Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 168 of 190
Found at i:27519689 original size:16 final size:16
Alignment explanation
Indices: 27519668--27519698 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27519658 TTACGGTTTT
27519668 GATTTTAGAGTTTGGA
1 GATTTTAGAGTTTGGA
*
27519684 GATTTTAGGGTTTGG
1 GATTTTAGAGTTTGG
27519699 GTTTTGTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (16 bp):
GATTTTAGAGTTTGGA
Found at i:27519742 original size:7 final size:7
Alignment explanation
Indices: 27519730--27519767 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
27519720 GATGTAAGGG
27519730 TTTGGAT
1 TTTGGAT
27519737 TTTGGAT
1 TTTGGAT
27519744 TTTGGAT
1 TTTGGAT
**
27519751 TTTGGGG
1 TTTGGAT
27519758 TTTGGAT
1 TTTGGAT
27519765 TTT
1 TTT
27519768 AGGGATTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.58
Consensus pattern (7 bp):
TTTGGAT
Found at i:27521246 original size:12 final size:11
Alignment explanation
Indices: 27521221--27521273 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 11
27521211 TTTTTGGGTA
27521221 TTTTGTATTATT
1 TTTTGTATT-TT
*
27521233 TTTGGTATTTTT
1 TTTTGTA-TTTT
27521245 TTTTGTATTTCAT
1 TTTTGTATTT--T
27521258 ATTTTGTATTTT
1 -TTTTGTATTTT
27521270 TTTT
1 TTTT
27521274 TTGTATTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 7 0.20
12 15 0.43
13 3 0.09
14 10 0.29
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.75
Consensus pattern (11 bp):
TTTTGTATTTT
Found at i:27521270 original size:27 final size:25
Alignment explanation
Indices: 27521221--27521280 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
27521211 TTTTTGGGTA
27521221 TTTTGTA-TTATTTTTGGTATTTTT
1 TTTTGTATTTATTTTTGGTATTTTT
27521245 TTTTGTATTTCATATTTT-GTATTTTTT
1 TTTTGTATTT-AT-TTTTGGTA-TTTTT
27521272 TTTTGTATT
1 TTTTGTATT
27521281 CTGGACAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.22
25 2 0.06
26 5 0.16
27 18 0.56
ACGTcount: A:0.13, C:0.02, G:0.10, T:0.75
Consensus pattern (25 bp):
TTTTGTATTTATTTTTGGTATTTTT
Found at i:27521997 original size:169 final size:174
Alignment explanation
Indices: 27521614--27521999 Score: 471
Period size: 176 Copynumber: 2.2 Consensus size: 174
27521604 TAAGGATTAG
** *
27521614 GATTAAACTATAAATCAGAGAATAAAGAGACC-AGGATTAAATAGCGAATCAAAAAATGACGTTA
1 GATTAAACCGTAAATCAAAGAATAAAGAGACCGA-GATTAAATAGCGAATCAAAAAATGACGTTA
* * * * *
27521678 ACTTGGATTGAATCGCAAGTTAAAAAAAATAAGAAGATCGAGAATAAATCATGAGTTAGAGGTTA
65 ACTTGGATTGAATCACAAGTTAAAAAAAATAAGAAGATCAAGAATAAACCACGAGTCAGAGGTTA
* * * *
27521743 ACAACAACAATTAAGATTAAACTACGATTTTAAATTAAAGAGATTGA
130 ACAACAACAATT-ACA-TAAACTACAATTTTAAATTAAAAAGATCGA
* * * * *
27521790 GATTAAACCGTAAATCGAAGAATAAAGAGACCGAGATTAAATCA-TGAGTTAGAAAATGACGTTA
1 GATTAAACCGTAAATCAAAGAATAAAGAGACCGAGATTAAAT-AGCGAATCAAAAAATGACGTTA
* *
27521854 ACTTGGATTGAATCACAAG-T-CAAAAAATAAGAAGATCAAGAATAAACCACGAGTCAGGGGTTA
65 ACTTGGATTGAATCACAAGTTAAAAAAAATAAGAAGATCAAGAATAAACCACGAGTCAGAGGTTA
* * *
27521917 ACAACGACAA-T-CA-AAACTATAATTTTAAATTAAAAATATCGA
130 ACAACAACAATTACATAAACTACAATTTTAAATTAAAAAGATCGA
* *
27521959 GATTGAATCGTAAATCAAAGAATAAAGAGACCGAGATTAAA
1 GATTAAACCGTAAATCAAAGAATAAAGAGACCGAGATTAAA
27522000 CCACGAGTCA
Statistics
Matches: 183, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
169 62 0.34
171 1 0.01
173 1 0.01
174 46 0.25
175 1 0.01
176 70 0.38
177 2 0.01
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (174 bp):
GATTAAACCGTAAATCAAAGAATAAAGAGACCGAGATTAAATAGCGAATCAAAAAATGACGTTAA
CTTGGATTGAATCACAAGTTAAAAAAAATAAGAAGATCAAGAATAAACCACGAGTCAGAGGTTAA
CAACAACAATTACATAAACTACAATTTTAAATTAAAAAGATCGA
Found at i:27522088 original size:105 final size:105
Alignment explanation
Indices: 27521879--27522543 Score: 734
Period size: 111 Copynumber: 6.3 Consensus size: 105
27521869 CAAGTCAAAA
* * * ** * * * *
27521879 AATAAGAAGATCAAGAATAAACCACGAGTCAGGGGTTAACAACGACAATC---A--AAACTATAA
1 AATAAAAAGATCGAGATTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGA
* * * ** *
27521939 TTTTAAATTAAAAATATCGAGATTGAATCGTAAATCAAAG
66 TTTTAAATTAAAGAGATCGAGATTGAACCGCGAATCGAAG
* *
27521979 AATAAAGAGACCGAGATTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGA
1 AATAAAAAGATCGAGATTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGA
* * *
27522044 TTTTAAATTAAAGAGATCGGGATTGAACCACGAACCGAAG
66 TTTTAAATTAAAGAGATCGAGATTGAACCGCGAATCGAAG
* * * *
27522084 AATAAAAAGATCAAGGATTAAACAACGAGTCAGAAGATAACAACAACAATCAAGATTAAACTGTA
1 AATAAAAAGATCGA-GATTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTG
* * *
27522149 ATTTTAAATTAAAGAGATCGGGATTGAATCGTGAATCGAAG
65 ATTTTAAATTAAAGAGATCGAGATTGAACCGCGAATCGAAG
* * *
27522190 AATAAAAAGATCGGGATTAAACCACGAGTTAGAAGATAATAACAACAATCGAGATTAAACTGTGA
1 AATAAAAAGATCGAGATTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGA
*
27522255 TTTTAAATTAAAAAGATCGAGATTGAACCGCGAATC-AGAG
66 TTTTAAATTAAAGAGATCGAGATTGAACCGCGAATCGA-AG
* * * * *
27522295 AATAAAAAGGTCGAAATTAAATCACAAGTCAAAGATTAAAGATAACAATAACAATCGAGATTAAA
1 AATAAAAAGATCGAGATTAAACCACGAGTC--AG----AAGATAACAACAACAATCGAGATTAAA
* * *
27522360 CTGTGATTTTAAATTAAAGAGATCGAGATTGAACTGTGAATC-AGAT
60 CTGTGATTTTAAATTAAAGAGATCGAGATTGAACCGCGAATCGA-AG
* * *
27522406 AATAAAAAGATC-AGGATTAAACCATGAGTCAAAGATTAAAGATAACAACAATAATCGCGATTAA
1 AATAAAAAGATCGA-GATTAAACCACGAGTC--AG----AAGATAACAACAACAATCGAGATTAA
* *
27522470 ACTGTGATTTTAAATTAAAGAGATCGAGATTGAACCACGAATCGGAG
59 ACTGTGATTTTAAATTAAAGAGATCGAGATTGAACCGCGAATCGAAG
27522517 AATAAAAAGATCGAGATTAAACCACGA
1 AATAAAAAGATCGAGATTAAACCACGA
27522544 ATCAAATATT
Statistics
Matches: 482, Mismatches: 67, Indels: 21
0.85 0.12 0.04
Matches are distributed among these distances:
100 41 0.09
103 1 0.00
104 1 0.00
105 153 0.32
106 96 0.20
107 2 0.00
110 1 0.00
111 186 0.39
112 1 0.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.22
Consensus pattern (105 bp):
AATAAAAAGATCGAGATTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGA
TTTTAAATTAAAGAGATCGAGATTGAACCGCGAATCGAAG
Found at i:27522178 original size:211 final size:211
Alignment explanation
Indices: 27521930--27522548 Score: 782
Period size: 211 Copynumber: 2.9 Consensus size: 211
27521920 ACGACAATCA
* * * * * *
27521930 AAACTATAATTTTAAATTAAAAATATCGAGATTGAATCGTAAATCAAAGAATAAAGAGACCGAGA
1 AAACTGTAATTTTAAATTAAAGAGATCGAGATTGAATCGTGAATCAAAGAATAAAAAGATCGAGA
27521995 TTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAGAGA
66 TTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAGAGA
* *
27522060 TCGGGATTGAACCACGAACCGAAGAATAAAAAGATCAAGGATTAAACAACGAGTC-AG-AAGATA
131 TCGAGATTGAACCACGAATCGAAGAATAAAAAGATCAA-GATTAAAC-ACGAGTCAAGAAAGATA
27522123 ACAACAACAATCAAGATT
194 ACAACAACAATCAAGATT
* * *
27522141 AAACTGTAATTTTAAATTAAAGAGATCGGGATTGAATCGTGAATCGAAGAATAAAAAGATCGGGA
1 AAACTGTAATTTTAAATTAAAGAGATCGAGATTGAATCGTGAATCAAAGAATAAAAAGATCGAGA
* * *
27522206 TTAAACCACGAGTTAGAAGATAATAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAAAGA
66 TTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAGAGA
* * *
27522271 TCGAGATTGAACCGCGAATC-AGAGAATAAAAAGGTCGAA-ATTAAATCACAAGTCAAAGATTAA
131 TCGAGATTGAACCACGAATCGA-AGAATAAAAAGATC-AAGATTAAA-CACGAGTC-AAG---AA
* *
27522334 AGATAACAATAACAATCGAGATT
189 AGATAACAACAACAATCAAGATT
* * *
27522357 AAACTGTGATTTTAAATTAAAGAGATCGAGATTGAA-CTGTGAATCAGATAATAAAAAGATC-AG
1 AAACTGTAATTTTAAATTAAAGAGATCGAGATTGAATC-GTGAATCAAAGAATAAAAAGATCGA-
* * *
27522420 GATTAAACCATGAGTCAAAGATTAAAGATAACAACAATAATCGCGATTAAACTGTGATTTTAAAT
64 GATTAAACCACGAGTC--AG----AAGATAACAACAACAATCGAGATTAAACTGTGATTTTAAAT
* * *
27522485 TAAAGAGATCGAGATTGAACCACGAATCGGAGAATAAAAAGATCGAGATTAAACCACGAATCAA
123 TAAAGAGATCGAGATTGAACCACGAATCGAAGAATAAAAAGATCAAGATTAAA-CACGAGTCAA
27522549 ATATTAAAGA
Statistics
Matches: 351, Mismatches: 38, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
210 13 0.04
211 149 0.42
212 4 0.01
215 1 0.00
216 90 0.26
218 2 0.01
221 3 0.01
222 89 0.25
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.22
Consensus pattern (211 bp):
AAACTGTAATTTTAAATTAAAGAGATCGAGATTGAATCGTGAATCAAAGAATAAAAAGATCGAGA
TTAAACCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAGAGA
TCGAGATTGAACCACGAATCGAAGAATAAAAAGATCAAGATTAAACACGAGTCAAGAAAGATAAC
AACAACAATCAAGATT
Found at i:27524257 original size:21 final size:20
Alignment explanation
Indices: 27524204--27524258 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
27524194 TGAAGATTCA
*
27524204 GATTTT-AGGGTTTTGGTTT
1 GATTTTAAGGTTTTTGGTTT
*
27524223 GAGTTTTGAGGGTTTTTGGGTTT
1 GA-TTTT-AAGGTTTTT-GGTTT
27524246 GATTTTAAGGTTT
1 GATTTTAAGGTTT
27524259 AGAGGGTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.07
20 4 0.14
21 6 0.21
22 10 0.34
23 7 0.24
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.55
Consensus pattern (20 bp):
GATTTTAAGGTTTTTGGTTT
Found at i:27525903 original size:19 final size:18
Alignment explanation
Indices: 27525879--27525915 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
27525869 ATTATTATTA
27525879 TTATTATTATTTAAAAAAT
1 TTATTATTA-TTAAAAAAT
27525898 TTATTATTATTAAAAAAT
1 TTATTATTATTAAAAAAT
27525916 GTAGACCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTATTATTAAAAAAT
Found at i:27525909 original size:3 final size:3
Alignment explanation
Indices: 27525859--27525889 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
27525849 ATTAAACCAA
27525859 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
27525890 TAAAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27526073 original size:2 final size:2
Alignment explanation
Indices: 27526068--27526101 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
27526058 TTTTTTACTA
*
27526068 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27526102 TGATTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27526362 original size:2 final size:2
Alignment explanation
Indices: 27526355--27526384 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27526345 TTTGTTTCTA
27526355 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
27526385 TTGATTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27527394 original size:26 final size:25
Alignment explanation
Indices: 27527365--27527445 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 25
27527355 CACATAACTT
27527365 TTTTATTATGTGACTTCCAATTAAAG
1 TTTTATTATGTGACTT-CAATTAAAG
* *
27527391 TTTTATAAT-T--CTT--ATTATAACTT
1 TTTTATTATGTGACTTCAATTA-AA--G
27527414 TTTTATTATGTGACTTCTAATTAAAG
1 TTTTATTATGTGACTTC-AATTAAAG
27527440 TTTTAT
1 TTTTAT
27527446 AATTTTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
20 4 0.10
21 2 0.05
23 11 0.26
24 1 0.02
25 1 0.02
26 17 0.40
28 2 0.05
29 4 0.10
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (25 bp):
TTTTATTATGTGACTTCAATTAAAG
Found at i:27527430 original size:49 final size:49
Alignment explanation
Indices: 27527358--27527457 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
27527348 GTTGTTACAC
27527358 ATAACTTTTTTATTATGTGACTTCCAATTAAAGTTTTATAATTCTTATT
1 ATAACTTTTTTATTATGTGACTTCCAATTAAAGTTTTATAATTCTTATT
* *
27527407 ATAACTTTTTTATTATGTGACTTCTAATTAAAGTTTTATAATTTTTATT
1 ATAACTTTTTTATTATGTGACTTCCAATTAAAGTTTTATAATTCTTATT
27527456 AT
1 AT
27527458 CATTGTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (49 bp):
ATAACTTTTTTATTATGTGACTTCCAATTAAAGTTTTATAATTCTTATT
Found at i:27527745 original size:15 final size:15
Alignment explanation
Indices: 27527725--27527755 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27527715 ATTTTAGTTG
27527725 TAACACTATTTTGAA
1 TAACACTATTTTGAA
27527740 TAACACTATTTTGAA
1 TAACACTATTTTGAA
27527755 T
1 T
27527756 TTTTGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
TAACACTATTTTGAA
Found at i:27537204 original size:18 final size:18
Alignment explanation
Indices: 27537167--27537204 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
27537157 ATTATAAAAT
*
27537167 ATTATTTTTAAATATTAA
1 ATTATTTTTAAATATAAA
27537185 ATTATATTTTAAAT-TAAA
1 ATTAT-TTTTAAATATAAA
27537203 AT
1 AT
27537205 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTTTTAAATATAAA
Found at i:27537208 original size:20 final size:18
Alignment explanation
Indices: 27537160--27537208 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
27537150 GTATAATATT
27537160 ATAAAATATTATTTTTAA
1 ATAAAATATTATTTTTAA
*
27537178 ATATTAA-ATTATATTTTAA
1 ATA-AAATATTAT-TTTTAA
27537197 ATTAAAATATTA
1 A-TAAAATATTA
27537209 AATAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAAATATTATTTTTAA
Found at i:27537211 original size:13 final size:13
Alignment explanation
Indices: 27537161--27537211 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
27537151 TATAATATTA
**
27537161 TAAAATATTATTT
1 TAAAATATTAAAT
*
27537174 TTAAATATTAAAT
1 TAAAATATTAAAT
* *
27537187 T-ATATTTTAAAT
1 TAAAATATTAAAT
27537199 TAAAATATTAAAT
1 TAAAATATTAAAT
27537212 AATAATTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAAATATTAAAT
Found at i:27550969 original size:24 final size:23
Alignment explanation
Indices: 27550925--27550974 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
27550915 CGTCCCTTAT
*
27550925 TTTTTTTTTCATTTAAAACAATAG
1 TTTTTTTTT-ATTTAAAACAAAAG
27550949 TTTTTTTTT-TTTAAATTACAAAAG
1 TTTTTTTTTATTTAAA--ACAAAAG
27550973 TT
1 TT
27550975 AAGAAACCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.26
24 17 0.74
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTTTTTTATTTAAAACAAAAG
Found at i:27551033 original size:22 final size:22
Alignment explanation
Indices: 27551008--27551088 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 22
27550998 ATTTAACAAA
27551008 TTTTATAATATAATATTTTTAC
1 TTTTATAATATAATATTTTTAC
* * * *
27551030 TTTTAAAATGTTGTAATATCAATTTAAAA
1 TTTTATAA---TATAATAT---TTT-TAC
27551059 TTTTATAATATAATATTTTTAC
1 TTTTATAATATAATATTTTTAC
27551081 TTTTATAA
1 TTTTATAA
27551089 CTCGTATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
22 16 0.36
23 3 0.07
25 7 0.16
26 7 0.16
28 3 0.07
29 8 0.18
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTATAATATAATATTTTTAC
Found at i:27556226 original size:31 final size:31
Alignment explanation
Indices: 27556159--27556226 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
27556149 ATTTGGGATA
* * * * *
27556159 ATGGTTTTCTTTTCCTTTTGGAATTAGGTTT
1 ATGGTTTCCTCTTCCTTTCGAAATTAGATTT
27556190 ATGGTTTCCTCTTCCTTTCGAAATTAAGATTT
1 ATGGTTTCCTCTTCCTTTCGAAATT-AGATTT
27556222 -TGGTT
1 ATGGTT
27556227 ATCTCTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (31 bp):
ATGGTTTCCTCTTCCTTTCGAAATTAGATTT
Found at i:27557846 original size:6 final size:6
Alignment explanation
Indices: 27557835--27557860 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27557825 TGTACATAAT
27557835 AGATAG AGATAG AGATAG AGATAG AG
1 AGATAG AGATAG AGATAG AGATAG AG
27557861 TTACCACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
AGATAG
Found at i:27579193 original size:15 final size:17
Alignment explanation
Indices: 27579174--27579205 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27579164 TATAAATTTG
27579174 AAAAAAA-TGTGATACT
1 AAAAAAAGTGTGATACT
27579190 AAAAAAAGTGTGATAC
1 AAAAAAAGTGTGATAC
27579206 CGGGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (17 bp):
AAAAAAAGTGTGATACT
Found at i:27579899 original size:24 final size:24
Alignment explanation
Indices: 27579867--27579972 Score: 133
Period size: 24 Copynumber: 4.2 Consensus size: 24
27579857 TTTGTTTATT
27579867 TTATTAGTTTATTTTAATTATTTA
1 TTATTAGTTTATTTTAATTATTTA
* *
27579891 TTATTAGTTTATTTGTTTATTTTATTA
1 TTATTAGTTTA-TT-TTAATTAT-TTA
27579918 GTTTATTAGTTTATTTTAATTATTTA
1 --TTATTAGTTTATTTTAATTATTTA
27579944 TTATTAGTTTATTTT-ATTATTATA
1 TTATTAGTTTATTTTAATTATT-TA
27579968 TTATT
1 TTATT
27579973 TATAGATATT
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
23 6 0.08
24 33 0.46
25 2 0.03
26 9 0.12
27 9 0.12
28 2 0.03
29 11 0.15
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (24 bp):
TTATTAGTTTATTTTAATTATTTA
Found at i:27579906 original size:45 final size:45
Alignment explanation
Indices: 27579843--27579972 Score: 162
Period size: 45 Copynumber: 2.9 Consensus size: 45
27579833 TATTCAAAGC
27579843 ATTT-TTATTATTTATTTGTTTATTTTATTAGTTTATT-TTAATT
1 ATTTATTATTATTTATTTGTTTATTTTATTAGTTTATTATTAATT
*
27579886 ATTTATTATTAGTTTATTTGTTTATTTTATTAGTTTATTAGTTTATT
1 ATTTATTATTA-TTTATTTGTTTATTTTATTAGTTTATTA-TTAATT
* *
27579933 -TTAATTATT-TATTATTAGTTTATTTTATTA-TTATATTATT
1 ATTTATTATTAT-TTATTTGTTTATTTTATTAGTT-TATTATT
27579973 TATAGATATT
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
43 4 0.05
44 11 0.14
45 50 0.64
46 8 0.10
47 5 0.06
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (45 bp):
ATTTATTATTATTTATTTGTTTATTTTATTAGTTTATTATTAATT
Found at i:27579948 original size:32 final size:33
Alignment explanation
Indices: 27579847--27579956 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 33
27579837 CAAAGCATTT
*
27579847 TTATTA-TTTATTTGTTTATTTT-ATTAGTTTA
1 TTATTAGTTTATTAGTTTATTTTAATTAGTTTA
* *
27579878 TTTTAATTA-TTTATTA--TTAGTTT-ATTTGTTTA
1 --TT-ATTAGTTTATTAGTTTATTTTAATTAGTTTA
27579910 TTTTATTAGTTTATTAGTTTATTTTAATTA-TTTA
1 --TTATTAGTTTATTAGTTTATTTTAATTAGTTTA
27579944 TTATTAGTTTATT
1 TTATTAGTTTATT
27579957 TTATTATTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
31 4 0.06
32 38 0.57
33 2 0.03
34 20 0.30
35 3 0.04
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (33 bp):
TTATTAGTTTATTAGTTTATTTTAATTAGTTTA
Found at i:27579986 original size:45 final size:45
Alignment explanation
Indices: 27579854--27579988 Score: 118
Period size: 45 Copynumber: 3.0 Consensus size: 45
27579844 TTTTTATTAT
* * * *
27579854 TTATTTGTTTATTTTATTAGTTTATT--TTAATTATTTATTA-TTA
1 TTATTAGTTTATTTTATTAGTTTATTAGTTTATGA-TAATTATTTA
* **
27579897 GTTTATTTGTTTATTTTATTAGTTTATTAGTTTATTTTAATTATTTA
1 --TTATTAGTTTATTTTATTAGTTTATTAGTTTATGATAATTATTTA
*
27579944 TTATTAGTTTATTTTATTA-TTATATTA-TTTATAGATATTTATTTA
1 TTATTAGTTTATTTTATTAGTT-TATTAGTTTAT-GATAATTATTTA
27579989 AATATAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
44 7 0.09
45 58 0.74
46 5 0.06
47 8 0.10
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (45 bp):
TTATTAGTTTATTTTATTAGTTTATTAGTTTATGATAATTATTTA
Found at i:27579989 original size:53 final size:53
Alignment explanation
Indices: 27579866--27579975 Score: 188
Period size: 53 Copynumber: 2.1 Consensus size: 53
27579856 ATTTGTTTAT
*
27579866 TTTATTAGTTTATTTTAATTATTTATTATTAGTTTATTTGTTTATTTTATTAG
1 TTTATTAGTTTATTTTAATTATTTATTATTAGTTTATTTGTTTATTATATTAG
27579919 TTTATTAGTTTATTTTAATTATTTATTATTAGTTTATTT-TATTATTATATTA-
1 TTTATTAGTTTATTTTAATTATTTATTATTAGTTTATTTGT-TTATTATATTAG
27579971 TTTAT
1 TTTAT
27579976 AGATATTTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
52 6 0.11
53 49 0.89
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (53 bp):
TTTATTAGTTTATTTTAATTATTTATTATTAGTTTATTTGTTTATTATATTAG
Found at i:27580032 original size:19 final size:18
Alignment explanation
Indices: 27579987--27580025 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
27579977 GATATTTATT
*
27579987 TAAATATAATTTAATATA
1 TAAATATAATTTAATAAA
27580005 TAAATATAATTTAAATAAA
1 TAAATATAATTT-AATAAA
27580024 TA
1 TA
27580026 TCTATAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATAATTTAATAAA
Found at i:27580915 original size:26 final size:26
Alignment explanation
Indices: 27580886--27580944 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
27580876 TTCGTGTTAT
*
27580886 TAAACAAATGAGTAATAAACAAATAA
1 TAAACAAACGAGTAATAAACAAATAA
** **
27580912 TAAACAAACGAGTTTTAAACAAATCT
1 TAAACAAACGAGTAATAAACAAATAA
27580938 TAAACAA
1 TAAACAA
27580945 GCTTGTTCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (26 bp):
TAAACAAACGAGTAATAAACAAATAA
Found at i:27587477 original size:19 final size:20
Alignment explanation
Indices: 27587446--27587518 Score: 55
Period size: 22 Copynumber: 3.8 Consensus size: 20
27587436 ACGTGAAGAG
*
27587446 ATTGGATGAGGTGGGGAGG-
1 ATTGGGTGAGGTGGGGAGGA
* *
27587465 ATTGGGT---GTGGTGAGGC
1 ATTGGGTGAGGTGGGGAGGA
*
27587482 ATTGGGGGGAAGGTGGGGAGGA
1 ATT-GGGTG-AGGTGGGGAGGA
*
27587504 ATTGGGTGTGGTGGG
1 ATTGGGTGAGGTGGG
27587519 ATGTTGGGGG
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
16 8 0.20
17 3 0.07
18 3 0.07
19 6 0.15
20 6 0.15
21 4 0.10
22 11 0.27
ACGTcount: A:0.16, C:0.01, G:0.59, T:0.23
Consensus pattern (20 bp):
ATTGGGTGAGGTGGGGAGGA
Found at i:27587515 original size:39 final size:38
Alignment explanation
Indices: 27587454--27587547 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 38
27587444 AGATTGGATG
27587454 AGGTGGGGAGGATTGGGTGTGGTGAGGCA-TT-GGGGGGA
1 AGGTGGGGAGGATTGGGTGTGGTG-GG-AGTTGGGGGGGA
27587492 AGGTGGGGAGGAATTGGGTGTGGTGGGATGTTGGGGGGGA
1 AGGTGGGGAGG-ATTGGGTGTGGTGGGA-GTTGGGGGGGA
*
27587532 AGGTGGAGAGGGATTG
1 AGGTGGGGA-GGATTG
27587548 ATGGGGGTGG
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
37 1 0.02
38 13 0.26
39 15 0.30
40 19 0.38
41 2 0.04
ACGTcount: A:0.17, C:0.01, G:0.61, T:0.21
Consensus pattern (38 bp):
AGGTGGGGAGGATTGGGTGTGGTGGGAGTTGGGGGGGA
Found at i:27587884 original size:26 final size:27
Alignment explanation
Indices: 27587828--27587884 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
27587818 TTTTTTGTTG
* *
27587828 TTTTGATATTTATATTATTGTCAATTC
1 TTTTGATATTTATATTATTCTCAATTA
*
27587855 TTTTGATA-TTATATTAATTCT-TATTA
1 TTTTGATATTTATATT-ATTCTCAATTA
27587881 TTTT
1 TTTT
27587885 TGTGTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (27 bp):
TTTTGATATTTATATTATTCTCAATTA
Found at i:27588072 original size:25 final size:26
Alignment explanation
Indices: 27588044--27588092 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
27588034 CTAAAAAATA
*
27588044 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
27588069 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
27588093 ATTTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:27589094 original size:6 final size:6
Alignment explanation
Indices: 27589083--27589114 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
27589073 GTCTAGATAA
*
27589083 TGATGG TGATGG TGATGG AGATGG TGATGG TG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TG
27589115 TGAATTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.50, T:0.31
Consensus pattern (6 bp):
TGATGG
Found at i:27589934 original size:6 final size:6
Alignment explanation
Indices: 27589923--27589950 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
27589913 ATAAGAGTTT
27589923 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
27589951 TACATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:27591470 original size:18 final size:18
Alignment explanation
Indices: 27591433--27591468 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
27591423 AGAATATATG
27591433 ATATGAAAAATGATAAAA
1 ATATGAAAAATGATAAAA
*
27591451 ATATG-AAAGTGATAAAA
1 ATATGAAAAATGATAAAA
27591468 A
1 A
27591469 ATCTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (18 bp):
ATATGAAAAATGATAAAA
Found at i:27591989 original size:11 final size:11
Alignment explanation
Indices: 27591967--27592001 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
27591957 GAAAAAGCCT
27591967 AAAAATTTTAA
1 AAAAATTTTAA
* *
27591978 AAGAATTGTAA
1 AAAAATTTTAA
27591989 AAAAATTTTAA
1 AAAAATTTTAA
27592000 AA
1 AA
27592002 TTCTAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:27592134 original size:12 final size:11
Alignment explanation
Indices: 27592108--27592148 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
27592098 AAATTTTAAA
27592108 TTTTAATTTT-
1 TTTTAATTTTC
*
27592118 TTTAAATTTTC
1 TTTTAATTTTC
27592129 TTTTAATTTT-
1 TTTTAATTTTC
*
27592139 TTATAATTTT
1 TTTTAATTTT
27592149 TAAAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTAATTTTC
Found at i:27592134 original size:21 final size:22
Alignment explanation
Indices: 27592089--27592189 Score: 80
Period size: 25 Copynumber: 4.3 Consensus size: 22
27592079 ATATTTTTGG
27592089 ATTTTTATTAAATTTTAAATTTTA
1 ATTTTT-TTAAATTTT-AATTTTA
*
27592113 ATTTTTTTAAATTTT-CTTTTA
1 ATTTTTTTAAATTTTAATTTTA
*
27592134 ATTTTTTATAATTTTTAAAATGTTT-
1 ATTTTTT-TAAATTTT--AAT-TTTA
*
27592159 ATATTTTTAAATTTTTAATTTTCA
1 ATTTTTTTAAA-TTTTAATTTT-A
27592183 GATTTTT
1 -ATTTTT
27592190 AAAAAATTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
21 12 0.19
22 10 0.16
23 12 0.19
24 9 0.15
25 16 0.26
26 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTTTTAAATTTTAATTTTA
Found at i:27592151 original size:17 final size:16
Alignment explanation
Indices: 27592101--27592190 Score: 64
Period size: 16 Copynumber: 5.8 Consensus size: 16
27592091 TTTTATTAAA
* *
27592101 TTTTAAATTTTAATTT
1 TTTTAAATTTTTATAT
*
27592117 TTTTAAA--TTT-T-C
1 TTTTAAATTTTTATAT
*
27592129 TTTTAATTTTTTATAAT
1 TTTTAAATTTTTAT-AT
*
27592146 TTTTAAAATGTTTATAT
1 TTTT-AAATTTTTATAT
27592163 TTTTAAATTTTTA-AT
1 TTTTAAATTTTTATAT
* *
27592178 TTTCAGATTTTTA
1 TTTTAAATTTTTA
27592191 AAAAATTTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.10
13 1 0.02
14 5 0.08
15 14 0.24
16 15 0.25
17 10 0.17
18 8 0.14
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTAAATTTTTATAT
Found at i:27592275 original size:14 final size:15
Alignment explanation
Indices: 27592253--27592283 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27592243 ATTTTCAAAA
*
27592253 AATTTTTAATTTTTT
1 AATTTTAAATTTTTT
27592268 AATTTTAAATTTTTT
1 AATTTTAAATTTTTT
27592283 A
1 A
27592284 TGTTTTTCTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
AATTTTAAATTTTTT
Found at i:27592359 original size:28 final size:27
Alignment explanation
Indices: 27592322--27592443 Score: 90
Period size: 28 Copynumber: 4.4 Consensus size: 27
27592312 TTTAAGAAAA
*
27592322 TTTTACTTTTATTAAAATTTTCAT-TT
1 TTTTAATTTTATTAAAATTTTCATATT
*
27592348 TTTCTAATTTT-TTAGAAATATTTTAT-TT
1 TTT-TAATTTTATTA-AAAT-TTTCATATT
* * *
27592376 TTTTGATTTCTTATTAAATTTTTGATATTT
1 TTTT-AATT-TTATTAAAATTTTCATA-TT
*
27592406 TTTTAAATTTATT-AAATTTTCATAATT
1 TTTTAATTTTATTAAAATTTTCAT-ATT
27592433 TTTTGAATTTT
1 TTTT-AATTTT
27592444 TATAATTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
26 6 0.08
27 25 0.33
28 29 0.38
29 7 0.09
30 9 0.12
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTTAATTTTATTAAAATTTTCATATT
Found at i:27592397 original size:19 final size:19
Alignment explanation
Indices: 27592375--27592415 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27592365 ATATTTTATT
27592375 TTTTTGAT-TTCTTATTAAA
1 TTTTTGATATT-TTATTAAA
*
27592394 TTTTTGATATTTTTTTAAA
1 TTTTTGATATTTTATTAAA
27592413 TTT
1 TTT
27592416 ATTAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTGATATTTTATTAAA
Found at i:27592424 original size:19 final size:19
Alignment explanation
Indices: 27592389--27592510 Score: 61
Period size: 19 Copynumber: 6.5 Consensus size: 19
27592379 TGATTTCTTA
*
27592389 TTAAATTTTTGATATTTTT
1 TTAAATTTTTGAAATTTTT
*
27592408 TTAAATTTATT-AAATTTTC
1 TTAAATTT-TTGAAATTTTT
* *
27592427 ATAATTTTTTG-AATTTTT
1 TTAAATTTTTGAAATTTTT
* ** * *
27592445 AT-AATTTTAAAAAATATT
1 TTAAATTTTTGAAATTTTT
* * ** *
27592463 TCAGATTTTTTTAACTTTT
1 TTAAATTTTTGAAATTTTT
*
27592482 TTATAATTTTTAAAATTTTT
1 TTA-AATTTTTGAAATTTTT
*
27592502 TTGAATTTT
1 TTAAATTTT
27592511 ATTGAAACAT
Statistics
Matches: 74, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
17 5 0.07
18 15 0.20
19 38 0.51
20 16 0.22
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (19 bp):
TTAAATTTTTGAAATTTTT
Found at i:27592443 original size:37 final size:36
Alignment explanation
Indices: 27592394--27592500 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 36
27592384 TCTTATTAAA
27592394 TTTTTGATATTTTTTTAAATTTATTAAATTTTCATAAT
1 TTTTTGA-ATTTTTTTAAATTTATTAAATTTTCA-AAT
* * ** *
27592432 TTTTTGAATTTTTATAATTTTAAAAAATATTTCAGAT
1 TTTTTGAATTTTTTTAAATTTATTAAAT-TTTCAAAT
* *
27592469 TTTTTTAACTTTTTTATAATTT-TTAAAATTTT
1 TTTTTGAATTTTTTTA-AATTTATT-AAATTTT
27592501 TTTGAATTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
37 35 0.64
38 20 0.36
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (36 bp):
TTTTTGAATTTTTTTAAATTTATTAAATTTTCAAAT
Found at i:27592500 original size:18 final size:18
Alignment explanation
Indices: 27592405--27592501 Score: 63
Period size: 18 Copynumber: 5.3 Consensus size: 18
27592395 TTTTGATATT
27592405 TTTTTA-AATTTATT-AAA
1 TTTTTATAATTT-TTAAAA
* **
27592422 TTTTCATAATTTTTTGAA
1 TTTTTATAATTTTTAAAA
*
27592440 TTTTTATAATTTTAAAAAA
1 TTTTTATAATTTT-TAAAA
* * * **
27592459 TATTTCAGATTTTTTTAACT
1 T-TTTTATA-ATTTTTAAAA
27592479 TTTTTATAATTTTTAAAA
1 TTTTTATAATTTTTAAAA
27592497 TTTTT
1 TTTTT
27592502 TTGAATTTTA
Statistics
Matches: 58, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
17 7 0.12
18 31 0.53
19 8 0.14
20 8 0.14
21 4 0.07
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTTTAAAA
Found at i:27597192 original size:36 final size:34
Alignment explanation
Indices: 27597151--27597258 Score: 106
Period size: 35 Copynumber: 3.3 Consensus size: 34
27597141 GATGATTATA
*
27597151 TAATTATGATACGAAGAGTATTATAGTAATTTTGAT
1 TAATTATGATA-TAAGA-TATTATAGTAATTTTGAT
*
27597187 TAATTATGATATAAGA-A-T-TA-T-A-TTCG--
1 TAATTATGATATAAGATATTATAGTAATTTTGAT
*
27597213 TAATTATGATATAAAAATATTATAGTAATTTTGAT
1 TAATTATGATAT-AAGATATTATAGTAATTTTGAT
27597248 TAATTATGATA
1 TAATTATGATA
27597259 GGAGTATTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
26 12 0.20
27 3 0.05
28 4 0.07
29 2 0.03
30 3 0.05
31 3 0.05
32 2 0.03
33 4 0.07
35 15 0.25
36 11 0.19
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.44
Consensus pattern (34 bp):
TAATTATGATATAAGATATTATAGTAATTTTGAT
Found at i:27597750 original size:19 final size:20
Alignment explanation
Indices: 27597726--27597764 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
27597716 TATTTATGTG
27597726 ATTATAGTAT-AAAAGCATA
1 ATTATAGTATGAAAAGCATA
27597745 ATTATAGTATGAAAAGCATA
1 ATTATAGTATGAAAAGCATA
27597765 GTAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTATAGTATGAAAAGCATA
Found at i:27598151 original size:22 final size:22
Alignment explanation
Indices: 27598106--27598151 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
27598096 CTTTTGATCG
** * *
27598106 ATTATGATAAAATTTTTTTGTA
1 ATTATGATAAAATGATATTATA
27598128 ATTATGATAAAATGATATTATA
1 ATTATGATAAAATGATATTATA
27598150 AT
1 AT
27598152 AATTTTAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (22 bp):
ATTATGATAAAATGATATTATA
Found at i:27598256 original size:24 final size:27
Alignment explanation
Indices: 27598203--27598256 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
27598193 TATTATAATA
27598203 ATTTTGATCAATTATAAAATAAAGAGT
1 ATTTTGATCAATTATAAAATAAAGAGT
*
27598230 ATTTTG-T-AATTATAATAT-AAGAGT
1 ATTTTGATCAATTATAAAATAAAGAGT
27598254 ATT
1 ATT
27598257 ATAGTAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.35
25 10 0.38
26 1 0.04
27 6 0.23
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (27 bp):
ATTTTGATCAATTATAAAATAAAGAGT
Found at i:27598263 original size:25 final size:25
Alignment explanation
Indices: 27598212--27598263 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
27598202 AATTTTGATC
*
27598212 AATTATAAAATAAAGAGTATTTTGT
1 AATTATAAAATAAAGAGTATTTAGT
*
27598237 AATTATAATAT-AAGAGTATTATAGT
1 AATTATAAAATAAAGAGTATT-TAGT
27598262 AA
1 AA
27598264 GTAATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (25 bp):
AATTATAAAATAAAGAGTATTTAGT
Found at i:27598440 original size:20 final size:20
Alignment explanation
Indices: 27598415--27598458 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
27598405 AGTATATTTT
*
27598415 CATAATTATGAAA-TAAAAAA
1 CATAATAAT-AAATTAAAAAA
*
27598435 CATAATAATAAATTTAAAAA
1 CATAATAATAAATTAAAAAA
27598455 CATA
1 CATA
27598459 TTAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
CATAATAATAAATTAAAAAA
Found at i:27598988 original size:24 final size:22
Alignment explanation
Indices: 27598931--27598992 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
27598921 AATATTTTTA
*
27598931 AATA-TTTATA-TTAAAAAAAT
1 AATATTTTATATTTTAAAAAAT
27598951 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
27598973 AATATTTTATTAATTTTAAA
1 AATATTTTA-T-ATTTTAAA
27598993 TCGAATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 4 0.11
21 6 0.16
22 18 0.49
23 1 0.03
24 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:27599009 original size:36 final size:38
Alignment explanation
Indices: 27598969--27599047 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 38
27598959 ATATTTTAAA
* *
27598969 AAATAATATTTTAT-TAATTTTAAATC-GAATTAAATT-
1 AAATAATA-TTTATGTAATATTAAATCAAAATTAAATTC
*
27599005 AAATATTATTTATGTAATATTAAATCAAAATTAAATTC
1 AAATAATATTTATGTAATATTAAATCAAAATTAAATTC
27599043 AAATA
1 AAATA
27599048 TAAAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.14
36 18 0.49
37 9 0.24
38 5 0.14
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (38 bp):
AAATAATATTTATGTAATATTAAATCAAAATTAAATTC
Found at i:27599053 original size:24 final size:24
Alignment explanation
Indices: 27599020--27599070 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
27599010 TTATTTATGT
* *
27599020 AATATTAAATCAAAATTAAATTCA
1 AATATAAAATCAAAATTAAATTAA
**
27599044 AATATAAAATTTAAATTAAATTAA
1 AATATAAAATCAAAATTAAATTAA
27599068 AAT
1 AAT
27599071 TTAATAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
AATATAAAATCAAAATTAAATTAA
Found at i:27599085 original size:17 final size:18
Alignment explanation
Indices: 27599031--27599087 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
27599021 ATATTAAATC
27599031 AAAA-TTAAATTCAAATAT
1 AAAATTTAAATT-AAATAT
27599049 AAAATTTAAATTAAAT-T
1 AAAATTTAAATTAAATAT
27599066 AAAATTT-AA-TAATATAT
1 AAAATTTAAATTAA-ATAT
27599083 AAAAT
1 AAAAT
27599088 AGAATCAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.08
16 4 0.11
17 14 0.39
18 8 0.22
19 7 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTTAAATTAAATAT
Found at i:27611828 original size:19 final size:18
Alignment explanation
Indices: 27611806--27611844 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
27611796 AATAAATAAG
27611806 AATTAAAAATTTAAAAATA
1 AATT-AAAATTTAAAAATA
* *
27611825 AATTTAAATTTTAAAATA
1 AATTAAAATTTAAAAATA
27611843 AA
1 AA
27611845 GAGTCAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAAATTTAAAAATA
Found at i:27621115 original size:175 final size:167
Alignment explanation
Indices: 27620799--27621132 Score: 443
Period size: 175 Copynumber: 2.0 Consensus size: 167
27620789 TTTTGTACAT
* ** * *
27620799 AAACATTTTAATTGATTTTTTTATTTTTTTAATAATTGATCAATTAAGACATTTATGTACAGAAA
1 AAACATCTTAATTGATCCTTTAATTTTTTTAATAATTGATCAATTAAGACATTTATGTACAAAAA
* * *
27620864 TATCTTAAATGATATTTTTTTTATAATGCCTTAATTGATCAATTATTTAGGGTGTTTTTATACAC
66 TACCTTAAATGATATTTTTTTTATAATGCCTTAATTGATCAATTATTCAAGGTGTTTTTATACAC
*
27620929 AAATATCTTAATTGATCCTTTTATTTTTTCTGTATAC
131 AAATATCTTAATTGATCATTTTATTTTTTCTGTATAC
***
27620966 AAACATCTTAATTGATCCTTTAATTTTTTTAATAATTGATCAATTAAGGTGTTTATGTACAAAAA
1 AAACATCTTAATTGATCCTTTAATTTTTTTAATAATTGATCAATTAAGACATTTATGTACAAAAA
* * *
27621031 TGCCTTTAATGATCTTTTTTTTTTATATATATAATGCCTTAATTGATCAATTATTCAAGGTGTTT
66 TACCTTAAATGA-----TATTTTT-T-T-TATAATGCCTTAATTGATCAATTATTCAAGGTGTTT
* *
27621096 TTATACATAAATGTCTTAATTGATCATTTTATTTTTT
123 TTATACACAAATATCTTAATTGATCATTTTATTTTTT
27621133 TTATAACTGA
Statistics
Matches: 142, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
167 66 0.46
172 6 0.04
173 1 0.01
174 1 0.01
175 68 0.48
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (167 bp):
AAACATCTTAATTGATCCTTTAATTTTTTTAATAATTGATCAATTAAGACATTTATGTACAAAAA
TACCTTAAATGATATTTTTTTTATAATGCCTTAATTGATCAATTATTCAAGGTGTTTTTATACAC
AAATATCTTAATTGATCATTTTATTTTTTCTGTATAC
Found at i:27621266 original size:134 final size:135
Alignment explanation
Indices: 27620961--27621311 Score: 347
Period size: 138 Copynumber: 2.6 Consensus size: 135
27620951 ATTTTTTCTG
* * *
27620961 TATACAAACATCTTAATTGATCCTTTAATTTTTTTAATAATTGATCAATTAAGGTGTTTATGTAC
1 TATACAAACGTCTTAATTGATCTTTTAATTTTTTT-ATAATTGATCAATTAAGGTATTTATGTAC
* * * * * *
27621026 AAAAATGCCTTT-AATGATCTTTTTTTTTTATATATATAATGCCTTAATTGATCAATTATTCAAG
65 AGAAATG-TTTTAAATGATCTTTTTTATTTATATATATAACGCCTTAATTGATAAATCATTCAAG
**
27621090 GTGTTTT
129 GCATTTT
* * * *
27621097 TATACATAAATGTCTTAATTGATCATTTTATTTTTTTTATAACTGATCAATTAAGGTATTTATAT
1 TATAC--AAACGTCTTAATTGATC-TTTTAATTTTTTTATAATTGATCAATTAAGGTATTTATGT
* *
27621162 ACAGAAACGTTTTAAATGAGTC-TTTTTATTT-T-T-T-TAACGCCTTAATTGATAAATCATTTA
63 ACAGAAATGTTTTAAATGA-TCTTTTTTATTTATATATATAACGCCTTAATTGATAAATCATTCA
27621222 AGGCATTTT
127 AGGCATTTT
* * * * * * *
27621231 AGTGTACAAACGTTTTAATTGATCTTTTTAA-TTTTTTCTAATTGATTAATTTAGATATTTTTGT
1 --TATACAAACGTCTTAATTGATC-TTTTAATTTTTTTATAATTGATCAATTAAGGTATTTATGT
*
27621295 ATAGAAATGTTTTAAAT
63 ACAGAAATGTTTTAAAT
27621312 TATCATATTT
Statistics
Matches: 177, Mismatches: 31, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
133 41 0.23
134 49 0.28
135 1 0.01
136 10 0.06
137 4 0.02
138 59 0.33
139 13 0.07
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (135 bp):
TATACAAACGTCTTAATTGATCTTTTAATTTTTTTATAATTGATCAATTAAGGTATTTATGTACA
GAAATGTTTTAAATGATCTTTTTTATTTATATATATAACGCCTTAATTGATAAATCATTCAAGGC
ATTTT
Found at i:27624108 original size:20 final size:20
Alignment explanation
Indices: 27624083--27624121 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27624073 ATGACATCTA
*
27624083 ATATCATGTTTATTATTTTT
1 ATATCATGTCTATTATTTTT
27624103 ATATCATGTCTATTATTTT
1 ATATCATGTCTATTATTTT
27624122 GCATGCGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (20 bp):
ATATCATGTCTATTATTTTT
Found at i:27624306 original size:13 final size:13
Alignment explanation
Indices: 27624288--27624312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27624278 TTTCTTTATA
27624288 ATTATTATTATTT
1 ATTATTATTATTT
27624301 ATTATTATTATT
1 ATTATTATTATT
27624313 ATTTGTTCAA
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTATTT
Found at i:27624307 original size:16 final size:16
Alignment explanation
Indices: 27624282--27624316 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27624272 ATTGTGTTTC
27624282 TTTATAATTATTATTA
1 TTTATAATTATTATTA
*
27624298 TTTATTATTATTATTA
1 TTTATAATTATTATTA
27624314 TTT
1 TTT
27624317 GTTCAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATAATTATTATTA
Found at i:27628270 original size:20 final size:20
Alignment explanation
Indices: 27628234--27628272 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27628224 AATGTCGTCG
*
27628234 AAAAATTTCGTCGAATTTTA
1 AAAAATTTCGTAGAATTTTA
27628254 AAAAATTTC-TAGAAATTTT
1 AAAAATTTCGTAG-AATTTT
27628273 CTATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (20 bp):
AAAAATTTCGTAGAATTTTA
Found at i:27628615 original size:3 final size:3
Alignment explanation
Indices: 27628602--27628697 Score: 65
Period size: 3 Copynumber: 32.3 Consensus size: 3
27628592 AAAAGAAAAG
* *
27628602 ATA AAA ATA ATA ATA ATA A-A ATAA ATA ATG ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA
** * * * *
27628648 ATA A-A CGA A-A AAA ATA ATG CTA ATA ATA ATA ATAA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
27628692 A-A ATA A
1 ATA ATA A
27628698 AAAATATAGG
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
2 7 0.10
3 57 0.78
4 9 0.12
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:27628622 original size:27 final size:29
Alignment explanation
Indices: 27628592--27628658 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
27628582 ATTAATCAAG
27628592 AAAAGAAAA-GATAAAAATAAT-AATAAT
1 AAAAGAAAATGATAAAAATAATAAATAAT
* *
27628619 AAAATAAATAATGATAATAATAATAAATAAT
1 AAAA-GAA-AATGATAAAAATAATAAATAAT
*
27628650 AAACGAAAA
1 AAAAGAAAA
27628659 AAATAATGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 4 0.12
30 13 0.41
31 9 0.28
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (29 bp):
AAAAGAAAATGATAAAAATAATAAATAAT
Found at i:27628672 original size:35 final size:36
Alignment explanation
Indices: 27628602--27628698 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 36
27628592 AAAAGAAAAG
*
27628602 ATAA-AAATAATAATAATAAAATAAATAATGATAATA
1 ATAATAAATAATAA-AAGAAAATAAATAATGATAATA
* *
27628638 ATAATAAATAATAAACGAAAA-AAATAATGCTAATA
1 ATAATAAATAATAAAAGAAAATAAATAATGATAATA
*
27628673 ATAAT-AATAAATAAAAATAAAATAAA
1 ATAATAAAT-AAT-AAAAGAAAATAAA
27628699 AAATATAGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
34 3 0.06
35 21 0.40
36 16 0.31
37 12 0.23
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (36 bp):
ATAATAAATAATAAAAGAAAATAAATAATGATAATA
Found at i:27630999 original size:16 final size:16
Alignment explanation
Indices: 27630978--27631012 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27630968 AATTAAGATA
*
27630978 TTTCTTCATTGAAGCG
1 TTTCTTCATTGAAACG
27630994 TTTCTTCATTGAAACG
1 TTTCTTCATTGAAACG
27631010 TTT
1 TTT
27631013 TAATTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTCTTCATTGAAACG
Found at i:27632047 original size:20 final size:21
Alignment explanation
Indices: 27632024--27632076 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
27632014 TTCGATTTTA
27632024 AATTAATCAAAACTT-AAGAT
1 AATTAATCAAAACTTAAAGAT
*
27632044 AATT-ATCAAAATTTGAAAGAT
1 AATTAATCAAAACTT-AAAGAT
27632065 -ATTATATCAAAA
1 AATTA-ATCAAAA
27632077 AAATGTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.32
20 7 0.25
21 5 0.18
22 7 0.25
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.32
Consensus pattern (21 bp):
AATTAATCAAAACTTAAAGAT
Found at i:27641256 original size:51 final size:51
Alignment explanation
Indices: 27641175--27641353 Score: 160
Period size: 51 Copynumber: 3.3 Consensus size: 51
27641165 TGATACTAGG
* * * *
27641175 TTGGAGCAGGCTGTTGAATCAAGAAAAGAAGTCGGAATATCTGGGAGAAGT
1 TTGGAGCAGGCAGCTGAACCAAGAAAAGAAGTCGGAATAGCTGGGAGAAGT
* * *
27641226 TTGGAGCAGGCAGCTGAACCTAGAAGAGAAGTTGGAATAGCTGGGAGAAGT
1 TTGGAGCAGGCAGCTGAACCAAGAAAAGAAGTCGGAATAGCTGGGAGAAGT
* * * * *
27641277 TTGGAGCCGAGCCAGCCAGCTGCTGAATCTAGAAAAGAAGTTGGAATAGTTGGGAGAACT
1 TTGGAG-C-AG---G-CA---GCTGAACCAAGAAAAGAAGTCGGAATAGCTGGGAGAAGT
*
27641337 TTGGAGCAGGGAGCTGA
1 TTGGAGCAGGCAGCTGA
27641354 TTCCAGAAAG
Statistics
Matches: 107, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
51 55 0.51
52 1 0.01
53 2 0.02
54 1 0.01
55 1 0.01
56 1 0.01
57 2 0.02
58 2 0.02
59 1 0.01
60 41 0.38
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (51 bp):
TTGGAGCAGGCAGCTGAACCAAGAAAAGAAGTCGGAATAGCTGGGAGAAGT
Found at i:27655261 original size:30 final size:29
Alignment explanation
Indices: 27655197--27655264 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
27655187 ACGGTTTAAA
* *
27655197 TATTTAATTTAGGATTAAATTTTTAATAT
1 TATTTATTTTAAGATTAAATTTTTAATAT
*
27655226 TATTTATTTTAAGATTAAATGTATTT-ATTT
1 TATTTATTTTAAGATTAAAT-T-TTTAATAT
27655256 TATTTATTT
1 TATTTATTT
27655265 CTTCTACATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 18 0.53
30 13 0.38
31 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (29 bp):
TATTTATTTTAAGATTAAATTTTTAATAT
Found at i:27659065 original size:42 final size:43
Alignment explanation
Indices: 27659012--27659098 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 43
27659002 AATTTTATTT
* *
27659012 ATTTCTTTAATACTTAATTTTTCTTTA-TTTAATTTAGGATTA
1 ATTTCTTTAATACTTAATTTTACTTTATTTTAATTTAAGATTA
* *
27659054 ATTTTTTTAATACTTAATTTTACTTTATTTTATTTTAAGATTA
1 ATTTCTTTAATACTTAATTTTACTTTATTTTAATTTAAGATTA
27659097 AT
1 AT
27659099 GGGCTATACG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 25 0.62
43 15 0.38
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (43 bp):
ATTTCTTTAATACTTAATTTTACTTTATTTTAATTTAAGATTA
Found at i:27663116 original size:14 final size:15
Alignment explanation
Indices: 27663099--27663143 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
27663089 TTTTTTTAAA
27663099 AAATATTTTATTAT-
1 AAATATTTTATTATC
27663113 AAATATTTTATCTATC
1 AAATATTTTAT-TATC
*
27663129 ACAATATTTTTTTAT
1 A-AATATTTTATTAT
27663144 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 4 0.15
17 9 0.33
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATATTTTATTATC
Found at i:27663183 original size:20 final size:18
Alignment explanation
Indices: 27663131--27663183 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
27663121 TATCTATCAC
27663131 AATATTTTTTTATTAAAA
1 AATATTTTTTTATTAAAA
* **
27663149 AATATCGTTGATATTAAAAA
1 AATAT-TTTTTTATT-AAAA
27663169 AATATTATTTTTATT
1 AATATT-TTTTTATT
27663184 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
20 15 0.58
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
AATATTTTTTTATTAAAA
Found at i:27664086 original size:21 final size:22
Alignment explanation
Indices: 27664062--27664104 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
27664052 ATGTGTTGAG
*
27664062 TTTTACTGAAC-ATTATATCTT
1 TTTTACTGAACAATTAAATCTT
*
27664083 TTTTATTGAACAATTAAATCTT
1 TTTTACTGAACAATTAAATCTT
27664105 CATTTGTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTACTGAACAATTAAATCTT
Found at i:27670198 original size:23 final size:22
Alignment explanation
Indices: 27670149--27670199 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
27670139 AAAGTATTAT
* *
27670149 AAAATAAAAAAATAATTCAATA
1 AAAATTAAAAAATAATTAAATA
* *
27670171 GAAATTAAAAAATTATTAATATA
1 AAAATTAAAAAATAATTAA-ATA
27670194 AAAATT
1 AAAATT
27670200 CTTTTTAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATTAAAAAATAATTAAATA
Found at i:27672640 original size:11 final size:11
Alignment explanation
Indices: 27672624--27672676 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
27672614 GTTCAATGAT
27672624 AAAAAAGAGAA
1 AAAAAAGAGAA
27672635 AAAAAAG-GAA
1 AAAAAAGAGAA
27672645 AAATAAA-AGAA
1 AAA-AAAGAGAA
*
27672656 AAAATAAAAGATA
1 AAAA-AAGAGA-A
27672669 AAAAAAGA
1 AAAAAAGA
27672677 ATGAATGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 7 0.19
11 18 0.50
12 6 0.17
13 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:27672652 original size:12 final size:12
Alignment explanation
Indices: 27672626--27672672 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
27672616 TCAATGATAA
*
27672626 AAAAGAGAAAA-
1 AAAAGAAAAAAT
*
27672637 AAAAGGAAAAAT
1 AAAAGAAAAAAT
27672649 AAAAGAAAAAAT
1 AAAAGAAAAAAT
27672661 AAAAGATAAAAA
1 AAAAGA-AAAAA
27672673 AAGAATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 9 0.29
12 17 0.55
13 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAAAT
Found at i:27672786 original size:19 final size:20
Alignment explanation
Indices: 27672753--27672810 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
27672743 ATAAAGGAAG
27672753 AAGAAAATAAA-GGAAA-AAA
1 AAGAAAA-AAAGGGAAAGAAA
*
27672772 AAGAAAAAAAGGGAAAGAGA
1 AAGAAAAAAAGGGAAAGAAA
27672792 AA-AAAAAAA--GAAAGAAA
1 AAGAAAAAAAGGGAAAGAAA
27672809 AA
1 AA
27672811 AGTGGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.26
18 3 0.09
19 19 0.54
20 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAAGGGAAAGAAA
Found at i:27672810 original size:16 final size:16
Alignment explanation
Indices: 27672745--27672811 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
27672735 TGTTTGGGAT
* *
27672745 AAAGGAAGAAGAAAATA
1 AAAGAAAGAA-AAAAAA
* *
27672762 AAGGAAAAAAAAGAAAA
1 AAAGAAAGAAAA-AAAA
27672779 AAAGGGAAAGAGAAAAAAA
1 AAA--GAAAGA-AAAAAAA
27672798 AAAGAAAGAAAAAA
1 AAAGAAAGAAAAAA
27672812 GTGGAAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 18 0.45
19 12 0.30
20 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (16 bp):
AAAGAAAGAAAAAAAA
Found at i:27676027 original size:59 final size:59
Alignment explanation
Indices: 27675941--27676068 Score: 152
Period size: 59 Copynumber: 2.2 Consensus size: 59
27675931 GATTTCTTTG
* * * *
27675941 AAATTAAAATTTTAGAAAAAAATATTTTGACGAAAAGTTGAAAATACCAATTTTT-TAAA
1 AAATAAAAATTATAGAAAAAAACATTTTAACGAAAAGTTGAAAATACCAATTTTTCT-AA
* * * *
27676000 AAATAAAAATTAT-GAAGAAAAACATTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTA
1 AAATAAAAATTATAGAA-AAAAACATTTTAACGAAAAGTTGAAAATACCAATTTTTCTAA
27676059 AAATAAAAAT
1 AAATAAAAAT
27676069 CTCCAAATGC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 3 0.05
59 55 0.93
60 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (59 bp):
AAATAAAAATTATAGAAAAAAACATTTTAACGAAAAGTTGAAAATACCAATTTTTCTAA
Found at i:27676204 original size:8 final size:8
Alignment explanation
Indices: 27676193--27676217 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27676183 TTTATTTTAT
27676193 TTTTTTTC
1 TTTTTTTC
27676201 TTTTTTTC
1 TTTTTTTC
27676209 TTTTTTTC
1 TTTTTTTC
27676217 T
1 T
27676218 GAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:27676958 original size:17 final size:17
Alignment explanation
Indices: 27676938--27676970 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27676928 GAGGTTTTAT
27676938 ATTCACAAAAATTTCAG
1 ATTCACAAAAATTTCAG
*
27676955 ATTCGCAAAAATTTCA
1 ATTCACAAAAATTTCA
27676971 ATTTTCATAA
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:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (17 bp):
ATTCACAAAAATTTCAG
Found at i:27676989 original size:18 final size:17
Alignment explanation
Indices: 27676965--27677012 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
27676955 ATTCGCAAAA
27676965 ATTTCAATTTTCATAAAG
1 ATTTCAA-TTTCATAAAG
* * *
27676983 GTTTCAAATTCGTAAAG
1 ATTTCAATTTCATAAAG
27677000 ATTTCAAGTTTCA
1 ATTTCAA-TTTCA
27677013 CATAGGTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (17 bp):
ATTTCAATTTCATAAAG
Found at i:27677004 original size:17 final size:17
Alignment explanation
Indices: 27676948--27677006 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
27676938 ATTCACAAAA
* * *
27676948 ATTTCAGATTCGCAAAA
1 ATTTCAAATTCGTAAAG
* *
27676965 ATTTCAATTTTCATAAAG
1 ATTTCAA-ATTCGTAAAG
*
27676983 GTTTCAAATTCGTAAAG
1 ATTTCAAATTCGTAAAG
27677000 ATTTCAA
1 ATTTCAA
27677007 GTTTCACATA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 20 0.62
18 12 0.38
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (17 bp):
ATTTCAAATTCGTAAAG
Found at i:27677033 original size:35 final size:35
Alignment explanation
Indices: 27676939--27677021 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 35
27676929 AGGTTTTATA
** * * * *
27676939 TTCACAAAAATTTCAGATTCGCAAAAATTTCAATT
1 TTCACAAAGGTTTCAAATTCGTAAAGATTTCAAGT
*
27676974 TTCATAAAGGTTTCAAATTCGTAAAGATTTCAAGT
1 TTCACAAAGGTTTCAAATTCGTAAAGATTTCAAGT
*
27677009 TTCACATAGGTTT
1 TTCACAAAGGTTT
27677022 TAGATTTGTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (35 bp):
TTCACAAAGGTTTCAAATTCGTAAAGATTTCAAGT
Found at i:27677060 original size:33 final size:33
Alignment explanation
Indices: 27677036--27677150 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
27677026 TTTGTAAAAG
* *
27677036 TTTAGATTCACAAAAAT-AGAAGATTCACAAGAC
1 TTTAGATTCACAAAAATGA-AAGATTCGCAAGAA
* *
27677069 TTTAGATTTACAAGAATGAAAGATTCGCAAGAA
1 TTTAGATTCACAAAAATGAAAGATTCGCAAGAA
* * * *
27677102 TTTAGAATCACAAAAATGTAAGATTTGTAAGAA
1 TTTAGATTCACAAAAATGAAAGATTCGCAAGAA
* *
27677135 TTTAAATTCAAAAAAA
1 TTTAGATTCACAAAAA
27677151 CTTTCAGATT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
33 67 0.99
34 1 0.01
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.28
Consensus pattern (33 bp):
TTTAGATTCACAAAAATGAAAGATTCGCAAGAA
Found at i:27677642 original size:35 final size:35
Alignment explanation
Indices: 27677570--27677649 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
27677560 ATTCATAAAA
* **
27677570 GTTTTAGATTCTAAAAGATTTCAATTTTCGTAGAG
1 GTTTTAGATTCTAAAAGATTTCAAGTTTCACAGAG
*
27677605 GTTTTAGATTC-ACAAAGATTTCAAGTTTCACATAG
1 GTTTTAGATTCTA-AAAGATTTCAAGTTTCACAGAG
*
27677640 GTTTCAGATT
1 GTTTTAGATT
27677650 TGTAAAAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (35 bp):
GTTTTAGATTCTAAAAGATTTCAAGTTTCACAGAG
Found at i:27677673 original size:17 final size:17
Alignment explanation
Indices: 27677640--27677672 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27677630 TTTCACATAG
*
27677640 GTTTCAGATTTGTAAAA
1 GTTTCAGATTCGTAAAA
27677657 GTTT-AGATTCGTAAAA
1 GTTTCAGATTCGTAAAA
27677673 ATAAAAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (17 bp):
GTTTCAGATTCGTAAAA
Found at i:27677812 original size:16 final size:16
Alignment explanation
Indices: 27677791--27677826 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
27677781 CAAAAAAACT
27677791 TTCAGATTCATAAGAC
1 TTCAGATTCATAAGAC
**
27677807 TTCAGATTTGTAAGAC
1 TTCAGATTCATAAGAC
27677823 TTCA
1 TTCA
27677827 AATATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (16 bp):
TTCAGATTCATAAGAC
Found at i:27677923 original size:16 final size:16
Alignment explanation
Indices: 27677904--27677959 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
27677894 TCATATTCAT
*
27677904 AAGAATTCATA-TTGGC
1 AAGAATTCA-AGTTCGC
*
27677920 AAGACTTCAAGTTCGC
1 AAGAATTCAAGTTCGC
* *
27677936 AAGAATTTAAGGTTCAC
1 AAGAATTCAA-GTTCGC
27677953 AAGAATT
1 AAGAATT
27677960 TTTAGTTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 1 0.03
16 20 0.61
17 12 0.36
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (16 bp):
AAGAATTCAAGTTCGC
Found at i:27677971 original size:18 final size:18
Alignment explanation
Indices: 27677930--27677977 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
27677920 AAGACTTCAA
*
27677930 GTTCGCAAGAA-TTTAAG
1 GTTCACAAGAATTTTAAG
*
27677947 GTTCACAAGAATTTTTAG
1 GTTCACAAGAATTTTAAG
* *
27677965 TTTCACAGGAATT
1 GTTCACAAGAATT
27677978 CAGATTCGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (18 bp):
GTTCACAAGAATTTTAAG
Found at i:27678001 original size:17 final size:17
Alignment explanation
Indices: 27677976--27678039 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
27677966 TTCACAGGAA
27677976 TTCAGATTCGTAAGAACT
1 TTCAGATTCGTAAGAA-T
*
27677994 TT-AGATTCGCAAGAAT
1 TTCAGATTCGTAAGAAT
*
27678010 TTCATATTCGTAA-AGAT
1 TTCAGATTCGTAAGA-AT
27678027 TTGCAGATT-GTAA
1 TT-CAGATTCGTAA
27678040 TTCACATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.10
17 28 0.72
18 7 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (17 bp):
TTCAGATTCGTAAGAAT
Found at i:27678204 original size:46 final size:46
Alignment explanation
Indices: 27678131--27678432 Score: 224
Period size: 46 Copynumber: 6.6 Consensus size: 46
27678121 AGGCTCATAG
* * * *
27678131 CCAAAA-TTCAAATATTCTCATTGAAAAAATTTCAGGATTTCACAT
1 CCAAAATTTCAAAGATTCTTATTCAAAAAATTTTAGGATTTCACAT
* * *
27678176 CCAAAGTTTTAAATATTCTTATTCAAAAAATTTTAGGATTT-ACAT
1 CCAAAATTTCAAAGATTCTTATTCAAAAAATTTTAGGATTTCACAT
* * * ** * * *
27678221 -CAAAAGTTTCAAAGATTCATATTCGAAAATTTTTAATATTTTAGAA
1 CCAAAA-TTTCAAAGATTCTTATTCAAAAAATTTTAGGATTTCACAT
* * ** * *
27678267 CCAAAATTTTAAAGATTCTCATTTGAAAAATTTTTGGGTTTCACAT
1 CCAAAATTTCAAAGATTCTTATTCAAAAAATTTTAGGATTTCACAT
* * *
27678313 CTAAAATTTCAAAGATTCATT-TT--TAAAACTTTATGG-TTTCACAT
1 CCAAAATTTCAAAGATTC-TTATTCAAAAAATTTTA-GGATTTCACAT
* * * * * *
27678357 CCAAAATTTTAAATATTCTTATTTGAAAAAAATTTTTGGTTTTC-TAT
1 CCAAAATTTCAAAGATTCTTA-TT-CAAAAAATTTTAGGATTTCACAT
*
27678404 CTAAAATTTCAAAGATTCTTATTCAAAAA
1 CCAAAATTTCAAAGATTCTTATTCAAAAA
27678433 GCTCACTTAA
Statistics
Matches: 201, Mismatches: 44, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
43 2 0.01
44 34 0.17
45 46 0.23
46 80 0.40
47 28 0.14
48 11 0.05
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (46 bp):
CCAAAATTTCAAAGATTCTTATTCAAAAAATTTTAGGATTTCACAT
Found at i:27678329 original size:92 final size:91
Alignment explanation
Indices: 27678166--27678432 Score: 283
Period size: 91 Copynumber: 2.9 Consensus size: 91
27678156 AAAATTTCAG
* * ** *
27678166 GATTTCACATCCAAAGTTTTAAATATTCTTATTCAAAAAATTTTAGGATTT-ACATC-AAAAGTT
1 GATTTCACAACCAAAATTTTAAATATTCTTATTTGAAAAATTTTTGGATTTCACATCTAAAA-TT
**
27678229 TCAAAGATTCATATTCGAAAATTTTTAAT
65 TCAAAGATTCATATTC-AAAAACTTT-AT
* * * * *
27678258 -ATTTTAGAACCAAAATTTTAAAGATTCTCATTTGAAAAATTTTTGGGTTTCACATCTAAAATTT
1 GATTTCACAACCAAAATTTTAAATATTCTTATTTGAAAAATTTTTGGATTTCACATCTAAAATTT
**
27678322 CAAAGATTCAT-TTTTAAAACTTTAT
66 CAAAGATTCATATTCAAAAACTTTAT
* * * *
27678347 GGTTTCACATCCAAAATTTTAAATATTCTTATTTGAAAAAAATTTTTGGTTTTC-TATCTAAAAT
1 GATTTCACAACCAAAATTTTAAATATTCTTATTTG--AAAAATTTTTGGATTTCACATCTAAAAT
*
27678411 TTCAAAGATTCTTATTCAAAAA
64 TTCAAAGATTCATATTCAAAAA
27678433 GCTCACTTAA
Statistics
Matches: 144, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
89 2 0.01
90 34 0.24
91 63 0.44
92 41 0.28
93 4 0.03
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (91 bp):
GATTTCACAACCAAAATTTTAAATATTCTTATTTGAAAAATTTTTGGATTTCACATCTAAAATTT
CAAAGATTCATATTCAAAAACTTTAT
Found at i:27679425 original size:12 final size:12
Alignment explanation
Indices: 27679402--27679436 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
27679392 TCAATTTAAG
27679402 TCTTTCTTTTTTT
1 TCTTT-TTTTTTT
27679415 TCTTTTTTTTTT
1 TCTTTTTTTTTT
27679427 TCTTTTTTTT
1 TCTTTTTTTT
27679437 GTTACACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:27684658 original size:32 final size:32
Alignment explanation
Indices: 27684610--27684677 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
27684600 AATCACAATC
* *
27684610 CTTTGATTTTTTAATTTTTTAA-TTTTTTTTA
1 CTTTGATTTTTTAATTTGTGAATTTTTTTTTA
*
27684641 CTTTTATTTTTTAAATTTGTGAATTTTTTTTTA
1 CTTTGATTTTTT-AATTTGTGAATTTTTTTTTA
27684674 CTTT
1 CTTT
27684678 ATAAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 11 0.34
32 8 0.25
33 13 0.41
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (32 bp):
CTTTGATTTTTTAATTTGTGAATTTTTTTTTA
Found at i:27684679 original size:32 final size:30
Alignment explanation
Indices: 27684610--27684679 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 30
27684600 AATCACAATC
* *
27684610 CTTTGATTTTTTAATTTTTTAATTTTTTTTA
1 CTTT-ATTTTTTAATTTGTGAATTTTTTTTA
27684641 CTTTTATTTTTTAAATTTGTGAATTTTTTTTTA
1 C-TTTATTTTTT-AATTTGTGAA-TTTTTTTTA
27684674 CTTTAT
1 CTTTAT
27684680 AAAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 8 0.24
32 16 0.47
33 10 0.29
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (30 bp):
CTTTATTTTTTAATTTGTGAATTTTTTTTA
Found at i:27686141 original size:58 final size:59
Alignment explanation
Indices: 27686071--27686190 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 59
27686061 GATTATATAA
* * * *
27686071 TACTTAAACTTTAATTTGGTTATGCAGGCACTAACTTTGTTGAATAGTGTCATGAAGGT
1 TACTTAAACTTTAATTTAGTTATACAAGCACTAACTTTGTTGAATAGTCTCATGAAGGT
* * *
27686130 TACTT-AACTTTAATTTAGTTATACAAGCATTAACTTTGTTGGATAGTCTCATGGAGGT
1 TACTTAAACTTTAATTTAGTTATACAAGCACTAACTTTGTTGAATAGTCTCATGAAGGT
27686188 TAC
1 TAC
27686191 CTGAAAATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 49 0.91
59 5 0.09
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (59 bp):
TACTTAAACTTTAATTTAGTTATACAAGCACTAACTTTGTTGAATAGTCTCATGAAGGT
Found at i:27688954 original size:22 final size:22
Alignment explanation
Indices: 27688908--27688952 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
27688898 GAACAATTAT
*
27688908 AATAATATAATATTGTAATGTA
1 AATAATATAATATTGTAATATA
27688930 AATAAT-T-ATATTAGTAATATA
1 AATAATATAATATT-GTAATATA
27688951 AA
1 AA
27688953 ATTGTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (22 bp):
AATAATATAATATTGTAATATA
Found at i:27689174 original size:236 final size:236
Alignment explanation
Indices: 27688763--27689207 Score: 567
Period size: 236 Copynumber: 1.9 Consensus size: 236
27688753 AAATTAGTAA
** *
27688763 AAATTAAAAAAACATATTGGTAATGTAAACAAGTGAGAAAAAATGTAAAATTAGTATAATTTAGC
1 AAATTAAAAAAACATATTGGTAATGTAAACAAGTGAGAAAAAACATAAAAGTAGTATAATTTAGC
* * * *
27688828 ATAAAATAGTTATAAATTATTGTAATACATTAAAAAGAGTTATAATAATTTTAAACATAATGGAA
66 ATAAAATAGTTATAAAGTATTGTAACACATTAAAAAGAGTTACAACAATTTTAAACATAATGGAA
* * * * * *
27688893 AGTAAGAACAATTATAATAATATAATATTGTAATGTAAATAATTATATT-AGTAATATAAAATTG
131 AGTAAAAACAATCATAAGAAGATAATATTGTAAAGTAAATAATTATATTGA-CAATATAAAATTG
27688957 TAATTAATTATTATTTTGCAAATAGCTAAGGAAAATAACTAT
195 TAATTAATTATTATTTTGCAAATAGCTAAGGAAAATAACTAT
* * *
27688999 AAATTAAAAAATA-A-ATTGGTAATTTAAACAAGTGAGAACAAACATAAAAGTAGTATAATTTGG
1 AAATTAAAAAA-ACATATTGGTAATGTAAACAAGTGAGAAAAAACATAAAAGTAGTATAATTTAG
** * ** * *
27689062 TGTAAAATAGTTATGAAGTATCT-TAACACATTAAAAAAGAGTTACGGCAATTTTGAATATAATG
65 CATAAAATAGTTATAAAGTAT-TGTAACACATT-AAAAAGAGTTACAACAATTTTAAACATAATG
* * *
27689126 GAAAGTAAAAACAA-CAGTGAGAAGATATTATTGTAAAGTAAATAATTATATTGACAATGTAAAA
128 GAAAGTAAAAACAATCA-TAAGAAGATAATATTGTAAAGTAAATAATTATATTGACAATATAAAA
*
27689190 TTTTAATTAATTATTATT
192 TTGTAATTAATTATTATT
27689208 CCTCTAAATA
Statistics
Matches: 177, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
235 69 0.39
236 106 0.60
237 2 0.01
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (236 bp):
AAATTAAAAAAACATATTGGTAATGTAAACAAGTGAGAAAAAACATAAAAGTAGTATAATTTAGC
ATAAAATAGTTATAAAGTATTGTAACACATTAAAAAGAGTTACAACAATTTTAAACATAATGGAA
AGTAAAAACAATCATAAGAAGATAATATTGTAAAGTAAATAATTATATTGACAATATAAAATTGT
AATTAATTATTATTTTGCAAATAGCTAAGGAAAATAACTAT
Found at i:27689406 original size:237 final size:233
Alignment explanation
Indices: 27688788--27689444 Score: 639
Period size: 237 Copynumber: 2.8 Consensus size: 233
27688778 ATTGGTAATG
* ** * * * * *
27688788 TAAACAAGTGAGAAAAAATGTAAAATTAGTATAATTTAGCA-TAAAATAGTTATAAATTATTGTA
1 TAAACAAGTGAGAACAAA-CAAAAAGTAGTATAATTT-GGAGTAAAATAGTTATGAAGTATCGTA
* * * **
27688852 ATACATTAAAAAGAGTTATAATAATTTTAAACATAATGGAAAGTAAGAACAATTATAATAA-TAT
64 ACACATTAAAAAAAGTTATAACAATTTTAAACATAATGGAAAGTAAGAACAATCGTAA-AAGTAT
* * * *
27688916 AATATTGTAATGTAAATAATTATATTAGTAATATAAAATTGTAATTAATTATTATTTTGCAAATA
128 ATTATTGTAATGTAAATAATTATATTA-TAATGTAAAATTTTAATTAATTATTATTCTGCAAATA
* * ** **
27688981 GCTAAGGAAAATAACTATAAATTAAAAAATAAATTGGTAATT
192 GATAAGAAAAATAACTATAAATTAAAAAATAAATTAATAACA
* *
27689023 TAAACAAGTGAGAACAAACATAAAAGTAGTATAATTTGGTGTAAAATAGTTATGAAGTATCTTAA
1 TAAACAAGTGAGAACAAACA-AAAAGTAGTATAATTTGGAGTAAAATAGTTATGAAGTATCGTAA
*** * * * *
27689088 CACATTAAAAAAGAGTTACGGCAATTTTGAATATAATGGAAAGTAAAAACAA-CAGTGAGAAG-A
65 CACATTAAAAAA-AGTTATAACAATTTTAAACATAATGGAAAGTAAGAACAATC-GT-AAAAGTA
* *
27689151 TATTATTGTAAAGTAAATAATTATATTGACAATGTAAAATTTTAATTAATTATTATTCCT-CTAA
127 TATTATTGTAATGTAAATAATTATATT-ATAATGTAAAATTTTAATTAATTATTATT-CTGC-AA
* * * *
27689215 ATATATTAGAAAAATAGCTA-AAATTTTAAAAATAAAATTAATAACA
189 ATAGATAAGAAAAATAACTATAAA-TTAAAAAAT-AAATTAATAACA
* * * * * *
27689261 TAAATAAG-GAAGAAGTAAAGC-AAAATTAGTATCATTTTGAGTAAAATGGATTA-GAAGTATCG
1 TAAACAAGTG-AGAA-CAAA-CAAAAAGTAGTATAATTTGGAGTAAAATAG-TTATGAAGTATCG
** **
27689323 TAACATGTTAAAAAAAGTTATAACAATTTTAAACATAATCAAAAGTAAGAACAATCGTAAAAGTA
62 TAACACATTAAAAAAAGTTATAACAATTTTAAACATAATGGAAAGTAAGAACAATCGTAAAAGTA
* *
27689388 TATTATTATAATGTAAATAATTATGATAATAATGTAAAATTTTAATTAATTATTATT
127 TATTATTGTAATGTAAATAATTAT-ATTATAATGTAAAATTTTAATTAATTATTATT
27689445 TTTTGCAAGT
Statistics
Matches: 343, Mismatches: 61, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
234 1 0.00
235 62 0.18
236 94 0.27
237 113 0.33
238 66 0.19
239 6 0.02
240 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.33
Consensus pattern (233 bp):
TAAACAAGTGAGAACAAACAAAAAGTAGTATAATTTGGAGTAAAATAGTTATGAAGTATCGTAAC
ACATTAAAAAAAGTTATAACAATTTTAAACATAATGGAAAGTAAGAACAATCGTAAAAGTATATT
ATTGTAATGTAAATAATTATATTATAATGTAAAATTTTAATTAATTATTATTCTGCAAATAGATA
AGAAAAATAACTATAAATTAAAAAATAAATTAATAACA
Found at i:27691152 original size:20 final size:20
Alignment explanation
Indices: 27691127--27691164 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27691117 AAATTCAAGA
27691127 ATCAATTGATCTCCTAATAG
1 ATCAATTGATCTCCTAATAG
*
27691147 ATCAATTGATCTTCTAAT
1 ATCAATTGATCTCCTAAT
27691165 GGACTTGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCAATTGATCTCCTAATAG
Found at i:27692713 original size:28 final size:28
Alignment explanation
Indices: 27692653--27692714 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
27692643 CATAATTAAG
*
27692653 ATAT-TTAATGAATTAATTTAGTTAAGT
1 ATATATTAATGAATTAATTTAGTAAAGT
27692680 ATTATATTAAT-AATTAATTTA-TAAATAGT
1 A-TATATTAATGAATTAATTTAGT-AA-AGT
27692709 ATATAT
1 ATATAT
27692715 AGTATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 2 0.07
28 19 0.63
29 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (28 bp):
ATATATTAATGAATTAATTTAGTAAAGT
Found at i:27695592 original size:2 final size:2
Alignment explanation
Indices: 27695585--27695615 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27695575 GTTGGCAGTT
27695585 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27695616 GCGGACACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27702785 original size:16 final size:16
Alignment explanation
Indices: 27702753--27702800 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
27702743 TATTATTTTT
* *
27702753 AAATATAAATATTTAA
1 AAATATATATATATAA
27702769 AAATATCAT-TATATAA
1 AAATAT-ATATATATAA
*
27702785 ATATATATATATATAA
1 AAATATATATATATAA
27702801 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.89
17 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATATATATAA
Found at i:27702798 original size:24 final size:24
Alignment explanation
Indices: 27702755--27702824 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
27702745 TTATTTTTAA
* *
27702755 ATATAAATATTTAAAAATATCATT
1 ATATAAATATATAAAAATATAATT
* *
27702779 ATATAAATATATATATATATAATT
1 ATATAAATATATAAAAATATAATT
* *
27702803 AAAAAAAT-TA-AAAAAT-TAATT
1 ATATAAATATATAAAAATATAATT
27702824 A
1 A
27702825 AAAAAATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 6 0.16
22 4 0.11
23 2 0.05
24 26 0.68
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATATAAAAATATAATT
Found at i:27705029 original size:29 final size:28
Alignment explanation
Indices: 27704980--27705061 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
27704970 TAAATTATAT
*
27704980 TTTAATTATATATAAATATAATATATTTA
1 TTTAATTAAATATAAATATAATA-ATTTA
*
27705009 TTTAATTAAAGTATTAA-ATAATAATTTGA
1 TTTAATTAAA-TATAAATATAATAATTT-A
*
27705038 -TTAATATAATATATAATTA-AATAA
1 TTTAAT-TAA-ATATAAATATAATAA
27705062 CTAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
28 9 0.20
29 28 0.64
30 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TTTAATTAAATATAAATATAATAATTTA
Found at i:27705040 original size:16 final size:16
Alignment explanation
Indices: 27705021--27705067 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
27705011 TAATTAAAGT
* *
27705021 ATTAAATAATAATTTG
1 ATTAAATAATAATATA
27705037 ATTAATATAAT-ATATA
1 ATTAA-ATAATAATATA
27705053 ATTAAATAACTAATA
1 ATTAAATAA-TAATA
27705068 AAAATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 14 0.54
17 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTAAATAATAATATA
Found at i:27706596 original size:16 final size:15
Alignment explanation
Indices: 27706571--27706630 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
27706561 TATTAAATAA
27706571 GAAAGAAGAAAAGAAG
1 GAAA-AAGAAAAGAAG
27706587 GAAAATAGAAAA-AA-
1 GAAAA-AGAAAAGAAG
27706601 GAAAAAGAAGAAGAAG
1 GAAAAAGAA-AAGAAG
*
27706617 AAGAAAAAAAAAAG
1 --GAAAAAGAAAAG
27706631 TCAGCTCATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 4 0.11
14 7 0.19
15 5 0.14
16 10 0.27
17 3 0.08
18 8 0.22
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAGAAG
Found at i:27706597 original size:23 final size:25
Alignment explanation
Indices: 27706565--27706629 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
27706555 TTATATTATT
*
27706565 AAATAAGAAAGAAG-AAAAGAAGGA
1 AAATAAGAAAAAAGAAAAAGAAGGA
27706589 AAAT-AGAAAAAAGAAAAAGAA-GA
1 AAATAAGAAAAAAGAAAAAGAAGGA
*
27706612 AGAAGAAGAAAAAA-AAAA
1 A-AATAAGAAAAAAGAAAA
27706630 GTCAGCTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 11 0.31
24 17 0.47
25 8 0.22
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (25 bp):
AAATAAGAAAAAAGAAAAAGAAGGA
Found at i:27706606 original size:24 final size:24
Alignment explanation
Indices: 27706565--27706630 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
27706555 TTATATTATT
*
27706565 AAATAAGAAAGAAGAAAAGAAGGA
1 AAATAAGAAAAAAGAAAAGAAGGA
27706589 AAAT-AGAAAAAAGAAAAAGAA-GA
1 AAATAAGAAAAAAG-AAAAGAAGGA
*
27706612 AGAAGAAGAAAAAA-AAAAG
1 A-AATAAGAAAAAAGAAAAG
27706631 TCAGCTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 16 0.43
24 13 0.35
25 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (24 bp):
AAATAAGAAAAAAGAAAAGAAGGA
Found at i:27706611 original size:9 final size:9
Alignment explanation
Indices: 27706572--27706624 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
27706562 ATTAAATAAG
27706572 AAAGAAG-A
1 AAAGAAGAA
*
27706580 AAAGAAGGA
1 AAAGAAGAA
*
27706589 AAA-TAG-A
1 AAAGAAGAA
27706596 AAA-AAGAA
1 AAAGAAGAA
27706604 AAAGAAGAA
1 AAAGAAGAA
*
27706613 GAAGAAGAA
1 AAAGAAGAA
27706622 AAA
1 AAA
27706625 AAAAAGTCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
7 6 0.16
8 13 0.34
9 19 0.50
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:27710095 original size:28 final size:28
Alignment explanation
Indices: 27710054--27710112 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
27710044 TGCTGGTGAG
27710054 CTTAATCTCAGATTCCTTTTCATTCTTT
1 CTTAATCTCAGATTCCTTTTCATTCTTT
* *
27710082 CTTAATCTCGGATTCCTTTTCTTTCTTT
1 CTTAATCTCAGATTCCTTTTCATTCTTT
27710110 CTT
1 CTT
27710113 TGTTTTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.14, C:0.25, G:0.05, T:0.56
Consensus pattern (28 bp):
CTTAATCTCAGATTCCTTTTCATTCTTT
Found at i:27710385 original size:43 final size:43
Alignment explanation
Indices: 27710324--27710421 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
27710314 ATACTGCCTT
* *
27710324 GTAATTGTATTATTCATTTTTCGTGTTACTAAGTTTAGGTCTA
1 GTAATTGTATTATTCATTTTTCATATTACTAAGTTTAGGTCTA
27710367 GTAATTGTATTATTCATTTTTCATATTACTAAGTTTAGGTCTA
1 GTAATTGTATTATTCATTTTTCATATTACTAAGTTTAGGTCTA
27710410 GTAATTGTATTA
1 GTAATTGTATTA
27710422 GGGATTCATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (43 bp):
GTAATTGTATTATTCATTTTTCATATTACTAAGTTTAGGTCTA
Found at i:27715284 original size:21 final size:22
Alignment explanation
Indices: 27715254--27715294 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
27715244 AGATTTTAAA
27715254 AGTTTATTTTTAA-TATTAATG
1 AGTTTATTTTTAAGTATTAATG
*
27715275 AGTTTTTTTTTAAGTATTAA
1 AGTTTATTTTTAAGTATTAA
27715295 ATTGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (22 bp):
AGTTTATTTTTAAGTATTAATG
Found at i:27718211 original size:2 final size:2
Alignment explanation
Indices: 27718204--27718230 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27718194 CAACCATTTT
27718204 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
27718231 GTATATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:27723911 original size:30 final size:30
Alignment explanation
Indices: 27723875--27723932 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
27723865 AACATTTATA
*
27723875 TTTATTATTTCATGCCTACTATAACAACTG
1 TTTATTATTTCATGCCTAATATAACAACTG
*
27723905 TTTATTATTTCATGTCTAATATAACAAC
1 TTTATTATTTCATGCCTAATATAACAAC
27723933 CATCTTCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTATTATTTCATGCCTAATATAACAACTG
Found at i:27725481 original size:26 final size:26
Alignment explanation
Indices: 27725445--27725495 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
27725435 GTATGGAGGC
27725445 TTTACAAAGGCAGCGGTGGTTTTAAG
1 TTTACAAAGGCAGCGGTGGTTTTAAG
*
27725471 TTTAGAAAGGCAGCGGTGGTTTTAA
1 TTTACAAAGGCAGCGGTGGTTTTAA
27725496 TTAGGGGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.31
Consensus pattern (26 bp):
TTTACAAAGGCAGCGGTGGTTTTAAG
Found at i:27725801 original size:20 final size:19
Alignment explanation
Indices: 27725748--27725803 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 19
27725738 AAATATTTTA
*
27725748 TTAATTAAAATAATAAAAAAT
1 TTAATT-AAATTAT-AAAAAT
* *
27725769 ATATTTAAA-TATAAAAAT
1 TTAATTAAATTATAAAAAT
27725787 TTAATTAAATTTATAAA
1 TTAATTAAA-TTATAAA
27725804 TTATTCGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 13 0.46
19 2 0.07
20 9 0.32
21 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAATTAAATTATAAAAAT
Done.