Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold427
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: 252688
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:166032 original size:17 final size:17
Alignment explanation
Indices: 165900--166088 Score: 92
Period size: 17 Copynumber: 10.9 Consensus size: 17
165890 GGCCATTTCA
165900 TTTTTT-ATTTTATTAT
1 TTTTTTGATTTTATTAT
*
165916 TTTATT-ATTTTGATT-T
1 TTTTTTGATTTT-ATTAT
* *
165932 TTTTGATGATTTTA-GA-
1 TTTT-TTGATTTTATTAT
* *
165948 TTTTTAGATTTTATTTT
1 TTTTTTGATTTTATTAT
*
165965 TACTTTTTGATTATTTTTTAT
1 T--TTTTTGA-T-TTTATTAT
165986 TTTTTT-ATTATT-TTAT
1 TTTTTTGATT-TTATTAT
*
166002 TTTATATTATATTTTATTAT
1 TTT-T-TT-GATTTTATTAT
166022 TTTTTTGATTTT-TTGAT
1 TTTTTTGATTTTATT-AT
* *
166039 TTCTTTGATTTTTTTGA-
1 TTTTTTGATTTTATT-AT
*
166056 TTTTTTGATTTT-TTGAA
1 TTTTTTGATTTTATT-AT
166073 TTTTTTGATTATTATT
1 TTTTTTGATT-TTATT
166089 TTAATTTTGT
Statistics
Matches: 138, Mismatches: 14, Indels: 39
0.72 0.07 0.20
Matches are distributed among these distances:
15 7 0.05
16 32 0.23
17 49 0.36
18 16 0.12
19 16 0.12
20 11 0.08
21 7 0.05
ACGTcount: A:0.19, C:0.01, G:0.07, T:0.73
Consensus pattern (17 bp):
TTTTTTGATTTTATTAT
Found at i:166033 original size:8 final size:8
Alignment explanation
Indices: 166022--166082 Score: 95
Period size: 8 Copynumber: 7.2 Consensus size: 8
166012 ATTTTATTAT
166022 TTTTTTGA
1 TTTTTTGA
166030 TTTTTTGA
1 TTTTTTGA
166038 TTTCTTTGA
1 TTT-TTTGA
166047 TTTTTTTGA
1 -TTTTTTGA
166056 TTTTTTGA
1 TTTTTTGA
166064 TTTTTTGAA
1 TTTTTTG-A
166073 TTTTTTGA
1 TTTTTTGA
166081 TT
1 TT
166083 ATTATTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
8 29 0.58
9 18 0.36
10 3 0.06
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (8 bp):
TTTTTTGA
Found at i:166069 original size:10 final size:10
Alignment explanation
Indices: 165968--166069 Score: 51
Period size: 9 Copynumber: 10.3 Consensus size: 10
165958 TTATTTTTAC
165968 TTTTTGATTAT
1 TTTTTGATT-T
165979 TTTTT-ATTT
1 TTTTTGATTT
*
165988 TTTTATTATTT
1 TTTT-TGATTT
165999 TATTTT-ATATT
1 T-TTTTGAT-TT
166010 ATATTTT-ATTATT
1 -T-TTTTGA-T-TT
166023 TTTTTGA--T
1 TTTTTGATTT
166031 TTTTTGA-TT
1 TTTTTGATTT
*
166040 TCTTTGA-TT
1 TTTTTGATTT
166049 TTTTTGA--T
1 TTTTTGATTT
166057 TTTTTGATTT
1 TTTTTGATTT
166067 TTT
1 TTT
166070 GAATTTTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 21
0.77 0.02 0.21
Matches are distributed among these distances:
8 16 0.20
9 20 0.25
10 10 0.13
11 17 0.22
12 12 0.15
13 4 0.05
ACGTcount: A:0.17, C:0.01, G:0.06, T:0.76
Consensus pattern (10 bp):
TTTTTGATTT
Found at i:166084 original size:63 final size:62
Alignment explanation
Indices: 165900--166096 Score: 153
Period size: 63 Copynumber: 3.2 Consensus size: 62
165890 GGCCATTTCA
* * *
165900 TTTTTTA--TTTT-ATTAT-TTT-ATTATTTTGATTTTTTTGATGATTTTAGATTTTTAGATT-T
1 TTTTTTATTTTTTGATTATCTTTGATTTTTTTGA-TTTTTTGAT-TTTTTA-ATTTTTTGATTAT
* * * * *
165959 TATTTTTACTTTTTGATTATTTTTTATTTTTTT-ATTATTTT-ATTTTAT-ATTATATTTTATTA
1 T-TTTTTATTTTTTGATTATCTTTGATTTTTTTGATT-TTTTGATTTTTTAATT-T-TTTGATTA
166021 T
62 T
166022 TTTTTTGATTTTTTGATT-TCTTTGATTTTTTTGATTTTTTGATTTTTTGAATTTTTTGATTAT
1 TTTTTT-ATTTTTTGATTATCTTTGATTTTTTTGATTTTTTGATTTTTT-AATTTTTTGATTAT
* *
166085 TATTTTAATTTT
1 TTTTTTATTTTT
166097 GTATCGAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
59 1 0.01
60 9 0.08
61 1 0.01
62 38 0.34
63 43 0.39
64 9 0.08
65 10 0.09
ACGTcount: A:0.19, C:0.01, G:0.07, T:0.73
Consensus pattern (62 bp):
TTTTTTATTTTTTGATTATCTTTGATTTTTTTGATTTTTTGATTTTTTAATTTTTTGATTAT
Found at i:168848 original size:28 final size:29
Alignment explanation
Indices: 168789--168862 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 29
168779 AATTTAAAAA
* *
168789 TTTAATAAATAATGATATATTAATCATTATT
1 TTTAATAAA-AATAATATATTAATCA-TAAT
*
168820 TTTAATAAAAATAATAT-TTAATTA-AAT
1 TTTAATAAAAATAATATATTAATCATAAT
*
168847 TTTAA-AAAAATTATAT
1 TTTAATAAAAATAATAT
168863 CAATAAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 10 0.26
27 7 0.18
29 6 0.15
30 7 0.18
31 9 0.23
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
TTTAATAAAAATAATATATTAATCATAAT
Found at i:168869 original size:24 final size:27
Alignment explanation
Indices: 168819--168871 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
168809 TAATCATTAT
*
168819 TTTTAATAAAAATAATATTTAATTAAA
1 TTTTAATAAAAATAATATTCAATTAAA
*
168846 TTTTAA-AAAAATTATA-TCAA-TAAA
1 TTTTAATAAAAATAATATTCAATTAAA
168870 TT
1 TT
168872 AAAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 3 0.12
26 9 0.38
27 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTTAATAAAAATAATATTCAATTAAA
Found at i:168996 original size:21 final size:21
Alignment explanation
Indices: 168939--169000 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
168929 ATTTTTAATA
* *
168939 AAATTAAAAATAA-TATTTAATT
1 AAATTAAAAA-AATTAATTAA-C
168961 AAATTAAAAAAATTACATTAAC
1 AAATTAAAAAAATTA-ATTAAC
*
168983 AAATT-AAAATATTAATTA
1 AAATTAAAAAAATTAATTA
169001 TATGTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 4 0.11
21 10 0.29
22 17 0.49
23 4 0.11
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATTAAAAAAATTAATTAAC
Found at i:169014 original size:116 final size:110
Alignment explanation
Indices: 168825--169103 Score: 330
Period size: 116 Copynumber: 2.5 Consensus size: 110
168815 TTATTTTTAA
* * *
168825 TAAAAATAATATTTAATTAAATTTTAAAAAAATTATATCAATAAATTAAAATATTAATTATTTTT
1 TAAAAATAATATTTAATTAAA-TTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTT
168890 TAAAATAAATAATTAAATTAAAAAAGGTTAATTATTATTA-TTTTTAATAAAAT
65 T-AAATAAA-AA-T-AA--AAAAAA--TTAATTATTATTATTTTTTAATAAAAT
168943 TAAAAATAATATTTAATTAAA-TTAAAAAAATTACATTAACAAATTAAAATATTAATTATATGTT
1 TAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAACAAATTAAAATATTAATTAT-T-TT
* ** **
169007 TT-TATAAAAATAAAAAGTATTTTTTATTATTATTTTTTAATAAAAT
64 TTAAATAAAAATAAAAAAAATTAATTATTATTATTTTTTAATAAAAT
* * *
169053 AAAAAATGATATTTAATTAAATTTAAAAACATTTACATTAACAAATTAAAA
1 TAAAAATAATATTTAATTAAATTTAAAAA-AATTACATTAACAAATTAAAA
169104 AAAATAACAT
Statistics
Matches: 145, Mismatches: 11, Indels: 16
0.84 0.06 0.09
Matches are distributed among these distances:
109 11 0.08
110 32 0.22
111 11 0.08
112 20 0.14
113 2 0.01
114 1 0.01
115 2 0.01
116 40 0.28
117 1 0.01
118 25 0.17
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (110 bp):
TAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTT
AAATAAAAATAAAAAAAATTAATTATTATTATTTTTTAATAAAAT
Found at i:169561 original size:124 final size:123
Alignment explanation
Indices: 169418--169780 Score: 463
Period size: 123 Copynumber: 2.9 Consensus size: 123
169408 AAAAAATATT
169418 ATTATAATAAAAAACTTTTTTTAATTTAAAATTTTTTATTTTTAGAAACATAATAATTAATATTT
1 ATTATAATAAAAAACTTTTTTTAATTTAAAATTTTTTATTTTTA-AAACATAATAATTAATATTT
169483 TAATTTGTTAATGTAAATTTTTAAAATTAATTAAATATTATTTTTTATTTTATT-AAAA
65 TAATTTGTTAATGTAAATTTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAAAA
* * *
169541 ATTATAATAAAAAACTTTTTTTATTTTAAAATTTTTTATTTTTATAAAAACATATTAAATAA-AT
1 ATTATAATAAAAAACTTTTTTTAATTTAAAATTTTTTA-TTTT-T-AAAACATAATAATTAATAT
*
169605 TTTAATTTGTTAATGT-AATTTTTAAAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
63 TTTAATTTGTTAATGTAAATTTTTAAAA-TTAATTAAATATTATTTTTTATTTTATTAAAAA
* ** * *
169666 ATAATAATAATCAACCCTTTTTATTTTTATTT-AAACTTTTTA-TTTT-AAA-A-AATAATTAAT
1 ATTATAATAA--AAAAC--TTT-TTTTAATTTAAAATTTTTTATTTTTAAAACATAATAATTAAT
* *
169726 ATTTTAATTTGTTAATATAAATTTCTTTAAAGTTAATTAAATATTATTTTTTATT
61 ATTTTAATTTGTTAATGTAAA-TT-TTTAAAATTAATTAAATATTATTTTTTATT
169781 AAAAGTAATA
Statistics
Matches: 211, Mismatches: 15, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
122 7 0.03
123 66 0.31
124 54 0.26
125 51 0.24
126 8 0.04
127 6 0.03
129 12 0.06
130 7 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (123 bp):
ATTATAATAAAAAACTTTTTTTAATTTAAAATTTTTTATTTTTAAAACATAATAATTAATATTTT
AATTTGTTAATGTAAATTTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAAAA
Found at i:173207 original size:52 final size:52
Alignment explanation
Indices: 173122--173246 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
173112 ATATGAAAAG
* *
173122 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
173174 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
173226 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
173247 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:173259 original size:52 final size:51
Alignment explanation
Indices: 173122--173267 Score: 213
Period size: 52 Copynumber: 2.8 Consensus size: 51
173112 ATATGAAAAG
*
173122 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
173174 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
173226 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
173268 TTTTTTTGGC
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:173328 original size:13 final size:13
Alignment explanation
Indices: 173310--173334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173300 CAAAAAAATA
173310 TGTATCGATACAT
1 TGTATCGATACAT
173323 TGTATCGATACA
1 TGTATCGATACA
173335 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:173330 original size:33 final size:33
Alignment explanation
Indices: 173288--173354 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
173278 AGTAGCTTAA
173288 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
173321 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
173354 A
1 A
173355 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:173584 original size:18 final size:18
Alignment explanation
Indices: 173558--173618 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 18
173548 GAATTGGTCC
173558 CCACATAGGTCGAATCCT
1 CCACATAGGTCGAATCCT
*
173576 CCACGTAGGTCGAATTGGTCC-
1 CCACATAGGTCGAA----TCCT
173597 CCACATAGGTCGAATCCT
1 CCACATAGGTCGAATCCT
173615 CCAC
1 CCAC
173619 CTATTAGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 3 0.08
18 17 0.47
21 13 0.36
22 3 0.08
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (18 bp):
CCACATAGGTCGAATCCT
Found at i:173605 original size:21 final size:21
Alignment explanation
Indices: 173548--173611 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
173538 CCATTTTTAT
173548 GAATTGGTCCCCACATAGGTC
1 GAATTGGTCCCCACATAGGTC
*
173569 GAA----TCCTCCACGTAGGTC
1 GAATTGGTCC-CCACATAGGTC
173587 GAATTGGTCCCCACATAGGTC
1 GAATTGGTCCCCACATAGGTC
173608 GAAT
1 GAAT
173612 CCTCCACCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 3 0.08
18 13 0.36
21 17 0.47
22 3 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (21 bp):
GAATTGGTCCCCACATAGGTC
Found at i:174462 original size:91 final size:92
Alignment explanation
Indices: 174161--174704 Score: 721
Period size: 91 Copynumber: 6.0 Consensus size: 92
174151 AAAAATTGAC
* * * * *
174161 TGATTGTAAATATCAGACTGCGATGATTAAACTAATGCATGAATTATATCTGAAAATCAGATTCT
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGA---T
174226 TCTTTTTTATAGAAAAAAAGAAAGACTGAT
63 TCTTTTTTATAGAAAAAAAGAAAGACTGAT
* * * * *
174256 TGATTGCAAATGTGAGACTGCAAGGATTAGACTCATGCATGAATTATA-CTGAAAATC-GAATTA
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAG-ATTC
*
174319 TTTTTTAT----AAAAA-AAAG-TTGAT
65 TTTTTTATAGAAAAAAAGAAAGACTGAT
* * * *
174341 TGATTATAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATATATGAGAATCAGATT-T
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCT
174405 TTTTTATAGAAAAAAAGAAAGACTGAT
66 TTTTTATAGAAAAAAAGAAAGACTGAT
* * *
174432 TAATTGTAAATGTCAGACTGCAAGAATTAGACTAATGCATGAATTATATCTAAGAATCAGATTCT
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCT
*
174497 TTTTTATAGAAAAAAAGAAAGACTAAT
66 TTTTTATAGAAAAAAAGAAAGACTGAT
* * * *
174524 TGATTGTAAATGTCATACTGCAAGGATTAGATTAATGCATGAATTAAATCTGAGAATCAGATTTT
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCT
* * *
174589 TTTTTTTAG-AAAAAAGAAAGGCTTAT
66 TTTTTATAGAAAAAAAGAAAGACTGAT
* *
174615 TGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGGATTCT
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCT
*
174680 TTTTTATAGGAAAAAAGAAAGACTG
66 TTTTTATAGAAAAAAAGAAAGACTG
174705 CAAGGATTAG
Statistics
Matches: 394, Mismatches: 44, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
85 55 0.14
86 14 0.04
87 6 0.02
89 5 0.01
90 4 0.01
91 152 0.39
92 106 0.27
93 1 0.00
94 10 0.03
95 41 0.10
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (92 bp):
TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCT
TTTTTATAGAAAAAAAGAAAGACTGAT
Found at i:174604 original size:183 final size:182
Alignment explanation
Indices: 174161--174703 Score: 717
Period size: 183 Copynumber: 3.0 Consensus size: 182
174151 AAAAATTGAC
* * * * *
174161 TGATTGTAAATATCAGACTGCGATGATTAAACTAATGCATGAATTATATCTGAAAATCAGATTCT
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATT-T
* * *
174226 TCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGCAAATGTGAGACTGCAAGGATTAGACTCA
65 T-TTTTTT-TAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAA
* * *
174291 TGCATGAATTATA-CTGAA-AATCGAATTATTTTTTAT---AAAAA-AAAG-TTGAT
128 TGCATGAATTATATCT-AAGAATCG-ATTCTTTTTTATAGAAAAAAGAAAGACTAAT
* * * *
174341 TGATTATAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATATATGAGAATCAGA-TTT
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTT
* * *
174405 TTTTTATAGAAAAAAAGAAAGACTGATTAATTGTAAATGTCAGACTGCAAGAATTAGACTAATGC
66 TTTTTTTAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGC
174470 ATGAATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTAAT
131 ATGAATTATATCTAAGAATC-GATTCTTTTTTATAG-AAAAAAGAAAGACTAAT
* * *
174524 TGATTGTAAATGTCATACTGCAAGGATTAGATTAATGCATGAATTAAATCTGAGAATCAGATTTT
1 TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTT
* * *
174589 TTTTTTTAG-AAAAAAGAAAGGCTTATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGC
66 TTTTTTTAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGC
*
174653 ATGAATTATATCTGAGAATCGGATTCTTTTTTATAGGAAAAAAGAAAGACT
131 ATGAATTATATCTAAGAATC-GATTCTTTTTTATA-GAAAAAAGAAAGACT
174704 GCAAGGATTA
Statistics
Matches: 319, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
176 66 0.21
177 22 0.07
178 3 0.01
179 1 0.00
180 52 0.16
181 5 0.02
182 4 0.01
183 154 0.48
184 12 0.04
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (182 bp):
TGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTT
TTTTTTTAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGC
ATGAATTATATCTAAGAATCGATTCTTTTTTATAGAAAAAAGAAAGACTAAT
Found at i:174791 original size:71 final size:70
Alignment explanation
Indices: 174629--174844 Score: 387
Period size: 70 Copynumber: 3.1 Consensus size: 70
174619 TGTAAATGTT
*
174629 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGGATTCTTTTTTATAGGAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
174694 AAGAA
66 AAGAA
*
174699 AGACTGCAAGGATTAGACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATAGGAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTC-TTTTTTATAGGAAA
174764 AAAGAA
65 AAAGAA
* *
174770 AGATTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
174835 AAGAA
66 AAGAA
174840 AGACT
1 AGACT
174845 AATTGATTGT
Statistics
Matches: 139, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
70 71 0.51
71 68 0.49
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (70 bp):
AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
AAGAA
Found at i:174967 original size:90 final size:91
Alignment explanation
Indices: 174774--175026 Score: 418
Period size: 90 Copynumber: 2.8 Consensus size: 91
174764 AAAGAAAGAT
174774 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGA
1 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAG-AAAAAAGA
*
174839 AAGACTAATTGATTGTAAATGTCATAC
65 AAGACTAATTGATTGTAAATGTCAGAC
* * * *
174866 TGCAAAGATTAGATTAATGCATGAATTATATCTAAGAATCAGATT-TTTTTTTTAGAAAAAAGAA
1 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAGAA
* *
174930 AGACTTATTGATTGTAAATGTTAGAC
66 AGACTAATTGATTGTAAATGTCAGAC
174956 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAAAAGA
1 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATA-GAAAAAAGA
175021 AAGACT
65 AAGACT
175027 GCAAGGATTA
Statistics
Matches: 148, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
90 74 0.50
91 17 0.11
92 57 0.39
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (91 bp):
TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAGAA
AGACTAATTGATTGTAAATGTCAGAC
Found at i:175065 original size:70 final size:70
Alignment explanation
Indices: 174952--175258 Score: 410
Period size: 70 Copynumber: 4.4 Consensus size: 70
174942 TGTAAATGTT
* *
174952 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
1 AGACTGCAAGGATTAAACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAGAAAA
175017 AAGAA
66 AAGAA
* *
175022 AGACTGCAAGGATTAAACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATAGGAAA
1 AGACTGCAAGGATTAAACTAATGCATGAATTATATCTGAGAATCAGATTC-TTTTTTATAAGAAA
*
175087 AAAAAA
65 AAAGAA
* * *
175093 AGATTGCAAGGATTAGACTAATGCATGAATTATATTTGAGAATCAGATTCTTTTTTATAAGAAAA
1 AGACTGCAAGGATTAAACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAGAAAA
175158 AAGAA
66 AAGAA
* * * * * *
175163 AGATTGCAAGAATTAAACTAATGCACGAATGATATATGAGAATC-GAATTCTTTTTCATAAG---
1 AGACTGCAAGGATTAAACTAATGCATGAATTATATCTGAGAATCAG-ATTCTTTTTTATAAGAAA
175224 -AA-AA
65 AAAGAA
* *
175228 AGACTGCAAAGATTAGACTAATGCATGAATT
1 AGACTGCAAGGATTAAACTAATGCATGAATT
175259 GTTCATGAGA
Statistics
Matches: 214, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
65 27 0.13
66 2 0.01
69 1 0.00
70 119 0.56
71 65 0.30
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (70 bp):
AGACTGCAAGGATTAAACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAGAAAA
AAGAA
Found at i:175158 original size:324 final size:324
Alignment explanation
Indices: 174450--175165 Score: 1319
Period size: 323 Copynumber: 2.2 Consensus size: 324
174440 AATGTCAGAC
* *
174450 TGCAAGAATTAGACTAATGCATGAATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAAAGA
1 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGA
* *
174515 AAGACTAATTGATTGTAAATGTCATACTGCAAGGATTAGATTAATGCATGAATTAAATCTGAGAA
66 AAGACTAATTGATTGTAAATGTCATACTGCAAAGATTAGATTAATGCATGAATTAAATCTAAGAA
*
174580 TCAGATTTTTTTTTTTAGAAAAAAGAAAGGCTTATTGATTGTAAATGTTAGACTGCAAGGATTAG
131 TCAGATTTTTTTTTTTAGAAAAAAGAAAGACTTATTGATTGTAAATGTTAGACTGCAAGGATTAG
*
174645 ACTAATGCATGAATTATATCTGAGAATCGGATTCTTTTTTATAGGAAAAAAGAAAGACTGCAAGG
196 ACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAAAAGAAAGACTGCAAGG
* *
174710 ATTAGACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATAGGAAAAAAGAAAGAT
261 ATTAAACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATAGGAAAAAAAAAAGAT
174774 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGA
1 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGA
*
174839 AAGACTAATTGATTGTAAATGTCATACTGCAAAGATTAGATTAATGCATGAATTATATCTAAGAA
66 AAGACTAATTGATTGTAAATGTCATACTGCAAAGATTAGATTAATGCATGAATTAAATCTAAGAA
174904 TCAGA-TTTTTTTTTTAGAAAAAAGAAAGACTTATTGATTGTAAATGTTAGACTGCAAGGATTAG
131 TCAGATTTTTTTTTTTAGAAAAAAGAAAGACTTATTGATTGTAAATGTTAGACTGCAAGGATTAG
174968 ACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAAAAGAAAGACTGCAAGG
196 ACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAAAAGAAAGACTGCAAGG
175033 ATTAAACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATAGGAAAAAAAAAAGAT
261 ATTAAACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATAGGAAAAAAAAAAGAT
*
175097 TGCAAGGATTAGACTAATGCATGAATTATATTTGAGAATCAGATTCTTTTTTATA-AGAAAAAAG
1 TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGA-AAAAAAG
175161 AAAGA
65 AAAGA
175166 TTGCAAGAAT
Statistics
Matches: 381, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
322 1 0.00
323 250 0.66
324 130 0.34
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.33
Consensus pattern (324 bp):
TGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGA
AAGACTAATTGATTGTAAATGTCATACTGCAAAGATTAGATTAATGCATGAATTAAATCTAAGAA
TCAGATTTTTTTTTTTAGAAAAAAGAAAGACTTATTGATTGTAAATGTTAGACTGCAAGGATTAG
ACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAAAAGAAAGACTGCAAGG
ATTAAACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATAGGAAAAAAAAAAGAT
Found at i:175213 original size:141 final size:135
Alignment explanation
Indices: 174952--175258 Score: 436
Period size: 141 Copynumber: 2.2 Consensus size: 135
174942 TGTAAATGTT
*
174952 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAGAAAA
* * * * * *
175017 AAGAAAGACTGCAAGGATTAAACTAATGTATGAATTATATCTGAGAATCAGATTCTTTTTTTATA
66 AAGAAAGACTGCAAGAATTAAACTAATGCACGAATGATATATGAGAATCAGATTC-TTTTTCAT-
175082 GGAAAAAAAAA
129 ----AAAAAAA
* *
175093 AGATTGCAAGGATTAGACTAATGCATGAATTATATTTGAGAATCAGATTCTTTTTTATAAGAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAGAAAA
*
175158 AAGAAAGATTGCAAGAATTAAACTAATGCACGAATGATATATGAGAATC-GAATTCTTTTTCATA
66 AAGAAAGACTGCAAGAATTAAACTAATGCACGAATGATATATGAGAATCAG-ATTCTTTTTCATA
*
175222 AGAAAA
130 AAAAAA
*
175228 AGACTGCAAAGATTAGACTAATGCATGAATT
1 AGACTGCAAGGATTAGACTAATGCATGAATT
175259 GTTCATGAGA
Statistics
Matches: 152, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
135 35 0.23
140 8 0.05
141 109 0.72
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (135 bp):
AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAAGAAAA
AAGAAAGACTGCAAGAATTAAACTAATGCACGAATGATATATGAGAATCAGATTCTTTTTCATAA
AAAAA
Found at i:179742 original size:123 final size:122
Alignment explanation
Indices: 179469--179814 Score: 461
Period size: 123 Copynumber: 2.8 Consensus size: 122
179459 TATTATTTTT
*
179469 AATAAAAAATAATATTTAATTAACTTTAAAAAAATTTATATTAACAAATTAAAA--T-ATTAATT
1 AATAAAAAATAATATTTAATTAAGTTT-AAAAAA-TTATATTAACAAATTAAAATTTAATT-ATT
* *
179531 AT-TTTTTAAAAATACAAAATTTAAATAAAAATAAAAAAGGTTGATTATTATTATTTTTTAATAA
63 ATGTTTTTAAAAATAAAAAATTT---T-AAAATAAAAAAGGTT-ATTATTATTAATTTTTAATAA
*
179595 AATTAAAAATAATATTTAATTAAGTTTAAAAAATTATATTAACAAATTAAAATTTAATTATTATG
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAATTATATTAACAAATTAAAATTTAATTATTATG
179660 TTTTTATAAAAGTAAAAAATTTTAAAATAAAAAAGGGTT-TTATTA-TAATTTTTAATAA
66 TTTTTA-AAAA-TAAAAAATTTTAAAATAAAAAA-GGTTATTATTATTAATTTTTAATAA
* * * *
179718 AATAAAAAATAATATTTAATTAAGTTTAAAAATTTACATGAATAAATTAAAATATTAATTATTAT
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAATTATATTAACAAATTAAAAT-TTAATTATTAT
*
179783 GTTTTTAAAAATAAAAAATTTTAAATTAAAAA
65 GTTTTTAAAAATAAAAAATTTTAAAATAAAAA
179815 GATATTTTAT
Statistics
Matches: 202, Mismatches: 10, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
122 20 0.10
123 64 0.32
124 43 0.21
125 17 0.08
126 36 0.18
127 9 0.04
128 4 0.02
129 9 0.04
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (122 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAAAATTATATTAACAAATTAAAATTTAATTATTATG
TTTTTAAAAATAAAAAATTTTAAAATAAAAAAGGTTATTATTATTAATTTTTAATAA
Found at i:180144 original size:23 final size:22
Alignment explanation
Indices: 180110--180170 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
180100 TTTATTTAAA
*
180110 TAATGATAATTTTTTTCATTCCT
1 TAATG-TAATTTTTTTAATTCCT
* **
180133 TAAATGTTATTTTTTTAATTTGT
1 T-AATGTAATTTTTTTAATTCCT
180156 TAATGTAATTTTTTT
1 TAATGTAATTTTTTT
180171 TAAATTCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 13 0.41
23 15 0.47
24 4 0.12
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (22 bp):
TAATGTAATTTTTTTAATTCCT
Found at i:180379 original size:110 final size:110
Alignment explanation
Indices: 180147--180347 Score: 278
Period size: 109 Copynumber: 1.8 Consensus size: 110
180137 TGTTATTTTT
* *
180147 TTAATTTGTTAATGTAATTTTTTTTAAATTCAATTAAATATTATTTTTATTTTATTAAAAATATT
1 TTAATTTGTTAATATAATTTTTTTTAAATTCAATTAAATATTATTTTTATTTTATTAAAAATAAT
* * ** *
180212 AATAAAAAAAACTTTTTATTTTTATAAAAACATATAATTAATATT
66 AATAAAAAAAACTTTTTAATTTAATAAAAACATATAAAAAATATA
*
180257 TTAATTTGTTAATATAA-TTTTTTTAAATTTAATTAAATATTATTTTTAATTTTATTAAAAAATA
1 TTAATTTGTTAATATAATTTTTTTTAAATTCAATTAAATATTATTTTT-ATTTTATT-AAAAATA
* **
180321 ATAATAATAAATCCTTTTTAATTTAAT
64 ATAATAAAAAAAACTTTTTAATTTAAT
180348 TTTTTATTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
109 29 0.36
110 24 0.30
111 28 0.35
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (110 bp):
TTAATTTGTTAATATAATTTTTTTTAAATTCAATTAAATATTATTTTTATTTTATTAAAAATAAT
AATAAAAAAAACTTTTTAATTTAATAAAAACATATAAAAAATATA
Found at i:180613 original size:15 final size:14
Alignment explanation
Indices: 180568--180621 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
180558 TAACGTATTC
*
180568 TTAAAAAAAAACTAT
1 TTAAAAAAATA-TAT
180583 TTAAAAAAATAT-T
1 TTAAAAAAATATAT
*
180596 TTATAAAAAATTTAT
1 TTA-AAAAAATATAT
*
180611 TTACAAAAATA
1 TTAAAAAAATA
180622 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 4 0.12
14 15 0.45
15 14 0.42
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAAAAATATAT
Found at i:181805 original size:38 final size:37
Alignment explanation
Indices: 181737--181810 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
181727 GGATAAAAAA
181737 AATTATGTTTATATTATTTTTATGTCGTATTATATTTT
1 AATTATGTTTATATTATTTTTATGTCGTATTA-ATTTT
* *
181775 AATTAT-TTTAATGTTATTTTTAT-TATGTATTAATTT
1 AATTATGTTT-ATATTATTTTTATGT-CGTATTAATTT
181811 AATCTCATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 8 0.25
38 24 0.75
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.64
Consensus pattern (37 bp):
AATTATGTTTATATTATTTTTATGTCGTATTAATTTT
Found at i:183222 original size:14 final size:14
Alignment explanation
Indices: 183198--183245 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
183188 GAAGAAACTG
*
183198 AGAGAAGAAAAGATA
1 AGAGAAAAAAAGA-A
183213 A-AGAAAAAAAGAA
1 AGAGAAAAAAAGAA
*
183226 AGAGAAAAAAAAAA
1 AGAGAAAAAAAGAA
183240 AGAGAA
1 AGAGAA
183246 GGAGAGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 2 0.07
14 27 0.90
15 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (14 bp):
AGAGAAAAAAAGAA
Found at i:183227 original size:18 final size:18
Alignment explanation
Indices: 183202--183242 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
183192 AAACTGAGAG
183202 AAGAAA-AGATAAAGAAAAA
1 AAGAAAGAGA-AAA-AAAAA
183221 AAGAAAGAGAAAAAAAAA
1 AAGAAAGAGAAAAAAAAA
183239 AAGA
1 AAGA
183243 GAAGGAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
19 9 0.43
20 3 0.14
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (18 bp):
AAGAAAGAGAAAAAAAAA
Found at i:183245 original size:20 final size:20
Alignment explanation
Indices: 183202--183250 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
183192 AAACTGAGAG
*
183202 AAGAAA-AGATAAAGAAAAA
1 AAGAAAGAGATAAAAAAAAA
183221 AAGAAAGAGA-AAAAAAAAA
1 AAGAAAGAGATAAAAAAAAA
*
183240 AGAGAAGGAGA
1 A-AGAAAGAGA
183251 GAGAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (20 bp):
AAGAAAGAGATAAAAAAAAA
Found at i:183554 original size:20 final size:21
Alignment explanation
Indices: 183525--183564 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
183515 CACGTTCATA
183525 TATTTATGTA-ATATTTATAT
1 TATTTATGTATATATTTATAT
*
183545 TATTTTTGTATTATATTTAT
1 TATTTATGTA-TATATTTAT
183565 TTAATATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TATTTATGTATATATTTATAT
Found at i:183571 original size:11 final size:11
Alignment explanation
Indices: 183523--183589 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
183513 GACACGTTCA
*
183523 TATATTTATGT
1 TATATTTATAT
*
183534 AATATTTATAT
1 TATATTTATAT
* *
183545 TATTTTTGTAT
1 TATATTTATAT
183556 TATATTTAT-T
1 TATATTTATAT
183566 TAATATCTTA-AT
1 T-ATAT-TTATAT
183578 T-TATTTTATAT
1 TATA-TTTATAT
183589 T
1 T
183590 TTAAATAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
10 7 0.16
11 32 0.73
12 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:183579 original size:17 final size:17
Alignment explanation
Indices: 183559--183593 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
183549 TTTGTATTAT
183559 ATTTATTTAATATCTTA
1 ATTTATTTAATATCTTA
* *
183576 ATTTATTTTATATTTTA
1 ATTTATTTAATATCTTA
183593 A
1 A
183594 ATAATTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTATTTAATATCTTA
Found at i:183771 original size:18 final size:19
Alignment explanation
Indices: 183740--183775 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
183730 TGAGAAAAAA
183740 TTTTATTTTATTAATTATT
1 TTTTATTTTATTAATTATT
183759 TTTTATTTT-TTAATTAT
1 TTTTATTTTATTAATTAT
183776 ATATTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTATTTTATTAATTATT
Found at i:183879 original size:7 final size:7
Alignment explanation
Indices: 183867--183907 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
183857 TTTAATAATT
183867 ATTTTTA
1 ATTTTTA
183874 ATTTTT-
1 ATTTTTA
*
183880 ATATTTA
1 ATTTTTA
183887 ATTTTTA
1 ATTTTTA
183894 ATTTTTA
1 ATTTTTA
183901 ATTTTTA
1 ATTTTTA
183908 TTAAGGGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:183879 original size:20 final size:21
Alignment explanation
Indices: 183856--183902 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
183846 TAAATAATTA
183856 TTTTAATAATT-ATTTTTAAT
1 TTTTAATAATTAATTTTTAAT
*
183876 TTTT-ATATTTAATTTTTAAT
1 TTTTAATAATTAATTTTTAAT
183896 TTTTAAT
1 TTTTAAT
183903 TTTTATTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 17 0.71
21 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAATAATTAATTTTTAAT
Found at i:183881 original size:13 final size:13
Alignment explanation
Indices: 183865--183909 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
183855 ATTTTAATAA
183865 TTATTTTTAATTT
1 TTATTTTTAATTT
*
183878 TTATATTTAATTT
1 TTATTTTTAATTT
183891 TTAATTTTTAATTT
1 TT-ATTTTTAATTT
183905 TTATT
1 TTATT
183910 AAGGGATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTTTAATTT
Found at i:184177 original size:13 final size:13
Alignment explanation
Indices: 184159--184188 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
184149 TTAATTAATT
*
184159 TTTAAATAATATA
1 TTTAAAGAATATA
184172 TTTAAAGAATATA
1 TTTAAAGAATATA
184185 TTTA
1 TTTA
184189 TTTAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TTTAAAGAATATA
Found at i:184731 original size:32 final size:32
Alignment explanation
Indices: 184638--184732 Score: 91
Period size: 32 Copynumber: 3.0 Consensus size: 32
184628 TTCATACTTG
* * * *
184638 AAAATAATTTAAATTTAAAATGAGTTGAATCT
1 AAAATAATTTAAATTCAAAATGATTTAAATTT
* * * * * *
184670 AAAATCATCTGAACTCGAAATGATCTAAATTT
1 AAAATAATTTAAATTCAAAATGATTTAAATTT
*
184702 AAAATAATTTAAATTCAAAATTATTTAAATT
1 AAAATAATTTAAATTCAAAATGATTTAAATT
184733 CGAAATAACT
Statistics
Matches: 46, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.37
Consensus pattern (32 bp):
AAAATAATTTAAATTCAAAATGATTTAAATTT
Found at i:184733 original size:16 final size:16
Alignment explanation
Indices: 184695--184740 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
184685 CGAAATGATC
*
184695 TAAATTTAAAATAATT
1 TAAATTCAAAATAATT
*
184711 TAAATTCAAAATTATT
1 TAAATTCAAAATAATT
*
184727 TAAATTCGAAATAA
1 TAAATTCAAAATAA
184741 CTCGAACTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (16 bp):
TAAATTCAAAATAATT
Found at i:184989 original size:49 final size:48
Alignment explanation
Indices: 184930--185027 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 48
184920 GATCAAACTT
* * * *
184930 AAAATTATTTAAAA-TCAAAATAATTTAAACTTGATATGATTTAAATTTA
1 AAAATAATTTAAAATTCAAAA-AATTTAAA-ATAATATAATTTAAATTTA
**
184979 AAAATAATTTAAAATTTTAAAAATTTAAAATAATATAATTTAAATTTA
1 AAAATAATTTAAAATTCAAAAAATTTAAAATAATATAATTTAAATTTA
185027 A
1 A
185028 TTCGTGGCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 17 0.40
49 21 0.50
50 4 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (48 bp):
AAAATAATTTAAAATTCAAAAAATTTAAAATAATATAATTTAAATTTA
Found at i:184995 original size:18 final size:18
Alignment explanation
Indices: 184968--185002 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
184958 ACTTGATATG
184968 ATTTAAA-TTTAAAAATA
1 ATTTAAATTTTAAAAATA
184985 ATTTAAAATTTTAAAAAT
1 ATTT-AAATTTTAAAAAT
185003 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 3 0.19
19 9 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTAAATTTTAAAAATA
Found at i:185028 original size:16 final size:16
Alignment explanation
Indices: 184949--185028 Score: 67
Period size: 16 Copynumber: 5.0 Consensus size: 16
184939 TAAAATCAAA
* *
184949 ATAATTTAAACTTGAT
1 ATAATTTAAATTTAAT
* *
184965 ATGATTTAAATTTAAAA
1 ATAATTTAAATTT-AAT
184982 ATAATTTAAAATTTTAA-
1 ATAATTT-AAA-TTTAAT
*
184999 A-AATTTAAA-ATAAT
1 ATAATTTAAATTTAAT
185013 ATAATTTAAATTTAAT
1 ATAATTTAAATTTAAT
185029 TCGTGGCCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
13 3 0.06
14 1 0.02
15 11 0.22
16 20 0.39
17 8 0.16
18 5 0.10
19 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (16 bp):
ATAATTTAAATTTAAT
Found at i:186357 original size:17 final size:18
Alignment explanation
Indices: 186323--186357 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
186313 TAAATATATA
*
186323 AAATATAAATTGTTAAAT
1 AAATAAAAATTGTTAAAT
186341 AAATAAAAATT-TTAAAT
1 AAATAAAAATTGTTAAAT
186358 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAATAAAAATTGTTAAAT
Found at i:186435 original size:5 final size:5
Alignment explanation
Indices: 186417--186484 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
186407 ATTTCAATAA
* *
186417 ATTAT ATT-T ATTAT ATTATT TTTAT ATT-T ATAAAT CATTAT ATTTAT
1 ATTAT ATTAT ATTAT ATTA-T ATTAT ATTAT AT-TAT -ATTAT A-TTAT
186464 ATTAT ATT-T -TTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATT
186485 TAAAATTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
3 2 0.04
4 9 0.18
5 26 0.51
6 12 0.24
7 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (5 bp):
ATTAT
Found at i:186443 original size:11 final size:11
Alignment explanation
Indices: 186418--186486 Score: 63
Period size: 11 Copynumber: 6.3 Consensus size: 11
186408 TTTCAATAAA
186418 TTATATT-TA-
1 TTATATTATAT
*
186427 TTATATTATTT
1 TTATATTATAT
186438 TTATATT-TAT
1 TTATATTATAT
**
186448 AAATCATTATAT
1 TTAT-ATTATAT
186460 TTATATTATATTT
1 TTATATTATA--T
186473 TTATATTATAT
1 TTATATTATAT
186484 TTA
1 TTA
186487 AAATTATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 7 0.15
10 5 0.10
11 20 0.42
12 5 0.10
13 11 0.23
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTATAT
Found at i:186448 original size:6 final size:6
Alignment explanation
Indices: 186418--186527 Score: 55
Period size: 6 Copynumber: 17.2 Consensus size: 6
186408 TTTCAATAAA
*
186418 TTATAT TTATTAT ATTATTT TTATAT TTATAAAT CATTATAT TTATA-
1 TTATAT TTA-TAT -TTATAT TTATAT TTAT--AT --TTATAT TTATAT
* * * *
186465 TTATAT TTTTAT ATTATAT TTAAAA TTATTAAA TTA-AT TTATAT TTATAT
1 TTATAT TTATAT -TTATAT TTATAT TTA-T-AT TTATAT TTATAT TTATAT
*
186515 ATT-TAT TTTTAT T
1 -TTATAT TTATAT T
186528 GGTAGTTCAT
Statistics
Matches: 83, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
5 11 0.13
6 44 0.53
7 12 0.14
8 12 0.14
10 4 0.05
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:186450 original size:33 final size:33
Alignment explanation
Indices: 186413--186526 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 33
186403 TCATATTTCA
186413 ATAAATTATATTTATTATATTATTTTTATATTT
1 ATAAATTATATTTATTATATTATTTTTATATTT
186446 ATAAATCATTATATTTA-TAT-TATATTTTTATA-TT
1 AT-AA--ATTATATTTATTATAT-TATTTTTATATTT
* * * * *
186480 AT-ATTTAAAATTATTAAATTA-ATTTATATTT
1 ATAAATTATATTTATTATATTATTTTTATATTT
*
186511 ATATATT-TATTT-TTAT
1 ATAAATTATATTTATTAT
186527 TGGTAGTTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
30 16 0.25
31 11 0.17
32 4 0.06
33 2 0.03
34 7 0.11
35 13 0.21
36 10 0.16
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (33 bp):
ATAAATTATATTTATTATATTATTTTTATATTT
Found at i:186457 original size:36 final size:36
Alignment explanation
Indices: 186417--186520 Score: 106
Period size: 38 Copynumber: 2.9 Consensus size: 36
186407 ATTTCAATAA
186417 ATTATATTTATTATATTATTTTTATATTTATAAATC
1 ATTATATTTATTATATTATTTTTATATTTATAAATC
* *
186453 ATTATATTTATATTATATTTTTATATTATATTTA-AAATT
1 ATTATA-TT-TATTATATTATT-T-TTATATTTATAAATC
* * *
186492 ATTAAATTAATT-TA-TATTTATATATTTAT
1 ATTATATTTATTATATTATTTTTATATTTAT
186521 TTTTATTGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
33 8 0.14
34 1 0.02
35 3 0.05
36 8 0.14
37 5 0.09
38 13 0.23
39 10 0.18
40 9 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (36 bp):
ATTATATTTATTATATTATTTTTATATTTATAAATC
Found at i:186462 original size:22 final size:20
Alignment explanation
Indices: 186418--186526 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
186408 TTTCAATAAA
* *
186418 TTATATTTATTATATTATTT
1 TTATATTTATAATATTATAT
186438 TTATATTTATAAATCATTATAT
1 TTATATTTAT-AAT-ATTATAT
* *
186460 TTATA-TTATATTTTTATA-
1 TTATATTTATAATATTATAT
* *
186478 TTATATTTAAAATTATTA-AA
1 TTATATTTATAA-TATTATAT
*
186498 TTA-ATTTAT-ATTTATATAT
1 TTATATTTATAATAT-TATAT
*
186517 TTATTTTTAT
1 TTATATTTAT
186527 TGGTAGTTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
17 2 0.03
18 8 0.11
19 19 0.27
20 24 0.34
21 6 0.09
22 11 0.16
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTTATAATATTATAT
Found at i:186477 original size:13 final size:13
Alignment explanation
Indices: 186459--186485 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
186449 AATCATTATA
186459 TTTATATTATATT
1 TTTATATTATATT
186472 TTTATATTATATT
1 TTTATATTATATT
186485 T
1 T
186486 AAAATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:186787 original size:13 final size:13
Alignment explanation
Indices: 186745--186787 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
186735 TTTACACAAA
186745 TTATTTTTTATAT
1 TTATTTTTTATAT
* *
186758 TAATCTTTTT-TAG
1 TTAT-TTTTTATAT
186771 TTATTTTTTATAT
1 TTATTTTTTATAT
186784 TTAT
1 TTAT
186788 AATAAGCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (13 bp):
TTATTTTTTATAT
Found at i:188281 original size:2 final size:2
Alignment explanation
Indices: 188263--188300 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
188253 AGTAGAATAC
* *
188263 AT AT AT AC AT AT CT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
188301 CACACGTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:189801 original size:121 final size:122
Alignment explanation
Indices: 189666--189908 Score: 461
Period size: 121 Copynumber: 2.0 Consensus size: 122
189656 AATTTCTTCT
189666 ATATATTCTTATATTAACAAATAAAAAATAATTCAGTTATTTTCATTTTATTTAGAAATAAGAG-
1 ATATATTCTTATATTAACAAATAAAAAATAATTCAGTTATTTTCATTTTATTTAGAAATAAGAGA
*
189730 AAAAAATATTAAGAATTTTGAATATAATCTGAAAAAAGAGTTCCAATATTAATCTTA
66 AAAAAATATTAAGAATTTTGAATATAATCTGAAAAAAGAATTCCAATATTAATCTTA
189787 ATATATTCTTATATTAACAAATAAAAAATAATTCAGTTATTTTCATTTTATTTAGAAATAAGAGA
1 ATATATTCTTATATTAACAAATAAAAAATAATTCAGTTATTTTCATTTTATTTAGAAATAAGAGA
*
189852 AAAAAATATTAAGAATTTTGAATATAATGTGAAAAAAGAATTCCAATATTAATCTTA
66 AAAAAATATTAAGAATTTTGAATATAATCTGAAAAAAGAATTCCAATATTAATCTTA
189909 GAAGTAAGTT
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
121 64 0.54
122 55 0.46
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (122 bp):
ATATATTCTTATATTAACAAATAAAAAATAATTCAGTTATTTTCATTTTATTTAGAAATAAGAGA
AAAAAATATTAAGAATTTTGAATATAATCTGAAAAAAGAATTCCAATATTAATCTTA
Found at i:193788 original size:31 final size:31
Alignment explanation
Indices: 193747--193809 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
193737 TCCCAGAAAG
*
193747 AACCATTTGAACCATATCAAATGGACATAAA
1 AACCACTTGAACCATATCAAATGGACATAAA
* *
193778 AACCACTTGAACCGTATCAAATGGACGTAAA
1 AACCACTTGAACCATATCAAATGGACATAAA
193809 A
1 A
193810 CTAGCACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (31 bp):
AACCACTTGAACCATATCAAATGGACATAAA
Found at i:194593 original size:14 final size:14
Alignment explanation
Indices: 194574--194611 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
194564 GGGAGAATAG
*
194574 AGTAAGAAGAGGAA
1 AGTAAGAAGAGAAA
194588 AGTAAGAAGGAGAAA
1 AGTAAGAA-GAGAAA
194603 AG-AAGAAGA
1 AGTAAGAAGA
194612 AGATTTAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 13 0.59
15 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (14 bp):
AGTAAGAAGAGAAA
Found at i:194757 original size:17 final size:18
Alignment explanation
Indices: 194731--194769 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
194721 TGAAACCAAA
*
194731 TAACAGAATT-TAACTAG
1 TAACAAAATTATAACTAG
194748 TAACAAAATTAATAACTAG
1 TAACAAAATT-ATAACTAG
194767 TAA
1 TAA
194770 AAGAAGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (18 bp):
TAACAAAATTATAACTAG
Found at i:194783 original size:19 final size:19
Alignment explanation
Indices: 194742--194783 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
194732 AACAGAATTT
* *
194742 AACTAGTAACAAAATTAAT
1 AACTAGTAACAAAAGTAAC
194761 AACTAGTAA-AAGAAGTAAC
1 AACTAGTAACAA-AAGTAAC
194780 AACT
1 AACT
194784 CATTAACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.21
Consensus pattern (19 bp):
AACTAGTAACAAAAGTAAC
Found at i:197772 original size:7 final size:7
Alignment explanation
Indices: 197757--197812 Score: 78
Period size: 7 Copynumber: 8.0 Consensus size: 7
197747 TAAAGGCATT
197757 AACCTTA
1 AACCTTA
*
197764 AATCTTA
1 AACCTTA
197771 AACCTTA
1 AACCTTA
197778 AACCTTA
1 AACCTTA
197785 AACCTTA
1 AACCTTA
*
197792 AATCTTAA
1 AACCTT-A
197800 AACC-TA
1 AACCTTA
197806 AACCTTA
1 AACCTTA
197813 TTTCATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.12
7 34 0.79
8 4 0.09
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (7 bp):
AACCTTA
Found at i:199559 original size:15 final size:14
Alignment explanation
Indices: 199523--199570 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 14
199513 TAGAGGTTAG
*
199523 AAAGAAAAGTATTAA
1 AAAGAATAGT-TTAA
199538 TAAAGAATCAGTTTAA
1 -AAAGAAT-AGTTTAA
*
199554 AAAGAATAGTGTAA
1 AAAGAATAGTTTAA
199568 AAA
1 AAA
199571 AAGAAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.31
15 7 0.24
16 10 0.34
17 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.15, T:0.23
Consensus pattern (14 bp):
AAAGAATAGTTTAA
Found at i:202176 original size:20 final size:19
Alignment explanation
Indices: 202130--202201 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
202120 TTTTACCTAG
* * *
202130 ATGTATTGATACATTTTTTA
1 ATGTATCGATACA-TCTTCA
* * *
202150 ATATATCGATACATGTATGA
1 ATGTATCGATACATCT-TCA
*
202170 ATGTATCGGTAC-TCTTCA
1 ATGTATCGATACATCTTCA
202188 ATGTATCGATACAT
1 ATGTATCGATACAT
202202 TTTGTGTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 13 0.32
19 5 0.12
20 23 0.56
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATCTTCA
Found at i:207252 original size:465 final size:465
Alignment explanation
Indices: 206365--207294 Score: 1163
Period size: 465 Copynumber: 2.0 Consensus size: 465
206355 AGACCATGTT
* * *
206365 AAGGCATGAATATTTTTAGATATTTACTATCCTCATTCACATTAATTTTTTTAATCAAAAATATC
1 AAGGCATGAATATTTTTACATATTTACCATCCTCATTCACATAAATTTTTTTAATCAAAAATATC
* * * ** ***
206430 AAAATTTTATTCATCGGGAATACTCTAGCCTTATTCTTCCGAGGGGATACTCTAACCTTGCTTTT
66 AAAATTTTATTCATAGGGAATACTCCAACCCCATTCTTCCGA-GGGATA-TCTAACCCCACTTTT
* * *
206495 AAACTTCTCAAGATTTAAATCTTATTTTTGCTTAAATCATCCTTGTCATGGACACTCCAACCCCA
129 AAACTTATCAAGATTTAAATCTTATTTTTGCTCAAATCATCCTTGTCAGGGACACTCCAACCCCA
* * * * * * *
206560 TTCTTCCGAGGAAATACTCTAACCTCGTCTTTCAACCAAAATTAAATCTTTTTCTCTCTCCTAAA
194 TTCCTCCAAGGAAATACTCCAACCTCATCTTTCAACAAAAATTAAATCTTTTTCGCTCTCCCAAA
* * * * *
206625 TTTTGAATCATACCTTTTTACTTTAATTAATCGAAGAATCTAAACAAATCTTTAAGTTGTCAAGT
259 TTTTGAATCATACCTTTTTACTTCAATTAATCAAAGAATCCAAACAAATCTCTAAGTTATCAAGT
* * * * * * *
206690 TAGTTATCTCAAGATAATCGGTGGCAATTACGAGATACATCACAACTATTACACTTTTCTTTTCT
324 TAGTTATCTAAAGATAATCAGTGGCAATTACAAGATAAATCACAACTATCACACTTTTCATTTCA
* * * * *
206755 CTTTTTGTTTGGCTTGGATGAATACTTTTATGTGATATCCTATGCTTTCATTATCTTACTAACGT
389 CCTTTTGTTTGGCTTAGATAAATACCTTTATGTAATATCCTATGCTTTCATTATCTTACTAACGT
206820 GTTTTCCTTGTC
454 GTTTTCCTTGTC
206832 AAGGCATGAATATTTTTACATATTTACCATCCTCATTCACATAAATTTTCTTT-ATCAAAAATAT
1 AAGGCATGAATATTTTTACATATTTACCATCCTCATTCACATAAATTTT-TTTAATCAAAAATAT
*
206896 CAAAATTTTATTCATTAGGG-ATACTCCAACCCCATTCTTCTGA-GGACT-TC-AACCCCACTTT
65 CAAAATTTTATTCA-TAGGGAATACTCCAACCCCATTCTTCCGAGGGA-TATCTAACCCCACTTT
* ** * * *
206957 TAAACTTATCGAGATTTAAATCTTATTTTTGCTCAAATCATCCTTGTTGGGGACACTCTAACTCT
128 TAAACTTATCAAGATTTAAATCTTATTTTTGCTCAAATCATCCTTGTCAGGGACACTCCAACCCC
* ** * * * *
207022 ATTCCTCTAAGGGGGATACTCCAACCAT-ATCTGTT-AATTAAAAATTAATTTTTTTTCGCTTTC
193 ATTCCTCCAA-GGAAATACTCCAACC-TCATCT-TTCAA-CAAAAATTAAATCTTTTTCGCTCTC
* *
207085 CCAAATTTTGAATTATACCTTTTTACTTCAATTAATCAAAGAATCCAGACAAATCTCTAAGTTAT
254 CCAAATTTTGAATCATACCTTTTTACTTCAATTAATCAAAGAATCCAAACAAATCTCTAAGTTAT
* * * * *
207150 CAAGTTAGTTTTTTAAAGATAATCAGTGGCAATTATAAGATAAATCGCGACTATCACACTTTTCA
319 CAAGTTAGTTATCTAAAGATAATCAGTGGCAATTACAAGATAAATCACAACTATCACACTTTTCA
* *
207215 TTTCACCTTTTGTTTGGCTTAGATAAATACCTTTATGTAATATCCTTTGCTTTCATTGTCTTACT
384 TTTCACCTTTTGTTTGGCTTAGATAAATACCTTTATGTAATATCCTATGCTTTCATTATCTTACT
* *
207280 AACTTGTTTTTCTTG
449 AACGTGTTTTCCTTG
207295 CGATGATTGT
Statistics
Matches: 393, Mismatches: 63, Indels: 16
0.83 0.13 0.03
Matches are distributed among these distances:
463 71 0.18
464 19 0.05
465 206 0.52
466 1 0.00
467 89 0.23
468 7 0.02
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (465 bp):
AAGGCATGAATATTTTTACATATTTACCATCCTCATTCACATAAATTTTTTTAATCAAAAATATC
AAAATTTTATTCATAGGGAATACTCCAACCCCATTCTTCCGAGGGATATCTAACCCCACTTTTAA
ACTTATCAAGATTTAAATCTTATTTTTGCTCAAATCATCCTTGTCAGGGACACTCCAACCCCATT
CCTCCAAGGAAATACTCCAACCTCATCTTTCAACAAAAATTAAATCTTTTTCGCTCTCCCAAATT
TTGAATCATACCTTTTTACTTCAATTAATCAAAGAATCCAAACAAATCTCTAAGTTATCAAGTTA
GTTATCTAAAGATAATCAGTGGCAATTACAAGATAAATCACAACTATCACACTTTTCATTTCACC
TTTTGTTTGGCTTAGATAAATACCTTTATGTAATATCCTATGCTTTCATTATCTTACTAACGTGT
TTTCCTTGTC
Found at i:209439 original size:16 final size:16
Alignment explanation
Indices: 209419--209457 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
209409 CTATTTCATT
*
209419 TTTTTCTTTTTTCTTTC
1 TTTTTC-TTTTTCTTCC
209436 TTTTTCTTTTTCTTCC
1 TTTTTCTTTTTCTTCC
209452 TTTTTC
1 TTTTTC
209458 CCCACCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTTCTTCC
Found at i:210034 original size:32 final size:32
Alignment explanation
Indices: 209998--210081 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
209988 GTTGCCACTA
*
209998 ACTTGTGTGGACTTTAAAGAAAGTTGCTAATG
1 ACTTGTGTGGGCTTTAAAGAAAGTTGCTAATG
210030 ACTTGTGTGGGCTTTAAAGAAAGTTGCTAATG
1 ACTTGTGTGGGCTTTAAAGAAAGTTGCTAATG
210062 ACTTGTGTGGGCTTTGAAAG
1 ACTTGTGTGGGCTTT-AAAG
210082 GATGCCACTG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 46 0.92
33 4 0.08
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.35
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTAAAGAAAGTTGCTAATG
Found at i:210109 original size:28 final size:29
Alignment explanation
Indices: 210067--210300 Score: 214
Period size: 28 Copynumber: 8.6 Consensus size: 29
210057 TAATGACTTG
210067 TGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
210095 TGT-GGCTTTGAAAA-GATGCCACTTACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
210122 TGTGGGCTTT-AAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
210150 TGTGGGCTTTGAAAAGG-TACCATTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
210178 TGTGGGCTTTG-AAAGGATGCCA-TAGACT
1 TGTGGGCTTTGAAAAGGATGCCACT-GACT
*
210206 TATGGGC-TT--------TGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
210226 TGTGGGCTTTGAAGAGGGTTGCCACAGACT
1 TGTGGGCTTTGAA-AAGGATGCCACTGACT
* *
210256 TATGGGCTTTGAAAA-GATGCCCCTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
210284 TGTGAGCTTTGAGAAGG
1 TGTGGGCTTTGAAAAGG
210301 TGCTGTCGCA
Statistics
Matches: 170, Mismatches: 18, Indels: 35
0.76 0.08 0.16
Matches are distributed among these distances:
20 15 0.09
21 3 0.02
27 34 0.20
28 88 0.52
29 8 0.05
30 22 0.13
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACT
Found at i:210250 original size:30 final size:28
Alignment explanation
Indices: 210214--210295 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 28
210204 CTTATGGGCT
*
210214 TTGCCACTGACTTGTGGGCTTTGAAGAGGG
1 TTGCCACTGACTTGTGGGCTTTGAA-A-AG
* *
210244 TTGCCACAGACTTATGGGCTTTGAAAAG
1 TTGCCACTGACTTGTGGGCTTTGAAAAG
* * *
210272 ATGCCCCTGACTTGTGAGCTTTGA
1 TTGCCACTGACTTGTGGGCTTTGA
210296 GAAGGTGCTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 20 0.45
29 1 0.02
30 23 0.52
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (28 bp):
TTGCCACTGACTTGTGGGCTTTGAAAAG
Found at i:210263 original size:50 final size:48
Alignment explanation
Indices: 210173--210266 Score: 152
Period size: 50 Copynumber: 1.9 Consensus size: 48
210163 AAGGTACCAT
*
210173 TGACTTGTGGGCTTTGAAAGGATGCCATAGACTTATGGGCTTTGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACAGACTTATGGGCTTTGCCAC
*
210221 TGACTTGTGGGCTTTGAAGAGGGTTGCCACAGACTTATGGGCTTTG
1 TGACTTGTGGGCTTTGAA-A-GGATGCCACAGACTTATGGGCTTTG
210267 AAAAGATGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 18 0.43
49 1 0.02
50 23 0.55
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (48 bp):
TGACTTGTGGGCTTTGAAAGGATGCCACAGACTTATGGGCTTTGCCAC
Found at i:210284 original size:78 final size:76
Alignment explanation
Indices: 210139--210294 Score: 188
Period size: 78 Copynumber: 2.0 Consensus size: 76
210129 TTTAAAAGGG
** * *
210139 TGCCACTAACTTGTGGGCTTTGAAAAGGTACCATTGACTTGTGGGCTTTGAAAGGATGCCATAGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGGTACCACAGACTTATGGGCTTTGAAAAGATGCCATAGA
*
210204 CTTATGGGCTT
66 CTTATGAGCTT
* * * *
210215 TGCCACTGACTTGTGGGCTTTGAAGAGGGTTGCCACAGACTTATGGGCTTTGAAAAGATGCCCCT
1 TGCCACTAACTTGTGGGCTTTGAA-AAGG-TACCACAGACTTATGGGCTTTGAAAAGATG-CCAT
*
210280 -GACTTGTGAGCTT
63 AGACTTATGAGCTT
210293 TG
1 TG
210295 AGAAGGTGCT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
76 23 0.34
77 3 0.04
78 38 0.57
79 3 0.04
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (76 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGGTACCACAGACTTATGGGCTTTGAAAAGATGCCATAGA
CTTATGAGCTT
Found at i:210285 original size:106 final size:105
Alignment explanation
Indices: 210111--210300 Score: 267
Period size: 106 Copynumber: 1.8 Consensus size: 105
210101 TTTGAAAAGA
* * * *
210111 TGCCACTTACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGTACCATTGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAACTTATGGGCTTTGAAAAGATACCACTGA
*
210176 CTTGTGGGCTTTGA-AAGGATGCCATAGACTTATGGGCTT
66 CTTGTGAGCTTTGAGAAGGATGCCATAGACTTATGGGCTT
* * *
210215 TGCCACTGACTTGTGGGCTTTGAAGAGGGTTGCCAC-AGACTTATGGGCTTTGAAAAGATGCCCC
1 TGCCACTGACTTGTGGGCTTT-AAAAGGG-TGCCACTA-ACTTATGGGCTTTGAAAAGATACCAC
210279 TGACTTGTGAGCTTTGAGAAGG
63 TGACTTGTGAGCTTTGAGAAGG
210301 TGCTGTCGCA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
104 20 0.27
105 7 0.09
106 43 0.58
107 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (105 bp):
TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAACTTATGGGCTTTGAAAAGATACCACTGA
CTTGTGAGCTTTGAGAAGGATGCCATAGACTTATGGGCTT
Found at i:213826 original size:20 final size:20
Alignment explanation
Indices: 213799--213853 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
213789 TAAAATTTCC
*
213799 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
213819 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
213839 AAATGTATCGATACA
1 AAATGTATCGATACA
213854 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:213897 original size:19 final size:18
Alignment explanation
Indices: 213873--213942 Score: 87
Period size: 19 Copynumber: 4.1 Consensus size: 18
213863 CAGTAGCTAA
213873 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
213892 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
213907 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
213924 TTATGTATCGATACAAAC
1 TTATGTATCGATACAAAC
213942 T
1 T
213943 GTTGAATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.24
14 1 0.02
16 2 0.04
18 6 0.13
19 25 0.56
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:213913 original size:13 final size:13
Alignment explanation
Indices: 213895--213919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213885 ACAATACTTA
213895 TGTATCGATACAT
1 TGTATCGATACAT
213908 TGTATCGATACA
1 TGTATCGATACA
213920 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:213917 original size:32 final size:32
Alignment explanation
Indices: 213876--213938 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
213866 TAGCTAATTA
*
213876 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
213908 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
213939 AACTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:214306 original size:27 final size:27
Alignment explanation
Indices: 214179--214586 Score: 375
Period size: 29 Copynumber: 14.3 Consensus size: 27
214169 AGGTGTCTAC
214179 AGGTGCCACTGACTTGTGGGCTTTGAAA
1 AGGTGCCACTGACTTGTGGGCTTTG-AA
* * *
214207 AGGGTTGTCACTGACTTATGGGCCTTGAA
1 A-GG-TGCCACTGACTTGTGGGCTTTGAA
*
214236 AGGATGCCATTGACTTGTGGGCTTTGAAAA
1 AGG-TGCCACTGACTTGTGGGCTTTG--AA
* * * * *
214266 ATGTGCCATTAACTTATAGGCTTTGAA
1 AGGTGCCACTGACTTGTGGGCTTTGAA
*
214293 AGGTGCCACTAACTTGTGGGCTTTGAA
1 AGGTGCCACTGACTTGTGGGCTTTGAA
214320 AGGTGCCACTGACTTGTGGGCTTTGAA
1 AGGTGCCACTGACTTGTGGGCTTTGAA
* *
214347 AGATGCCACTAACTTGTGGGCTTTGAAA
1 AGGTGCCACTGACTTGTGGGCTTTG-AA
* *
214375 ATGGTGCCACTGATTTGTAGGCTTTGAAA
1 A-GGTGCCACTGACTTGTGGGCTTTG-AA
* * **
214404 AGGTTACCACCGACTTGTGTGGGCTCTCAAAA
1 AGG-TGCCACTGAC-T-TGTGGGCT-T-TGAA
* * *
214436 AGTTGCCACTAACTTGTGGGCTTTAAAA
1 AGGTGCCACTGACTTGTGGGCTTT-GAA
214464 AGGGTGCCACTGACTTGTGGGCTTTGAA
1 A-GGTGCCACTGACTTGTGGGCTTTGAA
* *
214492 AGAGTGCCACTGACTTTTGGGCTTTAAA
1 AG-GTGCCACTGACTTGTGGGCTTTGAA
* * *
214520 AGAGTGCTACTAACTTGTAGGCTTTGAGA
1 AG-GTGCCACTGACTTGTGGGCTTTGA-A
* *
214549 AGAGTGCCACTGACTGGTGGGCTTTAAAA
1 AG-GTGCCACTGACTTGTGGGCTTT-GAA
214578 AGGTGCCAC
1 AGGTGCCAC
214587 GAAGTTGTAG
Statistics
Matches: 315, Mismatches: 49, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
27 75 0.24
28 86 0.27
29 109 0.35
30 26 0.08
31 14 0.04
32 5 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (27 bp):
AGGTGCCACTGACTTGTGGGCTTTGAA
Found at i:214443 original size:60 final size:60
Alignment explanation
Indices: 214361--214520 Score: 146
Period size: 60 Copynumber: 2.7 Consensus size: 60
214351 GCCACTAACT
* * * * * * *
214361 TGTGGGCTTTGAAAATGGTGCCACTGATTTGTAGGCTTTGAAAAGGTTACCACCGACTTG
1 TGTGGGCTCTCAAAAAGGTGCCACTAACTTGTAGGCTTTAAAAAGGGTACCACCGACTTG
* * * *
214421 TGTGGGCTCTCAAAAAGTTGCCACTAACTTGTGGGCTTTAAAAAGGGTGCCACTGAC-T-
1 TGTGGGCTCTCAAAAAGGTGCCACTAACTTGTAGGCTTTAAAAAGGGTACCACCGACTTG
* * * * * *
214479 TGTGGGCTTTGAAAGA-GTGCCACTGACTTTTGGGCTTTAAAA
1 TGTGGGCTCTCAAAAAGGTGCCACTAACTTGTAGGCTTTAAAA
214521 GAGTGCTACT
Statistics
Matches: 83, Mismatches: 17, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
57 23 0.28
58 13 0.16
59 1 0.01
60 46 0.55
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (60 bp):
TGTGGGCTCTCAAAAAGGTGCCACTAACTTGTAGGCTTTAAAAAGGGTACCACCGACTTG
Found at i:214780 original size:56 final size:56
Alignment explanation
Indices: 214565--214804 Score: 284
Period size: 56 Copynumber: 4.3 Consensus size: 56
214555 CCACTGACTG
* * * *
214565 GTGGGCTTTAAAAAGGTGCCACGAAGTTGTAGACTTAAAAA-GGTGCCACGAAGTT
1 GTGGACTTTAAAAGGGTGCCACGAAGTTGTAGACTTAAAAAGGGTGCCATGGAGTT
* * ** * * * * *
214620 GTAGACTTAAAAAGGGTGCCGTGGAGTTATGGACTAAAAAATGGTGCCATGGAGTT
1 GTGGACTTTAAAAGGGTGCCACGAAGTTGTAGACTTAAAAAGGGTGCCATGGAGTT
* * * * * *
214676 GCGAACTTTAAAAATGGTGCTACGGAGTTGTAGACTTAAAAAGAGTGCCATGGAGTT
1 GTGGACTTT-AAAAGGGTGCCACGAAGTTGTAGACTTAAAAAGGGTGCCATGGAGTT
*
214733 GTGGACTTTAAAAGGGTGCCACGAAGTTTTAGACTTAAAAAGGGTGCCATGGAGTT
1 GTGGACTTTAAAAGGGTGCCACGAAGTTGTAGACTTAAAAAGGGTGCCATGGAGTT
214789 GTGGACTTTAAAAGGG
1 GTGGACTTTAAAAGGG
214805 AGTGCCATTG
Statistics
Matches: 151, Mismatches: 32, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
55 31 0.21
56 75 0.50
57 45 0.30
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.25
Consensus pattern (56 bp):
GTGGACTTTAAAAGGGTGCCACGAAGTTGTAGACTTAAAAAGGGTGCCATGGAGTT
Found at i:214800 original size:85 final size:83
Alignment explanation
Indices: 214548--214834 Score: 281
Period size: 85 Copynumber: 3.4 Consensus size: 83
214538 AGGCTTTGAG
* * * * *
214548 AAGAGTGCCACT-GACTGGTGGGCTTTAAAAAGGTGCCACGAAGTTGTAGACTTAAAAAGGTGCC
1 AAGAGTGCCA-TGGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTTTAGACTTAAAAAGGTGCC
*
214612 ACGAAGTTGTAGACTTAAA
65 ACGGAGTTGTAGACTTAAA
* * * ** * * * **
214631 AAGGGTGCCGTGGAGTTATGGACTAAAAAATGGTGCCATGGAG-TTGCGAACTTTAAAAATGGTG
1 AAGAGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTTTAG-AC-TTAAAAA-GGTG
*
214695 CTACGGAGTTGTAGACTTAAA
63 CCACGGAGTTGTAGACTTAAA
214716 AAGAGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTTTAGACTTAAAAAGGGTGCC
1 AAGAGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTTTAGACTTAAAAA-GGTGCC
* *
214781 ATGGAGTTGTGGACTTTAAA
65 ACGGAGTTGTAGAC-TTAAA
* * * *
214801 AGGGAGTGCCATTGAATCGTGGACTTTGAAAAGG
1 A-AGAGTGCCATGGAGTTGTGGACTTT-AAAAGG
214835 TTACATTACC
Statistics
Matches: 162, Mismatches: 34, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
82 3 0.02
83 32 0.20
84 31 0.19
85 66 0.41
86 24 0.15
87 6 0.04
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (83 bp):
AAGAGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGAAGTTTTAGACTTAAAAAGGTGCCA
CGGAGTTGTAGACTTAAA
Found at i:214802 original size:28 final size:28
Alignment explanation
Indices: 214565--214834 Score: 218
Period size: 28 Copynumber: 9.5 Consensus size: 28
214555 CCACTGACTG
* * * *
214565 GTGGGCTTTAAAAAGGTGCCACGAAGTT
1 GTGGACTTTAAAAGGGTGCCATGGAGTT
* * * *
214593 GTAGAC-TTAAAAAGGTGCCACGAAGTT
1 GTGGACTTTAAAAGGGTGCCATGGAGTT
* * *
214620 GTAGACTTAAAAAGGGTGCCGTGGAGTT
1 GTGGACTTTAAAAGGGTGCCATGGAGTT
* ** *
214648 ATGGACTAAAAAATGGTGCCATGGAGTT
1 GTGGACTTTAAAAGGGTGCCATGGAGTT
* * * * *
214676 GCGAACTTTAAAAATGGTGCTACGGAGTT
1 GTGGACTTT-AAAAGGGTGCCATGGAGTT
* * *
214705 GTAGACTTAAAAAGAGTGCCATGGAGTT
1 GTGGACTTTAAAAGGGTGCCATGGAGTT
* *
214733 GTGGACTTTAAAAGGGTGCCACGAAGTT
1 GTGGACTTTAAAAGGGTGCCATGGAGTT
* * *
214761 TTAGACTTAAAAAGGGTGCCATGGAGTT
1 GTGGACTTTAAAAGGGTGCCATGGAGTT
* * *
214789 GTGGACTTTAAAAGGGAGTGCCATTGAATC
1 GTGGACTTTAAAA-GG-GTGCCATGGAGTT
214819 GTGGACTTTGAAAAGG
1 GTGGACTTT-AAAAGG
214835 TTACATTACC
Statistics
Matches: 194, Mismatches: 43, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
27 27 0.14
28 118 0.61
29 24 0.12
30 21 0.11
31 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (28 bp):
GTGGACTTTAAAAGGGTGCCATGGAGTT
Found at i:222674 original size:48 final size:47
Alignment explanation
Indices: 222603--222722 Score: 186
Period size: 48 Copynumber: 2.5 Consensus size: 47
222593 CTAATATGCC
* * *
222603 AATTCATGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCT
1 AATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGT-GAAAATGTGCT
222651 AATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGAAAATGTGCT
1 AATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGAAAATGTGCT
* *
222698 GATTCAAGGCCAGGAACATTGAGCT
1 AATTCAAGGCCAGCAACATTGAGCT
222723 GATAAAGATG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 33 0.49
48 34 0.51
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.20
Consensus pattern (47 bp):
AATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGTGAAAATGTGCT
Found at i:222716 original size:47 final size:48
Alignment explanation
Indices: 222603--222722 Score: 181
Period size: 47 Copynumber: 2.5 Consensus size: 48
222593 CTAATATGCC
* *
222603 AATTCATGGCCAGCG-ACATTGAGCTAAGGGAAAAGTGGACAATGTGCT
1 AATTCAAGGCCAG-GAACATTGAGCTAAGGGAAAAGTGGAAAATGTGCT
*
222651 AATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAGT-GAAAATGTGCT
1 AATTCAAGGCCAGGAACATTGAGCTAAGGGAAAAGTGGAAAATGTGCT
*
222698 GATTCAAGGCCAGGAACATTGAGCT
1 AATTCAAGGCCAGGAACATTGAGCT
222723 GATAAAGATG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
47 33 0.50
48 33 0.50
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.20
Consensus pattern (48 bp):
AATTCAAGGCCAGGAACATTGAGCTAAGGGAAAAGTGGAAAATGTGCT
Found at i:222886 original size:32 final size:29
Alignment explanation
Indices: 222850--223891 Score: 562
Period size: 28 Copynumber: 35.5 Consensus size: 29
222840 TAACTTATGC
**
222850 GGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
1 GGGCTTTGAAAAG-GTTGCCACTGAC-T-TGT
* *
222882 GGGCTTTG-AAAGGGTGACACTGACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
*
222910 AGGCTTTGAAAAAAGAGTTGCCACTGACTTGTGT
1 GGGCTTTG--AAAAG-GTTGCCACTGAC-T-TGT
*
222944 GGGCTTTG-AAAGGATGCCACTGACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* *
222972 GGGCTTTGAAAAGGATGCTACTGACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * *
223001 GGGCTTTTGAAAA-GATGCCACTAACTTAT
1 GGGC-TTTGAAAAGGTTGCCACTGACTTGT
* * *
223030 GGGATTTGAAAGGGCATGCCACTGACTTGT
1 GGGCTTTGAAAAGG-TTGCCACTGACTTGT
* *
223060 GGGCTTTG-AAAGGGTGCCACTGACTTAT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * *
223088 GGGCTTTG-GAAGGATGCCATTAACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * *
223116 GGG-TTTTAAAAGGGTGCCACGGACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
*
223144 GGGCTTTGAAATAGGTCGCCACTGACTTGT
1 GGGCTTTGAAA-AGGTTGCCACTGACTTGT
** *
223174 GAACTTTGAAATAGGTTGCCACCGACTTGTGT
1 GGGCTTTGAAA-AGGTTGCCACTGAC-T-TGT
* **
223206 GGGGTTTGAAATAGGTTGCCACCAACTTGT
1 GGGCTTTGAAA-AGGTTGCCACTGACTTGT
* * **
223236 GTAGGCTTTGAAATGGGTTGCTACCAACTTGTGT
1 G--GGCTTTGAAA-AGGTTGCCACTGAC-T-TGT
* * *
223270 GGGCTTTCAAATGAGTTGCCACCGACTTATGT
1 GGGCTTTGAAAAG-GTTGCCACTGAC-T-TGT
223302 GGGCTTT-AAAATGAGTTGCCACTGACTTGT
1 GGGCTTTGAAAA-G-GTTGCCACTGACTTGT
* *
223332 GGGCTTTGAAATGGGTTGCCACAGACTTGTGT
1 GGGCTTTGAAA-AGGTTGCCACTGAC-T-TGT
223364 GGGCTTTGAAATAGGTTGCCA-TCGACTTGTGT
1 GGGCTTTGAAA-AGGTTGCCACT-GAC-T-TGT
* * * *
223396 GGGCTTTCAAATGAGTTGCCACCGATTTGTGT
1 GGGCTTTGAAAAG-GTTGCCACTGA-CT-TGT
*
223428 GGGCTTTGAAATGAGTTGCCACTGACTTGT
1 GGGCTTTGAAAAG-GTTGCCACTGACTTGT
* *
223458 GGGCTTTG-AAATGATGCCACTGACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
*
223486 GGGCTTTG-AAAGGATGCCACTGACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * *
223514 GGGTTTTG-AAATGATGCCACTAACTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* *
223542 GGGCTTT-AAAAGGGTGCTGCCACGGAGTTGT
1 GGGCTTTGAAAA-GGT--TGCCACTGACTTGT
** * *
223573 GCAC-TT-AAAAGGATGCCAC-GAAGTTGT
1 GGGCTTTGAAAAGGTTGCCACTG-ACTTGT
* * * * *
223600 AGAC-TT-AAAAGGATGCCACAGAGTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * *
223627 GGAC-TT-AAAAGAG-TGCCACGGAGTGGT
1 GGGCTTTGAAAAG-GTTGCCACTGACTTGT
* * *
223654 GGACTTT-AAAAGAG-TGCCACGGAGTTGT
1 GGGCTTTGAAAAG-GTTGCCACTGACTTGT
* * * *
223682 GGAC-TT-AAAAGGGTGCCACGGAGTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * *
223709 GGAC-TTAAAAAGG-TGCCACGGAGTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * * *
223736 GGACTTT-AAAAGGGTGCCACGGAGTTAT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * * *
223764 GGACTTT--AAAGGGTGCCAATGAGTTAT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * * *
223791 GGACTTTAAAAAGG-TGCCACAGAGTTAT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* * * *
223819 GGACTTT-AAAAGGATGCCACAGAGTTGT
1 GGGCTTTGAAAAGGTTGCCACTGACTTGT
* ** *
223847 GGACTTTGAAAAGAAATGCCACTGAATTGT
1 GGGCTTTGAAAAG-GTTGCCACTGACTTGT
* *
223877 GGACTTTGAAGAGGT
1 GGGCTTTGAAAAGGT
223892 CACAGTACTA
Statistics
Matches: 865, Mismatches: 99, Indels: 95
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.00
27 146 0.17
28 256 0.30
29 67 0.08
30 151 0.17
31 39 0.05
32 188 0.22
33 2 0.00
34 14 0.02
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (29 bp):
GGGCTTTGAAAAGGTTGCCACTGACTTGT
Found at i:222932 original size:62 final size:59
Alignment explanation
Indices: 222850--223558 Score: 552
Period size: 62 Copynumber: 11.8 Consensus size: 59
222840 TAACTTATGC
** *
222850 GGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAAGGGTGACACTGACTTGT
1 GGGCTTTGAAAAGAGTTGCCACTGACTT-TGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* *
222910 AGGCTTTGAAAAAAGAGTTGCCACTGACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGT
1 GGGCTTTG--AAAAGAGTTGCCACTGACTT-TGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * * * * *
222972 GGGCTTTGAAAAG-GATGCTACTGAC-TTGTGGGCTTTTGAAAAGATGCCACTAACTTAT
1 GGGCTTTGAAAAGAGTTGCCACTGACTTTGTGGGC-TTTGAAAGGGTGCCACTGACTTGT
* * * *
223030 GGGATTTG-AAAGGGCATGCCACTGAC-TTGTGGGCTTTGAAAGGGTGCCACTGACTTAT
1 GGGCTTTGAAAAGAG-TTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * * * * * *
223088 GGGCTTTG-GAAG-GATGCCATTAAC-TTGTGGGTTTTAAAAGGGTGCCACGGACTTGT
1 GGGCTTTGAAAAGAGTTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* ** * *
223144 GGGCTTTGAAATAG-GTCGCCACTGAC-TTGTGAACTTTGAAATAGGTTGCCACCGACTTGTGT
1 GGGCTTTGAAA-AGAGTTGCCACTGACTTTGTGGGCTTTG-AA-AGGGTGCCACTGAC-T-TGT
* ** * * **
223206 GGGGTTTGAAATAG-GTTGCCACCAACTTGTGTAGGCTTTGAAATGGGTTGCTACCAACTTGTGT
1 GGGCTTTGAAA-AGAGTTGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T-TGT
* * * * *
223270 GGGCTTTCAAATGAGTTGCCACCGACTTATGTGGGCTTTAAAATGAGTTGCCACTGACTTGT
1 GGGCTTTGAAAAGAGTTGCCACTGACTT-TGTGGGCTTTGAAA-G-GGTGCCACTGACTTGT
* * * *
223332 GGGCTTTGAAATGGGTTGCCACAGACTTGTGTGGGCTTTGAAATAGGTTGCCA-TCGACTTGTGT
1 GGGCTTTGAAAAGAGTTGCCACTGACTT-TGTGGGCTTTG-AA-AGGGTGCCACT-GAC-T-TGT
* * * * *
223396 GGGCTTTCAAATGAGTTGCCACCGATTTGTGTGGGCTTTGAAATGAGTTGCCACTGACTTGT
1 GGGCTTTGAAAAGAGTTGCCACTGACTT-TGTGGGCTTTGAAA-G-GGTGCCACTGACTTGT
* *
223458 GGGCTTTGAAATGA--TGCCACTGAC-TTGTGGGCTTTGAAAGGATGCCACTGACTTGT
1 GGGCTTTGAAAAGAGTTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * * *
223514 GGGTTTTGAAATGA--TGCCACTAAC-TTGTGGGCTTTAAAAGGGTGC
1 GGGCTTTGAAAAGAGTTGCCACTGACTTTGTGGGCTTTGAAAGGGTGC
223559 TGCCACGGAG
Statistics
Matches: 551, Mismatches: 73, Indels: 54
0.81 0.11 0.08
Matches are distributed among these distances:
56 101 0.18
57 14 0.03
58 93 0.17
59 31 0.06
60 32 0.06
61 2 0.00
62 146 0.26
63 15 0.03
64 115 0.21
65 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (59 bp):
GGGCTTTGAAAAGAGTTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
Found at i:223333 original size:126 final size:126
Alignment explanation
Indices: 222924--223496 Score: 454
Period size: 126 Copynumber: 4.7 Consensus size: 126
222914 TTTGAAAAAA
* * * *
222924 GAGTTGCCACTGACTTGTGTGGGCTTTGAAA-G-GATGCCACTGACTTGTGGGCTTTGAAA-AGG
1 GAGTTGCCACCGACTTATGTGGGCTTTAAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATAGG
* * * * * * * *
222986 ATGCTACTGACTTGTG--GGCTTTTGAAA-A-GATGCCACTAAC-T-TATGGGATTTGAAA-
66 TTGCCACAGACTTGTGTAGGC-TTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTCAAAT
* * * * * * *
223041 GGGCATGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTGACTTATGGGCTTTG-GA-AG
1 GAG-TTGCCACCGACTTATGTGGGCTTTAAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATAG
* * * * ** *
223100 GATGCCATTA-ACTTGTG--GG-TTTTAAA-AGGGTGCCACGGAC-T-TGTGGGCTTTGAAAT
65 GTTGCCA-CAGACTTGTGTAGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTCAAAT
* * ** * * *
223156 -AGGTCGCCACTGAC-T-TGTGAACTTTGAAAT-AGGTTGCCACCGACTTGTGTGGGGTTTGAAA
1 GA-GTTGCCACCGACTTATGTGGGCTTTAAAATGA-GTTGCCACTGAC-T-TGTGGGCTTTGAAA
* *
223217 TAGGTTGCCACCA-ACTTGTGTAGGCTTTGAAATGGGTTGCTACCAACTTGTGTGGGCTTTCAAA
62 TAGGTTGCCA-CAGACTTGTGTAGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTCAAA
223281 T
126 T
*
223282 GAGTTGCCACCGACTTATGTGGGCTTTAAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATGGG
1 GAGTTGCCACCGACTTATGTGGGCTTTAAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATAGG
* * *
223347 TTGCCACAGACTTGTGTGGGCTTTGAAATAGGTTGCCATCGACTTGTGTGGGCTTTCAAAT
66 TTGCCACAGACTTGTGTAGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTCAAAT
* * *
223408 GAGTTGCCACCGATTTGTGTGGGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAT--G
1 GAGTTGCCACCGACTTATGTGGGCTTTAAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATAGG
* *
223471 ATGCCACTGACTTGTG--GGCTTTGAAA
66 TTGCCACAGACTTGTGTAGGCTTTGAAA
223497 GGATGCCACT
Statistics
Matches: 381, Mismatches: 52, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
113 7 0.02
114 44 0.12
115 19 0.05
116 47 0.12
117 4 0.01
118 19 0.05
119 1 0.00
120 16 0.04
122 12 0.03
123 6 0.02
124 24 0.06
125 3 0.01
126 152 0.40
127 3 0.01
128 23 0.06
129 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (126 bp):
GAGTTGCCACCGACTTATGTGGGCTTTAAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATAGG
TTGCCACAGACTTGTGTAGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTCAAAT
Found at i:223429 original size:158 final size:155
Alignment explanation
Indices: 222850--223542 Score: 528
Period size: 158 Copynumber: 4.6 Consensus size: 155
222840 TAACTTATGC
* ** * * * *
222850 GGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAA-GGGTGACACTGAC-T-TGTAG
1 GGGCTTTGAAATGAGTTGCCACTGAC-T-TGTGGGCTTTGAAATGGTTGCCACAGACTTGTGTGG
* ** * * * **
222912 GCTTTGAAAAAAGAGTTGCCACTGACTTGTGTGGGCTTTGAAA-G-GATGCCACTGAC-T-TGTG
64 GCTTTG-AAATAG-GTTGCCACCAACTTGTGTAGGCTTTCAAATGAGTTGCCACCAACTTGTGTG
* * * * *
222973 GGCTTTGAAAAG-GATGCTACTGACTTGT
127 GGCTTTCAAATGAGTTGCCACCGACTTGT
* * * * * * *
223001 GGGCTTTTGAAA--AGATGCCACTAACTTATGGGATTTGAAAGGGCATGCCACTGAC-T-TGTGG
1 GGGC-TTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATGG-TTGCCACAGACTTGTGTGG
* ** * ** * **
223062 GCTTTG-AA-AGGGTGCCACTGACTTATG--GGCTTTGGAA-G-GATGCCATTAAC-T-TGTGGG
64 GCTTTGAAATAGGTTGCCACCAACTTGTGTAGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGG
* * * *
223119 -TTTTAAAAG-GGTGCCACGGACTTGT
129 CTTTCAAATGAGTTGCCACCGACTTGT
* ** *
223144 GGGCTTTGAAAT-AGGTCGCCACTGACTTGTGAACTTTGAAATAGGTTGCCACCGACTTGTGTGG
1 GGGCTTTGAAATGA-GTTGCCACTGACTTGTGGGCTTTGAAAT-GGTTGCCACAGACTTGTGTGG
* * * *
223208 GGTTTGAAATAGGTTGCCACCAACTTGTGTAGGCTTTGAAATGGGTTGCTACCAACTTGTGTGGG
64 GCTTTGAAATAGGTTGCCACCAACTTGTGTAGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGG
223273 CTTTCAAATGAGTTGCCACCGACTTATGT
129 CTTTCAAATGAGTTGCCACCGAC-T-TGT
*
223302 GGGCTTTAAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACAGACTTGTGTGGG
1 GGGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAAT-GGTTGCCACAGACTTGTGTGGG
* * * * *
223367 CTTTGAAATAGGTTGCCATCGACTTGTGTGGGCTTTCAAATGAGTTGCCACCGATTTGTGTGGGC
65 CTTTGAAATAGGTTGCCACCAACTTGTGTAGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGGC
* *
223432 TTTGAAATGAGTTGCCACTGACTTGT
130 TTTCAAATGAGTTGCCACCGACTTGT
* * *
223458 GGGCTTTGAAATGA--TGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTGAC-T-TGTGGGT
1 GGGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATGGTTGCCACAGACTTGTGTGGGC
* *
223518 TTTGAAAT--GATGCCACTAACTTGTG
66 TTTGAAATAGGTTGCCACCAACTTGTG
223543 GGCTTTAAAA
Statistics
Matches: 456, Mismatches: 65, Indels: 45
0.81 0.11 0.08
Matches are distributed among these distances:
142 7 0.02
143 26 0.06
144 56 0.12
145 3 0.01
146 25 0.05
147 4 0.01
148 42 0.09
149 3 0.01
150 54 0.12
151 6 0.01
152 26 0.06
153 1 0.00
154 31 0.07
155 7 0.02
156 26 0.06
157 2 0.00
158 136 0.30
159 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (155 bp):
GGGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATGGTTGCCACAGACTTGTGTGGGC
TTTGAAATAGGTTGCCACCAACTTGTGTAGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGGCT
TTCAAATGAGTTGCCACCGACTTGT
Found at i:223584 original size:86 final size:85
Alignment explanation
Indices: 222879--223883 Score: 328
Period size: 82 Copynumber: 11.5 Consensus size: 85
222869 CACCAACTTG
* * * * * *
222879 TGTGGGCTTTGAAA-GGGTGACACTGACTTGTAGGCTTTGAAAAAAGAGTTGCCACTGACTTGTG
1 TGTGGGCTTTGAAATGAGTGCCACTAACTTGTGGGCTTT--AAAATGA--TGCCACGGAC-T-TG
** *
222943 TGGGCTTTGAAAGGATGCCACTGACT
60 TGCACTTTAAAAGGATGCCACTGACT
* * * ** *
222969 TGTGGGCTTTGAAAAG-GATGCTACTGACTTGTGGGCTTTTGAAAA-GATGCCACTAACTTATGG
1 TGTGGGCTTTGAAATGAG-TGCCACTAACTTGTGGGC-TTT-AAAATGATGCCACGGACTTGT-G
* *
223032 GA-TTTGAAAGGGCATGCCACTGACT
62 CACTTT-AAAAGG-ATGCCACTGACT
* * * ** * *** ***
223057 TGTGGGCTTTGAAA-GGGTGCCACTGACTTATGGGCTTTGGAAGGATGCCATTAACTTGTGGGTT
1 TGTGGGCTTTGAAATGAGTGCCACTAACTTGTGGGCTTTAAAATGATGCCACGGACTTGTGCACT
* *
223121 TTAAAAGGGTGCCACGGACT
66 TTAAAAGGATGCCACTGACT
* ** * * *
223141 TGTGGGCTTTGAAAT-AGGTCGCCACTGACTTGTGAACTTTGAAATAGGTTGCCACCGACTTGTG
1 TGTGGGCTTTGAAATGA-GT-GCCACTAACTTGTGGGCTTT-AAA-ATGATGCCACGGAC-T-TG
*** * **
223205 TGGGGTTTGAAATAGGTTGCCACCAACT
60 TGCACTTT-AAA-AGGATGCCACTGACT
* * * * *
223233 TGTGTAGGCTTTGAAATGGGTTGCTACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTT
1 TGTG--GGCTTTGAAATGAG-TGCCACTAAC-T-TGTGGGCTTTAAAATGA--TGCCACGGAC-T
** *
223298 ATGTGGGCTTTAAAATGAGTTGCCACTGACT
58 -TGTGCACTTTAAAA-G-GATGCCACTGACT
* * *
223329 TGTGGGCTTTGAAATGGGTTGCCAC-AGACTTGTGTGGGCTTTGAAATAGGTTGCCATC-GACTT
1 TGTGGGCTTTGAAATGAG-TGCCACTA-AC-T-TGTGGGCTTT-AAA-ATGATGCCA-CGGAC-T
** * * * *
223392 GTGTGGGCTTTCAAATGAGTTGCCACCGATTT
58 -TGTGCACTTT-AAAAG-GATGCCACTGA-CT
* * * **
223424 GTGTGGGCTTTGAAATGAGTTGCCACTGACTTGTGGGCTTTGAAATGATGCCACTGACTTGTGGG
1 -TGTGGGCTTTGAAATGAG-TGCCACTAACTTGTGGGCTTTAAAATGATGCCACGGACTTGTGCA
*
223489 CTTTGAAAGGATGCCACTGACT
64 CTTTAAAAGGATGCCACTGACT
* * *
223511 TGTGGGTTTTGAAATGA-TGCCACTAACTTGTGGGCTTTAAAAGGGTGCTGCCACGGAGTTGTGC
1 TGTGGGCTTTGAAATGAGTGCCACTAACTTGTGGGCTTTAAAA---TGATGCCACGGACTTGTGC
*
223575 AC-TTAAAAGGATGCCAC-GAAGT
63 ACTTTAAAAGGATGCCACTG-ACT
* * * * * * * * *
223597 TGTAGAC-TTAAAAGGA-TGCCAC-AGAGTTGTGGAC-TTAAAA-GAGTGCCACGGAGTGGTGGA
1 TGTGGGCTTTGAAATGAGTGCCACTA-ACTTGTGGGCTTTAAAATGA-TGCCACGGACTTGTGCA
* *
223657 CTTTAAAA-GAGTGCCACGGAGT
64 CTTTAAAAGGA-TGCCACTGACT
* * * ** * * * * * *
223679 TGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAAGGTGCCACGGAGTTGTGGACT
1 TGTGGGCTTTGAAATGAGTGCCACTAACTTGTGGGCTTTAAAATGATGCCACGGACTTGTGCACT
* * *
223741 TTAAAAGGGTGCCACGGAGT
66 TTAAAAGGATGCCACTGACT
* * * * * * * * * * * * * *
223761 TATGGACTTT-AAA-GGGTGCCAATGAGTTATGGACTTTAAAAAGGTGCCACAGAGTTATGGACT
1 TGTGGGCTTTGAAATGAGTGCCACTAACTTGTGGGCTTTAAAATGATGCCACGGACTTGTGCACT
* *
223824 TTAAAAGGATGCCACAGAGT
66 TTAAAAGGATGCCACTGACT
* * * *
223844 TGTGGACTTTGAAAAGAAATGCCACTGAA-TTGTGGACTTT
1 TGTGGGCTTTGAAATG-AGTGCCACT-AACTTGTGGGCTTT
223884 GAAGAGGTCA
Statistics
Matches: 754, Mismatches: 105, Indels: 116
0.77 0.11 0.12
Matches are distributed among these distances:
80 1 0.00
81 22 0.03
82 104 0.14
83 61 0.08
84 57 0.08
85 34 0.05
86 94 0.12
87 43 0.06
88 55 0.07
89 4 0.01
90 36 0.05
91 25 0.03
92 29 0.04
93 3 0.00
94 98 0.13
95 16 0.02
96 72 0.10
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (85 bp):
TGTGGGCTTTGAAATGAGTGCCACTAACTTGTGGGCTTTAAAATGATGCCACGGACTTGTGCACT
TTAAAAGGATGCCACTGACT
Found at i:223597 original size:27 final size:27
Alignment explanation
Indices: 223559--223882 Score: 350
Period size: 27 Copynumber: 11.7 Consensus size: 27
223549 AAAAGGGTGC
*
223559 TGCCACGGAGTTGTGCACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
223586 TGCCACGAAGTTGTAGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
223613 TGCCACAGAGTTGTGGACTTAAAA-GA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
223639 GTGCCACGGAGTGGTGGACTTTAAAA-GA
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGA
*
223667 GTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGA
223695 TGCCACGGAGTTGTGGACTTAAAAAGG-
1 TGCCACGGAGTTGTGGACTT-AAAAGGA
*
223722 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* * *
223750 TGCCACGGAGTTATGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
** *
223777 TGCCAATGAGTTATGGACTTTAAAAAGG-
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGA
* *
223805 TGCCACAGAGTTATGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
223833 TGCCACAGAGTTGTGGACTTTGAAAAGAAA
1 TGCCACGGAGTTGTGGAC-TT-AAAAG-GA
* *
223863 TGCCACTGAATTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
223883 TGAAGAGGTC
Statistics
Matches: 265, Mismatches: 21, Indels: 20
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.01
27 141 0.53
28 93 0.35
29 12 0.05
30 17 0.06
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:223674 original size:82 final size:82
Alignment explanation
Indices: 223559--223882 Score: 388
Period size: 82 Copynumber: 3.9 Consensus size: 82
223549 AAAAGGGTGC
* *
223559 TGCCACGGAGTTGTGCAC-TTAAAAGGATGCCACGAAGTTGTAGACTTAAAAGGATGCCACAGAG
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACAGAG
223623 TTGTGGACTT-AAAAGAG
66 TTGTGGACTTAAAAAG-G
* * * *
223640 TGCCACGGAGTGGTGGACTTTAAAA-GAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGA-TGCCACGAAGTTGTGGACTTAAAAGGATGCCACAGA
223704 GTTGTGGACTTAAAAAGG
65 GTTGTGGACTTAAAAAGG
* * * * *
223722 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTAAAGGGTGCCA-ATGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACA-GA
*
223786 GTTATGGACTTTAAAAAGG
65 GTTGTGGAC-TTAAAAAGG
* * *
223805 TGCCACAGAGTTATGGACTTTAAAAGGATGCCAC-AGAGTTGTGGACTTTGAAAAGAAATGCCAC
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGA-AGTTGTGGAC-TT-AAAAG-GATGCCAC
* *
223869 TGAATTGTGGACTT
62 AGAGTTGTGGACTT
223883 TGAAGAGGTC
Statistics
Matches: 209, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
81 18 0.09
82 114 0.55
83 55 0.26
84 2 0.01
85 6 0.03
86 14 0.07
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (82 bp):
TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACAGAG
TTGTGGACTTAAAAAGG
Found at i:223682 original size:55 final size:54
Alignment explanation
Indices: 223559--223883 Score: 368
Period size: 55 Copynumber: 5.9 Consensus size: 54
223549 AAAAGGGTGC
* * *
223559 TGCCACGGAGTTGTGCACTTAAAAG-GATGCCACGAAGTTGTAGAC-TTAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGAG-TGCCACGGAGTTGTGGACTTTAAAAGG
* *
223612 ATGCCACAGAGTTGTGGACTTAAAAGAGTGCCACGGAGTGGTGGACTTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAG-G
* *
223668 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGG
* * *
223722 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGG
** * * *
223777 TGCCAATGAGTTATGGACTTTAAAA-AGGTGCCACAGAGTTATGGACTTTAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGA-GTGCCACGGAGTTGTGGACTTTAAAAGG
* * * *
223832 ATGCCACAGAGTTGTGGACTTTGAAAAGAAATGCCACTGAATTGTGGACTTT
1 -TGCCACGGAGTTGTGGAC-TT-AAAAG-AGTGCCACGGAGTTGTGGACTTT
223884 GAAGAGGTCA
Statistics
Matches: 237, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
54 57 0.24
55 138 0.58
56 19 0.08
57 4 0.02
58 18 0.08
59 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGG
Found at i:233454 original size:14 final size:15
Alignment explanation
Indices: 233426--233455 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
233416 TCTTTACCAC
233426 ATTTATTGAAATGAT
1 ATTTATTGAAATGAT
233441 ATTTATTG-AATGAT
1 ATTTATTGAAATGAT
233455 A
1 A
233456 AGACGATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
ATTTATTGAAATGAT
Found at i:237436 original size:13 final size:13
Alignment explanation
Indices: 237418--237444 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
237408 ACATTATGCT
237418 TTGTATCGATACA
1 TTGTATCGATACA
237431 TTGTATCGATACA
1 TTGTATCGATACA
237444 T
1 T
237445 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:237459 original size:32 final size:33
Alignment explanation
Indices: 237400--237463 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
237390 TTACCCAGAG
*
237400 GTATCGATACATTATGCTTTGTATCGATACATT
1 GTATCGATACATTATGCATTGTATCGATACATT
237433 GTATCGATACATGT-T-CATTGTATCGATACAT
1 GTATCGATACAT-TATGCATTGTATCGATACAT
237464 GGACAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 13 0.45
34 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
GTATCGATACATTATGCATTGTATCGATACATT
Found at i:237474 original size:20 final size:19
Alignment explanation
Indices: 237428--237484 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
237418 TTGTATCGAT
*
237428 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
237447 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
237466 ACAATTGTATCAATACATG
1 AC-ATTGTATCGATACATG
237485 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:238449 original size:13 final size:13
Alignment explanation
Indices: 238431--238456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
238421 ATTTTTTTTG
238431 TGTATCGATACAT
1 TGTATCGATACAT
238444 TGTATCGATACAT
1 TGTATCGATACAT
238457 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:243043 original size:15 final size:15
Alignment explanation
Indices: 243023--243053 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
243013 ATTTCGTTTG
*
243023 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
243038 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
243053 G
1 G
243054 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:244883 original size:21 final size:21
Alignment explanation
Indices: 244854--244898 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
244844 AAGTTTTTAT
*
244854 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
244874 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
244896 TTT
1 TTT
244899 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:247137 original size:13 final size:13
Alignment explanation
Indices: 247119--247144 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247109 ATTTTTTTTG
247119 TGTATCGATACAT
1 TGTATCGATACAT
247132 TGTATCGATACAT
1 TGTATCGATACAT
247145 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:250591 original size:2 final size:2
Alignment explanation
Indices: 250584--250614 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
250574 AGATTTTCAA
*
250584 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
250615 CACATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:251603 original size:20 final size:18
Alignment explanation
Indices: 251561--251594 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
251551 AGTTGCGTTG
251561 TTTTTATTATTTTTTCAA
1 TTTTTATTATTTTTTCAA
251579 TTTTT-TTATTTTTTCA
1 TTTTTATTATTTTTTCA
251595 TAACTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATTATTTTTTCAA
Done.