Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 43 of 135
Found at i:16735937 original size:183 final size:183
Alignment explanation
Indices: 16735629--16735963 Score: 528
Period size: 183 Copynumber: 1.8 Consensus size: 183
16735619 TAAAATAAAA
* * * *
16735629 ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACGATGAATCTTATACCTTTGAAG
1 ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
* * * *
16735694 TTACAGAGGGTCGGATTAAATCTAATCGTATCAAACCTTATCTCACTGAGGTCGCAGTGGAGCAG
66 TTACAGAGGGTCGGATTAAACCTAATCATATCAAACATTACCTCACTGAGGTCGCAGTGGAGCAG
16735759 GTTGAAG-ATACAAGTCTTATCTTCCTGAAGTTACAGTGAAGTAGGCTAAAGCG
131 GTTGAAGCA-ACAAGTCTTATCTTCCTGAAGTTACAGTGAAGTAGGCTAAAGCG
*
16735812 ACTAATCTTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
1 ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
** * *
16735877 TTGTAGAGGGTCGGATTAAACCTTATCATATCAAACATTACCTCCCTGAGGTCGCAGTGGAGCAG
66 TTACAGAGGGTCGGATTAAACCTAATCATATCAAACATTACCTCACTGAGGTCGCAGTGGAGCAG
*
16735942 GTTGAGGCAACAAGTCTTATCT
131 GTTGAAGCAACAAGTCTTATCT
16735964 CCCTAACATT
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
183 136 0.99
184 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (183 bp):
ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
TTACAGAGGGTCGGATTAAACCTAATCATATCAAACATTACCTCACTGAGGTCGCAGTGGAGCAG
GTTGAAGCAACAAGTCTTATCTTCCTGAAGTTACAGTGAAGTAGGCTAAAGCG
Found at i:16737372 original size:18 final size:18
Alignment explanation
Indices: 16737346--16737454 Score: 65
Period size: 18 Copynumber: 5.6 Consensus size: 18
16737336 TTTAATAATG
*
16737346 TTATCATTATTTTTACTA
1 TTATTATTATTTTTACTA
* *
16737364 TTATTATTATGTTTAATA
1 TTATTATTATTTTTACTA
* * * * *
16737382 CTGTTATTACTATTACCTTTT
1 TTATTATTATTTTTA-C--TA
16737403 TTATTTATATATTTTTACTA
1 TTA-TTAT-TATTTTTACTA
16737423 TTATTATTATTATTTATCTA
1 TTATTATTATT-TTTA-CTA
*
16737443 TTTAATATTATT
1 -TTATTATTATT
16737455 GTTCATTTAT
Statistics
Matches: 67, Mismatches: 16, Indels: 13
0.70 0.17 0.14
Matches are distributed among these distances:
18 29 0.43
19 8 0.12
20 7 0.10
21 12 0.18
22 5 0.07
23 6 0.09
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTATTATTTTTACTA
Found at i:16737426 original size:20 final size:20
Alignment explanation
Indices: 16737407--16737454 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
16737397 CCTTTTTTAT
16737407 TTATATATT-TTTA-CTATTA
1 TTAT-TATTATTTATCTATTA
16737426 TTATTATTATTTATCTATTTA
1 TTATTATTATTTATCTA-TTA
*
16737447 ATATTATT
1 TTATTATT
16737455 GTTCATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 3 0.12
21 10 0.40
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATTATTTATCTATTA
Found at i:16737464 original size:29 final size:29
Alignment explanation
Indices: 16737402--16737465 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
16737392 TATTACCTTT
*
16737402 TTTATTTATATATTTTTACTATTATTATTA
1 TTTATTTATATA-TTTTAATATTATTATTA
* *
16737432 -TTATTTATCTA-TTTAATATTATTGTTCA
1 TTTATTTATATATTTTAATATTATTATT-A
16737460 TTTATT
1 TTTATT
16737466 AATGCATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 13 0.45
28 1 0.03
29 15 0.52
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTATTTATATATTTTAATATTATTATTA
Found at i:16749222 original size:19 final size:19
Alignment explanation
Indices: 16749198--16749234 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16749188 ATTCTATATA
* *
16749198 TCTGTTCTTCTTATCTGAT
1 TCTGTTATTCGTATCTGAT
16749217 TCTGTTATTCGTATCTGA
1 TCTGTTATTCGTATCTGA
16749235 AATGGACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.54
Consensus pattern (19 bp):
TCTGTTATTCGTATCTGAT
Found at i:16751473 original size:22 final size:22
Alignment explanation
Indices: 16751448--16751490 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16751438 ATAATAATAT
16751448 AATAATAAAATAACAACAAAAC
1 AATAATAAAATAACAACAAAAC
* * *
16751470 AATATTAAAATAGCAGCAAAA
1 AATAATAAAATAACAACAAAA
16751491 TAATGAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.16
Consensus pattern (22 bp):
AATAATAAAATAACAACAAAAC
Found at i:16751823 original size:18 final size:18
Alignment explanation
Indices: 16751792--16751826 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16751782 AAATTCTCAA
*
16751792 TTAAAAATAGTTTATTTT
1 TTAAAAATAATTTATTTT
*
16751810 TTAAACATAATTTATTT
1 TTAAAAATAATTTATTT
16751827 GTTTGAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAAAATAATTTATTTT
Found at i:16758895 original size:14 final size:13
Alignment explanation
Indices: 16758876--16758906 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
16758866 GTGCAACGGT
16758876 CACAGGGCCAAGC
1 CACAGGGCCAAGC
16758889 ACACAGGGCCAAGC
1 -CACAGGGCCAAGC
16758903 CACA
1 CACA
16758907 TGCCCGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.35, C:0.39, G:0.26, T:0.00
Consensus pattern (13 bp):
CACAGGGCCAAGC
Found at i:16761104 original size:15 final size:15
Alignment explanation
Indices: 16761084--16761113 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16761074 ATAAAATGTG
16761084 CCGATTTAGTTAGTC
1 CCGATTTAGTTAGTC
16761099 CCGATTTAGTTAGTC
1 CCGATTTAGTTAGTC
16761114 TGTCAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
CCGATTTAGTTAGTC
Found at i:16765987 original size:21 final size:21
Alignment explanation
Indices: 16765958--16766070 Score: 75
Period size: 21 Copynumber: 5.4 Consensus size: 21
16765948 CAGAAACCCG
* *
16765958 TAAGGGTTGAACGGAAGCTCA
1 TAAGAGTTGAACGGAAACTCA
*
16765979 TAAGAGTTGAACGGAAACCCA
1 TAAGAGTTGAACGGAAACTCA
* * * *
16766000 TAAGGGTTAAACTGAAGCTCA
1 TAAGAGTTGAACGGAAACTCA
* * * *
16766021 -AATGAGCTGAATGAAAACCCA
1 TAA-GAGTTGAACGGAAACTCA
* * *
16766042 TTAGGGTTGAACAGAAACTCA
1 TAAGAGTTGAACGGAAACTCA
*
16766063 TATGAGTT
1 TAAGAGTT
16766071 AACAGAAGCT
Statistics
Matches: 64, Mismatches: 26, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 2 0.03
21 61 0.95
22 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (21 bp):
TAAGAGTTGAACGGAAACTCA
Found at i:16765996 original size:42 final size:42
Alignment explanation
Indices: 16765950--16766070 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 42
16765940 GTACTAAACA
* *
16765950 GAAACCCGTAAGGGTTGAACGGAAGCTCATAAGAGTTGAACG
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTTGAACG
* * * *
16765992 GAAACCCATAAGGGTTAAACTGAAGCTCA-AATGAGCTGAATG
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAA-GAGTTGAACG
* * * *
16766034 AAAACCCATTAGGGTTGAACAGAAACTCATATGAGTT
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTT
16766071 AACAGAAGCT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 62 0.95
43 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.20
Consensus pattern (42 bp):
GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTTGAACG
Found at i:16766088 original size:20 final size:21
Alignment explanation
Indices: 16766051--16766099 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
16766041 ATTAGGGTTG
*
16766051 AACAGAAACTCATATGAG-TT
1 AACAGAAACTCATATGAGCTA
* * *
16766071 AACAGAAGCTCGTGTGAGCTA
1 AACAGAAACTCATATGAGCTA
16766092 AACAGAAA
1 AACAGAAA
16766100 GTAAATACGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATATGAGCTA
Found at i:16767984 original size:17 final size:17
Alignment explanation
Indices: 16767962--16768000 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
16767952 ATTCTTTTTA
16767962 TCAAAA-CAAAATAATTT
1 TCAAAATCAAAAT-ATTT
16767979 TCAAAATCAAAATATTT
1 TCAAAATCAAAATATTT
16767996 TCAAA
1 TCAAA
16768001 CTTTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (17 bp):
TCAAAATCAAAATATTT
Found at i:16768939 original size:17 final size:18
Alignment explanation
Indices: 16768894--16768939 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
16768884 TTTCGGTAAA
16768894 ATATATTCAATTAATATTT
1 ATATATT-AATTAATATTT
* *
16768913 -TGTATGAATTAA-ATTT
1 ATATATTAATTAATATTT
16768929 ATATATTAATT
1 ATATATTAATT
16768940 TTATATATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
ATATATTAATTAATATTT
Found at i:16784111 original size:20 final size:19
Alignment explanation
Indices: 16784086--16784124 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
16784076 GATCTAAATG
*
16784086 ATATAATATATAATAATAGA
1 ATATAATAT-TAAAAATAGA
16784106 ATATAATATTAAAAATAGA
1 ATATAATATTAAAAATAGA
16784125 GTTGCATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATATAATATTAAAAATAGA
Found at i:16786492 original size:20 final size:20
Alignment explanation
Indices: 16786461--16786522 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
16786451 TGCAAATCAT
*
16786461 TTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
* * * *
16786481 TTGAAATCATTTTGACCTGG
1 TTAAAATCATTTTAACTTGA
**
16786501 TTAAAATCATTTGCACTTGA
1 TTAAAATCATTTTAACTTGA
16786521 TT
1 TT
16786523 TTAAATTGTT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:16810533 original size:26 final size:26
Alignment explanation
Indices: 16810465--16810534 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
16810455 ACAAATCTTA
* *
16810465 AGAATCTAACAAATTAACTAACTTGG
1 AGAACCTAACAAATTAACTAACTAGG
* **
16810491 TGAACCTATTAAATTAACTAACTAGG
1 AGAACCTAACAAATTAACTAACTAGG
*
16810517 AGAACCTAACAAGTTAAC
1 AGAACCTAACAAATTAAC
16810535 AAACCTTGCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (26 bp):
AGAACCTAACAAATTAACTAACTAGG
Found at i:16816254 original size:17 final size:17
Alignment explanation
Indices: 16816232--16816267 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
16816222 GAAGTACGCT
16816232 TATTTTGGAGAAAATGA
1 TATTTTGGAGAAAATGA
16816249 TATTTTGGAGAAAATGA
1 TATTTTGGAGAAAATGA
16816266 TA
1 TA
16816268 CATTGCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (17 bp):
TATTTTGGAGAAAATGA
Found at i:16832217 original size:23 final size:23
Alignment explanation
Indices: 16832191--16832236 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16832181 AAATTATCTT
16832191 AGCCTTCTTGATTTGTTGTCAAA
1 AGCCTTCTTGATTTGTTGTCAAA
16832214 AGCCTTCTTGATTTGTTGTCAAA
1 AGCCTTCTTGATTTGTTGTCAAA
16832237 CTTATCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (23 bp):
AGCCTTCTTGATTTGTTGTCAAA
Found at i:16833012 original size:29 final size:29
Alignment explanation
Indices: 16832970--16833028 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
16832960 GCAACGTCGT
16832970 CATGACATACTGAGATAACCACGCCATGA
1 CATGACATACTGAGATAACCACGCCATGA
* *
16832999 CATGACATACTGAGATGACCACGTCATGA
1 CATGACATACTGAGATAACCACGCCATGA
16833028 C
1 C
16833029 GAAGTCGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (29 bp):
CATGACATACTGAGATAACCACGCCATGA
Found at i:16853747 original size:101 final size:101
Alignment explanation
Indices: 16853600--16853850 Score: 321
Period size: 101 Copynumber: 2.5 Consensus size: 101
16853590 CAAACATAAT
* * * *
16853600 ACCATGGTTGGACCATG-TAGTGTTTAAATGTAAGACCATAGTTGGGCTATGCCATTCCGATGAT
1 ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATGACATTCCGATGAT
* *
16853664 AAGACTATAACTGGGTTATGGCACTATGGATGCAAG
66 AAGACCATAACTGGGTTATGGCACTATGAATGCAAG
* ** *
16853700 ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGCTGGGCTATGACATTTTGATGGT
1 ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATGACATTCCGATGAT
*
16853765 AAGACCATAACTGGGTTATGGCACTATGAATGTAAG
66 AAGACCATAACTGGGTTATGGCACTATGAATGCAAG
** ** *
16853801 ACCATGGCAAGG-CCATGACA--ATGCATATGTAAGACCATAGTTGGACTATG
1 ACCATGG-TTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATG
16853851 GCACAAATGA
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
99 26 0.20
100 17 0.13
101 87 0.66
102 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (101 bp):
ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATGACATTCCGATGAT
AAGACCATAACTGGGTTATGGCACTATGAATGCAAG
Found at i:16853800 original size:33 final size:33
Alignment explanation
Indices: 16853626--16853805 Score: 103
Period size: 33 Copynumber: 5.4 Consensus size: 33
16853616 GTAGTGTTTA
** * * **
16853626 AATGTAAGACCATAGTTGGGCTATGCCATTCCG
1 AATGTAAGACCATAACTGGGCTATGACACTATG
* * *
16853659 -ATGATAAGACTATAACTGGGTTATGGCACTATG
1 AATG-TAAGACCATAACTGGGCTATGACACTATG
* * *** * * * *
16853692 GATGCAAGACCATGGTTGGACCATGACAGTATTT
1 AATGTAAGACCATAACTGGGCTATGACACTA-TG
* * *
16853726 ATATGTAAGACCATAGCTGGGCTATGACATTTTG
1 A-ATGTAAGACCATAACTGGGCTATGACACTATG
* *
16853760 -ATGGTAAGACCATAACTGGGTTATGGCACTATG
1 AAT-GTAAGACCATAACTGGGCTATGACACTATG
16853793 AATGTAAGACCAT
1 AATGTAAGACCAT
16853806 GGCAAGGCCA
Statistics
Matches: 108, Mismatches: 33, Indels: 12
0.71 0.22 0.08
Matches are distributed among these distances:
32 5 0.05
33 73 0.68
34 7 0.06
35 23 0.21
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (33 bp):
AATGTAAGACCATAACTGGGCTATGACACTATG
Found at i:16855973 original size:30 final size:31
Alignment explanation
Indices: 16855937--16856022 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
16855927 GTATATGTTT
*
16855937 TATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTCGTATATAGA
* *
16855967 TATACATTGCTGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTCGTATATAGA
* *
16855998 TATATATCGCCGAATTTGATTCGTA
1 TATACATTGCCGAATTTGATTCGTA
16856023 CATGGATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 13 0.27
31 36 0.73
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTCGTATATAGA
Found at i:16856019 original size:31 final size:31
Alignment explanation
Indices: 16855945--16856035 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 31
16855935 TTTATACATT
* * * *
16855945 GCCGAA-TTGATTTGTATATAGATATACATT
1 GCCGAATTTGATTCGTATATGGATATATATC
*
16855975 GCTGAATTTGATTCGTATATGGATATATATC
1 GCCGAATTTGATTCGTATATGGATATATATC
* *
16856006 GCCGAATTTGATTCGTACATGGATTTATAT
1 GCCGAATTTGATTCGTATATGGATATATAT
16856036 TGTTGAACTA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (31 bp):
GCCGAATTTGATTCGTATATGGATATATATC
Found at i:16856236 original size:43 final size:43
Alignment explanation
Indices: 16856174--16856289 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
16856164 TGTGATTTCA
* * * *
16856174 TGTAAAACCATGTCTGGGACATTTGCATCGAAGTGAGACAACG
1 TGTAAGACCATGTCTGGGACATTAGCATCGAAGAGAGAAAACG
* *
16856217 TGTAAGACCTTGTTTGGGACATTAGCATCGAAGAGAGAAAACG
1 TGTAAGACCATGTCTGGGACATTAGCATCGAAGAGAGAAAACG
*
16856260 TGTAAGACCATGTCTGGGACATTGGCATCG
1 TGTAAGACCATGTCTGGGACATTAGCATCG
16856290 TATATGATTC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTAGCATCGAAGAGAGAAAACG
Found at i:16883826 original size:75 final size:74
Alignment explanation
Indices: 16883654--16883915 Score: 242
Period size: 75 Copynumber: 3.5 Consensus size: 74
16883644 CATTTATAGT
* * * * * **
16883654 TGATATCTTTACGGTTTGCTGATTTAAAATCACGACCCTCGATTTTCTATTAGCTCGATGACCTA
1 TGATATATTTACGGTTCGCTGATTTAAGATCA-AACCCTCGAGTTTCTAACAGCTCGATGACCTA
* *
16883719 TATTCACATC
65 GATTCACAGC
* ** * * *
16883729 TGTTATATTTACTATTCACTGATTTAAGATCGAAACTCTCGAGTTTCTAACAGCTCAATGACCTA
1 TGATATATTTACGGTTCGCTGATTTAAGATC-AAACCCTCGAGTTTCTAACAGCTCGATGACCTA
16883794 GATTCACAGC
65 GATTCACAGC
* * * * *
16883804 TGATATCTTTACGG-TCTGCTGATTTAAGATCTCAACCCTCG-GTTTACTACCAACTCGATGACT
1 TGATATATTTACGGTTC-GCTGATTTAAGATC-AAACCCTCGAGTTT-CTAACAGCTCGATGACC
*
16883867 TATG-TTCATAGC
63 TA-GATTCACAGC
*
16883879 TGATATATTTATGGTTCGCTGATTTAAGATCACAACC
1 TGATATATTTACGGTTCGCTGATTTAAGATCA-AACC
16883916 TATCTATCTT
Statistics
Matches: 150, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
74 6 0.04
75 140 0.93
76 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (74 bp):
TGATATATTTACGGTTCGCTGATTTAAGATCAAACCCTCGAGTTTCTAACAGCTCGATGACCTAG
ATTCACAGC
Found at i:16884118 original size:105 final size:105
Alignment explanation
Indices: 16883898--16884124 Score: 256
Period size: 105 Copynumber: 2.2 Consensus size: 105
16883888 TATGGTTCGC
* * * * *
16883898 TGATTTAAGATCACAACCTATCTATCTTTAAGTTAGCTAATTTAAGATCGCAACTCCTAAACAAC
1 TGATTTAATATCGCAACCTATCTATCTTTAAGTTAGCTAATTTAAAATCACAACTCCTAAACAAA
** * *
16883963 TTGATGACCTACGTTAACAACTAATATTATAAAGGTTAGC
66 TCAATGACCTACGTTAACAAATAATATTATAAAGGTTAGA
** * * * ***
16884003 TGATCCAATATCGCAACCTATCTATCTTTGAGTTAGTTGATTTAAAATCATGGCTCCTAAACAAA
1 TGATTTAATATCGCAACCTATCTATCTTTAAGTTAGCTAATTTAAAATCACAACTCCTAAACAAA
* * * *
16884068 TCAATGACCTATGTTTACAAATGATATTATAAAGGTTGGA
66 TCAATGACCTACGTTAACAAATAATATTATAAAGGTTAGA
*
16884108 TGATTTAATATTGCAAC
1 TGATTTAATATCGCAAC
16884125 GCCTAAACAA
Statistics
Matches: 98, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (105 bp):
TGATTTAATATCGCAACCTATCTATCTTTAAGTTAGCTAATTTAAAATCACAACTCCTAAACAAA
TCAATGACCTACGTTAACAAATAATATTATAAAGGTTAGA
Found at i:16884250 original size:173 final size:173
Alignment explanation
Indices: 16883937--16884297 Score: 470
Period size: 173 Copynumber: 2.1 Consensus size: 173
16883927 AAGTTAGCTA
* * * *
16883937 ATTTAAGATCGCAACTCCTAAACAACTTGATGACCTACGTTAACAACTAATATTATAAAGGTTAG
1 ATTTAATATCGCAACGCCTAAACAACTCGATGAACTACGTTAACAACTAATATTATAAAGGTTAG
* **
16884002 CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGTTGATTTAAAATCATGGCTCCTAAACAA
66 CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGCTGATTTAAAATCACAGCTCCTAAACAA
** * * *
16884067 ATCAATGACCTATGTTTACAAATGATATTATAAAGGTTGGATG
131 ATCAATGACCTACATTCACAAATGATATTATAAAGGGTAGATG
* * * *
16884110 ATTTAATATTGCAACGCCTAAACAACTCGATGAACTACGTTCACAGCTGATATTATAAAGGTTAG
1 ATTTAATATCGCAACGCCTAAACAACTCGATGAACTACGTTAACAACTAATATTATAAAGGTTAG
** ** * *
16884175 CTGATTTAATATCTTAACCTATCTATCTTTGAGTTAGCTGATTTAATATCACAGCTCCTAAACAG
66 CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGCTGATTTAAAATCACAGCTCCTAAACAA
* * ** *
16884240 CTCGATGACCTACATTCACATCTGATATTATAAAGGGTAGCTG
131 ATCAATGACCTACATTCACAAATGATATTATAAAGGGTAGATG
*
16884283 ATTTAATATGGCAAC
1 ATTTAATATCGCAAC
16884298 CCATCTATCT
Statistics
Matches: 160, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
173 160 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (173 bp):
ATTTAATATCGCAACGCCTAAACAACTCGATGAACTACGTTAACAACTAATATTATAAAGGTTAG
CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGCTGATTTAAAATCACAGCTCCTAAACAA
ATCAATGACCTACATTCACAAATGATATTATAAAGGGTAGATG
Found at i:16884290 original size:105 final size:105
Alignment explanation
Indices: 16884108--16884539 Score: 426
Period size: 105 Copynumber: 4.1 Consensus size: 105
16884098 AAAGGTTGGA
* * * *
16884108 TGATTTAATATTGCAACGCCTAAACAACTCGATGAACTACGTTCACAGCTGATATTATAAAGGTT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
** *
16884173 AGCTGATTTAATATCTTAACCTATCTATCTTTGAGTTAGC
66 AGCTGATTTAATATCACAACCTATCTATATTTGAGTTAGC
* * * * *
16884213 TGATTTAATATCACAGCTCCTAAACAGCTCGATGACCTACATTCACATCTGATATTATAAAGGGT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
** * *
16884278 AGCTGATTTAATATGGCAACCCATCTATCTTTGAGTTAGC
66 AGCTGATTTAATATCACAACCTATCTATATTTGAGTTAGC
** * * * *
16884318 TGATTTACGATCGCAACTCCTAAATAGCTC-ATTGACCTACGTTCACGGCTAATGTTATAAAGGT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGA-TGACCTACGTTCACAGCTGATATTATAAAGGT
* ** *
16884382 TATCTGATTTAAGT-TCACAACCTAAGTTTATTTGAGTTCA-C
65 TAGCTGATTTAA-TATCACAACCTATCTATATTTGAGTT-AGC
* * * * * ** * *
16884423 TAATTTAAGATCGCAACTCCT-AATAGCTTGCTGACCTACGTTCACAATTGATATTATTAAGGCT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
* * * *
16884487 CGCTGATTTAAGATCAGAACC--TCTAATTATTTGAGTTAGT
66 AGCTGATTTAATATCACAACCTATCT-A-TATTTGAGTTAGC
16884527 TGATTTAATATCG
1 TGATTTAATATCG
16884540 TAATTCTGAA
Statistics
Matches: 266, Mismatches: 53, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
102 1 0.00
103 1 0.00
104 71 0.27
105 191 0.72
106 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (105 bp):
TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
AGCTGATTTAATATCACAACCTATCTATATTTGAGTTAGC
Found at i:16884378 original size:278 final size:278
Alignment explanation
Indices: 16883854--16884382 Score: 648
Period size: 278 Copynumber: 1.9 Consensus size: 278
16883844 GGTTTACTAC
* * * * *
16883854 CAACTCGATGACTTATGTTCATAGCTGATATATTTATGGTTCGCTGATTTAAGATCACAACCTAT
1 CAACTCGATGACTTACGTTCACAGCTGATATATTAAAGGTTAGCTGATTTAAGATCACAACCTAT
* * *
16883919 CTATCTTTAAGTTAGCTAATTTAAGATCGCAACTCCTAAACAACTTGATGACCTACGTTAACAAC
66 CTATCTTTAAGTTAGCTAATTTAAGATCACAACTCCTAAACAACTCGATGACCTACATTAACAAC
* * *
16883984 TAATATTATAAAGGTTAGCTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGTTGATTTAAA
131 TAATATTATAAAGGGTAGCTGATCCAATATCGCAACCCATCTATCTTTGAGTTAGCTGATTTAAA
*** * * *
16884049 ATCATGGCTCCTAAACAAATCAATGACCTATGTTTACAAATGATATTATAAAGGTTGGATGATTT
196 ATCACAACTCCTAAACAAATCAATGACCTACGTTCACAAATAATATTATAAAGGTTGGATGATTT
16884114 AATATTGCAACGCCTAAA
261 AATATTGCAACGCCTAAA
* **
16884132 CAACTCGATGAAC-TACGTTCACAGCTGATAT-TATAAAGGTTAGCTGATTTAATATCTTAACCT
1 CAACTCGATG-ACTTACGTTCACAGCTGATATAT-TAAAGGTTAGCTGATTTAAGATCACAACCT
* * * * * *
16884195 ATCTATCTTTGAGTTAGCTGATTTAATATCACAGCTCCTAAACAGCTCGATGACCTACATTCACA
64 ATCTATCTTTAAGTTAGCTAATTTAAGATCACAACTCCTAAACAACTCGATGACCTACATTAACA
* * ** *
16884260 TCTGATATTATAAAGGGTAGCTGATTTAATATGGCAACCCATCTATCTTTGAGTTAGCTGATTTA
129 ACTAATATTATAAAGGGTAGCTGATCCAATATCGCAACCCATCTATCTTTGAGTTAGCTGATTTA
** * * ** * *** *
16884325 CGATCGCAACTCCTAAATAGCTCATTGACCTACGTTCACGGCTAATGTTATAAAGGTT
194 AAATCACAACTCCTAAACAAATCAATGACCTACGTTCACAAATAATATTATAAAGGTT
16884383 ATCTGATTTA
Statistics
Matches: 207, Mismatches: 42, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
277 1 0.00
278 204 0.99
279 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (278 bp):
CAACTCGATGACTTACGTTCACAGCTGATATATTAAAGGTTAGCTGATTTAAGATCACAACCTAT
CTATCTTTAAGTTAGCTAATTTAAGATCACAACTCCTAAACAACTCGATGACCTACATTAACAAC
TAATATTATAAAGGGTAGCTGATCCAATATCGCAACCCATCTATCTTTGAGTTAGCTGATTTAAA
ATCACAACTCCTAAACAAATCAATGACCTACGTTCACAAATAATATTATAAAGGTTGGATGATTT
AATATTGCAACGCCTAAA
Found at i:16898527 original size:19 final size:20
Alignment explanation
Indices: 16898487--16898527 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
16898477 TCCAAAATTC
*
16898487 AAATAATAAAAATAATGAGA
1 AAATAATAAAAATAAAGAGA
16898507 AAATAA-AAAAATTAAAG-GA
1 AAATAATAAAAA-TAAAGAGA
16898526 AA
1 AA
16898528 TTATATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (20 bp):
AAATAATAAAAATAAAGAGA
Found at i:16905399 original size:44 final size:44
Alignment explanation
Indices: 16905336--16905420 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
16905326 GAAATATGAT
16905336 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTCGAC
1 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTCGAC
16905380 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTC
1 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTC
16905421 CACTAATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (44 bp):
AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTCGAC
Found at i:16907340 original size:26 final size:26
Alignment explanation
Indices: 16907293--16907342 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
16907283 AGAATCTAAC
* *
16907293 AAATTAACTAACTTCGTAAACCTATT
1 AAATTAACTAACTTAGGAAACCTATT
16907319 AAATTAACTAAC-TAGGAGAACCTA
1 AAATTAACTAACTTAGGA-AACCTA
16907343 ACAAGTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (26 bp):
AAATTAACTAACTTAGGAAACCTATT
Found at i:16916138 original size:3 final size:3
Alignment explanation
Indices: 16916130--16916182 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
16916120 ACCTCATATG
* * *
16916130 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AGT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16916178 AAT AA
1 AAT AA
16916183 ACTAATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:16929279 original size:18 final size:16
Alignment explanation
Indices: 16929243--16929276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16929233 ATACATATAC
*
16929243 ATATACATATATGAAA
1 ATATACATATAAGAAA
16929259 ATATACATATAAAGAAA
1 ATATACATAT-AAGAAA
16929276 A
1 A
16929277 ATAAATACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
ATATACATATAAGAAA
Found at i:16929534 original size:3 final size:3
Alignment explanation
Indices: 16929526--16929587 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
16929516 ACCTCATATG
* * *
16929526 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AGT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
16929574 AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AA
16929588 ACTAATTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16948730 original size:29 final size:29
Alignment explanation
Indices: 16948697--16948753 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
16948687 CAACGTCATC
* *
16948697 ATGACATGCTGAGATGACCACGCCATGAT
1 ATGACATACTGAGATAACCACGCCATGAT
*
16948726 ATGACATACTGAGATAACCACGTCATGA
1 ATGACATACTGAGATAACCACGCCATGA
16948754 CGAAGTCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (29 bp):
ATGACATACTGAGATAACCACGCCATGAT
Found at i:16949136 original size:24 final size:25
Alignment explanation
Indices: 16949080--16949136 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
16949070 CTTGATAGTC
16949080 ATTTATTATAATAAATAATTTAAAAT
1 ATTTA-TATAATAAATAATTTAAAAT
* *
16949106 -TACTATATAATAATTAA-TTAAAAT
1 AT-TTATATAATAAATAATTTAAAAT
16949130 ATTTATA
1 ATTTATA
16949137 GAAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
24 11 0.42
25 13 0.50
26 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTATATAATAAATAATTTAAAAT
Found at i:16956176 original size:22 final size:20
Alignment explanation
Indices: 16956135--16956171 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16956125 AAGGACAAAA
16956135 AATGTTATTTTCGTTGTTTT
1 AATGTTATTTTCGTTGTTTT
*
16956155 AATGTTATGTTC-TTGTT
1 AATGTTATTTTCGTTGTT
16956172 GTTTTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.62
Consensus pattern (20 bp):
AATGTTATTTTCGTTGTTTT
Found at i:16967553 original size:33 final size:32
Alignment explanation
Indices: 16967409--16967587 Score: 115
Period size: 33 Copynumber: 5.4 Consensus size: 32
16967399 AAGTGTTTAA
* * **
16967409 ATGTAAGACCATAGTTGGGCTATGGGATTCCG
1 ATGTAAGACCATAGCTGGGCTATGGCATTTTG
* * * * *
16967441 ATGATAAGACTATAACTGGGTTATGGCACTATGG
1 ATG-TAAGACCATAGCTGGGCTATGGCA-TTTTG
* * * * * * *
16967475 ATGCAAGACCATGGTTGGACAATGACAGTATTTAT
1 ATGTAAGACCATAGCTGGGCTATGGCA-T-TTT-G
16967510 ATGTAAGACCATAGCTGGGCTATGGCATTTTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTTTG
* * * *
16967542 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGCTGGGCTATGGCATTTTG
16967575 AATGTAAGACCAT
1 -ATGTAAGACCAT
16967588 GGCAGGGCCA
Statistics
Matches: 109, Mismatches: 32, Indels: 11
0.72 0.21 0.07
Matches are distributed among these distances:
32 6 0.06
33 72 0.66
34 10 0.09
35 21 0.19
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTTTG
Found at i:16967602 original size:101 final size:101
Alignment explanation
Indices: 16967377--16967589 Score: 320
Period size: 101 Copynumber: 2.1 Consensus size: 101
16967367 TATTCAAACA
* * *
16967377 TAAGACCATGGTTGGACCATGGA-AGTGTTTAAATGTAAGACCATAGTTGGGCTATGGGATTCCG
1 TAAGACCATGGTTGGACCAT-GACAGTATTTAAATGTAAGACCATAGCTGGGCTATGGCATTCCG
* *
16967441 ATGATAAGACTATAACTGGGTTATGGCACTATGGATG
65 ATGATAAGACCATAACTGGGTTATGGCACTATGAATG
* * * **
16967478 CAAGACCATGGTTGGACAATGACAGTATTTATATGTAAGACCATAGCTGGGCTATGGCATTTTGA
1 TAAGACCATGGTTGGACCATGACAGTATTTAAATGTAAGACCATAGCTGGGCTATGGCATTCCGA
16967543 TGATAAGACCATAACTGGGTTATGGCACTATGAATG
66 TGATAAGACCATAACTGGGTTATGGCACTATGAATG
16967579 TAAGACCATGG
1 TAAGACCATGG
16967590 CAGGGCCATG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 2 0.02
101 98 0.98
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAGTATTTAAATGTAAGACCATAGCTGGGCTATGGCATTCCGA
TGATAAGACCATAACTGGGTTATGGCACTATGAATG
Found at i:16967609 original size:13 final size:13
Alignment explanation
Indices: 16967591--16967616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16967581 AGACCATGGC
16967591 AGGGCCATGACAA
1 AGGGCCATGACAA
16967604 AGGGCCATGACAA
1 AGGGCCATGACAA
16967617 TGAATATGTA
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:0.38, C:0.23, G:0.31, T:0.08
Consensus pattern (13 bp):
AGGGCCATGACAA
Found at i:16969583 original size:30 final size:30
Alignment explanation
Indices: 16969547--16969688 Score: 124
Period size: 31 Copynumber: 4.7 Consensus size: 30
16969537 ATATGTTTTT
*
16969547 TACATTGCCGAATTGATTTGTATATAGATA
1 TACATTGCTGAATTGATTTGTATATAGATA
*
16969577 TACATTGTTGAATTGATTTGTATATAGATA
1 TACATTGCTGAATTGATTTGTATATAGATA
* * * *
16969607 TACATTACTAAATTTGATTCGTATATGGATA
1 TACATTGCTGAA-TTGATTTGTATATAGATA
* * *** *
16969638 TATAGTG-TCGAATTTGATTCAAATATGGATA
1 TACATTGCT-GAA-TTGATTTGTATATAGATA
* *
16969669 TATATTGTTGAATTGATTTG
1 TACATTGCTGAATTGATTTG
16969689 AGCATTGGAT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
30 44 0.47
31 48 0.52
32 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (30 bp):
TACATTGCTGAATTGATTTGTATATAGATA
Found at i:16969631 original size:31 final size:30
Alignment explanation
Indices: 16969557--16969639 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
16969547 TACATTGCCG
** *
16969557 AATTGATTTGTATATAGATATACATTGTTG
1 AATTGATTTGTATATAGATATACATTACTA
16969587 AATTGATTTGTATATAGATATACATTACTA
1 AATTGATTTGTATATAGATATACATTACTA
* *
16969617 AATTTGATTCGTATATGGATATA
1 AA-TTGATTTGTATATAGATATA
16969640 TAGTGTCGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 29 0.62
31 18 0.38
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (30 bp):
AATTGATTTGTATATAGATATACATTACTA
Found at i:16987953 original size:13 final size:14
Alignment explanation
Indices: 16987929--16987955 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16987919 TTGAATTTTG
16987929 CATTTAAAAAAAAA
1 CATTTAAAAAAAAA
16987943 CATTTAAAAAAAA
1 CATTTAAAAAAAA
16987956 GGGTGGCAGA
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:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (14 bp):
CATTTAAAAAAAAA
Found at i:17004758 original size:3 final size:3
Alignment explanation
Indices: 17004750--17004779 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17004740 TTCTCTCTTT
17004750 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17004780 GCCAGGGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17019720 original size:24 final size:24
Alignment explanation
Indices: 17019693--17019744 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
17019683 TCAGATTATG
* *
17019693 CAGCAGAAGCATCAA-CTAATGCAA
1 CAGCAGAAGCAGCAAGC-AAAGCAA
*
17019717 CAGCAGCAGCAGCAAGCAAAGCAA
1 CAGCAGAAGCAGCAAGCAAAGCAA
17019741 CAGC
1 CAGC
17019745 TGCCCACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.44, C:0.29, G:0.21, T:0.06
Consensus pattern (24 bp):
CAGCAGAAGCAGCAAGCAAAGCAA
Found at i:17023898 original size:20 final size:20
Alignment explanation
Indices: 17023859--17023897 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17023849 ATGTGCTATA
* *
17023859 AAAATATTTTTTATTATTTT
1 AAAATATTTATAATTATTTT
17023879 AAAATATTTATAATT-TTTT
1 AAAATATTTATAATTATTTT
17023898 TTTGAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AAAATATTTATAATTATTTT
Found at i:17025925 original size:3 final size:3
Alignment explanation
Indices: 17025917--17025945 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17025907 TATATAAATA
17025917 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
17025946 TAGGCCTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:17028488 original size:31 final size:31
Alignment explanation
Indices: 17028431--17028489 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17028421 CAAAAAAATA
* **
17028431 AAATATAAAGATTAAATTTTAAATTTAATCG
1 AAATATAAAAATTAAATGCTAAATTTAATCG
17028462 AAATATAAAAATTAAA-GCTAATATTTAA
1 AAATATAAAAATTAAATGCTAA-ATTTAA
17028490 CCTTTCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (31 bp):
AAATATAAAAATTAAATGCTAAATTTAATCG
Found at i:17028649 original size:17 final size:18
Alignment explanation
Indices: 17028624--17028658 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17028614 TTCGTAGTAG
17028624 TATAATTTAT-TTTTATT
1 TATAATTTATATTTTATT
*
17028641 TATATTTTATATTTTATT
1 TATAATTTATATTTTATT
17028659 GAAATGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATAATTTATATTTTATT
Found at i:17038852 original size:2 final size:2
Alignment explanation
Indices: 17038845--17038872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17038835 GAATTGGTAG
17038845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17038873 TATTGAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17039105 original size:41 final size:37
Alignment explanation
Indices: 17039058--17039163 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
17039048 TTCGACTTCG
*
17039058 AGTCGATGAGACACTGGGTGTTAATTCACTACTTCGGATTA
1 AGTCGATGAGACACTGGGTGTCAATT---TACTTCGG-TTA
* * * *
17039099 ATTCGATGAGGCACTGGGTGCCAATTTACTTCGGTTT
1 AGTCGATGAGACACTGGGTGTCAATTTACTTCGGTTA
*
17039136 AGCCGATGAGACACTGGGTGTCAATTTA
1 AGTCGATGAGACACTGGGTGTCAATTTA
17039164 TTTCTTCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 26 0.46
38 8 0.14
41 22 0.39
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (37 bp):
AGTCGATGAGACACTGGGTGTCAATTTACTTCGGTTA
Found at i:17044397 original size:21 final size:19
Alignment explanation
Indices: 17044355--17044397 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
17044345 AACTTAATAA
*
17044355 TAATTAAAAAGATATGAGT
1 TAATTAAAAAGATATGAAT
*
17044374 TAATGTAAAAAGATTTAGAAT
1 TAAT-TAAAAAGATAT-GAAT
17044395 TAA
1 TAA
17044398 GAATTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (19 bp):
TAATTAAAAAGATATGAAT
Found at i:17046346 original size:21 final size:21
Alignment explanation
Indices: 17046320--17046364 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17046310 GGTCGATGAT
* * *
17046320 AAAAAGTAAATATAAATTGTA
1 AAAAAGAAAAAATAAATTATA
*
17046341 AAAAAGAAAAAATATATTATA
1 AAAAAGAAAAAATAAATTATA
17046362 AAA
1 AAA
17046365 CTTTAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAAAGAAAAAATAAATTATA
Found at i:17048383 original size:19 final size:18
Alignment explanation
Indices: 17048359--17048398 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
17048349 TATAAATATT
*
17048359 TTTAAAAAGTTATATAAAA
1 TTTAAAAAATT-TATAAAA
*
17048378 TTTAAAAAATTTTTAAAA
1 TTTAAAAAATTTATAAAA
17048396 TTT
1 TTT
17048399 TTTCACTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTAAAAAATTTATAAAA
Found at i:17061418 original size:18 final size:19
Alignment explanation
Indices: 17061387--17061424 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17061377 GCTTTTGGTA
**
17061387 ACACCATCTTCAA-TTAGT
1 ACACCATCGCCAATTTAGT
17061405 ACACCATCGCCAATTTAGT
1 ACACCATCGCCAATTTAGT
17061424 A
1 A
17061425 TGCATTGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (19 bp):
ACACCATCGCCAATTTAGT
Found at i:17063021 original size:35 final size:35
Alignment explanation
Indices: 17062975--17063045 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
17062965 CGTTCAATTA
*
17062975 TGGCGAGAATAGAATCATGTGCCTTCTTGTTTGTT
1 TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
17063010 TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
1 TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
17063045 T
1 T
17063046 AGTAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.39
Consensus pattern (35 bp):
TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
Found at i:17068373 original size:21 final size:21
Alignment explanation
Indices: 17068331--17068373 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17068321 TAAATTTTTT
* *
17068331 TAAATAATGAAATTCATAAAC
1 TAAATAATAAAAATCATAAAC
17068352 TAAATAATAAAAAT-ATATAAC
1 TAAATAATAAAAATCATA-AAC
17068373 T
1 T
17068374 TTAACTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAATAATAAAAATCATAAAC
Found at i:17068819 original size:426 final size:426
Alignment explanation
Indices: 17068026--17068872 Score: 1678
Period size: 426 Copynumber: 2.0 Consensus size: 426
17068016 TATGAGATTT
17068026 CCTTTTCTTATTCCATAATAATTAGAATAATTCAAAGAATGGCTCAAGCGTCGGCAAATGTTTAT
1 CCTTTTCTTATTCCATAATAATTAGAATAATTCAAAGAATGGCTCAAGCGTCGGCAAATGTTTAT
17068091 TTTTATATTATTCAAAAATATCAATTTTTAAAATGTAAGAAAATAAACTTTTACATTTTTTTGGT
66 TTTTATATTATTCAAAAATATCAATTTTTAAAATGTAAGAAAATAAACTTTTACATTTTTTTGGT
17068156 TTTTTTTTTTTTTCATTTGTTCAAAGATCACTTGTACAGTTGTACATCACCAAAGGCAAATGTAA
131 TTTTTTTTTTTTTCATTTGTTCAAAGATCACTTGTACAGTTGTACATCACCAAAGGCAAATGTAA
17068221 AGGGGAGGGAGGCCTAACCCCCAAAAATGACAATTATAAATTTACCCTTTGTAAATTATTAAATT
196 AGGGGAGGGAGGCCTAACCCCCAAAAATGACAATTATAAATTTACCCTTTGTAAATTATTAAATT
17068286 ATTATAAATTTATTTTAAAGTAAAAAATATATATTTAAATTTTTTTAAATAATGAAATTCATAAA
261 ATTATAAATTTATTTTAAAGTAAAAAATATATATTTAAATTTTTTTAAATAATGAAATTCATAAA
17068351 CTAAATAATAAAAATATATAACTTTAACTTCTCTAAAATTTATAATTTAATTCGCCACTCCACTC
326 CTAAATAATAAAAATATATAACTTTAACTTCTCTAAAATTTATAATTTAATTCGCCACTCCACTC
17068416 CGCTCCACCATTACTGGTCCAAACACCACAAGATGA
391 CGCTCCACCATTACTGGTCCAAACACCACAAGATGA
17068452 CCTTTTCTTATTCCATAATAATTAGAATAATTCAAAGAATGGCTCAAGCGTCGGCAAATGTTTAT
1 CCTTTTCTTATTCCATAATAATTAGAATAATTCAAAGAATGGCTCAAGCGTCGGCAAATGTTTAT
17068517 TTTTATATTATTCAAAAATATCAATTTTTAAAATGTAAGAAAATAAACTTTTACATTTTTTTGGT
66 TTTTATATTATTCAAAAATATCAATTTTTAAAATGTAAGAAAATAAACTTTTACATTTTTTTGGT
17068582 TTTTTTTTTTTTTCATTTGTTCAAAGATCACTTGTACAGTTGTACATCACCAAAGGCAAATGTAA
131 TTTTTTTTTTTTTCATTTGTTCAAAGATCACTTGTACAGTTGTACATCACCAAAGGCAAATGTAA
17068647 AGGGGAGGGAGGCCTAACCCCCAAAAATGACAATTATAAATTTACCCTTTGTAAATTATTAAATT
196 AGGGGAGGGAGGCCTAACCCCCAAAAATGACAATTATAAATTTACCCTTTGTAAATTATTAAATT
17068712 ATTATAAATTTATTTTAAAGTAAAAAATATATATTTAAATTTTTTTAAAATAATGAAA-TCATAA
261 ATTATAAATTTATTTTAAAGTAAAAAATATATATTTAAATTTTTTT-AAATAATGAAATTCATAA
17068776 ACTAAATAATAAAAATATATAACTTTAACTTCTCTAAAATTTATAATTTAATTCGCCACTCCACT
325 ACTAAATAATAAAAATATATAACTTTAACTTCTCTAAAATTTATAATTTAATTCGCCACTCCACT
17068841 CCGCTCCACCATTACTGGTCCAAACACCACAA
390 CCGCTCCACCATTACTGGTCCAAACACCACAA
17068873 AGATTTCAGC
Statistics
Matches: 420, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
426 409 0.97
427 11 0.03
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (426 bp):
CCTTTTCTTATTCCATAATAATTAGAATAATTCAAAGAATGGCTCAAGCGTCGGCAAATGTTTAT
TTTTATATTATTCAAAAATATCAATTTTTAAAATGTAAGAAAATAAACTTTTACATTTTTTTGGT
TTTTTTTTTTTTTCATTTGTTCAAAGATCACTTGTACAGTTGTACATCACCAAAGGCAAATGTAA
AGGGGAGGGAGGCCTAACCCCCAAAAATGACAATTATAAATTTACCCTTTGTAAATTATTAAATT
ATTATAAATTTATTTTAAAGTAAAAAATATATATTTAAATTTTTTTAAATAATGAAATTCATAAA
CTAAATAATAAAAATATATAACTTTAACTTCTCTAAAATTTATAATTTAATTCGCCACTCCACTC
CGCTCCACCATTACTGGTCCAAACACCACAAGATGA
Found at i:17069672 original size:27 final size:27
Alignment explanation
Indices: 17069622--17069690 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
17069612 GGACATGATG
* *
17069622 CCTATCTGATAGGCGGCACCAGTGACC
1 CCTATTTGATAGGTGGCACCAGTGACC
** ***
17069649 CCTATTTGATAGGTGGCATTAGTGGTG
1 CCTATTTGATAGGTGGCACCAGTGACC
17069676 CCTATTTGATAGGTG
1 CCTATTTGATAGGTG
17069691 ACATACCTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (27 bp):
CCTATTTGATAGGTGGCACCAGTGACC
Found at i:17088271 original size:112 final size:110
Alignment explanation
Indices: 17088074--17088301 Score: 350
Period size: 112 Copynumber: 2.0 Consensus size: 110
17088064 AATATTTGAG
*
17088074 TATACAATTATAGATGGACCATAAGGAACCGTACATATTGACTAATAAAAACATTGCACGTTTTG
1 TATACAATTATAGATGGACCATAAGGAACCATACA-ATTGACTAATAAAAACATTGCACGTTTTG
* * *
17088139 TAGATAAATTAGACCACACTTTAGAGCTTAGTGTATGTCTTATGCTT
65 TAGATAAACTAAACCACACTTTAGAGCTTA-TATATGTCTTATGCTT
*
17088186 TATACATATATATAGATGGACCATAAGGAACCATAC-ATTGACTAATAAAAACATTGCATGTTTT
1 TATACA-AT-TATAGATGGACCATAAGGAACCATACAATTGACTAATAAAAACATTGCACGTTTT
* *
17088250 GTAGATAAACTAAACCACACTTTGGAGTTTATATATGTCTTATGCTT
64 GTAGATAAACTAAACCACACTTTAGAGCTTATATATGTCTTATGCTT
17088297 TATAC
1 TATAC
17088302 TGCAGTTTAC
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
111 20 0.19
112 60 0.56
113 2 0.02
114 25 0.23
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (110 bp):
TATACAATTATAGATGGACCATAAGGAACCATACAATTGACTAATAAAAACATTGCACGTTTTGT
AGATAAACTAAACCACACTTTAGAGCTTATATATGTCTTATGCTT
Found at i:17091765 original size:20 final size:19
Alignment explanation
Indices: 17091742--17091798 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
17091732 AAAAAATTTA
17091742 TTAAATTTTAATAAAAAAAT
1 TTAAATTTT-ATAAAAAAAT
*
17091762 TTAAATTTTGA-AAAAATAT
1 TTAAATTTT-ATAAAAAAAT
17091781 TGTAAAATTTTATAAAAA
1 T-T-AAATTTTATAAAAA
17091799 TCATATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 8 0.25
20 12 0.38
21 12 0.38
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TTAAATTTTATAAAAAAAT
Found at i:17092091 original size:9 final size:9
Alignment explanation
Indices: 17091989--17092139 Score: 60
Period size: 9 Copynumber: 15.9 Consensus size: 9
17091979 TGTTGGTACG
17091989 ATAATTTTT
1 ATAATTTTT
*
17091998 ATATTTCTTT
1 ATAATT-TTT
17092008 AT-ATTTTT
1 ATAATTTTT
17092016 ATAATTTTATT
1 ATAA-TTT-TT
* *
17092027 ACGAATTTAT
1 A-TAATTTTT
*
17092037 A-AAATTTT
1 ATAATTTTT
17092045 ATAAATTTTTT
1 AT-AA-TTTTT
* *
17092056 CTACATTTCT
1 ATA-ATTTTT
17092066 ATATATTTTCT
1 ATA-ATTTT-T
17092077 AT--TTTTT
1 ATAATTTTT
17092084 ATAATTTTT
1 ATAATTTTT
17092093 A-ATATTTTT
1 ATA-ATTTTT
*
17092102 ATATTCTTTT
1 ATAAT-TTTT
* *
17092112 ATTAAAATTTA
1 A-T-AATTTTT
*
17092123 ATAACTTTT
1 ATAATTTTT
17092132 ATAATTTT
1 ATAATTTT
17092140 ATTTTTTTAT
Statistics
Matches: 106, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
7 3 0.03
8 16 0.15
9 34 0.32
10 30 0.28
11 20 0.19
12 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:17092097 original size:28 final size:27
Alignment explanation
Indices: 17092040--17092113 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 27
17092030 AATTTATAAA
* *
17092040 ATTTTATAAATTTTTTCTACATTTCTAT
1 ATTTT-TATATTTTTTATACATTTCTAT
* *
17092068 ATATTTTCTATTTTTTATA-ATTTTTAAT
1 AT-TTTTATATTTTTTATACATTTCT-AT
17092096 ATTTTTATATTCTTTTAT
1 ATTTTTATATT-TTTTAT
17092114 TAAAATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 13 0.34
28 22 0.58
29 3 0.08
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTTATATTTTTTATACATTTCTAT
Found at i:17092261 original size:16 final size:16
Alignment explanation
Indices: 17092233--17092297 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
17092223 GGTTCGCTTA
17092233 ATTGGATTAGAGGTGT
1 ATTGGATTAGAGGTGT
* *
17092249 ATTGAATTGGAGGTGT
1 ATTGGATTAGAGGTGT
17092265 ATTGGATTAGAGGTGT
1 ATTGGATTAGAGGTGT
17092281 ATTGGATTAGAGGTGT
1 ATTGGATTAGAGGTGT
17092297 A
1 A
17092298 ATAGCAAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
ATTGGATTAGAGGTGT
Found at i:17092554 original size:18 final size:17
Alignment explanation
Indices: 17092533--17092567 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17092523 TTATTATTAA
*
17092533 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17092551 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17092568 TCTTANNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17098216 original size:110 final size:111
Alignment explanation
Indices: 17098023--17098243 Score: 426
Period size: 110 Copynumber: 2.0 Consensus size: 111
17098013 AATAATTTAA
17098023 TCATATTTAAACATAATAATTATTAAATATATTATAATTTGAATATTTTTTACACCATTAAGCGT
1 TCATATTTAAACATAATAATTATTAAATATATTATAATTTGAATATTTTTTACACCATTAAGCGT
17098088 TTTGAGTATAAGATGTTTATGGCATTTTTACTAT-GGAGTGCCATG
66 TTTGAGTATAAGATGTTTATGGCATTTTTACTATGGGAGTGCCATG
*
17098133 TCATATTTAAACATAATTATTATTAAATATATTATAATTTGAATATTTTTTACACCATTAAGCGT
1 TCATATTTAAACATAATAATTATTAAATATATTATAATTTGAATATTTTTTACACCATTAAGCGT
17098198 TTTGAGTATAAGATGTTTATGGCATTTTTACTATGGGAGTGCCATG
66 TTTGAGTATAAGATGTTTATGGCATTTTTACTATGGGAGTGCCATG
17098244 GGTTGATTAA
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
110 98 0.90
111 11 0.10
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (111 bp):
TCATATTTAAACATAATAATTATTAAATATATTATAATTTGAATATTTTTTACACCATTAAGCGT
TTTGAGTATAAGATGTTTATGGCATTTTTACTATGGGAGTGCCATG
Found at i:17105838 original size:31 final size:31
Alignment explanation
Indices: 17105803--17105870 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
17105793 TTAATAGCCC
* *
17105803 AGTGATTTAAATAAAAATTTTCGAATAATTT
1 AGTGATTTAAATAAAAACTTTCAAATAATTT
* *
17105834 AGTGACTTAAATGAAAACTTTCAAATAATTT
1 AGTGATTTAAATAAAAACTTTCAAATAATTT
*
17105865 AATGAT
1 AGTGAT
17105871 CAAATTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (31 bp):
AGTGATTTAAATAAAAACTTTCAAATAATTT
Found at i:17106415 original size:22 final size:23
Alignment explanation
Indices: 17106374--17106417 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17106364 ACGAATAAGT
17106374 ATCACGTGTAAATCTTTAATTCC
1 ATCACGTGTAAATCTTTAATTCC
*
17106397 ATCATGTGTAAA-CTTTAATTC
1 ATCACGTGTAAATCTTTAATTC
17106418 GATGAGTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (23 bp):
ATCACGTGTAAATCTTTAATTCC
Found at i:17108719 original size:46 final size:46
Alignment explanation
Indices: 17108628--17108719 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
17108618 AAAATATTCT
* * *
17108628 CTATGAACTATAAAATAAATATGAAAGGCACCTTCATTCTAAAGAA
1 CTATGAACTATAAAATAAATATAAAAGACACCTTCATTCCAAAGAA
* * * * *
17108674 CTATGGACTATAAAATAGATATAAAAGATACCTTTATTCCGAAGAA
1 CTATGAACTATAAAATAAATATAAAAGACACCTTCATTCCAAAGAA
17108720 AATTGATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (46 bp):
CTATGAACTATAAAATAAATATAAAAGACACCTTCATTCCAAAGAA
Found at i:17112948 original size:183 final size:183
Alignment explanation
Indices: 17112647--17112997 Score: 549
Period size: 183 Copynumber: 1.9 Consensus size: 183
17112637 CATAAACCCA
*
17112647 TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAGACCTGACAGAC
1 TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAAACCTGACAGAC
* * * *
17112712 TGAGTAACAGGCCCCTTTCGCAACGCTTCCTGCTCTTCGAACTCACAGAGGGCATATTGAATTCC
66 TGAGTAACAGACCCCTTTCGCAACCCTTCCAGCTCTTCAAACTCACAGAGGGCATATTGAATTCC
* *
17112777 TTGGCCATGTTCCAAACTATCACTAGTCTTTGATAAATTGTCCCATGAACTGG
131 TTGGCCATATTCCAAACTATCACTAGTCTTTAATAAATTGTCCCATGAACTGG
* * *
17112830 TTCTGTCTTCTAAGGGGATCTTTGGTTGATTTGAAGTCTCAACTACATCTTGAAACCTGGCAGAC
1 TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAAACCTGACAGAC
* * * *
17112895 TGAGTAACAGACCCCTTTTGCAACCCTTGCAGCTCTTCAAACTCGCTGAGGGCATATTGAATTCC
66 TGAGTAACAGACCCCTTTCGCAACCCTTCCAGCTCTTCAAACTCACAGAGGGCATATTGAATTCC
** *
17112960 TTGGCCATATTCTGAGCTATCACTAGTCTTTAATAAAT
131 TTGGCCATATTCCAAACTATCACTAGTCTTTAATAAAT
17112998 GACTGATTCT
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
183 151 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (183 bp):
TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAAACCTGACAGAC
TGAGTAACAGACCCCTTTCGCAACCCTTCCAGCTCTTCAAACTCACAGAGGGCATATTGAATTCC
TTGGCCATATTCCAAACTATCACTAGTCTTTAATAAATTGTCCCATGAACTGG
Found at i:17122150 original size:64 final size:64
Alignment explanation
Indices: 17122029--17122153 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 64
17122019 CATCCCGATT
* * * * **
17122029 GGTATTGATCCTGCATATGTTGCGGACATACCGCAGCTCTTTGTGAGTGTATTGATATATGATC
1 GGTATTGATCCTGCATATATTGCGAACATACCGCAGCTCTTTATGAGCGTACCGATATATGATC
* *
17122093 GGTATTGATCCTGCATGTATTGCGAACATACCGCAGCTCTTTATGAGCGTCCCGATATATG
1 GGTATTGATCCTGCATATATTGCGAACATACCGCAGCTCTTTATGAGCGTACCGATATATG
17122154 GCTCTTCATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (64 bp):
GGTATTGATCCTGCATATATTGCGAACATACCGCAGCTCTTTATGAGCGTACCGATATATGATC
Found at i:17123161 original size:13 final size:13
Alignment explanation
Indices: 17123143--17123169 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17123133 AATAATGTTA
17123143 TAGTAGAGTTTTC
1 TAGTAGAGTTTTC
17123156 TAGTAGAGTTTTC
1 TAGTAGAGTTTTC
17123169 T
1 T
17123170 TATATAAGGT
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:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TAGTAGAGTTTTC
Found at i:17124712 original size:25 final size:23
Alignment explanation
Indices: 17124667--17124724 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
17124657 TCTTACAAGT
17124667 TTCCTGTTATAGCCCAAATAAGC
1 TTCCTGTTATAGCCCAAATAAGC
* *
17124690 TTCCTGTTACATAGCTCACATAAGC
1 TTCCTGTT--ATAGCCCAAATAAGC
*
17124715 TTCCTATTAT
1 TTCCTGTTAT
17124725 GTGGCTCGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 10 0.33
25 20 0.67
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (23 bp):
TTCCTGTTATAGCCCAAATAAGC
Found at i:17126985 original size:25 final size:25
Alignment explanation
Indices: 17126907--17126987 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
17126897 CTCTCAAGCA
*
17126907 CTATAACGGGAAGCTCAT--TGAGC
1 CTATAACGGGAAGCTCATCCGGAGC
*
17126930 CTTGTAACGGGAAGCTCATCCGGA-C
1 C-TATAACGGGAAGCTCATCCGGAGC
* *
17126955 AATATAACGGGAAGCTTATCCGGAGC
1 -CTATAACGGGAAGCTCATCCGGAGC
17126981 CTATAAC
1 CTATAAC
17126988 AAGTAGCTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.02
24 16 0.34
25 27 0.57
26 3 0.06
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (25 bp):
CTATAACGGGAAGCTCATCCGGAGC
Found at i:17127011 original size:24 final size:24
Alignment explanation
Indices: 17126984--17127036 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
17126974 CCGGAGCCTA
*
17126984 TAACAAGTAGCTCCAAAGAGCAAT
1 TAACAAGTAGCTCCAAAGAGCAAC
* * *
17127008 TAACGAGTAGTTCCGAAGAGCAAC
1 TAACAAGTAGCTCCAAAGAGCAAC
17127032 TAACA
1 TAACA
17127037 GGAAGCACCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (24 bp):
TAACAAGTAGCTCCAAAGAGCAAC
Found at i:17127628 original size:21 final size:21
Alignment explanation
Indices: 17127604--17127645 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17127594 AAATTTAACA
* *
17127604 TCAATTTAATACAAGTTACAT
1 TCAATTCAATACAAGTCACAT
*
17127625 TCAATTCAATCCAAGTCACAT
1 TCAATTCAATACAAGTCACAT
17127646 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.33
Consensus pattern (21 bp):
TCAATTCAATACAAGTCACAT
Found at i:17155119 original size:2 final size:2
Alignment explanation
Indices: 17155112--17155150 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
17155102 TTAAAAAGAA
*
17155112 AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
17155151 GGTCGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17161876 original size:2 final size:2
Alignment explanation
Indices: 17161869--17161902 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17161859 GTAAGGTCTC
17161869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17161903 TCATTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17165625 original size:28 final size:28
Alignment explanation
Indices: 17165578--17165634 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 28
17165568 TATTTTAACG
17165578 TTAACATTTTTTCTTCATAT-TATCATTT
1 TTAACATTTTTTCTTCATATATAT-ATTT
17165606 TTAACAGTTTTATT-TT-ATATATATATTT
1 TTAACA-TTTT-TTCTTCATATATATATTT
17165634 T
1 T
17165635 ATTTATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
28 15 0.58
29 9 0.35
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (28 bp):
TTAACATTTTTTCTTCATATATATATTT
Found at i:17168963 original size:38 final size:39
Alignment explanation
Indices: 17168885--17168964 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
17168875 TGATCCTAAA
** *
17168885 TTAAAAATATATAAAAATACATAAATATTTTGAATAATT
1 TTAAAAATATATAAAAATACATAAATATCATAAATAATT
*
17168924 TTAAAATATATATAAAAATA-A-AAATATGCATAAATATTT
1 TTAAAA-ATATATAAAAATACATAAATAT-CATAAATAATT
17168963 TT
1 TT
17168965 GTTATAACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 6 0.17
39 16 0.46
40 13 0.37
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (39 bp):
TTAAAAATATATAAAAATACATAAATATCATAAATAATT
Found at i:17178082 original size:948 final size:948
Alignment explanation
Indices: 17176249--17178146 Score: 3796
Period size: 948 Copynumber: 2.0 Consensus size: 948
17176239 ATTATTAATT
17176249 TTTAAATTTAATGTTAAAACATAATTTCAATTTTTTTAGTTGTAATGTTAAAAACCATTTTTTAA
1 TTTAAATTTAATGTTAAAACATAATTTCAATTTTTTTAGTTGTAATGTTAAAAACCATTTTTTAA
17176314 CATTTTATGTTTTAAATATTTTTCTGTTAAAAATAAAATAATAATGTTATTAATTAAAAAGTAAA
66 CATTTTATGTTTTAAATATTTTTCTGTTAAAAATAAAATAATAATGTTATTAATTAAAAAGTAAA
17176379 TTCAAATTGAACATATATTAATAACCATATTCTCGTATGTACCAATTGAACAACATCAGCCCAAT
131 TTCAAATTGAACATATATTAATAACCATATTCTCGTATGTACCAATTGAACAACATCAGCCCAAT
17176444 CACTTTCTAGTTTAACTTTTTGAAAGCCTTCGTTTCAAGCCATCTCTAATTTGTCTCAAATAACC
196 CACTTTCTAGTTTAACTTTTTGAAAGCCTTCGTTTCAAGCCATCTCTAATTTGTCTCAAATAACC
17176509 CATAGTTCTGAATGAAAATAGCAAATAATAATTGGATTCGACTAATCACAATGCACACCAAGTTC
261 CATAGTTCTGAATGAAAATAGCAAATAATAATTGGATTCGACTAATCACAATGCACACCAAGTTC
17176574 ATGGTGCAAAGTATAGAATCAAAACTGCAAACAAATGTTGTCATTATAACATTACATTCATATGG
326 ATGGTGCAAAGTATAGAATCAAAACTGCAAACAAATGTTGTCATTATAACATTACATTCATATGG
17176639 ATATAAAAACAGAGTTGAGAAAAAAAAACGTATGATCCATCCTAAAAATGATTTTGATCTTGGCA
391 ATATAAAAACAGAGTTGAGAAAAAAAAACGTATGATCCATCCTAAAAATGATTTTGATCTTGGCA
17176704 CTAAAATTTTTCATTTTCAACTTTTAAACTTCATCTTATACTTGTGGAGTTGCATAAATAATGCG
456 CTAAAATTTTTCATTTTCAACTTTTAAACTTCATCTTATACTTGTGGAGTTGCATAAATAATGCG
17176769 GATTTTTTTAAATGCTATTATTTGAAAAAGATTAAATGTTGAATGTTATTTATAATGGTGAATCT
521 GATTTTTTTAAATGCTATTATTTGAAAAAGATTAAATGTTGAATGTTATTTATAATGGTGAATCT
17176834 TAATTTTAATTGATATATAACTATAACGTTAACTAAATGATAATTATTTTTTTAACTCTAATAAT
586 TAATTTTAATTGATATATAACTATAACGTTAACTAAATGATAATTATTTTTTTAACTCTAATAAT
17176899 TAATTAATTAATATACTCAATCGTGCAGTTCAAATGAAGAAAACTTTATTATACAAATAAAAAAA
651 TAATTAATTAATATACTCAATCGTGCAGTTCAAATGAAGAAAACTTTATTATACAAATAAAAAAA
17176964 AATATTGATATGATATTATTGAATGTGATTTATAATGGTAAATTTTAATTTTAATTGATATACAC
716 AATATTGATATGATATTATTGAATGTGATTTATAATGGTAAATTTTAATTTTAATTGATATACAC
17177029 TTATAACACTAATTAAATGATGACTAATTTAAACAAATAAAAGCAAATATTTTTTAATGTCAATT
781 TTATAACACTAATTAAATGATGACTAATTTAAACAAATAAAAGCAAATATTTTTTAATGTCAATT
17177094 TAGTAATATAATGAGCAATAAAATGTATTATTATCGATTCAAAAGTTTTAAAAATTCGTGGTTTT
846 TAGTAATATAATGAGCAATAAAATGTATTATTATCGATTCAAAAGTTTTAAAAATTCGTGGTTTT
17177159 ATATATATTATTATAGATTATAGATAAAGAATACATTA
911 ATATATATTATTATAGATTATAGATAAAGAATACATTA
17177197 TTTAAATTTAATGTTAAAACATAATTTCAATTTTTTTAGTTGTAATGTTAAAAACCATTTTTTAA
1 TTTAAATTTAATGTTAAAACATAATTTCAATTTTTTTAGTTGTAATGTTAAAAACCATTTTTTAA
17177262 CATTTTATGTTTTAAATATTTTTCTGTTAAAAATAAAATAATAATGTTATTAATTAAAAAGTAAA
66 CATTTTATGTTTTAAATATTTTTCTGTTAAAAATAAAATAATAATGTTATTAATTAAAAAGTAAA
17177327 TTCAAATTGAACATATATTAATAACCATATTCTCGTATGTACCAATTGAACAACATCAGCCCAAT
131 TTCAAATTGAACATATATTAATAACCATATTCTCGTATGTACCAATTGAACAACATCAGCCCAAT
17177392 CACTTTCTAGTTTAACTTTTTGAAAGCCTTCGTTTCAAGCCATCTCTAATTTGTCTCAAATAACC
196 CACTTTCTAGTTTAACTTTTTGAAAGCCTTCGTTTCAAGCCATCTCTAATTTGTCTCAAATAACC
17177457 CATAGTTCTGAATGAAAATAGCAAATAATAATTGGATTCGACTAATCACAATGCACACCAAGTTC
261 CATAGTTCTGAATGAAAATAGCAAATAATAATTGGATTCGACTAATCACAATGCACACCAAGTTC
17177522 ATGGTGCAAAGTATAGAATCAAAACTGCAAACAAATGTTGTCATTATAACATTACATTCATATGG
326 ATGGTGCAAAGTATAGAATCAAAACTGCAAACAAATGTTGTCATTATAACATTACATTCATATGG
17177587 ATATAAAAACAGAGTTGAGAAAAAAAAACGTATGATCCATCCTAAAAATGATTTTGATCTTGGCA
391 ATATAAAAACAGAGTTGAGAAAAAAAAACGTATGATCCATCCTAAAAATGATTTTGATCTTGGCA
17177652 CTAAAATTTTTCATTTTCAACTTTTAAACTTCATCTTATACTTGTGGAGTTGCATAAATAATGCG
456 CTAAAATTTTTCATTTTCAACTTTTAAACTTCATCTTATACTTGTGGAGTTGCATAAATAATGCG
17177717 GATTTTTTTAAATGCTATTATTTGAAAAAGATTAAATGTTGAATGTTATTTATAATGGTGAATCT
521 GATTTTTTTAAATGCTATTATTTGAAAAAGATTAAATGTTGAATGTTATTTATAATGGTGAATCT
17177782 TAATTTTAATTGATATATAACTATAACGTTAACTAAATGATAATTATTTTTTTAACTCTAATAAT
586 TAATTTTAATTGATATATAACTATAACGTTAACTAAATGATAATTATTTTTTTAACTCTAATAAT
17177847 TAATTAATTAATATACTCAATCGTGCAGTTCAAATGAAGAAAACTTTATTATACAAATAAAAAAA
651 TAATTAATTAATATACTCAATCGTGCAGTTCAAATGAAGAAAACTTTATTATACAAATAAAAAAA
17177912 AATATTGATATGATATTATTGAATGTGATTTATAATGGTAAATTTTAATTTTAATTGATATACAC
716 AATATTGATATGATATTATTGAATGTGATTTATAATGGTAAATTTTAATTTTAATTGATATACAC
17177977 TTATAACACTAATTAAATGATGACTAATTTAAACAAATAAAAGCAAATATTTTTTAATGTCAATT
781 TTATAACACTAATTAAATGATGACTAATTTAAACAAATAAAAGCAAATATTTTTTAATGTCAATT
17178042 TAGTAATATAATGAGCAATAAAATGTATTATTATCGATTCAAAAGTTTTAAAAATTCGTGGTTTT
846 TAGTAATATAATGAGCAATAAAATGTATTATTATCGATTCAAAAGTTTTAAAAATTCGTGGTTTT
17178107 ATATATATTATTATAGATTATAGATAAAGAATACATTA
911 ATATATATTATTATAGATTATAGATAAAGAATACATTA
17178145 TT
1 TT
17178147 AAAAAATAAT
Statistics
Matches: 950, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
948 950 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (948 bp):
TTTAAATTTAATGTTAAAACATAATTTCAATTTTTTTAGTTGTAATGTTAAAAACCATTTTTTAA
CATTTTATGTTTTAAATATTTTTCTGTTAAAAATAAAATAATAATGTTATTAATTAAAAAGTAAA
TTCAAATTGAACATATATTAATAACCATATTCTCGTATGTACCAATTGAACAACATCAGCCCAAT
CACTTTCTAGTTTAACTTTTTGAAAGCCTTCGTTTCAAGCCATCTCTAATTTGTCTCAAATAACC
CATAGTTCTGAATGAAAATAGCAAATAATAATTGGATTCGACTAATCACAATGCACACCAAGTTC
ATGGTGCAAAGTATAGAATCAAAACTGCAAACAAATGTTGTCATTATAACATTACATTCATATGG
ATATAAAAACAGAGTTGAGAAAAAAAAACGTATGATCCATCCTAAAAATGATTTTGATCTTGGCA
CTAAAATTTTTCATTTTCAACTTTTAAACTTCATCTTATACTTGTGGAGTTGCATAAATAATGCG
GATTTTTTTAAATGCTATTATTTGAAAAAGATTAAATGTTGAATGTTATTTATAATGGTGAATCT
TAATTTTAATTGATATATAACTATAACGTTAACTAAATGATAATTATTTTTTTAACTCTAATAAT
TAATTAATTAATATACTCAATCGTGCAGTTCAAATGAAGAAAACTTTATTATACAAATAAAAAAA
AATATTGATATGATATTATTGAATGTGATTTATAATGGTAAATTTTAATTTTAATTGATATACAC
TTATAACACTAATTAAATGATGACTAATTTAAACAAATAAAAGCAAATATTTTTTAATGTCAATT
TAGTAATATAATGAGCAATAAAATGTATTATTATCGATTCAAAAGTTTTAAAAATTCGTGGTTTT
ATATATATTATTATAGATTATAGATAAAGAATACATTA
Found at i:17179001 original size:28 final size:28
Alignment explanation
Indices: 17178968--17179025 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
17178958 TCTTTTAATG
*
17178968 AATGAAATCATACAATTCAGAAGAAA-AA
1 AATGAAACCATACAATTCAG-AGAAAGAA
17178996 AATGAAACCATACAATTCAGAGAAAGAA
1 AATGAAACCATACAATTCAGAGAAAGAA
17179024 AA
1 AA
17179026 AATAGTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (28 bp):
AATGAAACCATACAATTCAGAGAAAGAA
Found at i:17181416 original size:57 final size:57
Alignment explanation
Indices: 17181330--17181439 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
17181320 GAGTGATCCT
* *
17181330 ATCTTGATATAGCCCTCCCGAAGAGTATGTGTGAAAA-AGATCTAGCCCGGACGGGTG
1 ATCTTGATATAGCCCTCCCAAAGAATATGTG-GAAAATAGATCTAGCCCGGACGGGTG
*
17181387 ATCTTGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATTTAGCCCGGACG
1 ATCTTGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATCTAGCCCGGACG
17181440 ATAATCGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 5 0.10
57 44 0.90
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (57 bp):
ATCTTGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGTG
Found at i:17181679 original size:67 final size:67
Alignment explanation
Indices: 17181571--17181765 Score: 320
Period size: 67 Copynumber: 2.9 Consensus size: 67
17181561 TATATTACAA
*
17181571 GGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
17181636 AG
66 AG
*
17181638 GGGATTTAGCCTGGACTGGTAATCCCGTTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
17181703 AG
66 AG
* * * **
17181705 GGGATTTAGCCTGGACTGGTAATCCCACTGTAAG-GATGAGATTCGCAGGAGTGTGCTCTCT
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCT
17181766 GAAATGGAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 23 0.19
67 97 0.81
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.29
Consensus pattern (67 bp):
GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
AG
Found at i:17183699 original size:4 final size:4
Alignment explanation
Indices: 17183690--17183715 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17183680 TGTTTTAATT
17183690 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
17183716 AACAACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:17184737 original size:18 final size:18
Alignment explanation
Indices: 17184704--17184761 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
17184694 AAGACATTCT
17184704 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
17184719 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
* *
17184737 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
17184755 TATTGAT
1 TATTGAT
17184762 CGTGACCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
18 26 0.68
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:17195198 original size:13 final size:13
Alignment explanation
Indices: 17195180--17195230 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
17195170 ACACTCAAAT
17195180 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
**
17195193 TTTTCAAAAATAC
1 TTTTCAAAAGCAC
*
17195206 TTTTCTACAA-CAC
1 TTTTC-AAAAGCAC
17195219 TTTTCAAAAGCA
1 TTTTCAAAAGCA
17195231 ATGACCCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:17202343 original size:4 final size:4
Alignment explanation
Indices: 17202334--17202358 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17202324 AACATATCTG
17202334 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
17202359 TATTTGAAGA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:17208309 original size:32 final size:32
Alignment explanation
Indices: 17208271--17208334 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
17208261 AATTAATCAA
17208271 CATGAGTTG-TCAAATTAAATTAATT-AATTTAT
1 CATGAGTTGCT-AAATTAAATT-ATTCAATTTAT
*
17208303 CATGAGTTGCTAAATTCAATTATTCAATTTAT
1 CATGAGTTGCTAAATTAAATTATTCAATTTAT
17208335 AAGTTTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 3 0.10
32 25 0.86
33 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (32 bp):
CATGAGTTGCTAAATTAAATTATTCAATTTAT
Found at i:17209421 original size:21 final size:21
Alignment explanation
Indices: 17209393--17209456 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
17209383 AATCTTACTA
* *
17209393 CTACAGTATCCAATCTCATTG
1 CTACAGTAACCAATCTCATCG
* *
17209414 CTATAGTAACTAATCTCATCG
1 CTACAGTAACCAATCTCATCG
* *
17209435 CTACAGTAACTAATCTTATCG
1 CTACAGTAACCAATCTCATCG
17209456 C
1 C
17209457 CACCGCTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (21 bp):
CTACAGTAACCAATCTCATCG
Found at i:17213096 original size:18 final size:18
Alignment explanation
Indices: 17213053--17213087 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17213043 AATCCTTATG
*
17213053 ATTGAA-TTTGTTAATTA
1 ATTGAAGTTAGTTAATTA
17213070 ATTGAAGTTAGTTAATTA
1 ATTGAAGTTAGTTAATTA
17213088 GTTTGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
ATTGAAGTTAGTTAATTA
Found at i:17215244 original size:21 final size:22
Alignment explanation
Indices: 17215210--17215257 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
17215200 GTTTTTTTTT
17215210 TAAAAGTTACAAA-TATTGA-AA
1 TAAAAGTTACAAATTATT-ACAA
17215231 TAAAA-TTACTAAATTATTACAA
1 TAAAAGTTAC-AAATTATTACAA
17215253 TAAAA
1 TAAAA
17215258 AAAGTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.17
21 9 0.38
22 11 0.46
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAGTTACAAATTATTACAA
Found at i:17222394 original size:12 final size:11
Alignment explanation
Indices: 17222357--17222396 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
17222347 TCACAATAAT
17222357 AATAATAAA-G
1 AATAATAAATG
17222367 AATAAT-AAT-
1 AATAATAAATG
17222376 AATAATAAATG
1 AATAATAAATG
17222387 AATAAATAAA
1 AAT-AATAAA
17222397 AACAAGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.31
10 9 0.35
11 3 0.12
12 6 0.23
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (11 bp):
AATAATAAATG
Found at i:17231644 original size:86 final size:87
Alignment explanation
Indices: 17231545--17231718 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 87
17231535 ACTATTTTGC
17231545 TACCATCTCACTATTACATTACTACTATCTATTTTGTTAATGTTTGGATATTGTATAACACTTGT
1 TACCATCTCACTATTACATTACTACTATCTATTTTGTTAATGTTTGGATATTGTATAACACTTGT
17231610 TTTATTGTTAA-TTTGCTACTA
66 TTTATTGTTAATTTTGCTACTA
17231631 TACCATCTCACTATTACATTACTACTATCTATTTTGTTAATGTTTGGATATTGTATAACACTTGT
1 TACCATCTCACTATTACATTACTACTATCTATTTTGTTAATGTTTGGATATTGTATAACACTTGT
17231696 TTTATTGTTAATTTTGCTACTA
66 TTTATTGTTAATTTTGCTACTA
17231718 T
1 T
17231719 TTTAGAGGTA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 76 0.87
87 11 0.13
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (87 bp):
TACCATCTCACTATTACATTACTACTATCTATTTTGTTAATGTTTGGATATTGTATAACACTTGT
TTTATTGTTAATTTTGCTACTA
Found at i:17233049 original size:20 final size:21
Alignment explanation
Indices: 17233016--17233057 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17233006 AGTATCTTTC
*
17233016 TTTTAAAACCAAAATATTATT
1 TTTTAAAACCAAAATATAATT
*
17233037 TTTTAAAA-TAAAATATAATT
1 TTTTAAAACCAAAATATAATT
17233057 T
1 T
17233058 CATAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTAAAACCAAAATATAATT
Found at i:17237642 original size:20 final size:21
Alignment explanation
Indices: 17237604--17237643 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17237594 TCTTCAGTAT
* *
17237604 CCATGATGGTAAAGCATAGGC
1 CCATGACGGTAAAGAATAGGC
17237625 CCATGACGG-AAAGAATAGG
1 CCATGACGGTAAAGAATAGG
17237644 AGGTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (21 bp):
CCATGACGGTAAAGAATAGGC
Found at i:17240616 original size:15 final size:15
Alignment explanation
Indices: 17240592--17240626 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17240582 TATCGAAGAG
*
17240592 CTTCCGGCTCTTAAA
1 CTTCCGGCTCGTAAA
*
17240607 CTTCCTGCTCGTAAA
1 CTTCCGGCTCGTAAA
17240622 CTTCC
1 CTTCC
17240627 CCGTAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.11, T:0.34
Consensus pattern (15 bp):
CTTCCGGCTCGTAAA
Found at i:17242269 original size:22 final size:22
Alignment explanation
Indices: 17242243--17242286 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
17242233 GAATATCTTA
17242243 TTTTT-TAAAGATATTTTAATTC
1 TTTTTATAAAGA-ATTTTAATTC
*
17242265 TTTTTACTAAATAATTTTAATT
1 TTTTTA-TAAAGAATTTTAATT
17242287 TAAAGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTATAAAGAATTTTAATTC
Found at i:17245363 original size:50 final size:51
Alignment explanation
Indices: 17245288--17245395 Score: 164
Period size: 50 Copynumber: 2.1 Consensus size: 51
17245278 CTTACGTATG
* * *
17245288 ATCACTTATCACTTGTCCCTGATCAGATAAGTGCAGGT-AAGCTACCACTT
1 ATCACTTACCACTTGTCACTGATCAGATAAGTGCAGCTGAAGCTACCACTT
* *
17245338 ATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTACCACTTGTCACTGATCAGATAAGTGCAGCTGAAGCTACCACTT
17245389 ATCACTT
1 ATCACTT
17245396 GTCACTGATC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
50 34 0.65
51 18 0.35
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (51 bp):
ATCACTTACCACTTGTCACTGATCAGATAAGTGCAGCTGAAGCTACCACTT
Found at i:17266863 original size:19 final size:22
Alignment explanation
Indices: 17266834--17266873 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
17266824 ATATTGCATC
17266834 AAAAATAAATA-TTT-ATATTA
1 AAAAATAAATACTTTAATATTA
17266854 AAAAAT-AATACTTTAATATT
1 AAAAATAAATACTTTAATATT
17266874 TGTTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAAATACTTTAATATTA
Found at i:17270929 original size:19 final size:20
Alignment explanation
Indices: 17270901--17270944 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
17270891 TCAGAAAAAT
*
17270901 TATTAATTAT-TAATATTTA
1 TATTAATTATAAAATATTTA
*
17270920 TATTATTTATAAAATATTTA
1 TATTAATTATAAAATATTTA
17270940 -ATTAA
1 TATTAA
17270945 ATTGGTGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTAATTATAAAATATTTA
Found at i:17278102 original size:22 final size:24
Alignment explanation
Indices: 17278067--17278116 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
17278057 TATATTAAAA
*
17278067 AAATGTTAAGTATAATT-AA-TTTT
1 AAATGTTAAATAT-ATTAAATTTTT
17278090 AAAT-TTAAATATATTAAATTTTT
1 AAATGTTAAATATATTAAATTTTT
17278113 AAAT
1 AAAT
17278117 ATGTTAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 9 0.38
23 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATGTTAAATATATTAAATTTTT
Found at i:17278237 original size:78 final size:80
Alignment explanation
Indices: 17278092--17278238 Score: 199
Period size: 80 Copynumber: 1.9 Consensus size: 80
17278082 TTAATTTTAA
* * * * * *
17278092 ATTTAAATATATTAAATTTTTAAATATGTTAAAAGAAAATGATGAGTATAAACAATTTTAAATTT
1 ATTTAAATATATTAAAATTTTAAACATATTAAAAAAAAAT-ATAAGTATAAACAATTTTAAAATT
17278157 TTAATAACTGAATAAT
65 TTAATAACTGAATAAT
* *
17278173 ATTT-AATATATTAAAATTTTGAACATATTAAAAAAAAAT-TAAGTATAACCAATTTTAAAATTT
1 ATTTAAATATATTAAAATTTTAAACATATTAAAAAAAAATATAAGTATAAACAATTTTAAAATTT
17278236 TAA
66 TAA
17278239 AATTTCAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
78 24 0.41
80 30 0.52
81 4 0.07
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.40
Consensus pattern (80 bp):
ATTTAAATATATTAAAATTTTAAACATATTAAAAAAAAATATAAGTATAAACAATTTTAAAATTT
TAATAACTGAATAAT
Found at i:17280869 original size:14 final size:14
Alignment explanation
Indices: 17280833--17280872 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
17280823 AAAAACCCTA
17280833 TTTTTCCTT-TTTC
1 TTTTTCCTTCTTTC
*
17280846 -TTTTCTTTCTTTC
1 TTTTTCCTTCTTTC
17280859 TTTTTCCTTCTTTC
1 TTTTTCCTTCTTTC
17280873 CTTTCTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 12 0.52
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCCTTCTTTC
Found at i:17280876 original size:23 final size:21
Alignment explanation
Indices: 17280843--17280885 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
17280833 TTTTTCCTTT
*
17280843 TTCTTTTCTTTCTTTCTTTTTCC
1 TTCTTTCCTTTC--TCTTTTTCC
17280866 TTCTTTCCTTTCTCTTTTTC
1 TTCTTTCCTTTCTCTTTTTC
17280886 GTTTGCCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTCTTTCCTTTCTCTTTTTCC
Found at i:17282086 original size:29 final size:30
Alignment explanation
Indices: 17282030--17282101 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
17282020 TTTTTATATG
*
17282030 AATAATATAAAATAAATCAATATATACGAA
1 AATAAGATAAAATAAATCAATATATACGAA
* * * *
17282060 AATAAGATAACATGAAT-AATATTTACGAG
1 AATAAGATAAAATAAATCAATATATACGAA
17282089 AAT-AGATAAAATA
1 AATAAGATAAAATA
17282102 CACAGTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 8 0.23
29 13 0.37
30 14 0.40
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (30 bp):
AATAAGATAAAATAAATCAATATATACGAA
Found at i:17307240 original size:16 final size:16
Alignment explanation
Indices: 17307219--17307257 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17307209 TTGATTTGCT
*
17307219 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
17307235 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
17307251 ATTACAC
1 ATTACAC
17307258 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:17307258 original size:16 final size:16
Alignment explanation
Indices: 17307231--17307272 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
17307221 TACACAGCTT
17307231 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
17307247 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
* *
17307263 ATCCAATACA
1 TTCCATTACA
17307273 GCGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:17309072 original size:2 final size:2
Alignment explanation
Indices: 17309065--17309090 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17309055 TTAACAAATG
17309065 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17309091 TAAAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17311142 original size:2 final size:2
Alignment explanation
Indices: 17311135--17311161 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17311125 TACAATACTA
17311135 AT 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 AT A
17311162 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17311204 original size:2 final size:2
Alignment explanation
Indices: 17311199--17311231 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17311189 NNNTATATAT
*
17311199 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17311232 ACAAAAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17313684 original size:52 final size:52
Alignment explanation
Indices: 17313619--17313723 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
17313609 CACTGCATGT
17313619 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
1 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
17313671 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
1 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
17313723 A
1 A
17313724 TGCTTGCCAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (52 bp):
AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
Found at i:17328094 original size:3 final size:3
Alignment explanation
Indices: 17328086--17328117 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17328076 AGGTTATTAA
17328086 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
17328118 AAAGATGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:17329204 original size:105 final size:106
Alignment explanation
Indices: 17329022--17329241 Score: 424
Period size: 105 Copynumber: 2.1 Consensus size: 106
17329012 TTATAATAAT
17329022 AAGATAAATAATTAATTGGGTGGTAATAAGTTTAAAATTTTTAATAAGCTTGAAAATACCCGCAT
1 AAGATAAATAATTAATTGGGTGGTAATAAGTTTAAAATTTTTAATAAGCTTGAAAATACCCGCAT
17329087 TCAAAGTAATTCAGTGAAAGGCTTCGTCCTAAATTCT-CCA
66 TCAAAGTAATTCAGTGAAAGGCTTCGTCCTAAATTCTCCCA
*
17329127 AAGATAAATAATTAATTGGGTTGTAATAAGTTTAAAATTTTTAATAAGCTTGAAAATACCCGCAT
1 AAGATAAATAATTAATTGGGTGGTAATAAGTTTAAAATTTTTAATAAGCTTGAAAATACCCGCAT
17329192 TCAAAGTAATTCAGTGAAAGGCTTCGTCCTAAATTCTCCCA
66 TCAAAGTAATTCAGTGAAAGGCTTCGTCCTAAATTCTCCCA
17329233 AAGATAAAT
1 AAGATAAAT
17329242 TAAACCACTA
Statistics
Matches: 113, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 101 0.89
106 12 0.11
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (106 bp):
AAGATAAATAATTAATTGGGTGGTAATAAGTTTAAAATTTTTAATAAGCTTGAAAATACCCGCAT
TCAAAGTAATTCAGTGAAAGGCTTCGTCCTAAATTCTCCCA
Found at i:17347067 original size:17 final size:17
Alignment explanation
Indices: 17347045--17347083 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
17347035 AAATTTTAAT
17347045 AAAAATATAAAAA-ATAC
1 AAAAATA-AAAAATATAC
*
17347062 AAAAATAAAAAATATAT
1 AAAAATAAAAAATATAC
17347079 AAAAA
1 AAAAA
17347084 AGTGTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAAATATAC
Found at i:17347069 original size:15 final size:15
Alignment explanation
Indices: 17347042--17347075 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17347032 ATTAAATTTT
17347042 AATAAAAATATAAAA
1 AATAAAAATATAAAA
17347057 AATACAAAA-ATAAAA
1 AATA-AAAATATAAAA
17347072 AATA
1 AATA
17347076 TATAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAAAAATATAAAA
Found at i:17347072 original size:7 final size:7
Alignment explanation
Indices: 17347042--17347075 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
17347032 ATTAAATTTT
17347042 AATAAAA
1 AATAAAA
17347049 ATATAAAA
1 A-ATAAAA
17347057 AATACAAA
1 AATA-AAA
17347065 AATAAAA
1 AATAAAA
17347072 AATA
1 AATA
17347076 TATAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (7 bp):
AATAAAA
Found at i:17347121 original size:9 final size:9
Alignment explanation
Indices: 17347001--17347083 Score: 52
Period size: 9 Copynumber: 9.6 Consensus size: 9
17346991 CATGTGATAA
17347001 AAAAATTAT
1 AAAAATTAT
17347010 AAAAA--AT
1 AAAAATTAT
*
17347017 AAAAATTGT
1 AAAAATTAT
17347026 -AAAATTATT
1 AAAAATTA-T
**
17347035 AAATTTTAAT
1 AAAAATT-AT
17347045 AAAAA-TAT
1 AAAAATTAT
* *
17347053 AAAAAATAC
1 AAAAATTAT
17347062 AAAAA-TA-
1 AAAAATTAT
17347069 AAAAATATAT
1 AAAAAT-TAT
17347079 AAAAA
1 AAAAA
17347084 AGTGTAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
7 12 0.21
8 15 0.26
9 17 0.29
10 13 0.22
11 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Done.