Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 270 of 290
Found at i:93288606 original size:2 final size:2
Alignment explanation
Indices: 93288599--93288625 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
93288589 TTTTTCTTTT
93288599 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
93288626 TTTCTCTTAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:93289178 original size:19 final size:19
Alignment explanation
Indices: 93289154--93289192 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
93289144 TATGTATATA
*
93289154 ATCGAAACTAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
*
93289173 ATCGAACCCAAATTAAAAT
1 ATCGAAACCAAATTAAAAT
93289192 A
1 A
93289193 ATTTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.23
Consensus pattern (19 bp):
ATCGAAACCAAATTAAAAT
Found at i:93297226 original size:21 final size:20
Alignment explanation
Indices: 93297200--93297256 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
93297190 ATTTGGTAGA
93297200 AAAACATATATGAACATATTT
1 AAAACA-ATATGAACATATTT
93297221 AAAACAAGATAT-AACATATTT
1 AAAAC-A-ATATGAACATATTT
*
93297242 AAAACACTATGAACA
1 AAAACAATATGAACA
93297257 CATACAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 19 0.59
22 5 0.16
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAACAATATGAACATATTT
Found at i:93297232 original size:22 final size:21
Alignment explanation
Indices: 93297207--93297247 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
93297197 AGAAAAACAT
93297207 ATATGAACATATTTAAAACAAG
1 ATAT-AACATATTTAAAACAAG
93297229 ATATAACATATTTAAAACA
1 ATATAACATATTTAAAACA
93297248 CTATGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (21 bp):
ATATAACATATTTAAAACAAG
Found at i:93297452 original size:4 final size:4
Alignment explanation
Indices: 93297443--93297470 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
93297433 CAACTTTGCT
93297443 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
93297471 TACTCTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:93301901 original size:13 final size:13
Alignment explanation
Indices: 93301883--93301941 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
93301873 TTTAATATCG
93301883 ATAATTTTAAAAT
1 ATAATTTTAAAAT
*
93301896 ATAATTTAAATAAT
1 ATAATTTTAA-AAT
*
93301910 TTAAATTTTAAAA-
1 AT-AATTTTAAAAT
93301923 ACTAA-TTTAAAAT
1 A-TAATTTTAAAAT
93301936 AATAAT
1 -ATAAT
93301942 CATAATTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
12 7 0.19
13 14 0.39
14 8 0.22
15 7 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATTTTAAAAT
Found at i:93307171 original size:5 final size:5
Alignment explanation
Indices: 93307163--93307195 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
93307153 TGAGCTGGGC
*
93307163 TGGTA TGGTA TGGTA TGGTA TGGTA TGGAA TGG
1 TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGG
93307196 CTAATTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.36
Consensus pattern (5 bp):
TGGTA
Found at i:93309154 original size:50 final size:50
Alignment explanation
Indices: 93308996--93309147 Score: 191
Period size: 50 Copynumber: 3.1 Consensus size: 50
93308986 TACTAAATAG
* *
93308996 GCTTCCATCAAATCA--TAAAGAGACTTGTTTTATCATTTCAGTTATCAG
1 GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
* * * * *
93309044 GCTTCCATCAACTCATGCAAACAGACTTGTTTTATCATTTCAGTCGTTAA
1 GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
* * * *
93309094 ACTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATCTCGGCCATCAA
1 GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
93309144 GCTT
1 GCTT
93309148 TTATCAACTC
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
48 14 0.16
50 71 0.84
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (50 bp):
GCTTCCATCAAATCATGTAAAGAGACTTGTTTTATCATTTCAGTCATCAA
Found at i:93313309 original size:23 final size:22
Alignment explanation
Indices: 93313266--93313309 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
93313256 TTCTAAGTCG
93313266 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
93313289 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
93313310 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:93313418 original size:45 final size:45
Alignment explanation
Indices: 93313354--93313447 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
93313344 AACAGATACT
* * *
93313354 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
93313399 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
93313444 CGGT
1 CGGT
93313448 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:93315071 original size:23 final size:23
Alignment explanation
Indices: 93315038--93315089 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
93315028 ATAAGTGCCA
* *
93315038 CACTGATATGTAGTCAAAGCTAC
1 CACTGAAATGTAGCCAAAGCTAC
*
93315061 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCAAAGCTAC
93315084 CACTGA
1 CACTGA
93315090 TCAATAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCAAAGCTAC
Found at i:93315342 original size:18 final size:17
Alignment explanation
Indices: 93315316--93315354 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
93315306 ATTTTCCTTC
93315316 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
93315333 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
93315351 CACA
1 CACA
93315355 ATTTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:93317949 original size:30 final size:30
Alignment explanation
Indices: 93317913--93317989 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
93317903 GTTTAATTAG
93317913 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTATCATACTTTTTATCAAAAAAA
93317943 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTATCATACTTTTTATCAAAAAAA
*
93317973 AAACTTTTACCATACTT
1 AAACTTTTATCATACTT
93317990 ATAAAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (30 bp):
AAACTTTTATCATACTTTTTATCAAAAAAA
Found at i:93318005 original size:30 final size:30
Alignment explanation
Indices: 93317913--93318007 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
93317903 GTTTAATTAG
* * *
93317913 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTACCATACTTTATATAAAAAAAA
* * *
93317943 AAACTTTTATCATACTTTTTATCAAAAAAA
1 AAACTTTTACCATACTTTATATAAAAAAAA
* *
93317973 AAACTTTTACCATACTTATAAAATAAATAAAA
1 AAACTTTTACCATACTT-T-ATATAAAAAAAA
93318005 AAA
1 AAA
93318008 TTATCATGGC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 46 0.79
31 1 0.02
32 11 0.19
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.36
Consensus pattern (30 bp):
AAACTTTTACCATACTTTATATAAAAAAAA
Found at i:93318604 original size:19 final size:19
Alignment explanation
Indices: 93318558--93318594 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
93318548 AAAATCAAAA
93318558 AAATATTATAAAAATGTTT
1 AAATATTATAAAAATGTTT
*
93318577 AAATATTATAAAAGTGTT
1 AAATATTATAAAAATGTT
93318595 ATATATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATATTATAAAAATGTTT
Found at i:93334338 original size:21 final size:21
Alignment explanation
Indices: 93334312--93334352 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
93334302 AGACGAGCAA
* *
93334312 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
93334333 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
93334353 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:93336291 original size:16 final size:16
Alignment explanation
Indices: 93336258--93336291 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
93336248 GGAGATTGTT
* *
93336258 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
93336274 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
93336290 AA
1 AA
93336292 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:93356026 original size:37 final size:37
Alignment explanation
Indices: 93355965--93356110 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
93355955 TACGTATGAT
* *
93355965 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
93356000 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
93356037 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
93356074 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
93356111 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:93356127 original size:46 final size:46
Alignment explanation
Indices: 93356074--93356342 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
93356064 TAAGTGTAGC
* **
93356074 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
93356120 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
93356166 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
93356218 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
93356264 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
93356316 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
93356343 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:93356193 original size:52 final size:52
Alignment explanation
Indices: 93356117--93356336 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
93356107 TAGCTAAAGC
* *
93356117 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
93356170 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
93356222 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
93356268 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
93356320 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
93356337 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:93356239 original size:98 final size:98
Alignment explanation
Indices: 93356074--93356342 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
93356064 TAAGTGTAGC
* * *
93356074 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
93356139 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
93356173 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
93356238 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
93356271 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
93356336 GATCAGA
66 GATCAGA
93356343 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:93372132 original size:16 final size:16
Alignment explanation
Indices: 93372111--93372142 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
93372101 TAAAATATAG
93372111 AAATTAGTAGATGAAA
1 AAATTAGTAGATGAAA
*
93372127 AAATTAGTAGTTGAAA
1 AAATTAGTAGATGAAA
93372143 CTGATTTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
AAATTAGTAGATGAAA
Found at i:93373772 original size:3 final size:3
Alignment explanation
Indices: 93373764--93373788 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
93373754 TTATATTAGT
93373764 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
93373789 AAGGGCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:93380525 original size:20 final size:20
Alignment explanation
Indices: 93380502--93380566 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
93380492 ATTTAATTAG
*
93380502 AATATATAAATTATATTTTA
1 AATATTTAAATTATATTTTA
93380522 AATATTTAAA-TATAATTATTA
1 AATATTTAAATTAT-ATT-TTA
*
93380543 AATATTTGTAATTAGTATTTTA
1 AATATTT-AAATTA-TATTTTA
93380565 AA
1 AA
93380567 AATTATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 10 0.26
22 7 0.18
23 5 0.13
24 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AATATTTAAATTATATTTTA
Found at i:93380545 original size:21 final size:21
Alignment explanation
Indices: 93380497--93380566 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
93380487 ATAAAATTTA
*
93380497 ATTAGAATATATAAATTATATT
1 ATTA-AATATTTAAATTATATT
93380519 -TTAAATATTTAAA-TATAATT
1 ATTAAATATTTAAATTAT-ATT
*
93380539 ATTAAATATTTGTAATTAGTATT
1 ATTAAATATTT-AAATTA-TATT
93380562 -TTAAA
1 ATTAAA
93380567 AATTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 13 0.32
22 7 0.17
23 5 0.12
24 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTAAATATTTAAATTATATT
Found at i:93380545 original size:33 final size:31
Alignment explanation
Indices: 93380469--93380549 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 31
93380459 ATTTTTAAGT
*
93380469 AATA-AATATT-AATTATTTATAAA-ATTTA
1 AATATAATATTAAATTATTTTTAAATATTTA
* *
93380497 ATTAGAATATATAAATTATATTTTAAATATTTA
1 AATATAATAT-TAAATTAT-TTTTAAATATTTA
93380530 AATATAATTATTAAA-TATTT
1 AATATAA-TATTAAATTATTT
93380550 GTAATTAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 1 0.02
31 8 0.19
32 9 0.21
33 14 0.33
34 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (31 bp):
AATATAATATTAAATTATTTTTAAATATTTA
Found at i:93384272 original size:38 final size:38
Alignment explanation
Indices: 93384221--93384294 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
93384211 TCATAAGTTT
* * *
93384221 AGTAATTCGTTTGTTGTGTATTTCCCGGTTGGTGTCAA
1 AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTCAA
93384259 AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTC
1 AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTC
93384295 TGTCTCTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.45
Consensus pattern (38 bp):
AGTAATTCATTTGTTGAGTATTTCCCGGTTAGTGTCAA
Found at i:93385320 original size:22 final size:22
Alignment explanation
Indices: 93385295--93385337 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
93385285 TATTTAAAAA
93385295 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
*
93385317 ATAATAACAAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
93385338 AACAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:93385347 original size:22 final size:22
Alignment explanation
Indices: 93385300--93385347 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
93385290 AAAAAATAAC
* * *
93385300 AACAAAATAGTAGCAATATAAT
1 AACAAAATAGTAGCAAAACAAA
93385322 AACAAAAT-GATAGCAAAACAAA
1 AACAAAATAG-TAGCAAAACAAA
93385344 AACA
1 AACA
93385348 TAACAGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (22 bp):
AACAAAATAGTAGCAAAACAAA
Found at i:93392890 original size:3 final size:3
Alignment explanation
Indices: 93392882--93392914 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
93392872 TAGTCCCTAA
93392882 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
93392915 TTTGCTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:93408846 original size:5 final size:5
Alignment explanation
Indices: 93408836--93408860 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
93408826 CACCGTTCAC
93408836 TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA
93408861 AACTCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:93409291 original size:134 final size:132
Alignment explanation
Indices: 93409132--93409400 Score: 457
Period size: 134 Copynumber: 2.0 Consensus size: 132
93409122 ATATATATAT
93409132 ACAAAAAATATATATATATACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGACA
1 ACAAAAAATATATATATATACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGACA
* * *
93409197 ACTCGAACAAGTTACATGATTTCTCAACCAGTTATCTATGCAACTAAAATGAAAAACATGTTCGG
66 AATCGAACAAGTTAAATGATTTCTCAACCAGTTATCTATGCAACTAAAATGAAAAACATGTTCGC
93409262 AA
131 AA
* *
93409264 ACAAAAAGTATATATATACTTACATTCTCAATGTCATGCTCATACTATCTATTATACAATTCCGA
1 ACAAAAAATATATATATA--TACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGA
* *
93409329 CAAATCGGACAAGTTAAATGTTTTCTCAACCAGTTATCTATGCAACTAAAATGAAAAACATGTTC
64 CAAATCGAACAAGTTAAATGATTTCTCAACCAGTTATCTATGCAACTAAAATGAAAAACATGTTC
93409394 GCAA
129 GCAA
93409398 ACA
1 ACA
93409401 GGGAAAACCC
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
132 17 0.13
134 111 0.87
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (132 bp):
ACAAAAAATATATATATATACATTCTCAATGTCATGCTCATACTATCTACTATACAATTCCGACA
AATCGAACAAGTTAAATGATTTCTCAACCAGTTATCTATGCAACTAAAATGAAAAACATGTTCGC
AA
Found at i:93414026 original size:11 final size:10
Alignment explanation
Indices: 93414010--93414076 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 10
93414000 CATATAAATT
93414010 AAAAATTCATA
1 AAAAATT-ATA
93414021 AAAAATTATTA
1 AAAAATTA-TA
* *
93414032 GAAATTTATA
1 AAAAATTATA
*
93414042 AAAAATTATT
1 AAAAATTATA
*
93414052 TAAAA-TATA
1 AAAAATTATA
93414061 AAAAA-TATA
1 AAAAATTATA
*
93414070 GAAAATT
1 AAAAATT
93414077 TTTAAATGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
9 15 0.33
10 15 0.33
11 15 0.33
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:93414036 original size:10 final size:10
Alignment explanation
Indices: 93414007--93414066 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 10
93413997 TTTCATATAA
93414007 ATTAAAAATT
1 ATTAAAAATT
*
93414017 CATAAAAAATT
1 -ATTAAAAATT
*
93414028 ATTAGAAATTT
1 ATTA-AAAATT
*
93414039 ATAAAAAATT
1 ATTAAAAATT
*
93414049 ATTTAAAA-T
1 ATTAAAAATT
*
93414058 ATAAAAAAT
1 ATTAAAAAT
93414067 ATAGAAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
9 7 0.18
10 14 0.37
11 17 0.45
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:93414060 original size:19 final size:20
Alignment explanation
Indices: 93414007--93414066 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
93413997 TTTCATATAA
*
93414007 ATTAAAAATTCATAAAAAATT
1 ATTAGAAATT-ATAAAAAATT
93414028 ATTAGAAATTTATAAAAAATT
1 ATTAGAAA-TTATAAAAAATT
93414049 ATTTA-AAA-TATAAAAAAT
1 A-TTAGAAATTATAAAAAAT
93414067 ATAGAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 10 0.28
21 21 0.58
22 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTAGAAATTATAAAAAATT
Found at i:93414126 original size:31 final size:31
Alignment explanation
Indices: 93414080--93414152 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
93414070 GAAAATTTTT
*
93414080 AAATGTTATAAAATTTTTAGAAAAATATAGA
1 AAATATTATAAAATTTTTAGAAAAATATAGA
* * *
93414111 AAATATTATACAATTTTTTGAAAAATAT-CA
1 AAATATTATAAAATTTTTAGAAAAATATAGA
93414141 AAA-ATTATAAAA
1 AAATATTATAAAA
93414153 AAGAATAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.22
30 4 0.11
31 25 0.68
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (31 bp):
AAATATTATAAAATTTTTAGAAAAATATAGA
Found at i:93419024 original size:17 final size:17
Alignment explanation
Indices: 93419002--93419034 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
93418992 AAAATTGTAT
*
93419002 ATTCTTCTTTTGGTTTG
1 ATTCTTCTTTAGGTTTG
93419019 ATTCTTCTTTAGGTTT
1 ATTCTTCTTTAGGTTT
93419035 TCAAGCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.15, T:0.64
Consensus pattern (17 bp):
ATTCTTCTTTAGGTTTG
Found at i:93428955 original size:36 final size:37
Alignment explanation
Indices: 93428915--93428990 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
93428905 TGAAACATAG
* *
93428915 AAAATATATAAAA-GTATGTGTATATATATAT-TTATA
1 AAAAT-TAAAAAATGTATATGTATATATATATATTATA
* *
93428951 AAAATTAAAAAATGTGTATGTATATGTATATATTATA
1 AAAATTAAAAAATGTATATGTATATATATATATTATA
93428988 AAA
1 AAA
93428991 CGTATGTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 6 0.18
36 20 0.59
37 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.39
Consensus pattern (37 bp):
AAAATTAAAAAATGTATATGTATATATATATATTATA
Found at i:93429281 original size:28 final size:28
Alignment explanation
Indices: 93429249--93429305 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
93429239 ATAATGAATT
93429249 TGAAAATGAATAAAAAGAGAAAAAGAGA
1 TGAAAATGAATAAAAAGAGAAAAAGAGA
* *
93429277 TGAAAATGAATAATAAGGGAAAAAGAGA
1 TGAAAATGAATAAAAAGAGAAAAAGAGA
93429305 T
1 T
93429306 TTGAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (28 bp):
TGAAAATGAATAAAAAGAGAAAAAGAGA
Found at i:93433748 original size:21 final size:21
Alignment explanation
Indices: 93433716--93433756 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
93433706 AGGCTCGAGG
93433716 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
93433737 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
93433757 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:93440282 original size:13 final size:13
Alignment explanation
Indices: 93440264--93440290 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
93440254 TTTCGGTTTA
93440264 ATTTAAACAATAT
1 ATTTAAACAATAT
93440277 ATTTAAACAATAT
1 ATTTAAACAATAT
93440290 A
1 A
93440291 GTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAACAATAT
Found at i:93440541 original size:97 final size:97
Alignment explanation
Indices: 93440375--93440610 Score: 472
Period size: 97 Copynumber: 2.4 Consensus size: 97
93440365 TTAAATTATG
93440375 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTG
1 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTG
93440440 CATATTTTAATTAAAATATAATTCGGTACTTA
66 CATATTTTAATTAAAATATAATTCGGTACTTA
93440472 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTG
1 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTG
93440537 CATATTTTAATTAAAATATAATTCGGTACTTA
66 CATATTTTAATTAAAATATAATTCGGTACTTA
93440569 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
1 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
93440611 TGTTATTAAA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 139 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (97 bp):
TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATGTCCAAATTTAAGATTAAATCTG
CATATTTTAATTAAAATATAATTCGGTACTTA
Found at i:93440683 original size:23 final size:23
Alignment explanation
Indices: 93440648--93440692 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
93440638 CCTTATTTAA
**
93440648 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
93440671 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
93440693 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:93443993 original size:92 final size:91
Alignment explanation
Indices: 93443836--93444044 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
93443826 TTGATTTTAG
* * *
93443836 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
93443901 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
93443928 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
93443992 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
93444020 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
93444045 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:93444007 original size:24 final size:25
Alignment explanation
Indices: 93443972--93444019 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
93443962 TTATGAAATT
93443972 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
93443996 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
93444020 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:93444198 original size:120 final size:120
Alignment explanation
Indices: 93444060--93444352 Score: 473
Period size: 120 Copynumber: 2.4 Consensus size: 120
93444050 AATTATTTTA
* * * * *
93444060 AATTTTATTAAGTCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATT
* *
93444123 TTATAGTATCATATATTATGATTTTAATAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATATTAATTATTAAG
*
93444180 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTACTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
93444245 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATATTAATTATTAAG
93444300 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
93444353 TAAATATGAT
Statistics
Matches: 162, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
119 4 0.02
120 156 0.96
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATATTAATTATTAAG
Found at i:93444220 original size:15 final size:15
Alignment explanation
Indices: 93444185--93444226 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
93444175 TTAAGAATTT
*
93444185 TATTAAATTAT-ATA
1 TATTTAATTATAATA
93444199 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
93444213 TATTTAATAATAAT
1 TATTTAATTATAAT
93444227 TATGTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:93444318 original size:61 final size:59
Alignment explanation
Indices: 93444133--93444320 Score: 170
Period size: 61 Copynumber: 3.1 Consensus size: 59
93444123 TTATAGTATC
93444133 ATATATTATGATTTTAATAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGA-TTT-ATAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
93444194 ATATATT-TTAATTAT-AATAT-ATTTAATAATAATTATGTTACTTTA-TATTTTA-CAGTATC
1 ATATATTATGATTTATAAAT-TCATATAAGAAT-ATTA-ATTA-TTAAGAATTTTATTA-AATT
93444253 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTT-A-TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
93444314 ATATATT
1 ATATATT
93444321 TTAATTATAA
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
57 11 0.12
58 8 0.08
59 20 0.21
60 12 0.13
61 26 0.27
62 7 0.07
63 11 0.12
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (59 bp):
ATATATTATGATTTATAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:93444335 original size:16 final size:16
Alignment explanation
Indices: 93444314--93444355 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
93444304 TTATTAAATT
*
93444314 ATATATTTTAATTATA
1 ATATATTTTAATAATA
93444330 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
93444345 AT-TATGTTTAA
1 ATATAT-TTTAA
93444356 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:93444340 original size:15 final size:15
Alignment explanation
Indices: 93444305--93444346 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
93444295 TTAAGAATTT
*
93444305 TATTAAATTAT-ATA
1 TATTTAATTATAATA
93444319 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
93444333 TATTTAATAATAAT
1 TATTTAATTATAAT
93444347 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:93444469 original size:156 final size:156
Alignment explanation
Indices: 93444288--93444596 Score: 557
Period size: 156 Copynumber: 2.0 Consensus size: 156
93444278 TATAAGAATA
*
93444288 TTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
* * *
93444353 TAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACA
66 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
93444418 ATAATAATTTACCAAAACCAATTTCTG
131 ATAATAATTTACCAAAA-CAATTTCTG
93444445 TTAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
93444509 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
66 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
*
93444574 ATAATCATTTACCAAAACAATTT
131 ATAATAATTTACCAAAACAATTT
93444597 TATGCTAAGG
Statistics
Matches: 147, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
155 6 0.04
156 134 0.91
157 7 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
ATAATAATTTACCAAAACAATTTCTG
Found at i:93444483 original size:18 final size:17
Alignment explanation
Indices: 93444457--93444491 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
93444447 AATTATAAGA
*
93444457 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
93444474 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
93444492 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:93444748 original size:16 final size:16
Alignment explanation
Indices: 93444727--93444762 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
93444717 GATTTGCTAT
93444727 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
93444743 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
93444759 TACA
1 TACA
93444763 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:93455531 original size:4 final size:4
Alignment explanation
Indices: 93455522--93455568 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
93455512 GTTACTAGGG
* *
93455522 TGTT TGTT TGTT TGTT TGTT TGTT GTGTT T-TT T-TT TTTT TTTT TGTT
1 TGTT TGTT TGTT TGTT TGTT TGTT -TGTT TGTT TGTT TGTT TGTT TGTT
93455569 CTTTTCCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
3 6 0.15
4 30 0.75
5 4 0.10
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (4 bp):
TGTT
Found at i:93456815 original size:14 final size:14
Alignment explanation
Indices: 93456796--93456825 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
93456786 TATATTAAAC
*
93456796 TCTTTTTTTCTTTT
1 TCTTTTTTTCTCTT
93456810 TCTTTTTTTCTCTT
1 TCTTTTTTTCTCTT
93456824 TC
1 TC
93456826 CAAGTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TCTTTTTTTCTCTT
Found at i:93471224 original size:8 final size:8
Alignment explanation
Indices: 93471211--93471240 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
93471201 TCATTTTTAT
93471211 TTATTAAA
1 TTATTAAA
93471219 TTATTAAA
1 TTATTAAA
93471227 TTATTTAAA
1 TTA-TTAAA
93471236 TTATT
1 TTATT
93471241 TGTACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTATTAAA
Found at i:93471290 original size:20 final size:20
Alignment explanation
Indices: 93471265--93471332 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
93471255 TTGGGTCGAG
93471265 TTGGGTTTATATATATTGGA
1 TTGGGTTTATATATATTGGA
93471285 TTGGG--T-T-TATATT-GA
1 TTGGGTTTATATATATTGGA
93471300 GTTGGGTTTATATATATTGGA
1 -TTGGGTTTATATATATTGGA
93471321 TTGGGTTTATAT
1 TTGGGTTTATAT
93471333 TGCGTAGGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.05
16 11 0.26
17 1 0.02
18 2 0.05
19 1 0.02
20 23 0.55
21 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.51
Consensus pattern (20 bp):
TTGGGTTTATATATATTGGA
Found at i:93471297 original size:16 final size:16
Alignment explanation
Indices: 93471276--93471334 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 16
93471266 TGGGTTTATA
93471276 TATATTGGATTGGGTT
1 TATATTGGATTGGGTT
93471292 TATATT-GAGTTGGGTTTAT
1 TATATTGGA-TTGGG--T-T
93471311 ATATATTGGATTGGGTT
1 -TATATTGGATTGGGTT
93471328 TATATTG
1 TATATTG
93471335 CGTAGGACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.05
16 18 0.49
17 1 0.03
18 2 0.05
19 1 0.03
20 11 0.30
21 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (16 bp):
TATATTGGATTGGGTT
Found at i:93471309 original size:36 final size:36
Alignment explanation
Indices: 93471262--93471334 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
93471252 GGATTGGGTC
93471262 GAGTTGGGTTTATATATATTGGATTGGGTTTATATT
1 GAGTTGGGTTTATATATATTGGATTGGGTTTATATT
93471298 GAGTTGGGTTTATATATATTGGATTGGGTTTATATT
1 GAGTTGGGTTTATATATATTGGATTGGGTTTATATT
93471334 G
1 G
93471335 CGTAGGACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (36 bp):
GAGTTGGGTTTATATATATTGGATTGGGTTTATATT
Found at i:93476176 original size:42 final size:42
Alignment explanation
Indices: 93476085--93476189 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
93476075 TTAGGGTTAC
* * * * * *
93476085 TGAGACTATGTATAAAACCATATCTGGGATATGACATCTATA
1 TGAGACTTTGTGTAAGACCATATCTAGGATACGACATCGATA
*
93476127 TGAGACTTTGTGTAAGACCATATCTAGGATACGGCATCGATA
1 TGAGACTTTGTGTAAGACCATATCTAGGATACGACATCGATA
**
93476169 TGAGACTTCATGTAAGACCAT
1 TGAGACTTTGTGTAAGACCAT
93476190 GGTTAGGCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (42 bp):
TGAGACTTTGTGTAAGACCATATCTAGGATACGACATCGATA
Found at i:93479616 original size:47 final size:47
Alignment explanation
Indices: 93479550--93479650 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 47
93479540 GAAATGATAG
93479550 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
93479597 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
93479644 CAAGGCC
1 TAAGGCC
93479651 GAGTGGCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
Found at i:93479673 original size:47 final size:47
Alignment explanation
Indices: 93479551--93479690 Score: 145
Period size: 47 Copynumber: 3.0 Consensus size: 47
93479541 AAATGATAGT
* * * * * *
93479551 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGAT
1 AAGGCCGAATGGCCAACGTAATGAATGTGAAAGTGTATATATGTGAC
* * * *
93479598 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
1 AAGGCCGAATGGCCAACGTAATGAATGTGAAAGTGTATATATGTGAC
* * * * *
93479645 AAGGCCGAGTGGCCAACGTAATGGATGTGGAAGTGCATAAATGTGA
1 AAGGCCGAATGGCCAACGTAATGAATGTGAAAGTGTATATATGTGA
93479691 TAAGTCCCGA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 82 1.00
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.25
Consensus pattern (47 bp):
AAGGCCGAATGGCCAACGTAATGAATGTGAAAGTGTATATATGTGAC
Found at i:93479869 original size:37 final size:37
Alignment explanation
Indices: 93479813--93479891 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
93479803 CCGAGCTCTA
* *
93479813 AAGACCCGATGACTACGTGTGGGGATGT-TGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGAT-TATGTCCGGGT
* *
93479850 AAGACCCGATAACTTCGTGTGGAGATTATGTTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
93479887 AAGAC
1 AAGAC
93479892 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:93482813 original size:29 final size:27
Alignment explanation
Indices: 93482781--93482888 Score: 92
Period size: 27 Copynumber: 3.9 Consensus size: 27
93482771 GTCATTCTTT
93482781 TAGAGTGCACCACAAAGGCTTCATTTTCA
1 TAGAGTG--CCACAAAGGCTTCATTTTCA
* *
93482810 TAGATTGCCATAAAGGCTTCATTTTCA
1 TAGAGTGCCACAAAGGCTTCATTTTCA
* * * *
93482837 TAGATTGCTATC-AAGGCTCCCTTTTCA
1 TAGAGTGCCA-CAAAGGCTTCATTTTCA
* * * *
93482864 TAGATTGCTATAAAGGCTCCATTTT
1 TAGAGTGCCACAAAGGCTTCATTTT
93482889 TCTAGCATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 63 0.91
29 6 0.09
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (27 bp):
TAGAGTGCCACAAAGGCTTCATTTTCA
Found at i:93482829 original size:27 final size:27
Alignment explanation
Indices: 93482794--93482888 Score: 145
Period size: 27 Copynumber: 3.5 Consensus size: 27
93482784 AGTGCACCAC
* *
93482794 AAAGGCTTCATTTTCATAGATTGCCAT
1 AAAGGCTCCATTTTCATAGATTGCTAT
*
93482821 AAAGGCTTCATTTTCATAGATTGCTAT
1 AAAGGCTCCATTTTCATAGATTGCTAT
* *
93482848 CAAGGCTCCCTTTTCATAGATTGCTAT
1 AAAGGCTCCATTTTCATAGATTGCTAT
93482875 AAAGGCTCCATTTT
1 AAAGGCTCCATTTT
93482889 TCTAGCATGT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (27 bp):
AAAGGCTCCATTTTCATAGATTGCTAT
Found at i:93485710 original size:12 final size:12
Alignment explanation
Indices: 93485625--93485735 Score: 56
Period size: 12 Copynumber: 9.2 Consensus size: 12
93485615 CTTATCAAGA
*
93485625 TAAATATTAGAT
1 TAAATATTAAAT
93485637 TAAAT-TTAATAT
1 TAAATATTAA-AT
93485649 TAAACCTATTAAAT
1 TAAA--TATTAAAT
*
93485663 T-AATA-GAAAT
1 TAAATATTAAAT
* *
93485673 T-TATCTATAAGA-
1 TAAATAT-TAA-AT
93485685 TAAATATTAAAT
1 TAAATATTAAAT
93485697 TAAAT-TTAATAT
1 TAAATATTAA-AT
*
93485709 TAAGATA-AAAAT
1 TAA-ATATTAAAT
*
93485721 TTAATATTAAAT
1 TAAATATTAAAT
93485733 TAA
1 TAA
93485736 TAAAATACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 26
0.67 0.10 0.23
Matches are distributed among these distances:
10 7 0.09
11 13 0.17
12 37 0.49
13 10 0.13
14 4 0.05
15 4 0.05
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:93485737 original size:11 final size:11
Alignment explanation
Indices: 93485655--93485797 Score: 54
Period size: 11 Copynumber: 13.0 Consensus size: 11
93485645 ATATTAAACC
93485655 TATTAAATTAA
1 TATTAAATTAA
* *
93485666 TA-GAAATTTA
1 TATTAAATTAA
* *
93485676 TCTATAAGATAAA
1 TAT-TAA-ATTAA
93485689 TATTAAATTAA
1 TATTAAATTAA
93485700 -ATTTAATATTAA
1 TA-TTAA-ATTAA
* *
93485712 GATAAAAATTTAA
1 TAT-TAAA-TTAA
93485725 TATTAAATTAA
1 TATTAAATTAA
*
93485736 TA--AAA-TAC
1 TATTAAATTAA
93485744 TATCTAAA-TAA
1 TAT-TAAATTAA
93485755 GTATTAAATTAA
1 -TATTAAATTAA
*
93485767 TA--AAA-TAC
1 TATTAAATTAA
93485775 TATCTAAA-TAA
1 TAT-TAAATTAA
93485786 GTATTAAATTAA
1 -TATTAAATTAA
93485798 ATCTAATATT
Statistics
Matches: 99, Mismatches: 15, Indels: 35
0.66 0.10 0.23
Matches are distributed among these distances:
8 8 0.08
9 6 0.06
10 8 0.08
11 36 0.36
12 27 0.27
13 14 0.14
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
TATTAAATTAA
Found at i:93485753 original size:16 final size:16
Alignment explanation
Indices: 93485734--93485785 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
93485724 ATATTAAATT
93485734 AATAAAATACTATCTA
1 AATAAAATACTATCTA
* * ** *
93485750 AAT-AAGTATTAAATT
1 AATAAAATACTATCTA
93485765 AATAAAATACTATCTA
1 AATAAAATACTATCTA
93485781 AATAA
1 AATAA
93485786 GTATTAAATT
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (16 bp):
AATAAAATACTATCTA
Found at i:93485760 original size:31 final size:31
Alignment explanation
Indices: 93485725--93485797 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
93485715 AAAAATTTAA
93485725 TATTAAATTAATAAAATACTATCTAAATAAG
1 TATTAAATTAATAAAATACTATCTAAATAAG
93485756 TATTAAATTAATAAAATACTATCTAAATAAG
1 TATTAAATTAATAAAATACTATCTAAATAAG
93485787 TATTAAATTAA
1 TATTAAATTAA
93485798 ATCTAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (31 bp):
TATTAAATTAATAAAATACTATCTAAATAAG
Found at i:93487647 original size:3 final size:3
Alignment explanation
Indices: 93487639--93487672 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
93487629 ATTCGATCTT
93487639 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
93487673 ATTTTAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:93489236 original size:152 final size:150
Alignment explanation
Indices: 93488978--93489289 Score: 475
Period size: 153 Copynumber: 2.1 Consensus size: 150
93488968 CTTTATTTTT
* * *
93488978 AAAAAAATCACTACTTTTCTTAAAGATCAAAACTTTATTTTGAAATAATTGAAAAAGATCAAAAC
1 AAAAAAATCACTACTTTTCTAAAAGATCAAAACTTTATTTCGAAATAATTGAAAAAAATCAAAAC
93489043 TTTGTTTTAAAATTTTAAACTTCTCCTTTAAAACGACT-AAAAAACAGATTTTTATTCTTAAAAA
66 TTTGTTTTAAAATTTTAAACTTCTCCTTTAAAACGACTAAAAAAACAGATTTTTATT-TTAAAAA
* * *
93489107 TCTAAACTTTCTTTTTTTTAAT
130 TATAAACTTTC-TCTTTTTAAA
* *
93489129 TAAAAAATCACTACTTTTCTAAAAGATCAAAACTTTGATTTCGAAATAGTTGAAAAAAAATCAAA
1 AAAAAAATCACTACTTTTCTAAAAGATCAAAACTTT-ATTTCGAAATAATTG-AAAAAAATCAAA
* * *
93489194 ACTTTGTTTTAAAATTTTAAACTT-TCCTTTAAAATGACTAAAAAAACATATTTTTATTTTTAAA
64 ACTTTGTTTTAAAATTTTAAACTTCTCCTTTAAAACGACTAAAAAAACAGATTTTTATTTTAAAA
93489258 ATATAAACTTTCTCTTTTTAAA
129 ATATAAACTTTCTCTTTTTAAA
93489280 AAAAAAATCA
1 AAAAAAATCA
93489290 AAACTTTCCT
Statistics
Matches: 146, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
151 51 0.35
152 43 0.29
153 52 0.36
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (150 bp):
AAAAAAATCACTACTTTTCTAAAAGATCAAAACTTTATTTCGAAATAATTGAAAAAAATCAAAAC
TTTGTTTTAAAATTTTAAACTTCTCCTTTAAAACGACTAAAAAAACAGATTTTTATTTTAAAAAT
ATAAACTTTCTCTTTTTAAA
Found at i:93489626 original size:3 final size:3
Alignment explanation
Indices: 93489620--93489679 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
93489610 TAAAAAAAAG
* * * *
93489620 ATA ATA ATA TTTA ATA ATA ATA GTA GTA ATG ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
93489666 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
93489680 TTGTGCACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 48 0.96
4 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:93490305 original size:7 final size:7
Alignment explanation
Indices: 93490293--93490328 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
93490283 AAGACATAAT
93490293 TGTGAAA
1 TGTGAAA
93490300 TGTGAAA
1 TGTGAAA
93490307 TGTGAAA
1 TGTGAAA
93490314 TGTGAAA
1 TGTGAAA
93490321 TGTGAAA
1 TGTGAAA
93490328 T
1 T
93490329 TAAATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.31
Consensus pattern (7 bp):
TGTGAAA
Found at i:93493097 original size:27 final size:27
Alignment explanation
Indices: 93493039--93493177 Score: 147
Period size: 27 Copynumber: 5.1 Consensus size: 27
93493029 TGGCTGCCAA
** *
93493039 AACAGATAA-TGTGATAGAGTCACCAG
1 AACAGATAATTGTGGCAGAGCCACCAG
* *
93493065 ATACAGATAATCGTGGCAGGGCCACCAG
1 A-ACAGATAATTGTGGCAGAGCCACCAG
93493093 AACAGAT-ATATGTGGCAGAGCCACCAG
1 AACAGATAAT-TGTGGCAGAGCCACCAG
* *
93493120 ATCAGATATTTGTGGCAGAGCCACCAG
1 AACAGATAATTGTGGCAGAGCCACCAG
* * * *
93493147 ATCAAATATTTGTGGCATAGCCACCAG
1 AACAGATAATTGTGGCAGAGCCACCAG
93493174 AACA
1 AACA
93493178 CTTCCTCCAT
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.03
27 80 0.82
28 14 0.14
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
AACAGATAATTGTGGCAGAGCCACCAG
Found at i:93494823 original size:26 final size:26
Alignment explanation
Indices: 93494794--93494903 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
93494784 CATGAAATTC
93494794 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
93494820 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
93494846 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
93494872 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
93494898 TTATCA
1 TTATCA
93494904 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:93495030 original size:13 final size:13
Alignment explanation
Indices: 93495012--93495046 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
93495002 CATGCAAATC
93495012 CTCCTATTTTACA
1 CTCCTATTTTACA
93495025 CTCCTATTTTACA
1 CTCCTATTTTACA
93495038 CTCCTATTT
1 CTCCTATTT
93495047 ATTTGACCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (13 bp):
CTCCTATTTTACA
Found at i:93502873 original size:5 final size:5
Alignment explanation
Indices: 93502865--93502890 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
93502855 GAGATGGAAT
93502865 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
93502891 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:93503807 original size:9 final size:9
Alignment explanation
Indices: 93503793--93503829 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
93503783 TATAGTTTGA
93503793 TATTCGAAT
1 TATTCGAAT
93503802 TATTCGAAT
1 TATTCGAAT
*
93503811 TATTCGAGT
1 TATTCGAAT
93503820 TATTCGAAT
1 TATTCGAAT
93503829 T
1 T
93503830 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:93522355 original size:13 final size:12
Alignment explanation
Indices: 93522287--93522358 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
93522277 TTCTTGGTAC
93522287 TTAATTACAAAT-
1 TTAATTA-AAATA
93522299 TT-ATTAAAATTA
1 TTAATTAAAA-TA
93522311 TTAATTAAAA-A
1 TTAATTAAAATA
*
93522322 -TAA-AAAAATA
1 TTAATTAAAATA
**
93522332 TTTTTTAAAATA
1 TTAATTAAAATA
93522344 TTAATTACAAATA
1 TTAATTA-AAATA
93522357 TT
1 TT
93522359 TAATAGTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
9 4 0.09
10 7 0.15
11 7 0.15
12 15 0.32
13 14 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAATTAAAATA
Found at i:93523939 original size:64 final size:64
Alignment explanation
Indices: 93523867--93523994 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 64
93523857 TCATTCATAA
* *
93523867 CACATCTAGTTAGGAGCACTGGTTTCATTTTGATCATAGCATCCTAACTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCACTGGATTCATTTCGATCATAGCATCCTAACTATTTGACATAAGCAT
* * * * **
93523931 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGTATCCTAATTATTTGGTATAAGCAT
1 CACATCTAGTTAGGAGCACTGGATTCATTTCGATCATAGCATCCTAACTATTTGACATAAGCAT
93523995 AGATACATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCACTGGATTCATTTCGATCATAGCATCCTAACTATTTGACATAAGCAT
Found at i:93524337 original size:87 final size:87
Alignment explanation
Indices: 93524061--93524354 Score: 448
Period size: 88 Copynumber: 3.4 Consensus size: 87
93524051 GTGAATTCAC
* *
93524061 GAGCCTTAACCCTCTAAGCAGTAGGGAAACAGGCT-GAAAATTACAGATTTTATCTCCCTAAGCA
1 GAGCCTTAACCC-CTAAGCAGTAGGAAAACAGGCTAG-AAATTACAGATATTATCTCCCTAAGCA
93524125 GTAGTGGAGCAGATCGAAGATGGT
64 GTAGTGGAGCAGATCGAAGATGGT
* * *
93524149 GAGCCTTAGCCCCTTAAGCAGTAGGAAAATAGGCTAGAAATTACATATATTATCTCCCTAAGCAG
1 GAGCCTTAACCCC-TAAGCAGTAGGAAAACAGGCTAGAAATTACAGATATTATCTCCCTAAGCAG
93524214 TAGTGGAGCAGATCGAAGATGGT
65 TAGTGGAGCAGATCGAAGATGGT
* * *
93524237 GAGCTTTAACCCCTAAGCGGTAGGAAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
1 GAGCCTTAACCCCTAAGCAGTAGGAAAACAGGCTAGAAATTACAGATATTATCTCCCTAAGCAGT
*
93524302 -GTGGAACAGATCGAAGATGGT
66 AGTGGAGCAGATCGAAGATGGT
*
93524323 GAGCCTTAATCCCCTAAGCAGTAGGGAAACAG
1 GAGCCTTAA-CCCCTAAGCAGTAGGAAAACAG
93524355 ATCGAAGATG
Statistics
Matches: 188, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
86 28 0.15
87 69 0.37
88 90 0.48
89 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (87 bp):
GAGCCTTAACCCCTAAGCAGTAGGAAAACAGGCTAGAAATTACAGATATTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGT
Found at i:93524360 original size:44 final size:43
Alignment explanation
Indices: 93524204--93524399 Score: 152
Period size: 44 Copynumber: 4.5 Consensus size: 43
93524194 TATATTATCT
* *
93524204 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAGCTTTAA-C
1 CCCTAAGCAGTAG-GGAACAGATCGAAGATGGTGAGCCTTAATC
* * * * * *
93524247 CCCTAAGCGGTAGGAAAACAGGCTAGAA-AT--TACAGATCTT-ATC
1 CCCTAAGCAGTAGG-GAACA-GATCGAAGATGGT-GAG-CCTTAATC
93524290 TCCCTAAGCAGT-GTGGAACAGATCGAAGATGGTGAGCCTTAATC
1 -CCCTAAGCAGTAG-GGAACAGATCGAAGATGGTGAGCCTTAATC
** * *
93524334 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACCC
1 CCCTAAGCAGTAGGG-AACAGATCGAAGATGGTGAGCCTTAA-TC
93524379 CCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGG-AACAG
93524400 GCTGGAAATC
Statistics
Matches: 120, Mismatches: 19, Indels: 26
0.73 0.12 0.16
Matches are distributed among these distances:
41 1 0.01
42 9 0.08
43 43 0.36
44 45 0.38
45 22 0.18
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGAACAGATCGAAGATGGTGAGCCTTAATC
Found at i:93524399 original size:45 final size:43
Alignment explanation
Indices: 93524204--93524399 Score: 148
Period size: 43 Copynumber: 4.5 Consensus size: 43
93524194 TATATTATCT
* ** *
93524204 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAGCTTTAA-C
1 CCCTAAGCAGTAG-GGAACAGATCGAAGATGAAGAGCCTTAACC
* * * * * * * *
93524247 CCCTAAGCGGTAGGAAAACAGGCTAGAA-ATTACAGA-TCTTATCT
1 CCCTAAGCAGTAGG-GAACA-GATCGAAGATGA-AGAGCCTTAACC
** *
93524291 CCCTAAGCAGT-GTGGAACAGATCGAAGATGGTGAGCCTTAATC
1 CCCTAAGCAGTAG-GGAACAGATCGAAGATGAAGAGCCTTAACC
*
93524334 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACCC
1 CCCTAAGCAGTAGGG-AACAGATCGAAGATGAAGAGCCTTAA-CC
93524379 CCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGG-AACAG
93524400 GCTGGAAATC
Statistics
Matches: 115, Mismatches: 28, Indels: 18
0.71 0.17 0.11
Matches are distributed among these distances:
42 8 0.07
43 44 0.38
44 42 0.37
45 21 0.18
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGAACAGATCGAAGATGAAGAGCCTTAACC
Found at i:93524569 original size:88 final size:88
Alignment explanation
Indices: 93524414--93525024 Score: 820
Period size: 88 Copynumber: 7.0 Consensus size: 88
93524404 GAAATCAAGT
* * * * * *
93524414 CAGTGGTGGAGCAGATTGAAGACAGTGAGCCTTAACCCCCTAAGCAGTAGGAAAACAAGCTGAAA
1 CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGAA
93524479 ATTACAGATCTTATCTCCCTAAG
66 ATTACAGATCTTATCTCCCTAAG
* * * *
93524502 CAGTAGTGGAGCGGATCGAGGACAGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAAGCTGGAA
1 CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGAA
*
93524567 ATTACAAATCTTATCTCCCTAAG
66 ATTACAGATCTTATCTCCCTAAG
* * * * * *
93524590 CAGTACTGGAGCAGATCAAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGAGAAATAGGCCGAAA
1 CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGAA
*
93524655 ATTTCAGATCTTATCTCCCTAAG
66 ATTACAGATCTTATCTCCCTAAG
* * * * * *
93524678 CAAT-GTGGAATC-GATCGAAGATGGTGAGCCTTAACCTCCTAAGCA-TAGGGAAACTGGTTGGA
1 CAGTAGTGG-AGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGA
*
93524740 AATTACAGATCTTATATCCCTAAG
65 AATTACAGATCTTATCTCCCTAAG
* * *
93524764 CAGTAGTGGAGCAAATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAAGGAAACAGGCTAGAA
1 CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGAA
* * *
93524829 ATTACAGATCTCAACTCCTTAAG
66 ATTACAGATCTTATCTCCCTAAG
93524852 CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCT-GAA
1 CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGAA
* *
93524916 GATTATAGATCTCATCTCCCTAAG
66 -ATTACAGATCTTATCTCCCTAAG
* * *
93524940 CAGTAGTGGAGCGGATCGAAGATGGTGAGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCT-GAA
1 CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGAA
93525004 GATTACA-AGTCTTATCTCCCT
66 -ATTACAGA-TCTTATCTCCCT
93525025 CAAGTTGCAG
Statistics
Matches: 461, Mismatches: 56, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
86 38 0.08
87 71 0.15
88 352 0.76
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGGAA
ATTACAGATCTTATCTCCCTAAG
Found at i:93524587 original size:44 final size:44
Alignment explanation
Indices: 93524451--93524594 Score: 114
Period size: 44 Copynumber: 3.3 Consensus size: 44
93524441 AGCCTTAACC
* * *
93524451 CCCTAAGCAGTAGGAAAACAAGCTGAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGGGAAACAAGCTGGAAATTACAAATCTTATCT
* * * * * * * ** * *
93524495 CCCTAAGCAGTAGTGG-AGCGGATCGAGGACAGT--GAGCCTTAACC
1 CCCTAAGCAGTAG-GGAAAC-AAGC-TGGAAATTACAAATCTTATCT
93524539 CCCTAAGCAGTAGGGAAACAAGCTGGAAATTACAAATCTTATCT
1 CCCTAAGCAGTAGGGAAACAAGCTGGAAATTACAAATCTTATCT
93524583 CCCTAAGCAGTA
1 CCCTAAGCAGTA
93524595 CTGGAGCAGA
Statistics
Matches: 69, Mismatches: 25, Indels: 12
0.65 0.24 0.11
Matches are distributed among these distances:
42 5 0.07
43 4 0.06
44 53 0.77
45 3 0.04
46 4 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (44 bp):
CCCTAAGCAGTAGGGAAACAAGCTGGAAATTACAAATCTTATCT
Found at i:93524896 original size:44 final size:44
Alignment explanation
Indices: 93524757--93524989 Score: 147
Period size: 44 Copynumber: 5.3 Consensus size: 44
93524747 GATCTTATAT
*
93524757 CCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
* * * * * * * * *
93524801 CCCTAAGCAGTAAG-GAAACAGGCTAGAA-A--TTACAGATCTCAACT
1 CCCTAAGCAGT-AGTGGAGCA-GATCGAAGACGGT-GAG-CCTTAACC
*
93524845 CCTTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
* * *** * * * *
93524889 CCCTAAGCAGTAG-GGAAACAG-GCTGAAGATTAT-AGATCTCATCT
1 CCCTAAGCAGTAGTGG-AGCAGATC-GAAGACGGTGAG-CCTTAACC
* * *
93524933 CCCTAAGCAGTAGTGGAGCGGATCGAAGATGGTGAGCCTTATCC
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
93524977 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
93524990 GGAAACAGGC
Statistics
Matches: 137, Mismatches: 38, Indels: 28
0.67 0.19 0.14
Matches are distributed among these distances:
42 1 0.01
43 14 0.10
44 108 0.79
45 13 0.09
46 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (44 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
Found at i:93525005 original size:44 final size:44
Alignment explanation
Indices: 93524869--93525006 Score: 147
Period size: 44 Copynumber: 3.1 Consensus size: 44
93524859 GGAGCAGATC
* *
93524869 GAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCT
1 GAAGATGGTGAGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCT
** * * * * *
93524913 GAAGATTAT-AGATCTCATCTCCCTAAGCAGTAGTGG-AGC-GGAT
1 GAAGATGGTGAG-CCTTATCCCCCTAAGCAGTAG-GGAAACAGGCT
93524956 CGAAGATGGTGAGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCT
1 -GAAGATGGTGAGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCT
93525001 GAAGAT
1 GAAGAT
93525007 TACAAGTCTT
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
43 7 0.10
44 58 0.81
45 7 0.10
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (44 bp):
GAAGATGGTGAGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCT
Found at i:93525018 original size:44 final size:43
Alignment explanation
Indices: 93524882--93525024 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 43
93524872 GACGGTGAGC
* *
93524882 CTTAACCCCCTAAGCAGTAGGGAAACAGGCTGAAGATTATAGAT
1 CTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAGATTAAAG-T
* * * * * *
93524926 CTCATCTCCCTAAGCAGTAGTGG-AGC-GGATCGAAGATGGT-GAGC
1 CTTATCCCCCTAAGCAGTAG-GGAAACAGGCT-GAAGAT--TAAAGT
93524970 CTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAGATTACAAGT
1 CTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAGATTA-AAGT
*
93525014 CTTATCTCCCT
1 CTTATCCCCCT
93525025 CAAGTTGCAG
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
42 1 0.01
43 5 0.06
44 63 0.82
45 7 0.09
46 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (43 bp):
CTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAGATTAAAGT
Found at i:93529462 original size:14 final size:14
Alignment explanation
Indices: 93529443--93529471 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
93529433 ATACCCACTA
93529443 CGAACAGTATACTC
1 CGAACAGTATACTC
93529457 CGAACAGTATACTC
1 CGAACAGTATACTC
93529471 C
1 C
93529472 CCAGACTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (14 bp):
CGAACAGTATACTC
Found at i:93531593 original size:23 final size:23
Alignment explanation
Indices: 93531567--93531614 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
93531557 AGTACCAAAT
*
93531567 GTACCAAAGTACTAATAATAGAA
1 GTACCAAAGTACTAATAACAGAA
* * *
93531590 GTACTATAGTACTAGTAACAGAA
1 GTACCAAAGTACTAATAACAGAA
93531613 GT
1 GT
93531615 CCCCTATTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (23 bp):
GTACCAAAGTACTAATAACAGAA
Found at i:93531723 original size:88 final size:88
Alignment explanation
Indices: 93531574--93531751 Score: 302
Period size: 88 Copynumber: 2.0 Consensus size: 88
93531564 AATGTACCAA
*
93531574 AGTACTAATAATAGAAGTACTATAGTACTAGTAACAGAAGTCCCCTATTGGCATGCCAATCGTAT
1 AGTACTAATAATAGAAGTACTATAGTACTAGTAACAGAAGTCCCCTATTGACATGCCAATCGTAT
* *
93531639 GTTAACTCTTTAACTAAGCTACT
66 GCTAACTATTTAACTAAGCTACT
* * *
93531662 AGTACTAATAATAGAAGTACTATAGTGCTAGTAACAGAAGTTCCCTATTGACATTCCAATCGTAT
1 AGTACTAATAATAGAAGTACTATAGTACTAGTAACAGAAGTCCCCTATTGACATGCCAATCGTAT
93531727 GCTAACTATTTAACTAAGCTACT
66 GCTAACTATTTAACTAAGCTACT
93531750 AG
1 AG
93531752 AGCCTTTTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (88 bp):
AGTACTAATAATAGAAGTACTATAGTACTAGTAACAGAAGTCCCCTATTGACATGCCAATCGTAT
GCTAACTATTTAACTAAGCTACT
Found at i:93532571 original size:29 final size:28
Alignment explanation
Indices: 93532531--93532594 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
93532521 GAATCGAGTT
93532531 ATTTGAGTCAAATCGAATTT-TTTTCGA
1 ATTTGAGTCAAATCGAATTTGTTTTCGA
*
93532558 ATTTCGAGTTCAAATCGAGTTTGGTTTTCGA
1 ATTT-GAG-TCAAATCGAATTT-GTTTTCGA
93532589 ATTTGA
1 ATTTGA
93532595 ATAACTCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.12
28 3 0.09
29 12 0.38
30 2 0.06
31 11 0.34
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.44
Consensus pattern (28 bp):
ATTTGAGTCAAATCGAATTTGTTTTCGA
Found at i:93533076 original size:18 final size:18
Alignment explanation
Indices: 93533037--93533078 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
93533027 TTAAAAAATT
* *
93533037 ATATTTTTTACATTTAAT
1 ATATATTTTACATTTAAA
93533055 ATATATTTTA-ATTTCAAA
1 ATATATTTTACATTT-AAA
93533073 ATATAT
1 ATATAT
93533079 AGTGACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTTTACATTTAAA
Found at i:93540815 original size:5 final size:6
Alignment explanation
Indices: 93540786--93540813 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
93540776 ACCAATTGAA
93540786 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
93540814 GACCCTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:93543941 original size:17 final size:18
Alignment explanation
Indices: 93543919--93543952 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
93543909 TCACATTGAA
93543919 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
93543936 GTGTTTTCATTGAAAAC
1 GTGTTTTCAGTGAAAAC
93543953 TCTTCTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:93545100 original size:29 final size:29
Alignment explanation
Indices: 93545014--93545128 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
93545004 TACCTGTATC
* * *
93545014 TGGCCCACTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * **
93545042 TGACCCATTAGGCCCAAATCACCTAAATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
93545071 TGGCCCATTAGGCCTAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * * *
93545100 TAGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
93545128 T
1 T
93545129 TCATGCTCAC
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
28 24 0.35
29 45 0.65
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:93553053 original size:31 final size:32
Alignment explanation
Indices: 93553012--93553077 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
93553002 TTTAAATTAA
*
93553012 TTAATTAGATA-AATATTATTTTATTAATATT
1 TTAATGAGATATAATATTATTTTATTAATATT
* *
93553043 TTAATGAGATATTTATTATTATTTTATTATTATT
1 TTAATGAGATA--TAATATTATTTTATTAATATT
93553077 T
1 T
93553078 ATTTAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
34 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (32 bp):
TTAATGAGATATAATATTATTTTATTAATATT
Found at i:93554857 original size:32 final size:32
Alignment explanation
Indices: 93554761--93554873 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 32
93554751 TACCTAAAAG
* *
93554761 GTACAACTGGAAAAGGAAATGTACACTGTGTGT
1 GTACAACTTGAAAAGAAAATGTACACT-TGTGT
*
93554794 GTACAACTT-AAATAGAAAACGTACACTTTGTGT
1 GTACAACTTGAAA-AGAAAATGTACAC-TTGTGT
*
93554827 GTAC-ACTTGAAAAGAAAATGTACGGCTTGTGT
1 GTACAACTTGAAAAGAAAATGTAC-ACTTGTGT
93554859 GTACAA-TATGAAAAG
1 GTACAACT-TGAAAAG
93554874 TGGTAGCTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
32 28 0.41
33 40 0.58
34 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (32 bp):
GTACAACTTGAAAAGAAAATGTACACTTGTGT
Found at i:93554904 original size:31 final size:31
Alignment explanation
Indices: 93554867--93555044 Score: 275
Period size: 31 Copynumber: 5.7 Consensus size: 31
93554857 GTGTACAATA
*
93554867 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
* * *
93554898 TGAAAAGTGGTAGCTTCAGCTATCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
*
93554929 TGAAAAGTGGTAGCTTTGGCTACCTGATTAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
*
93554960 TGAAAAGTAGTAGCTTCGGCTACCTGATTAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
* *
93554991 TGAAAAGTGGTAGCTCCAGCTACCTGATTAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
*
93555022 TGAATAGTGGTAGCTTCGGCTAC
1 TGAAAAGTGGTAGCTTCGGCTAC
93555045 AAGTGATAAA
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 133 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
Found at i:93555167 original size:27 final size:27
Alignment explanation
Indices: 93555136--93555197 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
93555126 GTTGAACTAT
* * *
93555136 GCAAAGTGATAAAGTGTGTCAATCATG
1 GCAAAGTGATAAAGTGTGCCAAACATA
*
93555163 GCAAAGTGATATAGTGTGCCAAACATA
1 GCAAAGTGATAAAGTGTGCCAAACATA
93555190 GCAAAGTG
1 GCAAAGTG
93555198 TTTAGTGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (27 bp):
GCAAAGTGATAAAGTGTGCCAAACATA
Found at i:93555270 original size:34 final size:34
Alignment explanation
Indices: 93555239--93555313 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
93555229 ACCATGGTTG
93555239 ATCCATGAAAAAG-TGTGAAACGTAGGTATGGTAT
1 ATCCAT-AAAAAGCTGTGAAACGTAGGTATGGTAT
* *** *
93555273 TTCCATACCGAGCTGTGAAACGTAGGTATGGTGT
1 ATCCATAAAAAGCTGTGAAACGTAGGTATGGTAT
*
93555307 TTCCATA
1 ATCCATA
93555314 CTGAGTTGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 3 0.09
34 32 0.91
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (34 bp):
ATCCATAAAAAGCTGTGAAACGTAGGTATGGTAT
Found at i:93555314 original size:34 final size:34
Alignment explanation
Indices: 93555252--93555325 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
93555242 CATGAAAAAG
93555252 TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
1 TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
* * *
93555286 TGTGAAACGTAGGTATGGTGTTTCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
93555320 TGTGAA
1 TGTGAA
93555326 TCGTGGCACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (34 bp):
TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
Found at i:93561214 original size:15 final size:15
Alignment explanation
Indices: 93561194--93561228 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
93561184 TCAATATTAT
93561194 GCATATATAAACTAA
1 GCATATATAAACTAA
93561209 GCATATATAAACTAA
1 GCATATATAAACTAA
93561224 GCATA
1 GCATA
93561229 CATACACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (15 bp):
GCATATATAAACTAA
Found at i:93561955 original size:39 final size:39
Alignment explanation
Indices: 93561907--93562045 Score: 134
Period size: 45 Copynumber: 3.4 Consensus size: 39
93561897 TTATAATGCA
93561907 AACAGGAGCATAAATATGCTATCAAGAGCACCTAGTGCT
1 AACAGGAGCATAAATATGCTATCAAGAGCACCTAGTGCT
* * * * *
93561946 AACAAGAGCAAAAATGTGCTATCAGGAGCACTGTAGTGCT
1 AACAGGAGCATAAATATGCTATCAAGAGCAC-CTAGTGCT
* *
93561986 AACAGGAGCATGAATGTGCCATGCTATCATGAGCACCATAGTGCT
1 AACAGGAGCAT-AA-AT---ATGCTATCAAGAGCACC-TAGTGCT
* *
93562031 AACGGGAGCACAAAT
1 AACAGGAGCATAAAT
93562046 GTACTATCGG
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
39 27 0.34
40 16 0.20
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 30 0.38
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (39 bp):
AACAGGAGCATAAATATGCTATCAAGAGCACCTAGTGCT
Found at i:93562004 original size:20 final size:20
Alignment explanation
Indices: 93561941--93562004 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
93561931 AGAGCACCTA
* **
93561941 GTGCTAACAAGAGCAAAAAT
1 GTGCTAACAGGAGCATGAAT
* *
93561961 GTGCTATCAGGAGCACTGTA-
1 GTGCTAACAGGAGCA-TGAAT
93561981 GTGCTAACAGGAGCATGAAT
1 GTGCTAACAGGAGCATGAAT
93562001 GTGC
1 GTGC
93562005 CATGCTATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.09
20 31 0.89
21 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.20
Consensus pattern (20 bp):
GTGCTAACAGGAGCATGAAT
Found at i:93562422 original size:13 final size:13
Alignment explanation
Indices: 93562404--93562429 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
93562394 ATATAATAGT
93562404 TAAATTCAAAATA
1 TAAATTCAAAATA
93562417 TAAATTCAAAATA
1 TAAATTCAAAATA
93562430 CATTATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATTCAAAATA
Found at i:93562784 original size:16 final size:16
Alignment explanation
Indices: 93562763--93562830 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
93562753 TTTGGTTCGC
93562763 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
93562779 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
93562795 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
93562811 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
93562827 TGTA
1 TGTA
93562831 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:93563087 original size:18 final size:17
Alignment explanation
Indices: 93563066--93563100 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
93563056 TTATTATTAA
*
93563066 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
93563084 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
93563101 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:93564997 original size:30 final size:30
Alignment explanation
Indices: 93564961--93565020 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
93564951 TCTAGCACAT
93564961 TCCTGCTTCCATTATCACCAGCAATACTAA
1 TCCTGCTTCCATTATCACCAGCAATACTAA
*
93564991 TCCTGCTTCCATTATCACCTGCAATACTAA
1 TCCTGCTTCCATTATCACCAGCAATACTAA
93565021 GTATCCCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.32
Consensus pattern (30 bp):
TCCTGCTTCCATTATCACCAGCAATACTAA
Found at i:93571035 original size:93 final size:93
Alignment explanation
Indices: 93570927--93571098 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
93570917 CGCCCATAAG
* * * *
93570927 CGAACTCGGACTCAACTCATCGAGCTCGGGCGTTTGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
93570992 ACGAGTTCGGATGCCTGGTTACATCTCA
66 ACGAGTTCGGATGCCTGGTTACATCTCA
* *
93571020 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
93571085 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
93571099 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTGGTTACATCTCA
Found at i:93571095 original size:46 final size:46
Alignment explanation
Indices: 93570920--93571095 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
93570910 TGTAACCCGC
* * * *
93570920 CCATAAGCGAACTCGGACTCAACTCATCGAGCTCGGGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * *
93570966 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTGGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA--CAT--TTGCAT
* *
93571016 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
93571059 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
93571096 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 4 0.04
46 61 0.56
47 28 0.26
48 4 0.04
49 1 0.01
50 5 0.05
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:93571114 original size:46 final size:45
Alignment explanation
Indices: 93570971--93571114 Score: 132
Period size: 46 Copynumber: 3.1 Consensus size: 45
93570961 TGCATCCATA
* **
93570971 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTGGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATG-CT--CAACCATCT
* * * * *
93571018 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCT
93571064 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
93571110 AGTGA
1 AGTGA
93571115 CATGTCACTT
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 33 0.43
47 30 0.39
48 2 0.03
49 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:93590767 original size:45 final size:45
Alignment explanation
Indices: 93590658--93590832 Score: 223
Period size: 45 Copynumber: 4.0 Consensus size: 45
93590648 TTTTATCAAA
* *
93590658 TCACCGGCAT-TTAGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATT
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATT
* * * * * *
93590700 TCACCAGCATGATAGCCCGCTAGACTCGAAGGCCCGAATAGTATC
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATT
*
93590745 TCATCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATT
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATT
*
93590790 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCTCGAATAGTA
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
93590833 CTTTACGATA
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
42 9 0.08
43 16 0.14
44 5 0.04
45 84 0.73
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (45 bp):
TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATT
Found at i:93594327 original size:29 final size:29
Alignment explanation
Indices: 93594294--93594351 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
93594284 AGAAAAAAAG
* *
93594294 GTCTTTAAGTTCGGAATTGACCCGAACTA
1 GTCTTTAAGTTCGAAATTAACCCGAACTA
93594323 GTCTTTAAGTTCGAAATTAACCCGAACTA
1 GTCTTTAAGTTCGAAATTAACCCGAACTA
93594352 ACTACTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (29 bp):
GTCTTTAAGTTCGAAATTAACCCGAACTA
Found at i:93598268 original size:49 final size:50
Alignment explanation
Indices: 93598207--93598431 Score: 292
Period size: 49 Copynumber: 4.5 Consensus size: 50
93598197 TGAGGTCATG
* **
93598207 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTATT-GGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCACA
* * * * *
93598256 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TTAGGTCACA
* * ** *
93598307 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCACA
* *
93598357 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATT-GGTCTCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCACA
93598406 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
93598432 TGCGTACCAG
Statistics
Matches: 151, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
49 67 0.44
50 46 0.30
51 38 0.25
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCACA
Found at i:93598396 original size:101 final size:98
Alignment explanation
Indices: 93598207--93598443 Score: 312
Period size: 99 Copynumber: 2.4 Consensus size: 98
93598197 TGAGGTCATG
* * **
93598207 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTATTGGTTGCATGTGTAGTACTAAGTG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGATTGGTCACATGTGTAGTACTAAGTG
** *
93598272 CAGGCTACTATGCGTACCTGATAACTTCGATCACA
66 CAGGCTACTACACGTACCGGATAA-TT-GATCACA
* * *
93598307 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGATT-GGTCACATGTGTAGTACTAAGT
* * *
93598372 GCAGGCTACTACATGTACCGGATAATTGGTCTCA
65 GCAGGCTACTACACGTACCGGATAATTGATCACA
* *
93598406 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
93598444 AGCTTTGGCT
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
99 40 0.33
100 40 0.33
101 40 0.33
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (98 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGATTGGTCACATGTGTAGTACTAAGTG
CAGGCTACTACACGTACCGGATAATTGATCACA
Found at i:93602470 original size:46 final size:45
Alignment explanation
Indices: 93602403--93602574 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 45
93602393 AACCCGCCCC
*
93602403 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCA
**
93602449 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTATAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCA
* * * *
93602497 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCATCCA
* *
93602542 TAGGTGAACTTGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
93602575 ATGCTCATCC
Statistics
Matches: 105, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 1 0.01
46 59 0.56
47 28 0.27
48 3 0.03
49 2 0.02
50 2 0.02
51 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCA
Found at i:93602515 original size:93 final size:93
Alignment explanation
Indices: 93602408--93602578 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
93602398 GCCCCTAAGT
* *
93602408 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
93602473 CGAGTTCGGATGCCTAGTTATATCTCAC
66 CGAGTTCGGATGCCTAGTTATATCTCAC
* * * *
93602501 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAGGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
93602566 CGAGTTCGGATGC
66 CGAGTTCGGATGC
93602579 TCATCCTAGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTATATCTCAC
Found at i:93603908 original size:48 final size:48
Alignment explanation
Indices: 93603837--93604155 Score: 338
Period size: 48 Copynumber: 6.5 Consensus size: 48
93603827 GGATATTACA
* * * * *
93603837 AAGACCATGTTTGGTACATGGCATCAACGATGGTATATGTGCCAGTGT
1 AAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTGCCAGTGT
* *
93603885 AAGACCATGTCTGGGATATGGCATCAGCGATGATATATGTGCCAGTGT
1 AAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTGCCAGTGT
* * *
93603933 AAGACCATGTCTAGGACATGGCATTAGCGATGATATGTGTGCCTGTGT
1 AAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTGCCAGTGT
* * * *
93603981 AAGACCATGTTTGGGACATAGCACATATCATCGGTGATGATATGTGTGCCTGTGT
1 AAGACCATGTCTGGGACAT-G-GC--ATCA---GCGATGATATGTGTGCCAGTGT
** *
93604036 AAGACCATGTCTGGGACATGGCATTGGCGATGATATGTGTGCCAGCGT
1 AAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTGCCAGTGT
* * * *
93604084 AAGACCATGTTTGGGACATGGCATCGGTGATGATATGTG-GATTCA-TGT
1 AAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTG--CCAGTGT
93604132 AAGACCATGT-TGGAGACATGGCAT
1 AAGACCATGTCTGG-GACATGGCAT
93604156 TGGTACTTTA
Statistics
Matches: 234, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
47 4 0.02
48 180 0.77
49 3 0.01
50 1 0.00
51 2 0.01
52 3 0.01
53 1 0.00
54 1 0.00
55 39 0.17
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (48 bp):
AAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTGCCAGTGT
Found at i:93604053 original size:103 final size:103
Alignment explanation
Indices: 93603913--93604102 Score: 326
Period size: 103 Copynumber: 1.8 Consensus size: 103
93603903 TGGCATCAGC
*
93603913 GATGATATATGTGCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCGATGATATGTGTGCCTG
1 GATGATATATGTGCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCGATGATATGTGTGCCAG
*
93603978 TGTAAGACCATGTTTGGGACATAGCACATATCATCGGT
66 CGTAAGACCATGTTTGGGACATAGCACATATCATCGGT
* * * *
93604016 GATGATATGTGTGCCTGTGTAAGACCATGTCTGGGACATGGCATTGGCGATGATATGTGTGCCAG
1 GATGATATATGTGCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCGATGATATGTGTGCCAG
93604081 CGTAAGACCATGTTTGGGACAT
66 CGTAAGACCATGTTTGGGACAT
93604103 GGCATCGGTG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 81 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (103 bp):
GATGATATATGTGCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCGATGATATGTGTGCCAG
CGTAAGACCATGTTTGGGACATAGCACATATCATCGGT
Done.