Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 77 of 199
Found at i:27954931 original size:9 final size:9
Alignment explanation
Indices: 27954882--27955241 Score: 265
Period size: 9 Copynumber: 42.8 Consensus size: 9
27954872 AATTGCACGG
27954882 GTAAGTTAT
1 GTAAGTTAT
27954891 GT-A-TTAT
1 GTAAGTTAT
*
27954898 GTAAGCTAT
1 GTAAGTTAT
*
27954907 GTAAGTTGT
1 GTAAGTTAT
27954916 GT-A-TTAT
1 GTAAGTTAT
27954923 GTAAGTTAT
1 GTAAGTTAT
27954932 -T-A-TTAT
1 GTAAGTTAT
27954938 GTAAGTTAT
1 GTAAGTTAT
*
27954947 GTAAGTAAT
1 GTAAGTTAT
27954956 GT-A-TTAT
1 GTAAGTTAT
*
27954963 GTAAGTTGT
1 GTAAGTTAT
*
27954972 GT-A-TAAT
1 GTAAGTTAT
*
27954979 GTTAGTTAT
1 GTAAGTTAT
**
27954988 CAAAGTTAT
1 GTAAGTTAT
27954997 GT-A-TTAT
1 GTAAGTTAT
27955004 GTAAGTTAT
1 GTAAGTTAT
*
27955013 TTAAGTTAT
1 GTAAGTTAT
*
27955022 GTAAGTTGT
1 GTAAGTTAT
27955031 GT-A-TTAT
1 GTAAGTTAT
27955038 GTAAGTTAT
1 GTAAGTTAT
*
27955047 GTAAGTTGT
1 GTAAGTTAT
27955056 GT-A-TTAT
1 GTAAGTTAT
27955063 GTAAGTTAT
1 GTAAGTTAT
* *
27955072 GTAGGCTAT
1 GTAAGTTAT
* *
27955081 GTATGTTAA
1 GTAAGTTAT
*
27955090 GTAAGTCAT
1 GTAAGTTAT
27955099 GT-A-TTAT
1 GTAAGTTAT
*
27955106 GTAAGTTGT
1 GTAAGTTAT
27955115 GT-A-TTAT
1 GTAAGTTAT
27955122 GTAAGTTAT
1 GTAAGTTAT
**
27955131 CAAAGTTAT
1 GTAAGTTAT
27955140 GT-A-TTAT
1 GTAAGTTAT
27955147 GTAAGTTAT
1 GTAAGTTAT
* *
27955156 TTAAGTCAT
1 GTAAGTTAT
*
27955165 GTAAGTTGT
1 GTAAGTTAT
27955174 GT-A-TTAT
1 GTAAGTTAT
27955181 GTAAGTTAT
1 GTAAGTTAT
27955190 GT-AGTCTAT
1 GTAAGT-TAT
27955199 GT-A-TTAT
1 GTAAGTTAT
27955206 GTAAGTTAT
1 GTAAGTTAT
*
27955215 -TATGTTATTAT
1 GTAAG---TTAT
27955226 GTAAGTTAT
1 GTAAGTTAT
*
27955235 GCAAGTT
1 GTAAGTT
27955242 TATATATAAG
Statistics
Matches: 274, Mismatches: 45, Indels: 64
0.72 0.12 0.17
Matches are distributed among these distances:
6 4 0.01
7 64 0.23
8 32 0.12
9 167 0.61
11 4 0.01
12 3 0.01
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:27954966 original size:25 final size:25
Alignment explanation
Indices: 27954888--27955241 Score: 170
Period size: 25 Copynumber: 14.0 Consensus size: 25
27954878 ACGGGTAAGT
*
27954888 TATGTATTATGTAAGCTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGT
*
27954913 TGTGTATTATGTAAGTTAT-T-A-T
1 TATGTATTATGTAAGTTATGTAAGT
*
27954935 TATGTAAGTTATGTAAGTAATGT-A-T
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
27954960 TATGTAAGTTGTGT-A-TAATGTTAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
**
27954985 TATCAAAGTTATGT-A-TTATGTAAGT
1 TAT-GTA-TTATGTAAGTTATGTAAGT
* *
27955010 TATTTAAGTTATGTAAGTTGTGT-A-T
1 TATGT-A-TTATGTAAGTTATGTAAGT
*
27955035 TATGTAAGTTATGTAAGTTGTGT-A-T
1 TATGT-A-TTATGTAAGTTATGTAAGT
* * *
27955060 TATGTAAGTTATGTAGGCTATGTATGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
* *
27955087 TAAGTAAGTCATGT-A-TTATGTAAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
* **
27955112 TGTGTATTATGTAAGTTATCAAAGT
1 TATGTATTATGTAAGTTATGTAAGT
*
27955137 TATGTATTATGTAAGTTATTTAAGT
1 TATGTATTATGTAAGTTATGTAAGT
* *
27955162 CATGTAAGTTGTGT-A-TTATGTAAGT
1 TATGT-A-TTATGTAAGTTATGTAAGT
27955187 TATGTAGTCTATGT-A-TTATGTAAGTTAT
1 TATGTA-T-TATGTAAGTTATGTAAG---T
*
27955215 TATGTTATTATGTAAGTTATGCAAGT
1 TATG-TATTATGTAAGTTATGTAAGT
27955241 T
1 T
27955242 TATATATAAG
Statistics
Matches: 270, Mismatches: 37, Indels: 43
0.77 0.11 0.12
Matches are distributed among these distances:
22 5 0.02
23 13 0.05
24 20 0.07
25 181 0.67
26 6 0.02
27 28 0.10
28 7 0.03
29 10 0.04
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (25 bp):
TATGTATTATGTAAGTTATGTAAGT
Found at i:27955020 original size:34 final size:34
Alignment explanation
Indices: 27954919--27955189 Score: 207
Period size: 34 Copynumber: 7.9 Consensus size: 34
27954909 AAGTTGTGTA
*
27954919 TTATGTAAGTTAT-TATTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAGTTATTTAAG
* * *
27954952 TAATGT-A-TTATGTAAGTTGTGT-A-TAATGTT-AG
1 TTATGTAAGTTATGT-A-TTATGTAAGTTAT-TTAAG
**
27954984 TTATCAAAGTTATGTATTATGTAAGTTATTTAAG
1 TTATGTAAGTTATGTATTATGTAAGTTATTTAAG
* *
27955018 TTATGTAAGTTGTGTATTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAGTTATTTAAG
* * * * *
27955052 TTGTGT-A-TTATGTAAGTTATGTAGGCTATGTATG
1 TTATGTAAGTTATGT-A-TTATGTAAGTTATTTAAG
* *
27955086 TTAAGTAAGTCATGTATTATGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAA---GT-TA-T-T-TAAG
**
27955127 TTATCAAAGTTATGTATTATGTAAGTTATTTAAG
1 TTATGTAAGTTATGTATTATGTAAGTTATTTAAG
* *
27955161 TCATGTAAGTTGTGTATTATGTAAGTTAT
1 TTATGTAAGTTATGTATTATGTAAGTTAT
27955190 GTAGTCTATG
Statistics
Matches: 185, Mismatches: 33, Indels: 39
0.72 0.13 0.15
Matches are distributed among these distances:
31 4 0.02
32 20 0.11
33 15 0.08
34 106 0.57
35 3 0.02
36 6 0.03
37 3 0.02
38 4 0.02
39 1 0.01
41 23 0.12
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (34 bp):
TTATGTAAGTTATGTATTATGTAAGTTATTTAAG
Found at i:27955029 original size:59 final size:59
Alignment explanation
Indices: 27954887--27955235 Score: 294
Period size: 59 Copynumber: 6.0 Consensus size: 59
27954877 CACGGGTAAG
*
27954887 TTATGT-A-TTATGTAAGCTATGTAAGTTGTGTATTATGTAAGTTAT-T-A-TTATGTAA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTATGT-A
* * * **
27954942 GTTATGTAAGTAATGT-A-TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
1 -TTATGTAAGTTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTATGTA
* *
27955000 TTATGTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTATGTA
* * * ** * *
27955059 TTATGTAAGTTATGTAGGCTATGTATGTTAAGTAAGTCATGT-A-TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTGTGT-A-TTATGTAAGTTATGTAAGTTATGTA
** * * * *
27955118 TTATGTAAGTTATCAAAGTTATGT-A-TTATGTAAGTTATTTAAGTCATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTGTGT-A-TTATGTAAGTTATGTAAGTTATGTA
* *
27955177 TTATGTAAGTTATGT-AGTCTATGT-ATTATGTAAGTTATTATGTTA-TTATGTAAGTTATG
1 TTATGTAAGTTATGTAAGT-TATGTAAGT-TGT--G-TATTATGTAAGTTATGTAAGTTATG
27955236 CAAGTTTATA
Statistics
Matches: 241, Mismatches: 35, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
56 32 0.13
57 27 0.11
58 12 0.05
59 139 0.58
60 3 0.01
61 19 0.08
62 6 0.02
63 2 0.01
64 1 0.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.47
Consensus pattern (59 bp):
TTATGTAAGTTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTATGTA
Found at i:27955138 original size:143 final size:140
Alignment explanation
Indices: 27954882--27955216 Score: 537
Period size: 143 Copynumber: 2.4 Consensus size: 140
27954872 AATTGCACGG
* * * *
27954882 GTAAGTTATGTATTATGTAAGCTATGTAAGTTGTGTATTATGTAAGTTATTATTATGTAAGTTAT
1 GTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATTACTATGTAAGTTAA
*
27954947 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTA
66 GTAAGTAATGTATTATGTAAGTTGTGTATAATGTAAGTTATCAAAGTTATGTATTATGTAAGTTA
*
27955012 TTTAAGTTAT
131 TTTAAGTCAT
*
27955022 GTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATGT
1 GTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTAT-TA--CTATGTAAGT
* *
27955087 TAAGTAAGTCATGTATTATGTAAGTTGTGTATTATGTAAGTTATCAAAGTTATGTATTATGTAAG
63 TAAGTAAGTAATGTATTATGTAAGTTGTGTATAATGTAAGTTATCAAAGTTATGTATTATGTAAG
27955152 TTATTTAAGTCAT
128 TTATTTAAGTCAT
*
27955165 GTAAGTTGTGTATTATGTAAGTTATGT-AGTCTATGTATTATGTAAGTTATTA
1 GTAAGTTGTGTATTATGTAAGTTATGTAAGT-TGTGTATTATGTAAGTTATTA
27955217 TGTTATTATG
Statistics
Matches: 181, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
140 48 0.27
141 2 0.01
142 5 0.03
143 126 0.70
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.47
Consensus pattern (140 bp):
GTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATTACTATGTAAGTTAA
GTAAGTAATGTATTATGTAAGTTGTGTATAATGTAAGTTATCAAAGTTATGTATTATGTAAGTTA
TTTAAGTCAT
Found at i:27955201 original size:34 final size:34
Alignment explanation
Indices: 27954887--27955240 Score: 101
Period size: 34 Copynumber: 10.6 Consensus size: 34
27954877 CACGGGTAAG
*
27954887 TTATGT-A-TTATGTAAG-CTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTC-ATGTAAGTTATGTA
* *
27954919 TTATGTAAGTTATTATTATGTAAGTTATGTAAGTAATGTA
1 TTATGTAAG------TTATGTAAGTCATGTAAGTTATGTA
* * * **
27954959 TTATGTAAGTTGTGT-A-TAATGTTAGTTATCAAA
1 TTATGTAAGTTATGTAAGTCATGTAAGTTAT-GTA
* *
27954992 GTTATGT-A-TTATGTAAGTTATTTAAGTTATGTAA
1 -TTATGTAAGTTATGTAAGTCATGTAAGTTATGT-A
* * *
27955026 GTTGTGT-A-TTATGTAAGTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTAAGTCATGTAAGTTATGTA
* *
27955059 TTATGTAAGTTATGT-AGGC---TATG-TATG--
1 TTATGTAAGTTATGTAAGTCATGTAAGTTATGTA
* * * *
27955086 TTAAGTAAGTCATGT-A-TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTCATGTAAGTTATGTA
** *
27955118 TTATGTAAGTTATCAAAGTTATGT-A-TTATGTAA
1 TTATGTAAGTTATGTAAGTCATGTAAGTTATGT-A
* * **
27955151 GTTATTTAAGTCATGTAAGTTGTGT-A-TTATGTAA
1 -TTATGTAAGTTATGTAAGTCATGTAAGTTATGT-A
*
27955185 GTTATGT-AGTCTATGT-A-TTATGTAAGTTATTATGTTA
1 -TTATGTAAGT-TATGTAAGTCATGTAAG---TTATG-TA
*
27955222 TTATGTAAGTTATGCAAGT
1 TTATGTAAGTTATGTAAGT
27955241 TTATATATAA
Statistics
Matches: 243, Mismatches: 43, Indels: 66
0.69 0.12 0.19
Matches are distributed among these distances:
27 14 0.06
29 6 0.02
30 6 0.02
32 47 0.19
33 17 0.07
34 101 0.42
36 10 0.04
37 10 0.04
38 2 0.01
40 30 0.12
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTCATGTAAGTTATGTA
Found at i:27955225 original size:20 final size:19
Alignment explanation
Indices: 27954993--27955234 Score: 85
Period size: 16 Copynumber: 12.1 Consensus size: 19
27954983 GTTATCAAAG
27954993 TTATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
*
27955012 TT-T-AAGTTATGTAAGTTGTGTA
1 TTATGTA-TTATGTAA---GT-TA
27955034 TTATGTAAGTTATGTAAG---
1 TTATGT-A-TTATGTAAGTTA
*
27955052 TTGTGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
* *
27955071 TGTAGGCTATGTATGTTAAGTAA
1 T-TATG-TAT-TATG-TAAGTTA
*
27955094 GTCATGTATTATGTAAG---
1 -TTATGTATTATGTAAGTTA
*
27955111 TTGTGTATTATGTAAGTTATCAAA
1 TTATGTATTATGTAAG-T-T---A
27955135 GTTATGTATTATGTAAGTTA
1 -TTATGTATTATGTAAGTTA
* * *
27955155 TTTAAGTCATGTAAGT-TGTGTA
1 -TTATGT-AT-TATGTAAGT-TA
27955177 TTATGTAAGTTATGT-AG-T-
1 TTATGT-A-TTATGTAAGTTA
*
27955195 CTATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
27955214 TTATGTTATTATGTAAGTTA
1 TTATG-TATTATGTAAGTTA
27955234 T
1 T
27955235 GCAAGTTTAT
Statistics
Matches: 169, Mismatches: 21, Indels: 65
0.66 0.08 0.25
Matches are distributed among these distances:
16 29 0.17
17 5 0.03
18 20 0.12
19 8 0.05
20 27 0.16
21 24 0.14
22 19 0.11
23 10 0.06
24 2 0.01
25 25 0.15
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (19 bp):
TTATGTATTATGTAAGTTA
Found at i:27955430 original size:121 final size:120
Alignment explanation
Indices: 27955287--27955607 Score: 516
Period size: 121 Copynumber: 2.6 Consensus size: 120
27955277 TTATGTATCT
* * * *
27955287 TATTTATAATTATTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAAATGTAGGATATATAT
1 TATTTACAATTATTTTTAAAATTATAAAATTAATTTC-AATAAAATTGAAATATAGGTTATATAT
*
27955352 CCATATCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAA
65 CCATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAA
* *
27955408 TATTTACAATTATTTTTAAAATTATAAAATTTATTGACAATAAAATTGAAATATAGGTTATATAT
1 TATTTACAATTATTTTTAAAATTATAAAATTAATT-TCAATAAAATTGAAATATAGGTTATATAT
*
27955473 CCATACCATATATGGGGTGATATATTAAAAATATAGGTTTTAATATTTAAAAATAA
65 CCATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAA
* *
27955529 CATTTACAATTATTTTTAAAATTATAAAAAATAATTTACAATAAAATTGAAATATAGGTTATATA
1 TATTTACAATTATTTTTAAAATTAT-AAAATTAATTT-CAATAAAATTGAAATATAGGTTATATA
27955594 TCCATACCATATAT
64 TCCATACCATATAT
27955608 ATAAATTTTT
Statistics
Matches: 186, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
121 136 0.73
122 50 0.27
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (120 bp):
TATTTACAATTATTTTTAAAATTATAAAATTAATTTCAATAAAATTGAAATATAGGTTATATATC
CATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAA
Found at i:27955660 original size:18 final size:18
Alignment explanation
Indices: 27955637--27955725 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
27955627 ATATATAAAT
27955637 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
27955655 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
**
27955677 TTTTTGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
27955694 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
27955712 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
27955726 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.49
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:27955720 original size:31 final size:31
Alignment explanation
Indices: 27955639--27955743 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
27955629 ATATAAATTT
27955639 TAAGTAATGTAATATA--TT--TAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
* * *
27955666 TAAGT--TATAA-ATTTTTGTAAGTAA-TATATT
1 TAAGTAATGTAATATATTT-T-AGTAAGTA-ATG
27955696 TAAGTAATGTAATATATTTTAGTAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
27955727 TAAGTAATGTAATATAT
1 TAAGTAATGTAATATAT
27955744 ACTTTAATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
24 2 0.03
25 4 0.07
26 1 0.02
27 6 0.10
29 2 0.03
30 10 0.16
31 24 0.39
32 7 0.11
33 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (31 bp):
TAAGTAATGTAATATATTTTAGTAAGTAATG
Found at i:27955783 original size:13 final size:13
Alignment explanation
Indices: 27955767--27955857 Score: 82
Period size: 13 Copynumber: 6.8 Consensus size: 13
27955757 TAAGTCATGC
27955767 ATTTAAGTAATAT
1 ATTTAAGTAATAT
27955780 ATTTAAGTAA-AT
1 ATTTAAGTAATAT
*
27955792 -TCTAGTAAGTAATGT
1 AT-T--TAAGTAATAT
27955807 ATTTAAGTAATAT
1 ATTTAAGTAATAT
27955820 ATTTAAGTAA-AGT
1 ATTTAAGTAATA-T
*
27955833 -TTAGTAATTAATAT
1 ATT--TAAGTAATAT
27955847 ATTTAAGTAAT
1 ATTTAAGTAAT
27955858 GTAAGTTATA
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
11 1 0.02
12 6 0.09
13 37 0.58
14 14 0.22
15 5 0.08
16 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (13 bp):
ATTTAAGTAATAT
Found at i:27955811 original size:40 final size:39
Alignment explanation
Indices: 27955621--27955874 Score: 193
Period size: 40 Copynumber: 6.5 Consensus size: 39
27955611 AATTTTTAAT
*
27955621 ATATATATATATAAATTTTAAGTAATGTAATATATTTAAGTA
1 ATATATTTA-ATAAATTTT-AGTAA-GTAATATATTTAAGTA
* * *
27955663 ATGTAAGTT-ATAAATTTTTGTAAGTAATATATTTAAG--
1 ATAT-ATTTAATAAATTTTAGTAAGTAATATATTTAAGTA
* * * **
27955700 -TA-ATGTAATATATTTTAGTAAGTAATGTAAGTAATGTA
1 ATATATTTAATAAATTTTAGTAAGTAATATATTTAA-GTA
* **
27955738 ATATATACTT--T-AATTTTAGTAAGTCATGCATTTAAGTA
1 ATATAT--TTAATAAATTTTAGTAAGTAATATATTTAAGTA
* *
27955776 ATATATTTAAGTAAATTCTAGTAAGTAATGTATTTAAGTA
1 ATATATTTAA-TAAATTTTAGTAAGTAATATATTTAAGTA
* *
27955816 ATATATTTAAGTAAAGTTTAGTAATTAATATATTTAAGTA
1 ATATATTTAA-TAAATTTTAGTAAGTAATATATTTAAGTA
* *
27955856 ATGTAAGTT-ATAAATTTTA
1 ATAT-ATTTAATAAATTTTA
27955875 AAAATATATA
Statistics
Matches: 170, Mismatches: 28, Indels: 31
0.74 0.12 0.14
Matches are distributed among these distances:
34 2 0.01
35 22 0.13
36 4 0.02
38 9 0.05
39 44 0.26
40 71 0.42
41 12 0.07
42 4 0.02
43 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (39 bp):
ATATATTTAATAAATTTTAGTAAGTAATATATTTAAGTA
Found at i:27959517 original size:7 final size:7
Alignment explanation
Indices: 27959505--27959628 Score: 65
Period size: 7 Copynumber: 17.0 Consensus size: 7
27959495 CTTAATTGAC
27959505 ACCCTAA
1 ACCCTAA
27959512 ACCCTAA
1 ACCCTAA
27959519 ATCCCT-A
1 A-CCCTAA
*
27959526 ACCCTTA
1 ACCCTAA
27959533 ACCCTTAA
1 ACCC-TAA
*
27959541 ATCTCCTAG
1 A-C-CCTAA
*
27959550 CCCCTAA
1 ACCCTAA
*
27959557 ATTCCTAA
1 A-CCCTAA
*
27959565 CCCCT-A
1 ACCCTAA
27959571 ACTCCTAA
1 AC-CCTAA
*
27959579 CCCCTAA
1 ACCCTAA
27959586 ATCCCTAA
1 A-CCCTAA
*
27959594 CCCCTAA
1 ACCCTAA
*
27959601 CCCCTAA
1 ACCCTAA
*
27959608 ACCTTATA
1 ACCCTA-A
*
27959616 TCCC-AA
1 ACCCTAA
27959622 ACCCTAA
1 ACCCTAA
27959629 TAATCATATA
Statistics
Matches: 89, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
6 10 0.11
7 50 0.56
8 24 0.27
9 3 0.03
10 2 0.02
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.23
Consensus pattern (7 bp):
ACCCTAA
Found at i:27959526 original size:15 final size:15
Alignment explanation
Indices: 27959505--27959628 Score: 80
Period size: 14 Copynumber: 8.5 Consensus size: 15
27959495 CTTAATTGAC
27959505 ACCCTAAA-CCCTAA
1 ACCCTAAATCCCTAA
*
27959519 ATCCCT-AA-CCCTTA
1 A-CCCTAAATCCCTAA
*
27959533 ACCCTTAAATCTCCTAG
1 ACCC-TAAATC-CCTAA
* *
27959550 CCCCTAAATTCCTAA
1 ACCCTAAATCCCTAA
* *
27959565 CCCCTAACT-CCTAA
1 ACCCTAAATCCCTAA
*
27959579 CCCCTAAATCCCTAA
1 ACCCTAAATCCCTAA
* *
27959594 CCCCT-AACCCCTAA
1 ACCCTAAATCCCTAA
* *
27959608 ACCTTATATCCC-AA
1 ACCCTAAATCCCTAA
27959622 ACCCTAA
1 ACCCTAA
27959629 TAATCATATA
Statistics
Matches: 88, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
13 3 0.03
14 41 0.47
15 32 0.36
16 6 0.07
17 6 0.07
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.23
Consensus pattern (15 bp):
ACCCTAAATCCCTAA
Found at i:27959577 original size:29 final size:29
Alignment explanation
Indices: 27959543--27959625 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
27959533 ACCCTTAAAT
* *
27959543 CTCCTAGCCCCTAAATTCCTAACCCCTAA
1 CTCCTAACCCCTAAATCCCTAACCCCTAA
27959572 CTCCTAACCCCTAAATCCCTAACCCCTAA
1 CTCCTAACCCCTAAATCCCTAACCCCTAA
* * * * *
27959601 CCCCTAAACCTTATATCCCAAACCC
1 CTCCTAACCCCTAAATCCCTAACCC
27959626 TAATAATCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.30, C:0.47, G:0.01, T:0.22
Consensus pattern (29 bp):
CTCCTAACCCCTAAATCCCTAACCCCTAA
Found at i:27959591 original size:22 final size:22
Alignment explanation
Indices: 27959506--27959608 Score: 109
Period size: 22 Copynumber: 4.6 Consensus size: 22
27959496 TTAATTGACA
*
27959506 CCCTAAACCCTAAATCCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
* * *
27959528 CCTTAACCCTTAAATCTCCTAGC
1 CCCTAACCCCTAAATC-CCTAAC
** *
27959551 CCCTAAATTCCT-AACCCCTAAC
1 CCCT-AACCCCTAAATCCCTAAC
*
27959573 TCCTAACCCCTAAATCCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
27959595 CCCTAACCCCTAAA
1 CCCTAACCCCTAAA
27959609 CCTTATATCC
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 5 0.08
22 43 0.68
23 11 0.17
24 4 0.06
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.22
Consensus pattern (22 bp):
CCCTAACCCCTAAATCCCTAAC
Found at i:27959624 original size:22 final size:22
Alignment explanation
Indices: 27959505--27959625 Score: 77
Period size: 22 Copynumber: 5.5 Consensus size: 22
27959495 CTTAATTGAC
*
27959505 ACCCTAAA-CCCTAAATCCCTA
1 ACCCCAAACCCCTAAATCCCTA
** *
27959526 ACCCTTAACCCTTAAATCTCCTA
1 ACCCCAAACCCCTAAATC-CCTA
* ** *
27959549 GCCCCTAAATTCCT-AACCCCTA
1 ACCCC-AAACCCCTAAATCCCTA
* *
27959571 ACTCCTAACCCCTAAATCCCTA
1 ACCCCAAACCCCTAAATCCCTA
* *
27959593 ACCCCTAACCCCTAAA-CCTTA
1 ACCCCAAACCCCTAAATCCCTA
*
27959614 TATCCCAAACCC
1 -ACCCCAAACCC
27959626 TAATAATCAT
Statistics
Matches: 76, Mismatches: 19, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
21 16 0.21
22 46 0.61
23 10 0.13
24 4 0.05
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.22
Consensus pattern (22 bp):
ACCCCAAACCCCTAAATCCCTA
Found at i:27960683 original size:41 final size:42
Alignment explanation
Indices: 27960634--27960785 Score: 107
Period size: 41 Copynumber: 3.7 Consensus size: 42
27960624 TCAACAAAAA
27960634 CGCCGCTAAA-ACCCTAACATTAGCGGCGCTTATCATAGAAT
1 CGCCGCTAAAGACCCTAACATTAGCGGCGCTTATCATAGAAT
* * * * * * *
27960675 CGCCGCTAAAAATCTTAACTTTAGCGTCGCTTAT-ATAAAAA
1 CGCCGCTAAAGACCCTAACATTAGCGGCGCTTATCATAGAAT
* * * * *
27960716 CGCCACTATAAGA-CCAAATATTCGCGGCGC-T-TCAAAGAAAT
1 CGCCGCTA-AAGACCCTAACATTAGCGGCGCTTATCATAG-AAT
* * * *
27960757 CACCGCTAAATACCTTAACTTTAGCGGCG
1 CGCCGCTAAAGACCCTAACATTAGCGGCG
27960786 GTTGATTAAA
Statistics
Matches: 81, Mismatches: 25, Indels: 10
0.70 0.22 0.09
Matches are distributed among these distances:
39 1 0.01
40 6 0.07
41 52 0.64
42 22 0.27
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (42 bp):
CGCCGCTAAAGACCCTAACATTAGCGGCGCTTATCATAGAAT
Found at i:27964137 original size:48 final size:49
Alignment explanation
Indices: 27964057--27964192 Score: 159
Period size: 54 Copynumber: 2.7 Consensus size: 49
27964047 TTGTGGATTT
* *
27964057 GGTTTAGGCACTGGTGGTGGTTGCGGT-TTTGGTTCAGAAGGCAGGTTA
1 GGTTTAGTCACTGGTGGTGGTTGAGGTATTTGGTTCAGAAGGCAGGTTA
* *
27964105 GGTTTAGTCACTGGTGGTGGTTGAGGTATTGGTTTTGGTTCAGGAGGCGGGTTA
1 GGTTTAGTCACTGGTGGTGGTTGAGGTA-----TTTGGTTCAGAAGGCAGGTTA
* *
27964159 GGTTTAGTCACTGGTGCTGGTTGTGG-ATTTGGTT
1 GGTTTAGTCACTGGTGGTGGTTGAGGTATTTGGTT
27964193 TAGGCACTGG
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
48 32 0.42
53 1 0.01
54 43 0.57
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (49 bp):
GGTTTAGTCACTGGTGGTGGTTGAGGTATTTGGTTCAGAAGGCAGGTTA
Found at i:27964195 original size:30 final size:30
Alignment explanation
Indices: 27964159--27964222 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
27964149 AGGCGGGTTA
* * *
27964159 GGTTTAGTCACTGGTGCTGGTTGTGGATTT
1 GGTTTAGGCACTGGTGCTGGCTGCGGATTT
* *
27964189 GGTTTAGGCACTGGTGGTGGCTGCGGTTTT
1 GGTTTAGGCACTGGTGCTGGCTGCGGATTT
27964219 GGTT
1 GGTT
27964223 CAGAAGGCGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.08, C:0.11, G:0.41, T:0.41
Consensus pattern (30 bp):
GGTTTAGGCACTGGTGCTGGCTGCGGATTT
Found at i:27964198 original size:132 final size:126
Alignment explanation
Indices: 27963987--27964318 Score: 423
Period size: 132 Copynumber: 2.5 Consensus size: 126
27963977 GCTCCTCAGA
* * *
27963987 TGGTGGTTGCGGTTTTGGTTCTGAGGGAGGGTTAGGTTTA-GCAACTGGTGGTGGTGATGGTTGT
1 TGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGC-AC------TGGTGATGGTTGT
*
27964051 GGATTTGGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGTCAC
59 GGATTTGGTTTAGGCACTGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGTCAC
27964116 TGG
124 TGG
* * * *
27964119 TGGTGGTTGAGGTATTGGTTTTGGTTCAGGAGGCGGGTTAGGTTTAGTCACTGGTGCTGGTTGTG
1 TGGTGGTT---G---CGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCACTGGTGATGGTTGTG
* *
27964184 GATTTGGTTTAGGCACTGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTTGTCACT
60 GATTTGGTTTAGGCACTGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGTCACT
27964249 GG
125 GG
* * *
27964251 TGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCATTGGTGGTGGTTGTGGTTTTG
1 TGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCACTGGTGATGGTTGTGGATTTG
27964316 GTT
66 GTT
27964319 CAGAGGGCGG
Statistics
Matches: 177, Mismatches: 16, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
126 53 0.30
129 1 0.01
132 93 0.53
135 1 0.01
138 28 0.16
139 1 0.01
ACGTcount: A:0.11, C:0.08, G:0.42, T:0.38
Consensus pattern (126 bp):
TGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCACTGGTGATGGTTGTGGATTTG
GTTTAGGCACTGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGTCACTGG
Found at i:27964259 original size:180 final size:178
Alignment explanation
Indices: 27964057--27964444 Score: 502
Period size: 180 Copynumber: 2.2 Consensus size: 178
27964047 TTGTGGATTT
*
27964057 GGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGTCACTGGTGG
1 GGTTTA-GCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGGCACTGGTGG
27964122 TGGTTGAGGTATTGGTTTTGGTTCAG-GAGGCGGGTTAGGTTTAGTCACTGGTGCTGG-T-T-G-
65 TGGTT---G---TGGTTTTGGTTCAGAG-GGCGGGTTAGGTTTAGTCACTGGTGCTGGTTGTGGC
*
27964182 T-GGATTTGGTTTAGGCA-CTGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCGGGTTA
123 TCGGATTTGGTTTAGGAATC-GGTGGTGGCTGCGGTTTTGGTTCAGAAGGCGGGTTA
* * *
27964237 GGTTTTGTCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCATTGGTGG
1 GGTTTAG-CACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGGCACTGGTGG
* *
27964302 TGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGTCACTGTTGGTGGTTGTGGCTGCGGAT
65 TGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGTCACTGGTGCTGGTTGTGGCT-CGGAT
* * * *
27964367 TTGGTTTAGGAATCGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTC
129 TTGGTTTAGGAATCGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCGGGTTA
* *
27964417 GGTTTAGCTACCGGTGGTGGTTGTGGTT
1 GGTTTAGC-ACTGGTGGTGGTTGCGGTT
27964445 GCGGTTTTGG
Statistics
Matches: 184, Mismatches: 14, Indels: 20
0.84 0.06 0.09
Matches are distributed among these distances:
174 41 0.22
175 2 0.01
176 1 0.01
177 2 0.01
178 1 0.01
179 2 0.01
180 134 0.73
181 1 0.01
ACGTcount: A:0.11, C:0.10, G:0.43, T:0.37
Consensus pattern (178 bp):
GGTTTAGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGGCACTGGTGGT
GGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGTCACTGGTGCTGGTTGTGGCTCGGATTT
GGTTTAGGAATCGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCGGGTTA
Found at i:27964336 original size:24 final size:24
Alignment explanation
Indices: 27964213--27964337 Score: 73
Period size: 24 Copynumber: 5.2 Consensus size: 24
27964203 TGGTGGCTGC
*
27964213 GGTTTTGGTTCAGAAGGCGGGTTA
1 GGTTTTGGTTCAGAGGGCGGGTTA
** *
27964237 GGTTTT-G-TCACTGGTG-GTGGTTGC
1 GGTTTTGGTTCAGAGG-GCG-GGTT-A
*
27964261 GGTTTTGGTTCAGAAGGCGGGTTA
1 GGTTTTGGTTCAGAGGGCGGGTTA
* ** *
27964285 GGTTTAGG--CATTGGTG-GTGGTTGT
1 GGTTTTGGTTCAGAGG-GCG-GGTT-A
27964309 GGTTTTGGTTCAGAGGGCGGGTTA
1 GGTTTTGGTTCAGAGGGCGGGTTA
27964333 GGTTT
1 GGTTT
27964338 AGTCACTGTT
Statistics
Matches: 72, Mismatches: 17, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
22 9 0.12
23 11 0.15
24 31 0.43
25 11 0.15
26 10 0.14
ACGTcount: A:0.11, C:0.08, G:0.43, T:0.38
Consensus pattern (24 bp):
GGTTTTGGTTCAGAGGGCGGGTTA
Found at i:27964354 original size:132 final size:126
Alignment explanation
Indices: 27963987--27964577 Score: 370
Period size: 132 Copynumber: 4.6 Consensus size: 126
27963977 GCTCCTCAGA
* * * *
27963987 TGGTGGTTGCGGTTTTGGTTCTGAGGGAGGGTTAGGTTTA-GCAACTGGTGGTGGTGATGGTTGT
1 TGGTGGTTGTGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGC-AC---TGGT-G-G-TGGTTGT
* * * * * * *
27964051 GGATTTGGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCAGGTTAGGTTTAGTCAC
59 GGTTTTGGTTCAGGCACGGGTGGTGGCTACGGTTGTGGTTCAGAAGGCGGGTTAGGTTTAGTCAC
27964116 TGG
124 TGG
* * *
27964119 TGGTGGTTGAGGTATTGGTTTTGGTTCAGGAGGCGGGTTAGGTTTAGTCACTGGTGCTGGTTGTG
1 TGGTGGTT---G---TGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCACTGGTGGTGGTTGTG
* * * * * *
27964184 GATTTGGTTTAGGCACTGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTTGTCACT
60 GTTTTGGTTCAGGCACGGGTGGTGGCTACGGTTGTGGTTCAGAAGGCGGGTTAGGTTTAGTCACT
27964249 GG
125 GG
* *
27964251 TGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCATTGGTGGTGGTTGTGGTTTTG
1 TGGTGGTTGTGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCACTGGTGGTGGTTGTGGTTTTG
** * * ** *** * * * *
27964316 GTTCAGAGGGCGGGTTAGGTTTAG-TCACTGTTGGTGGTTGTGGCTGCGGATTTGGTTTAG-GAA
66 GTTCAG-GCACGGG-T-GG--TGGCT-ACGGTT-GTGGTTCAGAAGGCGGGTTAGGTTTAGTCAC
27964379 TCGG
124 T-GG
* * *
27964383 TGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTCGGTTTA-GCTACCGGTGGTGGTTGTGGTTGC
1 TGGTGGTTGTGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGC-A-C--TGGT-G--GTGGTTGT
* ** * *
27964447 GGTTTTGGTTCAGGCACTGGTGGTGGCTGTGGTTTTGGTTCAG-AGG-GCG--A-G-TT--T-A-
59 GGTTTTGGTTCAGGCACGGGTGGTGGCTACGGTTGTGGTTCAGAAGGCGGGTTAGGTTTAGTCAC
27964502 --G
124 TGG
* * * * *
27964503 TGGTAGTTGTGGTTTTGGTTCAGAGGGCGGATTAGGTTTAGGCACTGGTGGTAGTTGCT-GATTT
1 TGGTGGTTGTGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCACTGGTGGTGGTTG-TGGTTTT
27964567 GGTTCAGGCAC
65 GGTTCAGGCAC
27964578 TGGTTGCGGT
Statistics
Matches: 373, Mismatches: 60, Indels: 70
0.74 0.12 0.14
Matches are distributed among these distances:
114 21 0.06
116 1 0.00
117 4 0.01
119 1 0.00
120 39 0.10
121 2 0.01
124 1 0.00
126 57 0.15
127 5 0.01
128 1 0.00
129 3 0.01
130 2 0.01
131 11 0.03
132 152 0.41
133 5 0.01
134 2 0.01
135 11 0.03
136 2 0.01
137 4 0.01
138 48 0.13
139 1 0.00
ACGTcount: A:0.12, C:0.09, G:0.42, T:0.37
Consensus pattern (126 bp):
TGGTGGTTGTGGTTTTGGTTCAGAAGGCGGGTTAGGTTTAGGCACTGGTGGTGGTTGTGGTTTTG
GTTCAGGCACGGGTGGTGGCTACGGTTGTGGTTCAGAAGGCGGGTTAGGTTTAGTCACTGG
Found at i:27964358 original size:48 final size:48
Alignment explanation
Indices: 27964189--27964355 Score: 262
Period size: 48 Copynumber: 3.5 Consensus size: 48
27964179 TTGTGGATTT
*
27964189 GGTTTAGGCACTGGTGGTGGCTGCGGTTTTGGTTCAGAAGGCGGGTTA
1 GGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTA
* *
27964237 GGTTTTGTCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTA
1 GGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTA
* * *
27964285 GGTTTAGGCATTGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTA
1 GGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTA
* *
27964333 GGTTTAGTCACTGTTGGTGGTTG
1 GGTTTAGGCACTGGTGGTGGTTG
27964356 TGGCTGCGGA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 108 1.00
ACGTcount: A:0.11, C:0.10, G:0.43, T:0.37
Consensus pattern (48 bp):
GGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAAGGCGGGTTA
Found at i:27964385 original size:84 final size:84
Alignment explanation
Indices: 27964285--27964495 Score: 309
Period size: 84 Copynumber: 2.5 Consensus size: 84
27964275 AGGCGGGTTA
* * *
27964285 GGTTTAGGCATTGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAG-TCACTGTTG
1 GGTTTAGGCATCGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGCT-ACCGGTG
27964349 GTGGTTGTGGCTGCGGATTT
65 GTGGTTGTGGCTGCGGATTT
* *
27964369 GGTTTAGGAATCGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTCGGTTTAGCTACCGGTGG
1 GGTTTAGGCATCGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGCTACCGGTGG
* *
27964434 TGGTTGTGGTTGCGGTTTT
66 TGGTTGTGGCTGCGGATTT
* *
27964453 GGTTCAGGCA-CTGGTGGTGGCTGTGGTTTTGGTTCAGAGGGCG
1 GGTTTAGGCATC-GGTGGTGGTTGTGGTTTTGGTTCAGAGGGCG
27964496 AGTTTAGTGG
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
83 1 0.01
84 113 0.98
85 1 0.01
ACGTcount: A:0.09, C:0.10, G:0.44, T:0.37
Consensus pattern (84 bp):
GGTTTAGGCATCGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGCTACCGGTGG
TGGTTGTGGCTGCGGATTT
Found at i:27964522 original size:84 final size:83
Alignment explanation
Indices: 27964285--27964573 Score: 259
Period size: 84 Copynumber: 3.4 Consensus size: 83
27964275 AGGCGGGTTA
* *
27964285 GGTTTAGGCATTGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAG-GTTTAGTCACT-GTT
1 GGTTTAGGCAATGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGTTTAGTG-TTAGT-ACTGGTT
27964348 GGTGGTTGTGGCTGCGGATTT
64 -GTGGTTGTGGCTGCGGATTT
* * *
27964369 GGTTTAGG-AATCGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTTCG-GTTTAGCTACCGGT
1 GGTTTAGGCAAT-GGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGTTTAGTG-TTAG-TACTGGT
* * *
27964432 GGTGGTTGTGGTTGCGGTTTT
63 TGTGGTTGTGGCTGCGGATTT
* * * * ** *
27964453 GGTTCAGGCACTGGTGGTGGCTGTGGTTTTGGTTCAGAGGGCGAGTTTAGTGGTAGTTGTGGTTT
1 GGTTTAGGCAATGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCG-GTTTAGTGTTAGTACTGGTTG
* *
27964518 TGGTTCAGAGG--GCGGATTA
65 TGGTT--GTGGCTGCGGATTT
* * *
27964537 GGTTTAGGCACTGGTGGTAGTTGCT-GATTTGGTTCAG
1 GGTTTAGGCAATGGTGGTGGTTG-TGGTTTTGGTTCAG
27964574 GCACTGGTTG
Statistics
Matches: 172, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
83 2 0.01
84 153 0.89
85 13 0.08
86 4 0.02
ACGTcount: A:0.11, C:0.09, G:0.43, T:0.37
Consensus pattern (83 bp):
GGTTTAGGCAATGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGTTTAGTGTTAGTACTGGTTGT
GGTTGTGGCTGCGGATTT
Found at i:27964636 original size:30 final size:30
Alignment explanation
Indices: 27964578--27964641 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
27964568 GTTCAGGCAC
* * * *
27964578 TGGTTGCGGTTTTGGTTTAGGAATTGGTGG
1 TGGTTGCGGTTTTGGTTCAAGAACTGGTGA
**
27964608 TGGTTGCGGTTTTGGTTCAATTACTGGTGA
1 TGGTTGCGGTTTTGGTTCAAGAACTGGTGA
27964638 TGGT
1 TGGT
27964642 GGTTGTGGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.11, C:0.06, G:0.39, T:0.44
Consensus pattern (30 bp):
TGGTTGCGGTTTTGGTTCAAGAACTGGTGA
Found at i:27969388 original size:3 final size:3
Alignment explanation
Indices: 27969380--27969455 Score: 136
Period size: 3 Copynumber: 25.3 Consensus size: 3
27969370 TCTCAGGCCT
27969380 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27969428 ATA ATA ATA ATA ACTA A-A ATA ATA ATA A
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA A
27969456 CTAAAATGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 66 0.93
4 3 0.04
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27973742 original size:20 final size:20
Alignment explanation
Indices: 27973717--27973766 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
27973707 TGGCTTAAAA
27973717 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
27973737 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
27973754 GTGGTAGTGGATT
1 TTGGTAGTGGATT
27973767 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:27978371 original size:20 final size:20
Alignment explanation
Indices: 27978346--27978395 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
27978336 TGGCTTAAAA
27978346 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
27978366 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
27978383 GTGGTAGTGGATT
1 TTGGTAGTGGATT
27978396 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:27985684 original size:37 final size:39
Alignment explanation
Indices: 27985634--27985734 Score: 125
Period size: 37 Copynumber: 2.6 Consensus size: 39
27985624 AACACACCAG
***
27985634 ATTGGCACCCAGTGTCTCATCGGTTAAAT-CGAAG-TAA
1 ATTGGCACCCAGTGTCTCATCGAACAAATCCGAAGATAA
*
27985671 ATTGGCACCCAGTGCCTCATCGAACAAATCCGAAGTAATAA
1 ATTGGCACCCAGTGTCTCATCGAACAAATCCGAAG--ATAA
*
27985712 ATTGACACCCAGTGTCTCATCGA
1 ATTGGCACCCAGTGTCTCATCGA
27985735 CTCGAAGTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
37 25 0.46
38 5 0.09
41 24 0.44
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (39 bp):
ATTGGCACCCAGTGTCTCATCGAACAAATCCGAAGATAA
Found at i:27987653 original size:3 final size:3
Alignment explanation
Indices: 27987645--27987682 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
27987635 GCTTTGTTAT
27987645 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
27987683 ATTTTCACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:27990454 original size:41 final size:39
Alignment explanation
Indices: 27990356--27990467 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 39
27990346 TTAGATAATT
* **
27990356 CGAAGTATTAAATTGACACCCAGTGTCTTATCGGTTAAAC
1 CGAAGTA-TAAATTGACACCCAGTGTCTCATCGAATAAAC
* *
27990396 CGAAG--TAAATTGGCACCCAGTGCCTCATCGAATAAATC
1 CGAAGTATAAATTGACACCCAGTGTCTCATCGAATAAA-C
*
27990434 CGAAGTAATAAATTAACACCCAGTGTCTCATCGA
1 CGAAGT-ATAAATTGACACCCAGTGTCTCATCGA
27990468 CTTGAAGTCG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 26 0.43
38 6 0.10
40 5 0.08
41 23 0.38
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (39 bp):
CGAAGTATAAATTGACACCCAGTGTCTCATCGAATAAAC
Found at i:27991390 original size:21 final size:21
Alignment explanation
Indices: 27991347--27991390 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
27991337 CTTCGTGTCC
*
27991347 TTCTTTCTTTCCCTTTTTATT
1 TTCTTTCTTTCCCTTTCTATT
* *
27991368 TTCTTTCTTTTCCTTTCTGTT
1 TTCTTTCTTTCCCTTTCTATT
27991389 TT
1 TT
27991391 GTTGTGCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (21 bp):
TTCTTTCTTTCCCTTTCTATT
Found at i:27997261 original size:33 final size:33
Alignment explanation
Indices: 27997222--27997323 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
27997212 AAATGCATGC
* *
27997222 AATCATATTAGTATATATACAAAATAC-GATTGT
1 AATCATATTAATAGATATACAAAATACAGA-TGT
* *
27997255 AATCATATTAATAGATACACATAATACAGATGT
1 AATCATATTAATAGATATACAAAATACAGATGT
* **
27997288 AATCATATTAACAGATATACAAAATATGGATGT
1 AATCATATTAATAGATATACAAAATACAGATGT
27997321 AAT
1 AAT
27997324 TATACATACT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 57 0.97
34 2 0.03
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (33 bp):
AATCATATTAATAGATATACAAAATACAGATGT
Found at i:27997381 original size:2 final size:2
Alignment explanation
Indices: 27997369--27997401 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
27997359 TATCAGACAG
27997369 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27997402 GTAATGCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28002835 original size:12 final size:12
Alignment explanation
Indices: 28002818--28002844 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28002808 CTTTGTAGGA
28002818 GGACCATTTGTT
1 GGACCATTTGTT
28002830 GGACCATTTGTT
1 GGACCATTTGTT
28002842 GGA
1 GGA
28002845 GGTCCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (12 bp):
GGACCATTTGTT
Found at i:28009046 original size:12 final size:13
Alignment explanation
Indices: 28009029--28009065 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
28009019 GAACCGGACA
28009029 CGAACCGAA-CTC
1 CGAACCGAAGCTC
28009041 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
28009053 CGAACCGTAGCTC
1 CGAACCGAAGCTC
28009066 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:28011630 original size:41 final size:42
Alignment explanation
Indices: 28011556--28011754 Score: 212
Period size: 42 Copynumber: 4.8 Consensus size: 42
28011546 CCTTTCGGGT
* * *
28011556 CTTTAGCGGCGTTTTATTAAGAAGCGCCGCTAATGCTGTAGG-
1 CTTTAGCGGCGTTTTCTGAA-AAGCGCCGCTAATGCTGTGGGC
* * * *
28011598 CTTTAGCGGCATTTT-TGAATAAGCGCCACTAATTCTATGGG-
1 CTTTAGCGGCGTTTTCTGAA-AAGCGCCGCTAATGCTGTGGGC
*
28011639 CTTTAGCGGCGTTTT-TGTAAAAGCGCCGCTAATGCT-TTGGC
1 CTTTAGCGGCGTTTTCTG-AAAAGCGCCGCTAATGCTGTGGGC
* *
28011680 CTTTAGCGGCGTTTTCTGGAAAAGCACCGCTAATGCTG-GGGT
1 CTTTAGCGGCGTTTTCT-GAAAAGCGCCGCTAATGCTGTGGGC
*
28011722 CTTTAGCGGCGTTTTCTGGAAAAGCGCCACTAA
1 CTTTAGCGGCGTTTTCT-GAAAAGCGCCGCTAA
28011755 GGACATTTTA
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.02
41 65 0.48
42 67 0.49
43 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTCTGAAAAGCGCCGCTAATGCTGTGGGC
Found at i:28011727 original size:83 final size:84
Alignment explanation
Indices: 28011552--28011754 Score: 247
Period size: 83 Copynumber: 2.4 Consensus size: 84
28011542 CCTACCTTTC
28011552 GGGTCTTTAGCGGCGTTTTAT-TAAGAAGCGCCGCTAATGCTGTAGGCTTTAGCGGCATTTTTGA
1 GGGTCTTTAGCGGCGTTTTATGTAA-AAGCGCCGCTAATGCTGTAGGCTTTAGCGGCATTTTTGA
* * *
28011616 ATAAGCGCCACTAATTCTAT
65 ATAAGCACCACTAATGCTAG
* *
28011636 GGG-CTTTAGCGGCGTTTT-TGTAAAAGCGCCGCTAATGCT-TTGGCCTTTAGCGGCGTTTTCTG
1 GGGTCTTTAGCGGCGTTTTATGTAAAAGCGCCGCTAATGCTGTAGG-CTTTAGCGGCATTTT-T-
*
28011698 GAA-AAGCACCGCTAATGCT-G
63 GAATAAGCACCACTAATGCTAG
* * *
28011718 GGGTCTTTAGCGGCGTTTTCTGGAAAAGCGCCACTAA
1 GGGTCTTTAGCGGCGTTTTATGTAAAAGCGCCGCTAA
28011755 GGACATTTTA
Statistics
Matches: 105, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
81 3 0.03
82 34 0.32
83 47 0.45
84 21 0.20
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (84 bp):
GGGTCTTTAGCGGCGTTTTATGTAAAAGCGCCGCTAATGCTGTAGGCTTTAGCGGCATTTTTGAA
TAAGCACCACTAATGCTAG
Found at i:28012570 original size:7 final size:7
Alignment explanation
Indices: 28012558--28012582 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28012548 TAATAAATTT
28012558 GTTTAGG
1 GTTTAGG
28012565 GTTTAGG
1 GTTTAGG
28012572 GTTTAGG
1 GTTTAGG
28012579 GTTT
1 GTTT
28012583 TAATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:28012691 original size:21 final size:22
Alignment explanation
Indices: 28012619--28012693 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
28012609 AAGTTACTGT
*
28012619 TTTAAGGTTTATGGAGTAT-GGA
1 TTTAAGGTTTAAGGAGT-TGGGA
* * * *
28012641 TTTAGGGATTAAGGACTAGGGA
1 TTTAAGGTTTAAGGAGTTGGGA
*
28012663 -TTATGGTTTAAGG-GTTGGGA
1 TTTAAGGTTTAAGGAGTTGGGA
28012683 TTTAAGGTTTA
1 TTTAAGGTTTA
28012694 GGGGTTAGGG
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
20 5 0.12
21 20 0.49
22 16 0.39
ACGTcount: A:0.27, C:0.01, G:0.33, T:0.39
Consensus pattern (22 bp):
TTTAAGGTTTAAGGAGTTGGGA
Found at i:28012698 original size:21 final size:20
Alignment explanation
Indices: 28012659--28012699 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28012649 TTAAGGACTA
*
28012659 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
28012679 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
28012700 AGGGGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:28012701 original size:7 final size:7
Alignment explanation
Indices: 28012691--28012728 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
28012681 GATTTAAGGT
28012691 TTAGGGG
1 TTAGGGG
28012698 TTAGGGG
1 TTAGGGG
28012705 TTAGGGG
1 TTAGGGG
**
28012712 TTAGACG
1 TTAGGGG
28012719 TTAGGGG
1 TTAGGGG
28012726 TTA
1 TTA
28012729 AGAATTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.47, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:28013810 original size:83 final size:83
Alignment explanation
Indices: 28013723--28013879 Score: 196
Period size: 83 Copynumber: 1.9 Consensus size: 83
28013713 GCATTGATGT
* * * *
28013723 ATTAATGTTT-TTCAAAACGTCACCGTTTCTCTTCAG-GACTTGAAATT-TTAGTGGCGTTTTT-
1 ATTAAAGTTTCTT-AAAACGACACCGTTTCTATTCAGTAACTT--AATTCTTAGTGGCGTTTTTG
28013784 CGGGAAAACGCCGGAACTACGG
63 C-GGAAAACGCCGGAACTACGG
* *
28013806 ATTAAAGTTTCTTAAAACGACACCGTTTCTATTCAGTAAGTTAATTCTTAGTGGCGTTTTTGCGT
1 ATTAAAGTTTCTTAAAACGACACCGTTTCTATTCAGTAACTTAATTCTTAGTGGCGTTTTTGCGG
28013871 AAAACGCCG
66 AAAACGCCG
28013880 CAAATATATA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
82 4 0.06
83 54 0.84
84 6 0.09
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (83 bp):
ATTAAAGTTTCTTAAAACGACACCGTTTCTATTCAGTAACTTAATTCTTAGTGGCGTTTTTGCGG
AAAACGCCGGAACTACGG
Found at i:28013902 original size:450 final size:451
Alignment explanation
Indices: 28013041--28013938 Score: 1532
Period size: 450 Copynumber: 2.0 Consensus size: 451
28013031 TTGGATATAT
28013041 AGGACCACATTATAAGAAATAAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
1 AGGACCACATTATAAGAAATAAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
*
28013106 CCATTTTTTTGAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
66 CCATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
*
28013171 AAAACGCCATAAATATGTATTATAATTTATCAAAACGGCCCCATTTCAGAAGAGGAATGTAATCT
131 AAAACGCCATAAATATGTATTATAATTTATCAAAACGGCACCATTTCAGAAGAGGAATGTAATCT
* * * *
28013236 ATTAGTGGCGTTTATGCTAGAAACGCCGCAAGGATGTATTAATGTTTTTCAAAATGTCAACGTTT
196 ATTAGTGCCGTTTAAGCTAAAAACGCCGCAAGGATGTATTAATGTTTTTCAAAACGTCAACGTTT
* *
28013301 CACTTCAGGACTTGACATTTTAGTGGCGTTTTTCCGGAAAACGCCGGAAATATGGATTAAAGTTT
261 CACTTCAGGACTTGAAATTTTAGTGGCGTTTTTCCGGAAAACGCCGGAAATACGGATTAAAGTTT
* * **
28013366 CTTAAAACGGCACCGTTTCCTTTCAGTAAGTTAATTTTTAGTGGCGTTTTTGCTAAAAACGCTTC
326 CTTAAAACGACACCGTTTCCTTTCAGTAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAACGCCGC
* *
28013431 AACTATATATTGACGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTACGC
391 AAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTACGC
*
28013492 AGGACCACATTATAAGGAA-AAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
1 AGGACCACATTATAAGAAATAAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
*
28013556 CTATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
66 CCATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
* * *
28013621 AAAACGCCATAAATATGTATTATAATTTCTCAAAACGGCACCGTTTCAGAAGAGGAGTGTAATCT
131 AAAACGCCATAAATATGTATTATAATTTATCAAAACGGCACCATTTCAGAAGAGGAATGTAATCT
** *
28013686 ATTAGTGCCGTTTAAGCTAAAAACGCCGCATTGATGTATTAATGTTTTTCAAAACGTCACCGTTT
196 ATTAGTGCCGTTTAAGCTAAAAACGCCGCAAGGATGTATTAATGTTTTTCAAAACGTCAACGTTT
* * *
28013751 CTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTCGGGAAAACGCCGGAACTACGGATTAAAGTTT
261 CACTTCAGGACTTGAAATTTTAGTGGCGTTTTTCCGGAAAACGCCGGAAATACGGATTAAAGTTT
28013816 CTTAAAACGACACCGTTT-CTATTCAGTAAGTTAATTCTTAGTGGCGTTTTTGCGT-AAAACGCC
326 CTTAAAACGACACCGTTTCCT-TTCAGTAAGTTAATTCTTAGTGGCGTTTTTGC-TAAAAACGCC
28013879 GCAAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTA
389 GCAAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTA
28013939 TGGAAGCAAT
Statistics
Matches: 420, Mismatches: 25, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
449 2 0.00
450 399 0.95
451 19 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (451 bp):
AGGACCACATTATAAGAAATAAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
CCATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
AAAACGCCATAAATATGTATTATAATTTATCAAAACGGCACCATTTCAGAAGAGGAATGTAATCT
ATTAGTGCCGTTTAAGCTAAAAACGCCGCAAGGATGTATTAATGTTTTTCAAAACGTCAACGTTT
CACTTCAGGACTTGAAATTTTAGTGGCGTTTTTCCGGAAAACGCCGGAAATACGGATTAAAGTTT
CTTAAAACGACACCGTTTCCTTTCAGTAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAACGCCGC
AAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTACGC
Found at i:28014935 original size:12 final size:12
Alignment explanation
Indices: 28014920--28014951 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28014910 ATTCTTGGGT
28014920 TTTGTTTTCTAG
1 TTTGTTTTCTAG
28014932 TTTGTTTTCTAG
1 TTTGTTTTCTAG
*
28014944 TCTGTTTT
1 TTTGTTTT
28014952 GCGAGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.09, G:0.16, T:0.69
Consensus pattern (12 bp):
TTTGTTTTCTAG
Found at i:28016210 original size:9 final size:9
Alignment explanation
Indices: 28016192--28016411 Score: 146
Period size: 9 Copynumber: 25.8 Consensus size: 9
28016182 CTTATATATA
*
28016192 AACTTGCAT
1 AACTTACAT
28016201 AACTTACAT
1 AACTTACAT
*
28016210 AA-TAACATAAT
1 AACTTAC---AT
28016221 AACTTACAT
1 AACTTACAT
28016230 AA--TACAT
1 AACTTACAT
* *
28016237 AGCCTACAT
1 AACTTACAT
28016246 AACTTACAT
1 AACTTACAT
*
28016255 AA--TACAC
1 AACTTACAT
28016262 AACTTACAT
1 AACTTACAT
*
28016271 AACTTAAAT
1 AACTTACAT
28016280 AACTTACAT
1 AACTTACAT
28016289 AA--TACAT
1 AACTTACAT
**
28016296 AACTTTGAT
1 AACTTACAT
*
28016305 AACTAACAT
1 AACTTACAT
* *
28016314 TA--TACAC
1 AACTTACAT
28016321 AACTTACAT
1 AACTTACAT
28016330 AA--TACAT
1 AACTTACAT
* *
28016337 TACTTACTT
1 AACTTACAT
*
28016346 AACATACAT
1 AACTTACAT
* *
28016355 AGCCTACAT
1 AACTTACAT
28016364 AACTTACAT
1 AACTTACAT
*
28016373 AA--TACAC
1 AACTTACAT
28016380 AACTTACAT
1 AACTTACAT
*
28016389 AGCTTACAT
1 AACTTACAT
28016398 AA--TACAT
1 AACTTACAT
28016405 AACTTAC
1 AACTTAC
28016412 CCGTGCAATT
Statistics
Matches: 160, Mismatches: 33, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
7 42 0.26
8 3 0.02
9 108 0.68
11 4 0.03
12 3 0.02
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:28016224 original size:20 final size:19
Alignment explanation
Indices: 28016199--28016297 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 19
28016189 ATAAACTTGC
28016199 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
28016219 ATAACTTACATAATACATAGCCTA
1 ATAACTTACATAATAC--A---TA
28016243 CATAACTTACATAATAC---
1 -ATAACTTACATAATACATA
* *
28016260 ACAACTTACAT-A-ACTTAA
1 ATAACTTACATAATACAT-A
28016278 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
28016297 A
1 A
28016298 CTTTGATAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
14 2 0.03
15 1 0.02
16 10 0.16
18 10 0.16
19 5 0.08
20 17 0.27
21 1 0.02
24 2 0.03
25 16 0.25
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.29
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:28016249 original size:25 final size:23
Alignment explanation
Indices: 28016198--28016405 Score: 137
Period size: 25 Copynumber: 8.9 Consensus size: 23
28016188 TATAAACTTG
*
28016198 CATAACTTACATAATA-ACA-TA
1 CATAACTTACATAATACATACTA
28016219 -ATAACTTACATAATACATAGCCTA
1 CATAACTTACATAATACATA--CTA
*
28016243 CATAACTTACATAATACACAACTTA
1 CATAACTTACATAATACA-TAC-TA
* *
28016268 CATAACTTAAATAACTTACATAATA
1 CATAACTTACATAA--TACATACTA
**
28016293 CATAACTTTGATAACTAACATTA-TA
1 CATAACTTACATAA-T-ACA-TACTA
*
28016318 CACAACTTACATAATACAT--TA
1 CATAACTTACATAATACATACTA
* *
28016339 C-TTACTTA-A-CATACATAGCCTA
1 CATAACTTACATAATACATA--CTA
*
28016361 CATAACTTACATAATACACAACTTA
1 CATAACTTACATAATACA-TAC-TA
*
28016386 CATAGCTTACATAATACATA
1 CATAACTTACATAATACATA
28016406 ACTTACCCGT
Statistics
Matches: 148, Mismatches: 19, Indels: 37
0.73 0.09 0.18
Matches are distributed among these distances:
18 6 0.04
19 1 0.01
20 20 0.14
21 5 0.03
22 4 0.03
23 9 0.06
24 8 0.05
25 86 0.58
26 5 0.03
27 4 0.03
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (23 bp):
CATAACTTACATAATACATACTA
Found at i:28016282 original size:34 final size:34
Alignment explanation
Indices: 28016244--28016411 Score: 133
Period size: 34 Copynumber: 4.7 Consensus size: 34
28016234 CATAGCCTAC
*
28016244 ATAACTTACATAATACACAACTTACATAACTTAA
1 ATAACTTACATAATACATAACTTACATAACTTAA
*
28016278 ATAACTTACATAATACATAACTTTGATAACTAACATTATA
1 ATAACTTACATAATACATAAC-TT-A-CA-TAAC-TTA-A
* * * * *
28016318 CACAACTTACATAATACATTACTTACTTAACATAC
1 -ATAACTTACATAATACATAACTTACATAACTTAA
* * * *
28016353 ATAGCCTACATAACTTACATAA--TACACAACTTAC
1 ATAACTTACATAA--TACATAACTTACATAACTTAA
*
28016387 ATAGCTTACATAATACATAACTTAC
1 ATAACTTACATAATACATAACTTAC
28016412 CCGTGCAATT
Statistics
Matches: 107, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
32 7 0.07
34 54 0.50
35 2 0.02
36 9 0.08
37 5 0.05
38 4 0.04
39 4 0.04
40 3 0.03
41 19 0.18
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (34 bp):
ATAACTTACATAATACATAACTTACATAACTTAA
Found at i:28016288 original size:59 final size:59
Alignment explanation
Indices: 28016218--28016406 Score: 233
Period size: 59 Copynumber: 3.2 Consensus size: 59
28016208 ATAATAACAT
28016218 AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
1 AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
* * ** * *
28016277 AATAACTTACATAATACATAACTTTGATAACTAACATTATACACAACTTACATAA--TA
1 AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
* * * *
28016334 CATTACTTACTTAACATACATAGCCTACATAACTTACATAATACACAACTTACATAGCTTA
1 AATAACTTACAT-A-ATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
*
28016395 CATAA--TACATAA
1 AATAACTTACATAA
28016407 CTTACCCGTG
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
57 12 0.11
58 2 0.02
59 88 0.81
61 6 0.06
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (59 bp):
AATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTACATAACTTA
Found at i:28021917 original size:66 final size:66
Alignment explanation
Indices: 28021834--28021982 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 66
28021824 GAGGTAACAT
28021834 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGC-TACAACTTAAAGCAGATGCAG
1 CGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGCAT-CAACTTAAAGCAGATGCAG
*
28021897 CTG
64 CAG
* * **
28021900 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCATCAGCTTAAAGCAGATGTGGCA
1 CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCATCAACTTAAAGCAGATGCAGCA
28021965 G
66 G
* *
28021966 CAAGAGAAGCAGAGGTT
1 CGAGAGAAGCTGAGGTT
28021983 GCAGCGAGGG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 69 0.93
67 5 0.07
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.16
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCATCAACTTAAAGCAGATGCAGCA
G
Found at i:28021975 original size:21 final size:21
Alignment explanation
Indices: 28021951--28021999 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28021941 CATCAGCTTA
*
28021951 AAGCAGATGTGGCAGCAAGAG
1 AAGCAGAGGTGGCAGCAAGAG
* * *
28021972 AAGCAGAGGTTGCAGCGAGGG
1 AAGCAGAGGTGGCAGCAAGAG
28021993 AAGCAGA
1 AAGCAGA
28022000 ACAGCGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.41, T:0.08
Consensus pattern (21 bp):
AAGCAGAGGTGGCAGCAAGAG
Found at i:28022423 original size:43 final size:42
Alignment explanation
Indices: 28022351--28022582 Score: 243
Period size: 43 Copynumber: 5.4 Consensus size: 42
28022341 TTTTCGACAA
* *
28022351 AAAGCGCTGCTAAAAGATAAGAG-CGTTTAGCGGCGTTTGTAGAG
1 AAAGCGCCGCT-AAAGATAAG-GTC-TTTAGCGGCGTTTGTGGAG
* *
28022395 AAAGCGCAGCTAAAGATAATGGTCTTTAGCGGCATTTGTGGAG
1 AAAGCGCCGCTAAAGATAA-GGTCTTTAGCGGCGTTTGTGGAG
*
28022438 AAAGTGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAG
1 AAAGCGCCGCTAAAGATAA-GGTCTTTAGCGGCGTTTGTGGAG
* * * *
28022481 AAAGCGCCGCAAAAGATCAGGTTCTTTAGTGGCGTTTGTGGTG
1 AAAGCGCCGCTAAAGATAAGG-TCTTTAGCGGCGTTTGTGGAG
* * * **
28022524 GAAGCGCCGCTATAGATTAGGGTCTTTTCCGGCGTTTGTGG-G
1 AAAGCGCCGCTAAAGA-TAAGGTCTTTAGCGGCGTTTGTGGAG
*
28022566 AAAAGCCCCGCTAAAGA
1 -AAAGCGCCGCTAAAGA
28022583 CCCTAATCTT
Statistics
Matches: 160, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.02
43 142 0.89
44 15 0.09
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGATAAGGTCTTTAGCGGCGTTTGTGGAG
Found at i:28022854 original size:22 final size:21
Alignment explanation
Indices: 28022821--28022865 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
28022811 ATTTGCGGCG
*
28022821 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
28022842 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
28022864 CT
1 CT
28022866 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:28023638 original size:33 final size:33
Alignment explanation
Indices: 28023601--28023667 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
28023591 TTATATACAT
28023601 CACATCCTAAAATTTAATTTCATCTTGAAACAA
1 CACATCCTAAAATTTAATTTCATCTTGAAACAA
*
28023634 CACATCCTAAAATTTAGTTTCATCTTGAAACAA
1 CACATCCTAAAATTTAATTTCATCTTGAAACAA
28023667 C
1 C
28023668 GCGACCACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (33 bp):
CACATCCTAAAATTTAATTTCATCTTGAAACAA
Found at i:28024731 original size:16 final size:16
Alignment explanation
Indices: 28024698--28024731 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28024688 GAGAGATGTT
* *
28024698 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
28024714 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
28024730 AA
1 AA
28024732 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:28027557 original size:21 final size:21
Alignment explanation
Indices: 28027531--28027571 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28027521 AGACGAGCAA
* *
28027531 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
28027552 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
28027572 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:28029510 original size:16 final size:16
Alignment explanation
Indices: 28029477--28029510 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28029467 GGAGATTGTT
* *
28029477 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
28029493 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
28029509 AA
1 AA
28029511 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:28032570 original size:31 final size:30
Alignment explanation
Indices: 28032535--28032608 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
28032525 AAAAATTATT
*
28032535 ATTTTAGTCACTCCTA-TTAGATA-AGTTGTCA
1 ATTTTAGTCACTCC-AGTTA-ATACA-TTATCA
*
28032566 ATTTTAGTTACTCCAGTTAATACATTATCA
1 ATTTTAGTCACTCCAGTTAATACATTATCA
*
28032596 ATTTTAATCACTC
1 ATTTTAGTCACTC
28032609 TACCGTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (30 bp):
ATTTTAGTCACTCCAGTTAATACATTATCA
Found at i:28044223 original size:13 final size:14
Alignment explanation
Indices: 28044200--28044228 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28044190 ACAAGCATCC
28044200 AAGTCCCTTTGAAT
1 AAGTCCCTTTGAAT
28044214 AAGT-CCTTTGAAT
1 AAGTCCCTTTGAAT
28044227 AA
1 AA
28044229 CCTTGAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (14 bp):
AAGTCCCTTTGAAT
Found at i:28045554 original size:25 final size:24
Alignment explanation
Indices: 28045519--28045576 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
28045509 TACAATAAAT
*
28045519 TTTTTTA-TTTTAGAATGTATTTTA
1 TTTTTTATTTTTA-AATGTATGTTA
*
28045543 TTTTTTATTTTTAATTGTATGTTA
1 TTTTTTATTTTTAAATGTATGTTA
28045567 TTTTATTATT
1 TTTT-TTATT
28045577 CTCGTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 20 0.67
25 10 0.33
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (24 bp):
TTTTTTATTTTTAAATGTATGTTA
Found at i:28049072 original size:24 final size:23
Alignment explanation
Indices: 28049041--28049085 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
28049031 ACTAAATTAA
28049041 TAAATTTTTTA-AATTTTAAATGT
1 TAAATTTTTTAGAA-TTTAAATGT
28049064 TAAATTTTTTTAGAATTTAAAT
1 TAAA-TTTTTTAGAATTTAAAT
28049086 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 14 0.70
25 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TAAATTTTTTAGAATTTAAATGT
Found at i:28049074 original size:17 final size:17
Alignment explanation
Indices: 28049054--28049086 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28049044 ATTTTTTAAA
28049054 TTTTA-AATGTTAAATTT
1 TTTTAGAAT-TTAAATTT
28049071 TTTTAGAATTTAAATT
1 TTTTAGAATTTAAATT
28049087 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTTAGAATTTAAATTT
Found at i:28051551 original size:43 final size:41
Alignment explanation
Indices: 28051490--28051646 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 41
28051480 TATGTATTTT
28051490 CGTGTAAGACCACT-TCTGGGACGTTGGCATCGACTTGTGTATA
1 CGTGTAAGACCA-TGTCTGGGACGTTGGCATCGA-TTGTG-ATA
* * * *
28051533 CGTGTAAGACCATGTCTGGGACATTGACATTGTATT-TGATT
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCG-ATTGTGATA
* *
28051574 TGTGTAAGACCTTGTCTGGGACAG-TGGCATCGATATGTGATTA
1 CGTGTAAGACCATGTCTGGGAC-GTTGGCATCGAT-TGTGA-TA
* *
28051617 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCATGTCTGGGACGTTGGCAT
28051647 TGTACGAGCC
Statistics
Matches: 93, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
40 2 0.02
41 29 0.31
42 7 0.08
43 54 0.58
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (41 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATCGATTGTGATA
Found at i:28051634 original size:84 final size:84
Alignment explanation
Indices: 28051491--28051650 Score: 211
Period size: 84 Copynumber: 1.9 Consensus size: 84
28051481 ATGTATTTTC
* *
28051491 GTGTAAGACCACTTCTGGGACGTTGGCATCGACTTGTGTATACGTGTAAGACCATGTCTGGGACA
1 GTGTAAGACCACTTCTGGGACGTTGGCATCGACTTGTGTATACATGTAAGACCACGTCTGGGACA
28051556 TTGACATTGTATTTGATTT
66 TTGACATTGTATTTGATTT
*
28051575 GTGTAAGACC-TTGTCTGGGACAG-TGGCATCGA-TATGTG-ATTACATGTAAGACCACGTCTGG
1 GTGTAAGACCACT-TCTGGGAC-GTTGGCATCGACT-TGTGTA-TACATGTAAGACCACGTCTGG
* *
28051636 GACGTTGGCATTGTA
62 GACATTGACATTGTA
28051651 CGAGCCTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
83 3 0.04
84 63 0.94
85 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (84 bp):
GTGTAAGACCACTTCTGGGACGTTGGCATCGACTTGTGTATACATGTAAGACCACGTCTGGGACA
TTGACATTGTATTTGATTT
Found at i:28051844 original size:16 final size:17
Alignment explanation
Indices: 28051815--28051846 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28051805 TGAATTGATG
28051815 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
28051832 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
28051847 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:28054900 original size:19 final size:19
Alignment explanation
Indices: 28054876--28054916 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28054866 GCCTCTATTA
*
28054876 ATGTAAATATGATTCTAGC
1 ATGTAAATATAATTCTAGC
*
28054895 ATGTAAATTTAATTCTAGC
1 ATGTAAATATAATTCTAGC
28054914 ATG
1 ATG
28054917 CACATTAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (19 bp):
ATGTAAATATAATTCTAGC
Found at i:28061025 original size:29 final size:28
Alignment explanation
Indices: 28060946--28061030 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
28060936 TCTAGAGTAA
*
28060946 AATTAAAAAAAAATACATTAAAATTAAA--T
1 AATT-AAAAAAAAT--ATAAAAATTAAATTT
* * **
28060975 AATTCAAACAAATATATGAATTAAATTT
1 AATTAAAAAAAATATAAAAATTAAATTT
28061003 AATTAAAATAAAATATAAAAATTAAATT
1 AATTAAAA-AAAATATAAAAATTAAATT
28061031 ACTTTCAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
26 9 0.20
28 15 0.34
29 20 0.45
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.32
Consensus pattern (28 bp):
AATTAAAAAAAATATAAAAATTAAATTT
Found at i:28078309 original size:30 final size:29
Alignment explanation
Indices: 28078275--28078399 Score: 139
Period size: 29 Copynumber: 4.2 Consensus size: 29
28078265 TTTATTTTTG
*
28078275 CATTTTGACCCTTAAACTTTTCTAAAATTA
1 CATTTTGACCCCTAAAC-TTTCTAAAATTA
28078305 CATTTT-ACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCT-AAAATTA
*
28078334 CATTTCT-ACCCCTAAAATTTTCT-AAATTA
1 CATTT-TGACCCCT-AAACTTTCTAAAATTA
* * *
28078363 CATTTGGGCCCTTAAACTTTCTATAAATTA
1 CATTTTGACCCCTAAACTTTCTA-AAATTA
28078393 CATTTTG
1 CATTTTG
28078400 GTCATTTCTT
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
28 13 0.16
29 36 0.44
30 25 0.30
31 8 0.10
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTCTAAAATTA
Found at i:28078338 original size:59 final size:59
Alignment explanation
Indices: 28078275--28078399 Score: 157
Period size: 59 Copynumber: 2.1 Consensus size: 59
28078265 TTTATTTTTG
* * *
28078275 CATTTTGACCCTTAAACTTTTCTAAAATTACATTT-TACCCCTAAACTTTCTCA-AAATTA
1 CATTTTGACCCCTAAAATTTTCT-AAATTACATTTGGACCCCTAAACTTTCT-ATAAATTA
* *
28078334 CATTTCT-ACCCCTAAAATTTTCTAAATTACATTTGGGCCCTTAAACTTTCTATAAATTA
1 CATTT-TGACCCCTAAAATTTTCTAAATTACATTTGGACCCCTAAACTTTCTATAAATTA
28078393 CATTTTG
1 CATTTTG
28078400 GTCATTTCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
58 13 0.23
59 43 0.75
60 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (59 bp):
CATTTTGACCCCTAAAATTTTCTAAATTACATTTGGACCCCTAAACTTTCTATAAATTA
Found at i:28078673 original size:12 final size:11
Alignment explanation
Indices: 28078646--28078680 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28078636 ATTAAATTTT
28078646 GAGCAAAAAAA
1 GAGCAAAAAAA
*
28078657 GAGCAAAAACA
1 GAGCAAAAAAA
28078668 GCAGCAAAAAAA
1 G-AGCAAAAAAA
28078680 G
1 G
28078681 GCATACCGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.66, C:0.14, G:0.20, T:0.00
Consensus pattern (11 bp):
GAGCAAAAAAA
Found at i:28078794 original size:34 final size:32
Alignment explanation
Indices: 28078750--28078812 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
28078740 CAACTAGCAA
28078750 AACAACCAAAAAGCAAAAAAAAAGAGAAAGAAAC
1 AACAACC-AAAAG-AAAAAAAAAGAGAAAGAAAC
* *
28078784 AACAAGCAAAAGAGAAAAAAAGAGAAAGA
1 AACAACCAAAAGAAAAAAAAAGAGAAAGA
28078813 GAAAAGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 16 0.59
33 5 0.19
34 6 0.22
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (32 bp):
AACAACCAAAAGAAAAAAAAAGAGAAAGAAAC
Found at i:28078811 original size:16 final size:16
Alignment explanation
Indices: 28078766--28078822 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
28078756 CAAAAAGCAA
28078766 AAAAAAAGAGAAAGA-
1 AAAAAAAGAGAAAGAG
*
28078781 AACAACAAGCA-AAAGAG
1 AA-AAAAAG-AGAAAGAG
28078798 AAAAAAAGAGAAAGAG
1 AAAAAAAGAGAAAGAG
*
28078814 AAAAGAAGA
1 AAAAAAAGA
28078823 AAGATGGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 3 0.09
16 29 0.83
17 3 0.09
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAGAAAGAG
Found at i:28078946 original size:13 final size:13
Alignment explanation
Indices: 28078928--28079004 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 13
28078918 TGATTGGGAA
28078928 AGAAAGAAAAAAG
1 AGAAAGAAAAAAG
28078941 AGAAAG--AAAAG
1 AGAAAGAAAAAAG
28078952 AG-AAGAAAAAAG
1 AGAAAGAAAAAAG
*
28078964 AAAGAAGAAGGAAGAAG
1 AGA-AAGAA--AA-AAG
* *
28078981 AAAAAGAAAGAAG
1 AGAAAGAAAAAAG
*
28078994 A-AAATAAAAAA
1 AGAAAGAAAAAA
28079005 TTTAATTCAG
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
10 3 0.06
11 7 0.13
12 14 0.26
13 10 0.19
14 6 0.11
16 7 0.13
17 6 0.11
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (13 bp):
AGAAAGAAAAAAG
Found at i:28078958 original size:23 final size:22
Alignment explanation
Indices: 28078926--28078992 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 22
28078916 GCTGATTGGG
28078926 AAAGA-AAGAAAAAAGAGAAAGA
1 AAAGAGAAGAAAAAA-AGAAAGA
28078948 AAAGAGAAG-AAAAAAGAAAGA
1 AAAGAGAAGAAAAAAAGAAAGA
28078969 AGAAG-GAAGAAGAAAAAGAAAGA
1 A-AAGAGAAGAA-AAAAAGAAAGA
28078992 A
1 A
28078993 GAAAATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.29
22 14 0.34
23 15 0.37
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (22 bp):
AAAGAGAAGAAAAAAAGAAAGA
Found at i:28078963 original size:17 final size:17
Alignment explanation
Indices: 28078943--28079002 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
28078933 GAAAAAAGAG
28078943 AAAGAAAAGAGAAGAAA
1 AAAGAAAAGAGAAGAAA
*
28078960 AAAG-AAAGAAGAAGGAA
1 AAAGAAAAG-AGAAGAAA
*
28078977 GAAGAAAA-AGAAAGAAGA
1 AAAGAAAAGAG-AAGAA-A
*
28078995 AAATAAAA
1 AAAGAAAA
28079003 AATTTAATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.18
17 18 0.53
18 10 0.29
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (17 bp):
AAAGAAAAGAGAAGAAA
Found at i:28078971 original size:7 final size:7
Alignment explanation
Indices: 28078927--28078996 Score: 65
Period size: 7 Copynumber: 9.9 Consensus size: 7
28078917 CTGATTGGGA
28078927 AAGAAAG
1 AAGAAAG
*
28078934 AAAAAAG
1 AAGAAAG
28078941 -AGAAAG
1 AAGAAAG
28078947 AA-AAGAG
1 AAGAA-AG
*
28078954 AAGAAAA
1 AAGAAAG
28078961 AAGAAAG
1 AAGAAAG
28078968 AAGAAGGAAG
1 AAG-A--AAG
28078978 AAGAAA-
1 AAGAAAG
28078984 AAGAAAG
1 AAGAAAG
28078991 AAGAAA
1 AAGAAA
28078997 ATAAAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 13 0.25
7 29 0.56
8 3 0.06
9 1 0.02
10 6 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:28079301 original size:14 final size:14
Alignment explanation
Indices: 28079279--28079346 Score: 63
Period size: 13 Copynumber: 5.0 Consensus size: 14
28079269 GAAGCAGGCC
28079279 AGAAAAAAAAAGAG
1 AGAAAAAAAAAGAG
* *
28079293 AG-AAGAAAAACAG
1 AGAAAAAAAAAGAG
28079306 AG-AAAAAAAAGA-
1 AGAAAAAAAAAGAG
*
28079318 AAAAAGAAAAAAGAG
1 AGAAA-AAAAAAGAG
28079333 A-ACAAAAAAAAGAG
1 AGA-AAAAAAAAGAG
28079347 GTTCAATTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
12 1 0.02
13 21 0.47
14 20 0.44
15 3 0.07
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAGAG
Found at i:28079306 original size:25 final size:26
Alignment explanation
Indices: 28079278--28079346 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
28079268 AGAAGCAGGC
28079278 CAGA-AAAAAAAAGAGAGAAGAAAAA
1 CAGAGAAAAAAAAGAGAGAAGAAAAA
* *
28079303 CAGAGAAAAAAAAGAAAAAAGAAAAA
1 CAGAGAAAAAAAAGAGAGAAGAAAAA
*
28079329 -AGAGAACAAAAAAAAGAG
1 CAGAGAA-AAAAAAGAGAG
28079347 GTTCAATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.27
26 27 0.73
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (26 bp):
CAGAGAAAAAAAAGAGAGAAGAAAAA
Found at i:28079327 original size:16 final size:16
Alignment explanation
Indices: 28079306--28079343 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28079296 AGAAAAACAG
28079306 AGAAAAAAAAGAAAAA
1 AGAAAAAAAAGAAAAA
* *
28079322 AGAAAAAAGAGAACAA
1 AGAAAAAAAAGAAAAA
28079338 A-AAAAA
1 AGAAAAA
28079344 GAGGTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAGAAAAA
Found at i:28079534 original size:16 final size:16
Alignment explanation
Indices: 28079498--28079537 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28079488 TTTGTATCTA
28079498 TATTTTAATTTAATTC
1 TATTTTAATTTAATTC
* * *
28079514 AATTTTAATTTTATTT
1 TATTTTAATTTAATTC
28079530 TATTTTAA
1 TATTTTAA
28079538 ATAATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTAATTTAATTC
Found at i:28079706 original size:15 final size:16
Alignment explanation
Indices: 28079673--28079704 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28079663 AAATATTCTA
28079673 AAATTCTCGTGTTTTTT
1 AAATTCTCGTG-TTTTT
28079690 AAATTCTCGTGTTTT
1 AAATTCTCGTGTTTT
28079705 AATAGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (16 bp):
AAATTCTCGTGTTTTT
Found at i:28079893 original size:39 final size:40
Alignment explanation
Indices: 28079831--28079929 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 40
28079821 TCGTGTTTCA
* * *
28079831 AAAAATTTTCGTGTTTTC--AAAAAAATTTCTCGTAT-TTC
1 AAAAATTCTCATGTTTTCAAAAAAAAAATT-TCGTATCTTC
* *
28079869 AAAAATTC-CTTGTTTTCAAAAAAAAAATTTCGTGTCTTC
1 AAAAATTCTCATGTTTTCAAAAAAAAAATTTCGTATCTTC
28079908 AAAAATTCTCATG-TTTCAAAAA
1 AAAAATTCTCATGTTTTCAAAAA
28079930 TCTTCGTGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
37 8 0.15
38 12 0.23
39 29 0.56
40 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (40 bp):
AAAAATTCTCATGTTTTCAAAAAAAAAATTTCGTATCTTC
Found at i:28079895 original size:22 final size:22
Alignment explanation
Indices: 28079869--28079912 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28079859 CTCGTATTTC
* *
28079869 AAAAATTCCTTGTTTTCAAAAA
1 AAAAATTCCGTGTCTTCAAAAA
*
28079891 AAAAATTTCGTGTCTTCAAAAA
1 AAAAATTCCGTGTCTTCAAAAA
28079913 TTCTCATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAAATTCCGTGTCTTCAAAAA
Found at i:28079913 original size:17 final size:16
Alignment explanation
Indices: 28079891--28079966 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 16
28079881 TTTTCAAAAA
28079891 AAAAATTTCGTGTCTTC
1 AAAAATTTCGTGT-TTC
*
28079908 AAAAATTCTCATGTTTC
1 AAAAATT-TCGTGTTTC
28079925 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTG-TTTC
*
28079943 -AAAATTCCAGTGTTTC
1 AAAAATTTC-GTGTTTC
28079959 AAAAATTT
1 AAAAATTT
28079967 TTGTGTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
16 6 0.12
17 34 0.68
18 10 0.20
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:28079928 original size:16 final size:16
Alignment explanation
Indices: 28079909--28079962 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
28079899 CGTGTCTTCA
28079909 AAAATTCTCATGTTTC
1 AAAATTCTCATGTTTC
* *
28079925 AAAAATCTTCGTGTTTTC
1 AAAATTC-TCATG-TTTC
28079943 AAAATTC-CAGTGTTTC
1 AAAATTCTCA-TGTTTC
28079959 AAAA
1 AAAA
28079963 ATTTTTGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 15 0.48
17 6 0.19
18 10 0.32
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (16 bp):
AAAATTCTCATGTTTC
Found at i:28079947 original size:34 final size:34
Alignment explanation
Indices: 28079891--28080154 Score: 126
Period size: 34 Copynumber: 7.7 Consensus size: 34
28079881 TTTTCAAAAA
*
28079891 AAAAATTTCGTGTCTTCAAAAATTCTCA-TGTTTC
1 AAAAATTTCGTGTTTTCAAAAATTC-CAGTGTTTC
28079925 AAAAATCTTCGTGTTTTC-AAAATTCCAGTGTTTC
1 AAAAAT-TTCGTGTTTTCAAAAATTCCAGTGTTTC
* * **
28079959 AAAAATTTTTGTGTTTTTTTAAAAA----AAAG----
1 AAAAA-TTTCGTG--TTTTCAAAAATTCCAGTGTTTC
** * *
28079988 AAACTTTTTCGTGTTTTCAAAAATT-AAGGTGTTTT
1 AAA-AATTTCGTGTTTTCAAAAATTCCA-GTGTTTC
* * *
28080023 AAAAACTTTCGTGTTTTCAGAAACTTCGA-TG-ATC
1 AAAAA-TTTCGTGTTTTCA-AAAATTCCAGTGTTTC
*
28080057 AAAAAAATATTTCGTGTTTTTCAAAAAATTTC-GTGTTTC
1 ---AAAA-ATTTCGTG-TTTTC-AAAAATTCCAGTGTTTC
* * *
28080096 AAAAATTTTCATGTTTTCAAAAATTCC-CTGTTTT
1 AAAAA-TTTCGTGTTTTCAAAAATTCCAGTGTTTC
28080130 AAAAATTTCCGTGTTTTCAAAAATT
1 AAAAATTT-CGTGTTTTCAAAAATT
28080155 TTCGTGTTTT
Statistics
Matches: 176, Mismatches: 26, Indels: 56
0.68 0.10 0.22
Matches are distributed among these distances:
27 9 0.05
29 9 0.05
30 1 0.01
31 1 0.01
33 7 0.04
34 63 0.36
35 35 0.20
36 19 0.11
37 16 0.09
38 13 0.07
39 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (34 bp):
AAAAATTTCGTGTTTTCAAAAATTCCAGTGTTTC
Found at i:28079972 original size:17 final size:17
Alignment explanation
Indices: 28079821--28080223 Score: 136
Period size: 18 Copynumber: 21.8 Consensus size: 17
28079811 CTTAAAAAAA
28079821 TCGTGTTTCAAAAAATTT
1 TCGTGTTTC-AAAAATTT
28079839 TCGTGTTTTCAAAAAAATTT
1 TCGTG-TTTC--AAAAATTT
*
28079859 CTCGTATTTCAAAAATTCCT
1 -TCGTGTTTCAAAAATT--T
*
28079879 T-GT-TTTCAAAAAAAAAATT
1 TCGTGTTTC----AAAAATTT
*
28079898 TCGTGTCTTCAAAAATTC
1 TCGTGT-TTCAAAAATTT
* *
28079916 TCATGTTTCAAAAATCT
1 TCGTGTTTCAAAAATTT
28079933 TCGTGTTTTC-AAAA-TT
1 TCGTG-TTTCAAAAATTT
*
28079949 CCAGTGTTTCAAAAATTT
1 TC-GTGTTTCAAAAATTT
* *
28079967 TTGTGTTTTTTTAAAAAAAAGAAACTTTT
1 TCGTG----TTT-----CAA-AAA--TTT
*
28079996 TCGTGTTTTCAAAAATTA
1 TCGTG-TTTCAAAAATTT
** * *
28080014 AGGTGTTTTAAAAACTT
1 TCGTGTTTCAAAAATTT
* *
28080031 TCGTGTTTTCAGAAA-CT
1 TCGTG-TTTCAAAAATTT
*
28080048 TCGATG-ATCAAAAAAATATT
1 TCG-TGTTTC--AAAAAT-TT
*
28080068 TCGTGTTTTTCAAAAAATT
1 TCGTG--TTTCAAAAATTT
28080087 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
28080104 TCATGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
* * *
28080121 CCCTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
*
28080138 CCGTGTTTTCAAAAATTT
1 TCGTG-TTTCAAAAATTT
* **
28080156 TCGTGTTTTTATGAATTT
1 TCGTG-TTTCAAAAATTT
* * *
28080174 TCGTGTCTCTAAAATTC
1 TCGTGTTTCAAAAATTT
* *
28080191 TCGTGTTTTAAAATTTTT
1 TCGTGTTTCAAAA-ATTT
28080209 TCGTGTTTTCAAAAA
1 TCGTG-TTTCAAAAA
28080224 AATAATTATT
Statistics
Matches: 288, Mismatches: 55, Indels: 84
0.67 0.13 0.20
Matches are distributed among these distances:
16 16 0.06
17 89 0.31
18 95 0.33
19 23 0.08
20 28 0.10
21 16 0.06
22 5 0.02
26 6 0.02
27 3 0.01
29 7 0.02
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:28091211 original size:14 final size:13
Alignment explanation
Indices: 28091179--28091218 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
28091169 TATTATGCCT
* *
28091179 AAAAAAACAACAA
1 AAAAAAAGAAAAA
28091192 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
28091205 AAGAAAAAGAAAAA
1 AA-AAAAAGAAAAA
28091219 TCAAGATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:28092434 original size:80 final size:79
Alignment explanation
Indices: 28092092--28092838 Score: 950
Period size: 77 Copynumber: 9.6 Consensus size: 79
28092082 CAATTACTGC
*
28092092 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTAAGGTA--T
1 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
28092155 TTTT-AATTTCTATT
66 TTTTAAATTTCTA-T
* *
28092169 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCTTCAGGTCACGCTGAGGTA--T
1 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
28092232 TTTT-AATTTCTGT
66 TTTTAAATTTCTAT
* *
28092245 CTTTTTTT--AAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCACGCTGAGGCA--
1 -TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
28092306 TTTTT-AATTTCTGT
65 TTTTTAAATTTCTAT
*
28092320 CTTTTTTT---AAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 -TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
28092382 TCTTTTAAATTTCTAT
65 T-TTTTAAATTTCTAT
* *
28092398 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGGTCACGCTAAGGTATTT
1 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
28092463 CTTTTAAATTTCTGT
66 -TTTTAAATTTCTAT
* * *
28092478 TTTTTTTCAAAAACCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGGTCACGCCGAGGTATTT
1 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
28092543 CTTTTAAATTTC---
66 -TTTTAAATTTCTAT
* *
28092555 TGTTTTTCAAAAATCAACTCATAATACGAGAGGTAAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
* *
28092620 TTTT-TATTTCT-G
66 TTTTAAATTTCTAT
* *
28092632 TTGTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGTTGAGGTA--T
1 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
28092695 TTTTAAATTTCTA-
66 TTTTAAATTTCTAT
* * * ** * *
28092708 TTTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGACCATGCCGAGGTAT
1 TTTTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
28092773 TTCTTTTAAA-TT-TA-
64 TT-TTTTAAATTTCTAT
* * * *
28092787 TGTTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTC
1 TTTTTTTC-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
28092839 GCATGCCGAG
Statistics
Matches: 612, Mismatches: 41, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
74 49 0.08
75 82 0.13
76 19 0.03
77 207 0.34
78 96 0.16
79 9 0.01
80 143 0.23
81 7 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (79 bp):
TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
TTTTAAATTTCTAT
Found at i:28093103 original size:29 final size:30
Alignment explanation
Indices: 28093070--28093146 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
28093060 GACCCTATAC
*
28093070 TTTTCTAAAATTGCATTT-TAACCCCTAAAA
1 TTTTCTAAAATTACATTTCT-ACCCCTAAAA
28093100 -TTTCTCAAAATTACATTTCTACCCCTAAAA
1 TTTTCT-AAAATTACATTTCTACCCCTAAAA
28093130 TTTTCT-AAATTACATTT
1 TTTTCTAAAATTACATTT
28093147 GGGCCCTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 16 0.37
30 21 0.49
31 6 0.14
ACGTcount: A:0.35, C:0.21, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTTCTAAAATTACATTTCTACCCCTAAAA
Found at i:28093117 original size:59 final size:59
Alignment explanation
Indices: 28093054--28093178 Score: 130
Period size: 59 Copynumber: 2.1 Consensus size: 59
28093044 TTTATTTTTG
* * * *
28093054 CATTTTGA-CCCTATACTTTTCTAAAATTGCATTTTAACCCCTAAAATTTCTCA-AAATTA
1 CATTTTGACCCCTAAAATTTTCT-AAATTACATTTGAACCCCTAAAATTTCT-ATAAATTA
** * *
28093113 CATTTCT-ACCCCTAAAATTTTCTAAATTACATTTGGGCCCTTAAACTTTCTATAAATTA
1 CATTT-TGACCCCTAAAATTTTCTAAATTACATTTGAACCCCTAAAATTTCTATAAATTA
28093172 CATTTTG
1 CATTTTG
28093179 GCCATTTCCT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
58 2 0.04
59 39 0.72
60 13 0.24
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (59 bp):
CATTTTGACCCCTAAAATTTTCTAAATTACATTTGAACCCCTAAAATTTCTATAAATTA
Found at i:28093157 original size:29 final size:30
Alignment explanation
Indices: 28093091--28093181 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
28093081 TGCATTTTAA
* **
28093091 CCCCTAAAATTTCTCAAAATTACATTTCTA
1 CCCCTAAAATTTCTCTAAATTACATTTCGG
*
28093121 CCCCTAAAATTT-TCTAAATTACATTTGGG
1 CCCCTAAAATTTCTCTAAATTACATTTCGG
* * * *
28093150 CCCTTAAACTTTCTATAAATTACATTTTGG
1 CCCCTAAAATTTCTCTAAATTACATTTCGG
28093180 CC
1 CC
28093182 ATTTCCTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 23 0.44
30 29 0.56
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (30 bp):
CCCCTAAAATTTCTCTAAATTACATTTCGG
Found at i:28093452 original size:12 final size:11
Alignment explanation
Indices: 28093425--28093459 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28093415 AATAAATTTT
28093425 GAGCAAAAAAA
1 GAGCAAAAAAA
*
28093436 GAGCAAAAACA
1 GAGCAAAAAAA
28093447 GTAGCAAAAAAA
1 G-AGCAAAAAAA
28093459 G
1 G
28093460 GCATACCGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.66, C:0.11, G:0.20, T:0.03
Consensus pattern (11 bp):
GAGCAAAAAAA
Found at i:28093575 original size:36 final size:34
Alignment explanation
Indices: 28093529--28093595 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
28093519 CAACTAGCAA
28093529 AACAACCAAAAAGCAAAAAAAAAAAGAGAAAGAAAC
1 AACAACC-AAAAG-AAAAAAAAAAAGAGAAAGAAAC
* *
28093565 AACAAGCAAAAGAGAAAAAAAAAGAGAAAGA
1 AACAACCAAAAGAAAAAAAAAAAGAGAAAGA
28093596 GAAAAGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 18 0.62
35 5 0.17
36 6 0.21
ACGTcount: A:0.75, C:0.10, G:0.15, T:0.00
Consensus pattern (34 bp):
AACAACCAAAAGAAAAAAAAAAAGAGAAAGAAAC
Found at i:28093594 original size:18 final size:18
Alignment explanation
Indices: 28093545--28093600 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
28093535 CAAAAAGCAA
28093545 AAAAAAAAAGAG-AA-AG
1 AAAAAAAAAGAGAAAGAG
* *
28093561 AAACAACAAGCA-AAAGAG
1 AAAAAAAAAG-AGAAAGAG
28093579 AAAAAAAAAGAGAAAGAG
1 AAAAAAAAAGAGAAAGAG
28093597 AAAA
1 AAAA
28093601 GAAGAAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 8 0.25
17 4 0.12
18 20 0.62
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAGAAAGAG
Found at i:28093606 original size:14 final size:13
Alignment explanation
Indices: 28093572--28093609 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
28093562 AACAACAAGC
28093572 AAAAGAGAAA-AA
1 AAAAGAGAAAGAA
*
28093584 AAAAGAGAAAGAG
1 AAAAGAGAAAGAA
28093597 AAAAGAAGAAAGA
1 AAAAG-AGAAAGA
28093610 TGGGGGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAGAA
Found at i:28093719 original size:4 final size:4
Alignment explanation
Indices: 28093710--28093786 Score: 68
Period size: 4 Copynumber: 18.8 Consensus size: 4
28093700 GCTGATCGGA
* *
28093710 AAAG AAAG AAAA AAGAG AAAG AAAAG AGAAG AAAG AAAG AAAG AAAG AATG
1 AAAG AAAG AAAG AA-AG AAAG -AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
* *
28093761 -AAG AATG -AAG AAGAA AAAG AAAG AAA
1 AAAG AAAG AAAG AA-AG AAAG AAAG AAA
28093787 AAAAATAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
3 4 0.07
4 41 0.69
5 14 0.24
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:28093755 original size:35 final size:34
Alignment explanation
Indices: 28093710--28093791 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
28093700 GCTGATCGGA
28093710 AAAGAAAGAAAAAAG-AGAAAGAAAAGAGAAGAAAG
1 AAAGAAAGAAAAAAGAAGAAAGAAAA-AGAA-AAAG
* * *
28093745 AAAGAAAGAAAGAATGAAGAATGAAGAAGAAAAAG
1 AAAGAAAGAAA-AAAGAAGAAAGAAAAAGAAAAAG
28093780 AAAGAAA-AAAAA
1 AAAGAAAGAAAAA
28093792 TAAAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 2 0.05
34 3 0.07
35 22 0.52
36 7 0.17
37 8 0.19
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (34 bp):
AAAGAAAGAAAAAAGAAGAAAGAAAAAGAAAAAG
Found at i:28093981 original size:26 final size:25
Alignment explanation
Indices: 28093928--28093981 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
28093918 AAAAAAAGAA
* **
28093928 CAGGCCATTTCCAGCAGCCCAAGTG
1 CAGGCCAATTCCAGCAGCCCAACAG
*
28093953 CAGGCCCAATTCCAGCAGCCCACCAG
1 CAGG-CCAATTCCAGCAGCCCAACAG
28093979 CAG
1 CAG
28093982 TCTCCCAGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.26, C:0.41, G:0.22, T:0.11
Consensus pattern (25 bp):
CAGGCCAATTCCAGCAGCCCAACAG
Found at i:28094085 original size:13 final size:12
Alignment explanation
Indices: 28094058--28094113 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
28094048 AAGCAGGCCA
*
28094058 AAAAAAAAGAGAG
1 AAAAAAAA-ATAG
28094071 AAGAAAAAAATAG
1 AA-AAAAAAATAG
*
28094084 AAAAAAAAAGA-
1 AAAAAAAAATAG
*
28094095 AAAAAGAAAAAAG
1 AAAAA-AAAATAG
28094108 AAAAAA
1 AAAAAA
28094114 GAGAACAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 5 0.14
12 14 0.38
13 12 0.32
14 6 0.16
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAAAAATAG
Found at i:28094090 original size:11 final size:10
Alignment explanation
Indices: 28094071--28094115 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
28094061 AAAAAGAGAG
28094071 AAGAAAAAAA
1 AAGAAAAAAA
*
28094081 TAGAAAAAAA
1 AAGAAAAAAA
28094091 AAGAAAAAAGA
1 AAGAAAAAA-A
28094102 AA-AAAGAAAA
1 AAGAAA-AAAA
28094112 AAGA
1 AAGA
28094116 GAACAGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:28094113 original size:7 final size:7
Alignment explanation
Indices: 28094060--28094129 Score: 63
Period size: 7 Copynumber: 10.1 Consensus size: 7
28094050 GCAGGCCAAA
28094060 AAAAAAG
1 AAAAAAG
* *
28094067 AGAGAAG
1 AAAAAAG
28094074 AAAAAA-
1 AAAAAAG
*
28094080 ATAGAAA-
1 A-AAAAAG
28094087 AAAAAAG
1 AAAAAAG
28094094 AAAAAAG
1 AAAAAAG
28094101 AAAAAAG
1 AAAAAAG
28094108 AAAAAAG
1 AAAAAAG
* *
28094115 AGAACAG
1 AAAAAAG
*
28094122 AAGAAAG
1 AAAAAAG
28094129 A
1 A
28094130 GGTTCAATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
6 5 0.10
7 45 0.90
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:28094306 original size:21 final size:20
Alignment explanation
Indices: 28094282--28094324 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
28094272 TGTGTATCTA
*
28094282 TATTTTAATTTAATTCAATTT
1 TATTTTAATTTAAAT-AATTT
*
28094303 TATTTTATTTTAAATAATTT
1 TATTTTAATTTAAATAATTT
28094323 TA
1 TA
28094325 ATAAATAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTAATTTAAATAATTT
Found at i:28094626 original size:21 final size:21
Alignment explanation
Indices: 28094600--28094681 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
28094590 ATCCTGTTTC
28094600 AAAAATTTTTCGTGTTTTCAA
1 AAAAATTTTTCGTGTTTTCAA
*
28094621 AAAAATTTCTCGTG-TTTC--
1 AAAAATTTTTCGTGTTTTCAA
*
28094639 AAAAATTCTT--TGTTTTCAA
1 AAAAATTTTTCGTGTTTTCAA
** *
28094658 AAAAAAATTTCGTGTCTTCAA
1 AAAAATTTTTCGTGTTTTCAA
28094679 AAA
1 AAA
28094682 TTCTCATGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.04
17 4 0.08
18 8 0.16
19 7 0.14
20 4 0.08
21 24 0.49
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (21 bp):
AAAAATTTTTCGTGTTTTCAA
Found at i:28094638 original size:20 final size:21
Alignment explanation
Indices: 28094600--28094715 Score: 78
Period size: 17 Copynumber: 6.1 Consensus size: 21
28094590 ATCCTGTTTC
*
28094600 AAAAATTTTTCGTGTTTTCAA
1 AAAAATTTCTCGTGTTTTCAA
28094621 AAAAATTTCTCGTG-TTTC--
1 AAAAATTTCTCGTGTTTTCAA
*
28094639 AAAAA-TTCT-TTGTTTTCAAA
1 AAAAATTTCTCGTGTTTTC-AA
* *
28094659 AAAAAATT-TCGTGTCTTC--
1 AAAAATTTCTCGTGTTTTCAA
*
28094677 AAAAA-TTCTCATG-TTTC--
1 AAAAATTTCTCGTGTTTTCAA
*
28094694 AAAAATCT-TCGTGTTTTCAA
1 AAAAATTTCTCGTGTTTTCAA
28094714 AA
1 AA
28094716 TTCCAGTGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
16 2 0.03
17 22 0.29
18 19 0.25
20 12 0.16
21 21 0.28
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (21 bp):
AAAAATTTCTCGTGTTTTCAA
Found at i:28094647 original size:17 final size:18
Alignment explanation
Indices: 28094596--28094982 Score: 229
Period size: 18 Copynumber: 21.5 Consensus size: 18
28094586 AAAAATCCTG
*
28094596 TTTCAAAAATTTTTCGTGT
1 TTTCAAAAA-TTCTCGTGT
28094615 TTTCAAAAAAATTTCTCGTG-
1 TTTC--AAAAA-TTCTCGTGT
*
28094635 TTTCAAAAATTCT-TTGT
1 TTTCAAAAATTCTCGTGT
28094652 TTTCAAAAAAAAATT-TCGTGT
1 TTTC----AAAAATTCTCGTGT
* *
28094673 CTTCAAAAATTCTCATG-
1 TTTCAAAAATTCTCGTGT
28094690 TTTCAAAAA-TCTTCGTGT
1 TTTCAAAAATTC-TCGTGT
28094708 TTTC-AAAATTC-CAGTG-
1 TTTCAAAAATTCTC-GTGT
* *
28094724 TTTCGAAAATTTTCGTGT
1 TTTCAAAAATTCTCGTGT
*
28094742 TTTCAAAAATCCTCGTGT
1 TTTCAAAAATTCTCGTGT
28094760 TTTCAAAAATT-TCGGTGT
1 TTTCAAAAATTCTC-GTGT
28094778 TTT-AAAAACTT-TCGTGT
1 TTTCAAAAA-TTCTCGTGT
*
28094795 TTTCAAAAATT-TC-TAT
1 TTTCAAAAATTCTCGTGT
** * *
28094811 GATCAAAATTTTTTTTTCGTGTT
1 TTTCAAAA----ATTCTCGTG-T
28094834 TTTCAAAAAATT-TCGTG-
1 TTTC-AAAAATTCTCGTGT
* *
28094851 TTTCAAAAATTTTCATGT
1 TTTCAAAAATTCTCGTGT
*
28094869 TTTCAAAAATTC-CCTGT
1 TTTCAAAAATTCTCGTGT
28094886 TTT-AAAAATT-TCCGTGT
1 TTTCAAAAATTCT-CGTGT
* *
28094903 TTTCAAAAATTTTCATGT
1 TTTCAAAAATTCTCGTGT
* ** *
28094921 TTTTATGAATTTTCGTG-
1 TTTCAAAAATTCTCGTGT
* * *
28094938 TCTCTAAAATTGTCGTGT
1 TTTCAAAAATTCTCGTGT
*
28094956 TTT-AAAAATTTTTCGTGT
1 TTTCAAAAA-TTCTCGTGT
28094974 TTTCAAAAA
1 TTTCAAAAA
28094983 AATAATTATT
Statistics
Matches: 294, Mismatches: 38, Indels: 72
0.73 0.09 0.18
Matches are distributed among these distances:
16 31 0.11
17 98 0.33
18 105 0.36
19 15 0.05
20 9 0.03
21 28 0.10
22 1 0.00
23 3 0.01
24 4 0.01
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTCAAAAATTCTCGTGT
Found at i:28094661 original size:38 final size:37
Alignment explanation
Indices: 28094594--28094698 Score: 124
Period size: 38 Copynumber: 2.8 Consensus size: 37
28094584 AAAAAAATCC
* *
28094594 TGTTTCAAAAATTTTTCGTGTTTTC-AAAAAAATTTCTCG
1 TGTTTCAAAAATTCTT--TGTTTTCAAAAAAAAATT-TCG
28094633 TGTTTCAAAAATTCTTTGTTTTCAAAAAAAAATTTCG
1 TGTTTCAAAAATTCTTTGTTTTCAAAAAAAAATTTCG
*
28094670 TGTCTTCAAAAATTCTCATG-TTTCAAAAA
1 TGT-TTCAAAAATTCT-TTGTTTTCAAAAA
28094699 TCTTCGTGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
37 13 0.22
38 30 0.50
39 17 0.28
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (37 bp):
TGTTTCAAAAATTCTTTGTTTTCAAAAAAAAATTTCG
Found at i:28094966 original size:34 final size:34
Alignment explanation
Indices: 28094594--28094982 Score: 261
Period size: 35 Copynumber: 10.9 Consensus size: 34
28094584 AAAAAAATCC
*
28094594 TGTTTCAAAAATTTTTCGTGTTTTCAAAAAAATTTCTCG
1 TGTTTTAAAAA-TTTTCGTGTTTTC--AAAAA-TT-TCG
*
28094633 TGTTTCAAAAATTCTT--TGTTTTCAAAAAAAAATTTCG
1 TGTTTTAAAAATT-TTCGTGTTTTC----AAAAATTTCG
* * *
28094670 TGTCTTCAAAAATTCTCATG-TTTCAAAAATCTTCG
1 TGT-TTTAAAAATTTTCGTGTTTTCAAAAAT-TTCG
* * *
28094705 TGTTTTCAAAA-TTCCAGTG-TTTCGAAAATTTTCG
1 TGTTTTAAAAATTTTC-GTGTTTTC-AAAAATTTCG
**
28094739 TGTTTTCAAAAATCCTCGTGTTTTCAAAAATTTCGG
1 TGTTTT-AAAAATTTTCGTGTTTTCAAAAATTTC-G
*
28094775 TGTTTTAAAAACTTTCGTGTTTTCAAAAATTTC-
1 TGTTTTAAAAATTTTCGTGTTTTCAAAAATTTCG
* * * *
28094808 TATGATCAAAATTTTTTTTTCGTGTTTTTCAAAAAATTTCG
1 TGT-TTTAAAA----ATTTTCGTG-TTTTC-AAAAATTTCG
* * * *
28094849 TGTTTCAAAAATTTTCATGTTTTCAAAAATTCCC
1 TGTTTTAAAAATTTTCGTGTTTTCAAAAATTTCG
* *
28094883 TGTTTTAAAAATTTCCGTGTTTTCAAAAATTTTCA
1 TGTTTTAAAAATTTTCGTGTTTTCAAAAA-TTTCG
** * *
28094918 TGTTTTTATGAATTTTCGTG-TCTCTAAAATTGTCG
1 TG-TTTTAAAAATTTTCGTGTTTTCAAAAATT-TCG
28094953 TGTTTTAAAAATTTTTCGTGTTTTCAAAAA
1 TGTTTTAAAAA-TTTTCGTGTTTTCAAAAA
28094983 AATAATTATT
Statistics
Matches: 283, Mismatches: 41, Indels: 55
0.75 0.11 0.15
Matches are distributed among these distances:
33 4 0.01
34 76 0.27
35 80 0.28
36 40 0.14
37 14 0.05
38 25 0.09
39 27 0.10
40 15 0.05
41 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (34 bp):
TGTTTTAAAAATTTTCGTGTTTTCAAAAATTTCG
Found at i:28095797 original size:49 final size:50
Alignment explanation
Indices: 28095744--28095883 Score: 151
Period size: 49 Copynumber: 2.8 Consensus size: 50
28095734 CTATAAACGG
* * *
28095744 GAAGCTCTGGAGAGCCATTAATCGGAAAGCTCATGCGAGCCAA-TATCAA
1 GAAGCTCTGAAGAGCCATTAATCGAAAAGCTCATGAGAGCCAATTATCAA
* * *
28095793 GAAGCTCTGAAGAGCTATTAATCGAAAAGCTCGTGAGAGCCAATTATCGA
1 GAAGCTCTGAAGAGCCATTAATCGAAAAGCTCATGAGAGCCAATTATCAA
* * * * *
28095843 GAAGCTCAT-ACGAGCCA-TAAACTAGAAGCTCAAGAGAGCCA
1 GAAGCTC-TGAAGAGCCATTAATCGAAAAGCTCATGAGAGCCA
28095884 TATAACGAGA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 57 0.75
50 18 0.24
51 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (50 bp):
GAAGCTCTGAAGAGCCATTAATCGAAAAGCTCATGAGAGCCAATTATCAA
Found at i:28095874 original size:24 final size:25
Alignment explanation
Indices: 28095754--28095906 Score: 88
Period size: 25 Copynumber: 6.2 Consensus size: 25
28095744 GAAGCTCTGG
*
28095754 AGAGCCAT-TAATCG-GAAAGCTCATG
1 AGAGCCATATAA-CGAG-AAGCTCATA
* * *
28095779 CGAGCCA-ATATCAAGAAGCTC-TGA
1 AGAGCCATATAACGAGAAGCTCAT-A
* * * *
28095803 AGAGCTAT-TAATCGAAAAGCTCGTG
1 AGAGCCATATAA-CGAGAAGCTCATA
*
28095828 AGAGCCA-ATTATCGAGAAGCTCATA
1 AGAGCCATA-TAACGAGAAGCTCATA
* *
28095853 CGAGCCATA-AACTAGAAGCTCA-A
1 AGAGCCATATAACGAGAAGCTCATA
*
28095876 GAGAGCCATATAACGAGACGCTCATA
1 -AGAGCCATATAACGAGAAGCTCATA
28095902 AGAGC
1 AGAGC
28095907 TGTGGTGAGT
Statistics
Matches: 95, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
23 2 0.02
24 33 0.35
25 55 0.58
26 5 0.05
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (25 bp):
AGAGCCATATAACGAGAAGCTCATA
Found at i:28095905 original size:25 final size:24
Alignment explanation
Indices: 28095840--28095906 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
28095830 AGCCAATTAT
*
28095840 CGAGAAGCTCATACGAGCCATAAA
1 CGAGAAGCTCATAAGAGCCATAAA
*
28095864 CTAGAAGCTCA-AGAGAGCCATATAA
1 CGAGAAGCTCATA-AGAGCCATA-AA
*
28095889 CGAGACGCTCATAAGAGC
1 CGAGAAGCTCATAAGAGC
28095907 TGTGGTGAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 1 0.03
24 18 0.50
25 16 0.44
26 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (24 bp):
CGAGAAGCTCATAAGAGCCATAAA
Found at i:28099161 original size:13 final size:15
Alignment explanation
Indices: 28099131--28099162 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28099121 ATATTTCATG
28099131 CATTTCATCAATAAT
1 CATTTCATCAATAAT
28099146 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
28099159 CATT
1 CATT
28099163 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:28099458 original size:45 final size:44
Alignment explanation
Indices: 28099394--28099555 Score: 218
Period size: 45 Copynumber: 3.6 Consensus size: 44
28099384 GTAATGGTAG
* *
28099394 CAGTAACAGTAACAGTATTCAACACACAAAGTGCTAAATCTGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATC-GTAA
* *
28099439 CAGTAATAGTAACAGTATTCGACACACAAAGCGCTGAATCGATAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCG-TAA
*
28099484 CAGTAACAGTAACAGCATTCGACACACAAAGTG-TCGAATCAGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCT-GAATC-GTAA
*
28099529 TCAGTAACAGTAACAGTAGTCGACACA
1 -CAGTAACAGTAACAGTATTCGACACA
28099556 TAAGTGCCTA
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
44 2 0.02
45 77 0.74
46 25 0.24
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.20
Consensus pattern (44 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCGTAA
Found at i:28106815 original size:18 final size:19
Alignment explanation
Indices: 28106784--28106819 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28106774 GTGTATGAAT
*
28106784 ATAAAAATCGTAAAAATAA
1 ATAAAAATCATAAAAATAA
28106803 ATAAAAAT-ATAAAAATA
1 ATAAAAATCATAAAAATA
28106820 TGCTTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (19 bp):
ATAAAAATCATAAAAATAA
Found at i:28108878 original size:45 final size:44
Alignment explanation
Indices: 28108822--28109391 Score: 337
Period size: 45 Copynumber: 12.8 Consensus size: 44
28108812 GCCAATACAT
* *
28108822 GAAGACAAGATCTGCTTTCTTTGATCTGTTCCACCACCAGTATGG
1 GAAGATAAGATCTGCTTTCTTTGATCTCTT-CACCACCAGTATGG
* ** ** * * * * *
28108867 GGAGATAAGATCTGCTACCTACGATCCACTTCGCTACCAATATAG
1 GAAGATAAGATCTGCTTTCTTTGAT-CTCTTCACCACCAGTATGG
* * * * *
28108912 GAAGATAGGATTTACTTTCTTCGATTTACTTCACCACCAGTATGG
1 GAAGATAAGATCTGCTTTCTTTGATCT-CTTCACCACCAGTATGG
* *
28108957 GAAGACAAGATCTG-TTATCTTTGATCTACTCCACCACCAGTATGG
1 GAAGATAAGATCTGCTT-TCTTTGATCT-CTTCACCACCAGTATGG
* * ** * * * * * *
28109002 GGAGATAAGATATG-TTATCTACGATCCACTCCGCTACCAATATAG
1 GAAGATAAGATCTGCTT-TCTTTGAT-CTCTTCACCACCAGTATGG
* * *
28109047 GAAGACAGGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGATAAGATCTGCTTTCTTTGATCT-CTTCACCACCAGTATGG
* * ***
28109092 GAAGAT-AGATCTGCTATCTTTGATCTACTTCA-CGCCAGTACAT
1 GAAGATAAGATCTGCTTTCTTTGATCT-CTTCACCACCAGTATGG
* * *
28109135 GAAGACAAGATCTGTTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGATAAGATCTGCTTTCTTTGATCT-CTTCACCACCAGTATGG
* * ** ***
28109180 GAATG-CAAGATCTGCTATCTTTGATCTACTTCA-TGCCAGTACAT
1 GAA-GATAAGATCTGCTTTCTTTGATCT-CTTCACCACCAGTATGG
* * *
28109224 GAAGACAAGATCTG-TTTTTTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGATAAGATCTGCTTTCTTT-GATCT-CTTCACCACCAGTATGG
** * * ***
28109269 GAAGGCAAGATCTGCTATCTTTGATCTACTTCA-CGCCAGTACAT
1 GAAGATAAGATCTGCTTTCTTTGATCT-CTTCACCACCAGTATGG
* ** * *
28109313 GAAGACAAGATCTATTTTCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGATAAGATCTGCTTTCTTTGATCT-CTTCACCACCAGTATGG
** * *
28109358 GAAGGCAAGATCTGCTATCTTTAATCTACTTCAC
1 GAAGATAAGATCTGCTTTCTTTGATCT-CTTCAC
28109392 GCCAGCATAT
Statistics
Matches: 394, Mismatches: 117, Indels: 28
0.73 0.22 0.05
Matches are distributed among these distances:
43 18 0.05
44 107 0.27
45 257 0.65
46 12 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
GAAGATAAGATCTGCTTTCTTTGATCTCTTCACCACCAGTATGG
Found at i:28108982 original size:135 final size:135
Alignment explanation
Indices: 28108822--28109387 Score: 444
Period size: 135 Copynumber: 4.2 Consensus size: 135
28108812 GCCAATACAT
** *
28108822 GAAGACAAGATCTGCTT-TCTTTGATCTGTTCCACCACCAGTATGGGGAGATAAGATCTGCTACC
1 GAAGACAAGATCTG-TTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATATGCTACC
* * * *
28108886 TACGATCCACTTCGCTACCAATATAGGAAGATAGGATTTACTTTCTTCGATTTACTTCACCACCA
65 TACGATCCACTCCGCTACCAATATAGGAAGACAGGATCTACTTTCTTCGATCTACTTCACCACCA
28108951 GTATGG
130 GTATGG
* *
28108957 GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATATGTTATCT
1 GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATATGCTACCT
* * * *
28109022 ACGATCCACTCCGCTACCAATATAGGAAGACAGGATCTGCTTTCTTTGATCTGCTTCGCCACCAG
66 ACGATCCACTCCGCTACCAATATAGGAAGACAGGATCTACTTTCTTCGATCTACTTCACCACCAG
28109087 TATGG
131 TATGG
* * * * *** * * * * **
28109092 GAAGA-TAGATCTGCTATCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATATGCTACCT
** ** * * * * * * * * **
28109155 TTGATCTGCTTCGCCACCAGTATGGGAATG-CAAGATCTGCTATCTTTGATCTACTTCA-TGCCA
66 ACGATCCACTCCGCTACCAATATAGGAA-GACAGGATCTACTTTCTTCGATCTACTTCACCACCA
***
28109218 GTACAT
130 GTATGG
* * * * * ** * *
28109224 GAAGACAAGATCTGTT-TTTTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGCTATC
1 GAAGACAAGATCTGTTATCTTT-GATCTACTCCACCACCAGTATGGGGAGATAAGATATGCTACC
** * * * * * * * * * * *
28109288 TTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTATTTTCTTCGATCTGCTTCGCCACCA
65 TACGATCCACTCCGCTACCAATATAGGAAGACAGGATCTACTTTCTTCGATCTACTTCACCACCA
28109352 GTATGG
130 GTATGG
* * *
28109358 GAAGGCAAGATCTGCTATCTTTAATCTACT
1 GAAGACAAGATCTGTTATCTTTGATCTACT
28109388 TCACGCCAGC
Statistics
Matches: 348, Mismatches: 75, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
132 16 0.05
133 115 0.33
134 89 0.26
135 128 0.37
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (135 bp):
GAAGACAAGATCTGTTATCTTTGATCTACTCCACCACCAGTATGGGGAGATAAGATATGCTACCT
ACGATCCACTCCGCTACCAATATAGGAAGACAGGATCTACTTTCTTCGATCTACTTCACCACCAG
TATGG
Done.