Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 44 of 163
Found at i:14247232 original size:41 final size:39
Alignment explanation
Indices: 14247169--14247306 Score: 115
Period size: 41 Copynumber: 3.5 Consensus size: 39
14247159 GACTTCGAGT
* * * *
14247169 CGATGAGACACTAGATGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGCCAA-TTA-TACTTCGGATTAATC
*
14247210 CGATGAGGCACTGGGTGCCAATT-TACTTC-GATTTAA-C
1 CGATGAGACACTGGGTGCCAATTATACTTCGGA-TTAATC
* *
14247247 CGATGAGAC-CTGGGTGTCAAGTTATTACTTCGAATT-ATC
1 CGATGAGACACTGGGTGCCAA-TTA-TACTTCGGATTAATC
* *
14247286 CAATGAGGCACTGGGTGCCAA
1 CGATGAGACACTGGGTGCCAA
14247307 ACTGGTGTGT
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
36 10 0.13
37 12 0.15
38 11 0.14
39 16 0.20
40 13 0.16
41 17 0.22
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (39 bp):
CGATGAGACACTGGGTGCCAATTATACTTCGGATTAATC
Found at i:14271528 original size:24 final size:26
Alignment explanation
Indices: 14271487--14271537 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
14271477 AAGTAAAAAC
14271487 AAATTATAGTAGTATAAAAATA-GTG
1 AAATTATAGTAGTATAAAAATATGTG
14271512 AAATTA-AGTA-TACTAAAAATATGTG
1 AAATTATAGTAGTA-TAAAAATATGTG
14271537 A
1 A
14271538 GACCCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.08
24 12 0.50
25 10 0.42
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (26 bp):
AAATTATAGTAGTATAAAAATATGTG
Found at i:14282075 original size:21 final size:21
Alignment explanation
Indices: 14282051--14282103 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
14282041 CGCTGTTTCT
*
14282051 AATCTCACCACTACAATATCC
1 AATCTCACCACTACAATAACC
* * * *
14282072 AATCACACCACTATAGTAACT
1 AATCTCACCACTACAATAACC
14282093 AATCTCACCAC
1 AATCTCACCAC
14282104 CACCGTTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.36, G:0.02, T:0.23
Consensus pattern (21 bp):
AATCTCACCACTACAATAACC
Found at i:14287298 original size:45 final size:45
Alignment explanation
Indices: 14287237--14288084 Score: 1036
Period size: 45 Copynumber: 19.0 Consensus size: 45
14287227 GGTTAAAAAA
* *
14287237 ATAGTAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
14287282 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
*
14287327 ATAGCATATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * *
14287372 ATAACAGATCTTATCTTCCTGTATTGGCAGCAAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
14287417 ATAGAAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* ** *
14287462 ATAGTAGATCTTGTCTTCCTGTAAAGGCAGCGAAATAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
*
14287507 ATAGCAGATCTTGTCTTCC-----TGGCAGCGAAATAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
*
14287547 ATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
*
14287592 ATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * *** * ** *
14287637 ATACCAG-CCTTAT-TTCCCTG-AGCAGCAGC-AGAGTAGGTTAAAA
1 ATAGCAGATCTTGTCTT-CCTGTATTGGCAGCGA-AGTAGATCGAAG
* * *
14287680 ATAACAGATCTTATCTT-CTGTATTGGTAAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGG-CAGCGAAGTAGATCGAAG
* * * *
14287725 ATAGCGGATCTTGTCTTCTTATATTGGCAGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * *
14287770 ATAGCAGATCTTGTCTTCCTTTATTGGTAGCGAAATAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * * *
14287815 ATAGCAGATCTTATCTTCCTGTACTAGCAGCG-AGTAAATCGAAT
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * *
14287859 ATAGCAAATCTTGTCTTTCTGTATTGGCAGTGATA-TAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA-AGTAGATCGAAG
* * * **
14287904 ATAGTAGATCTAGTCTTCCTGTACTGGCAGTAAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * *
14287949 ATAGCAGATCTTGTCTTCTTGTAATGGCAGCGAAGTAAATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * *
14287994 ATAGCAGATCTTGTCTTCCTGTAATAGCAACGAAGTAGATCGAAA
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * *
14288039 ATAGCAGATATTGTCTTCCTATACTGGCAGCAAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
14288084 A
1 A
14288085 CACAAGTCTT
Statistics
Matches: 688, Mismatches: 99, Indels: 32
0.84 0.12 0.04
Matches are distributed among these distances:
40 39 0.06
42 1 0.00
43 25 0.04
44 51 0.07
45 563 0.82
46 9 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
Found at i:14288284 original size:89 final size:87
Alignment explanation
Indices: 14288044--14288285 Score: 256
Period size: 89 Copynumber: 2.7 Consensus size: 87
14288034 CGAAAATAGC
* * * * *
14288044 AGATATTGTCTTCCTATACTGGCAGCAAAGTAGATCGAAGACA-CAAGTCTTGCCTCCCTAACTT
1 AGAT-TTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACACCAA-CCTTGCCT-CCTGAGTT
*
14288108 TGCAGTGGAGCAGACTGAAGATAAA
63 TGCAGCGGAGCAGACTGAAGATAAA
* * * * *
14288133 ATATTTCGCCTTCCTGTACTGGCAGTGAAGTAGATCAAAGACACCAGCC-TGACCTCCTTGAGTT
1 AGATTT-GTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACACCAACCTTG-CCTCC-TGAGTT
* *
14288197 TGCAGCGGAGTAGACTGAAGATAAT
63 TGCAGCGGAGCAGACTGAAGATAAA
*
14288222 AGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGACA-ACACCAACCTTGCCTCTCTGAGTT
1 AGAT-TTGTCTTCCTGTACTGGCAGCGAAGTAGATCGA-AGACACCAACCTTGCCTC-CTGAGTT
14288286 GGCAATGGAA
Statistics
Matches: 126, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
88 6 0.05
89 112 0.89
90 8 0.06
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (87 bp):
AGATTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCTGAGTTTGC
AGCGGAGCAGACTGAAGATAAA
Found at i:14288380 original size:51 final size:51
Alignment explanation
Indices: 14288316--14288438 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
14288306 CTACGATAGT
* * * * *
14288316 GAATCTTACTTCCCTAGTGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGC
1 GAATCTTATTTCCCTAGCGTTGCAGCGGAACAGATAAAAGCTAAAGGCAGC
* * ** * *
14288367 GAATCTTGTTTCCCTGGCGTTGCAGCGGAGTAGATAAAAGCTGAGGGCAGC
1 GAATCTTATTTCCCTAGCGTTGCAGCGGAACAGATAAAAGCTAAAGGCAGC
*
14288418 GAATCTTATCTCCCTAGCGTT
1 GAATCTTATTTCCCTAGCGTT
14288439 AAGACTTGGA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (51 bp):
GAATCTTATTTCCCTAGCGTTGCAGCGGAACAGATAAAAGCTAAAGGCAGC
Found at i:14288855 original size:45 final size:43
Alignment explanation
Indices: 14288668--14288910 Score: 175
Period size: 44 Copynumber: 5.5 Consensus size: 43
14288658 GAAGATGGCG
* * *
14288668 AATCTTATCTCCTTGAAGTTACAATGGAGCAGATTAAA-ACCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATA--AAT
* * * *
14288712 AATCCTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAATAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAAT
* * * ****
14288755 AAATCTAATCCCCCTGAAGTTGCAGTGGGGCAGATTCAAGATGGCG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-ATAAAT
* *
14288801 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAAGTTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAA-TAAAT
* * * ** *
14288846 AATCATATCTCCCTAAAGTTGTAGCAGAGCGGATTAAA-ATAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATA-AAT
**
14288889 AGATCTTATCTCTTTGAAGTTG
1 A-ATCTTATCTCCCTGAAGTTG
14288911 TAGAGAGTAG
Statistics
Matches: 153, Mismatches: 39, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
43 7 0.05
44 80 0.52
45 64 0.42
46 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAAT
Found at i:14289690 original size:13 final size:14
Alignment explanation
Indices: 14289659--14289691 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
14289649 ATACAGTACC
14289659 AAAAAGATACTGAA
1 AAAAAGATACTGAA
14289673 AAAAAGATAC-GAA
1 AAAAAGATACTGAA
14289686 GAAAAA
1 -AAAAA
14289692 TCAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.70, C:0.06, G:0.15, T:0.09
Consensus pattern (14 bp):
AAAAAGATACTGAA
Found at i:14290408 original size:25 final size:25
Alignment explanation
Indices: 14290360--14290408 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
14290350 ATTGTTATTA
* * *
14290360 TATTTTATATTACTATTATTTTTAG
1 TATTTTAGATTACTATCATATTTAG
14290385 TATTTTAGATTACTATCATATTTA
1 TATTTTAGATTACTATCATATTTA
14290409 TTTATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (25 bp):
TATTTTAGATTACTATCATATTTAG
Found at i:14290857 original size:18 final size:20
Alignment explanation
Indices: 14290817--14290858 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
14290807 TGCTGCCCTA
*
14290817 TTGTATGTTGTATTGTTTAT
1 TTGTATGTTGTATTGATTAT
*
14290837 TTGTAT-TT-TATTGATTCT
1 TTGTATGTTGTATTGATTAT
14290855 TTGT
1 TTGT
14290859 TGCTAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 2 0.10
20 6 0.30
ACGTcount: A:0.14, C:0.02, G:0.17, T:0.67
Consensus pattern (20 bp):
TTGTATGTTGTATTGATTAT
Found at i:14291962 original size:20 final size:19
Alignment explanation
Indices: 14291939--14291980 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
14291929 GCATATTTTC
14291939 TTTCTATATTATTAATATTA
1 TTTCTATATTATTAATA-TA
14291959 TTTCTATATTATTAATATA
1 TTTCTATATTATTAATATA
14291978 TTT
1 TTT
14291981 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTCTATATTATTAATATA
Found at i:14291990 original size:20 final size:19
Alignment explanation
Indices: 14291943--14292009 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
14291933 ATTTTCTTTC
*
14291943 TATATTATTAATATTATTTC
1 TATATTATTAATA-TATTTT
14291963 TATATTATTAATATATTTT
1 TATATTATTAATATATTTT
* * *
14291982 TATTTTTATTTATATATATT
1 TA-TATTATTAATATATTTT
*
14292002 TAAATTAT
1 TATATTAT
14292010 ATATTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.28
20 29 0.73
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTATTAATATATTTT
Found at i:14292012 original size:13 final size:13
Alignment explanation
Indices: 14291994--14292019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14291984 TTTTTATTTA
14291994 TATATATTTAAAT
1 TATATATTTAAAT
14292007 TATATATTTAAAT
1 TATATATTTAAAT
14292020 GATAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATTTAAAT
Found at i:14292045 original size:15 final size:15
Alignment explanation
Indices: 14292021--14292058 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
14292011 TATTTAAATG
*
14292021 ATAAATAATAATAAA
1 ATAAACAATAATAAA
14292036 ATAAACAATAATAAA
1 ATAAACAATAATAAA
14292051 ATAAACAA
1 ATAAACAA
14292059 ACCAAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAACAATAATAAA
Found at i:14292401 original size:29 final size:29
Alignment explanation
Indices: 14292341--14292402 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
14292331 GCTAGAAGTG
* *
14292341 TTTTTCAAAAATAACCTATTCCCGCAATT
1 TTTTTCAAAAATAACCTATTCACACAATT
* *
14292370 TTTTTCTAAAATTAACCTATTCACATAATT
1 TTTTTC-AAAAATAACCTATTCACACAATT
14292400 TTT
1 TTT
14292403 GCCTGACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (29 bp):
TTTTTCAAAAATAACCTATTCACACAATT
Found at i:14295511 original size:54 final size:54
Alignment explanation
Indices: 14295433--14295566 Score: 216
Period size: 54 Copynumber: 2.5 Consensus size: 54
14295423 GGAGTTAATG
* * *
14295433 CTGTAGGAGACTTCGCAATAGGACCAGGAGCCAGAGCAGGAACCGGAGATGATC
1 CTGTGGGAGGCTTTGCAATAGGACCAGGAGCCAGAGCAGGAACCGGAGATGATC
14295487 CTGTGGGAGGCTTTGCAATAGGACCAGGAGCCAGAGCAGGAACCGGAGATGATC
1 CTGTGGGAGGCTTTGCAATAGGACCAGGAGCCAGAGCAGGAACCGGAGATGATC
*
14295541 CTGTGGGTGGCTTTGCAACT-GGACCA
1 CTGTGGGAGGCTTTGCAA-TAGGACCA
14295567 TGGTGATAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 74 0.99
55 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.35, T:0.16
Consensus pattern (54 bp):
CTGTGGGAGGCTTTGCAATAGGACCAGGAGCCAGAGCAGGAACCGGAGATGATC
Found at i:14299797 original size:5 final size:6
Alignment explanation
Indices: 14299771--14299803 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
14299761 AATAGTAAAA
14299771 AAATTT AAATTT AAATTT AAA-TT AAATTAT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATT-T AAA
14299804 AATATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 16 0.64
7 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AAATTT
Found at i:14309986 original size:40 final size:39
Alignment explanation
Indices: 14309938--14310047 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
14309928 TTTTTTATCC
14309938 AAATGCCGCTAAAGATTGAGAATTAGCGGCGCTATTCA-GA
1 AAATGCCGCTAAAGATTGAGAATTAGCGGCGCT-TT-AGGA
*
14309978 AAATGCCGCTAAAGATCGA-ACATTAGCGGCGCTTTATGGA
1 AAATGCCGCTAAAGATTGAGA-ATTAGCGGCGCTTTA-GGA
* * *
14310018 AAACGCCGCTAAA-AATAAGAATTAGCGGCG
1 AAATGCCGCTAAAGATTGAGAATTAGCGGCG
14310048 TTTTTCAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
38 1 0.02
39 15 0.25
40 45 0.74
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (39 bp):
AAATGCCGCTAAAGATTGAGAATTAGCGGCGCTTTAGGA
Found at i:14310064 original size:39 final size:38
Alignment explanation
Indices: 14309919--14310071 Score: 101
Period size: 40 Copynumber: 3.8 Consensus size: 38
14309909 AAACAGGCTT
* * * * *
14309919 TTAGCGGCGTTTTTTATCCAAATGCCGCTAAAGATTGAGAA
1 TTAGCGGCGTTTTTCA--AAAACGCCGCTAAA-AATAAGAA
* * * * *
14309960 TTAGCGGCGCTATTCAGAAAATGCCGCTAAAGATCGAA-CA
1 TTAGCGGCGTTTTTCA-AAAACGCCGCTAAAAAT--AAGAA
* **
14310000 TTAGCGGCGCTTTATGGAAAACGCCGCTAAAAATAAGAA
1 TTAGCGGCG-TTTTTCAAAAACGCCGCTAAAAATAAGAA
*
14310039 TTAGCGGCGTTTTTCAAAAAGCGCCGCAAAAAA
1 TTAGCGGCGTTTTTCAAAAA-CGCCGCTAAAAA
14310072 CCTATGCCCA
Statistics
Matches: 86, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
38 10 0.12
39 22 0.26
40 38 0.44
41 16 0.19
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (38 bp):
TTAGCGGCGTTTTTCAAAAACGCCGCTAAAAATAAGAA
Found at i:14310174 original size:41 final size:41
Alignment explanation
Indices: 14310110--14310358 Score: 270
Period size: 41 Copynumber: 6.1 Consensus size: 41
14310100 CTTTCGGGGT
* * *
14310110 TTTAGCGGTGTTTTTGAGAAAGCGCGGCTAATGCTCTGGGA
1 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCTGGGA
*
14310151 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
1 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCTGGGA
* * * * * *
14310192 TTTAGCGGCGTTTTTTAGGAAGCGCAGCTATTGCTCAGTGC
1 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCTGGGA
* * *
14310233 TTTAGCGGCGTTTTTTAGAAAGCACCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCTGGGA
* ***
14310274 TTTAGCGGCG-TTTTT-GAAGTAGCGCCGCTAGTGCTCT-ATT
1 TTTAGCGGCGTTTTTTAGAA--AGCGCCGCTAATGCTCTGGGA
* * **
14310314 TTTAGCGGCGTTTTTTAAAAAGCGTCGCTAATGCTCACGGA
1 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCTGGGA
14310355 TTTA
1 TTTA
14310359 AAATAATTTA
Statistics
Matches: 175, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.02
40 29 0.17
41 141 0.81
42 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCTGGGA
Found at i:14311338 original size:14 final size:15
Alignment explanation
Indices: 14311321--14311362 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
14311311 TATGGTTTAT
14311321 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
*
14311335 GGTTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
14311350 GG-TTAAGGGTTAG
1 GGTTTAAGGGTTAG
14311363 ATGTTAGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.36
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:14311340 original size:21 final size:21
Alignment explanation
Indices: 14311314--14311353 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14311304 TATAGATTAT
*
14311314 GGTTTATGGTTTAAGGGTTGG
1 GGTTTAAGGTTTAAGGGTTGG
*
14311335 GGTTTAAGGTTTAGGGGTT
1 GGTTTAAGGTTTAAGGGTT
14311354 AAGGGTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (21 bp):
GGTTTAAGGTTTAAGGGTTGG
Found at i:14311382 original size:14 final size:14
Alignment explanation
Indices: 14311324--14311393 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
14311314 GGTTTATGGT
14311324 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
*
14311337 TTTAAGGTTTAGGGG
1 -TTAAGGGTTAGGGG
**
14311352 TTAAGGGTTAGATG
1 TTAAGGGTTAGGGG
*
14311366 TT-AGTGGTTAAGGG
1 TTAAG-GGTTAGGGG
*
14311380 TTAGGGGTTTAGGG
1 TTAAGGG-TTAGGG
14311394 TTTATGTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
13 2 0.05
14 31 0.72
15 10 0.23
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:14311395 original size:21 final size:21
Alignment explanation
Indices: 14311341--14311395 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
14311331 TTGGGGTTTA
14311341 AGGTTTAGGGGTTAAGGGTTAG
1 AGGTTTA-GGGTTAAGGGTTAG
*
14311363 ATG-TTAGTGGTTAAGGGTTAG
1 AGGTTTAG-GGTTAAGGGTTAG
*
14311384 GGGTTTAGGGTT
1 AGGTTTAGGGTT
14311396 TATGTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.04
21 21 0.75
22 6 0.21
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (21 bp):
AGGTTTAGGGTTAAGGGTTAG
Found at i:14315668 original size:43 final size:43
Alignment explanation
Indices: 14315598--14315836 Score: 307
Period size: 43 Copynumber: 5.6 Consensus size: 43
14315588 GAGCTATAGT
* * * **
14315598 GTCTGGGTCTTTAGAAGCATTTGTGGGAAAATTGCCGCTAAAG
1 GTCTTGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAG
* * *
14315641 GTTTTGGTTTTTAGCAGCGTTTGTGGGAAAAGCGTCGCTAAAG
1 GTCTTGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAG
* * *
14315684 GTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAG
1 GTCTTGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAG
* * * *
14315727 GTCCTGGTCTTTAGCGGCGTTTGTAGGAAAAGCACCGCTAAAG
1 GTCTTGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAG
* *
14315770 GTCTTGGTATTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1 GTCTTGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAG
* *
14315813 GTCTTGGTCTTTAGTAGCATTTGT
1 GTCTTGGTCTTTAGCAGCGTTTGT
14315837 TTCTAAAAAC
Statistics
Matches: 171, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 171 1.00
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (43 bp):
GTCTTGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAG
Found at i:14317500 original size:73 final size:75
Alignment explanation
Indices: 14317420--14317570 Score: 245
Period size: 74 Copynumber: 2.0 Consensus size: 75
14317410 TTTCGATGTT
*
14317420 TGTGTTTAA-TGCGGATTTAGTCCTTTAATTTTGAAACA-AGTTTTAATTAAATACTGA-TTTTT
1 TGTGTTTAATTGCGGATTTAGTCCTTCAATTTTGAAACAGA-TTTTAATTAAATACTGATTTTTT
14317482 TTTAAATTCAA
65 TTTAAATTCAA
* *
14317493 TGTGTTTAATTGCGGATTTAGTCCTTCAATTTTGAAGCAGATTTTAATTAAATATTGATTTTTTT
1 TGTGTTTAATTGCGGATTTAGTCCTTCAATTTTGAAACAGATTTTAATTAAATACTGATTTTTTT
14317558 TTAAATTCAA
66 TTAAATTCAA
14317568 TGT
1 TGT
14317571 TTTTTTAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
73 9 0.12
74 43 0.60
75 20 0.28
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (75 bp):
TGTGTTTAATTGCGGATTTAGTCCTTCAATTTTGAAACAGATTTTAATTAAATACTGATTTTTTT
TTAAATTCAA
Found at i:14319853 original size:20 final size:20
Alignment explanation
Indices: 14319828--14319872 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
14319818 AATGTGTCTT
14319828 GTCTTAACCAAATTAATTGG
1 GTCTTAACCAAATTAATTGG
** *
14319848 GTCTTAACTTAATTAATTGT
1 GTCTTAACCAAATTAATTGG
14319868 GTCTT
1 GTCTT
14319873 GTTCTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
GTCTTAACCAAATTAATTGG
Found at i:14326719 original size:20 final size:20
Alignment explanation
Indices: 14326694--14326738 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
14326684 AATGTGTCTT
14326694 GTCTTAACCAAATTAATTGG
1 GTCTTAACCAAATTAATTGG
** *
14326714 GTCTTAACTTAATTAATTGT
1 GTCTTAACCAAATTAATTGG
14326734 GTCTT
1 GTCTT
14326739 GTTCTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
GTCTTAACCAAATTAATTGG
Found at i:14329461 original size:25 final size:25
Alignment explanation
Indices: 14329428--14329488 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
14329418 CCCACAGGAA
* *
14329428 TTAT-AAAAATGA-ATTTAATAATT
1 TTATCAAAAATGATAGTAAATAATT
14329451 TCTATCAAAAA-GATAGTAAATAATT
1 T-TATCAAAAATGATAGTAAATAATT
14329476 TTATCATAAAATG
1 TTATCA-AAAATG
14329489 GATCTAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 10 0.32
25 19 0.61
26 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.38
Consensus pattern (25 bp):
TTATCAAAAATGATAGTAAATAATT
Found at i:14343388 original size:15 final size:15
Alignment explanation
Indices: 14343368--14343401 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
14343358 TGTGTGTGTG
*
14343368 TATTTATTTATTGTT
1 TATTTATTTATTATT
14343383 TATTTATTTATTATT
1 TATTTATTTATTATT
14343398 TATT
1 TATT
14343402 AACATTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TATTTATTTATTATT
Found at i:14346183 original size:22 final size:21
Alignment explanation
Indices: 14346156--14346211 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
14346146 ATTAAGACTT
**
14346156 TTTTATTTTTAAGTTTATCTTA
1 TTTTATTTTTAA-TTTAGATTA
*
14346178 TTTTATTATTAATTTAGATTA
1 TTTTATTTTTAATTTAGATTA
14346199 TTATTATTATTTA
1 TT-TTATT-TTTA
14346212 GGGAGCAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.32
22 16 0.57
23 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTATTTTTAATTTAGATTA
Found at i:14347234 original size:28 final size:27
Alignment explanation
Indices: 14347148--14347247 Score: 75
Period size: 27 Copynumber: 3.6 Consensus size: 27
14347138 TTTTCCATAA
*
14347148 AAAATGATTAAAAATCATA-AAACGTTA-T
1 AAAAT-ATT-AAAATTATATAAAC-TTATT
* *
14347176 AAAATATTAAATATTA-ATAATA-TAATA
1 AAAATATTAAA-ATTATATAA-ACTTATT
14347203 AAAATATTAAAATTGATATAAACTTATT
1 AAAATATTAAAATT-ATATAAACTTATT
14347231 AAAACTA-TAAAATTATA
1 AAAA-TATTAAAATTATA
14347248 AAATATAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
26 9 0.15
27 24 0.41
28 24 0.41
29 2 0.03
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAATATTAAAATTATATAAACTTATT
Found at i:14347241 original size:17 final size:15
Alignment explanation
Indices: 14347218--14347257 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
14347208 ATTAAAATTG
*
14347218 ATATAAACTTATTAAA
1 ATATAAAATTA-TAAA
14347234 ACTATAAAATTATAAA
1 A-TATAAAATTATAAA
14347250 ATATAAAA
1 ATATAAAA
14347258 AATCTAANNN
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATAAAATTATAAA
Found at i:14347247 original size:8 final size:8
Alignment explanation
Indices: 14347154--14347257 Score: 52
Period size: 8 Copynumber: 12.1 Consensus size: 8
14347144 ATAAAAAATG
14347154 ATTA-AAA
1 ATTATAAA
*
14347161 ATCATAAA
1 ATTATAAA
14347169 ACGTTATAAA
1 A--TTATAAA
14347179 A-TATTAAA
1 ATTA-TAAA
*
14347187 TATTAATAAT
1 -ATT-ATAAA
*
14347197 ATAATAAA
1 ATTATAAA
*
14347205 AATATTAAA
1 ATTA-TAAA
14347214 ATTGATATAA
1 ATT-ATA-AA
14347224 ACTTATTAAA
1 A-TTA-TAAA
*
14347234 ACTATAAA
1 ATTATAAA
14347242 ATTATAAA
1 ATTATAAA
14347250 A-TATAAA
1 ATTATAAA
14347257 A
1 A
14347258 AATCTAANNN
Statistics
Matches: 75, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
7 12 0.16
8 26 0.35
9 13 0.17
10 19 0.25
11 5 0.07
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (8 bp):
ATTATAAA
Found at i:14347486 original size:39 final size:39
Alignment explanation
Indices: 14347438--14347566 Score: 149
Period size: 39 Copynumber: 3.4 Consensus size: 39
14347428 TAAAATGAAT
14347438 AAAACTTATTTAAAATATTTAAAATTAAAAAGAACGTATC
1 AAAA-TTATTTAAAATATTTAAAATTAAAAAGAACGTATC
* * * ** *
14347478 AAAATTATTTAAAA-A-TAAAAAATATTAAA-ATTGAAT-
1 AAAATTATTTAAAATATTTAAAATTA-AAAAGAACGTATC
*
14347514 AAACTTATTTAAAATATTTAAAATTAAAAAGAACGTATC
1 AAAATTATTTAAAATATTTAAAATTAAAAAGAACGTATC
14347553 AAAATTATTTAAAA
1 AAAATTATTTAAAA
14347567 ATAAAAAATA
Statistics
Matches: 70, Mismatches: 14, Indels: 11
0.74 0.15 0.12
Matches are distributed among these distances:
36 13 0.19
37 15 0.21
38 15 0.21
39 23 0.33
40 4 0.06
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (39 bp):
AAAATTATTTAAAATATTTAAAATTAAAAAGAACGTATC
Found at i:14347515 original size:76 final size:76
Alignment explanation
Indices: 14347428--14347597 Score: 310
Period size: 75 Copynumber: 2.3 Consensus size: 76
14347418 AAATAACTTA
14347428 TAAAA-TGAATAAAACTTATTTAAAATATTTAAAATTAAAAAGAACGTATCAAAATTATTTAAAA
1 TAAAATTGAATAAAACTTATTTAAAATATTTAAAATTAAAAAGAACGTATCAAAATTATTTAAAA
14347492 ATAAAAAATAT
66 ATAAAAAATAT
14347503 TAAAATTGAAT-AAACTTATTTAAAATATTTAAAATTAAAAAGAACGTATCAAAATTATTTAAAA
1 TAAAATTGAATAAAACTTATTTAAAATATTTAAAATTAAAAAGAACGTATCAAAATTATTTAAAA
14347567 ATAAAAAATAT
66 ATAAAAAATAT
14347578 TAAAATTG-ATATAAACTTAT
1 TAAAATTGAATA-AAACTTAT
14347598 AAAAAATTTA
Statistics
Matches: 92, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
74 2 0.02
75 77 0.84
76 13 0.14
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (76 bp):
TAAAATTGAATAAAACTTATTTAAAATATTTAAAATTAAAAAGAACGTATCAAAATTATTTAAAA
ATAAAAAATAT
Found at i:14349532 original size:13 final size:13
Alignment explanation
Indices: 14349514--14349538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14349504 GCTTTGAGCT
14349514 CTTACTAAGTACA
1 CTTACTAAGTACA
14349527 CTTACTAAGTAC
1 CTTACTAAGTAC
14349539 GTTAGCTCAC
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:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
CTTACTAAGTACA
Found at i:14358903 original size:22 final size:23
Alignment explanation
Indices: 14358857--14358907 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
14358847 AAAATATATC
*
14358857 AAAAGAAATAGTTGATGTTTTTA
1 AAAAGAAATAGTTGATGTTTATA
* *
14358880 AAAAGTAATATTTGAT-TTTATA
1 AAAAGAAATAGTTGATGTTTATA
14358902 AAAAGA
1 AAAAGA
14358908 TGAATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (23 bp):
AAAAGAAATAGTTGATGTTTATA
Found at i:14358979 original size:32 final size:33
Alignment explanation
Indices: 14358920--14358985 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
14358910 AATTAAAAAT
* * *
14358920 AAAACAACTTGAAAAAAATATATTTATTAATTA
1 AAAAAAACTTGAAAAAAACATAATTATTAATTA
* *
14358953 AAAAAAACTT-AAAACAACATAATTATTATTTA
1 AAAAAAACTTGAAAAAAACATAATTATTAATTA
14358985 A
1 A
14358986 TGTGTCGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.32
Consensus pattern (33 bp):
AAAAAAACTTGAAAAAAACATAATTATTAATTA
Found at i:14360682 original size:8 final size:8
Alignment explanation
Indices: 14360671--14360713 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
14360661 TAAAATTTAA
14360671 TAAAAAAT
1 TAAAAAAT
14360679 TAAAAAAT
1 TAAAAAAT
*
14360687 AGAAAAAAT
1 -TAAAAAAT
*
14360696 TATAAAAAA
1 TA-AAAAAT
14360705 TAAAAAAT
1 TAAAAAAT
14360713 T
1 T
14360714 GTAAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 15 0.52
9 14 0.48
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (8 bp):
TAAAAAAT
Found at i:14360684 original size:27 final size:26
Alignment explanation
Indices: 14360645--14360730 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
14360635 AAAAATCAAC
*
14360645 AAAAGTTATAAAATATTAAAATTTAATA
1 AAAAATTA-AAAATATTAAAATTT-ATA
** *
14360673 AAAAATTAAAAAATAGAAAAAATTATA
1 AAAAATT-AAAAATATTAAAATTTATA
*
14360700 AAAAATAAAAAAT-TGTAAAATTTTATA
1 AAAAATTAAAAATAT-TAAAA-TTTATA
14360727 AAAA
1 AAAA
14360731 TCATAAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
26 10 0.21
27 18 0.38
28 18 0.38
29 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (26 bp):
AAAAATTAAAAATATTAAAATTTATA
Found at i:14360694 original size:17 final size:17
Alignment explanation
Indices: 14360672--14360719 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
14360662 AAAATTTAAT
14360672 AAAAAATTA-AAAAATAG
1 AAAAAATTATAAAAA-AG
*
14360689 AAAAAATTATAAAAAAT
1 AAAAAATTATAAAAAAG
*
14360706 AAAAAATTGTAAAA
1 AAAAAATTATAAAA
14360720 TTTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (17 bp):
AAAAAATTATAAAAAAG
Found at i:14361340 original size:92 final size:90
Alignment explanation
Indices: 14361167--14361332 Score: 212
Period size: 92 Copynumber: 1.8 Consensus size: 90
14361157 TTTTTTAATC
* * *
14361167 AGGGCCTTTTTGGTGCATTGTGAAAGTTCAAGTACCCAATTGAGCGTTAAAAAAAAGCTAGGGAC
1 AGGGCCTTTTTGATGCATTGTGAAAGTTCAAATACCCAAGTGA-CGTTAAAAAAAA-CTAGGGAC
14361232 TAATTGCTTTTTAAAAAAAAAAGTTTG
64 TAATTGCTTTTTAAAAAAAAAAGTTTG
* * * *
14361259 AGGGCCTTTTTTATGCATTTTGAAAGTTTAAATACCCAAGTGA-G-TACAAAAAAA-TAGGGGCT
1 AGGGCCTTTTTGATGCATTGTGAAAGTTCAAATACCCAAGTGACGTTA-AAAAAAACTAGGGAC-
14361321 TAATTGCTTTTT
64 TAATTGCTTTTT
14361333 TTGAAAAAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
88 6 0.09
89 14 0.22
90 8 0.12
92 37 0.57
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (90 bp):
AGGGCCTTTTTGATGCATTGTGAAAGTTCAAATACCCAAGTGACGTTAAAAAAAACTAGGGACTA
ATTGCTTTTTAAAAAAAAAAGTTTG
Found at i:14362354 original size:18 final size:18
Alignment explanation
Indices: 14362322--14362361 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
14362312 AAATATATTA
14362322 ATTTAAATTTATAAATAT
1 ATTTAAATTTATAAATAT
14362340 ATTTATAATTT-TAAATAT
1 ATTTA-AATTTATAAATAT
14362358 ATTT
1 ATTT
14362362 TGAATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAAATTTATAAATAT
Found at i:14362367 original size:18 final size:17
Alignment explanation
Indices: 14362302--14362372 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 17
14362292 TTCTTCAAAT
*
14362302 TTTTATTTTTAAATATA
1 TTTTAATTTTAAATATA
14362319 TTAATTTAAATTTATAAATATA
1 -T--TTT-AATTT-TAAATATA
14362341 TTTATAATTTTAAATATA
1 TTT-TAATTTTAAATATA
*
14362359 TTTTGAATTATAAA
1 TTTT-AATTTTAAA
14362373 CCAATCCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
17 1 0.02
18 20 0.44
19 7 0.16
20 4 0.09
21 5 0.11
22 8 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTTAATTTTAAATATA
Found at i:14362412 original size:20 final size:19
Alignment explanation
Indices: 14362387--14362433 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
14362377 TCCATATAAT
*
14362387 TAAAAAAATTATAAAAACTA
1 TAAAAAAAGTATAAAAA-TA
* *
14362407 TAAAAAAAGTATTAAAATT
1 TAAAAAAAGTATAAAAATA
14362426 TAAAAAAA
1 TAAAAAAA
14362434 AAAACTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAAAAAGTATAAAAATA
Found at i:14368860 original size:17 final size:16
Alignment explanation
Indices: 14368837--14368894 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
14368827 GTTTATTTAA
14368837 TATATAATAATATAAT
1 TATATAATAATATAAT
14368853 TAATATAAT-ATAATATAT
1 T-ATATAATAAT-ATA-AT
*
14368871 TATATAATAAAATAAT
1 TATATAATAATATAAT
14368887 ATATATAA
1 -TATATAA
14368895 AACATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.14
17 27 0.75
18 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAATAATATAAT
Found at i:14368861 original size:5 final size:5
Alignment explanation
Indices: 14368834--14368894 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
14368824 TTGGTTTATT
14368834 TAATA T-ATAA TAATA TAAT- TAATA TAATA TAATA TATTATA TAATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TA--ATA TAATA
14368880 -AA-A TAATA T-ATA TAA
1 TAATA TAATA TAATA TAA
14368895 AACATAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
3 1 0.02
4 14 0.29
5 26 0.54
6 2 0.04
7 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:14370379 original size:44 final size:46
Alignment explanation
Indices: 14370295--14370382 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 46
14370285 ACTGTAGTGG
*
14370295 AATAGAGCTGTAATCAGTAATTCAGTTGTTTGGTTGAATGGAATGA
1 AATAGAGCTGTAATCAATAATTCAGTTGTTTGGTTGAATGGAATGA
* *
14370341 AATAGAGCTGTAAT-AAT-ATTC-TTGTGTTTGGTTTAATGGAAT
1 AATAGAGCTGTAATCAATAATTCAGT-TGTTTGGTTGAATGGAAT
14370383 AGATGTTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 21 0.55
45 2 0.05
46 14 0.37
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.39
Consensus pattern (46 bp):
AATAGAGCTGTAATCAATAATTCAGTTGTTTGGTTGAATGGAATGA
Found at i:14370471 original size:20 final size:20
Alignment explanation
Indices: 14370443--14370544 Score: 52
Period size: 20 Copynumber: 5.0 Consensus size: 20
14370433 AGCATAATTT
*
14370443 TTTAGTAAAATAATATATAA
1 TTTAATAAAATAATATATAA
* **
14370463 TTTAATAAATTTTTAATATAA
1 TTTAATAAAATAAT-ATATAA
* *
14370484 -TTATTATTAA-AATATA-AA
1 TTTAATA-AAATAATATATAA
14370502 -TTAATAAAAATCATAATATATAA
1 TTTAAT--AAA--ATAATATATAA
14370525 TGTTAA-AAAATAATATATAA
1 T-TTAATAAAATAATATATAA
14370545 CCTACTTTAT
Statistics
Matches: 61, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
18 6 0.10
19 4 0.07
20 28 0.46
21 8 0.13
22 9 0.15
23 2 0.03
25 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
TTTAATAAAATAATATATAA
Found at i:14373660 original size:14 final size:14
Alignment explanation
Indices: 14373641--14373667 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14373631 ATTATAATGT
14373641 ATTTGGAATTAATA
1 ATTTGGAATTAATA
14373655 ATTTGGAATTAAT
1 ATTTGGAATTAAT
14373668 TATTATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
ATTTGGAATTAATA
Found at i:14374494 original size:5 final size:5
Alignment explanation
Indices: 14374484--14374509 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
14374474 TGAACATTCG
14374484 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
14374510 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:14375531 original size:16 final size:16
Alignment explanation
Indices: 14375510--14375540 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14375500 GGGGAAAATA
*
14375510 AAAAGTTTTAGGGAAT
1 AAAAGTTTGAGGGAAT
14375526 AAAAGTTTGAGGGAA
1 AAAAGTTTGAGGGAA
14375541 AGTAAATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (16 bp):
AAAAGTTTGAGGGAAT
Found at i:14376396 original size:23 final size:23
Alignment explanation
Indices: 14376363--14376479 Score: 164
Period size: 23 Copynumber: 5.1 Consensus size: 23
14376353 TCATGCATTT
14376363 CAGTATCAAAATCAGTTCGGTAA
1 CAGTATCAAAATCAGTTCGGTAA
* * *
14376386 CAATATCAAAATTAGTTTGGTAA
1 CAGTATCAAAATCAGTTCGGTAA
*
14376409 CAGTATCAAAATCAGTAT-GGTAG
1 CAGTATCAAAATCAGT-TCGGTAA
*
14376432 CAGTATCAAAATCAATTCGGTAA
1 CAGTATCAAAATCAGTTCGGTAA
*
14376455 CAGTATCAAAATCAGTTCGATAA
1 CAGTATCAAAATCAGTTCGGTAA
14376478 CA
1 CA
14376480 ATATTAGCAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
22 1 0.01
23 80 0.98
24 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (23 bp):
CAGTATCAAAATCAGTTCGGTAA
Found at i:14382511 original size:31 final size:31
Alignment explanation
Indices: 14382474--14382607 Score: 95
Period size: 31 Copynumber: 4.4 Consensus size: 31
14382464 AAAACATAAT
14382474 TTTTTAAATAATTTTTATTTATAAAATAGAA
1 TTTTTAAATAATTTTTATTTATAAAATAGAA
* **
14382505 TTTTTAAATAA---TTATCTATAATTTTAGAA
1 TTTTTAAATAATTTTTATTTATAA-AATAGAA
* * * * *
14382534 TTATGT---T-AGTTTTA-TAAGAACAAACAGAA
1 TT-TTTAAATAATTTTTATTTA-TA-AAATAGAA
14382563 TTTTTTAAATAATTTTTATTTATAAAATAGAA
1 -TTTTTAAATAATTTTTATTTATAAAATAGAA
14382595 TTTTTAAATAATT
1 TTTTTAAATAATT
14382608 ATCTATAATT
Statistics
Matches: 75, Mismatches: 15, Indels: 26
0.65 0.13 0.22
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 10 0.13
29 17 0.23
30 5 0.07
31 24 0.32
32 8 0.11
33 7 0.09
34 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTTTAAATAATTTTTATTTATAAAATAGAA
Found at i:14382602 original size:90 final size:90
Alignment explanation
Indices: 14382449--14382627 Score: 331
Period size: 90 Copynumber: 2.0 Consensus size: 90
14382439 ACATCTTCTT
* *
14382449 TTAGTTTTATAATAAAAAACATAATTTTTTAAATAATTTTTATTTATAAAATAGAATTTTTAAAT
1 TTAGTTTTATAAGAAAAAACAGAATTTTTTAAATAATTTTTATTTATAAAATAGAATTTTTAAAT
14382514 AATTATCTATAATTTTAGAATTATG
66 AATTATCTATAATTTTAGAATTATG
*
14382539 TTAGTTTTATAAGAACAAACAGAATTTTTTAAATAATTTTTATTTATAAAATAGAATTTTTAAAT
1 TTAGTTTTATAAGAAAAAACAGAATTTTTTAAATAATTTTTATTTATAAAATAGAATTTTTAAAT
14382604 AATTATCTATAATTTTAGAATTAT
66 AATTATCTATAATTTTAGAATTAT
14382628 TTAAAAAACA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (90 bp):
TTAGTTTTATAAGAAAAAACAGAATTTTTTAAATAATTTTTATTTATAAAATAGAATTTTTAAAT
AATTATCTATAATTTTAGAATTATG
Found at i:14385675 original size:31 final size:33
Alignment explanation
Indices: 14385610--14385686 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
14385600 ATTCTAAATT
*
14385610 ATTAAATTAATAATTTATTTTAATTATACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
* *
14385643 ATTAAATTATTAATTT-TTCTATTTA-ACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
14385674 ATTAAA-TAATAAT
1 ATTAAATTAATAAT
14385687 AACTTAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.15
31 12 0.30
32 7 0.17
33 15 0.38
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (33 bp):
ATTAAATTAATAATTTATTCTAATTATACTTAA
Found at i:14385691 original size:20 final size:20
Alignment explanation
Indices: 14385666--14385705 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
14385656 TTTTTCTATT
*
14385666 TAACTTAAATTAAATAATAA
1 TAACTTAAATGAAATAATAA
14385686 TAACTTAAATGAAATAATAA
1 TAACTTAAATGAAATAATAA
14385706 AAAATTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
TAACTTAAATGAAATAATAA
Found at i:14385744 original size:11 final size:11
Alignment explanation
Indices: 14385728--14385755 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
14385718 AGACTAAATA
14385728 TAAATAATAAC
1 TAAATAATAAC
14385739 TAAATAATAAC
1 TAAATAATAAC
14385750 TAAATA
1 TAAATA
14385756 GAAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAATAATAAC
Found at i:14385747 original size:3 final size:3
Alignment explanation
Indices: 14385730--14385840 Score: 65
Period size: 3 Copynumber: 36.3 Consensus size: 3
14385720 ACTAAATATA
14385730 AAT AAT AACT AAAT AAT AACT AAAT AGA- AAT AAT AAT -AT ATAT AAT
1 AAT AAT AA-T -AAT AAT AA-T -AAT A-AT AAT AAT AAT AAT A-AT AAT
* *
14385776 AAT -AT TAT AAG AAT AAT -AT AAT AAT AGAT AAT -AT AAT AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT
*
14385820 -AG AAT AAT AA- AAT AAAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT A
14385841 TAGAAATATA
Statistics
Matches: 87, Mismatches: 5, Indels: 32
0.70 0.04 0.26
Matches are distributed among these distances:
2 12 0.14
3 55 0.63
4 16 0.18
5 4 0.05
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:14385774 original size:12 final size:12
Alignment explanation
Indices: 14385759--14385842 Score: 75
Period size: 12 Copynumber: 6.9 Consensus size: 12
14385749 CTAAATAGAA
14385759 ATAATAATATAT
1 ATAATAATATAT
14385771 ATAATAATAT-T
1 ATAATAATATAT
*
14385782 ATAAGAATA-AT
1 ATAATAATATAT
14385793 ATAATAATAGATAAT
1 ATAATAAT--AT-AT
*
14385808 ATAATAATAGAT
1 ATAATAATATAT
* *
14385820 AGAATAATA-AA
1 ATAATAATATAT
14385831 ATAAATAATATA
1 AT-AATAATATA
14385843 GAAATATAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
11 19 0.32
12 27 0.46
13 3 0.05
15 10 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:14385790 original size:11 final size:11
Alignment explanation
Indices: 14385759--14385801 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
14385749 CTAAATAGAA
14385759 ATAATAATATAT
1 ATAATAATAT-T
14385771 ATAATAATATT
1 ATAATAATATT
* *
14385782 ATAAGAATAAT
1 ATAATAATATT
14385793 ATAATAATA
1 ATAATAATA
14385802 GATAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATAATAATATT
Found at i:14385790 original size:29 final size:29
Alignment explanation
Indices: 14385761--14385814 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
14385751 AAATAGAAAT
*
14385761 AATAATAT-AT-ATA-ATAATATTATAAG
1 AATAATATAATAATAGATAATATAATAAG
14385787 AATAATATAATAATAGATAATATAATAA
1 AATAATATAATAATAGATAATATAATAA
14385815 TAGATAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 2 0.08
28 3 0.12
29 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (29 bp):
AATAATATAATAATAGATAATATAATAAG
Found at i:14385810 original size:15 final size:14
Alignment explanation
Indices: 14385730--14385840 Score: 94
Period size: 15 Copynumber: 8.1 Consensus size: 14
14385720 ACTAAATATA
14385730 AATAATAACTA-AAT
1 AATAATAA-TATAAT
14385744 AATAACTAA-ATAGA-
1 AATAA-TAATATA-AT
14385758 AATAATAATAT-AT
1 AATAATAATATAAT
*
14385771 -ATAATAATATTAT
1 AATAATAATATAAT
*
14385784 AAGAATAATATAAT
1 AATAATAATATAAT
14385798 AATAGATAATATAAT
1 AATA-ATAATATAAT
14385813 AATAGATAGA-ATAAT
1 AATA-ATA-ATATAAT
14385828 AA-AATAA-ATAAT
1 AATAATAATATAAT
14385840 A
1 A
14385841 TAGAAATATA
Statistics
Matches: 85, Mismatches: 3, Indels: 20
0.79 0.03 0.19
Matches are distributed among these distances:
12 18 0.21
13 9 0.11
14 28 0.33
15 29 0.34
16 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (14 bp):
AATAATAATATAAT
Found at i:14385839 original size:32 final size:37
Alignment explanation
Indices: 14385758--14385842 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
14385748 ACTAAATAGA
*
14385758 AATAAT-AATATATATAATAATATTATAAGAATAATAT
1 AATAATAAATA-ATATAATAATATGATAAGAATAATAT
*
14385795 AATAATAGATAATATAATAATA-GAT-AGAAT-A-AT
1 AATAATAAATAATATAATAATATGATAAGAATAATAT
14385828 AA-AATAAATAATATA
1 AATAATAAATAATATA
14385843 GAAATATAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 12 0.27
33 4 0.09
34 1 0.02
35 5 0.11
36 2 0.05
37 17 0.39
38 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (37 bp):
AATAATAAATAATATAATAATATGATAAGAATAATAT
Found at i:14385883 original size:14 final size:14
Alignment explanation
Indices: 14385864--14385904 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
14385854 TTATAAATCG
14385864 AAATATATTAATAT
1 AAATATATTAATAT
*
14385878 AAATATAATAATAT
1 AAATATATTAATAT
14385892 AAATATTATTAAT
1 AAATA-TATTAAT
14385905 TACTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATTAATAT
Found at i:14390274 original size:14 final size:13
Alignment explanation
Indices: 14390255--14390306 Score: 86
Period size: 14 Copynumber: 3.8 Consensus size: 13
14390245 TAGCTCTCAC
14390255 TTTTTTTTTCACAA
1 TTTTTTTTTCA-AA
14390269 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
14390282 TTTTTTTTTTCAAA
1 -TTTTTTTTTCAAA
14390296 TTTTTTTTTCA
1 TTTTTTTTTCA
14390307 CAACTTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
13 13 0.35
14 24 0.65
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:14390366 original size:16 final size:15
Alignment explanation
Indices: 14390347--14390385 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
14390337 TGGAAACTAG
*
14390347 TTTTTTTTTTCGAAA
1 TTTTTTTTTTTGAAA
14390362 TTTTTTTTTTTGAAA
1 TTTTTTTTTTTGAAA
14390377 TTTTTTTTT
1 TTTTTTTTT
14390386 CGAGTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTTTGAAA
Found at i:14390367 original size:14 final size:14
Alignment explanation
Indices: 14390348--14390398 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
14390338 GGAAACTAGT
14390348 TTTTTTTTTCGAAA
1 TTTTTTTTTCGAAA
*
14390362 TTTTTTTTTTTGAAA
1 -TTTTTTTTTCGAAA
*
14390377 TTTTTTTTTCG-AG
1 TTTTTTTTTCGAAA
14390390 TTTTTTTTT
1 TTTTTTTTT
14390399 GAAGAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 10 0.30
14 10 0.30
15 13 0.39
ACGTcount: A:0.14, C:0.04, G:0.08, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTCGAAA
Found at i:14390367 original size:15 final size:15
Alignment explanation
Indices: 14390347--14390398 Score: 72
Period size: 14 Copynumber: 3.6 Consensus size: 15
14390337 TGGAAACTAG
14390347 TTTTTTTTTTCGAAA
1 TTTTTTTTTTCGAAA
*
14390362 TTTTTTTTTTTGAAA
1 TTTTTTTTTTCGAAA
*
14390377 -TTTTTTTTTCG-AG
1 TTTTTTTTTTCGAAA
14390390 TTTTTTTTT
1 TTTTTTTTT
14390399 GAAGAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 1 0.03
14 18 0.55
15 14 0.42
ACGTcount: A:0.13, C:0.04, G:0.08, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTTCGAAA
Found at i:14390405 original size:29 final size:29
Alignment explanation
Indices: 14390348--14390405 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
14390338 GGAAACTAGT
**
14390348 TTTTTTTTTCGAAATTTTTTTTTTTGAAA
1 TTTTTTTTTCGAAATTTTTTTTTAAGAAA
*
14390377 TTTTTTTTTCG-AGTTTTTTTTTGAAGAAA
1 TTTTTTTTTCGAAATTTTTTTTT-AAGAAA
14390406 CTACTATACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (29 bp):
TTTTTTTTTCGAAATTTTTTTTTAAGAAA
Found at i:14391774 original size:19 final size:19
Alignment explanation
Indices: 14391743--14391808 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
14391733 AAAAACATAA
14391743 ATTTTGAAATTTTTATAAAT
1 ATTTTG-AATTTTTATAAAT
*
14391763 ATTTTGAA-TTTTAAAAAT
1 ATTTTGAATTTTTATAAAT
*
14391781 -TATTTAAACTTTTT-TAAAAT
1 AT-TTTGAA-TTTTTAT-AAAT
14391801 ATTTTGAA
1 ATTTTGAA
14391809 ACTTTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 1 0.03
18 14 0.38
19 2 0.05
20 19 0.51
21 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTTTGAATTTTTATAAAT
Found at i:14391828 original size:21 final size:21
Alignment explanation
Indices: 14391743--14391818 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
14391733 AAAAACATAA
14391743 ATTTTGAAA--TTTTTATAAAT
1 ATTTTGAAACTTTTTTA-AAAT
14391763 ATTTTG-AA---TTTTAAAA-
1 ATTTTGAAACTTTTTTAAAAT
*
14391779 ATTATTTAAACTTTTTTAAAAT
1 ATT-TTGAAACTTTTTTAAAAT
14391801 ATTTTGAAACTTTTTTAA
1 ATTTTGAAACTTTTTTAA
14391819 TTTTTGTTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
16 3 0.06
17 5 0.10
18 7 0.15
19 2 0.04
20 6 0.12
21 22 0.46
22 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTTTGAAACTTTTTTAAAAT
Found at i:14391974 original size:23 final size:23
Alignment explanation
Indices: 14391947--14392000 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
14391937 TCGAACTCAA
* *
14391947 AACTCGAATTACT-TATTCAAGTT
1 AACTCGAATAACTCGATTCAA-TT
*
14391970 GACTCGAATAACTCGATTCAATT
1 AACTCGAATAACTCGATTCAATT
14391993 AACTCGAA
1 AACTCGAA
14392001 ATTTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (23 bp):
AACTCGAATAACTCGATTCAATT
Found at i:14397379 original size:19 final size:19
Alignment explanation
Indices: 14397355--14397395 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
14397345 TTCTATATTT
*
14397355 TTTTATAGTT-TTTAATAAA
1 TTTTATAATTATTT-ATAAA
14397374 TTTTATAATTATTTATAAA
1 TTTTATAATTATTTATAAA
14397393 TTT
1 TTT
14397396 CTAATAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTATAATTATTTATAAA
Found at i:14398360 original size:16 final size:16
Alignment explanation
Indices: 14398339--14398394 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
14398329 CGTTTGATTC
14398339 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
14398355 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
14398371 GGTGTAATGGAATAAA
1 GCTGTAATGGAATAGA
14398387 GCTGTAAT
1 GCTGTAAT
14398395 AGTAATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:14398428 original size:45 final size:44
Alignment explanation
Indices: 14398376--14398468 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
14398366 ATAGAGGTGT
14398376 AATGGAATA-AAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAA-CTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
14398421 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
14398465 AATG
1 AATG
14398469 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 19 0.42
46 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:14408264 original size:2 final size:2
Alignment explanation
Indices: 14408259--14408283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14408249 ATAATTATTA
14408259 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14408284 AACATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14408609 original size:11 final size:11
Alignment explanation
Indices: 14408593--14408634 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
14408583 TAAAGAAATA
14408593 TGTTGTTTTCT
1 TGTTGTTTTCT
*
14408604 TGTTGTTTTCC
1 TGTTGTTTTCT
* *
14408615 TATGGTTTTCT
1 TGTTGTTTTCT
14408626 TGTTGTTTT
1 TGTTGTTTT
14408635 GGTGTCATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.02, C:0.10, G:0.19, T:0.69
Consensus pattern (11 bp):
TGTTGTTTTCT
Found at i:14409734 original size:7 final size:7
Alignment explanation
Indices: 14409714--14409743 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
14409704 TTTTTCTGTC
14409714 CTTTCTT
1 CTTTCTT
14409721 C-TTCTT
1 CTTTCTT
14409727 CTTTCTT
1 CTTTCTT
14409734 CTTTCTT
1 CTTTCTT
14409741 CTT
1 CTT
14409744 CCTCCCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
CTTTCTT
Found at i:14410293 original size:15 final size:15
Alignment explanation
Indices: 14410273--14410301 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14410263 TAAATAAAAA
14410273 AATTTAAAACCAAAT
1 AATTTAAAACCAAAT
14410288 AATTTAAAACCAAA
1 AATTTAAAACCAAA
14410302 AATAAAAGTC
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:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTTAAAACCAAAT
Found at i:14410306 original size:17 final size:17
Alignment explanation
Indices: 14410268--14410306 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
14410258 CCGCATAAAT
14410268 AAAAA-AATTTAAAACC
1 AAAAATAATTTAAAACC
14410284 --AAATAATTTAAAACC
1 AAAAATAATTTAAAACC
14410299 AAAAATAA
1 AAAAATAA
14410307 AAGTCCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 3 0.15
15 11 0.55
17 6 0.30
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAATTTAAAACC
Found at i:14410797 original size:3 final size:3
Alignment explanation
Indices: 14410789--14410825 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
14410779 TTTAGTTGTT
14410789 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
14410826 CATTTTACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:14411537 original size:3 final size:3
Alignment explanation
Indices: 14411531--14411606 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
14411521 ATAATTTTGA
* *
14411531 TAT TAT TAT TAT TAT TAT TAT TACT T-T CAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* **
14411576 TAG TAT TAT TGC TAT TAT TGA- TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T
14411607 TGCTTATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:14419049 original size:12 final size:12
Alignment explanation
Indices: 14419034--14419069 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
14419024 AAAAGAGTCA
14419034 ATAAACGAGCTT
1 ATAAACGAGCTT
*
14419046 ATAAATGAGCTT
1 ATAAACGAGCTT
*
14419058 TTAAACGAGCTT
1 ATAAACGAGCTT
14419070 GTTCTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:14419294 original size:5 final size:5
Alignment explanation
Indices: 14419278--14419328 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
14419268 TGTGAAACTT
** *
14419278 TTAAA TTAAAA TTAAA TTAAA TTATAA AAAAA TTAAA CT-AA TTAAA TTAAA
1 TTAAA TT-AAA TTAAA TTAAA TTA-AA TTAAA TTAAA TTAAA TTAAA TTAAA
14419329 ACTTTTCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 26 0.70
6 8 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (5 bp):
TTAAA
Found at i:14419299 original size:16 final size:16
Alignment explanation
Indices: 14419278--14419328 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
14419268 TGTGAAACTT
14419278 TTAAATTAAAATTAAA
1 TTAAATTAAAATTAAA
*
14419294 TTAAATTATAAA-AAAA
1 TTAAATTA-AAATTAAA
*
14419310 TTAAACT--AATTAAA
1 TTAAATTAAAATTAAA
14419324 TTAAA
1 TTAAA
14419329 ACTTTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.27
16 17 0.57
17 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAATTAAAATTAAA
Found at i:14419502 original size:124 final size:125
Alignment explanation
Indices: 14419283--14419555 Score: 507
Period size: 124 Copynumber: 2.2 Consensus size: 125
14419273 AACTTTTAAA
*
14419283 TTAAAATTAAATTAAATTATAAAAAAATTAAACTAATTAAATTAAAACTTTTCAATTTTTATATG
1 TTAACATTAAATTAAATTATAAAAAAATTAAACTAATTAAATTAAAACTTTTCAATTTTTATATG
14419348 CACTCTCTCTCCCCACTATTCTTTGTGCTCTTTTAACGGATTTTTTTTATAGAAA-TTAT
66 CACTCTCTCTCCCCACTATTCTTTGTGCTCTTTTAACGGATTTTTTTTATAGAAATTTAT
14419407 TTAACATTAAATTAAATTATAAAAAAATTAAACTAATTAAATTAAAACTTTTCAATTTTTATATG
1 TTAACATTAAATTAAATTATAAAAAAATTAAACTAATTAAATTAAAACTTTTCAATTTTTATATG
14419472 CACTCTCTCTCCCCACTATTCTTTGTGCTCTTTTAACGGATTTTTTTTATAGAAATTTAT
66 CACTCTCTCTCCCCACTATTCTTTGTGCTCTTTTAACGGATTTTTTTTATAGAAATTTAT
*
14419532 TTAACATT-AATT-ATTTATAAAAAA
1 TTAACATTAAATTAAATTATAAAAAA
14419556 TATATATTTT
Statistics
Matches: 146, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
123 11 0.08
124 123 0.84
125 12 0.08
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (125 bp):
TTAACATTAAATTAAATTATAAAAAAATTAAACTAATTAAATTAAAACTTTTCAATTTTTATATG
CACTCTCTCTCCCCACTATTCTTTGTGCTCTTTTAACGGATTTTTTTTATAGAAATTTAT
Found at i:14424135 original size:28 final size:28
Alignment explanation
Indices: 14424103--14424156 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
14424093 ACTATTTTAC
14424103 TTTTACTTCAAAGTCAAAGAGTTTTATA
1 TTTTACTTCAAAGTCAAAGAGTTTTATA
14424131 TTTTACTTCAAAGTCAAAGAGTTTTA
1 TTTTACTTCAAAGTCAAAGAGTTTTA
14424157 CTTTCAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (28 bp):
TTTTACTTCAAAGTCAAAGAGTTTTATA
Found at i:14426559 original size:18 final size:18
Alignment explanation
Indices: 14426510--14426550 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
14426500 TATTGCTTCT
*
14426510 AAAAAACACTTTTGGGAC
1 AAAAAGCACTTTTGGGAC
14426528 AAAAAGCACTTTTGGGAC
1 AAAAAGCACTTTTGGGAC
14426546 AAAAA
1 AAAAA
14426551 TTACTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (18 bp):
AAAAAGCACTTTTGGGAC
Found at i:14433651 original size:41 final size:42
Alignment explanation
Indices: 14433570--14433665 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 42
14433560 AGCAGGCGTC
* * * * *
14433570 ATGCCAGTGTATT-AATTTAGGCTTTGTGCCTAGTAGGCTTT
1 ATGCCGGTGTATTGAATTTAGGCCTTGAGCCTAGCAAGCTTT
14433611 GA-GCCGGTGTATTGAA-TTAGGCCTTGAGCCTAGCAAGCTTT
1 -ATGCCGGTGTATTGAATTTAGGCCTTGAGCCTAGCAAGCTTT
*
14433652 ATGCCGGCGTATTG
1 ATGCCGGTGTATTG
14433666 TATCAAGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 42 0.91
42 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (42 bp):
ATGCCGGTGTATTGAATTTAGGCCTTGAGCCTAGCAAGCTTT
Found at i:14448746 original size:6 final size:6
Alignment explanation
Indices: 14448737--14448763 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
14448727 TTATTTTTAG
14448737 TTTGGT TTTGGT TTTGGT TTTGGT TTT
1 TTTGGT TTTGGT TTTGGT TTTGGT TTT
14448764 TTAGCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (6 bp):
TTTGGT
Found at i:14450372 original size:4 final size:4
Alignment explanation
Indices: 14450363--14450387 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
14450353 TGGCACTGCT
14450363 CTCC CTCC CTCC CTCC CTCC CTCC C
1 CTCC CTCC CTCC CTCC CTCC CTCC C
14450388 CCTCTCTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CTCC
Found at i:14458142 original size:18 final size:19
Alignment explanation
Indices: 14458103--14458145 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
14458093 AAAATTATAA
*
14458103 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
*
14458122 AAAATTCAAAGT-ATTTAT
1 AAAATTCAAAATAATTTAT
14458140 AAAATT
1 AAAATT
14458146 TCTGAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:14458191 original size:21 final size:22
Alignment explanation
Indices: 14458158--14458198 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
14458148 TGAAATTTAT
*
14458158 ATTTTTAAAAAAAT-TAAAATA
1 ATTTTAAAAAAAATCTAAAATA
14458179 ATTTTAAAAAAAATCTAAAA
1 ATTTTAAAAAAAATCTAAAA
14458199 ATATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
ATTTTAAAAAAAATCTAAAATA
Found at i:14460077 original size:13 final size:13
Alignment explanation
Indices: 14460059--14460083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14460049 TAATTTATAT
14460059 GTGTGAAAATTTC
1 GTGTGAAAATTTC
14460072 GTGTGAAAATTT
1 GTGTGAAAATTT
14460084 TTATCGTTTG
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:14466867 original size:39 final size:39
Alignment explanation
Indices: 14466824--14466898 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
14466814 AATGATATTT
*
14466824 AAATTTATTAATATTATGATATATGAAATATATAAACTC
1 AAATTGATTAATATTATGATATATGAAATATATAAACTC
*
14466863 AAATTGGTTAATATTATGATATATGAAATATATAAA
1 AAATTGATTAATATTATGATATATGAAATATATAAA
14466899 TTTTGATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (39 bp):
AAATTGATTAATATTATGATATATGAAATATATAAACTC
Found at i:14478702 original size:2 final size:2
Alignment explanation
Indices: 14478695--14478719 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14478685 AAGAAATGAA
14478695 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14478720 ATAGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14478875 original size:17 final size:19
Alignment explanation
Indices: 14478841--14478880 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
14478831 GAATAAATAT
14478841 ATACATAATAAAGGAATAAA
1 ATACATAATAAA-GAATAAA
14478861 ATACATAAT-AA-AATAAA
1 ATACATAATAAAGAATAAA
14478878 ATA
1 ATA
14478881 AAAGTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
ATACATAATAAAGAATAAA
Found at i:14478927 original size:3 final size:3
Alignment explanation
Indices: 14478921--14478951 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
14478911 AATAACATCT
*
14478921 ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
14478952 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:14478978 original size:16 final size:16
Alignment explanation
Indices: 14478957--14478995 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
14478947 AATAAAATTT
14478957 AAAAAACACAAAAA-A
1 AAAAAACACAAAAAGA
*
14478972 AACAAAATACAAAAAGA
1 AA-AAAACACAAAAAGA
14478989 AAAAAAC
1 AAAAAAC
14478996 CAATAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 15 0.75
17 3 0.15
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAAACACAAAAAGA
Found at i:14481024 original size:52 final size:52
Alignment explanation
Indices: 14480926--14481026 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
14480916 TATAAATTAC
*
14480926 AATATTGTCATAAGTTAAACATAATTTATTTTTCAATTAATATATGTAATCT
1 AATATTGTCATAAGTTAAACATAATTTATTTTTCAATCAATATATGTAATCT
*
14480978 AATATTGTCATATGTTAAACATAATTTATTTTTCAATCAATATATGTAA
1 AATATTGTCATAAGTTAAACATAATTTATTTTTCAATCAATATATGTAA
14481027 GCTTTGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (52 bp):
AATATTGTCATAAGTTAAACATAATTTATTTTTCAATCAATATATGTAATCT
Found at i:14495820 original size:21 final size:21
Alignment explanation
Indices: 14495787--14495831 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
14495777 TGAAATTAGT
*
14495787 TACTGTAATGGTGAGATTGGA
1 TACTGTAACGGTGAGATTGGA
*
14495808 TACTGTAGCGGTGAGATTGGA
1 TACTGTAACGGTGAGATTGGA
14495829 TAC
1 TAC
14495832 GGTGAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.31
Consensus pattern (21 bp):
TACTGTAACGGTGAGATTGGA
Found at i:14506029 original size:87 final size:86
Alignment explanation
Indices: 14505933--14506095 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 86
14505923 TTAAATTCGT
* * *
14505933 TGAATTCATCAAGTCCGTTTCAATAGGACCACCCAAA-CTCTAGGATATAAACTCATTAAGATTA
1 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACCT-TAGGATATAAACTCATTAAGAGTA
14505997 AGAAACTCAACCTCACATGTCGG
65 AGAAA-TCAACCTCACATGTCGG
* * * *
14506020 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACCTTGGGGTATGAATTCATTAAGAGTAA
1 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACCTTAGGATATAAACTCATTAAGAGTAA
14506085 GAAATCAACCT
66 GAAATCAACCT
14506096 TATGCATGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 7 0.10
87 59 0.87
88 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (86 bp):
TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACCTTAGGATATAAACTCATTAAGAGTAA
GAAATCAACCTCACATGTCGG
Found at i:14513705 original size:90 final size:90
Alignment explanation
Indices: 14513602--14513880 Score: 416
Period size: 90 Copynumber: 3.1 Consensus size: 90
14513592 GCATATTGAA
* * *
14513602 TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATACTAATTGAATTCGTTTGAT
1 TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATATTGATTGAATTCATTTGAT
*
14513667 TGACCAAATTATGCAACTTGTATAT
66 TGACTAAATTATGCAACTTGTATAT
* * *
14513692 TTGTATAAATATTTGCTTGATTTCCGATAGTATATAGTAACTTATATTGATTGAATTCATTTGAT
1 TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATATTGATTGAATTCATTTGAT
*
14513757 TGATTAAATTATGCAACTTGTATAT
66 TGACTAAATTATGCAACTTGTATAT
*
14513782 TTGTATAAATATTTTCTTGA-TTTCTGATAGTATATCGTAACTTGATATTGATTGAATTCATATG
1 TTGTATAAATATTTTCTTGATTTTC-GATAGTATATCGTAACTT-ATATTGATTGAATTCATTTG
* * * *
14513846 ATTTAGTGAATTATGCAAGTTGTATAT
64 ATTGACTAAATTATGCAACTTGTATAT
14513873 TTGTATAA
1 TTGTATAA
14513881 CTCACCATTG
Statistics
Matches: 171, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
89 3 0.02
90 118 0.69
91 50 0.29
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (90 bp):
TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATATTGATTGAATTCATTTGAT
TGACTAAATTATGCAACTTGTATAT
Found at i:14517314 original size:40 final size:40
Alignment explanation
Indices: 14517270--14517371 Score: 159
Period size: 40 Copynumber: 2.5 Consensus size: 40
14517260 TGCTATACTC
* * *
14517270 TCTGTTTGGTGTGTTTTGGTTGGATCAGCTCTTATGAGCT
1 TCTGTTTGGCGTGTTTCGGTTGGACCAGCTCTTATGAGCT
*
14517310 TCTGTTTGGCATGTTTCGGTTGGACCAGCTCTTATGAGCT
1 TCTGTTTGGCGTGTTTCGGTTGGACCAGCTCTTATGAGCT
*
14517350 TCTGTTTGGGGTGTTTCGGTTG
1 TCTGTTTGGCGTGTTTCGGTTG
14517372 ATTTGACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.09, C:0.15, G:0.31, T:0.45
Consensus pattern (40 bp):
TCTGTTTGGCGTGTTTCGGTTGGACCAGCTCTTATGAGCT
Found at i:14521196 original size:12 final size:11
Alignment explanation
Indices: 14521174--14521214 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
14521164 AATTTCCTTG
14521174 AGCTTCTTTTC
1 AGCTTCTTTTC
14521185 AGCTTCCTTTTC
1 AGCTT-CTTTTC
14521197 AGC-TCTTTT-
1 AGCTTCTTTTC
*
14521206 AGCTGCTTT
1 AGCTTCTTT
14521215 GGCTGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 3 0.11
10 9 0.33
11 6 0.22
12 9 0.33
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (11 bp):
AGCTTCTTTTC
Found at i:14524695 original size:7 final size:7
Alignment explanation
Indices: 14524670--14524707 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
14524660 ACGGCAGCTG
14524670 AAAT-AA
1 AAATAAA
14524676 AAATAATAA
1 AAAT-A-AA
14524685 AAATAAA
1 AAATAAA
14524692 AAATAAA
1 AAATAAA
14524699 AAATAAA
1 AAATAAA
14524706 AA
1 AA
14524708 GTAGGTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.14
7 18 0.62
8 1 0.03
9 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:14525467 original size:14 final size:14
Alignment explanation
Indices: 14525448--14525487 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
14525438 TTGATTGGCA
14525448 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
14525462 GTAAAATATTTTCT
1 GTAAAATGTTTTCC
*
14525476 GGAAAATGTTTT
1 GTAAAATGTTTT
14525488 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:14525495 original size:20 final size:20
Alignment explanation
Indices: 14525470--14525510 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
14525460 CCGTAAAATA
*
14525470 TTTTCTGGAAAATGTTTTAC
1 TTTTCTGGAAAATGATTTAC
*
14525490 TTTTCTGTAAAATGATTTAC
1 TTTTCTGGAAAATGATTTAC
14525510 T
1 T
14525511 GGAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTTCTGGAAAATGATTTAC
Found at i:14525500 original size:34 final size:35
Alignment explanation
Indices: 14525456--14525522 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
14525446 CAGTAAAATG
* *
14525456 TTTTCCGTAAAAT-ATTTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
14525490 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
14525523 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:14525526 original size:14 final size:15
Alignment explanation
Indices: 14525450--14525526 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
14525440 GATTGGCAGT
* *
14525450 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
14525464 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
*
14525478 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
14525498 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
14525513 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
14525527 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 11 0.22
16 1 0.02
19 1 0.02
20 13 0.26
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:14528030 original size:14 final size:14
Alignment explanation
Indices: 14528008--14528064 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
14527998 GAATATGCTG
* *
14528008 AGAAGAGAAGATGA
1 AGAACAGAAGAAGA
14528022 AGAACAGAAGAAGA
1 AGAACAGAAGAAGA
14528036 A-AA-AG--GAATGA
1 AGAACAGAAGAA-GA
*
14528047 AGAACGGAAGAAGA
1 AGAACAGAAGAAGA
14528061 AGAA
1 AGAA
14528065 GGAGCCTTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
10 3 0.09
11 3 0.09
12 4 0.11
13 3 0.09
14 19 0.54
15 3 0.09
ACGTcount: A:0.61, C:0.04, G:0.32, T:0.04
Consensus pattern (14 bp):
AGAACAGAAGAAGA
Found at i:14528066 original size:25 final size:25
Alignment explanation
Indices: 14528018--14528067 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
14528008 AGAAGAGAAG
14528018 ATGAAGAACAGAAGAAGAAAAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
* *
14528043 ATGAAGAACGGAAGAAGAAGAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
14528068 GCCTTACCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.04, G:0.32, T:0.04
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGAAAAAGGA
Found at i:14528150 original size:18 final size:18
Alignment explanation
Indices: 14528127--14528164 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
14528117 TTTGCAGCAC
14528127 AAGGGGAAGGGAAAAGGG
1 AAGGGGAAGGGAAAAGGG
*
14528145 AAGGGGAAGGGAAAGGGG
1 AAGGGGAAGGGAAAAGGG
14528163 AA
1 AA
14528165 AGGAAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGAAAAGGG
Found at i:14540824 original size:29 final size:29
Alignment explanation
Indices: 14540737--14540830 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
14540727 ACACATGACT
* * *
14540737 GTGTGTCGTGCATGACCTACCACACGGTC
1 GTGTGGCGCGCATGACCTACCACACGGCC
* * *
14540766 ATGTAGCGCGCACGACCTACCACACGGCC
1 GTGTGGCGCGCATGACCTACCACACGGCC
*
14540795 GTGTGGCGCGCATAACCTACCACACGGCC
1 GTGTGGCGCGCATGACCTACCACACGGCC
14540824 GTGTGGC
1 GTGTGGC
14540831 ATCGACAAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.17
Consensus pattern (29 bp):
GTGTGGCGCGCATGACCTACCACACGGCC
Found at i:14545629 original size:21 final size:21
Alignment explanation
Indices: 14545605--14545644 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14545595 TGCCAAGCTA
*
14545605 TTTTAGGGTTTTAGTTAGTAG
1 TTTTAGGATTTTAGTTAGTAG
*
14545626 TTTTAGGATTTTATTTAGT
1 TTTTAGGATTTTAGTTAGT
14545645 TTAGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (21 bp):
TTTTAGGATTTTAGTTAGTAG
Found at i:14550301 original size:42 final size:43
Alignment explanation
Indices: 14550241--14550385 Score: 161
Period size: 43 Copynumber: 3.4 Consensus size: 43
14550231 ACTAAGATTA
14550241 CGTGTAAGACCATATCTGGGATA-TGGCATCGATATGATAATTT
1 CGTGTAAGACCATATCTGGGATATTGGCATCGATATG-TAATTT
* *
14550284 -GTGTAAGACCATATCTGGGATATTGGCATAGATATGTGATTT
1 CGTGTAAGACCATATCTGGGATATTGGCATCGATATGTAATTT
* ** * * * *
14550326 CGCGTAAGACCATGGCTGGGCTATTGGCATCAATACG-AGATTA
1 CGTGTAAGACCATATCTGGGATATTGGCATCGATATGTA-ATTT
*
14550369 CATGTAAGACCATATCT
1 CGTGTAAGACCATATCT
14550386 AGAATATGAC
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
42 27 0.32
43 57 0.68
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCATATCTGGGATATTGGCATCGATATGTAATTT
Found at i:14557881 original size:34 final size:34
Alignment explanation
Indices: 14557836--14557906 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
14557826 AGTGTAGCCC
* *
14557836 AATCTTATTTTAATCGGATCGG-ATCAGTTGATTG
1 AATCTTATTTTAATCAGATCGGAAT-AGTTAATTG
* *
14557870 AATCTTGTTTTAATTAGATCGGAATAGTTAATTG
1 AATCTTATTTTAATCAGATCGGAATAGTTAATTG
14557904 AAT
1 AAT
14557907 TGATTAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 30 0.94
35 2 0.06
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.42
Consensus pattern (34 bp):
AATCTTATTTTAATCAGATCGGAATAGTTAATTG
Found at i:14559043 original size:20 final size:20
Alignment explanation
Indices: 14559010--14559048 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
14559000 TGATTTTTAT
*
14559010 TTTTTTAAAATTTATAATTA
1 TTTTTTAAAATTTAAAATTA
* *
14559030 TTTTTTGAATTTTAAAATT
1 TTTTTTAAAATTTAAAATT
14559049 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTTAAAATTTAAAATTA
Done.