Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 19 of 21
Found at i:3225221 original size:6 final size:6
Alignment explanation
Indices: 3225210--3225235 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3225200 TCCATCATCG
3225210 TGATCA TGATCA TGATCA TGATCA TG
1 TGATCA TGATCA TGATCA TGATCA TG
3225236 TTGTCATCAT
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:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (6 bp):
TGATCA
Found at i:3234941 original size:39 final size:39
Alignment explanation
Indices: 3234890--3234972 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 39
3234880 GTTTCAAGTG
3234890 TTATATATTTA-TATAATTTT-TA-TAAATTTTAA-CATAT
1 TTATAT-TTTATTAT-ATTTTATATTAAATTTTAATCATAT
* *
3234927 TTATATTTTATTATATTTTATATTATATTTTAATTATAT
1 TTATATTTTATTATATTTTATATTAAATTTTAATCATAT
3234966 TTATATT
1 TTATATT
3234973 ATATAATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 9 0.22
37 11 0.28
38 9 0.22
39 11 0.28
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (39 bp):
TTATATTTTATTATATTTTATATTAAATTTTAATCATAT
Found at i:3234943 original size:5 final size:5
Alignment explanation
Indices: 3234927--3234985 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
3234917 TTTAACATAT
* *
3234927 TTATA TTTTA TTATA TTTTATA TTATA TTTTAA TTATA TTTATA TTATA
1 TTATA TTATA TTATA --TTATA TTATA TTAT-A TTATA -TTATA TTATA
3234976 -TA-A TTATA TT
1 TTATA TTATA TT
3234986 GTGTTTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 25 0.57
6 9 0.20
7 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:3234948 original size:17 final size:17
Alignment explanation
Indices: 3234926--3234976 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
3234916 TTTTAACATA
3234926 TTTATATTTTATTATAT
1 TTTATATTTTATTATAT
* *
3234943 TTTATATTATATTTTA-
1 TTTATATTTTATTATAT
*
3234959 ATTATATTTATATTATAT
1 TTTATATTT-TATTATAT
3234977 AATTATATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTTTATTATAT
Found at i:3234954 original size:22 final size:22
Alignment explanation
Indices: 3234927--3234976 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3234917 TTTAACATAT
3234927 TTATATTTT-ATTATATTTTATA
1 TTATATTTTAATTATA-TTTATA
3234949 TTATATTTTAATTATATTTATA
1 TTATATTTTAATTATATTTATA
3234971 TTATAT
1 TTATAT
3234977 AATTATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATTTTAATTATATTTATA
Found at i:3237140 original size:22 final size:23
Alignment explanation
Indices: 3237115--3237172 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
3237105 ATATTTAACC
*
3237115 AATTAAAATTTTA-T-ATTATTAA
1 AATTAAAATTTAATTAATT-TTAA
3237137 AATT-AAATTTAATTAATTTTAA
1 AATTAAAATTTAATTAATTTTAA
3237159 AATTTAAAATTTAA
1 AA-TTAAAATTTAA
3237173 AATTTATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 7 0.23
22 11 0.35
23 5 0.16
24 8 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTAAAATTTAATTAATTTTAA
Found at i:3237166 original size:7 final size:7
Alignment explanation
Indices: 3237133--3237178 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
3237123 TTTTATATTA
3237133 TTAAAA-
1 TTAAAAT
3237139 TT-AAAT
1 TTAAAAT
3237145 TTAATTAATT
1 TTAA--AA-T
3237155 TTAAAAT
1 TTAAAAT
3237162 TTAAAAT
1 TTAAAAT
3237169 TTAAAAT
1 TTAAAAT
3237176 TTA
1 TTA
3237179 TAATATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 3 0.09
6 4 0.11
7 19 0.54
8 2 0.06
9 2 0.06
10 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTAAAAT
Found at i:3237176 original size:22 final size:22
Alignment explanation
Indices: 3237117--3237186 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
3237107 ATTTAACCAA
* *
3237117 TTAAAATTTTATATTATTAAAA-
1 TTAAAATTTAAAATT-TTAAAAT
3237139 TT-AAATTTAATTAATTTTAAAAT
1 TTAAAATTTAA--AATTTTAAAAT
*
3237162 TTAAAATTTAAAATTTATAATAT
1 TTAAAATTTAAAATTT-TAAAAT
3237185 TT
1 TT
3237187 TATTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.17
22 13 0.32
23 12 0.30
24 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAAATTTAAAATTTTAAAAT
Found at i:3237241 original size:24 final size:24
Alignment explanation
Indices: 3237215--3237268 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3237205 TTATATATAA
3237215 AAAATT-TATAATAT-TTATAAGTT
1 AAAATTATATAATATGTT-TAAGTT
3237238 AAAATTATATAATATGTTTAAG-T
1 AAAATTATATAATATGTTTAAGTT
3237261 AAATATTA
1 AAA-ATTA
3237269 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 10 0.36
24 16 0.57
25 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (24 bp):
AAAATTATATAATATGTTTAAGTT
Found at i:3251671 original size:2 final size:2
Alignment explanation
Indices: 3251664--3251727 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3251654 CGTATGAGTG
3251664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3251706 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3251728 AAGGTTGAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3257045 original size:37 final size:37
Alignment explanation
Indices: 3256995--3257072 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
3256985 ACCTTTACTA
3256995 TTGTTGTTGAAATTTAATAATAAAGGATCCTCAAGTT
1 TTGTTGTTGAAATTTAATAATAAAGGATCCTCAAGTT
3257032 TTGTTGTTGAAATTTAATAATAAAGGATCCTCAAGTT
1 TTGTTGTTGAAATTTAATAATAAAGGATCCTCAAGTT
3257069 TTGT
1 TTGT
3257073 CGATCACTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (37 bp):
TTGTTGTTGAAATTTAATAATAAAGGATCCTCAAGTT
Found at i:3263218 original size:41 final size:41
Alignment explanation
Indices: 3263173--3263358 Score: 291
Period size: 41 Copynumber: 4.5 Consensus size: 41
3263163 ACTATTTTTT
*
3263173 TTTGATAAGGCGTGGGCACGCTAAGAAAACGGAAGCTCTCG
1 TTTGATAAGGCGTGGGCACGCTAAGAAAACAGAAGCTCTCG
* * *
3263214 TTTGATAAGGCGTGGGTACGTTAATAAAACAGAAGCTCTCG
1 TTTGATAAGGCGTGGGCACGCTAAGAAAACAGAAGCTCTCG
* *
3263255 TTTGATAAGGCGTGGGCACGTTAATAAAACAGAAGCTCTCG
1 TTTGATAAGGCGTGGGCACGCTAAGAAAACAGAAGCTCTCG
* * *
3263296 TTTGATAAGGCGTGGGGACACTAAGAAAAAAGAAGCTCTCG
1 TTTGATAAGGCGTGGGCACGCTAAGAAAACAGAAGCTCTCG
3263337 TTTGATAAGGCGTGGGCACGCT
1 TTTGATAAGGCGTGGGCACGCT
3263359 CTATGAAAAG
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.23
Consensus pattern (41 bp):
TTTGATAAGGCGTGGGCACGCTAAGAAAACAGAAGCTCTCG
Found at i:3269181 original size:3 final size:3
Alignment explanation
Indices: 3269173--3269199 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3269163 AGATTGGTCT
3269173 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
3269200 CAGTAGTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:3272641 original size:38 final size:38
Alignment explanation
Indices: 3272590--3272671 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
3272580 AGCAGATGGT
* *
3272590 ACTACTTGCTAGCTGATTAACTTTTCCATTATTTAATA
1 ACTACTTGCTAGCTAATTAACTTTTCCATTAATTAATA
3272628 ACTACTTGCTAGCTAATTAACTTTTCCATTAATTAATA
1 ACTACTTGCTAGCTAATTAACTTTTCCATTAATTAATA
3272666 ACTACT
1 ACTACT
3272672 ATTTCAAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.43
Consensus pattern (38 bp):
ACTACTTGCTAGCTAATTAACTTTTCCATTAATTAATA
Found at i:3273406 original size:2 final size:2
Alignment explanation
Indices: 3273399--3273439 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3273389 AATAAGACTG
* * *
3273399 AT AT AT AT TT AT TT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3273440 AATGATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3274997 original size:3 final size:3
Alignment explanation
Indices: 3274989--3275016 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3274979 GATGACTCCC
3274989 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
3275017 CAATTGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:3275247 original size:3 final size:3
Alignment explanation
Indices: 3275233--3275275 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
3275223 TTGTGATCAG
*
3275233 AAT AAC AAT AAT AAT AAT AAT AATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
3275276 GGCAATAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3275262 original size:16 final size:16
Alignment explanation
Indices: 3275241--3275272 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3275231 AGAATAACAA
3275241 TAATAATAATAATAAT
1 TAATAATAATAATAAT
3275257 TAATAATAATAATAAT
1 TAATAATAATAATAAT
3275273 AATGGCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATAATAATAAT
Found at i:3275263 original size:19 final size:19
Alignment explanation
Indices: 3275239--3275275 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3275229 TCAGAATAAC
3275239 AATAATAATAATAATAATT
1 AATAATAATAATAATAATT
3275258 AATAATAATAATAATAAT
1 AATAATAATAATAATAAT
3275276 GGCAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATAATAATAATAATAATT
Found at i:3275339 original size:2 final size:2
Alignment explanation
Indices: 3275332--3275369 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3275322 ATAAAAATGG
3275332 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3275370 ACGGACTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3275610 original size:2 final size:2
Alignment explanation
Indices: 3275591--3275624 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3275581 ACGTAACTCG
* *
3275591 AT AT AG AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3275625 TTATTACTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3276495 original size:20 final size:20
Alignment explanation
Indices: 3276455--3276505 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
3276445 AACAAGTCAC
*
3276455 TATAATAAAAAAAATTAAAA
1 TATAATATAAAAAATTAAAA
3276475 T-TAAATATAAAAAA-TATAAA
1 TAT-AATATAAAAAATTA-AAA
3276495 TATAATATAAA
1 TATAATATAAA
3276506 TTTATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAATATAAAAAATTAAAA
Found at i:3276513 original size:19 final size:18
Alignment explanation
Indices: 3276476--3276565 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
3276466 AAATTAAAAT
3276476 TAAATATAA-AAAA--TA
1 TAAATATAATAAAATTTA
3276491 TAAATATAATATAAATTTA
1 TAAATATAATA-AAATTTA
*
3276510 TAAATAT-TTAAAATTTTTA
1 TAAATATAATAAAA--TTTA
* *
3276529 TATAATACAA-AAGATTT-
1 TA-AATATAATAAAATTTA
3276546 TAAATATAATAAAATTTA
1 TAAATATAATAAAATTTA
3276564 TA
1 TA
3276566 TAACTATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
15 9 0.15
16 7 0.12
17 14 0.24
18 7 0.12
19 15 0.25
20 7 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (18 bp):
TAAATATAATAAAATTTA
Found at i:3276576 original size:19 final size:18
Alignment explanation
Indices: 3276479--3276576 Score: 62
Period size: 19 Copynumber: 5.3 Consensus size: 18
3276469 TTAAAATTAA
**
3276479 ATATAAAAAATATA-AAT
1 ATATAAAATTTATATAAT
3276496 ATAATATAAATTTATA-AAT
1 AT-ATA-AAATTTATATAAT
*
3276515 ATTTAAAATTTTTATATAAT
1 ATATAAAA--TTTATATAAT
*
3276535 ACA-AAAGATTT-TA-AAT
1 ATATAAA-ATTTATATAAT
3276551 ATAATAAAATTTATATAACT
1 AT-ATAAAATTTATATAA-T
3276571 ATATAA
1 ATATAA
3276577 TTTTTAAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
16 4 0.06
17 12 0.19
18 13 0.20
19 27 0.42
20 8 0.12
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAAAATTTATATAAT
Found at i:3278471 original size:2 final size:2
Alignment explanation
Indices: 3278466--3278492 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3278456 TTTTTTTTCT
3278466 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
3278493 CTTTATTATA
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:3279879 original size:7 final size:8
Alignment explanation
Indices: 3279864--3279888 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3279854 ATATGATAAT
3279864 ATAAAAAA
1 ATAAAAAA
3279872 ATAAAAAA
1 ATAAAAAA
3279880 ATAAAAAA
1 ATAAAAAA
3279888 A
1 A
3279889 ACCTTGGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:3280607 original size:2 final size:2
Alignment explanation
Indices: 3280600--3280637 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3280590 CACAAAAGAA
3280600 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3280638 GGCTGCTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3283180 original size:3 final size:3
Alignment explanation
Indices: 3283174--3283199 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3283164 TCAATATAAA
3283174 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
3283200 TAACTACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3294369 original size:2 final size:2
Alignment explanation
Indices: 3294362--3294391 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3294352 ACAGGTTGAC
3294362 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
3294392 AGAAAGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3295446 original size:4 final size:4
Alignment explanation
Indices: 3295439--3295468 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3295429 CTAATCTTTC
*
3295439 TTAT TTAT TTAT TTGT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
3295469 TCTAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:3296231 original size:27 final size:27
Alignment explanation
Indices: 3296185--3296236 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
3296175 TTAATCAGCT
*
3296185 AATTTTTTTAAAATATTATATTAAATC
1 AATTTTTTTAAAATATTATAATAAATC
3296212 AATTATTTTTATAAA-A-TATAATAAA
1 AATT-TTTTTA-AAATATTATAATAAA
3296237 AATAATATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 12 0.55
28 7 0.32
29 3 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTTTTTAAAATATTATAATAAATC
Found at i:3303971 original size:27 final size:26
Alignment explanation
Indices: 3303921--3303970 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3303911 ATATGTTTTC
*
3303921 AAAATATTTTAAAAATATAATTTTAA
1 AAAATATATTAAAAATATAATTTTAA
3303947 AAAATACTATTAAAAATA-AATTTT
1 AAAATA-TATTAAAAATATAATTTT
3303971 TTATCTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATATATTAAAAATATAATTTTAA
Found at i:3306067 original size:30 final size:32
Alignment explanation
Indices: 3306033--3306106 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 32
3306023 TTAAAAATAT
*
3306033 ATTTTTATATAAATAATAAATTAA-TTT-ATA
1 ATTTTTATATAAATAATAAATTAATTTTAAAA
* *
3306063 A-TTTT-T-TAAAGAATAATTTAATTTTAAAA
1 ATTTTTATATAAATAATAAATTAATTTTAAAA
3306092 ATTTTTATGATAAAT
1 ATTTTTAT-ATAAAT
3306107 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
27 13 0.38
28 4 0.12
29 7 0.21
30 5 0.15
31 1 0.03
33 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
ATTTTTATATAAATAATAAATTAATTTTAAAA
Found at i:3307438 original size:24 final size:24
Alignment explanation
Indices: 3307411--3307461 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3307401 ATACATATTT
*
3307411 TTAAATA-ATTAATAATAATGTATA
1 TTAAATACAATAATAAT-ATGTATA
*
3307435 TTAAATACAATAATAATATTTATA
1 TTAAATACAATAATAATATGTATA
3307459 TTA
1 TTA
3307462 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAATACAATAATAATATGTATA
Found at i:3314126 original size:2 final size:2
Alignment explanation
Indices: 3314119--3314158 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3314109 AAGTACTCAA
* *
3314119 AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3314159 CATGGAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3314210 original size:2 final size:2
Alignment explanation
Indices: 3314203--3314237 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3314193 ACAAAATCTT
* *
3314203 TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3314238 CAATCAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3314750 original size:6 final size:6
Alignment explanation
Indices: 3314739--3314771 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3314729 TTTCCCTCCA
3314739 CCATTG CCATTG CCATTG CCATTG CCATTG CCA
1 CCATTG CCATTG CCATTG CCATTG CCATTG CCA
3314772 CCTCCACCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.36, G:0.15, T:0.30
Consensus pattern (6 bp):
CCATTG
Found at i:3314778 original size:6 final size:6
Alignment explanation
Indices: 3314769--3314795 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3314759 ATTGCCATTG
3314769 CCACCT CCACCT CCACCT CCACCT CCA
1 CCACCT CCACCT CCACCT CCACCT CCA
3314796 ACATTACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.67, G:0.00, T:0.15
Consensus pattern (6 bp):
CCACCT
Found at i:3316683 original size:2 final size:2
Alignment explanation
Indices: 3316676--3316703 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3316666 GAGTAAGTAT
3316676 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
3316704 ATTATCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3319177 original size:2 final size:2
Alignment explanation
Indices: 3319166--3319198 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3319156 AAAATGTTAA
3319166 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3319199 TTGGATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3322723 original size:2 final size:2
Alignment explanation
Indices: 3322716--3322743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3322706 ACGATGACAA
3322716 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
3322744 TTCAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3323548 original size:2 final size:2
Alignment explanation
Indices: 3323541--3323572 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3323531 TAAACTTTAA
3323541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3323573 TAAAAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3326652 original size:12 final size:12
Alignment explanation
Indices: 3326625--3326657 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3326615 AAATTAATTA
3326625 AATTATA-TTTT
1 AATTATATTTTT
*
3326636 GATTATATTTTT
1 AATTATATTTTT
3326648 AATTATATTT
1 AATTATATTT
3326658 AAAGCCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (12 bp):
AATTATATTTTT
Found at i:3326873 original size:28 final size:30
Alignment explanation
Indices: 3326828--3326888 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
3326818 AAAATATATC
* * *
3326828 ATAAAAAACTAATGAAAATATGATAT-AAT
1 ATAAAAAACAAATAAAAAGATGATATGAAT
3326857 ATAAAAAA-AAATAAAAAGATGATATGAAT
1 ATAAAAAACAAATAAAAAGATGATATGAAT
3326886 ATA
1 ATA
3326889 TAAATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.25
Consensus pattern (30 bp):
ATAAAAAACAAATAAAAAGATGATATGAAT
Found at i:3327466 original size:12 final size:12
Alignment explanation
Indices: 3327449--3327473 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3327439 ATTATAAAAA
3327449 ATTTACACTAAT
1 ATTTACACTAAT
3327461 ATTTACACTAAT
1 ATTTACACTAAT
3327473 A
1 A
3327474 CGAGGGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTACACTAAT
Found at i:3331779 original size:3 final size:3
Alignment explanation
Indices: 3331719--3331761 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3331709 CTATATGTCT
3331719 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3331762 ATTTTACACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3346817 original size:32 final size:33
Alignment explanation
Indices: 3346771--3346835 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
3346761 ATAGACAGAA
3346771 CATTAGAAAATTAATGAAACAAACAACTTAAAT
1 CATTAGAAAATTAATGAAACAAACAACTTAAAT
* * *
3346804 CATT-GAAACTTAATGAAACAAATAGCTTAAAT
1 CATTAGAAAATTAATGAAACAAACAACTTAAAT
3346836 TGAAACTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (33 bp):
CATTAGAAAATTAATGAAACAAACAACTTAAAT
Found at i:3348883 original size:60 final size:60
Alignment explanation
Indices: 3348789--3348917 Score: 215
Period size: 60 Copynumber: 2.1 Consensus size: 60
3348779 TTTCATTCCC
*
3348789 ATCCTTTTTACAAACCCATTGGCTTTTCAATCAACAACCAACGCTTTTAAATAAATT-AA
1 ATCCTTTTTACAAACCCATTGGCTTTTCAATCAACAACCAACGCCTTTAAATAAATTAAA
* *
3348848 ATCCTTTTTACAAACCCCTTTGGCTTTTCAATCAACAGCCAACGCCTTTAAATAAATTAAA
1 ATCCTTTTTACAAA-CCCATTGGCTTTTCAATCAACAACCAACGCCTTTAAATAAATTAAA
3348909 ATCCTTTTT
1 ATCCTTTTT
3348918 CTTGTTAAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 14 0.22
60 40 0.62
61 11 0.17
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (60 bp):
ATCCTTTTTACAAACCCATTGGCTTTTCAATCAACAACCAACGCCTTTAAATAAATTAAA
Found at i:3349154 original size:22 final size:22
Alignment explanation
Indices: 3349096--3349155 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
3349086 TTTATTTAAG
*
3349096 TTATTA-TTTATAATAAATATT
1 TTATTATTTTATGATAAATATT
**
3349117 TTA-TATTAAATAGATAAA-AGTT
1 TTATTATTTTAT-GATAAATA-TT
3349139 TTATTATTTTATGATAA
1 TTATTATTTTATGATAA
3349156 TAATAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.07
21 7 0.23
22 15 0.50
23 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTATTATTTTATGATAAATATT
Found at i:3349477 original size:2 final size:2
Alignment explanation
Indices: 3349470--3349496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3349460 TTTTTATAAT
3349470 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
3349497 TTTGAATTTG
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:3377442 original size:20 final size:18
Alignment explanation
Indices: 3377417--3377453 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
3377407 AAAAATTCAA
3377417 GATAATGACATTGAGAAATG
1 GATAATGA-ATTGA-AAATG
3377437 GATAATGAATTGAAAAT
1 GATAATGAATTGAAAAT
3377454 CCAAATCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.27
Consensus pattern (18 bp):
GATAATGAATTGAAAATG
Found at i:3380107 original size:2 final size:2
Alignment explanation
Indices: 3380100--3380134 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3380090 CTCTTTATCA
3380100 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3380135 ATAAACACGT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:3381057 original size:337 final size:339
Alignment explanation
Indices: 3380406--3381061 Score: 786
Period size: 344 Copynumber: 1.9 Consensus size: 339
3380396 TTTTATAAAT
* ** * * * *
3380406 AATCATGGTGAAGCAAGGCTATTGGATTAAAGGATACACTATAGTCTCTGCATATTTACGTCTCT
1 AATCATGGTGAAACAAGGCTATTGGACGAAAGGATACACCATAGCCTATACATATTTACGTCTCT
* * * * * *
3380471 ATTTCGTTATATTTCTTAAATTTTTTTTTTATATTTTGTCGTAGTCATGAACACAAGGAAAATTT
66 ATTTCCTTATATTTCTTAAA-TTTTTTTTAAAATTTAGTCGTAGTCATGAACACAAGAAAAAATT
* * * *
3380536 ATGACTATTGCCATAACCAGATCGTCGTGTATTATCAATGCATTCATAATTGTAGGCTATCTTTT
130 ATGACTATTGCCATAACCAGACCGTCGTGCAATATCAATGCATTCATAATTGTAGGCTATCTTAT
* * * * *
3380601 AAGTGATTATTTTTTTTTCTCTTATTTTGTTGGAATGCTTATATATTTCATACGATAGTATAAAA
195 AAGCG-----TTTTTTCTCCCCTATTTTGTTGGAATGCTTATATATTTCATACGATAATATAAAA
** * * *
3380666 ATTTAATTGATGAGATTTTAGTGTAGCTTTGAATTTAGAAAAGAAATATAAAGCAAAGTCCCCCC
255 ACCTAATTGATAAGATTTTAGTGTAACTTTCAATTTAGAAAAGAAATATAAAGCAAAGTCCCCCC
3380731 CCCCCCCCCCCCCTCTCAAG
320 CCCCCCCCCCCCCTCTCAAG
*
3380751 AATCATGGTGAAACAAGGCTATT-GACCGAAAGGATACACCATAGCCTATACATATTTTCGTCTC
1 AATCATGGTGAAACAAGGCTATTGGA-CGAAAGGATACACCATAGCCTATACATATTTACGTCTC
* *
3380815 TATTTCCTTCTATTTCTTAACA-TTTTTTTAAAATTTAGTCGTAGTCATGAGCACAA-AATAAAA
65 TATTTCCTTATATTTCTTAA-ATTTTTTTTAAAATTTAGTCGTAGTCATGAACACAAGAA-AAAA
* * * * *
3380878 TTATGATTCTTGCTATAATCAGACCTTCGTGCAATATCAATGCATTCATAATTGTAGGCT-TACT
128 TTATGACTATTGCCATAACCAGACCGTCGTGCAATATCAATGCATTCATAATTGTAGGCTAT-CT
* * * * *
3380942 TATAAGCG-TTTTTCTCCCCT-TTTTGTTTGACTGTTTATATATTTCATATGGTAATATAAAAAC
192 TATAAGCGTTTTTTCTCCCCTATTTTGTTGGAATGCTTATATATTTCATACGATAATATAAAAAC
* *
3381005 CTAATTGATAA-AGTTTTAGTGTAATTTTCAATTTAGAAGAGAAATATAAAGCAAAGT
257 CTAATTGATAAGA-TTTTAGTGTAACTTTCAATTTAGAAAAGAAATATAAAGCAAAGT
3381062 TTCTTCTTCT
Statistics
Matches: 264, Mismatches: 42, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
336 1 0.00
337 85 0.32
338 9 0.03
343 2 0.01
344 95 0.36
345 71 0.27
346 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (339 bp):
AATCATGGTGAAACAAGGCTATTGGACGAAAGGATACACCATAGCCTATACATATTTACGTCTCT
ATTTCCTTATATTTCTTAAATTTTTTTTAAAATTTAGTCGTAGTCATGAACACAAGAAAAAATTA
TGACTATTGCCATAACCAGACCGTCGTGCAATATCAATGCATTCATAATTGTAGGCTATCTTATA
AGCGTTTTTTCTCCCCTATTTTGTTGGAATGCTTATATATTTCATACGATAATATAAAAACCTAA
TTGATAAGATTTTAGTGTAACTTTCAATTTAGAAAAGAAATATAAAGCAAAGTCCCCCCCCCCCC
CCCCCCCTCTCAAG
Found at i:3384580 original size:2 final size:2
Alignment explanation
Indices: 3384573--3384604 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3384563 CATCCGCAAC
3384573 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3384605 TCACCGTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3385005 original size:18 final size:18
Alignment explanation
Indices: 3384982--3385017 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3384972 CATGTATTGT
*
3384982 AAAGTTCTGAATTTTTCA
1 AAAGTTCCGAATTTTTCA
*
3385000 AAAGTTCCGGATTTTTCA
1 AAAGTTCCGAATTTTTCA
3385018 GTTAAAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (18 bp):
AAAGTTCCGAATTTTTCA
Found at i:3387051 original size:2 final size:2
Alignment explanation
Indices: 3387046--3387080 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3387036 TTTGTTTCTC
* *
3387046 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3387081 CCCTTTATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3388543 original size:2 final size:2
Alignment explanation
Indices: 3388536--3388598 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
3388526 GCGTTAAGTG
* *
3388536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A CA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3388577 TC TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3388599 GATTATTCGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3390259 original size:2 final size:2
Alignment explanation
Indices: 3390252--3390277 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3390242 GAGAGGAAGC
3390252 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3390278 TAGTTGTTTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3390911 original size:18 final size:18
Alignment explanation
Indices: 3390879--3390918 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3390869 ATTTTTATAC
*
3390879 ATTAATAATATAAATATT
1 ATTAATAATATAAATAAT
3390897 ATTAATAA-ATAAAATAAT
1 ATTAATAATAT-AAATAAT
3390915 ATTA
1 ATTA
3390919 TTTTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAATAATATAAATAAT
Found at i:3390950 original size:25 final size:26
Alignment explanation
Indices: 3390895--3390946 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
3390885 AATATAAATA
3390895 TTATTAATAAATAAAATAATATTATT
1 TTATTAATAAATAAAATAATATTATT
* *
3390921 TTATTAA-AAATAAGATTAT-TTATT
1 TTATTAATAAATAAAATAATATTATT
3390945 TT
1 TT
3390947 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 10 0.42
26 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTATTAATAAATAAAATAATATTATT
Found at i:3392486 original size:2 final size:2
Alignment explanation
Indices: 3392479--3392504 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3392469 TTCATTGTCA
3392479 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
3392505 TTATTGATTG
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):
AT
Found at i:3393522 original size:3 final size:3
Alignment explanation
Indices: 3393514--3393548 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3393504 GTAACAAATG
3393514 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3393549 CACAGAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3396438 original size:2 final size:2
Alignment explanation
Indices: 3396433--3396486 Score: 69
Period size: 2 Copynumber: 27.5 Consensus size: 2
3396423 ACACACACGC
3396433 AT AT AT AT GA- AT AT AT AT AT AT AT AT AT AT AT GA- AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
3396475 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
3396487 CACTTATTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3397561 original size:3 final size:3
Alignment explanation
Indices: 3397555--3397585 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3397545 ACTAATTACA
3397555 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
3397586 TCATCAGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3399278 original size:2 final size:2
Alignment explanation
Indices: 3399271--3399314 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3399261 TAAAAGATGC
3399271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3399313 TA
1 TA
3399315 AGCTTTTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3404101 original size:11 final size:12
Alignment explanation
Indices: 3404087--3404115 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3404077 TAAATATTAA
3404087 TTAAAATTTA-T
1 TTAAAATTTATT
3404098 TTAAAATTTATT
1 TTAAAATTTATT
3404110 TTAAAA
1 TTAAAA
3404116 AATATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:3405758 original size:24 final size:24
Alignment explanation
Indices: 3405712--3405773 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
3405702 GGGTTGTTTA
* *
3405712 GGCTTTTTCTCCTTTGGCACTTTT
1 GGCTTCTTCTCCTTTGGCACTTTG
3405736 GGCTTCTTCTCCTTTGG-AGCTTTG
1 GGCTTCTTCTCCTTTGGCA-CTTTG
* *
3405760 GGTTTCTTTTCCTT
1 GGCTTCTTCTCCTT
3405774 GACTGGCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.03, C:0.24, G:0.19, T:0.53
Consensus pattern (24 bp):
GGCTTCTTCTCCTTTGGCACTTTG
Found at i:3407296 original size:15 final size:16
Alignment explanation
Indices: 3407276--3407306 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3407266 CTGAAATCAT
3407276 AAACAACA-ACTAACA
1 AAACAACAGACTAACA
3407291 AAACAACAGACTAACA
1 AAACAACAGACTAACA
3407307 GAAAATAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.26, G:0.03, T:0.06
Consensus pattern (16 bp):
AAACAACAGACTAACA
Found at i:3410445 original size:18 final size:18
Alignment explanation
Indices: 3410422--3410459 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3410412 AGTAACAAAA
*
3410422 ATGCACAGACAAGAATAT
1 ATGCACAGAAAAGAATAT
3410440 ATGCACAGAAAAGAATAT
1 ATGCACAGAAAAGAATAT
3410458 AT
1 AT
3410460 CTCTATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (18 bp):
ATGCACAGAAAAGAATAT
Found at i:3425738 original size:5 final size:6
Alignment explanation
Indices: 3425723--3425753 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3425713 AAACGCAATG
*
3425723 AAAAAC AAAAAC AAAAAT AAAAAC AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC A
3425754 CAACAGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:3426069 original size:2 final size:2
Alignment explanation
Indices: 3426020--3426056 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
3426010 ATGAATATCC
*
3426020 AT AT AT AT AT AT AT AT AT AT AT AT AT AA ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
3426057 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3426542 original size:2 final size:2
Alignment explanation
Indices: 3426535--3426563 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3426525 ACCTTCTAAA
3426535 TC 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 TC T
3426564 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3426568 original size:2 final size:2
Alignment explanation
Indices: 3426563--3426588 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3426553 TCTCTCTCTC
3426563 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
3426589 AAATCACATT
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:3442047 original size:2 final size:2
Alignment explanation
Indices: 3442040--3442065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3442030 CTCGAGTATG
3442040 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
3442066 GCATATGTTT
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):
AT
Found at i:3445172 original size:120 final size:121
Alignment explanation
Indices: 3444948--3445189 Score: 423
Period size: 120 Copynumber: 2.0 Consensus size: 121
3444938 TCAAGGCTAG
* * *
3444948 ATGTTCATGAATTTACATATTTTGTGGTATTACTTTGGCTTACTGTTATCGAACTAGCCCTATAG
1 ATGTTCATGAATTTACATATTTTGTGGTATTACTTGGGCTTACTGTTATCGAACTAGCCATACAG
*
3445013 GAATTAAGAAAGCAGATTAATCAGTTCAAAAAGTCTAAAAATCTTTAAAAATTACT
66 GAATTAAGAAAGCAGATCAATCAGTTCAAAAAGTCTAAAAATCTTTAAAAATTACT
3445069 ATGTT-ATGAATTTACATATTTTGTGGTATTACTTGGGCTTACTGTTATCGAACTAGCCATACAG
1 ATGTTCATGAATTTACATATTTTGTGGTATTACTTGGGCTTACTGTTATCGAACTAGCCATACAG
* *
3445133 GAATTAAGAAAGCAGATCAATCAGTTCAAAAAGTTTAAAAATCTTTTAAAATTACT
66 GAATTAAGAAAGCAGATCAATCAGTTCAAAAAGTCTAAAAATCTTTAAAAATTACT
3445189 A
1 A
3445190 GAAAACTAAT
Statistics
Matches: 115, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
120 110 0.96
121 5 0.04
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (121 bp):
ATGTTCATGAATTTACATATTTTGTGGTATTACTTGGGCTTACTGTTATCGAACTAGCCATACAG
GAATTAAGAAAGCAGATCAATCAGTTCAAAAAGTCTAAAAATCTTTAAAAATTACT
Found at i:3454074 original size:31 final size:31
Alignment explanation
Indices: 3454033--3454137 Score: 81
Period size: 31 Copynumber: 3.3 Consensus size: 31
3454023 GATATGTCCT
*
3454033 TGTTTCAAATTAATAGTTTCACAACATGTTA
1 TGTTTAAAATTAATAGTTTCACAACATGTTA
** * *
3454064 TGTTTAAAATT-AT-GCATCACATTA-ATATCTCCT
1 TGTTTAAAATTAATAGTTTCACA--ACATGT-T--A
* *
3454097 TGTTTCAAATTAATAGTTTCGCAACATGTTA
1 TGTTTAAAATTAATAGTTTCACAACATGTTA
3454128 TGTTTAAAAT
1 TGTTTAAAAT
3454138 CATGCATCGC
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
29 6 0.11
30 5 0.09
31 21 0.39
33 12 0.22
34 5 0.09
35 5 0.09
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (31 bp):
TGTTTAAAATTAATAGTTTCACAACATGTTA
Found at i:3454108 original size:64 final size:64
Alignment explanation
Indices: 3454024--3454152 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
3454014 GCAAAATGTG
* *
3454024 ATATGTCCTTGTTTCAAATTAATAGTTTCACAACATGTTATGTTTAAAATTATGCATCACATTA
1 ATATCTCCTTGTTTCAAATTAATAGTTTCACAACATGTTATGTTTAAAATCATGCATCACATTA
* *
3454088 ATATCTCCTTGTTTCAAATTAATAGTTTCGCAACATGTTATGTTTAAAATCATGCATCGCATTA
1 ATATCTCCTTGTTTCAAATTAATAGTTTCACAACATGTTATGTTTAAAATCATGCATCACATTA
3454152 A
1 A
3454153 GTAATTGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (64 bp):
ATATCTCCTTGTTTCAAATTAATAGTTTCACAACATGTTATGTTTAAAATCATGCATCACATTA
Found at i:3460853 original size:12 final size:12
Alignment explanation
Indices: 3460817--3460858 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3460807 ACCCAAGAGG
3460817 GAAAGAAAAAAA
1 GAAAGAAAAAAA
* *
3460829 AAAAAAAAAAAA
1 GAAAGAAAAAAA
*
3460841 GAAAGAAAGAAA
1 GAAAGAAAAAAA
3460853 GAAAGA
1 GAAAGA
3460859 GGGAACGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
GAAAGAAAAAAA
Found at i:3461046 original size:7 final size:7
Alignment explanation
Indices: 3461034--3461082 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
3461024 CTCAATTTCG
3461034 AAGAAGA
1 AAGAAGA
3461041 AAGAAGTA
1 AAGAAG-A
*
3461049 TAGAAGA
1 AAGAAGA
3461056 AAGAAGA
1 AAGAAGA
**
3461063 ACCAAGA
1 AAGAAGA
*
3461070 AAGGAGA
1 AAGAAGA
3461077 AAGAAG
1 AAGAAG
3461083 TGTGACAGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.63, C:0.04, G:0.29, T:0.04
Consensus pattern (7 bp):
AAGAAGA
Found at i:3463975 original size:19 final size:19
Alignment explanation
Indices: 3463951--3463988 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3463941 ATCTGACTTC
3463951 CTTTCTCTCCCCTTCCTTT
1 CTTTCTCTCCCCTTCCTTT
3463970 CTTTCTCTCCCCTTCCTTT
1 CTTTCTCTCCCCTTCCTTT
3463989 TGTTATAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (19 bp):
CTTTCTCTCCCCTTCCTTT
Found at i:3466254 original size:24 final size:23
Alignment explanation
Indices: 3466197--3466254 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
3466187 GCTTTTGGAT
*
3466197 CTTTTGATCTATGATATTTTAGT
1 CTTTTGATCTATGATATTTTAGC
**
3466220 CTTTACCATCTATGATATTTTAGC
1 CTTT-TGATCTATGATATTTTAGC
3466244 CTTTTGGATCT
1 CTTTT-GATCT
3466255 TTTGATTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.52
Consensus pattern (23 bp):
CTTTTGATCTATGATATTTTAGC
Found at i:3466632 original size:2 final size:2
Alignment explanation
Indices: 3466625--3466669 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3466615 GGTTTTATGT
3466625 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3466667 TC T
1 TC T
3466670 GTTTTCCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3478133 original size:36 final size:36
Alignment explanation
Indices: 3478082--3478154 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
3478072 TTTTTAGCTA
* *
3478082 TGGATTTCAGCGTTTAATTGATATAGCACTGATCTT
1 TGGATTTCAACGTTTAATTGAGATAGCACTGATCTT
*
3478118 TGGATTTCAATGTTTAATTGAGATAGCACTGATCTT
1 TGGATTTCAACGTTTAATTGAGATAGCACTGATCTT
3478154 T
1 T
3478155 TGTTCCACGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (36 bp):
TGGATTTCAACGTTTAATTGAGATAGCACTGATCTT
Found at i:3483003 original size:20 final size:20
Alignment explanation
Indices: 3482978--3483015 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3482968 AGAGCAGACC
3482978 TTTCTTGTTGC-TGTTTTCCA
1 TTTCTTGTT-CTTGTTTTCCA
3482998 TTTCTTGTTCTTGTTTTC
1 TTTCTTGTTCTTGTTTTC
3483016 GACACACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.03, C:0.18, G:0.13, T:0.66
Consensus pattern (20 bp):
TTTCTTGTTCTTGTTTTCCA
Found at i:3487662 original size:6 final size:6
Alignment explanation
Indices: 3487651--3487683 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3487641 AAATTTTCTT
3487651 CTACTG CTACTG CTACTG CTACTG CTACTG CTA
1 CTACTG CTACTG CTACTG CTACTG CTACTG CTA
3487684 GTGCGAGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (6 bp):
CTACTG
Found at i:3487694 original size:18 final size:18
Alignment explanation
Indices: 3487653--3487695 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3487643 ATTTTCTTCT
*
3487653 ACTGCTACTGCTACTGCT
1 ACTGCTACTGCTACTGCG
*
3487671 ACTGCTACTGCTAGTGCG
1 ACTGCTACTGCTACTGCG
*
3487689 AGTGCTA
1 ACTGCTA
3487696 GGATTCCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (18 bp):
ACTGCTACTGCTACTGCG
Found at i:3488674 original size:2 final size:2
Alignment explanation
Indices: 3488663--3488703 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3488653 CTAAACTACA
*
3488663 CT CT -T CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3488704 TAGTTCGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.46, G:0.02, T:0.51
Consensus pattern (2 bp):
CT
Found at i:3489347 original size:2 final size:2
Alignment explanation
Indices: 3489340--3489369 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3489330 CACAACAAAT
3489340 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
3489370 ACAGATCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3496183 original size:2 final size:2
Alignment explanation
Indices: 3496176--3496203 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3496166 GCTGCACCAT
3496176 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
3496204 GAGGGATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3497760 original size:2 final size:2
Alignment explanation
Indices: 3497753--3497797 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3497743 TTGTATACCT
3497753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3497795 TA T
1 TA T
3497798 CCTTATTCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3499261 original size:20 final size:20
Alignment explanation
Indices: 3499232--3499316 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 20
3499222 TTTAATTATT
*
3499232 AAAAATTATATTTTTCATTC
1 AAAAAATATATTTTTCATTC
* *
3499252 AAAAAATATATTTTTTATCC
1 AAAAAATATATTTTTCATTC
** *
3499272 AATCAATATATCATTTCATTC
1 AAAAAATATAT-TTTTCATTC
*
3499293 -AAAAATAT-CTTTTCA-T-
1 AAAAAATATATTTTTCATTC
3499309 AAAAAATA
1 AAAAAATA
3499317 ATGTCTATAT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
17 8 0.16
18 5 0.10
20 32 0.63
21 6 0.12
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAAATATATTTTTCATTC
Found at i:3499306 original size:18 final size:18
Alignment explanation
Indices: 3499239--3499308 Score: 52
Period size: 18 Copynumber: 3.7 Consensus size: 18
3499229 ATTAAAAATT
3499239 ATAT-TTTTCATTCAAAAA
1 ATATCTTTTCATTC-AAAA
* * *
3499257 ATATATTTTTTATCCAATCAA
1 ATAT-CTTTTCATTCAA--AA
*
3499278 TATATCATTTCATTCAAAA
1 -ATATCTTTTCATTCAAAA
3499297 ATATCTTTTCAT
1 ATATCTTTTCAT
3499309 AAAAAATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
18 15 0.38
19 4 0.10
20 7 0.17
21 10 0.25
22 4 0.10
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATCTTTTCATTCAAAA
Found at i:3499313 original size:17 final size:18
Alignment explanation
Indices: 3499279--3499316 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3499269 TCCAATCAAT
*
3499279 ATATCATTTCATTCAAAA
1 ATATCATTTCATTAAAAA
*
3499297 ATATCTTTTCA-TAAAAA
1 ATATCATTTCATTAAAAA
3499314 ATA
1 ATA
3499317 ATGTCTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATCATTTCATTAAAAA
Found at i:3503472 original size:215 final size:215
Alignment explanation
Indices: 3503101--3503531 Score: 853
Period size: 215 Copynumber: 2.0 Consensus size: 215
3503091 ATGATGTAGT
3503101 TTCACTAAATTAACTATTCTAAATTTGAGAAGTTTGATTTCTCTTCTGCTTTTTTTATTTGTTTT
1 TTCACTAAATTAACTATTCTAAATTTGAGAAGTTTGATTTCTCTTCTGCTTTTTTTATTTGTTTT
*
3503166 AATGTTCAAATGAAGTTTATAGCAAACAGTCCTGAGTCGTAGCTATGTTCCTTGGAGCTAGAAAA
66 AATGTTCAAATGAAGTTCATAGCAAACAGTCCTGAGTCGTAGCTATGTTCCTTGGAGCTAGAAAA
3503231 GTGTTCCATTCTTAGCGATTTTCTTTTCTTTTGCTTGTTAAACATTCTAGCTTGATGCCTACTAG
131 GTGTTCCATTCTTAGCGATTTTCTTTTCTTTTGCTTGTTAAACATTCTAGCTTGATGCCTACTAG
3503296 CTTGATTTCCTGATTCTCTA
196 CTTGATTTCCTGATTCTCTA
3503316 TTCACTAAATTAACTATTCTAAATTTGAGAAGTTTGATTTCTCTTCTGCTTTTTTTATTTGTTTT
1 TTCACTAAATTAACTATTCTAAATTTGAGAAGTTTGATTTCTCTTCTGCTTTTTTTATTTGTTTT
3503381 AATGTTCAAATGAAGTTCATAGCAAACAGTCCTGAGTCGTAGCTATGTTCCTTGGAGCTAGAAAA
66 AATGTTCAAATGAAGTTCATAGCAAACAGTCCTGAGTCGTAGCTATGTTCCTTGGAGCTAGAAAA
3503446 GTGTTCCATTCTTAGCGATTTTCTTTTCTTTTGCTTGTTAAACATTCTAGCTTGATGCCTACTAG
131 GTGTTCCATTCTTAGCGATTTTCTTTTCTTTTGCTTGTTAAACATTCTAGCTTGATGCCTACTAG
3503511 CTTGATTTCCTGATTCTCTA
196 CTTGATTTCCTGATTCTCTA
3503531 T
1 T
3503532 ATGAGGTTAG
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 215 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.45
Consensus pattern (215 bp):
TTCACTAAATTAACTATTCTAAATTTGAGAAGTTTGATTTCTCTTCTGCTTTTTTTATTTGTTTT
AATGTTCAAATGAAGTTCATAGCAAACAGTCCTGAGTCGTAGCTATGTTCCTTGGAGCTAGAAAA
GTGTTCCATTCTTAGCGATTTTCTTTTCTTTTGCTTGTTAAACATTCTAGCTTGATGCCTACTAG
CTTGATTTCCTGATTCTCTA
Found at i:3517924 original size:17 final size:18
Alignment explanation
Indices: 3517885--3517918 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3517875 AGTAAATATG
*
3517885 TTTATCAATTCTATATAA
1 TTTATCAATTCTACATAA
3517903 TTTAT-AATTCTACATA
1 TTTATCAATTCTACATA
3517919 GATTATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATCAATTCTACATAA
Found at i:3521768 original size:24 final size:25
Alignment explanation
Indices: 3521741--3521790 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
3521731 CTCCCTAAAA
3521741 AAATTTATAAAAATATAAAT-TTAT
1 AAATTTATAAAAATATAAATATTAT
*
3521765 AAATTTATAAAAATATGAATATTAT
1 AAATTTATAAAAATATAAATATTAT
3521790 A
1 A
3521791 TTTTCCCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATTTATAAAAATATAAATATTAT
Found at i:3522860 original size:20 final size:22
Alignment explanation
Indices: 3522819--3522860 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3522809 ATAATATAAA
3522819 AATATGATACTTTTAATAAATAT
1 AATATGATACTTTT-ATAAATAT
3522842 AATATGATA-TTTT-TAAATA
1 AATATGATACTTTTATAAATA
3522861 AGATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 4 0.21
23 9 0.47
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
AATATGATACTTTTATAAATAT
Found at i:3522868 original size:24 final size:23
Alignment explanation
Indices: 3522819--3522875 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
3522809 ATAATATAAA
*
3522819 AATATGATACTTTTAATAAATAT
1 AATATGATATTTTTAATAAATAT
3522842 AATATGATATTTTTAAATAAGAT-T
1 AATATGATATTTTT-AATAA-ATAT
3522866 AATATGATAT
1 AATATGATAT
3522876 GCTTATACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 13 0.42
24 16 0.52
25 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (23 bp):
AATATGATATTTTTAATAAATAT
Found at i:3522921 original size:17 final size:17
Alignment explanation
Indices: 3522899--3522943 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3522889 TCATATTCAT
3522899 ATTTAATATTTTAACAC
1 ATTTAATATTTTAACAC
* *
3522916 ATTTAAAATTCTTATCAC
1 ATTTAATATT-TTAACAC
3522934 ATTT-ATATTT
1 ATTTAATATTT
3522944 ACATAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 13 0.54
18 10 0.42
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATATTTTAACAC
Found at i:3522936 original size:18 final size:17
Alignment explanation
Indices: 3522899--3522938 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3522889 TCATATTCAT
*
3522899 ATTTAATATTTTAACAC
1 ATTTAAAATTTTAACAC
*
3522916 ATTTAAAATTCTTATCAC
1 ATTTAAAATT-TTAACAC
3522934 ATTTA
1 ATTTA
3522939 TATTTACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAAAATTTTAACAC
Found at i:3526491 original size:2 final size:2
Alignment explanation
Indices: 3526484--3526539 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
3526474 TAAAAGGTAA
3526484 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3526526 AG AG AG AG A- AG AG A
1 AG AG AG AG AG AG AG A
3526540 AAAATTACTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3531724 original size:12 final size:13
Alignment explanation
Indices: 3531701--3531743 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
3531691 TCATGTATTT
3531701 TTATATTTTAAAA
1 TTATATTTTAAAA
*
3531714 TTATATTTAAAATA
1 TTATATTTTAAA-A
3531728 TTTTATATTTTAAAA
1 --TTATATTTTAAAA
3531743 T
1 T
3531744 ATTAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 12 0.48
14 1 0.04
15 1 0.04
16 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATTTTAAAA
Found at i:3531741 original size:17 final size:17
Alignment explanation
Indices: 3531699--3531746 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
3531689 TGTCATGTAT
3531699 TTTTATATTTT-AAA-A
1 TTTTATATTTTAAAATA
3531714 --TTATA-TTTAAAATA
1 TTTTATATTTTAAAATA
3531728 TTTTATATTTTAAAATA
1 TTTTATATTTTAAAATA
3531745 TT
1 TT
3531747 AATAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 1 0.04
16 5 0.18
17 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATATTTTAAAATA
Found at i:3537706 original size:26 final size:28
Alignment explanation
Indices: 3537670--3537723 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3537660 TCATCATATA
3537670 CATTATATA-T-TATATATATGGTGGTG
1 CATTATATATTATATATATATGGTGGTG
3537696 CATTATATATTATATATATATGGTGGTG
1 CATTATATATTATATATATATGGTGGTG
3537724 TGACTGAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 9 0.35
27 1 0.04
28 16 0.62
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (28 bp):
CATTATATATTATATATATATGGTGGTG
Found at i:3539470 original size:2 final size:2
Alignment explanation
Indices: 3539463--3539503 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3539453 GTTTTCATCT
3539463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3539504 CTTCAGGCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3548963 original size:2 final size:2
Alignment explanation
Indices: 3548956--3548985 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3548946 TAAATTAAGA
*
3548956 AT AT AT AT AC 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
3548986 TTAAAAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3560266 original size:2 final size:2
Alignment explanation
Indices: 3560259--3560291 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3560249 AATCAACTAT
*
3560259 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3560292 GTATCCTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3578080 original size:12 final size:12
Alignment explanation
Indices: 3578063--3578101 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
3578053 CCTTGCACCT
3578063 TTTTTTTTTTAA
1 TTTTTTTTTTAA
3578075 TTTTTTTTTTAA
1 TTTTTTTTTTAA
*
3578087 TTTTTTTTATAA
1 TTTTTTTTTTAA
3578099 TTT
1 TTT
3578102 AATAATAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:3583459 original size:2 final size:2
Alignment explanation
Indices: 3583446--3583475 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3583436 GATATAACAA
*
3583446 AT AT AT AC 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
3583476 TTGGCCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3594786 original size:3 final size:3
Alignment explanation
Indices: 3594778--3594824 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3594768 GGGAAAACAA
3594778 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3594825 GGACAGAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3602932 original size:5 final size:5
Alignment explanation
Indices: 3602922--3602954 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
3602912 TTCTTCTCAA
3602922 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
3602955 GGAAAAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3602960 original size:15 final size:15
Alignment explanation
Indices: 3602922--3602960 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3602912 TTCTTCTCAA
*
3602922 AAAATAAAATAAAAT
1 AAAAGAAAATAAAAT
*
3602937 AAAATAAAATAAAAT
1 AAAAGAAAATAAAAT
*
3602952 AAAGGAAAA
1 AAAAGAAAA
3602961 AGATGATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (15 bp):
AAAAGAAAATAAAAT
Found at i:3607096 original size:5 final size:5
Alignment explanation
Indices: 3607066--3607126 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
3607056 CATTGTAGAC
*
3607066 ATAAT ATAA- A-AA- ATAATT AAAAT ATAAT ATAAT AT-A- ATAAT ATTAAT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT
3607113 ATAAT ATTAAT ATA
1 ATAAT A-TAAT ATA
3607127 TAAACATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 5 0.11
4 5 0.11
5 24 0.51
6 13 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:3607129 original size:37 final size:40
Alignment explanation
Indices: 3607077--3607164 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 40
3607067 TAATATAAAA
* *
3607077 AATAATTAAAATAT-AATATAATATAATAATA-TT-AATAT
1 AATAATTAATATATAAACATAATA-AATAATATTTAAATAT
* *
3607115 AAT-ATTAATATATAAACATATTAAATATTATTTAAATAT
1 AATAATTAATATATAAACATAATAAATAATATTTAAATAT
3607154 AATAATTAATA
1 AATAATTAATA
3607165 AATTAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
37 15 0.36
38 12 0.29
39 8 0.19
40 7 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (40 bp):
AATAATTAATATATAAACATAATAAATAATATTTAAATAT
Found at i:3607166 original size:16 final size:17
Alignment explanation
Indices: 3607141--3607190 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
3607131 CATATTAAAT
*
3607141 ATTATTTAAATATAATA
1 ATTATATAAATATAATA
3607158 ATTA-ATAAAT-TAA-A
1 ATTATATAAATATAATA
3607172 ATTTATATAAATA-AATA
1 A-TTATATAAATATAATA
3607189 AT
1 AT
3607191 GTTTTAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
14 2 0.07
15 6 0.21
16 14 0.50
17 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATATAAATATAATA
Found at i:3611338 original size:3 final size:3
Alignment explanation
Indices: 3611330--3611359 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3611320 TCATAACTTG
3611330 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3611360 TAAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3614539 original size:21 final size:20
Alignment explanation
Indices: 3614492--3614540 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3614482 ATTCTTATAA
3614492 TAATT-TTTAAAAATAATAT
1 TAATTATTTAAAAATAATAT
* *
3614511 TAACTATTTAAAAATTATAT
1 TAATTATTTAAAAATAATAT
3614531 TAAATTATTT
1 T-AATTATTT
3614541 TTTTACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 14 0.56
21 7 0.28
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTATTTAAAAATAATAT
Found at i:3626730 original size:5 final size:5
Alignment explanation
Indices: 3626720--3626745 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3626710 TTATTCAAGA
3626720 GTTTT GTTTT GTTTT GTTTT GTTTT G
1 GTTTT GTTTT GTTTT GTTTT GTTTT G
3626746 CTAACATTAA
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:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (5 bp):
GTTTT
Found at i:3629153 original size:22 final size:23
Alignment explanation
Indices: 3629088--3629166 Score: 97
Period size: 22 Copynumber: 3.4 Consensus size: 23
3629078 GACGGTTTTT
*
3629088 TTAATTTTTACATAAATTATTAATA
1 TTAATTTATA-ATAAATTATT-ATA
* *
3629113 TTAATTTAAAATAAATTATTATT
1 TTAATTTATAATAAATTATTATA
*
3629136 TTAATTTATAA-AAATTATTAAA
1 TTAATTTATAATAAATTATTATA
3629158 TTAATTTAT
1 TTAATTTAT
3629167 TTATTTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.38
23 12 0.25
24 10 0.21
25 8 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTTATAATAAATTATTATA
Found at i:3629215 original size:15 final size:15
Alignment explanation
Indices: 3629195--3629225 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3629185 TTATTATTTT
3629195 TTAAAAATAATATTA
1 TTAAAAATAATATTA
*
3629210 TTAAAAATATTATTA
1 TTAAAAATAATATTA
3629225 T
1 T
3629226 GTTGATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAAATAATATTA
Done.