Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 168 of 199
Found at i:49178935 original size:24 final size:23
Alignment explanation
Indices: 49178884--49178953 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
49178874 TATTATTTAT
* *
49178884 TTTAATTTGTTTTACATATTATTTAC
1 TTTAAATTGTTTT--ATA-TATTCAC
49178910 TTTAAATTGTTTTATACTATTCAC
1 TTTAAATTGTTTTATA-TATTCAC
* *
49178934 TTCAAATTGTTCTATATATT
1 TTTAAATTGTTTTATATATT
49178954 ATTTTGTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 4 0.10
24 23 0.59
26 12 0.31
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTAAATTGTTTTATATATTCAC
Found at i:49184024 original size:1 final size:1
Alignment explanation
Indices: 49184020--49184073 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
49184010 TTACTTTTTT
* * * ** *
49184020 AAAAAAAAAGAAAAAAAAAAGAAAAAAAAGAAAACGAAAATAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
49184074 GGAGAAGCCG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.02, G:0.07, T:0.02
Consensus pattern (1 bp):
A
Found at i:49184036 original size:11 final size:11
Alignment explanation
Indices: 49184020--49184070 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
49184010 TTACTTTTTT
49184020 AAAAAAAAAGA
1 AAAAAAAAAGA
49184031 AAAAAAAAAG-
1 AAAAAAAAAGA
49184041 -AAAAAAAAGA
1 AAAAAAAAAGA
** *
49184051 AAACGAAAATA
1 AAAAAAAAAGA
49184062 AAAAAAAAA
1 AAAAAAAAA
49184071 AAAGGAGAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 9 0.27
11 24 0.73
ACGTcount: A:0.88, C:0.02, G:0.08, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:49184044 original size:20 final size:20
Alignment explanation
Indices: 49184021--49184073 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
49184011 TACTTTTTTA
49184021 AAAAAAAAGAAAAAAAAAAG
1 AAAAAAAAGAAAAAAAAAAG
** *
49184041 AAAAAAAAGAAAACGAAAAT
1 AAAAAAAAGAAAAAAAAAAG
49184061 AAAAAAAA-AAAAA
1 AAAAAAAAGAAAAA
49184074 GGAGAAGCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.89, C:0.02, G:0.08, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAAAAG
Found at i:49186234 original size:48 final size:45
Alignment explanation
Indices: 49186178--49186331 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 45
49186168 AATCCTATAC
49186178 CCTTGAAGTTGCAGTGGGATGGATTGAAGATCATATCAAACCTTATCT
1 CCTTGAAGTTGCAGTGGGATGGATTGAAGAT--TA-CAAACCTTATCT
* * **
49186226 CCTTGAAGTTACAGT-GGAGTAGG-TTGAAG-TTACTAGTCTTATCT
1 CCTTGAAGTTGCAGTGGGA-T-GGATTGAAGATTACAAACCTTATCT
* * * *
49186270 CCTTGAAGTTGCAGTGGAGA-AGATTGAAGA-TAGCGAATCTTATTT
1 CCTTGAAGTTGCAGTGG-GATGGATTGAAGATTA-CAAACCTTATCT
*
49186315 CCCTGAAGTTGCAGTGG
1 CCTTGAAGTTGCAGTGG
49186332 AACAGATTGA
Statistics
Matches: 89, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
43 1 0.01
44 31 0.35
45 28 0.31
46 2 0.02
47 4 0.04
48 21 0.24
49 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (45 bp):
CCTTGAAGTTGCAGTGGGATGGATTGAAGATTACAAACCTTATCT
Found at i:49186325 original size:45 final size:43
Alignment explanation
Indices: 49186219--49186890 Score: 368
Period size: 44 Copynumber: 14.8 Consensus size: 43
49186209 CATATCAAAC
* * * * * *
49186219 CTTATCTCCTTGAAGTTACAGTGGAGTAGGTTGAAGTTACTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AAT
* *
49186263 CTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-C-AAT
* *
49186308 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG------A-TACA-AT
* * * * * *
49186359 CTTATCTCTCTAAAGTTGTAGTAGAGCAGA-TCATG-T-CAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAT
* * * *
49186399 CATTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGT
1 C-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AAT
* *
49186444 CTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-C-AAT
* * *
49186489 CTTATTTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG------A-TACA-AT
* * * * * *
49186540 CTTATCTCTCTGAAGTTGCAATAGAGCAGA-T-CATAT-CAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AAT
* * * * * * *
49186581 CTAATCTCCCTGAAGTTGTAGTGAAGTAGGTTGAAGTTACTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AAT
* * *
49186625 CTTATCTCCTTGAAGTTGCAGTGGAGTAGACTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-C-AAT
* * *
49186670 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G--A-AGA-TA---CA-AT
* * * ** **
49186724 CTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAGCCACTAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AAT
** *
49186768 CTTATCTCCCTGAAGTTGTGGTGGAGCAGACTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAT
* * * * *
49186812 CTTATCTCCCTAAAGTTACAGTGGAGCAAATTAAAGCTACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AAT
* *
49186856 CCTATCTCTCTGAAGTTGCAGTGGAGC-GAATTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTGAA
49186891 ACGATAAATT
Statistics
Matches: 475, Mismatches: 111, Indels: 84
0.71 0.17 0.13
Matches are distributed among these distances:
40 3 0.01
41 49 0.10
42 7 0.01
43 5 0.01
44 198 0.42
45 104 0.22
47 1 0.00
48 2 0.00
49 2 0.00
50 7 0.01
51 58 0.12
52 6 0.01
53 1 0.00
54 32 0.07
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAT
Found at i:49186434 original size:92 final size:91
Alignment explanation
Indices: 49186305--49186754 Score: 329
Period size: 92 Copynumber: 4.9 Consensus size: 91
49186295 GAAGATAGCG
* *
49186305 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTATCTCTCT
1 AATCTTATCTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTACAGATCTTATCTCTCT
* *
49186370 AAAGTTGTAGTAGAGCAGATCATGTC
66 GAAGTTGCAGTAGAGCAGATCATGTC
* * * * * *
49186396 AATCATTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAAG-T-T--ACT--AG-TCTTATCTCCC
1 AATC-TTATCTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTACAGATCTTATCTCTC
* * * *
49186454 TGAAGTTACAGTGGAGCAGACTGAAGATAGC
65 TGAAGTTGCAGTAGAGCAGA-TCATG-T--C
*
49186485 GAATCTTATTTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTACAGATCTTATCTCTC
1 -AATCTTATCTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTACAGATCTTATCTCTC
* *
49186550 TGAAGTTGCAATAGAGCAGATCATATC
65 TGAAGTTGCAGTAGAGCAGATCATGTC
* * * ** * *
49186577 AAACCTAATCTCCCTGAAGTTGTAGTGAAGTAGGTTGAAG-T-T--ACT--AG-TCTTATCTC-C
1 -AATCTTATCTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTACAGATCTTATCTCTC
* * * *
49186634 TTGAAGTTGCAGTGGAGTAGACTGAAGATAGC
65 -TGAAGTTGCAGTAGAGCAGA-TCATG-T--C
* * * *
49186666 GAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCAGATCTTATCT
1 -AATCTTATCTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTA---CAGATCTTATCT
* *
49186731 -TCCTGAAGTTACAGTGGAGCAGAT
62 CT-CTGAAGTTGCAGTAGAGCAGAT
49186755 TAAAGCCACT
Statistics
Matches: 275, Mismatches: 54, Indels: 53
0.72 0.14 0.14
Matches are distributed among these distances:
84 1 0.00
85 52 0.19
86 9 0.03
87 2 0.01
88 4 0.01
89 62 0.23
90 8 0.03
91 7 0.03
92 64 0.23
93 4 0.01
94 1 0.00
95 4 0.01
96 27 0.10
98 3 0.01
99 26 0.09
100 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (91 bp):
AATCTTATCTCCCTGAAGTTGCAGTGAAACAGATTGAAGCTATAAATTACAGATCTTATCTCTCT
GAAGTTGCAGTAGAGCAGATCATGTC
Found at i:49186509 original size:181 final size:181
Alignment explanation
Indices: 49186205--49186880 Score: 861
Period size: 181 Copynumber: 3.7 Consensus size: 181
49186195 GATGGATTGA
* * *
49186205 AGATCATATCAAACCTTATCTCCTTGAAGTTACAGTGGAGTAGGTTGAAGTTACTAGTCTTATCT
1 AGATCATATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCT
* * * *
49186270 CCTTGAAGTTGCAGTGGAGAAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAAC
66 CCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAAC
* *
49186335 AGATTGAAGCTATAAATTACAGATCTTATCTCTCTAAAGTTGTAGTAGAGC
131 AGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
* * * *
49186386 AGATCATGTCAATCATTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCT
1 AGATCATATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCT
*
49186451 CCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGAAAC
66 CCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAAC
*
49186516 AGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGC
131 AGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
* * * *
49186567 AGATCATATCAAACCTAATCTCCCTGAAGTTGTAGTGAAGTAGGTTGAAGTTACTAGTCTTATCT
1 AGATCATATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCT
* * *
49186632 CCTTGAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAAC
66 CCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAAC
* * * *
49186697 AGATTAAAGCTACAAATTATGGCAGATCTTATCT-TCCTGAAGTTACAGTGGAGC
131 AGATTGAAGCTATAAATTA---CAGATCTTATCTCT-CTGAAGTTGCAGTAGAGC
* * * * ** ** * * *
49186751 AGATTAAAGCCACTAGCCTTATCTCCCTGAAGTTGTGGTGGAGCAGACTGAAGATACCAATCTTA
1 AGATCATA-TCA--AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTA
* * * * * * * * *
49186816 TCTCCCTAAAGTTACAGTGGAGCAAATTAAAGCTA-CTAATCCTATCTCTCTGAAGTTGCAGTGG
63 TCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGG
49186880 A
128 A
49186881 GCGAATTGAA
Statistics
Matches: 433, Mismatches: 55, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
181 303 0.70
183 1 0.00
184 33 0.08
185 2 0.00
186 26 0.06
187 68 0.16
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (181 bp):
AGATCATATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCT
CCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAAC
AGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
Found at i:49188078 original size:7 final size:7
Alignment explanation
Indices: 49188066--49188093 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
49188056 GTCCCTTTGA
49188066 TTTATTT
1 TTTATTT
49188073 TTTATTT
1 TTTATTT
49188080 TTTATTT
1 TTTATTT
49188087 TTTATTT
1 TTTATTT
49188094 AATTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:49188376 original size:29 final size:25
Alignment explanation
Indices: 49188336--49188399 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 25
49188326 TGTTATTCAT
*
49188336 TTATTTATTTTAAACCTTTTTCTTATATA
1 TTATTTATTTTAAA--TTATT-TTAT-TA
49188365 TTATTTATTTTAAATTATTTTATTA
1 TTATTTATTTTAAATTATTTTATTA
49188390 TTATTTATTT
1 TTATTTATTT
49188400 CAAGTTTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.35
26 4 0.12
27 4 0.12
29 14 0.41
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATTTATTTTAAATTATTTTATTA
Found at i:49188391 original size:25 final size:28
Alignment explanation
Indices: 49188336--49188731 Score: 104
Period size: 26 Copynumber: 15.4 Consensus size: 28
49188326 TGTTATTCAT
*
49188336 TTATTTATTTTAAACCTTTTTCTTATATA
1 TTATTTATTTTAAA-CTTATTCTTATATA
49188365 TTATTTATTTTAAA-TTATT-TTAT-TA
1 TTATTTATTTTAAACTTATTCTTATATA
* * * *
49188390 TTATTTA-TTTCAAGTT-TTC-CATATG
1 TTATTTATTTTAAACTTATTCTTATATA
* * * *
49188415 TCATGTATTTTAAAC-TATT-TCAAACTA
1 TTATTTATTTTAAACTTATTCTTATA-TA
* *
49188442 TTATCTA--TT----TT-TT-GTATATA
1 TTATTTATTTTAAACTTATTCTTATATA
*
49188462 TTATTTATTTTTAAAC-TATT-ATATATA
1 TTATTTA-TTTTAAACTTATTCTTATATA
* * *
49188489 TTATTTATTTTGAA-TTGTTTTTATATA
1 TTATTTATTTTAAACTTATTCTTATATA
* * *
49188516 CCTCATTTATTTTTTAAAC-TGTT-TTGTATA
1 --TTATTTA--TTTTAAACTTATTCTTATATA
* * * * *
49188546 TTAGTTATTTGAAACTTCTTTTTACATA
1 TTATTTATTTTAAACTTATTCTTATATA
49188574 TTATTTATTTTAAA--T-TT-TT-TATA
1 TTATTTATTTTAAACTTATTCTTATATA
* * *
49188597 -TA-TTATTTTAAA-TT-GTCTCATATG
1 TTATTTATTTTAAACTTATTCTTATATA
** * *
49188621 TTATTTATTTTAAA-TTGCT-TTGTGTA
1 TTATTTATTTTAAACTTATTCTTATATA
49188647 TTATTTATTTT-AA-TT-TGT-TTATATA
1 TTATTTATTTTAAACTTAT-TCTTATATA
* *
49188672 TTATTTACTTTAAA-TT-GT-TT-TATA
1 TTATTTATTTTAAACTTATTCTTATATA
* * *
49188696 CTATTTACTTCAAA-TTATTC-TATATA
1 TTATTTATTTTAAACTTATTCTTATATA
49188722 TTATTT-TTTT
1 TTATTTATTTT
49188732 CGTTTTCTTT
Statistics
Matches: 280, Mismatches: 51, Indels: 76
0.69 0.13 0.19
Matches are distributed among these distances:
20 8 0.03
21 14 0.05
22 5 0.02
23 6 0.02
24 32 0.11
25 51 0.18
26 71 0.25
27 35 0.12
28 22 0.08
29 20 0.07
30 6 0.02
31 10 0.04
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (28 bp):
TTATTTATTTTAAACTTATTCTTATATA
Found at i:49188490 original size:20 final size:19
Alignment explanation
Indices: 49188436--49188495 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
49188426 AAACTATTTC
*
49188436 AAACTATTATCTATTTTTTGT
1 AAACTATTAT-TATATTTT-T
*
49188457 ATA-TATTATT-TATTTTT
1 AAACTATTATTATATTTTT
49188474 AAACTATTATATATATTATTT
1 AAACTATTAT-TATATT-TTT
49188495 A
1 A
49188496 TTTTGAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 3 0.09
18 11 0.34
19 2 0.06
20 10 0.31
21 6 0.19
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (19 bp):
AAACTATTATTATATTTTT
Found at i:49188524 original size:56 final size:55
Alignment explanation
Indices: 49188459--49188604 Score: 147
Period size: 57 Copynumber: 2.7 Consensus size: 55
49188449 TTTTTTGTAT
* * * *
49188459 ATATTATTTATTTTTAAACTATTATATATATTATTTATTTTG-AA-TTGTTTTTAT
1 ATATCATTTATTTTTAAACTATTTTATATATTATTTA-TTTGAAACTTCTTTTTAC
* * *
49188513 ATACCTCATTTATTTTTTAAACTGTTTTGTATATTAGTTATTTGAAACTTCTTTTTAC
1 ATA--TCATTTA-TTTTTAAACTATTTTATATATTATTTATTTGAAACTTCTTTTTAC
* *
49188571 ATATTATTTA-TTTTAAA-TTTTTTATATATTATTT
1 ATATCATTTATTTTTAAACTATTTTATATATTATTT
49188605 TAAATTGTCT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
53 14 0.18
54 10 0.13
56 16 0.21
57 25 0.33
58 11 0.14
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.61
Consensus pattern (55 bp):
ATATCATTTATTTTTAAACTATTTTATATATTATTTATTTGAAACTTCTTTTTAC
Found at i:49188604 original size:21 final size:23
Alignment explanation
Indices: 49188575--49188728 Score: 125
Period size: 26 Copynumber: 6.4 Consensus size: 23
49188565 TTTTACATAT
49188575 TATTTATTTTAAATT-TTTTATA
1 TATTTATTTTAAATTGTTTTATA
* *
49188597 TA-TTATTTTAAATTGTCTCATATGT
1 TATTTATTTTAAATTGT-T-TTAT-A
*
49188622 TATTTATTTTAAATTGCTTTGTGTA
1 TATTTATTTTAAATTG-TTT-TATA
*
49188647 TTATTTATTTTAATTTGTTTATATA
1 -TATTTATTTTAAATTGTTT-TATA
*
49188672 TTATTTACTTTAAATTGTTTTATA
1 -TATTTATTTTAAATTGTTTTATA
* * * *
49188696 CTATTTACTTCAAATTATTCTATA
1 -TATTTATTTTAAATTGTTTTATA
49188720 TA-TTATTTT
1 TATTTATTTT
49188729 TTTCGTTTTC
Statistics
Matches: 108, Mismatches: 16, Indels: 16
0.77 0.11 0.11
Matches are distributed among these distances:
21 12 0.11
22 8 0.07
23 3 0.03
24 27 0.25
25 26 0.24
26 31 0.29
27 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (23 bp):
TATTTATTTTAAATTGTTTTATA
Found at i:49188619 original size:22 final size:21
Alignment explanation
Indices: 49188578--49188626 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
49188568 TACATATTAT
* *
49188578 TTATTTTAAATTTTTTATATA
1 TTATTTTAAATTTCTCATATA
*
49188599 TTATTTTAAATTGTCTCATATG
1 TTATTTTAAATT-TCTCATATA
49188621 TTATTT
1 TTATTT
49188627 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (21 bp):
TTATTTTAAATTTCTCATATA
Found at i:49192424 original size:22 final size:22
Alignment explanation
Indices: 49192399--49192443 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
49192389 ATATTATAAC
49192399 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
49192421 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
49192443 T
1 T
49192444 AAAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTTTATTTACCAAAATATA
Found at i:49192542 original size:27 final size:27
Alignment explanation
Indices: 49192503--49192575 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
49192493 CCTTGGTCAC
* *
49192503 GCCAAAACGATTGGCGGCACCAAAGGT
1 GCCAAAGCCATTGGCGGCACCAAAGGT
* *
49192530 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAAAGCCATTGGCGGCACCAAAGGT
*
49192557 GCCAAAGGCATTGGCGGCA
1 GCCAAAGCCATTGGCGGCA
49192576 TTACTCGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (27 bp):
GCCAAAGCCATTGGCGGCACCAAAGGT
Found at i:49192815 original size:3 final size:3
Alignment explanation
Indices: 49192809--49192840 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
49192799 ATTATTATTA
49192809 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
49192841 AGTATTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:49193021 original size:27 final size:27
Alignment explanation
Indices: 49192991--49193043 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
49192981 AATTGGTAGG
*
49192991 TACATGCATGGACGGCATTGAAGATAA
1 TACATGCATGGACGGCAATGAAGATAA
49193018 TACATGCATGGACGGCAATGAAGATA
1 TACATGCATGGACGGCAATGAAGATA
49193044 CTTCAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACGGCAATGAAGATAA
Found at i:49197758 original size:15 final size:15
Alignment explanation
Indices: 49197738--49197766 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49197728 GTCTCGAGAA
49197738 GAATTCTCTGCCGAT
1 GAATTCTCTGCCGAT
49197753 GAATTCTCTGCCGA
1 GAATTCTCTGCCGA
49197767 GGATTATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (15 bp):
GAATTCTCTGCCGAT
Found at i:49199047 original size:18 final size:16
Alignment explanation
Indices: 49199024--49199063 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
49199014 AAATCCTTGT
49199024 TAAAATAAAATACAATAG
1 TAAAATAAAATA-AA-AG
49199042 TAAAATAAAATAAAAG
1 TAAAATAAAATAAAAG
49199058 TAAAAT
1 TAAAAT
49199064 TTATATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (16 bp):
TAAAATAAAATAAAAG
Found at i:49199320 original size:7 final size:6
Alignment explanation
Indices: 49199290--49199316 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
49199280 ATCTGTGTGC
49199290 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
49199317 TATTATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:49200711 original size:31 final size:30
Alignment explanation
Indices: 49200676--49200737 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
49200666 GTCCCTCATG
*
49200676 TTAGATAAATTATTGATTTGAGTCACTTCTA
1 TTAGATAAATTATTAATTTGAGTCAC-TCTA
* * *
49200707 TTAGATAAGTTGTTAATTTTAGTCACTCTA
1 TTAGATAAATTATTAATTTGAGTCACTCTA
49200737 T
1 T
49200738 CATTAAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (30 bp):
TTAGATAAATTATTAATTTGAGTCACTCTA
Found at i:49201400 original size:2 final size:2
Alignment explanation
Indices: 49201395--49201453 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
49201385 AGTAGTAGTA
49201395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49201437 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
49201454 ACTTTGGTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49201932 original size:17 final size:17
Alignment explanation
Indices: 49201910--49201952 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
49201900 ATTTAGGGTT
49201910 TAAGAAGAGAAA-AAGAA
1 TAAGAAGA-AAAGAAGAA
*
49201927 TAAGAAGAAAAGGAGAA
1 TAAGAAGAAAAGAAGAA
49201944 TAAGAAGAA
1 TAAGAAGAA
49201953 GAAGGAGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.07
Consensus pattern (17 bp):
TAAGAAGAAAAGAAGAA
Found at i:49202885 original size:3 final size:3
Alignment explanation
Indices: 49202877--49202921 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
49202867 AATAAAATGC
*
49202877 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49202922 TGTAATAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49209388 original size:3 final size:3
Alignment explanation
Indices: 49209380--49209407 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49209370 GATAAGTCTT
49209380 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
49209408 GAATTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49213776 original size:2 final size:2
Alignment explanation
Indices: 49213769--49213795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49213759 TGCAGCAGAT
49213769 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
49213796 CAAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49219995 original size:69 final size:69
Alignment explanation
Indices: 49219884--49220241 Score: 466
Period size: 69 Copynumber: 5.2 Consensus size: 69
49219874 TATGATGTAT
* * * * * ** *
49219884 TATGTATATGCTGCCCATTTGTTGTATATATACTATTCAATTTTGGTGTAAAATTGCTACTCAAT
1 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
49219949 TTGG
66 TTGG
* * * *
49219953 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTTGTGTAAAAATGCTGCTCAAT
1 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
*
49220018 TTAG
66 TTGG
* * *
49220022 TATGTATATGATGCCCATTTGTTGTATATATGTTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
1 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
49220087 TTGG
66 TTGG
* * * * *
49220091 TATGTATATGTTGCCTATTTGCTATATATATGCTGTTAAATTTTGGTGTAAAAGTGCTATTAAAA
1 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
49220156 TTGG
66 TTGG
** *
49220160 TATGTATATGCTGCCTATTTACTGTATATATGCTGTTAAATTTTGGTGTATAAA-TGCTGTTTAA
1 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTA-AAAGTGCTGTTAAA
49220224 TTTGG
65 TTTGG
* *
49220229 TATATAAATGCTG
1 TATGTATATGCTG
49220242 TCCAAATTGA
Statistics
Matches: 257, Mismatches: 31, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
69 254 0.99
70 3 0.01
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (69 bp):
TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
TTGG
Found at i:49220209 original size:24 final size:23
Alignment explanation
Indices: 49219969--49220242 Score: 121
Period size: 24 Copynumber: 11.9 Consensus size: 23
49219959 TATGCTGCCT
*
49219969 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTGTTAA
* * * * *
49219992 ATTTTTGTGTAAAAATGCTGCTCA
1 A-TTTGGTGTATATATGCTGTTAA
* * * * ***
49220016 ATTTAGTATGTATATGATG-CCC
1 ATTTGGTGTATATATGCTGTTAA
* *
49220038 ATTTGTTGTATATATGTTGTTAA
1 ATTTGGTGTATATATGCTGTTAA
*
49220061 ATTTTGGTGTA-AAAGTGCTGTTAA
1 A-TTTGGTGTATATA-TGCTGTTAA
* * * *
49220085 ATTTGGTATGTATATGTTGCCT--
1 ATTTGGTGTATATATGCTG-TTAA
* *
49220107 ATTTGCTATATATATGCTGTTAA
1 ATTTGGTGTATATATGCTGTTAA
* *
49220130 ATTTTGGTGTA-AAAGTGCTATTAA
1 A-TTTGGTGTATATA-TGCTGTTAA
* * * *
49220154 AATTGGTATGTATATGCTGCCT--
1 ATTTGGTGTATATATGCTG-TTAA
**
49220176 ATTTACTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTGTTAA
* *
49220199 ATTTTGGTGTATAAATGCTGTTTA
1 A-TTTGGTGTATATATGCTGTTAA
* *
49220223 ATTTGGTATATAAATGCTGT
1 ATTTGGTGTATATATGCTGT
49220243 CCAAATTGAT
Statistics
Matches: 181, Mismatches: 55, Indels: 30
0.68 0.21 0.11
Matches are distributed among these distances:
21 2 0.01
22 45 0.25
23 59 0.33
24 75 0.41
ACGTcount: A:0.27, C:0.07, G:0.19, T:0.46
Consensus pattern (23 bp):
ATTTGGTGTATATATGCTGTTAA
Found at i:49220234 original size:23 final size:24
Alignment explanation
Indices: 49220046--49220242 Score: 96
Period size: 23 Copynumber: 8.5 Consensus size: 24
49220036 CCATTTGTTG
* * *
49220046 TATATATGTTGTTAAATTTTGGTG
1 TATAAATGCTGTTAAATTTTGGTA
49220070 TA-AAAGTGCTGTTAAA-TTTGGTA
1 TATAAA-TGCTGTTAAATTTTGGTA
* * * * *
49220093 TGTATATGTTGCCT--A-TTTGCTA
1 TATAAATGCTG-TTAAATTTTGGTA
* *
49220115 TATATATGCTGTTAAATTTTGGTG
1 TATAAATGCTGTTAAATTTTGGTA
* *
49220139 TA-AAAGTGCTATTAAA-ATTGGTA
1 TATAAA-TGCTGTTAAATTTTGGTA
* * *
49220162 TGTATATGCTGCCT--ATTTACT-GTA
1 TATAAATGCTG-TTAAATTT--TGGTA
*
49220186 TAT--ATGCTGTTAAATTTTGGTG
1 TATAAATGCTGTTAAATTTTGGTA
*
49220208 TATAAATGCTGTTTAA-TTTGGTA
1 TATAAATGCTGTTAAATTTTGGTA
49220231 TATAAATGCTGT
1 TATAAATGCTGT
49220243 CCAAATTGAT
Statistics
Matches: 129, Mismatches: 27, Indels: 35
0.68 0.14 0.18
Matches are distributed among these distances:
21 3 0.02
22 28 0.22
23 49 0.38
24 48 0.37
25 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (24 bp):
TATAAATGCTGTTAAATTTTGGTA
Found at i:49220249 original size:24 final size:23
Alignment explanation
Indices: 49220182--49220266 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
49220172 GCCTATTTAC
* *
49220182 TGTATATATGCTGTTAAATTTTGG
1 TGTATAAATGCTGTCAAA-TTTGG
**
49220206 TGTATAAATGCTGTTTAATTTGG
1 TGTATAAATGCTGTCAAATTTGG
* *
49220229 TATATAAATGCTGTCCAAA-TTGA
1 TGTATAAATGCTGT-CAAATTTGG
49220252 TGTATAAGA-GCTGTC
1 TGTATAA-ATGCTGTC
49220267 CAAACAAGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 19 0.37
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (23 bp):
TGTATAAATGCTGTCAAATTTGG
Found at i:49221406 original size:14 final size:14
Alignment explanation
Indices: 49221387--49221414 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49221377 AAGCATACAT
49221387 TTGCTAAATACTAA
1 TTGCTAAATACTAA
49221401 TTGCTAAATACTAA
1 TTGCTAAATACTAA
49221415 CTAAAAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TTGCTAAATACTAA
Found at i:49230086 original size:16 final size:16
Alignment explanation
Indices: 49230065--49230099 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
49230055 TCTCTCTTCA
49230065 TCTTCTTCCTCTCAAT
1 TCTTCTTCCTCTCAAT
49230081 TCTTCTTCCTCTCAAT
1 TCTTCTTCCTCTCAAT
49230097 TCT
1 TCT
49230100 CTTTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.37, G:0.00, T:0.51
Consensus pattern (16 bp):
TCTTCTTCCTCTCAAT
Found at i:49233437 original size:30 final size:31
Alignment explanation
Indices: 49233413--49233471 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
49233403 GTAAATACTC
* **
49233413 AAAATTTGAAGGGTTAA-AGTGTAAATATGA
1 AAAAGTTGAAGGACTAATAGTGTAAATATGA
49233443 AAAAGTTGAAGGACTAATAGTGTAAATAT
1 AAAAGTTGAAGGACTAATAGTGTAAATAT
49233472 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (31 bp):
AAAAGTTGAAGGACTAATAGTGTAAATATGA
Found at i:49235791 original size:45 final size:45
Alignment explanation
Indices: 49235726--49235871 Score: 238
Period size: 45 Copynumber: 3.2 Consensus size: 45
49235716 ATGTGCCGAC
* *
49235726 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
*
49235771 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
49235816 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
49235861 TACTGTTACTG
1 TACTGTTACTG
49235872 CTACTGTTAC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 94 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:49235866 original size:6 final size:6
Alignment explanation
Indices: 49235855--49235903 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
49235845 GTGTGTTGAA
* *
49235855 TACTGT TACTGT TACTGC TACTGT TACCGT TACTGAT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG-T TACTG
49235904 GTGTGTTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
6 25 0.68
7 12 0.32
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:49240776 original size:44 final size:43
Alignment explanation
Indices: 49240694--49240777 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
49240684 TAAAAATTAC
* ***
49240694 AAAAAATTAAAATATTTGTAAAAATTTCAAATTTTATATATTT
1 AAAAAATTAAAATATTTGTAAAAAATTCAAAAAATATATATTT
*
49240737 AAAAAATTATAAA-ATTTTTAAAAAATTCTAAAAAATATATA
1 AAAAAATTA-AAATATTTGTAAAAAATTC-AAAAAATATATA
49240778 AAGAAAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 22 0.65
44 12 0.35
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (43 bp):
AAAAAATTAAAATATTTGTAAAAAATTCAAAAAATATATATTT
Found at i:49240803 original size:19 final size:19
Alignment explanation
Indices: 49240752--49240812 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
49240742 ATTATAAAAT
* *
49240752 TTTTAAAAAATTCTAAAAAA
1 TTTTAAAAAAGTC-AAAAGA
*
49240772 TATATAAAGAAAGTCAAAAGA
1 T-TTTAAA-AAAGTCAAAAGA
*
49240793 TTTTAAAAAAGTTAAAAGA
1 TTTTAAAAAAGTCAAAAGA
49240812 T
1 T
49240813 AATAATTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 12 0.35
20 6 0.18
21 11 0.32
22 5 0.15
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (19 bp):
TTTTAAAAAAGTCAAAAGA
Found at i:49244173 original size:107 final size:107
Alignment explanation
Indices: 49243987--49244287 Score: 498
Period size: 107 Copynumber: 2.8 Consensus size: 107
49243977 GAGGTGAAAG
* *
49243987 AGGATATTTGGCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTA-GGACATGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGA-ACGTTTTCTC
*
49244051 GAATTTCCAAACGCAAAATATTGCCTTACTTTGAATTTTTAAA
65 GAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
*
49244094 AGGATATTTGGCTATTTGGTCGAACGAAAAAATCAAAACCCAGCACATTAGGGAACGTTTTCTCG
1 AGGATATTTGGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTCG
*
49244159 AATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAGA
66 AATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* * *
49244201 AGGATATTTGGCTATTTGGTCGAACG-AGAAATCGAAACTCAGCACATTAGGGCACGTTTTCTCG
1 AGGATATTTGGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTCG
*
49244265 AATTTCCAAATGCAAAATATTGC
66 AATTTCCAAACGCAAAATATTGC
49244288 TTTATTTAGA
Statistics
Matches: 183, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
106 56 0.31
107 124 0.68
108 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (107 bp):
AGGATATTTGGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTCG
AATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
Found at i:49244369 original size:20 final size:21
Alignment explanation
Indices: 49244326--49244370 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
49244316 GTATGGTGTT
*
49244326 AATATGTATAATGGAATAACA
1 AATATGTATAATGAAATAACA
49244347 AATATG-ATAATGTAAATAA-A
1 AATATGTATAATG-AAATAACA
49244367 AATA
1 AATA
49244371 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (21 bp):
AATATGTATAATGAAATAACA
Found at i:49244586 original size:27 final size:28
Alignment explanation
Indices: 49244547--49244604 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
49244537 ATATATAAAT
49244547 ATATATATATATGT-ACA-TATAAGAAAA
1 ATATATATATATGTGA-ATTATAAGAAAA
* *
49244574 ATATATATGTATGTGAATTATAATAAAA
1 ATATATATATATGTGAATTATAAGAAAA
49244602 ATA
1 ATA
49244605 AAAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (28 bp):
ATATATATATATGTGAATTATAAGAAAA
Found at i:49246707 original size:44 final size:44
Alignment explanation
Indices: 49246480--49246772 Score: 179
Period size: 44 Copynumber: 6.6 Consensus size: 44
49246470 CCGCTCCTAA
* * * **
49246480 TGCAACTTCAGGGAGATAGGATTAGTAGCTTCAGTCTG-CTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCCT-CAC
* * * * * *
49246524 TACAACTTCAGTGAGATAAGACTTGCATATTCAACCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCCTCAC
* * * * ** * *
49246568 TGC-ACTT-TGGGGGATAAGGTTTATGGC-TCTAATCTGCTTCAC
1 TGCAACTTCAGGGAGATAAGATTTGTATCTTC-AACCTGCCTCAC
* * * *
49246610 TGCGACTTCAAGGAGATAAGATTTGTAGCCGGTCTTCAATCT-ACTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGTA-----TCTTCAACCTGCCT-CAC
*
49246659 TGCAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCCTCAT
1 TGCAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCCTCAC
* *
49246703 TGCAACTTCAGAGG-GATAAGGTTTGT-TAGTTCAACCTG-CTCTAC
1 TGCAACTTCAG-GGAGATAAGATTTGTAT-CTTCAACCTGCCTC-AC
* *
49246747 TGCAACTTCAGAGAGATAAGGTTTGT
1 TGCAACTTCAGGGAGATAAGATTTGT
49246773 GATTTATAGC
Statistics
Matches: 190, Mismatches: 43, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
41 2 0.01
42 22 0.12
43 13 0.07
44 111 0.58
45 5 0.03
48 1 0.01
49 34 0.18
50 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATTTGTATCTTCAACCTGCCTCAC
Found at i:49250015 original size:45 final size:45
Alignment explanation
Indices: 49249808--49250007 Score: 292
Period size: 45 Copynumber: 4.4 Consensus size: 45
49249798 TCGCTTAGGG
* * * * * *
49249808 AGACAGGATCTACAATCTTCAATCTACTTCGCTGCTAATATAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
*
49249853 AGACAAGATCTGCTATCTTCGATCTACTTTGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* *
49249898 AGATAAGATCTACTATCTTCGATCTACTTCGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* **
49249943 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGGCAATACAATA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
49249988 AGACAAGATCTGCTATCTTC
1 AGACAAGATCTGCTATCTTC
49250008 AACCTACTCC
Statistics
Matches: 140, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 140 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (45 bp):
AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
Found at i:49250447 original size:132 final size:132
Alignment explanation
Indices: 49249988--49250419 Score: 684
Period size: 132 Copynumber: 3.3 Consensus size: 132
49249978 CAATACAATA
* * * * *
49249988 AGACAAGATCTGCTATCTTCAACCTACTCCATTGCTTCTCAGGGAGATAAGGCTAGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTTCTCAGGGAGACAAGGCTAGTGGCTTAAA
* * * * *
49250053 TCTGCTTCCCTATTACCTTGAGAAGATAAGATTCGCCGTCTTCGATCTGTTTCACTACTGCTTAG
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTGCTTAG
49250118 GG
131 GG
* *
49250120 AGACAAGATCTACAATCTTCAACCTACTCCACTGCTTCTCAGTGAGACAAGGCTAGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTTCTCAGGGAGACAAGGCTAGTGGCTTAAA
* *
49250185 TCTGTTTCCCTACTACCTTGGGAAGATAAGATTCGTCGTCTTCTATCTGCTCCACTACTGCTTAG
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTGCTTAG
49250250 GG
131 GG
* *
49250252 AGACAGGATCTACAATCTTTAACCTACTCCACTGCTTCTCAAGGAGACAAGGCTAGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTTCTCAGGGAGACAAGGCTAGTGGCTTAAA
*
49250317 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTACTTAG
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTGCTTAG
49250382 GG
131 GG
* * *
49250384 AGATAGGATCTACAATCTTCGACCTACTCTACTGCT
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCT
49250420 GCTTCGGGAG
Statistics
Matches: 277, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 277 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (132 bp):
AGACAGGATCTACAATCTTCAACCTACTCCACTGCTTCTCAGGGAGACAAGGCTAGTGGCTTAAA
TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTGCTTAG
GG
Found at i:49252863 original size:30 final size:30
Alignment explanation
Indices: 49252827--49252916 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 30
49252817 ATGATACACG
*
49252827 AACTTTGATTTGGTGCAATGATACACATGA
1 AACTTTGATTTGGTTCAATGATACACATGA
* *
49252857 AACTTTGATTGTGGTTTAAATG-TATACATGA
1 AACTTTGATT-TGG-TTCAATGATACACATGA
* * *
49252888 AACTTTAACTTTGATTCAATCATACACAT
1 AACTTTGA-TTTGGTTCAATGATACACAT
49252917 TTAAAGAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
30 15 0.31
31 26 0.54
32 7 0.15
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (30 bp):
AACTTTGATTTGGTTCAATGATACACATGA
Found at i:49267658 original size:54 final size:54
Alignment explanation
Indices: 49267598--49267700 Score: 206
Period size: 54 Copynumber: 1.9 Consensus size: 54
49267588 TAAATATCTT
49267598 CCAACAAATTGAAAATAAATTTTAAAAAATATGTAGACTTAAATAACACATTTC
1 CCAACAAATTGAAAATAAATTTTAAAAAATATGTAGACTTAAATAACACATTTC
49267652 CCAACAAATTGAAAATAAATTTTAAAAAATATGTAGACTTAAATAACAC
1 CCAACAAATTGAAAATAAATTTTAAAAAATATGTAGACTTAAATAACAC
49267701 TAAGATAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (54 bp):
CCAACAAATTGAAAATAAATTTTAAAAAATATGTAGACTTAAATAACACATTTC
Found at i:49267768 original size:30 final size:30
Alignment explanation
Indices: 49267725--49267786 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
49267715 CTTAAAAAGT
49267725 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* * *
49267755 AAATGTCTTTAAAATGATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
49267785 AA
1 AA
49267787 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:49267836 original size:14 final size:14
Alignment explanation
Indices: 49267817--49267846 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49267807 ATCCAAACAA
49267817 TAGCAACAAAATAG
1 TAGCAACAAAATAG
*
49267831 TAGCAACATAATAG
1 TAGCAACAAAATAG
49267845 TA
1 TA
49267847 AAATGGTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
TAGCAACAAAATAG
Found at i:49268051 original size:22 final size:22
Alignment explanation
Indices: 49268026--49268068 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
49268016 TATCCAAACA
49268026 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
49268048 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
49268069 AATATGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:49269286 original size:21 final size:21
Alignment explanation
Indices: 49269257--49269298 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
49269247 TTAATTTGTT
49269257 CGTGAGATTTTGAATACAGCA
1 CGTGAGATTTTGAATACAGCA
* *
49269278 CGTGGGATTTTGAATATAGCA
1 CGTGAGATTTTGAATACAGCA
49269299 TGGCCGACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (21 bp):
CGTGAGATTTTGAATACAGCA
Found at i:49273083 original size:29 final size:29
Alignment explanation
Indices: 49273049--49273112 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
49273039 AAATAATTTT
* *
49273049 ATCTTTATCCAGCCAATTTCAAATTATCA
1 ATCTTTATCCAACCAACTTCAAATTATCA
*
49273078 ATCTTTATCCAACCAACTTCAAATTTTCA
1 ATCTTTATCCAACCAACTTCAAATTATCA
49273107 ATCTTT
1 ATCTTT
49273113 CAATCTACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.41
Consensus pattern (29 bp):
ATCTTTATCCAACCAACTTCAAATTATCA
Found at i:49283326 original size:2 final size:2
Alignment explanation
Indices: 49283319--49283348 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49283309 AAGATTACTA
49283319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49283349 GAGAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49286394 original size:15 final size:16
Alignment explanation
Indices: 49286374--49286406 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49286364 CTTTTACATT
49286374 TTTTTA-TCAATTTGA
1 TTTTTATTCAATTTGA
*
49286389 TTTTTATTTAATTTGA
1 TTTTTATTCAATTTGA
49286405 TT
1 TT
49286407 ATCAATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTTATTCAATTTGA
Found at i:49288448 original size:105 final size:106
Alignment explanation
Indices: 49288148--49288458 Score: 355
Period size: 106 Copynumber: 3.0 Consensus size: 106
49288138 TCTTCTCCCC
** **
49288148 TAATTGTGGTGGCTGCAGGGCTC-TTTTCCCAAAGGTTATAATTGTGTAGACTCATAG-TTTTAT
1 TAATTGTGGTGATTGCAGGGCTCTTTTTCCC-AAGGTTATAATAATGTAGACTCATAGTTTTTAT
* *
49288211 ATC-CTTTGTTTTGCATAGTTGTGTATCTTCATGTATTTAGAT
65 A-CACTTTGTTTTGCATAATTGTGTATCTCCATGTATTTAGAT
** ** * * * * *
49288253 TCTTTGTGGCAATTGCATGGATCTTTTTTTCCAAGGTTATAATGATGTAGGCTCATAGTTTTGTA
1 TAATTGTGGTGATTGCAGGGCTC-TTTTTCCCAAGGTTATAATAATGTAGACTCATAGTTTT-TA
* *
49288318 T--ACTTTGTTTTGCATAATTGTGTATCTCCGTGTATTTGGAT
64 TACACTTTGTTTTGCATAATTGTGTATCTCCATGTATTTAGAT
** *
49288359 TAATTGTGGTGATTGCAGGGCTCTTTTTCCCAAGG-TATAATAAAATAGACTTATAGTTTTTATA
1 TAATTGTGGTGATTGCAGGGCTCTTTTTCCCAAGGTTATAATAATGTAGACTCATAGTTTTTATA
*
49288423 CACTTTGTTTTGCATATTTGTGTATCTCCATGTATT
66 CACTTTGTTTTGCATAATTGTGTATCTCCATGTATT
49288459 ATTTTTTGGG
Statistics
Matches: 169, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
103 3 0.02
104 20 0.12
105 59 0.35
106 75 0.44
107 9 0.05
108 3 0.02
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.46
Consensus pattern (106 bp):
TAATTGTGGTGATTGCAGGGCTCTTTTTCCCAAGGTTATAATAATGTAGACTCATAGTTTTTATA
CACTTTGTTTTGCATAATTGTGTATCTCCATGTATTTAGAT
Found at i:49290561 original size:30 final size:31
Alignment explanation
Indices: 49290518--49290576 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
49290508 TTAGTAAAAA
**
49290518 AAAGTTATAATTT-AGTTATTGAACTATTCG
1 AAAGTTATAATTTAAGTTACCGAACTATTCG
* *
49290548 AAAGTTTTTATTTAAGTTACCGAACTATT
1 AAAGTTATAATTTAAGTTACCGAACTATT
49290577 TAAAAGCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (31 bp):
AAAGTTATAATTTAAGTTACCGAACTATTCG
Found at i:49291385 original size:14 final size:14
Alignment explanation
Indices: 49291366--49291404 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
49291356 TTGTTTCACT
*
49291366 GAAAATGGCTTCCG
1 GAAAATGACTTCCG
* *
49291380 GAAAATGATTTCTG
1 GAAAATGACTTCCG
49291394 GAAAATGACTT
1 GAAAATGACTT
49291405 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:49292940 original size:54 final size:54
Alignment explanation
Indices: 49292882--49293001 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 54
49292872 TCCTCACCCA
* *
49292882 TGTAACTCACTGAG-TAGCCCCACAAGCCCGTGTGTCAGGCCGTGTGCTAGGCCG
1 TGTAACTCACTGAGTTA-CCACACAAGCCCATGTGTCAGGCCGTGTGCTAGGCCG
* * * *
49292936 TGTAACTCTCTGAGTTACCACACATGCCCATGTGTTAGGCTGTGTGCTAGGCCG
1 TGTAACTCACTGAGTTACCACACAAGCCCATGTGTCAGGCCGTGTGCTAGGCCG
*
49292990 TGTAATTCACTG
1 TGTAACTCACTG
49293002 GCTTGAACAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 55 0.96
55 2 0.04
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (54 bp):
TGTAACTCACTGAGTTACCACACAAGCCCATGTGTCAGGCCGTGTGCTAGGCCG
Found at i:49293779 original size:40 final size:40
Alignment explanation
Indices: 49293721--49293827 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 40
49293711 GTTACCAAAG
49293721 TACAAACA-GGGCACGTATGTGCATTCAGGGGTATCGAAA
1 TACAAACAGGGGCACGTATGTGCATTCAGGGGTATCGAAA
* *
49293760 TACAAACAGGGGCACGTATGTGCATTTAGGGGTATCGAAG
1 TACAAACAGGGGCACGTATGTGCATTCAGGGGTATCGAAA
* *
49293800 TACAAACAGGGGCACGCATGTGTATTCA
1 TACAAACAGGGGCACGTATGTGCATTCA
49293828 ACAATAATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
39 8 0.13
40 54 0.87
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (40 bp):
TACAAACAGGGGCACGTATGTGCATTCAGGGGTATCGAAA
Found at i:49293810 original size:20 final size:20
Alignment explanation
Indices: 49293746--49293811 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
49293736 TATGTGCATT
*
49293746 CAGGGGTATCGAAATACAAA
1 CAGGGGTATCGAAGTACAAA
* * * **
49293766 CAGGGGCA-CGTATGTGCATT
1 CAGGGGTATCG-AAGTACAAA
*
49293786 TAGGGGTATCGAAGTACAAA
1 CAGGGGTATCGAAGTACAAA
49293806 CAGGGG
1 CAGGGG
49293812 CACGCATGTG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.18
Consensus pattern (20 bp):
CAGGGGTATCGAAGTACAAA
Found at i:49296504 original size:38 final size:38
Alignment explanation
Indices: 49296453--49296526 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
49296443 ACCTCAACAC
49296453 AAAATCGCCAATTTCATTAAATTTCTTGCATAAATATT
1 AAAATCGCCAATTTCATTAAATTTCTTGCATAAATATT
49296491 AAAATCGCCAATTTCATTAAATTTCTTGCATAAATA
1 AAAATCGCCAATTTCATTAAATTTCTTGCATAAATA
49296527 CTAACACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (38 bp):
AAAATCGCCAATTTCATTAAATTTCTTGCATAAATATT
Found at i:49300283 original size:17 final size:17
Alignment explanation
Indices: 49300261--49300320 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
49300251 TTTTCAATAA
49300261 TTTTAATAATTTTAAAT
1 TTTTAATAATTTTAAAT
* *
49300278 TTTTAA-AA-ATAAAAT
1 TTTTAATAATTTTAAAT
49300293 TTTT-ATAATTTTTAAAT
1 TTTTAATAA-TTTTAAAT
*
49300310 TTTTAAAAATT
1 TTTTAATAATT
49300321 AATTAAATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 2 0.06
17 17 0.50
18 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAATAATTTTAAAT
Found at i:49300301 original size:31 final size:32
Alignment explanation
Indices: 49300259--49300319 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
49300249 ACTTTTCAAT
49300259 AATTTTAATAA-TTTTAAATTTTTAAAAATAA
1 AATTTTAATAATTTTTAAATTTTTAAAAATAA
*
49300290 AATTTTTATAATTTTTAAATTTTTAAAAAT
1 AATTTTAATAATTTTTAAATTTTTAAAAAT
49300320 TAATTAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATTTTAATAATTTTTAAATTTTTAAAAATAA
Found at i:49300304 original size:9 final size:8
Alignment explanation
Indices: 49300270--49300316 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
49300260 ATTTTAATAA
49300270 TTTTAAAT
1 TTTTAAAT
49300278 TTTTAAA-
1 TTTTAAAT
** *
49300285 AATAAAAT
1 TTTTAAAT
49300293 TTTTATAAT
1 TTTTA-AAT
49300302 TTTTAAAT
1 TTTTAAAT
49300310 TTTTAAA
1 TTTTAAA
49300317 AATTAATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
7 4 0.13
8 19 0.61
9 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTTTAAAT
Found at i:49301062 original size:25 final size:25
Alignment explanation
Indices: 49301028--49301081 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
49301018 TAAACCCTAA
49301028 GTACATGTCATTTACAATCAAAAGG
1 GTACATGTCATTTACAATCAAAAGG
49301053 GTACATGTCATTTACAATCAAAAGG
1 GTACATGTCATTTACAATCAAAAGG
49301078 GTAC
1 GTAC
49301082 TTTACAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (25 bp):
GTACATGTCATTTACAATCAAAAGG
Found at i:49301730 original size:19 final size:19
Alignment explanation
Indices: 49301718--49301754 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
49301708 GGCACATAAT
*
49301718 GTGCATTCTGGCACACGAA
1 GTGCATCCTGGCACACGAA
49301737 GTGCATCCTGGCACACGA
1 GTGCATCCTGGCACACGA
49301755 GGTACGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.19
Consensus pattern (19 bp):
GTGCATCCTGGCACACGAA
Found at i:49302029 original size:16 final size:17
Alignment explanation
Indices: 49302008--49302040 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49301998 AATTCCTGCT
49302008 ATTTTA-CATTTTATTC
1 ATTTTAGCATTTTATTC
*
49302024 ATTTTAGCCTTTTATTC
1 ATTTTAGCATTTTATTC
49302041 TGAGAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.21, C:0.15, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTTAGCATTTTATTC
Found at i:49303539 original size:74 final size:74
Alignment explanation
Indices: 49303418--49303558 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 74
49303408 TTGCTATCTA
* *
49303418 CTAATTTATATTTTCAAGTAGATCTCGATAACCTAACACGTGTCATGGTTTTACA-CTAACCAAT
1 CTAATTTATATTTTCAAGTAGATCTCGATAACCTAACACCTGTCATGG-TTTACACCAAACCAAT
49303482 AAAGAGGAAT
65 AAAGAGGAAT
**
49303492 CTAATTTATATTTTCAAGTA-AGTCTCGATAGTCTAACACCTGTCATGGTTTACACCAAACCAAT
1 CTAATTTATATTTTCAAGTAGA-TCTCGATAACCTAACACCTGTCATGGTTTACACCAAACCAAT
49303556 AAA
65 AAA
49303559 AAGTTATTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
73 7 0.11
74 54 0.89
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (74 bp):
CTAATTTATATTTTCAAGTAGATCTCGATAACCTAACACCTGTCATGGTTTACACCAAACCAATA
AAGAGGAAT
Found at i:49303859 original size:2 final size:2
Alignment explanation
Indices: 49303852--49303902 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
49303842 TACATTATTA
49303852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49303894 AT AT AT AT A
1 AT AT AT AT A
49303903 ACTGATGGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49304538 original size:89 final size:89
Alignment explanation
Indices: 49304355--49304560 Score: 210
Period size: 89 Copynumber: 2.3 Consensus size: 89
49304345 AACCAATTAA
* * * * *
49304355 TTTTTTTTTGCATTAAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGACCCTCAAACTTTT
1 TTTTTGTTTGCACTCAATTGGGTACTTGAACTTGCAAAATGCATAAAAAAGACCCTCAAACTTTT
49304420 TCAAAAACAACAATTAAGCCTCTAC
66 TCAAAAACAACAATTAAG-CTCTAC
**
49304445 TTTTT-TTTTTACTCAATTGGGTACTTGAA-TTGCAAAATTGCATAAAAAATG-CCCTCTAAA-T
1 TTTTTGTTTGCACTCAATTGGGTACTTGAACTTGCAAAA-TGCATAAAAAA-GACCCTC-AAACT
*
49304506 TTTTCAAAAAAAAGAAGCAATTAAG-TC-A-
63 TTTTC---AAAAACAA-CAATTAAGCTCTAC
*
49304534 TTTTTGTTTGCACTCAATTGAGTACTT
1 TTTTTGTTTGCACTCAATTGGGTACTT
49304561 AAACAGCCAA
Statistics
Matches: 98, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
88 7 0.07
89 46 0.47
90 28 0.29
91 2 0.02
92 7 0.07
93 8 0.08
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (89 bp):
TTTTTGTTTGCACTCAATTGGGTACTTGAACTTGCAAAATGCATAAAAAAGACCCTCAAACTTTT
TCAAAAACAACAATTAAGCTCTAC
Found at i:49304775 original size:19 final size:18
Alignment explanation
Indices: 49304724--49304776 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
49304714 AAAAAATCAA
*
49304724 TAAAATTTATAAAAATGT
1 TAAAATTTTTAAAAATGT
49304742 T-AAATTTTAATAAAATAT-T
1 TAAAATTTT--TAAAA-ATGT
49304761 TAAAATTTTTAAAAAT
1 TAAAATTTTTAAAAAT
49304777 TAGAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
17 8 0.27
18 6 0.20
19 7 0.23
20 9 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAAATTTTTAAAAATGT
Found at i:49305034 original size:19 final size:18
Alignment explanation
Indices: 49305010--49305058 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
49305000 GTACGATAAT
49305010 TTTTATATTTTTTTACGAA
1 TTTTATATTTTTTTAC-AA
* *
49305029 TTTTATATTTCTTTACAT
1 TTTTATATTTTTTTACAA
49305047 TTTTATAATTTT
1 TTTTAT-ATTTT
49305059 CTTATGACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATATTTTTTTACAA
Found at i:49305160 original size:20 final size:21
Alignment explanation
Indices: 49305135--49305178 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
49305125 ATTTTACAAA
49305135 AATTTTTTATAA-ATTTTTAC
1 AATTTTTTATAATATTTTTAC
*
49305155 AATTTTTTATAATTTTTTTAC
1 AATTTTTTATAATATTTTTAC
49305176 AAT
1 AAT
49305179 GTGGGGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTTTTTATAATATTTTTAC
Found at i:49305172 original size:10 final size:10
Alignment explanation
Indices: 49305135--49305172 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
49305125 ATTTTACAAA
49305135 AATTTTTTAT
1 AATTTTTTAT
* *
49305145 AAATTTTTAC
1 AATTTTTTAT
49305155 AATTTTTTAT
1 AATTTTTTAT
49305165 AATTTTTT
1 AATTTTTT
49305173 TACAATGTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:49307054 original size:20 final size:19
Alignment explanation
Indices: 49307025--49307065 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
49307015 ACATGTGAAA
49307025 AATAATAAAA-TAAATAAAT
1 AATAATAAAATTAAA-AAAT
49307044 AATACATAAAATTAAAAAAT
1 AATA-ATAAAATTAAAAAAT
49307064 AA
1 AA
49307066 CTCTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAATAAAATTAAAAAAT
Found at i:49308877 original size:9 final size:9
Alignment explanation
Indices: 49308856--49308940 Score: 98
Period size: 9 Copynumber: 9.4 Consensus size: 9
49308846 TTTGGTTAAA
*
49308856 AATTAGCCG
1 AATTAACCG
*
49308865 AATTAACCA
1 AATTAACCG
*
49308874 AATTAACTG
1 AATTAACCG
*
49308883 AATTACCCG
1 AATTAACCG
49308892 AATTAACCG
1 AATTAACCG
* *
49308901 AATTACCCA
1 AATTAACCG
*
49308910 AATTACCCG
1 AATTAACCG
49308919 AATTAACCG
1 AATTAACCG
*
49308928 AATTAACCT
1 AATTAACCG
49308937 AATT
1 AATT
49308941 GAATCATACA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 64 1.00
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:49308892 original size:27 final size:27
Alignment explanation
Indices: 49308855--49308940 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 27
49308845 TTTTGGTTAA
* * *
49308855 AAATTAGCCGAATTAACCAAATTAACT
1 AAATTACCCGAATTAACCGAATTAACC
* *
49308882 GAATTACCCGAATTAACCGAATTACCC
1 AAATTACCCGAATTAACCGAATTAACC
49308909 AAATTACCCGAATTAACCGAATTAACC
1 AAATTACCCGAATTAACCGAATTAACC
*
49308936 TAATT
1 AAATT
49308941 GAATCATACA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (27 bp):
AAATTACCCGAATTAACCGAATTAACC
Found at i:49312513 original size:42 final size:42
Alignment explanation
Indices: 49312461--49312560 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
49312451 GCTCTCGGTA
*
49312461 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATCCAACATCATCATTTTAATT
* *
49312503 TTGCACACTTAGTGCCCGTTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCGTTATCCAACATCATCATTTTAATT
49312545 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
49312561 GTTCATATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATCCAACATCATCATTTTAATT
Found at i:49314313 original size:17 final size:17
Alignment explanation
Indices: 49314291--49314323 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
49314281 GGCCTAGACT
49314291 TTTATTTGTTTTTGTTG
1 TTTATTTGTTTTTGTTG
49314308 TTTATTTGTTTTTGTT
1 TTTATTTGTTTTTGTT
49314324 TTGTTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.00, G:0.15, T:0.79
Consensus pattern (17 bp):
TTTATTTGTTTTTGTTG
Found at i:49315202 original size:44 final size:43
Alignment explanation
Indices: 49315154--49315299 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 43
49315144 CTTCAAAGCT
49315154 ATAAGATTCGTAGTTTCAATCTGCTCCACTTCAACTTTAGGGAG
1 ATAAGATTCGTAGTTT-AATCTGCTCCACTTCAACTTTAGGGAG
****
49315198 ATAAGATTCGCTATGGTAAACTTAATCCAAACCACTGT-AACTTTAGGG-G
1 ATAAGATTCG-TA--GT----TTAATCTGCTCCACT-TCAACTTTAGGGAG
* * *
49315247 TATAAGATTTGTAGCTTTAATTTGCTCCACTGCAACTTTAGGGAG
1 -ATAAGATTCGTAG-TTTAATCTGCTCCACTTCAACTTTAGGGAG
49315292 ATAAGATT
1 ATAAGATT
49315300 TGTTATGGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
44 38 0.48
45 3 0.04
47 3 0.04
48 1 0.01
49 3 0.04
50 28 0.35
51 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (43 bp):
ATAAGATTCGTAGTTTAATCTGCTCCACTTCAACTTTAGGGAG
Found at i:49315242 original size:375 final size:376
Alignment explanation
Indices: 49314626--49315644 Score: 928
Period size: 375 Copynumber: 2.8 Consensus size: 376
49314616 CCATTGCAAC
* * *
49314626 TTCAGAGAGATAAAATTCGCTATGGTAACTTAAATTTGACCCACTACAACTTTAGGGGTATAGGA
1 TTCAGAGAGATAAAATTCGCTATGATAACTTAAATCTGACCCACTACAACTTTAGGGGTACAGGA
* * * * * * ** * * *
49314691 TTTGTGGCTTTAATCTGCTCTACTATAACTTCAGGGAGATAAGATTCGTTATGCTAGATTCAATC
66 TTTGTAGCATTAATATACTCCACTACAACTTCAAAGAGATAAGATTAGCTATGATAGATTCAATC
* * * *
49314756 CAACCCACTGCAACTTCAGAGGTATAGGATTTGTAGCTTTAATCTGCTCCACTATAACTTCAGGG
131 CAACCCACTGCAACTTCAAAGCTATAAGATTCGTAGCTTTAATCTGCTCCACTATAACTTCAGGG
* * * *
49314821 AGATAAGATTCGTTATAGTAGATTCAATCCGATCCACTGCAACTTTAAGGGTATAAGATTTGTAG
196 AGATAAGATTCGCTATAGTAAATTCAATCCAAACCACTGCAACTTTAAGGGTATAAGATTTGTAG
* * * *
49314886 C-TTCATCTGTTTCACTGCAACTTTAGGGAGATAAGATTCACTATGGTAACTTTAATCCAACCCA
261 CTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCACTATGGTAAATTTAATCCAACCCA
49314950 CTGCAACTTCAAGGGTATAGGATTTTTAGCTTCAATCTGCTCTACTATAAT
326 CTGCAACTTCAAGGGTATAGGATTTTTAGCTTCAATCTGCTCTACTATAAT
* ** * * *
49315001 TTCAGATAGATAAGGTTCGCTATGATAGA-TTTAATCTGACCCACTGCATCTTTAGGGGTACAGG
1 TTCAGAGAGATAAAATTCGCTATGATA-ACTTAAATCTGACCCACTACAACTTTAGGGGTACAGG
* *
49315065 ATTTGTATCATTAATATACTCCACTGCAACTTCAAAGAGATAAGATTAGCTATGATA-ACTTCAA
65 ATTTGTAGCATTAATATACTCCACTACAACTTCAAAGAGATAAGATTAGCTATGATAGA-TTCAA
*** *
49315129 TTTGACCCACTGCAACTTCAAAGCTATAAGATTCGTAG-TTTCAATCTGCTCCACT-TCAACTTT
129 TCCAACCCACTGCAACTTCAAAGCTATAAGATTCGTAGCTTT-AATCTGCTCCACTAT-AACTTC
* * *
49315192 AGGGAGATAAGATTCGCTATGGTAAACTT-AATCCAAACCACTGTAACTTTAGGGGTATAAGATT
192 AGGGAGATAAGATTCGCTATAGTAAA-TTCAATCCAAACCACTGCAACTTTAAGGGTATAAGATT
* *** *
49315256 TGTAGCTTTAATTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTTATGGTAAATTTAATCCG
256 TGTAGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCACTATGGTAAATTTAATCCA
* * * * **
49315321 ATCCACT---A--T-AA----CT---A----T---TTCAATCTGTTCTATTGCAACT
321 ACCCACTGCAACTTCAAGGGTATAGGATTTTTAGCTTCAATCTGCTCTACTATAA-T
* * * * * * ** * *
49315358 TT-AGAGAGATAAGATTCGTTATGGTAAATTTAATCTGATCCACTGTAACTTCAGGGGTATAGGA
1 TTCAGAGAGATAAAATTCGCTATGATAACTTAAATCTGACCCACTACAACTTTAGGGGTACAGGA
* * * * ** * *
49315422 TTTGTAGC-TTCAATTTGCTCTA-TGCAACTTCAGGGAGATAGGATTCA-CTATGGTAGATTCAA
66 TTTGTAGCATT-AATATACTCCACTACAACTTCAAAGAGATAAGATT-AGCTATGATAGATTCAA
* * * * ** * * * *
49315484 TTCGACCCACTACAACTTTAGGGGTATAAGATTTGTAGCTTCAATCTGCTCTACTATAACTTCAG
129 TCCAACCCACTGCAACTTCAAAGCTATAAGATTCGTAGCTTTAATCTGCTCCACTATAACTTCAG
* ** ** * * * *
49315549 GGAGATAATATTCATTATAGTAAATTCAATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGT
194 GGAGATAAGATTCGCTATAGTAAATTCAATCCAAACCACTGCAACTTTAAGGGTATAAGATTTGT
* * *
49315614 AGCTTCAATCTGCTCTACTGTAACTTTAGGG
259 AGCTTTAATCTGCTCCACTGCAACTTTAGGG
49315645 GTATAAAATT
Statistics
Matches: 537, Mismatches: 93, Indels: 48
0.79 0.14 0.07
Matches are distributed among these distances:
354 2 0.00
355 164 0.31
356 87 0.16
357 3 0.01
359 1 0.00
363 1 0.00
366 1 0.00
370 2 0.00
371 1 0.00
373 1 0.00
374 5 0.01
375 211 0.39
376 58 0.11
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (376 bp):
TTCAGAGAGATAAAATTCGCTATGATAACTTAAATCTGACCCACTACAACTTTAGGGGTACAGGA
TTTGTAGCATTAATATACTCCACTACAACTTCAAAGAGATAAGATTAGCTATGATAGATTCAATC
CAACCCACTGCAACTTCAAAGCTATAAGATTCGTAGCTTTAATCTGCTCCACTATAACTTCAGGG
AGATAAGATTCGCTATAGTAAATTCAATCCAAACCACTGCAACTTTAAGGGTATAAGATTTGTAG
CTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCACTATGGTAAATTTAATCCAACCCA
CTGCAACTTCAAGGGTATAGGATTTTTAGCTTCAATCTGCTCTACTATAAT
Found at i:49315333 original size:94 final size:94
Alignment explanation
Indices: 49314591--49315327 Score: 688
Period size: 94 Copynumber: 7.9 Consensus size: 94
49314581 CTTTAAAGAG
* * * * *
49314591 ATAAGATTTGTAGC-TTCATCTTGCTCCATTGCAACTTCAGAGAGATAAAATTCGCTATGGTAAC
1 ATAAGATTTGTAGCTTTAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAA
* ** *
49314655 TTAAATTTGACCCACTACAACTTTAGGGGT
65 TTTAATCCGACCCACTGCAACTTTAGGGGT
* * * ** * * *
49314685 ATAGGATTTGTGGCTTTAATCTGCTCTACTATAACTTCAGGGAGATAAGATTCGTTATGCTAGAT
1 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAAT
* * * *
49314750 TCAATCCAACCCACTGCAACTTCAGAGGT
66 TTAATCCGACCCACTGCAACTTTAGGGGT
* ** * * *
49314779 ATAGGATTTGTAGCTTTAATCTGCTCCACTATAACTTCAGGGAGATAAGATTCGTTATAGTAGAT
1 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAAT
* * *
49314844 TCAATCCGATCCACTGCAACTTTAAGGGT
66 TTAATCCGACCCACTGCAACTTTAGGGGT
* * * * * *
49314873 ATAAGATTTGTAGC-TTCATCTGTTTCACTGCAACTTTAGGGAGATAAGATTCACTATGGTAACT
1 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAAT
* * *
49314937 TTAATCCAACCCACTGCAACTTCAAGGGT
66 TTAATCCGACCCACTGCAACTTTAGGGGT
* * * * ** * ** * * *
49314966 ATAGGATTTTTAGCTTCAATCTGCTCTACTATAATTTCAGATAGATAAGGTTCGCTATGATAGAT
1 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAAT
* *
49315031 TTAATCTGACCCACTGCATCTTTAGGGGT
66 TTAATCCGACCCACTGCAACTTTAGGGGT
* * * * * * ** * * *
49315060 ACAGGATTTGTATCATTAATATACTCCACTGCAACTTCAAAGAGATAAGATTAGCTATGATAACT
1 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAAT
* ** * ** *
49315125 TCAATTTGACCCACTGCAACTTCAAAGCT
66 TTAATCCGACCCACTGCAACTTTAGGGGT
* * *
49315154 ATAAGATTCGTAG-TTTCAATCTGCTCCACTTCAACTTTAGGGAGATAAGATTCGCTATGGTAAA
1 ATAAGATTTGTAGCTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAA
* * * *
49315218 CTTAATCCAAACCACTGTAACTTTAGGGGT
65 TTTAATCCGACCCACTGCAACTTTAGGGGT
* * * *
49315248 ATAAGATTTGTAGCTTTAATTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTTATGGTAAAT
1 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAAT
*
49315313 TTAATCCGATCCACT
66 TTAATCCGACCCACT
49315328 ATAACTATTT
Statistics
Matches: 514, Mismatches: 125, Indels: 8
0.79 0.19 0.01
Matches are distributed among these distances:
93 78 0.15
94 428 0.83
95 8 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (94 bp):
ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAAAT
TTAATCCGACCCACTGCAACTTTAGGGGT
Found at i:49315594 original size:94 final size:94
Alignment explanation
Indices: 49315336--49315644 Score: 406
Period size: 94 Copynumber: 3.3 Consensus size: 94
49315326 CTATAACTAT
* * * * * * *
49315336 TTCAATCTGTTCTATTGCAACTTTAGAGAGATAAGATTCGTTATGGTAAATTTAATCTGATCCAC
1 TTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTCATTATGGTAAATTCAATCTGACCCAC
*
49315401 TGTAACTTCAGGGGTATAGGATTTGTAGC
66 TGCAACTTCAGGGGTATAGGATTTGTAGC
* * * *
49315430 TTCAATTTGCTCTA-TGCAACTTCAGGGAGATAGGATTCACTATGGTAGATTCAAT-TCGACCCA
1 TTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTCATTATGGTAAATTCAATCT-GACCCA
* * *
49315493 CTACAACTTTAGGGGTATAAGATTTGTAGC
65 CTGCAACTTCAGGGGTATAGGATTTGTAGC
** * *
49315523 TTCAATCTGCTCTACTATAACTTCAGGGAGATAATATTCATTATAGTAAATTCAATCTGACCCAC
1 TTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTCATTATGGTAAATTCAATCTGACCCAC
49315588 TGCAACTTCAGGGGTATAGGATTTGTAGC
66 TGCAACTTCAGGGGTATAGGATTTGTAGC
* *
49315617 TTCAATCTGCTCTACTGTAACTTTAGGG
1 TTCAATCTGCTCTACTGCAACTTCAGGG
49315645 GTATAAAATT
Statistics
Matches: 185, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
92 1 0.01
93 78 0.42
94 105 0.57
95 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (94 bp):
TTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTCATTATGGTAAATTCAATCTGACCCAC
TGCAACTTCAGGGGTATAGGATTTGTAGC
Found at i:49315639 original size:44 final size:44
Alignment explanation
Indices: 49315389--49315649 Score: 181
Period size: 44 Copynumber: 5.7 Consensus size: 44
49315379 TGGTAAATTT
* *
49315389 AATCTGATCCACTGTAACTTCAGGGGTATAGGATTTGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTC
* * *
49315433 AATTTGCTCTA-TGCAACTTCAGGGAG-ATAGGATTCACTATGGTAGATTC
1 AATCTGCTCCACTGCAACTTCAGGG-GTATAGGA-T---T-T-GTAGCTTC
* * *
49315482 AAT-TCGAC-CCACTACAACTTTAGGGGTATAAGATTTGTAGCTTC
1 AATCT-G-CTCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTC
* ** ** **
49315526 AATCTGCTCTACTATAACTTCAGGGAGATAATATTCATTATAGTAAATTC
1 AATCTGCTCCACTGCAACTTCAGGG-G-T-ATA-GGATT-T-GTAGCTTC
49315576 AATCTGAC-CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTC
1 AATCTG-CTCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTC
* * *
49315620 AATCTGCTCTACTGTAACTTTAGGGGTATA
1 AATCTGCTCCACTGCAACTTCAGGGGTATA
49315650 AAATTTATGG
Statistics
Matches: 169, Mismatches: 27, Indels: 42
0.71 0.11 0.18
Matches are distributed among these distances:
43 20 0.12
44 66 0.39
45 4 0.02
46 5 0.03
47 7 0.04
48 6 0.04
49 17 0.10
50 43 0.25
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTC
Found at i:49320332 original size:8 final size:8
Alignment explanation
Indices: 49320328--49320357 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
49320318 GAAATAATAA
49320328 AATAAAAT
1 AATAAAAT
49320336 AATAAAAT
1 AATAAAAT
49320344 AA-AAAAT
1 AATAAAAT
49320351 AATAAAA
1 AATAAAA
49320358 AGTAGGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AATAAAAT
Found at i:49320337 original size:13 final size:13
Alignment explanation
Indices: 49320319--49320352 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
49320309 AAAGTGCTTG
49320319 AAATAATAAAATA
1 AAATAATAAAATA
49320332 AAATAATAAAATA
1 AAATAATAAAATA
49320345 AAA-AATAA
1 AAATAATAA
49320353 TAAAAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAATAAAATA
Found at i:49332125 original size:39 final size:39
Alignment explanation
Indices: 49331832--49332128 Score: 328
Period size: 39 Copynumber: 7.6 Consensus size: 39
49331822 AACCTGGTAA
* * *
49331832 GCACAAAGCCCGAATAATCA-CTGGCACACAGTCTGCTAG
1 GCACATAGCCCGAATAATCATC-GGCACAAAGCCTGCTAG
* * *
49331871 GCACATAGCCCAAATAATCATCGGCACAAAGCTTGTTAG
1 GCACATAGCCCGAATAATCATCGGCACAAAGCCTGCTAG
* * *
49331910 GCACATAGCTCGAATAATTA-CTGGCACAAAGCCTACTAG
1 GCACATAGCCCGAATAATCATC-GGCACAAAGCCTGCTAG
* * * * *
49331949 ACACATAGCTCAAATAATCATCGACACACAGCCTGCTAG
1 GCACATAGCCCGAATAATCATCGGCACAAAGCCTGCTAG
* * * * *
49331988 ACACATAACCAGAATAATCACCGGTACAAAGCCTGCTAG
1 GCACATAGCCCGAATAATCATCGGCACAAAGCCTGCTAG
* * * * *
49332027 GCACATAACCCGAATAATCACCGGTAAAAAGCCTACTAG
1 GCACATAGCCCGAATAATCATCGGCACAAAGCCTGCTAG
*
49332066 GCACATAGCCCGAATAATCATCGGCACAAAGCCTACTAG
1 GCACATAGCCCGAATAATCATCGGCACAAAGCCTGCTAG
*
49332105 GTACATAGCCCGAATAATCATCGG
1 GCACATAGCCCGAATAATCATCGG
49332129 ATTTCTATTT
Statistics
Matches: 220, Mismatches: 35, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
38 1 0.00
39 217 0.99
40 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (39 bp):
GCACATAGCCCGAATAATCATCGGCACAAAGCCTGCTAG
Found at i:49333303 original size:2 final size:2
Alignment explanation
Indices: 49333296--49333339 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
49333286 TTAAACTAGA
49333296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49333338 AT
1 AT
49333340 GGAAATCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49334113 original size:47 final size:48
Alignment explanation
Indices: 49334054--49334152 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
49334044 AATTGATATA
49334054 TTTATGATTTTGATTATATGAAATTGATGAATACATAAACATTCAGAT
1 TTTATGATTTTGATTATATGAAATTGATGAATACATAAACATTCAGAT
*
49334102 TTTA-GATTTTGATTATATGAATTTGATGAATACATAAACATTCAGAT
1 TTTATGATTTTGATTATATGAAATTGATGAATACATAAACATTCAGAT
49334149 TTTA
1 TTTA
49334153 CATGCTTGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 46 0.92
48 4 0.08
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.43
Consensus pattern (48 bp):
TTTATGATTTTGATTATATGAAATTGATGAATACATAAACATTCAGAT
Found at i:49336596 original size:9 final size:10
Alignment explanation
Indices: 49336575--49336599 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49336565 AAAAGTTCAT
49336575 AAAAATTTAA
1 AAAAATTTAA
49336585 AAAAATTTAA
1 AAAAATTTAA
49336595 AAAAA
1 AAAAA
49336600 CCCCATGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:49341710 original size:14 final size:14
Alignment explanation
Indices: 49341691--49341722 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
49341681 TTTTTTTTGA
49341691 GCTTCCAACAATCT
1 GCTTCCAACAATCT
49341705 GCTTCCAACAATCT
1 GCTTCCAACAATCT
49341719 GCTT
1 GCTT
49341723 TCACATGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.34, G:0.09, T:0.31
Consensus pattern (14 bp):
GCTTCCAACAATCT
Found at i:49343778 original size:2 final size:2
Alignment explanation
Indices: 49343773--49343797 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49343763 ATATATATAT
49343773 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
49343798 ATAAAACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49345210 original size:21 final size:21
Alignment explanation
Indices: 49345172--49345212 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49345162 AAATAATTTC
*
49345172 ATTTTATTCGACTTGACTCGA
1 ATTTTATTCGACTCGACTCGA
49345193 ATTTTATTTC-ACTCGACTCG
1 ATTTTA-TTCGACTCGACTCG
49345213 TTTTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (21 bp):
ATTTTATTCGACTCGACTCGA
Found at i:49348690 original size:32 final size:32
Alignment explanation
Indices: 49348645--49348849 Score: 284
Period size: 32 Copynumber: 6.4 Consensus size: 32
49348635 GAGTTAGTTG
* *
49348645 AGGCCAATATGTTGATTTTGTTCATTCCGCTA
1 AGGCCAATATGTTGATTTTGTCCATTCCTCTA
* *
49348677 AGGTCAATATGTTGATTTTCTCCATTCCTCTA
1 AGGCCAATATGTTGATTTTGTCCATTCCTCTA
*
49348709 AGGCCAATATGTTGGTTTTGTCCATTCCTCTA
1 AGGCCAATATGTTGATTTTGTCCATTCCTCTA
* * *
49348741 AGGCCAATATGTTGGTTTTGTCCATTCCACTG
1 AGGCCAATATGTTGATTTTGTCCATTCCTCTA
* * * *
49348773 AGGTCAATATGTCGATTTTGTTCATTCCGCTA
1 AGGCCAATATGTTGATTTTGTCCATTCCTCTA
* *
49348805 AGGCCAACATGTTGGTTTTGTCCATTCCTCTA
1 AGGCCAATATGTTGATTTTGTCCATTCCTCTA
49348837 AGGCCAATATGTT
1 AGGCCAATATGTT
49348850 TAAGGCCAAT
Statistics
Matches: 151, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 151 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (32 bp):
AGGCCAATATGTTGATTTTGTCCATTCCTCTA
Found at i:49348809 original size:96 final size:96
Alignment explanation
Indices: 49348645--49348849 Score: 329
Period size: 96 Copynumber: 2.1 Consensus size: 96
49348635 GAGTTAGTTG
* * * *
49348645 AGGCCAATATGTTGATTTTGTTCATTCCGCTAAGGTCAATATGTTGATTTTCTCCATTCCTCTAA
1 AGGCCAATATGTTGATTTTGTCCATTCCACTAAGGTCAATATGTCGATTTTCTCCATTCCGCTAA
*
49348710 GGCCAATATGTTGGTTTTGTCCATTCCTCTA
66 GGCCAACATGTTGGTTTTGTCCATTCCTCTA
* * * *
49348741 AGGCCAATATGTTGGTTTTGTCCATTCCACTGAGGTCAATATGTCGATTTTGTTCATTCCGCTAA
1 AGGCCAATATGTTGATTTTGTCCATTCCACTAAGGTCAATATGTCGATTTTCTCCATTCCGCTAA
49348806 GGCCAACATGTTGGTTTTGTCCATTCCTCTA
66 GGCCAACATGTTGGTTTTGTCCATTCCTCTA
49348837 AGGCCAATATGTT
1 AGGCCAATATGTT
49348850 TAAGGCCAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 100 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (96 bp):
AGGCCAATATGTTGATTTTGTCCATTCCACTAAGGTCAATATGTCGATTTTCTCCATTCCGCTAA
GGCCAACATGTTGGTTTTGTCCATTCCTCTA
Found at i:49348855 original size:15 final size:15
Alignment explanation
Indices: 49348835--49348864 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49348825 TCCATTCCTC
49348835 TAAGGCCAATATGTT
1 TAAGGCCAATATGTT
49348850 TAAGGCCAATATGTT
1 TAAGGCCAATATGTT
49348865 GGTAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TAAGGCCAATATGTT
Found at i:49348891 original size:50 final size:47
Alignment explanation
Indices: 49348803--49348899 Score: 131
Period size: 50 Copynumber: 2.0 Consensus size: 47
49348793 TTCATTCCGC
* * *
49348803 TAAGGCCAACATGTTGGTTTTGTCCATTCCTCTAAGGCCAATATGTT
1 TAAGGCCAACATGTTGGTTTTGTCCACTCCGCTAAGGCCAACATGTT
*
49348850 TAAGGCCAATATGTTGGTAATTTTGTCCACTCCGCTAAGGCCAACATGTT
1 TAAGGCCAACATGTTGG---TTTTGTCCACTCCGCTAAGGCCAACATGTT
49348900 GGTTTTGTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 16 0.37
50 27 0.63
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (47 bp):
TAAGGCCAACATGTTGGTTTTGTCCACTCCGCTAAGGCCAACATGTT
Found at i:49356914 original size:50 final size:50
Alignment explanation
Indices: 49356843--49356988 Score: 177
Period size: 50 Copynumber: 2.9 Consensus size: 50
49356833 TTTCCTTTAC
* * **
49356843 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCAAGATATGGTCTTACATGGGACCTCTCATATCGG
* ** *
49356893 TGCCCATGCCATGTCCAAGATATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCAAGATATGGTCTTACATGGGACCTCTCATATCGG
* * *
49356943 TGCCAACGCCATGTCCCAA-ACATGGTCTTATATGGGACCTCTCATA
1 TGCCAATGCCATGT-CCAAGATATGGTCTTACATGGGACCTCTCATA
49356989 ATCTTAATAA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
50 76 0.95
51 4 0.05
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCAAGATATGGTCTTACATGGGACCTCTCATATCGG
Found at i:49360117 original size:13 final size:13
Alignment explanation
Indices: 49360099--49360133 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
49360089 GCTTCTTCTG
49360099 TTTTCTTTTTCCC
1 TTTTCTTTTTCCC
* *
49360112 TTTTCTTTTTTCG
1 TTTTCTTTTTCCC
49360125 TTTTCTTTT
1 TTTTCTTTT
49360134 CTGTGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTCTTTTTCCC
Found at i:49360117 original size:20 final size:18
Alignment explanation
Indices: 49360094--49360137 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
49360084 CTTTTGCTTC
*
49360094 TTCTGTTTTCTTTTTCCCTT
1 TTCTGTTTTCGTTTT--CTT
*
49360114 TTCTTTTTTCGTTTTCTT
1 TTCTGTTTTCGTTTTCTT
49360132 TTCTGT
1 TTCTGT
49360138 GTTTGTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 8 0.38
20 13 0.62
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (18 bp):
TTCTGTTTTCGTTTTCTT
Found at i:49360779 original size:3 final size:3
Alignment explanation
Indices: 49360771--49360888 Score: 65
Period size: 3 Copynumber: 40.3 Consensus size: 3
49360761 TTTATAATAC
* * * *
49360771 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAC TAT TAT TAG TA- TAGG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* *
49360816 TAT TAT TAT CA- TAT TAG T-T TA- TAT CTATT TATT TACT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TA-T TA-T TAT TAT TAT
49360860 TA- TAT TAT T-T TAT T-T TAT TAT GTAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
49360889 TTGTAATGCT
Statistics
Matches: 91, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
2 16 0.18
3 59 0.65
4 15 0.16
5 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:49360890 original size:20 final size:21
Alignment explanation
Indices: 49360847--49360890 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
49360837 TATCTATTTA
*
49360847 TTTACTTTTATTTTATATTAT
1 TTTACTTTTATTATATATTAT
*
49360868 TTTA-TTTTATTATGTATTAT
1 TTTACTTTTATTATATATTAT
49360888 TTT
1 TTT
49360891 GTAATGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTACTTTTATTATATATTAT
Found at i:49366861 original size:22 final size:22
Alignment explanation
Indices: 49366842--49366883 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
49366832 TTCAATTTAT
49366842 TTTA-TTATATATAAATATTTG
1 TTTATTTATATATAAATATTTG
* *
49366863 TTTATTTATATTTATATATTT
1 TTTATTTATATATAAATATTT
49366884 TTGTTCGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTATTTATATATAAATATTTG
Found at i:49367126 original size:49 final size:49
Alignment explanation
Indices: 49367069--49367163 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
49367059 ATTTTCCTAG
*
49367069 GATTTTAATCAATATATATATACCAAACGTTGTAAAATAACTTTCTTGA
1 GATTTTAATCAATACATATATACCAAACGTTGTAAAATAACTTTCTTGA
* ** *
49367118 GATTTTAATCAATACATATATATCTGACGTTGTAAAGTAACTTTCT
1 GATTTTAATCAATACATATATACCAAACGTTGTAAAATAACTTTCT
49367164 CGATAATCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (49 bp):
GATTTTAATCAATACATATATACCAAACGTTGTAAAATAACTTTCTTGA
Found at i:49370594 original size:13 final size:13
Alignment explanation
Indices: 49370548--49370598 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
49370538 TGCCTGCAAT
*
49370548 AAATCAAAAGTTGA
1 AAAT-AAAAATTGA
*
49370562 AAATAAAAATTCA
1 AAATAAAAATTGA
* *
49370575 CATTAAAAATTGA
1 AAATAAAAATTGA
49370588 AAATAAAAATT
1 AAATAAAAATT
49370599 TAGTCCCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (13 bp):
AAATAAAAATTGA
Found at i:49371078 original size:9 final size:9
Alignment explanation
Indices: 49371064--49371094 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49371054 GTTAAAGGAA
49371064 TCGAGTTAT
1 TCGAGTTAT
*
49371073 TCGAGTTAA
1 TCGAGTTAT
49371082 TCGAGTTAT
1 TCGAGTTAT
49371091 TCGA
1 TCGA
49371095 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:49371164 original size:9 final size:9
Alignment explanation
Indices: 49371150--49371192 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
49371140 GTTTTCAAAT
49371150 TCGAATAAC
1 TCGAATAAC
*
49371159 TCGAATAAT
1 TCGAATAAC
49371168 TCGAATAAC
1 TCGAATAAC
*
49371177 TCGAATAAT
1 TCGAATAAC
49371186 TCGAATA
1 TCGAATA
49371193 TCAAACTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (9 bp):
TCGAATAAC
Found at i:49371170 original size:18 final size:18
Alignment explanation
Indices: 49371147--49371192 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
49371137 TGAGTTTTCA
49371147 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
49371165 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
49371183 AATTCGAATA
1 AATTCGAATA
49371193 TCAAACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:49371254 original size:21 final size:21
Alignment explanation
Indices: 49371228--49371272 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
49371218 ACCCTAAACT
* *
49371228 CTCAAACATTTTTACT-TTTCC
1 CTCAAA-ACTTTTACTCCTTCC
49371249 CTCAAAACTTTTACTCCTTCC
1 CTCAAAACTTTTACTCCTTCC
49371270 CTC
1 CTC
49371273 TTTCTCCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.22, C:0.36, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTACTCCTTCC
Found at i:49371304 original size:32 final size:30
Alignment explanation
Indices: 49371242--49371304 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 30
49371232 AACATTTTTA
*
49371242 CTTTTCCCTCAAAACTTTTACTCCTTCCCT
1 CTTTTCCCTCAAAACTTTTACTCCTCCCCT
49371272 CTTTCTCCC-CAAAACTTTTACCCTCCTCCCCT
1 CTTT-TCCCTCAAAACTTTTA--CTCCTCCCCT
49371304 C
1 C
49371305 CCAACCCCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 15 0.52
31 4 0.14
32 10 0.34
ACGTcount: A:0.16, C:0.46, G:0.00, T:0.38
Consensus pattern (30 bp):
CTTTTCCCTCAAAACTTTTACTCCTCCCCT
Found at i:49371478 original size:7 final size:7
Alignment explanation
Indices: 49371466--49371498 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
49371456 TCTCTTCCGA
49371466 TCCCACC
1 TCCCACC
49371473 TCCCACC
1 TCCCACC
49371480 TCCCACC
1 TCCCACC
49371487 TCCCACC
1 TCCCACC
49371494 TCCCA
1 TCCCA
49371499 TCTAGGGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.70, G:0.00, T:0.15
Consensus pattern (7 bp):
TCCCACC
Found at i:49371644 original size:13 final size:13
Alignment explanation
Indices: 49371626--49371659 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
49371616 TGAAATTTTT
49371626 TCGGTTAATAAGG
1 TCGGTTAATAAGG
49371639 TCGGTTAATAAGG
1 TCGGTTAATAAGG
49371652 TCGGTTAA
1 TCGGTTAA
49371660 CCGAATTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (13 bp):
TCGGTTAATAAGG
Found at i:49371716 original size:9 final size:9
Alignment explanation
Indices: 49371702--49371733 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
49371692 TTTGGTTAAA
49371702 AATTACCTG
1 AATTACCTG
49371711 AATTACCTG
1 AATTACCTG
*
49371720 AATTACCCG
1 AATTACCTG
49371729 AATTA
1 AATTA
49371734 ATCGAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (9 bp):
AATTACCTG
Found at i:49371739 original size:9 final size:9
Alignment explanation
Indices: 49371727--49371760 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
49371717 CTGAATTACC
49371727 CGAATTAAT
1 CGAATTAAT
49371736 CGAATTAAT
1 CGAATTAAT
*
49371745 CGAATTAAC
1 CGAATTAAT
49371754 CGAATTA
1 CGAATTA
49371761 CTGAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (9 bp):
CGAATTAAT
Found at i:49371740 original size:18 final size:18
Alignment explanation
Indices: 49371719--49371787 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
49371709 TGAATTACCT
49371719 GAATTACCCGAATTAATC
1 GAATTACCCGAATTAATC
** *
49371737 GAATTAATCGAATTAACC
1 GAATTACCCGAATTAATC
*
49371755 GAATTA-CTGAAAATT-ATC
1 GAATTACCCG--AATTAATC
49371773 TGAATTACCCGAATT
1 -GAATTACCCGAATT
49371788 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
17 1 0.03
18 27 0.68
19 10 0.25
20 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (18 bp):
GAATTACCCGAATTAATC
Found at i:49371740 original size:27 final size:25
Alignment explanation
Indices: 49371709--49371787 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 25
49371699 AAAAATTACC
49371709 TGAATTACCTGAATTACCCGAATTAA
1 TGAATTA-CTGAATTACCCGAATTAA
* * *
49371735 TCGAATTAATCGAATTAACCGAATTAC
1 T-GAATTACT-GAATTACCCGAATTAA
49371762 TGAAAATTATCTGAATTACCCGAATT
1 TG--AATTA-CTGAATTACCCGAATT
49371788 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 3 0.07
27 21 0.49
28 18 0.42
29 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (25 bp):
TGAATTACTGAATTACCCGAATTAA
Found at i:49372114 original size:30 final size:30
Alignment explanation
Indices: 49372078--49372149 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
49372068 CCTAAAAAAT
*
49372078 TCGGTTAACCGACCGATTAACTGAATTCGG
1 TCGGTTAACCGACCGATTAACCGAATTCGG
49372108 TCGGTTAACCGACCGATTAACCGAATTCGG
1 TCGGTTAACCGACCGATTAACCGAATTCGG
49372138 TCGGTTAACCGA
1 TCGGTTAACCGA
49372150 ACTTTTTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (30 bp):
TCGGTTAACCGACCGATTAACCGAATTCGG
Found at i:49373341 original size:10 final size:10
Alignment explanation
Indices: 49373306--49373365 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
49373296 ACTTTTATTA
49373306 AATTTTTTA-
1 AATTTTTTAG
* *
49373315 ACTTTCTTTAT
1 AATTT-TTTAG
49373326 ATATTTTTTAG
1 A-ATTTTTTAG
*
49373337 AATTTTTTTG
1 AATTTTTTAG
*
49373347 AAATTTTTAG
1 AATTTTTTAG
49373357 AATTTTTTA
1 AATTTTTTA
49373366 AATATATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 4 0.10
10 28 0.68
11 6 0.15
12 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.63
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:49387235 original size:15 final size:15
Alignment explanation
Indices: 49387206--49387234 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
49387196 AGGGGTATAG
49387206 TAAACTATTAAAAAA
1 TAAACTATTAAAAAA
49387221 TAAA-TATTAAAAAA
1 TAAACTATTAAAAAA
49387235 AAAGACTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAACTATTAAAAAA
Found at i:49393247 original size:2 final size:2
Alignment explanation
Indices: 49393240--49393264 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49393230 ATAATTTGAT
49393240 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 T
49393265 TTTGTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.