Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 19 of 198
Found at i:5697014 original size:23 final size:22
Alignment explanation
Indices: 5696960--5697015 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
5696950 AAGGTTTAGA
5696960 TAGGGTTTAGGAAAAATTAAAT
1 TAGGGTTTAGGAAAAATTAAAT
5696982 TAGGGTTTAGGAAAAATTAAAT
1 TAGGGTTTAGGAAAAATTAAAT
5697004 TAGGGTATTAGG
1 TAGGGT-TTAGG
5697016 TTTTTTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (22 bp):
TAGGGTTTAGGAAAAATTAAAT
Found at i:5699358 original size:19 final size:18
Alignment explanation
Indices: 5699336--5699420 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 18
5699326 TTCAAAACTT
5699336 AAAAATTCAGAAATTATAA
1 AAAAATTCA-AAATTATAA
*
5699355 AAAATATT-AATAATTATTTA
1 AAAA-ATTCAA-AATTA-TAA
*
5699375 AAAAATCTAAAAAATTAT-A
1 AAAAAT-T-CAAAATTATAA
* *
5699394 AAAAATTGAAAATT-GAA
1 AAAAATTCAAAATTATAA
5699411 AAAAATTCAA
1 AAAAATTCAA
5699421 GTTTTTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
17 16 0.29
18 2 0.04
19 19 0.35
20 11 0.20
21 5 0.09
22 2 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAAATTCAAAATTATAA
Found at i:5699390 original size:21 final size:19
Alignment explanation
Indices: 5699346--5699399 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
5699336 AAAAATTCAG
*
5699346 AAATTATAAAAAATATTAA
1 AAATTATAAAAAATATAAA
* *
5699365 TAATTATTTAAAAAATCTAAA
1 AAATTA--TAAAAAATATAAA
5699386 AAATTATAAAAAAT
1 AAATTATAAAAAAT
5699400 TGAAAATTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTATAAAAAATATAAA
Found at i:5699399 original size:10 final size:10
Alignment explanation
Indices: 5699346--5699400 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
5699336 AAAAATTCAG
5699346 AAATTATAAA
1 AAATTATAAA
*
5699356 AAA-TATTAA
1 AAATTATAAA
*
5699365 TAATTATTTAAA
1 AAATTA--TAAA
*
5699377 AAA-TCTAAA
1 AAATTATAAA
5699386 AAATTATAAA
1 AAATTATAAA
5699396 AAATT
1 AAATT
5699401 GAAAATTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 14 0.40
10 15 0.43
11 1 0.03
12 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATTATAAA
Found at i:5699894 original size:2 final size:2
Alignment explanation
Indices: 5699887--5699916 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5699877 TCATATTCGA
5699887 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
5699917 TATTAATAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5700180 original size:21 final size:20
Alignment explanation
Indices: 5700150--5700188 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5700140 TTAATTAATT
5700150 TTTATTTTTTTTAAAAAATA
1 TTTATTTTTTTTAAAAAATA
5700170 TTTATTTTTTTTAAAAAAT
1 TTTATTTTTTTTAAAAAAT
5700189 CAAACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTTTTTAAAAAATA
Found at i:5705408 original size:22 final size:22
Alignment explanation
Indices: 5705365--5705428 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
5705355 TTATTTAAAA
5705365 TTAAATATTAAATATAAT-TATATT
1 TTAAATA--AAATATAATATA-ATT
*
5705389 ATTTAATAAAATATAATATAATT
1 -TTAAATAAAATATAATATAATT
*
5705412 TTAAATAAAATAAAATA
1 TTAAATAAAATATAATA
5705429 AAATAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 15 0.43
23 12 0.34
24 2 0.06
25 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAATAAAATATAATATAATT
Found at i:5707494 original size:11 final size:11
Alignment explanation
Indices: 5707478--5707502 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5707468 CTTCATGTAT
5707478 GTTTGTATGAA
1 GTTTGTATGAA
5707489 GTTTGTATGAA
1 GTTTGTATGAA
5707500 GTT
1 GTT
5707503 CGTGTTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (11 bp):
GTTTGTATGAA
Found at i:5718974 original size:18 final size:18
Alignment explanation
Indices: 5718951--5718990 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5718941 TAATTTTTTA
*
5718951 AAAAATA-TATAATACATT
1 AAAAATACTA-AAAACATT
5718969 AAAAATACTAAAAACATT
1 AAAAATACTAAAAACATT
5718987 AAAA
1 AAAA
5718991 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATACTAAAAACATT
Found at i:5720403 original size:17 final size:18
Alignment explanation
Indices: 5720376--5720413 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5720366 TAAATAAAAA
5720376 TTTACTTTTAA-ATTATTT
1 TTTACTTTTAAGA-TATTT
5720394 TTTA-TTTTAAGATATTT
1 TTTACTTTTAAGATATTT
5720411 TTT
1 TTT
5720414 TTAATGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTACTTTTAAGATATTT
Found at i:5720616 original size:17 final size:17
Alignment explanation
Indices: 5720596--5720670 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
5720586 ATTAAACAAA
5720596 TAAAATAAATAGATATT
1 TAAAATAAATAGATATT
5720613 TAAAA-AAATTA-A-ATT
1 TAAAATAAA-TAGATATT
*
5720628 TAAATTAAAATAGAT-TT
1 TAAAAT-AAATAGATATT
*
5720645 TATAAGTAAATAG-TAATT
1 TA-AAATAAATAGAT-ATT
5720663 T-AAATAAA
1 TAAAATAAA
5720671 ATTTAGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 17
0.70 0.04 0.25
Matches are distributed among these distances:
15 7 0.15
16 13 0.28
17 21 0.45
18 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
TAAAATAAATAGATATT
Found at i:5728063 original size:9 final size:9
Alignment explanation
Indices: 5728051--5728273 Score: 134
Period size: 9 Copynumber: 25.0 Consensus size: 9
5728041 AATTAAATAT
5728051 CTTACATAA
1 CTTACATAA
5728060 CTTACATAA
1 CTTACATAA
*
5728069 ATTA-AGTAA
1 CTTACA-TAA
*
5728078 TTTACATAA
1 CTTACATAA
5728087 CTTACATAA
1 CTTACATAA
* * *
5728096 ATTAAATAT
1 CTTACATAA
*
5728105 CTTGCATAA
1 CTTACATAA
*
5728114 TTTACATAA
1 CTTACATAA
*
5728123 ATTA-AGTAA
1 CTTACA-TAA
* * *
5728132 ATTAAATAT
1 CTTACATAA
*
5728141 CTTGCATAA
1 CTTACATAA
*
5728150 TTTACATAA
1 CTTACATAA
* * *
5728159 ATTAAATAT
1 CTTACATAA
5728168 CTTACATAA
1 CTTACATAA
5728177 CTTACATAA
1 CTTACATAA
* * *
5728186 ATTAAATAT
1 CTTACATAA
*
5728195 CTTACATTA
1 CTTACATAA
*
5728204 CTTACATAG
1 CTTACATAA
*
5728213 CTTACATTA
1 CTTACATAA
**
5728222 CTTACATGGGG
1 CTTACAT--AA
*
5728233 CATACATAA
1 CTTACATAA
5728242 --TACATAA
1 CTTACATAA
*
5728249 --TACAGAA
1 CTTACATAA
5728256 CTTACATAA
1 CTTACATAA
5728265 CTTACATAA
1 CTTACATAA
5728274 TACATAAAAA
Statistics
Matches: 162, Mismatches: 44, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
7 13 0.08
8 2 0.01
9 139 0.86
10 2 0.01
11 6 0.04
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (9 bp):
CTTACATAA
Found at i:5728082 original size:27 final size:27
Alignment explanation
Indices: 5728039--5728211 Score: 195
Period size: 27 Copynumber: 6.1 Consensus size: 27
5728029 NNNAATTAAG
5728039 TAAATTAAATATCTTACATAACTTACA
1 TAAATTAAATATCTTACATAACTTACA
*
5728066 TAAATTAAGTAAT-TTACATAACTTACA
1 TAAATTAAAT-ATCTTACATAACTTACA
* *
5728093 TAAATTAAATATCTTGCATAATTTACATAAATTAA
1 TAAATTAAATATCTTACATAACTTAC--------A
* *
5728128 GTAAATTAAATATCTTGCATAATTTACA
1 -TAAATTAAATATCTTACATAACTTACA
5728156 TAAATTAAATATCTTACATAACTTACA
1 TAAATTAAATATCTTACATAACTTACA
*
5728183 TAAATTAAATATCTTACATTACTTACA
1 TAAATTAAATATCTTACATAACTTACA
5728210 TA
1 TA
5728212 GCTTACATTA
Statistics
Matches: 128, Mismatches: 7, Indels: 22
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.02
27 96 0.75
28 3 0.02
35 1 0.01
36 26 0.20
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAATTAAATATCTTACATAACTTACA
Found at i:5728115 original size:36 final size:36
Alignment explanation
Indices: 5728075--5728163 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
5728065 ATAAATTAAG
*
5728075 TAATTTACATAACTTACA-TAAATTAAATATCTTGCA
1 TAATTTACATAAATTA-AGTAAATTAAATATCTTGCA
5728111 TAATTTACATAAATTAAGTAAATTAAATATCTTGCA
1 TAATTTACATAAATTAAGTAAATTAAATATCTTGCA
5728147 TAATTTACATAAATTAA
1 TAATTTACATAAATTAA
5728164 ATATCTTACA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 1 0.02
36 50 0.98
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.39
Consensus pattern (36 bp):
TAATTTACATAAATTAAGTAAATTAAATATCTTGCA
Found at i:5745682 original size:126 final size:124
Alignment explanation
Indices: 5745488--5745739 Score: 369
Period size: 126 Copynumber: 2.0 Consensus size: 124
5745478 GTTTGTGAAA
*
5745488 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGAACAAGCGCCGCTAAAGAACATGAT
1 TAAGCGCCGCTAAAGAACACGACTTTTAGCGGCGTTTTTGAACAAGCGCCGCTAAAGAACATGAT
* * *
5745553 CTTTAGCGGCGTTTGTTTCTATGCGTCGCTAAAGAACATGATCTTTAGGGGCGCTTTTTT
66 CTTTAGCGGCGTTTGTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTT
* * * *** *
5745613 TAAGCGCCGCTAAAGCACACGATTTTTAGGGGCGTTTTTTTTCAAAGCGCTGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACACGACTTTTAGCGGCGTTTTTGAAC-AAGCGCCGCTAAAGAACATGA
* *
5745678 TCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
65 TCTTTAGCGGCGTTTGTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
5745738 TA
1 TA
5745740 TGTAAGCGCC
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
125 44 0.39
126 69 0.61
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (124 bp):
TAAGCGCCGCTAAAGAACACGACTTTTAGCGGCGTTTTTGAACAAGCGCCGCTAAAGAACATGAT
CTTTAGCGGCGTTTGTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
Found at i:5745738 original size:42 final size:42
Alignment explanation
Indices: 5745488--5745738 Score: 312
Period size: 42 Copynumber: 6.0 Consensus size: 42
5745478 GTTTGTGAAA
**
5745488 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TTC
*
5745531 -AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * * *
5745572 TATGCGTCGCTAAAGAACATGATCTTTAGGGGCGCTTTTTT-
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * * *
5745613 TAAGCGCCGCTAAAGCACACGATTTTTAGGGGCGTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTC
* * *
5745656 AAAGCGCTGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
5745698 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
5745739 ATGTAAGCGC
Statistics
Matches: 180, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.17
42 120 0.67
43 29 0.16
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:5745859 original size:22 final size:22
Alignment explanation
Indices: 5745828--5745870 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5745818 TAGTGGCGTT
* *
5745828 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
5745850 AAAAAACGCCGCTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
5745871 GTTCTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:5747124 original size:8 final size:8
Alignment explanation
Indices: 5747111--5747136 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5747101 ATATATATAT
5747111 TTTAATTA
1 TTTAATTA
5747119 TTTAATTA
1 TTTAATTA
5747127 TTTAATTA
1 TTTAATTA
5747135 TT
1 TT
5747137 ATATCTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTAATTA
Found at i:5747851 original size:17 final size:17
Alignment explanation
Indices: 5747830--5747920 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
5747820 TTTTTCTATT
5747830 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
*
5747847 --CTT--TTTTAAAAT-
1 TTTTTAATTTTAAAATA
5747859 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
* *
5747876 TTTTTAAAATACTTTTAAATT
1 TTTTT--AAT--TTTAAAATA
*
5747897 TTTTTAATTTTTAAATA
1 TTTTTAATTTTAAAATA
5747914 TTTTTAA
1 TTTTTAA
5747921 AATAAAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 9 0.15
14 2 0.03
15 2 0.03
16 9 0.15
17 20 0.33
19 6 0.10
21 12 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTAATTTTAAAATA
Found at i:5747863 original size:12 final size:13
Alignment explanation
Indices: 5747837--5747891 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
5747827 ATTTTTTTAA
5747837 TTTTAAAATACTT
1 TTTTAAAATACTT
**
5747850 TTTTAAAATTTTTT
1 TTTTAAAA-TACTT
5747864 AATTTTAAAATA--T
1 --TTTTAAAATACTT
5747877 TTTTAAAATACTT
1 TTTTAAAATACTT
5747890 TT
1 TT
5747892 AAATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
11 10 0.29
13 12 0.35
14 3 0.09
15 1 0.03
16 8 0.24
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTAAAATACTT
Found at i:5747869 original size:38 final size:36
Alignment explanation
Indices: 5747817--5747924 Score: 101
Period size: 38 Copynumber: 2.8 Consensus size: 36
5747807 CGAATACAAT
*
5747817 AAATTTTTCT-ATTTTTTTAATTTTAAAATACTTTTTTA
1 AAATTTTT-TAATTTTTATAATTTTAAAATAC--TTTTA
* *
5747855 AAATTTTTTAATTTTAAAATATTTTTAAAATACTTTTA
1 AAATTTTTTAATTTT--TATAATTTTAAAATACTTTTA
* *
5747893 AATTTTTTTAATTTTTAAATATTTTTAAAATA
1 AAATTTTTTAATTTTT--ATAATTTTAAAATA
5747925 AAATTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
37 1 0.02
38 46 0.77
40 13 0.22
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (36 bp):
AAATTTTTTAATTTTTATAATTTTAAAATACTTTTA
Found at i:5747898 original size:29 final size:28
Alignment explanation
Indices: 5747829--5747885 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
5747819 ATTTTTCTAT
5747829 TTTTTTAATTTTAAAATACTTTTTTAAAA
1 TTTTTTAATTTTAAAATAC-TTTTTAAAA
5747858 TTTTTTAATTTTAAAATA-TTTTTAAAA
1 TTTTTTAATTTTAAAATACTTTTTAAAA
5747885 T
1 T
5747886 ACTTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 10 0.36
29 18 0.64
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTTAATTTTAAAATACTTTTTAAAA
Found at i:5747924 original size:11 final size:10
Alignment explanation
Indices: 5747849--5747921 Score: 59
Period size: 10 Copynumber: 7.8 Consensus size: 10
5747839 TTAAAATACT
5747849 TTTTTAAA-A
1 TTTTTAAATA
*
5747858 TTTTT-TA-A
1 TTTTTAAATA
*
5747866 TTTTAAAATA
1 TTTTTAAATA
5747876 TTTTTAAAATA
1 TTTTT-AAATA
*
5747887 CTTTTAAAT-
1 TTTTTAAATA
*
5747896 TTTTT-TA-A
1 TTTTTAAATA
5747904 TTTTTAAATA
1 TTTTTAAATA
5747914 TTTTTAAA
1 TTTTTAAA
5747922 ATAAAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
8 12 0.24
9 11 0.22
10 18 0.36
11 9 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:5747951 original size:34 final size:32
Alignment explanation
Indices: 5747891--5747965 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
5747881 AAAATACTTT
5747891 TAAATTTTTTTAATTTTTAAATATTTTTAAAA
1 TAAATTTTTTTAATTTTTAAATATTTTTAAAA
**
5747923 TAAAATTTTTTT-ATTTTTGATTTAATTTTTAAAA
1 T-AAATTTTTTTAATTTTT-AAAT-ATTTTTAAAA
5747957 TAAATTTTT
1 TAAATTTTT
5747966 GGTATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 7 0.18
33 20 0.53
34 11 0.29
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (32 bp):
TAAATTTTTTTAATTTTTAAATATTTTTAAAA
Found at i:5748497 original size:29 final size:30
Alignment explanation
Indices: 5748432--5748510 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
5748422 ATTAATAACA
5748432 AAGGATTAAAATGTCAACTTTTCAAACATAC
1 AAGGATTAAAATGT-AACTTTTCAAACATAC
* *
5748463 AAGGATTAAAATGT-TCTTTTCAATA-ATAG
1 AAGGATTAAAATGTAACTTTTCAA-ACATAC
*
5748492 AGGGATTAAAATG-AACTTT
1 AAGGATTAAAATGTAACTTT
5748511 ATGATATAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 27 0.64
30 1 0.02
31 14 0.33
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (30 bp):
AAGGATTAAAATGTAACTTTTCAAACATAC
Found at i:5757885 original size:51 final size:51
Alignment explanation
Indices: 5757772--5758212 Score: 346
Period size: 51 Copynumber: 8.7 Consensus size: 51
5757762 TATCGATGAA
* * * * * * *
5757772 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGCATCGATAAG-TAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAAGAAGCT-TTGAT
* * * * *
5757823 CACATGAGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAAGAAGCTTTGAT
* * * * * * ** *
5757874 CACGTGTGTAGTACTGTGTGAATGTTACTACGTGT-CTCGATAAACTACGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTAC-CAAGAAGCTTTGAT
* * * *
5757925 TACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAAGAAGCTTTGAT
* * * * * * ** *
5757976 CACGTGTGTAGTACTGTGTGAATGTTACTACGTGT-CTCGATAAACTACGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTAC-CAAGAAGCTTTGAT
* * * *
5758027 TACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAAGAAGCTTTGAT
* *
5758078 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTG-AGCCGTAA-AA--ATTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CC--AAGAAGCTTTGAT
* *
5758128 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAA-AA-C--TGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTAC--CAAGAAGCTTTGAT
*
5758177 CACGTGTGCAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
5758213 TCGAATGATA
Statistics
Matches: 303, Mismatches: 75, Indels: 26
0.75 0.19 0.06
Matches are distributed among these distances:
49 38 0.13
50 46 0.15
51 212 0.70
52 5 0.02
53 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAAGAAGCTTTGAT
Found at i:5757948 original size:102 final size:102
Alignment explanation
Indices: 5757772--5758216 Score: 575
Period size: 102 Copynumber: 4.4 Consensus size: 102
5757762 TATCGATGAA
* * * *
5757772 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTG-CATCGAT-AAGTAATGGTCACATGAGTAGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTC-TCGATAAACT-ACGGTTACATGTGTAGT
*
5757835 ACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
64 ACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
* *
5757874 CACGTGTGTAGTACTGTGTGAATGTTACTACGTGTCTCGATAAACTACGGTTACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTCTCGATAAACTACGGTTACATGTGTAGTAC
5757939 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
66 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
* *
5757976 CACGTGTGTAGTACTGTGTGAATGTTACTACGTGTCTCGATAAACTACGGTTACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTCTCGATAAACTACGGTTACATGTGTAGTAC
5758041 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
66 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
* * * * * *
5758078 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAGC-CG-TAAA-AATTGATCACGTGTGTAGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTG-TCTCGATAAACTA-CGGTTACATGTGTAGT
* * * *
5758140 ACTATGTGAAGGCTACTACGTGAACTGTAA-AA-C--TGAT
64 ACTAAGTGAAGGCTACTATGTGTAC--CAAGAAGCTTTGAT
* * *
5758177 CACGTGTGCAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTCTCGA
5758217 ATGATAAAAA
Statistics
Matches: 312, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
99 38 0.12
100 1 0.00
101 39 0.12
102 227 0.73
103 7 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTCTCGATAAACTACGGTTACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAT
Found at i:5760263 original size:19 final size:16
Alignment explanation
Indices: 5760208--5760263 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
5760198 GATTAATAAA
*
5760208 AAATATATAAAATTATT
1 AAATAT-TAAAATAATT
5760225 AAATATTAAAATAATAT
1 AAATATTAAAATAAT-T
5760242 AAATATTTTAAAATAAATT
1 AAATA--TTAAAAT-AATT
5760261 AAA
1 AAA
5760264 AATAATATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
16 8 0.24
17 12 0.35
19 11 0.32
20 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATTAAAATAATT
Found at i:5762253 original size:89 final size:89
Alignment explanation
Indices: 5762079--5762345 Score: 304
Period size: 89 Copynumber: 3.0 Consensus size: 89
5762069 AAAAGCTCTT
* * * * * *
5762079 AAACTTTTTCAAAAAAAGTAATTAAGCCTTTACTCTTTTTTTTTATACTCATTTGGGTACTTGAG
1 AAACTTTTTCAAAAAAAGCAATTAAGCC---CCTATTTTTTTTTACACTCAATTGGGTACTTGAA
* * *
5762144 CTTTTAAAATGCATCAAAAAGGCCCTC
63 CTGTCAAAATGCATAAAAAAGGCCCTC
* * * *
5762171 AAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTATTTTGCACTCAATTGGGTATTTAAACTG
1 AAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTTACACTCAATTGGGTACTTGAACTG
* **
5762236 TCAAAATGCATAAAAAAGACTTTC
66 TCAAAATGCATAAAAAAGGCCCTC
*
5762260 AAAC-TTTT-AAAAAAATGCAATTAAGCCCCTACTTTTTTTTTTCACTCAATTAGGGTACTTGAA
1 AAACTTTTTCAAAAAAA-GCAATTAAGCCCCTA-TTTTTTTTTACACTCAATT-GGGTACTTGAA
*
5762323 CTGCCAAAATGCATAAAAAAGGC
63 CTGTCAAAATGCATAAAAAAGGC
5762346 TAGGGGCGGA
Statistics
Matches: 150, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
87 7 0.05
88 19 0.13
89 67 0.45
90 30 0.20
92 27 0.18
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (89 bp):
AAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTTACACTCAATTGGGTACTTGAACTG
TCAAAATGCATAAAAAAGGCCCTC
Found at i:5762904 original size:29 final size:30
Alignment explanation
Indices: 5762844--5762928 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 30
5762834 AAAAAGTTGT
* *
5762844 AAAATTTTATAAAAATCAT-AAAATATTATAG
1 AAAATTATA-AAAAAT-ATAAAAAAATTATAG
* *
5762875 AATA-TATAGAAATATATAAAAAAATT-TAG
1 AAAATTATA-AAAAATATAAAAAAATTATAG
*
5762904 AAAATTATAAAAAATGTAAAAAAAT
1 AAAATTATAAAAAATATAAAAAAAT
5762929 ATAAAATCCG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 22 0.50
30 19 0.43
31 3 0.07
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAATTATAAAAAATATAAAAAAATTATAG
Found at i:5762916 original size:9 final size:9
Alignment explanation
Indices: 5762779--5762934 Score: 54
Period size: 9 Copynumber: 16.3 Consensus size: 9
5762769 TTTTAATAAC
5762779 AAAATATATA
1 AAAAT-TATA
5762789 AAAGATT-TA
1 AAA-ATTATA
* *
5762798 AAACTTGTTA
1 AAAATT-ATA
*
5762808 AAAATTAGA
1 AAAATTATA
5762817 AAAA-TATA
1 AAAATTATA
5762825 AAAATCGTA-A
1 AAAAT--TATA
*
5762835 AAAAGTTGTA
1 AAAA-TTATA
*
5762845 AAATTTTATA
1 AAA-ATTATA
*
5762855 AAAATCATA
1 AAAATTATA
5762864 AAATATTAT-
1 AAA-ATTATA
*
5762873 AGAATATATA
1 AAAAT-TATA
*
5762883 GAAATATATAAA
1 -AAA-AT-TATA
5762895 AAAATT-TA
1 AAAATTATA
5762903 GAAAATTATAA
1 -AAAATTAT-A
5762914 AAAATGTA-A
1 AAAAT-TATA
*
5762923 AAAAATATA
1 AAAATTATA
5762932 AAA
1 AAA
5762935 TCCGTAAAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 39
0.67 0.10 0.23
Matches are distributed among these distances:
8 14 0.13
9 39 0.35
10 39 0.35
11 13 0.12
12 6 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:5762917 original size:19 final size:19
Alignment explanation
Indices: 5762888--5762934 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5762878 ATATAGAAAT
* *
5762888 ATATAAAAAAATTTAGAAAA
1 ATAT-AAAAAATGTAAAAAA
*
5762908 TTATAAAAAATGTAAAAAA
1 ATATAAAAAATGTAAAAAA
5762927 ATATAAAA
1 ATATAAAA
5762935 TCCGTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
ATATAAAAAATGTAAAAAA
Found at i:5763539 original size:90 final size:94
Alignment explanation
Indices: 5763363--5763556 Score: 234
Period size: 90 Copynumber: 2.1 Consensus size: 94
5763353 TAATTGAGTG
* * **
5763363 AAAAAAAAAGCAGGGGATTAATTGCTTGTTTTTGAAAAAGTTTGAGGGCATTTTTTTTATGAATT
1 AAAAAAAAAACAAGGGATTAATTGCTTGTTTTTGAAAAAGTTTGA-GGCA-TTAATTTATGAATT
** * * *
5763428 TTGGCAGTTTAAGTACCCAATTGAGTGCAAA
64 TTGAAAGTTCAAATACCCAATTGAATGCAAA
* *
5763459 AAAAAAAAAACAAGGGCTTAATTGCTT-TTTTTGAAAAAGTTTGA-G-A-TAATTTATGCATTTT
1 AAAAAAAAAACAAGGGATTAATTGCTTGTTTTTGAAAAAGTTTGAGGCATTAATTTATGAATTTT
*
5763520 GAAAGTTCAAATACCCAATTGAATGTAAA
66 GAAAGTTCAAATACCCAATTGAATGCAAA
5763549 AAAAAAAA
1 AAAAAAAA
5763557 GTAGACTTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
90 43 0.50
92 1 0.01
93 1 0.01
95 17 0.20
96 24 0.28
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (94 bp):
AAAAAAAAAACAAGGGATTAATTGCTTGTTTTTGAAAAAGTTTGAGGCATTAATTTATGAATTTT
GAAAGTTCAAATACCCAATTGAATGCAAA
Found at i:5766377 original size:254 final size:248
Alignment explanation
Indices: 5765556--5766421 Score: 1247
Period size: 251 Copynumber: 3.5 Consensus size: 248
5765546 GTCAGAAATC
** * * * *
5765556 GCTCAAGGTAATGATGATCCAAGATGAATACCCTA-TCGTTTACCAGTGCCTGCCATATAGTGTT
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTT-CCATTGCCTGCCATATAGTGTT
* * * *
5765620 GTGTATGTATTCATAAAGTAATTAATTTGAAAGGAAAAGAAATACATAAGCTTGTTTTTCCTTTT
65 ATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTG-TTTTCTTTTT
* * * ** * * * *
5765685 TACCTTAAAAAAATC-TCGCCATTGC-GGCTGGTTATACTGCTTTTCCTGTTGAACCTGCAAACG
129 TACCTTAAACAAATCTTC-CCATT-CTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGC-AACG
*
5765748 TTTAAAATATTGGATTCTAAGCTCAAACATTATATGTTAT-AACCTAGGAAAGAGATT
191 TTTAAAATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
*
5765805 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTTCCTGCCATATAGTGTTA
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
*
5765870 TGTACGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
66 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
* * * *
5765935 CCTTAAGCAAATATTCTTTCCGTT-TCTGTGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGT
131 CCTTAAAC-AA-A-TCTTCCCATTCT-TGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGT
* *
5765999 TTAAAATATTGGATTGTAAGCTCGAACATTATATGTTATAAACCTAGGAAATAGATT
192 TTAAAATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
* *
5766056 GCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATATTGTTA
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
* *
5766121 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAATGAAAAACATAAACTTGTTTTCTTTTTTA
66 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
5766186 CCGGCTTAAACAAATCTTCCCATTCTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGTT
131 -C--CTTAAACAAATCTTCCCATTCTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGTT
5766251 TAAAATATTGGATTAATGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
193 TAAAATATTGGA-T--TGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
*
5766310 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTTCCTGCCATATAGTGTTA
1 GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
* *
5766375 TGTATGTATTCATAAAGTTGTTAATTTGAAAGGAAAAGAGATACATA
66 TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
5766422 TCTCTGCAAA
Statistics
Matches: 555, Mismatches: 47, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
248 17 0.03
249 104 0.19
250 47 0.08
251 228 0.41
252 5 0.01
253 2 0.00
254 152 0.27
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (248 bp):
GCTCAAGGTAATGGCGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTA
TGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTTTTA
CCTTAAACAAATCTTCCCATTCTTGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGTTTAA
AATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATT
Found at i:5770843 original size:21 final size:21
Alignment explanation
Indices: 5770817--5770891 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
5770807 TTAAAAATAG
*
5770817 CGGTGGCGGTGAGATTAGTTA
1 CGGTAGCGGTGAGATTAGTTA
* *
5770838 CGGTGGCGGTGAGATTAGTTT
1 CGGTAGCGGTGAGATTAGTTA
* * *
5770859 CTGTAACGGTGAGATTAGATA
1 CGGTAGCGGTGAGATTAGTTA
*
5770880 CTGTAGCGGTGA
1 CGGTAGCGGTGA
5770892 TGTAATCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.21, C:0.11, G:0.39, T:0.29
Consensus pattern (21 bp):
CGGTAGCGGTGAGATTAGTTA
Found at i:5771118 original size:30 final size:30
Alignment explanation
Indices: 5770964--5771111 Score: 149
Period size: 30 Copynumber: 5.0 Consensus size: 30
5770954 AATTTTTTTG
*
5770964 CATTTTGACCCCTGAAATTTTC-CAAAATTA
1 CATTTTGACCCCT-AAACTTTCTCAAAATTA
* * *
5770994 CATTTTGACCCTTAAACTTTCCCAAAACTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
** * *
5771024 CATTTCAACCCCTAAA-TTTTTTAAAA-TA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* * *
5771052 CATTTTGGCCCCTAAACTTTATCTAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* *
5771082 TATTTTGACCCATAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
5771112 TGTTTTGCCC
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
28 15 0.16
29 21 0.22
30 59 0.62
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTCAAAATTA
Found at i:5771458 original size:7 final size:7
Alignment explanation
Indices: 5771446--5771539 Score: 75
Period size: 7 Copynumber: 13.3 Consensus size: 7
5771436 CCGAACGGAG
5771446 AAGAAAA
1 AAGAAAA
*
5771453 AAGAAAG
1 AAGAAAA
**
5771460 AAGAAGG
1 AAGAAAA
*
5771467 AAG-AAG
1 AAGAAAA
*
5771473 AAGAAGA
1 AAGAAAA
5771480 AAGAAAGA
1 AAGAAA-A
5771488 AAG-AAA
1 AAGAAAA
5771494 AAGAGAAA
1 AAGA-AAA
5771502 AAGAGAAA
1 AAGA-AAA
*
5771510 AAGAGAA
1 AAGAAAA
5771517 AAGAAAA
1 AAGAAAA
*
5771524 AGGAAAA
1 AAGAAAA
*
5771531 AGGAAAA
1 AAGAAAA
5771538 AA
1 AA
5771540 AAATTTGACA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
6 9 0.12
7 45 0.62
8 19 0.26
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:5771463 original size:14 final size:14
Alignment explanation
Indices: 5771444--5771539 Score: 83
Period size: 14 Copynumber: 6.8 Consensus size: 14
5771434 GGCCGAACGG
5771444 AGAAGAAAAAAGAA
1 AGAAGAAAAAAGAA
**
5771458 AGAAGAAGGAAG-A
1 AGAAGAAAAAAGAA
*
5771471 AGAAGAAGAAAGAA
1 AGAAGAAAAAAGAA
5771485 AGAAAGAAAAAGAGAA
1 AG-AAGAAAAA-AGAA
5771501 A-AAGAGAAAAAGAGA
1 AGAAGA-AAAAAGA-A
*
5771516 A-AAGAAAAAGGAA
1 AGAAGAAAAAAGAA
5771529 A-AAGGAAAAAA
1 AGAA-GAAAAAA
5771540 AAATTTGACA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
13 16 0.23
14 32 0.46
15 17 0.24
16 5 0.07
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAAGAA
Found at i:5771483 original size:10 final size:9
Alignment explanation
Indices: 5771444--5771518 Score: 57
Period size: 8 Copynumber: 8.0 Consensus size: 9
5771434 GGCCGAACGG
5771444 AGAAGAAAAA
1 AGAAG-AAAA
5771454 AGAAAGAAGAA
1 AG-AAGAA-AA
* *
5771465 GGAAGAAGA
1 AGAAGAAAA
5771474 AGAAGAAAGAA
1 AGAAG-AA-AA
5771485 AGAAAGAAAA
1 AG-AAGAAAA
5771495 AG-AGAAAA
1 AGAAGAAAA
5771503 AG-AGAAAA
1 AGAAGAAAA
5771511 AG-AGAAAA
1 AGAAGAAAA
5771519 GAAAAAGGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
8 22 0.39
9 5 0.09
10 15 0.27
11 11 0.20
12 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:5771831 original size:8 final size:8
Alignment explanation
Indices: 5771820--5771849 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5771810 CCAGCAGAAA
5771820 AAAAAGAG
1 AAAAAGAG
5771828 AAAAAGAAG
1 AAAAAG-AG
5771837 AAAAAGAG
1 AAAAAGAG
5771845 AAAAA
1 AAAAA
5771850 AAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:5771840 original size:17 final size:18
Alignment explanation
Indices: 5771815--5771859 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5771805 GCAGCCCAGC
*
5771815 AGAAAAAAAAGAG-AAAA
1 AGAAGAAAAAGAGAAAAA
5771832 AGAAGAAAAAGAGAAAAA
1 AGAAGAAAAAGAGAAAAA
*
5771850 AAAAGAAAAA
1 AGAAGAAAAA
5771860 AGAGGTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AGAAGAAAAAGAGAAAAA
Found at i:5771860 original size:19 final size:18
Alignment explanation
Indices: 5771819--5771863 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
5771809 CCCAGCAGAA
*
5771819 AAAAAAGAGAAAAAGAAG
1 AAAAAAGAGAAAAAAAAG
5771837 -AAAAAGAGAAAAAAAAAG
1 AAAAAAGAG-AAAAAAAAG
5771855 AAAAAAGAG
1 AAAAAAGAG
5771864 GTTCAATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:5772230 original size:22 final size:21
Alignment explanation
Indices: 5772200--5772240 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5772190 GTGTTTTAAG
*
5772200 AATTTTCGTGTTTCTAAAAAAA
1 AATTCTCGTGTTTC-AAAAAAA
5772222 AATTCTCGTGTTTCAAAAA
1 AATTCTCGTGTTTCAAAAA
5772241 TTGTCGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
AATTCTCGTGTTTCAAAAAAA
Found at i:5772248 original size:39 final size:36
Alignment explanation
Indices: 5772181--5772257 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 36
5772171 GAAAATATTC
* * *
5772181 AAAAAATTTGTGTTTTAAGAATTTTCGTGTTTCTAAA
1 AAAAAATTTGTGTTTCAAAAATTGTCGTGTTT-TAAA
5772218 AAAAAATTCTCGTGTTTCAAAAATTGTCGTGTTTTAAA
1 AAAAAATT-T-GTGTTTCAAAAATTGTCGTGTTTTAAA
5772256 AA
1 AA
5772258 TTTTCATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
37 8 0.23
38 7 0.20
39 20 0.57
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (36 bp):
AAAAAATTTGTGTTTCAAAAATTGTCGTGTTTTAAA
Found at i:5772257 original size:18 final size:18
Alignment explanation
Indices: 5772178--5772484 Score: 248
Period size: 17 Copynumber: 17.4 Consensus size: 18
5772168 ATCGAAAATA
*
5772178 TTCAAAAAATTT-GTGTT
1 TTCAAAAATTTTCGTGTT
*
5772195 TT-AAGAATTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
* *
5772212 TCTAAAAAAAAATTCTCGTG-T
1 T-T---CAAAAATTTTCGTGTT
*
5772233 TTCAAAAATTGTCGTGTT
1 TTCAAAAATTTTCGTGTT
*
5772251 TT-AAAAATTTTCATG-T
1 TTCAAAAATTTTCGTGTT
* *
5772267 TTC-TAAATTTTCGT-AT
1 TTCAAAAATTTTCGTGTT
5772283 TTCAAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
*
5772301 TTC-AAAGTTTTGCGTG-T
1 TTCAAAAATTTT-CGTGTT
*
5772318 TTCAAAAATCTTCGTGTT
1 TTCAAAAATTTTCGTGTT
5772336 TTCAAAAA-TTTCG-GTGT
1 TTCAAAAATTTTCGTGT-T
** **
5772353 TTCAAAAAAATTCCCGTT
1 TTCAAAAATTTTCGTGTT
5772371 TT-AAAAATTTTCAG-GTT
1 TTCAAAAATTTTC-GTGTT
*
5772388 TTCAAAATTTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
* *
5772406 TTCAAAAAATTCTCTTG-T
1 TTC-AAAAATTTTCGTGTT
**
5772424 TTCAAAAATCCTCGTGTT
1 TTCAAAAATTTTCGTGTT
*
5772442 TTCAAAAATTTTGGTGTT
1 TTCAAAAATTTTCGTGTT
*
5772460 TT-GAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
5772477 TTCAAAAA
1 TTCAAAAA
5772485 AAATCTCGTG
Statistics
Matches: 234, Mismatches: 33, Indels: 45
0.75 0.11 0.14
Matches are distributed among these distances:
16 25 0.11
17 109 0.47
18 74 0.32
19 12 0.05
20 1 0.00
21 2 0.01
22 11 0.05
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (18 bp):
TTCAAAAATTTTCGTGTT
Found at i:5772332 original size:35 final size:34
Alignment explanation
Indices: 5772178--5772510 Score: 244
Period size: 35 Copynumber: 9.4 Consensus size: 34
5772168 ATCGAAAATA
*
5772178 TTCAAAAAATTT-GTGTTTT-AAGAATTTTCGTGT
1 TTCAAAAATTTTCGTGTTTTCAA-AATTTTCGTGT
* *
5772211 TTCTAAAAAAAAATTCTCGTG-TTTCAAAAATTGTCGTGT
1 TTC-----AAAAATTTTCGTGTTTTC-AAAATTTTCGTGT
* * * *
5772250 TTTAAAAATTTTCATG-TTTCTAAATTTTCGTAT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTTCGTGT
*
5772283 TTCAAAAATTTTCGTGTTTTCAAAGTTTTGCGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTT-CGTGT
* *
5772318 TTCAAAAATCTTCGTGTTTTCAAAAATTTCGGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTTC-GTGT
** ** *
5772353 TTCAAAAAAATTCCCGTTTTAAAAATTTTCAG-GTT
1 TTCAAAAATTTTCGTGTTTTCAAAATTTTC-GTG-T
* * *
5772388 TTCAAAATTTTTCGTGTTTTCAAAAAATTCTCTTGT
1 TTCAAAAATTTTCGTGTTTTC--AAAATTTTCGTGT
** *
5772424 TTCAAAAATCCTCGTGTTTTCAAAAATTTTGGTGT
1 TTCAAAAATTTTCGTGTTTTC-AAAATTTTCGTGT
** * *
5772459 TTTGAAAATTTTCGTGTTTTCAAAAAAAATCTCGTGT
1 TTCAAAAATTTTCGTGTTTTC---AAAATTTTCGTGT
*
5772496 TTCATAAATTTTCGT
1 TTCAAAAATTTTCGT
5772511 TTTAAAAAAA
Statistics
Matches: 235, Mismatches: 48, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
33 27 0.11
34 27 0.11
35 103 0.44
36 19 0.08
37 32 0.14
38 10 0.04
39 15 0.06
40 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (34 bp):
TTCAAAAATTTTCGTGTTTTCAAAATTTTCGTGT
Found at i:5772545 original size:17 final size:17
Alignment explanation
Indices: 5772178--5772545 Score: 239
Period size: 17 Copynumber: 21.1 Consensus size: 17
5772168 ATCGAAAATA
*
5772178 TTCAAAAAATTT-GTGT
1 TTCAAAAATTTTCGTGT
* *
5772194 TTTAAGAATTTTCGTGT
1 TTCAAAAATTTTCGTGT
*
5772211 TTCTAAAAAAAAATTCTCGTGT
1 TTC-----AAAAATTTTCGTGT
*
5772233 TTCAAAAATTGTCGTGT
1 TTCAAAAATTTTCGTGT
* *
5772250 TTTAAAAATTTTCATGT
1 TTCAAAAATTTTCGTGT
* *
5772267 TTC-TAAATTTTCGTAT
1 TTCAAAAATTTTCGTGT
5772283 TTCAAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
*
5772301 TTC-AAAGTTTTGCGTGT
1 TTCAAAAATTTT-CGTGT
*
5772318 TTCAAAAATCTTCGTGTT
1 TTCAAAAATTTTCGTG-T
5772336 TTCAAAAA-TTTCGGTGT
1 TTCAAAAATTTTC-GTGT
** **
5772353 TTCAAAAAAATTCCCGT
1 TTCAAAAATTTTCGTGT
*
5772370 TTTAAAAATTTTCAG-GTT
1 TTCAAAAATTTTC-GTG-T
*
5772388 TTCAAAATTTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
* *
5772406 TTCAAAAAATTCTCTTGT
1 TTC-AAAAATTTTCGTGT
**
5772424 TTCAAAAATCCTCGTGTT
1 TTCAAAAATTTTCGTG-T
*
5772442 TTCAAAAATTTTGGTGT
1 TTCAAAAATTTTCGTGT
**
5772459 TTTGAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
* *
5772477 TTCAAAAAAAATCTCGTGT
1 TTC--AAAAATTTTCGTGT
*
5772496 TTCATAAATTTTCGT-T
1 TTCAAAAATTTTCGTGT
* **
5772512 TTAAAAAAATAAT--TGT
1 TT-CAAAAATTTTCGTGT
*
5772528 TTCAAAAATCTTCGTGT
1 TTCAAAAATTTTCGTGT
5772545 T
1 T
5772546 AAAAAAAATT
Statistics
Matches: 273, Mismatches: 54, Indels: 49
0.73 0.14 0.13
Matches are distributed among these distances:
15 8 0.03
16 28 0.10
17 130 0.48
18 68 0.25
19 14 0.05
20 10 0.04
22 15 0.05
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTCAAAAATTTTCGTGT
Found at i:5776025 original size:7 final size:7
Alignment explanation
Indices: 5776013--5776078 Score: 105
Period size: 7 Copynumber: 9.1 Consensus size: 7
5776003 TCTTGAAATC
5776013 AACCCTA
1 AACCCTA
5776020 AACCCTA
1 AACCCTA
5776027 AACCCTA
1 AACCCTA
5776034 AACCCTA
1 AACCCTA
5776041 AACCCTA
1 AACCCTA
5776048 AACCCTAA
1 AACCCT-A
*
5776056 AACCTTAA
1 AACCCT-A
5776064 AACCCTA
1 AACCCTA
5776071 AACCCTA
1 AACCCTA
5776078 A
1 A
5776079 CCATTCACTT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
7 43 0.77
8 13 0.23
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCCTA
Found at i:5779967 original size:1 final size:1
Alignment explanation
Indices: 5779956--5780042 Score: 57
Period size: 1 Copynumber: 87.0 Consensus size: 1
5779946 TATTATGCTT
* * * * * * * * **
5779956 AAAAAACAAAAAAAATAGAAAAAAAAAAAACAACAAAAAAAAAAAGACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
5780021 AAAAGAAAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
5780043 TCAAGATGAA
Statistics
Matches: 62, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.01
Consensus pattern (1 bp):
A
Found at i:5779982 original size:16 final size:15
Alignment explanation
Indices: 5779956--5780042 Score: 84
Period size: 15 Copynumber: 5.5 Consensus size: 15
5779946 TATTATGCTT
*
5779956 AAAAAACAAAAAAAAT
1 AAAAAA-AAAAAAAAG
* *
5779972 AGAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAG
*
5779987 AACAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
5780002 ACAAAACAAAAAAAAGG
1 A-AAAA-AAAAAAAAAG
*
5780019 AAAAAAGAAAAAAAG
1 AAAAAAAAAAAAAAG
5780034 AAAGAAAAA
1 AAA-AAAAA
5780043 TCAAGATGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
15 32 0.55
16 16 0.28
17 10 0.17
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:5779983 original size:17 final size:16
Alignment explanation
Indices: 5779956--5780042 Score: 70
Period size: 16 Copynumber: 5.5 Consensus size: 16
5779946 TATTATGCTT
*
5779956 AAAAAACAAAAAAAA-
1 AAAAAAAAAAAAAAAG
* *
5779971 TAGAAAAAAAAAAAA-
1 AAAAAAAAAAAAAAAG
* *
5779986 CAACAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAG
* *
5780002 ACAAAACAAAAAAAAG
1 AAAAAAAAAAAAAAAG
* *
5780018 GAAAAAAGAAAAAAAG
1 AAAAAAAAAAAAAAAG
5780034 AAAGAAAAA
1 AAA-AAAAA
5780043 TCAAGATGAA
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
15 24 0.44
16 26 0.48
17 4 0.07
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:5779996 original size:19 final size:19
Alignment explanation
Indices: 5779956--5780042 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 19
5779946 TATTATGCTT
* * *
5779956 AAAAAACAA-AAAAAATAG
1 AAAAAAAAAGAAAAAACAA
*
5779974 AAAAAAAAA-AAACAACAA
1 AAAAAAAAAGAAAAAACAA
*
5779992 AAAAAAAAAGACAAAAC--
1 AAAAAAAAAGAAAAAACAA
* *
5780009 AAAAAAAAGGAAAAAAGAA
1 AAAAAAAAAGAAAAAACAA
*
5780028 AAAAAGAAAGAAAAA
1 AAAAAAAAAGAAAAA
5780043 TCAAGATGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
17 14 0.25
18 23 0.42
19 18 0.33
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.01
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAACAA
Found at i:5780022 original size:8 final size:8
Alignment explanation
Indices: 5779964--5780041 Score: 63
Period size: 8 Copynumber: 9.9 Consensus size: 8
5779954 TTAAAAAACA
*
5779964 AAAAAAAT
1 AAAAAAAG
*
5779972 AGAAAAA-
1 AAAAAAAG
*
5779979 AAAAAAAC
1 AAAAAAAG
*
5779987 AACAAAA-
1 AAAAAAAG
5779994 AAAAAAAG
1 AAAAAAAG
*
5780002 ACAAAACA-
1 A-AAAAAAG
5780010 AAAAAAAG
1 AAAAAAAG
*
5780018 GAAAAAAG
1 AAAAAAAG
5780026 AAAAAAAG
1 AAAAAAAG
5780034 AAAGAAAA
1 AAA-AAAA
5780042 ATCAAGATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
7 17 0.30
8 31 0.54
9 9 0.16
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5781362 original size:230 final size:228
Alignment explanation
Indices: 5780893--5781670 Score: 799
Period size: 230 Copynumber: 3.4 Consensus size: 228
5780883 TTTCAAGAAA
* * ** * *
5780893 TATTTTTTACTTTCTGTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAAATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * ** * *
5780957 T-CACGCTGAGGTATTTTTAATTTATGTCTTTTTTTAAAAAATCAACTCATAATGCGAGAGGTGA
65 TCCACGCTGAGGTATTTTAAATTTATG---TTTTTCAAAAAATCAACAAAAAATGCAAGAGGTGA
* *** * *
5781021 GTTGAACCT--AGGGTCACGCTGAGGTATTTTCAATTTATGTTTCTCTG-TTTTTCAAAAAAATC
127 GTTGAGCCTCGAGACACACGCCGAGGTATTTT-AA---A---TT-TCTGATTTTT--GAAAAATC
* *
5781083 AACTCATATTGCGAGAAGTGAGTTGAGCCCCGGGTCGCACGCTGAGG
182 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
* * *
5781130 TATTTCTTTTAAATTTCT-CTTTTCAAAAAATCAACTCATAATGTGAGAGGTGAGTTGAGCCTCG
1 TA--T-TTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* **** **
5781194 GGT-CACGCTGAGGTATTTTCAATTTATG-TTTTCTAACTGTTTTTACAAAAAAT-CAAGAGGTG
63 GGTCCACGCTGAGGTATTTTAAATTTATGTTTTTC-AA-AAAATCAACAAAAAATGCAAGAGGTG
* *
5781256 AGTTGAGCCTC-AGACACATGCCGAGGTATTTATTTTAAATTTCT-ATTTTT-CAAAATCAACTC
126 AGTTGAGCCTCGAGACACACGCCGAGG----TATTTTAAATTTCTGATTTTTGAAAAATCAACTC
*
5781318 ATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGG
187 ATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
*
5781360 TA-TTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT
1 TATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* ** * * * *
5781424 CACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGATAGGTGAGT
66 C-CACGCTGAGGTA-TTTTAAATTTATGTTTTTCAAAAAATCAACAAAAAATGCAAGAGGTGAGT
* *** * * *
5781489 TGAGCCTCGGGTTGCACGCTGAGGTATTTTAAATTTTTGTTTTTTGAAAAATCAACTCATATTGC
129 TGAGCCTCGAGACACACGCCGAGGTATTTTAAATTTCTGATTTTTGAAAAATCAACTCATATTGC
5781554 GAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
194 GAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
5781589 TATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
5781654 CGCACGCTGAGGTATTT
66 C-CACGCTGAGGTATTT
5781671 CTTTTAAATT
Statistics
Matches: 460, Mismatches: 59, Indels: 52
0.81 0.10 0.09
Matches are distributed among these distances:
226 12 0.03
227 58 0.13
228 5 0.01
229 75 0.16
230 157 0.34
231 14 0.03
233 8 0.02
234 2 0.00
235 4 0.01
236 19 0.04
237 20 0.04
238 21 0.05
239 47 0.10
240 12 0.03
241 6 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (228 bp):
TATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
CCACGCTGAGGTATTTTAAATTTATGTTTTTCAAAAAATCAACAAAAAATGCAAGAGGTGAGTTG
AGCCTCGAGACACACGCCGAGGTATTTTAAATTTCTGATTTTTGAAAAATCAACTCATATTGCGA
GAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
Found at i:5781363 original size:153 final size:151
Alignment explanation
Indices: 5780911--5781747 Score: 863
Period size: 153 Copynumber: 5.4 Consensus size: 151
5780901 ACTTTCTGTT
* * * *
5780911 TTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTATTT
* * * * * *
5780973 TTAATTTATGTCTTTTTTTAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAACCTAGGGT--C
66 TTAA---ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGC
*
5781036 ACGCTGAGGTATTTTCAATTTATGTTTCTCTG
128 ACGCTGAGGTATTTT-AA---A---TT-TATG
* * * *
5781068 TTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCCCGGGTCGCACGCTGAGGTAT
1 TTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTA-
* * *
5781133 TTCTTTTAAATTTCT-CTTTTCAAAAAATCAACTCATAATGTGAGAGGTGAGTTGAGCCTCGGGT
63 -T-TTTTAAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
5781197 --CACGCTGAGGTATTTTCAATTTATG
125 CGCACGCTGAGGTATTTTAAATTTATG
*** ** ** * * * * * *
5781222 -TTTTCTAACTGTTTTTACAAAAAAT-CAAGAGGTGAGTTGAGCCTC-AGACACATGCCGAGGTA
1 TTTTTC-AA--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTA
*
5781284 TTTATTTTAAATTTCTATTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
63 --T-TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
5781348 CACACGCTGAGGTATTTTAAATTTCTG
125 CGCACGCTGAGGTATTTTAAATTTATG
5781375 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTATT
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTATT
* *
5781440 TTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCGGGTTGCA
65 TTTAAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCA
*
5781505 CGCTGAGGTATTTTAAATTTTTG
129 CGCTGAGGTATTTTAAATTTATG
* * *
5781528 TTTTTTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATT
1 -TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTATT
5781593 TTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCA
65 TTTAAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCA
*
5781658 CGCTGAGGTATTTCTTTTAAATTTCTG
129 CGCTGAGGTA----TTTTAAATTTATG
* * * * * * *
5781685 -TTTTCAAAAATCAACTCATATTTCGAAAGGTGAGTTGAGCTTTGAGTCGCACGCCGAGCTATT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTATT
5781748 CTCGATTTCT
Statistics
Matches: 586, Mismatches: 70, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
151 57 0.10
152 36 0.06
153 262 0.45
154 35 0.06
155 57 0.10
157 17 0.03
158 1 0.00
159 17 0.03
160 20 0.03
161 5 0.01
162 72 0.12
164 1 0.00
165 6 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (151 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGAGGTATTT
TTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACG
CTGAGGTATTTTAAATTTATG
Found at i:5781406 original size:76 final size:76
Alignment explanation
Indices: 5780903--5781747 Score: 883
Period size: 77 Copynumber: 10.9 Consensus size: 76
5780893 TATTTTTTAC
** * *
5780903 TTTCTGTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT--CACGCTG
1 TTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTG
*
5780965 AGGTATTTTTAA
65 AGGTATTTTAAA
* * * * *
5780977 TTTATGTCTTTTTTTAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAACCTAGGGT--CACGC
1 TTTCTG---TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGC
5781040 TGAGGTATTTTCAATTTA
63 TGAGGTATTTT-AA---A
* *
5781058 TGTTTCTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCCCGGGTCGCAC
1 ---TT-TCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCAC
5781123 GCTGAGGTATTTCTTTTAAA
61 GCTGAGGTA----TTTTAAA
* * *
5781143 TTTCT-CTTTTCAAAAAATCAACTCATAATGTGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGA
1 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
*
5781205 GGTATTTTCAA
66 GGTATTTTAAA
* **** ** ** * * * * * * * *
5781216 TTTATG-TTTTCTAACTGTTTTTACAAAAAAT-CAAGAGGTGAGTTGAGCCTC-AGACACATGCC
1 TTTCTGTTTTTC-AA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCT
5781278 GAGGTATTTATTTTAAA
64 GAGG----TATTTTAAA
* *
5781295 TTTCTATTTTTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGA
1 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
5781358 GGTATTTTAAA
66 GGTATTTTAAA
* *
5781369 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCTGA
1 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
5781434 GGTATTTTTAAA
66 GGTA-TTTTAAA
* *
5781446 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCGGGTTGCACGCTGA
1 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
5781511 GGTATTTTAAA
66 GGTATTTTAAA
* **
5781522 TTTTTGTTTTTTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
1 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
5781587 GGTATTTTTAAA
66 GGTA-TTTTAAA
5781599 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
1 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
5781664 GGTATTTCTTTTAAA
66 GGTA----TTTTAAA
* * * * * *
5781679 TTTCTG-TTTTC-AAAAATCAACTCATATTTCGAAAGGTGAGTTGAGCTTTGAGTCGCACGCCGA
1 TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
*
5781742 GCTATT
66 GGTATT
5781748 CTCGATTTCT
Statistics
Matches: 659, Mismatches: 75, Indels: 74
0.82 0.09 0.09
Matches are distributed among these distances:
73 16 0.02
74 47 0.07
75 15 0.02
76 156 0.24
77 212 0.32
78 61 0.09
79 56 0.08
80 23 0.03
81 4 0.01
82 7 0.01
83 38 0.06
84 2 0.00
85 16 0.02
88 2 0.00
89 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (76 bp):
TTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
GGTATTTTAAA
Found at i:5781958 original size:30 final size:29
Alignment explanation
Indices: 5781927--5782075 Score: 163
Period size: 30 Copynumber: 5.0 Consensus size: 29
5781917 TAATTTTTTG
* *
5781927 CATTTTGACCCCTGAAATTTTCTAAAATTG
1 CATTTTGACCCCT-AAACTTTCTAAAATTA
*
5781957 CATTTTGACCCCTAAACTTTCTTAAAACTA
1 CATTTTGACCCCTAAACTTTC-TAAAATTA
** * * *
5781987 CATTTCAACCCCTAAAATTTTTTAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAATTA
*
5782016 CATTTTAACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCT-AAAATTA
* *
5782046 CATTTTGACGCATAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCT-AAAATTA
5782076 TGTTTTGGCC
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
29 32 0.32
30 69 0.68
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTCTAAAATTA
Found at i:5782029 original size:59 final size:60
Alignment explanation
Indices: 5781934--5782050 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 60
5781924 TTGCATTTTG
* * * *
5781934 ACCCCTGAAATTTTCTAAAATTGCATTTTGACCCCTAAACTTTCTTAAAACTACATTTCA
1 ACCCCTAAAATTTTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAACTACATTTCA
* *
5781994 ACCCCTAAAATTTT-TTAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACATTT
1 ACCCCTAAAATTTTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAACTACATTT
5782051 TGACGCATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 38 0.75
60 13 0.25
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (60 bp):
ACCCCTAAAATTTTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAACTACATTTCA
Found at i:5782426 original size:7 final size:7
Alignment explanation
Indices: 5782409--5782497 Score: 66
Period size: 7 Copynumber: 13.3 Consensus size: 7
5782399 TCGAACGGAG
5782409 AAGAAGA
1 AAGAAGA
5782416 AAGAA-A
1 AAGAAGA
*
5782422 GAAGAAGG
1 -AAGAAGA
5782430 AAGAAG-
1 AAGAAGA
*
5782436 AATAAGA
1 AAGAAGA
5782443 AAGAAAGA
1 AAG-AAGA
5782451 AAGAA-A
1 AAGAAGA
5782457 AA-AAGA
1 AAGAAGA
*
5782463 AAAAAGA
1 AAGAAGA
*
5782470 AAAAAGA
1 AAGAAGA
5782477 AA-AAGA
1 AAGAAGA
5782483 GAA-AAGA
1 -AAGAAGA
5782490 AA-AAGA
1 AAGAAGA
5782496 AA
1 AA
5782498 AGAAAAAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
5 2 0.03
6 24 0.33
7 39 0.54
8 7 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (7 bp):
AAGAAGA
Found at i:5782426 original size:14 final size:14
Alignment explanation
Indices: 5782407--5782496 Score: 80
Period size: 14 Copynumber: 6.5 Consensus size: 14
5782397 GGTCGAACGG
5782407 AGAAGAAGAAAGAA
1 AGAAGAAGAAAGAA
*
5782421 AGAAGAAGGAAG-A
1 AGAAGAAGAAAGAA
*
5782434 AGAATAAGAAAGAA
1 AGAAGAAGAAAGAA
*
5782448 AGAAAGAAAAAAAGAA
1 AG-AAG-AAGAAAGAA
* *
5782464 AAAAGAAAAAAGAA
1 AGAAGAAGAAAGAA
5782478 A-AAG-AGAAAAGAA
1 AGAAGAAG-AAAGAA
5782491 A-AAGAA
1 AGAAGAA
5782497 AAGAAAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
12 1 0.02
13 24 0.38
14 25 0.39
15 5 0.08
16 9 0.14
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (14 bp):
AGAAGAAGAAAGAA
Found at i:5782505 original size:7 final size:7
Alignment explanation
Indices: 5782442--5782505 Score: 74
Period size: 7 Copynumber: 8.4 Consensus size: 7
5782432 GAAGAATAAG
5782442 AAAGAAA
1 AAAGAAA
5782449 GAAAGAAAA
1 -AAAG-AAA
5782458 AAAGAAA
1 AAAGAAA
5782465 AAAGAAA
1 AAAGAAA
5782472 AAAGAAA
1 AAAGAAA
5782479 AAGAGAAA
1 AA-AGAAA
*
5782487 AGAAAAAGA
1 A-AAGAA-A
5782496 AAAGAAA
1 AAAGAAA
5782503 AAA
1 AAA
5782506 ATAATTGACA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
7 23 0.46
8 21 0.42
9 6 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:5782505 original size:13 final size:13
Alignment explanation
Indices: 5782442--5782506 Score: 66
Period size: 12 Copynumber: 5.2 Consensus size: 13
5782432 GAAGAATAAG
*
5782442 AAAG-AAAGAAAG
1 AAAGAAAAGAAAA
5782454 AAA-AAAAGAAAA
1 AAAGAAAAGAAAA
*
5782466 AAGAAAAAAGAAAA
1 AA-AGAAAAGAAAA
*
5782480 AGAGAAAAG--AA
1 AAAGAAAAGAAAA
5782491 AAAGAAAAGAAAA
1 AAAGAAAAGAAAA
5782504 AAA
1 AAA
5782507 TAATTGACAG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 10 0.23
12 12 0.27
13 12 0.27
14 10 0.23
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAAA
Found at i:5782506 original size:8 final size:8
Alignment explanation
Indices: 5782442--5782506 Score: 73
Period size: 8 Copynumber: 8.4 Consensus size: 8
5782432 GAAGAATAAG
*
5782442 AAAGAAAG
1 AAAGAAAA
5782450 AAAGAAAA
1 AAAGAAAA
5782458 AAAG-AAA
1 AAAGAAAA
5782465 AAAG-AAA
1 AAAGAAAA
5782472 AAAGAAAA
1 AAAGAAAA
*
5782480 AGAGAAAA
1 AAAGAAAA
*
5782488 GAAA-AAGA
1 -AAAGAAAA
5782496 AAAGAAAA
1 AAAGAAAA
5782504 AAA
1 AAA
5782507 TAATTGACAG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
7 17 0.35
8 30 0.61
9 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:5782506 original size:27 final size:27
Alignment explanation
Indices: 5782407--5782506 Score: 102
Period size: 27 Copynumber: 3.7 Consensus size: 27
5782397 GGTCGAACGG
* *
5782407 AGAAGAAGAAAGAAAGAAGAAG-GAAGA
1 AGAAAAAGAAAGAAAGAAAAAGAGAA-A
*
5782434 AGAATAAGAAAGAAAGAAAGAA-A-AAA
1 AGAAAAAGAAAGAAAGAAA-AAGAGAAA
5782460 AGAAAAAAGAAA-AAAGAAAAAGAGAAA
1 AG-AAAAAGAAAGAAAGAAAAAGAGAAA
5782487 AGAAAAAGAAAAGAAA-AAAA
1 AGAAAAAG-AAAGAAAGAAAA
5782507 TAATTGACAG
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
25 2 0.03
26 17 0.27
27 39 0.62
28 5 0.08
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (27 bp):
AGAAAAAGAAAGAAAGAAAAAGAGAAA
Found at i:5782806 original size:9 final size:8
Alignment explanation
Indices: 5782788--5782817 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5782778 CAGCAGAAAA
5782788 AAAAAGAG
1 AAAAAGAG
5782796 AAAAAGAAG
1 AAAAAG-AG
5782805 AAAAAGAG
1 AAAAAGAG
5782813 AAAAA
1 AAAAA
5782818 AAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:5782810 original size:17 final size:18
Alignment explanation
Indices: 5782784--5782827 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5782774 AGCCCAGCAG
5782784 AAAA-AAAAAGAG-AAAA
1 AAAAGAAAAAGAGAAAAA
*
5782800 AGAAGAAAAAGAGAAAAA
1 AAAAGAAAAAGAGAAAAA
5782818 AAAAGAAAAA
1 AAAAGAAAAA
5782828 AGAGGTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAGAAAAA
Found at i:5782828 original size:19 final size:18
Alignment explanation
Indices: 5782787--5782831 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
5782777 CCAGCAGAAA
*
5782787 AAAAAAGAGAAAAAGAAG
1 AAAAAAGAGAAAAAAAAG
5782805 -AAAAAGAGAAAAAAAAAG
1 AAAAAAGAG-AAAAAAAAG
5782823 AAAAAAGAG
1 AAAAAAGAG
5782832 GTTCAATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:5783207 original size:21 final size:21
Alignment explanation
Indices: 5783183--5783224 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5783173 TCGTGTTTCT
* *
5783183 AAAATTTTCATGTTTTAAAAA
1 AAAATTCTCATGTTTCAAAAA
*
5783204 AAAATTCTCGTGTTTCAAAAA
1 AAAATTCTCATGTTTCAAAAA
5783225 TTGTCGTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAATTCTCATGTTTCAAAAA
Found at i:5783218 original size:38 final size:38
Alignment explanation
Indices: 5783168--5783241 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
5783158 GTGTTTTAAG
* * *
5783168 AATTTTCGTGTTTCTAAAATTTTCATGTTTTAAAAAAA
1 AATTCTCGTGTTTCAAAAATTGTCATGTTTTAAAAAAA
*
5783206 AATTCTCGTGTTTCAAAAATTGTCGTGTTTTAAAAA
1 AATTCTCGTGTTTCAAAAATTGTCATGTTTTAAAAA
5783242 TTTTCGTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (38 bp):
AATTCTCGTGTTTCAAAAATTGTCATGTTTTAAAAAAA
Found at i:5783223 original size:18 final size:17
Alignment explanation
Indices: 5783146--5783509 Score: 247
Period size: 17 Copynumber: 20.9 Consensus size: 17
5783136 ATAAAAAATA
*
5783146 TTCAAAAAATTT-GTGT
1 TTCAAAAATTTTCGTGT
* *
5783162 TTTAAGAATTTTCGTGT
1 TTCAAAAATTTTCGTGT
* *
5783179 TTCTAAAATTTTCATGTT
1 TTCAAAAATTTTCGTG-T
* *
5783197 TTAAAAAAAAATTCTCGTGT
1 TT---CAAAAATTTTCGTGT
*
5783217 TTCAAAAATTGTCGTGT
1 TTCAAAAATTTTCGTGT
*
5783234 TTTAAAAATTTTCGTGT
1 TTCAAAAATTTTCGTGT
* *
5783251 TTC-TAAATTTTCGTAT
1 TTCAAAAATTTTCGTGT
5783267 TTCAAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
5783285 TTCAAAAA-TTTCGGTGT
1 TTCAAAAATTTTC-GTGT
** **
5783302 TTCAAAAAAATTCCCGT
1 TTCAAAAATTTTCGTGT
* *
5783319 TTTAAAAATTTTCGGGTT
1 TTCAAAAATTTTCGTG-T
*
5783337 TTCAAAATTTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
* *
5783355 TTCAAAAAATTCTCTTGT
1 TTC-AAAAATTTTCGTGT
**
5783373 TTCAAAAATCCTCGTGTT
1 TTCAAAAATTTTCGTG-T
5783391 TTCAAAAA-TTTCGGTGT
1 TTCAAAAATTTTC-GTGT
**
5783408 TTTGAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTG-T
* *
5783426 TTCAAAAAAAATCTCGTGT
1 TTC--AAAAATTTTCGTGT
*
5783445 TTCATAAATTTTCGT-T
1 TTCAAAAATTTTCGTGT
* **
5783461 TTAAAAAAATAAT--TGT
1 TT-CAAAAATTTTCGTGT
5783477 TTCAAAAATTTTCGTGT
1 TTCAAAAATTTTCGTGT
**
5783494 TAAAAAAATTTCTCGT
1 TTCAAAAATTT-TCGT
5783510 ATTTTGATCG
Statistics
Matches: 270, Mismatches: 56, Indels: 42
0.73 0.15 0.11
Matches are distributed among these distances:
15 8 0.03
16 29 0.11
17 132 0.49
18 64 0.24
19 14 0.05
20 13 0.05
21 10 0.04
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (17 bp):
TTCAAAAATTTTCGTGT
Found at i:5783305 original size:35 final size:34
Alignment explanation
Indices: 5783150--5783494 Score: 256
Period size: 35 Copynumber: 9.9 Consensus size: 34
5783140 AAAATATTCA
* *
5783150 AAAAATTT-GTGTTTTAAGAATTTTCGTG-TTTC
1 AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
* * * *
5783182 TAAAATTTTCATGTTTTAAAAAAAAATTCTCGTG-TTTC
1 -AAAAATTTCGTG-TTT---CAAAAATTTTCGTGTTTTC
*
5783220 AAAAATTGTCGTGTTTTAAAAATTTTCGTG-TTTC
1 AAAAATT-TCGTGTTTCAAAAATTTTCGTGTTTTC
* * *
5783254 TAAATTTTCGTATTTCAAAAATTTTCGTGTTTTC
1 AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
** **
5783288 AAAAATTTCGGTGTTTCAAAAAAATTCCCGTTTT-
1 AAAAATTTC-GTGTTTCAAAAATTTTCGTGTTTTC
* *
5783322 AAAAATTTTCGGGTTTTCAAAATTTTTCGTGTTTTC
1 AAAAA-TTTCGTG-TTTCAAAAATTTTCGTGTTTTC
* **
5783358 AAAAAATTCTCTTGTTTCAAAAATCCTCGTGTTTTC
1 -AAAAATT-TCGTGTTTCAAAAATTTTCGTGTTTTC
**
5783394 AAAAATTTCGGTGTTTTGAAAATTTTCGTGTTTTC
1 AAAAATTTC-GTGTTTCAAAAATTTTCGTGTTTTC
* * **
5783429 AAAAAAAATCTCGTGTTTCATAAATTTTCGT-TTTAA
1 ---AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
*
5783465 AAAAATAAT--TGTTTCAAAAATTTTCGTGTT
1 AAAAAT-TTCGTGTTTCAAAAATTTTCGTGTT
5783495 AAAAAAATTT
Statistics
Matches: 249, Mismatches: 44, Indels: 38
0.75 0.13 0.11
Matches are distributed among these distances:
32 17 0.07
33 35 0.14
34 44 0.18
35 69 0.28
36 24 0.10
37 33 0.13
38 27 0.11
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (34 bp):
AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
Found at i:5783468 original size:32 final size:32
Alignment explanation
Indices: 5783442--5783502 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
5783432 AAAAATCTCG
* *
5783442 TGTTTCATAAATTTTCGTTTTAAAAAAATAAT
1 TGTTTCAAAAATTTTCGTGTTAAAAAAATAAT
5783474 TGTTTCAAAAATTTTCGTGTTAAAAAAAT
1 TGTTTCAAAAATTTTCGTGTTAAAAAAAT
5783503 TTCTCGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (32 bp):
TGTTTCAAAAATTTTCGTGTTAAAAAAATAAT
Found at i:5792036 original size:14 final size:14
Alignment explanation
Indices: 5791997--5792036 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
5791987 AAATTTATAT
5791997 TTTGATTATTACAA
1 TTTGATTATTACAA
*
5792011 TTTAATTTATTACAA
1 TTTGA-TTATTACAA
5792026 TTTGATTATTA
1 TTTGATTATTA
5792037 ATATTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (14 bp):
TTTGATTATTACAA
Found at i:5792411 original size:24 final size:23
Alignment explanation
Indices: 5792357--5792421 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 23
5792347 AATTTTGATT
5792357 AATAAAAAAAATAAAATTATTAA
1 AATAAAAAAAATAAAATTATTAA
*
5792380 ATATTAAAATAATATAAATATT-TTAA
1 A-A-TAAAA-AAAATAAA-ATTATTAA
5792406 AATAAATTAAAAATAA
1 AATAAA--AAAAATAA
5792422 TATGGGCGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
23 1 0.03
24 5 0.15
25 12 0.35
26 13 0.38
27 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAAAAAAAATAAAATTATTAA
Found at i:5792416 original size:19 final size:16
Alignment explanation
Indices: 5792368--5792416 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 16
5792358 ATAAAAAAAA
*
5792368 TAAAATTATTAAATAT
1 TAAAATAATTAAATAT
5792384 TAAAATAATATAAATATTT
1 TAAAATAAT-TAAATA--T
5792403 TAAAATAAATTAAA
1 TAAAAT-AATTAAA
5792417 AATAATATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
19 11 0.39
20 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATAATTAAATAT
Found at i:5792440 original size:2 final size:2
Alignment explanation
Indices: 5792433--5792462 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5792423 ATGGGCGGGA
5792433 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
5792463 TTGCAAATTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5794511 original size:38 final size:38
Alignment explanation
Indices: 5794469--5794617 Score: 104
Period size: 38 Copynumber: 3.9 Consensus size: 38
5794459 ATAAAAGTTG
* *
5794469 TAAAAGTTATTAAATTTTAAAAAAATATATAAAATATT
1 TAAAAATTATTAAATTTTAAAAAAATATATAAAATATA
* * ** * *
5794507 TAAAACTTGTTAAAAATTAGAAAAATATA-AAAATCGTA
1 TAAAAATTATTAAATTTTAAAAAAATATATAAAAT-ATA
* * *
5794545 AAAAAATTATAAAATTTTATTAAAAAT-TATAAAATATA
1 TAAAAATTATTAAATTTTA-AAAAAATATATAAAATATA
* * * * *
5794583 TAGAAATATATAAAAAATTTAGAAAATTATATAAA
1 TAAAAAT-TAT-TAAATTTTAAAAAAATATATAAA
5794618 GTTGTAAGAA
Statistics
Matches: 85, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
37 5 0.06
38 47 0.55
39 19 0.22
40 14 0.16
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (38 bp):
TAAAAATTATTAAATTTTAAAAAAATATATAAAATATA
Found at i:5794530 original size:9 final size:9
Alignment explanation
Indices: 5794450--5794613 Score: 75
Period size: 10 Copynumber: 17.2 Consensus size: 9
5794440 AGATCAAAAT
5794450 TAAAAATTAA
1 TAAAAATT-A
* *
5794460 TAAAAGTTG
1 TAAAAATTA
*
5794469 TAAAAGTTA
1 TAAAAATTA
**
5794478 TTAAATTTTA
1 -TAAAAATTA
*
5794488 AAAAAATATA
1 TAAAAAT-TA
5794498 TAAAATATT-
1 TAAAA-ATTA
* *
5794507 TAAAACTTGT
1 TAAAAATT-A
5794517 TAAAAATTA
1 TAAAAATTA
*
5794526 GAAAAA-TA
1 TAAAAATTA
5794534 TAAAAATCGTA
1 TAAAAAT--TA
*
5794545 AAAAAATTA
1 TAAAAATTA
*
5794554 TAAAATTTTA
1 TAAAA-ATTA
5794564 TTAAAAATTA
1 -TAAAAATTA
5794574 T-AAAATATA
1 TAAAAAT-TA
*
5794583 TAGAAATATA
1 TAAAAAT-TA
5794593 TAAAAAATT-
1 T-AAAAATTA
5794602 TAGAAAATTA
1 TA-AAAATTA
5794612 TA
1 TA
5794614 TAAAGTTGTA
Statistics
Matches: 119, Mismatches: 20, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
8 15 0.13
9 39 0.33
10 45 0.38
11 20 0.17
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:5794596 original size:19 final size:20
Alignment explanation
Indices: 5794567--5794617 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
5794557 AATTTTATTA
*
5794567 AAAAT-TATAAAATATATAG
1 AAAATATATAAAAAATATAG
*
5794586 -AAATATATAAAAAATTTAG
1 AAAATATATAAAAAATATAG
5794605 AAAATTATATAAA
1 AAAA-TATATAAA
5794618 GTTGTAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 3 0.11
21 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAATATATAAAAAATATAG
Found at i:5795148 original size:95 final size:93
Alignment explanation
Indices: 5795039--5795218 Score: 243
Period size: 95 Copynumber: 1.9 Consensus size: 93
5795029 ACCCCTGGCC
* * * * *
5795039 TTTTTGATGCATTTTAGCAGTTCAAGTATCTAATTGAGTGGAAAAAAAAAAGCAGGGGCTTAATT
1 TTTTTGATGAATTTTAGCAATTCAAGTACCCAATTGAGT-GAAAAAAAAAAGCAAGGGCTTAATT
* *
5795104 GTTTGTTTTTGAAAAAGTTTGAAGGCATTT
65 GCTT-TCTTTGAAAAAGTTTGAAGGCATTT
* * * *
5795134 TTTTTTATGAATTTTAGCAATTGAAGTACCCAATTGAGTGCAAAAAAAAAGCAATGGCTTAATTG
1 TTTTTGATGAATTTTAGCAATTCAAGTACCCAATTGAGTGAAAAAAAAAAGCAAGGGCTTAATTG
5795199 CTTTCTTTGAAAAAGTTTGA
66 CTTTCTTTGAAAAAGTTTGA
5795219 GATATTTTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
93 16 0.22
94 25 0.34
95 33 0.45
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (93 bp):
TTTTTGATGAATTTTAGCAATTCAAGTACCCAATTGAGTGAAAAAAAAAAGCAAGGGCTTAATTG
CTTTCTTTGAAAAAGTTTGAAGGCATTT
Found at i:5795256 original size:87 final size:92
Alignment explanation
Indices: 5795070--5795266 Score: 217
Period size: 87 Copynumber: 2.2 Consensus size: 92
5795060 TCAAGTATCT
* * *
5795070 AATTGAGTGGAAAAAAAAAAGCAGGGGCTTAATTGTTTGTTTTTGAAAAAGTTTGAAGGCATTTT
1 AATTGAGT-GAAAAAAAAAAGCAAGGGCTTAATTGCTTGTCTTTGAAAAAGTTTGAAGGCA--TT
* * * *
5795135 TTTTTATGAATTTTAGCAATTGAAGTACCC
63 ATTTTATGAATTTTAGAAATTAAAATACCC
* *
5795165 AATTGAGTGCAAAAAAAAAGCAATGGCTTAATTGCTT-TCTTTGAAAAAGTTTG-A-G-A-TATT
1 AATTGAGTGAAAAAAAAAAGCAAGGGCTTAATTGCTTGTCTTTGAAAAAGTTTGAAGGCATTATT
*
5795225 TTATGCATTTTA-AAAGTTAAAATACCC
66 TTATGAATTTTAGAAA-TTAAAATACCC
*
5795252 AATTGAGTGTAAAAA
1 AATTGAGTGAAAAAA
5795267 TATTAATTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
86 2 0.02
87 37 0.41
90 1 0.01
91 1 0.01
92 1 0.01
93 15 0.17
94 25 0.28
95 8 0.09
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (92 bp):
AATTGAGTGAAAAAAAAAAGCAAGGGCTTAATTGCTTGTCTTTGAAAAAGTTTGAAGGCATTATT
TTATGAATTTTAGAAATTAAAATACCC
Found at i:5797767 original size:248 final size:248
Alignment explanation
Indices: 5797327--5797937 Score: 1062
Period size: 248 Copynumber: 2.5 Consensus size: 248
5797317 ATTGTCAGAA
* * * * *
5797327 ATTGCTCAAGGTAATGATGATCCAAGATGAATACCCTA-TCGTTTACCAGTGCCTGCCATATAGT
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTT-CCATTGCCTGCCATATAGT
*
5797391 GTTGTGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTT
65 GTTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTT
*
5797456 TTCACCTTAAACAAATCTTCCAATTTCTGCGGGTTCGACTTCATTTCCTGTAGAACAAGCAACGT
130 TTCACCTTAAACAAATCTCCCAATTTCTGCGGGTTCGACTTCATTTCCTGTAGAACAAGCAACGT
*
5797521 TTAAAATATTGGATTGGAAGCTCAAACATTATATGTTATAAACCTAAGAAAGAG
195 TTAAAATATTGGATTGGAAGCTCAAACATTATATATTATAAACCTAAGAAAGAG
5797575 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
*
5797640 TTATGTATGTATTCATAAAGTAGTTAATTTGGAAGGAAAAGAAATACATAAACTTGTTTTCTTTT
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTT
* *
5797705 TCACCTTAAACAAATCTCCCCATTTCTGCGGGTTCGACTTCATTTCCTGTAGAACCAGCAACGTT
131 TCACCTTAAACAAATCTCCCAATTTCTGCGGGTTCGACTTCATTTCCTGTAGAACAAGCAACGTT
* *
5797770 TAAAATATTGGATTGTAAGCTCAAACATTATATATTATAAACCTAGGAAAGAG
196 TAAAATATTGGATTGGAAGCTCAAACATTATATATTATAAACCTAAGAAAGAG
5797823 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
* * *
5797888 TTATGTATGTATTCTTAAAGTGGTTAATTTGAAAGGAAAAGAGATACATA
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
5797938 TCTCTGCAAA
Statistics
Matches: 345, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
248 341 0.99
249 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (248 bp):
ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTT
TCACCTTAAACAAATCTCCCAATTTCTGCGGGTTCGACTTCATTTCCTGTAGAACAAGCAACGTT
TAAAATATTGGATTGGAAGCTCAAACATTATATATTATAAACCTAAGAAAGAG
Found at i:5803456 original size:8 final size:9
Alignment explanation
Indices: 5803416--5803462 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
5803406 ATATATATTT
5803416 ATTTTTAAA
1 ATTTTTAAA
5803425 ATTTTTAAA
1 ATTTTTAAA
**
5803434 ATATTTT-TT
1 AT-TTTTAAA
5803443 ATTTTTAAA
1 ATTTTTAAA
5803452 ATTTTTAAA
1 ATTTTTAAA
5803461 AT
1 AT
5803463 AAATTTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 4 0.12
9 24 0.75
10 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:5803469 original size:27 final size:27
Alignment explanation
Indices: 5803404--5803469 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
5803394 AATATATAAT
5803404 AAATATATATTTATTTTTAAAATTTTTA
1 AAATATAT-TTTATTTTTAAAATTTTTA
*
5803432 AAATATTTTTTATTTTTAAAATTTTTA
1 AAATATATTTTATTTTTAAAATTTTTA
*
5803459 AAATAAATTTT
1 AAATATATTTT
5803470 TGGTGTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 28 0.80
28 7 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
AAATATATTTTATTTTTAAAATTTTTA
Found at i:5805238 original size:19 final size:19
Alignment explanation
Indices: 5805194--5805251 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
5805184 AAAAATCAAT
* *
5805194 TAATAAAAATA-TATAAAA
1 TAATATAAATATTTTAAAA
5805212 TAAT-TAAATATTTTAAAA
1 TAATATAAATATTTTAAAA
*
5805230 TAATATAAAGATTTTAAAA
1 TAATATAAATATTTTAAAA
5805249 TAA
1 TAA
5805252 ATTAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.14
18 14 0.40
19 16 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TAATATAAATATTTTAAAA
Found at i:5805257 original size:19 final size:18
Alignment explanation
Indices: 5805207--5805257 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
5805197 TAAAAATATA
*
5805207 TAAAATAATTAAATATTT
1 TAAAATAATTAAAGATTT
5805225 TAAAATAATATAAAGATTT
1 TAAAATAAT-TAAAGATTT
5805244 TAAAATAAATTAAA
1 TAAAAT-AATTAAA
5805258 AATAATATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.30
19 18 0.60
20 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAAATAATTAAAGATTT
Found at i:5806305 original size:16 final size:16
Alignment explanation
Indices: 5806284--5806323 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
5806274 TTAAGCTTGA
5806284 AAAACTTTGAAAGGCC
1 AAAACTTTGAAAGGCC
5806300 AAAACTTTGAAAGGCC
1 AAAACTTTGAAAGGCC
*
5806316 ATAACTTT
1 AAAACTTT
5806324 TCGCTCGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (16 bp):
AAAACTTTGAAAGGCC
Found at i:5807369 original size:10 final size:10
Alignment explanation
Indices: 5807334--5807419 Score: 63
Period size: 10 Copynumber: 8.8 Consensus size: 10
5807324 ATTAGAAAAA
5807334 TATAAAA-AT
1 TATAAAATAT
* *
5807343 CATAAAAAAAT
1 TAT-AAAATAT
* *
5807354 TGTAAAATTT
1 TATAAAATAT
5807364 TATAAAA-AT
1 TATAAAATAT
*
5807373 CATAAAATAT
1 TATAAAATAT
5807383 TATAAAATA-
1 TATAAAATAT
5807392 TATAGAAATA-
1 TATA-AAATAT
*
5807402 TATAAAAAAT
1 TATAAAATAT
*
5807412 TAGAAAAT
1 TATAAAAT
5807420 TATATAAAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
9 17 0.28
10 40 0.67
11 3 0.05
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (10 bp):
TATAAAATAT
Found at i:5807370 original size:19 final size:19
Alignment explanation
Indices: 5807356--5807409 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
5807346 AAAAAAATTG
*
5807356 TAAAATTTTATAAAAATCA
1 TAAAATATTATAAAAATCA
5807375 TAAAATATTATAAAATAT-A
1 TAAAATATTATAAAA-ATCA
5807394 TAGAAATA-TATAAAAA
1 TA-AAATATTATAAAAA
5807410 ATTAGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.03
19 24 0.75
20 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAATATTATAAAAATCA
Found at i:5807370 original size:30 final size:30
Alignment explanation
Indices: 5807333--5807427 Score: 108
Period size: 29 Copynumber: 3.2 Consensus size: 30
5807323 AATTAGAAAA
5807333 ATATAAAAATCATAAAAAAATTGTAAAATT
1 ATATAAAAATCATAAAAAAATTGTAAAATT
* * *
5807363 TTATAAAAATCAT-AAAATATTATAAAA-T
1 ATATAAAAATCATAAAAAAATTGTAAAATT
*
5807391 ATATAGAAAT-ATATAAAAAATTAG-AAAATT
1 ATATAAAAATCATA-AAAAAATT-GTAAAATT
5807421 ATATAAA
1 ATATAAA
5807428 GTTGCAAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
27 2 0.04
28 9 0.17
29 23 0.43
30 19 0.36
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (30 bp):
ATATAAAAATCATAAAAAAATTGTAAAATT
Found at i:5807419 original size:19 final size:19
Alignment explanation
Indices: 5807329--5807427 Score: 64
Period size: 19 Copynumber: 5.1 Consensus size: 19
5807319 TAAAAATTAG
5807329 AAAAATATA-AAAATCATA-A
1 AAAAAT-TAGAAAAT-ATATA
*
5807348 AAAAATT-GTAAAAT-TTTA
1 AAAAATTAG-AAAATATATA
* *
5807366 TAAAAATCATAAAATATTATA
1 -AAAAATTAGAAAATA-TATA
*
5807387 AAATATATAG-AAATATATA
1 AAAAAT-TAGAAAATATATA
5807406 AAAAATTAGAAAATTATATA
1 AAAAATTAGAAAA-TATATA
5807426 AA
1 AA
5807428 GTTGCAAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
17 1 0.02
18 5 0.08
19 34 0.55
20 18 0.29
21 4 0.06
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAATTAGAAAATATATA
Found at i:5810648 original size:248 final size:247
Alignment explanation
Indices: 5810139--5810747 Score: 908
Period size: 248 Copynumber: 2.4 Consensus size: 247
5810129 TCAGAAATTT
* * * * * * *
5810139 CTCAAGGTACTGATGATCCAAGATGAATACCCTA-TCGTTTACCAGTGCCTGCCATATAGTGTTG
1 CTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTT-CCATTGCCTGCCATATAGTGTTA
5810203 TGTATGTATTCATAAAGTAGTTAATTTGAAAAGG-AAAGAAATACATATAAACTTGTTTTTCCTT
65 TGTATGTATTCATAAAGTAGTTAATTTG-AAAGGAAAAGAAATAC--ATAAACTTGTTTTTCCTT
* *
5810267 TTTACCTTATAAAAATCTTGCCATTGCGGCTGGTTAAACTTTTCCTGTAGAACGCCAGCAACGTT
127 TTTACCTTATAAAAAGCTTCCCATTGCGGCTGGTTAAACTTTTCCTGTAGAAC-CCAGCAACGTT
* *
5810332 TAAAATATTGGATTGTAAGCTTAAACATTATATGTTATAAACCTAGGAAAGAGATTG
191 TAAAATATTGGACTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATTG
*
5810389 CTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCTATATAGTGTTAT
1 CTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTAT
*
5810454 GTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTG-TTTTCTTTTTTA
66 GTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCCTTTTTA
* * **
5810518 CCTTA-AACAAAGCTTCCCAATT-CTGCTTGTTCCACTTCATTTCCTGTAGAA-CCAGCAACGTT
131 CCTTATAA-AAAGCTTCCC-ATTGCGGCTGGTTAAAC-T--TTTCCTGTAGAACCCAGCAACGTT
5810580 TAAAATATTGGACTGTAAGCTCAAACATTATATGTTATAAA-CTAAGGAAAGAGATTG
191 TAAAATATTGGACTGTAAGCTCAAACATTATATGTTATAAACCT-AGGAAAGAGATTG
5810637 CTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTAT
1 CTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTAT
*
5810702 GTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAGATACATA
66 GTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
5810748 TCTCTGCAAA
Statistics
Matches: 332, Mismatches: 19, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
246 2 0.01
247 35 0.11
248 185 0.56
249 5 0.02
250 101 0.30
251 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (247 bp):
CTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTGTTAT
GTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCCTTTTTA
CCTTATAAAAAGCTTCCCATTGCGGCTGGTTAAACTTTTCCTGTAGAACCCAGCAACGTTTAAAA
TATTGGACTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAGATTG
Found at i:5816241 original size:4 final size:4
Alignment explanation
Indices: 5816232--5816257 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5816222 GACTAAAAAG
5816232 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
5816258 GGTTAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:5816745 original size:18 final size:18
Alignment explanation
Indices: 5816724--5816758 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5816714 ATTTTGTAAT
*
5816724 TAGTTTGAATTTAATTTC
1 TAGTTTAAATTTAATTTC
*
5816742 TAGTTTAAATTTGATTT
1 TAGTTTAAATTTAATTT
5816759 TTAAGTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:5817488 original size:19 final size:19
Alignment explanation
Indices: 5817419--5817573 Score: 67
Period size: 19 Copynumber: 8.2 Consensus size: 19
5817409 AATTTTTTAT
*
5817419 TAAAATATT-TAAAACTTG
1 TAAAATATTATAAAAATTG
* * *
5817437 TTAAA-ATTAGAAAAA-TA
1 TAAAATATTATAAAAATTG
*
5817454 TAAAA-ATCGTAAAAAAATTG
1 TAAAATAT--TATAAAAATTG
**
5817474 TAAAATATTATAAAAATCA
1 TAAAATATTATAAAAATTG
* *
5817493 TAAAATTTTAT-AAAATATA
1 TAAAATATTATAAAAAT-TG
*
5817512 TAGAAATA-TAGAAAAAATT-
1 TA-AAATATTA-TAAAAATTG
*
5817531 TAGAAA-ATTATATAAAGTTG
1 TA-AAATATTATA-AAAATTG
*
5817551 TAAGAAAATTATAAAAA-TG
1 TAA-AATATTATAAAAATTG
5817570 TAAA
1 TAAA
5817574 GAAATATAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
17 10 0.09
18 16 0.15
19 49 0.46
20 18 0.17
21 13 0.12
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (19 bp):
TAAAATATTATAAAAATTG
Found at i:5817505 original size:10 final size:10
Alignment explanation
Indices: 5817474--5817520 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
5817464 AAAAAAATTG
5817474 TAAAATATTA
1 TAAAATATTA
*
5817484 TAAAA-ATCA
1 TAAAATATTA
*
5817493 TAAAATTTTA
1 TAAAATATTA
5817503 TAAAATA-TA
1 TAAAATATTA
5817512 TAGAAATAT
1 TA-AAATAT
5817521 AGAAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
9 12 0.40
10 18 0.60
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
TAAAATATTA
Found at i:5818182 original size:84 final size:85
Alignment explanation
Indices: 5818037--5818220 Score: 223
Period size: 84 Copynumber: 2.2 Consensus size: 85
5818027 TTGCTCTTTT
* ** * * *
5818037 TTTTTTTGAAAAAGTTTGAGGGCATTTTTTATGAATTTTGGCAGTTTAAGTACTCAATTGAGTG-
1 TTTTTTTGAAAAAGTTTGA-GGCATATTTTATGAATTTTGAAAGTTCAAATACCCAATTGAGTGT
*
5818101 AAAAAAAAGTAAGGACTTAATTGC
65 AAAAAAAAG--A-GACTTAATTAC
*
5818125 -TTTTTTGAAAAAGTTTGA-G-ATATTTTATGCATTTTGAAAGTTCAAATACCCAATTGAGTGTT
1 TTTTTTTGAAAAAGTTTGAGGCATATTTTATGAATTTTGAAAGTTCAAATACCCAATTGAGTG-T
5818187 AAAAAAAAGAGACTTAATTAC
65 AAAAAAAAGAGACTTAATTAC
5818208 TTTTTTTGAAAAA
1 TTTTTTTGAAAAA
5818221 AATTTAAAGT
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
83 10 0.12
84 47 0.55
85 1 0.01
86 9 0.11
87 18 0.21
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (85 bp):
TTTTTTTGAAAAAGTTTGAGGCATATTTTATGAATTTTGAAAGTTCAAATACCCAATTGAGTGTA
AAAAAAAGAGACTTAATTAC
Found at i:5822493 original size:20 final size:20
Alignment explanation
Indices: 5822457--5822494 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5822447 GGGAAATGGG
*
5822457 AAAATAGAAAATGTATTTTA
1 AAAATAGAAAATATATTTTA
5822477 AAAATA-AAATATATATTT
1 AAAATAGAAA-ATATATTT
5822495 ATTATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAATAGAAAATATATTTTA
Found at i:5823084 original size:14 final size:14
Alignment explanation
Indices: 5823067--5823116 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
5823057 CTAAACTCGT
*
5823067 AACCCGTAACCCCA
1 AACCCTTAACCCCA
* *
5823081 AACCCTTAAACCCT
1 AACCCTTAACCCCA
5823095 AA-CCTTGAACCCCA
1 AACCCTT-AACCCCA
5823109 AA-CCTTAA
1 AACCCTTAA
5823117 ACATTGATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 6 0.20
14 24 0.80
ACGTcount: A:0.38, C:0.42, G:0.04, T:0.16
Consensus pattern (14 bp):
AACCCTTAACCCCA
Found at i:5823086 original size:28 final size:27
Alignment explanation
Indices: 5823054--5823118 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
5823044 CGGGCCTTAG
*
5823054 ACCCTAAACTCGTAACCCGT-AACCCCAA
1 ACCCTAAAC-CCTAA-CCGTGAACCCCAA
*
5823082 ACCCTTAAACCCTAACCTTGAACCCCAA
1 ACCC-TAAACCCTAACCGTGAACCCCAA
*
5823110 ACCTTAAAC
1 ACCCTAAAC
5823119 ATTGATCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 8 0.25
28 19 0.59
29 5 0.16
ACGTcount: A:0.37, C:0.42, G:0.05, T:0.17
Consensus pattern (27 bp):
ACCCTAAACCCTAACCGTGAACCCCAA
Found at i:5831325 original size:77 final size:77
Alignment explanation
Indices: 5831198--5831351 Score: 247
Period size: 77 Copynumber: 2.0 Consensus size: 77
5831188 CAAAGACTCC
* *
5831198 CTTGAAAATGCCAGAGGTGTGGCAAACCAATGTGAAGCATGTTGATTTATCGGT-GAGGCTACCA
1 CTTGAAAATGCCAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAG-GGCTACCA
5831262 CATATGAGAGAGG
65 CATATGAGAGAGG
*
5831275 CTTGAAAATGCTAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAGGGCTACCAC
1 CTTGAAAATGCCAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAGGGCTACCAC
* *
5831340 CTATGAGTGAGG
66 ATATGAGAGAGG
5831352 TGAGTTGTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
77 70 0.99
78 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.24
Consensus pattern (77 bp):
CTTGAAAATGCCAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAGGGCTACCAC
ATATGAGAGAGG
Found at i:5832768 original size:15 final size:15
Alignment explanation
Indices: 5832748--5832777 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5832738 ATCACAAGTA
5832748 TAAAAGATGATCCAC
1 TAAAAGATGATCCAC
5832763 TAAAAGATGATCCAC
1 TAAAAGATGATCCAC
5832778 ATAATGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
TAAAAGATGATCCAC
Found at i:5837859 original size:34 final size:34
Alignment explanation
Indices: 5837816--5837885 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
5837806 CAAATAGGGT
* *
5837816 TTAGGGTTTAGGGTTTCAAATGCATACCAAACTA
1 TTAGGGTTTAGGGTTCCAAATACATACCAAACTA
*
5837850 TTAGGGTTTAGGGTTCCAAATACATGCCAAACTA
1 TTAGGGTTTAGGGTTCCAAATACATACCAAACTA
5837884 TT
1 TT
5837886 TCTTTCACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (34 bp):
TTAGGGTTTAGGGTTCCAAATACATACCAAACTA
Found at i:5840489 original size:35 final size:36
Alignment explanation
Indices: 5840422--5840496 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
5840412 TGTAACATTA
* *
5840422 AAAAATATATTTAATTTTTTATATTAAAATTTTAAT
1 AAAAACATATTTAATTTATTATATTAAAATTTTAAT
* *
5840458 AAAAACATA-TTAATTTATTAT-TTATATATTTTTAT
1 AAAAACATATTTAATTTATTATATTA-AAATTTTAAT
5840493 AAAA
1 AAAA
5840497 TTTAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 3 0.09
35 23 0.68
36 8 0.24
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
AAAAACATATTTAATTTATTATATTAAAATTTTAAT
Found at i:5840511 original size:14 final size:15
Alignment explanation
Indices: 5840489--5840518 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5840479 TTATATATTT
5840489 TTATAAAATTTAAAA
1 TTATAAAATTTAAAA
5840504 TTAT-AAATTTAAAA
1 TTATAAAATTTAAAA
5840518 T
1 T
5840519 ATATTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATAAAATTTAAAA
Found at i:5843286 original size:22 final size:22
Alignment explanation
Indices: 5843247--5843311 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
5843237 CTTAGAAAAA
*
5843247 TAATACATATAAAATTAAAATGG
1 TAATACA-ATAAATTTAAAATGG
*
5843270 TAATACAATAAATTTAAACAATGT
1 TAATACAATAAATTT-AA-AATGG
5843294 TAAT--AATAAATTTAAAAT
1 TAATACAATAAATTTAAAAT
5843312 AATATTAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 3 0.08
21 2 0.05
22 16 0.42
23 9 0.24
24 8 0.21
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (22 bp):
TAATACAATAAATTTAAAATGG
Found at i:5845463 original size:46 final size:46
Alignment explanation
Indices: 5845363--5845698 Score: 475
Period size: 46 Copynumber: 7.6 Consensus size: 46
5845353 TACGTATGAT
5845363 CACTTATCACTTGTC-C-C-TGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTT-TCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
5845406 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
5845452 CACTTATCACTTTCTCACTTGATCAGATAAGAGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
5845498 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
5845544 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A-G----
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
5845580 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
5845626 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
5845672 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTCTCACTTGATCAGA
5845699 AGTACTCAAA
Statistics
Matches: 268, Mismatches: 11, Indels: 25
0.88 0.04 0.08
Matches are distributed among these distances:
36 28 0.10
38 2 0.01
39 1 0.00
40 2 0.01
41 2 0.01
42 3 0.01
43 14 0.05
44 3 0.01
45 18 0.07
46 195 0.73
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:5845585 original size:36 final size:36
Alignment explanation
Indices: 5845544--5845616 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
5845534 CTAAGGCTAA
*
5845544 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
5845580 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
5845616 C
1 C
5845617 TAATGCTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:5845592 original size:82 final size:82
Alignment explanation
Indices: 5845498--5845662 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 82
5845488 CTAAGGCTAC
* *
5845498 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCTCT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTCACT
5845563 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
* * *
5845580 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTCACT
5845645 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
5845662 C
1 C
5845663 TAATGCTACC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTCACT
TGATCAGATAAGTGTAG
Found at i:5845592 original size:128 final size:128
Alignment explanation
Indices: 5845452--5845698 Score: 431
Period size: 128 Copynumber: 1.9 Consensus size: 128
5845442 CTAAGGCTAC
5845452 CACTTATCACTTTCTCACTTGATCAGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACT
* *
5845517 TGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* * *
5845580 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACT
* *
5845645 TGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTATCACTTGATCAGA
66 TGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTATCACTTGATCAGA
5845699 AGTACTCAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 112 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (128 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACT
TGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:5848560 original size:132 final size:132
Alignment explanation
Indices: 5848322--5848905 Score: 857
Period size: 132 Copynumber: 4.4 Consensus size: 132
5848312 CGCTGCCTTC
* * * *
5848322 GATCTGCTCCACTACTGCTTAGGGAGACATGATATAAAATCTTCAACCTACTCCACTACTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
* * * *
5848387 AGGAGATAGGATTTGTGGTTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
66 AGGAGACAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
5848452 TT
131 TT
* * * * * * *
5848454 AATCTGGTCCATTATTGTTTAGGGAGAC-GGAATCTACATTCTTCAACCTACTCCACTGTTGCTC
1 GATCTGCTCCACTACTGCTTAGGGAGACAGG-ATCTACAATCTTCAACCTACTCCACTGCTGCTC
*
5848518 AAGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTC
65 AAGGAGACAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTC
5848583 -TT
130 TTT
5848585 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
* * * * *
5848650 AGGAGACATGAATGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATGAGATTCACCATCT
66 AGGAGACAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
5848715 TT
131 TT
* *
5848717 GATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACAGCTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
* * * * ** *
5848782 GGGAGACAGGACTGGTGGCTTAAACCTGCTTCCCTACTACCTTGAGAAGATAAGATTCATTGTAT
66 AGGAGACAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
5848847 TT
131 TT
* *
5848849 GATCTGCTCCACTACTGCTTAGGGAGACAGGACCTAAAATCTTCAACCTACTCCACT
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACT
5848906 ACTACTCAGG
Statistics
Matches: 405, Mismatches: 44, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
131 116 0.29
132 289 0.71
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
AGGAGACAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
TT
Found at i:5848800 original size:263 final size:264
Alignment explanation
Indices: 5848322--5848913 Score: 873
Period size: 263 Copynumber: 2.2 Consensus size: 264
5848312 CGCTGCCTTC
* *
5848322 GATCTGCTCCACTACTGCTTAGGGAGACATGATATAAAATCTTCAACCTACTCCACTACTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAAAATCTTCAACCTACTCCACTACTGCTCA
* * * * * *
5848387 AGGAGATAGGATTTGTGGTTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
66 AGGAGACAGGAATGGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGATAAGATTCACCATCT
** * * * * * *
5848452 TTAATCTGGTCCATTATTGTTTAGGGAGACGGAATCTACATTCTTCAACCTACTCCACTGTTGCT
131 TTAATCTACTCCACTACTGCTTAGGGAGACGGAATCTACAATCTTCAACCTACTCCACAGCTGCT
* * * *
5848517 CAAGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT
196 CAAGGAGACAGGACTGGTGGCTTAAACCTGCTTCCCTACTACCTTGAGAAGATAAGATTCACCGT
5848582 -CTT
261 ACTT
* *
5848585 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAAAATCTTCAACCTACTCCACTACTGCTCA
* * *
5848650 AGGAGACATGAATGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATGAGATTCACCATCT
66 AGGAGACAGGAATGGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGATAAGATTCACCATCT
*
5848715 TTGATCTACTCCACTACTGCTTAGGGAGACAGG-ATCTACAATCTTCAACCTACTCCACAGCTGC
131 TTAATCTACTCCACTACTGCTTAGGGAGAC-GGAATCTACAATCTTCAACCTACTCCACAGCTGC
* **
5848779 TCAGGGAGACAGGACTGGTGGCTTAAACCTGCTTCCCTACTACCTTGAGAAGATAAGATTCATTG
195 TCAAGGAGACAGGACTGGTGGCTTAAACCTGCTTCCCTACTACCTTGAGAAGATAAGATTCACCG
*
5848844 TATTT
260 TACTT
* *
5848849 GATCTGCTCCACTACTGCTTAGGGAGACAGGACCTAAAATCTTCAACCTACTCCACTACTACTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAAAATCTTCAACCTACTCCACTACTGCTCA
5848914 GGGAAATAGG
Statistics
Matches: 293, Mismatches: 34, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
263 228 0.78
264 65 0.22
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (264 bp):
GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAAAATCTTCAACCTACTCCACTACTGCTCA
AGGAGACAGGAATGGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGATAAGATTCACCATCT
TTAATCTACTCCACTACTGCTTAGGGAGACGGAATCTACAATCTTCAACCTACTCCACAGCTGCT
CAAGGAGACAGGACTGGTGGCTTAAACCTGCTTCCCTACTACCTTGAGAAGATAAGATTCACCGT
ACTT
Found at i:5849084 original size:45 final size:44
Alignment explanation
Indices: 5849027--5849351 Score: 223
Period size: 45 Copynumber: 7.3 Consensus size: 44
5849017 GCTATCTTCG
*
5849027 ATCTACTTCACTGCCAATACAGGAATACAAGATCTGTTATTTCCA
1 ATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTATTT-CA
* * * * * * *** *
5849072 ACCTACTCCACTGCTGC-CTAGA-G-AGATAAG-CCTGGGGTCTTCG
1 ATCTACTTCACTGC--CAATACAGGAAGACAAGATCTGTTAT-TTCA
* *
5849115 ATCTACTTCACTGCTAATACAGGAAGACAAGATCTGCTATTTTCA
1 ATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTA-TTTCA
* *** * * *
5849160 ATCTACTCCACTGCTGCT-CAAGG-AGACAAG-GCTTGTGACTTCA
1 ATCTACTTCACTGCCAATAC-AGGAAGACAAGATC-TGTTATTTCA
* * *
5849203 ATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGTTATCTTCG
1 ATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTAT-TTCA
** * * *
5849248 ATCTACTTCGTTGCCAATACAGGAAGACAAGATCTGCTAACTTCG
1 ATCTACTTCACTGCCAATACAGGAAGACAAGATCTG-TTATTTCA
* *
5849293 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
1 ATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTAT-TTCA
* *
5849338 ACCTACTCCACTGC
1 ATCTACTTCACTGC
5849352 TGCTCAGGGA
Statistics
Matches: 213, Mismatches: 51, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
42 3 0.01
43 39 0.18
44 37 0.17
45 127 0.60
46 6 0.03
47 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (44 bp):
ATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTATTTCA
Found at i:5849134 original size:88 final size:88
Alignment explanation
Indices: 5849021--5849363 Score: 334
Period size: 88 Copynumber: 3.9 Consensus size: 88
5849011 AGGCTTGCTA
*
5849021 TCTTCGATCTACTTCACTGCCAATACAGGAATACAAGATCTGTTATTTCCAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTATTTCCAACCTACTCCACTGC
* *
5849086 TGC-CTAGAGAGATAAGCCTGGGG
66 TGCTCAAG-GAGACAAGCCTGGGG
* * * *
5849109 TCTTCGATCTACTTCACTGCTAATACAGGAAGACAAGATCTGCTATTTTCAATCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTATTTCCAACCTACTCCACTGC
* * *
5849174 TGCTCAAGGAGACAAGGCTTGTG
66 TGCTCAAGGAGACAAGCCTGGGG
* * * * * * * **
5849197 ACTTCAATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGTTATCTT-CGATCTACTTCGTTG
1 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTAT-TTCCAACCTACTCCACTG
*** * ***
5849261 CCAAT-ACAGGAAGACAAGATCTGCTA
65 CTGCTCA-AGG-AGACAAG-CCTGGGG
* * *
5849287 ACTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT-CAACCTACTCCACTG
1 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTAT-TTCCAACCTACTCCACTG
*
5849351 CTGCTCAGGGAGA
65 CTGCTCAAGGAGA
5849364 TAAGGCATTG
Statistics
Matches: 210, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
87 1 0.00
88 130 0.62
89 15 0.07
90 63 0.30
91 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGTTATTTCCAACCTACTCCACTGC
TGCTCAAGGAGACAAGCCTGGGG
Found at i:5850726 original size:62 final size:62
Alignment explanation
Indices: 5850609--5850726 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
5850599 TCTTTATTTA
* * * *
5850609 TTTTTTTGGACTCAAGGCGCCCTTTACAGGTTTTCACCTTGGTCTTCTTTTCTTTTTTCCTT
1 TTTTTTTGGACTCAAAGCGCCCTTTACAGATTTTCACCTTGATCTTCTTTCCTTTTTTCCTT
*
5850671 TTTTTTTGGACTCAAAGCGCCCTTTGCAGATTTTCACCTTGATCTT-TTCTCCTTTT
1 TTTTTTTGGACTCAAAGCGCCCTTTACAGATTTTCACCTTGATCTTCTT-TCCTTTT
5850727 AGGTGCTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
61 2 0.04
62 48 0.96
ACGTcount: A:0.12, C:0.25, G:0.14, T:0.50
Consensus pattern (62 bp):
TTTTTTTGGACTCAAAGCGCCCTTTACAGATTTTCACCTTGATCTTCTTTCCTTTTTTCCTT
Found at i:5867424 original size:41 final size:44
Alignment explanation
Indices: 5867367--5867468 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
5867357 TGACATGTAT
* * * *
5867367 TGTCTGGGACATTGGCATC-GTATTTGATT-CGTGTAAGACC-C
1 TGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCAC
5867408 TGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCAC
1 TGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCAC
5867452 -GTCTGGGAC-GTTGGCAT
1 TGTCTGGGACAG-TGGCAT
5867469 TGTACGAGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
41 18 0.34
42 9 0.17
43 25 0.47
44 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (44 bp):
TGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCAC
Found at i:5867658 original size:16 final size:17
Alignment explanation
Indices: 5867629--5867660 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5867619 TGAATTGATG
5867629 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
5867646 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
5867661 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:5875872 original size:22 final size:23
Alignment explanation
Indices: 5875839--5875884 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5875829 AATTCGTTTG
*
5875839 TCATCTGG-AAAAGTTCTATAGC
1 TCATCTGGAAAAAGGTCTATAGC
5875861 TCAT-TGGAAAAAAGGTCTATAGC
1 TCATCTGG-AAAAAGGTCTATAGC
5875884 T
1 T
5875885 AGTTTGGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 4 0.19
23 14 0.67
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (23 bp):
TCATCTGGAAAAAGGTCTATAGC
Found at i:5892738 original size:44 final size:43
Alignment explanation
Indices: 5892660--5892789 Score: 142
Period size: 43 Copynumber: 3.0 Consensus size: 43
5892650 CATAGGATTC
* * *
5892660 CGATATGAG-TTATCGTGTAAGACCACGTCAGGGACGTTGGCGT
1 CGATATTAGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
5892703 CGAT-TTGAGATTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATATT-AGA-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* *
5892747 CGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTAGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
5892790 TGTATGAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
42 2 0.03
43 35 0.47
44 31 0.42
45 6 0.08
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
CGATATTAGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:5895443 original size:23 final size:23
Alignment explanation
Indices: 5895401--5895444 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5895391 TAAATATTAT
*
5895401 TTTATTAATATTTTGCTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
5895424 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
5895445 AAAATGGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Done.