Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 45 of 131
Found at i:9436383 original size:11 final size:11
Alignment explanation
Indices: 9436364--9436405 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
9436354 GAAGAATAAT
9436364 GAAAAAAAATA
1 GAAAAAAAATA
*
9436375 GAAAGAAAAAAA
1 GAAA-AAAAATA
9436387 GAAAAAAAATA
1 GAAAAAAAATA
9436398 GAAAAAAA
1 GAAAAAAA
9436406 GAAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (11 bp):
GAAAAAAAATA
Found at i:9436394 original size:23 final size:24
Alignment explanation
Indices: 9436349--9436405 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
9436339 AATCGAATAA
*
9436349 AGAAAGAAGAATAATGAAAAAAAAT
1 AGAAAGAA-AATAAAGAAAAAAAAT
9436374 AGAAAGAAAA-AAAGAAAAAAAAT
1 AGAAAGAAAATAAAGAAAAAAAAT
9436397 AGAAA-AAAA
1 AGAAAGAAAA
9436406 GAAAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 4 0.13
23 17 0.55
24 2 0.06
25 8 0.26
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (24 bp):
AGAAAGAAAATAAAGAAAAAAAAT
Found at i:9436402 original size:17 final size:17
Alignment explanation
Indices: 9436378--9436414 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
9436368 AAAAATAGAA
9436378 AGAAAAAAAGAAAAAAAAT
1 AGAAAAAAAG--AAAAAAT
9436397 AGAAAAAAAGAAAAAAT
1 AGAAAAAAAGAAAAAAT
9436414 A
1 A
9436415 TAATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AGAAAAAAAGAAAAAAT
Found at i:9436427 original size:3 final size:3
Alignment explanation
Indices: 9436414--9436477 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
9436404 AAGAAAAAAT
*
9436414 ATA AT- ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9436461 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
9436478 TATTATTATT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9436482 original size:3 final size:3
Alignment explanation
Indices: 9436476--9436513 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
9436466 AATAATAATA
9436476 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9436514 AAATACAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9436766 original size:44 final size:43
Alignment explanation
Indices: 9436670--9436991 Score: 342
Period size: 44 Copynumber: 7.2 Consensus size: 43
9436660 TTAATAACAT
* * * * *
9436670 TTTTGAAAATTTAAAAAGCTCATCTGAGTAAAGACTCAATAAC
1 TTTTAAAAATTTAAAAAGCTCCTCTAAGTAGAGGCTCAATAAC
* * * *
9436713 TTTTAAAAATTTAAAGAGGCTCCTCTAAGCAGAGGCTTAATTAC
1 TTTTAAAAATTTAAA-AAGCTCCTCTAAGTAGAGGCTCAATAAC
* *
9436757 TTTTGAAAATTTAAAAAGGCTCCTCTAAGTAGAGGCTCAATGAC
1 TTTTAAAAATTTAAAAA-GCTCCTCTAAGTAGAGGCTCAATAAC
* *
9436801 TTTTAAAAATTTAAAGAAGCTCCTCTAAGTAGAGGTTCAACAAC
1 TTTTAAAAATTTAAA-AAGCTCCTCTAAGTAGAGGCTCAATAAC
* *
9436845 TTTTGAAAATTTTAAAAAGCTCCTCTAAGTAGAGGCTCAACAAC
1 TTTT-AAAAATTTAAAAAGCTCCTCTAAGTAGAGGCTCAATAAC
* *
9436889 TTTTAAAAATTTAAAAACGCTCTTCTAAATAGAGGCTCAATAA-
1 TTTTAAAAATTTAAAAA-GCTCCTCTAAGTAGAGGCTCAATAAC
* *
9436932 TTTTAAAATTCATCATCTCGAAAAAGCTCATCTAAGTAGAGGCTCAACAA-
1 TTTTAAAA---AT--T-T--AAAAAGCTCCTCTAAGTAGAGGCTCAATAAC
9436982 TTTTAAAAAT
1 TTTTAAAAAT
9436992 CCATCATCTT
Statistics
Matches: 239, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
43 35 0.15
44 151 0.63
45 12 0.05
46 2 0.01
47 2 0.01
48 1 0.00
49 1 0.00
50 30 0.13
51 5 0.02
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (43 bp):
TTTTAAAAATTTAAAAAGCTCCTCTAAGTAGAGGCTCAATAAC
Found at i:9436977 original size:50 final size:50
Alignment explanation
Indices: 9436901--9437109 Score: 231
Period size: 50 Copynumber: 4.1 Consensus size: 50
9436891 TTAAAAATTT
** * * *
9436901 AAAAACGCTCTTCTAAATAGAGGCTCAATAATTTTAAAATTCATCATCTCG
1 AAAAA-GCTCTTCTAAGCAGAGGCTCAACAACTTTAAAATTCATCATCTTG
* * * *
9436952 AAAAAGCTCATCTAAGTAGAGGCTCAACAATTTTAAAAATCCATCATCTTG
1 AAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTT-AAAATTCATCATCTTG
* * *
9437003 GAAAAGCT-TGTCTAAGCAGAGACTCAACAACTTTAAAATTCATCATATTG
1 AAAAAGCTCT-TCTAAGCAGAGGCTCAACAACTTTAAAATTCATCATCTTG
*
9437053 GAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTATTCTTG
1 AAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTT-AAAAT-TCATC-A-TCTTG
9437107 AAA
1 AAA
9437110 CCGAGTTTTC
Statistics
Matches: 136, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
50 71 0.52
51 53 0.39
52 5 0.04
53 1 0.01
54 6 0.04
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.29
Consensus pattern (50 bp):
AAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTTAAAATTCATCATCTTG
Found at i:9437954 original size:11 final size:10
Alignment explanation
Indices: 9437918--9437956 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
9437908 CTTTTTCACT
9437918 TTTTGTTTTTGC
1 TTTT-TTTTT-C
9437930 TTTTTTTTTC
1 TTTTTTTTTC
*
9437940 TTTTTTTTTA
1 TTTTTTTTTC
9437950 TTTTTTT
1 TTTTTTT
9437957 AAGCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.65
11 5 0.19
12 4 0.15
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:9443460 original size:25 final size:26
Alignment explanation
Indices: 9443418--9443466 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
9443408 CATAGATTAT
9443418 TCAAAACATTCATCAAA-TCATAATG
1 TCAAAACATTCATCAAATTCATAATG
*
9443443 TCAAAACATTTCGT-AAATTCATAA
1 TCAAAACA-TTCATCAAATTCATAA
9443467 ATCAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (26 bp):
TCAAAACATTCATCAAATTCATAATG
Found at i:9443572 original size:10 final size:10
Alignment explanation
Indices: 9443559--9443585 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9443549 CAGTCATTAA
9443559 AAATCATTGT
1 AAATCATTGT
9443569 AAATCATTGT
1 AAATCATTGT
9443579 AAATCAT
1 AAATCAT
9443586 CTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (10 bp):
AAATCATTGT
Found at i:9443668 original size:20 final size:20
Alignment explanation
Indices: 9443643--9443717 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
9443633 TCTTTATATA
9443643 AAAATCATGGATCAATCTTT
1 AAAATCATGGATCAATCTTT
*
9443663 AAAATCATCGTAAATC-ATCTTTATAT
1 AAAATCAT-G--GATCAATC--T-T-T
9443689 ACAAATCATGGATCAATCTTT
1 A-AAATCATGGATCAATCTTT
9443710 AAAATCAT
1 AAAATCAT
9443718 CATAAATCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
20 15 0.34
21 3 0.07
22 4 0.09
23 4 0.09
24 4 0.09
25 4 0.09
26 3 0.07
27 7 0.16
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAATCATGGATCAATCTTT
Found at i:9443685 original size:47 final size:47
Alignment explanation
Indices: 9443569--9443727 Score: 264
Period size: 47 Copynumber: 3.4 Consensus size: 47
9443559 AAATCATTGT
* *
9443569 AAATCATTGTAAATCATCTTTATATATAAATCATGGATCAATCTTTAA
1 AAATCATCGTAAATCATCTTTATATAAAAATCATGGATCAATCTTT-A
*
9443617 AAATCATTGTAAATCATCTTTATATAAAAATCATGGATCAATCTTTA
1 AAATCATCGTAAATCATCTTTATATAAAAATCATGGATCAATCTTTA
*
9443664 AAATCATCGTAAATCATCTTTATATACAAATCATGGATCAATCTTTA
1 AAATCATCGTAAATCATCTTTATATAAAAATCATGGATCAATCTTTA
*
9443711 AAATCATCATAAATCAT
1 AAATCATCGTAAATCAT
9443728 TATTATCATT
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
47 62 0.58
48 45 0.42
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (47 bp):
AAATCATCGTAAATCATCTTTATATAAAAATCATGGATCAATCTTTA
Found at i:9451314 original size:17 final size:16
Alignment explanation
Indices: 9451277--9451315 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
9451267 TGTAATGTTG
*
9451277 ATTTTTTTTTATTTGA
1 ATTTTTTTTTATTTAA
*
9451293 TTTTTTTTCTTATTTAA
1 ATTTTTTT-TTATTTAA
9451310 ATTTTT
1 ATTTTT
9451316 GACAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (16 bp):
ATTTTTTTTTATTTAA
Found at i:9452800 original size:14 final size:14
Alignment explanation
Indices: 9452771--9452799 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9452761 TGAACCGAAT
9452771 AAGGAAAGAAGAAA
1 AAGGAAAGAAGAAA
9452785 AAGGAAA-AAGAAA
1 AAGGAAAGAAGAAA
9452798 AA
1 AA
9452800 AATATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGGAAAGAAGAAA
Found at i:9453111 original size:79 final size:78
Alignment explanation
Indices: 9452846--9453224 Score: 259
Period size: 79 Copynumber: 4.7 Consensus size: 78
9452836 CATTTATAAC
* * * *
9452846 AAAAAATTGAAAATTTAAAACAAATTTTAATCAAATACTGCGTTACTTTTTATTATAATGTAGTA
1 AAAAAATTTAAAATTTAAAACAAATTTTAATCAAATACTGTGTTACTTTTTATTATAACGTAATA
*
9452911 ATTAAGTTCTTTAGAAT
66 ATTGAGTT-TTT---AT
* * * * * * **
9452928 AAAAAATTTAAAATTCAAAATAAATTTTAATCAAATGCTGTATTAATCTTTATTATAACACAATA
1 AAAAAATTTAAAATTTAAAACAAATTTTAATCAAATACTGTGTTACTTTTTATTATAACGTAATA
*
9452993 ATTGGGAG-TCTTAT
66 ATT--GAGTTTTTAT
* * * * ** * *
9453007 CCAAACAA-TTCACATTTTAAA-AAATTACAATCAAATACTATGTTACTTTTTATTACAACGTAA
1 --AAAAAATTTAAAATTTAAAACAAATTTTAATCAAATACTGTGTTACTTTTTATTATAACGTAA
9453070 TAATTGAGTTTTTAT
64 TAATTGAGTTTTTAT
* * * * * * *
9453085 TAAAAATTTGAAAATTTAAAACAAATTTTAATCAAATA-TTTCATTAATTTTTATTATAATGCAG
1 AAAAAATTT-AAAATTTAAAACAAATTTTAATCAAATACTGT-GTTACTTTTTATTATAACGTAA
9453149 TAATTGGGAGTTTTATAT
64 TAATT--GAGTTTT-TAT
* * ** *
9453167 AAAAGAA-TTGATATTT-AAA-AAATTATATAATCAAATACTGCATTACTTTTTCTTATAA
1 AAAA-AATTTAAAATTTAAAACAAATT-T-TAATCAAATACTGTGTTACTTTTTATTATAA
9453225 GTGATACCAT
Statistics
Matches: 230, Mismatches: 51, Indels: 33
0.73 0.16 0.11
Matches are distributed among these distances:
76 4 0.02
77 5 0.02
78 15 0.07
79 79 0.34
80 13 0.06
81 42 0.18
82 67 0.29
83 3 0.01
84 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (78 bp):
AAAAAATTTAAAATTTAAAACAAATTTTAATCAAATACTGTGTTACTTTTTATTATAACGTAATA
ATTGAGTTTTTAT
Found at i:9453184 original size:158 final size:161
Alignment explanation
Indices: 9452874--9453217 Score: 385
Period size: 158 Copynumber: 2.1 Consensus size: 161
9452864 AACAAATTTT
* * * *
9452874 AATCAAATACTGCGTTACTTTTTATTATAATGTAGTAATTAAGTTCTTTAGAATAAAAAATTTAA
1 AATCAAATACTACGTTACTTTTTATTACAACGTAATAATTAAGTTCTTT--AATAAAAAATTTAA
* *
9452939 AATTCAAAATAAATTTTAATCAAATGCTGTATTAATCTTTATTATAACACAATAATTGGGAGTCT
64 AATTCAAAACAAATTTTAATCAAATGATGTATTAATCTTTATTATAACACAATAATTGGGAGTCT
*
9453004 TATCCAAACAATTCACATTTTAAAAAA-T-TAC
129 TATCAAAACAATTCACATTTTAAAAAATTATAC
* * *
9453035 AATCAAATACTATGTTACTTTTTATTACAACGTAATAATTGAGTT-TTT-ATTAAAAATTTGAAA
1 AATCAAATACTACGTTACTTTTTATTACAACGTAATAATTAAGTTCTTTAATAAAAAATTT-AAA
* * * ** * *
9453098 ATTTAAAACAAATTTTAATCAAAT-ATTTCATTAATTTTTATTATAATGCAGTAATTGGGAGTTT
65 ATTCAAAACAAATTTTAATCAAATGATGT-ATTAATCTTTATTATAACACAATAATTGGGAGTCT
* * * * *
9453162 TATATAAAAGAATTGATA-TTTAAAAAATTATAT
129 TAT-CAAAACAATTCACATTTTAAAAAATTATAC
* *
9453195 AATCAAATACTGCATTACTTTTT
1 AATCAAATACTACGTTACTTTTT
9453218 CTTATAAGTG
Statistics
Matches: 153, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
157 12 0.08
158 67 0.44
159 10 0.07
160 25 0.16
161 39 0.25
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (161 bp):
AATCAAATACTACGTTACTTTTTATTACAACGTAATAATTAAGTTCTTTAATAAAAAATTTAAAA
TTCAAAACAAATTTTAATCAAATGATGTATTAATCTTTATTATAACACAATAATTGGGAGTCTTA
TCAAAACAATTCACATTTTAAAAAATTATAC
Found at i:9459104 original size:14 final size:14
Alignment explanation
Indices: 9459068--9459117 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
9459058 CATATGGCAG
*
9459068 CATATACATACATA
1 CATATACATATATA
9459082 CATACATACATATATA
1 CAT--ATACATATATA
*
9459098 TATATACATATATA
1 CATATACATATATA
9459112 CATATA
1 CATATA
9459118 TATCATCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 19 0.61
16 12 0.39
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (14 bp):
CATATACATATATA
Found at i:9459116 original size:8 final size:8
Alignment explanation
Indices: 9459069--9459119 Score: 70
Period size: 8 Copynumber: 6.6 Consensus size: 8
9459059 ATATGGCAGC
9459069 ATATACAT
1 ATATACAT
*
9459077 ACATACAT
1 ATATACAT
*
9459085 ACATACAT
1 ATATACAT
9459093 ATAT--AT
1 ATATACAT
9459099 ATATACAT
1 ATATACAT
9459107 ATATACAT
1 ATATACAT
9459115 ATATA
1 ATATA
9459120 TCATCTAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 6 0.15
8 33 0.85
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (8 bp):
ATATACAT
Found at i:9459118 original size:22 final size:22
Alignment explanation
Indices: 9459068--9459120 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
9459058 CATATGGCAG
*
9459068 CATATACATACATACATACATA
1 CATATATATACATACATACATA
* *
9459090 CATATATATATATACATATATA
1 CATATATATACATACATACATA
9459112 CATATATAT
1 CATATATAT
9459121 CATCTAGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (22 bp):
CATATATATACATACATACATA
Found at i:9464211 original size:16 final size:15
Alignment explanation
Indices: 9464162--9464212 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
9464152 TGATAAAATA
9464162 TTAAATTTT-TAATT
1 TTAAATTTTATAATT
* *
9464176 TTAATTATTTATGA-T
1 TTAAAT-TTTATAATT
9464191 TTAAATTTTAATAATT
1 TTAAATTTT-ATAATT
9464207 TTAAAT
1 TTAAAT
9464213 ATAAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 8 0.28
15 12 0.41
16 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TTAAATTTTATAATT
Found at i:9464354 original size:42 final size:42
Alignment explanation
Indices: 9464307--9464388 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
9464297 CTCAAATCAA
* * *
9464307 AATTAAATCTAATATTTATTTCAAATTAGGATTAAACATTAG
1 AATTAAATCAAATATTTATTTCAAATCAAGATTAAACATTAG
*
9464349 AATTAAATCAAATATTTATTTCAAATCAAGATTATACATT
1 AATTAAATCAAATATTTATTTCAAATCAAGATTAAACATT
9464389 TTGAGGGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (42 bp):
AATTAAATCAAATATTTATTTCAAATCAAGATTAAACATTAG
Found at i:9465437 original size:20 final size:20
Alignment explanation
Indices: 9465412--9465455 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9465402 CTTAAATTTT
*
9465412 ATTTAGGGTTAACTTATAAA
1 ATTTAGGGTTAAATTATAAA
*
9465432 ATTTAGGGTTAAATTATAAT
1 ATTTAGGGTTAAATTATAAA
9465452 ATTT
1 ATTT
9465456 GATTACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTTAGGGTTAAATTATAAA
Found at i:9465625 original size:93 final size:92
Alignment explanation
Indices: 9465499--9465945 Score: 319
Period size: 99 Copynumber: 4.7 Consensus size: 92
9465489 AAAGCTGTTT
* * * *
9465499 AAAAAATTTATTAAAAAAGAAAATTTTTGAAATTTATTTATTTTAAATTATAAAACTAGATAAAA
1 AAAAAACTTATTAAAAAAGAAAA-TTTTAAAATTTATTTATTTTAAATTATAAAATTTGATAAAA
**
9465564 TATAAAAATATATTATATCTAAAA-ATTA
65 TATAAAAATATATTATAT-TAAAATAAAA
* * *
9465592 AAAAAACTTCTTAAAAATATAAAATTTTAAAATTTATTTATTTTAAACTATAAAATTTGA-AAAA
1 AAAAAACTTATTAAAAA-AGAAAATTTTAAAATTTATTTATTTTAAATTATAAAATTTGATAAAA
9465656 -A-AACAAAT-T-TT-T-TTAAAAGTAAAA
65 TATAA-AAATATATTATATTAAAA-TAAAA
* * * *
9465680 AAAAAACTTATTCAAAAAGAAAATTTTGAAATTTATTTATTTTAAATTGTAATATTTGATAAAAT
1 AAAAAACTTATTAAAAAAGAAAATTTTAAAATTTATTTATTTTAAATTATAAAATTTGAT-AAA-
9465745 ATATTAAAAATATATATTATATTTGAAAATAAAA
64 ATA-T-AAAA-ATATATTATA-TT-AAAATAAAA
* * * * *
9465779 ACAAAAACTTCTTTAAAATAG-AAATTTTAAAAACTTATTTA-TTTACATTATAGAATTTGGA-A
1 A-AAAAACTT-ATTAAAAAAGAAAATTTT-AAAATTTATTTATTTTAAATTATAAAATTT-GATA
** *
9465841 ATGTGTTAAAAATATATATTATGATTCAAAAATAAAA
62 AAAT-AT-AAAA-ATATATTAT-ATT--AAAATAAAA
* * * * * *
9465878 ACAAAAGA-TAATTTAAAATAA-AATATTTTGAAATTT-TTAATTTTAAATTGTAATATTTGATA
1 A-AAAA-ACTTA-TTAAAA-AAGAAAATTTTAAAATTTATTTATTTTAAATTATAAAATTTGATA
9465940 AAATAT
62 AAATAT
9465946 TTTAATTTCT
Statistics
Matches: 280, Mismatches: 43, Indels: 57
0.74 0.11 0.15
Matches are distributed among these distances:
86 5 0.02
87 38 0.14
88 18 0.06
89 5 0.02
90 4 0.01
91 6 0.02
92 4 0.01
93 49 0.17
94 9 0.03
95 1 0.00
96 2 0.01
97 1 0.00
98 25 0.09
99 54 0.19
100 40 0.14
101 19 0.07
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (92 bp):
AAAAAACTTATTAAAAAAGAAAATTTTAAAATTTATTTATTTTAAATTATAAAATTTGATAAAAT
ATAAAAATATATTATATTAAAATAAAA
Found at i:9465696 original size:23 final size:24
Alignment explanation
Indices: 9465652--9465696 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
9465642 TAAAATTTGA
* * *
9465652 AAAAAAACAAATTTTTTTAAAAGT
1 AAAAAAACAAACTTATTCAAAAGT
9465676 AAAAAAA-AAACTTATTCAAAA
1 AAAAAAACAAACTTATTCAAAA
9465697 AGAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAAAAACAAACTTATTCAAAAGT
Found at i:9465717 original size:87 final size:90
Alignment explanation
Indices: 9465499--9465837 Score: 280
Period size: 93 Copynumber: 3.6 Consensus size: 90
9465489 AAAGCTGTTT
* * *
9465499 AAAAAATTTATTAAAAAAGAAAATTTTTGAAATTTATTTATTTTAAATTATAAAACTAGATAAAA
1 AAAAAACTTATTAAAAAAGAAAA-TTTTGAAATTTATTTATTTTAAATTATAAAATTTGA-AAAA
**
9465564 TATAAAAATATATTATATCTAAAAATTA
64 -ATAAAAATATATTATATCTAAAAAAAA
* * * *
9465592 AAAAAACTTCTTAAAAATATAAAATTTTAAAATTTATTTATTTTAAACTATAAAATTTGAAAAAA
1 AAAAAACTTATTAAAAA-AGAAAATTTTGAAATTTATTTATTTTAAATTATAAAATTTGAAAAAA
9465657 -AACAAAT-T-TT-T-T-TAAAAGTAAAA
65 TAA-AAATATATTATATCTAAAA--AAAA
* * *
9465680 AAAAAACTTATTCAAAAAGAAAATTTTGAAATTTATTTATTTTAAATTGTAATATTTGATAAAAT
1 AAAAAACTTATTAAAAAAGAAAATTTTGAAATTTATTTATTTTAAATTATAAAATTTG--AAAA-
*
9465745 ATATTAAAAATATATATTATATTTGAAAATAAAA
63 A-A-T-AAAA-ATATATTATATCT-AAAA-AAAA
* * * * * *
9465779 ACAAAAACTTCTTTAAAATAG-AAATTTTAAAAACTTATTTA-TTTACATTATAGAATTTG
1 A-AAAAACTT-ATTAAAAAAGAAAATTTT-GAAATTTATTTATTTTAAATTATAAAATTTG
9465838 GAAATGTGTT
Statistics
Matches: 200, Mismatches: 25, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
86 5 0.03
87 37 0.19
88 18 0.09
89 6 0.03
90 4 0.02
91 6 0.03
92 4 0.02
93 49 0.25
94 9 0.05
95 1 0.00
96 2 0.01
97 1 0.00
98 1 0.00
99 7 0.04
100 33 0.17
101 17 0.09
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (90 bp):
AAAAAACTTATTAAAAAAGAAAATTTTGAAATTTATTTATTTTAAATTATAAAATTTGAAAAAAT
AAAAATATATTATATCTAAAAAAAA
Found at i:9466347 original size:2 final size:2
Alignment explanation
Indices: 9466340--9466373 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9466330 GTAGGTTTAC
9466340 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
9466374 CAATATCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9471448 original size:20 final size:21
Alignment explanation
Indices: 9471411--9471451 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9471401 AGCTATTAGT
* *
9471411 TTTTTTTTAAATTGTTTTTAA
1 TTTTTTTCAAATTATTTTTAA
9471432 TTTTTTTCAAA-TATTTTTAA
1 TTTTTTTCAAATTATTTTTAA
9471452 AAGTTAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTTTCAAATTATTTTTAA
Found at i:9474737 original size:3 final size:3
Alignment explanation
Indices: 9474729--9474767 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
9474719 ATTAATTACA
9474729 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9474768 TTAGTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9475055 original size:24 final size:25
Alignment explanation
Indices: 9475015--9475063 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
9475005 TGAAAAAAAG
9475015 GGATTTTGGTTAATATTAA-ATAAA
1 GGATTTTGGTTAATATTAATATAAA
*
9475039 GGATTTTGG-TATTTATTAATATAAA
1 GGATTTTGGTTA-ATATTAATATAAA
9475064 TATAGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 2 0.09
24 15 0.68
25 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
GGATTTTGGTTAATATTAATATAAA
Found at i:9475183 original size:26 final size:26
Alignment explanation
Indices: 9475154--9475233 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 26
9475144 AGGCCTGATC
* * *
9475154 AGGCTTATTGACATCCCGGCCCAATT
1 AGGCATATTGACATTCAGGCCCAATT
* *
9475180 AGGCACATTGATATTCAGGCCCAATT
1 AGGCATATTGACATTCAGGCCCAATT
* * **
9475206 AGGCCTGTTGACATTTGGGCCCAATT
1 AGGCATATTGACATTCAGGCCCAATT
9475232 AG
1 AG
9475234 ACCAATTTGT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (26 bp):
AGGCATATTGACATTCAGGCCCAATT
Found at i:9475394 original size:32 final size:32
Alignment explanation
Indices: 9475306--9475402 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 32
9475296 TATAAATTAT
* * *
9475306 TATTATTATTATTGTTATTATTACTTTCCTTTTT
1 TATTATTATTATTATTATT-TT-CTTTTCTTTTA
* * *
9475340 TATCT-TTCTTTTTATGT-GTTTCTTTTCTTTTA
1 TAT-TATTATTATTAT-TATTTTCTTTTCTTTTA
9475372 TATTATTATTATTATTATTTTCTTTTCTTTT
1 TATTATTATTATTATTATTTTCTTTTCTTTT
9475403 TCTCTTCTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
31 2 0.04
32 33 0.66
33 2 0.04
34 11 0.22
35 2 0.04
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.71
Consensus pattern (32 bp):
TATTATTATTATTATTATTTTCTTTTCTTTTA
Found at i:9487836 original size:54 final size:54
Alignment explanation
Indices: 9487661--9487838 Score: 139
Period size: 54 Copynumber: 3.2 Consensus size: 54
9487651 AACATCGTCT
* * * *
9487661 TAGTCATTTGATCTTGACTTAGGTTAGATTATCTTCAGACTCGTGACATCAATC
1 TAGTCATTTAATCTCGACTTAGGTTAGATCATCTTCAGACTTGTGACATCAATC
* * * * *
9487715 TAGTCATTT-ATTTACGACCTCGACTCGGACTT-GGTCACCTTTC-GACTTGCGACATC-ATC
1 TAGTCATTTAATCT-CGA-CT----TAGG--TTAGATCATC-TTCAGACTTGTGACATCAATC
*
9487774 TTAATCATTTAATCTCGACTTAGGTTAGATCATCTTCAGACTTGTGACATCAATC
1 -TAGTCATTTAATCTCGACTTAGGTTAGATCATCTTCAGACTTGTGACATCAATC
*
9487829 CAGTCATTTA
1 TAGTCATTTA
9487839 TTTACAACCT
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
53 8 0.09
54 36 0.38
55 8 0.09
59 8 0.09
60 26 0.28
61 8 0.09
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (54 bp):
TAGTCATTTAATCTCGACTTAGGTTAGATCATCTTCAGACTTGTGACATCAATC
Found at i:9487883 original size:60 final size:60
Alignment explanation
Indices: 9487705--9487884 Score: 153
Period size: 60 Copynumber: 3.1 Consensus size: 60
9487695 TCAGACTCGT
* * *
9487705 GACATCAATCTAGTCATTTATTTACGACCTCGACTCGGA-CTTGGTCACCTTTCGACTTGC
1 GACATCAATCCAGTCATTTATTTACAACCTCGACT-TGATCTTGGTCACCTTTCGACTTGC
* * * * * * * * *
9487765 GACATC-AT-C--TTAATCATTT--AATCTCGACTTAGGT-TAGATCATC-TTCAGACTTGT
1 GACATCAATCCAGTCATTTATTTACAACCTCGACTT-GATCTTGGTCACCTTTC-GACTTGC
*
9487819 GACATCAATCCAGTCATTTATTTACAACCTCGACTTGATCTTGGTCACCTTTCGACTTAC
1 GACATCAATCCAGTCATTTATTTACAACCTCGACTTGATCTTGGTCACCTTTCGACTTGC
9487879 GACATC
1 GACATC
9487885 GTCCCAATCA
Statistics
Matches: 87, Mismatches: 22, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
53 3 0.03
54 27 0.31
55 2 0.02
56 8 0.09
58 7 0.08
59 4 0.05
60 33 0.38
61 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (60 bp):
GACATCAATCCAGTCATTTATTTACAACCTCGACTTGATCTTGGTCACCTTTCGACTTGC
Found at i:9487979 original size:228 final size:230
Alignment explanation
Indices: 9487547--9487982 Score: 558
Period size: 228 Copynumber: 1.9 Consensus size: 230
9487537 ATCGTCCCAG
* *
9487547 TCATTTGATCTCGACTCAAGTTAAATCATCGTCAGACTCGTGACATCAATCCGATCATTTATTTT
1 TCATTTAATCTCGACTCAAGTTAAATCATCGTCAGACTCGTGACATCAATCCGATCATTTATTTA
** * ** *
9487612 TGACCTCGACTCGATCCTGGTCACTTCATTTTGACTCACAACATCGTCTTAGTCATTTGATCTTG
66 CAACCTCGACTCGATCCTGGTCAC-TCATTTCGACTCACAACATCGTCCCAATCATTTGATCTTG
* * * * * *
9487677 ACTTAGGTTAGATTATCTTCAGACTCGTGACATCAATCTAGTCATTTATTTACGACCTCGACTCG
130 ACTCAGGTCAAATCATCTTCAGACTCGCGACATCAATCTAGTCATTTATTTACGACCTCAACTCG
9487742 GACTTGGTCACCTTTCGACTTGCGACATCATCTTAA
195 GACTTGGTCACCTTTCGACTTGCGACATCATCTTAA
* * * * *
9487778 TCATTTAATCTCGACTTAGGTTAGATCATCTTCAGACTTGTGACATCAATCC-AGTCATTTATTT
1 TCATTTAATCTCGACTCAAGTTAAATCATCGTCAGACTCGTGACATCAATCCGA-TCATTTATTT
* * * *
9487842 ACAACCTCGACTTGATCTTGGTCAC-C-TTTCGACTTACGACATCGTCCCAATCATTTGATCTTG
65 ACAACCTCGACTCGATCCTGGTCACTCATTTCGACTCACAACATCGTCCCAATCATTTGATCTTG
* * *
9487905 ACTCAGGTCAAATCATCTTCAGACTCGCGACATTAGTCTAGGT-ATTTATTTACGATCTCAACTC
130 ACTCAGGTCAAATCATCTTCAGACTCGCGACATCAATCTA-GTCATTTATTTACGACCTCAACTC
*
9487969 -GATTTTGGTCACCT
194 GGA-CTTGGTCACCT
9487983 CCTAACTCGC
Statistics
Matches: 175, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
227 2 0.01
228 93 0.53
229 3 0.02
230 1 0.01
231 76 0.43
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (230 bp):
TCATTTAATCTCGACTCAAGTTAAATCATCGTCAGACTCGTGACATCAATCCGATCATTTATTTA
CAACCTCGACTCGATCCTGGTCACTCATTTCGACTCACAACATCGTCCCAATCATTTGATCTTGA
CTCAGGTCAAATCATCTTCAGACTCGCGACATCAATCTAGTCATTTATTTACGACCTCAACTCGG
ACTTGGTCACCTTTCGACTTGCGACATCATCTTAA
Found at i:9487996 original size:114 final size:114
Alignment explanation
Indices: 9487536--9488016 Score: 502
Period size: 114 Copynumber: 4.2 Consensus size: 114
9487526 TGATTCGTAG
* * * * * * *
9487536 CATCGTCCCAGTCATTTGATCTCGACTCAAGTTAAATCATCGTCAGACTCGTGACATCAATC-CG
1 CATCGTCCCAATCATTTGATCTTGACTTAGGTTAGATCATCTTCAGACTCGTGACATCAATCTAG
** * * ** *
9487600 ATCATTTATTTTTGACCTCGACTCGATCCTGGTCACTTCATTTTGACTCACAA
66 -TCATTTATTTACGACCTCGACTCGATCTTGGTCAC--C-TTTCGACTTGCGA
** * *
9487653 CATCGTCTTAGTCATTTGATCTTGACTTAGGTTAGATTATCTTCAGACTCGTGACATCAATCTAG
1 CATCGTCCCAATCATTTGATCTTGACTTAGGTTAGATCATCTTCAGACTCGTGACATCAATCTAG
9487718 TCATTTATTTACGACCTCGACTCGGA-CTTGGTCACCTTTCGACTTGCGA
66 TCATTTATTTACGACCTCGACTC-GATCTTGGTCACCTTTCGACTTGCGA
* ** * * * *
9487767 CATCATCTTAATCATTTAATCTCGACTTAGGTTAGATCATCTTCAGACTTGTGACATCAATCCAG
1 CATCGTCCCAATCATTTGATCTTGACTTAGGTTAGATCATCTTCAGACTCGTGACATCAATCTAG
* * *
9487832 TCATTTATTTACAACCTCGACTTGATCTTGGTCACCTTTCGACTTACGA
66 TCATTTATTTACGACCTCGACTCGATCTTGGTCACCTTTCGACTTGCGA
* * * * * *
9487881 CATCGTCCCAATCATTTGATCTTGACTCAGGTCAAATCATCTTCAGACTCGCGACATTAGTCTAG
1 CATCGTCCCAATCATTTGATCTTGACTTAGGTTAGATCATCTTCAGACTCGTGACATCAATCTA-
* * * * * *
9487946 GT-ATTTATTTACGATCTCAACTCGATTTTGGTCACC-TCCTAACTCGCGA
65 GTCATTTATTTACGACCTCGACTCGATCTTGGTCACCTTTC-GACTTGCGA
*
9487995 CATCGTCCCAGTCATTTGATCT
1 CATCGTCCCAATCATTTGATCT
9488017 CAGCTTTGGT
Statistics
Matches: 310, Mismatches: 49, Indels: 13
0.83 0.13 0.03
Matches are distributed among these distances:
113 4 0.01
114 217 0.70
115 3 0.01
117 83 0.27
118 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (114 bp):
CATCGTCCCAATCATTTGATCTTGACTTAGGTTAGATCATCTTCAGACTCGTGACATCAATCTAG
TCATTTATTTACGACCTCGACTCGATCTTGGTCACCTTTCGACTTGCGA
Found at i:9488375 original size:12 final size:12
Alignment explanation
Indices: 9488358--9488392 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9488348 TTTTTTATAA
9488358 ATTGTTATTATC
1 ATTGTTATTATC
*
9488370 ATTGTTATTATT
1 ATTGTTATTATC
*
9488382 ATTATTATTAT
1 ATTGTTATTAT
9488393 TATTACTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (12 bp):
ATTGTTATTATC
Found at i:9488380 original size:3 final size:3
Alignment explanation
Indices: 9488362--9488397 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
9488352 TTATAAATTG
* *
9488362 TTA TTA TCA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9488398 CTTTCCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:9488448 original size:3 final size:3
Alignment explanation
Indices: 9488436--9488515 Score: 58
Period size: 3 Copynumber: 27.7 Consensus size: 3
9488426 TTCTTTTCTT
* ** * *
9488436 TTA TTA -TA TTA TTA CTA TTA TTA TTA CCA TTA TTA ATA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
9488483 TT- TTT TTA TTT TTA TTT TTA TT- TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9488516 TTTCTCTTCT
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 6 0.10
3 54 0.90
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9488497 original size:14 final size:14
Alignment explanation
Indices: 9488475--9488518 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
9488465 TTATTAATAA
*
9488475 TATTATTATTTTTT
1 TATTTTTATTTTTT
9488489 TATTTTTATTTTTAT
1 TATTTTTATTTTT-T
9488504 T-TTTTTATTATTTT
1 TATTTTTATT-TTTT
9488518 T
1 T
9488519 CTCTTCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
TATTTTTATTTTTT
Found at i:9488500 original size:12 final size:11
Alignment explanation
Indices: 9488477--9488518 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
9488467 ATTAATAATA
*
9488477 TTATTATTTTT
1 TTATTTTTTTT
9488488 TTATTTTTATTT
1 TTATTTTT-TTT
*
9488500 TTATTTTTTTA
1 TTATTTTTTTT
9488511 TTATTTTT
1 TTATTTTT
9488519 CTCTTCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:9488503 original size:20 final size:20
Alignment explanation
Indices: 9488475--9488512 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9488465 TTATTAATAA
9488475 TATTATTATTTTTTTATTTT
1 TATTATTATTTTTTTATTTT
*
9488495 TATTTTTATTTTTTTATT
1 TATTATTATTTTTTTATT
9488513 ATTTTTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (20 bp):
TATTATTATTTTTTTATTTT
Found at i:9488971 original size:9 final size:10
Alignment explanation
Indices: 9488958--9488983 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9488948 GTTTTTTATT
9488958 TTTTTTTAGG
1 TTTTTTTAGG
9488968 TTTTTTTAGG
1 TTTTTTTAGG
9488978 TTTTTT
1 TTTTTT
9488984 GAAAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (10 bp):
TTTTTTTAGG
Found at i:9494211 original size:42 final size:42
Alignment explanation
Indices: 9494152--9494380 Score: 160
Period size: 44 Copynumber: 5.3 Consensus size: 42
9494142 TCTAGTTATG
* *
9494152 AATTTTTAAAGTTTCAAAGCTTCTATT-GATGGAAGCCTTTTA
1 AATTTTCAAAGTTTCAAAGCTTCTATTAGA-GGAAGCATTTTA
* * * * *
9494194 AATTTTCAAAGTTTCAAAACTTCTGTTAAAGAAAAGCCTTTTA
1 AATTTTCAAAGTTTCAAAGCTTCTATTAGAG-GAAGCATTTTA
* * * * * **
9494237 AATGTTCCAAGGTTTCAAAGCTTTTGTTAAGAGGTAGGTTTTTA
1 AAT-TTTCAAAGTTTCAAAGCTTCTATT-AGAGGAAGCATTTTA
* * * *
9494281 AATTTCTCAAAGTTTCAAAGTTTTTATTGGGAAGAAGCATTTTA
1 AATTT-TCAAAGTTTCAAAGCTTCTATT-AGAGGAAGCATTTTA
* *
9494325 AATTTTTC--AGTTTCAAAACCTCTATTGAGAGGGAA-CATTTTA
1 AA-TTTTCAAAGTTTCAAAGCTTCTATT-AGA-GGAAGCATTTTA
*
9494367 AATTTCCAAAGTTT
1 AATTTTCAAAGTTT
9494381 AAAAACTTTT
Statistics
Matches: 147, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
41 4 0.03
42 51 0.35
43 24 0.16
44 62 0.42
45 6 0.04
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (42 bp):
AATTTTCAAAGTTTCAAAGCTTCTATTAGAGGAAGCATTTTA
Found at i:9494691 original size:6 final size:6
Alignment explanation
Indices: 9494682--9494757 Score: 73
Period size: 6 Copynumber: 12.3 Consensus size: 6
9494672 TTTTAATCCA
* * * *
9494682 TTATTT TTATTTT TTATTT TTA-TT TGATTT TTAATT TAATTT TTGTTT
1 TTATTT TTA-TTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
9494730 TTATTT TTATTA TTATTACT TTATTT TT
1 TTATTT TTATTT TTATT--T TTATTT TT
9494758 TGTTTTTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
5 4 0.07
6 41 0.73
7 6 0.11
8 5 0.09
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:9495653 original size:7 final size:7
Alignment explanation
Indices: 9495641--9495757 Score: 78
Period size: 7 Copynumber: 15.7 Consensus size: 7
9495631 AACCGTAAGT
9495641 TTTTTTA
1 TTTTTTA
9495648 TTTTTTA
1 TTTTTTA
9495655 TTTTTTA
1 TTTTTTA
9495662 TTTTTTGA
1 TTTTTT-A
*
9495670 -TTTTGA
1 TTTTTTA
9495676 TTTTGATT-
1 TTTT--TTA
9495684 TTGATTTTA
1 TT--TTTTA
*
9495693 TTTTTAA
1 TTTTTTA
*
9495700 TTTTTAA
1 TTTTTTA
9495707 TTTTTAATA
1 TTTTT--TA
9495716 TATTTTT-
1 T-TTTTTA
*
9495723 TTCTTTTG
1 TT-TTTTA
9495731 TTTTTTA
1 TTTTTTA
9495738 GTTTTTTA
1 -TTTTTTA
*
9495746 TTTATTA
1 TTTTTTA
9495753 TTTTT
1 TTTTT
9495758 AATTGTGATT
Statistics
Matches: 90, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.02
7 62 0.69
8 15 0.17
9 5 0.06
10 6 0.07
ACGTcount: A:0.17, C:0.01, G:0.05, T:0.77
Consensus pattern (7 bp):
TTTTTTA
Found at i:9495839 original size:26 final size:26
Alignment explanation
Indices: 9495809--9495883 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 26
9495799 GGAAACTTTA
**
9495809 GCATGATTTTTATTATGATATTTATG
1 GCATGATTTTTATTATGATATTTACC
*
9495835 GCATGATTTTTATTTTGATATTTACC
1 GCATGATTTTTATTATGATATTTACC
* *
9495861 ACATGATTTTTATTATAATATTT
1 GCATGATTTTTATTATGATATTT
9495884 TCAAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.55
Consensus pattern (26 bp):
GCATGATTTTTATTATGATATTTACC
Found at i:9501396 original size:52 final size:52
Alignment explanation
Indices: 9501310--9501466 Score: 210
Period size: 52 Copynumber: 3.0 Consensus size: 52
9501300 TATAACCATA
* * *
9501310 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
9501362 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* **
9501414 CAAACTTACCTATTAAGAATCCTCTTT-CTCTT-GAAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-CTTTCCTCTTAG-AATTCTTCTCCTGCAAGT
9501466 C
1 C
9501467 TTCTTGTCCA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 1 0.01
52 90 0.95
53 4 0.04
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:9501520 original size:11 final size:11
Alignment explanation
Indices: 9501491--9501521 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
9501481 GCAATATCTG
*
9501491 ACAAATCCCAA
1 ACAAATCTCAA
9501502 ACAAATCTCAA
1 ACAAATCTCAA
9501513 ACAAATCTC
1 ACAAATCTC
9501522 TTATGGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:9501859 original size:2 final size:2
Alignment explanation
Indices: 9501852--9501888 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9501842 TGAAAATGTG
9501852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9501889 GAAAGATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9502736 original size:69 final size:69
Alignment explanation
Indices: 9502661--9502797 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 69
9502651 TGTCCTATCG
* * *
9502661 TTAAAATTACCTTCTCTTATCTAGTATTATTTTATAAAAACTTTTCAACAGGAAAGTAAGCGGTA
1 TTAAAATTACCTTCTCTTATCTACTATTATTTTATAAAAACTTTTCAACAGGAAAATAAACGGTA
9502726 AAAA
66 AAAA
**
9502730 TTAAAATTACCTTCTCTTATCTACTATTATTTTATAAAAACTTTTCGGCAGGAAAATAAACGGTA
1 TTAAAATTACCTTCTCTTATCTACTATTATTTTATAAAAACTTTTCAACAGGAAAATAAACGGTA
9502795 AAA
66 AAA
9502798 GAAATAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (69 bp):
TTAAAATTACCTTCTCTTATCTACTATTATTTTATAAAAACTTTTCAACAGGAAAATAAACGGTA
AAAA
Found at i:9503945 original size:17 final size:18
Alignment explanation
Indices: 9503925--9503997 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
9503915 GATGGGGCAT
9503925 AAAAA-AAACAAAAACAA
1 AAAAACAAACAAAAACAA
* *
9503942 AAAAA-AAGCAAAAAGGAA
1 AAAAACAAACAAAAA-CAA
* * * *
9503960 AAAAACATAGAAAGATAA
1 AAAAACAAACAAAAACAA
*
9503978 AAAAACAAAAAAAAACAA
1 AAAAACAAACAAAAACAA
9503996 AA
1 AA
9503998 GGACATCTTC
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
17 13 0.30
18 25 0.58
19 5 0.12
ACGTcount: A:0.82, C:0.08, G:0.07, T:0.03
Consensus pattern (18 bp):
AAAAACAAACAAAAACAA
Found at i:9505695 original size:18 final size:18
Alignment explanation
Indices: 9505672--9505720 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
9505662 ATTCGCATTC
* *
9505672 TTGCATTTGCATTGACAT
1 TTGCATTAGCATCGACAT
9505690 TTGCATTCA-CATCGACAT
1 TTGCATT-AGCATCGACAT
*
9505708 TTCCATTAGCATC
1 TTGCATTAGCATC
9505721 ATTTGATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (18 bp):
TTGCATTAGCATCGACAT
Found at i:9507750 original size:106 final size:104
Alignment explanation
Indices: 9507569--9507760 Score: 240
Period size: 106 Copynumber: 1.8 Consensus size: 104
9507559 TCTTTTAAAC
* * * *
9507569 ATTTTAAAGTTTATTGCCTTTGATTGGGAGGAGCATTCGAAGACTTCAAAATTTCTAAGACCTCT
1 ATTTTAAAGTTTATTGCCTTTGATTAGAAAGAGCATTCAAAGACTTCAAAATTTCTAAGACCTCT
* *
9507634 AGGCACAATCTTTTAGACCTCATGGTAAAAGATTTTTAA
66 AGGCACAATCTCTAAGACCTCATGGTAAAAGATTTTTAA
* ** * *
9507673 ATTTTAAAAGTTTCATTGCCTTTGATTAGAAAGAGCATTCAAAGATTTTGATATTTGTAAGACCT
1 ATTTT-AAAGTTT-ATTGCCTTTGATTAGAAAGAGCATTCAAAGACTTCAAAATTTCTAAGACCT
* * *
9507738 TTGGGCATAATCTCTAAGACCTC
64 CTAGGCACAATCTCTAAGACCTC
9507761 CAAGTATAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
104 5 0.07
105 7 0.10
106 60 0.83
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (104 bp):
ATTTTAAAGTTTATTGCCTTTGATTAGAAAGAGCATTCAAAGACTTCAAAATTTCTAAGACCTCT
AGGCACAATCTCTAAGACCTCATGGTAAAAGATTTTTAA
Found at i:9507882 original size:22 final size:22
Alignment explanation
Indices: 9507854--9507902 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
9507844 TTTTTAGATT
**
9507854 TAAGACTTTCGGGTATAATCTC
1 TAAGACTTTCAAGTATAATCTC
*
9507876 TAAGACTTTCAAGTATAATTTC
1 TAAGACTTTCAAGTATAATCTC
9507898 TAAGA
1 TAAGA
9507903 GCTCCGGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
TAAGACTTTCAAGTATAATCTC
Found at i:9507915 original size:22 final size:23
Alignment explanation
Indices: 9507890--9507985 Score: 137
Period size: 22 Copynumber: 4.3 Consensus size: 23
9507880 ACTTTCAAGT
*
9507890 ATAATTTCT-AAGAGCTCCGGAC
1 ATAATTTCTCAAGACCTCCGGAC
9507912 ATAATTTCT-AAGACCTCCGGAC
1 ATAATTTCTCAAGACCTCCGGAC
* *
9507934 ATAATTT-TCAAGACCTTCGAAC
1 ATAATTTCTCAAGACCTCCGGAC
9507956 ATAATTT-TCAAGACCTCCGGAC
1 ATAATTTCTCAAGACCTCCGGAC
9507978 ATAATTTC
1 ATAATTTC
9507986 GACTTGCGGT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
21 1 0.01
22 66 0.99
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (23 bp):
ATAATTTCTCAAGACCTCCGGAC
Found at i:9508136 original size:36 final size:37
Alignment explanation
Indices: 9507982--9508241 Score: 124
Period size: 37 Copynumber: 7.1 Consensus size: 37
9507972 CCGGACATAA
* * *
9507982 TTTCGACTTGCGGTGTTGTC-CTAGTCG-TTTTTTTTT
1 TTTCGACTTACGGTGTTGTCTC-AATCGATTTTTTATT
* * *
9508018 ATTTCAACTTACGGTGTTATCTCGATCGATTTTTTATCT
1 -TTTCGACTTACGGTGTTGTCTCAATCGATTTTTTAT-T
* * * *
9508057 TTT-GATTTACGATGTTGTCTCGATC-ATTCTTCT-TT
1 TTTCGACTTACGGTGTTGTCTCAATCGATT-TTTTATT
* *
9508092 ATTCGACTTACGGTGTTGTC-CTAATCGAGTTTTTATT
1 TTTCGACTTACGGTGTTGTCTC-AATCGATTTTTTATT
* * * * *
9508129 TTT-GACTTACAGTATTATCCCAATC-ATTTTCTTTATC
1 TTTCGACTTACGGTGTTGTCTCAATCGA-TTT-TTTATT
* * * * * * * *
9508166 ATTCAACTTGCAGTGTTATCCCAATTGATTCTTTATT
1 TTTCGACTTACGGTGTTGTCTCAATCGATTTTTTATT
* * * * *
9508203 TCTCGACTCACGGTGTTGTCCCTATCG-TTCTTTATT
1 TTTCGACTTACGGTGTTGTCTCAATCGATTTTTTATT
9508239 TTT
1 TTT
9508242 TAACTCAAGG
Statistics
Matches: 170, Mismatches: 40, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
35 5 0.03
36 54 0.32
37 78 0.46
38 31 0.18
39 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (37 bp):
TTTCGACTTACGGTGTTGTCTCAATCGATTTTTTATT
Found at i:9508219 original size:37 final size:36
Alignment explanation
Indices: 9508178--9508260 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
9508168 TCAACTTGCA
* * *
9508178 GTGTTATCCCAATTGATTCTTTATTTCTCGACTCACG
1 GTGTTATCCCAATCG-TTCTTTATTTCTCAACTCAAG
* * * *
9508215 GTGTTGTCCCTATCGTTCTTTATTTTTTAACTCAAG
1 GTGTTATCCCAATCGTTCTTTATTTCTCAACTCAAG
9508251 GTGTTATCCC
1 GTGTTATCCC
9508261 GATCATTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 26 0.68
37 12 0.32
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (36 bp):
GTGTTATCCCAATCGTTCTTTATTTCTCAACTCAAG
Found at i:9509141 original size:127 final size:126
Alignment explanation
Indices: 9508915--9509304 Score: 512
Period size: 127 Copynumber: 3.1 Consensus size: 126
9508905 TAAAGCACTT
* * *
9508915 AAACACCCCAACTCTAAAAGACCCAGGCACCAGTCCCCATACCCCAAGCATTCACCCTCATCAAC
1 AAACA-CCCAACTCTAAAAGACCAAGGCACCAGTCTCCATACCCCAAGCATTCACCCTCACCAAC
* * * ** * *
9508980 ATTGTCAAAGTCATAGCCTATACCCACACACCACCAACCTTGTGTTTAGCCTCCGCCCACAC
65 ACTGTCAAAGTCATAGCCCACACCCATGCACCACCAACCTTGTGCTTAGCCTCCACCCACAC
* * * ** *
9509042 AAACACCTCAACTTTAAAAGACCTATGCACCAGTCTCCATACCCTGAGCATTCACCCTCACCAGC
1 AAACACC-CAACTCTAAAAGACCAAGGCACCAGTCTCCATACCCCAAGCATTCACCCTCACCAAC
** * * *
9509107 ACTGTCAAAGTCGCAGCCCACACCCATGCACCACCAGCCTAGTGCTTAACCTCCACCCACAC
65 ACTGTCAAAGTCATAGCCCACACCCATGCACCACCAACCTTGTGCTTAGCCTCCACCCACAC
*
9509169 AAACACCCTAACTCTAAAAAACCAAGGCACCAGTACT-CATACCCCAAGCATTCACCCTCACCAA
1 AAACACCC-AACTCTAAAAGACCAAGGCACCAGT-CTCCATACCCCAAGCATTCACCCTCACCAA
* * *
9509233 CACTATCAAAGTCATAGCCCACACCCATGCACCACCAACCTTGTGCTTAGCCTCCACCTATAC
64 CACTGTCAAAGTCATAGCCCACACCCATGCACCACCAACCTTGTGCTTAGCCTCCACCCACAC
9509296 AAACACCCA
1 AAACACCCA
9509305 GCCACAACAA
Statistics
Matches: 225, Mismatches: 35, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
126 4 0.02
127 219 0.97
128 2 0.01
ACGTcount: A:0.33, C:0.41, G:0.09, T:0.17
Consensus pattern (126 bp):
AAACACCCAACTCTAAAAGACCAAGGCACCAGTCTCCATACCCCAAGCATTCACCCTCACCAACA
CTGTCAAAGTCATAGCCCACACCCATGCACCACCAACCTTGTGCTTAGCCTCCACCCACAC
Found at i:9509919 original size:7 final size:8
Alignment explanation
Indices: 9509900--9509947 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
9509890 TTAAAGTAAT
9509900 TTTTTATA
1 TTTTTATA
9509908 TTTTTATA
1 TTTTTATA
*
9509916 TTTTTAAA
1 TTTTTATA
9509924 TTTTTTATA
1 -TTTTTATA
9509933 TTATTT-TA
1 TT-TTTATA
*
9509941 GTTTTAT
1 TTTTTAT
9509948 TAATACATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 3 0.09
8 21 0.62
9 10 0.29
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTTATA
Found at i:9509920 original size:17 final size:16
Alignment explanation
Indices: 9509900--9509934 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
9509890 TTAAAGTAAT
*
9509900 TTTTTATATTTTTATA
1 TTTTTAAATTTTTATA
9509916 TTTTTAAATTTTTTATA
1 TTTTTAAA-TTTTTATA
9509933 TT
1 TT
9509935 ATTTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAAATTTTTATA
Found at i:9509945 original size:25 final size:25
Alignment explanation
Indices: 9509897--9509946 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
9509887 TGGTTAAAGT
*
9509897 AATTTTTTATATTTTTATATTTTTA
1 AATTTTTTATATTTTTATAGTTTTA
9509922 AATTTTTTATATTATTT-TAGTTTTA
1 AATTTTTTATATT-TTTATAGTTTTA
9509947 TTAATACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (25 bp):
AATTTTTTATATTTTTATAGTTTTA
Found at i:9510125 original size:12 final size:12
Alignment explanation
Indices: 9510089--9510132 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
9510079 CCAAGTGTTA
9510089 AATAAAAATAAAT
1 AATAAAAAT-AAT
* *
9510102 AATAATATTAAT
1 AATAAAAATAAT
9510114 AATAAAAATAAT
1 AATAAAAATAAT
*
9510126 TATAAAA
1 AATAAAA
9510133 CAAACTAGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:9510429 original size:14 final size:14
Alignment explanation
Indices: 9510410--9510517 Score: 76
Period size: 14 Copynumber: 7.4 Consensus size: 14
9510400 CCAAATCCTT
9510410 AAAACCCCAAAATC
1 AAAACCCCAAAATC
* *
9510424 AAAACCCTAAAGCCTTC
1 AAAACCCCAAA---ATC
9510441 -AAACCCCAAAATC
1 AAAACCCCAAAATC
* *
9510454 AAAACCTC-AAACC
1 AAAACCCCAAAATC
* *
9510467 TTAAACCCCAAAATT
1 -AAAACCCCAAAATC
* *
9510482 AAAACCCCAAACCTTT
1 AAAACCCCAAA--ATC
9510498 AAAACCCCAAAATC
1 AAAACCCCAAAATC
9510512 AAAACC
1 AAAACC
9510518 TTAAACCTCA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
13 6 0.08
14 39 0.54
15 3 0.04
16 22 0.31
17 2 0.03
ACGTcount: A:0.51, C:0.35, G:0.01, T:0.13
Consensus pattern (14 bp):
AAAACCCCAAAATC
Found at i:9510503 original size:58 final size:57
Alignment explanation
Indices: 9510395--9510552 Score: 208
Period size: 58 Copynumber: 2.7 Consensus size: 57
9510385 CATTTTTTCT
* * *
9510395 AAACCCCAAATCCTTAAAACCCCAAAATCAAAACCCTAAAGCCTTCAAACCCCAAAATCA
1 AAACCTCAAA-CCTT-AAACCCCAAAATTAAAACCCTAAA-CCTTAAAACCCCAAAATCA
*
9510455 AAACCTCAAACCTTAAACCCCAAAATTAAAACCCCAAACCTTTAAAACCCCAAAATCA
1 AAACCTCAAACCTTAAACCCCAAAATTAAAACCCTAAACC-TTAAAACCCCAAAATCA
* * * *
9510513 AAACCTTAAACCTCAAACTCTAAAATTAAAACCCTAAACC
1 AAACCTCAAACCTTAAACCCCAAAATTAAAACCCTAAACC
9510553 CTTAGAATCA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.02
58 73 0.83
59 4 0.05
60 9 0.10
ACGTcount: A:0.49, C:0.34, G:0.01, T:0.16
Consensus pattern (57 bp):
AAACCTCAAACCTTAAACCCCAAAATTAAAACCCTAAACCTTAAAACCCCAAAATCA
Found at i:9510550 original size:28 final size:29
Alignment explanation
Indices: 9510395--9510552 Score: 178
Period size: 30 Copynumber: 5.4 Consensus size: 29
9510385 CATTTTTTCT
* *
9510395 AAACCCCAAATCCTTAAAACCCCAAAATCA
1 AAACCCTAAA-CCTTCAAACCCCAAAATCA
9510425 AAACCCTAAAGCCTTCAAACCCCAAAATCA
1 AAACCCTAAA-CCTTCAAACCCCAAAATCA
*
9510455 AAA-CCTCAAACCTT-AAACCCCAAAATTA
1 AAACCCT-AAACCTTCAAACCCCAAAATCA
* *
9510483 AAACCCCAAACCTTTAAAACCCCAAAATCA
1 AAACCCTAAACC-TTCAAACCCCAAAATCA
* * * *
9510513 AAACCTTAAACC-TCAAACTCTAAAATTA
1 AAACCCTAAACCTTCAAACCCCAAAATCA
9510541 AAACCCTAAACC
1 AAACCCTAAACC
9510553 CTTAGAATCA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
28 44 0.40
29 11 0.10
30 56 0.50
ACGTcount: A:0.49, C:0.34, G:0.01, T:0.16
Consensus pattern (29 bp):
AAACCCTAAACCTTCAAACCCCAAAATCA
Found at i:9510565 original size:28 final size:28
Alignment explanation
Indices: 9510417--9510567 Score: 103
Period size: 28 Copynumber: 5.2 Consensus size: 28
9510407 CTTAAAACCC
* * *
9510417 CAAAATCAAAACCCTAAAGCCTTCAAACCC
1 CAAAATTAAAACCCTAAACCCTT-AAA-CT
* *
9510447 CAAAATCAAAA-CCTCAAA-CCTTAAACCC
1 CAAAATTAAAACCCT-AAACCCTTAAA-CT
* * *
9510475 CAAAATTAAAACCCCAAACCTTTAAAACCC
1 CAAAATTAAAACCCTAAACCCTT-AAA-CT
* * *
9510505 CAAAATCAAAACCTTAAA-CCTCAAACT
1 CAAAATTAAAACCCTAAACCCTTAAACT
9510532 CTAAAATTAAAACCCTAAACCCTTAGAA-T
1 C-AAAATTAAAACCCTAAACCCTTA-AACT
9510561 CAAAATT
1 CAAAATT
9510568 TTTAAACCCT
Statistics
Matches: 102, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
27 2 0.02
28 43 0.42
29 20 0.20
30 37 0.36
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.18
Consensus pattern (28 bp):
CAAAATTAAAACCCTAAACCCTTAAACT
Found at i:9510633 original size:29 final size:29
Alignment explanation
Indices: 9510577--9510659 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
9510567 TTTTAAACCC
* * **
9510577 TCCAAACCCTAAAAACCTTAAACCTTAAAA
1 TCCAAAACCT-AAAACCCTAAATTTTAAAA
9510607 TCCAAAACCTAAAACCCTAAATTTTAAAA
1 TCCAAAACCTAAAACCCTAAATTTTAAAA
* *
9510636 TTCAAAACTTAAAA-CCTCAAATTT
1 TCCAAAACCTAAAACCCT-AAATTT
9510660 GGTACACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.07
29 34 0.74
30 9 0.20
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (29 bp):
TCCAAAACCTAAAACCCTAAATTTTAAAA
Found at i:9512182 original size:116 final size:116
Alignment explanation
Indices: 9512054--9512327 Score: 315
Period size: 116 Copynumber: 2.4 Consensus size: 116
9512044 TTAAAACATT
* * * * *
9512054 TTTTTAAGGAAAATTGGTACTTCCAACTTTTTCC-C-AAAATGTTTTTCT-GAAACTTTAATTTC
1 TTTTCAAGGAAAATTGATACTT-CAACCTTTTCCTCAAAAATATTTTT-TAGAAA-ATTAATTTC
*
9512116 GAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAGATTTTA
63 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAGATTTTA
** *
9512170 TTTTCAAGGAAAATTGATACTTTTACCTTTTCCTCAAAAATATTTTTTAGAAAATTATTTTCAAG
1 TTTTCAAGGAAAATTGATACTTCAACCTTTTCCTCAAAAATATTTTTTAGAAAATTAATTTCAAG
* * ** * **
9512235 AAAAATTGATACTTTCAACTTTTTCTCGAAAATA-TTTTTTAGAAAACTTA
66 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAGATTTTA
* *
9512285 TTTTCAAGGAAAATTAATATTTTCAA-CTTTTCCTCAAAAATAT
1 TTTTCAAGGAAAATTGATA-CTTCAACCTTTTCCTCAAAAATAT
9512328 ATTGTTTTAG
Statistics
Matches: 134, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
115 54 0.40
116 66 0.49
117 14 0.10
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (116 bp):
TTTTCAAGGAAAATTGATACTTCAACCTTTTCCTCAAAAATATTTTTTAGAAAATTAATTTCAAG
AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAGATTTTA
Found at i:9512355 original size:58 final size:57
Alignment explanation
Indices: 9512051--9512356 Score: 313
Period size: 57 Copynumber: 5.3 Consensus size: 57
9512041 TTCTTAAAAC
* * *
9512051 ATTT-TTTT-AAGGAAAATTGGTACTTCCAACTTTTTCC-C-AAAATGTTTTTCT-GAA
1 ATTTATTTTCAAGGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTT-TAGAA
* * *
9512105 ACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAG-A
1 A-TTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA---TTTTTTAGAA
* * *
9512165 TTTTATTTTCAAGGAAAATTGATACTTTTACCTTTTCCTCAAAAATATTTTTTAGAA
1 ATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAA
* * * *
9512222 AATTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTTAGAAA
1 ATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAG-AA
* * *
9512280 ACTTATTTTCAAGGAAAATTAATATTTTCAACTTTTCCTCAAAAATATATTGTTTTAGAA
1 ATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATATT-TTTTAGAA
*
9512340 TTTTATTTT-AA-GAAAAT
1 ATTTATTTTCAAGGAAAAT
9512357 CATTTTAAAA
Statistics
Matches: 211, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
54 1 0.00
55 3 0.01
56 17 0.08
57 68 0.32
58 48 0.23
59 46 0.22
60 16 0.08
61 12 0.06
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.45
Consensus pattern (57 bp):
ATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAA
Found at i:9512377 original size:12 final size:12
Alignment explanation
Indices: 9512362--9512404 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
9512352 AAAATCATTT
9512362 TAAAAAATAAAA
1 TAAAAAATAAAA
*
9512374 TAAAATA-AAAA
1 TAAAAAATAAAA
9512385 T-AAAAATAAAA
1 TAAAAAATAAAA
9512396 TAAAAAATA
1 TAAAAAATA
9512405 CCAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.15
11 10 0.37
12 13 0.48
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:9512378 original size:11 final size:11
Alignment explanation
Indices: 9512364--9512401 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
9512354 AATCATTTTA
9512364 AAAAATAAAAT
1 AAAAATAAAAT
9512375 -AAAATAAAAAT
1 AAAAAT-AAAAT
9512386 AAAAATAAAAT
1 AAAAATAAAAT
9512397 AAAAA
1 AAAAA
9512402 ATACCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:9512384 original size:6 final size:6
Alignment explanation
Indices: 9512364--9512401 Score: 55
Period size: 5 Copynumber: 6.8 Consensus size: 6
9512354 AATCATTTTA
9512364 AAAAAT -AAAAT -AAAAT AAAAAT AAAAAT -AAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
9512402 ATACCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.50
6 15 0.50
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:9512384 original size:17 final size:17
Alignment explanation
Indices: 9512362--9512404 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
9512352 AAAATCATTT
9512362 TAAAAAATAAAATAAAA
1 TAAAAAATAAAATAAAA
9512379 T-AAAAATAAAAATAAAA
1 TAAAAAAT-AAAATAAAA
9512396 TAAAAAATA
1 TAAAAAATA
9512405 CCAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 12 0.50
18 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAAAAATAAAATAAAA
Found at i:9512438 original size:3 final size:3
Alignment explanation
Indices: 9512430--9512477 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
9512420 CTAATCAATA
* *
9512430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAGA AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
9512476 AA
1 AA
9512478 AAAATGAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:9513270 original size:16 final size:15
Alignment explanation
Indices: 9513245--9513344 Score: 69
Period size: 16 Copynumber: 6.5 Consensus size: 15
9513235 AATAATAGAA
*
9513245 AAATATATATACTAAT
1 AAATAAATATA-TAAT
9513261 AAATAAATATATTAAT
1 AAATAAATATA-TAAT
**
9513277 TGATAAATA-ATAAT
1 AAATAAATATATAAT
* *
9513291 AAAAAATATATATTAAA
1 AAATAA-ATATA-TAAT
* *
9513308 AAATACATTTATAAAT
1 AAATAAATATAT-AAT
*
9513324 AAATAAATAAATAA-
1 AAATAAATATATAAT
9513338 AAATAAA
1 AAATAAA
9513345 AATGCAAATA
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
14 14 0.22
15 7 0.11
16 37 0.57
17 7 0.11
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (15 bp):
AAATAAATATATAAT
Found at i:9513311 original size:27 final size:30
Alignment explanation
Indices: 9513257--9513328 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
9513247 ATATATATAC
* *
9513257 TAATAAATAAATATATTAATTGATAAATAA
1 TAATAAATAAATATATTAATTAAAAAATAA
9513287 TAATAAA-AAATATA-T-ATTAAAAAATACA
1 TAATAAATAAATATATTAATTAAAAAATA-A
*
9513315 TTTATAAATAAATA
1 -TAATAAATAAATA
9513329 AATAAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.25
28 2 0.06
29 13 0.36
30 12 0.33
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (30 bp):
TAATAAATAAATATATTAATTAAAAAATAA
Found at i:9513330 original size:47 final size:48
Alignment explanation
Indices: 9513209--9513340 Score: 132
Period size: 47 Copynumber: 2.8 Consensus size: 48
9513199 AAAGATGAAG
*
9513209 TAAAAAAT-AATA-AT-AATAATATTAATAATAATAGAAAAATATATATA
1 TAAAAAATAAATATATAAATAA-ATAAATAATAATA-AAAAATATATATA
* * **
9513256 CTAATAAATAAATATATTAATTGATAAATAATAATAAAAAATATATAT-
1 -TAAAAAATAAATATATAAATAAATAAATAATAATAAAAAATATATATA
* *
9513304 TAAAAAATACATTTATAAATAAATAAAT-A-AATAAAAA
1 TAAAAAATAAATATATAAATAAATAAATAATAATAAAAA
9513341 TAAAAATGCA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
45 8 0.11
46 1 0.01
47 22 0.31
48 7 0.10
49 16 0.23
50 14 0.20
51 3 0.04
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (48 bp):
TAAAAAATAAATATATAAATAAATAAATAATAATAAAAAATATATATA
Found at i:9513626 original size:42 final size:42
Alignment explanation
Indices: 9513537--9513884 Score: 299
Period size: 45 Copynumber: 7.9 Consensus size: 42
9513527 TTGATTAAGT
*
9513537 TCCTCTAAACAAAGGCTCAACGACTTTGAAAAAATAAACAAAGC
1 TCCTCTAAA-AGAGGCTCAACGACTTTG-AAAAATAAACAAAGC
* *
9513581 TCCTCTAATAAGAGGCT-AACAACTTTGGAAAAT-AACTAAAGC
1 TCCTCTAA-AAGAGGCTCAACGACTTTGAAAAATAAAC-AAAGC
* * *
9513623 TCCTCTAATTAA-AGGCTCAATGGCTTTTAGTAAAATAAACAAAGC
1 TCCTCTAA--AAGAGGCTCAACGAC-TTT-GAAAAATAAACAAAGC
* * *
9513668 TCATCTAAACAGAGGCTCAACGATTTTGAAAAATAAATAAAGC
1 TCCTCTAAA-AGAGGCTCAACGACTTTGAAAAATAAACAAAGC
* *
9513711 TCCTCTAATTAGAGGCTCAACGACTTTTAGTAAAATAAACAAAGC
1 TCCTCTAA-AAGAGGCTCAACGAC-TTT-GAAAAATAAACAAAGC
* * *
9513756 TCCTCTGAACAGAGGCTCAACGATTTTG-AAAATAAATAAAGC
1 TCCTCT-AAAAGAGGCTCAACGACTTTGAAAAATAAACAAAGC
* * *
9513798 TCCTTTAAATAGAGGCTCAACGACTTTTAGTGAAATAAACAAAGAAAGC
1 TCCTCTAAA-AGAGGCTCAACGAC--TT--TG-AA-AAATAAACAAAGC
* *
9513847 TCCTCTAAACAGAGGCTCAACAACTTTCAAAAAATAAA
1 TCCTCTAAA-AGAGGCTCAACGACTTT-GAAAAATAAA
9513885 TTGCTCCTTT
Statistics
Matches: 251, Mismatches: 31, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
41 5 0.02
42 54 0.22
43 51 0.20
44 35 0.14
45 64 0.25
46 7 0.03
47 2 0.01
48 1 0.00
49 32 0.13
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (42 bp):
TCCTCTAAAAGAGGCTCAACGACTTTGAAAAATAAACAAAGC
Found at i:9513738 original size:88 final size:88
Alignment explanation
Indices: 9513549--9513885 Score: 439
Period size: 88 Copynumber: 3.8 Consensus size: 88
9513539 CTCTAAACAA
* * * *
9513549 AGGCTCAACGACTTTGA-AAAAATAAACAAAGCTCCTCTAATA-AGAGGCT-AACAACTTTGGAA
1 AGGCTCAACGACTTTTAGTAAAATAAACAAAGCTCCTCTAA-ACAGAGGCTCAACAATTTTGAAA
* *
9513611 AATAACTAAAGCTCCTCTAATTAA
65 AATAAATAAAGCTCCTCTAATTAG
* * * *
9513635 AGGCTCAATGGCTTTTAGTAAAATAAACAAAGCTCATCTAAACAGAGGCTCAACGATTTTGAAAA
1 AGGCTCAACGACTTTTAGTAAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACAATTTTGAAAA
9513700 ATAAATAAAGCTCCTCTAATTAG
66 ATAAATAAAGCTCCTCTAATTAG
* *
9513723 AGGCTCAACGACTTTTAGTAAAATAAACAAAGCTCCTCTGAACAGAGGCTCAACGATTTTG-AAA
1 AGGCTCAACGACTTTTAGTAAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACAATTTTGAAAA
* *
9513787 ATAAATAAAGCTCCTTTAAATAG
66 ATAAATAAAGCTCCTCTAATTAG
* *
9513810 AGGCTCAACGACTTTTAGTGAAATAAACAAAGAAAGCTCCTCTAAACAGAGGCTCAACAACTTTC
1 AGGCTCAACGACTTTTAGTAAAATAAAC----AAAGCTCCTCTAAACAGAGGCTCAACAA-TTTT
*
9513875 AAAAAATAAAT
61 GAAAAATAAAT
9513886 TGCTCCTTTA
Statistics
Matches: 221, Mismatches: 21, Indels: 11
0.87 0.08 0.04
Matches are distributed among these distances:
86 15 0.07
87 79 0.36
88 89 0.40
91 26 0.12
92 3 0.01
93 9 0.04
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (88 bp):
AGGCTCAACGACTTTTAGTAAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACAATTTTGAAAA
ATAAATAAAGCTCCTCTAATTAG
Found at i:9513827 original size:175 final size:176
Alignment explanation
Indices: 9513549--9513885 Score: 448
Period size: 175 Copynumber: 1.9 Consensus size: 176
9513539 CTCTAAACAA
9513549 AGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAATAAGAGGCTAACAACTTTGGAAAAT
1 AGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAATAAGAGGCTAACAACTTTGGAAAAT
* * * *
9513614 AACTAAAGCTCCTCTAATTAAAGGCTCAATGGCTTTTAGTAAAATAAAC-AAAGCTCATCTAAAC
66 AAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTTAGTAAAATAAACAAAAGCTCATCTAAAC
* **
9513678 AGAGGCTCAACGA-TTTTGAAAAATAAATAAAGCTCCTCTAATTAG
131 AGAGGCTCAACAACTTTCAAAAAATAAATAAAGCTCCTCTAATTAG
* * * * *
9513723 AGGCTCAACGACTTTTAGTAAAATAAACAAAGCTCCTCTGAA-CAGAGGCTCAACGA-TTTTGAA
1 AGGCTCAACGACTTTGA-AAAAATAAACAAAGCTCCTCT-AATAAGAGGCT-AACAACTTTGGAA
* * * *
9513786 AATAAATAAAGCTCCTTTAAATAGAGGCTCAACGACTTTTAGTGAAATAAACAAAGAAAGCTCCT
63 AATAAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTTAGTAAAATAAAC--A-AAAGCTCAT
9513851 CTAAACAGAGGCTCAACAACTTTCAAAAAATAAAT
125 CTAAACAGAGGCTCAACAACTTTCAAAAAATAAAT
9513886 TGCTCCTTTA
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
174 16 0.12
175 78 0.56
176 6 0.04
179 26 0.19
180 13 0.09
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (176 bp):
AGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAATAAGAGGCTAACAACTTTGGAAAAT
AAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTTAGTAAAATAAACAAAAGCTCATCTAAAC
AGAGGCTCAACAACTTTCAAAAAATAAATAAAGCTCCTCTAATTAG
Found at i:9514171 original size:21 final size:21
Alignment explanation
Indices: 9514142--9514195 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
9514132 AATGTAGTAT
9514142 ATGCTATGCAAAATTCAATAC
1 ATGCTATGCAAAATTCAATAC
*
9514163 ATGCGATGCAAAATTCAATAC
1 ATGCTATGCAAAATTCAATAC
9514184 ATGCTATGCAAA
1 ATGCTATGCAAA
9514196 TACTGGCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26
Consensus pattern (21 bp):
ATGCTATGCAAAATTCAATAC
Found at i:9514912 original size:18 final size:18
Alignment explanation
Indices: 9514891--9514929 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9514881 TTGCCTTGAG
9514891 TTTTCCTTTTTCATTCCT
1 TTTTCCTTTTTCATTCCT
* **
9514909 TTTTTCTTTTTTTTTCCT
1 TTTTCCTTTTTCATTCCT
9514927 TTT
1 TTT
9514930 CATTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCCTTTTTCATTCCT
Found at i:9516629 original size:58 final size:57
Alignment explanation
Indices: 9516565--9517013 Score: 556
Period size: 58 Copynumber: 7.7 Consensus size: 57
9516555 TTGTGCAGGA
* * *
9516565 AAAATTGATACTTTTAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATT-TTTTGAAACTTTATTTTCGAGG
* * **
9516623 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAACTTTATTTTCGAGG
* *
9516682 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAC-TTTATTTTCGAGG
* * * * * **
9516740 AAAATTGATATTTTTAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTGAAACTTTATTTTCGAGG
*
9516798 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTTATTTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAAC-TTTATTTTCGAGG
* *
9516857 AAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTGAAACTTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAC-TTTATTTTCGAGG
* * * ** *
9516915 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTAAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAACTTTATTTTCGAGG
* *
9516974 AAAATTGATATTTTCAACTTTTCCTCAAAAACTTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTT
9517014 TTGAAAATTT
Statistics
Matches: 341, Mismatches: 42, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
57 17 0.05
58 167 0.49
59 143 0.42
60 14 0.04
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAACTTTATTTTCGAGG
Found at i:9516771 original size:117 final size:116
Alignment explanation
Indices: 9516565--9517029 Score: 646
Period size: 117 Copynumber: 4.0 Consensus size: 116
9516555 TTGTGCAGGA
*
9516565 AAAATTGATACTTTTAACTTTTCCCCAAAAATATTCTTTTGAAAC-TTTAATTTCGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATT-TTTTGAAACTTTTAATTTCGAGGAAAATT
9516629 GATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTAAAATTTATTTTTAAGG
65 GATACTTTCAACTTTTCCTCAAAAATTT-TTTTTTTAAAATTTATTTTTAAGG
9516682 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGGAAAATTG
* * *
9516747 ATATTTTTAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGG
66 ATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTAAAATTTATTTTTAAGG
*
9516798 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTTATTTTCGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAACTTTTAATTTCGAGGAAAATT
* * * * * **
9516863 GATACTTTCAACTTTTCTTCAAAAA-TATTTTTTGAAACTTTTAATTTCGAGG
65 GATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTAAA-ATTTATTTTTAAGG
* * * ** * ** *
9516915 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTAAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTGAAACTTTTAATTTCGAGGAAAATT
* *
9516980 GATATTTTCAACTTTTCCTCAAAAACTTTTTTTTTTGAAAATTTTTTTTT
65 GATACTTTCAACTTTTCCTCAAAAA-TTTTTTTTTT-AAAATTTATTTTT
9517030 TTTTTTAGAA
Statistics
Matches: 310, Mismatches: 31, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
116 81 0.26
117 207 0.67
118 6 0.02
119 13 0.04
120 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGGAAAATTG
ATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTAAAATTTATTTTTAAGG
Found at i:9516860 original size:175 final size:174
Alignment explanation
Indices: 9516565--9517028 Score: 678
Period size: 175 Copynumber: 2.6 Consensus size: 174
9516555 TTGTGCAGGA
* * * * * * **
9516565 AAAATTGATACTTTTAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGGAAAATTG
1 AAAATTGATACTTTTAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGGAAAATTG
* *
9516630 ATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTAAAATTTATTTTTAAGGAAAATTGATACTT
66 ATACTTTCAACTTTTCCTCAAAAA-TTATTTTTTGAAAATTTATTTTCAAGGAAAATTGATACTT
9516695 TCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGG
130 TCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGG
*
9516740 AAAATTGATATTTTTAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGGAAAATTG
1 AAAATTGATACTTTTAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGGAAAATTG
* * *
9516805 ATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGGAAACTTTTATTTTCGAGGAAAATTGATACT
66 ATACTTTCAACTTTTCCTCAAAAATTATTTTTT-GAAA-ATTTATTTTCAAGGAAAATTGATACT
**
9516869 TTCAACTTTTCTTCAAAAATATTTTTTGAAACTTTTAATTTCGAGG
129 TTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGG
* *
9516915 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTAAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTTAACTTTTCCTCAAAAATCTTTTTTTT-AAAATTTATTTTTAAGGAAAATT
* * *
9516980 GATATTTTCAACTTTTCCTCAAAAACTTTTTTTTTTGAAAATTTTTTTT
65 GATACTTTCAACTTTTCCTCAAAAA--TTATTTTTTGAAAATTTATTTT
9517029 TTTTTTTAGA
Statistics
Matches: 259, Mismatches: 24, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
173 8 0.03
174 3 0.01
175 185 0.71
176 45 0.17
177 7 0.03
178 4 0.02
179 7 0.03
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (174 bp):
AAAATTGATACTTTTAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGGAAAATTG
ATACTTTCAACTTTTCCTCAAAAATTATTTTTTGAAAATTTATTTTCAAGGAAAATTGATACTTT
CAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGG
Found at i:9517031 original size:16 final size:16
Alignment explanation
Indices: 9517001--9517030 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9516991 CTTTTCCTCA
9517001 AAAACTTTTTTTTTTG
1 AAAACTTTTTTTTTTG
9517017 AAAA-TTTTTTTTTT
1 AAAACTTTTTTTTTT
9517031 TTTTTAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
AAAACTTTTTTTTTTG
Found at i:9519182 original size:20 final size:20
Alignment explanation
Indices: 9519154--9519224 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
9519144 AAAAGAAAAT
9519154 AAATAAAAAAAATAAATCATA
1 AAATAAAAAAAA-AAATCATA
* *
9519175 AAATAAAAATAAAAATGATA
1 AAATAAAAAAAAAAATCATA
* *
9519195 AATATGAAATAACAAAATC-TA
1 AA-AT-AAAAAAAAAAATCATA
9519216 AAATAAAAA
1 AAATAAAAA
9519225 TGAATAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 4 0.10
20 11 0.27
21 17 0.41
22 9 0.22
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATAAAAAAAAAAATCATA
Found at i:9519184 original size:27 final size:26
Alignment explanation
Indices: 9519154--9519206 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
9519144 AAAAGAAAAT
9519154 AAATAAAAAAAATAAATCATAAAATAA
1 AAATAAAAAAAATAAAT-ATAAAATAA
** *
9519181 AAATAAAAATGATAAATATGAAATAA
1 AAATAAAAAAAATAAATATAAAATAA
9519207 CAAAATCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (26 bp):
AAATAAAAAAAATAAATATAAAATAA
Found at i:9519189 original size:12 final size:13
Alignment explanation
Indices: 9519149--9519190 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
9519139 TAATCAAAAG
*
9519149 AAAATAAATAAAA
1 AAAATAAATAATA
*
9519162 AAAATAAATCAT-
1 AAAATAAATAATA
9519174 AAAATAAA-AATA
1 AAAATAAATAATA
9519186 AAAAT
1 AAAAT
9519191 GATAAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 2 0.08
12 13 0.52
13 10 0.40
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:9519596 original size:15 final size:14
Alignment explanation
Indices: 9519570--9519608 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
9519560 AGAGGTAATT
9519570 TTTTTATTTTTTTTC
1 TTTTT-TTTTTTTTC
*
9519585 TTGTTTTTTTTTTTG
1 TT-TTTTTTTTTTTC
9519600 TTTTTTTTT
1 TTTTTTTTT
9519609 AAAGCTCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 12 0.55
16 3 0.14
ACGTcount: A:0.03, C:0.03, G:0.05, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:9519608 original size:12 final size:12
Alignment explanation
Indices: 9519568--9519608 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
9519558 ACAGAGGTAA
*
9519568 TTTTTTTATTTT
1 TTTTTTTGTTTT
*
9519580 TTTTCTTGTTTT
1 TTTTTTTGTTTT
9519592 TTTTTTTGTTTT
1 TTTTTTTGTTTT
9519604 TTTTT
1 TTTTT
9519609 AAAGCTCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.02, C:0.02, G:0.05, T:0.90
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:9519669 original size:41 final size:41
Alignment explanation
Indices: 9519612--9520039 Score: 642
Period size: 41 Copynumber: 10.4 Consensus size: 41
9519602 TTTTTTTAAA
* * *
9519612 GCTCCTCTAAACAGAGGCTCAACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
** *
9519653 GCTCCTCTAAACAGAGGCACCGTGACTTTGAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
9519694 ACTCCTTTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
9519735 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
9519776 GCTCCTCTAAACAGAGGAACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
9519817 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* *
9519859 GCTCCTTTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * * *
9519900 ACTCTTCTAAACAGAAGCACCACGATTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
9519941 GCTCCTCTAAACAGAGACACCACGACTTT-AGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
*
9519982 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
9520023 GCTCCTCTAAATAGAGG
1 GCTCCTCTAAACAGAGG
9520040 TAACGGAACT
Statistics
Matches: 349, Mismatches: 35, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
40 1 0.00
41 308 0.88
42 40 0.11
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:9519965 original size:206 final size:205
Alignment explanation
Indices: 9519612--9520039 Score: 687
Period size: 206 Copynumber: 2.1 Consensus size: 205
9519602 TTTTTTTAAA
* * **
9519612 GCTCCTCTAAACAGAGGCTCAACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCGTG
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
* *
9519677 ACTTTGAAAATTAAATTACTCCTTTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTC
66 ACTTTGAAAAATAAATTACTCCTTTAAACAGAAGCACCACGACTTTGAAAAGTAAATTGCTCCTC
* * * *
9519742 TAAACAGAGGCACCACGACTTTGGAAATTAAATTGCTCCTCTAAACAGAGGAACCACGACTTTGG
131 TAAACAGAGACACCACGACTTTAGAAAGTAAATTGCTCCTCTAAACAGAGGAACCACGACTTTGA
*
9519807 AAAGTAAATT
196 AAAATAAATT
* *
9519817 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACAACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
9519882 GACTTTGAAAAATAAATTACT-CTTCTAAACAGAAGCACCACGATTTTGAAAAGTAAATTGCTCC
65 GACTTTGAAAAATAAATTACTCCTT-TAAACAGAAGCACCACGACTTTGAAAAGTAAATTGCTCC
*
9519946 TCTAAACAGAGACACCACGACTTTAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
129 TCTAAACAGAGACACCACGACTTTAGAAAGTAAATTGCTCCTCTAAACAGAGGAACCACGACTTT
9520011 GAAAAATAAATT
194 GAAAAATAAATT
*
9520023 GCTCCTCTAAATAGAGG
1 GCTCCTCTAAACAGAGG
9520040 TAACGGAACT
Statistics
Matches: 205, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
205 27 0.13
206 178 0.87
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (205 bp):
GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAATAAATTACTCCTTTAAACAGAAGCACCACGACTTTGAAAAGTAAATTGCTCCTC
TAAACAGAGACACCACGACTTTAGAAAGTAAATTGCTCCTCTAAACAGAGGAACCACGACTTTGA
AAAATAAATT
Found at i:9520417 original size:43 final size:42
Alignment explanation
Indices: 9520365--9520446 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
9520355 TTTGGCAAAC
* * *
9520365 TTGGAATTCATATCCAAAAA-TCTAAAGCTTTTCGTTTGAATT
1 TTGGAATTCACATCCAAAAATTC-AAAGCTTCTCATTTGAATT
9520407 TTGGAGATTCACATCCAAAAATTCAAAGCTTCTCATTTGA
1 TTGGA-ATTCACATCCAAAAATTCAAAGCTTCTCATTTGA
9520447 GTTCAAATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 5 0.14
43 28 0.80
44 2 0.06
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATTCAAAGCTTCTCATTTGAATT
Found at i:9521792 original size:21 final size:21
Alignment explanation
Indices: 9521766--9521811 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
9521756 AATTTGAATA
*
9521766 TTTTTTGTTCATTT-TCTCTTT
1 TTTTTTCTTC-TTTCTCTCTTT
*
9521787 TTTTTTCTTCTTTCTTTCTTT
1 TTTTTTCTTCTTTCTCTCTTT
9521808 TTTT
1 TTTT
9521812 CTTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTCTTCTTTCTCTCTTT
Found at i:9521826 original size:8 final size:8
Alignment explanation
Indices: 9521777--9521829 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
9521767 TTTTTGTTCA
*
9521777 TTTTCTCT
1 TTTTCTTT
9521785 TTTT-TTT
1 TTTTCTTT
*
9521792 TCTTCTTT
1 TTTTCTTT
*
9521800 CTTTCTTT
1 TTTTCTTT
9521808 TTTTCTTTTT
1 TTTTC--TTT
9521818 TTTTCTTT
1 TTTTCTTT
9521826 TTTT
1 TTTT
9521830 AATCATCTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 5 0.14
8 24 0.65
10 8 0.22
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTCTTT
Found at i:9526558 original size:233 final size:232
Alignment explanation
Indices: 9526151--9526658 Score: 790
Period size: 233 Copynumber: 2.2 Consensus size: 232
9526141 TTTTGTGTAG
** *
9526151 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTTTCCAAAAATATT-TTTTGAAACTTTAATTTAGAGAAAAAT
** *
9526216 TGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTAAAATTTATTTTTAAAGAAAATTGATAC
65 TGATACTTTCAACTTTTCCTCAAAAACCTATTTTTTGAAAATTTATTTTTAAAGAAAATTGATAC
* *
9526281 TTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTGATATTTTAAAC
130 TTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTGATACTTTAAAC
9526346 TTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAA
195 TTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAA
*
9526384 GGAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGGAAACTTTTATTTTAGA-AGAAA
1 GGAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTT-GAAAC-TTTAATTTAGAGA-AAA
9526448 ATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTGAAAATTTATTTTT-AAGAAAAATTGA
63 ATTGATACTTTCAACTTTTCCTCAAAAACCTATTTTTTGAAAATTTATTTTTAAAG-AAAATTGA
* *
9526511 TACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTGATGCTTTC
127 TACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTGATACTTTA
*
9526576 AACTTTTCCTTAAAAATCTTTTTTTTAAAATTTATTTTTAA
192 AACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAA
* * *
9526617 GAAAAATTGATATTTTCAACTTTTCTT-CAAAATTTATTTTTT
1 GGAAAATTGATACTTTCAACTTTT-TTCCAAAA-ATATTTTTT
9526659 TTTAGAAAAA
Statistics
Matches: 254, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
232 7 0.03
233 196 0.77
234 51 0.20
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (232 bp):
GGAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAACTTTAATTTAGAGAAAAATT
GATACTTTCAACTTTTCCTCAAAAACCTATTTTTTGAAAATTTATTTTTAAAGAAAATTGATACT
TTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTGATACTTTAAACT
TTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAA
Found at i:9526641 original size:116 final size:116
Alignment explanation
Indices: 9526153--9526641 Score: 786
Period size: 117 Copynumber: 4.2 Consensus size: 116
9526143 TTGTGTAGGG
9526153 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAAC-TTTAATTTCGAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATT-TTTTGAAACTTTTAATTTCGAGAAAAATT
*
9526217 GATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTAAAATTTATTTTTAA-A
65 GATACTTTCAACTTTTCCTCAAAAATCT-TTTTTTTAAAATTTATTTTTAAGA
*
9526269 GAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATT
1 -AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATT
* * *
9526334 GATATTTTAAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGG
65 GATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGA
** * *
9526386 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGGAAACTTTTATTTTAGA-AGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAACTTTTAATTTCGAGA-AAAAT
* *
9526450 TGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTGAAAATTTATTTTTAAGA
64 TGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGA
9526503 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTG
* *
9526568 ATGCTTTCAACTTTTCCTTAAAAATCTTTTTTTTAAAATTTATTTTTAAGA
66 ATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGA
*
9526619 AAAATTGATATTTTCAACTTTTC
1 AAAATTGATACTTTCAACTTTTC
9526642 TTCAAAATTT
Statistics
Matches: 345, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
116 161 0.47
117 184 0.53
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGAAAAATTG
ATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGA
Found at i:9526659 original size:58 final size:57
Alignment explanation
Indices: 9526153--9526658 Score: 563
Period size: 58 Copynumber: 8.7 Consensus size: 57
9526143 TTGTGTAGGG
* * * **
9526153 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATT-TTTTGAAAATTTATTTTTAAGA
*
9526211 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTAAAATTTATTTTTAA-A
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAAATTTATTTTTAAGA
* * **
9526269 GAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGAAACTTTTAATTTCGAGA
1 -AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTGAAA-ATTTATTTTTAAGA
* * * * *
9526328 AAAATTGATATTTTAAACTTTTCCTCAAAAATCTTTTTTTTAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTGAAAATTTATTTTTAAGA
* * *
9526386 AAAATTGATACTTTCAACTTTT-TTCCAAAAATATTTTTTGGAAACTTTTATTTTAGAAG-
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTT-GAAA-ATTTATTTT-TAAGA
9526445 AAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAAATTTATTTTTAAGA
* * * **
9526503 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAACTTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAA-ATTTATTTTTAAGA
* * * *
9526561 AAAATTGATGCTTTCAACTTTTCCTTAAAAATCTTTTTTTTAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTGAAAATTTATTTTTAAGA
* * *
9526619 AAAATTGATATTTTCAACTTTTCTTCAAAATTTATTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAA-ATATTTTTT
9526659 TTTAGAAAAA
Statistics
Matches: 378, Mismatches: 50, Indels: 40
0.81 0.11 0.09
Matches are distributed among these distances:
56 1 0.00
57 37 0.10
58 220 0.58
59 99 0.26
60 20 0.05
61 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTATTTTTAAGA
Found at i:9528841 original size:20 final size:21
Alignment explanation
Indices: 9528799--9528868 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
9528789 CAAAAGAAAA
9528799 AAAATAAAGAAAATAAATCAT
1 AAAATAAAGAAAATAAATCAT
*
9528820 AAAATAAA-AATAA-AAATGAT
1 AAAATAAAGAA-AATAAATCAT
* *
9528840 AAATATGAAATAACA-AAATC-T
1 AAA-AT-AAAGAAAATAAATCAT
9528861 AAAATAAA
1 AAAATAAA
9528869 AATGAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
19 3 0.07
20 13 0.31
21 16 0.38
22 8 0.19
23 2 0.05
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAATAAAGAAAATAAATCAT
Found at i:9528850 original size:26 final size:27
Alignment explanation
Indices: 9528794--9528852 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
9528784 ATAATCAAAA
9528794 GAAA-AAAAATAAAGAAAATAAATCAT
1 GAAATAAAAATAAAGAAAATAAATCAT
* *
9528820 AAAATAAAAATAAA-AATGATAAAT-AT
1 GAAATAAAAATAAAGAA-AATAAATCAT
9528846 GAAATAA
1 GAAATAA
9528853 CAAAATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.19
Consensus pattern (27 bp):
GAAATAAAAATAAAGAAAATAAATCAT
Found at i:9535064 original size:15 final size:15
Alignment explanation
Indices: 9535043--9535077 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9535033 TTACTTTGTT
*
9535043 AAATGTATTGAATGA
1 AAATGTAATGAATGA
*
9535058 GAATGTAATGAATGA
1 AAATGTAATGAATGA
9535073 AAATG
1 AAATG
9535078 CATGCATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (15 bp):
AAATGTAATGAATGA
Found at i:9538426 original size:57 final size:57
Alignment explanation
Indices: 9538347--9538557 Score: 203
Period size: 57 Copynumber: 3.7 Consensus size: 57
9538337 TATTTTAAGG
* ** * * * ** *
9538347 AAAATTGGTACTTCCAAC-TTTTCTCCAAAATGTTTTTCTTGAACTTTAATTTCGAAA
1 AAAATTGATACTTTTAACATTTTCTCAAAAATATTTTT-TAGAAAATTAATTTCAAAA
* *
9538404 AAAATTGATACTTTT-ACATTTTCCTCAAAAATATTTTTTAGAAAATTATTTTTAAAA
1 AAAATTGATACTTTTAACATTTT-CTCAAAAATATTTTTTAGAAAATTAATTTCAAAA
* * * * **
9538461 AAAATTGATATTTTTAACTTTTTCTCGAAAATATTTTTTAGAAAACTTATTTTCAAGG
1 AAAATTGATACTTTTAACATTTTCTCAAAAATATTTTTTAGAAAA-TTAATTTCAAAA
*
9538519 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT
1 AAAATTGATACTTTTAACATTTT-CTCAAAAATATTTTTT
9538558 TTAGAATTTT
Statistics
Matches: 129, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
56 2 0.02
57 68 0.53
58 59 0.46
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTTAACATTTTCTCAAAAATATTTTTTAGAAAATTAATTTCAAAA
Found at i:9538484 original size:58 final size:58
Alignment explanation
Indices: 9538396--9538557 Score: 229
Period size: 58 Copynumber: 2.8 Consensus size: 58
9538386 TGAACTTTAA
*
9538396 TTTCGAAAAAAATTGATACTTTT-ACATTTTCCTCAAAAATATTTTTTAGAAAA-TTAT
1 TTTCAAAAAAAATTGATACTTTTAAC-TTTTCCTCAAAAATATTTTTTAGAAAACTTAT
* * * *
9538453 TTTTAAAAAAAATTGATATTTTTAACTTTTTCTCGAAAATATTTTTTAGAAAACTTAT
1 TTTCAAAAAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTAGAAAACTTAT
** *
9538511 TTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 TTTCAAAAAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTT
9538558 TTAGAATTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
57 45 0.49
58 46 0.51
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (58 bp):
TTTCAAAAAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTAGAAAACTTAT
Found at i:9538941 original size:20 final size:20
Alignment explanation
Indices: 9538908--9538957 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
9538898 TTCTTCGGAT
9538908 TTCCCTTCTCTTTTC-CTCTCC
1 TTCCCTT-TCTTTTCTC-CTCC
9538929 TTCCCTTTCTTTTCTCCTCC
1 TTCCCTTTCTTTTCTCCTCC
*
9538949 TTCTCTTTC
1 TTCCCTTTC
9538958 AACAATCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (20 bp):
TTCCCTTTCTTTTCTCCTCC
Found at i:9539402 original size:3 final size:3
Alignment explanation
Indices: 9539394--9539436 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
9539384 ATGAAGTCAA
9539394 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9539437 GAAAAAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9539454 original size:20 final size:20
Alignment explanation
Indices: 9539429--9539520 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 20
9539419 ATAATAATAA
9539429 TAAT-AATAGAAAAAATATAT
1 TAATAAATA-AAAAAATATAT
*
9539449 TAATAAATAAATAAATATAT
1 TAATAAATAAAAAAATATAT
* *
9539469 TAAT---T-GATAAATA-A-
1 TAATAAATAAAAAAATATAT
*
9539483 TAAT-ATTAAAAAAATATAT
1 TAATAAATAAAAAAATATAT
* *
9539502 TTATAAATAAATAAATATA
1 TAATAAATAAAAAAATATA
9539521 AATACAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 4 0.07
15 1 0.02
16 8 0.14
17 7 0.12
18 1 0.02
19 3 0.05
20 30 0.52
21 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
TAATAAATAAAAAAATATAT
Found at i:9539513 original size:16 final size:16
Alignment explanation
Indices: 9539455--9539514 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
9539445 ATATTAATAA
*
9539455 ATAAATAAATATATTA
1 ATAAATAAATATATTT
**
9539471 ATTGATAAATAATAATATT
1 ATAAATAAAT-AT-AT-TT
9539490 A-AAA-AAATATATTT
1 ATAAATAAATATATTT
9539504 ATAAATAAATA
1 ATAAATAAATA
9539515 AATATAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
14 3 0.09
15 5 0.15
16 15 0.44
17 6 0.18
18 3 0.09
19 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAAATAAATATATTT
Found at i:9546362 original size:16 final size:16
Alignment explanation
Indices: 9546326--9546366 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
9546316 AAGTTCTGTT
9546326 TATTAAT-ATTAAAAC
1 TATTAATAATTAAAAC
9546341 TAATTAATAATTAAATA-
1 T-ATTAATAATTAAA-AC
9546358 TATTAATAA
1 TATTAATAA
9546367 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 7 0.30
18 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTAATAATTAAAAC
Found at i:9546404 original size:22 final size:20
Alignment explanation
Indices: 9546365--9546407 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
9546355 ATATATTAAT
*
9546365 AAGAAAAAAAATAAAAAAGC
1 AAGAAAAAAAAAAAAAAAGC
9546385 AAGAAAAAAAGAAAACAAAAGC
1 AAGAAAAAAA-AAAA-AAAAGC
9546407 A
1 A
9546408 GAGGGCTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAAAAAAAAAAGC
Found at i:9546481 original size:31 final size:32
Alignment explanation
Indices: 9546443--9546502 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
9546433 CGCCTCCTGT
* *
9546443 CCAGCCA-CACCTACAATCTACCCTAGCCCGA
1 CCAGCCACCACCTACAACCTACCCCAGCCCGA
*
9546474 CCAGCCACCCCCTACAACCTACCCCAGCC
1 CCAGCCACCACCTACAACCTACCCCAGCC
9546503 ACTCCCTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.27, C:0.55, G:0.08, T:0.10
Consensus pattern (32 bp):
CCAGCCACCACCTACAACCTACCCCAGCCCGA
Found at i:9548110 original size:7 final size:7
Alignment explanation
Indices: 9548075--9548194 Score: 75
Period size: 7 Copynumber: 17.1 Consensus size: 7
9548065 TAAAAAAAAT
9548075 ACCCTAA
1 ACCCTAA
9548082 ATCCTCTAA
1 A-CC-CTAA
9548091 ACCCTAA
1 ACCCTAA
*
9548098 A-ACTAA
1 ACCCTAA
9548104 ACCCTAA
1 ACCCTAA
*
9548111 A-ACTAA
1 ACCCTAA
*
9548117 ACCATAA
1 ACCCTAA
*
9548124 AACCTCAA
1 ACCCT-AA
9548132 ACCCTAA
1 ACCCTAA
** *
9548139 AATCAAA
1 ACCCTAA
9548146 ACCCTAA
1 ACCCTAA
*
9548153 ACACTAA
1 ACCCTAA
9548160 ACCCTAA
1 ACCCTAA
** *
9548167 AATCAAA
1 ACCCTAA
*
9548174 ACCTTAA
1 ACCCTAA
*
9548181 ACCTTAA
1 ACCCTAA
9548188 A-CCTAA
1 ACCCTAA
9548194 A
1 A
9548195 ACCAAACCAT
Statistics
Matches: 84, Mismatches: 24, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
6 15 0.18
7 54 0.64
8 10 0.12
9 5 0.06
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (7 bp):
ACCCTAA
Found at i:9548149 original size:14 final size:13
Alignment explanation
Indices: 9548087--9548202 Score: 117
Period size: 14 Copynumber: 8.5 Consensus size: 13
9548077 CCTAAATCCT
9548087 CTAAACCCTAAAA
1 CTAAACCCTAAAA
9548100 CTAAACCCTAAAA
1 CTAAACCCTAAAA
*
9548113 CTAAACCATAAAA
1 CTAAACCCTAAAA
9548126 CCTCAAACCCTAAAA
1 -CT-AAACCCTAAAA
*
9548141 TCAAAACCCTAAACA
1 -CTAAACCCTAAA-A
9548156 CTAAACCCTAAAA
1 CTAAACCCTAAAA
* * *
9548169 TCAAAACCTTAAAC
1 -CTAAACCCTAAAA
9548183 CTTAAA-CCTAAAA
1 C-TAAACCCTAAAA
*
9548196 CCAAACC
1 CTAAACC
9548203 ATTAAAGGCC
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
12 3 0.04
13 34 0.40
14 36 0.42
15 12 0.14
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.16
Consensus pattern (13 bp):
CTAAACCCTAAAA
Found at i:9548154 original size:28 final size:27
Alignment explanation
Indices: 9548089--9548200 Score: 129
Period size: 28 Copynumber: 4.1 Consensus size: 27
9548079 TAAATCCTCT
* *
9548089 AAACCCTAAAACTAAACCCTAAAA-CT
1 AAACCCTAAACCTAAACCCTAAAATCA
*
9548115 AAACCATAAAACCTCAAACCCTAAAATCA
1 AAACCCT-AAACCT-AAACCCTAAAATCA
9548144 AAACCCTAAACACTAAACCCTAAAATCA
1 AAACCCTAAAC-CTAAACCCTAAAATCA
* *
9548172 AAACCTTAAACCTTAAA-CCTAAAACCA
1 AAACCCTAAACC-TAAACCCTAAAATCA
9548199 AA
1 AA
9548201 CCATTAAAGG
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.08
27 17 0.23
28 43 0.57
29 9 0.12
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.15
Consensus pattern (27 bp):
AAACCCTAAACCTAAACCCTAAAATCA
Found at i:9548319 original size:13 final size:14
Alignment explanation
Indices: 9548301--9548330 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9548291 CATCGAAACT
9548301 CCAAACCC-TAAAA
1 CCAAACCCTTAAAA
9548314 CCAAACCCTTAAAA
1 CCAAACCCTTAAAA
9548328 CCA
1 CCA
9548331 TAGATCCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (14 bp):
CCAAACCCTTAAAA
Found at i:9548418 original size:15 final size:15
Alignment explanation
Indices: 9548364--9548419 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
9548354 CAAAACTCTT
9548364 AAAA-TCTAAAATCC
1 AAAATTCTAAAATCC
* ** *
9548378 CAAACCCTAAAATTC
1 AAAATTCTAAAATCC
9548393 AAAACTT-TAAAATCC
1 AAAA-TTCTAAAATCC
9548408 AAAATTCTAAAA
1 AAAATTCTAAAA
9548420 ACCCTAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 5 0.16
15 27 0.84
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATTCTAAAATCC
Found at i:9548429 original size:38 final size:38
Alignment explanation
Indices: 9548340--9548427 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
9548330 ATAGATCCTC
* * * * *
9548340 AAAACCTTGAAATCCAAAACTCTTAAAATCTAAAATCC
1 AAAACCCTAAAATTCAAAACTCTTAAAATCCAAAATCA
*
9548378 CAAACCCTAAAATTCAAAACT-TTAAAATCCAAAATTCTA
1 AAAACCCTAAAATTCAAAACTCTTAAAATCCAAAA-TC-A
9548417 AAAACCCTAAA
1 AAAACCCTAAA
9548428 TTTAGCACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
37 12 0.29
38 19 0.46
39 10 0.24
ACGTcount: A:0.52, C:0.24, G:0.01, T:0.23
Consensus pattern (38 bp):
AAAACCCTAAAATTCAAAACTCTTAAAATCCAAAATCA
Found at i:9550255 original size:17 final size:17
Alignment explanation
Indices: 9550229--9550262 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9550219 AGCATTATCC
*
9550229 AATAAGAAAAAAAAAAG
1 AATAACAAAAAAAAAAG
*
9550246 AATAACAAAAAATAAAG
1 AATAACAAAAAAAAAAG
9550263 GTTTATCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AATAACAAAAAAAAAAG
Found at i:9556283 original size:22 final size:22
Alignment explanation
Indices: 9556248--9556294 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
9556238 GTCAATTCTG
* *
9556248 TAAGACCTCCGGGTATGATTTT
1 TAAGACCTCCGGGTATAATCTT
**
9556270 TAAGACCTTTGGGTATAATCTT
1 TAAGACCTCCGGGTATAATCTT
9556292 TAA
1 TAA
9556295 AAGCTTCGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (22 bp):
TAAGACCTCCGGGTATAATCTT
Found at i:9556662 original size:37 final size:35
Alignment explanation
Indices: 9556592--9557088 Score: 210
Period size: 37 Copynumber: 13.6 Consensus size: 35
9556582 ATCTTCGATT
* * *
9556592 GATTCTTTAATTTTGACTCACGCTATTGTCCCAGTC
1 GATTCTTT-ATTTTGACTTACGGTGTTGTCCCAGTC
9556628 GATTCTTTATTTCTCGACTTACGGTGTTGTCCCAGTC
1 GATTCTTTATTT-T-GACTTACGGTGTTGTCCCAGTC
*** *
9556665 GATTCTTTAATTTTGACTCGTGGTGTTG-CCTTAGTC
1 GATTCTTT-ATTTTGACTTACGGTGTTGTCC-CAGTC
*
9556701 GATTCTTTATTTTTCGACTTACGGTGTTGTCTCAGTC
1 GATTCTTTA-TTTT-GACTTACGGTGTTGTCCCAGTC
* * * *
9556738 GATTCATTAATTTTGACTCACGGTATTGTCCCAATC
1 GATTC-TTTATTTTGACTTACGGTGTTGTCCCAGTC
* * * ** * * *
9556774 AATTATTTATTTCTTGATTTACAATATTAT-CCTGATC
1 GATTCTTTA-TT-TTGACTTACGGTGTTGTCCCAG-TC
* * * * *
9556811 GATTCTTTATTTTTCAACTTACGATGTTATCTCAATC
1 GATTCTTTA-TTTT-GACTTACGGTGTTGTCCCAGTC
* ** *
9556848 GATTCTTTAATTTTGACTTGCAATGTTGTCCCAATC
1 GATTCTTT-ATTTTGACTTACGGTGTTGTCCCAGTC
* * * *** * * * *
9556884 AATTCTATATTTCTCAACTTGTAGTGTTATCTCAATT
1 GATTCTTTATTT-T-GACTTACGGTGTTGTCCCAGTC
* ** *
9556921 GATTCTTTAATCTTGACTTACAATATTGTCCCAGTC
1 GATTCTTT-ATTTTGACTTACGGTGTTGTCCCAGTC
* * * *** *
9556957 AATTCTTTAATTTTGATTTGCGGTGTTGTCTTGGTT
1 GATTCTTT-ATTTTGACTTACGGTGTTGTCCCAGTC
* * * *
9556993 GATTCTTTACTTTTTAACTTGCAGT-TTCATCCC-GATC
1 GATTCTTTA--TTTTGACTTACGGTGTT-GTCCCAG-TC
* * * *
9557030 AATTCTTTATCTTCTGACTTACGGTATTGTCTCAGTT
1 GATTCTTTAT-TT-TGACTTACGGTGTTGTCCCAGTC
9557067 GATTCTTTATTTTTTGACTTAC
1 GATTCTTTA--TTTTGACTTAC
9557089 AGTATTATCC
Statistics
Matches: 346, Mismatches: 88, Indels: 53
0.71 0.18 0.11
Matches are distributed among these distances:
35 16 0.05
36 137 0.40
37 174 0.50
38 18 0.05
39 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (35 bp):
GATTCTTTATTTTGACTTACGGTGTTGTCCCAGTC
Done.