Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 8 of 20
Found at i:1225856 original size:14 final size:14
Alignment explanation
Indices: 1225833--1225876 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1225823 AAATTATATT
*
1225833 TATTTTAATTTAAA
1 TATTTAAATTTAAA
*
1225847 TATTTAAATTTAAT
1 TATTTAAATTTAAA
* *
1225861 TAATTAAAATTAAA
1 TATTTAAATTTAAA
1225875 TA
1 TA
1225877 AATTTATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTAAATTTAAA
Found at i:1232593 original size:3 final size:3
Alignment explanation
Indices: 1232587--1232611 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1232577 ATTGATAACT
1232587 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1232612 CAACGCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1232892 original size:21 final size:21
Alignment explanation
Indices: 1232868--1232908 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1232858 GATTGGTAAA
* *
1232868 TTACTTTTTGTTAATCAAAAG
1 TTACTTTTAGTTAAACAAAAG
1232889 TTACTTTTAGTTAAACAAAA
1 TTACTTTTAGTTAAACAAAA
1232909 ATTGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (21 bp):
TTACTTTTAGTTAAACAAAAG
Found at i:1233238 original size:23 final size:24
Alignment explanation
Indices: 1233204--1233248 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1233194 AACTTAGGAT
*
1233204 TAATATTTTTAA-TATTAATATAA
1 TAATATTTTTAATTATAAATATAA
1233227 TAAT-TTTGTTAATTATAAATAT
1 TAATATTT-TTAATTATAAATAT
1233249 TAAATATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 8 0.42
24 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TAATATTTTTAATTATAAATATAA
Found at i:1234404 original size:26 final size:25
Alignment explanation
Indices: 1234356--1234417 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
1234346 AAATCATGAG
*
1234356 AAAAATAAT-TAAATTTAACATGACAT
1 AAAAA-AATATAAATTCAACATGA-AT
*
1234382 AAAAAAATATAAATTCAATATGAAT
1 AAAAAAATATAAATTCAACATGAAT
* *
1234407 ATAAAATTATA
1 AAAAAAATATA
1234418 TCAAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (25 bp):
AAAAAAATATAAATTCAACATGAAT
Found at i:1234719 original size:4 final size:4
Alignment explanation
Indices: 1234702--1234737 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1234692 CTCCTATCAT
* *
1234702 AATA AGTA AGTA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
1234738 GGTGGGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:1234973 original size:15 final size:16
Alignment explanation
Indices: 1234953--1234984 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1234943 TAAAAATAAT
1234953 AAATTTATA-TATTTA
1 AAATTTATATTATTTA
1234968 AAATTTATATTATTTA
1 AAATTTATATTATTTA
1234984 A
1 A
1234985 TTTTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTATATTATTTA
Found at i:1235072 original size:16 final size:15
Alignment explanation
Indices: 1235039--1235071 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1235029 TTTTTTAAAT
1235039 AAATTTAATAATTTA
1 AAATTTAATAATTTA
1235054 AAATTTAA-ATATTTA
1 AAATTTAATA-ATTTA
1235069 AAA
1 AAA
1235072 AAATTACAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTAATAATTTA
Found at i:1235696 original size:2 final size:2
Alignment explanation
Indices: 1235689--1235718 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1235679 CAATTAGCAA
1235689 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
1235719 TTTAAAAGTG
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:1236693 original size:2 final size:2
Alignment explanation
Indices: 1236686--1236724 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1236676 TCCAAAAATT
1236686 TA TA TA TA 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 TA TA TA TA T
1236725 TACTTCCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1237327 original size:20 final size:19
Alignment explanation
Indices: 1237294--1237331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1237284 CATAATACAA
1237294 AAATATTTTATTAATATTT
1 AAATATTTTATTAATATTT
*
1237313 AAATAATTTTGTTAATATT
1 AAAT-ATTTTATTAATATT
1237332 ATTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
AAATATTTTATTAATATTT
Found at i:1237394 original size:21 final size:22
Alignment explanation
Indices: 1237370--1237410 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1237360 TAAAAAGTAA
1237370 AATAATA-AAAAAATTAAATTT
1 AATAATATAAAAAATTAAATTT
*
1237391 AATAATATAAAAATTTAAAT
1 AATAATATAAAAAATTAAAT
1237411 ATTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATAATATAAAAAATTAAATTT
Found at i:1237920 original size:15 final size:15
Alignment explanation
Indices: 1237900--1237933 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1237890 TTTATATATT
1237900 ATTAATTAATAA-AAA
1 ATTAATTAA-AATAAA
1237915 ATTAATTAAAATAAA
1 ATTAATTAAAATAAA
1237930 ATTA
1 ATTA
1237934 TTTATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATTAAAATAAA
Found at i:1239987 original size:2 final size:2
Alignment explanation
Indices: 1239980--1240019 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1239970 CACTTTACCC
1239980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1240020 AGGGGGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1240213 original size:24 final size:25
Alignment explanation
Indices: 1240162--1240207 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1240152 TGCATCTATA
1240162 AAAAAAATAAATATATAAATTAACT
1 AAAAAAATAAATATATAAATTAACT
*
1240187 AAAAAACT-AATAT-TAAATTAA
1 AAAAAAATAAATATATAAATTAA
1240208 ATTAAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAAAATAAATATATAAATTAACT
Found at i:1241868 original size:11 final size:13
Alignment explanation
Indices: 1241843--1241875 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1241833 ATAAATTTAA
1241843 ATTTAAATATATT
1 ATTTAAATATATT
1241856 A-TTAAAT-TATT
1 ATTTAAATATATT
1241867 ATTTAAATA
1 ATTTAAATA
1241876 AAAAATGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.28
12 12 0.67
13 1 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAATATATT
Found at i:1242227 original size:20 final size:21
Alignment explanation
Indices: 1242197--1242253 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
1242187 ATATTATTTT
1242197 ATTTATTTATAGTTT-TA-GTAA
1 ATTT-TTTATA-TTTATATGTAA
1242218 ATTTTTTATATTTAATATGTAA
1 ATTTTTTATATTT-ATATGTAA
1242240 ATTTTTTATATTTA
1 ATTTTTTATATTTA
1242254 ATATACTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
21 7 0.21
22 17 0.52
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTTTTATATTTATATGTAA
Found at i:1242241 original size:22 final size:22
Alignment explanation
Indices: 1242214--1242257 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1242204 TATAGTTTTA
1242214 GTAAATTTTTTATATTTAATAT
1 GTAAATTTTTTATATTTAATAT
1242236 GTAAATTTTTTATATTTAATAT
1 GTAAATTTTTTATATTTAATAT
1242258 ACTATTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
GTAAATTTTTTATATTTAATAT
Found at i:1242270 original size:22 final size:21
Alignment explanation
Indices: 1242212--1242273 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
1242202 TTTATAGTTT
1242212 TAGTAAATTTTTTATATTTAA
1 TAGTAAATTTTTTATATTTAA
1242233 TATGTAAATTTTTTATATTTAA
1 TA-GTAAATTTTTTATATTTAA
*
1242255 TA-TACTATTTTGTTATATT
1 TAGTA-AATTTT-TTATATT
1242274 AAAAAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 2 0.05
21 7 0.19
22 28 0.76
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TAGTAAATTTTTTATATTTAA
Found at i:1242299 original size:36 final size:37
Alignment explanation
Indices: 1242246--1242317 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 37
1242236 GTAAATTTTT
*
1242246 TATATTTAATATACTATT-TTGTT-ATATTAAAAAAA
1 TATATTTAATATACTATTATTGTTCATAATAAAAAAA
* * *
1242281 TATATATTAATTTTCTATTATTTTTCATAATAAAAAA
1 TATAT-TTAATATACTATTATTGTTCATAATAAAAAA
1242318 TTTAAAATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
35 5 0.17
36 11 0.37
37 4 0.13
38 10 0.33
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (37 bp):
TATATTTAATATACTATTATTGTTCATAATAAAAAAA
Found at i:1246813 original size:29 final size:26
Alignment explanation
Indices: 1246781--1246850 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 26
1246771 AATTAATTGA
1246781 TAATATATTTTTATTTAA-TTTTTAATAAT
1 TAATATATTTTTA-TTAAGTTTTT--T-AT
1246810 TAATTATATTTTTATTAAGTTTTTTAT
1 TAA-TATATTTTTATTAAGTTTTTTAT
1246837 TAATATTATTTTTA
1 TAATA-TATTTTTA
1246851 AAAATACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 2 0.05
27 13 0.34
28 1 0.03
29 7 0.18
30 15 0.39
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (26 bp):
TAATATATTTTTATTAAGTTTTTTAT
Found at i:1248827 original size:2 final size:2
Alignment explanation
Indices: 1248820--1248844 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1248810 ATCGTTTACA
1248820 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1248845 CATGCTAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1251169 original size:21 final size:22
Alignment explanation
Indices: 1251143--1251220 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 22
1251133 TAATATTTAA
1251143 TATATTATTAAAATAT-TATTT
1 TATATTATTAAAATATATATTT
**
1251164 TATATTATT-ATTTATATATTT
1 TATATTATTAAAATATATATTT
1251185 TATAATTAAATTAAAAATATATATTT
1 TAT-ATT--ATT-AAAATATATATTT
1251211 T-TATTATTAA
1 TATATTATTAA
1251221 GTCGATGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.09
21 19 0.40
22 6 0.13
24 6 0.13
25 1 0.02
26 11 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATTATTAAAATATATATTT
Found at i:1251172 original size:13 final size:14
Alignment explanation
Indices: 1251156--1251187 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1251146 ATTATTAAAA
1251156 TATTATTT-TATAT
1 TATTATTTATATAT
1251169 TATTATTTATATAT
1 TATTATTTATATAT
1251183 T-TTAT
1 TATTAT
1251188 AATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTATTTATATAT
Found at i:1251172 original size:24 final size:24
Alignment explanation
Indices: 1251136--1251219 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
1251126 TTTACTTTAA
*
1251136 TATTTAATA-TATTATTAAAATAT
1 TATTTTATATTATTATTAAAATAT
*
1251159 TATTTTATATTATTATT--TATA-
1 TATTTTATATTATTATTAAAATAT
*
1251180 TATTTTATAATTA-AATTAAAAATAT
1 TATTTTAT-ATTATTATT-AAAATAT
1251205 ATATTTT-TATTATTA
1 -TATTTTATATTATTA
1251220 AGTCGATGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
21 11 0.23
22 7 0.15
23 8 0.17
24 14 0.29
25 2 0.04
26 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTTATATTATTATTAAAATAT
Found at i:1256315 original size:2 final size:2
Alignment explanation
Indices: 1256310--1256340 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1256300 ACACACACAC
1256310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1256341 CCACAAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1256748 original size:20 final size:21
Alignment explanation
Indices: 1256725--1256764 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1256715 TAAAAAGATA
1256725 AATTTTATTTT-TTTT-ATCAT
1 AATTTT-TTTTATTTTGATCAT
1256745 AATTTTTTTTATTTTGATCA
1 AATTTTTTTTATTTTGATCA
1256765 CCCAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (21 bp):
AATTTTTTTTATTTTGATCAT
Found at i:1257311 original size:16 final size:16
Alignment explanation
Indices: 1257290--1257329 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1257280 GAACATTGAT
1257290 AATTAA-ATCATTAAAA
1 AATTAATAT-ATTAAAA
1257306 AATTAATATATTAAAA
1 AATTAATATATTAAAA
*
1257322 TATTAATA
1 AATTAATA
1257330 ATTTCACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAATATATTAAAA
Found at i:1259603 original size:2 final size:2
Alignment explanation
Indices: 1259596--1259629 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1259586 TCAACAGTAC
1259596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1259630 CATACCACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1260243 original size:7 final size:7
Alignment explanation
Indices: 1260231--1260261 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1260221 TGCTGACTGG
1260231 TATATAT
1 TATATAT
1260238 TATATAT
1 TATATAT
1260245 TATATAT
1 TATATAT
1260252 TATATAT
1 TATATAT
1260259 TAT
1 TAT
1260262 CAGTACGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:1260708 original size:20 final size:20
Alignment explanation
Indices: 1260685--1260722 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260675 GATTTAAAAT
1260685 AAATT-TTTTAAATTTGAATC
1 AAATTGTTTT-AATTTGAATC
1260705 AAATTGTTTTAATTTGAA
1 AAATTGTTTTAATTTGAA
1260723 ATAATTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
AAATTGTTTTAATTTGAATC
Found at i:1261033 original size:26 final size:23
Alignment explanation
Indices: 1260988--1261050 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 23
1260978 CTTTAGTCTG
*
1260988 TTTTAATTATATAATATATATTAA
1 TTTTTATTATATAATATATA-TAA
1261012 TTTTATATTTATATACAT-TATATAA
1 TTTT-TA-TTATATA-ATATATATAA
1261037 TTTTTATTATATAA
1 TTTTTATTATATAA
1261051 AAAATAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 1 0.03
23 7 0.20
24 6 0.17
25 8 0.23
26 11 0.31
27 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTATTATATAATATATATAA
Found at i:1261085 original size:13 final size:13
Alignment explanation
Indices: 1261067--1261092 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1261057 AATATATAAT
1261067 ATATATAATATTA
1 ATATATAATATTA
1261080 ATATATAATATTA
1 ATATATAATATTA
1261093 TAATTTAAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATAATATTA
Found at i:1261180 original size:13 final size:13
Alignment explanation
Indices: 1261162--1261206 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1261152 TATATAATTA
1261162 TTAAAAATTAAAT
1 TTAAAAATTAAAT
1261175 TT-AAAA--AAAT
1 TTAAAAATTAAAT
*
1261185 TATAAAAATTTAAT
1 T-TAAAAATTAAAT
1261199 TTAAAAAT
1 TTAAAAAT
1261207 ATAATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
10 5 0.19
11 1 0.04
12 8 0.30
13 9 0.33
14 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAAATTAAAT
Found at i:1261190 original size:24 final size:24
Alignment explanation
Indices: 1261157--1261220 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
1261147 AATTTTATAT
1261157 AATTATTAAAAATTAAATTTAAAAA
1 AATTA-TAAAAATTAAATTTAAAAA
*
1261182 AATTATAAAAATTTAATTTAAAAA
1 AATTATAAAAATTAAATTTAAAAA
* * *
1261206 TATAATATAAATTAA
1 AATTATAAAAATTAA
1261221 TATAAATAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATTATAAAAATTAAATTTAAAAA
Found at i:1261255 original size:41 final size:41
Alignment explanation
Indices: 1261209--1261302 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1261199 TTAAAAATAT
* *
1261209 AATATAAATTAATATAAAT-AAGTTTAAATTATT-TATTTATA
1 AATATAAATTAATATAAATAAAATTAAAATT-TTATATTT-TA
* * *
1261250 AATATAAATAAATTTATATAAAATTAAAATTTTATATTTTA
1 AATATAAATTAATATAAATAAAATTAAAATTTTATATTTTA
1261291 AAT-TAAATTAAT
1 AATATAAATTAAT
1261303 TTTAAATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
40 8 0.18
41 23 0.51
42 14 0.31
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (41 bp):
AATATAAATTAATATAAATAAAATTAAAATTTTATATTTTA
Found at i:1261338 original size:43 final size:46
Alignment explanation
Indices: 1261264--1261348 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 46
1261254 TAAATAAATT
* * *
1261264 TATATAAAATTAAAATTTTATATTTTAAATTAAAT-TAATTTTAAA
1 TATATAAAAATAAAATTTAATATTATAAATTAAATCTAATTTTAAA
*
1261309 TATATAAAAATAATA-TTAATATTAT-AATTAAATCTAATTT
1 TATATAAAAATAAAATTTAATATTATAAATTAAATCTAATTT
1261349 AATTTATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 8 0.23
44 14 0.40
45 13 0.37
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (46 bp):
TATATAAAAATAAAATTTAATATTATAAATTAAATCTAATTTTAAA
Found at i:1262591 original size:22 final size:25
Alignment explanation
Indices: 1262542--1262589 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1262532 AAAAAAATAA
1262542 AATAATTTTTATAATATTATATTAT
1 AATAATTTTTATAATATTATATTAT
1262567 AATAATTATTTA-AAT-TTATATTA
1 AATAATT-TTTATAATATTATATTA
1262590 ATGATTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATAATTTTTATAATATTATATTAT
Found at i:1262833 original size:12 final size:12
Alignment explanation
Indices: 1262813--1262841 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1262803 TCAAACTTAT
1262813 AAAAA-TAAAAA
1 AAAAATTAAAAA
1262824 AAAAATTAAAAA
1 AAAAATTAAAAA
1262836 AAAAAT
1 AAAAAT
1262842 ATAGAAGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATTAAAAA
Found at i:1263024 original size:25 final size:24
Alignment explanation
Indices: 1262977--1263024 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1262967 AAATTAAAAA
*
1262977 ATTTAAATATTAAATATAATTAAT
1 ATTTAAAAATTAAATATAATTAAT
* *
1263001 ATTTAAAAATATATATATAGTTAA
1 ATTTAAAAAT-TAAATATAATTAA
1263025 ATAGATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTTAAAAATTAAATATAATTAAT
Found at i:1263421 original size:2 final size:2
Alignment explanation
Indices: 1263414--1263443 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1263404 GGATTATTAT
1263414 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1263444 CACTAATGTT
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):
TA
Found at i:1263740 original size:2 final size:2
Alignment explanation
Indices: 1263733--1263761 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1263723 CTTTATAAAC
1263733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1263762 ATCAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1267576 original size:18 final size:18
Alignment explanation
Indices: 1267553--1267587 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1267543 CTTCAAGTGA
1267553 ATTGATTAAA-TAAAAATT
1 ATTGA-TAAATTAAAAATT
1267571 ATTGATAAATTAAAAAT
1 ATTGATAAATTAAAAAT
1267588 ACCGAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
ATTGATAAATTAAAAATT
Found at i:1270376 original size:23 final size:23
Alignment explanation
Indices: 1270349--1270393 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1270339 AAAGTATATT
* *
1270349 AATAATATTTATATTTATGTATA
1 AATAATATATAAATTTATGTATA
1270372 AATAATATATAAATTTATGTAT
1 AATAATATATAAATTTATGTAT
1270394 TATCAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AATAATATATAAATTTATGTATA
Found at i:1270401 original size:23 final size:22
Alignment explanation
Indices: 1270345--1270418 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
1270335 TTTAAAAGTA
*
1270345 TATTAATAATATTTATATTTATG
1 TATT-ATAATATTTAAATTTATG
* *
1270368 TATAAATAATATATAAATTTATG
1 TAT-TATAATATTTAAATTTATG
1270391 TATTATCAATAATTTAAATTATAT-
1 TATTAT-AAT-ATTTAAATT-TATG
1270415 TATT
1 TATT
1270419 TTATTAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.05
23 25 0.60
24 12 0.29
25 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
TATTATAATATTTAAATTTATG
Found at i:1270528 original size:18 final size:19
Alignment explanation
Indices: 1270505--1270542 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1270495 TTATTATTTT
1270505 TAATAAATTAAATGA-GAA
1 TAATAAATTAAATGATGAA
* *
1270523 TAATAATTTATATGATGAA
1 TAATAAATTAAATGATGAA
1270542 T
1 T
1270543 TTAAAGTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (19 bp):
TAATAAATTAAATGATGAA
Found at i:1271077 original size:17 final size:17
Alignment explanation
Indices: 1271031--1271079 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1271021 AATAATATAA
*
1271031 TTTATATAATTTTTATAT
1 TTTATATAAATTTTA-AT
*
1271049 ATTA-AT-AA-TTTAAT
1 TTTATATAAATTTTAAT
1271063 TTTATATAAATTTTAAT
1 TTTATATAAATTTTAAT
1271080 ATAATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 3 0.12
17 8 0.32
18 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATATAAATTTTAAT
Found at i:1271079 original size:22 final size:23
Alignment explanation
Indices: 1271034--1271091 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
1271024 AATATAATTT
*
1271034 ATATAATTTT-TATATATTAATA
1 ATATAATTTTATATAAATTAATA
* *
1271056 ATTTAATTTTATATAAATT-TTA
1 ATATAATTTTATATAAATTAATA
*
1271078 ATATAATTATATAT
1 ATATAATTTTATAT
1271092 TTATATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATAATTTTATATAAATTAATA
Found at i:1271101 original size:11 final size:11
Alignment explanation
Indices: 1271087--1271144 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
1271077 AATATAATTA
1271087 TATATTTATAT
1 TATATTTATAT
*
1271098 TATATTCATAT
1 TATATTTATAT
1271109 TAT-TTTATAT
1 TATATTTATAT
*
1271119 T-TTTATTATAT
1 TATAT-TTATAT
1271130 TATATTTATAT
1 TATATTTATAT
1271141 TATA
1 TATA
1271145 CTTAAAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 1 0.02
10 8 0.20
11 30 0.73
12 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1271101 original size:33 final size:32
Alignment explanation
Indices: 1271021--1271102 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 32
1271011 TTATGTTTTA
* *
1271021 AATAATATAAT-TTATATAATTTTTATATATT
1 AATAATTTAATATTATATAATTTTAATATATT
*
1271052 AATAATTTAATTTTATATAAATTTTAATATAATT
1 AATAATTTAATATTATAT-AATTTTAATAT-ATT
1271086 -ATATATTT-ATATTATAT
1 AATA-ATTTAATATTATAT
1271103 TCATATTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 10 0.23
32 6 0.14
33 21 0.48
34 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
AATAATTTAATATTATATAATTTTAATATATT
Found at i:1271108 original size:27 final size:26
Alignment explanation
Indices: 1271025--1271134 Score: 84
Period size: 27 Copynumber: 4.2 Consensus size: 26
1271015 GTTTTAAATA
*
1271025 ATATAATTTATATAATTTTTA-TATATT
1 ATATAA-TTATAT-ATTTATATTATATT
* *
1271052 A-ATAATT-TA-ATTTTATATAAATTTT
1 ATATAATTATATA-TTTATAT-TATATT
1271077 AATATAATTATATATTTATATTATATT
1 -ATATAATTATATATTTATATTATATT
* * *
1271104 CATATTATTTTATATTTTTATTATATT
1 -ATATAATTATATATTTATATTATATT
1271131 ATAT
1 ATAT
1271135 TTATATTATA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.01
23 5 0.07
24 2 0.03
25 6 0.09
26 9 0.13
27 34 0.51
28 9 0.13
29 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (26 bp):
ATATAATTATATATTTATATTATATT
Found at i:1271111 original size:16 final size:16
Alignment explanation
Indices: 1271087--1271144 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
1271077 AATATAATTA
1271087 TATATTTATATTATATT
1 TATA-TTATATTATATT
* *
1271104 CATATTATTTTATATT
1 TATATTATATTATATT
*
1271120 TTTATTATATTATATT
1 TATATTATATTATATT
1271136 TATATTATA
1 TATATTATA
1271145 CTTAAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
16 32 0.91
17 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTATATTATATT
Found at i:1271138 original size:27 final size:27
Alignment explanation
Indices: 1271087--1271144 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
1271077 AATATAATTA
*
1271087 TATATTTATATTATATTCATATTATTT
1 TATATTTATATTATATTCATATTATAT
*
1271114 TATATTTTTATTATATT-ATATTTATAT
1 TATATTTATATTATATTCATA-TTATAT
1271141 TATA
1 TATA
1271145 CTTAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TATATTTATATTATATTCATATTATAT
Found at i:1279132 original size:11 final size:11
Alignment explanation
Indices: 1279112--1279153 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1279102 AATCCATGTA
1279112 TTTT-TATTAT
1 TTTTATATTAT
1279122 TTTTATATTAT
1 TTTTATATTAT
1279133 TTTATATATTAT
1 TTT-TATATTAT
*
1279145 ATTTATATT
1 TTTTATATT
1279154 TAAATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.14
11 15 0.52
12 10 0.34
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:1279165 original size:26 final size:28
Alignment explanation
Indices: 1279136--1279208 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 28
1279126 ATATTATTTT
1279136 ATATATTATATTTATATTTAA-ATA-TA
1 ATATATTATATTTATATTTAATATATTA
* *
1279162 ATATATTATATATAAAATTTAATATATTA
1 ATATATTATAT-TTATATTTAATATATTA
*
1279191 ATAATATTATATATATAT
1 AT-ATATTATATTTATAT
1279209 ATATCGTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 11 0.29
27 8 0.21
28 3 0.08
29 7 0.18
30 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATATATTATATTTATATTTAATATATTA
Found at i:1279166 original size:21 final size:22
Alignment explanation
Indices: 1279136--1279212 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 22
1279126 ATATTATTTT
*
1279136 ATATATTATATTTATAT-TTAA
1 ATATAATATATTTATATATTAA
*
1279157 ATATAATATA-TTATATATAAA
1 ATATAATATATTTATATATTAA
* * *
1279178 ATTTAATATATTAATAATATTAT
1 ATATAATATATTTAT-ATATTAA
1279201 ATATATATATAT
1 ATATA-ATATAT
1279213 CGTTTAATTG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.13
21 21 0.47
22 3 0.07
23 9 0.20
24 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATAATATATTTATATATTAA
Found at i:1279199 original size:9 final size:8
Alignment explanation
Indices: 1279142--1279206 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 8
1279132 TTTTATATAT
*
1279142 TATATTTA
1 TATATTAA
1279150 TAT-TTAA
1 TATATTAA
1279157 -ATA-TAA
1 TATATTAA
1279163 TATATT-A
1 TATATTAA
1279170 TATA-TAA
1 TATATTAA
*
1279177 AAT-TTAA
1 TATATTAA
1279184 TATATTAA
1 TATATTAA
1279192 TAATATTATA
1 T-ATATTA-A
1279202 TATAT
1 TATAT
1279207 ATATATCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
6 6 0.13
7 19 0.41
8 9 0.20
9 10 0.22
10 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TATATTAA
Found at i:1280152 original size:36 final size:36
Alignment explanation
Indices: 1280105--1280176 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1280095 ATAGCAACAA
1280105 CAATCCATATCTCACGCGTGATTGTTGGATTTAGAC
1 CAATCCATATCTCACGCGTGATTGTTGGATTTAGAC
*
1280141 CAATCCATATCTCTCGCGTGATTGTTGGATTTAGAC
1 CAATCCATATCTCACGCGTGATTGTTGGATTTAGAC
1280177 TTAACCGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (36 bp):
CAATCCATATCTCACGCGTGATTGTTGGATTTAGAC
Found at i:1280838 original size:21 final size:20
Alignment explanation
Indices: 1280814--1280871 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
1280804 TTATATCAAT
1280814 ATTTATATAATTTATAATTAA
1 ATTTATATAATTTA-AATTAA
1280835 ATTTA-ATTAAATTTAAATTAA
1 ATTTATA-T-AATTTAAATTAA
* *
1280856 GTATATGATAATTTAA
1 ATTTAT-ATAATTTAA
1280872 GTAAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 1 0.03
21 22 0.71
22 7 0.23
23 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (20 bp):
ATTTATATAATTTAAATTAA
Found at i:1280911 original size:24 final size:25
Alignment explanation
Indices: 1280883--1280930 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1280873 TAAAATCAAA
1280883 TAAAATT-ATATTAA-AAAATTTAAT
1 TAAAATTGA-ATTAATAAAATTTAAT
*
1280907 TAAAATTGAATTAATCAAATTTAA
1 TAAAATTGAATTAATAAAATTTAA
1280931 CTTATTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TAAAATTGAATTAATAAAATTTAAT
Found at i:1281728 original size:20 final size:20
Alignment explanation
Indices: 1281682--1281743 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
1281672 ATTAAAAATT
* *
1281682 TTAATTTTAAAATAAATT-GA
1 TTAA-TTTAAATTAAATTAAA
1281702 TTCAATTTAAATTAAATTAAA
1 TT-AATTTAAATTAAATTAAA
* *
1281723 TTAATTAAAATTTAA-TAAA
1 TTAATTTAAATTAAATTAAA
1281742 TT
1 TT
1281744 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 6 0.17
20 25 0.69
21 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAATTTAAATTAAATTAAA
Found at i:1282185 original size:2 final size:2
Alignment explanation
Indices: 1282173--1282226 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
1282163 ATGTGAACCA
* *
1282173 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1282215 AT AT GT AT AT AT
1 AT AT AT AT AT AT
1282227 GTATCAATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1282645 original size:17 final size:17
Alignment explanation
Indices: 1282619--1282651 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1282609 TTATAAAATT
1282619 AAAATGTATTTATATAA
1 AAAATGTATTTATATAA
*
1282636 AAAATTTATTTATATA
1 AAAATGTATTTATATA
1282652 GTAATTTATA
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:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAATGTATTTATATAA
Found at i:1283439 original size:28 final size:28
Alignment explanation
Indices: 1283385--1283439 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1283375 AGATTTAAAA
*
1283385 TAAAAAATAATATATTTTTAAATTTTTT
1 TAAAAAATAATATATTTTAAAATTTTTT
* * *
1283413 TAAAAATTTATATA-TTTAAAATATTTT
1 TAAAAAATAATATATTTTAAAATTTTTT
1283440 ATATTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAAAAAATAATATATTTTAAAATTTTTT
Found at i:1283440 original size:18 final size:16
Alignment explanation
Indices: 1283411--1283446 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1283401 TTTAAATTTT
1283411 TTTAAAAATTTATATA
1 TTTAAAAATTTATATA
1283427 TTTAAAATATTT-TATA
1 TTTAAAA-ATTTATATA
1283443 TTTA
1 TTTA
1283447 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAAAATTTATATA
Found at i:1283451 original size:22 final size:23
Alignment explanation
Indices: 1283423--1283473 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
1283413 TAAAAATTTA
*
1283423 TATATTTAAAATATTTTAT-ATT
1 TATATTTAAAATATATTATAATT
**
1283445 TATATTTTTAATATATTATAATT
1 TATATTTAAAATATATTATAATT
1283468 TATATT
1 TATATT
1283474 ATATAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATATTTAAAATATATTATAATT
Found at i:1283454 original size:24 final size:23
Alignment explanation
Indices: 1283417--1283473 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
1283407 TTTTTTTAAA
*
1283417 AATTTATATATTTAAAATATTTT
1 AATTTATATTTTTAAAATATTTT
* *
1283440 ATATTTATATTTTTAATATATTAT
1 A-ATTTATATTTTTAAAATATTTT
1283464 AATTTATATT
1 AATTTATATT
1283474 ATATAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTATATTTTTAAAATATTTT
Found at i:1283551 original size:15 final size:15
Alignment explanation
Indices: 1283433--1283544 Score: 64
Period size: 16 Copynumber: 7.8 Consensus size: 15
1283423 TATATTTAAA
1283433 ATATTTTAT-AT-TT
1 ATATTTTATAATATT
1283446 ATATTTT-TAATATATT
1 ATATTTTAT-A-ATATT
* *
1283462 ATAATTTATATTATAT
1 ATATTTTATAATAT-T
* *
1283478 AAATTTTAAAATA-T
1 ATATTTTATAATATT
*
1283492 ACATTTATATAAATATT
1 ATATTT-TAT-AATATT
1283509 ATA-TTT-T--TA-T
1 ATATTTTATAATATT
1283519 -TATTTTATAATATT
1 ATATTTTATAATATT
1283533 ATATTTTATAAT
1 ATATTTTATAAT
1283545 CATATATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 28
0.67 0.08 0.25
Matches are distributed among these distances:
9 2 0.03
10 4 0.05
11 3 0.04
12 1 0.01
13 9 0.12
14 8 0.11
15 19 0.25
16 25 0.33
17 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTTATAATATT
Found at i:1284281 original size:24 final size:24
Alignment explanation
Indices: 1284220--1284282 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
1284210 TCCATCAGCT
* *
1284220 CCTCCGCCTTCAACCACCCCATCC
1 CCTCCGCCTTCATCCACCCCATCA
* * **
1284244 CCTCCTCCTCCATCCACTTCATCA
1 CCTCCGCCTTCATCCACCCCATCA
1284268 CCTCCGCCTTCATCC
1 CCTCCGCCTTCATCC
1284283 TCTACCTCCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.14, C:0.59, G:0.03, T:0.24
Consensus pattern (24 bp):
CCTCCGCCTTCATCCACCCCATCA
Found at i:1284295 original size:24 final size:24
Alignment explanation
Indices: 1284220--1284299 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
1284210 TCCATCAGCT
* * **
1284220 CCTCCGCCTTCAACCACCCCATCC
1 CCTCCGCCTCCATCCACTACATCC
* * *
1284244 CCTCCTCCTCCATCCACTTCATCA
1 CCTCCGCCTCCATCCACTACATCC
* * *
1284268 CCTCCGCCTTCATCCTCTACCTCC
1 CCTCCGCCTCCATCCACTACATCC
1284292 CCTCCGCC
1 CCTCCGCC
1284300 CCCGGCCACT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.12, C:0.60, G:0.04, T:0.24
Consensus pattern (24 bp):
CCTCCGCCTCCATCCACTACATCC
Found at i:1291142 original size:100 final size:99
Alignment explanation
Indices: 1290970--1291168 Score: 308
Period size: 100 Copynumber: 2.0 Consensus size: 99
1290960 GGTCATCTTT
* *
1290970 TTGAAAATGCCTAGTATGCATTACAGAAATCCGAAGTCGTTTGAACTGTTCATTACTATAATTAG
1 TTGAAAATGCCTAGCATGCATTACAGAAATCCAAAGTCGTTTGAACTGTTCATTACTATAATTAG
*
1291035 AAGATATTCAAGCTGAAAAACGATGAATAGGCAA
66 AAGATATTCAAGCGGAAAAACGATGAATAGGCAA
* * *
1291069 TTGAAAATGCCTAGCATGCATTGCAGAAATCCAAAGCTCTTTTGAATTGTTCATTACTATAATTA
1 TTGAAAATGCCTAGCATGCATTACAGAAATCCAAAG-TCGTTTGAACTGTTCATTACTATAATTA
** *
1291134 GAAGATATTTGAGCGGAAAAATGATGAATAGGCAA
65 GAAGATATTCAAGCGGAAAAACGATGAATAGGCAA
1291169 GATAATGAGA
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 33 0.37
100 57 0.63
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (99 bp):
TTGAAAATGCCTAGCATGCATTACAGAAATCCAAAGTCGTTTGAACTGTTCATTACTATAATTAG
AAGATATTCAAGCGGAAAAACGATGAATAGGCAA
Found at i:1295601 original size:16 final size:16
Alignment explanation
Indices: 1295560--1295592 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1295550 TTGAGGTAAT
*
1295560 TTAAATTTGA-ATTAA
1 TTAAATTTAATATTAA
1295575 TTAAATTTAATATTAA
1 TTAAATTTAATATTAA
1295591 TT
1 TT
1295593 TATTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTAAATTTAATATTAA
Found at i:1295648 original size:22 final size:21
Alignment explanation
Indices: 1295623--1295664 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1295613 GAATTGAATT
*
1295623 TATTAATTTTAAAATAAAATAA
1 TATTAAATTT-AAATAAAATAA
1295645 TATTAAATTTAAATAAAATA
1 TATTAAATTTAAATAAAATA
1295665 TCTTTTCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAATTTAAATAAAATAA
Found at i:1295965 original size:23 final size:23
Alignment explanation
Indices: 1295929--1295978 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1295919 TTCAGATTTA
*
1295929 TTTATATTTATAAATATATAATT
1 TTTATAGTTATAAATATATAATT
* *
1295952 TTTATAGTTGTAAATGTATAATT
1 TTTATAGTTATAAATATATAATT
1295975 TTTA
1 TTTA
1295979 GGTCAGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTATAGTTATAAATATATAATT
Found at i:1296460 original size:19 final size:18
Alignment explanation
Indices: 1296425--1296460 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1296415 TTCACAATCT
*
1296425 AAATAAAAAATTTTATAA
1 AAATAAAAAAATTTATAA
1296443 AAATAAATAAAATTTATA
1 AAATAAA-AAAATTTATA
1296461 TTTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAAAAAATTTATAA
Found at i:1300802 original size:3 final size:3
Alignment explanation
Indices: 1300794--1300841 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1300784 ATAATTCTTT
1300794 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1300842 AAATTGTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1310279 original size:20 final size:20
Alignment explanation
Indices: 1310253--1310294 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1310243 ACTTAGATAG
1310253 TTTTAT-TTA-TTTAAATTT
1 TTTTATATTATTTTAAATTT
1310271 TTTTATATTATTTTAAATTT
1 TTTTATATTATTTTAAATTT
1310291 TTTT
1 TTTT
1310295 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
19 3 0.14
20 13 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATATTATTTTAAATTT
Found at i:1310308 original size:20 final size:20
Alignment explanation
Indices: 1310262--1310306 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1310252 GTTTTATTTA
**
1310262 TTTAAATTTTTTTATATTAT
1 TTTAAATTTTTTTATAAAAT
1310282 TTTAAATTTTTTT-TAAAAT
1 TTTAAATTTTTTTATAAAAT
1310301 TTTAAA
1 TTTAAA
1310307 ATATAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTTTATAAAAT
Found at i:1310342 original size:14 final size:15
Alignment explanation
Indices: 1310312--1310352 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1310302 TTAAAATATA
* *
1310312 AATAATATA-ATTTT
1 AATATTATATATTAT
1310326 AATATT-TATATTAT
1 AATATTATATATTAT
1310340 AATATTATATATT
1 AATATTATATATT
1310353 TATTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 15 0.65
15 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATATTATATATTAT
Found at i:1310353 original size:21 final size:20
Alignment explanation
Indices: 1310317--1310355 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1310307 ATATAAATAA
*
1310317 TATAATTTTAATATTTATAT
1 TATAATATTAATATTTATAT
1310337 TATAATATTATATATTTAT
1 TATAATATTA-ATATTTAT
1310356 TTTTAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATAATATTAATATTTATAT
Found at i:1310931 original size:3 final size:3
Alignment explanation
Indices: 1310912--1310956 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1310902 TGGTGGACTC
* *
1310912 TGG TGG TGA TGG AGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1310957 AGATGGAGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.04, C:0.00, G:0.64, T:0.31
Consensus pattern (3 bp):
TGG
Found at i:1315153 original size:11 final size:11
Alignment explanation
Indices: 1315137--1315161 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1315127 TATGTTTTGG
1315137 AAAAAAAAAGA
1 AAAAAAAAAGA
1315148 AAAAAAAAAGA
1 AAAAAAAAAGA
1315159 AAA
1 AAA
1315162 GCAAACCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:1321240 original size:25 final size:25
Alignment explanation
Indices: 1321206--1321256 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1321196 AAACAAAATC
1321206 ACATTAAGCTCCCTATTATATAAGT
1 ACATTAAGCTCCCTATTATATAAGT
* *
1321231 ACATTAAGCTCTCTATTCTATAAGT
1 ACATTAAGCTCCCTATTATATAAGT
1321256 A
1 A
1321257 AGTACTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (25 bp):
ACATTAAGCTCCCTATTATATAAGT
Found at i:1321720 original size:14 final size:15
Alignment explanation
Indices: 1321692--1321729 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1321682 ACAACCTAAT
*
1321692 AAAAAGAGAACAAAA
1 AAAAAGAGAAAAAAA
1321707 AAAAAGA-AAAAAAA
1 AAAAAGAGAAAAAAA
*
1321721 GAAAAGAGA
1 AAAAAGAGA
1321730 TTCAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAAA
Found at i:1321983 original size:20 final size:23
Alignment explanation
Indices: 1321958--1322008 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 23
1321948 TTTTATAATA
1321958 TAAATATAAA-ATAAT-TA-TTT
1 TAAATATAAATATAATATAGTTT
1321978 TAAATATAAATATAATATATGTTT
1 TAAATATAAATATAATATA-GTTT
1322002 TAAATAT
1 TAAATAT
1322009 GTGAAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.37
21 5 0.19
22 2 0.07
24 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATATAAATATAATATAGTTT
Found at i:1322002 original size:24 final size:26
Alignment explanation
Indices: 1321948--1322008 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1321938 TTTTGTGTTT
1321948 TTTTATAATATAAATATAAAATAATTA
1 TTTTA-AATATAAATATAAAATAATTA
* *
1321975 TTTTAAATATAAATATAATAT-A-TG
1 TTTTAAATATAAATATAAAATAATTA
1321999 TTTTAAATAT
1 TTTTAAATAT
1322009 GTGAAGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 11 0.34
25 1 0.03
26 15 0.47
27 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTAAATATAAATATAAAATAATTA
Found at i:1324483 original size:2 final size:2
Alignment explanation
Indices: 1324478--1324503 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1324468 TATATATATA
1324478 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1324504 ACACTTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1327120 original size:11 final size:11
Alignment explanation
Indices: 1327106--1327134 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1327096 AAATCCATGT
1327106 TAAAATAAAAA
1 TAAAATAAAAA
1327117 TAAAAT-AAAA
1 TAAAATAAAAA
1327127 TAAAATAA
1 TAAAATAA
1327135 GGAGTGACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:1327612 original size:38 final size:40
Alignment explanation
Indices: 1327576--1327654 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
1327566 GATTTCTTCA
**
1327576 CAAAAATGGATATTCAATTAAGTTTTTTATCATCTTCTGAAC
1 CAAAAATAAATATTCAATTAAGTTTTTTATCATCTTC--AAC
***
1327618 CATTTATAAATATTCAATTAAGTTTTTTATCATCTTC
1 CAAAAATAAATATTCAATTAAGTTTTTTATCATCTTC
1327655 TGAACCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (40 bp):
CAAAAATAAATATTCAATTAAGTTTTTTATCATCTTCAAC
Found at i:1327632 original size:42 final size:42
Alignment explanation
Indices: 1327585--1327671 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
1327575 ACAAAAATGG
1327585 ATATTCAATTAAGTTTTTTATCATCTTCTGAACCATTTATAA
1 ATATTCAATTAAGTTTTTTATCATCTTCTGAACCATTTATAA
*
1327627 ATATTCAATTAAGTTTTTTATCATCTTCTGAACCATTTATGA
1 ATATTCAATTAAGTTTTTTATCATCTTCTGAACCATTTATAA
1327669 ATA
1 ATA
1327672 GAAGCAGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (42 bp):
ATATTCAATTAAGTTTTTTATCATCTTCTGAACCATTTATAA
Found at i:1334883 original size:2 final size:2
Alignment explanation
Indices: 1334878--1334902 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1334868 ATATATATAT
1334878 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1334903 ATAAAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1336947 original size:2 final size:2
Alignment explanation
Indices: 1336940--1336970 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1336930 AAATACAAAC
*
1336940 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1336971 GTAAACACGG
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1338021 original size:22 final size:21
Alignment explanation
Indices: 1337975--1338021 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
1337965 ATTTTTAATG
*
1337975 TTTAAAAAATATTTATTTATA
1 TTTAAAAAATATTTAATTATA
*
1337996 TTTAAATAAA-ATTATAATTATT
1 TTTAAA-AAATATT-TAATTATA
1338018 TTTA
1 TTTA
1338022 GTTGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAAAAAATATTTAATTATA
Found at i:1338151 original size:11 final size:10
Alignment explanation
Indices: 1338129--1338220 Score: 53
Period size: 10 Copynumber: 8.7 Consensus size: 10
1338119 ATAATAAAAA
1338129 TTTAATTATT
1 TTTAATTATT
1338139 TTTAATTATT
1 TTTAATTATT
1338149 TTTAAATTAATT
1 TTT-AATT-ATT
*
1338161 TATT-ATTAAT
1 T-TTAATTATT
*
1338171 TTTATATTTTAT
1 TTTA-ATTAT-T
1338183 TTTAAGTTA-T
1 TTTAA-TTATT
** *
1338193 CATAAATATT
1 TTTAATTATT
*
1338203 TTAAATTTATT
1 TTTAA-TTATT
1338214 TTTAATT
1 TTTAATT
1338221 TAATTATATA
Statistics
Matches: 61, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
9 4 0.07
10 25 0.41
11 19 0.31
12 11 0.18
13 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTAATTATT
Found at i:1338292 original size:23 final size:23
Alignment explanation
Indices: 1338243--1338288 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1338233 AATTTTAAAA
* *
1338243 TAAATTTATTAAAATATTTTTAT
1 TAAATTAATTAAAATATTGTTAT
*
1338266 TAAATTAATT-AATTATTGTTAT
1 TAAATTAATTAAAATATTGTTAT
1338288 T
1 T
1338289 TAAAAATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TAAATTAATTAAAATATTGTTAT
Found at i:1338635 original size:29 final size:30
Alignment explanation
Indices: 1338606--1338660 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
1338596 ATTTATTTTA
1338606 TATT-AAATTTTAAAAA-TAAA-AAAATAT
1 TATTCAAATTTTAAAAATTAAATAAAATAT
1338633 TATTCAAATTTTAAAAATTAAATAAAAT
1 TATTCAAATTTTAAAAATTAAATAAAAT
1338661 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 4 0.16
28 12 0.48
29 4 0.16
30 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TATTCAAATTTTAAAAATTAAATAAAATAT
Found at i:1353264 original size:24 final size:26
Alignment explanation
Indices: 1353237--1353287 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1353227 GTTGTTGTTG
* *
1353237 TATTT-AATTTTTTTAAT-TTTTATA
1 TATTTAAAATTTTTTAATATATTATA
1353261 TATTTAAAATTTTTTAATATATTATA
1 TATTTAAAATTTTTTAATATATTATA
1353287 T
1 T
1353288 TATTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 11 0.48
26 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTTAAAATTTTTTAATATATTATA
Found at i:1353624 original size:2 final size:2
Alignment explanation
Indices: 1353619--1353647 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1353609 TGCTTGCCCC
1353619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1353648 CACATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1354720 original size:20 final size:20
Alignment explanation
Indices: 1354695--1354738 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1354685 CACTCTCAGG
*
1354695 GGGCCTAAACTCCTAGAGCA
1 GGGCCTAAACTCCTAAAGCA
1354715 GGGCCTAAACTCCTAAAGCA
1 GGGCCTAAACTCCTAAAGCA
1354735 GGGC
1 GGGC
1354739 TCAACATTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.14
Consensus pattern (20 bp):
GGGCCTAAACTCCTAAAGCA
Found at i:1355078 original size:27 final size:26
Alignment explanation
Indices: 1355041--1355093 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
1355031 AAATAATATC
*
1355041 AAAAATATTTACTTGTCTAAACCCAT
1 AAAAATATTTACTTATCTAAACCCAT
1355067 AAAATATATTTACTTATCTAAACCCAT
1 AAAA-ATATTTACTTATCTAAACCCAT
1355094 TTAACCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAAATATTTACTTATCTAAACCCAT
Found at i:1362539 original size:28 final size:27
Alignment explanation
Indices: 1362508--1362603 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 27
1362498 AATTTCTTAA
1362508 ATATTTTATTTTTAAAATAATTTTTTAT
1 ATATTTTATTTTTAAAATAATTTTTT-T
*
1362536 ATATTTATTTTATTTAAATATATATTTATTTT
1 ATATTT-TATT-TTTAAA-ATA-ATTT-TTTT
* *
1362568 -TA-TTTATATTT-AAATAA-ATTTTT
1 ATATTTTATTTTTAAAATAATTTTTTT
1362591 AT-TTTTATTTTTA
1 ATATTTTATTTTTA
1362604 TTTAAATAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
23 4 0.07
24 10 0.18
25 1 0.02
26 3 0.05
27 2 0.04
28 9 0.16
29 5 0.09
30 8 0.15
31 5 0.09
32 5 0.09
33 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
ATATTTTATTTTTAAAATAATTTTTTT
Found at i:1362556 original size:17 final size:16
Alignment explanation
Indices: 1362518--1362566 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1362508 ATATTTTATT
1362518 TTTAAA-ATA-ATTT-
1 TTTAAATATATATTTA
* *
1362531 TTTATATATTTATTTTA
1 TTTAAATATATA-TTTA
1362548 TTTAAATATATATTTA
1 TTTAAATATATATTTA
1362564 TTT
1 TTT
1362567 TTATTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 5 0.18
14 2 0.07
15 1 0.04
16 10 0.36
17 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAAATATATATTTA
Found at i:1362557 original size:21 final size:22
Alignment explanation
Indices: 1362533--1362573 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1362523 AATAATTTTT
1362533 TATATATTTA-TTTTATTTAAA
1 TATATATTTATTTTTATTTAAA
1362554 TATATATTTATTTTTATTTA
1 TATATATTTATTTTTATTTA
1362574 TATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATATTTATTTTTATTTAAA
Found at i:1362575 original size:16 final size:16
Alignment explanation
Indices: 1362535--1362579 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1362525 TAATTTTTTA
1362535 TATATTTAT-TTTATT
1 TATATTTATATTTATT
* *
1362550 TAAATATATATTTATT
1 TATATTTATATTTATT
*
1362566 TTTATTTATATTTA
1 TATATTTATATTTA
1362580 AATAAATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTATATTTATT
Found at i:1362605 original size:28 final size:28
Alignment explanation
Indices: 1362511--1362623 Score: 135
Period size: 28 Copynumber: 4.1 Consensus size: 28
1362501 TTCTTAAATA
*
1362511 TTTTATTTTTA---AAATAATTTTTTAT
1 TTTTATTTTTATTTAAATAAATTTTTAT
* *
1362536 ATATTTA-TTTTATTTAAATATATATTTAT
1 -T-TTTATTTTTATTTAAATAAATTTTTAT
*
1362565 TTTTATTTATATTTAAATAAATTTTTAT
1 TTTTATTTTTATTTAAATAAATTTTTAT
*
1362593 TTTTATTTTTATTTAAATAAAATTTTAT
1 TTTTATTTTTATTTAAATAAATTTTTAT
1362621 TTT
1 TTT
1362624 ATATGAGATA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.08
27 8 0.11
28 49 0.66
29 11 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTATTTTTATTTAAATAAATTTTTAT
Found at i:1362679 original size:30 final size:30
Alignment explanation
Indices: 1362643--1362714 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
1362633 ATTGATTTAT
*
1362643 ATTAAAAGA-TAAGAATTTA-TTTAAGTATAA
1 ATTAAAA-ATTAAAAATTTATTTTAA-TATAA
1362673 ATTAAAAATTAAAAATTTATTTTAATATAA
1 ATTAAAAATTAAAAATTTATTTTAATATAA
1362703 ATTAAAAATTAA
1 ATTAAAAATTAA
1362715 TTATTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.85
31 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (30 bp):
ATTAAAAATTAAAAATTTATTTTAATATAA
Found at i:1362919 original size:2 final size:2
Alignment explanation
Indices: 1362912--1362941 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1362902 ACATATTCAT
1362912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1362942 GTACAATGCT
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):
TA
Found at i:1373811 original size:22 final size:22
Alignment explanation
Indices: 1373785--1373829 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1373775 AATTACAAGC
*
1373785 ATAAATC-TTACATAATATTTTG
1 ATAAATCTTTACAAAAT-TTTTG
1373807 ATAAATCTTTACAAAATTTTTG
1 ATAAATCTTTACAAAATTTTTG
1373829 A
1 A
1373830 ATATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (22 bp):
ATAAATCTTTACAAAATTTTTG
Found at i:1374391 original size:2 final size:2
Alignment explanation
Indices: 1374384--1374415 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1374374 ATCCGAAAAC
1374384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1374416 TCCTGTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1374571 original size:9 final size:9
Alignment explanation
Indices: 1374528--1374676 Score: 71
Period size: 9 Copynumber: 16.4 Consensus size: 9
1374518 CACGATATAA
*
1374528 ATAAAAAAT
1 ATAAAATAT
1374537 A-AAAATA-
1 ATAAAATAT
1374544 ATATAAATATT
1 ATA-AAATA-T
1374555 ATATAAATAT
1 ATA-AAATAT
*
1374565 ATAAAATTT
1 ATAAAATAT
*
1374574 TTAAAATAT
1 ATAAAATAT
1374583 ATATAATATATT
1 ATA-AA-ATA-T
**
1374595 ATTGAATAT
1 ATAAAATAT
*
1374604 -TAAAATTT
1 ATAAAATAT
1374612 ATAAAA-AT
1 ATAAAATAT
1374620 AT----TAT
1 ATAAAATAT
1374625 ATAAAATAT
1 ATAAAATAT
* *
1374634 TTTAAATATT
1 ATAAAATA-T
*
1374644 ATTATAATAT
1 A-TAAAATAT
1374654 ATTAAAATAT
1 A-TAAAATAT
*
1374664 ATAAATTAT
1 ATAAAATAT
1374673 ATAA
1 ATAA
1374677 TATAAATTAT
Statistics
Matches: 107, Mismatches: 18, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
5 4 0.04
7 1 0.01
8 14 0.13
9 46 0.43
10 21 0.20
11 18 0.17
12 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATAAAATAT
Found at i:1374579 original size:39 final size:39
Alignment explanation
Indices: 1374536--1374698 Score: 126
Period size: 39 Copynumber: 4.1 Consensus size: 39
1374526 AAATAAAAAA
1374536 TAAAAATA-ATATAAATATTATATAAATATATAAAATT-T
1 TAAAAATATATATAAATATTAT-TAAATATATAAAATTAT
* *
1374574 TTAAAATATATATAATATATTATTGAATAT-TAAAATT-T
1 TAAAAATATATATAA-ATATTATTAAATATATAAAATTAT
*
1374612 ATAAAAATATTATATAAAATATT-TTAAATATTATTATAATATAT
1 -TAAAAATA-TATAT-AAATATTATTAAATA-TA-TAAAAT-TAT
* *
1374656 T-AAAATATATA-AATTATATAATATAAAT-TATTAAATTAT
1 TAAAAATATATATAA--ATATTAT-TAAATATATAAAATTAT
1374695 TAAA
1 TAAA
1374699 TTTAAAAACG
Statistics
Matches: 102, Mismatches: 8, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
38 15 0.15
39 31 0.30
40 24 0.24
41 12 0.12
42 12 0.12
43 7 0.07
44 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (39 bp):
TAAAAATATATATAAATATTATTAAATATATAAAATTAT
Found at i:1374629 original size:13 final size:12
Alignment explanation
Indices: 1374535--1374657 Score: 60
Period size: 11 Copynumber: 10.9 Consensus size: 12
1374525 TAAATAAAAA
*
1374535 ATAAAA-ATAAT
1 ATAAAATATTAT
1374546 AT-AAATATTAT
1 ATAAAATATTAT
1374557 AT--AA-A-TAT
1 ATAAAATATTAT
1374565 ATAAAAT-TT-T
1 ATAAAATATTAT
1374575 -TAAAATA-TAT
1 ATAAAATATTAT
1374585 ATAATATATTATTGAAT
1 ATAA-A-A-TATT--AT
1374602 ATTAAAAT-TTAT
1 A-TAAAATATTAT
1374614 A-AAAATATTAT
1 ATAAAATATTAT
1374625 ATAAAATATT-T
1 ATAAAATATTAT
1374636 -T-AAATATTATT
1 ATAAAATATTA-T
*
1374647 ATAATATATTA
1 ATAAAATATTA
1374658 AAATATATAA
Statistics
Matches: 89, Mismatches: 2, Indels: 40
0.68 0.02 0.31
Matches are distributed among these distances:
8 5 0.06
9 15 0.17
10 15 0.17
11 19 0.21
12 13 0.15
13 8 0.09
14 4 0.04
15 2 0.02
16 1 0.01
17 4 0.04
18 3 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (12 bp):
ATAAAATATTAT
Found at i:1374629 original size:22 final size:24
Alignment explanation
Indices: 1374575--1374649 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 24
1374565 ATAAAATTTT
*
1374575 TAAAATATATATAATATATTATTGAATA
1 TAAAATAT-TATAA-ATAATATT--ATA
1374603 TTAAAAT-TTATAAA-AATATTATA
1 -TAAAATATTATAAATAATATTATA
* *
1374626 TAAAATATTTTAAATATTATTATA
1 TAAAATATTATAAATAATATTATA
1374650 ATATATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 6 0.15
23 9 0.22
24 8 0.20
25 5 0.12
26 1 0.02
27 5 0.12
28 1 0.02
29 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
TAAAATATTATAAATAATATTATA
Found at i:1374650 original size:22 final size:21
Alignment explanation
Indices: 1374562--1374668 Score: 68
Period size: 20 Copynumber: 5.4 Consensus size: 21
1374552 ATTATATAAA
1374562 TATATAAAAT-TTTTAAA-AT
1 TATATAAAATATTTTAAATAT
* *
1374581 ATATATAATATATTATTGAATAT
1 -TATATAAAATATT-TTAAATAT
** **
1374604 TA-A-AATTTA-TAAAAATAT
1 TATATAAAATATTTTAAATAT
1374622 TATATAAAATATTTTAAATAT
1 TATATAAAATATTTTAAATAT
* *
1374643 TAT-TATAATATATTAAA-A-
1 TATATAAAATATTTTAAATAT
1374661 TATATAAA
1 TATATAAA
1374669 TTATATAATA
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
18 10 0.15
19 6 0.09
20 30 0.45
21 13 0.19
22 6 0.09
23 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
TATATAAAATATTTTAAATAT
Found at i:1374663 original size:60 final size:60
Alignment explanation
Indices: 1374562--1374676 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
1374552 ATTATATAAA
*
1374562 TATATAAAATTTTTAAAATATATATAATATATTATTGAATAT-TAAAATT-TATAAAAATAT
1 TATATAAAATTTTTAAAATATATATAATATATTA-TAAATATAT-AAATTATATAAAAATAT
1374622 TATATAAAATATTTT-AAATATTATTATAATATATTA-AAATATATAAATTATATAA
1 TATATAAAAT-TTTTAAAATA-TA-TATAATATATTATAAATATATAAATTATATAA
1374677 TATAAATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
60 25 0.51
61 12 0.24
62 12 0.24
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (60 bp):
TATATAAAATTTTTAAAATATATATAATATATTATAAATATATAAATTATATAAAAATAT
Found at i:1374665 original size:12 final size:11
Alignment explanation
Indices: 1374601--1374663 Score: 71
Period size: 10 Copynumber: 6.0 Consensus size: 11
1374591 TATTATTGAA
1374601 TATTAAAAT-T
1 TATTAAAATAT
*
1374611 TATAAAAATAT
1 TATTAAAATAT
1374622 TATATAAAATAT
1 TAT-TAAAATAT
1374634 T-TT-AAATAT
1 TATTAAAATAT
*
1374643 TATTATAATA-
1 TATTAAAATAT
1374653 TATTAAAATAT
1 TATTAAAATAT
1374664 ATAAATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
9 7 0.16
10 20 0.45
11 9 0.20
12 8 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATTAAAATAT
Found at i:1374674 original size:90 final size:88
Alignment explanation
Indices: 1374538--1374706 Score: 209
Period size: 90 Copynumber: 1.9 Consensus size: 88
1374528 ATAAAAAATA
* * * *
1374538 AAAATAATATAAATATTATATAAATATATAAAATTTTTAAAATATAT-ATAATATATTATTGAA-
1 AAAATAATATAAATATTATATAAATATATAAAATATATAAAATATATAAT-ATAAATTATTAAAT
1374601 TATTAAAATTTATAAAAATATTATAT
65 TATT-AAATTTA-AAAAATATTATAT
* * *
1374627 AAAATATTTTAAATATTAT-TATAATATATTAAAATATATAAATTATATAATATAAATTATTAAA
1 AAAATAATATAAATATTATATA-AATATA-TAAAATATATAAAATATATAATATAAATTATTAAA
1374691 TTATTAAATTTAAAAA
64 TTATTAAATTTAAAAA
1374707 CGGCTGATAC
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
88 2 0.03
89 27 0.39
90 34 0.49
91 6 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (88 bp):
AAAATAATATAAATATTATATAAATATATAAAATATATAAAATATATAATATAAATTATTAAATT
ATTAAATTTAAAAAATATTATAT
Found at i:1374692 original size:8 final size:8
Alignment explanation
Indices: 1374641--1374700 Score: 54
Period size: 8 Copynumber: 7.4 Consensus size: 8
1374631 TATTTTAAAT
1374641 ATTATTATA
1 ATTATTA-A
1374650 ATATATTAA
1 AT-TATTAA
*
1374659 AATATATAA
1 ATTAT-TAA
1374668 ATTA-TATA
1 ATTATTA-A
1374676 A-TA-TAA
1 ATTATTAA
1374682 ATTATTAA
1 ATTATTAA
1374690 ATTATTAA
1 ATTATTAA
1374698 ATT
1 ATT
1374701 TAAAAACGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
6 2 0.05
7 8 0.18
8 19 0.43
9 10 0.23
10 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTATTAA
Found at i:1374704 original size:22 final size:23
Alignment explanation
Indices: 1374655--1374705 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1374645 TTATAATATA
1374655 TTAAAATATATAAATTATATAAT
1 TTAAAATATATAAATTATATAAT
* *
1374678 ATAAATTAT-TAAATTAT-TAAAT
1 TTAAAATATATAAATTATAT-AAT
1374700 TTAAAA
1 TTAAAA
1374706 ACGGCTGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.65
23 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAATATATAAATTATATAAT
Found at i:1377307 original size:2 final size:2
Alignment explanation
Indices: 1377300--1377329 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1377290 ACCTGTTTTG
1377300 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1377330 AATTATACAA
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):
TA
Done.