Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 175 of 378
Found at i:50835241 original size:47 final size:47
Alignment explanation
Indices: 50835183--50835435 Score: 389
Period size: 47 Copynumber: 5.4 Consensus size: 47
50835173 GATGTACAAG
*
50835183 GTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * *
50835230 CTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
50835277 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * *
50835324 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* *
50835371 GTGTATATATGTGATAAAGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
50835418 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
50835436 TCCCGAAGGG
Statistics
Matches: 185, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 185 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:50842915 original size:13 final size:13
Alignment explanation
Indices: 50842897--50842936 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
50842887 GAAGTAATCG
50842897 CACACGGGCGTGT
1 CACACGGGCGTGT
50842910 CACACGGGCGTGT
1 CACACGGGCGTGT
50842923 CACACGGGCGTGT
1 CACACGGGCGTGT
50842936 C
1 C
50842937 TCTGCCGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.38, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:50845752 original size:28 final size:27
Alignment explanation
Indices: 50845689--50845758 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
50845679 ATAGTGAGTC
50845689 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
50845716 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
50845744 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
50845759 GTACAAGTTT
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:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:50852984 original size:28 final size:27
Alignment explanation
Indices: 50852921--50852990 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
50852911 ATAGTGAGTC
50852921 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
50852948 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
50852976 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
50852991 GTACAAGTTT
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:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:50854006 original size:15 final size:16
Alignment explanation
Indices: 50853970--50853999 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50853960 ACATATCATT
50853970 TATTTCATTATATCAA
1 TATTTCATTATATCAA
50853986 TATTTCA-TATATCA
1 TATTTCATTATATCA
50854000 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:50855888 original size:30 final size:30
Alignment explanation
Indices: 50855854--50855914 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
50855844 TTCTTAACTC
50855854 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
50855884 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
50855914 A
1 A
50855915 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:50863372 original size:34 final size:34
Alignment explanation
Indices: 50863323--50863388 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
50863313 AAAAAAACAT
*
50863323 AGAAATTGGGCAAATTGCTCTTGAAGACCTTCAA
1 AGAAATTGGGAAAATTGCTCTTGAAGACCTTCAA
*
50863357 AGAAATTGTGAAAATTGCTCTTGAAGACCTTC
1 AGAAATTGGGAAAATTGCTCTTGAAGACCTTC
50863389 TAATTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (34 bp):
AGAAATTGGGAAAATTGCTCTTGAAGACCTTCAA
Found at i:50872063 original size:40 final size:40
Alignment explanation
Indices: 50871958--50872109 Score: 175
Period size: 40 Copynumber: 3.8 Consensus size: 40
50871948 GTTATAATAG
** *
50871958 CTCGCACAAATGCCTTCGGGA-CTTAACCCGAATTTGGGAA
1 CTCGCACAAATGCCTTC-GGATCTTAGTCCGGATTTGGGAA
50871998 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTGGGAA
1 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTGGGAA
* ** **
50872038 CTCGCATAAATGCCTTCGGATCTTAGTCCGGACATGGTCA
1 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTGGGAA
*
50872078 CTCAGCACAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CTC-GCACAAATGCCTTC-GGATCTTAGTCCGGA
50872110 CATCATTCGA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 87 0.88
41 9 0.09
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTGGGAA
Found at i:50872112 original size:40 final size:40
Alignment explanation
Indices: 50871929--50872109 Score: 170
Period size: 40 Copynumber: 4.5 Consensus size: 40
50871919 TCGCTCTAAA
* * *** *
50871929 GCCTTCGGGACATAGCCCGGTTATAATAGCTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATGGGAACTCGCACAAAT
* * *
50871969 GCCTTCGGGACTTAACCCGAATTTGGGAACTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATGGGAACTCGCACAAAT
* * *
50872009 GCCTTC-GGATCTTAGTCCGGATTTGGGAACTCGCATAAAT
1 GCCTTCGGGA-CTTAGCCCGGATATGGGAACTCGCACAAAT
* * **
50872049 GCCTTC-GGATCTTAGTCCGGACATGGTCACTCAGCACAAA-
1 GCCTTCGGGA-CTTAGCCCGGATATGGGAACTC-GCACAAAT
50872089 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAGCCCGGA
50872110 CATCATTCGA
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.03
40 107 0.90
41 9 0.08
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATGGGAACTCGCACAAAT
Found at i:50875185 original size:38 final size:38
Alignment explanation
Indices: 50875139--50875299 Score: 173
Period size: 38 Copynumber: 4.2 Consensus size: 38
50875129 GCTTAAAGAT
*
50875139 CCGCAGGCTAT-ATGCTGGAATTATATCCAGGTTAAATC
1 CCGCAGGCT-TCATGCTGGTATTATATCCAGGTTAAATC
* * *
50875177 CCGTAGGCTTCCTACTGGTATTATATCCAGGTTAAATC
1 CCGCAGGCTTCATGCTGGTATTATATCCAGGTTAAATC
* **
50875215 CCGCAGGCTTCGTGCTGGTATTATATCTGGGTTAAATC
1 CCGCAGGCTTCATGCTGGTATTATATCCAGGTTAAATC
* * * *
50875253 CCGCTGGCTT-AGTGCTAGTATTATATTCGAGCTTAAAGTC
1 CCGCAGGCTTCA-TGCTGGTATTATA-TCCAGGTTAAA-TC
50875293 CCGCAGG
1 CCGCAGG
50875300 TTTTGTGCTG
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
37 1 0.01
38 86 0.83
39 8 0.08
40 8 0.08
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (38 bp):
CCGCAGGCTTCATGCTGGTATTATATCCAGGTTAAATC
Found at i:50875231 original size:76 final size:78
Alignment explanation
Indices: 50875129--50875310 Score: 194
Period size: 76 Copynumber: 2.4 Consensus size: 78
50875119 GTGTATCCGG
* *
50875129 GCTTAAAGAT-CCGCAGGCTAT-ATGCTGGAATTATATCCAGGTTAAATCCCG-TAGGCTTCCTA
1 GCTTAAAG-TCCCGCAGGCT-TCGTGCTGGAATTATATCCAGGTTAAATCCCGCT-GGCTTACTA
*
50875191 CTGGTATTATA-TCCA
63 CTAGTATTATATTCCA
* * ** * *
50875206 GGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTATATCTGGGTTAAATCCCGCTGGCTTAGTGCTA
1 GCTTAAAGTCCCGCAGGCTTCGTGCTGGAATTATATCCAGGTTAAATCCCGCTGGCTTACTACTA
*
50875270 GTATTATATTCGA
66 GTATTATATTCCA
* *
50875283 GCTTAAAGTCCCGCAGGTTTTGTGCTGG
1 GCTTAAAGTCCCGCAGGCTTCGTGCTGG
50875311 TGGCTGGATT
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
75 2 0.02
76 51 0.59
77 16 0.18
78 18 0.21
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (78 bp):
GCTTAAAGTCCCGCAGGCTTCGTGCTGGAATTATATCCAGGTTAAATCCCGCTGGCTTACTACTA
GTATTATATTCCA
Found at i:50877270 original size:29 final size:27
Alignment explanation
Indices: 50877228--50877290 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 27
50877218 TTTTTCATTT
* * *
50877228 ATTTCACATTTTAACCACTAAATTTCCA
1 ATTTCACAATTTAACC-CAAAATTTACA
50877256 CATTTCACAATTTAACCCAAAATTTACA
1 -ATTTCACAATTTAACCCAAAATTTACA
50877284 ATTTCAC
1 ATTTCAC
50877291 TAATAATTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 7 0.23
28 9 0.29
29 15 0.48
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTTCACAATTTAACCCAAAATTTACA
Found at i:50879197 original size:45 final size:45
Alignment explanation
Indices: 50879036--50879206 Score: 188
Period size: 45 Copynumber: 3.7 Consensus size: 45
50879026 GGTTGAGCAT
* *
50879036 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGG
* * * *
50879082 CCGAACTTGTTGAGTTGAGTCCGAG-T---TTGTGAAATGTAACTAGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAAC--GG
50879126 CATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGG
1 C---CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGG
*
50879174 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
50879207 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 11, Indels: 21
0.76 0.08 0.15
Matches are distributed among these distances:
42 6 0.06
43 3 0.03
44 2 0.02
45 32 0.31
46 24 0.23
47 23 0.22
48 4 0.04
50 6 0.06
51 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGG
Found at i:50887344 original size:27 final size:27
Alignment explanation
Indices: 50887287--50887346 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
50887277 ATATATCTCA
*
50887287 TAGGGGCATATCAGTCATTTTACCATG
1 TAGGGGCATATCAGTCATTTTACAATG
*
50887314 TAGGGGCATTTCAGTCATTTTATCAAT-
1 TAGGGGCATATCAGTCATTTTA-CAATG
50887341 TAGGGG
1 TAGGGG
50887347 GTCTAGGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (27 bp):
TAGGGGCATATCAGTCATTTTACAATG
Found at i:50887421 original size:12 final size:12
Alignment explanation
Indices: 50887404--50887435 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
50887394 GTGACCCGTG
50887404 CGACCCATATTA
1 CGACCCATATTA
*
50887416 CGACCCATATTG
1 CGACCCATATTA
50887428 CGACCCAT
1 CGACCCAT
50887436 TGATACGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.38, G:0.12, T:0.22
Consensus pattern (12 bp):
CGACCCATATTA
Found at i:50898575 original size:52 final size:52
Alignment explanation
Indices: 50898492--50898594 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
50898482 ATTTCCACTC
*
50898492 GAGTATCATAATCGGCTGAAGCAATCTAGTAGGTACCTGATGTTTGGCTTTT
1 GAGTATCATAATCGGCTGAAGCAATCCAGTAGGTACCTGATGTTTGGCTTTT
50898544 GAGTATCATAATCGGCTGAAGCAATCCAGTAGGTACCTGATGTTTGGCTTT
1 GAGTATCATAATCGGCTGAAGCAATCCAGTAGGTACCTGATGTTTGGCTTT
50898595 CACTTGCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (52 bp):
GAGTATCATAATCGGCTGAAGCAATCCAGTAGGTACCTGATGTTTGGCTTTT
Found at i:50902354 original size:17 final size:18
Alignment explanation
Indices: 50902321--50902354 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50902311 CAATTCAAGA
*
50902321 TTTATAATCACATCAAAG
1 TTTATAATCAAATCAAAG
50902339 TTTATAAT-AAATCAAA
1 TTTATAATCAAATCAAA
50902355 TATCAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (18 bp):
TTTATAATCAAATCAAAG
Found at i:50907111 original size:43 final size:43
Alignment explanation
Indices: 50907064--50907157 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
50907054 GTCCCGGATG
* *
50907064 TGGTCTTACATGT-AAT-TCAATATCGATGCCTCTGTCCCAGACA
1 TGGTCTTACACGTAAATCTC-A-ATCGAGGCCTCTGTCCCAGACA
* *
50907107 TGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACA
1 TGGTCTTACACGTAAATCTCAATCGAGGCCTCTGTCCCAGACA
*
50907150 CGGTCTTA
1 TGGTCTTA
50907158 TACGATGTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
43 38 0.86
44 4 0.09
45 2 0.05
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
TGGTCTTACACGTAAATCTCAATCGAGGCCTCTGTCCCAGACA
Found at i:50909759 original size:29 final size:28
Alignment explanation
Indices: 50909718--50909772 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
50909708 ATCTGAAGTA
50909718 CTGATATCATGGCCCGAAGCCAAATCAG
1 CTGATATCATGGCCCGAAGCCAAATCAG
50909746 CTGATATTCATGGCCCGAAGCCAAATC
1 CTGATA-TCATGGCCCGAAGCCAAATC
50909773 GGTATAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (28 bp):
CTGATATCATGGCCCGAAGCCAAATCAG
Found at i:50915776 original size:30 final size:30
Alignment explanation
Indices: 50915740--50915840 Score: 127
Period size: 28 Copynumber: 3.5 Consensus size: 30
50915730 GACAAGATTG
* * *
50915740 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
50915770 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
50915798 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
50915827 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
50915841 GATTCACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.37
29 20 0.32
30 19 0.31
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:50915834 original size:29 final size:29
Alignment explanation
Indices: 50915740--50915840 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 29
50915730 GACAAGATTG
* * * *
50915740 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTGAAAA-TATATA
*
50915770 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-TTGAAAATATATA
*
50915798 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTTGAAAATATATA
50915827 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
50915841 GATTCACTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 20 0.33
29 22 0.36
30 15 0.25
31 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTGAAAATATATA
Found at i:50922908 original size:30 final size:30
Alignment explanation
Indices: 50922872--50922972 Score: 127
Period size: 28 Copynumber: 3.5 Consensus size: 30
50922862 GACAAGATTG
* * *
50922872 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
50922902 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
50922930 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
50922959 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
50922973 GATTCACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.37
29 20 0.32
30 19 0.31
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:50922966 original size:29 final size:29
Alignment explanation
Indices: 50922872--50922972 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 29
50922862 GACAAGATTG
* * * *
50922872 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTGAAAA-TATATA
*
50922902 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-TTGAAAATATATA
*
50922930 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTTGAAAATATATA
50922959 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
50922973 GATTCACTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 20 0.33
29 22 0.36
30 15 0.25
31 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTGAAAATATATA
Found at i:50926889 original size:29 final size:29
Alignment explanation
Indices: 50926856--50926987 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
50926846 TACTCGATTT
** * *
50926856 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* *** * *
50926885 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
50926914 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
50926943 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
50926972 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
50926988 ATCTAGTCAC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 2 0.02
29 85 0.98
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:50931495 original size:29 final size:30
Alignment explanation
Indices: 50931433--50931551 Score: 126
Period size: 29 Copynumber: 4.2 Consensus size: 30
50931423 TACATACATG
* *
50931433 CATATGGCCTA-CTGGGCCCAA-TC-TCATT
1 CATATGGCCCATCTAGGCCCAATTCAT-ATT
*
50931461 CATATGGCCCATCT-GGCCTAATTCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
50931490 CTTATGGCCCA-CTAGGCCCAATTCACATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
*
50931519 CATATGGCCCAT-TAGGCCCAAATCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
50931548 -ATAT
1 CATAT
50931552 TCATGCTTAC
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
28 22 0.28
29 55 0.71
30 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (30 bp):
CATATGGCCCATCTAGGCCCAATTCATATT
Found at i:50931529 original size:58 final size:57
Alignment explanation
Indices: 50931435--50931547 Score: 156
Period size: 58 Copynumber: 2.0 Consensus size: 57
50931425 CATACATGCA
* * * * *
50931435 TATGGCCTACTGGGCCCAATCTCATTCATATGGCCCATCT-GGCCTAATTCATATTCT
1 TATGGCCCACTAGGCCCAATCACATTCATATGGCCCAT-TAGGCCCAAATCATATTCT
50931492 TATGGCCCACTAGGCCCAATTCACATTCATATGGCCCATTAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCACATTCATATGGCCCATTAGGCCCAAATCATATT
50931548 ATATTCATGC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 18 0.37
58 31 0.63
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCACATTCATATGGCCCATTAGGCCCAAATCATATTCT
Found at i:50931809 original size:16 final size:16
Alignment explanation
Indices: 50931785--50931844 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
50931775 GTAGCCCAAC
* *
50931785 TTTCAGCTTTTTGGTA
1 TTTCGGCTTTTCGGTA
50931801 TTTCGGCTTTTCGGCT-
1 TTTCGGCTTTTCGG-TA
*
50931817 TTTCGACTTTTCGGTA
1 TTTCGGCTTTTCGGTA
50931833 TTTCGGCATTTT
1 TTTCGGC-TTTT
50931845 GGCTTTTGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.03
16 31 0.84
17 5 0.14
ACGTcount: A:0.08, C:0.18, G:0.20, T:0.53
Consensus pattern (16 bp):
TTTCGGCTTTTCGGTA
Found at i:50931814 original size:8 final size:8
Alignment explanation
Indices: 50931801--50931851 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
50931791 CTTTTTGGTA
50931801 TTTCGGCT
1 TTTCGGCT
50931809 TTTCGGCT
1 TTTCGGCT
*
50931817 TTTCGACT
1 TTTCGGCT
50931825 TTTCGG-T
1 TTTCGGCT
50931832 ATTTCGGCAT
1 -TTTCGGC-T
50931842 TTT-GGCT
1 TTTCGGCT
50931849 TTT
1 TTT
50931852 GCCGATTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
7 5 0.13
8 29 0.76
9 3 0.08
10 1 0.03
ACGTcount: A:0.06, C:0.20, G:0.22, T:0.53
Consensus pattern (8 bp):
TTTCGGCT
Found at i:50931833 original size:32 final size:32
Alignment explanation
Indices: 50931791--50931851 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
50931781 CAACTTTCAG
*
50931791 CTTTTTGGTATTTCGGC-TTTTCGGCTTTTCGA
1 CTTTTCGGTATTTCGGCATTTT-GGCTTTTCGA
50931823 CTTTTCGGTATTTCGGCATTTTGGCTTTT
1 CTTTTCGGTATTTCGGCATTTTGGCTTTT
50931852 GCCGATTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.07, C:0.18, G:0.21, T:0.54
Consensus pattern (32 bp):
CTTTTCGGTATTTCGGCATTTTGGCTTTTCGA
Found at i:50933538 original size:20 final size:20
Alignment explanation
Indices: 50933513--50933553 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
50933503 ATACCACAGC
50933513 TAATAACTATTTTTAAGTGG
1 TAATAACTATTTTTAAGTGG
50933533 TAATAACTATTTTTAAGTGG
1 TAATAACTATTTTTAAGTGG
50933553 T
1 T
50933554 GGTGTAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (20 bp):
TAATAACTATTTTTAAGTGG
Found at i:50940002 original size:17 final size:17
Alignment explanation
Indices: 50939959--50940005 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
50939949 ATATTAAAAA
* *
50939959 ATTATTTAAACATAATT
1 ATTATATAAATATAATT
*
50939976 A-AATATTAAATATAATT
1 ATTATA-TAAATATAATT
50939993 ATTATATAAATAT
1 ATTATATAAATAT
50940006 TAATAAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 19 0.79
18 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATATAAATATAATT
Found at i:50940066 original size:21 final size:22
Alignment explanation
Indices: 50940037--50940090 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
50940027 TGTTTAGACT
* **
50940037 TTTAGAATTTTAGGTCTTA-AA
1 TTTAAAATTTTAGGATTTAGAA
50940058 TTTAAAA-TTTAGGATTTAGAA
1 TTTAAAATTTTAGGATTTAGAA
*
50940079 TTTAAGATTTTA
1 TTTAAAATTTTA
50940091 AAATTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (22 bp):
TTTAAAATTTTAGGATTTAGAA
Found at i:50940095 original size:15 final size:14
Alignment explanation
Indices: 50940053--50940097 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
50940043 ATTTTAGGTC
50940053 TTAA-ATTTAAAAT
1 TTAAGATTTAAAAT
* *
50940066 TTAGGATTTAGAAT
1 TTAAGATTTAAAAT
50940080 TTAAGATTTTAAAAT
1 TTAAGA-TTTAAAAT
50940095 TTA
1 TTA
50940098 TTTATAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 3 0.12
14 13 0.50
15 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
TTAAGATTTAAAAT
Found at i:50946162 original size:6 final size:6
Alignment explanation
Indices: 50946144--50946246 Score: 68
Period size: 6 Copynumber: 16.8 Consensus size: 6
50946134 AAGAAACATT
* * *
50946144 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACACA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * * *
50946193 ATCAGA ATCAGA ATCAGT ATCAGGTA AT-AGA AACAAA ATAAGA ATCAGT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA
50946242 ATCAG
1 ATCAG
50946247 GTAACAGAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
5 4 0.05
6 63 0.85
7 4 0.05
8 3 0.04
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:50946237 original size:37 final size:37
Alignment explanation
Indices: 50946159--50946246 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 37
50946149 AACTAGAATC
* * * * *
50946159 AGAATCAGAATCAGAATTAGGTGACACAATCAGAATC
1 AGAATCAGAATCAGAATCAGGTAACACAAACAAAATA
* * *
50946196 AGAATCAGAATCAGTATCAGGTAATAGAAACAAAATA
1 AGAATCAGAATCAGAATCAGGTAACACAAACAAAATA
*
50946233 AGAATCAGTATCAG
1 AGAATCAGAATCAG
50946247 GTAACAGAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCAGGTAACACAAACAAAATA
Found at i:50946240 original size:31 final size:32
Alignment explanation
Indices: 50946202--50946269 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
50946192 AATCAGAATC
* *
50946202 AGAATCAGTATCAGGTAATAGAA-ACAAAATA
1 AGAATCAGTATCAGGTAACAGAATAAAAAATA
*
50946233 AGAATCAGTATCAGGTAACAGAATAAAAAATC
1 AGAATCAGTATCAGGTAACAGAATAAAAAATA
50946265 AGAAT
1 AGAAT
50946270 GTGAATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.19
Consensus pattern (32 bp):
AGAATCAGTATCAGGTAACAGAATAAAAAATA
Found at i:50946448 original size:27 final size:26
Alignment explanation
Indices: 50946406--50946507 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
50946396 GCTCAGTTAT
* *
50946406 CAGATATTGTGACAGAGCCACAAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
50946432 CAGATATTTGTGGCAGAGCCACCAGAA
1 CAGATA-TTGTGGCAGAGCCACCAGAA
*
50946459 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
50946487 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
50946508 TTAACAGAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
26 6 0.09
27 55 0.80
28 8 0.12
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:50946694 original size:22 final size:22
Alignment explanation
Indices: 50946666--50946730 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
50946656 GCAAATACGT
* *
50946666 TTGGCACACATCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
50946688 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
50946710 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
50946731 AAGGCTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:50947006 original size:16 final size:16
Alignment explanation
Indices: 50946985--50947015 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50946975 ATCCCAACCC
*
50946985 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
50947001 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
50947016 CCCATATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:50947213 original size:27 final size:27
Alignment explanation
Indices: 50947174--50947374 Score: 264
Period size: 27 Copynumber: 7.4 Consensus size: 27
50947164 TACCCCACAA
* * *
50947174 GGTATCTCGGTAATTGC-ACCCTATAGG
1 GGTATTTCGATAATT-CTACCCTACAGG
*
50947201 GGTATTT-TAGTAATTCTACCCTACAGG
1 GGTATTTCGA-TAATTCTACCCTACAGG
* *
50947228 GGTATTGCGATAATTCTACCCTATAGG
1 GGTATTTCGATAATTCTACCCTACAGG
50947255 GGTATTTCGATAATTCTACCCTACAGG
1 GGTATTTCGATAATTCTACCCTACAGG
50947282 GGTATTTCGATAATTCTACCCTACAGG
1 GGTATTTCGATAATTCTACCCTACAGG
50947309 GGTATTTC-AGTAATTCTACCCTACAGG
1 GGTATTTCGA-TAATTCTACCCTACAGG
* * *
50947336 GGTATTCCGGTAATTCTACCATACAGG
1 GGTATTTCGATAATTCTACCCTACAGG
*
50947363 GGTATTTTGATA
1 GGTATTTCGATA
50947375 TTTTACAAAT
Statistics
Matches: 154, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.01
27 151 0.98
28 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (27 bp):
GGTATTTCGATAATTCTACCCTACAGG
Found at i:50947412 original size:27 final size:27
Alignment explanation
Indices: 50947359--50947514 Score: 124
Period size: 27 Copynumber: 5.8 Consensus size: 27
50947349 TTCTACCATA
*
50947359 CAGGGGTATTTTGAT-ATTTTACAAAT
1 CAGGAGTATTTTGATAATTTTACAAAT
*
50947385 C-GAGAGTATTTTGATAATTTCACAAAT
1 CAG-GAGTATTTTGATAATTTTACAAAT
* * *
50947412 CAGGGGTATTTTGGTAAATTTTACAAAC
1 CAGGAGTATTTTGAT-AATTTTACAAAT
* *
50947440 CAGGGGTATTTT-AGTAATTTTACAAAC
1 CAGGAGTATTTTGA-TAATTTTACAAAT
* * **
50947467 CAGG-GCTATTTTGGTTATTTTACTGAT
1 CAGGAG-TATTTTGATAATTTTACAAAT
*
50947494 CGAGG-GTATTTTGGTAATTTT
1 C-AGGAGTATTTTGATAATTTT
50947515 GTAAACTAAG
Statistics
Matches: 109, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
25 1 0.01
26 13 0.12
27 67 0.61
28 28 0.26
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (27 bp):
CAGGAGTATTTTGATAATTTTACAAAT
Found at i:50947458 original size:55 final size:55
Alignment explanation
Indices: 50947359--50947513 Score: 158
Period size: 55 Copynumber: 2.9 Consensus size: 55
50947349 TTCTACCATA
* *
50947359 CAGGGGTATTTT-G-ATATTTTACAAATCGAGAGTATTTTGATAATTTCACAAAT
1 CAGGGGTATTTTGGTATATTTTACAAACCGAGAGTATTTTGATAATTTCACAAAC
* * *
50947412 CAGGGGTATTTTGGTAAATTTTACAAACC-AGGGGTATTTT-AGTAATTTTACAAAC
1 CAGGGGTATTTTGGTATATTTTACAAACCGA-GAGTATTTTGA-TAATTTCACAAAC
* ** * * *
50947467 CAGGGCTATTTTGGT-TATTTTACTGATCGAGGGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTATATTTTACAAACCGAGAGTATTTTGATAATTT
50947514 TGTAAACTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
53 12 0.14
54 27 0.32
55 46 0.54
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (55 bp):
CAGGGGTATTTTGGTATATTTTACAAACCGAGAGTATTTTGATAATTTCACAAAC
Found at i:50947565 original size:27 final size:27
Alignment explanation
Indices: 50947543--50947876 Score: 445
Period size: 27 Copynumber: 12.4 Consensus size: 27
50947533 AATAATTTTG
* ** * *
50947543 TAAATCGAGGATAAAACAGTAATTTTG
1 TAAATCGAGGGTAAAATGGTAATTCTA
* *
50947570 TAAATCGAGGGTAAAATAGTAATTATA
1 TAAATCGAGGGTAAAATGGTAATTCTA
* *
50947597 TAAATCAAGGGTAAAATGGTAATTATA
1 TAAATCGAGGGTAAAATGGTAATTCTA
* *
50947624 TAAATCGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAATGGTAATTCTA
*
50947651 TAAATCGAGGGTAAAATAGTAATTCTA
1 TAAATCGAGGGTAAAATGGTAATTCTA
* * *
50947678 TAAATCAAGGGTAAAATGGTAATTTTG
1 TAAATCGAGGGTAAAATGGTAATTCTA
50947705 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAATGGTAATTCTA
**
50947732 TAAATCGAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAATGGTAATTCTA
*
50947759 TAAATCGAGGGTAAAATGGTAATTCTG
1 TAAATCGAGGGTAAAATGGTAATTCTA
*
50947786 TAAATCGAGGGTAAAATGGTAATTTTA
1 TAAATCGAGGGTAAAATGGTAATTCTA
* * *
50947813 TAAATCGAGGGTAAAATGATAATTTTG
1 TAAATCGAGGGTAAAATGGTAATTCTA
* *
50947840 TAAATCGAGGGTGAAA-CGTAATTCTA
1 TAAATCGAGGGTAAAATGGTAATTCTA
50947866 TAAATCGAGGG
1 TAAATCGAGGG
50947877 CATTTCAGTA
Statistics
Matches: 273, Mismatches: 34, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
26 17 0.06
27 256 0.94
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (27 bp):
TAAATCGAGGGTAAAATGGTAATTCTA
Found at i:50949452 original size:25 final size:24
Alignment explanation
Indices: 50949395--50949468 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
50949385 ACCACAACTA
50949395 GTATGAGCTTACCGATTTCAGCTC
1 GTATGAGCTTACCGATTTCAGCTC
* * *
50949419 ATAAGAGCTTACTGATTCTCAGCTC
1 GTATGAGCTTACCGATT-TCAGCTC
* *
50949444 GTATTAGCTTACCAATTTCTAGCTC
1 GTATGAGCTTACCGATTTC-AGCTC
50949469 ATCAGAGCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
24 16 0.40
25 24 0.60
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (24 bp):
GTATGAGCTTACCGATTTCAGCTC
Found at i:50949493 original size:50 final size:49
Alignment explanation
Indices: 50949395--50949501 Score: 137
Period size: 50 Copynumber: 2.2 Consensus size: 49
50949385 ACCACAACTA
*
50949395 GTATGAGCTTACCGATTTCAGCTCATAAGAGCTTACTGATTCTCAGCTC
1 GTATGAGCTTACCAATTTCAGCTCATAAGAGCTTACTGATTCTCAGCTC
* * *
50949444 GTATTAGCTTACCAATTTCTAGCTCATCAGAGCATTTCT-ATTCAT-AGCTC
1 GTATGAGCTTACCAATTTC-AGCTCATAAGAGC-TTACTGATTC-TCAGCTC
50949494 GTATGAGC
1 GTATGAGC
50949502 ATACATGTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
49 17 0.34
50 28 0.56
51 5 0.10
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (49 bp):
GTATGAGCTTACCAATTTCAGCTCATAAGAGCTTACTGATTCTCAGCTC
Found at i:50954321 original size:29 final size:28
Alignment explanation
Indices: 50954281--50954359 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
50954271 TTTGGCCCCT
* *
50954281 TTAGGCCCAATCTCATTCATATGGCCAA
1 TTAGGCCCAATCACATTCATATGACCAA
* *
50954309 TTAGGCCCAAATCACTTTCATATGACCCA
1 TTAGGCCC-AATCACATTCATATGACCAA
50954338 TT-GGCCCCAATCACATTCATAT
1 TTAGG-CCCAATCACATTCATAT
50954360 AGCCCATCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
28 23 0.52
29 21 0.48
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.29
Consensus pattern (28 bp):
TTAGGCCCAATCACATTCATATGACCAA
Found at i:50954365 original size:28 final size:27
Alignment explanation
Indices: 50954286--50954376 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 27
50954276 CCCCTTTAGG
* *
50954286 CCCAATCTCATTCATATGGCCAATTAGGC
1 CCCAATCACATTCATAT-GCCCATT-GGC
* *
50954315 CCAAATCACTTTCATATGACCCATTGGC
1 CCCAATCACATTCATATG-CCCATTGGC
**
50954343 CCCAATCACATTCATATAGCCCATCAGC
1 CCCAATCACATTCATAT-GCCCATTGGC
50954371 CCCAAT
1 CCCAAT
50954377 GTAACACCCC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 32 0.62
29 20 0.38
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.25
Consensus pattern (27 bp):
CCCAATCACATTCATATGCCCATTGGC
Found at i:50955248 original size:37 final size:37
Alignment explanation
Indices: 50955190--50955371 Score: 292
Period size: 37 Copynumber: 4.9 Consensus size: 37
50955180 GCTCAGACGA
* * * *
50955190 AATCTCCACACGAAGTTATCGGGTCTTACCTGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
50955227 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
* *
50955264 ACTCTCCACACGTAGTCATCGGGTCTTACCCTGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
50955301 AATCTCCACACGTAGTCATTGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
50955338 AATCTCCACACGTAGTCATCGGGTCTCACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
50955372 ATATATTTCC
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:50955572 original size:48 final size:48
Alignment explanation
Indices: 50955518--50955652 Score: 198
Period size: 48 Copynumber: 2.8 Consensus size: 48
50955508 GCACATCGCC
*
50955518 TACATATTTCACACTAGCCATTAGGCTTTACCACATATACATACCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
* *
50955566 TACATATTTCGCACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
* * * * *
50955614 TACATATGTCACATTAGCAATTCGGCCTTATCACATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA
50955653 TGCATGTTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
Found at i:50955687 original size:47 final size:47
Alignment explanation
Indices: 50955633--50955871 Score: 390
Period size: 47 Copynumber: 5.1 Consensus size: 47
50955623 CACATTAGCA
50955633 ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
1 ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
* * * *
50955680 ATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCC
1 ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
50955727 ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
1 ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
* * * *
50955774 ATTCGGCCTTATCACACATATGCATG-CCAACATTCATCACATTGGCC
1 ATTCGGCCTTATCACATATATGCATGTTC-ATATTCATCATATTGGCC
50955821 ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
1 ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
50955868 ATTC
1 ATTC
50955872 AATACCAGAT
Statistics
Matches: 174, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.01
47 172 0.99
48 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.35
Consensus pattern (47 bp):
ATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCC
Found at i:50955731 original size:94 final size:94
Alignment explanation
Indices: 50955622--50955871 Score: 466
Period size: 94 Copynumber: 2.7 Consensus size: 94
50955612 CATACATATG
* *
50955622 TCACATTAGCAATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCCATTCGGC
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCCATTCGGC
50955687 CTTATCACACATATGCATGCTC-ACATTCA
66 CTTATCACACATATGCATGC-CAACATTCA
50955716 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCCATTCGGC
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCCATTCGGC
50955781 CTTATCACACATATGCATGCCAACATTCA
66 CTTATCACACATATGCATGCCAACATTCA
50955810 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCCATTC
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCCATTC
50955872 AATACCAGAT
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
93 1 0.01
94 152 0.99
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.34
Consensus pattern (94 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCATATTGGCCATTCGGC
CTTATCACACATATGCATGCCAACATTCA
Found at i:50960453 original size:28 final size:28
Alignment explanation
Indices: 50960382--50960482 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
50960372 GACAAGATTG
* * * *
50960382 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
*
50960412 GAACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
50960440 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
50960469 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
50960483 GATTCACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.37
29 20 0.32
30 17 0.27
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:50960476 original size:29 final size:28
Alignment explanation
Indices: 50960414--50960482 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 28
50960404 ATTGTACAGA
*
50960414 ACTAAGTGTGCGAGTTTGATTATATAGC
1 ACTAAGTGTGCGAGTCTGATTATATAGC
50960442 ACTAAGTGTGCGAG-CTGAATGTATATAGC
1 ACTAAGTGTGCGAGTCTG-AT-TATATAGC
50960471 ACTAAGTGTGCG
1 ACTAAGTGTGCG
50960483 GATTCACTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 16 0.42
29 20 0.53
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (28 bp):
ACTAAGTGTGCGAGTCTGATTATATAGC
Found at i:50970586 original size:68 final size:67
Alignment explanation
Indices: 50970514--50970663 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
50970504 CATCATGTGT
* * * *
50970514 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
50970576 ATGTAG
62 ATGTAG
** * *
50970582 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
50970647 AG
66 AG
50970649 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
50970664 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:50970619 original size:64 final size:64
Alignment explanation
Indices: 50970538--50970721 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
50970528 AGACATTATG
* *
50970538 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
50970602 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
50970667 AA
63 AA
* * * *
50970669 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
50970722 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:50975032 original size:68 final size:67
Alignment explanation
Indices: 50974960--50975109 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
50974950 CATCATGTGT
* * * *
50974960 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
50975022 ATGTAG
62 ATGTAG
** * *
50975028 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
50975093 AG
66 AG
50975095 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
50975110 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:50975065 original size:64 final size:64
Alignment explanation
Indices: 50974984--50975167 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
50974974 AGACATTATG
* *
50974984 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
50975048 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
50975113 AA
63 AA
* * * *
50975115 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
50975168 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:50982550 original size:11 final size:11
Alignment explanation
Indices: 50982514--50982569 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
50982504 CATGGTATGT
50982514 ATGATATGCAC
1 ATGATATGCAC
* *
50982525 ATGACATG--T
1 ATGATATGCAC
50982534 ATGATATGCAC
1 ATGATATGCAC
*
50982545 ATGATATG--T
1 ATGATATGCAC
50982554 ATGATATGCAC
1 ATGATATGCAC
50982565 ATGAT
1 ATGAT
50982570 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:50982569 original size:20 final size:20
Alignment explanation
Indices: 50982503--50982569 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
50982493 ATTTTGATAA
*
50982503 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
50982523 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
50982543 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
50982563 ACATGAT
1 ACATGAT
50982570 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:50982677 original size:24 final size:24
Alignment explanation
Indices: 50982618--50982738 Score: 174
Period size: 24 Copynumber: 5.0 Consensus size: 24
50982608 GGAGGAAGTG
50982618 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
50982642 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
*
50982667 TAAAAGGGCTTATGCCCCAATTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
50982691 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
50982714 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
50982739 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
23 18 0.20
24 39 0.44
25 31 0.35
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:50982970 original size:31 final size:31
Alignment explanation
Indices: 50982935--50982994 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
50982925 TTACAGTAAA
50982935 GGCTTCGGCCCAGTAATATGAAATATGAAAT
1 GGCTTCGGCCCAGTAATATGAAATATGAAAT
**
50982966 GGCTTCGGCCCAGTGTTATGAAATATGAA
1 GGCTTCGGCCCAGTAATATGAAATATGAA
50982995 GTGTGAAAAG
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:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (31 bp):
GGCTTCGGCCCAGTAATATGAAATATGAAAT
Found at i:50984908 original size:46 final size:46
Alignment explanation
Indices: 50984858--50984983 Score: 209
Period size: 46 Copynumber: 2.7 Consensus size: 46
50984848 TGGTTGAGCA
*
50984858 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
50984904 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
50984950 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
50984984 GGGGCGGGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 2 0.03
46 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:50985013 original size:16 final size:16
Alignment explanation
Indices: 50984992--50985025 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
50984982 TAGGGGCGGG
50984992 TTACATGATTTCTTGA
1 TTACATGATTTCTTGA
50985008 TTACATGATTTCTTGA
1 TTACATGATTTCTTGA
50985024 TT
1 TT
50985026 TTAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (16 bp):
TTACATGATTTCTTGA
Found at i:50996769 original size:46 final size:46
Alignment explanation
Indices: 50996719--50996840 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
50996709 TGGTTGAGCA
*
50996719 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
50996765 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
50996811 -CCTGAGCTCATTGAGTTGAGTCCGAGTTCA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCA
50996841 GTTAGGGACG
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 2 0.03
46 69 0.97
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:50996874 original size:16 final size:16
Alignment explanation
Indices: 50996853--50996886 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
50996843 TAGGGACGGG
50996853 TTACATGATTTCTTGA
1 TTACATGATTTCTTGA
50996869 TTACATGATTTCTTGA
1 TTACATGATTTCTTGA
50996885 TT
1 TT
50996887 TTAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (16 bp):
TTACATGATTTCTTGA
Found at i:51000911 original size:30 final size:30
Alignment explanation
Indices: 51000875--51001031 Score: 193
Period size: 30 Copynumber: 5.4 Consensus size: 30
51000865 GACAAGATTG
* * * * *
51000875 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
51000905 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
51000933 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
51000962 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
51000992 GCACTAAGTGTGCTAGCTG--AA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
51001019 GCACTAAGTGTGC
1 GCACTAAGTGTGC
51001032 TGATTCACTA
Statistics
Matches: 116, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
27 21 0.18
28 24 0.21
29 29 0.25
30 40 0.34
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:51001002 original size:59 final size:57
Alignment explanation
Indices: 51000875--51001031 Score: 194
Period size: 57 Copynumber: 2.7 Consensus size: 57
51000865 GACAAGATTG
* * * * * *
51000875 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATATA
51000933 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATATA
*
51000992 GCACTAAGTGTGCTAGCTG--AATATATAGCACTAAGTGTGC
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGC
51001032 TGATTCACTA
Statistics
Matches: 89, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
56 2 0.02
57 41 0.46
58 20 0.22
59 26 0.29
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATATA
Found at i:51001044 original size:27 final size:27
Alignment explanation
Indices: 51000904--51001032 Score: 123
Period size: 29 Copynumber: 4.6 Consensus size: 27
51000894 AAAATTGTAC
* * * *
51000904 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCTAG-CTCAATATAT
* *
51000932 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCTAGCT--CAATATAT
* *
51000961 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCTAGCT--CAA-TATAT
*
51000991 AGCACTAAGTGTGCTAGCTGAATATAT
1 AGCACTAAGTGTGCTAGCTCAATATAT
51001018 AGCACTAAGTGTGCT
1 AGCACTAAGTGTGCT
51001033 GATTCACTAT
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
27 21 0.23
28 19 0.20
29 30 0.32
30 23 0.25
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCTAGCTCAATATAT
Found at i:51007369 original size:20 final size:20
Alignment explanation
Indices: 51007303--51007369 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
51007293 ATTTTGATAA
*
51007303 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* * *
51007323 ACATGAAATCTATGATATGT
1 ACATGATATGTATGATATGC
51007343 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
51007363 ACATGAT
1 ACATGAT
51007370 GTATTCATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:51007448 original size:25 final size:24
Alignment explanation
Indices: 51007418--51007539 Score: 176
Period size: 25 Copynumber: 5.0 Consensus size: 24
51007408 GGAGGAAGTG
51007418 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
51007442 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
51007467 TAAAAAGGGCTTATGCCCCAGTTAT
1 T-AAAAGGGCTTATGCCCCAGTTAT
51007492 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
51007515 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
51007540 ATGATAAAGC
Statistics
Matches: 90, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
23 19 0.21
24 17 0.19
25 53 0.59
26 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:51007536 original size:48 final size:50
Alignment explanation
Indices: 51007418--51007548 Score: 173
Period size: 48 Copynumber: 2.6 Consensus size: 50
51007408 GGAGGAAGTG
51007418 TAAAAG-GGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGAGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
*
51007467 TAAAA-AGGGCTTATGCCCCAGTTATTA-AAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGA-GGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
*
51007515 TAAAAGAGGC-TAGGCCTCCAGTTATATGATAAAG
1 TAAAAGAGGCTTATGCC-CCAG-T-TATGATAAAG
51007549 CAGCTATGCT
Statistics
Matches: 72, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
47 5 0.07
48 24 0.33
49 16 0.22
50 23 0.32
51 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (50 bp):
TAAAAGAGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
Found at i:51007768 original size:31 final size:31
Alignment explanation
Indices: 51007733--51007792 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
51007723 CGTTTACAGT
51007733 AAAGGCTTCGGCCCAGTAATATGAAATATAA
1 AAAGGCTTCGGCCCAGTAATATGAAATATAA
**
51007764 AAAGGCTTCGGCCCAGTGTTATGAAATAT
1 AAAGGCTTCGGCCCAGTAATATGAAATAT
51007793 GAAGTGTGAA
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:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATAA
Found at i:51013382 original size:40 final size:40
Alignment explanation
Indices: 51013224--51013368 Score: 204
Period size: 40 Copynumber: 3.6 Consensus size: 40
51013214 ATGTCCGGAC
** * * **
51013224 TAAGTCCCGAAGGC-TTTGTGCTGAGTGACCATATCTGGAC
1 TAAGTCCCGAAGGCATTTGTGC-GAGTTCCCAAATCCGGGT
51013264 TAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAATCCGGGT
1 TAAG-TCCCGAAGGCATTTGTGCGAGTTCCCAAATCCGGGT
51013304 TAAGTCCCGAAGGCATTTGTGCGAGTTCCCAAATCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTCCCAAATCCGGGT
51013344 TAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCGAG
51013369 CTATTATAAC
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
39 1 0.01
40 87 0.91
41 8 0.08
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTCCCAAATCCGGGT
Found at i:51013382 original size:80 final size:79
Alignment explanation
Indices: 51013217--51013435 Score: 203
Period size: 80 Copynumber: 2.7 Consensus size: 79
51013207 TCGAATGATG
* * *
51013217 TCCGGACTAAGTCCCGAAGGCTTTGTGCTGAGTGACCATATCTGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGC-GAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* *
51013282 GTGCGAGTTCCCAAA
65 GTGCGAGCTACCAAA
* ** **
51013297 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTCCCAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
**
51013361 TGTGCGAGCTATTATAA
64 TGTGCGAGCTACCA-AA
** * * *
51013378 -CCGGGCTATCTCCCGAAGGCTTTTGAGCGAGTCG-CTATATCCGGA-TAAGATCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGT-GACCAAATCCGGACTAAGATCCGAAGG
51013436 TACGTGATTC
Statistics
Matches: 113, Mismatches: 21, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
79 12 0.11
80 92 0.81
81 9 0.08
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGCTACCAAA
Found at i:51013392 original size:40 final size:40
Alignment explanation
Indices: 51013217--51013408 Score: 149
Period size: 40 Copynumber: 4.8 Consensus size: 40
51013207 TCGAATGATG
* * *
51013217 TCCGGACTAAGTCCCGAAGGC-TTTGTGCTGAG-TGACCATA
1 TCCGGGCTAACTCCCGAAGGCATTTGTGC-GAGCT-ACCAAA
* * * * *
51013257 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAA-CTCCCGAAGGCATTTGTGCGAGCTACCAAA
* * * *
51013297 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAACTCCCGAAGGCATTTGTGCGAGCTACCAAA
* * **
51013337 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 TCCGGGCTAACTCCCGAAGGCATTTGTGCGAGCTACCA-AA
* * *
51013378 -CCGGGCTATCTCCCGAAGGCTTTTGAGCGAG
1 TCCGGGCTAACTCCCGAAGGCATTTGTGCGAG
51013409 TCGCTATATC
Statistics
Matches: 130, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 118 0.91
41 11 0.08
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAACTCCCGAAGGCATTTGTGCGAGCTACCAAA
Found at i:51015075 original size:41 final size:41
Alignment explanation
Indices: 51015030--51015112 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
51015020 CAAGACAGAC
*
51015030 TTAAAAGGCAAATTTCAAGACCGCGCCACAAATCCTCTGTA
1 TTAAAAGGAAAATTTCAAGACCGCGCCACAAATCCTCTGTA
51015071 TTAAAAGGAAAATTTCAAGACCGCGCCACAAATCCTCTGTA
1 TTAAAAGGAAAATTTCAAGACCGCGCCACAAATCCTCTGTA
51015112 T
1 T
51015113 GCATAATAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.23
Consensus pattern (41 bp):
TTAAAAGGAAAATTTCAAGACCGCGCCACAAATCCTCTGTA
Found at i:51018757 original size:27 final size:27
Alignment explanation
Indices: 51018727--51018787 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
51018717 TAAGGCGATC
* *
51018727 CTTTCTTAATTCGCCTCAAAGGCTTTT
1 CTTTCATAATTCGCCACAAAGGCTTTT
** * *
51018754 CTTTCATGTTTTGTCACAAAGGCTTTT
1 CTTTCATAATTCGCCACAAAGGCTTTT
51018781 CTTTCAT
1 CTTTCAT
51018788 GACGAGTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (27 bp):
CTTTCATAATTCGCCACAAAGGCTTTT
Found at i:51024775 original size:25 final size:25
Alignment explanation
Indices: 51024745--51024794 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
51024735 CAAAAGAGAT
51024745 GAAGAAAATAGGAGGATTTTGGCTA
1 GAAGAAAATAGGAGGATTTTGGCTA
51024770 GAAGAAAATAGGAGGATTTTGGCTA
1 GAAGAAAATAGGAGGATTTTGGCTA
51024795 TAGAGGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.24
Consensus pattern (25 bp):
GAAGAAAATAGGAGGATTTTGGCTA
Found at i:51025944 original size:27 final size:27
Alignment explanation
Indices: 51025664--51025936 Score: 330
Period size: 27 Copynumber: 10.1 Consensus size: 27
51025654 CCTTAACCGA
* **
51025664 TAAAATGACTGTTTTGTCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* *
51025691 TAAAATAATTGTTTTGCCCTTATAAGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* * **
51025718 GAAAATGATTGTTTTGCCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* *
51025745 TAAAATGGCTGTTTTGCACTTATAAGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* *
51025772 TAAAATGACTATTTTGCCTTTATAAGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
*
51025799 TAAAATGACTGTTTTTCCCTTATAAGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* * **
51025826 TAAAATGATTGTTTTTCCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* *
51025853 TAAAATGACTGTTTTTCCCTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* *
51025880 TAAAATGACTATTTTGCCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
* *
51025907 TAAAATGACTGTTTTGCCCTTTTATGG
1 TAAAATGACTGTTTTGCCCTTATAAGG
51025934 TAA
1 TAA
51025937 GATAACTGCT
Statistics
Matches: 213, Mismatches: 33, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 213 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.41
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATAAGG
Found at i:51026255 original size:18 final size:18
Alignment explanation
Indices: 51026232--51026268 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
51026222 GGACTTGCAT
*
51026232 ACTGTTTACTGTTACTGC
1 ACTGTTTACTATTACTGC
51026250 ACTGTTTACTATTACTGC
1 ACTGTTTACTATTACTGC
51026268 A
1 A
51026269 ATGGGCCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (18 bp):
ACTGTTTACTATTACTGC
Found at i:51030308 original size:93 final size:93
Alignment explanation
Indices: 51030196--51030367 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
51030186 GCCCATAAGT
* *
51030196 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
51030261 CGAGTTCGGATGCCTAGTTATATCTCAC
66 CGAGTTCGGATGCCTAGTTATATCTCAC
*
51030289 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
51030354 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
51030368 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTATATCTCAC
Found at i:51030363 original size:46 final size:46
Alignment explanation
Indices: 51030188--51030363 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
51030178 TGTAACCCGC
* * *
51030188 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
**
51030234 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ATAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
51030284 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
51030327 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
51030364 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 2 0.02
50 2 0.02
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:51032389 original size:28 final size:29
Alignment explanation
Indices: 51032283--51032399 Score: 173
Period size: 29 Copynumber: 4.1 Consensus size: 29
51032273 CACATACCTG
* *
51032283 TATATAGCCCACTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* *
51032312 TATATGGCCCATGAGGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
51032341 TATATGGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* *
51032370 CATATGG-CCATTAGGCCCAAAACACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
51032398 TA
1 TA
51032400 CAGTCATGCT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 21 0.27
29 58 0.73
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:51044274 original size:6 final size:6
Alignment explanation
Indices: 51044263--51044298 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
51044253 TACATACATG
51044263 TATTTT TATTTT TATTTT T-TTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT T
51044299 TTAATTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TATTTT
Found at i:51044287 original size:17 final size:17
Alignment explanation
Indices: 51044265--51044300 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
51044255 CATACATGTA
51044265 TTTTTATTTTTATTTTT
1 TTTTTATTTTTATTTTT
51044282 TTTTTATTTTTATTTTT
1 TTTTTATTTTTATTTTT
51044299 TT
1 TT
51044301 AATTAGGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTATTTTTATTTTT
Found at i:51054377 original size:40 final size:40
Alignment explanation
Indices: 51054269--51054438 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
51054259 CGGGATTTAA
* * * * *
51054269 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
51054309 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
51054349 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
51054389 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
51054429 CCGGATATAT
1 CCGGATATAT
51054439 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:51062404 original size:40 final size:40
Alignment explanation
Indices: 51062296--51062505 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
51062286 CGGGATTTAA
* * * * *
51062296 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
51062336 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
51062376 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
51062416 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
51062456 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
51062496 CCGGATATAT
1 CCGGATATAT
51062506 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:51068139 original size:50 final size:50
Alignment explanation
Indices: 51068064--51068164 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
51068054 AAAATGCTCA
*
51068064 GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTGGAG
1 GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
*
51068114 GTAGTAAACACATGGGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
1 GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
51068164 G
1 G
51068165 CCACGGCCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.26, C:0.22, G:0.35, T:0.18
Consensus pattern (50 bp):
GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
Found at i:51069732 original size:39 final size:39
Alignment explanation
Indices: 51069689--51069800 Score: 170
Period size: 39 Copynumber: 2.9 Consensus size: 39
51069679 TTCGAGCACG
* * * *
51069689 TAGCCTGCAGACTTCAAGTCCGGATATATTTCCAGCATA
1 TAGCCTGCGGACCTCATGTCCGGATATATTCCCAGCATA
* *
51069728 TAGCCTGCGGACCTCATGTCTGGGTATATTCCCAGCATA
1 TAGCCTGCGGACCTCATGTCCGGATATATTCCCAGCATA
51069767 TAGCCTGCGGACCTCATGTCCGGATATATTCCCA
1 TAGCCTGCGGACCTCATGTCCGGATATATTCCCA
51069801 ATATCATGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (39 bp):
TAGCCTGCGGACCTCATGTCCGGATATATTCCCAGCATA
Found at i:51072469 original size:37 final size:37
Alignment explanation
Indices: 51072415--51072515 Score: 141
Period size: 37 Copynumber: 2.7 Consensus size: 37
51072405 TTTGAGTACG
* *
51072415 TGTAAGACCATAGCTGGGCTATGGCATCGTAATGACA
1 TGTAAGACCATATCTGGGCTATGGCATCGTAATCACA
* *
51072452 TGTAAGACCATATCTGGGCTATGGCATCGTGATCCCA
1 TGTAAGACCATATCTGGGCTATGGCATCGTAATCACA
*
51072489 TGTAAGACCATGTCTGGGAC-ATGGCAT
1 TGTAAGACCATATCTGGG-CTATGGCAT
51072516 TGGCATCGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 57 0.98
38 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (37 bp):
TGTAAGACCATATCTGGGCTATGGCATCGTAATCACA
Found at i:51072535 original size:48 final size:48
Alignment explanation
Indices: 51072480--51072659 Score: 279
Period size: 48 Copynumber: 3.8 Consensus size: 48
51072470 CTATGGCATC
51072480 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
* *
51072528 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAT
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
* * * *
51072576 GTGATCCTATGTAAGACCATGTCTAGGACATGGCTTTGGCATCTATAT
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
** *
51072624 GTGATTTCGTGTAAGACCATGTCTGGGACATGGCAT
1 GTGATCCCATGTAAGACCATGTCTGGGACATGGCAT
51072660 CGATATGGGA
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 118 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (48 bp):
GTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT
Found at i:51078220 original size:19 final size:19
Alignment explanation
Indices: 51078183--51078231 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
51078173 TTCTTATTAT
* *
51078183 TTTATTATTTTATTTTTAG
1 TTTATTATTATATTGTTAG
*
51078202 TTTATTATTATCTTGTTAG
1 TTTATTATTATATTGTTAG
* *
51078221 TGTATTCTTAT
1 TTTATTATTAT
51078232 TATGATTCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTATTATTATATTGTTAG
Found at i:51082713 original size:57 final size:58
Alignment explanation
Indices: 51082595--51082717 Score: 151
Period size: 57 Copynumber: 2.1 Consensus size: 58
51082585 ATTTCTAGGT
* *
51082595 CATTTTCATTTTCAATTTGGAGAAAAAGCACATTCATTTCCAGATAATTCCATTTCTC
1 CATTTTCATTTTCAATTTGGAGAAAAAGCACAATCATTTCCAAATAATTCCATTTCTC
* * * * * *
51082653 CATTTTTATTTTTATTTTGGAG-AAAGGCATAATCATTTCCAAAT-GTTCTCATTTCTC
1 CATTTTCATTTTCAATTTGGAGAAAAAGCACAATCATTTCCAAATAATTC-CATTTCTC
51082710 CATTTTCA
1 CATTTTCA
51082718 CAATTTCTGT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
56 3 0.05
57 33 0.60
58 19 0.35
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (58 bp):
CATTTTCATTTTCAATTTGGAGAAAAAGCACAATCATTTCCAAATAATTCCATTTCTC
Found at i:51083502 original size:13 final size:13
Alignment explanation
Indices: 51083484--51083510 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51083474 GTCTATAGAC
51083484 CTCAGATGTGATT
1 CTCAGATGTGATT
51083497 CTCAGATGTGATT
1 CTCAGATGTGATT
51083510 C
1 C
51083511 CCAATATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (13 bp):
CTCAGATGTGATT
Found at i:51092054 original size:28 final size:28
Alignment explanation
Indices: 51091985--51092085 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
51091975 GACAAGATTG
* * * *
51091985 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
51092015 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
51092043 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
51092072 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
51092086 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:51092079 original size:29 final size:28
Alignment explanation
Indices: 51092014--51092085 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
51092004 AAAATTGTAC
*
51092014 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
51092042 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
51092071 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
51092086 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:51100134 original size:28 final size:28
Alignment explanation
Indices: 51100065--51100165 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
51100055 GACAAGATTG
* * * *
51100065 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
51100095 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
51100123 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
51100152 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
51100166 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:51100159 original size:29 final size:28
Alignment explanation
Indices: 51100094--51100165 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
51100084 AAAATTGTAC
*
51100094 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
51100122 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
51100151 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
51100166 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:51104556 original size:87 final size:84
Alignment explanation
Indices: 51104432--51104711 Score: 235
Period size: 87 Copynumber: 3.2 Consensus size: 84
51104422 AGCTTCAGGT
* * * *
51104432 ATCGAATATGGAAAGGGATAGTTTCGACTATCTATTATGAAAAGGGATGGTGACAACCATCAACT
1 ATCGAATATGAAAAGGGATAGTTT-GGCTATCGATTATGAAAAGGGATGGTGACAACCATC-ATT
51104497 ATGAAAAGGGATGGTGATGACC
64 ATGAAAAGGGATGGT-ATGACC
* * * *
51104519 ATCGAATATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAAGGATAGCT-TCAACTATCGAT
1 ATCGAATATGAAAAGGGATAG-TTTGGCTATCGATTATGAAAAGGGAT-GGTGACAACCATC-AT
* *
51104583 TATGAAAAGGGATGGCT-TCGGCT
63 TATGAAAAGGGATGG-TAT-GACC
* * * ** * * *
51104606 ATCGATTATGAAAAAGGATGGTGACGAGC-ATCGATTATGAAAAGGGATAGTGACGACCATTCGT
1 ATCGAATATGAAAAGGGATAGT-TTG-GCTATCGATTATGAAAAGGGATGGTGACAACCA-TCAT
*
51104670 TAATGAAAAGGGATGGTTACGACC
63 T-ATGAAAAGGGATGG-TATGACC
51104694 AAT-GAATATGAAAAGGGA
1 -ATCGAATATGAAAAGGGA
51104712 CGGTTACGAC
Statistics
Matches: 153, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
86 3 0.02
87 108 0.71
88 40 0.26
89 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (84 bp):
ATCGAATATGAAAAGGGATAGTTTGGCTATCGATTATGAAAAGGGATGGTGACAACCATCATTAT
GAAAAGGGATGGTATGACC
Found at i:51104678 original size:30 final size:29
Alignment explanation
Indices: 51104432--51104726 Score: 213
Period size: 29 Copynumber: 10.1 Consensus size: 29
51104422 AGCTTCAGGT
* * * ** *
51104432 ATCGAATATGGAAAGGGATAGTTTCGACT
1 ATCGATTATGAAAAGGGATGGTGACGACC
* *
51104461 ATCTATTATGAAAAGGGATGGTGACAACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* * *
51104490 ATCAACTATGAAAAGGGATGGTGATGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* * ** * *
51104519 ATCGAATATGAAAAGGGATAGCT-TTGGCT
1 ATCGATTATGAAAAGGGAT-GGTGACGACC
* * * * *
51104548 ATCGATTATGAAAAAGGATAGCT-TCAACT
1 ATCGATTATGAAAAGGGAT-GGTGACGACC
* * *
51104577 ATCGATTATGAAAAGGGATGGCT-TCGGCT
1 ATCGATTATGAAAAGGGATGG-TGACGACC
* *
51104606 ATCGATTATGAAAAAGGATGGTGACGAGC
1 ATCGATTATGAAAAGGGATGGTGACGACC
*
51104635 ATCGATTATGAAAAGGGATAGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
*
51104664 ATTCG-TTAATGAAAAGGGATGGTTACGACC
1 A-TCGATT-ATGAAAAGGGATGGTGACGACC
* * *
51104694 AAT-GAATATGAAAAGGGACGGTTACGACC
1 -ATCGATTATGAAAAGGGATGGTGACGACC
51104723 ATCG
1 ATCG
51104727 TTTAACACAC
Statistics
Matches: 219, Mismatches: 39, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
28 4 0.02
29 187 0.85
30 27 0.12
31 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATGGTGACGACC
Found at i:51104705 original size:59 final size:58
Alignment explanation
Indices: 51104613--51104728 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 58
51104603 GCTATCGATT
* * *
51104613 ATGAAAAAGGATGGTGACGAGCATCGATTATGAAAAGGGATAGTGACGACCATTCGTTA
1 ATGAAAAAGGATGGTGACGACCATCGAATATGAAAAGGGACAGTGACGACCA-TCGTTA
* * * *
51104672 ATGAAAAGGGATGGTTACGACCAAT-GAATATGAAAAGGGACGGTTACGACCATCGTT
1 ATGAAAAAGGATGGTGACGACC-ATCGAATATGAAAAGGGACAGTGACGACCATCGTT
51104729 TAACACACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 5 0.10
59 42 0.86
60 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (58 bp):
ATGAAAAAGGATGGTGACGACCATCGAATATGAAAAGGGACAGTGACGACCATCGTTA
Found at i:51107296 original size:34 final size:34
Alignment explanation
Indices: 51107252--51107337 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
51107242 GTACTGAATT
*
51107252 GGGCTAAGGCCCACACTGATACTGTTAC-AGTAA
1 GGGCTAAGGCCCACACTGATACTGCTACTAGTAA
* * * *
51107285 CGGGCTGAGGCCCACATTGATATTGCTACTATTAA
1 -GGGCTAAGGCCCACACTGATACTGCTACTAGTAA
* *
51107320 GGGCTTAGGCCCAGACTG
1 GGGCTAAGGCCCACACTG
51107338 TTTGCACTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 39 0.91
35 4 0.09
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (34 bp):
GGGCTAAGGCCCACACTGATACTGCTACTAGTAA
Found at i:51116204 original size:43 final size:43
Alignment explanation
Indices: 51116157--51116282 Score: 98
Period size: 42 Copynumber: 3.0 Consensus size: 43
51116147 CCCGGACGTG
*
51116157 GTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACAAA
1 GTCTTACATGTAATTCAATATCGATGCCTATGTCCCAGACAAA
* * * * **
51116200 GTCTTAGATG-AAATCAGATA-AGATGCCAATGTCCCAGACATG
1 GTCTTACATGTAATTCA-ATATCGATGCCTATGTCCCAGACAAA
* * * *
51116242 GTCTTATACGTAAATCTC-A-ATCGAGGCCTGTGTCCCAGACA
1 GTCTTACATGT-AAT-TCAATATCGATGCCTATGTCCCAGACA
51116283 CGGTTTTATA
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
42 31 0.48
43 29 0.45
44 2 0.03
45 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCTTACATGTAATTCAATATCGATGCCTATGTCCCAGACAAA
Found at i:51118581 original size:42 final size:42
Alignment explanation
Indices: 51118534--51118640 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
51118524 TATTGGTCTC
51118534 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
51118576 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
51118618 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
51118641 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:51118705 original size:27 final size:28
Alignment explanation
Indices: 51118648--51118717 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
51118638 AAAATTGTAC
**
51118648 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
51118676 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
51118703 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
51118718 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:51128914 original size:15 final size:15
Alignment explanation
Indices: 51128894--51128927 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
51128884 CAGGTCTCAA
51128894 AAAGGTTGTTGGTCC
1 AAAGGTTGTTGGTCC
51128909 AAAGGTTGTTGGTCC
1 AAAGGTTGTTGGTCC
51128924 AAAG
1 AAAG
51128928 TTTAATGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (15 bp):
AAAGGTTGTTGGTCC
Found at i:51132711 original size:25 final size:27
Alignment explanation
Indices: 51132683--51132738 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
51132673 TTTGTTATGA
* *
51132683 TATGAT-TCTAAATTGGTATG-GTTGG
1 TATGATGTCAAAAGTGGTATGTGTTGG
*
51132708 TATG-TGTCAAAAGTGGTATGTTTTGG
1 TATGATGTCAAAAGTGGTATGTGTTGG
51132734 TATGA
1 TATGA
51132739 AGGTATGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 1 0.04
25 16 0.64
26 8 0.32
ACGTcount: A:0.25, C:0.04, G:0.29, T:0.43
Consensus pattern (27 bp):
TATGATGTCAAAAGTGGTATGTGTTGG
Found at i:51136690 original size:40 final size:40
Alignment explanation
Indices: 51136614--51136797 Score: 237
Period size: 40 Copynumber: 4.6 Consensus size: 40
51136604 CAAACTCAAG
* * *
51136614 TGCCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAGA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAA
* *
51136653 TGCCTTCGGGTCTTAGCCTGGATATAGTCAATAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* * *
51136693 AGCCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* *
51136733 TGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* *
51136773 TGCCCTCGGGACTTAACCCGGATAT
1 TGCCTTCGGGACTTAGCCCGGATAT
51136798 CATTCGAATA
Statistics
Matches: 128, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 14 0.11
40 111 0.87
41 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
Found at i:51143963 original size:22 final size:20
Alignment explanation
Indices: 51143920--51143958 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
51143910 CAATTTAAAA
51143920 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
51143940 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
51143959 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:51144081 original size:20 final size:20
Alignment explanation
Indices: 51144056--51144095 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
51144046 AAATATTTTC
51144056 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
51144076 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
51144096 TCATTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:51144097 original size:34 final size:33
Alignment explanation
Indices: 51144046--51144110 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
51144036 AAACACCAGA
51144046 AAATATTTTCAGTAAATCATTTTCCAGAAAAGT
1 AAATATTTTCAGTAAATCATTTTCCAGAAAAGT
*
51144079 AAATCATTTTCCAG-AAATCATTTTCTAGAAAA
1 AAAT-ATTTT-CAGTAAATCATTTTCCAGAAAA
51144111 CATTTTACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 22 0.76
35 3 0.10
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (33 bp):
AAATATTTTCAGTAAATCATTTTCCAGAAAAGT
Found at i:51144098 original size:14 final size:14
Alignment explanation
Indices: 51144079--51144116 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
51144069 CCAGAAAAGT
51144079 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
51144093 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
51144107 AAAACATTTT
1 AAATCATTTT
51144117 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:51146505 original size:40 final size:40
Alignment explanation
Indices: 51146426--51146575 Score: 167
Period size: 40 Copynumber: 3.8 Consensus size: 40
51146416 CGGATGATAA
* * ** *
51146426 CCGGACTAAGATCCGAAGGCATTCGTGCGAATTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
*** * *
51146466 CCGGGCTATCTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTG-CTATAT
*
51146506 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* *
51146546 CTGGGCTAAGACCCGAAGGCATTTGTGCGA
1 CCGGGCTAAGACCCGAAGGCATTTATGCGA
51146576 TTATGTGTTT
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.02
40 87 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
Found at i:51153040 original size:40 final size:40
Alignment explanation
Indices: 51152961--51153137 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
51152951 CGGATGATAA
* * * *
51152961 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
51153001 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
51153041 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
51153081 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
51153121 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
51153138 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.12
40 102 0.85
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:51153405 original size:22 final size:22
Alignment explanation
Indices: 51153365--51153406 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
51153355 GAATGTGCAT
*
51153365 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
51153387 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
51153407 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:51172553 original size:39 final size:40
Alignment explanation
Indices: 51172506--51172648 Score: 182
Period size: 39 Copynumber: 3.6 Consensus size: 40
51172496 AATGTTCGAG
51172506 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* * *
51172545 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* * *
51172584 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
** * *
51172624 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAGTCCCGAAGG
51172649 TGTTTGAACG
Statistics
Matches: 89, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 51 0.57
40 38 0.43
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (40 bp):
TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
Found at i:51180561 original size:39 final size:40
Alignment explanation
Indices: 51180514--51180657 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
51180504 AATGTTCGAG
51180514 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* * *
51180553 TGATATCCGGGCTAAG-CCCGAAGGAAATTGTGCAAAGTTG
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGC-GAGTTA
* * *
51180593 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
** * *
51180633 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAGTCCCGAAGG
51180658 TGTTTTGAAC
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 32 0.36
40 42 0.47
41 15 0.17
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (40 bp):
TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
Found at i:51186337 original size:38 final size:39
Alignment explanation
Indices: 51186245--51186367 Score: 185
Period size: 39 Copynumber: 3.2 Consensus size: 39
51186235 TGTGAATGAA
*
51186245 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
51186284 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGG-AAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
51186322 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
51186362 TGTGCG
1 TGTGCG
51186368 GGTTACCATA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
38 27 0.36
39 40 0.53
40 8 0.11
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:51186385 original size:77 final size:78
Alignment explanation
Indices: 51186245--51186396 Score: 200
Period size: 78 Copynumber: 2.0 Consensus size: 78
51186235 TGTGAATGAA
** *
51186245 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTATGATATCCGGGCTAA
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTACCATAACCGGGCTAA
51186310 G-CCCGAAGGAAT
66 GTCCCGAAGGAAT
* * * * *
51186322 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACC-GGCTA
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGCTACCATAACCGGGCTA
*
51186386 TGTCCCGAAGG
65 AGTCCCGAAGG
51186397 TGTTTTGAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
77 31 0.48
78 33 0.52
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (78 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTACCATAACCGGGCTAA
GTCCCGAAGGAAT
Found at i:51189303 original size:40 final size:40
Alignment explanation
Indices: 51189234--51189427 Score: 182
Period size: 40 Copynumber: 4.8 Consensus size: 40
51189224 GGATATAACG
* * * *
51189234 ACTCGCTCGATTGTCTTCGGGACA-TAGCCCGG-TTATAGTG
1 ACTCGCACGAATGCCTTCGGGA-ATTAGCCCGGATT-TAGTA
*
51189274 ATTCGCAC-AATTGCCTTCGGGAATTAGCCCGGATTTAGTA
1 ACTCGCACGAA-TGCCTTCGGGAATTAGCCCGGATTTAGTA
* * *
51189314 ACTCGCACGAATGCCTTC-GGAACTTAACCCGGTTTTGGTA
1 ACTCGCACGAATGCCTTCGGGAA-TTAGCCCGGATTTAGTA
*
51189354 ACTCGCACGAATGCCTTCGGGAATT-GACCCGGATTTAGTC
1 ACTCGCACGAATGCCTTCGGGAATTAG-CCCGGATTTAGTA
* * * *
51189394 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACGAATGCCTTCGGGAATTAGCCCGGA
51189428 CACCATTCGA
Statistics
Matches: 128, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
39 6 0.05
40 88 0.69
41 33 0.26
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGAATTAGCCCGGATTTAGTA
Done.