Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 52 of 145
Found at i:16992375 original size:50 final size:50
Alignment explanation
Indices: 16992271--16992380 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
16992261 TGTCCATGTT
* * ** * *
16992271 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTA
1 TGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATA
* * *
16992321 TGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATC
1 TGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATA
*
16992371 TGGGATATGG
1 TGGGACATGG
16992381 AATTGGCAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
TGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATA
Found at i:16998525 original size:125 final size:126
Alignment explanation
Indices: 16997941--16998586 Score: 888
Period size: 126 Copynumber: 5.1 Consensus size: 126
16997931 GGCCAAACAT
* *
16997941 GAACTACTGTAGTAAAAGAGCGTCCACATGGGAGCTTTTTTCAGT-AATTTT-TCTGACAGTGCA
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCA-TCAATTTTGT-TGACAGTGCA
* * * *
16998004 TCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTTTTAG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
* * * * *
16998067 GAACTATTGTAGAAAAAGAGCATCCACGTGGGAGCCTTTTTCAGCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
* * * * *
16998132 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTTTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
* * * *
16998193 GAACTACTGTAGAAAAATAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGATAGTGCACC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
* *
16998258 CTGCTTGAAGCGTTTTTAACACTATTTGTTCAG-AATCGTCTTTTCAAAATTATTTTTTC-A
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAT-GTCTTCTCAAAATTATTTTTTCAA
* * * * *
16998318 GAAACCACTATAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGCAATTTTGTTGGCAGTGCAT
1 G-AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCAT
**
16998383 CCTGCTTGAAGTATTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
* * * *
16998445 GAACTACTGTAG-AAAAGAGCATCCACATGGGAGCATTTTTCATCAATTTTGTTGACAGTGCTTC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
* * * *
16998509 CTTCTTGAAGCGTTTTTGGCACTATTTGTTTAGAACTGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
16998570 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
16998587 AAAACCAAAA
Statistics
Matches: 459, Mismatches: 54, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
125 115 0.25
126 339 0.74
127 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
Found at i:16998700 original size:34 final size:34
Alignment explanation
Indices: 16998651--16998759 Score: 100
Period size: 34 Copynumber: 3.3 Consensus size: 34
16998641 CAATATTATT
*
16998651 TTTAAAAAAACTAAACCCAATTTTAATTCATTT-
1 TTTAAAAAAACTAAACCCAAATTTAATTCATTTA
*
16998684 TCTTAAAAACAA-TAAACCCAAATTTAATTTATTTA
1 T-TTAAAAA-AACTAAACCCAAATTTAATTCATTTA
*** ** *
16998719 TTTAAAACCCCTAAACCTTAATTTAATT-AATT-
1 TTTAAAAAAACTAAACCCAAATTTAATTCATTTA
16998751 TTTAAAAAA
1 TTTAAAAAA
16998760 GAACACTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
32 7 0.11
33 4 0.06
34 48 0.77
35 3 0.05
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (34 bp):
TTTAAAAAAACTAAACCCAAATTTAATTCATTTA
Found at i:16998885 original size:15 final size:15
Alignment explanation
Indices: 16998865--16998903 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
16998855 TTATTTTAAC
* **
16998865 AAAACCCTAACCCTA
1 AAAACCCTAAACAAA
16998880 AAAACCCTAAACAAA
1 AAAACCCTAAACAAA
16998895 AAAACCCTA
1 AAAACCCTA
16998904 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAACCCTAAACAAA
Found at i:16998889 original size:42 final size:42
Alignment explanation
Indices: 16998795--16998885 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
16998785 AAAAATTCTT
* * *
16998795 AAAACCTAGAACCCTAAATTATTTTCACAAAATCCTAAACCTTA
1 AAAACCT--AACCCTAAATTATTTTAACAAAACCCTAAACCCTA
*
16998839 CAAACCTAACCCTAAATTATTTTAACAAAACCCT-AACCCTA
1 AAAACCTAACCCTAAATTATTTTAACAAAACCCTAAACCCTA
16998880 AAAACC
1 AAAACC
16998886 CTAAACAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 11 0.26
42 25 0.60
44 6 0.14
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (42 bp):
AAAACCTAACCCTAAATTATTTTAACAAAACCCTAAACCCTA
Found at i:17000483 original size:2 final size:2
Alignment explanation
Indices: 17000476--17000518 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
17000466 TGAAATTTTC
**
17000476 AT AT AT AT AT AT AT AT NNN 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 AT AT AT AT
17000519 GATCTTGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17007500 original size:30 final size:30
Alignment explanation
Indices: 17007466--17007538 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
17007456 AAAATATCAA
17007466 ACATAAAAAAGTATCATACATTAGTTTTAC
1 ACATAAAAAAGTATCATACATTAGTTTTAC
*
17007496 ACATAAAAAAGCATCATACATTAGTTTTAC
1 ACATAAAAAAGTATCATACATTAGTTTTAC
*
17007526 ACGTAAAAAAGTA
1 ACATAAAAAAGTA
17007539 GTATAGTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (30 bp):
ACATAAAAAAGTATCATACATTAGTTTTAC
Found at i:17029643 original size:6 final size:6
Alignment explanation
Indices: 17029632--17029670 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
17029622 ATCAAGGATG
* *
17029632 GGGGAA GGGGAA GGGAAA GGGGAA GGGAAA GGGGAA GGG
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGG
17029671 AAGATTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:17029653 original size:12 final size:12
Alignment explanation
Indices: 17029636--17029672 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
17029626 AGGATGGGGG
17029636 AAGGGGAAGGGA
1 AAGGGGAAGGGA
17029648 AAGGGGAAGGGA
1 AAGGGGAAGGGA
17029660 AAGGGGAAGGGA
1 AAGGGGAAGGGA
17029672 A
1 A
17029673 GATTGGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
AAGGGGAAGGGA
Found at i:17035566 original size:19 final size:19
Alignment explanation
Indices: 17035542--17035595 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
17035532 AATCATATCT
17035542 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
17035561 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
17035580 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
17035596 CTTAAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:17035591 original size:38 final size:40
Alignment explanation
Indices: 17035519--17035595 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
17035509 AAATTAAATC
17035519 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
17035561 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
17035596 CTTAAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:17036201 original size:45 final size:45
Alignment explanation
Indices: 17036144--17036272 Score: 179
Period size: 45 Copynumber: 2.9 Consensus size: 45
17036134 TTGTTTATTT
* * * *
17036144 AGTCTGCCCCACTGCAATTTTAGAGG-GATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAACTTCAG-GGAGATAAGACTCGATTTCTTG
*
17036189 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* *
17036234 GGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGAT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGAT
17036273 GCGATCTGCT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
44 2 0.03
45 73 0.97
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:17036462 original size:44 final size:45
Alignment explanation
Indices: 17036356--17036620 Score: 144
Period size: 44 Copynumber: 6.1 Consensus size: 45
17036346 TTGGCTTTAA
17036356 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTCATCTTCAG
* * *
17036401 TCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTT-G-CTTACTT-AG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAA-GATTCGTCAT-CTTCAG
* * ** *
17036445 TCTGCTCCACTGCAACTTTAGAGAGATAAGA--C-T-AGATGC-G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTCATCTTCAG
* * * * * * *
17036485 ATCTACT-CTCTGCAACTTTAGAGAGATAAGA-TCTGTTAT-TTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GTCATCTTCAG
* * * * * * * * *
17036529 TCCGCTCCACTGCGACTTCAGGGAGAGAGGATT-ATTAGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTCATCTTCAG
* *
17036573 TCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTCATCTTCAG
17036618 TCT
1 TCT
17036621 TTTAAATTGC
Statistics
Matches: 163, Mismatches: 38, Indels: 38
0.68 0.16 0.16
Matches are distributed among these distances:
40 25 0.15
41 6 0.04
43 10 0.06
44 81 0.50
45 38 0.23
46 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTCATCTTCAG
Found at i:17036967 original size:44 final size:44
Alignment explanation
Indices: 17036919--17037038 Score: 147
Period size: 44 Copynumber: 2.7 Consensus size: 44
17036909 ATCTGTTATT
*
17036919 TTCAACCTACTCCACTGGTGCTCAGGGAGATAAGA-TTCACAATC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTT-ACAATC
* * *
17036963 TTCAACATACTCCACTACTGAC-CAAGGAGATAAGACTTACAATC
1 TTCAACCTACTCCACTGCTG-CTCAGGGAGATAAGACTTACAATC
*
17037007 TTCAACCTATTCCACTGCTG-TCTAGGGAGATA
1 TTCAACCTACTCCACTGCTGCTC-AGGGAGATA
17037039 GGGTTGCGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 60 0.94
45 3 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (44 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTTACAATC
Found at i:17037168 original size:88 final size:88
Alignment explanation
Indices: 17037051--17038057 Score: 1512
Period size: 88 Copynumber: 11.4 Consensus size: 88
17037041 GTTGCGGTCA
* * * *
17037051 TCGATTTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
17037116 CTAGGGAGACAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * **
17037139 TCAATCTGCTTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
17037204 CTAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
17037227 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* * *
17037292 CTAGGGAGTCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
17037315 TCGATCTGCTTCGCTATCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
17037380 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
17037403 TCGATCTGCTTCCCTGTCGGTGCAGGAAGGCAAGTTCTGTTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* * *
17037468 CCAGAGAGGCAAGGTTAGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
17037491 TCGATCTGCTTCGCTGTAGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTACTTCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
17037556 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
17037579 TCGATCTGCTTCCCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
17037644 CCAGAGAGGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
17037667 TCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAATATCTGCTATTTTTAACCTACTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
17037732 CCAGGTAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * **
17037755 TTGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCT-ATAATTTTTAACTTGCTCCACTGTAA
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT-ATTTTTAACCTGCTCCGCTACAA
* * *
17037819 ACCAGGGAGGCAATGCTGATGTCT
65 CCCAGGGAGGCAAGGCTGGTGTCT
* *
17037843 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTCTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
17037908 CCAGGGAGGCAAGGCTGGGGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
17037931 TTGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCTGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
17037996 CCAGGGAGGGAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
17038019 TCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTG
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
17038058 TTATCTTCAC
Statistics
Matches: 829, Mismatches: 88, Indels: 4
0.90 0.10 0.00
Matches are distributed among these distances:
87 1 0.00
88 827 1.00
89 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:17037216 original size:44 final size:44
Alignment explanation
Indices: 17037078--17037392 Score: 131
Period size: 44 Copynumber: 7.2 Consensus size: 44
17037068 CGATGCAGGA
*
17037078 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAACCTAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGTAACCTAGGG
* * * * * * * * **** *
17037122 AGACAAG-GCTGGTGTCTTCAATCTGCTTCACTGTCGGTGTAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGT-AACCTAGGG
*
17037166 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACCTAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGTAACCTAGGG
* * * * ** * * * *
17037210 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGTTGT--CGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGTAAC-CT--AGGG
* * **
17037254 AGGCAAGATCTACTATTTTTAACCTGCTCCGCTACAACCTAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGTAACCTAGGG
* * * * * ** * * * *
17037298 AGTCAAGGT-TGGTGTCTTCGATCTGCTTCGC--TATCGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGTAAC-CT--AGGG
** *
17037342 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACCCAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGTAACCTAGGG
17037386 AGGCAAG
1 AGGCAAG
17037393 GCTGGTGTCT
Statistics
Matches: 177, Mismatches: 80, Indels: 28
0.62 0.28 0.10
Matches are distributed among these distances:
41 3 0.02
42 2 0.01
43 51 0.29
44 67 0.38
45 50 0.28
46 1 0.01
47 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGTAACCTAGGG
Found at i:17037434 original size:44 final size:43
Alignment explanation
Indices: 17037210--17037788 Score: 129
Period size: 44 Copynumber: 13.2 Consensus size: 43
17037200 TAACCTAGGG
*
17037210 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
* ** * * ** * * * *** *
17037254 AGGCAAGATCTACTATTTTTAACCTGCTCCGCTAC-AACCTAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTTCGGTGC-AGGA
* *
17037298 AGTCAAGGTTGGTGTCTTCGATCTGCTTCGCTATCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
* * * * ** * * **** *
17037342 AGGCAAGATCTGCTATTTTTAACCTGCTTCGCTACAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
*
17037386 AGGCAAGGCTGGTGTCTTCGATCTGCTTCCCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
* * * * ** * * * ****
17037430 AGGCAAGTTCTGTTATTTTTAACCTGCTCCGCTACAACCCA-GA
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
* * * *
17037473 GAGGCAAGGTTAGTGTCTTCGATCTGCTTCGCTGTAGGTGCAAGA
1 -AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
* * * * ** * * * **** *
17037518 AGGCAAGATCTGCTATTTTTAACCTACTTCGCTACAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
*
17037562 AGGCAAGGCTGGTGTCTTCGATCTGCTTCCCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
* * * * ** * * * * ****
17037606 AGGCAAGATCTGCTATTTTTAACCTACTCCGCTACAACCCA-GA
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
* *
17037649 GAGGCAAGGTTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGA
1 -AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
** * * * ** * * * * **** *
17037694 AGGCAATATCTGCTATTTTTAACCTACTCCGCTACAACCCAGGT
1 AGGCAA-GGCTGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
*
17037738 AGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
17037782 AGGCAAG
1 AGGCAAG
17037789 ATCTATAATT
Statistics
Matches: 330, Mismatches: 187, Indels: 36
0.60 0.34 0.07
Matches are distributed among these distances:
43 99 0.30
44 134 0.41
45 97 0.29
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (43 bp):
AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
Found at i:17039406 original size:14 final size:15
Alignment explanation
Indices: 17039383--17039415 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17039373 ATTAACGCTT
17039383 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
17039397 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
17039412 TTCC
1 TTCC
17039416 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:17044316 original size:3 final size:3
Alignment explanation
Indices: 17044308--17044345 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17044298 GCACATGAAT
17044308 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17044346 GATACAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17044602 original size:15 final size:15
Alignment explanation
Indices: 17044565--17044604 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
17044555 AAGAGATTTG
*
17044565 AAATCAACAATATAC
1 AAATCAATAATATAC
17044580 AAATCAATAATATAC
1 AAATCAATAATATAC
17044595 AAATCAATAA
1 AAATCAATAA
17044605 ATAAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATCAATAATATAC
Found at i:17044606 original size:23 final size:23
Alignment explanation
Indices: 17044580--17044624 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17044570 AACAATATAC
* *
17044580 AAATCAATAATATACAAATCAAT
1 AAATAAATAATACACAAATCAAT
*
17044603 AAATAAATTATACACAAATCAA
1 AAATAAATAATACACAAATCAA
17044625 CAAAATAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
AAATAAATAATACACAAATCAAT
Found at i:17044857 original size:19 final size:19
Alignment explanation
Indices: 17044833--17044881 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
17044823 TTATATCTTT
17044833 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
* *
17044852 TAAGATTACGTATCATATC
1 TAAGATTGCATATCATATC
17044871 TAAGATTGCAT
1 TAAGATTGCAT
17044882 GTCCTTGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:17047391 original size:27 final size:26
Alignment explanation
Indices: 17047361--17047418 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
17047351 ATGTAACAAG
* *
17047361 CACATTTGCAAACTTAGTTCACCAAAA
1 CACATTTACAAAC-AAGTTCACCAAAA
**
17047388 CACATTTACAAACAAGTTTGCCAAAA
1 CACATTTACAAACAAGTTCACCAAAA
17047414 CACAT
1 CACAT
17047419 CTGTGAGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (26 bp):
CACATTTACAAACAAGTTCACCAAAA
Found at i:17048119 original size:33 final size:33
Alignment explanation
Indices: 17048082--17048148 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
17048072 TAATTACTTA
17048082 AGTATGAACATGTAAATTAAGAAAATATCAATC
1 AGTATGAACATGTAAATTAAGAAAATATCAATC
17048115 AGTATGAACATGTAAATTAAGAAAATATCAATC
1 AGTATGAACATGTAAATTAAGAAAATATCAATC
17048148 A
1 A
17048149 AATTCAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (33 bp):
AGTATGAACATGTAAATTAAGAAAATATCAATC
Found at i:17049302 original size:31 final size:31
Alignment explanation
Indices: 17049264--17049334 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
17049254 AAACACAAGC
* *
17049264 GAACCTAGGTTC-ACACTGTTAATCTTTTGGT
1 GAACCTAGGTCCGACA-TGCTAATCTTTTGGT
*
17049295 GAACCTAGGTCCGTACATGCTAGTCTTTTGGT
1 GAACCTAGGTCCG-ACATGCTAATCTTTTGGT
17049327 GAACCTAG
1 GAACCTAG
17049335 TTTCCTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 11 0.31
32 21 0.60
33 3 0.09
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (31 bp):
GAACCTAGGTCCGACATGCTAATCTTTTGGT
Found at i:17051143 original size:24 final size:24
Alignment explanation
Indices: 17051116--17051162 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
17051106 TAACATATTT
*
17051116 AATTTTATTTAATTTAAATCGAAC
1 AATTTTATTTAATTCAAATCGAAC
*
17051140 AATTTTATTTAATTCAATTCGAA
1 AATTTTATTTAATTCAAATCGAA
17051163 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (24 bp):
AATTTTATTTAATTCAAATCGAAC
Found at i:17051390 original size:3 final size:3
Alignment explanation
Indices: 17051382--17051425 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
17051372 TAGTAAACCC
17051382 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17051426 ATTAATGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17056765 original size:2 final size:2
Alignment explanation
Indices: 17056758--17056788 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17056748 TATGTTTAGA
*
17056758 AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17056789 ACAGCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
AG
Found at i:17058199 original size:30 final size:29
Alignment explanation
Indices: 17058163--17058222 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
17058153 ATGGTTTAAC
17058163 GTGTAATTTGTATACATGAAA-TTTGATTTT
1 GTGTAATTT-TATACAT-AAAGTTTGATTTT
17058193 GTGTAATTTTATACATAAAGTTTTGATTTT
1 GTGTAATTTTATACATAAAG-TTTGATTTT
17058223 ATTTAATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 3 0.11
29 7 0.25
30 18 0.64
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (29 bp):
GTGTAATTTTATACATAAAGTTTGATTTT
Found at i:17058230 original size:30 final size:30
Alignment explanation
Indices: 17058164--17058230 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
17058154 TGGTTTAACG
*
17058164 TGTAATTTGTATACATGAAATTTGATTTTG
1 TGTAATTTGTATACATGAAATTTGATTTTA
17058194 TGTAATTT-TATACAT-AAAGTTTTGATTTTA
1 TGTAATTTGTATACATGAAA--TTTGATTTTA
*
17058224 TTTAATT
1 TGTAATT
17058231 CTTGTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.09
29 7 0.21
30 23 0.70
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTAATTTGTATACATGAAATTTGATTTTA
Found at i:17058446 original size:29 final size:30
Alignment explanation
Indices: 17058414--17058474 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
17058404 TTTCACGTGA
* *
17058414 ATAATTGCAC-TAAATTAAAGTTCATGTAT
1 ATAATTACACATAAATCAAAGTTCATGTAT
17058443 ATAATTACACATTAAATCAAAGTTCATGTAT
1 ATAATTACACA-TAAATCAAAGTTCATGTAT
17058474 A
1 A
17058475 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
31 19 0.68
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (30 bp):
ATAATTACACATAAATCAAAGTTCATGTAT
Found at i:17069732 original size:116 final size:113
Alignment explanation
Indices: 17069580--17069809 Score: 370
Period size: 116 Copynumber: 2.0 Consensus size: 113
17069570 AAATTGAATG
*
17069580 AAATAATTGTATAGACCGGATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAGAT
1 AAATAATTGTATAGACAGGATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAGAT
* *
17069645 TAGTCCTTAAAGTTTCAACTTGTTTGCTATTTTTCTCAGGTAGGTTCAT
66 TAGTCCTTAAAGTTTCAACTTG-TTGCTATTTTTCCCAAGTAGGTTCAT
* * * *
17069694 AAATAATTGTATAGACTAGGAATTGGATCAAACTAGAGATAGTTGGGGAAAAGCAAAAATTTTAG
1 AAATAATTGTATAGAC-AGG-ATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAG
17069759 ATTAGTCCTTAAAGTTTCAACTTGTTGCTATTTTTCCCAAGTAGGTTCAT
64 ATTAGTCCTTAAAGTTTCAACTTGTTGCTATTTTTCCCAAGTAGGTTCAT
17069809 A
1 A
17069810 TAGTACTTAC
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 16 0.15
115 27 0.25
116 64 0.60
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (113 bp):
AAATAATTGTATAGACAGGATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAGAT
TAGTCCTTAAAGTTTCAACTTGTTGCTATTTTTCCCAAGTAGGTTCAT
Found at i:17073671 original size:39 final size:38
Alignment explanation
Indices: 17073617--17073749 Score: 149
Period size: 39 Copynumber: 3.4 Consensus size: 38
17073607 TATTATAGAT
* *
17073617 TATAATGAGATCTAGCATTTGTTGCAGATCCTCGAGTAA
1 TATAACGAGATCTAGCATTTGTTGCAGATTCT-GAGTAA
* * *
17073656 TATAACAAGATCTAGCCTTTGTTGCAGATTCTTGGGTAA
1 TATAACGAGATCTAGCATTTGTTGCAGATTC-TGAGTAA
* * * *
17073695 TATAATGAGATCTAGCATCTATTGCAGATTCTTAGGTAA
1 TATAACGAGATCTAGCATTTGTTGCAGATTCTGA-GTAA
*
17073734 TATATCGAGATCTAGC
1 TATAACGAGATCTAGC
17073750 CCATTTTGTG
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.01
39 76 0.97
40 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (38 bp):
TATAACGAGATCTAGCATTTGTTGCAGATTCTGAGTAA
Found at i:17073771 original size:78 final size:78
Alignment explanation
Indices: 17073617--17073776 Score: 189
Period size: 78 Copynumber: 2.1 Consensus size: 78
17073607 TATTATAGAT
* * * *
17073617 TATAATGAGATCTAGCATTTGTTGCAGATCCTCGAGTAATATAACAAGATCTAGCCTTTGTTGCA
1 TATAATGAGATCTAGCATCTATTGCAGATCCTAGAGTAATATAACAAGATCTAGCCATTGTTGCA
*
17073682 GATTCTTGGGTAA
66 GATTCTCGGGTAA
* * *
17073695 TATAATGAGATCTAGCATCTATTGCAGATTCTTAG-GTAATATATCGAGATCTAGCCCATT-TTG
1 TATAATGAGATCTAGCATCTATTGCAGA-TCCTAGAGTAATATAACAAGATCTAG-CCATTGTTG
** *
17073758 TGGGTTCTCGGGTAA
64 CAGATTCTCGGGTAA
17073773 TATA
1 TATA
17073777 TGACATAGGT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 61 0.88
79 8 0.12
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (78 bp):
TATAATGAGATCTAGCATCTATTGCAGATCCTAGAGTAATATAACAAGATCTAGCCATTGTTGCA
GATTCTCGGGTAA
Found at i:17075602 original size:19 final size:20
Alignment explanation
Indices: 17075578--17075617 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
17075568 TGAGCTAGTT
*
17075578 GGAGCTGGAA-TGAGCTAAA
1 GGAGCTGAAATTGAGCTAAA
17075597 GGAGCTGAAATTGAGCTAAA
1 GGAGCTGAAATTGAGCTAAA
17075617 G
1 G
17075618 TCAGCTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.10, G:0.35, T:0.17
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAA
Found at i:17082671 original size:89 final size:89
Alignment explanation
Indices: 17082520--17082698 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
17082510 GATCATATGT
* *
17082520 ATATAAATGATTAACTTACCTTATATAACAAGTACATAGGTTAAACTAATGTGTATAATCAAATT
1 ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
17082585 TACCTAACATATCAAAACGCAATC
66 TACCTAACATATCAAAACGCAATC
17082609 ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
1 ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
17082674 TACCTAACATATCAAAACGCAATC
66 TACCTAACATATCAAAACGCAATC
17082698 A
1 A
17082699 CAATCAAGTG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (89 bp):
ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
TACCTAACATATCAAAACGCAATC
Found at i:17083605 original size:35 final size:35
Alignment explanation
Indices: 17083559--17083628 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
17083549 AAAACATACA
*
17083559 TAGATTCACAATATAACATCTATAATGATTTAAAC
1 TAGATTCACAATATAAAATCTATAATGATTTAAAC
*
17083594 TAGATTCACAATATAAAATTTATAATGATTTAAAC
1 TAGATTCACAATATAAAATCTATAATGATTTAAAC
17083629 ATAATTACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (35 bp):
TAGATTCACAATATAAAATCTATAATGATTTAAAC
Found at i:17087193 original size:12 final size:12
Alignment explanation
Indices: 17087178--17087207 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
17087168 TTTGGGGTAA
17087178 ATGGGAGGTGGG
1 ATGGGAGGTGGG
17087190 ATGGGAGGTGGG
1 ATGGGAGGTGGG
17087202 ATGGGA
1 ATGGGA
17087208 AGAGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.63, T:0.17
Consensus pattern (12 bp):
ATGGGAGGTGGG
Found at i:17087425 original size:21 final size:21
Alignment explanation
Indices: 17087391--17087431 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17087381 GGAGGGAAGT
*
17087391 GGGAAGAAGTAAAAGTTTTGA
1 GGGAAGAAGTAAAAGGTTTGA
17087412 GGGAA-AAGTAAAAAGGTTTG
1 GGGAAGAAGT-AAAAGGTTTG
17087432 GGAGTTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAGAAGTAAAAGGTTTGA
Found at i:17087483 original size:9 final size:9
Alignment explanation
Indices: 17087469--17087505 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17087459 TATAGTTTGA
17087469 TATTCGAAT
1 TATTCGAAT
17087478 TATTCGAAT
1 TATTCGAAT
*
17087487 TATTCGAGT
1 TATTCGAAT
*
17087496 TATTTGAAT
1 TATTCGAAT
17087505 T
1 T
17087506 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17087574 original size:9 final size:9
Alignment explanation
Indices: 17087557--17087587 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17087547 TCGAGTTGAT
17087557 TCGAATAAC
1 TCGAATAAC
*
17087566 TCGATTAAC
1 TCGAATAAC
17087575 TCGAATAAC
1 TCGAATAAC
17087584 TCGA
1 TCGA
17087588 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:17089189 original size:20 final size:21
Alignment explanation
Indices: 17089147--17089199 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
17089137 TATTAATAAA
* *
17089147 AATATTT-TTATTATTCATGT
1 AATATTTATTTTTATTAATGT
17089167 AATATTTATTTTTATTAAT-T
1 AATATTTATTTTTATTAATGT
*
17089187 AAT-TTTAATTTTA
1 AATATTTATTTTTA
17089200 ATATAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.31
20 11 0.38
21 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
AATATTTATTTTTATTAATGT
Found at i:17090705 original size:9 final size:9
Alignment explanation
Indices: 17090691--17090922 Score: 70
Period size: 9 Copynumber: 25.1 Consensus size: 9
17090681 TAAACGATTT
17090691 TTTTTATAA
1 TTTTTATAA
*
17090700 TTTTTATAC
1 TTTTTATAA
**
17090709 TTTTTA-GC
1 TTTTTATAA
*
17090717 TTTTTATGA
1 TTTTTATAA
*
17090726 TTTATTAGAA
1 TTT-TTATAA
*
17090736 TTTATAT-A
1 TTTTTATAA
17090744 TTATTTATAAA
1 TT-TTTAT-AA
*
17090755 TTTTTAGTGA
1 TTTTTA-TAA
17090765 TTTTT-TAA
1 TTTTTATAA
17090773 GTTTTTATAAA
1 -TTTTTAT-AA
* *
17090784 ATTTTAAATA
1 TTTTTATA-A
17090794 TGTTTTATAAA
1 T-TTTTAT-AA
*
17090805 TTGTATCATAA
1 TT-T-TTATAA
*
17090816 TTTAT-TAA
1 TTTTTATAA
17090824 TTTTTATAA
1 TTTTTATAA
*
17090833 TTTTTTGTAA
1 -TTTTTATAA
** *
17090843 AATTTACAA
1 TTTTTATAA
* *
17090852 GTTTTTTTTA
1 -TTTTTATAA
17090862 TTTTTATAA
1 TTTTTATAA
*
17090871 CTTTATATCAA
1 -TTTTTAT-AA
17090882 -TTTTAT--
1 TTTTTATAA
*
17090888 TTTTT-TAT
1 TTTTTATAA
17090896 TTTTTA-ACA
1 TTTTTATA-A
*
17090905 TTTTTATGA
1 TTTTTATAA
17090914 TTTTT-TAA
1 TTTTTATAA
17090922 T
1 T
17090923 GATTTCTATG
Statistics
Matches: 163, Mismatches: 35, Indels: 51
0.65 0.14 0.20
Matches are distributed among these distances:
6 1 0.01
7 4 0.02
8 28 0.17
9 62 0.38
10 44 0.27
11 20 0.12
12 4 0.02
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17090927 original size:20 final size:19
Alignment explanation
Indices: 17090894--17090933 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17090884 TTATTTTTTT
*
17090894 ATTTTTTAACATTTTTATG
1 ATTTTTTAACATTTCTATG
*
17090913 ATTTTTTAATGATTTCTATG
1 ATTTTTTAA-CATTTCTATG
17090933 A
1 A
17090934 GAAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
ATTTTTTAACATTTCTATG
Found at i:17091328 original size:3 final size:3
Alignment explanation
Indices: 17091320--17091354 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17091310 TGCTTTTTCT
17091320 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
17091355 TTTTTNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:17097097 original size:38 final size:39
Alignment explanation
Indices: 17097035--17097108 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
17097025 CACAAAAAAA
*
17097035 TATTTTAAAAATAAAAAATAAAAAAATATATTTTTAAAG
1 TATTTTAAAAATAAAAAATAAAAAAATATATATTTAAAG
*
17097074 TATTTTAAAATTAAAAAAT-AAAAAATATATATTTA
1 TATTTTAAAAATAAAAAATAAAAAAATATATATTTA
17097109 TTATATTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (39 bp):
TATTTTAAAAATAAAAAATAAAAAAATATATATTTAAAG
Found at i:17108359 original size:23 final size:22
Alignment explanation
Indices: 17108332--17108380 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
17108322 AAATATATGA
*
17108332 AATTTGAATTC-ACTTTAAATTTT
1 AATTTG-ATTCAACTGT-AATTTT
17108355 AATTTTGATTCAACTGTAATTTT
1 AA-TTTGATTCAACTGTAATTTT
17108378 AAT
1 AAT
17108381 CTTTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 1 0.04
23 14 0.61
24 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (22 bp):
AATTTGATTCAACTGTAATTTT
Found at i:17109774 original size:2 final size:2
Alignment explanation
Indices: 17109769--17109801 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17109759 AAAATTGAAC
*
17109769 AT AT AT AT AT GT 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 AT AT AT A
17109802 ATAGGACACG
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17110857 original size:6 final size:6
Alignment explanation
Indices: 17110846--17110870 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17110836 CAATATAATA
17110846 TCCATT TCCATT TCCATT TCCATT T
1 TCCATT TCCATT TCCATT TCCATT T
17110871 TCAACCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TCCATT
Found at i:17117040 original size:30 final size:30
Alignment explanation
Indices: 17117004--17117061 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
17116994 AAACCTTTTA
*
17117004 TTTT-CCCTCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCT-AAAACTTTTACTCCCTTCCAC
*
17117034 TTTTCCCCTAAAACTTTTATTCCCTTCC
1 TTTTCCCCTAAAACTTTTACTCCCTTCC
17117062 CATCCCACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCAC
Found at i:17119144 original size:18 final size:18
Alignment explanation
Indices: 17119121--17119155 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17119111 ATACATATAC
*
17119121 TTTTATAATTTATAATTT
1 TTTTATAATTTAAAATTT
*
17119139 TTTTATATTTTAAAATT
1 TTTTATAATTTAAAATT
17119156 ATATATATTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATAATTTAAAATTT
Found at i:17120423 original size:18 final size:18
Alignment explanation
Indices: 17120400--17120434 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17120390 ATACATATAC
*
17120400 TTTTATAATTTATAATTT
1 TTTTATAATTTAAAATTT
*
17120418 TTTTATATTTTAAAATT
1 TTTTATAATTTAAAATT
17120435 ATATATATTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATAATTTAAAATTT
Found at i:17121278 original size:22 final size:22
Alignment explanation
Indices: 17121231--17121280 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
17121221 AAAAAAATGA
* *
17121231 ATTTATAAGTGAATATCTTGTC
1 ATTTATAAGAGAATATATTGTC
*
17121253 ATTTATAATGAGAATATATT-TT
1 ATTTATAA-GAGAATATATTGTC
17121275 ATTTAT
1 ATTTAT
17121281 TATTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTATAAGAGAATATATTGTC
Found at i:17136852 original size:38 final size:38
Alignment explanation
Indices: 17136784--17136899 Score: 144
Period size: 38 Copynumber: 3.1 Consensus size: 38
17136774 AACTTTTATT
* **
17136784 ACACCGGCAATAA-CCTGCTAGGCACCAAGCCTGAATA
1 ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
** ** *
17136821 ACATTGGCACTAAGCCTGCTAGGCATAAAGCCCAAATT
1 ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
*
17136859 ACACCGGCACCAAGCCTGCTAGGCATAAAGCCTGAATA
1 ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
17136897 ACA
1 ACA
17136900 GTATAATTCA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
37 10 0.16
38 54 0.84
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (38 bp):
ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
Found at i:17143494 original size:50 final size:50
Alignment explanation
Indices: 17143383--17143629 Score: 178
Period size: 50 Copynumber: 4.8 Consensus size: 50
17143373 ATTTGGGGAA
* * *
17143383 AGAGATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCA-C--CGA-G--ATG
* *
17143439 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAGATG
* *** * * * *
17143489 AGAGGTCCCCCATAAGACCATGTATGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAGATG
* * * * * * *
17143539 AGA-ACTCCCATTTAAGACCATATATTGGATATGGTATTGGCA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCG-AGATG
* * *
17143588 AAACATCCCATGTAAGACCATGTCTCGGACATGGCT-TTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGG-TATTGGCA
17143630 TGTTATTATC
Statistics
Matches: 157, Mismatches: 30, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 79 0.50
52 1 0.01
53 2 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAGATG
Found at i:17154608 original size:25 final size:25
Alignment explanation
Indices: 17154575--17154648 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
17154565 CGAGCTACAT
* * *
17154575 AACGGTAAGCTCCTTCGAGCTGAAC
1 AACGATAAGCTCATGCGAGCTGAAC
* **
17154600 AACTATAAGCTCATGCGAGCTGAGT
1 AACGATAAGCTCATGCGAGCTGAAC
**
17154625 AACGATAAGCTCATATGAGCTGAA
1 AACGATAAGCTCATGCGAGCTGAA
17154649 ATCAGTAACC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (25 bp):
AACGATAAGCTCATGCGAGCTGAAC
Found at i:17158732 original size:19 final size:19
Alignment explanation
Indices: 17158708--17158746 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
17158698 CCAATTGTCA
17158708 GCCAAAAATAATTAAACAT
1 GCCAAAAATAATTAAACAT
17158727 GCCAAAAATAATTAAACAT
1 GCCAAAAATAATTAAACAT
17158746 G
1 G
17158747 TCAATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (19 bp):
GCCAAAAATAATTAAACAT
Found at i:17162083 original size:61 final size:61
Alignment explanation
Indices: 17161916--17162098 Score: 149
Period size: 61 Copynumber: 3.0 Consensus size: 61
17161906 TTATTCGTCT
* * * * * *
17161916 AATAACAAAATTAGTCCTCTAATATTTAC-ACATTCTATCAATTT-GATCCTAAATAT-AAAAA
1 AATAATAAATTTAGCCCTC-AATATTTACAAAATT-TATCACTTTAG-TCCTAACTATAAAAAA
* * * * ** * *
17161977 ATTCAACAAATTTAGCCCTCAGTGTTTACAAAATTTATCTGTTTAGTTCTAATTATAAAAAA
1 AAT-AATAAATTTAGCCCTCAATATTTACAAAATTTATCACTTTAGTCCTAACTATAAAAAA
* *
17162039 AATAATAAATTTGGCCCTCAATATTTACAAAATCTT-TCACTTTAGTCCTAACTCTAAAAA
1 AATAATAAATTTAGCCCTCAATATTTACAAAAT-TTATCACTTTAGTCCTAACTATAAAAA
17162099 TAAAAAAAAT
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
61 69 0.71
62 28 0.29
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (61 bp):
AATAATAAATTTAGCCCTCAATATTTACAAAATTTATCACTTTAGTCCTAACTATAAAAAA
Found at i:17162597 original size:60 final size:60
Alignment explanation
Indices: 17162463--17162598 Score: 139
Period size: 60 Copynumber: 2.2 Consensus size: 60
17162453 TTAAAAATAT
* * * ** ** *
17162463 ATTTTTAAATTTTTTAGAGTTAGGACTGAATTGACTGATTTTGTAAATGTTGAGAGCTGA
1 ATTTTTAAATTTTTTAGAATTAGGACTAAAATGACAAATTTTGTAAACATTGAGAGCTAA
* * * *
17162523 ATTTATTGATTTTTTTAGAATTA-GACTAAAATGACAAATTTTTTAAACATTGAGGGCTAA
1 ATTT-TTAAATTTTTTAGAATTAGGACTAAAATGACAAATTTTGTAAACATTGAGAGCTAA
17162583 ATTTGTTAAATTTTTT
1 ATTT-TTAAATTTTTT
17162599 TTATATTTGG
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
60 45 0.75
61 15 0.25
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (60 bp):
ATTTTTAAATTTTTTAGAATTAGGACTAAAATGACAAATTTTGTAAACATTGAGAGCTAA
Found at i:17165389 original size:3 final size:3
Alignment explanation
Indices: 17165381--17165463 Score: 72
Period size: 3 Copynumber: 30.0 Consensus size: 3
17165371 TTCCATTTTC
*
17165381 TCT TCT TCT T-T TCT TCT TCT TC- TCC TCT TCT TCT T-T TCT TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
17165425 T-T TCT TCT TC- TCA TAT TCT TCT TTT TC- TCT TGT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
17165464 ACCGCCCAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
2 14 0.21
3 52 0.79
ACGTcount: A:0.02, C:0.29, G:0.01, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:17165394 original size:8 final size:8
Alignment explanation
Indices: 17165378--17165463 Score: 70
Period size: 8 Copynumber: 10.5 Consensus size: 8
17165368 TCCTTCCATT
*
17165378 TTCTCTTC
1 TTCTTTTC
17165386 TTCTTTTC
1 TTCTTTTC
17165394 TTCTTCTTC
1 TTCTT-TTC
* *
17165403 TCCTCTTC
1 TTCTTTTC
17165411 TTCTTTTC
1 TTCTTTTC
17165419 TTCTTTT-
1 TTCTTTTC
17165426 TTCTTCTTC
1 TTCTT-TTC
*
17165435 -TCATATTC
1 TTC-TTTTC
17165443 TTCTTTT-
1 TTCTTTTC
17165450 TCTCTTGTTC
1 T-TCTT-TTC
17165460 TTCT
1 TTCT
17165464 ACCGCCCAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
7 6 0.10
8 42 0.67
9 14 0.22
10 1 0.02
ACGTcount: A:0.02, C:0.29, G:0.01, T:0.67
Consensus pattern (8 bp):
TTCTTTTC
Found at i:17165400 original size:14 final size:14
Alignment explanation
Indices: 17165376--17165463 Score: 65
Period size: 14 Copynumber: 6.1 Consensus size: 14
17165366 AGTCCTTCCA
17165376 TTTTC-TCTTCTTC
1 TTTTCTTCTTCTTC
17165389 TTTTCTTCTTCTTC
1 TTTTCTTCTTCTTC
17165403 TCCTCTTCTTCTTTTCTTC
1 T--T-TTCTTC--TTCTTC
17165422 TTTT-TTCTTCTTC
1 TTTTCTTCTTCTTC
** *
17165435 TCATATTCTTCTT-
1 TTTTCTTCTTCTTC
*
17165448 TTTCTCTTGTTCTTC
1 TTT-TCTTCTTCTTC
17165463 T
1 T
17165464 ACCGCCCAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
13 14 0.23
14 25 0.42
15 4 0.07
16 3 0.05
17 7 0.12
19 7 0.12
ACGTcount: A:0.02, C:0.28, G:0.01, T:0.68
Consensus pattern (14 bp):
TTTTCTTCTTCTTC
Found at i:17165455 original size:11 final size:11
Alignment explanation
Indices: 17165381--17165449 Score: 77
Period size: 11 Copynumber: 6.1 Consensus size: 11
17165371 TTCCATTTTC
17165381 TCTTCTTCTTT
1 TCTTCTTCTTT
17165392 TCTTCTTCTTCT
1 TCTTCTTCTT-T
17165404 CCTCTTCTTCTTT
1 --TCTTCTTCTTT
17165417 TCTTCTT-TTT
1 TCTTCTTCTTT
**
17165427 TCTTCTTCTCA
1 TCTTCTTCTTT
*
17165438 TATTCTTCTTT
1 TCTTCTTCTTT
17165449 T
1 T
17165450 TCTCTTGTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 10 0.20
11 27 0.55
12 1 0.02
13 1 0.02
14 10 0.20
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (11 bp):
TCTTCTTCTTT
Found at i:17167998 original size:1 final size:1
Alignment explanation
Indices: 17167992--17168021 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
17167982 CAACCCTTTA
17167992 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17168022 GAGTTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17168639 original size:59 final size:59
Alignment explanation
Indices: 17168547--17168666 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
17168537 TTACATTGTT
* *
17168547 ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTTGAAATTCATGCTTAGACATCTCA
1 ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACATCTCA
* *
17168606 ATTCTCAGCTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACGTCTCA
1 ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACATCTCA
17168665 AT
1 AT
17168667 CTTCGTAGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.40
Consensus pattern (59 bp):
ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACATCTCA
Found at i:17169566 original size:16 final size:16
Alignment explanation
Indices: 17169545--17169577 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17169535 AAATCTTTTT
17169545 TCTTGTAATTTCTATA
1 TCTTGTAATTTCTATA
17169561 TCTTGTAATTTCTATA
1 TCTTGTAATTTCTATA
17169577 T
1 T
17169578 TTTTGAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (16 bp):
TCTTGTAATTTCTATA
Found at i:17170438 original size:42 final size:42
Alignment explanation
Indices: 17170381--17170595 Score: 200
Period size: 42 Copynumber: 5.1 Consensus size: 42
17170371 TTTGATTATG
* * *
17170381 CACTTACGTGTCAGTATATTTTCTTCAGTATATCCGATGATA
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * *
17170423 CACTTATGTGACAGTATATTTTCTTCGATATATCCAATGATA
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * * * *
17170465 CATTTATGTGCCAGTATATTTTCTTTGGTACATCCGATAATG
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * * ** * *
17170507 CACTTACGTGCCAGCATAATTGATTCGGTTTATCCGATGATG
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * *
17170549 CAC-TATGTGTTCCAGTATATTTCCTTCGGTTTA-CTCGATGATG
1 CACTTATGTG--CCAGTATATTTTCTTCGGTATATC-CGATGATA
17170592 CACT
1 CACT
17170596 GCGGTGCCAG
Statistics
Matches: 141, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
41 5 0.04
42 107 0.76
43 29 0.21
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (42 bp):
CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
Found at i:17179062 original size:19 final size:18
Alignment explanation
Indices: 17179018--17179078 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 18
17179008 ATTAAAAAAA
17179018 TAAAAAATTATTAAATTT
1 TAAAAAATTATTAAATTT
17179036 TAGAAAAATTATTAAATTT
1 TA-AAAAATTATTAAATTT
* *
17179055 TAATAAAAATATAAAAATTT
1 TAA-AAAATTAT-TAAATTT
17179075 TAAA
1 TAAA
17179079 TTTATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 3 0.08
19 26 0.68
20 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAAAATTATTAAATTT
Found at i:17179070 original size:27 final size:27
Alignment explanation
Indices: 17179039--17179095 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
17179029 TAAATTTTAG
17179039 AAAAATTATTAAATTTTAATAAAAA-TAT
1 AAAAATT-TTAAA-TTTAATAAAAATTAT
*
17179067 AAAAATTTTAAATTTATTAAAAATTAT
1 AAAAATTTTAAATTTAATAAAAATTAT
17179094 AA
1 AA
17179096 TTTTTAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.37
27 10 0.37
28 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AAAAATTTTAAATTTAATAAAAATTAT
Found at i:17179078 original size:9 final size:10
Alignment explanation
Indices: 17178987--17179093 Score: 57
Period size: 10 Copynumber: 11.4 Consensus size: 10
17178977 ACCCATGCTC
17178987 TTATTAAAAA
1 TTATTAAAAA
*
17178997 TTA-GAAAAA
1 TTATTAAAAA
**
17179006 AAATTAAAAA
1 TTATTAAAAA
* *
17179016 -AATAAAAAA
1 TTATTAAAAA
**
17179025 TTATTAAATT
1 TTATTAAAAA
*
17179035 TTA-GAAAAA
1 TTATTAAAAA
**
17179044 TTATTAAATT
1 TTATTAAAAA
*
17179054 TTAATAAAAA
1 TTATTAAAAA
17179064 -TA-TAAAAA
1 TTATTAAAAA
*
17179072 TT-TT-AAAT
1 TTATTAAAAA
17179080 TTATTAAAAA
1 TTATTAAAAA
17179090 TTAT
1 TTAT
17179094 AATTTTTAAG
Statistics
Matches: 70, Mismatches: 20, Indels: 14
0.67 0.19 0.13
Matches are distributed among these distances:
8 11 0.16
9 26 0.37
10 33 0.47
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:17179080 original size:46 final size:44
Alignment explanation
Indices: 17179009--17179102 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 44
17178999 AGAAAAAAAA
17179009 TTAAAAAAATAAAAAATTATTAAATTT-TAGAAAAATTATTAAATT
1 TTAAAAAAATAAAAAATTATTAAATTTAT-GAAAAATTA-TAAATT
* *
17179054 TTAATAAAAATATAAAAATT-TTAAATTTATTAAAAATTATAATTT
1 TTAA-AAAAATA-AAAAATTATTAAATTTATGAAAAATTATAAATT
17179099 TTAA
1 TTAA
17179103 GGGGTCGTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
45 13 0.30
46 23 0.52
47 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (44 bp):
TTAAAAAAATAAAAAATTATTAAATTTATGAAAAATTATAAATT
Found at i:17179264 original size:49 final size:48
Alignment explanation
Indices: 17179142--17179264 Score: 110
Period size: 48 Copynumber: 2.5 Consensus size: 48
17179132 AAAAATTTAC
* *
17179142 AATTTTTTATATTTTTATGATTTTTATAAAAAAATTTCTAAAGTTTAATA
1 AATTTTTTATTTTTTTAT-ATTTTT-TAAAAAAATTTCTAAAATTTAATA
* * **
17179192 AA-TTTTAATTTTTTTCGTA-TTTTTATTAAAA-TT-TAATAATTTAATA
1 AATTTTTTATTTTTTT-ATATTTTTTAAAAAAATTTCTAA-AATTTAATA
17179238 AATTTTTTTATTTTTTTATAATTTTTT
1 AA-TTTTTTATTTTTTTAT-ATTTTTT
17179265 TTCTAATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
45 3 0.05
46 12 0.20
47 7 0.12
48 17 0.29
49 17 0.29
50 3 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (48 bp):
AATTTTTTATTTTTTTATATTTTTTAAAAAAATTTCTAAAATTTAATA
Found at i:17179274 original size:22 final size:21
Alignment explanation
Indices: 17179231--17179280 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
17179221 AATTTAATAA
* *
17179231 TTTAATAA-ATTTTTTTATTT
1 TTTAATAATTTTTTTTTAATT
*
17179251 TTTTATAATTTTTTTTCTAATT
1 TTTAATAATTTTTTTT-TAATT
17179273 TTTAATAA
1 TTTAATAA
17179281 AGCCAAGGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTAATAATTTTTTTTTAATT
Found at i:17179384 original size:89 final size:89
Alignment explanation
Indices: 17179291--17179460 Score: 234
Period size: 89 Copynumber: 1.9 Consensus size: 89
17179281 AGCCAAGGGA
** * * * *
17179291 TTAATTACTTTTTTTTTAAAA-GTTTGAGGGTTTTTTTTATGCATTTTGAAAGTTCAAGTACCCA
1 TTAATTAC-TTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
* *
17179355 ATTGAATGTAAAAAAAAGTAGGGGC
65 AATGAATGCAAAAAAAAGTAGGGGC
*
17179380 TTAATTGCTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
1 TTAATTACTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
*
17179445 ATGAGTGCAAAAAAAA
66 ATGAATGCAAAAAAAA
17179461 TGCAAAAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
88 10 0.14
89 60 0.86
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (89 bp):
TTAATTACTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
ATGAATGCAAAAAAAAGTAGGGGC
Found at i:17179482 original size:89 final size:88
Alignment explanation
Indices: 17179290--17179483 Score: 217
Period size: 89 Copynumber: 2.2 Consensus size: 88
17179280 AAGCCAAGGG
** * * * *
17179290 ATTAATTACTTTTTTTTTAAAAGTTTGAGGGTTTTTTTTATGCATTTTGAAAGTTCAAGTACCCA
1 ATTAATTAC-TTTTTTGAAAAAGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
* * * ****
17179355 ATTGAATGTAAAAAAAAGTAGGGG
65 AATGAATGCAAAAAAAAGCAAAAA
* *
17179379 CTTAATTGCTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
1 ATTAATTACTTTTTTGAAAAA-GTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
*
17179444 AATGAGTGCAAAAAAAATGCAAAAA
65 AATGAATGCAAAAAAAA-GCAAAAA
17179469 ATTAATTACTTTTTT
1 ATTAATTACTTTTTT
17179484 TTTTTTAAGT
Statistics
Matches: 85, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
88 10 0.12
89 60 0.71
90 15 0.18
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (88 bp):
ATTAATTACTTTTTTGAAAAAGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
ATGAATGCAAAAAAAAGCAAAAA
Found at i:17181042 original size:243 final size:241
Alignment explanation
Indices: 17180673--17181308 Score: 735
Period size: 241 Copynumber: 2.6 Consensus size: 241
17180663 TCCCCCATTT
* * * *
17180673 TCTTCATTTTTATTTCTCAATTGTTTATTTC-A-CCGTCT-GTTCGTGGGATTTGGTTTTCCATT
1 TCTTCATTTTT-TTTCTCAATTGTTAATTTCAATGCG-CTAGTTCGTGGAATTTGGTTTTTCATT
** * *
17180735 TCTGA-CAGTATTTAGGGCAAAAATAGGATCGTAGAATTCTAAATTTATATTCAATTAAATCAGC
64 TC-GAGTTGTATTTAGGGGAAAAAAAGGATCGTAGAA-TCTAAATTTATATTCAATTAAATCAGC
* * * * *
17180799 CTAACATTTTTGTTAATAATTGTTTTTAATAAAGTTTCGTAGCTAATAAATTTATTAATCTGAAT
127 CTAACATTTTTGTTAATTATTGTTTTTAAT----TTCCGTACCTAACAAATTGATTAATCTGAAT
* *
17180864 TA-TTATTTATT-TTGCGAAATTTG-A-T-A-AAAA-ATTATGTTGTTTTTTCTTTG
188 AAGTTATTTATTATT---AAATTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
* *
17180914 TCTTCATTTTTGTTTCTCAATTGTTAATTCCAATGCGCTAGTTCGTGGAATTAGGTTTTTCATTT
1 TCTTCATTTTT-TTTCTCAATTGTTAATTTCAATGCGCTAGTTCGTGGAATTTGGTTTTTCATTT
* * * *
17180979 CGAGTTGTATATAGGGGAAAAGAAAAGATCGTAGAATCTAAATTTATAGTCAATTATATCAGCCT
65 CGAGTTGTATTTAGGGGAAAA-AAAGGATCGTAGAATCTAAATTTATATTCAATTAAATCAGCCT
*
17181044 AACATTTTTGTTAATTATTG--TTTCATTTCCGTACCTAACAAATTGATTAATCTGAATAAGTTA
129 AACATTTTTGTTAATTATTGTTTTTAATTTCCGTACCTAACAAATTGATTAATCTGAATAAGTTA
* *
17181107 TTTATTATTTATTTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
194 TTTATTATTAAATTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
* * * *
17181155 TCTTCATTTTTTCTTCTCAATTATTAATTTCAATGCGCCATTTTGTGGAATTTGGTTTTTCATTT
1 TCTTCATTTTTT-TTCTCAATTGTTAATTTCAATGCGCTAGTTCGTGGAATTTGGTTTTTCATTT
* *
17181220 TG-GATTGTATTTAGGGGGAAAAAATAGGATCGTGGAAT-TGAAATTTATATTCAATTAAATCAG
65 CGAG-TTGTATTTA-GGGGAAAAAA-AGGATCGTAGAATCT-AAATTTATATTCAATTAAATCAG
17181283 CCTAACATTTTTGTTAATTATTGTTT
126 CCTAACATTTTTGTTAATTATTGTTT
17181309 GTTTCTAATC
Statistics
Matches: 339, Mismatches: 37, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
236 5 0.01
237 29 0.09
238 10 0.03
239 3 0.01
240 6 0.02
241 121 0.36
242 68 0.20
243 84 0.25
244 13 0.04
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (241 bp):
TCTTCATTTTTTTTCTCAATTGTTAATTTCAATGCGCTAGTTCGTGGAATTTGGTTTTTCATTTC
GAGTTGTATTTAGGGGAAAAAAAGGATCGTAGAATCTAAATTTATATTCAATTAAATCAGCCTAA
CATTTTTGTTAATTATTGTTTTTAATTTCCGTACCTAACAAATTGATTAATCTGAATAAGTTATT
TATTATTAAATTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
Found at i:17193205 original size:276 final size:276
Alignment explanation
Indices: 17192712--17193262 Score: 1021
Period size: 276 Copynumber: 2.0 Consensus size: 276
17192702 CTGCATTTTA
*
17192712 GTTGTTATCCTACTGCTGCTGGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
1 GTTGTTATCCTACTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
*
17192777 TAATAAATCCAAGTGTTGCTAATTTCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
66 TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
17192842 GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
131 GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
*
17192907 GTACATGAATTTTGATTTTGTGCAGTTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
196 GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
17192972 ACACTAACACTGTTTG
261 ACACTAACACTGTTTG
*
17192988 GTTGTTATCCTATTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
1 GTTGTTATCCTACTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
17193053 TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
66 TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
* *
17193118 GAACTGAATTTTTTCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
131 GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
*
17193183 GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACATA
196 GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
* *
17193248 GCACTGACACTGTTT
261 ACACTAACACTGTTT
17193263 TCGACATAAC
Statistics
Matches: 266, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
276 266 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (276 bp):
GTTGTTATCCTACTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
ACACTAACACTGTTTG
Found at i:17193399 original size:31 final size:31
Alignment explanation
Indices: 17193364--17193427 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
17193354 AATGTTTACG
*
17193364 ATTGAATCAATATCAAAGTTTCATATATATA
1 ATTGAATCAAAATCAAAGTTTCATATATATA
* * * *
17193395 ATTGAATTAAAATCAAATTTTCATGTGTATA
1 ATTGAATCAAAATCAAAGTTTCATATATATA
17193426 AT
1 AT
17193428 ACTATCACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTGAATCAAAATCAAAGTTTCATATATATA
Found at i:17200188 original size:4 final size:4
Alignment explanation
Indices: 17200179--17200224 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
17200169 ATATTAGAAT
*
17200179 ATAC ATAC ATAC ATAC ATAC ATAC ATAA ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
17200225 TAATGTTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:17203350 original size:16 final size:16
Alignment explanation
Indices: 17203329--17203360 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17203319 ATTTTACTAT
17203329 ATAGTGGTTCATAAAA
1 ATAGTGGTTCATAAAA
17203345 ATAGTGGTTCATAAAA
1 ATAGTGGTTCATAAAA
17203361 GGTTGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATAGTGGTTCATAAAA
Found at i:17205810 original size:22 final size:24
Alignment explanation
Indices: 17205785--17205838 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
17205775 TTATAAATTC
17205785 AATTTAA-AATATATAAT-ACAAT
1 AATTTAAGAATATATAATAACAAT
* *
17205807 AATTTCAAGCATATTTAATAACAAT
1 AATTT-AAGAATATATAATAACAAT
*
17205832 AGTTTAA
1 AATTTAA
17205839 TCATCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
23 2 0.08
24 10 0.38
25 9 0.35
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (24 bp):
AATTTAAGAATATATAATAACAAT
Found at i:17207209 original size:183 final size:183
Alignment explanation
Indices: 17206894--17207259 Score: 543
Period size: 183 Copynumber: 2.0 Consensus size: 183
17206884 TATTTTCCTT
* * *
17206894 CGTTTTCGCACGCGGTTAGTGCTTGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
1 CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
* * * * * * **
17206959 TCTCTTAACGACTTAAGTGGTAATGTTTTTTCTCTGCGATTTGGACATAGGGGGAGGCTTGGACT
66 TCTCTTAACAACTGAAGTGATAATGTTTTTTCTCTACGATTTGGACATAAGGAGAGGCTCAGACT
*
17207024 GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAATGGAGGGTTATCATTGG
131 GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCATTGG
** *
17207077 CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTTTGTTTCTGTCATGAA
1 CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
* * * *
17207142 TCTCTTAACAACTGAAGTGATAATGTTTTTTCTTTATGATTTGGGCGTAAGGAGAGGCTCAGACT
66 TCTCTTAACAACTGAAGTGATAATGTTTTTTCTCTACGATTTGGACATAAGGAGAGGCTCAGACT
* *
17207207 GGTGAATTCGGTGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCGTTGG
131 GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCATTGG
17207260 TGGTAAGTTG
Statistics
Matches: 162, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
183 162 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (183 bp):
CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
TCTCTTAACAACTGAAGTGATAATGTTTTTTCTCTACGATTTGGACATAAGGAGAGGCTCAGACT
GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCATTGG
Found at i:17221952 original size:17 final size:16
Alignment explanation
Indices: 17221918--17221970 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
17221908 GATTTGTTAT
17221918 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17221934 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
17221951 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17221967 TACA
1 TACA
17221971 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17222228 original size:20 final size:20
Alignment explanation
Indices: 17222199--17222247 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17222189 CAAACAATAA
*
17222199 ATATCTATACTT-TGAACATT
1 ATATCGATACTTATGAA-ATT
*
17222219 ATATCGATACTTATTAAATT
1 ATATCGATACTTATGAAATT
17222239 -TATCGATAC
1 ATATCGATAC
17222248 CAATTTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 14 0.54
21 3 0.12
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
ATATCGATACTTATGAAATT
Found at i:17222659 original size:5 final size:5
Alignment explanation
Indices: 17222649--17222673 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
17222639 CATAAGCTCG
17222649 GGCCC GGCCC GGCCC GGCCC GGCCC
1 GGCCC GGCCC GGCCC GGCCC GGCCC
17222674 CTTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.40, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:17222714 original size:11 final size:11
Alignment explanation
Indices: 17222694--17222813 Score: 71
Period size: 11 Copynumber: 11.5 Consensus size: 11
17222684 ATAAATACCA
17222694 AAAAATTATTTT
1 AAAAA-TATTTT
17222706 AAAAATATTTT
1 AAAAATATTTT
*
17222717 --TAA-A--TT
1 AAAAATATTTT
17222723 AAAAA-ATTTT
1 AAAAATATTTT
*
17222733 ACAAAGTATTTT
1 A-AAAATATTTT
17222745 AAAAATATTTT
1 AAAAATATTTT
*
17222756 --AAA-A-TTA
1 AAAAATATTTT
* *
17222763 AAAAAAATTTA
1 AAAAATATTTT
17222774 AAAAAGTATTTT
1 AAAAA-TATTTT
*
17222786 AAAAGTATTTT
1 AAAAATATTTT
*
17222797 AAAAGTATTTT
1 AAAAATATTTT
*
17222808 TAAAAT
1 AAAAAT
17222814 TAAAAAAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 5 0.06
9 8 0.09
10 4 0.05
11 47 0.54
12 19 0.22
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:17222747 original size:39 final size:40
Alignment explanation
Indices: 17222693--17222800 Score: 155
Period size: 41 Copynumber: 2.7 Consensus size: 40
17222683 AATAAATACC
* *
17222693 AAAAAATTATTTTAAAAATATTTTTAAATT-AAAAAATTT
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTT
* *
17222732 TACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTT
1 AAAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAAATTT
*
17222773 AAAAAAGTATTTTAAAAGTATTTTAAAA
1 AAAAAAGTATTTTAAAAATATTTTAAAA
17222801 GTATTTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 26 0.43
41 34 0.57
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (40 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTT
Found at i:17222829 original size:52 final size:53
Alignment explanation
Indices: 17222728--17222829 Score: 154
Period size: 52 Copynumber: 1.9 Consensus size: 53
17222718 AAATTAAAAA
**
17222728 ATTTTACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTTAAAAAAGT
1 ATTTTACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATAAAAAAAAGT
*
17222781 ATTTTA-AAAGTATTTTAAAAGTATTTTTAAAATT-AAAAAAATAAAAAAA
1 ATTTTACAAAGTATTTTAAAAATA-TTTTAAAATTAAAAAAAATAAAAAAA
17222830 TAAAATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 29 0.64
53 16 0.36
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (53 bp):
ATTTTACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATAAAAAAAAGT
Found at i:17227293 original size:2 final size:2
Alignment explanation
Indices: 17227286--17227320 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17227276 ATCAATTAAA
17227286 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17227321 ACTTAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17227733 original size:7 final size:7
Alignment explanation
Indices: 17227721--17227745 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17227711 AGTTGAGGGT
17227721 GGAAGAG
1 GGAAGAG
17227728 GGAAGAG
1 GGAAGAG
17227735 GGAAGAG
1 GGAAGAG
17227742 GGAA
1 GGAA
17227746 AAGAAGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GGAAGAG
Found at i:17239914 original size:24 final size:23
Alignment explanation
Indices: 17239887--17239952 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 23
17239877 CCCTTCTATT
17239887 TTATTTTATTTATTATTTCTTATA
1 TTATTTTATTTATTA-TTCTTATA
17239911 TTA-TTTATTT-TTATT-TTACTA
1 TTATTTTATTTATTATTCTTA-TA
17239932 --ATTTTATTTATTATTCTTATA
1 TTATTTTATTTATTATTCTTATA
17239953 CTTAGATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 11 0.29
22 6 0.16
23 7 0.18
24 3 0.08
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTTTATTTATTATTCTTATA
Found at i:17239954 original size:24 final size:24
Alignment explanation
Indices: 17239889--17239963 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 24
17239879 CTTCTATTTT
*
17239889 ATTTTATTTATTATTTCTTATA-TT
1 ATTTTATTTATTA-TTCTTATACTA
17239913 A-TTTATTT-TTA-T-TT-TACTA
1 ATTTTATTTATTATTCTTATACTA
17239932 ATTTTATTTATTATTCTTATACTTA
1 ATTTTATTTATTATTCTTATAC-TA
17239957 GATTTTA
1 -ATTTTA
17239964 AATTTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 8 0.19
21 3 0.07
22 4 0.10
23 9 0.21
24 4 0.10
25 2 0.05
26 6 0.14
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (24 bp):
ATTTTATTTATTATTCTTATACTA
Found at i:17240090 original size:24 final size:22
Alignment explanation
Indices: 17240056--17240119 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
17240046 TATCATTTAG
*
17240056 TTTATTATTATTATTTTTTCCGT
1 TTTATTTTTATTATTTTTT-CGT
* *
17240079 TTTATTTTTTATT-TATCTTTCTT
1 TTTA-TTTTTATTAT-TTTTTCGT
17240102 TTTATTTTT-TTATTTTTT
1 TTTATTTTTATTATTTTTT
17240120 AAACTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 6 0.18
22 6 0.18
23 11 0.32
24 11 0.32
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTATTTTTATTATTTTTTCGT
Found at i:17244937 original size:40 final size:40
Alignment explanation
Indices: 17244884--17245022 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
17244874 AACACACTAG
* *
17244884 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * * *
17244924 TTTGACACACAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * * *
17244962 TTAG-CACCCAATGCCTCATC-GATTAATCCAAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATCCGAAGTAATAA
* *
17245001 ATTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
17245023 ACTCGAAGTC
Statistics
Matches: 76, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
36 1 0.01
37 22 0.29
38 5 0.07
39 5 0.07
40 43 0.57
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
Found at i:17245474 original size:24 final size:23
Alignment explanation
Indices: 17245446--17245491 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
17245436 GGCTTTCTCT
17245446 TTCCTTTCTTTCCTTTTTCTTTTC
1 TTCCTTTCTTT-CTTTTTCTTTTC
17245470 TTCCTTTCTTTCTTTTTCTTTT
1 TTCCTTTCTTTCTTTTTCTTTT
17245492 TGTTTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (23 bp):
TTCCTTTCTTTCTTTTTCTTTTC
Found at i:17245482 original size:4 final size:4
Alignment explanation
Indices: 17245443--17245517 Score: 55
Period size: 4 Copynumber: 18.2 Consensus size: 4
17245433 TGTGGCTTTC
* * *
17245443 TCTT TCCTT TCTT TCCT T-TT TCTTT TCTT CCTT TCTT TCTT T-TT CTTTT
1 TCTT T-CTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT TCTT TCTT -TCTT
* *
17245492 TGTT TCATT TCTA TCTT TCTT TCTT T
1 TCTT TC-TT TCTT TCTT TCTT TCTT T
17245518 TTATTTATTC
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
3 4 0.07
4 39 0.68
5 14 0.25
ACGTcount: A:0.03, C:0.24, G:0.01, T:0.72
Consensus pattern (4 bp):
TCTT
Found at i:17246522 original size:15 final size:15
Alignment explanation
Indices: 17246502--17246530 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17246492 AATAATATTA
17246502 ATAATAATGATAATG
1 ATAATAATGATAATG
17246517 ATAATAATGATAAT
1 ATAATAATGATAAT
17246531 TTAAAGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
ATAATAATGATAATG
Found at i:17251204 original size:6 final size:7
Alignment explanation
Indices: 17251177--17251202 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17251167 ATATTTATTT
17251177 ATTTTTA
1 ATTTTTA
17251184 ATTTTTA
1 ATTTTTA
17251191 ATTTTTA
1 ATTTTTA
17251198 ATTTT
1 ATTTT
17251203 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Found at i:17251246 original size:26 final size:26
Alignment explanation
Indices: 17251210--17251270 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
17251200 TTTAAAATAC
* *
17251210 TTTTAAAAT-AATTTTTATTTTTTTAT
1 TTTTAAAATAAATTTTTA-ATGTTTAT
17251236 TTTTAAAATAAATTTTTAATGTTTAT
1 TTTTAAAATAAATTTTTAATGTTTAT
*
17251262 TTTAAAAAT
1 TTTTAAAAT
17251271 GGGACAGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTAAAATAAATTTTTAATGTTTAT
Found at i:17273046 original size:28 final size:27
Alignment explanation
Indices: 17273003--17273071 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
17272993 AAATAAAAAA
*
17273003 TTACCAAAATGT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTAT
17273030 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
17273057 TTACCAAAATATATA
1 TTACCAAAATATATA
17273072 AAAAAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:17273158 original size:27 final size:27
Alignment explanation
Indices: 17273128--17273194 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
17273118 AAGGAAGCAG
17273128 GTTGGCGGCACCAAACAAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
****
17273155 GTTGGCGGCACCAGTGGAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
17273182 GTTGGCGGCACCA
1 GTTGGCGGCACCA
17273195 CCCTTGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.16
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGATCCCT
Found at i:17273264 original size:18 final size:17
Alignment explanation
Indices: 17273241--17273318 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 17
17273231 GAAGGAGAGG
17273241 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
17273259 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
17273276 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
17273292 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
17273310 GGAAAGAAA
1 GG-AAGAAA
17273319 AGGAAAGGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
15 9 0.18
16 4 0.08
17 4 0.08
18 20 0.39
19 14 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:17273274 original size:10 final size:10
Alignment explanation
Indices: 17273243--17273314 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
17273233 AGGAGAGGGG
*
17273243 AAGAAGAAGA
1 AAGAAAAAGA
17273253 AAGAAAGGAAGA
1 AAGAAA--AAGA
17273265 AAGAAAAAGA
1 AAGAAAAAGA
* *
17273275 AGGAAAAGGA
1 AAGAAAAAGA
17273285 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
17273299 AAGAAAAAGA
1 AAGAAAAAGA
*
17273309 AGGAAA
1 AAGAAA
17273315 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:17273274 original size:22 final size:23
Alignment explanation
Indices: 17273243--17273325 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
17273233 AGGAGAGGGG
*
17273243 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
17273265 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
17273287 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
*
17273313 AAGAAAAGGAAAG
1 AAGAAAAAGAAAG
17273326 GGGAGGAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
22 12 0.26
23 10 0.21
24 21 0.45
25 3 0.06
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:17273280 original size:14 final size:13
Alignment explanation
Indices: 17273246--17273319 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
17273236 AGAGGGGAAG
17273246 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
17273258 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
17273271 AAGAAGGAAAAGGAAA
1 AAGAA-G-AAA-GAAA
17273287 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
17273305 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
17273319 A
1 A
17273320 GGAAAGGGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 4 0.08
16 5 0.10
18 5 0.10
19 4 0.08
20 2 0.04
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:17273301 original size:28 final size:28
Alignment explanation
Indices: 17273246--17273325 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
17273236 AGAGGGGAAG
17273246 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
17273271 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
17273305 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
17273326 GGGAGGAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.17
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:17273319 original size:38 final size:36
Alignment explanation
Indices: 17273261--17273419 Score: 137
Period size: 38 Copynumber: 4.3 Consensus size: 36
17273251 GAAAGAAAGG
17273261 AAGAAAGAAAAAGAAG--GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
*
17273295 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAGAGGA
* * * *
17273333 AATAAAGAAAAATAAGGAAAGAAGAGGAAATGAGAAGAGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAG-AG-GA
* * *
17273373 AA-AAAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGGAA
1 AAGAAAGAA-AAAGAAGAAGAAAAGGAAAGGAGAGG-A
*
17273409 AAAAAAGAAAA
1 AAGAAAGAAAA
17273420 TAAGGTAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
34 15 0.14
35 2 0.02
36 7 0.07
37 5 0.05
38 59 0.56
39 8 0.08
40 9 0.09
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (36 bp):
AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
Found at i:17273321 original size:10 final size:10
Alignment explanation
Indices: 17273263--17273387 Score: 64
Period size: 10 Copynumber: 12.7 Consensus size: 10
17273253 AAGAAAGGAA
*
17273263 GAAAGAAAAA
1 GAAAGAAAAG
*
17273273 GAAGGAAAAG
1 GAAAGAAAAG
* *
17273283 GAAAGGAGAG
1 GAAAGAAAAG
17273293 GAAAG-AAA-
1 GAAAGAAAAG
17273301 GAAA-AAGAAG
1 GAAAGAA-AAG
17273311 GAAAGAAAAG
1 GAAAGAAAAG
***
17273321 GAAAGGGGAG
1 GAAAGAAAAG
*
17273331 GAAA-TAAA-
1 GAAAGAAAAG
17273339 GAAA-AATAAG
1 GAAAGAA-AAG
*
17273349 GAAAGAAGAG
1 GAAAGAAAAG
*
17273359 GAAATGAGAAG
1 GAAA-GAAAAG
* *
17273370 AGAAAAAAAAA
1 -GAAAGAAAAG
17273381 GAAAGAA
1 GAAAGAA
17273388 GAAGAAGAGG
Statistics
Matches: 86, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
8 10 0.12
9 7 0.08
10 54 0.63
11 11 0.13
12 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.02
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:17273325 original size:18 final size:19
Alignment explanation
Indices: 17273277--17273325 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
17273267 GAAAAAGAAG
17273277 GAAAAGGAAAGGAGAGGAAA
1 GAAAAGGAAA-GAGAGGAAA
*
17273297 G-AAA-GAAAAAGAAGGAAA
1 GAAAAGGAAAGAG-AGGAAA
17273315 GAAAAGGAAAG
1 GAAAAGGAAAG
17273326 GGGAGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.08
18 11 0.46
19 6 0.25
20 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
GAAAAGGAAAGAGAGGAAA
Found at i:17274051 original size:27 final size:28
Alignment explanation
Indices: 17274001--17274069 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
17273991 ATATAAAAAA
17274001 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
17274029 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
17274056 TTACCAAAATATAT
1 TTACCAAAATATAT
17274070 CAAAAAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.57
28 12 0.30
29 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:17274085 original size:9 final size:9
Alignment explanation
Indices: 17274071--17274114 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
17274061 AAAATATATC
*
17274071 AAAAAAGTA
1 AAAAAAATA
*
17274080 AAAAAAACA
1 AAAAAAATA
17274089 AAAAAAATA
1 AAAAAAATA
*
17274098 AAAAAAACA
1 AAAAAAATA
17274107 GAAAAAAA
1 -AAAAAAA
17274115 ACACACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.05
Consensus pattern (9 bp):
AAAAAAATA
Found at i:17274092 original size:18 final size:19
Alignment explanation
Indices: 17274071--17274114 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
17274061 AAAATATATC
*
17274071 AAAAAAGTAAAAAAAACA-
1 AAAAAAATAAAAAAAACAG
17274089 AAAAAAATAAAAAAAACAG
1 AAAAAAATAAAAAAAACAG
17274108 AAAAAAA
1 AAAAAAA
17274115 ACACACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.05
Consensus pattern (19 bp):
AAAAAAATAAAAAAAACAG
Found at i:17275316 original size:17 final size:17
Alignment explanation
Indices: 17275294--17275330 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
17275284 ATGGGGTAAG
17275294 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
17275311 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
17275328 ATG
1 ATG
17275331 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:17276325 original size:15 final size:14
Alignment explanation
Indices: 17276285--17276313 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17276275 TTTTTGTATC
17276285 AATTTAATTATTCT
1 AATTTAATTATTCT
17276299 AATTTAATTATTCT
1 AATTTAATTATTCT
17276313 A
1 A
17276314 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:17279445 original size:31 final size:32
Alignment explanation
Indices: 17279393--17279542 Score: 92
Period size: 38 Copynumber: 4.3 Consensus size: 32
17279383 AATACCTTAT
17279393 TTTCTTTTTTTTCCTTCCTT-CCCTCTT-CTTCTTC
1 TTTCTTTTTTTT-C-TCCTTCCCCT-TTCCTT-TTC
17279427 TTTCTTTTTTTTCT-CTTCCCCTTTCCTTTTC
1 TTTCTTTTTTTTCTCCTTCCCCTTTCCTTTTC
17279458 TTTCCTTATTTTTCTTTCTTTCC-TCCCCTTTCCTTTTC
1 TTT-C---TTTTT-TTTC--TCCTTCCCCTTTCCTTTTC
* *
17279496 TTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTC
1 TTT-CTT-TTTTT-TCTCCTT-C-C-CCTTTCCTTTTC
*
17279534 CTTCTTTTT
1 TTTCTTTTT
17279543 CTTGCTTCCT
Statistics
Matches: 97, Mismatches: 3, Indels: 30
0.75 0.02 0.23
Matches are distributed among these distances:
31 11 0.11
32 9 0.09
33 1 0.01
34 14 0.14
35 10 0.10
36 12 0.12
37 4 0.04
38 35 0.36
39 1 0.01
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTCTTTTTTTTCTCCTTCCCCTTTCCTTTTC
Found at i:17279475 original size:18 final size:18
Alignment explanation
Indices: 17279454--17279564 Score: 86
Period size: 18 Copynumber: 6.1 Consensus size: 18
17279444 CCCCTTTCCT
*
17279454 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTCTTTTTC
* * *
17279472 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-TCTTTTTC
17279491 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
*
17279510 TTTCTTTCC-TCTCCTTTC
1 TTTCTTTCCTTCT-TTTTC
*
17279528 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
*
17279544 TTGC-TTCCTTTCTTTCTTC
1 TTTCTTTCC-TTCTTT-TTC
17279563 TT
1 TT
17279565 CTTCCCCTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.12
17 11 0.15
18 29 0.40
19 14 0.19
20 10 0.14
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:17279516 original size:28 final size:28
Alignment explanation
Indices: 17279485--17279564 Score: 76
Period size: 34 Copynumber: 2.8 Consensus size: 28
17279475 CTTTCCTCCC
*
17279485 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTG
17279513 CTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTG
1 CTTT-C-CT--TTT-C-TTTCCTTCTTTTTCTTG
17279547 C-TTCC-TTTCTTT-CTTCTT
1 CTTTCCTTTTCTTTCCTTCTT
17279565 CTTCCCCTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
27 1 0.02
28 7 0.16
29 1 0.02
30 2 0.04
31 1 0.02
32 4 0.09
33 3 0.07
34 17 0.38
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTG
Found at i:17279555 original size:38 final size:38
Alignment explanation
Indices: 17279443--17279533 Score: 164
Period size: 38 Copynumber: 2.4 Consensus size: 38
17279433 TTTTTTCTCT
17279443 TCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
1 TCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
*
17279481 TCCCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
*
17279519 TCTCCTTTCCTTTTC
1 TCCCCTTTCCTTTTC
17279534 CTTCTTTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.63
Consensus pattern (38 bp):
TCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
Found at i:17279560 original size:22 final size:23
Alignment explanation
Indices: 17279525--17279567 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
17279515 TTCCTCTCCT
*
17279525 TTCCTTTTCCTTCTTTTTCTTGC
1 TTCCTTTTCCTTCTTCTTCTTGC
*
17279548 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
17279568 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTGC
Found at i:17279565 original size:28 final size:30
Alignment explanation
Indices: 17279487--17279568 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 30
17279477 TTCCTCCCCT
*
17279487 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
* *
17279519 TCTCCTTTCCTTT-TCCTTCTT-TTTC-TTGC
1 T-TCCTTT-CTTTCTTCTTCTTCTTTCTTTCC
17279548 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
17279569 CCCTCTCCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
27 4 0.10
28 13 0.31
29 4 0.10
30 4 0.10
31 6 0.14
32 4 0.10
33 7 0.17
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Done.