Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008745.1 Hibiscus syriacus cultivar Beakdansim tig00111834_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1915556
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:843877 original size:17 final size:17
Alignment explanation
Indices: 843855--843888 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
843845 GATTGTGATG
843855 CTTTTGGCAATGAATGA
1 CTTTTGGCAATGAATGA
*
843872 CTTTTGGCGATGAATGA
1 CTTTTGGCAATGAATGA
843889 GGTCATAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (17 bp):
CTTTTGGCAATGAATGA
Found at i:845475 original size:19 final size:19
Alignment explanation
Indices: 845451--845509 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
845441 CGGGCCTGGT
845451 ATATATATATTTAAATTAA
1 ATATATATATTTAAATTAA
* *
845470 ATATATAAATATTATA-TAA
1 ATATATATAT-TTAAATTAA
*
845489 ATAT-TTTAATTTAAATTAA
1 ATATATAT-ATTTAAATTAA
845508 AT
1 AT
845510 TTATTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.16
19 23 0.72
20 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATATATTTAAATTAA
Found at i:845516 original size:19 final size:19
Alignment explanation
Indices: 845459--845517 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
845449 GTATATATAT
* *
845459 ATTTAAATTAAATATATAA
1 ATTTAAATTAAATTTATTA
*
845478 ATATTATA-TAAATATT-TTA
1 AT-TTAAATTAAAT-TTATTA
845497 ATTTAAATTAAATTTATTA
1 ATTTAAATTAAATTTATTA
845516 AT
1 AT
845518 ATTATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 6 0.19
19 21 0.66
20 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAAATTAAATTTATTA
Found at i:846058 original size:60 final size:60
Alignment explanation
Indices: 845936--846065 Score: 138
Period size: 60 Copynumber: 2.1 Consensus size: 60
845926 GTCGGGTGAC
* * * * *
845936 CATTTTATAACTTTTAATAGTCGAATGACTAAACAAAATAGCACTTTATAGTCGGAGTAT
1 CATTTTGTAACTTTTAATAGTCGAATGACTAAACAAAACAGCACTCTAGAGTCAGAGTAT
* * * *
845996 CATTTTGTAACTTTTAATAGTCGAGTGACTTAATAAAACAGTA-TACTAGAGTCAAGAG-AT
1 CATTTTGTAACTTTTAATAGTCGAATGACTAAACAAAACAGCACT-CTAGAGTC-AGAGTAT
846056 CATTTGTGTA
1 CATTT-TGTA
846066 TTTTACCCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.02
60 50 0.86
61 7 0.12
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAATGACTAAACAAAACAGCACTCTAGAGTCAGAGTAT
Found at i:849930 original size:31 final size:31
Alignment explanation
Indices: 849894--849952 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
849884 AACTTAAAAG
* *
849894 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
849925 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
849953 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:850002 original size:22 final size:22
Alignment explanation
Indices: 849976--850018 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
849966 ATAATAATTA
849976 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
849998 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
850019 CTAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:850029 original size:54 final size:54
Alignment explanation
Indices: 849970--850738 Score: 221
Period size: 54 Copynumber: 14.3 Consensus size: 54
849960 ACTACAATAA
849970 TAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
1 TAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
* *
850024 TAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACAATCCATACTA
1 TAATTATTTAAAATAAATCAATCCAT---A-T---TTTA-AAAT-AA---AT-CAATCCATACTA
850089 AT
53 AT
* *** *
850091 AAATTATTTAAAAT-AATCAATCCATACAACTACATAAT-AATCAATCCATA-T-TT
1 TAATTATTTAAAATAAATCAATCCATA-TTTTA-A-AATAAATCAATCCATACTAAT
* * * * *
850144 TAA--A-AT-AAATCAATCTATACAAATAAATTATTTAAAATAAATCAATCTATACTAAT
1 TAATTATTTAAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAAT
* * * *
850200 AAATTA-TTAAAATAAATCAATCCATATTTTAAAAT-AATCAATTCATATTTTAAAA
1 TAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA--CT-AAT
* ** * * * *
850255 TAATCATCCATACT-AATAAAT---TA-TTT-AAATAAATCAATCCATA-T-TT
1 TAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
* * * * * *
850301 TAA--A-AT-AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATAC-AAC
1 TAATTATTTAAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAAT
* *
850356 TACA--A--T--ATTAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAT
1 TA-ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
* *
850405 AAATTATTTAAAATAAATCATACTACTAATAAATTATTTAAAATAAATCAATCCATACTAA-
1 TAATTATTTAAAATAAATCA-A-T-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAAT
*
850466 TAATTATTTAAAAT-AATCAATCCATATTTTAAAATAAATCAATCCATA-T-TT
1 TAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
* * * ** *
850517 TAA--AATAAATCAATACATACTAATAAAT-TATTTAAAATAAATCAATCCATA-T-TT
1 TAATTATTTAA--AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAAT
* * * * * *
850571 TAA--A-AT-AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAC-AAC
1 TAATTATTTAAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAAT
*
850626 TACA--A--T--AAT-AATC-ATCCATA-TTTAAAATAAATCAGTCCATACTAA-
1 TA-ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
* *
850671 TAATTATTTAAAAT-AATCAATCTATATTTT-AAATAAATC-ATTCATACTAA-
1 TAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
*
850721 TAATTATTTTAAATAAAT
1 TAATTATTTAAAATAAAT
850739 TATTTTAAAA
Statistics
Matches: 548, Mismatches: 80, Indels: 177
0.68 0.10 0.22
Matches are distributed among these distances:
42 2 0.00
43 5 0.01
44 2 0.00
45 22 0.04
46 6 0.01
48 28 0.05
49 13 0.02
50 53 0.10
51 42 0.08
52 46 0.08
53 25 0.05
54 133 0.24
55 32 0.06
56 15 0.03
57 5 0.01
58 7 0.01
59 12 0.02
60 9 0.02
61 19 0.03
62 28 0.05
63 4 0.01
66 13 0.02
67 27 0.05
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
Found at i:850034 original size:32 final size:32
Alignment explanation
Indices: 849998--850117 Score: 129
Period size: 32 Copynumber: 3.7 Consensus size: 32
849988 CAATCCATAT
*
849998 TTTAAAATAAATCAATCCATACTAATTAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
850030 TTTAAAATAAATCAATCCATAC-AACTACAA-TA
1 TTTAAAATAAATCAATCCATACTAA-TA-AATTA
* * **
850062 ATAAATCAATCCATACAATCCATACTAATAAATTA
1 TTTAA--AATAAAT-CAATCCATACTAATAAATTA
850097 TTTAAAAT-AATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
850118 AACTACATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
31 12 0.16
32 30 0.41
33 5 0.07
34 7 0.10
35 17 0.23
36 2 0.03
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:850089 original size:67 final size:64
Alignment explanation
Indices: 850010--850140 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 64
850000 TAAAATAAAT
*
850010 CAATCCATACTAATTAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCA
1 CAATCCATACTAATAAATTATTTAAAAT-AATCAATCCATACAACTAC-ATAAT-AATCAATCCA
850075 TA
63 TA
850077 CAATCCATACTAATAAATTATTTAAAATAATCAATCCATACAACTACATAATAATCAATCCATA
1 CAATCCATACTAATAAATTATTTAAAATAATCAATCCATACAACTACATAATAATCAATCCATA
850141 TTTTAAAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
64 12 0.19
65 5 0.08
66 19 0.30
67 27 0.43
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (64 bp):
CAATCCATACTAATAAATTATTTAAAATAATCAATCCATACAACTACATAATAATCAATCCATA
Found at i:850117 original size:40 final size:44
Alignment explanation
Indices: 850061--850165 Score: 128
Period size: 40 Copynumber: 2.4 Consensus size: 44
850051 CAACTACAAT
* *
850061 AATAAATCAATCCATACAA-TCCATACTAATAAAT-TA-TTTAA
1 AATAAATCAATCCATACAACTACATAATAATAAATCTATTTTAA
*
850102 AAT-AATCAATCCATACAACTACATAATAATCAATCCATATTTTAA
1 AATAAATCAATCCATACAACTACATAATAATAAAT-C-TATTTTAA
*
850147 AATAAATCAATCTATACAA
1 AATAAATCAATCCATACAA
850166 ATAAATTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 15 0.28
41 15 0.28
44 2 0.04
45 8 0.15
46 14 0.26
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.30
Consensus pattern (44 bp):
AATAAATCAATCCATACAACTACATAATAATAAATCTATTTTAA
Found at i:850167 original size:18 final size:18
Alignment explanation
Indices: 850146--850203 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
850136 CCATATTTTA
850146 AAATAAATCAATCTATAC
1 AAATAAATCAATCTATAC
*
850164 AAATAAAT-TAT-T-TA-
1 AAATAAATCAATCTATAC
850178 AAATAAATCAATCTATAC
1 AAATAAATCAATCTATAC
*
850196 TAATAAAT
1 AAATAAAT
850204 TATTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
16 2 0.06
17 4 0.12
18 15 0.45
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATCAATCTATAC
Found at i:850181 original size:32 final size:32
Alignment explanation
Indices: 850142--850563 Score: 150
Period size: 32 Copynumber: 12.5 Consensus size: 32
850132 CAATCCATAT
850142 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
850174 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
850206 -TTAAAATAAATCAATCCATATTTTA-AAATAATCAATTCATA
1 TTTAAAATAAATCAAT-C-TA---TACAAAT-A--AA-T--TA
* *
850247 TTTTAAAAT-AATC-ATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCTATACAAATAAATTA
*
850278 TTT-AAATAAATCAATCCATATTTTA-AAATAAATCAA
1 TTTAAAATAAATCAAT-C-TA---TACAAATAAAT-TA
* * * *
850314 TCCATACTAATAAAT-TAT-T-TA-AAATAAATCAA
1 T--TTA-AAATAAATCAATCTATACAAATAAAT-TA
* * **
850346 TCTATACAACTACAAT--AT-TAAATC-AATCCA-TA
1 T-T-TA-AAATA-AATCAATCTATA-CAAATAAATTA
*
850378 TTTTAAAATAAATCAATCCATACAAATAAATTA
1 -TTTAAAATAAATCAATCTATACAAATAAATTA
*
850411 TTTAAAATAAATC-A--TACTACTAATAAATTA
1 TTTAAAATAAATCAATCTA-TACAAATAAATTA
* *
850441 TTTAAAATAAATCAATCCATACTAAT-AATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
850472 TTTAAAAT-AATCAATCCATATTTTA-AAATAAATCAATCCATA
1 TTTAAAATAAATCAAT-C-TA---TACAAAT--A--AAT---TA
*
850514 TTTTAAAATAAATCAATAC-ATACTAATAAATTA
1 -TTTAAAATAAATCAAT-CTATACAAATAAATTA
850547 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
850564 CATATTTTAA
Statistics
Matches: 304, Mismatches: 29, Indels: 115
0.68 0.06 0.26
Matches are distributed among these distances:
29 8 0.03
30 43 0.14
31 42 0.14
32 101 0.33
33 14 0.05
34 9 0.03
35 12 0.04
36 14 0.05
37 3 0.01
38 4 0.01
39 9 0.03
40 11 0.04
41 4 0.01
42 7 0.02
43 15 0.05
44 8 0.03
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACAAATAAATTA
Found at i:850224 original size:109 final size:103
Alignment explanation
Indices: 850077--850297 Score: 309
Period size: 109 Copynumber: 2.1 Consensus size: 103
850067 TCAATCCATA
850077 CAATCCATACTAATAAATTATTTAAAATAATCAATCCATACAACTACATAATAATCAATCCATAT
1 CAATCCATACTAATAAATTATTTAAAATAATCAATCCATA-AACTA-A-AATAATCAATCCATAT
*
850142 TTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAAT
63 TTTAAAAT-AATC-ATCCATACAAATAAATTATTT-AAATAAAT
* *** *
850186 CAATCTATACTAATAAATTA-TTAAAATAAATCAATCCATATTTTAAAATAATCAATTCATATTT
1 CAATCCATACTAATAAATTATTTAAAAT-AATCAATCCATAAACTAAAATAATCAATCCATATTT
*
850250 TAAAATAATCATCCATACTAATAAATTATTTAAATAAAT
65 TAAAATAATCATCCATACAAATAAATTATTTAAATAAAT
850289 CAATCCATA
1 CAATCCATA
850298 TTTTAAAATA
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
103 16 0.16
104 19 0.18
105 4 0.04
106 23 0.22
107 1 0.01
108 9 0.09
109 31 0.30
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (103 bp):
CAATCCATACTAATAAATTATTTAAAATAATCAATCCATAAACTAAAATAATCAATCCATATTTT
AAAATAATCATCCATACAAATAAATTATTTAAATAAAT
Found at i:850274 original size:21 final size:21
Alignment explanation
Indices: 850206--850266 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
850196 TAATAAATTA
850206 TTAAAATAAATCAATCCATATT
1 TTAAAAT-AATCAATCCATATT
*
850228 TTAAAATAATCAATTCATATT
1 TTAAAATAATCAATCCATATT
850249 TTAAAATAATC-ATCCATA
1 TTAAAATAATCAATCCATA
850267 CTAATAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.16
21 24 0.65
22 7 0.19
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAATAATCAATCCATATT
Found at i:850282 original size:30 final size:30
Alignment explanation
Indices: 850248--850491 Score: 142
Period size: 30 Copynumber: 8.6 Consensus size: 30
850238 CAATTCATAT
850248 TTTAAAATAATCATCCATACTAATAAATTA
1 TTTAAAATAATCATCCATACTAATAAATTA
* *
850278 TTT-AAATAA--ATCAAT-C-CAT--A-T-
1 TTTAAAATAATCATCCATACTAATAAATTA
850299 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAAT-AATC-ATCCATACTAATAAATTA
*
850331 TTTAAAATAAATCAATCTATAC-AACTACAA-TA
1 TTTAAAAT-AATC-ATCCATACTAA-TA-AATTA
* **
850363 -TT-AAATCA--ATCCATA-TTTTAAA--A
1 TTTAAAATAATCATCCATACTAATAAATTA
* *
850386 --T-AAATCA--ATCCATACAAATAAATTA
1 TTTAAAATAATCATCCATACTAATAAATTA
*
850411 TTTAAAATAAATCATAC-TACTAATAAATTA
1 TTTAAAAT-AATCATCCATACTAATAAATTA
850441 TTTAAAATAAATCAATCCATACTAAT-AATTA
1 TTTAAAAT-AATC-ATCCATACTAATAAATTA
850472 TTTAAAATAATCAATCCATA
1 TTTAAAATAATC-ATCCATA
850492 TTTTAAAATA
Statistics
Matches: 173, Mismatches: 16, Indels: 50
0.72 0.07 0.21
Matches are distributed among these distances:
21 3 0.02
22 19 0.11
23 8 0.05
24 2 0.01
25 5 0.03
26 12 0.07
27 7 0.04
28 6 0.03
29 8 0.05
30 45 0.26
31 24 0.14
32 32 0.18
33 2 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.35
Consensus pattern (30 bp):
TTTAAAATAATCATCCATACTAATAAATTA
Found at i:850328 original size:22 final size:21
Alignment explanation
Indices: 850280--850328 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
850270 ATAAATTATT
**
850280 TAAATAAATCAATCCATATTT
1 TAAATAAATCAATCCATATAA
850301 TAAAATAAATCAATCCATACTAA
1 T-AAATAAATCAATCCATA-TAA
850324 TAAAT
1 TAAAT
850329 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.88
23 2 0.08
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATAAATCAATCCATATAA
Found at i:850418 original size:14 final size:14
Alignment explanation
Indices: 850401--850452 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
850391 CAATCCATAC
850401 AAATAAATTATTTA
1 AAATAAATTATTTA
* *
850415 AAATAAATCATACTA
1 AAATAAATTAT-TTA
*
850430 CTAATAAATTATTTA
1 -AAATAAATTATTTA
850445 AAATAAAT
1 AAATAAAT
850453 CAATCCATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 17 0.57
15 4 0.13
16 9 0.30
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:850508 original size:22 final size:22
Alignment explanation
Indices: 850472--850535 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
850462 CTAATAATTA
850472 TTTAAAAT-AATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
850493 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
850515 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATCCATA
850536 CTAATAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 8 0.20
22 33 0.80
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:850522 original size:18 final size:20
Alignment explanation
Indices: 850480--850589 Score: 74
Period size: 22 Copynumber: 5.6 Consensus size: 20
850470 TATTTAAAAT
850480 AATCAATCCATATTTTAAAATA
1 AATCAATCCATATTTT--AATA
850502 AATCAATCCATATTTTAAAATA
1 AATCAATCCATATTTT--AATA
* *
850524 AATCAATACATA--CTAATA
1 AATCAATCCATATTTTAATA
**
850542 AAT---T--AT-TTAAAATA
1 AATCAATCCATATTTTAATA
850556 AATCAATCCATATTTTAAAATA
1 AATCAATCCATATTTT--AATA
850578 AATCAATCCATA
1 AATCAATCCATA
850590 CTAATAAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 20
0.73 0.06 0.20
Matches are distributed among these distances:
13 2 0.03
14 7 0.10
15 1 0.01
17 1 0.01
18 7 0.10
19 2 0.03
20 3 0.04
22 49 0.68
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.35
Consensus pattern (20 bp):
AATCAATCCATATTTTAATA
Found at i:850573 original size:22 final size:22
Alignment explanation
Indices: 850547--850589 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
850537 TAATAAATTA
850547 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
850569 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
850590 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:850582 original size:76 final size:74
Alignment explanation
Indices: 850441--850589 Score: 271
Period size: 76 Copynumber: 2.0 Consensus size: 74
850431 TAATAAATTA
*
850441 TTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAATCAATCCATATTTTAAAATAAATC
1 TTTAAAATAAATCAATACATACTAATAATTATTTAAAATAATCAATCCATATTTTAAAATAAATC
850506 AATCCATAT
66 AATCCATAT
850515 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATACATACTAAT-AATTATTTAAAAT-AATCAATCCATATTTTAAAATAAA
850580 TCAATCCATA
64 TCAATCCATA
850590 CTAATAAATT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
74 25 0.35
75 13 0.18
76 34 0.47
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.36
Consensus pattern (74 bp):
TTTAAAATAAATCAATACATACTAATAATTATTTAAAATAATCAATCCATATTTTAAAATAAATC
AATCCATAT
Found at i:850598 original size:22 final size:22
Alignment explanation
Indices: 850549--850597 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
850539 ATAAATTATT
**
850549 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
850571 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
850594 TAAA
1 TAAA
850598 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:850625 original size:270 final size:263
Alignment explanation
Indices: 850142--850773 Score: 917
Period size: 267 Copynumber: 2.4 Consensus size: 263
850132 CAATCCATAT
* *
850142 TTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTA-
1 TTTAAAATAAATCAA-C--TACTAATAAATTATTTAAAATAAATCAATCCATACTAAT-AATTAT
* *
850206 TTAAAATAAATCAATCCATATTTTAAAAT-AATCAATTCATATTTTAAAAT-AATCATCCATACT
62 TTAAAAT-AATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCATACATACT
850269 AATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
126 AATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
*
850334 AAAATAAATCAATCTATACAACTACAATATTAAATCAATCCATATTTTAAAATAAATCAATCCAT
191 AAAATAAATCAATCTATACAACTACAATAAT-AATC-ATCCATA-TTTAAAATAAATCAATCCAT
850399 ACAAATAAATTA
253 ACAAAT-AATTA
850411 TTTAAAATAAATCATACTACTAATAAATTATTTAAAATAAATCAATCCATACTAATAATTATTTA
1 TTTAAAATAAATCA-ACTACTAATAAATTATTTAAAATAAATCAATCCATACTAATAATTATTTA
850476 AAATAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAAT
65 AAATAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATC-ATACATACTAAT
850541 AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
129 AAATTATTT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
850606 AATAAATCAAT-TCATACAACTACAATAATAATCATCCATATTTAAAATAAATCAGTCCATACTA
193 AATAAATCAATCT-ATACAACTACAATAATAATCATCCATATTTAAAATAAATCAATCCATACAA
850670 ATAATTA
257 ATAATTA
* *
850677 TTTAAAAT-AATCAA-T-CT-AT--A-T-TTT-AAATAAATC-ATTCATACTAATAATTATTTTA
1 TTTAAAATAAATCAACTACTAATAAATTATTTAAAATAAATCAATCCATACTAATAATTATTTAA
*
850732 AAT-A--AAT---TATTTTAAAATAAATCAATCCATATTTTATAATAA
66 AATAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAA
850774 TTTATTTTAA
Statistics
Matches: 346, Mismatches: 10, Indels: 34
0.89 0.03 0.09
Matches are distributed among these distances:
249 34 0.10
252 3 0.01
254 1 0.00
255 23 0.07
256 9 0.03
257 3 0.01
258 1 0.00
259 1 0.00
261 2 0.01
262 2 0.01
263 1 0.00
264 1 0.00
265 5 0.01
266 39 0.11
267 88 0.25
268 11 0.03
269 40 0.12
270 82 0.24
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.36
Consensus pattern (263 bp):
TTTAAAATAAATCAACTACTAATAAATTATTTAAAATAAATCAATCCATACTAATAATTATTTAA
AATAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCATACATACTAATAA
ATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT
AAATCAATCTATACAACTACAATAATAATCATCCATATTTAAAATAAATCAATCCATACAAATAA
TTA
Found at i:850719 original size:50 final size:50
Alignment explanation
Indices: 850632--850762 Score: 164
Period size: 50 Copynumber: 2.7 Consensus size: 50
850622 CAACTACAAT
850632 AATAATCATCCATATTTAAAATAAATCAGTCCATACTAATAATTATTTAA
1 AATAATCATCCATATTTAAAATAAATCAGTCCATACTAATAATTATTTAA
* * * *
850682 AATAATCAATCTATATTTTAAATAAATCA-TTCATACTAATAATTATTTTA
1 AATAATC-ATCCATATTTAAAATAAATCAGTCCATACTAATAATTATTTAA
* *
850732 AATAA--AT-TAT-TTTAAAATAAATCAATCCATA
1 AATAATCATCCATATTTAAAATAAATCAGTCCATA
850763 TTTTATAATA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
45 13 0.18
46 8 0.11
47 2 0.03
50 31 0.42
51 19 0.26
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (50 bp):
AATAATCATCCATATTTAAAATAAATCAGTCCATACTAATAATTATTTAA
Found at i:850751 original size:15 final size:15
Alignment explanation
Indices: 850722--850865 Score: 173
Period size: 15 Copynumber: 9.2 Consensus size: 15
850712 TCATACTAAT
850722 AATTATTTT-AAATA
1 AATTATTTTAAAATA
850736 AATTATTTTAAAATAAA
1 AATTATTTTAAAAT--A
*
850753 TCAATCCATATTTTATAATA
1 --AAT---TATTTTAAAATA
* *
850773 ATTTATTTTAAAGTA
1 AATTATTTTAAAATA
*
850788 AATTATTTTATAATA
1 AATTATTTTAAAATA
*
850803 AATTATTTCAAAATA
1 AATTATTTTAAAATA
850818 AATTATTTTAAAATA
1 AATTATTTTAAAATA
850833 AATTATTTTAAAATA
1 AATTATTTTAAAATA
850848 AATTATTTTAAAATA
1 AATTATTTTAAAATA
850863 AAT
1 AAT
850866 AACCTTATTA
Statistics
Matches: 112, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.08
15 86 0.77
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (15 bp):
AATTATTTTAAAATA
Found at i:850764 original size:66 final size:67
Alignment explanation
Indices: 850668--850820 Score: 185
Period size: 67 Copynumber: 2.3 Consensus size: 67
850658 CAGTCCATAC
*
850668 TAAT-AATTA-TTTAAAAT-AATCAATCTATATTTTA-AATAAATCATTCATACTAA-T-AATTA
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATCATT-ATA--AAGTAAATTA
850727 TTTTA
63 TTTTA
* * *
850732 -AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAGTAAATTATTT
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATCATTATAAAGTAAATTATTT
850796 TA
66 TA
*
850798 TAATAAATTATTTCAAAATAAAT
1 TAATAAATTATTTTAAAATAAAT
850821 TATTTTAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
63 3 0.04
64 7 0.09
65 9 0.12
66 28 0.36
67 30 0.39
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (67 bp):
TAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATCATTATAAAGTAAATTATTT
TA
Found at i:858694 original size:19 final size:20
Alignment explanation
Indices: 858649--858704 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
858639 ATAATTTTTT
*
858649 AAATATATAATTTTTTTATAA
1 AAATATATAA-TTATTTATAA
**
858670 TTATATATAATTATTTA-AA
1 AAATATATAATTATTTATAA
*
858689 AAATATTATAGTTATT
1 AAATA-TATAATTATT
858705 ATTTTCAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.18
20 15 0.54
21 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAATATATAATTATTTATAA
Found at i:863985 original size:26 final size:27
Alignment explanation
Indices: 863933--863985 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
863923 TAAAAAAAGA
* * *
863933 TAAATTTAAATTTGTAAAATTTTAAGG
1 TAAACTTAAATTTATAAAATTATAAGG
863960 TAAACTTAAATTTAT-AAATTATAAGG
1 TAAACTTAAATTTATAAAATTATAAGG
863986 GAATGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (27 bp):
TAAACTTAAATTTATAAAATTATAAGG
Found at i:864860 original size:6 final size:7
Alignment explanation
Indices: 864839--864863 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
864829 ATTAATAACA
864839 TTAATTT
1 TTAATTT
864846 TTAATTT
1 TTAATTT
864853 TTAATTT
1 TTAATTT
864860 TTAA
1 TTAA
864864 AATTTCAGTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTAATTT
Found at i:866817 original size:19 final size:19
Alignment explanation
Indices: 866793--866900 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 19
866783 AAATGACCAA
*
866793 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGATTT
* *
866812 CAAATTCACAAC-CCAGTTT
1 CAAATTCGCAACGCGA-TTT
* **
866831 CCAATTTCGCAACGCGAAGT
1 -CAAATTCGCAACGCGATTT
*
866851 CAAATTCGCAACTG-AATTT
1 CAAATTCGCAAC-GCGATTT
*
866870 CAAATTCGCAACGTGAATTT
1 CAAATTCGCAACGCG-ATTT
*
866890 -AATTTCGCAAC
1 CAAATTCGCAAC
866901 AGGTTTTAGT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
18 3 0.04
19 48 0.70
20 16 0.23
21 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (19 bp):
CAAATTCGCAACGCGATTT
Found at i:870491 original size:20 final size:20
Alignment explanation
Indices: 870455--870492 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
870445 TTGCGATAGT
**
870455 CAAATTCGCAATGCGAAAGA
1 CAAATTCGCAACACGAAAGA
870475 CAAATTCGCAACACGAAA
1 CAAATTCGCAACACGAAA
870493 TCGCAAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.13
Consensus pattern (20 bp):
CAAATTCGCAACACGAAAGA
Found at i:870541 original size:20 final size:20
Alignment explanation
Indices: 870501--870557 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
870491 AATCGCAAAT
*
870501 CGAATTTGACTTTTGCATTG
1 CGAATTTGACTTTCGCATTG
*
870521 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCATTG
* * *
870541 CAAATATGACTATCGCA
1 CGAATTTGACTTTCGCA
870558 ACGCGAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (20 bp):
CGAATTTGACTTTCGCATTG
Found at i:870685 original size:25 final size:25
Alignment explanation
Indices: 870647--870696 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
870637 AAATCAATTA
*
870647 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
*
870672 AACATTGTTATGGGTATATTATTTG
1 AACATTGTTATGGGTACATTATTTG
870697 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:871126 original size:24 final size:24
Alignment explanation
Indices: 871075--871127 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
871065 TTTCATATGT
* * *
871075 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
*
871099 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTCAATATA
871123 AATTT
1 AATTT
871128 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:871477 original size:39 final size:39
Alignment explanation
Indices: 871430--871516 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
871420 TCTGATGCTC
* *
871430 ATCAAAATCCAAAGCTCATATGGTGCTAAGCAAAAGGAA
1 ATCAAAATCCAAAGCACATATGGTGCCAAGCAAAAGGAA
* *
871469 ATCCAAATCCAAATCACATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCACATATGGTGCCAAGCAAAAGGAA
871508 ATCAAAATC
1 ATCAAAATC
871517 TACAACTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCACATATGGTGCCAAGCAAAAGGAA
Found at i:871702 original size:20 final size:20
Alignment explanation
Indices: 871674--871713 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
871664 ATGTTGCGAT
* *
871674 CAACGCGAAAGTTAAATTCG
1 CAACACGAAAGTCAAATTCG
871694 CAACACGAAAGTCAAATTCG
1 CAACACGAAAGTCAAATTCG
871714 TAAACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
CAACACGAAAGTCAAATTCG
Found at i:871804 original size:19 final size:20
Alignment explanation
Indices: 871780--871818 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
871770 CGCTTATTTC
871780 GCGTTGCGAATTTG-ACTTT
1 GCGTTGCGAATTTGTACTTT
871799 GCGTTGCGAATTTGTACTTT
1 GCGTTGCGAATTTGTACTTT
871819 CAACAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (20 bp):
GCGTTGCGAATTTGTACTTT
Found at i:875896 original size:22 final size:22
Alignment explanation
Indices: 875841--875898 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
875831 GATGGAGATA
*
875841 GACGGATTTAGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
875863 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
*
875885 GACGGATGTCGTCG
1 GACGGATTTCGTCG
875899 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.21, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:876116 original size:20 final size:21
Alignment explanation
Indices: 876067--876120 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
876057 CGATTTACAT
876067 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTGGAA
* *
876088 ACT-GGGTTGCGAAATT-GAA
1 ATTCGCGTTGCGAAATTGGAA
876107 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
876121 TTTGTTGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.18
20 21 0.75
21 2 0.07
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAA
Found at i:880520 original size:54 final size:54
Alignment explanation
Indices: 880456--880563 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
880446 TATAGAATAT
*
880456 TATTTTGTTAAGTATCTCGACTATTAAGAGTTATAAATTGTTCACCCGACTAGA
1 TATTTTGTTAAGTATCTCGACTATTAAAAGTTATAAATTGTTCACCCGACTAGA
880510 TATTTTGTTAAGTATCTCGACTATTAAAAGTTATAAATTGTTCACCCGACTAGA
1 TATTTTGTTAAGTATCTCGACTATTAAAAGTTATAAATTGTTCACCCGACTAGA
880564 GATTATGCTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (54 bp):
TATTTTGTTAAGTATCTCGACTATTAAAAGTTATAAATTGTTCACCCGACTAGA
Found at i:882247 original size:19 final size:18
Alignment explanation
Indices: 882212--882267 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
882202 TTTACCCTTT
*
882212 TTATTTTTGT-AAGATAAA
1 TTATTTTT-TAAAAATAAA
882230 GTTATTTTTTAAAAATAAA
1 -TTATTTTTTAAAAATAAA
*
882249 -TATAATTTTAAAAATAAA
1 TTAT-TTTTTAAAAATAAA
882267 T
1 T
882268 AGAATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.09
18 14 0.44
19 15 0.47
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATTTTTTAAAAATAAA
Found at i:882923 original size:9 final size:9
Alignment explanation
Indices: 882909--882935 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
882899 TCCTAAACTA
882909 TTAAATTTT
1 TTAAATTTT
882918 TTAAATTTT
1 TTAAATTTT
882927 TTAAATTTT
1 TTAAATTTT
882936 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTAAATTTT
Found at i:882956 original size:23 final size:23
Alignment explanation
Indices: 882916--882989 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
882906 CTATTAAATT
*
882916 TTTTAAATTT-TTTAAATTTTAAA
1 TTTT-AATTTATTTTAATTTTAAA
**
882939 TTTTAATTTATTTTAATTTTCTA
1 TTTTAATTTATTTTAATTTTAAA
882962 TTATT-ATCTATATTTTAATTTTTAAA
1 TT-TTAAT-T-TATTTTAA-TTTTAAA
882988 TT
1 TT
882990 AATATCTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
22 5 0.12
23 18 0.44
24 3 0.07
25 8 0.20
26 7 0.17
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTAATTTATTTTAATTTTAAA
Found at i:882995 original size:26 final size:25
Alignment explanation
Indices: 882947--882996 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
882937 AATTTTAATT
*
882947 TATTTTAATTTTCTATTATTATCTA
1 TATTTTAATTTTCTATTAATATCTA
882972 TATTTTAATTTT-TAAATTAATATCT
1 TATTTTAATTTTCT--ATTAATATCT
882997 TGACTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 12 0.55
26 9 0.41
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTTAATTTTCTATTAATATCTA
Found at i:886534 original size:20 final size:20
Alignment explanation
Indices: 886509--886548 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
886499 AAAATACAGC
886509 TTTGTAATCATCGTTTATTA
1 TTTGTAATCATCGTTTATTA
886529 TTTGTAATCATCGTTTATTA
1 TTTGTAATCATCGTTTATTA
886549 ATGAAATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTGTAATCATCGTTTATTA
Found at i:889466 original size:20 final size:20
Alignment explanation
Indices: 889443--889532 Score: 58
Period size: 20 Copynumber: 4.3 Consensus size: 20
889433 TATTAAATTT
889443 ATTAAATTATTATAAAAACA
1 ATTAAATTATTATAAAAACA
* *
889463 ATTAAAATATTA-AAATGACA
1 ATTAAATTATTATAAA-AACA
* ***
889483 A-TAAATTTAATATTTATTAAATTT
1 ATTAAA--T--TA-TTATAAAAACA
889507 ATTAAATTATTATAAAAACA
1 ATTAAATTATTATAAAAACA
889527 ATTAAA
1 ATTAAA
889533 ATACTAAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 16
0.64 0.15 0.21
Matches are distributed among these distances:
19 7 0.14
20 28 0.56
21 2 0.04
23 3 0.06
24 4 0.08
25 6 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (20 bp):
ATTAAATTATTATAAAAACA
Found at i:889507 original size:64 final size:64
Alignment explanation
Indices: 889433--889628 Score: 365
Period size: 64 Copynumber: 3.1 Consensus size: 64
889423 ATCAAATAAA
*
889433 TATTAAATTTATTAAATTATTATAAAAACAATTAAAATATTAAAATGACAATAAATTTAATATT
1 TATTAAATTTATTAAATTATTATAAAAACAATTAAAATATTAAAATGATAATAAATTTAATATT
*
889497 TATTAAATTTATTAAATTATTATAAAAACAATTAAAATACTAAAATGATAATAAATTTAATATT
1 TATTAAATTTATTAAATTATTATAAAAACAATTAAAATATTAAAATGATAATAAATTTAATATT
*
889561 TATTAAATTTATTAAATTATTATAAAAACAATTAAAATATTAAAATGATAATAAATTTAATAAT
1 TATTAAATTTATTAAATTATTATAAAAACAATTAAAATATTAAAATGATAATAAATTTAATATT
889625 TATT
1 TATT
889629 TTACCATAAT
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 128 1.00
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (64 bp):
TATTAAATTTATTAAATTATTATAAAAACAATTAAAATATTAAAATGATAATAAATTTAATATT
Found at i:891312 original size:2 final size:2
Alignment explanation
Indices: 891305--891344 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
891295 CAAGGAATTA
891305 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
891345 TTTCAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:891330 original size:15 final size:15
Alignment explanation
Indices: 891305--891344 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
891295 CAAGGAATTA
891305 ATATA-TATATATAT
1 ATATATTATATATAT
891319 ATATATTATATATAT
1 ATATATTATATATAT
891334 ATATATTATAT
1 ATATATTATAT
891345 TTTCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATTATATATAT
Found at i:898982 original size:64 final size:63
Alignment explanation
Indices: 898895--899055 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
898885 TTATTTAAGG
* * * * * *
898895 TGCATCGATGCACATGCAATGCATCGATGCAT-TAATTTAAAAAGAAAACATTGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATAGAATAGGATTTA
* * *
898959 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATAGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATAGAATAGGATTTA
*
899023 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
899056 ACCTCCATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.72
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATAGAATAGGATTTA
Found at i:899381 original size:30 final size:25
Alignment explanation
Indices: 899320--899375 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
899310 ATGATAGTAT
899320 TTCATATTATGATATATGACATGAA
1 TTCATATTATGATATATGACATGAA
899345 TTCATATTATGATATATGACATGAA
1 TTCATATTATGATATATGACATGAA
899370 TTCATA
1 TTCATA
899376 CCATATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (25 bp):
TTCATATTATGATATATGACATGAA
Found at i:899766 original size:103 final size:103
Alignment explanation
Indices: 899541--899758 Score: 402
Period size: 103 Copynumber: 2.1 Consensus size: 103
899531 GTAGAGGGTC
899541 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
899606 TTGATTCTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATTCTTGGCATATGTATATGATTCTTAAAGAATGA
*
899644 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
899709 TTGA-TCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATTC-TTGGCATATGTATATGATTCTTAAAGAATGA
899747 TATGTGGTCCTT
1 TATGTGGTCCTT
899759 ATGGACATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
102 2 0.02
103 109 0.98
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATTCTTGGCATATGTATATGATTCTTAAAGAATGA
Found at i:899809 original size:23 final size:22
Alignment explanation
Indices: 899775--899837 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 22
899765 ATTATTATAT
899775 GGCACTACGGTGCAATTCTACGC
1 GGCACTA-GGTGCAATTCTACGC
* *
899798 GGCACTCAGGTGCAATTCTATGT
1 GGCACT-AGGTGCAATTCTACGC
899821 GGCACTTAGGTGCAATT
1 GGCAC-TAGGTGCAATT
899838 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 34 0.94
24 2 0.06
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (22 bp):
GGCACTAGGTGCAATTCTACGC
Found at i:899842 original size:23 final size:23
Alignment explanation
Indices: 899765--899842 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
899755 CCTTATGGAC
*
899765 ATTATTATATGGCAC-TACGGTGCA
1 ATTA-TATGTGGCACTTA-GGTGCA
* * * *
899789 ATTCTACGCGGCACTCAGGTGCA
1 ATTATATGTGGCACTTAGGTGCA
*
899812 ATTCTATGTGGCACTTAGGTGCA
1 ATTATATGTGGCACTTAGGTGCA
899835 ATTATATG
1 ATTATATG
899843 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTTAGGTGCA
Found at i:905311 original size:2 final size:2
Alignment explanation
Indices: 905294--905326 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
905284 CTAAACAAAA
*
905294 AT AT TT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
905327 TTGGCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:907650 original size:15 final size:15
Alignment explanation
Indices: 907623--907673 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
907613 AAAATAAATT
*
907623 TTAAAGTTAGAGTGA
1 TTAAAGTTAGAGTAA
907638 TTAAA-TTAGGAGTAA
1 TTAAAGTTA-GAGTAA
907653 TTAGAAAGTTA-AGTAA
1 TT--AAAGTTAGAGTAA
907669 TTAAA
1 TTAAA
907674 TTTAAAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 6 0.19
15 12 0.39
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
TTAAAGTTAGAGTAA
Found at i:921484 original size:16 final size:16
Alignment explanation
Indices: 921465--921505 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
921455 AGATTCTACT
921465 TCAGAAAATTGCGACA
1 TCAGAAAATTGCGACA
921481 TCAGAAAATTGCGACA
1 TCAGAAAATTGCGACA
921497 TCAGAAAAT
1 TCAGAAAAT
921506 CCTGCAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (16 bp):
TCAGAAAATTGCGACA
Found at i:922317 original size:20 final size:20
Alignment explanation
Indices: 922288--922325 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
922278 GTTGATCGGC
* *
922288 TGTTTTGGTACTGTAATTCT
1 TGTTTAGGTACTGCAATTCT
922308 TGTTTAGGTACTGCAATT
1 TGTTTAGGTACTGCAATT
922326 GATCAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.50
Consensus pattern (20 bp):
TGTTTAGGTACTGCAATTCT
Found at i:922771 original size:14 final size:15
Alignment explanation
Indices: 922752--922784 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
922742 TTCAATAATC
922752 ATTGCAGAAATCT-A
1 ATTGCAGAAATCTGA
*
922766 ATTGCAGGAATCTGA
1 ATTGCAGAAATCTGA
922781 ATTG
1 ATTG
922785 TGTTGCCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (15 bp):
ATTGCAGAAATCTGA
Found at i:930772 original size:78 final size:78
Alignment explanation
Indices: 930654--931083 Score: 238
Period size: 78 Copynumber: 5.6 Consensus size: 78
930644 CGCTTTGCAG
* * * * * * * *
930654 CAGAAAAAGGCATCATTCTCCGATGTTAAAAGCGTCATCATGGAAGATACCAAGTCGAAACGGGA
1 CAGAAGAAGGTATCATTCTCTGATGTTGAAAGCATAATCATGGAAGATACCAAGTCAAAACCGGA
930719 GATTGGTCCTAAC
66 GATTGGTCCTAAC
* * ** * * * *
930732 CAGAAGAAGGTATCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAA-T-TAACCCAA
1 CAGAAGAAGGTATCATTCTCTGATGTTGAAAGCATAATCATGGAAGATAC-CAAGTCAAAACC-G
** *
930795 GAGATCAGT-TTGAAC
64 GAGATTGGTCCT-AAC
* ** * * * *
930810 CAG-A-AA-GTCTCATTCTCTGATGTT-AAGAGTGTCATGATGGTAGATACCGAGTCAAAACCGG
1 CAGAAGAAGGTATCATTCTCTGATGTTGAA-AGCATAATCATGGAAGATACCAAGTCAAAACCGG
* *
930871 AGATTGGTCCGAAA
65 AGATTGGTCCTAAC
* * * ** * ** *
930885 CAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAA-TCAACCCCAG
1 CAGAAGAAGGTATCATTCTCTGATGTTGAAAGCATAATCATGGAAGATAC-CAAGTCAAAACCGG
** *
930949 AGATCAGT-TTGAAC
65 AGATTGGTCCT-AAC
* * ** * * *
930963 C---AGAAGGTCTCATTCTCCGATGTT-AAGAGTGTCATGATGGAAGATACCGAGTCAAAACCGG
1 CAGAAGAAGGTATCATTCTCTGATGTTGAA-AGCATAATCATGGAAGATACCAAGTCAAAACCGG
*
931024 AGATTGGTCCGAAC
65 AGATTGGTCCTAAC
* * * *
931038 CAGAAGAAGTTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAG
1 CAGAAGAAGGTATCATTCTCTGATGTTGAAAGCATAATCATGGAAG
931084 GCACTGAATC
Statistics
Matches: 246, Mismatches: 86, Indels: 40
0.66 0.23 0.11
Matches are distributed among these distances:
74 6 0.02
75 91 0.37
76 7 0.03
77 7 0.03
78 128 0.52
79 7 0.03
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (78 bp):
CAGAAGAAGGTATCATTCTCTGATGTTGAAAGCATAATCATGGAAGATACCAAGTCAAAACCGGA
GATTGGTCCTAAC
Found at i:930874 original size:75 final size:74
Alignment explanation
Indices: 930666--931195 Score: 265
Period size: 75 Copynumber: 6.9 Consensus size: 74
930656 GAAAAAGGCA
* * * * * *
930666 TCATTCTCCGATGTTAAAAGCGTCATCATGGAAGATACC-AAGTCGAAACGGGAGATTGGTCCT-
1 TCATTCTCTGATGTT-AAAGTGTCATCATGGAAGATACCGAA-TCAAAACCGGAGATTAGT-TTG
*
930729 AACCAGAAGAAGGTA
63 AACCAG-A-AA-GTC
* ** * * ** * * * * *
930744 TCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAAT-TAACCCAAGAGATCAGTTTGA
1 TCATTCTCTGATGTT-AAAGTGTCATCATGGAAGATACCGAATCAAAACC-GGAGATTAGTTTGA
930808 ACCAGAAAGTC
64 ACCAGAAAGTC
* * * * **
930819 TCATTCTCTGATGTTAAGAGTGTCATGATGGTAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
1 TCATTCTCTGATGTTAA-AGTGTCATCATGGAAGATACCGAATCAAAACCGGAGATTAGTTTGAA
* *
930884 ACAGAAGAAGGTT
65 CCAG-A-AA-GTC
* ** * * ** * ** * *
930897 TCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCCCAGAGATCAGTTTGAA
1 TCATTCTCTGATGTT-AAAGTGTCATCATGGAAGATACCGAATCAAAACCGGAGATTAGTTTGAA
*
930962 CCAGAAGGTC
65 CCAGAAAGTC
* * * * **
930972 TCATTCTCCGATGTTAAGAGTGTCATGATGGAAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
1 TCATTCTCTGATGTTAA-AGTGTCATCATGGAAGATACCGAATCAAAACCGGAGATTAGTTTGAA
*
931037 CCAGAAGAAGTTT
65 CCAG-A-AAG-TC
* ** * * ** * ** * *
931050 TCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAATCCCAGACATTAGTTTGAA
1 TCATTCTCTGATGTT-AAAGTGTCATCATGGAAGATACCGAATCAAAACCGGAGATTAGTTTGAA
*
931115 CCAGAAGGTC
65 CCAGAAAGTC
* * * * * **
931125 TCATTCTCCGATGTTAAAAGTGTCATCATGGACGATACCGATTCGAAACCGGAGATTGGTTCCAA
1 TCATTCTCTGATGTT-AAAGTGTCATCATGGAAGATACCGAATCAAAACCGGAGATTAGTTTGAA
931190 CCAGAA
65 CCAGAA
931196 GATGGTTACG
Statistics
Matches: 320, Mismatches: 118, Indels: 31
0.68 0.25 0.07
Matches are distributed among these distances:
74 4 0.01
75 146 0.46
76 11 0.03
77 11 0.03
78 142 0.44
79 6 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (74 bp):
TCATTCTCTGATGTTAAAGTGTCATCATGGAAGATACCGAATCAAAACCGGAGATTAGTTTGAAC
CAGAAAGTC
Found at i:930891 original size:153 final size:152
Alignment explanation
Indices: 930666--931222 Score: 855
Period size: 153 Copynumber: 3.6 Consensus size: 152
930656 GAAAAAGGCA
* * * * *
930666 TCATTCTCCGATGTTAAAAGCGTCATCATGGAAGATACCAAGTCGAAACGGGAGATTGGTCCTAA
1 TCATTCTCCGATGTTAAAAGTGTCATCATGGAAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
* *
930731 CCAGAAGAAGGTATCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATTAACCCAAG
66 CCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC-AG
*
930796 AGATCAGTTTGAACCAGAAAGTC
130 AGATCAGTTTGAACCAGAAGGTC
* * * *
930819 TCATTCTCTGATGTTAAGAGTGTCATGATGGTAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
1 TCATTCTCCGATGTTAAAAGTGTCATCATGGAAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
*
930884 ACAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCCCAG
66 CCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAA-CCCAG
930949 AGATCAGTTTGAACCAGAAGGTC
130 AGATCAGTTTGAACCAGAAGGTC
* *
930972 TCATTCTCCGATGTTAAGAGTGTCATGATGGAAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
1 TCATTCTCCGATGTTAAAAGTGTCATCATGGAAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
*
931037 CCAGAAGAAGTTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAATCCCAG
66 CCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAA-CCCAG
* *
931102 ACATTAGTTTGAACCAGAAGGTC
130 AGATCAGTTTGAACCAGAAGGTC
* * *
931125 TCATTCTCCGATGTTAAAAGTGTCATCATGGACGATACCGATTCGAAACCGGAGATTGGTTCC-A
1 TCATTCTCCGATGTTAAAAGTGTCATCATGGAAGATACCGAGTCAAAACCGGAGATTGG-TCCGA
* * *
931189 ACCAGAAGATGGTTACGTTCTCCGATGTTGAAAG
65 ACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAG
931223 GACTGAATCA
Statistics
Matches: 373, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
153 367 0.98
154 6 0.02
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (152 bp):
TCATTCTCCGATGTTAAAAGTGTCATCATGGAAGATACCGAGTCAAAACCGGAGATTGGTCCGAA
CCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCCAGA
GATCAGTTTGAACCAGAAGGTC
Found at i:931116 original size:78 final size:77
Alignment explanation
Indices: 930729--931144 Score: 310
Period size: 75 Copynumber: 5.4 Consensus size: 77
930719 GATTGGTCCT
* *
930729 AACCAGAAGAAGGTATCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAAT-TAACCC
1 AACCAGAAGAA-GTCTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAAACCC
*
930793 AAGAGATCAGTTTG
65 -AGAGATTAGTTTG
* ** * * * * ** * * *
930807 AACCAG-A-AAGTCTCATTCTCTGATGTT-AAGAGTGTCATGATGGTAGATACCGAGTCAAAACC
1 AACCAGAAGAAGTCTCGTTCTCTGATGTTGAA-AGCATAATCATTGAAGGCACTGAATCAAACCC
* * **
930869 GGAGATTGGTCCG
65 AGAGATTAGTTTG
* * *
930882 AAACAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCCC
1 AACCAGAAGAA-GTCTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAAACCC
*
930947 AGAGATCAGTTTG
65 AGAGATTAGTTTG
* * ** * * * ** * * *
930960 AACCAGAAG--GTCTCATTCTCCGATGTT-AAGAGTGTCATGATGGAAGATACCGAGTCAAAACC
1 AACCAGAAGAAGTCTCGTTCTCTGATGTTGAA-AGCATAATCATTGAAGGCACTGAATCAAACCC
* * **
931022 GGAGATTGGTCCG
65 AGAGATTAGTTTG
* *
931035 AACCAGAAGAAGTTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAATCCC
1 AACCAGAAGAAG-TCTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAAACCC
*
931100 AGACATTAGTTTG
65 AGAGATTAGTTTG
* * *
931113 AACCAGAAG--GTCTCATTCTCCGATGTTAAAAG
1 AACCAGAAGAAGTCTCGTTCTCTGATGTTGAAAG
931145 TGTCATCATG
Statistics
Matches: 245, Mismatches: 82, Indels: 25
0.70 0.23 0.07
Matches are distributed among these distances:
74 4 0.02
75 115 0.47
76 8 0.03
77 4 0.02
78 110 0.45
79 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (77 bp):
AACCAGAAGAAGTCTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAAACCCA
GAGATTAGTTTG
Found at i:940579 original size:16 final size:16
Alignment explanation
Indices: 940558--940591 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
940548 CAAAGAAGTG
940558 CACATTTTTCAT-ATTT
1 CACATTTTT-ATCATTT
940574 CACATTTTTATCATTT
1 CACATTTTTATCATTT
940590 CA
1 CA
940592 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (16 bp):
CACATTTTTATCATTT
Found at i:940598 original size:2 final size:2
Alignment explanation
Indices: 940591--940624 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
940581 TTATCATTTC
940591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
940625 GCAAGAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:943409 original size:18 final size:18
Alignment explanation
Indices: 943369--943410 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
943359 ATTATTTTAT
*
943369 AATAAACATTAAAAAATT
1 AATAAACATTAAAAAATA
*
943387 CATAAACCATT-AAAAATA
1 AATAAA-CATTAAAAAATA
943405 AATAAA
1 AATAAA
943411 ATAGATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAAACATTAAAAAATA
Found at i:954897 original size:27 final size:27
Alignment explanation
Indices: 954859--954936 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
954849 CGCGAGTTAC
954859 TCGGTCAAAGCTCGATAAATACTCTAT
1 TCGGTCAAAGCTCGATAAATACTCTAT
*
954886 TCGGTCAAAGCTCAATAAATACTCTAT
1 TCGGTCAAAGCTCGATAAATACTCTAT
954913 TCGGTCAAAGCTCGATAAATACTC
1 TCGGTCAAAGCTCGATAAATACTC
954937 GAATGGATTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (27 bp):
TCGGTCAAAGCTCGATAAATACTCTAT
Found at i:957085 original size:39 final size:39
Alignment explanation
Indices: 957039--957133 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 39
957029 AATTTATATT
957039 ATTAAAATATATTATTT-AAT-TATTAAAAATAAAAAATA
1 ATTAAAATATATTATTTAAATGT-TTAAAAATAAAAAATA
* *
957077 ATCTAAAATATATTAATTTAAATGTTTAAATATAATAAATA
1 AT-TAAAATATATT-ATTTAAATGTTTAAAAATAAAAAATA
957118 ATTATAAATAT-TTATT
1 ATTA-AAATATATTATT
957134 AGAAAATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
38 2 0.04
39 14 0.28
40 8 0.16
41 25 0.50
42 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (39 bp):
ATTAAAATATATTATTTAAATGTTTAAAAATAAAAAATA
Found at i:959744 original size:42 final size:42
Alignment explanation
Indices: 959659--959747 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
959649 CGGCGGCGGC
* *
959659 GGAGGTGGTGGTGTACATTTCGGTACAGGTGGGGGAGGAGGT
1 GGAGGTGGTGGTGTACATTTCGGTACAGGAGGCGGAGGAGGT
* ** * *
959701 GGAGGTGGTGGTGTACATTTTGGTTTAGGAGGCGGTGGTGGT
1 GGAGGTGGTGGTGTACATTTCGGTACAGGAGGCGGAGGAGGT
959743 GGAGG
1 GGAGG
959748 AGGAGGAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.15, C:0.06, G:0.53, T:0.27
Consensus pattern (42 bp):
GGAGGTGGTGGTGTACATTTCGGTACAGGAGGCGGAGGAGGT
Found at i:959749 original size:3 final size:3
Alignment explanation
Indices: 959743--959789 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
959733 CGGTGGTGGT
* * * *
959743 GGA GGA GGA GGA GGA GGC GGT GGT GGT GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
959790 TGGTGGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.23, C:0.02, G:0.68, T:0.06
Consensus pattern (3 bp):
GGA
Found at i:959753 original size:21 final size:21
Alignment explanation
Indices: 959740--959789 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
959730 AGGCGGTGGT
959740 GGTGGAGGAGGAGGAGGAGGC
1 GGTGGAGGAGGAGGAGGAGGC
* * *
959761 GGTGGTGGTGGAGGAGGAGGA
1 GGTGGAGGAGGAGGAGGAGGC
*
959782 GGAGGAGG
1 GGTGGAGG
959790 TGGTGGTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.68, T:0.08
Consensus pattern (21 bp):
GGTGGAGGAGGAGGAGGAGGC
Found at i:959757 original size:27 final size:27
Alignment explanation
Indices: 959727--959822 Score: 138
Period size: 27 Copynumber: 3.6 Consensus size: 27
959717 ATTTTGGTTT
*
959727 AGGAGGCGGTGGTGGTGGAGGAGGAGG
1 AGGAGGAGGTGGTGGTGGAGGAGGAGG
*
959754 AGGAGGCGGTGGTGGTGGAGGAGGAGG
1 AGGAGGAGGTGGTGGTGGAGGAGGAGG
* *
959781 AGGAGGAGGTGGTGGTGGTGGCGGAGG
1 AGGAGGAGGTGGTGGTGGAGGAGGAGG
* *
959808 CGGCGGAGGTGGTGG
1 AGGAGGAGGTGGTGG
959823 GGGAAGTTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.16, C:0.05, G:0.67, T:0.12
Consensus pattern (27 bp):
AGGAGGAGGTGGTGGTGGAGGAGGAGG
Found at i:960292 original size:21 final size:21
Alignment explanation
Indices: 960268--960312 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
960258 AAATTACTCA
*
960268 TTTAGTACTTAAACTATCAGT
1 TTTAGTACCTAAACTATCAGT
* *
960289 TTTAGTACCTAAACTTTCATT
1 TTTAGTACCTAAACTATCAGT
960310 TTT
1 TTT
960313 CTAAAATCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAGT
Found at i:965164 original size:59 final size:60
Alignment explanation
Indices: 965101--965234 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
965091 TGAATATTTT
* * *
965101 AATTTTATCATCAAACTATAATC-TCATTTTAAATTAGTCCTTAAATGTTTAAA-CATTCC
1 AATTTTATCCTCAAACTATAATCATCATTTTAAATTAGTACTCAAATGTTTAAATC-TTCC
* * * * * *
965160 AATTTAATCCTTAAATTATGATCATCATTTTAAATTGGTACTCAAATTTTTAAATCTTCC
1 AATTTTATCCTCAAACTATAATCATCATTTTAAATTAGTACTCAAATGTTTAAATCTTCC
965220 AATTTTATCCTCAAA
1 AATTTTATCCTCAAA
965235 TTCATCCAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 18 0.29
60 43 0.69
61 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (60 bp):
AATTTTATCCTCAAACTATAATCATCATTTTAAATTAGTACTCAAATGTTTAAATCTTCC
Found at i:965624 original size:60 final size:59
Alignment explanation
Indices: 965551--965677 Score: 191
Period size: 60 Copynumber: 2.1 Consensus size: 59
965541 AATAAATACA
* **
965551 TAGAATGAAGCTAATTGTTTGTGACGAAATTGAAATGTTCAAAAAGTTTGGGGACTAATT
1 TAGAATGAAGCTAATTGTTTGGGACGAAATTGAAATGTTC-AAAAGTTTAAGGACTAATT
* * *
965611 TAGAATGAAGCTAATTGTTTGGGATGAAATTGAAATGTTCAAGAGTTTAATGACTAATT
1 TAGAATGAAGCTAATTGTTTGGGACGAAATTGAAATGTTCAAAAGTTTAAGGACTAATT
965670 TAGAATGA
1 TAGAATGA
965678 CAACCATAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 23 0.38
60 38 0.62
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (59 bp):
TAGAATGAAGCTAATTGTTTGGGACGAAATTGAAATGTTCAAAAGTTTAAGGACTAATT
Found at i:975576 original size:31 final size:31
Alignment explanation
Indices: 975541--975646 Score: 151
Period size: 31 Copynumber: 3.5 Consensus size: 31
975531 TTAGGGAAAA
975541 GAAACTCAGGGACTAATATGGGAAAAATAGC
1 GAAACTCAGGGACTAATATGGGAAAAATAGC
**
975572 GAAACTCAGGGACTAATA-GGGGGAAATAGC
1 GAAACTCAGGGACTAATATGGGAAAAATAGC
* *
975602 GAAACTCAGAGACTAATATGGGAAAAGTAGC
1 GAAACTCAGGGACTAATATGGGAAAAATAGC
* *
975633 TAAAATCAGGGACT
1 GAAACTCAGGGACT
975647 GAGTCTTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
30 27 0.42
31 38 0.58
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.16
Consensus pattern (31 bp):
GAAACTCAGGGACTAATATGGGAAAAATAGC
Found at i:975601 original size:30 final size:30
Alignment explanation
Indices: 975541--975646 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
975531 TTAGGGAAAA
*
975541 GAAACTCAGGGACTAATATGGGAAAAATAGC
1 GAAACTCAGGGACTAATA-GGGGAAAATAGC
*
975572 GAAACTCAGGGACTAATAGGGGGAAATAGC
1 GAAACTCAGGGACTAATAGGGGAAAATAGC
* *
975602 GAAACTCAGAGACTAATATGGGAAAAGTAGC
1 GAAACTCAGGGACTAATAGGGGAAAA-TAGC
* *
975633 TAAAATCAGGGACT
1 GAAACTCAGGGACT
975647 GAGTCTTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
30 33 0.50
31 33 0.50
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.16
Consensus pattern (30 bp):
GAAACTCAGGGACTAATAGGGGAAAATAGC
Found at i:979446 original size:18 final size:18
Alignment explanation
Indices: 979423--979459 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
979413 ACCACATCAT
979423 CGTCCACGAAGCCAGCAG
1 CGTCCACGAAGCCAGCAG
*
979441 CGTCCACGAAGGCAGCAG
1 CGTCCACGAAGCCAGCAG
979459 C
1 C
979460 AACAAAGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.38, G:0.30, T:0.05
Consensus pattern (18 bp):
CGTCCACGAAGCCAGCAG
Found at i:983973 original size:52 final size:52
Alignment explanation
Indices: 983890--983988 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
983880 TTTAAATTAG
**
983890 GTCATTTCGGGGTTCAATTTTATTCGGGTATATAGTAAGTCGAGTCAAGTCA
1 GTCATTTCGGGGTTCAATTTTATTCAAGTATATAGTAAGTCGAGTCAAGTCA
* * * *
983942 GTCATTTTGGGTTTCGATTTTATTCAAGTATATAGTAAGTCGGGTCA
1 GTCATTTCGGGGTTCAATTTTATTCAAGTATATAGTAAGTCGAGTCA
983989 GTTTGGGTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (52 bp):
GTCATTTCGGGGTTCAATTTTATTCAAGTATATAGTAAGTCGAGTCAAGTCA
Found at i:989146 original size:32 final size:32
Alignment explanation
Indices: 989105--989166 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
989095 TTCAGGGCCC
989105 GTTTGGAATTAACTTTTAAAAAATAACTTTCA
1 GTTTGGAATTAACTTTTAAAAAATAACTTTCA
*
989137 GTTTGGAATTAACTTTTGAAAAATAACTTT
1 GTTTGGAATTAACTTTTAAAAAATAACTTT
989167 TAAAAGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (32 bp):
GTTTGGAATTAACTTTTAAAAAATAACTTTCA
Found at i:991461 original size:2 final size:2
Alignment explanation
Indices: 991454--991478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
991444 AGCAATCGAA
991454 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
991479 ATGTGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:994857 original size:115 final size:114
Alignment explanation
Indices: 994610--994948 Score: 570
Period size: 115 Copynumber: 2.9 Consensus size: 114
994600 TGTTGGCAAT
* *
994610 ATTGTTTTATATGAAAAAAATGAAGCTTGATTGTGGTTTTCTTATGTTTGTTTCAGAAATTTAGG
1 ATTGTTTTATTTGAAAAAAATGAAGCTTGATTATGGTTTTCTTATGTTTGTTTCAGAAATTTAGG
*
994675 AGAATTGGGATGTTTCCAATCGTTCTTGCCTCTGAATAGCATGGTCAAA
66 AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
994724 ATTGTTTTATTTGAAAAAAAATGAAGCTTGATTATGGTTTTCTTATGTTTGTTTCAGAAATTTAG
1 ATTGTTTTATTTG-AAAAAAATGAAGCTTGATTATGGTTTTCTTATGTTTGTTTCAGAAATTTAG
*
994789 GAGAATTGGGATGTTTTCCAATCATTCTAGCCTCTGAATAGCATGGTCAAA
65 GAGAATTGGGATG-TTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
* * * *
994840 ATTGATTTATTTGAAAAAAATGAAGCTTGATTATGGTTTTCTTTTTGTTTTTTTCAGAAATTTTG
1 ATTGTTTTATTTGAAAAAAATGAAGCTTGATTATGGTTTTC-TTATGTTTGTTTCAGAAATTTAG
*
994905 GAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCATG
65 GAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATG
994949 ATTCCCACAG
Statistics
Matches: 212, Mismatches: 10, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
114 12 0.06
115 120 0.57
116 80 0.38
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (114 bp):
ATTGTTTTATTTGAAAAAAATGAAGCTTGATTATGGTTTTCTTATGTTTGTTTCAGAAATTTAGG
AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
Found at i:996444 original size:14 final size:14
Alignment explanation
Indices: 996425--996452 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
996415 TTGATTGAAA
996425 TTGAATAACAAATG
1 TTGAATAACAAATG
996439 TTGAATAACAAATG
1 TTGAATAACAAATG
996453 AATTTGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
TTGAATAACAAATG
Found at i:998377 original size:18 final size:18
Alignment explanation
Indices: 998354--998398 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
998344 AACATTCTCA
998354 GTAATCTTATTCCCACCG
1 GTAATCTTATTCCCACCG
*
998372 GTAATCTTATTCCCGCCG
1 GTAATCTTATTCCCACCG
*
998390 ATAATCTTA
1 GTAATCTTA
998399 CATTCCGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (18 bp):
GTAATCTTATTCCCACCG
Found at i:999538 original size:21 final size:21
Alignment explanation
Indices: 999514--999558 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
999504 AAACTACGTG
*
999514 TTTAATATTTAAATTATTAAT
1 TTTAATATCTAAATTATTAAT
* *
999535 TTTAGTATCTAAATTTTTAAT
1 TTTAATATCTAAATTATTAAT
999556 TTT
1 TTT
999559 TCCTAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAATATCTAAATTATTAAT
Found at i:999820 original size:32 final size:31
Alignment explanation
Indices: 999747--999820 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
999737 TTTTTAACCA
* * *
999747 TGAGTAGTAAAATGAAACAAAAATTAAACTT
1 TGAGTACTAAAACGAAACAAAAATAAAACTT
* *
999778 T-ACGTACTAAAACGAACCAAAAATAAATAGTT
1 TGA-GTACTAAAACGAAACAAAAATAAA-ACTT
999810 TGAGTACTAAA
1 TGAGTACTAAA
999821 TACGTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.03
31 21 0.60
32 12 0.34
33 1 0.03
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (31 bp):
TGAGTACTAAAACGAAACAAAAATAAAACTT
Found at i:1001865 original size:11 final size:11
Alignment explanation
Indices: 1001849--1001879 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1001839 GTGAGGTAGT
1001849 AAAATAAAATG
1 AAAATAAAATG
1001860 AAAATAAAATG
1 AAAATAAAATG
1001871 AAAACTAAA
1 AAAA-TAAA
1001880 CGTTAGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:1003469 original size:20 final size:20
Alignment explanation
Indices: 1003444--1003488 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1003434 GTCATCTAAT
* *
1003444 TTTTTAAACCTCAGATCGGA
1 TTTTTAAACCCCAGACCGGA
1003464 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
1003484 TTTTT
1 TTTTT
1003489 TTCCAGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:1003627 original size:19 final size:20
Alignment explanation
Indices: 1003588--1003628 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1003578 CGGTTATACT
* *
1003588 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTTAAAAAAACCG
1003608 ATCCGG-TTTAAAAAAACCG
1 ATCCGGTTTTAAAAAAACCG
1003627 AT
1 AT
1003629 TTTTCCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCCGGTTTTAAAAAAACCG
Found at i:1009317 original size:44 final size:44
Alignment explanation
Indices: 1009217--1009442 Score: 231
Period size: 44 Copynumber: 5.1 Consensus size: 44
1009207 ATTGAAAAAA
* * * * *
1009217 TGATATCCCCATCTAAGTCAATCCAAATATTATCTAAACAACAAG
1 TGATATACCCATCTAAGCCGATCCAAATA-TAACTAAACGACAAG
* *
1009262 TGATATCCCCATCTAAGCCGATCCAAGTATAACTAAACGACAAG
1 TGATATACCCATCTAAGCCGATCCAAATATAACTAAACGACAAG
* * * * *
1009306 TGAAAAACCCATCTAAGACAATCCATATATAACTAAACGACAAG
1 TGATATACCCATCTAAGCCGATCCAAATATAACTAAACGACAAG
* * * * *
1009350 TGATGTACCCAGCTGAA-CTTG-TCCAAATATAACTAAACAACACG
1 TGATATACCCATCT-AAGC-CGATCCAAATATAACTAAACGACAAG
* * *
1009394 TGATATCCCCTTCTAAGCCGATCCAAATATAACTAAGCGACAAG
1 TGATATACCCATCTAAGCCGATCCAAATATAACTAAACGACAAG
1009438 TGATA
1 TGATA
1009443 GCCACTTTTA
Statistics
Matches: 147, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
43 3 0.02
44 116 0.79
45 28 0.19
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.23
Consensus pattern (44 bp):
TGATATACCCATCTAAGCCGATCCAAATATAACTAAACGACAAG
Found at i:1020760 original size:27 final size:28
Alignment explanation
Indices: 1020720--1020777 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
1020710 TCCTAACGTA
*
1020720 AAATCTTATATTATAAATCT-TAAACCCT
1 AAATCATATATTAT-AATCTCTAAACCCT
* *
1020748 AAATCATA-ATTATTATCTCTAAACTCT
1 AAATCATATATTATAATCTCTAAACCCT
1020775 AAA
1 AAA
1020778 CCTTAAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 15 0.58
28 7 0.27
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATCATATATTATAATCTCTAAACCCT
Found at i:1023412 original size:2 final size:2
Alignment explanation
Indices: 1023405--1023433 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1023395 TAGCTCCATG
1023405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1023434 ATACTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1026645 original size:16 final size:16
Alignment explanation
Indices: 1026606--1026647 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
1026596 ACCCGAAAGT
1026606 TCCGGGTACCCAAAAA
1 TCCGGGTACCCAAAAA
*
1026622 T-CGAGTACCCAAAAA
1 TCCGGGTACCCAAAAA
1026637 TCCGGGTACCC
1 TCCGGGTACCC
1026648 GAATTTGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.14
Consensus pattern (16 bp):
TCCGGGTACCCAAAAA
Found at i:1027766 original size:30 final size:32
Alignment explanation
Indices: 1027730--1027788 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
1027720 ATTTTAAAAT
*
1027730 AAATTAA-ACTTTAAGTACTAAA-ATATATCA
1 AAATTAATACTTTAAATACTAAATATATATCA
*
1027760 AAATTAATAGTTTAAATACTAAATATATA
1 AAATTAATACTTTAAATACTAAATATATA
1027789 ATTTATCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 13 0.52
32 5 0.20
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (32 bp):
AAATTAATACTTTAAATACTAAATATATATCA
Found at i:1028433 original size:15 final size:15
Alignment explanation
Indices: 1028381--1028433 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1028371 ATATGATTAC
*
1028381 TTTTTTTAAATTTAG
1 TTTTTATAAATTTAG
*
1028396 TTTTATATTAATTT-G
1 TTTT-TATAAATTTAG
*
1028411 TATATTATAAATTTAG
1 T-TTTTATAAATTTAG
1028427 TTTTTAT
1 TTTTTAT
1028434 GTTAATTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTATAAATTTAG
Found at i:1028452 original size:31 final size:31
Alignment explanation
Indices: 1028387--1028455 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
1028377 TTACTTTTTT
*
1028387 TAAATTTAGTTTTATATTAATTTGTATATTA
1 TAAATTTAGTTTTATATTAATTTGCATATTA
*
1028418 TAAATTTAGTTTTTATGTTAATTT-CA-ATTCA
1 TAAATTTAG-TTTTATATTAATTTGCATATT-A
1028449 TAAATTT
1 TAAATTT
1028456 CTTTTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 18 0.53
32 13 0.38
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (31 bp):
TAAATTTAGTTTTATATTAATTTGCATATTA
Found at i:1033117 original size:2 final size:2
Alignment explanation
Indices: 1033112--1033161 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1033102 TATATGTTTA
1033112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1033154 AT AT AT AT
1 AT AT AT AT
1033162 GGTTTATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1033184 original size:31 final size:31
Alignment explanation
Indices: 1033146--1033228 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 31
1033136 ATATATATAT
1033146 ATATATATATATATATGGTTTATTGATGTTG
1 ATATATATATATATATGGTTTATTGATGTTG
*
1033177 --ATATATATATAT-TGGTTTATTGTTGTTG
1 ATATATATATATATATGGTTTATTGATGTTG
* *
1033205 ATGTA-A-ATGATATATGATTTATTG
1 ATATATATAT-ATATATGGTTTATTG
1033229 TTGTAATGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 17 0.38
29 17 0.38
30 11 0.24
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (31 bp):
ATATATATATATATATGGTTTATTGATGTTG
Found at i:1033238 original size:29 final size:31
Alignment explanation
Indices: 1033183--1033240 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1033173 GTTGATATAT
* *
1033183 ATATATTGGTTTATTGTTGTTGATGTAAATG
1 ATATATTGATTTATTGTTGTTAATGTAAATG
1033214 ATATA-TGATTTATTGTTG-TAATGTAAA
1 ATATATTGATTTATTGTTGTTAATGTAAA
1033241 CTAACCATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 12 0.48
31 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (31 bp):
ATATATTGATTTATTGTTGTTAATGTAAATG
Found at i:1035924 original size:15 final size:15
Alignment explanation
Indices: 1035883--1035925 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1035873 TTAACTTAGT
*
1035883 AAATATAATTTAATA
1 AAATAAAATTTAATA
* *
1035898 AAATCAAGTTTAATA
1 AAATAAAATTTAATA
*
1035913 AGATAAAATTTAA
1 AAATAAAATTTAA
1035926 ATTTAATTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (15 bp):
AAATAAAATTTAATA
Found at i:1036131 original size:17 final size:17
Alignment explanation
Indices: 1036109--1036149 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1036099 TTAAAAAGTA
* *
1036109 ATCATATTACTTTAATT
1 ATCATAATAATTTAATT
1036126 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
1036143 ATCATAA
1 ATCATAA
1036150 GTTTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:1046372 original size:27 final size:29
Alignment explanation
Indices: 1046317--1046372 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
1046307 TGAAGTGAAC
*
1046317 GTATAAGTTTATTTATTTATTAAATATATA
1 GTATAAGTTTA-TTATTTATTAAAAATATA
1046347 GTATAAGTTTA-T-TTTATTAAAAATAT
1 GTATAAGTTTATTATTTATTAAAAATAT
1046373 TTTTTAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 1 0.04
30 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (29 bp):
GTATAAGTTTATTATTTATTAAAAATATA
Found at i:1046921 original size:21 final size:21
Alignment explanation
Indices: 1046895--1046934 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1046885 AACCGACCGA
1046895 ACCGAATTAATTCGGTCGGCC
1 ACCGAATTAATTCGGTCGGCC
*
1046916 ACCGAATTAGTTCGGTCGG
1 ACCGAATTAATTCGGTCGG
1046935 GGAACGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
ACCGAATTAATTCGGTCGGCC
Found at i:1047336 original size:188 final size:188
Alignment explanation
Indices: 1047015--1047415 Score: 653
Period size: 188 Copynumber: 2.1 Consensus size: 188
1047005 ATAAAATTTT
* *
1047015 AAATATTAAATATAT-TATATATAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATA
1 AAATATTAAATATATATATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAATA
* *
1047079 ATTTAAGATCCAATAATTTTTAAAAATAAATCAATATTAATTAATTAAAAATTTTATATAAAATT
66 ATTTAAGATCCAATAACTTTTAAAAATAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
*
1047144 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAAC-TATTTTTTTGAATTAAA
131 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACGTATTTTTTTGAATTAAA
1047201 AAATATTAAATATATTATATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAAT
1 AAATATTAAATATA-TATATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAAT
* ** *
1047266 AATTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATT
65 AATTTAAGATCCAATAACTTTTAAAAATAAATCAATATTAATTAATTAAAAAATTTATATAAAAT
* *
1047331 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTTTGAATTATA
130 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAAC-GTATTTTTTTGAATTAAA
* *
1047391 AAATATTTAATTTATATATATATAA
1 AAATATTAAATATATATATATATAA
1047416 ATTAGAAAAT
Statistics
Matches: 198, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
186 14 0.07
187 1 0.01
188 145 0.73
189 11 0.06
190 27 0.14
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (188 bp):
AAATATTAAATATATATATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAATA
ATTTAAGATCCAATAACTTTTAAAAATAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
TTTATTTTATAATTATATATTATTTAAATTAATTATAAACGTATTTTTTTGAATTAAA
Found at i:1047348 original size:22 final size:21
Alignment explanation
Indices: 1047323--1047419 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 21
1047313 AAAAAATTTA
*
1047323 TATAAATTTTTTATTTTATAAT
1 TATAAATTATTTATTTT-TAAT
* **
1047345 TATATATTATTTA-AATTAAT
1 TATAAATTATTTATTTTTAAT
* * *
1047365 TATAAACTGTTTTTTTTTGAAT
1 TATAAATTATTTATTTTT-AAT
* *
1047387 TATAAAATATTTAATTTATATAT
1 TATAAATTATTT-ATTTTTA-AT
1047410 ATATAAATTA
1 -TATAAATTA
1047420 GAAAATTTTA
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
20 13 0.24
21 3 0.05
22 25 0.45
23 6 0.11
24 8 0.15
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (21 bp):
TATAAATTATTTATTTTTAAT
Found at i:1051351 original size:67 final size:67
Alignment explanation
Indices: 1051269--1051399 Score: 244
Period size: 67 Copynumber: 2.0 Consensus size: 67
1051259 TTACCCCTCC
*
1051269 GATTGATTAAGTCGTTTTATCATATGTAAATTCGCTCGACATTTATTCCTATTTAAATCTTATCT
1 GATTAATTAAGTCGTTTTATCATATGTAAATTCGCTCGACATTTATTCCTATTTAAATCTTATCT
1051334 CT
66 CT
*
1051336 GATTAATTAAGTCGTTTTATCATATGTAAATTCGTTCGACATTTATTCCTATTTAAATCTTATC
1 GATTAATTAAGTCGTTTTATCATATGTAAATTCGCTCGACATTTATTCCTATTTAAATCTTATC
1051400 GTATGCGAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (67 bp):
GATTAATTAAGTCGTTTTATCATATGTAAATTCGCTCGACATTTATTCCTATTTAAATCTTATCT
CT
Found at i:1061385 original size:22 final size:22
Alignment explanation
Indices: 1061360--1061459 Score: 76
Period size: 22 Copynumber: 4.4 Consensus size: 22
1061350 TTTTAAAATA
1061360 ATTTATTATAAAATATGGATTG
1 ATTTATTATAAAATATGGATTG
* ** *
1061382 ATTTATTTTAAAATAATTTATTTTA
1 ATTTATTATAAAAT-ATGGA--TTG
* * * *
1061407 AATAATT-TATTAGTATGGATTG
1 ATTTATTATA-AAATATGGATTG
*
1061429 ATTTATTTTAAAATATGGATTG
1 ATTTATTATAAAATATGGATTG
1061451 ATTTATTAT
1 ATTTATTAT
1061460 TGTAGTTGTA
Statistics
Matches: 57, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
22 38 0.67
23 5 0.09
24 5 0.09
25 9 0.16
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
ATTTATTATAAAATATGGATTG
Found at i:1061411 original size:14 final size:15
Alignment explanation
Indices: 1061105--1061417 Score: 484
Period size: 15 Copynumber: 20.5 Consensus size: 15
1061095 TAATAAGATT
1061105 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1061120 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1061135 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1061150 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1061165 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1061180 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1061195 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1061210 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1061225 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1061240 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1061255 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1061270 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1061285 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1061300 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1061315 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1061330 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1061345 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1061360 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1061379 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1061397 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1061411 ATTTATT
1 ATTTATT
1061418 AGTATGGATT
Statistics
Matches: 281, Mismatches: 10, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
14 12 0.04
15 248 0.88
16 4 0.01
17 2 0.01
18 1 0.00
19 1 0.00
20 2 0.01
21 4 0.01
22 7 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1061491 original size:80 final size:79
Alignment explanation
Indices: 1061397--1062017 Score: 586
Period size: 80 Copynumber: 7.8 Consensus size: 79
1061387 TTTTAAAATA
1061397 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1061462 TAGTTGTATGGATTG
66 TA-TTGTATGGATTG
*
1061477 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
*
1061542 ATAATTTATTAGTATGGATTG
62 AT--TGTATT-GTATGGATTG
* *
1061563 ATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
1061628 TAGTTGTATGAATTG
66 TA-TTGTATGGATTG
* * * *
1061643 ATTTATTTTAAAATAATTTATT--T-T-AAATAATTTA--TT--AATATGAATTGATTTA-T-TT
1 ATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATT
*** *
1061698 -TAAAATATGGATTA
65 GTATTGTATGGATTG
* ** **
1061712 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATT
**
1061769 GATT-TACTT-TA-AAATATGG
62 -ATTGTA-TTGTATGGAT-T-G
*
1061788 ATTGGTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAG-TTGATTTATT
1 A----TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--
*
1061852 TTAAATAATTTATTAGTATGGATTG
60 TT--AT--TGTATT-GTATGGATTG
*
1061877 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
1061942 TAGTTGTATGAATTG
66 TA-TTGTATGGATTG
*
1061957 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1062018 TTAAATAATT
Statistics
Matches: 450, Mismatches: 43, Indels: 96
0.76 0.07 0.16
Matches are distributed among these distances:
62 3 0.01
63 2 0.00
64 3 0.01
65 1 0.00
66 7 0.02
67 2 0.00
68 2 0.00
69 15 0.03
70 7 0.02
71 3 0.01
72 4 0.01
73 16 0.04
74 2 0.00
75 9 0.02
76 1 0.00
77 7 0.02
78 1 0.00
79 1 0.00
80 154 0.34
81 16 0.04
82 8 0.02
83 3 0.01
84 9 0.02
85 55 0.12
86 103 0.23
87 4 0.01
88 3 0.01
89 4 0.01
90 3 0.01
91 2 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (79 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TATTGTATGGATTG
Found at i:1061509 original size:32 final size:32
Alignment explanation
Indices: 1061467--1061606 Score: 167
Period size: 32 Copynumber: 4.7 Consensus size: 32
1061457 TATTGTAGTT
*
1061467 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
1061499 GTATGAATTGATTTATTTT-AA-AA--TA-T-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
1061525 G---G-ATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
* *
1061553 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGAATTGATTTATTTTAAATAATTTATTA
1061585 GTAT-AGATTGATTTATTTTAAA
1 GTATGA-ATTGATTTATTTTAAA
1061607 ATATGGATTG
Statistics
Matches: 94, Mismatches: 3, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
22 13 0.14
23 3 0.03
24 2 0.02
26 3 0.03
27 2 0.02
28 3 0.03
30 2 0.02
31 3 0.03
32 63 0.67
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:1061525 original size:22 final size:22
Alignment explanation
Indices: 1061500--1061542 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1061490 AATTTATTAG
1061500 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1061522 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1061543 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1061533 original size:54 final size:54
Alignment explanation
Indices: 1061468--1062032 Score: 435
Period size: 54 Copynumber: 10.6 Consensus size: 54
1061458 ATTGTAGTTG
*
1061468 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1061522 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * ***
1061575 TA---ATTTATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
* * * *
1061634 TATGAATTGATTTATTTTAAAATAATTTATT--T-T-AAATAATTTA--TT--AA
1 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* ** * ***
1061681 TATGAATTGATTTATTTTAAA-ATATGGATTA--AT---TT-A-TTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGATTGATTTATTTTA-AAA
*
1061729 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
1061783 TATGGATTGGTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
1061837 TATAG-TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * * * ***
1061889 TA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
*
1061948 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
1062002 TATTGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
1062033 TTTTAGTTGT
Statistics
Matches: 405, Mismatches: 62, Indels: 88
0.73 0.11 0.16
Matches are distributed among these distances:
43 3 0.01
44 1 0.00
45 3 0.01
46 8 0.02
47 19 0.05
48 26 0.06
49 4 0.01
50 32 0.08
51 1 0.00
52 9 0.02
53 50 0.12
54 165 0.41
55 17 0.04
56 7 0.02
57 4 0.01
58 15 0.04
59 4 0.01
60 2 0.00
61 2 0.00
62 23 0.06
63 9 0.02
64 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:1061537 original size:261 final size:257
Alignment explanation
Indices: 1061270--1061923 Score: 845
Period size: 261 Copynumber: 2.5 Consensus size: 257
1061260 TTATAAAATA
* * * *
1061270 ATTTATTATAAAATAATTTATTA-TA-AAATAATTTATTTTAAAATAATTTATTTTAAAATAATT
1 ATTTATT-TTAAATAATTTATTAGTAGGATTGATTTATTTTAAAATAATTTATTTTAAAATAATT
*
1061333 TATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGATTGATTTATTTTAAAATAA
65 TATTATAAAAT-ATTTATTTT-AAATAATTTATT-T--AGTATGGATTGATTTATTTTAAAATAA
* * *
1061398 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
125 TTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTGT
*
1061463 AGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGA
190 AGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTACTTTAAAATATGGA
1061528 TTG
255 TTG
* *
1061531 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATAATTTATTTGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTA-GGATTGATTTATTTTAAAATAATTTATTT-TA-A-AATA
* ** * * * *
1061595 ATTTATTTTAAAATATGGATTGATT-TATTATTGTAGTT-GTATGAATTGATTTATTTTAAAATA
62 ATTTATTATAAAATATTTATT--TTAAATAATT-TATTTAGTATGGATTGATTTATTTTAAAATA
1061658 ATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTG
124 ATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTG
*
1061723 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAATATGG
189 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTACTTTAAAATATGG
1061788 ATTG
254 ATTG
*
1061792 GTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGTTGATTTATTTT-AA
1 ATTTATTTTAAATAATTTATTAGTA-GGATTGATTTATTTT-AAA-ATA----ATTTATTTTAAA
* *
1061856 ATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTT-GTATGGATTGATTTATTTTAA
59 ATAATTTATTA-TA--AAAT-ATTTATTTTAAATAATTTATTTAGTATGGATTGATTTATTTTAA
1061920 AATA
120 AATA
1061924 TGGATTGATT
Statistics
Matches: 341, Mismatches: 31, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
260 14 0.04
261 201 0.59
262 13 0.04
263 15 0.04
264 24 0.07
265 21 0.06
266 32 0.09
267 8 0.02
268 13 0.04
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (257 bp):
ATTTATTTTAAATAATTTATTAGTAGGATTGATTTATTTTAAAATAATTTATTTTAAAATAATTT
ATTATAAAATATTTATTTTAAATAATTTATTTAGTATGGATTGATTTATTTTAAAATAATTTATT
TTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGT
ATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTACTTTAAAATATGGATTG
Found at i:1061598 original size:18 final size:16
Alignment explanation
Indices: 1061526--1061605 Score: 60
Period size: 14 Copynumber: 5.0 Consensus size: 16
1061516 TTAAAATATG
1061526 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
* * *
1061542 -A-TAATTTATTAGTATG
1 GATTGATTTATT-TTA-A
1061558 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
*
1061574 -A-TAATTTATTTGTATA
1 GATTGATTTATTT-TA-A
1061590 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
1061606 AATATGGATT
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
14 17 0.35
15 6 0.12
16 2 0.04
17 6 0.12
18 17 0.35
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (16 bp):
GATTGATTTATTTTAA
Found at i:1061615 original size:22 final size:22
Alignment explanation
Indices: 1061590--1061718 Score: 78
Period size: 22 Copynumber: 5.5 Consensus size: 22
1061580 TATTTGTATA
1061590 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
***
1061612 GATTGATTTATTATTGTAGTTGTATG
1 GATTGATTTA-T-TT-TA-AAATATG
* *
1061638 AATTGATTTATTTTAAAATAATT
1 GATTGATTTATTTTAAAAT-ATG
* * ** * *
1061661 TATTTTAAATAATTTATTAATATG
1 GA-TTGATTTATTTTA-AAATATG
*
1061685 AATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
*
1061707 GATTAATTTATT
1 GATTGATTTATT
1061719 ATTGTAGTTG
Statistics
Matches: 77, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
22 27 0.35
23 15 0.19
24 16 0.21
25 6 0.08
26 13 0.17
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:1061643 original size:48 final size:48
Alignment explanation
Indices: 1061583--1061749 Score: 202
Period size: 48 Copynumber: 3.5 Consensus size: 48
1061573 AATAATTTAT
*
1061583 TTGTAT-AGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAG
1 TTGTATGA-ATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAG
* *
1061631 TTGTATGAATTGATTTATTTTAAAATA---ATTTATTTTAAATAATT-TA-
1 TTGTATGAATTGATTTATTTTAAAATATGGA-TTAATTT--ATTATTGTAG
*
1061677 TTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAG
1 TT-GTATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAG
*
1061726 TTGTATGGATTGATTTATTTTAAA
1 TTGTATGAATTGATTTATTTTAAA
1061750 TAATTTATTA
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
45 1 0.01
46 7 0.07
47 31 0.31
48 52 0.51
49 9 0.09
50 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (48 bp):
TTGTATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAG
Found at i:1061672 original size:14 final size:15
Alignment explanation
Indices: 1061643--1061678 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
1061633 GTATGAATTG
1061643 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1061658 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1061672 ATTTATT
1 ATTTATT
1061679 AATATGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1061678 original size:95 final size:94
Alignment explanation
Indices: 1061563--1061758 Score: 331
Period size: 95 Copynumber: 2.1 Consensus size: 94
1061553 GTATGGATTG
** *
1061563 ATTTATTTTAAATAATTTATTTGTAT-AGATTGATTTATTTTAAAATATGGATTGATTTATTATT
1 ATTTATTTTAAATAATTTATTAATATGA-ATTGATTTATTTTAAAATATGGATTAATTTATTATT
1061627 GTAGTTGTATGAATTGATTTATTTTAAAATA
65 GTAGTTGTATGAATTGATTTATTTT-AAATA
1061658 ATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTG
1 ATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTG
*
1061723 TAGTTGTATGGATTGATTTATTTTAAATA
66 TAGTTGTATGAATTGATTTATTTTAAATA
1061752 ATTTATT
1 ATTTATT
1061759 AGTATGGATT
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
94 12 0.12
95 83 0.86
96 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (94 bp):
ATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTG
TAGTTGTATGAATTGATTTATTTTAAATA
Found at i:1061697 original size:32 final size:32
Alignment explanation
Indices: 1061520--1061701 Score: 119
Period size: 32 Copynumber: 5.7 Consensus size: 32
1061510 TTTATTTTAA
*
1061520 AATATGGATTGATTTATTTTAAATAATTTATT
1 AATATGAATTGATTTATTTTAAATAATTTATT
* *
1061552 AGTATGGATTGATTTATTTTAAATAATTTATT
1 AATATGAATTGATTTATTTTAAATAATTTATT
** **
1061584 TGTAT-AGATTGATTTATTTTAAA-ATATGGATT
1 AATATGA-ATTGATTTATTTTAAATA-ATTTATT
* * * *
1061616 GAT-T-TATT-ATTGTAGTTGTATGAATTGATTTATT
1 AATATGAATTGATT-TA-TT-T-T-AAATAATTTATT
* * *
1061650 --T-TAAAATAATTTATTTTAAATAATTTATT
1 AATATGAATTGATTTATTTTAAATAATTTATT
1061679 AATATGAATTGATTTATTTTAAA
1 AATATGAATTGATTTATTTTAAA
1061702 ATATGGATTA
Statistics
Matches: 118, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
29 13 0.11
30 6 0.05
31 6 0.05
32 78 0.66
33 5 0.04
34 10 0.08
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
AATATGAATTGATTTATTTTAAATAATTTATT
Found at i:1061769 original size:32 final size:32
Alignment explanation
Indices: 1061728--1061835 Score: 128
Period size: 32 Copynumber: 3.7 Consensus size: 32
1061718 TATTGTAGTT
1061728 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1061760 GTATGGATTGATTTA-CTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1061783 -TATGGATTGGTTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1061814 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1061836 ATATAGTTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
22 13 0.21
23 3 0.05
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 3 0.05
32 35 0.56
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Done.