Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 129 of 163
Found at i:35373425 original size:41 final size:42
Alignment explanation
Indices: 35373347--35373446 Score: 148
Period size: 41 Copynumber: 2.4 Consensus size: 42
35373337 GCTAATTCAC
* *
35373347 ACCTTTAGTGGCGCTTTTCTAATAAGCGCCGCTAATGACAAG
1 ACCTTTAGCGGCGCTTTTCTAATAAGCGCCACTAATGACAAG
* **
35373389 ACCTTTAGCGACGCTTTTCT-ATAAGCGCCACTAATGACCCG
1 ACCTTTAGCGGCGCTTTTCTAATAAGCGCCACTAATGACAAG
35373430 ACCTTTAGCGGCGCTTT
1 ACCTTTAGCGGCGCTTT
35373447 CCACAAAGCG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 34 0.65
42 18 0.35
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (42 bp):
ACCTTTAGCGGCGCTTTTCTAATAAGCGCCACTAATGACAAG
Found at i:35381744 original size:26 final size:26
Alignment explanation
Indices: 35381676--35381744 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
35381666 ACATTAACAC
* *
35381676 AAATATGGTAATATTTAGTCGCTAGAT
1 AAATATGGTAATATCT-GTCACTAGAT
* * *
35381703 AAATGT-GTAACATCTGTCACTAGTT
1 AAATATGGTAATATCTGTCACTAGAT
35381728 AAATATGGTAATATCTG
1 AAATATGGTAATATCTG
35381745 CGATTAATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 13 0.38
26 16 0.47
27 5 0.15
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (26 bp):
AAATATGGTAATATCTGTCACTAGAT
Found at i:35385078 original size:31 final size:33
Alignment explanation
Indices: 35385014--35385094 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 33
35385004 TCATTAACTT
* * *
35385014 TTTAATCAATTTTAGT-TTTTATATTTTTTGAA
1 TTTAATCAATTTTAATCTTTTATACTTTTCGAA
35385046 -TTAATCAATTTTAATCTTTT-TACTTTTCGAA
1 TTTAATCAATTTTAATCTTTTATACTTTTCGAA
35385077 TTTTAA--AATTTTAATCTT
1 -TTTAATCAATTTTAATCTT
35385095 AACCCAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 35 0.81
32 4 0.09
33 4 0.09
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (33 bp):
TTTAATCAATTTTAATCTTTTATACTTTTCGAA
Found at i:35394643 original size:23 final size:22
Alignment explanation
Indices: 35394613--35394737 Score: 106
Period size: 23 Copynumber: 5.5 Consensus size: 22
35394603 ACGCTAGCGC
35394613 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
*
35394636 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
* ** * *
35394659 GCCTACTGATTTGTGCTATGTGC
1 GCTTACTG-TTTGCACTTTGTGT
* * *
35394682 GCCTACTGATTGCACTGTGTGT
1 GCTTACTGTTTGCACTTTGTGT
* * *
35394704 GCCTACTGGATTGCACTGTGTGT
1 GCTTACT-GTTTGCACTTTGTGT
35394727 GCTTACTGTTT
1 GCTTACTGTTT
35394738 CCCCAGTACT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
22 19 0.22
23 64 0.74
24 3 0.03
ACGTcount: A:0.11, C:0.22, G:0.25, T:0.42
Consensus pattern (22 bp):
GCTTACTGTTTGCACTTTGTGT
Found at i:35394734 original size:45 final size:46
Alignment explanation
Indices: 35394616--35394734 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 46
35394606 CTAGCGCGCT
* *
35394616 TACTG-TTTCGCACTTTGTGTGCTTACTGTTTCGCACCTTGTGTGCC
1 TACTGATTT-GCACTATGTGTGCTTACTGATTCGCACCTTGTGTGCC
** * *
35394662 TACTGATTTGTGCTATGTGCGCCTACTGATT-GCA-CTGTGTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACCT-TGTGTGCC
*
35394707 TACTGGA-TTGCACTGTGTGTGCTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
35394735 TTTCCCCAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
44 2 0.03
45 31 0.53
46 23 0.39
47 3 0.05
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTCGCACCTTGTGTGCC
Found at i:35395578 original size:2 final size:2
Alignment explanation
Indices: 35395573--35395598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35395563 AAAAAAAAAA
35395573 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
35395599 TTGAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35408075 original size:21 final size:21
Alignment explanation
Indices: 35408041--35408080 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35408031 CTGAAAAGAA
* *
35408041 TTAAAAAATGTAAACAAATAT
1 TTAAAAAATATAAAAAAATAT
*
35408062 TTAAAAATTATAAAAAAAT
1 TTAAAAAATATAAAAAAAT
35408081 TCAAGATCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
TTAAAAAATATAAAAAAATAT
Found at i:35412048 original size:19 final size:19
Alignment explanation
Indices: 35412024--35412084 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 19
35412014 CTTGTCACTG
35412024 TATATTTTTAAATTAAAAA
1 TATATTTTTAAATTAAAAA
35412043 TATA---TTAAATGTAAAAA
1 TATATTTTTAAAT-TAAAAA
*
35412060 TATATTTTTTAA-TAAAAA
1 TATATTTTTAAATTAAAAA
35412078 TTATATT
1 -TATATT
35412085 AAAGATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
16 6 0.17
17 10 0.28
18 6 0.17
19 10 0.28
20 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATATTTTTAAATTAAAAA
Found at i:35421054 original size:30 final size:30
Alignment explanation
Indices: 35421020--35421084 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
35421010 TAACTTAGCA
* * *
35421020 AACAAATGCCTCTAAAATAGTAACAAAATT
1 AACAAATACCTCTAAAACAATAACAAAATT
*
35421050 AACAAATACCTCTAAAACAATAACGAAATT
1 AACAAATACCTCTAAAACAATAACAAAATT
35421080 AACAA
1 AACAA
35421085 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.18, G:0.05, T:0.20
Consensus pattern (30 bp):
AACAAATACCTCTAAAACAATAACAAAATT
Found at i:35421201 original size:21 final size:22
Alignment explanation
Indices: 35421155--35421201 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
35421145 AAATTGTAGC
*
35421155 AAAATAGAAATAAAACAACAAG
1 AAAATAGAAATAAAACAACAAA
* *
35421177 AAAATAGCATTAAAA-AACAAA
1 AAAATAGAAATAAAACAACAAA
35421198 AAAA
1 AAAA
35421202 ATGCAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAATAGAAATAAAACAACAAA
Found at i:35422373 original size:32 final size:32
Alignment explanation
Indices: 35422332--35422397 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
35422322 CACACAAGAA
35422332 GACCTAAAGTGACCCACAATATATAGGCCCCT
1 GACCTAAAGTGACCCACAATATATAGGCCCCT
35422364 GACCTAAAGTGACCCACAATATATAGGCCCCT
1 GACCTAAAGTGACCCACAATATATAGGCCCCT
35422396 GA
1 GA
35422398 ATTGGAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (32 bp):
GACCTAAAGTGACCCACAATATATAGGCCCCT
Found at i:35423716 original size:4 final size:4
Alignment explanation
Indices: 35423709--35423765 Score: 62
Period size: 4 Copynumber: 13.8 Consensus size: 4
35423699 CGGGCAGAAG
* *
35423709 AAGA AAGA AAGAA AAAA AAGAA AAAA AAGA AAGA AAGA AA-A GAAGA AAGA
1 AAGA AAGA AAG-A AAGA AAG-A AAGA AAGA AAGA AAGA AAGA -AAGA AAGA
35423759 AAGA AAG
1 AAGA AAG
35423766 GTAGTGTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 1 0.02
4 37 0.82
5 7 0.16
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:35423730 original size:9 final size:9
Alignment explanation
Indices: 35423706--35423749 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
35423696 AAACGGGCAG
35423706 AAGAAGAAAGA
1 AAGAA-AAA-A
35423717 AAGAAAAAA
1 AAGAAAAAA
35423726 AAGAAAAAA
1 AAGAAAAAA
*
35423735 AAG-AAAGA
1 AAGAAAAAA
35423743 AAGAAAA
1 AAGAAAA
35423750 GAAGAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 7 0.23
9 16 0.52
10 3 0.10
11 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:35423730 original size:13 final size:13
Alignment explanation
Indices: 35423712--35423760 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
35423702 GCAGAAGAAG
35423712 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
35423725 AAAGAAA-AAAAA
1 AAAGAAAGAAAAA
35423737 GAAAGAAAG-AAAA
1 -AAAGAAAGAAAAA
*
35423750 GAAGAAAGAAA
1 AAAGAAAGAAA
35423761 GAAAGGTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAA
Found at i:35423750 original size:9 final size:9
Alignment explanation
Indices: 35423712--35423764 Score: 67
Period size: 9 Copynumber: 6.2 Consensus size: 9
35423702 GCAGAAGAAG
35423712 AAAGAAAGA
1 AAAGAAAGA
*
35423721 AAAAAAAGA
1 AAAGAAAGA
*
35423730 AAAAAAAG-
1 AAAGAAAGA
35423738 AAAGAAAGA
1 AAAGAAAGA
35423747 AAAG-AAG-
1 AAAGAAAGA
35423754 AAAGAAAGA
1 AAAGAAAGA
35423763 AA
1 AA
35423765 GGTAGTGTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 4 0.10
8 13 0.33
9 22 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAGAAAGA
Found at i:35429533 original size:13 final size:13
Alignment explanation
Indices: 35429515--35429543 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35429505 ACAAATTAAA
35429515 AAATTTTAAAAAT
1 AAATTTTAAAAAT
35429528 AAA-TTTAAAAAT
1 AAATTTTAAAAAT
35429540 AAAT
1 AAAT
35429544 ACATTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:35429581 original size:4 final size:4
Alignment explanation
Indices: 35429572--35429612 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
35429562 TTTCCTTCTC
*
35429572 CTTT CTTT CTTCT CATT C-TT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTT-T CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
35429613 AATACCCGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.82
5 3 0.09
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:35429603 original size:28 final size:26
Alignment explanation
Indices: 35429551--35429610 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 26
35429541 AATACATTAC
35429551 CTTTC-TCTCATTTTCCTTCTCCTTT
1 CTTTCTTCTCATTTTCCTTCTCCTTT
* *
35429576 CTTTCTTCTCATTCTTCTTTCTTTCTTT
1 CTTTCTTCTCATT-TTCCTTC-TCCTTT
35429604 CTTTCTT
1 CTTTCTT
35429611 TCAATACCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 7 0.23
27 6 0.20
28 12 0.40
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (26 bp):
CTTTCTTCTCATTTTCCTTCTCCTTT
Found at i:35436290 original size:7 final size:7
Alignment explanation
Indices: 35436278--35436322 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
35436268 AAGATCATAT
35436278 AACAGCA
1 AACAGCA
35436285 AACAGCA
1 AACAGCA
35436292 AACAGCA
1 AACAGCA
35436299 AACAGCA
1 AACAGCA
35436306 AACAGCA
1 AACAGCA
35436313 AACAGCA
1 AACAGCA
35436320 AAC
1 AAC
35436323 GATACTACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.58, C:0.29, G:0.13, T:0.00
Consensus pattern (7 bp):
AACAGCA
Found at i:35436642 original size:30 final size:30
Alignment explanation
Indices: 35436606--35436667 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
35436596 TGACGACACA
*
35436606 TTATTGGTCTCACCTCTGTAAGTACGTGAC
1 TTATTGGTCTCACCTCTGTAAGTACGCGAC
35436636 TTATTGGTCTCACCTCTGTAAGTACGCGAC
1 TTATTGGTCTCACCTCTGTAAGTACGCGAC
35436666 TT
1 TT
35436668 GTTCCTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (30 bp):
TTATTGGTCTCACCTCTGTAAGTACGCGAC
Found at i:35441258 original size:154 final size:154
Alignment explanation
Indices: 35440978--35441644 Score: 782
Period size: 154 Copynumber: 4.3 Consensus size: 154
35440968 CACAATTAGC
35440978 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
1 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
35441043 GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCTATT
66 GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCTATT
35441108 AAAAAATAATGAAAAATTCAAACA
131 AAAAAATAATGAAAAATTCAAACA
35441132 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
1 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
35441197 GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCTATT
66 GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCTATT
35441262 AAAAAATAATGAAAAATTCAAACA
131 AAAAAATAATGAAAAATTCAAACA
***
35441286 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAA-CACTAAAAAT-
1 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCAC-ACCCATA
* * * ** *** * *** *
35441349 GTTAAC-ACAT-TTAC-TTTTGGGTACCAAAACATATAACTTTTGTCA-AA-TAGAGGTACTAAA
65 G--GACTATATATGACAAATTAATTA-CAAAA-TTA-AACAAAT-TCACAATTA-A---ATTAAA
* * * ** * * *
35441409 TTCAAGT-T-TT-AGAGTTGATTTGATGAGAATTCATAATTA
120 TT-TATTCTATTAAAAAAT-A-ATGA--AAAATTCA-AA-CA
* * *
35441448 GCTAATAATATTAGCAATTCATTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACATCCAT
1 --TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCAT
* * *
35441513 AGGACTATATTTGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTGTTCAA
64 AGGACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCTA
* *
35441578 TTAAAAAATCAT-AAAAAATCAAACA
129 TTAAAAAATAATGAAAAATTCAAACA
35441603 TAATAATATTAGCAATTAAC-TTCATCAAATCAACCCTAAAAC
1 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAAC
35441645 TTGAATTAAA
Statistics
Matches: 427, Mismatches: 56, Indels: 62
0.78 0.10 0.11
Matches are distributed among these distances:
152 26 0.06
153 30 0.07
154 217 0.51
155 10 0.02
156 8 0.02
157 9 0.02
158 11 0.03
159 4 0.01
160 15 0.04
161 4 0.01
162 7 0.02
163 9 0.02
164 61 0.14
165 12 0.03
166 4 0.01
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.30
Consensus pattern (154 bp):
TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCTATT
AAAAAATAATGAAAAATTCAAACA
Found at i:35441545 original size:318 final size:316
Alignment explanation
Indices: 35441132--35441726 Score: 1046
Period size: 318 Copynumber: 1.9 Consensus size: 316
35441122 AATTCAAACA
35441132 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
1 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
*
35441197 GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCTATT
66 GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCAATT
*
35441262 AAAAAATAATGAAAAATTCAAACATAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAA
131 AAAAAATAAT-AAAAAATCAAACATAATAATATTAGCAATTAAC-TTCATCAAATCAACCCTAAA
35441327 ACCCAAATTAAACACTAAAAATGTTAACACATTTACTTTTGGGTACCAAAACATATAACTTTTGT
194 ACCCAAATTAAACACTAAAAATGTTAACACATTTACTTTTGGGTACCAAAACATATAACTTTTGT
*
35441392 CAAATAGAGGTACTAAATTCAAGTTTTAGAGTTGATTTGATGAGAATTCATAATTAGC
259 CAAATACAGGTACTAAATTCAAGTTTTAGAGTTGATTTGATGAGAATTCATAATTAGC
* * *
35441450 TAATAATATTAGCAATTCATTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACATCCATAG
1 TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
* *
35441515 GACTATATTTGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTGTTCAATT
66 GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCAATT
*
35441580 AAAAAATCATAAAAAATCAAACATAATAATATTAGCAATTAACTTCATCAAATCAACCCTAAAAC
131 AAAAAATAATAAAAAATCAAACATAATAATATTAGCAATTAACTTCATCAAATCAACCCTAAAAC
*** *
35441645 TTGAATTAAACACTAAAAATGTTAACACATTTACTTTTGGGTACCAAAATATATAACTTTTGTCA
196 CCAAATTAAACACTAAAAATGTTAACACATTTACTTTTGGGTACCAAAACATATAACTTTTGTCA
*
35441710 AATACATGTACTAAATT
261 AATACAGGTACTAAATT
35441727 GGACCAAAAA
Statistics
Matches: 263, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
316 98 0.37
317 32 0.12
318 133 0.51
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (316 bp):
TAATAATATTAGCAATTAACTTTCATCAAATCAACCCTAAAACCCAAATTAAATCACACCCATAG
GACTATATATGACAAATTAATTACAAAATTAAACAAATTCACAATTAAATTAAATTTATTCAATT
AAAAAATAATAAAAAATCAAACATAATAATATTAGCAATTAACTTCATCAAATCAACCCTAAAAC
CCAAATTAAACACTAAAAATGTTAACACATTTACTTTTGGGTACCAAAACATATAACTTTTGTCA
AATACAGGTACTAAATTCAAGTTTTAGAGTTGATTTGATGAGAATTCATAATTAGC
Found at i:35449445 original size:14 final size:14
Alignment explanation
Indices: 35449426--35449455 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
35449416 TTGTATTTAA
35449426 TTTATATTTATCTT
1 TTTATATTTATCTT
35449440 TTTATATTTATCTT
1 TTTATATTTATCTT
35449454 TT
1 TT
35449456 AGAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:35453795 original size:19 final size:19
Alignment explanation
Indices: 35453773--35453816 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
35453763 TTTATAAGGG
35453773 TTTAATATTTAAGATAT-TA
1 TTTAATATTTAA-ATATGTA
* *
35453792 TTTATTATTTAAATTTGTA
1 TTTAATATTTAAATATGTA
35453811 TTTAAT
1 TTTAAT
35453817 TTATGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTAATATTTAAATATGTA
Found at i:35463236 original size:23 final size:23
Alignment explanation
Indices: 35463209--35463254 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35463199 TTGGGTGCAA
*
35463209 CTACCACTCTAACTCCCATGGTG
1 CTACCACTCCAACTCCCATGGTG
35463232 CTACCACTCCAACTCCCATGGTG
1 CTACCACTCCAACTCCCATGGTG
35463255 AGTGCTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.41, G:0.13, T:0.24
Consensus pattern (23 bp):
CTACCACTCCAACTCCCATGGTG
Found at i:35483547 original size:21 final size:21
Alignment explanation
Indices: 35483523--35483576 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
35483513 GAAATTTAAA
35483523 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
* *
35483544 ACAAATATTATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
35483565 ACAAACATAATG
1 ACAAACATAATG
35483577 CTTTGTAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.22
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:35484989 original size:26 final size:26
Alignment explanation
Indices: 35484924--35484997 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
35484914 TTTAGTAAAA
35484924 AATAAAAGAAAA-TCAATTAAGCCCTT
1 AATAAAA-AAAATTCAATTAAGCCCTT
*** *
35484950 AA-AATAATGTATTCAATTGAGCCCTT
1 AATAA-AAAAAATTCAATTAAGCCCTT
*
35484976 AATAAAAAAAATTCAACTAAGC
1 AATAAAAAAAATTCAATTAAGC
35484998 TTTCTCGATA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
25 3 0.08
26 31 0.86
27 2 0.06
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (26 bp):
AATAAAAAAAATTCAATTAAGCCCTT
Found at i:35486294 original size:18 final size:16
Alignment explanation
Indices: 35486280--35486315 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
35486270 GAAAATATTA
35486280 ATTTTTTC--AAAAAT
1 ATTTTTTCTTAAAAAT
35486294 ATTTTTTCTTAAAAAT
1 ATTTTTTCTTAAAAAT
35486310 ATTTTT
1 ATTTTT
35486316 GAGAAACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
16 12 0.60
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTTCTTAAAAAT
Found at i:35492692 original size:9 final size:9
Alignment explanation
Indices: 35492678--35492708 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
35492668 GTTGTAAGAT
35492678 AAAAATAAA
1 AAAAATAAA
35492687 AAAAAT-AA
1 AAAAATAAA
35492695 AAAAATAAA
1 AAAAATAAA
35492704 AAAAA
1 AAAAA
35492709 ACACCCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:35492696 original size:8 final size:8
Alignment explanation
Indices: 35492678--35492707 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
35492668 GTTGTAAGAT
35492678 AAAAATAAA
1 AAAAAT-AA
35492687 AAAAATAA
1 AAAAATAA
35492695 AAAAATAA
1 AAAAATAA
35492703 AAAAA
1 AAAAA
35492708 AACACCCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:35493113 original size:7 final size:7
Alignment explanation
Indices: 35493101--35493172 Score: 67
Period size: 7 Copynumber: 10.1 Consensus size: 7
35493091 TCTCGACCTC
35493101 TCTTTTT
1 TCTTTTT
35493108 TCTTTTT
1 TCTTTTT
*
35493115 T-TCTTT
1 TCTTTTT
*
35493121 T-TTTCT
1 TCTTTTT
*
35493127 TCTCTTT
1 TCTTTTT
35493134 TCTTTTT
1 TCTTTTT
35493141 TCTTTTTT
1 TC-TTTTT
35493149 TCTTTCTT
1 TCTTT-TT
35493157 TCCTTTTT
1 T-CTTTTT
*
35493165 TATTTTT
1 TCTTTTT
35493172 T
1 T
35493173 TGGGTGAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
6 9 0.17
7 28 0.52
8 13 0.24
9 4 0.07
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (7 bp):
TCTTTTT
Found at i:35493114 original size:8 final size:8
Alignment explanation
Indices: 35493103--35493173 Score: 90
Period size: 8 Copynumber: 8.8 Consensus size: 8
35493093 TCGACCTCTC
35493103 TTTTTTCT
1 TTTTTTCT
35493111 TTTTTTCT
1 TTTTTTCT
35493119 TTTTTTCT
1 TTTTTTCT
35493127 TCTCTTTTC-
1 T-T-TTTTCT
35493136 TTTTTTCT
1 TTTTTTCT
35493144 TTTTTTCT
1 TTTTTTCT
* *
35493152 TTCTTTCC
1 TTTTTTCT
*
35493160 TTTTTTAT
1 TTTTTTCT
35493168 TTTTTT
1 TTTTTT
35493174 GGGTGAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
7 5 0.09
8 43 0.78
9 2 0.04
10 5 0.09
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:35493145 original size:25 final size:24
Alignment explanation
Indices: 35493105--35493173 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
35493095 GACCTCTCTT
35493105 TTTTCTTTTTTTCTTTTTTTCTTCTC
1 TTTTC-TTTTTTCTTTTTTTCTT-TC
35493131 TTTTCTTTTTTCTTTTTTTCTTTC
1 TTTTCTTTTTTCTTTTTTTCTTTC
* *
35493155 TTTCCTTTTTTATTTTTTT
1 TTTTCTTTTTTCTTTTTTT
35493174 GGGTGAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 19 0.46
25 17 0.41
26 5 0.12
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTCTTTTTTCTTTTTTTCTTTC
Found at i:35494111 original size:20 final size:22
Alignment explanation
Indices: 35494088--35494130 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
35494078 TGGGTTTTCA
35494088 TCTTGACTT-TT-TCTTTTTTT
1 TCTTGACTTCTTCTCTTTTTTT
**
35494108 TCTTTCCTTCTTCTCTTTTTTT
1 TCTTGACTTCTTCTCTTTTTTT
35494130 T
1 T
35494131 GATCTCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (22 bp):
TCTTGACTTCTTCTCTTTTTTT
Found at i:35498462 original size:30 final size:30
Alignment explanation
Indices: 35498296--35498525 Score: 138
Period size: 30 Copynumber: 7.8 Consensus size: 30
35498286 TAAGGAAAAT
35498296 AGGGTTAAAATCATAA-TTTTAGAAAGTTT-
1 AGGGTTAAAATCA-AATTTTTAGAAAGTTTA
**
35498325 AGGGTTAAAATGC-AA-TTTTA-AAAAATTA
1 AGGGTTAAAAT-CAAATTTTTAGAAAGTTTA
* * ** **
35498353 GGGGTCAAAATGTAATTTTTATG-AAGTTCG
1 AGGGTTAAAATCAAATTTTTA-GAAAGTTTA
* * * *
35498383 TGAGTCAAAA-CGTAATTTTTAGAAAGTTTA
1 AGGGTTAAAATC-AAATTTTTAGAAAGTTTA
* *
35498413 AGAGTCAAAA-CATAATTTTTAGAAAGTTTA
1 AGGGTTAAAATCA-AATTTTTAGAAAGTTTA
* * *
35498443 AGGGCTAAAATCAATTTTTTGGAAAGTTT-
1 AGGGTTAAAATCAAATTTTTAGAAAGTTTA
* * **
35498472 AGGGTTACAAT-AAATTTTTTTGAAAGTACA
1 AGGGTTAAAATCAAA-TTTTTAGAAAGTTTA
*
35498502 AGGGTTAAAATCAAATTTTGAGAA
1 AGGGTTAAAATCAAATTTTTAGAA
35498526 GTTCGGGGTC
Statistics
Matches: 158, Mismatches: 30, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.03
28 20 0.13
29 37 0.23
30 91 0.58
31 5 0.03
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (30 bp):
AGGGTTAAAATCAAATTTTTAGAAAGTTTA
Found at i:35501613 original size:18 final size:19
Alignment explanation
Indices: 35501587--35501626 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
35501577 CTTTAATATA
35501587 TTTAATTCAC-CAATTTAT
1 TTTAATTCACTCAATTTAT
* *
35501605 TTTATTTCACTTAATTTAT
1 TTTAATTCACTCAATTTAT
35501624 TTT
1 TTT
35501627 GCAATCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATTCACTCAATTTAT
Found at i:35501675 original size:3 final size:3
Alignment explanation
Indices: 35501669--35501704 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35501659 ATTTGTTGTT
35501669 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35501705 ACTTTATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35502379 original size:15 final size:15
Alignment explanation
Indices: 35502359--35502390 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
35502349 ACCGTTGTCG
35502359 AATTTCTAACCACGT
1 AATTTCTAACCACGT
35502374 AATTTCTAACCACGT
1 AATTTCTAACCACGT
35502389 AA
1 AA
35502391 CTCGTGCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (15 bp):
AATTTCTAACCACGT
Found at i:35503067 original size:6 final size:7
Alignment explanation
Indices: 35503049--35503076 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
35503039 AAATTTCAAC
35503049 TAAAAAT
1 TAAAAAT
35503056 TAAAAAT
1 TAAAAAT
35503063 TAAAAAT
1 TAAAAAT
35503070 TAAAAAT
1 TAAAAAT
35503077 ATTATCAACT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TAAAAAT
Found at i:35508138 original size:40 final size:41
Alignment explanation
Indices: 35508004--35508172 Score: 122
Period size: 38 Copynumber: 4.3 Consensus size: 41
35507994 TTCCCTGGTG
* * *
35508004 TTTATCGGG-TTTAGTGCCTAG-TAGACTTTGTGCCAATG--
1 TTTATCGGGCTTTAGTGCCTAGCAAG-CTTAGTGCCGATGTA
** * * *
35508042 TTTATTAGGC-TTAGTGCCTAGGAGGCTTCGTGCCGATG--
1 TTTATCGGGCTTTAGTGCCTAGCAAGCTTAGTGCCGATGTA
* *
35508080 TTTATCGAGC-TTAGTGCCTAGCAAGCTTAGTGTCGATGTA
1 TTTATCGGGCTTTAGTGCCTAGCAAGCTTAGTGCCGATGTA
* * * *
35508120 TTTATCGGGCTTTA-TGCCTAGTAGGCTTCGTGCCGGTGTA
1 TTTATCGGGCTTTAGTGCCTAGCAAGCTTAGTGCCGATGTA
*
35508160 TATTATCAGGCTT
1 T-TTATCGGGCTT
35508173 CGAGCCTAGT
Statistics
Matches: 105, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
38 60 0.57
39 1 0.01
40 31 0.30
41 13 0.12
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (41 bp):
TTTATCGGGCTTTAGTGCCTAGCAAGCTTAGTGCCGATGTA
Found at i:35515401 original size:144 final size:144
Alignment explanation
Indices: 35515052--35515414 Score: 406
Period size: 144 Copynumber: 2.5 Consensus size: 144
35515042 ATCGGGGTTG
*
35515052 AAAATGAGACTTTTTGGATACCCGGGGGCAAAATGGTAATTTTAGACTCTAGAAGGG-AAAATGG
1 AAAATGAGACTTTTTGGATACCCGGGGGCAAAATGGTAATTTTAGACTCTCG-AGGGTAAAATGG
* * ** *
35515116 TAATTTTGGGAAATTTGGGATTAGAAATGACATTTTATATGATCAGGGGTAAAACGATAATTTTC
65 TAATTTTGGAAAATTTGGGATTAGAAATGACATTTTAGACAATCAGGGGTAAAACGATAATTTTA
35515181 GAAAGAATTGGGATC
130 GAAAGAATTGGGATC
* * * *
35515196 AAAACGGGACTTTTTGGATGCCCGAGGGCAAAATGGTAATTTTAGACTCTCGAGGGTAAAATGGT
1 AAAATGAGACTTTTTGGATACCCGGGGGCAAAATGGTAATTTTAGACTCTCGAGGGTAAAATGGT
*
35515261 AATTTTAGGAAAATTTGAGG-TTA-AAATGATATTTTAGACAATC-GAGGG--AAAC-AGTAATT
66 AATTTT-GGAAAATTTG-GGATTAGAAATGACATTTTAGACAATCAG-GGGTAAAACGA-TAA--
35515320 TTTTAGAAA-AATTGGGATC
125 TTTTAGAAAGAATTGGGATC
* * * * *
35515339 AAAAATGAGA-TTTTTGGACATCCGGGGGTAAAATGGTAATTTTGAGAGTTTCG-GGGTCAAAAT
1 -AAAATGAGACTTTTTGGATACCCGGGGGCAAAATGGTAATTTT-AGACTCTCGAGGGT-AAAAT
35515402 GG-AATTTTTGGAA
63 GGTAA-TTTTGGAA
35515415 GTTTGGGGTA
Statistics
Matches: 188, Mismatches: 20, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
141 1 0.01
142 7 0.04
143 53 0.28
144 113 0.60
145 12 0.06
146 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (144 bp):
AAAATGAGACTTTTTGGATACCCGGGGGCAAAATGGTAATTTTAGACTCTCGAGGGTAAAATGGT
AATTTTGGAAAATTTGGGATTAGAAATGACATTTTAGACAATCAGGGGTAAAACGATAATTTTAG
AAAGAATTGGGATC
Found at i:35515410 original size:29 final size:29
Alignment explanation
Indices: 35515363--35515765 Score: 181
Period size: 30 Copynumber: 13.8 Consensus size: 29
35515353 TGGACATCCG
35515363 GGGGT-AAAATGGTAA-TTTTGAGAGTTTC
1 GGGGTCAAAAT-GTAATTTTTGAGAGTTTC
*
35515391 GGGGTCAAAATGGAATTTTTG-GAAGTTT-
1 GGGGTCAAAATGTAATTTTTGAG-AGTTTC
* * *
35515419 GGGGTAAAAAATG-AAATTTTGGGAAGTTT-
1 GGGGT-CAAAATGTAATTTTTGAG-AGTTTC
*
35515448 GAGAG-CAAAAATGTAATTTTTG-GAAGTTTC
1 G-GGGTC-AAAATGTAATTTTTGAG-AGTTTC
* ** * *
35515478 GAGGTCAAAATGTAATTTTCAAAAGTTTT
1 GGGGTCAAAATGTAATTTTTGAGAGTTTC
** * *
35515507 AAGGTCAAAAATGGAATTGTTG-GAAG-TTC
1 GGGGTC-AAAATGTAATTTTTGAG-AGTTTC
* *
35515536 GAGGGTCAAAAATGGAATTTTTG-GAGGTTTA
1 G-GGGTC-AAAATGTAATTTTTGAGA-GTTTC
* * *
35515567 GGGGTAAAAATGTAATTTTTGGAAAATTT-
1 GGGGTCAAAATGTAATTTTT-GAGAGTTTC
* * *
35515596 GAGGTCAAAAATGTAATTTTAG-GAAGTTTT
1 GGGGTC-AAAATGTAATTTTTGAG-AGTTTC
* *
35515626 AGGGTCAAAATGGAATTTTTGA-AG-TTC
1 GGGGTCAAAATGTAATTTTTGAGAGTTTC
* * * *
35515653 AAGGGT-AGAAATATAATTTTTGAAAGTTTT
1 -GGGGTCA-AAATGTAATTTTTGAGAGTTTC
* * *
35515683 GAGGTCAAAAATGTAATTTTAGAGAAATTTC
1 GGGGTC-AAAATGTAATTTTTGAG-AGTTTC
* * * *
35515714 GGGGTTAAAATGTAATTTTAGAAAAGTTTA
1 GGGGTCAAAATGTAATTTTTG-AGAGTTTC
**
35515744 GGGGTCAAAATACAATTTTTGA
1 GGGGTCAAAATGTAATTTTTGA
35515766 ACAGATTAGG
Statistics
Matches: 289, Mismatches: 56, Indels: 59
0.72 0.14 0.15
Matches are distributed among these distances:
27 3 0.01
28 41 0.14
29 110 0.38
30 121 0.42
31 14 0.05
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTTGAGAGTTTC
Found at i:35515469 original size:30 final size:30
Alignment explanation
Indices: 35515368--35515732 Score: 287
Period size: 29 Copynumber: 12.4 Consensus size: 30
35515358 ATCCGGGGGT
35515368 AAAATGGTAA-TTTT-GAGAGTTTCG-GGGTC-
1 AAAAT-GTAATTTTTGGA-AGTTT-GAGGGTCA
* *
35515397 AAAATGGAATTTTTGGAAGTTTG-GGGTAA
1 AAAATGTAATTTTTGGAAGTTTGAGGGTCA
* * *
35515426 AAAATGAAATTTTGGGAAGTTTGAGAG-CA
1 AAAATGTAATTTTTGGAAGTTTGAGGGTCA
35515455 AAAATGTAATTTTTGGAAGTTTCGA-GGTC-
1 AAAATGTAATTTTTGGAAGTTT-GAGGGTCA
*** * *
35515484 AAAATGTAATTTTCAAAAGTTTTAAGGTCA
1 AAAATGTAATTTTTGGAAGTTTGAGGGTCA
* * *
35515514 AAAATGGAATTGTTGGAAGTTCGAGGGTCA
1 AAAATGTAATTTTTGGAAGTTTGAGGGTCA
* *
35515544 AAAATGGAATTTTTGGAGGTTT-AGGGGT-A
1 AAAATGTAATTTTTGGAAGTTTGA-GGGTCA
*
35515573 AAAATGTAATTTTTGGAAAATTTGA-GGTCA
1 AAAATGTAATTTTTGG-AAGTTTGAGGGTCA
* *
35515603 AAAATGTAATTTTAGGAAGTTTTAGGGTC-
1 AAAATGTAATTTTTGGAAGTTTGAGGGTCA
* **
35515632 AAAATGGAATTTTT-GAAGTTCAAGGGT-A
1 AAAATGTAATTTTTGGAAGTTTGAGGGTCA
* * *
35515660 GAAATATAATTTTTGAAAGTTTTGA-GGTCA
1 AAAATGTAATTTTTGGAAG-TTTGAGGGTCA
* * *
35515690 AAAATGTAATTTTAGAGAAATTTCG-GGGT-T
1 AAAATGTAATTTTTG-GAAGTTT-GAGGGTCA
35515720 AAAATGTAATTTT
1 AAAATGTAATTTT
35515733 AGAAAAGTTT
Statistics
Matches: 270, Mismatches: 46, Indels: 39
0.76 0.13 0.11
Matches are distributed among these distances:
28 31 0.11
29 124 0.46
30 108 0.40
31 7 0.03
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGTCA
Found at i:35515545 original size:59 final size:58
Alignment explanation
Indices: 35515337--35515742 Score: 237
Period size: 59 Copynumber: 6.9 Consensus size: 58
35515327 AAAATTGGGA
* * * * ***
35515337 TCAAAAAT-GAGATTTTTGGACA-TCCGGGGGT-AAAATGGTAATTTTGAGAGTTTCGGGG
1 TCAAAAATGGA-ATTTTTGGA-AGTTCGAGGGTCAAAAT-GTAATTTTAAAAGTTTTAAGG
* * * ** *
35515395 TC-AAAATGGAATTTTTGGAAGTTTG-GGGTAAAAAATGAAATTTTGGGAAG-TTTGAGAG
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGT-CAAAATGTAATTTT-AAAAGTTTTAAG-G
*
35515453 -CAAAAATGTAATTTTTGGAAGTTTCGA-GGTCAAAATGTAATTTTCAAAAGTTTTAAGG
1 TCAAAAATGGAATTTTTGGAAG-TTCGAGGGTCAAAATGTAATTTT-AAAAGTTTTAAGG
* * *** * *
35515511 TCAAAAATGGAATTGTTGGAAGTTCGAGGGTCAAAAATGGAATTTTTGGAGGTTTAGGGG
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTC-AAAATGTAATTTTAAAAGTTTTA-AGG
* * * * *
35515571 T-AAAAATGTAATTTTTGGAAAATTTGA-GGTCAAAAATGTAATTTTAGGAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGG-AAGTTCGAGGGTC-AAAATGTAATTTTA-AAAGTTTTAAGG
* * * *
35515630 TC-AAAATGGAATTTTT-GAAGTTCAAGGGT-AGAAATATAATTTTTGAAAGTTTTGAGG
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTCA-AAATGTAA-TTTTAAAAGTTTTAAGG
* * * *
35515687 TCAAAAATGTAATTTTAGAGAAATTTCG-GGGTTAAAATGTAATTTTAGAAAAGTTT
1 TCAAAAATGGAATTTTTG-G-AAGTTCGAGGGTCAAAATGTAATTTT--AAAAGTTT
35515743 AGGGGTCAAA
Statistics
Matches: 275, Mismatches: 46, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
56 6 0.02
57 51 0.19
58 72 0.26
59 93 0.34
60 40 0.15
61 13 0.05
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.34
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGGAAGTTCGAGGGTCAAAATGTAATTTTAAAAGTTTTAAGG
Found at i:35516859 original size:3 final size:3
Alignment explanation
Indices: 35516853--35516916 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
35516843 TTTTTATATA
** * *
35516853 ATT ATT AATT ATT AATT AAA AT- ATT ATT ATT AAT ATC ATT ATT ATT
1 ATT ATT -ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
35516899 ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
35516917 TAATGCAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:35516895 original size:18 final size:18
Alignment explanation
Indices: 35516874--35516916 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
35516864 TTAATTAAAA
35516874 TATTATTATTAATATCAT
1 TATTATTATTAATATCAT
*
35516892 TATTATTATTATTATCAT
1 TATTATTATTAATATCAT
35516910 TATTATT
1 TATTATT
35516917 TAATGCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATTATTAATATCAT
Found at i:35517767 original size:13 final size:13
Alignment explanation
Indices: 35517749--35517782 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
35517739 TTTGGCCCAG
35517749 TTGGACTTGTAAA
1 TTGGACTTGTAAA
*
35517762 TTGGACATGTAAA
1 TTGGACTTGTAAA
*
35517775 TTAGACTT
1 TTGGACTT
35517783 TATTTAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (13 bp):
TTGGACTTGTAAA
Found at i:35517828 original size:6 final size:6
Alignment explanation
Indices: 35517817--35517867 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
35517807 TACAATGATA
* * *
35517817 TTAAAT TTAAAT TTAAA- TTAAAA TTGAAT TTAAA- ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
35517863 TTAAA
1 TTAAA
35517868 ATAGATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
5 9 0.24
6 29 0.76
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:35517834 original size:12 final size:12
Alignment explanation
Indices: 35517817--35517867 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 12
35517807 TACAATGATA
35517817 TTAAATTTAAAT
1 TTAAATTTAAAT
*
35517829 TTAAA-TTAAAA
1 TTAAATTTAAAT
*
35517840 TTGAATTTAAA-
1 TTAAATTTAAAT
*
35517851 ATAAATTTAAAT
1 TTAAATTTAAAT
35517863 TTAAA
1 TTAAA
35517868 ATAGATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 18 0.56
12 14 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:35517836 original size:17 final size:17
Alignment explanation
Indices: 35517818--35517895 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
35517808 ACAATGATAT
*
35517818 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAA
* *
35517835 TAAAATTGAATTTAAAA
1 TAAATTTAAATTTAAAA
35517852 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
35517869 TAGATTT-AATTTCAAAG
1 TAAATTTAAATTT-AAAA
35517886 TAAATTTAAA
1 TAAATTTAAA
35517896 ATGGTTTAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
16 5 0.10
17 44 0.86
18 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:35518713 original size:3 final size:3
Alignment explanation
Indices: 35518707--35518732 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35518697 TTTTTATTAT
35518707 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
35518733 ATGTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:35519638 original size:40 final size:42
Alignment explanation
Indices: 35519572--35519673 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
35519562 GCATAGTGGT
35519572 CACACGAGCTAGACACACGGGTGTGTGCCTAGTCGTGTGTCA
1 CACACGAGCTAGACACACGGGTGTGTGCCTAGTCGTGTGTCA
* * *
35519614 CACATGAGCTGGACACACGGGTGTGTGCCTCGTCGTGTGTCA
1 CACACGAGCTAGACACACGGGTGTGTGCCTAGTCGTGTGTCA
*
35519656 CACACGAGCAAG-CACACG
1 CACACGAGCTAGACACACG
35519674 ACCGTGCGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
41 6 0.11
42 48 0.89
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (42 bp):
CACACGAGCTAGACACACGGGTGTGTGCCTAGTCGTGTGTCA
Found at i:35519918 original size:40 final size:40
Alignment explanation
Indices: 35519871--35519966 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
35519861 ATAGACTAGC
* *
35519871 AGTGACACTGTAAACATTACGATATCATTACT-GAACTGGA
1 AGTGACACTGTAAACATTACGAAATCACTA-TGGAACTGGA
* * *
35519911 AGTGACACTGTAAACATTGCGAAATCACTATGGAATTGGT
1 AGTGACACTGTAAACATTACGAAATCACTATGGAACTGGA
35519951 AGTGACACTGTAAACA
1 AGTGACACTGTAAACA
35519967 CCGTGCTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (40 bp):
AGTGACACTGTAAACATTACGAAATCACTATGGAACTGGA
Found at i:35521340 original size:13 final size:13
Alignment explanation
Indices: 35521322--35521346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35521312 CCCATTTAAT
35521322 CATTTTTAGCATG
1 CATTTTTAGCATG
35521335 CATTTTTAGCAT
1 CATTTTTAGCAT
35521347 TTTTAACTTA
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:35521382 original size:21 final size:20
Alignment explanation
Indices: 35521343--35521382 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
35521333 TGCATTTTTA
* *
35521343 GCATTTTTAACTTAGTGATT
1 GCATTTTTAACTCAATGATT
35521363 GCATTTTCTAACTCAATGAT
1 GCATTTT-TAACTCAATGAT
35521383 GCTTGGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (20 bp):
GCATTTTTAACTCAATGATT
Found at i:35535278 original size:19 final size:21
Alignment explanation
Indices: 35535254--35535299 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
35535244 ATTCTATCAT
*
35535254 GTGATTGCA-TTT-TAACTTA
1 GTGATTGCATTTTCTAACTCA
35535273 GTGATTGCATTTTCTAACTCA
1 GTGATTGCATTTTCTAACTCA
35535294 GTGATT
1 GTGATT
35535300 CTTGATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 12 0.50
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (21 bp):
GTGATTGCATTTTCTAACTCA
Found at i:35541352 original size:12 final size:12
Alignment explanation
Indices: 35541337--35541366 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
35541327 CGGTAGGTTC
35541337 CTCTTCTTCTTT
1 CTCTTCTTCTTT
35541349 CTCTTCTTCTTT
1 CTCTTCTTCTTT
35541361 CTCTTC
1 CTCTTC
35541367 CTCGTCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
CTCTTCTTCTTT
Found at i:35554041 original size:37 final size:37
Alignment explanation
Indices: 35553962--35554042 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
35553952 ATTCTTACGA
* * * *
35553962 CGACAGTTTTGGGTGCAATCTGGAAGTGCTCATGCGG
1 CGACATTTTTGGGCGCAATCTAGAAGTGCTCATGCAG
35553999 CGACATTTTTGGGCGCAATCTAGAAGTGCTCATGCAG
1 CGACATTTTTGGGCGCAATCTAGAAGTGCTCATGCAG
*
35554036 TGACATT
1 CGACATT
35554043 AGTAGTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (37 bp):
CGACATTTTTGGGCGCAATCTAGAAGTGCTCATGCAG
Found at i:35557633 original size:37 final size:38
Alignment explanation
Indices: 35557592--35557686 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
35557582 GTACATGTTC
35557592 ATGCAGCGACATTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
* * * *
35557629 ATGCAGTGATAGTT-CTGGATGCAATTTGAAGAATATTT
1 ATGCAGCGACA-TTCCTGGGTGCAATTTGAAGAATACTT
* *
35557667 ATGCAGCGACAATCTTGGGT
1 ATGCAGCGACATTCCTGGGT
35557687 ACATTCCGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 19 0.41
38 27 0.59
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (38 bp):
ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
Found at i:35557787 original size:37 final size:37
Alignment explanation
Indices: 35557709--35557788 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
35557699 TATTCCTGCT
* * **
35557709 GCGACAGTTTTGGGTGCAATCTAGAAGTGCTTATATG
1 GCGACAGTTTTGGGCGCAATCTAGAAGTGCTCATACA
*
35557746 GCGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGCA
1 GCGACAGTTTTGGGCGCAATCTAGAAGTGCTCATACA
35557783 GCGACA
1 GCGACA
35557789 TTAGTAGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
GCGACAGTTTTGGGCGCAATCTAGAAGTGCTCATACA
Found at i:35562697 original size:38 final size:38
Alignment explanation
Indices: 35562646--35562833 Score: 227
Period size: 38 Copynumber: 4.9 Consensus size: 38
35562636 AACTCCCTGG
* * * *
35562646 TGTTTATCGGGCTTAATGCCTAGAAGGCTTCATGCCGA
1 TGTTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGCCGA
*
35562684 TGTTTATC-AGGCTTAGTGCCTAGGAGGCTTCGTGCCGA
1 TGTTTATCGA-GCTTAGTGCCTAGCAGGCTTCGTGCCGA
*
35562722 TGTTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGCTGA
1 TGTTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGCCGA
* *
35562760 TGTTTATCGAGCTTAGTGCCTAGCAGGCTTAGTGTC-A
1 TGTTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGCCGA
* * *
35562797 GTGTATTTATCAAGCTTTGTGCCTAGTAGGCTTCGTG
1 -TG--TTTATCGAGCTTAGTGCCTAGCAGGCTTCGTG
35562834 TCAATGTATA
Statistics
Matches: 132, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
37 1 0.01
38 102 0.77
39 1 0.01
40 28 0.21
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.35
Consensus pattern (38 bp):
TGTTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGCCGA
Found at i:35562862 original size:41 final size:40
Alignment explanation
Indices: 35562739--35562867 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
35562729 CGAGCTTAGT
* * * * *
35562739 GCCTAGCAGGCTTCGTG-CTGATGT-T-TATCGAGCTTAGT
1 GCCTAGCAGGCTTAGTGTC-AATGTATCTATCAAGCTTTGA
* * *
35562777 GCCTAGCAGGCTTAGTGTCAGTGTATTTATCAAGCTTTGT
1 GCCTAGCAGGCTTAGTGTCAATGTATCTATCAAGCTTTGA
* * *
35562817 GCCTAGTAGGCTTCGTGTCAATGTATACTATCACGCTTTGA
1 GCCTAGCAGGCTTAGTGTCAATGTAT-CTATCAAGCTTTGA
35562858 GCCTAGCAGG
1 GCCTAGCAGG
35562868 TTTTACACCG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
38 19 0.25
39 2 0.03
40 34 0.45
41 20 0.27
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (40 bp):
GCCTAGCAGGCTTAGTGTCAATGTATCTATCAAGCTTTGA
Found at i:35566578 original size:11 final size:11
Alignment explanation
Indices: 35566562--35566586 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35566552 ACAGTACAGA
35566562 TCAAATCCTTC
1 TCAAATCCTTC
35566573 TCAAATCCTTC
1 TCAAATCCTTC
35566584 TCA
1 TCA
35566587 TTTGATTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (11 bp):
TCAAATCCTTC
Found at i:35581641 original size:16 final size:17
Alignment explanation
Indices: 35581617--35581649 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35581607 TGCATACTTA
35581617 GGATAATTTGC-ATTAG
1 GGATAATTTGCAATTAG
*
35581633 GGATCATTTGCAATTAG
1 GGATAATTTGCAATTAG
35581650 TTTAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.36
Consensus pattern (17 bp):
GGATAATTTGCAATTAG
Found at i:35583017 original size:13 final size:13
Alignment explanation
Indices: 35582999--35583024 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35582989 GAATTAACAT
35582999 CAAAATAGGAGTG
1 CAAAATAGGAGTG
35583012 CAAAATAGGAGTG
1 CAAAATAGGAGTG
35583025 GACAAGGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (13 bp):
CAAAATAGGAGTG
Found at i:35592021 original size:19 final size:18
Alignment explanation
Indices: 35591997--35592034 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
35591987 TAATTTTAAA
*
35591997 ATTAATTTTTATATTTTTT
1 ATTAATTTTAAT-TTTTTT
35592016 ATTAATTTTAATTTTTTT
1 ATTAATTTTAATTTTTTT
35592034 A
1 A
35592035 AAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTAATTTTAATTTTTTT
Found at i:35592037 original size:40 final size:41
Alignment explanation
Indices: 35591981--35592064 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
35591971 CATGTCAACA
* *
35591981 TTTAATTAATTTT-AAAATTAATTTTTATATTTTTTATTAAT
1 TTTAATTAATTTTAAAAAATAATTTTTATATATTTTA-TAAT
* *
35592022 TTTAATT-TTTTTAAAAAATATTTTTTATATATTTTATAAT
1 TTTAATTAATTTTAAAAAATAATTTTTATATATTTTATAAT
35592062 TTT
1 TTT
35592065 TTACCTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 11 0.29
41 27 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (41 bp):
TTTAATTAATTTTAAAAAATAATTTTTATATATTTTATAAT
Found at i:35594346 original size:54 final size:54
Alignment explanation
Indices: 35594272--35594379 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
35594262 TTTCTAAGAA
*
35594272 AGAATCAACATTATATATACTTTTACTTTTATCGCTTTACCCCTAACTTTTCTT
1 AGAATCAACATTATATATACTTTTACTTTTATCACTTTACCCCTAACTTTTCTT
35594326 AGAATCAACATTATATATACTTTTACTTTTATCACTTTACCCCTAACTTTTCTT
1 AGAATCAACATTATATATACTTTTACTTTTATCACTTTACCCCTAACTTTTCTT
35594380 TAAATTACTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.46
Consensus pattern (54 bp):
AGAATCAACATTATATATACTTTTACTTTTATCACTTTACCCCTAACTTTTCTT
Found at i:35594359 original size:27 final size:27
Alignment explanation
Indices: 35594275--35594359 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
35594265 CTAAGAAAGA
35594275 ATCAACATTATATATACTTTTACTTTT
1 ATCAACATTATATATACTTTTACTTTT
* * ** **
35594302 ATC-GCTTTACCCCTA-ACTTTT-CTTAGA
1 ATCAACATTA--TATATACTTTTACTT-TT
35594329 ATCAACATTATATATACTTTTACTTTT
1 ATCAACATTATATATACTTTTACTTTT
35594356 ATCA
1 ATCA
35594360 CTTTACCCCT
Statistics
Matches: 40, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
26 9 0.22
27 22 0.55
28 9 0.22
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47
Consensus pattern (27 bp):
ATCAACATTATATATACTTTTACTTTT
Found at i:35594374 original size:27 final size:26
Alignment explanation
Indices: 35594290--35594380 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 26
35594280 CATTATATAT
*
35594290 ACTTTTACTTTTATCGCTTTACCCCTA
1 ACTTTT-CTTTTATCACTTTACCCCTA
** * **
35594317 ACTTTTCTTAGAATCAACATTA--TATA
1 ACTTTTCTT-TTATC-ACTTTACCCCTA
35594343 TACTTTTACTTTTATCACTTTACCCCTA
1 -ACTTTT-CTTTTATCACTTTACCCCTA
35594371 ACTTTTCTTT
1 ACTTTTCTTT
35594381 AAATTACTGA
Statistics
Matches: 47, Mismatches: 11, Indels: 13
0.66 0.15 0.18
Matches are distributed among these distances:
26 14 0.30
27 24 0.51
28 9 0.19
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.49
Consensus pattern (26 bp):
ACTTTTCTTTTATCACTTTACCCCTA
Found at i:35594645 original size:8 final size:8
Alignment explanation
Indices: 35594634--35594673 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
35594624 AAAAATAAAA
35594634 ATATTTTT
1 ATATTTTT
35594642 ATATTTTT
1 ATATTTTT
35594650 ATATTTTT
1 ATATTTTT
35594658 ATATTTTT
1 ATATTTTT
*
35594666 AAATTTTT
1 ATATTTTT
35594674 TAAAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATATTTTT
Found at i:35595268 original size:30 final size:30
Alignment explanation
Indices: 35595234--35595298 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
35595224 CAACTTAACA
*
35595234 AACAAATACCTCTAAAATAGTAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
* *
35595264 AACAAATACCTCTGAAATAATAACAAAGTT
1 AACAAATACCTCTAAAATAATAACAAAATT
35595294 AACAA
1 AACAA
35595299 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.22
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:35598411 original size:59 final size:59
Alignment explanation
Indices: 35598340--35598659 Score: 382
Period size: 59 Copynumber: 5.4 Consensus size: 59
35598330 ATTTTTGACT
* * *
35598340 TTTGGGGGTAAAAAT-GTAATTTTTGGTAGAATTGGGGTTAAAAATGGGATTTTAGAAAG
1 TTTGAGGGT-AAAATGGTAATTTTTGGTAGAATCGGGGTTAAAAATGGGATTTTGGAAAG
* * * *
35598399 TTTGAGGATAAAATGGTAATTTTTGGGTAAAATCGGGGTTAAAGATGGGATTTTTGAAAG
1 TTTGAGGGTAAAATGGTAATTTTT-GGTAGAATCGGGGTTAAAAATGGGATTTTGGAAAG
* * * * *
35598459 TTCGAGGGTAAAATGATAATTTTTGGTA-AAACTGGGGTT-AAAATGAGATTTTGGGAAG
1 TTTGAGGGTAAAATGGTAATTTTTGGTAGAATC-GGGGTTAAAAATGGGATTTTGGAAAG
* * *
35598517 TTTGGGGGTAAAATGGTAATTTTTGG-AGAAATCAGGGTTAAAAATGGAATTTTGGAAAG
1 TTTGAGGGTAAAATGGTAATTTTTGGTAG-AATCGGGGTTAAAAATGGGATTTTGGAAAG
* * *
35598576 -TTCAGAGGTAAAATGGTAATTTTTTGT-GAAATCGGGGTTAAAAATGGAATTTTGGAAAG
1 TTTGAG-GGTAAAATGGTAATTTTTGGTAG-AATCGGGGTTAAAAATGGGATTTTGGAAAG
35598635 TTTGAGGGTAAAATGGTAATTTTTG
1 TTTGAGGGTAAAATGGTAATTTTTG
35598660 AATAGTTTAG
Statistics
Matches: 224, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.00
58 54 0.24
59 113 0.50
60 56 0.25
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (59 bp):
TTTGAGGGTAAAATGGTAATTTTTGGTAGAATCGGGGTTAAAAATGGGATTTTGGAAAG
Found at i:35598480 original size:29 final size:29
Alignment explanation
Indices: 35598380--35598666 Score: 129
Period size: 29 Copynumber: 9.8 Consensus size: 29
35598370 ATTGGGGTTA
* * * *
35598380 AAAATGG-GATTTTAGAAAGTTTGAGGAT
1 AAAATGGTAATTTTTGAAAGTTCGAGGGT
*
35598408 AAAATGGTAATTTTTGGGTAAA-ATCG-GGGTT
1 AAAATGGTAATTTTT--G-AAAGTTCGAGGG-T
*
35598439 AAAGATGG-GATTTTTGAAAGTTCGAGGGT
1 AAA-ATGGTAATTTTTGAAAGTTCGAGGGT
* **
35598468 AAAATGATAATTTTTGGTAAAACT-G-GGGTT
1 AAAATGGTAATTTTT-G-AAAGTTCGAGGG-T
* * * *
35598498 AAAAT-G-AGATTTTGGGAAGTTTGGGGGT
1 AAAATGGTA-ATTTTTGAAAGTTCGAGGGT
*
35598526 AAAATGGTAATTTTTGGAGAA-ATC-AGGGTT
1 AAAATGGTAATTTTT-GA-AAGTTCGAGGG-T
*
35598556 AAAAATGG-AATTTTGGAAAGTTC-AGAGGT
1 -AAAATGGTAATTTTTGAAAGTTCGAG-GGT
35598585 AAAATGGTAATTTTTTGTGAAA--TCG-GGGTT
1 AAAATGGTAA--TTTT-TGAAAGTTCGAGGG-T
* *
35598615 AAAAATGG-AATTTTGGAAAGTTTGAGGGT
1 -AAAATGGTAATTTTTGAAAGTTCGAGGGT
35598644 AAAATGGTAATTTTTGAATAGTT
1 AAAATGGTAATTTTTGAA-AGTT
35598667 TAGGGACCTA
Statistics
Matches: 197, Mismatches: 27, Indels: 68
0.67 0.09 0.23
Matches are distributed among these distances:
27 7 0.04
28 42 0.21
29 62 0.31
30 38 0.19
31 37 0.19
32 11 0.06
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGAAAGTTCGAGGGT
Found at i:35598620 original size:31 final size:29
Alignment explanation
Indices: 35598526--35598628 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 29
35598516 GTTTGGGGGT
* *
35598526 AAAATGGTAATTTTTGGAGAAATCAGGGTTA
1 AAAATGG-AATTTTTTG-GAAATCGGGGTTA
*
35598557 AAAATGGAA--TTTTGGAAAGTTCAGAGG-T-
1 AAAATGGAATTTTTTGGAAA--TC-GGGGTTA
35598585 AAAATGGTAATTTTTTGTGAAATCGGGGTTA
1 AAAATGG-AATTTTTTG-GAAATCGGGGTTA
35598616 AAAATGGAATTTT
1 AAAATGGAATTTT
35598629 GGAAAGTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
27 4 0.07
28 11 0.19
29 8 0.14
30 13 0.22
31 19 0.32
32 4 0.07
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTTGGAAATCGGGGTTA
Found at i:35600699 original size:28 final size:29
Alignment explanation
Indices: 35600639--35600699 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
35600629 CTAAATGTAT
* *
35600639 TTAAATTTAAAACAAAATTTAAATTTAAA
1 TTAAATTTAAAACAAAATTCAAACTTAAA
**
35600668 -TAAATTTAAAA-TTAATTCAAACTTAAA
1 TTAAATTTAAAACAAAATTCAAACTTAAA
35600695 TTAAA
1 TTAAA
35600700 AATCCAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAATTTAAAACAAAATTCAAACTTAAA
Found at i:35601502 original size:201 final size:201
Alignment explanation
Indices: 35601016--35601857 Score: 1223
Period size: 201 Copynumber: 4.2 Consensus size: 201
35601006 TGACCTGATC
* * * * * *
35601016 TTCTTCCCTGTGTCTCATCAGGAAAATGACTGCAATC-ATCTGTTTTAATTCGCTTCTCTGGATC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGC-CTCGCT-TGTTTTGATTCGCTTCTCTGGATC
* * *
35601080 TCCTCAAGAAAACGAATCTGGTCTACTTCCCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCT
64 TCCTCAGGAAAACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCT
* * ** * * *
35601145 TCGACTTGCTTCTCAGTGTCTCGTCTTGAAGCTGGGTTCGAAGATTTGCTGGTGTTTGA-CGTTG
129 TCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTA
*
35601209 AGTTAGTG
194 AGTTGGTG
* *
35601217 TTCTTTTCTGTATCTCATCAGGAAGATGACTACCTCGCTTGTTTTGATTCGCTTCTCTGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTC
* * *
35601282 CTCAGGAAGACGAATCTGGTCCACTTCTTTGTGTCTTATCAGGAAGCTAACCTTTTTATTGCTTC
66 CTCAGGAAAACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTC
* * *
35601347 GACTTGCTTCTCGGTGTCTCATCTA-GAAGCTGGGTTCGAAGATTTACTCGTGTTTGAGCGCTAA
131 GACCTGCTTCTCAGTGTCTCATC-AGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTAA
35601411 GTTGGTG
195 GTTGGTG
*
35601418 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCTTGTTTTGATTCGCTTCTCTAGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTC
* * *
35601483 CTTAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC
66 CTCAGGAAAACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTC
*
35601548 GTCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTAAG
131 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTAAG
*
35601613 TTGGCG
196 TTGGTG
*
35601619 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTG---T--TTCGCTTCTCTGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTC
* * *
35601679 CTCAGGAAAATGAATCTGGTCCACTTCTCTATGTCTCATCAAGAAGCTAACCTTTTTATTGCTTC
66 CTCAGGAAAACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTC
* * * *
35601744 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGAGTCTGAGCGTTGAG
131 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTAAG
*
35601809 TTGGTA
196 TTGGTG
* *
35601815 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCTTGTT
35601858 GAACTACTCC
Statistics
Matches: 585, Mismatches: 50, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
196 180 0.31
198 1 0.00
200 138 0.24
201 266 0.45
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (201 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTC
CTCAGGAAAACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTC
GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTAAG
TTGGTG
Found at i:35601813 original size:397 final size:397
Alignment explanation
Indices: 35601016--35601857 Score: 1213
Period size: 397 Copynumber: 2.1 Consensus size: 397
35601006 TGACCTGATC
* * * * * *
35601016 TTCTTCCCTGTGTCTCATCAGGAAAATGACTGCAATCATCTGTTTTAATTCGCTTCTCTGGATCT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGC-CTCCT-TGTTTTAATTCGCTTCTCTAGATCT
* *
35601081 CCTCAAGAAAACGAATCTGGTCTACTTCCCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTT
64 CCTCAAGAAAACGAATCTGGTCCACTTCCCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTT
* * ** * * *
35601146 CGACTTGCTTCTCAGTGTCTCGTCTTGAAGCTGGGTTCGAAGATTTGCTGGTGTTTGACGTTGAG
129 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGACGCTAAG
* * *
35601211 TTAGTGTTCTTTTCTGTATCTCATCAGGAAGATGACTACCTCGCTTGTTTTGATTCGCTTCTCTG
194 TTAGCGTTCTTCTCTGTATCTCATCAGGAAGATGACCACCTCGCTTG--TT-ATTCGCTTCTCTG
* * * * *
35601276 GATCTCCTCAGGAAGACGAATCTGGTCCACTTCTTTGTGTCTTATCAGGAAGCTAACCTTTTTAT
256 GATCTCCTCAGGAAAACGAATCTGGTCCACTTCTCTATGTCTCATCAAGAAGCTAACCTTTTTAT
* * * *
35601341 TGCTTCGACTTGCTTCTCGGTGTCTCATCTAGAAGCTGGGTTCGAAGATTTACTCGTGTTTGAGC
321 TGCTTCGACCTGCTTCTCAGTGTCTCATCTAGAAGCTGGGTTCGAAGATTTACTCGAGTCTGAGC
*
35601406 GCTAAGTTGGTG
386 GCTAAGTTGGTA
*
35601418 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCTTGTTTTGATTCGCTTCTCTAGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTC-CTTGTTTTAATTCGCTTCTCTAGATCTC
* * * *
35601483 CTTAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC
65 CTCAAGAAAACGAATCTGGTCCACTTCCCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC
*
35601548 GTCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTAAG
130 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGA-CGCTAAG
* *
35601613 TTGGCGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTG-T-TTCGCTTCTCTGGAT
194 TTAGCGTTCTTCTCTGTATCTCATCAGGAAGATGACCACCTCGCTTGTTATTCGCTTCTCTGGAT
*
35601676 CTCCTCAGGAAAATGAATCTGGTCCACTTCTCTATGTCTCATCAAGAAGCTAACCTTTTTATTGC
259 CTCCTCAGGAAAACGAATCTGGTCCACTTCTCTATGTCTCATCAAGAAGCTAACCTTTTTATTGC
* *
35601741 TTCGACCTGCTTCTCAGTGTCTCATC-AGGAAGCTGGGTTCGAAGATTTGCTCGAGTCTGAGCGT
324 TTCGACCTGCTTCTCAGTGTCTCATCTA-GAAGCTGGGTTCGAAGATTTACTCGAGTCTGAGCGC
*
35601805 TGAGTTGGTA
388 TAAGTTGGTA
*
35601815 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTC-CTTGTT
35601858 GAACTACTCC
Statistics
Matches: 395, Mismatches: 42, Indels: 11
0.88 0.09 0.02
Matches are distributed among these distances:
396 1 0.00
397 179 0.45
399 1 0.00
401 136 0.34
402 78 0.20
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (397 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCCTTGTTTTAATTCGCTTCTCTAGATCTCC
TCAAGAAAACGAATCTGGTCCACTTCCCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCG
ACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGACGCTAAGTT
AGCGTTCTTCTCTGTATCTCATCAGGAAGATGACCACCTCGCTTGTTATTCGCTTCTCTGGATCT
CCTCAGGAAAACGAATCTGGTCCACTTCTCTATGTCTCATCAAGAAGCTAACCTTTTTATTGCTT
CGACCTGCTTCTCAGTGTCTCATCTAGAAGCTGGGTTCGAAGATTTACTCGAGTCTGAGCGCTAA
GTTGGTA
Found at i:35614160 original size:58 final size:58
Alignment explanation
Indices: 35614087--35614364 Score: 271
Period size: 59 Copynumber: 4.7 Consensus size: 58
35614077 ATTTTTGACT
* *
35614087 TTCGGGGGTAAAAAT-GTAATTTTTGGTAGAATTTGGGTTAAAAATGAGATTTTGGAAAG
1 TTCGAGGGT-AAAATGGTAATTTTTGGT-GAATTAGGGTTAAAAATGAGATTTTGGAAAG
* *
35614146 TTCGAGGATAAAATGGTAATTTTTGGGTGAAATTAGGGTT-AAAATGAGATTTTAGAAAG
1 TTCGAGGGTAAAATGGTAATTTTT-GGTG-AATTAGGGTTAAAAATGAGATTTTGGAAAG
* * * * * *
35614205 TTTGGGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAAGGTA-ATTTTGGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAATTAG-GGTTAAAAATG-AGATTTTGGAAAG
* * * * * *
35614263 TTTGGGGGTAAAAAT-GTAATTTTTGGTGAAATCAAGGTTAAAAATG-GAATTTGAAAAG
1 TTCGAGGGT-AAAATGGTAATTTTTGGTG-AATTAGGGTTAAAAATGAGATTTTGGAAAG
* *
35614321 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAA
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAATTAG-GGTTAAAAA
35614365 GGTAATTTTT
Statistics
Matches: 181, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
56 4 0.02
57 15 0.08
58 73 0.40
59 75 0.41
60 14 0.08
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.33
Consensus pattern (58 bp):
TTCGAGGGTAAAATGGTAATTTTTGGTGAATTAGGGTTAAAAATGAGATTTTGGAAAG
Found at i:35614275 original size:117 final size:117
Alignment explanation
Indices: 35614087--35614382 Score: 354
Period size: 117 Copynumber: 2.5 Consensus size: 117
35614077 ATTTTTGACT
* * *
35614087 TTCGGGGGTAAAAAT-GTAATTTTTGGTAGAATTTG-GGTTAAAAATG-AGATTTTGGAAAGTTC
1 TTCGGGGGT-AAAATGGTAATTTTTGGT-GAAATCGAGGTTAAAAAGGTA-ATTTTGGAAAGTTC
* * *
35614149 GAGGAT-AAAATGGTAATTTTTGGGTGAAATTAGGGTT-AAAAT-GAGATTTTAGAAAG
63 GAGGATAAAAAT-GTAATTTTT-GGTGAAATCAAGGTTAAAAATGGA-ATTTGA-AAAG
* * * *
35614205 TTTGGGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAAGGTAATTTTGGGAAGTTTGGG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGGTAATTTTGGAAAGTTCGAG
*
35614269 GGTAAAAATGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTGAAAAG
66 GATAAAAATGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTGAAAAG
* *
35614321 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGGTAATTTTTGAATAGTT
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGGTAATTTTGGAA-AGTT
35614383 TAGGGACCTA
Statistics
Matches: 155, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
116 39 0.25
117 92 0.59
118 24 0.15
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (117 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGGTAATTTTGGAAAGTTCGAG
GATAAAAATGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTGAAAAG
Found at i:35614372 original size:58 final size:57
Alignment explanation
Indices: 35614087--35614372 Score: 278
Period size: 58 Copynumber: 4.9 Consensus size: 57
35614077 ATTTTTGACT
* * * *
35614087 TTCGGGGGTAAAAAT-GTAATTTTTGGTAGAATTTG-GGTTAAAAATGAGATTTTGGAAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGGT-GAAATCGAGGTTAAAAA-G-GAATTTGAAAAG
* * * * *
35614146 TTCGAGGATAAAATGGTAATTTTTGGGTGAAAT-TAGGGTT-AAAATGAGATTTTAGAAAG
1 TTCGGGGGTAAAATGGTAATTTTT-GGTGAAATCGA-GGTTAAAAAGGA-ATTTGA-AAAG
* **
35614205 TTTGGGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAAGGTAATTTTGGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGG-AA-TTTGAAAAG
* *
35614263 TTTGGGGGTAAAAAT-GTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTGAAAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAA-GGAATTTGAAAAG
*
35614321 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGGTAATTT
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGG-AATTT
35614373 TTGAATAGTT
Statistics
Matches: 190, Mismatches: 22, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
57 21 0.11
58 82 0.43
59 78 0.41
60 9 0.05
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (57 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGGAATTTGAAAAG
Found at i:35614375 original size:30 final size:29
Alignment explanation
Indices: 35614213--35614373 Score: 143
Period size: 30 Copynumber: 5.5 Consensus size: 29
35614203 AGTTTGGGGG
*
35614213 TAAAATGGTAATTTTGGTGAAATCGAGGT
1 TAAAAAGGTAATTTTGGTGAAATCGAGGT
* * * *
35614242 TAAAAAGGTAATTTTGG-GAAGTTTGGGGG
1 TAAAAAGGTAATTTTGGTGAA-ATCGAGGT
* *
35614271 TAAAAATGTAATTTTTGGTGAAATCAAGGT
1 TAAAAAGGTAA-TTTTGGTGAAATCGAGGT
* *
35614301 TAAAAATGG-AA-TTT-G-AAAAGTTCGAGGG
1 TAAAAA-GGTAATTTTGGTGAAA--TCGAGGT
*
35614329 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAAAGGTAA-TTTTGGTGAAATCGAGGT
35614359 TAAAAAGGTAATTTT
1 TAAAAAGGTAATTTT
35614374 TGAATAGTTT
Statistics
Matches: 102, Mismatches: 19, Indels: 22
0.71 0.13 0.15
Matches are distributed among these distances:
26 3 0.03
27 3 0.03
28 18 0.18
29 34 0.33
30 36 0.35
31 5 0.05
32 3 0.03
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
TAAAAAGGTAATTTTGGTGAAATCGAGGT
Found at i:35617068 original size:2 final size:2
Alignment explanation
Indices: 35617061--35617101 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35617051 ATCATGACAA
35617061 AG AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG AG A
35617102 AAATGCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35618204 original size:14 final size:14
Alignment explanation
Indices: 35618187--35618230 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
35618177 TAAATGGGAT
35618187 AAAAATAAATAAAG
1 AAAAATAAATAAAG
* *
35618201 AAAAACAAATAAAT
1 AAAAATAAATAAAG
35618215 AAAATATAAAATAAAG
1 AAAA-AT-AAATAAAG
35618231 GGGAGCATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 16 0.67
15 1 0.04
16 7 0.29
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAAATAAATAAAG
Found at i:35619942 original size:38 final size:38
Alignment explanation
Indices: 35619893--35619993 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
35619883 AGTAAGCCTG
*
35619893 CTAGGCACTAAGCTCGATAAACATCGGCACG-AAGTCTC
1 CTAGGCACTAAGCTCGATAAACATCGGCACGAAACT-TC
** * *
35619931 CTAGGTTCTAAGC-CTGATAAACATTGGCACGAAACTTG
1 CTAGGCACTAAGCTC-GATAAACATCGGCACGAAACTTC
35619969 CTAGGCACTAAGCTCGATAAACATC
1 CTAGGCACTAAGCTCGATAAACATC
35619994 AGGGAATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
37 1 0.02
38 47 0.90
39 4 0.08
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (38 bp):
CTAGGCACTAAGCTCGATAAACATCGGCACGAAACTTC
Found at i:35621399 original size:28 final size:28
Alignment explanation
Indices: 35621357--35621450 Score: 134
Period size: 28 Copynumber: 3.3 Consensus size: 28
35621347 CGAAGCATCG
*
35621357 AAGTGCTATTACAGAACAGAGAGCACACA
1 AAGTGCTAAT-CAGAACAGAGAGCACACA
* *
35621386 AAGTGCTAATCAGAATAGAAAGCACACA
1 AAGTGCTAATCAGAACAGAGAGCACACA
* *
35621414 AAGTGCTAATCAAAACAGAGGGCACACA
1 AAGTGCTAATCAGAACAGAGAGCACACA
35621442 AAGTGCTAA
1 AAGTGCTAA
35621451 ATACATGTAG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 49 0.84
29 9 0.16
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (28 bp):
AAGTGCTAATCAGAACAGAGAGCACACA
Found at i:35624671 original size:16 final size:16
Alignment explanation
Indices: 35624650--35624690 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
35624640 TATTAAACTA
35624650 AATGCAAATGATTCCT
1 AATGCAAATGATTCCT
35624666 AATGCAAATGATTCCT
1 AATGCAAATGATTCCT
35624682 AATGCAAAT
1 AATGCAAAT
35624691 TATCCTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (16 bp):
AATGCAAATGATTCCT
Found at i:35632642 original size:26 final size:26
Alignment explanation
Indices: 35632610--35632847 Score: 105
Period size: 26 Copynumber: 9.2 Consensus size: 26
35632600 ACTTCGAGCT
35632610 GGTGATTAAATAGCAAGCCTTGAGTC
1 GGTGATTAAATAGCAAGCCTTGAGTC
* * * *
35632636 GATGATTAATTAGCAGGCCTTAAG-C
1 GGTGATTAAATAGCAAGCCTTGAGTC
* * *
35632661 TGGTGATTAACTA-CCAGGCTTCGAGTC
1 -GGTGATTAAATAGCAAGCCTT-GAGTC
*
35632688 GGTGATTAAATAGCAGGCCTTGAG-C
1 GGTGATTAAATAGCAAGCCTTGAGTC
* * ** *
35632713 TGGTGATTTACTAGC-AGGTTTCAAG-C
1 -GGTGATTAAATAGCAAGCCTT-GAGTC
* * *
35632739 TGGTGATTAAATAGTAGGCCTTGAGGC
1 -GGTGATTAAATAGCAAGCCTTGAGTC
** * * *
35632766 AATGACT-ATTAGCAAG-CTATGAGCC
1 GGTGATTAAATAGCAAGCCT-TGAGTC
* * *
35632791 GATGATTAATTAGCCAG-CTTCGAGTC
1 GGTGATTAAATAGCAAGCCTT-GAGTC
* ** *
35632817 GGTGACTAAATAGCTGGCCTTGAGCC
1 GGTGATTAAATAGCAAGCCTTGAGTC
35632843 GGTGA
1 GGTGA
35632848 CTTTTAGCAG
Statistics
Matches: 156, Mismatches: 44, Indels: 24
0.70 0.20 0.11
Matches are distributed among these distances:
24 2 0.01
25 27 0.17
26 114 0.73
27 13 0.08
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GGTGATTAAATAGCAAGCCTTGAGTC
Found at i:35632730 original size:78 final size:78
Alignment explanation
Indices: 35632601--35632748 Score: 203
Period size: 78 Copynumber: 1.9 Consensus size: 78
35632591 AATGAGAAGA
*
35632601 CTTCGAGCTGGTGATTAAATAGCAAGCCTTGAGTCGATGATTAATTAGCAGGCCTT-AAGCTGGT
1 CTTCGAGCTGGTGATTAAATAGCAAGCCTTGAGTCGATGATTAACTAGCAGG-CTTCAAGCTGGT
35632665 GATTAACTACCAGG
65 GATTAACTACCAGG
* * * *
35632679 CTTCGAG-TCGGTGATTAAATAGCAGGCCTTGAG-CTGGTGATTTACTAGCAGGTTTCAAGCTGG
1 CTTCGAGCT-GGTGATTAAATAGCAAGCCTTGAGTC-GATGATTAACTAGCAGGCTTCAAGCTGG
35632742 TGATTAA
64 TGATTAA
35632749 ATAGTAGGCC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
77 4 0.06
78 58 0.94
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (78 bp):
CTTCGAGCTGGTGATTAAATAGCAAGCCTTGAGTCGATGATTAACTAGCAGGCTTCAAGCTGGTG
ATTAACTACCAGG
Found at i:35632744 original size:52 final size:52
Alignment explanation
Indices: 35632605--35632763 Score: 178
Period size: 52 Copynumber: 3.1 Consensus size: 52
35632595 AGAAGACTTC
* * * * * *
35632605 GAGCTGGTGATTAAATAGCAAGCCTT-GAGTCGATGATTAATTAGCAGGCCTT
1 GAGCTGGTGATTAACTA-CCAGGCTTCAAGTCGGTGATTAAATAGCAGGCCTT
* *
35632657 AAGCTGGTGATTAACTACCAGGCTTCGAGTCGGTGATTAAATAGCAGGCCTT
1 GAGCTGGTGATTAACTACCAGGCTTCAAGTCGGTGATTAAATAGCAGGCCTT
* * * *
35632709 GAGCTGGTGATTTACTAGCAGGTTTCAAG-CTGGTGATTAAATAGTAGGCCTT
1 GAGCTGGTGATTAACTACCAGGCTTCAAGTC-GGTGATTAAATAGCAGGCCTT
35632761 GAG
1 GAG
35632764 GCAATGACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 7 0.08
52 86 0.92
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (52 bp):
GAGCTGGTGATTAACTACCAGGCTTCAAGTCGGTGATTAAATAGCAGGCCTT
Found at i:35638730 original size:28 final size:28
Alignment explanation
Indices: 35638699--35638759 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
35638689 AAAATGAGAC
* *
35638699 TTTGGA-TGCCCGGGAGTAAAATGGTAAT
1 TTTGGACT-CCCGAGAGCAAAATGGTAAT
*
35638727 TTTGGACTCTCGAGAGCAAAATGGTAAT
1 TTTGGACTCCCGAGAGCAAAATGGTAAT
35638755 TTTGG
1 TTTGG
35638760 GGAAATTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (28 bp):
TTTGGACTCCCGAGAGCAAAATGGTAAT
Found at i:35638884 original size:28 final size:29
Alignment explanation
Indices: 35638843--35638903 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
35638833 AAAACGGGAC
*
35638843 TTTTTGGATTCTCGAGGGCAAAATGGCAA
1 TTTTTGGACTCTCGAGGGCAAAATGGCAA
*
35638872 TTTTT-GACTCTCGAGGGCAAAATGGTAA
1 TTTTTGGACTCTCGAGGGCAAAATGGCAA
35638900 TTTT
1 TTTT
35638904 GAGAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTTTGGACTCTCGAGGGCAAAATGGCAA
Found at i:35638892 original size:146 final size:146
Alignment explanation
Indices: 35638716--35638993 Score: 432
Period size: 146 Copynumber: 1.9 Consensus size: 146
35638706 GCCCGGGAGT
* * *
35638716 AAAATGGTAATTTTGGACTCTCGAGAGCAAAATGGTAATTTTGGGGAAATTTGGGGTTAAAAATG
1 AAAATGGCAATTTTGGACTCTCGAGAGCAAAATGGTAATTTTGAGAAAATTTGGGGTT-AAAATG
* * *
35638781 ATATTTTAGACACTTAAGGGTAAAATGGTAATTTTT-GAAAGAATCGAAATAAAAAACGGGACTT
65 ACATTTTAGACACTTAAGGGTAAAACGATAATTTTTCGAAAGAATCGAAATAAAAAACGGGACTT
35638845 TTTGGATTCTCGAGGGC
130 TTTGGATTCTCGAGGGC
* *
35638862 AAAATGGCAATTTTTGACTCTCGAGGGCAAAATGGTAATTTTGAGAAAATTTGGGGTTAAAATGA
1 AAAATGGCAATTTTGGACTCTCGAGAGCAAAATGGTAATTTTGAGAAAATTTGGGGTTAAAATGA
* * **
35638927 CATTTTAGACACTTGAGGGTAAAACGATAATTTTTCGGAAGAATCGGGATAAAAAACGGGACTTT
66 CATTTTAGACACTTAAGGGTAAAACGATAATTTTTCGAAAGAATCGAAATAAAAAACGGGACTTT
35638992 TT
131 TT
35638994 CAGAAAAGGG
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
145 38 0.32
146 81 0.68
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (146 bp):
AAAATGGCAATTTTGGACTCTCGAGAGCAAAATGGTAATTTTGAGAAAATTTGGGGTTAAAATGA
CATTTTAGACACTTAAGGGTAAAACGATAATTTTTCGAAAGAATCGAAATAAAAAACGGGACTTT
TTGGATTCTCGAGGGC
Found at i:35639498 original size:17 final size:17
Alignment explanation
Indices: 35639437--35639498 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
35639427 TTTTTATTTC
*
35639437 AAAATAAATTTAAACTC
1 AAAATAAATTTAAACTT
* * * *
35639454 CAAACAAGTTTTAAATTT
1 AAAATAA-ATTTAAACTT
*
35639472 ACAATAAATTTAAACTT
1 AAAATAAATTTAAACTT
*
35639489 AAAATGAATT
1 AAAATAAATT
35639499 AAAAATCTAA
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATAAATTTAAACTT
Found at i:35640607 original size:91 final size:91
Alignment explanation
Indices: 35640089--35641365 Score: 2137
Period size: 91 Copynumber: 14.0 Consensus size: 91
35640079 TAGTGCTGAA
* * ** *
35640089 GCTTTATCTTGCTCTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCGTCTTTGCTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
35640154 TCAAGAGGATA-GAAATTGATGTTTGAA
66 TCAAGAGGATAGGAAA-TGATG-TTGAT
* * ** *
35640181 GTTTCATCTTGCTCTTACTACTACAACTACAGAGAGATAAAGACTTGCTATCCGTCTTCACTACA
1 GCTTCATCTTGCTC-T--TACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACA
* *
35640246 ACTGCAAGAGGATAGGAATTGATGTTTGAT
63 ACTTCAAGAGGATAGGAAATGATG-TTGAT
35640276 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
35640341 TCAAGAGGATAGGAATTGATGTTTAAT
66 TCAAGAGGATAGGAAATGATG-TTGAT
35640368 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
35640433 TCAAGAGGATAGGAATTGATGTTTGAT
66 TCAAGAGGATAGGAAATGATG-TTGAT
*
35640460 GCTTCATCTTGCTCTTACTACAACTTTAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
35640525 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
*
35640551 GCTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
35640616 TCAAGAGGATAGGAAATTATGTTGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
* *
35640642 TCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAAAT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
35640707 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
*
35640733 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAATT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
35640798 TCAAGAGGATAGAAAATGATGTTGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
* *
35640824 TCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
35640889 TCAAGAGGATAAGAAATGATGTTGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
35640915 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
35640980 TCAAGAGGATAGGAAATGATATT-AGT
66 TCAAGAGGATAGGAAATGATGTTGA-T
35641006 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
35641071 TCAAGAGGATAGGAAATGATATTGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
35641097 GCTTCATCTTGCT-TTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
35641161 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
35641187 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
35641252 TCAAGAGGATAGGAAATGATGTTGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
* *
35641278 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTACAAAT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
35641343 TCAAGAGGATAGGAAATGATGTT
66 TCAAGAGGATAGGAAATGATGTT
35641366 ATTTTGATTT
Statistics
Matches: 1130, Mismatches: 48, Indels: 15
0.95 0.04 0.01
Matches are distributed among these distances:
90 88 0.08
91 700 0.62
92 258 0.23
93 1 0.00
94 1 0.00
95 79 0.07
96 3 0.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (91 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
TCAAGAGGATAGGAAATGATGTTGAT
Found at i:35642979 original size:1 final size:1
Alignment explanation
Indices: 35642964--35643035 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
35642954 CGACCTCTCC
* * * * * * * * *
35642964 TTTTCTTTTTCTTTTTTCTTTTTTCTTTTTTTTCTTCTTTTTTCTTTTTTTTTTCTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
35643029 TCTTTTT
1 TTTTTTT
35643036 ATTTATTGAA
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:35642981 original size:7 final size:7
Alignment explanation
Indices: 35642964--35643027 Score: 82
Period size: 7 Copynumber: 9.6 Consensus size: 7
35642954 CGACCTCTCC
35642964 TTTTC-T
1 TTTTCTT
35642970 TTTTCTT
1 TTTTCTT
35642977 TTTTCTT
1 TTTTCTT
35642984 TTTTC-T
1 TTTTCTT
35642990 TTTT-TT
1 TTTTCTT
*
35642996 TCTTCTT
1 TTTTCTT
35643003 TTTTCTT
1 TTTTCTT
35643010 TTTT-TT
1 TTTTCTT
35643016 TTCTTCTT
1 TT-TTCTT
35643024 TTTT
1 TTTT
35643028 TTCTTTTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
6 18 0.35
7 29 0.57
8 4 0.08
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:35642986 original size:19 final size:18
Alignment explanation
Indices: 35642964--35643035 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 18
35642954 CGACCTCTCC
35642964 TTTTCTTTTTCTTTTTTCTT
1 TTTTC-TTTT-TTTTTTCTT
35642984 TTTTCTTTTTTTTCTTCTT
1 TTTTCTTTTTTTT-TTCTT
35643003 TTTTCTTTTTTTTTTCTT
1 TTTTCTTTTTTTTTTCTT
35643021 CTTTT-TTTTCTTTTT
1 -TTTTCTTTT-TTTTT
35643036 ATTTATTGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.27
19 31 0.63
20 5 0.10
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTCTTTTTTTTTTCTT
Found at i:35643011 original size:33 final size:33
Alignment explanation
Indices: 35642969--35643032 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
35642959 TCTCCTTTTC
35642969 TTTTTCTTTTTTCTTTT-TTCTTTTTTTTCTTCT
1 TTTTTCTTTTTT-TTTTCTTCTTTTTTTTCTTCT
35643002 TTTTTCTTTTTTTTTTCTTCTTTTTTTTCTT
1 TTTTTCTTTTTTTTTTCTTCTTTTTTTTCTT
35643033 TTTATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (33 bp):
TTTTTCTTTTTTTTTTCTTCTTTTTTTTCTTCT
Found at i:35648775 original size:118 final size:118
Alignment explanation
Indices: 35648580--35648830 Score: 378
Period size: 118 Copynumber: 2.1 Consensus size: 118
35648570 TCTCGAGAGC
* * *
35648580 AAAATGGTAATTTTGGGAAAATTTAGGGTTAAAAATGATATTTTAGACACTTAAGGGTAAAATGA
1 AAAATGGTAATTTTGAGAAAATGTAGGGTTAAAAATGATATTTTAGACACTTAAGGGTAAAACGA
* *
35648645 TAATTTTCGAAAGAATCGAGATAAAAAAGGGGACTTTTTGGATGCCCTAGGGA-
66 TAATTTTCGAAAGAATCGAGATAAAAAAGGGGACTTTTTAGATGCCCGA-GGAT
* * * *
35648698 AAAAGGGTAATTTTGAGAAAATGTGGGGTTAAAAATGATGTTTTAGACACTTGAGGGTAAAACGA
1 AAAATGGTAATTTTGAGAAAATGTAGGGTTAAAAATGATATTTTAGACACTTAAGGGTAAAACGA
* * *
35648763 TAATTTTTGAAAGAATCGGGATAAAAAATGGGACTTTTTAGATGCCCGAGGAT
66 TAATTTTCGAAAGAATCGAGATAAAAAAGGGGACTTTTTAGATGCCCGAGGAT
35648816 AAAATGGTAATTTTG
1 AAAATGGTAATTTTG
35648831 GACTCTCGAG
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
117 3 0.03
118 116 0.97
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (118 bp):
AAAATGGTAATTTTGAGAAAATGTAGGGTTAAAAATGATATTTTAGACACTTAAGGGTAAAACGA
TAATTTTCGAAAGAATCGAGATAAAAAAGGGGACTTTTTAGATGCCCGAGGAT
Found at i:35648996 original size:146 final size:146
Alignment explanation
Indices: 35648696--35648974 Score: 343
Period size: 146 Copynumber: 1.9 Consensus size: 146
35648686 ATGCCCTAGG
* * ** *
35648696 GAAAAAGGGTAATTTTGAGAAAATGTGGGGTTAAAAATGATGTTTTAGACACTTGAGGGTAAAAC
1 GAAAAATGGTAATTTTGGGAAAATGTGGGGTTAAAAATGAAATTTTAGACACTTGAGGGTAAAAA
** * * **
35648761 GATAATTTTTGAAAGAATCGGGATAAAAAATGGGACTTTTTAGATGCCCGAGGATAAAATGGTAA
66 GATAATTTTCAAAAGAATCGAGATAAAAAATGAGACTTTTTAGACACCCGAGGATAAAATGGTAA
35648826 TTTTGGACTCTCGAGA
131 TTTTGGACTCTCGAGA
* ** *
35648842 GAAAAATGGTAATTTTGGGAAAATTTGGGGTTAAAAATGAAATTTTAGA-TTTTTAGGGGTAAAA
1 GAAAAATGGTAATTTTGGGAAAATGTGGGGTTAAAAATGAAATTTTAGACACTTGA-GGGTAAAA
* * *
35648906 TAGA-AATTTTCAAAAGAATCGAGATCAAAAATGAGA-TTTTTGGACATCCG-GGATAAAAT-GT
65 -AGATAATTTTCAAAAGAATCGAGATAAAAAATGAGACTTTTTAGACACCCGAGGATAAAATGGT
35648967 AATTTTGG
129 AATTTTGG
35648975 GAAGTTTCAT
Statistics
Matches: 113, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
143 10 0.09
144 9 0.08
145 13 0.12
146 79 0.70
147 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.30
Consensus pattern (146 bp):
GAAAAATGGTAATTTTGGGAAAATGTGGGGTTAAAAATGAAATTTTAGACACTTGAGGGTAAAAA
GATAATTTTCAAAAGAATCGAGATAAAAAATGAGACTTTTTAGACACCCGAGGATAAAATGGTAA
TTTTGGACTCTCGAGA
Found at i:35650228 original size:3 final size:3
Alignment explanation
Indices: 35650222--35650293 Score: 74
Period size: 3 Copynumber: 23.7 Consensus size: 3
35650212 CTTTTTTGAC
* * * *
35650222 TTA TTA TTA TTAA TTA TTAA TTA -AA ATA TTA TTA CTA ATA TTA TTA
1 TTA TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
35650268 TTA TTA TTA TTA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
35650294 TAATGCAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 51 0.88
4 6 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:35652105 original size:59 final size:58
Alignment explanation
Indices: 35652027--35652333 Score: 422
Period size: 59 Copynumber: 5.2 Consensus size: 58
35652017 ACCCAAGGGC
*
35652027 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAA-GTTCAGGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTC-GGGGT
*
35652085 AAAATGGTAATTTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAA-GTTCGAGGGT
1 AAAATGGTAA-TTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG-GGGT
* * *
35652144 AAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGATT-GGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGG-TTCGGGGT
* * * *
35652202 AAAATGGTAATTTTTTGTGAAACCGGGGTTAAAAACGGAATTTTAGAAGGTTCGAGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG-GGGT
* * * *
35652261 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAACGGAATTTTAGAAGGTTTGGGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGG-TTCGGGGT
35652320 AAAATGGTAATTTT
1 AAAATGGTAATTTT
35652334 GGAAATTTTA
Statistics
Matches: 231, Mismatches: 11, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
57 2 0.01
58 95 0.41
59 129 0.56
60 5 0.02
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGT
Found at i:35652215 original size:117 final size:116
Alignment explanation
Indices: 35651984--35652333 Score: 463
Period size: 117 Copynumber: 3.0 Consensus size: 116
35651974 AAAGAAACGA
* ** * * *
35651984 TAAAATCGGGTGTTGAAAATGGAACTTTTGGATA-CCCAAGGGCAAAATGGTAATTTTTGGTAAA
1 TAAAATCGGG-GTTAAAAATGGAA-TTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGGTGAA
*
35652048 ATCGGGGTTAAAAATGGAATTTTGGAA-GTTCAGGGGTAAAATGGTAATTTTTTGG
63 ATCGGGGTTAAAAATGGAATTTTAGAAGGTT-AGGGGTAAAATGGTAATTTTTT-G
*
35652103 TAAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTCGGTGAAATC
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATC
*
35652168 GAGGTTAAAAATGGAATTTTAGAAGGATT-GGGGTAAAATGGTAATTTTTTG
66 GGGGTTAAAAATGGAATTTTAGAAGG-TTAGGGGTAAAATGGTAATTTTTTG
* * * * *
35652219 TGAAACCGGGGTTAAAAACGGAATTTTAGAAGGTTCGAGGGTAAAATGGTAATTTTTGGTGAAAC
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAA-GTTCGAGGGTAAAATGGTAATTTTTGGTGAAAT
* *
35652284 CGGGGTTAAAAACGGAATTTTAGAAGGTTTGGGGGTAAAATGGTAATTTT
65 CGGGGTTAAAAATGGAATTTTAGAAGG-TTAGGGGTAAAATGGTAATTTT
35652334 GGAAATTTTA
Statistics
Matches: 208, Mismatches: 18, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
116 29 0.14
117 135 0.65
118 32 0.15
119 12 0.06
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.31
Consensus pattern (116 bp):
TAAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATC
GGGGTTAAAAATGGAATTTTAGAAGGTTAGGGGTAAAATGGTAATTTTTTG
Found at i:35652244 original size:30 final size:30
Alignment explanation
Indices: 35652210--35652304 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
35652200 GTAAAATGGT
35652210 AATTTTTTGTGAAACCGGGGTTAAAAACGG
1 AATTTTTTGTGAAACCGGGGTTAAAAACGG
* ** *
35652240 AA--TTTT-AGAAGGTTCGAGGG-T-AAAATGG
1 AATTTTTTGTGAA--ACCG-GGGTTAAAAACGG
*
35652268 TAATTTTTGGTGAAACCGGGGTTAAAAACGG
1 -AATTTTTTGTGAAACCGGGGTTAAAAACGG
35652299 AATTTT
1 AATTTT
35652305 AGAAGGTTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
27 3 0.06
28 10 0.21
29 8 0.17
30 14 0.30
31 9 0.19
32 3 0.06
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (30 bp):
AATTTTTTGTGAAACCGGGGTTAAAAACGG
Found at i:35652757 original size:162 final size:162
Alignment explanation
Indices: 35652463--35652798 Score: 550
Period size: 162 Copynumber: 2.1 Consensus size: 162
35652453 AGGCATCTAG
* * * *
35652463 CAGTCAAAGGACGAATTTGTAAATCTTGAAGAATTCTTGGGCCAATTTCGTAATTAAGTAAAAGT
1 CAGTCAAAGGACGAATTTATAAACCTTGAAAAATGCTTGGGCCAATTTCGTAATTAAGTAAAAGT
* *
35652528 TGATTTAGGATTAAATTTAAACAAATTAAAAATGTTAGGGACTAAATGCAGAAATAAACCAAAAA
66 TGATTTAGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCAGAAATAAACCAAAAA
*
35652593 AATGACTCGTGACAGCCTCTGGTGCAGTCAAA
131 AATGACACGTGACAGCCTCTGGTGCAGTCAAA
*
35652625 CAGTCAAAGGACGAATTTATGAACCTTGAAAAATGCTTGGGCCAATTTCGTAATTAAGTAAAAGT
1 CAGTCAAAGGACGAATTTATAAACCTTGAAAAATGCTTGGGCCAATTTCGTAATTAAGTAAAAGT
35652690 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGCG-CTAAATGCAGAAATAAACC-AA
66 TGATTTA-GGATTAAATTAAAACAAATTAAAAATGTCAGG-GACTAAATGCAGAAATAAACCAAA
* *
35652753 AAAATGACACGTGGCAGTCTCTGGTGCAGTCAAA
129 AAAATGACACGTGACAGCCTCTGGTGCAGTCAAA
35652787 CAGTCAAAGGAC
1 CAGTCAAAGGAC
35652799 TAAATTGAAA
Statistics
Matches: 162, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
162 112 0.69
163 49 0.30
164 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (162 bp):
CAGTCAAAGGACGAATTTATAAACCTTGAAAAATGCTTGGGCCAATTTCGTAATTAAGTAAAAGT
TGATTTAGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCAGAAATAAACCAAAAA
AATGACACGTGACAGCCTCTGGTGCAGTCAAA
Found at i:35654396 original size:17 final size:17
Alignment explanation
Indices: 35654376--35654440 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
35654366 TTAATATTAT
* *
35654376 TTTAAATTAAGTTTAAA
1 TTTAAAATAAATTTAAA
35654393 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
*
35654410 --T-AAGTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
35654424 TTTAAGATAAATTTAAA
1 TTTAAAATAAATTTAAA
35654441 ATGAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 26 0.65
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:35654403 original size:11 final size:11
Alignment explanation
Indices: 35654389--35654458 Score: 65
Period size: 11 Copynumber: 6.5 Consensus size: 11
35654379 AAATTAAGTT
35654389 TAAATTTAAAA
1 TAAATTTAAAA
35654400 TAAATTT-AAA
1 TAAATTTAAAA
* *
35654410 T-AA-GTAAATT
1 TAAATTTAAA-A
*
35654420 TAAATTTAAGA
1 TAAATTTAAAA
35654431 TAAATTTAAAA
1 TAAATTTAAAA
*
35654442 TGAATTTAAAA
1 TAAATTTAAAA
*
35654453 TTAATT
1 TAAATT
35654459 CAAACTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 5 0.11
11 34 0.72
12 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:35654875 original size:76 final size:76
Alignment explanation
Indices: 35654747--35655494 Score: 929
Period size: 76 Copynumber: 9.8 Consensus size: 76
35654737 TGCTCTTCAG
* * * *
35654747 AGAGATAAAGACTTTGCTATCCAACTTTACTTCAATTTCAGGAGAATAGGAAATGATTTTGCTCT
1 AGAGATAAAGAC-TTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
*
35654812 TACTTCAATTTT
65 TACTTCAATTTC
* * * ** * *
35654824 GGAGATAAAGACTTGTTATCCAACTCTACTTCAGCTTCAAGCGGATAGGAAATGA-CGTTGCACT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCT
35654888 TACTTCAATTTC
65 TACTTCAATTTC
* * * *
35654900 AGAGATAAATTCAGAGATAAAGACGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGA
1 AGAGAT-AA---AGA-CT-----TGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
*
35654965 TCTTGCTCTTACTTCAATTTT
56 TCTTGCTCTTACTTCAATTTC
* *
35654986 AGAGATAAAGACTTGATATCTAACTTTACTTCAATTTCAAGAGGATAAGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
*
35655051 ACTTCATTTTC
66 ACTTCAATTTC
* * *
35655062 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGGATTGATCTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
*
35655127 ACTTCATTTTC
66 ACTTCAATTTC
* * *
35655138 AGAGATAAAGACTTGATATCCAGCTTTACTTCAAATTCAAGAGGATAGGAAATGA-CGTTGTTCT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCT
35655202 TACTTCAATTTC
65 TACTTCAATTTC
* * *
35655214 AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
35655279 ACTTCAATTTC
66 ACTTCAATTTC
* * *
35655290 AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
35655355 ACTTCAATTTC
66 ACTTCAATTTC
* * *
35655366 AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
*
35655424 ACTTTAATTTC
66 ACTTCAATTTC
* * * * * *
35655435 AGAGATAAAGACGTGTTATCCAGCTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTG
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTG
35655495 GTGCGGTCTG
Statistics
Matches: 596, Mismatches: 54, Indels: 43
0.86 0.08 0.06
Matches are distributed among these distances:
69 61 0.10
71 1 0.00
72 2 0.00
73 2 0.00
74 1 0.00
75 1 0.00
76 444 0.74
77 14 0.02
80 3 0.01
81 2 0.00
82 3 0.01
85 2 0.00
86 59 0.10
87 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (76 bp):
AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
ACTTCAATTTC
Found at i:35663591 original size:24 final size:27
Alignment explanation
Indices: 35663541--35663591 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 27
35663531 TATGTTAATA
* *
35663541 GTATGCAAGATATGATGCAAAATGCAT
1 GTATGCAAGATACGATGCAAAAGGCAT
35663568 GTATGCAA-ATACGA-G-AAAAGGCAT
1 GTATGCAAGATACGATGCAAAAGGCAT
35663592 TGATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 5 0.23
27 8 0.36
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (27 bp):
GTATGCAAGATACGATGCAAAAGGCAT
Found at i:35667801 original size:59 final size:59
Alignment explanation
Indices: 35667600--35667913 Score: 449
Period size: 58 Copynumber: 5.4 Consensus size: 59
35667590 TGGATACCTA
* * * * *
35667600 GGGGCAAAATCGTAATTTTTAGTAAAATCGGGGTTAAAAATGGAATTTTGGAA-GTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG
* *
35667658 AGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAA-GTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG
* *
35667716 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGATCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG
* *
35667775 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAGAAGGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG
* * *
35667834 GGGGTAAAATGGTAATTTTT-G-GAAGTTTTGGGGTTAAAAATAGAATTTTAGAAGGTTC-
1 GGGGTAAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG
35667892 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
35667914 AAATTTTGGG
Statistics
Matches: 236, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
57 3 0.01
58 124 0.53
59 109 0.46
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCG
Found at i:35667822 original size:117 final size:117
Alignment explanation
Indices: 35667600--35667913 Score: 438
Period size: 117 Copynumber: 2.7 Consensus size: 117
35667590 TGGATACCTA
* * * * *
35667600 GGGGCAAAATCGTAATTTTTAGTAAAATCGGGGTTAAAAATGGAATTTTGGAA-GTTCGAGGGTA
1 GGGGTAAAATGGTAA-TTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGTA
* * *
35667664 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAA-GTTCG
65 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAGAAGGTTCG
* *
35667716 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGATCGGGGGTA
1 GGGGTAAAATGGTAATTTT-AGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGTA
35667781 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAGAAGGTTCG
65 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAGAAGGTTCG
* * * *
35667834 GGGGTAAAATGGTAATTTTTG-GAAGTTTTGGGGTTAAAAATAGAATTTTAGAAGGTTC-GGGGT
1 GGGGTAAAATGGTAATTTTAGTGAA--ATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
35667897 AAAATGGTAATTTTTGG
64 AAAATGGTAATTTTTGG
35667914 AAATTTTGGG
Statistics
Matches: 178, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
115 4 0.02
116 46 0.26
117 76 0.43
118 52 0.29
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.32
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGTAA
AATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAGAAGGTTCG
Found at i:35667842 original size:29 final size:29
Alignment explanation
Indices: 35667627--35667910 Score: 161
Period size: 30 Copynumber: 9.8 Consensus size: 29
35667617 TTTAGTAAAA
* *
35667627 TCGGGGTTAAAAATGGAATTTTGGAA-GT
1 TCGGGGGTAAAAATGGAATTTTAGAAGGT
* * ** **
35667655 TCGAGGGT-AAAATGGTAATTTTTGGTGAAA
1 TCGGGGGTAAAAATGG-AATTTTAGAAG-GT
* *
35667685 TCGGGGTTAAAAATGGAATTTTGGAA-GT
1 TCGGGGGTAAAAATGGAATTTTAGAAGGT
* ** **
35667713 TCGGGGGT-AAAATGGTAATTTTCGGTGAAA
1 TCGGGGGTAAAAATGG-AATTTTAGAAG-GT
* *
35667743 TCGGGGTTAAAAATGGAATTTTAGAAGGA
1 TCGGGGGTAAAAATGGAATTTTAGAAGGT
* ** **
35667772 TCGGGGGT-AAAATGGTAATTTTTGGTGAAA
1 TCGGGGGTAAAAATGG-AATTTTAGAAG-GT
* * *
35667802 TCGAGGTTAAAAATAGAATTTTAGAAGGT
1 TCGGGGGTAAAAATGGAATTTTAGAAGGT
* *
35667831 TCGGGGGT-AAAATGGTAATTTTTGGAAGTT
1 TCGGGGGTAAAAATGG-AA-TTTTAGAAGGT
* * *
35667861 TTGGGGTTAAAAATAGAATTTTAGAAGGT
1 TCGGGGGTAAAAATGGAATTTTAGAAGGT
35667890 TC-GGGGT-AAAATGGTAATTTT
1 TCGGGGGTAAAAATGG-AATTTT
35667911 TGGAAATTTT
Statistics
Matches: 190, Mismatches: 51, Indels: 30
0.70 0.19 0.11
Matches are distributed among these distances:
27 20 0.11
28 50 0.26
29 34 0.18
30 60 0.32
31 26 0.14
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (29 bp):
TCGGGGGTAAAAATGGAATTTTAGAAGGT
Found at i:35667911 original size:29 final size:29
Alignment explanation
Indices: 35667605--35667939 Score: 152
Period size: 29 Copynumber: 11.5 Consensus size: 29
35667595 ACCTAGGGGC
* **
35667605 AAAATCGTAATTTTTAGTAAAATCGGGGTTA
1 AAAATGGTAATTTTTAG-AAGTTCGGGG-TA
*
35667636 AAAATGG-AA-TTTTGGAAGTTCGAGGGT-
1 AAAATGGTAATTTTTAGAAGTTCG-GGGTA
* *
35667663 AAAATGGTAATTTTTGGTGAA-ATCGGGGTTA
1 AAAATGGTAATTTTT--AGAAGTTCGGGG-TA
*
35667694 AAAATGG-AA-TTTTGGAAGTTCGGGGGT-
1 AAAATGGTAATTTTTAGAAGTTC-GGGGTA
*
35667721 AAAATGGTAATTTTCGGT-GAA-ATCGGGGTTA
1 AAAATGGTAATTTT---TAGAAGTTCGGGG-TA
*
35667752 AAAATGG-AA-TTTTAGAAGGATCGGGGGT-
1 AAAATGGTAATTTTTAGAA-GTTC-GGGGTA
* * *
35667780 AAAATGGTAATTTTTGGTGAA-ATCGAGGTTA
1 AAAATGGTAATTTTT--AGAAGTTCG-GGGTA
*
35667811 AAAATAG-AA-TTTTAGAAGGTTCGGGGGT-
1 AAAATGGTAATTTTTAGAA-GTTC-GGGGTA
* *
35667839 AAAATGGTAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGTAATTTTTAGAAG-TTCGGGG-TA
*
35667870 AAAATAG-AA-TTTTAGAAGGTTCGGGGT-
1 AAAATGGTAATTTTTAGAA-GTTCGGGGTA
* * * *
35667897 AAAATGGTAATTTTTGGAAATTTTGGGGTC
1 AAAATGGTAATTTTTAG-AAGTTCGGGGTA
35667927 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
35667940 CTGAAATTTT
Statistics
Matches: 240, Mismatches: 25, Indels: 80
0.70 0.07 0.23
Matches are distributed among these distances:
26 1 0.00
27 29 0.12
28 29 0.12
29 89 0.37
30 50 0.21
31 38 0.16
32 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGAAGTTCGGGGTA
Found at i:35667945 original size:29 final size:29
Alignment explanation
Indices: 35667834--35667972 Score: 110
Period size: 29 Copynumber: 4.8 Consensus size: 29
35667824 AGAAGGTTCG
*
35667834 GGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 GGGGTCAAAAT-GTAATTTTTGGAAATTTT
* * ** *
35667863 GGGGTTAAAAATAG-AA-TTTTAGAAGGTTC
1 GGGG-TCAAAAT-GTAATTTTTGGAAATTTT
35667892 GGGGT-AAAATGGTAATTTTTGGAAATTTT
1 GGGGTCAAAAT-GTAATTTTTGGAAATTTT
35667921 GGGGTCAAAATGTAATTTTCT-GAAATTTT
1 GGGGTCAAAATGTAATTTT-TGGAAATTTT
* *
35667950 GGGAG-CAAAATGCAATTTCTGGA
1 GGG-GTCAAAATGTAATTTTTGGA
35667973 CTGTTTGGGG
Statistics
Matches: 91, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
27 6 0.07
28 4 0.04
29 65 0.71
30 10 0.11
31 6 0.07
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTTGGAAATTTT
Found at i:35669755 original size:37 final size:35
Alignment explanation
Indices: 35669705--35669779 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
35669695 TTCAACCCAA
**
35669705 TTGGGCTTTTTGTAATCGGGCCTTTAATTTGGGCTT
1 TTGGGCTTTTTGTAATCGGGCC-CCAATTTGGGCTT
* *
35669741 TTGGGTTTATTTGTAATTGGGCCCCAATTTGGGCTT
1 TTGGGCTT-TTTGTAATCGGGCCCCAATTTGGGCTT
35669777 TTG
1 TTG
35669780 TAAATGGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 21 0.62
37 13 0.38
ACGTcount: A:0.12, C:0.13, G:0.28, T:0.47
Consensus pattern (35 bp):
TTGGGCTTTTTGTAATCGGGCCCCAATTTGGGCTT
Found at i:35669842 original size:17 final size:17
Alignment explanation
Indices: 35669822--35669891 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 17
35669812 TAATATTATT
* *
35669822 TTAAATTAAGTTTAAAA
1 TTAAAATAAATTTAAAA
35669839 TTAAAATAAATTT-AAA
1 TTAAAATAAATTTAAAA
* *
35669855 -T-AAGTAAATTTAAAT
1 TTAAAATAAATTTAAAA
*
35669870 TTAAGATAAATTTAAAA
1 TTAAAATAAATTTAAAA
*
35669887 ATAAA
1 TTAAA
35669892 TTTAAAATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
14 9 0.22
15 3 0.07
16 4 0.10
17 25 0.61
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (17 bp):
TTAAAATAAATTTAAAA
Found at i:35669848 original size:22 final size:22
Alignment explanation
Indices: 35669804--35669850 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35669794 ATTTTAATTT
* ***
35669804 ATTAAGTTTAATATTATTTTAA
1 ATTAAGTTTAAAATTAAAATAA
35669826 ATTAAGTTTAAAATTAAAATAA
1 ATTAAGTTTAAAATTAAAATAA
35669848 ATT
1 ATT
35669851 TAAATAAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTAAGTTTAAAATTAAAATAA
Found at i:35669879 original size:31 final size:29
Alignment explanation
Indices: 35669832--35669902 Score: 106
Period size: 31 Copynumber: 2.4 Consensus size: 29
35669822 TTAAATTAAG
35669832 TTTAAAATTAAAATAAATTTAAATAAGTAAA
1 TTTAAAATTAAAATAAATTTAAA-AA-TAAA
* *
35669863 TTTAAATTTAAGATAAATTTAAAAATAAA
1 TTTAAAATTAAAATAAATTTAAAAATAAA
35669892 TTTAAAATTAA
1 TTTAAAATTAA
35669903 TTCAAACTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 14 0.38
30 2 0.05
31 21 0.57
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTAAAATTAAAATAAATTTAAAAATAAA
Found at i:35669881 original size:11 final size:11
Alignment explanation
Indices: 35669834--35669904 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
35669824 AAATTAAGTT
*
35669834 TAAAATTAAAA
1 TAAATTTAAAA
35669845 TAAATTT-AAA
1 TAAATTTAAAA
* *
35669855 T-AA-GTAAATT
1 TAAATTTAAA-A
*
35669865 TAAATTTAAGA
1 TAAATTTAAAA
35669876 TAAATTTAAAAA
1 TAAATTT-AAAA
35669888 TAAATTTAAAA
1 TAAATTTAAAA
*
35669899 TTAATT
1 TAAATT
35669905 CAAACTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 5 0.11
11 24 0.51
12 13 0.28
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Done.