Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 38 of 378
Found at i:9424321 original size:44 final size:44
Alignment explanation
Indices: 9424222--9424311 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 44
9424212 TGTTCAGGGA
* *
9424222 TACTTCGACCTCGAGTCGATGAGGCACTATAGGTGTCGTACTGT
1 TACTTCGACTTCAAGTCGATGAGGCACTATAGGTGTCGTACTGT
9424266 TACTTCGACTTCAAGTCGATGAGGCACCT-T-GTGTGTCGTACTGT
1 TACTTCGACTTCAAGTCGATGAGGCA-CTATAG-GTGTCGTACTGT
9424310 TA
1 TA
9424312 TTATTACTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 39 0.93
45 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (44 bp):
TACTTCGACTTCAAGTCGATGAGGCACTATAGGTGTCGTACTGT
Found at i:9424565 original size:18 final size:18
Alignment explanation
Indices: 9424510--9424566 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
9424500 ATTACTGTAC
9424510 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
* * *
9424528 TG-AT---TGTTTGATAC
1 TGAATAACTGATTGTTAT
9424542 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
9424560 TGAATAA
1 TGAATAA
9424567 AAATAAGCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.31
15 2 0.07
17 2 0.07
18 16 0.55
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:9425894 original size:30 final size:30
Alignment explanation
Indices: 9425860--9425922 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
9425850 ACTTAACAAG
9425860 CAAATGCCTCTAAAATAATAAC-AAAATTAA
1 CAAATGCCTCTAAAATAAT-ACTAAAATTAA
*
9425890 CAAATGCCTTTAAAATAATACTAAAATTAA
1 CAAATGCCTCTAAAATAATACTAAAATTAA
9425920 CAA
1 CAA
9425923 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATACTAAAATTAA
Found at i:9430841 original size:31 final size:31
Alignment explanation
Indices: 9430806--9430880 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
9430796 TTTAACGACC
* *
9430806 TAGTGACTTAAATAAAAACTTTTGAGTGGTT
1 TAGTGACTTAAATAAAAACTTTTGAATAGTT
**
9430837 TAGTGACTTAAATAAAATTTTTTGAATAGTT
1 TAGTGACTTAAATAAAAACTTTTGAATAGTT
*
9430868 TAATGACTTAAAT
1 TAGTGACTTAAAT
9430881 GAAACATTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTTGAATAGTT
Found at i:9430895 original size:31 final size:31
Alignment explanation
Indices: 9430809--9430895 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
9430799 AACGACCTAG
* * * *
9430809 TGACTTAAATAAAA-ACTTTTGAGTGGTTTAG
1 TGACTTAAATAAAACA-TTTCGAATAGTTTAA
** *
9430840 TGACTTAAATAAAATTTTTTGAATAGTTTAA
1 TGACTTAAATAAAACATTTCGAATAGTTTAA
*
9430871 TGACTTAAATGAAACATTTCGAATA
1 TGACTTAAATAAAACATTTCGAATA
9430896 ATTCAAGGAC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (31 bp):
TGACTTAAATAAAACATTTCGAATAGTTTAA
Found at i:9433603 original size:3 final size:3
Alignment explanation
Indices: 9433595--9433639 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
9433585 TATAGTTTAC
9433595 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9433640 AAGCTTGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9433993 original size:3 final size:3
Alignment explanation
Indices: 9433985--9434030 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
9433975 CGTATCCTTC
9433985 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
9434031 GTCATATTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:9434338 original size:29 final size:29
Alignment explanation
Indices: 9434243--9434339 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
9434233 CACATGCCCA
*
9434243 TGTTTTCATAGTTATATGTATCTCAT-CT
1 TGTTTTCATAGTTATATTTATCTCATGCT
* * * * * * *
9434271 TGGTTACATTAGCTTTTATTAATTTAAATGACCA
1 TGTTTTCA-TAG-TTATATTTATCT-CATG--CT
9434305 TGTTTTCATAGTTATATTTATCTCATGCT
1 TGTTTTCATAGTTATATTTATCTCATGCT
9434334 TGTTTT
1 TGTTTT
9434340 TAAAAAAGGA
Statistics
Matches: 48, Mismatches: 15, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
28 6 0.12
29 10 0.21
30 8 0.17
31 5 0.10
32 9 0.19
33 3 0.06
34 7 0.15
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.53
Consensus pattern (29 bp):
TGTTTTCATAGTTATATTTATCTCATGCT
Found at i:9435793 original size:2 final size:2
Alignment explanation
Indices: 9435786--9435814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9435776 ATTTAATGTT
9435786 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 T
9435815 GTGTGAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9437400 original size:10 final size:10
Alignment explanation
Indices: 9437385--9437413 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
9437375 TTGCATGTGG
9437385 GATGTGAATA
1 GATGTGAATA
9437395 GATGTGAATA
1 GATGTGAATA
9437405 GATGTGAAT
1 GATGTGAAT
9437414 GAAAGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (10 bp):
GATGTGAATA
Found at i:9440906 original size:25 final size:25
Alignment explanation
Indices: 9440877--9440924 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
9440867 TATTAGCTCA
9440877 ATTTTTATTATTTCATTTAACAATT
1 ATTTTTATTATTTCATTTAACAATT
9440902 ATTTTTATTATTTCATTTAACAA
1 ATTTTTATTATTTCATTTAACAA
9440925 AATCCTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTTTATTATTTCATTTAACAATT
Found at i:9441871 original size:23 final size:23
Alignment explanation
Indices: 9441841--9441885 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
9441831 TTGCAAACTG
9441841 TTAAAGCCTTTATTGTCCTATAT
1 TTAAAGCCTTTATTGTCCTATAT
9441864 TTAAAGCCTTTATTGTCCTATA
1 TTAAAGCCTTTATTGTCCTATA
9441886 CTTGTAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (23 bp):
TTAAAGCCTTTATTGTCCTATAT
Found at i:9443029 original size:35 final size:34
Alignment explanation
Indices: 9442990--9443055 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
9442980 TAATTGTATT
*
9442990 ATTAATTTATTAT-TTTAAATTCTAAATTTAAATTC
1 ATTAATTT-TTATATTT-AATTCTAAAGTTAAATTC
*
9443025 ATTAATTTTTATATTTAATTTTAAAGTTAAA
1 ATTAATTTTTATATTTAATTCTAAAGTTAAA
9443056 ATTTTCATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (34 bp):
ATTAATTTTTATATTTAATTCTAAAGTTAAATTC
Found at i:9443058 original size:35 final size:35
Alignment explanation
Indices: 9442990--9443058 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
9442980 TAATTGTATT
*
9442990 ATTAATTTATTATTTTAAATTCTAAATTTAAATTC
1 ATTAATTTATTATTTTAAATTCTAAATTAAAATTC
*
9443025 ATTAATTT-TTATATTT-AATTTTAAAGTTAAAATT
1 ATTAATTTATTAT-TTTAAATTCTAAA-TTAAAATT
9443059 TTCATAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (35 bp):
ATTAATTTATTATTTTAAATTCTAAATTAAAATTC
Found at i:9443211 original size:17 final size:17
Alignment explanation
Indices: 9443164--9443211 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
9443154 TATCATAGAA
*
9443164 GAAAATATTATTT-AAT
1 GAAAATAATATTTAAAT
* *
9443180 TAAAATAAATTTTTAAAT
1 GAAAAT-AATATTTAAAT
9443198 GAAAATAATATTTA
1 GAAAATAATATTTA
9443212 TCAATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.20
17 12 0.48
18 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (17 bp):
GAAAATAATATTTAAAT
Found at i:9443330 original size:31 final size:32
Alignment explanation
Indices: 9443289--9443362 Score: 132
Period size: 31 Copynumber: 2.3 Consensus size: 32
9443279 ATTTTAATTT
9443289 AAATAGTAACTCAAAATAGATGAAAAATTAAC
1 AAATAGTAACTCAAAATAGATGAAAAATTAAC
9443321 AAATA-TAACTCAAAATAGATGAAAAATTAAC
1 AAATAGTAACTCAAAATAGATGAAAAATTAAC
*
9443352 AAATATTAACT
1 AAATAGTAACT
9443363 TTATTAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 31 0.76
32 10 0.24
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.24
Consensus pattern (32 bp):
AAATAGTAACTCAAAATAGATGAAAAATTAAC
Found at i:9446557 original size:13 final size:13
Alignment explanation
Indices: 9446539--9446565 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9446529 CAATTAAAGG
9446539 GTTAAAATTTAAA
1 GTTAAAATTTAAA
9446552 GTTAAAATTTAAA
1 GTTAAAATTTAAA
9446565 G
1 G
9446566 ATAATAATCA
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:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:9446659 original size:36 final size:36
Alignment explanation
Indices: 9446618--9446694 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
9446608 AACTTTAGAT
*
9446618 CATAACTTATATAAACATATATCATATCATAACTTA
1 CATAACTTACATAAACATATATCATATCATAACTTA
*
9446654 CATAACTTACATAAATATATATCATATCATAACTTA
1 CATAACTTACATAAACATATATCATATCATAACTTA
9446690 CATAA
1 CATAA
9446695 AACTTTGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (36 bp):
CATAACTTACATAAACATATATCATATCATAACTTA
Found at i:9457285 original size:7 final size:8
Alignment explanation
Indices: 9457270--9457294 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9457260 AATCTTATTA
9457270 TATTTTTT
1 TATTTTTT
9457278 TATTTTTT
1 TATTTTTT
9457286 TATTTTTT
1 TATTTTTT
9457294 T
1 T
9457295 CAATTGAATT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:9460273 original size:19 final size:19
Alignment explanation
Indices: 9460251--9460287 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
9460241 AGACTTATGA
9460251 CATGTTTTAACTTTTATTG
1 CATGTTTTAACTTTTATTG
9460270 CATGTTTTAACTTTTATT
1 CATGTTTTAACTTTTATT
9460288 TTCTTTTCTG
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:0.22, C:0.11, G:0.08, T:0.59
Consensus pattern (19 bp):
CATGTTTTAACTTTTATTG
Found at i:9462266 original size:30 final size:30
Alignment explanation
Indices: 9462220--9462279 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9462210 TTCCCGAGCC
*
9462220 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
9462250 TAGGGGTAAAAATGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
9462280 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:9468994 original size:25 final size:25
Alignment explanation
Indices: 9468966--9469094 Score: 95
Period size: 25 Copynumber: 5.0 Consensus size: 25
9468956 ATCGGATTAT
*
9468966 TTTTATATATATTTATTTTAACTTG
1 TTTTATATATATTTATTTTAAATTG
* **
9468991 TTTTATGTACT-TTTATTCGAAATTG
1 TTTTATATA-TATTTATTTTAAATTG
9469016 TTTTAT-TATA--TATTTTAAATTG
1 TTTTATATATATTTATTTTAAATTG
* *
9469038 CCTTATATATATTTATTTATTTCTAAATTAT
1 --TT-T-TATATATATTTATTT-TAAATT-G
9469069 TTTATATATATTATTTATTTTAAATT
1 TTT-TATATA-TATTTATTTTAAATT
9469095 CTTTCCCCAT
Statistics
Matches: 83, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
22 10 0.12
23 1 0.01
24 4 0.05
25 26 0.31
26 4 0.05
27 3 0.04
28 13 0.16
29 16 0.19
30 6 0.07
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTTATATATATTTATTTTAAATTG
Found at i:9469074 original size:30 final size:28
Alignment explanation
Indices: 9469019--9469094 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
9469009 GAAATTGTTT
* ***
9469019 TATTATATATTTTAAATTGCCTTATATA
1 TATTATTTATTTTAAATTATTTTATATA
9469047 TATTTATTTATTTCTAAATTATTTTATATA
1 TA-TTATTTATTT-TAAATTATTTTATATA
9469077 TATTATTTATTTTAAATT
1 TATTATTTATTTTAAATT
9469095 CTTTCCCCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 8 0.19
29 19 0.45
30 15 0.36
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (28 bp):
TATTATTTATTTTAAATTATTTTATATA
Found at i:9469264 original size:24 final size:24
Alignment explanation
Indices: 9469222--9469277 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
9469212 TAGTATATAA
*
9469222 ATTTTAAATTAACTTATATTACTT
1 ATTTTAAATTAACTTATATGACTT
* *
9469246 ATTTTAAATT-ATTTCATATGCCTT
1 ATTTTAAATTAACTT-ATATGACTT
9469270 ATTTTAAA
1 ATTTTAAA
9469278 CTCTTTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTAAATTAACTTATATGACTT
Found at i:9469314 original size:24 final size:24
Alignment explanation
Indices: 9469286--9469343 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
9469276 AACTCTTTTC
* *
9469286 ATTTATTTTAA-ATTTTTTATTATT
1 ATTTATTTTAATATTCTTTA-TAAT
*
9469310 ATTTACTTTAATATTCTTTATAAT
1 ATTTATTTTAATATTCTTTATAAT
9469334 ATTTATTTTA
1 ATTTATTTTA
9469344 CACTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
ATTTATTTTAATATTCTTTATAAT
Found at i:9469373 original size:30 final size:31
Alignment explanation
Indices: 9469314--9469373 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
9469304 ATTATTATTT
* *
9469314 ACTTTAATATTCTTTATAATATTTATTTTAC
1 ACTTTAATATTCTATATAATATCTATTTTAC
* *
9469345 ACTTTTATATT-TATATACTATCTATTTTA
1 ACTTTAATATTCTATATAATATCTATTTTA
9469374 AAATTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (31 bp):
ACTTTAATATTCTATATAATATCTATTTTAC
Found at i:9469380 original size:28 final size:26
Alignment explanation
Indices: 9469349--9469410 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 26
9469339 TTTTACACTT
9469349 TTATATTTATATACTATCTATTTTAAAA
1 TTATATTTATATA--ATCTATTTTAAAA
*
9469377 TTATA--TATATAATCTATTTTTAAA
1 TTATATTTATATAATCTATTTTAAAA
*
9469401 TCAT-TTTATA
1 TTATATTTATA
9469411 CATAGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 15 0.50
25 4 0.13
26 6 0.20
28 5 0.17
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (26 bp):
TTATATTTATATAATCTATTTTAAAA
Found at i:9477029 original size:37 final size:38
Alignment explanation
Indices: 9476978--9477062 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 38
9476968 GAATTAGAAT
9476978 TATTTAAATCATCGTTGTACT-AAAATATATAAACATA
1 TATTTAAATCATCGTTGTACTAAAAATATATAAACATA
*
9477015 TATTTAAATTATCGTTGTACTAAAAAATATATAAACATA
1 TATTTAAATCATCGTTGTACT-AAAAATATATAAACATA
9477054 TATTTAAAT
1 TATTTAAAT
9477063 ATTAAAATGC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 20 0.44
39 25 0.56
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (38 bp):
TATTTAAATCATCGTTGTACTAAAAATATATAAACATA
Found at i:9478147 original size:16 final size:15
Alignment explanation
Indices: 9478123--9478152 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9478113 CAAATACTAA
9478123 TATTTATAAATATAT
1 TATTTATAAATATAT
9478138 TATTTGATAAATATA
1 TATTT-ATAAATATA
9478153 ATTTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TATTTATAAATATAT
Found at i:9480443 original size:2 final size:2
Alignment explanation
Indices: 9480436--9480460 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9480426 TGACTTTGTA
9480436 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9480461 AATCTAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9483785 original size:17 final size:16
Alignment explanation
Indices: 9483763--9483795 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
9483753 TGTACTTGGT
9483763 AGAAAATAAAAGTGAGA
1 AGAAAATAAAA-TGAGA
9483780 AGAAAATAAAATGAGA
1 AGAAAATAAAATGAGA
9483796 GATCATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (16 bp):
AGAAAATAAAATGAGA
Found at i:9483986 original size:2 final size:2
Alignment explanation
Indices: 9483979--9484019 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
9483969 AACCTATAAA
9483979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9484020 GTTCCAACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9485304 original size:20 final size:21
Alignment explanation
Indices: 9485271--9485311 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
9485261 ATAATTGTTC
9485271 AATTTAAAAATTAAT-TAAAA
1 AATTTAAAAATTAATATAAAA
**
9485291 AATTTAAATCTTAATATAAAA
1 AATTTAAAAATTAATATAAAA
9485312 TTAATTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTTAAAAATTAATATAAAA
Found at i:9489200 original size:13 final size:15
Alignment explanation
Indices: 9489169--9489203 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
9489159 GTATTTAGTC
9489169 TTATTTTTATATATT
1 TTATTTTTATATATT
9489184 TTATTTTTAT-T-TT
1 TTATTTTTATATATT
9489197 TTATTTT
1 TTATTTT
9489204 GGGAATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 1 0.05
15 10 0.50
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTATATATT
Found at i:9489252 original size:38 final size:38
Alignment explanation
Indices: 9489228--9489310 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
9489218 TTTCTCTTTG
9489228 TTTTTCACGTTCTCCTTTTCCTTTTTGGCTTTTATTTC
1 TTTTTCACGTTCTCCTTTTCCTTTTTGGCTTTTATTTC
*
9489266 TTTTTCACGTTTTCCTTTTCCTTTTTGGCTTTTATTTTC
1 TTTTTCACGTTCTCCTTTTCCTTTTTGGCTTTTA-TTTC
9489305 TTTTTC
1 TTTTTC
9489311 TCCTTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 33 0.77
39 10 0.23
ACGTcount: A:0.05, C:0.22, G:0.07, T:0.66
Consensus pattern (38 bp):
TTTTTCACGTTCTCCTTTTCCTTTTTGGCTTTTATTTC
Found at i:9495054 original size:13 final size:13
Alignment explanation
Indices: 9495036--9495061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9495026 CTATAAATGT
9495036 TTTTGCAATGTTG
1 TTTTGCAATGTTG
9495049 TTTTGCAATGTTG
1 TTTTGCAATGTTG
9495062 GGTAGTTTAA
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:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (13 bp):
TTTTGCAATGTTG
Found at i:9495827 original size:7 final size:6
Alignment explanation
Indices: 9495808--9495841 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
9495798 ACGTTAGTTC
* *
9495808 TTTCTT TTTCTT TTTCCT TTTCTT TTTTTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
9495842 GACTTTTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:9496516 original size:62 final size:63
Alignment explanation
Indices: 9496447--9496671 Score: 219
Period size: 62 Copynumber: 3.6 Consensus size: 63
9496437 GTGTAGGTTT
*
9496447 CACACGGCCAAGG-ACTCGGGCGTGTGCCCAGGCCGTGTAACTCACTATTTGGGGTATAAAAC
1 CACACGGCCAAGGAACACGGGCGTGTGCCCAGGCCGTGTAACTCACTATTTGGGGTATAAAAC
* * * * * *
9496509 CACACGGCC-AGGAACACGGGCTTTTGTCCAGGCCATATAACTCACTGTTTGGGGTATAAAAC
1 CACACGGCCAAGGAACACGGGCGTGTGCCCAGGCCGTGTAACTCACTATTTGGGGTATAAAAC
* * * ** * * * * *
9496571 CATACAGCC-AGGGACACGGGAATGTGCCCAAGACC-TGTAACTTATTTTTTGGGGTATAAGAC
1 CACACGGCCAAGGAACACGGGCGTGTGCCC-AGGCCGTGTAACTCACTATTTGGGGTATAAAAC
*
9496633 CACACGGCCAAGG--CACGTAGGTGTGTGCCCAGGCCGTGT
1 CACACGGCCAAGGAACACG--GGCGTGTGCCCAGGCCGTGT
9496672 GGTAGAATAT
Statistics
Matches: 132, Mismatches: 25, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
61 7 0.05
62 106 0.80
63 19 0.14
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (63 bp):
CACACGGCCAAGGAACACGGGCGTGTGCCCAGGCCGTGTAACTCACTATTTGGGGTATAAAAC
Found at i:9497465 original size:26 final size:26
Alignment explanation
Indices: 9497436--9497488 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9497426 ATTTGTTTTA
9497436 GAATGTTATGGATTTATGAAGATTAT
1 GAATGTTATGGATTTATGAAGATTAT
9497462 GAATGTTATGGATTTATGAAGATTAT
1 GAATGTTATGGATTTATGAAGATTAT
9497488 G
1 G
9497489 TCTTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.42
Consensus pattern (26 bp):
GAATGTTATGGATTTATGAAGATTAT
Found at i:9499076 original size:14 final size:14
Alignment explanation
Indices: 9499057--9499083 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9499047 TGTTTAGATT
9499057 ATTTTAAAATTAAC
1 ATTTTAAAATTAAC
9499071 ATTTTAAAATTAA
1 ATTTTAAAATTAA
9499084 GACATTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAAATTAAC
Found at i:9512759 original size:9 final size:9
Alignment explanation
Indices: 9512740--9512783 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
9512730 TAGTACTTAT
9512740 TTTTTTCTTC
1 TTTTTT-TTC
9512750 TTTTTTTTC
1 TTTTTTTTC
9512759 -TTTTTTTC
1 TTTTTTTTC
**
9512767 TTTTTTTGA
1 TTTTTTTTC
9512776 TTTTTTTT
1 TTTTTTTT
9512784 AAATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 8 0.27
9 16 0.53
10 6 0.20
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:9512779 original size:17 final size:17
Alignment explanation
Indices: 9512741--9512782 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
9512731 AGTACTTATT
**
9512741 TTTTTCTTCTTTTTTTTC
1 TTTTT-TTCTTTTTTTGA
9512759 TTTTTTTCTTTTTTTGA
1 TTTTTTTCTTTTTTTGA
9512776 TTTTTTT
1 TTTTTTT
9512783 TAAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTGA
Found at i:9513084 original size:118 final size:117
Alignment explanation
Indices: 9512909--9513138 Score: 379
Period size: 118 Copynumber: 2.0 Consensus size: 117
9512899 TATTTCCGGT
9512909 TAGCGGAGTTTTACCCAACACGTCAACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACC
1 TAGCGGAGTTTTACCCAACACGTCAACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACC
* *
9512974 CTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
****
9513026 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCA-ACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
**
9513091 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCTGTACTCATAACC
65 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACC
9513139 ATGGAAAACA
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 21 0.20
118 83 0.80
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (117 bp):
TAGCGGAGTTTTACCCAACACGTCAACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACC
CTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:9513853 original size:43 final size:42
Alignment explanation
Indices: 9513806--9513896 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 42
9513796 TGAAAAGGGG
* * * *
9513806 TGTTTGGCTGCAG-GTTTTGGGGATTCTAAGGCTGGAATAGGAC
1 TGTTTGGCTGCAGAGATAT-GGCATTCT-AGGCTGGAATAGAAC
*
9513849 TGTTTGGCTGCAGAGATATGGCATTCTGGGCTGGAATAGAAC
1 TGTTTGGCTGCAGAGATATGGCATTCTAGGCTGGAATAGAAC
9513891 TGTTTG
1 TGTTTG
9513897 ACAGCATGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 19 0.45
43 20 0.48
44 3 0.07
ACGTcount: A:0.20, C:0.12, G:0.35, T:0.33
Consensus pattern (42 bp):
TGTTTGGCTGCAGAGATATGGCATTCTAGGCTGGAATAGAAC
Found at i:9514042 original size:25 final size:25
Alignment explanation
Indices: 9514006--9514072 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 25
9513996 TATTTAACTA
*
9514006 AAAT-AAAATAAAAATAAAAAAAAT
1 AAATAAAAATAAAAAGAAAAAAAAT
9514030 -AATAAATAAT-AAAAGAAAAAAAAT
1 AAATAAA-AATAAAAAGAAAAAAAAT
9514054 AAATAAAAATAAAAAGAAA
1 AAATAAAAATAAAAAGAAA
9514073 GATGGGTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 3 0.08
24 18 0.47
25 17 0.45
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (25 bp):
AAATAAAAATAAAAAGAAAAAAAAT
Found at i:9523173 original size:2 final size:2
Alignment explanation
Indices: 9523166--9523192 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9523156 CAATTAACTC
9523166 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9523193 GACCAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9526238 original size:19 final size:19
Alignment explanation
Indices: 9526214--9526279 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
9526204 ATTAGAAAAA
*
9526214 AAATTTTATAAAACATAAT
1 AAATTTTATAAAATATAAT
* * *
9526233 AAATTTTAGAAAATTTATT
1 AAATTTTATAAAATATAAT
9526252 AAATTTTAATAAGAATATAA-
1 AAATTTT-ATAA-AATATAAT
9526272 AAATTTTA
1 AAATTTTA
9526280 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 23 0.61
20 10 0.26
21 5 0.13
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (19 bp):
AAATTTTATAAAATATAAT
Found at i:9526273 original size:28 final size:28
Alignment explanation
Indices: 9526250--9526302 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
9526240 AGAAAATTTA
* *
9526250 TTAAATTTTAATAAGAA-TATAAAAATT
1 TTAAATTTTAAAAAAAATTATAAAAATT
9526277 TTAAATTTTAAAAAAAATTATAAAAA
1 TTAAATTTTAAAAAAAATTATAAAAA
9526303 AATTTTAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
TTAAATTTTAAAAAAAATTATAAAAATT
Found at i:9526566 original size:19 final size:19
Alignment explanation
Indices: 9526542--9526608 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
9526532 TTCTATATAC
9526542 TTTATATTTTTTTACGATT
1 TTTATATTTTTTTACGATT
*** *
9526561 TTTATAAAATTTTACAATT
1 TTTATATTTTTTTACGATT
*
9526580 TTT-TATATTTTTTATGATT
1 TTTATAT-TTTTTTACGATT
9526599 TTTATATTTT
1 TTTATATTTT
9526609 ATCTAATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
18 2 0.05
19 32 0.86
20 3 0.08
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATATTTTTTTACGATT
Found at i:9526589 original size:28 final size:28
Alignment explanation
Indices: 9526505--9526661 Score: 94
Period size: 28 Copynumber: 5.6 Consensus size: 28
9526495 TTCTTACAAC
**
9526505 TTTATAAAATTTTATGCTTTTTTATATT
1 TTTATAAAATTTTATAATTTTTTATATT
* * * * *
9526533 TCTAT-ATACTTTATATTTTTTTACGATT
1 TTTATAAAATTTTATAATTTTTTA-TATT
*
9526561 TTTATAAAATTTTACAATTTTTTATATT
1 TTTATAAAATTTTATAATTTTTTATATT
**
9526589 TTT-TATGATTTT-TATATTTTATCTA-ATT
1 TTTATAAAATTTTATA-ATTTT-T-TATATT
* *
9526617 TTTA-ATAAATTTT-TAATATTTGA-ATT
1 TTTATA-AAATTTTATAATTTTTTATATT
*
9526643 TTTATTAAAATTTAATAAT
1 TTTA-TAAAATTTTATAAT
9526662 ATTTATAGCT
Statistics
Matches: 99, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
26 9 0.09
27 33 0.33
28 34 0.34
29 23 0.23
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTATAAAATTTTATAATTTTTTATATT
Found at i:9526618 original size:56 final size:55
Alignment explanation
Indices: 9526505--9526631 Score: 132
Period size: 56 Copynumber: 2.3 Consensus size: 55
9526495 TTCTTACAAC
*** *
9526505 TTTATAAAATTTTATGCTTTTTTATATTTCTATATACTTTATATTTTTTTACGATT
1 TTTATAAAATTTTACAATTTTTTATATTTCTATATACTTTATATTTTTCTAC-ATT
* *
9526561 TTTATAAAATTTTACAATTTTTTATATTT-TTTATGATTTTTATATTTTATCTA-ATT
1 TTTATAAAATTTTACAATTTTTTATATTTCTATAT-A-CTTTATATTTT-TCTACATT
*
9526617 TTTAATAAATTTTTA
1 TTT-ATAAAATTTTA
9526632 ATATTTGAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
55 4 0.07
56 33 0.55
57 20 0.33
58 3 0.05
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (55 bp):
TTTATAAAATTTTACAATTTTTTATATTTCTATATACTTTATATTTTTCTACATT
Found at i:9526642 original size:26 final size:28
Alignment explanation
Indices: 9526613--9526665 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
9526603 TATTTTATCT
*
9526613 AATTTTTAAT-AAATTT-TTAATATTTG
1 AATTTTTAATAAAATTTAATAATATTTG
*
9526639 AATTTTTATTAAAATTTAATAATATTT
1 AATTTTTAATAAAATTTAATAATATTT
9526666 ATAGCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 6 0.26
28 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
AATTTTTAATAAAATTTAATAATATTTG
Found at i:9526705 original size:10 final size:9
Alignment explanation
Indices: 9526558--9526701 Score: 55
Period size: 9 Copynumber: 15.8 Consensus size: 9
9526548 TTTTTTTACG
9526558 ATTTTTATAA
1 ATTTTTAT-A
* *
9526568 AATTTTACA
1 ATTTTTATA
9526577 ATTTTTTATA
1 A-TTTTTATA
* *
9526587 TTTTTTATG
1 ATTTTTATA
9526596 ATTTTTAT-
1 ATTTTTATA
*
9526604 ATTTTATCTA
1 ATTTT-TATA
9526614 ATTTTTAATA
1 ATTTTT-ATA
*
9526624 AATTTT-TA
1 ATTTTTATA
* *
9526632 ATATTT-GA
1 ATTTTTATA
9526640 ATTTTTATTAA
1 ATTTTTA-T-A
* *
9526651 AATTTAATA
1 ATTTTTATA
*
9526660 ATATTTATA
1 ATTTTTATA
** *
9526669 GCTTTTATTG
1 ATTTTTA-TA
9526679 A-TTTTA-A
1 ATTTTTATA
*
9526686 GTTTTTATA
1 ATTTTTATA
9526695 ATTTTTA
1 ATTTTTA
9526702 ATAAAAGTAG
Statistics
Matches: 96, Mismatches: 28, Indels: 21
0.66 0.19 0.14
Matches are distributed among these distances:
8 22 0.23
9 42 0.44
10 26 0.27
11 6 0.06
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:9528411 original size:35 final size:36
Alignment explanation
Indices: 9528372--9528443 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
9528362 CGTTTAATGC
*
9528372 TTAAAATTATGGTCTTTTAAATTCAAA-TTTATTGT
1 TTAAAATTATGATCTTTTAAATTCAAATTTTATTGT
9528407 TTAAAATTATGATCTTTTAAATTCAAATTTTATTGT
1 TTAAAATTATGATCTTTTAAATTCAAATTTTATTGT
9528443 T
1 T
9528444 GATGGGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 26 0.74
36 9 0.26
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.53
Consensus pattern (36 bp):
TTAAAATTATGATCTTTTAAATTCAAATTTTATTGT
Found at i:9528993 original size:13 final size:13
Alignment explanation
Indices: 9528975--9528999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9528965 ATAATGGAGT
9528975 TTAAAATTAAAAA
1 TTAAAATTAAAAA
9528988 TTAAAATTAAAA
1 TTAAAATTAAAA
9529000 CAAAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:9531764 original size:15 final size:14
Alignment explanation
Indices: 9531726--9531778 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
9531716 TGATAAATTA
*
9531726 AAAATTAAGTGTTG
1 AAAATTAAGAGTTG
*
9531740 AATAAATAAGAGTTGG
1 AA-AATTAAGAGTT-G
9531756 AAAATTAAGTA-TTG
1 AAAATTAAG-AGTTG
9531770 AAAATTAAG
1 AAAATTAAG
9531779 TACTGAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.36
15 17 0.52
16 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (14 bp):
AAAATTAAGAGTTG
Found at i:9531772 original size:14 final size:14
Alignment explanation
Indices: 9531726--9531785 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
9531716 TGATAAATTA
*
9531726 AAAATTAAGTGTTG
1 AAAATTAAGTATTG
*
9531740 AATAAATAAG-AGTTGG
1 AA-AATTAAGTA-TT-G
9531756 AAAATTAAGTATTG
1 AAAATTAAGTATTG
*
9531770 AAAATTAAGTACTG
1 AAAATTAAGTATTG
9531784 AA
1 AA
9531786 TTTAAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 18 0.47
15 16 0.42
16 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.30
Consensus pattern (14 bp):
AAAATTAAGTATTG
Found at i:9532228 original size:31 final size:31
Alignment explanation
Indices: 9532180--9532253 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
9532170 TAGAAAATAT
* *
9532180 TAAATTAATTTTAATTTATTAAAAAGTTGAGA
1 TAAATT-ATCTTAATTTATTAAAAAGTTGAAA
9532212 TAAATTATCTTAATTTATTAAAAAGTTGAAA
1 TAAATTATCTTAATTTATTAAAAAGTTGAAA
9532243 TAAATTATCTT
1 TAAATTATCTT
9532254 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 34 0.85
32 6 0.15
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (31 bp):
TAAATTATCTTAATTTATTAAAAAGTTGAAA
Found at i:9535349 original size:44 final size:44
Alignment explanation
Indices: 9535299--9535604 Score: 155
Period size: 44 Copynumber: 6.8 Consensus size: 44
9535289 AGGATTTAGT
*
9535299 TTCAATCTACTCCACTACAACTTTAAGGAGATAAGGCTTGTAAC
1 TTCAATCTACTCCACTACAACTTTAAGGAGATAAGACTTGTAAC
* * * *
9535343 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAAC
1 TTCAATCTACTCCACTACAACTTTAAGGAGATAAGACTTGTAAC
* * *** * * * **
9535387 TTGTAGCTTTAATCTATTCCACTGCAACTTCGGGGAAATAAGATTTTTGGC
1 -T-T--C---AATCTACTCCACTACAACTTTAAGGAGATAAGACTTGTAAC
* * * * * * * *
9535438 CTCAATATACTCCACTACAACTTCAAGAAGATTAGATTTATAGC
1 TTCAATCTACTCCACTACAACTTTAAGGAGATAAGACTTGTAAC
* * * ** * *
9535482 TTTAATCTGCTTCACTGTAACTTCAGGGAGATAAGACTTGTAAC
1 TTCAATCTACTCCACTACAACTTTAAGGAGATAAGACTTGTAAC
* * * * * * * *
9535526 TTCAATCTTCTCCACTGCAACTTTAGGGATATTAGATTTATAGC
1 TTCAATCTACTCCACTACAACTTTAAGGAGATAAGACTTGTAAC
* * * * *
9535570 TTTAATCTGCTCTATTGCAACTTT-AGGAGATAAGA
1 TTCAATCTACTCCACTACAACTTTAAGGAGATAAGA
9535605 TTCACTATAG
Statistics
Matches: 201, Mismatches: 54, Indels: 15
0.74 0.20 0.06
Matches are distributed among these distances:
43 8 0.04
44 155 0.77
45 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
51 33 0.16
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (44 bp):
TTCAATCTACTCCACTACAACTTTAAGGAGATAAGACTTGTAAC
Found at i:9535411 original size:51 final size:51
Alignment explanation
Indices: 9535335--9535432 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
9535325 GGAGATAAGG
* * *
9535335 CTTGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAA
1 CTTGTAACTTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTGTAA
* * * *
9535386 CTTGTAGCTTTAATCTATTCCACTGCAACTTCGGGGAAATAAGATTT
1 CTTGTAACTTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTT
9535433 TTGGCCTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (51 bp):
CTTGTAACTTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTGTAA
Found at i:9535539 original size:88 final size:89
Alignment explanation
Indices: 9535309--9535604 Score: 258
Period size: 88 Copynumber: 3.3 Consensus size: 89
9535299 TTCAATCTAC
* * * * *
9535309 TCCACTACAACTTTAAGGAGATAAGGCTTGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTACTCCACTGCAACTTTA---AG-
* * * *
9535374 TAAGATTTGTAACTTGTAGCTTTAATCT-AT
62 -AAGATTAG--ATTTATAGCTTTAATCTGCT
* * * * ** * * * *
9535404 TCCACTGCAACTTCGGGGAAATAAGATTTTTGGCCTCAATATACTCCACTACAACTTCAAGAAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTACTCCACTGCAACTTTAAGAAGA
9535469 TTAGATTTATAGCTTTAATCTGCT
66 TTAGATTTATAGCTTTAATCTGCT
* * * * *
9535493 T-CACTGTAACTTCAGGGAGATAAGACTTGTAACTTCAATCTTCTCCACTGCAACTTTAGGGATA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTACTCCACTGCAACTTTAAGAAGA
9535557 TTAGATTTATAGCTTTAATCTGC-
66 TTAGATTTATAGCTTTAATCTGCT
* * *
9535580 TCTATTGCAACTTTA-GGAGATAAGA
1 TCCACTGCAACTTCAGGGAGATAAGA
9535605 TTCACTATAG
Statistics
Matches: 161, Mismatches: 38, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
87 11 0.07
88 95 0.59
89 2 0.01
90 7 0.04
92 2 0.01
95 44 0.27
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (89 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTACTCCACTGCAACTTTAAGAAGA
TTAGATTTATAGCTTTAATCTGCT
Found at i:9535900 original size:13 final size:13
Alignment explanation
Indices: 9535882--9535907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9535872 AACGTATATG
9535882 AATGTATATGAAT
1 AATGTATATGAAT
9535895 AATGTATATGAAT
1 AATGTATATGAAT
9535908 GTTATTCATC
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:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
AATGTATATGAAT
Found at i:9537221 original size:18 final size:19
Alignment explanation
Indices: 9537182--9537221 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
9537172 TTTGATAAAG
* *
9537182 TTCGTCTTTGAAAAAATCA
1 TTCGTATTTAAAAAAATCA
9537201 TTCGTATTTAAAAAAAT-A
1 TTCGTATTTAAAAAAATCA
9537219 TTC
1 TTC
9537222 ATTTTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (19 bp):
TTCGTATTTAAAAAAATCA
Found at i:9537843 original size:169 final size:169
Alignment explanation
Indices: 9537560--9537874 Score: 567
Period size: 169 Copynumber: 1.9 Consensus size: 169
9537550 AATTTGGGCC
* *
9537560 TTTGCCCAATCGGATATAGTTTCACAATTATATTAGAGCCTTGGCCCATATCAGATACAGAATGC
1 TTTGCCCAATCGGATACAGTTTCACAATAATATTAGAGCCTTGGCCCATATCAGATACAGAATGC
* *
9537625 AAACACAGTAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTCCGTCTAGCCCTACACAC
66 AAACACAGTAAATCAGAATCCTACCCACCAACCTCTACACACCATCTCCGTCCAGCCCTACACAC
9537690 CATGTGGGGATTAAATCAACCCACCCATCCCTACACACT
131 CATGTGGGGATTAAATCAACCCACCCATCCCTACACACT
* *
9537729 TTTGCCCAATCGGTTACAGTTTCACAATAATATTAGAGTCTTGGCCCATATCAGATACAGAATGC
1 TTTGCCCAATCGGATACAGTTTCACAATAATATTAGAGCCTTGGCCCATATCAGATACAGAATGC
*
9537794 AAACACAGTAAATCAGAATCCTACCCACCAACCTCTACACACTATCTCCGTCCAGCCCTACACAC
66 AAACACAGTAAATCAGAATCCTACCCACCAACCTCTACACACCATCTCCGTCCAGCCCTACACAC
9537859 CATGTGGGGATTAAAT
131 CATGTGGGGATTAAAT
9537875 AATGTAACAC
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
169 139 1.00
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (169 bp):
TTTGCCCAATCGGATACAGTTTCACAATAATATTAGAGCCTTGGCCCATATCAGATACAGAATGC
AAACACAGTAAATCAGAATCCTACCCACCAACCTCTACACACCATCTCCGTCCAGCCCTACACAC
CATGTGGGGATTAAATCAACCCACCCATCCCTACACACT
Found at i:9539003 original size:21 final size:21
Alignment explanation
Indices: 9538975--9539060 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
9538965 CCTGATCAGT
* *
9538975 ATACGACACATAAAGTGCCTA
1 ATACGACACACAAAGTGCCTG
* * *
9538996 AAACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
* *
9539017 ATACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
*
9539038 ATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCTG
9539059 AT
1 AT
9539061 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (21 bp):
ATACGACACACAAAGTGCCTG
Found at i:9540522 original size:12 final size:13
Alignment explanation
Indices: 9540500--9540528 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
9540490 ATTCTCCCTT
9540500 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
9540513 TTTC-TTTCTTTC
1 TTTCTTTTCTTTC
9540525 TTTC
1 TTTC
9540529 CTTCCCCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:9545581 original size:18 final size:17
Alignment explanation
Indices: 9545558--9545600 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
9545548 CGTAAGATTC
9545558 TTCTTCTCCAGTATGCAT
1 TTCTTCTCCAGTAT-CAT
9545576 TTCTTCAT-CAGTATCAT
1 TTCTTC-TCCAGTATCAT
*
9545593 TTATTCTC
1 TTCTTCTC
9545601 TCATCCGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 1 0.05
17 8 0.36
18 12 0.55
19 1 0.05
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49
Consensus pattern (17 bp):
TTCTTCTCCAGTATCAT
Found at i:9546889 original size:21 final size:21
Alignment explanation
Indices: 9546861--9546946 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
9546851 CCTGATCAGT
* *
9546861 ATACGACACATAAAGTGCCTA
1 ATACGACACACAAAGTGCCTG
* * *
9546882 AAACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
* *
9546903 ATACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
*
9546924 ATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCTG
9546945 AT
1 AT
9546947 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (21 bp):
ATACGACACACAAAGTGCCTG
Found at i:9548416 original size:16 final size:17
Alignment explanation
Indices: 9548381--9548416 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
9548371 CCTAATTCTC
9548381 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
9548397 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
9548412 CCTTC
1 CCTTC
9548417 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:9548474 original size:14 final size:14
Alignment explanation
Indices: 9548455--9548483 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9548445 CTTTTCTTTG
9548455 TTCTTTCTTTTATT
1 TTCTTTCTTTTATT
9548469 TTCTTTCTTTTATT
1 TTCTTTCTTTTATT
9548483 T
1 T
9548484 GTTTTAGTTG
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:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTCTTTTATT
Found at i:9558181 original size:20 final size:21
Alignment explanation
Indices: 9558158--9558199 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9558148 TATCAAAAAA
* *
9558158 TTTAATT-AATTCAATCAATT
1 TTTAATTCAAATCAATAAATT
9558178 TTTAATTCAAATCAATAAATT
1 TTTAATTCAAATCAATAAATT
9558199 T
1 T
9558200 ACAGATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAATTCAAATCAATAAATT
Found at i:9560570 original size:4 final size:4
Alignment explanation
Indices: 9560553--9560587 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
9560543 TATAGATTGT
* *
9560553 ATAC ATAC AAAC ATAC ATAC ATTC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
9560588 TATATGTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:9561868 original size:2 final size:2
Alignment explanation
Indices: 9561863--9561894 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9561853 ATTTTTTAAG
9561863 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
9561895 GTATGTATGT
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:9577480 original size:15 final size:15
Alignment explanation
Indices: 9577460--9577490 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9577450 TGAATCAAAG
9577460 TTTTGTCTCTTGATA
1 TTTTGTCTCTTGATA
9577475 TTTTGTCTCTTGATA
1 TTTTGTCTCTTGATA
9577490 T
1 T
9577491 ATGGAAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTTGTCTCTTGATA
Found at i:9585373 original size:2 final size:2
Alignment explanation
Indices: 9585366--9585397 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9585356 GAATTTGAAT
*
9585366 TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9585398 CCTGTACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:9585588 original size:39 final size:39
Alignment explanation
Indices: 9585544--9585620 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
9585534 TAGTTTTCAA
*
9585544 CCACATTCATGTTTGCATACTTTCAATGGTTAATTTTAG
1 CCACATTCATGTTTGCATACTTTCAATGGTAAATTTTAG
9585583 CCACATTCATGTTTGCATACTTTCAATGGTAAATTTTA
1 CCACATTCATGTTTGCATACTTTCAATGGTAAATTTTA
9585621 AGTGAACATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (39 bp):
CCACATTCATGTTTGCATACTTTCAATGGTAAATTTTAG
Found at i:9591716 original size:31 final size:30
Alignment explanation
Indices: 9591681--9591738 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
9591671 CAGGTTATTA
* *
9591681 TAAAATAATTAAA-TTTTTTTTATATTTTACT
1 TAAAA-AATAAAAGTTTTATTTAT-TTTTACT
9591712 TAAAAAATAAAAGTTTTATTTATTTTT
1 TAAAAAATAAAAGTTTTATTTATTTTT
9591739 GGTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (30 bp):
TAAAAAATAAAAGTTTTATTTATTTTTACT
Found at i:9599300 original size:21 final size:21
Alignment explanation
Indices: 9599276--9599315 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9599266 CACCGGGCTT
9599276 CAACACCCTCA-CCATCTCCCC
1 CAACACCCTCATCC-TCTCCCC
9599297 CAACACCCTCATCCTCTCC
1 CAACACCCTCATCCTCTCC
9599316 GCCGCTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.23, C:0.60, G:0.00, T:0.17
Consensus pattern (21 bp):
CAACACCCTCATCCTCTCCCC
Found at i:9601581 original size:25 final size:25
Alignment explanation
Indices: 9601548--9601609 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
9601538 ACTTAAAGAA
*
9601548 AAATATTTAAAAAATATTATATGAT
1 AAATGTTTAAAAAATATTATATGAT
9601573 AAATGTTTAAAAAATATTATATGAT
1 AAATGTTTAAAAAATATTATATGAT
9601598 AAATGTTTAAAA
1 AAATGTTTAAAA
9601610 TATTATCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
AAATGTTTAAAAAATATTATATGAT
Found at i:9603315 original size:81 final size:81
Alignment explanation
Indices: 9603212--9603364 Score: 279
Period size: 81 Copynumber: 1.9 Consensus size: 81
9603202 TATTAAAATA
* * *
9603212 TTGATAAAAATATAGATGAAATTATAAAATATTTCATTTAAATAACAGTAAAAATTAGAAAATAT
1 TTGATAAAAATATAGATAAAATTATAAAATATTTCATTTAAAGAACAATAAAAATTAGAAAATAT
9603277 ATAGTCAGGCTCAATT
66 ATAGTCAGGCTCAATT
9603293 TTGATAAAAATATAGATAAAATTATAAAATATTTCATTTAAAGAACAATAAAAATTAGAAAATAT
1 TTGATAAAAATATAGATAAAATTATAAAATATTTCATTTAAAGAACAATAAAAATTAGAAAATAT
9603358 ATAGTCA
66 ATAGTCA
9603365 AGCTTAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (81 bp):
TTGATAAAAATATAGATAAAATTATAAAATATTTCATTTAAAGAACAATAAAAATTAGAAAATAT
ATAGTCAGGCTCAATT
Found at i:9603676 original size:22 final size:23
Alignment explanation
Indices: 9603651--9603694 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9603641 ATTATAATAA
*
9603651 TATTTAAAAA-ATTATATATTTT
1 TATTAAAAAATATTATATATTTT
*
9603673 TATTAAAAAATATTATGTATTT
1 TATTAAAAAATATTATATATTT
9603695 ATTTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTAAAAAATATTATATATTTT
Found at i:9604775 original size:16 final size:16
Alignment explanation
Indices: 9604754--9604786 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9604744 TTTCAATTTG
9604754 GACTGTAAATTGGACC
1 GACTGTAAATTGGACC
9604770 GACTGTAAATTGGACC
1 GACTGTAAATTGGACC
9604786 G
1 G
9604787 TTAAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (16 bp):
GACTGTAAATTGGACC
Found at i:9613924 original size:14 final size:15
Alignment explanation
Indices: 9613897--9613928 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9613887 AATGATCATA
9613897 TTCCAAATTTTTTTC
1 TTCCAAATTTTTTTC
9613912 TTCCAAATTTTTTTC
1 TTCCAAATTTTTTTC
9613927 TT
1 TT
9613929 TCTTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCCAAATTTTTTTC
Found at i:9615267 original size:23 final size:24
Alignment explanation
Indices: 9615232--9615277 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
9615222 GTCTTTATAT
*
9615232 TTTTTATTAATTTATATATTATCA
1 TTTTAATTAATTTATATATTATCA
*
9615256 TTTTAATT-ATTTTTATATTATC
1 TTTTAATTAATTTATATATTATC
9615278 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTAATTAATTTATATATTATCA
Found at i:9615358 original size:21 final size:20
Alignment explanation
Indices: 9615325--9615367 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
9615315 TCGTAAGATA
9615325 TTAATAATGTTTTTATAATAT
1 TTAATAATGTTTTTATAA-AT
* * *
9615346 TTAATATTTTTTTTCTAAAT
1 TTAATAATGTTTTTATAAAT
9615366 TT
1 TT
9615368 TATGATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTAATAATGTTTTTATAAAT
Found at i:9615404 original size:20 final size:18
Alignment explanation
Indices: 9615363--9615406 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
9615353 TTTTTTTCTA
9615363 AATTTTATGATATTTAAT
1 AATTTTATGATATTTAAT
9615381 AATTTTGATAGAT-TTTATAT
1 AATTTT-AT-GATATTTA-AT
9615401 AATTTT
1 AATTTT
9615407 CAAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
AATTTTATGATATTTAAT
Found at i:9616162 original size:17 final size:17
Alignment explanation
Indices: 9616112--9616163 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 17
9616102 TTTCAAATAA
9616112 TTTATTTTCA--ATTAT
1 TTTATTTTCATTATTAT
**
9616127 TTTATTTT--TTAAAAT
1 TTTATTTTCATTATTAT
9616142 TTTATTTTCATTATTAT
1 TTTATTTTCATTATTAT
9616159 TTTAT
1 TTTAT
9616164 AATTTATAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 19 0.66
17 10 0.34
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATTTTCATTATTAT
Found at i:9616182 original size:32 final size:32
Alignment explanation
Indices: 9616112--9616182 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
9616102 TTTCAAATAA
**
9616112 TTTATTTTCA--ATTATTTTATTTTTTAAAAT
1 TTTATTTTCATTATTATTTTATAATTTAAAAT
*
9616142 TTTATTTTCATTATTATTTTATAATTTATAAGT
1 TTTATTTTCATTATTATTTTATAATTTA-AAAT
9616175 TTT-TTTTC
1 TTTATTTTC
9616183 TAGAATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.29
32 19 0.54
33 6 0.17
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (32 bp):
TTTATTTTCATTATTATTTTATAATTTAAAAT
Found at i:9616623 original size:27 final size:27
Alignment explanation
Indices: 9616575--9616626 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
9616565 CTTTGAGAGT
* *
9616575 TTTTGAGAAATAATATTTTATATATAA
1 TTTTAAGAAATAATATTATATATATAA
9616602 TTTTAAGAAATAATGA-TATATATAT
1 TTTTAAGAAATAAT-ATTATATATAT
9616627 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (27 bp):
TTTTAAGAAATAATATTATATATATAA
Found at i:9617134 original size:24 final size:24
Alignment explanation
Indices: 9617107--9617174 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
9617097 ATAACTCTTT
9617107 TATGTATATAAATAAAATA-ATAAA
1 TATGTATATAAATAAAATATAT-AA
*
9617131 TATGTAATTATATAATAAAATATATAT
1 TATGT-A-TATA-AATAAAATATATAA
* *
9617158 TATATATAAAAATAAAA
1 TATGTATATAAATAAAA
9617175 GATTTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 12 0.32
25 4 0.11
26 5 0.14
27 14 0.38
28 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
TATGTATATAAATAAAATATATAA
Found at i:9617147 original size:19 final size:19
Alignment explanation
Indices: 9617123--9617168 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
9617113 TATAAATAAA
*
9617123 ATAAT-AAATATGTAATTAT
1 ATAATAAAATATAT-ATTAT
9617142 ATAATAAAATATATATTAT
1 ATAATAAAATATATATTAT
9617161 AT-ATAAAA
1 ATAATAAAA
9617169 ATAAAAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 12 0.48
20 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATAAAATATATATTAT
Found at i:9617182 original size:24 final size:22
Alignment explanation
Indices: 9617130--9617191 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
9617120 AAAATAATAA
* *
9617130 ATATGTAATTATATAATAAAATAT
1 ATAT-TAATTA-AAAATAAAAGAT
9617154 ATATTATATATAAAAATAAAAGAT
1 ATATTA-AT-TAAAAATAAAAGAT
*
9617178 TTATTAATTAAAAA
1 ATATTAATTAAAAA
9617192 GATAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 21 0.64
25 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
ATATTAATTAAAAATAAAAGAT
Found at i:9618147 original size:15 final size:15
Alignment explanation
Indices: 9618127--9618155 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9618117 AGAATAATCA
9618127 GACAATAACATATGT
1 GACAATAACATATGT
9618142 GACAATAACATATG
1 GACAATAACATATG
9618156 ACATGTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
GACAATAACATATGT
Found at i:9618777 original size:34 final size:35
Alignment explanation
Indices: 9618691--9618804 Score: 103
Period size: 34 Copynumber: 3.3 Consensus size: 35
9618681 GTAATATGAG
* *
9618691 ATACTTATAATAGATT-AATACGGTAACATTTAAT
1 ATACTTATAACAGATTCAATACGGTAACAATTAAT
* *
9618725 ATGA-TTTTAATAGA-TCAATACGGTAACAATTAAT
1 AT-ACTTATAACAGATTCAATACGGTAACAATTAAT
**
9618759 ATACTTATAACA-ATTCAATAAAGTAGA-AATTAAT
1 ATACTTATAACAGATTCAATACGGTA-ACAATTAAT
**
9618793 ATGTTTATAACA
1 ATACTTATAACA
9618805 AATCAATTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
33 3 0.04
34 62 0.93
35 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
ATACTTATAACAGATTCAATACGGTAACAATTAAT
Found at i:9621668 original size:11 final size:11
Alignment explanation
Indices: 9621639--9621679 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
9621629 TTCTAATACG
9621639 TATATATA-T-
1 TATATATATTA
*
9621648 TATATGTATTA
1 TATATATATTA
9621659 TATATATATTA
1 TATATATATTA
*
9621670 TGTATATATT
1 TATATATATT
9621680 TTTAATGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 7 0.26
10 1 0.04
11 19 0.70
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
TATATATATTA
Found at i:9621819 original size:3 final size:3
Alignment explanation
Indices: 9621811--9621862 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
9621801 GATGTGTATA
* ** * *
9621811 TAT TAT TAT TACT AAT TAT TAT TAT TGC TAG TAT TAT TAT AAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9621857 TAT TAT
1 TAT TAT
9621863 GTTAGTGTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:9621832 original size:16 final size:15
Alignment explanation
Indices: 9621811--9621850 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
9621801 GATGTGTATA
*
9621811 TATTATTATTACTAAT
1 TATTATTATTACT-AG
*
9621827 TATTATTATTGCTAG
1 TATTATTATTACTAG
9621842 TATTATTAT
1 TATTATTAT
9621851 AATTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (15 bp):
TATTATTATTACTAG
Found at i:9621979 original size:17 final size:19
Alignment explanation
Indices: 9621959--9622001 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
9621949 GTAGCTTTTG
*
9621959 TATTTTA-AT-ATTGTTAT
1 TATTTTATATCATTATTAT
9621976 TATTATTATATCATTATTAT
1 TATT-TTATATCATTATTAT
9621996 TATTTT
1 TATTTT
9622002 TGTATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 3 0.14
19 4 0.18
20 11 0.50
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTATATCATTATTAT
Found at i:9621980 original size:3 final size:3
Alignment explanation
Indices: 9621967--9622072 Score: 55
Period size: 3 Copynumber: 36.3 Consensus size: 3
9621957 TGTATTTTAA
* *
9621967 TAT TGT TAT TAT TAT TA- TAT CAT TAT TAT TAT T-T T-T GTAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT
* * * * *
9622011 TAT TCA- TAC TAT CAT TAT TA- TAT TAT TAT CAC TAT TA- CATT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
9622055 TA- TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
9622073 GCTATCATTA
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
2 11 0.14
3 61 0.78
4 6 0.08
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:9622034 original size:23 final size:26
Alignment explanation
Indices: 9622006--9622061 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 26
9621996 TATTTTTGTA
9622006 TATATTATTCAT-ACTA-T-CA-TTAT
1 TATATTATT-ATCACTATTACATTTAT
9622029 TATATTATTATCACTATTACATTTAT
1 TATATTATTATCACTATTACATTTAT
9622055 TATATTA
1 TATATTA
9622062 GTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 2 0.07
23 13 0.45
24 1 0.03
25 2 0.07
26 11 0.38
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATTATTATCACTATTACATTTAT
Found at i:9622046 original size:17 final size:18
Alignment explanation
Indices: 9622020--9622057 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9622010 TTATTCATAC
* *
9622020 TATCATTATTATA-TTAT
1 TATCACTATTACATTTAT
9622037 TATCACTATTACATTTAT
1 TATCACTATTACATTTAT
9622055 TAT
1 TAT
9622058 ATTAGTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (18 bp):
TATCACTATTACATTTAT
Found at i:9623840 original size:55 final size:55
Alignment explanation
Indices: 9623756--9623868 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
9623746 TGCAATCATT
9623756 TTATTCTTAAGTAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTGC
1 TTATTCTTAAGTAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTGC
9623811 TTATTCTTAAGTAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTGC
1 TTATTCTTAAGTAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTGC
9623866 TTA
1 TTA
9623869 ATTTTCTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (55 bp):
TTATTCTTAAGTAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTGC
Found at i:9624768 original size:2 final size:2
Alignment explanation
Indices: 9624761--9624785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9624751 AACTCATGGA
9624761 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9624786 CATGTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9638914 original size:40 final size:40
Alignment explanation
Indices: 9638855--9638938 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
9638845 ACCTCCAATG
9638855 CTTA-CCATATGCAAGAAATCAAAATGCAATAATTTACAA
1 CTTAGCCATATGCAAGAAATCAAAATGCAATAATTTACAA
9638894 CTTAGCCATATGCAAGAAATCAAAATGCAATAATTTACAA
1 CTTAGCCATATGCAAGAAATCAAAATGCAATAATTTACAA
9638934 CTTAG
1 CTTAG
9638939 TTCAGATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 4 0.09
40 40 0.91
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (40 bp):
CTTAGCCATATGCAAGAAATCAAAATGCAATAATTTACAA
Found at i:9641789 original size:18 final size:18
Alignment explanation
Indices: 9641766--9641800 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9641756 GAGTTAAACG
9641766 AATCGAGTTATTAAAGTT
1 AATCGAGTTATTAAAGTT
*
9641784 AATCGAGTTATTCAAGT
1 AATCGAGTTATTAAAGT
9641801 CAACTTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTAAAGTT
Found at i:9641871 original size:9 final size:9
Alignment explanation
Indices: 9641852--9641888 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
9641842 TGAGTTTTCG
*
9641852 AATTTGAAT
1 AATTCGAAT
*
9641861 AACTCGAAT
1 AATTCGAAT
9641870 AATTCGAAT
1 AATTCGAAT
9641879 AATTCGAAT
1 AATTCGAAT
9641888 A
1 A
9641889 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:9643158 original size:25 final size:25
Alignment explanation
Indices: 9643124--9643175 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
9643114 TGATTTGGAG
*
9643124 AATGACTATTTCTTGGTAAAGTTCC
1 AATGAATATTTCTTGGTAAAGTTCC
*
9643149 AATGAATATTTCTTGGTCAAGTTCC
1 AATGAATATTTCTTGGTAAAGTTCC
9643174 AA
1 AA
9643176 AATGATGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (25 bp):
AATGAATATTTCTTGGTAAAGTTCC
Found at i:9647221 original size:46 final size:46
Alignment explanation
Indices: 9647161--9647434 Score: 415
Period size: 46 Copynumber: 6.0 Consensus size: 46
9647151 TTTGACATGA
* * * * *
9647161 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *** * *
9647207 TGCCATGGTATCTTTCAACTATGGTCTTGTTCATTTCATATTACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
9647253 TGCCATGGTATCTTTCAACCATGGTCTTACGCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
9647299 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
9647345 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
9647391 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
9647435 AGAGCACACT
Statistics
Matches: 213, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 4 0.02
46 209 0.98
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:9653124 original size:21 final size:21
Alignment explanation
Indices: 9653100--9653141 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9653090 AACTTAACAC
* *
9653100 CAATTTAATAAAATTCACATT
1 CAATTCAACAAAATTCACATT
*
9653121 CAATTCAACCAAATTCACATT
1 CAATTCAACAAAATTCACATT
9653142 TAGGCAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (21 bp):
CAATTCAACAAAATTCACATT
Found at i:9655504 original size:20 final size:20
Alignment explanation
Indices: 9655467--9655514 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
9655457 TATCAAAAAT
9655467 TATTATTTTAGAATTTTTTTATA
1 TATT-TTTTAGAA-TTTTTTA-A
9655490 TATTTTTTAG-A-TTTTTAA
1 TATTTTTTAGAATTTTTTAA
9655508 TATTTTT
1 TATTTTT
9655515 AAAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 6 0.24
21 1 0.04
22 6 0.24
23 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTTTTAGAATTTTTTAA
Found at i:9655522 original size:19 final size:19
Alignment explanation
Indices: 9655500--9655563 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
9655490 TATTTTTTAG
9655500 ATTTTTA-ATATTTTTAAAA
1 ATTTTTAGA-ATTTTTAAAA
*
9655519 A-TTTTAGAATTTTTATAA
1 ATTTTTAGAATTTTTAAAA
*
9655537 ATATTTT-GAATTTTAAAAA
1 AT-TTTTAGAATTTTTAAAA
9655556 ATATTTTA
1 AT-TTTTA
9655564 TTTTTTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 15 0.39
19 19 0.50
20 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTTTAGAATTTTTAAAA
Found at i:9655523 original size:18 final size:18
Alignment explanation
Indices: 9655509--9655557 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
9655499 GATTTTTAAT
9655509 ATTTTTAAAAATTTTAGA
1 ATTTTTAAAAATTTTAGA
9655527 ATTTTTATAAATATTTT-GA
1 ATTTTTA-AAA-ATTTTAGA
*
9655546 ATTTTAAAAAAT
1 ATTTTTAAAAAT
9655558 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 10 0.36
19 11 0.39
20 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATTTTTAAAAATTTTAGA
Found at i:9657367 original size:7 final size:7
Alignment explanation
Indices: 9657313--9657357 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
9657303 TTAGAGTTAA
9657313 AAATAAG
1 AAATAAG
9657320 AAATAAG
1 AAATAAG
9657327 AAATAAG
1 AAATAAG
9657334 AAATAAG
1 AAATAAG
9657341 AAATAAG
1 AAATAAG
9657348 AAATAAG
1 AAATAAG
9657355 AAA
1 AAA
9657358 AAAAGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAATAAG
Found at i:9665476 original size:19 final size:19
Alignment explanation
Indices: 9665452--9665491 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
9665442 TAGGTTTCAA
9665452 CAACATGAAGAGGCAAAAG
1 CAACATGAAGAGGCAAAAG
*
9665471 CAACATGAAGAGGTAAAAG
1 CAACATGAAGAGGCAAAAG
9665490 CA
1 CA
9665492 TTTATTGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.25, T:0.07
Consensus pattern (19 bp):
CAACATGAAGAGGCAAAAG
Found at i:9670785 original size:26 final size:26
Alignment explanation
Indices: 9670723--9670786 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
9670713 AGTTTGGCGA
9670723 TGCTTTTGAAAAATACTTTTGAAAAG
1 TGCTTTTGAAAAATACTTTTGAAAAG
* * * *
9670749 TG-TTGTGGAAAAGTATTTTTGAGAAG
1 TGCTT-TTGAAAAATACTTTTGAAAAG
9670775 TGCTTTTGAAAA
1 TGCTTTTGAAAA
9670787 CTTTGGTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 2 0.06
26 27 0.87
27 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (26 bp):
TGCTTTTGAAAAATACTTTTGAAAAG
Found at i:9680332 original size:14 final size:15
Alignment explanation
Indices: 9680313--9680350 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
9680303 TGCTACCACT
9680313 AAAAT-ATTTTTCAA
1 AAAATAATTTTTCAA
*
9680327 AAAATAATTTTT-GA
1 AAAATAATTTTTCAA
9680341 AAAATAATTT
1 AAAATAATTT
9680351 ATTTTTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (15 bp):
AAAATAATTTTTCAA
Found at i:9680483 original size:18 final size:18
Alignment explanation
Indices: 9680457--9680499 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
9680447 AAAAATTATT
*
9680457 TTTAAATATATTAATAAA
1 TTTATATATATTAATAAA
9680475 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
9680493 TTTATAT
1 TTTATAT
9680500 TTTAAATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:9681368 original size:15 final size:15
Alignment explanation
Indices: 9681348--9681402 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
9681338 ACCAGAAAAC
9681348 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
9681363 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
9681382 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
9681397 ATTTAT
1 ATTTAT
9681403 AGTGAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 15 0.45
16 1 0.03
17 7 0.21
18 1 0.03
19 9 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:9681470 original size:13 final size:13
Alignment explanation
Indices: 9681428--9681473 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
9681418 TAATAGATCA
*
9681428 AAAATATTATTTA
1 AAAATATTATTTT
9681441 AAAATATTATTTCT
1 AAAATATTATTT-T
9681455 AAAAT-TTATTATT
1 AAAATATTATT-TT
9681468 AAAATA
1 AAAATA
9681474 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATATTATTTT
Found at i:9681501 original size:20 final size:20
Alignment explanation
Indices: 9681476--9681515 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9681466 TTAAAATAAA
*
9681476 ATTAAAATATTAAATAATTT
1 ATTAAAATAATAAATAATTT
*
9681496 ATTAAAATAATAAATTATTT
1 ATTAAAATAATAAATAATTT
9681516 TAATAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAAATAATAAATAATTT
Done.