTCCCGCAGGTATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
53959718 TTATATCCGGGCTAAGTCCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
53959747 TGTGTTGGAA
Statistics
Matches: 163, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 163 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:53964620 original size:7 final size:7
Alignment explanation
Indices: 53964610--53964651 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
53964600 GGGGAATAGG
53964610 GAAGGGA
1 GAAGGGA
53964617 GAAGGGA
1 GAAGGGA
*
53964624 GAAGGAA
1 GAAGGGA
*
53964631 GAATGGA
1 GAAGGGA
53964638 GAAGGGA
1 GAAGGGA
53964645 GAAGGGA
1 GAAGGGA
53964652 ACATAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.02
Consensus pattern (7 bp):
GAAGGGA
Found at i:53967455 original size:10 final size:10
Alignment explanation
Indices: 53967440--53967464 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53967430 TAATGAAAGT
53967440 TTAAACAAAA
1 TTAAACAAAA
53967450 TTAAACAAAA
1 TTAAACAAAA
53967460 TTAAA
1 TTAAA
53967465 GAATGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
TTAAACAAAA
Found at i:53969778 original size:3 final size:3
Alignment explanation
Indices: 53969772--53969818 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
53969762 CCTCATCCCT
* * *
53969772 TTC TTC TTC TTT TTC TTC TTC GTC -TC GTC TTC TTC TCTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC
53969817 TT
1 TT
53969819 TTATTGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.00, C:0.32, G:0.04, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:53972589 original size:17 final size:17
Alignment explanation
Indices: 53972542--53972591 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
53972532 TTTTAGAAAA
* *
53972542 TTTTTAAAATTTTAACT
1 TTTTTAAAATTTTTATT
* *
53972559 TTTTTATATTTTTTATT
1 TTTTTAAAATTTTTATT
53972576 TTTTTAAAATTTTTAT
1 TTTTTAAAATTTTTAT
53972592 AAATATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAAAATTTTTATT
Found at i:53973033 original size:19 final size:19
Alignment explanation
Indices: 53972998--53973059 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
53972988 CTTATGCGTT
* *
53972998 AGGATACACCTCATGTGCC
1 AGGATACACTTCGTGTGCC
* *
53973017 AGGATCCACTTCGTGTGTC
1 AGGATACACTTCGTGTGCC
* *
53973036 AGTATACACTTCGTGTGCT
1 AGGATACACTTCGTGTGCC
53973055 AGGAT
1 AGGAT
53973060 GTGCTTCATG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (19 bp):
AGGATACACTTCGTGTGCC
Found at i:53975281 original size:15 final size:15
Alignment explanation
Indices: 53975261--53975292 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53975251 AATCCTGTAG
*
53975261 AAATTAAATATAACT
1 AAATTAAATAAAACT
53975276 AAATTAAATAAAACT
1 AAATTAAATAAAACT
53975291 AA
1 AA
53975293 TGGAAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATTAAATAAAACT
Found at i:53978490 original size:35 final size:35
Alignment explanation
Indices: 53978451--53978531 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
53978441 ACTCTATGTT
** * *
53978451 TTGGTGTGTTTTAGTTGGATTAGGTTTTATGAGCA
1 TTGGTGTGTTTTAGAGGGATTAGCTCTTATGAGCA
*
53978486 TTGGTGTGTTTTGGAGGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTTAGAGGGATTAGCTCTTATGAGCA
53978521 TTGGTGTGTTT
1 TTGGTGTGTTT
53978532 GGGTGGTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.15, C:0.05, G:0.33, T:0.47
Consensus pattern (35 bp):
TTGGTGTGTTTTAGAGGGATTAGCTCTTATGAGCA
Found at i:53980002 original size:18 final size:18
Alignment explanation
Indices: 53979969--53980003 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53979959 TTAATATATA
53979969 TATAGGTTATAAAATAAT
1 TATAGGTTATAAAATAAT
53979987 TATA-GTTATAATAATAA
1 TATAGGTTATAA-AATAA
53980004 ATACAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TATAGGTTATAAAATAAT
Found at i:53982084 original size:34 final size:34
Alignment explanation
Indices: 53982041--53982108 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
53982031 AGAAAAGAAG
53982041 AAAACTTTGTTGTCTTTACAATTTGATCCTTCTA
1 AAAACTTTGTTGTCTTTACAATTTGATCCTTCTA
53982075 AAAACTTTGTTGTCTTTACAATTTGATCCTTCTA
1 AAAACTTTGTTGTCTTTACAATTTGATCCTTCTA
53982109 CCACAAATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (34 bp):
AAAACTTTGTTGTCTTTACAATTTGATCCTTCTA
Found at i:53984951 original size:15 final size:15
Alignment explanation
Indices: 53984914--53984949 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
53984904 ATCTTATTTC
53984914 ATTTTTATTTGTTTT
1 ATTTTTATTTGTTTT
*
53984929 ATTTTTATCTTTTTTT
1 ATTTTTAT-TTGTTTT
53984945 ATTTT
1 ATTTT
53984950 ATTCTTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (15 bp):
ATTTTTATTTGTTTT
Found at i:53984955 original size:16 final size:16
Alignment explanation
Indices: 53984904--53984949 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
53984894 TTTTAATTCC
* *
53984904 ATCTTATTTCATTTTT
1 ATCTTTTTTTATTTTT
*
53984920 AT-TTGTTTTATTTTT
1 ATCTTTTTTTATTTTT
53984935 ATCTTTTTTTATTTT
1 ATCTTTTTTTATTTT
53984950 ATTCTTGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (16 bp):
ATCTTTTTTTATTTTT
Found at i:53985430 original size:19 final size:19
Alignment explanation
Indices: 53985408--53985490 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 19
53985398 CATACTTTTT
53985408 TTATATTATTTCATTATTA
1 TTATATTATTTCATTATTA
53985427 TTATCATTATTATCA-TA-TA
1 TTAT-ATTATT-TCATTATTA
* * * *
53985446 GTATTATTAATTAAATATT-
1 TTA-TATTATTTCATTATTA
53985465 TTATTATTATTTC-TTATTA
1 TTA-TATTATTTCATTATTA
*
53985484 TTGTATT
1 TTATATT
53985491 CATTATAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
18 10 0.20
19 27 0.54
20 10 0.20
21 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATATTATTTCATTATTA
Found at i:53986975 original size:46 final size:45
Alignment explanation
Indices: 53986826--53987047 Score: 211
Period size: 46 Copynumber: 4.8 Consensus size: 45
53986816 TCATTTGTGT
* * * *
53986826 GAGCTAGTGTAAGACATGTCTGGGACATGCGTCGGCT-GCATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCG-A-GACGA
* *
53986872 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TCGAGACGA
* * *
53986920 GTGCTAGTGTAAGACATGTCTGGGACATGCTTCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTCGAGACG-A
53986967 -AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-A--A
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCT-CGAGACGA
* *
53987009 TGTGTCAGTGTAAGACTATGTCTGGGACATGGCATCGGC
1 -GAGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGC
53987048 ATAGATATTC
Statistics
Matches: 150, Mismatches: 15, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
42 1 0.01
44 12 0.08
45 16 0.11
46 68 0.45
47 28 0.19
48 22 0.15
49 2 0.01
50 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (45 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGACGA
Found at i:53991850 original size:93 final size:93
Alignment explanation
Indices: 53991742--53991912 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
53991732 GCCCCTAAGT
* * * *
53991742 GAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
53991807 TGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
53991835 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
53991900 CGAGTTCGGATGC
66 CGAGTTCGGATGC
53991913 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:53991909 original size:46 final size:46
Alignment explanation
Indices: 53991741--53991909 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 46
53991731 CGCCCCTAAG
* * * * * *
53991741 TGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
* * * *
53991787 TGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAAA
*
53991834 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
53991880 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
53991910 TGCTCAACCA
Statistics
Matches: 100, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 56 0.56
47 28 0.28
48 1 0.01
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
Found at i:53992365 original size:30 final size:30
Alignment explanation
Indices: 53992331--53992388 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53992321 CATTTAATAC
53992331 AAACTTTGGAAAAATTAAACTTTTGCCCCT
1 AAACTTTGGAAAAATTAAACTTTTGCCCCT
* * * *
53992361 AAACTTTTGCATAATTACACTTTTGCCC
1 AAACTTTGGAAAAATTAAACTTTTGCCC
53992389 TTAGGCTCGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTAAACTTTTGCCCCT
Found at i:53993421 original size:40 final size:40
Alignment explanation
Indices: 53993364--53993447 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
53993354 GAAAGCATGA
53993364 GATGGCATAAAACGTTGCCTTAAATGGAACCTATGGCATT
1 GATGGCATAAAACGTTGCCTTAAATGGAACCTATGGCATT
*
53993404 GATGGCATAAAATGTTGCCTTAAATGGAACCTATGGCATT
1 GATGGCATAAAACGTTGCCTTAAATGGAACCTATGGCATT
53993444 GATG
1 GATG
53993448 ATGCAGTTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (40 bp):
GATGGCATAAAACGTTGCCTTAAATGGAACCTATGGCATT
Found at i:53996611 original size:15 final size:15
Alignment explanation
Indices: 53996593--53996626 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
53996583 GGAGGGAAAA
53996593 AAAATTCTTAAATGT
1 AAAATTCTTAAATGT
53996608 AAAATTCTTAAATGT
1 AAAATTCTTAAATGT
53996623 AAAA
1 AAAA
53996627 GAACTAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
AAAATTCTTAAATGT
Found at i:53998063 original size:9 final size:9
Alignment explanation
Indices: 53998049--53998088 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
53998039 GGAAAGGGAG
*
53998049 GGTGGTAGT
1 GGTGGTAGA
*
53998058 GGTGGTGGA
1 GGTGGTAGA
53998067 GGTGGTAGA
1 GGTGGTAGA
*
53998076 GGTGGCAGA
1 GGTGGTAGA
53998085 GGTG
1 GGTG
53998089 TTTGTATTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.60, T:0.23
Consensus pattern (9 bp):
GGTGGTAGA
Found at i:54000094 original size:19 final size:19
Alignment explanation
Indices: 54000072--54000118 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54000062 TTATACCATG
*
54000072 TATATAT-TTTTATAAATAT
1 TATATATATATTA-AAATAT
*
54000091 TATATATATATTAATATAT
1 TATATATATATTAAAATAT
54000110 TATATATAT
1 TATATATAT
54000119 TGTGTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATATATATTAAAATAT
Found at i:54014364 original size:19 final size:19
Alignment explanation
Indices: 54014340--54014376 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
54014330 ATAAATTAAT
54014340 AAATATTATTTAATAGTAA
1 AAATATTATTTAATAGTAA
54014359 AAATATTATTTAATAGTA
1 AAATATTATTTAATAGTA
54014377 GAAAGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
AAATATTATTTAATAGTAA
Found at i:54019348 original size:9 final size:9
Alignment explanation
Indices: 54019323--54019408 Score: 68
Period size: 9 Copynumber: 9.6 Consensus size: 9
54019313 TATTTATGTA
54019323 TTATGTAAG
1 TTATGTAAG
*
54019332 TTAAGTAAG
1 TTATGTAAG
54019341 CTT-TGTAAG
1 -TTATGTAAG
54019350 TTATGTAAG
1 TTATGTAAG
* *
54019359 TTACGTTA-
1 TTATGTAAG
* * *
54019367 TGATATACAT
1 TTATGTA-AG
*
54019377 TTATATAAG
1 TTATGTAAG
*
54019386 GTATGTAAG
1 TTATGTAAG
54019395 TTATGTAAG
1 TTATGTAAG
54019404 TTATG
1 TTATG
54019409 ATATGATATA
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
8 5 0.08
9 47 0.78
10 8 0.13
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:54019428 original size:13 final size:13
Alignment explanation
Indices: 54019410--54019439 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
54019400 TAAGTTATGA
54019410 TATGATATATATT
1 TATGATATATATT
54019423 TATGATATATATT
1 TATGATATATATT
54019436 TATG
1 TATG
54019440 TATTATGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATGATATATATT
Found at i:54020391 original size:50 final size:51
Alignment explanation
Indices: 54020300--54020406 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 51
54020290 TAACATAACG
* * *
54020300 TATAAATGTTACGAGTTAAATTTGTTAAATTATGACTAAATTGACAGAATA
1 TATAAATATTACGAGTTAAATTTGTTAAATCAAGACTAAATTGACAGAATA
* *
54020351 TATAAATATTACGA-TTTAATTTGTTAAATCAAGA-TCAAATTGATAGAATA
1 TATAAATATTACGAGTTAAATTTGTTAAATCAAGACT-AAATTGACAGAATA
54020401 TATAAA
1 TATAAA
54020407 CTTAAGATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.02
50 36 0.72
51 13 0.26
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (51 bp):
TATAAATATTACGAGTTAAATTTGTTAAATCAAGACTAAATTGACAGAATA
Found at i:54022439 original size:19 final size:16
Alignment explanation
Indices: 54022399--54022431 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54022389 TTGAGTGCTG
54022399 AGCATTAACAACAGAA
1 AGCATTAACAACAGAA
54022415 AGCATTAACAACAGAA
1 AGCATTAACAACAGAA
54022431 A
1 A
54022432 TCTGCATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (16 bp):
AGCATTAACAACAGAA
Found at i:54022931 original size:84 final size:84
Alignment explanation
Indices: 54022790--54022982 Score: 314
Period size: 84 Copynumber: 2.3 Consensus size: 84
54022780 GTTTTTTTGC
* * **
54022790 GGCGTTTCTAGGATAGCGCCACTAATTCCTAAACCTTGCCACATAAAACGACGTAGTTTTCATTC
1 GGCGTTTATAAGATAGCGCCACTAATTCCTAAACCGCGCCACATAAAACGACGTAGTTTTCATTC
54022855 GGTTTCTCATATTCTTAGT
66 GGTTTCTCATATTCTTAGT
* * *
54022874 GGCGTTTATACGATAGCACCACTAATTCCTAAACCGCGCCACATAAAATGACGTAGTTTTCATTC
1 GGCGTTTATAAGATAGCGCCACTAATTCCTAAACCGCGCCACATAAAACGACGTAGTTTTCATTC
*
54022939 GGTTTCTCATATTTTTAGT
66 GGTTTCTCATATTCTTAGT
54022958 GGCGTTTATAAGATAGCGCCACTAA
1 GGCGTTTATAAGATAGCGCCACTAA
54022983 ATCCACTACC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 100 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (84 bp):
GGCGTTTATAAGATAGCGCCACTAATTCCTAAACCGCGCCACATAAAACGACGTAGTTTTCATTC
GGTTTCTCATATTCTTAGT
Found at i:54023331 original size:15 final size:15
Alignment explanation
Indices: 54023307--54023433 Score: 56
Period size: 14 Copynumber: 8.9 Consensus size: 15
54023297 GCCCAAAACT
54023307 AATACACTAAACCCC
1 AATACACTAAACCCC
*
54023322 AATACCCTAAA-CCC
1 AATACACTAAACCCC
* * *
54023336 TATAGACTAAACCCT
1 AATACACTAAACCCC
* *
54023351 AA-AC-C-AAATACCT
1 AATACACTAAA-CCCC
54023364 AATACACTAAA-CCC
1 AATACACTAAACCCC
* * *
54023378 TATAGACTAAACCCT
1 AATACACTAAACCCC
*
54023393 AA-AC-C-AAATACCC
1 AATACACTAAA-CCCC
*
54023406 AATACCCTAAA-CCC
1 AATACACTAAACCCC
* *
54023420 TATAGACTAAACCC
1 AATACACTAAACCC
54023434 TAAACCCAAT
Statistics
Matches: 82, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
12 6 0.07
13 11 0.13
14 39 0.48
15 20 0.24
16 6 0.07
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (15 bp):
AATACACTAAACCCC
Found at i:54023347 original size:14 final size:14
Alignment explanation
Indices: 54023328--54023435 Score: 89
Period size: 14 Copynumber: 7.7 Consensus size: 14
54023318 CCCCAATACC
54023328 CTAAACCCTATAGA
1 CTAAACCCTATAGA
54023342 CTAAACCCTA-A-A
1 CTAAACCCTATAGA
* * *
54023354 CCAAATACCTAATACA
1 CTAAA-CCCT-ATAGA
54023370 CTAAACCCTATAGA
1 CTAAACCCTATAGA
54023384 CTAAACCCTA-A-A
1 CTAAACCCTATAGA
* * **
54023396 CCAAATACCCAATACC
1 -CTAA-ACCCTATAGA
54023412 CTAAACCCTATAGA
1 CTAAACCCTATAGA
54023426 CTAAACCCTA
1 CTAAACCCTA
54023436 AACCCAATAC
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
12 6 0.08
13 8 0.11
14 47 0.64
15 8 0.11
16 5 0.07
ACGTcount: A:0.45, C:0.33, G:0.03, T:0.19
Consensus pattern (14 bp):
CTAAACCCTATAGA
Found at i:54023349 original size:21 final size:21
Alignment explanation
Indices: 54023325--54023440 Score: 128
Period size: 21 Copynumber: 5.5 Consensus size: 21
54023315 AAACCCCAAT
54023325 ACCCTAAACCCTATAGACTAA
1 ACCCTAAACCCTATAGACTAA
** *
54023346 ACCCTAAACCAAATA-CCTAA
1 ACCCTAAACCCTATAGACTAA
*
54023366 TACACTAAACCCTATAGACTAA
1 -ACCCTAAACCCTATAGACTAA
** * *
54023388 ACCCTAAACCAAATA-CCCAA
1 ACCCTAAACCCTATAGACTAA
54023408 TACCCTAAACCCTATAGACTAA
1 -ACCCTAAACCCTATAGACTAA
54023430 ACCCTAAACCC
1 ACCCTAAACCC
54023441 AATACCCATT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
20 7 0.09
21 61 0.81
22 7 0.09
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.17
Consensus pattern (21 bp):
ACCCTAAACCCTATAGACTAA
Found at i:54023377 original size:28 final size:30
Alignment explanation
Indices: 54023301--54023440 Score: 104
Period size: 28 Copynumber: 5.0 Consensus size: 30
54023291 AATTAAGCCC
*
54023301 AAAA-CTAATACACTAAACCCCAATACCCT
1 AAAACCTAATACACTAAACCCTAATACCCT
* *
54023330 AAACCCT-ATAGACTAAACCCTAA-A-CC-
1 AAAACCTAATACACTAAACCCTAATACCCT
**
54023356 AAATACCTAATACACTAAACCCT-ATAGACT
1 AAA-ACCTAATACACTAAACCCTAATACCCT
* *
54023386 AAACCCTAA-AC-CAAATACCC-AATACCCT
1 AAAACCTAATACACTAA-ACCCTAATACCCT
* *
54023414 AAACCCT-ATAGACTAAACCCTAA-ACCC
1 AAAACCTAATACACTAAACCCTAATACCC
54023441 AATACCCATT
Statistics
Matches: 88, Mismatches: 12, Indels: 23
0.72 0.10 0.19
Matches are distributed among these distances:
26 3 0.03
27 10 0.11
28 42 0.48
29 28 0.32
30 5 0.06
ACGTcount: A:0.46, C:0.34, G:0.02, T:0.17
Consensus pattern (30 bp):
AAAACCTAATACACTAAACCCTAATACCCT
Found at i:54023381 original size:42 final size:42
Alignment explanation
Indices: 54023319--54023489 Score: 261
Period size: 42 Copynumber: 4.1 Consensus size: 42
54023309 TACACTAAAC
54023319 CCCAATACCCTAAACCCTATAGACTAAACCCTAAACCAAATA
1 CCCAATACCCTAAACCCTATAGACTAAACCCTAAACCAAATA
* *
54023361 CCTAATACACTAAACCCTATAGACTAAACCCTAAACCAAATA
1 CCCAATACCCTAAACCCTATAGACTAAACCCTAAACCAAATA
*
54023403 CCCAATACCCTAAACCCTATAGACTAAACCCTAAACCCAATA
1 CCCAATACCCTAAACCCTATAGACTAAACCCTAAACCAAATA
* * * ** *
54023445 CCCATTACCCTAAACCTTATAAACTAAATTCTAAACCCAATA
1 CCCAATACCCTAAACCCTATAGACTAAACCCTAAACCAAATA
54023487 CCC
1 CCC
54023490 TAAACCTTGA
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 119 1.00
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (42 bp):
CCCAATACCCTAAACCCTATAGACTAAACCCTAAACCAAATA
Found at i:54023454 original size:21 final size:21
Alignment explanation
Indices: 54023388--54023460 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
54023378 TATAGACTAA
* *
54023388 ACCCTAAACCAAATACCCAAT
1 ACCCTAAACCCAATACCCATT
* ** *
54023409 ACCCTAAACCCTATAGAC-TAA
1 ACCCTAAACCCAATACCCAT-T
54023430 ACCCTAAACCCAATACCCATT
1 ACCCTAAACCCAATACCCATT
54023451 ACCCTAAACC
1 ACCCTAAACC
54023461 TTATAAACTA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.42, C:0.40, G:0.01, T:0.16
Consensus pattern (21 bp):
ACCCTAAACCCAATACCCATT
Found at i:54023961 original size:22 final size:22
Alignment explanation
Indices: 54023933--54023986 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
54023923 AAAATTTATT
* *
54023933 TTTAAGATTTTAGGGTTTAT-G
1 TTTAAGAGTTTAGGGCTTATAG
54023954 ATTTAAGAGTTTAGGGCTTATAG
1 -TTTAAGAGTTTAGGGCTTATAG
54023977 TTTAAG-GTTT
1 TTTAAGAGTTT
54023987 GAGATTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 4 0.14
22 24 0.83
23 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (22 bp):
TTTAAGAGTTTAGGGCTTATAG
Found at i:54026115 original size:11 final size:11
Alignment explanation
Indices: 54026094--54026122 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54026084 TGTAACTGTG
54026094 AAAAT-AAAAT
1 AAAATAAAAAT
54026104 AAAATAAAAAT
1 AAAATAAAAAT
54026115 AAAATAAA
1 AAAATAAA
54026123 GAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:54030499 original size:5 final size:5
Alignment explanation
Indices: 54030489--54030533 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
54030479 CCAATTTGTG
54030489 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAA
54030534 GAACACACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 33 0.87
7 5 0.13
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:54032723 original size:43 final size:43
Alignment explanation
Indices: 54032639--54032788 Score: 126
Period size: 43 Copynumber: 3.5 Consensus size: 43
54032629 TCTGAGACAT
* * * * *
54032639 CGTGTAAGATCGTGTCTGGGACACAGGCCTCGAT-TGAGATTTA
1 CGTGTAAGACCATGTCTGGGACAGAGGCATCGATAT-TGATTTA
* **
54032682 CGTATAAGACCATGTCTGGGACATCGGCATCG-TATCTGATTT-
1 CGTGTAAGACCATGTCTGGGACAGAGGCATCGATAT-TGATTTA
* * * * *
54032724 TGTGTAAGACCCTATCTGGGATAGAGGCATCGATATTGAATTA
1 CGTGTAAGACCATGTCTGGGACAGAGGCATCGATATTGATTTA
* *
54032767 CATGTAAGACCACGTCTGGGAC
1 CGTGTAAGACCATGTCTGGGAC
54032789 GTTGGCATTG
Statistics
Matches: 82, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
42 31 0.38
43 51 0.62
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACAGAGGCATCGATATTGATTTA
Found at i:54037125 original size:28 final size:28
Alignment explanation
Indices: 54037085--54037167 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
54037075 CTGTATCTGG
* * *
54037085 CCCATTAAGCCCATTCATATTCATATGA
1 CCCATTAGGCCCAATCACATTCATATGA
* *
54037113 CCCATTAGGCCCAAATCACATTTATATGG
1 CCCATTAGGCCC-AATCACATTCATATGA
* * *
54037142 CCCGTTAGGCCTAGTCACATTCATAT
1 CCCATTAGGCCCAATCACATTCATAT
54037168 TCATGCTCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 23 0.51
29 22 0.49
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (28 bp):
CCCATTAGGCCCAATCACATTCATATGA
Found at i:54037256 original size:18 final size:18
Alignment explanation
Indices: 54037217--54037268 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
54037207 TTCAGTTTTT
54037217 GCCCATCGGGCCCA-ACA
1 GCCCATCGGGCCCATACA
**
54037234 GCCCATCGGGCCCATTTA
1 GCCCATCGGGCCCATACA
*
54037252 GCCCATTCAGGCCCATA
1 GCCCA-TCGGGCCCATA
54037269 TGGCCAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 14 0.48
18 6 0.21
19 9 0.31
ACGTcount: A:0.21, C:0.42, G:0.21, T:0.15
Consensus pattern (18 bp):
GCCCATCGGGCCCATACA
Found at i:54041674 original size:16 final size:17
Alignment explanation
Indices: 54041642--54041677 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
54041632 AGAAAGAAAG
54041642 TTTGGGATTTCGGGATT
1 TTTGGGATTTCGGGATT
*
54041659 TTTGGG-TTTTGGGATT
1 TTTGGGATTTCGGGATT
54041675 TTT
1 TTT
54041678 AGGGCGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.08, C:0.03, G:0.33, T:0.56
Consensus pattern (17 bp):
TTTGGGATTTCGGGATT
Found at i:54051154 original size:29 final size:29
Alignment explanation
Indices: 54051112--54051170 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
54051102 GACCATGTGT
*
54051112 ATGCAAATCATGTGCTTTGATATAAGTGG
1 ATGCAAATCATGTGCTTTAATATAAGTGG
54051141 ATGCAAATCATGTGCTTTAATATAAGTGG
1 ATGCAAATCATGTGCTTTAATATAAGTGG
54051170 A
1 A
54051171 GCTTATGCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGCAAATCATGTGCTTTAATATAAGTGG
Found at i:54059569 original size:40 final size:40
Alignment explanation
Indices: 54059514--54059620 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
54059504 TATTCGGATG
54059514 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
* * *
54059554 ATATCCGGACTAAGATCCAAAGGCAATTGTGCTAGTTATT
1 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
* **
54059594 ATAACCGGGTTAAG-TCCCGAAGGCATT
1 ATATCCGGACTAAGAT-CCGAAGGCATT
54059621 CCTGCTGGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (40 bp):
ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
Found at i:54063706 original size:39 final size:40
Alignment explanation
Indices: 54063629--54063735 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
54063619 TAGCTCCTCG
* * *
54063629 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
54063669 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
54063708 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
54063736 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:54063734 original size:79 final size:80
Alignment explanation
Indices: 54063635--54063855 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
54063625 CTCGTTCAAG
* * * ** * *
54063635 TGCCTTCGGGACATAGCCCGG-TTATATTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
54063698 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
54063714 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
54063779 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
54063794 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
54063856 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
79 36 0.31
80 75 0.64
81 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:54063786 original size:80 final size:80
Alignment explanation
Indices: 54063675--54063855 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
54063665 CTCATTCAAT
* * *
54063675 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
54063738 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
54063754 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
54063818 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
54063835 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
54063856 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:54063815 original size:40 final size:40
Alignment explanation
Indices: 54063672--54063855 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
54063662 TAACTCATTC
* *
54063672 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
54063712 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
54063752 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
54063792 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
54063833 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54063856 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:54070708 original size:40 final size:40
Alignment explanation
Indices: 54070646--54070750 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
54070636 TATTCGGATG
*
54070646 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTACT
* * *
54070686 ATATTCGGACTAAGATCTGAAGGCAATTGTGCTAGTTATT
1 ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTACT
* **
54070726 ATAACCGGGTTAAG-TCCCGAAGGCA
1 ATATCCGGACTAAGAT-CCGAAGGCA
54070751 TTCCTGCGGG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.02
40 54 0.98
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (40 bp):
ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTACT
Found at i:54070764 original size:40 final size:40
Alignment explanation
Indices: 54070720--54070802 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
54070710 AATTGTGCTA
54070720 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCCTGCGG
1 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCCTGCGG
* * *
54070760 GTTATTATAACCGGGTTAAGTCTCGAAGGCATTCGTGCTG
1 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCCTGCGG
54070800 GTT
1 GTT
54070803 GTTACATCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (40 bp):
GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCCTGCGG
Found at i:54082037 original size:38 final size:38
Alignment explanation
Indices: 54081990--54082130 Score: 135
Period size: 38 Copynumber: 3.7 Consensus size: 38
54081980 GGCTTAAAGA
* * *
54081990 CCCGCAGGCTATATGCTAGAATTATATCTGGGTTAAAT
1 CCCGCAGGCTATGTGCTGGTATTATATCTGGGTTAAAT
* *
54082028 CCCGTAGGCT-TCGTGCTGGTATTATATCCGGGTTAAAT
1 CCCGCAGGCTAT-GTGCTGGTATTATATCTGGGTTAAAT
* *
54082066 CCCGCAGGCCTA-GTGCTGGTATTATATCTAAGTTTAAAGT
1 CCCGCAGG-CTATGTGCTGGTATTATATCT-GGGTTAAA-T
* *
54082106 CCCGTAGGCT-TCGTGCTGGTGTTAT
1 CCCGCAGGCTAT-GTGCTGGTATTAT
54082131 GTTCAGGTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
37 1 0.01
38 54 0.64
39 10 0.12
40 20 0.24
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (38 bp):
CCCGCAGGCTATGTGCTGGTATTATATCTGGGTTAAAT
Found at i:54082073 original size:76 final size:80
Alignment explanation
Indices: 54081974--54082130 Score: 207
Period size: 78 Copynumber: 2.0 Consensus size: 80
54081964 ATTTGATGTG
*
54081974 TATCCGGGCTTAAAGACCCGCAGG-CTATATGCTAGAATTATATCT-GGGTTAAA-TCCCGTAGG
1 TATCCGGGCTTAAAGACCCGCAGGCCTA-ATGCTAGAATTATATCTAAGGTTAAAGTCCCGTAGG
54082036 CTTCGTGCTGGTATTA
65 CTTCGTGCTGGTATTA
* * * * *
54082052 TATCCGGG-TTAAA-TCCCGCAGGCCTAGTGCTGGTATTATATCTAAGTTTAAAGTCCCGTAGGC
1 TATCCGGGCTTAAAGACCCGCAGGCCTAATGCTAGAATTATATCTAAGGTTAAAGTCCCGTAGGC
*
54082115 TTCGTGCTGGTGTTA
66 TTCGTGCTGGTATTA
54082130 T
1 T
54082131 GTTCAGGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
76 22 0.32
77 14 0.20
78 33 0.48
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (80 bp):
TATCCGGGCTTAAAGACCCGCAGGCCTAATGCTAGAATTATATCTAAGGTTAAAGTCCCGTAGGC
TTCGTGCTGGTATTA
Found at i:54082122 original size:40 final size:38
Alignment explanation
Indices: 54082010--54082130 Score: 143
Period size: 38 Copynumber: 3.1 Consensus size: 38
54082000 ATATGCTAGA
**
54082010 ATTATATCTGGGTTAAATCCCGTAGGCTTCGTGCTGGT
1 ATTATATCAAGGTTAAATCCCGTAGGCTTCGTGCTGGT
** * * *
54082048 ATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGT
1 ATTATATCAAGGTTAAATCCCGTAGGCTTCGTGCTGGT
*
54082086 ATTATATCTAAGTTTAAAGTCCCGTAGGCTTCGTGCTGGT
1 ATTATATC-AAGGTTAAA-TCCCGTAGGCTTCGTGCTGGT
*
54082126 GTTAT
1 ATTAT
54082131 GTTCAGGTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
38 42 0.60
39 6 0.09
40 22 0.31
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (38 bp):
ATTATATCAAGGTTAAATCCCGTAGGCTTCGTGCTGGT
Found at i:54092405 original size:15 final size:15
Alignment explanation
Indices: 54092347--54092406 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
54092337 CACGGTATTG
*
54092347 TATCTTGGATATCTT
1 TATCTTGGATTTCTT
*
54092362 TATCTTGGATTTCTC
1 TATCTTGGATTTCTT
** *
54092377 TATCTCAGACTTCTT
1 TATCTTGGATTTCTT
*
54092392 TATCTTGGTTTTCTT
1 TATCTTGGATTTCTT
54092407 GCTATCTATA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.55
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:54095703 original size:43 final size:43
Alignment explanation
Indices: 54095646--54095731 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
54095636 GATATATGTG
* *
54095646 GCATCCGAGCTCGTTGAGTGGTCCGAGTTCATTATGGATGCGA
1 GCATCCGAGCTCGTTGAGTGGTCCAAGTTCATAATGGATGCGA
*
54095689 GCATCCGAGCTCGTTGAGTGGTTCAAGTTCATAATGGATGCGA
1 GCATCCGAGCTCGTTGAGTGGTCCAAGTTCATAATGGATGCGA
54095732 TACATGTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAGTGGTCCAAGTTCATAATGGATGCGA
Found at i:54100177 original size:21 final size:20
Alignment explanation
Indices: 54100153--54100222 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
54100143 TCTCACAGGC
54100153 TTCTGTTTAACTCATATGAGT
1 TTCTGTTTAACTC-TATGAGT
* * *
54100174 TTCTGTTCAGCTCTATTGAGC
1 TTCTGTTTAACTCTA-TGAGT
* *
54100195 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAACTC-TATGAGT
54100216 TTCTGTT
1 TTCTGTT
54100223 CAGCTCTTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.90
22 2 0.05
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.49
Consensus pattern (20 bp):
TTCTGTTTAACTCTATGAGT
Found at i:54100231 original size:21 final size:21
Alignment explanation
Indices: 54100153--54100301 Score: 63
Period size: 21 Copynumber: 7.2 Consensus size: 21
54100143 TCTCACAGGC
* * * *
54100153 TTCTGTTTAACTCATATGAGT
1 TTCTGTTCAGCTCTTATGGGT
* *
54100174 TTCTGTTCAGCTC-TATTGAGC
1 TTCTGTTCAGCTCTTA-TGGGT
* * *
54100195 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAGCTCTTATGGGT
* * *
54100216 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGGGT
* * * *
54100237 ATCCGTTCAACACTTATGGGT
1 TTCTGTTCAGCTCTTATGGGT
* * * *
54100258 TTTTGTTTAGCTCTCATGAGCT
1 TTCTGTTCAGCTCTTATG-GGT
*
54100280 TT-TGTTCAGC-CTT-TGGGC
1 TTCTGTTCAGCTCTTATGGGT
54100298 TTCT
1 TTCT
54100302 AAAAATGATG
Statistics
Matches: 91, Mismatches: 33, Indels: 10
0.68 0.25 0.07
Matches are distributed among these distances:
18 3 0.03
19 3 0.03
20 4 0.04
21 75 0.82
22 6 0.07
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGGGT
Found at i:54100287 original size:42 final size:42
Alignment explanation
Indices: 54100151--54100287 Score: 141
Period size: 42 Copynumber: 3.3 Consensus size: 42
54100141 GCTCTCACAG
* * * *
54100151 GCTTCTGTTTAACTCATATGAGTTTCTGTTCAGCTCT-ATTGA
1 GCTTCTGTTCAACACTTATGGGTTTCTGTTCAGCTCTCA-TGA
* * * *
54100193 GCTTCTGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTACGA
1 GCTTCTGTTCAACACTTATGGGTTTCTGTTCAGCTCTCATGA
* * * *
54100235 GCATCCGTTCAACACTTATGGGTTTTTGTTTAGCTCTCATGA
1 GCTTCTGTTCAACACTTATGGGTTTCTGTTCAGCTCTCATGA
*
54100277 GCTTTTGTTCA
1 GCTTCTGTTCA
54100288 GCCTTTGGGC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 78 0.99
43 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
GCTTCTGTTCAACACTTATGGGTTTCTGTTCAGCTCTCATGA
Found at i:54101696 original size:25 final size:24
Alignment explanation
Indices: 54101546--54101699 Score: 208
Period size: 24 Copynumber: 6.4 Consensus size: 24
54101536 CACTGGGCCT
*
54101546 AGCCTCTTTTAATAACT-GGGCCT-
1 AGCC-CTTTTAATAACTGGGGCATA
54101569 AGCCTCTTTTAATAACTGGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
54101593 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
54101617 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
54101641 AGCCCTTTATCATAACT-GGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
*
54101665 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
*
54101690 AGACCTTTTA
1 AGCCCTTTTA
54101700 CACTTCCTCC
Statistics
Matches: 122, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
23 35 0.29
24 66 0.54
25 21 0.17
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:54101773 original size:20 final size:20
Alignment explanation
Indices: 54101748--54101794 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
54101738 TTATGAATAC
54101748 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54101768 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54101788 ACCATGT
1 ATCATGT
54101795 TTATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54109436 original size:29 final size:30
Alignment explanation
Indices: 54109388--54109445 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
54109378 CCTTTTCATA
54109388 TTTCATATTTCATAACACTGGGCCGAAGCT
1 TTTCATATTTCATAACACTGGGCCGAAGCT
**
54109418 TTTCA-ATTTCATATTACTGGGCCGAAGC
1 TTTCATATTTCATAACACTGGGCCGAAGC
54109446 CTTTACTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (30 bp):
TTTCATATTTCATAACACTGGGCCGAAGCT
Found at i:54109749 original size:25 final size:24
Alignment explanation
Indices: 54109643--54109763 Score: 183
Period size: 24 Copynumber: 5.0 Consensus size: 24
54109633 GCTTTATCAT
*
54109643 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
54109668 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54109691 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
54109715 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
54109740 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54109764 CACTTCCTCC
Statistics
Matches: 90, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.20
24 41 0.46
25 31 0.34
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:54109757 original size:49 final size:48
Alignment explanation
Indices: 54109634--54109763 Score: 183
Period size: 49 Copynumber: 2.6 Consensus size: 48
54109624 AGCATAGCTG
*
54109634 CTTTATCATATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAGCC
1 CTTTATC--ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAGCC
*
54109685 CTTT-TAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCA-AAGCC
54109733 CTTTATCATAACTGGGGCATAAGCCCTTTTA
1 CTTTATCATAACTGGGGCATAAGCCCTTTTA
54109764 CACTTCCTCC
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
47 22 0.30
48 21 0.29
49 25 0.34
50 1 0.01
51 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (48 bp):
CTTTATCATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAGCC
Found at i:54109837 original size:20 final size:20
Alignment explanation
Indices: 54109812--54109878 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
54109802 TTATGAATAC
54109812 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54109832 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54109852 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54109872 ACCATGT
1 ATCATGT
54109879 TTCTCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54109843 original size:11 final size:11
Alignment explanation
Indices: 54109812--54109867 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54109802 TTATGAATAC
54109812 ATCATGTGCAT
1 ATCATGTGCAT
*
54109823 ATCA--TACAT
1 ATCATGTGCAT
54109832 ATCATGTGCAT
1 ATCATGTGCAT
*
54109843 ATCA--TACAT
1 ATCATGTGCAT
*
54109852 GTCATGTGCAT
1 ATCATGTGCAT
54109863 ATCAT
1 ATCAT
54109868 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:54113580 original size:40 final size:40
Alignment explanation
Indices: 54113520--54113701 Score: 222
Period size: 40 Copynumber: 4.5 Consensus size: 40
54113510 TATTCGAATG
* *
54113520 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * * * *
54113560 ATATCTGGACTAAGATCCGAAGGCATTTGTTCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGACT
* * *
54113600 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * *
54113640 ATATCCGGGCTAAGTCCCGGAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
54113680 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
54113702 CCCTTGTGCG
Statistics
Matches: 117, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 114 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:54121360 original size:27 final size:27
Alignment explanation
Indices: 54121330--54121507 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54121320 ATATTGAGTC
* * * *
54121330 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54121357 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54121384 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54121412 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54121439 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54121466 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54121493 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54121508 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54121469 original size:82 final size:81
Alignment explanation
Indices: 54121351--54121506 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54121341 TGCTATATAA
* *
54121351 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54121416 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54121433 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54121497 CACTTAGTGC
65 CACTTAGTGC
54121507 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54130643 original size:27 final size:27
Alignment explanation
Indices: 54130613--54130790 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54130603 ATATTGAGTC
* * * *
54130613 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54130640 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54130667 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54130695 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54130722 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54130749 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54130776 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54130791 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54130752 original size:82 final size:81
Alignment explanation
Indices: 54130634--54130789 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54130624 TGCTATATAA
* *
54130634 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54130699 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54130716 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54130780 CACTTAGTGC
65 CACTTAGTGC
54130790 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54134619 original size:40 final size:40
Alignment explanation
Indices: 54134559--54134740 Score: 235
Period size: 40 Copynumber: 4.5 Consensus size: 40
54134549 TATTCGAATG
*
54134559 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
54134599 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
54134639 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
54134679 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
54134719 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGATCCGAAG
54134741 CCCTTGTGCG
Statistics
Matches: 124, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 120 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:54134692 original size:80 final size:80
Alignment explanation
Indices: 54134559--54134740 Score: 260
Period size: 80 Copynumber: 2.3 Consensus size: 80
54134549 TATTCGAATG
* * *
54134559 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
54134623 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* *
54134639 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
54134704 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
54134719 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
54134741 CCCTTGTGCG
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.03
80 89 0.97
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:54137908 original size:28 final size:27
Alignment explanation
Indices: 54137858--54137942 Score: 111
Period size: 27 Copynumber: 3.1 Consensus size: 27
54137848 AGCATGGCTG
* *
54137858 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
54137884 CCAGATACAGATAATTGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
*
54137912 CCAGAACAGAT-ATATGTGGCATAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
54137939 CCAG
1 CCAG
54137943 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
26 7 0.13
27 30 0.57
28 16 0.30
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:54145079 original size:20 final size:20
Alignment explanation
Indices: 54145054--54145097 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
54145044 TTTGATTAAG
54145054 TCATTTTTAGGAAAATATTT
1 TCATTTTTAGGAAAATATTT
*
54145074 TCA--TTTCGGAAAATATTT
1 TCATTTTTAGGAAAATATTT
54145092 TCATTT
1 TCATTT
54145098 CGGAAGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 17 0.81
20 4 0.19
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
TCATTTTTAGGAAAATATTT
Found at i:54145086 original size:18 final size:18
Alignment explanation
Indices: 54145063--54145102 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
54145053 GTCATTTTTA
54145063 GGAAAATATTTTCATTTC
1 GGAAAATATTTTCATTTC
54145081 GGAAAATATTTTCATTTC
1 GGAAAATATTTTCATTTC
54145099 GGAA
1 GGAA
54145103 GCTTTGCTTG
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:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (18 bp):
GGAAAATATTTTCATTTC
Found at i:54145740 original size:27 final size:26
Alignment explanation
Indices: 54145676--54145787 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
54145666 AGCATGGCTG
* *
54145676 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* *
54145702 CTAGATATAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
54145730 CCAGAACAGATATATGTGGCGGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
** *
54145757 CCAGATTAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
54145784 CCAG
1 CCAG
54145788 GATGCTTTCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.07
27 50 0.70
28 16 0.23
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:54145767 original size:54 final size:54
Alignment explanation
Indices: 54145676--54145787 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
54145666 AGCATGGCTG
* *
54145676 CCAGAACAGATAATGTGACAGAGTCACTAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATATAGATAATCGTGGCAGAGCCA
* * * *
54145730 CCAGAACAGATATATGTGGCGGAGCCACCAGAT-TAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATATAGATAATCGTGGCAGAGCCA
54145784 CCAG
1 CCAG
54145788 GATGCTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 35 0.69
55 16 0.31
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATATAGATAATCGTGGCAGAGCCA
Found at i:54152938 original size:19 final size:18
Alignment explanation
Indices: 54152912--54152947 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
54152902 ATTAGAATGT
*
54152912 AAAAATTAAATTAAAAAC
1 AAAAATTAAAGTAAAAAC
54152930 AAAATATTAAAGTAAAAA
1 AAAA-ATTAAAGTAAAAA
54152948 AAAGGCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAAATTAAAGTAAAAAC
Found at i:54156435 original size:21 final size:22
Alignment explanation
Indices: 54156398--54156439 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
54156388 ATTATGTGAT
54156398 AATAACAAAATTAATATTAATG
1 AATAACAAAATTAATATTAATG
54156420 AATAA-AAAAGTT-ATATTAAT
1 AATAACAAAA-TTAATATTAAT
54156440 TTGAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AATAACAAAATTAATATTAATG
Found at i:54156606 original size:18 final size:17
Alignment explanation
Indices: 54156583--54156625 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
54156573 ATTTAATTAA
54156583 ATAAATATCATTTTATAT
1 ATAAATATCATTTTAT-T
*
54156601 ATAAATATGATTTTATT
1 ATAAATATCATTTTATT
*
54156618 TTAAATAT
1 ATAAATAT
54156626 AATAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
ATAAATATCATTTTATT
Found at i:54159354 original size:62 final size:62
Alignment explanation
Indices: 54159264--54159381 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
54159254 CTTCAGATAT
* * *
54159264 TTTTTATTTAATACTTATAACATCTCGAACTAAGATATAATAAATGCCTTATACTCGTAAGA
1 TTTTTATTTAATACTTATAACATCTCGAACCAAAATATAATAAATGCCCTATACTCGTAAGA
* * *
54159326 TTTTTATTTAATACTTGTAACGTTTCGAACCAAAATATAATAAATGCCCTATACTC
1 TTTTTATTTAATACTTATAACATCTCGAACCAAAATATAATAAATGCCCTATACTC
54159382 ATGAGATATA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (62 bp):
TTTTTATTTAATACTTATAACATCTCGAACCAAAATATAATAAATGCCCTATACTCGTAAGA
Found at i:54165627 original size:7 final size:8
Alignment explanation
Indices: 54165609--54165636 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
54165599 CTAGATCGGC
54165609 AAAAGTCA
1 AAAAGTCA
54165617 AAAAGTCA
1 AAAAGTCA
54165625 AAAAGTCA
1 AAAAGTCA
54165633 AAAA
1 AAAA
54165637 ACCAGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAGTCA
Found at i:54175336 original size:27 final size:27
Alignment explanation
Indices: 54175322--54175375 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
54175312 CATATTTATT
*
54175322 TTCAATAACTTAATTTAAATATGATAA
1 TTCAATAACTTAATTCAAATATGATAA
*
54175349 TTCAATAACTTAATTTAAATATGATAA
1 TTCAATAACTTAATTCAAATATGATAA
54175376 AAAAATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (27 bp):
TTCAATAACTTAATTCAAATATGATAA
Found at i:54175382 original size:27 final size:27
Alignment explanation
Indices: 54175325--54175382 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
54175315 ATTTATTTTC
***
54175325 AATAACTTAATTTAAATATGATAATTC
1 AATAACTTAATTTAAATATGATAAAAA
54175352 AATAACTTAATTTAAATATGATAAAAA
1 AATAACTTAATTTAAATATGATAAAAA
54175379 AATA
1 AATA
54175383 CTTTTATGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.36
Consensus pattern (27 bp):
AATAACTTAATTTAAATATGATAAAAA
Found at i:54181039 original size:16 final size:16
Alignment explanation
Indices: 54181018--54181050 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54181008 AAACGGAGTA
54181018 AAAACCAAATTTCATG
1 AAAACCAAATTTCATG
54181034 AAAACCAAATTTCATG
1 AAAACCAAATTTCATG
54181050 A
1 A
54181051 TCCATTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAACCAAATTTCATG
Found at i:54188829 original size:36 final size:36
Alignment explanation
Indices: 54188746--54188845 Score: 146
Period size: 39 Copynumber: 2.7 Consensus size: 36
54188736 TGATACCAAC
*
54188746 ATAAAATTTTAACACGAATATTTAATAGTATCATCA
1 ATAAAATTTTAACACGAATATTTAATAGCATCATCA
* *
54188782 ATAATTCAATTTTAACACAAATATTTAATGGCATCATCA
1 ATAA---AATTTTAACACGAATATTTAATAGCATCATCA
54188821 ATAAAATTTTAACACGAATATTTAA
1 ATAAAATTTTAACACGAATATTTAA
54188846 AGGGGGGTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
36 24 0.42
39 33 0.58
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (36 bp):
ATAAAATTTTAACACGAATATTTAATAGCATCATCA
Found at i:54194285 original size:47 final size:47
Alignment explanation
Indices: 54194163--54194702 Score: 712
Period size: 47 Copynumber: 11.4 Consensus size: 47
54194153 AACAGCTCGT
* *
54194163 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
54194210 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * *
54194259 AGTGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
54194306 AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
54194355 CA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 -AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * * *
54194402 CA-TGCATATATGAGGTAAGGCCGAATAGCCAATGTGATGAATGTGAA
1 -AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
54194449 CA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 -AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
54194496 CA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 -AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
54194543 CA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 -AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * * *
54194590 CGTGCATATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * *
54194637 AGTGTATATATGTGGTAAGGCCGAATGGCCAATGTGATGGATGTGGA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
54194684 AGCGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
54194703 TCCCGAAGGG
Statistics
Matches: 453, Mismatches: 34, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
47 363 0.80
49 89 0.20
50 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
Found at i:54200160 original size:20 final size:21
Alignment explanation
Indices: 54200132--54200170 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
54200122 CTCTCTTGAT
54200132 CTAAATTAAT-ACAAATTTCA
1 CTAAATTAATCACAAATTTCA
*
54200152 CTAATTTAATCACAAATTT
1 CTAAATTAATCACAAATTT
54200171 AATCAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
CTAAATTAATCACAAATTTCA
Found at i:54212133 original size:49 final size:51
Alignment explanation
Indices: 54212061--54212207 Score: 199
Period size: 49 Copynumber: 2.9 Consensus size: 51
54212051 CACTTGTAGC
* * *
54212061 CAAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-
1 CAAAGTTATATGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGAT
* * * *
54212111 CCAA-TTATATGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAT
1 CAAAGTTATATGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGAT
**
54212161 CAAAGTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACACG
1 CAAAGTTATATGGTACGCATAGTAGCCTGCACTTAGTACTACACACG
54212208 TGACCTCACA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
49 39 0.47
50 6 0.07
51 38 0.46
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (51 bp):
CAAAGTTATATGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGAT
Found at i:54212197 original size:51 final size:50
Alignment explanation
Indices: 54212061--54212211 Score: 214
Period size: 51 Copynumber: 3.0 Consensus size: 50
54212051 CACTTGTAGC
* * *
54212061 CAAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA
1 CAAAGTTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * *
54212111 CCAA-TTATATGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA
1 CAAAGTTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
*
54212160 TCAAAGTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
1 -CAAAGTTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
54212211 C
1 C
54212212 CTCACAATAG
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 39 0.45
50 7 0.08
51 41 0.47
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (50 bp):
CAAAGTTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
Found at i:54223328 original size:56 final size:56
Alignment explanation
Indices: 54223242--54223361 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
54223232 ACAAGGGATG
*
54223242 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAAAAAGAAGC
*
54223298 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAAAAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAAAAAGAAGC
54223354 ATGGGCAA
1 ATGGGCAA
54223362 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAAAAAGAAGC
Done.