Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 409 of 438
Found at i:127176939 original size:14 final size:14
Alignment explanation
Indices: 127176920--127176949 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
127176910 TACATCATTT
127176920 TTTTTAATACTATA
1 TTTTTAATACTATA
127176934 TTTTTAATACTATA
1 TTTTTAATACTATA
127176948 TT
1 TT
127176950 ATGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAATACTATA
Found at i:127177028 original size:64 final size:58
Alignment explanation
Indices: 127176920--127177076 Score: 136
Period size: 64 Copynumber: 2.5 Consensus size: 58
127176910 TACATCATTT
* * * *
127176920 TTTTTAATACTATATTTTTAATACTATATTATGTATATATTTTTACAT-GCATTATGTACATA
1 TTTTTAATA-TATATATGT-ATA-TAT-TTATGTACATACTTTTA-ATAGCATTATGTACATA
** **
127176982 TTTTCAATAACTATATCATATGTATATATTTTATGTACATACTTTTAATATTATTATGTATTTA
1 TTTT---TAA-TATAT-ATATGTATATA-TTTATGTACATACTTTTAATAGCATTATGTACATA
127177046 TTTTTAATATATATATGTATATATTTATGTA
1 TTTTTAATATATATATGTATATATTTATGTA
127177077 GTATTATTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
58 8 0.10
59 11 0.14
60 5 0.06
61 3 0.04
62 4 0.05
63 2 0.03
64 31 0.39
65 10 0.12
66 6 0.08
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.54
Consensus pattern (58 bp):
TTTTTAATATATATATGTATATATTTATGTACATACTTTTAATAGCATTATGTACATA
Found at i:127177039 original size:23 final size:23
Alignment explanation
Indices: 127177007--127177064 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
127176997 TCATATGTAT
127177007 ATATT-TTATGTACATACTTTTA
1 ATATTATTATGTACATACTTTTA
** *
127177029 ATATTATTATGTATTTATTTTTA
1 ATATTATTATGTACATACTTTTA
127177052 ATA-TATATATGTA
1 ATATTAT-TATGTA
127177065 TATATTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (23 bp):
ATATTATTATGTACATACTTTTA
Found at i:127177071 original size:23 final size:23
Alignment explanation
Indices: 127176930--127177013 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
127176920 TTTTTAATAC
127176930 TATATTTTTAATACTATATTATGTA
1 TATATTTTTAATA-TATA-TATGTA
**
127176955 TATATTTTTACATGCAT-TATGTA
1 TATATTTTTA-ATATATATATGTA
*
127176978 CATATTTTCAATAACTATATCATATGTA
1 TATATTTT---TAA-TATAT-ATATGTA
127177006 TATATTTT
1 TATATTTT
127177014 ATGTACATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
23 13 0.28
25 13 0.28
26 7 0.15
28 13 0.28
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (23 bp):
TATATTTTTAATATATATATGTA
Found at i:127177174 original size:2 final size:2
Alignment explanation
Indices: 127177169--127177203 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
127177159 ATATATTACG
127177169 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 T
127177204 CTTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:127177309 original size:29 final size:29
Alignment explanation
Indices: 127177260--127177321 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
127177250 ACTATATTAC
* *
127177260 TTTTTTTACATATTATCTTATGTATATAT
1 TTTTTTTACATACTATATTATGTATATAT
*
127177289 TTTTTTTA-ATAACTATATTATGTATGTAT
1 TTTTTTTACAT-ACTATATTATGTATATAT
127177318 TTTT
1 TTTT
127177322 AACGCTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTTTTACATACTATATTATGTATATAT
Found at i:127177354 original size:25 final size:25
Alignment explanation
Indices: 127177291--127177354 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
127177281 GTATATATTT
**
127177291 TTTTTAATAACTATATTATGTATGTA
1 TTTTTAAT-ACTATATTATGTACATA
**
127177317 TTTTTAACGCTATATTATGTACATA
1 TTTTTAATACTATATTATGTACATA
127177342 TTTTTAATACTAT
1 TTTTTAATACTAT
127177355 GTATATACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (25 bp):
TTTTTAATACTATATTATGTACATA
Found at i:127178421 original size:20 final size:19
Alignment explanation
Indices: 127178392--127178432 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
127178382 CTAGACATGT
*
127178392 TTATATTTTATTTTATCTTC
1 TTATACTTTATTTTAT-TTC
127178412 TTATACTTTATTTTATTTC
1 TTATACTTTATTTTATTTC
127178431 TT
1 TT
127178433 TCTTTCAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATACTTTATTTTATTTC
Found at i:127180808 original size:48 final size:48
Alignment explanation
Indices: 127180694--127180794 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
127180684 CACAATATAT
* *
127180694 ATATACACATCTCATACATATTTCACATTACCCATTTGGCTTTACCAC
1 ATATACATAGCTCATACATATTTCACATTACCCATTTGGCTTTACCAC
* * *
127180742 ATATGCATGGCTCATACATATTTCACATTAGCC-TTTCGGCTTTACCAC
1 ATATACATAGCTCATACATATTTCACATTACCCATTT-GGCTTTACCAC
127180790 ATATA
1 ATATA
127180795 TATATCTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 3 0.07
48 43 0.93
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.36
Consensus pattern (48 bp):
ATATACATAGCTCATACATATTTCACATTACCCATTTGGCTTTACCAC
Found at i:127183034 original size:5 final size:5
Alignment explanation
Indices: 127183021--127183067 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
127183011 AGTCCATTTG
*
127183021 TTTTC TTTTA TTTTTA TTTTTA TTTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA -TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT
127183068 CTTATACTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 23 0.57
6 17 0.43
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:127183037 original size:6 final size:6
Alignment explanation
Indices: 127183026--127183067 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
127183016 ATTTGTTTTC
127183026 TTTTAT TTTTAT TTTTAT TTTTA- TTTTA- TTTTA- TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
127183068 CTTATACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.43
6 20 0.57
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:127183059 original size:10 final size:11
Alignment explanation
Indices: 127183021--127183067 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
127183011 AGTCCATTTG
*
127183021 TTTTCTTTTAT
1 TTTTATTTTAT
127183032 TTTTATTTTTAT
1 TTTTA-TTTTAT
127183044 TTTTATTTTA-
1 TTTTATTTTAT
127183054 TTTTATTTTAT
1 TTTTATTTTAT
127183065 TTT
1 TTT
127183068 CTTATACTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 10 0.30
11 12 0.36
12 11 0.33
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:127186512 original size:11 final size:11
Alignment explanation
Indices: 127186496--127186520 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
127186486 TATGTTAATG
127186496 ATAATATTGAA
1 ATAATATTGAA
127186507 ATAATATTGAA
1 ATAATATTGAA
127186518 ATA
1 ATA
127186521 TTGAAATCAT
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:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAATATTGAA
Found at i:127186850 original size:3 final size:3
Alignment explanation
Indices: 127186844--127186883 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
127186834 TTCATCATCA
127186844 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
127186884 GAACTTTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:127199359 original size:4 final size:4
Alignment explanation
Indices: 127199350--127199384 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
127199340 GAGTGAACGT
127199350 GAAA GAAA G-AA GAAA GAAA GAAA GAAA GAAA -AAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
127199385 GGAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:127200077 original size:15 final size:15
Alignment explanation
Indices: 127200057--127200113 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
127200047 CGATGAATTT
127200057 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
127200072 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
127200087 ATTGAATTTATATTG
1 ATTGAATTTATATTG
127200102 ATTGAA-TTATAT
1 ATTGAATTTATAT
127200114 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:127200532 original size:21 final size:21
Alignment explanation
Indices: 127200508--127200566 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
127200498 GTGTCGTATT
127200508 TCAGGCACCTCGTGTGTCATA
1 TCAGGCACCTCGTGTGTCATA
*
127200529 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCATA
127200550 TCAGGCACCTCGTGTGT
1 TCAGGCACCTCGTGTGT
127200567 AGTTTTAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCATA
Found at i:127200576 original size:21 final size:21
Alignment explanation
Indices: 127200508--127200578 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
127200498 GTGTCGTATT
127200508 TCAGGCACCTCGTGTGTCA-TA
1 TCAGGCACCTCGTGTGT-AGTA
*
127200529 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTAGTA
*
127200550 TCAGGCACCTCGTGTGTAGTT
1 TCAGGCACCTCGTGTGTAGTA
*
127200571 TTAGGCAC
1 TCAGGCAC
127200579 TTTATGTGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTAGTA
Found at i:127200577 original size:42 final size:42
Alignment explanation
Indices: 127200487--127200592 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
127200477 TTTATCGATT
* *
127200487 AGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCATATC
1 AGGCACCTCATGTGTCGTA--TCAGGCACCTCGTGTGTCATATC
* * *
127200531 AGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGT-AGTTTT
1 AGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCA-TATC
* *
127200573 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
127200593 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 36 0.68
44 16 0.30
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (42 bp):
AGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCATATC
Found at i:127209010 original size:48 final size:49
Alignment explanation
Indices: 127208944--127209041 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
127208934 ATATTTACTT
127208944 TTGGTGAAACAGGATTAGAACAATTTCAGGATTCCCTGTTCTGA-TTTA
1 TTGGTGAAACAGGATTAGAACAATTTCAGGATTCCCTGTTCTGACTTTA
*
127208992 TTGGTGAAACAGGATTAGAACAATTTCTGGATTCCCTGTTCTGACTTTA
1 TTGGTGAAACAGGATTAGAACAATTTCAGGATTCCCTGTTCTGACTTTA
127209041 T
1 T
127209042 AAATTCACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 43 0.90
49 5 0.10
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (49 bp):
TTGGTGAAACAGGATTAGAACAATTTCAGGATTCCCTGTTCTGACTTTA
Found at i:127211779 original size:16 final size:16
Alignment explanation
Indices: 127211754--127211803 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
127211744 AGTAATTTAT
*
127211754 TTATTATTATTATTAA
1 TTATTTTTATTATTAA
**
127211770 TTATTTTTATTAACAA
1 TTATTTTTATTATTAA
*
127211786 TTTTTTTTATTATATAA
1 TTATTTTTATTAT-TAA
127211803 T
1 T
127211804 ATCAAATCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 24 0.89
17 3 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTTTATTATTAA
Found at i:127219641 original size:20 final size:21
Alignment explanation
Indices: 127219612--127219652 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
127219602 ATTAAACTTA
*
127219612 TAAAATTA-TTATGTATTTTT
1 TAAAAATATTTATGTATTTTT
*
127219632 TAAAAATATTTATTTATTTTT
1 TAAAAATATTTATGTATTTTT
127219653 AATATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TAAAAATATTTATGTATTTTT
Found at i:127222310 original size:5 final size:5
Alignment explanation
Indices: 127222300--127222340 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
127222290 TGCCTTTGGT
*
127222300 TTTTA TTTTA TTTTA TTTATA TTTTA TTATA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA
127222341 ATGACTCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:127229880 original size:27 final size:27
Alignment explanation
Indices: 127229850--127229902 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
127229840 TTTATCGAGG
*
127229850 TTATTAGTTTATCGATAAATGAATATT
1 TTATTAATTTATCGATAAATGAATATT
* *
127229877 TTATTAATTTATTGATAAATTAATAT
1 TTATTAATTTATCGATAAATGAATAT
127229903 ATATATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATGAATATT
Found at i:127234241 original size:46 final size:46
Alignment explanation
Indices: 127234174--127234346 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
127234164 TGTAACCCGC
127234174 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
* *
127234220 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G--T-GTTCGCAT
* * **
127234270 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GG-ACTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
* *
127234311 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG
127234347 ATGCCCAAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 1 0.01
43 2 0.02
44 27 0.25
45 1 0.01
46 36 0.34
47 25 0.23
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
Found at i:127234338 original size:91 final size:93
Alignment explanation
Indices: 127234181--127234351 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 93
127234171 CGCCCATAAG
**
127234181 CGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGGTACTCGCATCCATAAGTGAACTCGGACTCAACTCA
127234246 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
127234274 CGAACTCGGACTCAACTCAACGAGTTC-GG-ACTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGGTACTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
127234337 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
127234352 CAAATATCCA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
91 46 0.62
92 2 0.03
93 26 0.35
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGGTACTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:127236782 original size:15 final size:15
Alignment explanation
Indices: 127236734--127236802 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
127236724 ACAAGAAAAC
127236734 GAATAAA-AAATCCA
1 GAATAAAGAAATCCA
* *
127236748 -AGATAGAGAAA-CCC
1 GA-ATAAAGAAATCCA
127236762 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
127236777 GAATAAAGAGATCCA
1 GAATAAAGAAATCCA
*
127236792 GGATAAAGAAA
1 GAATAAAGAAA
127236803 CCCAAGATAC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
13 1 0.02
14 14 0.32
15 29 0.66
ACGTcount: A:0.58, C:0.13, G:0.17, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:127236811 original size:15 final size:15
Alignment explanation
Indices: 127236736--127236811 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
127236726 AAGAAAACGA
127236736 ATAAA-AAATCCAAG
1 ATAAAGAAATCCAAG
* * *
127236750 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
127236764 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
127236778 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
127236794 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
127236809 ATA
1 ATA
127236812 CGATACTATG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
13 1 0.02
14 14 0.29
15 32 0.67
16 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:127239868 original size:93 final size:93
Alignment explanation
Indices: 127239738--127239910 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
127239728 CGCCCATAAG
* * ** * *
127239738 CGAACTTGGACTCAACTCAATGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCA
127239803 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
127239831 CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCA
*
127239896 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
127239911 CAAATATCCC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:127239906 original size:46 final size:46
Alignment explanation
Indices: 127239739--127239909 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 46
127239729 GCCCATAAGC
* * * * *
127239739 GAACTTGGACTCAACTCAATGAGCTCGGGTGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCATCCATAAAT
* * * ** *
127239785 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATG-CTCGCATCCAT-AAAT
* *
127239832 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAAT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCATCCATAAAT
*
127239878 GAACTCGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGC
127239910 CCAAATATCC
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
46 67 0.66
47 35 0.34
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCATCCATAAAT
Found at i:127244439 original size:22 final size:22
Alignment explanation
Indices: 127244412--127244456 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
127244402 TTACCAGTAG
127244412 CACTGAAAATATAATACTGGAA
1 CACTGAAAATATAATACTGGAA
127244434 CACTGAAAATATAATACTGGAA
1 CACTGAAAATATAATACTGGAA
127244456 C
1 C
127244457 GATATTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (22 bp):
CACTGAAAATATAATACTGGAA
Found at i:127249670 original size:16 final size:15
Alignment explanation
Indices: 127249651--127249718 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
127249641 TTTTATGTGT
127249651 TATAAATTACATA-AGA
1 TATAAATTA-ATATA-A
127249667 TATAAAATTAATATAA
1 TAT-AAATTAATATAA
* * **
127249683 TATAAATTATTTTTT
1 TATAAATTAATATAA
127249698 TGATAAA-TAATATAA
1 T-ATAAATTAATATAA
127249713 TATAAA
1 TATAAA
127249719 ATATTACAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
14 5 0.12
15 14 0.34
16 15 0.37
17 7 0.17
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (15 bp):
TATAAATTAATATAA
Found at i:127249952 original size:4 final size:4
Alignment explanation
Indices: 127249943--127250009 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
127249933 GTTGGATAAC
* ** * *
127249943 GGGA GGGA GGGA GGGA GGGA GGGA AGGA AAGA GGGA GAGAGA GAGA GAGA
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA G-G-GA GGGA GGGA
*
127249993 GAGA GGGA GGGA GGGA G
1 GGGA GGGA GGGA GGGA G
127250010 AGCAAGGGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
4 51 0.93
5 1 0.02
6 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:127249990 original size:10 final size:10
Alignment explanation
Indices: 127249972--127250035 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
127249962 AGGGAAGGAA
*
127249972 AGAGGGAGAG
1 AGAGAGAGAG
127249982 AGAGAGAGAG
1 AGAGAGAGAG
*
127249992 AGAGAGGGAG
1 AGAGAGAGAG
* *
127250002 GGAGGGAGAG
1 AGAGAGAGAG
*
127250012 CA-AGGGAGAG
1 -AGAGAGAGAG
*
127250022 AGAAAGAGAG
1 AGAGAGAGAG
127250032 AGAG
1 AGAG
127250036 GAAGACGAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 1 0.02
10 42 0.98
ACGTcount: A:0.44, C:0.02, G:0.55, T:0.00
Consensus pattern (10 bp):
AGAGAGAGAG
Found at i:127250021 original size:38 final size:38
Alignment explanation
Indices: 127249957--127250036 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
127249947 GGGAGGGAGG
* *
127249957 GAGGGAGGGAAGGAAAGAGGGAGAGAGAGAGAGAGAGA
1 GAGGGAGGGAAGGAAAGAAGGAGAGAGAGAAAGAGAGA
* *
127249995 GAGGGAGGGAGGGAGAGCAAGG-GAGAGAGAAAGAGAGA
1 GAGGGAGGGAAGGAAAG-AAGGAGAGAGAGAAAGAGAGA
127250033 GAGG
1 GAGG
127250037 AAGACGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 34 0.92
39 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.56, T:0.00
Consensus pattern (38 bp):
GAGGGAGGGAAGGAAAGAAGGAGAGAGAGAAAGAGAGA
Found at i:127250024 original size:4 final size:4
Alignment explanation
Indices: 127249972--127250035 Score: 58
Period size: 4 Copynumber: 16.0 Consensus size: 4
127249962 AGGGAAGGAA
* * * * *
127249972 AGAG GGAG AGAG AGAG AGAG AGAG AGGG AGGG AGGG AGAG CA-AG GGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG -AGAG AGAG
*
127250020 AGAG AAAG AGAG AGAG
1 AGAG AGAG AGAG AGAG
127250036 GAAGACGAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
4 49 0.98
5 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.55, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:127255610 original size:24 final size:23
Alignment explanation
Indices: 127255560--127255613 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
127255550 AATCAAATAA
** *
127255560 AAATTAATTAACCGAAATAACAT
1 AAATTAATTAAAAGAAATAACAC
127255583 AAATTAATTAAAAGTAAATAACAC
1 AAATTAATTAAAAG-AAATAACAC
127255607 AAATTAA
1 AAATTAA
127255614 CAATCGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (23 bp):
AAATTAATTAAAAGAAATAACAC
Found at i:127257523 original size:24 final size:24
Alignment explanation
Indices: 127257496--127257549 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
127257486 CCTATATATA
*
127257496 AGCTTCCTAATTATGGCTCTTATG
1 AGCTTCCTAATTATGACTCTTATG
*
127257520 AGCTTCCTGATTATGACTCTTATG
1 AGCTTCCTAATTATGACTCTTATG
*
127257544 AACTTC
1 AGCTTC
127257550 TCATTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (24 bp):
AGCTTCCTAATTATGACTCTTATG
Found at i:127260008 original size:3 final size:3
Alignment explanation
Indices: 127260000--127260045 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
127259990 ATGAGGTAAC
127260000 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
127260046 GAGATTAGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:127263869 original size:24 final size:24
Alignment explanation
Indices: 127263842--127263895 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
127263832 GAGTAAGCTT
127263842 ATGTAAGCTTAGTAAGTTCATAGG
1 ATGTAAGCTTAGTAAGTTCATAGG
127263866 ATGTAAGCTTAGTAAGTTCATAGG
1 ATGTAAGCTTAGTAAGTTCATAGG
127263890 ATGTAA
1 ATGTAA
127263896 AGATAAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.33
Consensus pattern (24 bp):
ATGTAAGCTTAGTAAGTTCATAGG
Found at i:127271958 original size:67 final size:67
Alignment explanation
Indices: 127271846--127271982 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 67
127271836 TCCCTCCTCT
* *
127271846 AATAGGTTTTGGTTTTAGAATTAACCCAATTGGAAATGTAGCATTGTTACATGAATATAGAAATC
1 AATAGGTTTTGGTTTCAGAATTAACCCAATTGGAAATGTAACATTGTTACATGAATATAGAAATC
127271911 AA
66 AA
*
127271913 AATAGGTTTTGGTTTCAGAATTAACCCAATTGGGAATGTAACATTGTTACATGAATATAGAAATC
1 AATAGGTTTTGGTTTCAGAATTAACCCAATTGGAAATGTAACATTGTTACATGAATATAGAAATC
127271978 AA
66 AA
127271980 AAT
1 AAT
127271983 GGGGTTTCTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (67 bp):
AATAGGTTTTGGTTTCAGAATTAACCCAATTGGAAATGTAACATTGTTACATGAATATAGAAATC
AA
Found at i:127272854 original size:62 final size:62
Alignment explanation
Indices: 127272757--127272881 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
127272747 ACATAGGCAG
*
127272757 AAGAGCTGAAAACCAACATATTCAGCATGAAAATAAAGAATGACCTCTTCTTTTTTTCAAAA
1 AAGAGCTGAAAACCAACATATTCAGCATGAAAATAAAGAATAACCTCTTCTTTTTTTCAAAA
127272819 AAGAGCTGAAAACCAACATATTCAGCACT-AAAATAAAGAATAACCTCTTCTTTTTTTCAAAA
1 AAGAGCTGAAAACCAACATATTCAGCA-TGAAAATAAAGAATAACCTCTTCTTTTTTTCAAAA
127272881 A
1 A
127272882 CGTCCTTACA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 60 0.98
63 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (62 bp):
AAGAGCTGAAAACCAACATATTCAGCATGAAAATAAAGAATAACCTCTTCTTTTTTTCAAAA
Found at i:127273878 original size:18 final size:17
Alignment explanation
Indices: 127273855--127273898 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
127273845 TAATTAACCC
127273855 CTCAATTAAACTAATTTT
1 CTCAATTAAA-TAATTTT
127273873 CTCAATT-AATAATTTT
1 CTCAATTAAATAATTTT
*
127273889 CTCAGTTAAA
1 CTCAATTAAA
127273899 GTTATCCCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 13 0.54
17 4 0.17
18 7 0.29
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (17 bp):
CTCAATTAAATAATTTT
Found at i:127279378 original size:22 final size:21
Alignment explanation
Indices: 127279343--127279418 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
127279333 AAAAGGTATC
* *
127279343 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
127279364 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
127279387 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
127279406 TGC-AATCATATCT
1 TACAAATCATATCT
127279419 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:127279403 original size:19 final size:19
Alignment explanation
Indices: 127279379--127279469 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
127279369 AATCATATCT
127279379 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
127279398 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
127279416 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
127279433 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
127279452 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
127279470 TGAAAATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:127279435 original size:35 final size:37
Alignment explanation
Indices: 127279372--127279469 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
127279362 ATTACAAAAT
127279372 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
127279408 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
127279443 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
127279470 TGAAAATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:127279878 original size:45 final size:45
Alignment explanation
Indices: 127279829--127280044 Score: 170
Period size: 45 Copynumber: 4.8 Consensus size: 45
127279819 TGCTATATTT
127279829 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
** * * * *
127279874 GATCTGCTCCCCGTCTAATACAGAGACACAAAATTTGCT-TCTCC
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
* * * * *
127279918 AATCTGCTCCCTGTCTAATAGAGAGATGCCAAATCTGTCATCTTG
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
* ** * * * * * *
127279963 GATTTG-T-TTCGATGTAA-ACACATGAATGTCAGATCTACTATGTCTTC
1 GATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAAATCT-GT-TATCTTC
*
127280010 GATCTGCTCCCCGTCTAATATAGAGATGCCAAATC
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
127280045 ATCTTAGATC
Statistics
Matches: 123, Mismatches: 39, Indels: 16
0.69 0.22 0.09
Matches are distributed among these distances:
43 4 0.03
44 40 0.33
45 50 0.41
46 1 0.01
47 17 0.14
48 6 0.05
49 5 0.04
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (45 bp):
GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
Found at i:127280206 original size:79 final size:78
Alignment explanation
Indices: 127279984--127280279 Score: 405
Period size: 78 Copynumber: 3.8 Consensus size: 78
127279974 ATGTAAACAC
*
127279984 ATGAATGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATCT
*
127280049 TAGATCTGCTTCA
66 TGGATCTGCTTCA
** *
127280062 ATGAAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATC
127280126 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * ** *
127280140 ATGAAGGTCAGATCTACTGTGTTTTCGATCTGTTTCCCTTTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGTCAGATCTACTATGTCTTCGATCTG-CTCCCCGTCTAATATAGAGATGCCAAATCATC
127280205 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * * * * *
127280219 ATGAATGTCAGATCTGCTATGTCTTCGATCTACTCTCCGTCAAATATGGAGATGCTAAATC
1 ATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATC
127280280 TGTTTCTTCG
Statistics
Matches: 188, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
77 2 0.01
78 115 0.61
79 71 0.38
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (78 bp):
ATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:127280271 original size:157 final size:156
Alignment explanation
Indices: 127279984--127280279 Score: 423
Period size: 157 Copynumber: 1.9 Consensus size: 156
127279974 ATGTAAACAC
* *
127279984 ATGAATGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
* * * *
127280049 TAGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATATAGAGA
66 TAGATCTGCTTCAATGAAGGTCCAATCTGCTATGTCTTCGATCTACTCCCCGTCAAATATAGAGA
127280114 TGCCAAATCATCTTGGATCTGCTTCA
131 TGCCAAATCATCTTGGATCTGCTTCA
* * * **
127280140 ATGAAGGTCAGATCTACTGTGTTTTCGATCTGTTTCCCTTTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGTCAGATCTACTATGTCTTCGATCTG-CTCCCCGTCTAATACAGAGATGCCAAATCATC
* * * *
127280205 TTGGATCTGCTTCAATGAATGT-CAGATCTGCTATGTCTTCGATCTACTCTCCGTCAAATATGGA
65 TTAGATCTGCTTCAATGAAGGTCCA-ATCTGCTATGTCTTCGATCTACTCCCCGTCAAATATAGA
*
127280269 GATGCTAAATC
129 GATGCCAAATC
127280280 TGTTTCTTCG
Statistics
Matches: 122, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
156 31 0.25
157 91 0.75
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (156 bp):
ATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TAGATCTGCTTCAATGAAGGTCCAATCTGCTATGTCTTCGATCTACTCCCCGTCAAATATAGAGA
TGCCAAATCATCTTGGATCTGCTTCA
Found at i:127289117 original size:22 final size:21
Alignment explanation
Indices: 127289082--127289157 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 21
127289072 AAAAGGTATC
* *
127289082 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
127289103 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
127289126 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
127289145 TGC-AATCATATCT
1 TACAAATCATATCT
127289158 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 10 0.22
20 1 0.02
21 3 0.07
22 15 0.33
23 11 0.24
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:127289171 original size:17 final size:18
Alignment explanation
Indices: 127289118--127289189 Score: 101
Period size: 17 Copynumber: 3.9 Consensus size: 18
127289108 AATCATATCT
*
127289118 TCTAAGATTACATATCATA
1 TCTAAGATTGC-TATCATA
*
127289137 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
127289155 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
127289172 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
127289190 TGAAGATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
17 16 0.33
18 16 0.33
19 16 0.33
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:127289716 original size:18 final size:19
Alignment explanation
Indices: 127289681--127289720 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
127289671 AAGTACATAT
127289681 TTTTAAAAAAATTATAAAA
1 TTTTAAAAAAATTATAAAA
* *
127289700 TTTTGAAAATATT-TAAAA
1 TTTTAAAAAAATTATAAAA
127289718 TTT
1 TTT
127289721 GAAGAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TTTTAAAAAAATTATAAAA
Found at i:127291624 original size:2 final size:2
Alignment explanation
Indices: 127291617--127291646 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
127291607 GGTGTTAAAC
127291617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127291647 GCGTGAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127295287 original size:2 final size:2
Alignment explanation
Indices: 127295280--127295304 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
127295270 TTGTAAAGTG
127295280 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
127295305 GTATGTATTT
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:127295659 original size:4 final size:4
Alignment explanation
Indices: 127295650--127295678 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
127295640 CCATGCCAAC
127295650 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
127295679 GTTACTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:127297454 original size:2 final size:2
Alignment explanation
Indices: 127297447--127297478 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127297437 TTATGCAAAT
127297447 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
127297479 AAGAGAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:127298052 original size:22 final size:22
Alignment explanation
Indices: 127298027--127298072 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
127298017 TGCAAAATAA
*
127298027 AAATAAAAAATGAAG-AGGATGC
1 AAATAAAAAA-GAAGAAGAATGC
*
127298049 AAATGAAAAAGAAGAAGAATGC
1 AAATAAAAAAGAAGAAGAATGC
127298071 AA
1 AA
127298073 GTGGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (22 bp):
AAATAAAAAAGAAGAAGAATGC
Found at i:127298171 original size:1 final size:1
Alignment explanation
Indices: 127298165--127298190 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
127298155 TTCAAAGTTT
127298165 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
127298191 CCATGCCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:127298759 original size:2 final size:2
Alignment explanation
Indices: 127298752--127298778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
127298742 TTGCAACACT
127298752 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 T
127298779 TTCCAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:127308278 original size:3 final size:3
Alignment explanation
Indices: 127308270--127308313 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
127308260 AATTGATTAG
127308270 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
127308314 GCTAATGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:127317162 original size:137 final size:137
Alignment explanation
Indices: 127317004--127317251 Score: 365
Period size: 137 Copynumber: 1.8 Consensus size: 137
127316994 TGGACTCGAG
* * *
127317004 ACTCAATAATGTAATTACAACTATCTAACCATCTAACAAAAGGACTAATATGTTAAAAAACATTA
1 ACTCAATAATGTAATTACAACTATCTAACCATCAAACAAAAGAACTAATATGCTAAAAAA-A-TA
*
127317069 ATT-AAAATATAAAAAGCTTCAAACAACATGAAA-AAAAATATAAATACAAGTAGGAGATTAATC
64 ATTAAAAATATAAAAAGCTTCAAACAACATGAAAGAAAAATACAAATACAAGTAGGAGATTAATC
127317132 GAACTCAAA
129 GAACTCAAA
* * *
127317141 ACTCAATGATGTAATTGCAACTATCTAACCATCAAACCAAAGAACTAATATGCTAAAAAAATAAT
1 ACTCAATAATGTAATTACAACTATCTAACCATCAAACAAAAGAACTAATATGCTAAAAAAATAAT
* * *
127317206 TAAAAATTTAAAAAGCTTGAAGCAACATGAAATGAAAAATACAAAT
66 TAAAAATATAAAAAGCTTCAAACAACATGAAA-GAAAAATACAAAT
127317252 GTGAATAAGA
Statistics
Matches: 98, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
135 5 0.05
136 28 0.29
137 54 0.55
138 11 0.11
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (137 bp):
ACTCAATAATGTAATTACAACTATCTAACCATCAAACAAAAGAACTAATATGCTAAAAAAATAAT
TAAAAATATAAAAAGCTTCAAACAACATGAAAGAAAAATACAAATACAAGTAGGAGATTAATCGA
ACTCAAA
Found at i:127317310 original size:138 final size:137
Alignment explanation
Indices: 127316936--127317311 Score: 323
Period size: 137 Copynumber: 2.8 Consensus size: 137
127316926 AGCTAATATG
* * *
127316936 TTAAAAAAAAAAAAACTTGAAGCAACATGAAATAAAAAATACAAATGTG--T-AGA-AG-AATTG
1 TTAAAATATAAAAAGCTTGAAGCAACATGAAAT-AAAAATACAAATGTGAATAAGAGAGTAATTG
* * * *
127316996 GACTCGAGACTC-A-ATAATGTAATTAC-AACTATCTAACCATCTAACAAAAGGACTAATATGTT
65 AACTCGAGACTCAAGATAA-G-AA--ACTAACTATCTAACCATCAAACAAAAGAACTAATATGCT
127317058 AAAAAACATTAA
126 AAAAAACATTAA
* * * ** * * *
127317070 TTAAAATATAAAAAGCTTCAAACAACATGAAA-AAAAATATAAAT-ACAAGTAGGAGATTAATCG
1 TTAAAATATAAAAAGCTTGAAGCAACATGAAATAAAAATACAAATGTGAA-TAAGAGAGTAATTG
* * * * *
127317133 AACTCAAAACTCAATGAT--GTAATTGCAACTATCTAACCATCAAACCAAAGAACTAATATGCTA
65 AACTCGAGACTCAA-GATAAGAAACT--AACTATCTAACCATCAAACAAAAGAACTAATATGCTA
127317196 AAAAA-A-TAA
127 AAAAACATTAA
*
127317205 TTAAAAATTTAAAAAGCTTGAAGCAACATGAAATGAAAAATACAAATGTGAATAAGAGAGTAATT
1 TT-AAAATATAAAAAGCTTGAAGCAACATGAAAT-AAAAATACAAATGTGAATAAGAGAGTAATT
* *
127317270 GAACTTGAGACTCAAGGATAAGAACACTAAC-ATTTAACCATC
64 GAACTCGAGACTCAA-GATAAGAA-ACTAACTATCTAACCATC
127317312 TAGACAAAGT
Statistics
Matches: 187, Mismatches: 36, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
132 11 0.06
134 29 0.16
135 7 0.04
136 30 0.16
137 52 0.28
138 47 0.25
139 5 0.03
140 4 0.02
141 2 0.01
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.23
Consensus pattern (137 bp):
TTAAAATATAAAAAGCTTGAAGCAACATGAAATAAAAATACAAATGTGAATAAGAGAGTAATTGA
ACTCGAGACTCAAGATAAGAAACTAACTATCTAACCATCAAACAAAAGAACTAATATGCTAAAAA
ACATTAA
Found at i:127317320 original size:138 final size:136
Alignment explanation
Indices: 127316936--127317320 Score: 323
Period size: 138 Copynumber: 2.8 Consensus size: 136
127316926 AGCTAATATG
* * *
127316936 TTAAAAAAAAAAAAACTTGAAGCAACATGAAATAAAAAATACAAATGTG--T-AGA-AG-AATTG
1 TTAAAATATAAAAAGCTTGAAGCAACATGAAAT-AAAAATACAAATGTGAATAAGAGAGTAATTG
* * *
127316996 GACTCGAGACTC-A-ATAATGTAATTAC-AACTATCTAACCATCTAACAAAAGGACTAATATGTT
65 AACTCGAGACTCAAGATAA-G-AA--ACTAACTATCTAACCATCTAAC-AAAGAACTAATATGCT
127317058 AAAAAACATTAA
125 AAAAAACATTAA
* * * ** * * *
127317070 TTAAAATATAAAAAGCTTCAAACAACATGAAA-AAAAATATAAAT-ACAAGTAGGAGATTAATCG
1 TTAAAATATAAAAAGCTTGAAGCAACATGAAATAAAAATACAAATGTGAA-TAAGAGAGTAATTG
* * * * *
127317133 AACTCAAAACTCAATGAT--GTAATTGCAACTATCTAACCATCAAACCAAAGAACTAATATGCTA
65 AACTCGAGACTCAA-GATAAGAAACT--AACTATCTAACCATCTAA-CAAAGAACTAATATGCTA
127317196 AAAAA-A-TAA
126 AAAAACATTAA
*
127317205 TTAAAAATTTAAAAAGCTTGAAGCAACATGAAATGAAAAATACAAATGTGAATAAGAGAGTAATT
1 TT-AAAATATAAAAAGCTTGAAGCAACATGAAAT-AAAAATACAAATGTGAATAAGAGAGTAATT
* *
127317270 GAACTTGAGACTCAAGGATAAGAACACTAAC-ATTTAACCATCTAGACAAAG
64 GAACTCGAGACTCAA-GATAAGAA-ACTAACTATCTAACCATCTA-ACAAAG
127317321 TTAAGAACAC
Statistics
Matches: 194, Mismatches: 36, Indels: 38
0.72 0.13 0.14
Matches are distributed among these distances:
132 11 0.06
134 29 0.15
135 7 0.04
136 30 0.15
137 51 0.26
138 54 0.28
139 6 0.03
140 4 0.02
141 2 0.01
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (136 bp):
TTAAAATATAAAAAGCTTGAAGCAACATGAAATAAAAATACAAATGTGAATAAGAGAGTAATTGA
ACTCGAGACTCAAGATAAGAAACTAACTATCTAACCATCTAACAAAGAACTAATATGCTAAAAAA
CATTAA
Found at i:127322758 original size:13 final size:12
Alignment explanation
Indices: 127322735--127322798 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 12
127322725 TAGAAACGAA
127322735 AAGAGAAAAGAG
1 AAGAGAAAAGAG
*
127322747 AAGAGTAAAAGAA
1 AAGAG-AAAAGAG
127322760 AAGAGTAAAAGA-
1 AAGAG-AAAAGAG
127322772 AA-ACGAAAAGAG
1 AAGA-GAAAAGAG
*
127322784 AGGAG-AAAGAG
1 AAGAGAAAAGAG
127322795 AAGA
1 AAGA
127322799 AACAAGATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
11 16 0.36
12 10 0.22
13 19 0.42
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.03
Consensus pattern (12 bp):
AAGAGAAAAGAG
Found at i:127322790 original size:18 final size:17
Alignment explanation
Indices: 127322738--127322796 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
127322728 AAACGAAAAG
127322738 AGAAAAGAGAAGAGTAAA
1 AGAAAAGAGAAGAG-AAA
*
127322756 AGAAAAGAGTAAAAGAAA
1 AGAAAAGAG-AAGAGAAA
*
127322774 ACGAAAAGAGAGGAGAAA
1 A-GAAAAGAGAAGAGAAA
127322792 GAGAA
1 -AGAA
127322797 GAAACAAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.66, C:0.02, G:0.29, T:0.03
Consensus pattern (17 bp):
AGAAAAGAGAAGAGAAA
Found at i:127324949 original size:24 final size:24
Alignment explanation
Indices: 127324911--127324965 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
127324901 TTCCATTATT
* * *
127324911 TAGCTCGGAAGAGCTTACCATTTA
1 TAGCTCGAAAAAGCTTACAATTTA
*
127324935 TAGCTCGAAAAAGCTTATAATTTA
1 TAGCTCGAAAAAGCTTACAATTTA
*
127324959 CAGCTCG
1 TAGCTCG
127324966 TATGAGCATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (24 bp):
TAGCTCGAAAAAGCTTACAATTTA
Found at i:127330012 original size:30 final size:30
Alignment explanation
Indices: 127329978--127330072 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
127329968 AGAAAAACAA
*
127329978 CTACAATTACAACAACAACAACAACAATGG
1 CTACAATTACAACAACTACAACAACAATGG
** * *
127330008 CTAC-ACCACAAGTAAGTACAACAACAATGG
1 CTACAATTACAA-CAACTACAACAACAATGG
* * *
127330038 CTACACTCT-CAGCAGCTACAACAACAATGG
1 CTACAAT-TACAACAACTACAACAACAATGG
127330068 CTACA
1 CTACA
127330073 GCGGGAACTA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
29 5 0.10
30 43 0.86
31 2 0.04
ACGTcount: A:0.45, C:0.29, G:0.11, T:0.15
Consensus pattern (30 bp):
CTACAATTACAACAACTACAACAACAATGG
Found at i:127330083 original size:27 final size:27
Alignment explanation
Indices: 127329989--127330121 Score: 95
Period size: 30 Copynumber: 4.7 Consensus size: 27
127329979 TACAATTACA
* *
127329989 ACAACAACAACAACAATGGCTACACCACA
1 ACAACTACAACAACAATGGCTACA--ACG
* * * *
127330018 AGTAAGTACAACAACAATGGCTACACTCTC
1 A-CAACTACAACAACAATGGCTACA-AC-G
* *
127330048 AGCAGCTACAACAACAATGGCTACAGCG
1 A-CAACTACAACAACAATGGCTACAACG
** * * *
127330076 GGAACTACAACACCAATGGGTACAATG
1 ACAACTACAACAACAATGGCTACAACG
127330103 ACAACTACAACAACAATGG
1 ACAACTACAACAACAATGG
127330122 GTATGAGACA
Statistics
Matches: 82, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
27 36 0.44
29 4 0.05
30 42 0.51
ACGTcount: A:0.44, C:0.28, G:0.15, T:0.13
Consensus pattern (27 bp):
ACAACTACAACAACAATGGCTACAACG
Found at i:127330122 original size:27 final size:27
Alignment explanation
Indices: 127330053--127330124 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
127330043 CTCTCAGCAG
* * **
127330053 CTACAACAACAATGGCTACAGCGGGAA
1 CTACAACAACAATGGGTACAACGACAA
* *
127330080 CTACAACACCAATGGGTACAATGACAA
1 CTACAACAACAATGGGTACAACGACAA
127330107 CTACAACAACAATGGGTA
1 CTACAACAACAATGGGTA
127330125 TGAGACAGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14
Consensus pattern (27 bp):
CTACAACAACAATGGGTACAACGACAA
Found at i:127336316 original size:25 final size:26
Alignment explanation
Indices: 127336273--127336378 Score: 198
Period size: 25 Copynumber: 4.2 Consensus size: 26
127336263 ATAAATTCCC
127336273 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
127336299 ATCATGGAA-ATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
127336324 ATCAT-GAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
127336349 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
127336375 ATCA
1 ATCA
127336379 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
24 3 0.04
25 42 0.54
26 33 0.42
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:127337239 original size:92 final size:92
Alignment explanation
Indices: 127337131--127337348 Score: 303
Period size: 92 Copynumber: 2.4 Consensus size: 92
127337121 TTGATATCTA
* * *
127337131 AACTATCAAAATGTGTTTTATTATGGTACCT-GTACATTCATAAAATGTCAAATGTGATACCTGC
1 AACTATCAATATGTGTTTTATTATGGTACCTGGT-CATTCATAAAATGTCAAATATAATACCTGC
* *
127337195 ACTTTGAAAATGTTCAATATGGTATTTG
65 ACTTTGAAAATATCCAATATGGTATTTG
* * **
127337223 AACTATCAATATGTGTTTTATTATGGTACTTGGTCTTTCATAAAATGTCAAATATAATATTTGCA
1 AACTATCAATATGTGTTTTATTATGGTACCTGGTCATTCATAAAATGTCAAATATAATACCTGCA
*
127337288 CTTTGAAAATATCCAATATGGTGTTTG
66 CTTTGAAAATATCCAATATGGTATTTG
* * *
127337315 AACTATCAATATATGCTTTATTATGGTACTTGGT
1 AACTATCAATATGTGTTTTATTATGGTACCTGGT
127337349 GTTAACATCG
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 111 0.98
93 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.41
Consensus pattern (92 bp):
AACTATCAATATGTGTTTTATTATGGTACCTGGTCATTCATAAAATGTCAAATATAATACCTGCA
CTTTGAAAATATCCAATATGGTATTTG
Found at i:127338056 original size:19 final size:22
Alignment explanation
Indices: 127338014--127338057 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
127338004 AAATACTTTA
127338014 ATTATTATTTGAAGTTATTATT
1 ATTATTATTTGAAGTTATTATT
127338036 ATTATTA-TTGAAG-TATT-TT
1 ATTATTATTTGAAGTTATTATT
127338055 ATT
1 ATT
127338058 TTTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 4 0.18
21 6 0.27
22 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
ATTATTATTTGAAGTTATTATT
Found at i:127338947 original size:20 final size:21
Alignment explanation
Indices: 127338912--127338951 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
127338902 TTTATGCCAC
*
127338912 ATCAGTATTCTTATCCTGAAA
1 ATCAGGATTCTTATCCTGAAA
127338933 ATCAGGATT-TTATCCTGAA
1 ATCAGGATTCTTATCCTGAA
127338952 TTTCAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
ATCAGGATTCTTATCCTGAAA
Found at i:127346349 original size:18 final size:19
Alignment explanation
Indices: 127346328--127346363 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
127346318 AAATAATACA
127346328 TTAAATTAAA-AAAATAAC
1 TTAAATTAAAGAAAATAAC
*
127346346 TTAATTTAAAGAAAATAA
1 TTAAATTAAAGAAAATAA
127346364 ATGGAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
TTAAATTAAAGAAAATAAC
Found at i:127346987 original size:32 final size:32
Alignment explanation
Indices: 127346951--127347045 Score: 85
Period size: 29 Copynumber: 3.2 Consensus size: 32
127346941 TAATAGTATA
127346951 AATATAGATACATACAAAATACTAAGTGGGTG
1 AATATAGATACATACAAAATACTAAGTGGGTG
* *** * * *
127346983 AATATTG--AC-TTTTAAATAAT-AGT--ATA
1 AATATAGATACATACAAAATACTAAGTGGGTG
127347009 AATATAGATACATACAAAATACTAAGTGGGTG
1 AATATAGATACATACAAAATACTAAGTGGGTG
127347041 AATAT
1 AATAT
127347046 TTAAAATATA
Statistics
Matches: 43, Mismatches: 14, Indels: 12
0.62 0.20 0.17
Matches are distributed among these distances:
26 7 0.16
28 5 0.12
29 14 0.33
30 5 0.12
32 12 0.28
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (32 bp):
AATATAGATACATACAAAATACTAAGTGGGTG
Found at i:127347003 original size:58 final size:58
Alignment explanation
Indices: 127346933--127347046 Score: 228
Period size: 58 Copynumber: 2.0 Consensus size: 58
127346923 CTTAGTCAAC
127346933 CTTTTAAATAATAGTATAAATATAGATACATACAAAATACTAAGTGGGTGAATATTGA
1 CTTTTAAATAATAGTATAAATATAGATACATACAAAATACTAAGTGGGTGAATATTGA
127346991 CTTTTAAATAATAGTATAAATATAGATACATACAAAATACTAAGTGGGTGAATATT
1 CTTTTAAATAATAGTATAAATATAGATACATACAAAATACTAAGTGGGTGAATATT
127347047 TAAAATATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (58 bp):
CTTTTAAATAATAGTATAAATATAGATACATACAAAATACTAAGTGGGTGAATATTGA
Found at i:127350220 original size:6 final size:6
Alignment explanation
Indices: 127350201--127350245 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
127350191 GTCGAAACTT
* *
127350201 TTGCCC TTGACC TTGCCC TTGCCC TTGCCC TTGCCT TTGCCC TTG
1 TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTG
127350246 ATAAACAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (6 bp):
TTGCCC
Found at i:127357839 original size:2 final size:2
Alignment explanation
Indices: 127357832--127357857 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
127357822 TTATTTGAAT
127357832 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
127357858 CATGAGTTAT
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:127361615 original size:21 final size:20
Alignment explanation
Indices: 127361569--127361616 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
127361559 CTATTTCATC
**
127361569 TTTT-AATTTTGAAACATTT
1 TTTTAAATTTTGAAACATAA
127361588 TTCTTAAATTTTGAAACCATAA
1 TT-TTAAATTTTGAAA-CATAA
127361610 TTTTAAA
1 TTTTAAA
127361617 CTCCAAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 15 0.62
22 5 0.21
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTAAATTTTGAAACATAA
Found at i:127362900 original size:16 final size:16
Alignment explanation
Indices: 127362881--127362922 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
127362871 TTACTTGATC
127362881 AAAATTAATTTTTCCA
1 AAAATTAATTTTTCCA
127362897 AAAATTAATTTTTCCA
1 AAAATTAATTTTTCCA
*
127362913 AAAATCAATT
1 AAAATTAATT
127362923 AGATTTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTAATTTTTCCA
Found at i:127362906 original size:20 final size:18
Alignment explanation
Indices: 127362881--127362934 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 18
127362871 TTACTTGATC
127362881 AAAATTAATTTTTCC--A
1 AAAATTAATTTTTCCAAA
127362897 AAAATTAATTTTTCCAAA
1 AAAATTAATTTTTCCAAA
127362915 AATCAATTAGA-TTTTCCAAA
1 AA--AATTA-ATTTTTCCAAA
127362935 TTAAGTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 15 0.45
18 3 0.09
20 14 0.42
21 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTAATTTTTCCAAA
Found at i:127364075 original size:15 final size:15
Alignment explanation
Indices: 127364051--127364082 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
127364041 TATGCATGCA
*
127364051 AAATATAAAAGACAT
1 AAATACAAAAGACAT
127364066 AAATACAAAAGACAT
1 AAATACAAAAGACAT
127364081 AA
1 AA
127364083 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:127365068 original size:51 final size:51
Alignment explanation
Indices: 127365005--127365109 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
127364995 ACACTATCTT
127365005 TTGGAGATTGATTGTCTGAATGTTGAGCTACCTTAAGGATATCCTCTTTGG
1 TTGGAGATTGATTGTCTGAATGTTGAGCTACCTTAAGGATATCCTCTTTGG
*
127365056 TTGGAGATTGATTGTCTGAATGTTGAGCTACCTTAAGGATCTCCTCTTTGG
1 TTGGAGATTGATTGTCTGAATGTTGAGCTACCTTAAGGATATCCTCTTTGG
127365107 TTG
1 TTG
127365110 TTAAACCGTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (51 bp):
TTGGAGATTGATTGTCTGAATGTTGAGCTACCTTAAGGATATCCTCTTTGG
Found at i:127366750 original size:15 final size:15
Alignment explanation
Indices: 127366725--127366775 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
127366715 TAATAAAATC
*
127366725 ATAAT-TATATTAAT
1 ATAATATATATTAAA
127366739 ATAATATATATTAAA
1 ATAATATATATTAAA
* *
127366754 ATAATATTTATCTTAA
1 ATAATATATAT-TAAA
127366770 ATAATA
1 ATAATA
127366776 ATTAAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 18 0.56
16 9 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATATATTAAA
Found at i:127366758 original size:20 final size:20
Alignment explanation
Indices: 127366704--127366760 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
127366694 TATGTCTCTA
* *
127366704 CATAATAAAAATAATAAAAT
1 CATAATTAAAATAATATAAT
* *
127366724 CATAATTATATTAATATAAT
1 CATAATTAAAATAATATAAT
127366744 -ATATATTAAAATAATAT
1 CATA-ATTAAAATAATAT
127366761 TTATCTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
CATAATTAAAATAATATAAT
Found at i:127366769 original size:17 final size:16
Alignment explanation
Indices: 127366718--127366775 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
127366708 ATAAAAATAA
*
127366718 TAAAATCATAATTATAT
1 TAAAATAAT-ATTATAT
*
127366735 TAATATAATA-TATAT
1 TAAAATAATATTATAT
127366750 TAAAATAATATT-TAT
1 TAAAATAATATTATAT
*
127366765 CTTAAATAATA
1 -TAAAATAATA
127366776 ATTAAAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 17 0.49
16 11 0.31
17 7 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATAATATTATAT
Found at i:127373046 original size:20 final size:20
Alignment explanation
Indices: 127373021--127373062 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
127373011 TCAAACTCTT
127373021 ATGACCTCAAAAACATAAAA
1 ATGACCTCAAAAACATAAAA
127373041 ATGACCTCAAAAACATAAAA
1 ATGACCTCAAAAACATAAAA
127373061 AT
1 AT
127373063 TATAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.17
Consensus pattern (20 bp):
ATGACCTCAAAAACATAAAA
Found at i:127373238 original size:14 final size:15
Alignment explanation
Indices: 127373207--127373248 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
127373197 CTTATATACT
*
127373207 TTAATTAAAAGTTAA
1 TTAATTATAAGTTAA
127373222 TTAATTATAAG-TAA
1 TTAATTATAAGTTAA
127373236 TTAATTAT-AGTTA
1 TTAATTATAAGTTA
127373249 TAATTAACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 2 0.08
14 13 0.52
15 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
TTAATTATAAGTTAA
Found at i:127374269 original size:17 final size:17
Alignment explanation
Indices: 127374247--127374281 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
127374237 GATATGATTC
127374247 TAAAAT-TATTAAAAAAA
1 TAAAATATA-TAAAAAAA
127374264 TAAAATATATAAAAAAA
1 TAAAATATATAAAAAAA
127374281 T
1 T
127374282 CAGGGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATATATAAAAAAA
Found at i:127374280 original size:18 final size:17
Alignment explanation
Indices: 127374247--127374280 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
127374237 GATATGATTC
*
127374247 TAAAATTATTAAAAAAA
1 TAAAATTATAAAAAAAA
127374264 TAAAATATATAAAAAAA
1 TAAAAT-TATAAAAAAA
127374281 TCAGGGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATTATAAAAAAAA
Found at i:127374570 original size:22 final size:21
Alignment explanation
Indices: 127374535--127374610 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
127374525 AAAAGGTATC
* *
127374535 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
127374556 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
127374579 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
127374598 TGC-AATCATATCT
1 TACAAATCATATCT
127374611 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:127374627 original size:35 final size:37
Alignment explanation
Indices: 127374564--127374661 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
127374554 ATTACAAAAT
127374564 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
127374600 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
127374635 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
127374662 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:127374669 original size:17 final size:19
Alignment explanation
Indices: 127374571--127374661 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
127374561 AATCATATCT
127374571 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
127374590 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
127374608 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
127374625 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
127374644 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
127374662 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:127374817 original size:21 final size:20
Alignment explanation
Indices: 127374780--127374818 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
127374770 TTGGACTTCG
**
127374780 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
127374800 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
127374819 TCTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:127375066 original size:45 final size:45
Alignment explanation
Indices: 127375011--127375210 Score: 240
Period size: 45 Copynumber: 4.5 Consensus size: 45
127375001 AGAAGGCAAT
* * * *
127375011 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATATAGAGACGTCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
*
127375056 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCTAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * * *
127375101 ATCTGCT-TCTTCAATCTACTCACCATCTAATACAGATATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * *
127375145 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
127375190 ATCTGTCATCTTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCT
127375211 TCGATGTAAA
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
44 36 0.28
45 93 0.72
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:127375353 original size:78 final size:78
Alignment explanation
Indices: 127375224--127375518 Score: 484
Period size: 78 Copynumber: 3.8 Consensus size: 78
127375214 ATGTAAACAT
* *
127375224 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTTCCCGTCTAACACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
127375289 TGGATCTGCTTCA
66 TGGATCTGCTTCA
*
127375302 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
127375366 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* *
127375380 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
127375445 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * * *
127375458 ATGAAGGTGAGATCTGCCATGTCTTCGATCTGCTCTCCGTCGAATATAGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
127375519 TGTTTCTTCG
Statistics
Matches: 202, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
77 2 0.01
78 198 0.98
79 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:127375728 original size:78 final size:78
Alignment explanation
Indices: 127375600--127376261 Score: 941
Period size: 78 Copynumber: 8.3 Consensus size: 78
127375590 TGAAAGCCAA
**
127375600 ATCTGCTATGTCTTCGATCTGCTCCCTTTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
127375665 CAATGAAGGTCCA-
66 CAATGAAGGT-CAG
* *
127375678 ATCTGTTATGTCTTCGATCTGCTCCCCGTTTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
127375743 CAATGAAGGTCAG
66 CAATGAAGGTCAG
* * *
127375756 ATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCTGTCATCTTGGATCT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATCT
127375821 GCTTCGATGTAAACAGATGAAGGTCAG
62 G---C--T-T---CA-ATGAAGGTCAG
* * *
127375848 ATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATAATTTTGGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
127375913 CAATGAAGGTCCA-
66 CAATGAAGGT-CAG
* * * *
127375926 ATTTGTTAAGTCTTCGATATGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
* *
127375991 CAATGAAGGTTAA
66 CAATGAAGGTCAG
* * *
127376004 ATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGTTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
127376069 CAATGAAGGTCAG
66 CAATGAAGGTCAG
* * *
127376082 TTCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGTTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
127376147 CAATGAAGGTCAG
66 CAATGAAGGTCAG
* * *
127376160 ATCTGCTGTGTCTTTGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
127376225 CAATGAAGGTCAG
66 CAATGAAGGTCAG
127376238 ATCTGCTATGTCTTCGATCTGCTC
1 ATCTGCTATGTCTTCGATCTGCTC
127376262 TCCGACGAAT
Statistics
Matches: 527, Mismatches: 40, Indels: 34
0.88 0.07 0.06
Matches are distributed among these distances:
77 3 0.01
78 431 0.82
79 4 0.01
82 15 0.03
83 1 0.00
85 2 0.00
87 1 0.00
88 13 0.02
91 2 0.00
92 55 0.10
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (78 bp):
ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
CAATGAAGGTCAG
Found at i:127375861 original size:248 final size:236
Alignment explanation
Indices: 127375600--127376288 Score: 999
Period size: 248 Copynumber: 2.9 Consensus size: 236
127375590 TGAAAGCCAA
*
127375600 ATCTGCTATGTCTTCGATCTGCTCCCTTTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCC-GTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
*
127375665 CAATGAAGGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTTTAATACAGAGATGCCAAATCAT
65 CAATGAAGGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCAT
127375730 CTTGGATCTGCTTCAATGAAGGTCAGATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATATAGA
130 CTTGGATCTGCTTCAATGAAGGTCAGATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATATAGA
127375795 GATGCCAAATCTGTCATCTTGGATCTGCTTCGATGTAAACAGATGAAGGTCAG
195 GATGCCAAATCT-TCATCTTGGATCTG--T---T-T---CA-ATGAAGGTCAG
* * *
127375848 ATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATAATTTTGGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCT-CCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
* * *
127375913 CAATGAAGGTCCAATTTGTTAAGTCTTCGATATGCTCCCCGTCTAATACAGAGATGCCAAATCAT
65 CAATGAAGGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCAT
* * *
127375978 CTTGGATCTGCTTCAATGAAGGTTAAATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATACAGA
130 CTTGGATCTGCTTCAATGAAGGTCAGATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATATAGA
127376043 GATGCCAAA---TCATCTTGGATCTGTTTCAATGAAGGTCAG
195 GATGCCAAATCTTCATCTTGGATCTGTTTCAATGAAGGTCAG
* *
127376082 TTCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGTTT
1 ATCTGCTATGTCTTCGATCTGCTC-CCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTT
* * * *
127376147 CAATGAAGGT-CAGATCTGCTGTGTCTTTGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCA
65 CAATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
* * * * * *
127376211 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGACGAATATGG
129 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATATAG
*
127376276 AGATGTCAAATCT
194 AGATGCCAAATCT
127376289 ATTTCTTCAA
Statistics
Matches: 402, Mismatches: 33, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
233 3 0.01
234 188 0.47
235 2 0.00
238 1 0.00
239 1 0.00
242 1 0.00
244 14 0.03
248 189 0.47
249 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (236 bp):
ATCTGCTATGTCTTCGATCTGCTCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTC
AATGAAGGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
TTGGATCTGCTTCAATGAAGGTCAGATCTGTTGTGTCTTCGATCTGCTCCCCGTCTAATATAGAG
ATGCCAAATCTTCATCTTGGATCTGTTTCAATGAAGGTCAG
Found at i:127376630 original size:220 final size:220
Alignment explanation
Indices: 127376230--127376802 Score: 903
Period size: 220 Copynumber: 2.6 Consensus size: 220
127376220 TGCTTCAATG
* * * *
127376230 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGACGAATATGGAGATGTCAAATCTATTTCT
1 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
127376295 TCAATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGT
66 TCAATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGT
* * *
127376360 GAAGGCCAAATTTGCTATGTCTTCGATCTGCTCCTTGTCAATGCAAGGATGCCAAATCATCTTGG
131 GAAAGCCAAATATGCTATGTCTTCGATCTGCTCCTTGTCAATGCAAGGATGCCAAATAATCTTGG
*
127376425 ATCTACTTTGATGTGAAAAAATCCA
196 ATCTACTTAGATGTGAAAAAATCCA
*
127376450 AAGGTTAGATCTTCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
1 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
*
127376515 TCAATTTGTTCTCTGACAGTATAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGT
66 TCAATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGT
* *
127376580 GAAAGCCAAATATGCTATGTCTTCGATCTGTTCCTTGTCAATGTAAGGATGCCAAATAATCTTGG
131 GAAAGCCAAATATGCTATGTCTTCGATCTGCTCCTTGTCAATGCAAGGATGCCAAATAATCTTGG
* **
127376645 ATCTACTTAGATGTGAAAACATCTG
196 ATCTACTTAGATGTGAAAAAATCCA
* * * *
127376670 AAGGTTAGTTCTGCTATGTCTTAGATCTGCTCTCCGTCAAATATGGAGATGCCAAATTTGTTTCT
1 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
* * ** * ** *
127376735 TCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTGGATCCACTTCAGCGTAAACACCT
66 TCAATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGT
127376800 GAA
131 GAA
127376803 GGTCAAATCT
Statistics
Matches: 324, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
220 324 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (220 bp):
AAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
TCAATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGT
GAAAGCCAAATATGCTATGTCTTCGATCTGCTCCTTGTCAATGCAAGGATGCCAAATAATCTTGG
ATCTACTTAGATGTGAAAAAATCCA
Found at i:127385598 original size:36 final size:36
Alignment explanation
Indices: 127385522--127385599 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
127385512 CATATCTTCT
*
127385522 AAGATTGCATATCATATCTAAGATTGTATCATATCT
1 AAGATTGCATATCATATCTAAGATTGTATCATATCG
127385558 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCTAAGATTG--TATCATATCG
127385594 AAGATT
1 AAGATT
127385600 ATATTTCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 32 0.82
37 1 0.03
38 6 0.15
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (36 bp):
AAGATTGCATATCATATCTAAGATTGTATCATATCG
Found at i:127385599 original size:17 final size:19
Alignment explanation
Indices: 127385519--127385591 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
127385509 AATCATATCT
127385519 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
127385538 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
127385555 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
127385574 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
127385592 TGAAGATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.33
19 35 0.67
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:127385747 original size:21 final size:20
Alignment explanation
Indices: 127385710--127385748 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
127385700 TTGGACTTCG
**
127385710 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
127385730 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
127385749 TCTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:127391998 original size:12 final size:12
Alignment explanation
Indices: 127391981--127392010 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
127391971 ACAAAATTTG
127391981 AATTTAATTTCC
1 AATTTAATTTCC
*
127391993 AATTTAATTTCT
1 AATTTAATTTCC
127392005 AATTTA
1 AATTTA
127392011 TTTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:127392570 original size:6 final size:6
Alignment explanation
Indices: 127392526--127392551 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
127392516 CAAATTTTAT
127392526 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
127392552 TTAAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:127395711 original size:30 final size:30
Alignment explanation
Indices: 127395677--127395734 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
127395667 CACAGCCATG
127395677 ACACACGGGCATGTGG-TCTACCCGTGTGTC
1 ACACACGGGCATGTGGAT-TACCCGTGTGTC
**
127395707 ACACACGGGTGTGTGGATTACCCGTGTG
1 ACACACGGGCATGTGGATTACCCGTGTG
127395735 GGACTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (30 bp):
ACACACGGGCATGTGGATTACCCGTGTGTC
Found at i:127401027 original size:13 final size:13
Alignment explanation
Indices: 127401011--127401035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127401001 TTAAATCAGT
127401011 TAATTAGTTTAAA
1 TAATTAGTTTAAA
127401024 TAATTAGTTTAA
1 TAATTAGTTTAA
127401036 TAAATAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:127406432 original size:6 final size:6
Alignment explanation
Indices: 127406398--127406466 Score: 95
Period size: 6 Copynumber: 11.5 Consensus size: 6
127406388 TCCTCCTATT
* * *
127406398 TTTTTA TTATTTA CTCTTA TTTATA -TTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
127406446 TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTT
127406467 CAATTTTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
5 4 0.07
6 46 0.84
7 5 0.09
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:127406472 original size:24 final size:22
Alignment explanation
Indices: 127406398--127406486 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 22
127406388 TCCTCCTATT
* *
127406398 TTTTTATTATTTACTCTTATTTA
1 TTTTTATT-TTTATTTTTATTTA
127406421 TATTTTATTTTTATTTTTATTTTTA
1 T-TTTTATTTTTATTTTTA--TTTA
127406446 TTTTTATTTTTATTTTTATTTCA
1 TTTTTATTTTTATTTTTATTT-A
*
127406469 ATTTTATTATTTTATTTT
1 TTTTTA-T-TTTTATTTT
127406487 GAAAGACATC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
22 3 0.05
23 15 0.26
24 25 0.44
25 14 0.25
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTATTTTTATTTTTATTTA
Found at i:127409398 original size:13 final size:13
Alignment explanation
Indices: 127409382--127409406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127409372 TTAAATCAGT
127409382 TAATTAGTTTAAA
1 TAATTAGTTTAAA
127409395 TAATTAGTTTAA
1 TAATTAGTTTAA
127409407 TAAATAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:127427181 original size:35 final size:35
Alignment explanation
Indices: 127427142--127427237 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 35
127427132 AATCCAACCA
* **
127427142 AAACACACCAATGCTCGTAAGAGCTAATCCCTTTG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
* *
127427177 AAACACACCAATGCTCATAAAAGTTAATCCCTCCG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
*
127427212 AAACACACCAATGCCCATAAGAGCTA
1 AAACACACCAATGCTCATAAGAGCTA
127427238 GTCAAACCAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
Found at i:127429387 original size:23 final size:23
Alignment explanation
Indices: 127429322--127429389 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
127429312 CTTAGTGTCG
* *
127429322 TTCTGGTGTGTTTGGGTAGATTA
1 TTCTGGTGTGTTTGGGTGGATCA
127429345 TTCTGGTGTGTTTGGGTGGATCA
1 TTCTGGTGTGTTTGGGTGGATCA
* *
127429368 TTCTGGTATGTTTGGTTGGATC
1 TTCTGGTGTGTTTGGGTGGATC
127429390 CGTGTATCCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.10, C:0.07, G:0.35, T:0.47
Consensus pattern (23 bp):
TTCTGGTGTGTTTGGGTGGATCA
Found at i:127433134 original size:43 final size:42
Alignment explanation
Indices: 127433070--127433188 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 42
127433060 CAGTCACAGG
* *
127433070 CTATAATGAACTCGGATCACTCAACAAGATCGAATGCTCGCAT
1 CTATAATGAACTCGGACCACTCAACAAGATCGAATGC-CACAT
* *
127433113 CTATAATGAACTCGGACCACTCAACGAGCTC-AGATGCCACAT
1 CTATAATGAACTCGGACCACTCAACAAGATCGA-ATGCCACAT
* * * *
127433155 ATCTCAA-GAACTTGGACCACTCAACAAGTTCGAA
1 CTAT-AATGAACTCGGACCACTCAACAAGATCGAA
127433189 ATCTCATACA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 29 0.45
43 35 0.55
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (42 bp):
CTATAATGAACTCGGACCACTCAACAAGATCGAATGCCACAT
Found at i:127433172 original size:42 final size:42
Alignment explanation
Indices: 127433120--127433232 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 42
127433110 CATCTATAAT
* * *
127433120 GAACTCGGACCACTCAACGAGCTCAGATGC-CACATATCTCAA
1 GAACTTGGACCACTCAACGAGCTCAGAT-CTCACACATATCAA
* * * * *
127433162 GAACTTGGACCACTCAACAAGTTCGAAATCTCATACATATCAC
1 GAACTTGGACCACTCAACGAGCTC-AGATCTCACACATATCAA
*
127433205 GAAATTGGACCACTCAACGAGCTCAGAT
1 GAACTTGGACCACTCAACGAGCTCAGAT
127433233 TTCTTAATTC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 25 0.44
43 32 0.56
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.19
Consensus pattern (42 bp):
GAACTTGGACCACTCAACGAGCTCAGATCTCACACATATCAA
Found at i:127437127 original size:3 final size:3
Alignment explanation
Indices: 127437002--127437116 Score: 123
Period size: 3 Copynumber: 38.7 Consensus size: 3
127436992 TTGAAGAGAA
127437002 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
127437050 AAT AA- AAC AACT AA- AAC AA- AATT AAA AAG AA- AGAT AAAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AA-T AAT AAT AAT A-AT -AAT AAT AAT
127437095 AAT AA- AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
127437117 ACTAAATAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 18
0.83 0.02 0.15
Matches are distributed among these distances:
2 9 0.09
3 84 0.84
4 6 0.06
5 1 0.01
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:127437259 original size:16 final size:16
Alignment explanation
Indices: 127437210--127437272 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
127437200 TAGCAAAATT
127437210 AAAATTAAAAT-TAAA
1 AAAATTAAAATATAAA
* *
127437225 ATAA-TAAAAGTATATA
1 AAAATTAAAA-TATAAA
127437241 AAAATTAAAATATAAA
1 AAAATTAAAATATAAA
127437257 AAAATTAGAAATATAA
1 AAAATTA-AAATATAA
127437273 GTATAAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 5 0.12
15 4 0.10
16 18 0.45
17 13 0.32
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAATTAAAATATAAA
Found at i:127437348 original size:22 final size:20
Alignment explanation
Indices: 127437304--127437355 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
127437294 TATTAATTAG
* *
127437304 TAAAATAAAAATAAATCATA
1 TAAAATAAAAATAAATAAAA
127437324 TAACAATTAAAAATAAATAAAA
1 TAA-AA-TAAAAATAAATAAAA
127437346 TAAAATAAAA
1 TAAAATAAAA
127437356 TTGGGGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
22 16 0.57
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAATAAAAATAAATAAAA
Found at i:127441600 original size:30 final size:30
Alignment explanation
Indices: 127441556--127441616 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
127441546 CACGGGCTGG
* * *
127441556 CACATGGGCATGTGGTTTGCCTGTGTGGAT
1 CACATGGGCATGTGGTCTGCCCGTGTAGAT
* *
127441586 CACATTGGCGTGTGGTCTGCCCGTGTAGAT
1 CACATGGGCATGTGGTCTGCCCGTGTAGAT
127441616 C
1 C
127441617 CTGAAAACTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.13, C:0.21, G:0.34, T:0.31
Consensus pattern (30 bp):
CACATGGGCATGTGGTCTGCCCGTGTAGAT
Found at i:127443293 original size:33 final size:30
Alignment explanation
Indices: 127443249--127443318 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
127443239 TACTAAGAAT
*
127443249 ATATATATATATATAAATAATAGTATTAGAA
1 ATATATATATATATAAATAATAATATTA-AA
* *
127443280 ATCATATAGTATATATAACTGATAATATTAAA
1 AT-ATATA-TATATATAAATAATAATATTAAA
127443312 ATATATA
1 ATATATA
127443319 CATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 18 0.53
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATATATATATATATAAATAATAATATTAAA
Found at i:127443543 original size:3 final size:3
Alignment explanation
Indices: 127443535--127443760 Score: 147
Period size: 3 Copynumber: 72.0 Consensus size: 3
127443525 ACAAGGATAT
127443535 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
* * ** * * * *
127443583 A-A ACA CAAA AGCC ATT ATA ATA AAA ATA TTA A-A ATA A-A GTA ATA
1 ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
127443627 GA-A ATA TTA CTA CATA TATA TATA TATA CACA CATGA AGA TATA CACTA
1 -ATA ATA ATA ATA -ATA -ATA -ATA -ATA -ATA -AT-A ATA -ATA -A-TA
* * *
127443676 AT- GTA TTTCA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
127443722 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
127443761 TTGAAATGCG
Statistics
Matches: 182, Mismatches: 27, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
2 7 0.04
3 143 0.79
4 28 0.15
5 4 0.02
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:127444255 original size:11 final size:12
Alignment explanation
Indices: 127444239--127444276 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
127444229 AGAAAAAAAA
127444239 GAAGAGAG-AGG
1 GAAGAGAGAAGG
127444250 GAAGAGAGAAGG
1 GAAGAGAGAAGG
127444262 GAA-AGAGAAGG
1 GAAGAGAGAAGG
127444273 GAAG
1 GAAG
127444277 GGAATCCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Done.