Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 54 of 106
Found at i:20411455 original size:31 final size:28
Alignment explanation
Indices: 20411356--20411459 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 28
20411346 AGGCTGCTTT
*
20411356 AATATGTTTGTCTTAA-TT-GACAATAA
1 AATATGTTTGTCTTAATTTAGACAAGAA
* * *
20411382 AACATGTTTAATTTTAATTTAGACAAGAA
1 AATATGTTT-GTCTTAATTTAGACAAGAA
*
20411411 AATATGTTTGTCTTAATTTAATACAAGAAA
1 AATATGTTTGTCTTAATTT-AGACAAG-AA
*
20411441 AATATTTTTTGTCTTAATT
1 AATA-TGTTTGTCTTAATT
20411460 ACAGAAAAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 8 0.13
27 5 0.08
28 10 0.16
29 21 0.33
30 6 0.10
31 13 0.21
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (28 bp):
AATATGTTTGTCTTAATTTAGACAAGAA
Found at i:20412756 original size:19 final size:20
Alignment explanation
Indices: 20412719--20412763 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
20412709 AATTCTGTTA
*
20412719 TTATAAAAATATATATATTT
1 TTATTAAAATATATATATTT
20412739 TCTATTAAAATAT-T-TATTT
1 T-TATTAAAATATATATATTT
20412758 TTATTA
1 TTATTA
20412764 TAAAAGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
20 2 0.09
21 10 0.43
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTAAAATATATATATTT
Found at i:20412856 original size:32 final size:31
Alignment explanation
Indices: 20412800--20412859 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
20412790 TGCTATAGAG
*
20412800 TAGCACACAGCCCCTGCTGTGTGCTGTTCGA
1 TAGCACACAGCCACTGCTGTGTGCTGTTCGA
* *
20412831 TAGCACATAGCACACTGTTGTGTGCTGTT
1 TAGCACACAGC-CACTGCTGTGTGCTGTT
20412860 GCCGAACAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (31 bp):
TAGCACACAGCCACTGCTGTGTGCTGTTCGA
Found at i:20418352 original size:29 final size:29
Alignment explanation
Indices: 20418316--20418538 Score: 198
Period size: 29 Copynumber: 7.6 Consensus size: 29
20418306 AACAAGCTTT
*
20418316 AACATGTTTTGTCTTCATTTAGACAAAAA
1 AACATGTTTTGTCTTAATTTAGACAAAAA
* * * *
20418345 AATATG-TTTATCTTAATTTAGACTAGAA
1 AACATGTTTTGTCTTAATTTAGACAAAAA
* * * *
20418373 AACATGTTATGTCTTAAATTAGACGAGAA
1 AACATGTTTTGTCTTAATTTAGACAAAAA
* * *
20418402 AACATGTTATGTATTAGTTTAGACAAAAAAA
1 AACATGTTTTGTCTTAATTTAGAC--AAAAA
*
20418433 AACTTGTTTTGTCTTAATTTAGACAAGAAA
1 AACATGTTTTGTCTTAATTTAGACAA-AAA
* * * *
20418463 AATATGTTTTATCTTAATCTAAACAAGAAA
1 AACATGTTTTGTCTTAATTTAGACAA-AAA
* * * * *
20418493 AACAT-ATTTGTCTCAATTTATACAAGAT
1 AACATGTTTTGTCTTAATTTAGACAAAAA
20418521 AACATGTTTTGTCTTAAT
1 AACATGTTTTGTCTTAAT
20418539 CAAAGACAAG
Statistics
Matches: 155, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
28 29 0.19
29 71 0.46
30 32 0.21
31 23 0.15
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (29 bp):
AACATGTTTTGTCTTAATTTAGACAAAAA
Found at i:20418773 original size:20 final size:21
Alignment explanation
Indices: 20418729--20418774 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20418719 AGAGTTTTAT
20418729 TTTATTAAGAACTCTAAATGA
1 TTTATTAAGAACTCTAAATGA
*
20418750 -TTATTAAAGAA-T-TAAATTA
1 TTTATT-AAGAACTCTAAATGA
20418769 TTTATT
1 TTTATT
20418775 CTTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (21 bp):
TTTATTAAGAACTCTAAATGA
Found at i:20426065 original size:2 final size:2
Alignment explanation
Indices: 20426060--20426091 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20426050 TATATATATC
20426060 TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
20426092 AGTGATAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:20426226 original size:38 final size:38
Alignment explanation
Indices: 20426183--20426306 Score: 119
Period size: 38 Copynumber: 3.2 Consensus size: 38
20426173 GGGAGTGTGA
*
20426183 ATGATGATATTGCCTATGTGCACGATGTGGGGGAGCAC
1 ATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCAC
** * *
20426221 ATGATGGCATTAG--T-TGTGTGTGATGTGGGGGAGCACAC
1 ATGATGATATT-GCCTATGTGCGCGATGTGGGGGAG--CAC
20426259 AATGATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCAC
1 ----ATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCAC
20426301 ATGATG
1 ATGATG
20426307 GCTTTAGTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
36 16 0.24
37 1 0.01
38 18 0.27
39 1 0.01
41 1 0.01
42 12 0.18
43 1 0.01
44 17 0.25
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.27
Consensus pattern (38 bp):
ATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCAC
Found at i:20426247 original size:36 final size:36
Alignment explanation
Indices: 20426206--20426337 Score: 122
Period size: 36 Copynumber: 3.4 Consensus size: 36
20426196 CTATGTGCAC
*
20426206 GATGTGGGGGAGCACATGATGGCATTAGTTGTGTGT
1 GATGTGGGGGAGCACATGATGGCATTAGTTGTGCGT
* *
20426242 GATGTGGGGGAGCACACAATGATGATG-ATATTGCCTATGTGCGC
1 GATGTGGGGGAG--CAC-ATGATG--GCAT-TAG--T-TGTGCGT
*
20426286 GATGTGGGGGAGCACATGATGGCTTTAGTTGTGCGT
1 GATGTGGGGGAGCACATGATGGCATTAGTTGTGCGT
**
20426322 GATGTACGGGAGCACA
1 GATGTGGGGGAGCACA
20426338 CAAACATGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
36 32 0.41
37 1 0.01
38 3 0.04
39 9 0.12
40 3 0.04
41 9 0.12
42 3 0.04
43 1 0.01
44 17 0.22
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.27
Consensus pattern (36 bp):
GATGTGGGGGAGCACATGATGGCATTAGTTGTGCGT
Found at i:20426271 original size:80 final size:80
Alignment explanation
Indices: 20426183--20426350 Score: 273
Period size: 80 Copynumber: 2.1 Consensus size: 80
20426173 GGGAGTGTGA
* *
20426183 ATGATGATATTGCCTATGTGCACGATGTGGGGGAGCACATGATGGCATTAGTTGTGTGTGATGTG
1 ATGATGATATTGCCTATGTGCACGATGTGGGGGAGCACATGATGGCATTAGTTGTGCGTGATGTA
* **
20426248 GGGGAGCACACAATG
66 CGGGAGCACACAAAC
* *
20426263 ATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCACATGATGGCTTTAGTTGTGCGTGATGTA
1 ATGATGATATTGCCTATGTGCACGATGTGGGGGAGCACATGATGGCATTAGTTGTGCGTGATGTA
20426328 CGGGAGCACACAAAC
66 CGGGAGCACACAAAC
20426343 ATGATGAT
1 ATGATGAT
20426351 GTTGAAATGT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.27
Consensus pattern (80 bp):
ATGATGATATTGCCTATGTGCACGATGTGGGGGAGCACATGATGGCATTAGTTGTGCGTGATGTA
CGGGAGCACACAAAC
Found at i:20428061 original size:68 final size:68
Alignment explanation
Indices: 20427952--20428208 Score: 311
Period size: 68 Copynumber: 3.8 Consensus size: 68
20427942 ATGCTTACTT
* * * ** *
20427952 ATCTCATA-AGGTATATGGAATTTACATTATATACATAATCTCATGGCATTTATCATGCTTGGTC
1 ATCTCATATA-GTATATGGAATTTACATCATATACATAATCTCATGGCATTCATCATGCATACTT
20428016 AATC
65 AATC
20428020 ATCTCATATAGTATATGGAATTTACATCATATACATAATCTCCA-GGCATTCATCATGCATACTT
1 ATCTCATATAGTATATGGAATTTACATCATATACATAATCT-CATGGCATTCATCATGCATACTT
20428084 AATC
65 AATC
* * * * * * * * * * * *
20428088 ACCTCATATGGTTTATGAAATCTACATCATATATACAATCTTATAGTATACATCATGCATACTTG
1 ATCTCATATAGTATATGGAATTTACATCATATACATAATCTCATGGCATTCATCATGCATACTTA
20428153 ATC
66 ATC
*
20428156 ATCTCATATAGTATATGGAATTTACATCATATACATAATCTTATGGCATTCAT
1 ATCTCATATAGTATATGGAATTTACATCATATACATAATCTCATGGCATTCAT
20428209 TATTGGTATA
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
67 1 0.01
68 154 0.97
69 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (68 bp):
ATCTCATATAGTATATGGAATTTACATCATATACATAATCTCATGGCATTCATCATGCATACTTA
ATC
Found at i:20430919 original size:12 final size:12
Alignment explanation
Indices: 20430883--20430919 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
20430873 TCTAGGGAAA
20430883 ATGTATCGATAC
1 ATGTATCGATAC
20430895 AT-TAT-GA-AC
1 ATGTATCGATAC
20430904 ATGTATCGATAC
1 ATGTATCGATAC
20430916 ATGT
1 ATGT
20430920 TCATTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:20431159 original size:16 final size:16
Alignment explanation
Indices: 20431138--20431183 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
20431128 ATTTAGATTC
*
20431138 AATAAAAATATAAAAA
1 AATAAAAATCTAAAAA
*
20431154 AATAAAAATCTAAAAG
1 AATAAAAATCTAAAAA
*
20431170 AATCAAAATCTAAA
1 AATAAAAATCTAAA
20431184 TTTTGCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (16 bp):
AATAAAAATCTAAAAA
Found at i:20432571 original size:28 final size:28
Alignment explanation
Indices: 20432514--20432675 Score: 175
Period size: 28 Copynumber: 5.6 Consensus size: 28
20432504 TAGCAGCTTT
*
20432514 AACATGTTTATCTTAATTTAGACAATG-A
1 AACATGTTTGTCTTAATTTAGACAA-GAA
20432542 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
20432571 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * *
20432601 AATATTTTTTGTCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* *
20432630 AACATATTTGTCTTAATTTAAACAAG-A
1 AACATGTTTGTCTTAATTTAGACAAGAA
* *
20432657 TACAATATTTGTCTTAATT
1 AAC-ATGTTTGTCTTAATT
20432676 AAAGATAAGA
Statistics
Matches: 119, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
27 3 0.03
28 54 0.45
29 36 0.30
30 13 0.11
31 13 0.11
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:20432627 original size:59 final size:59
Alignment explanation
Indices: 20432514--20432666 Score: 188
Period size: 59 Copynumber: 2.6 Consensus size: 59
20432504 TAGCAGCTTT
* * * *
20432514 AACATGTTTATCTTAATTT-AGACAATG--AAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAAGACAA-GAAAAATATTTTTGGTCTTAATCTAGACAAGAA
* *
20432571 AATATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTGGTCTTAATCTAGACAAGAA
* *
20432630 AACATATTTGTCTTAATTTAA-ACAAGATACAATATTT
1 AACATGTTTGTCTTAATTTAAGACAAGA-AAAATATTT
20432667 GTCTTAATTA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 18 0.22
58 12 0.14
59 53 0.64
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (59 bp):
AACATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTGGTCTTAATCTAGACAAGAA
Found at i:20432692 original size:22 final size:22
Alignment explanation
Indices: 20432665--20432727 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
20432655 GATACAATAT
20432665 TTGTCTT-AATTAAAGATAAGAG
1 TTGTCTTAAATT-AAGATAAGAG
20432687 TTGTCTTAAATTAAGATAAGAG
1 TTGTCTTAAATTAAGATAAGAG
20432709 TTGTCTTAAATTAAGATAA
1 TTGTCTTAAATTAAGATAA
20432728 TGCTAGGAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 36 0.90
23 4 0.10
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (22 bp):
TTGTCTTAAATTAAGATAAGAG
Found at i:20432869 original size:17 final size:17
Alignment explanation
Indices: 20432849--20432881 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20432839 ATAATAATAA
20432849 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
20432866 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
20432882 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:20437035 original size:13 final size:13
Alignment explanation
Indices: 20437017--20437041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20437007 TTTCAGAAAA
20437017 TTTATAAAATCAT
1 TTTATAAAATCAT
20437030 TTTATAAAATCA
1 TTTATAAAATCA
20437042 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20443247 original size:20 final size:20
Alignment explanation
Indices: 20443230--20443267 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20443220 CCTCAAATCT
20443230 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
20443250 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
20443268 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:20445775 original size:17 final size:18
Alignment explanation
Indices: 20445732--20445779 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
20445722 TACCATCTTT
20445732 CATGAGATTA-AAGTTGA
1 CATGAGATTATAAGTTGA
* *
20445749 AAT-TGATTATAA-TTGA
1 CATGAGATTATAAGTTGA
20445765 CATGAGATTATAAGT
1 CATGAGATTATAAGT
20445780 GAATGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
16 11 0.46
17 12 0.50
18 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (18 bp):
CATGAGATTATAAGTTGA
Found at i:20447295 original size:18 final size:18
Alignment explanation
Indices: 20447272--20447313 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
20447262 ATATATATAT
20447272 ATATATTGAAGATTATTG
1 ATATATTGAAGATTATTG
*
20447290 ATATATTGAATATTATTG
1 ATATATTGAAGATTATTG
20447308 ATATAT
1 ATATAT
20447314 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (18 bp):
ATATATTGAAGATTATTG
Found at i:20454178 original size:22 final size:22
Alignment explanation
Indices: 20454113--20454178 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
20454103 TTTAAAACAA
* *
20454113 CTTTAAACCCAAAAGCTCTAAT
1 CTTTAAAACCAAAAGCTCTGAT
* * *
20454135 CTTTCAAACTAAAAGCTATGAT
1 CTTTAAAACCAAAAGCTCTGAT
20454157 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAGCTCTGAT
20454179 ACCACTCTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTGAT
Found at i:20457933 original size:67 final size:67
Alignment explanation
Indices: 20457823--20457997 Score: 255
Period size: 67 Copynumber: 2.6 Consensus size: 67
20457813 GCTTAGCCAA
* *
20457823 AACCTTTCAAAATGGTTTTAC-CGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGACTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGACTCAACC
20457887 AC
66 AC
** * *
20457889 AACCTTTCACAATGGTTTTTCACTAGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGACTCAACC
20457954 AC
66 AC
* *
20457956 AACC-TACAACAATGGTTTTTCACGGGATCAACTAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
20457998 CAACTAACTT
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
66 21 0.22
67 75 0.78
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.25
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGACTCAACC
AC
Found at i:20457942 original size:32 final size:31
Alignment explanation
Indices: 20457849--20457977 Score: 125
Period size: 32 Copynumber: 3.9 Consensus size: 31
20457839 TTTACCGGGA
20457849 TCAACCAAAACCCAAAGTGGTTTTTCAAAGAC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAG-C
* *
20457881 TCAACCACAACCTTTCACAA-TGGTTTTTCACTAGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCA-AAGC
20457916 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAA-GC
* *
20457948 TCAACCACAACCTACAACAATGGTTTTTCA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCA
20457978 CGGGATCAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
31 3 0.04
32 36 0.44
34 3 0.04
35 35 0.43
36 4 0.05
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.26
Consensus pattern (31 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGC
Found at i:20457987 original size:35 final size:32
Alignment explanation
Indices: 20457830--20457997 Score: 126
Period size: 35 Copynumber: 5.1 Consensus size: 32
20457820 CAAAACCTTT
* *
20457830 CAAAATGGTTTTAC-CGGGATCAACCAAAACC
1 CAAAATGGTTTTTCACAGGATCAACCAAAACC
* * *
20457861 CAAAGTGGTTTTTCA-AAGACTCAACCACAACC
1 CAAAATGGTTTTTCACAGGA-TCAACCAAAACC
* *
20457893 TTTCACAATGGTTTTTCACTA-GCTCAACCAAAACC
1 ---CAAAATGGTTTTTCAC-AGGATCAACCAAAACC
* * * *
20457928 CAAAGTGGTTTTTCAAAGGCTCAACCACAACC
1 CAAAATGGTTTTTCACAGGATCAACCAAAACC
* *
20457960 TACAACAATGGTTTTTCACGGGATCAACTAAAACC
1 --CAA-AATGGTTTTTCACAGGATCAACCAAAACC
20457995 CAA
1 CAA
20457998 CAACTAACTT
Statistics
Matches: 107, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
31 15 0.14
32 37 0.35
33 3 0.03
34 3 0.03
35 47 0.44
36 1 0.01
37 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (32 bp):
CAAAATGGTTTTTCACAGGATCAACCAAAACC
Found at i:20459173 original size:37 final size:37
Alignment explanation
Indices: 20459132--20459207 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
20459122 CATCAGCATC
* *
20459132 CAAATCCTAACCATCAACAATTATCACAGCAGAATGT
1 CAAATCCTAACCATCAACAATTATCACAACAAAATGT
*
20459169 CAAATCCTAACCATCAGCAATTATCACAACAAAATGT
1 CAAATCCTAACCATCAACAATTATCACAACAAAATGT
20459206 CA
1 CA
20459208 TAAGCAACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (37 bp):
CAAATCCTAACCATCAACAATTATCACAACAAAATGT
Found at i:20462848 original size:42 final size:42
Alignment explanation
Indices: 20462793--20462918 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
20462783 GTAATGATAT
* ** *
20462793 TGACCCGGTTATGTGCGAGTAAGAATGTGCATAAGCTGATGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGTGCATAAGCTGATGC
* * * *
20462835 TGACCTGGCTATGTGAGAGTGGGAGTGCGCATAAGTTGATGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGTGCATAAGCTGATGC
* *
20462877 TGACCCGGCTATATGCGAGTGGGAGTGTGCATAAGCCGATGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGTGCATAAGCTGATGC
20462919 ATATAATCTG
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTGGGAGTGTGCATAAGCTGATGC
Found at i:20462966 original size:2 final size:2
Alignment explanation
Indices: 20462959--20463004 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
20462949 ATGATGATTG
* *
20462959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT GT AT NAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
20463002 AT A
1 AT A
20463005 ATCTGATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20463010 original size:81 final size:80
Alignment explanation
Indices: 20462919--20463082 Score: 310
Period size: 81 Copynumber: 2.0 Consensus size: 80
20462909 AAGCCGATGC
20462919 ATATAATCTGATGATGATGGGAGGGTGTGCATGATGATTGATATATATATATATATATATATATA
1 ATATAATCTGATGATGATGGGAGGGTGTGCATGATGATTGATATATATATATATATATATATATA
20462984 TATACATATATGTAT
66 TATACATATATGTAT
20462999 NATATAATCTGATGATGATGGGAGGGTGTGCATGATGATTGATATATATATATATATATATATAT
1 -ATATAATCTGATGATGATGGGAGGGTGTGCATGATGATTGATATATATATATATATATATATAT
20463064 ATATACATATATGGTAT
65 ATATACATATAT-GTAT
20463081 AT
1 AT
20463083 GGTTGTAATG
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 78 0.95
82 4 0.05
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (80 bp):
ATATAATCTGATGATGATGGGAGGGTGTGCATGATGATTGATATATATATATATATATATATATA
TATACATATATGTAT
Found at i:20463047 original size:2 final size:2
Alignment explanation
Indices: 20463040--20463075 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
20463030 ATGATGATTG
*
20463040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20463076 GGTATATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20465725 original size:30 final size:29
Alignment explanation
Indices: 20465600--20465790 Score: 244
Period size: 29 Copynumber: 6.6 Consensus size: 29
20465590 GACAGCTTTT
20465600 ACATG-TTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* *
20465628 ACATGATTTGTCTTAATTTAGACAATAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * *
20465657 ATATGTTATGCCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
20465686 ACATGTTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
20465715 A-ATTTGTTTTGTCTTAATATAGACAAGAAA
1 ACA--TGTTTTGTCTTAATTTAGACAAGAAA
* * * *
20465745 ACACG-TTTGTCTCAATTTAGATAAGATA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
20465773 ACATGTTTTGTTTTAATT
1 ACATGTTTTGTCTTAATT
20465791 AAAGAAAAGA
Statistics
Matches: 140, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
28 29 0.21
29 84 0.60
30 26 0.19
31 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
ACATGTTTTGTCTTAATTTAGACAAGAAA
Found at i:20474752 original size:26 final size:26
Alignment explanation
Indices: 20474705--20474774 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
20474695 TTTAAGCTAC
*
20474705 TATAAACATA-TTCAACACTTATACGTT
1 TATAAA-ATATTTCAA-AATTATACGTT
*
20474732 TATAAAATATTTCAAAATTATATGTT
1 TATAAAATATTTCAAAATTATACGTT
20474758 TATAAAATATTTCAAAA
1 TATAAAATATTTCAAAA
20474775 GCCCACACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 29 0.73
27 11 0.28
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (26 bp):
TATAAAATATTTCAAAATTATACGTT
Found at i:20476411 original size:15 final size:15
Alignment explanation
Indices: 20476391--20476423 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
20476381 GTTTCTCGCT
20476391 GCAGCGAGAAACAGG
1 GCAGCGAGAAACAGG
20476406 GCAGCGAGAAACAGG
1 GCAGCGAGAAACAGG
20476421 GCA
1 GCA
20476424 CCTAAGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (15 bp):
GCAGCGAGAAACAGG
Found at i:20476725 original size:38 final size:40
Alignment explanation
Indices: 20476636--20476728 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
20476626 CACACCCGGC
* *
20476636 TCATGTGCATCCCCCTACATTGTGCACATAGCCGGCGCCA
1 TCATGTGCATCCCCCCACATTGTGCACATAGCCAGCGCCA
* * * *
20476676 TCGTATGCATCCCCCCACATTGTGCACA-A-TCAGTGCCA
1 TCATGTGCATCCCCCCACATTGTGCACATAGCCAGCGCCA
*
20476714 TCATGTACATCCCCC
1 TCATGTGCATCCCCC
20476729 ATATCGTGCA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 18 0.41
39 1 0.02
40 25 0.57
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (40 bp):
TCATGTGCATCCCCCCACATTGTGCACATAGCCAGCGCCA
Found at i:20476863 original size:2 final size:2
Alignment explanation
Indices: 20476856--20476883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20476846 ATCATGCACA
20476856 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
20476884 CATCATAATG
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:20480195 original size:106 final size:106
Alignment explanation
Indices: 20480006--20480220 Score: 367
Period size: 106 Copynumber: 2.0 Consensus size: 106
20479996 TTTGTTTTGT
*
20480006 TTGGGATTAGTTGAATTGGGCGATGAGAAATGGAATCTGTGTTTTGTGGGATGAATGAGTAGTAG
1 TTGGGATTAGTTGAATTGGGCGATGAGAAATGGAATCTGTCTTTTGTGGGATGAATGAGTAGTAG
** *
20480071 ATTATTGTTTTTTGGGGGAATTATCAGATTATGGGGTTAAA
66 ATTATTGTTTTTACGGGGAATTATCAGATTATGAGGTTAAA
* * *
20480112 TTGGGATTAGTTGAATTTGGCGATGAGAAATGGAATCTGTCTTTTGTGGGATGGATGAGTAGTGG
1 TTGGGATTAGTTGAATTGGGCGATGAGAAATGGAATCTGTCTTTTGTGGGATGAATGAGTAGTAG
20480177 ATTATTGTTTTTACGGGGAATTATCAGATTATGAGGTTAAA
66 ATTATTGTTTTTACGGGGAATTATCAGATTATGAGGTTAAA
20480218 TTG
1 TTG
20480221 AAATGATCAG
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.26, C:0.04, G:0.32, T:0.38
Consensus pattern (106 bp):
TTGGGATTAGTTGAATTGGGCGATGAGAAATGGAATCTGTCTTTTGTGGGATGAATGAGTAGTAG
ATTATTGTTTTTACGGGGAATTATCAGATTATGAGGTTAAA
Found at i:20483187 original size:13 final size:13
Alignment explanation
Indices: 20483169--20483196 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20483159 GGCATGTTTA
20483169 TAGAGTAAATCTT
1 TAGAGTAAATCTT
20483182 TAGAGTAAATCTT
1 TAGAGTAAATCTT
20483195 TA
1 TA
20483197 TTTGTGGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
TAGAGTAAATCTT
Found at i:20489741 original size:31 final size:31
Alignment explanation
Indices: 20489703--20489775 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
20489693 AACGTTGGTA
20489703 TGTTACAACATTTTACGTTATATACATGGCG
1 TGTTACAACATTTTACGTTATATACATGGCG
*
20489734 TGTTACAACATTTTACGTTATATGCATGGCG
1 TGTTACAACATTTTACGTTATATACATGGCG
20489765 TGTTACAACAT
1 TGTTACAACAT
20489776 GACTGACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (31 bp):
TGTTACAACATTTTACGTTATATACATGGCG
Found at i:20493732 original size:118 final size:118
Alignment explanation
Indices: 20493588--20493835 Score: 370
Period size: 118 Copynumber: 2.1 Consensus size: 118
20493578 CAATCACATC
* *
20493588 TTGTGGTGACACACTAAGTGGAAGCAGATAGTTGGCGTGACATGCTAAGTGCATGCAGATTTTGG
1 TTGTGGTGACACACTAAGTGGAAGCAGATAGTTGGCGTGACACGCTAAGTGCATGCAGATTTCGG
* *
20493653 TGGTGACACGTTGACTTCTTGCAGTATTGTGGAGTGACACGACACACCCCATA
66 TGGTGACACATTGACTTCTTGCAATATTGTGGAGTGACACGACACACCCCATA
* * * * *
20493706 TTGTGGTGACACATTGAGTGGAAGCAGATAGTTGGCGTGACACGTTGAGTGCATGTAGATTTCGG
1 TTGTGGTGACACACTAAGTGGAAGCAGATAGTTGGCGTGACACGCTAAGTGCATGCAGATTTCGG
* * * * *
20493771 TGGTGACACATTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCTATC
66 TGGTGACACATTGACTTCTTGCAATATTGTGGAGTGACACGACACACCCCATA
20493824 TTGTGGTGACAC
1 TTGTGGTGACAC
20493836 GCTGACTTCT
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (118 bp):
TTGTGGTGACACACTAAGTGGAAGCAGATAGTTGGCGTGACACGCTAAGTGCATGCAGATTTCGG
TGGTGACACATTGACTTCTTGCAATATTGTGGAGTGACACGACACACCCCATA
Found at i:20493860 original size:56 final size:56
Alignment explanation
Indices: 20493770--20493896 Score: 209
Period size: 56 Copynumber: 2.3 Consensus size: 56
20493760 GTAGATTTCG
** * * *
20493770 GTGGTGACACATTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCTATCTT
1 GTGGTGACACGCTGACTTCTTGCAATATTATGGGGTGACACGGCACACCCCATCTT
20493826 GTGGTGACACGCTGACTTCTTGCAATATTATGGGGTGACACGGCACACCCCATCTT
1 GTGGTGACACGCTGACTTCTTGCAATATTATGGGGTGACACGGCACACCCCATCTT
20493882 GTGGTGACACGCTGA
1 GTGGTGACACGCTGA
20493897 GTGGAACCAG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (56 bp):
GTGGTGACACGCTGACTTCTTGCAATATTATGGGGTGACACGGCACACCCCATCTT
Found at i:20493920 original size:56 final size:56
Alignment explanation
Indices: 20493804--20493923 Score: 134
Period size: 56 Copynumber: 2.1 Consensus size: 56
20493794 ATATTGTGGG
* * * *** * *
20493804 GTGACACGGCACGCCCTATCTTGTGGTGACACGCTGACTTCTTGCAATATTATGGG
1 GTGACACGGCACACCCCATCTTGTGGTGACACGCTGACTGCAACCAATACTATGGC
* *
20493860 GTGACACGGCACACCCCATCTTGTGGTGACACGCTGAGTGGAACCAGATACT-TGGC
1 GTGACACGGCACACCCCATCTTGTGGTGACACGCTGACTGCAACCA-ATACTATGGC
20493916 GTGACACG
1 GTGACACG
20493924 CTGAGTGCAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 49 0.92
57 4 0.08
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Consensus pattern (56 bp):
GTGACACGGCACACCCCATCTTGTGGTGACACGCTGACTGCAACCAATACTATGGC
Found at i:20493942 original size:174 final size:174
Alignment explanation
Indices: 20493652--20494010 Score: 538
Period size: 174 Copynumber: 2.1 Consensus size: 174
20493642 GCAGATTTTG
* * *
20493652 GTGGTGACACGTTGACTTCTTGCAGTATTGTGGAGTGACACGACACACCCCATATTGTGGTGACA
1 GTGGTGACACGCTGACTTCTTGCAATATTATGGAGTGACACGACACACCCCATATTGTGGTGACA
* * * * * * * *
20493717 CATTGAGTGGAAGCAGATAGTTGGCGTGACACGTTGAGTGCATGTAGATTTCGGTGGTGACACAT
66 CACTGAGTGGAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCGATAGTGACACAC
*
20493782 TGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCTATCTT
131 TGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTT
* * *
20493826 GTGGTGACACGCTGACTTCTTGCAATATTATGGGGTGACACGGCACACCCCATCTTGTGGTGACA
1 GTGGTGACACGCTGACTTCTTGCAATATTATGGAGTGACACGACACACCCCATATTGTGGTGACA
* *
20493891 CGCTGAGTGGAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCGATAGTGACACGC
66 CACTGAGTGGAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCGATAGTGACACAC
* *
20493956 TGACTTCTTGCAGTATTGTGGGGTGACATGGCACGCCCCATCTT
131 TGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTT
*
20494000 ATGGTGACACG
1 GTGGTGACACG
20494011 TTGAGTGGAA
Statistics
Matches: 165, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
174 165 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (174 bp):
GTGGTGACACGCTGACTTCTTGCAATATTATGGAGTGACACGACACACCCCATATTGTGGTGACA
CACTGAGTGGAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCGATAGTGACACAC
TGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTT
Found at i:20494119 original size:292 final size:292
Alignment explanation
Indices: 20493584--20494132 Score: 846
Period size: 292 Copynumber: 1.9 Consensus size: 292
20493574 ATGTCAATCA
* * *
20493584 CATCTTGTGGTGACACACTAAGTGGAAGCAGATAGTTGGCGTGACATGCTAAGTGCATGCAGATT
1 CATCTTGTGGTGACACACTAAGTGGAACCAGATACTTGGCGTGACACGCTAAGTGCATGCAGATT
* * * * *
20493649 TTGGTGGTGACACGTTGACTTCTTGCAGTATTGTGGAGTGACACGACACACCCCATATTGTGGTG
66 TCGATAGTGACACGCTGACTTCTTGCAGTATTGTGGAGTGACACGACACACCCCATATTATGGTG
* * * *
20493714 ACACATTGAGTGGAAGCAGATAGTTGGCGTGACACGTTGAGTGCATGTAGATTTCGGTGGTGACA
131 ACACATTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCATGCAAATTTCAGTGGTGACA
* *
20493779 CATTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCTATCTTGTGGTGACACGCTGACTT
196 CATTAACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGACACGCTGACTT
20493844 CTTGCAATATTATGGGGTGACACGGCACACCC
261 CTTGCAATATTATGGGGTGACACGGCACACCC
* * *
20493876 CATCTTGTGGTGACACGCTGAGTGGAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATT
1 CATCTTGTGGTGACACACTAAGTGGAACCAGATACTTGGCGTGACACGCTAAGTGCATGCAGATT
* * * * *
20493941 TCGATAGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGACATGGCACGCCCCATCTTATGGTG
66 TCGATAGTGACACGCTGACTTCTTGCAGTATTGTGGAGTGACACGACACACCCCATATTATGGTG
* *
20494006 ACACGTTGAGTGGAATCAGATACTTGGCGTGACACGTTGAGTGCATGCAAATTTCAGTGGTGACA
131 ACACATTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCATGCAAATTTCAGTGGTGACA
* * * *
20494071 CGTTAACTTCTTGCAGTATTGTGGGGTGACACGGCACTCCCCATCTTGTGGTGACATGCTGA
196 CATTAACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGACACGCTGA
20494133 GTGAAACCAG
Statistics
Matches: 229, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
292 229 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (292 bp):
CATCTTGTGGTGACACACTAAGTGGAACCAGATACTTGGCGTGACACGCTAAGTGCATGCAGATT
TCGATAGTGACACGCTGACTTCTTGCAGTATTGTGGAGTGACACGACACACCCCATATTATGGTG
ACACATTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCATGCAAATTTCAGTGGTGACA
CATTAACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGACACGCTGACTT
CTTGCAATATTATGGGGTGACACGGCACACCC
Found at i:20494309 original size:118 final size:118
Alignment explanation
Indices: 20493826--20494275 Score: 650
Period size: 118 Copynumber: 3.8 Consensus size: 118
20493816 GCCCTATCTT
* *
20493826 GTGGTGACACGCTGACTTCTTGCAATATTATGGGGTGACACGGCACACCCCATCTTGTGGTGACA
1 GTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGACA
*
20493891 CGCTGAGTGGAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTC-
66 CGCTGAGTGAAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCA
* * * *
20493943 GATAGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGACATGGCACGCCCCATCTTATGGTGAC
1 G-TGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGAC
* * * * *
20494008 ACGTTGAGTGGAATCAGATACTTGGCGTGACACGTTGAGTGCATGCAAATTTCA
65 ACGCTGAGTGAAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCA
* * * *
20494062 GTGGTGACACGTTAACTTCTTGCAGTATTGTGGGGTGACACGGCACTCCCCATCTTGTGGTGACA
1 GTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGACA
* * * **
20494127 TGCTGAGTGAAACCAGATACTTGGCGTGACACACTAAGTGCATGCAGATTTTG
66 CGCTGAGTGAAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCA
* *
20494180 GTGGTGACACGCTGACTTCTTTCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGCTGACA
1 GTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGACA
* * *
20494245 CACTGAGTGAAACTAGATACTTGGAGTGACA
66 CGCTGAGTGAAACCAGATACTTGGCGTGACA
20494276 TGTTGACTTC
Statistics
Matches: 295, Mismatches: 36, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
117 1 0.00
118 293 0.99
119 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (118 bp):
GTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGTGACA
CGCTGAGTGAAACCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTCA
Found at i:20496802 original size:145 final size:145
Alignment explanation
Indices: 20496603--20496889 Score: 439
Period size: 145 Copynumber: 2.0 Consensus size: 145
20496593 CCGACGGGGG
** ** *
20496603 GTTAGCACTGTGCTTCTGAGGAAAACCTCTCAGTGGTTGAGGAGCTATTGTCGCATGGTCCAATT
1 GTTAGCACTGTGAGTCTGAGGAAAACCTCTCAGTGGTTGAGGAGCTATCATCGCATGGTCCAACT
*
20496668 GCAAACACAGATATGTTATTCGATAATCACATATGGAATTGTTGAACACAAACCATTATAACCGT
66 GCAAACACAGATATGTTATTCGATAATCACATATGGAATTGTTGAACACAAACCATTAGAACCGT
20496733 CCTTACAGGCTCGTC
131 CCTTACAGGCTCGTC
** * * *
20496748 GTTAGCACTGTGAGTCTGAGGAGTACCTCTCGGTGGTTGTGGAGCTGTCATCGCATGGTCCAACT
1 GTTAGCACTGTGAGTCTGAGGAAAACCTCTCAGTGGTTGAGGAGCTATCATCGCATGGTCCAACT
* **
20496813 GCAAACACATATATGTTATTCGATAATCACATATGGAATTGTTGAACACAAACTGTTAGAACCGT
66 GCAAACACAGATATGTTATTCGATAATCACATATGGAATTGTTGAACACAAACCATTAGAACCGT
*
20496878 CCTTACCGGCTC
131 CCTTACAGGCTC
20496890 TTCACTACCA
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
145 127 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (145 bp):
GTTAGCACTGTGAGTCTGAGGAAAACCTCTCAGTGGTTGAGGAGCTATCATCGCATGGTCCAACT
GCAAACACAGATATGTTATTCGATAATCACATATGGAATTGTTGAACACAAACCATTAGAACCGT
CCTTACAGGCTCGTC
Found at i:20498323 original size:31 final size:31
Alignment explanation
Indices: 20498280--20498674 Score: 513
Period size: 31 Copynumber: 12.7 Consensus size: 31
20498270 GTTAACCCAT
* * *
20498280 AATGTGTTAACACACCATACATATAAC-TGAA
1 AATGTGGTAACACGCCATGCATATAACGT-AA
* ** *
20498311 AATATGGTAACACAACATGCATATAACGGAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
20498342 AATGTGGTAACACACCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
20498373 AATGTGGTAACACGCCATTCACATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* * *
20498404 ACTCTGGGAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* * * *
20498435 ACTCTAGTAACACGCCATGAATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
20498466 ATTGTGGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
20498497 AATGTGGTAACATGCCATGCATATAACATAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
20498528 ACTGTGGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* * * *
20498559 ACTGTAGTAACATGCCATGCATATAACATAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
20498590 ACTGTGGTAACTCGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
20498621 AATGTGGTAACACGCCATGCATATAACATAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
20498652 AATGTTGTAACACGCCATGCATA
1 AATGTGGTAACACGCCATGCATA
20498675 ACAAGTCAAA
Statistics
Matches: 323, Mismatches: 40, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
31 323 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (31 bp):
AATGTGGTAACACGCCATGCATATAACGTAA
Found at i:20499393 original size:24 final size:24
Alignment explanation
Indices: 20499360--20499410 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
20499350 ATAGAGTCTG
*
20499360 ACAAACTCTAAACGTTGACGTGTC
1 ACAAACTCTAAACGTTGACATGTC
* * *
20499384 ACAAATTCTAAATGTTGGCATGTC
1 ACAAACTCTAAACGTTGACATGTC
20499408 ACA
1 ACA
20499411 GATTGCCTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (24 bp):
ACAAACTCTAAACGTTGACATGTC
Found at i:20499548 original size:47 final size:47
Alignment explanation
Indices: 20499404--20499537 Score: 178
Period size: 47 Copynumber: 2.9 Consensus size: 47
20499394 AATGTTGGCA
* * *
20499404 TGTCACAGATTGCCTCCATGGCATGTCACGAACTCTGAACGCAAGCG
1 TGTCACAGATTACCTCCATGGCCTGTCACGAACTCTGAACGCTAGCG
* * *
20499451 TGTCACAGATTACCTCCATGGCCTGTCATGAACTTTGAACGCTGGCG
1 TGTCACAGATTACCTCCATGGCCTGTCACGAACTCTGAACGCTAGCG
* * * *
20499498 TGTCTCATATTCCCTCCATGGCCTGTCACAAACTCTGAAC
1 TGTCACAGATTACCTCCATGGCCTGTCACGAACTCTGAAC
20499538 ATTAGAGTGT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (47 bp):
TGTCACAGATTACCTCCATGGCCTGTCACGAACTCTGAACGCTAGCG
Found at i:20499548 original size:94 final size:94
Alignment explanation
Indices: 20499416--20499595 Score: 220
Period size: 94 Copynumber: 1.9 Consensus size: 94
20499406 TCACAGATTG
* * * *
20499416 CCTCCATGGCATGTCACGAACTCTGAACGCAAGCGTGTCAC-AGATTACCTCC-ATGGCCTGTCA
1 CCTCCATGGCATGTCACAAACTCTGAACACAAGAGTGTCACGA-ATTACC-CCTATGGCATGTCA
* *
20499479 TGAACTTTGAACGCTGGCGTGTCTCATATTC
64 CGAACTTTAAACGCTGGCGTGTCTCATATTC
* ** * *
20499510 CCTCCATGGCCTGTCACAAACTCTGAACATTAGAGTGTCACGAATTTCCCCTATGGCATGTGACG
1 CCTCCATGGCATGTCACAAACTCTGAACACAAGAGTGTCACGAATTACCCCTATGGCATGTCACG
*
20499575 AACTTTAAACGCTGGTGTGTC
66 AACTTTAAACGCTGGCGTGTC
20499596 ACCAACTCTG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
93 2 0.03
94 69 0.96
95 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (94 bp):
CCTCCATGGCATGTCACAAACTCTGAACACAAGAGTGTCACGAATTACCCCTATGGCATGTCACG
AACTTTAAACGCTGGCGTGTCTCATATTC
Found at i:20504587 original size:29 final size:28
Alignment explanation
Indices: 20504558--20504723 Score: 161
Period size: 29 Copynumber: 5.6 Consensus size: 28
20504548 TGACATATTG
*
20504558 GTCTTAATTTAGACAAGAAAACATGCTTG
1 GTCTTAATTTAGACAAGAAAACATG-TTT
*
20504587 GTCTTAATTTAGACAAGAAAATATGTTT
1 GTCTTAATTTAGACAAGAAAACATGTTT
* * *
20504615 GCCTTAATTTAAGACAAGAAAAATATTTTTT
1 GTCTTAATTT-AGACAAG-AAAACA-TGTTT
* *
20504646 GTCTTAATTTAGTCAAGAAAACATATTT
1 GTCTTAATTTAGACAAGAAAACATGTTT
* * *
20504674 GTCTCAATTTAGACAAGATACAATATTTTTT
1 GTCTTAATTTAGACAAGA-A-AACA-TGTTT
*
20504705 GTCTTAATTACAGACAAGA
1 GTCTTAATT-TAGACAAGA
20504724 GTTGTCTTAA
Statistics
Matches: 116, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
28 31 0.27
29 37 0.32
30 15 0.13
31 25 0.22
32 8 0.07
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (28 bp):
GTCTTAATTTAGACAAGAAAACATGTTT
Found at i:20504656 original size:59 final size:58
Alignment explanation
Indices: 20504550--20504723 Score: 197
Period size: 59 Copynumber: 3.0 Consensus size: 58
20504540 GGCAGCTTTG
* * * ** *
20504550 ACATATTGGTCTTAATTTAGACAAG-AAAACATGCTTGGTCTTAATTTAGACAAGAAA
1 ACATATTTGCCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
20504607 ATATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATATTTGCCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * * *
20504666 ACATATTTGTCTCAATTTAGACAAGATACAATATTTTTTGTCTTAATTACAGACAAGA
1 ACATATTTGCCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAATT-TAGACAAGA
20504724 GTTGTCTTAA
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
57 14 0.14
58 15 0.15
59 61 0.63
60 7 0.07
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (58 bp):
ACATATTTGCCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:20512386 original size:21 final size:21
Alignment explanation
Indices: 20512361--20512401 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20512351 CACAAAATAA
*
20512361 AAAGTAAATATATTTATATTT
1 AAAGTAAATATATATATATTT
*
20512382 AAAGTACATATATATATATT
1 AAAGTAAATATATATATATT
20512402 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:20515633 original size:2 final size:2
Alignment explanation
Indices: 20515626--20515673 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
20515616 NNNNNNNNNN
20515626 AT AT AT AT 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 AT AT AT AT
20515668 AT AT AT
1 AT AT AT
20515674 TGGGTGAGGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20516328 original size:17 final size:16
Alignment explanation
Indices: 20516288--20516332 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
20516278 AAAGGGAAGG
20516288 AAAAAGACA-AAAGAGA
1 AAAAAGA-AGAAAGAGA
*
20516304 AGAAAGAAGAAAGAGGA
1 AAAAAGAAGAAAGA-GA
20516321 AAAAAGAAGAAA
1 AAAAAGAAGAAA
20516333 TAGGGGGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 13 0.52
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAAGAGA
Found at i:20516613 original size:72 final size:67
Alignment explanation
Indices: 20516464--20516711 Score: 234
Period size: 72 Copynumber: 3.6 Consensus size: 67
20516454 GAAGAAGAAG
* * * *
20516464 AGGGAAGAAAGAAG-AAAGAACAAGAAAAAGAATGAAAGAAGGAGCAGCTGCAGAGGAG-AAGAA
1 AGGGAAGAAAGAAGAAAAGAAAAAGAAAAA-AAGGAGAGAAGGAGCAG-TGCAGAGGAGAAAAAA
*
20516527 AAAG
64 AAAA
*
20516531 AGGGAAGAAAGAAGAAAAAGAAAAAGAAGAAAAAGGAGAGAAGGAGCCGTGACAGAGGAGAATAA
1 AGGGAAGAAAGAAG-AAAAGAAAAAGAA-AAAAAGGAGAGAAGGAGCAGTG-CAGAGGAG-A-AA
20516596 AAAAAAA
61 AAAAAAA
* * * * * *
20516603 AGGGAAGAAAGAAGAAAAAGAAAAATAAGAAGAAGAAGAGAAGGAGCAGCGGTAGAGGAGAAGAA
1 AGGGAAGAAAGAAG-AAAAGAAAAAGAA-AAAAAGGAGAGAAGGAGCAG-TGCAGAGGAGAAAAA
* *
20516668 AGAGA
63 AAAAA
*
20516673 A-GGAAGAAAGAAGAAAA-AAAAAGAAAAAACAAGAGAGAA
1 AGGGAAGAAAGAAGAAAAGAAAAAGAAAAAA-AGGAGAGAA
20516712 TATTTAAGTA
Statistics
Matches: 153, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
66 3 0.02
67 28 0.18
68 6 0.04
69 45 0.29
70 10 0.07
71 1 0.01
72 59 0.39
73 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.31, T:0.02
Consensus pattern (67 bp):
AGGGAAGAAAGAAGAAAAGAAAAAGAAAAAAAGGAGAGAAGGAGCAGTGCAGAGGAGAAAAAAAA
AA
Found at i:20517306 original size:60 final size:61
Alignment explanation
Indices: 20517212--20517517 Score: 364
Period size: 62 Copynumber: 5.0 Consensus size: 61
20517202 ATTTGATTGT
* * * * * * *
20517212 AAAGGGGGACCTAAAGCCCCGATTCATATTTGGTGACGTGGGCAGTTCCCACAAGTAGGCA
1 AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGGAA
* *
20517273 AAA-GGGGACCTGAAGCCCCGATTTATATATGGTGGTGTGGGCAGATTCCACGAGTAGGGAA
1 AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTA-GGAA
* * * * *
20517334 AAAAGGGGACTTGAAGCCCCGATTTATATACGATGGCGTGGGCAGATCTCACGAGTAGGCAA
1 AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGG-AA
* *
20517396 AAATGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGAGAA
1 AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAG-GAA
* * * * *
20517458 AAAGGGGGACCTGAAG-CCCTATTTTATATATGGTGGCATTGGTAGTTTCCCACGAGTAGG
1 AAAGGGGGACCTGAAGCCCCGA-TTTATATATGGTGGCGTGGGCAG-ATCCCACGAGTAGG
20517518 TGATGATGTT
Statistics
Matches: 213, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
60 45 0.21
61 15 0.07
62 140 0.66
63 13 0.06
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (61 bp):
AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGGAA
Found at i:20518511 original size:22 final size:22
Alignment explanation
Indices: 20518464--20518518 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
20518454 TTAATTATTT
* * * *
20518464 AATTTAATCAATTAAGCTCGAT
1 AATTTAATTAATTAAGCACAAC
20518486 AATTTAATTAATTAAGCACAAC
1 AATTTAATTAATTAAGCACAAC
20518508 AATTTAATTAA
1 AATTTAATTAA
20518519 ACAATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.36
Consensus pattern (22 bp):
AATTTAATTAATTAAGCACAAC
Found at i:20518535 original size:36 final size:36
Alignment explanation
Indices: 20518488--20518671 Score: 200
Period size: 36 Copynumber: 5.2 Consensus size: 36
20518478 AGCTCGATAA
* * * *
20518488 TTTAATTAATTAAGCACAACAATTTAATTAAACAAT
1 TTTAATCAATTAGGCACAATAACTTAATTAAACAAT
*
20518524 TTTAATCAATTAGGTC-CAATGACTTAATTAAACAAT
1 TTTAATCAATTAGG-CACAATAACTTAATTAAACAAT
* *
20518560 TTTAATCAACTAGGCCCAATAACTTAATTAAACAA-
1 TTTAATCAATTAGGCACAATAACTTAATTAAACAAT
* * * *
20518595 TTTAATTAATTAGGCCCAATGACTTAATTAAGCAAT
1 TTTAATCAATTAGGCACAATAACTTAATTAAACAAT
*
20518631 TTT-ATTAATTAGGCAC---AACTTAATTAAACAAT
1 TTTAATCAATTAGGCACAATAACTTAATTAAACAAT
*
20518663 TTGAATCAA
1 TTTAATCAA
20518672 GTGCTTGAGT
Statistics
Matches: 128, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
32 16 0.12
33 4 0.03
35 44 0.34
36 63 0.49
37 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (36 bp):
TTTAATCAATTAGGCACAATAACTTAATTAAACAAT
Found at i:20518561 original size:71 final size:70
Alignment explanation
Indices: 20518486--20518671 Score: 234
Period size: 71 Copynumber: 2.7 Consensus size: 70
20518476 TAAGCTCGAT
* *
20518486 AATTTAATTAATTAAGCACAACAATTTAATTAAACAATTTTAATCAATTAGGTCCAATGACTTAA
1 AATTTAATTAATTAGGCACAACAA-TTAATTAAACAATTTTAATCAATTAGGCCCAATGACTTAA
20518551 TTAAAC
65 TTAAAC
* * * * *
20518557 AATTTTAATCAACTAGGCCCAATAACTTAATTAAACAA-TTTAATTAATTAGGCCCAATGACTTA
1 AA-TTTAATTAATTAGGCACAACAA-TTAATTAAACAATTTTAATCAATTAGGCCCAATGACTTA
*
20518621 ATTAAGC
64 ATTAAAC
* *
20518628 AATTTTATTAATTAGGCACAAC--TTAATTAAACAATTTGAATCAA
1 AATTTAATTAATTAGGCACAACAATTAATTAAACAATTTTAATCAA
20518672 GTGCTTGAGT
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
67 12 0.12
68 7 0.07
70 15 0.15
71 34 0.35
72 29 0.30
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (70 bp):
AATTTAATTAATTAGGCACAACAATTAATTAAACAATTTTAATCAATTAGGCCCAATGACTTAAT
TAAAC
Found at i:20520181 original size:17 final size:17
Alignment explanation
Indices: 20520151--20520201 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
20520141 AAATAGAAAG
*
20520151 TAAA-TATATTTATATT
1 TAAAGTATATATATATT
*
20520167 TAAAGTATATATATAAT
1 TAAAGTATATATATATT
*
20520184 AAAAGTATTAGTATATAT
1 TAAAGTA-TA-TATATAT
20520202 ATATAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 2 0.07
19 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TAAAGTATATATATATT
Found at i:20524349 original size:47 final size:47
Alignment explanation
Indices: 20524275--20524391 Score: 171
Period size: 47 Copynumber: 2.5 Consensus size: 47
20524265 GATTTGTTTA
* * *
20524275 ACTTGTTTAGTTCATTGTGTTACTGTGTCAACTTGTATAACTAATTT
1 ACTTGTTTAGTTAATTGTGTTATTGTGTCAACTTATATAACTAATTT
*
20524322 ACTTGTTTAGTTAATTGTGTTATTGTGTCAACTTATATAACTTATTT
1 ACTTGTTTAGTTAATTGTGTTATTGTGTCAACTTATATAACTAATTT
* * *
20524369 ACTTATTTAATTAATCGTGTTAT
1 ACTTGTTTAGTTAATTGTGTTAT
20524392 CACTGTCCAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (47 bp):
ACTTGTTTAGTTAATTGTGTTATTGTGTCAACTTATATAACTAATTT
Found at i:20524800 original size:13 final size:12
Alignment explanation
Indices: 20524782--20524822 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
20524772 AGTATCCATC
20524782 TTTTTTATTATAA
1 TTTTTTATTAT-A
*
20524795 TTTTTTATTATC
1 TTTTTTATTATA
*
20524807 TTTTTTAATATA
1 TTTTTTATTATA
20524819 TTTT
1 TTTT
20524823 GTAATATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTTATTATA
Found at i:20524810 original size:12 final size:12
Alignment explanation
Indices: 20524779--20524813 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
20524769 ATGAGTATCC
20524779 ATCTTTTTTATT
1 ATCTTTTTTATT
*
20524791 ATAATTTTTTATT
1 AT-CTTTTTTATT
20524804 ATCTTTTTTA
1 ATCTTTTTTA
20524814 ATATATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
ATCTTTTTTATT
Found at i:20524822 original size:12 final size:12
Alignment explanation
Indices: 20524782--20524829 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
20524772 AGTATCCATC
*
20524782 TTTTTTATTATAA
1 TTTTTTAATAT-A
* *
20524795 TTTTTTATTATC
1 TTTTTTAATATA
20524807 TTTTTTAATATA
1 TTTTTTAATATA
*
20524819 TTTTGTAATAT
1 TTTTTTAATAT
20524830 TGATTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 20 0.65
13 11 0.35
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTTTAATATA
Found at i:20525146 original size:6 final size:6
Alignment explanation
Indices: 20525129--20525159 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20525119 GGTTCTCTTT
*
20525129 TGTTGA TATTGA TGTTGA TGTTGA TGTTGA T
1 TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA T
20525160 TGATTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (6 bp):
TGTTGA
Found at i:20531765 original size:30 final size:30
Alignment explanation
Indices: 20531715--20531788 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
20531705 ATATACATTC
*
20531715 CCACACCACATCATCACCGGCA-TGTGCACTT
1 CCACACCACA-CACCACCGGCACTGT-CACTT
20531746 CCACACCACACACCACCGGCACTGTCACTT
1 CCACACCACACACCACCGGCACTGTCACTT
* *
20531776 GCACTCC-CACACC
1 CCACACCACACACC
20531789 GCACATGCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 6 0.15
30 20 0.51
31 13 0.33
ACGTcount: A:0.26, C:0.49, G:0.11, T:0.15
Consensus pattern (30 bp):
CCACACCACACACCACCGGCACTGTCACTT
Found at i:20545076 original size:36 final size:35
Alignment explanation
Indices: 20545035--20545122 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 35
20545025 TCATCAGCTT
*
20545035 ATGTGCACTCCCACACCGCACATAGCTAGA-ATCATC
1 ATGTGCACTCCCACACCGCACAAAGC-A-ATATCATC
*
20545071 ATGTGCACTCCTACACCGCACAAAGCAATATCATC
1 ATGTGCACTCCCACACCGCACAAAGCAATATCATC
* *
20545106 ATATACACTCCCACACC
1 ATGTGCACTCCCACACC
20545123 ACATCATCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.02
35 21 0.46
36 24 0.52
ACGTcount: A:0.33, C:0.38, G:0.10, T:0.19
Consensus pattern (35 bp):
ATGTGCACTCCCACACCGCACAAAGCAATATCATC
Found at i:20545115 original size:35 final size:36
Alignment explanation
Indices: 20545040--20545122 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 36
20545030 AGCTTATGTG
* * *
20545040 CACTCCCACACCGCACATAGCTAGAATCATCATGTG
1 CACTCCCACACCGCACAAAGCTAGAATCATCATATA
*
20545076 CACTCCTACACCGCACAAAGC-A-ATATCATCATATA
1 CACTCCCACACCGCACAAAGCTAGA-ATCATCATATA
20545111 CACTCCCACACC
1 CACTCCCACACC
20545123 ACATCATCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 1 0.02
35 21 0.51
36 19 0.46
ACGTcount: A:0.34, C:0.40, G:0.08, T:0.18
Consensus pattern (36 bp):
CACTCCCACACCGCACAAAGCTAGAATCATCATATA
Found at i:20546432 original size:20 final size:20
Alignment explanation
Indices: 20546390--20546446 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
20546380 CTCCTATAAA
* * * *
20546390 AACATAAAATAAATATAAAT
1 AACATAAAACAAACATTATT
*
20546410 AACATAAAACTAACATTATT
1 AACATAAAACAAACATTATT
*
20546430 AACTTAAAACAAACATT
1 AACATAAAACAAACATT
20546447 TAAACACAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.26
Consensus pattern (20 bp):
AACATAAAACAAACATTATT
Found at i:20551113 original size:180 final size:179
Alignment explanation
Indices: 20550798--20551142 Score: 487
Period size: 180 Copynumber: 1.9 Consensus size: 179
20550788 TTATCTTTAA
* * * * * * *
20550798 GAATTTATTTCTAATAAAATTTATCCTGATTGATAACTCATGGAGCTATTGTAGAATAAATTTTC
1 GAATTTAATTCTAATAAAAATTATCCTAATAGATAACTCAAGGAACTATTCTAGAATAAATTTTC
* *
20550863 AAGATTTTAGGAGCTGATTTGGCTATTCAAAAAATTAAAAAACCTTGACCTTTATCTGCATGTAG
66 AAAATTTTAGGAGCTGATTTGGCTATTCAAAAAATTAAAAAACCATGACCTTTATCTGCATGTAG
*
20550928 TAGAATC-GATTTTTGAGACATTTTGAAACTCTTTGTGACTTAAACTTAG
131 TAGAATCAG-CTTTTGAGACATTTTGAAACTCTTTGTGACTTAAACTTAG
20550977 GAATTTAATTCTTAATAAAAATTATCCTAATAGATAACTCAAGGAACTATTCTAGAATAAATTTT
1 GAATTTAATTC-TAATAAAAATTATCCTAATAGATAACTCAAGGAACTATTCTAGAATAAATTTT
* * * *
20551042 CAAAATTTTAGGAGGTGATTTGGTTATTCCAAAAATTAAAAAACCATGACCTTTATTTGC-TGGT
65 CAAAATTTTAGGAGCTGATTTGGCTATTCAAAAAATTAAAAAACCATGACCTTTATCTGCAT-GT
* * * *
20551106 GGTAGAATCAGCTTTTGAGTCTTTTTGAAACTGTTTG
129 AGTAGAATCAGCTTTTGAGACATTTTGAAACTCTTTG
20551143 GTGGTGTAAA
Statistics
Matches: 145, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
179 11 0.08
180 133 0.92
181 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (179 bp):
GAATTTAATTCTAATAAAAATTATCCTAATAGATAACTCAAGGAACTATTCTAGAATAAATTTTC
AAAATTTTAGGAGCTGATTTGGCTATTCAAAAAATTAAAAAACCATGACCTTTATCTGCATGTAG
TAGAATCAGCTTTTGAGACATTTTGAAACTCTTTGTGACTTAAACTTAG
Found at i:20552801 original size:20 final size:19
Alignment explanation
Indices: 20552763--20552801 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
20552753 AAGAAAACCT
*
20552763 AGGTGAAAATTCAAAGAAA
1 AGGTGAAAAATCAAAGAAA
*
20552782 AGGTGAAGAAATCAATGAAA
1 AGGTGAA-AAATCAAAGAAA
20552802 CAAGCTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (19 bp):
AGGTGAAAAATCAAAGAAA
Found at i:20553864 original size:21 final size:20
Alignment explanation
Indices: 20553831--20553987 Score: 97
Period size: 20 Copynumber: 8.2 Consensus size: 20
20553821 GGGAGTGCGC
20553831 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
*
20553851 ATGAGCTGGGTGATTATGATG
1 ATGAGCT-GGTGATGATGATG
* *
20553872 ATGGGGTTGGTGA-GATGATG
1 AT-GAGCTGGTGATGATGATG
20553892 ATGA--TGG-G-T-AT-AT-
1 ATGAGCTGGTGATGATGATG
*
20553905 ATNGAG-TAGG-GA-G-TG-CG
1 AT-GAGCT-GGTGATGATGATG
20553922 CATGAGCTGGTGATGATGATG
1 -ATGAGCTGGTGATGATGATG
*
20553943 ATGAGCTGGTGATGATGAGG
1 ATGAGCTGGTGATGATGATG
* *
20553963 ATGGGTTGGTGAAATGATGATG
1 ATGAGCTGGTG--ATGATGATG
20553985 ATG
1 ATG
20553988 GTATATACGT
Statistics
Matches: 108, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
13 2 0.02
14 4 0.04
15 3 0.03
16 5 0.05
17 8 0.07
18 5 0.05
19 2 0.02
20 45 0.42
21 20 0.19
22 14 0.13
ACGTcount: A:0.25, C:0.04, G:0.41, T:0.29
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:20565453 original size:13 final size:13
Alignment explanation
Indices: 20565437--20565472 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
20565427 TTTAGTTTAA
*
20565437 ATTTTGGTTAATT
1 ATTTTAGTTAATT
20565450 ATTTTAGTTAATT
1 ATTTTAGTTAATT
*
20565463 AATTTAGTTA
1 ATTTTAGTTA
20565473 TTTGATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (13 bp):
ATTTTAGTTAATT
Found at i:20570466 original size:74 final size:73
Alignment explanation
Indices: 20570361--20570564 Score: 227
Period size: 73 Copynumber: 2.8 Consensus size: 73
20570351 TCAGATAGAG
* * * * *
20570361 AGCTCTTAGTTGAGTAAC-ATACTTCTTAGTCGATTAAGTCGT-TTCTGTCTTTTGATACC-AG-
1 AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTT-TGTC-TCT-AAACCTAGT
*
20570422 ATTCTGGCAGTA
63 A-TCTGGCAATA
*
20570434 AGCTTTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTTTGTCTCTAAACCTAGTATC
1 AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTTTGTCTCTAAACCTAGTATC
*
20570499 TGGCAATG
66 TGGCAATA
* * * * *
20570507 AGCTCTTAGTCGACTAACAATGCTTCTCAGTCGATTATGTCTTCTTTATCTCTGAACC
1 AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTTTGTCTCTAAACC
20570565 CAGCCAACTT
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
72 4 0.04
73 79 0.70
74 28 0.25
75 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (73 bp):
AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTTTGTCTCTAAACCTAGTATC
TGGCAATA
Found at i:20571292 original size:22 final size:22
Alignment explanation
Indices: 20571266--20571309 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20571256 CCTAAATTAC
20571266 CCCTAAATTACTTCTACTTTCT
1 CCCTAAATTACTTCTACTTTCT
*
20571288 CCCTAAATTTCTTCTACTTTCT
1 CCCTAAATTACTTCTACTTTCT
20571310 ATCTCTGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (22 bp):
CCCTAAATTACTTCTACTTTCT
Found at i:20576602 original size:20 final size:20
Alignment explanation
Indices: 20576577--20576617 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20576567 ATAAGCCTTG
*
20576577 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
20576597 TTGATTTATATGAAATGAAA
1 TTGATTTATATGAAATGAAA
20576617 T
1 T
20576618 GAGATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:20576633 original size:25 final size:25
Alignment explanation
Indices: 20576586--20576635 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20576576 GTTGATTTTT
*
20576586 ATGAAATGAAATTGATTTATATGAA
1 ATGAAATGAAATTGATGTATATGAA
*
20576611 ATGAAATGAGATTTGATGT-TATGAA
1 ATGAAATGA-AATTGATGTATATGAA
20576636 TCATATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (25 bp):
ATGAAATGAAATTGATGTATATGAA
Found at i:20582284 original size:20 final size:20
Alignment explanation
Indices: 20582259--20582299 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20582249 GTAAGCCTTG
*
20582259 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
20582279 TTGATTTATATGAAATGAAA
1 TTGATTTATATGAAATGAAA
20582299 T
1 T
20582300 GAGATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:20582315 original size:25 final size:25
Alignment explanation
Indices: 20582268--20582317 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20582258 GTTGATTTTT
*
20582268 ATGAAATGAAATTGATTTATATGAA
1 ATGAAATGAAATTGATGTATATGAA
*
20582293 ATGAAATGAGATTTGATGT-TATGAA
1 ATGAAATGA-AATTGATGTATATGAA
20582318 TCATATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (25 bp):
ATGAAATGAAATTGATGTATATGAA
Found at i:20589308 original size:40 final size:40
Alignment explanation
Indices: 20589253--20589356 Score: 142
Period size: 38 Copynumber: 2.6 Consensus size: 40
20589243 ACCCAGCTCA
*
20589253 TGTGCATCCCCCCACATCGTGCACATAGCTAGA-GTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCTA-ATGCCATCG
* *
20589293 TGTGCATCCCCCCACATTGTG--CATAGTTAATGCCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCTAATGCCATCG
*
20589331 TGTGCATCGCCCCACATCGTGCACAT
1 TGTGCATCCCCCCACATCGTGCACAT
20589357 GGGCAATATC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
37 1 0.02
38 32 0.57
40 23 0.41
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAGCTAATGCCATCG
Found at i:20589474 original size:2 final size:2
Alignment explanation
Indices: 20589467--20589493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20589457 TATGACATAG
20589467 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20589494 CAATATTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20590097 original size:22 final size:22
Alignment explanation
Indices: 20590072--20590115 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20590062 TCTTCCATCA
20590072 AACACT-TTCTAAGTTTACATGT
1 AACACTATTCTAA-TTTACATGT
*
20590094 AACACTATTCTCATTTACATGT
1 AACACTATTCTAATTTACATGT
20590116 TGCCACCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (22 bp):
AACACTATTCTAATTTACATGT
Found at i:20593788 original size:29 final size:29
Alignment explanation
Indices: 20593746--20593804 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20593736 AAGTATGCAA
20593746 AGAGTTTTTGCTATTTTTGAGCTTTTTTT
1 AGAGTTTTTGCTATTTTTGAGCTTTTTTT
20593775 AGAGTTTTTGCTATTTTTGAGCTTTTTTT
1 AGAGTTTTTGCTATTTTTGAGCTTTTTTT
20593804 A
1 A
20593805 TCTTGGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.15, C:0.07, G:0.17, T:0.61
Consensus pattern (29 bp):
AGAGTTTTTGCTATTTTTGAGCTTTTTTT
Found at i:20594098 original size:73 final size:73
Alignment explanation
Indices: 20593971--20594178 Score: 247
Period size: 73 Copynumber: 2.8 Consensus size: 73
20593961 CTAGACAGAG
** * * * * **
20593971 AGCTCTTAGTTAACTAAC-ATACTTCTTAGTCGATTAAGTCGTTTCTATCTTCTGATCTTAGCTT
1 AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTC-TCTGAACCCAGCTT
* *
20594035 CTGGCAGTA
65 CTAGCAATA
* * *
20594044 AGCTCTTAGTCGACTAACAATGTTTCTTAGTCGATTAAGTCATCTCTGTCTCTGAACCCAGTTTC
1 AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACCCAGCTTC
*
20594109 TAGCAATG
66 TAGCAATA
* * *
20594117 AGCTCTTAGTCGACTAACAATGCTTCTTAGTCAATTAAGTTGTCTCTGTCTCTAAACCCAGC
1 AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACCCAGC
20594179 CAAATTCATT
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
73 88 0.77
74 26 0.23
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (73 bp):
AGCTCTTAGTCGACTAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTCTCTGAACCCAGCTTC
TAGCAATA
Found at i:20602761 original size:37 final size:37
Alignment explanation
Indices: 20602720--20602834 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
20602710 GTTGTGTGAG
20602720 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
20602757 GATGTT-AGAGTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTGA-AGTGTGCGAGTAGGGAGTGCACACATGAT
* *
20602794 GATGTTGAAATGTGCGAGTAAGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
20602831 GATG
1 GATG
20602835 AATGCATATG
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
36 1 0.01
37 72 0.97
38 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24
Consensus pattern (37 bp):
GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
Found at i:20603036 original size:52 final size:52
Alignment explanation
Indices: 20602958--20603061 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
20602948 ATGACTTTTG
20602958 ATGTAACAAGACCCATTTCAATTAAAATGCTCTGTTTCTCGCTGCAACGAGA
1 ATGTAACAAGACCCATTTCAATTAAAATGCTCTGTTTCTCGCTGCAACGAGA
* *
20603010 ATGTAACAAGACCTATTTCAATTAAAATGCTCTGTTTCTCGCTGCAGCGAGA
1 ATGTAACAAGACCCATTTCAATTAAAATGCTCTGTTTCTCGCTGCAACGAGA
20603062 TTCATTTTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (52 bp):
ATGTAACAAGACCCATTTCAATTAAAATGCTCTGTTTCTCGCTGCAACGAGA
Found at i:20616152 original size:2 final size:2
Alignment explanation
Indices: 20616145--20616188 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
20616135 TTTACAAACT
*
20616145 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20616187 TA
1 TA
20616189 CGTAAACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20617461 original size:2 final size:2
Alignment explanation
Indices: 20617454--20617482 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20617444 ATAATATTTC
20617454 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20617483 CTAGGCTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20618705 original size:16 final size:17
Alignment explanation
Indices: 20618683--20618727 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
20618673 TAAGCCAAGG
20618683 ATAAAAAATTTGAATAT
1 ATAAAAAATTTGAATAT
*
20618700 -TAAAAACATATGAATAT
1 ATAAAAA-ATTTGAATAT
*
20618717 ATAAACAATTT
1 ATAAAAAATTT
20618728 AAACTCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.26
17 12 0.52
18 5 0.22
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (17 bp):
ATAAAAAATTTGAATAT
Found at i:20621401 original size:255 final size:252
Alignment explanation
Indices: 20620944--20621533 Score: 670
Period size: 255 Copynumber: 2.3 Consensus size: 252
20620934 TGCGACCAAC
** * * * *
20620944 AAAACAAGTATTGTCAAAATATTGGTGTAAATTTATAATATTTAACGTAAAAAGTCAATTAAGT-
1 AAAACAAACATTGTCAAAATATTGATGTAAATGTATAA-ATTTAACATAACAAGTCAATTAAGTC
* * * * * * ***
20621008 AAAAAAAATATAATTTTTGTGAAAATTAAATATTTAAATTTATGTTATTGAGTTAAAAGTTTTTA
65 AAAATAAATATATTTTTTGTGAAAATTAAACATTTAAATTGATATTATTGAGATAAAAGTTAACA
* *
20621073 ACGGTTTACAAATTTTAATTTATAATGAAATAATAGTAAGGATAAAAATACATATAATGAAAATT
130 ACAGTTTACAAATTTTAATTTATAATGAAATAATAATAAGGATAAAAATACATATAATGAAAATT
* * * *
20621138 CGCAATTGAAAAACCTTGACATAAACTTGTAAGAAGTAATGTAAAAAATAATAAAAG-T
195 AGCAATTGAAAAACCTTGACATAAACCTATAAGAAGTAACGTAAAAAATAAT-AAAGTT
** * * * *
20621196 GGAACGAGCATTGTCAAAATATTGACGTAAATGTATGAAATTTAACATAACAAGTCAATTAATTC
1 AAAACAAACATTGTCAAAATATTGATGTAAATGTAT-AAATTTAACATAACAAGTCAATTAAGTC
*
20621261 AAAATAAATATATTTTTT-TGGAAAATTAAACATTTAAATTGATATTGTTGAGATAAAAGTATAA
65 AAAATAAATATATTTTTTGT-GAAAATTAAACATTTAAATTGATATTATTGAGATAAAAGT-TAA
** * *
20621325 CATACAGTTTGTAGATTTTAATTTATAAATG-AATAATAATAAGGATAAAAATA-ATTATAGTGA
128 CA-ACAGTTTACAAATTTTAATTTAT-AATGAAATAATAATAAGGATAAAAATACA-TATAATGA
** * *
20621388 AAATTAGCAATTGAAAAACCTTGATGTAAACCTATAAGAATTAACGTAAAAAATTATAAAGTT
190 AAATTAGCAATTGAAAAACCTTGACATAAACCTATAAGAAGTAACGTAAAAAATAATAAAGTT
* * * * * *
20621451 AAAACAAACATTGTTAAAATATCGATGTAAATGCATTAAATTTAATATAACAAATCTA-TAAGTC
1 AAAACAAACATTGTCAAAATATTGATGTAAATGTA-TAAATTTAACATAACAAGTCAATTAAGTC
20621515 AAAATAAATATAATTTTTT
65 AAAATAAATAT-ATTTTTT
20621534 AAAAGTTAAA
Statistics
Matches: 282, Mismatches: 46, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
252 52 0.18
253 53 0.19
254 23 0.08
255 149 0.53
256 5 0.02
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.34
Consensus pattern (252 bp):
AAAACAAACATTGTCAAAATATTGATGTAAATGTATAAATTTAACATAACAAGTCAATTAAGTCA
AAATAAATATATTTTTTGTGAAAATTAAACATTTAAATTGATATTATTGAGATAAAAGTTAACAA
CAGTTTACAAATTTTAATTTATAATGAAATAATAATAAGGATAAAAATACATATAATGAAAATTA
GCAATTGAAAAACCTTGACATAAACCTATAAGAAGTAACGTAAAAAATAATAAAGTT
Found at i:20624888 original size:4 final size:4
Alignment explanation
Indices: 20624861--20624911 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
20624851 TATTCGAGCT
* *
20624861 TTTC TCTTC TTTT TTTC TTTTC TTTC TTTCC TTTC -TTC TTTC TTCC TTTC
1 TTTC T-TTC TTTC TTTC -TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC
20624911 T
1 T
20624912 CTCTCTTAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 3 0.08
4 24 0.62
5 12 0.31
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:20624888 original size:9 final size:9
Alignment explanation
Indices: 20624859--20624897 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
20624849 CTTATTCGAG
20624859 CTTTTCTCTT
1 CTTTTCT-TT
20624869 CTTTT-TTT
1 CTTTTCTTT
20624877 CTTTTCTTT
1 CTTTTCTTT
*
20624886 CTTTCCTTT
1 CTTTTCTTT
20624895 CTT
1 CTT
20624898 CTTTCTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 7 0.26
9 15 0.56
10 5 0.19
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
CTTTTCTTT
Found at i:20631837 original size:35 final size:35
Alignment explanation
Indices: 20631791--20631861 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
20631781 CTAAGTGAAA
20631791 GATAATTGTCGAGGAAATAATTCAAGAAGAAAATG
1 GATAATTGTCGAGGAAATAATTCAAGAAGAAAATG
* *
20631826 GATAATTGTCGAGGATATAATTCAAGGAGAAAATG
1 GATAATTGTCGAGGAAATAATTCAAGAAGAAAATG
20631861 G
1 G
20631862 GTGACCTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.25, T:0.24
Consensus pattern (35 bp):
GATAATTGTCGAGGAAATAATTCAAGAAGAAAATG
Found at i:20632612 original size:25 final size:25
Alignment explanation
Indices: 20632580--20632639 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
20632570 TGGTCTATTA
20632580 TTATACGTGGCAAGACCACGAGTTG
1 TTATACGTGGCAAGACCACGAGTTG
* *
20632605 TTATACGTGGCTAGGCCACGAGTTG
1 TTATACGTGGCAAGACCACGAGTTG
*
20632630 ATATACGTGG
1 TTATACGTGG
20632640 TTGCAATCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (25 bp):
TTATACGTGGCAAGACCACGAGTTG
Found at i:20634490 original size:37 final size:37
Alignment explanation
Indices: 20634436--20634551 Score: 216
Period size: 37 Copynumber: 3.2 Consensus size: 37
20634426 TGATGTTGGG
*
20634436 TGATGATG-TTGAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATCGAGTGTGCGAGTAGGGAGTGCACACA
20634472 TGATGATGATCGAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATCGAGTGTGCGAGTAGGGAGTGCACACA
20634509 TGATGATGATCGAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATCGAGTGTGCGAGTAGGGAGTGCACACA
20634546 TGATGA
1 TGATGA
20634552 CGATGTATGT
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
36 8 0.10
37 70 0.90
ACGTcount: A:0.27, C:0.12, G:0.38, T:0.23
Consensus pattern (37 bp):
TGATGATGATCGAGTGTGCGAGTAGGGAGTGCACACA
Found at i:20634784 original size:21 final size:22
Alignment explanation
Indices: 20634738--20634784 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
20634728 GGTGCCCTGC
*
20634738 TTCTCGTTGCAGCGAGAAAGCA
1 TTCTCGCTGCAGCGAGAAAGCA
*
20634760 TTCTCGCTGCAGTGAGAAA-CA
1 TTCTCGCTGCAGCGAGAAAGCA
20634781 TTCT
1 TTCT
20634785 ATTTTGGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (22 bp):
TTCTCGCTGCAGCGAGAAAGCA
Found at i:20637728 original size:35 final size:34
Alignment explanation
Indices: 20637659--20637794 Score: 132
Period size: 35 Copynumber: 4.0 Consensus size: 34
20637649 CCACCAAGCT
* ** * * *
20637659 TTTACAATGGCTTTTCACAAGCTCAGCCACAACC
1 TTTACAATGGTTTTTCACGGGATCAACCAAAACC
*
20637693 TTTCACAATAGTTTTTCACGGGATCAACCAAAACC
1 TTT-ACAATGGTTTTTCACGGGATCAACCAAAACC
* * ** *
20637728 --TAAAATGGCTTTTCAAAGGCTCAACCAAAACC
1 TTTACAATGGTTTTTCACGGGATCAACCAAAACC
20637760 TTTAACAATGGTTTTTCACGGGATCAACCAAAACC
1 TTT-ACAATGGTTTTTCACGGGATCAACCAAAACC
20637795 CCAAACTAAC
Statistics
Matches: 80, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
32 25 0.31
33 1 0.01
34 4 0.05
35 50 0.62
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (34 bp):
TTTACAATGGTTTTTCACGGGATCAACCAAAACC
Found at i:20637774 original size:67 final size:67
Alignment explanation
Indices: 20637664--20637794 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
20637654 AAGCTTTTAC
* * *
20637664 AATGGCTTTTCACAAGCTCAGCCACAACCTTTCACAATAGTTTTTCACGGGATCAACCAAAACCT
1 AATGGCTTTTCACAAGCTCAACCAAAACCTTTAACAATAGTTTTTCACGGGATCAACCAAAACCT
20637729 AA
66 AA
*
20637731 AATGGCTTTTCA-AAGGCTCAACCAAAACCTTTAACAATGGTTTTTCACGGGATCAACCAAAACC
1 AATGGCTTTTCACAA-GCTCAACCAAAACCTTTAACAATAGTTTTTCACGGGATCAACCAAAACC
20637795 CCAAACTAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 2 0.03
67 57 0.97
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (67 bp):
AATGGCTTTTCACAAGCTCAACCAAAACCTTTAACAATAGTTTTTCACGGGATCAACCAAAACCT
AA
Found at i:20638514 original size:56 final size:56
Alignment explanation
Indices: 20638438--20638549 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
20638428 TTCATTATCC
* *
20638438 AACTAAAAGGCTTCTATTTTGTTGATCAATTGTGTCTCCTTATTCATGTGATTTTT
1 AACTAAAAGGCTTCTATTTTGTTGATCAATTGTGGCTCCTTATTCATATGATTTTT
* *
20638494 AACTAAGAGGCTTCTGTTTTGTTGATCAATTGTGGCTCCTTATTCATATGATTTTT
1 AACTAAAAGGCTTCTATTTTGTTGATCAATTGTGGCTCCTTATTCATATGATTTTT
20638550 GATATGTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.47
Consensus pattern (56 bp):
AACTAAAAGGCTTCTATTTTGTTGATCAATTGTGGCTCCTTATTCATATGATTTTT
Found at i:20639201 original size:29 final size:29
Alignment explanation
Indices: 20639168--20639226 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20639158 TGATCATTTT
20639168 GTCATAATCAAAACTATAATAATTTTAAA
1 GTCATAATCAAAACTATAATAATTTTAAA
20639197 GTCATAATCAAAACTATAATAATTTTAAA
1 GTCATAATCAAAACTATAATAATTTTAAA
20639226 G
1 G
20639227 CTAACAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (29 bp):
GTCATAATCAAAACTATAATAATTTTAAA
Found at i:20642260 original size:31 final size:31
Alignment explanation
Indices: 20642178--20642260 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
20642168 GACCCCATCA
* * *
20642178 ACCTTGGGTTGGCAATGTACATCCCCATTGC
1 ACCTTGGGCTGGCAATGTATAACCCCATTGC
* * *
20642209 ACCTTGGGCTGGCAACGTATAACCCTATTGT
1 ACCTTGGGCTGGCAATGTATAACCCCATTGC
*
20642240 ACCTTGGGCTAGCAATGTATA
1 ACCTTGGGCTGGCAATGTATA
20642261 TTCTGTCACA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (31 bp):
ACCTTGGGCTGGCAATGTATAACCCCATTGC
Found at i:20655859 original size:37 final size:37
Alignment explanation
Indices: 20655818--20655936 Score: 211
Period size: 37 Copynumber: 3.2 Consensus size: 37
20655808 AATGCAATAT
*
20655818 CATCATTATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
*
20655855 CATCATCATGTGTGCACTCCCTACTCGCACACTCCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
*
20655892 CATCATCATGTGTGCACTCCCTACTCGTACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
20655929 CATCATCA
1 CATCATCA
20655937 CAAAACATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 78 1.00
ACGTcount: A:0.25, C:0.37, G:0.10, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:20656636 original size:20 final size:20
Alignment explanation
Indices: 20656611--20656651 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20656601 GAAAAAGAAT
20656611 AAGAAGCTGCTGGAAAAATG
1 AAGAAGCTGCTGGAAAAATG
*
20656631 AAGAAGCTGCTGGAGAAATG
1 AAGAAGCTGCTGGAAAAATG
20656651 A
1 A
20656652 GATATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.32, T:0.15
Consensus pattern (20 bp):
AAGAAGCTGCTGGAAAAATG
Found at i:20661752 original size:225 final size:224
Alignment explanation
Indices: 20661361--20661810 Score: 891
Period size: 225 Copynumber: 2.0 Consensus size: 224
20661351 ACCCGACAAT
20661361 GTTCACCATACAAGTAATGCCTCTAGTTTTTTAAAGCAAACACCACTACTGCTAACTCTAAATCG
1 GTTCACCATACAAGTAATGCCTCTAGTTTTTTAAAGCAAACACCACTACTGCTAACTCTAAATCG
20661426 TGGGTAGGATAATTTACTTCATGCCTCTTTAGTTGTCTAGAAGCATAAGCCAACAACTTTTTCAT
66 TGGGTAGGATAATTTACTTCATGCCTCTTTAGTTGTCTAGAAGCATAAGCCAACAACTTTTTCAT
20661491 TTTGCATCAGTACGCACCCCAACCCCAACTTTAAGGCATCACTATAAACTACAAATCCCTTACCA
131 TTTGCATCAGTACGCACCCCAACCCCAACTTTAAGGCATCACTATAAACTACAAATCCCTTACCA
20661556 CTCACAGGAAGTGCTAAAACGGGAGTGGA
196 CTCACAGGAAGTGCTAAAACGGGAGTGGA
20661585 NGTTCACCATACAAGTAATGCCTCTAGTTTTTTAAAGCAAACACCACTACTGCTAACTCTAAATC
1 -GTTCACCATACAAGTAATGCCTCTAGTTTTTTAAAGCAAACACCACTACTGCTAACTCTAAATC
20661650 GTGGGTAGGATAATTTACTTCATGCCTCTTTAGTTGTCTAGAAGCATAAGCCAACAACTTTTTCA
65 GTGGGTAGGATAATTTACTTCATGCCTCTTTAGTTGTCTAGAAGCATAAGCCAACAACTTTTTCA
20661715 TTTTGCATCAGTACGCACCCCAACCCCAACTTTAAGGCATCACTATAAACTACAAATCCCTTACC
130 TTTTGCATCAGTACGCACCCCAACCCCAACTTTAAGGCATCACTATAAACTACAAATCCCTTACC
20661780 ACTCACAGGAAGTGCTAAAACGGGAGTGGA
195 ACTCACAGGAAGTGCTAAAACGGGAGTGGA
20661810 G
1 G
20661811 GTTAACTGGT
Statistics
Matches: 225, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
224 1 0.00
225 224 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (224 bp):
GTTCACCATACAAGTAATGCCTCTAGTTTTTTAAAGCAAACACCACTACTGCTAACTCTAAATCG
TGGGTAGGATAATTTACTTCATGCCTCTTTAGTTGTCTAGAAGCATAAGCCAACAACTTTTTCAT
TTTGCATCAGTACGCACCCCAACCCCAACTTTAAGGCATCACTATAAACTACAAATCCCTTACCA
CTCACAGGAAGTGCTAAAACGGGAGTGGA
Found at i:20668318 original size:68 final size:68
Alignment explanation
Indices: 20668157--20668488 Score: 349
Period size: 68 Copynumber: 4.9 Consensus size: 68
20668147 CACATACATG
* * * *
20668157 CTTACTCATCTCATA-ACGTATATGGAATTTACATCATATACATAATCTCATGGC---AATAATG
1 CTTAATCATCTCATATA-GTATATGGAATATACATCATATACATATTCTCATGGCATTAATCATG
20668218 C-TA
65 CATA
* * *
20668221 GCTCAATCATCTCATGTAGTACATGGAATATACATCATATACATATTCTCATGGCATTAATCATG
1 -CTTAATCATCTCATATAGTATATGGAATATACATCATATACATATTCTCATGGCATTAATCATG
20668286 CATA
65 CATA
* * *
20668290 CTTAATCATCTCATGTAGTATATGGAATATACATTATATACATATTCTCATGGAATTAATCATGC
1 CTTAATCATCTCATATAGTATATGGAATATACATCATATACATATTCTCATGGCATTAATCATGC
20668355 ATA
66 ATA
* * * * * *
20668358 CTTAATCACCTCATATGGTATATGGAATTTACATCATATACACCATCCT-AT--AATATACATCA
1 CTTAATCATCTCATATAGTATATGGAATATACATCATATACA-TATTCTCATGGCAT-TA-ATCA
20668420 TGCATA
63 TGCATA
* * * * * *
20668426 CTTGATCATCTCATATGGTACATGGAAT-TCACATCATATACATAATCTTATGGCATTCATCAT
1 CTTAATCATCTCATATAGTATATGGAATAT-ACATCATATACATATTCTCATGGCATTAATCAT
20668489 ACCAACATGC
Statistics
Matches: 229, Mismatches: 26, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
65 46 0.20
66 4 0.02
67 6 0.03
68 164 0.72
69 7 0.03
70 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (68 bp):
CTTAATCATCTCATATAGTATATGGAATATACATCATATACATATTCTCATGGCATTAATCATGC
ATA
Found at i:20669709 original size:15 final size:16
Alignment explanation
Indices: 20669689--20669721 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
20669679 AGATTCAATA
20669689 AAAATCCAAAA-AATC
1 AAAATCCAAAAGAATC
20669704 AAAATCCAAAAGAATC
1 AAAATCCAAAAGAATC
20669720 AA
1 AA
20669722 GATCTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.67, C:0.18, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAATCCAAAAGAATC
Found at i:20670419 original size:28 final size:28
Alignment explanation
Indices: 20670383--20670546 Score: 177
Period size: 29 Copynumber: 5.6 Consensus size: 28
20670373 TGCAAACTTT
20670383 AATATGTTTGTCTTAATTTAGACAAAAA
1 AATATGTTTGTCTTAATTTAGACAAAAA
* *
20670411 AACATGTTTGTTCTTAATTTAGACAAGAA
1 AATATGTTTG-TCTTAATTTAGACAAAAA
20670440 AATATGTTTGTCTTAATTTAAGACAAAAAA
1 AATATGTTTGTCTTAATTT-AGAC-AAAAA
* *
20670470 AATATTTTTTGTCTT-ATATTAGACAAGAA
1 AATA-TGTTTGTCTTAAT-TTAGACAAAAA
* * *
20670499 AACATATTTGTCTCAATTTAGACAAGATAA
1 AATATGTTTGTCTTAATTTAGACAA-A-AA
* *
20670529 AATATTTTTATCTTAATT
1 AATATGTTTGTCTTAATT
20670547 AAAGACAAGA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
28 34 0.30
29 39 0.34
30 30 0.26
31 11 0.10
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (28 bp):
AATATGTTTGTCTTAATTTAGACAAAAA
Found at i:20670498 original size:59 final size:59
Alignment explanation
Indices: 20670383--20670537 Score: 201
Period size: 59 Copynumber: 2.6 Consensus size: 59
20670373 TGCAAACTTT
* *
20670383 AATATGTTTGTCTTAATTTAGAC-AAAAAAACA-TGTTTGTTCTTAATTTAGACAAGAA
1 AATATGTTTGTCTTAATTTAGACAAAAAAAATATTTTTTGTTCTTAATTTAGACAAGAA
20670440 AATATGTTTGTCTTAATTTAAGACAAAAAAAATATTTTTTG-TCTT-ATATTAGACAAGAA
1 AATATGTTTGTCTTAATTT-AGACAAAAAAAATATTTTTTGTTCTTAAT-TTAGACAAGAA
* * * *
20670499 AACATATTTGTCTCAATTTAGACAAGATAAAATATTTTT
1 AATATGTTTGTCTTAATTTAGACAA-AAAAAATATTTTT
20670538 ATCTTAATTA
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
57 19 0.22
58 12 0.14
59 51 0.59
60 5 0.06
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (59 bp):
AATATGTTTGTCTTAATTTAGACAAAAAAAATATTTTTTGTTCTTAATTTAGACAAGAA
Found at i:20670553 original size:59 final size:54
Alignment explanation
Indices: 20670389--20670556 Score: 183
Period size: 59 Copynumber: 2.9 Consensus size: 54
20670379 CTTTAATATG
* * *
20670389 TTTGTCTTAATTTAGACAAAAAAACATGTTTGTTCTTAATTTAGACAAGAAAATATG
1 TTTGTCTTAATTTAGACAAAAAAATAT-TTT-TTCTTAA-TTAGACAAGAAAACATA
20670446 TTTGTCTTAATTTAAGACAAAAAAAATATTTTTTGTCTTATATTAGACAAGAAAACATA
1 TTTGTCTTAATTT-AGAC-AAAAAAATA-TTTTT-TCTTA-ATTAGACAAGAAAACATA
*
20670505 TTTGTCTCAATTTAGACAAGATAAAATATTTTTATCTTAATTAAAGACAAGA
1 TTTGTCTTAATTTAGACAA-A-AAAATATTTTT-TCTTAATT--AGACAAGA
20670557 GTTGTCTTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
57 18 0.19
58 20 0.21
59 57 0.59
60 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (54 bp):
TTTGTCTTAATTTAGACAAAAAAATATTTTTTCTTAATTAGACAAGAAAACATA
Found at i:20670720 original size:17 final size:17
Alignment explanation
Indices: 20670698--20670730 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20670688 ATAATAATAA
20670698 AATAAG-AGTTATTATTC
1 AATAAGAAGTT-TTATTC
20670715 AATAAGAAGTTTTATT
1 AATAAGAAGTTTTATT
20670731 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAAGAAGTTTTATTC
Found at i:20673763 original size:28 final size:28
Alignment explanation
Indices: 20673726--20673820 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
20673716 CAGCCCCAAT
*
20673726 TGTGTACTGTTCGATAGCACA-AAGCATC
1 TGTGTGCTGTTCGATAGCACACAA-CATC
* *
20673754 TGTGTGCTGTTTGATTGCACACAACATC
1 TGTGTGCTGTTCGATAGCACACAACATC
* *
20673782 TGTGTGCTATTCGATAGCACACAACATT
1 TGTGTGCTGTTCGATAGCACACAACATC
*
20673810 TGTGTGTTGTT
1 TGTGTGCTGTT
20673821 AGGTAACAGC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 55 0.96
29 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (28 bp):
TGTGTGCTGTTCGATAGCACACAACATC
Found at i:20675166 original size:18 final size:19
Alignment explanation
Indices: 20675143--20675182 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
20675133 CTAGTGGAGA
20675143 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
20675161 ATTTTATGAATAAAATAAT
1 ATTTTATGAATAAAATAAT
20675180 ATT
1 ATT
20675183 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:20676679 original size:19 final size:19
Alignment explanation
Indices: 20676655--20676691 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20676645 CCATTTAACT
*
20676655 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
20676674 TATTGGAGTATAATTTGA
1 TATTGGAGTATAATTTGA
20676692 TGGTTTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:20676905 original size:28 final size:28
Alignment explanation
Indices: 20676874--20676947 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
20676864 TCAGTTTTTG
*
20676874 GGGCAAAAATGTAATTTTGCCACCTCGA
1 GGGCAAAAAGGTAATTTTGCCACCTCGA
*
20676902 GGGCAAAACGGTAATTTTGCCACCTCG-
1 GGGCAAAAAGGTAATTTTGCCACCTCGA
* *
20676929 GAGGTAAAATGGTAATTTT
1 G-GGCAAAAAGGTAATTTT
20676948 TCACCCCTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (28 bp):
GGGCAAAAAGGTAATTTTGCCACCTCGA
Found at i:20679941 original size:39 final size:39
Alignment explanation
Indices: 20679891--20680064 Score: 210
Period size: 39 Copynumber: 4.5 Consensus size: 39
20679881 GTGTCGGTAG
** **
20679891 TGTGCGGTGTGGGAGAGCACGCGCCGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* *
20679930 TGTGTGGTGTGGGAGAGCACATGATGATGATATATGTCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
*
20679969 TGTGTGGTGTGGGAGAGCACATGATGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * * *
20680008 TGTACGGTGTGGGAGTGCACATGAGGAT-AT-TA-GCTA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* *
20680044 TGTGTGGTGTGGGAGTGCACA
1 TGTGCGGTGTGGGAGAGCACA
20680065 AGAGCTGAGT
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
36 22 0.18
37 2 0.02
38 2 0.02
39 95 0.79
ACGTcount: A:0.23, C:0.12, G:0.38, T:0.27
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
Found at i:20689128 original size:29 final size:28
Alignment explanation
Indices: 20689081--20689221 Score: 120
Period size: 29 Copynumber: 4.9 Consensus size: 28
20689071 GGCAGCTTTG
* * *
20689081 ACATGTTTATGTTAATTTAGACAATAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
* *
20689109 ACATGTTTGGTCTTAATTTACAAAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
20689138 ATATGTTTGTCTTAATCTAAGACAAGAAA
1 ACATGTTTGTCTTAAT-TTAGACAAGAAA
*** * * *
20689167 TTTTTTTTTATCTTAATCTAGACAAGAAA
1 -ACATGTTTGTCTTAATTTAGACAAGAAA
* *
20689196 ACATATTTGTCTCAATTTAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA
20689222 TAAAATATTT
Statistics
Matches: 88, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
28 35 0.40
29 41 0.47
30 12 0.14
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:20689167 original size:28 final size:29
Alignment explanation
Indices: 20689099--20689238 Score: 99
Period size: 28 Copynumber: 4.8 Consensus size: 29
20689089 ATGTTAATTT
* * *
20689099 AGACAATAAAACATGTTTGGTCTTAATTTA
1 AGACAAGAAAATATGTTT-GTCTTAATCTA
20689129 CA-A-AAGAAAATATGTTTGTCTTAATCTA
1 -AGACAAGAAAATATGTTTGTCTTAATCTA
* * * *
20689157 AGACAAGAAATTTTTTTTTATCTTAATCT-
1 AGACAAGAAA-ATATGTTTGTCTTAATCTA
* * * *
20689186 AGACAAGAAAACATATTTGTCTCAAT-TT
1 AGACAAGAAAATATGTTTGTCTTAATCTA
*
20689214 AGACAAGATAAAATATTTTTGTCTT
1 AGACAAG--AAAATATGTTTGTCTT
20689239 CATTACAGAC
Statistics
Matches: 87, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
27 2 0.02
28 28 0.32
29 28 0.32
30 28 0.32
31 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
AGACAAGAAAATATGTTTGTCTTAATCTA
Found at i:20689413 original size:17 final size:17
Alignment explanation
Indices: 20689391--20689423 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20689381 ATAATAATAA
20689391 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
20689408 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
20689424 TTGTCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:20699593 original size:13 final size:13
Alignment explanation
Indices: 20699575--20699599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20699565 GGAAAAATTG
20699575 TGATTTTATAAAA
1 TGATTTTATAAAA
20699588 TGATTTTATAAA
1 TGATTTTATAAA
20699600 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20703957 original size:38 final size:39
Alignment explanation
Indices: 20703915--20704017 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 39
20703905 ATAGTGCCTG
*
20703915 TGTGCACGATGTGGGGGGATGTACACGAT-AGCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGAGC-CGGATA
* * * *
20703953 TGTGCACGATGTGGGGGGATGCACATGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGAT-GAGCCGGATA
20703993 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
20704018 TGAGCCGGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 27 0.48
39 3 0.05
40 26 0.46
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGTACACGATGAGCCGGATA
Found at i:20704008 original size:40 final size:38
Alignment explanation
Indices: 20703915--20704020 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 38
20703905 ATAGTGCCTG
* *
20703915 TGTGCACGATGTGGGGGGATGTACACGATAGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATAGCACGGAT
* * *
20703953 TGTGCACGATGTGGGGGGATGCACATGATGGTGC-CGGCT
1 TGTGCACGATGTGGGGGGATGTACATGAT--AGCACGGAT
20703992 ATGTGCACGATGTGGGGGGATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
20704021 GCCGGGAGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
38 27 0.46
39 3 0.05
40 29 0.49
ACGTcount: A:0.21, C:0.15, G:0.41, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATAGCACGGAT
Done.