Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 357 of 438
Found at i:111461948 original size:94 final size:92
Alignment explanation
Indices: 111461728--111461999 Score: 270
Period size: 94 Copynumber: 2.9 Consensus size: 92
111461718 ATTTGTTTGT
* * *
111461728 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAG-AA-CCAGTGTAAGACCA
1 GAGCTAATGTAAGACATGTCTGGGACATGCATCGGCCTC--GA-GAGTAAGCCAGTGTAAGACCA
* *
111461791 TGTCTGGGACATGGCATCGGCATTGAGATGA
63 TGTCTGGGACAT-GAATCGGCATCGAGATGA
*
111461822 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGCCAGTGTAAGA-CATG
1 GAGCTAATGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA-GTAAGCCAGTGTAAGACCATG
*
111461886 TCTGGGACATGAATTGGC-TACGAGATGA
65 TCTGGGACATGAATCGGCAT-CGAGATGA
* ** * *
111461914 TAG-TCAATGTAAGACCATGTCTGGGACATGGCATC-AACTTGATA-TATGAGCCAGTGTAAGAC
1 GAGCT-AATGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGAGTA--AGCCAGTGTAAGAC
*
111461976 CATGTCTGGGACATGGCATCGGCA
61 CATGTCTGGGACAT-GAATCGGCA
111462000 CCTTGCCCAC
Statistics
Matches: 153, Mismatches: 13, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
91 6 0.04
92 25 0.16
93 48 0.31
94 68 0.44
95 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (92 bp):
GAGCTAATGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAGTAAGCCAGTGTAAGACCATGT
CTGGGACATGAATCGGCATCGAGATGA
Found at i:111461985 original size:140 final size:141
Alignment explanation
Indices: 111461733--111461998 Score: 369
Period size: 140 Copynumber: 1.9 Consensus size: 141
111461723 TTTGTGAGCT
* * *
111461733 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAACCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGAATCGGCCACATGATGAGAACCAATGTAAGACCATGTCTGG
** *
111461798 GACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCG
66 GACATGGCATCAACATTGAGATGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCG
111461862 AGACGTAAGCC
131 AGACGTAAGCC
* * * **
111461873 AGTGTAAGACATGTCTGGGACATGAATTGGCTACGA-GATGATAGTCAATGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTGGGACATGAATCGGCCAC-ATGATGAGAACCAATGTAAGACCATGTCTG
*
111461937 GGACATGGCATCAAC-TTGATAT-ATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
65 GGACATGGCATCAACATTGAGATGA-GAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGC
111461999 ACCTTGCCCA
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
138 1 0.01
139 19 0.17
140 81 0.74
141 9 0.08
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATGTCTGGGACATGAATCGGCCACATGATGAGAACCAATGTAAGACCATGTCTGG
GACATGGCATCAACATTGAGATGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCG
AGACGTAAGCC
Found at i:111471009 original size:5 final size:5
Alignment explanation
Indices: 111470999--111471027 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
111470989 AATTAATAAT
111470999 AATTA AATTA AATTA AATTA AATTA AATT
1 AATTA AATTA AATTA AATTA AATTA AATT
111471028 GCAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:111471009 original size:15 final size:15
Alignment explanation
Indices: 111470978--111471025 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
111470968 AAGAGAATGA
111470978 AAAAGTAAATT-AATT
1 AAAA-TAAATTAAATT
111470993 AATAAT-AATTAAATT
1 AA-AATAAATTAAATT
*
111471008 AAATTAAATTAAATT
1 AAAATAAATTAAATT
111471023 AAA
1 AAA
111471026 TTGCAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 6 0.21
15 21 0.72
16 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATAAATTAAATT
Found at i:111479554 original size:22 final size:23
Alignment explanation
Indices: 111479523--111479565 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
111479513 GGGTGAACTT
111479523 GATAGGAAAAACACAGGTGTGGG
1 GATAGGAAAAACACAGGTGTGGG
* *
111479546 GATA-GAAAACCACGGGTGTG
1 GATAGGAAAAACACAGGTGTG
111479566 CCACGAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.12, G:0.37, T:0.14
Consensus pattern (23 bp):
GATAGGAAAAACACAGGTGTGGG
Found at i:111481939 original size:28 final size:27
Alignment explanation
Indices: 111481876--111481945 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
111481866 ATAGTGAGTC
111481876 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
111481903 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
111481931 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
111481946 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:111484843 original size:6 final size:5
Alignment explanation
Indices: 111484818--111484894 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
111484808 AATCCTCCTT
111484818 TTTTA TTTTA TTTTA -TTTA TTCTTA TTTTTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTTA
111484868 TTTT- TCTTTGA TTTTTA TTTTTA TTTT
1 TTTTA T-TTT-A -TTTTA -TTTTA TTTT
111484895 CACTTCAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
4 9 0.14
5 36 0.56
6 13 0.20
7 5 0.08
8 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:111484853 original size:26 final size:25
Alignment explanation
Indices: 111484817--111484919 Score: 113
Period size: 25 Copynumber: 4.2 Consensus size: 25
111484807 GAATCCTCCT
111484817 TTTTTATTTTATTTTATTTATTCTTA
1 TTTTTATTTTATTTTATTTATT-TTA
111484843 TTTTTATTTTATTTTATTTATTTTA
1 TTTTTATTTTATTTTATTTATTTTA
* * *
111484868 TTTTTCTTTGATTTT-TAT-TTTTA
1 TTTTTATTTTATTTTATTTATTTTA
* **
111484891 TTTTCACTTCAATTTTA-TTATTTTA
1 TTTTTA-TTTTATTTTATTTATTTTA
111484916 TTTT
1 TTTT
111484920 GAAAAACACA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
23 9 0.14
24 10 0.15
25 25 0.38
26 22 0.33
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTTTATTTTATTTTATTTATTTTA
Found at i:111484884 original size:31 final size:32
Alignment explanation
Indices: 111484817--111484894 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
111484807 GAATCCTCCT
*
111484817 TTTTTATTTTATTTTATTTATTCTTATTTTTA
1 TTTTTATTTTATTTTATTTATTCTTATTTTGA
111484849 -TTTTATTTTA-TTTATTTTATT-TT-TCTTTGA
1 TTTTTATTTTATTTTA-TTTATTCTTAT-TTTGA
111484879 TTTTTATTTTTATTTT
1 TTTTTA-TTTTATTTT
111484895 CACTTCAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
29 1 0.03
30 10 0.25
31 21 0.52
32 5 0.12
33 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (32 bp):
TTTTTATTTTATTTTATTTATTCTTATTTTGA
Found at i:111487050 original size:40 final size:39
Alignment explanation
Indices: 111486984--111487134 Score: 153
Period size: 40 Copynumber: 3.8 Consensus size: 39
111486974 AAATTGAATG
* * *
111486984 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GGTAATT
* * ***
111487023 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GGTAATT
*
111487063 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCG-GTAATT
* *
111487103 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
111487135 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
39 16 0.17
40 74 0.80
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGGTAATT
Found at i:111487148 original size:40 final size:39
Alignment explanation
Indices: 111487021--111487150 Score: 161
Period size: 40 Copynumber: 3.3 Consensus size: 39
111487011 ATGCTGGAAA
* *
111487021 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-TGG
* * * **
111487061 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATGG
*
111487101 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA-ATGG
111487141 TTATATCCGG
1 TTATATCCGG
111487151 TTATATTCCG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 72 0.97
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATGG
Found at i:111495074 original size:39 final size:39
Alignment explanation
Indices: 111494993--111495158 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 39
111494983 AAATTGAATG
* *
111494993 ATATCCGGGCTAAG-CCCGAAGACAATTATGC--TGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTGG---TT
* *
111495032 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTGGTT
**
111495071 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGC-AGTGGTT
* * *
111495111 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCA-GTGGTT
111495151 ATATCCGG
1 ATATCCGG
111495159 TTATATTCCG
Statistics
Matches: 106, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
38 3 0.03
39 42 0.40
40 56 0.53
41 2 0.02
42 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTGGTT
Found at i:111512137 original size:2 final size:2
Alignment explanation
Indices: 111512130--111512171 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
111512120 ACATTCGGCC
111512130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111512172 GCATGTGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111512687 original size:29 final size:29
Alignment explanation
Indices: 111512626--111512724 Score: 168
Period size: 28 Copynumber: 3.5 Consensus size: 29
111512616 AATGAGATTG
111512626 GCACTAAGTGTGCGAGTTT-AATTGTATA
1 GCACTAAGTGTGCGAGTTTGAATTGTATA
111512654 GCACTAAGTGTGCGAGTTTGAATTGTATA
1 GCACTAAGTGTGCGAGTTTGAATTGTATA
111512683 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
1 GCACTAAGTGTGCGAGTTTGAAT-TGTATA
111512711 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
111512725 GACTTACTGT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 34 0.49
29 34 0.49
30 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.32
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTTGAATTGTATA
Found at i:111521256 original size:2 final size:2
Alignment explanation
Indices: 111521249--111521284 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
111521239 TTGTAAGCTC
111521249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111521285 GTATGTGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111522600 original size:18 final size:19
Alignment explanation
Indices: 111522560--111522606 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
111522550 GGTCATTTCC
111522560 CTCTTCATCGTAAACCAAG
1 CTCTTCATCGTAAACCAAG
*
111522579 -TCTTCATTGTAAACC-AG
1 CTCTTCATCGTAAACCAAG
*
111522596 CTCTTCTTCGT
1 CTCTTCATCGT
111522607 TGCTACCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (19 bp):
CTCTTCATCGTAAACCAAG
Found at i:111525962 original size:48 final size:48
Alignment explanation
Indices: 111525885--111526216 Score: 227
Period size: 48 Copynumber: 6.9 Consensus size: 48
111525875 GGTGAGTTGT
* * * * *
111525885 CGATTCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGC
* * *** * *
111525933 CGATGCCATGTCCCAGAAATGATCTTACACTAGCTCTTGTCTCAATGTC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA-GGC
* * * ** *
111525982 TG-TGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAAGGC
* * * * * * *
111526029 CTATGTCATCTCCTATACATGGTCTTACACTAGCGCACATATCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGC
* * * **
111526077 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACAACATCGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGC
* * * * * * ** *
111526125 CAATGACATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGC
* * * * * *
111526173 CGATGCCATATCCCAAACGTGGGCTTACACTGGCACACATATCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCA
111526217 CCCAAATGTC
Statistics
Matches: 215, Mismatches: 65, Indels: 8
0.75 0.23 0.03
Matches are distributed among these distances:
47 3 0.01
48 208 0.97
49 4 0.02
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGC
Found at i:111526161 original size:144 final size:142
Alignment explanation
Indices: 111525883--111526216 Score: 375
Period size: 144 Copynumber: 2.3 Consensus size: 142
111525873 ACGGTGAGTT
* * * * * *
111525883 GTCGATTCCATGTTCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCCGATGCCATGTCCCA
1 GTCGATGCCATATCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCGATGCCATGTCCCA
* * ** * *
111525948 GAAATGATCTTACACTAGCTCTTGTCTCAATGTCTGTGCCATGTCCCAGACATGGTCTTACACTG
66 GAAATGATCTTACACTAGCTC-T-TCACAATGCCAATGACATGTCCCAAACATGGTCTTACACTG
111526013 GCTCTCATAAT-GTG
129 GCTCTCAT-ATCGTG
* * * * * * *
111526027 GTCTATGTCATCTCCTATACATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCA
1 GTCGATGCCATATCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCGATGCCATGTCCCA
* * *
111526092 GACATGGTCTTACACTAGCTC-TCACAACATCGCCAATGACATGTTCCAAACATGGTCTTACACT
66 GAAATGATCTTACACTAGCTCTTCAC-A-AT-GCCAATGACATGTCCCAAACATGGTCTTACACT
111526156 GGCTCTCATATCGTG
128 GGCTCTCATATCGTG
* * *
111526171 GTCGATGCCATATCCCAAACGTGGGCTTACACTGGCACACATATCA
1 GTCGATGCCATATCCCAAACATGGTCTTACACTAGCACACATATCA
111526217 CCCAAATGTC
Statistics
Matches: 157, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
141 3 0.02
142 1 0.01
143 4 0.03
144 149 0.95
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (142 bp):
GTCGATGCCATATCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCGATGCCATGTCCCA
GAAATGATCTTACACTAGCTCTTCACAATGCCAATGACATGTCCCAAACATGGTCTTACACTGGC
TCTCATATCGTG
Found at i:111533631 original size:20 final size:20
Alignment explanation
Indices: 111533602--111533639 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
111533592 ACTGACAAGA
*
111533602 TGTATGGGTAGAAATGGACT
1 TGTATCGGTAGAAATGGACT
*
111533622 TGTATCGGTAGAATTGGA
1 TGTATCGGTAGAAATGGA
111533640 TGTAACAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (20 bp):
TGTATCGGTAGAAATGGACT
Found at i:111534421 original size:13 final size:13
Alignment explanation
Indices: 111534403--111534427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111534393 TGTTGTATTA
111534403 AAATTTTATTATG
1 AAATTTTATTATG
111534416 AAATTTTATTAT
1 AAATTTTATTAT
111534428 TTAGATAGTT
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
AAATTTTATTATG
Found at i:111536806 original size:28 final size:29
Alignment explanation
Indices: 111536739--111536839 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
111536729 ATAGTGAATC
*
111536739 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
111536768 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
111536796 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
111536826 CGCACACTTAGTGC
1 CGCACACTTAGTGC
111536840 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:111543684 original size:6 final size:6
Alignment explanation
Indices: 111543670--111543714 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
111543660 TGGAAAATGA
*
111543670 TTGGGG TTGGCG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTG
1 TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTG
111543715 AGATAGGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.02, G:0.62, T:0.36
Consensus pattern (6 bp):
TTGGGG
Found at i:111544763 original size:14 final size:14
Alignment explanation
Indices: 111544744--111544781 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
111544734 GTATAATTGG
*
111544744 TTTAGGGTTTAGAA
1 TTTAGGGTTTAAAA
111544758 TTTAGGGTTTAAAA
1 TTTAGGGTTTAAAA
*
111544772 TTTAAGGTTT
1 TTTAGGGTTT
111544782 GGGTTCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAAAA
Found at i:111546443 original size:19 final size:20
Alignment explanation
Indices: 111546419--111546465 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
111546409 TATTGTTATT
*
111546419 ATATTTATAATTATAATA-A
1 ATATTTATAATTAAAATATA
*
111546438 ATATTTATTATTAAAATATTA
1 ATATTTATAATTAAAATA-TA
111546459 ATATTTA
1 ATATTTA
111546466 ATATTTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.67
21 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTTATAATTAAAATATA
Found at i:111546515 original size:15 final size:17
Alignment explanation
Indices: 111546490--111546526 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
111546480 ATGTAAAGAA
111546490 TATTATTTAAAATT-AT
1 TATTATTTAAAATTCAT
111546506 TATT-TTTAAAATTCAT
1 TATTATTTAAAATTCAT
111546522 TATTA
1 TATTA
111546527 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATTTAAAATTCAT
Found at i:111546653 original size:22 final size:21
Alignment explanation
Indices: 111546626--111546668 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
111546616 ATGTTTAATA
111546626 ATATTAAAAAATATAATATTTT
1 ATATTAAAAAAT-TAATATTTT
* *
111546648 ATATTAATATATTAATATTTT
1 ATATTAAAAAATTAATATTTT
111546669 TAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTAAAAAATTAATATTTT
Found at i:111549065 original size:25 final size:24
Alignment explanation
Indices: 111549021--111549067 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
111549011 TATTATATAT
111549021 AATAAAACAAATAAAGAAAGAATA
1 AATAAAACAAATAAAGAAAGAATA
*
111549045 AATAAATAGAAATAGAA-AAAGAA
1 AATAAA-ACAAATA-AAGAAAGAA
111549068 AGCCAAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (24 bp):
AATAAAACAAATAAAGAAAGAATA
Found at i:111549108 original size:21 final size:21
Alignment explanation
Indices: 111549084--111549123 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
111549074 AGCAGAAACG
111549084 AAAGAGAGAAG-GAAAGAAATA
1 AAAGAGA-AAGAGAAAGAAATA
111549105 AAAGAGAAAGAGAAAGAAA
1 AAAGAGAAAGAGAAAGAAA
111549124 AGAGAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (21 bp):
AAAGAGAAAGAGAAAGAAATA
Found at i:111549124 original size:17 final size:17
Alignment explanation
Indices: 111549098--111549130 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
111549088 AGAGAAGGAA
*
111549098 AGAAATAAAAGAGAAAG
1 AGAAAGAAAAGAGAAAG
111549115 AGAAAGAAAAGAGAAA
1 AGAAAGAAAAGAGAAA
111549131 AAGTTAGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
AGAAAGAAAAGAGAAAG
Found at i:111554134 original size:5 final size:5
Alignment explanation
Indices: 111554124--111554167 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
111554114 TTGTTTTTAT
*
111554124 TATAA TATAA TATAA TATAA TATAG TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
111554168 CTTAATTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:111555958 original size:63 final size:63
Alignment explanation
Indices: 111555797--111555958 Score: 164
Period size: 63 Copynumber: 2.6 Consensus size: 63
111555787 ATCCCTAAAG
** * * ** *
111555797 AATGTGTTGATGCAGGGAATAATTACGCGTGC-TGTGGTGCTTATGTAAAATAAACTAGTGCTG
1 AATGTGTTGATGCAGGGAATAATTGTGCGT-CTTGTGGTACTTATGTAAAATAAACCAAAGCTA
** * * * * * *
111555860 GTTATGTTGATGCAGAGAATGATTGTGCATGTTGTGGTACTTGTGTAAAATAAACCAAAGCTA
1 AATGTGTTGATGCAGGGAATAATTGTGCGTCTTGTGGTACTTATGTAAAATAAACCAAAGCTA
*
111555923 AATGTGTTGATGCAGGGAATAAGTGTGCGTCTTGTG
1 AATGTGTTGATGCAGGGAATAATTGTGCGTCTTGTG
111555959 ATGCTTGCGA
Statistics
Matches: 75, Mismatches: 23, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.33
Consensus pattern (63 bp):
AATGTGTTGATGCAGGGAATAATTGTGCGTCTTGTGGTACTTATGTAAAATAAACCAAAGCTA
Found at i:111557933 original size:19 final size:19
Alignment explanation
Indices: 111557911--111557947 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
111557901 CATAAAACCT
*
111557911 TTGACATGACATGAAAATC
1 TTGACATGAAATGAAAATC
*
111557930 TTGAGATGAAATGAAAAT
1 TTGACATGAAATGAAAAT
111557948 GACTTGAAAG
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:0.08, G:0.19, T:0.27
Consensus pattern (19 bp):
TTGACATGAAATGAAAATC
Found at i:111558015 original size:17 final size:17
Alignment explanation
Indices: 111557993--111558029 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
111557983 GTTACTTGAT
111557993 TGATATGAAGATTTTGG
1 TGATATGAAGATTTTGG
111558010 TGATATGAAGATTTTGG
1 TGATATGAAGATTTTGG
111558027 TGA
1 TGA
111558030 CTAACATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (17 bp):
TGATATGAAGATTTTGG
Found at i:111559025 original size:22 final size:21
Alignment explanation
Indices: 111558975--111559025 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
111558965 GTCCTAGGGT
111558975 CACACGGGCGTTTCCCTTGGA
1 CACACGGGCGTTTCCCTTGGA
*
111558996 C-CACGGGCGTTTCTCTTGGA
1 CACACGGGCGTTTCCCTTGGA
111559016 CCACACGGGC
1 -CACACGGGC
111559026 ATGTAAACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 18 0.67
21 2 0.07
22 7 0.26
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.22
Consensus pattern (21 bp):
CACACGGGCGTTTCCCTTGGA
Found at i:111564842 original size:11 final size:11
Alignment explanation
Indices: 111564813--111564842 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
111564803 TTGTTTTAGA
111564813 TTTA-TTTTAT
1 TTTATTTTTAT
111564823 TTTATTTTTAT
1 TTTATTTTTAT
111564834 TTTATTTTT
1 TTTATTTTT
111564843 GGAAGTGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:111599346 original size:46 final size:45
Alignment explanation
Indices: 111599293--111599468 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
111599283 TATTTGGGCA
*
111599293 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
111599339 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
111599386 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
111599432 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
111599469 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:111599448 original size:93 final size:93
Alignment explanation
Indices: 111599289--111599461 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
111599279 AGGATATTTG
* * *
111599289 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
111599354 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
111599382 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
111599447 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
111599462 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:111601817 original size:22 final size:22
Alignment explanation
Indices: 111601787--111601830 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
111601777 CAAAATAATA
*
111601787 AAAAATAATAAAAATTTATTAT
1 AAAAATAATAAAAATTCATTAT
* *
111601809 AAAATTAATTAAAATTCATTAT
1 AAAAATAATAAAAATTCATTAT
111601831 GTTAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATAATAAAAATTCATTAT
Found at i:111603412 original size:39 final size:39
Alignment explanation
Indices: 111603353--111603431 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
111603343 ACAAGTTAGT
*
111603353 CACAGAATCTTATATGAATATCAAGTAAACATAGATGAG
1 CACAGAATCTCATATGAATATCAAGTAAACATAGATGAG
*
111603392 CACATAATCTCATATGAATATCAAGTAAACATAGATGAG
1 CACAGAATCTCATATGAATATCAAGTAAACATAGATGAG
111603431 C
1 C
111603432 CTAGCACATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (39 bp):
CACAGAATCTCATATGAATATCAAGTAAACATAGATGAG
Found at i:111603429 original size:21 final size:21
Alignment explanation
Indices: 111603366--111603429 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
111603356 AGAATCTTAT
111603366 ATGAATATCAAGTAAACATAG
1 ATGAATATCAAGTAAACATAG
** * *
111603387 ATGAGCA-C-A-TAATC-TCAT
1 ATGAATATCAAGTAAACAT-AG
111603405 ATGAATATCAAGTAAACATAG
1 ATGAATATCAAGTAAACATAG
111603426 ATGA
1 ATGA
111603430 GCCTAGCACA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 1 0.03
18 10 0.33
19 2 0.07
20 2 0.07
21 14 0.47
22 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (21 bp):
ATGAATATCAAGTAAACATAG
Found at i:111604064 original size:40 final size:38
Alignment explanation
Indices: 111603996--111604079 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 38
111603986 AGTCTTGAGC
* * *
111603996 TTAGTATCAGTAGCGTTGGGCCTTAGCCCAACTCAGTA
1 TTAGTATCAGTAGCCTAGGGCCTTAGCCCAACACAGTA
*
111604034 TTAGTATCAGTATGCACTAGGGCCTTAGCCCATCACAGTA
1 TTAGTATCAGTA-GC-CTAGGGCCTTAGCCCAACACAGTA
*
111604074 TCAGTA
1 TTAGTA
111604080 ACAAATATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 12 0.31
39 2 0.05
40 25 0.64
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (38 bp):
TTAGTATCAGTAGCCTAGGGCCTTAGCCCAACACAGTA
Found at i:111604641 original size:18 final size:18
Alignment explanation
Indices: 111604603--111604637 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
111604593 ATCCCACACA
*
111604603 CCCGTGTGGACCCACATG
1 CCCGTGTAGACCCACATG
111604621 CCCGTGTAG-CCCACATG
1 CCCGTGTAGACCCACATG
111604638 GCCCAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (18 bp):
CCCGTGTAGACCCACATG
Found at i:111606996 original size:49 final size:49
Alignment explanation
Indices: 111606940--111607184 Score: 265
Period size: 49 Copynumber: 4.9 Consensus size: 49
111606930 TAGCCAAAGC
* * *
111606940 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * * *
111606989 TATCTGGTACACGTAGTAGTCTGCATTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC-AAT
* * * * **
111607039 CATCTGATACACGTAGGAGCCTGCACTTAGTACTACACACGTGATTAAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-T
* * * * *
111607090 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACGCATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * * *
111607139 AATCCGATACACGTAGTAGCTTGCACTTAGTACTACACATGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
111607185 TCACAATAGA
Statistics
Matches: 159, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 79 0.50
50 45 0.28
51 35 0.22
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
Found at i:111607460 original size:27 final size:27
Alignment explanation
Indices: 111607430--111607483 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
111607420 TCATACAACC
* *
111607430 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
111607457 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
111607484 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:111618309 original size:45 final size:45
Alignment explanation
Indices: 111618242--111618415 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
111618232 TGATATGTGT
* *
111618242 GCTAGTGTAAGACATGTTTGGGACATGCATTAGCCA-CAGCAT-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CATCAG-ATGAGA
*
111618287 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCA-TCAGATGAGA
* * * * * *
111618333 GCTAGTGTAAGACATGTCTGGGACATGCACCGGCCTCGCGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATC-AGAT-GA-GA
*
111618381 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAGC
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGC
111618416 TTGTTGTGTG
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
44 2 0.02
45 34 0.31
46 40 0.37
47 1 0.01
48 26 0.24
49 6 0.06
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCAGATGAGA
Found at i:111621574 original size:40 final size:40
Alignment explanation
Indices: 111621525--111621711 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 40
111621515 ATAACCACAT
* *
111621525 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA
* ** * *
111621565 GCACAAATGCCTTCGGGTATTAGCCCGGATTTAACAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA
* *
111621605 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GTCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACG--ACTA
* * * ** *
111621645 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTACCA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA
* * *
111621685 GCATAAATGTCTTCGGGACTTAGCCCG
1 GCACAAATGCCTTCGGGTCTTAGCCCG
111621712 ATATCATTCA
Statistics
Matches: 119, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 117 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA
Found at i:111621658 original size:80 final size:80
Alignment explanation
Indices: 111621525--111621674 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 80
111621515 ATAACCACAT
* *
111621525 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATGCCTTCGGGTATTAACC
111621590 CGGATTTAACAACTC
66 CGGATTTAACAACTC
* * *
111621605 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GTCACTAGCACAATTGCCTTCGGGTCTTAA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACG--ACTAGCACAAATGCCTTCGGGTATTAA
111621668 CCCGGAT
64 CCCGGAT
111621675 ATAATTACCA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
78 1 0.02
79 2 0.03
80 60 0.95
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (80 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATGCCTTCGGGTATTAACC
CGGATTTAACAACTC
Found at i:111621699 original size:80 final size:80
Alignment explanation
Indices: 111621512--111621711 Score: 210
Period size: 80 Copynumber: 2.5 Consensus size: 80
111621502 AATACGACCA
* * *
111621512 GATATAACCACAT-GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATGCC
1 GATATAACAAC-TCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATGCC
*
111621576 TTCGGGTATTAGCCCG
65 TTCGGGTATTAACCCG
* * * *
111621592 GATTTAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GTCACTAGCACAATTGC
1 GATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACG--ACTAGCACAAATGC
*
111621655 CTTCGGGTCTTAACCCG
64 CTTCGGGTATTAACCCG
** * * *
111621672 GATATAATTAC-CAGCATAAATGTCTTCGGGACTTAGCCCG
1 GATATAACAACTC-GCACAAATGCCTTCGGGTCTTAGCCCG
111621712 ATATCATTCA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 4 0.04
80 97 0.95
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
GATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATGCCT
TCGGGTATTAACCCG
Found at i:111625020 original size:29 final size:29
Alignment explanation
Indices: 111624987--111625088 Score: 195
Period size: 29 Copynumber: 3.5 Consensus size: 29
111624977 GTGACGAGAT
111624987 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
111625016 TGGCAATAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
111625045 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
111625074 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
111625089 GAGCTCGAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:111625104 original size:29 final size:29
Alignment explanation
Indices: 111624987--111625148 Score: 116
Period size: 29 Copynumber: 5.6 Consensus size: 29
111624977 GTGACGAGAT
* **
111624987 TGGCACTAAGTGTGC-ATGCTGGAAATATA
1 TGGCACTAAGTGTGCGA-GCTCGAAACGTA
* * **
111625016 TGGCAATAAGTGTGC-ATGCTGGAAATATA
1 TGGCACTAAGTGTGCGA-GCTCGAAACGTA
* **
111625045 TGGCACTAAGTGTGC-ATGCTGGAAATATA
1 TGGCACTAAGTGTGCGA-GCTCGAAACGTA
**
111625074 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGAGCTCGAAACGTA
* * * *
111625103 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAA-CGTA
111625132 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
111625149 AATCGAGTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
28 2 0.02
29 114 0.97
30 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTCGAAACGTA
Found at i:111625105 original size:58 final size:59
Alignment explanation
Indices: 111624983--111625148 Score: 196
Period size: 58 Copynumber: 2.9 Consensus size: 59
111624973 TACGGTGACG
* *
111624983 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCAATAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA
*
111625040 ATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA
* * * ** * **
111625098 GGGTATGGCACTATGTGTGCGGGCT-TAAATCGCATGGCACTAAGTGTGCGA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
111625149 AATCGAGTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
57 7 0.07
58 86 0.91
59 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (59 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA
Found at i:111629642 original size:58 final size:59
Alignment explanation
Indices: 111629520--111629685 Score: 205
Period size: 58 Copynumber: 2.9 Consensus size: 59
111629510 TACGGTGACG
*
111629520 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA
*
111629577 ATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA
* * * ** * **
111629635 GGGTATGGCACTATGTGTGCGGGCT-TAAATCGCATGGCACTAAGTGTGCGA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
111629686 AATCGAGTAT
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
57 7 0.07
58 87 0.92
59 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.26
Consensus pattern (59 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA
Found at i:111629647 original size:29 final size:29
Alignment explanation
Indices: 111629524--111629625 Score: 204
Period size: 29 Copynumber: 3.5 Consensus size: 29
111629514 GTGACGAGAT
111629524 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
111629553 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
111629582 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
111629611 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
111629626 GAGCTCGAAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:111638258 original size:13 final size:13
Alignment explanation
Indices: 111638225--111638258 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
111638215 GTGTTACATA
111638225 GGCATGTCACACG
1 GGCATGTCACACG
*
111638238 GGCGTGTCACACG
1 GGCATGTCACACG
*
111638251 TGCATGTC
1 GGCATGTC
111638259 CCTGCCGAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.29, G:0.32, T:0.21
Consensus pattern (13 bp):
GGCATGTCACACG
Found at i:111641585 original size:27 final size:27
Alignment explanation
Indices: 111641555--111641644 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
111641545 GGGCATAATC
* * * *
111641555 GTCATTTTACCATACAAGGATATTATG
1 GTCATTTTACCCTATAGGGGTATTATG
* *
111641582 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGTATTATG
*
111641609 GTCATTTTACCCTGTAGGGGTATTATG
1 GTCATTTTACCCTATAGGGGTATTATG
111641636 GTCATTTTA
1 GTCATTTTA
111641645 ACTATTTTAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTATG
Found at i:111646748 original size:46 final size:45
Alignment explanation
Indices: 111646695--111646870 Score: 162
Period size: 46 Copynumber: 3.8 Consensus size: 45
111646685 TATTTGGGCA
111646695 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AAATG
* * *
111646741 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGAAGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATG-AA--ATG
* * **
111646786 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGATCG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAT-G
* * *
111646834 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
111646871 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
42 1 0.01
43 6 0.06
44 1 0.01
45 2 0.02
46 62 0.58
47 28 0.26
48 1 0.01
49 1 0.01
50 4 0.04
51 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAATG
Found at i:111646844 original size:93 final size:93
Alignment explanation
Indices: 111646691--111646863 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
111646681 GGGATATTTG
* *
111646691 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAG
111646756 TTGAGTCCGAGTTCGAGAGAAGTAACTA
66 TTGAGTCCGAGTTCGAGAGAAGTAACTA
* ** *
111646784 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATG-TGATCGCCCGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAAT-GCCCGAACTCGTTGA
111646848 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
111646864 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGAAGTAACTA
Found at i:111663595 original size:2 final size:2
Alignment explanation
Indices: 111663588--111663618 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
111663578 TATAATTGTG
111663588 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
111663619 GATTCACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111678780 original size:40 final size:40
Alignment explanation
Indices: 111678731--111678881 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
111678721 ATAACCACGT
*
111678731 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC
* * *
111678771 GCACGAA-TGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATAGAATG--TCTC
* * *
111678811 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-C
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC
* * *
111678850 AGCATAATTGTCTTCGGGGCTTAGCCCGGATA
1 -GCACAATTGCCTTCGGGTCTTAGCCCGGATA
111678882 TTATTCAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 83 0.91
41 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC
Found at i:111678865 original size:80 final size:80
Alignment explanation
Indices: 111678731--111678880 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
111678721 ATAACCACGT
* *
111678731 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
111678796 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * * * *
111678811 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGGCTTAG
111678874 CCCGGAT
64 CCCGGAT
111678881 ATTATTCAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 3 0.05
80 58 0.95
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:111694148 original size:46 final size:46
Alignment explanation
Indices: 111694098--111694270 Score: 196
Period size: 46 Copynumber: 3.7 Consensus size: 46
111694088 TGGTTGAGCA
*
111694098 TCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
111694144 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
*
111694189 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
111694237 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
111694271 GGGGCAGGTT
Statistics
Matches: 108, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
42 6 0.06
43 5 0.05
45 4 0.04
46 55 0.51
47 26 0.24
48 2 0.02
50 4 0.04
51 6 0.06
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:111694254 original size:93 final size:93
Alignment explanation
Indices: 111694095--111694264 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
111694085 GGATGGTTGA
*
111694095 GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
111694160 TGAGTCCGAGTTTGTGAGATGTAACTAG
66 TGAGTCCGAGTTTGTGAGATGTAACTAG
* *
111694188 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
111694252 TTGAGTCCGAGTT
65 TTGAGTCCGAGTT
111694265 CACTTAGGGG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTTGTGAGATGTAACTAG
Found at i:111701544 original size:46 final size:46
Alignment explanation
Indices: 111701494--111701666 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
111701484 TGGTTGAGCA
*
111701494 TCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
111701540 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
111701585 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
111701633 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
111701667 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 58 0.55
47 28 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:111701650 original size:93 final size:93
Alignment explanation
Indices: 111701491--111701661 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
111701481 GGATGGTTGA
* *
111701491 GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
111701556 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
111701584 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
111701649 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
111701662 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGGCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:111704178 original size:34 final size:34
Alignment explanation
Indices: 111704104--111704200 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 34
111704094 CTTTCAGTTT
* * * **
111704104 CAGTCTGGGCCTGAGCCCCTTTTTTAGTAACAGTCG
1 CAGTCTGGGCCTGAG-CCC-ATTTCAGTAACAATAA
*
111704140 CAGTCTGGGCTTGAGCCCATTTCAGTAACAATAA
1 CAGTCTGGGCCTGAGCCCATTTCAGTAACAATAA
* *
111704174 CAGTCTGGGCCTAAGCCCGTTTCAGTA
1 CAGTCTGGGCCTGAGCCCATTTCAGTA
111704201 CAGTATGCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 35 0.67
35 3 0.06
36 14 0.27
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (34 bp):
CAGTCTGGGCCTGAGCCCATTTCAGTAACAATAA
Found at i:111708805 original size:30 final size:29
Alignment explanation
Indices: 111708740--111708806 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
111708730 TTTCAGTAAA
* **
111708740 ATGGACTAAATTGTGAAAATGTGAAATTG
1 ATGGACTAAAATGTGAAAAAATGAAATTG
*
111708769 AGGGACTAAAATGTGAAATAAATGAAATATG
1 ATGGACTAAAATGTGAAA-AAATGAAAT-TG
111708800 -TGGACTA
1 ATGGACTA
111708807 GTATGAGTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 16 0.52
30 13 0.42
31 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.24, T:0.27
Consensus pattern (29 bp):
ATGGACTAAAATGTGAAAAAATGAAATTG
Found at i:111717941 original size:46 final size:46
Alignment explanation
Indices: 111717748--111717941 Score: 130
Period size: 46 Copynumber: 4.2 Consensus size: 46
111717738 GTAACCCGCC
* * * ** * **
111717748 CCTAAGTGAAATCAGACTCAACTCAACGAGCTCGGGCGTTC-GTAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
* *
111717793 CCATAAATGAACTCGGACTCAACTCAACTAGTTCGGATGC-CTAGTTACAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACAT
* * * *** *
111717843 -CTCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTC-GCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
111717886 CCGTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAA-CAT
111717934 CCT-AGTGA
1 CCTAAGTGA
111717942 CATGTCACTT
Statistics
Matches: 112, Mismatches: 25, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 5 0.04
46 64 0.57
47 28 0.25
48 8 0.07
49 1 0.01
50 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
Found at i:111736986 original size:13 final size:13
Alignment explanation
Indices: 111736968--111736992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111736958 GTGTTTGGGC
111736968 CCACACGGGCATT
1 CCACACGGGCATT
111736981 CCACACGGGCAT
1 CCACACGGGCAT
111736993 GTGTGTTTTT
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:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (13 bp):
CCACACGGGCATT
Found at i:111740604 original size:19 final size:19
Alignment explanation
Indices: 111740567--111740602 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
111740557 ATATGTGATG
*
111740567 TTAATAAATAATTTAAAAT
1 TTAAAAAATAATTTAAAAT
111740586 TTAAAAAAT-ATTTAAAA
1 TTAAAAAATAATTTAAAA
111740603 ATAAGAGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAAATAATTTAAAAT
Found at i:111741952 original size:154 final size:154
Alignment explanation
Indices: 111741662--111741966 Score: 511
Period size: 154 Copynumber: 2.0 Consensus size: 154
111741652 AGAAGGGAGA
* * **
111741662 CTAAAGTATATTGCTTAAGGGAGTAAAAGTGGGAATAAGATCCCTTTTGTATTGTATGTTGGGTA
1 CTAAAGTATATTGCTAAAGGGAGTAAAAGTGGGAAGAAGATCAATTTTGTATTGTATGTTGGGTA
* *
111741727 TATATAGGGAGAAAGTCTCCTTGCTTGTAATGTCACGTCATCAACAACACGAGTGGTGGCCTGCT
66 TATATAGGGAGAAAGTCTCCTTGCTTGTAATGTCACGTCATCAACAACACGAGCGATGGCCTGCT
* *
111741792 CGTGTGGTCAGTCAAGTGGCAAGT
131 CATGTGGCCAGTCAAGTGGCAAGT
*
111741816 CTAAGGTATATTGCTAAAGGGAGTAAAAGTGGGAAGAAGATCAATTTTGTATTGTATGTTGGGTA
1 CTAAAGTATATTGCTAAAGGGAGTAAAAGTGGGAAGAAGATCAATTTTGTATTGTATGTTGGGTA
* *
111741881 TATATAGGGAGAAGGTCTCCTTGCTTGTAATGTCACGTCATCAACAGCACGAGCGATGGCCTGCT
66 TATATAGGGAGAAAGTCTCCTTGCTTGTAATGTCACGTCATCAACAACACGAGCGATGGCCTGCT
111741946 CATGTGGCCAGTCAAGTGGCA
131 CATGTGGCCAGTCAAGTGGCA
111741967 GGCCTGTTAT
Statistics
Matches: 140, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 140 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (154 bp):
CTAAAGTATATTGCTAAAGGGAGTAAAAGTGGGAAGAAGATCAATTTTGTATTGTATGTTGGGTA
TATATAGGGAGAAAGTCTCCTTGCTTGTAATGTCACGTCATCAACAACACGAGCGATGGCCTGCT
CATGTGGCCAGTCAAGTGGCAAGT
Found at i:111742809 original size:5 final size:5
Alignment explanation
Indices: 111742799--111742823 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
111742789 CCCTCAACTT
111742799 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
111742824 CTAGGAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:111743695 original size:22 final size:24
Alignment explanation
Indices: 111743669--111743717 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
111743659 GAGTCATTCA
*
111743669 AAAAGTAAAG-ATTCAAT-CAAAC
1 AAAAGTAAAGAATTAAATCCAAAC
*
111743691 AAAAGTAATGAATTAAATCCAAAC
1 AAAAGTAAAGAATTAAATCCAAAC
111743715 AAA
1 AAA
111743718 TTGATAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 6 0.26
24 8 0.35
ACGTcount: A:0.61, C:0.12, G:0.08, T:0.18
Consensus pattern (24 bp):
AAAAGTAAAGAATTAAATCCAAAC
Found at i:111747835 original size:40 final size:40
Alignment explanation
Indices: 111747780--111747861 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
111747770 CAATGCTTGC
* *
111747780 TTTGTGGGATGAATTATTAAAGGTTGCATCGCAGCTGAGT
1 TTTGTGGGATGAATTATTAAAGGTTGCATCACAACTGAGT
111747820 TTTGTGGGATGAATTATTAAAGGTTGCATCACAACTGAGT
1 TTTGTGGGATGAATTATTAAAGGTTGCATCACAACTGAGT
111747860 TT
1 TT
111747862 CAGTGATCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (40 bp):
TTTGTGGGATGAATTATTAAAGGTTGCATCACAACTGAGT
Found at i:111750575 original size:20 final size:20
Alignment explanation
Indices: 111750550--111750593 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
111750540 ATCCATTTGC
111750550 AAACAATAGCTCATCCATAT
1 AAACAATAGCTCATCCATAT
**
111750570 AAACAATATTTCATCCATAT
1 AAACAATAGCTCATCCATAT
111750590 AAAC
1 AAAC
111750594 TGTAACAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (20 bp):
AAACAATAGCTCATCCATAT
Found at i:111751346 original size:40 final size:40
Alignment explanation
Indices: 111751259--111751369 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 40
111751249 CGACTATGTT
* *
111751259 TGGCACTAAGTGTGCG-ATTCAAAATAGCTTTGGCTATAAA
1 TGGCACTAAGTGTGCGAATT-GAAATAGTTTTGGCTATAAA
** *
111751299 TAACACTAAGTGTGCGAATTGAAATAGTTTTGGCTATACGA
1 TGGCACTAAGTGTGCGAATTGAAATAGTTTTGGCTATA-AA
* *
111751340 -GGCACTAAGTGTGTGATATTGAGATAGTTT
1 TGGCACTAAGTGTGCGA-ATTGAAATAGTTT
111751370 CGATTATTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
40 43 0.73
41 16 0.27
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (40 bp):
TGGCACTAAGTGTGCGAATTGAAATAGTTTTGGCTATAAA
Found at i:111753158 original size:33 final size:33
Alignment explanation
Indices: 111753115--111753193 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
111753105 GAACAAACTG
* *
111753115 GGCCTAAGCCCA-TATTAATCGCAATATCAGTGT
1 GGCCTTAGCCCATTA-TAATAGCAATATCAGTGT
* * *
111753148 GGCCTTAGCCCATTATAGTATCAGTATCAGTGT
1 GGCCTTAGCCCATTATAATAGCAATATCAGTGT
*
111753181 GGGCTTAGCCCAT
1 GGCCTTAGCCCAT
111753194 CTCAGTACAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (33 bp):
GGCCTTAGCCCATTATAATAGCAATATCAGTGT
Found at i:111755133 original size:40 final size:40
Alignment explanation
Indices: 111755076--111755297 Score: 292
Period size: 40 Copynumber: 5.5 Consensus size: 40
111755066 ACCCAAGTAT
* *
111755076 CTTC-GGATTTAG-CCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
* **
111755114 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
111755154 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
*
111755194 CTTCGGGACTTAG-CCGGGTATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATGC
* *
111755236 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
111755276 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
111755298 CATCCGAATA
Statistics
Matches: 164, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
38 5 0.03
39 19 0.12
40 103 0.63
41 1 0.01
42 23 0.14
43 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
Found at i:111755257 original size:82 final size:79
Alignment explanation
Indices: 111755076--111755297 Score: 281
Period size: 82 Copynumber: 2.8 Consensus size: 79
111755066 ACCCAAGTAT
* * *
111755076 CTTC-GGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAG-CCGGATATAG
**
111755138 TCACTAGCATGAATGC
64 TCACTAGCACAAATGC
*
111755154 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCGGGTATAG-C
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAGTC
111755218 AACTACTCGCACAAATGC
66 -ACTA---GCACAAATGC
* *
111755236 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAG-CCGGATAT
111755298 CATCCGAATA
Statistics
Matches: 127, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
78 5 0.04
79 20 0.16
80 35 0.28
81 1 0.01
82 59 0.46
83 7 0.06
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAGTC
ACTAGCACAAATGC
Found at i:111763287 original size:40 final size:40
Alignment explanation
Indices: 111763209--111763432 Score: 310
Period size: 40 Copynumber: 5.5 Consensus size: 40
111763199 ACCCAAGTAT
* *
111763209 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
111763248 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
111763288 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
111763328 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
111763371 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
111763411 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
111763433 CATCCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 12 0.07
40 117 0.70
41 1 0.01
43 36 0.22
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:111763405 original size:83 final size:80
Alignment explanation
Indices: 111763209--111763432 Score: 317
Period size: 83 Copynumber: 2.8 Consensus size: 80
111763199 ACCCAAGTAT
* * * *
111763209 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
111763273 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
111763288 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
111763352 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
111763371 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
111763433 CATCCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.10
80 49 0.38
83 67 0.52
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:111771415 original size:40 final size:40
Alignment explanation
Indices: 111771337--111771559 Score: 317
Period size: 40 Copynumber: 5.5 Consensus size: 40
111771327 ACCCAAGTAT
* *
111771337 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
111771376 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
111771416 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
111771456 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA--GCACAAATGC
* *
111771498 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
111771538 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
111771560 CATCCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
39 12 0.07
40 117 0.70
41 1 0.01
42 36 0.22
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:111771532 original size:82 final size:80
Alignment explanation
Indices: 111771337--111771559 Score: 324
Period size: 82 Copynumber: 2.8 Consensus size: 80
111771327 ACCCAAGTAT
* * * *
111771337 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
111771401 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
111771416 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
111771480 CAACTACTGCACAAATGC
66 C-ACTA--GCACAAATGC
*
111771498 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
111771560 CATCCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
79 13 0.10
80 49 0.38
82 67 0.52
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:111773241 original size:14 final size:14
Alignment explanation
Indices: 111773222--111773250 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
111773212 CAACCCAAAG
111773222 AACAAACACTTCAA
1 AACAAACACTTCAA
111773236 AACAAACACTTCAA
1 AACAAACACTTCAA
111773250 A
1 A
111773251 GTACCAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (14 bp):
AACAAACACTTCAA
Found at i:111775580 original size:46 final size:46
Alignment explanation
Indices: 111775527--111775702 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
111775517 TATTTGGGCA
111775527 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
111775573 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
111775620 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
111775666 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
111775703 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:111775682 original size:93 final size:93
Alignment explanation
Indices: 111775523--111775694 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
111775513 GGGATATTTG
* *
111775523 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
111775588 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
111775616 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
111775681 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
111775695 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:111778672 original size:15 final size:15
Alignment explanation
Indices: 111778652--111778720 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
111778642 GTATCTTGGG
111778652 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
111778667 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
111778682 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
111778697 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
111778712 TTTCTTTAT
1 TTTCTTTAT
111778721 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:111778721 original size:30 final size:30
Alignment explanation
Indices: 111778643--111778730 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
111778633 CATAGTATCG
* * * *
111778643 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
111778673 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
111778703 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
111778731 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:111786160 original size:40 final size:40
Alignment explanation
Indices: 111786111--111786281 Score: 195
Period size: 40 Copynumber: 4.3 Consensus size: 40
111786101 TCTTCGGAAT
* * *
111786111 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* * *** *
111786150 TTAACCCGGATTTCGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
111786190 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
111786230 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTC-GGAC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
111786269 TTAGCCCGGATAT
1 TTAGCCCGGATAT
111786282 CATTCAAATG
Statistics
Matches: 110, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 19 0.17
40 90 0.82
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
Found at i:111795237 original size:34 final size:34
Alignment explanation
Indices: 111795198--111795264 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
111795188 GATGCTTCGC
* *
111795198 TATAAATCACAAATTTTTTACCCGATTCTGGCTA
1 TATAAATCACAAAATCTTTACCCGATTCTGGCTA
*
111795232 TATAAATCACAAAATCTTTACCCGATTTTGGCT
1 TATAAATCACAAAATCTTTACCCGATTCTGGCT
111795265 GTACTAACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (34 bp):
TATAAATCACAAAATCTTTACCCGATTCTGGCTA
Found at i:111799066 original size:27 final size:26
Alignment explanation
Indices: 111799010--111799120 Score: 159
Period size: 27 Copynumber: 4.2 Consensus size: 26
111799000 AGCATGGCTG
* *
111799010 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
111799036 CCAGAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
111799063 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
111799090 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
111799117 CCAG
1 CCAG
111799121 GACGCTTCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
26 15 0.19
27 61 0.78
28 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:111800522 original size:12 final size:12
Alignment explanation
Indices: 111800505--111800599 Score: 50
Period size: 12 Copynumber: 7.9 Consensus size: 12
111800495 GCCAACTCTT
*
111800505 GCTCCTTGATCA
1 GCTCCTTAATCA
* *
111800517 GCTCCTAAATCT
1 GCTCCTTAATCA
* *
111800529 TCTCCTTTATCA
1 GCTCCTTAATCA
* *
111800541 GCTCCTAAATCC
1 GCTCCTTAATCA
*
111800553 TCTCCCTT-ATCA
1 GCT-CCTTAATCA
* *
111800565 GCTCCTAAATCC
1 GCTCCTTAATCA
*
111800577 TCTCCCTT-ATCA
1 GCT-CCTTAATCA
*
111800589 GCTCCTAAATC
1 GCTCCTTAATC
111800600 TTCTCCTGAC
Statistics
Matches: 57, Mismatches: 22, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
11 6 0.11
12 45 0.79
13 6 0.11
ACGTcount: A:0.21, C:0.38, G:0.06, T:0.35
Consensus pattern (12 bp):
GCTCCTTAATCA
Found at i:111800534 original size:24 final size:23
Alignment explanation
Indices: 111800501--111800606 Score: 149
Period size: 24 Copynumber: 4.4 Consensus size: 23
111800491 GCCGGCCAAC
111800501 TCTTGCTCCTTGATCAGCTCCTAAA
1 TCTT-CTCCTT-ATCAGCTCCTAAA
111800526 TCTTCTCCTTTATCAGCTCCTAAA
1 TCTTCTCC-TTATCAGCTCCTAAA
*
111800550 TCCTCTCCCTTATCAGCTCCTAAA
1 TCTTCT-CCTTATCAGCTCCTAAA
*
111800574 TCCTCTCCCTTATCAGCTCCTAAA
1 TCTTCT-CCTTATCAGCTCCTAAA
111800598 TCTTCTCCT
1 TCTTCTCCT
111800607 GACAGCCTGT
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
23 3 0.04
24 66 0.86
25 8 0.10
ACGTcount: A:0.19, C:0.38, G:0.06, T:0.38
Consensus pattern (23 bp):
TCTTCTCCTTATCAGCTCCTAAA
Found at i:111802995 original size:24 final size:24
Alignment explanation
Indices: 111802963--111803060 Score: 133
Period size: 24 Copynumber: 4.0 Consensus size: 24
111802953 AACTCTTGCT
**
111802963 CCTTGATCAGCTCCTAAATATTCTC
1 CCTT-ATCAGCTCCTAAATCCTCTC
* * *
111802988 CTTTATCAACTCCAAAATCCTCTC
1 CCTTATCAGCTCCTAAATCCTCTC
111803012 CCTTATCAGCTCCTAAATCCTCTC
1 CCTTATCAGCTCCTAAATCCTCTC
*
111803036 CCTTATCAGCTCCTAAATCTTCTC
1 CCTTATCAGCTCCTAAATCCTCTC
111803060 C
1 C
111803061 AGCCATTCAC
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
24 61 0.95
25 3 0.05
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.35
Consensus pattern (24 bp):
CCTTATCAGCTCCTAAATCCTCTC
Found at i:111805550 original size:50 final size:50
Alignment explanation
Indices: 111805478--111805756 Score: 254
Period size: 50 Copynumber: 5.7 Consensus size: 50
111805468 TCAGCCACTT
* *
111805478 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGAGA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGA
* * *
111805528 TATGAAAGCTAGTATAACACCATGTCTGGGACATGGCATCGGCTT-GAG-
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGA
* * * ** *
111805576 -AT--G-TCTCAGTGTAAGACCATGTCTAGGACATGGCATTGGCACCGACA
1 TATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGA
* * * * *
111805623 GATGAGAGCCAGTGTAAGACCATGTCTGGGATATGGCATCGGCCTCGATA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGA
* * *
111805673 TATGAGAG-TCAATGTAAGACCATGTCTGGGACATGGCATCGACTT--TGA
1 TATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGA
* * * *
111805721 TGTGTA-AGCCAGTGTAAGACCATGCCCGGGACATGG
1 TATG-AGAGCTAGTGTAAGACCATGTCTGGGACATGG
111805757 TTTCGGCATC
Statistics
Matches: 184, Mismatches: 35, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
44 2 0.01
45 29 0.16
46 2 0.01
47 2 0.01
48 31 0.17
49 4 0.02
50 113 0.61
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGA
Found at i:111805595 original size:95 final size:98
Alignment explanation
Indices: 111805487--111805756 Score: 271
Period size: 95 Copynumber: 2.8 Consensus size: 98
111805477 TTATGAGAGC
* * *
111805487 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGAGATATGAAAGCTAGTATAACACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGACAGATGAAAGCCAGTATAACACCATG
* *
111805552 TCTGGGACATGGCATCGG-CTTG-AGAT-GTCT
66 TCTGGGACATGGCATCGGCCTCGAAGATAGACT
* * * ** * * *
111805582 CAGTGTAAGACCATGTCTAGGACATGGCATTGGCACCGACAGATGAGAGCCAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGACAGATGAAAGCCAGTATAACACCATG
* * *
111805647 TCTGGGATATGGCATCGGCCTCGATATATGAGAGT
66 TCTGGGACATGGCATCGGCCTCGA-AGAT-AGACT
* * * * * *
111805682 CAATGTAAGACCATGTCTGGGACATGGCATCGACTTTGA-TG-TGTAAGCCAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGACAGATGAAAGCCAGTATAACACCATG
* *
111805745 CCCGGGACATGG
66 TCTGGGACATGG
111805757 TTTCGGCATC
Statistics
Matches: 141, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
95 71 0.50
96 3 0.02
98 32 0.23
99 1 0.01
100 34 0.24
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (98 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTCGACAGATGAAAGCCAGTATAACACCATG
TCTGGGACATGGCATCGGCCTCGAAGATAGACT
Found at i:111809678 original size:12 final size:12
Alignment explanation
Indices: 111809661--111809685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
111809651 AGGACACCAT
111809661 GTAGACAAGAGA
1 GTAGACAAGAGA
111809673 GTAGACAAGAGA
1 GTAGACAAGAGA
111809685 G
1 G
111809686 CTACGTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.36, T:0.08
Consensus pattern (12 bp):
GTAGACAAGAGA
Found at i:111809729 original size:83 final size:83
Alignment explanation
Indices: 111809590--111809756 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
111809580 TGTATCCCAT
111809590 GTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGA
1 GTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGA
111809655 CACCATGTAGACAAGAGA
66 CACCATGTAGACAAGAGA
111809673 GTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGA
1 GTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGA
111809738 CACCATGTAGACAAGAGA
66 CACCATGTAGACAAGAGA
111809756 G
1 G
111809757 CTACGAGACA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (83 bp):
GTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGA
CACCATGTAGACAAGAGA
Found at i:111814764 original size:48 final size:48
Alignment explanation
Indices: 111814714--111814996 Score: 313
Period size: 48 Copynumber: 5.9 Consensus size: 48
111814704 GCCACATTAC
* *
111814714 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
* *
111814762 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGC-TTGAGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
* * *
111814809 --GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TG-AGAT
* * * *
111814857 GAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATCTAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA--GAT
* * * * *
111814907 GAGAGTCAGTGTAATACCATGTTTGGGACATGGCATCGACTTTGATG-T
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GAT
* * * *
111814955 GTGAGCTAGTGTAAGACCATGTCCGGGACATGGCATTGGCAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
111814997 CTTACCCTAT
Statistics
Matches: 197, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
45 34 0.17
46 1 0.01
47 7 0.04
48 78 0.40
49 1 0.01
50 76 0.39
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (48 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
Found at i:111814887 original size:50 final size:50
Alignment explanation
Indices: 111814714--111814997 Score: 289
Period size: 50 Copynumber: 5.9 Consensus size: 50
111814704 GCCACATTAC
* * *
111814714 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAT-TG-AGAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
* * *
111814762 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGC-T-TG-AGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
* *
111814809 --GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
* * * **
111814857 GAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATCTAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
* * * * * * *
111814907 GAGAGTCAGTGTAATACCATGTTTGGGACATGGCATCGACTTTGAT-G-T
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
* * * *
111814955 GTGAGCTAGTGTAAGACCATGTCCGGGACATGGCATTGGCATC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC
111814998 TTACCCTATG
Statistics
Matches: 199, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
45 34 0.17
46 1 0.01
47 7 0.04
48 77 0.39
50 80 0.40
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (50 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGGTAGAT
Found at i:111819057 original size:49 final size:49
Alignment explanation
Indices: 111819002--111819326 Score: 527
Period size: 47 Copynumber: 6.8 Consensus size: 49
111818992 ATGTACAAGA
111819002 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
111819051 TATG--TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
*
111819098 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA--AG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
* *
111819145 TATATATATATGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
*
111819194 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
* *
111819243 TATG--TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTA
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
* * *
111819290 TATATATATATGATAAGGCCGAATGGTCAATGTGATG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATG
111819327 GAAGTGGAAG
Statistics
Matches: 259, Mismatches: 11, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
47 136 0.53
49 123 0.47
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTG
Found at i:111819166 original size:96 final size:96
Alignment explanation
Indices: 111819002--111819341 Score: 574
Period size: 96 Copynumber: 3.5 Consensus size: 96
111818992 ATGTACAAGA
*
111819002 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAGGTGTATGTATGTGATAAGG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
111819067 CCGAATGGCCAATGTGATGAATGTGAAGGTG
66 CCGAATGGCCAATGTGATGAATGTGAAGGTG
* * *
111819098 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATATATGATAAGG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
111819163 CCGAATGGCCAATGTGATGAATGTGAAGGTG
66 CCGAATGGCCAATGTGATGAATGTGAAGGTG
111819194 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
* *
111819259 CCGAATGGCCAATGTGATGAATGTGAAAGTA
66 CCGAATGGCCAATGTGATGAATGTGAAGGTG
* * * *
111819290 TATATATATATGATAAGGCCGAATGGTCAATGTGATGGAA-GTGGAAGTGTAT
1 TATGTATATGTGATAAGGCCGAATGGCCAATGTGAT-GAATGTGAAAGTGTAT
111819342 AACTGTGATA
Statistics
Matches: 230, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
96 227 0.99
97 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29
Consensus pattern (96 bp):
TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
CCGAATGGCCAATGTGATGAATGTGAAGGTG
Found at i:111829757 original size:26 final size:26
Alignment explanation
Indices: 111829718--111829771 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
111829708 GTTTTTGCAT
*
111829718 GCAAAACAATATAGAAACAAATATTA
1 GCAAAACAAAATAGAAACAAATATTA
*
111829744 GCAAAACAAAATAGAAGCAAATATTA
1 GCAAAACAAAATAGAAACAAATATTA
111829770 GC
1 GC
111829772 TCACTTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.59, C:0.13, G:0.11, T:0.17
Consensus pattern (26 bp):
GCAAAACAAAATAGAAACAAATATTA
Found at i:111832451 original size:48 final size:47
Alignment explanation
Indices: 111832376--111832695 Score: 274
Period size: 48 Copynumber: 6.6 Consensus size: 47
111832366 AGGGTAAGCT
* * * *
111832376 GCCGACGCCATG-CCTCGGACATGGTCTTACACTGGCTCACACATTAAA
1 GCCGATGCCATGTCC-CAGACATGGTCTTACACTGGCTCTCAC-TTAAG
* **
111832424 GTCGATGCCATGTCCCAGACATGGTCTTACACTTACTCTCA-TATATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACT-TA---AG
* * **
111832474 GCCGATGCCATGTCCTAGGCATGGTCTTACACTGGCTCTCATCTGTCGG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-CT-TAAG
* * ** * *
111832523 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGATCTTGTCTCAAT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCACTTAAG
* * *
111832572 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTTAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-CTTAAG
*
111832620 GCCGATTCCATGTCCCAGACATGGTCTTACACTGGCTCTCA--TAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACTTAA---G
*
111832668 GCTGATG-CATGTCCCAGACAT-GTCTTAC
1 GCCGATGCCATGTCCCAGACATGGTCTTAC
111832696 TCTAGCACAC
Statistics
Matches: 223, Mismatches: 36, Indels: 28
0.78 0.13 0.10
Matches are distributed among these distances:
45 3 0.01
46 8 0.04
47 16 0.07
48 117 0.52
49 3 0.01
50 73 0.33
51 1 0.00
52 2 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACTTAAG
Found at i:111838763 original size:50 final size:50
Alignment explanation
Indices: 111838700--111838960 Score: 177
Period size: 50 Copynumber: 5.6 Consensus size: 50
111838690 ATATCAAAGT
* *
111838700 CGATGCCATGTCCCAGACATGGTCTTACACTTACTCTTATATACCGAG-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATACCG-GTGC
* ** * * *
111838750 CGATGCCATGTCCCAAACATGGTCTTACACTGGTTCTCATCTATCGGTGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATACCGGTGC
* *
111838800 CGATGCCATATCCCAGACATGGTCTTACAC--A-TATC--A-A-----GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATACCGGTGC
* *
111838839 CGATGCCATGTCCCAGACATGGTCTTACACT-AGCTCTCATCTTA---ATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCAT-ATACCGGTGC
* * * * * *
111838887 CGATACTATGTCCCATATATGGTCTTACACTGGCTCTCATA-A--TGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATACCGGT-GC
111838935 CGATG-CATGTCCCAGACAT-GTCTTAC
1 CGATGCCATGTCCCAGACATGGTCTTAC
111838961 TCTAGCACAC
Statistics
Matches: 170, Mismatches: 28, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
39 30 0.18
40 1 0.01
42 3 0.02
44 1 0.01
46 9 0.05
47 15 0.09
48 42 0.25
49 1 0.01
50 68 0.40
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (50 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATACCGGTGC
Found at i:111838937 original size:48 final size:47
Alignment explanation
Indices: 111838837--111838966 Score: 147
Period size: 48 Copynumber: 2.7 Consensus size: 47
111838827 CACATATCAA
**
111838837 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTTAAT
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCATAATAAT
* * * * *
111838885 GCCGATACTATGTCCCATATATGGTCTTACACTGGCTCTCATAAT-GT
1 GCCGATGC-ATGTCCCAGACATGGTCTTACACTAGCTCTCATAATAAT
*
111838932 GGCCGATGCATGTCCCAGACAT-GTCTTACTCTAGC
1 -GCCGATGCATGTCCCAGACATGGTCTTACACTAGC
111838967 ACACATATCA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
46 11 0.16
47 13 0.19
48 44 0.65
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.30
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATAAT
Found at i:111840231 original size:29 final size:29
Alignment explanation
Indices: 111840189--111840247 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
111840179 AATGTGTTAC
111840189 ATTCGAAAATGAATGTGGTTTTCTCACTA
1 ATTCGAAAATGAATGTGGTTTTCTCACTA
111840218 ATTCGAAAATGAATGTGGTTTTCTCACTA
1 ATTCGAAAATGAATGTGGTTTTCTCACTA
111840247 A
1 A
111840248 GTATGGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
ATTCGAAAATGAATGTGGTTTTCTCACTA
Found at i:111841374 original size:45 final size:45
Alignment explanation
Indices: 111841323--111841420 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 45
111841313 ATACTTAACT
* *
111841323 TTTAATTAAACTACTAATCACTAATTTAATGGTTATTGTTCTTCC
1 TTTAATTAAACTACTAATCACTAATATAATGGTTATTATTCTTCC
111841368 TTTAATTAAACTACTAATCACTAATATAATGGTTATTATTCTTCC
1 TTTAATTAAACTACTAATCACTAATATAATGGTTATTATTCTTCC
111841413 -TTAATTAA
1 TTTAATTAA
111841421 GCAAGTCGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 8 0.16
45 43 0.84
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (45 bp):
TTTAATTAAACTACTAATCACTAATATAATGGTTATTATTCTTCC
Found at i:111843389 original size:19 final size:20
Alignment explanation
Indices: 111843352--111843392 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
111843342 TTTTGTACGC
111843352 TTTTCCTTTTTCTGAATGAT
1 TTTTCCTTTTTCTGAATGAT
111843372 TTTTCCTGTTTT-TG-ATGAT
1 TTTTCCT-TTTTCTGAATGAT
111843391 TT
1 TT
111843393 GTTTGTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 9 0.45
21 4 0.20
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.63
Consensus pattern (20 bp):
TTTTCCTTTTTCTGAATGAT
Found at i:111849686 original size:19 final size:19
Alignment explanation
Indices: 111849638--111849702 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
111849628 ACGCATACTA
*
111849638 GCACACGAAGCACATATTG
1 GCACACGAAGCGCATATTG
* *
111849657 GCGCACAAAGCGCATATTG
1 GCACACGAAGCGCATATTG
* **
111849676 GCATACGAAGCGCATCCTG
1 GCACACGAAGCGCATATTG
111849695 GCACACGA
1 GCACACGA
111849703 TGTGCATCCT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.32, C:0.29, G:0.25, T:0.14
Consensus pattern (19 bp):
GCACACGAAGCGCATATTG
Found at i:111856995 original size:28 final size:28
Alignment explanation
Indices: 111856963--111857031 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
111856953 GCGTAGATCA
*
111856963 CGAAATTACCCCTAAAGAGTAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
111856991 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
111857019 CGATA-TACCCCTA
1 CGAAATTACCCCTA
111857032 GGGTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:111864710 original size:12 final size:12
Alignment explanation
Indices: 111864693--111864727 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
111864683 ATGGGCAACA
111864693 ATTTTGGGCCTG
1 ATTTTGGGCCTG
111864705 ATTTTGGGCCTG
1 ATTTTGGGCCTG
111864717 ATTTTGGGCCT
1 ATTTTGGGCCT
111864728 AATCGGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.09, C:0.17, G:0.31, T:0.43
Consensus pattern (12 bp):
ATTTTGGGCCTG
Found at i:111865318 original size:18 final size:17
Alignment explanation
Indices: 111865291--111865324 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
111865281 CAGCTGTGCT
*
111865291 GTTTTTTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
111865309 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
111865325 TTCTTCCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.09, C:0.15, G:0.09, T:0.68
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:111866227 original size:25 final size:25
Alignment explanation
Indices: 111866198--111866245 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
111866188 TTATAATATG
* * *
111866198 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
111866223 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
111866246 GTTTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:111866316 original size:9 final size:9
Alignment explanation
Indices: 111866284--111866360 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
111866274 TTTGATAAAC
111866284 ATGATATGT
1 ATGATATGT
* *
111866293 ATGGTATGCAC
1 ATGATATG--T
111866304 ATGATATGT
1 ATGATATGT
*
111866313 ATGATATGCAC
1 ATGATATG--T
*
111866324 ATGACATGT
1 ATGATATGT
*
111866333 ATGATATGCAC
1 ATGATATG--T
111866344 ATGATATGT
1 ATGATATGT
111866353 ATGATATG
1 ATGATATG
111866361 CACACGAGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
9 30 0.58
11 22 0.42
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:111866372 original size:20 final size:20
Alignment explanation
Indices: 111866282--111866364 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
111866272 ATTTTGATAA
*
111866282 ACATGATATGTATGGTATGC
1 ACATGATATGTATGATATGC
111866302 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
111866322 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
111866342 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
111866362 ACA
1 ACA
111866365 CGAGATGTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:111866492 original size:48 final size:48
Alignment explanation
Indices: 111866419--111866511 Score: 161
Period size: 48 Copynumber: 1.9 Consensus size: 48
111866409 AGGAAGTGCA
111866419 AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTT-TGCCCCAGTTATGAT
*
111866467 AAAGGGCTTATGCCCCAGTTGTTAAAAGGGCTTTGCCCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTGCCCCAGTTAT
111866512 TAAAAGAGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
48 34 0.79
49 9 0.21
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (48 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTGCCCCAGTTATGAT
Found at i:111866516 original size:23 final size:24
Alignment explanation
Indices: 111866418--111866522 Score: 160
Period size: 23 Copynumber: 4.4 Consensus size: 24
111866408 GAGGAAGTGC
111866418 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
111866442 -AAAGGGCTTATGCCCCAGTTATG
1 AAAAGGGCTTATGCCCCAGTTATT
*
111866465 ATAAAGGGCTTATGCCCCAGTTGTT
1 A-AAAGGGCTTATGCCCCAGTTATT
111866490 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
111866513 AAAAGAGGCT
1 AAAAG-GGCT
111866523 AGGCCTCCGG
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 39 0.53
24 13 0.18
25 22 0.30
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:111866769 original size:31 final size:31
Alignment explanation
Indices: 111866731--111866812 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
111866721 CGTTTACAGT
*
111866731 AAAGGCTTCGTCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
111866762 AAAGGCTTCGGCCCAGTGTTATGAAATATGAA
1 AAAGGCTTCGGCCCAGTAATATGAAATATG-A
111866794 AAAGGGCTAT-GGCCCAGTA
1 AAA-GGCT-TCGGCCCAGTA
111866813 CATGTTGAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 27 0.61
32 4 0.09
33 12 0.27
34 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:111873164 original size:18 final size:17
Alignment explanation
Indices: 111873137--111873170 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
111873127 CAGCTGTGCT
*
111873137 GTTTTTTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
111873155 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
111873171 TTCTTCCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.09, C:0.15, G:0.09, T:0.68
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:111874069 original size:25 final size:25
Alignment explanation
Indices: 111874040--111874087 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
111874030 TTATAATATG
* * *
111874040 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
111874065 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
111874088 GTTTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Done.