Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:423332 original size:55 final size:54
Alignment explanation
Indices: 423259--423679 Score: 470
Period size: 55 Copynumber: 7.5 Consensus size: 54
423249 TAGAAGGGAA
* * * *
423259 TGCCACTGACTTGCGGACTTAAAAAGGGTGCCATGATGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGA-GTTGTGGACTTAAAAGGG
* *
423314 TGCCACAGAGTTGTGGACTTTAAAAGGGTGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCA-CGAGTTGTGGACTTAAAAGGG
* * * *
423369 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGAAATTGTGGACTCTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACG-AGTTGTGGACT-TAAAAGGG
423425 TGCCACAGAGTTGTGGACTGTTGTGGACTTAAAAGGGTGCCACGAAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGAC---T-T--A---AAAAGGGTGCCACG-AGTTGTGGACTTAAAAGGG
* *
423489 TGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACAGAGTTGTGGACTTTAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCAC-GAGTTGTGGACTTAAAAGGG
* * * *
423543 TGCCACGGAGTTGTGGACTTTAAAGGGGTGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCAC-GAGTTGTGGAC-TTAAAAGGG
* **
423599 TGCCAC-GAAGTTGTGGACTT-AAAAGGATGCCACGGAGTTGTGGACTTAAAAGAA
1 TGCCACAG-AGTTGTGGACTTAAAAAGGGTGCCAC-GAGTTGTGGACTTAAAAGGG
423653 TGCCACAGAGTTGTGGACTTTAAAAAG
1 TGCCACAGAGTTGTGGAC-TTAAAAAG
423680 AAATGCCACT
Statistics
Matches: 325, Mismatches: 22, Indels: 37
0.85 0.06 0.10
Matches are distributed among these distances:
54 76 0.23
55 139 0.43
56 57 0.18
59 1 0.00
60 2 0.01
61 1 0.00
64 25 0.08
65 24 0.07
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (54 bp):
TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGAGTTGTGGACTTAAAAGGG
Found at i:423462 original size:37 final size:38
Alignment explanation
Indices: 423407--423480 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 38
423397 TGCCACGAAA
423407 TTGTGGACTCTAAAAGGGTGCCAC-AGAGTTGTGGACTG
1 TTGTGGACTCTAAAAGGGTGCCACGA-AGTTGTGGACTG
423445 TTGTGGACT-TAAAAGGGTGCCACGAAGTTGTGGACT
1 TTGTGGACTCTAAAAGGGTGCCACGAAGTTGTGGACT
423481 TAAAAGGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 25 0.71
38 10 0.29
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (38 bp):
TTGTGGACTCTAAAAGGGTGCCACGAAGTTGTGGACTG
Found at i:423482 original size:27 final size:27
Alignment explanation
Indices: 423444--423677 Score: 319
Period size: 27 Copynumber: 8.6 Consensus size: 27
423434 GTTGTGGACT
423444 GTTGTGGACTTAAAAGGGTGCCACGAA
1 GTTGTGGACTTAAAAGGGTGCCACGAA
*
423471 GTTGTGGACTTAAAAGGGTGCCACGGA
1 GTTGTGGACTTAAAAGGGTGCCACGAA
423498 GTTGTGGACTTAAAAGGGTGCCAC-AGA
1 GTTGTGGACTTAAAAGGGTGCCACGA-A
* *
423525 GTTGTGGACTTTAAAGGGTGCCACGGA
1 GTTGTGGACTTAAAAGGGTGCCACGAA
* *
423552 GTTGTGGACTTTAAAGGGGTGCCACGGA
1 GTTGTGGAC-TTAAAAGGGTGCCACGAA
*
423580 GTTGTGGACTTTAAAAGGATGCCACGAA
1 GTTGTGGAC-TTAAAAGGGTGCCACGAA
* *
423608 GTTGTGGACTTAAAAGGATGCCACGGA
1 GTTGTGGACTTAAAAGGGTGCCACGAA
**
423635 GTTGTGGACTTAAAAGAATGCCAC-AGA
1 GTTGTGGACTTAAAAGGGTGCCACGA-A
423662 GTTGTGGACTTTAAAA
1 GTTGTGGAC-TTAAAA
423678 AGAAATGCCA
Statistics
Matches: 190, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
27 134 0.71
28 56 0.29
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (27 bp):
GTTGTGGACTTAAAAGGGTGCCACGAA
Found at i:423528 original size:54 final size:54
Alignment explanation
Indices: 423444--423677 Score: 351
Period size: 54 Copynumber: 4.3 Consensus size: 54
423434 GTTGTGGACT
* *
423444 GTTGTGGACTTAAAAGGGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGGA
1 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGA
* * *
423498 GTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAGGGTGCCACGGA
1 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGA
* *
423552 GTTGTGGACTTTAAAGGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGAA
1 GTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGA
* * *
423608 GTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGAATGCCACAGA
1 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGA
423662 GTTGTGGACTTTAAAA
1 GTTGTGGAC-TTAAAA
423678 AGAAATGCCA
Statistics
Matches: 164, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
54 84 0.51
55 56 0.34
56 24 0.15
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (54 bp):
GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGA
Found at i:434212 original size:17 final size:17
Alignment explanation
Indices: 434190--434224 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
434180 ATTTTCTTTC
*
434190 ATGTTCCTTGCATGCAT
1 ATGTTCATTGCATGCAT
*
434207 ATGTTCATTTCATGCAT
1 ATGTTCATTGCATGCAT
434224 A
1 A
434225 AACATTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (17 bp):
ATGTTCATTGCATGCAT
Found at i:435753 original size:24 final size:24
Alignment explanation
Indices: 435726--435782 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
435716 GAAGCAATAT
435726 GAGCAAAGGAGACCAACAAAGGGC
1 GAGCAAAGGAGACCAACAAAGGGC
* * **
435750 GAGCAAATGAGAGCAGTAAAGGGC
1 GAGCAAAGGAGACCAACAAAGGGC
435774 GAGCAAAGG
1 GAGCAAAGG
435783 GAAGATGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.37, T:0.04
Consensus pattern (24 bp):
GAGCAAAGGAGACCAACAAAGGGC
Found at i:447162 original size:20 final size:19
Alignment explanation
Indices: 447111--447163 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
447101 ACATTATGCT
**
447111 TTGTATCGATACATGTTCA
1 TTGTATCGATACATACTCA
* *
447130 TTATATTGATACATACTCAA
1 TTGTATCGATACATACTC-A
447150 TTGTATCGATACAT
1 TTGTATCGATACAT
447164 GAAACTGGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACATACTCA
Found at i:448828 original size:3 final size:3
Alignment explanation
Indices: 448820--448848 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
448810 GATAATGAAT
448820 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
448849 AAAGTAGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:453484 original size:21 final size:20
Alignment explanation
Indices: 453460--453507 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
453450 TAAATCCTTT
453460 TCAAAATTCATC-ATTTTCACA
1 TCAAAATT-ATCTATTTT-ACA
* *
453481 TCAAAACTATCTATTTTTCA
1 TCAAAATTATCTATTTTACA
453501 TCAAAAT
1 TCAAAAT
453508 CTTCATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
TCAAAATTATCTATTTTACA
Found at i:459404 original size:44 final size:44
Alignment explanation
Indices: 459262--459967 Score: 369
Period size: 44 Copynumber: 16.2 Consensus size: 44
459252 AGTCTACCTC
** * ** *
459262 TCAGCTTTGACCCTATAGACTTCC-TTATCCTCAAGTCTATCTG
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCCAG
* * * * * * * *
459305 TCGGCTTTAACCCTAGAAACTT-CTTTTTCCTCAAGTTTGTCTA-
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTG-CCAG
* *
459348 TC-GACTTTGACCCTGGAGACTTCCTTTATCTTTAACTCTGCCAG
1 TCAG-CTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCCAG
* * * * *
459392 TTAGCTTTGACCCTTGAGACTT-CTTTTTCCCTCAAGTCTGCCTG
1 TCAGCTTTGACCCTGGAGACTTCCTTTAT-CCTTAAGTCTGCCAG
* * *
459436 TCAGCTTTGTCCCTAGAGACTTCCTTTATCCTCAAGTCTGCCTA-
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCC-AG
* * * **
459480 TCGGCTTTGA-CCTGGAGACTT-CTTTTTCTCTTAAGTCTACTTG
1 TCAGCTTTGACCCTGGAGACTTCCTTTATC-CTTAAGTCTGCCAG
* * * *
459523 TCAGCTTTGACCTTGGAGACTTCCTTTACCCTAAAGTTTGCCTA-
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCC-AG
* * * * *
459567 TC-GACTTTGACCTTGGAGACTTCTTTTA-CCCTCA-TCTGCCTG
1 TCAG-CTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCCAG
* * * *
459609 TCAGCTTTGACCTTGGAGACTTTCTTTATCCTTAAGTCTATCTA-
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCT-GCCAG
* * *
459653 TCGGCTTTGACCTTAGAGACTTCCTTTATCCTTAAGTCTGCCTA-
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCC-AG
** * ** * * **
459697 TTGGCTTTGTCCCCAGAGACTT-CTTTTTCCTTCAAGTCTACTTG
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTT-AAGTCTGCCAG
* * * ** *
459741 TCAGTTTTGTCCTTGGAGACTTCCTTTATCCTTAAGTCTATCTG
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCCAG
* * * * * *
459785 TCAGCTTTGACCTTAGAGATTTCATTT-TCCCTCAAGTCTGCTTA-
1 TCAGCTTTGACCCTGGAGACTTCCTTTAT-CCTTAAGTCTGC-CAG
* * * * * * *
459829 TCGGCTTTAACACTGGAGATTTTC-TT-TCATTAAGTCTACCTA-
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCC-AG
* * * *
459871 TCGGCTTT-ATCCCTGGAGACTTTCTTTA-CCTTCAAGTCTACCTG
1 TCAGCTTTGA-CCCTGGAGACTTCCTTTATCCTT-AAGTCTGCCAG
** * * *
459915 TTGGCTCTGA-CCTAGAGACTTCCTTTATCCTTAAGTCTGCCTG
1 TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCCAG
*
459958 TCGGCTTTGA
1 TCAGCTTTGA
459968 TCTTAGAGAC
Statistics
Matches: 514, Mismatches: 115, Indels: 68
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.00
42 67 0.13
43 143 0.28
44 281 0.55
45 22 0.04
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (44 bp):
TCAGCTTTGACCCTGGAGACTTCCTTTATCCTTAAGTCTGCCAG
Found at i:459796 original size:218 final size:216
Alignment explanation
Indices: 459345--459988 Score: 651
Period size: 218 Copynumber: 3.0 Consensus size: 216
459335 TCAAGTTTGT
* * ** * * *
459345 CTATCGACTTTGACCCTGGAGACTTCCTTTATCTTTAACTCTGCCAGTTAGCTTTGACCCTT-GA
1 CTATCGACTTTGACCTTGGAGACTTCTTTTA-CCCTCACTCTGCCTGTCAGCTTTGA-CCTTGGA
* * * * * *
459409 GAC-TTCTTTTTCCCTCAAGTCTGCCTGTCAGCTTTGTCCCTAGAGACTTCCTTTATCCTCAAGT
64 GACTTTC-TTTT-CCTTAAGTCTACCTATCGGCTTTGACCCTAGAGACTTCCTTTATCCTTAAGT
* *
459473 CTGCCTATCGGCTTTGACCTGGAGACTTCTTTTTCTCTTAAGTCTACTTGTCAGCTTTGACCTTG
127 CTGCCTATTGGCTTTGACCTAGAGACTTCTTTTTC-CTTAAGTCTACTTGTCAGCTTTGACCTTG
* *
459538 GAGACTTCCTTTACCCTAAAGTTTGC
191 GAGACTTCCTTTACCCTAAAGTCTAC
459564 CTATCGACTTTGACCTTGGAGACTTCTTTTACCCTCA-TCTGCCTGTCAGCTTTGACCTTGGAGA
1 CTATCGACTTTGACCTTGGAGACTTCTTTTACCCTCACTCTGCCTGTCAGCTTTGACCTTGGAGA
* *
459628 CTTTCTTTATCCTTAAGTCTATCTATCGGCTTTGACCTTAGAGACTTCCTTTATCCTTAAGTCTG
66 CTTTCTTT-TCCTTAAGTCTACCTATCGGCTTTGACCCTAGAGACTTCCTTTATCCTTAAGTCTG
* * * *
459693 CCTATTGGCTTTGTCCCCAGAGACTTCTTTTTCCTTCAAGTCTACTTGTCAGTTTTGTCCTTGGA
130 CCTATTGGCTTTG-ACCTAGAGACTTCTTTTTCCTT-AAGTCTACTTGTCAGCTTTGACCTTGGA
* * *
459758 GACTTCCTTTATCCTTAAGTCTAT
193 GACTTCCTTTACCCTAAAGTCTAC
* * * * * * * *
459782 CTGTC-AGCTTTGACCTTAGAGATTTCATTTT-CCCTCAAGTCTGCTTATCGGCTTTAACAC-TG
1 CTATCGA-CTTTGACCTTGGAGACTTC-TTTTACCCTC-ACTCTGCCTGTCAGCTTTGAC-CTTG
* * * *
459844 GAGATTTTC-TTTCATTAAGTCTACCTATCGGCTTT-ATCCCTGGAGACTTTCTTTA-CCTTCAA
62 GAGACTTTCTTTTCCTTAAGTCTACCTATCGGCTTTGA-CCCTAGAGACTTCCTTTATCCTT-AA
* * * * * * * *
459906 GTCTACCTGTTGGCTCTGACCTAGAGACTTCCTTTATCCTTAAGTCTGCCTGTCGGCTTTGATCT
125 GTCTGCCTATTGGCTTTGACCTAGAGACTT-CTTTTTCCTTAAGTCTACTTGTCAGCTTTGACCT
* *
459971 TAGAGACTTTCTTT-CCCT
189 TGGAGACTTCCTTTACCCT
459989 TTGTTTCCCT
Statistics
Matches: 358, Mismatches: 54, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
216 7 0.02
217 132 0.37
218 157 0.44
219 36 0.10
220 25 0.07
221 1 0.00
ACGTcount: A:0.17, C:0.27, G:0.16, T:0.40
Consensus pattern (216 bp):
CTATCGACTTTGACCTTGGAGACTTCTTTTACCCTCACTCTGCCTGTCAGCTTTGACCTTGGAGA
CTTTCTTTTCCTTAAGTCTACCTATCGGCTTTGACCCTAGAGACTTCCTTTATCCTTAAGTCTGC
CTATTGGCTTTGACCTAGAGACTTCTTTTTCCTTAAGTCTACTTGTCAGCTTTGACCTTGGAGAC
TTCCTTTACCCTAAAGTCTAC
Found at i:459874 original size:42 final size:44
Alignment explanation
Indices: 459816--459965 Score: 128
Period size: 43 Copynumber: 3.5 Consensus size: 44
459806 TCATTTTCCC
* * *
459816 TCAAGTCTGCTTATCGGCTTTAACACTGGAGATTTTCTTT-CAT
1 TCAAGTCTACCTATCGGCTTTAACACTGGAGACTTTCTTTACAT
* * *
459859 T-AAGTCTACCTATCGGCTTTATCCCTGGAGACTTTCTTTACCT
1 TCAAGTCTACCTATCGGCTTTAACACTGGAGACTTTCTTTACAT
* * * * * * *
459902 TCAAGTCTACCTGTTGGCTCTGAC-CTAGAGACTTCCTTTATCCT
1 TCAAGTCTACCTATCGGCTTTAACACTGGAGACTTTCTTTA-CAT
* *
459946 T-AAGTCTGCCTGTCGGCTTT
1 TCAAGTCTACCTATCGGCTTT
459966 GATCTTAGAG
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 33 0.38
43 34 0.39
44 21 0.24
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (44 bp):
TCAAGTCTACCTATCGGCTTTAACACTGGAGACTTTCTTTACAT
Found at i:459935 original size:305 final size:305
Alignment explanation
Indices: 459251--459984 Score: 777
Period size: 305 Copynumber: 2.4 Consensus size: 305
459241 TTTTTATCTC
* ** * * * *
459251 AAGTCTACCTCTC-AGCTTTGACCCTATAGACTTC-CTTATCCTCAAGTCTATCTGTCGGCTTTA
1 AAGTCTACCTATCGA-CTTTGACCCTGGAGACTTCTTTTACCCTCAAGTCTACCTGTCGGCTTTG
* * * * * * *
459314 ACCCTAGAAAC-TTCTTTTTCCTCAAGTTTGTCTATCGACTTTGACCCTGGAGACTTCCTTTATC
65 A-CCTAGAGACTTTCTTTATCCTTAAGTCTGTCTATCGGCTTTGACCTTAGAGACTTCCTTTATC
* ** *
459378 TTTAACTCTGCCAGTTAGCTTTGACCCTTGAGACTTCTTTTTCCCTCAAGTCTGCCTGTCAGCTT
129 CTTAACTCTGCCAGTTAGCTTTGACCCCAGAGACTTCTTTTTCCCTCAAGTCTACCTGTCAGCTT
* * * *
459443 TGTCCCTAGAGACTTCCTTTATCCTCAAGTCTGCCTATCGGCTTTGACCTGGAGACTTCTTTTTC
194 TGTCCCTAGAGACTTCCTTTATCCTCAAGTCTACCTATCAGCTTTGACCTAGAGACTTCATTTTC
* * * * *
459508 TCTTAAGTCTACTTGTCAGCTTTGACCTTGGAGACTTCCTTTACCCTA
259 CCTCAAGTCTACTTATCAGCTTTAACCTTGGAGACTTCCTTTA-CATA
* * * * *
459556 AAGTTTGCCTATCGACTTTGACCTTGGAGACTTCTTTTACCCTC-A-TCTGCCTGTCAGCTTTGA
1 AAGTCTACCTATCGACTTTGACCCTGGAGACTTCTTTTACCCTCAAGTCTACCTGTCGGCTTTGA
* *
459619 CCTTGGAGACTTTCTTTATCCTTAAGTCTATCTATCGGCTTTGACCTTAGAGACTTCCTTTATCC
66 CC-TAGAGACTTTCTTTATCCTTAAGTCTGTCTATCGGCTTTGACCTTAGAGACTTCCTTTATCC
* * * * * *
459684 TTAAGTCTGCCTA-TTGGCTTTGTCCCCAGAGACTTCTTTTTCCTTCAAGTCTACTTGTCAGTTT
130 TTAACTCTGCC-AGTTAGCTTTGACCCCAGAGACTTCTTTTTCCCTCAAGTCTACCTGTCAGCTT
* * * * * *
459748 TGTCCTTGGAGACTTCCTTTATCCTTAAGTCTATCTGTCAGCTTTGACCTTAGAGATTTCATTTT
194 TGTCCCTAGAGACTTCCTTTATCCTCAAGTCTACCTATCAGCTTTGACC-TAGAGACTTCATTTT
* * * * *
459813 CCCTCAAGTCTGCTTATCGGCTTTAACAC-TGGAGATTTTCTTT-CATT
258 CCCTCAAGTCTACTTATCAGCTTTAAC-CTTGGAGACTTCCTTTACATA
* * * *
459860 AAGTCTACCTATCGGCTTT-ATCCCTGGAGACTT-TCTTTACCTTCAAGTCTACCTGTTGGCTCT
1 AAGTCTACCTATCGACTTTGA-CCCTGGAGACTTCT-TTTACCCTCAAGTCTACCTGTCGGCTTT
* * * * *
459923 GACCTAGAGACTTCCTTTATCCTTAAGTCTGCCTGTCGGCTTTGATCTTAGAGACTTTCTTT
64 GACCTAGAGACTTTCTTTATCCTTAAGTCTGTCTATCGGCTTTGACCTTAGAGACTTCCTTT
459985 CCCTTTGTTT
Statistics
Matches: 351, Mismatches: 67, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
303 4 0.01
304 56 0.16
305 220 0.63
306 70 0.20
307 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (305 bp):
AAGTCTACCTATCGACTTTGACCCTGGAGACTTCTTTTACCCTCAAGTCTACCTGTCGGCTTTGA
CCTAGAGACTTTCTTTATCCTTAAGTCTGTCTATCGGCTTTGACCTTAGAGACTTCCTTTATCCT
TAACTCTGCCAGTTAGCTTTGACCCCAGAGACTTCTTTTTCCCTCAAGTCTACCTGTCAGCTTTG
TCCCTAGAGACTTCCTTTATCCTCAAGTCTACCTATCAGCTTTGACCTAGAGACTTCATTTTCCC
TCAAGTCTACTTATCAGCTTTAACCTTGGAGACTTCCTTTACATA
Found at i:460009 original size:42 final size:42
Alignment explanation
Indices: 459954--460038 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
459944 CTTAAGTCTG
* * * *
459954 CCTGTCGGCTTTGATCTTAGAGACTTTCTTTCCCTTTGTTTC
1 CCTGTCGGCTTTGACCCTAGAAACTTCCTTTCCCTTTGTTTC
*
459996 CCTGTCGGTTTTGACCCTAGAAACTTCCTTTCCCTTTGTTTC
1 CCTGTCGGCTTTGACCCTAGAAACTTCCTTTCCCTTTGTTTC
460038 C
1 C
460039 TTATCAGCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.11, C:0.29, G:0.15, T:0.45
Consensus pattern (42 bp):
CCTGTCGGCTTTGACCCTAGAAACTTCCTTTCCCTTTGTTTC
Found at i:463321 original size:79 final size:79
Alignment explanation
Indices: 463104--463358 Score: 284
Period size: 79 Copynumber: 3.2 Consensus size: 79
463094 GAGATAATAA
* * * * *
463104 CGGGGTTGGAGTATTCTCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTG-TGAAAAATCGATG
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC-GATGATGAAAAATTGATG
* **
463168 -ATTAGGAAATAAAAT
65 TTTTA-GAAATAAAGC
* * * * * *
463183 CGAGATTAGAGTATCCCCTCGGAAATAAGGGGGTTGGAGTATCCCCGACT-ATAAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA-TGATGAAAAATTGATG
463247 TTTTAGAAATAAAGC
65 TTTTAGAAATAAAGC
* * *
463262 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATTGATGT
463327 TTTAGAAATAAAGC
66 TTTAGAAATAAAGC
*
463341 CAGGGTTGG-GTTATCCCC
1 CGGGGTTGGAG-TATCCCC
463359 GATTGTGGAG
Statistics
Matches: 147, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
78 3 0.02
79 141 0.96
80 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATTGATGT
TTTAGAAATAAAGC
Found at i:465869 original size:19 final size:21
Alignment explanation
Indices: 465845--465883 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
465835 GATGTATCGA
465845 TACAAA-G-ATCGATACATTC
1 TACAAATGTATCGATACATTC
465864 TACAAATGTATCGATACATT
1 TACAAATGTATCGATACATT
465884 TCCTTGGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (21 bp):
TACAAATGTATCGATACATTC
Found at i:465937 original size:19 final size:21
Alignment explanation
Indices: 465913--465962 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
465903 AGCGATACAC
*
465913 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
465932 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
465953 TGTATCGATA
1 TGTATCGATA
465963 TAAATTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:466795 original size:42 final size:43
Alignment explanation
Indices: 466740--466840 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
466730 CCATTTTTCG
* * *
466740 AGGACAAAGGAAAAAGGGAAACGAAA-TACGTCCTGCTCTGTA
1 AGGAAAAAAGAAAAAGGGAAAAGAAAGTACGTCCTGCTCTGTA
* * * * *
466782 AGGATAAAAGAAAAA-GGAAAATAAAGTGCGTCCTGCTCTTTG
1 AGGAAAAAAGAAAAAGGGAAAAGAAAGTACGTCCTGCTCTGTA
466824 AGGAAAAAAGAGAAAAG
1 AGGAAAAAAGA-AAAAG
466841 AAGGGAAGGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 8 0.17
42 36 0.75
43 4 0.08
ACGTcount: A:0.48, C:0.12, G:0.26, T:0.15
Consensus pattern (43 bp):
AGGAAAAAAGAAAAAGGGAAAAGAAAGTACGTCCTGCTCTGTA
Found at i:466949 original size:61 final size:60
Alignment explanation
Indices: 466854--467145 Score: 303
Period size: 61 Copynumber: 4.9 Consensus size: 60
466844 GGAAGGAAGT
* * **
466854 GTGTCCTACTCTTTGAA-GACTGAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAAAAA
1 GTGTCCTGCTCTTT-AAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAA
* * *
466914 GGTGTCCTGCCCTTTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAA
1 -GTGTCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAAAAAAA
** * * * *
466976 GCATCCTGCTCTTTGAA-GACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAG
1 GTGTCCTGCTCTTT-AAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA-AAAAA
* * * * *
467037 GTGTCCTGCTTTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTT------AAAA
1 GTGTCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAA
*
467091 GTCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
1 GT-GTCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
467146 GGCGTCCTGC
Statistics
Matches: 191, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
54 5 0.03
55 44 0.23
60 7 0.04
61 125 0.65
62 10 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (60 bp):
GTGTCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAA
Found at i:467080 original size:122 final size:116
Alignment explanation
Indices: 466857--467145 Score: 389
Period size: 122 Copynumber: 2.4 Consensus size: 116
466847 AGGAAGTGTG
* **
466857 TCCTACTCTTTGAAGACTGAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAAAAAGGTGTCCT
1 TCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGGTGTCCT
*
466922 GCCCTTTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAGCA
66 GCCCTTTAAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTT---AAAAG---GCA
* **
466979 TCCTGCTCTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTGTCCT
1 TCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGGTGTCCT
** * * * *
467044 GCTTTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGTCG
66 GCCCTTTAAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGCA
* *
467095 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
1 TCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA
467146 GGCGTCCTGC
Statistics
Matches: 151, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
116 49 0.32
119 5 0.03
122 97 0.64
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (116 bp):
TCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGGTGTCCT
GCCCTTTAAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGCA
Found at i:467121 original size:55 final size:55
Alignment explanation
Indices: 466979--467172 Score: 230
Period size: 55 Copynumber: 3.4 Consensus size: 55
466969 AAAGAAAGCA
* * *
466979 TCCTGCTCTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGT-G
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----A--AAA-GTCG
* * * *
467040 TCCTGCTTTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGTCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGTCG
* *
467095 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGTCG
467150 TCCTGCTCTTTGAGGACT-AAAGG
1 TCCTGCTCTTTGAGGACTGAAAGG
467173 GTGAAAGGAG
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
54 7 0.06
55 71 0.60
57 1 0.01
61 40 0.34
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGTCG
Found at i:467254 original size:61 final size:60
Alignment explanation
Indices: 467186--467677 Score: 477
Period size: 61 Copynumber: 8.4 Consensus size: 60
467176 AAAGGAGAGA
467186 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAG
* *
467247 GCATCCTGCTCTTTGAGGACTGAGAA-GTGCCACCAACTCGTATGGGCTTT----G-AAAG
1 GCATCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG
* ** * *
467302 GCGTCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTCGTGTAGGCTTT----G-AAAG
1 GCATCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG
*
467357 GCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAG
* * * * * * *
467417 GCGTCCTGCTCTTCGAGGACTAAAAGTTGTCACCAAATTGTGTGGGCTTTAAAAAAGAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAG
** * *
467478 GCGCCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA-AAAG
* * * * *
467539 GCATCCTGCTCTTTGAGGATTGGAAGGTGCCACCAA-TTGGAGTGGTCTTTAAAAGGAGGAA-
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTT-GTGTGGGCTTTAAAA-GA-AAAG
** *
467600 GCATCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTCGTGTGGGCTTT----G-AAAG
1 GCATCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG
* *
467656 GCGTCTTGCTCTTTGAGGACTA
1 GCATCCTGCTCTTTGAGGACTA
467678 AGGGGTGAAA
Statistics
Matches: 372, Mismatches: 41, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
53 1 0.00
54 25 0.07
55 73 0.20
56 21 0.06
57 1 0.00
59 1 0.00
60 35 0.09
61 182 0.49
62 32 0.09
63 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (60 bp):
GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG
Found at i:467302 original size:155 final size:161
Alignment explanation
Indices: 467040--467840 Score: 594
Period size: 155 Copynumber: 4.9 Consensus size: 161
467030 AGGAAAGGTG
* * * * *
467040 TCCTGCTTTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTT-----AAAAGTCGTCCTG
1 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTG
* *
467100 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
66 CTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
** *
467165 ACT-AAAGGGTG-A-AA-G-G-A-GAGA-GCA
131 ACTGAAA-AATGCACAACGTGTATGAAAGGCA
*
467189 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT
1 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCGTCCT
467254 GCTCTTTGAGGACTGAGAA-GTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCTCTTTGA
65 GCTCTTTGAGGACTGA-AAGGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCTCTTTGA
*
467318 GGACTGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGCG
129 GGACTGAAAAATG-CA-CAA--CGTGTA-----TGAAAGGCA
467360 TCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCT
* * * * * * * *
467424 GCTCTTCGAGGACTAAAAGTTGTCACCAAATTGTGTGGGCTTTAAAAAAGAAAGGCGCCCTGCTC
65 GCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTTT------GAAAGGCGTCCTGCTC
* ** *
467489 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCA
124 TTTGAGGACTGAAAAATG-CA-CAAC----GT--G-TATG--AA-AG---GCA
* * * * * *
467542 TCCTGCTCTTTGAGGATTGGAAGGTGCCACCAA-TTGGAGTGGTCTTTAAAAGGAGGAA-GCATC
1 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTT-GTGTGGGCTTTAAAA-GA-AAAGGCGTC
** * *
467605 CTGCTCTTTGAGGACTAGAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCTTGCTCTTT
63 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCTCTTT
*** * *
467670 GAGGACT-AAGGGGTG-A-AA-G-G-A-GAGA-GCG
127 GAGGACTGAA-AAATGCACAACGTGTATGAAAGGCA
* * * * * *
467698 TCCTGCGCTTTGAGGACTAGGAA-GTGCCACTAACTGGAGTGGTCTTTAAAAGGAAAAGGCATCC
1 TCCTGCTCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCGTCC
* *
467762 TGCTCTTTAAGGACTGAGAA-GTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
64 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCTCTTTG
* *
467826 AGGACAGGAAAATGC
128 AGGACTGAAAAATGC
467841 CACCAACTCG
Statistics
Matches: 535, Mismatches: 60, Indels: 107
0.76 0.09 0.15
Matches are distributed among these distances:
149 43 0.08
155 129 0.24
156 73 0.14
157 5 0.01
159 2 0.00
160 1 0.00
161 1 0.00
162 1 0.00
163 2 0.00
164 1 0.00
166 1 0.00
169 3 0.01
170 75 0.14
171 25 0.05
174 3 0.01
176 40 0.07
177 1 0.00
178 32 0.06
179 2 0.00
180 1 0.00
181 1 0.00
182 25 0.05
183 43 0.08
184 25 0.05
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (161 bp):
TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTG
CTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
ACTGAAAAATGCACAACGTGTATGAAAGGCA
Found at i:467337 original size:210 final size:210
Alignment explanation
Indices: 466975--467382 Score: 642
Period size: 210 Copynumber: 1.9 Consensus size: 210
466965 GCAAAAAGAA
**
466975 AGCATCCTGCTCTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
1 AGCATCCTGCTCTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCA
* * * *
467040 TCCTGCTTTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGTCGTCCTGCTCTT
66 TCCTGCTCTTTGAGGACTGGAGAGTGCCACCAACTCGTATGGGCTTTAAAAGGCGTCCTGCTCTT
** * *
467105 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAA
131 TGAGGACTGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAA
467170 AGGGTGAAAGGAGAG
196 AGGGTGAAAGGAGAG
* * *
467185 AGCATCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGG
1 AGCATCCTGCTCTTTGAAGACTGA-AAAGTACCACCAACTTGTGTGGGCTTTGAAAAGG-AAAGG
*
467248 CATCCTGCTCTTTGAGGACT-GAGAAGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCT
64 CATCCTGCTCTTTGAGGACTGGAG-AGTGCCACCAACTCGTATGGGCTTTAAAAGGCGTCCTGCT
467312 CTTTGAGGACTGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGCGTCCTGCTCTTTGAGGAC
128 CTTTGAGGACTGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGCGTCCTGCTCTTTGAGGAC
467377 TAAAGG
193 TAAAGG
467383 TGCCACCAAC
Statistics
Matches: 181, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
209 10 0.06
210 171 0.94
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (210 bp):
AGCATCCTGCTCTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCA
TCCTGCTCTTTGAGGACTGGAGAGTGCCACCAACTCGTATGGGCTTTAAAAGGCGTCCTGCTCTT
TGAGGACTGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAA
AGGGTGAAAGGAGAG
Found at i:467751 original size:156 final size:155
Alignment explanation
Indices: 467533--467830 Score: 456
Period size: 156 Copynumber: 1.9 Consensus size: 155
467523 GCTTTGCAAA
* * * *
467533 GAGAAAGCATCCTGCTCTTTGAGGATTGGAAGGTGCCACCAATTGGAGTGGTCTTTAAAAGGAGG
1 GAGAAAGCATCCTGCGCTTTGAGGATAGGAAGGTGCCACCAACTGGAGTGGTCTTTAAAAGGA-A
* *
467598 AA-GCATCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCT
65 AAGGCATCCTGCTCTTTAAGGACT-GAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCC
467662 TGCTCTTTGAGGACTAAGGGGTGAAAG
129 TGCTCTTTGAGGACTAAGGGGTGAAAG
* * *
467689 GAGAGAGCGTCCTGCGCTTTGAGGACTAGGAA-GTGCCACTAACTGGAGTGGTCTTTAAAAGGAA
1 GAGAAAGCATCCTGCGCTTTGAGGA-TAGGAAGGTGCCACCAACTGGAGTGGTCTTTAAAAGGAA
* *
467753 AAGGCATCCTGCTCTTTAAGGACTGAGAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCT
65 AAGGCATCCTGCTCTTTAAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCT
467818 GCTCTTTGAGGAC
130 GCTCTTTGAGGAC
467831 AGGAAAATGC
Statistics
Matches: 129, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
155 53 0.41
156 71 0.55
157 5 0.04
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (155 bp):
GAGAAAGCATCCTGCGCTTTGAGGATAGGAAGGTGCCACCAACTGGAGTGGTCTTTAAAAGGAAA
AGGCATCCTGCTCTTTAAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTG
CTCTTTGAGGACTAAGGGGTGAAAG
Found at i:467830 original size:509 final size:502
Alignment explanation
Indices: 466856--467888 Score: 1480
Period size: 509 Copynumber: 2.0 Consensus size: 502
466846 AAGGAAGTGT
* * *
466856 GTCCTACTCTTTGAAGACTGAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAAAAAGGTGTCC
1 GTCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAAAAAGGCGTCC
* ** * * *
466921 TGCCCTTTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAGCATCCTGCT
65 TGCCCTTCAAGGACTAAAAGGTGCCACCAAATTGTGTGGGCTTTGAAAAAAGAAAGCACCCTGCT
** *
466986 CTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTGTCCTGCTTTTT
130 CTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCATCCTGCTCTTT
* * * *
467051 GAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGTCGTCCTGCTCTTTGAGGACTGAA
195 GAGGACTGGAAGGTGCCACCAACTCGAGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTGAA
** *
467116 AGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGAAAGG
260 AAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGAAAGG
* * *
467181 AGAGAGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
325 AGAGAGCATCCTGCGCTTTGAGGACTAGAAGGTGCCACCAACTGGAGTGGGCTTTAAAAGGAAAA
*
467246 GGCATCCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGC
390 GGCATCCTGCTCTTTAAGGACTGAGAAGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGC
*
467311 TCTTTGAGGACTGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGC
455 TCTTTGAGGACAGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGC
* **
467359 GTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAA-AAAAGGCGTCC
* * * * *
467423 TGCTCTTCGAGGACTAAAAGTTGTCACCAAATTGTGTGGGCTTT-AAAAAAGAAAGGCGCCCTGC
65 TGCCCTTCAAGGACTAAAAGGTGCCACCAAATTGTGTGGGCTTTGAAAAAAGAAA-GCACCCTGC
* * * * *
467487 TCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GCATCCTGCTCT
129 TCTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAG-GAAAGGCATCCTGCTCT
* * * *
467551 TTGAGGATTGGAAGGTGCCACCAATTGGAGTGGTCTTTAAAAGGAGGAAGCATCCTGCTCTTTGA
193 TTGAGGACTGGAAGGTGCCACCAACTCGAGTGGGCTTT-AAA--A-G--GCATCCTGCTCTTTGA
* *
467616 GGACTAGAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACTAAGG
252 GGACT-GAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAG
* * *
467681 GGTGAAAGGAGAGAGCGTCCTGCGCTTTGAGGACTAGGAA-GTGCCACTAACTGGAGTGGTCTTT
316 GGTGAAAGGAGAGAGCATCCTGCGCTTTGAGGACTA-GAAGGTGCCACCAACTGGAGTGGGCTTT
*
467745 AAAAGGAAAAGGCATCCTGCTCTTTAAGGACTGAGAAGTGCCACCAACTCGTGTGGGCTTTGAAA
380 AAAAGGAAAAGGCATCCTGCTCTTTAAGGACTGAGAAGTGCCACCAACTCGTATGGGCTTTGAAA
* *
467810 GGCGTCCTGCTCTTTGAGGACAGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGC
445 GGCGTCCTGCTCTTTGAGGACAGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGC
*
467868 GTCCTGCTCTTTAAGGACTAA
1 GTCCTGCTCTTTGAGGACTAA
467889 GGAGAAAAGG
Statistics
Matches: 469, Mismatches: 50, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
501 14 0.03
502 161 0.34
503 24 0.05
505 1 0.00
506 1 0.00
508 19 0.04
509 246 0.52
510 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (502 bp):
GTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAAAAAGGCGTCCT
GCCCTTCAAGGACTAAAAGGTGCCACCAAATTGTGTGGGCTTTGAAAAAAGAAAGCACCCTGCTC
TTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCATCCTGCTCTTTG
AGGACTGGAAGGTGCCACCAACTCGAGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTGAAA
AATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
GAGAGCATCCTGCGCTTTGAGGACTAGAAGGTGCCACCAACTGGAGTGGGCTTTAAAAGGAAAAG
GCATCCTGCTCTTTAAGGACTGAGAAGTGCCACCAACTCGTATGGGCTTTGAAAGGCGTCCTGCT
CTTTGAGGACAGAAAAATGCCACCAACTCGTGTAGGCTTTGAAAGGC
Found at i:467842 original size:55 final size:55
Alignment explanation
Indices: 467752--467885 Score: 216
Period size: 55 Copynumber: 2.4 Consensus size: 55
467742 TTTAAAAGGA
* * *
467752 AAAGGCATCCTGCTCTTTAAGGACTGAGAAGTGCCACCAACTCGTGTGGGCTTTG
1 AAAGGCGTCCTGCTCTTTAAGGACGGAGAAATGCCACCAACTCGTGTGGGCTTTG
*
467807 AAAGGCGTCCTGCTCTTTGAGGACAGGA-AAATGCCACCAACTCGTGTGGGCTTTG
1 AAAGGCGTCCTGCTCTTTAAGGAC-GGAGAAATGCCACCAACTCGTGTGGGCTTTG
467862 AAAGGCGTCCTGCTCTTTAAGGAC
1 AAAGGCGTCCTGCTCTTTAAGGAC
467886 TAAGGAGAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
55 71 0.97
56 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (55 bp):
AAAGGCGTCCTGCTCTTTAAGGACGGAGAAATGCCACCAACTCGTGTGGGCTTTG
Found at i:467878 original size:210 final size:212
Alignment explanation
Indices: 467482--468109 Score: 612
Period size: 210 Copynumber: 2.9 Consensus size: 212
467472 AGAAAGGCGC
* ** * * * ** *
467482 CCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAG-AGAAA-GCATCC
1 CCTGCGCTTTGAGGACTAAAAAGTGCCACCAACTGGAGTGGGCTTTAAAAAGAAAAAAGGCATCC
* * * * * * * * *
467545 TGCTCTTTGAGGATTGGAAGGTGCCACCAATTGGAGTGGTCTTTA-AAAGGAGGAAGCATCCTGC
66 TACTCTTTAAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAGAAA--A-G--GCGTCCTGC
*
467609 TCTTTGAGGACTAGAAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGG
125 TCTTTGAGGACTAG-AAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
* * *
467674 ACTAAGGGGTGAAAGGAGAGAG-CGT
189 ACTAAGGAG-AAAAGGA-AAAGTCGT
** * * *
467699 CCTGCGCTTTGAGGACTAGGAAGTGCCACTAACTGGAGTGGTCTTT-AAAAG-GAAAAGGCATCC
1 CCTGCGCTTTGAGGACTAAAAAGTGCCACCAACTGGAGTGGGCTTTAAAAAGAAAAAAGGCATCC
*
467762 TGCTCTTTAAGGACTGAGAA-GTGCCACCAACTCGTGTGGGCTTT-G-AAAGGCGTCCTGCTCTT
66 TACTCTTTAAGGACT-A-AAGGTGCCACCAACTCGTGTGGGCTTTAGAAAAGGCGTCCTGCTCTT
*
467824 TGAGGAC-AGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTAAGGACTA
129 TGAGGACTA-GAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTA
467888 AGGAGAAAAGGAAAAGTCGT
193 AGGAGAAAAGGAAAAGTCGT
* * * * *
467908 CCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCT
1 CCTGCGCTTTGAGGACTAAAAAGTGCCACCAACTGGAGTGGGCTTTAAAAAGAAAAAAGGCATCC
* **
467973 TACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAGGCGTCCTAATC
66 TACTCTTTAAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTT----AGAAAAGGCGTCCTGCTC
** * *
468038 TTTGAGGACTA-AAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAGGCGTCCTGCTCTTTG
127 TTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTT-----G-AAAGGCGTCCTGCTCTTTG
468102 AGGACTAA
186 AGGACTAA
468110 AAGGTGCCAC
Statistics
Matches: 347, Mismatches: 43, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
208 3 0.01
209 50 0.14
210 87 0.25
211 42 0.12
213 1 0.00
214 1 0.00
215 24 0.07
216 31 0.09
217 79 0.23
218 2 0.01
220 1 0.00
221 26 0.07
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (212 bp):
CCTGCGCTTTGAGGACTAAAAAGTGCCACCAACTGGAGTGGGCTTTAAAAAGAAAAAAGGCATCC
TACTCTTTAAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAGAAAAGGCGTCCTGCTCTTTG
AGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAGG
AGAAAAGGAAAAGTCGT
Found at i:468055 original size:60 final size:61
Alignment explanation
Indices: 467893--468146 Score: 395
Period size: 60 Copynumber: 4.2 Consensus size: 61
467883 GACTAAGGAG
* * * *
467893 AAAAGGAAAAGTCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* *
467954 AAAAAGAAAAAAGGCGTCTTACTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTT
1 AAAAAG--AAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* *
468016 AAAAAGAAAAGGCGTCCTAATCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTAGGCTTT
1 AAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
*
468076 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
468137 AAAAAGAAAA
1 AAAAAGAAAA
468147 AATGCGTCAT
Statistics
Matches: 177, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
60 80 0.45
61 42 0.24
62 32 0.18
63 23 0.13
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (61 bp):
AAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:474380 original size:79 final size:79
Alignment explanation
Indices: 474285--474539 Score: 266
Period size: 79 Copynumber: 3.2 Consensus size: 79
474275 GAGATAATAA
* ** *
474285 CGGGGTTGGAGTATCCCCTTGAAGATAACGGGGTTGGAGTATCCCCGGTTG-TGAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTAGAA-ATAACGGGGTTGGAGTATCCCCGGACGATAAAAAATTGATG
*
474349 -ATTAGGAAATAAAAT
65 TATTA-GAAATAAAAC
* **
474364 CGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCATC-GACGATAAAAAATTGATG
1 CGGGGTTGGAGTATCCCCT-AGAAATAACGGGGTTGGAGTATCCCCGGACGATAAAAAATTGATG
*
474428 TTTTAGAAATAAAAC
65 TATTAGAAATAAAAC
* * * * * *
474443 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC-GATGATGAGAAATTAATA
1 CGGGGTTGGAGTATCCCCTAG-AAATAACGGGGTTGGAGTATCCCCGGACGATAAAAAATTGATG
* * *
474507 TTTTAAAAATAAAGC
65 TATTAGAAATAAAAC
* *
474522 CAGGGTTGGGGTATCCCC
1 CGGGGTTGGAGTATCCCC
474540 GATTGTGGAG
Statistics
Matches: 150, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
78 3 0.02
79 141 0.94
80 6 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTAGAAATAACGGGGTTGGAGTATCCCCGGACGATAAAAAATTGATGT
ATTAGAAATAAAAC
Found at i:474537 original size:51 final size:51
Alignment explanation
Indices: 474473--474590 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
474463 GAAAATAACG
*
474473 GGGTTGGAGTATCCCCGA-TGAT-GAGAAATTAATATTTTAAAAATAAAGCCA
1 GGGTTGGAGTATCCCCGATTG-TGGAG-AATTAATATTTTAAAAATAAAACCA
* ** * * *
474524 GGGTTGGGGTATCCCCGATTGTGGAGAATTGGTGTTTTAAAAATAAAATCG
1 GGGTTGGAGTATCCCCGATTGTGGAGAATTAATATTTTAAAAATAAAACCA
474575 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
474591 TCAGAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
51 52 0.91
52 5 0.09
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGGAGAATTAATATTTTAAAAATAAAACCA
Found at i:474696 original size:130 final size:128
Alignment explanation
Indices: 474434--474698 Score: 279
Period size: 130 Copynumber: 2.0 Consensus size: 128
474424 GATGTTTTAG
474434 AAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAGA
1 AAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGA-GAGA
* * * * *** *
474499 AATTAATATTTTAAAAATAAAGCCAGGGTTGGGGTATCCCCGATTGTGGAGAATTGGTGTTTTAA
65 AATTAATATTTTAAAAATAAAGCCAGGGCTGGAGTATCCCCGA-TGTGAAAAATTGAAATTTCAA
*
474564 AAATAAAATCGGGGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCGATGA-A-A
1 AAATAAAACCGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATGAGAGA
* * ** * *
474626 AATTGATGTTTTGGAAATGGAA-CCGGGGCTGGAGTATCCCCGA-GATGAAAAATCTAGAAATTT
65 AATTAATATTTTAAAAAT-AAAGCCAGGGCTGGAGTATCCCCGATG-TGAAAAAT-T-GAAATTT
474689 AACAA
126 --CAA
474694 AAATA
1 AAATA
474699 CTTAGGTTTA
Statistics
Matches: 113, Mismatches: 15, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
125 1 0.01
126 6 0.05
127 34 0.30
128 7 0.06
129 1 0.01
130 64 0.57
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (128 bp):
AAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAGAGAA
ATTAATATTTTAAAAATAAAGCCAGGGCTGGAGTATCCCCGATGTGAAAAATTGAAATTTCAA
Found at i:476703 original size:13 final size:13
Alignment explanation
Indices: 476685--476710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
476675 ACAAAGATCG
476685 ATGTATCGATACA
1 ATGTATCGATACA
476698 ATGTATCGATACA
1 ATGTATCGATACA
476711 TTCTACAAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:476721 original size:21 final size:21
Alignment explanation
Indices: 476697--476754 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
476687 GTATCGATAC
476697 AATGTATCGATACATTCTACA
1 AATGTATCGATACATTCTACA
*
476718 AATGTATCAATACATTCTACA
1 AATGTATCGATACATTCTACA
476739 AATGTATCGATACATT
1 AATGTATCGATACATT
476755 TCTTTGGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTCTACA
Found at i:476808 original size:19 final size:21
Alignment explanation
Indices: 476784--476835 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
476774 AGCGATACAC
*
476784 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
476803 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
476824 TGTATCGATACA
1 TGTATCGATACA
476836 AATTATTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:479746 original size:170 final size:170
Alignment explanation
Indices: 479464--479830 Score: 529
Period size: 170 Copynumber: 2.2 Consensus size: 170
479454 GTTAAGAACT
479464 AAAATGCAAATATCCAAAGTTTAGGGACTTGTATGCAAAACTGATTTTTTCTAGAAATGTTGTAC
1 AAAATGCAAATATCCAAAGTTTAGGGACTTGTATGCAAAACTGATTTTTTCTAGAAATGTTGTAC
* * *
479529 ATGGCCGAACCTAAGATATTTCTTTGCTGTATTTTTGCTGCTGTTGTTGAGCTGATTTCATGCTT
66 ATGGCCGAACCTAAGATATTTCTTGGCCGTAATTTTGCTGCTGTTGTTGAGCTGATTTCATGCTT
* *
479594 TAAATGATGTGTTCCCATGTTATTTTGATGTATAGGGACC
131 TAAATGATGAGTTCCCATGTTATTTTGACGTATAGGGACC
* * * *
479634 AAAATGCAAATATCCAAAGTTTAGGGATTTGTATGCAAAATTGATTTTTCTTTAGAAATGTTGTG
1 AAAATGCAAATATCCAAAGTTTAGGGACTTGTATGCAAAACTGATTTTT-TCTAGAAATGTTGTA
** * ** * *
479699 TTTGGTCGAATTTAAGATATTTCTTGGCCG-AATTTTGCTGTTGTTGTTGAGTTGATTTCATGCT
65 CATGGCCGAACCTAAGATATTTCTTGGCCGTAATTTTGCTGCTGTTGTTGAGCTGATTTCATGCT
*
479763 TTAAATGATGAGTTCTCATGTTATTTTGACGTATAGGGACC
130 TTAAATGATGAGTTCCCATGTTATTTTGACGTATAGGGACC
* **
479804 AAAACGCAAATACTAAAAAGTTTAGGG
1 AAAATGCAAATA-TCCAAAGTTTAGGG
479831 CCATTTAGCA
Statistics
Matches: 175, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
170 127 0.73
171 48 0.27
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (170 bp):
AAAATGCAAATATCCAAAGTTTAGGGACTTGTATGCAAAACTGATTTTTTCTAGAAATGTTGTAC
ATGGCCGAACCTAAGATATTTCTTGGCCGTAATTTTGCTGCTGTTGTTGAGCTGATTTCATGCTT
TAAATGATGAGTTCCCATGTTATTTTGACGTATAGGGACC
Found at i:480460 original size:161 final size:162
Alignment explanation
Indices: 480015--480479 Score: 688
Period size: 162 Copynumber: 2.9 Consensus size: 162
480005 CTTAGTGGTA
* * *
480015 AATATTTAGTTTTTTCTAATC-TTTATATTCCTATGGGCATCCGTAGAGGTACAAAATATTTCAA
1 AATATTTA-TTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAA
* *
480079 AAACCTTTCGTATTCTTTCGGGCTTCCATTAGGATACGAACTGGTATTTTCAAAAATAAATAAAA
65 AAACCTTTCGTATTCTTTCGGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAAAA
*
480144 TTAACTTAAATTGGTATTATTGGGATAAATTTC
130 TTAACTTAAATTAGTATTATTGGGATAAATTTC
* *
480177 AATATTT-TATTTTTCTAATTTTTTATATTCCTATGGGCATCCGTAAGGGTATAAAAGATTTCAA
1 AATATTTAT-TTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAA
* * * *
480241 AAACCTTTCATATTCTTTCGGGCTTCTATTAGAGTACGAAATAGTATTTTCAAAAATAAATAAAA
65 AAACCTTTCGTATTCTTTCGGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAAAA
480306 TTAACTTAAATTAGTATTATTGGGATAAA-TTC
130 TTAACTTAAATTAGTATTATTGGGATAAATTTC
* * *
480338 TAATATTTATTTTTTCTAATCTTTTATATTTCTATGGGCATCCATCGGGGTATAAAAGATTTC-A
1 -AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAA
* *
480402 AAACCAATTCGTATTC-TTCGGGCTTCCATTAGGGTACGAAATGGTATTTTTAAAAATAAATAAA
65 AAACC-TTTCGTATTCTTTCGGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAAA
* *
480466 ATTAAATTGAATTA
129 ATTAACTTAAATTA
480480 ATACTTTTGA
Statistics
Matches: 273, Mismatches: 25, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
160 1 0.00
161 75 0.27
162 196 0.72
163 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (162 bp):
AATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAAA
AACCTTTCGTATTCTTTCGGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAAAAT
TAACTTAAATTAGTATTATTGGGATAAATTTC
Found at i:484162 original size:19 final size:19
Alignment explanation
Indices: 484117--484168 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
484107 ACTGCCAGTT
484117 TCATGTATCGATAAGATTG
1 TCATGTATCGATAAGATTG
484136 TGCATGTATCGATACA-A-TG
1 T-CATGTATCGATA-AGATTG
484155 ATCATGTATCGATA
1 -TCATGTATCGATA
484169 GCATGTATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 15 0.50
20 14 0.47
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATAAGATTG
Found at i:484175 original size:13 final size:13
Alignment explanation
Indices: 484157--484181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
484147 ATACAATGAT
484157 CATGTATCGATAG
1 CATGTATCGATAG
484170 CATGTATCGATA
1 CATGTATCGATA
484182 TAAAGCATAA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
CATGTATCGATAG
Found at i:484178 original size:32 final size:33
Alignment explanation
Indices: 484137--484201 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
484127 ATAAGATTGT
* *
484137 GCATGTATCGATACAATG-ATCATGTATCGATA
1 GCATGTATCGATACAAAGCATAATGTATCGATA
*
484169 GCATGTATCGATATAAAGCATAATGTATCGATA
1 GCATGTATCGATACAAAGCATAATGTATCGATA
484202 CATCTAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (33 bp):
GCATGTATCGATACAAAGCATAATGTATCGATA
Found at i:486689 original size:13 final size:13
Alignment explanation
Indices: 486670--486709 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
486660 ATAGTAACCC
486670 ATGTATCGATACA
1 ATGTATCGATACA
*
486683 TTGTATCGATACA
1 ATGTATCGATACA
486696 ATGTATCGATACA
1 ATGTATCGATACA
486709 A
1 A
486710 AGAACATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:488954 original size:21 final size:20
Alignment explanation
Indices: 488906--488946 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
488896 GATTCATCAA
488906 AAACAACGTGGATTGATTCT
1 AAACAACGTGGATTGATTCT
488926 AAAGCAACGTGGATTGATTCT
1 AAA-CAACGTGGATTGATTCT
488947 TCAACAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (20 bp):
AAACAACGTGGATTGATTCT
Found at i:491272 original size:15 final size:15
Alignment explanation
Indices: 491254--491288 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
491244 CCAGTCAACT
491254 TCATCATTATCATCA
1 TCATCATTATCATCA
*
491269 TCATCATTATCTTCA
1 TCATCATTATCATCA
491284 TCATC
1 TCATC
491289 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:492903 original size:20 final size:20
Alignment explanation
Indices: 492878--492931 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
492868 GTTTGAGACA
492878 ATGTATCGATACAAT-T-CTTC
1 ATGTATCGATACAATATGC--C
492898 ATGTATCGATACAATATGCC
1 ATGTATCGATACAATATGCC
492918 ATGTATCGATACAA
1 ATGTATCGATACAA
492932 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATATGCC
Found at i:492999 original size:13 final size:13
Alignment explanation
Indices: 492981--493007 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
492971 ACAATTGTGC
492981 ATGTATCGATACA
1 ATGTATCGATACA
492994 ATGTATCGATACA
1 ATGTATCGATACA
493007 A
1 A
493008 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:494703 original size:22 final size:21
Alignment explanation
Indices: 494653--494710 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
494643 AAAACACAAT
494653 ATTATATTGATACAATATGGCC
1 ATTATATTGATACAATA-GGCC
494675 -TTATATTGATACAAT-GAGCAC
1 ATTATATTGATACAATAG-GC-C
*
494696 ATTATATTGACACAA
1 ATTATATTGATACAA
494711 GGTCATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 16 0.50
22 13 0.41
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (21 bp):
ATTATATTGATACAATAGGCC
Found at i:495249 original size:22 final size:21
Alignment explanation
Indices: 495219--495271 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
495209 ATTTTATTCA
*
495219 AAATTAAAATAAATAAT-AATA
1 AAATAAAAATAAA-AATAAATA
*
495240 CAAATAAAAATAAAAGTAAATA
1 -AAATAAAAATAAAAATAAATA
495262 AAATAAAAAT
1 AAATAAAAAT
495272 GCAATAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (21 bp):
AAATAAAAATAAAAATAAATA
Found at i:497384 original size:2 final size:2
Alignment explanation
Indices: 497377--497415 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
497367 ATGTTTTGAG
497377 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
497416 GAGTTTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:498014 original size:16 final size:16
Alignment explanation
Indices: 497985--498040 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
497975 TTAAAACTCT
497985 AATTCTAAAA-TATTTA
1 AATT-TAAAATTATTTA
498001 AATTTAAAATTATTTA
1 AATTTAAAATTATTTA
* * *
498017 AATCTAAAATTACTAA
1 AATTTAAAATTATTTA
498033 AATTTAAA
1 AATTTAAA
498041 TATCTAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 5 0.14
16 30 0.86
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAATTATTTA
Found at i:498665 original size:22 final size:19
Alignment explanation
Indices: 498634--498683 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 19
498624 GCATCTTTAC
498634 TTTTTAATTTTTTATAATATA
1 TTTTTAATTTTTTATAA-A-A
498655 TTTTTAGATTTTTTATAAAA
1 TTTTTA-ATTTTTTATAAAA
498675 TTTTTAATT
1 TTTTTAATT
498684 AAATTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.11
20 7 0.25
21 7 0.25
22 11 0.39
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTAATTTTTTATAAAA
Found at i:500672 original size:21 final size:21
Alignment explanation
Indices: 500612--500672 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
500602 ATTATTATTT
500612 AATAAAAT--TTATTTA-TAA
1 AATAAAATAATTATTTATTAA
* * *
500630 AAT-ATATAAATATTAATATAA
1 AATAAAATAATTATTTAT-TAA
500651 AATAAAATAATTATTTATTAA
1 AATAAAATAATTATTTATTAA
500672 A
1 A
500673 TTTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
17 3 0.09
18 3 0.09
19 5 0.16
21 10 0.31
22 11 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAAAATAATTATTTATTAA
Found at i:500844 original size:2 final size:2
Alignment explanation
Indices: 500839--500896 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
500829 CCCCTCTCTG
500839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
500881 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
500897 AATAAGATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:501617 original size:24 final size:24
Alignment explanation
Indices: 501559--501617 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
501549 GTTTACCTTC
* * *
501559 TTTTAATTGATATCAAAATATATTT
1 TTTTAATTTA-ATCAAAATAAAATT
* *
501584 TTTTTA-TTAATTAAAATAAAATT
1 TTTTAATTTAATCAAAATAAAATT
501607 TTTTAATTTAA
1 TTTTAATTTAA
501618 GTAAGTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 16 0.59
24 6 0.22
25 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTAATTTAATCAAAATAAAATT
Found at i:501987 original size:29 final size:27
Alignment explanation
Indices: 501955--502011 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
501945 ATTTTTATGT
*
501955 TTATAACATATTTATATTATTTTTTAATA
1 TTATAACATATTT-TAAT-TTTTTTAATA
*
501984 TTATATCATATTTTAATTTTTTTAATA
1 TTATAACATATTTTAATTTTTTTAATA
502011 T
1 T
502012 AAATCAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 11 0.42
28 3 0.12
29 12 0.46
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATAACATATTTTAATTTTTTTAATA
Found at i:501989 original size:18 final size:18
Alignment explanation
Indices: 501966--502000 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
501956 TATAACATAT
* *
501966 TTATATTATTTTTTAATA
1 TTATATCATATTTTAATA
501984 TTATATCATATTTTAAT
1 TTATATCATATTTTAAT
502001 TTTTTTAATA
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:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATCATATTTTAATA
Found at i:502451 original size:20 final size:21
Alignment explanation
Indices: 502396--502459 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 21
502386 ACTTATTTGA
*
502396 TTTTTTAAAATTACTTTTTAATT
1 TTTTTTATAATTA-TTTTT-ATT
*
502419 TTTTTGTCTTAATTATTTTTA-T
1 TTTTT-T-ATAATTATTTTTATT
*
502441 TTTTTTATAATTATATTTA
1 TTTTTTATAATTATTTTTA
502460 AAAATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 11 0.31
21 1 0.03
22 6 0.17
23 6 0.17
24 6 0.17
25 5 0.14
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTATAATTATTTTTATT
Found at i:502613 original size:2 final size:2
Alignment explanation
Indices: 502600--502638 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
502590 TTACATTTGG
*
502600 AT AT AA AT AT AT 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 AT AT AT AT AT AT A
502639 ATAGAGGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:503501 original size:10 final size:10
Alignment explanation
Indices: 503488--503520 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
503478 TTTTTATATT
503488 TTTTTCTTCC
1 TTTTTCTTCC
503498 TTTTTCTT--
1 TTTTTCTTCC
503506 TTTTTCTTCC
1 TTTTTCTTCC
503516 TTTTT
1 TTTTT
503521 TCTTTAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTTCC
Found at i:503509 original size:18 final size:19
Alignment explanation
Indices: 503486--503525 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
503476 TTTTTTTATA
503486 TTTTTTTCTTCC-TTTTTC
1 TTTTTTTCTTCCTTTTTTC
503504 TTTTTTTCTTCCTTTTTTC
1 TTTTTTTCTTCCTTTTTTC
503523 TTT
1 TTT
503526 AACCAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTCTTCCTTTTTTC
Found at i:503685 original size:28 final size:25
Alignment explanation
Indices: 503654--503710 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
503644 TATAACATAC
503654 ATTTGAATTAGAATATAACTTAA-TAATA
1 ATTT-AATT-GAATATAA-TTAAGT-ATA
*
503682 ATTTAATTTAATATAATTAAGTATA
1 ATTTAATTGAATATAATTAAGTATA
503707 ATTT
1 ATTT
503711 TAATGTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 11 0.41
26 8 0.30
27 4 0.15
28 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (25 bp):
ATTTAATTGAATATAATTAAGTATA
Found at i:503695 original size:26 final size:27
Alignment explanation
Indices: 503665--503719 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
503655 TTTGAATTAG
503665 AATATAACTTAA-TAATAA-TTTAAT-TT
1 AATATAA-TTAAGT-ATAATTTTAATGTT
503691 AATATAATTAAGTATAATTTTAATGTT
1 AATATAATTAAGTATAATTTTAATGTT
503718 AA
1 AA
503720 CAAATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (27 bp):
AATATAATTAAGTATAATTTTAATGTT
Found at i:513966 original size:33 final size:33
Alignment explanation
Indices: 513928--514015 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 33
513918 TGAAAAGGGT
**
513928 TGCCACCGACTTGCATGGGCTTTTAAAAAAAGG
1 TGCCACCGACTTGTGTGGGCTTTTAAAAAAAGG
** * * *
513961 TGCCACTAACTTGTGTGGGC-TTTGAAAAGAGT
1 TGCCACCGACTTGTGTGGGCTTTTAAAAAAAGG
513993 TGCCACCGACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTT
514016 GGAAAGAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTTAAAAAAAGG
Found at i:514042 original size:30 final size:30
Alignment explanation
Indices: 513916--514249 Score: 231
Period size: 28 Copynumber: 11.2 Consensus size: 30
513906 AAAGTGGTGA
* *
513916 TTTGAAAAGGGTTGCCACCGACTTGCATGGGC
1 TTTGAAAAGAGTTGCCACTGACTTG--TGGGC
* * * *
513948 TTTTAAAAAAAGGTGCCACTAACTTGTGTGGGC
1 -TTTGAAAAGAGTTGCCACTGAC-T-TGTGGGC
*
513981 TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGAGTTGCCACTGAC-T-TGTGGGC
* * *
514013 TTTGGAAAGAGTTACCATTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* * *
514043 TTTGATAAGAGTTACCACT-AGCTTGTAGGC
1 TTTGAAAAGAGTTGCCACTGA-CTTGTGGGC
* * *
514073 TTTGAAAAG-GGTGCCACTAACTTATGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
*
514102 TTT-AAAAG-GGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
514130 TTTGAAAAGA--TGCTACTGAATTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* **
514158 TTTG-AAAG-GATGCCACTGACTTGTGGTTT
1 TTTGAAAAGAGTTGCCACTGACTTGTGG-GC
* * *
514187 TTTG--AAGAGATGCCACTAACTTGT-GGT
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
*** * * *
514214 TTTTTTAAGAGATGCCACTGACCTGTAGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
514244 TTTGAA
1 TTTGAA
514250 GAGATGAACG
Statistics
Matches: 247, Mismatches: 41, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
27 8 0.03
28 64 0.26
29 60 0.24
30 45 0.18
31 1 0.00
32 45 0.18
33 21 0.09
34 1 0.00
35 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (30 bp):
TTTGAAAAGAGTTGCCACTGACTTGTGGGC
Found at i:514125 original size:57 final size:56
Alignment explanation
Indices: 513955--514255 Score: 212
Period size: 57 Copynumber: 5.1 Consensus size: 56
513945 GGCTTTTAAA
* * * *
513955 AAAAGGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTT-AAAAG-GATGCCACTGAC-T-TGTAGGCTTT-G
* * * * * * *
514018 AAAGAGTTACCATTGACTTGTGGGCTTTGATAAGAGTTACCACT-AGCTTGTAGGCTTTG
1 AAA-AGATGCCACTAACTTGTGGGCTTT-AAAAG-GATGCCACTGA-CTTGTAGGCTTTG
* * * *
514077 AAAAGGGTGCCACTAACTTATGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAA-GATGCCACTAACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTAGGCTTTG
* * *
514134 AAAAGATGCTACTGAA-TTGTGGGCTTTGAAAGGATGCCACTGACTTGT-GGTTTTTTG
1 AAAAGATGCCACT-AACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTAGG--CTTTG
* ** ** *
514191 AAGAGATGCCACTAACTTGTGGTTTTTTTAAGAGATGCCACTGACCTGTAGGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTTAAAAG-GATGCCACTGACTTGTAGGCTTTG
*
514248 AAGAGATG
1 AAAAGATG
514256 AACGTTTTAG
Statistics
Matches: 197, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
55 2 0.01
56 38 0.19
57 64 0.32
58 21 0.11
59 24 0.12
60 9 0.05
61 2 0.01
62 24 0.12
63 4 0.02
64 9 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (56 bp):
AAAAGATGCCACTAACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTAGGCTTTG
Found at i:515455 original size:9 final size:9
Alignment explanation
Indices: 515441--515511 Score: 74
Period size: 10 Copynumber: 7.7 Consensus size: 9
515431 TCTAGACCCA
515441 TTTTTTGGT
1 TTTTTTGGT
515450 TTTTTT-GT
1 TTTTTTGGT
515458 TTTTTTGTGT
1 TTTTTTG-GT
*
515468 TTTTTATGTT
1 TTTTT-TGGT
515478 TTTTTTGTGT
1 TTTTTTG-GT
515488 TTTTTT-GT
1 TTTTTTGGT
*
515496 TTTTTGTTGT
1 TTTTT-TGGT
515506 TTTTTT
1 TTTTTT
515512 TCTTGGTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
8 15 0.28
9 10 0.19
10 27 0.50
11 2 0.04
ACGTcount: A:0.01, C:0.00, G:0.15, T:0.83
Consensus pattern (9 bp):
TTTTTTGGT
Found at i:515462 original size:10 final size:10
Alignment explanation
Indices: 515449--515536 Score: 90
Period size: 10 Copynumber: 8.8 Consensus size: 10
515439 CATTTTTTGG
515449 TTTTTTTGTT
1 TTTTTTTGTT
*
515459 TTTTTGTG-T
1 TTTTTTTGTT
*
515468 TTTTTATG-T
1 TTTTTTTGTT
*
515477 TTTTTTTGTG
1 TTTTTTTGTT
515487 TTTTTTTGTT
1 TTTTTTTGTT
*
515497 TTTTGTTGTTT
1 TTTTTTTG-TT
*
515508 TTTTTCTTGGT
1 TTTTT-TTGTT
*
515519 TTTTTTTCTT
1 TTTTTTTGTT
515529 TTTTTTTG
1 TTTTTTTG
515537 GTACAAAGGA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
9 16 0.25
10 33 0.52
11 12 0.19
12 3 0.05
ACGTcount: A:0.01, C:0.02, G:0.14, T:0.83
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:515512 original size:20 final size:19
Alignment explanation
Indices: 515449--515536 Score: 97
Period size: 19 Copynumber: 4.4 Consensus size: 19
515439 CATTTTTTGG
515449 TTTTTTTG-TTTTTTTGTGT
1 TTTTTTTGTTTTTTTTGT-T
* *
515468 TTTTTATGTTTTTTTTGTG
1 TTTTTTTGTTTTTTTTGTT
515487 TTTTTTTGTTTTTTGTTGTTT
1 TTTTTTTGTTTTTT-TTG-TT
*
515508 TTTTTCTTGGTTTTTTTTCTT
1 TTTTT-TT-GTTTTTTTTGTT
515529 TTTTTTTG
1 TTTTTTTG
515537 GTACAAAGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
19 21 0.36
20 14 0.24
21 13 0.22
22 4 0.07
23 7 0.12
ACGTcount: A:0.01, C:0.02, G:0.14, T:0.83
Consensus pattern (19 bp):
TTTTTTTGTTTTTTTTGTT
Found at i:515522 original size:30 final size:30
Alignment explanation
Indices: 515449--515532 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
515439 CATTTTTTGG
515449 TTTTTTTGTTTTTTTGTGTTTTTTATGTTT
1 TTTTTTTGTTTTTTTGTGTTTTTTATGTTT
*
515479 TTTTTGTGTTTTTTTGT-TTTTTGT-TGTTT
1 TTTTTTTGTTTTTTTGTGTTTTT-TATGTTT
*
515508 TTTTTCTTGGTTTTTTT-TCTTTTTT
1 TTTTT-TT-GTTTTTTTGTGTTTTTT
515533 TTTGGTACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
29 15 0.31
30 20 0.42
31 13 0.27
ACGTcount: A:0.01, C:0.02, G:0.13, T:0.83
Consensus pattern (30 bp):
TTTTTTTGTTTTTTTGTGTTTTTTATGTTT
Found at i:515523 original size:15 final size:14
Alignment explanation
Indices: 515476--515530 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
515466 GTTTTTTATG
515476 TTTTTTTTGTGTTTT
1 TTTTTTTTG-GTTTT
*
515491 TTTGTTTTTTGTTGTT
1 TTT-TTTTTGGTT-TT
515507 TTTTTTCTTGGTTTT
1 TTTTTT-TTGGTTTT
515522 TTTTCTTTT
1 TTTT-TTTT
515531 TTTTTGGTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 17 0.50
16 17 0.50
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.84
Consensus pattern (14 bp):
TTTTTTTTGGTTTT
Found at i:515526 original size:13 final size:12
Alignment explanation
Indices: 515495--515535 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
515485 TGTTTTTTTG
*
515495 TTTTTTGTTGTT
1 TTTTTTCTTGTT
515507 TTTTTTCTTGGTT
1 TTTTTTCTT-GTT
515520 TTTTTTCTT-TT
1 TTTTTTCTTGTT
515531 TTTTT
1 TTTTT
515536 GGTACAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.26
12 8 0.30
13 12 0.44
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTGTT
Found at i:515534 original size:9 final size:9
Alignment explanation
Indices: 515441--515512 Score: 99
Period size: 9 Copynumber: 7.7 Consensus size: 9
515431 TCTAGACCCA
*
515441 TTTTTTGGT
1 TTTTTTGTT
515450 TTTTTTGTT
1 TTTTTTGTT
515459 TTTTTGTGTT
1 TTTTT-TGTT
*
515469 TTTTATGTT
1 TTTTTTGTT
515478 TTTTTTGTGT
1 TTTTTTGT-T
515488 TTTTTTGTT
1 TTTTTTGTT
515497 TTTTGTTGTT
1 TTTT-TTGTT
515507 TTTTTT
1 TTTTTT
515513 CTTGGTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
9 31 0.54
10 26 0.46
ACGTcount: A:0.01, C:0.00, G:0.15, T:0.83
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:533316 original size:59 final size:59
Alignment explanation
Indices: 533244--533502 Score: 281
Period size: 59 Copynumber: 4.4 Consensus size: 59
533234 TACGACTCCC
* * *
533244 CTCAGATCGCCACCAAGATGACCCAAACTTAAACATTAAGTGATGCCAAGTCACTTAAA
1 CTCAGATCACCACCAAGATGACCCAAACTTAAACACTAAGTGATGCCAAGTCACTCAAA
* *
533303 CTCAGATCACCACCAACG-TGACCCAAA-TTCAAACACTAAGTCATGCCAACTCACTCAAA
1 CTCAGATCACCACCAA-GATGACCCAAACTT-AAACACTAAGTGATGCCAAGTCACTCAAA
* *** *
533362 CTCAGATCATCACCAAGGCAACCCAAACTTAAACACTAAGTGATGCCAAGTCCCTCAAA
1 CTCAGATCACCACCAAGATGACCCAAACTTAAACACTAAGTGATGCCAAGTCACTCAAA
* * * * * * * * *
533421 CTCAGATCGCCACCAAGACGACCCAAATTTGAAGACTAAGTAATGCTAAGTCACTTAGA
1 CTCAGATCACCACCAAGATGACCCAAACTTAAACACTAAGTGATGCCAAGTCACTCAAA
* * *
533480 TTAAGATCACCA-CAAGGTGACCC
1 CTCAGATCACCACCAAGATGACCC
533503 CTATCCAAAC
Statistics
Matches: 168, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
58 12 0.07
59 153 0.91
60 3 0.02
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (59 bp):
CTCAGATCACCACCAAGATGACCCAAACTTAAACACTAAGTGATGCCAAGTCACTCAAA
Found at i:538809 original size:51 final size:51
Alignment explanation
Indices: 538743--539019 Score: 224
Period size: 51 Copynumber: 5.3 Consensus size: 51
538733 TGAAAATAAT
538743 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGTC
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGTC
* * * * *
538794 GGGGTTGAAGTATCCCCAATTGTGAGAAATCGATATTTTGGCAACA-AAGCT-
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAG-AA-ATAAGGTC
*** * ** * * ***
538845 GGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATGAAATAA--T-
1 GGGGTTGGAGTAT-CCC-CGATTGTGA-GA-AAT-CAATAT--TTTA-GAAATAAGGTC
*
538901 GGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTAGAAATAAGGTC
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGTC
** * *
538952 GGGGTTAAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAG-C
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGTC
539002 TGGGGTTGGAGTATCCCC
1 -GGGGTTGGAGTATCCCC
539020 TCGGAAATAA
Statistics
Matches: 172, Mismatches: 39, Indels: 30
0.71 0.16 0.12
Matches are distributed among these distances:
48 7 0.04
49 1 0.01
50 2 0.01
51 112 0.65
52 10 0.06
53 7 0.04
54 7 0.04
55 3 0.02
56 17 0.10
57 1 0.01
58 4 0.02
59 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGTC
Found at i:538920 original size:28 final size:27
Alignment explanation
Indices: 538844--538920 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
538834 GCAACAAAGC
538844 TGGGGTTGGAGTATCCCCTCGA-AAATAA
1 TGGGGTTGGAGTAT--CCTCGATAAATAA
* * *
538872 CGAGGTTGGAGTATCCCCGATGAAATAA
1 TGGGGTTGGAGTATCCTCGAT-AAATAA
538900 TGGGGTTGGAGTATCCTCGAT
1 TGGGGTTGGAGTATCCTCGAT
538921 TGTGAGAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.12
28 36 0.88
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (27 bp):
TGGGGTTGGAGTATCCTCGATAAATAA
Found at i:539010 original size:158 final size:158
Alignment explanation
Indices: 538722--539208 Score: 594
Period size: 158 Copynumber: 3.1 Consensus size: 158
538712 ATCGAGATTA
* *
538722 GAGTATCCCTG-TGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAA
1 GAGTATCCCCGATG-AAATAATGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTAGAA
* * *
538786 ATAAGGTCGGGGTTGAAGTATCCCCAATTGTGAGAAATCGATATTTTGGCAACAAAGCTGGGGTT
65 ATAAGGTCGGGGTTAAAGTATCCCCAATTGTGAGAAATCGATATTTTGGAAATAAAGCTGGGGTT
538851 GGAGTATCCCCTCGAAAATAACGAGGTTG
130 GGAGTATCCCCTCGAAAATAACGAGGTTG
538880 GAGTATCCCCGATGAAATAATGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTAGAAA
1 GAGTATCCCCGATGAAATAATGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTAGAAA
* *
538945 TAAGGTCGGGGTTAAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCTGGGGTTG
66 TAAGGTCGGGGTTAAAGTATCCCCAATTGTGAGAAATCGATATTTTGGAAATAAAGCTGGGGTTG
* *
539010 GAGTATCCCCTCGGAAATAA-TAGGGTTG
131 GAGTATCCCCTCGAAAATAACGA-GGTTG
* * * * *** *
539038 GAGTATCCTCGATGAAATAATGGGGTTAGAGTAT-CTCCGATTATGAAAAATTGGTGTTTT-GAA
1 GAGTATCCCCGATGAAATAATGGGGTTGGAGTATCCT-CGATTGTGAGAAATCAATATTTTAG-A
** * * * * * * * *
539101 AATAAAATCGGAGTTAGAGTATCCCCAATTGTG-GAGAATTGGTGTTTTAGAAATAAA-ATCAGG
64 AATAAGGTCGGGGTTAAAGTATCCCCAATTGTGAGA-AATCGATATTTTGGAAATAAAGCT-GGG
*
539164 GTTGGAGTATCCCCAC-AGAAATAACG-GGATTG
127 GTTGGAGTATCCCCTCGA-AAATAACGAGG-TTG
539196 GAGTATCCCCGAT
1 GAGTATCCCCGAT
539209 TATGAAAAAT
Statistics
Matches: 287, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
157 9 0.03
158 276 0.96
159 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (158 bp):
GAGTATCCCCGATGAAATAATGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTAGAAA
TAAGGTCGGGGTTAAAGTATCCCCAATTGTGAGAAATCGATATTTTGGAAATAAAGCTGGGGTTG
GAGTATCCCCTCGAAAATAACGAGGTTG
Found at i:539039 original size:28 final size:28
Alignment explanation
Indices: 539004--539072 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
538994 AATAAAGCTG
539004 GGGTTGGAGTATCCCCTCG-GAAATAATA
1 GGGTTGGAGTAT-CCCTCGAGAAATAATA
*
539032 GGGTTGGAGTAT-CCTCGATGAAATAATG
1 GGGTTGGAGTATCCCTCGA-GAAATAATA
*
539060 GGGTTAGAGTATC
1 GGGTTGGAGTATC
539073 TCCGATTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 5 0.14
28 31 0.86
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.28
Consensus pattern (28 bp):
GGGTTGGAGTATCCCTCGAGAAATAATA
Found at i:539120 original size:51 final size:51
Alignment explanation
Indices: 539060--539178 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 51
539050 TGAAATAATG
* *
539060 GGGTTAGAGTATCTCCGATTATGAAAAATTGGTGTTTT-GAAAATAAAATC-
1 GGGTTAGAGTATCCCCAATTATGAAAAATTGGTGTTTTAG-AAATAAAATCA
* * *
539110 GGAGTTAGAGTATCCCCAATTGTGGAGAATTGGTGTTTTAGAAATAAAATCA
1 GG-GTTAGAGTATCCCCAATTATGAAAAATTGGTGTTTTAGAAATAAAATCA
*
539162 GGGTTGGAGTATCCCCA
1 GGGTTAGAGTATCCCCA
539179 CAGAAATAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
50 2 0.03
51 55 0.92
52 3 0.05
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GGGTTAGAGTATCCCCAATTATGAAAAATTGGTGTTTTAGAAATAAAATCA
Found at i:539200 original size:79 final size:79
Alignment explanation
Indices: 539117--539366 Score: 297
Period size: 79 Copynumber: 3.2 Consensus size: 79
539107 ATCGGAGTTA
* * * *
539117 GAGTATCCCCAATTGTGGAGAATTGGTGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCCACAG
1 GAGTATCCCCAATTATGGAGAATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAG
*
539182 AAATAACGGGATTG
66 AAATAACGGGGTTG
* * * * * * * *
539196 GAGTATCCCCGATTATGAAAAATTGATGTTTCAGAAATAAAACCGGGGTTGGAGTATTCTCTCAA
1 GAGTATCCCCAATTATGGAGAATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAG
* *
539261 AAATAATGGGGTTA
66 AAATAACGGGGTTG
* * * *
539275 GAGTATCCCCGATTAT-GAGAAATTAATATTTTAGAAATAAAGCC-GAGGTTGGAGTATCCCCTC
1 GAGTATCCCCAATTATGGAG-AATTGATGTTTTAGAAATAAAACCAG-GGTTGGAGTATCCCCTC
539338 AGAAATAACGGGGTTG
64 AGAAATAACGGGGTTG
539354 GAGTATCCCCAAT
1 GAGTATCCCCAAT
539367 AAAAAATTGA
Statistics
Matches: 142, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
78 2 0.01
79 140 0.99
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
GAGTATCCCCAATTATGGAGAATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAG
AAATAACGGGGTTG
Found at i:539421 original size:158 final size:157
Alignment explanation
Indices: 539113--539411 Score: 383
Period size: 158 Copynumber: 1.9 Consensus size: 157
539103 TAAAATCGGA
* ** * *
539113 GTTAGAGTATCCCCAATTGTGGAGAATTGGTGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
1 GTTAGAGTATCCCCAATTATGGAGAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCC
* *
539178 ACAGAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTTCAGAAATAAAACCGGG
66 ACAGAAATAACGGGATTGGAGTATCCCCGA-TATAAAAAATTGATGTTTCAGAAATAAAACCGCG
* *
539243 GTTGGAGTATTCTCTCAAAAATAATGGG
130 ATTGGAGTATCCTCTCAAAAATAATGGG
* *
539271 GTTAGAGTATCCCCGATTAT-GAGAAATTAATATTTTAGAAATAAAGCC-GAGGTTGGAGTATCC
1 GTTAGAGTATCCCCAATTATGGAG-AATTAATATTTTAGAAATAAAACCAG-GGTTGGAGTATCC
* * * **
539334 CCTCAGAAATAACGGGGTTGGAGTATCCCC-A-ATAAAAAATTGATG-TTCTGGAAATGGAACCG
64 CCACAGAAATAACGGGATTGGAGTATCCCCGATATAAAAAATTGATGTTTC-AGAAATAAAACCG
539396 CGATTGGAGTATCCTC
128 CGATTGGAGTATCCTC
539412 GAGATAAAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
154 3 0.02
155 36 0.30
157 5 0.04
158 78 0.64
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (157 bp):
GTTAGAGTATCCCCAATTATGGAGAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCC
ACAGAAATAACGGGATTGGAGTATCCCCGATATAAAAAATTGATGTTTCAGAAATAAAACCGCGA
TTGGAGTATCCTCTCAAAAATAATGGG
Found at i:541781 original size:20 final size:20
Alignment explanation
Indices: 541706--541812 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
541696 AAAATGCCTG
* *
541706 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGC
* *
541726 AATGCATCGATAAAATGAGC
1 AATGTATCGATACAATGAGC
541746 AATGTATCG-----AT-A-C
1 AATGTATCGATACAATGAGC
*
541759 AATGTATCGTTACAATGAGC
1 AATGTATCGATACAATGAGC
*
541779 AATGTATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGC
541799 AATGTATCGATACA
1 AATGTATCGATACA
541813 TCTGGGTAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
13 10 0.14
14 1 0.01
15 2 0.03
18 2 0.03
19 2 0.03
20 53 0.75
21 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:541794 original size:13 final size:13
Alignment explanation
Indices: 541745--541775 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
541735 ATAAAATGAG
541745 CAATGTATCGATA
1 CAATGTATCGATA
*
541758 CAATGTATCGTTA
1 CAATGTATCGATA
541771 CAATG
1 CAATG
541776 AGCAATGTAT
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:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:542526 original size:40 final size:41
Alignment explanation
Indices: 542477--542579 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 41
542467 GTCCCACTTT
* * * *
542477 TTGAGGACAAAGGAAAAGAG-AATGAAATAGGTCTTGCTCC
1 TTGAAGACAAAGGAAAAGAGAAAAGAAAAAGGTCCTGCTCC
* * * * *
542517 TTGATGACAAAGAAAAAAAGAAAAGAAAAATGTCCTGCTTC
1 TTGAAGACAAAGGAAAAGAGAAAAGAAAAAGGTCCTGCTCC
542558 TTGAAGACAAAGTGGAAAAGAG
1 TTGAAGACAAA--GGAAAAGAG
542580 TACGTCTTGC
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
40 17 0.35
41 25 0.51
43 7 0.14
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (41 bp):
TTGAAGACAAAGGAAAAGAGAAAAGAAAAAGGTCCTGCTCC
Found at i:542723 original size:45 final size:43
Alignment explanation
Indices: 542610--542749 Score: 124
Period size: 42 Copynumber: 3.2 Consensus size: 43
542600 TAAAGGAAAA
* * * *
542610 AAAAGGAAAACAAAATGCGTCCTACTCTTTGAGGACAAAA--G
1 AAAAGAAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGGG
* *
542651 AAAGAGAAAAATAAAGTGCATCATGCTCTTTGAGGACAAAAGGG
1 AAA-AGAAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGGG
* * * *
542695 AAAAGAAGGGAATGAAGTGTGTCCTGCTCTTTGAAGAC-AAAGGAG
1 AAAAGAA--AAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGG-G
*
542740 AAAAGGAAAA
1 AAAAGAAAAA
542750 GGCATCCTAC
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
41 3 0.04
42 31 0.39
43 6 0.08
44 9 0.11
45 30 0.38
ACGTcount: A:0.46, C:0.12, G:0.25, T:0.17
Consensus pattern (43 bp):
AAAAGAAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGGG
Found at i:542816 original size:62 final size:60
Alignment explanation
Indices: 542739--542991 Score: 285
Period size: 62 Copynumber: 4.1 Consensus size: 60
542729 AGACAAAGGA
*
542739 GAAAAGGAAAAGGCATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
1 GAAAA-GAAAA-GCATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* ** *
542801 GAAAAGAAAAGGGCATCCTACTCTTGGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGAAAA--GCATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
542863 GCAAAGAGAAAGCATCCTGCTCTTTGAGGACTGGAAAA-TGCTACCAACTAATGTGTGGGCTTT
1 GAAAAGA-AAAGCATCCTACTCTTTGAGGACT-AAAAAGTGCCACCAACT--TGTGTGGGCTTT
* * * **
542926 GAAAGGAAAAGCTGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGAAAAGC-ATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
542987 -AAAAG
1 GAAAAG
542992 GGAAAAGAAA
Statistics
Matches: 165, Mismatches: 19, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
60 4 0.02
61 46 0.28
62 67 0.41
63 48 0.29
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (60 bp):
GAAAAGAAAAGCATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:542909 original size:61 final size:60
Alignment explanation
Indices: 542751--542996 Score: 266
Period size: 61 Copynumber: 4.0 Consensus size: 60
542741 AAAGGAAAAG
* *
542751 GCATCCTACTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA-AGAAAA
1 GCATCCTACTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGAG-AAA
* **
542811 GGGCATCCTACTCTTGGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA
1 --GCATCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGAGAAA
* *
542874 GCATCCTGCTCTTTGAGGACTGGAAAATGCTACCAACTAATGTGTGGGCTTTGAAAG-GAAAA
1 GCATCCTACTCTTTGAGGACTGGAAAATGCCACCAACT--TGTGTGGGCTTTGAAAGAG-AAA
* * * * *
542936 GCTGTCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAA
1 GC-ATCCTACTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAGAAA
542997 AGAAAGAAAT
Statistics
Matches: 161, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
61 53 0.33
62 53 0.33
63 51 0.32
64 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (60 bp):
GCATCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAGAAA
Found at i:543045 original size:46 final size:44
Alignment explanation
Indices: 542987--543251 Score: 218
Period size: 43 Copynumber: 6.0 Consensus size: 44
542977 TGTGGGCTTT
* *
542987 AAAAGGGAAAAGAAAGAAATGAAGTGCGTCCTACTCTTTGAGGAC
1 AAAAGAGAAAAGAAA-AAATGAAGTGCGTCCTGCTCTTTGAGGAC
543032 AATAAGAGAAAAGAAAAGAATGGAACGT--GTCCTGCTCTTTGAGGAC
1 AA-AAGAGAAAAGAAAA-AAT-GAA-GTGCGTCCTGCTCTTTGAGGAC
* * *
543078 AAAGGAGAAAA-AGAAAATAAAGTGCGTCCTGCT-TCTTGAGGAC
1 AAAAGAGAAAAGAAAAAATGAAGTGCGTCCTGCTCT-TTGAGGAC
** * * * * * *
543121 GGAGGCGGAAAG-GAAAATAAAGTGCGTCTTGCTCTTTGAGGAC
1 AAAAGAGAAAAGAAAAAATGAAGTGCGTCCTGCTCTTTGAGGAC
* * *
543164 AAAAGGGAAAAGAAGGAAACGAAGTGCGTCCTGCTCTTTGAGGAC
1 AAAAGAGAAAAGAA-AAAATGAAGTGCGTCCTGCTCTTTGAGGAC
** * * * * *
543209 AAGGGGGAAGAG-GAAAATAAAGTGCGTCATGCTCTTTGAGGAC
1 AAAAGAGAAAAGAAAAAATGAAGTGCGTCCTGCTCTTTGAGGAC
543252 TAGGATGTGC
Statistics
Matches: 181, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.01
42 3 0.02
43 87 0.48
44 4 0.02
45 46 0.25
46 34 0.19
47 3 0.02
48 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.18
Consensus pattern (44 bp):
AAAAGAGAAAAGAAAAAATGAAGTGCGTCCTGCTCTTTGAGGAC
Found at i:543208 original size:88 final size:86
Alignment explanation
Indices: 543064--543251 Score: 256
Period size: 88 Copynumber: 2.2 Consensus size: 86
543054 GAACGTGTCC
* *
543064 TGCTCTTTGAGGACAAAGGAGAAAAAGAAAATAAAGTGCGTCCTGCTTCTTGAGGACGGAGGCGG
1 TGCTCTTTGAGGACAAAGGAGAAAAAGAAAACAAAGTGCGTCCTGCTTCTTGAGGAC-AAGGCGG
*
543129 AA-AGGAAAATAAAGTGCGTCT
65 AAGAGGAAAATAAAGTGCGTCA
* *
543150 TGCTCTTTGAGGACAAAAGG-GAAAAGAAGGAAACGAAGTGCGTCCTGC-TCTTTGAGGACAAGG
1 TGCTCTTTGAGGAC-AAAGGAG-AAA-AAGAAAACAAAGTGCGTCCTGCTTC-TTGAGGACAAGG
*
543213 GGGAAGAGGAAAATAAAGTGCGTCA
62 CGGAAGAGGAAAATAAAGTGCGTCA
543238 TGCTCTTTGAGGAC
1 TGCTCTTTGAGGAC
543252 TAGGATGTGC
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
86 15 0.16
87 17 0.19
88 59 0.65
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (86 bp):
TGCTCTTTGAGGACAAAGGAGAAAAAGAAAACAAAGTGCGTCCTGCTTCTTGAGGACAAGGCGGA
AGAGGAAAATAAAGTGCGTCA
Found at i:543248 original size:131 final size:132
Alignment explanation
Indices: 543003--543251 Score: 335
Period size: 131 Copynumber: 1.9 Consensus size: 132
542993 GAAAAGAAAG
* **
543003 AAATGAAGTGCGTCCTACTCTTTGAGGACAATAAGAGAAAAGAAAAGAATGGAACGTGTCCTGCT
1 AAATAAAGTGCGTCCTACTCTTTGAGGACAATAAGAGAAAAGAAAAGAAACGAACGTGTCCTGCT
*
543068 CTTTGAGGACAAAGGAGAAAAAGAAAATAAAGTGCGTCCTGCTTCTTGAGGACGGAGGCGGAAAG
66 CTTTGAGGACAAAGGAGAAAAAGAAAATAAAGTGCGTCATGCTTCTTGAGGACGGAGGCGGAAAG
543133 GA
131 GA
* * * *
543135 AAATAAAGTGCGTCTTGCTCTTTGAGGACAA-AAGGGAAAAG-AAGGAAACGAA-GTGCGTCCTG
1 AAATAAAGTGCGTCCTACTCTTTGAGGACAATAAGAGAAAAGAAAAGAAACGAACGT--GTCCTG
* * * *
543197 CTCTTTGAGGACAAGGGGGAAGAGGAAAATAAAGTGCGTCATGC-TCTTTGAGGAC
64 CTCTTTGAGGACAAAGGAGAAAAAGAAAATAAAGTGCGTCATGCTTC-TTGAGGAC
543252 TAGGATGTGC
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
129 2 0.02
130 10 0.10
131 62 0.61
132 28 0.27
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (132 bp):
AAATAAAGTGCGTCCTACTCTTTGAGGACAATAAGAGAAAAGAAAAGAAACGAACGTGTCCTGCT
CTTTGAGGACAAAGGAGAAAAAGAAAATAAAGTGCGTCATGCTTCTTGAGGACGGAGGCGGAAAG
GA
Found at i:543537 original size:62 final size:61
Alignment explanation
Indices: 543227--544223 Score: 1119
Period size: 61 Copynumber: 16.5 Consensus size: 61
543217 AGAGGAAAAT
* * * *
543227 AAAGTGCGTCATGCTCTTTGAGGACTAGG-ATGTGCCACCAATTTGTGTGGGCTTTAAAAAGAAA
1 AAAG-GCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GA
* * * * *
543291 AAAGACGTCCTGCTCTTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTT-GAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
543351 GAAGGCGTCCTGCTCTTTAAGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * ** *
543412 AAAGGCGTCTTTCTCTTTGAGGAC-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAACGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GGA
* * * *
543473 AAAGGCATCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTTGTGTAGGC-TTCAAAGGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-A
* * * **
543534 AAAAGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT------A
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
543589 AAAGGCGTCCTGCTCTTTGAGGACTGAAAAGGTGCCACCAACTTGTGTAGGCTTT-----G-
1 AAAGGCGTCCTGCTCTTTGAGGACTG-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
** *
543645 AAAGGTATCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGGGGGCTTT------A
1 AAAGGCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * *
543700 AAAGGTGTCATGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * * *
543761 AAAGGTGTCTTACTCTTTGAGGACTAGCAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * *
543823 AAAGGCATCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACATGTGTGGGCTTTAAAAAGAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTGG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GA
* * * *
543887 AAAGGCGTCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
** *
543948 AAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTT-T-TGGGCTTTAAAAAGAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GA
* * * * *
544009 AAAGGCATCCTGCTCTTTAAGGATTGGAAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
544070 AAAGGTGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
544131 AAAGGTGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
544193 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGG
544224 GCTAAAAGAG
Statistics
Matches: 809, Mismatches: 96, Indels: 59
0.84 0.10 0.06
Matches are distributed among these distances:
54 3 0.00
55 90 0.11
56 52 0.06
57 1 0.00
59 9 0.01
60 82 0.10
61 293 0.36
62 171 0.21
63 77 0.10
64 31 0.04
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (61 bp):
AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:550546 original size:52 final size:52
Alignment explanation
Indices: 550458--550577 Score: 172
Period size: 52 Copynumber: 2.3 Consensus size: 52
550448 TGAAAGTAAT
*
550458 GGGGTTGGAGTAT-CCCTGATTGTGAGAAATCAATATTTTAGAAAT-AAGACC
1 GGGGTTGGAGTATCCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAG-CC
* ** *
550509 GGGGTTGAAGTATCCCCCGATTGTGAGAAATTGATATTTTGGAAATAAAGCC
1 GGGGTTGGAGTATCCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
550561 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
550578 TCAAAAATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 12 0.20
52 46 0.75
53 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (52 bp):
GGGGTTGGAGTATCCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
Found at i:550618 original size:79 final size:80
Alignment explanation
Indices: 550508--550656 Score: 228
Period size: 79 Copynumber: 1.9 Consensus size: 80
550498 GAAATAAGAC
** * **
550508 CGGGGTTGAAGTATCCCCCGATTGTGAGAAATTGATATTTTGGAAATAAAGCCGGGGTTGGAGTA
1 CGGGGTTGAAGTATCCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAAAGTA
550573 TCCCCTCAAAAATAA
66 TCCCCTCAAAAATAA
* *
550588 CGGGGTTGGAGTAT-CCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTTAAAGTA
1 CGGGGTTGAAGTATCCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAAAGTA
550652 TCCCC
66 TCCCC
550657 GATTGTGAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 49 0.79
80 13 0.21
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (80 bp):
CGGGGTTGAAGTATCCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAAAGTA
TCCCCTCAAAAATAA
Found at i:550655 original size:51 final size:51
Alignment explanation
Indices: 550588--550706 Score: 193
Period size: 51 Copynumber: 2.3 Consensus size: 51
550578 TCAAAAATAA
*
550588 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
** *
550639 CGGGGTTAAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
*
550690 AGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
550707 TTCGGTAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
Found at i:550726 original size:130 final size:131
Alignment explanation
Indices: 550458--550738 Score: 456
Period size: 130 Copynumber: 2.2 Consensus size: 131
550448 TGAAAGTAAT
* *
550458 GGGGTTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAGACCGGGGTTGAAGTATC
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGACCGGGGTTAAAGTATC
** *
550523 CCCCGATTGTGAGAAATTGATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCAAAAATAA
66 CCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCAAAAATAA
550588 C
131 C
*
550589 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTTAAAGTAT-
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGACCGGGGTTAAAGTATC
* ***
550653 CCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCTTCGGTAATAA
66 CCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCAAAAATAA
550718 C
131 C
*
550719 GGGGTTGGAGTATCCTCGAT
1 GGGGTTGGAGTATCCCCGAT
550739 GAAATAATAG
Statistics
Matches: 139, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 78 0.56
131 61 0.44
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (131 bp):
GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGACCGGGGTTAAAGTATC
CCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCAAAAATAA
C
Found at i:550744 original size:28 final size:28
Alignment explanation
Indices: 550691--550766 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
550681 AAATAAAGCA
*
550691 GGGGTTGGAGTATCCCTTCG--GTAATAAC
1 GGGGTTGGAGTAT-CC-TCGATGAAATAAC
*
550719 GGGGTTGGAGTATCCTCGATGAAATAAT
1 GGGGTTGGAGTATCCTCGATGAAATAAC
* * *
550747 AGGGTTAGAGTATCCCCGAT
1 GGGGTTGGAGTATCCTCGAT
550767 TGGGAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 36 0.88
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.28
Consensus pattern (28 bp):
GGGGTTGGAGTATCCTCGATGAAATAAC
Found at i:550813 original size:51 final size:51
Alignment explanation
Indices: 550749--550865 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
550739 GAAATAATAG
* *
550749 GGTTAGAGTATCCCCGATTG-GGAAAAATTGGTGTTTTGGAAATAAAATCG-
1 GGTTGGAGTATCCCCGATTGTGG-AAAATTGGTGTTTTAGAAATAAAATCGC
*
550799 GAGTTGGAGTATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAATCGC
1 G-GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGC
550851 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
550866 TCAAAAATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
50 1 0.02
51 57 0.93
52 3 0.05
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGC
Found at i:550885 original size:79 final size:79
Alignment explanation
Indices: 550801--551097 Score: 352
Period size: 79 Copynumber: 3.8 Consensus size: 79
550791 TAAAATCGGA
* * *
550801 GTTGGAGTATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAATCGCGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGGAGAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCC
*
550866 TCAAAAATAACGGG
66 TCGAAAATAACGGG
* * * * *
550880 ATTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGGAGAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCC
*
550945 TCGAAAATAATGGG
66 TCGAAAATAACGGG
* * **
550959 GTTGGAGTATCCCCGATTAT-GAGAAATTTATATTTTAGAAATAAAGCCGAGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATGGAG-AATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCC
* *
551023 CTTGGAAATAACGGG
65 CTCGAAAATAACGGG
* * * **
551038 GTTGGAGTATCCCCGA-TA--AAAAATTGATGTTTTGGAAATGGAATCG-GGATTGGAGTATCC
1 GTTGGAGTATCCCCGATTATGGAGAATTGATGTTTTAGAAATAAAATCGAGG-TTGGAGTATCC
551098 TCGAGACAAA
Statistics
Matches: 186, Mismatches: 30, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
75 2 0.01
76 29 0.16
77 1 0.01
78 3 0.02
79 151 0.81
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (79 bp):
GTTGGAGTATCCCCGATTATGGAGAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCC
TCGAAAATAACGGG
Found at i:550963 original size:158 final size:155
Alignment explanation
Indices: 550801--551097 Score: 407
Period size: 158 Copynumber: 1.9 Consensus size: 155
550791 TAAAATCGGA
* * * * *
550801 GTTGGAGTATCCCCGATTGTG-GAGAATTGGTGTTTTAGAAATAAAATCGCGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAGA-AATTGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCC
550865 CTCAAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGG
65 CTCAAAAATAACGGGATTGGAGTATCCCCGA-TA--AAAAATTGATGTTTTAGAAATAAAATCGG
*
550930 GGTTAGAGTATCCCCTCGAAAATAATGGG
127 GATTAGAGTATCCCCTCGAAAATAATGGG
* *
550959 GTTGGAGTATCCCCGATTATGAGAAATTTATATTTTAGAAATAAAGCCGAGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAGAAATTGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
*** * * **
551024 TTGGAAATAACGGGGTTGGAGTATCCCCGATAAAAAATTGATGTTTTGGAAATGGAATCGGGATT
66 TCAAAAATAACGGGATTGGAGTATCCCCGATAAAAAATTGATGTTTTAGAAATAAAATCGGGATT
*
551089 GGAGTATCC
131 AGAGTATCC
551098 TCGAGACAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
155 37 0.30
157 2 0.02
158 81 0.66
159 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (155 bp):
GTTGGAGTATCCCCGATTATGAGAAATTGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
TCAAAAATAACGGGATTGGAGTATCCCCGATAAAAAATTGATGTTTTAGAAATAAAATCGGGATT
AGAGTATCCCCTCGAAAATAATGGG
Found at i:553412 original size:18 final size:19
Alignment explanation
Indices: 553389--553563 Score: 101
Period size: 20 Copynumber: 8.8 Consensus size: 19
553379 AAAATGTCTG
*
553389 AATGTATCGATAC-ATTAC
1 AATGTATCGATACAATAAC
553407 AATGTATCGATACAATAAGC
1 AATGTATCGATACAATAA-C
553427 AATGTATCGATACAATGCAA-
1 AATGTATCGATACAAT--AAC
*
553447 AATGTATCGATACATCTGGGTAAACC
1 AATGTATCGATACA-----AT-AA-C
* * *
553473 CA-GAAT-G-TATCGAT-AC
1 AATGTATCGATA-CAATAAC
553489 AATGTATCGATACAATGAAC
1 AATGTATCGATACAAT-AAC
*
553509 AATATATCGATACAATGAAC
1 AATGTATCGATACAAT-AAC
* * *
553529 AATATATCGATATAATGTAC
1 AATGTATCGATACAAT-AAC
553549 AATGTATCGATACAA
1 AATGTATCGATACAA
553564 ATTGTGAAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 32
0.73 0.09 0.19
Matches are distributed among these distances:
16 2 0.02
17 4 0.03
18 17 0.14
19 6 0.05
20 83 0.66
22 2 0.02
23 2 0.02
24 4 0.03
25 4 0.03
26 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAATAAC
Found at i:553516 original size:20 final size:20
Alignment explanation
Indices: 553487--553563 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
553477 ATGTATCGAT
*
553487 ACAATGTATCGATACAATGA
1 ACAATATATCGATACAATGA
553507 ACAATATATCGATACAATGA
1 ACAATATATCGATACAATGA
* *
553527 ACAATATATCGATATAATGT
1 ACAATATATCGATACAATGA
*
553547 ACAATGTATCGATACAA
1 ACAATATATCGATACAA
553564 ATTGTGAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (20 bp):
ACAATATATCGATACAATGA
Found at i:553524 original size:13 final size:13
Alignment explanation
Indices: 553476--553505 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
553466 GTAAACCCAG
553476 AATGTATCGATAC
1 AATGTATCGATAC
553489 AATGTATCGATAC
1 AATGTATCGATAC
553502 AATG
1 AATG
553506 AACAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:556444 original size:20 final size:20
Alignment explanation
Indices: 556419--556504 Score: 111
Period size: 20 Copynumber: 4.2 Consensus size: 20
556409 TAAAAAATGC
*
556419 CTTGCTTTTGAATATTATTT
1 CTTGCTTTTGAATATTGTTT
556439 CTTGCTTTTGAATATTGTTT
1 CTTGCTTTTGAATATTGTTT
*
556459 CTTGCTAGTTT-AACCATTGTTT
1 CTTGCT--TTTGAA-TATTGTTT
*
556481 TTTGCTTTTGAATATTGTTT
1 CTTGCTTTTGAATATTGTTT
556501 CTTG
1 CTTG
556505 ATTCTTATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
20 38 0.67
21 4 0.07
22 15 0.26
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (20 bp):
CTTGCTTTTGAATATTGTTT
Found at i:556841 original size:15 final size:15
Alignment explanation
Indices: 556821--556850 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
556811 AGATTTTTGG
556821 AATTAAATTATTATT
1 AATTAAATTATTATT
*
556836 AATTAATTTATTATT
1 AATTAAATTATTATT
556851 TACACGAAAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTAAATTATTATT
Found at i:557576 original size:47 final size:47
Alignment explanation
Indices: 557525--557633 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 47
557515 AATTTAAATG
* *
557525 TCAAACTCAAATTATTTAAATCT-AAAATAACTCAAA-TTTAAATTAAT
1 TCAAACTAAAATTATTTAAAT-TAAAAATAACTCAAATTTTAAA-TAAA
* *
557572 TCAAA-TAAAAATGATTTAAATTAAAAATAACTTAAATTTTAAATAAA
1 TCAAACT-AAAATTATTTAAATTAAAAATAACTCAAATTTTAAATAAA
557619 TCAAACATAAAATTA
1 TCAAAC-TAAAATTA
557634 ATTCAAACGT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
46 2 0.04
47 37 0.71
48 12 0.23
49 1 0.02
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (47 bp):
TCAAACTAAAATTATTTAAATTAAAAATAACTCAAATTTTAAATAAA
Found at i:557596 original size:16 final size:16
Alignment explanation
Indices: 557548--557609 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
557538 ATTTAAATCT
* *
557548 AAAATAACTCAAATTT
1 AAAATAACTTAAATTA
*
557564 AAATTAA-TTCAAA-TA
1 AAAATAACTT-AAATTA
* *
557579 AAAATGATTTAAATTA
1 AAAATAACTTAAATTA
557595 AAAATAACTTAAATT
1 AAAATAACTTAAATT
557610 TTAAATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 10 0.28
16 26 0.72
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATAACTTAAATTA
Found at i:557610 original size:22 final size:22
Alignment explanation
Indices: 557538--557615 Score: 54
Period size: 25 Copynumber: 3.4 Consensus size: 22
557528 AACTCAAATT
*
557538 ATTTAAATCT-AAAATAACTCAA
1 ATTTAAAT-TAAAAATAACTAAA
557560 ATTTAAATTAATTCAAATAA--AAA
1 ATTTAAATTAA---AAATAACTAAA
557583 TGATTTAAATTAAAAATAACTTAAA
1 --ATTTAAATTAAAAATAAC-TAAA
*
557608 TTTTAAAT
1 ATTTAAAT
557616 AAATCAAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
21 1 0.02
22 15 0.33
23 9 0.20
25 20 0.44
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.37
Consensus pattern (22 bp):
ATTTAAATTAAAAATAACTAAA
Found at i:557961 original size:9 final size:10
Alignment explanation
Indices: 557934--558053 Score: 56
Period size: 9 Copynumber: 12.0 Consensus size: 10
557924 ATTATACAAA
557934 TATAATAT-T
1 TATAATATAT
*
557943 TATAAAATAT
1 TATAATATAT
557953 T-TAATATAT
1 TATAATATAT
557962 GATATAATATGA-
1 --TATAATAT-AT
557974 -AT-ATATAT
1 TATAATATAT
*
557982 TAAAATATA-
1 TATAATATAT
557991 TATAATATGAAT
1 TATAATAT--AT
* *
558003 GATTAATTTAT
1 TA-TAATATAT
* *
558014 TAAAATATTT
1 TATAATATAT
558024 TA-AATATAAT
1 TATAATAT-AT
*
558034 TATAATATAA
1 TATAATATAT
*
558044 TAAAATATAT
1 TATAATATAT
558054 AAAATGTAAC
Statistics
Matches: 83, Mismatches: 14, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
7 1 0.01
8 4 0.05
9 29 0.35
10 26 0.31
11 10 0.12
12 7 0.08
13 6 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (10 bp):
TATAATATAT
Found at i:557988 original size:18 final size:16
Alignment explanation
Indices: 557926--558052 Score: 66
Period size: 18 Copynumber: 7.7 Consensus size: 16
557916 TAAATATGAT
*
557926 TATACAAATATAATATT
1 TATA-AAATATAATATA
557943 TATAAAATATTTAATATA
1 TATAAAATA--TAATATA
*
557961 TGATATAATATGAATATA
1 T-ATAAAATAT-AATATA
557979 TATTAAAATAT-ATATA
1 TA-TAAAATATAATATA
* *
557995 -ATATGAATGATTAATTTA
1 TATA-AAAT-A-TAATATA
** *
558013 T-TAAAATATTTTAAA
1 TATAAAATATAATATA
*
558028 TAT-AATTATAATATA
1 TATAAAATATAATATA
558043 -ATAAAATATA
1 TATAAAATATA
558053 TAAAATGTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
14 4 0.05
15 22 0.27
16 13 0.16
17 10 0.12
18 27 0.33
19 7 0.08
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.43
Consensus pattern (16 bp):
TATAAAATATAATATA
Found at i:558015 original size:32 final size:31
Alignment explanation
Indices: 557976--558090 Score: 93
Period size: 30 Copynumber: 3.9 Consensus size: 31
557966 TAATATGAAT
557976 ATATATTAAAATATATAT-AATATGAATGATTA
1 ATATATTAAAATATATATAAATAT-AATGA-TA
* * *
558008 ATTTATTAAAATAT-TTTAAATATAATTATA
1 ATATATTAAAATATATATAAATATAATGATA
* * *
558038 ATATAATAAAATATATA-AAATGTAA-CATA
1 ATATATTAAAATATATATAAATATAATGATA
558067 A-ATA-TATAAAT-TATA-AAATATAAT
1 ATATATTA-AAATATATATAAATATAAT
558091 CTTACTATTT
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
27 13 0.19
28 7 0.10
29 4 0.06
30 21 0.30
31 7 0.10
32 18 0.26
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (31 bp):
ATATATTAAAATATATATAAATATAATGATA
Found at i:558894 original size:13 final size:13
Alignment explanation
Indices: 558878--558902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
558868 TATATTAAAA
558878 ATAAATATATATC
1 ATAAATATATATC
558891 ATAAATATATAT
1 ATAAATATATAT
558903 AATATTATAA
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAATATATATC
Found at i:558896 original size:17 final size:18
Alignment explanation
Indices: 558876--558921 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
558866 TTTATATTAA
558876 AAATAAATAT-ATATCAT
1 AAATAAATATAATATCAT
* *
558893 AAATATATATAATATTAT
1 AAATAAATATAATATCAT
558911 AATATAAATAT
1 AA-ATAAATAT
558922 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.38
18 8 0.33
19 7 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAAATATAATATCAT
Found at i:559137 original size:3 final size:3
Alignment explanation
Indices: 559129--559164 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
559119 AACAAATATG
559129 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
559165 TATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:559169 original size:3 final size:3
Alignment explanation
Indices: 559163--559191 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
559153 AATAATAATA
559163 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
559192 GCTTTTGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:559246 original size:14 final size:14
Alignment explanation
Indices: 559227--559260 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
559217 ATATTTTATA
559227 AATAAATAAA-AGTT
1 AATAAATAAATA-TT
559241 AATAAATAAATATT
1 AATAAATAAATATT
559255 AATAAA
1 AATAAA
559261 AATTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AATAAATAAATATT
Found at i:560595 original size:2 final size:2
Alignment explanation
Indices: 560588--560616 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
560578 AAGAATTGCT
560588 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
560617 GCCACAAGAT
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:562894 original size:33 final size:33
Alignment explanation
Indices: 562833--562903 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
562823 ATTCTCTCAT
* *
562833 TGATACATTTAAGATGGAGGATATATTTAAAGA
1 TGATACATTTAAGATAGAGGATACATTTAAAGA
** * * *
562866 TGATACATTTGTGATAGATGATACATTTAGAGT
1 TGATACATTTAAGATAGAGGATACATTTAAAGA
562899 TGATA
1 TGATA
562904 AGGATAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (33 bp):
TGATACATTTAAGATAGAGGATACATTTAAAGA
Found at i:563960 original size:19 final size:16
Alignment explanation
Indices: 563938--563977 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
563928 TAGCTACACT
563938 AATAAAAAATAGAATAATA
1 AATAAAAAAT-GAA-AA-A
563957 AATAAAAAATGAAAAA
1 AATAAAAAATGAAAAA
563973 AATAA
1 AATAA
563978 TTACATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 2 0.10
18 3 0.14
19 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (16 bp):
AATAAAAAATGAAAAA
Found at i:566877 original size:13 final size:13
Alignment explanation
Indices: 566859--566884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
566849 CAATTTTTTG
566859 TGTATCGATACAT
1 TGTATCGATACAT
566872 TGTATCGATACAT
1 TGTATCGATACAT
566885 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:567636 original size:45 final size:47
Alignment explanation
Indices: 567587--567686 Score: 150
Period size: 49 Copynumber: 2.1 Consensus size: 47
567577 ATCTCCCCCG
567587 TTTATT-A-ATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAA
1 TTTATTCACATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAA
**
567632 TTTATTTGCACATACCTCTCCCCCTTAATCAAGTAATTCACATCAAAAA
1 TTTA-TT-CACATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAA
567681 TTTATT
1 TTTATT
567687 TGCACATACC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
45 4 0.08
46 2 0.04
48 3 0.06
49 40 0.82
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (47 bp):
TTTATTCACATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAA
Found at i:567655 original size:49 final size:49
Alignment explanation
Indices: 567599--567697 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
567589 TATTAATAAA
567599 TCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATACC
1 TCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATACC
567648 TCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATACC
1 TCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATACC
567697 T
1 T
567698 ATTTTCTCTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (49 bp):
TCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATACC
Found at i:569509 original size:13 final size:13
Alignment explanation
Indices: 569471--569509 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
569461 ATAATCACCC
*
569471 TGTATCGATACAC
1 TGTATCGATACAA
569484 TGTATCGATACAA
1 TGTATCGATACAA
569497 TGTATCGATACAA
1 TGTATCGATACAA
569510 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Done.