Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 8 of 27
Found at i:1030837 original size:124 final size:124
Alignment explanation
Indices: 1030613--1031667 Score: 1287
Period size: 124 Copynumber: 8.6 Consensus size: 124
1030603 GAATGTGTCT
** * * *
1030613 TGCTCTTTGAGGACTAAAGTGG-GCCACCAACTCGTGTACGTTTTGAAAAGAAAAAGGTGTCCTA
1 TGCTCTTTGAGGACTAAAG-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTG
* *
1030677 CTCTTTGAGGACAAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
65 CTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* *** *
1030737 TGCTCTTTGAGCACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGTTATCCTAC
1 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
* * *
1030802 TCTTTGGGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAATAAAAAGGCATCC
66 TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* **
1030861 TACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGTTGTCCTGC
1 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
* * * *
1030926 TCTTTGGGGACTAAAAGGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGGCGTCC
66 TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * * * * *
1030985 TACTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGAAAAGGCATCCTAC
1 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
* * * * * * *
1031050 TCTTTGAGGACAAAATGATGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGCATCT
66 TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * * *
1031109 TGCTTTTTGAGGACAAAAGGATGCCACCAA-------------TGAAAAGAAAAAGACGTCCTGC
1 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
*
1031161 TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCC
66 TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * * *
1031220 TACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGATAAAGGCATCTTGC
1 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
* * * * *
1031285 TCTTTGAGGACAAAAGGATGCCACCAACTCGTATGGGCTTTGAAAAGAAAAATGCGTCC
66 TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * * * * *
1031344 TGCTTTTTTAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTCAAAAGGAAAAGACGTCTTGC
1 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
* * * *
1031409 TCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTT-AAAAGGAAAAGGTGTCT
66 TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * * * * *
1031467 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGAAAAGGCATCTTGT
1 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
* * *
1031532 TTTTTGAGGACTAAAAGGGTGCCACCAACTCATATGGGCTTTGAAAAGAAAAAGGTGT-C
66 TCTTTGAGGACT-AAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * * * * * * *
1031591 TGGCTCTTTAAGGACGAAAGGGTGCTACCAACTCATGTGGGCTTTAAAAAGGAAAAGGTGTCCTA
1 T-GCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTG
1031656 CTCTTTGAGGAC
65 CTCTTTGAGGAC
1031668 AAAATGGCTA
Statistics
Matches: 809, Mismatches: 105, Indels: 33
0.85 0.11 0.03
Matches are distributed among these distances:
111 96 0.12
123 84 0.10
124 551 0.68
125 78 0.10
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (124 bp):
TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGC
TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGTCC
Found at i:1031167 original size:49 final size:49
Alignment explanation
Indices: 1031090--1031187 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
1031080 GTGTAGGCTT
* * *
1031090 TGAAAAGAAAAAGGCATCTTGCTTTTTGAGGACAAAAGGATGCCACCAA
1 TGAAAAGAAAAAGACATCCTGCTCTTTGAGGACAAAAGGATGCCACCAA
* * *
1031139 TGAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAA
1 TGAAAAGAAAAAGACATCCTGCTCTTTGAGGACAAAAGGATGCCACCAA
1031188 CTCATGTGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (49 bp):
TGAAAAGAAAAAGACATCCTGCTCTTTGAGGACAAAAGGATGCCACCAA
Found at i:1031236 original size:62 final size:62
Alignment explanation
Indices: 1031139--1031667 Score: 666
Period size: 62 Copynumber: 8.5 Consensus size: 62
1031129 ATGCCACCAA
*
1031139 TGAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
* * *
1031201 TGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTT
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
* * * * * * *
1031263 TGAAAAGATAAAGGCATCTTGCTCTTTGAGGACAAAAGGATGCCACCAACTCGTATGGGCTT
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
* * * *
1031325 TGAAAAGAAAAATGCGTCCTGCTTTTTTAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTT
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
* * * * *
1031387 TCAAAAGGAAAAGACGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTT
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
* * * * *
1031449 T-AAAAGGAAAAGGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTT
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
* * * * * * *
1031510 TAAAAAGGAAAAGGCATCTTGTTTTTTGAGGACTAAAAGGGTGCCACCAACTCATATGGGCTT
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTCATGTGGGCTT
* * * *
1031573 TGAAAAGAAAAAGGTGT-CTGGCTCTTTAAGGACGAAAGGGTGCTACCAACTCATGTGGGCTT
1 TGAAAAGAAAAAGGCGTCCT-GCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
* * * *
1031635 TAAAAAGGAAAAGGTGTCCTACTCTTTGAGGAC
1 TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGAC
1031668 AAAATGGCTA
Statistics
Matches: 410, Mismatches: 53, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
61 58 0.14
62 302 0.74
63 50 0.12
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (62 bp):
TGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTT
Found at i:1037814 original size:52 final size:51
Alignment explanation
Indices: 1037729--1037852 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
1037719 ATATGAAAAG
* *
1037729 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
1037780 CTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
1037832 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1037853 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:1037879 original size:13 final size:13
Alignment explanation
Indices: 1037861--1037885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1037851 CAAAGATCAG
1037861 TGTATCGATACAA
1 TGTATCGATACAA
1037874 TGTATCGATACA
1 TGTATCGATACA
1037886 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1037963 original size:33 final size:33
Alignment explanation
Indices: 1037926--1037992 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1037916 AGTAGCTTAA
1037926 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1037959 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1037992 A
1 A
1037993 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1037966 original size:13 final size:13
Alignment explanation
Indices: 1037948--1037972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1037938 CAAAAAAATA
1037948 TGTATCGATACAT
1 TGTATCGATACAT
1037961 TGTATCGATACA
1 TGTATCGATACA
1037973 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1044214 original size:101 final size:100
Alignment explanation
Indices: 1044082--1044522 Score: 321
Period size: 101 Copynumber: 4.4 Consensus size: 100
1044072 GAGAAGAATG
* * * * *
1044082 CCAATGTGCTGATTCAAGGTCAGTGAAATTAGGCTTAGGAATGTTAAAGATGCCAATATGTTAAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAGGAA-GTTGAAGATGCCAATATGCTAAT
* *
1044147 TCAAGGCCAGCGATATCGAACTTAAAGATTAAAGCA
65 TCAAGGCCAACGATATCGAACTTAAAGATTAAAGTA
* * * * * *
1044183 CCAATGTGGTGATTCAAGGCCAACGACATTAGACTT--GAAGATGAAGGTACCAATATGCTAATT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAGGAAGTTGAAGATGCCAATATGCTAATT
* * * * * *
1044246 CAAGGCCAACGATGT-TAGGCTTAGGAATATTGAAGATG
66 CAAGGCCAACGATATCGA-ACTTA--AAGATTAAAG-TA
* * * * *
1044284 CCAATATGCTTATTCAAGGCCAGCGATATTGGGCTTA--AA---G-A-ATGCCAATATGCTGATT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAGGAAGTTGAAGATGCCAATATGCTAATT
* * * * *
1044342 CAGGGCCAACGATATCAAACTTAAAGATGAAGGTG
66 CAAGGCCAACGATATCGAACTTAAAGATTAAAGTA
* * *
1044377 CCAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAGGAATATTGAAGATGCCAATATGTTGA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTAGG-CTTAGGAA-GTTGAAGATGCCAATATGCTAA
* * ** * *
1044441 TTCAAGGCCAGCGATATTGGGCTTAAAGATAACAAAGGTG
64 TTCAAGGCCAACGATATCGAACTTAAAGAT--TAAA-GTA
* * ** *
1044481 CCAATATGTTGATTCAAGGCCAATGACATTGGGCTTA-GAAGT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAGGAAGT
1044523 AGGTGCCACT
Statistics
Matches: 267, Mismatches: 54, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
92 2 0.01
93 33 0.12
94 6 0.02
95 2 0.01
96 31 0.12
97 3 0.01
98 37 0.14
99 4 0.01
100 9 0.03
101 99 0.37
102 1 0.00
103 5 0.02
104 33 0.12
105 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (100 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAGGAAGTTGAAGATGCCAATATGCTAATT
CAAGGCCAACGATATCGAACTTAAAGATTAAAGTA
Found at i:1044293 original size:52 final size:51
Alignment explanation
Indices: 1044074--1044521 Score: 302
Period size: 52 Copynumber: 8.9 Consensus size: 51
1044064 TTGAAGATGA
* * * *
1044074 GAAGAATGCCAATGTGCTGATTCAAGGTCAGTGAAATTAGGCTTAGGAATG-TT
1 GAAG-ATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTA-GAA-GATT
* * * * *
1044127 AAAGATGCCAATATGTTAATTCAAGGCCAGCGATA-TCGAACTTA-AAGATT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAG-GCTTAGAAGATT
* * * * * *
1044177 AAAGCA--CCAATGTGGTGATTCAAGGCCAACGACATTAGACTT-GAAGA-T
1 GAAG-ATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAGAAGATT
* * * * * *
1044225 GAAGGTACCAATATGCTAATTCAAGGCCAACGATGTTAGGCTTAGGAATATT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTA-GAAGATT
* *
1044277 GAAGATGCCAATATGCTTATTCAAGGCCAGCGATATTGGGCTT--AA-A--
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAGAAGATT
* * * **
1044323 G-A-ATGCCAATATGCTGATTCAGGGCCAACGATATCAAACTTA-AAGA-T
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAGAAGATT
* * * *
1044370 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAGGAATATT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTA-GAAGATT
* * *
1044422 GAAGATGCCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTA-AAGATAAC
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAGAAGAT--T
* * * ** * *
1044474 AAAGGTGCCAATATGTTGATTCAAGGCCAATGACATTGGGCTTAGAAG
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAGAAG
1044522 TAGGTGCCAC
Statistics
Matches: 315, Mismatches: 57, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
44 32 0.10
45 3 0.01
46 2 0.01
47 1 0.00
48 6 0.02
49 95 0.30
50 14 0.04
51 10 0.03
52 144 0.46
53 8 0.03
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (51 bp):
GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAGAAGATT
Found at i:1044398 original size:49 final size:49
Alignment explanation
Indices: 1043972--1044517 Score: 289
Period size: 52 Copynumber: 10.9 Consensus size: 49
1043962 AAGAGTGATA
* * * * *
1043972 AAGGTGCCAACATGCTGATTTAAGACCAACAATATTGGGCTTAAAGATGCG
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT--G
* ** * * * * * *
1044023 AAGAATGTTAA-AGTGCTGATTCACGGTCAACGACAATAGACTTGAAGATGAG
1 AAG-GTGCCAATA-TGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT--G
* * * ** * * *
1044075 AAGAATGCCAATGTGCTGATTCAAGGTCAGTGAAATTAGG-CTTAGGAATGTTA
1 AAG-GTGCCAATATGCTGATTCAAGGCCAACGATATT-GGACTTA--AA-GATG
* * * * * * *
1044128 AAGATGCCAATATGTTAATTCAAGGCCAGCGATATCGAACTTAAAGATT
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG
* ** * * * * *
1044177 AAAGCACCAATGTGGTGATTCAAGGCCAACGACATTAGACTTGAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG
* * * *
1044226 AAGGTACCAATATGCTAATTCAAGGCCAACGATGTTAGG-CTTAGGAATATTG
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATT-GGACTTA--AAGA-TG
* * * *
1044278 AAGATGCCAATATGCTTATTCAAGGCCAGCGATATTGGGCTT-AA-A-G
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG
* ***
1044324 AA--TGCCAATATGCTGATTCAGGGCCAACGATATCAAACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG
* * * *
1044371 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATATTG
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA--AAGA-TG
* * * * *
1044423 AAGATGCCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTAAAGATAACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT---G
* * * *
1044475 AAGGTGCCAATATGTTGATTCAAGGCCAATGACATTGGGCTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA
1044518 GAAGTAGGTG
Statistics
Matches: 380, Mismatches: 91, Indels: 47
0.73 0.18 0.09
Matches are distributed among these distances:
44 31 0.08
45 2 0.01
46 4 0.01
47 3 0.01
48 1 0.00
49 104 0.27
50 6 0.02
51 13 0.03
52 208 0.55
53 4 0.01
54 2 0.01
55 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG
Found at i:1044415 original size:145 final size:146
Alignment explanation
Indices: 1044036--1044469 Score: 498
Period size: 145 Copynumber: 2.9 Consensus size: 146
1044026 AATGTTAAAG
* * * * *
1044036 TGCTGATTCACGGTCAACGACAAT-AGACTTGAAGATGAGAAGAATGCCAATGTGCTGATTCAAG
1 TGCTGATTCAAGGCCAACGAC-ATCAAACTTAAAGAT--GAAG-GTGCCAATGTGCTGATTCAAG
* * * * *
1044100 GTCAGTGAAATTAGGCTTAGGAATGTTAAAGATGCCAATATGTTAATTCAAGGCCAGCGATATCG
62 GCCAGCGAAATTAGGCTTAGGAATATTGAAGATGCCAATATGTTAATTCAAGGCCAGCGATATTG
** *
1044165 AACTTAAAGATTAAAGCACCAATG
127 GGCTTAAAG---AAAG-ACCAATA
* * * * * * *
1044189 TGGTGATTCAAGGCCAACGACATTAGACTTGAAGATGAAGGTACCAATATGCTAATTCAAGGCCA
1 TGCTGATTCAAGGCCAACGACATCAAACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* **
1044254 ACGATGTTAGGCTTAGGAATATTGAAGATGCCAATATGCTT-ATTCAAGGCCAGCGATATTGGGC
66 GCGAAATTAGGCTTAGGAATATTGAAGATGCCAATATG-TTAATTCAAGGCCAGCGATATTGGGC
*
1044318 TTAAAGAATG-CCAATA
130 TTAAAGAAAGACCAATA
* *
1044334 TGCTGATTCAGGGCCAACGATATCAAACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAACGACATCAAACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
1044399 GCGACATT-GGACTTAGGAATATTGAAGATGCCAATATGTTGATTCAAGGCCAGCGATATTGGGC
66 GCGAAATTAGG-CTTAGGAATATTGAAGATGCCAATATGTTAATTCAAGGCCAGCGATATTGGGC
1044463 TTAAAGA
130 TTAAAGA
1044470 TAACAAAGGT
Statistics
Matches: 246, Mismatches: 31, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
144 4 0.02
145 123 0.50
147 3 0.01
150 78 0.32
151 6 0.02
152 2 0.01
153 30 0.12
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (146 bp):
TGCTGATTCAAGGCCAACGACATCAAACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGAAATTAGGCTTAGGAATATTGAAGATGCCAATATGTTAATTCAAGGCCAGCGATATTGGGCT
TAAAGAAAGACCAATA
Found at i:1044593 original size:31 final size:31
Alignment explanation
Indices: 1044525--1044594 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
1044515 TTAGAAGTAG
* * *
1044525 GTGCCACTAACTTGTGTGGGCTTTTGAAAGG
1 GTGCCACCAACTTGTGTGGGCTATTGAAAGA
1044556 GTTGCCACCAACTTGTGTGGGC-ATTGAAAAGA
1 G-TGCCACCAACTTGTGTGGGCTATTG-AAAGA
1044588 GTGCCAC
1 GTGCCAC
1044595 GAAGTTATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.29
32 24 0.71
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (31 bp):
GTGCCACCAACTTGTGTGGGCTATTGAAAGA
Found at i:1044686 original size:27 final size:26
Alignment explanation
Indices: 1044648--1044791 Score: 132
Period size: 27 Copynumber: 5.3 Consensus size: 26
1044638 GTTTGAAAAG
* *
1044648 AAAAAGGTGCCATAGAGCTGTGGACTT
1 AAAAGGGTGCCACAGAGCTGTGG-CTT
*
1044675 AAAAGGGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGCTGT-GGCTT
* * *
1044702 AAAAAGGTTCCACAGAGTCAT-CGGCTT
1 AAAAGGGTGCCACAGAG-C-TGTGGCTT
*
1044729 AAAAGGGTGCCACAGAG-TCGTGAACTT
1 AAAAGGGTGCCACAGAGCT-GTG-GCTT
1044756 AAAAGGGTGCCACAGAGTCATG-GGCTT
1 AAAAGGGTGCCACAGAG-C-TGTGGCTT
1044783 AAAAGGGTG
1 AAAAGGGTG
1044792 AGGAGTGTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
24 1 0.01
26 1 0.01
27 88 0.92
28 3 0.03
29 2 0.02
30 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.31, T:0.20
Consensus pattern (26 bp):
AAAAGGGTGCCACAGAGCTGTGGCTT
Found at i:1044733 original size:54 final size:54
Alignment explanation
Indices: 1044672--1044791 Score: 186
Period size: 54 Copynumber: 2.2 Consensus size: 54
1044662 GAGCTGTGGA
* ** *
1044672 CTTAAAAGGGTGCCACAGAGTTGTGGGCTTAAAAAGGTTCCACAGAGTCATCGG
1 CTTAAAAGGGTGCCACAGAGTCGTGAACTTAAAAAGGTGCCACAGAGTCATCGG
* *
1044726 CTTAAAAGGGTGCCACAGAGTCGTGAACTTAAAAGGGTGCCACAGAGTCATGGG
1 CTTAAAAGGGTGCCACAGAGTCGTGAACTTAAAAAGGTGCCACAGAGTCATCGG
1044780 CTTAAAAGGGTG
1 CTTAAAAGGGTG
1044792 AGGAGTGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (54 bp):
CTTAAAAGGGTGCCACAGAGTCGTGAACTTAAAAAGGTGCCACAGAGTCATCGG
Found at i:1046261 original size:8 final size:8
Alignment explanation
Indices: 1046231--1046365 Score: 67
Period size: 8 Copynumber: 15.5 Consensus size: 8
1046221 ATCCGGGCCC
1046231 TTTTTGTT
1 TTTTTGTT
*
1046239 GTTTAT-TT
1 -TTTTTGTT
1046247 TTTTTGTT
1 TTTTTGTT
*
1046255 GTTTTGTT
1 TTTTTGTT
1046263 TTTTTGGTT
1 TTTTT-GTT
1046272 TTTTTGTTCTT
1 TTTTTG---TT
1046283 TTTTTGGTT
1 TTTTT-GTT
*
1046292 TTTTAATCTTT
1 TTTT--T-GTT
*
1046303 TTTTTGGT
1 TTTTTGTT
1046311 TTTTTGTCT
1 TTTTTGT-T
*
1046320 TTTTTATTT
1 TTTTT-GTT
*
1046329 TTTTTGTC
1 TTTTTGTT
*
1046337 TTCTTGTT
1 TTTTTGTT
*
1046345 TTCTTGTCT
1 TTTTTGT-T
1046354 TCTTTT-TT
1 T-TTTTGTT
1046362 TTTT
1 TTTT
1046366 ACGAGGGATG
Statistics
Matches: 99, Mismatches: 15, Indels: 26
0.71 0.11 0.19
Matches are distributed among these distances:
7 7 0.07
8 39 0.39
9 34 0.34
10 4 0.04
11 14 0.14
12 1 0.01
ACGTcount: A:0.03, C:0.06, G:0.12, T:0.79
Consensus pattern (8 bp):
TTTTTGTT
Found at i:1046264 original size:17 final size:17
Alignment explanation
Indices: 1046231--1046286 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
1046221 ATCCGGGCCC
*
1046231 TTTTTGTTG-TTTATTT
1 TTTTTGTTGTTTTGTTT
1046247 TTTTTGTTGTTTTGTTT
1 TTTTTGTTGTTTTGTTT
* *
1046264 TTTTGGTTTTTTTGTTCT
1 TTTTTGTTGTTTTGTT-T
1046282 TTTTT
1 TTTTT
1046287 TGGTTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 9 0.26
17 20 0.59
18 5 0.15
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.82
Consensus pattern (17 bp):
TTTTTGTTGTTTTGTTT
Found at i:1046284 original size:20 final size:18
Alignment explanation
Indices: 1046244--1046338 Score: 88
Period size: 20 Copynumber: 5.1 Consensus size: 18
1046234 TTGTTGTTTA
*
1046244 TTTTTTTTGTTGTTTTG--
1 TTTTTTTGGTT-TTTTGTC
1046261 TTTTTTTGGTTTTTTTGTTC
1 TTTTTTTGG-TTTTTTG-TC
*
1046281 TTTTTTTGGTTTTTTAATC
1 TTTTTTTGGTTTTTT-GTC
1046300 TTTTTTTTGGTTTTTTGTC
1 -TTTTTTTGGTTTTTTGTC
*
1046319 TTTTTTAT-TTTTTTTGTC
1 TTTTTT-TGGTTTTTTGTC
1046337 TT
1 TT
1046339 CTTGTTTTCT
Statistics
Matches: 67, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
17 13 0.19
18 19 0.28
19 11 0.16
20 24 0.36
ACGTcount: A:0.03, C:0.04, G:0.13, T:0.80
Consensus pattern (18 bp):
TTTTTTTGGTTTTTTGTC
Found at i:1055674 original size:14 final size:14
Alignment explanation
Indices: 1055628--1055683 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
1055618 ATGCCTACAC
1055628 TATTTTTAAAAACAT
1 TATTTTT-AAAACAT
* *
1055643 TAATTTTTATATCA-
1 T-ATTTTTAAAACAT
1055657 TATTTTTAAAACAT
1 TATTTTTAAAACAT
*
1055671 TATTTTGAAAACA
1 TATTTTTAAAACA
1055684 AAATTTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 10 0.29
14 13 0.38
15 5 0.15
16 6 0.18
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (14 bp):
TATTTTTAAAACAT
Found at i:1055724 original size:12 final size:12
Alignment explanation
Indices: 1055691--1055724 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1055681 ACAAAATTTT
1055691 AATATTATTTCA
1 AATATTATTTCA
* *
1055703 AAAATAATTTCA
1 AATATTATTTCA
1055715 AATATTATTT
1 AATATTATTT
1055725 TTAAATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATTATTTCA
Found at i:1055748 original size:25 final size:27
Alignment explanation
Indices: 1055720--1055789 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 27
1055710 TTTCAAATAT
1055720 TATTTTTAAATATAATTTATACT-A-A
1 TATTTTTAAATATAATTTATACTGATA
** * * *
1055745 TATTTTTGGATATTATTTTTATTGATA
1 TATTTTTAAATATAATTTATACTGATA
*
1055772 TATTTTTAAAAATAATTT
1 TATTTTTAAATATAATTT
1055790 TATTAATTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 18 0.53
26 1 0.03
27 15 0.44
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (27 bp):
TATTTTTAAATATAATTTATACTGATA
Found at i:1056199 original size:25 final size:24
Alignment explanation
Indices: 1056171--1056222 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
1056161 AAAGCTCATT
1056171 TTATTGTTTA-AAAAATATTAAATAA
1 TTATT-TTTATAAAAATATT-AATAA
* *
1056196 TTATTTTTATAATAATATTTATAA
1 TTATTTTTATAAAAATATTAATAA
1056220 TTA
1 TTA
1056223 AATTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATTTTTATAAAAATATTAATAA
Found at i:1057572 original size:17 final size:18
Alignment explanation
Indices: 1057534--1057578 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1057524 AGACTTGATC
1057534 ATTTTTTAAATAAATTTA
1 ATTTTTTAAATAAATTTA
**
1057552 ATTTTTTATTTAAATTT-
1 ATTTTTTAAATAAATTTA
1057569 ATTTTTTAAA
1 ATTTTTTAAA
1057579 CTTAACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTTTAAATAAATTTA
Found at i:1062571 original size:24 final size:25
Alignment explanation
Indices: 1062540--1062587 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1062530 AAAATTAATT
1062540 TATTTTAA-AATAAAAATAATATAA
1 TATTTTAATAATAAAAATAATATAA
*
1062564 TATTTTAATAATAAAATTAATATA
1 TATTTTAATAATAAAAATAATATA
1062588 TAATTGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TATTTTAATAATAAAAATAATATAA
Found at i:1063954 original size:32 final size:32
Alignment explanation
Indices: 1063870--1063955 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
1063860 TTGAAAGTTA
**
1063870 TATTTTGTTAAATTAATAAAACATTCTGTATT
1 TATTTTGTTAAATTAATAAATTATTCTGTATT
* *
1063902 TAATCTT-TTAAATTAATAAATTATTTTGTATT
1 T-ATTTTGTTAAATTAATAAATTATTCTGTATT
1063934 TATTTTGTTAAATTAATAAATT
1 TATTTTGTTAAATTAATAAATT
1063956 TAATCATTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 4 0.09
32 39 0.83
33 4 0.09
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (32 bp):
TATTTTGTTAAATTAATAAATTATTCTGTATT
Found at i:1063980 original size:37 final size:32
Alignment explanation
Indices: 1063868--1063980 Score: 111
Period size: 32 Copynumber: 3.4 Consensus size: 32
1063858 TATTGAAAGT
** *
1063868 TATATTTTGTTAAATTAATAAAACATTCTGTA
1 TATATTTTGTTAAATTAATAAATTATTTTGTA
* *
1063900 TTTAATCTT-TTAAATTAATAAATTATTTTGTA
1 TAT-ATTTTGTTAAATTAATAAATTATTTTGTA
*
1063932 TTTATTTTGTTAAATTAATAAATTTAATCATTTGTTA
1 TATATTTTGTTAAATTAATAAA-TT-AT--TTTG-TA
1063969 TATATTTTGTTA
1 TATATTTTGTTA
1063981 TGTTATAATT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
31 4 0.06
32 38 0.57
33 6 0.09
34 2 0.03
36 4 0.06
37 13 0.19
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (32 bp):
TATATTTTGTTAAATTAATAAATTATTTTGTA
Found at i:1064703 original size:134 final size:134
Alignment explanation
Indices: 1064425--1064692 Score: 459
Period size: 134 Copynumber: 2.0 Consensus size: 134
1064415 ATTAAAAAAA
1064425 AAACGTTCATTAGGTATAAAAGAATGAACTCTTTCAAGTAAATTACATTTATTATTCATAATTTT
1 AAAC-TTCATTAGGTATAAAAGAATGAACTCTTTCAAGTAAATTACATTTATTATTCATAATTTT
*
1064490 ATCCAATATTTTATTTTTATTCGTAATTTTGATATTCAATCTTTTGCTGCTTTGAATTTAAACAT
65 ATCCAATATTTTATTTTTATTCGTAATTTTGATATTCAATCTTTTGATGCTTTGAATTTAAACAT
*
1064555 TTCAT
130 TCCAT
* *
1064560 AAACTTCATTAGGTATAAAAGAATGAACTCTTTCAAGTAAATTATATTTATTATTTATAATTTTA
1 AAACTTCATTAGGTATAAAAGAATGAACTCTTTCAAGTAAATTACATTTATTATTCATAATTTTA
*
1064625 TCCGATA-TTTATTTTTATAT-GTAATTTTGATATTCAATCTTTTGATGCTTTGAATTTAAACAT
66 TCCAATATTTTATTTTTAT-TCGTAATTTTGATATTCAATCTTTTGATGCTTTGAATTTAAACAT
1064688 TCCAT
130 TCCAT
1064693 CAATTTTCAT
Statistics
Matches: 127, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
133 57 0.45
134 66 0.52
135 4 0.03
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (134 bp):
AAACTTCATTAGGTATAAAAGAATGAACTCTTTCAAGTAAATTACATTTATTATTCATAATTTTA
TCCAATATTTTATTTTTATTCGTAATTTTGATATTCAATCTTTTGATGCTTTGAATTTAAACATT
CCAT
Found at i:1072141 original size:25 final size:25
Alignment explanation
Indices: 1072113--1072206 Score: 75
Period size: 27 Copynumber: 3.6 Consensus size: 25
1072103 AATGCACCCA
1072113 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGGTTA-T
*
1072139 TTGTGTTTGCCAAAAATGGTGGTT-T
1 TT-TGTTTGTCAAAAATGGTGGTTAT
* *
1072164 CCTTTGGATTTGTCAAATATGGAGGCTTA-
1 --TTT-G-TTTGTCAAAAATGGTGG-TTAT
*
1072193 TTTATTTGTCAAAA
1 TTTGTTTGTCAAAA
1072207 TTTGTGGCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
25 10 0.18
26 3 0.05
27 26 0.47
28 14 0.25
29 2 0.04
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (25 bp):
TTTGTTTGTCAAAAATGGTGGTTAT
Found at i:1072955 original size:2 final size:2
Alignment explanation
Indices: 1072944--1072979 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1072934 CAGTTGTGAG
1072944 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1072980 CCTTAAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1073592 original size:22 final size:22
Alignment explanation
Indices: 1073567--1073608 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1073557 ATATTTTATT
1073567 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1073589 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1073609 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1075083 original size:71 final size:74
Alignment explanation
Indices: 1074962--1075120 Score: 225
Period size: 71 Copynumber: 2.2 Consensus size: 74
1074952 TCTTGGCATA
* * * * *
1074962 AATATAATTTTAATAATTTTTTTATAATTATTGCTCAACATAGATATAATTTTAA-T-CTATATT
1 AATATAAATATAATAATTTTTTTATAATTATTACACAACATAGATATAATTTTAATTAATATATT
1075025 TTATTATTT
66 TTATTATTT
*
1075034 AATATAAATATAATAA-TTTTTTATAATTATTACACAACATAGATTTAATTTTAATTTTAATATA
1 AATATAAATATAATAATTTTTTTATAATTATTACACAACATAGATATAATTTTAA--TTAATATA
1075098 TTTTATTATTT
64 TTTTATTATTT
1075109 AATATAAATATA
1 AATATAAATATA
1075121 GCTTTAATAA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
71 35 0.45
72 14 0.18
74 1 0.01
75 27 0.35
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (74 bp):
AATATAAATATAATAATTTTTTTATAATTATTACACAACATAGATATAATTTTAATTAATATATT
TTATTATTT
Found at i:1075143 original size:35 final size:34
Alignment explanation
Indices: 1075089--1075155 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
1075079 TAATTTTAAT
1075089 TTTAATATATTTTATTATTTAATATAAATATAGC
1 TTTAATATATTTTATTATTTAATATAAATATAGC
* *
1075123 TTTAATA-ATTTTTCATTATTTATTATATATATA
1 TTTAATATA-TTTT-ATTATTTAATATAAATATA
1075156 TATGTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.03
34 11 0.38
35 17 0.59
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (34 bp):
TTTAATATATTTTATTATTTAATATAAATATAGC
Found at i:1075304 original size:21 final size:20
Alignment explanation
Indices: 1075258--1075304 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1075248 ACCACAAATT
*
1075258 TTAATCTTATTATTATAATA
1 TTAATCTTATTATTACAATA
*
1075278 TCTAATCTTATTATTACCATAA
1 T-TAATCTTATTATTACAAT-A
1075300 TTAAT
1 TTAAT
1075305 TTCACCGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATCTTATTATTACAATA
Found at i:1083162 original size:51 final size:52
Alignment explanation
Indices: 1083085--1083193 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 52
1083075 AAATGTGCAA
1083085 ACATTTAGGTCAAAAACCCAGAATGTATCGATACAATAAAAAATGTATCGAT
1 ACATTTAGGTCAAAAACCCAGAATGTATCGATACAATAAAAAATGTATCGAT
* * * *
1083137 GCATTTAGGTC-AAAACCTAGAATGTATCGATATAATGAAAAATGTATCGAT
1 ACATTTAGGTCAAAAACCCAGAATGTATCGATACAATAAAAAATGTATCGAT
1083188 ACATTT
1 ACATTT
1083194 CCTTTCTAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
51 42 0.81
52 10 0.19
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (52 bp):
ACATTTAGGTCAAAAACCCAGAATGTATCGATACAATAAAAAATGTATCGAT
Found at i:1083296 original size:21 final size:20
Alignment explanation
Indices: 1083249--1083302 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
1083239 CATTTCAAGC
*
1083249 ATGTATCGATACATTCACTT
1 ATGTATTGATACATTCACTT
1083269 ATGTATTGATACATTCACTT
1 ATGTATTGATACATTCACTT
1083289 ATTGTATTGATACA
1 A-TGTATTGATACA
1083303 AATCGTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (20 bp):
ATGTATTGATACATTCACTT
Found at i:1095335 original size:27 final size:27
Alignment explanation
Indices: 1095297--1095349 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1095287 ATTTAAAAAC
1095297 GGGGTTGGAGTATCCCCGATGAATAAT
1 GGGGTTGGAGTATCCCCGATGAATAAT
1095324 GGGGTTGGAGTATCCCCGATGAATAA
1 GGGGTTGGAGTATCCCCGATGAATAA
1095350 AATTTGGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATGAATAAT
Found at i:1095616 original size:17 final size:17
Alignment explanation
Indices: 1095594--1095627 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1095584 CTGATCGGAA
1095594 GGTTTTAGAGGGTGGAC
1 GGTTTTAGAGGGTGGAC
1095611 GGTTTTAGAGGGTGGAC
1 GGTTTTAGAGGGTGGAC
1095628 ATGGTACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.47, T:0.29
Consensus pattern (17 bp):
GGTTTTAGAGGGTGGAC
Found at i:1098334 original size:61 final size:61
Alignment explanation
Indices: 1098238--1098369 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
1098228 AAATGATGAG
** *
1098238 GATGAGAAGAGTGATAAAGATGCCAATATGCTGATTCAGGGCCAGCGATATTGGGCTTAAA
1 GATGAGAAGAGTGATAAAGATGCCAATATGCTGATTCAAAGCCAACGATATTGGGCTTAAA
* * * * *
1098299 GATGAGGAGGGTGATAAAGGTGCCAATATGTTGATTTAAAGCCAACGATATTGGGCTTAAA
1 GATGAGAAGAGTGATAAAGATGCCAATATGCTGATTCAAAGCCAACGATATTGGGCTTAAA
* *
1098360 GGTGCGAAGA
1 GATGAGAAGA
1098370 ATGTCAATGT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.23
Consensus pattern (61 bp):
GATGAGAAGAGTGATAAAGATGCCAATATGCTGATTCAAAGCCAACGATATTGGGCTTAAA
Found at i:1098600 original size:52 final size:51
Alignment explanation
Indices: 1098313--1098808 Score: 355
Period size: 52 Copynumber: 9.9 Consensus size: 51
1098303 AGGAGGGTGA
* * * * * *
1098313 TAAAGGTGCCAATATGTTGATTTAAAGCCAACGATATTGGGCTTAAAGGTG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
** * * * * * * * *
1098364 CGAAGAATGTCAATGTGCTGATTCACGGCTAGCGACATTAGACTTGAAGATG
1 TAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * * ** * *
1098416 -AGAAGAATGCCAATATGCTGATTCAAGGCTAGCAACATTGGGGTTTAGGAATG
1 TA-AAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-ATG
* * *
1098469 TTAAAGATGCCAATATGTTGATTCAAGGCCAGCGATATCGGACTTAAAGATG
1 -TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * *
1098521 --AAGGTGCCAATGTACTGATTCAAGGCCAGTGACATTGGACTTAAAGATGG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G
* * *
1098571 TAAAGGTGCCAATATGCTAATTCAGGGCCAACGATATTGGA--T-----T-
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * * *
1098614 TAAAGGTGCCAATGTACTAATTCAAGGCCAGCGACATTGGACTTGAAGATGG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G
* *
1098666 CAAAGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGAC-------T-
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
* * * *
1098709 TAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G
* * *
1098761 CAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1098809 GTACCAATGT
Statistics
Matches: 348, Mismatches: 71, Indels: 51
0.74 0.15 0.11
Matches are distributed among these distances:
43 73 0.21
45 3 0.01
49 41 0.12
50 4 0.01
51 3 0.01
52 183 0.53
53 37 0.11
54 3 0.01
55 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (51 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:1098610 original size:154 final size:156
Alignment explanation
Indices: 1098313--1098602 Score: 345
Period size: 154 Copynumber: 1.9 Consensus size: 156
1098303 AGGAGGGTGA
* * * * * *
1098313 TAAAGGTGCCAATATGTTGATTTAAAGCCAACGATATTGGGCTTAAAGGTGCGAAGAATGTCAAT
1 TAAAGATGCCAATATGTTGATTCAAAGCCAACGATATCGGACTTAAAGAT-CGAAGAATGCCAAT
* * * * *
1098378 GTGCTGATTCACGGCTAGCGACATTAGACTTGAAGATGAGAAGAATGCCAATATGCTGATTCAAG
65 GTACTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAATGCCAATATGCTAATTCAAG
* *
1098443 GCTAGCAACATTGGGGTTTAGGAATGT
130 GCCAACAACATTGGGGTTTAGGAATGT
* * *
1098470 TAAAGATGCCAATATGTTGATTCAAGGCCAGCGATATCGGACTTAAAGAT-GAAG-GTGCCAATG
1 TAAAGATGCCAATATGTTGATTCAAAGCCAACGATATCGGACTTAAAGATCGAAGAATGCCAATG
* * * *
1098533 TACTGATTCAAGGCCAGTGACATTGGACTTAAAGATG-GTAA-AGGTGCCAATATGCTAATTCAG
66 TACTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAG-AAGA-ATGCCAATATGCTAATTCAA
1098596 GGCCAAC
129 GGCCAAC
1098603 GATATTGGAT
Statistics
Matches: 111, Mismatches: 20, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
153 2 0.02
154 62 0.56
155 4 0.04
157 43 0.39
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (156 bp):
TAAAGATGCCAATATGTTGATTCAAAGCCAACGATATCGGACTTAAAGATCGAAGAATGCCAATG
TACTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAATGCCAATATGCTAATTCAAGG
CCAACAACATTGGGGTTTAGGAATGT
Found at i:1098634 original size:43 final size:43
Alignment explanation
Indices: 1098571--1098844 Score: 215
Period size: 43 Copynumber: 6.0 Consensus size: 43
1098561 TTAAAGATGG
* *
1098571 TAAAGGTGCCAATATGCTAATTCAGGGCCAACGATATTGGATT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGATT
* * *
1098614 TAAAGGTGCCAATGTACTAATTCAAGGCCAGCGACATTGGACTT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGA-TT
* * *
1098658 GAAGATGGCAAAGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGACT
1 -----T---AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGATT
* * * *
1098709 TAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGA-TT
* *
1098753 AAAGATAACAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACT
1 -----T---AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGATT
* * * * *
1098804 TAAAGGTACCAATGTGCTGATTCAAAGCCAGCGACATTGGA
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGA
1098845 CCTAAAGGGA
Statistics
Matches: 185, Mismatches: 28, Indels: 36
0.74 0.11 0.14
Matches are distributed among these distances:
43 106 0.57
44 3 0.02
46 2 0.01
49 2 0.01
51 2 0.01
52 70 0.38
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGATT
Found at i:1098654 original size:95 final size:95
Alignment explanation
Indices: 1098521--1098851 Score: 518
Period size: 95 Copynumber: 3.5 Consensus size: 95
1098511 CTTAAAGATG
* *
1098521 AAGGTGCCAATGTACTGATTCAAGGCCAGTGACATTGGACTTAAAGATGGTAAAGGTGCCAATAT
1 AAGGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGCAAAGGTGCCAATAT
*
1098586 GCTAATTCAGGGCCAACGATATTGGATTTA
66 GCTAATTCAGGGCCAACGATATTGGACTTA
* *
1098616 AAGGTGCCAATGTACTAATTCAAGGCCAGCGACATTGGACTTGAAGATGGCAAAGGTGCCAATAT
1 AAGGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGCAAAGGTGCCAATAT
* *
1098681 GCTGATTCAGGGCCAGCGATATTGGACTTA
66 GCTAATTCAGGGCCAACGATATTGGACTTA
* * **
1098711 AAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAACAAAGGTGCCAATAT
1 AAGGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGCAAAGGTGCCAATAT
*
1098776 GCTAATTCAAGGCCAACGATATTGGACTTA
66 GCTAATTCAGGGCCAACGATATTGGACTTA
* * * *
1098806 AAGGTACCAATGTGCTGATTCAAAGCCAGCGACATTGGACCTAAAG
1 AAGGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAG
1098852 GGAGATGCAA
Statistics
Matches: 216, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 216 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (95 bp):
AAGGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGCAAAGGTGCCAATAT
GCTAATTCAGGGCCAACGATATTGGACTTA
Found at i:1098754 original size:190 final size:192
Alignment explanation
Indices: 1098471--1098845 Score: 556
Period size: 190 Copynumber: 1.9 Consensus size: 192
1098461 TAGGAATGTT
*
1098471 AAAGATGCCAATATGTTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGGTGCCAATGTAC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTT--A-A-GAAGGTGCCAATGTAC
* *** *
1098536 TGATTCAAGGCCAGTGACATTGGACTTAAAGATGGTAAAGGTGCCAATATGCTAATTCAGGGCCA
62 TGATTCAAGGCCAGCGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTAATTCAAGGCCA
* * *
1098601 ACGATATTGGATTTAAAGGTGCCAATGTACTAATTCAAGGCCAGCGACATTGGACTTGAAGATGG
127 ACGATATTGGACTTAAAGGTACCAATGTACTAATTCAAAGCCAGCGACATTGGACTTGAAGATGG
1098666 C
192 C
* * * *
1098667 AAAGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGACTT-A-AAGGTGCCAATGTGCTGAT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAGAAGGTGCCAATGTACTGAT
*
1098730 TCAAGGCTAGCGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTAATTCAAGGCCAACGA
66 TCAAGGCCAGCGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTAATTCAAGGCCAACGA
* *
1098795 TATTGGACTTAAAGGTACCAATGTGCTGATTCAAAGCCAGCGACATTGGAC
131 TATTGGACTTAAAGGTACCAATGTACTAATTCAAAGCCAGCGACATTGGAC
1098846 CTAAAGGGAG
Statistics
Matches: 163, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
190 123 0.75
192 1 0.01
196 39 0.24
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (192 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAGAAGGTGCCAATGTACTGAT
TCAAGGCCAGCGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTAATTCAAGGCCAACGA
TATTGGACTTAAAGGTACCAATGTACTAATTCAAAGCCAGCGACATTGGACTTGAAGATGGC
Found at i:1098956 original size:27 final size:27
Alignment explanation
Indices: 1098918--1099726 Score: 332
Period size: 27 Copynumber: 27.0 Consensus size: 27
1098908 TTTTGAAAAG
* * *
1098918 AAAAAGGTGCCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
1098945 AAAAGGGTGCCATGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
***
1098973 AAAA-GGTGCCATAAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
1098999 AAAA-GGTACCACGAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
1099025 ACAAGGGCGCCACGGGGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
1099053 GAAAAGAAAAAAAAAGTGCCACGGAATTGTGGACTT
1 -AAAAG--------GGTGCCACGGAGTTGTGGACTT
*
1099089 AAAAGGGTGCCACGGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
1099116 CGAAAAGAAAAAGGTGCCATGGAGTTGT-GACTT
1 --AAAAG-----GGTGCCACGGAGTTGTGGACTT
**
1099149 AAAAGGGTGCCATAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
**
1099176 CGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
1 --AAAAG-----GGTGCCACGGAGTTGTGGACTT
* *
1099210 AAAAGGGTGCCACGGAGTTATGGGCTGT
1 AAAAGGGTGCCACGGAGTTGTGGACT-T
1099238 AAAAGGAAAAGGGTGCCAC-GAGTTGTGGACTT
1 ------AAAAGGGTGCCACGGAGTTGTGGACTT
**
1099270 AAAAGGGTGCCACAAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
1099297 AAAAGGGTGCCACAGAGTTAT-GAGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGA-C-TT
* *
1099325 GAAAAGAAAAAGGTGCCACAGAGTTGTAGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
* *
1099358 AAAAAGGAAAAGGTGCCACAGAGTTGTAGACTT
1 -AAAA-G----GGTGCCACGGAGTTGTGGACTT
* **
1099391 AAAAGGGTGCCACAGAGTTGTGGGTTTT
1 AAAAGGGTGCCACGGAGTTGT-GGACTT
* *
1099419 GAAAAGAAAAAGGTGCCACGAAGTTGTAGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
* *
1099452 AAAAGGGTGCCATGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
1099480 GAAAAGAAAAAAGTGCCACGGAGTTGTGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
1099513 AAAAGGAAATGATGCCACGGAGTTGTGGACTT
1 AAAAGG----G-TGCCACGGAGTTGTGGACTT
* * *
1099545 AAAAGGGTGCCACAGAGTTATGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * * *
1099573 GAAAAGAAAAAAGTGCCATGGAGTTATAGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
** *
1099606 AAAAGGGTGCCACAAAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
1099634 AAAAGGAAAAAGGGTTCCACAGAGTTGTGGACTT
1 -------AAAAGGGTGCCACGGAGTTGTGGACTT
1099668 AAAAGGAAAAGATGCCACGGAGTTGTGGACTT
1 AAAAGG----G-TGCCACGGAGTTGTGGACTT
* *
1099700 AAAAGGATGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
1099727 GGAGAAGAGA
Statistics
Matches: 625, Mismatches: 73, Indels: 168
0.72 0.08 0.19
Matches are distributed among these distances:
26 58 0.09
27 214 0.34
28 21 0.03
29 34 0.05
31 8 0.01
32 75 0.12
33 54 0.09
34 115 0.18
35 29 0.05
36 2 0.00
37 15 0.02
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:1099156 original size:60 final size:60
Alignment explanation
Indices: 1098999--1099727 Score: 496
Period size: 61 Copynumber: 11.9 Consensus size: 60
1098989 TTGTGGACTT
* * * * * * *
1098999 AAAAGGTACCACGAAGTTGTGGACTTACAAGGGCGCCACGGGGTTGTGGGCTTTGAAAAGAAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTGAAAAG---A
* * * *
1099063 AAAAAGTGCCACGGAATTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTCGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT-GAAAAGA
* *
1099124 AAAAGGTGCCATGGAGTTGT-GACTTAAAAGGGTGCCATAGAGTTGTGGACTTCGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT-GAAAAGA
** * * *
1099184 AAAAGGTGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGGC-TGTAAAAGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTG-AAAA-GA
* *
1099245 AAAGGGTGCCAC-GAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTT-AAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAAGA
* * * *
1099302 ----GGTGCCACAGAGTTAT-GAGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTAGACTTAAAA
1 AAAAGGTGCCACGGAGTTGTGGA-C-TT-AAAAG-----GGTGCCACAGAGTTGTGGACTTGAAA
*
1099362 AGG
58 AGA
* * **
1099365 AAAAGGTGCCACAGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGTTTTGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGT-GGACTTGAAAAGA
* * ** *
1099426 AAAAGGTGCCACGAAGTTGTAGACTTAAAAGGGTGCCATGGAGTTGTGGGCTTTGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTGAAAAGA
* *
1099487 AAAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAATGATGCCACGGAGTTGTGGACTT-AAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGG----G-TGCCACAGAGTTGTGGACTTGAAAAGA
* * * * ** * *
1099550 ----GGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTATAGACTT-AAAA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAG-----GGTGCCACAGAGTTGTGGACTTGAAAA
1099610 G-
59 GA
** * *
1099611 ----GGTGCCACAAAGTTGTGGGCTTTAAAAGGAAAAAGGGTTCCACAGAGTTGTGGACTT-AAA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-------AAAAGGGTGCCACAGAGTTGTGGACTTGAAA
*
1099671 AGG
58 AGA
* *
1099674 AAAAGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTG
1099728 GAGAAGAGAT
Statistics
Matches: 549, Mismatches: 69, Indels: 98
0.77 0.10 0.14
Matches are distributed among these distances:
53 10 0.02
54 7 0.01
55 2 0.00
56 5 0.01
58 1 0.00
59 46 0.08
60 115 0.21
61 214 0.39
62 27 0.05
63 2 0.00
64 53 0.10
65 8 0.01
66 20 0.04
67 37 0.07
68 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (60 bp):
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAAGA
Found at i:1099217 original size:121 final size:120
Alignment explanation
Indices: 1098999--1099727 Score: 516
Period size: 121 Copynumber: 6.0 Consensus size: 120
1098989 TTGTGGACTT
* * * * * * *
1098999 AAAAGGTACCACGAAGTTGTGGACTTACAAGGGCGCCACGGGGTTGTGGGCTTTGAAAAGAAAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTGAAAAG---AA
* * *
1099064 AAAAGTGCCACGGAATTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTCGAAAAGA
62 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTT-GAAAAGA
* *
1099124 AAAAGGTGCCATGGAGTTGT-GACTTAAAAGGGTGCCATAGAGTTGTGGACTTCGAAAAGAAAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT-GAAAAGAAAAA
* * * *
1099188 GGTGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGGC-TGTAAAAGGA
65 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTG-AAAA-GA
* *
1099245 AAAGGGTGCCAC-GAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTT-AAAAG-----G
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAAGAAAAAG
* * * *
1099303 GTGCCACAGAGTTAT-GAGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTAGACTTAAAAAGG
66 GTGCCACAGAGTTGTGGA-C-TT-AAAAG-----GGTGCCACGGAGTTGTAGACTTGAAAAGA
* * **
1099365 AAAAGGTGCCACAGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGTTTTGAAAAGAAAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGT-GGACTTGAAAAGAAAAA
* * * *
1099430 GGTGCCAC-GAAGTTGTAGACTTAAAAGGGTGCCATGGAGTTGTGGGCTTTGAAAAGA
65 GGTGCCACAG-AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGAC-TTGAAAAGA
* *
1099487 AAAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAATGATGCCACGGAGTTGTGGACTT-AAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGG----G-TGCCACAGAGTTGTGGACTTGAAAAGA
* * * * *
1099550 ----GGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTATAGACTT-AAAA
61 AAAAGGTGCCACAGAGTTGTGGAC-TT-AAAAG-----GGTGCCACGGAGTTGTAGACTTGAAAA
1099610 G-
119 GA
** * *
1099611 ----GGTGCCACAAAGTTGTGGGCTTTAAAAGGAAAAAGGGTTCCACAGAGTTGTGGACTT-AAA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-------AAAAGGGTGCCACAGAGTTGTGGACTTGAAA
* * * * * *
1099671 AGGAAAAGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTG
58 AGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTG
1099728 GAGAAGAGAT
Statistics
Matches: 484, Mismatches: 69, Indels: 105
0.74 0.10 0.16
Matches are distributed among these distances:
113 2 0.00
114 15 0.03
115 2 0.00
116 5 0.01
119 6 0.01
120 55 0.11
121 176 0.36
122 46 0.10
123 30 0.06
124 31 0.06
125 27 0.06
126 17 0.04
127 34 0.07
128 36 0.07
129 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (120 bp):
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAAGAAAAAG
GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTGAAAAGA
Found at i:1099261 original size:94 final size:91
Alignment explanation
Indices: 1099149--1099456 Score: 383
Period size: 94 Copynumber: 3.3 Consensus size: 91
1099139 GTTGTGACTT
* * * *
1099149 AAAAGGGTGCCATAGAGTTGTGGACTTCGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTTAAAA
1 AAAAAGGTGCCA-CGAGTTGTAGACTT--AAAAG-AAAAGGTGCCACAGAGTTGTGGACTTAAAA
* *
1099214 GGGTGCCACGGAGTTATGGGCTGT-AAAAGG
62 GGGTGCCACAGAGTTATGGGCTTTGAAAA-G
* * *
1099244 AAAAGGGTGCCACGAGTTGTGGACTTAAAAG----GGTGCCACAAAGTTGTGGACTTAAAAGGGT
1 AAAAAGGTGCCACGAGTTGTAGACTTAAAAGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGT
*
1099305 GCCACAGAGTTATGAGCTTTGAAAAG
66 GCCACAGAGTTATGGGCTTTGAAAAG
*
1099331 AAAAAGGTGCCACAGAGTTGTAGACTTAAAAAGGAAAAGGTGCCACAGAGTTGTAGACTTAAAAG
1 AAAAAGGTGCCAC-GAGTTGTAGACTT-AAAA-GAAAAGGTGCCACAGAGTTGTGGACTTAAAAG
* *
1099396 GGTGCCACAGAGTTGTGGGTTTTGAAAAG
63 GGTGCCACAGAGTTATGGGCTTTGAAAAG
1099425 AAAAAGGTGCCACGAAGTTGTAGACTTAAAAG
1 AAAAAGGTGCCACG-AGTTGTAGACTTAAAAG
1099457 GGTGCCATGG
Statistics
Matches: 191, Mismatches: 13, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
87 58 0.30
88 16 0.08
89 4 0.02
90 1 0.01
92 6 0.03
93 5 0.03
94 89 0.47
95 12 0.06
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (91 bp):
AAAAAGGTGCCACGAGTTGTAGACTTAAAAGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGT
GCCACAGAGTTATGGGCTTTGAAAAG
Found at i:1099479 original size:155 final size:154
Alignment explanation
Indices: 1099063--1099722 Score: 783
Period size: 155 Copynumber: 4.3 Consensus size: 154
1099053 GAAAAGAAAA
* * * * * *
1099063 AAAAAGTGCCACGGAATTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTCGAAAAGAAAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAA
* * * * *
1099128 GGTGCCATGGAGTTGT-GACTTAAAAGGGTGCCATAGAGTTGTGGACTTCGAAAAGAAAAAGGTG
66 GGTGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTG
*
1099192 CCATAGAGTTGTGGACTTAAAA-G
131 CCACAGAGTTGTGGACTTAAAAGG
* * *
1099215 ----GGTGCCACGGAGTTATGGGCTGTAAAAGGAAAAGGGTGCCAC-GAGTTGTGGAC-TT-AAA
1 AAAAGGTGCCACGGAGTTGTGGACT-T------AAAAGGGTGCCACAGAGTTGTGGGCTTTGAAA
* * * *
1099273 AG-----GGTGCCACAAAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGAGCTTTGAAAAGAA
59 AGAAAAAGGTGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAA
*
1099333 AAAGGTGCCACAGAGTTGTAGACTTAAAAAGG
124 AAAGGTGCCACAGAGTTGTGGACTT-AAAAGG
* * *
1099365 AAAAGGTGCCACAGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGTTTTGAAAAGAAAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAA
** *
1099430 GGTGCCACGAAGTTGTAGACTTAAAAGGGTGCCATGGAGTTGTGGGCTTTGAAAAGAAAAAAGTG
66 GGTGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTG
*
1099495 CCACGGAGTTGTGGACTTAAAAGG
131 CCACAGAGTTGTGGACTTAAAAGG
* * *
1099519 AAATGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAA
* * * * *
1099584 AGTGCCATGGAGTTATAGACTTAAAAGGGTGCCACAAAGTTGTGGGCTTT-AAAAGGAAAAAGGG
66 GGTGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAA-GAAAAA-GG
*
1099648 TTCCACAGAGTTGTGGACTTAAAAGG
129 TGCCACAGAGTTGTGGACTTAAAAGG
* *
1099674 AAAAGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGG
1099723 ACTTGGAGAA
Statistics
Matches: 434, Mismatches: 50, Indels: 45
0.82 0.09 0.09
Matches are distributed among these distances:
147 26 0.06
148 85 0.20
149 7 0.02
150 6 0.01
152 5 0.01
153 6 0.01
154 141 0.32
155 158 0.36
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.22
Consensus pattern (154 bp):
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAA
GGTGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTG
CCACAGAGTTGTGGACTTAAAAGG
Found at i:1099531 original size:93 final size:93
Alignment explanation
Indices: 1099432--1099611 Score: 288
Period size: 93 Copynumber: 1.9 Consensus size: 93
1099422 AAGAAAAAGG
** *
1099432 TGCCACGAAGTTGTAGACTTAAAAGGGTGCCATGGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCC
1 TGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCC
* *
1099497 ACGGAGTTGTGGACTTAAAAGGAAATGA
66 ACGGAGTTATAGACTTAAAAGGAAATGA
* *
1099525 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCC
1 TGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCC
*
1099590 ATGGAGTTATAGACTTAAAAGG
66 ACGGAGTTATAGACTTAAAAGG
1099612 GTGCCACAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.23
Consensus pattern (93 bp):
TGCCACGAAGTTGTAGACTTAAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCC
ACGGAGTTATAGACTTAAAAGGAAATGA
Found at i:1099645 original size:35 final size:34
Alignment explanation
Indices: 1099606--1099706 Score: 134
Period size: 32 Copynumber: 3.0 Consensus size: 34
1099596 TTATAGACTT
* *
1099606 AAAAGGGTGCCACAAAGTTGTGGGCTTTAAAAGGA
1 AAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGA
*
1099641 AAAAGGGTTCCACAGAGTTGTGGACTTAAAAGG-
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
1099674 AAAA-GATGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1099707 TGCCACAGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
32 25 0.42
33 4 0.07
34 8 0.14
35 22 0.37
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.20
Consensus pattern (34 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1099699 original size:94 final size:96
Alignment explanation
Indices: 1099545--1099722 Score: 245
Period size: 94 Copynumber: 1.9 Consensus size: 96
1099535 TTGTGGACTT
* *
1099545 AAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTATAGACTTAAAA
1 AAAAGGGTGCCACAGAGTTATGGACTTTGAAAAGAAAAAAGTGCCACGGAGTTATAGACTTAAAA
*
1099610 GGGTGCCACAAAGTTGTGGGCTTTAAAAGGA
66 GGATGCCACAAAGTTGTGGGCTTTAAAAGGA
* * * * *
1099641 AAAAGGGTTCCACAGAGTTGTGGAC-TT-AAAAG-GAAAAGATGCCACGGAGTTGTGGACTTAAA
1 AAAAGGGTGCCACAGAGTTATGGACTTTGAAAAGAAAAAAG-TGCCACGGAGTTATAGACTTAAA
*
1099703 AGGATGCCACAGAGTTGTGG
65 AGGATGCCACAAAGTTGTGG
1099723 ACTTGGAGAA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
93 5 0.07
94 43 0.60
95 2 0.03
96 22 0.31
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (96 bp):
AAAAGGGTGCCACAGAGTTATGGACTTTGAAAAGAAAAAAGTGCCACGGAGTTATAGACTTAAAA
GGATGCCACAAAGTTGTGGGCTTTAAAAGGA
Found at i:1099741 original size:30 final size:30
Alignment explanation
Indices: 1099650--1100043 Score: 205
Period size: 33 Copynumber: 12.6 Consensus size: 30
1099640 AAAAAGGGTT
* **
1099650 CCACAGAGTTGTGGACTTAAAAGGAAAAGATG
1 CCACAGAGTCGTGGACTT-GGA-GAAAAGATG
* * *
1099682 CCACGGAGTTGTGGACTT--A-AAAGGATG
1 CCACAGAGTCGTGGACTTGGAGAAAAGATG
* *
1099709 CCACAGAGTTGTGGACTTGGAGAAGAGATG
1 CCACAGAGTCGTGGACTTGGAGAAAAGATG
** *
1099739 CCATTGAGTCGTGGACTTTGAAGAAAAAAGATG
1 CCACAGAGTCGTGGAC-TTG--GAGAAAAGATG
* *
1099772 CCACTA-AGTCGTGGACTTTGACAAAAAAGGATG
1 CCAC-AGAGTCGTGGAC-TTG-GAGAAAA-GATG
* * *
1099805 CCACTA-AGTCATTGACTTTGAAGAAAAAAGATG
1 CCAC-AGAGTCGTGGAC-TTG--GAGAAAAGATG
* * *
1099838 CCACTGAGTCGTGGACTTGAAGAAGAGATG
1 CCACAGAGTCGTGGACTTGGAGAAAAGATG
* * **
1099868 CCACTGAGTCATGGACTTTTGGA-AGGAGATG
1 CCACAGAGTCGTGGAC--TTGGAGAAAAGATG
*
1099899 CCACTGAGTCGTGGACTTTGGGAGAAAAAGGATG
1 CCACAGAGTCGTGGAC-TT-GGAG-AAAA-GATG
* *
1099933 CGACTA-AGTCATGGACTTGGAAGAAAAAAGATG
1 CCAC-AGAGTCGTGGACTTGG-AG--AAAAGATG
*
1099966 CCACTA-AGTCATGGACTTGGA-AAAGAGATG
1 CCAC-AGAGTCGTGGACTTGGAGAAA-AGATG
* * * *
1099996 CCACTGAGTTGTGGACTTGAAGAAGAGATG
1 CCACAGAGTCGTGGACTTGGAGAAAAGATG
1100026 CCACTA-AGTCGTGGACTT
1 CCAC-AGAGTCGTGGACTT
1100044 TAGGAAGGAT
Statistics
Matches: 300, Mismatches: 39, Indels: 48
0.78 0.10 0.12
Matches are distributed among these distances:
27 24 0.08
29 5 0.02
30 86 0.29
31 30 0.10
32 34 0.11
33 93 0.31
34 28 0.09
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (30 bp):
CCACAGAGTCGTGGACTTGGAGAAAAGATG
Found at i:1099774 original size:33 final size:33
Alignment explanation
Indices: 1099734--1100044 Score: 306
Period size: 33 Copynumber: 9.7 Consensus size: 33
1099724 CTTGGAGAAG
* *
1099734 AGATGCCATTGAGTCGTGGACTTTGAAGAAAAA
1 AGATGCCACTAAGTCGTGGACTTTGAAGAAAAA
1099767 AGATGCCACTAAGTCGTGGACTTTGACA-AAAAA
1 AGATGCCACTAAGTCGTGGACTTTGA-AGAAAAA
* * *
1099800 GGATGCCACTAAGTCATTGACTTTGAAGAAAAA
1 AGATGCCACTAAGTCGTGGACTTTGAAGAAAAA
* *
1099833 AGATGCCACTGAGTCGTGGAC-TTGAAG--AAG
1 AGATGCCACTAAGTCGTGGACTTTGAAGAAAAA
* * **
1099863 AGATGCCACTGAGTCATGGACTTTTG--G-AAGG
1 AGATGCCACTAAGTCGTGGAC-TTTGAAGAAAAA
* *
1099894 AGATGCCACTGAGTCGTGGACTTTGGGAGAAAAA
1 AGATGCCACTAAGTCGTGGACTTT-GAAGAAAAA
* * * *
1099928 GGATGCGACTAAGTCATGGACTTGGAAGAAAAA
1 AGATGCCACTAAGTCGTGGACTTTGAAGAAAAA
* *
1099961 AGATGCCACTAAGTCATGGAC-TTG--GAAAAG
1 AGATGCCACTAAGTCGTGGACTTTGAAGAAAAA
* * *
1099991 AGATGCCACTGAGTTGTGGAC-TTGAAG--AAG
1 AGATGCCACTAAGTCGTGGACTTTGAAGAAAAA
1100021 AGATGCCACTAAGTCGTGGACTTT
1 AGATGCCACTAAGTCGTGGACTTT
1100045 AGGAAGGATA
Statistics
Matches: 236, Mismatches: 30, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
30 74 0.31
31 25 0.11
32 13 0.06
33 102 0.43
34 22 0.09
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (33 bp):
AGATGCCACTAAGTCGTGGACTTTGAAGAAAAA
Found at i:1099799 original size:155 final size:156
Alignment explanation
Indices: 1099321--1100029 Score: 472
Period size: 155 Copynumber: 4.5 Consensus size: 156
1099311 GAGTTATGAG
* * *
1099321 CTTTGAAAAGAAAAAGG-TGCCACAGAGTTGTAGACTTAAAAAGGAAAAGGTGCCACAGAGTTGT
1 CTTT-AAAAGAAAAAGGATGCCACAGAGTTGTGGACTT-AAAAGGAAAAGATGCCACGGAGTTGT
* * * ** * * * * * *
1099385 AGACTTAAAAGGGTGCCACAGAGTTGTGGGTTTTGAAAAGAAAAAGGTGCCA-CGAAGTTGTAGA
64 GGACTTAAAAGGATGCCACAGAGTTATGGACTTTG--GAG-AAGAGATGCCATTG-AGTCGTGGA
* * * *
1099449 C-TT----AAAAGGGTGCCA-TGGAGTTGTGGG
125 CTTTGAGAAAAAGGATGCCACT-AAGTCGTGGA
* * *
1099476 CTTTGAAAAGAAAAAAG-TGCCACGGAGTTGTGGACTTAAAAGGAAATGATGCCACGGAGTTGTG
1 CTTT-AAAAGAAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTGTG
* * * * * * ** *
1099540 GACTTAAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTATAGAC-
65 GACTTAAAAGGATGCCACAGAGTTATGGACTTTG--GAGAAGAGA-TGCCATTGAGTCGTGGACT
* * * *
1099604 TT----AAAAGGGTGCCACAAAGTTGTGGG
127 TTGAGAAAAAGGATGCCACTAAGTCGTGGA
* *
1099630 CTTTAAAAGGAAAAAGGGTTCCACAGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTGTG
1 CTTTAAAA-GAAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTGTG
*
1099695 GACTTAAAAGGATGCCACAGAGTTGTGGAC-TTGGAGAAGAGATGCCATTGAGTCGTGGACTTTG
65 GACTTAAAAGGATGCCACAGAGTTATGGACTTTGGAGAAGAGATGCCATTGAGTCGTGGACTTTG
*
1099759 AAGAAAAAAGATGCCACTAAGTCGTGGA
130 -AGAAAAAGGATGCCACTAAGTCGTGGA
* * ** * ** * * *
1099787 CTTTGACA-AAAAAGGATGCCACTA-AGTCATTGACTTTGAAGAAAAAAGATGCCACTGAGTCGT
1 CTTTAAAAGAAAAAGGATGCCAC-AGAGTTGTGGACTTAAAAG-GAAAAGATGCCACGGAGTTGT
* * * *
1099850 GGACTTGAAGAAGAGATGCCACTGAGTCATGGACTTTTGGA-AGGAGATGCCACTGAGTCGTGGA
64 GGACTT-AA-AAG-GATGCCACAGAGTTATGGAC-TTTGGAGAAGAGATGCCATTGAGTCGTGGA
* *
1099914 CTTTGGGAGAAAAAGGATGCGACTAAGTCATGGA
125 CTTT--GAGAAAAAGGATGCCACTAAGTCGTGGA
** * ** ** * *
1099948 C-TTGGAAGAAAAAAGATGCCACTA-AGTCATGGACTTGGAA--AAGAGATGCCACTGAGTTGTG
1 CTTTAAAAGAAAAAGGATGCCAC-AGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTGTG
1100009 GACTTGAAGAAGAGATGCCAC
65 GACTT-AA-AAG-GATGCCAC
1100030 TAAGTCGTGG
Statistics
Matches: 472, Mismatches: 61, Indels: 39
0.83 0.11 0.07
Matches are distributed among these distances:
151 14 0.03
152 8 0.02
153 8 0.02
154 111 0.24
155 130 0.28
156 25 0.05
157 27 0.06
158 43 0.09
159 17 0.04
160 29 0.06
161 59 0.12
162 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.22
Consensus pattern (156 bp):
CTTTAAAAGAAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTGTGG
ACTTAAAAGGATGCCACAGAGTTATGGACTTTGGAGAAGAGATGCCATTGAGTCGTGGACTTTGA
GAAAAAGGATGCCACTAAGTCGTGGA
Found at i:1099981 original size:128 final size:126
Alignment explanation
Indices: 1099720--1100044 Score: 429
Period size: 128 Copynumber: 2.5 Consensus size: 126
1099710 CACAGAGTTG
* * *
1099720 TGGACTTGGAGAAGAGATGCCATTGAGTCGTGGAC-TTTGAAGAAAAAAGATGCCACTAAGTCGT
1 TGGACTTGAAGAAGAGATGCCACTGAGTCGTGGACTTTTG--G--AAGAGATGCCACTAAGTCGT
* * * *
1099784 GGACTTTGACAAAAAAGGATGCCACTAAGTCATTGACTTTGAAGAAAAAAGATGCCACTGAGTCG
62 GGACTTTGACAAAAAAGGATGCCACTAAGTCATGGACTTGGAAGAAAAAAGATGCCACTAAGTCA
* *
1099849 TGGACTTGAAGAAGAGATGCCACTGAGTCATGGACTTTTGGAAGGAGATGCCACTGAGTCGTGGA
1 TGGACTTGAAGAAGAGATGCCACTGAGTCGTGGACTTTTGGAA-GAGATGCCACTAAGTCGTGGA
** *
1099914 CTTTGGGAGAAAAAGGATGCGACTAAGTCATGGACTTGGAAGAAAAAAGATGCCACTAAGTCA
65 CTTTGACA-AAAAAGGATGCCACTAAGTCATGGACTTGGAAGAAAAAAGATGCCACTAAGTCA
* ***
1099977 TGGACTTGGAA-AAGAGATGCCACTGAGTTGTGGACTTGAAGAAGAGATGCCACTAAGTCGTGGA
1 TGGACTT-GAAGAAGAGATGCCACTGAGTCGTGGACTTTTGGAAGAGATGCCACTAAGTCGTGGA
1100041 CTTT
65 CTTT
1100045 AGGAAGGATA
Statistics
Matches: 174, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
126 2 0.01
127 49 0.28
128 84 0.48
129 35 0.20
130 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (126 bp):
TGGACTTGAAGAAGAGATGCCACTGAGTCGTGGACTTTTGGAAGAGATGCCACTAAGTCGTGGAC
TTTGACAAAAAAGGATGCCACTAAGTCATGGACTTGGAAGAAAAAAGATGCCACTAAGTCA
Found at i:1106112 original size:27 final size:27
Alignment explanation
Indices: 1106062--1106114 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1106052 ATTCAAAAAC
**
1106062 GGGGTTGGAGTATCCCCTCGGAATAAT
1 GGGGTTGGAGTATCCCCGAGGAATAAT
*
1106089 GGGGTTGGAGTATCCCCGATGAATAA
1 GGGGTTGGAGTATCCCCGAGGAATAA
1106115 AATTTGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGAGGAATAAT
Found at i:1110179 original size:25 final size:26
Alignment explanation
Indices: 1110122--1110179 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1110112 AGACCAACCT
*
1110122 TTTAAATACATTATTGAAAAATAAAA
1 TTTAAATACATTAATGAAAAATAAAA
**
1110148 TAAAAATA-ATTAAT-AAAAATAAATA
1 TTTAAATACATTAATGAAAAATAAA-A
1110173 TTTAAAT
1 TTTAAAT
1110180 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 9 0.35
25 11 0.42
26 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TTTAAATACATTAATGAAAAATAAAA
Found at i:1111272 original size:21 final size:20
Alignment explanation
Indices: 1111234--1111285 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1111224 TTTATTGAGG
*
1111234 TTAATATTTGAAAATTTAAAT
1 TTAA-ATTTTAAAATTTAAAT
*
1111255 TTAAATTTTAAAATTTTATAT
1 TTAAATTTTAAAA-TTTAAAT
*
1111276 TTAAAATTTA
1 TTAAATTTTA
1111286 TGATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTAAATTTTAAAATTTAAAT
Found at i:1111291 original size:14 final size:14
Alignment explanation
Indices: 1111261--1111311 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
1111251 AAATTTAAAT
1111261 TTTAAAATTTTAT-A
1 TTTAAAA-TTTATGA
1111275 TTTAAAATTTATGA
1 TTTAAAATTTATGA
* *
1111289 TTTTTAAATTCATGA
1 -TTTAAAATTTATGA
1111304 TTTGAAAA
1 TTT-AAAA
1111312 AATTTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 5 0.16
14 11 0.35
15 15 0.48
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (14 bp):
TTTAAAATTTATGA
Found at i:1112356 original size:2 final size:2
Alignment explanation
Indices: 1112351--1112398 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1112341 TGTATGTAAT
*
1112351 TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1112393 CA TA TA
1 TA TA TA
1112399 AATCCAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1115796 original size:50 final size:50
Alignment explanation
Indices: 1115742--1115883 Score: 266
Period size: 50 Copynumber: 2.8 Consensus size: 50
1115732 GTCATTTCTC
* *
1115742 ATGCTTAGGAATTTCTATATCATTTCATACATTTTTATGTCACATTTTTT
1 ATGCTTAGAAATTTTTATATCATTTCATACATTTTTATGTCACATTTTTT
1115792 ATGCTTAGAAATTTTTATATCATTTCATACATTTTTATGTCACATTTTTT
1 ATGCTTAGAAATTTTTATATCATTTCATACATTTTTATGTCACATTTTTT
1115842 ATGCTTAGAAATTTTTATATCATTTCATACATTTTTATGTCA
1 ATGCTTAGAAATTTTTATATCATTTCATACATTTTTATGTCA
1115884 TTTTAGTTAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (50 bp):
ATGCTTAGAAATTTTTATATCATTTCATACATTTTTATGTCACATTTTTT
Found at i:1115982 original size:58 final size:56
Alignment explanation
Indices: 1115856--1116005 Score: 183
Period size: 58 Copynumber: 2.6 Consensus size: 56
1115846 TTAGAAATTT
* * * *
1115856 TTATATCATTTCATACATTTTTATGTCATTTTAGTTATTTTCATGAATTAAGTACTA
1 TTATATCATTTCATGCA-TTTTATATCATTTTAGTCATTTTCATGAATTAAGGACTA
* *
1115913 TTATGTCATTTCATGCATCTTTGTATCATTTTAGTCATTTTTCATGAATTAAGGACTA
1 TTATATCATTTCATGCAT-TTTATATCATTTTAGTCA-TTTTCATGAATTAAGGACTA
* * *
1115971 TTATATAATTTCACGTATTTTATGATCATTTTAGT
1 TTATATCATTTCATGCATTTTAT-ATCATTTTAGT
1116006 TCTATGTTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
56 1 0.01
57 34 0.43
58 44 0.56
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.51
Consensus pattern (56 bp):
TTATATCATTTCATGCATTTTATATCATTTTAGTCATTTTCATGAATTAAGGACTA
Found at i:1121124 original size:2 final size:2
Alignment explanation
Indices: 1121117--1121142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1121107 CAATTGCATA
1121117 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
1121143 TTCTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1128073 original size:77 final size:76
Alignment explanation
Indices: 1127976--1128149 Score: 312
Period size: 77 Copynumber: 2.3 Consensus size: 76
1127966 ATAAAAGTAG
* * *
1127976 AATTAAGAAGATGACAAACGATTGTATTTAATTGAATTTAGAATTTAACTTAATTATATAATTAC
1 AATTAAGAAAATAACAAACGATTGTATTTAATTGAATTTAAAATTTAACTTAATTATATAATTAC
1128041 TTTTTAAAATGT
66 -TTTTAAAATGT
1128053 AATTAAGAAAATAACAAACGATTGTATTTAATTGAATTTAAAATTTAACTTAATTATATAATTAC
1 AATTAAGAAAATAACAAACGATTGTATTTAATTGAATTTAAAATTTAACTTAATTATATAATTAC
1128118 TTTTAAAATGT
66 TTTTAAAATGT
1128129 AATTAAGAAAATAACAAACGA
1 AATTAAGAAAATAACAAACGA
1128150 CATATATTAA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
76 32 0.34
77 62 0.66
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (76 bp):
AATTAAGAAAATAACAAACGATTGTATTTAATTGAATTTAAAATTTAACTTAATTATATAATTAC
TTTTAAAATGT
Found at i:1128353 original size:22 final size:21
Alignment explanation
Indices: 1128322--1128374 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
1128312 AATTTTTATT
* *
1128322 TAAATTTAATTTTAAAATATA
1 TAAATTTAATATAAAAATATA
1128343 TAAATATTAATATAAAAATA-A
1 TAAAT-TTAATATAAAAATATA
*
1128364 T-ATTTTAATAT
1 TAAATTTAATAT
1128375 TTTAAATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 7 0.25
20 2 0.07
21 7 0.25
22 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:1131791 original size:26 final size:26
Alignment explanation
Indices: 1131768--1131820 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1131758 CTAAAATCTC
1131768 AAATAAAATTCAACTTTAGTAATCCT
1 AAATAAAATTCAACTTTAGTAATCCT
* *
1131794 AAATAAAGTTGAACTTTA-TCAATCCT
1 AAATAAAATTCAACTTTAGT-AATCCT
1131820 A
1 A
1131821 TCTTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (26 bp):
AAATAAAATTCAACTTTAGTAATCCT
Found at i:1132722 original size:20 final size:20
Alignment explanation
Indices: 1132681--1132722 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1132671 ACAAATAGTA
* *
1132681 AATGTATTGATACATGAGTG
1 AATGCATTGATACATGACTG
*
1132701 AATGCATTGATACATGCCTG
1 AATGCATTGATACATGACTG
1132721 AA
1 AA
1132723 ATGTATCGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
AATGCATTGATACATGACTG
Found at i:1137110 original size:13 final size:13
Alignment explanation
Indices: 1137092--1137116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1137082 CAAAAAAATA
1137092 TGTATCGATACAT
1 TGTATCGATACAT
1137105 TGTATCGATACA
1 TGTATCGATACA
1137117 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1137127 original size:33 final size:33
Alignment explanation
Indices: 1137070--1137136 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1137060 AGTAGCTTAA
*
1137070 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
* ***
1137103 ATTGTATCGATACAACACTTTATGTATCAATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
1137136 A
1 A
1137137 AATCATTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCAATAC
Found at i:1141583 original size:20 final size:21
Alignment explanation
Indices: 1141533--1141583 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1141523 TTCTATAATT
*
1141533 TGTATCAATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
* *
1141554 TGTA-CTGATACATA-AGTGAA
1 TGTATC-GATACAAACAGTAAA
1141574 TGTATCGATA
1 TGTATCGATA
1141584 TATGCCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:1144245 original size:78 final size:78
Alignment explanation
Indices: 1144050--1144378 Score: 279
Period size: 79 Copynumber: 4.2 Consensus size: 78
1144040 TTTTATCTCG
* * *
1144050 GGGATACTCCAACCCCGTTTTTTATTTCTAAATATTAAATTTTTCATCTCAAGGATACTCCAGCC
1 GGGATACTCCAACCCC-ATTTTTATTTCAAAATATTAAAATTTTCATCTCAAGGATACTCCAGCC
*
1144115 CCGTTATTTTCGAA
65 CCGTTATTTTCCAA
* * * * * * * *
1144129 GAGATACTCTAACCCCGTTTTTATTTTTAAAATATTAAAATTTTCCTCTCGAGGGTACTTCAGCC
1 GGGATACTCCAACCCCATTTTTA-TTTCAAAATATTAAAATTTTCATCTCAAGGATACTCCAGCC
**
1144194 TTGTTA-TTTCCAA
65 CCGTTATTTTCCAA
* * *
1144207 GGGATACTCCAACCTCATTTTTATTTCCAAAATATTAAAATTTTCATCT-TAGAGATACTCCAAC
1 GGGATACTCCAACCCCATTTTTATTT-CAAAATATTAAAATTTTCATCTCAAG-GATACTCCAGC
* ** **
1144271 CCC-ATGGTTTCCGC
64 CCCGTTATTTTCCAA
* * * * ** * * *
1144285 GAGGATCCTCTAACCCTATTTTCATTTCCAAAATATTAATTTTTTTATCTTAAGGATACTCCAAC
1 G-GGATACTCCAACCCCATTTTTATTT-CAAAATATTAAAATTTTCATCTCAAGGATACTCCAGC
*
1144350 CCCGTTA-TTTCTAA
64 CCCGTTATTTTCCAA
1144364 GGGAATACTCCAACC
1 GGG-ATACTCCAACC
1144379 TCGTTATTTT
Statistics
Matches: 197, Mismatches: 45, Indels: 16
0.76 0.17 0.06
Matches are distributed among these distances:
77 6 0.03
78 68 0.35
79 120 0.61
80 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (78 bp):
GGGATACTCCAACCCCATTTTTATTTCAAAATATTAAAATTTTCATCTCAAGGATACTCCAGCCC
CGTTATTTTCCAA
Found at i:1144407 original size:28 final size:27
Alignment explanation
Indices: 1144338--1144407 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
1144328 TTTATCTTAA
*
1144338 GGATACTCCAACCCCGTTATTTCTAAG
1 GGATACTCCAACCTCGTTATTTCTAAG
*
1144365 GGAATACTCCAACCTCGTTATTTTTGAAG
1 GG-ATACTCCAACCTCGTTATTTCT-AAG
*
1144394 GGATACTCAAACCT
1 GGATACTCCAACCT
1144408 TGCTTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 31 0.82
29 5 0.13
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (27 bp):
GGATACTCCAACCTCGTTATTTCTAAG
Found at i:1146994 original size:26 final size:26
Alignment explanation
Indices: 1146965--1147023 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
1146955 TCTTATCTAA
1146965 AATCCTAGATAAAGTTGAACTTTATT
1 AATCCTAGATAAAGTTGAACTTTATT
1146991 AATCCTAGATAAAGTTGAACTTTATT
1 AATCCTAGATAAAGTTGAACTTTATT
1147017 AATCCTA
1 AATCCTA
1147024 TTTCTATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (26 bp):
AATCCTAGATAAAGTTGAACTTTATT
Found at i:1150613 original size:78 final size:77
Alignment explanation
Indices: 1150387--1150639 Score: 280
Period size: 78 Copynumber: 3.2 Consensus size: 77
1150377 TTGGGAAGCG
* * * * * * * * *
1150387 AAAACGGGGTTGGAGTATCCTTTCAGAAGTGATGGGGTTGGAGTATCCTGGATGGTGAAAAATTG
1 AAAACGAGGTTGGAGTATCCTCTCAAAAAT-ATGGGGTTAGAGTATCCTCGA-GATGAAAATTTA
1150452 ATATTTT-AGAAATA
64 ATATTTTGA-AAATA
* * * *
1150466 AAAACG-GGATCGGAGTATCCCCTCGAAAATACGGGGTTAGAGTATCC-CGAGATGAAAATTTTA
1 AAAACGAGG-TTGGAGTATCCTCTCAAAAATATGGGGTTAGAGTATCCTCGAGATGAAAA-TTTA
1150529 ATATTTTGAAAATA
64 ATATTTTGAAAATA
1150543 AAAACGAGGTTGGAGTATCCTCTCAAAAATAATGGGGTTAGAGTATCCTCGCA-ATGAAAATTTA
1 AAAACGAGGTTGGAGTATCCTCTCAAAAAT-ATGGGGTTAGAGTATCCTCG-AGATGAAAATTTA
*
1150607 ATATTTTGGAAATA
64 ATATTTTGAAAATA
*
1150621 AAAACGAGGTTAGAGTATC
1 AAAACGAGGTTGGAGTATC
1150640 TCCTAAGATG
Statistics
Matches: 149, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
76 7 0.05
77 40 0.27
78 71 0.48
79 30 0.20
80 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (77 bp):
AAAACGAGGTTGGAGTATCCTCTCAAAAATATGGGGTTAGAGTATCCTCGAGATGAAAATTTAAT
ATTTTGAAAATA
Found at i:1153229 original size:21 final size:21
Alignment explanation
Indices: 1153205--1153261 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1153195 CCGCTGGGAC
*
1153205 CATGTATTAATACATGAAAGG
1 CATGTATCAATACATGAAAGG
*
1153226 CATGTATCGATACATGAAAGG
1 CATGTATCAATACATGAAAGG
*
1153247 CATGTATCGATACAT
1 CATGTATCAATACAT
1153262 CTAAGCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (21 bp):
CATGTATCAATACATGAAAGG
Found at i:1156233 original size:6 final size:7
Alignment explanation
Indices: 1156218--1156251 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1156208 AAAAATACTG
1156218 AAAATAA
1 AAAATAA
1156225 AAAATAA
1 AAAATAA
1156232 AAAATAA
1 AAAATAA
**
1156239 AAACGAA
1 AAAATAA
1156246 AAAATA
1 AAAATA
1156252 GAAAGCCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:1156556 original size:15 final size:14
Alignment explanation
Indices: 1156523--1156568 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1156513 ATTATTTTTA
1156523 TATTATATTTATAT
1 TATTATATTTATAT
*
1156537 AATTATATTTGATAT
1 TATTATATTT-ATAT
* *
1156552 TATTAAATTTATTT
1 TATTATATTTATAT
1156566 TAT
1 TAT
1156569 ATCTGCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TATTATATTTATAT
Found at i:1157476 original size:12 final size:14
Alignment explanation
Indices: 1157442--1157481 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1157432 TTTTTTTATC
1157442 AAAATATATCTTAA
1 AAAATATATCTTAA
* *
1157456 AAAATATATATTTA
1 AAAATATATCTTAA
1157470 AAAATATGATCT
1 AAAATAT-ATCT
1157482 ATACACCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (14 bp):
AAAATATATCTTAA
Found at i:1162801 original size:181 final size:181
Alignment explanation
Indices: 1162497--1162856 Score: 549
Period size: 181 Copynumber: 2.0 Consensus size: 181
1162487 AAATAATTAC
* * *
1162497 TTCCACTAGCAACCGCCAAAGGAAGATAAGCCTAACCAAAGCCAAAGCACTTACCAATAGGGTAA
1 TTCCACTAGCAACCGCCAAAGGAAGACAAGCCCAACCAAAGCCAAAGCACTTACCAATAAGGTAA
* *
1162562 AAAGAGAGAATAGGCTCCTTACTACTCTTAGTATGTATCATACACTCTTTTCACTACTAATAGAA
66 AAAGAGAGAATAGGCTCCTTACTACTCCTAGTATGAATCATACACTCTTTTCACTACTAATAGAA
* * * *
1162627 CCCCAATCCTTAGTACTATAATGTGGAATGGATTGGTGGAAAGACCCTTGT
131 CCCAAATCCTTAATACCATAATGTGGAATAGATTGGTGGAAAGACCCTTGT
* * * * * *
1162678 TTCCACTAGCTATCGCCAAAGGAAGACAAGCCCAACCAAAGCTAGAGCACTTACTAGTAAGGTAA
1 TTCCACTAGCAACCGCCAAAGGAAGACAAGCCCAACCAAAGCCAAAGCACTTACCAATAAGGTAA
* *
1162743 AAAGAGAGAATGGGCTCCTTACTACTCCTAGTGTGAATCATACACTCTTTTCACTACTAATAGAA
66 AAAGAGAGAATAGGCTCCTTACTACTCCTAGTATGAATCATACACTCTTTTCACTACTAATAGAA
* *
1162808 CCTAAATCCTTAATACCATAATGTTGAATAGATTGGTGGAAAGACCCTT
131 CCCAAATCCTTAATACCATAATGTGGAATAGATTGGTGGAAAGACCCTT
1162857 ACCAATGAAG
Statistics
Matches: 160, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
181 160 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (181 bp):
TTCCACTAGCAACCGCCAAAGGAAGACAAGCCCAACCAAAGCCAAAGCACTTACCAATAAGGTAA
AAAGAGAGAATAGGCTCCTTACTACTCCTAGTATGAATCATACACTCTTTTCACTACTAATAGAA
CCCAAATCCTTAATACCATAATGTGGAATAGATTGGTGGAAAGACCCTTGT
Found at i:1169383 original size:202 final size:203
Alignment explanation
Indices: 1168974--1169475 Score: 635
Period size: 202 Copynumber: 2.5 Consensus size: 203
1168964 GTTATATTAT
* * **
1168974 TTTTAGTTTATTATATTATTGAGTTAAAAATG-AAAAGCCCCAG-ACATTCAGAGTAAAGTTGCC
1 TTTTAGTTTATTATATTATTAAGTTAAAAATGTAAAAGCCAC-GTAC-TTCAGAGTAAAGTTTTC
* *
1169037 AATAAAAGAACGATGTGACATTCACCAACTTTTAGCAGTATGATCGCAAAATTAAAAGGACTTTT
64 AATAAAAGAATGATGTGACATTCACCAACTTTTAGCAG-ATGATCGCAAAACTAAAAGGACTTTT
* * * * * *
1169102 CGGCGCTCATCTCGGTCGGCCGATCCAGACCACATTTTAAGGGAAATCGCACGATCCTTGCGAGT
128 AGGAGCTCATCGCGGTCGGCCGACCCAGACCACATTTTAAGGGAAATCGCACGATCCTCGCAAGT
1169167 CTCCCTTACAC
193 CTCCCTTACAC
1169178 TTTTAGTTTATTATATTATTAAGTTAAAAATGTAAAAGCCACGTACGTTCAGAGTAAAGTTTTCA
1 TTTTAGTTTATTATATTATTAAGTTAAAAATGTAAAAGCCACGTAC-TTCAGAGTAAAGTTTTCA
* * * * * * *
1169243 ATAAAAGAATAATGTGGCATTCACTAACTTTTGGCAG-T-ATCGTAATACTGAAAGGACTTTTAG
65 ATAAAAGAATGATGTGACATTCACCAACTTTTAGCAGATGATCGCAAAACTAAAAGGACTTTTAG
* * * *
1169306 GAGCTCATCGCGGTCGGCCGACCCAGACTAC-TTTTCAAGGTAGATCGCACGATTCTCGCAAGTC
130 GAGCTCATCGCGGTCGGCCGACCCAGACCACATTTT-AAGGGAAATCGCACGATCCTCGCAAGTC
*
1169370 TCCCTTGCAC
194 TCCCTTACAC
* * * * *
1169380 TTTTAGTTTATTATATTTTTAGGTTAAAAATGTAAAAGCCA--TA-TTAAGAGAAAAATTTT-AA
1 TTTTAGTTTATTATATTATTAAGTTAAAAATGTAAAAGCCACGTACTTCAGAGTAAAGTTTTCAA
1169441 TAAAAGAATGATGTGACATTCACCAACTTTTAGCA
66 TAAAAGAATGATGTGACATTCACCAACTTTTAGCA
1169476 TTATGACGGT
Statistics
Matches: 261, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
197 33 0.13
198 13 0.05
200 2 0.01
201 4 0.02
202 118 0.45
203 1 0.00
204 32 0.12
205 58 0.22
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (203 bp):
TTTTAGTTTATTATATTATTAAGTTAAAAATGTAAAAGCCACGTACTTCAGAGTAAAGTTTTCAA
TAAAAGAATGATGTGACATTCACCAACTTTTAGCAGATGATCGCAAAACTAAAAGGACTTTTAGG
AGCTCATCGCGGTCGGCCGACCCAGACCACATTTTAAGGGAAATCGCACGATCCTCGCAAGTCTC
CCTTACAC
Found at i:1173026 original size:13 final size:13
Alignment explanation
Indices: 1173008--1173032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1172998 TTCAAATTAA
1173008 AATTTTTTAATTC
1 AATTTTTTAATTC
1173021 AATTTTTTAATT
1 AATTTTTTAATT
1173033 TCTTAATCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTTAATTC
Found at i:1173827 original size:15 final size:15
Alignment explanation
Indices: 1173807--1173857 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
1173797 TGGATTTGAT
* *
1173807 ATTTAACTTATTTAA
1 ATTTAAATTATTCAA
*
1173822 ATTTAAATTATTCGA
1 ATTTAAATTATTCAA
*
1173837 ATTTAATTTATT-AA
1 ATTTAAATTATTCAA
*
1173851 TTTTAAA
1 ATTTAAA
1173858 ATCAAATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTAAATTATTCAA
Found at i:1175038 original size:2 final size:2
Alignment explanation
Indices: 1175033--1175063 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1175023 TGTGTGTGTG
*
1175033 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1175064 GTGAGATGTT
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:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1180820 original size:90 final size:90
Alignment explanation
Indices: 1180668--1180834 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 90
1180658 CACTGAATCG
* * * * *
1180668 AGTCTTAGAAATGGGGTAACAACTCTTGAACCAAATTTCATGTCTATACTGTAATTTAAACCTCA
1 AGTCTTAGAAATGAGGTAACAACTCTTAAACCAAATTCCATGTCTATACTGCAACTTAAACCTCA
*
1180733 TAATTCTCAGCAATCCTTTGAACTC
66 TAATTCTAAGCAATCCTTTGAACTC
* * * *
1180758 AGTCTTGGAAATGAGGTAACATA-TCTTAAACCAAATTCCATGTTTATAAC-GCAGCTTGAACCT
1 AGTCTTAGAAATGAGGTAACA-ACTCTTAAACCAAATTCCATGTCTAT-ACTGCAACTTAAACCT
*
1180821 TATAATTCTAAGCA
64 CATAATTCTAAGCA
1180835 TGACCTACCT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
90 61 0.95
91 3 0.05
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (90 bp):
AGTCTTAGAAATGAGGTAACAACTCTTAAACCAAATTCCATGTCTATACTGCAACTTAAACCTCA
TAATTCTAAGCAATCCTTTGAACTC
Found at i:1185162 original size:24 final size:24
Alignment explanation
Indices: 1185126--1185174 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1185116 TTTGTTTTGA
*
1185126 TTTTCTTAAGTGCTAGTTCTTCTG
1 TTTTCTTAAGTGCTAGTTATTCTG
*
1185150 TTTTCTTAGGTGCTAGTTATTCTG
1 TTTTCTTAAGTGCTAGTTATTCTG
1185174 T
1 T
1185175 ATCGGACAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.55
Consensus pattern (24 bp):
TTTTCTTAAGTGCTAGTTATTCTG
Found at i:1188441 original size:32 final size:32
Alignment explanation
Indices: 1188405--1188468 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1188395 GCTTAAAGAG
1188405 TATGAGACCAAGCACAGAAACTTCTAACAGAT
1 TATGAGACCAAGCACAGAAACTTCTAACAGAT
*
1188437 TATGAGACCAAGCACAGAAACTTCTATCAGAT
1 TATGAGACCAAGCACAGAAACTTCTAACAGAT
1188469 CTTCTATAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (32 bp):
TATGAGACCAAGCACAGAAACTTCTAACAGAT
Found at i:1191241 original size:3 final size:3
Alignment explanation
Indices: 1191233--1191263 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1191223 CTTGATAAGG
1191233 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1191264 TAACAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1194622 original size:18 final size:18
Alignment explanation
Indices: 1194596--1194630 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1194586 TTTCTTTTAT
1194596 AAAAATAAAAAT-TATAC
1 AAAAATAAAAATATATAC
1194613 AAAAAGTAAAAATATATA
1 AAAAA-TAAAAATATATA
1194631 TATACACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAAATAAAAATATATAC
Found at i:1194903 original size:20 final size:20
Alignment explanation
Indices: 1194865--1194901 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1194855 TATTTAAAAA
*
1194865 ATTTTAAAAATTATATTTAT
1 ATTTTAAAAATTAAATTTAT
1194885 ATTTT-AAAATTAAATTT
1 ATTTTAAAAATTAAATTT
1194902 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTAAAAATTAAATTTAT
Found at i:1195723 original size:19 final size:22
Alignment explanation
Indices: 1195697--1195749 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 22
1195687 TTTAAATTAC
1195697 TTATTTTTATTTTA-ATTTTAA
1 TTATTTTTATTTTATATTTTAA
*
1195718 -TA-TTTT-TTTAATATTTTAA
1 TTATTTTTATTTTATATTTTAA
1195737 TTATTTTTATTTT
1 TTATTTTTATTTT
1195750 TTAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 4 0.15
19 11 0.42
20 4 0.15
21 4 0.15
22 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTTTTATTTTATATTTTAA
Found at i:1195724 original size:44 final size:44
Alignment explanation
Indices: 1195675--1195765 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
1195665 CTTATAATAG
*
1195675 ATTTTTATATTATTTAAATTACTTATTT-TTATTTTAA-T-TTTAAT
1 ATTTTTATAATATTTAAATTA-TT-TTTATT-TTTTAATTATTTAAT
* *
1195719 ATTTTTTTAATATTTTAATTATTTTTATTTTTTAATTATTTAAT
1 ATTTTTATAATATTTAAATTATTTTTATTTTTTAATTATTTAAT
1195763 ATT
1 ATT
1195766 AAAATATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
42 9 0.22
43 5 0.12
44 27 0.66
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (44 bp):
ATTTTTATAATATTTAAATTATTTTTATTTTTTAATTATTTAAT
Found at i:1195751 original size:17 final size:18
Alignment explanation
Indices: 1195711--1195759 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1195701 TTTTATTTTA
*
1195711 ATTTTAATATTTTTTTAAT
1 ATTTTAAT-TATTTTTAAT
1195730 ATTTTAATTATTTTT-AT
1 ATTTTAATTATTTTTAAT
*
1195747 TTTTTAATTATTT
1 ATTTTAATTATTT
1195760 AATATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.50
18 6 0.21
19 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTAATTATTTTTAAT
Found at i:1196114 original size:7 final size:7
Alignment explanation
Indices: 1196092--1196124 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1196082 ATTATATTAA
1196092 TATTATT
1 TATTATT
*
1196099 TTTTA-T
1 TATTATT
1196105 TATTATT
1 TATTATT
1196112 TATTATT
1 TATTATT
1196119 TATTAT
1 TATTAT
1196125 ATTAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTATT
Found at i:1202116 original size:21 final size:22
Alignment explanation
Indices: 1202061--1202158 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 22
1202051 CCATTTAAAC
*
1202061 ATAATATAAAATATGATTAAAAA
1 ATAATATTAAATAT-ATTAAAAA
1202084 ATAATATT-AATATATT-AAAA
1 ATAATATTAAATATATTAAAAA
* * *
1202104 TTTATATTAAATATAATT--ATA
1 ATAATATTAAATAT-ATTAAAAA
1202125 ATAA-ATTAAA-ATA-TAAAAA
1 ATAATATTAAATATATTAAAAA
*
1202144 TAAAATA-TAAATATA
1 -ATAATATTAAATATA
1202159 CGAATATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 4 0.07
20 23 0.38
21 16 0.27
22 8 0.13
23 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (22 bp):
ATAATATTAAATATATTAAAAA
Found at i:1202149 original size:13 final size:13
Alignment explanation
Indices: 1202121--1202169 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1202111 TAAATATAAT
1202121 TATAATAAATTAAAA
1 TATAA-AAA-TAAAA
1202136 TATAAAAATAAAA
1 TATAAAAATAAAA
* *
1202149 TATAAATATACGAA
1 TATAAAAATA-AAA
1202163 TATAAAA
1 TATAAAA
1202170 TTTAATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 14 0.47
14 11 0.37
15 5 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (13 bp):
TATAAAAATAAAA
Found at i:1203223 original size:24 final size:23
Alignment explanation
Indices: 1203196--1203256 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
1203186 CCAATCCACG
1203196 ATATCTAATAAATATTTAAGCATA
1 ATATCTAATAAATATTT-AGCATA
*
1203220 ATATCTAATAAACATTTAGCATA
1 ATATCTAATAAATATTTAGCATA
*
1203243 ATATTTAATAAATA
1 ATATCTAATAAATA
1203257 AATCTTTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (23 bp):
ATATCTAATAAATATTTAGCATA
Found at i:1204538 original size:8 final size:8
Alignment explanation
Indices: 1204527--1204571 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
1204517 TTATATTTAC
*
1204527 ATATAAAT
1 ATATATAT
*
1204535 ATATATAA
1 ATATATAT
1204543 ATATATAT
1 ATATATAT
1204551 ATATATAT
1 ATATATAT
*
1204559 ATATATAC
1 ATATATAT
1204567 ATATA
1 ATATA
1204572 CAATAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATATAT
Found at i:1204540 original size:10 final size:10
Alignment explanation
Indices: 1204527--1204576 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
1204517 TTATATTTAC
1204527 ATATAAATAT
1 ATATAAATAT
1204537 ATATAAATAT
1 ATATAAATAT
*
1204547 ATATATATAT
1 ATATAAATAT
* *
1204557 ATATATATAC
1 ATATAAATAT
1204567 ATATACAATA
1 ATATA-AATA
1204577 AAAGTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
10 33 0.92
11 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATAAATAT
Found at i:1204987 original size:20 final size:20
Alignment explanation
Indices: 1204962--1205010 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1204952 AAATAGAGGC
1204962 TCCCTCTTCCCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
1204982 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
1205002 TCCCTCTTC
1 TCCCTCTTC
1205011 AATTCTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Found at i:1206293 original size:38 final size:38
Alignment explanation
Indices: 1206250--1206377 Score: 179
Period size: 38 Copynumber: 3.3 Consensus size: 38
1206240 ATTTTTTTTC
1206250 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
1 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
1206288 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
1 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
* *
1206326 TTCATGCATGCATAATTTTCATTTCATGCTTTTCACGTAACAT
1 AT--TGCATGC---ATTTTCATTTCATGTTTTTCACGTAACAT
1206369 -TT-CATGCAT
1 ATTGCATGCAT
1206378 GCATAATTTT
Statistics
Matches: 83, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
36 2 0.02
38 39 0.47
39 5 0.06
40 8 0.10
42 1 0.01
43 28 0.34
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (38 bp):
ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
Found at i:1206344 original size:43 final size:43
Alignment explanation
Indices: 1206259--1206396 Score: 223
Period size: 43 Copynumber: 3.3 Consensus size: 43
1206249 CATTGCATGC
*
1206259 ATTTTCATTTCATGTTTTTCACGTAACATAT--TGCATGC---
1 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1206297 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
*
1206340 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1206383 ATTTTCATTTCATG
1 ATTTTCATTTCATG
1206397 CATTTCAAAA
Statistics
Matches: 93, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
38 30 0.32
40 7 0.08
43 56 0.60
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (43 bp):
ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
Found at i:1206351 original size:22 final size:22
Alignment explanation
Indices: 1206323--1206399 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
1206313 TTTCACGTAA
1206323 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* *
1206345 CATTTCATGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
1206366 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
1206388 CATTTCATGCAT
1 CATTTCATGCAT
1206400 TTCAAAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 10 0.23
22 22 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:1206371 original size:21 final size:21
Alignment explanation
Indices: 1206302--1206375 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
1206292 CATGCATTTT
*
1206302 CATTTCATGTTTTTCACGTAA
1 CATTTCATGCTTTTCACGTAA
* *
1206323 CATTTCATGC-ATGCA--TAA
1 CATTTCATGCTTTTCACGTAA
1206341 TTTTCATTTCATGCTTTTCACGTAA
1 ----CATTTCATGCTTTTCACGTAA
1206366 CATTTCATGC
1 CATTTCATGC
1206376 ATGCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 19 0.46
22 10 0.24
23 3 0.07
25 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (21 bp):
CATTTCATGCTTTTCACGTAA
Found at i:1206424 original size:5 final size:5
Alignment explanation
Indices: 1206414--1206503 Score: 83
Period size: 5 Copynumber: 18.0 Consensus size: 5
1206404 AAAACATTTT
* * * *
1206414 ATTGC ATTGC ACTT-C ATTTC ATTTC ATTGC ATTTC ATTGC ATTGC ATTTC
1 ATTGC ATTGC A-TTGC ATTGC ATTGC ATTGC ATTGC ATTGC ATTGC ATTGC
* * * * *
1206464 ATTTC ATTTC ATTTC ATTGC ATTGC ATTTC ATTAC ATTGC
1 ATTGC ATTGC ATTGC ATTGC ATTGC ATTGC ATTGC ATTGC
1206504 TTTCATGCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
4 2 0.03
5 71 0.95
6 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (5 bp):
ATTGC
Found at i:1206431 original size:10 final size:10
Alignment explanation
Indices: 1206418--1206513 Score: 106
Period size: 10 Copynumber: 9.8 Consensus size: 10
1206408 CATTTTATTG
*
1206418 CATTGCACTT
1 CATTGCATTT
*
1206428 CATTTCATTT
1 CATTGCATTT
1206438 CATTGCATTT
1 CATTGCATTT
*
1206448 CATTGCATTG
1 CATTGCATTT
*
1206458 CATTTCATTT
1 CATTGCATTT
*
1206468 CATTTCATTT
1 CATTGCATTT
*
1206478 CATTGCATTG
1 CATTGCATTT
* *
1206488 CATTTCATTA
1 CATTGCATTT
1206498 CATTGC-TTT
1 CATTGCATTT
1206507 CA-TGCAT
1 CATTGCAT
1206514 GAAATGGCCG
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
8 3 0.04
9 5 0.07
10 65 0.89
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (10 bp):
CATTGCATTT
Found at i:1206446 original size:15 final size:15
Alignment explanation
Indices: 1206418--1206513 Score: 126
Period size: 15 Copynumber: 6.5 Consensus size: 15
1206408 CATTTTATTG
1206418 CATTGCACTT-CATTT
1 CATTGCA-TTGCATTT
*
1206433 CATTTCATTGCATTT
1 CATTGCATTGCATTT
1206448 CATTGCATTGCATTT
1 CATTGCATTGCATTT
* *
1206463 CATTTCATTTCATTT
1 CATTGCATTGCATTT
1206478 CATTGCATTGCATTT
1 CATTGCATTGCATTT
*
1206493 CATTACATTGC-TTT
1 CATTGCATTGCATTT
1206507 CA-TGCAT
1 CATTGCAT
1206514 GAAATGGCCG
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.06
14 7 0.10
15 61 0.85
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (15 bp):
CATTGCATTGCATTT
Found at i:1219746 original size:42 final size:41
Alignment explanation
Indices: 1219695--1220414 Score: 611
Period size: 42 Copynumber: 16.8 Consensus size: 41
1219685 TTTTGTTTTC
1219695 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
*
1219736 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
1 CCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* *
1219778 CCCTTAGTCTACCTGTTGGCTTTGACCCTGGAGACTTTGGAGACTTTCCTAT
1 -CCTTAGTCTGCCTGTCGGCTTTGA-CC------C--TGGAGACTTTCCT-T
* * *
1219830 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGAC-TGCC-T
1 -CCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* *
1219871 CATTTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
1 C-CTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* *
1219915 CCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGATTTTCCTT
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * * ***
1219957 CCCTTAGTCTGCTTGTCGGCTTTGTCCCTGAAGACTTTTCAAC
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * *
1220000 CCTCAATCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTT
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * * * *
1220042 CCCTAAGTCTGCCTATCGGCTTCGTCCCTAGAGACTTTCTTT
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * * *
1220084 CCCTCAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTTCTTT
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * *
1220127 CCCTAAGTCTGCCTGTCGGCTTTGGCCCTAGAGACTTTTCTT
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1220169 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* ** * *
1220211 CCCTTCAGTCTGCCTGTCAGCTTTGATTCTAGAGAC-TGCC-T
1 -CCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * *
1220252 CATTTAAAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTTCTT
1 C-CTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
* * *
1220296 CCCTTAGTCTGCCTGTCGGCCTTGACCCTGGAGACTTTTCATC
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * *
1220339 CCTTAGTCTGCCTGTCGGTTTTAACCTTGGAGACTTTTCTTT
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTT
* * * * *
1220381 CCCTAAGTCTACCCGTTGGCTTTGACCCGGGAGA
1 -CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA
1220415 GTATTTTCTT
Statistics
Matches: 561, Mismatches: 89, Indels: 56
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.00
41 10 0.02
42 358 0.64
43 138 0.25
44 13 0.02
45 2 0.00
46 1 0.00
49 1 0.00
51 12 0.02
52 7 0.01
53 17 0.03
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.36
Consensus pattern (41 bp):
CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
Found at i:1219846 original size:53 final size:51
Alignment explanation
Indices: 1219764--1219866 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 51
1219754 GCTTTGACCC
* **
1219764 TGGAGACTTTTCTTCCCTTAGTCTACCTGTTGGCTTTGACCCTGGAGACTT
1 TGGAGACTTTCCTTCCCTTAGTCTACCTGTCAGCTTTGACCCTGGAGACTT
* *
1219815 TGGAGACTTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACT
1 TGGAGACTTTCCT-TCCCTT-AGTCTACCTGTCAGCTTTGACCCTGGAGACT
1219867 GCCTCATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 12 0.27
52 6 0.13
53 27 0.60
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (51 bp):
TGGAGACTTTCCTTCCCTTAGTCTACCTGTCAGCTTTGACCCTGGAGACTT
Found at i:1220070 original size:85 final size:85
Alignment explanation
Indices: 1219817--1220404 Score: 622
Period size: 85 Copynumber: 6.9 Consensus size: 85
1219807 GGAGACTTTG
* * * ** *
1219817 GAGACTTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTT---AAA
1 GAGACTTTTCT-TCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTC-TTTCCCTAA
* *
1219879 GTCTGCCTGTCGGCTTTGACCCTG
62 GTCTGCCTGTCGGCTTTGTCCCTA
* * *
1219903 GAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGA-TTTTCCTTCCCTTAGTCT
1 GAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGTCT
*
1219967 GCTTGTCGGCTTTGTCCCT-
66 GCCTGTCGGCTTTGTCCCTA
** * * *
1219986 GAAGACTTTTCAACCCTCAATCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGTC
1 G-AGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGTC
* *
1220051 TGCCTATCGGCTTCGTCCCTA
65 TGCCTGTCGGCTTTGTCCCTA
* * *
1220072 GAGAC-TTTCTTTCCCTCAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTTCTTTCCCTAAGTC
1 GAGACTTTTC-TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGTC
*
1220136 TGCCTGTCGGCTTTGGCCCTA
65 TGCCTGTCGGCTTTGTCCCTA
* *
1220157 GAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTTCCCTTCAGTC
1 GAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCC-TAAGTC
* *
1220221 TGCCTGTCAGCTTTGAT-TCTA
65 TGCCTGTCGGCTTTG-TCCCTA
* * ** * *
1220242 GAGAC--TGCCTCATTTAAAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTTC-TTCCCTTAGT
1 GAGACTTTTCTTCCCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGT
* * *
1220304 CTGCCTGTCGGCCTTGACCCTG
64 CTGCCTGTCGGCTTTGTCCCTA
* * * *
1220326 GAGACTTTTCATCCCTTAGTCTGCCTGTCGGTTTTAACCTTGGAGACTTTTCTTTCCCTAAGTCT
1 GAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGTCT
* * *
1220391 ACCCGTTGGCTTTG
66 GCCTGTCGGCTTTG
1220405 ACCCGGGAGA
Statistics
Matches: 424, Mismatches: 61, Indels: 35
0.82 0.12 0.07
Matches are distributed among these distances:
81 2 0.00
82 2 0.00
83 8 0.02
84 156 0.37
85 231 0.54
86 25 0.06
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (85 bp):
GAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGTCT
GCCTGTCGGCTTTGTCCCTA
Found at i:1220101 original size:127 final size:127
Alignment explanation
Indices: 1219817--1220414 Score: 643
Period size: 127 Copynumber: 4.7 Consensus size: 127
1219807 GGAGACTTTG
* * * ** * **
1219817 GAGACTTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGAC-TGCCTCA-TTTAAAG
1 GAGACTTTCCT-TCCC-TCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTTACCCT-AAG
*
1219880 TCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTA
63 TCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * * *
1219945 GAGATTTTCCTTCCCTTAGTCTGCTTGTCGGCTTTGTCCCT-GAAGACTTTTC-AACCCTCAA-T
1 GAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTTTCTTACCCT-AAGT
* * * *
1220007 CTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTTCCCTAAGTCTGCCTATCGGCTTCGTCCCTA
64 CTACCTGTCGGCTTTGACCCTGGAGACTTTTC-TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTA
* * *
1220072 GAGACTTTCTTTCCCTCAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTTCTTTCCCTAAGTCT
1 GAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTTACCCTAAGTCT
* * * *
1220137 GCCTGTCGGCTTTGGCCCTAGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTG
66 ACCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTA
* ** ** * **
1220199 GAGACTTTCCTTCCCTTCAGTCTGCCTGTCAGCTTTGATTCTAGAGAC-TGCCTCA-TTTAAAGT
1 GAGACTTTCCTTCCC-TCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTTACCCT-AAGT
* * * *
1220262 CTGCCTGTCAGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCCTTGACCCTG
64 CTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * * * * * *
1220326 GAGACTTTTCATCCCTTAGTCTGCCTGTCGGTTTTAACCTTGGAGACTTTTCTTTCCCTAAGTCT
1 GAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTTACCCTAAGTCT
* * *
1220391 ACCCGTTGGCTTTGACCCGGGAGA
66 ACCTGTCGGCTTTGACCCTGGAGA
1220415 GTATTTTCTT
Statistics
Matches: 390, Mismatches: 69, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
125 1 0.00
126 83 0.21
127 232 0.59
128 74 0.19
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.36
Consensus pattern (127 bp):
GAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTTACCCTAAGTCT
ACCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTA
Found at i:1220888 original size:38 final size:38
Alignment explanation
Indices: 1220845--1220972 Score: 179
Period size: 38 Copynumber: 3.3 Consensus size: 38
1220835 ATTTTTTTTC
1220845 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
1 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
1220883 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
1 ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
* *
1220921 TTCATGCATGCATAATTTTCATTTCATGCTTTTCACGTAACAT
1 AT--TGCATGC---ATTTTCATTTCATGTTTTTCACGTAACAT
1220964 -TT-CATGCAT
1 ATTGCATGCAT
1220973 GCATAATTTT
Statistics
Matches: 83, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
36 2 0.02
38 39 0.47
39 5 0.06
40 8 0.10
42 1 0.01
43 28 0.34
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (38 bp):
ATTGCATGCATTTTCATTTCATGTTTTTCACGTAACAT
Found at i:1220939 original size:43 final size:43
Alignment explanation
Indices: 1220854--1220991 Score: 223
Period size: 43 Copynumber: 3.3 Consensus size: 43
1220844 CATTGCATGC
*
1220854 ATTTTCATTTCATGTTTTTCACGTAACATAT--TGCATGC---
1 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1220892 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
*
1220935 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1220978 ATTTTCATTTCATG
1 ATTTTCATTTCATG
1220992 CATTTCAAAA
Statistics
Matches: 93, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
38 30 0.32
40 7 0.08
43 56 0.60
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (43 bp):
ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
Found at i:1220946 original size:22 final size:22
Alignment explanation
Indices: 1220918--1220994 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
1220908 TTTCACGTAA
1220918 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* *
1220940 CATTTCATGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
1220961 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
1220983 CATTTCATGCAT
1 CATTTCATGCAT
1220995 TTCAAAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 10 0.23
22 22 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:1220966 original size:21 final size:21
Alignment explanation
Indices: 1220897--1220970 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
1220887 CATGCATTTT
*
1220897 CATTTCATGTTTTTCACGTAA
1 CATTTCATGCTTTTCACGTAA
* *
1220918 CATTTCATGC-ATGCA--TAA
1 CATTTCATGCTTTTCACGTAA
1220936 TTTTCATTTCATGCTTTTCACGTAA
1 ----CATTTCATGCTTTTCACGTAA
1220961 CATTTCATGC
1 CATTTCATGC
1220971 ATGCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 19 0.46
22 10 0.24
23 3 0.07
25 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (21 bp):
CATTTCATGCTTTTCACGTAA
Found at i:1221029 original size:5 final size:5
Alignment explanation
Indices: 1221021--1221101 Score: 108
Period size: 5 Copynumber: 16.2 Consensus size: 5
1221011 TGCATTGCAC
* * *
1221021 TTCAT TTCAT TTCAT TGCAT TTCAT TGCAT TGCAT TTCAT TTCAT TTCAT
1 TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT
* * *
1221071 TTCAT TTCAT TGCAT TGCAT TTCAT TACAT T
1 TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT T
1221102 GCTTTCATGC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 69 1.00
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (5 bp):
TTCAT
Found at i:1221041 original size:15 final size:15
Alignment explanation
Indices: 1221023--1221113 Score: 123
Period size: 15 Copynumber: 6.2 Consensus size: 15
1221013 CATTGCACTT
1221023 CATTTCATTTCATTG
1 CATTTCATTTCATTG
*
1221038 CATTTCATTGCATTG
1 CATTTCATTTCATTG
*
1221053 CATTTCATTTCATTT
1 CATTTCATTTCATTG
1221068 CATTTCATTTCATTG
1 CATTTCATTTCATTG
* *
1221083 CATTGCATTTCATTA
1 CATTTCATTTCATTG
*
1221098 CATTGC-TTTCA-TG
1 CATTTCATTTCATTG
1221111 CAT
1 CAT
1221114 GAAATGGCCG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
13 4 0.06
14 5 0.07
15 60 0.87
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.51
Consensus pattern (15 bp):
CATTTCATTTCATTG
Found at i:1221502 original size:36 final size:36
Alignment explanation
Indices: 1221455--1221548 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
1221445 CAACTTCTAG
1221455 CCACGAACACTGGCAGCAGCTCCATCAGCTTCCAAC
1 CCACGAACACTGGCAGCAGCTCCATCAGCTTCCAAC
1221491 CCACGAACACTGGCAGCAGCTCCATCAGCTTCCAAC
1 CCACGAACACTGGCAGCAGCTCCATCAGCTTCCAAC
*
1221527 CCACGAACACCGGCAGCAGCTC
1 CCACGAACACTGGCAGCAGCTC
1221549 TGCAACCTTC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.28, C:0.43, G:0.18, T:0.12
Consensus pattern (36 bp):
CCACGAACACTGGCAGCAGCTCCATCAGCTTCCAAC
Found at i:1224626 original size:21 final size:22
Alignment explanation
Indices: 1224597--1224642 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1224587 TGTTCAGACA
** *
1224597 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1224619 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1224640 AGT
1 AGT
1224643 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1226693 original size:20 final size:19
Alignment explanation
Indices: 1226664--1226701 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1226654 CTATAAATAG
*
1226664 AAGCTCCCTCTTCCCTCTT
1 AAGCTCCCTCATCCCTCTT
1226683 AAGCATCCCTCATCCCTCT
1 AAGC-TCCCTCATCCCTCT
1226702 CTTGTATCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.16, C:0.47, G:0.05, T:0.32
Consensus pattern (19 bp):
AAGCTCCCTCATCCCTCTT
Found at i:1228400 original size:5 final size:5
Alignment explanation
Indices: 1228390--1228423 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1228380 AATAAAAGTT
1228390 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1228424 AAGGTTTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:1230216 original size:18 final size:18
Alignment explanation
Indices: 1230195--1230229 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1230185 ATTAAGGATG
1230195 CTTATTTTATTT-ATTTTC
1 CTTA-TTTATTTAATTTTC
1230213 CTTATTTATTTAATTTT
1 CTTATTTATTTAATTTT
1230230 TTTCATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTATTTATTTAATTTTC
Done.