Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 165 of 167
Found at i:54649770 original size:18 final size:16
Alignment explanation
Indices: 54649739--54649772 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
54649729 AAAAAAATTC
54649739 AAAAAAAAATTGAAAA
1 AAAAAAAAATTGAAAA
54649755 AAAAACAAAATCTGAAAA
1 AAAAA-AAAAT-TGAAAA
54649773 TTTGAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAAAAATTGAAAA
Found at i:54651959 original size:21 final size:21
Alignment explanation
Indices: 54651895--54651968 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
54651885 AAAAAAATTA
54651895 GAAAAAGAAAACAAAAGAG-AG
1 GAAAAAGAAAA-AAAAGAGAAG
**
54651916 TG-AAAAG-AAAATCAGTA-AA-
1 -GAAAAAGAAAAAAAAG-AGAAG
54651935 GAAAAAGAAAAAAAAGAGAAG
1 GAAAAAGAAAAAAAAGAGAAG
**
54651956 GAAATTGAAAAAA
1 GAAAAAGAAAAAA
54651969 TGAGTTTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 1 0.03
19 9 0.22
20 13 0.32
21 16 0.40
22 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAGAGAAG
Found at i:54653161 original size:19 final size:19
Alignment explanation
Indices: 54653137--54653176 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54653127 AGCTCCCATG
54653137 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
54653156 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
54653175 TA
1 TA
54653177 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:54654858 original size:12 final size:12
Alignment explanation
Indices: 54654843--54654885 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
54654833 TAAAAAAATA
54654843 AAAAAAAATTCG
1 AAAAAAAATTCG
*
54654855 AAAAAAAAATC-
1 AAAAAAAATTCG
54654866 AAAAGAAAATT-G
1 AAAA-AAAATTCG
54654878 AAAAAAAA
1 AAAAAAAA
54654886 GTGATTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:54654864 original size:23 final size:23
Alignment explanation
Indices: 54654834--54654885 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
54654824 TATACAAGTT
54654834 AAAAAAAT-AAAAAAAAATTCGAA
1 AAAAAAATCAAAAAAAAATT-GAA
*
54654857 AAAAAAATCAAAAGAAAATTGAA
1 AAAAAAATCAAAAAAAAATTGAA
54654880 AAAAAA
1 AAAAAA
54654886 GTGATTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAAAAATCAAAAAAAAATTGAA
Found at i:54660131 original size:19 final size:19
Alignment explanation
Indices: 54660107--54660146 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54660097 AGCTCCCATG
54660107 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
* * *
54660126 TAGCTCGAGACTAGCTCAT
1 TAGCTCCACACCAGCTCAT
54660145 TA
1 TA
54660147 TCAACTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:54660742 original size:31 final size:32
Alignment explanation
Indices: 54660689--54660748 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
54660679 AATTCGTTCA
*
54660689 CACCTATGTTCACATGGCAAGACTATTCAGTT
1 CACCTATGTTCACATAGCAAGACTATTCAGTT
*
54660721 CACCT-TGTTCACACTAG-AAGACTCTTCA
1 CACCTATGTTCACA-TAGCAAGACTATTCA
54660749 ACACTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (32 bp):
CACCTATGTTCACATAGCAAGACTATTCAGTT
Found at i:54666368 original size:26 final size:26
Alignment explanation
Indices: 54666332--54666722 Score: 755
Period size: 26 Copynumber: 15.0 Consensus size: 26
54666322 TACAAATTGG
*
54666332 TAATAGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
* *
54666358 TAATGGATTAGGTAAATATTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666384 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666410 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666436 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666462 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666488 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666514 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666540 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666566 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666592 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666618 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666644 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666670 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666696 TAATGGGTTAGGTAAATGTTCCATGA
1 TAATGGGTTAGGTAAATGTTCCATGA
54666722 T
1 T
54666723 GGGCATTTCA
Statistics
Matches: 360, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 360 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (26 bp):
TAATGGGTTAGGTAAATGTTCCATGA
Found at i:54668343 original size:27 final size:26
Alignment explanation
Indices: 54668303--54668406 Score: 127
Period size: 27 Copynumber: 3.9 Consensus size: 26
54668293 AGGAAGCATC
*
54668303 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAA-TATCTGAT
*
54668330 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACA-ATATCTGAT
*
54668357 CTGGTGGCTCTGCCATAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTG-AT
* * *
54668384 CTGGTGACTTTGTCACAATATCT
1 CTGGTGGCTCTGCCACAATATCT
54668407 AGTAGCCTCG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 7 0.10
27 59 0.88
28 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACAATATCTGAT
Found at i:54669385 original size:333 final size:333
Alignment explanation
Indices: 54668779--54669446 Score: 1309
Period size: 333 Copynumber: 2.0 Consensus size: 333
54668769 TTTTCTTCTG
*
54668779 GTGAACTGGACATCCTTTTAATTACGTTTGAGGTTTTGGGCTTTTAAATGTAATAAGGCCGCTTA
1 GTGAACTGGACATCCTTTTAATTACGTTTGAGGTTTTGGGCTTTTAAATGTAATAAAGCCGCTTA
*
54668844 TTTATTTTTGATGGTTTTTGTATGTTTTATTAAGATAGGTAATATTTATATTTAACTGTTGAAAT
66 TTTATTTTTGATGGTTTTTATATGTTTTATTAAGATAGGTAATATTTATATTTAACTGTTGAAAT
54668909 TGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAATAAGACGAAAACAAGTAA
131 TGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAATAAGACGAAAACAAGTAA
54668974 AGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCG
196 AGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCG
54669039 GTTTCCTAGAAATATACATGACGTTAAGGTATGGCAATGGTGGTTTGCATGTCTAGGATTGGATC
261 GTTTCCTAGAAATATACATGACGTTAAGGTATGGCAATGGTGGTTTGCATGTCTAGGATTGGATC
54669104 CGAAGGGA
326 CGAAGGGA
*
54669112 GTGAACTGGACATCTTTTTAATTACGTTTGAGGTTTTGGGCTTTTAAATGTAATAAAGCCGCTTA
1 GTGAACTGGACATCCTTTTAATTACGTTTGAGGTTTTGGGCTTTTAAATGTAATAAAGCCGCTTA
54669177 TTTATTTTTGATGGTTTTTATATGTTTTATTAAGATAGGTAATATTTATATTTAACTGTTGAAAT
66 TTTATTTTTGATGGTTTTTATATGTTTTATTAAGATAGGTAATATTTATATTTAACTGTTGAAAT
54669242 TGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAATAAGACGAAAACAAGTAA
131 TGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAATAAGACGAAAACAAGTAA
54669307 AGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCG
196 AGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCG
54669372 GTTTCCTAGAAATATACATGACGTTAAGGTATGGCAATGGTGGTTTGCATGTCTAGGATTGGATC
261 GTTTCCTAGAAATATACATGACGTTAAGGTATGGCAATGGTGGTTTGCATGTCTAGGATTGGATC
54669437 CGAAGGGA
326 CGAAGGGA
54669445 GT
1 GT
54669447 TTGGTACTTA
Statistics
Matches: 332, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
333 332 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (333 bp):
GTGAACTGGACATCCTTTTAATTACGTTTGAGGTTTTGGGCTTTTAAATGTAATAAAGCCGCTTA
TTTATTTTTGATGGTTTTTATATGTTTTATTAAGATAGGTAATATTTATATTTAACTGTTGAAAT
TGGATAGCTTTAGGGCGCGTTTTCAAAAACAGTAATTGATTTCAAAATAAGACGAAAACAAGTAA
AGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCG
GTTTCCTAGAAATATACATGACGTTAAGGTATGGCAATGGTGGTTTGCATGTCTAGGATTGGATC
CGAAGGGA
Found at i:54674906 original size:64 final size:64
Alignment explanation
Indices: 54674834--54675216 Score: 577
Period size: 64 Copynumber: 6.0 Consensus size: 64
54674824 CATTCATAAC
* * *
54674834 ACATCTAGTTAGGAGCATTTAATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
1 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
54674898 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
1 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
54674962 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
1 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
* * *
54675026 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGGCATAAGCATC
1 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
* * ** * ** *
54675090 ACATCTAATTAGGAGTATTTGATTCATTTCGATCATAATATCCTAATTATTTGACATCAGCATC
1 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
* ** * * * *
54675154 ACATCTAGTTAGGAGTATTTGATTCATTTTGATCATAGCATTCTAGTTATTTGGCATAAGCAT
1 ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCAT
54675217 GATACATGAA
Statistics
Matches: 296, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 296 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (64 bp):
ACATCTAGTTAAGAACATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATCAGCATT
Found at i:54675716 original size:177 final size:177
Alignment explanation
Indices: 54675414--54675736 Score: 402
Period size: 177 Copynumber: 1.8 Consensus size: 177
54675404 CAAAGACGAT
* *
54675414 AAATATTATCTCCATGTATTGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTT
1 AAATATTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTA
* * * * *
54675479 GCAGTAGAGCTGGCTCAATATATGAATCTTATCTTTCTAAGGTAGCAAGGAAGTAGACTGAA-AT
66 GAAGTAGAGCAGGCTCAATATATGAATCTAATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAGA-
*
54675543 TTGCAGATATTATCTCCCTAGACAGTAGTGGGGCAGATCGAAGATGGC
130 TTGAAGATATTATCTCCCTAGACAGTAGTGGGGCAGATCGAAGATGGC
* * * * * *
54675591 AAATGTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCGCTAGCCTTATCTCTCTGAGGTA
1 AAATATTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTA
* * * * *
54675656 GTAAG-AGAGCAGGTTGGCGAT-TGT-AGTCTAATCTTCCTGAGGTAGCAAGGAAGCAGACTGAA
66 G-AAGTAGAGCAGGCT--CAATATATGAATCTAATCTTCCTAAGGTAGCAAGGAAGCAGACTGAA
*
54675718 GATTGAAGATTTTATCTCC
128 GATTGAAGATATTATCTCC
54675737 TTGAAGTTGT
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
177 114 0.93
178 5 0.04
179 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (177 bp):
AAATATTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTA
GAAGTAGAGCAGGCTCAATATATGAATCTAATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAGAT
TGAAGATATTATCTCCCTAGACAGTAGTGGGGCAGATCGAAGATGGC
Found at i:54675758 original size:45 final size:45
Alignment explanation
Indices: 54675707--54675802 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
54675697 GTAGCAAGGA
* * * *
54675707 AGCAGACTGAAGATTGAAGATTTTATCTCCTTGAAGTTGTAGTGG
1 AGCAGACTGAAGATAGAAGATCTTATCTCATTGAAGTTGCAGTGG
* *
54675752 AGCAGACTGAAGATAGCAGATCTTGTCTCATTGAAGTTGCAGTGG
1 AGCAGACTGAAGATAGAAGATCTTATCTCATTGAAGTTGCAGTGG
54675797 AGCAGA
1 AGCAGA
54675803 TCGAAGCCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (45 bp):
AGCAGACTGAAGATAGAAGATCTTATCTCATTGAAGTTGCAGTGG
Found at i:54690101 original size:49 final size:50
Alignment explanation
Indices: 54690021--54690266 Score: 325
Period size: 49 Copynumber: 4.9 Consensus size: 50
54690011 AGCTATTGTA
54690021 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
54690071 -GGTCGCCTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * **
54690121 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
54690171 AGGTCACGTGTGTAGTATTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
54690221 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
54690267 CCTTCGGCTA
Statistics
Matches: 167, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
49 82 0.49
50 47 0.28
51 38 0.23
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:54690158 original size:28 final size:27
Alignment explanation
Indices: 54690126--54690209 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
54690116 AACTTCGATC
54690126 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTA-TAAGTGCAGGCTACT
* * *
54690154 ACGTGTATCAG-AT-GGT-TAGG-T-C-
1 ACGTGTGT-AGTATAAGTGCAGGCTACT
54690176 ACGTGTGTAGTATTAAGTGCAGGCTACT
1 ACGTGTGTAGTA-TAAGTGCAGGCTACT
54690204 ACGTGT
1 ACGTGT
54690210 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (27 bp):
ACGTGTGTAGTATAAGTGCAGGCTACT
Found at i:54692706 original size:40 final size:40
Alignment explanation
Indices: 54692651--54692776 Score: 200
Period size: 40 Copynumber: 3.1 Consensus size: 40
54692641 AAACCAAGTA
* * *
54692651 CCTTCGGGACTTAGCCCGG-ATATAGTAACTCGCATAAATG
1 CCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCACAAATG
*
54692691 CCTTCGGGACTTAGCCCGAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
54692731 CCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
54692771 CCTTCG
1 CCTTCG
54692777 TTATCATCCG
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 78 0.98
41 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
Found at i:54704238 original size:3 final size:3
Alignment explanation
Indices: 54704230--54704274 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
54704220 TACTGCCATG
*
54704230 GAA GAA GAA GAA GAA GAA GAA G-A GAA GAA GAA G-A GGA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
54704275 GGGCGGCGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54704257 original size:14 final size:14
Alignment explanation
Indices: 54704230--54704274 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
54704220 TACTGCCATG
54704230 GAAGAAGAAGAAGAA
1 GAAGAAG-AGAAGAA
54704245 GAAGAAGAGAAGAA
1 GAAGAAGAGAAGAA
*
54704259 GAAGAGGAGAAGAA
1 GAAGAAGAGAAGAA
54704273 GA
1 GA
54704275 GGGCGGCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 22 0.76
15 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (14 bp):
GAAGAAGAGAAGAA
Found at i:54704276 original size:11 final size:11
Alignment explanation
Indices: 54704230--54704275 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
54704220 TACTGCCATG
54704230 GAAGAAGAAGAA
1 GAAGAAGAAG-A
54704242 GAAGAAGAAGA
1 GAAGAAGAAGA
54704253 GAAGAAGAAGA
1 GAAGAAGAAGA
*
54704264 GGAGAAGAAGA
1 GAAGAAGAAGA
54704275 G
1 G
54704276 GGCGGCGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 23 0.70
12 10 0.30
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (11 bp):
GAAGAAGAAGA
Found at i:54704310 original size:24 final size:25
Alignment explanation
Indices: 54704283--54704330 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
54704273 GAGGGCGGCG
*
54704283 AAAAAGGAA-AGAAAGA-AAGAAAA
1 AAAAAAGAAGAGAAAGAGAAGAAAA
*
54704306 AAAAAAGAAGAGAGAGAGAAGAAAA
1 AAAAAAGAAGAGAAAGAGAAGAAAA
54704331 GAGAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAGAGAAAGAGAAGAAAA
Found at i:54704825 original size:30 final size:31
Alignment explanation
Indices: 54704765--54704824 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
54704755 TTGTATGTAT
*
54704765 TGTTATTTTAAAAGTCGGTATAATTTTTTTA
1 TGTTATTTTAAAAGTCGATATAATTTTTTTA
*
54704796 TGTTATTTTAAAAGTTGATATAATTTTTT
1 TGTTATTTTAAAAGTCGATATAATTTTTT
54704825 AACTCATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.57
Consensus pattern (31 bp):
TGTTATTTTAAAAGTCGATATAATTTTTTTA
Found at i:54705183 original size:20 final size:20
Alignment explanation
Indices: 54705168--54705204 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54705158 TAATAATAAT
54705168 AAATTAAATTTTATAACAAA
1 AAATTAAATTTTATAACAAA
*
54705188 AAATTACATTTT-TAACA
1 AAATTAAATTTTATAACA
54705205 CTTTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTAAATTTTATAACAAA
Found at i:54714700 original size:42 final size:42
Alignment explanation
Indices: 54714631--54714775 Score: 166
Period size: 42 Copynumber: 3.5 Consensus size: 42
54714621 CAATGTCATG
* * ** *
54714631 TCCCAGACATGGTCTTACAAGGGATCTCATATCGATGCCATA
1 TCCCAGATATGGTCTTACACGAAATCTCATATAGATGCCATA
* * * *
54714673 TCCCAGAAATGGTCTTATACGAAATCTCATTTAGATGCCATG
1 TCCCAGATATGGTCTTACACGAAATCTCATATAGATGCCATA
* * *
54714715 TCCTAGATGTGGTCTTACACGAAATCTCATATTA-ACGCCATA
1 TCCCAGATATGGTCTTACACGAAATCTCATA-TAGATGCCATA
54714757 TCCCAGATATGGTCTTACA
1 TCCCAGATATGGTCTTACA
54714776 TGATAACACA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
TCCCAGATATGGTCTTACACGAAATCTCATATAGATGCCATA
Found at i:54735753 original size:20 final size:20
Alignment explanation
Indices: 54735728--54735773 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
54735718 TTCCCTTATT
54735728 AGATTTGACTCTAATCTGCC
1 AGATTTGACTCTAATCTGCC
54735748 AGATTTGACTCTAATCTGCC
1 AGATTTGACTCTAATCTGCC
54735768 AGATTT
1 AGATTT
54735774 ATGTTGTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (20 bp):
AGATTTGACTCTAATCTGCC
Found at i:54738028 original size:41 final size:41
Alignment explanation
Indices: 54737962--54738161 Score: 177
Period size: 41 Copynumber: 4.9 Consensus size: 41
54737952 AAACACCGCA
* * * * *
54737962 AAAAACTAAACAATAACGGCATTTTTGGCCCAAACGCCATT
1 AAAAACTGATCAATAGCGGCGTTTTTGGCCCAAACGCCACT
* * * **
54738003 AAAAACTGATCGATAGCAGCGTTTTTTAGCTAAAACGCCACT
1 AAAAACTGATCAATAGCGGCG-TTTTTGGCCCAAACGCCACT
* *****
54738045 AAAAACTGATCAATAGCGGCATTTTTATATAAAACGCCACT
1 AAAAACTGATCAATAGCGGCGTTTTTGGCCCAAACGCCACT
* * ** *
54738086 AAAAACTAAGCAATAGTTGCGTTTTTGGTCCAAACGCCACT
1 AAAAACTGATCAATAGCGGCGTTTTTGGCCCAAACGCCACT
* *
54738127 -AAAATTGATCAATAGCGGCGTTTTTGGTCCAAACG
1 AAAAACTGATCAATAGCGGCGTTTTTGGCCCAAACG
54738162 TCGCAAAAAA
Statistics
Matches: 128, Mismatches: 30, Indels: 3
0.80 0.19 0.02
Matches are distributed among these distances:
40 30 0.23
41 64 0.50
42 34 0.27
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (41 bp):
AAAAACTGATCAATAGCGGCGTTTTTGGCCCAAACGCCACT
Found at i:54738039 original size:42 final size:41
Alignment explanation
Indices: 54737993--54738101 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 41
54737983 TTTTTGGCCC
* * *
54737993 AAACGCCATTAAAAACTGATCGATAGCAGCGTTTTT-TAGCTA
1 AAACGCCACTAAAAACTGATCAATAGCAGCATTTTTATA--TA
*
54738035 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTATATA
1 AAACGCCACTAAAAACTGATCAATAGCAGCATTTTTATATA
* *
54738076 AAACGCCACTAAAAACTAAGCAATAG
1 AAACGCCACTAAAAACTGATCAATAG
54738102 TTGCGTTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 26 0.43
42 32 0.53
43 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (41 bp):
AAACGCCACTAAAAACTGATCAATAGCAGCATTTTTATATA
Found at i:54738090 original size:83 final size:81
Alignment explanation
Indices: 54737993--54738151 Score: 194
Period size: 81 Copynumber: 1.9 Consensus size: 81
54737983 TTTTTGGCCC
* * * *
54737993 AAACGCCATTAAAAACTGATCGATAGCAGCGTTTTTTAGCT-AAAACGCCACTAAAAACTGATCA
1 AAACGCCACTAAAAACTAAGCAATAGCAGCG-TTTTT-GCTCAAAACGCCACT-AAAACTGATCA
54738057 ATAGCGGCATTTTTATATA
63 ATAGCGGCATTTTTATATA
** * * *
54738076 AAACGCCACTAAAAACTAAGCAATAGTTGCGTTTTTGGTCCAAACGCCACTAAAATTGATCAATA
1 AAACGCCACTAAAAACTAAGCAATAGCAGCGTTTTTGCTCAAAACGCCACTAAAACTGATCAATA
*
54738141 GCGGCGTTTTT
66 GCGGCATTTTT
54738152 GGTCCAAACG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
81 25 0.38
82 15 0.23
83 25 0.38
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (81 bp):
AAACGCCACTAAAAACTAAGCAATAGCAGCGTTTTTGCTCAAAACGCCACTAAAACTGATCAATA
GCGGCATTTTTATATA
Found at i:54738515 original size:14 final size:14
Alignment explanation
Indices: 54738490--54738537 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
54738480 ATGGCTTTCT
54738490 CTAAACCCTTAAATC
1 CTAAA-CCTTAAATC
54738505 CTAAACCTTAAA-C
1 CTAAACCTTAAATC
* *
54738518 CTTAAACCCTAAATT
1 C-TAAACCTTAAATC
54738533 CTAAA
1 CTAAA
54738538 AACATAAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 21 0.72
15 6 0.21
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (14 bp):
CTAAACCTTAAATC
Found at i:54738545 original size:29 final size:28
Alignment explanation
Indices: 54738490--54738584 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 28
54738480 ATGGCTTTCT
* *
54738490 CTAAACCCTTAAATCCTAAACCTTAAACC
1 CTAAACCC-TAAATCCTAAAACATAAACC
* *
54738519 TTAAACCCTAAATTCTAAAAACATAAACC
1 CTAAACCCTAAATCCT-AAAACATAAACC
* *
54738548 CTAAACACT-AATCC-ATAAACTCTAAAACC
1 CTAAACCCTAAATCCTA-AAAC-AT-AAACC
54738577 CTAAACCC
1 CTAAACCC
54738585 CCCAAAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 4 0.08
28 12 0.23
29 36 0.68
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (28 bp):
CTAAACCCTAAATCCTAAAACATAAACC
Found at i:54738803 original size:34 final size:35
Alignment explanation
Indices: 54738729--54738808 Score: 108
Period size: 38 Copynumber: 2.2 Consensus size: 35
54738719 GTTTAAAGCC
* *
54738729 TATGGTTTAGGGTTCAATGGTAGTATATATTTTAAGTT
1 TATGGTTTAGGGCTCAATGGTAG---ATATGTTAAGTT
54738767 TATGGTTTAGGGCTCAATGGTAG-TATGTTAAGTT
1 TATGGTTTAGGGCTCAATGGTAGATATGTTAAGTT
54738801 TATGGTTT
1 TATGGTTT
54738809 GGGTCGGGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 18 0.45
38 22 0.55
ACGTcount: A:0.24, C:0.04, G:0.26, T:0.46
Consensus pattern (35 bp):
TATGGTTTAGGGCTCAATGGTAGATATGTTAAGTT
Found at i:54739988 original size:82 final size:82
Alignment explanation
Indices: 54739877--54740040 Score: 215
Period size: 82 Copynumber: 2.0 Consensus size: 82
54739867 CTCCAGCGAC
*
54739877 ATTAGCGGCGCTTTTTTGAAAAACACCACTAAAGATCGAGAGTTAGCGGCGC-TTTTGTAAAAAT
1 ATTAGCGGCGCTTTTTTGAAAAACACCACTAAAGATCGAGAGTTAGCGGCACTTTTTGTAAAAAT
* *
54739941 GCCGGAAAAGATCGAGA
66 ACCGCAAAAGATCGAGA
** * * *
54739958 ATTAGCGGCAG-TTTTTTCGAAAAATGCCACTAAAGTTCGAGATTTAGCGGCACTTTTTTTAAAA
1 ATTAGCGGC-GCTTTTTT-GAAAAACACCACTAAAGATCGAGAGTTAGCGGCACTTTTTGTAAAA
*
54740022 ATACCGCTAAAGATCGAGA
64 ATACCGCAAAAGATCGAGA
54740041 TTTATTGGCT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
81 15 0.21
82 31 0.44
83 25 0.35
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (82 bp):
ATTAGCGGCGCTTTTTTGAAAAACACCACTAAAGATCGAGAGTTAGCGGCACTTTTTGTAAAAAT
ACCGCAAAAGATCGAGA
Found at i:54739998 original size:42 final size:40
Alignment explanation
Indices: 54739877--54740040 Score: 159
Period size: 42 Copynumber: 4.0 Consensus size: 40
54739867 CTCCAGCGAC
*
54739877 ATTAGCGGCGCTTTTTTGAAAAACACCACTAAAGATCGAGA
1 ATTAGCGGCG-TTTTTTGAAAAATACCACTAAAGATCGAGA
* * * ***
54739918 GTTAGCGGCG-CTTTTGTAAAAATGCCGGAAAAGATCGAGA
1 ATTAGCGGCGTTTTTTG-AAAAATACCACTAAAGATCGAGA
* *
54739958 ATTAGCGGCAGTTTTTTCGAAAAATGCCACTAAAGTTCGAGA
1 ATTAGCGGC-GTTTTTT-GAAAAATACCACTAAAGATCGAGA
* * * *
54740000 TTTAGCGGCACTTTTTTTAAAAATACCGCTAAAGATCGAGA
1 ATTAGCGGC-GTTTTTTGAAAAATACCACTAAAGATCGAGA
54740041 TTTATTGGCT
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
39 5 0.05
40 26 0.26
41 30 0.30
42 38 0.38
43 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (40 bp):
ATTAGCGGCGTTTTTTGAAAAATACCACTAAAGATCGAGA
Found at i:54740041 original size:41 final size:41
Alignment explanation
Indices: 54739878--54740044 Score: 183
Period size: 41 Copynumber: 4.1 Consensus size: 41
54739868 TCCAGCGACA
* * *
54739878 TTAGCGGCGCTTTTTTGAAAAACACCACTAAAGATCGAGAG
1 TTAGCGGCACTTTTTTGAAAAATACCACTAAAGATCGAGAT
* * * *** *
54739919 TTAGCGGCGCTTTTGT-AAAAATGCCGGAAAAGATCGAGAA
1 TTAGCGGCACTTTTTTGAAAAATACCACTAAAGATCGAGAT
* * *
54739959 TTAGCGGCAGTTTTTTCGAAAAATGCCACTAAAGTTCGAGAT
1 TTAGCGGCACTTTTTT-GAAAAATACCACTAAAGATCGAGAT
* *
54740001 TTAGCGGCACTTTTTTTAAAAATACCGCTAAAGATCGAGAT
1 TTAGCGGCACTTTTTTGAAAAATACCACTAAAGATCGAGAT
54740042 TTA
1 TTA
54740045 TTGGCTTTCT
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
40 31 0.30
41 39 0.38
42 34 0.33
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (41 bp):
TTAGCGGCACTTTTTTGAAAAATACCACTAAAGATCGAGAT
Found at i:54741057 original size:85 final size:87
Alignment explanation
Indices: 54740938--54741112 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 87
54740928 GTGAACTGTG
** * *
54740938 AAGCAATCTATTAACATTTTAAACCTCAGCTAAACAACTCTTCTACCTATAAAGAACATTT-AC-
1 AAGCAATCTATTAACATTTTAAACCTCAGCTAAACAACTCTTCTACAAACAAAAAACATTTGACT
*
54741001 TATACCATTGCAATTATTACTC
66 TATACCATTGCAATTATTACCC
* * *
54741023 AAGCAATTTATTAACATTTTAAACCTCAGTTAAACAAGTCTTCTACAAACAAAAAACATTTGACT
1 AAGCAATCTATTAACATTTTAAACCTCAGCTAAACAACTCTTCTACAAACAAAAAACATTTGACT
* *
54741088 TTTATCATTGCAATTATTACCC
66 TATACCATTGCAATTATTACCC
54741110 AAG
1 AAG
54741113 AACAAGGCCT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 54 0.69
86 2 0.03
87 22 0.28
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (87 bp):
AAGCAATCTATTAACATTTTAAACCTCAGCTAAACAACTCTTCTACAAACAAAAAACATTTGACT
TATACCATTGCAATTATTACCC
Found at i:54743195 original size:16 final size:16
Alignment explanation
Indices: 54743171--54743204 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54743161 TAATACTAAT
*
54743171 TAATTTTTGATATTAA
1 TAATGTTTGATATTAA
*
54743187 TAATGTTTGATTTTAA
1 TAATGTTTGATATTAA
54743203 TA
1 TA
54743205 TTTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TAATGTTTGATATTAA
Found at i:54743495 original size:22 final size:22
Alignment explanation
Indices: 54743437--54743558 Score: 108
Period size: 22 Copynumber: 5.7 Consensus size: 22
54743427 TCATCTCAAG
54743437 ATAAGTTTAAAAGGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
* **
54743459 ATAA--ATAAATTGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
54743479 ATAAGTTTAAAAGGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
* ** *** * *
54743501 ATTA--TCCAAATCCATCTCAAG
1 ATAAGTTTAAAAGGTAT-TTAAT
54743522 ATAAGTTTAAAAGGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
54743544 ATAAGTTTAAAAGGT
1 ATAAGTTTAAAAGGT
54743559 TGGGTTTCAT
Statistics
Matches: 73, Mismatches: 22, Indels: 10
0.70 0.21 0.10
Matches are distributed among these distances:
20 23 0.32
21 6 0.08
22 38 0.52
23 6 0.08
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (22 bp):
ATAAGTTTAAAAGGTATTTAAT
Found at i:54743540 original size:43 final size:43
Alignment explanation
Indices: 54743412--54743545 Score: 175
Period size: 43 Copynumber: 3.1 Consensus size: 43
54743402 CTTTAGTTGC
54743412 AATATTATCCAAATCTCATCTCAAGATAAGTTTAAAAGGTATTT
1 AATATTATCCAAATC-CATCTCAAGATAAGTTTAAAAGGTATTT
* ** * *
54743456 AATATAAAT--AAATTGTAT-TTAATATAAGTTTAAAAGGTATTT
1 AATAT-TATCCAAA-TCCATCTCAAGATAAGTTTAAAAGGTATTT
54743498 AATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGTATTT
1 AATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGTATTT
54743541 AATAT
1 AATAT
54743546 AAGTTTAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
41 2 0.03
42 30 0.40
43 35 0.47
44 6 0.08
45 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (43 bp):
AATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGTATTT
Found at i:54743641 original size:246 final size:246
Alignment explanation
Indices: 54743342--54743936 Score: 1181
Period size: 246 Copynumber: 2.4 Consensus size: 246
54743332 ATTTAAAAGC
54743342 TTCAATGTAATTAGTTAAACAAAGTTTCAATTTAGGTTCGTCATTACAAAATAGTTTATACTTTA
1 TTCAATGTAATTAGTTAAACAAAGTTTCAATTTAGGTTCGTCATTACAAAATAGTTTATACTTTA
54743407 GTTGCAATATTATCCAAATCTCATCTCAAGATAAGTTTAAAAGGTATTTAATATAAATAAATTGT
66 GTTGCAATATTATCCAAATCTCATCTCAAGATAAGTTTAAAAGGTATTTAATATAAATAAATTGT
54743472 ATTTAATATAAGTTTAAAAGGTATTTAATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGT
131 ATTTAATATAAGTTTAAAAGGTATTTAATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGT
54743537 ATTTAATATAAGTTTAAAAGGTTGGGTTTCATCCATTTCCTCATTTGCAAG
196 ATTTAATATAAGTTTAAAAGGTTGGGTTTCATCCATTTCCTCATTTGCAAG
54743588 TTCAATGTAATTAGTTAAACAAAGTTTCAATTTAGGTTCGTCATTACAAAATAGTTTATACTTTA
1 TTCAATGTAATTAGTTAAACAAAGTTTCAATTTAGGTTCGTCATTACAAAATAGTTTATACTTTA
54743653 GTTGCAATATTATCCAAATCTCATCTCAAGATAAGTTTAAAAGGTATTTAATATAAATAAATTGT
66 GTTGCAATATTATCCAAATCTCATCTCAAGATAAGTTTAAAAGGTATTTAATATAAATAAATTGT
54743718 ATTTAATATAAGTTTAAAAGGTATTTAATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGT
131 ATTTAATATAAGTTTAAAAGGTATTTAATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGT
54743783 ATTTAATATAAGTTTAAAAGGTTGGGTTTCATCCATTTCCTCATTTGCAAG
196 ATTTAATATAAGTTTAAAAGGTTGGGTTTCATCCATTTCCTCATTTGCAAG
54743834 TTCAATGTAATTAGTTAAACAAAGTTTCAATTTAGGTTCGTCATTACAAAATAGTTTATACTTTA
1 TTCAATGTAATTAGTTAAACAAAGTTTCAATTTAGGTTCGTCATTACAAAATAGTTTATACTTTA
*
54743899 GTTGCAATATTATCCAAATCCCATCTCAAGATAAGTTT
66 GTTGCAATATTATCCAAATCTCATCTCAAGATAAGTTT
54743937 TTGAATATTA
Statistics
Matches: 348, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 348 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (246 bp):
TTCAATGTAATTAGTTAAACAAAGTTTCAATTTAGGTTCGTCATTACAAAATAGTTTATACTTTA
GTTGCAATATTATCCAAATCTCATCTCAAGATAAGTTTAAAAGGTATTTAATATAAATAAATTGT
ATTTAATATAAGTTTAAAAGGTATTTAATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGT
ATTTAATATAAGTTTAAAAGGTTGGGTTTCATCCATTTCCTCATTTGCAAG
Found at i:54743741 original size:22 final size:22
Alignment explanation
Indices: 54743683--54743804 Score: 108
Period size: 22 Copynumber: 5.7 Consensus size: 22
54743673 TCATCTCAAG
54743683 ATAAGTTTAAAAGGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
* **
54743705 ATAA--ATAAATTGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
54743725 ATAAGTTTAAAAGGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
* ** *** * *
54743747 ATTA--TCCAAATCCATCTCAAG
1 ATAAGTTTAAAAGGTAT-TTAAT
54743768 ATAAGTTTAAAAGGTATTTAAT
1 ATAAGTTTAAAAGGTATTTAAT
54743790 ATAAGTTTAAAAGGT
1 ATAAGTTTAAAAGGT
54743805 TGGGTTTCAT
Statistics
Matches: 73, Mismatches: 22, Indels: 10
0.70 0.21 0.10
Matches are distributed among these distances:
20 23 0.32
21 6 0.08
22 38 0.52
23 6 0.08
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (22 bp):
ATAAGTTTAAAAGGTATTTAAT
Found at i:54743786 original size:43 final size:43
Alignment explanation
Indices: 54743658--54743791 Score: 175
Period size: 43 Copynumber: 3.1 Consensus size: 43
54743648 CTTTAGTTGC
54743658 AATATTATCCAAATCTCATCTCAAGATAAGTTTAAAAGGTATTT
1 AATATTATCCAAATC-CATCTCAAGATAAGTTTAAAAGGTATTT
* ** * *
54743702 AATATAAAT--AAATTGTAT-TTAATATAAGTTTAAAAGGTATTT
1 AATAT-TATCCAAA-TCCATCTCAAGATAAGTTTAAAAGGTATTT
54743744 AATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGTATTT
1 AATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGTATTT
54743787 AATAT
1 AATAT
54743792 AAGTTTAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
41 2 0.03
42 30 0.40
43 35 0.47
44 6 0.08
45 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (43 bp):
AATATTATCCAAATCCATCTCAAGATAAGTTTAAAAGGTATTT
Found at i:54744023 original size:9 final size:9
Alignment explanation
Indices: 54744011--54744306 Score: 141
Period size: 9 Copynumber: 33.6 Consensus size: 9
54744001 TATATCATAT
54744011 CATAACTTA
1 CATAACTTA
54744020 CATAACTTA
1 CATAACTTA
*
54744029 CATAACCTA
1 CATAACTTA
*
54744038 TATAACTTA
1 CATAACTTA
* *
54744047 GATAA-ATA
1 CATAACTTA
* *
54744055 TATAACATA
1 CATAACTTA
* *
54744064 GATAA-ATA
1 CATAACTTA
*
54744072 TATAACTTA
1 CATAACTTA
54744081 CATAACTTA
1 CATAACTTA
* *
54744090 CACAA-ATA
1 CATAACTTA
* * *
54744098 TATATCATA
1 CATAACTTA
54744107 TCATAACTTA
1 -CATAACTTA
54744117 CATAA--TA
1 CATAACTTA
*
54744124 CATAA-ATA
1 CATAACTTA
* * *
54744132 TATATCATA
1 CATAACTTA
54744141 TCATAACTTA
1 -CATAACTTA
54744151 CATAACTTA
1 CATAACTTA
54744160 CATAACTTA
1 CATAACTTA
*
54744169 TATAACTTA
1 CATAACTTA
* *
54744178 GATAA-ATA
1 CATAACTTA
*
54744186 TATAACTTA
1 CATAACTTA
*
54744195 CACAACTTTA
1 CATAAC-TTA
*
54744205 CATAA-ATA
1 CATAACTTA
* * *
54744213 TATATCATA
1 CATAACTTA
*
54744222 TCATATCTTA
1 -CATAACTTA
54744232 CATAACTTA
1 CATAACTTA
54744241 CATAATACTTA
1 CAT-A-ACTTA
* *
54744252 AAT-ATTTA
1 CATAACTTA
54744260 TCAT-A--T-
1 -CATAACTTA
*
54744266 CATATCTTA
1 CATAACTTA
54744275 CATAACTTA
1 CATAACTTA
*
54744284 CAAAACTTA
1 CATAACTTA
*
54744293 CTTAACTTA
1 CATAACTTA
54744302 CATAA
1 CATAA
54744307 TAAATAAATA
Statistics
Matches: 223, Mismatches: 46, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
5 3 0.01
7 8 0.04
8 38 0.17
9 140 0.63
10 27 0.12
11 7 0.03
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:54744058 original size:17 final size:17
Alignment explanation
Indices: 54744021--54744196 Score: 93
Period size: 17 Copynumber: 10.6 Consensus size: 17
54744011 CATAACTTAC
*
54744021 ATAACTTACATAACCTAT
1 ATAACTTACATAA-ATAT
*
54744039 ATAACTTAGATAAATAT
1 ATAACTTACATAAATAT
* *
54744056 ATAACATAGATAAATAT
1 ATAACTTACATAAATAT
54744073 ATAACTTAC--------
1 ATAACTTACATAAATAT
*
54744082 ATAACTTACACAAATAT
1 ATAACTTACATAAATAT
* * * *
54744099 ATATCATATCATAACTTAC
1 ATAACTTA-CATAA-ATAT
54744118 ATAA--TACATAAATAT
1 ATAACTTACATAAATAT
* * * *
54744133 ATATCATATCATAACTTAC
1 ATAACTTA-CATAA-ATAT
*
54744152 ATAACTTACATAACTTAT
1 ATAACTTACATAA-ATAT
*
54744170 ATAACTTAGATAAATAT
1 ATAACTTACATAAATAT
54744187 ATAACTTACA
1 ATAACTTACA
54744197 CAACTTTACA
Statistics
Matches: 122, Mismatches: 22, Indels: 29
0.71 0.13 0.17
Matches are distributed among these distances:
9 9 0.07
15 5 0.04
16 5 0.04
17 48 0.39
18 42 0.34
19 13 0.11
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAACTTACATAAATAT
Found at i:54744086 original size:43 final size:44
Alignment explanation
Indices: 54744007--54744209 Score: 189
Period size: 43 Copynumber: 4.6 Consensus size: 44
54743997 TATATATATC
* * *
54744007 ATATCATAACTTACATAACTTACATAACCTATATAACTTAGATAA
1 ATAT-ATAACATACATAACTTACATAACTTACATAACTTAGATAA
* * * * *
54744052 ATATATAACATAGATAA-ATATATAACTTACATAACTTACACAA
1 ATATATAACATACATAACTTACATAACTTACATAACTTAGATAA
* * * *
54744095 ATATATATCATATCATAACTTACATAA--TACATAA-ATATATATC
1 ATATATAACATA-CATAACTTACATAACTTACATAACTTAGATA-A
* *
54744138 ATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAA
1 ATAT-ATAACATACATAACTTACATAACTTACATAACTTAGATAA
* *
54744183 ATATATAACTTACACAACTTTACATAA
1 ATATATAACATACATAAC-TTACATAA
54744210 ATATATATCA
Statistics
Matches: 127, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
42 4 0.03
43 56 0.44
44 34 0.27
45 28 0.22
46 5 0.04
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (44 bp):
ATATATAACATACATAACTTACATAACTTACATAACTTAGATAA
Found at i:54744263 original size:43 final size:41
Alignment explanation
Indices: 54744207--54744292 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 41
54744197 CAACTTTACA
54744207 TAAATATATATCATATCATATCTTACATAACTTACATAATACT
1 TAAATATATATCATATCATATCTTACATAACTTACA-AA-ACT
*
54744250 TAAATATTTATCATATCATATCTTACATAACTTACAAAACT
1 TAAATATATATCATATCATATCTTACATAACTTACAAAACT
54744291 TA
1 TA
54744293 CTTAACTTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 5 0.12
42 2 0.05
43 35 0.83
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (41 bp):
TAAATATATATCATATCATATCTTACATAACTTACAAAACT
Found at i:54744291 original size:124 final size:129
Alignment explanation
Indices: 54743998--54744306 Score: 391
Period size: 124 Copynumber: 2.4 Consensus size: 129
54743988 TTAATGTTAT
*
54743998 ATATATATCATATCATAACTTACATAACTTACATAACCTATATAACTTAGATAAATATATAACAT
1 ATATATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACAT
* * * *
54744063 AGATAAATATATAACTTACATAACTTACACAAATATATATCATATCATAACTTACATAATACATA
66 ACACAAATATATAACATAAATAAC-TACAC-AATATATATCATATCATAACTTACATAATACATA
54744128 A
129 A
*
54744129 ATATATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTT
1 ATATATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACAT
* * * *
54744194 ACACAACT-T-T-ACATAAATATA-TA-TC-ATATCATATCTTA-CATAACTTACATAATACTTA
66 ACACAAATATATAACATAAATA-ACTACACAATAT-ATATCATATCATAACTTACATAATACATA
54744252 A
129 A
* * * *
54744253 ATATTTATCATATCATATCTTACATAACTTACAAAACTTACT-TAACTTACATAA
1 ATATATATCATATCATAACTTACATAACTTACATAACTTA-TATAACTTAGATAA
54744307 TAAATAAATA
Statistics
Matches: 161, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
124 72 0.45
125 8 0.05
126 1 0.01
127 2 0.01
128 7 0.04
129 2 0.01
130 1 0.01
131 68 0.42
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (129 bp):
ATATATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACAT
ACACAAATATATAACATAAATAACTACACAATATATATCATATCATAACTTACATAATACATAA
Found at i:54750051 original size:47 final size:47
Alignment explanation
Indices: 54749982--54750075 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
54749972 CATTGAATTT
54749982 TTGAAGTATCATTTAGATTTGCTGTTATTGGTTGGATTTGATGTTGC
1 TTGAAGTATCATTTAGATTTGCTGTTATTGGTTGGATTTGATGTTGC
*
54750029 TTGAAGTATCATTTAGGTTTGCTGTTATTGGTTGGATTTGATGTTGC
1 TTGAAGTATCATTTAGATTTGCTGTTATTGGTTGGATTTGATGTTGC
54750076 AGGAAGGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.49
Consensus pattern (47 bp):
TTGAAGTATCATTTAGATTTGCTGTTATTGGTTGGATTTGATGTTGC
Found at i:54757158 original size:42 final size:41
Alignment explanation
Indices: 54757097--54757258 Score: 119
Period size: 42 Copynumber: 3.9 Consensus size: 41
54757087 AGATACCAAT
* * * *
54757097 GCCATGTCCCAGACGTGGTCTTACATGGGATCTCACATCGAC
1 GCCATATCCCAGACATGGTCTTACA-GGAATCTCATATCGAC
* * * * *
54757139 GCCATATCCCAGATATGGTCTTATACGAAATCTCATTTCGAT
1 GCCATATCCCAGACATGGTCTTACA-GGAATCTCATATCGAC
* ** * * *
54757181 GCCATGTCCTTGACGTGGTCTTACACGAAGTCTCATATCAAC
1 GCCATATCCCAGACATGGTCTTACAGGAA-TCTCATATCGAC
* *
54757223 GCCATATCCCAGATATGGTTTTATACAGG-ATCTCAT
1 GCCATATCCCAGACATGG-TCT-TACAGGAATCTCAT
54757259 CAAACCAAAT
Statistics
Matches: 89, Mismatches: 28, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
41 2 0.02
42 79 0.89
43 3 0.03
44 5 0.06
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (41 bp):
GCCATATCCCAGACATGGTCTTACAGGAATCTCATATCGAC
Found at i:54757258 original size:84 final size:84
Alignment explanation
Indices: 54757095--54757248 Score: 229
Period size: 84 Copynumber: 1.8 Consensus size: 84
54757085 TAAGATACCA
* * *
54757095 ATGCCATGTCCCAGACGTGGTCTTACATGGGATCTCACATCGACGCCATATCCCAGATATGGTCT
1 ATGCCATGTCCCAGACGTGGTCTTACACGAGATCTCACATCAACGCCATATCCCAGATATGGTCT
54757160 TATACGAAATCTCATTTCG
66 TATACGAAATCTCATTTCG
** * *
54757179 ATGCCATGTCCTTGACGTGGTCTTACACGA-AGTCTCATATCAACGCCATATCCCAGATATGGTT
1 ATGCCATGTCCCAGACGTGGTCTTACACGAGA-TCTCACATCAACGCCATATCCCAGATATGGTC
54757243 TTATAC
65 TTATAC
54757249 AGGATCTCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
83 1 0.02
84 61 0.98
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (84 bp):
ATGCCATGTCCCAGACGTGGTCTTACACGAGATCTCACATCAACGCCATATCCCAGATATGGTCT
TATACGAAATCTCATTTCG
Found at i:54757523 original size:58 final size:57
Alignment explanation
Indices: 54757433--54757547 Score: 212
Period size: 58 Copynumber: 2.0 Consensus size: 57
54757423 CACAAACTTA
*
54757433 CCTCGGAACAAAATATGGACAATTAATTCGATTTAGTCCAAGATCTTGCTCTTTCCC
1 CCTCGGAACAAAATATGGACAATTAATTCGATTTAGTCCAAGATCTGGCTCTTTCCC
54757490 NCCTCGGAACAAAATATGGACAATTAATTCGATTTAGTCCAAGATCTGGCTCTTTCCC
1 -CCTCGGAACAAAATATGGACAATTAATTCGATTTAGTCCAAGATCTGGCTCTTTCCC
54757548 TGGTTGAAGC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (57 bp):
CCTCGGAACAAAATATGGACAATTAATTCGATTTAGTCCAAGATCTGGCTCTTTCCC
Found at i:54759485 original size:29 final size:27
Alignment explanation
Indices: 54759451--54759532 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 27
54759441 TGATTCATCC
54759451 ATGGAAAATAAAATAAAAAAATGATGAA
1 ATGGAAAATAAAATAAAAAAATGAT-AA
* *
54759479 ATTGGAAAGTGAAATAATAAAAGATGATAA
1 A-TGGAAAATAAAATAA-AAAA-ATGATAA
* * *
54759509 ATGATAAAAAAAAAGAAAAAAATG
1 ATG-GAAAATAAAATAAAAAAATG
54759533 TCATTTATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
28 4 0.09
29 19 0.44
30 15 0.35
31 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (27 bp):
ATGGAAAATAAAATAAAAAAATGATAA
Found at i:54762057 original size:271 final size:271
Alignment explanation
Indices: 54761572--54762117 Score: 975
Period size: 271 Copynumber: 2.0 Consensus size: 271
54761562 TTGGCCAATA
54761572 TTGGCATATAAATGCTTTAATTGTAACTAGCCATTGGAATGGCTTATGATGAATATGTTTGGTAT
1 TTGGCATATAAATGCTTTAATTGTAACTAGCCATTGGAATGGCTTATGATGAATATGTTTGGTAT
54761637 GCGTTTGAAATGGTTGATTGATAGAAATTATATTGGCATATTGATGATTGAATTAAGTTAGCATA
66 GCGTTTGAAATGGTTGATTGATAGAAATTATATTGGCATATTGATGATTGAATTAAGTTAGCATA
*
54761702 TTTGATAAGATATGCATATATGTGAACTTGGTAATTTAAGTAAATGTGTATACTTGATTATATGA
131 TTTGATAAGATATGCATATATGTGAACTTGGTAATTTAAGTAAATGTGTATACTTGATTATAAGA
*
54761767 GGTATTATATCATGTATAGGACTTGATTTTGAGTTGGGTTAAATGACCTATGATAGCTTGTGAAT
196 GGTATTATATCAGGTATAGGACTTGATTTTGAGTTGGGTTAAATGACCTATGATAGCTTGTGAAT
*
54761832 GTGTGAAAGTG
261 GTGTGAAACTG
* ** *
54761843 TTGGCATATAAATGCTTTAATTGTAATTAGTTATTGGAATGGCTTATGATGGATATGTTTGGTAT
1 TTGGCATATAAATGCTTTAATTGTAACTAGCCATTGGAATGGCTTATGATGAATATGTTTGGTAT
* *
54761908 GCGTTTGAAGTGGTTGATTGATAGAAATTATTTTGGCATATTGATGATTGAATTAAGTTAGCATA
66 GCGTTTGAAATGGTTGATTGATAGAAATTATATTGGCATATTGATGATTGAATTAAGTTAGCATA
** *
54761973 TTTGATAATCTATGCATATATGTGAACTTGGTAATTTAAGTAAGTGTGTATACTTGATTATAAGA
131 TTTGATAAGATATGCATATATGTGAACTTGGTAATTTAAGTAAATGTGTATACTTGATTATAAGA
54762038 GGTATTATATCAGGTATAGGACTTGATTTTGAGTTGGGTTAAATGACCTATGATAGCTTGTGAAT
196 GGTATTATATCAGGTATAGGACTTGATTTTGAGTTGGGTTAAATGACCTATGATAGCTTGTGAAT
*
54762103 GTGTTAAACTG
261 GTGTGAAACTG
54762114 TTGG
1 TTGG
54762118 TGTAGGAGGA
Statistics
Matches: 262, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
271 262 1.00
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.40
Consensus pattern (271 bp):
TTGGCATATAAATGCTTTAATTGTAACTAGCCATTGGAATGGCTTATGATGAATATGTTTGGTAT
GCGTTTGAAATGGTTGATTGATAGAAATTATATTGGCATATTGATGATTGAATTAAGTTAGCATA
TTTGATAAGATATGCATATATGTGAACTTGGTAATTTAAGTAAATGTGTATACTTGATTATAAGA
GGTATTATATCAGGTATAGGACTTGATTTTGAGTTGGGTTAAATGACCTATGATAGCTTGTGAAT
GTGTGAAACTG
Found at i:54766757 original size:28 final size:28
Alignment explanation
Indices: 54766694--54766819 Score: 191
Period size: 28 Copynumber: 4.5 Consensus size: 28
54766684 ATATTAAGTC
*
54766694 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
54766721 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
54766749 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
54766777 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
54766806 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54766820 CAATCTCATG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.24
28 51 0.55
29 19 0.21
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54774646 original size:29 final size:27
Alignment explanation
Indices: 54774628--54774697 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
54774618 ATATTAAGTC
54774628 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
54774655 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
54774683 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
54774698 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:54774691 original size:28 final size:28
Alignment explanation
Indices: 54774628--54774725 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
54774618 ATATTAAGTC
*
54774628 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
54774655 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
54774683 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
*
54774712 CGCGCACTTAGTGC
1 CGCACACTTAGTGC
54774726 CAATCTCATG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 22 0.35
28 23 0.37
29 18 0.29
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54776794 original size:56 final size:56
Alignment explanation
Indices: 54776727--54776838 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
54776717 CATCATAGGC
54776727 CTTCAGAATTTGGCCAAAATGACATGACACATATCACAAAATAACCAAGGCCCCTA
1 CTTCAGAATTTGGCCAAAATGACATGACACATATCACAAAATAACCAAGGCCCCTA
54776783 CTTCAGAATTTGGCCAAAATGACATGACACATATCACAAAATAACCAAGGCCCCTA
1 CTTCAGAATTTGGCCAAAATGACATGACACATATCACAAAATAACCAAGGCCCCTA
54776839 TACATGCCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (56 bp):
CTTCAGAATTTGGCCAAAATGACATGACACATATCACAAAATAACCAAGGCCCCTA
Found at i:54784537 original size:19 final size:20
Alignment explanation
Indices: 54784513--54784550 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
54784503 GGTACCACCA
54784513 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
54784532 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
54784551 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:54784889 original size:93 final size:93
Alignment explanation
Indices: 54784780--54784950 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
54784770 GCCCCTAAGT
* * * *
54784780 GAACTCGGACTTAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
54784845 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
54784873 GAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
54784938 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54784951 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54784947 original size:46 final size:46
Alignment explanation
Indices: 54784775--54784947 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
54784765 AACCCGCCCC
* * * * **
54784775 TAAGTGAACTCGGACTTAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
* *
54784821 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTACATCCA
* *
54784869 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
54784914 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54784948 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 7 0.07
44 2 0.02
45 2 0.02
46 59 0.55
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
Found at i:54785404 original size:30 final size:30
Alignment explanation
Indices: 54785370--54785429 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
54785360 ATTTAATATG
*
54785370 AACTTTAAAAAAATTCCACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
54785400 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
54785430 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:54793092 original size:38 final size:38
Alignment explanation
Indices: 54793049--54793130 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
54793039 TTCCTTATGA
54793049 CATGTTTTCTCATTGGTCAAGTTTTAATAAGCCTTTGT
1 CATGTTTTCTCATTGGTCAAGTTTTAATAAGCCTTTGT
*
54793087 CATGTTTTCTCATTGGTCAAGTTTTAATAAGTCTTTGT
1 CATGTTTTCTCATTGGTCAAGTTTTAATAAGCCTTTGT
54793125 CA-GTTT
1 CATGTTT
54793131 CAATTAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 4 0.09
38 39 0.91
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.49
Consensus pattern (38 bp):
CATGTTTTCTCATTGGTCAAGTTTTAATAAGCCTTTGT
Found at i:54795295 original size:42 final size:42
Alignment explanation
Indices: 54795248--54795339 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
54795238 TGGCCCTTAG
* ** *
54795248 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
54795290 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
54795332 GCCCATTT
1 GCCCATTT
54795340 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:54795580 original size:26 final size:26
Alignment explanation
Indices: 54795484--54795761 Score: 382
Period size: 26 Copynumber: 10.8 Consensus size: 26
54795474 CCTCTTTAAT
*
54795484 AACTGGGGCA-AAGCCCTTTTTGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* *
54795509 AACTAGGGCA-AAGCCCTTTTTGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
54795534 AACTGGGGCA-AAGCCTTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
54795559 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
54795585 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
54795611 GACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
54795637 GACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* *
54795663 GACTGGGGCATAAGCCCTTTTCGGTC
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
54795689 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
***
54795715 AACTGGGGCATAAGCCCTTTTTAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
54795741 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
54795762 GCACTTCCTC
Statistics
Matches: 232, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
25 54 0.23
26 178 0.77
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:54796645 original size:27 final size:27
Alignment explanation
Indices: 54796566--54796653 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
54796556 TATTCGTCAT
* * *
54796566 TTTACCATAC-AGGGGTATTACGGTCAC
1 TTTACCTTACAAGGGCT-TTACGGTCTC
* *
54796593 TTTACCCTACAGGGGCTTTACGGTCTC
1 TTTACCTTACAAGGGCTTTACGGTCTC
*
54796620 TTTACCTTACAAGGGCTTTACGGTCTT
1 TTTACCTTACAAGGGCTTTACGGTCTC
54796647 TTTACCT
1 TTTACCT
54796654 AATAGGGGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
27 49 0.92
28 4 0.08
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (27 bp):
TTTACCTTACAAGGGCTTTACGGTCTC
Found at i:54796726 original size:27 final size:27
Alignment explanation
Indices: 54796683--54797018 Score: 190
Period size: 27 Copynumber: 12.4 Consensus size: 27
54796673 TTTCATCCTA
* * *
54796683 CAAGGGTGTTTTGGTAAATTTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* **
54796710 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* ** * *
54796737 CAATGGTATTTCCATAATTTTTAGAAAGT
1 CAAGGGTATTTCGGTAA-TTTTACAAA-C
* ** ** *
54796766 CAAGGGTATTTCTGTAACATTGTAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * * *
54796793 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
** * *
54796820 TGAGGGTATTTCAGTAATTTCACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
*
54796847 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTCGGTAATTTTACAAAC
* * * * *
54796874 TAGGGGTATTTTGGTAATTTTACTAAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
**
54796901 TGAGGGTATTTCGGTAATTTTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* ** * * *
54796928 CAGGGGTATTTTAGCAATTTTATAGA-
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * ** *
54796954 CTAGGGTATTTTGGTAATTTTACTGAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * **
54796981 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
*
54797008 CAAGGGCATTT
1 CAAGGGTATTT
54797019 TAGTAATTCT
Statistics
Matches: 236, Mismatches: 68, Indels: 10
0.75 0.22 0.03
Matches are distributed among these distances:
26 22 0.09
27 187 0.79
28 13 0.06
29 14 0.06
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTCGGTAATTTTACAAAC
Found at i:54796855 original size:54 final size:54
Alignment explanation
Indices: 54796796--54797040 Score: 219
Period size: 54 Copynumber: 4.6 Consensus size: 54
54796786 TGTAAATTAG
* * *
54796796 GGGTATTTTGGTAATTTTACAAATTGA-GGGTATTTCAGTAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTAGTAATTTTACAAACCA
* * ***
54796849 GTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACTAATTGA
1 G-GGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTAGTAATTTTAC-AAACCA
* * * * * *
54796904 GGGTATTTCGGTAATTTTACAAA-CCAGGGGTATTTTAGCAATTTTATAGACTA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTAGTAATTTTACAAACCA
** * **
54796957 GGGTATTTTGGTAATTTTACTGATCGA-GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTAGTAATTTTACAAACC-A
* * * **
54797011 GGGCATTTTAGTAATTCTGTAAATCGAGGG
1 GGGTATTTTGGTAATTTTACAAATCGAGGG
54797041 TAAAACGGTA
Statistics
Matches: 153, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
53 44 0.29
54 103 0.67
55 6 0.04
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTAGTAATTTTACAAACCA
Found at i:54796888 original size:81 final size:81
Alignment explanation
Indices: 54796793--54797000 Score: 310
Period size: 81 Copynumber: 2.6 Consensus size: 81
54796783 CATTGTAAAT
* * *
54796793 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTT
1 TAGGGGTATTTTGGTAATTTTACTAATTGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTT
* *
54796858 TGGTAATTTTACAAAC
66 TAGCAATTTTACAAAC
*
54796874 TAGGGGTATTTTGGTAATTTTACTAATTGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTT
1 TAGGGGTATTTTGGTAATTTTACTAATTGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTT
* *
54796939 TAGCAATTTTATAGAC
66 TAGCAATTTTACAAAC
* * *
54796955 TA-GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTT
1 TAGGGGTATTTTGGTAATTTTACTAATTGAGGGTATTTCGGTAATTT
54797001 TGTAAACCAA
Statistics
Matches: 116, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
80 41 0.35
81 75 0.65
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (81 bp):
TAGGGGTATTTTGGTAATTTTACTAATTGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTT
TAGCAATTTTACAAAC
Found at i:54797104 original size:27 final size:27
Alignment explanation
Indices: 54796796--54797134 Score: 179
Period size: 27 Copynumber: 12.6 Consensus size: 27
54796786 TGTAAATTAG
* * *
54796796 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTCTATAAATCGA
** * *
54796823 GGGTATTTCAGTAATT-TCACAAA-CCA
1 GGGTATTTTGGTAATTCT-ATAAATCGA
* * *
54796849 GTGGTATTTTGGTAATTTTACAAA-CTA
1 G-GGTATTTTGGTAATTCTATAAATCGA
* *
54796876 GGGGTATTTTGGTAATTTTACT-AATTGA
1 -GGGTATTTTGGTAATTCTA-TAAATCGA
* * * *
54796904 GGGTATTTCGGTAATTTTACAAA-CCA
1 GGGTATTTTGGTAATTCTATAAATCGA
* * * * *
54796930 GGGGTATTTTAGCAATTTTATAGA-CTA
1 -GGGTATTTTGGTAATTCTATAAATCGA
* *
54796957 GGGTATTTTGGTAATTTTACT-GATCGA
1 GGGTATTTTGGTAATTCTA-TAAATCGA
* * * *
54796984 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTCTATAAATCGA
* * *
54797011 GGGCATTTTAGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTCTATAAATCGA
****
54797038 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTCTATAAATCGA
****
54797065 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTCTATAAATCGA
* * * * *
54797092 GGGTACTTTGGTAATTTTACAATTTGA
1 GGGTATTTTGGTAATTCTATAAATCGA
*
54797119 GGGTATTTTAGTAATT
1 GGGTATTTTGGTAATT
54797135 TGGTAAACTA
Statistics
Matches: 252, Mismatches: 49, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
26 24 0.10
27 225 0.89
28 3 0.01
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTCTATAAATCGA
Found at i:54797133 original size:54 final size:53
Alignment explanation
Indices: 54796796--54797135 Score: 211
Period size: 54 Copynumber: 6.3 Consensus size: 53
54796786 TGTAAATTAG
* * ** * * ***
54796796 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTATAATTGA
* *
54796849 GTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACTAATTGA
1 G-GGTATTTTGGTAATTTTATAAATCGA-GGGTATTTTGGTAATTTTA-TAATTGA
* * * * * *
54796904 GGGTATTTCGGTAATTTTACAAA-CCAGGGGTATTTTAGCAATTTTATAGACT-A
1 GGGTATTTTGGTAATTTTATAAATCGA-GGGTATTTTGGTAATTTTATA-ATTGA
* * ***
54796957 GGGTATTTTGGTAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTA-TAAATCGAGGGTATTTTGGTAATTTTAT-AATTGA
* * * * **** * *
54797011 GGGCATTTTAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTAT-AATTGA
**** * * *
54797065 GGGTAAAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAATTTGA
1 GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTATAA-TTGA
*
54797119 GGGTATTTTAGTAATTT
1 GGGTATTTTGGTAATTT
54797136 GGTAAACTAA
Statistics
Matches: 222, Mismatches: 55, Indels: 19
0.75 0.19 0.06
Matches are distributed among these distances:
53 46 0.21
54 172 0.77
55 4 0.02
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTATAATTGA
Found at i:54805342 original size:27 final size:27
Alignment explanation
Indices: 54805320--54805462 Score: 169
Period size: 27 Copynumber: 5.3 Consensus size: 27
54805310 AGAATTACTG
**
54805320 AAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCTTGGTTTGTAAAATTACCA
* *
54805347 AAATACCCCTAGTTTGTAAAATTACCA
1 AAATACCCTTGGTTTGTAAAATTACCA
54805374 AAATACCCTTGGTTTGTAAAATTACCA
1 AAATACCCTTGGTTTGTAAAATTACCA
* ** *
54805401 AAATACCCCTAATTTGTGAAATTACCA
1 AAATACCCTTGGTTTGTAAAATTACCA
****
54805428 AAATACCCTCAACTTGTAAAATTACCA
1 AAATACCCTTGGTTTGTAAAATTACCA
*
54805455 AAGTACCC
1 AAATACCC
54805463 CCGATTTACA
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 101 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATACCCTTGGTTTGTAAAATTACCA
Found at i:54805395 original size:54 final size:54
Alignment explanation
Indices: 54805320--54805463 Score: 207
Period size: 54 Copynumber: 2.7 Consensus size: 54
54805310 AGAATTACTG
** *
54805320 AAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCA
1 AAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCA
*
54805374 AAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACCA
1 AAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCA
**** *
54805428 AAATACCCTCAACTTGTAAAATTACCAAAGTACCCC
1 AAATACCCTTGGTTTGTAAAATTACCAAAATACCCC
54805464 CGATTTACAG
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (54 bp):
AAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCA
Found at i:54805515 original size:27 final size:27
Alignment explanation
Indices: 54805445--54805517 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
54805435 CTCAACTTGT
*
54805445 AAAATTA-CCAAAGTACCCCCGATTTAC
1 AAAATTATCGAAA-TACCCCCGATTTAC
* *** *
54805472 AGAATTATCGTTTTACCCTCGATTTAC
1 AAAATTATCGAAATACCCCCGATTTAC
*
54805499 AAAATTATTGAAATACCCC
1 AAAATTATCGAAATACCCC
54805518 TATAGGGTAG
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (27 bp):
AAAATTATCGAAATACCCCCGATTTAC
Found at i:54805567 original size:54 final size:54
Alignment explanation
Indices: 54805509--54805616 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
54805499 AAAATTATTG
*
54805509 AAATACCCCTATAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAAA-TACCA
1 AAATACCCCTATAGGGTAGAATTACCGAAATACCCTTGTAGGGTA-AAATTACCA
* *
54805563 AAATACCCCTATAGGGTAGAATTACCGAGATACCCTTGTGGGGTAAAATTACCA
1 AAATACCCCTATAGGGTAGAATTACCGAAATACCCTTGTAGGGTAAAATTACCA
54805617 TTTTGCCCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 3 0.06
54 47 0.94
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (54 bp):
AAATACCCCTATAGGGTAGAATTACCGAAATACCCTTGTAGGGTAAAATTACCA
Found at i:54805606 original size:27 final size:27
Alignment explanation
Indices: 54805508--54805615 Score: 126
Period size: 27 Copynumber: 4.0 Consensus size: 27
54805498 CAAAATTATT
* * *
54805508 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
*
54805535 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
54805562 AAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
54805589 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
54805616 ATTTTGCCCT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:54806431 original size:27 final size:27
Alignment explanation
Indices: 54806348--54806452 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 27
54806338 ATTCTGTTAA
* *
54806348 GTGGCTTTGCCACAATATCTGTTGC-TA
1 GTGGCTCTGCCACAATATCTGTT-CATG
*
54806375 GTGGCTATGCCACAAATATCTGTTCA-G
1 GTGGCTCTGCCAC-AATATCTGTTCATG
54806402 GTGGCTCTGCCACAATATCTGTAT-ATG
1 GTGGCTCTGCCACAATATCTGT-TCATG
* *
54806429 GTGACTCTGTCACAATATCTGTTC
1 GTGGCTCTGCCACAATATCTGTTC
54806453 TGGCAACCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.16
27 47 0.69
28 10 0.15
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTCATG
Found at i:54806443 original size:54 final size:53
Alignment explanation
Indices: 54806340--54806452 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 53
54806330 TGCCACGTAT
* * *
54806340 TCTGTT-AAGTGGCTTTGCCACAATATCTGTTGCTAGTGGCTATGCCACAAATA
1 TCTGTTCAAGTGGCTCTGCCACAATATCTGTTGATAGTGACTATGCCAC-AATA
* * * *
54806393 TCTGTTCAGGTGGCTCTGCCACAATATCTGTAT-ATGGTGACTCTGTCACAATA
1 TCTGTTCAAGTGGCTCTGCCACAATATCTGT-TGATAGTGACTATGCCACAATA
54806446 TCTGTTC
1 TCTGTTC
54806453 TGGCAACCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
53 17 0.33
54 33 0.65
55 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (53 bp):
TCTGTTCAAGTGGCTCTGCCACAATATCTGTTGATAGTGACTATGCCACAATA
Found at i:54806582 original size:6 final size:6
Alignment explanation
Indices: 54806573--54806793 Score: 112
Period size: 6 Copynumber: 35.8 Consensus size: 6
54806563 TTGCATTCAC
* * * * *
54806573 ATTCTG ATTCTA ATTCTG -TTACCTG ATACAG ATTCTG ATTCT- ATCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
*
54806623 ATTCTG ATTCTG ATTCTG ATTTTG ATTCTG ATTCTG ATTCTG -TTACCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * * * * *
54806672 ATACTG ATTGTA ATTCTG -TCACCTA ACTCTG ATTCTA ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* ** * * *
54806721 ATTCTG ATCCTG -TTACTTG ACACTG ATTTTG ATTCTG -TCACCTA ATTCTG
1 ATTCTG ATTCTG ATT-C-TG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
*
54806771 ATTCTG ATTCTG ACTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
54806794 ACCACCTGAT
Statistics
Matches: 158, Mismatches: 39, Indels: 36
0.68 0.17 0.15
Matches are distributed among these distances:
5 9 0.06
6 129 0.82
7 15 0.09
8 5 0.03
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.45
Consensus pattern (6 bp):
ATTCTG
Found at i:54806606 original size:25 final size:25
Alignment explanation
Indices: 54806576--54806714 Score: 122
Period size: 25 Copynumber: 5.6 Consensus size: 25
54806566 CATTCACATT
54806576 CTGATTCTAATTCTGTTACCTGATA
1 CTGATTCTAATTCTGTTACCTGATA
* * * * * *
54806601 CAGATTCTGATTCTATCACCTAATT
1 CTGATTCTAATTCTGTTACCTGATA
* * *
54806626 CTGATTCTGATTCTGATT--TTGATT
1 CTGATTCTAATTCTG-TTACCTGATA
*
54806650 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTAATTCTGTTACCTGATA
* * *
54806675 CTGATTGTAATTCTGTCACCTAACT-
1 CTGATTCTAATTCTGTTACCTGA-TA
54806700 CTGATTCTAATTCTG
1 CTGATTCTAATTCTG
54806715 ATTCTGATTC
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.02
24 19 0.21
25 69 0.75
26 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (25 bp):
CTGATTCTAATTCTGTTACCTGATA
Found at i:54806663 original size:74 final size:74
Alignment explanation
Indices: 54806573--54806793 Score: 292
Period size: 74 Copynumber: 3.1 Consensus size: 74
54806563 TTGCATTCAC
* * *
54806573 ATTCTGATTCTAATTCTGTTACCTGATACAGATTCTGATTCTATCACCTAATTCTGATTCTGATT
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTGATTCTGATT
*
54806638 CTGATTTTG
66 CTGATTCTG
* *
54806647 ATTCTGATTCTGATTCTGTTACCTGATACTGATTGTAATTCTGTCACCTAA--C----TCTGATT
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTGATTCTGATT
*
54806706 CTAATTCTG
66 CTGATTCTG
* * * *
54806715 ATTCTGATTCTGATCCTGTTACTTGACACTGATTTTGATTCTGTCACCTAATTCTGATTCTGATT
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTGATTCTGATT
*
54806780 CTGACTCTG
66 CTGATTCTG
54806789 ATTCT
1 ATTCT
54806794 ACCACCTGAT
Statistics
Matches: 127, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
68 60 0.47
70 1 0.01
72 1 0.01
74 65 0.51
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.45
Consensus pattern (74 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTGATTCTGATT
CTGATTCTG
Found at i:54806703 original size:68 final size:68
Alignment explanation
Indices: 54806573--54806793 Score: 271
Period size: 68 Copynumber: 3.2 Consensus size: 68
54806563 TTGCATTCAC
* * *
54806573 ATTCTGATTCTAATTCTGTTACCTGATACAGATTCTGATTCTATCACCTAATTCTGATTCTGATT
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAA--C----TCTGATT
*
54806638 CTGATTTTG
60 CTGATTCTG
* * *
54806647 ATTCTGATTCTGATTCTGTTACCTGATACTGATTGTAATTCTGTCACCTAACTCTGATTCTAATT
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAACTCTGATTCTGATT
54806712 CTG
66 CTG
* * * * *
54806715 ATTCTGATTCTGATCCTGTTACTTGACACTGATTTTGATTCTGTCACCTAATTCTGATTCTGATT
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAACTCTGATTCTGATT
54806780 CTG
66 CTG
*
54806783 ACTCTGATTCT
1 ATTCTGATTCT
54806794 ACCACCTGAT
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
68 85 0.64
72 1 0.01
74 46 0.35
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.45
Consensus pattern (68 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAACTCTGATTCTGATT
CTG
Found at i:54806828 original size:37 final size:37
Alignment explanation
Indices: 54806743--54806831 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
54806733 TTACTTGACA
** *
54806743 CTGATTTTGATTCTGTCACCTAATTCTGATTCTGATT
1 CTGATTTTGATTCTACCACCTAATTCTGATTCTGATC
* * * *
54806780 CTGACTCTGATTCTACCACCTGATTTTGATTCTGATC
1 CTGATTTTGATTCTACCACCTAATTCTGATTCTGATC
*
54806817 CTTATTTTGATTCTA
1 CTGATTTTGATTCTA
54806832 GTTCTGATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.47
Consensus pattern (37 bp):
CTGATTTTGATTCTACCACCTAATTCTGATTCTGATC
Found at i:54808745 original size:27 final size:27
Alignment explanation
Indices: 54808723--54808865 Score: 153
Period size: 27 Copynumber: 5.3 Consensus size: 27
54808713 AGAATTACTG
* **
54808723 AAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCATGGTTTGTAAAATTACCA
* * *
54808750 AAATACCCCTGCTTTGTAAAATTACCC
1 AAATACCCATGGTTTGTAAAATTACCA
54808777 AAATACCCATGGTTTGTAAAATTACCA
1 AAATACCCATGGTTTGTAAAATTACCA
* * * *
54808804 AAATACCCCTGATGTGTGAAATTACCA
1 AAATACCCATGGTTTGTAAAATTACCA
**
54808831 AAATACCC-TCGACTTGTAAAATTACCA
1 AAATACCCAT-GGTTTGTAAAATTACCA
*
54808858 AAGTACCC
1 AAATACCC
54808866 CCAATTTATA
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 98 0.99
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.27
Consensus pattern (27 bp):
AAATACCCATGGTTTGTAAAATTACCA
Found at i:54808798 original size:54 final size:53
Alignment explanation
Indices: 54808723--54808866 Score: 180
Period size: 54 Copynumber: 2.7 Consensus size: 53
54808713 AGAATTACTG
** * * *
54808723 AAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGCTTTGTAAAATTACCC
1 AAATACCC-TGGTTTGTAAAATTACCAAAATACCCCTGATGTGTAAAATTACCA
*
54808777 AAATACCCATGGTTTGTAAAATTACCAAAATACCCCTGATGTGTGAAATTACCA
1 AAATACCC-TGGTTTGTAAAATTACCAAAATACCCCTGATGTGTAAAATTACCA
** *
54808831 AAATACCCTCGACTTGTAAAATTACCAAAGTACCCC
1 AAATACCCT-GGTTTGTAAAATTACCAAAATACCCC
54808867 CAATTTATAG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 78 0.99
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (53 bp):
AAATACCCTGGTTTGTAAAATTACCAAAATACCCCTGATGTGTAAAATTACCA
Found at i:54808880 original size:27 final size:27
Alignment explanation
Indices: 54808740--54808884 Score: 78
Period size: 27 Copynumber: 5.4 Consensus size: 27
54808730 CTTGGTTTAC
** *
54808740 AAAATTACCAAAATA-CCCCTGCTTTGT
1 AAAATTACCAAAATACCCCCAAC-TTAT
* ***** *
54808767 AAAATTACCCAAATACCCATGGTTTGT
1 AAAATTACCAAAATACCCCCAACTTAT
** *
54808794 AAAATTACCAAAATACCCCTGA-TGTGT
1 AAAATTACCAAAATACCCCCAACT-TAT
* * * *
54808821 GAAATTACCAAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCCCAACTTAT
* *
54808848 AAAATTACCAAAGTACCCCCAATTTAT
1 AAAATTACCAAAATACCCCCAACTTAT
*
54808875 AGAATTACCA
1 AAAATTACCA
54808885 TTTTACCCTC
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.01
27 92 0.95
28 4 0.04
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCCAACTTAT
Found at i:54808881 original size:54 final size:54
Alignment explanation
Indices: 54808740--54808884 Score: 168
Period size: 54 Copynumber: 2.7 Consensus size: 54
54808730 CTTGGTTTAC
* * * **
54808740 AAAATTACCAAAATACCCCTGCTTTGTAAAATTACCCAAATACCCATGGTTTGT
1 AAAATTACCAAAATACCCCTGATTTGTAGAATTACCAAAATACCCATGACTTGT
*
54808794 AAAATTACCAAAATACCCCTGATGTGT-GAAATTACCAAAATACCC-TCGACTTGT
1 AAAATTACCAAAATACCCCTGATTTGTAG-AATTACCAAAATACCCAT-GACTTGT
* ** *
54808848 AAAATTACCAAAGTACCCCCAATTTATAGAATTACCA
1 AAAATTACCAAAATACCCCTGATTTGTAGAATTACCA
54808885 TTTTACCCTC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 1 0.01
54 75 0.97
55 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTGATTTGTAGAATTACCAAAATACCCATGACTTGT
Found at i:54808934 original size:27 final size:27
Alignment explanation
Indices: 54808911--54809045 Score: 182
Period size: 27 Copynumber: 5.0 Consensus size: 27
54808901 CAAAATTATT
* *
54808911 GAAATACCTCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
54808938 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
54808965 AAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
54808992 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
54809019 GAGATACCCTTGT-GAGGTAAAATTACC
1 GAAATACCCCTGTAG-GGTAGAATTACC
54809046 ATTTTGCCCT
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 95 0.99
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:54809055 original size:27 final size:27
Alignment explanation
Indices: 54809025--54809086 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
54809015 TACCGAGATA
*
54809025 CCCTTGTGAG-GTAAAATTACCATTTTG
1 CCCTTGTG-GTGTAAAATGACCATTTTG
* * *
54809052 CCCTAG-GGTGTTAAATGACTATTTTG
1 CCCTTGTGGTGTAAAATGACCATTTTG
54809078 CCCTTGTGG
1 CCCTTGTGG
54809087 GCAAGTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 1 0.04
26 20 0.71
27 7 0.25
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (27 bp):
CCCTTGTGGTGTAAAATGACCATTTTG
Found at i:54809598 original size:22 final size:22
Alignment explanation
Indices: 54809573--54809621 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
54809563 ATGGCTTTAC
54809573 GCCAACCT-ACATATGGCTCTGT
1 GCCAACCTGA-ATATGGCTCTGT
* *
54809595 GCCAACCTGATTATGGCTGTGT
1 GCCAACCTGAATATGGCTCTGT
54809617 GCCAA
1 GCCAA
54809622 ACGTATTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (22 bp):
GCCAACCTGAATATGGCTCTGT
Found at i:54809809 original size:27 final size:27
Alignment explanation
Indices: 54809779--54809887 Score: 96
Period size: 27 Copynumber: 4.1 Consensus size: 27
54809769 TATTCTGTTA
*
54809779 AGTGGCTTTGCCACATTATCTGTTTCT
1 AGTGGCTTTGCCACAATATCTGTTTCT
*
54809806 AGTGGCTATGCCACAAATATCTG-TTCT
1 AGTGGCTTTGCCAC-AATATCTGTTTCT
* * * *
54809833 GGTAGTTTTGCCACAATATCTGTATCT
1 AGTGGCTTTGCCACAATATCTGTTTCT
* * * **
54809860 GGTGACTCTATCACAATATCTG-TTCT
1 AGTGGCTTTGCCACAATATCTGTTTCT
54809886 AG
1 AG
54809888 CAGGCATGCT
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
26 12 0.18
27 46 0.71
28 7 0.11
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (27 bp):
AGTGGCTTTGCCACAATATCTGTTTCT
Found at i:54810016 original size:6 final size:6
Alignment explanation
Indices: 54810005--54810228 Score: 122
Period size: 6 Copynumber: 36.3 Consensus size: 6
54809995 TTGCGTTCAC
* *
54810005 ATTCTG ATTCTG ATTCTG ATTCTG -TTACCTG ATACAG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
* * * *
54810054 -TCACCTA ATTTTG ATTCTG ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* * * *
54810104 ATTCTG ATTTTG -TCACCTA ACTCTG ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
54810153 -TTACTTG ATACTG ATTCTG ATTCT- -TTCACCTA ATTTTG ATTTTG ATTCTG
1 ATT-C-TG ATTCTG ATTCTG ATTCTG ATT---CTG ATTCTG ATTCTG ATTCTG
* *
54810203 ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
54810229 AATGTTTCTT
Statistics
Matches: 167, Mismatches: 29, Indels: 44
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.01
5 9 0.05
6 135 0.81
7 15 0.09
8 4 0.02
9 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:54810036 original size:25 final size:25
Alignment explanation
Indices: 54810008--54810202 Score: 120
Period size: 25 Copynumber: 7.8 Consensus size: 25
54809998 CGTTCACATT
54810008 CTGATTCTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGATTCTGTTAC
* * *
54810033 CTGATACAGATTCTGATTCTGTCAC
1 CTGATTCTGATTCTGATTCTGTTAC
* *
54810058 CTAATTTTGATTCTGATTCTGATT--
1 CTGATTCTGATTCTGATTCTG-TTAC
*
54810082 CTGATTCTG-TTACCTGATACTGATT--
1 CTGATTCTGATT--CTGATTCTG-TTAC
* * * *
54810107 CTGATTTTG-TCACCTAACTCTGATT--
1 CTGATTCTGAT--TCTGATTCTG-TTAC
54810132 CTGATTCTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGATTCTGTTAC
* *
54810157 TTGATACTGATTCTGATTCT-TTCAC
1 CTGATTCTGATTCTGATTCTGTT-AC
* * *
54810182 CTAATTTTGATTTTGATTCTG
1 CTGATTCTGATTCTGATTCTG
54810203 ATTCTCATTT
Statistics
Matches: 133, Mismatches: 27, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
23 4 0.03
24 16 0.12
25 111 0.83
26 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (25 bp):
CTGATTCTGATTCTGATTCTGTTAC
Found at i:54810074 original size:37 final size:37
Alignment explanation
Indices: 54810033--54810111 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
54810023 ATTCTGTTAC
**
54810033 CTGATACAGATTCTGATTCTGTCACCTAATTTTGATT
1 CTGATACAGATTCTGATTCTGTCACCTAATACTGATT
* * * *
54810070 CTGATTCTGATTCTGATTCTGTTACCTGATACTGATT
1 CTGATACAGATTCTGATTCTGTCACCTAATACTGATT
54810107 CTGAT
1 CTGAT
54810112 TTTGTCACCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (37 bp):
CTGATACAGATTCTGATTCTGTCACCTAATACTGATT
Found at i:54810107 original size:62 final size:62
Alignment explanation
Indices: 54810005--54810207 Score: 343
Period size: 62 Copynumber: 3.3 Consensus size: 62
54809995 TTGCGTTCAC
*
54810005 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACAGATTCTGATTCTGTCACCTAATTTTG
1 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTTTG
* * *
54810067 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTTTGTCACCTAACTCTG
1 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTTTG
* *
54810129 ATTCTGATTCTGATTCTGATTCTGTTACTTGATACTGATTCTGATTCTTTCACCTAATTTTG
1 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTTTG
*
54810191 ATTTTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
54810208 CATTTTGATT
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 131 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.48
Consensus pattern (62 bp):
ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTTTG
Found at i:54810112 original size:37 final size:37
Alignment explanation
Indices: 54810041--54810176 Score: 118
Period size: 37 Copynumber: 4.0 Consensus size: 37
54810031 ACCTGATACA
* **
54810041 GATTCTGATTCTGTCACCTAATTTTGATTCTGATTCT
1 GATTCTGATTCTGTTACCTAATACTGATTCTGATTCT
*
54810078 GATTCTGATTCTGTTACCTGATACTGATTCTGA---T
1 GATTCTGATTCTGTTACCTAATACTGATTCTGATTCT
54810112 --TT-TG--TC----ACCTAACT-CTGATTCTGATTCT
1 GATTCTGATTCTGTTACCTAA-TACTGATTCTGATTCT
* *
54810140 GATTCTGATTCTGTTACTTGATACTGATTCTGATTCT
1 GATTCTGATTCTGTTACCTAATACTGATTCTGATTCT
54810177 TTCACCTAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 28
0.69 0.06 0.25
Matches are distributed among these distances:
25 15 0.19
26 1 0.01
28 1 0.01
29 2 0.03
30 2 0.03
31 4 0.05
32 2 0.03
33 2 0.03
34 1 0.01
36 1 0.01
37 47 0.60
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (37 bp):
GATTCTGATTCTGTTACCTAATACTGATTCTGATTCT
Found at i:54813943 original size:40 final size:40
Alignment explanation
Indices: 54813843--54814014 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
54813833 GCTCCTCGTT
* * *
54813843 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
54813883 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
54813922 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
54813962 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
54814002 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54814015 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54821910 original size:39 final size:40
Alignment explanation
Indices: 54821865--54822049 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
54821855 GCTCCTCGTT
* * *
54821865 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
54821905 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
54821944 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
54821984 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
54822025 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
54822050 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54821965 original size:40 final size:39
Alignment explanation
Indices: 54821832--54822049 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
54821822 AAATCACGTA
* * **
54821832 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
54821871 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
54821910 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
54821950 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
54821990 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
54822030 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
54822050 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:54829097 original size:43 final size:42
Alignment explanation
Indices: 54829050--54829191 Score: 119
Period size: 43 Copynumber: 3.3 Consensus size: 42
54829040 TCTTGCATGT
*
54829050 AATCAAATATCAATGCCACTATCCCAGACAGGGTCTTACACAA
1 AATCAAATATCAATGCCA-TGTCCCAGACAGGGTCTTACACAA
* * * * * *
54829093 AATCAAAT-GCGATGACGATGTCCCAAACATGGTCTTACATGAA
1 AATCAAATATCAATG-CCATGTCCCAGACAGGGTCTTACA-CAA
* *
54829136 AATCTCAA-ATCAATGCCAATGTCCCAGAC-GTGGTCTTACACGA
1 AATC-AAATATCAATGCC-ATGTCCCAGACAG-GGTCTTACACAA
*
54829179 AATCACATATCAA
1 AATCAAATATCAA
54829192 AAATTCTATG
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
42 23 0.31
43 27 0.36
44 25 0.33
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (42 bp):
AATCAAATATCAATGCCATGTCCCAGACAGGGTCTTACACAA
Found at i:54829129 original size:42 final size:41
Alignment explanation
Indices: 54829071--54829183 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 41
54829061 AATGCCACTA
* * *
54829071 TCCCAGACAGGGTCTTACACAAAATCAAATGCGATGACGATG
1 TCCCAGACATGGTCTTACACAAAATCAAAT-CAATGACAATG
* * *
54829113 TCCCAAACATGGTCTTACATGAAAATCTCAAATCAATGCCAATG
1 TCCCAGACATGGTCTTACA-CAAAA--TCAAATCAATGACAATG
* *
54829157 TCCCAGACGTGGTCTTACACGAAATCA
1 TCCCAGACATGGTCTTACACAAAATCA
54829184 CATATCAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
41 3 0.05
42 17 0.29
43 7 0.12
44 25 0.43
45 6 0.10
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (41 bp):
TCCCAGACATGGTCTTACACAAAATCAAATCAATGACAATG
Found at i:54832852 original size:39 final size:39
Alignment explanation
Indices: 54832798--54832872 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
54832788 TTTAAGTCTC
54832798 CTTCACCGAAACTCCATAGTTTCAACTTCTCCAAGCAGA
1 CTTCACCGAAACTCCATAGTTTCAACTTCTCCAAGCAGA
* *
54832837 CTTCACTGAAACTCCATAGTTTCAACTTCTCTAAGC
1 CTTCACCGAAACTCCATAGTTTCAACTTCTCCAAGC
54832873 TTCGGTCTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (39 bp):
CTTCACCGAAACTCCATAGTTTCAACTTCTCCAAGCAGA
Found at i:54834997 original size:46 final size:46
Alignment explanation
Indices: 54834848--54835006 Score: 176
Period size: 46 Copynumber: 3.4 Consensus size: 46
54834838 TCACTGGTGT
* * * * * *
54834848 GAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCACAATATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
* *
54834894 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* * * *
54834942 GTGCTAGTGTAAGACATGTTTGGGACATGCATCAGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
54834989 -AGCCAGTGTAAGACATGT
1 GAGCCAGTGTAAGACATGT
54835007 GTAACACCCT
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
46 43 0.46
47 28 0.30
48 23 0.24
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:54837006 original size:29 final size:29
Alignment explanation
Indices: 54836974--54837071 Score: 144
Period size: 29 Copynumber: 3.4 Consensus size: 29
54836964 TTTGGGTCGG
54836974 ATGGGCCATATGAACGTGATTTGGGCCTA
1 ATGGGCCATATGAACGTGATTTGGGCCTA
54837003 ATGGGCCATATGAACGTGATTTGGGCCTA
1 ATGGGCCATATGAACGTGATTTGGGCCTA
* * *
54837032 ATAGGCCATATGAATGAGA-TTGGGCCTA
1 ATGGGCCATATGAACGTGATTTGGGCCTA
* *
54837060 GTGGGCAATATG
1 ATGGGCCATATG
54837072 CATGTATGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 18 0.29
29 45 0.71
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.27
Consensus pattern (29 bp):
ATGGGCCATATGAACGTGATTTGGGCCTA
Found at i:54838606 original size:46 final size:49
Alignment explanation
Indices: 54838488--54838613 Score: 159
Period size: 46 Copynumber: 2.6 Consensus size: 49
54838478 CGAGATGTGT
* * *
54838488 CAGTGTAAGACCATGTCTAGGACATGGCATCGGCACGAATAGGTGAGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATC-GCACGAATAGATAAGAGC
* * *
54838538 TAGTGTAAGACCATGTCTGGGACATGGCATC-CTCG-AT-GATAATAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGCACGAATAGATAAGAGC
*
54838584 CAGTGTAAGACCATGTCCGGGACATGGCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCAT
54838614 TAGCAACTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 34 0.50
47 2 0.03
48 3 0.04
50 29 0.43
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGCACGAATAGATAAGAGC
Found at i:54841571 original size:29 final size:30
Alignment explanation
Indices: 54841539--54841601 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
54841529 CACGGGCCGC
*
54841539 CACATGGTTGTGTGCCACACACG-CCACCT
1 CACATGGTCGTGTGCCACACACGACCACCT
* *
54841568 CACATGGTCGTGTGCCATACACGACCACTT
1 CACATGGTCGTGTGCCACACACGACCACCT
54841598 CACA
1 CACA
54841602 CGACCATGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.21
Consensus pattern (30 bp):
CACATGGTCGTGTGCCACACACGACCACCT
Found at i:54842897 original size:43 final size:43
Alignment explanation
Indices: 54842850--54842937 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
54842840 TCTTAGTGAT
54842850 TTTTATTATTTATGCCTCATTACCTTAAGCACTGATGGTTGAA
1 TTTTATTATTTATGCCTCATTACCTTAAGCACTGATGGTTGAA
*
54842893 TTTTATTATTTATGTCTCATTACCTTAAGCACTGATGGTTGAA
1 TTTTATTATTTATGCCTCATTACCTTAAGCACTGATGGTTGAA
54842936 TT
1 TT
54842938 ACTTGATTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (43 bp):
TTTTATTATTTATGCCTCATTACCTTAAGCACTGATGGTTGAA
Found at i:54846888 original size:163 final size:163
Alignment explanation
Indices: 54846611--54846927 Score: 465
Period size: 163 Copynumber: 1.9 Consensus size: 163
54846601 CAAAACCAAA
* * * * *
54846611 TCATTAGATGGATTTTATTGCTCCAAGAATTCAACATCGAGATTCGAGACAAGAAGGGATGCAGA
1 TCATTAGATGGAATTTACTACTCCAAGAATTCAACATCAAGATTCGAGACAAGAAAGGATGCAGA
*
54846676 AACTTAGTGGCTAACCACTTGAGTAGGTTAAAAACACCTTGTAATGACACTCCTATAAAGGATGA
66 AACTTAGTGGCTAACCACATGAGTAGGTTAAAAACACCTTGTAATGACACTCCTATAAAGGATGA
54846741 GTTTCCTGATGAGGGCCTATTTTCGACCAAGAC
131 GTTTCCTGATGAGGGCCTATTTTCGACCAAGAC
* * * * *
54846774 TCATTAGATGGAATTTACTACTTCAAGAATTCGACATCAAGCTTCGAGATACGAAAGGATGC-GA
1 TCATTAGATGGAATTTACTACTCCAAGAATTCAACATCAAGATTCGAGACAAGAAAGGATGCAG-
* * * *
54846838 AAACTTGGTGGTTGACCACATGAGTAGGTTAAAAACACCTTGTGATGACACTCCTATAAAGGATG
65 AAACTTAGTGGCTAACCACATGAGTAGGTTAAAAACACCTTGTAATGACACTCCTATAAAGGATG
* *
54846903 AGTTTCTTGATGATGGCCTATTTTC
130 AGTTTCCTGATGAGGGCCTATTTTC
54846928 AGCCAAAGTG
Statistics
Matches: 136, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
162 1 0.01
163 135 0.99
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (163 bp):
TCATTAGATGGAATTTACTACTCCAAGAATTCAACATCAAGATTCGAGACAAGAAAGGATGCAGA
AACTTAGTGGCTAACCACATGAGTAGGTTAAAAACACCTTGTAATGACACTCCTATAAAGGATGA
GTTTCCTGATGAGGGCCTATTTTCGACCAAGAC
Found at i:54851048 original size:105 final size:105
Alignment explanation
Indices: 54850866--54851058 Score: 237
Period size: 105 Copynumber: 1.8 Consensus size: 105
54850856 AAAATTAAGA
* * *
54850866 GTGTGTTGGGCTGAGTAACCGTGGTAGGGTGCTAGGGTTGTCATTCCACTTCGCATCAAAAGGGC
1 GTGTGTTGGGCTGAGTAACCGAGGTAGGGTGCTAGGGTTGTCATCCCACTTCACATCAAAAGGGC
* *
54850931 CAAAACGCTCTTAACCAAAAATAGTATAATAATAAAATAG
66 CAAAACACTCTTAACAAAAAATAGTATAATAATAAAATAG
* ** *
54850971 GTGTGTTGGGTTGAGTAATTGAGGT-GAGGTGCCT-GGGTTGTCATCCCTCTTCACATCAAAAGG
1 GTGTGTTGGGCTGAGTAACCGAGGTAG-GGTG-CTAGGGTTGTCATCCCACTTCACATCAAAAGG
* * * *
54851034 GTCAATACATTCTTAAGAAAAAATA
64 GCCAAAACACTCTTAACAAAAAATA
54851059 CAAAAAAAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
104 1 0.01
105 70 0.96
106 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (105 bp):
GTGTGTTGGGCTGAGTAACCGAGGTAGGGTGCTAGGGTTGTCATCCCACTTCACATCAAAAGGGC
CAAAACACTCTTAACAAAAAATAGTATAATAATAAAATAG
Found at i:54858640 original size:23 final size:23
Alignment explanation
Indices: 54858550--54858667 Score: 107
Period size: 23 Copynumber: 5.0 Consensus size: 23
54858540 GCGACTCACC
54858550 TCAGCTCGCAT-GAGCTTACTGCTAT
1 TCAGCTCG-ATAGAGCTTACTG-T-T
54858575 ATCAGCTCG-TAAGAGCTTACTGTT
1 -TCAGCTCGAT-AGAGCTTACTGTT
*
54858599 CTCAGCTC-ATATGAACTTACTGTT
1 -TCAGCTCGATA-GAGCTTACTGTT
* * *
54858623 TTAGCTCGTTAGAGCTTACCGTT
1 TCAGCTCGATAGAGCTTACTGTT
*
54858646 TCAGCTCAATAGAGCTTACTGT
1 TCAGCTCGATAGAGCTTACTGT
54858668 CCATCAGCTC
Statistics
Matches: 77, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
23 35 0.45
24 23 0.30
25 1 0.01
26 18 0.23
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (23 bp):
TCAGCTCGATAGAGCTTACTGTT
Found at i:54858640 original size:47 final size:46
Alignment explanation
Indices: 54858578--54858667 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 46
54858568 CTGCTATATC
*
54858578 AGCTCGTAAGAGCTTACTGTTCTCAGCTC-ATATGAACTTACTGTTTT
1 AGCTCGTAAGAGCTTACCGTT-TCAGCTCAATA-GAACTTACTGTTTT
* *
54858625 AGCTCGTTAGAGCTTACCGTTTCAGCTCAATAGAGCTTACTGT
1 AGCTCGTAAGAGCTTACCGTTTCAGCTCAATAGAACTTACTGT
54858668 CCATCAGCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
46 17 0.44
47 22 0.56
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (46 bp):
AGCTCGTAAGAGCTTACCGTTTCAGCTCAATAGAACTTACTGTTTT
Found at i:54862362 original size:10 final size:10
Alignment explanation
Indices: 54862344--54862384 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
54862334 GTAAAAGCCT
*
54862344 AAAATTTAAA
1 AAAAATTAAA
54862354 AAAAATT-AA
1 AAAAATTAAA
*
54862363 AAAATTTAAA
1 AAAAATTAAA
54862373 AAAAATTAAA
1 AAAAATTAAA
54862383 AA
1 AA
54862385 CATATAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:54862366 original size:19 final size:19
Alignment explanation
Indices: 54862344--54862384 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
54862334 GTAAAAGCCT
54862344 AAAATTTAAAAAAAATTAA
1 AAAATTTAAAAAAAATTAA
54862363 AAAATTTAAAAAAAATTAA
1 AAAATTTAAAAAAAATTAA
54862382 AAA
1 AAA
54862385 CATATAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATTTAAAAAAAATTAA
Found at i:54862419 original size:18 final size:18
Alignment explanation
Indices: 54862396--54862433 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54862386 ATATAGTTTA
*
54862396 TATTCGATTTATTCAAAT
1 TATTCGAGTTATTCAAAT
*
54862414 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCAAAT
54862432 TA
1 TA
54862434 GAAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (18 bp):
TATTCGAGTTATTCAAAT
Found at i:54862459 original size:6 final size:6
Alignment explanation
Indices: 54862442--54862472 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
54862432 TAGAAAATTT
54862442 AACTCG -ACTCG AACTCG AACTCG AACTCG AA
1 AACTCG AACTCG AACTCG AACTCG AACTCG AA
54862473 ATTCAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
AACTCG
Found at i:54863395 original size:53 final size:53
Alignment explanation
Indices: 54863326--54863428 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
54863316 GGATCTTCTA
* * * * *
54863326 ATCTTCCACTAACATAATGCGTCAGCAAGAACTATTTATCTTCTAACCTCCCG
1 ATCTTCCACTAACATAACGAGTCAACAAGAACTACTTATCTTCCAACCTCCCG
54863379 ATCTTCCACTAACATAACGAGTCAACAAGAACTACTTATCTTCCAACCTC
1 ATCTTCCACTAACATAACGAGTCAACAAGAACTACTTATCTTCCAACCTC
54863429 ACAGTCCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (53 bp):
ATCTTCCACTAACATAACGAGTCAACAAGAACTACTTATCTTCCAACCTCCCG
Found at i:54873277 original size:23 final size:23
Alignment explanation
Indices: 54873250--54873293 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54873240 TTTTCACAAA
54873250 AAAATAATAATTTTA-TATTTTAT
1 AAAATAA-AATTTTATTATTTTAT
*
54873273 AAAATAAATTTTTATTATTTT
1 AAAATAAAATTTTATTATTTT
54873294 GAAAATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAATAAAATTTTATTATTTTAT
Found at i:54873298 original size:22 final size:23
Alignment explanation
Indices: 54873250--54873299 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
54873240 TTTTCACAAA
*
54873250 AAAATAATAATTTTATATTTTAT
1 AAAATAATAATTTTATATTTTAG
*
54873273 AAAATAA-ATTTTTATTATTTT-G
1 AAAATAATAATTTTA-TATTTTAG
54873295 AAAAT
1 AAAAT
54873300 TGTTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAATAATAATTTTATATTTTAG
Found at i:54873398 original size:5 final size:5
Alignment explanation
Indices: 54873388--54873428 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
54873378 AATGGTTAAA
**
54873388 TTTCT TTTC- TTT-T TTTAA TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
54873429 GAAATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
4 6 0.19
5 25 0.81
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:54874869 original size:27 final size:27
Alignment explanation
Indices: 54874815--54874885 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
54874805 GTGCCATCAG
* * *
54874815 GGCATTTCTTTCAAAGTTCACCACGAA
1 GGCATCTCTTTCATATTTCACCACGAA
* *
54874842 GG-ATACTCTTTCATATTTCTCCATGAA
1 GGCAT-CTCTTTCATATTTCACCACGAA
*
54874869 GGCATTTCTTTCATATT
1 GGCATCTCTTTCATATT
54874886 GTGCCACAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 2 0.06
27 32 0.89
28 2 0.06
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (27 bp):
GGCATCTCTTTCATATTTCACCACGAA
Found at i:54874897 original size:27 final size:27
Alignment explanation
Indices: 54874849--54874960 Score: 107
Period size: 27 Copynumber: 4.1 Consensus size: 27
54874839 GAAGGATACT
* * ** *
54874849 CTTTCATATTTCTCCATGAAGGCATTT
1 CTTTCATATTGCGCCACAAAGGCATTC
* *
54874876 CTTTCATATTGTGCCACAAAGGCGTTC
1 CTTTCATATTGCGCCACAAAGGCATTC
* * * *
54874903 CTTTCGTATTACGTCACAAAGGCGTTC
1 CTTTCATATTGCGCCACAAAGGCATTC
* *
54874930 CTTTCATATTGCACCACAAAGACATTC
1 CTTTCATATTGCGCCACAAAGGCATTC
54874957 CTTT
1 CTTT
54874961 AAGGTTCGTC
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (27 bp):
CTTTCATATTGCGCCACAAAGGCATTC
Found at i:54875954 original size:6 final size:6
Alignment explanation
Indices: 54875943--54875993 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
54875933 TGAAAAAATT
* * *
54875943 AGAATC AGAATC AGTATC AGGTAA-C AGAATC AAAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAATC
54875992 AG
1 AG
54875994 GTAACAGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
5 2 0.05
6 31 0.84
7 3 0.08
8 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:54876000 original size:31 final size:31
Alignment explanation
Indices: 54875914--54876016 Score: 127
Period size: 31 Copynumber: 3.3 Consensus size: 31
54875904 CTAGAATTAG
* * * * *
54875914 AATCAGAATCAGAATTAGGTGAA-AAAATTAG
1 AATCAGAATCAGTATCAGGT-AACAGAATAAA
*
54875945 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATAAA
54875976 AATCAGAATCAGTATCAGGTAACAGAATAAAA
1 AATCAGAATCAGTATCAGGTAACAGAAT-AAA
54876008 AATCAGAAT
1 AATCAGAAT
54876017 GTAAATGCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
30 2 0.03
31 51 0.80
32 11 0.17
ACGTcount: A:0.51, C:0.12, G:0.17, T:0.20
Consensus pattern (31 bp):
AATCAGAATCAGTATCAGGTAACAGAATAAA
Done.