Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 33 of 279
Found at i:11145867 original size:43 final size:43
Alignment explanation
Indices: 11145798--11145964 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 43
11145788 CGCTATATGT
* ** *
11145798 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTTTGCA
1 AACGCCGTTAAAGGCCATGACCTTTAGCGGCGCTTTTTTAGCA
* *
11145841 AATGCCGTTAAAGGCCATGACCTTTAGCGGCGCTTTTTTCGCA
1 AACGCCGTTAAAGGCCATGACCTTTAGCGGCGCTTTTTTAGCA
* * * * *
11145884 AACGTCGTTAAAGGCTATGGCCTTTAACGGCGCTTTTTGAGCA
1 AACGCCGTTAAAGGCCATGACCTTTAGCGGCGCTTTTTTAGCA
* * * *
11145927 AACGCCGCTAAAGGCCATGGCTTTTAGCGGCACTTTTT
1 AACGCCGTTAAAGGCCATGACCTTTAGCGGCGCTTTTT
11145965 CTAAAAACGC
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (43 bp):
AACGCCGTTAAAGGCCATGACCTTTAGCGGCGCTTTTTTAGCA
Found at i:11145973 original size:43 final size:42
Alignment explanation
Indices: 11145798--11146024 Score: 197
Period size: 43 Copynumber: 5.3 Consensus size: 42
11145788 CGCTATATGT
** *
11145798 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTTTGCA
1 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGC-TTTTTTACA
* * *
11145841 AATGCCGTTAAAGGCCATGACCTTTAGCGGCGCTTTTTTCGCA
1 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTT-ACA
* * * * * *
11145884 AACGTCGTTAAAGGCTATGGCCTTTAACGGCGCTTTTTGAGCA
1 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTTA-CA
* * * *
11145927 AACGCCGCTAAAGGCCATGGCTTTTAGCGGCACTTTTTCTAAA
1 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTT-TACA
* * ** *
11145970 AACGCCACTATA--TAATAGACCTTTAGCGACGCTTTTTTCACA
1 AACGCCGCTAAAGGCCAT-GACCTTTAGCGGCGCTTTTTT-ACA
11146012 AACGCCGCTAAAG
1 AACGCCGCTAAAG
11146025 AATATAAACT
Statistics
Matches: 148, Mismatches: 30, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
41 3 0.02
42 34 0.23
43 110 0.74
44 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (42 bp):
AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTTACA
Found at i:11146218 original size:17 final size:17
Alignment explanation
Indices: 11146178--11146212 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11146168 GATTTACACA
*
11146178 AATAAATAGAAGACAAG
1 AATAAATAAAAGACAAG
11146195 AATAAATAAAAGACAAG
1 AATAAATAAAAGACAAG
11146212 A
1 A
11146213 GAAAATGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (17 bp):
AATAAATAAAAGACAAG
Found at i:11146383 original size:75 final size:75
Alignment explanation
Indices: 11146257--11146407 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
11146247 AAGCAATCAG
*
11146257 AAAGAATAGTACAGGAAATTCTTAGTATCCTACTTGAAGAAAGCATAGGAAAATATAAAGAGGAT
1 AAAGAATAGTACAGGAAATTCTTAGTATCCTACCTGAAGAAAGCATAGGAAAATATAAAGAGGAT
*
11146322 GAGGATGAGT
66 GAGAATGAGT
*
11146332 AAAGAATAGTACAGGAAATTCTTAGTATCCTACCTGAAGAAAGCATCGGAAAATATAAAGAGGAT
1 AAAGAATAGTACAGGAAATTCTTAGTATCCTACCTGAAGAAAGCATAGGAAAATATAAAGAGGAT
11146397 GAGAATGAGT
66 GAGAATGAGT
11146407 A
1 A
11146408 CAAGGAAGCA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (75 bp):
AAAGAATAGTACAGGAAATTCTTAGTATCCTACCTGAAGAAAGCATAGGAAAATATAAAGAGGAT
GAGAATGAGT
Found at i:11150218 original size:14 final size:14
Alignment explanation
Indices: 11150201--11150230 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11150191 AATATTTATT
*
11150201 ATTATTTTTTATAA
1 ATTAGTTTTTATAA
11150215 ATTAGTTTTTATAA
1 ATTAGTTTTTATAA
11150229 AT
1 AT
11150231 AAAAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
ATTAGTTTTTATAA
Found at i:11150881 original size:8 final size:7
Alignment explanation
Indices: 11150863--11151039 Score: 68
Period size: 7 Copynumber: 24.7 Consensus size: 7
11150853 ACTAATTAAT
11150863 CTAAACC
1 CTAAACC
11150870 CTAAATCC
1 CTAAA-CC
*
11150878 CTAACCC
1 CTAAACC
*
11150885 CTAACCC
1 CTAAACC
11150892 CTAAACC
1 CTAAACC
* *
11150899 TTAAACA
1 CTAAACC
* *
11150906 ATAAAAC
1 CTAAACC
*
11150913 ATAAACC
1 CTAAACC
* *
11150920 CTTAACA
1 CTAAACC
*
11150927 CTTAACC
1 CTAAACC
*
11150934 CTTAACAC
1 CTAAAC-C
*
11150942 ATAAACC
1 CTAAACC
*
11150949 TTAAACC
1 CTAAACC
* *
11150956 CCAACCC
1 CTAAACC
*
11150963 TCTAAAAC
1 -CTAAACC
*
11150971 TTAAACC
1 CTAAACC
11150978 CT-AACC
1 CTAAACC
* *
11150984 ATTAATCC
1 -CTAAACC
*
11150992 ATAAACC
1 CTAAACC
*
11150999 ATAAACC
1 CTAAACC
* *
11151006 ATAATCC
1 CTAAACC
11151013 CTAAACC
1 CTAAACC
*
11151020 CATAATCC
1 C-TAAACC
*
11151028 ATAAACC
1 CTAAACC
*
11151035 TTAAA
1 CTAAA
11151040 ATAGTAATTC
Statistics
Matches: 129, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
6 4 0.03
7 102 0.79
8 23 0.18
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:11150956 original size:22 final size:20
Alignment explanation
Indices: 11150930--11151039 Score: 76
Period size: 22 Copynumber: 5.1 Consensus size: 20
11150920 CTTAACACTT
11150930 AACCCTTAACACATAAACCTTA
1 AACCC-TAAC-CATAAACCTTA
* * *
11150952 AACCCCAACCCTCTAAAACTTA
1 AACCCTAA-CC-ATAAACCTTA
* *
11150974 AACCCTAACCATTAATCCATA
1 AACCCTAACCA-TAAACCTTA
* * *
11150995 AACCATAAACCATAATCCCTA
1 AACCCT-AACCATAAACCTTA
11151016 AACCCATAATCCATAAACCTTA
1 AACCC-TAA-CCATAAACCTTA
11151038 AA
1 AA
11151040 ATAGTAATTC
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
21 30 0.43
22 39 0.57
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCCTAACCATAAACCTTA
Found at i:11151336 original size:40 final size:40
Alignment explanation
Indices: 11151248--11151352 Score: 108
Period size: 39 Copynumber: 2.6 Consensus size: 40
11151238 ATTTTTTGTA
*
11151248 GCGTTTTTTAAAAAAGCGCCGCTAAAGGTGTACATATAGAG
1 GCGTTTTTTAAAAAA-CGCCGCTAAACGTGTACATATAGAG
* * * *
11151289 GCATTTTTTAAAAAACGCCGCTAATACTTG-ATC-TTTAGTG
1 GCGTTTTTTAAAAAACGCCGCTAA-ACGTGTA-CATATAGAG
*
11151329 GCG-TTTTTAAAAAGCGCCGCTAAA
1 GCGTTTTTTAAAAAACGCCGCTAAA
11151353 GCCACTAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.02
39 19 0.35
40 17 0.31
41 18 0.33
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (40 bp):
GCGTTTTTTAAAAAACGCCGCTAAACGTGTACATATAGAG
Found at i:11151482 original size:40 final size:41
Alignment explanation
Indices: 11151407--11151506 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 41
11151397 TTTGCTGCGT
*
11151407 TTTTCTAAAAA-CACCGCTAAAGATCTAGAATTAGCGAC-A
1 TTTTCTAAAAAGCACCGCTAAAGATCTACAATTAGCGACGA
* * * *
11151446 TTTTCTAAAAAGCACCGCTAAAGGTGTAC-ATATAGCGGCGC
1 TTTTCTAAAAAGCACCGCTAAAGATCTACAAT-TAGCGACGA
*
11151487 TTTT-AAAAAAGCACCGCTAA
1 TTTTCTAAAAAGCACCGCTAA
11151507 TACTCAATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
39 13 0.25
40 35 0.67
41 4 0.08
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (41 bp):
TTTTCTAAAAAGCACCGCTAAAGATCTACAATTAGCGACGA
Found at i:11161982 original size:40 final size:40
Alignment explanation
Indices: 11161955--11162056 Score: 195
Period size: 40 Copynumber: 2.5 Consensus size: 40
11161945 TCTCAAATCC
11161955 CACACTAAGTGCCAAATTTAGCCGAAGCTATACTGAACCG
1 CACACTAAGTGCCAAATTTAGCCGAAGCTATACTGAACCG
11161995 CACACTAAGTGCCAAATTTAGCCGAAGCTATACTGAACCG
1 CACACTAAGTGCCAAATTTAGCCGAAGCTATACTGAACCG
*
11162035 CACACTAAGTGCCATATTTAGC
1 CACACTAAGTGCCAAATTTAGC
11162057 TGATATGTCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (40 bp):
CACACTAAGTGCCAAATTTAGCCGAAGCTATACTGAACCG
Found at i:11165624 original size:42 final size:42
Alignment explanation
Indices: 11165576--11165658 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
11165566 ATCTCTGTCG
*
11165576 CAATCTTAATTAATTAGAGAATTAGTGTTAGTTTAAAAACAA
1 CAATCTTAATTAATCAGAGAATTAGTGTTAGTTTAAAAACAA
*
11165618 CAATCTTAGTTAATCAGAGAATTAGTGTTAGTTTAAAAACA
1 CAATCTTAATTAATCAGAGAATTAGTGTTAGTTTAAAAACA
11165659 TTCTCTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (42 bp):
CAATCTTAATTAATCAGAGAATTAGTGTTAGTTTAAAAACAA
Found at i:11170383 original size:27 final size:27
Alignment explanation
Indices: 11170353--11170530 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
11170343 ATATTGAGTC
* * * *
11170353 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
11170380 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11170407 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
11170435 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
11170462 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
11170489 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11170516 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11170531 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:11170492 original size:82 final size:81
Alignment explanation
Indices: 11170374--11170529 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
11170364 TGCTATATAA
* *
11170374 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
11170439 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
11170456 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
11170520 CACTTAGTGC
65 CACTTAGTGC
11170530 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:11178446 original size:27 final size:27
Alignment explanation
Indices: 11178416--11178593 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
11178406 ATATTGAGTC
* * * *
11178416 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
11178443 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11178470 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
11178498 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
11178525 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
11178552 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11178579 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11178594 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:11178555 original size:82 final size:81
Alignment explanation
Indices: 11178437--11178592 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
11178427 TGCTATATAA
* *
11178437 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
11178502 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
11178519 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
11178583 CACTTAGTGC
65 CACTTAGTGC
11178593 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:11185628 original size:23 final size:24
Alignment explanation
Indices: 11185583--11185630 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11185573 TTTCTTTTTA
* *
11185583 TTTTATTTTTATTTTTGCGTTTCT
1 TTTTATTTTTATTTATGCATTTCT
*
11185607 TTTTGTTTTTATTTAT-CATTTCT
1 TTTTATTTTTATTTATGCATTTCT
11185630 T
1 T
11185631 GAAAGACATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.75
Consensus pattern (24 bp):
TTTTATTTTTATTTATGCATTTCT
Found at i:11189867 original size:12 final size:12
Alignment explanation
Indices: 11189850--11189883 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11189840 ACCACACGGG
*
11189850 CGTGTGGTCGCC
1 CGTGTGGTAGCC
*
11189862 CGTGTGGTAGGC
1 CGTGTGGTAGCC
11189874 CGTGTGGTAG
1 CGTGTGGTAG
11189884 TACCCGGGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.21, G:0.47, T:0.26
Consensus pattern (12 bp):
CGTGTGGTAGCC
Found at i:11196035 original size:96 final size:97
Alignment explanation
Indices: 11195864--11196047 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 97
11195854 ATTTAATTTA
** * * * * *
11195864 TTTATTTTTACTTAGGAATATATTGAACCTTTTGATGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAACAACATATCGAACCTTTTGACGCAAAGAGAGATGACAACCAAGCACCCCA
** *
11195929 CCCCGGTTACTCAATCCAACATACTCCTAATT
66 CCCCAATTACTCAACCCAACATACTCCTAATT
* *
11195961 TTTATTTTT-CTTAACAACATATCGAACCTTTTGACGCAAAGAGAGATGACAATCAAGCACCTCA
1 TTTATTTTTACTTAACAACATATCGAACCTTTTGACGCAAAGAGAGATGACAACCAAGCACCCCA
* *
11196025 CCCTAATTACTCAGCCCAACATA
66 CCCCAATTACTCAACCCAACATA
11196048 TTCTTAAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
96 64 0.88
97 9 0.12
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (97 bp):
TTTATTTTTACTTAACAACATATCGAACCTTTTGACGCAAAGAGAGATGACAACCAAGCACCCCA
CCCCAATTACTCAACCCAACATACTCCTAATT
Found at i:11196962 original size:21 final size:21
Alignment explanation
Indices: 11196937--11196986 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
11196927 AATAATTAAG
* *
11196937 TAATAAATCATTAAGATAAAA
1 TAATAAATAATTAAAATAAAA
11196958 TAATAAATAATTAAAATAAAA
1 TAATAAATAATTAAAATAAAA
11196979 TAATAAAT
1 TAATAAAT
11196987 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
TAATAAATAATTAAAATAAAA
Found at i:11197008 original size:16 final size:16
Alignment explanation
Indices: 11196970--11197031 Score: 79
Period size: 16 Copynumber: 3.7 Consensus size: 16
11196960 ATAAATAATT
11196970 AAAATAAAATAATAAATGA
1 AAAAT-AAA-AATAAA-GA
11196989 AAAATAAAAATAAAGA
1 AAAATAAAAATAAAGA
*
11197005 AAAATAACAATAAAGA
1 AAAATAAAAATAAAGA
*
11197021 GAAATAAAAAT
1 AAAATAAAAAT
11197032 TGGGTTGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
16 26 0.65
17 6 0.15
18 3 0.08
19 5 0.12
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAATAAAAATAAAGA
Found at i:11197029 original size:22 final size:23
Alignment explanation
Indices: 11196976--11197031 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
11196966 AATTAAAATA
*
11196976 AAATAATAAATGAAAAATAAAAAT
1 AAATAA-AAATGAAAAATAAAAAG
* * *
11197000 AAAGAAAAAT-AACAATAAAGAG
1 AAATAAAAATGAAAAATAAAAAG
11197022 AAATAAAAAT
1 AAATAAAAAT
11197032 TGGGTTGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.67
23 4 0.15
24 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
AAATAAAAATGAAAAATAAAAAG
Found at i:11207569 original size:25 final size:25
Alignment explanation
Indices: 11207541--11207598 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
11207531 TTTTCTTTTC
*
11207541 TTTTCTTTTCATTTTTTAGTTTAG-
1 TTTTCTTTTCATTTTTTAGATTAGA
*
11207565 TTTT-TTCTCTCTTTTTTTAGATTAGA
1 TTTTCTT-T-TCATTTTTTAGATTAGA
11207591 TTTTCTTT
1 TTTTCTTT
11207599 GTTGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
24 5 0.18
25 14 0.50
26 5 0.18
27 2 0.07
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (25 bp):
TTTTCTTTTCATTTTTTAGATTAGA
Found at i:11215913 original size:46 final size:46
Alignment explanation
Indices: 11215858--11216033 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
11215848 TATTTGGGCA
11215858 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
11215904 TCTGAACTCGTTAAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
*
11215949 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * *
11215997 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11216034 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 61 0.57
47 26 0.24
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:11215965 original size:93 final size:93
Alignment explanation
Indices: 11215854--11216026 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
11215844 AGGATATTTG
* * *
11215854 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAACTCGTTAAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTAAG
11215919 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
11215947 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTAAG
11216012 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
11216027 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTAAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:11223935 original size:26 final size:26
Alignment explanation
Indices: 11223899--11223949 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
11223889 CCATGCAATA
*
11223899 AAAGCCTTTGTGGCGTAATATGAAAT
1 AAAGCCTTTGTGGCGGAATATGAAAT
*
11223925 AAAGCTTTTGTGGCGGAATATGAAA
1 AAAGCCTTTGTGGCGGAATATGAAA
11223950 GGAATGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (26 bp):
AAAGCCTTTGTGGCGGAATATGAAAT
Found at i:11224332 original size:19 final size:19
Alignment explanation
Indices: 11224308--11224353 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
11224298 TATGAATAAT
11224308 GAAGTGATAAGATATAGAA
1 GAAGTGATAAGATATAGAA
*
11224327 GAAGTGATTAGATATAGAA
1 GAAGTGATAAGATATAGAA
11224346 GAAGTGAT
1 GAAGTGAT
11224354 GGATAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (19 bp):
GAAGTGATAAGATATAGAA
Found at i:11225001 original size:13 final size:13
Alignment explanation
Indices: 11224970--11224999 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11224960 GTTATATCTA
11224970 TATTTACTCATTG
1 TATTTACTCATTG
11224983 TATTTACTCA-TG
1 TATTTACTCATTG
11224995 TATTT
1 TATTT
11225000 TAGTTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (13 bp):
TATTTACTCATTG
Found at i:11227727 original size:25 final size:27
Alignment explanation
Indices: 11227699--11227750 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
11227689 ACTAATTGCT
*
11227699 ATATTTCTTTTAT-GAATTAT-ATTTC
1 ATATTCCTTTTATAGAATTATAATTTC
*
11227724 ATATTCCTTTTATATAATTATAATTTC
1 ATATTCCTTTTATAGAATTATAATTTC
11227751 GAACTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 6 0.26
27 5 0.22
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.58
Consensus pattern (27 bp):
ATATTCCTTTTATAGAATTATAATTTC
Found at i:11227896 original size:41 final size:41
Alignment explanation
Indices: 11227851--11227945 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
11227841 TGACGAAAAC
*
11227851 TTAAATTAGT-TGA-AATTTAATATTTTTAATGATTTATTCTT
1 TTAAATTAGTCT-ACAA-TTAATATTTTTAATAATTTATTCTT
*
11227892 TTAAATTTGTCTACAATTAATATTTTTAATAATTTATTCTT
1 TTAAATTAGTCTACAATTAATATTTTTAATAATTTATTCTT
*
11227933 TTAAATTTGTCTA
1 TTAAATTAGTCTA
11227946 TAATAAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
41 47 0.94
42 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (41 bp):
TTAAATTAGTCTACAATTAATATTTTTAATAATTTATTCTT
Found at i:11229103 original size:24 final size:24
Alignment explanation
Indices: 11229071--11229119 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11229061 AATGTAAGCA
11229071 AATGTTGCTTATTGGTTGTCTATT
1 AATGTTGCTTATTGGTTGTCTATT
11229095 AATGTTGCTTATTGGTTGTCTATT
1 AATGTTGCTTATTGGTTGTCTATT
11229119 A
1 A
11229120 GTCAACTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.53
Consensus pattern (24 bp):
AATGTTGCTTATTGGTTGTCTATT
Found at i:11230481 original size:32 final size:32
Alignment explanation
Indices: 11230445--11230507 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
11230435 TTCTGTTTTC
11230445 ACCCTAAATAAAAGAGAGAAAACATTTTTCTT
1 ACCCTAAATAAAAGAGAGAAAACATTTTTCTT
11230477 ACCCTAAATAAAAGAGAGAAAACATTTTTCT
1 ACCCTAAATAAAAGAGAGAAAACATTTTTCT
11230508 AGTTCTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.27
Consensus pattern (32 bp):
ACCCTAAATAAAAGAGAGAAAACATTTTTCTT
Found at i:11231295 original size:47 final size:47
Alignment explanation
Indices: 11231235--11231329 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
11231225 CAAGGTCAAG
11231235 TACTAATATTTTCATTAACTCTATGTTTAACAAACAAAAAGGTTATA
1 TACTAATATTTTCATTAACTCTATGTTTAACAAACAAAAAGGTTATA
*
11231282 TACTAATGTTTTCATTAACTCTATGTTTAACAAACAAAAAGGTTATA
1 TACTAATATTTTCATTAACTCTATGTTTAACAAACAAAAAGGTTATA
11231329 T
1 T
11231330 GATGTTATCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (47 bp):
TACTAATATTTTCATTAACTCTATGTTTAACAAACAAAAAGGTTATA
Found at i:11233177 original size:654 final size:658
Alignment explanation
Indices: 11231914--11233493 Score: 1986
Period size: 654 Copynumber: 2.4 Consensus size: 658
11231904 TATTAATTAG
11231914 TGTTGAGTAATTTTATCTCTTGTCTTATTAATGGGAGTATTCGAGTATTTATACATGCTATTACA
1 TGTTGAGTAATTTTATCTCTTGTCTTATTAATGGGAGTATTCGAGTATTTATACATGCTATTACA
*
11231979 GCTCACGATATGACCCCACTA-TTTTGTCTTGAC-TCTGCCGTTCCTAGTACTGACATTCTGTGT
66 GCTCACGATATGACCCCACTAGTTTTGTCTTGACTTCT--CGTTCCTAGTACTGACATTCCGTGT
* * * * * * *
11232042 GGACTTCAGACCTACTGAATACATGTTTCACTCTATGTTGCCCGCGGAGCATGCGGTCCCTCTTC
129 GGACTTCAGGCCTACTGGACACGTGTTT--CTCTAGGTTGCCTGTGGAGCATGCGGTCCC-CTTC
* *
11232107 TACGAGCTCCTTGGA-AGCATGCGAACTAAGA-TCGTGGCCTTCCCTTGGTTCGTGCGAGCTAGA
191 TACGAGCTCCTTGGACA-CATGCGAACTAAGACT-GTGGCTTTCCCTTGGTTCGTGCAAGCTAGA
* * *
11232170 TCTACAAGCCTGCTTTGCAATCTGGGTCCGTGAACTCCCCTTGCTATCCTCTCGCAATTCACTTT
254 TCTACAAGCCTGCCTTGCAATCTGGATCCGTAAACTCCCCTTGCTA----CTC-CAATT-AC--T
*** * * ** * *
11232235 GCACTCAATCATCTGATAGGACCTATCTGGGTCACGAGGTGACCCGGATCTTATCTAGGACTCAA
311 GCACTCAATCATCTGATAGGACCTATCCAAGTCACGAGATGAACCAAATCCTATCTAGGACCCAA
11232300 ATTGGTGATCACTGATGTATAACAATAGTCCCCCCTTTAGTGGGTCTAAGGAGGGTTACAAAGTG
376 ATTGGTGATCACTGATGTATAACAATAGTCCCCCCTTTAGTGGGTCTAAGGAGGGTTACAAAGTG
* * * *
11232365 GCACTTCTTAGATCCATCACATCGAGTTTAAATTCAGCTTGTTGGGTACACTACGAGCTGTGATG
441 GCACTTCTTAAATCAATCACATCGAGTTTAAATGCAGCTTGTTGGGTACACTACAAGCTGTGATG
* * * *
11232430 CACAATGGCTATTCTGCCACATGTATGAATGGGTTTTGGGTGCATGTATCTGACCGTCGAAAATT
506 CACAACGGCTATTCTACCACAGGTATGAATGGGTTTTGAGTGCATGTATCTGACCGTCGAAAATT
* * * * * *
11232495 GAACCATTTCTATCTGCTTGAATCTGGATCGTTGATCTTCTTCAGTCATATGAAGGTCGCGTGTT
571 GAACCATTTCCATCTGCTCGAATCTGGATCGTTAATCTTCCTCAGTCATATAAAGGTCACGTGTT
*
11232560 CGATCCACGCTTACCACACCAAT
636 CGATCCACGCTCACCACACCAAT
* *
11232583 TGTTGAGTAATTTTGTCTCTTGTCTTATTAATGGGAGTATTCGAGTATTTATACATGTTATTACA
1 TGTTGAGTAATTTTATCTCTTGTCTTATTAATGGGAGTATTCGAGTATTTATACATGCTATTACA
* * *
11232648 GCTCATGATATGACCCCA-TAGTTTTGTCTTGACTTCATCGTTCCTAGTATTGACATTCCGTGGG
66 GCTCACGATATGACCCCACTAGTTTTGTCTTGACTTC-TCGTTCCTAGTACTGACATTCCGTGTG
* * **
11232712 GACTTCAGGCCTACTGGACACGTGTTT-TCTGGGTTGCTTGTGGAGCACACGGTCCTCCTTCTAC
130 GACTTCAGGCCTACTGGACACGTGTTTCTCTAGGTTGCCTGTGGAGCATGCGGTCC-CCTTCTAC
* * * * *
11232776 AAGCTCCTTGGACACATGCGAACTAAGACTATGGATTTCCCTTAGTTCGTGCTAGCTAGATCTAC
194 GAGCTCCTTGGACACATGCGAACTAAGACTGTGGCTTTCCCTTGGTTCGTGCAAGCTAGATCTAC
* *
11232841 AAGCCTGCCTTGCGAGT-TGGATTCGTAAACTCCCCTTGCTA-T-C-A-T-C-GCACTCAATCAT
259 AAGCCTGCCTTGC-AATCTGGATCCGTAAACTCCCCTTGCTACTCCAATTACTGCACTCAATCAT
* * ***
11232899 CTGGTGGGACCTATCCAAGTCACAGGTAGATGAACCAAATCCTATCTAGGACCCGGGTTGGTGAT
323 CTGATAGGACCTATCCAAGTCAC--G-AGATGAACCAAATCCTATCTAGGACCCAAATTGGTGAT
* *
11232964 CACTGATGTATAACAATAGTCCCCCC-TTAGTGGGTCTAAGGAGGGTTACAAATTGGCGCTTCTT
385 CACTGATGTATAACAATAGTCCCCCCTTTAGTGGGTCTAAGGAGGGTTACAAAGTGGCACTTCTT
* *
11233028 AAATCAATCACATTGAGTTTAAATGCAGCTTGTTGGGTACACTCCAAGCTGTGATGCACAACGGC
450 AAATCAATCACATCGAGTTTAAATGCAGCTTGTTGGGTACACTACAAGCTGTGATGCACAACGGC
* * * **
11233093 TATTCTACCACGGGTATGAATGGGTTTTGAGTGCATGTATTTGACCGTTGAAAATTGAACTGTTT
515 TATTCTACCACAGGTATGAATGGGTTTTGAGTGCATGTATCTGACCGTCGAAAATTGAACCATTT
* ** * * * ** *
11233158 CCATCTGCTCGCATCTGGATTTTTAATCTTCCTCGGTCATCTAAAGGTCACGTGTTTGATTTATG
580 CCATCTGCTCGAATCTGGATCGTTAATCTTCCTCAGTCATATAAAGGTCACGTGTTCGATCCACG
11233223 CTCACCACACCAAT
645 CTCACCACACCAAT
* *
11233237 TGTTGAGTAATTTTATCTCTTATCTTATTAATGGGAGTATTCAAGTATTTATACATGCTATTACA
1 TGTTGAGTAATTTTATCTCTTGTCTTATTAATGGGAGTATTCGAGTATTTATACATGCTATTACA
* * * * *
11233302 GCTTACGATATGACCCCACT-GTTTTCTCTTGACTCCGTCGTTCCTAATACTGACATTTCGTGTG
66 GCTCACGATATGACCCCACTAGTTTTGTCTTGACTTC-TCGTTCCTAGTACTGACATTCCGTGTG
** * *
11233366 GACTTCAGGCCTGTTGGACACGTATTTCACTCTAGGTTGCCTGTGGAGCATGCAGTCCCCCTTCT
130 GACTTCAGGCCTACTGGACACGTGTTT--CTCTAGGTTGCCTGTGGAGCATGCGGT-CCCCTTCT
* * * * *
11233431 ACGAGCTCGTTGGACGCATGTGAATTAAGACCGTGGCCTTT-CCTTGGTTCGTGCAAGCTAGAT
192 ACGAGCTCCTTGGACACATGCGAACTAAGACTGTGG-CTTTCCCTTGGTTCGTGCAAGCTAGAT
11233494 TGCGAGCTGG
Statistics
Matches: 789, Mismatches: 106, Indels: 44
0.84 0.11 0.05
Matches are distributed among these distances:
652 30 0.04
654 353 0.45
655 57 0.07
657 77 0.10
658 6 0.01
659 1 0.00
661 1 0.00
666 116 0.15
667 5 0.01
668 2 0.00
669 138 0.17
670 2 0.00
671 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (658 bp):
TGTTGAGTAATTTTATCTCTTGTCTTATTAATGGGAGTATTCGAGTATTTATACATGCTATTACA
GCTCACGATATGACCCCACTAGTTTTGTCTTGACTTCTCGTTCCTAGTACTGACATTCCGTGTGG
ACTTCAGGCCTACTGGACACGTGTTTCTCTAGGTTGCCTGTGGAGCATGCGGTCCCCTTCTACGA
GCTCCTTGGACACATGCGAACTAAGACTGTGGCTTTCCCTTGGTTCGTGCAAGCTAGATCTACAA
GCCTGCCTTGCAATCTGGATCCGTAAACTCCCCTTGCTACTCCAATTACTGCACTCAATCATCTG
ATAGGACCTATCCAAGTCACGAGATGAACCAAATCCTATCTAGGACCCAAATTGGTGATCACTGA
TGTATAACAATAGTCCCCCCTTTAGTGGGTCTAAGGAGGGTTACAAAGTGGCACTTCTTAAATCA
ATCACATCGAGTTTAAATGCAGCTTGTTGGGTACACTACAAGCTGTGATGCACAACGGCTATTCT
ACCACAGGTATGAATGGGTTTTGAGTGCATGTATCTGACCGTCGAAAATTGAACCATTTCCATCT
GCTCGAATCTGGATCGTTAATCTTCCTCAGTCATATAAAGGTCACGTGTTCGATCCACGCTCACC
ACACCAAT
Found at i:11233751 original size:19 final size:17
Alignment explanation
Indices: 11233727--11233775 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
11233717 TTTAATTAAA
11233727 TAAATATAACTTTTATCTT
1 TAAATATAA-TTTTAT-TT
*
11233746 TAAATATGATTTTATTT
1 TAAATATAATTTTATTT
*
11233763 TATAATAAAATTT
1 TA-AATATAATTT
11233776 CATGTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 14 0.54
19 8 0.31
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TAAATATAATTTTATTT
Found at i:11234000 original size:13 final size:14
Alignment explanation
Indices: 11233982--11234010 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11233972 ATAAATTTTT
11233982 ATTTA-TAAATATG
1 ATTTATTAAATATG
11233995 ATTTATTAAATATG
1 ATTTATTAAATATG
11234009 AT
1 AT
11234011 AATAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTTATTAAATATG
Found at i:11234180 original size:24 final size:23
Alignment explanation
Indices: 11234153--11234197 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
11234143 TTTTTAATTT
*
11234153 ATATAAAAATTCAAAAGAAAATAA
1 ATATAAAAATT-AAAACAAAATAA
* *
11234177 ATATTATAATTAAAACAAAAT
1 ATATAAAAATTAAAACAAAAT
11234198 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
ATATAAAAATTAAAACAAAATAA
Found at i:11234411 original size:20 final size:19
Alignment explanation
Indices: 11234367--11234416 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
11234357 AATTTTTTTA
11234367 AATAT-ATA-AAAATAATG
1 AATATAATATAAAATAATG
* *
11234384 AATGTAATATAAAATAATT
1 AATATAATATAAAATAATG
11234403 AACTATAATTATAA
1 AA-TATAA-TATAA
11234417 TTATAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 3 0.12
19 10 0.38
20 4 0.15
21 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (19 bp):
AATATAATATAAAATAATG
Found at i:11234518 original size:15 final size:15
Alignment explanation
Indices: 11234498--11234528 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11234488 ATTGTAGTTA
11234498 TTTTATTAATAATGT
1 TTTTATTAATAATGT
*
11234513 TTTTATTATTAATGT
1 TTTTATTAATAATGT
11234528 T
1 T
11234529 ATACTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTATTAATAATGT
Found at i:11242920 original size:30 final size:30
Alignment explanation
Indices: 11242886--11242945 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
11242876 ATTTAATACG
11242886 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
11242916 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
11242946 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:11244305 original size:15 final size:15
Alignment explanation
Indices: 11244285--11244315 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11244275 AAACTTGTAA
11244285 AAATTAAATAAAACT
1 AAATTAAATAAAACT
11244300 AAATTAAATAAAACT
1 AAATTAAATAAAACT
11244315 A
1 A
11244316 CTAACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAATAAAACT
Found at i:11253744 original size:34 final size:34
Alignment explanation
Indices: 11253701--11253768 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
11253691 ACACAGGCTA
11253701 CCACACGGGCAGACCACACGTCCGTGCGGCGTCG
1 CCACACGGGCAGACCACACGTCCGTGCGGCGTCG
11253735 CCACACGGGCAGACCACACGTCCGTGCGGCGTCG
1 CCACACGGGCAGACCACACGTCCGTGCGGCGTCG
11253769 ACAGGCCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.18, C:0.41, G:0.32, T:0.09
Consensus pattern (34 bp):
CCACACGGGCAGACCACACGTCCGTGCGGCGTCG
Found at i:11260978 original size:11 final size:11
Alignment explanation
Indices: 11260962--11261053 Score: 64
Period size: 11 Copynumber: 8.5 Consensus size: 11
11260952 AGAGTTATAC
11260962 AATAATAACAA
1 AATAATAACAA
*
11260973 AATAATAATAA
1 AATAATAACAA
* ***
11260984 TATAATAGTGA
1 AATAATAACAA
*
11260995 AATAGTAACAA
1 AATAATAACAA
11261006 AATAA-AGA-AA
1 AATAATA-ACAA
* *
11261016 AACAATAAAAA
1 AATAATAACAA
* *
11261027 AATAACAACAG
1 AATAATAACAA
11261038 AATAATAA-AA
1 AATAATAACAA
11261048 AATAAT
1 AATAAT
11261054 TTTTTTTGCA
Statistics
Matches: 61, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
10 15 0.25
11 46 0.75
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (11 bp):
AATAATAACAA
Found at i:11260990 original size:25 final size:25
Alignment explanation
Indices: 11260939--11260990 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
11260929 GCAACAAAAT
* * *
11260939 TAATAATAAAATAAGAGTTATACAA
1 TAATAACAAAATAAGAATAATACAA
* *
11260964 TAATAACAAAATAATAATAATATAA
1 TAATAACAAAATAAGAATAATACAA
11260989 TA
1 TA
11260991 GTGAAATAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
TAATAACAAAATAAGAATAATACAA
Found at i:11264485 original size:51 final size:51
Alignment explanation
Indices: 11264409--11264510 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
11264399 CAAGTTATGT
11264409 ACTACTAAATGACACCTTTTTTAATAGGAAATTACACTTTGAAAGAAAGTG
1 ACTACTAAATGACACCTTTTTTAATAGGAAATTACACTTTGAAAGAAAGTG
11264460 ACTACTAAATGACACCTTTTTTAATAGGAAATTACACTTTGAAAGAAAGTG
1 ACTACTAAATGACACCTTTTTTAATAGGAAATTACACTTTGAAAGAAAGTG
11264511 TTTTCACATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (51 bp):
ACTACTAAATGACACCTTTTTTAATAGGAAATTACACTTTGAAAGAAAGTG
Found at i:11269539 original size:31 final size:31
Alignment explanation
Indices: 11269501--11269564 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
11269491 GGATCCATTC
11269501 TTTGGTTAAATC-AAATTTTGCCCCTGAATTA
1 TTTGGTTAAATCAAAATTTT-CCCCTGAATTA
11269532 TTTGGTTAAATCAAAATTTTCCCCTGAATTA
1 TTTGGTTAAATCAAAATTTTCCCCTGAATTA
11269563 TT
1 TT
11269565 CATTTGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTGGTTAAATCAAAATTTTCCCCTGAATTA
Found at i:11271653 original size:33 final size:33
Alignment explanation
Indices: 11271593--11271663 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
11271583 AGTAGCAGTT
* *
11271593 GTTTCCTCACCCAAGTTTGCAGGAATGGT-TGTA
1 GTTTCCTCACCCAAGGTTGCAGAAATGGTCTG-A
* *
11271626 GTTTCCTCACCCATGGTTGTAGAAATGGTCTGA
1 GTTTCCTCACCCAAGGTTGCAGAAATGGTCTGA
11271659 GTTTC
1 GTTTC
11271664 TGGACCCGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (33 bp):
GTTTCCTCACCCAAGGTTGCAGAAATGGTCTGA
Found at i:11271738 original size:33 final size:34
Alignment explanation
Indices: 11271688--11271773 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 34
11271678 CTGGAACAGT
* * * * *
11271688 AGGAGTTCCCTCACTGAAAGGAT-GAGGAATTGT
1 AGGAGTTTCTTCACTGAAAGGATGGAAGAATGGC
** *
11271721 AGGAGTTTCTTTGCTG-AATGATGGAAGAATGGC
1 AGGAGTTTCTTCACTGAAAGGATGGAAGAATGGC
11271754 AGGAGTTTCTTCACTGAAAG
1 AGGAGTTTCTTCACTGAAAG
11271774 TCAGAGGAAC
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
32 5 0.12
33 33 0.82
34 2 0.05
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.28
Consensus pattern (34 bp):
AGGAGTTTCTTCACTGAAAGGATGGAAGAATGGC
Found at i:11279007 original size:31 final size:31
Alignment explanation
Indices: 11278966--11279035 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
11278956 AGAGAGAGAG
*
11278966 AGAGAGAAAGAAAAGATTTGTATTAAATAGA
1 AGAGAAAAAGAAAAGATTTGTATTAAATAGA
*
11278997 AGAGAAAAAGAAAAGATTTGTGTTAAATAGA
1 AGAGAAAAAGAAAAGATTTGTATTAAATAGA
11279028 AGAGAAAA
1 AGAGAAAA
11279036 CAAATTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (31 bp):
AGAGAAAAAGAAAAGATTTGTATTAAATAGA
Found at i:11283786 original size:29 final size:29
Alignment explanation
Indices: 11283754--11283856 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
11283744 AGGTCACCAC
* * *
11283754 AAAGGCTTTCTTATAATAGAGATTGCCGA
1 AAAGGCTTTCTTATAATTGAGATAGCCAA
*
11283783 AAAGGC-TTCATTATAATTGAGATCGCCAA
1 AAAGGCTTTC-TTATAATTGAGATAGCCAA
* * * *
11283812 AAAGACTTCCTTATAATTGAGATAGCTAC
1 AAAGGCTTTCTTATAATTGAGATAGCCAA
11283841 AAAGGCTTTCTTATAA
1 AAAGGCTTTCTTATAA
11283857 CAAAGATAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 57 0.92
30 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (29 bp):
AAAGGCTTTCTTATAATTGAGATAGCCAA
Found at i:11287166 original size:115 final size:114
Alignment explanation
Indices: 11286958--11287363 Score: 408
Period size: 115 Copynumber: 3.6 Consensus size: 114
11286948 CCAGTGCCAA
* * * * * * **
11286958 AAGTATTGATACCCA-ATGCTTGTATCGATACTAAATTCGGC-TTCGATGTTTTGAAAAATATGA
1 AAGTATTGATACCCATA-GCTGGTATCGATACCAATTTAGACTTTTGATGTTTACAAAAA-ATGA
* * *
11287021 AAAATAAATACTAAGTATCGATACATTCACCAAGGTATCGATACCAGGGAC-T
64 AAAATAAATCCTAAGTATCGATACAATCACCAAAGTATCGATACCA--GACAT
* ** * * ***
11287073 AAGAATTGATACCCATAGCTATTATCGATACCAATTTTGTCTTTTGATGTTTAGGGAAAATGAAA
1 AAGTATTGATACCCATAGCTGGTATCGATACCAATTTAGACTTTTGATGTTTACAAAAAATGAAA
*
11287138 AATAAATCCTAAGTATCGATACAATCACCAAAGTATTGATACCAGACCAT
66 AATAAATCCTAAGTATCGATACAATCACCAAAGTATCGATACCAGA-CAT
** * * * *
11287188 AAGTATCAATACCCATAGCTGGTATCAATACCAATTTCGAC-TTCGATGTTTTCAAAAAATGAAA
1 AAGTATTGATACCCATAGCTGGTATCGATACCAATTTAGACTTTTGATGTTTACAAAAAATGAAA
* * * * *
11287252 AATAAATCCTAAGTATCGATACCATCACCAATGTATCAATATCAAGCCAT
66 AATAAATCCTAAGTATCGATACAATCACCAAAGTATCGATA-CCAGACAT
* * * *
11287302 AACTATTGATACCCATAGTTGGTATCGATACCAATTTAGGCTTTT-ATGTTTTCAAAAAATGA
1 AAGTATTGATACCCATAGCTGGTATCGATACCAATTTAGACTTTTGATGTTTACAAAAAATGA
11287364 GGAAAAATTA
Statistics
Matches: 243, Mismatches: 42, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
113 2 0.01
114 110 0.45
115 117 0.48
116 14 0.06
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (114 bp):
AAGTATTGATACCCATAGCTGGTATCGATACCAATTTAGACTTTTGATGTTTACAAAAAATGAAA
AATAAATCCTAAGTATCGATACAATCACCAAAGTATCGATACCAGACAT
Found at i:11287279 original size:114 final size:114
Alignment explanation
Indices: 11286958--11287363 Score: 444
Period size: 114 Copynumber: 3.5 Consensus size: 114
11286948 CCAGTGCCAA
* * * *
11286958 AAGTATTGATACCCA-ATGCTTGTATCGATACTAAATTCGGCTTCGATGTTTTGAAAAATATGAA
1 AAGTATTGATACCCATA-GCTGGTATCGATACCAATTTCGGCTTCGATGTTTTCAAAAA-ATGAA
* *
11287022 AAATAAATACTAAGTATCGATA-CATTCACCAAGGTATCGATACCAGGGA-C-T
64 AAATAAATCCTAAGTATCGATACCA-TCACCAAAGTATCGATACCA--GACCAT
* ** * * * ****
11287073 AAGAATTGATACCCATAGCTATTATCGATACCAATTTTGTCTTTTGATGTTTAGGGAAAATGAAA
1 AAGTATTGATACCCATAGCTGGTATCGATACCAATTTCGGC-TTCGATGTTTTCAAAAAATGAAA
* *
11287138 AATAAATCCTAAGTATCGATACAATCACCAAAGTATTGATACCAGACCAT
65 AATAAATCCTAAGTATCGATACCATCACCAAAGTATCGATACCAGACCAT
** * *
11287188 AAGTATCAATACCCATAGCTGGTATCAATACCAATTTCGACTTCGATGTTTTCAAAAAATGAAAA
1 AAGTATTGATACCCATAGCTGGTATCGATACCAATTTCGGCTTCGATGTTTTCAAAAAATGAAAA
* * *
11287253 ATAAATCCTAAGTATCGATACCATCACCAATGTATCAATATCA-AGCCAT
66 ATAAATCCTAAGTATCGATACCATCACCAAAGTATCGATACCAGA-CCAT
* * * **
11287302 AACTATTGATACCCATAGTTGGTATCGATACCAATTTAGGCTTTTATGTTTTCAAAAAATGA
1 AAGTATTGATACCCATAGCTGGTATCGATACCAATTTCGGCTTCGATGTTTTCAAAAAATGA
11287364 GGAAAAATTA
Statistics
Matches: 243, Mismatches: 42, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
113 3 0.01
114 115 0.47
115 110 0.45
116 15 0.06
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (114 bp):
AAGTATTGATACCCATAGCTGGTATCGATACCAATTTCGGCTTCGATGTTTTCAAAAAATGAAAA
ATAAATCCTAAGTATCGATACCATCACCAAAGTATCGATACCAGACCAT
Found at i:11292564 original size:18 final size:18
Alignment explanation
Indices: 11292541--11292578 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
11292531 TTTCCTTATT
11292541 TTCCCCTAAAACTTTTAC
1 TTCCCCTAAAACTTTTAC
11292559 TTCCCCTAAAACTTTTAC
1 TTCCCCTAAAACTTTTAC
11292577 TT
1 TT
11292579 TCCTCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (18 bp):
TTCCCCTAAAACTTTTAC
Found at i:11292625 original size:25 final size:26
Alignment explanation
Indices: 11292562--11292615 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
11292552 CTTTTACTTC
*
11292562 CCCT-AAAACTTTTACTTTCCTCAAA
1 CCCTCAAAACTTTTACTTCCCTCAAA
11292587 CCCTCAAAACTTTTACTTCCCTCAAA
1 CCCTCAAAACTTTTACTTCCCTCAAA
11292613 CCC
1 CCC
11292616 CCAATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.31
Consensus pattern (26 bp):
CCCTCAAAACTTTTACTTCCCTCAAA
Found at i:11292900 original size:18 final size:17
Alignment explanation
Indices: 11292879--11292912 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11292869 TTAAAAAAGC
*
11292879 ATATTTTTTTTACATTTA
1 ATATATTTTTTA-ATTTA
11292897 ATATATTTTTTAATTT
1 ATATATTTTTTAATTT
11292913 CAAAATACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
ATATATTTTTTAATTTA
Found at i:11299470 original size:40 final size:40
Alignment explanation
Indices: 11299415--11299495 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
11299405 AATAGGAAAT
*
11299415 GCATACAGTTGGTTTCATGTGTATATGTTGATGTTCAAAG
1 GCATACAGTTGGTTTCATGTGTACATGTTGATGTTCAAAG
11299455 GCATACAGTTGGTTTCATGTGTACATGTTGATGTTCAAAG
1 GCATACAGTTGGTTTCATGTGTACATGTTGATGTTCAAAG
11299495 G
1 G
11299496 AATGGTAGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (40 bp):
GCATACAGTTGGTTTCATGTGTACATGTTGATGTTCAAAG
Found at i:11301736 original size:78 final size:76
Alignment explanation
Indices: 11301581--11301779 Score: 220
Period size: 77 Copynumber: 2.6 Consensus size: 76
11301571 ACAGGAAAAG
* * ** * *
11301581 AATCCTGAAACATAATTATTCAATTGATTTCTGTTTGAAACAAAAAAATTGAACAAATCCTTTTA
1 AATCCTGAAACAAAATTATTCAATTGATTTTTGTTTGAAAC--AAAAATCAAACAAATCCTATCA
11301646 AACAACAAGAATA
64 AACAACAAGAATA
* *
11301659 ACATCCTGAAACAAAATTTTTCAATTGCTTTTTTGTTTGAAACAAAAATCAAACAAATCCTATCA
1 A-ATCCTGAAACAAAATTATTCAATTG-ATTTTTGTTTGAAACAAAAATCAAACAAATCCTATCA
** *
11301724 AACAGTAGGAATA
64 AACAACAAGAATA
* *
11301737 AA-CCTTGAAACAAGATTGTTCAATTGAATTTTTGTTTGAAACA
1 AATCC-TGAAACAAAATTATTCAATTG-ATTTTTGTTTGAAACA
11301780 TAATACAATC
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
76 2 0.02
77 35 0.34
78 30 0.29
79 23 0.22
80 13 0.13
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (76 bp):
AATCCTGAAACAAAATTATTCAATTGATTTTTGTTTGAAACAAAAATCAAACAAATCCTATCAAA
CAACAAGAATA
Found at i:11311830 original size:15 final size:15
Alignment explanation
Indices: 11311810--11311842 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11311800 ACTCCATTTT
11311810 ATTTATATTAGGATA
1 ATTTATATTAGGATA
11311825 ATTTATATTAGGATA
1 ATTTATATTAGGATA
11311840 ATT
1 ATT
11311843 ATTAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (15 bp):
ATTTATATTAGGATA
Found at i:11316480 original size:40 final size:40
Alignment explanation
Indices: 11316375--11316631 Score: 396
Period size: 40 Copynumber: 6.5 Consensus size: 40
11316365 CGGATGATAA
* *
11316375 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
11316415 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
11316454 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
11316494 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
11316534 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
11316574 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
11316614 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
11316632 TACTTGGTTT
Statistics
Matches: 204, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
39 51 0.25
40 153 0.75
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:11316612 original size:120 final size:119
Alignment explanation
Indices: 11316371--11316631 Score: 402
Period size: 119 Copynumber: 2.2 Consensus size: 119
11316361 TATTCGGATG
*
11316371 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
* * *
11316436 TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
*
11316490 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAG-CCCGAAGGC
11316554 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
64 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTA-CT
* * *
11316610 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
11316632 TACTTGGTTT
Statistics
Matches: 131, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
118 2 0.02
119 65 0.50
120 64 0.49
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
Found at i:11328913 original size:22 final size:21
Alignment explanation
Indices: 11328887--11328947 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
11328877 AGGCAACCCA
11328887 ATTTATATTTA-TATTTTATTT
1 ATTTATATTTATTATTTTA-TT
11328908 ATTT-TATCTTATTATTTTATT
1 ATTTATAT-TTATTATTTTATT
11328929 ATTTATTATTTATTATTTT
1 ATTTA-TATTTATTATTTT
11328948 CAGATATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 17 0.47
23 3 0.08
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTATATTTATTATTTTATT
Found at i:11328935 original size:7 final size:7
Alignment explanation
Indices: 11328887--11328946 Score: 56
Period size: 7 Copynumber: 8.6 Consensus size: 7
11328877 AGGCAACCCA
11328887 ATTTA-T
1 ATTTATT
11328893 ATTTA-T
1 ATTTATT
11328899 A-TT-TT
1 ATTTATT
11328904 ATTTATTTT
1 ATTTA--TT
11328913 ATCTTATT
1 AT-TTATT
11328921 ATTTTATT
1 A-TTTATT
11328929 ATTTATT
1 ATTTATT
11328936 ATTTATT
1 ATTTATT
11328943 ATTT
1 ATTT
11328947 TCAGATATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
5 4 0.09
6 9 0.19
7 17 0.36
8 9 0.19
9 5 0.11
10 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:11330547 original size:15 final size:15
Alignment explanation
Indices: 11330527--11330559 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11330517 ACTCCATTTT
11330527 ATTTATATTAGGATA
1 ATTTATATTAGGATA
11330542 ATTTATATTAGGATA
1 ATTTATATTAGGATA
11330557 ATT
1 ATT
11330560 ATTAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (15 bp):
ATTTATATTAGGATA
Found at i:11332242 original size:21 final size:21
Alignment explanation
Indices: 11332216--11332257 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11332206 ATTCAATATT
*
11332216 GATACTTACCTTATAATTTTA
1 GATACTGACCTTATAATTTTA
11332237 GATACTGACCTTATAATTTTA
1 GATACTGACCTTATAATTTTA
11332258 CTTACCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (21 bp):
GATACTGACCTTATAATTTTA
Found at i:11341979 original size:324 final size:324
Alignment explanation
Indices: 11341390--11342038 Score: 1298
Period size: 324 Copynumber: 2.0 Consensus size: 324
11341380 AAACTTCTCA
11341390 ATCTCATTTCTATTTATTTCATCGCATATAAACATTATATAAACAATATGTATTATACACGAACT
1 ATCTCATTTCTATTTATTTCATCGCATATAAACATTATATAAACAATATGTATTATACACGAACT
11341455 AACCTCAGACGTAAAATCGACGATATTAGTCGATCAATCGAGTACTTTGTTTTTACCTCGATCTA
66 AACCTCAGACGTAAAATCGACGATATTAGTCGATCAATCGAGTACTTTGTTTTTACCTCGATCTA
11341520 GGTCCGAATTTCTCCTTTCTTGATCTATATGTATTCAAAATTAACTCATAATCACGAACACATTC
131 GGTCCGAATTTCTCCTTTCTTGATCTATATGTATTCAAAATTAACTCATAATCACGAACACATTC
11341585 GATTTAATATACAAACACATCTTTGGACATTTTTGTTCTTTAGCCCCTAAAATTACACATTTTGA
196 GATTTAATATACAAACACATCTTTGGACATTTTTGTTCTTTAGCCCCTAAAATTACACATTTTGA
11341650 CATTTTAGTCCTTATTACACAAAACACCAAATATACAAAATTCATTAAAACAATGCCTTAGCTG
261 CATTTTAGTCCTTATTACACAAAACACCAAATATACAAAATTCATTAAAACAATGCCTTAGCTG
11341714 ATCTCATTTCTATTTATTTCATCGCATATAAACATTATATAAACAATATGTATTATACACGAACT
1 ATCTCATTTCTATTTATTTCATCGCATATAAACATTATATAAACAATATGTATTATACACGAACT
11341779 AACCTCAGACGTAAAATCGACGATATTAGTCGATCAATCGAGTACTTTGTTTTTACCTCGATCTA
66 AACCTCAGACGTAAAATCGACGATATTAGTCGATCAATCGAGTACTTTGTTTTTACCTCGATCTA
11341844 GGTCCGAATTTCTCCTTTCTTGATCTATATGTATTCAAAATTAACTCATAATCACGAACACATTC
131 GGTCCGAATTTCTCCTTTCTTGATCTATATGTATTCAAAATTAACTCATAATCACGAACACATTC
11341909 GATTTAATATACAAACACATCTTTGGACATTTTTGTTCTTTAGCCCCTAAAATTACACATTTTGA
196 GATTTAATATACAAACACATCTTTGGACATTTTTGTTCTTTAGCCCCTAAAATTACACATTTTGA
11341974 CATTTTAGTCCTTATTACACAAAACACCAAATATACAAAATTCATTAAAACAATGCCTTAGCTG
261 CATTTTAGTCCTTATTACACAAAACACCAAATATACAAAATTCATTAAAACAATGCCTTAGCTG
11342038 A
1 A
11342039 ATTTTCCTAT
Statistics
Matches: 325, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
324 325 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (324 bp):
ATCTCATTTCTATTTATTTCATCGCATATAAACATTATATAAACAATATGTATTATACACGAACT
AACCTCAGACGTAAAATCGACGATATTAGTCGATCAATCGAGTACTTTGTTTTTACCTCGATCTA
GGTCCGAATTTCTCCTTTCTTGATCTATATGTATTCAAAATTAACTCATAATCACGAACACATTC
GATTTAATATACAAACACATCTTTGGACATTTTTGTTCTTTAGCCCCTAAAATTACACATTTTGA
CATTTTAGTCCTTATTACACAAAACACCAAATATACAAAATTCATTAAAACAATGCCTTAGCTG
Found at i:11345142 original size:43 final size:42
Alignment explanation
Indices: 11345079--11345198 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 42
11345069 TACCATACCA
* *
11345079 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCGTATCG
1 ATGCCATAGCCCAGATATGGTCTTACACGAAATCTCGTATCG
* * *
11345121 ATGCCAATAGCCTAGTTATGGTCTTACACGAAGTCTCGTATCG
1 ATGCC-ATAGCCCAGATATGGTCTTACACGAAATCTCGTATCG
* *
11345164 ATGCCATATCCCAGATATGGTCTTACACGTAATCT
1 ATGCCATAGCCCAGATATGGTCTTACACGAAATCT
11345199 TAGTAAACCT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 30 0.45
43 37 0.55
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGCCATAGCCCAGATATGGTCTTACACGAAATCTCGTATCG
Found at i:11351911 original size:21 final size:21
Alignment explanation
Indices: 11351869--11351911 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11351859 TTATGGCCTT
*
11351869 AAATGATTGGTTTATGTATGG
1 AAATGATTGGTATATGTATGG
* *
11351890 AAATGATTGGTATGTGTTTGG
1 AAATGATTGGTATATGTATGG
11351911 A
1 A
11351912 GATATTTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (21 bp):
AAATGATTGGTATATGTATGG
Found at i:11367223 original size:21 final size:22
Alignment explanation
Indices: 11367197--11367241 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
11367187 ATATAGTTAC
* *
11367197 AATTAAAGA-ATAAATATGGTT
1 AATTAAAGACATAAACATGATT
*
11367218 AATTAATGACATAAACATGATT
1 AATTAAAGACATAAACATGATT
11367240 AA
1 AA
11367242 CTAAGTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (22 bp):
AATTAAAGACATAAACATGATT
Found at i:11374214 original size:13 final size:13
Alignment explanation
Indices: 11374196--11374222 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11374186 CTTTATTTTA
11374196 TATATATATGATG
1 TATATATATGATG
11374209 TATATATATGATG
1 TATATATATGATG
11374222 T
1 T
11374223 TCATGTAGCA
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATATATATGATG
Found at i:11377441 original size:33 final size:32
Alignment explanation
Indices: 11377404--11377497 Score: 82
Period size: 33 Copynumber: 2.8 Consensus size: 32
11377394 TGAATGTTGG
**
11377404 AGGAACAGATGGAGTTTCTTCATCCAAGGTTTC
1 AGGAACAG-TGGAGTTTCTTCATCCAAGGTCAC
* * * *
11377437 AGGAATACTGGGGCTTTCCTC-TGCCAAGGTCAC
1 AGGAACAGTGGAG-TTTCTTCAT-CCAAGGTCAC
*
11377470 AGGATCAGTAGGAGTTTCTTCATCCAAG
1 AGGAACAGT-GGAGTTTCTTCATCCAAG
11377498 TTAGTTGGAA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
32 5 0.11
33 37 0.80
34 4 0.09
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (32 bp):
AGGAACAGTGGAGTTTCTTCATCCAAGGTCAC
Found at i:11387100 original size:25 final size:25
Alignment explanation
Indices: 11387038--11387091 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
11387028 TTTTTGGGTT
*
11387038 TTAATAATTATTTTTATATTTAAAC
1 TTAATAATTATTTTTATATTAAAAC
*
11387063 TTAATAATTATTTTTATATTAAAAT
1 TTAATAATTATTTTTATATTAAAAC
11387088 TTAA
1 TTAA
11387092 GTTTTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAATAATTATTTTTATATTAAAAC
Found at i:11388216 original size:20 final size:20
Alignment explanation
Indices: 11388179--11388216 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11388169 CTTTGCAGAG
*
11388179 TAAGGGACGAAACTTTCCTC
1 TAAGGGACGAAACCTTCCTC
11388199 TAAGGGAC-AATACCTTCC
1 TAAGGGACGAA-ACCTTCC
11388217 ATTGTTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
TAAGGGACGAAACCTTCCTC
Found at i:11389789 original size:48 final size:48
Alignment explanation
Indices: 11389662--11389831 Score: 120
Period size: 48 Copynumber: 3.7 Consensus size: 48
11389652 TGGTTAACGA
* * * * *
11389662 GATCCCCTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATACGC
1 GATCCCGTATAAGACCATGTCTAGGACATGGCATCGGCACCGATAAGC
* * * * * * *
11389710 GATCCCGTGTAAGACCTTATC-AGGGATATGGCTTCGGCACCGGTAAGT
1 GATCCCGTATAAGACCATGTCTA-GGACATGGCATCGGCACCGATAAGC
** * *
11389758 GATTTCGTATAAGACCATGTCTAGGACATGGCAT---CA---ATATGA
1 GATCCCGTATAAGACCATGTCTAGGACATGGCATCGGCACCGATAAGC
* *
11389800 GGTCCCGTATAAGACCATGTCTGGGACATGGC
1 GATCCCGTATAAGACCATGTCTAGGACATGGC
11389832 GTTGGCACTG
Statistics
Matches: 96, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
42 31 0.32
45 2 0.02
48 62 0.65
49 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (48 bp):
GATCCCGTATAAGACCATGTCTAGGACATGGCATCGGCACCGATAAGC
Found at i:11389839 original size:90 final size:89
Alignment explanation
Indices: 11389712--11389930 Score: 213
Period size: 90 Copynumber: 2.4 Consensus size: 89
11389702 CGATACGCGA
* * * * * * * *
11389712 TCCCGTGTAAGACCTTATCAGGGATATGGCTTCGGCACCGGTAAGTGATTTCGTATAAGACCATG
1 TCCCGTGTAAGACCATGTCTGGGACATGGCTT-GGCACCGATAAGAGACTTCGTATAAGACCATA
*
11389777 TCTAGGACATGGCATCAATATGAGG
65 CCTAGGACATGGCATCAATATGAGG
* * **
11389802 TCCCGTATAAGACCATGTCTGGGACATGGCGTTGGCACTGATTTGAGACTTCGTATAAGACCATA
1 TCCCGTGTAAGACCATGTCTGGGACATGGC-TTGGCACCGATAAGAGACTTCGTATAAGACCATA
* * ** * *
11389867 CCTGGGATATGGCATTGATGTGTGG
65 CCTAGGACATGGCATCAATATGAGG
* * *
11389892 TCCCATGTAAGACTATGTCTAGGACATGGCTTTGGCACC
1 TCCCGTGTAAGACCATGTCTGGGACATGGC-TTGGCACC
11389931 CTATTTGGTG
Statistics
Matches: 103, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
90 101 0.98
91 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (89 bp):
TCCCGTGTAAGACCATGTCTGGGACATGGCTTGGCACCGATAAGAGACTTCGTATAAGACCATAC
CTAGGACATGGCATCAATATGAGG
Found at i:11392281 original size:46 final size:46
Alignment explanation
Indices: 11392214--11392350 Score: 265
Period size: 46 Copynumber: 3.0 Consensus size: 46
11392204 TGGTAAATTT
11392214 CGTTCGCATCCATGAGTGAACTCGGACTCAACTCAACGAGCTCGGG
1 CGTTCGCATCCATGAGTGAACTCGGACTCAACTCAACGAGCTCGGG
11392260 CGTTCGCATCCATGAGTGAACTCGGACTCAACTCAACGAGCTCGGG
1 CGTTCGCATCCATGAGTGAACTCGGACTCAACTCAACGAGCTCGGG
*
11392306 CGTTCGCATCCATGAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CGTTCGCATCCATGAGTGAACTCGGACTCAACTCAACGAGCTCGG
11392351 ATGCCCAAAT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 90 1.00
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.20
Consensus pattern (46 bp):
CGTTCGCATCCATGAGTGAACTCGGACTCAACTCAACGAGCTCGGG
Found at i:11407238 original size:24 final size:24
Alignment explanation
Indices: 11407164--11407238 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
11407154 TATCCGGTGC
11407164 TTCCTGA-TAATAACTCTT-TGGAGT
1 TTCCTGATTAA-AACTCTTAT-GAGT
* * *
11407188 TACCT-ATT-AAGCT-TTATGAGC
1 TTCCTGATTAAAACTCTTATGAGT
*
11407209 TCCCTGATTAAAACTCTTATGAGT
1 TTCCTGATTAAAACTCTTATGAGT
11407233 TTCCTG
1 TTCCTG
11407239 TTTAGCCTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
21 9 0.23
22 7 0.18
23 6 0.15
24 17 0.44
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (24 bp):
TTCCTGATTAAAACTCTTATGAGT
Found at i:11409162 original size:17 final size:17
Alignment explanation
Indices: 11409142--11409174 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11409132 CTCAAGTTAA
11409142 TAAATTAAT-TTCTCAAT
1 TAAA-TAATCTTCTCAAT
11409159 TAAATAATCTTCTCAA
1 TAAATAATCTTCTCAA
11409175 CCTAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATAATCTTCTCAAT
Found at i:11417139 original size:53 final size:53
Alignment explanation
Indices: 11417057--11417266 Score: 278
Period size: 53 Copynumber: 4.0 Consensus size: 53
11417047 CCATAGCATT
* * * *
11417057 AAAGAAGACCATATTGTGTAAGACCGTAACTGGTGGGTTATGACATCATATGG
1 AAAGAAGACCATATCGTGTAAGACCATAACTGGTGGGTTATGGCATCATATAG
* * **
11417110 AAAGAAGAACATATCGTGTATGACTGTAACTGGTGGGTTATGGCATCATATAG
1 AAAGAAGACCATATCGTGTAAGACCATAACTGGTGGGTTATGGCATCATATAG
* * *
11417163 AAAGAAGACCATA-CTATGTAAGATCATAACTAGTGGGTTATGGCATCATATAG
1 AAAGAAGACCATATC-GTGTAAGACCATAACTGGTGGGTTATGGCATCATATAG
* * *
11417216 AAATAAGACCATATTGTGTAAGACCATAATTGGTGGGTTATGGCATCATAT
1 AAAGAAGACCATATCGTGTAAGACCATAACTGGTGGGTTATGGCATCATAT
11417267 GGGAAAAATT
Statistics
Matches: 136, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
52 1 0.01
53 135 0.99
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (53 bp):
AAAGAAGACCATATCGTGTAAGACCATAACTGGTGGGTTATGGCATCATATAG
Found at i:11417521 original size:28 final size:28
Alignment explanation
Indices: 11417484--11417574 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
11417474 AAAACTCTGG
* * *
11417484 AAAGGTAAGCCTCTGTGGCAATCCTGTT
1 AAAGGTAAGCCTTTGTGGCAAACCTATT
* *
11417512 AAAGGAAAGCCTTTGTGGCAAAACTCTA-G
1 AAAGGTAAGCCTTTGTGGC-AAAC-CTATT
11417541 AAAGGTAAGCCTTTGTGGCAAACCTATT
1 AAAGGTAAGCCTTTGTGGCAAACCTATT
11417569 AAAGGT
1 AAAGGT
11417575 GGAAAATCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 3 0.06
28 27 0.51
29 21 0.40
30 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (28 bp):
AAAGGTAAGCCTTTGTGGCAAACCTATT
Found at i:11417523 original size:57 final size:57
Alignment explanation
Indices: 11417456--11417573 Score: 173
Period size: 57 Copynumber: 2.1 Consensus size: 57
11417446 GCATTTGTGG
* * * *
11417456 AAGGATAGCCTTTGTGAAAAAACTCTGGAAAGGTAAGCCTCTGTGGCAATCCTGTTA
1 AAGGAAAGCCTTTGTGAAAAAACTCTAGAAAGGTAAGCCTCTGTGGCAAACCTATTA
** *
11417513 AAGGAAAGCCTTTGTGGCAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTATTA
1 AAGGAAAGCCTTTGTGAAAAAACTCTAGAAAGGTAAGCCTCTGTGGCAAACCTATTA
11417570 AAGG
1 AAGG
11417574 TGGAAAATCT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (57 bp):
AAGGAAAGCCTTTGTGAAAAAACTCTAGAAAGGTAAGCCTCTGTGGCAAACCTATTA
Found at i:11417558 original size:29 final size:28
Alignment explanation
Indices: 11417462--11417562 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 28
11417452 GTGGAAGGAT
**
11417462 AGCCTTTGTGAAAAAACTCTGGAAAGGTA
1 AGCCTTTGTGGCAAAACTCT-GAAAGGTA
* ** * * *
11417491 AGCCTCTGTGGCAATCCTGTTAAAGGAA
1 AGCCTTTGTGGCAAAACTCTGAAAGGTA
11417519 AGCCTTTGTGGCAAAACTCTAGAAAGGTA
1 AGCCTTTGTGGCAAAACTCT-GAAAGGTA
11417548 AGCCTTTGTGGCAAA
1 AGCCTTTGTGGCAAA
11417563 CCTATTAAAG
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 22 0.39
29 35 0.61
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (28 bp):
AGCCTTTGTGGCAAAACTCTGAAAGGTA
Found at i:11435967 original size:13 final size:13
Alignment explanation
Indices: 11435949--11435975 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11435939 GAATCTGAAT
11435949 TACCCGCTCAGAC
1 TACCCGCTCAGAC
11435962 TACCCGCTCAGAC
1 TACCCGCTCAGAC
11435975 T
1 T
11435976 GATCATCAGT
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:0.44, G:0.15, T:0.19
Consensus pattern (13 bp):
TACCCGCTCAGAC
Found at i:11451140 original size:49 final size:49
Alignment explanation
Indices: 11451083--11451308 Score: 283
Period size: 49 Copynumber: 4.6 Consensus size: 49
11451073 CTGGTATGCA
*
11451083 TAGTAGCCTGCACTTAGTACTACACA-GACGACCAATGATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACG-CGACCAATTATCCGGTACACG
* * * *
11451132 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAATCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACACG
* ** * ** *
11451182 TAGTAGCCTGCACTTAGTGCTACACACATGATCGAAGTTATTGGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACG
*
11451233 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
*
11451282 TAGTAGCCTGTACTTAGTACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
11451309 ATGACCTCAC
Statistics
Matches: 151, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
49 66 0.44
50 48 0.32
51 37 0.25
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
Found at i:11451250 original size:101 final size:98
Alignment explanation
Indices: 11451083--11451314 Score: 311
Period size: 100 Copynumber: 2.3 Consensus size: 98
11451073 CTGGTATGCA
* * *
11451083 TAGTAGCCTGCACTTAGTACTACACAGACGACCAATGATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACATGACCAATGATCCGGTACACATAGTAGCCTGCACTTA
* *
11451148 GTACTACACACGTGACCTAATCATCTGATACACG
66 GTACTACACACGCGACC-AATCATCCGATACACG
* * * **
11451182 TAGTAGCCTGCACTTAGTGCTACACACATGATCGAAGTTATTGGGTACACATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACATGA-CCAA-TGATCCGGTACACATAGTAGCCTGCACT
* * *
11451247 TAGTACTACACATGCGACCAATTATCCGGTACACG
64 TAGTACTACACACGCGACCAATCATCCGATACACG
*
11451282 TAGTAGCCTGTACTTAGTACTACACACATGACC
1 TAGTAGCCTGCACTTAGTACTACACACATGACC
11451315 TCACAATAGA
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 29 0.25
100 45 0.39
101 41 0.36
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACATGACCAATGATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCAATCATCCGATACACG
Found at i:11455505 original size:17 final size:17
Alignment explanation
Indices: 11455483--11455516 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11455473 TGATTTAGTT
11455483 ATAACCATTTCATTACA
1 ATAACCATTTCATTACA
11455500 ATAACCATTTCATTACA
1 ATAACCATTTCATTACA
11455517 CTTTCTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAACCATTTCATTACA
Found at i:11456258 original size:25 final size:23
Alignment explanation
Indices: 11456229--11456281 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
11456219 AGTCTGTAAA
11456229 TATTAAATATGGATATTTACAAATT
1 TATTAAATATGGATA-TTA-AAATT
*
11456254 TATT--ATATTGATATTAAAATT
1 TATTAAATATGGATATTAAAATT
11456275 TAGTTAA
1 TA-TTAA
11456282 GTAATTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 8 0.33
25 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (23 bp):
TATTAAATATGGATATTAAAATT
Found at i:11456275 original size:21 final size:23
Alignment explanation
Indices: 11456235--11456276 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11456225 TAAATATTAA
11456235 ATATGGATATTTACAAATTTATT
1 ATATGGATATTTACAAATTTATT
*
11456258 ATATTGATA-TTA-AAATTTA
1 ATATGGATATTTACAAATTTA
11456277 GTTAAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (23 bp):
ATATGGATATTTACAAATTTATT
Found at i:11456541 original size:16 final size:17
Alignment explanation
Indices: 11456509--11456541 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11456499 TAAGTAAATG
*
11456509 AATTAAGTTTAATTATA
1 AATTAAGTTTAAGTATA
11456526 AATTAA-TTTAAGTATA
1 AATTAAGTTTAAGTATA
11456542 CAAGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
AATTAAGTTTAAGTATA
Found at i:11463356 original size:19 final size:19
Alignment explanation
Indices: 11463332--11463369 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
11463322 ATCTCTGGTT
11463332 TAAAGACTAAATTGAATAA
1 TAAAGACTAAATTGAATAA
11463351 TAAAGACTAAATTGAATAA
1 TAAAGACTAAATTGAATAA
11463370 GTTGCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (19 bp):
TAAAGACTAAATTGAATAA
Found at i:11476718 original size:18 final size:19
Alignment explanation
Indices: 11476681--11476724 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
11476671 TGCATGGCAA
* *
11476681 TATAAATTCGTTAGATATG
1 TATAAATTCATTAAATATG
11476700 TATAAATT-ATTAAATATG
1 TATAAATTCATTAAATATG
11476718 TATAAAT
1 TATAAAT
11476725 AAGTTGAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (19 bp):
TATAAATTCATTAAATATG
Found at i:11482155 original size:46 final size:46
Alignment explanation
Indices: 11482045--11482258 Score: 184
Period size: 46 Copynumber: 4.6 Consensus size: 46
11482035 TATTTGTGTC
* * * *
11482045 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCATGT--A-GCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTC-TCATCTCGAGGCT
* *
11482091 GATGCATGTCCCAGACATGTCTTACACTGGCTTTTATCTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCT
* * * * * * * ** *
11482137 AATGCATGTCCCAAACATGTCGTACACTAGCACTCGTCTCAATACC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCT
* *
11482183 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAGGCT
11482231 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
11482259 AGCACACAAA
Statistics
Matches: 132, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
43 4 0.03
44 12 0.09
45 15 0.11
46 53 0.40
47 27 0.20
48 20 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCT
Found at i:11482207 original size:94 final size:92
Alignment explanation
Indices: 11482089--11482263 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 92
11482079 CATCATGTAG
* * *
11482089 CCGATGCATGTCCCAGACATGTCTTACACTGGCTTTTAT-CTCGAGGCTAATGCATGTCCCAAAC
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAAT-GAGGCTAATGCATGTCCCAAAC
11482153 ATGTCGTACACTAGCACTCGTCTCAATA
65 ATGTCGTACACTAGCACTCGTCTCAATA
* * *
11482181 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAGA
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGAGGCTAATGCATGTCCCAAA
*
11482246 CATGTCTTACACTAGCAC
64 CATGTCGTACACTAGCAC
11482264 ACAAATATCC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
92 6 0.08
93 14 0.19
94 52 0.71
95 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (92 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCTAATGCATGTCCCAAACA
TGTCGTACACTAGCACTCGTCTCAATA
Found at i:11483727 original size:85 final size:87
Alignment explanation
Indices: 11483588--11483850 Score: 275
Period size: 87 Copynumber: 3.0 Consensus size: 87
11483578 AACAGACACT
* * * *
11483588 AAAAACAAAAATTGAAAATAACTCAGCACGTGAGCC-AAGGCTCAACTCACCTCTCGCAATGTGA
1 AAAAACAGAAATTGAAAATACCTCA--ACGTG-CCCTAAGGCTCAACTCACCTCTCGCAATATGA
* * *
11483652 GTTGGTTTTTGAAA-CT-TAATTTG
63 GTTGATTTTTGAAAGATATAAATTG
* * ** * * *
11483675 GAAAGCAGATTTTGAAAATA-CTGCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGT
1 AAAAACAGAAATTGAAAATACCT-CAACGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGT
11483739 TGATTTTTGAAAGATATAAATTG
65 TGATTTTTGAAAGATATAAATTG
* ** * *
11483762 AAAAATAGAAATTGAAAATACCTCAACGTTTCTTAAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAACGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTT
*
11483827 GATTTTTGAAA-ATAGAAATTG
66 GATTTTTGAAAGATATAAATTG
11483848 AAA
1 AAA
11483851 GTAGCTCAGC
Statistics
Matches: 145, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
84 2 0.01
85 42 0.29
86 15 0.10
87 84 0.58
88 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAACGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAGATATAAATTG
Found at i:11483764 original size:14 final size:14
Alignment explanation
Indices: 11483745--11483779 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11483735 GAGTTGATTT
* *
11483745 TTGAAAGATATAAA
1 TTGAAAAATAGAAA
11483759 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
11483773 TTGAAAA
1 TTGAAAA
11483780 TACCTCAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:11483841 original size:72 final size:73
Alignment explanation
Indices: 11483763--11483926 Score: 215
Period size: 74 Copynumber: 2.2 Consensus size: 73
11483753 TATAAATTGA
** * *
11483763 AAAATAGAAATTGAAAATACCTCA-ACGT-TTCTTAAGGCTCAACTCACTTCTCGCAATATGAGT
1 AAAATAGAAATTGAAAATACCTCACACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGT
11483826 TGATTTTTG
65 TGATTTTTG
* * *
11483835 AAAATAGAAATTGAAAGTAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATGTGAGT
1 AAAATAGAAATTGAAAATACCTCA-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
11483900 TGATTTTTG
65 TGATTTTTG
*
11483909 AAAAGCAGAAATTGAAAA
1 AAAA-TAGAAATTGAAAA
11483927 ACAGAAATTG
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
72 22 0.28
74 45 0.57
75 12 0.15
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (73 bp):
AAAATAGAAATTGAAAATACCTCACACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTG
Found at i:11483886 original size:161 final size:165
Alignment explanation
Indices: 11483710--11484016 Score: 446
Period size: 161 Copynumber: 1.9 Consensus size: 165
11483700 GCGTGCCCTG
* * *
11483710 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTG-AAAGATATAAATTGAAAAATAGAAAT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAG-CAGAAATTGAAAAACAGAAAT
* *
11483774 TGAAAATACCTCAACGTT-T-CTTAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-G-
65 TGAAAATACCTCAAC-TTATACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGA
*
11483835 A-AAATAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
129 AGAAACAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
* *
11483871 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAGCAGAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAGCAGAAATTGAAAAACAGAAATT
* * *
11483936 GAAATTACCTCAGCTTATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
66 GAAAATACCTCAACTTAT-ACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
11484001 GAAACAGAAATTGAAA
130 GAAACAGAAATTGAAA
11484017 AATGAAATTT
Statistics
Matches: 128, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
160 2 0.02
161 68 0.53
162 4 0.03
163 38 0.30
164 1 0.01
165 1 0.01
166 14 0.11
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (165 bp):
AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAGCAGAAATTGAAAAACAGAAATT
GAAAATACCTCAACTTATACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAG
AAACAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
Found at i:11483925 original size:14 final size:14
Alignment explanation
Indices: 11483906--11483939 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11483896 GAGTTGATTT
*
11483906 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
11483920 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
11483934 TTGAAA
1 TTGAAA
11483940 TTACCTCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:11484162 original size:173 final size:169
Alignment explanation
Indices: 11483960--11484270 Score: 430
Period size: 169 Copynumber: 1.8 Consensus size: 169
11483950 TTATGACCTG
11483960 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGGAAGAAACAGAAATTGAAAAATG-AA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAA-AAACAGAAATTG-AAAA-GCAA
** * *
11484023 ATTTTGAAAATACCTCAGCATGTGGCCC-GAGGCTCAACTCATCTTTCGAAATATGAGTTGACTT
63 A-AATGAAAATACCTCAGC--GT-GCCCTGAGGCTCAACTCACCTCTCGAAATATGAGTTGACTT
*
11484087 TTGAAAAGTATAAATAAAAACTAAAAATGCCTCAGCATGTGAGCCA
124 TTGAAAAATATAAATAAAAACTAAAAATGCCTCAGCATGTGAGCCA
* ** *
11484133 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAGATTGAAAAGCAAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAGAAATTGAAAAGCAAAAA
* * *
11484198 TGAAAATTCCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
66 TGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGAAATATGAGTTGACTTTTGAAAA
11484263 ATATAAAT
131 ATATAAAT
11484271 TGAAAAACAG
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
168 4 0.03
169 48 0.39
171 15 0.12
172 7 0.06
173 41 0.33
174 8 0.07
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (169 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAGAAATTGAAAAGCAAAAA
TGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGAAATATGAGTTGACTTTTGAAAA
ATATAAATAAAAACTAAAAATGCCTCAGCATGTGAGCCA
Found at i:11484275 original size:14 final size:14
Alignment explanation
Indices: 11484256--11484290 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11484246 GAGTTGATTT
* *
11484256 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
11484270 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
11484284 TTGAAAA
1 TTGAAAA
11484291 TACTTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.23
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:11484317 original size:87 final size:86
Alignment explanation
Indices: 11483871--11484352 Score: 453
Period size: 87 Copynumber: 5.5 Consensus size: 86
11483861 ACGTGAGCCA
* ** *
11483871 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAGCAGAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACA-AAAAT
* * *
11483936 GAAATTACCTCAGCTTATGACCTG
65 GAAAATACCTCAGCGTA--CCCTG
* *
11483960 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAACAGAAATTGAAAAATGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAA-AAATAGAAATTGAAAAA-CAAA-
** *
11484025 TTTGAAAATACCTCAGCATGTGGCCC-G
62 AATGAAAATACCTCAGC--GT-ACCCTG
* * * * * *
11484052 AGGCTCAACTCATCTTTCGAAATATGAGTTGACTTTTGAAAAGTATAAA-T-AAAAACTAAAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAAC-AAAAAT
* *
11484115 G------CCTCAGCATGTGAGCC-A
65 GAAAATACCTCAGC--GT-ACCCTG
* * *
11484133 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAGATTGAAAAGCAAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATAGAAATTGAAAAACAAAAA
* *
11484198 TGAAAATTCCTCAGCGTGCCCTG
64 TGAAAATACCTCAGCGTACCCTG
* *
11484221 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACA-AAAAT
* *
11484286 GAAAATACTTCAGCGTATCCTG
65 GAAAATACCTCAGCGTACCCTG
* **
11484308 AGGTTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAATA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATA
11484353 AAAACATCAA
Statistics
Matches: 330, Mismatches: 43, Indels: 42
0.80 0.10 0.10
Matches are distributed among these distances:
81 43 0.13
83 14 0.04
84 8 0.02
85 5 0.02
86 23 0.07
87 68 0.21
88 42 0.13
89 37 0.11
90 16 0.05
91 21 0.06
92 50 0.15
93 2 0.01
94 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (86 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAAAAATG
AAAATACCTCAGCGTACCCTG
Found at i:11496239 original size:13 final size:15
Alignment explanation
Indices: 11496215--11496251 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
11496205 AAAATATAAT
*
11496215 AATAACATTAATA-A
1 AATAATATTAATACA
11496229 AAT-ATATTAATACA
1 AATAATATTAATACA
11496243 AATAATATT
1 AATAATATT
11496252 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 8 0.40
14 7 0.35
15 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATTAATACA
Found at i:11496248 original size:22 final size:22
Alignment explanation
Indices: 11496205--11496249 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11496195 TAGAATACCA
*
11496205 AAAATATAATAATAACATTAAT
1 AAAATATAATAATAACAATAAT
*
11496227 AAAATATATTAAT-ACAAATAAT
1 AAAATATAATAATAAC-AATAAT
11496249 A
1 A
11496250 TTGAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATATAATAATAACAATAAT
Found at i:11496276 original size:21 final size:21
Alignment explanation
Indices: 11496234--11496276 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11496224 AATAAAATAT
* **
11496234 ATTAATACAAATAATATTGAA
1 ATTAAAACAAATAATAAGGAA
11496255 ATTAAAACAAATAATAAGGAA
1 ATTAAAACAAATAATAAGGAA
11496276 A
1 A
11496277 AGTAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (21 bp):
ATTAAAACAAATAATAAGGAA
Found at i:11500330 original size:13 final size:13
Alignment explanation
Indices: 11500312--11500336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11500302 CCCGGGGGAC
11500312 ACATGACCGTGTA
1 ACATGACCGTGTA
11500325 ACATGACCGTGT
1 ACATGACCGTGT
11500337 GTTGCACATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
ACATGACCGTGTA
Found at i:11500559 original size:23 final size:22
Alignment explanation
Indices: 11500529--11500572 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
11500519 TCTCAATTCA
*
11500529 TAAATAAATTCATACCAAAACT
1 TAAATAAAATCATACCAAAACT
*
11500551 TAAACTAAAATCATACCTAAAC
1 TAAA-TAAAATCATACCAAAAC
11500573 ATACGATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAATAAAATCATACCAAAACT
Found at i:11506870 original size:46 final size:46
Alignment explanation
Indices: 11506760--11506973 Score: 184
Period size: 46 Copynumber: 4.6 Consensus size: 46
11506750 TATTTGTGTC
* * * *
11506760 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCATGT--A-GCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTC-TCATCTCGAGGCT
* *
11506806 GATGCATGTCCCAGACATGTCTTACACTGGCTTTTATCTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCT
* * * * * * * ** *
11506852 AATGCATGTCCCAAACATGTCGTACACTAGCACTCGTCTCAATACC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCT
* *
11506898 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAGGCT
11506946 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
11506974 AGCACACAAA
Statistics
Matches: 132, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
43 4 0.03
44 12 0.09
45 15 0.11
46 53 0.40
47 27 0.20
48 20 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCT
Found at i:11506922 original size:94 final size:92
Alignment explanation
Indices: 11506804--11506978 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 92
11506794 CATCATGTAG
* * *
11506804 CCGATGCATGTCCCAGACATGTCTTACACTGGCTTTTAT-CTCGAGGCTAATGCATGTCCCAAAC
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAAT-GAGGCTAATGCATGTCCCAAAC
11506868 ATGTCGTACACTAGCACTCGTCTCAATA
65 ATGTCGTACACTAGCACTCGTCTCAATA
* * *
11506896 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAGA
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGAGGCTAATGCATGTCCCAAA
*
11506961 CATGTCTTACACTAGCAC
64 CATGTCGTACACTAGCAC
11506979 ACAAATATCC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
92 6 0.08
93 14 0.19
94 52 0.71
95 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (92 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCTAATGCATGTCCCAAACA
TGTCGTACACTAGCACTCGTCTCAATA
Found at i:11511873 original size:15 final size:15
Alignment explanation
Indices: 11511853--11511881 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11511843 AGACATAATA
11511853 ATACTAAATATATAC
1 ATACTAAATATATAC
11511868 ATACTAAATATATA
1 ATACTAAATATATA
11511882 TACATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
ATACTAAATATATAC
Found at i:11511910 original size:32 final size:35
Alignment explanation
Indices: 11511850--11511914 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 35
11511840 TATAGACATA
11511850 ATAATACTAAATATATACATACTAAATATATATAC
1 ATAATACTAAATATATACATACTAAATATATATAC
11511885 ATAATA-TAAATA-A-ACATA-TACAATATATAT
1 ATAATACTAAATATATACATACTA-AATATATAT
11511915 TAGGAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 2 0.07
32 14 0.48
33 1 0.03
34 6 0.21
35 6 0.21
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (35 bp):
ATAATACTAAATATATACATACTAAATATATATAC
Found at i:11512674 original size:22 final size:21
Alignment explanation
Indices: 11512645--11512691 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
11512635 ACACATACAT
*
11512645 AATATATACGTATTATATATA
1 AATATATACGTATAATATATA
* *
11512666 AATACTATATGTATAATATATT
1 AATA-TATACGTATAATATATA
11512688 AATA
1 AATA
11512692 GAAACATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
AATATATACGTATAATATATA
Found at i:11512933 original size:13 final size:15
Alignment explanation
Indices: 11512909--11512945 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
11512899 AAAATATAAT
*
11512909 AATAACATTAATA-A
1 AATAATATTAATACA
11512923 AAT-ATATTAATACA
1 AATAATATTAATACA
11512937 AATAATATT
1 AATAATATT
11512946 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 8 0.40
14 7 0.35
15 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATTAATACA
Found at i:11512942 original size:22 final size:22
Alignment explanation
Indices: 11512899--11512943 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11512889 TAGAATACCA
*
11512899 AAAATATAATAATAACATTAAT
1 AAAATATAATAATAACAATAAT
*
11512921 AAAATATATTAAT-ACAAATAAT
1 AAAATATAATAATAAC-AATAAT
11512943 A
1 A
11512944 TTGAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATATAATAATAACAATAAT
Found at i:11514821 original size:85 final size:87
Alignment explanation
Indices: 11514682--11514944 Score: 293
Period size: 87 Copynumber: 3.0 Consensus size: 87
11514672 AACAGACACT
* * * * *
11514682 AAAAACAAAAATTGAAAATAACTCAGCACGTGAGCC-AAGGCTCAACTCACCTCTCGCAATGTGA
1 AAAAACAGAAATTGAAAATACCTCA--ACGTG-CCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
11514746 GTTGGTTTTTGAAA-CT-TAATTTG
63 GTTGATTTTTGAAAGATATAAATTG
* * ** *
11514769 GAAAGCAGATTTTGAAAATA-CTGCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAACAGAAATTGAAAATACCT-CAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
11514833 TGATTTTTGAAAGATATAAATTG
65 TGATTTTTGAAAGATATAAATTG
* * * *
11514856 AAAAATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
11514921 GATTTTTGAAA-ATAGAAATTG
66 GATTTTTGAAAGATATAAATTG
11514942 AAA
1 AAA
11514945 GTAGCTCAGC
Statistics
Matches: 149, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
84 2 0.01
85 43 0.29
86 15 0.10
87 87 0.58
88 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAGATATAAATTG
Found at i:11514858 original size:14 final size:14
Alignment explanation
Indices: 11514839--11514873 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11514829 GAGTTGATTT
* *
11514839 TTGAAAGATATAAA
1 TTGAAAAATAGAAA
11514853 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
11514867 TTGAAAA
1 TTGAAAA
11514874 TACCTCAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:11514935 original size:72 final size:73
Alignment explanation
Indices: 11514857--11515020 Score: 224
Period size: 74 Copynumber: 2.2 Consensus size: 73
11514847 TATAAATTGA
* ** *
11514857 AAAATAGAAATTGAAAATACCTCA-ACGTG-TCTTGAGGCTCAACTCACTTCTCGCAATATGAGT
1 AAAATAGAAATTGAAAATACCTCACACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGT
11514920 TGATTTTTG
65 TGATTTTTG
* * *
11514929 AAAATAGAAATTGAAAGTAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATGTGAGT
1 AAAATAGAAATTGAAAATACCTCA-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
11514994 TGATTTTTG
65 TGATTTTTG
11515003 AAAAGTAGAAATTGAAAA
1 AAAA-TAGAAATTGAAAA
11515021 ACAGAAATTG
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
72 22 0.28
74 45 0.56
75 13 0.16
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (73 bp):
AAAATAGAAATTGAAAATACCTCACACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTG
Found at i:11514985 original size:161 final size:165
Alignment explanation
Indices: 11514804--11515110 Score: 471
Period size: 161 Copynumber: 1.9 Consensus size: 165
11514794 GCGTGCCCTG
* *
11514804 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAGATATAAATTGAAAAATAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAG-TAGAAATTGAAAAACAGAAAT
* * * *
11514868 TGAAAATACCTCAAC-GTGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-G-A
65 TGAAAATACCTCAACTATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
*
11514930 -AAATAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
130 GAAACAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
*
11514965 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
* *
11515030 GAAATTACCTCAGCTTATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
66 GAAAATACCTCAAC-TATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
11515095 GAAACAGAAATTGAAA
130 GAAACAGAAATTGAAA
11515111 AATGAAATTT
Statistics
Matches: 130, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
161 69 0.53
162 4 0.03
163 41 0.32
164 1 0.01
165 1 0.01
166 14 0.11
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (165 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
GAAAATACCTCAACTATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAG
AAACAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
Found at i:11515170 original size:92 final size:90
Alignment explanation
Indices: 11514929--11515263 Score: 318
Period size: 89 Copynumber: 3.8 Consensus size: 90
11514919 TTGATTTTTG
* * * * * *
11514929 AAAATAGAAATTGAAAGTAGCTCAGCACGTGAG-CCAAGGCTCAACTCACCTCTCGCAATGTGAG
1 AAAACAGAAATTGAAAATACCTCAGCATGTG-GCCCGAGGCTCAACTCACCTCTCGCAATATGAG
**
11514993 TTGATTTTT-GAAAAGTAGAAATTGA
65 TTGATTTTTGGAAAAACAGAAATTGA
* * * * *
11515018 AAAACAGAAATTGAAATTACCTCAGCTTATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGCATGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
11515083 TGATTTTTGGAAGAAACAGAAATTGA
66 TGATTTTTGGAA-AAACAGAAATTGA
* * * *
11515109 AAAA-TGAAATTTTGAAAATACCTCAGCATGTGGCCCGAGGCTCAACTCATCTTTCGAAATATGA
1 AAAACAGAAA--TTGAAAATACCTCAGCATGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
11515173 GTTGACTTTT-G--AAA-AG-TA-T-A
64 GTTGATTTTTGGAAAAACAGAAATTGA
* * * * *
11515193 AATA-A-AAACTAAAAATGCCTCAGCATGTGAG-CCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAACAGAAATTGAAAATACCTCAGCATGTG-GCCCGAGGCTCAACTCACCTCTCGCAATATGAG
11515255 TTGATTTTT
65 TTGATTTTT
11515264 TTGAAAAGNN
Statistics
Matches: 207, Mismatches: 33, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
81 53 0.26
82 1 0.00
83 3 0.01
84 4 0.02
85 1 0.00
86 1 0.00
87 2 0.01
88 3 0.01
89 62 0.30
90 7 0.03
91 16 0.08
92 54 0.26
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (90 bp):
AAAACAGAAATTGAAAATACCTCAGCATGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTGGAAAAACAGAAATTGA
Found at i:11529309 original size:85 final size:86
Alignment explanation
Indices: 11529171--11529431 Score: 280
Period size: 86 Copynumber: 3.0 Consensus size: 86
11529161 ACAGACACTA
* * * *
11529171 AAAACAAAAATTGAAAATAACTCAGCACGTGAGCC-AAGGCTCAACTCACCTCTCGCAATGTGAG
1 AAAACAGAAATTGAAAATACCTCA--ACGTG-CCCTAAGGCTCAACTCACCTCTCGCAATATGAG
* * *
11529235 TTGGTTTTTGAAA-CT-TAATTTGG
63 TTGATTTTTGAAAGATATAAATT-G
* ** * *
11529258 AAAGCAGATTTTGAAAATA-CTGCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAACAGAAATTGAAAATACCT-CAACGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTT
11529322 GATTTTTGAAAGATATAAATTG
65 GATTTTTGAAAGATATAAATTG
* ** * *
11529344 AAAATAGAAATTGAAAATACCTCAACGTTTCTTAAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
11529409 ATTTTTGAAA-ATAGAAATTG
66 ATTTTTGAAAGATATAAATTG
11529429 AAA
1 AAA
11529432 GTAGCTCAGC
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
84 2 0.01
85 55 0.37
86 66 0.45
87 24 0.16
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (86 bp):
AAAACAGAAATTGAAAATACCTCAACGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAGATATAAATTG
Found at i:11529356 original size:13 final size:13
Alignment explanation
Indices: 11529327--11529362 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
11529317 GAGTTGATTT
*
11529327 TTGAAAGATATAAA
1 TTGAAA-ATAGAAA
11529341 TTGAAAATAGAAA
1 TTGAAAATAGAAA
11529354 TTGAAAATA
1 TTGAAAATA
11529363 CCTCAACGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (13 bp):
TTGAAAATAGAAA
Found at i:11529431 original size:72 final size:73
Alignment explanation
Indices: 11529341--11529507 Score: 230
Period size: 74 Copynumber: 2.3 Consensus size: 73
11529331 AAGATATAAA
** * *
11529341 TTGAAAATAGAAATTGAAAATACCTCA-ACGT-TTCTTAAGGCTCAACTCACTTCTCGCAATATG
1 TTGAAAATAGAAATTGAAAATACCTCACACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATG
11529404 AGTTGATTT
65 AGTTGATTT
* * *
11529413 TTGAAAATAGAAATTGAAAGTAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATGTG
1 TTGAAAATAGAAATTGAAAATACCTCA-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATG
11529478 AGTTGATTT
65 AGTTGATTT
11529487 TTGAAAAGTAGAAATTGAAAA
1 TTGAAAA-TAGAAATTGAAAA
11529508 ACAGAAATTG
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
72 25 0.30
74 45 0.54
75 13 0.16
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (73 bp):
TTGAAAATAGAAATTGAAAATACCTCACACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:11529470 original size:160 final size:165
Alignment explanation
Indices: 11529292--11529926 Score: 466
Period size: 181 Copynumber: 3.8 Consensus size: 165
11529282 GCGTGCCCTG
* *
11529292 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAGATATAAATTG-AAAATAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAG-TAGAAATTGAAAAACAGAAAT
* *
11529355 TGAAAATACCTCAACGTT-T-CTTAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-G-
65 TGAAAATACCTCAAC-TTATACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGA
*
11529416 A-AAATAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
129 AGAAACAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
*
11529452 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
* * *
11529517 GAAATTACCTCAGCTTATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
66 GAAAATACCTCAACTTAT-ACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAA
* * *
11529582 GAAACAGAAATTGAAAAATGAAATTTTGAAAATACCTCAGCATGTG-GCCCG
130 GAAACAGAAA-T------TGAAA----G----TAGCTCAGCACGTGAG-CCA
* * * * *
11529633 AGGCTCAACTCATCTTTCGAAATATGAGTTGACTTTTGAAAAGTATAAA-T-AAAAAC------T
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
* * * * *
11529690 AAAAATGCCTCAGCATGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
66 GAAAATACCTCAACTTAT-A-CCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG
* * * ** * *
11529754 AAAAGCAGAGACTGAAAAGCAAAAATGAAAATTCCTCAG--CGTG-CCCTG
127 ----G-A-AGA---AACAG--AAATTGAAAGTAGCTCAGCACGTGAGCC-A
* *
11529802 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
* * * * * **
11529867 GAAAATACTTCAGCGTAT-CCTGAGGTTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
66 GAAAATACCTCAACTTATACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
11529927 AAAAATAAAA
Statistics
Matches: 383, Mismatches: 44, Indels: 83
0.75 0.09 0.16
Matches are distributed among these distances:
160 47 0.12
161 28 0.07
163 38 0.10
164 1 0.00
165 1 0.00
166 8 0.02
167 1 0.00
168 2 0.01
169 48 0.13
170 1 0.00
171 13 0.03
173 59 0.15
174 4 0.01
175 35 0.09
177 15 0.04
179 12 0.03
180 3 0.01
181 60 0.16
184 4 0.01
186 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (165 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATTGAAAAACAGAAATT
GAAAATACCTCAACTTATACCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAG
AAACAGAAATTGAAAGTAGCTCAGCACGTGAGCCA
Done.