Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 178 of 187
Found at i:53255260 original size:21 final size:21
Alignment explanation
Indices: 53255202--53255263 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
53255192 ATTTGTATAG
* *
53255202 TATTTTTAAGTTATTTAAAAT
1 TATTTTGAATTTATTTAAAAT
* ** *
53255223 GATTATTGAATAAATTTAAATT
1 TATT-TTGAATTTATTTAAAAT
53255245 TATTTTGAATTTATTTAAA
1 TATTTTGAATTTATTTAAA
53255264 GTTAATTATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (21 bp):
TATTTTGAATTTATTTAAAAT
Found at i:53262913 original size:2 final size:2
Alignment explanation
Indices: 53262902--53262930 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53262892 CGACATAAAG
53262902 TA TA -A 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
53262931 GGTTCATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:53268225 original size:25 final size:25
Alignment explanation
Indices: 53268194--53268244 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53268184 TATGAAATAC
**
53268194 TTTGTATATTGCCATTGTGGCGTAT
1 TTTGTATATCACCATTGTGGCGTAT
* *
53268219 TTTGTATGTCACCTTTGTGGCGTAT
1 TTTGTATATCACCATTGTGGCGTAT
53268244 T
1 T
53268245 CTGTCTGGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.49
Consensus pattern (25 bp):
TTTGTATATCACCATTGTGGCGTAT
Found at i:53271499 original size:18 final size:18
Alignment explanation
Indices: 53271465--53271499 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53271455 CATGGTGGAA
*
53271465 TAAATTTTATATGTTTTC
1 TAAATTTTATATATTTTC
*
53271483 TAAATTTTATGTATTTT
1 TAAATTTTATATATTTT
53271500 TTATTTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (18 bp):
TAAATTTTATATATTTTC
Found at i:53281740 original size:17 final size:18
Alignment explanation
Indices: 53281720--53281754 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53281710 TATTTTTCTA
53281720 AATAAATTT-TAAAATAC
1 AATAAATTTATAAAATAC
*
53281737 AATAATTTTATAAAATAC
1 AATAAATTTATAAAATAC
53281755 TCTAACATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATTTATAAAATAC
Found at i:53294715 original size:13 final size:13
Alignment explanation
Indices: 53294697--53294724 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53294687 ATAAAATTGG
53294697 AAAGATGAAAAAT
1 AAAGATGAAAAAT
53294710 AAAGATGAAAAAT
1 AAAGATGAAAAAT
53294723 AA
1 AA
53294725 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGATGAAAAAT
Found at i:53295766 original size:26 final size:26
Alignment explanation
Indices: 53295736--53295822 Score: 106
Period size: 26 Copynumber: 3.4 Consensus size: 26
53295726 ACAGTTCTTA
*
53295736 TGAGCATCCCGA-TATATGGCTCTTCG
1 TGAGCTTCCCGATTA-ATGGCTCTTCG
* *
53295762 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAATGGCTCTTCG
**
53295788 TGAGCTTCTTGATTAATGGCTCTTCG
1 TGAGCTTCCCGATTAATGGCTCTTCG
53295814 -GAGCTTCCC
1 TGAGCTTCCC
53295823 AATATTGGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 7 0.14
26 42 0.82
27 2 0.04
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.34
Consensus pattern (26 bp):
TGAGCTTCCCGATTAATGGCTCTTCG
Found at i:53298968 original size:18 final size:17
Alignment explanation
Indices: 53298945--53298978 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53298935 TATTTCGATA
53298945 TTTTAATAAAATGTAATC
1 TTTTAA-AAAATGTAATC
*
53298963 TTTTAAATAATGTAAT
1 TTTTAAAAAATGTAAT
53298979 GTGACTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
TTTTAAAAAATGTAATC
Found at i:53299058 original size:11 final size:11
Alignment explanation
Indices: 53299040--53299072 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
53299030 TACACCAATG
53299040 AATAACAAACA
1 AATAACAAACA
*
53299051 ATTAACAAACA
1 AATAACAAACA
53299062 AAT-ACAAACA
1 AATAACAAACA
53299072 A
1 A
53299073 GCATAGCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (11 bp):
AATAACAAACA
Found at i:53299712 original size:14 final size:14
Alignment explanation
Indices: 53299693--53299722 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53299683 AAACAGAAGT
*
53299693 AAAAAGAGAAAAAG
1 AAAAAGAAAAAAAG
53299707 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
53299721 AA
1 AA
53299723 TGATGGGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:53311760 original size:21 final size:20
Alignment explanation
Indices: 53311730--53311786 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
53311720 GGATTTAATT
53311730 AATT-TTTTTAAATATATAAA
1 AATTATTTTTAAATATA-AAA
53311750 AATTATTTTTAAATCATAAAA
1 AATTATTTTTAAAT-ATAAAA
*
53311771 AAATATTTTTAAATAT
1 AATTATTTTTAAATAT
53311787 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.18
21 25 0.74
22 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTATTTTTAAATATAAAA
Found at i:53316441 original size:22 final size:22
Alignment explanation
Indices: 53316416--53316459 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53316406 TTAACCATAT
*
53316416 ATTTAGTTATTTT-TTTAATTTA
1 ATTTAATT-TTTTATTTAATTTA
*
53316438 ATTTAATTTTTTATTTTATTTA
1 ATTTAATTTTTTATTTAATTTA
53316460 TTTTTCTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTAATTTTTTATTTAATTTA
Found at i:53316449 original size:18 final size:16
Alignment explanation
Indices: 53316426--53316464 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
53316416 ATTTAGTTAT
53316426 TTTTTTAATTTAATTTAA
1 TTTTTT-ATTTAATTT-A
*
53316444 TTTTTTATTTTATTTA
1 TTTTTTATTTAATTTA
53316460 TTTTT
1 TTTTT
53316465 CTACATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTATTTAATTTA
Found at i:53318238 original size:43 final size:42
Alignment explanation
Indices: 53318172--53318296 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 42
53318162 ATACACTTAC
* * * * *
53318172 GTGCCAACATGATTACTTTGGTTTATCCGATGATGCACT-GT
1 GTGCCAATATAATTGCTTCGGTTTGTCCGATGATGCACTCGT
* * *
53318213 GCATGCCAATATAATTGGTTCGGTTTGTCCAATGGTGCACCTCGT
1 G--TGCCAATATAATTGCTTCGGTTTGTCCGATGATGCA-CTCGT
* *
53318258 GTGCCAGTATAATTGCTTCAGTTTGTCCGATGATGCACT
1 GTGCCAATATAATTGCTTCGGTTTGTCCGATGATGCACT
53318297 ATTTGTGCTA
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 59 0.88
44 2 0.03
45 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (42 bp):
GTGCCAATATAATTGCTTCGGTTTGTCCGATGATGCACTCGT
Found at i:53318304 original size:43 final size:42
Alignment explanation
Indices: 53318192--53318310 Score: 114
Period size: 43 Copynumber: 2.8 Consensus size: 42
53318182 GATTACTTTG
* * * *
53318192 GTTTATCCGATGATGCAC-TGTGCATGCCAATATAATTGGTTCG
1 GTTTGTCCGATGATGCACTTGTG--TGCCAGTATAATTGCTTCA
* * *
53318235 GTTTGTCCAATGGTGCACCTCGTGTGCCAGTATAATTGCTTCA
1 GTTTGTCCGATGATGCA-CTTGTGTGCCAGTATAATTGCTTCA
* *
53318278 GTTTGTCCGATGATGCACTATTTGTGCTAGTAT
1 GTTTGTCCGATGATGCACT-TGTGTGCCAGTAT
53318311 CTTTCCTTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 2 0.03
43 55 0.90
44 1 0.02
45 3 0.05
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (42 bp):
GTTTGTCCGATGATGCACTTGTGTGCCAGTATAATTGCTTCA
Found at i:53318342 original size:36 final size:36
Alignment explanation
Indices: 53318295--53318376 Score: 157
Period size: 36 Copynumber: 2.3 Consensus size: 36
53318285 CGATGATGCA
53318295 CTATTT-GTGCTAGTATCTTTCCTTCAGTAGGTTGT
1 CTATTTCGTGCTAGTATCTTTCCTTCAGTAGGTTGT
53318330 CTATTTCGTGCTAGTATCTTTCCTTCAGTAGGTTGT
1 CTATTTCGTGCTAGTATCTTTCCTTCAGTAGGTTGT
53318366 CTATTTCGTGC
1 CTATTTCGTGC
53318377 ACAAATAGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 6 0.13
36 40 0.87
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.48
Consensus pattern (36 bp):
CTATTTCGTGCTAGTATCTTTCCTTCAGTAGGTTGT
Found at i:53328408 original size:132 final size:133
Alignment explanation
Indices: 53328169--53328687 Score: 579
Period size: 132 Copynumber: 3.9 Consensus size: 133
53328159 ACTTTAATTT
* * * * * **
53328169 ATGAACAAATTTTATTTGAGTTAGCTGATCTC-ATATTGCAAC-TCTTAATAGCTCGCTGGTTTA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACTTC-AAACAGCTCGCTAATTTA
** ** * * *
53328232 AGATTGCAACTGATATTGTTAAGGTTCGTTAATTTAATATTGCAACCTAAGTTCATTCGGTTTAA
65 AGATCACAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAA
53328297 GATC
130 GATC
* *
53328301 AAGAACAAATTTTATTTGAGTTAGTTGATC-CAAGATCGCAACTTCAAACAGCTTGCTAATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACTTCAAACAGCTCGCTAATTTAA
*
53328365 GATCGCAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
66 GATCACAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
*
53328430 ACC
131 ATC
* * *
53328433 ATGAACAAATTTTATTTGAGTTAGTTGATCTC-AGATCGCAACTCCGAACAACTCGCTAATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACTTCAAACAGCTCGCTAATTTAA
* * * * * *
53328497 TATCACAGCTGATGTTGTTAAGGTT-AGCTGATTTAATATCGCAACCTAAGTTCATTCAATTTAA
66 GATCACAACTGATATTGTTAAGGTTCA-CTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAA
*
53328561 GATT
130 GATC
* * * * *
53328565 GTGAACAAATTTTATTTGAGTTTGTTGATCT-TAGATCGCAACTCTGAATA-A-CTCACTAATTT
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACT-TCAA-ACAGCTCGCTAATTT
* * * * * *
53328627 AAGATCATAGCTAATATTGTTAAGGTTCGA-TGATTTAAGATCGTAACCTAAGCTCATTCGA
64 AAGATCACAACTGATATTGTTAAGGTTC-ACTGATTTAAGATTGCAACCTAAGTTCATTCGA
53328688 AATTTTATTT
Statistics
Matches: 334, Mismatches: 44, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
131 2 0.01
132 325 0.97
133 5 0.01
134 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (133 bp):
ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACTTCAAACAGCTCGCTAATTTAA
GATCACAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
ATC
Found at i:53328646 original size:264 final size:253
Alignment explanation
Indices: 53328169--53328835 Score: 751
Period size: 264 Copynumber: 2.6 Consensus size: 253
53328159 ACTTTAATTT
* * * ** * *
53328169 ATGAACAAATTTTATTTGAGTTAGCTGATCTCATATTGCAACTCTTAATAGCTCGCTGGTTTAAG
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAG
** * * *
53328234 ATTGCAACTGATATTGTTAAGGTTCGTTAATTTAATATTGCAACCTAAGTTCATTCGGTTTAAGA
66 ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
* **
53328299 TCAAGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTTGCTAATTTA
131 TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTCACTAATTTA
* * *
53328364 AGATCGCAACTGATATTGTTAAGGTTC-ACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTA
196 AGATCACAACTAATATTGTTAAGGTTCGA-TGATTTAAGATCGCAACCTAAG--C--TC-A-TT-
53328428 AGACC
253 ----C
* * * * *
53328433 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACTCCGAACAACTCGCTAATTTAAT
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAG
* * * * *
53328498 ATCACAGCTGATGTTGTTAAGGTTAGCTGATTTAATATCGCAACCTAAGTTCATTCAATTTAAGA
66 ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
** * ** *
53328563 TTGTGAACAAATTTTATTTGAGTTTGTTGATCTTAGATCGCAACTCTGAATA-A-CTCACTAATT
131 TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACT-TCAA-ACAGCTCACTAATT
* * *
53328626 TAAGATCATAGCTAATATTGTTAAGGTTCGATGATTTAAGATCGTAACCTAAGCTCATTC
194 TAAGATCACAACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTC
*
53328686 --G---AAATTTTATTTGAGTTAGTTGATCTGAAATC-CTAACTCCAAACAGCTCGCTGATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGC-AACTCCAAACAGCTCGCTGATTTAA
* * *
53328745 GATCATAACTGATATTGTTAAGTTTCGCTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
65 GATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
*
53328810 ATCATGATCAAA-TTTATTTGAGTTAG
130 ATCATGAACAAATTTTATTTGAGTTAG
53328836 CTAATTTAAT
Statistics
Matches: 346, Mismatches: 53, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
247 14 0.04
248 116 0.34
251 1 0.00
253 1 0.00
258 2 0.01
259 1 0.00
260 2 0.01
262 1 0.00
264 202 0.58
265 5 0.01
266 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (253 bp):
ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAG
ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTCACTAATTTA
AGATCACAACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTC
Found at i:53328777 original size:116 final size:116
Alignment explanation
Indices: 53328571--53328803 Score: 306
Period size: 116 Copynumber: 2.0 Consensus size: 116
53328561 GATTGTGAAC
* * * ** *
53328571 AAATTTTATTTGAGTTTGTTGATCTTAGATCGCAACTCTGAATAACTCACTAATTTAAGATCATA
1 AAATTTTATTTGAGTTAGTTGATCTGAAATCGCAACTCCAAACAACTCACTAATTTAAGATCATA
* *
53328636 GCTAATATTGTTAAGGTTCGATGATTTAAGATCGTAACCTAAGCTCATTCG
66 ACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
* * *
53328687 AAATTTTATTTGAGTTAGTTGATCTGAAATC-CTAACTCCAAACAGCTCGCTGATTTAAGATCAT
1 AAATTTTATTTGAGTTAGTTGATCTGAAATCGC-AACTCCAAACAACTCACTAATTTAAGATCAT
* * * * *
53328751 AACTGATATTGTTAAGTTTCGCTGATTTAAGATTGCAACCTAAGTTCATTCG
65 AACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
53328803 A
1 A
53328804 TTTAAGATCA
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
115 1 0.01
116 99 0.99
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (116 bp):
AAATTTTATTTGAGTTAGTTGATCTGAAATCGCAACTCCAAACAACTCACTAATTTAAGATCATA
ACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
Found at i:53335309 original size:20 final size:21
Alignment explanation
Indices: 53335261--53335314 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
53335251 AACTTGTCGA
* * *
53335261 TTGTCTCGAGATAATGACCCC
1 TTGTCTCGAGACAAAGACCAC
53335282 TATGTCTCGAGACAAAG-CCAC
1 T-TGTCTCGAGACAAAGACCAC
53335303 TTGTCTCGAGAC
1 TTGTCTCGAGAC
53335315 CCTAAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
21 5 0.17
22 13 0.45
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (21 bp):
TTGTCTCGAGACAAAGACCAC
Found at i:53336869 original size:26 final size:26
Alignment explanation
Indices: 53336840--53336891 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
53336830 GATTAAACTA
* *
53336840 AATAAATTACTTACCTTAAATTAACC
1 AATAAATTACTTACATAAAATTAACC
53336866 AATAAATTACTTACATAAAATTAACC
1 AATAAATTACTTACATAAAATTAACC
53336892 TAATGTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAAATTACTTACATAAAATTAACC
Found at i:53338093 original size:46 final size:46
Alignment explanation
Indices: 53338018--53338258 Score: 401
Period size: 46 Copynumber: 5.2 Consensus size: 46
53338008 TGCCCTGTTT
53338018 TGGACAGCATTTATACATCAAATTGGACAGCATTAATATGCTCAAAA
1 TGGACAGCA-TTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* * *
53338065 TGGATAGCATTATACATCAAATTAGACAGCATCAATATGCTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* *
53338111 TGGACAGCATTATACATCAAATTGGACAGCTTTAATATGCTCAAAT
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* *
53338157 TGGACAGCATTATACATCAAATTGGACAACATCAATATGCTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
*
53338203 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAT
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
53338249 TGGACAGCAT
1 TGGACAGCAT
53338259 CATAACATAT
Statistics
Matches: 179, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
46 171 0.96
47 8 0.04
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (46 bp):
TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
Found at i:53338968 original size:41 final size:40
Alignment explanation
Indices: 53338905--53339053 Score: 156
Period size: 41 Copynumber: 3.6 Consensus size: 40
53338895 AATGTTTCGT
* * * *
53338905 ACACTAATTGCCATTGCATAGCCGAAGCTATTATAATCTCAC
1 ACACTAAGTGCCA-TACATAGCCGAAGCTATT-CAATCTCGC
* * *
53338947 ACACTAAGTGCCTTACATAGCCAAAGCTATCTCAGTCTCGC
1 ACACTAAGTGCCATACATAGCCGAAGCTAT-TCAATCTCGC
* *
53338988 ACACTAAGTGCCATATATAGCCGAAGCTATTCCAA-ATCGC
1 ACACTAAGTGCCATACATAGCCGAAGCTATT-CAATCTCGC
* *
53339028 ACACTAAGTGCAATAAATAGCCGAAG
1 ACACTAAGTGCCATACATAGCCGAAG
53339054 TCTCGTGTAT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 29 0.32
41 50 0.55
42 12 0.13
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (40 bp):
ACACTAAGTGCCATACATAGCCGAAGCTATTCAATCTCGC
Found at i:53343110 original size:26 final size:24
Alignment explanation
Indices: 53343080--53343138 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
53343070 TACATCCTTG
53343080 ATATATAC-TTTATAATTTATATATAC
1 ATATATACATTT-TAA-TT-TATATAC
* *
53343106 ATATACACATTTTAATTTATGTAC
1 ATATATACATTTTAATTTATATAC
53343130 ATATATACA
1 ATATATACA
53343139 CATATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.48
25 2 0.07
26 10 0.34
27 3 0.10
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATATACATTTTAATTTATATAC
Found at i:53343139 original size:26 final size:26
Alignment explanation
Indices: 53343092--53343141 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
53343082 ATATACTTTA
*
53343092 TAATTTATATATACATATACACATTT
1 TAATTTATATACACATATACACATTT
* *
53343118 TAATTTATGTACATATATACACAT
1 TAATTTATATACACATATACACAT
53343142 ATTTTCATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTTATATACACATATACACATTT
Found at i:53343240 original size:2 final size:2
Alignment explanation
Indices: 53343235--53343306 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
53343225 TTTATATTTC
* * *
53343235 AT AT AT AT AT AT TT AT AT AT -T CT AC A- 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 AT
* * * *
53343275 AT AT AT AT AC AT A- AT AA AT AC AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53343307 CGTTTTGATT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:53343243 original size:22 final size:23
Alignment explanation
Indices: 53343204--53343280 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 23
53343194 CTTAAAATCC
* * *
53343204 ATATTTTTCTTATGTATATATTT
1 ATATATTTCATATATATATATTT
53343227 -TATATTTCATATATATATATTT
1 ATATATTTCATATATATATATTT
*
53343249 ATATATTCTACAATATATATATATAT
1 ATATATT-T-C-ATATATATATATTT
53343275 ATATAT
1 ATATAT
53343281 ATACATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 19 0.41
23 6 0.13
24 1 0.02
25 1 0.02
26 19 0.41
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (23 bp):
ATATATTTCATATATATATATTT
Found at i:53345168 original size:22 final size:22
Alignment explanation
Indices: 53345143--53345214 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
53345133 TTGCTAAACC
53345143 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
53345165 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
53345187 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
53345209 CTCATG
1 CTCATG
53345215 TTTGATATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:53348822 original size:97 final size:97
Alignment explanation
Indices: 53348656--53348943 Score: 481
Period size: 97 Copynumber: 3.0 Consensus size: 97
53348646 ATTCATTTCG
*
53348656 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTTTCAATAAAATTT
53348721 CATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
*
53348753 TATCTTAGCAAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTTTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTTTCAATAAAATTT
53348818 CATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* * * *
53348850 TAT-TCTAGAAAAATTTGCTATCTTCATTAATTTATTCATTTCAAGCTTTG-TTCTCAATAAAAT
1 TATCT-TAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTT-TCAATAAAAT
*
53348913 TTCATCTTGTCCATTGTGATAATCTTTTTCA
64 TTCATCTTATCCATTGTGATAATCTTTTTCA
53348944 AGCAGTTTTC
Statistics
Matches: 181, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
96 3 0.02
97 178 0.98
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (97 bp):
TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTTTCAATAAAATTT
CATCTTATCCATTGTGATAATCTTTTTCATCT
Found at i:53350111 original size:44 final size:44
Alignment explanation
Indices: 53350033--53350137 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
53350023 TGGAAGCTAT
* * *
53350033 AAATTACAAACCTTATCTCTTCGAAGGCGTAGTAGAGTAGGTTG
1 AAATAACAAACCTTATCTCTTCGAAGGCGCAGTAGAGCAGGTTG
*
53350077 AAATAACAAACCTTGTCTC-TCTGAA-GCTGCAGTAGAGCAGGTTG
1 AAATAACAAACCTTATCTCTTC-GAAGGC-GCAGTAGAGCAGGTTG
* * *
53350121 AAGTCACTAACCTTATC
1 AAATAACAAACCTTATC
53350138 CCCCTGAAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.08
44 47 0.92
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
AAATAACAAACCTTATCTCTTCGAAGGCGCAGTAGAGCAGGTTG
Found at i:53350145 original size:44 final size:44
Alignment explanation
Indices: 53350063--53350167 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
53350053 TCGAAGGCGT
* * * * *
53350063 AGTAGAGTAGGTTGAAATAACAAACCTTGTCTCTCTGAAGCTGC
1 AGTAGAGCAGGTTGAAGTAACAAACCTTATCCCCCTGAAGCTGC
* * *
53350107 AGTAGAGCAGGTTGAAGTCACTAACCTTATCCCCCTGAAGTTGC
1 AGTAGAGCAGGTTGAAGTAACAAACCTTATCCCCCTGAAGCTGC
* * *
53350151 AGTTGGGCAAGTTGAAG
1 AGTAGAGCAGGTTGAAG
53350168 ATATGAGTCC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
AGTAGAGCAGGTTGAAGTAACAAACCTTATCCCCCTGAAGCTGC
Found at i:53350456 original size:139 final size:139
Alignment explanation
Indices: 53350195--53350460 Score: 397
Period size: 139 Copynumber: 1.9 Consensus size: 139
53350185 TTAAAGTTGC
** * * * * *
53350195 AGTGGAGCGGGTCAAAATGATGGATCTTATCCCTCTAAAGTTGCAGTAGGTTGGATTAAATTTAC
1 AGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTGGCAGTAGGTTGGATTAAATTTAC
* *
53350260 CATGACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAGACCTTATCTCCC
66 CATGACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAACATAGCAAACCTTATCTCCC
53350325 TGACATTGT
131 TGACATTGT
*
53350334 AGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTGGCTGTAGGTTGGATTAAATTTAC
1 AGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTGGCAGTAGGTTGGATTAAATTTAC
* * * * *
53350399 CATGACAAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCATATCAAACCTTATCT
66 CATGACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAACATAGCAAACCTTATCT
53350461 TACTGAGGTT
Statistics
Matches: 112, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
139 112 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (139 bp):
AGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTGGCAGTAGGTTGGATTAAATTTAC
CATGACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAACATAGCAAACCTTATCTCCC
TGACATTGT
Found at i:53350530 original size:45 final size:46
Alignment explanation
Indices: 53350410--53350569 Score: 150
Period size: 45 Copynumber: 3.6 Consensus size: 46
53350400 ATGACAAGTT
* *
53350410 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-ATCATATCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATCATAGCAAACC
** * ** * * *
53350455 TTATCTTACTGAGGTTGCAGTAAAGTAGACTGAAT-ATAGCGAGCC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATCATAGCAAACC
* * *
53350500 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAAC-TA-CTAATCC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATCATAGC-AAACC
*
53350545 -TATCTCCCTGAAGTTGCAATGGAGC
1 TTATCTCCCTGAAGTTGCAGTGGAGC
53350570 GAATTAAAAT
Statistics
Matches: 90, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
44 24 0.27
45 64 0.71
46 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (46 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATCATAGCAAACC
Found at i:53352208 original size:3 final size:3
Alignment explanation
Indices: 53352195--53352257 Score: 92
Period size: 3 Copynumber: 20.7 Consensus size: 3
53352185 TTTACTATCG
*
53352195 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
53352241 -TA TTA TTA TTA CTTA TT
1 TTA TTA TTA TTA -TTA TT
53352258 TATTTATACC
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 1 0.02
3 50 0.91
4 4 0.07
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:53352338 original size:16 final size:17
Alignment explanation
Indices: 53352319--53352352 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53352309 ATATATACCC
53352319 ACTTTTT-TTTATATAT
1 ACTTTTTATTTATATAT
53352335 ACTTTTTAATTTATATAT
1 ACTTTTT-ATTTATATAT
53352353 GCATATACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
ACTTTTTATTTATATAT
Found at i:53352384 original size:26 final size:26
Alignment explanation
Indices: 53352328--53352390 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
53352318 CACTTTTTTT
* * **
53352328 TATATATACTTTTTAATTTATATATG
1 TATATACACATTTTAATTTATATACA
* *
53352354 CATATACACATTTTAATTTATGTACA
1 TATATACACATTTTAATTTATATACA
53352380 TATATACACAT
1 TATATACACAT
53352391 ATTTTCATAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (26 bp):
TATATACACATTTTAATTTATATACA
Found at i:53352503 original size:16 final size:17
Alignment explanation
Indices: 53352453--53352503 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
53352443 CTTAAAATCC
* *
53352453 ATATTTTTCTTATGTAT
1 ATATTTTTATTATATAT
53352470 ATATTTTATATT-TCATAT
1 ATATTTT-TATTAT-ATAT
53352488 ATATTTTT-TTATATAT
1 ATATTTTTATTATATAT
53352504 TCTACAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 6 0.21
17 10 0.34
18 13 0.45
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (17 bp):
ATATTTTTATTATATAT
Found at i:53356900 original size:29 final size:30
Alignment explanation
Indices: 53356847--53356916 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
53356837 ACTATCAACA
* *
53356847 TAGTCACTTTTATTTGACTCATGTTACATTT
1 TAGTCACTTATATTTGAC-AATGTTACATTT
*
53356878 TAGTCACTTATATTTGA-AATGTTACGTTT
1 TAGTCACTTATATTTGACAATGTTACATTT
*
53356907 TGGTCACTTA
1 TAGTCACTTA
53356917 CGTTATCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (30 bp):
TAGTCACTTATATTTGACAATGTTACATTT
Found at i:53357143 original size:3 final size:3
Alignment explanation
Indices: 53357135--53357190 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
53357125 CAGAACCACA
53357135 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53357183 AAT AAT AA
1 AAT AAT AA
53357191 ATGGACGCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:53364973 original size:27 final size:26
Alignment explanation
Indices: 53364943--53364993 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
53364933 ATGAAATTCT
*
53364943 TACAAA-CAATATGATTGATTAACAATA
1 TACAAAGCAA-ATGA-TGAATAACAATA
53364970 TACAAAGCAAATGATGAATAACAA
1 TACAAAGCAAATGATGAATAACAA
53364994 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (26 bp):
TACAAAGCAAATGATGAATAACAATA
Found at i:53367446 original size:9 final size:10
Alignment explanation
Indices: 53367422--53367446 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53367412 TCCCATAATT
53367422 ATTTTTTACA
1 ATTTTTTACA
53367432 ATTTTTTACA
1 ATTTTTTACA
53367442 ATTTT
1 ATTTT
53367447 CCAAAGTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTTACA
Found at i:53367994 original size:51 final size:50
Alignment explanation
Indices: 53367932--53368070 Score: 179
Period size: 51 Copynumber: 2.7 Consensus size: 50
53367922 ATGTTTGGTT
* *
53367932 CACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCA-AACCATCCGATA
* * * * *
53367983 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCAAACCATCCGATA
* *
53368034 CGCATAGTAGCCTGCACATAGTACTACACATGCGACC
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACC
53368071 TGTAACACCT
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
50 1 0.01
51 72 0.96
52 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCAAACCATCCGATA
Found at i:53369934 original size:48 final size:48
Alignment explanation
Indices: 53369864--53370008 Score: 146
Period size: 48 Copynumber: 3.0 Consensus size: 48
53369854 AAAACAGATT
* * * * *
53369864 TCTCAGTGGCCTACACACAGTCCGTACCACCTTTGTGTAATAACAGAC
1 TCTCGGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGAA
* * **
53369912 TCTCGGTGGCCTGCACAAAGTCCGTGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGAA
* * ** * **
53369960 TATTGGTGGCCTGCACACAGTCTATGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGAA
53370008 T
1 T
53370009 ATTGGTATGC
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 83 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
TCTCGGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGAA
Found at i:53370009 original size:48 final size:48
Alignment explanation
Indices: 53369916--53370014 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
53369906 ACAGACTCTC
*
53369916 GGTGGCCTGCACAAAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
1 GGTGGCCTGCACAAAGTCCATGCCACCCTTGTATCTTAACAGAATATT
* *
53369964 GGTGGCCTGCACACAGTCTATGCCACCCTTGTATCTTAACAGAATATT
1 GGTGGCCTGCACAAAGTCCATGCCACCCTTGTATCTTAACAGAATATT
53370012 GGT
1 GGT
53370015 ATGCATAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (48 bp):
GGTGGCCTGCACAAAGTCCATGCCACCCTTGTATCTTAACAGAATATT
Found at i:53370218 original size:51 final size:51
Alignment explanation
Indices: 53370142--53370244 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
53370132 TCTATTTTTG
53370142 AGGTTCAATCGGGAAATGTTTACTTTTAAATATTTTACCAGTTCTTCTCTA
1 AGGTTCAATCGGGAAATGTTTACTTTTAAATATTTTACCAGTTCTTCTCTA
53370193 AGGTTCAATCGGGAAATGTTTACTTTTAAATATTTTACCAGTTCTTCTCTA
1 AGGTTCAATCGGGAAATGTTTACTTTTAAATATTTTACCAGTTCTTCTCTA
53370244 A
1 A
53370245 CCAATATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (51 bp):
AGGTTCAATCGGGAAATGTTTACTTTTAAATATTTTACCAGTTCTTCTCTA
Found at i:53375538 original size:62 final size:60
Alignment explanation
Indices: 53375462--53375608 Score: 160
Period size: 57 Copynumber: 2.5 Consensus size: 60
53375452 ATTGGCGTTA
*
53375462 AAAAGGATCTAGCCCGGACGGGTGATCCTATCTTGATATAGCCCTCCCGAAGAATATGTGTGG
1 AAAAGGATCTAGCCCGGACGGGTGATCC-ATCTTGATATAACCCTCCCGAAGAATA--TGTGG
** *
53375525 AAAA-GATCTAGCCCGGAAAGGTG----ATCTTGATATAACCCTCCCGAATAATATGTGG
1 AAAAGGATCTAGCCCGGACGGGTGATCCATCTTGATATAACCCTCCCGAAGAATATGTGG
* * *
53375580 AAAATGGATTTAGCCCGAACGGGTAATCC
1 AAAA-GGATCTAGCCCGGACGGGTGATCC
53375609 GAATTAGGGT
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
55 9 0.13
57 39 0.57
62 17 0.25
63 4 0.06
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (60 bp):
AAAAGGATCTAGCCCGGACGGGTGATCCATCTTGATATAACCCTCCCGAAGAATATGTGG
Found at i:53375838 original size:67 final size:67
Alignment explanation
Indices: 53375730--53375859 Score: 251
Period size: 67 Copynumber: 1.9 Consensus size: 67
53375720 GTTTATATTA
*
53375730 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
53375795 TG
66 TG
53375797 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCT
53375860 TTGAATTGGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
TG
Found at i:53396903 original size:25 final size:25
Alignment explanation
Indices: 53396850--53396900 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53396840 TAAAAATAGT
* *
53396850 ATATGTTTTAAATGATATTGAATGA
1 ATATGTTTTAAATGATATTAAAAGA
*
53396875 ATATGTTTTAAATTATTATTAAAAGA
1 ATATGTTTTAAATGA-TATTAAAAGA
53396901 TATCTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (25 bp):
ATATGTTTTAAATGATATTAAAAGA
Found at i:53403836 original size:80 final size:80
Alignment explanation
Indices: 53403742--53403906 Score: 321
Period size: 80 Copynumber: 2.1 Consensus size: 80
53403732 TACTATGAGA
53403742 TAGAATGTTGAACGATTATTGAATGAACGAATTGAAAGATCTAATTATATTGCATATACATGGGG
1 TAGAATGTTGAACGATTATTGAATGAACGAATTGAAAGATCTAATTATATTGCATATACATGGGG
53403807 GGATGTTATGAAAGG
66 GGATGTTATGAAAGG
*
53403822 TAGAATGTTGAACGATTATTGAATGAACGAATTGAAATATCTAATTATATTGCATATACATGGGG
1 TAGAATGTTGAACGATTATTGAATGAACGAATTGAAAGATCTAATTATATTGCATATACATGGGG
53403887 GGATGTTATGAAAGG
66 GGATGTTATGAAAGG
53403902 TAGAA
1 TAGAA
53403907 GAACGACAGT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (80 bp):
TAGAATGTTGAACGATTATTGAATGAACGAATTGAAAGATCTAATTATATTGCATATACATGGGG
GGATGTTATGAAAGG
Found at i:53407196 original size:19 final size:18
Alignment explanation
Indices: 53407154--53407197 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
53407144 TTACTAACAT
* *
53407154 TAATTATACAAATTAAAT
1 TAATTATAAAAATTAAAA
53407172 TAAATTATTAAAAATTAAAA
1 T-AATTA-TAAAAATTAAAA
53407192 TAATTA
1 TAATTA
53407198 AATGTGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 10 0.45
20 11 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTATAAAAATTAAAA
Found at i:53421134 original size:24 final size:22
Alignment explanation
Indices: 53421105--53421150 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
53421095 TGTCTATTTT
53421105 TTGAATAAAATATATGAAAATATA
1 TTGAATAAAA-ATATG-AAATATA
*
53421129 TTGAATAAAAATGTGAAATATA
1 TTGAATAAAAATATGAAATATA
53421151 AAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 4 0.19
24 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.33
Consensus pattern (22 bp):
TTGAATAAAAATATGAAATATA
Found at i:53421789 original size:60 final size:60
Alignment explanation
Indices: 53421696--53421815 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
53421686 ATGGTGATAA
*
53421696 GGCATTTCCAGTTCATAACTTTAAGCTCAAACCTTGAAGAAATTGAATTGATCAAGTTCC
1 GGCATTTCCAGCTCATAACTTTAAGCTCAAACCTTGAAGAAATTGAATTGATCAAGTTCC
53421756 GGCATTTCCAGCTCATAACTTTAAGCTCAAACCTTGAAGAAATTGAATTGATCAAGTTCC
1 GGCATTTCCAGCTCATAACTTTAAGCTCAAACCTTGAAGAAATTGAATTGATCAAGTTCC
53421816 AATCCTCAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (60 bp):
GGCATTTCCAGCTCATAACTTTAAGCTCAAACCTTGAAGAAATTGAATTGATCAAGTTCC
Found at i:53429544 original size:22 final size:22
Alignment explanation
Indices: 53429502--53429546 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
53429492 TAATTTCTAA
* *
53429502 TATAATTTTGTCATTATATTTT
1 TATAATGTTATCATTATATTTT
53429524 TATAATGTTATCAGTTA-ATTTT
1 TATAATGTTATCA-TTATATTTT
53429546 T
1 T
53429547 TTATTAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (22 bp):
TATAATGTTATCATTATATTTT
Found at i:53430277 original size:2 final size:2
Alignment explanation
Indices: 53430270--53430318 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
53430260 TGAAAATTAG
*
53430270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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 AT
53430312 AT AT AT A
1 AT AT AT A
53430319 ATCTAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53430953 original size:14 final size:15
Alignment explanation
Indices: 53430931--53431007 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
53430921 CAATCAAACA
53430931 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
53430945 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
53430960 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
53430980 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
53430994 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
53431008 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:53430972 original size:20 final size:20
Alignment explanation
Indices: 53430947--53430986 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53430937 AATATTTTCC
*
53430947 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
53430967 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
53430987 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:53430992 original size:34 final size:35
Alignment explanation
Indices: 53430935--53431001 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53430925 CAAACACCAG
*
53430935 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
53430970 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
53431002 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53432056 original size:17 final size:18
Alignment explanation
Indices: 53432018--53432056 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
53432008 ATTAAATGAA
53432018 AATTATCTCAATTAAAAT
1 AATTATCTCAATTAAAAT
*
53432036 -ATTATTTCAA-TAAAAT
1 AATTATCTCAATTAAAAT
53432052 AATTA
1 AATTA
53432057 AATTTCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTATCTCAATTAAAAT
Found at i:53438460 original size:29 final size:29
Alignment explanation
Indices: 53438392--53438471 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
53438382 ATTGATAGTC
*
53438392 CAAATACCACAATGGAA-ATTTTCAAAGTA
1 CAAATACCAC-ATTGAACATTTTCAAAGTA
*
53438421 CAAGTACCACATTGAACATTTTCAAAGTA
1 CAAATACCACATTGAACATTTTCAAAGTA
* *
53438450 TAAATATCACATTGAACATTTT
1 CAAATACCACATTGAACATTTT
53438472 ATAAAAATAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 5 0.11
29 40 0.89
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (29 bp):
CAAATACCACATTGAACATTTTCAAAGTA
Found at i:53439991 original size:21 final size:19
Alignment explanation
Indices: 53439929--53440009 Score: 74
Period size: 19 Copynumber: 4.1 Consensus size: 19
53439919 TAAATTAATG
* *
53439929 AATTAATTGTAGATAAACTT
1 AATTAATTTTAGTTAAA-TT
53439949 -ATTACATTTTAGTTAAATT
1 AATTA-ATTTTAGTTAAATT
*
53439968 AATTAATTTTATTTATATATT
1 AATTAATTTTAGTTA-A-ATT
**
53439989 AATTAATTTTAAATAAATT
1 AATTAATTTTAGTTAAATT
53440008 AA
1 AA
53440010 AATTACATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
19 20 0.38
20 16 0.31
21 16 0.31
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
AATTAATTTTAGTTAAATT
Found at i:53442323 original size:15 final size:15
Alignment explanation
Indices: 53442298--53442332 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53442288 AACTCTAATT
*
53442298 TAATT-ATATTACGA
1 TAATTAATATTAAGA
53442312 TAATTAATATTAAGA
1 TAATTAATATTAAGA
53442327 TAATTA
1 TAATTA
53442333 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:53446306 original size:14 final size:15
Alignment explanation
Indices: 53446287--53446352 Score: 53
Period size: 17 Copynumber: 4.1 Consensus size: 15
53446277 AGTAACTCAA
*
53446287 TTTTTA-TTCTTATT
1 TTTTTATTTATTATT
53446301 TTTTTATTTATTATTTT
1 TTTTTATTTATTA--TT
53446318 TTCTTTACTTTATTTATT
1 TT-TTTA-TTTA-TTATT
*
53446336 ATTTTATTTTATTATT
1 TTTTTA-TTTATTATT
53446352 T
1 T
53446353 ATTACTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 6 0.14
15 5 0.12
16 5 0.12
17 12 0.29
18 7 0.17
19 4 0.10
20 3 0.07
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATTTATTATT
Found at i:53446316 original size:7 final size:7
Alignment explanation
Indices: 53446296--53446369 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 7
53446286 ATTTTTATTC
53446296 TTATT-T
1 TTATTAT
53446302 TT-TTAT
1 TTATTAT
53446308 TTATTAT
1 TTATTAT
* *
53446315 TTTTTCT
1 TTATTAT
53446322 TTACTTTAT
1 TTA--TTAT
53446331 TTATTA-
1 TTATTAT
53446337 TT-TTATT
1 TTATTA-T
53446344 TTATTAT
1 TTATTAT
*
53446351 TTATTAC
1 TTATTAT
*
53446358 TTATTAC
1 TTATTAT
53446365 TTATT
1 TTATT
53446370 TGTATATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
5 5 0.09
6 7 0.12
7 35 0.62
8 3 0.05
9 6 0.11
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTAT
Found at i:53446330 original size:23 final size:21
Alignment explanation
Indices: 53446286--53446356 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 21
53446276 AAGTAACTCA
53446286 ATTT-TTATTCTTATTTT-TTT
1 ATTTATTATT-TTATTTTATTT
*
53446306 ATTTATTATTTTTTCTTTACTTT
1 ATTTATTATTTTAT-TTTA-TTT
53446329 ATTTATTATTTTATTTTA-TT
1 ATTTATTATTTTATTTTATTT
53446349 ATTTATTA
1 ATTTATTA
53446357 CTTATTACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
20 17 0.38
21 8 0.18
22 4 0.09
23 16 0.36
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
ATTTATTATTTTATTTTATTT
Found at i:53446363 original size:14 final size:12
Alignment explanation
Indices: 53446289--53446370 Score: 55
Period size: 12 Copynumber: 6.6 Consensus size: 12
53446279 TAACTCAATT
53446289 TTTATTCTTATT-
1 TTTATT-TTATTA
*
53446301 TTTTTATTTATTA
1 TTTAT-TTTATTA
53446314 TTT-TTTCT-TTA
1 TTTATTT-TATTA
53446325 CTTTA-TTTATTA
1 -TTTATTTTATTA
53446337 TTTTATTTTATTA
1 -TTTATTTTATTA
53446350 TTTATTACTTATTA
1 TTTATT--TTATTA
*
53446364 CTTATTT
1 TTTATTT
53446371 GTATATTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
11 6 0.10
12 30 0.52
13 11 0.19
14 11 0.19
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:53447854 original size:15 final size:15
Alignment explanation
Indices: 53447834--53447873 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
53447824 AGCAAAATTA
53447834 AGGATAATTAATATT
1 AGGATAATTAATATT
53447849 AGGATAATTAATATT
1 AGGATAATTAATATT
*
53447864 AAGATAATTA
1 AGGATAATTA
53447874 TTAAGGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (15 bp):
AGGATAATTAATATT
Found at i:53470715 original size:75 final size:75
Alignment explanation
Indices: 53470570--53470716 Score: 163
Period size: 75 Copynumber: 2.0 Consensus size: 75
53470560 GTGTAGGAAC
* * * * * * * * * *
53470570 TGGGGGCTTATATGGGGGAGTTGGTGCTTTAGTTGGCGGTGCTGGTGCTGGAGTTGGTGCTTTGG
1 TGGGGGCTTATATGGGGGAGTAGGGGCTTGAGCTGGAGGTGCCGGTGCGGGAGTAGGGGCTTTGA
53470635 TTGGGGGTGT
66 TTGGGGGTGT
*
53470645 TGGGGGCTTATATGGGGGAGTAGGGGCCTTGA-CTGGAGGTGCCGGTGCGGGAGTAGGGGGTTT-
1 TGGGGGCTTATATGGGGGAGTAGGGG-CTTGAGCTGGAGGTGCCGGTGCGGGAGTAGGGGCTTTG
53470708 ATATGGGGG
65 AT-TGGGGG
53470717 AGTAGGAGCC
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
74 1 0.02
75 54 0.92
76 4 0.07
ACGTcount: A:0.10, C:0.09, G:0.51, T:0.30
Consensus pattern (75 bp):
TGGGGGCTTATATGGGGGAGTAGGGGCTTGAGCTGGAGGTGCCGGTGCGGGAGTAGGGGCTTTGA
TTGGGGGTGT
Found at i:53470733 original size:96 final size:91
Alignment explanation
Indices: 53470631--53470929 Score: 332
Period size: 96 Copynumber: 3.1 Consensus size: 91
53470621 AGTTGGTGCT
* * ** *
53470631 TTGGTTGG-GGGTGTTGGGGGCTTATATGGGGGAGTAGGGGCCTTGACTGGAGGTGCCGGTGCGG
1 TTGGTTGGTGGGTGTTGGGGGCTTATATGGTGGAGTAGGAGCCTTG---GTTGGT---GGTGCAG
53470695 GAG-TAGGGGGTTTATATGGGGGAGTAGGAGCC
60 GAGCT-GGGGGTTTATATGGGGGAGTAGGAGCC
* *
53470727 TTGGTTGGTGGTGCTGGTGCTGGGGGCTTAAATGGTGGAGTTGGAGCCTTGGTTGGTGGTGCAGG
1 TTGGTTGGTGG-G-T-GT--TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGG
* *
53470792 AGCTGGGGGCTTATATGGTGGAGTAGGAGCC
61 AGCTGGGGGTTTATATGGGGGAGTAGGAGCC
* *
53470823 TTGGTTGGTGGTGCAGGAGCTGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGG
1 TTGG-T--TGGTG--GGTGTTGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGG
53470888 AGCTGGGGGTTTATATGGGGGAGTAGGAGCC
61 AGCTGGGGGTTTATATGGGGGAGTAGGAGCC
53470919 TTGGTTGGTGG
1 TTGGTTGGTGG
53470930 TTTATATGGT
Statistics
Matches: 176, Mismatches: 15, Indels: 29
0.80 0.07 0.13
Matches are distributed among these distances:
91 1 0.01
93 5 0.03
95 1 0.01
96 122 0.69
97 4 0.02
98 2 0.01
99 10 0.06
100 3 0.02
101 1 0.01
102 27 0.15
ACGTcount: A:0.13, C:0.09, G:0.50, T:0.28
Consensus pattern (91 bp):
TTGGTTGGTGGGTGTTGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCTG
GGGGTTTATATGGGGGAGTAGGAGCC
Found at i:53470767 original size:48 final size:48
Alignment explanation
Indices: 53470700--53470930 Score: 390
Period size: 48 Copynumber: 4.8 Consensus size: 48
53470690 TGCGGGAGTA
* * * *
53470700 GGGGGTTTATATGGGGGAGTAGGAGCCTTGGTTGGTGGTGCTGGTGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
* *
53470748 GGGGGCTTAAATGGTGGAGTTGGAGCCTTGGTTGGTGGTGCAGGAGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
53470796 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
53470844 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
* *
53470892 GGGGGTTTATATGGGGGAGTAGGAGCCTTGGTTGGTGGT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGT
53470931 TTATATGGTG
Statistics
Matches: 173, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 173 1.00
ACGTcount: A:0.13, C:0.09, G:0.49, T:0.29
Consensus pattern (48 bp):
GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
Found at i:53470810 original size:27 final size:27
Alignment explanation
Indices: 53470780--53470869 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 27
53470770 GAGCCTTGGT
*
53470780 TGGTGGTGCAGGAGCTGGGGGCTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
* *
53470807 TGGTGGAGTAGGAGC------CTTGGT-
1 TGGTGGAGCAGGAGCTGGGGGCTT-ATA
*
53470828 TGGTGGTGCAGGAGCTGGGGGCTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
*
53470855 TGGTGGAGTAGGAGC
1 TGGTGGAGCAGGAGC
53470870 CTTGGTTGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
21 16 0.34
22 1 0.02
26 1 0.02
27 29 0.62
ACGTcount: A:0.16, C:0.10, G:0.49, T:0.26
Consensus pattern (27 bp):
TGGTGGAGCAGGAGCTGGGGGCTTATA
Found at i:53470937 original size:33 final size:33
Alignment explanation
Indices: 53470892--53470971 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
53470882 TGCAGGAGCT
*
53470892 GGGGGTTTATATGGGGGAGTAGGAGCCTTGGTT
1 GGGGGTTTATATGGGGGAGTAGGAGCCTTGGTA
* * * *
53470925 GGTGGTTTATATGGTGGAGTGGGGGCCTTGGTA
1 GGGGGTTTATATGGGGGAGTAGGAGCCTTGGTA
*
53470958 GGGGGTTTGTATGG
1 GGGGGTTTATATGG
53470972 AGTGGGGCCC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.05, G:0.50, T:0.33
Consensus pattern (33 bp):
GGGGGTTTATATGGGGGAGTAGGAGCCTTGGTA
Found at i:53473163 original size:25 final size:25
Alignment explanation
Indices: 53473115--53473165 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
53473105 TGATCATTAA
* **
53473115 TATCAATAGGCAATATTTTTCTATC
1 TATCAATAAGCAATATTTCACTATC
53473140 TATCAATAAGCAATATTTCACTATC
1 TATCAATAAGCAATATTTCACTATC
53473165 T
1 T
53473166 CAATTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (25 bp):
TATCAATAAGCAATATTTCACTATC
Found at i:53473638 original size:23 final size:23
Alignment explanation
Indices: 53473549--53473638 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
53473539 ACCTGATCAG
53473549 TATACGACACAT-AAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
** *
53473571 -A-ACGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
53473592 AATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
53473615 TATACGACGCATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
53473638 T
1 T
53473639 CGACAGAACC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.14
21 10 0.17
22 1 0.02
23 39 0.67
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:53474258 original size:3 final size:3
Alignment explanation
Indices: 53474250--53474288 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
53474240 TAGCTACGAA
53474250 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53474289 TGAATTTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53474901 original size:23 final size:23
Alignment explanation
Indices: 53474875--53474921 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
53474865 AATAAGTATG
53474875 TACATATATTAATTATAAATGTA
1 TACATATATTAATTATAAATGTA
* *
53474898 TACATATATTTATTATACATGTA
1 TACATATATTAATTATAAATGTA
53474921 T
1 T
53474922 TTATAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (23 bp):
TACATATATTAATTATAAATGTA
Found at i:53474916 original size:15 final size:15
Alignment explanation
Indices: 53474896--53474925 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53474886 ATTATAAATG
53474896 TATACATATATTTAT
1 TATACATATATTTAT
*
53474911 TATACATGTATTTAT
1 TATACATATATTTAT
53474926 AATTACCACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (15 bp):
TATACATATATTTAT
Found at i:53477649 original size:34 final size:34
Alignment explanation
Indices: 53477518--53477637 Score: 204
Period size: 34 Copynumber: 3.5 Consensus size: 34
53477508 TAAAAGTTAT
*
53477518 ATGATTTACATGGTTTATAAGTTACATAAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
53477552 ATGATTTACATGGTTTATAAGTTATATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
53477586 ATGATTTACATGGTTTATAAGCTACATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
53477620 ATGATTTACATGGATTAT
1 ATGATTTACATGGTTTAT
53477638 TTGTTATATG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 81 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (34 bp):
ATGATTTACATGGTTTATAAGTTACATGAAATAC
Found at i:53489217 original size:13 final size:13
Alignment explanation
Indices: 53489199--53489227 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53489189 ACATTCGGCT
53489199 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
53489212 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
53489225 GAA
1 GAA
53489228 AAAAGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (13 bp):
GAAGGAGAAGAAA
Found at i:53489232 original size:20 final size:19
Alignment explanation
Indices: 53489204--53489319 Score: 65
Period size: 20 Copynumber: 5.8 Consensus size: 19
53489194 CGGCTGAAGG
53489204 AGAAGAAAGAAGGAGAAGAA
1 AGAA-AAAGAAGGAGAAGAA
* *
53489224 AGAAAAAAGAAAGAAAAGGAA
1 AG-AAAAAGAAGGAGAA-GAA
* * *
53489245 AGGAGAATA-AAGAAAAAGAA
1 A-GA-AAAAGAAGGAGAAGAA
* *
53489265 AGAAAAGGAAAGGAGAATAA
1 AGAAAAAG-AAGGAGAAGAA
* * *
53489285 AGGAAAGGAAATGAGAAG-A
1 AGAAAAAG-AAGGAGAAGAA
53489304 AGAAAAAGAAGGAGAA
1 AGAAAAAGAAGGAGAA
53489320 AGAGGCGCAG
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
18 9 0.12
19 9 0.12
20 39 0.53
21 13 0.18
22 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (19 bp):
AGAAAAAGAAGGAGAAGAA
Found at i:53489245 original size:10 final size:10
Alignment explanation
Indices: 53489219--53489276 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
53489209 AAAGAAGGAG
53489219 AAGAAAGAAAA
1 AAGAAAG-AAA
53489230 AAGAAAGAAA
1 AAGAAAGAAA
* * *
53489240 AGGAAAGGAG
1 AAGAAAGAAA
*
53489250 AATAAAGAAA
1 AAGAAAGAAA
53489260 AAGAAAGAAA
1 AAGAAAGAAA
*
53489270 AGGAAAG
1 AAGAAAG
53489277 GAGAATAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
10 31 0.82
11 7 0.18
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:53489263 original size:30 final size:30
Alignment explanation
Indices: 53489213--53489295 Score: 130
Period size: 30 Copynumber: 2.7 Consensus size: 30
53489203 GAGAAGAAAG
*
53489213 AAGGAGAAGAAAGAAAAAAGAAAGAAAAGGA
1 AAGGAGAATAAAG-AAAAAGAAAGAAAAGGA
53489244 AAGGAGAATAAAGAAAAAGAAAGAAAAGGA
1 AAGGAGAATAAAGAAAAAGAAAGAAAAGGA
* *
53489274 AAGGAGAATAAAGGAAAGGAAA
1 AAGGAGAATAAAGAAAAAGAAA
53489296 TGAGAAGAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 37 0.76
31 12 0.24
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (30 bp):
AAGGAGAATAAAGAAAAAGAAAGAAAAGGA
Found at i:53489286 original size:15 final size:15
Alignment explanation
Indices: 53489238--53489293 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
53489228 AAAAGAAAGA
53489238 AAAGGAAAGGAGAAT
1 AAAGGAAAGGAGAAT
* * *
53489253 AAAGAAAAAGA-AAGA
1 AAAGGAAAGGAGAA-T
53489268 AAAGGAAAGGAGAAT
1 AAAGGAAAGGAGAAT
53489283 AAAGGAAAGGA
1 AAAGGAAAGGA
53489294 AATGAGAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 2 0.06
15 29 0.88
16 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (15 bp):
AAAGGAAAGGAGAAT
Found at i:53489348 original size:43 final size:43
Alignment explanation
Indices: 53489284--53489397 Score: 97
Period size: 43 Copynumber: 2.7 Consensus size: 43
53489274 AAGGAGAATA
* * * *
53489284 AAGGAAAGGAAATGAGA-AGAAGAAAAAGAAGGAGAAAGAGGCG
1 AAGGAAAGAAAAAGAAAGAGAAGAAAAAGAAGAAGAAAGAGG-G
* * * * **
53489327 CAGGAAA-AAAGAGAAAGAGAAGGAGAAGAAGAAGATGGAGGG
1 AAGGAAAGAAAAAGAAAGAGAAGAAAAAGAAGAAGAAAGAGGG
* *
53489369 AAGGAAAGAAAAAGAAAGAAAAAAAAAAG
1 AAGGAAAGAAAAAGAAAGAGAAGAAAAAG
53489398 GGGAAGGTAA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
42 12 0.23
43 41 0.77
ACGTcount: A:0.62, C:0.02, G:0.34, T:0.02
Consensus pattern (43 bp):
AAGGAAAGAAAAAGAAAGAGAAGAAAAAGAAGAAGAAAGAGGG
Found at i:53489656 original size:15 final size:16
Alignment explanation
Indices: 53489624--53489657 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53489614 AAATAGCATT
53489624 AAAAATAAAATACTGA
1 AAAAATAAAATACTGA
53489640 AAAAATAAAATAC-GA
1 AAAAATAAAATACTGA
53489655 AAA
1 AAA
53489658 TAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAAATAAAATACTGA
Found at i:53489665 original size:16 final size:16
Alignment explanation
Indices: 53489624--53489665 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
53489614 AAATAGCATT
*
53489624 AAAAATAAAATACTGA
1 AAAAAAAAAATACTGA
*
53489640 AAAAATAAAATAC-GA
1 AAAAAAAAAATACTGA
53489655 AAATAAAAAAA
1 AAA-AAAAAAA
53489666 AAACAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (16 bp):
AAAAAAAAAATACTGA
Found at i:53489893 original size:159 final size:160
Alignment explanation
Indices: 53489654--53490077 Score: 649
Period size: 160 Copynumber: 2.7 Consensus size: 160
53489644 ATAAAATACG
* * ** *
53489654 AAAATAAAAAAAAAACAAAAATAGTATATTTACTGAAAGAAATAAAATTCA--AAAATAAGAAAA
1 AAAAT-AATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAGGAAAA-AAGAAAA
53489717 ATACGAACAAAGGGCCAAAATAAGGGTTTTTTTACTAAATTTA-AAAAAAAACACACTAAATTAA
64 ATACGAACAAAGGGCCAAAATAAGGGTTTTTTTACTAAATTTATAAAAAAAACACACTAAATTAA
* * *
53489781 TACATTTCAAACATAATGTAGTAAGATAATAT
129 TAAATTTCAAACATAATGTACTAAAATAATAT
*
53489813 AAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCAGGAAAAAAGAAAAAT
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAGGAAAAAAGAAAAAT
* * *
53489878 AGGAACAAAGGGCCAAAATAAGGTTTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATA
66 ACGAACAAAGGGCCAAAATAAGGGTTTTTTTACTAAATTTATAAAAAAAACACACTAAATTAATA
53489943 AATTTCAAACATAATGTACTAAAATAATAT
131 AATTTCAAACATAATGTACTAAAATAATAT
* *
53489973 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCCGGGAAAAAATGAAAAA
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAGGAAAAAA-GAAAAA
* *
53490038 TACGAACAAAGGGTCAAAATAAGGG-TTTTTTACTATATTT
65 TACGAACAAAGGGCCAAAATAAGGGTTTTTTTACTAAATTT
53490078 GTTTTGAAGT
Statistics
Matches: 242, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
158 39 0.16
159 53 0.22
160 122 0.50
161 28 0.12
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (160 bp):
AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAGGAAAAAAGAAAAAT
ACGAACAAAGGGCCAAAATAAGGGTTTTTTTACTAAATTTATAAAAAAAACACACTAAATTAATA
AATTTCAAACATAATGTACTAAAATAATAT
Found at i:53492245 original size:40 final size:40
Alignment explanation
Indices: 53492185--53492282 Score: 187
Period size: 40 Copynumber: 2.4 Consensus size: 40
53492175 GAATTATTTC
53492185 AAATGAATTATACTTTTTACAACTTAATTTGGAAACCATAT
1 AAAT-AATTATACTTTTTACAACTTAATTTGGAAACCATAT
53492226 AAATAATTATACTTTTTACAACTTAATTTGGAAACCATAT
1 AAATAATTATACTTTTTACAACTTAATTTGGAAACCATAT
53492266 AAATAATTATACTTTTT
1 AAATAATTATACTTTTT
53492283 TCATTATATT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 53 0.93
41 4 0.07
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (40 bp):
AAATAATTATACTTTTTACAACTTAATTTGGAAACCATAT
Found at i:53495280 original size:3 final size:3
Alignment explanation
Indices: 53495272--53495317 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
53495262 TAACTAACAC
53495272 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
53495318 GTTTTTTACT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53495351 original size:39 final size:39
Alignment explanation
Indices: 53495296--53495394 Score: 114
Period size: 40 Copynumber: 2.6 Consensus size: 39
53495286 TAATAATAAT
* **
53495296 AATAA-TAATAATAATAATAATAGTTTTTTACTAAAAAG
1 AATAACTAATAACAATAATAATAGGGTTTTACTAAAAAG
*
53495334 AAT-ACTAACTAACAATAATAATTAGGGTTTTACTAAAAAT
1 AATAACTAA-TAACAATAATAA-TAGGGTTTTACTAAAAAG
*
53495374 AATAACTAATAATAAT-ATAAT
1 AATAACTAATAACAATAATAAT
53495395 GTAAAAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
37 1 0.02
38 7 0.13
39 15 0.29
40 24 0.46
41 5 0.10
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (39 bp):
AATAACTAATAACAATAATAATAGGGTTTTACTAAAAAG
Found at i:53499936 original size:28 final size:28
Alignment explanation
Indices: 53499854--53499930 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
53499844 TTTGGGTTTA
* *
53499854 ATATTTGGGGTTTAAGGTTTGAGATTTT
1 ATATTTAGGGTTTAAGGTTTAAGATTTT
* **
53499882 AGATTTAGGGTTTAATTTTTAAGATTTT
1 ATATTTAGGGTTTAAGGTTTAAGATTTT
*
53499910 ATATTTAGAGTTTAAGGTTTA
1 ATATTTAGGGTTTAAGGTTTA
53499931 GTATTTCAGG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (28 bp):
ATATTTAGGGTTTAAGGTTTAAGATTTT
Found at i:53500349 original size:49 final size:49
Alignment explanation
Indices: 53500272--53500368 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
53500262 TTATGCTATG
* * *
53500272 CATTTCTAAACTTGGTCTTCCACTGTCTATACTCTTATCTA-TATTTATA
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATC-ACTATTTATA
53500321 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
53500369 CCCTTCTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.98
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTATA
Found at i:53501692 original size:43 final size:43
Alignment explanation
Indices: 53501644--53501729 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
53501634 TCATATTTCA
* *
53501644 TTTCTCGTCTCATAATCATTTCTCATATTTGCCTTTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
* * *
53501687 TTTCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
53501730 CAATCACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.21, C:0.24, G:0.02, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
Found at i:53502938 original size:3 final size:3
Alignment explanation
Indices: 53502932--53502982 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
53502922 TGTTTTCATT
53502932 TTA TTA TCT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53502977 TTA TTA
1 TTA TTA
53502983 AAGTTACTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53502945 original size:9 final size:8
Alignment explanation
Indices: 53502915--53502982 Score: 66
Period size: 9 Copynumber: 7.9 Consensus size: 8
53502905 TTTCTATTTC
53502915 TTTATTAT
1 TTTATTAT
*
53502923 GTTT-TCAT
1 -TTTATTAT
53502931 TTTATTAT
1 TTTATTAT
53502939 CTTTATTAT
1 -TTTATTAT
53502948 TATTATTAT
1 T-TTATTAT
53502957 TATTATTAT
1 T-TTATTAT
53502966 TATTATTAT
1 T-TTATTAT
53502975 TATTATTA
1 T-TTATTA
53502983 AAGTTACTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
7 3 0.06
8 7 0.13
9 44 0.81
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (8 bp):
TTTATTAT
Found at i:53509667 original size:14 final size:15
Alignment explanation
Indices: 53509648--53509682 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
53509638 CCTTATACTC
53509648 TTATTTTTAAA-AAT
1 TTATTTTTAAATAAT
53509662 TTATTTTTAAATAAT
1 TTATTTTTAAATAAT
53509677 TT-TTTT
1 TTATTTT
53509683 ATACAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTTTAAATAAT
Found at i:53527900 original size:103 final size:104
Alignment explanation
Indices: 53527715--53527909 Score: 306
Period size: 103 Copynumber: 1.9 Consensus size: 104
53527705 NNNNNNNNNN
* * **
53527715 TTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCTG
1 TTGCTAAGTGCTGATTCCACCGTATCTGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
53527780 AGGGGTTGCTAAGTGCTGATTCCCCGACCCATTTAGTGG
66 AGGGGTTGCTAAGTGCTGATTCCCCGACCCATTTAGTGG
53527819 TTGCTAAGTGCTGATTCCACC-TCATCTGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
1 TTGCTAAGTGCTGATTCCACCGT-ATCTGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
53527882 AAGGGGTTGCTGTA-TGCTGATTCCCCGA
65 AAGGGGTTGCT-AAGTGCTGATTCCCCGA
53527910 TTCATTGGTG
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
103 52 0.62
104 32 0.38
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.31
Consensus pattern (104 bp):
TTGCTAAGTGCTGATTCCACCGTATCTGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
AGGGGTTGCTAAGTGCTGATTCCCCGACCCATTTAGTGG
Found at i:53535416 original size:33 final size:28
Alignment explanation
Indices: 53535345--53535426 Score: 103
Period size: 27 Copynumber: 2.8 Consensus size: 28
53535335 AATGTGAAAG
53535345 GGGGTTGCTAAGTGCTGATT-CCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCCCGA
*
53535372 GGGGTTGCTAAGTGCTGATTCCCCTACCTA
1 GGGGTTGCTAAGTGCTGATTCCCC--CCGA
53535402 TTGGTGGTTGCTAAGTGCTGATTCC
1 --GG-GGTTGCTAAGTGCTGATTCC
53535427 ACCGTATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 20 0.42
28 3 0.06
30 3 0.06
32 2 0.04
33 20 0.42
ACGTcount: A:0.15, C:0.23, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGGTTGCTAAGTGCTGATTCCCCCCGA
Found at i:53535448 original size:103 final size:102
Alignment explanation
Indices: 53535268--53535468 Score: 341
Period size: 103 Copynumber: 2.0 Consensus size: 102
53535258 TTGCATATAA
**
53535268 AGGGGTTGCTGTGTGCTGATTCCCCTATACATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCTATACATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
*
53535333 TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGT-AAAAGGGGTTGCTAAGTGCTGATTCCCCCG
*
53535371 AGGGGTTGCTAAGTGCTGATTCCCCTA-CCTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCCTATAC-ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
53535435 TTAAATGTAAAAGGGGTTGCTAAGTGCTGATTCC
65 TTAAATGTAAAAGGGGTTGCTAAGTGCTGATTCC
53535469 ACCGTATTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
102 26 0.28
103 67 0.72
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCTATACATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
TAAATGTAAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:53535466 original size:42 final size:43
Alignment explanation
Indices: 53535407--53535511 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 43
53535397 ACCTATTGGT
53535407 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAA-GG
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGG
53535449 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGG
53535492 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
53535512 CCCGAGGGGT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 40 0.65
43 22 0.35
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGG
Found at i:53535474 original size:145 final size:146
Alignment explanation
Indices: 53535304--53535614 Score: 507
Period size: 145 Copynumber: 2.1 Consensus size: 146
53535294 ATACATTGGT
*
53535304 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCC
* * * * *
53535369 CGAGGGGTTGCTAAGTGCTGATTCCCCTACCTA-TTGGTGGTTGCTAAGTGCTGATTCCACCGTA
66 CGAGGGGTTGCTAAGTACTGATTCCCCGACCCATTTGGTGATTGCTAAGTGCTGATTCCACCGCA
* *
53535433 TTTTAAATGTAAAAGG
131 TCTGAAATGTAAAAGG
53535449 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCC
* *
53535514 CGAGGGGTTGCTAAGTACTGATTCCCCGACCCATTTTGTGATTGCTAAGTGCTGATTTCACCGCA
66 CGAGGGGTTGCTAAGTACTGATTCCCCGACCCATTTGGTGATTGCTAAGTGCTGATTCCACCGCA
* *
53535579 TCTGAAATGTGAAGGG
131 TCTGAAATGTAAAAGG
53535595 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
53535615 CCCAAGGGGT
Statistics
Matches: 153, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
145 94 0.61
146 59 0.39
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (146 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCC
CGAGGGGTTGCTAAGTACTGATTCCCCGACCCATTTGGTGATTGCTAAGTGCTGATTCCACCGCA
TCTGAAATGTAAAAGG
Found at i:53535638 original size:103 final size:104
Alignment explanation
Indices: 53535451--53535645 Score: 302
Period size: 103 Copynumber: 1.9 Consensus size: 104
53535441 GTAAAAGGGG
* * * *
53535451 TTGCTAAGTGCTGATTCCACCGTATTTTAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
1 TTGCTAAGTGCTGATTCCACCGCATCTGAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
53535516 AGGGGTTGCTAAGTACTGATTCCCCGACCCATTTTGTGA
66 AGGGGTTGCTAAGTACTGATTCCCCGACCCATTTTGTGA
* *
53535555 TTGCTAAGTGCTGATTTCACCGCATCTGAAATGT-GAAGGGGGTTGCTAAGTGCTGATTCCCCCA
1 TTGCTAAGTGCTGATTCCACCGCATCTGAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
** *
53535619 AGGGGTTGCTGTGTGCTGATTCCCCGA
66 AGGGGTTGCTAAGTACTGATTCCCCGA
53535646 TTCATTGGTG
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
103 52 0.63
104 30 0.37
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.31
Consensus pattern (104 bp):
TTGCTAAGTGCTGATTCCACCGCATCTGAAATGTAAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
AGGGGTTGCTAAGTACTGATTCCCCGACCCATTTTGTGA
Found at i:53539743 original size:103 final size:103
Alignment explanation
Indices: 53539393--53539746 Score: 460
Period size: 103 Copynumber: 3.4 Consensus size: 103
53539383 GGTTCCGCAG
* * * *
53539393 TTAACAACCACTAATGAATCGGGGAATCAGCACACAACAACCCATTGGGGGAATCAGCACTTAGC
1 TTAACAACCACCAATGAATAGGGGAATCAGCACACAACAACCCCTCGGGGGAATCAGCACTTAGC
* * *
53539458 AACCCCC-TTCACATTTCAGATGCGGTGGAATCAGCAC
66 AACCCCCTTTCACATTTAAAATACGGTGGAATCAGCAC
* ** * * * ** * *
53539495 TTAGCAACCACCAAATGGGTCGGAGAATTAGCACTTAGCAACCCCTCGGGGGAATCATCACTTAG
1 TTAACAACCACC-AATGAATAGGGGAATCAGCACACAACAACCCCTCGGGGGAATCAGCACTTAG
*
53539560 CAACCCCCTTTTACATTTAAAATACGGTGGAATCAGCAC
65 CAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCAC
* * * ** *
53539599 TTAGCAACCACCAAT-AGGTAGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAG
1 TTAACAACCACCAATGA-ATAGGGGAATCAGCACACAACAACCCCTCGGGGGAATCAGCACTTAG
53539663 CAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCAC
65 CAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCAC
53539702 TTAACAACCACCAATGAATAGGGGAATCAGCACACAACAACCCCT
1 TTAACAACCACCAATGAATAGGGGAATCAGCACACAACAACCCCT
53539747 TTATATGCAA
Statistics
Matches: 219, Mismatches: 29, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
102 10 0.05
103 170 0.78
104 39 0.18
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (103 bp):
TTAACAACCACCAATGAATAGGGGAATCAGCACACAACAACCCCTCGGGGGAATCAGCACTTAGC
AACCCCCTTTCACATTTAAAATACGGTGGAATCAGCAC
Found at i:53541031 original size:13 final size:13
Alignment explanation
Indices: 53541010--53541040 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
53541000 TAAAGTGAAA
*
53541010 TTTACTTTTATTT
1 TTTATTTTTATTT
53541023 TTTATTTTTATTT
1 TTTATTTTTATTT
53541036 TTTAT
1 TTTAT
53541041 CGTGGGCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:53545707 original size:41 final size:41
Alignment explanation
Indices: 53545659--53545744 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
53545649 TGACATGGGG
53545659 TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
1 TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
* *
53545700 TTATATTTTACACAAATATAATATTCTTCTTGTTTTGTTCA
1 TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
53545741 TTAT
1 TTAT
53545745 TATATTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (41 bp):
TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
Found at i:53555678 original size:2 final size:2
Alignment explanation
Indices: 53555671--53555722 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
53555661 CTTGGACCAC
53555671 AT AT AT AT AT 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 AT AT AT AT AT
53555713 AT AT ACT AT A
1 AT AT A-T AT A
53555723 CTACGTTCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53556470 original size:21 final size:21
Alignment explanation
Indices: 53556444--53556496 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
53556434 AGTGGTGGCG
*
53556444 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
*
53556465 GTGAGATTGGATACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
53556486 GTGAGATTAGA
1 GTGAGATTAGA
53556497 AACAGCGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:53561877 original size:6 final size:6
Alignment explanation
Indices: 53561868--53561896 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53561858 GACACCAACA
53561868 CCGACC CCGACC CCGACC CCGACC CCGAC
1 CCGACC CCGACC CCGACC CCGACC CCGAC
53561897 TTGGAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.66, G:0.17, T:0.00
Consensus pattern (6 bp):
CCGACC
Found at i:53563567 original size:33 final size:32
Alignment explanation
Indices: 53563526--53563593 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
53563516 AATAAAAGAA
*
53563526 GAAAGCCTCCAATAATCCACTTAGATTGCTCT
1 GAAAGCCTCCAATAATCCACTTAAATTGCTCT
*
53563558 GAAAGGCCTCCAATAATCCACTTAAATTGCTTT
1 GAAA-GCCTCCAATAATCCACTTAAATTGCTCT
53563591 GAA
1 GAA
53563594 TCAAAAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (32 bp):
GAAAGCCTCCAATAATCCACTTAAATTGCTCT
Found at i:53565081 original size:2 final size:2
Alignment explanation
Indices: 53565074--53565115 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
53565064 TGGAAATGGA
53565074 AT AT AT AT AT 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 AT AT AT AT AT
53565116 GAGTTAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53574820 original size:24 final size:25
Alignment explanation
Indices: 53574781--53574829 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
53574771 TATAAACATA
*
53574781 AACATATATATATAAT-TATTATTT
1 AACATATATATATAATATAATATTT
53574805 AACATATATA-ATTAATATAATATTT
1 AACATATATATA-TAATATAATATTT
53574830 TCTATAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 14 0.64
25 7 0.32
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
AACATATATATATAATATAATATTT
Found at i:53583003 original size:6 final size:6
Alignment explanation
Indices: 53582992--53583019 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53582982 AGTATTATCA
53582992 CTTCAT CTTCAT CTTCAT CTTCAT CTTC
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTC
53583020 GTTGTGACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTCAT
Found at i:53587596 original size:2 final size:2
Alignment explanation
Indices: 53587589--53587618 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53587579 GTCCACTTTG
*
53587589 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53587619 TAGTTCACGT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53591655 original size:19 final size:19
Alignment explanation
Indices: 53591615--53591662 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
53591605 AAGAGTTTAG
*
53591615 TAAACAAAAAAACTAATAT
1 TAAACAAATAAACTAATAT
*
53591634 TAAACAAATAATCTTAAT-T
1 TAAACAAATAAAC-TAATAT
*
53591653 TAAATAAATA
1 TAAACAAATA
53591663 TTAAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAACAAATAAACTAATAT
Found at i:53604937 original size:11 final size:11
Alignment explanation
Indices: 53604923--53604949 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
53604913 ATTTTGTTAC
53604923 TATTTTAGAGT
1 TATTTTAGAGT
53604934 TATTTTAGAGT
1 TATTTTAGAGT
53604945 TATTT
1 TATTT
53604950 AAGTATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (11 bp):
TATTTTAGAGT
Found at i:53607579 original size:12 final size:12
Alignment explanation
Indices: 53607562--53607587 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53607552 CCTCTTCCTC
53607562 CATCATCATCTT
1 CATCATCATCTT
53607574 CATCATCATCTT
1 CATCATCATCTT
53607586 CA
1 CA
53607588 AGCCCTTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (12 bp):
CATCATCATCTT
Found at i:53615474 original size:2 final size:2
Alignment explanation
Indices: 53615467--53615496 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53615457 GTACTAAGTA
53615467 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
53615497 CCATTTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53617859 original size:17 final size:18
Alignment explanation
Indices: 53617837--53617876 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
53617827 CCAGTACTTA
53617837 TTTTTTCAACACTT-ATT
1 TTTTTTCAACACTTAATT
*
53617854 TTTTTTCAGCACTTAATT
1 TTTTTTCAACACTTAATT
53617872 TTTTT
1 TTTTT
53617877 AGTTTATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.20, C:0.15, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTTCAACACTTAATT
Found at i:53617873 original size:15 final size:15
Alignment explanation
Indices: 53617817--53617874 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
53617807 AAAATTCAAT
* *
53617817 ACTTAATTTTCCAGT
1 ACTTAATTTTTCAGC
* *
53617832 ACTTATTTTTTCAAC
1 ACTTAATTTTTCAGC
*
53617847 ACTTATTTTTTTTCAGC
1 ACTTA--ATTTTTCAGC
53617864 ACTTAATTTTT
1 ACTTAATTTTT
53617875 TTAGTTTATC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 21 0.60
17 14 0.40
ACGTcount: A:0.24, C:0.17, G:0.03, T:0.55
Consensus pattern (15 bp):
ACTTAATTTTTCAGC
Found at i:53640900 original size:13 final size:13
Alignment explanation
Indices: 53640854--53640887 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53640844 TTCATACCTT
*
53640854 TTTTAAATATGTA
1 TTTTATATATGTA
53640867 TTTTATATATGTA
1 TTTTATATATGTA
53640880 TTTTATAT
1 TTTTATAT
53640888 TTTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TTTTATATATGTA
Found at i:53646526 original size:13 final size:13
Alignment explanation
Indices: 53646480--53646513 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53646470 TTCATACCTT
*
53646480 TTTTAAATATGTA
1 TTTTATATATGTA
53646493 TTTTATATATGTA
1 TTTTATATATGTA
53646506 TTTTATAT
1 TTTTATAT
53646514 TTTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TTTTATATATGTA
Done.