Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 87 of 91
Found at i:33573208 original size:15 final size:15
Alignment explanation
Indices: 33573188--33573222 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33573178 GGTTAGTTGG
*
33573188 ATAATACCAATTTTT
1 ATAATACCAATGTTT
*
33573203 ATAATATCAATGTTT
1 ATAATACCAATGTTT
33573218 ATAAT
1 ATAAT
33573223 TTGTGGGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (15 bp):
ATAATACCAATGTTT
Found at i:33573796 original size:20 final size:20
Alignment explanation
Indices: 33573765--33573811 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
33573755 CTTCCAACTC
* * *
33573765 TTTCTCTTTCTTTTCTCTTTA
1 TTTCT-TTTCTTTCCCCTTAA
33573786 TTTCTTTTCTTTCCCCTTAA
1 TTTCTTTTCTTTCCCCTTAA
33573806 TTTCTT
1 TTTCTT
33573812 GTTCGTGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCTTTTCTTTCCCCTTAA
Found at i:33573984 original size:27 final size:27
Alignment explanation
Indices: 33573932--33573984 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
33573922 ATCAGGAAAA
*
33573932 TTTATTAATTAATAGATGAATGAATAG
1 TTTATTAATTAATACATGAATGAATAG
* * *
33573959 TTTATTAATTTATACATTAATTAATA
1 TTTATTAATTAATACATGAATGAATA
33573985 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTATTAATTAATACATGAATGAATAG
Found at i:33574538 original size:17 final size:18
Alignment explanation
Indices: 33574516--33574552 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
33574506 TAATTGTCAA
33574516 TATTTTTTAA-AATATAT
1 TATTTTTTAATAATATAT
*
33574533 TA-TTTTTAATAATATTT
1 TATTTTTTAATAATATAT
33574550 TAT
1 TAT
33574553 ATTAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTTAATAATATAT
Found at i:33595380 original size:15 final size:15
Alignment explanation
Indices: 33595356--33595411 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
33595346 AAATTAAAAT
33595356 AAAATGTATAATATAA
1 AAAAT-TATAATATAA
33595372 AAAATTAT-AT-TAA
1 AAAATTATAATATAA
* * *
33595385 AAAATAAAAATATAT
1 AAAATTATAATATAA
*
33595400 AAGATTATAATA
1 AAAATTATAATA
33595412 AGAAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
13 9 0.28
14 4 0.12
15 14 0.44
16 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (15 bp):
AAAATTATAATATAA
Found at i:33595397 original size:28 final size:28
Alignment explanation
Indices: 33595365--33595424 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
33595355 TAAAATGTAT
*
33595365 AATATAAAAAATTATATTAAAAAATAAA
1 AATATAAAAAATTATAATAAAAAATAAA
* * *
33595393 AATATATAAGATTATAATAAGAAATAAA
1 AATATAAAAAATTATAATAAAAAATAAA
33595421 AATA
1 AATA
33595425 ACATATATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (28 bp):
AATATAAAAAATTATAATAAAAAATAAA
Found at i:33595680 original size:15 final size:15
Alignment explanation
Indices: 33595651--33595698 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
33595641 TTTTTCCTGC
* *
33595651 AATCACATTATTTGT
1 AATCATATTACTTGT
*
33595666 AATTATATTACTTGT
1 AATCATATTACTTGT
33595681 AATCATATTACATTGT
1 AATCATATTAC-TTGT
33595697 AA
1 AA
33595699 AATACTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (15 bp):
AATCATATTACTTGT
Found at i:33607464 original size:2 final size:2
Alignment explanation
Indices: 33607457--33607488 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33607447 ATCAAACCAC
33607457 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
33607489 TTTGTGCAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33610227 original size:76 final size:76
Alignment explanation
Indices: 33610101--33610251 Score: 221
Period size: 76 Copynumber: 2.0 Consensus size: 76
33610091 TAAAAAATAG
* * *
33610101 ATAAGCTAAGAATAAGTTATGCCAAACAGGCACTAAGAAGTTTATGAGACTAGTAAGAGACTGAA
1 ATAAGCTAAAAATAAGTTAAGCCAAACAGGCACTAAGAAGTCTATGAGACTAGTAAGAGACTGAA
33610166 GAGATTCCATC
66 GAGATTCCATC
* * * * * *
33610177 ATAAGCTAAAAATACGTTAAGTCAAATAGGTACTAAGAAGTCTATGAGACTGGTAAGAGATTGAA
1 ATAAGCTAAAAATAAGTTAAGCCAAACAGGCACTAAGAAGTCTATGAGACTAGTAAGAGACTGAA
33610242 GAGATTCCAT
66 GAGATTCCAT
33610252 TGTTCTTTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (76 bp):
ATAAGCTAAAAATAAGTTAAGCCAAACAGGCACTAAGAAGTCTATGAGACTAGTAAGAGACTGAA
GAGATTCCATC
Found at i:33620212 original size:40 final size:40
Alignment explanation
Indices: 33620164--33620244 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
33620154 TTCTTGTTTG
*
33620164 TGAGCTTAACTGGCAGCAGGCCAAAGTCTGTTGCTTCTGA
1 TGAGCTTAACCGGCAGCAGGCCAAAGTCTGTTGCTTCTGA
33620204 TGAGCTTAACCGGCAGCAGGCCAAAGTCTGTTGCTTCTGA
1 TGAGCTTAACCGGCAGCAGGCCAAAGTCTGTTGCTTCTGA
33620244 T
1 T
33620245 TTTATCAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
TGAGCTTAACCGGCAGCAGGCCAAAGTCTGTTGCTTCTGA
Found at i:33622794 original size:21 final size:20
Alignment explanation
Indices: 33622753--33622794 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
33622743 TAATTTAGAT
**
33622753 TGTAATTTACTAATTATATA
1 TGTAATTTACTAAAGATATA
33622773 TGTAATTTACTAAAAGATATA
1 TGTAATTTACT-AAAGATATA
33622794 T
1 T
33622795 ATTCTCAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
TGTAATTTACTAAAGATATA
Found at i:33625899 original size:15 final size:15
Alignment explanation
Indices: 33625881--33625923 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 15
33625871 TAAAAAGTTT
33625881 AAATAAAAATTACAG
1 AAATAAAAATTACAG
33625896 AAATAATTCAAATTACAG
1 AAATAA---AAATTACAG
33625914 AAATATAAAA
1 AAATA-AAAA
33625924 AGTAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
18 14 0.58
19 1 0.04
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (15 bp):
AAATAAAAATTACAG
Found at i:33634310 original size:46 final size:46
Alignment explanation
Indices: 33634241--33634331 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
33634231 ATATAAATAG
* * *
33634241 TAAGATATTTACGATCTTGAGTTATATCTTAGATCATAATCATAAC
1 TAAGATACTAACGATCTTAAGTTATATCTTAGATCATAATCATAAC
*
33634287 TAAGATACTAACGATCTTAAGTTATATCTTAGATCATAATTATAA
1 TAAGATACTAACGATCTTAAGTTATATCTTAGATCATAATCATAA
33634332 TCATCGTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (46 bp):
TAAGATACTAACGATCTTAAGTTATATCTTAGATCATAATCATAAC
Found at i:33635890 original size:17 final size:18
Alignment explanation
Indices: 33635868--33635907 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
33635858 ATACGGCATG
33635868 TTCTTTGGTTTTT-TCCT
1 TTCTTTGGTTTTTGTCCT
**
33635885 TTCTTTTTTTTTTGTCCT
1 TTCTTTGGTTTTTGTCCT
33635903 TTCTT
1 TTCTT
33635908 CTTTTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.75
Consensus pattern (18 bp):
TTCTTTGGTTTTTGTCCT
Found at i:33635902 original size:18 final size:18
Alignment explanation
Indices: 33635876--33635913 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
33635866 TGTTCTTTGG
33635876 TTTTTTCCTTTCTT-TTT
1 TTTTTTCCTTTCTTCTTT
33635893 TTTTTGTCCTTTCTTCTTT
1 TTTTT-TCCTTTCTTCTTT
33635912 TT
1 TT
33635914 CATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTCCTTTCTTCTTT
Found at i:33635912 original size:17 final size:17
Alignment explanation
Indices: 33635876--33635913 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
33635866 TGTTCTTTGG
*
33635876 TTTTTTCCTTTCTTTTT
1 TTTTTTCCTTTCTTTCT
33635893 TTTTTGTCCTTTC-TTCT
1 TTTTT-TCCTTTCTTTCT
33635910 TTTT
1 TTTT
33635914 CATTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTTCCTTTCTTTCT
Found at i:33638516 original size:18 final size:19
Alignment explanation
Indices: 33638483--33638522 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
33638473 TTTATTTCAT
* *
33638483 TTAATTAAATTTTTA-TTA
1 TTAATTAAAATATTATTTA
33638501 TTAATTAAAATATTATTTA
1 TTAATTAAAATATTATTTA
33638520 TTA
1 TTA
33638523 TTTTATATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATTAAAATATTATTTA
Found at i:33648153 original size:2 final size:2
Alignment explanation
Indices: 33648146--33648178 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
33648136 TCATTTTTCG
33648146 TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
33648179 ATATATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:33649074 original size:2 final size:2
Alignment explanation
Indices: 33649067--33649110 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
33649057 CTCATATCCT
33649067 TA 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 TA
33649109 TA
1 TA
33649111 AATTGGATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33661700 original size:55 final size:53
Alignment explanation
Indices: 33661611--33661720 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 53
33661601 ATTCATCCAA
*
33661611 TTACGAGAGAGAGAGAGAGAGACTGCTTTATATGGATTCAGTTTAGTGTTTCTT
1 TTACTAGAGAGAGAGAGAGAGACTGCTTTATATGGATTCAGTTTAGTG-TTCTT
33661665 TNTACTAGAGAGAGAGAGAGAGACTGCTTTATATGGATTCAGTTTAGTGTTCTT
1 T-TACTAGAGAGAGAGAGAGAGACTGCTTTATATGGATTCAGTTTAGTGTTCTT
33661719 TT
1 TT
33661721 TTTTTTTTCT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
53 1 0.02
54 7 0.13
55 46 0.85
ACGTcount: A:0.27, C:0.09, G:0.26, T:0.36
Consensus pattern (53 bp):
TTACTAGAGAGAGAGAGAGAGACTGCTTTATATGGATTCAGTTTAGTGTTCTT
Found at i:33662017 original size:3 final size:3
Alignment explanation
Indices: 33662009--33662056 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
33661999 GTCACAGGAG
33662009 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
33662057 GTAAGATTAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33662205 original size:24 final size:24
Alignment explanation
Indices: 33662160--33662205 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
33662150 TATATTTCAT
*
33662160 TTAAAATAAAATCTAAAAAATTAA
1 TTAAAATAAAATCAAAAAAATTAA
*
33662184 TTAAAATATAAT-AAAAATAATT
1 TTAAAATAAAATCAAAAA-AATT
33662206 TTAAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
TTAAAATAAAATCAAAAAAATTAA
Found at i:33665221 original size:29 final size:29
Alignment explanation
Indices: 33665167--33665222 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
33665157 CTTCATGTGA
***
33665167 TACTATTTACTATATGTTTTTTTTTTAAG
1 TACTATTTACTATATGTTTAACTTTTAAG
33665196 TACTATTTACTATAT-TCTTAACTTTTA
1 TACTATTTACTATATGT-TTAACTTTTA
33665223 CTCCTCCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.59
Consensus pattern (29 bp):
TACTATTTACTATATGTTTAACTTTTAAG
Found at i:33665239 original size:2 final size:2
Alignment explanation
Indices: 33665232--33665344 Score: 87
Period size: 2 Copynumber: 58.5 Consensus size: 2
33665222 ACTCCTCCTC
* * *
33665232 TA TA TA TA TA TA TA TA TA TT TA TA TT TA -A NA 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 TA
** *
33665273 TA TA TA TA TA TA TA TA TA -A GT- TA -A GGG TA -A T- TGG TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA T-A TA TA
*
33665310 TA TA CA 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 T
33665345 TTGAATGGTT
Statistics
Matches: 90, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
1 7 0.08
2 82 0.91
3 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33671399 original size:18 final size:18
Alignment explanation
Indices: 33671376--33671411 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33671366 CATAAATTTT
33671376 ATTATTAGAATATTAAAA
1 ATTATTAGAATATTAAAA
* *
33671394 ATTATTATAATTTTAAAA
1 ATTATTAGAATATTAAAA
33671412 TTTTAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTATTAGAATATTAAAA
Found at i:33684910 original size:21 final size:19
Alignment explanation
Indices: 33684865--33684914 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
33684855 ATTATATTAA
* *
33684865 AAATTTTAAATATATTTTT
1 AAATTTTTATTATATTTTT
*
33684884 ATATTTTTATTATATTTAATT
1 AAATTTTTATTATATTT--TT
33684905 AAATTTTTAT
1 AAATTTTTAT
33684915 ATTTTTACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 14 0.56
21 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATTTTTATTATATTTTT
Found at i:33686523 original size:16 final size:15
Alignment explanation
Indices: 33686502--33686531 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33686492 TTTAAAAATT
33686502 TTAATTTAATATTAAA
1 TTAATTTAA-ATTAAA
33686518 TTAATTTAAATTAA
1 TTAATTTAAATTAA
33686532 TAAATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTTAAATTAAA
Found at i:33696588 original size:27 final size:27
Alignment explanation
Indices: 33696489--33696581 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
33696479 ACTTGTAGTC
* * * * *
33696489 GTAGTACCTGGAGCAAAGCTCACGGTC
1 GTAGTGCCTAGAGAAAAGCTCAGGGTT
* *
33696516 GTAGTGCCTGGAGAAAAGCTCATGGTT
1 GTAGTGCCTAGAGAAAAGCTCAGGGTT
*
33696543 GTAGTGCCTAGAGAAAAGCTCGGGGTT
1 GTAGTGCCTAGAGAAAAGCTCAGGGTT
33696570 GTAGTGCCTAGA
1 GTAGTGCCTAGA
33696582 CTAAAGCCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (27 bp):
GTAGTGCCTAGAGAAAAGCTCAGGGTT
Found at i:33703949 original size:50 final size:50
Alignment explanation
Indices: 33703895--33704001 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
33703885 CTAAAATAAA
*
33703895 AAAAAAAACC-TTCAAATCTAAAAAAACAACGCAACTTTGATATAAGGTGT
1 AAAAAAAACCTTTCAAATCT-AAAAAACAACGCAACTTTGACATAAGGTGT
* * * * * **
33703945 AAAAAAAACCTTTTAAATGTCAAAAACAATGTAGTTTTGACATAAGGTGT
1 AAAAAAAACCTTTCAAATCTAAAAAACAACGCAACTTTGACATAAGGTGT
33703995 AAAAAAA
1 AAAAAAA
33704002 GTTAATTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 41 0.85
51 7 0.15
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (50 bp):
AAAAAAAACCTTTCAAATCTAAAAAACAACGCAACTTTGACATAAGGTGT
Found at i:33704420 original size:10 final size:10
Alignment explanation
Indices: 33704405--33704434 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
33704395 TTGAAAAATC
33704405 AATTGAAACA
1 AATTGAAACA
*
33704415 AATTGAAAGA
1 AATTGAAACA
33704425 AATTGAAACA
1 AATTGAAACA
33704435 TCTTACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (10 bp):
AATTGAAACA
Found at i:33707981 original size:24 final size:23
Alignment explanation
Indices: 33707907--33707981 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 23
33707897 ATTAACTAAT
*
33707907 AATATTACAATATAATGTTAATTA
1 AATATTATAATATAAT-TTAATTA
* *
33707931 AATATTATAATATAA-TTACTAA
1 AATATTATAATATAATTTAATTA
*
33707953 CAATATTATAATACAAATTTAATTA
1 -AATATTATAATA-TAATTTAATTA
33707978 AATA
1 AATA
33707982 ATTTATAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 5 0.12
23 12 0.29
24 20 0.48
25 5 0.12
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (23 bp):
AATATTATAATATAATTTAATTA
Found at i:33710291 original size:2 final size:2
Alignment explanation
Indices: 33710284--33710328 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
33710274 TTAAAAAGGT
33710284 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33710326 GA G
1 GA G
33710329 GAGGAGGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33713418 original size:21 final size:21
Alignment explanation
Indices: 33713393--33713433 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33713383 TTAATTTTAA
33713393 AAAATTAAAATAATAAAAAAT
1 AAAATTAAAATAATAAAAAAT
* *
33713414 AAAATTCACATAATAAAAAA
1 AAAATTAAAATAATAAAAAA
33713434 AATGACAAAT
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:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAATTAAAATAATAAAAAAT
Found at i:33713589 original size:21 final size:22
Alignment explanation
Indices: 33713551--33713632 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 22
33713541 ATAGAAAAAA
33713551 AAATAATATATATATATTAAAT
1 AAATAATATATATATATTAAAT
*
33713573 AAATAAT-TATTTATATTAATTACT
1 AAATAATATATATATATTAA--A-T
*
33713597 AAATAA-A-A-ATCATTTTAAA-
1 AAATAATATATAT-ATATTAAAT
*
33713616 AAATATTATATATATAT
1 AAATAATATATATATAT
33713633 ATAGAGAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 17
0.68 0.07 0.25
Matches are distributed among these distances:
19 5 0.11
20 1 0.02
21 16 0.34
22 10 0.21
23 8 0.17
24 7 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATAATATATATATATTAAAT
Found at i:33720717 original size:31 final size:31
Alignment explanation
Indices: 33720676--33720734 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
33720666 AGAGCTAGAG
*
33720676 AGAGGTATTTCTTTACATAAAGAAAAAATAA
1 AGAGGGATTTCTTTACATAAAGAAAAAATAA
* *
33720707 AGAGGGATTTCTTTATATAAAGAGAAAA
1 AGAGGGATTTCTTTACATAAAGAAAAAA
33720735 GACTAACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (31 bp):
AGAGGGATTTCTTTACATAAAGAAAAAATAA
Found at i:33763690 original size:49 final size:49
Alignment explanation
Indices: 33763617--33763736 Score: 204
Period size: 49 Copynumber: 2.4 Consensus size: 49
33763607 AGTCAGCTAC
* *
33763617 ATGAACCATATCGGGCCACCGTGATACACATAGGTTTCCACCCAATTAT
1 ATGAACCATATCGGGCCACTGTGATACACATAGATTTCCACCCAATTAT
33763666 ATGAACCATATCGGGCCACTGTGATACACATAGATTTCCACCCAATTAT
1 ATGAACCATATCGGGCCACTGTGATACACATAGATTTCCACCCAATTAT
* *
33763715 ATGAACCATATCAGACCACTGT
1 ATGAACCATATCGGGCCACTGT
33763737 TTTCTATTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (49 bp):
ATGAACCATATCGGGCCACTGTGATACACATAGATTTCCACCCAATTAT
Found at i:33764136 original size:3 final size:3
Alignment explanation
Indices: 33764128--33764169 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
33764118 CATAGCATAG
33764128 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
33764170 ACATTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:33770446 original size:15 final size:17
Alignment explanation
Indices: 33770416--33770449 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
33770406 AATAAATTTT
33770416 ATTAAATAATTAATAAA
1 ATTAAATAATTAATAAA
33770433 ATTAAA-AA-TAATAAA
1 ATTAAATAATTAATAAA
33770448 AT
1 AT
33770450 GATATTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 2 0.12
17 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAAATAATTAATAAA
Found at i:33784157 original size:10 final size:11
Alignment explanation
Indices: 33784126--33784166 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
33784116 ATCTTACTTA
*
33784126 AATAA-TTTTA
1 AATAATTTTTT
33784136 AATAATTATTTT
1 AATAATT-TTTT
33784148 AATAATTTTTT
1 AATAATTTTTT
33784159 AA-AATTTT
1 AATAATTTT
33784167 ATAAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 11 0.39
11 7 0.25
12 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATAATTTTTT
Found at i:33784277 original size:31 final size:31
Alignment explanation
Indices: 33784215--33784277 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
33784205 AATTTTGCAC
* *
33784215 TTTTGTTTTGTTATATTTGATGTTATTATTA
1 TTTTGTTTTGTTATATTTGATATTATAATTA
33784246 TTTTGTTTTGTTATAATATT-ATATT-TAATTA
1 TTTTGTTTTGTTAT-AT-TTGATATTATAATTA
33784277 T
1 T
33784278 AAATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 20 0.71
32 6 0.21
33 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (31 bp):
TTTTGTTTTGTTATATTTGATATTATAATTA
Found at i:33787126 original size:2 final size:2
Alignment explanation
Indices: 33787119--33787143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33787109 CGATAAGTAA
33787119 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
33787144 ATTATGAGGT
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:33787641 original size:17 final size:18
Alignment explanation
Indices: 33787618--33787656 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
33787608 TTTTTAAAGG
33787618 AATTTTTTTTTTAGTCGA
1 AATTTTTTTTTTAGTCGA
*
33787636 ANTTTTTTTTTTAGTCGA
1 AATTTTTTTTTTAGTCGA
33787654 AAT
1 AAT
33787657 AGGTGTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.59
Consensus pattern (18 bp):
AATTTTTTTTTTAGTCGA
Found at i:33787863 original size:29 final size:29
Alignment explanation
Indices: 33787810--33787898 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 29
33787800 GTATTAAAGT
* * *
33787810 ATAACAAAATGTTTTTGAATGTGACGTGCA
1 ATAACAATAT-TTTTTCAATATGACGTGCA
*
33787840 ATAACAATATTTTTTCAATATGACGTGTA
1 ATAACAATATTTTTTCAATATGACGTGCA
*
33787869 ACAACAATATTTTTTTTTCAATATGACGTG
1 ATAACAATA---TTTTTTCAATATGACGTG
33787899 TAAAAATCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 24 0.47
30 9 0.18
32 18 0.35
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
ATAACAATATTTTTTCAATATGACGTGCA
Found at i:33787946 original size:45 final size:45
Alignment explanation
Indices: 33787915--33788305 Score: 387
Period size: 45 Copynumber: 8.8 Consensus size: 45
33787905 TCTAATTATA
*
33787915 ACGTGTCACATGTTTTTGTACATGACGTGTAACAACATAACCATG
1 ACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
* *
33787960 ACGTGTCACAT-TTTTTTTACATG-CGTGTAACAACCTAACCATG
1 ACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
* * * *
33788003 ACGTGTTACATGTTTAT-TACATGATGTGTAACAACCTAACCATG
1 ACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
*
33788047 ACGTGTCACATGTTTTTGTACATGACATGTAACAACTTAACCAT-
1 ACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
* * *
33788091 AGTGTGTCACATGTTTTTGTACATGACGTGTAATAACTTAATCATG
1 A-CGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
* * * *** *
33788137 ACGCGTCACGTATTTTTGTACATGGTATGTAACAACTTAATCATG
1 ACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
* * * * * *
33788182 ACGTGCCACGA-GTTTTTGTATATCATGTGTAACAACCTAATCATG
1 ACGTGTCAC-ATGTTTTTGTACATGACGTGTAACAACTTAACCATG
* * * * * * * * *
33788227 ATGCGCCACATGTTTTTGTATATGAAGTGCAATAACCTAACCATA
1 ACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
* * * * *
33788272 ACGTGTCATATGCTTTTATATATGGCGTGTAACA
1 ACGTGTCACATGTTTTTGTACATGACGTGTAACA
33788306 TATTTTTGTA
Statistics
Matches: 290, Mismatches: 49, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
43 35 0.12
44 51 0.18
45 203 0.70
46 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (45 bp):
ACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATG
Found at i:33788008 original size:21 final size:21
Alignment explanation
Indices: 33787979--33788052 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
33787969 ATTTTTTTTA
33787979 CATG-CGTGTAACAACCTAAC
1 CATGACGTGTAACAACCTAAC
* ***
33787999 CATGACGTGTTACATGTTTATTA-
1 CATGACGTGTAACA-ACCTA--AC
*
33788022 CATGATGTGTAACAACCTAAC
1 CATGACGTGTAACAACCTAAC
33788043 CATGACGTGT
1 CATGACGTGT
33788053 CACATGTTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 9
0.67 0.17 0.16
Matches are distributed among these distances:
20 5 0.13
21 17 0.44
22 4 0.10
23 12 0.31
24 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (21 bp):
CATGACGTGTAACAACCTAAC
Found at i:33788350 original size:69 final size:69
Alignment explanation
Indices: 33788234--33788372 Score: 188
Period size: 69 Copynumber: 2.0 Consensus size: 69
33788224 ATGATGCGCC
* * * * * *
33788234 ACATGTTTTTGTATATGAAGTGCAATAACCTAACCATAACGTGTCATATGCTTTTATATATGGCG
1 ACATATTTTTGTACATGAAGTGCAACAACCTAACCACAACGTGTCATATGCTTTTATACATGACG
33788299 TGTA
66 TGTA
* * * *
33788303 ACATATTTTTGTACATGACGTGTAACAACCTAACCACAACGTGTCATATGTTTTTGTACATGACG
1 ACATATTTTTGTACATGAAGTGCAACAACCTAACCACAACGTGTCATATGCTTTTATACATGACG
33788368 TGTA
66 TGTA
33788372 A
1 A
33788373 TAACCTAACC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (69 bp):
ACATATTTTTGTACATGAAGTGCAACAACCTAACCACAACGTGTCATATGCTTTTATACATGACG
TGTA
Found at i:33788399 original size:45 final size:45
Alignment explanation
Indices: 33788308--33788419 Score: 145
Period size: 45 Copynumber: 2.5 Consensus size: 45
33788298 GTGTAACATA
* * *
33788308 TTTTTGTACATGACGTGTAACAACCTAACCACAACGTGTCATATG
1 TTTTTGTACATGACGTGTAATAACCTAACCACAACCTATCATATG
**
33788353 TTTTTGTACATGACGTGTAATAACCTAACCATGACCTAT-ATCATG
1 TTTTTGTACATGACGTGTAATAACCTAACCACAACCTATCAT-ATG
* *
33788398 TTTTTGTATATGACGTATAATA
1 TTTTTGTACATGACGTGTAATA
33788420 TCATAACATG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 2 0.03
45 57 0.97
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (45 bp):
TTTTTGTACATGACGTGTAATAACCTAACCACAACCTATCATATG
Found at i:33788532 original size:30 final size:31
Alignment explanation
Indices: 33788464--33788538 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
33788454 ATAATTAAAG
* * *
33788464 TTATAAAAAATATTATTTTTTAAAACATCTT
1 TTATATAAAATATTATTTTTAAAAACACCTT
* * *
33788495 ATCTATAAAA-ATTATTTTTAAAAATACCTT
1 TTATATAAAATATTATTTTTAAAAACACCTT
33788525 TTATATAAATATAT
1 TTATATAAA-ATAT
33788539 CATCAGCTCC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
30 24 0.71
31 8 0.24
32 2 0.06
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (31 bp):
TTATATAAAATATTATTTTTAAAAACACCTT
Found at i:33802077 original size:2 final size:2
Alignment explanation
Indices: 33802070--33802108 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
33802060 TACTAATTCT
33802070 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
33802109 GTGGTTTTGG
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:33810991 original size:2 final size:2
Alignment explanation
Indices: 33810986--33811011 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33810976 TCTACCCTCC
33810986 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
33811012 GAATAAGAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33811822 original size:29 final size:27
Alignment explanation
Indices: 33811790--33811858 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 27
33811780 ATTATTATTC
**
33811790 ATAAAATTTTATTTATTTAAAATAAAAA
1 ATAAAATTTTATTTAAATAAAAT-AAAA
* * *
33811818 TATAAAAATTTAATTAAATATAATAAAA
1 -ATAAAATTTTATTTAAATAAAATAAAA
33811846 ATAAAATTTTATT
1 ATAAAATTTTATT
33811859 CAAAAATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 11 0.33
28 4 0.12
29 18 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAAAATTTTATTTAAATAAAATAAAA
Found at i:33811828 original size:21 final size:21
Alignment explanation
Indices: 33811804--33811847 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33811794 AATTTTATTT
33811804 ATTTAAAATAAAAAT-ATAAAA
1 ATTT-AAATAAAAATAATAAAA
* *
33811825 ATTTAATTAAATATAATAAAA
1 ATTTAAATAAAAATAATAAAA
33811846 AT
1 AT
33811848 AAAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTTAAATAAAAATAATAAAA
Found at i:33811851 original size:26 final size:25
Alignment explanation
Indices: 33811800--33811856 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
33811790 ATAAAATTTT
* *
33811800 ATTTATTTAAAATAAAAATATAAAA
1 ATTTAATTAAAATAAAAAAATAAAA
33811825 ATTTAATTAAATATAATAAAAATAAAA
1 ATTTAATTAAA-ATAA-AAAAATAAAA
*
33811852 TTTTA
1 ATTTA
33811857 TTCAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 10 0.37
26 4 0.15
27 13 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTTAATTAAAATAAAAAAATAAAA
Found at i:33817892 original size:2 final size:2
Alignment explanation
Indices: 33817846--33817878 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33817836 ACGTATATCT
33817846 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 T
33817879 CAACCAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33819284 original size:2 final size:2
Alignment explanation
Indices: 33819277--33819303 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33819267 CATCTACAAG
33819277 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
33819304 TATATAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:33821875 original size:24 final size:25
Alignment explanation
Indices: 33821833--33821879 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
33821823 TTATTTGCCC
* *
33821833 TTTTCTTTTTATTTGTTGGGTACAA
1 TTTTCTTTTTACTTCTTGGGTACAA
33821858 TTTTC-TTTTACTTCTTGGGTAC
1 TTTTCTTTTTACTTCTTGGGTAC
33821880 TATTCAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.60
Consensus pattern (25 bp):
TTTTCTTTTTACTTCTTGGGTACAA
Found at i:33830819 original size:2 final size:2
Alignment explanation
Indices: 33830812--33830836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33830802 GTACAAGAAT
33830812 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 T
33830837 TTTGTAAGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33831541 original size:13 final size:13
Alignment explanation
Indices: 33831523--33831550 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33831513 CCGGCATCCC
33831523 ATTATTATTATTA
1 ATTATTATTATTA
33831536 ATTATTATTATTA
1 ATTATTATTATTA
33831549 AT
1 AT
33831551 GAAAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:33842741 original size:232 final size:226
Alignment explanation
Indices: 33842335--33842792 Score: 756
Period size: 232 Copynumber: 2.0 Consensus size: 226
33842325 AATAGCTGGG
* *
33842335 CATGTTTTTGCTTATTGGTATTGGTTCACTTGCTGTTTCGAACTTCTGGTGATCAAAGAAGTTTT
1 CATGTTTTTGCTTATCGGTAGTGGTTCACTTGCTGTTTCGAACTTCTGGTGATCAAAGAAGTTTT
* *
33842400 TGATTCAGGGATTTAATGGTCTTGGATGTGATTTTCTTTGTTAATTTGACATTGTTTAGGTCAAT
66 TGATTCAGGGATTTAATGGTCTTGGATGTGATCTTCTTTGTTAATTTAACATTGTTTAGGTCAAT
33842465 GTAAGTAATGGCATGGGTAATGGTATTGTTCAGGCAGGAAAAAGTTCCACATGGAAATGTTTAGG
131 GTAAGTAATGGCATGGGTAATGGTATTGTTCAGGCAGGAAAAAGTTCCACATGG-AA----TAGG
33842530 AGCCAAACATTTCAGAAAAAAAAGTGCTTTTCCTATA
191 AGCCAAACATTTCAG-AAAAAAAGTGCTTTTCCTATA
*
33842567 CATGTTTTTGCTTATCGGTAGTGGTTCACTTGCTG-TTCTGAACTTTTGGTGATCAAAGAAGTTT
1 CATGTTTTTGCTTATCGGTAGTGGTTCACTTGCTGTTTC-GAACTTCTGGTGATCAAAGAAGTTT
* *
33842631 TTGATTCAGGGCTTTAATGGTCTTGGATGTGATCTTCTTTGTTAATTTAACATTGTTTTGGTCAA
65 TTGATTCAGGGATTTAATGGTCTTGGATGTGATCTTCTTTGTTAATTTAACATTGTTTAGGTCAA
* *
33842696 TGTAAGTAATGGCATGGGTAATGGTATTGTTCTGGCTGGAAAAAGTTCCACATGGAATAGGAGCC
130 TGTAAGTAATGGCATGGGTAATGGTATTGTTCAGGCAGGAAAAAGTTCCACATGGAATAGGAGCC
*
33842761 AAACATTTCAGAAAAAAAGTGCTTTTCTTATA
195 AAACATTTCAGAAAAAAAGTGCTTTTCCTATA
33842793 AGGCTTTAGC
Statistics
Matches: 215, Mismatches: 10, Indels: 8
0.92 0.04 0.03
Matches are distributed among these distances:
226 20 0.09
227 19 0.09
231 5 0.02
232 171 0.80
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (226 bp):
CATGTTTTTGCTTATCGGTAGTGGTTCACTTGCTGTTTCGAACTTCTGGTGATCAAAGAAGTTTT
TGATTCAGGGATTTAATGGTCTTGGATGTGATCTTCTTTGTTAATTTAACATTGTTTAGGTCAAT
GTAAGTAATGGCATGGGTAATGGTATTGTTCAGGCAGGAAAAAGTTCCACATGGAATAGGAGCCA
AACATTTCAGAAAAAAAGTGCTTTTCCTATA
Found at i:33851209 original size:31 final size:31
Alignment explanation
Indices: 33851172--33851245 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
33851162 TAGATAATAT
*
33851172 ATGATGTGAATTATCAAAACGAACAAGGTAG
1 ATGATGTGAAGTATCAAAACGAACAAGGTAG
33851203 ATGATGTGAAGTATCAAAACGAACAAGGTAG
1 ATGATGTGAAGTATCAAAACGAACAAGGTAG
33851234 ATGATGTGAAGT
1 ATGATGTGAAGT
33851246 GAGTTATAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.43, C:0.08, G:0.26, T:0.23
Consensus pattern (31 bp):
ATGATGTGAAGTATCAAAACGAACAAGGTAG
Found at i:33852891 original size:29 final size:29
Alignment explanation
Indices: 33852857--33852915 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
33852847 TTTTCTGTAC
33852857 ATTTTCTCCATTGCTAATGGTTGTACCTA
1 ATTTTCTCCATTGCTAATGGTTGTACCTA
* *
33852886 ATTTTCTCCATTGCTATTTGTTGTACCTA
1 ATTTTCTCCATTGCTAATGGTTGTACCTA
33852915 A
1 A
33852916 AATTCGAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (29 bp):
ATTTTCTCCATTGCTAATGGTTGTACCTA
Found at i:33857399 original size:30 final size:28
Alignment explanation
Indices: 33857359--33857444 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 28
33857349 TATTAAACTA
*
33857359 AAAAAATTATTTAATTTAAAATAAAAATAT
1 AAAAAATTATTTAA-ATAAAATAAAAAT-T
* *
33857389 AAAAATTTATTTAAATACAATAAAAATT
1 AAAAAATTATTTAAATAAAATAAAAATT
*
33857417 AAAAAACCTTAATTAAAT-AAATAAAAAT
1 AAAAAA--TTATTTAAATAAAATAAAAAT
33857445 AATACAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
28 6 0.12
29 20 0.42
30 22 0.46
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAAAATTATTTAAATAAAATAAAAATT
Found at i:33857410 original size:29 final size:29
Alignment explanation
Indices: 33857357--33857454 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
33857347 TTTATTAAAC
*
33857357 TAAAAAAATTATTTAATTTAAAATAAAAATA
1 TAAAAAAATTATTTAA-AT-AAATAAAAATA
*
33857388 T-AAAAATTTATTTAAATACAATAAAAAT-
1 TAAAAAAATTATTTAAATA-AATAAAAATA
* *
33857416 TAAAAAACCTTAATTAAATAAATAAAAATAA
1 TAAAAAA-ATTATTTAAATAAATAAAAAT-A
*
33857447 TACAAAAA
1 TAAAAAAA
33857455 CCTTTTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 2 0.04
29 24 0.43
30 23 0.41
31 7 0.12
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (29 bp):
TAAAAAAATTATTTAAATAAATAAAAATA
Found at i:33858300 original size:7 final size:7
Alignment explanation
Indices: 33858288--33858332 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
33858278 GATGATGATG
*
33858288 GTGGTGA
1 GTGGCGA
*
33858295 GTGGTGA
1 GTGGCGA
33858302 GTGGCGA
1 GTGGCGA
33858309 GTGGCGA
1 GTGGCGA
33858316 GTGGCGA
1 GTGGCGA
33858323 GTGGCGA
1 GTGGCGA
33858330 GTG
1 GTG
33858333 TATGTACAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.13, C:0.09, G:0.58, T:0.20
Consensus pattern (7 bp):
GTGGCGA
Found at i:33888809 original size:2 final size:2
Alignment explanation
Indices: 33888802--33888859 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
33888792 TGTACAATGA
33888802 AT AT AT AT A- AT -T AT AT AT AT AT AT AT -T AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
33888840 AT AT AT A- AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
33888860 GTAGTCTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
1 5 0.10
2 45 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33888827 original size:20 final size:19
Alignment explanation
Indices: 33888802--33888859 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 19
33888792 TGTACAATGA
33888802 ATATATATAAT-TATATAT
1 ATATATATAATATATATAT
*
33888820 ATATATATTATATATAT-T
1 ATATATATAATATATATAT
*
33888838 ATATATATAAAATATATAT
1 ATATATATAATATATATAT
33888857 ATA
1 ATA
33888860 GTAGTCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 26 0.74
19 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATATAATATATATAT
Found at i:33892324 original size:42 final size:42
Alignment explanation
Indices: 33892277--33892452 Score: 111
Period size: 40 Copynumber: 4.2 Consensus size: 42
33892267 TAAATATTAA
* *
33892277 TATTTTATTTAATTTAAATATTATTATGATTAATTTTTATTT
1 TATTTTATTTAATTAAAATATTATTATGATTAATTTATATTT
* *
33892319 TATTTTATTT--TTAAAATATTAATAATTGA-TAATTTAAATATTAA
1 TATTTTATTTAATTAAAATATT-ATTA-TGATTAATTT--ATATT-T
* * * * *
33892363 TATTTTATTTATAATTTAATTATT-TATAT-TTTAA--AATATCAT
1 TATTTTA-TT-TAATTAAAATATTAT-TATGATTAATTTATAT-TT
*
33892405 TATTTTATTTAATTAAAATATTATTATGATCAA--T-TATTT
1 TATTTTATTTAATTAAAATATTATTATGATTAATTTATATTT
33892444 TATTTTATT
1 TATTTTATT
33892453 CTTAAATATT
Statistics
Matches: 103, Mismatches: 17, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
39 10 0.10
40 26 0.25
41 15 0.15
42 24 0.23
43 4 0.04
44 7 0.07
45 2 0.02
46 6 0.06
47 1 0.01
48 8 0.08
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (42 bp):
TATTTTATTTAATTAAAATATTATTATGATTAATTTATATTT
Found at i:33892378 original size:26 final size:26
Alignment explanation
Indices: 33892347--33892776 Score: 101
Period size: 26 Copynumber: 16.8 Consensus size: 26
33892337 TTAATAATTG
33892347 ATAATTTAAATATTAATATTTTATTT
1 ATAATTTAAATATTAATATTTTATTT
* *
33892373 ATAATTTAATTATTTATATTTTA---
1 ATAATTTAAATATTAATATTTTATTT
* * * * *
33892396 A-AATATCATTATT-TTA-TTTAATT
1 ATAATTTAAATATTAATATTTTATTT
* * *
33892419 AAAATATTATTATGATCAATTATTTTATTT
1 ATAAT-TTA-AAT-ATTAA-TATTTTATTT
* *
33892449 -TATTCTTAAATATTATTAATTGATTATTT
1 ATAAT-TTAAATATTAAT-ATT--TTATTT
* **
33892478 AT--TTCAAATATTAATA----ATAG
1 ATAATTTAAATATTAATATTTTATTT
* *
33892498 ATCATTTAAACATTAATATTTTATTT
1 ATAATTTAAATATTAATATTTTATTT
33892524 ATAATTT-AATCATTAATATTTT-TATT
1 ATAATTTAAAT-ATTAATATTTTAT-TT
* *
33892550 -TAATTTAAATATTATTATTAT-TTT
1 ATAATTTAAATATTAATATTTTATTT
** *
33892574 ATTTTTTAAATATTAATAATTGGTAATTT
1 ATAATTTAAATATTAAT-ATT--TTATTT
* *
33892603 AT--TTAAAATATTAATA----ATTG
1 ATAATTTAAATATTAATATTTTATTT
* *
33892623 ATGATTTAATTATTAATATTTTA--T
1 ATAATTTAAATATTAATATTTTATTT
* *
33892647 ATAATTTAAATGATATTATGCTTATTTATTT
1 ATAATTTAAAT-AT-TAAT--AT-TTTATTT
* ** * ** *
33892678 TTAATTTATTTTTTAAATAGAAATAATTT
1 ATAATTTAAATATT-AAT--ATTTTATTT
** *
33892707 ATAATTTATTTTATTAATA----ATTG
1 ATAATTTA-AATATTAATATTTTATTT
*
33892730 ATAATTTAAATATCAATATTTTATTT
1 ATAATTTAAATATTAATATTTTATTT
33892756 ATAATTT-AATATTAATATTTT
1 ATAATTTAAATATTAATATTTT
33892777 TAAATATTAA
Statistics
Matches: 294, Mismatches: 63, Indels: 95
0.65 0.14 0.21
Matches are distributed among these distances:
20 13 0.04
21 2 0.01
22 41 0.14
23 13 0.04
24 14 0.05
25 48 0.16
26 66 0.22
27 31 0.11
28 4 0.01
29 38 0.13
30 15 0.05
31 9 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
ATAATTTAAATATTAATATTTTATTT
Found at i:33892406 original size:22 final size:22
Alignment explanation
Indices: 33892322--33892414 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 22
33892312 TTTATTTTAT
*
33892322 TTTAT-TTTTAAAATATTAATAA
1 TTTATATTTTAAAATA-TAATTA
* *
33892344 TTGATAATTT-AAATATTAA-TA
1 TTTATATTTTAAAATA-TAATTA
* *
33892365 TTT-TA-TTTATAATTTAATTA
1 TTTATATTTTAAAATATAATTA
*
33892385 TTTATATTTTAAAATATCATTA
1 TTTATATTTTAAAATATAATTA
33892407 TTT-TATTT
1 TTTATATTT
33892415 AATTAAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
19 6 0.11
20 10 0.18
21 10 0.18
22 28 0.49
23 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (22 bp):
TTTATATTTTAAAATATAATTA
Found at i:33892408 original size:86 final size:86
Alignment explanation
Indices: 33892237--33892427 Score: 219
Period size: 86 Copynumber: 2.2 Consensus size: 86
33892227 ATAATCTAGA
*
33892237 ATTTAGTTAAAACATTAATAAATAATAATTTAAATATTAATATTTTATTTAATTTAAATATTATT
1 ATTTA-TTAAAATATTAATAAATAATAATTTAAATATTAATATTTTATTTAATTTAAATATTATT
** *
33892302 ATGATTAATTTTTATTTTATTTT
65 ATGATTAA-TAATATATTATTTT
* * *
33892325 ATTT-TTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATTATT-T
1 ATTTATTAAAATATTAATAAATAATAATTTAAATATTAATATTTTA-TT-TAATTTAAATATTAT
*
33892388 ATAT-TTTAA-AATATCATTATTTT
64 -TATGATTAATAATAT-ATTATTTT
33892411 ATTTAATTAAAATATTA
1 ATTT-ATTAAAATATTA
33892428 TTATGATCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
85 3 0.03
86 49 0.55
87 7 0.08
88 30 0.34
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (86 bp):
ATTTATTAAAATATTAATAAATAATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTA
TGATTAATAATATATTATTTT
Found at i:33892488 original size:27 final size:28
Alignment explanation
Indices: 33892447--33892505 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
33892437 ATTATTTTAT
* * * *
33892447 TTTATTCTTAAATATTATTAATTGATTA
1 TTTATTCTCAAATATTAATAATAGATCA
33892475 TTTATT-TCAAATATTAATAATAGATCA
1 TTTATTCTCAAATATTAATAATAGATCA
33892502 TTTA
1 TTTA
33892506 AACATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTATTCTCAAATATTAATAATAGATCA
Found at i:33892594 original size:125 final size:120
Alignment explanation
Indices: 33892437--33892796 Score: 374
Period size: 125 Copynumber: 3.1 Consensus size: 120
33892427 ATTATGATCA
* * * *
33892437 ATTATT-TTATTTTA-TTCTTAAATATTATTAATTGATTATTTATTTCAAATATTAATAATAGAT
1 ATTATTATTATTTTATTTTTTAAATATTAATAATTGATAATTTATTT-AAATATTAATAATTGAT
* * *
33892500 CATTTAAACATTAATATTTTATTTATAATTTAATCATTAATATTTTTATTTAATTTAAAT
65 AATTTAAATATTAATATTTTATTTATAATTTAAT-ATTAATATTTTTACTT-ATTT--AT
*
33892560 ATTATTATTATTTTATTTTTTAAATATTAATAATTGGTAATTTATTTAAAATATTAATAATTGAT
1 ATTATTATTATTTTATTTTTTAAATATTAATAATTGATAATTTATTT-AAATATTAATAATTGAT
* * * * *
33892625 GATTTAATTATTAATATTTTA--TATAATTTAA-A-TGATA-TTATGCTTATTTAT
65 AATTTAAATATTAATATTTTATTTATAATTTAATATTAATATTTTTACTTATTTAT
** *
33892676 -TT-TTA--A-TTTATTTTTTAAATAGAAATAATTTATAATTTATTT---TATTAATAATTGATA
1 ATTATTATTATTTTATTTTTTAAATATTAATAATTGATAATTTATTTAAATATTAATAATTGATA
* ** *
33892733 ATTTAAATATCAATATTTTATTTATAATTTAATATTAATATTTTTAAATATTAAT
66 ATTTAAATATTAATATTTTATTTATAATTTAATATTAATATTTTTACTTATTTAT
33892788 ATT-TTATTA
1 ATTATTATTA
33892797 AAAATTAGAA
Statistics
Matches: 201, Mismatches: 26, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
107 32 0.16
109 10 0.05
110 1 0.00
111 36 0.18
112 10 0.05
113 5 0.02
114 3 0.01
115 3 0.01
116 2 0.01
118 4 0.02
119 5 0.02
120 4 0.02
121 1 0.00
123 16 0.08
124 8 0.04
125 61 0.30
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (120 bp):
ATTATTATTATTTTATTTTTTAAATATTAATAATTGATAATTTATTTAAATATTAATAATTGATA
ATTTAAATATTAATATTTTATTTATAATTTAATATTAATATTTTTACTTATTTAT
Found at i:33892629 original size:27 final size:26
Alignment explanation
Indices: 33892574--33892630 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
33892564 TTATTATTTT
*
33892574 ATTT-TTTAAATATTAATAATTGGTA
1 ATTTATTTAAATATTAATAATTGATA
*
33892599 ATTTATTTAAAATATTAATAATTGATG
1 ATTTATTT-AAATATTAATAATTGATA
33892626 ATTTA
1 ATTTA
33892631 ATTATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 21 0.75
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:33892750 original size:107 final size:109
Alignment explanation
Indices: 33892561--33892764 Score: 277
Period size: 111 Copynumber: 1.9 Consensus size: 109
33892551 AATTTAAATA
* ** * *
33892561 TTATTATTATTTTATTTTTTAAATATTAATAATTGGTAATTTATTTAAAATATTAATAATTGATG
1 TTATTATTAATTTATTTTTTAAATAGAAATAATTGATAATTTATTT---ATATTAATAATTGATA
* *
33892626 ATTTAATTATTAATATTTTA-TATAATTTAAATGATATTATGCTTAT
63 ATTTAAATATCAATATTTTATTATAATTTAAATGATATTATGCTTAT
* *
33892672 TTATTTTTAATTTATTTTTTAAATAGAAATAATTTATAATTTATTT-TATTAATAATTGATAATT
1 TTATTATTAATTTATTTTTTAAATAGAAATAATTGATAATTTATTTATATTAATAATTGATAATT
33892736 TAAATATCAATATTTTATTTATAATTTAA
66 TAAATATCAATATTTTA-TTATAATTTAA
33892765 TATTAATATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
107 32 0.39
109 10 0.12
111 40 0.49
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (109 bp):
TTATTATTAATTTATTTTTTAAATAGAAATAATTGATAATTTATTTATATTAATAATTGATAATT
TAAATATCAATATTTTATTATAATTTAAATGATATTATGCTTAT
Found at i:33898256 original size:22 final size:22
Alignment explanation
Indices: 33898224--33898302 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 22
33898214 TTAAATTATA
*
33898224 AATAAAATATTAATATTTAAAT
1 AATAAATTATTAATATTTAAAT
*
33898246 GATAAATTATTAATATTATAAAT
1 AATAAATTATTAATATT-TAAAT
*
33898269 AAAATATAAATTATTAATATTTAAAA
1 ---A-ATAAATTATTAATATTTAAAT
33898295 AATAAATT
1 AATAAATT
33898303 GAAATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
22 22 0.46
23 6 0.12
26 4 0.08
27 16 0.33
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
AATAAATTATTAATATTTAAAT
Found at i:33898279 original size:27 final size:27
Alignment explanation
Indices: 33898242--33898293 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
33898232 ATTAATATTT
33898242 AAATGATAAATTATTAATATTATAAATA
1 AAATGATAAATTATTAATATT-TAAATA
33898270 AAAT-ATAAATTATTAATATTTAAA
1 AAATGATAAATTATTAATATTTAAA
33898294 AAATAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATGATAAATTATTAATATTTAAATA
Found at i:33898403 original size:28 final size:28
Alignment explanation
Indices: 33898372--33898431 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
33898362 TATTAATATT
* *
33898372 TAAACTAT-CAATTTTTAATATTTTAAAA
1 TAAACTATAC-ATTATTAATATTTAAAAA
* *
33898400 TAAATTATACATTATTAATGTTTAAAAA
1 TAAACTATACATTATTAATATTTAAAAA
33898428 TAAA
1 TAAA
33898432 ATAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (28 bp):
TAAACTATACATTATTAATATTTAAAAA
Found at i:33898427 original size:131 final size:130
Alignment explanation
Indices: 33898214--33898470 Score: 367
Period size: 131 Copynumber: 2.0 Consensus size: 130
33898204 ATAATAAAAT
*
33898214 TTAAATTATAAATAAAATATTAATATTTAAATGATAAATTATTAATATTATAAATAAAATATAAA
1 TTAAAGTATAAATAAAATATTAATATTTAAATGATAAATTATTAATATTATAAATAAAATATAAA
*
33898279 TTATTAATATTTAAAAAATAAATTGAA-ATAAAAATAAATAATCACAATAACATTTAATATTAAT
66 TTATTAATATTTAAAAAATAAAAT-AATATAAAAATAAATAATCACAATAACATTTAA-ATTAAT
33898343 GA
129 GA
* * * *
33898345 TTAAAGTATAAATAAAATATTAATATTTAAACT-ATCAATTTTTAATATTTTAAAATAAATTATA
1 TTAAAGTATAAATAAAATATTAATATTTAAA-TGATAAATTATTAATATTAT-AAATAAAATATA
* * * *
33898409 CATTATTAATGTTT-AAAAATAAAATAATTTAAAAATAAATAATCATAATAACATTTAAATTA
64 AATTATTAATATTTAAAAAATAAAATAATATAAAAATAAATAATCACAATAACATTTAAATTA
33898471 TGCATAAAAT
Statistics
Matches: 113, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
130 6 0.05
131 83 0.73
132 24 0.21
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (130 bp):
TTAAAGTATAAATAAAATATTAATATTTAAATGATAAATTATTAATATTATAAATAAAATATAAA
TTATTAATATTTAAAAAATAAAATAATATAAAAATAAATAATCACAATAACATTTAAATTAATGA
Found at i:33898448 original size:15 final size:16
Alignment explanation
Indices: 33898420--33898451 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33898410 ATTATTAATG
33898420 TTTAAAAATAAAATAA
1 TTTAAAAATAAAATAA
33898436 TTTAAAAAT-AAATAA
1 TTTAAAAATAAAATAA
33898451 T
1 T
33898452 CATAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTAAAAATAAAATAA
Found at i:33902103 original size:30 final size:28
Alignment explanation
Indices: 33902048--33902169 Score: 101
Period size: 30 Copynumber: 4.2 Consensus size: 28
33902038 TTTATAATGT
33902048 TATAAT-TAAAATAAAAAATATTAAAATAATA
1 TATAATATAAAAT--AAAA-ATTAAAATAA-A
33902079 TATATATATAAAATAAAAATTAAAATAAA
1 TATA-ATATAAAATAAAAATTAAAATAAA
* * **
33902108 -ATAA-A-ATATTAAAAATTAAAATTTA
1 TATAATATAAAATAAAAATTAAAATAAA
33902133 TATAATATAAGTAA-AAGAAATTAAAATAAA
1 TATAATATAA--AATAA-AAATTAAAATAAA
33902163 TATAATA
1 TATAATA
33902170 ATATAAAATA
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
25 16 0.21
26 5 0.07
27 2 0.03
28 4 0.05
29 3 0.04
30 29 0.39
31 8 0.11
32 2 0.03
33 6 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
TATAATATAAAATAAAAATTAAAATAAA
Found at i:33902108 original size:17 final size:18
Alignment explanation
Indices: 33902086--33902121 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
33902076 ATATATATAT
33902086 ATAAAATAAAA-ATTAAA
1 ATAAAATAAAATATTAAA
33902103 ATAAAATAAAATATTAAA
1 ATAAAATAAAATATTAAA
33902121 A
1 A
33902122 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAATAAAATATTAAA
Found at i:33902126 original size:55 final size:55
Alignment explanation
Indices: 33902054--33902180 Score: 154
Period size: 55 Copynumber: 2.3 Consensus size: 55
33902044 ATGTTATAAT
*
33902054 TAAAATAAAAAATATTAAAATAATATATATATATAA-AATAA-AAATTAAAATAAA-A
1 TAAAATATAAAATATTAAAAT-ATATATA-ATATAAGAA-AAGAAATTAAAATAAATA
*
33902109 TAAAATATTAAAA-ATTAAAATTTATATAATATAAGTAAAAGAAATTAAAATAAATA
1 TAAAATA-TAAAATATTAAAATATATATAATATAAG-AAAAGAAATTAAAATAAATA
33902165 TAATAATATAAAATAT
1 TAA-AATATAAAATAT
33902181 ATTANATTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
53 6 0.10
54 8 0.13
55 30 0.48
56 13 0.21
57 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (55 bp):
TAAAATATAAAATATTAAAATATATATAATATAAGAAAAGAAATTAAAATAAATA
Found at i:33902426 original size:15 final size:15
Alignment explanation
Indices: 33902406--33902450 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
33902396 TATTATTTTT
*
33902406 TCTACAATTACATTA
1 TCTACAATCACATTA
* *
33902421 TTTACAACCACATTA
1 TCTACAATCACATTA
*
33902436 TCTATAATCACATTA
1 TCTACAATCACATTA
33902451 CATTATAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (15 bp):
TCTACAATCACATTA
Found at i:33906364 original size:59 final size:57
Alignment explanation
Indices: 33906263--33906376 Score: 156
Period size: 59 Copynumber: 2.0 Consensus size: 57
33906253 AAAATTTTTT
* ** *
33906263 ATATATTACATATATTTTTAATGAACTCAAAATTTTTTTTATTGAATTATTAATACA
1 ATATATTACATATATTTTTAATAAACTCAAAATAATTTTTATTAAATTATTAATACA
* *
33906320 ATATGTTATATATATTTTTAATAAACCTCTAAAATAATTTTTATTAAATTATTAATA
1 ATATATTACATATATTTTTAATAAA-CTC-AAAATAATTTTTATTAAATTATTAATA
33906377 TAAATAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 22 0.45
58 3 0.06
59 24 0.49
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (57 bp):
ATATATTACATATATTTTTAATAAACTCAAAATAATTTTTATTAAATTATTAATACA
Found at i:33906593 original size:17 final size:18
Alignment explanation
Indices: 33906551--33906603 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
33906541 TTTTTATTTA
33906551 TATTATTATTACTATTATTTT
1 TATT-TTATT-CTATT-TTTT
33906572 TA-TTTATT-TATTTTTT
1 TATTTTATTCTATTTTTT
33906588 TAATTTTATTCTATTT
1 T-ATTTTATTCTATTT
33906604 GATCATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.17
17 5 0.17
18 6 0.21
19 10 0.34
20 1 0.03
21 2 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTATTCTATTTTTT
Found at i:33907002 original size:19 final size:19
Alignment explanation
Indices: 33906980--33907026 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
33906970 TAAAAAATTA
33906980 TTAATT-TTATATATTATAT
1 TTAATTATT-TATATTATAT
33906999 TTAATTATTTATATTATAT
1 TTAATTATTTATATTATAT
*
33907018 GT-ATTATTT
1 TTAATTATTT
33907027 TTCATCTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 17 0.65
20 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTAATTATTTATATTATAT
Found at i:33916686 original size:16 final size:16
Alignment explanation
Indices: 33916662--33916714 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
33916652 TTGTAATTAT
* * *
33916662 GTAATAAATCAAGCAG
1 GTAAAAAATAAAGCAA
33916678 GTAAAAAATAAAGCAA
1 GTAAAAAATAAAGCAA
*
33916694 GTAAAAATGATAATGCAA
1 GTAAAAA--ATAAAGCAA
33916712 GTA
1 GTA
33916715 GGATAGCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 20 0.65
18 11 0.35
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.19
Consensus pattern (16 bp):
GTAAAAAATAAAGCAA
Found at i:33931624 original size:2 final size:2
Alignment explanation
Indices: 33931617--33931646 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33931607 CTATGTGGAC
33931617 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
33931647 ACTANATCCG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33946580 original size:10 final size:10
Alignment explanation
Indices: 33946553--33946586 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
33946543 ATAGATCTTT
*
33946553 TTATGATTAA
1 TTATTATTAA
33946563 TTATTTATTAA
1 TTA-TTATTAA
33946574 TTATTATTAA
1 TTATTATTAA
33946584 TTA
1 TTA
33946587 AAATGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
TTATTATTAA
Found at i:33952777 original size:2 final size:2
Alignment explanation
Indices: 33952770--33952798 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33952760 TATTTGCAAA
33952770 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
33952799 ATTAGGAGGA
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:33955723 original size:127 final size:127
Alignment explanation
Indices: 33955487--33955742 Score: 332
Period size: 127 Copynumber: 2.0 Consensus size: 127
33955477 TAAAGATCTT
* * * * * * *
33955487 ATCAATATAAAATAATTACTAATTTCTTGTAATATTTATCTTATATATATATAATTAATGGCTAA
1 ATCAATATAAAATAATTACTAATTTATAGTAACATCTATCTTATATATATAAAATAAATAGCTAA
* * * * *
33955552 AGGTTGTCAAATTCAATTGATTTGTTTATTCAATAATGACTGTGTGTTATGTATATTGAGAA
66 AAGTTGTCAAATTCAATTGATTTGTATATTAAATAATGACTGTGTGCTATGTATATTAAGAA
* * * * * *
33955614 ATCAATATAAAATAGTTATTAATTTATAGTAGCATCTGTCTTTTATATATAAAATAAATAGTTAA
1 ATCAATATAAAATAATTACTAATTTATAGTAACATCTATCTTATATATATAAAATAAATAGCTAA
* *
33955679 AAGTTGTCAAATTCAATTGATTTGTATATTAAATGATGATTGTGTGCTATGTATATTAAGAA
66 AAGTTGTCAAATTCAATTGATTTGTATATTAAATAATGACTGTGTGCTATGTATATTAAGAA
33955741 AT
1 AT
33955743 TAGTAAATTT
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
127 109 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (127 bp):
ATCAATATAAAATAATTACTAATTTATAGTAACATCTATCTTATATATATAAAATAAATAGCTAA
AAGTTGTCAAATTCAATTGATTTGTATATTAAATAATGACTGTGTGCTATGTATATTAAGAA
Found at i:33958589 original size:22 final size:22
Alignment explanation
Indices: 33958547--33958589 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
33958537 TCAACCAGTC
*
33958547 ATGCAATGCCTAAAAATTAGTA
1 ATGCAATGCCTAAAAAGTAGTA
*
33958569 ATGCAATGCCTAAAAGGTAGT
1 ATGCAATGCCTAAAAAGTAGT
33958590 CACACAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (22 bp):
ATGCAATGCCTAAAAAGTAGTA
Found at i:33958922 original size:15 final size:16
Alignment explanation
Indices: 33958902--33958936 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
33958892 ATATGAGTCG
33958902 ATTTTATT-AAAAATA
1 ATTTTATTCAAAAATA
*
33958917 ATTTTATTCAAAATTA
1 ATTTTATTCAAAAATA
33958933 ATTT
1 ATTT
33958937 ATTTTGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTATTCAAAAATA
Found at i:33958949 original size:20 final size:20
Alignment explanation
Indices: 33958917--33958955 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33958907 ATTAAAAATA
*
33958917 ATTTTATTCAAAATTAATTT
1 ATTTTATTCAAAAATAATTT
33958937 ATTTTGATT-AAAAATAATT
1 ATTTT-ATTCAAAAATAATT
33958956 AAAATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTTATTCAAAAATAATTT
Found at i:33959009 original size:30 final size:30
Alignment explanation
Indices: 33958973--33959048 Score: 143
Period size: 30 Copynumber: 2.5 Consensus size: 30
33958963 TAAAAAGAAA
*
33958973 TATTTTTAAAAATAACTTTATGTGTAAGGG
1 TATTTTTGAAAATAACTTTATGTGTAAGGG
33959003 TATTTTTGAAAATAACTTTATGTGTAAGGG
1 TATTTTTGAAAATAACTTTATGTGTAAGGG
33959033 TATTTTTGAAAATAAC
1 TATTTTTGAAAATAAC
33959049 CTTTTAGTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (30 bp):
TATTTTTGAAAATAACTTTATGTGTAAGGG
Found at i:33971173 original size:14 final size:15
Alignment explanation
Indices: 33971154--33971192 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
33971144 CTTAAATTTT
*
33971154 TTTATTTGTA-TATA
1 TTTATTTATATTATA
33971168 TTTATTTATATTATA
1 TTTATTTATATTATA
*
33971183 TTTTTTTATA
1 TTTATTTATA
33971193 AATCAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTATTTATATTATA
Found at i:33979013 original size:20 final size:18
Alignment explanation
Indices: 33978978--33979016 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
33978968 AGTAAATATT
*
33978978 TATTTTTTATTTAAAATA
1 TATTTTTTATTGAAAATA
33978996 TATTTTTTAAATTGAAAATA
1 TATTTTTT--ATTGAAAATA
33979016 T
1 T
33979017 GTGATGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTTTTATTGAAAATA
Found at i:33985254 original size:25 final size:24
Alignment explanation
Indices: 33985204--33985251 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33985194 CGAAAACTAA
** *
33985204 AAAAAAAAGAGTAAAATAACATTT
1 AAAAAAAAGAAAAAAAAAACATTT
33985228 AAAAAAAAGAAAAAAAAAACATTT
1 AAAAAAAAGAAAAAAAAAACATTT
33985252 TAAGCTTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAAAACATTT
Found at i:34039737 original size:1 final size:1
Alignment explanation
Indices: 34039731--34039760 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
34039721 TGCTATTACC
*
34039731 AAAAAAAAAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
34039761 CGATAGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:34042139 original size:30 final size:30
Alignment explanation
Indices: 34042067--34042197 Score: 160
Period size: 30 Copynumber: 4.4 Consensus size: 30
34042057 ATTATTAATC
*
34042067 ATAAAAGTTTATTT-GATTTAAAATAAAAAT
1 ATAAGAGTTTATTTAG-TTTAAAATAAAAAT
34042097 ATAA-A-TACTTATTTAGTTTAAAATAAAAAT
1 ATAAGAGT--TTATTTAGTTTAAAATAAAAAT
* *
34042127 TTAAGAGTTTATTTAGTTTAAAATGAAAAT
1 ATAAGAGTTTATTTAGTTTAAAATAAAAAT
* *
34042157 TTAAGAGTTTATTTAGTTTAAAATGAAAAT
1 ATAAGAGTTTATTTAGTTTAAAATAAAAAT
*
34042187 ATAAGGGTTTA
1 ATAAGAGTTTA
34042198 ATGTAATAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.01
29 1 0.01
30 87 0.95
31 2 0.02
32 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.11, T:0.41
Consensus pattern (30 bp):
ATAAGAGTTTATTTAGTTTAAAATAAAAAT
Found at i:34052542 original size:2 final size:2
Alignment explanation
Indices: 34052535--34052714 Score: 122
Period size: 2 Copynumber: 97.0 Consensus size: 2
34052525 CTGATCATCT
* * * *
34052535 TA TA TA TA TA TA TA TT TA TA TA TA T- TA TT TT TA TA TC T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
34052575 TG T- TGA TA TA TA TA TA TT TA TA TA TA TA TA TA -A TA T- TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* ** * *
34052615 TA TA TA TA T- TA TA TA CTA T- TA T- TA T- TT TA NC CA AA T- TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
34052653 -A TA T- TA TA TA TA TA -A TA TA TA TA TA -A TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
34052690 TA TA -A TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
34052715 AATGGTAAAT
Statistics
Matches: 143, Mismatches: 17, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
1 16 0.11
2 124 0.87
3 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34059514 original size:4 final size:4
Alignment explanation
Indices: 34059499--34059553 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
34059489 AAAAGAACGA
** * *
34059499 AAAG AGAAG AAAG AAA- AAAG AAAG AGTG ACAG ACAG AAAG AAAG AAAG
1 AAAG A-AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
34059547 AAAG AAA
1 AAAG AAA
34059554 AGACAAAGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
3 3 0.07
4 37 0.84
5 4 0.09
ACGTcount: A:0.69, C:0.04, G:0.25, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:34061399 original size:22 final size:22
Alignment explanation
Indices: 34061323--34061400 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
34061313 ATGATTATGT
* * * *
34061323 TATTTTATTTTTTAAGTATTAA
1 TATTTTATTTATAAAATACTAA
34061345 TATTTTATTTAT--AAT-CTAA
1 TATTTTATTTATAAAATACTAA
**
34061364 TCA-TCAATATTATAAAATACTAA
1 T-ATTTTAT-TTATAAAATACTAA
34061387 TATTTTATTTATAA
1 TATTTTATTTATAA
34061401 TTTAAATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
19 7 0.16
20 7 0.16
22 21 0.49
23 8 0.19
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (22 bp):
TATTTTATTTATAAAATACTAA
Found at i:34061437 original size:15 final size:16
Alignment explanation
Indices: 34061417--34061449 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34061407 TATTATTATG
34061417 ATTA-TTCATTTTTAA
1 ATTATTTCATTTTTAA
*
34061432 ATTATTTTATTTTTAA
1 ATTATTTCATTTTTAA
34061448 AT
1 AT
34061450 ATTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATTTCATTTTTAA
Found at i:34062212 original size:22 final size:24
Alignment explanation
Indices: 34062113--34062213 Score: 68
Period size: 22 Copynumber: 4.2 Consensus size: 24
34062103 AAATTAATAT
*
34062113 TTTAAAATATTATTATTTTATTTATAA
1 TTTAAAATATTAATATTTTA--TA-AA
* *
34062140 TGTAAATATATT-ATA-ATTA-AAA
1 TTTAAA-ATATTAATATTTTATAAA
* *
34062162 TATAAAAATATTAATATTTTTTAAA
1 T-TTAAAATATTAATATTTTATAAA
*
34062187 TTTAAAATATT-A-ATTTTATAAG
1 TTTAAAATATTAATATTTTATAAA
34062209 TTTAA
1 TTTAA
34062214 GTTTGTAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
22 21 0.36
23 8 0.14
24 11 0.19
25 4 0.07
26 3 0.05
27 7 0.12
28 5 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTAAAATATTAATATTTTATAAA
Found at i:34083665 original size:17 final size:17
Alignment explanation
Indices: 34083636--34083670 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34083626 CACACAAAAA
34083636 AATTATAATATAATTAT
1 AATTATAATATAATTAT
34083653 AATT-TAATGATAATTAT
1 AATTATAAT-ATAATTAT
34083670 A
1 A
34083671 TATATACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTATAATATAATTAT
Found at i:34084084 original size:3 final size:3
Alignment explanation
Indices: 34084078--34084103 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34084068 TTTGATACTT
34084078 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
34084104 TACATAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34092640 original size:2 final size:2
Alignment explanation
Indices: 34092633--34092665 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34092623 GACCCCATTA
34092633 AT 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 AT A
34092666 GTAATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34106085 original size:94 final size:94
Alignment explanation
Indices: 34105924--34106112 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
34105914 TTCAGCCCCG
34105924 ACTAAAACTCAAACTTGACAAATGCCCCTTATGCCACCAGATCTTTCTTAGTTCTTTGCAGAATG
1 ACTAAAACTCAAACTTGACAAATGCCCCTTATGCCACCAGATCTTTCTTAGTTCTTTGCAGAATG
34105989 CAACTGGTAATTATTGATCAAGAACCAGA
66 CAACTGGTAATTATTGATCAAGAACCAGA
34106018 ACTAAAACTCAAACTTGACAAATGCCCCTTATGCCACCAGATCTTTCTTAGTTCTTTGCAGAATG
1 ACTAAAACTCAAACTTGACAAATGCCCCTTATGCCACCAGATCTTTCTTAGTTCTTTGCAGAATG
34106083 CAACTGGTAATTATTGATCAAGAACCAGA
66 CAACTGGTAATTATTGATCAAGAACCAGA
34106112 A
1 A
34106113 AAATTCAACT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (94 bp):
ACTAAAACTCAAACTTGACAAATGCCCCTTATGCCACCAGATCTTTCTTAGTTCTTTGCAGAATG
CAACTGGTAATTATTGATCAAGAACCAGA
Found at i:34106658 original size:6 final size:7
Alignment explanation
Indices: 34106642--34106678 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
34106632 AAGAAGTTGG
*
34106642 TTTCGTT
1 TTTCTTT
34106649 TTTC-TT
1 TTTCTTT
34106655 TTTCTTT
1 TTTCTTT
34106662 TTTCTTT
1 TTTCTTT
34106669 TTTCTTT
1 TTTCTTT
34106676 TTT
1 TTT
34106679 GGGCGTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTCTTT
Found at i:34112760 original size:14 final size:14
Alignment explanation
Indices: 34112741--34112779 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
34112731 TGGCTTTAAA
*
34112741 TTTTTCAATTAATT
1 TTTTTCAATAAATT
34112755 TTTTTCAA-AAATT
1 TTTTTCAATAAATT
*
34112768 TATTTCAATAAA
1 TTTTTCAATAAA
34112780 AAAAATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTTCAATAAATT
Found at i:34113349 original size:21 final size:22
Alignment explanation
Indices: 34113324--34113366 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
34113314 ATAAAAAATG
34113324 AAAAATAATTAAATT-ATATTA
1 AAAAATAATTAAATTGATATTA
*
34113345 AAAAATAATTAGATTGATATTA
1 AAAAATAATTAAATTGATATTA
34113367 TTAACTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAAATAATTAAATTGATATTA
Found at i:34118244 original size:57 final size:57
Alignment explanation
Indices: 34118157--34118277 Score: 181
Period size: 57 Copynumber: 2.1 Consensus size: 57
34118147 GGTGCTCGCA
*
34118157 TGGGAG-CATCAGCCATGACAAAGCCCGAAATTCCTGAGAAGAAGTTGGTTAGTCCT
1 TGGGAGTCATCAGCCATGACAAAGCCCGAAATTCCTGAGAAGAAGTTGGTTAGTCCC
* * **
34118213 TGGGAGTCATCAGTCATGACTAAGCTTGAAATTCCTGAGAAGAAGTTGGTTAGTCCC
1 TGGGAGTCATCAGCCATGACAAAGCCCGAAATTCCTGAGAAGAAGTTGGTTAGTCCC
*
34118270 CGGGAGTC
1 TGGGAGTC
34118278 TGAATCGACG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 6 0.10
57 52 0.90
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (57 bp):
TGGGAGTCATCAGCCATGACAAAGCCCGAAATTCCTGAGAAGAAGTTGGTTAGTCCC
Found at i:34133110 original size:7 final size:6
Alignment explanation
Indices: 34133095--34133179 Score: 75
Period size: 6 Copynumber: 14.3 Consensus size: 6
34133085 ACCATCTAAC
* * ***
34133095 ATACAT ATACAT -TATAT AT-CTT AATACAT ATACAT ATACAT ATATGC
1 ATACAT ATACAT ATACAT ATACAT -ATACAT ATACAT ATACAT ATACAT
* * *
34133142 ATACAT ATACAT ATACAT ATATAT ATATAT ATATAT AT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT AT
34133180 TATATATTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
5 5 0.08
6 58 0.89
7 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (6 bp):
ATACAT
Found at i:34133137 original size:24 final size:24
Alignment explanation
Indices: 34133095--34133163 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
34133085 ACCATCTAAC
* * *
34133095 ATACATATACAT-TATATATCTTA
1 ATACATATACATATACATATATGA
*
34133118 ATACATATACATATACATATATGC
1 ATACATATACATATACATATATGA
34133142 ATACATATACATATACATATAT
1 ATACATATACATATACATATAT
34133164 ATATATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 12 0.29
24 29 0.71
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.38
Consensus pattern (24 bp):
ATACATATACATATACATATATGA
Found at i:34133165 original size:2 final size:2
Alignment explanation
Indices: 34133122--34133201 Score: 74
Period size: 2 Copynumber: 41.0 Consensus size: 2
34133112 ATCTTAATAC
* * ** * * *
34133122 AT AT AC AT AT AC AT AT AT GC AT AC AT AT AC AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
34133164 AT AT AT AT AT AT AT AT -T AT AT AT TT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34133202 TCAAATCACT
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
1 2 0.03
2 58 0.97
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:34142626 original size:3 final size:3
Alignment explanation
Indices: 34142618--34142649 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
34142608 CGTTCTTTTG
34142618 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
34142650 GTAGTTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34146484 original size:17 final size:17
Alignment explanation
Indices: 34146459--34146496 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
34146449 TAGTCAATCC
34146459 ATTTAATCTTGAAAT-AT
1 ATTTAATCTT-AAATAAT
*
34146476 ATTTGATCTTAAATAAT
1 ATTTAATCTTAAATAAT
34146493 ATTT
1 ATTT
34146497 TATTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTAATCTTAAATAAT
Found at i:34146733 original size:18 final size:17
Alignment explanation
Indices: 34146710--34146743 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34146700 AAATATGTTA
34146710 TTTTATTAAATTTTTTAC
1 TTTTATT-AATTTTTTAC
*
34146728 TTTTATTTATTTTTTA
1 TTTTATTAATTTTTTA
34146744 TAAACAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTAATTTTTTAC
Found at i:34147945 original size:22 final size:21
Alignment explanation
Indices: 34147918--34147962 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
34147908 TGTAAGAATT
*
34147918 TATTTAATTTAATATAAAAATA
1 TATTTAATTTAA-AAAAAAATA
34147940 TATTTAATTTAAAAAAAAATA
1 TATTTAATTTAAAAAAAAATA
34147961 TA
1 TA
34147963 AAAACTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TATTTAATTTAAAAAAAAATA
Done.