Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 13 of 333
Found at i:3599030 original size:43 final size:43
Alignment explanation
Indices: 3598969--3599061 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
3598959 GCAGATTTTT
*
3598969 CACAGCTCATGTAAGCAGCACCGTGTAGCCTAACATCTTAACC
1 CACAGCTCATATAAGCAGCACCGTGTAGCCTAACATCTTAACC
* *
3599012 CACAGCTCATATGAGCAGCATCGTGTAGCCTAACATCTTAACC
1 CACAGCTCATATAAGCAGCACCGTGTAGCCTAACATCTTAACC
3599055 CACAGCT
1 CACAGCT
3599062 TATGTGAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (43 bp):
CACAGCTCATATAAGCAGCACCGTGTAGCCTAACATCTTAACC
Found at i:3600962 original size:13 final size:13
Alignment explanation
Indices: 3600944--3600968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3600934 TGGTGCCCAA
3600944 AAGCAATGTTGGC
1 AAGCAATGTTGGC
3600957 AAGCAATGTTGG
1 AAGCAATGTTGG
3600969 AGGATTCTCT
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:0.12, G:0.32, T:0.24
Consensus pattern (13 bp):
AAGCAATGTTGGC
Found at i:3605668 original size:94 final size:94
Alignment explanation
Indices: 3605507--3605693 Score: 329
Period size: 94 Copynumber: 2.0 Consensus size: 94
3605497 TTACCTACCT
3605507 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
1 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
* *
3605572 GCATTATCTAAGCTATTATGCGAAATAAG
66 GCATTACCTAAACTATTATGCGAAATAAG
* *
3605601 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGCGAGGATGGCTGCTTTTG
1 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
*
3605666 GCATTACCTAAATTATTATGCGAAATAA
66 GCATTACCTAAACTATTATGCGAAATAA
3605694 AATTTTGTAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (94 bp):
TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
GCATTACCTAAACTATTATGCGAAATAAG
Found at i:3607871 original size:59 final size:59
Alignment explanation
Indices: 3607799--3607916 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
3607789 GAAAGGAGTA
3607799 AGAATGGAAAATTTGCTAATCAAATGGTTAAGATTCATAATTACTTTCTTACTTTATAG
1 AGAATGGAAAATTTGCTAATCAAATGGTTAAGATTCATAATTACTTTCTTACTTTATAG
3607858 AGAATGGAAAATTTGCTAATCAAATGGTTAAGATTCATAATTACTTTCTTACTTTATAG
1 AGAATGGAAAATTTGCTAATCAAATGGTTAAGATTCATAATTACTTTCTTACTTTATAG
3607917 TTTAACCATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (59 bp):
AGAATGGAAAATTTGCTAATCAAATGGTTAAGATTCATAATTACTTTCTTACTTTATAG
Found at i:3614484 original size:60 final size:59
Alignment explanation
Indices: 3614410--3614527 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 59
3614400 TCGGAGATTA
* *
3614410 ACTTCAGCATTAAAACGAGTTTCAAAAGTCAAATTTTCAATAGATTCTAATATTTCATTC
1 ACTTCAACATTAAAACGAGTTCCAAAAGTCAAA-TTTCAATAGATTCTAATATTTCATTC
* * * *
3614470 ACTTCAACATTAAAACGAGTTCCGAAGGTCAAATTTCGATAGATTCTAATGTTTCATT
1 ACTTCAACATTAAAACGAGTTCCAAAAGTCAAATTTCAATAGATTCTAATATTTCATT
3614528 TAAAGCATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 23 0.44
60 29 0.56
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (59 bp):
ACTTCAACATTAAAACGAGTTCCAAAAGTCAAATTTCAATAGATTCTAATATTTCATTC
Found at i:3620492 original size:12 final size:13
Alignment explanation
Indices: 3620475--3620503 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3620465 TATATTTTGT
3620475 ATTTAAATTTAA-
1 ATTTAAATTTAAG
3620487 ATTTAAATTTAAG
1 ATTTAAATTTAAG
3620500 ATTT
1 ATTT
3620504 TATTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATTTAAATTTAAG
Found at i:3620510 original size:48 final size:49
Alignment explanation
Indices: 3620415--3620510 Score: 108
Period size: 48 Copynumber: 2.0 Consensus size: 49
3620405 ATAAAAAAGA
* * *
3620415 TTATAATTTTGTATTGATATTAATATTTAAATCTTATGTTATGTTTTAT
1 TTATAATTTTGTATTGAAATTAATATTTAAATCTTAAGTTATATTTTAT
* *
3620464 TTAT-ATTTTGTATTTAAATTTAA-ATTTAAAT-TTAAGATTTTATTTTA
1 TTATAATTTTGTATTGAAA-TTAATATTTAAATCTTAAG-TTATATTTTA
3620511 ATATATTGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
47 4 0.10
48 28 0.70
49 8 0.20
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.59
Consensus pattern (49 bp):
TTATAATTTTGTATTGAAATTAATATTTAAATCTTAAGTTATATTTTAT
Found at i:3620537 original size:15 final size:15
Alignment explanation
Indices: 3620513--3620560 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3620503 TTATTTTAAT
*
3620513 ATATTGTAATAAAAA
1 ATATTTTAATAAAAA
* *
3620528 ATATTTTAAT--TAT
1 ATATTTTAATAAAAA
3620541 ATATTTTAATAAAAA
1 ATATTTTAATAAAAA
3620556 ATATT
1 ATATT
3620561 GAATTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATATTTTAATAAAAA
Found at i:3621953 original size:18 final size:19
Alignment explanation
Indices: 3621932--3621988 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
3621922 AAATTCAAAA
3621932 AAATATAAAAATATA-TTT
1 AAATATAAAAATATATTTT
*
3621950 AAATATGAAAAT-TATTTT
1 AAATATAAAAATATATTTT
3621968 AAATATATAAAATATAATTTT
1 AAATATA-AAAATAT-ATTTT
3621989 TAAAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 2 0.06
18 20 0.61
19 5 0.15
20 1 0.03
21 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATATAAAAATATATTTT
Found at i:3635917 original size:6 final size:6
Alignment explanation
Indices: 3635906--3635935 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3635896 TACAAGCCTG
3635906 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
3635936 ATCACCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:3635946 original size:18 final size:18
Alignment explanation
Indices: 3635907--3635947 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3635897 ACAAGCCTGC
* * *
3635907 TCTCCCTCTCCCTCTCCC
1 TCTCCCTCTCCATCACCA
3635925 TCTCCCTCTCCATCACCA
1 TCTCCCTCTCCATCACCA
3635943 TCTCC
1 TCTCC
3635948 TACATTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.61, G:0.00, T:0.32
Consensus pattern (18 bp):
TCTCCCTCTCCATCACCA
Found at i:3640796 original size:170 final size:171
Alignment explanation
Indices: 3640490--3640833 Score: 654
Period size: 170 Copynumber: 2.0 Consensus size: 171
3640480 TCATGAGCTA
3640490 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
1 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
3640555 AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
66 AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
3640620 GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
131 GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
3640661 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
1 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
* *
3640726 -AAAATAAGGGATGGGATGATGAGTATAGATTAAGTTGCAGCTTTGATGGAAGCCACCGCTTTGA
66 AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
*
3640790 GTAGAAAGGCAAAGAGAAGAGTAGGCATGGAGAAAAATGGG
131 GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
3640831 CTG
1 CTG
3640834 TGATCACTTT
Statistics
Matches: 170, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
170 105 0.62
171 65 0.38
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (171 bp):
CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
Found at i:3649291 original size:5 final size:5
Alignment explanation
Indices: 3649276--3649308 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3649266 CGCCGTTACG
*
3649276 CTTCT CATCT CTTCT CTTCT CTTCT CTTCT CTT
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTT
3649309 TGTTTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (5 bp):
CTTCT
Found at i:3656312 original size:22 final size:22
Alignment explanation
Indices: 3656284--3656328 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3656274 GTGAGTGGCA
3656284 TAGGGCTGTAAATGAATTGGGT
1 TAGGGCTGTAAATGAATTGGGT
3656306 TAGGGCTGTAAATGAATTGGGT
1 TAGGGCTGTAAATGAATTGGGT
3656328 T
1 T
3656329 TGAACGCATG
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:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (22 bp):
TAGGGCTGTAAATGAATTGGGT
Found at i:3656557 original size:18 final size:17
Alignment explanation
Indices: 3656536--3656569 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3656526 TATAAATATT
3656536 AATAATTATATTGAACAA
1 AATAATTATATT-AACAA
*
3656554 AATAATTTTATTAACA
1 AATAATTATATTAACA
3656570 TATGTGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
AATAATTATATTAACAA
Found at i:3661939 original size:12 final size:11
Alignment explanation
Indices: 3661923--3661950 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3661913 AACAAAATAG
3661923 GAAAAAAAAAA
1 GAAAAAAAAAA
3661934 GAAAAAAAAAA
1 GAAAAAAAAAA
3661945 GAAAAA
1 GAAAAA
3661951 GATAGATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:3666631 original size:75 final size:74
Alignment explanation
Indices: 3666544--3666714 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 74
3666534 GTTTTCCTCA
** * * * **
3666544 TTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAACT
1 TTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACATACATTTCACAACT
3666608 CAGTATGGAT
65 CAGTATGGAT
*
3666618 TTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACATACATTTCACAACT
1 TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACATACATTTCACAACT
3666683 CAGTATGGA-
65 CAGTATGGAT
*
3666692 -TG--ACACCATACCTACATTTCACA
1 TTGAAATACCATACCTACATTTCACA
3666715 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 20 0.23
73 2 0.02
74 7 0.08
75 57 0.66
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (74 bp):
TTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACATACATTTCACAACTC
AGTATGGAT
Found at i:3666712 original size:35 final size:35
Alignment explanation
Indices: 3666549--3666714 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
3666539 CCTCATTGAA
** * *
3666549 ATACCATACCTACATTTTTCAACTCGGTATGGGA-A
1 ATACCATACCTACATTTCACAACTCAGTAT-GGATG
* **
3666584 ATGCCATACCTACATTTCTTAACTCAGTATGGATTTG
1 ATACCATACCTACATTTCACAACTCAGTATGGA--TG
* *
3666621 ATAATACCATACCTACATTTCACAGCTCAGTATGGATA
1 ---ATACCATACCTACATTTCACAACTCAGTATGGATG
*
3666659 ATACCATACATACATTTCACAACTCAGTATGGATG
1 ATACCATACCTACATTTCACAACTCAGTATGGATG
*
3666694 ACACCATACCTACATTTCACA
1 ATACCATACCTACATTTCACA
3666715 CTTTGCCATG
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
34 3 0.03
35 77 0.70
38 1 0.01
40 29 0.26
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
ATACCATACCTACATTTCACAACTCAGTATGGATG
Found at i:3673940 original size:6 final size:6
Alignment explanation
Indices: 3673931--3674040 Score: 60
Period size: 6 Copynumber: 17.8 Consensus size: 6
3673921 AGACTGAGCC
* * * ** **
3673931 TGAAGT TGAAGA TGAAGA TGAA-A GTGAAGA TGAGGT TGGGGA TGGGGA
1 TGAAGA TGAAGA TGAAGA TGAAGA -TGAAGA TGAAGA TGAAGA TGAAGA
* * * * *
3673979 TGAAGA TGAGGATGA TGAAGA AGAAGA CGAAGA AGAAGA AGAAGA CGAAGA
1 TGAAGA TGA--A-GA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA
*
3674030 CGAAGA TGAAG
1 TGAAGA TGAAG
3674041 CCGACGCCGA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
5 1 0.01
6 78 0.90
7 2 0.02
8 1 0.01
9 5 0.06
ACGTcount: A:0.45, C:0.03, G:0.39, T:0.14
Consensus pattern (6 bp):
TGAAGA
Found at i:3674010 original size:9 final size:9
Alignment explanation
Indices: 3673998--3674029 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3673988 GGATGATGAA
3673998 GAAGAAGAC
1 GAAGAAGAC
*
3674007 GAAGAAGAA
1 GAAGAAGAC
3674016 GAAGAAGAC
1 GAAGAAGAC
3674025 GAAGA
1 GAAGA
3674030 CGAAGATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.34, T:0.00
Consensus pattern (9 bp):
GAAGAAGAC
Found at i:3674016 original size:18 final size:18
Alignment explanation
Indices: 3673995--3674040 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
3673985 TGAGGATGAT
3673995 GAAGAAGAAGACGAAGAA
1 GAAGAAGAAGACGAAGAA
*
3674013 GAAGAAGAAGACGAAGAC
1 GAAGAAGAAGACGAAGAA
*
3674031 GAAGATGAAG
1 GAAGAAGAAG
3674041 CCGACGCCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.57, C:0.07, G:0.35, T:0.02
Consensus pattern (18 bp):
GAAGAAGAAGACGAAGAA
Found at i:3676290 original size:31 final size:31
Alignment explanation
Indices: 3676255--3676334 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
3676245 TATTTTTCAT
* *
3676255 TTGCTTCAATTTCTATGCTTATTCC-CCGTTA
1 TTGCTTCAATTTCCATGCTTATACCTCC-TTA
*
3676286 TTGCTTCAATTTCCATGATTATACCTCCTTA
1 TTGCTTCAATTTCCATGCTTATACCTCCTTA
3676317 TTGCTTCAATTTCCATGC
1 TTGCTTCAATTTCCATGC
3676335 CTTACAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.46
Consensus pattern (31 bp):
TTGCTTCAATTTCCATGCTTATACCTCCTTA
Found at i:3677844 original size:3 final size:3
Alignment explanation
Indices: 3677838--3677866 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3677828 CGTCATATTA
3677838 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
3677867 ATGAAGTTAT
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:3683254 original size:13 final size:13
Alignment explanation
Indices: 3683234--3683272 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
3683224 CTTTTTTGAC
3683234 TTTTTTTTTATGT
1 TTTTTTTTTATGT
3683247 TTTGTTTTTTATGT
1 TTT-TTTTTTATGT
*
3683261 TTATTTATTTAT
1 TT-TTTTTTTAT
3683273 TTATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 19 0.83
15 1 0.04
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTATGT
Found at i:3683373 original size:21 final size:19
Alignment explanation
Indices: 3683349--3683410 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 19
3683339 TTAAATATAT
3683349 ATTTTGAAATTACTTTTTTAA
1 ATTTT-AAATTA-TTTTTTAA
3683370 ATTTTAAATATTATTTTTTAA
1 ATTTT-AA-ATTATTTTTTAA
*
3683391 ATATTAAATATATTTTTTAA
1 ATTTTAAAT-TATTTTTTAA
3683411 TAATATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 19 0.51
22 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTAAATTATTTTTTAA
Found at i:3683421 original size:22 final size:20
Alignment explanation
Indices: 3683362--3683423 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
3683352 TTGAAATTAC
* *
3683362 TTTTTTAAATTTTAAATATTA
1 TTTTTTAAATATAAAATA-TA
*
3683383 TTTTTTAAATATTAAATATA
1 TTTTTTAAATATAAAATATA
3683403 TTTTTTAATAATATAAAATAT
1 TTTTTT-A-AATATAAAATAT
3683424 TTAAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 8 0.22
21 18 0.49
22 11 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTTAAATATAAAATATA
Found at i:3683425 original size:20 final size:20
Alignment explanation
Indices: 3683362--3683410 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
3683352 TTGAAATTAC
*
3683362 TTTTTTAAATTTTAAATATTA
1 TTTTTTAAATATTAAATA-TA
3683383 TTTTTTAAATATTAAATATA
1 TTTTTTAAATATTAAATATA
3683403 TTTTTTAA
1 TTTTTTAA
3683411 TAATATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTAAATATTAAATATA
Found at i:3683586 original size:46 final size:46
Alignment explanation
Indices: 3683519--3683609 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
3683509 AAAAAAATAA
3683519 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTTT
1 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTTT
3683565 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTT
1 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTT
3683610 GAATGGTTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (46 bp):
TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTTT
Found at i:3684894 original size:17 final size:18
Alignment explanation
Indices: 3684874--3684907 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3684864 AAAAGATTTA
3684874 TTTATTGAAAAA-ATATG
1 TTTATTGAAAAATATATG
*
3684891 TTTATTTAAAAATATAT
1 TTTATTGAAAAATATAT
3684908 ATATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTATTGAAAAATATATG
Found at i:3684953 original size:20 final size:20
Alignment explanation
Indices: 3684899--3684958 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
3684889 TGTTTATTTA
3684899 AAAATATATATATTAAAAAGT
1 AAAA-ATATATATTAAAAAGT
* *
3684920 AAAAATTTAAATTAAAAAGT
1 AAAAATATATATTAAAAAGT
3684940 AAAAATATATATTATAAAA
1 AAAAATATATATTA-AAAA
3684959 TCACATCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAATATATATTAAAAAGT
Found at i:3685423 original size:20 final size:20
Alignment explanation
Indices: 3685400--3685464 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
3685390 ATAATTTTTT
3685400 AATTTTAGTACACATTTATA
1 AATTTTAGTACACATTTATA
* * *
3685420 AATTTATA-TATTA-ATTTTTT
1 AATTT-TAGTA-CACATTTATA
*
3685440 AATTTTAGTACACATTCATA
1 AATTTTAGTACACATTTATA
3685460 AATTT
1 AATTT
3685465 ATGTACTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (20 bp):
AATTTTAGTACACATTTATA
Found at i:3685435 original size:40 final size:41
Alignment explanation
Indices: 3685391--3685475 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 41
3685381 GTGTTGGTTA
*
3685391 TAATTTTTTAATTTTAGTACACATTTATAAATTTATATA-T
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
*
3685431 TAATTTTTTAATTTTAGTACACATTCATAAATTTATGTACT
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
3685472 TAAT
1 TAAT
3685476 ATATATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 37 0.88
41 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (41 bp):
TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
Found at i:3685486 original size:40 final size:40
Alignment explanation
Indices: 3685399--3685486 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
3685389 TATAATTTTT
* * *
3685399 TAATTTTAGTACACATTTATAAATTTATATATTAATTTTT
1 TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
*
3685439 TAATTTTAGTACACATTCATAAATTTATGTACTTAA-TATA
1 TAATTTTAGTACACATTCATAAATTTATATA-TTAATTATA
*
3685479 TATTTTTA
1 TAATTTTA
3685487 ATAGATAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (40 bp):
TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
Found at i:3690652 original size:184 final size:184
Alignment explanation
Indices: 3690337--3690693 Score: 466
Period size: 184 Copynumber: 1.9 Consensus size: 184
3690327 ATAGTCAACA
* * *** *
3690337 CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCGCCCATGGCCCTCATGGTTTTGTTTTTGGGAGG
1 CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCACCCATAGCCCTCATAACTTTGTTCTTGGGAGG
** *
3690402 GCTCATACACCCCTAAAAGGTCTCTTTCCACTTAAGTGTTGCTACCCCTTTATATAGGCTAGGTC
66 GCTCATACACCCCTAAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATATACGCTAGGTC
*** * * * *
3690467 TCTCTTGTGTTTTTCCAATGTGGGATTTGCCTAGGGTGTTACATTGATAAATTT
131 TCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACATTGATAAATTT
* * * * * *
3690521 CCCATCCCGGTAAAATATTGTTTGCTTTGGGTACTCATAGCCGTCATAACTTTGTTCTTGGGAGG
1 CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCACCCATAGCCCTCATAACTTTGTTCTTGGGAGG
* *
3690586 GCTCATACA-CCTTCAAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATGTAACGC-AGG
66 GCTCATACACCCCT-AAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATAT-ACGCTAGG
3690649 TCTCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACA
129 TCTCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACA
3690694 AAGTACATAA
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
183 3 0.02
184 141 0.96
185 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (184 bp):
CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCACCCATAGCCCTCATAACTTTGTTCTTGGGAGG
GCTCATACACCCCTAAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATATACGCTAGGTC
TCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACATTGATAAATTT
Found at i:3693848 original size:22 final size:26
Alignment explanation
Indices: 3693823--3693874 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 26
3693813 CAAGAATGTC
3693823 TTATAT-TACGATT-A-TTGTTTT-T
1 TTATATCTACGATTAACTTGTTTTAT
*
3693845 TTAT-TCTATGATTAACTTGTTTTAT
1 TTATATCTACGATTAACTTGTTTTAT
3693870 TTATA
1 TTATA
3693875 CATTAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 10 0.42
23 1 0.04
24 7 0.29
25 5 0.21
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.62
Consensus pattern (26 bp):
TTATATCTACGATTAACTTGTTTTAT
Found at i:3694630 original size:44 final size:44
Alignment explanation
Indices: 3694581--3694701 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 44
3694571 ATTAGGTAGT
* * *
3694581 ACAAAATTAGTTGAAAAC-TCTAGAAGAGATAATTATTTGATAGC
1 ACAAAATTAGTTGAAAACTTC-AAAAGAGATAATCATTCGATAGC
* *
3694625 ACAAAATTAGTTGAAAGCTTCAAAAGAGATAATCATTCGTTAGC
1 ACAAAATTAGTTGAAAACTTCAAAAGAGATAATCATTCGATAGC
* *
3694669 ACAAAATTAGTTG-AAATTTCTAAAAGAGGTAAT
1 ACAAAATTAGTTGAAAACTTC-AAAAGAGATAAT
3694702 ATATCAATAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.07
44 60 0.90
45 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (44 bp):
ACAAAATTAGTTGAAAACTTCAAAAGAGATAATCATTCGATAGC
Found at i:3696876 original size:30 final size:30
Alignment explanation
Indices: 3696842--3696899 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3696832 AATTGTTTTT
* *
3696842 TGATAATATTGATTGTGATGAATGAAATTA
1 TGATAATATTGATTGTGATAAAAGAAATTA
* *
3696872 TGATAATGTTGCTTGTGATAAAAGAAAT
1 TGATAATATTGATTGTGATAAAAGAAAT
3696900 GAGAAACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (30 bp):
TGATAATATTGATTGTGATAAAAGAAATTA
Found at i:3703841 original size:5 final size:5
Alignment explanation
Indices: 3703825--3703854 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3703815 TATTTGTATT
3703825 CTTCC C-TCC CTTCC CTTCC CTTCC CTTCC C
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC C
3703855 GTGAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (5 bp):
CTTCC
Found at i:3721369 original size:23 final size:23
Alignment explanation
Indices: 3721343--3721386 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3721333 TGGAAACTTA
3721343 ATTTGGTATAATAGTTTCATCTC
1 ATTTGGTATAATAGTTTCATCTC
3721366 ATTTGGTATAATAGTTTCATC
1 ATTTGGTATAATAGTTTCATC
3721387 AGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (23 bp):
ATTTGGTATAATAGTTTCATCTC
Found at i:3728895 original size:27 final size:24
Alignment explanation
Indices: 3728836--3728899 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
3728826 CTGTTGCTGA
3728836 TGCAGCTGCTGCTGTTCCTCATAT
1 TGCAGCTGCTGCTGTTCCTCATAT
3728860 TGCAGCTGCTGCTGTTCCTCATAT
1 TGCAGCTGCTGCTGTTCCTCATAT
*
3728884 TGCAGCTCCTGCTGTT
1 TGCAGCTGCTGCTGTT
3728900 GTTGATCACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.11, C:0.30, G:0.22, T:0.38
Consensus pattern (24 bp):
TGCAGCTGCTGCTGTTCCTCATAT
Found at i:3731511 original size:20 final size:22
Alignment explanation
Indices: 3731481--3731527 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
3731471 CAAAAGTTAC
3731481 AAAATAATTCAAA-ATAATTTT
1 AAAATAATTCAAACATAATTTT
*
3731502 AAAA-AATTCAAACCTAATTTT
1 AAAATAATTCAAACATAATTTT
3731523 AAAAT
1 AAAAT
3731528 TTAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAATTCAAACATAATTTT
Found at i:3731555 original size:17 final size:17
Alignment explanation
Indices: 3731517--3731558 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3731507 ATTCAAACCT
*
3731517 AATTT-TAAAATTTAAA
1 AATTTATAAAATTCAAA
*
3731533 ATATTTATAAAATTCCAA
1 A-ATTTATAAAATTCAAA
3731551 AATTTATA
1 AATTTATA
3731559 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 11 0.50
18 10 0.45
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTATAAAATTCAAA
Found at i:3734771 original size:19 final size:18
Alignment explanation
Indices: 3734743--3734782 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3734733 ACGAAATTTT
3734743 AATTAGTATTATGAGATAA
1 AATTAGTATTATGAGA-AA
* *
3734762 AATTATTATTATTAGAAA
1 AATTAGTATTATGAGAAA
3734780 AAT
1 AAT
3734783 AATACTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
AATTAGTATTATGAGAAA
Found at i:3734899 original size:15 final size:15
Alignment explanation
Indices: 3734881--3734909 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3734871 ATATTTATAA
3734881 AATTATTATTATTAT
1 AATTATTATTATTAT
3734896 AATTATTATTATTA
1 AATTATTATTATTA
3734910 GATAGGGAAA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:3737168 original size:20 final size:20
Alignment explanation
Indices: 3737143--3737180 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3737133 TTGTTATGGA
3737143 CCAACTGTATTAAAATGGGC
1 CCAACTGTATTAAAATGGGC
* *
3737163 CCAACTGTGTTAATATGG
1 CCAACTGTATTAAAATGG
3737181 CCAAGGCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (20 bp):
CCAACTGTATTAAAATGGGC
Found at i:3737251 original size:60 final size:59
Alignment explanation
Indices: 3737175--3737311 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
3737165 AACTGTGTTA
* * *
3737175 ATATGGCCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * *
3737235 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAAGGGCTATGGCCTAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
3737295 ATATGGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
3737312 GTTAACACTG
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
59 1 0.01
60 51 0.76
61 15 0.22
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:3739519 original size:19 final size:19
Alignment explanation
Indices: 3739495--3739563 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
3739485 CGTGTTTGCT
3739495 TTCCGTTTAGCCTTCGGGC
1 TTCCGTTTAGCCTTCGGGC
3739514 TTCCGTTTAGCACTT-GTGTGC
1 TTCCGTTTAGC-CTTCG-G-GC
*
3739535 TTCAG-TTAGCCTTCGGGC
1 TTCCGTTTAGCCTTCGGGC
3739553 TTCCGTTTAGC
1 TTCCGTTTAGC
3739564 ACTTATGTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
18 6 0.14
19 21 0.49
20 10 0.23
21 6 0.14
ACGTcount: A:0.09, C:0.28, G:0.25, T:0.39
Consensus pattern (19 bp):
TTCCGTTTAGCCTTCGGGC
Found at i:3739547 original size:39 final size:39
Alignment explanation
Indices: 3739501--3739594 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
3739491 TGCTTTCCGT
*
3739501 TTAGCCTTCGGGCTTCCGTTTAGCACTTGTGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
3739540 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
* *
3739579 CTAGACTTCGGGCTTC
1 TTAGCCTTCGGGCTTC
3739595 AGATCACGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (39 bp):
TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
Found at i:3748296 original size:50 final size:50
Alignment explanation
Indices: 3748211--3748376 Score: 219
Period size: 50 Copynumber: 3.3 Consensus size: 50
3748201 GCTAAATGAC
* *
3748211 CTTGTATATTCGGCCATA-AAGGTATGCACAAATGTGATATTATATTTGAAT
1 CTTGTATATTCGGCCATATAA-GTAAGCACATATGTGATATTATATTTG-AT
* *
3748262 -TTGTATATTCGGCCATATAAGTAAGTACATATGTGATATTAAATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTATATTTGAT
* * * *
3748311 CTTGCATATTCGACCATATAGGTAAGCACATATGTGATATTGTATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTATATTTGAT
*
3748361 CTTGTATATTTGGCCA
1 CTTGTATATTCGGCCA
3748377 AATGAGTGGT
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.02
50 96 0.96
51 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (50 bp):
CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTATATTTGAT
Found at i:3748530 original size:26 final size:26
Alignment explanation
Indices: 3748500--3748551 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3748490 TTATTGAAAT
3748500 GTTTATTTGCTTATGACTTACTAAGC
1 GTTTATTTGCTTATGACTTACTAAGC
3748526 GTTTATTTGCTTATGACTTACTAAGC
1 GTTTATTTGCTTATGACTTACTAAGC
3748552 TAAGTTAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (26 bp):
GTTTATTTGCTTATGACTTACTAAGC
Found at i:3748969 original size:21 final size:21
Alignment explanation
Indices: 3748945--3748987 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3748935 AATGGTAGTG
*
3748945 TAAATATGTTTGTATGTTTGC
1 TAAATATGTTTGTATCTTTGC
3748966 TAAATATGTTTGTATCTTTGC
1 TAAATATGTTTGTATCTTTGC
3748987 T
1 T
3748988 TGTAGATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.53
Consensus pattern (21 bp):
TAAATATGTTTGTATCTTTGC
Found at i:3753056 original size:16 final size:16
Alignment explanation
Indices: 3753032--3753062 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3753022 TAAAAAAATA
3753032 AATACATCAATCTATC
1 AATACATCAATCTATC
*
3753048 AATATATCAATCTAT
1 AATACATCAATCTAT
3753063 ACAAGTCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
AATACATCAATCTATC
Found at i:3767815 original size:21 final size:21
Alignment explanation
Indices: 3767777--3767817 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3767767 TTGTTAAGGG
*
3767777 TTTAGGGTTCATGGTTCATGA
1 TTTAGGGTTCATGATTCATGA
3767798 TTTAGGGTTCGA-GATTCATG
1 TTTAGGGTTC-ATGATTCATG
3767818 GTTCAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (21 bp):
TTTAGGGTTCATGATTCATGA
Found at i:3768087 original size:17 final size:17
Alignment explanation
Indices: 3768036--3768095 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 17
3768026 CAATCAATTT
3768036 AAATTTTCAATATTTATA
1 AAATTTTCAAT-TTTATA
3768054 AAATTTATCACATTTTATA
1 AAATTT-TCA-ATTTTATA
3768073 ATAATTTT-AATTTTAATA
1 A-AATTTTCAATTTT-ATA
3768091 AAATT
1 AAATT
3768096 AAATAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.24
18 11 0.29
19 11 0.29
20 7 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTTCAATTTTATA
Found at i:3768363 original size:43 final size:44
Alignment explanation
Indices: 3768305--3768389 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
3768295 CATTTGATTG
3768305 TTTTTTATATTATTGTA-TCACATTACAATAATATTATATATGT
1 TTTTTTATATTATTGTATTCACATTACAATAATATTATATATGT
3768348 TTTTTTATATTATTGTATTCACATTACAATAATATTATATAT
1 TTTTTTATATTATTGTATTCACATTACAATAATATTATATAT
3768390 TAGTAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 17 0.41
44 24 0.59
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (44 bp):
TTTTTTATATTATTGTATTCACATTACAATAATATTATATATGT
Found at i:3768448 original size:23 final size:21
Alignment explanation
Indices: 3768422--3768465 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
3768412 ATTAAAGATG
*
3768422 AAATTATATTTTGTATTTACATT
1 AAATTATACTTT-TA-TTACATT
3768445 AAATTATACTTTTATTACATT
1 AAATTATACTTTTATTACATT
3768466 TTCAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTATACTTTTATTACATT
Found at i:3771546 original size:38 final size:38
Alignment explanation
Indices: 3771491--3771564 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
3771481 AAAAATTATT
* *
3771491 TTAATTTTATAATATTAT-TATATATTGATATAATTTCC
1 TTAATTTTATAAGATTATAAATAT-TTGATATAATTTCC
*
3771529 TTAATTTTATAAGATTATAAATATTTGATTTAATTT
1 TTAATTTTATAAGATTATAAATATTTGATATAATTT
3771565 TTTTTTGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (38 bp):
TTAATTTTATAAGATTATAAATATTTGATATAATTTCC
Found at i:3776938 original size:18 final size:17
Alignment explanation
Indices: 3776891--3776939 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
3776881 AAATGTGACA
3776891 AAAAAT-TATAAAATAT
1 AAAAATATATAAAATAT
*
3776907 AAAAATATAAAAAATATT
1 AAAAATATATAAAATA-T
* *
3776925 TAAAATATTTAAAAT
1 AAAAATATATAAAAT
3776940 TTACTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 6 0.22
17 8 0.30
18 13 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATATATAAAATAT
Found at i:3777025 original size:21 final size:21
Alignment explanation
Indices: 3776982--3777027 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3776972 AAAAAATTGT
* *
3776982 AAAATTTTATAAAAACCATCA
1 AAAAATTTATAAAAACCAACA
**
3777003 AAAAATTTATAAAATGCAACA
1 AAAAATTTATAAAAACCAACA
3777024 AAAA
1 AAAA
3777028 GACCCTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAATTTATAAAAACCAACA
Found at i:3777239 original size:10 final size:10
Alignment explanation
Indices: 3777224--3777253 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
3777214 TTTTACAAAT
3777224 TTTACATTTC
1 TTTACATTTC
3777234 TTTACATTTC
1 TTTACATTTC
3777244 TTTATCATTT
1 TTTA-CATTT
3777254 TCTTATGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTACATTTC
Found at i:3777339 original size:20 final size:19
Alignment explanation
Indices: 3777291--3777343 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3777281 TTTTTCTATA
*
3777291 TTTCTAATATTTTATATTTT
1 TTTCTAAT-TTTTATATCTT
3777311 TTTAC-AATTTTTATAATCTT
1 TTT-CTAATTTTTAT-ATCTT
3777331 TTTCTAATTTTTA
1 TTTCTAATTTTTA
3777344 ACAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 7 0.24
20 21 0.72
21 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTCTAATTTTTATATCTT
Found at i:3782894 original size:15 final size:16
Alignment explanation
Indices: 3782874--3782908 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3782864 CTTTTAATAT
3782874 TATTTAATATTA-TTA
1 TATTTAATATTATTTA
*
3782889 TATTTACTATTATTTA
1 TATTTAATATTATTTA
3782905 TATT
1 TATT
3782909 ATTCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAATATTATTTA
Found at i:3783059 original size:24 final size:24
Alignment explanation
Indices: 3783016--3783079 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
3783006 TTCTAACATG
* * *
3783016 TATATACTATGTAAATATTT-TAA
1 TATATATTATGTATACATTTCTAA
*
3783039 TACTATATTATGTATACATTTCTTA
1 TA-TATATTATGTATACATTTCTAA
*
3783064 TATATATTACGTATAC
1 TATATATTATGTATAC
3783080 GTATCTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.06
24 28 0.82
25 4 0.12
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (24 bp):
TATATATTATGTATACATTTCTAA
Found at i:3783229 original size:101 final size:103
Alignment explanation
Indices: 3783055--3783258 Score: 394
Period size: 101 Copynumber: 2.0 Consensus size: 103
3783045 ATTATGTATA
3783055 CATTTCTTATATATATTACGTATACGTATCTTTTTAATATTATATTATATATATTATTATGTATA
1 CATTTCTTATATATATTACGTATACGTATCTTTTTAATATTATATTATATATATTATTATGTATA
3783120 TGTCTTTAATGTTATTAGTTGTATATGTTTATTATACT
66 TGTCTTTAATGTTATTAGTTGTATATGTTTATTATACT
3783158 CATTTCTTATATATATTACGTATACGTATCTTTTTAATATTATA-T-TATATATTATTATGTATA
1 CATTTCTTATATATATTACGTATACGTATCTTTTTAATATTATATTATATATATTATTATGTATA
3783221 TGTCTTTAATGTTATTAGTTGTATATGTTTATTATACT
66 TGTCTTTAATGTTATTAGTTGTATATGTTTATTATACT
3783259 ATTCCATGTA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
101 56 0.55
102 1 0.01
103 44 0.44
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.55
Consensus pattern (103 bp):
CATTTCTTATATATATTACGTATACGTATCTTTTTAATATTATATTATATATATTATTATGTATA
TGTCTTTAATGTTATTAGTTGTATATGTTTATTATACT
Found at i:3783540 original size:13 final size:13
Alignment explanation
Indices: 3783524--3783603 Score: 63
Period size: 13 Copynumber: 6.1 Consensus size: 13
3783514 TTTTATTTTA
3783524 ATATATTATGTAT
1 ATATATTATGTAT
*
3783537 ATATATTCT-TCAT
1 ATATATTATGT-AT
* *
3783550 ATATGTTATGTAC
1 ATATATTATGTAT
* * *
3783563 ATACATTTTTTGAT
1 ATATATTATGT-AT
* *
3783577 ATTTATTATATAT
1 ATATATTATGTAT
3783590 ATATATTATGTAT
1 ATATATTATGTAT
3783603 A
1 A
3783604 CATTTTAACA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
12 1 0.02
13 39 0.80
14 9 0.18
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (13 bp):
ATATATTATGTAT
Found at i:3784467 original size:28 final size:28
Alignment explanation
Indices: 3784435--3784492 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
3784425 CCTTTTTAGT
*
3784435 AAAATCGCAAGTCGATTTTCAAATTTTC
1 AAAATCGCAAGTCGATATTCAAATTTTC
*
3784463 AAAATCGCAAGTCGGTATTCAAATTTTC
1 AAAATCGCAAGTCGATATTCAAATTTTC
3784491 AA
1 AA
3784493 TAAATCGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (28 bp):
AAAATCGCAAGTCGATATTCAAATTTTC
Found at i:3792447 original size:21 final size:20
Alignment explanation
Indices: 3792419--3792460 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3792409 AAATAGAGCA
3792419 TGTTGAGA-ACCTCAGGAAGT
1 TGTTGAGAGA-CTCAGGAAGT
*
3792439 TGTTCGAGAGACTGAGGAAGT
1 TGTT-GAGAGACTCAGGAAGT
3792460 T
1 T
3792461 CCAGCTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 14 0.74
22 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (20 bp):
TGTTGAGAGACTCAGGAAGT
Found at i:3795996 original size:76 final size:76
Alignment explanation
Indices: 3795898--3796087 Score: 301
Period size: 76 Copynumber: 2.5 Consensus size: 76
3795888 TTCTGTTTTC
* * *
3795898 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCATGACACGTTAAGG-AATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTTCAATTT
3795962 CTATCTTTAAAA
66 CTATCTTT-AAA
* * *
3795974 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCTGAGGTAATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTTCAATTT
*
3796039 CTATCTTTCAA
66 CTATCTTTAAA
3796050 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
3796088 GGGCCACATG
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
76 85 0.81
77 20 0.19
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (76 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTTCAATTT
CTATCTTTAAA
Found at i:3796109 original size:77 final size:77
Alignment explanation
Indices: 3795898--3796112 Score: 292
Period size: 76 Copynumber: 2.8 Consensus size: 77
3795888 TTCTGTTTTC
* * * ***
3795898 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCATGACACGTTAAGG-AATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCCGAGGTAATTTTCAATTT
3795962 CTATCTTTAAAA
66 CTATCTTTAAAA
* *
3795974 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCTGAGGTAATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCCGAGGTAATTTTCAATTT
*
3796039 CTATCTTT-CAA
66 CTATCTTTAAAA
**
3796050 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACATGCCGAGGT-ATTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACATGCCGAGGTAATTTTCAA
3796113 AATTCCATTT
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
76 86 0.69
77 28 0.22
78 11 0.09
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (77 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCCGAGGTAATTTTCAATTT
CTATCTTTAAAA
Found at i:3796279 original size:90 final size:87
Alignment explanation
Indices: 3796029--3796442 Score: 388
Period size: 88 Copynumber: 4.6 Consensus size: 87
3796019 GCTGAGGTAA
* * *
3796029 TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC-C
1 TTTTCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGGCTC
*
3796093 ACATGCCGAGGTATTTTCAAAATTCCAT
62 ACATGCTGAGGTATTTTCAAAATT--AT
* *
3796121 TTTTCAATTTCTGTTTCTTCTAAAAATTAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCA
1 TTTTCAATTTCTG-TT-TTC-AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCA
*
3796186 CATGCTGAGGTATTTTCAATTGATGT-T
63 CATGCTGAGGTATTTTCAA--AAT-TAT
* * * * *
3796213 TTTTCAGTTTATGCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTTAGG-TTAC
1 TTTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTT-GGCTCAC
*
3796277 ATGTTGAGGTATTTTCAAAATCTAT
64 ATGCTGAGGTATTTTCAAAAT-TAT
* * * * *
3796302 TTTTCAAATTCTGTTGTCAAAAGTCAACTCATATTGCAAGAAGTGAGTTGAGCCTTGGCTCACGT
1 TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACAT
* **
3796367 GCTGAGCTATTTTCAATTTCTAT
66 GCTGAGGTATTTTCAAAAT-TAT
* * * * **
3796390 TTTT-AATGTT-TGTTTTTAAAGATTCAATTCATATTGCGAGAAATGAGTTGAGC
1 TTTTCAAT-TTCTGTTTTCAAA-AATCAACTCATATTGCAAGAGGTGAGTTGAGC
3796443 TCAGGATCAC
Statistics
Matches: 272, Mismatches: 39, Indels: 26
0.81 0.12 0.08
Matches are distributed among these distances:
87 12 0.04
88 98 0.36
89 11 0.04
90 54 0.20
91 8 0.03
92 82 0.30
93 4 0.01
94 2 0.01
95 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (87 bp):
TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACAT
GCTGAGGTATTTTCAAAATTAT
Found at i:3798142 original size:15 final size:16
Alignment explanation
Indices: 3798122--3798156 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3798112 CTTTTAATAT
3798122 TATTTAATATTA-TTA
1 TATTTAATATTATTTA
*
3798137 TATTTACTATTATTTA
1 TATTTAATATTATTTA
3798153 TATT
1 TATT
3798157 ATTCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAATATTATTTA
Found at i:3798786 original size:25 final size:25
Alignment explanation
Indices: 3798739--3798786 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3798729 TTTACTATCT
* **
3798739 TATGTATATATTTTGAATGCTATGC
1 TATGTATATATTTTAAACACTATGC
3798764 TATGTATATATTTTAAACACTAT
1 TATGTATATATTTTAAACACTAT
3798787 TTATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (25 bp):
TATGTATATATTTTAAACACTATGC
Found at i:3800775 original size:15 final size:15
Alignment explanation
Indices: 3800736--3800777 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3800726 ATTTGGTAAA
3800736 TTGAAAAATTAAGTG
1 TTGAAAAATTAAGTG
* *
3800751 CTAAAAAATTAAGTG
1 TTGAAAAATTAAGTG
*
3800766 TTGAATAATTAA
1 TTGAAAAATTAA
3800778 ACATGGACAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.33
Consensus pattern (15 bp):
TTGAAAAATTAAGTG
Found at i:3804942 original size:12 final size:12
Alignment explanation
Indices: 3804925--3804951 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3804915 AGTTTTTGTG
3804925 AAAAATAAAATA
1 AAAAATAAAATA
3804937 AAAAATAAAATA
1 AAAAATAAAATA
3804949 AAA
1 AAA
3804952 TAAAGAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:3807661 original size:28 final size:27
Alignment explanation
Indices: 3807630--3807723 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 27
3807620 CCCGATCTCA
3807630 CACACATAGTGCTCGGTTAATAATTTCG
1 CACACATAGTGCTC-GTTAATAATTTCG
* ** * *
3807658 CACACATATTGC-C-TTACACCCGATCTAG
1 CACACATAGTGCTCGTTA-A--TAATTTCG
*
3807686 CATACATAGTGCTCGATTAATAATTTCG
1 CACACATAGTGCTCG-TTAATAATTTCG
3807714 CACACATAGT
1 CACACATAGT
3807724 ACATATATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 1 0.02
28 38 0.79
29 1 0.02
30 1 0.02
31 3 0.06
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
CACACATAGTGCTCGTTAATAATTTCG
Found at i:3807678 original size:56 final size:56
Alignment explanation
Indices: 3807590--3807723 Score: 198
Period size: 56 Copynumber: 2.4 Consensus size: 56
3807580 ATATTCCCTA
* *
3807590 AATAATTTCGCACACACACAGTGCCTTACACCCGATCTCA-CACACATAGTGCTCGGTT
1 AATAATTTCG--CACACATAGTGCCTTACACCCGATCT-AGCACACATAGTGCTCGATT
* *
3807648 AATAATTTCGCACACATATTGCCTTACACCCGATCTAGCATACATAGTGCTCGATT
1 AATAATTTCGCACACATAGTGCCTTACACCCGATCTAGCACACATAGTGCTCGATT
3807704 AATAATTTCGCACACATAGT
1 AATAATTTCGCACACATAGT
3807724 ACATATATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
55 1 0.01
56 59 0.84
58 10 0.14
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (56 bp):
AATAATTTCGCACACATAGTGCCTTACACCCGATCTAGCACACATAGTGCTCGATT
Found at i:3808759 original size:22 final size:23
Alignment explanation
Indices: 3808715--3808765 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
3808705 TTTTTGTCCA
3808715 TTTTAATCATTTATAGAATTTTT
1 TTTTAATCATTTATAGAATTTTT
3808738 TTTTAATCATTTATAGAATTTTT
1 TTTTAATCATTTATAGAATTTTT
3808761 TTTTA
1 TTTTA
3808766 CTTAGTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTAATCATTTATAGAATTTTT
Found at i:3820860 original size:25 final size:24
Alignment explanation
Indices: 3820830--3820896 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
3820820 GCTACAGTTA
3820830 ATGGTTTTGATATGATGGTTGATTT
1 ATGGTTTTGAT-TGATGGTTGATTT
3820855 ATGGTTTTGATT--TGGTTGATTT
1 ATGGTTTTGATTGATGGTTGATTT
* *
3820877 ATGATTTTAATCTGATGGTT
1 ATGGTTTTGAT-TGATGGTT
3820897 TATGGTCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 19 0.51
23 1 0.03
24 1 0.03
25 16 0.43
ACGTcount: A:0.19, C:0.01, G:0.25, T:0.54
Consensus pattern (24 bp):
ATGGTTTTGATTGATGGTTGATTT
Found at i:3829427 original size:3 final size:3
Alignment explanation
Indices: 3829419--3829453 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3829409 TAGAAATTTA
3829419 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3829454 GATGCAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3830584 original size:20 final size:21
Alignment explanation
Indices: 3830547--3830585 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3830537 TATTTTTCGA
3830547 TAAAATATTAAGAATATTATT
1 TAAAATATTAAGAATATTATT
3830568 TAAAAT-TTAA-AATTATTA
1 TAAAATATTAAGAA-TATTA
3830586 CTAATGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TAAAATATTAAGAATATTATT
Found at i:3831737 original size:30 final size:30
Alignment explanation
Indices: 3831652--3831737 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
3831642 TATTTTATTA
* * *
3831652 TTAATTTTGTTATTATTTTAAAAGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCACTTG
3831682 TTAATTTTGTTATTATTTTAAAGGCACTTG
1 TTAATTTTGTTATTATTTTAAAGGCACTTG
*
3831712 TTAATTTTGTTATTATTTTAGAGGCA
1 TTAATTTTGTTATTATTTTAAAGGCA
3831738 TTTGCTTGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCACTTG
Found at i:3836042 original size:34 final size:31
Alignment explanation
Indices: 3836004--3836072 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 31
3835994 AGTAGTTGTA
*
3836004 TTATAAAGACGTAATTTTTGTACGTAAAATTATC
1 TTATAAAGACATAA--TTT-TACGTAAAATTATC
* *
3836038 TTATAAAGATATAATTTTATGTAAAATTATC
1 TTATAAAGACATAATTTTACGTAAAATTATC
3836069 TTAT
1 TTAT
3836073 TAAACAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 17 0.53
32 3 0.09
34 12 0.38
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (31 bp):
TTATAAAGACATAATTTTACGTAAAATTATC
Found at i:3838423 original size:13 final size:13
Alignment explanation
Indices: 3838405--3838429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3838395 TCTAACTTGA
3838405 TTAAGCTTATATT
1 TTAAGCTTATATT
3838418 TTAAGCTTATAT
1 TTAAGCTTATAT
3838430 ATATTTAAAC
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:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TTAAGCTTATATT
Found at i:3847785 original size:25 final size:25
Alignment explanation
Indices: 3847749--3847802 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
3847739 TGTTATACTT
*
3847749 CATGAATGCATGAAAACCCCATTTG
1 CATGAATACATGAAAACCCCATTTG
*
3847774 CATGAATACATGAAAACCTCATTTG
1 CATGAATACATGAAAACCCCATTTG
3847799 CATG
1 CATG
3847803 CATGCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (25 bp):
CATGAATACATGAAAACCCCATTTG
Found at i:3850015 original size:43 final size:44
Alignment explanation
Indices: 3849954--3850046 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
3849944 TCCTAATTGG
3849954 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
3849997 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
3850041 -AAAATA
1 GAAAATA
3850047 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:3850090 original size:19 final size:18
Alignment explanation
Indices: 3850068--3850107 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
3850058 TGAATAAAAC
3850068 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
3850087 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
3850105 TTA
1 TTA
3850108 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:3856873 original size:43 final size:44
Alignment explanation
Indices: 3856812--3856904 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
3856802 TCCTAATTGG
3856812 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
3856855 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
3856899 -AAAATA
1 GAAAATA
3856905 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:3856948 original size:19 final size:18
Alignment explanation
Indices: 3856926--3856965 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
3856916 TGAATAAAAC
3856926 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
3856945 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
3856963 TTA
1 TTA
3856966 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:3857985 original size:17 final size:18
Alignment explanation
Indices: 3857965--3858002 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3857955 TTAGAATCGG
*
3857965 ATTG-GAAAAATAATTTA
1 ATTGAGAAAAATAATTAA
*
3857982 ATTGAGAGAAATAATTAA
1 ATTGAGAAAAATAATTAA
3858000 ATT
1 ATT
3858003 AAATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (18 bp):
ATTGAGAAAAATAATTAA
Found at i:3859067 original size:61 final size:61
Alignment explanation
Indices: 3858958--3859079 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
3858948 AGAATAAAAA
* * *
3858958 TATATGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGGGGGGTGGAAACTTTATAGTTT
1 TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
3859019 TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
1 TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
3859080 AGAGCCATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (61 bp):
TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
Found at i:3865821 original size:17 final size:17
Alignment explanation
Indices: 3865799--3865833 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3865789 AAACTGTTTG
3865799 ACAAAGTTTATAACATT
1 ACAAAGTTTATAACATT
3865816 ACAAAGTTTATAACATT
1 ACAAAGTTTATAACATT
3865833 A
1 A
3865834 AATACTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (17 bp):
ACAAAGTTTATAACATT
Found at i:3867338 original size:17 final size:18
Alignment explanation
Indices: 3867318--3867353 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3867308 TTTATATATA
3867318 TTATATTAA-TTTTTACT
1 TTATATTAATTTTTTACT
3867335 TTATATTAATTTTTTACT
1 TTATATTAATTTTTTACT
3867353 T
1 T
3867354 CTTTCTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTAATTTTTTACT
Found at i:3872123 original size:6 final size:6
Alignment explanation
Indices: 3872112--3872158 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
3872102 ATCCGAAGAG
* * * *
3872112 GAGGAA GAGGAA GAGGAA GAGGAA GGGGAC GAGGAT GAGGAT GAGGA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
3872159 GACTAAAGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.40, C:0.02, G:0.53, T:0.04
Consensus pattern (6 bp):
GAGGAA
Found at i:3873003 original size:2 final size:2
Alignment explanation
Indices: 3872996--3873032 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3872986 AGAAATAATC
3872996 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3873033 ACTCACTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3876268 original size:9 final size:9
Alignment explanation
Indices: 3876254--3876467 Score: 87
Period size: 9 Copynumber: 22.3 Consensus size: 9
3876244 TTTTATCATA
3876254 AAAAATTAT
1 AAAAATTAT
3876263 AAAAATATCAT
1 AAAAAT-T-AT
3876274 AAAAA--AT
1 AAAAATTAT
* *
3876281 AAATATTTAC
1 AAA-AATTAT
3876291 ATAAAATTAT
1 A-AAAATTAT
*
3876301 AGAAATTAT
1 AAAAATTAT
*
3876310 AGAAAAATTAG
1 --AAAAATTAT
** *
3876321 AGTACTTAT
1 AAAAATTAT
*
3876330 AAAAAATAT
1 AAAAATTAT
3876339 AAAAATTCAT
1 AAAAATT-AT
*
3876349 AAAAGGTTAT
1 AAAA-ATTAT
*
3876359 AAATATTAT
1 AAAAATTAT
*
3876368 AAAATTTTAT
1 AAAA-ATTAT
*
3876378 AAAAATTCT
1 AAAAATTAT
3876387 AATAAATTAT
1 AA-AAATTAT
**
3876397 AAAAAAAAT
1 AAAAATTAT
3876406 AAAACA-TAT
1 AAAA-ATTAT
3876415 AAAAGCA-TATT
1 AAAA--ATTA-T
* *
3876426 CAAAATTTTT
1 -AAAAATTAT
3876436 AAAAGATTAT
1 AAAA-ATTAT
3876446 -AAAATTCAT
1 AAAAATT-AT
3876455 AAAAACTTAT
1 AAAAA-TTAT
3876465 AAA
1 AAA
3876468 TAATATGATA
Statistics
Matches: 153, Mismatches: 31, Indels: 41
0.68 0.14 0.18
Matches are distributed among these distances:
7 5 0.03
8 4 0.03
9 65 0.42
10 53 0.35
11 22 0.14
12 4 0.03
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3876318 original size:20 final size:19
Alignment explanation
Indices: 3876251--3876397 Score: 72
Period size: 19 Copynumber: 7.7 Consensus size: 19
3876241 TATTTTTATC
*
3876251 ATAAAAAATTATAAAAATAT
1 ATAAAAAATTATAGAAAT-T
*
3876271 CATAAAAAA-TA-A-ATATT
1 -ATAAAAAATTATAGAAATT
3876288 -TACATAAAATTATAGAAATT
1 ATA-A-AAAATTATAGAAATT
* * *
3876308 ATAGAAAAATTAGAGTACTT
1 ATA-AAAAATTATAGAAATT
*
3876328 ATAAAAAA-TATAAAAATT
1 ATAAAAAATTATAGAAATT
**
3876346 CATAAAAGGTTATA-AATATT
1 -ATAAAAAATTATAGAA-ATT
** *
3876366 ATAAAATTTTATAAAAATT
1 ATAAAAAATTATAGAAATT
* *
3876385 CTAATAAATTATA
1 ATAAAAAATTATA
3876398 AAAAAAATAA
Statistics
Matches: 98, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
15 2 0.02
16 1 0.01
17 5 0.05
18 11 0.11
19 38 0.39
20 30 0.31
21 11 0.11
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (19 bp):
ATAAAAAATTATAGAAATT
Found at i:3876345 original size:38 final size:36
Alignment explanation
Indices: 3876251--3876352 Score: 98
Period size: 38 Copynumber: 2.7 Consensus size: 36
3876241 TATTTTTATC
*
3876251 ATAAAAAATTATAAAAATATCATAAAAAATAAATATTT
1 ATAAAAAA-TATAAAAAT-TCATAAAAAATAAATACTT
* * * *
3876289 ACATAAAATTATAGAAATT-ATAGAAAAATTAGAGTACTT
1 ATA-AAAAATATAAAAATTCATA-AAAAA-TA-AATACTT
3876328 ATAAAAAATATAAAAATTCATAAAA
1 ATAAAAAATATAAAAATTCATAAAA
3876353 GGTTATAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
36 3 0.06
37 6 0.12
38 28 0.55
39 14 0.27
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (36 bp):
ATAAAAAATATAAAAATTCATAAAAAATAAATACTT
Found at i:3876358 original size:29 final size:29
Alignment explanation
Indices: 3876326--3876381 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
3876316 ATTAGAGTAC
3876326 TTATAAAAAATATAAAAATTCATAAAAGG
1 TTATAAAAAATATAAAAATTCATAAAAGG
* * * *
3876355 TTATAAATATTATAAAATTTTATAAAA
1 TTATAAAAAATATAAAAATTCATAAAA
3876382 ATTCTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (29 bp):
TTATAAAAAATATAAAAATTCATAAAAGG
Found at i:3880280 original size:21 final size:20
Alignment explanation
Indices: 3880232--3880281 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3880222 TCGTGTCAGT
*
3880232 AAAAAAAGTTTGAAAAAGAA
1 AAAAAAAGGTTGAAAAAGAA
* *
3880252 AAACAAAGGTTGGAAAAGCAA
1 AAAAAAAGGTTGAAAAAG-AA
3880273 AAAAAAAGG
1 AAAAAAAGG
3880282 GGAGCCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.66, C:0.04, G:0.20, T:0.10
Consensus pattern (20 bp):
AAAAAAAGGTTGAAAAAGAA
Found at i:3882463 original size:116 final size:116
Alignment explanation
Indices: 3882254--3882483 Score: 295
Period size: 116 Copynumber: 2.0 Consensus size: 116
3882244 AGCGTTATCC
* *
3882254 TTTTAGCACCCTGATTGATGACTGTTTGATTTTATTTGATGGAGGTTGGGTGATTGAGATTAAAC
1 TTTTAGCACCCTGATTGATGACTGGTTGACTTTATTTGATGGAGGTTGGGTGATTGAGATTAAAC
** * *
3882319 ATATTATTTGTAAGGGCAAAAAGCGTACAAATCAC-TAGGATTCTTTAACAG
66 ATATTATTTCCAAGGACAAAAAGCGTACAAATCACTTA-AATTCTTTAACAG
* * *
3882370 TTTTAGCACCCTGATTGATGATTGGTTGACTTTGTTTGAT-GAGGGTTGGGTGATTGAGATTAGA
1 TTTTAGCACCCTGATTGATGACTGGTTGACTTTATTTGATGGA-GGTTGGGTGATTGAGATTAAA
* * * *
3882434 CATATTCTTTCCAAGGACAATGAA-TGTACAAATGACTTAAATTCTTTAAC
65 CATATTATTTCCAAGGACAA-AAAGCGTACAAATCACTTAAATTCTTTAAC
3882484 GTAAGGATCC
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
115 2 0.02
116 92 0.94
117 4 0.04
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (116 bp):
TTTTAGCACCCTGATTGATGACTGGTTGACTTTATTTGATGGAGGTTGGGTGATTGAGATTAAAC
ATATTATTTCCAAGGACAAAAAGCGTACAAATCACTTAAATTCTTTAACAG
Found at i:3885523 original size:18 final size:18
Alignment explanation
Indices: 3885500--3885534 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3885490 ATTTCCATAC
3885500 ATTTTTCATA-ATTAATTA
1 ATTTTT-ATATATTAATTA
3885518 ATTTTTATATATTAATT
1 ATTTTTATATATTAATT
3885535 GGGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATATATTAATTA
Found at i:3917796 original size:64 final size:64
Alignment explanation
Indices: 3917717--3917843 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
3917707 AGGTTTTAAC
3917717 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
1 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
*
3917781 TTGACCATAATCTGTTTTATGTTCTCTCATGTAGGTTTGAAGTCCATCTCGAGATGTTCAAAA
1 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAA
3917844 CTATCTATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (64 bp):
TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
Found at i:3918907 original size:16 final size:16
Alignment explanation
Indices: 3918886--3918917 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3918876 CATCTAAAAG
3918886 GAAACCATGATTTTTC
1 GAAACCATGATTTTTC
3918902 GAAACCATGATTTTTC
1 GAAACCATGATTTTTC
3918918 AGGGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
GAAACCATGATTTTTC
Found at i:3919953 original size:15 final size:16
Alignment explanation
Indices: 3919923--3919955 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3919913 TTAAAAAAAA
3919923 TAATTTTTATAAATTT
1 TAATTTTTATAAATTT
*
3919939 TAATTTTT-TAGATTT
1 TAATTTTTATAAATTT
3919954 TA
1 TA
3919956 TATAATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TAATTTTTATAAATTT
Found at i:3924235 original size:21 final size:21
Alignment explanation
Indices: 3924197--3924239 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3924187 AAAAAATTAA
*
3924197 AAATATATTTTTATAATTTTT
1 AAATATATTTTAATAATTTTT
*
3924218 AAATA-ATTTTAATAAATTTT
1 AAATATATTTTAATAATTTTT
3924238 AA
1 AA
3924240 CTTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATATATTTTAATAATTTTT
Found at i:3925267 original size:25 final size:25
Alignment explanation
Indices: 3925221--3925290 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
3925211 GGTTTATTTT
3925221 ATTTAATATTAATA-TAATTATATTC
1 ATTTAATATTAATATTAA-TATATTC
*
3925246 ATTTAATATTAATATTAATATA-AC
1 ATTTAATATTAATATTAATATATTC
*
3925270 ATTTAA-ATT--TATTATTATATT
1 ATTTAATATTAATATTAATATATT
3925291 TTTTTGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.22
23 3 0.08
24 7 0.17
25 18 0.45
26 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTAATATTAATATTAATATATTC
Found at i:3925329 original size:23 final size:26
Alignment explanation
Indices: 3925276--3925398 Score: 80
Period size: 25 Copynumber: 4.8 Consensus size: 26
3925266 TAACATTTAA
*
3925276 ATTTATTATTATATTTTTTTGAAAAT
1 ATTTATTATTATATTATTTTGAAAAT
*
3925302 ATTTATTGTTATA-TATTTT-AAAAT
1 ATTTATTATTATATTATTTTGAAAAT
* * *
3925326 -TTTATATATTATTATTCCTTGTCAACAAT
1 ATTTAT-TATTA-TATT-ATTTTGAA-AAT
*
3925355 -TTT-TTAAATATATT-TTTTGAAAAT
1 ATTTATT-ATTATATTATTTTGAAAAT
*
3925379 ATTTA-TATTTATATTTTTTT
1 ATTTATTA-TTATATTATTTT
3925399 TATATATTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
23 5 0.06
24 13 0.17
25 22 0.29
26 17 0.22
27 8 0.10
28 6 0.08
29 6 0.08
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (26 bp):
ATTTATTATTATATTATTTTGAAAAT
Found at i:3931197 original size:22 final size:22
Alignment explanation
Indices: 3931162--3931203 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3931152 TTAATTTTGT
*
3931162 TTTTATACTGTAAAATTAAATA
1 TTTTATACTGTAAAAATAAATA
* *
3931184 TTTTATATTTTAAAAATAAA
1 TTTTATACTGTAAAAATAAA
3931204 ATAATTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTATACTGTAAAAATAAATA
Found at i:3932198 original size:18 final size:18
Alignment explanation
Indices: 3932166--3932207 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3932156 TAAAATTTCA
3932166 TAAAAATAATAAAAA-TT
1 TAAAAATAATAAAAACTT
*
3932183 TAAAATATATTAAAAACTT
1 TAAAA-ATAATAAAAACTT
3932202 TAAAAA
1 TAAAAA
3932208 CCGGTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 10 0.45
19 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATAATAAAAACTT
Found at i:3945550 original size:66 final size:65
Alignment explanation
Indices: 3945445--3945568 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 65
3945435 CTTGAATCTT
*
3945445 TATAAAATTTTTTGAGTAATCCCAAAATCTTTCAATATGTTTATAAGCCTTTTCAAAGTAGGATC
1 TATAAAATTTTTTGAGTAATCCCAAAACCTTTCAATATGTTTATAAGCCTTTTCAAAGTAGGATC
* * *
3945510 TATAAAGATTTTTTTGAGTACT-CCAAGACCTTTGAATATGTTTATAAGCCTTTTCAAAG
1 TATAAA-A-TTTTTTGAGTAATCCCAAAACCTTTCAATATGTTTATAAGCCTTTTCAAAG
3945569 CAGGTTTTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
65 6 0.11
66 35 0.66
67 12 0.23
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (65 bp):
TATAAAATTTTTTGAGTAATCCCAAAACCTTTCAATATGTTTATAAGCCTTTTCAAAGTAGGATC
Found at i:3951025 original size:21 final size:21
Alignment explanation
Indices: 3950999--3951039 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3950989 AGACGAGCAA
* *
3950999 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3951020 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3951040 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3957347 original size:15 final size:17
Alignment explanation
Indices: 3957326--3957366 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
3957316 TAATTATTTA
3957326 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
3957342 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
3957358 AAAATTATA
1 AAAATTATA
3957367 TTTCTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:3957367 original size:26 final size:26
Alignment explanation
Indices: 3957317--3957366 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
3957307 AATTTGGTTT
*
3957317 AATTATTTAAAAATTATAAAAATATA
1 AATTATTTAAAAATGATAAAAATATA
*
3957343 AATTA-TT-AAAATGATAAAATTATA
1 AATTATTTAAAAATGATAAAAATATA
3957367 TTTCTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AATTATTTAAAAATGATAAAAATATA
Found at i:3970411 original size:29 final size:29
Alignment explanation
Indices: 3970354--3970437 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 29
3970344 ATATTAAAAT
* * *
3970354 TATATATAAATTTTAATTTAATGTGTAATAA
1 TATACATAAATTTTAATTT--GGTATAATAA
*
3970385 TATACATAAATTTTAATTTGGTATAATTA
1 TATACATAAATTTTAATTTGGTATAATAA
* *
3970414 TATACGTGAAATTATAATTGTGGT
1 TATACAT-AAATTTTAATT-TGGT
3970438 TTGAATGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.29
30 10 0.22
31 22 0.49
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.46
Consensus pattern (29 bp):
TATACATAAATTTTAATTTGGTATAATAA
Found at i:3970624 original size:29 final size:29
Alignment explanation
Indices: 3970599--3970655 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
3970589 ATTTGTAAGA
3970599 ATTAAATC-AAATCAAAATTTTATGTATAAT
1 ATTAAA-CAAAATCAAAA-TTTATGTATAAT
*
3970629 ATTATACAAAATCAAAATTTATGTATA
1 ATTAAACAAAATCAAAATTTATGTATA
3970656 TAATTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (29 bp):
ATTAAACAAAATCAAAATTTATGTATAAT
Found at i:3977497 original size:15 final size:15
Alignment explanation
Indices: 3977477--3977511 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3977467 TATTTTAATA
3977477 TATTATCATCATTAT
1 TATTATCATCATTAT
*
3977492 TATTATCATTATTAT
1 TATTATCATCATTAT
3977507 TATTA
1 TATTA
3977512 ACCTTATTAT
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:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATCATCATTAT
Found at i:3977507 original size:12 final size:12
Alignment explanation
Indices: 3977451--3977509 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
3977441 TTGAGTACTT
* *
3977451 TTATTATTCTCT
1 TTATTATTATCA
* *
3977463 TTATTATTTTAA
1 TTATTATTATCA
*
3977475 TATATTATCATCA
1 T-TATTATTATCA
3977488 TTATTATTATCA
1 TTATTATTATCA
3977500 TTATTATTAT
1 TTATTATTAT
3977510 TAACCTTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
12 30 0.77
13 9 0.23
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATTATTATCA
Found at i:3977518 original size:15 final size:15
Alignment explanation
Indices: 3977477--3977523 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3977467 TATTTTAATA
* *
3977477 TATTATCATCATTAT
1 TATTAACATTATTAT
*
3977492 TATTATCATTATTAT
1 TATTAACATTATTAT
*
3977507 TATTAACCTTATTAT
1 TATTAACATTATTAT
3977522 TA
1 TA
3977524 CTAGTAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAACATTATTAT
Found at i:3990396 original size:39 final size:37
Alignment explanation
Indices: 3990292--3990397 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 37
3990282 CGGATTAAAG
* *
3990292 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCA
1 GATCTTATCTC-CTG-AGTTACAGT-G-GAAGACCAAATCA
*
3990333 GGTCTTAT-TCCCTGAGTTACAGTGGAAGACCAGAATTCA
1 GATCTTATCT-CCTGAGTTACAGTGGAAGACCA-AA-TCA
3990372 GATCTTATCTCCTGAGTTACAGTGGA
1 GATCTTATCTCCTGAGTTACAGTGGA
3990398 GCAGATTGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
37 7 0.12
38 2 0.04
39 35 0.61
40 5 0.09
41 8 0.14
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (37 bp):
GATCTTATCTCCTGAGTTACAGTGGAAGACCAAATCA
Found at i:3990483 original size:85 final size:82
Alignment explanation
Indices: 3990377--3990532 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 82
3990367 ATTCAGATCT
* * * *
3990377 TATCTCCTGAGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATACAGCGGA
1 TATCTCCTGAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATACAGCAGA
3990441 GCAGATCGAGACACTATCC
65 G-AGATCGAGACACTATCC
* * * *
3990460 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGTTACAGCAG
1 TATCT-CCTG-AGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATACAGCAG
3990525 AGAGATCG
64 AGAGATCG
3990533 CATCAGTCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
83 5 0.08
84 10 0.16
85 45 0.73
86 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (82 bp):
TATCTCCTGAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATACAGCAGAG
AGATCGAGACACTATCC
Done.