Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 59 of 145
Found at i:20408170 original size:30 final size:30
Alignment explanation
Indices: 20408106--20408174 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
20408096 AAGTGTAGAA
20408106 AACCTCTC-TCTATCCACTTTTGATCCACC
1 AACCTCTCTTCTATCCACTTTTGATCCACC
* * *
20408135 AACCTCTCTTCATATCTACTTTT-ATCTATC
1 AACCTCTCTTC-TATCCACTTTTGATCCACC
20408165 AACCTCTCTT
1 AACCTCTCTT
20408175 TCTTTGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 17 0.49
31 10 0.29
ACGTcount: A:0.22, C:0.36, G:0.01, T:0.41
Consensus pattern (30 bp):
AACCTCTCTTCTATCCACTTTTGATCCACC
Found at i:20412369 original size:40 final size:40
Alignment explanation
Indices: 20412314--20412389 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
20412304 GCTCAGCTCG
20412314 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAAATAT
1 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAAATAT
20412354 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAA
1 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAA
20412390 TAGACCTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (40 bp):
AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAAATAT
Found at i:20413269 original size:16 final size:16
Alignment explanation
Indices: 20413248--20413319 Score: 99
Period size: 16 Copynumber: 4.5 Consensus size: 16
20413238 CGTTTGGTTC
20413248 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
20413264 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
* *
20413280 GCTATAATGGAACAGA
1 GCTGTAATGGAATAGA
*
20413296 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
20413312 ACTGTAAT
1 GCTGTAAT
20413320 AGTAATTCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:20413359 original size:45 final size:44
Alignment explanation
Indices: 20413301--20413393 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
20413291 ACAGAGGTGT
20413301 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGATTGAATAG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGATTGAATAG
* *
20413346 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATAG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGATTGAATAG
20413390 AATG
1 AATG
20413394 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 22 0.49
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGATTGAATAG
Found at i:20413704 original size:23 final size:24
Alignment explanation
Indices: 20413664--20413710 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
20413654 TCATAATATC
20413664 CAAACATAATATTCATAT-ATTAA
1 CAAACATAATATTCATATAATTAA
20413687 CAAACATAATATTCATATAATTAA
1 CAAACATAATATTCATATAATTAA
20413711 TAAAAGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (24 bp):
CAAACATAATATTCATATAATTAA
Found at i:20416577 original size:25 final size:25
Alignment explanation
Indices: 20416549--20416598 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20416539 TGAAGGAAAA
20416549 GATGAAGCTGAGGGCAGAAAAGTTT
1 GATGAAGCTGAGGGCAGAAAAGTTT
20416574 GATGAAGCTGAGGGCAGAAAAGTTT
1 GATGAAGCTGAGGGCAGAAAAGTTT
20416599 CTAACTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.20
Consensus pattern (25 bp):
GATGAAGCTGAGGGCAGAAAAGTTT
Found at i:20418585 original size:51 final size:51
Alignment explanation
Indices: 20418509--20418608 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
20418499 ACTTAAACAC
*
20418509 CGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTTGCTTTAT
1 CGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTCGCTTTAT
*
20418560 CGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTTTTGAATCTCGCTTT
1 CGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTCGCTTT
20418609 CTTTCTTCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (51 bp):
CGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTCGCTTTAT
Found at i:20418946 original size:21 final size:21
Alignment explanation
Indices: 20418873--20419077 Score: 123
Period size: 21 Copynumber: 9.5 Consensus size: 21
20418863 TGTTACTGAA
20418873 TTTGTTGTTTTAAATCGATTC
1 TTTGTTGTTTTAAATCGATTC
* * *
20418894 TTT-TAT-TCTTTGAATCAATTG
1 TTTGT-TGT-TTTAAATCGATTC
*
20418915 TTTGTTGTTTTAAATTGATTC
1 TTTGTTGTTTTAAATCGATTC
* *
20418936 TTTGCTT-TTTTGAAGCGATTC
1 TTTG-TTGTTTTAAATCGATTC
* * *
20418957 ATGATTTTTGTTTTAAATTGATCC
1 -T--TTGTTGTTTTAAATCGATTC
*
20418981 ATGATTGTTGTTTTAAATCGATTA
1 -T--TTGTTGTTTTAAATCGATTC
* * *
20419005 TTTGCTT-CTTTAAATTGATTTT
1 TTTG-TTGTTTTAAATCGA-TTC
20419027 TTTGTTGTTTTAAATCGATTC
1 TTTGTTGTTTTAAATCGATTC
* * * *
20419048 ATTATT-ATTTGAATCGATTC
1 TTTGTTGTTTTAAATCGATTC
20419068 TTTGTTGTTT
1 TTTGTTGTTT
20419078 AGCTTGATTC
Statistics
Matches: 139, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
20 18 0.13
21 64 0.46
22 22 0.16
23 3 0.02
24 32 0.23
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.57
Consensus pattern (21 bp):
TTTGTTGTTTTAAATCGATTC
Found at i:20422043 original size:29 final size:29
Alignment explanation
Indices: 20422011--20422143 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
20422001 TCACACGGCT
* *
20422011 GACCACACACCCGTGTGGTGCACATGATC
1 GACCACACGCCCGTGTGGTGCACATGACC
* * * * *
20422040 GACCACACGCTCATGTAGTGAACATGACA
1 GACCACACGCCCGTGTGGTGCACATGACC
* * * * *
20422069 AACTATATGCCTGTGTGGTGCACATGACC
1 GACCACACGCCCGTGTGGTGCACATGACC
*
20422098 GACCACACGCCTGTGTGGTGCACATGACC
1 GACCACACGCCCGTGTGGTGCACATGACC
*
20422127 GACCACATGCCCGTGTG
1 GACCACACGCCCGTGTG
20422144 ACGCAGTGTA
Statistics
Matches: 81, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (29 bp):
GACCACACGCCCGTGTGGTGCACATGACC
Found at i:20427057 original size:20 final size:20
Alignment explanation
Indices: 20427034--20427087 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
20427024 AATCTCGAGT
*
20427034 AATTGTTATTAAAATAAGTG
1 AATTGTTATTAAAATAAGTA
*
20427054 AATT-TTACTT--AATTAGTA
1 AATTGTTA-TTAAAATAAGTA
20427072 ATATTGTTATTAAAAT
1 A-ATTGTTATTAAAAT
20427088 TGTGCTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
18 7 0.26
19 8 0.30
20 9 0.33
21 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (20 bp):
AATTGTTATTAAAATAAGTA
Found at i:20427901 original size:36 final size:36
Alignment explanation
Indices: 20427847--20427916 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
20427837 GAGCACATCA
20427847 GTCAAAATAGATCCGAAAGGTTGCTGAACTGAATTG
1 GTCAAAATAGATCCGAAAGGTTGCTGAACTGAATTG
* ** *
20427883 GTCATAATAGATTTGAAAGGTTGCTGAATTGAAT
1 GTCAAAATAGATCCGAAAGGTTGCTGAACTGAAT
20427917 AGAGTTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (36 bp):
GTCAAAATAGATCCGAAAGGTTGCTGAACTGAATTG
Found at i:20433115 original size:35 final size:35
Alignment explanation
Indices: 20433069--20433138 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
20433059 ACCTCCAAAG
20433069 ATTTTTCCCTTCTCTATTCTCTTTAACTTTCCCTT
1 ATTTTTCCCTTCTCTATTCTCTTTAACTTTCCCTT
20433104 ATTTTTCCCTTCTCTATTCTCTTTAACTTTCCCTT
1 ATTTTTCCCTTCTCTATTCTCTTTAACTTTCCCTT
20433139 CTTTCAATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.11, C:0.31, G:0.00, T:0.57
Consensus pattern (35 bp):
ATTTTTCCCTTCTCTATTCTCTTTAACTTTCCCTT
Found at i:20435072 original size:12 final size:12
Alignment explanation
Indices: 20435055--20435081 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20435045 GTCTCTTTGC
20435055 AGACTGAATTAT
1 AGACTGAATTAT
20435067 AGACTGAATTAT
1 AGACTGAATTAT
20435079 AGA
1 AGA
20435082 GATGCACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (12 bp):
AGACTGAATTAT
Found at i:20436180 original size:22 final size:22
Alignment explanation
Indices: 20436109--20436180 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
20436099 TGAATCACGG
* *
20436109 AAATATTTT-TTTTAAAATAGC
1 AAATATTTTAATTTAAAATAGA
* * *
20436130 CAATA-TTTAATTTAAAAAATTA
1 AAATATTTTAATTTAAAATA-GA
*
20436152 AGA-ATTTTAATTTAAAATAGA
1 AAATATTTTAATTTAAAATAGA
20436173 AAATATTT
1 AAATATTT
20436181 GTTGGCACTC
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
20 3 0.08
21 16 0.43
22 18 0.49
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (22 bp):
AAATATTTTAATTTAAAATAGA
Found at i:20437947 original size:122 final size:122
Alignment explanation
Indices: 20437725--20437971 Score: 422
Period size: 122 Copynumber: 2.0 Consensus size: 122
20437715 TCATGCTACC
* * *
20437725 AATGTGGTATGAAAATGCATTGGTCACATACCTGTCGTATGTTTAAGCATTTAGTAAAACTTTAT
1 AATGGGGTATGAAAATGCATTGGTCACATACCTATCGTATGTTTAAGCATTTAGTAAAAATTTAT
* *
20437790 CAAAGCATCCACTAAAACAAAAGGGAAACAATATTGAGATAAATTTCGTTATCCCAA
66 CAAAGCATCCACTAAAACAAAAGGAAAACAATATTGAGACAAATTTCGTTATCCCAA
*
20437847 AATGGGGTATGAAAATGCATTGGTCACGTACCTATCGTATGTTTAAGCATTTAGTAAAAATTTAT
1 AATGGGGTATGAAAATGCATTGGTCACATACCTATCGTATGTTTAAGCATTTAGTAAAAATTTAT
* *
20437912 CAAAGCATCCATTAAAACAAAAGGAAAACAGTATTGAGACAAATTTCGTTATCCCAA
66 CAAAGCATCCACTAAAACAAAAGGAAAACAATATTGAGACAAATTTCGTTATCCCAA
20437969 AAT
1 AAT
20437972 AATGAAATAG
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 117 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (122 bp):
AATGGGGTATGAAAATGCATTGGTCACATACCTATCGTATGTTTAAGCATTTAGTAAAAATTTAT
CAAAGCATCCACTAAAACAAAAGGAAAACAATATTGAGACAAATTTCGTTATCCCAA
Found at i:20439177 original size:27 final size:27
Alignment explanation
Indices: 20439147--20439198 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
20439137 AACCTAGGTG
**
20439147 TAAATTTATTATATATATGATAATAAC
1 TAAATTTAAAATATATATGATAATAAC
*
20439174 TAAATTTAAAATATATATTATAATA
1 TAAATTTAAAATATATATGATAATA
20439199 TGTTTACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAATTTAAAATATATATGATAATAAC
Found at i:20440055 original size:23 final size:22
Alignment explanation
Indices: 20440028--20440122 Score: 58
Period size: 23 Copynumber: 4.2 Consensus size: 22
20440018 ACTATTGAAT
20440028 TGAAATGAATATATGTGTTAATA
1 TGAAATGAATAT-TGTGTTAATA
*
20440051 TGAAAATTGGATATTG-GTT-ATA
1 TG-AAA-TGAATATTGTGTTAATA
*
20440073 TTG-AATG--TATTGACTATTGAAT-
1 -TGAAATGAATATTG--TGTT-AATA
20440095 TGAAATGAATATATGTGTTAATA
1 TGAAATGAATAT-TGTGTTAATA
20440118 TGAAA
1 TGAAA
20440123 ATTGGATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 26
0.66 0.04 0.31
Matches are distributed among these distances:
18 5 0.09
20 2 0.04
21 6 0.11
22 10 0.18
23 17 0.30
24 8 0.14
25 8 0.14
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.40
Consensus pattern (22 bp):
TGAAATGAATATTGTGTTAATA
Found at i:20440075 original size:67 final size:67
Alignment explanation
Indices: 20440003--20440138 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
20439993 TGGTAGATAC
20440003 ATATTGAATGTATTGACTATTGAATTGAAATGAATATATGTGTTAATATGAAAATTGGATATTGG
1 ATATTGAATGTATTGACTATTGAATTGAAATGAATATATGTGTTAATATGAAAATTGGATATTGG
20440068 TT
66 TT
20440070 ATATTGAATGTATTGACTATTGAATTGAAATGAATATATGTGTTAATATGAAAATTGGATATTGG
1 ATATTGAATGTATTGACTATTGAATTGAAATGAATATATGTGTTAATATGAAAATTGGATATTGG
20440135 TT
66 TT
20440137 AT
1 AT
20440139 GTCTGAAATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (67 bp):
ATATTGAATGTATTGACTATTGAATTGAAATGAATATATGTGTTAATATGAAAATTGGATATTGG
TT
Found at i:20440137 original size:23 final size:23
Alignment explanation
Indices: 20440044--20440137 Score: 60
Period size: 23 Copynumber: 4.2 Consensus size: 23
20440034 GAATATATGT
20440044 GTTAATATGAAAATTGGATATTG
1 GTTAATATGAAAATTGGATATTG
*
20440067 GTT-ATATTGAATGTATT-GACTATT-
1 GTTAATA-TGAA--AATTGGA-TATTG
*
20440091 G--AAT-TG-AAA-TGAATATATG
1 GTTAATATGAAAATTGGATAT-TG
20440110 TGTTAATATGAAAATTGGATATTG
1 -GTTAATATGAAAATTGGATATTG
20440134 GTTA
1 GTTA
20440138 TGTCTGAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 28
0.62 0.05 0.33
Matches are distributed among these distances:
17 4 0.08
18 3 0.06
20 2 0.04
21 2 0.04
22 6 0.11
23 15 0.28
24 8 0.15
25 13 0.25
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.41
Consensus pattern (23 bp):
GTTAATATGAAAATTGGATATTG
Found at i:20442341 original size:17 final size:18
Alignment explanation
Indices: 20442319--20442355 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20442309 GTTGAGTTCT
20442319 AATAGCTA-AAGGTATTA
1 AATAGCTATAAGGTATTA
*
20442336 AATAGCTATAAGGTTTTA
1 AATAGCTATAAGGTATTA
20442354 AA
1 AA
20442356 GTGGAAGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (18 bp):
AATAGCTATAAGGTATTA
Found at i:20451113 original size:18 final size:18
Alignment explanation
Indices: 20451086--20451120 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20451076 AACACAAACG
*
20451086 AAAAAAAATTGAAAACAT
1 AAAAAAAATTCAAAACAT
*
20451104 AAAAATAATTCAAAACA
1 AAAAAAAATTCAAAACA
20451121 CAATACTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAAAATTCAAAACAT
Found at i:20458701 original size:13 final size:13
Alignment explanation
Indices: 20458677--20458715 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
20458667 ATCTCCTTAC
20458677 ATATA-AGG-TAT
1 ATATATAGGATAT
20458688 ATATATAGGATAT
1 ATATATAGGATAT
20458701 ATATATAGGA-AT
1 ATATATAGGATAT
20458713 ATA
1 ATA
20458716 CTACTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.19
12 8 0.31
13 13 0.50
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (13 bp):
ATATATAGGATAT
Found at i:20459405 original size:16 final size:16
Alignment explanation
Indices: 20459384--20459445 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
20459374 TGTATTGGAT
*
20459384 TAGAGGCGTAATAGAA
1 TAGAGGTGTAATAGAA
* *
20459400 TAGAGGTGTAATGGAT
1 TAGAGGTGTAATAGAA
*
20459416 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATAGAA
20459432 TAGAGGTGTAATAG
1 TAGAGGTGTAATAG
20459446 CAAATCAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.37, C:0.02, G:0.35, T:0.26
Consensus pattern (16 bp):
TAGAGGTGTAATAGAA
Found at i:20459420 original size:32 final size:32
Alignment explanation
Indices: 20459374--20459443 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
20459364 TTTGGTCCAC
*
20459374 TGTATTGGATTAGAGGCGTAATAGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATAGAATAGAGG
* *
20459406 TGTAATGGATTAGAGGTGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATAGAATAGAGG
20459438 TGTAAT
1 TGTAAT
20459444 AGCAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.01, G:0.34, T:0.30
Consensus pattern (32 bp):
TGTAATGGATTAGAGGCGTAATAGAATAGAGG
Found at i:20459696 original size:18 final size:17
Alignment explanation
Indices: 20459675--20459709 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20459665 TTATTATTAA
*
20459675 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20459693 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20459710 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20473429 original size:34 final size:34
Alignment explanation
Indices: 20473391--20473459 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
20473381 ACTATTAAAG
20473391 TTAGTTTCCAACGATATCAATGATAATTTATTGA
1 TTAGTTTCCAACGATATCAATGATAATTTATTGA
*
20473425 TTAGTTTCCAACGATATCAATGATGATTTATTGA
1 TTAGTTTCCAACGATATCAATGATAATTTATTGA
20473459 T
1 T
20473460 ATCTGATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (34 bp):
TTAGTTTCCAACGATATCAATGATAATTTATTGA
Found at i:20505335 original size:32 final size:32
Alignment explanation
Indices: 20505284--20505419 Score: 168
Period size: 32 Copynumber: 4.3 Consensus size: 32
20505274 GAATGGCTAC
* * *
20505284 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
20505315 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
** * *
20505347 CTGCCATCAGTAATGGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
20505379 CAA-CCATCAGTAATGGTAATATGATCGGCACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
20505411 AAGCCATCA
1 AAGCCATCA
20505420 ATAGCATCGC
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
31 12 0.13
32 78 0.87
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:20505399 original size:64 final size:64
Alignment explanation
Indices: 20505298--20505419 Score: 192
Period size: 64 Copynumber: 1.9 Consensus size: 64
20505288 CATAAGTACA
* **
20505298 GTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACTGCCATCAGTAATG
1 GTAATATGATTGGCACAAAGCCATCAGTAATAGTAATATGATCGGCACAAAGCCATCAGTAATG
*
20505362 GTAATATGATTGGCACACAA-CCATCAGTAATGGTAATATGATCGGCACAAAGCCATCA
1 GTAATATGATTGGCACA-AAGCCATCAGTAATAGTAATATGATCGGCACAAAGCCATCA
20505420 ATAGCATCGC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 51 0.96
65 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (64 bp):
GTAATATGATTGGCACAAAGCCATCAGTAATAGTAATATGATCGGCACAAAGCCATCAGTAATG
Found at i:20505641 original size:24 final size:25
Alignment explanation
Indices: 20505614--20505678 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 25
20505604 ACAAATCACA
* *
20505614 GACAAATCAGTCATTTACATC-TCG
1 GACAAATCAATCATTTACATCATAG
*
20505638 GACAAATCATTCATTTACATCATAG
1 GACAAATCAATCATTTACATCATAG
20505663 G-CAAATCAATCATTTA
1 GACAAATCAATCATTTA
20505679 ACCACGAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 34 0.92
25 3 0.08
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (25 bp):
GACAAATCAATCATTTACATCATAG
Found at i:20505727 original size:27 final size:27
Alignment explanation
Indices: 20505697--20505924 Score: 267
Period size: 27 Copynumber: 8.4 Consensus size: 27
20505687 GGGCAAAATA
* *
20505697 GTCACTTTACCCTACAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
20505724 GTCATTTCACCCTACAGGGGCAATACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * *
20505751 ACCATTTTACCCTATAGGGGCAATACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * *
20505778 ACCATTTTACCCTATAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
20505805 GTCATTTTACCCTACAAGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* *
20505832 GTCATTTTACCCTATAGGTGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
20505859 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
20505886 GTTATTTTACCTTACAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
*
20505913 GTCATCTTACCC
1 GTCATTTTACCC
20505925 ATCGAGGGTA
Statistics
Matches: 173, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 173 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:20505945 original size:54 final size:54
Alignment explanation
Indices: 20505703--20505952 Score: 191
Period size: 54 Copynumber: 4.6 Consensus size: 54
20505693 AATAGTCACT
* * * * * * * * *
20505703 TTACCCTACAGGGGCATTATGGTCATTTCACCCTACAGGGGCAATAC-GACCATT
1 TTACCCTATAGGGGCATTACGATTATTTTACCTTACAGGGGCATTACAG-TCATC
* ** * * ** *
20505757 TTACCCTATAGGGGCAATACGACCATTTTACCCTATAGGGGCATTATGGTCATT
1 TTACCCTATAGGGGCATTACGATTATTTTACCTTACAGGGGCATTACAGTCATC
* * * * * * * *
20505811 TTACCCTACAAGGGCATTAC-AGTCATTTTACCCTATAGGTGCATTACGGTCATT
1 TTACCCTATAGGGGCATTACGA-TTATTTTACCTTACAGGGGCATTACAGTCATC
*
20505865 TTACCCTATAGGGGCATTACGGTTATTTTACCTTACAGGGGCATTACAGTCATC
1 TTACCCTATAGGGGCATTACGATTATTTTACCTTACAGGGGCATTACAGTCATC
* * *
20505919 TTACCC-ATCGAGGGTATTTCGATTATTTTACCTT
1 TTACCCTATAG-GGGCATTACGATTATTTTACCTT
20505953 TCGGGGTATT
Statistics
Matches: 163, Mismatches: 29, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
53 4 0.02
54 158 0.97
55 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (54 bp):
TTACCCTATAGGGGCATTACGATTATTTTACCTTACAGGGGCATTACAGTCATC
Found at i:20505947 original size:81 final size:81
Alignment explanation
Indices: 20505702--20505978 Score: 303
Period size: 81 Copynumber: 3.4 Consensus size: 81
20505692 AAATAGTCAC
* * * *
20505702 TTTACCCTACAGGGGCATTATGGTCATTTCACCCTACAGGGGCAATAC-GACCATTTTACCCTAT
1 TTTACCCTATAGGGGCATTATGGTCATTTTACCCTACAGGGGCATTACAG-TCATTTTACCCTAT
* *
20505766 -AGGGGCAATACGACCAT
65 GA-GGGCATTACGATCAT
*
20505783 TTTACCCTATAGGGGCATTATGGTCATTTTACCCTACAAGGGCATTACAGTCATTTTACCCTAT-
1 TTTACCCTATAGGGGCATTATGGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATG
*
20505847 AGGTGCATTACGGTCAT
66 AGG-GCATTACGATCAT
* * * *
20505864 TTTACCCTATAGGGGCATTACGGTTATTTTACCTTACAGGGGCATTACAGTCATCTTACCC-ATC
1 TTTACCCTATAGGGGCATTATGGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTAT-
* * *
20505928 GAGGGTATTTCGATTAT
65 GAGGGCATTACGATCAT
* * * * *
20505945 TTTA-CCTTTCGGGGTATTTTGATCATTTTACCCT
1 TTTACCCTATAGGGGCATTATGGTCATTTTACCCT
20505979 TCGAGGGTAT
Statistics
Matches: 167, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
80 26 0.16
81 137 0.82
82 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (81 bp):
TTTACCCTATAGGGGCATTATGGTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTATG
AGGGCATTACGATCAT
Found at i:20505960 original size:26 final size:28
Alignment explanation
Indices: 20505919--20506046 Score: 140
Period size: 27 Copynumber: 4.8 Consensus size: 28
20505909 TACAGTCATC
* *
20505919 TTACCCATCGAGGGTATTTCGA-TTATT
1 TTACCCTTCGAGGGTATTTCGAGTAATT
* * *
20505946 TTACCTTTCG-GGGTATTTTGA-TCATT
1 TTACCCTTCGAGGGTATTTCGAGTAATT
*
20505972 TTACCCTTCGAGGGTA-TTCTAGTAATT
1 TTACCCTTCGAGGGTATTTCGAGTAATT
* *
20505999 TTATCATTCGAGGGTATTTC-AGTAATT
1 TTACCCTTCGAGGGTATTTCGAGTAATT
*
20506026 TTACCCTTCAAGGGTATTTCG
1 TTACCCTTCGAGGGTATTTCG
20506047 GTCCAACCTT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
26 26 0.31
27 55 0.65
28 3 0.04
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (28 bp):
TTACCCTTCGAGGGTATTTCGAGTAATT
Found at i:20505984 original size:53 final size:55
Alignment explanation
Indices: 20505911--20506046 Score: 154
Period size: 53 Copynumber: 2.5 Consensus size: 55
20505901 AGGGGCATTA
* * * *
20505911 CAGTCATCTTACCCATCGAGGGTATTTCGA-TTATTTTACCTTTCG-GGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCGAGTAATTTTACCATTCGAGGGTATTT
* * *
20505964 -TGATCATTTTACCCTTCGAGGGTA-TTCTAGTAATTTTATCATTCGAGGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTTCGAGTAATTTTACCATTCGAGGGTATTT
* *
20506018 CAGTAATTTTACCCTTCAAGGGTATTTCG
1 CAGTCATTTTACCCTTCGAGGGTATTTCG
20506047 GTCCAACCTT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
52 5 0.07
53 31 0.46
54 27 0.40
55 4 0.06
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (55 bp):
CAGTCATTTTACCCTTCGAGGGTATTTCGAGTAATTTTACCATTCGAGGGTATTT
Found at i:20511154 original size:18 final size:17
Alignment explanation
Indices: 20511131--20511165 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20511121 ATTGGGCTAA
20511131 AATGGGTCGTGTGGGCCC
1 AATGGG-CGTGTGGGCCC
*
20511149 AATGGGCTTGTGGGCCC
1 AATGGGCGTGTGGGCCC
20511166 CACACGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.23, G:0.43, T:0.23
Consensus pattern (17 bp):
AATGGGCGTGTGGGCCC
Found at i:20511396 original size:27 final size:27
Alignment explanation
Indices: 20511357--20511601 Score: 269
Period size: 27 Copynumber: 9.1 Consensus size: 27
20511347 AATGTTTGTC
*
20511357 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** *
20511384 GAATGATTGAAATACCCCTATAGGG--
1 AAATGACCGAAATACCCCCATAGGGTA
* *
20511409 AAATGACTGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
20511436 AAATAATAGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
20511463 AAATGACCAAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
20511490 AAATGACCAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
20511517 AAATTATCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
20511544 AAATGACCGTAATACCCCCATAAGGTT
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
20511571 AAATAATCGAAATACCCCTATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
20511598 AAAT
1 AAAT
20511602 AATCGTAATG
Statistics
Matches: 182, Mismatches: 34, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
25 21 0.12
27 161 0.88
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:20511531 original size:81 final size:80
Alignment explanation
Indices: 20511364--20511606 Score: 317
Period size: 81 Copynumber: 3.0 Consensus size: 80
20511354 GTCAAATGAC
* ** *
20511364 CGAAATACCCTCATAGGGTAGAATGATTGAAATACCCCTATAGGG-AAATGACTGAAATACCCCC
1 CGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAATGACCGAAATACCCCC
20511428 ATAAGGTAAAATAAT
66 ATAAGGTAAAATAAT
* * * *
20511443 AGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGACCAAAATACCCC
1 CGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCTATAGGGT-AAATGACCGAAATACCCC
* *
20511508 CATAGGGTAAAATTAT
65 CATAAGGTAAAATAAT
* * * * *
20511524 CGAAATACCCTCATAGGGTAAAATGACCGTAATACCCCCATAAGGTTAAATAATCGAAATACCCC
1 CGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCTAT-AGGGTAAATGACCGAAATACCCC
*
20511589 TATAAGGTAAAATAAT
65 CATAAGGTAAAATAAT
20511605 CG
1 CG
20511607 TAATGTCCTT
Statistics
Matches: 139, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
79 39 0.28
81 96 0.69
82 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (80 bp):
CGAAATACCCTCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAATGACCGAAATACCCCC
ATAAGGTAAAATAAT
Found at i:20511733 original size:24 final size:24
Alignment explanation
Indices: 20511649--20511721 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
20511639 CCATCGAGTG
* *
20511649 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACTGATTTGTCTGTGATT
*
20511673 TAAATGACTAATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
20511697 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
20511721 T
1 T
20511722 GTATGAATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:20511946 original size:32 final size:32
Alignment explanation
Indices: 20511905--20512075 Score: 236
Period size: 32 Copynumber: 5.4 Consensus size: 32
20511895 ACTGCGATGC
* *
20511905 TACTGATGGCTTTGTGCTGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
20511937 TACTGATGGCTTTATGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
20511969 TACTGATGGATTTATGCCGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * *
20512001 TACTGATGGCTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
20512033 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
20512064 TACTTATGGCTT
1 TACTGATGGCTT
20512076 ATAGCCATTC
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 11 0.09
32 115 0.91
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:20515881 original size:19 final size:17
Alignment explanation
Indices: 20515842--20515882 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
20515832 AAAATAAGAT
20515842 AAAAATAAAATAATAAG
1 AAAAATAAAATAATAAG
*
20515859 AAAAATAATAATAAATGAG
1 AAAAATAA-AAT-AATAAG
20515878 AAAAA
1 AAAAA
20515883 GGGTACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 3 0.14
19 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
AAAAATAAAATAATAAG
Found at i:20517223 original size:24 final size:23
Alignment explanation
Indices: 20517180--20517236 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
20517170 AAAAGTCACC
*
20517180 TTTGATTTCTTTTGTATTTTGTT-
1 TTTGATTTTTTTTGTATTTT-TTG
20517203 TTTCGATTTTTTTTG-AGTTTTTTG
1 TTT-GATTTTTTTTGTA-TTTTTTG
20517227 TTTGATTTTT
1 TTTGATTTTT
20517237 ATTTCTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.09, C:0.04, G:0.14, T:0.74
Consensus pattern (23 bp):
TTTGATTTTTTTTGTATTTTTTG
Found at i:20517923 original size:44 final size:44
Alignment explanation
Indices: 20517899--20518157 Score: 191
Period size: 44 Copynumber: 5.9 Consensus size: 44
20517889 AGGATTTGTC
*
20517899 ACTTTAATCTGCTCTACCGCAACTTCAGGGAGATTAGATTTATA
1 ACTTTAATCTGCTCCACCGCAACTTCAGGGAGATTAGATTTATA
* * * * * **
20517943 ACTTTAATCTGCTCCACTGTAACTTCAGGGAGATGAAACTCGTA
1 ACTTTAATCTGCTCCACCGCAACTTCAGGGAGATTAGATTTATA
* * * * * *
20517987 TCTTCAATCTACTCCA-CGACAACCTCAGGGAGATAAGATTTGTA
1 ACTTTAATCTGCTCCACCG-CAACTTCAGGGAGATTAGATTTATA
* * * * * *
20518031 ACTTCAATCTACTCCACAGCAACCTCAGGGAGATAAGATTTGTA
1 ACTTTAATCTGCTCCACCGCAACTTCAGGGAGATTAGATTTATA
* * * * * * *
20518075 ACTTCAATATACTCCACGGTAATTTCAGGGAGA-TAGATTTGTA
1 ACTTTAATCTGCTCCACCGCAACTTCAGGGAGATTAGATTTATA
* * * * *
20518118 A-TTTCAATCTGCTTCACTGTAACTTTAGGGAGATAAGATT
1 ACTTT-AATCTGCTCCACCGCAACTTCAGGGAGATTAGATT
20518158 CACTACGGTG
Statistics
Matches: 177, Mismatches: 34, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
42 2 0.01
43 33 0.19
44 141 0.80
45 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
ACTTTAATCTGCTCCACCGCAACTTCAGGGAGATTAGATTTATA
Found at i:20517996 original size:88 final size:88
Alignment explanation
Indices: 20517756--20518155 Score: 310
Period size: 88 Copynumber: 4.5 Consensus size: 88
20517746 AGAGGCATAG
** * * * * * **
20517756 GATTTGTTTCTTTAATCTGCTCCATTGCAACTTTAGGGAGATAAGACTTGTAGCTTCAAT-TGTT
1 GATTTGTAACTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTCGTAACTTCAATCTACT
* * * *
20517820 CCACTGTAACTTCAAGGAGATAA
66 CCACCGCAACTTCAGGGAGATTA
* * * * * * * *
20517843 GATTTGTGACTTGATTTAATCCGAC-CCACTGTAACTTCAGAGG-TATAGGATTTGTCACTTTAA
1 GATTTGTAAC----TTTAATCTG-CTCCACTGTAACTTCAG-GGAGATAAGACTCGTAACTTCAA
* *
20517906 TCTGCTCTACCGCAACTTCAGGGAGATTA
60 TCTACTCCACCGCAACTTCAGGGAGATTA
* *
20517935 GATTTATAACTTTAATCTGCTCCACTGTAACTTCAGGGAGATGAA-ACTCGTATCTTCAATCTAC
1 GATTTGTAACTTTAATCTGCTCCACTGTAACTTCAGGGAGAT-AAGACTCGTAACTTCAATCTAC
* *
20517999 TCCA-CGACAACCTCAGGGAGATAA
65 TCCACCG-CAACTTCAGGGAGATTA
* * * * * * * *
20518023 GATTTGTAACTTCAATCTACTCCACAGCAACCTCAGGGAGATAAGATTTGTAACTTCAATATACT
1 GATTTGTAACTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTCGTAACTTCAATCTACT
* * *
20518088 CCACGGTAATTTCAGGGAGA-TA
66 CCACCGCAACTTCAGGGAGATTA
* *
20518110 GATTTGTAA-TTTCAATCTGCTTCACTGTAACTTTAGGGAGATAAGA
1 GATTTGTAACTTT-AATCTGCTCCACTGTAACTTCAGGGAGATAAGA
20518156 TTCACTACGG
Statistics
Matches: 245, Mismatches: 54, Indels: 28
0.75 0.17 0.09
Matches are distributed among these distances:
86 2 0.01
87 52 0.21
88 122 0.50
89 2 0.01
91 35 0.14
92 32 0.13
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (88 bp):
GATTTGTAACTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTCGTAACTTCAATCTACT
CCACCGCAACTTCAGGGAGATTA
Found at i:20518196 original size:50 final size:50
Alignment explanation
Indices: 20518138--20518247 Score: 175
Period size: 50 Copynumber: 2.2 Consensus size: 50
20518128 GCTTCACTGT
* *
20518138 AACTTTAGGGAGATAAGATTCACTACGGTGACCTCAATCCATCCCAGTAC
1 AACTTTAGGGAGATAAGATTCACTACAGTGACCTCAATCCATCCCACTAC
* * *
20518188 AACTTTAGGGAGATAAGATTCACTACAGTGACTTCAATTCATCCCACTGC
1 AACTTTAGGGAGATAAGATTCACTACAGTGACCTCAATCCATCCCACTAC
20518238 AACTTTAGGG
1 AACTTTAGGG
20518248 TTATAGGATT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (50 bp):
AACTTTAGGGAGATAAGATTCACTACAGTGACCTCAATCCATCCCACTAC
Found at i:20519496 original size:23 final size:23
Alignment explanation
Indices: 20519470--20519522 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
20519460 ATAACCGCCA
20519470 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20519493 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20519516 CCCTGAT
1 CACTGAT
20519523 CAATAACCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20532973 original size:21 final size:20
Alignment explanation
Indices: 20532934--20532973 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20532924 ATCCTGCATG
*
20532934 TCTTTCTACATTTGTTCTAA
1 TCTTTCTACATTTGATCTAA
*
20532954 TCTTTCTAACCTTTGATCTA
1 TCTTTCT-ACATTTGATCTA
20532974 TGGCTCTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.53
Consensus pattern (20 bp):
TCTTTCTACATTTGATCTAA
Found at i:20537626 original size:13 final size:13
Alignment explanation
Indices: 20537608--20537638 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20537598 TGAAATAAAA
*
20537608 TAAAATTAAATGG
1 TAAAATTAAAAGG
20537621 TAAAATTAAAAGG
1 TAAAATTAAAAGG
20537634 TAAAA
1 TAAAA
20537639 AGGACTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (13 bp):
TAAAATTAAAAGG
Found at i:20537819 original size:2 final size:2
Alignment explanation
Indices: 20537812--20537841 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20537802 TAGCACCCCC
20537812 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
20537842 ATCTATAAAA
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:20543206 original size:6 final size:6
Alignment explanation
Indices: 20543195--20543253 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
20543185 CATATTATGG
20543195 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
20543243 ATGTAT ATGTA
1 ATGTAT ATGTA
20543254 CACATCTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
ATGTAT
Found at i:20544640 original size:44 final size:43
Alignment explanation
Indices: 20544538--20544653 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 43
20544528 AGCTCGTACA
* *
20544538 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAACATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAACATAG
*
20544581 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAATCTCAA-ATAG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGT-AATC-AAACATAG
*
20544625 ATGCCAACGTACCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
20544654 AATAACTCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
42 2 0.03
43 26 0.41
44 31 0.49
45 4 0.06
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAACATAG
Found at i:20546216 original size:42 final size:41
Alignment explanation
Indices: 20546169--20546268 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 41
20546159 CACGGCCTAA
*
20546169 GACATGAGCGTGTGTCTCGGT-CGTGTACGACACAC-GCCATGC
1 GACATG-GCGTGTGTCTC-GTCCGGGTACGACACACAG-CATGC
*
20546211 GACATGGGCGTGTGTCTCGTCCGGGTGCGACACACAGCATGC
1 GACAT-GGCGTGTGTCTCGTCCGGGTACGACACACAGCATGC
20546253 GACATGGTCGTGTGTC
1 GACATGG-CGTGTGTC
20546269 CCTTGTAGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
41 4 0.08
42 46 0.88
43 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.22
Consensus pattern (41 bp):
GACATGGCGTGTGTCTCGTCCGGGTACGACACACAGCATGC
Found at i:20547991 original size:24 final size:24
Alignment explanation
Indices: 20547943--20547989 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20547933 ACTGGTCATA
*
20547943 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
20547967 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
20547990 GGGATTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:20548696 original size:27 final size:27
Alignment explanation
Indices: 20548658--20548740 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
20548648 TCCATATCTG
20548658 GACTAAAATACCCTCGAAGGGTAAAAT
1 GACTAAAATACCCTCGAAGGGTAAAAT
* * *
20548685 GACTGAAATACCCTTGATGGGTAAAAT
1 GACTAAAATACCCTCGAAGGGTAAAAT
* *
20548712 GACTAAAATGCCCAC-ATAGGGTAAAAT
1 GACTAAAATACCCTCGA-AGGGTAAAAT
20548739 GA
1 GA
20548741 TCGTAATGCC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (27 bp):
GACTAAAATACCCTCGAAGGGTAAAAT
Found at i:20548748 original size:27 final size:27
Alignment explanation
Indices: 20548675--20548964 Score: 257
Period size: 27 Copynumber: 10.8 Consensus size: 27
20548665 ATACCCTCGA
* * * *
20548675 AGGGTAAAATGACTGAAATACCCTTGAT
1 AGGGTAAAATGACCGTAATGCCCCT-AT
***
20548703 -GGGTAAAATGACTAAAATGCCCAC-AT
1 AGGGTAAAATGACCGTAATGCCC-CTAT
* *
20548729 AGGGTAAAATGATCGTAATGCCTCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * *
20548756 AAGGTAAAATGACCATAATACCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
*
20548783 AGGGT-AAATGACCGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * * *
20548809 AGTGTAAAATGACCATAATACCCCTTGT
1 AGGGTAAAATGACCGTAATGCCCC-TAT
* * *
20548837 AGGGTAAAAT-AGTCGTAATGCCCTTGT
1 AGGGTAAAATGA-CCGTAATGCCCCTAT
* *
20548864 AGGGT-AAATGACGGTAATGCCCTTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * *
20548890 AGGGTAAAACGACTGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * *
20548917 AAGGTAAAATAACCGTAATACCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
20548944 AGGGTAAAATGACCGTAATGC
1 AGGGTAAAATGACCGTAATGC
20548965 TCTGATGGGT
Statistics
Matches: 213, Mismatches: 41, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
26 46 0.22
27 147 0.69
28 20 0.09
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
AGGGTAAAATGACCGTAATGCCCCTAT
Found at i:20548762 original size:54 final size:54
Alignment explanation
Indices: 20548704--20548964 Score: 289
Period size: 54 Copynumber: 4.9 Consensus size: 54
20548694 ACCCTTGATG
* * * * * *
20548704 GGTAAAATGACTAAAATGCCCAC-ATAGGGTAAAATGATCGTAATGCCTCTATAA
1 GGTAAAATGACCATAATACCC-CTATAGGGTAAAATGACCGTAATGCCCCTGTAA
20548758 GGTAAAATGACCATAATACCCCTATAGGGT-AAATGACCGTAATGCCCCTGT-A
1 GGTAAAATGACCATAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAA
* * * *
20548810 GTGTAAAATGACCATAATACCCCTTGTAGGGTAAAAT-AGTCGTAATGCCCTTGTAG
1 G-GTAAAATGACCATAATACCCC-TATAGGGTAAAATGA-CCGTAATGCCCCTGTAA
** * * * *
20548866 GGT-AAATGACGGTAATGCCCTTATAGGGTAAAACGACTGTAATGCCCCTGTAA
1 GGTAAAATGACCATAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAA
* *
20548919 GGTAAAATAACCGTAATACCCCTATAGGGTAAAATGACCGTAATGC
1 GGTAAAATGACCATAATACCCCTATAGGGTAAAATGACCGTAATGC
20548965 TCTGATGGGT
Statistics
Matches: 173, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
52 2 0.01
53 67 0.39
54 84 0.49
55 19 0.11
56 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (54 bp):
GGTAAAATGACCATAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAA
Found at i:20549196 original size:27 final size:27
Alignment explanation
Indices: 20549153--20549212 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
20549143 TGAAGTATTG
* *
20549153 TACTAGTGGCTCTGCCACA-ATCACTGT
1 TACTGGTGGCTCTGCCACATAT-ACTAT
20549180 TACTGGTGGCT-TAGCCACATATACTAT
1 TACTGGTGGCTCT-GCCACATATACTAT
20549207 TACTGG
1 TACTGG
20549213 CAGCTTTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 26 0.90
28 2 0.07
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACATATACTAT
Found at i:20549218 original size:27 final size:27
Alignment explanation
Indices: 20549166--20549218 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
20549156 TAGTGGCTCT
* **
20549166 GCCACAATCACTGTTACTGGTGGCTTA
1 GCCACAATCACTATTACTGGCAGCTTA
20549193 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
20549219 TGTCGGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTA
Found at i:20549297 original size:32 final size:32
Alignment explanation
Indices: 20549256--20549495 Score: 161
Period size: 32 Copynumber: 7.5 Consensus size: 32
20549246 GCTGCGATAC
*
20549256 TACTGATGGCTTTCTGCTGATCATAGTACCGT
1 TACTGATGGCTTTGTGCTGATCATAGTACCGT
* * *
20549288 TACTGATGGCTTCGTGCTGATCACAGTACCAT
1 TACTGATGGCTTTGTGCTGATCATAGTACCGT
* * *
20549320 TACTGATGGCTTTGTG-TCGATCATATTATCAT
1 TACTGATGGCTTTGTGCT-GATCATAGTACCGT
* * * * *
20549352 TA-TCGATGG-TTGTCTACCGATCAT-TTCACTGT
1 TACT-GATGGCTT-TGTGCTGATCATAGT-ACCGT
* ** * *
20549384 TACTGATGGCTGTGTGCCAATCATA-TCACTGC
1 TACTGATGGCTTTGTGCTGATCATAGT-ACCGT
* *
20549416 TATTGATGGCTTTGTGCTAATCAT-GTTACCGT
1 TACTGATGGCTTTGTGCTGATCATAG-TACCGT
* * * *
20549448 TACTGATGGCTGTGTGCCGATCATA-TCACTGC
1 TACTGATGGCTTTGTGCTGATCATAGT-ACCGT
20549480 TACTGATGGCTTTGTG
1 TACTGATGGCTTTGTG
20549496 ATAATCACAT
Statistics
Matches: 165, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
31 7 0.04
32 155 0.94
33 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCTGATCATAGTACCGT
Found at i:20549424 original size:64 final size:63
Alignment explanation
Indices: 20549382--20549502 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 63
20549372 TCATTTCACT
*
20549382 GTTACTGATGGCTGTGTGCCAATCATATCACTGCTATTGATGGCTTTGTGCTAATCATGTTACC
1 GTTACTGATGGCTGTGTGCCAATCATATCACTGCTACTGATGGC-TTGTGCTAATCATGTTACC
* *
20549446 GTTACTGATGGCTGTGTGCCGATCATATCACTGCTACTGATGGCTTTGTGATAATCA
1 GTTACTGATGGCTGTGTGCCAATCATATCACTGCTACTGATGGC-TTGTGCTAATCA
20549503 CATTACTGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (63 bp):
GTTACTGATGGCTGTGTGCCAATCATATCACTGCTACTGATGGCTTGTGCTAATCATGTTACC
Found at i:20560622 original size:18 final size:19
Alignment explanation
Indices: 20560592--20560628 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
20560582 GCATTCACAT
20560592 CTTTCCTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTTTCCA
20560611 CTTTCC-CTCTTCTTTCCA
1 CTTTCCTCTCTTCTTTCCA
20560629 TTCCAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTTTCCA
Found at i:20564411 original size:42 final size:42
Alignment explanation
Indices: 20564352--20564435 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
20564342 CAATCTAGCT
20564352 AAGGTACTAAGGCGATGCGAAGAAACAAACCTTGTACTTAAC
1 AAGGTACTAAGGCGATGCGAAGAAACAAACCTTGTACTTAAC
20564394 AAGGTACTAAGGCGATGCGAAGAAACAAACCTTGTACTTAAC
1 AAGGTACTAAGGCGATGCGAAGAAACAAACCTTGTACTTAAC
20564436 TGGGAAAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (42 bp):
AAGGTACTAAGGCGATGCGAAGAAACAAACCTTGTACTTAAC
Found at i:20591010 original size:3 final size:3
Alignment explanation
Indices: 20591002--20591040 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20590992 TTTAAATTCA
20591002 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20591041 TTCGTAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20592874 original size:4 final size:4
Alignment explanation
Indices: 20592858--20592908 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
20592848 TTACCATATT
* * * *
20592858 TTTA TTCA TTTA TTTA -TTA TTTA ATTA TTTT TTTAA TTTA TTTA TTAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
20592906 TTT
1 TTT
20592909 CCTTATTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 3 0.08
4 31 0.84
5 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:20592888 original size:29 final size:28
Alignment explanation
Indices: 20592854--20592989 Score: 115
Period size: 29 Copynumber: 4.9 Consensus size: 28
20592844 CTATTTACCA
20592854 TATTTTTATTCATTTATTTATTATTTAAT
1 TATTTTT-TTCATTTATTTATTATTTAAT
* **
20592883 TATTTTTTTAATTTATTTATTAATTTCCT
1 TATTTTTTTCATTTATTTATT-ATTTAAT
*
20592912 TATTTTTTTC-TTCTACTTA-T-TTTAATT
1 TATTTTTTTCATT-TATTTATTATTTAA-T
* *
20592939 TATTTTTTTCCATTTAGTAATT-TTATAAT
1 TATTTTTTT-CATTTATTTATTATT-TAAT
20592968 TATTTTTTT-A-TTA-TTATTATTT
1 TATTTTTTTCATTTATTTATTATTT
20592990 TGCATGATAC
Statistics
Matches: 89, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
25 5 0.06
26 8 0.09
27 11 0.12
28 21 0.24
29 41 0.46
30 3 0.03
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (28 bp):
TATTTTTTTCATTTATTTATTATTTAAT
Found at i:20594744 original size:6 final size:6
Alignment explanation
Indices: 20594733--20594819 Score: 147
Period size: 6 Copynumber: 14.0 Consensus size: 6
20594723 AGTTTATTTC
20594733 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
20594781 TTTTAT TTTTAT TTTTAT TTTTAGT TAATTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTA-T T--TTTAT TTTTAT
20594820 GTTCCTAAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
6 70 0.90
7 2 0.03
8 2 0.03
9 4 0.05
ACGTcount: A:0.18, C:0.00, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:20595452 original size:14 final size:14
Alignment explanation
Indices: 20595433--20595461 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20595423 CATACATTTT
20595433 TCATGTTCATTCTA
1 TCATGTTCATTCTA
20595447 TCATGTTCATTCTA
1 TCATGTTCATTCTA
20595461 T
1 T
20595462 TATTGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.52
Consensus pattern (14 bp):
TCATGTTCATTCTA
Found at i:20601261 original size:23 final size:22
Alignment explanation
Indices: 20601233--20601277 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20601223 AAATTAAATG
20601233 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
20601256 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
20601278 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:20601280 original size:19 final size:19
Alignment explanation
Indices: 20601256--20601368 Score: 181
Period size: 19 Copynumber: 5.8 Consensus size: 19
20601246 AATCATATCT
20601256 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
20601275 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
20601296 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
20601315 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
20601334 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
20601353 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
20601369 CCTGAAGATT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 67 0.78
21 19 0.22
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:20602277 original size:31 final size:31
Alignment explanation
Indices: 20602242--20602302 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20602232 AAAATTTTAA
*
20602242 AATTCGAAAAG-TAAAAAAATTAAAATTGATC
1 AATTC-AAAAGATAAAAAAACTAAAATTGATC
* *
20602273 AATTCAAAAGATATAGAAACTAAAATTGAT
1 AATTCAAAAGATAAAAAAACTAAAATTGAT
20602303 TAAATTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (31 bp):
AATTCAAAAGATAAAAAAACTAAAATTGATC
Found at i:20602979 original size:7 final size:7
Alignment explanation
Indices: 20602939--20602972 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
20602929 TTTCCTTCTG
*
20602939 TTTTTTG
1 TTTTTTA
20602946 TTTTTTA
1 TTTTTTA
20602953 TTTTTTA
1 TTTTTTA
20602960 TTTTTTA
1 TTTTTTA
20602967 TTTTTT
1 TTTTTT
20602973 CTATTTTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:20602979 original size:21 final size:21
Alignment explanation
Indices: 20602939--20602980 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20602929 TTTCCTTCTG
* *
20602939 TTTTTTGTTTTTTATTTTTTA
1 TTTTTTATTTTTTATATTTTA
*
20602960 TTTTTTATTTTTTCTATTTTA
1 TTTTTTATTTTTTATATTTTA
20602981 GTTCCCATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTTTATTTTTTATATTTTA
Found at i:20605888 original size:70 final size:70
Alignment explanation
Indices: 20605775--20605916 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 70
20605765 CGTGATCGTC
*
20605775 ATCAACATGTTGATTTCGATATGGAACACCATTATCAGGTTGATATATTCAATGTTGCTATAGAT
1 ATCAACATGTTGATTTCGATATGGAACACCATTATCAGGTTGATATATTCAATGCTGCTATAGAT
20605840 TCTCA
66 TCTCA
*
20605845 ATCAACATGTTGATTTCGATATGGAACACCATTATTAGGTTGATATATTCAATGCTGCTATAGAT
1 ATCAACATGTTGATTTCGATATGGAACACCATTATCAGGTTGATATATTCAATGCTGCTATAGAT
20605910 TCTCA
66 TCTCA
20605915 AT
1 AT
20605917 TTCTTGAGCG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (70 bp):
ATCAACATGTTGATTTCGATATGGAACACCATTATCAGGTTGATATATTCAATGCTGCTATAGAT
TCTCA
Found at i:20611196 original size:60 final size:60
Alignment explanation
Indices: 20611119--20611239 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
20611109 GAAGTCGTAT
*
20611119 ACTCAACACACCAGCTTTCGATTTCTTATCTATTTGAACTTAAACTTCTACTTACATCAA
1 ACTCAACACACCAGCTTTCGACTTCTTATCTATTTGAACTTAAACTTCTACTTACATCAA
* *
20611179 ACTCAACACACCGGCTTTCGACTTCTTATCTATTTGAACTTAAACTTTTACTTACATCAA
1 ACTCAACACACCAGCTTTCGACTTCTTATCTATTTGAACTTAAACTTCTACTTACATCAA
20611239 A
1 A
20611240 GTATATGAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.36
Consensus pattern (60 bp):
ACTCAACACACCAGCTTTCGACTTCTTATCTATTTGAACTTAAACTTCTACTTACATCAA
Found at i:20611402 original size:25 final size:24
Alignment explanation
Indices: 20611369--20611416 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
20611359 TGAGAGATTT
20611369 TTATTTTATTTAATATTAATATAA
1 TTATTTTATTTAATATTAATATAA
20611393 TTATATTTATTTAATATTAATATA
1 TTAT-TTTATTTAATATTAATATA
20611417 GAATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTTTATTTAATATTAATATAA
Found at i:20615244 original size:26 final size:27
Alignment explanation
Indices: 20615185--20615244 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
20615175 ATGTGTTTTT
* *
20615185 CTATTTTTTTAAAATAAAAAATGAAAA
1 CTATTTTCTGAAAATAAAAAATGAAAA
*
20615212 CTCTTTTCTGAAAAT-AAAAATAGAAAA
1 CTATTTTCTGAAAATAAAAAAT-GAAAA
20615239 -TATTTT
1 CTATTTT
20615245 AAAAAACCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (27 bp):
CTATTTTCTGAAAATAAAAAATGAAAA
Found at i:20620373 original size:21 final size:22
Alignment explanation
Indices: 20620348--20620391 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20620338 CAAATATAAG
*
20620348 TATTGTAT-TAACCAAATCATT
1 TATTGAATATAACCAAATCATT
20620369 TATTGAATATAACCAAATCATT
1 TATTGAATATAACCAAATCATT
20620391 T
1 T
20620392 TCAGATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTGAATATAACCAAATCATT
Found at i:20620386 original size:44 final size:44
Alignment explanation
Indices: 20620144--20620369 Score: 452
Period size: 44 Copynumber: 5.1 Consensus size: 44
20620134 GTCTCGACTT
20620144 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
20620188 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
20620232 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
20620276 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
20620320 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
20620364 TCATTT
1 TCATTT
20620370 ATTGAATATA
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 182 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.42
Consensus pattern (44 bp):
TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
Found at i:20621714 original size:5 final size:5
Alignment explanation
Indices: 20621704--20621729 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20621694 CTCAAAAATT
20621704 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
20621730 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:20621774 original size:13 final size:13
Alignment explanation
Indices: 20621753--20621803 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
20621743 CTACTCAAAT
20621753 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
* *
20621766 TTCTTAAAAGAAC
1 TTCTCAAAAGCAC
*
20621779 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
20621792 TTCTCAAAAGCA
1 TTCTCAAAAGCA
20621804 ATAAAGAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:20628151 original size:8 final size:8
Alignment explanation
Indices: 20628138--20628167 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
20628128 TCATTTAGCA
20628138 TCCAAGTG
1 TCCAAGTG
20628146 TCCAAGT-
1 TCCAAGTG
20628153 TCCAAGTG
1 TCCAAGTG
20628161 TCCAAGT
1 TCCAAGT
20628168 TTGACACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (8 bp):
TCCAAGTG
Found at i:20628158 original size:15 final size:15
Alignment explanation
Indices: 20628138--20628168 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20628128 TCATTTAGCA
20628138 TCCAAGTGTCCAAGT
1 TCCAAGTGTCCAAGT
20628153 TCCAAGTGTCCAAGT
1 TCCAAGTGTCCAAGT
20628168 T
1 T
20628169 TGACACTTTT
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:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (15 bp):
TCCAAGTGTCCAAGT
Found at i:20628761 original size:7 final size:8
Alignment explanation
Indices: 20628730--20628768 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
20628720 AAAATGTCAA
20628730 ACTCAAAT
1 ACTCAAAT
20628738 ACTCAAAT
1 ACTCAAAT
20628746 ACTCAAAT
1 ACTCAAAT
20628754 AC-CAAAT
1 ACTCAAAT
20628761 AC-CAAAT
1 ACTCAAAT
20628768 A
1 A
20628769 AAAATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.21
Consensus pattern (8 bp):
ACTCAAAT
Found at i:20635995 original size:23 final size:23
Alignment explanation
Indices: 20635955--20635998 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20635945 AATCTGGATT
*
20635955 TTAAAATTTGAAAGATAAAAAAA
1 TTAAAATTTGAAAAATAAAAAAA
* *
20635978 TTAAATTTTTAAAAATAAAAA
1 TTAAAATTTGAAAAATAAAAA
20635999 TAAAATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
TTAAAATTTGAAAAATAAAAAAA
Found at i:20636615 original size:20 final size:21
Alignment explanation
Indices: 20636577--20636615 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20636567 CATTCTTATT
*
20636577 TTAATATTAAATAAAGAAATA
1 TTAATATTAAACAAAGAAATA
*
20636598 TTAATA-TAAACAATGAAA
1 TTAATATTAAACAAAGAAA
20636616 CTTATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (21 bp):
TTAATATTAAACAAAGAAATA
Found at i:20644270 original size:7 final size:7
Alignment explanation
Indices: 20644258--20644283 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20644248 TATTTGTCTA
20644258 TATATTT
1 TATATTT
20644265 TATATTT
1 TATATTT
20644272 TATATTT
1 TATATTT
20644279 TATAT
1 TATAT
20644284 AAACGCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:20647120 original size:18 final size:18
Alignment explanation
Indices: 20647097--20647132 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20647087 CTCGGTTACT
*
20647097 ATGTTTCGTCAATTTTCA
1 ATGTTTCATCAATTTTCA
20647115 ATGTTTCATCAATTTTCA
1 ATGTTTCATCAATTTTCA
20647133 TACAATGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (18 bp):
ATGTTTCATCAATTTTCA
Found at i:20648824 original size:12 final size:12
Alignment explanation
Indices: 20648807--20648838 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
20648797 ATTTTTACCC
20648807 AATTTCTTCAAT
1 AATTTCTTCAAT
20648819 AATTTCTTCAAT
1 AATTTCTTCAAT
20648831 AATTTCTT
1 AATTTCTT
20648839 TTTCTAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTCTTCAAT
Found at i:20654153 original size:151 final size:150
Alignment explanation
Indices: 20653937--20654239 Score: 461
Period size: 151 Copynumber: 2.0 Consensus size: 150
20653927 TATTTTTTTT
20653937 AAAAAGAGAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAATCATTTTAAAGGAAAATTT-
1 AAAAAGAGAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAATCATTTTAAAGGAAAATTTA
*
20654001 AAATTTTAAAACAAAGTTTTAAT-TTTTTTAACTATTTCGAAATAAGAGT-TTTGATATTTAAGA
66 AAATTTTAAAACAAAGTTTTAATGTTTTTCAACTATTTCGAAATAA-A-TCTTTGATATTTAAG-
20654064 AAAATAGTGATTTTTAAAAAGAA
128 AAAATAGTGATTTTTAAAAAGAA
* *
20654087 AAAAAGA-AAGTTTAGATTTTTAAAAATAAAAATATGTGTTTTTTAGTCATTTTAAAGGAAAGTT
1 AAAAAGAGAAGTTTAGATTTTTAAAAATAAAAATA--TGTTTTTTAATCATTTTAAAGGAAAATT
* * *
20654151 TAAAATTTTAAAACAAAGTTTTGATGTTTTTCAACTATTTCGGAATAAATCTTTGATTTTTAAGA
64 TAAAATTTTAAAACAAAGTTTTAATGTTTTTCAACTATTTCGAAATAAATCTTTGATATTTAAGA
**
20654216 AAATAGTGATTTTTTTAAAGAA
129 AAATAGTGATTTTTAAAAAGAA
20654238 AA
1 AA
20654240 CTTTGATTTT
Statistics
Matches: 140, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
149 27 0.19
150 7 0.05
151 51 0.36
152 35 0.25
153 20 0.14
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.41
Consensus pattern (150 bp):
AAAAAGAGAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAATCATTTTAAAGGAAAATTTA
AAATTTTAAAACAAAGTTTTAATGTTTTTCAACTATTTCGAAATAAATCTTTGATATTTAAGAAA
ATAGTGATTTTTAAAAAGAA
Found at i:20654744 original size:10 final size:10
Alignment explanation
Indices: 20654729--20654792 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
20654719 CCCTTGTATA
20654729 ATTTTTATTT
1 ATTTTTATTT
20654739 ATTTTTATTT
1 ATTTTTATTT
* *
20654749 CGTCTTTATTT
1 -ATTTTTATTT
20654760 ATTTTTATGTCT
1 ATTTTTAT-T-T
*
20654772 ATTTATATTT
1 ATTTTTATTT
20654782 ATGTTTT-TTT
1 AT-TTTTATTT
20654792 A
1 A
20654793 CACATTCTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 23 0.52
11 13 0.30
12 8 0.18
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:20654792 original size:16 final size:16
Alignment explanation
Indices: 20654755--20654785 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20654745 ATTTCGTCTT
*
20654755 TATTTATTTTTATGTC
1 TATTTATATTTATGTC
20654771 TATTTATATTTATGT
1 TATTTATATTTATGT
20654786 TTTTTTACAC
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:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTTATATTTATGTC
Found at i:20659419 original size:30 final size:30
Alignment explanation
Indices: 20659337--20659422 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 30
20659327 TTTGAGGGAT
20659337 TTAATGAGAATTTTCAAAAAA-TTTGGTAGGC
1 TTAATGAGAA-TTT-AAAAAATTTTGGTAGGC
* * *
20659368 CTAATTAGAACTTTAACAAATTTTGG-AGGC
1 TTAATGAGAA-TTTAAAAAATTTTGGTAGGC
*
20659398 TTAATGAGAGTTCTAAAAAATTTTG
1 TTAATGAGAATT-TAAAAAATTTTG
20659423 AAATGCTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
29 2 0.04
30 27 0.60
31 16 0.36
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.36
Consensus pattern (30 bp):
TTAATGAGAATTTAAAAAATTTTGGTAGGC
Found at i:20659845 original size:22 final size:23
Alignment explanation
Indices: 20659800--20659847 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20659790 AATTTTATCA
* * *
20659800 TTTTAATAGATTATATTTATAAT
1 TTTTAAAAGATTATAATTAAAAT
20659823 TTTTAAAAGATTA-AATTAAAAT
1 TTTTAAAAGATTATAATTAAAAT
20659845 TTT
1 TTT
20659848 ATATAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTTAAAAGATTATAATTAAAAT
Found at i:20659882 original size:11 final size:11
Alignment explanation
Indices: 20659866--20659890 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20659856 GATCTAAATG
20659866 TAAAGTATGCA
1 TAAAGTATGCA
20659877 TAAAGTATGCA
1 TAAAGTATGCA
20659888 TAA
1 TAA
20659891 GAATATTATG
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (11 bp):
TAAAGTATGCA
Found at i:20660170 original size:45 final size:44
Alignment explanation
Indices: 20660081--20660178 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 44
20660071 ATTACAACAT
20660081 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
20660125 CATTCCATTCAACCAAACA-ATTGAATTACTATTAC-GTCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGT-TCTATTC
20660170 CATTCCATT
1 CATTCCATT
20660179 ACACCTCTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
43 1 0.02
44 24 0.48
45 25 0.50
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:20661391 original size:14 final size:15
Alignment explanation
Indices: 20661372--20661400 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20661362 CACCCCATTC
20661372 ACAGATACAG-AATA
1 ACAGATACAGTAATA
20661386 ACAGATACAGTAATA
1 ACAGATACAGTAATA
20661401 TCATGCATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (15 bp):
ACAGATACAGTAATA
Found at i:20667922 original size:102 final size:101
Alignment explanation
Indices: 20667722--20667955 Score: 326
Period size: 102 Copynumber: 2.3 Consensus size: 101
20667712 AGTTGCTAGG
* *
20667722 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATGAAAGGTCACATGTGTAGTAC
* *
20667787 TATGTGCAGGCTACTATACGTATCGAATAGCTTCGA
66 TATGTGCAGGCTACTACACGTACCGAATAGCTTCGA
* ** * * *
20667823 TCACGTGTGTGGTACTATGTATAGGCTACTACGTGTA-TCGGATGAAAATGGTCACGTGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATG-AAA-GGTCACATGTGTAGT
** *
20667887 ACTATGTGCAGGCTACTACGTGTACCGGATAGCTTCGA
64 ACTATGTGCAGGCTACTACACGTACCGAATAGCTTCGA
20667925 TCACGTGTGTAGTACTATGTGCAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
20667956 TGTGAACCGG
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
100 5 0.04
101 36 0.31
102 74 0.64
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATGAAAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTACACGTACCGAATAGCTTCGA
Found at i:20667965 original size:51 final size:51
Alignment explanation
Indices: 20667722--20667965 Score: 260
Period size: 51 Copynumber: 4.8 Consensus size: 51
20667712 AGTTGCTAGG
* * *
20667722 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGA-ATG-ATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GCATCGA
* * *** * * *
20667772 TCGCATGTGTAGTACTATGTGCAGGCTACTATACGTATCGAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGCATCGA
* ** * ** *
20667823 TCACGTGTGTGGTACTATGTATAGGCTACTACGTGTATCGGATGAAAAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-AGCATCGA
*
20667874 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGCATCGA
* *
20667925 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
20667966 GTATCATTTA
Statistics
Matches: 156, Mismatches: 34, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
50 37 0.24
51 117 0.75
52 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGCATCGA
Found at i:20672335 original size:20 final size:20
Alignment explanation
Indices: 20672296--20672335 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20672286 GATGTCAAAT
* *
20672296 TTTTGGGAAGAAAGAGAAAA
1 TTTTGAGAAGAAAAAGAAAA
*
20672316 TTTTGAGAAGAAAAATAAAA
1 TTTTGAGAAGAAAAAGAAAA
20672336 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (20 bp):
TTTTGAGAAGAAAAAGAAAA
Found at i:20672342 original size:6 final size:7
Alignment explanation
Indices: 20672326--20672353 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
20672316 TTTTGAGAAG
20672326 AAAAATA
1 AAAAATA
20672333 AAAAATA
1 AAAAATA
20672340 AAAAATA
1 AAAAATA
20672347 AAAAATA
1 AAAAATA
20672354 TTCGATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:20681388 original size:19 final size:21
Alignment explanation
Indices: 20681356--20681400 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
20681346 AACTTGTCTT
20681356 TTAT-ATTATCTTTTTTTAAA
1 TTATAATTATCTTTTTTTAAA
20681376 -TATAATTAT-TTTTTTTAAA
1 TTATAATTATCTTTTTTTAAA
20681395 TTATAA
1 TTATAA
20681401 ATAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATAATTATCTTTTTTTAAA
Found at i:20684856 original size:11 final size:11
Alignment explanation
Indices: 20684842--20684866 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20684832 AAAGAGGTAG
20684842 AGAATTACCAA
1 AGAATTACCAA
20684853 AGAATTACCAA
1 AGAATTACCAA
20684864 AGA
1 AGA
20684867 GGCGGAGAAA
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:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (11 bp):
AGAATTACCAA
Found at i:20688188 original size:16 final size:17
Alignment explanation
Indices: 20688164--20688199 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20688154 ACCTACAATT
*
20688164 ATAATTATAAATT-AGA
1 ATAAATATAAATTAAGA
20688180 ATAAATATAAATTAAGA
1 ATAAATATAAATTAAGA
20688197 ATA
1 ATA
20688200 GCAATAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATAAATATAAATTAAGA
Found at i:20688411 original size:31 final size:31
Alignment explanation
Indices: 20688376--20688440 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
20688366 TATAATTTGA
***
20688376 TCATTGAACTATTTGTAAGTTTTTAGTTAAG
1 TCATTGAACTATTAAAAAGTTTTTAGTTAAG
* *
20688407 TCATTGATCTATTAAAAAGTTTTTATTTAAG
1 TCATTGAACTATTAAAAAGTTTTTAGTTAAG
20688438 TCA
1 TCA
20688441 CTAAGTTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (31 bp):
TCATTGAACTATTAAAAAGTTTTTAGTTAAG
Found at i:20694116 original size:36 final size:36
Alignment explanation
Indices: 20694075--20694178 Score: 190
Period size: 36 Copynumber: 2.9 Consensus size: 36
20694065 CTTTAGCTAC
*
20694075 ACTTATCTGATCAAGTGAAAAAGTAATAAGTGTTAT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
20694111 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
*
20694147 ACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTG
20694179 GTAGCTTAGC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (36 bp):
ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
Found at i:20694162 original size:21 final size:21
Alignment explanation
Indices: 20694102--20694163 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
20694092 AAAAAGTAAT
20694102 AAGTGTTATACTTATCTGATC
1 AAGTGTTATACTTATCTGATC
* **
20694123 AAGTG--A-A--AAAGTGAT-
1 AAGTGTTATACTTATCTGATC
20694138 AAGTGTTATACTTATCTGATC
1 AAGTGTTATACTTATCTGATC
20694159 AAGTG
1 AAGTG
20694164 ACAAAGTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
15 5 0.17
16 5 0.17
17 1 0.03
18 2 0.07
19 1 0.03
20 5 0.17
21 10 0.34
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
AAGTGTTATACTTATCTGATC
Found at i:20702080 original size:21 final size:21
Alignment explanation
Indices: 20702056--20702096 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20702046 GAATTAAATT
20702056 AATATACATTTGAAGAATTAC
1 AATATACATTTGAAGAATTAC
* * *
20702077 AATATGCCTTTGATGAATTA
1 AATATACATTTGAAGAATTA
20702097 GCTATAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AATATACATTTGAAGAATTAC
Found at i:20707208 original size:28 final size:28
Alignment explanation
Indices: 20707177--20707233 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
20707167 CCAATTAGGG
20707177 GTTAAAT-TGTGAAA-TGTGAAAATTTTAT
1 GTTAAATGTGTGAAATTGTG--AATTTTAT
20707205 GTTAAATGTGTGAAATTGTGAATTTTAT
1 GTTAAATGTGTGAAATTGTGAATTTTAT
20707233 G
1 G
20707234 GGCTGATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 16 0.59
29 7 0.26
30 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (28 bp):
GTTAAATGTGTGAAATTGTGAATTTTAT
Found at i:20713658 original size:41 final size:42
Alignment explanation
Indices: 20713606--20713719 Score: 128
Period size: 42 Copynumber: 2.7 Consensus size: 42
20713596 AGTTAACTCA
*
20713606 TATGAGTTTCAGTTTAACCCTATTGGGTTTCTT-TT-AGCTCT
1 TATGAGCTTCAGTTTAACCCT-TTGGGTTTCTTGTTCAGCTCT
*
20713647 T-TCGAGCTTCAGTTTAACCCTTATGAGTTT-TTGTTCAGCTCT
1 TAT-GAGCTTCAGTTTAACCCTT-TGGGTTTCTTGTTCAGCTCT
* *
20713689 TATGAGCTTCCGTTCAACCCTTTTGGGTTTC
1 TATGAGCTTCAGTTTAACCC-TTTGGGTTTC
20713720 CGTTTAGCAC
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
40 4 0.07
41 26 0.43
42 28 0.46
43 3 0.05
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.46
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTTGGGTTTCTTGTTCAGCTCT
Found at i:20715412 original size:13 final size:14
Alignment explanation
Indices: 20715394--20715422 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20715384 TCCGATATAT
20715394 GTAAAATAAC-AAA
1 GTAAAATAACTAAA
20715407 GTAAAATAACTAAA
1 GTAAAATAACTAAA
20715421 GT
1 GT
20715423 TTAATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (14 bp):
GTAAAATAACTAAA
Found at i:20727836 original size:18 final size:18
Alignment explanation
Indices: 20727797--20727834 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
20727787 TCACATCAAT
20727797 AAATATTTAAAAATTAAA
1 AAATATTTAAAAATTAAA
20727815 AAATA-TTAAAAATTAAA
1 AAATATTTAAAAATTAAA
20727832 AAA
1 AAA
20727835 ATCAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATTTAAAAATTAAA
Found at i:20736982 original size:20 final size:20
Alignment explanation
Indices: 20736954--20736994 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20736944 ACTCTGTTGC
*
20736954 TTGAGTTTGCCGCTGGAATT
1 TTGACTTTGCCGCTGGAATT
* *
20736974 TTGACTTTGCTGCTTGAATT
1 TTGACTTTGCCGCTGGAATT
20736994 T
1 T
20736995 ACTGCTTGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGACTTTGCCGCTGGAATT
Found at i:20737886 original size:20 final size:20
Alignment explanation
Indices: 20737861--20737903 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
20737851 AAATAAAAGT
*
20737861 ATGGTGATTAAACAGGTGGC
1 ATGGTGATTAAACAGGCGGC
20737881 ATGGTGATTAAACAGGCGGC
1 ATGGTGATTAAACAGGCGGC
20737901 ATG
1 ATG
20737904 TATTAAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (20 bp):
ATGGTGATTAAACAGGCGGC
Found at i:20742586 original size:236 final size:236
Alignment explanation
Indices: 20742173--20742647 Score: 842
Period size: 236 Copynumber: 2.0 Consensus size: 236
20742163 TTATTGGGGG
* *
20742173 AAAACATACGGACTGTTGGCCTTGAATTAAGTAGGAGCATTTCCTCCGAGAAAGTAATTTAAGAA
1 AAAACATACGAACTGTTGGCCTTGAATTAAGTAGGAGCATTGCCTCCGAGAAAGTAATTTAAGAA
* *
20742238 AGTGCTCAAAAATTATATCCGGCCTTATAAAAAGTAGAATGATTAACTGAGGATGAACCCTATCG
66 AGTGCTCAAAAATTATATCCGACCTTATAAAAAGTAGAAGGATTAACTGAGGATGAACCCTATCG
* * * *
20742303 TGTATTGAGCAAAATTCCTGACTATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTTAG
131 TGCATTGAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
20742368 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
196 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
20742409 AAAACATACGAACTGTTGGCCTTGAATTAAGTAGGAGCATTGCCTCCGAGAAAGTAATTTAAGAA
1 AAAACATACGAACTGTTGGCCTTGAATTAAGTAGGAGCATTGCCTCCGAGAAAGTAATTTAAGAA
* * *
20742474 AGTGCTCAAAAATTATATCCGACCTTATAAAAAGTAGAAGGATTAATTGAGGATGAGCGCTATCG
66 AGTGCTCAAAAATTATATCCGACCTTATAAAAAGTAGAAGGATTAACTGAGGATGAACCCTATCG
*
20742539 TGCGTTGAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
131 TGCATTGAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
20742604 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
196 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
20742645 AAA
1 AAA
20742648 TCATGGTTGT
Statistics
Matches: 227, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
236 227 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (236 bp):
AAAACATACGAACTGTTGGCCTTGAATTAAGTAGGAGCATTGCCTCCGAGAAAGTAATTTAAGAA
AGTGCTCAAAAATTATATCCGACCTTATAAAAAGTAGAAGGATTAACTGAGGATGAACCCTATCG
TGCATTGAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
Found at i:20742958 original size:24 final size:24
Alignment explanation
Indices: 20742912--20742958 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20742902 AATATGTTAT
* *
20742912 TTATTATTTTTATAATATTATATA
1 TTATGATTTTTATAATATCATATA
20742936 TTATGATTTTTATTAAT-TCATAT
1 TTATGATTTTTA-TAATATCATAT
20742959 TTTAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATGATTTTTATAATATCATATA
Found at i:20743212 original size:16 final size:16
Alignment explanation
Indices: 20743193--20743241 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
20743183 AATTACTAAA
*
20743193 TACAACTCTAATCCAT
1 TACAACTCTATTCCAT
*
20743209 TACATCTCTATTCCAT
1 TACAACTCTATTCCAT
*
20743225 TACAACCCTATTCCAT
1 TACAACTCTATTCCAT
20743241 T
1 T
20743242 CACCCTAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.37
Consensus pattern (16 bp):
TACAACTCTATTCCAT
Found at i:20745704 original size:6 final size:6
Alignment explanation
Indices: 20745693--20745726 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
20745683 TTTTGAGCCT
*
20745693 TATATC TATATC TATATC TATATC TATATA TATA
1 TATATC TATATC TATATC TATATC TATATC TATA
20745727 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:20745790 original size:2 final size:2
Alignment explanation
Indices: 20745783--20745822 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
20745773 NNNNNNNNNN
20745783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20745823 TATTGGCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20747511 original size:321 final size:321
Alignment explanation
Indices: 20746929--20747572 Score: 1272
Period size: 321 Copynumber: 2.0 Consensus size: 321
20746919 TTGACAAGTC
20746929 AAGATAGTAGTATAAAAAACAGAGCAATTAACAACACATCATAAATTACGTGGTTTAGTCAATTG
1 AAGATAGTAGTATAAAAAACAGAGCAATTAACAACACATCATAAATTACGTGGTTTAGTCAATTG
20746994 TGAGACCAAATTCATACAAGTACGAAAAGAAAGAAATTAACAATACATTCAAATTCAATCAATTG
66 TGAGACCAAATTCATACAAGTACGAAAAGAAAGAAATTAACAATACATTCAAATTCAATCAATTG
20747059 TGAAGACATTTTCGCCAAAGTACTTGAAATCTCCCTCTTTTATAGGTTGAGTATTAAATTACTTC
131 TGAAGACATTTTCGCCAAAGTACTTGAAATCTCCCTCTTTTATAGGTTGAGTATTAAATTACTTC
20747124 TTATATTATATTAACTTTTTTTTAAATTTTAAGTAAATAAATATATAGTTATTAAATAATTTATT
196 TTATATTATATTAACTTTTTTTTAAATTTTAAGTAAATAAATATATAGTTATTAAATAATTTATT
20747189 GTAAAAAAAATATTATACTTGTTTAAAATTTGTTAACAATAAAAATAATATTGCATTATTA
261 GTAAAAAAAATATTATACTTGTTTAAAATTTGTTAACAATAAAAATAATATTGCATTATTA
20747250 AAGATAGTAGTATAAAAAACAGAGCAATTAACAACACATCATAAATTACGTGGTTTAGTCAATTG
1 AAGATAGTAGTATAAAAAACAGAGCAATTAACAACACATCATAAATTACGTGGTTTAGTCAATTG
20747315 TGAGACCAAATTCATACAAGTACGAAAAGAAAGAAATTAACAATACATTCAAATTCAATCAATTG
66 TGAGACCAAATTCATACAAGTACGAAAAGAAAGAAATTAACAATACATTCAAATTCAATCAATTG
20747380 TGAAGACATTTTCGCCAAAGTACTTGAAATCTCCCTCTTTTATAGGTTGAGTATTAAATTACTTC
131 TGAAGACATTTTCGCCAAAGTACTTGAAATCTCCCTCTTTTATAGGTTGAGTATTAAATTACTTC
20747445 TTATATTATATTAACTTTTTTTTAAATTTTAAGTAAATTAAATATATA-TTATTAAATAATTTAT
196 TTATATTATATTAACTTTTTTTTAAATTTTAAGTAAA-TAAATATATAGTTATTAAATAATTTAT
20747509 TGTAAAAAAAATATTATACTTGTTTAAAATTTGTTAACAATAAAAATAATATTGCATTATTA
260 TGTAAAAAAAATATTATACTTGTTTAAAATTTGTTAACAATAAAAATAATATTGCATTATTA
20747571 AA
1 AA
20747573 TATTTAAACA
Statistics
Matches: 322, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
321 312 0.97
322 10 0.03
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (321 bp):
AAGATAGTAGTATAAAAAACAGAGCAATTAACAACACATCATAAATTACGTGGTTTAGTCAATTG
TGAGACCAAATTCATACAAGTACGAAAAGAAAGAAATTAACAATACATTCAAATTCAATCAATTG
TGAAGACATTTTCGCCAAAGTACTTGAAATCTCCCTCTTTTATAGGTTGAGTATTAAATTACTTC
TTATATTATATTAACTTTTTTTTAAATTTTAAGTAAATAAATATATAGTTATTAAATAATTTATT
GTAAAAAAAATATTATACTTGTTTAAAATTTGTTAACAATAAAAATAATATTGCATTATTA
Found at i:20752641 original size:49 final size:49
Alignment explanation
Indices: 20752585--20752999 Score: 422
Period size: 49 Copynumber: 8.5 Consensus size: 49
20752575 CTATCTTGGT
* * *
20752585 TGGCCCGACAACGATTGCTTTCACTATCTGCATATTCTACCATCCCAGG
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAGG
* * * *
20752634 TGGCCCGACAACTATAGCTTTCACTATTTGCATATTCTACCAT-CCTGAA
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAG-G
* * *
20752683 TGGCCCGACAATGATGGTTTCCACTATTTGCATATTCTACCATCCC-GAG
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAG-G
* * * *
20752732 TGACCCGACAATGATGGTTTTCACTATTTGCATATTCTACCATCTCAGG
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAGG
* ** * * ***
20752781 TGGCTCGATTACAATAGTTTTCACTATTTACATATTCTACCATCTTGGG
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAGG
* *
20752830 TGGCCTGACAACGATGGTTTTCACTATTTGCATATTCTACCATCCCAGG
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAGG
* * * * * ***
20752879 TGGCTCGATAACGATAGTTTTCAGTATTTACATATTCTACTATCTTGGG
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAGG
* * * * *
20752928 TGGCCCGACAACAATGGCTTTCACTATTTACATATTCTACCAT-CCTGAG
1 TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAG-G
** *
20752977 TGGCCTAACAACGATGGTTTTCA
1 TGGCCCGACAACGATAGTTTTCA
20753000 ATCACTATAT
Statistics
Matches: 304, Mismatches: 58, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
48 4 0.01
49 297 0.98
50 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (49 bp):
TGGCCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCCCAGG
Found at i:20752840 original size:147 final size:147
Alignment explanation
Indices: 20752588--20752996 Score: 550
Period size: 147 Copynumber: 2.8 Consensus size: 147
20752578 TCTTGGTTGG
* * * * *
20752588 CCCGACAACGATTGCTTTCACTATCTGCATATTCTACCATCCCAGGTGGCCCGACAACTATAGCT
1 CCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCTCAGGTGGCCCGACAACAATAGCT
* * * *
20752653 TTCACTATTTGCATATTCTACCATCCTGAATGGCCCGACAATGATGGTTTCCACTATTTGCATAT
66 TTCACTATTTACATATTCTACCATCCTGAGTGGCCTGACAACGATGGTTTCCACTATTTGCATAT
20752718 TCTACCATCCC-GAGTGA
131 TCTACCATCCCAG-GTGA
* * * ** *
20752735 CCCGACAATGATGGTTTTCACTATTTGCATATTCTACCATCTCAGGTGGCTCGATTACAATAGTT
1 CCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCTCAGGTGGCCCGACAACAATAGCT
* * *
20752800 TTCACTATTTACATATTCTACCATCTTGGGTGGCCTGACAACGATGGTTTTCACTATTTGCATAT
66 TTCACTATTTACATATTCTACCATCCTGAGTGGCCTGACAACGATGGTTTCCACTATTTGCATAT
*
20752865 TCTACCATCCCAGGTGG
131 TCTACCATCCCAGGTGA
* * * * * ** *
20752882 CTCGATAACGATAGTTTTCAGTATTTACATATTCTACTATCTTGGGTGGCCCGACAACAATGGCT
1 CCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCTCAGGTGGCCCGACAACAATAGCT
*
20752947 TTCACTATTTACATATTCTACCATCCTGAGTGGCCTAACAACGATGGTTT
66 TTCACTATTTACATATTCTACCATCCTGAGTGGCCTGACAACGATGGTTT
20752997 TCAATCACTA
Statistics
Matches: 226, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
147 225 1.00
148 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (147 bp):
CCCGACAACGATAGTTTTCACTATTTGCATATTCTACCATCTCAGGTGGCCCGACAACAATAGCT
TTCACTATTTACATATTCTACCATCCTGAGTGGCCTGACAACGATGGTTTCCACTATTTGCATAT
TCTACCATCCCAGGTGA
Done.