Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold354
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1097647
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.30
Warning! 124483 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:678 original size:21 final size:21
Alignment explanation
Indices: 654--819 Score: 210
Period size: 21 Copynumber: 7.9 Consensus size: 21
644 ATTTATATTT
*
654 AAGTTTCGCGTTTAATCGCGA
1 AAGTTTCGCGTTTATTCGCGA
*
675 AAGTTTCGCGTTTAGTCGCGA
1 AAGTTTCGCGTTTATTCGCGA
* **
696 AACTAACGCG-TTATATCGCGA
1 AAGTTTCGCGTTTAT-TCGCGA
717 AAGTTTCGCGTTTATTCGCGA
1 AAGTTTCGCGTTTATTCGCGA
* *
738 AAGTTACGCGTTTATTCGAGA
1 AAGTTTCGCGTTTATTCGCGA
*
759 AAGTTTCGCGTTTATTTGCGA
1 AAGTTTCGCGTTTATTCGCGA
* *
780 AACTTACGCGTTTAATT-GCGA
1 AAGTTTCGCGTTT-ATTCGCGA
801 AAGTTTCGCGTTTATTCGC
1 AAGTTTCGCGTTTATTCGC
820 AAAAAAAAAA
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
20 6 0.05
21 111 0.90
22 7 0.06
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
AAGTTTCGCGTTTATTCGCGA
Found at i:1076 original size:4 final size:4
Alignment explanation
Indices: 1067--1152 Score: 172
Period size: 4 Copynumber: 21.5 Consensus size: 4
1057 TCTTCAGTAC
1067 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1115 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
1153 TGACTTGGAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:5233 original size:18 final size:18
Alignment explanation
Indices: 5196--5235 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5186 AACACTAAAC
* *
5196 TAAAAACTATATAATATA
1 TAAAAACTAAAAAATATA
*
5214 TAAAAACTAAAAAATGTA
1 TAAAAACTAAAAAATATA
5232 TAAA
1 TAAA
5236 CACCGGATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAAACTAAAAAATATA
Found at i:8622 original size:2 final size:2
Alignment explanation
Indices: 8615--8640 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8605 ACAACACTAT
8615 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
8641 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11180 original size:11 final size:11
Alignment explanation
Indices: 11164--11195 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
11154 GCAATACATA
11164 TAGCTTAAAGG
1 TAGCTTAAAGG
11175 TAGCTTAAAGG
1 TAGCTTAAAGG
*
11186 TGGCTTAAAG
1 TAGCTTAAAG
11196 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:11217 original size:11 final size:11
Alignment explanation
Indices: 11201--11239 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
11191 TAAAGATCGT
11201 CTTTAAGCTAC
1 CTTTAAGCTAC
*
11212 CTTTAAAC-AC
1 CTTTAAGCTAC
*
11222 CTTTAAGCTAT
1 CTTTAAGCTAC
11233 CTTTAAG
1 CTTTAAG
11240 GAGGACTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:15849 original size:22 final size:21
Alignment explanation
Indices: 15819--15965 Score: 117
Period size: 19 Copynumber: 7.1 Consensus size: 21
15809 CAAAAAATAT
*
15819 TTTTGAATTTGATATAACGAA
1 TTTTGAATTTGTTATAACGAA
*
15840 TTCTTGAATTTGTTAAAACGAA
1 TT-TTGAATTTGTTATAACGAA
*
15862 -TTTGAA-TCGTTATAACGAA
1 TTTTGAATTTGTTATAACGAA
** *
15881 TTTTTGAATCCGTTATTACGAA
1 -TTTTGAATTTGTTATAACGAA
* *
15903 --TTAAATTTGTTATAACAAA
1 TTTTGAATTTGTTATAACGAA
*
15922 TTTTAGGAATTCGTTATAACGAA
1 TTTT--GAATTTGTTATAACGAA
* *
15945 -TTT-AATCTGTTATAACAAA
1 TTTTGAATTTGTTATAACGAA
15964 TT
1 TT
15966 CGATGAATTC
Statistics
Matches: 100, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
19 38 0.38
20 6 0.06
21 11 0.11
22 31 0.31
23 14 0.14
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (21 bp):
TTTTGAATTTGTTATAACGAA
Found at i:15956 original size:42 final size:42
Alignment explanation
Indices: 15831--15980 Score: 162
Period size: 42 Copynumber: 3.6 Consensus size: 42
15821 TTGAATTTGA
* * * *
15831 TATAACGAATTCT-TGAATTTGTTAAAACGAATTTGAATC-GT
1 TATAACAAATTTTATGAATTCGTTATAACGAATTT-AATCTGT
* * * * *
15872 TATAACGAATTTT-TGAATCCGTTATTACGAATTAAATTTGT
1 TATAACAAATTTTATGAATTCGTTATAACGAATTTAATCTGT
*
15913 TATAACAAATTTTAGGAATTCGTTATAACGAATTTAATCTGT
1 TATAACAAATTTTATGAATTCGTTATAACGAATTTAATCTGT
**
15955 TATAACAAATTCGATGAATTCGTTAT
1 TATAACAAATTTTATGAATTCGTTAT
15981 TTCAAAGTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
40 3 0.03
41 42 0.46
42 46 0.51
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (42 bp):
TATAACAAATTTTATGAATTCGTTATAACGAATTTAATCTGT
Found at i:17668 original size:21 final size:21
Alignment explanation
Indices: 17637--17694 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
17627 TCTATCCATA
* * *
17637 ACCCCTCACCAAGGTCTGTGT
1 ACCCATCACCAGGGTCTGTAT
*
17658 GCCCATCACCAGGGTCTGTAT
1 ACCCATCACCAGGGTCTGTAT
17679 ACCCATCACCAGGGTC
1 ACCCATCACCAGGGTC
17695 AGAGTACGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (21 bp):
ACCCATCACCAGGGTCTGTAT
Found at i:17710 original size:21 final size:21
Alignment explanation
Indices: 17683--17736 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
17673 CTGTATACCC
17683 ATCACCAGGGTCAGAGTACGT
1 ATCACCAGGGTCAGAGTACGT
* * ** *
17704 ATTACCAGAGTGGGTGTACGT
1 ATCACCAGGGTCAGAGTACGT
17725 ATCACCAGGGTC
1 ATCACCAGGGTC
17737 TGTATATGCA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (21 bp):
ATCACCAGGGTCAGAGTACGT
Found at i:18025 original size:21 final size:21
Alignment explanation
Indices: 18001--18110 Score: 58
Period size: 21 Copynumber: 5.1 Consensus size: 21
17991 ATATACAGAA
18001 TCAGTATACCCATCACCAGGG
1 TCAGTATACCCATCACCAGGG
* * * *
18022 TCAGTTTACCTATAACCAAGG
1 TCAGTATACCCATCACCAGGG
* * * * * *
18043 TTAGTGTACACAATTACAAGTG
1 TCAGTATAC-CCATCACCAGGG
* * * *
18065 TACATGTATACGCGTTACCAGAG
1 T-CA-GTATACCCATCACCAGGG
*
18088 TCAGTATACCCATCACCTGGG
1 TCAGTATACCCATCACCAGGG
18109 TC
1 TC
18111 TCAATACCTA
Statistics
Matches: 63, Mismatches: 23, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
21 39 0.62
22 10 0.16
23 9 0.14
24 5 0.08
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (21 bp):
TCAGTATACCCATCACCAGGG
Found at i:18252 original size:21 final size:21
Alignment explanation
Indices: 18228--18295 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
18218 TGGGCACAGA
18228 GACCCTGGTAATACG-ATCACT
1 GACCCTGGTAATACGTA-CACT
*
18249 GACCCTGGTGATACGTACACT
1 GACCCTGGTAATACGTACACT
* * *
18270 GACCCTGATGATATGTACACT
1 GACCCTGGTAATACGTACACT
18291 GACCC
1 GACCC
18296 AGGTTATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GACCCTGGTAATACGTACACT
Found at i:19808 original size:42 final size:41
Alignment explanation
Indices: 19758--19907 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 41
19748 AAAATTTGAA
** *
19758 ATAACGAATTCAGCGAATTTGTTATAACAGATTAAATTCGTG
1 ATAACGAATTCA-AAAATTCGTTATAACAGATTAAATTCGTG
* * * *
19800 ATAACGAATTCCTAAAAATT-GTTAAAACAAATTTAATTCGTT
1 ATAACGAATT-C-AAAAATTCGTTATAACAGATTAAATTCGTG
*
19842 ATAACGGATTCAAAAATTCGTTATAAC-GATTTAAATTCGTTG
1 ATAACGAATTCAAAAATTCGTTATAACAGA-TTAAATTCG-TG
* *
19884 -TAACAAATTCAAGAATTCGTTATA
1 ATAACGAATTCAAAAATTCGTTATA
19908 TCAAATTCAA
Statistics
Matches: 89, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
40 8 0.09
41 37 0.42
42 38 0.43
43 5 0.06
44 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (41 bp):
ATAACGAATTCAAAAATTCGTTATAACAGATTAAATTCGTG
Found at i:19859 original size:22 final size:22
Alignment explanation
Indices: 19834--19921 Score: 92
Period size: 22 Copynumber: 4.1 Consensus size: 22
19824 AAACAAATTT
**
19834 AATTCGTTATAACGGATTCAAA
1 AATTCGTTATAACAAATTCAAA
* *
19856 AATTCGTTATAAC-GATT--TA
1 AATTCGTTATAACAAATTCAAA
* *
19875 AATTCGTTGTAACAAATTCAAG
1 AATTCGTTATAACAAATTCAAA
*
19897 AATTCGTTATATCAAATTCAAA
1 AATTCGTTATAACAAATTCAAA
19919 AAT
1 AAT
19922 ATTTTTTGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
19 13 0.24
20 3 0.05
21 4 0.07
22 35 0.64
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (22 bp):
AATTCGTTATAACAAATTCAAA
Found at i:19879 original size:19 final size:20
Alignment explanation
Indices: 19773--19907 Score: 73
Period size: 19 Copynumber: 6.5 Consensus size: 20
19763 GAATTCAGCG
*
19773 AATTTGTTATAACAGA-TTA
1 AATTCGTTATAACAGATTTA
*
19792 AATTCGTGATAAC-GAATTCCTAAA
1 AATTCGTTATAACAG-ATT--T--A
* *
19816 AATT-GTTAAAACAAATTT-
1 AATTCGTTATAACAGATTTA
* *
19834 AATTCGTTATAACGGATTCAAA
1 AATTCGTTATAACAGATT--TA
19856 AATTCGTTATAAC-GATTTA
1 AATTCGTTATAACAGATTTA
* * *
19875 AATTCGTTGTAACAAATTCAA
1 AATTCGTTATAACAGATT-TA
19896 GAATTCGTTATA
1 -AATTCGTTATA
19908 TCAAATTCAA
Statistics
Matches: 88, Mismatches: 14, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
18 5 0.06
19 35 0.40
20 4 0.05
21 6 0.07
22 24 0.27
23 9 0.10
24 5 0.06
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
AATTCGTTATAACAGATTTA
Found at i:19894 original size:41 final size:42
Alignment explanation
Indices: 19759--19907 Score: 146
Period size: 41 Copynumber: 3.6 Consensus size: 42
19749 AAATTTGAAA
** *
19759 TAACGAATTCAGCGAATTTGTTATAACAGA-TTAAATTCG-TG
1 TAACGAATTCA-AAAATTCGTTATAACAGATTTAAATTCGTTG
* * *
19800 ATAACGAATTCCTAAAAATT-GTTAAAACAAATTT-AATTCGTTA
1 -TAACGAATT-C-AAAAATTCGTTATAACAGATTTAAATTCGTTG
*
19843 TAACGGATTCAAAAATTCGTTATAAC-GATTTAAATTCGTTG
1 TAACGAATTCAAAAATTCGTTATAACAGATTTAAATTCGTTG
* *
19884 TAACAAATTCAAGAATTCGTTATA
1 TAACGAATTCAAAAATTCGTTATA
19908 TCAAATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
40 11 0.12
41 37 0.42
42 32 0.36
43 8 0.09
44 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (42 bp):
TAACGAATTCAAAAATTCGTTATAACAGATTTAAATTCGTTG
Found at i:26386 original size:12 final size:12
Alignment explanation
Indices: 26369--26398 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
26359 TTTTTCTTGC
*
26369 GTGTGTGTGTTT
1 GTGTGTGTGTAT
26381 GTGTGTGTGTAT
1 GTGTGTGTGTAT
26393 GTGTGT
1 GTGTGT
26399 CTGTCTGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.00, G:0.43, T:0.53
Consensus pattern (12 bp):
GTGTGTGTGTAT
Found at i:26437 original size:16 final size:16
Alignment explanation
Indices: 26396--26440 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
26386 TGTGTATGTG
26396 TGTCTGTCTGTCCCTT
1 TGTCTGTCTGTCCCTT
** *
26412 TGTCCCTCTGTCCTTT
1 TGTCTGTCTGTCCCTT
26428 TGTCTGTCTGTCC
1 TGTCTGTCTGTCC
26441 GTAACAAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.18, T:0.49
Consensus pattern (16 bp):
TGTCTGTCTGTCCCTT
Found at i:33723 original size:2 final size:2
Alignment explanation
Indices: 33718--33765 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
33708 TAACACACAC
* *
33718 AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33760 AT AT AT
1 AT AT AT
33766 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:36932 original size:52 final size:53
Alignment explanation
Indices: 36870--36984 Score: 178
Period size: 53 Copynumber: 2.2 Consensus size: 53
36860 ACGTTTGAGA
* *
36870 TTTGCCGGCATCT-AAGAATTGCCGGCAAATCAAATATAACTCGTGGTTACTT
1 TTTGCCGGCATCTCAAGAATTGCCGGCAAATCAAACACAACTCGTGGTTACTT
* *
36922 TTTGCCGGCATTTCAGGAATTGCCGGCAAATCAAACACAACTCGTGGTTACTT
1 TTTGCCGGCATCTCAAGAATTGCCGGCAAATCAAACACAACTCGTGGTTACTT
36975 TTTGTCCGGC
1 TTTG-CCGGC
36985 CCATATCGGC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
52 12 0.21
53 40 0.70
54 5 0.09
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (53 bp):
TTTGCCGGCATCTCAAGAATTGCCGGCAAATCAAACACAACTCGTGGTTACTT
Found at i:44841 original size:17 final size:18
Alignment explanation
Indices: 44819--44852 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44809 TCAATAAATG
*
44819 ATTAATATATAC-ATCAT
1 ATTAATAAATACGATCAT
44836 ATTAATAAATACGATCA
1 ATTAATAAATACGATCA
44853 ATCAATTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (18 bp):
ATTAATAAATACGATCAT
Found at i:55721 original size:2 final size:2
Alignment explanation
Indices: 55714--55740 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55704 NNNNNNNNNN
55714 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55741 GATAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70935 original size:4 final size:4
Alignment explanation
Indices: 70926--70988 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
70916 AATCTCTCCC
70926 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
70974 TCTA TCTA TCTA TCT
1 TCTA TCTA TCTA TCT
70989 CTGTCTGTCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.24, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:73885 original size:13 final size:14
Alignment explanation
Indices: 73860--73888 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
73850 GCTTTGCATA
73860 AACAAAAACAATTC
1 AACAAAAACAATTC
73874 AACAAAAA-AATTC
1 AACAAAAACAATTC
73887 AA
1 AA
73889 TGATATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (14 bp):
AACAAAAACAATTC
Found at i:89891 original size:11 final size:11
Alignment explanation
Indices: 89875--89900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
89865 CAGAAACTCA
89875 AAAAGGTAGAT
1 AAAAGGTAGAT
89886 AAAAGGTAGAT
1 AAAAGGTAGAT
89897 AAAA
1 AAAA
89901 AGAGTCAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (11 bp):
AAAAGGTAGAT
Found at i:89901 original size:12 final size:12
Alignment explanation
Indices: 89874--89902 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
89864 GCAGAAACTC
89874 AAAAAGGTAGAT
1 AAAAAGGTAGAT
89886 -AAAAGGTAGAT
1 AAAAAGGTAGAT
89897 AAAAAG
1 AAAAAG
89903 AGTCAAGCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (12 bp):
AAAAAGGTAGAT
Found at i:95184 original size:39 final size:39
Alignment explanation
Indices: 95130--95282 Score: 279
Period size: 39 Copynumber: 3.9 Consensus size: 39
95120 ACAGATTAAT
95130 GTCAAAGTATATTTAAGATTATTACCGAGACCCATTGTA
1 GTCAAAGTATATTTAAGATTATTACCGAGACCCATTGTA
95169 GTCAAAGTATATTTAAGATTATTACCGAGACCCATTGTA
1 GTCAAAGTATATTTAAGATTATTACCGAGACCCATTGTA
*
95208 GTCAAAGTATATTTAAGATTATTACCGAGATCCATTGTA
1 GTCAAAGTATATTTAAGATTATTACCGAGACCCATTGTA
* *
95247 GTCAAAGTATATTTAAGATTATTACAGAAACCCATT
1 GTCAAAGTATATTTAAGATTATTACCGAGACCCATT
95283 ATATTAAAGA
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (39 bp):
GTCAAAGTATATTTAAGATTATTACCGAGACCCATTGTA
Found at i:97552 original size:46 final size:46
Alignment explanation
Indices: 97481--97631 Score: 162
Period size: 46 Copynumber: 3.3 Consensus size: 46
97471 AATAAATTTC
*
97481 ACGTCACACAACATTGAGTCT-ACTCACCAATGAGTGTAGCCATCAT
1 ACGTCACACAACATTGAGT-TAACTCACCAATGAGTGTAGTCATCAT
* * * * * * * *
97527 ATGTCACACAACATTAAGTTAACTCACTAATAAAT-TAATTAATTAT
1 ACGTCACACAACATTGAGTTAACTCACCAATGAGTGT-AGTCATCAT
* * *
97573 ACGTCATACAACATTGAGTCAACTCACCAATGAGTGTAGTCGTCAT
1 ACGTCACACAACATTGAGTTAACTCACCAATGAGTGTAGTCATCAT
97619 ACGTCACACAACA
1 ACGTCACACAACA
97632 GTGGTCATCA
Statistics
Matches: 81, Mismatches: 21, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
45 2 0.02
46 78 0.96
47 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (46 bp):
ACGTCACACAACATTGAGTTAACTCACCAATGAGTGTAGTCATCAT
Found at i:98478 original size:2 final size:2
Alignment explanation
Indices: 98471--98504 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
98461 AATTTGCTGC
98471 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
98505 TTACACGTGA
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):
AG
Found at i:99475 original size:57 final size:57
Alignment explanation
Indices: 99387--99503 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
99377 AATATTATTT
99387 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTTCA
1 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTTCA
99444 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTTCA
1 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTTCA
99501 TTA
1 TTA
99504 TTATTATTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.48
Consensus pattern (57 bp):
TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTTCA
Found at i:99515 original size:22 final size:23
Alignment explanation
Indices: 99485--99527 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
99475 CTTGTTATTC
99485 TATTGTTTCTTTTTCATTATTAT
1 TATTGTTTCTTTTTCATTATTAT
*
99508 TATT-TTTCTTTTTCTTTATT
1 TATTGTTTCTTTTTCATTATT
99528 TTTCTGACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (23 bp):
TATTGTTTCTTTTTCATTATTAT
Found at i:106006 original size:167 final size:161
Alignment explanation
Indices: 105730--106083 Score: 492
Period size: 167 Copynumber: 2.2 Consensus size: 161
105720 CTTGGAAACA
* *
105730 TCTGCAAAGAAAATGAACTGAAACTGCAAATAATTGGAATTTTTCTACATCCAAGAGGCATAACT
1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAATTGGAATTTTTCTACATCCAAGAGGCATAACT
* * **
105795 CTGTCGAAAATTGCTTGATCGTACCCAAAATCAAACTTGACCTAGATATTATTAAGATAAACCTG
66 CTGTCGAAAATTGCTCGATCGTACCCAAAATCAAACTTGACCTAGATACTATTAAGATAAACAAG
*
105860 TATACCAAATTTCATTTCAATATGTGCATCC
131 TATACCAAATTTCATTTCAATAAGTGCATCC
* * *
105891 TCTGCGAAGAAAATAAACGGAAACTGCAAATAATTGGAATTTTTCTACGTCCAAGGGGCATACAT
1 TCTGCGAAGAAAATGAACGGAAACTGCAAATAATTGGAATTTTTCTACATCCAAGAGG----CA-
* ** *
105956 GTAACTCTGTCGAAAATTGCTCGATTGTACCCAAAATTGAACTTGACCTAGATACTATTATGATA
61 -TAACTCTGTCGAAAATTGCTCGATCGTACCCAAAATCAAACTTGACCTAGATACTATTAAGATA
* *
106021 AACAAGTATACTAAATTTCATTTCAATAAGTGTATCC
125 AACAAGTATACCAAATTTCATTTCAATAAGTGCATCC
* *
106058 TCTGTGAAGAAAATGAATGGAAACTG
1 TCTGCGAAGAAAATGAACGGAAACTG
106084 TTGGTGAACC
Statistics
Matches: 168, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
161 53 0.32
165 2 0.01
167 113 0.67
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (161 bp):
TCTGCGAAGAAAATGAACGGAAACTGCAAATAATTGGAATTTTTCTACATCCAAGAGGCATAACT
CTGTCGAAAATTGCTCGATCGTACCCAAAATCAAACTTGACCTAGATACTATTAAGATAAACAAG
TATACCAAATTTCATTTCAATAAGTGCATCC
Found at i:111179 original size:17 final size:17
Alignment explanation
Indices: 111135--111179 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
111125 TCCGAAAAAT
111135 AAAA-GCGAGATTTTCA
1 AAAATGCGAGATTTTCA
** *
111151 AATCTGCCAGATTTTCA
1 AAAATGCGAGATTTTCA
111168 AAAATGCGAGAT
1 AAAATGCGAGAT
111180 GTTCTTCTGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (17 bp):
AAAATGCGAGATTTTCA
Found at i:120870 original size:14 final size:14
Alignment explanation
Indices: 120851--120877 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
120841 TAAAGTTAGC
120851 TACTAGTAACTGGT
1 TACTAGTAACTGGT
120865 TACTAGTAACTGG
1 TACTAGTAACTGG
120878 CTACGAGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
TACTAGTAACTGGT
Found at i:120913 original size:37 final size:37
Alignment explanation
Indices: 120865--121005 Score: 185
Period size: 37 Copynumber: 3.8 Consensus size: 37
120855 AGTAACTGGT
*
120865 TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGT
1 TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGC
* * ** *
120902 TACTAGTAACTGGCTACGAG-ATTAAATAAAAATTGGC
1 TACTAGTAACTGGCTACGAGAAGT-AAGAAAAGCTAGC
*
120939 TACTAGTAACTGGCTACAAGAAGTAAGAAAAGCTAGC
1 TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGC
* *
120976 TACTAGTAACTGGCTACGAGATGAAAGAAA
1 TACTAGTAACTGGCTACGAGAAGTAAGAAA
121006 CTTGGCTTCT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.02
37 83 0.95
38 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (37 bp):
TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGC
Found at i:121982 original size:177 final size:177
Alignment explanation
Indices: 121765--122449 Score: 796
Period size: 177 Copynumber: 3.9 Consensus size: 177
121755 CTTCAAGGGT
*
121765 TGCTAATATCAACATTCCT-TCAAGTCACCCACATAATATTACGACACAATTACTCAGATATCTC
1 TGCTAATATCAACATT-CTATCAAGTCATCCACATAATATTACGACACAATTACTCAGATATCTC
121829 TCATT-ATGTAGTAAGCTACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGACGGTTTTGTC
65 TC-TTAATGTAGTAAGCTACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGACGGTTTTGTC
121893 AATATATCTCAAGAAGCTGTATATATAAATTGAAGATATATGCCAGACA
129 AATATATCTCAAGAAGCTGTATATATAAATTGAAGATATATGCCAGACA
* * * * *
121942 TGCTTATATCAATATTCCT-TCAAATCATCCACATAATATTACGACACATTTACTTAGATATCTC
1 TGCTAATATCAACATT-CTATCAAGTCATCCACATAATATTACGACACAATTACTCAGATATCTC
* * * * * * *
122006 TCTTTATGAAGTCAGCAACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGGCAGTTTTTTCA
65 TCTTAATGTAGTAAGCTACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGACGGTTTTGTCA
* * * * *
122071 ATATATCTCAAGTAGCTGTATATATAGATTGAAGATATACGCCAGTCT
130 ATATATCTCAAGAAGCTGTATATATAAATTGAAGATATATGCCAGACA
* * *
122119 TTCTAATATCAACATTCTGTCAACTCATCCACATAATATTACGACACAATTACTCAGATATCTCT
1 TGCTAATATCAACATTCTATCAAGTCATCCACATAATATTACGACACAATTACTCAGATATCTCT
* * * * *
122184 CTTCATGTAGTCAA-CTATTAGTGCATTTTGTTACAAATATATTTATTTTTTGGCGGTGTTGTCA
66 CTTAATGTAGT-AAGCTACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGACGGTTTTGTCA
* * * * * **
122248 ATATATCTCAAGTAGCTGTATATATTAATTGAAGATATCT-ACAAATG
130 ATATATCTCAAGAAGCTGTATATATAAATTGAAGATATATGCCAGACA
* * * * *
122295 TGGTCAATTTGAACATTCTAT-AAGGTCA-CCTACATGATATTACGACACAATTACTCAGATATA
1 TGCT-AATATCAACATTCTATCAA-GTCATCC-ACATAATATTACGACACAATTACTCAGATATC
* * * ** * * *
122358 TCT-TTAAAGCTCGTCAGCTACTAGTAAATTATGTTACAATTATCTTTATTTTTT-AGGGTTTTG
63 TCTCTTAATG-TAGTAAGCTACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGACGGTTTTG
*
122421 TCAACATATCTCAAGTAA-CTGTATATATA
127 TCAATATATCTCAAG-AAGCTGTATATATA
122450 GATTCATAAG
Statistics
Matches: 434, Mismatches: 65, Indels: 19
0.84 0.13 0.04
Matches are distributed among these distances:
176 47 0.11
177 386 0.89
178 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (177 bp):
TGCTAATATCAACATTCTATCAAGTCATCCACATAATATTACGACACAATTACTCAGATATCTCT
CTTAATGTAGTAAGCTACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGACGGTTTTGTCAA
TATATCTCAAGAAGCTGTATATATAAATTGAAGATATATGCCAGACA
Found at i:122395 original size:354 final size:353
Alignment explanation
Indices: 121767--122453 Score: 906
Period size: 354 Copynumber: 1.9 Consensus size: 353
121757 TCAAGGGTTG
*
121767 CTAATATCAACATTCCTTCAAGTCACCCACATAATATTACGACACAATTACTCAGATATCTCTCA
1 CTAATATCAACATTCCTTCAACTCACCCACATAATATTACGACACAATTACTCAGATATCTCTCA
* *
121832 TTATGTAGTAAGCTACTAGTGCATTTTGTTACAAATATCTTTATTTTTTGACGGTTTTGTCAATA
66 TTATGTAGTAAGCTACTAGTGCATTTTGTTACAAATATATTTATTTTTTGACGGTGTTGTCAATA
* * * *
121897 TATCTCAAGAAGCTGTATATATAAATTGAAGATATATGCCAGACATGCTTATATCAATATTCCTT
131 TATCTCAAGAAGCTGTATATATAAATTGAAGATATATGACAAACATGCTAATATCAACATTCCTT
* * * * *
121962 CAAATCATCCACATAATATTACGACACATTTACTTAGATATCTCTCTTTATGAAGTCAGCAACTA
196 CAAATCATCCACATAATATTACGACACAATTACTCAGATATATCTCTTAAAGAAGTCAGCAACTA
** * * * *
122027 GTGCATTTTGTTACAAATATCTTTATTTTTT-GGCAGTTTTTTCAATATATCTCAAGTAGCTGTA
261 GTAAATTATGTTACAAATATCTTTATTTTTTAGG--GTTTTGTCAACATATCTCAAGTAACTGTA
122091 TATATAGATTGAAGATATACGCCAGTCTTT
324 TATATAGATTGAAGATATACGCCAGTCTTT
*
122121 CTAATATCAACATT-CTGTCAACTCATCCACATAATATTACGACACAATTACTCAGATATCTCTC
1 CTAATATCAACATTCCT-TCAACTCACCCACATAATATTACGACACAATTACTCAGATATCTCTC
* *
122185 -TTCATGTAGTCAA-CTATTAGTGCATTTTGTTACAAATATATTTATTTTTTGGCGGTGTTGTCA
65 ATT-ATGTAGT-AAGCTACTAGTGCATTTTGTTACAAATATATTTATTTTTTGACGGTGTTGTCA
* * * ** * * *
122248 ATATATCTCAAGTAGCTGTATATATTAATTGAAGATATCT-ACAAATGTGGTCAATTTGAACATT
128 ATATATCTCAAGAAGCTGTATATATAAATTGAAGATATATGACAAACATGCT-AATATCAACATT
* * **
122312 -CTAT-AAGGTCA-CCTACATGATATTACGACACAATTACTCAGATATATCT-TTAAAGCTCGTC
192 CCT-TCAA-ATCATCC-ACATAATATTACGACACAATTACTCAGATATATCTCTTAAAG-AAGTC
* *
122373 AGCTACTAGTAAATTATGTTACAATTATCTTTATTTTTTAGGGTTTTGTCAACATATCTCAAGTA
253 AGCAACTAGTAAATTATGTTACAAATATCTTTATTTTTTAGGGTTTTGTCAACATATCTCAAGTA
122438 ACTGTATATATAGATT
318 ACTGTATATATAGATT
122454 CATAAGATTG
Statistics
Matches: 289, Mismatches: 35, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
353 56 0.19
354 229 0.79
355 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (353 bp):
CTAATATCAACATTCCTTCAACTCACCCACATAATATTACGACACAATTACTCAGATATCTCTCA
TTATGTAGTAAGCTACTAGTGCATTTTGTTACAAATATATTTATTTTTTGACGGTGTTGTCAATA
TATCTCAAGAAGCTGTATATATAAATTGAAGATATATGACAAACATGCTAATATCAACATTCCTT
CAAATCATCCACATAATATTACGACACAATTACTCAGATATATCTCTTAAAGAAGTCAGCAACTA
GTAAATTATGTTACAAATATCTTTATTTTTTAGGGTTTTGTCAACATATCTCAAGTAACTGTATA
TATAGATTGAAGATATACGCCAGTCTTT
Found at i:123181 original size:10 final size:11
Alignment explanation
Indices: 123166--123194 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
123156 TTACTTTTAA
123166 GGTTTACTC-G
1 GGTTTACTCTG
123176 GGTTTACTCTG
1 GGTTTACTCTG
123187 GGTTTACT
1 GGTTTACT
123195 TTTTGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.10, C:0.17, G:0.28, T:0.45
Consensus pattern (11 bp):
GGTTTACTCTG
Found at i:123232 original size:11 final size:11
Alignment explanation
Indices: 123218--123260 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
123208 GGTCCTTTCA
123218 GGGTTTACTTT
1 GGGTTTACTTT
**
123229 GGGTTTACTCG
1 GGGTTTACTTT
*
123240 GGGTTAACTTT
1 GGGTTTACTTT
123251 GGGTTTACTT
1 GGGTTTACTT
123261 GGAAATTGCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.30, T:0.47
Consensus pattern (11 bp):
GGGTTTACTTT
Found at i:123243 original size:22 final size:22
Alignment explanation
Indices: 123218--123259 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
123208 GGTCCTTTCA
*
123218 GGGTTTACTTTGGGTTTACTCG
1 GGGTTAACTTTGGGTTTACTCG
123240 GGGTTAACTTTGGGTTTACT
1 GGGTTAACTTTGGGTTTACT
123260 TGGAAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.45
Consensus pattern (22 bp):
GGGTTAACTTTGGGTTTACTCG
Found at i:126735 original size:15 final size:15
Alignment explanation
Indices: 126715--126744 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
126705 CCTAGGTGGG
126715 GGACTCCGAGACTCA
1 GGACTCCGAGACTCA
*
126730 GGACTCGGAGACTCA
1 GGACTCCGAGACTCA
126745 AATCCTGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (15 bp):
GGACTCCGAGACTCA
Found at i:128016 original size:177 final size:177
Alignment explanation
Indices: 127705--128038 Score: 445
Period size: 177 Copynumber: 1.9 Consensus size: 177
127695 AACCCATCAC
* *
127705 AAAATAAAGACATTTGTAACAAAATGTTGATATTAGCTGACGACATAAAGAGAGATATCTGAGTA
1 AAAATAAAGACATTTGTAACAAAATG-TCATAGTAGCTGACGACATAAAGAGAGATATCTGAGTA
* * * * * * *** *
127770 ATTGTGTCGTAATATTATGTGGATGACTTGAAGGAATGTTGATATTAGCTATACTGGCTTATTTC
65 ATTGTGTCGTAATATGATGTGGATGACTTGAAGGAATCTTGATATGAACAACACTGGAAGATGTC
* *
127835 TTTAATCTGTATATACAGCTACTTGAGATATATTGACAAAACCGCCAA
130 TTTAATCTCTATATACAGCTACCTGAGATATATTGACAAAACCGCCAA
* * * *
127883 AAAATAAATATATTTGTAACAAAATG-CACTAGTAGCTGACTACATAAAGAGATATATCTGAGTA
1 AAAATAAAGACATTTGTAACAAAATGTCA-TAGTAGCTGACGACATAAAGAGAGATATCTGAGTA
* *
127947 ATTGTGTCGTAATATGATGTGGATGACTTGAAGGAATCTTGATATGAACAACCCTTGAAGATGTC
65 ATTGTGTCGTAATATGATGTGGATGACTTGAAGGAATCTTGATATGAACAACACTGGAAGATGTC
* *
128012 TTTAATCTCTATTTACGGCTACCTGAG
130 TTTAATCTCTATATACAGCTACCTGAG
128039 TTGCATGAAC
Statistics
Matches: 133, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
176 1 0.01
177 108 0.81
178 24 0.18
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (177 bp):
AAAATAAAGACATTTGTAACAAAATGTCATAGTAGCTGACGACATAAAGAGAGATATCTGAGTAA
TTGTGTCGTAATATGATGTGGATGACTTGAAGGAATCTTGATATGAACAACACTGGAAGATGTCT
TTAATCTCTATATACAGCTACCTGAGATATATTGACAAAACCGCCAA
Found at i:128783 original size:21 final size:20
Alignment explanation
Indices: 128759--128871 Score: 138
Period size: 21 Copynumber: 5.4 Consensus size: 20
128749 CTGTGTCACC
*
128759 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGAT-CTTATGTCG
128780 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATCTT-ATGTCG
128801 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATCTT-ATGTCG
*
128822 ACTTGTCAGATCTTTAT-ACTG
1 ACTTGTCAGATC-TTATGTC-G
*
128843 ACTTGTCTGATCTTTATGTCG
1 ACTTGTCAGATC-TTATGTCG
128864 ACTTGTCA
1 ACTTGTCA
128872 CTTATCCACG
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
20 3 0.04
21 77 0.93
22 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
ACTTGTCAGATCTTATGTCG
Found at i:128974 original size:21 final size:21
Alignment explanation
Indices: 128948--129102 Score: 136
Period size: 21 Copynumber: 7.4 Consensus size: 21
128938 CATAATATTT
128948 TCTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
128969 TCTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
* * *
128990 TCTAAAAAGTCGACATAATCA
1 TCTGACAAGTCGACATAATTA
*** *
129011 TCTTTTAAGTCGACATCACTT-
1 TCTGACAAGTCGACAT-AATTA
* *
129032 TCT-AGCTAGTCGTCATAATTA
1 TCTGA-CAAGTCGACATAATTA
*
129053 TCTGACAAGTTGACATAATT-
1 TCTGACAAGTCGACATAATTA
* * * *
129073 TCCTTACAAGTCAACATCATAA
1 T-CTGACAAGTCGACATAATTA
129095 TCTGACAA
1 TCTGACAA
129103 AGCGACTCAA
Statistics
Matches: 106, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
20 4 0.04
21 98 0.92
22 4 0.04
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (21 bp):
TCTGACAAGTCGACATAATTA
Found at i:129084 original size:63 final size:63
Alignment explanation
Indices: 128932--129102 Score: 152
Period size: 63 Copynumber: 2.7 Consensus size: 63
128922 TGTGCCTCCC
*
128932 AGTTGACATAATATTTTCTGACAAGTCGACAT-AATTATCTGACAAGTCGACATAATTATCTAAA
1 AGTTGACAT-A-A-TTTCTTACAAGTCGACATCAATTATCTGACAAGTCGACATAATTATCTAAA
128996 A
63 A
* * ** * * * * *
128997 AGTCGACATAATCATCTTTTAAGTCGACATCACTT-TCT-AGCTAGTCGTCATAATTATCTGACA
1 AGTTGACATAAT-TTCTTACAAGTCGACATCAATTATCTGA-CAAGTCGACATAATTATCTAAAA
* *
129060 AGTTGACATAATTTCCTTACAAGTCAACATC-ATAATCTGACAA
1 AGTTGACATAATTT-CTTACAAGTCGACATCAATTATCTGACAA
129103 AGCGACTCAA
Statistics
Matches: 82, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
62 4 0.05
63 65 0.79
64 5 0.06
65 8 0.10
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (63 bp):
AGTTGACATAATTTCTTACAAGTCGACATCAATTATCTGACAAGTCGACATAATTATCTAAAA
Found at i:130033 original size:165 final size:166
Alignment explanation
Indices: 129727--130107 Score: 504
Period size: 165 Copynumber: 2.3 Consensus size: 166
129717 TTTATAATTC
* * * *
129727 TTTAGCCTGAATGTTCAAACAAATTTTCGTCATAGATTTCTCAGCAACTATTTATTGCAGATGCT
1 TTTAGCCTAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATTGCAGAAGCT
* * * *
129792 TGACATTTTAATACACTATTTGTTGAGGCATGCCATAACGTGGCAAATATTTTTGTACCAATCGC
66 TGACAATATAACACACTATTTGTTGAGGCATGCCATAACGTGGCAAATATGTTTGTACCAATCGC
* * *
129857 ATGTCAACTTCCTGTTAAATAATGCCTTTGTTTATT
131 ACGTCAACTTCCTGTTAAATAACGACTTTGTTTATT
*
129893 ATTTAGCCTAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATTGCAGAAGC
1 -TTTAGCCTAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATTGCAGAAGC
* * * *
129958 TTGA-AATAT-ACACAGTGTTTGTTGAGGCATGCCATATCGTGGCATATATGTTTGTACCAATCG
65 TTGACAATATAACACACTATTTGTTGAGGCATGCCATAACGTGGCAAATATGTTTGTACCAATCG
* * *
130021 GACGTCAACTTCCTGTTCAATGACGACTTTGTTTATT
130 CACGTCAACTTCCTGTTAAATAACGACTTTGTTTATT
* * * *
130058 TGT-G--TAAATTTT-ACACAAATTTTCGTCAAAGATTTATCAACAACTATTTA
1 TTTAGCCTAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTA
130108 AATTGAAAAA
Statistics
Matches: 190, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
160 34 0.18
161 8 0.04
163 1 0.01
164 2 0.01
165 79 0.42
166 3 0.02
167 63 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (166 bp):
TTTAGCCTAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATTGCAGAAGCT
TGACAATATAACACACTATTTGTTGAGGCATGCCATAACGTGGCAAATATGTTTGTACCAATCGC
ACGTCAACTTCCTGTTAAATAACGACTTTGTTTATT
Found at i:132175 original size:10 final size:10
Alignment explanation
Indices: 132156--132190 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
132146 ATCACATGTG
132156 GTAA-TACAT
1 GTAATTACAT
132165 GTAATTACAT
1 GTAATTACAT
*
132175 GTAATTTCAT
1 GTAATTACAT
132185 GTAATT
1 GTAATT
132191 GTGCTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (10 bp):
GTAATTACAT
Found at i:133197 original size:4 final size:4
Alignment explanation
Indices: 133178--133254 Score: 136
Period size: 4 Copynumber: 19.2 Consensus size: 4
133168 GACTTATTGA
* *
133178 ATAG CTAG ACAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
133226 ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
133255 CAGACAGACA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.49, C:0.03, G:0.25, T:0.23
Consensus pattern (4 bp):
ATAG
Found at i:135479 original size:21 final size:21
Alignment explanation
Indices: 135455--135540 Score: 118
Period size: 21 Copynumber: 4.1 Consensus size: 21
135445 CCACCTCTTT
*
135455 TCAGATAATTATGTCGACTTG
1 TCAGATAATTATGTTGACTTG
*
135476 TCAGATAATTATGTTGACCTG
1 TCAGATAATTATGTTGACTTG
* *
135497 TCAGATATTTATGTTAACTTG
1 TCAGATAATTATGTTGACTTG
**
135518 TCAGATCTTTATGTTGACTTG
1 TCAGATAATTATGTTGACTTG
135539 TC
1 TC
135541 CGAAAATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (21 bp):
TCAGATAATTATGTTGACTTG
Found at i:135644 original size:21 final size:21
Alignment explanation
Indices: 135612--135734 Score: 149
Period size: 21 Copynumber: 5.9 Consensus size: 21
135602 CACTTGTCAT
135612 CATAAT-ATCTGACAAGTCGA
1 CATAATGATCTGACAAGTCGA
*
135632 CATAATCATCTGACAAGTCGA
1 CATAATGATCTGACAAGTCGA
* *
135653 CATGATTATCTGACAAGTCGA
1 CATAATGATCTGACAAGTCGA
* *
135674 AATAAAGATCTGACAAGTCGA
1 CATAATGATCTGACAAGTCGA
* **
135695 CATAAAGATCTGACAAGTTAA
1 CATAATGATCTGACAAGTCGA
* *
135716 CATGATTATCTGACAAGTC
1 CATAATGATCTGACAAGTC
135735 TGCTTATTGA
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
20 6 0.07
21 83 0.93
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (21 bp):
CATAATGATCTGACAAGTCGA
Found at i:140342 original size:16 final size:17
Alignment explanation
Indices: 140321--140354 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
140311 TTAAATCCAT
140321 GTTTAT-TATTTCTTTG
1 GTTTATATATTTCTTTG
*
140337 GTTTATATATTTTTTTG
1 GTTTATATATTTCTTTG
140354 G
1 G
140355 AAAACCAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.68
Consensus pattern (17 bp):
GTTTATATATTTCTTTG
Found at i:145654 original size:13 final size:13
Alignment explanation
Indices: 145636--145665 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
145626 CCGTAACACC
145636 CTGTATATCCTAT
1 CTGTATATCCTAT
*
145649 CTGTATATTCTAT
1 CTGTATATCCTAT
145662 CTGT
1 CTGT
145666 TCACCTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (13 bp):
CTGTATATCCTAT
Found at i:146534 original size:29 final size:29
Alignment explanation
Indices: 146454--146549 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 29
146444 TTCCTTTCTG
**
146454 GCACAGATTCCATTAGGAATTT-TCCCCA
1 GCACAGATTCCATTAGGAATTTCTTTCCA
* * **
146482 GCACTGATT-CATTAGGAATATCTTTATA
1 GCACAGATTCCATTAGGAATTTCTTTCCA
*
146510 GCACAGATTCCATTAAGAATTTCTTTCCA
1 GCACAGATTCCATTAGGAATTTCTTTCCA
*
146539 GCACGGATTCC
1 GCACAGATTCC
146550 TTCCTTGGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
27 11 0.20
28 18 0.33
29 25 0.46
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (29 bp):
GCACAGATTCCATTAGGAATTTCTTTCCA
Found at i:148319 original size:37 final size:37
Alignment explanation
Indices: 148285--148581 Score: 303
Period size: 37 Copynumber: 8.1 Consensus size: 37
148275 GTTTGATTGG
* *
148285 TTAACAAGTATCTAAAATTGTTTTATATAATGATTAA
1 TTAACAAGTATCTAAAAGTGTTTGATATAATGATTAA
* * *
148322 TTAACAAGTACCTACAAGTGTTTGATATAATAATTAA
1 TTAACAAGTATCTAAAAGTGTTTGATATAATGATTAA
* * * * *
148359 TTTACAAG-ATCTACAATTGTTTGCTATAATAATTAA
1 TTAACAAGTATCTAAAAGTGTTTGATATAATGATTAA
* * * *
148395 TTTATAAATATCTAAAAGTGTTTGATGTAATGATTAA
1 TTAACAAGTATCTAAAAGTGTTTGATATAATGATTAA
* *
148432 -TACACAAATATCTAAAAGTGCTTGATATAATGATTAA
1 TTA-ACAAGTATCTAAAAGTGTTTGATATAATGATTAA
* * ** *
148469 TTTACAAATATCTGCAAGTGTTTGATAAAATGATTAA
1 TTAACAAGTATCTAAAAGTGTTTGATATAATGATTAA
* * * *
148506 TCAA-AATATATCTACAAGTGTTTGATGTAATGATTAA
1 TTAACAA-GTATCTAAAAGTGTTTGATATAATGATTAA
* * *
148543 TTAACAAATATCTACAAGTGTTTGATGTAATGATTAA
1 TTAACAAGTATCTAAAAGTGTTTGATATAATGATTAA
148580 TT
1 TT
148582 NNNNNNNNNN
Statistics
Matches: 224, Mismatches: 31, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
36 34 0.15
37 187 0.83
38 3 0.01
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (37 bp):
TTAACAAGTATCTAAAAGTGTTTGATATAATGATTAA
Found at i:148469 original size:74 final size:73
Alignment explanation
Indices: 148288--148580 Score: 336
Period size: 74 Copynumber: 4.0 Consensus size: 73
148278 TGATTGGTTA
* * * * *
148288 ACAAGTATCTAAAATTGTTTTATATAATGATTAATTAACAAGTACCTACAAGTGTTTGATATAAT
1 ACAAATATCTAAAAGTGTTTGATATAATGATTAATTAACAAATATCTACAAGTGTTTGATATAAT
* *
148353 AATTAATTT
66 GATTAA-TC
* * * * * * * * *
148362 AC-AAGATCTACAATTGTTTGCTATAATAATTAATTTATAAATATCTAAAAGTGTTTGATGTAAT
1 ACAAATATCTAAAAGTGTTTGATATAATGATTAATTAACAAATATCTACAAGTGTTTGATATAAT
148426 GATTAATAC
66 GATTAAT-C
* * * *
148435 ACAAATATCTAAAAGTGCTTGATATAATGATTAATTTACAAATATCTGCAAGTGTTTGATAAAAT
1 ACAAATATCTAAAAGTGTTTGATATAATGATTAATTAACAAATATCTACAAGTGTTTGATATAAT
148500 GATTAATC
66 GATTAATC
* * * *
148508 AAAATATATCTACAAGTGTTTGATGTAATGATTAATTAACAAATATCTACAAGTGTTTGATGTAA
1 ACAA-ATATCTAAAAGTGTTTGATATAATGATTAATTAACAAATATCTACAAGTGTTTGATATAA
148573 TGATTAAT
65 TGATTAAT
148581 TNNNNNNNNN
Statistics
Matches: 183, Mismatches: 33, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
72 1 0.01
73 61 0.33
74 121 0.66
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.39
Consensus pattern (73 bp):
ACAAATATCTAAAAGTGTTTGATATAATGATTAATTAACAAATATCTACAAGTGTTTGATATAAT
GATTAATC
Found at i:148539 original size:111 final size:110
Alignment explanation
Indices: 148293--148581 Score: 375
Period size: 111 Copynumber: 2.6 Consensus size: 110
148283 GGTTAACAAG
* * * * * *
148293 TATCTAAAATTGTTTTATATAATGATTAATTAACAAGTACCTACAAGTGTTTGATATAATAATTA
1 TATCTAAAAGTGTTTGATGTAATGATTAATTAACAAATATCTACAAGTGTTTGATATAATGATTA
* * * * *
148358 ATTTACAAGATCTACAATTGTTTGCTATAATAATTAATTTATAAA
66 ATTTACAAGATCTACAAGTGTTTGATAAAATAATTAATTCAAAAA
* *
148403 TATCTAAAAGTGTTTGATGTAATGATTAA-TACACAAATATCTAAAAGTGCTTGATATAATGATT
1 TATCTAAAAGTGTTTGATGTAATGATTAATTA-ACAAATATCTACAAGTGTTTGATATAATGATT
* * *
148467 AATTTACAAATATCTGCAAGTGTTTGATAAAATGATTAA-TCAAAATA
65 AATTTAC-AAGATCTACAAGTGTTTGATAAAATAATTAATTCAAAA-A
* *
148514 TATCTACAAGTGTTTGATGTAATGATTAATTAACAAATATCTACAAGTGTTTGATGTAATGATTA
1 TATCTAAAAGTGTTTGATGTAATGATTAATTAACAAATATCTACAAGTGTTTGATATAATGATTA
148579 ATT
66 ATT
148582 NNNNNNNNNN
Statistics
Matches: 155, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
109 2 0.01
110 64 0.41
111 87 0.56
112 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (110 bp):
TATCTAAAAGTGTTTGATGTAATGATTAATTAACAAATATCTACAAGTGTTTGATATAATGATTA
ATTTACAAGATCTACAAGTGTTTGATAAAATAATTAATTCAAAAA
Found at i:169587 original size:89 final size:89
Alignment explanation
Indices: 169404--169587 Score: 323
Period size: 89 Copynumber: 2.1 Consensus size: 89
169394 AATAAGAGGT
169404 CTTTTGATTTCGATACATTTTGTGTAAAAACTTATTTGTAACCGTTCTTGATTTATCTGGAAGAG
1 CTTTTGATTTCGATACATTTTGTGTAAAAACTTATTTGTAACCGTTCTTGATTTATCTGGAAGAG
*
169469 ATCATGGGAACTGATAACAAACAN
66 ATCATGGGAACTGATAACAAACAA
* *
169493 CTTTTGATTTTGATACATTTTGTGTAAAAAGTTATTTGTAACCGTTCTTGATTTATCTGGAAGAG
1 CTTTTGATTTCGATACATTTTGTGTAAAAACTTATTTGTAACCGTTCTTGATTTATCTGGAAGAG
*
169558 ATCGTGGGAACTGATAACAAACAA
66 ATCATGGGAACTGATAACAAACAA
*
169582 GTTTTG
1 CTTTTG
169588 GTTGCAGATT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (89 bp):
CTTTTGATTTCGATACATTTTGTGTAAAAACTTATTTGTAACCGTTCTTGATTTATCTGGAAGAG
ATCATGGGAACTGATAACAAACAA
Found at i:170851 original size:56 final size:55
Alignment explanation
Indices: 170769--171041 Score: 399
Period size: 56 Copynumber: 4.8 Consensus size: 55
170759 TAAGGGAAAC
* *
170769 AGAAACAAAGCAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAA
1 AGAAACAAAG-AATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAAA
170825 AGAAACAATAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAAA
1 AGAAACAA-AGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAAA
*
170881 AGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC---TAAAA
1 AGAAA-CAAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAAA
*
170934 AGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAGGGAAA
1 AGAAA-CAAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAAT-A---AAA
170994 CAGAAACAAAGCAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACC
1 -AGAAACAAAG-AATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACC
171042 TTAACTAGAG
Statistics
Matches: 202, Mismatches: 4, Indels: 17
0.91 0.02 0.08
Matches are distributed among these distances:
53 53 0.26
56 96 0.48
57 5 0.02
60 7 0.03
61 41 0.20
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (55 bp):
AGAAACAAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAAA
Found at i:170972 original size:109 final size:113
Alignment explanation
Indices: 170764--171042 Score: 426
Period size: 109 Copynumber: 2.5 Consensus size: 113
170754 AATAATAAGG
*
170764 GAAACAGAAACAAAGCAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAAAGAA
1 GAAACAGAAACAAAGCAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACC-T-ATAAAAAGAA
170829 ACAATAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAAT-A
64 ACAATAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAA
* *
170878 -AAA-AGAAACCGAAG-AATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACC-CTAAAAAGAAA
1 GAAACAGAAA-CAAAGCAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCTATAAAAAGAAA
*
170939 CCGA-AGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAA
65 -CAATAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAA
170988 GGGAAACAGAAACAAAGCAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCT
1 --GAAACAGAAACAAAGCAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCT
171043 TAACTAGAGC
Statistics
Matches: 151, Mismatches: 5, Indels: 17
0.87 0.03 0.10
Matches are distributed among these distances:
109 53 0.35
110 3 0.02
112 40 0.26
113 14 0.09
114 41 0.27
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (113 bp):
GAAACAGAAACAAAGCAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCTATAAAAAGAAAC
AATAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAA
Found at i:172640 original size:56 final size:56
Alignment explanation
Indices: 172563--172672 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 56
172553 AGTATAATAA
*
172563 TAATAAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTAAAAACGGAAGACAT
1 TAATAAAAAGAAACCAAAGAATAACAAGAGGGTCTTCCGTTAAAAACGGAAGACAT
**
172619 TAATAAAAAGAAA-CAATAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGAC
1 TAATAAAAAGAAACCAA-AGAATAACAAGAGGGTCTTCCGTTAAAAACGGAAGAC
172673 CCTAATAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 2 0.04
56 48 0.96
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.16
Consensus pattern (56 bp):
TAATAAAAAGAAACCAAAGAATAACAAGAGGGTCTTCCGTTAAAAACGGAAGACAT
Found at i:172717 original size:78 final size:78
Alignment explanation
Indices: 172623--172833 Score: 386
Period size: 78 Copynumber: 2.7 Consensus size: 78
172613 AGACATTAAT
** * *
172623 AAAAAGAAACAATAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAATAATAAT
1 AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAATAATAAT
172688 AAGGATAAGAAAA
66 AAGGATAAGAAAA
172701 AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAATAATAAT
1 AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAATAATAAT
172766 AAGGATAAGAAAA
66 AAGGATAAGAAAA
172779 AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAA
1 AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAA
172834 CAAGAAACCG
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 129 1.00
ACGTcount: A:0.51, C:0.14, G:0.20, T:0.15
Consensus pattern (78 bp):
AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAATAATAAT
AAGGATAAGAAAA
Found at i:172877 original size:52 final size:54
Alignment explanation
Indices: 172781--172945 Score: 208
Period size: 58 Copynumber: 3.0 Consensus size: 54
172771 TAAGAAAAAA
*
172781 AAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAA-
1 AAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAAG
* * * *
172834 CAAGAAACCGAAGAATATCAAGAGGGTC-TCCGTTGGAAACGGAAGACCCTAATAATAG
1 AAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCC---T-A-AG
*
172892 AAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGATGGAAAACGGAAGACCCTAA
1 AAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGG-AAACGGAAGACCCTAA
172946 TAATGACTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
52 21 0.22
53 23 0.24
55 2 0.02
56 2 0.02
57 2 0.02
58 24 0.26
59 7 0.07
60 13 0.14
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (54 bp):
AAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAAG
Found at i:172899 original size:58 final size:58
Alignment explanation
Indices: 172780--172949 Score: 226
Period size: 53 Copynumber: 3.0 Consensus size: 58
172770 ATAAGAAAAA
*
172780 AAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCC---T-A-
1 AAAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT
* * * *
172833 ACAAGAAACCGAAGAATATCAAGAGGGTC-TCCGTTGGAAACGGAAGACCCTAATAAT
1 AAAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT
*
172890 AGAAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGATGGAAAACGGAAGACCCTAATAAT
1 A-AAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGG-AAACGGAAGACCCTAATAAT
172950 GACTATCCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
52 21 0.21
53 24 0.24
55 1 0.01
56 1 0.01
57 1 0.01
58 24 0.24
59 7 0.07
60 20 0.20
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (58 bp):
AAAAGAAACCGAAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT
Found at i:181330 original size:179 final size:174
Alignment explanation
Indices: 180872--181420 Score: 682
Period size: 179 Copynumber: 3.1 Consensus size: 174
180862 GGAAATTGGA
* *
180872 GTACAATAGGGGTACCCTATATGCAATATTCTGAGAGAAAATTACTAAGTTCAA-AAGCTGGTA-
1 GTACAATAGGGGTACCATATATGCAATATTCTGAGAGAAAATGACTAAGTTCAACAA-CTGGTAT
** *
180935 TTTTTTCATAAATCCTCATAAATCAAAATCCTAGCAATATGCACACCTCCTATATATGTACAATT
65 TTTTTTCATAAATTATCAGAAATCAAAATCCTAGCAATATGCACACCT-CTATATATG----ATT
*
181000 GATCTGC--AA-AACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCC
125 GATCTGCAAAACAACAACTTCCTATCTTGAAAACTGTA-GAGGAGTTATCC
* * *
181048 GTACAATAGGGGTACCCTATATGCAATATTCTGCA-AGAATATGACTAAGTTCAACAGCTGGTAT
1 GTACAATAGGGGTACCATATATGCAATATTCTG-AGAGAAAATGACTAAGTTCAACAACTGGTAT
* * *
181112 TTTTTTCATAAATTACCAGAAATCAAAATACTAGCAATATGCACATCTCTGATATATG-TTGATC
65 TTTTTTCATAAATTATCAGAAATCAAAATCCTAGCAATATGCACACCTCT-ATATATGATTGATC
181176 TGCAAAACAACAACTTCCTATCTTGAAAACTGTACGAGGAGTTATCC
129 TGCAAAACAACAACTTCCTATCTTGAAAACTGTA-GAGGAGTTATCC
* * *
181223 GTACAATAGGGGTATCCAAAATATATACAATATTCTGTGAGAAAATGATTAAGTTCAACAACTGG
1 GTACAATAGGGGTA-CC---ATATATGCAATATTCTGAGAGAAAATGACTAAGTTCAACAACTGG
* * *
181288 TATTTTTTTCATAGATTATCAGATATCAAAATCCTTGCAATATGCACACCTTCTATATATGTACA
62 TATTTTTTTCATAAATTATCAGAAATCAAAATCCTAGCAATATGCACACC-TCTATATATG----
* *
181353 ATTGATCGGCAAAACAACAGCTTCCTATCTTGAAAACTGTAG-GGAGTTATCC
122 ATTGATCTGCAAAACAACAACTTCCTATCTTGAAAACTGTAGAGGAGTTATCC
*
181405 GTACAATAGAGGTACC
1 GTACAATAGGGGTACC
181421 TTTTTGGCAG
Statistics
Matches: 329, Mismatches: 26, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
172 9 0.03
174 2 0.01
175 51 0.16
176 60 0.18
177 51 0.16
179 89 0.27
180 3 0.01
181 2 0.01
182 23 0.07
183 1 0.00
184 38 0.12
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (174 bp):
GTACAATAGGGGTACCATATATGCAATATTCTGAGAGAAAATGACTAAGTTCAACAACTGGTATT
TTTTTCATAAATTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTATATATGATTGATCTG
CAAAACAACAACTTCCTATCTTGAAAACTGTAGAGGAGTTATCC
Found at i:185267 original size:167 final size:167
Alignment explanation
Indices: 184859--185488 Score: 992
Period size: 167 Copynumber: 3.8 Consensus size: 167
184849 GTGAATATGC
* * * * * * *
184859 AAAAGAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * * * *
184924 ATATAGCATGCCTAAACAAACACTGTGTAAAAATTTCAAGCATCTCCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTAAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
*
184989 AATCTTTGATGAAAATTTGTTTGAAAATTTTGGC-AA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAA
* * * *
185025 AAAATAAACAAAGTCATTATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * *
185090 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
*
185155 ATTCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAA
*
185192 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
*
185257 ATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
* *
185322 AATCTTTGACGAATATTTGTTTGAAAATTTTGGTTAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAA
*
185359 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * *
185424 ATATGGCATGCCTTAACAAACACTGTTTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
185489 TAAATGCGAC
Statistics
Matches: 428, Mismatches: 35, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
166 143 0.33
167 285 0.67
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (167 bp):
AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
ATATGGCATGCCTAAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAA
Found at i:200853 original size:62 final size:62
Alignment explanation
Indices: 200756--200879 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
200746 AAATGTGAGA
*
200756 GACACAAAAAATGCTGTTACATATACTATTTCTAGCATTTTGGATGCACGTCTGAAGAACAG
1 GACACAAAAAATGCTGATACATATACTATTTCTAGCATTTTGGATGCACGTCTGAAGAACAG
200818 GACACAAAAAATGCTGATACATATACTATTTCTAGCATTTTGGATGCACGTCTGAAGAACAG
1 GACACAAAAAATGCTGATACATATACTATTTCTAGCATTTTGGATGCACGTCTGAAGAACAG
200880 AACATATCAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (62 bp):
GACACAAAAAATGCTGATACATATACTATTTCTAGCATTTTGGATGCACGTCTGAAGAACAG
Found at i:202968 original size:18 final size:18
Alignment explanation
Indices: 202945--202986 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
202935 GCTATTTTGA
202945 ATAGCTTTAT-AAAGCTAT
1 ATAGCTTT-TCAAAGCTAT
*
202963 ATAGCTTTTCCAAGCTAT
1 ATAGCTTTTCAAAGCTAT
202981 ATAGCT
1 ATAGCT
202987 AAATCAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (18 bp):
ATAGCTTTTCAAAGCTAT
Found at i:207412 original size:167 final size:167
Alignment explanation
Indices: 207055--207667 Score: 716
Period size: 168 Copynumber: 3.7 Consensus size: 167
207045 CCCTTCATGT
* * * *
207055 CCTGAACCCCTGACCAAGGGGCCATGAATTCCACAA-TTTAGGTAAAGGAGATTC-TGGATATC-
1 CCTGAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTA-GTAGAGG-GCTTCATGGACATCA
** *
207117 TGAACCATATATTCAGTTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTA
64 T-AACCATGCATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGA-TTTTTAAGATTTA
*
207182 AAACACTTTTACTATATGGCCATATTGGCCCCACCCTAGAG
127 AAACACTTTTACTATATGGCCACATTGGCCCCACCCTAGAG
* * * * *
207223 CCTGAACACCTAACAAAGGGGTCATGAATTTCACAGTTTTAGTAGA-GGCTCTCATGGACATCAT
1 CCTGAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTAGTAGAGGGCT-TCATGGACATCAT
* *
207287 AACCATGTATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTAAGATCTAAAA
65 AACCATGCATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTAAGATTTAAAA
* *
207352 CAGTTTTACTATATGGCCACATTGGCCCCATCCTAGAG
130 CACTTTTACTATATGGCCACATTGGCCCCACCCTAGAG
* * * *
207390 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAATAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA
* * ** * * * * *
207455 ATCATGCATTTAGTTTTTAAC-AAGTATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
66 ACCATGCATTCAGTTTTTTGCTCA-CATGTGTGGGAGTAGAGAAGAAGATTTT-TAAGATTTAAA
* *
207519 ACATTTTTACTATTTGGCCACATTGGCCCCACCCTAGAG
129 ACACTTTTACTATATGGCCACATTGGCCCCACCCTAGAG
* ** * * * *
207558 CCAGAACCCCTGACCCTGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTTATGGATATCATA
1 CCTGAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA
* * * * *
207623 ACCATGCA-ACTGGTTTTTTCCTCACATGCGTGGGATTAGAGAAGA
66 ACCATGCATTC-AGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGA
207668 TTTTTGAAAA
Statistics
Matches: 379, Mismatches: 57, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
166 3 0.01
167 148 0.39
168 222 0.59
169 6 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (167 bp):
CCTGAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA
ACCATGCATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTAAGATTTAAAAC
ACTTTTACTATATGGCCACATTGGCCCCACCCTAGAG
Found at i:216298 original size:166 final size:165
Alignment explanation
Indices: 215928--217214 Score: 1672
Period size: 166 Copynumber: 7.6 Consensus size: 165
215918 GCTTATGCTT
* * * * * *
215928 ATGATTTTCACAACGTT-AAATCTACACTACATTAGGATGCTTCAACGTAAGTGTCAGCTTTCCT
1 ATGATTTTCACAAC-TTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCT
* * *
215992 GGCTGATTGGTTTCTGAGAAGAAGATTTTTAAAATATAATCTATATTTTCCTATGTAAAAATTCG
65 GGCTGATTGGTTTCTGAGAAGAAGATTTTTAAAATTTACTCTATATATTCCTATGTAAAAATTC-
216057 ACATCCCCCCCCATTGTGGCCCCGACCTACCCCCGGGGGTC
129 A-A---CCCCCCATTGTGGCCCCGACCTACCCCCGGGGGTC
*
216098 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCCTTCCTG
1 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
* *
216163 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAATTTCA
66 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAA-ATTTACTCTATATATTCCTATGTAAAAATTCA
* *
216228 ACCCCCTATTGTGGCCCC-ACCCTACCCCCAGGGGTC
130 ACCCCCCATTGTGGCCCCGA-CCTACCCCCGGGGGTC
* * *
216264 ATGATTTTCACAACTTGGAATCTACACAACCTGAGGATGCTTCCACAAAAGTTTCAGCTTTTCTG
1 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
* *
216329 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAAATATAATCTATATATTCCTATGTAAAAATTCGA
66 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAAATTTACTCTATATATTCCTATGTAAAAATTC-A
* *
216394 CCCCCCCCCCCCCCATTGTGGCCCCGACCTACCCCTGGGGGTC
130 -------ACCCCCCATTGTGGCCCCGACCTACCCCCGGGGGTC
* *
216437 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTGCCACATAAGTTTCAGCTTTTCTG
1 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
* * *
216502 GCTGATTGGTTTCT--G-AGAAGATGTTTAAAATATAATCTATATATTCCTATGTAAAAATTCGA
66 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAAATTTACTCTATATATTCCTATGTAAAAATTC-A
* **
216564 CCCCCCCCCCCCCCATTGTGGCCCCGACCTACATCCGGGGGTC
130 -------ACCCCCCATTGTGGCCCCGACCTACCCCCGGGGGTC
* * *
216607 ATGATTTTCACAACTTGGAATTTACGCTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTTCTG
1 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
* *
216672 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAAGAATTACTCTATATATTCCAATGTAAAAATTCA
66 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAA-ATTTACTCTATATATTCCTATGTAAAAATTCA
* *
216737 A-CCCCCATCGTGGCCCC-ATCCTACCCCCAGGGGTC
130 ACCCCCCATTGTGGCCCCGA-CCTACCCCCGGGGGTC
* *
216772 ATGATTTTCACAACTTGGAATCTACACTACATGAGGATGCTTCCACATAAGTGTCAGCTTTCCTG
1 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
**
216837 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAATTTG
66 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAA-ATTTACTCTATATATTCCTATGTAAAAATTCA
*
216902 ACCCCCCATTGTGGCCCCGACCTACCCCTGGGGGTC
130 ACCCCCCATTGTGGCCCCGACCTACCCCCGGGGGTC
** * * *
216938 ATGATTTTCACAACTTTAAATCTACACTACATTAGGATGCTTCCACATAAGTGTCAGCTTTCCTG
1 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
*
217003 GCTGATTGGTTTCTGAGAAGATGATTTTTAAAGATTTACTCTATATCTATTCCTATGTAAAAAAA
66 GCTGATTGGTTTCTGAGAAGAAGATTTTTAAA-ATTTACTCTATA--TATTCCTATGT-----AA
** *
217068 AAATTGCCCCCTCCCCATTGTGGCCCC-ACCCTACCCCAGGGGGTC
123 AAATT-CAACC-CCCCATTGTGGCCCCGA-CCTACCCCCGGGGGTC
* * *
217113 ATGATTTTCACAACTTGGAATCTACACTACCTAAAGATGCTTCCACATAAGTTTCAGCTTCCCTG
1 ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
* *
217178 ACTGATTGGTTCCTGAGAAGAAGATTTTTGAAAATTT
66 GCTGATTGGTTTCTGAGAAGAAGATTTTT-AAAATTT
217215 CACAAAAATT
Statistics
Matches: 1011, Mismatches: 76, Indels: 55
0.89 0.07 0.05
Matches are distributed among these distances:
164 1 0.00
165 179 0.18
166 259 0.26
167 1 0.00
168 11 0.01
169 3 0.00
170 249 0.25
171 28 0.03
172 1 0.00
173 127 0.13
174 31 0.03
175 118 0.12
176 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (165 bp):
ATGATTTTCACAACTTGGAATCTACACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTG
GCTGATTGGTTTCTGAGAAGAAGATTTTTAAAATTTACTCTATATATTCCTATGTAAAAATTCAA
CCCCCCATTGTGGCCCCGACCTACCCCCGGGGGTC
Found at i:217393 original size:12 final size:12
Alignment explanation
Indices: 217376--217406 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
217366 TGAAAAGTTT
217376 ACAGACGGACAG
1 ACAGACGGACAG
*
217388 ACAGACGGGCAG
1 ACAGACGGACAG
217400 ACAGACG
1 ACAGACG
217407 ATAGACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:217584 original size:77 final size:77
Alignment explanation
Indices: 217457--217607 Score: 284
Period size: 77 Copynumber: 2.0 Consensus size: 77
217447 GCTCAGGTGA
217457 GCTAAAAATGAAAAGCATGAATATTATGTATGAATTAATTAAATTATTGTTAATTAAACAACTAA
1 GCTAAAAATGAAAAGCATGAATATTATGTATGAATTAATTAAATTATTGTTAATTAAACAACTAA
217522 TTATATAACGGG
66 TTATATAACGGG
* *
217534 GCTAAAAATGAAAAGCATGAATATTTTGTATGATTTAATTAAATTATTGTTAATTAAACAACTAA
1 GCTAAAAATGAAAAGCATGAATATTATGTATGAATTAATTAAATTATTGTTAATTAAACAACTAA
217599 TTATATAAC
66 TTATATAAC
217608 AGGGTTTGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (77 bp):
GCTAAAAATGAAAAGCATGAATATTATGTATGAATTAATTAAATTATTGTTAATTAAACAACTAA
TTATATAACGGG
Found at i:219258 original size:24 final size:24
Alignment explanation
Indices: 219231--219276 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
219221 CAAATCAAAC
219231 AGATACTGTCATTCTGAGGACATG
1 AGATACTGTCATTCTGAGGACATG
* *
219255 AGATACTGTTATTCTGGGGACA
1 AGATACTGTCATTCTGAGGACA
219277 GTTTACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (24 bp):
AGATACTGTCATTCTGAGGACATG
Found at i:226870 original size:2 final size:2
Alignment explanation
Indices: 226863--226911 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
226853 TGTTTTATAT
226863 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
226905 TC TC TC T
1 TC TC TC T
226912 TCGGTGAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:231757 original size:2 final size:2
Alignment explanation
Indices: 231750--231804 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
231740 TTTATTACAA
231750 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
231792 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
231805 ATGCCTTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:243095 original size:23 final size:24
Alignment explanation
Indices: 243065--243110 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
243055 AAATCAAGAA
243065 GTTCCAGT-AAAAAAACCCACCTT
1 GTTCCAGTCAAAAAAACCCACCTT
243088 GTTCCAGTCAAAAAAACCCACCT
1 GTTCCAGTCAAAAAAACCCACCT
243111 CCTGTCCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.20
Consensus pattern (24 bp):
GTTCCAGTCAAAAAAACCCACCTT
Found at i:249567 original size:16 final size:15
Alignment explanation
Indices: 249548--249580 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
249538 CTAGGCTTTT
249548 ATATTTATAAAAAAAA
1 ATATTTA-AAAAAAAA
249564 ATATTTAAAAAAAAA
1 ATATTTAAAAAAAAA
249579 AT
1 AT
249581 GTTATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATTTAAAAAAAAA
Found at i:254897 original size:16 final size:17
Alignment explanation
Indices: 254876--254907 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
254866 AAGATATTAT
254876 ATATTTTAA-TTTAAAC
1 ATATTTTAACTTTAAAC
254892 ATATTTTAACTTTAAA
1 ATATTTTAACTTTAAA
254908 AATCTGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTTAACTTTAAAC
Found at i:268027 original size:2 final size:2
Alignment explanation
Indices: 268020--268067 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
268010 TTTCATGATA
268020 CT CT CT CT CT CT CT CT CT CAT -T CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT
268062 CT CT CT
1 CT CT CT
268068 AATTACTACA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:269963 original size:18 final size:19
Alignment explanation
Indices: 269932--269976 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
269922 AAATTTGATG
269932 CCCACAATTTTTTTTGAAA
1 CCCACAATTTTTTTTGAAA
269951 CCCACAATTTTTTTTGAAA
1 CCCACAATTTTTTTTGAAA
269970 -CCACAAT
1 CCCACAAT
269977 ACATGTATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (19 bp):
CCCACAATTTTTTTTGAAA
Found at i:288982 original size:13 final size:13
Alignment explanation
Indices: 288961--288992 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
288951 TGTAAAAGTA
*
288961 GTCCGGGACATAT
1 GTCCCGGACATAT
288974 GTCCCGGACATAT
1 GTCCCGGACATAT
288987 GTCCCG
1 GTCCCG
288993 CGATGTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.31, G:0.28, T:0.22
Consensus pattern (13 bp):
GTCCCGGACATAT
Found at i:290588 original size:13 final size:13
Alignment explanation
Indices: 290570--290601 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
290560 TGGGACATCG
290570 CGGGACATATGTC
1 CGGGACATATGTC
290583 CGGGACATATGTC
1 CGGGACATATGTC
*
290596 CCGGAC
1 CGGGAC
290602 TACTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (13 bp):
CGGGACATATGTC
Found at i:293831 original size:11 final size:11
Alignment explanation
Indices: 293808--293844 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
293798 AACTTGGAAA
*
293808 AAAAGTAACTG
1 AAAAGTAATTG
*
293819 AAATGTAATTG
1 AAAAGTAATTG
293830 AAAAGTAATTG
1 AAAAGTAATTG
293841 AAAA
1 AAAA
293845 TACACAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (11 bp):
AAAAGTAATTG
Found at i:300067 original size:6 final size:6
Alignment explanation
Indices: 300056--300082 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
300046 AGGTCAGCCT
300056 GGACAG GGACAG GGACAG GGACAG GGA
1 GGACAG GGACAG GGACAG GGACAG GGA
300083 TCCCAGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.52, T:0.00
Consensus pattern (6 bp):
GGACAG
Found at i:304594 original size:16 final size:17
Alignment explanation
Indices: 304573--304606 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
304563 CGAATCCACT
304573 TTTTGTA-TTATGTGTG
1 TTTTGTATTTATGTGTG
304589 TTTTGTATTTATGTGTG
1 TTTTGTATTTATGTGTG
304606 T
1 T
304607 GCGTGTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.65
Consensus pattern (17 bp):
TTTTGTATTTATGTGTG
Found at i:305761 original size:16 final size:16
Alignment explanation
Indices: 305727--305774 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
305717 GTTGATATGT
305727 TTATTGTTTTGTATTTCA
1 TTATTGTTTTG--TTTCA
*
305745 TTTTTGTTTTGTTTCA
1 TTATTGTTTTGTTTCA
*
305761 TTATGGTTTTGTTT
1 TTATTGTTTTGTTT
305775 TCTTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 17 0.63
18 10 0.37
ACGTcount: A:0.10, C:0.04, G:0.15, T:0.71
Consensus pattern (16 bp):
TTATTGTTTTGTTTCA
Found at i:306732 original size:15 final size:17
Alignment explanation
Indices: 306702--306733 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
306692 GGCGAAGAAC
306702 TCAACCGGTATTATTTA
1 TCAACCGGTATTATTTA
306719 TCAA-CGGT-TTATTTA
1 TCAACCGGTATTATTTA
306734 CAAAAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (17 bp):
TCAACCGGTATTATTTA
Found at i:311410 original size:2 final size:2
Alignment explanation
Indices: 311403--311460 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
311393 GGTATGGTAG
311403 GA GA GA GA 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 GA GA GA GA
311445 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
311461 TGCAATATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:315331 original size:17 final size:17
Alignment explanation
Indices: 315309--315344 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
315299 AAATACCGGT
* *
315309 AGAACTTATGTGTGTAA
1 AGAACTTATATGTATAA
315326 AGAACTTATATGTATAA
1 AGAACTTATATGTATAA
315343 AG
1 AG
315345 TACACCGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (17 bp):
AGAACTTATATGTATAA
Found at i:327057 original size:1 final size:1
Alignment explanation
Indices: 327051--327077 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
327041 GGCCCTCTTT
327051 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
327078 GGATCCGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:329016 original size:477 final size:476
Alignment explanation
Indices: 328122--329075 Score: 1899
Period size: 477 Copynumber: 2.0 Consensus size: 476
328112 TTGTAAAAAT
328122 AACTGAAAATCAGATAAAATATGGCAAGACAGCAGCATAATGAGTTGAAATTGACCCAAAAACAA
1 AACTGAAAATCAGATAAAATATGGCAAGACAGCAGCATAATGAGTTGAAATTGACCCAAAAACAA
328187 TATTGCTACTTTGTAAACACAAAACAACTACATTCCTTGAAAAATATTGCAATCAAAGTCAAAGA
66 TATTGCTACTTTGTAAACACAAAACAACTACATTCCTTGAAAAATATTGCAATCAAAGTCAAAGA
328252 ACACCAGATTAAATAAATCTGAATTTTTTTTTGATTCATAAAAAAACAAAGGGATTTGCTTATTA
131 ACACCAGATTAAATAAATCTGAATTTTTTTTTGATTCATAAAAAAACAAAGGGATTTGCTTATTA
328317 TATTATTGTATTAGGGTTTTTTGTCAATTGTACCCAATAAAGCATGACACTACAAAACCATTATC
196 TATTATTGTATTAGGGTTTTTTGTCAATTGTACCCAATAAAGCATGACACTACAAAACCATTATC
328382 TCTAAAAGCGTGCTGGAGTTAATTTCTTCTTATAATGCAAGAAAGAAAATACAAAAAAAAGGACA
261 TCTAAAAGCGTGCTGGAGTTAATTTCTTCTTATAATGCAAGAAAGAAAATACAAAAAAAAGGACA
328447 AGAATAGAATCGATGATGCACTGTCACCATCTACACTGTTAAATGCAAACACTGGTATGTGTGGA
326 AGAATAGAATCGATGATGCACTGTCACCATCTACACTGTTAAATGCAAACACTGGTATGTGTGGA
328512 GAAGTCATTGAATGCACTGCTTCATAATCACTCTGTACCCAACAGAGGCACTTCTCTGATTAAAA
391 GAAGTCATTGAATGCACTGCTTCATAATCACTCTGTACCCAACAGAGGCACTTCTCTGATTAAAA
328577 CTAATTCTATTAAATCCTGTA
456 CTAATTCTATTAAATCCTGTA
328598 NAACTGAAAATCAGATAAAATATGGCAAGACAGCAGCATAATGAGTTGAAATTGACCCAAAAACA
1 -AACTGAAAATCAGATAAAATATGGCAAGACAGCAGCATAATGAGTTGAAATTGACCCAAAAACA
328663 ATATTGCTACTTTGTAAACACAAAACAACTACATTCCTTGAAAAATATTGCAATCAAAGTCAAAG
65 ATATTGCTACTTTGTAAACACAAAACAACTACATTCCTTGAAAAATATTGCAATCAAAGTCAAAG
328728 AACACCAGATTAAATAAATCTGAATTTTTTTTTGATTCATAAAAAAACAAAGGGATTTGCTTATT
130 AACACCAGATTAAATAAATCTGAATTTTTTTTTGATTCATAAAAAAACAAAGGGATTTGCTTATT
328793 ATATTATTGTATTAGGGTTTTTTGTCAATTGTACCCAATAAAGCATGACACTACAAAACCATTAT
195 ATATTATTGTATTAGGGTTTTTTGTCAATTGTACCCAATAAAGCATGACACTACAAAACCATTAT
328858 CTCTAAAAGCGTGCTGGAGTTAATTTCTTCTTATAATGCAAGAAAGAAAATACAAAAAAAAGGAC
260 CTCTAAAAGCGTGCTGGAGTTAATTTCTTCTTATAATGCAAGAAAGAAAATACAAAAAAAAGGAC
328923 AAGAATAGAATCGATGATGCACTGTCACCATCTACACTGTTAAATGCAAACACTGGTATGTGTGG
325 AAGAATAGAATCGATGATGCACTGTCACCATCTACACTGTTAAATGCAAACACTGGTATGTGTGG
328988 AGAAGTCATTGAATGCACTGCTTCATAATCACTCTGTACCCAACAGAGGCACTTCTCTGATTAAA
390 AGAAGTCATTGAATGCACTGCTTCATAATCACTCTGTACCCAACAGAGGCACTTCTCTGATTAAA
329053 ACTAATTCTATTAAATCCTGTA
455 ACTAATTCTATTAAATCCTGTA
329075 A
1 A
329076 TAGGTAATGA
Statistics
Matches: 477, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
476 1 0.00
477 476 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (476 bp):
AACTGAAAATCAGATAAAATATGGCAAGACAGCAGCATAATGAGTTGAAATTGACCCAAAAACAA
TATTGCTACTTTGTAAACACAAAACAACTACATTCCTTGAAAAATATTGCAATCAAAGTCAAAGA
ACACCAGATTAAATAAATCTGAATTTTTTTTTGATTCATAAAAAAACAAAGGGATTTGCTTATTA
TATTATTGTATTAGGGTTTTTTGTCAATTGTACCCAATAAAGCATGACACTACAAAACCATTATC
TCTAAAAGCGTGCTGGAGTTAATTTCTTCTTATAATGCAAGAAAGAAAATACAAAAAAAAGGACA
AGAATAGAATCGATGATGCACTGTCACCATCTACACTGTTAAATGCAAACACTGGTATGTGTGGA
GAAGTCATTGAATGCACTGCTTCATAATCACTCTGTACCCAACAGAGGCACTTCTCTGATTAAAA
CTAATTCTATTAAATCCTGTA
Found at i:342298 original size:143 final size:142
Alignment explanation
Indices: 342040--342319 Score: 551
Period size: 143 Copynumber: 2.0 Consensus size: 142
342030 CCAAAGCGTG
342040 TGGGATGGGAACACTTAAACAAAAACCCTTTCTTTGGTGATTTATGCCGGATATTAAGGTGGCGA
1 TGGGATGGGAACACTTAAACAAAAACCCTTTCTTTGGTGATTTATGCCGGATATTAAGGTGGCGA
342105 CAGTGCAGAAAAAAATAACATAACCCGTGTTAGCGGGCTATGAATTTTTTCCTGCAATCATCGCT
66 CAGTGCAGAAAAAAATAACATAACCCGTGTTAGCGGGCTATGAATTTTTTCCTGCAATCATCGCT
342170 ACTTTCATAACT
131 ACTTTCATAACT
342182 NTGGGATGGGAACACTTAAACAAAAACCCTTTCTTTGGTGATTTATGCCGGATATTAAGGTGGCG
1 -TGGGATGGGAACACTTAAACAAAAACCCTTTCTTTGGTGATTTATGCCGGATATTAAGGTGGCG
342247 ACAGTGCAGAAAAAAATAACATAACCCGTGTTAGCGGGCTATGAATTTTTTCCTGCAATCATCGC
65 ACAGTGCAGAAAAAAATAACATAACCCGTGTTAGCGGGCTATGAATTTTTTCCTGCAATCATCGC
342312 TACTTTCA
130 TACTTTCA
342320 CAGTGTTTCA
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 137 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (142 bp):
TGGGATGGGAACACTTAAACAAAAACCCTTTCTTTGGTGATTTATGCCGGATATTAAGGTGGCGA
CAGTGCAGAAAAAAATAACATAACCCGTGTTAGCGGGCTATGAATTTTTTCCTGCAATCATCGCT
ACTTTCATAACT
Found at i:352667 original size:18 final size:18
Alignment explanation
Indices: 352643--352684 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
352633 GCTACTCTGA
352643 ATAGCTTAATAAAGCTAT
1 ATAGCTTAATAAAGCTAT
* * *
352661 TTAGCTTATTCAAGCTAT
1 ATAGCTTAATAAAGCTAT
352679 ATAGCT
1 ATAGCT
352685 AAATCTGGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
ATAGCTTAATAAAGCTAT
Found at i:354362 original size:180 final size:180
Alignment explanation
Indices: 354060--354958 Score: 1604
Period size: 180 Copynumber: 5.0 Consensus size: 180
354050 GGCTGCCAAA
*
354060 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
354125 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
* * *
354190 AAAAATACCAGCTTTGGAACCTGGTCATTTTTTGGCAAAATGTTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
354240 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
354305 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATC-A
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
* **
354369 AAAAAAACCCAGCTTTTGAACTTAGTCATTTTTTAACAAAATGTTGCATAT
131 AAAAATA-CCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
354420 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
354485 GATTAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
* * *
354550 TAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCTTAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
*
354600 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
354665 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
* *
354730 TAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
354780 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
354845 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATATCTGATAATTTAT-GA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCG-
*
354909 AAAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATA
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATA
354959 AACATGTAGG
Statistics
Matches: 693, Mismatches: 23, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
179 8 0.01
180 679 0.98
181 6 0.01
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
Found at i:361346 original size:247 final size:246
Alignment explanation
Indices: 360910--361392 Score: 957
Period size: 247 Copynumber: 2.0 Consensus size: 246
360900 CAAAATTAAA
360910 AAAAAAAAAAATCCGCGAATTTAAAACGTACGAGTTGGTTAATAAAACTGGTTCTTATTTTTTAC
1 AAAAAAAAAAATCCGCGAATTTAAAACGTACGAGTTGGTTAATAAAACTGGTTCTTATTTTTTAC
360975 TGCAGCCGGTTCAGATGGCCAAGAACTAGTTTTTCTATTGGAAAAATTACGTTATCGATTTTCTT
66 TGCAGCCGGTTCAGATGGCCAAGAACTAGTTTTTCTATTGGAAAAATTACGTTATCGATTTTCTT
361040 TGGAAGACAAATTGGCAAATGAATGAAATGACTGCACAACACGAGAGACACAGGAATTGATTATT
131 TGGAAGACAAATTGGCAAATGAATGAAATGACTGCACAACACGAGAGACACAGGAATTGATTATT
361105 CAAAAAGTAGAGGAATAATTTAGGGACGGAAATGATAAAATNAAAAAAAATC
196 CAAAAAGTAGAGGAATAATTTAGGGACGGAAATGATAAAAT-AAAAAAAATC
361157 AAAAAAAAAAATCCGCGAATTTAAAACGTACGAGTTGGTTAATAAAACTGGTTCTTATTTTTTAC
1 AAAAAAAAAAATCCGCGAATTTAAAACGTACGAGTTGGTTAATAAAACTGGTTCTTATTTTTTAC
361222 TGCAGCCGGTTCAGATGGCCAAGAACTAGTTTTTCTATTGGAAAAATTACGTTATCGATTTTCTT
66 TGCAGCCGGTTCAGATGGCCAAGAACTAGTTTTTCTATTGGAAAAATTACGTTATCGATTTTCTT
361287 TGGAAGACAAATTGGCAAATGAATGAAATGACTGCACAACACGAGAGACACAGGAATTGATTATT
131 TGGAAGACAAATTGGCAAATGAATGAAATGACTGCACAACACGAGAGACACAGGAATTGATTATT
361352 CAAAAAGTAGAGGAATAATTTAGGGACGGAAATGATAAAAT
196 CAAAAAGTAGAGGAATAATTTAGGGACGGAAATGATAAAAT
361393 TCTTGCATAG
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 236 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (246 bp):
AAAAAAAAAAATCCGCGAATTTAAAACGTACGAGTTGGTTAATAAAACTGGTTCTTATTTTTTAC
TGCAGCCGGTTCAGATGGCCAAGAACTAGTTTTTCTATTGGAAAAATTACGTTATCGATTTTCTT
TGGAAGACAAATTGGCAAATGAATGAAATGACTGCACAACACGAGAGACACAGGAATTGATTATT
CAAAAAGTAGAGGAATAATTTAGGGACGGAAATGATAAAATAAAAAAAATC
Found at i:372456 original size:1 final size:1
Alignment explanation
Indices: 372450--372483 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
372440 CTGTACCCGA
*
372450 CCCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
372484 ATCTTGCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:374592 original size:14 final size:14
Alignment explanation
Indices: 374573--374612 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
374563 ATTAATATAC
*
374573 AAGAGAGAGAGACA
1 AAGAGAAAGAGACA
*
374587 AAGAGACAGAGACA
1 AAGAGAAAGAGACA
*
374601 GAGAGAAAGAGA
1 AAGAGAAAGAGA
374613 AAGAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.35, T:0.00
Consensus pattern (14 bp):
AAGAGAAAGAGACA
Found at i:375747 original size:1 final size:1
Alignment explanation
Indices: 375741--375766 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
375731 CTGTACAGGA
375741 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
375767 GGGGGGGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:386223 original size:2 final size:2
Alignment explanation
Indices: 386216--386245 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
386206 NNNNNNNNNN
386216 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
386246 CAGAAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:387533 original size:2 final size:2
Alignment explanation
Indices: 387526--387570 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
387516 ACATTTCTTA
387526 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
387568 TG T
1 TG T
387571 ATGACATGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:396120 original size:2 final size:2
Alignment explanation
Indices: 396113--396137 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
396103 TTACAAAGGG
396113 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
396138 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:403204 original size:2 final size:2
Alignment explanation
Indices: 403197--403235 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
403187 ATTGATAAAA
403197 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
403236 CTAAAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:404361 original size:18 final size:18
Alignment explanation
Indices: 404338--404381 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
404328 TTCGAGGACT
*
404338 TCTTCCACCTCTTGTACC
1 TCTTCCACCTCTCGTACC
404356 TCTTCCACCTCTCGTACC
1 TCTTCCACCTCTCGTACC
404374 TCTTCCAC
1 TCTTCCAC
404382 GTGACTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.11, C:0.48, G:0.05, T:0.36
Consensus pattern (18 bp):
TCTTCCACCTCTCGTACC
Found at i:413250 original size:113 final size:114
Alignment explanation
Indices: 413039--413251 Score: 356
Period size: 113 Copynumber: 1.9 Consensus size: 114
413029 AAAAATTATA
* *
413039 ATATGATTGTTAGAAAGTCTTAAACGATTAAAAAAAAAGGTATCCTATAGATTTTTTATTCTCTC
1 ATATGATCGTTAGAAAGTCTTAAAAGATT--AAAAAAAGGTATCCTATAGATTTTTTATTCTCTC
*
413104 TTGTAAATTTTAAAAGGTTCAAACTTATTAAATATACAAAATATACATGAT
64 TTGTAAATTTTAAAAGGTTCAAACTTATCAAATATACAAAATATACATGAT
413155 ATATGATCGTTAGAAAGTCTTAAAAGATT-AAAAAAGGTATCCTATAGATTTTTTATTCTCTCTT
1 ATATGATCGTTAGAAAGTCTTAAAAGATTAAAAAAAGGTATCCTATAGATTTTTTATTCTCTCTT
* *
413219 GTAAATTTTAAAAGGTTTAAATTTATCAAATAT
66 GTAAATTTTAAAAGGTTCAAACTTATCAAATAT
413252 TATAATACAA
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
113 65 0.71
116 27 0.29
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (114 bp):
ATATGATCGTTAGAAAGTCTTAAAAGATTAAAAAAAGGTATCCTATAGATTTTTTATTCTCTCTT
GTAAATTTTAAAAGGTTCAAACTTATCAAATATACAAAATATACATGAT
Found at i:417483 original size:2 final size:2
Alignment explanation
Indices: 417476--417512 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
417466 TTTCATAAAA
417476 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
417513 TTGATTAAGG
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:419465 original size:2 final size:2
Alignment explanation
Indices: 419460--419485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
419450 CCCCCCCCCC
419460 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
419486 GGTATAATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:425316 original size:2 final size:2
Alignment explanation
Indices: 425309--425397 Score: 162
Period size: 2 Copynumber: 45.0 Consensus size: 2
425299 GGGTAGGGTT
425309 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
425350 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA TA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
425392 GA GA GA
1 GA GA GA
425398 TATTTAAAAC
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 83 0.99
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
GA
Found at i:425668 original size:20 final size:18
Alignment explanation
Indices: 425652--425698 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
425642 AATGAAAATT
425652 AAAAACAAACGATGAAAA
1 AAAAACAAACGATGAAAA
* *
425670 AAAAAAAGAACGATTAAAA
1 AAAAACA-AACGATGAAAA
425689 CAAAAACAAA
1 -AAAAACAAA
425699 ATTTAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.74, C:0.11, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAACAAACGATGAAAA
Found at i:426495 original size:2 final size:2
Alignment explanation
Indices: 426488--426528 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
426478 TGTGTATAGT
426488 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
426529 AAATAATGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:433149 original size:117 final size:118
Alignment explanation
Indices: 432927--433162 Score: 370
Period size: 117 Copynumber: 2.0 Consensus size: 118
432917 TTCATCGTTA
* *
432927 TCATCCTGGTCTGTTGCAATGCAAAATCCCCGTATACACTTTTTTTAGTCGTGTATTGAAACATG
1 TCATCCGGGTCTGTTGCAATACAAAATCCCCGTATACACTTTTTTTAGTCGTGTATTGAAACATG
*
432992 ATAATCTAGAGGGGGCATTTCAAAAGAGAAATCTTAGAAACTTTTCATACTTT
66 ATAATCTAGAGAGGGCATTTCAAAAGAGAAATCTTAGAAACTTTTCATACTTT
433045 TCATCCGGGTCTGTTGCAATACAAAATCCCCGTATACAC-TTTTTTA-TCCGTGTATTGAAACAT
1 TCATCCGGGTCTGTTGCAATACAAAATCCCCGTATACACTTTTTTTAGT-CGTGTATTGAAACAT
** * *
433108 GATAAGT-TAGAGAGGGTGTTTCAAAGGAGAAATCTTGGAAACTTTTCATACTTT
65 GATAA-TCTAGAGAGGGCATTTCAAAAGAGAAATCTTAGAAACTTTTCATACTTT
433162 T
1 T
433163 GATTGAACAT
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
116 1 0.01
117 70 0.64
118 38 0.35
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (118 bp):
TCATCCGGGTCTGTTGCAATACAAAATCCCCGTATACACTTTTTTTAGTCGTGTATTGAAACATG
ATAATCTAGAGAGGGCATTTCAAAAGAGAAATCTTAGAAACTTTTCATACTTT
Found at i:433978 original size:11 final size:11
Alignment explanation
Indices: 433964--433993 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
433954 AAAATCAAGA
433964 AAAAAACCCTT
1 AAAAAACCCTT
433975 AAAAAATCCCTT
1 AAAAAA-CCCTT
433987 AAAAAAC
1 AAAAAAC
433994 TCACTACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAACCCTT
Found at i:434862 original size:2 final size:2
Alignment explanation
Indices: 434855--434913 Score: 77
Period size: 2 Copynumber: 30.0 Consensus size: 2
434845 GAGGAATATC
* *
434855 AG AG AG AG AG AG AG -G AG AG AG AG AA AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
434896 AG AG AG AG -G CAG AG AG AG
1 AG AG AG AG AG -AG AG AG AG
434914 TACAACGGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:443376 original size:2 final size:2
Alignment explanation
Indices: 443369--443409 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
443359 CATCAACAAT
443369 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
443410 GCATTTAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:444986 original size:161 final size:161
Alignment explanation
Indices: 444760--445219 Score: 627
Period size: 161 Copynumber: 2.9 Consensus size: 161
444750 TTGGAATATT
* * * * * *
444760 TCCAAGGGGCATAACTCTGTCGGAAATTGCTCTGTCATACCCAAAATCAAACTTGACCAAGATAT
1 TCCAAGGGCCATAACTCTGTCGAAAATTGCTCTATCGTACCCAATATCAAACTTGACCTAGATAT
* * *
444825 TATTTAGATAAACCTATATACCAAATTTCATATT-AATATGTGCACCCTCTGCAAAGAAAATGAG
66 TATTAAGATAAACCTATATACCAAATTTCAT-TTCAATATGTTCATCCTCTGCAAAGAAAATGAG
*
444889 CGGAAACTGCAAATAACTCGAATTTTTCTAGG
130 CGGAAACTGCAAATAACTCGAATTTTTCTAAG
**
444921 TCCAAGGGCCATAACTCTGTCGAAAATTGCTCTATCGTACCCAATATCAAACTAAACCTAGATAT
1 TCCAAGGGCCATAACTCTGTCGAAAATTGCTCTATCGTACCCAATATCAAACTTGACCTAGATAT
* *
444986 TATCAAGATAAACC-AGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAG
66 TATTAAGATAAACCTA-TATACCAAATTTCATTTCAATATGTTCATCCTCTGCAAAGAAAATGAG
*
445050 CGGAACCTGCAAATAACTCGAATTTTTCTAAG
130 CGGAAACTGCAAATAACTCGAATTTTTCTAAG
* * * * * *
445082 TCCAAGGCCCATAACTCCGTCGAAAATTGCTCGATCGAACCCAATATCGAACTTGACCTAAATAT
1 TCCAAGGGCCATAACTCTGTCGAAAATTGCTCTATCGTACCCAATATCAAACTTGACCTAGATAT
* * * * * * * *
445147 TATCATGATAAATCTGTATACAAAATTTCATTTCAATATGTTTATCCTTTGCAAAGAAAATGAAC
66 TATTAAGATAAACCTATATACCAAATTTCATTTCAATATGTTCATCCTCTGCAAAGAAAATGAGC
445212 GGAAACTG
131 GGAAACTG
445220 TTGGTGGACC
Statistics
Matches: 264, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
160 3 0.01
161 261 0.99
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (161 bp):
TCCAAGGGCCATAACTCTGTCGAAAATTGCTCTATCGTACCCAATATCAAACTTGACCTAGATAT
TATTAAGATAAACCTATATACCAAATTTCATTTCAATATGTTCATCCTCTGCAAAGAAAATGAGC
GGAAACTGCAAATAACTCGAATTTTTCTAAG
Found at i:458876 original size:68 final size:68
Alignment explanation
Indices: 458764--458899 Score: 211
Period size: 68 Copynumber: 2.0 Consensus size: 68
458754 TATTAATCTC
* * *
458764 AAAATCTTGAACGCATTTGCTGTAATTGCAGATGATAAATACATAAAATTACCCTGTTTTGACGT
1 AAAATCTTGAACGCATTTACTGTAATTGCAAATGAAAAATACATAAAATTACCCTGTTTTGACGT
458829 TAA
66 TAA
* *
458832 AAAATCTTGAACGCCTTTACTGTGACTT-CAAATGAAAAATACATAAAATTACCCTGTTTTGACG
1 AAAATCTTGAACGCATTTACTGT-AATTGCAAATGAAAAATACATAAAATTACCCTGTTTTGACG
458896 TTAA
65 TTAA
458900 CGTTAATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 59 0.95
69 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (68 bp):
AAAATCTTGAACGCATTTACTGTAATTGCAAATGAAAAATACATAAAATTACCCTGTTTTGACGT
TAA
Found at i:459997 original size:24 final size:25
Alignment explanation
Indices: 459970--460024 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
459960 TGAGTCTGTA
* *
459970 ATATGTTTAAC-GTATTTTTTAAAC
1 ATATGTTTAACAATATTTTTCAAAC
459994 ATATG-TTAACAATATTTTTCAAAC
1 ATATGTTTAACAATATTTTTCAAAC
460018 ATATGTT
1 ATATGTT
460025 CACATACTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 21 0.78
25 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.47
Consensus pattern (25 bp):
ATATGTTTAACAATATTTTTCAAAC
Found at i:460061 original size:11 final size:11
Alignment explanation
Indices: 460045--460083 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
460035 GAAAAATTCA
*
460045 TATGTTTAACG
1 TATGTTCAACG
460056 TATGTTCAACG
1 TATGTTCAACG
*
460067 TATGTTCAACA
1 TATGTTCAACG
460078 TATGTT
1 TATGTT
460084 ACTCGAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (11 bp):
TATGTTCAACG
Found at i:464319 original size:15 final size:15
Alignment explanation
Indices: 464299--464328 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
464289 ATCGTTGCAA
464299 ACAGATGAAACATAT
1 ACAGATGAAACATAT
*
464314 ACAGATGAAATATAT
1 ACAGATGAAACATAT
464329 GAAAAACACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (15 bp):
ACAGATGAAACATAT
Found at i:469772 original size:21 final size:21
Alignment explanation
Indices: 469748--469839 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
469738 ATCTGCCACC
469748 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
*
469769 ACTTGTCAGAT-CTTGATGTCG
1 ACTTGTCAGATAATT-ATGTCG
469790 ACTTGTCAGATAATTATGTTC-
1 ACTTGTCAGATAATTATG-TCG
* * ** *
469811 ACTTGTTAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTCG
469832 ACTTGTCA
1 ACTTGTCA
469840 CTTATTAACG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.07
21 51 0.86
22 4 0.07
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:469795 original size:42 final size:42
Alignment explanation
Indices: 469748--469839 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
469738 ATCTGCCACC
*
469748 ACTTGTCAGATAATTATG-TCGACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATTATGTTC-ACTTGTCAGATCTTGAAGTCG
* * *
469790 ACTTGTCAGATAATTATGTTCACTTGTTAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCG
469832 ACTTGTCA
1 ACTTGTCA
469840 CTTATTAACG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (42 bp):
ACTTGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCG
Found at i:469976 original size:21 final size:21
Alignment explanation
Indices: 469916--469985 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
469906 AATAATATTT
**
469916 TCTGACAAGTCGACATAAGGA
1 TCTGACAAGTCGACATAATTA
469937 TCTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
*
469958 TCTGACAAGTAGACATAATTA
1 TCTGACAAGTCGACATAATTA
*
469979 TTTGACA
1 TCTGACA
469986 GGACGACAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (21 bp):
TCTGACAAGTCGACATAATTA
Done.