Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 90 of 175
Found at i:28636296 original size:18 final size:18
Alignment explanation
Indices: 28636270--28636311 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28636260 GATTGGGAAA
* *
28636270 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
28636288 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
28636306 AGGATA
1 AGGATA
28636312 TTCACCTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:28644645 original size:6 final size:6
Alignment explanation
Indices: 28644636--28644669 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
28644626 AGGATTAAGA
28644636 CATGCT CATGCT CATGCT CATGCT CATGCT CATG
1 CATGCT CATGCT CATGCT CATGCT CATGCT CATG
28644670 TTACAGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (6 bp):
CATGCT
Found at i:28644875 original size:72 final size:72
Alignment explanation
Indices: 28644758--28644902 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
28644748 ATGGTCCAGA
28644758 AAAACAAAAAAAGAGAAAAAGGGCCTTGGTGTCCCTGGGTTGAACTTGATCCAACTGTTGACTGC
1 AAAACAAAAAAAGAGAAAAAGGGCCTTGGTGTCCCTGGGTTGAACTTGATCCAACTGTTGACTGC
28644823 CAAAGCC
66 CAAAGCC
28644830 AAAACAAAAAAAGAGAAAAAGGGCCTTGGTGTCCCTGGGTTGAACTTGATCCAACTGTTGACTGC
1 AAAACAAAAAAAGAGAAAAAGGGCCTTGGTGTCCCTGGGTTGAACTTGATCCAACTGTTGACTGC
28644895 CAAAGCC
66 CAAAGCC
28644902 A
1 A
28644903 GCTTTTGGAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (72 bp):
AAAACAAAAAAAGAGAAAAAGGGCCTTGGTGTCCCTGGGTTGAACTTGATCCAACTGTTGACTGC
CAAAGCC
Found at i:28645133 original size:135 final size:134
Alignment explanation
Indices: 28644892--28645134 Score: 432
Period size: 135 Copynumber: 1.8 Consensus size: 134
28644882 AACTGTTGAC
* *
28644892 TGCCAAAGCCAGCTTTTGGATCTGATCAATATATAAAAACTTCGTCTTTCAGTTTTATCAGTCAA
1 TGCCAAAGCCAGCTTTTGAATCTGATCAATATATAAAAACTTCGTCTATCAGTTTTATCAGTCAA
*
28644957 TGAGACAAAGATGTCAATTTCACTTTAGTTCGGGTTTTTGCATGACTTTCATATTCTCTCCCTTT
66 TGAGACAAAGATGTCAATTTCACTTTAGATCGGGTTTTTGCATGACTTTCATATTCTCTCCCTTT
28645022 TTTA
131 TTTA
*
28645026 TGCCAAAGCCAGCTTTTGAATCTGATCATTATATAAAAACTTCCGTCTATCAGTTTTATCAGTCA
1 TGCCAAAGCCAGCTTTTGAATCTGATCAATATATAAAAACTT-CGTCTATCAGTTTTATCAGTCA
*
28645091 ATGAGACAAAGATGTCAATTTTACTTTAGATCGGGTTTTTGCAT
65 ATGAGACAAAGATGTCAATTTCACTTTAGATCGGGTTTTTGCAT
28645135 TTTGTTTTAG
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
134 40 0.39
135 63 0.61
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (134 bp):
TGCCAAAGCCAGCTTTTGAATCTGATCAATATATAAAAACTTCGTCTATCAGTTTTATCAGTCAA
TGAGACAAAGATGTCAATTTCACTTTAGATCGGGTTTTTGCATGACTTTCATATTCTCTCCCTTT
TTTA
Found at i:28645655 original size:29 final size:30
Alignment explanation
Indices: 28645623--28645679 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
28645613 ATTATTTATT
28645623 TTTAGATA-TTTAATAAATTA-TTAATATAA
1 TTTA-ATATTTTAATAAATTATTTAATATAA
* *
28645652 TTTATTATTTTAGTAAATTATTTAATAT
1 TTTAATATTTTAATAAATTATTTAATAT
28645680 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.62
30 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (30 bp):
TTTAATATTTTAATAAATTATTTAATATAA
Found at i:28645729 original size:16 final size:15
Alignment explanation
Indices: 28645689--28645729 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
28645679 TTTTAATTTT
28645689 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
28645703 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
28645717 ATTTTAAATAATA
1 ATTTTAAATAATA
28645730 TTCTTCACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:28648084 original size:18 final size:18
Alignment explanation
Indices: 28648061--28648095 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28648051 CAAGAACAGA
28648061 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
* *
28648079 AAGCATGAAGATAGTTT
1 AAGCATCAAAATAGTTT
28648096 GACACGTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:28659371 original size:21 final size:21
Alignment explanation
Indices: 28659326--28659371 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28659316 TTCTCATTTT
*
28659326 CAACAATTTCCTCTTCTTTAG
1 CAACAATTTCCTCTTCTTTAA
*
28659347 CAACAATTTCCT-TTTTTGTAA
1 CAACAATTTCCTCTTCTT-TAA
28659368 CAAC
1 CAAC
28659372 TTTTGCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.41
Consensus pattern (21 bp):
CAACAATTTCCTCTTCTTTAA
Found at i:28665496 original size:21 final size:21
Alignment explanation
Indices: 28665463--28665526 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
28665453 ATTGGGTGAA
*
28665463 TCAACTTTTACGAGCTTCTGT
1 TCAACTCTTACGAGCTTCTGT
*
28665484 TCAGCTCTTACGAGCTTCTGT
1 TCAACTCTTACGAGCTTCTGT
28665505 TCAACTCTTACGAGCTTCTGT
1 TCAACTCTTACGAGCTTCTGT
28665526 T
1 T
28665527 GACATAATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.17, C:0.27, G:0.16, T:0.41
Consensus pattern (21 bp):
TCAACTCTTACGAGCTTCTGT
Found at i:28682912 original size:37 final size:37
Alignment explanation
Indices: 28682869--28682976 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
28682859 GCTCGGACGT
* * *
28682869 AATCTCCACACGAAGTTATCGGATCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
*
28682906 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
*
28682943 AATCTCCACACGTAGTCATCGGGTCTCACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28682977 ATATATTTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
Found at i:28683191 original size:47 final size:47
Alignment explanation
Indices: 28683139--28683447 Score: 174
Period size: 48 Copynumber: 6.5 Consensus size: 47
28683129 TTTCACACTA
* ** *
28683139 GCCATTCGGCTTTACCGCATATATGCATTTTCATATTCACCACATTG
1 GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
* * * *
28683186 GCCATTCGGCCTTATCACATATATGCATGCTCACATTTATCACATTG
1 GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
* * * *
28683233 GCCATTCGGCTTTACCACATATA--CATATCACACATAT-ATTTCACATTA
1 GCCATTCGGCTTTACCACATATATGCAT-GCTCACAT-TCA--CCACATTG
* ** *
28683281 GCCATTCGGCTTTACCACATATA--CATATCTCATACATAT-TTCACATTC
1 GCCATTCGGCTTTACCACATATATGCAT-GCTC--ACAT-TCACCACATTG
* * * *
28683329 GCCATTCGGCTTTACCACATATA--CATATCACACATAT-ATTTCACATTA
1 GCCATTCGGCTTTACCACATATATGCAT-GCTCACAT-TCA--CCACATTG
* ** *
28683377 GCCATTCGGCTTTACCACATATA--CATATCTCATACATAT-TTCACATTC
1 GCCATTCGGCTTTACCACATATATGCAT-GCTC--ACAT-TCACCACATTG
28683425 GCCATTCGGCTTTACCACATATA
1 GCCATTCGGCTTTACCACATATA
28683448 CATATCACAC
Statistics
Matches: 230, Mismatches: 22, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
45 3 0.01
46 13 0.06
47 61 0.27
48 141 0.61
50 12 0.05
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
Found at i:28683289 original size:48 final size:48
Alignment explanation
Indices: 28683225--28683497 Score: 438
Period size: 48 Copynumber: 5.6 Consensus size: 48
28683215 CTCACATTTA
*
28683225 TCACATTGGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
* * *
28683273 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
*
28683321 TCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
* * *
28683369 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
*
28683417 TCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
*
28683465 TCACATTAGCCATTCGGCCTTATCACACATATA
1 TCACATTAGCCATTCGGCTTTA-C-CACATATA
28683498 TATACGGGTT
Statistics
Matches: 205, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
48 196 0.96
49 1 0.00
50 8 0.04
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
Found at i:28683350 original size:96 final size:96
Alignment explanation
Indices: 28683179--28683497 Score: 511
Period size: 96 Copynumber: 3.3 Consensus size: 96
28683169 TCATATTCAC
* * * *
28683179 CACATTGGCCATTCGGCCTTATCACATATATGCAT-GCTC--ACAT-TTATCACATTGGCCATTC
1 CACATTAGCCATTCGGCCTTACCACATATA--CATATCTCATACATATT-TCACATTCGCCATTC
28683240 GGCTTTACCACATATACATATCACACATATATTT
63 GGCTTTACCACATATACATATCACACATATATTT
*
28683274 CACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCGGC
1 CACATTAGCCATTCGGCCTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCGGC
28683339 TTTACCACATATACATATCACACATATATTT
66 TTTACCACATATACATATCACACATATATTT
*
28683370 CACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCGGC
1 CACATTAGCCATTCGGCCTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCGGC
28683435 TTTACCACATATACATATCACACATATATTT
66 TTTACCACATATACATATCACACATATATTT
28683466 CACATTAGCCATTCGGCCTTATCACACATATA
1 CACATTAGCCATTCGGCCTTA-C-CACATATA
28683498 TATACGGGTT
Statistics
Matches: 212, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
93 3 0.01
94 3 0.01
95 27 0.13
96 168 0.79
97 3 0.01
98 8 0.04
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (96 bp):
CACATTAGCCATTCGGCCTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCGGC
TTTACCACATATACATATCACACATATATTT
Found at i:28683416 original size:144 final size:142
Alignment explanation
Indices: 28683123--28683497 Score: 456
Period size: 144 Copynumber: 2.6 Consensus size: 142
28683113 GCACATCGCC
* * *
28683123 TACATATTTCACACTAGCCATTCGGCTTTACCGCATATATGCAT-T-T--T-CATATTCACCACA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA--CATATCTCATACATATT--TCACA
* * * *
28683183 TTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTTATCACATTGGCCATTCGGCTTTAC
62 TTAGCCATTCGGCCTTACCACATATA-GCATGCACACATTTATCACATTAGCCATTCGGCTTTAC
28683248 CACATATACATATCACA
126 CACATATACATATCACA
* * *
28683265 CATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCG
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
* * *
28683330 CCATTCGGCTTTACCACATATA-CATATCACACATATATTTCACATTAGCCATTCGGCTTTACCA
66 CCATTCGGCCTTACCACATATAGCAT-GCACACAT-T-TATCACATTAGCCATTCGGCTTTACCA
*
28683394 CATATACATATCTCA
128 CATATACATATCACA
* * * *
28683409 TACATATTTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTAG
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
28683474 CCATTCGGCCTTATCACACATATA
66 CCATTCGGCCTTA-C-CACATATA
28683498 TATACGGGTT
Statistics
Matches: 202, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
140 3 0.01
141 4 0.02
142 42 0.21
143 28 0.14
144 110 0.54
145 7 0.03
146 8 0.04
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (142 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCGGCCTTACCACATATAGCATGCACACATTTATCACATTAGCCATTCGGCTTTACCACAT
ATACATATCACA
Found at i:28687060 original size:44 final size:44
Alignment explanation
Indices: 28687012--28687100 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
28687002 AGGGTAAATC
* * *
28687012 CAACAACCCATGTTTATCTTTTCCTATTTTTAAATTCTTCTTTT
1 CAACAACCCAAGATTATCTTCTCCTATTTTTAAATTCTTCTTTT
* *
28687056 CAACAACCCAAGATTATCTTCTCCTATTTTTTAATTCTTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTATTTTTAAATTCTTCTTTT
28687100 C
1 C
28687101 TAGGATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.51
Consensus pattern (44 bp):
CAACAACCCAAGATTATCTTCTCCTATTTTTAAATTCTTCTTTT
Found at i:28693535 original size:26 final size:26
Alignment explanation
Indices: 28693506--28693556 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
28693496 ATCATGATCT
28693506 TTAGCGGCGTTTGTGGTAAAAGCGCG
1 TTAGCGGCGTTTGTGGTAAAAGCGCG
28693532 TTAGCGGCGTTTGTGGTAAAAGCGC
1 TTAGCGGCGTTTGTGGTAAAAGCGC
28693557 CGCTAAAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.37, T:0.27
Consensus pattern (26 bp):
TTAGCGGCGTTTGTGGTAAAAGCGCG
Found at i:28693578 original size:69 final size:69
Alignment explanation
Indices: 28693471--28693599 Score: 204
Period size: 69 Copynumber: 1.9 Consensus size: 69
28693461 CTTTAGCAGT
* * ** *
28693471 GTTTGTGGAAAAAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTGTGGTAAAAGCGCGTTAG
1 GTTTGTGGAAAAAGCGCCGCTAAAGACCATGATATTTAGCAACGTTTGGGGTAAAAGCGCGTTAG
28693536 CGGC
66 CGGC
*
28693540 GTTTGTGGTAAAAGCGCCGCTAAAGACCATGATATTTAGCAACGTTTGGGGTAAAAGCGC
1 GTTTGTGGAAAAAGCGCCGCTAAAGACCATGATATTTAGCAACGTTTGGGGTAAAAGCGC
28693600 TGCTAAAGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (69 bp):
GTTTGTGGAAAAAGCGCCGCTAAAGACCATGATATTTAGCAACGTTTGGGGTAAAAGCGCGTTAG
CGGC
Found at i:28693629 original size:43 final size:43
Alignment explanation
Indices: 28693532--28693629 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
28693522 TAAAAGCGCG
*
28693532 TTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACCATGATAT
1 TTAGCGGCGTTTGGGGTAAAAGCGCCGCTAAAGACCATGATAT
** * *
28693575 TTAGCAACGTTTGGGGTAAAAGCGCTGCTAAAGACCATGATCT
1 TTAGCGGCGTTTGGGGTAAAAGCGCCGCTAAAGACCATGATAT
28693618 TTAGCGGCGTTT
1 TTAGCGGCGTTT
28693630 TTTCACATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGGGGTAAAAGCGCCGCTAAAGACCATGATAT
Found at i:28700928 original size:20 final size:21
Alignment explanation
Indices: 28700888--28700928 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28700878 AAACGCCGCA
28700888 AAAAATCATTTCATTTCGAAC
1 AAAAATCATTTCATTTCGAAC
*
28700909 AAAAATCATTTTATTT-GAAC
1 AAAAATCATTTCATTTCGAAC
28700929 TAATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
AAAAATCATTTCATTTCGAAC
Found at i:28700946 original size:10 final size:11
Alignment explanation
Indices: 28700920--28701124 Score: 66
Period size: 12 Copynumber: 17.5 Consensus size: 11
28700910 AAAATCATTT
*
28700920 TATTTGAACTAA
1 TATTTAAACT-A
28700932 TATTTAAA-TA
1 TATTTAAACTA
* *
28700942 TATTTATTAATTC
1 TATTTA--AACTA
28700955 TATTTAAACTAA
1 TATTTAAACT-A
28700967 TATTTAAA-TA
1 TATTTAAACTA
* *
28700977 TATTTATTAATTC
1 TATTTA--AACTA
28700990 TATTTAAACTAA
1 TATTTAAACT-A
28701002 TATTT-AA--A
1 TATTTAAACTA
*
28701010 TATTTAAATATA
1 TATTTAAA-CTA
28701022 TTTTATTTAAACT-
1 ---TATTTAAACTA
* *
28701035 TATTTATTAATTC
1 TATTTA--AACTA
28701048 TATTTAAACTAA
1 TATTTAAACT-A
*
28701060 TATTTAAATATA
1 TATTTAAA-CTA
28701072 TTTTATTTAAACT-
1 ---TATTTAAACTA
* *
28701085 TATTTATTAATTC
1 TATTTA--AACTA
28701098 TATTTAAACTAA
1 TATTTAAACT-A
28701110 TATTTAAA-TA
1 TATTTAAACTA
28701120 TATTT
1 TATTT
28701125 TATTTAAACT
Statistics
Matches: 150, Mismatches: 16, Indels: 56
0.68 0.07 0.25
Matches are distributed among these distances:
8 6 0.04
9 2 0.01
10 32 0.21
11 17 0.11
12 48 0.32
13 27 0.18
14 2 0.01
15 16 0.11
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTTAAACTA
Found at i:28700966 original size:35 final size:35
Alignment explanation
Indices: 28700920--28701124 Score: 213
Period size: 35 Copynumber: 5.8 Consensus size: 35
28700910 AAAATCATTT
*
28700920 TATTTGAACTAATATTTAAATATATTTATTAATTC
1 TATTTAAACTAATATTTAAATATATTTATTAATTC
28700955 TATTTAAACTAATATTTAAATATATTTATTAATTC
1 TATTTAAACTAATATTTAAATATATTTATTAATTC
* * *
28700990 TATTTAAACTAATATTTAAATAT-TTAAATATATTT
1 TATTTAAACTAATATTTAAATATATTTATTA-ATTC
* * * * **
28701025 TATTTAAACTTATTTATTAATTCTATTTA--AACTAA
1 TATTTAAACTAATAT-TTAAATATATTTATTAA-TTC
28701060 TATTTAAA-TATATTTTATTTAAACT-TATTTATTAATTC
1 TATTTAAACTA-A---TATTTAAA-TATATTTATTAATTC
28701098 TATTTAAACTAATATTTAAATATATTT
1 TATTTAAACTAATATTTAAATATATTT
28701125 TATTTAAACT
Statistics
Matches: 141, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
34 8 0.06
35 97 0.69
36 6 0.04
37 13 0.09
38 13 0.09
39 4 0.03
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (35 bp):
TATTTAAACTAATATTTAAATATATTTATTAATTC
Found at i:28701065 original size:50 final size:50
Alignment explanation
Indices: 28701008--28701172 Score: 321
Period size: 50 Copynumber: 3.3 Consensus size: 50
28700998 CTAATATTTA
28701008 AATATTTAAATATATTTTATTTAAACTTATTTATTAATTCTATTTAAACT
1 AATATTTAAATATATTTTATTTAAACTTATTTATTAATTCTATTTAAACT
28701058 AATATTTAAATATATTTTATTTAAACTTATTTATTAATTCTATTTAAACT
1 AATATTTAAATATATTTTATTTAAACTTATTTATTAATTCTATTTAAACT
*
28701108 AATATTTAAATATATTTTATTTAAACTTATTTATTAATTCTATTTAAATT
1 AATATTTAAATATATTTTATTTAAACTTATTTATTAATTCTATTTAAACT
28701158 AATATTTAAATATAT
1 AATATTTAAATATAT
28701173 CAAATGGTTT
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 114 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (50 bp):
AATATTTAAATATATTTTATTTAAACTTATTTATTAATTCTATTTAAACT
Found at i:28701147 original size:100 final size:94
Alignment explanation
Indices: 28700932--28701172 Score: 337
Period size: 100 Copynumber: 2.5 Consensus size: 94
28700922 TTTGAACTAA
*
28700932 TATTTAAA-TATATTTATTAATTCTATTTAAACTAATATTTAAATATA-TTTATTAATTCTATTT
1 TATTTAAACT-TATTTATTAATTCTATTTAAACTAATATTTAAATATATTTTATTAACTCTATTT
28700995 AAACTAATATTTAAATATTTAAATATATTT
65 AAACTAATATTTAAATATTTAAATATATTT
28701025 TATTTAAACTTATTTATTAATTCTATTTAAACTAATATTTAAATATATTTTATTTAAACT-TATT
1 TATTTAAACTTATTTATTAATTCTATTTAAACTAATATTTAAATATATTTTA-TT-AACTCTATT
**
28701089 TATTAA-TTCTATTTAAACTAATATTTAAATATATTT
64 TA--AACTAATATTT--A--AATATTTAAATATATTT
*
28701125 TATTTAAACTTATTTATTAATTCTATTTAAATTAATATTTAAATATAT
1 TATTTAAACTTATTTATTAATTCTATTTAAACTAATATTTAAATATAT
28701173 CAAATGGTTT
Statistics
Matches: 134, Mismatches: 4, Indels: 13
0.89 0.03 0.09
Matches are distributed among these distances:
93 45 0.34
94 5 0.04
95 8 0.06
96 9 0.07
97 2 0.01
98 1 0.01
100 64 0.48
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (94 bp):
TATTTAAACTTATTTATTAATTCTATTTAAACTAATATTTAAATATATTTTATTAACTCTATTTA
AACTAATATTTAAATATTTAAATATATTT
Found at i:28701551 original size:8 final size:8
Alignment explanation
Indices: 28701499--28701562 Score: 57
Period size: 8 Copynumber: 8.6 Consensus size: 8
28701489 CATAAAGTCT
*
28701499 AACCCCCA
1 AACCCCTA
28701507 AACCCCT-
1 AACCCCTA
28701514 AA-CCCTA
1 AACCCCTA
*
28701521 AA-CCTTA
1 AACCCCTA
*
28701528 AATCCC--
1 AACCCCTA
*
28701534 AACCCTTA
1 AACCCCTA
28701542 AACCCCTA
1 AACCCCTA
28701550 AACCCCTA
1 AACCCCTA
28701558 AACCC
1 AACCC
28701563 TAACCCGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 8 0.17
7 10 0.22
8 28 0.61
ACGTcount: A:0.38, C:0.48, G:0.00, T:0.14
Consensus pattern (8 bp):
AACCCCTA
Found at i:28701577 original size:57 final size:58
Alignment explanation
Indices: 28701455--28701578 Score: 130
Period size: 57 Copynumber: 2.2 Consensus size: 58
28701445 CCCGACCTCT
* * ** *
28701455 GAATCCCTAAACCTTAAATCTCTAACTCTTAACCCATAAAGTCTAACCCCCAAACCCC
1 GAATCCCTAAACCTTAAATCTCCAACCCTTAACCCATAAACCCTAACACCCAAACCCC
* * *
28701513 TAA-CCCTAAACCTTAAATC-CCAACCCTTAAACCCCTAAACCCCTAA-ACCCTAA-CCC
1 GAATCCCTAAACCTTAAATCTCCAACCCTT-AACCCATAAA-CCCTAACACCCAAACCCC
28701569 GAATCCCTAA
1 GAATCCCTAA
28701579 CCCCTAAACT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
56 12 0.22
57 36 0.67
58 6 0.11
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.20
Consensus pattern (58 bp):
GAATCCCTAAACCTTAAATCTCCAACCCTTAACCCATAAACCCTAACACCCAAACCCC
Found at i:28701581 original size:43 final size:43
Alignment explanation
Indices: 28701499--28701587 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
28701489 CATAAAGTCT
* *
28701499 AACCCCCAAACCCCTAACCCTAAACCTTAAATCCCAACCCTTA
1 AACCCCCAAACCCCTAACCCTAAACCTCAAATCCCAACCCCTA
* *
28701542 AACCCCTAAACCCCTAAACCCT-AACC-CGAATCCCTAACCCCTA
1 AACCCCCAAACCCCT-AACCCTAAACCTCAAATCCC-AACCCCTA
28701585 AAC
1 AAC
28701588 TCTAACCTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
42 6 0.15
43 28 0.70
44 6 0.15
ACGTcount: A:0.37, C:0.47, G:0.01, T:0.15
Consensus pattern (43 bp):
AACCCCCAAACCCCTAACCCTAAACCTCAAATCCCAACCCCTA
Found at i:28701582 original size:27 final size:27
Alignment explanation
Indices: 28701545--28701605 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
28701535 ACCCTTAAAC
28701545 CCCTAAACCCCTAAACCCTAACCCGAAT
1 CCCT-AACCCCTAAACCCTAACCCGAAT
* *
28701573 CCCTAACCCCTAAACTCTAACCTGAAT
1 CCCTAACCCCTAAACCCTAACCCGAAT
28701600 CCCTAA
1 CCCTAA
28701606 ACCAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.34, C:0.44, G:0.03, T:0.18
Consensus pattern (27 bp):
CCCTAACCCCTAAACCCTAACCCGAAT
Found at i:28701594 original size:14 final size:14
Alignment explanation
Indices: 28701507--28701594 Score: 74
Period size: 14 Copynumber: 6.3 Consensus size: 14
28701497 CTAACCCCCA
28701507 AACCCCT-AACCCT
1 AACCCCTAAACCCT
* *
28701520 AAACCTTAAATCCC-
1 AACCCCTAAA-CCCT
*
28701534 AACCCTTAAACCCCT
1 AACCCCTAAA-CCCT
28701549 AAACCCCTAAACCCT
1 -AACCCCTAAACCCT
* *
28701564 AA-CCCGAATCCCT
1 AACCCCTAAACCCT
*
28701577 AACCCCTAAACTCT
1 AACCCCTAAACCCT
28701591 AACC
1 AACC
28701595 TGAATCCCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
13 16 0.27
14 28 0.47
15 7 0.12
16 9 0.15
ACGTcount: A:0.36, C:0.45, G:0.01, T:0.17
Consensus pattern (14 bp):
AACCCCTAAACCCT
Found at i:28701846 original size:14 final size:15
Alignment explanation
Indices: 28701827--28701859 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
28701817 CTTAAACCAA
28701827 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
28701841 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
28701856 AATC
1 AATC
28701860 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:28701930 original size:14 final size:14
Alignment explanation
Indices: 28701908--28701944 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
28701898 ATCCTAAATT
28701908 AACCATATACCCTA
1 AACCATATACCCTA
*
28701922 AATCATATACCCTA
1 AACCATATACCCTA
28701936 AACCATATA
1 AACCATATA
28701945 TATTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:28702437 original size:123 final size:122
Alignment explanation
Indices: 28702257--28702612 Score: 453
Period size: 123 Copynumber: 2.9 Consensus size: 122
28702247 AAATATTTTT
* * * * * *
28702257 GCGGCACTTTTTCAAAAACGCCGCTAAAGCACCGAGAATTAGCGGTGCTTTTCCAAAAACGCCGC
1 GCGGCGCTTTTTTAAAAATGCCGCTAAAGC-CCGAGCATTAGCGGTGCTTTTTCAAAAATGCCGC
* * * * *
28702322 AAAAGACTAGAGCATTAGCGGCACTTTTCCAAAAATGCCGCTAAAGACTAGAGCATTA
65 TAAAGACTAGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCATTA
* * * *
28702380 GCGGCGCTTTTTTAAAAATGCCGCCAAAGTCCCGACCATTAGCGGCGCTTTTTCAAAAATACCGC
1 GCGGCGCTTTTTTAAAAATGCCGCTAAAG-CCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCGC
* * * *
28702445 TAAAGACCAGAGCATTAGCGGCGCTTTTTCAAAACCGCCGCTAAAGCCCCGAGCATTA
65 TAAAGACTAGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCATTA
* *
28702503 GCGGCGC-TTTTTCAAAATGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTTTCAAAAATGTCGC
1 GCGGCGCTTTTTTAAAAATGCCGCTAAAGCCC-GAGCATTAGCGGTGCTTTTTCAAAAATGCCGC
* * * *
28702567 TAACGTCTAGAGCATTAGCGGCGCTTTTTCAAAAACACCTCTAAAG
65 TAAAGACTAGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG
28702613 CCTAGAAAGG
Statistics
Matches: 200, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
121 3 0.01
122 87 0.44
123 109 0.55
124 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (122 bp):
GCGGCGCTTTTTTAAAAATGCCGCTAAAGCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCGCT
AAAGACTAGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCATTA
Found at i:28702618 original size:41 final size:41
Alignment explanation
Indices: 28702257--28702618 Score: 401
Period size: 41 Copynumber: 8.9 Consensus size: 41
28702247 AAATATTTTT
* * * *
28702257 GCGGCACTTTTTCAAAAACGCCGCTAAAGCAC-CGAGAATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGC-CTAGAGCATTA
* * * * *
28702298 GCGGTGCTTTTCCAAAAACGCCGCAAAAGACTAGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTAGAGCATTA
* * *
28702339 GCGGCACTTTTCCAAAAATGCCGCTAAAGACTAGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTAGAGCATTA
* * * *
28702380 GCGGCGCTTTTTTAAAAATGCCGCCAAAGTCC-CGACCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAG-CCTAGAGCATTA
*
28702421 GCGGCGCTTTTTCAAAAATACCGCTAAAGACC-AGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAG-CCTAGAGCATTA
** **
28702462 GCGGCGCTTTTTCAAAACCGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTAGAGCATTA
28702503 GCGGCGCTTTTTC-AAAATGCCGCTAAAGCCCT-GAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAG-CCTAGAGCATTA
* * * *
28702543 GCGGTGCTTTTTCAAAAATGTCGCTAACGTCTAGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTAGAGCATTA
** *
28702584 GCGGCGCTTTTTCAAAAACACCTCTAAAGCCTAGA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTAGA
28702619 AAGGTCAGAA
Statistics
Matches: 273, Mismatches: 42, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
40 38 0.14
41 234 0.86
42 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTAGAGCATTA
Found at i:28709888 original size:19 final size:19
Alignment explanation
Indices: 28709866--28709918 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
28709856 GATGAGCAAG
28709866 AAAAGAAAAATGAAAAAT-A
1 AAAAGAAAAA-GAAAAATGA
*
28709885 AAAAG-AAGAGAAAAATGA
1 AAAAGAAAAAGAAAAATGA
*
28709903 CAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
28709919 GAGTCAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 7 0.24
18 8 0.28
19 14 0.48
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAAGAAAAATGA
Found at i:28709896 original size:24 final size:24
Alignment explanation
Indices: 28709863--28709917 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
28709853 ACGGATGAGC
*
28709863 AAGAAAAGAAAAATGAAAAATAAA
1 AAGAAAAGAAAAATGAAAAAGAAA
* *
28709887 AAGAAGAGAAAAATGACAAAGAAA
1 AAGAAAAGAAAAATGAAAAAGAAA
28709911 AAGAAAA
1 AAGAAAA
28709918 AGAGTCAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.05
Consensus pattern (24 bp):
AAGAAAAGAAAAATGAAAAAGAAA
Found at i:28709915 original size:6 final size:6
Alignment explanation
Indices: 28709866--28709920 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
28709856 GATGAGCAAG
* * *
28709866 AAAAGA AAAATGA AAAATA AAAAG- AAGAGA AAAATGA CAAAGA AAAAGA
1 AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA
28709915 AAAAGA
1 AAAAGA
28709921 GTCAGAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 4 0.10
6 25 0.62
7 11 0.28
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:28712107 original size:20 final size:20
Alignment explanation
Indices: 28712082--28712121 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28712072 TAAATAGGTG
*
28712082 GCTGGACATTCATTTATGCA
1 GCTGGACATTCATTCATGCA
28712102 GCTGGACATTCATTCATGCA
1 GCTGGACATTCATTCATGCA
28712122 TGTTGCCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (20 bp):
GCTGGACATTCATTCATGCA
Found at i:28712995 original size:27 final size:27
Alignment explanation
Indices: 28712965--28713018 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
28712955 TAAGAATCGG
28712965 GTCCATAATCTTTATTACAGGTTCATT
1 GTCCATAATCTTTATTACAGGTTCATT
* *
28712992 GTCCTTAATCTTTATTACGGGTTCATT
1 GTCCATAATCTTTATTACAGGTTCATT
28713019 CTTGTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (27 bp):
GTCCATAATCTTTATTACAGGTTCATT
Found at i:28715576 original size:18 final size:18
Alignment explanation
Indices: 28715550--28715584 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28715540 ACGATGTGCC
*
28715550 AAACTATTTTCATGCTTG
1 AAACCATTTTCATGCTTG
*
28715568 AAACCATTTTGATGCTT
1 AAACCATTTTCATGCTT
28715585 CCTATTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
AAACCATTTTCATGCTTG
Found at i:28716678 original size:18 final size:17
Alignment explanation
Indices: 28716650--28716684 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28716640 TTTAACTAAT
28716650 TAAAATAATAAAATAAA
1 TAAAATAATAAAATAAA
*
28716667 TAAAACTAATAAGATAAA
1 TAAAA-TAATAAAATAAA
28716685 AGAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAATAAAATAAA
Found at i:28717075 original size:41 final size:41
Alignment explanation
Indices: 28716994--28717152 Score: 291
Period size: 41 Copynumber: 3.9 Consensus size: 41
28716984 TTTCTACCTT
28716994 TCAGATCTTTAGCGGCGTTTTTAAAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTT-AAAAAAGCGCCGCTAATGC
* *
28717036 TCATATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
28717077 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
28717118 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGC
28717153 AAAAACATTT
Statistics
Matches: 113, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 92 0.81
42 21 0.19
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (41 bp):
TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
Found at i:28717263 original size:27 final size:26
Alignment explanation
Indices: 28717219--28717276 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
28717209 AAAATGGATA
**
28717219 AATTTGAAATAATGACAT-GTAAAAAT
1 AATTTGAAATAAAAACATAG-AAAAAT
28717245 AATTTGAAATAAAAAACATAGAAAAAT
1 AATTTGAAAT-AAAAACATAGAAAAAT
28717272 -ATTTG
1 AATTTG
28717277 TTAAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 15 0.54
27 12 0.43
28 1 0.04
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.29
Consensus pattern (26 bp):
AATTTGAAATAAAAACATAGAAAAAT
Found at i:28717556 original size:14 final size:15
Alignment explanation
Indices: 28717528--28717558 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28717518 AAGGTTTATA
28717528 GATTATGGAATTAGG
1 GATTATGGAATTAGG
28717543 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
28717557 GA
1 GA
28717559 CTCTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:28717601 original size:7 final size:7
Alignment explanation
Indices: 28717580--28717644 Score: 60
Period size: 7 Copynumber: 9.3 Consensus size: 7
28717570 GGGTTGTGAT
*
28717580 TTAAGGT
1 TTAAGGG
*
28717587 TTATGGG
1 TTAAGGG
28717594 TTAAGGG
1 TTAAGGG
*
28717601 TTAGGGG
1 TTAAGGG
28717608 TTAAGGG
1 TTAAGGG
28717615 TT-AGAGG
1 TTAAG-GG
*
28717622 TTAAGAG
1 TTAAGGG
*
28717629 TTAAGGA
1 TTAAGGG
*
28717636 TTTAGGG
1 TTAAGGG
28717643 TT
1 TT
28717645 TATAGATTCG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
6 2 0.04
7 42 0.91
8 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (7 bp):
TTAAGGG
Found at i:28717748 original size:50 final size:49
Alignment explanation
Indices: 28717667--28717770 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 49
28717657 GTCAGATTAG
* *
28717667 GGTTT-AGGGTTTAGATTAATTAGTGCATTTTAATTTATATATTAAGTAA
1 GGTTTAAGGATTTAGATTAATTAGTGCATTTT-ATTTATATATTAAATAA
* ** *
28717716 TGTTTAAGGATTTAGATTAATTAGTGTTTTTTATTTTTATATTAAATAA
1 GGTTTAAGGATTTAGATTAATTAGTGCATTTTATTTATATATTAAATAA
28717765 GGTTTA
1 GGTTTA
28717771 GAGGTTAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 24 0.51
50 23 0.49
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (49 bp):
GGTTTAAGGATTTAGATTAATTAGTGCATTTTATTTATATATTAAATAA
Found at i:28718810 original size:117 final size:118
Alignment explanation
Indices: 28718663--28719004 Score: 523
Period size: 118 Copynumber: 2.9 Consensus size: 118
28718653 ATAATTTTTT
* *
28718663 GCGGCG-TTTTA-AAGAAAAACGCCACAAAAAATAATTTAACTTTAAAAAATAGCCATTTTATAT
1 GCGGCGTTTTTATAA-AAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATAT
* *
28718726 AGCAAAATATTTAGTGGCGTTTTTATAAAAAAACGCCGCAAAATGTAAGCAATA
65 AGCAAAATATTTAGCGGCGTTTTTATAAAAAAACGCCGCAAAAGGTAAGCAATA
* *
28718780 GCGGCGTTTTTATAAAAAAAGGCCACAAAAAATCATTTTACTTTAAAAAATAGTCATTTTATATA
1 GCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATATA
* * *
28718845 GCAAAACATTTTGCGGCGTTTTCAT-AAAAAACGCCGCAAAAGGTAAGCAATA
66 GCAAAATATTTAGCGGCGTTTTTATAAAAAAACGCCGCAAAAGGTAAGCAATA
28718897 GCGGCGTTTTTAT-AAAAAACGCCAC-AAAAATAATTTTACTTTAAAAAATAGTCATTTTATATA
1 GCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATATA
*
28718960 GCAAAATATTTAGCGGCGTTTTTATAATATAAAAACGCCACAAAA
66 GCAAAATATTTAGCGGCGTTTTTAT-A-A-AAAAACGCCGCAAAA
28719005 AATAATTTTA
Statistics
Matches: 204, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
115 59 0.29
116 11 0.05
117 45 0.22
118 73 0.36
119 16 0.08
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (118 bp):
GCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATATA
GCAAAATATTTAGCGGCGTTTTTATAAAAAAACGCCGCAAAAGGTAAGCAATA
Found at i:28718976 original size:75 final size:76
Alignment explanation
Indices: 28718895--28719245 Score: 526
Period size: 76 Copynumber: 4.5 Consensus size: 76
28718885 AGGTAAGCAA
28718895 TAGCGGCGTTTTTATAAAAAACGCCAC-AAAAATAATTTTACTTTAAAAAATAGTCATTTTATAT
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATAT
*
28718959 AGCAAAATATT
66 AGCAAAACATT
*
28718970 TAGCGGCGTTTTTATAATATAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGGCATTTT
1 TAGCGGCG-TTTT-T-ATA-AAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTT
28719035 ATATAGCAAAACATT
62 ATATAGCAAAACATT
*
28719050 TAGCGGCGTTTTTATACAAAACGCCACAAAAAATAATTTTACTTT-AAAAATAGTCATTTTATAT
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATAT
28719114 AGCAAAACATT
66 AGCAAAACATT
* ** *
28719125 TAGCGGCATTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAACCAGTTTAT
1 TAGCGGCGTTTTTAT-AAAAAACGCCACAAAAAATAATTTTACTTT-AAAAAATAGTCATTTTAT
* *
28719190 ATAGAAAAATATT
64 ATAGCAAAACATT
*
28719203 TAGCGGCGTTTTTATAAAAAAATGCCACAAAAAAATAATTTTA
1 TAGCGGCGTTTTTAT-AAAAAACGCCAC-AAAAAATAATTTTA
28719246 TAAAAAAATA
Statistics
Matches: 254, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
75 51 0.20
76 61 0.24
77 4 0.02
78 55 0.22
79 29 0.11
80 54 0.21
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (76 bp):
TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATAT
AGCAAAACATT
Found at i:28719072 original size:155 final size:153
Alignment explanation
Indices: 28718895--28719245 Score: 553
Period size: 155 Copynumber: 2.3 Consensus size: 153
28718885 AGGTAAGCAA
28718895 TAGCGGCGTTTTTATAAAAAACGCCAC-AAAAATAATTTTACTTTAAAAAATAGTCATTTTATAT
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTT-AAAAATAGTCATTTTATAT
* *
28718959 AGCAAAATATTTAGCGGCGTTTTTATAATATAAAAACGCCACAAAAAATAATTTTACTTT-AAAA
65 AGCAAAACATTTAGCGGCATTTTTAT-A-A-AAAAACGCCACAAAAAATAATTTTACTTTAAAAA
** * *
28719023 AATAGGCATTTTATATAGCAAAACATT
127 AATAACCAGTTTATATAGAAAAACATT
*
28719050 TAGCGGCGTTTTTATACAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGTCATTTTATATA
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGTCATTTTATATA
28719115 GCAAAACATTTAGCGGCATTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATA
66 GCAAAACATTTAGCGGCATTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATA
*
28719180 ACCAGTTTATATAGAAAAATATT
131 ACCAGTTTATATAGAAAAACATT
*
28719203 TAGCGGCGTTTTTATAAAAAAATGCCACAAAAAAATAATTTTA
1 TAGCGGCGTTTTTAT-AAAAAACGCCAC-AAAAAATAATTTTA
28719246 TAAAAAAATA
Statistics
Matches: 182, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
152 29 0.16
153 42 0.23
154 11 0.06
155 83 0.46
156 17 0.09
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (153 bp):
TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGTCATTTTATATA
GCAAAACATTTAGCGGCATTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATA
ACCAGTTTATATAGAAAAACATT
Found at i:28719147 original size:76 final size:77
Alignment explanation
Indices: 28718895--28719245 Score: 539
Period size: 80 Copynumber: 4.5 Consensus size: 77
28718885 AGGTAAGCAA
28718895 TAGCGGCGTTTTTAT-AAAAAACGCCAC-AAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
1 TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
*
28718958 TAGCAAAATATT
66 TAGCAAAACATT
*
28718970 TAGCGGCGTTTTTATAATATAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGGCATTTT
1 TAGCGGCGTTTTTAT-A-A-AAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTT
28719035 ATATAGCAAAACATT
63 ATATAGCAAAACATT
*
28719050 TAGCGGCGTTTTTAT-ACAAAACGCCACAAAAAATAATTTTACTTT-AAAAATAGTCATTTTATA
1 TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
28719113 TAGCAAAACATT
66 TAGCAAAACATT
* ** *
28719125 TAGCGGCATTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAACCAGTTTAT
1 TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTT-AAAAAATAGTCATTTTAT
* *
28719190 ATAGAAAAATATT
65 ATAGCAAAACATT
*
28719203 TAGCGGCGTTTTTATAAAAAAATGCCACAAAAAAATAATTTTA
1 TAGCGGCGTTTTTATAAAAAAACGCCAC-AAAAAATAATTTTA
28719246 TAAAAAAATA
Statistics
Matches: 254, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
75 58 0.23
76 57 0.22
77 1 0.00
78 52 0.20
79 25 0.10
80 61 0.24
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (77 bp):
TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
TAGCAAAACATT
Found at i:28720541 original size:24 final size:24
Alignment explanation
Indices: 28720496--28720555 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28720486 AGAGACTACT
*
28720496 GTTATCTA-TCCTAAGTTGTTTAA
1 GTTATCTATTTCTAAGTTGTTTAA
* * *
28720519 TTTATCTATTTCTAATTTTTTTAA
1 GTTATCTATTTCTAAGTTGTTTAA
28720543 GTTATCTATTTCT
1 GTTATCTATTTCT
28720556 GCCTTCAACG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (24 bp):
GTTATCTATTTCTAAGTTGTTTAA
Found at i:28723636 original size:43 final size:43
Alignment explanation
Indices: 28723602--28723872 Score: 434
Period size: 43 Copynumber: 6.3 Consensus size: 43
28723592 GAATTGTACT
** * *
28723602 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
28723645 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
28723688 TTCAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
28723731 TTCAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
28723774 TTCAGCGGCGTTTGTGGGACAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
28723817 TTTAGCTGCGTTTGTGGGAAAAACGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
28723860 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
28723873 AGTTATAAAA
Statistics
Matches: 214, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 214 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:28723963 original size:22 final size:22
Alignment explanation
Indices: 28723936--28723977 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28723926 CCGCGCTTCT
*
28723936 AAAAGCGCCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
28723958 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
28723978 GTTTTGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:28725765 original size:21 final size:21
Alignment explanation
Indices: 28725741--28725780 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28725731 TTTTGGCATA
28725741 TTTTGAGCT-TGTTTAATTGTG
1 TTTTGAG-TATGTTTAATTGTG
28725762 TTTTGAGTATGTTTAATTG
1 TTTTGAGTATGTTTAATTG
28725781 CTGGTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (21 bp):
TTTTGAGTATGTTTAATTGTG
Found at i:28734445 original size:19 final size:20
Alignment explanation
Indices: 28734407--28734442 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
28734397 AATAAAATTT
28734407 TAAAATTAATATTAATAATA
1 TAAAATTAATATTAATAATA
28734427 TAAAA-TAAT-TTAATAA
1 TAAAATTAATATTAATAA
28734443 ATACATTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAATTAATATTAATAATA
Found at i:28736419 original size:22 final size:22
Alignment explanation
Indices: 28736391--28736447 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
28736381 TCACTTACCG
28736391 ACACGCCCGTGTGCAA-CCTCTC
1 ACACGCCCGTGTGCAAGCC-CTC
*
28736413 ACACGCCGGTGTGCAAGCCCTC
1 ACACGCCCGTGTGCAAGCCCTC
*
28736435 ACACTCCCGTGTG
1 ACACGCCCGTGTG
28736448 GACAGGCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.18, C:0.42, G:0.23, T:0.18
Consensus pattern (22 bp):
ACACGCCCGTGTGCAAGCCCTC
Found at i:28737669 original size:14 final size:14
Alignment explanation
Indices: 28737650--28737682 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
28737640 TTGCCATTTT
28737650 CCAATATTTAATTA
1 CCAATATTTAATTA
28737664 CCAATATTTAATTA
1 CCAATATTTAATTA
28737678 CCAAT
1 CCAAT
28737683 TGTAACACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (14 bp):
CCAATATTTAATTA
Found at i:28739106 original size:22 final size:21
Alignment explanation
Indices: 28739078--28739119 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
28739068 AAAATTATTT
28739078 TTTTTTAAAATATTTTATTAAA
1 TTTTTTAAAATATTTT-TTAAA
* *
28739100 TTTTTTAGATTATTTTTTAA
1 TTTTTTAAAATATTTTTTAA
28739120 TCGATTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTTAAAATATTTTTTAAA
Found at i:28742750 original size:37 final size:37
Alignment explanation
Indices: 28742640--28742723 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
28742630 AGTACAGTAG
* * *
28742640 TTCAGTATATTTAATAGATAATACTC-GATTGAGC-TTA
1 TTCAGTATA-TCAATAAATAACACTCAG-TTGAGCTTTA
28742677 TTCAGTATATCAATAAATAACACTCAGTTGAGCTTTA
1 TTCAGTATATCAATAAATAACACTCAGTTGAGCTTTA
28742714 TTCAGTATAT
1 TTCAGTATAT
28742724 TAGTAGATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 19 0.45
37 23 0.55
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (37 bp):
TTCAGTATATCAATAAATAACACTCAGTTGAGCTTTA
Found at i:28744221 original size:40 final size:38
Alignment explanation
Indices: 28744177--28744258 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 38
28744167 AAATTGGCAA
* *
28744177 GGGAGGAGAGCATTGAAGAAGAAAATAGAAGAATAAATAG
1 GGGAGGAGAGAATTGAAAAAGAAAAT-GAAGAATAAAT-G
* *
28744217 GGGAGGAGAGAATTGAAAAAGATAATGAGGAATAAATG
1 GGGAGGAGAGAATTGAAAAAGAAAATGAAGAATAAATG
28744255 GGGA
1 GGGA
28744259 TAATACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 5 0.13
39 10 0.26
40 23 0.61
ACGTcount: A:0.50, C:0.01, G:0.35, T:0.13
Consensus pattern (38 bp):
GGGAGGAGAGAATTGAAAAAGAAAATGAAGAATAAATG
Found at i:28744345 original size:22 final size:22
Alignment explanation
Indices: 28744313--28744360 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28744303 ATTAGTATTT
28744313 TAATATATTAAAT-TATTAAATA
1 TAATATATTAAATAT-TTAAATA
* *
28744335 TAATATTTTAAATATTTTAATA
1 TAATATATTAAATATTTAAATA
28744357 TAAT
1 TAAT
28744361 TCAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATATTAAATATTTAAATA
Found at i:28744385 original size:39 final size:39
Alignment explanation
Indices: 28744308--28744385 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
28744298 GAATTATTAG
* *
28744308 TATTTTAATATATTAAATTATTAAATATAATATTTTAAA
1 TATTTTAATATATTAAATTATTAAAAATAATATATTAAA
*
28744347 TATTTTAATATAATTCAA-TA-TAAAAATAACTATATTAAA
1 TATTTTAATAT-ATTAAATTATTAAAAATAA-TATATTAAA
28744386 AATATTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 8 0.24
39 21 0.62
40 5 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (39 bp):
TATTTTAATATATTAAATTATTAAAAATAATATATTAAA
Found at i:28748856 original size:125 final size:126
Alignment explanation
Indices: 28748628--28749143 Score: 712
Period size: 126 Copynumber: 4.2 Consensus size: 126
28748618 TAAGGTCAAG
* *
28748628 CAAGAACTACTATAGAAAAAGAGCGTCCACA-TGAGAGTTTTTTTTAGTACTTTTGCTGACAGTG
1 CAAGAACTACTGTAGAAAAAGAGCGTCCA-AGTGAGAGCTTTTTTTAGTACTTTTGCTGACAGTG
* *
28748692 CATCCTGCTTGAAGCATTTTTGACGCTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
65 CATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* ** * * *
28748754 CAGGAACTACT-TAGAAAAAGAGCGTTTAAGTGAGAGCTTTTTTCAATACTTTTGCTGACAATGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCAAGTGAGAGCTTTTTTTAGTACTTTTGCTGACAGTGC
*
28748818 ATCCTACTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * * * *
28748879 CAAGAACTATTGTAGAAAAAGAGCGTCTAAGTGGGAGCTTTTTTGAGTTCTTTTGCTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCAAGTGAGAGCTTTTTTTAGTACTTTTGCTGACAGTGC
* *
28748944 ATCCTGCTTGAAGCATTTTTGTCACTATTTTTTCAAAACCGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * * *
28749005 CAAG-A--AC--TAGAAATA-AGTGTCCAAGTG-GAAGATTTTTTTAGTACTTTTGCTTACAGTG
1 CAAGAACTACTGTAGAAAAAGAGCGTCCAAGTGAG-AGCTTTTTTTAGTACTTTTGCTGACAGTG
* *
28749063 CAT-CTGCTTGAAGCGTTTTTGTCACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
65 CATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
28749124 C-AGAAACTACTGTAGAAAAA
1 CAAG-AACTACTGTAGAAAAA
28749144 AAACAAAATC
Statistics
Matches: 349, Mismatches: 32, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
118 2 0.01
119 58 0.17
120 39 0.11
121 7 0.02
122 2 0.01
123 1 0.00
124 8 0.02
125 113 0.32
126 119 0.34
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (126 bp):
CAAGAACTACTGTAGAAAAAGAGCGTCCAAGTGAGAGCTTTTTTTAGTACTTTTGCTGACAGTGC
ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:28749254 original size:35 final size:34
Alignment explanation
Indices: 28749202--28749289 Score: 81
Period size: 35 Copynumber: 2.6 Consensus size: 34
28749192 ACCCTTTTAC
*
28749202 AAAAACCTTATAA-CCTAA-ACACAAAATTATTTTT
1 AAAAATCTTA-AACCCTAATACA-AAAATTATTTTT
** ** *
28749236 AAAAATCTCTAAACCCTAATTTAATTATTTTTTTT
1 AAAAATCT-TAAACCCTAATACAAAAATTATTTTT
28749271 AAAAATCTTAAACCCTAAT
1 AAAAATCTTAAACCCTAAT
28749290 TAATTAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
34 20 0.44
35 24 0.53
36 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (34 bp):
AAAAATCTTAAACCCTAATACAAAAATTATTTTT
Found at i:28749269 original size:34 final size:33
Alignment explanation
Indices: 28749231--28749307 Score: 120
Period size: 35 Copynumber: 2.3 Consensus size: 33
28749221 CACAAAATTA
*
28749231 TTTTTAAAAATCTCTAAACCCTAATTTAATTATTT
1 TTTTTAAAAATCT-TAAACCCTAA-TTAATTATAT
28749266 TTTTTAAAAATCTTAAACCCTAATTAATTA-AT
1 TTTTTAAAAATCTTAAACCCTAATTAATTATAT
28749298 TTTTTAAAAA
1 TTTTTAAAAA
28749308 AAAAATCCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 11 0.27
33 7 0.17
34 10 0.24
35 13 0.32
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (33 bp):
TTTTTAAAAATCTTAAACCCTAATTAATTATAT
Found at i:28749293 original size:33 final size:35
Alignment explanation
Indices: 28749226--28749308 Score: 125
Period size: 33 Copynumber: 2.4 Consensus size: 35
28749216 CTAAACACAA
28749226 AATTATTTTTAAAAATCTCTAAACCCTAATTTAATT
1 AATT-TTTTTAAAAATCTCTAAACCCTAATTTAATT
*
28749262 ATTTTTTTTAAAAATCT-TAAACCCTAA-TTAATT
1 AATTTTTTTAAAAATCTCTAAACCCTAATTTAATT
*
28749295 AATTTTTTAAAAAA
1 AATTTTTTTAAAAA
28749309 AAAATCCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 18 0.41
34 10 0.23
35 13 0.30
36 3 0.07
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (35 bp):
AATTTTTTTAAAAATCTCTAAACCCTAATTTAATT
Found at i:28749312 original size:37 final size:33
Alignment explanation
Indices: 28749236--28749339 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 33
28749226 AATTATTTTT
**
28749236 AAAAATCTCTAAACCCTAATTTAATTATTTTTTTT
1 AAAAATCT-TAAACCCTAA-TTAATTATTTTTTAA
28749271 AAAAATCTTAAACCCTAATTAATTAATTTTTTAAAAA
1 AAAAATCTTAAACCCTAATTAATT-ATTTTTT---AA
*
28749308 AAAAATCCTAAACCCTAA-T--TTATTTTTTAA
1 AAAAATCTTAAACCCTAATTAATTATTTTTTAA
28749338 AA
1 AA
28749340 TCCCTACACC
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
30 4 0.06
33 13 0.21
34 19 0.31
35 8 0.13
36 1 0.02
37 17 0.27
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.41
Consensus pattern (33 bp):
AAAAATCTTAAACCCTAATTAATTATTTTTTAA
Found at i:28749335 original size:34 final size:33
Alignment explanation
Indices: 28749236--28749339 Score: 93
Period size: 37 Copynumber: 3.0 Consensus size: 33
28749226 AATTATTTTT
****
28749236 AAAAATCTCTAAACCCTAATTTAATTATTTT-TTTT
1 AAAAATC-CTAAACCCTAATTT-ATT-TTTTAAAAA
*
28749271 AAAAATCTTAAACCCTAATTAATTAATTTTTTAAAAA
1 AAAAATCCTAAACCCTAA-T--TT-ATTTTTTAAAAA
28749308 AAAAATCCTAAACCCTAATTTATTTTTTAAAA
1 AAAAATCCTAAACCCTAATTTATTTTTTAAAA
28749340 TCCCTACACC
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
33 11 0.19
34 12 0.20
35 8 0.14
36 5 0.08
37 23 0.39
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.41
Consensus pattern (33 bp):
AAAAATCCTAAACCCTAATTTATTTTTTAAAAA
Found at i:28749361 original size:27 final size:27
Alignment explanation
Indices: 28749309--28749368 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
28749299 TTTTAAAAAA
28749309 AAAATCCTAAACCCTAATTTATTTTTT
1 AAAATCCTAAACCCTAATTTATTTTTT
* *
28749336 AAAATCCCTACACCTTAATTTATTTTTT
1 AAAAT-CCTAAACCCTAATTTATTTTTT
28749364 AAAAT
1 AAAAT
28749369 ATCTAACCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAATCCTAAACCCTAATTTATTTTTT
Found at i:28749385 original size:27 final size:27
Alignment explanation
Indices: 28749309--28749385 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
28749299 TTTTAAAAAA
*
28749309 AAAAT-CCTAAACCCTAATTTATTTTTT
1 AAAATACCT-AACCATAATTTATTTTTT
* *
28749336 AAAATCCCTACACCTTAATTTATTTTTT
1 AAAATACCTA-ACCATAATTTATTTTTT
* *
28749364 AAAATATCTAACCATAAATTAT
1 AAAATACCTAACCATAATTTAT
28749386 AAACTCTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
27 16 0.37
28 27 0.63
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAATACCTAACCATAATTTATTTTTT
Found at i:28766210 original size:51 final size:51
Alignment explanation
Indices: 28766136--28766324 Score: 258
Period size: 51 Copynumber: 3.7 Consensus size: 51
28766126 CGATGAACAT
*
28766136 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-ACTTGGTCAC
* * * * *
28766187 ATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGATTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-ACTTGGTCAC
* *
28766238 GTGTGTAGTACTATGTGAAGGCTACTACGTGGATCG-TAAAACTTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAACTTGGTCAC
*
28766288 GTGTGTAGTACTATGTGAAGGCTATTACGTGTATCGA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
28766325 ATGATAATAA
Statistics
Matches: 120, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 46 0.38
51 74 0.62
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (51 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAACTTGGTCAC
Found at i:28766217 original size:26 final size:26
Alignment explanation
Indices: 28766137--28766219 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
28766127 GATGAACATG
*
28766137 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* *
28766163 CGTGTA-T-CGATAAAT-AATGG-TCAC-A
1 TGTGTAGTAC--TAAGTGAA-GGCT-ACTA
28766188 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
28766214 TGTGTA
1 TGTGTA
28766220 CCGAAAAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
24 1 0.02
25 18 0.42
26 23 0.53
27 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:28766350 original size:101 final size:102
Alignment explanation
Indices: 28766140--28766357 Score: 253
Period size: 101 Copynumber: 2.1 Consensus size: 102
28766130 GAACATGTGT
* *
28766140 GTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTATGTGAAGGCTACTACGTGGATCGATAAATAATGATCACATGTGTAGTACTAAGTGA
* * ** * * *
28766205 AGGCTACTATGTGTACCGAAAAGATTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATATAATAACATGA
* * *
28766242 GTAGTACTATGTGAAGGCTACTACGTGGATCG-TAAA-ACTTGATCACGTGTGTAGTACTATGTG
1 GTAGTACTATGTGAAGGCTACTACGTGGATCGATAAATA-ATGATCACATGTGTAGTACTAAGTG
* * *
28766305 AAGGCTATTACGTGTATCG-AATGATAATAATAACATGA
65 AAGGCTACTACGTGTACCGAAAAGAT-ATAATAACATGA
*
28766343 GTGGTACTATGTGAA
1 GTAGTACTATGTGAA
28766358 AACCCCAAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
100 6 0.06
101 61 0.62
102 31 0.32
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (102 bp):
GTAGTACTATGTGAAGGCTACTACGTGGATCGATAAATAATGATCACATGTGTAGTACTAAGTGA
AGGCTACTACGTGTACCGAAAAGATATAATAACATGA
Found at i:28773850 original size:12 final size:12
Alignment explanation
Indices: 28773804--28773853 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
28773794 ACTTAGTCAC
28773804 TTTAATATTAAA
1 TTTAATATTAAA
28773816 -TTAATATAATAAA
1 TTTAATAT--TAAA
*
28773829 TATT-AGATTAAA
1 T-TTAATATTAAA
28773841 TTTAATATTAAA
1 TTTAATATTAAA
28773853 T
1 T
28773854 CTTATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
11 9 0.29
12 13 0.42
13 4 0.13
14 3 0.10
15 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:28776924 original size:28 final size:28
Alignment explanation
Indices: 28776861--28777042 Score: 312
Period size: 28 Copynumber: 6.5 Consensus size: 28
28776851 ATATTAAGTC
* *
28776861 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28776888 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28776916 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28776944 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28776972 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
28777000 CGTACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28777028 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28777043 GTACAATTTA
Statistics
Matches: 149, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.15
28 127 0.85
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:28784868 original size:28 final size:28
Alignment explanation
Indices: 28784805--28784958 Score: 265
Period size: 28 Copynumber: 5.5 Consensus size: 28
28784795 ATATTAAGTC
* *
28784805 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28784832 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28784860 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28784888 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28784916 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
28784944 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28784959 GTACAATTTA
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
27 22 0.18
28 101 0.82
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:28787454 original size:12 final size:12
Alignment explanation
Indices: 28787437--28787461 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28787427 CCTTATACAC
28787437 ATTACACATTGA
1 ATTACACATTGA
28787449 ATTACACATTGA
1 ATTACACATTGA
28787461 A
1 A
28787462 ATCAGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:28792322 original size:45 final size:45
Alignment explanation
Indices: 28792256--28792375 Score: 186
Period size: 45 Copynumber: 2.6 Consensus size: 45
28792246 TGACCTTTTG
28792256 ACCCATTTACGTACCAAAACCTATACCATTTCGTACATACACCAAA
1 ACCCATTT-CGTACCAAAACCTATACCATTTCGTACATACACCAAA
* * *
28792302 TCCCATTTTGTACCAAAACCTATACCATTTCGTACCTACACCAAA
1 ACCCATTTCGTACCAAAACCTATACCATTTCGTACATACACCAAA
* *
28792347 ACCCATTTCGTACCTAAACTTATACCATT
1 ACCCATTTCGTACCAAAACCTATACCATT
28792376 CCATAACTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
45 60 0.90
46 7 0.10
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.28
Consensus pattern (45 bp):
ACCCATTTCGTACCAAAACCTATACCATTTCGTACATACACCAAA
Found at i:28792336 original size:22 final size:22
Alignment explanation
Indices: 28792258--28792375 Score: 103
Period size: 23 Copynumber: 5.2 Consensus size: 22
28792248 ACCTTTTGAC
28792258 CCATTTACGTACCAAAACCTATA
1 CCATTT-CGTACCAAAACCTATA
* * *
28792281 CCATTTCGTA-CATACACCAAATC
1 CCATTTCGTACCA-AAACC-TATA
*
28792304 CCATTTTGTACCAAAACCTATA
1 CCATTTCGTACCAAAACCTATA
* * * *
28792326 CCATTTCGTACCTACACCAAAA
1 CCATTTCGTACCAAAACCTATA
* *
28792348 CCCATTTCGTACCTAAACTTATA
1 -CCATTTCGTACCAAAACCTATA
28792371 CCATT
1 CCATT
28792376 CCATAACTAA
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
21 2 0.03
22 32 0.43
23 39 0.52
24 2 0.03
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.29
Consensus pattern (22 bp):
CCATTTCGTACCAAAACCTATA
Found at i:28792394 original size:45 final size:44
Alignment explanation
Indices: 28792256--28792394 Score: 163
Period size: 45 Copynumber: 3.1 Consensus size: 44
28792246 TGACCTTTTG
28792256 ACCCATTTACGTACCAAAACCTATACCATTTCGT-ACATACACCAA
1 ACCCATTT-CGTACCAAAACCTATACCATTTCGTAAC-TACACCAA
* *
28792301 ATCCCATTTTGTACCAAAACCTATACCATTTCGTACCTACACCAAA
1 A-CCCATTTCGTACCAAAACCTATACCATTTCGTAACTACACC-AA
* * * * *
28792347 ACCCATTTCGTACCTAAACTTATACCATTCCATAACTAAACCTAA
1 ACCCATTTCGTACCAAAACCTATACCATTTCGTAACTACACC-AA
28792392 ACC
1 ACC
28792395 ATATTTGACC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
45 70 0.86
46 11 0.14
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.27
Consensus pattern (44 bp):
ACCCATTTCGTACCAAAACCTATACCATTTCGTAACTACACCAA
Found at i:28800341 original size:15 final size:15
Alignment explanation
Indices: 28800323--28800361 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28800313 GTGAGAGGAA
28800323 AAAAGAAAGTGAGTG
1 AAAAGAAAGTGAGTG
* *
28800338 AAAACAAAATGAGTG
1 AAAAGAAAGTGAGTG
*
28800353 AAGAGAAAG
1 AAAAGAAAG
28800362 AGAACAAAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.28, T:0.10
Consensus pattern (15 bp):
AAAAGAAAGTGAGTG
Found at i:28812134 original size:15 final size:14
Alignment explanation
Indices: 28812114--28812161 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
28812104 ACTCTCATTT
28812114 TCTTTTTCTTTTATC
1 TCTTTTTCTTTT-TC
28812129 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
* *
28812143 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTC
28812158 TCTT
1 TCTT
28812162 CTCAGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:28812153 original size:21 final size:21
Alignment explanation
Indices: 28812099--28812164 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
28812089 CTCACTCTCA
*
28812099 CTCTCACTCTCATTTTCTTTTT
1 CTCTCA-TCTCTTTTTCTTTTT
* *
28812121 CTTTTATCTCTTTTTCTTTTT
1 CTCTCATCTCTTTTTCTTTTT
* *
28812142 CTCTCATTTCTTTTT-TTCTT
1 CTCTCATCTCTTTTTCTTTTT
28812162 CTC
1 CTC
28812165 AGAATTTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
20 7 0.19
21 26 0.70
22 4 0.11
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (21 bp):
CTCTCATCTCTTTTTCTTTTT
Found at i:28813232 original size:11 final size:11
Alignment explanation
Indices: 28813212--28813240 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28813202 AACAATTGTA
28813212 TTTCAA-TTTT
1 TTTCAATTTTT
28813222 TTTCAATTTTT
1 TTTCAATTTTT
28813233 TTTCAATT
1 TTTCAATT
28813241 ACAATATCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTCAATTTTT
Found at i:28813280 original size:32 final size:32
Alignment explanation
Indices: 28813239--28813306 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
28813229 TTTTTTTCAA
28813239 TTACAATATCGTAATGCCAAAAATGTCGATTC
1 TTACAATATCGTAATGCCAAAAATGTCGATTC
*
28813271 TTACAATATCGTAATGCCGAAAATGTCGATTC
1 TTACAATATCGTAATGCCAAAAATGTCGATTC
28813303 TTAC
1 TTAC
28813307 TCCGATTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTACAATATCGTAATGCCAAAAATGTCGATTC
Found at i:28823394 original size:37 final size:37
Alignment explanation
Indices: 28823344--28823487 Score: 234
Period size: 37 Copynumber: 3.9 Consensus size: 37
28823334 ATCTTTAGCT
* * *
28823344 CGGACGTAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
* * *
28823381 CGGACAAAATCTCCACACGTTGTCATCAGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
28823418 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
28823455 CGGACATAATCTCCACACGTAGTCATCGGGTCT
1 CGGACATAATCTCCACACGTAGTCATCGGGTCT
28823488 CACTCGGAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:28823711 original size:47 final size:47
Alignment explanation
Indices: 28823658--28823918 Score: 171
Period size: 48 Copynumber: 5.5 Consensus size: 47
28823648 TTTCACACTA
* ** *
28823658 GCCATTCGGCTTTACCGCATATATGCATTTTCATATTCACCACATTG
1 GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
* * * *
28823705 GCCATTCGGCCTTATCACATATATGCATGCTCACATTTATCACATTG
1 GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
* * * *
28823752 GCCATTCGGCTTTACCACATATA--CATATCACACATAT-ATTTCACATTA
1 GCCATTCGGCTTTACCACATATATGCAT-GCTCACAT-TCA--CCACATTG
* ** *
28823800 GCCATTCGGCTTTACCACATATA--CATATCTCATACATAT-TTCACATTC
1 GCCATTCGGCTTTACCACATATATGCAT-GCTC--ACAT-TCACCACATTG
* ** *
28823848 GCCATTCGGCTTTACCACATATA--CATATCTCATACATAT-TTCACATTC
1 GCCATTCGGCTTTACCACATATATGCAT-GCTC--ACAT-TCACCACATTG
28823896 GCCATTCGGCTTTACCACATATA
1 GCCATTCGGCTTTACCACATATA
28823919 CATATCACAC
Statistics
Matches: 192, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
45 3 0.02
46 7 0.04
47 61 0.32
48 115 0.60
50 6 0.03
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
Found at i:28823808 original size:48 final size:48
Alignment explanation
Indices: 28823736--28824162 Score: 604
Period size: 48 Copynumber: 8.8 Consensus size: 48
28823726 TATGCATGCT
*
28823736 CACAT-TTATCACATTGGCCATTCGGCTTTACCACATATACATATCACA
1 CACATATT-TCACATTAGCCATTCGGCTTTACCACATATACATATCACA
* *
28823784 CATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 CACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACA
* * *
28823832 TACATATTTCACATTCGCCATTCGGCTTTACCACATATACATATCTCA
1 CACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACA
* *
28823880 TACATATTTCACATTCGCCATTCGGCTTTACCACATATACATATCACA
1 CACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACA
* * *
28823928 CATATATTTCACATTAGCCATTCGGCTTTACCACCTATACATATCTCA
1 CACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACA
* * *
28823976 TACATATTTCACATTCGCCATTCGGCTTTACCACATATACATATCAGA
1 CACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACA
* * * *
28824024 CATATATTTCACATTAGCCATTCGGCCTTATCACACATATATATATCTCA
1 CACATATTTCACATTAGCCATTCGGCTTTA-C-CACATATACATATCACA
* *
28824074 TACATATTTCACATTCGCCATTCGGCTTTACCACATATACATATCACA
1 CACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACA
* *
28824122 CATATATTTCACATTAGCCATTCGGCCTTATCACACATATA
1 CACATATTTCACATTAGCCATTCGGCTTTA-C-CACATATA
28824163 TATACGGGTT
Statistics
Matches: 339, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
48 286 0.84
49 5 0.01
50 48 0.14
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
CACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACA
Found at i:28823869 original size:96 final size:96
Alignment explanation
Indices: 28823645--28824162 Score: 683
Period size: 96 Copynumber: 5.4 Consensus size: 96
28823635 CATCGCCTAC
* * * *
28823645 ATATTTCACACTAGCCATTCGGCTTTACCGCATATATGCAT-T-T--T-CATATTCACCACATTG
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATA--CATATCTCATACATATT--TCACATTC
* * * *
28823705 GCCATTCGGCCTTATCACATATATGCAT-GCTCACAT
62 GCCATTCGGCTTTACCACATATA--CATATCACACAT
* * * * * *
28823741 -T-TATCACATTGGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTAGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
* * *
28823804 TTCGGCTTTACCACATATACATATCTCATAC
66 TTCGGCTTTACCACATATACATATCACACAT
*
28823835 ATATTTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
28823900 TTCGGCTTTACCACATATACATATCACACAT
66 TTCGGCTTTACCACATATACATATCACACAT
*
28823931 ATATTTCACATTAGCCATTCGGCTTTACCACCTATACATATCTCATACATATTTCACATTCGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
*
28823996 TTCGGCTTTACCACATATACATATCAGACAT
66 TTCGGCTTTACCACATATACATATCACACAT
* *
28824027 ATATTTCACATTAGCCATTCGGCCTTATCACACATATATATATCTCATACATATTTCACATTCGC
1 ATATTTCACATTAGCCATTCGGCTTTA-C-CACATATACATATCTCATACATATTTCACATTCGC
28824092 CATTCGGCTTTACCACATATACATATCACACAT
64 CATTCGGCTTTACCACATATACATATCACACAT
*
28824125 ATATTTCACATTAGCCATTCGGCCTTATCACACATATA
1 ATATTTCACATTAGCCATTCGGCTTTA-C-CACATATA
28824163 TATACGGGTT
Statistics
Matches: 382, Mismatches: 30, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
92 3 0.01
93 4 0.01
94 34 0.09
95 29 0.08
96 203 0.53
97 6 0.02
98 103 0.27
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (96 bp):
ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
TTCGGCTTTACCACATATACATATCACACAT
Found at i:28823916 original size:144 final size:143
Alignment explanation
Indices: 28823645--28824162 Score: 647
Period size: 144 Copynumber: 3.6 Consensus size: 143
28823635 CATCGCCTAC
* * * *
28823645 ATATTTCACACTAGCCATTCGGCTTTACCGCATATATGCAT-T-T--T-CATATTCACCACATTG
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATA--CATATCTCATACATATT--TCACATTC
* * *
28823705 GCCATTCGGCCTTATCACATATATGCAT-GCTC-ACAT-TTATCACATTGGCCATTCGGCTTTAC
62 GCCATTCGGCCTTACCACATATA--CATATCTCAACATATT-TCACATTAGCCATTCGGCTTTAC
28823767 CACATATACATATCACACAT
124 CACATATACATATCACACAT
28823787 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
* *
28823852 TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCGGCTTTACCACATA
66 TTCGGCCTTACCACATATACATATCTCA-ACATATTTCACATTAGCCATTCGGCTTTACCACATA
28823917 TACATATCACACAT
130 TACATATCACACAT
*
28823931 ATATTTCACATTAGCCATTCGGCTTTACCACCTATACATATCTCATACATATTTCACATTCGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
* ** * *
28823996 TTCGGCTTTACCACATATACATATCAGACATATATTTCACATTAGCCATTCGGCCTTATCACACA
66 TTCGGCCTTACCACATATACATATCTCA-ACATATTTCACATTAGCCATTCGGCTTTA-C-CACA
* * * *
28824061 TATATATATCTCATAC
128 TATACATATCACACAT
* * * * *
28824077 ATATTTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTAGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
28824142 TTCGGCCTTATCACACATATA
66 TTCGGCCTTA-C-CACATATA
28824163 TATACGGGTT
Statistics
Matches: 337, Mismatches: 26, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
140 3 0.01
141 4 0.01
142 38 0.11
143 27 0.08
144 163 0.48
145 9 0.03
146 84 0.25
147 1 0.00
148 8 0.02
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (143 bp):
ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCA
TTCGGCCTTACCACATATACATATCTCAACATATTTCACATTAGCCATTCGGCTTTACCACATAT
ACATATCACACAT
Found at i:28824233 original size:98 final size:97
Alignment explanation
Indices: 28823744--28824212 Score: 459
Period size: 96 Copynumber: 4.8 Consensus size: 97
28823734 CTCACATTTA
* * * * * * * *
28823744 TCACATTGGCCATTCGGCTTTA-C-CACATATACATATCACACATATATTTCACATTAGCCATTC
1 TCACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTC
* * * *
28823807 GGCTTTACCACATATACATATCTCATACATA-TT
66 GGCCTTACCACATACACATA--TCACACATACAT
* * * * *
28823840 TCACATTCGCCATTCGGCTTTA-C-CACATATACATATCTCATACATATTTCACATTCGCCATTC
1 TCACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTC
* * *
28823903 GGCTTTACCACATATACATATCACACATATATT
66 GGCCTTACCACATACACATATCACACATACA-T
* * * * *
28823936 TCACATTAGCCATTCGGCTTTA-C-CACCTATACATATCTCATACATATTTCACATTCGCCATTC
1 TCACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTC
* * * *
28823999 GGCTTTACCACATATACATATCAGACATATATT
66 GGCCTTACCACATACACATATCACACATACA-T
* *
28824032 TCACATTAGCCATTCGGCCTTATCACACATATATATATCTCATACATATTTCACATTCGCCATTC
1 TCACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTC
* * *
28824097 GGCTTTACCACATATACATATCACACATATATT
66 GGCCTTACCACATACACATATCACACATACA-T
** * *
28824130 TCACATTAGCCATTCGGCCTTATCACACATATATATA-CGGGTTCACATTCATCACATTGGCCAT
1 TCACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATT--TCACATTCGCCAT
28824194 TCGGCCTTATCACACATAC
64 TCGGCCTTA-C-CACATAC
28824213 GCATGTTCAC
Statistics
Matches: 343, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
94 8 0.02
96 193 0.56
97 8 0.02
98 107 0.31
99 20 0.06
100 1 0.00
101 6 0.02
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (97 bp):
TCACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTC
GGCCTTACCACATACACATATCACACATACAT
Found at i:28838265 original size:23 final size:24
Alignment explanation
Indices: 28838231--28838275 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
28838221 GTTGTTGAGT
28838231 TTTCTTTCTTTTTGTCA-TCCTCG
1 TTTCTTTCTTTTTGTCAGTCCTCG
*
28838254 TTTC-TTCATTTTTTTCAGTCCT
1 TTTCTTTC-TTTTTGTCAGTCCT
28838276 ATATCTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 12 0.63
24 4 0.21
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.62
Consensus pattern (24 bp):
TTTCTTTCTTTTTGTCAGTCCTCG
Found at i:28840540 original size:20 final size:22
Alignment explanation
Indices: 28840506--28840560 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
28840496 TAATGAAATG
*
28840506 AAGA-CAAAAAAAGAAATCAAA
1 AAGAGCAAAAAGAGAAATCAAA
*
28840527 AA-AG-AAAAAGAG-AATGAAA
1 AAGAGCAAAAAGAGAAATCAAA
28840546 AAGAGCAAAAAGAGA
1 AAGAGCAAAAAGAGA
28840561 TTGAGATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 8 0.29
20 10 0.36
21 10 0.36
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.04
Consensus pattern (22 bp):
AAGAGCAAAAAGAGAAATCAAA
Found at i:28840546 original size:19 final size:21
Alignment explanation
Indices: 28840513--28840560 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28840503 ATGAAGACAA
28840513 AAAAAGA-AATCAAAAA-AG-
1 AAAAAGAGAATCAAAAAGAGC
*
28840531 AAAAAGAGAATGAAAAAGAGC
1 AAAAAGAGAATCAAAAAGAGC
28840552 AAAAAGAGA
1 AAAAAGAGA
28840561 TTGAGATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 2 0.08
21 9 0.35
ACGTcount: A:0.73, C:0.04, G:0.19, T:0.04
Consensus pattern (21 bp):
AAAAAGAGAATCAAAAAGAGC
Found at i:28847132 original size:20 final size:20
Alignment explanation
Indices: 28847098--28847151 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
28847088 TAAGTTGTCT
* *
28847098 TGTCTTAGTTAAATTAAATA
1 TGTCTTAATTTAATTAAATA
* * *
28847118 TGTCTTGATTTAATTAAGTT
1 TGTCTTAATTTAATTAAATA
28847138 TGTCTTAATTTAAT
1 TGTCTTAATTTAAT
28847152 ACATGTGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (20 bp):
TGTCTTAATTTAATTAAATA
Found at i:28850632 original size:28 final size:28
Alignment explanation
Indices: 28850586--28850646 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
28850576 AATGAGTGAT
*
28850586 AAAAAAAGAGAGAACGATGCA-AAAGAAA
1 AAAAAAAGAGACAACGATG-AGAAAGAAA
** *
28850614 AAAAAAAGAGACAGTGATGAGAATGAAA
1 AAAAAAAGAGACAACGATGAGAAAGAAA
28850642 AAAAA
1 AAAAA
28850647 GAGTTTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.67, C:0.05, G:0.21, T:0.07
Consensus pattern (28 bp):
AAAAAAAGAGACAACGATGAGAAAGAAA
Found at i:28857545 original size:47 final size:48
Alignment explanation
Indices: 28857467--28857561 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 48
28857457 TCAGCTGCAA
* * *
28857467 CAAAGACAAGTTTAATGACTAGATTCGGCTGGACAAATTAAATAGCAG
1 CAAAGACAAGATTAATGACTAAATTCAGCTGGACAAATTAAATAGCAG
28857515 CAAAGACAA-ATTAATGACTAAATTCAGCTGGACAAATTAAATAGCAG
1 CAAAGACAAGATTAATGACTAAATTCAGCTGGACAAATTAAATAGCAG
28857562 TAGCTAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 35 0.80
48 9 0.20
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (48 bp):
CAAAGACAAGATTAATGACTAAATTCAGCTGGACAAATTAAATAGCAG
Found at i:28864116 original size:51 final size:51
Alignment explanation
Indices: 28864057--28864203 Score: 144
Period size: 50 Copynumber: 2.9 Consensus size: 51
28864047 CATGATTTTA
*
28864057 TTAA-GATGCAAACTAAATGAATAA-AT-GAGTTACTTAATGCATGAC-TAAAT
1 TTAATGATGCAAACTAAA--AATAACATGGAGTTACATAATGCATGACAT-AAT
* * * *
28864107 TTAATGATGCAGACTTAAACTAACATGGGAGTTACATAATGCATGTCATAAT
1 TTAATGATGCAAACTAAAAATAACAT-GGAGTTACATAATGCATGACATAAT
* *
28864159 TT-ATGATGCAAACT-TAACTAACATGAGAGTTACATAATGCATGAC
1 TTAATGATGCAAACTAAAAATAACATG-GAGTTACATAATGCATGAC
28864204 TTTATTAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
49 5 0.06
50 33 0.40
51 22 0.27
52 22 0.27
53 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (51 bp):
TTAATGATGCAAACTAAAAATAACATGGAGTTACATAATGCATGACATAAT
Found at i:28864193 original size:50 final size:52
Alignment explanation
Indices: 28864083--28864204 Score: 178
Period size: 50 Copynumber: 2.4 Consensus size: 52
28864073 ATGAATAAAT
* * *
28864083 GAGTTACTTAATGCATGACTAAATTTAATGATGCAGACTTAAACTAACATGG
1 GAGTTACATAATGCATGACTAAATTTAATGATGCAAACTTAAACTAACATGA
*
28864135 GAGTTACATAATGCATGTC-ATAATTT-ATGATGCAAACTT-AACTAACATGA
1 GAGTTACATAATGCATGACTA-AATTTAATGATGCAAACTTAAACTAACATGA
28864185 GAGTTACATAATGCATGACT
1 GAGTTACATAATGCATGACT
28864205 TTATTAAATG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 28 0.44
51 13 0.21
52 22 0.35
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (52 bp):
GAGTTACATAATGCATGACTAAATTTAATGATGCAAACTTAAACTAACATGA
Found at i:28871831 original size:27 final size:27
Alignment explanation
Indices: 28871801--28871978 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
28871791 ATATCGAGTC
* * * *
28871801 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28871828 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28871855 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28871883 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28871910 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28871937 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28871964 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28871979 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28871940 original size:82 final size:81
Alignment explanation
Indices: 28871822--28871977 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
28871812 TGCTATATAA
*
28871822 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28871887 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28871904 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28871968 CACTTAGTGC
65 CACTTAGTGC
28871978 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28883161 original size:20 final size:20
Alignment explanation
Indices: 28883104--28883170 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
28883094 GCACGTTAAG
*
28883104 ATGAGCTGAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
* * *** *
28883124 ATAAGCTAAGGACAAGCTCA
1 ATGAGCTAAAGTTGAGCTGA
28883144 ATGAGCTAAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
28883164 ATGAGCT
1 ATGAGCT
28883171 TGAAGTAGAG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAGCTGA
Found at i:28886192 original size:8 final size:9
Alignment explanation
Indices: 28886170--28886242 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
28886160 TTTAAAAAAT
28886170 TATTA-AAA
1 TATTATAAA
28886178 TATTATAAA
1 TATTATAAA
28886187 TATATATGAAAA
1 TAT-TAT--AAA
28886199 TATTA-AAA
1 TATTATAAA
* *
28886207 CATCATAAAA
1 TATTAT-AAA
*
28886217 TATTATAGA
1 TATTATAAA
* *
28886226 TAATACAAA
1 TATTATAAA
28886235 TATTATAA
1 TATTATAA
28886243 TAATGTTAGG
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
8 11 0.22
9 20 0.41
10 10 0.20
11 2 0.04
12 6 0.12
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (9 bp):
TATTATAAA
Found at i:28886937 original size:18 final size:20
Alignment explanation
Indices: 28886898--28886939 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
28886888 TATTATGGGA
*
28886898 AATTACGAGTTTTAGGCTTT
1 AATTACGAGTTTAAGGCTTT
28886918 AATT-CGAGTTTAAGGC-TT
1 AATTACGAGTTTAAGGCTTT
28886936 AATT
1 AATT
28886940 TTGTTTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (20 bp):
AATTACGAGTTTAAGGCTTT
Found at i:28888031 original size:10 final size:10
Alignment explanation
Indices: 28888000--28888090 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 10
28887990 AAATCTTCTC
*
28888000 TAAAATATT-
1 TAAAAAATTA
**
28888009 TAAAAAAACA
1 TAAAAAATTA
28888019 TAAAAAATTA
1 TAAAAAATTA
*
28888029 TAAGAAATTA
1 TAAAAAATTA
28888039 T--AAAATTA
1 TAAAAAATTA
*
28888047 TATAAAA-TA
1 TAAAAAATTA
*
28888056 TAATTTAAA-TA
1 TAA--AAAATTA
*
28888067 TGAAAAA-TA
1 TAAAAAATTA
*
28888076 TAACAAATTA
1 TAAAAAATTA
28888086 TAAAA
1 TAAAA
28888091 TTATATGTTA
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
8 7 0.11
9 20 0.32
10 28 0.45
11 7 0.11
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:28888045 original size:18 final size:17
Alignment explanation
Indices: 28888022--28888095 Score: 61
Period size: 18 Copynumber: 4.5 Consensus size: 17
28888012 AAAAACATAA
28888022 AAAATTATAAGAAATTAT
1 AAAATTATAA-AAATTAT
28888040 AAAATTATATAAAA-TAT
1 AAAATTATA-AAAATTAT
* *
28888057 --AATT-TAAATATGA-
1 AAAATTATAAAAATTAT
28888070 AAAA-TATAACAAATTAT
1 AAAATTATAA-AAATTAT
28888087 AAAATTATA
1 AAAATTATA
28888096 TGTTATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
13 3 0.07
14 4 0.09
15 9 0.20
16 4 0.09
17 7 0.16
18 16 0.36
19 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATTAT
Found at i:28888361 original size:19 final size:19
Alignment explanation
Indices: 28888337--28888383 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
28888327 GTCAAATTTG
*
28888337 TTTTATAATTTTATAATAT
1 TTTTATAATTTTAAAATAT
*
28888356 TTTTATAGTTTTAAAATAT
1 TTTTATAATTTTAAAATAT
28888375 TTTTATAAT
1 TTTTATAAT
28888384 ATGTTATGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTAAAATAT
Found at i:28888446 original size:11 final size:10
Alignment explanation
Indices: 28888397--28888484 Score: 54
Period size: 11 Copynumber: 8.2 Consensus size: 10
28888387 TTATGCTTTC
28888397 ATAATTTTTA
1 ATAATTTTTA
28888407 TATAATTTTT-
1 -ATAATTTTTA
28888417 ATAATTTTCT-
1 ATAATTTT-TA
* *
28888427 ATTAGTTTTA
1 ATAATTTTTA
28888437 ATAAGTTTTTTA
1 ATAA--TTTTTA
*
28888449 AGGAATTTTTA
1 A-TAATTTTTA
*
28888460 ATAAGTTTTTTT
1 ATAA--TTTTTA
28888472 ATAATTTTGTA
1 ATAATTTT-TA
28888483 AT
1 AT
28888485 TTTATAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
9 9 0.15
10 16 0.26
11 19 0.31
12 15 0.25
13 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:28888479 original size:10 final size:10
Alignment explanation
Indices: 28888397--28888479 Score: 51
Period size: 10 Copynumber: 7.8 Consensus size: 10
28888387 TTATGCTTTC
28888397 ATAATTTTTAT
1 ATAATTTTT-T
28888408 ATAA-TTTTT
1 ATAATTTTTT
*
28888417 ATAATTTTCT
1 ATAATTTTTT
* * *
28888427 ATTAGTTTTA
1 ATAATTTTTT
28888437 ATAAGTTTTTT
1 ATAA-TTTTTT
* *
28888448 AAGGAATTTTTA
1 -A-TAATTTTTT
28888460 ATAAGTTTTTTT
1 ATAA--TTTTTT
28888472 ATAATTTT
1 ATAATTTT
28888480 GTAATTTTAT
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
9 5 0.09
10 23 0.43
11 9 0.17
12 15 0.28
13 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:28888503 original size:16 final size:17
Alignment explanation
Indices: 28888466--28888503 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
28888456 TTTAATAAGT
28888466 TTTTTTATAATTTTGTA
1 TTTTTTATAATTTTGTA
*
28888483 -ATTTTATAATTTT-TA
1 TTTTTTATAATTTTGTA
28888498 TTTTTT
1 TTTTTT
28888504 GAATATCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTATAATTTTGTA
Found at i:28891839 original size:75 final size:75
Alignment explanation
Indices: 28891748--28891894 Score: 231
Period size: 75 Copynumber: 2.0 Consensus size: 75
28891738 GAAAACCAAA
* * * * * *
28891748 ATTATTCCCTTCTTAATAGATAAGGCAAATGGAAAGTTAGAAAAATGAAATATATTCTTTTCGAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAAATATATTCTTTCCAAA
28891813 AGAATATAGG
66 AGAATATAGG
*
28891823 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAATTATATTCTTTCCAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAAATATATTCTTTCCAAA
28891888 AGAATAT
66 AGAATAT
28891895 TAATTTCCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.32
Consensus pattern (75 bp):
ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAAATATATTCTTTCCAAA
AGAATATAGG
Found at i:28892025 original size:30 final size:30
Alignment explanation
Indices: 28891967--28892025 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28891957 GAACAAACCT
* **
28891967 TTGTTCATGTTCGTTTGTTTATTTTTAAGC
1 TTGTTCATGTTCGTTTGTGTATCGTTAAGC
28891997 TTGTTCATGTTCAGTTTGTGT-TCGTTAAG
1 TTGTTCATGTTC-GTTTGTGTATCGTTAAG
28892026 AATTTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.14, C:0.10, G:0.20, T:0.56
Consensus pattern (30 bp):
TTGTTCATGTTCGTTTGTGTATCGTTAAGC
Found at i:28892110 original size:23 final size:23
Alignment explanation
Indices: 28892084--28892153 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
28892074 TTCATTTAAC
*
28892084 TTAATCGAACATGTTTACGAACA
1 TTAATCGAACATGTTCACGAACA
* * *
28892107 TTAAACAAACATGTTCATGAACAA
1 TTAATCGAACATGTTCACGAAC-A
* * *
28892131 ATAATTGAACATATTCACGAACA
1 TTAATCGAACATGTTCACGAACA
28892154 ATGTTAATAA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:28892168 original size:4 final size:4
Alignment explanation
Indices: 28892159--28892196 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
28892149 GAACAATGTT
*
28892159 AATA AATA AATA AATA AA-A TAATA AATA AATA CATA AA
1 AATA AATA AATA AATA AATA -AATA AATA AATA AATA AA
28892197 AACACATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 1 0.03
4 28 0.93
5 1 0.03
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:28892183 original size:20 final size:20
Alignment explanation
Indices: 28892158--28892197 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28892148 CGAACAATGT
28892158 TAATAAATAAATAAATAAAA
1 TAATAAATAAATAAATAAAA
*
28892178 TAATAAATAAATACATAAAA
1 TAATAAATAAATAAATAAAA
28892198 ACACATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
TAATAAATAAATAAATAAAA
Found at i:28892358 original size:12 final size:12
Alignment explanation
Indices: 28892332--28892392 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
28892322 TCATTAATAA
*
28892332 ATAAACGAG-TT
1 ATAAATGAGCTT
*
28892343 ATAAACGAGCTT
1 ATAAATGAGCTT
**
28892355 ATAAATGAGCCA
1 ATAAATGAGCTT
28892367 ATAAATGAGCTT
1 ATAAATGAGCTT
* *
28892379 TTTAATGAGCTT
1 ATAAATGAGCTT
28892391 AT
1 AT
28892393 TCATGAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
11 9 0.22
12 32 0.78
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (12 bp):
ATAAATGAGCTT
Found at i:28898523 original size:21 final size:22
Alignment explanation
Indices: 28898493--28898533 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
28898483 TTGAGTCAAA
28898493 AAAAGATGAAAAAATGAAAATT
1 AAAAGATGAAAAAATGAAAATT
28898515 AAAA-ATGAAAAAATGAAAA
1 AAAAGATGAAAAAATGAAAA
28898534 AGTTAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (22 bp):
AAAAGATGAAAAAATGAAAATT
Found at i:28899987 original size:44 final size:44
Alignment explanation
Indices: 28899921--28900185 Score: 223
Period size: 44 Copynumber: 5.8 Consensus size: 44
28899911 GGAAATGGTG
28899921 AATCTTATCTCCCTGATG-TTACAGTGGAGCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGA-GATTACAGTGGAGCAGATTGAAGCCAGA
** * *
28899965 AATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* * * *
28900009 AATCCTATCTCCATGAGATTACAGTGGAGCAGATT-AAACTA-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* *
28900051 AGGATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 A--ATCTTATCTCCCTGAGA-TTACAGT---G--GA--G---CAGATTGAAGCCAGA
* * *
28900107 AATCTTATCTCCCTGAGATTACAGCGGAGCTGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* * * *
28900151 AATCCTATTTCCCTAAGATTACAGTGGAGCGGATT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT
28900186 AAAATAAAGG
Statistics
Matches: 178, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
42 1 0.01
43 8 0.04
44 129 0.72
47 2 0.01
49 4 0.02
51 2 0.01
54 24 0.13
55 6 0.03
56 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
Found at i:28900116 original size:142 final size:142
Alignment explanation
Indices: 28899950--28900236 Score: 493
Period size: 142 Copynumber: 2.0 Consensus size: 142
28899940 TACAGTGGAG
*
28899950 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCT
* *
28900015 ATCTCCATGAGATTACAGTGGAGCAGATTAAACTAAAGGATCTTATCTCTCTAAAGTTACAGTAG
66 ATCTCCATAAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
28900080 AGTAGATCGCAT
131 AGTAGATCGCAT
* *
28900092 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCTGATTGAAGCCAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCT
* * * *
28900157 ATTTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTATAGTAG
66 ATCTCCATAAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
28900222 AGTAGATCGCAT
131 AGTAGATCGCAT
28900234 CAG
1 CAG
28900237 TTCTTATCTC
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 136 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCT
ATCTCCATAAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
AGTAGATCGCAT
Found at i:28900470 original size:100 final size:100
Alignment explanation
Indices: 28900292--28900570 Score: 387
Period size: 100 Copynumber: 2.8 Consensus size: 100
28900282 GATCTTAGTT
* * **
28900292 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCTTAACATTGCAG
1 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCCAACATTGCAG
* *
28900357 TTAAAAAGATTAAAGCTACAACAGCGAATCTTACC
66 TTAAAAAGATTAAAGCCACAACAGCGAATCTTAAC
* * *
28900392 TCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCCGACATTGCAG
1 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCCAACATTGCAG
*
28900457 TTAAAAAGATTAAAGCCACAACAGCGAATCTTAAT
66 TTAAAAAGATTAAAGCCACAACAGCGAATCTTAAC
* * * * * **
28900492 TCCCTGGCGATGCAGTGGAACGGATTAAATCTACAATGGTGAATCTTGTTTCCCCAACATCACAG
1 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCCAACATTGCAG
**
28900557 TTAAGTAGATTAAA
66 TTAAAAAGATTAAA
28900571 ATTGCGAGTT
Statistics
Matches: 157, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 157 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (100 bp):
TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCCAACATTGCAG
TTAAAAAGATTAAAGCCACAACAGCGAATCTTAAC
Found at i:28900545 original size:50 final size:50
Alignment explanation
Indices: 28900291--28900545 Score: 199
Period size: 50 Copynumber: 5.1 Consensus size: 50
28900281 AGATCTTAGT
*
28900291 TTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
1 TTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
* * ** ** * * * * *
28900341 CTCCTTAAC-ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
1 TTCCCTGGCGA-TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
* * * **
28900391 CTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGC
1 TTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
* * ** * * * **
28900441 TTCCCCGAC-ATTGCAGTTAAAAAGATTAAAGCCACAACAGCGAATCTTAA
1 TTCCCTGGCGA-TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
* * * * *
28900491 TTCCCTGGCGATGCAGTGGAACGGATTAAATCTACAATGGTGAATCTTGT
1 TTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
28900541 TTCCC
1 TTCCC
28900546 CAACATCACA
Statistics
Matches: 149, Mismatches: 52, Indels: 8
0.71 0.25 0.04
Matches are distributed among these distances:
50 148 0.99
51 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (50 bp):
TTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC
Found at i:28908483 original size:138 final size:138
Alignment explanation
Indices: 28908230--28908714 Score: 742
Period size: 138 Copynumber: 3.5 Consensus size: 138
28908220 GGGTGTTACA
* *
28908230 GTTTATATTAATAAATT-CGGTAAAATATATCCAATTAATATTTTATATAAATCAAATTCATATA
1 GTTTATATTAATAAATTAC-GTAAAATATATACAATTAATATTTTATATGAATCAAATTCATATA
* * * *
28908294 CTAATTATATTCTTTCCAAAAGAATATTAATTTCCTTGTTTTTTATATTTTGACCAAAATTAATT
65 TTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATT
28908359 AATATAATT
130 AATATAATT
* * * *
28908368 GTTTGTATTAATAAA-TACGATAAAATATATACTATTAATATTTTGTATGAATCAAATTCATAAA
1 GTTTATATTAATAAATTACG-TAAAATATATACAATTAATATTTTATATGAATCAAATTCATATA
* *
28908432 TTAATTATATTCTTTCCAAAATAATATTAATTTCCATGTCTTTTATTTTTTGACCGAAATTAATT
65 TTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATT
28908497 AATATAATT
130 AATATAATT
28908506 GTTTATATTAATAAATTTA-GTAAAATATATACAATTAATATTTTATATGAATCAAATTCATATA
1 GTTTATATTAATAAA-TTACGTAAAATATATACAATTAATATTTTATATGAATCAAATTCATATA
* **
28908570 TTAATTATATTCTTTTCAAAAGAATATTAATTTTTATGTCTTTTATATTTTGACCGAAATTAATT
65 TTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATT
**
28908635 AATATAACA
130 AATATAATT
* *
28908644 GTTTATATTAATAAATTAAGTAAAATATATACAATTAATATTTTTGTATGAATCAAATTCATATA
1 GTTTATATTAATAAATTACGTAAAATATATACAATTAATA-TTTTATATGAATCAAATTCATATA
28908709 TTAATT
65 TTAATT
28908715 TTATCTATGT
Statistics
Matches: 317, Mismatches: 24, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
137 5 0.02
138 280 0.88
139 30 0.09
140 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (138 bp):
GTTTATATTAATAAATTACGTAAAATATATACAATTAATATTTTATATGAATCAAATTCATATAT
TAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTA
ATATAATT
Done.