Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 74 of 93
Found at i:28499435 original size:2 final size:2
Alignment explanation
Indices: 28499428--28499528 Score: 141
Period size: 2 Copynumber: 51.0 Consensus size: 2
28499418 ACATACATAC
28499428 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * ** * *
28499469 AT AT GT GT NC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28499511 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
28499529 GTGTGTCCAA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
1 1 0.01
2 88 0.99
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28499835 original size:23 final size:23
Alignment explanation
Indices: 28499794--28499847 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
28499784 CACTAATCCC
28499794 ATCT-TCT-TCTTCTTTCTCTCT
1 ATCTCTCTCTCTTCTTTCTCTCT
*
28499815 CTCTCTCTCTCTT-TTTCCTCTCT
1 ATCTCTCTCTCTTCTTT-CTCTCT
*
28499838 ATCTGTCTCT
1 ATCTCTCTCT
28499848 AAAAACTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.11
22 6 0.22
23 18 0.67
ACGTcount: A:0.04, C:0.37, G:0.02, T:0.57
Consensus pattern (23 bp):
ATCTCTCTCTCTTCTTTCTCTCT
Found at i:28507841 original size:15 final size:16
Alignment explanation
Indices: 28507816--28507845 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28507806 TAAAAAAAAT
28507816 AAAATCTTTATATTTA
1 AAAATCTTTATATTTA
28507832 AAAATC-TTATATTT
1 AAAATCTTTATATTT
28507846 TGCACGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
AAAATCTTTATATTTA
Found at i:28509821 original size:20 final size:20
Alignment explanation
Indices: 28509790--28509838 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28509780 TTAGCATAAA
*
28509790 GACCCAAATGGGTCAAATTT
1 GACCCAATTGGGTCAAATTT
* *
28509810 GATCCAATTGGGTCACATTT
1 GACCCAATTGGGTCAAATTT
28509830 GACCCAATT
1 GACCCAATT
28509839 AAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
GACCCAATTGGGTCAAATTT
Found at i:28510642 original size:28 final size:28
Alignment explanation
Indices: 28510602--28510662 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
28510592 GGAGGAGGGG
28510602 GGATTCGAACCCTACTCTTTAGGCAGGA
1 GGATTCGAACCCTACTCTTTAGGCAGGA
* *
28510630 GGATTCGAACCCTGCTCTTTAGGCAGGG
1 GGATTCGAACCCTACTCTTTAGGCAGGA
28510658 GGATT
1 GGATT
28510663 ATGCACCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (28 bp):
GGATTCGAACCCTACTCTTTAGGCAGGA
Found at i:28515313 original size:19 final size:20
Alignment explanation
Indices: 28515280--28515318 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
28515270 GTAATTGGTT
28515280 AAAAAAATTCAAAAA-AAAG
1 AAAAAAATTCAAAAATAAAG
**
28515299 AAAAAAATTTTAAAATAAAG
1 AAAAAAATTCAAAAATAAAG
28515319 TCAGAGCCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAAAATTCAAAAATAAAG
Found at i:28516198 original size:17 final size:16
Alignment explanation
Indices: 28516164--28516198 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
28516154 TGGTTTAGAA
28516164 TTTTGTTAGTTTATTT
1 TTTTGTTAGTTTATTT
28516180 TTTTAGTTAGCTTTATTT
1 TTTT-GTTAG-TTTATTT
28516198 T
1 T
28516199 AAGATATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.14, C:0.03, G:0.11, T:0.71
Consensus pattern (16 bp):
TTTTGTTAGTTTATTT
Found at i:28516687 original size:24 final size:24
Alignment explanation
Indices: 28516656--28516827 Score: 92
Period size: 24 Copynumber: 7.4 Consensus size: 24
28516646 CTATGATGTT
*
28516656 ACACGCCATGTACAAAAACCTGTG
1 ACACGCCATGTACAAAAATCTGTG
* ** *
28516680 ACAAGCCATG---ATTAA-CGTGTT
1 ACACGCCATGTACAAAAATC-TGTG
* * *
28516701 ACACGCTATGTACAAAAATATATG
1 ACACGCCATGTACAAAAATCTGTG
* *
28516725 ACACGCCATATATAAAAATCTGTG
1 ACACGCCATGTACAAAAATCTGTG
* * * *
28516749 ACAAGCCATGGT-----TAGCGTGTT
1 ACACGCCAT-GTACAAAAATC-TGTG
* *
28516770 ACACGCTATGTACAAAAATATGTG
1 ACACGCCATGTACAAAAATCTGTG
*
28516794 ACACGCCATGTACAACAATCTGTG
1 ACACGCCATGTACAAAAATCTGTG
*
28516818 ACAAGCCATG
1 ACACGCCATG
28516828 GTTAGCGTGT
Statistics
Matches: 105, Mismatches: 31, Indels: 24
0.66 0.19 0.15
Matches are distributed among these distances:
20 5 0.05
21 24 0.23
24 74 0.70
25 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (24 bp):
ACACGCCATGTACAAAAATCTGTG
Found at i:28516768 original size:69 final size:69
Alignment explanation
Indices: 28516656--28516872 Score: 337
Period size: 69 Copynumber: 3.1 Consensus size: 69
28516646 CTATGATGTT
* * *
28516656 ACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAACGTGTTACACGCTATGTACAAAAATA
1 ACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
28516721 TATG
66 TATG
* *
28516725 ACACGCCATATATAAAAATCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
1 ACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
*
28516790 TGTG
66 TATG
* *
28516794 ACACGCCATGTACAACAATCTGTGACAAGCCATGGTTAGCGTGTTACACG-TCATGTATAAAAAT
1 ACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAGCGTGTTACACGCT-ATGTACAAAAAT
28516858 ATATG
65 ATATG
*
28516863 ACAAGCCATG
1 ACACGCCATG
28516873 GTTTGCTTGT
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
68 1 0.01
69 134 0.99
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (69 bp):
ACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
TATG
Found at i:28516853 original size:114 final size:114
Alignment explanation
Indices: 28516725--28517228 Score: 530
Period size: 114 Copynumber: 4.4 Consensus size: 114
28516715 AAAATATATG
* * *
28516725 ACACGCCATATATAAAAATCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
1 ACACGCCATGTACAAAAATATGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
* * *
28516790 TGTGACACGCCATGTACAACAATCTGTGACAAGCCATGGTTAGCGTGTT
66 TGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTT
* * * * * ** * *
28516839 ACACGTCATGTATAAAAATATATGACAAGCCATGGTTTGCTTGTTACATTCCATGTATAAAAATA
1 ACACGCCATGTACAAAAATATGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
* *
28516904 TGTGACAAGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTT
66 TGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTT
* * ** *
28516953 ACATGCCAAGTACAAAAACCTGTGACAAGCCATGGTTAGTGTGTTACACGCTATGTACAAAAATA
1 ACACGCCATGTACAAAAATATGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
* *
28517018 TGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTATCACGTT
66 TGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTT
* **** * * * * * *
28517067 ACACGCTATGTACAAAAATATGTGACAAGCCAAATACAAAAACCTATGACAAGCTATGGT---TA
1 ACACGCCATGTACAAAAATATGTGACAAGCC--AT-GGTTAGCGTGTTACACGCTAT-GTACAAA
** * * * *
28517129 GCT-TGTTACACGCCATGTACAAAAACCTATGACAAGCCATAGTTAGCTTGTT
62 AATATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTT
* ** * *
28517181 ACACGTCATGTACAAAAACCTATGACAAGCCATGGTTAGCTTGTTACA
1 ACACGCCATGTACAAAAATATGTGACAAGCCATGGTTAGCGTGTTACA
28517229 TGCCATGTTG
Statistics
Matches: 317, Mismatches: 69, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
111 7 0.02
112 2 0.01
114 291 0.92
115 2 0.01
116 2 0.01
117 11 0.03
118 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (114 bp):
ACACGCCATGTACAAAAATATGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATA
TGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTT
Found at i:28516865 original size:45 final size:45
Alignment explanation
Indices: 28516816--28516917 Score: 152
Period size: 45 Copynumber: 2.3 Consensus size: 45
28516806 CAACAATCTG
28516816 TGACAAGCCATGGTTAGCGTGTTACACGT-CATGTATAAAAATATA
1 TGACAAGCCATGGTTAGCGTGTTACA-GTCCATGTATAAAAATATA
* * * *
28516861 TGACAAGCCATGGTTTGCTTGTTACATTCCATGTATAAAAATATG
1 TGACAAGCCATGGTTAGCGTGTTACAGTCCATGTATAAAAATATA
28516906 TGACAAGCCATG
1 TGACAAGCCATG
28516918 TACAAAAACC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (45 bp):
TGACAAGCCATGGTTAGCGTGTTACAGTCCATGTATAAAAATATA
Found at i:28516918 original size:69 final size:69
Alignment explanation
Indices: 28516845--28516986 Score: 194
Period size: 69 Copynumber: 2.1 Consensus size: 69
28516835 TGTTACACGT
* * * * * * *
28516845 CATGTATAAAAATATATGACAAGCCATGGTTTGCTTGTTACATTCCATGTATAAAAATATGTGAC
1 CATGTACAAAAACATATGACAAGCCATGGTTAGCTTGTTACATGCCAAGTACAAAAACATGTGAC
28516910 AAGC
66 AAGC
* * *
28516914 CATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACATGCCAAGTACAAAAACCTGTGAC
1 CATGTACAAAAACATATGACAAGCCATGGTTAGCTTGTTACATGCCAAGTACAAAAACATGTGAC
28516979 AAGC
66 AAGC
28516983 CATG
1 CATG
28516987 GTTAGTGTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (69 bp):
CATGTACAAAAACATATGACAAGCCATGGTTAGCTTGTTACATGCCAAGTACAAAAACATGTGAC
AAGC
Found at i:28516924 original size:24 final size:24
Alignment explanation
Indices: 28516889--28517055 Score: 89
Period size: 24 Copynumber: 7.2 Consensus size: 24
28516879 TTGTTACATT
* *
28516889 CCATGTATAAAAATATGTGACAAG
1 CCATGTACAAAAATCTGTGACAAG
*
28516913 CCATGTACAAAAACCTGTGACAAG
1 CCATGTACAAAAATCTGTGACAAG
* ** * *
28516937 CCATGGT---TAGCT-TGTTACATG
1 CCAT-GTACAAAAATCTGTGACAAG
* *
28516958 CCAAGTACAAAAACCTGTGACAAG
1 CCATGTACAAAAATCTGTGACAAG
* * * * *
28516982 CCATGGT----TAGTGTGTTACACG
1 CCAT-GTACAAAAATCTGTGACAAG
* * *
28517003 CTATGTACAAAAATATGTGACACG
1 CCATGTACAAAAATCTGTGACAAG
*
28517027 CCATGTACAAAAACCTGTGACAAG
1 CCATGTACAAAAATCTGTGACAAG
28517051 CCATG
1 CCATG
28517056 GTTATCACGT
Statistics
Matches: 101, Mismatches: 32, Indels: 20
0.66 0.21 0.13
Matches are distributed among these distances:
20 4 0.04
21 21 0.21
22 1 0.01
23 1 0.01
24 70 0.69
25 4 0.04
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
CCATGTACAAAAATCTGTGACAAG
Found at i:28516968 original size:45 final size:45
Alignment explanation
Indices: 28516912--28517236 Score: 232
Period size: 45 Copynumber: 7.2 Consensus size: 45
28516902 TATGTGACAA
*
28516912 GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACAT
1 GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACAC
*
28516957 GCCAAGTACAAAAACCTGTGACAAGCCATGGTTAG-TGTGTTACAC
1 GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCT-TGTTACAC
* ** * * * * * *
28517002 GCTATGTACAAAAATATGTGACACGCCAT-GTACAAAAACCTGTGACAA
1 GCCATGTACAAAAACCTGTGACAAGCCATGGT----TAGCTTGTTACAC
* ** * * * * ** * *
28517050 GCCATGGT--TATCA-C-GTTACACGCTAT-GTACAAAAATATGTGACAA
1 GCCAT-GTACAAAAACCTGTGACAAGCCATGGT---TAGCT-TGTTACAC
** * *
28517095 GCCAAATACAAAAACCTATGACAAGCTATGGTTAGCTTGTTACAC
1 GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACAC
* *
28517140 GCCATGTACAAAAACCTATGACAAGCCATAGTTAGCTTGTTACAC
1 GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACAC
* * *
28517185 GTCATGTACAAAAACCTATGACAAGCCATGGTTAGCTTGTTACAT
1 GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACAC
28517230 GCCATGT
1 GCCATGT
28517237 TGAAAAAAAA
Statistics
Matches: 223, Mismatches: 44, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
44 8 0.04
45 184 0.83
46 4 0.02
47 3 0.01
48 20 0.09
49 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (45 bp):
GCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCTTGTTACAC
Found at i:28517035 original size:69 final size:68
Alignment explanation
Indices: 28516957--28517167 Score: 289
Period size: 69 Copynumber: 3.1 Consensus size: 68
28516947 CTTGTTACAT
28516957 GCCAAGTACAAAAACCTGTGACAAGCCATGGTTAGTGTGTTACACGCTATGTACAAAAATATGTG
1 GCCAAGTACAAAAACCTGTGACAAGCCATGGTTAGT-TGTTACACGCTATGTACAAAAATATGTG
*
28517022 ACAC
65 ACAA
* *
28517026 GCCATGTACAAAAACCTGTGACAAGCCATGGTTA-TCACGTTACACGCTATGTACAAAAATATGT
1 GCCAAGTACAAAAACCTGTGACAAGCCATGGTTAGT--TGTTACACGCTATGTACAAAAATATGT
28517090 GACAA
64 GACAA
* * * * ** *
28517095 GCCAAATACAAAAACCTATGACAAGCTATGGTTAGCTTGTTACACGCCATGTACAAAAACCTATG
1 GCCAAGTACAAAAACCTGTGACAAGCCATGGTTAG-TTGTTACACGCTATGTACAAAAATATGTG
28517160 ACAA
65 ACAA
28517164 GCCA
1 GCCA
28517168 TAGTTAGCTT
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
68 1 0.01
69 124 0.98
71 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (68 bp):
GCCAAGTACAAAAACCTGTGACAAGCCATGGTTAGTTGTTACACGCTATGTACAAAAATATGTGA
CAA
Found at i:28517243 original size:45 final size:45
Alignment explanation
Indices: 28517101--28517236 Score: 236
Period size: 45 Copynumber: 3.0 Consensus size: 45
28517091 ACAAGCCAAA
*
28517101 TACAAAAACCTATGACAAGCTATGGTTAGCTTGTTACACGCCATG
1 TACAAAAACCTATGACAAGCCATGGTTAGCTTGTTACACGCCATG
* *
28517146 TACAAAAACCTATGACAAGCCATAGTTAGCTTGTTACACGTCATG
1 TACAAAAACCTATGACAAGCCATGGTTAGCTTGTTACACGCCATG
*
28517191 TACAAAAACCTATGACAAGCCATGGTTAGCTTGTTACATGCCATG
1 TACAAAAACCTATGACAAGCCATGGTTAGCTTGTTACACGCCATG
28517236 T
1 T
28517237 TGAAAAAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 85 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (45 bp):
TACAAAAACCTATGACAAGCCATGGTTAGCTTGTTACACGCCATG
Found at i:28517285 original size:24 final size:25
Alignment explanation
Indices: 28517252--28517326 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 25
28517242 AAAAATACTG
28517252 TTGTTACACGCCATATAAAAAAACA
1 TTGTTACACGCCATATAAAAAAACA
* * *
28517277 -TGTTACACGCCATGGTTAAAAAAGA
1 TTGTTACACGCCAT-ATAAAAAAACA
*
28517302 TTGTTACACGCTATATTGAAAAAAA
1 TTGTTACACGCCATA-T-AAAAAAA
28517327 AATATTATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
24 13 0.32
25 8 0.20
26 13 0.32
27 6 0.15
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (25 bp):
TTGTTACACGCCATATAAAAAAACA
Found at i:28517323 original size:26 final size:25
Alignment explanation
Indices: 28517252--28517325 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
28517242 AAAAATACTG
*
28517252 TTGTTACACGCCATATAAAAAAACA
1 TTGTTACACGCCATATTAAAAAACA
* *
28517277 -TGTTACACGCCATGGTTAAAAAAGA
1 TTGTTACACGCCAT-ATTAAAAAACA
*
28517302 TTGTTACACGCTATATTGAAAAAA
1 TTGTTACACGCCATATT-AAAAAA
28517326 AAATATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 13 0.32
25 10 0.24
26 18 0.44
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (25 bp):
TTGTTACACGCCATATTAAAAAACA
Found at i:28517338 original size:32 final size:32
Alignment explanation
Indices: 28517301--28517385 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 32
28517291 GTTAAAAAAG
28517301 ATTGTTACACGCTATATTGAAAAAAAAATATT
1 ATTGTTACACGCTATATTGAAAAAAAAATATT
* * *
28517333 ATTGTTACATGTTATGTTG---AAAAAATATT
1 ATTGTTACACGCTATATTGAAAAAAAAATATT
* *
28517362 GTTGTTACACGAC-ATATTCAAAAA
1 ATTGTTACACG-CTATATTGAAAAA
28517386 CATTTTGTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
29 23 0.56
32 18 0.44
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (32 bp):
ATTGTTACACGCTATATTGAAAAAAAAATATT
Found at i:28517384 original size:29 final size:28
Alignment explanation
Indices: 28517323--28517398 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
28517313 TATATTGAAA
* ** * *
28517323 AAAAAATATTATTGTTACATGTTATGTTG
1 AAAAAATATT-TTGTTACACGACATATTC
28517352 AAAAAATATTGTTGTTACACGACATATTC
1 AAAAAATATT-TTGTTACACGACATATTC
*
28517381 -AAAAACATTTTGTTACAC
1 AAAAAATATTTTGTTACAC
28517399 TTTAATGCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.22
28 8 0.20
29 23 0.57
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (28 bp):
AAAAAATATTTTGTTACACGACATATTC
Found at i:28528340 original size:24 final size:24
Alignment explanation
Indices: 28528312--28528444 Score: 87
Period size: 24 Copynumber: 5.7 Consensus size: 24
28528302 CTATAATTAG
* *
28528312 TATGTTACACGCTATGTACAAAAA
1 TATGTGACACGCCATGTACAAAAA
28528336 TATGTGACACGCCATGTACAAAAA
1 TATGTGACACGCCATGTACAAAAA
** * * * *
28528360 CCTGTGACAAGCCGTGGT----TAG
1 TATGTGACACGCCAT-GTACAAAAA
** * * *
28528381 CGTGTTACACGCTATATACAAAAA
1 TATGTGACACGCCATGTACAAAAA
28528405 TATGTGACACGCCATGTACAAAAA
1 TATGTGACACGCCATGTACAAAAA
*
28528429 CT-TGTGACAAGCCATG
1 -TATGTGACACGCCATG
28528445 GTTAGCGTGT
Statistics
Matches: 81, Mismatches: 22, Indels: 12
0.70 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 11 0.14
24 66 0.81
25 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (24 bp):
TATGTGACACGCCATGTACAAAAA
Found at i:28528387 original size:69 final size:69
Alignment explanation
Indices: 28528273--28528558 Score: 380
Period size: 69 Copynumber: 4.1 Consensus size: 69
28528263 CTATGATATT
* * * **
28528273 ACACGCCATGTACAAAAATCTGTGACAAGCTATAATTAGTATGTTACACGCTATGTACAAAAATA
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATAGTTAGCGTGTTACACGCTATGTACAAAAATA
28528338 TGTG
66 TGTG
* * *
28528342 ACACGCCATGTACAAAAACCTGTGACAAGCCGTGGTTAGCGTGTTACACGCTATATACAAAAATA
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATAGTTAGCGTGTTACACGCTATGTACAAAAATA
28528407 TGTG
66 TGTG
* * *
28528411 ACACGCCATGTACAAAAACTTGTGACAAGCCATGGTTAGCGTGTTACATGCTATGTACAAAAATA
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATAGTTAGCGTGTTACACGCTATGTACAAAAATA
28528476 TGTG
66 TGTG
* * * *
28528480 ACAAGCCAAGTACAAAATCCTGTGACAAGCTATAGTTAG-GTTGTTACACG-TCATGTACAAAAA
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATAGTTAGCG-TGTTACACGCT-ATGTACAAAAA
28528543 CT-TGTG
64 -TATGTG
*
28528549 ACAAGCCATG
1 ACACGCCATG
28528559 GTTAGGTTGT
Statistics
Matches: 194, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
68 2 0.01
69 191 0.98
70 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (69 bp):
ACACGCCATGTACAAAAACCTGTGACAAGCCATAGTTAGCGTGTTACACGCTATGTACAAAAATA
TGTG
Found at i:28528587 original size:45 final size:45
Alignment explanation
Indices: 28528489--28528580 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
28528479 GACAAGCCAA
* * *
28528489 GTACAAAATCCTGTGACAAGCTATAGTTAGGTTGTTACACGTCAT
1 GTACAAAAACTTGTGACAAGCCATAGTTAGGTTGTTACACGTCAT
*
28528534 GTACAAAAACTTGTGACAAGCCATGGTTAGGTTGTTACACGTCAT
1 GTACAAAAACTTGTGACAAGCCATAGTTAGGTTGTTACACGTCAT
28528579 GT
1 GT
28528581 TGAAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (45 bp):
GTACAAAAACTTGTGACAAGCCATAGTTAGGTTGTTACACGTCAT
Found at i:28528635 original size:24 final size:26
Alignment explanation
Indices: 28528597--28528644 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
28528587 AAAATACTGT
*
28528597 TGTTACACGTAATG-T-AAAAAAACA
1 TGTTACACGCAATGTTGAAAAAAACA
*
28528621 TGTTACACGCCATGTTGAAAAAAA
1 TGTTACACGCAATGTTGAAAAAAA
28528645 AATATTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 1 0.05
26 7 0.35
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (26 bp):
TGTTACACGCAATGTTGAAAAAAACA
Found at i:28528644 original size:29 final size:31
Alignment explanation
Indices: 28528612--28528675 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
28528602 CACGTAATGT
28528612 AAAAAA-A-CATGTTACACGCCATGTTGAAA
1 AAAAAATATCATGTTACACGCCATGTTGAAA
**
28528641 AAAAAATATTGTTGTTACACGCCATGTTGAAA
1 AAAAAATA-TCATGTTACACGCCATGTTGAAA
28528673 AAA
1 AAA
28528676 TATTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 6 0.20
30 1 0.03
32 23 0.77
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (31 bp):
AAAAAATATCATGTTACACGCCATGTTGAAA
Found at i:28528676 original size:29 final size:30
Alignment explanation
Indices: 28528564--28528688 Score: 111
Period size: 29 Copynumber: 4.3 Consensus size: 30
28528554 CCATGGTTAG
* *
28528564 GTTGTTACACGTCATGTTGAAAAAAAATACT
1 GTTGTTACACGCCATGTTG-AAAAAAATATT
** *
28528595 GTTGTTACACGTAATG-T-AAAAAAACA--
1 GTTGTTACACGCCATGTTGAAAAAAATATT
28528621 --TGTTACACGCCATGTTGAAAAAAAAATATT
1 GTTGTTACACGCCATGTTG--AAAAAAATATT
28528651 GTTGTTACACGCCATGTTG-AAAAAATATT
1 GTTGTTACACGCCATGTTGAAAAAAATATT
* *
28528680 ATTATTACA
1 GTTGTTACA
28528689 TGACATATTC
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
24 12 0.15
25 1 0.01
28 16 0.20
29 17 0.22
30 1 0.01
31 15 0.19
32 17 0.22
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (30 bp):
GTTGTTACACGCCATGTTGAAAAAAATATT
Found at i:28528702 original size:29 final size:29
Alignment explanation
Indices: 28528641--28528703 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
28528631 CATGTTGAAA
* * * * *
28528641 AAAAAATATTGTTGTTACACGCCATGTTG
1 AAAAAATATTATTATTACACGACATATTC
*
28528670 AAAAAATATTATTATTACATGACATATTC
1 AAAAAATATTATTATTACACGACATATTC
28528699 AAAAA
1 AAAAA
28528704 CATTTTGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (29 bp):
AAAAAATATTATTATTACACGACATATTC
Found at i:28529935 original size:29 final size:29
Alignment explanation
Indices: 28529867--28529944 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 29
28529857 ATATTATGTG
28529867 TTAGTTATTATGGATATTCAATATATCTTGC
1 TTAGTTATTATGGATATTC-A-ATATCTTGC
**
28529898 TTAACTATTATGGATATTGC-ATATCTTGC
1 TTAGTTATTATGGATATT-CAATATCTTGC
28529927 TTAGTTATTATGGATATT
1 TTAGTTATTATGGATATT
28529945 ATAAATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 25 0.60
31 16 0.38
32 1 0.02
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (29 bp):
TTAGTTATTATGGATATTCAATATCTTGC
Found at i:28542317 original size:6 final size:6
Alignment explanation
Indices: 28542306--28542330 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28542296 CTTCTCCTTA
28542306 GGCTTG GGCTTG GGCTTG GGCTTG G
1 GGCTTG GGCTTG GGCTTG GGCTTG G
28542331 CTACAGCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGCTTG
Found at i:28546721 original size:30 final size:29
Alignment explanation
Indices: 28546659--28546722 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
28546649 AGTGATAAAG
* *
28546659 GCTTATTAGACTCAAAATAAAATATAATA
1 GCTTATTAGACTCAAAATAAAATACAAAA
28546688 GCTTATTTAG-CTCAAAATAAAAATACAAAA
1 GCTTA-TTAGACTCAAAAT-AAAATACAAAA
28546718 GCTTA
1 GCTTA
28546723 ATTGAACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (29 bp):
GCTTATTAGACTCAAAATAAAATACAAAA
Found at i:28549424 original size:29 final size:29
Alignment explanation
Indices: 28549338--28549427 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
28549328 AATGTTAAAG
28549338 TTTTAATTATAAATTA-TAAAAAGTTAATA
1 TTTTAATTATAAATTATTAAAAA-TTAATA
*
28549367 TTTTAAATT-TAAA-AATT--AAATTAGA-A
1 TTTT-AATTATAAATTATTAAAAATTA-ATA
28549393 TTTTAATTATAAATTATTAAAAATTAATA
1 TTTTAATTATAAATTATTAAAAATTAATA
28549422 TTTTAA
1 TTTTAA
28549428 AGTTAAAGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
25 4 0.08
26 12 0.24
27 7 0.14
28 2 0.04
29 22 0.43
30 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTAATTATAAATTATTAAAAATTAATA
Found at i:28549479 original size:44 final size:43
Alignment explanation
Indices: 28549393--28549479 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
28549383 TAAATTAGAA
**
28549393 TTTTAATTATAAATTATTAAAAATTAATATTTTAAAGTTAAAG
1 TTTTAATTATAAATTATTAAAAATTAATATTTTAAAAATAAAG
**
28549436 TTTTAATTATAAATT-TTGAATATTTTAATATTTTAAAAATAAAG
1 TTTTAATTATAAATTATT-AA-AAATTAATATTTTAAAAATAAAG
28549480 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.05
43 17 0.45
44 19 0.50
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (43 bp):
TTTTAATTATAAATTATTAAAAATTAATATTTTAAAAATAAAG
Found at i:28549552 original size:27 final size:27
Alignment explanation
Indices: 28549517--28549568 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28549507 TTAATGTTTT
*
28549517 AATTGTAAAATATTAATACTTTAAATG
1 AATTATAAAATATTAATACTTTAAATG
* *
28549544 AATTATAAATTATTAATATTTTAAA
1 AATTATAAAATATTAATACTTTAAA
28549569 CTATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTATAAAATATTAATACTTTAAATG
Found at i:28550640 original size:16 final size:17
Alignment explanation
Indices: 28550619--28550655 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
28550609 AATTTTAAAT
28550619 AATAGTTAAAT-ATATA
1 AATAGTTAAATAATATA
28550635 AATAGTTAAATAATATA
1 AATAGTTAAATAATATA
28550652 AATA
1 AATA
28550656 AATAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
AATAGTTAAATAATATA
Found at i:28552310 original size:109 final size:108
Alignment explanation
Indices: 28552111--28552311 Score: 264
Period size: 109 Copynumber: 1.9 Consensus size: 108
28552101 TGTTACACGC
* *
28552111 CATGTTGAAAATATAGTTGTTACATGCTAAGTTGAAAATTTAATTGTTACACGTCATGTTAAAAA
1 CATGTTGAAAATATAGTTGCTACATGCCAAGTTGAAAATTTAATTGTTACACGTCATGTTAAAAA
*
28552176 TGTAGTTGTTACACGCTATGTTGAAAATTTAGTTGTTACATAT
66 TGTAGTTGTTACACGCTATGATGAAAATTTAGTTGTTACATAT
* * * *
28552219 CATGTTGAAAAATGTAGTTGCTACATGCCATA-TTGAAGATTTACTTGTTACATG-CATGTTGAA
1 CATGTTG-AAAATATAGTTGCTACATGCCA-AGTTGAAAATTTAATTGTTACACGTCATGTT-AA
* *
28552282 AAATTTAGTTGTTACATG-TCATGATGAAAA
63 AAATGTAGTTGTTACACGCT-ATGATGAAAA
28552312 AGTTGTTACA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
108 14 0.17
109 65 0.81
110 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (108 bp):
CATGTTGAAAATATAGTTGCTACATGCCAAGTTGAAAATTTAATTGTTACACGTCATGTTAAAAA
TGTAGTTGTTACACGCTATGATGAAAATTTAGTTGTTACATAT
Found at i:28552311 original size:27 final size:27
Alignment explanation
Indices: 28552027--28552311 Score: 231
Period size: 27 Copynumber: 10.6 Consensus size: 27
28552017 AATATTATTA
* *
28552027 ATGTCATATTGAGAAATGTAG-TGTTAC
1 ATGTCATGTTGA-AAATTTAGTTGTTAC
* * * * *
28552054 GTGCCATGTTCTAAAATTTAGCTGTTAA
1 ATGTCATGTT-GAAAATTTAGTTGTTAC
* * *
28552082 ATGTTATGTTGGAAA--TAATTGTTAC
1 ATGTCATGTTGAAAATTTAGTTGTTAC
* * *
28552107 ACGCCATGTTGAAAATATAGTTGTTAC
1 ATGTCATGTTGAAAATTTAGTTGTTAC
* *
28552134 ATG-CTAAGTTGAAAATTTAATTGTTAC
1 ATGTC-ATGTTGAAAATTTAGTTGTTAC
* * *
28552161 ACGTCATGTTAAAAATGTAGTTGTTAC
1 ATGTCATGTTGAAAATTTAGTTGTTAC
*
28552188 ACG-CTATGTTGAAAATTTAGTTGTTAC
1 ATGTC-ATGTTGAAAATTTAGTTGTTAC
* * *
28552215 ATATCATGTTGAAAAATGTAGTTGCTAC
1 ATGTCATGTTG-AAAATTTAGTTGTTAC
* * * *
28552243 ATGCCATATTGAAGATTTACTTGTTAC
1 ATGTCATGTTGAAAATTTAGTTGTTAC
28552270 ATG-CATGTTGAAAAATTTAGTTGTTAC
1 ATGTCATGTTG-AAAATTTAGTTGTTAC
*
28552297 ATGTCATGATGAAAA
1 ATGTCATGTTGAAAA
28552312 AGTTGTTACA
Statistics
Matches: 202, Mismatches: 45, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
25 18 0.09
26 8 0.04
27 133 0.66
28 43 0.21
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (27 bp):
ATGTCATGTTGAAAATTTAGTTGTTAC
Found at i:28554628 original size:20 final size:20
Alignment explanation
Indices: 28554602--28554647 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
28554592 AATCTTACCT
* *
28554602 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
28554623 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
28554644 TTTT
1 TTTT
28554648 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:28554649 original size:22 final size:22
Alignment explanation
Indices: 28554607--28554647 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28554597 TACCTTTTTT
*
28554607 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
28554629 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
28554648 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:28568811 original size:26 final size:26
Alignment explanation
Indices: 28568751--28568812 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
28568741 ACCATATACC
*
28568751 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
28568777 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
28568803 CATCATCATC
1 CATCATCATC
28568813 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:28569105 original size:42 final size:42
Alignment explanation
Indices: 28569047--28569169 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
28569037 ATGGAGGCAA
* *
28569047 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
28569089 CAACGGCTTATATGCACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
28569131 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
28569170 TCAAATCAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:28580527 original size:32 final size:32
Alignment explanation
Indices: 28580490--28580612 Score: 122
Period size: 32 Copynumber: 3.8 Consensus size: 32
28580480 TTTACACTAG
* * *
28580490 TTTTTCATAGGCTAAACTAAAACCCAAAGTGA
1 TTTTTCAAAGGCTCAACCAAAACCCAAAGTGA
* *
28580522 TTTTTCAAAGGCTCAACCACAACCTTTCACAA-TGG
1 TTTTTCAAAGGCTCAACCAAAACC---CA-AAGTGA
** *
28580557 TTTTTCATGGGCTCAACCAAAACCCAACGTGA
1 TTTTTCAAAGGCTCAACCAAAACCCAAAGTGA
*
28580589 TTTTTCAAAGGCTCAACCACAACC
1 TTTTTCAAAGGCTCAACCAAAACC
28580613 TACAAGAATG
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
31 1 0.01
32 45 0.62
35 25 0.34
36 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (32 bp):
TTTTTCAAAGGCTCAACCAAAACCCAAAGTGA
Found at i:28580583 original size:67 final size:67
Alignment explanation
Indices: 28580475--28580613 Score: 215
Period size: 67 Copynumber: 2.1 Consensus size: 67
28580465 GTTTAGCCAA
* * *
28580475 AACCTTTTACACTAGTTTTTCATAGGCTAAACTAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
1 AACCTTTCACAATAGTTTTTCATAGGCTAAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
28580540 AC
66 AC
* * * *
28580542 AACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCCAACGTGATTTTTCAAAGGCTCAACC
1 AACCTTTCACAATAGTTTTTCATAGGCTAAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
28580607 AC
66 AC
28580609 AACCT
1 AACCT
28580614 ACAAGAATGT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.28
Consensus pattern (67 bp):
AACCTTTCACAATAGTTTTTCATAGGCTAAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
AC
Found at i:28580628 original size:35 final size:34
Alignment explanation
Indices: 28580519--28580630 Score: 106
Period size: 35 Copynumber: 3.3 Consensus size: 34
28580509 AAACCCAAAG
*
28580519 TGATTTTTCAAAGGCTCAACCACAACCTTTC-ACAA
1 TGATTTTTCAAAGGCTCAACCACAACC--TCAAGAA
* ** *
28580554 TGGTTTTTCATGGGCTCAACCAAAACC-CAACG--
1 TGATTTTTCAAAGGCTCAACCACAACCTCAA-GAA
28580586 TGATTTTTCAAAGGCTCAACCACAACCTACAAGAA
1 TGATTTTTCAAAGGCTCAACCACAACCT-CAAGAA
*
28580621 TGTTTTTTCA
1 TGATTTTTCA
28580631 CTAGATCAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
32 24 0.39
33 2 0.03
34 3 0.05
35 32 0.52
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (34 bp):
TGATTTTTCAAAGGCTCAACCACAACCTCAAGAA
Found at i:28580628 original size:67 final size:67
Alignment explanation
Indices: 28580489--28580630 Score: 205
Period size: 67 Copynumber: 2.1 Consensus size: 67
28580479 TTTTACACTA
* *
28580489 GTTTTTCATAGGCTAAACTAAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTTCACAA
1 GTTTTTCATAGGCTAAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTACACAA
28580554 TG
66 TG
* * * *
28580556 GTTTTTCATGGGCTCAACCAAAACCCAACGTGATTTTTCAAAGGCTCAACCACAACC-TACAAGA
1 GTTTTTCATAGGCTAAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTAC-ACA
28580620 ATG
65 ATG
*
28580623 TTTTTTCA
1 GTTTTTCA
28580631 CTAGATCAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 2 0.03
67 65 0.97
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (67 bp):
GTTTTTCATAGGCTAAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTACACAA
TG
Found at i:28580640 original size:67 final size:67
Alignment explanation
Indices: 28580508--28580645 Score: 190
Period size: 67 Copynumber: 2.1 Consensus size: 67
28580498 AGGCTAAACT
* * *
28580508 AAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTTCACAATGGTTTTTCATGGGCTCAA
1 AAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTACACAATGGTTTTTCATGAGATCAA
28580573 CC
66 CC
* * *
28580575 AAAACCCAACGTGATTTTTCAAAGGCTCAACCACAACC-TACAAGAATGTTTTTTCACT-AGATC
1 AAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTAC-ACAATGGTTTTTCA-TGAGATC
28580638 AACC
64 AACC
28580642 AAAA
1 AAAA
28580646 TTCAACACCT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
66 2 0.03
67 60 0.95
68 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (67 bp):
AAAACCCAAAGTGATTTTTCAAAGGCTCAACCACAACCTTACACAATGGTTTTTCATGAGATCAA
CC
Found at i:28590520 original size:42 final size:42
Alignment explanation
Indices: 28590405--28590521 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
28590395 ATCTCATATG
* *
28590405 CAACGGCTTATGCGCACTTCC-ACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCA-TTCCTACTCGCACATAGTCGGGTCAA
* * *
28590447 CAACGGTTTATGTGCA-TGCTCACTCGTACATAGTCGGGTCAA
1 CAACGGCTTATGTGCATTCCT-ACTCGCACATAGTCGGGTCAA
* *
28590489 CAACAGCTTATGTGCATTCCTACTCACACATAG
1 CAACGGCTTATGTGCATTCCTACTCGCACATAG
28590522 CCGAGTCCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.03
42 57 0.92
43 3 0.05
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.26
Consensus pattern (42 bp):
CAACGGCTTATGTGCATTCCTACTCGCACATAGTCGGGTCAA
Found at i:28613459 original size:35 final size:35
Alignment explanation
Indices: 28613413--28613482 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
28613403 TAAAGAGACC
*
28613413 ATCAAGCTTATCTTTCCTTTTTAGCATTCATCTTA
1 ATCAAGCTTATCTTTCCTTTCTAGCATTCATCTTA
*
28613448 ATCAAGCTTATCTTTTCTTTCTAGCATTCATCTTA
1 ATCAAGCTTATCTTTCCTTTCTAGCATTCATCTTA
28613483 GTCTTCCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (35 bp):
ATCAAGCTTATCTTTCCTTTCTAGCATTCATCTTA
Found at i:28613766 original size:36 final size:36
Alignment explanation
Indices: 28613718--28613786 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
28613708 TTTATGGATT
*
28613718 GTGTAAGAGTTATCACTTGATCTTGTGAAAAAGTCG
1 GTGTAAGAGTTATCACTTGATCTCGTGAAAAAGTCG
*
28613754 GTGTAA-AGGTTATCACTTGATCTCGTTAAAAAG
1 GTGTAAGA-GTTATCACTTGATCTCGTGAAAAAG
28613787 AAAAAATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (36 bp):
GTGTAAGAGTTATCACTTGATCTCGTGAAAAAGTCG
Found at i:28613767 original size:89 final size:88
Alignment explanation
Indices: 28613665--28613918 Score: 343
Period size: 89 Copynumber: 2.9 Consensus size: 88
28613655 TGAAAAGTTA
*
28613665 GTGTAAGGGTTATCACTTGATCTCGTTAAAAAGAAAAAATTCCTTTATGGATTGTGTAAGAGTTA
1 GTGTAAAGGTTATCACTTGATCTCGTTAAAAAGAAAAAATTCCTTTATGGATTGTGTAAGAGTTA
*
28613730 TCACTTGATCTTGTGAAAAAGTCG
66 TCACTTGATCTTGTG-AAAAGCCG
* *
28613754 GTGTAAAGGTTATCACTTGATCTCGTTAAAAAGAAAAAATTCTTTTGTGGATTGTGTAAGAGTTA
1 GTGTAAAGGTTATCACTTGATCTCGTTAAAAAGAAAAAATTCCTTTATGGATTGTGTAAGAGTTA
*
28613819 TCACATGATCTTGTGAAAAGCCG
66 TCACTTGATCTTGTGAAAAGCCG
* * * * * ** *
28613842 GTGT-AAGGGT-T-ACTTGATCTCATTAAAAAGCAAAGAATCCCTTTTTACATTGCGTAAGAGTT
1 GTGTAAAGGTTATCACTTGATCTCGTTAAAAAG-AAAAAATTCCTTTATGGATTGTGTAAGAGTT
*
28613904 ATCGCTTGATCTTGT
65 ATCACTTGATCTTGT
28613919 TAAAGAGCAA
Statistics
Matches: 148, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
85 18 0.12
86 38 0.26
87 5 0.03
88 11 0.07
89 76 0.51
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (88 bp):
GTGTAAAGGTTATCACTTGATCTCGTTAAAAAGAAAAAATTCCTTTATGGATTGTGTAAGAGTTA
TCACTTGATCTTGTGAAAAGCCG
Found at i:28615218 original size:7 final size:7
Alignment explanation
Indices: 28615206--28615247 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
28615196 ACAACGGGAG
28615206 AAAAGAA
1 AAAAGAA
28615213 AAAAG-A
1 AAAAGAA
28615219 AAAAGAA
1 AAAAGAA
* *
28615226 AAAACTAG
1 AAAA-GAA
28615234 AAAAGAA
1 AAAAGAA
28615241 AAAAGAA
1 AAAAGAA
28615248 TAGCTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 18 0.62
8 5 0.17
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:28615237 original size:15 final size:14
Alignment explanation
Indices: 28615203--28615246 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
28615193 GCAACAACGG
28615203 GAGAAAAGAAAAAA
1 GAGAAAAGAAAAAA
28615217 GA-AAAAGAAAAAA
1 GAGAAAAGAAAAAA
*
28615230 CTAGAAAAGAAAAAA
1 -GAGAAAAGAAAAAA
28615245 GA
1 GA
28615247 ATAGCTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.02
Consensus pattern (14 bp):
GAGAAAAGAAAAAA
Found at i:28615946 original size:60 final size:58
Alignment explanation
Indices: 28615849--28616016 Score: 221
Period size: 60 Copynumber: 2.8 Consensus size: 58
28615839 AAAAATGGGT
*
28615849 ACCTGAAGCCCCAATTTATATTAGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGA
1 ACCTGAAG-CCCGATTTATATT-GGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGA
* * *
28615909 ACCTGAAGCCTCGATTTATATTGGGTGGCGTGAGTAGTTCCCACAAGTAGGTAAAGGGGG
1 ACCTGAAGCC-CGATTTATATT-GGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGA
* * *
28615969 ACCTGAAGCCCTGATTCATA-TGATGGCGTGGGCAGTTCCCACGAGTAG
1 ACCTGAAGCCC-GATTTATATTGGTGGCGTGGGTAGTTCCCACGAGTAG
28616017 CTGATGATGT
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
58 23 0.24
59 4 0.04
60 69 0.72
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.24
Consensus pattern (58 bp):
ACCTGAAGCCCGATTTATATTGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGA
Found at i:28619672 original size:2 final size:2
Alignment explanation
Indices: 28619665--28619695 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28619655 TATCTTTTCT
28619665 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 T
28619696 TTTTGGGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28623526 original size:22 final size:23
Alignment explanation
Indices: 28623500--28623545 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28623490 CGGCAGTGGC
* *
28623500 TTCCTC-TTTCTTTTCTTTCCCT
1 TTCCTCGTTTCTTCTCTTCCCCT
28623522 TTCCTCGTTTCTTCTCTTCCCCT
1 TTCCTCGTTTCTTCTCTTCCCCT
28623545 T
1 T
28623546 CCTTCTGCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (23 bp):
TTCCTCGTTTCTTCTCTTCCCCT
Found at i:28623547 original size:22 final size:22
Alignment explanation
Indices: 28623499--28623548 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
28623489 CCGGCAGTGG
*
28623499 CTTCCTCTTTCTTTTCTTTCCC
1 CTTCCTCTTTCTTCTCTTTCCC
*
28623521 TTTCCTCGTTTCTTCTC-TTCCC
1 CTTCCTC-TTTCTTCTCTTTCCC
28623543 CTTCCT
1 CTTCCT
28623549 TCTGCCGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.00, C:0.42, G:0.02, T:0.56
Consensus pattern (22 bp):
CTTCCTCTTTCTTCTCTTTCCC
Found at i:28651691 original size:18 final size:19
Alignment explanation
Indices: 28651668--28651703 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28651658 ATGAAGCTCA
28651668 ATCATGG-AAAACATGCTT
1 ATCATGGAAAAACATGCTT
28651686 ATCATGGAAAAACATGCT
1 ATCATGGAAAAACATGCT
28651704 GAAAAATGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (19 bp):
ATCATGGAAAAACATGCTT
Found at i:28652417 original size:27 final size:26
Alignment explanation
Indices: 28652387--28652455 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
28652377 GTTTCCGCAC
*
28652387 TTGGAAGGTCCTTGGGTACTT-TCGTGA
1 TTGGAAGG-CCTTGGGCACTTCT-GTGA
* *
28652414 TTGGAATGCCCTTGGGCACTTCTGTGC
1 TTGGAA-GGCCTTGGGCACTTCTGTGA
28652441 TTGGAACGGCCTTGG
1 TTGGAA-GGCCTTGG
28652456 ACGGTTCCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.33
Consensus pattern (26 bp):
TTGGAAGGCCTTGGGCACTTCTGTGA
Found at i:28652517 original size:18 final size:18
Alignment explanation
Indices: 28652491--28652536 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
28652481 GGGCGCTTTT
*
28652491 GCACTTGGAACCCCTTAA
1 GCACTTGGAACCCCCTAA
* *
28652509 GCGCTTGGAACCCCCTAG
1 GCACTTGGAACCCCCTAA
28652527 GCACTTGGAA
1 GCACTTGGAA
28652537 TTCCTGTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (18 bp):
GCACTTGGAACCCCCTAA
Found at i:28652586 original size:27 final size:26
Alignment explanation
Indices: 28652543--28652605 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
28652533 GGAATTCCTG
*
28652543 TGGGCATTTCTATGCTTAGAACTCCCT
1 TGGGCATTTCTACGCTTAGAAC-CCCT
*
28652570 TGGGCATTTTTACGCTTAGAACCCCT
1 TGGGCATTTCTACGCTTAGAACCCCT
* *
28652596 TAGGCGTTTC
1 TGGGCATTTC
28652606 CGTGATTGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TGGGCATTTCTACGCTTAGAACCCCT
Found at i:28652632 original size:26 final size:27
Alignment explanation
Indices: 28652603--28652670 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
28652593 CCTTAGGCGT
28652603 TTCCGTGATTGGAACGCCCTAG-GTGC
1 TTCCGTGATTGGAACGCCCTAGTGTGC
* * *
28652629 TTCC-TCACTTGGAACTCCCTTGTGTGC
1 TTCCGTGA-TTGGAACGCCCTAGTGTGC
* *
28652656 TTCTGTGCTTGGAAC
1 TTCCGTGATTGGAAC
28652671 ACGCACTTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 2 0.06
26 16 0.48
27 14 0.42
28 1 0.03
ACGTcount: A:0.13, C:0.28, G:0.25, T:0.34
Consensus pattern (27 bp):
TTCCGTGATTGGAACGCCCTAGTGTGC
Found at i:28656411 original size:19 final size:19
Alignment explanation
Indices: 28656387--28656424 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28656377 CCATTTGACT
28656387 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
28656406 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
28656425 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:28664351 original size:17 final size:17
Alignment explanation
Indices: 28664298--28664355 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
28664288 AACACTACGT
28664298 ATTAAATACTCATACTC
1 ATTAAATACTCATACTC
* *
28664315 ATT-ACTTCTCATA---
1 ATTAAATACTCATACTC
**
28664328 AAAAAATACTCATACTC
1 ATTAAATACTCATACTC
28664345 ATTAAATACTC
1 ATTAAATACTC
28664356 GATTAAAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
13 1 0.03
14 8 0.28
16 8 0.28
17 12 0.41
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAATACTCATACTC
Found at i:28667291 original size:12 final size:14
Alignment explanation
Indices: 28667261--28667294 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
28667251 TTCATAATGG
28667261 ATACAAGTTGTTAA
1 ATACAAGTTGTTAA
28667275 ATACAA-TTGTT-A
1 ATACAAGTTGTTAA
28667287 ATACAAGT
1 ATACAAGT
28667295 AGGTTGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.37
13 6 0.32
14 6 0.32
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (14 bp):
ATACAAGTTGTTAA
Found at i:28668049 original size:2 final size:2
Alignment explanation
Indices: 28668042--28668084 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28668032 ATGTCTTTTA
28668042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28668084 A
1 A
28668085 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28672958 original size:21 final size:21
Alignment explanation
Indices: 28672932--28672973 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28672922 AAAGTTTTCC
28672932 TTCATCAATAAGACATCAATT
1 TTCATCAATAAGACATCAATT
*
28672953 TTCATCAATAAGATATCAATT
1 TTCATCAATAAGACATCAATT
28672974 ATAACAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TTCATCAATAAGACATCAATT
Found at i:28674071 original size:35 final size:35
Alignment explanation
Indices: 28674001--28674248 Score: 277
Period size: 35 Copynumber: 7.1 Consensus size: 35
28673991 CACTTGATTA
* * *
28674001 AAATTGTTTAATT-A--TGTTGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
28674033 AAATTGTTTAATTAAATCATTAGACCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* *
28674068 AAATTGTGTAATTAAGTTATTTGGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
**** *
28674103 AAATTAAACAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* *
28674138 AAATTTGTTTAATTAAGTCATTGGGCCTAATTGATT
1 AAA-TTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
28674174 AAATTGTTTAATTAAATTGTTGTGCTTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
*
28674209 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
28674244 AAATT
1 AAATT
28674249 AAACTGAAAT
Statistics
Matches: 179, Mismatches: 33, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
32 13 0.07
33 1 0.01
35 135 0.75
36 30 0.17
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:28674159 original size:106 final size:106
Alignment explanation
Indices: 28674021--28674248 Score: 307
Period size: 106 Copynumber: 2.2 Consensus size: 106
28674011 ATTATGTTGT
* * *
28674021 GCCTAATTAACTAAA-TTGTTTAATTAAATCATTAGACCTAATTAATTAAATTGTGTAATTAAGT
1 GCCTAATTGATTAAATTTGTTTAATTAAATCATTAGACCTAATTAATTAAATTGTGTAATTAAAT
*
28674085 TATT-TGGCCTAATTAATTAAATTAAACAATTAAGTTATTGG
66 TGTTGT-GCCTAATTAATTAAATTAAACAATTAAGTTATTGG
* * * * *
28674126 GCCTAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAATTGTTTAATTAAAT
1 GCCTAATTGATTAAATTTGTTTAATTAAATCATTAGACCTAATTAATTAAATTGTGTAATTAAAT
* ****
28674191 TGTTGTGCTTAATTAATTAAATTGTTTAATTAAGTTATTGG
66 TGTTGTGCCTAATTAATTAAATTAAACAATTAAGTTATTGG
28674232 GCCTAATTGATTAAATT
1 GCCTAATTGATTAAATT
28674249 AAACTGAAAT
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
105 13 0.12
106 93 0.87
107 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (106 bp):
GCCTAATTGATTAAATTTGTTTAATTAAATCATTAGACCTAATTAATTAAATTGTGTAATTAAAT
TGTTGTGCCTAATTAATTAAATTAAACAATTAAGTTATTGG
Found at i:28674204 original size:141 final size:138
Alignment explanation
Indices: 28673994--28674252 Score: 367
Period size: 141 Copynumber: 1.9 Consensus size: 138
28673984 TCTCAAGCAC
* *
28673994 TTGATTAAAATTGTTTAATTATGTTGTGCCTAATTAACTAAATTGTTTAATTAAATCATTAGACC
1 TTGATTAAAATTGTTTAATTATATTGGGCCTAATTAACTAAATTGTTTAATTAAATCATTAGACC
*
28674059 TAATTAATTAAATTGTGTAATTAAGTTATTTGGCCTAATTAATTAAATTAAACAATTAAGTTATT
66 TAATTAATTAAATTGTGTAATTAAGTTATTGGGCCTAATTAATTAAATTAAACAATTAAGTTATT
28674124 GGGCCTAA
131 GGGCCTAA
* * * **
28674132 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAATTGTTTAATTAAATTGTT-G
1 TTGATTAAAATTGTTTAATT-A-T-ATTGGGCCTAATTAACTAAATTGTTTAATTAAATCATTAG
* * * *
28674196 TGCTTAATTAATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAAC
63 -ACCTAATTAATTAAATTGTGTAATTAAGTTATTGGGCCTAATTAATTAAATTAAAC
28674253 TGAAATGCCC
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
138 19 0.18
139 1 0.01
140 2 0.02
141 83 0.79
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (138 bp):
TTGATTAAAATTGTTTAATTATATTGGGCCTAATTAACTAAATTGTTTAATTAAATCATTAGACC
TAATTAATTAAATTGTGTAATTAAGTTATTGGGCCTAATTAATTAAATTAAACAATTAAGTTATT
GGGCCTAA
Found at i:28674822 original size:19 final size:19
Alignment explanation
Indices: 28674798--28674834 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
28674788 CCATTTGACT
28674798 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
28674817 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
28674835 CGATTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:28677543 original size:13 final size:13
Alignment explanation
Indices: 28677525--28677555 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
28677515 TTGGGTTTAA
28677525 TTAATTAAATTAT
1 TTAATTAAATTAT
28677538 TTAATTAAATTAT
1 TTAATTAAATTAT
28677551 TTAAT
1 TTAAT
28677556 CAAAATAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTAAATTAT
Found at i:28686786 original size:74 final size:74
Alignment explanation
Indices: 28686598--28686798 Score: 262
Period size: 73 Copynumber: 2.7 Consensus size: 74
28686588 TATGGCCAGT
* * * *
28686598 TCAGAA-ACAGAGACGACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCAG
1 TCAGAAGATAGAGACGACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTCACTACCAA
* * *
28686662 AAGCTGGGT
66 AAACTAGGA
* ** *
28686671 TCAG-AGATAGAGATGACTTAATCGACTAAGAAATATTGTTAGTTGACTAAGAGCTCACTACCAA
1 TCAGAAGATAGAGACGACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTCACTACCAA
28686735 AAACTAGGA
66 AAACTAGGA
* * *
28686744 TCAGAAGATAGAGACGACTTAATCTACTAAGAAGCATAGTTAGTCAACTAAGAGC
1 TCAGAAGATAGAGACGACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGC
28686799 ATTTTGTCAG
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
72 1 0.01
73 64 0.59
74 43 0.40
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (74 bp):
TCAGAAGATAGAGACGACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTCACTACCAA
AAACTAGGA
Found at i:28703633 original size:21 final size:20
Alignment explanation
Indices: 28703592--28703647 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
28703582 CTTGGTCTAT
*
28703592 AAATTGAATTAGTTAATTTA
1 AAATTGAATTAATTAATTTA
*
28703612 AAATTGAATATAATTCATTT-
1 AAATTGAAT-TAATTAATTTA
28703632 AAATT-AATTAATTAAT
1 AAATTGAATTAATTAAT
28703648 AAAATTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.22
19 3 0.09
20 14 0.44
21 8 0.25
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTGAATTAATTAATTTA
Found at i:28704687 original size:29 final size:30
Alignment explanation
Indices: 28704649--28704722 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
28704639 TTTAAAAATT
* ***
28704649 TTAAATAAATTTTTATTTTTTTATTACGAG
1 TTAATTAAATTTTTATACGTTTATTACGAG
* *
28704679 -TAATTAAATTTGTATACGTTTATTATGAG
1 TTAATTAAATTTTTATACGTTTATTACGAG
*
28704708 TTAATTAAAGTTTTA
1 TTAATTAAATTTTTA
28704723 AAACTAATGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (30 bp):
TTAATTAAATTTTTATACGTTTATTACGAG
Found at i:28720954 original size:276 final size:270
Alignment explanation
Indices: 28720542--28721072 Score: 683
Period size: 276 Copynumber: 1.9 Consensus size: 270
28720532 TCCCATTTAA
* *
28720542 TCCTCATAATTTTGATGCAACTGCTTAAGTACCAGAATAGTAAGTCAGGAGTGTCATTGACTTGT
1 TCCTCATAATTTTGATGCAACTGCTTAAGTACCAGAATAGTAAGTAACGAGTG--ATTGACTTGT
** * * *
28720607 CAACTCAAGTTTGGAAGAAGAAGCAATAGAGTGCTTACAATGACTAAATAATACAGGCAATAAAA
64 CAACTCAAGTTTGGAAGAAGAAGCAATAGAGCACTTACAATAACAAAATAATACAGGCAACAAAA
* *
28720672 TGGCCAGAATTTCAAATTCTACTGCAGAGCTATTGCAAAAGCATAAGCAGCTAATGAATCCATTG
129 TGGCCAGAATGTCAAATTCTACTGCAGAACTATTGCAAAA-CATAAGCAGCTAATGAATCCATT-
*
28720737 ATATTTAAGTTACAAGATGACTTCATTCTACAATTACATAGGAGTATCTTTTTGATGAAATTGAA
192 -TATTT-AGTT--AACATGACTTCATTCTACAATTACATAGGAGT-TC-TTTTGATGAAATTGAA
28720802 GTATATTTTAAGATTGCATG
251 GTATATTTTAAGATTGCATG
* * *
28720822 TCCTCATAATTTTGATGCAAACTGC-TACAGTACTAGAATTGTACGTAACGAGTG-TT-A-TTGT
1 TCCTCATAATTTTGATGC-AACTGCTTA-AGTACCAGAATAGTAAGTAACGAGTGATTGACTTGT
* * * * * * *
28720883 CAAGTCAAGTTTGGCAGCAGAAGCAATGGAGCATTTGCAATAACAAAATAATACAGGCAACAAAG
64 CAACTCAAGTTTGGAAGAAGAAGCAATAGAGCACTTACAATAACAAAATAATACAGGCAACAAAA
* * * *
28720948 TGGCCAGAATGTCAAATTTTGCTGCAGAACTATTGCAATACATAAGTAGCTAATGAATCCATTTA
129 TGGCCAGAATGTCAAATTCTACTGCAGAACTATTGCAAAACATAAGCAGCTAATGAATCCATTTA
* * *
28721013 TTTAGTTAACCTGACTTCATTCTGCAATTACATAGGAGTTCTTTTGATGGAATTGAAGTA
194 TTTAGTTAACATGACTTCATTCTACAATTACATAGGAGTTCTTTTGATGAAATTGAAGTA
28721073 CTTTTTACAA
Statistics
Matches: 222, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
268 18 0.08
269 2 0.01
270 29 0.13
272 4 0.02
273 5 0.02
275 22 0.10
276 92 0.41
277 1 0.00
278 2 0.01
280 20 0.09
281 27 0.12
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (270 bp):
TCCTCATAATTTTGATGCAACTGCTTAAGTACCAGAATAGTAAGTAACGAGTGATTGACTTGTCA
ACTCAAGTTTGGAAGAAGAAGCAATAGAGCACTTACAATAACAAAATAATACAGGCAACAAAATG
GCCAGAATGTCAAATTCTACTGCAGAACTATTGCAAAACATAAGCAGCTAATGAATCCATTTATT
TAGTTAACATGACTTCATTCTACAATTACATAGGAGTTCTTTTGATGAAATTGAAGTATATTTTA
AGATTGCATG
Found at i:28723239 original size:38 final size:36
Alignment explanation
Indices: 28723187--28723278 Score: 94
Period size: 38 Copynumber: 2.5 Consensus size: 36
28723177 ATTTTTATTA
* * *
28723187 AATAATTTAATTTTTAAAAATATTATATTTAAATTTAT
1 AATATTTTTATTTTTAAAAATATT-TAATTAAATTT-T
* ***
28723225 AATATTTTTATTTTTTATTGTATTTAATTAAATTTT
1 AATATTTTTATTTTTAAAAATATTTAATTAAATTTT
*
28723261 TATATTTTTATTTTTAAA
1 AATATTTTTATTTTTAAA
28723279 TCAAATAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
36 16 0.36
37 10 0.23
38 18 0.41
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (36 bp):
AATATTTTTATTTTTAAAAATATTTAATTAAATTTT
Found at i:28724095 original size:32 final size:33
Alignment explanation
Indices: 28724031--28724102 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
28724021 AGAAAATTTT
28724031 ATATTTTTTATTATTTAGATAAATTTTCG-AAA
1 ATATTTTTTATTATTTAGATAAATTTTCGAAAA
* * * *
28724063 ATATTTTTTGTTGTTTAGAT-CATTTTATGAAAA
1 ATATTTTTTATTATTTAGATAAATTTT-CGAAAA
28724096 ATATTTT
1 ATATTTT
28724103 CCATCATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.15
32 19 0.56
33 10 0.29
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (33 bp):
ATATTTTTTATTATTTAGATAAATTTTCGAAAA
Found at i:28724456 original size:73 final size:73
Alignment explanation
Indices: 28724379--28724516 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 73
28724369 CCTATACTTA
* * * *
28724379 TAAATATGTGTTCATTAAATTACAATCATTGAAATATTTTTTATTATAATTATTAGTAAGATTTA
1 TAAATATGTATTCATCAAATGACAATCATTAAAATATTTTTTATTATAATTATTAGTAAGATTTA
28724444 AACTTATT
66 AACTTATT
* ** *
28724452 TAAATGTGTATTCATCAAATGATGATTATTAAAATATTTTTTATTATAATTATTAGTAAGATTTA
1 TAAATATGTATTCATCAAATGACAATCATTAAAATATTTTTTATTATAATTATTAGTAAGATTTA
28724517 TTCCATTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (73 bp):
TAAATATGTATTCATCAAATGACAATCATTAAAATATTTTTTATTATAATTATTAGTAAGATTTA
AACTTATT
Found at i:28724610 original size:41 final size:37
Alignment explanation
Indices: 28724565--28724681 Score: 122
Period size: 35 Copynumber: 3.2 Consensus size: 37
28724555 TTTCATTAAA
28724565 AATATTTTATTAATTTAATAGTGTTGTATAAATTAAATATT
1 AATATTTTATTAATTTAATA-T-TT-T-TAAATTAAATATT
28724606 AATATTTTA--AA-TTAAT-TTTTTAAAGTTAAATATT
1 AATATTTTATTAATTTAATATTTTTAAA-TTAAATATT
*
28724640 AATATTTTTATT--TTTAATA-TTTTAAGTTAAATATT
1 AATA-TTTTATTAATTTAATATTTTTAAATTAAATATT
28724675 AATATTT
1 AATATTT
28724682 ATCAAATTTA
Statistics
Matches: 69, Mismatches: 1, Indels: 19
0.78 0.01 0.21
Matches are distributed among these distances:
33 4 0.06
34 17 0.25
35 20 0.29
36 12 0.17
38 5 0.07
39 2 0.03
41 9 0.13
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (37 bp):
AATATTTTATTAATTTAATATTTTTAAATTAAATATT
Found at i:28727532 original size:17 final size:17
Alignment explanation
Indices: 28727509--28727543 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28727499 TAAAAAGGAA
*
28727509 AAAAAAAGTTTAATATTT
1 AAAAAAA-TTAAATATTT
28727527 AAAAAAATTAAATATTT
1 AAAAAAATTAAATATTT
28727544 TTTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAAAAATTAAATATTT
Found at i:28727576 original size:29 final size:29
Alignment explanation
Indices: 28727544--28727612 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
28727534 TTAAATATTT
**
28727544 TTTTTATATTTT-TATTACGTTAAATTAA
1 TTTTTATATTTTATATTAAATTAAATTAA
* *
28727572 GTTTTAATATTTTATTTTAAATTAAATTAA
1 -TTTTTATATTTTATATTAAATTAAATTAA
28727602 TTTTTATATTT
1 TTTTTATATTT
28727613 AAATTTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTTTATATTTTATATTAAATTAAATTAA
Found at i:28727619 original size:30 final size:30
Alignment explanation
Indices: 28727563--28727645 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
28727553 TTTTATTACG
* *
28727563 TTAAATTAAGTTTTAATATTT-TATTTTAAA
1 TTAAATTAA-TTTTTATATTTAAATTTTAAA
*
28727593 TTAAATTAATTTTTATATTTAAATTTTGAA
1 TTAAATTAATTTTTATATTTAAATTTTAAA
* * * *
28727623 TCAAATAAATCTTTATAATTAAA
1 TTAAATTAATTTTTATATTTAAA
28727646 AAATATCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 10 0.22
30 35 0.78
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TTAAATTAATTTTTATATTTAAATTTTAAA
Found at i:28727754 original size:33 final size:32
Alignment explanation
Indices: 28727680--28727754 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
28727670 ATATGAAGTT
* *
28727680 GATGTGATATACTAAATATAATAATTGAGAAT
1 GATGTGATATACTAAATATAATAATTAAGAAC
* * *
28727712 GATGAGATATATTAACATATTATAATTAATG-AC
1 GATGTGATATACTAA-ATATAATAATTAA-GAAC
28727745 GATGTGATAT
1 GATGTGATAT
28727755 GATAGTATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
32 13 0.37
33 21 0.60
34 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (32 bp):
GATGTGATATACTAAATATAATAATTAAGAAC
Found at i:28727884 original size:30 final size:30
Alignment explanation
Indices: 28727850--28727919 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
28727840 ATTAATCAAT
* *
28727850 ATTTATTTGATCTAAAAT-AAAAATATAGAA
1 ATTTATTTGATATAAAATAAAAAATA-AAAA
* *
28727880 ATTTAATTGA-ATATAATAAAAAATAAAAA
1 ATTTATTTGATATAAAATAAAAAATAAAAA
*
28727909 ATTTATATGAT
1 ATTTATTTGAT
28727920 TTTTTAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (30 bp):
ATTTATTTGATATAAAATAAAAAATAAAAA
Found at i:28742047 original size:122 final size:120
Alignment explanation
Indices: 28741848--28742082 Score: 362
Period size: 122 Copynumber: 1.9 Consensus size: 120
28741838 ACATAAAAAG
* * *
28741848 AAAAAGAAAAAGAAAAGGAGAAAAATAAATTAGGAGAATATTATAACCTTCATCTTCAAATGCAA
1 AAAAAGAAAAAGAAAAGGAGAAAAATAAACTAGGACAATAGTATAACCTTCATCTTCAAATGCAA
* *
28741913 TCAAGCTTCTTGCATTGCGTGATTCCCTTCCCATTGTGACCTCAGGAACAGAACAT
66 TCAAGCTTCTTGCATTGCATGATTCCCTTCCCATTGTGA-CTAAGGAACAGAACAT
* * * *
28741969 AAAAGGAAAAAGAGAAAGGAGAAAAATTAACTAGGACAATAGTATAACCTTCATCTTGAAATGTA
1 AAAAAGAAAAAGA-AAAGGAGAAAAATAAACTAGGACAATAGTATAACCTTCATCTTCAAATGCA
*
28742034 ATCAAGCTTCTTGCTTTGCATGATTCCCTTCCCATTGTGACTAAGGAAC
65 ATCAAGCTTCTTGCATTGCATGATTCCCTTCCCATTGTGACTAAGGAAC
28742083 CTTAAAGGTT
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
121 20 0.19
122 83 0.81
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (120 bp):
AAAAAGAAAAAGAAAAGGAGAAAAATAAACTAGGACAATAGTATAACCTTCATCTTCAAATGCAA
TCAAGCTTCTTGCATTGCATGATTCCCTTCCCATTGTGACTAAGGAACAGAACAT
Found at i:28747408 original size:25 final size:25
Alignment explanation
Indices: 28747379--28747444 Score: 62
Period size: 29 Copynumber: 2.4 Consensus size: 25
28747369 AATAATGTTT
28747379 TATAATTTAATATATTATGA-ATATA
1 TATAATTTAATATATTAT-ATATATA
28747404 TATAACTGTATAAATATATTATATATATA
1 TATAA-T-T-T-AATATATTATATATATA
*
28747433 CATATATTTAAT
1 TATA-ATTTAAT
28747445 TATACATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 2 0.06
28 3 0.09
29 19 0.56
30 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
TATAATTTAATATATTATATATATA
Found at i:28747728 original size:2 final size:2
Alignment explanation
Indices: 28747721--28747775 Score: 53
Period size: 2 Copynumber: 28.5 Consensus size: 2
28747711 CATTAATTTC
* * *
28747721 AT AT AT AT AT AT AT AT AT AT AT A- AT AA AGT A- AT AC AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
28747762 AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
28747776 AAATTAACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:28748949 original size:8 final size:8
Alignment explanation
Indices: 28748934--28748964 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
28748924 AAGTTAAATA
28748934 CAAA-AAT
1 CAAATAAT
28748941 CAAATAAT
1 CAAATAAT
28748949 CAAATAAT
1 CAAATAAT
28748957 CAAATAAT
1 CAAATAAT
28748965 ATATTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.23
Consensus pattern (8 bp):
CAAATAAT
Found at i:28751275 original size:107 final size:108
Alignment explanation
Indices: 28751071--28751278 Score: 330
Period size: 107 Copynumber: 1.9 Consensus size: 108
28751061 TATCACTCGT
*
28751071 GGACAAAATTTGAGATTTTGTGAGAATTTAAGATCACATTTGACAAATTGGAGAATGGTATGAAT
1 GGACAAAATTTGAGATTTTGAGAGAATTTAAGATCACATTTGACAAATTGGAGAATGGTATGAAT
**** *
28751136 ATAAGGGATGAAAAATATGTTANNNNGTAATTTTTCCACCCGC
66 ATAAGGGATGAAAAATATGTTAATGGGCAATTTTTCCACCCGC
*
28751179 GGACAAAATTTGAGATTTTGAGAGAATTT-AGATCACATTTGACAAATTGGAGAATGGTATGAGT
1 GGACAAAATTTGAGATTTTGAGAGAATTTAAGATCACATTTGACAAATTGGAGAATGGTATGAAT
28751243 ATAAGGGATGAAAAATATGTCT-ATGGGCAATTTTTC
66 ATAAGGGATGAAAAATATGT-TAATGGGCAATTTTTC
28751279 AATTTTTTTG
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 63 0.68
108 29 0.32
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.31
Consensus pattern (108 bp):
GGACAAAATTTGAGATTTTGAGAGAATTTAAGATCACATTTGACAAATTGGAGAATGGTATGAAT
ATAAGGGATGAAAAATATGTTAATGGGCAATTTTTCCACCCGC
Found at i:28764524 original size:6 final size:7
Alignment explanation
Indices: 28764502--28764527 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28764492 ATCTACTTTT
28764502 AAATTAA
1 AAATTAA
28764509 AAATTAA
1 AAATTAA
28764516 AAATTAA
1 AAATTAA
28764523 AAATT
1 AAATT
28764528 TTAGAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:28768079 original size:26 final size:25
Alignment explanation
Indices: 28768028--28768079 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
28768018 AGAAAAATAA
*
28768028 AGTTATATTTTAAAAAAAAATCAAGG
1 AGTTATATTTGAAAAAAAAA-CAAGG
28768054 AGTTATATTTGGAAAAATAAAA-AAGG
1 AGTTATATTT-GAAAAA-AAAACAAGG
28768080 CATAATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 14 0.61
27 5 0.22
28 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (25 bp):
AGTTATATTTGAAAAAAAAACAAGG
Found at i:28773002 original size:21 final size:21
Alignment explanation
Indices: 28772972--28773019 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28772962 TTTTAATGAA
* *
28772972 TTATTTTAATTTTA-TATTTAT
1 TTATTATAATTTGATTA-TTAT
28772993 TTATTATAATTTGATTATTAT
1 TTATTATAATTTGATTATTAT
28773014 TTATTA
1 TTATTA
28773020 ATTTAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTATAATTTGATTATTAT
Found at i:28773042 original size:20 final size:20
Alignment explanation
Indices: 28773017--28773055 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28773007 TTATTATTTA
28773017 TTAA-TTTAAAAGAATAAGAC
1 TTAATTTTAAAA-AATAAGAC
28773037 TTAATTTTAAAAAATAAGA
1 TTAATTTTAAAAAATAAGA
28773056 TGTTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
TTAATTTTAAAAAATAAGAC
Found at i:28773340 original size:18 final size:18
Alignment explanation
Indices: 28773274--28773343 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
28773264 TACATATATA
* * *
28773274 TCTTTATTTCTTCTTCTC
1 TCTTTATCTCTTTTTCTT
*
28773292 TCATTTTTCTCTTTTTTCTT
1 TC-TTTATCTC-TTTTTCTT
*
28773312 T-TTT-CCTTCTTTTTCTT
1 TCTTTATC-TCTTTTTCTT
28773329 TCTTTATCTCTTTTT
1 TCTTTATCTCTTTTT
28773344 TTTTTATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
17 10 0.24
18 17 0.41
19 7 0.17
20 7 0.17
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (18 bp):
TCTTTATCTCTTTTTCTT
Found at i:28774834 original size:20 final size:22
Alignment explanation
Indices: 28774795--28774836 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
28774785 TATTTAAATA
*
28774795 TTAACTAATATATTAATATTAT
1 TTAACTAATATATAAATATTAT
28774817 TTAACT-ATA-ATAAATATTAT
1 TTAACTAATATATAAATATTAT
28774837 AAAGAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAACTAATATATAAATATTAT
Found at i:28774871 original size:45 final size:45
Alignment explanation
Indices: 28774811--28774897 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
28774801 AATATATTAA
* *
28774811 TATTATTTAACTATAATAAATATTATAAAGAATATTATTTAATAT
1 TATTATTTAACTATAATAAATATAATAAAAAATATTATTTAATAT
*
28774856 TATTATTTGAA-TATAATAAATGTAATAAAAAATATTATTTAA
1 TATTATTT-AACTATAATAAATATAATAAAAAATATTATTTAA
28774898 ATTTAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 36 0.95
46 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (45 bp):
TATTATTTAACTATAATAAATATAATAAAAAATATTATTTAATAT
Found at i:28774899 original size:23 final size:23
Alignment explanation
Indices: 28774872--28774953 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
28774862 TTGAATATAA
*
28774872 TAAATGTAATAAAAAATATTATT
1 TAAATTTAATAAAAAATATTATT
* *
28774895 TAAATTTAATGAAGAATATATATT
1 TAAATTTAATAAAAAATAT-TATT
**
28774919 T---TTTAATATTAAATATTATT
1 TAAATTTAATAAAAAATATTATT
28774939 T-AATTATAATAAAAA
1 TAAATT-TAATAAAAA
28774954 TATGTTTGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
20 5 0.11
21 11 0.24
22 2 0.04
23 23 0.50
24 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAATTTAATAAAAAATATTATT
Found at i:28791103 original size:63 final size:62
Alignment explanation
Indices: 28791016--28791180 Score: 188
Period size: 63 Copynumber: 2.6 Consensus size: 62
28791006 GTAATTGATG
* * ** *
28791016 TAACCGTGTATGTGCGAAGTGGGCAATGCATATGCCGGTTGAATGACGATGTTGTCACAAC-TA
1 TAACCGTGCATGTGCG-AGTGGGCAGTGCATATGCCGGTCAAATGACAATGTTGTCAC-ACTTA
* *
28791079 TAACCGTGCATATGCAGAGTGGGCAGTGCATATGCCGGTCAAATGACAATGTTGTGACACTTA
1 TAACCGTGCATGTGC-GAGTGGGCAGTGCATATGCCGGTCAAATGACAATGTTGTCACACTTA
* * * *
28791142 CAACTGTGCATGTGCGGAGTGGGCAGTGCACATACCGGT
1 TAACCGTGCATGTGC-GAGTGGGCAGTGCATATGCCGGT
28791181 AATGATGTGC
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
62 2 0.02
63 84 0.97
64 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (62 bp):
TAACCGTGCATGTGCGAGTGGGCAGTGCATATGCCGGTCAAATGACAATGTTGTCACACTTA
Found at i:28791249 original size:2 final size:2
Alignment explanation
Indices: 28791237--28791312 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
28791227 TATTTGTGTT
*
28791237 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28791279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28791313 NAGAGTGGGC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28799774 original size:26 final size:26
Alignment explanation
Indices: 28799717--28799776 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
28799707 ACTAATTAGT
*
28799717 AAAAAAAATTCACAAATTATTAATTG
1 AAAAAAAATTCACAAATTATCAATTG
*
28799743 AGAAAAAACTT-ACAAATTATC-ATATG
1 A-AAAAAAATTCACAAATTATCAAT-TG
28799769 AAAAAAAA
1 AAAAAAAA
28799777 AATTAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 8 0.28
26 13 0.45
27 8 0.28
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (26 bp):
AAAAAAAATTCACAAATTATCAATTG
Found at i:28799793 original size:24 final size:27
Alignment explanation
Indices: 28799717--28799787 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
28799707 ACTAATTAGT
*
28799717 AAAAAAAATTCACAAATTATTA-ATTG-A
1 AAAAAAAATT-ACAAATTATCATA-TGAA
* *
28799744 GAAAAAACTTACAAATTATCATATGAA
1 AAAAAAAATTACAAATTATCATATGAA
28799771 AAAAAAAATTA-AAATTA
1 AAAAAAAATTACAAATTA
28799788 CAATGATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 18 0.49
27 19 0.51
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (27 bp):
AAAAAAAATTACAAATTATCATATGAA
Found at i:28802207 original size:52 final size:53
Alignment explanation
Indices: 28802129--28802229 Score: 186
Period size: 52 Copynumber: 1.9 Consensus size: 53
28802119 TGGTATATCT
28802129 GATATATTTATGCTTTTCTTATTTGGAG-TTGGATATGAAATGCAGTTAATCA
1 GATATATTTATGCTTTTCTTATTTGGAGTTTGGATATGAAATGCAGTTAATCA
*
28802181 GATATATTTATGCTTTTCTTATTTGGAGTTTGGATATGAAATGTAGTTA
1 GATATATTTATGCTTTTCTTATTTGGAGTTTGGATATGAAATGCAGTTA
28802230 TTGTTGGTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 28 0.60
53 19 0.40
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.47
Consensus pattern (53 bp):
GATATATTTATGCTTTTCTTATTTGGAGTTTGGATATGAAATGCAGTTAATCA
Found at i:28804146 original size:43 final size:43
Alignment explanation
Indices: 28804083--28804166 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
28804073 GTGTTTAACA
* *
28804083 TTCATTAGTATCTCATTTTGTTGGAAATTAAATTGATGATCCT
1 TTCATTAGTATCTCACTTTGTTAGAAATTAAATTGATGATCCT
* *
28804126 TTCATTCGTATTTCACTTTGTTAGAAATTAAATTGATGATC
1 TTCATTAGTATCTCACTTTGTTAGAAATTAAATTGATGATC
28804167 ATTCCATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (43 bp):
TTCATTAGTATCTCACTTTGTTAGAAATTAAATTGATGATCCT
Found at i:28805737 original size:188 final size:188
Alignment explanation
Indices: 28805369--28805751 Score: 538
Period size: 188 Copynumber: 2.0 Consensus size: 188
28805359 AACCAGCGTC
* * * **
28805369 TCAAAAGCTGCATGCCTGCATTAGGCTTTATTAGATATGAAATTTCTGCCTTTGAGATGATCATA
1 TCAACAGCTGCATGCCTGCATTAGACTTTATTAGATATGAAACTTCTGCCTTTGAGACAATCATA
* *
28805434 TGAAAAGTCTATTTTGATTTCTGCAATGCTGCAATGGCCTTTGTTCTACATGTTGCTTTATGTTC
66 TGAAAAGTCTAGTTTGATTTCTGCAATGCTGCAATGGCCTTTATTCTACATGTTGCTTTATGTTC
* * * * * *
28805499 GAGTTTCATTTATGTTGACCTTGACACGGCTATGCAGCTAGTTTTAAAAAGGCATATT
131 GAGGTTCATTGATGTTGACCTTGACACGGCAATACAACGAGTTTTAAAAAGGCATATT
* * *
28805557 TCGACAGCTGCATGCCTGCTTTAGAC-TTATTATG-TGTGAAACTTCTGCCTTTGAGACAATCAT
1 TCAACAGCTGCATGCCTGCATTAGACTTTATTA-GATATGAAACTTCTGCCTTTGAGACAATCAT
* ** *
28805620 ATGAAAAGTCTGGTTTGATTTCTGTGATGCTGCAATGGCCTTTATTCTACATTTTGCTTTTATGT
65 ATGAAAAGTCTAGTTTGATTTCTGCAATGCTGCAATGGCCTTTATTCTACATGTTGC-TTTATGT
28805685 T-GAAGGTTCATTGATGTTGACCTTGACACGGCAATACAACGAGTTTTAAAAAGGCATATT
129 TCG-AGGTTCATTGATGTTGACCTTGACACGGCAATACAACGAGTTTTAAAAAGGCATATT
28805745 TCAACAG
1 TCAACAG
28805752 GTAATGGATC
Statistics
Matches: 171, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
187 83 0.49
188 88 0.51
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (188 bp):
TCAACAGCTGCATGCCTGCATTAGACTTTATTAGATATGAAACTTCTGCCTTTGAGACAATCATA
TGAAAAGTCTAGTTTGATTTCTGCAATGCTGCAATGGCCTTTATTCTACATGTTGCTTTATGTTC
GAGGTTCATTGATGTTGACCTTGACACGGCAATACAACGAGTTTTAAAAAGGCATATT
Found at i:28806913 original size:14 final size:14
Alignment explanation
Indices: 28806894--28806931 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28806884 AATTTGATTA
28806894 TTATTTGAATTA-AT
1 TTATTT-AATTAGAT
28806908 TTATTTAATTAGAT
1 TTATTTAATTAGAT
*
28806922 TTTTTTAATT
1 TTATTTAATT
28806932 GAGAGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (14 bp):
TTATTTAATTAGAT
Found at i:28834381 original size:31 final size:30
Alignment explanation
Indices: 28834340--28834405 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
28834330 AATCAATTTT
* *
28834340 TTATATTTTTATTTTCAGTGAAATAAACTC
1 TTATATTTTTATTTTCAATCAAATAAACTC
* *
28834370 TTATACTTTTTATTTTGAATCAAATAAATTC
1 TTATA-TTTTTATTTTCAATCAAATAAACTC
28834401 TTATA
1 TTATA
28834406 ACTAATACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.52
Consensus pattern (30 bp):
TTATATTTTTATTTTCAATCAAATAAACTC
Found at i:28834768 original size:31 final size:30
Alignment explanation
Indices: 28834711--28834769 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
28834701 TTAAATGTAA
**
28834711 TAAAAATATAAAAATTTATTTAAATATTTT
1 TAAAAATATAAAAATACATTTAAATATTTT
* *
28834741 TAAATAATTTAAAAATACATTTGAATATT
1 TAAA-AATATAAAAATACATTTAAATATT
28834770 ATACTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
TAAAAATATAAAAATACATTTAAATATTTT
Found at i:28836237 original size:20 final size:22
Alignment explanation
Indices: 28836212--28836253 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28836202 CATAATATTT
28836212 CTCTT-ACTT-TTGGTTTTTTG
1 CTCTTAACTTGTTGGTTTTTTG
*
28836232 CTCTTAACTTGTTTGTTTTTTG
1 CTCTTAACTTGTTGGTTTTTTG
28836254 TGTGTTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.64
Consensus pattern (22 bp):
CTCTTAACTTGTTGGTTTTTTG
Found at i:28843680 original size:160 final size:161
Alignment explanation
Indices: 28843218--28844181 Score: 1808
Period size: 161 Copynumber: 6.0 Consensus size: 161
28843208 AGCGAGAGTG
* * *
28843218 AGCAAGCAGAGCTTTGCTCTTCCCTGCC-AAAGCACTAATCAGCCTCAGGCAGATTTACAAGTAT
1 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
*
28843282 AACATAAAAGAAAGCTTAAGAATTCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
66 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
28843347 TAATAGAGGAGGAGGAATGAAAACCTCACTA
131 TAATAGAGGAGGAGGAATGAAAACCTCACTA
28843378 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
1 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
28843443 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
66 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
28843508 TAATAGAGGAGGAGGAATGAAAACCTCACTA
131 TAATAGAGGAGGAGGAATGAAAACCTCACTA
* *
28843539 AGCAAGTAGAGCTTTGATCTTCCCCGCCAAAAGCACT-ATCAGCCTCAGGCAGATTTACAAGTAG
1 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
28843603 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
66 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
28843668 TAATAGAGGAGGAGGAATGAAAACCTCACTA
131 TAATAGAGGAGGAGGAATGAAAACCTCACTA
28843699 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
1 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
28843764 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
66 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
28843829 TAATAGAGGAGGAGGAATGAAAACCTCACTA
131 TAATAGAGGAGGAGGAATGAAAACCTCACTA
*
28843860 AGCAAGCAGAGCTTTGATCTTCCCCGCCAAAAGCACT-ATCAGCCTCAGGCAGATTTACAAGTAG
1 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
*
28843924 AACATAAAAGAAAGCTTAAGAATCCAACTAACAAAGAGGATTAATATAACGAAATTATTAGAAAA
66 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
28843989 TAATAGAGGAGGAGGAATGAAAACCTCACTA
131 TAATAGAGGAGGAGGAATGAAAACCTCACTA
*
28844020 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAACCTCAGGCAGATTTACAAGTAG
1 AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
28844085 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
66 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
* *
28844150 TAACAAAGGAGGAGGAATGAAAACCTCACTA
131 TAATAGAGGAGGAGGAATGAAAACCTCACTA
28844181 A
1 A
28844182 TCCAAAGCTA
Statistics
Matches: 786, Mismatches: 15, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
160 343 0.44
161 443 0.56
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.20
Consensus pattern (161 bp):
AGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCACTGATCAGCCTCAGGCAGATTTACAAGTAG
AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
TAATAGAGGAGGAGGAATGAAAACCTCACTA
Found at i:28843807 original size:321 final size:321
Alignment explanation
Indices: 28843218--28844181 Score: 1831
Period size: 321 Copynumber: 3.0 Consensus size: 321
28843208 AGCGAGAGTG
* * *
28843218 AGCAAGCAGAGCTTTGCTCTTCCCTGCC-AAAGCACTAATCAGCCTCAGGCAGATTTACAAGTAT
1 AGCAAGCAGAGCTTTGATCTTCCCCGCCAAAAGCACT-ATCAGCCTCAGGCAGATTTACAAGTAG
*
28843282 AACATAAAAGAAAGCTTAAGAATTCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
65 AACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAA
28843347 TAATAGAGGAGGAGGAATGAAAACCTCACTAAGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGC
130 TAATAGAGGAGGAGGAATGAAAACCTCACTAAGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGC
28843412 ACTGATCAGCCTCAGGCAGATTTACAAGTAGAACATAAAAGAAAGCTTAAGAATCCAACTAAAAA
195 ACTGATCAGCCTCAGGCAGATTTACAAGTAGAACATAAAAGAAAGCTTAAGAATCCAACTAAAAA
28843477 AGAGGATTAATATAACGAAATTATTAGAAAATAATAGAGGAGGAGGAATGAAAACCTCACTA
260 AGAGGATTAATATAACGAAATTATTAGAAAATAATAGAGGAGGAGGAATGAAAACCTCACTA
*
28843539 AGCAAGTAGAGCTTTGATCTTCCCCGCCAAAAGCACTATCAGCCTCAGGCAGATTTACAAGTAGA
1 AGCAAGCAGAGCTTTGATCTTCCCCGCCAAAAGCACTATCAGCCTCAGGCAGATTTACAAGTAGA
28843604 ACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAAT
66 ACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAAT
28843669 AATAGAGGAGGAGGAATGAAAACCTCACTAAGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCA
131 AATAGAGGAGGAGGAATGAAAACCTCACTAAGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCA
28843734 CTGATCAGCCTCAGGCAGATTTACAAGTAGAACATAAAAGAAAGCTTAAGAATCCAACTAAAAAA
196 CTGATCAGCCTCAGGCAGATTTACAAGTAGAACATAAAAGAAAGCTTAAGAATCCAACTAAAAAA
28843799 GAGGATTAATATAACGAAATTATTAGAAAATAATAGAGGAGGAGGAATGAAAACCTCACTA
261 GAGGATTAATATAACGAAATTATTAGAAAATAATAGAGGAGGAGGAATGAAAACCTCACTA
28843860 AGCAAGCAGAGCTTTGATCTTCCCCGCCAAAAGCACTATCAGCCTCAGGCAGATTTACAAGTAGA
1 AGCAAGCAGAGCTTTGATCTTCCCCGCCAAAAGCACTATCAGCCTCAGGCAGATTTACAAGTAGA
*
28843925 ACATAAAAGAAAGCTTAAGAATCCAACTAACAAAGAGGATTAATATAACGAAATTATTAGAAAAT
66 ACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAAT
28843990 AATAGAGGAGGAGGAATGAAAACCTCACTAAGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCA
131 AATAGAGGAGGAGGAATGAAAACCTCACTAAGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCA
*
28844055 CTGATCAACCTCAGGCAGATTTACAAGTAGAACATAAAAGAAAGCTTAAGAATCCAACTAAAAAA
196 CTGATCAGCCTCAGGCAGATTTACAAGTAGAACATAAAAGAAAGCTTAAGAATCCAACTAAAAAA
* *
28844120 GAGGATTAATATAACGAAATTATTAGAAAATAACAAAGGAGGAGGAATGAAAACCTCACTA
261 GAGGATTAATATAACGAAATTATTAGAAAATAATAGAGGAGGAGGAATGAAAACCTCACTA
28844181 A
1 A
28844182 TCCAAAGCTA
Statistics
Matches: 632, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
321 624 0.99
322 8 0.01
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.20
Consensus pattern (321 bp):
AGCAAGCAGAGCTTTGATCTTCCCCGCCAAAAGCACTATCAGCCTCAGGCAGATTTACAAGTAGA
ACATAAAAGAAAGCTTAAGAATCCAACTAAAAAAGAGGATTAATATAACGAAATTATTAGAAAAT
AATAGAGGAGGAGGAATGAAAACCTCACTAAGCAAGCAGAGCTTTGCTCTTCCCCGCCAAAAGCA
CTGATCAGCCTCAGGCAGATTTACAAGTAGAACATAAAAGAAAGCTTAAGAATCCAACTAAAAAA
GAGGATTAATATAACGAAATTATTAGAAAATAATAGAGGAGGAGGAATGAAAACCTCACTA
Found at i:28844608 original size:6 final size:6
Alignment explanation
Indices: 28844597--28844621 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28844587 ATAATCACCA
28844597 CGGTCC CGGTCC CGGTCC CGGTCC C
1 CGGTCC CGGTCC CGGTCC CGGTCC C
28844622 TAAACTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.32, T:0.16
Consensus pattern (6 bp):
CGGTCC
Found at i:28851205 original size:2 final size:2
Alignment explanation
Indices: 28851200--28851233 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28851190 ATATATATAT
*
28851200 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28851234 TTGTAATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:28852440 original size:74 final size:74
Alignment explanation
Indices: 28852353--28852494 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
28852343 AAACTTATAC
* * * *
28852353 TTATAAATATGTATTAATTAAATGACAATTATTGAAATATTTTTTATTGTAATTATTAGTAAGAT
1 TTATAAATATGTATTAATCAAATGACAATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
28852418 TTAAACCTA
66 TTAAACCTA
* * **
28852427 TTATAAATGTGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
1 TTATAAATATGTATTAATCAAATGACAATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
28852492 TTA
66 TTA
28852495 TTCCATTTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTAATCAAATGACAATCATTGAAATATTTTTTATTATAATTATTAATAAGAT
TTAAACCTA
Found at i:28852603 original size:13 final size:13
Alignment explanation
Indices: 28852585--28852634 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
28852575 TAATTTAAAT
28852585 ATTAATATTTTAA
1 ATTAATATTTTAA
*
28852598 ATTAATTTTTTAA
1 ATTAATATTTTAA
*
28852611 ATTTAA-ATATT-A
1 A-TTAATATTTTAA
28852623 A-TAATATTTTAA
1 ATTAATATTTTAA
28852635 TATTTTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.10
11 4 0.13
12 3 0.10
13 16 0.53
14 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTAATATTTTAA
Found at i:28852637 original size:8 final size:8
Alignment explanation
Indices: 28852586--28852642 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
28852576 AATTTAAATA
28852586 TTAATATT
1 TTAATATT
28852594 TTAA-A--
1 TTAATATT
*
28852599 TTAATTTT
1 TTAATATT
28852607 TTAA-ATT
1 TTAATATT
*
28852614 TAAATATT
1 TTAATATT
*
28852622 AATAATATT
1 -TTAATATT
28852631 TTAATATT
1 TTAATATT
28852639 TTAA
1 TTAA
28852643 GTTAAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
5 4 0.11
7 6 0.16
8 22 0.58
9 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTAATATT
Found at i:28852648 original size:37 final size:34
Alignment explanation
Indices: 28852576--28852659 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 34
28852566 TGTGTTGTAT
28852576 AATTTAAATATTAATATTTTAAATTAATTTTTTA
1 AATTTAAATATTAATATTTTAAATTAATTTTTTA
* *
28852610 AATTTAAATATTAATAATATT---TTAATATTTT-
1 AATTTAAATATTAAT-ATTTTAAATTAATTTTTTA
*
28852641 AAGTTAAATATTAATATTT
1 AATTTAAATATTAATATTT
28852660 ATTAAACTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.07
31 14 0.31
32 9 0.20
34 15 0.33
35 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
AATTTAAATATTAATATTTTAAATTAATTTTTTA
Found at i:28860262 original size:36 final size:36
Alignment explanation
Indices: 28860219--28860291 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
28860209 GCATGCCTGG
28860219 CTGGGAGCCTGGACTAGCCCATGCGGCTGCCAAGAA
1 CTGGGAGCCTGGACTAGCCCATGCGGCTGCCAAGAA
28860255 CTGGGAGCCTGGACTAGCCCATGCGGCTGCCAAGAA
1 CTGGGAGCCTGGACTAGCCCATGCGGCTGCCAAGAA
28860291 C
1 C
28860292 AAGAAGCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.32, G:0.33, T:0.14
Consensus pattern (36 bp):
CTGGGAGCCTGGACTAGCCCATGCGGCTGCCAAGAA
Found at i:28868976 original size:2 final size:2
Alignment explanation
Indices: 28868969--28868999 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28868959 ATTGTTTGAT
28868969 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28869000 ATGAATATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28871191 original size:76 final size:75
Alignment explanation
Indices: 28871065--28871214 Score: 212
Period size: 76 Copynumber: 2.0 Consensus size: 75
28871055 GTATTCACGC
** * * *
28871065 GCCACTTAACTTTTAATTAAATAAAAATTTAATTGACTGTTAATTGGCGCGTAAATAACTGTTAA
1 GCCACTTAACTGCTAATCAAATAAAAATTTAAATGACTGTTAATTGGCGCGTAAATAACTATTAA
28871130 TCAAATAAACG
66 TC-AATAAACG
* *
28871141 GCCACTTAACTGCTAATCAGATAAAAATTTAAATGA-TCGTTAATTGGCGCGTAAATAACTATTG
1 GCCACTTAACTGCTAATCAAATAAAAATTTAAATGACT-GTTAATTGGCGCGTAAATAACTATTA
28871205 ATCAATAAAC
65 ATCAATAAAC
28871215 TATTAAGATG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 8 0.12
76 58 0.88
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (75 bp):
GCCACTTAACTGCTAATCAAATAAAAATTTAAATGACTGTTAATTGGCGCGTAAATAACTATTAA
TCAATAAACG
Found at i:28873809 original size:30 final size:32
Alignment explanation
Indices: 28873751--28873810 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
28873741 ATAATAAACG
*
28873751 TAATAAAAAATAATATTTAGTATTTTTTAAATT
1 TAATAAAAAATAATATTTA-TATCTTTTAAATT
*
28873784 TAATGAAAAAT-ATATTT-TATCTTTTAA
1 TAATAAAAAATAATATTTATATCTTTTAA
28873811 TGTTAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
32 6 0.24
33 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (32 bp):
TAATAAAAAATAATATTTATATCTTTTAAATT
Found at i:28874653 original size:30 final size:31
Alignment explanation
Indices: 28874613--28874686 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
28874603 AATTATTTAT
* * *
28874613 AAAGATTTATTTGA-TTCGAAATAAAAGTAA
1 AAAGACTTATTTGAGCTCAAAATAAAAGTAA
*
28874643 AAAGACTTATTT-AGCTCAAAATAAAAGTAT
1 AAAGACTTATTTGAGCTCAAAATAAAAGTAA
*
28874673 AAAGACTTAATTGA
1 AAAGACTTATTTGA
28874687 ACGCAATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.03
30 35 0.95
31 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (31 bp):
AAAGACTTATTTGAGCTCAAAATAAAAGTAA
Done.