Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:3636645 original size:55 final size:49
Alignment explanation
Indices: 3636522--3636862 Score: 205
Period size: 48 Copynumber: 7.0 Consensus size: 49
3636512 AATAAATTAA
* * *
3636522 TATATAGGTTATAATATACTAATGAAAT-TTTCA-ATATAGTT-TATATA-
1 TATATAGG-TAT-ATATACTAATGAACTATATAATATATAGTTGTATATAC
* *
3636569 TAATATA-GTTTATATAGTAATGAACTATATAATATATAGTTTGTATACCATATAC
1 T-ATATAGGTATATATACTAATGAACTATATAATATATAG-TTG--T---ATATAC
*
3636624 TATATAGGTATATATACTAATGCACTATAT-A-ATATAGTTGTATATAC
1 TATATAGGTATATATACTAATGAACTATATAATATATAGTTGTATATAC
* * *
3636671 TA-ATAGTTTATATATACTAATGAACTACAT-A-ATATAGTTTATATATAC
1 TATATAG-GTATATATACTAATGAACTATATAATATATAG-TTGTATATAC
** ** * *
3636719 TA-AT-GAAATATATA-TAATGTAGTTATATATACCATATAGTT-TATATAT
1 TATATAGGTATATATACTAATG-AACTATATA-A-TATATAGTTGTATATAC
* * * *
3636767 TATATA-GTTTATATA-TAATAAACTATATAATGTATAGTTTTTATATAC
1 TATATAGGTATATATACTAATGAACTATATAATATATAG-TTGTATATAC
* * *
3636815 CATATA-GTTTATATACTAATGAACGACTATATATATATAGTT-TATATA
1 TATATAGGTATATATACTAATGAACTA-TATA-ATATATAGTTGTATATA
3636863 TATTATACAG
Statistics
Matches: 237, Mismatches: 31, Indels: 50
0.75 0.10 0.16
Matches are distributed among these distances:
45 18 0.08
46 26 0.11
47 47 0.20
48 56 0.24
49 28 0.12
50 13 0.05
51 8 0.03
52 3 0.01
53 6 0.03
54 11 0.05
55 21 0.09
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.43
Consensus pattern (49 bp):
TATATAGGTATATATACTAATGAACTATATAATATATAGTTGTATATAC
Found at i:3636703 original size:102 final size:101
Alignment explanation
Indices: 3636522--3636706 Score: 243
Period size: 102 Copynumber: 1.8 Consensus size: 101
3636512 AATAAATTAA
* *
3636522 TATATAGGTTATAATATACTAATGAAATTTTCAATATAGTTTATATATAATATAGTTTATATAGT
1 TATATAGGTTATAATATACTAATGAAATTATCAATATAGTTTATATATAATATA-TTTATATACT
*
3636587 AATGAACTATATAATATATAGTTTGTATACCATATAC
65 AATGAACTACATAATATATAGTTTGTATACCATATAC
* *
3636624 TATATAGG-TAT-ATATACTAATGCACTATAT-AATATAGTTGTATATACTAATAGT-TTATATA
1 TATATAGGTTATAATATACTAATGAAAT-TATCAATATAGTT-TATATA-TAATA-TATT-TATA
3636685 TACTAATGAACTACATAATATA
61 TACTAATGAACTACATAATATA
3636707 GTTTATATAT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
100 22 0.30
101 13 0.18
102 37 0.51
103 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (101 bp):
TATATAGGTTATAATATACTAATGAAATTATCAATATAGTTTATATATAATATATTTATATACTA
ATGAACTACATAATATATAGTTTGTATACCATATAC
Found at i:3636828 original size:97 final size:95
Alignment explanation
Indices: 3636535--3636880 Score: 300
Period size: 100 Copynumber: 3.5 Consensus size: 95
3636525 ATAGGTTATA
* * *
3636535 ATATACTAATGAA-AT-TTTCAATATAGTT-TATATATAATATAGTTTATATAGTAATGAACTAT
1 ATATACTAATGAAGATATAT-AATATAGTTATATATATTATATAGTTTATATACTAATGAACTAT
3636597 ATAATATATAGTTTGTATACCATATACTATATAGGTAT
65 ATAAT-TATAGTTT-T-T---ATATACTATATA-GTAT
* * * *
3636635 ATATACTAATGCA-CTATATAATATAGTTGTATATACTA-ATAGTTTATATATACTAATGAACTA
1 ATATACTAATGAAGATATATAATATAGTTATATATATTATATAG-TT-TATATACTAATGAACTA
* * *
3636698 CATAA-TATAGTTTATATATACTA-AT-GAAAT
64 TATAATTATAGTTTTTATATACTATATAG-TAT
* *
3636728 ATATA-TAATGTAGTTATATATACCATATAGTT-TATATATTATATAGTTTATATA-TAATAAAC
1 ATATACTAATGAAG--ATATATA--ATATAGTTATATATATTATATAGTTTATATACTAATGAAC
* *
3636790 TATATAATGTATAGTTTTTATATACCATATAGTTT
62 TATATAAT-TATAGTTTTTATATACTATATAGTAT
*
3636825 ATATACTAATGAACGACTATATATATATAGTTTATATATATTATACAGTTTATATA
1 ATATACTAATGAA-GA-TATATA-ATATAG-TTATATATATTATATAGTTTATATA
3636881 TACTATAGTA
Statistics
Matches: 205, Mismatches: 21, Indels: 41
0.77 0.08 0.15
Matches are distributed among these distances:
92 7 0.03
93 7 0.03
94 15 0.07
95 20 0.10
96 26 0.13
97 27 0.13
98 16 0.08
99 22 0.11
100 34 0.17
101 11 0.05
102 20 0.10
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (95 bp):
ATATACTAATGAAGATATATAATATAGTTATATATATTATATAGTTTATATACTAATGAACTATA
TAATTATAGTTTTTATATACTATATAGTAT
Found at i:3636874 original size:18 final size:17
Alignment explanation
Indices: 3636842--3636887 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
3636832 AATGAACGAC
*
3636842 TATATATATATAGTTTA
1 TATATATATACAGTTTA
3636859 TATATATTATACAGTTTA
1 TATATA-TATACAGTTTA
3636877 TATATACTATA
1 TATATA-TATA
3636888 GTATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATATATACAGTTTA
Found at i:3636979 original size:7 final size:7
Alignment explanation
Indices: 3636963--3637075 Score: 67
Period size: 7 Copynumber: 16.7 Consensus size: 7
3636953 TCATATGTAA
*
3636963 ATATACT
1 ATATAGT
3636970 ATATAGT
1 ATATAGT
3636977 ATATAGT
1 ATATAGT
*
3636984 TTATA-T
1 ATATAGT
*
3636990 ATATAAT
1 ATATAGT
3636997 ATATAGT
1 ATATAGT
*
3637004 ATATA-A
1 ATATAGT
*
3637010 ATATA-A
1 ATATAGT
3637016 ACTATAGT
1 A-TATAGT
*
3637024 ATGTAGT
1 ATATAGT
*
3637031 ATATA-A
1 ATATAGT
*
3637037 ATATA-A
1 ATATAGT
3637043 ACTATAGT
1 A-TATAGT
*
3637051 TTAT-GT
1 ATATAGT
*
3637057 ATATGGT
1 ATATAGT
*
3637064 ATATACT
1 ATATAGT
3637071 ATATA
1 ATATA
3637076 AATAGTTTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
6 24 0.28
7 61 0.71
8 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (7 bp):
ATATAGT
Found at i:3636994 original size:20 final size:20
Alignment explanation
Indices: 3636963--3637041 Score: 81
Period size: 20 Copynumber: 3.9 Consensus size: 20
3636953 TCATATGTAA
*
3636963 ATATACTATATAGTATATAGT
1 ATATA-TATATAATATATAGT
*
3636984 TTATATATATAATATATAGT
1 ATATATATATAATATATAGT
*
3637004 ATATAAATATAA-ACTATAGT
1 ATATATATATAATA-TATAGT
*
3637024 ATGTAGTATATAA-ATATA
1 ATATA-TATATAATATATA
3637042 AACTATAGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 38 0.76
21 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.42
Consensus pattern (20 bp):
ATATATATATAATATATAGT
Found at i:3637049 original size:27 final size:27
Alignment explanation
Indices: 3636960--3637060 Score: 109
Period size: 27 Copynumber: 3.8 Consensus size: 27
3636950 AGTTCATATG
* **
3636960 TAAA-TATACTATATAGTATATAGTTTA
1 TAAACTATAGTATATAGTATATA-AATA
* *
3636987 TATA-TATAATATATAGTATATAAATA
1 TAAACTATAGTATATAGTATATAAATA
*
3637013 TAAACTATAGTATGTAGTATATAAATA
1 TAAACTATAGTATATAGTATATAAATA
*
3637040 TAAACTATAGTTTAT-GTATAT
1 TAAACTATAGTATATAGTATAT
3637061 GGTATATACT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.17
27 53 0.83
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (27 bp):
TAAACTATAGTATATAGTATATAAATA
Found at i:3637110 original size:24 final size:24
Alignment explanation
Indices: 3637070--3637132 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
3637060 TGGTATATAC
* *
3637070 TATATAAA-TAGTTTATATAGTTCA
1 TATATAAACTA-TATATATAGGTCA
3637094 CTA-ATAAACTATATATATAGGTCA
1 -TATATAAACTATATATATAGGTCA
*
3637118 TATGTAAACTATATA
1 TATATAAACTATATA
3637133 GTTTATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 27 0.82
25 4 0.12
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (24 bp):
TATATAAACTATATATATAGGTCA
Found at i:3637197 original size:39 final size:39
Alignment explanation
Indices: 3637144--3637257 Score: 139
Period size: 39 Copynumber: 2.9 Consensus size: 39
3637134 TTTATATAAG
*
3637144 ATATGT-AACTATAGTTCATATGTAAATATCAACTATTT
1 ATATGTAAACTATAGTTCATATATAAATATCAACTATTT
3637182 ATATGTAAACTATAGTT-AGTATATTAAACTAT--A-TAGTTT
1 ATATGTAAACTATAGTTCA-TATA-TAAA-TATCAACTA-TTT
*
3637221 ATATGTAAACTATAATTCATATATAAATATCAACTAT
1 ATATGTAAACTATAGTTCATATATAAATATCAACTAT
3637258 AGTATATATA
Statistics
Matches: 65, Mismatches: 2, Indels: 17
0.77 0.02 0.20
Matches are distributed among these distances:
37 3 0.05
38 13 0.20
39 39 0.60
40 7 0.11
41 3 0.05
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (39 bp):
ATATGTAAACTATAGTTCATATATAAATATCAACTATTT
Found at i:3637218 original size:21 final size:20
Alignment explanation
Indices: 3637153--3637234 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 20
3637143 GATATGTAAC
*
3637153 TATAGTTCATATGTAAA-TA
1 TATAGTTTATATGTAAACTA
3637172 TCAACTA-TTTATATGTAAAC--
1 T--A-TAGTTTATATGTAAACTA
3637192 TATAGTTAGTATAT-TAAACTA
1 TATAGTT--TATATGTAAACTA
3637213 TATAGTTTATATGTAAACTA
1 TATAGTTTATATGTAAACTA
3637233 TA
1 TA
3637235 ATTCATATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 19
0.72 0.01 0.26
Matches are distributed among these distances:
17 2 0.04
18 3 0.06
19 11 0.21
20 15 0.29
21 19 0.37
22 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (20 bp):
TATAGTTTATATGTAAACTA
Found at i:3637223 original size:19 final size:20
Alignment explanation
Indices: 3637107--3637234 Score: 81
Period size: 20 Copynumber: 6.2 Consensus size: 20
3637097 ATAAACTATA
* *
3637107 TATATAGGTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
3637127 TATATAGTTTATATAAGATATGTAAC
1 TATATAGTTTATAT--G-TA---AAC
*
3637153 --TATAGTTCATATGTAAA-
1 TATATAGTTTATATGTAAAC
3637170 TATCAACTA-TTTATATGTAAAC
1 TAT--A-TAGTTTATATGTAAAC
3637192 --TATAGTTAGTATAT-TAAAC
1 TATATAGTT--TATATGTAAAC
3637211 TATATAGTTTATATGTAAAC
1 TATATAGTTTATATGTAAAC
3637231 TATA
1 TATA
3637235 ATTCATATAT
Statistics
Matches: 86, Mismatches: 4, Indels: 36
0.68 0.03 0.29
Matches are distributed among these distances:
17 2 0.02
18 5 0.06
19 11 0.13
20 27 0.31
21 21 0.24
22 4 0.05
23 2 0.02
24 11 0.13
26 3 0.03
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (20 bp):
TATATAGTTTATATGTAAAC
Found at i:3637243 original size:20 final size:19
Alignment explanation
Indices: 3637181--3637244 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
3637171 ATCAACTATT
*
3637181 TATATGTAAACTATAGTTA
1 TATATGTAAACTATAATTA
3637200 GTATAT-TAAACTATATAGTT-
1 -TATATGTAAACTATA-A-TTA
3637220 TATATGTAAACTATAATTCA
1 TATATGTAAACTATAATT-A
3637240 TATAT
1 TATAT
3637245 AAATATCAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.05
19 15 0.39
20 19 0.50
21 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (19 bp):
TATATGTAAACTATAATTA
Found at i:3637244 original size:29 final size:28
Alignment explanation
Indices: 3637211--3637298 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 28
3637201 TATATTAAAC
*
3637211 TATATAGTTTATATGTAAACTATAATTCA
1 TATATAG-TTATATGTAAACTATAGTTCA
* *
3637240 TATATA---A-ATATCAACTATAGTAT-A
1 TATATAGTTATATGTAAACTATAGT-TCA
3637264 TATATAGTTCATATGTAAACTATAGTTCA
1 TATATAGTT-ATATGTAAACTATAGTTCA
3637293 TATATA
1 TATATA
3637299 TAGTATATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
24 18 0.38
25 2 0.04
28 2 0.04
29 25 0.53
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (28 bp):
TATATAGTTATATGTAAACTATAGTTCA
Found at i:3637305 original size:18 final size:17
Alignment explanation
Indices: 3637211--3637305 Score: 57
Period size: 18 Copynumber: 5.4 Consensus size: 17
3637201 TATATTAAAC
* *
3637211 TATATAGTTTATATGTA
1 TATATAGTTCATATATA
* *
3637228 AACTATAATTCATATATA
1 TA-TATAGTTCATATATA
* **
3637246 AATATCAACT-ATAGTATA
1 TATAT-AGTTCATA-TATA
*
3637264 TATATAGTTCATATGTA
1 TATATAGTTCATATATA
*
3637281 AACTATAGTTCATATATA
1 TA-TATAGTTCATATATA
3637299 TAGTATA
1 TA-TATA
3637306 TAATTATAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
17 13 0.22
18 47 0.78
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (17 bp):
TATATAGTTCATATATA
Found at i:3637316 original size:33 final size:32
Alignment explanation
Indices: 3637240--3637355 Score: 132
Period size: 33 Copynumber: 3.7 Consensus size: 32
3637230 CTATAATTCA
*
3637240 TATATAAATATCAACTATAG-TATATATATAG
1 TATATAAATATAAACTATAGTTATATATATAG
*
3637271 T-TCAT--ATGTAAACTATAGTTCATATATATAG
1 TAT-ATAAATATAAACTATAGTT-ATATATATAG
* *
3637302 TATATAATTATAAACTATAGTTTATATAAATAG
1 TATATAAATATAAACTATAG-TTATATATATAG
*
3637335 TATATAAATATAAATTATAGT
1 TATATAAATATAAACTATAGT
3637356 ATGTAGTTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
29 11 0.15
30 2 0.03
31 16 0.23
32 2 0.03
33 38 0.54
34 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (32 bp):
TATATAAATATAAACTATAGTTATATATATAG
Found at i:3637320 original size:20 final size:18
Alignment explanation
Indices: 3637296--3637387 Score: 54
Period size: 20 Copynumber: 5.3 Consensus size: 18
3637286 TAGTTCATAT
3637296 ATATAGTATATAATTATAA
1 ATATAGTATATAA-TATAA
3637315 ACTATAGT-T-T-ATAT-A
1 A-TATAGTATATAATATAA
3637330 A-ATAGTATATAAATATAA
1 ATATAGTATAT-AATATAA
* * * *
3637348 ATTATAGTATGTAGTTTAT
1 A-TATAGTATATAATATAA
*
3637367 ATA-AATATA-AATATAA
1 ATATAGTATATAATATAA
3637383 ATATA
1 ATATA
3637388 AACCCTAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
15 3 0.05
16 10 0.18
17 10 0.18
18 5 0.09
19 7 0.13
20 14 0.25
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (18 bp):
ATATAGTATATAATATAA
Found at i:3637339 original size:40 final size:40
Alignment explanation
Indices: 3637293--3637389 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 40
3637283 CTATAGTTCA
*
3637293 TATATATAGTATATAATTATA-AACTATAGTTTATATAAATAG
1 TATATA-AATATA-AATTATAGAA-TATAGTTTATATAAATAG
* *
3637335 TATATAAATATAAATTATAGTATGTAGTTTATATAAATA-
1 TATATAAATATAAATTATAGAATATAGTTTATATAAATAG
3637374 TAAATATAAATATAAA
1 T--ATATAAATATAAA
3637390 CCCTAAACCC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
39 1 0.02
40 23 0.47
41 19 0.39
42 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (40 bp):
TATATAAATATAAATTATAGAATATAGTTTATATAAATAG
Found at i:3637376 original size:6 final size:6
Alignment explanation
Indices: 3637365--3637389 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3637355 TATGTAGTTT
3637365 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
3637390 CCCTAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:3637398 original size:7 final size:7
Alignment explanation
Indices: 3637386--3637426 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
3637376 AATATAAATA
3637386 TAAACCC
1 TAAACCC
3637393 TAAACCC
1 TAAACCC
*
3637400 TAATCCC
1 TAAACCC
3637407 TAAACCC
1 TAAACCC
*
3637414 TAATCCC
1 TAAACCC
3637421 TAAACC
1 TAAACC
3637427 ATATATACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:3637409 original size:14 final size:14
Alignment explanation
Indices: 3637390--3637426 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
3637380 TAAATATAAA
3637390 CCCTAAACCCTAAT
1 CCCTAAACCCTAAT
3637404 CCCTAAACCCTAAT
1 CCCTAAACCCTAAT
3637418 CCCTAAACC
1 CCCTAAACC
3637427 ATATATACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (14 bp):
CCCTAAACCCTAAT
Found at i:3637452 original size:22 final size:22
Alignment explanation
Indices: 3637421--3637482 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
3637411 CCCTAATCCC
*
3637421 TAAACCATATA-TACTATA-TATA
1 TAAACTATATAGT-CTATATTA-A
3637443 TAAACTATATAGTCTATATTAA
1 TAAACTATATAGTCTATATTAA
*
3637465 TAAACTATATAGTTTATA
1 TAAACTATATAGTCTATA
3637483 CAATATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAACTATATAGTCTATATTAA
Found at i:3637540 original size:20 final size:20
Alignment explanation
Indices: 3637515--3637659 Score: 114
Period size: 20 Copynumber: 7.1 Consensus size: 20
3637505 TAATATATAA
*
3637515 ATATAAATTGTATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
3637535 ATATAATTCATATATAATTTAT
1 ATATAAAT--TATATAGTTTAT
* * *
3637557 ATATAAACTATGTAGTTTCT
1 ATATAAATTATATAGTTTAT
* * *
3637577 ACAT-AGTTCA-ATAGTTCAT
1 ATATAAATT-ATATAGTTTAT
*
3637596 ATATAAACTATATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
3637616 ATATATAATCCATATACTTTAT
1 ATATA-AAT-TATATAGTTTAT
*
3637638 ATATAAACTATATAGTTTAT
1 ATATAAATTATATAGTTTAT
3637658 AT
1 AT
3637660 TATATATATT
Statistics
Matches: 94, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
19 12 0.13
20 47 0.50
21 4 0.04
22 31 0.33
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (20 bp):
ATATAAATTATATAGTTTAT
Found at i:3637560 original size:13 final size:11
Alignment explanation
Indices: 3637525--3637562 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3637515 ATATAAATTG
*
3637525 TATAGTTTATA
1 TATAATTTATA
*
3637536 TATAATTCATA
1 TATAATTTATA
3637547 TATAATTTATA
1 TATAATTTATA
3637558 TATAA
1 TATAA
3637563 ACTATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:3638158 original size:215 final size:216
Alignment explanation
Indices: 3637748--3638665 Score: 1536
Period size: 216 Copynumber: 4.3 Consensus size: 216
3637738 TTGATCCCTT
3637748 TGTGTTGTTTAATTTATTTAAA-TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* *
3637812 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGCCCCATAAC
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAAC
* *
3637877 TTTTTAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCA-AATTTTAAAATTATT
131 TTTTTAAATGGGTATAATTTAATACTTTTTTGTATTAATTTCAACCTCACAA-TTTAAAATTATT
* *
3637941 TCGATTTGATCCTTCATCAATG
195 TCGACTTGATCCCTCATCAATG
* *
3637963 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTAATATTTATTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* *
3638028 TTTTATTTCCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAAC
* *
3638093 TTTTTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAAATATTT
131 TTTTTAAATGGGTATAATTTAATACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTT
*
3638157 CGATTTGATCCCTCATCAATG
196 CGACTTGATCCCTCATCAATG
*
3638178 TGTGTTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * **
3638243 TTTTATTTGCATATGAAATTGATCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAGT
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAAC
*
3638308 TTTTTAAATGGGTATAATTTAATACTTTTTTGTAGTAATTTCAACCTCACAATTTAAAATTATTT
131 TTTTTAAATGGGTATAATTTAATACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTT
**
3638373 TTACTTGATCCCTCATCAATG
196 CGACTTGATCCCTCATCAATG
*
3638394 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCATTTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * **
3638459 TTTTATTTGCATCTGAAATTGATCCATACTTATTACTTAATTCTATTTTTTAATTGTCCCATAGT
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAAC
3638524 TTTTTAAATGGGTATAATTTAATACTTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
131 TTTTTAAATGGGTATAATTTAATAC-TTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
**
3638589 TTTACTTGATCCCTCATCAATG
195 TCGACTTGATCCCTCATCAATG
*
3638611 TGTATTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
3638666 ATTCTTAAAT
Statistics
Matches: 670, Mismatches: 29, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
215 222 0.33
216 335 0.50
217 113 0.17
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.51
Consensus pattern (216 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAAC
TTTTTAAATGGGTATAATTTAATACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTT
CGACTTGATCCCTCATCAATG
Found at i:3644181 original size:16 final size:16
Alignment explanation
Indices: 3644160--3644192 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3644150 TAAAAAATAA
3644160 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
3644176 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
3644192 A
1 A
3644193 AAATTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3644305 original size:16 final size:16
Alignment explanation
Indices: 3644254--3644306 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
3644244 CGTTCATTTA
*
3644254 ATAAAT-AA-ACGAAT
1 ATAAATGAACACGAAC
*
3644268 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
3644284 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
3644300 ATAAATG
1 ATAAATG
3644307 TTGGAGATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 27 0.79
ACGTcount: A:0.58, C:0.15, G:0.11, T:0.15
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:3645422 original size:24 final size:24
Alignment explanation
Indices: 3645395--3645467 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
3645385 ATAAATGAAT
*
3645395 GAACATAAACGAACATAACCGACC
1 GAACATAAACGAACATAACCGAAC
* * *
3645419 GAACATAAACGAATATAACTGAAT
1 GAACATAAACGAACATAACCGAAC
3645443 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
3645467 G
1 G
3645468 TTCACGAACG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.52, C:0.22, G:0.14, T:0.12
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:3647995 original size:14 final size:14
Alignment explanation
Indices: 3647976--3648026 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
3647966 TTCGTTTATG
3647976 TTATGTTCATTTGT
1 TTATGTTCATTTGT
3647990 TTATG-T--TTTGT
1 TTATGTTCATTTGT
* *
3648001 TCATGTTCATTCGT
1 TTATGTTCATTTGT
3648015 TTATGTTCATTT
1 TTATGTTCATTT
3648027 ATGTTCTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.63
Consensus pattern (14 bp):
TTATGTTCATTTGT
Found at i:3647997 original size:25 final size:25
Alignment explanation
Indices: 3647969--3648032 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
3647959 TAATCCGTTC
*
3647969 GTTTATGTTATGTTCATTTGTTTAT
1 GTTTATGTTATGTTCATTCGTTTAT
3647994 GTTT-TGTTCATGTTCATTCGTTTAT
1 GTTTATGTT-ATGTTCATTCGTTTAT
*
3648019 GTTCAT-TTATGTTC
1 GTTTATGTTATGTTC
3648033 TCCATACCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 10 0.29
25 24 0.69
26 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.61
Consensus pattern (25 bp):
GTTTATGTTATGTTCATTCGTTTAT
Found at i:3648246 original size:20 final size:20
Alignment explanation
Indices: 3648217--3648254 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3648207 ATTTTATGTT
*
3648217 CGTTCGTTTATGTTTGTTTG
1 CGTTCATTTATGTTTGTTTG
3648237 CGTTCATTTATGTTTGTT
1 CGTTCATTTATGTTTGTT
3648255 CATTTGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.11, G:0.21, T:0.61
Consensus pattern (20 bp):
CGTTCATTTATGTTTGTTTG
Found at i:3648260 original size:24 final size:24
Alignment explanation
Indices: 3648233--3648295 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
3648223 TTTATGTTTG
* * **
3648233 TTTGCGTTCATTTATGTTTGTTCA
1 TTTGTGTTCGTTTATGTTCATTCA
*
3648257 TTTGTGTTCGTTTACGTTCATTCA
1 TTTGTGTTCGTTTATGTTCATTCA
3648281 TTTGTGTTCGTTTAT
1 TTTGTGTTCGTTTAT
3648296 CATTTAAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (24 bp):
TTTGTGTTCGTTTATGTTCATTCA
Found at i:3648275 original size:34 final size:34
Alignment explanation
Indices: 3648209--3648278 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
3648199 CTCAATTAAT
* * *
3648209 TTTATGTTCGTTCGTTTATGTTTGTTTGCGTTCA
1 TTTATGTTCGTTCATTTATGTTCGTTTACGTTCA
* *
3648243 TTTATGTTTGTTCATTTGTGTTCGTTTACGTTCA
1 TTTATGTTCGTTCATTTATGTTCGTTTACGTTCA
3648277 TT
1 TT
3648279 CATTTGTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.10, C:0.11, G:0.19, T:0.60
Consensus pattern (34 bp):
TTTATGTTCGTTCATTTATGTTCGTTTACGTTCA
Found at i:3648289 original size:34 final size:34
Alignment explanation
Indices: 3648212--3648295 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
3648202 AATTAATTTT
* * * * *
3648212 ATGTTCGTTCGTTTATGTTTGTTTGCGTTCATTT
1 ATGTTTGTTCATTTATGTTCGTTTACGTTCATTC
*
3648246 ATGTTTGTTCATTTGTGTTCGTTTACGTTCATTC
1 ATGTTTGTTCATTTATGTTCGTTTACGTTCATTC
*
3648280 AT-TTGTGTTCGTTTAT
1 ATGTT-TGTTCATTTAT
3648296 CATTTAAACG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 2 0.05
34 39 0.95
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (34 bp):
ATGTTTGTTCATTTATGTTCGTTTACGTTCATTC
Found at i:3650059 original size:21 final size:20
Alignment explanation
Indices: 3650012--3650065 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3650002 AACTTGATAA
* *
3650012 TGGTATTGATACTAGACCCT
1 TGGTATCGATACTACACCCT
*
3650032 TGGTATCGATACTACATCCT
1 TGGTATCGATACTACACCCT
3650052 TCGGTATCGATACT
1 T-GGTATCGATACT
3650066 TCTTGAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACTACACCCT
Found at i:3651010 original size:13 final size:13
Alignment explanation
Indices: 3650990--3651019 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3650980 TTATCTTTGA
3650990 AAAT-GTTTTATG
1 AAATGGTTTTATG
3651002 AAATGGTTTTATG
1 AAATGGTTTTATG
3651015 AAATG
1 AAATG
3651020 TTGGGAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (13 bp):
AAATGGTTTTATG
Found at i:3652875 original size:15 final size:15
Alignment explanation
Indices: 3652852--3652883 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3652842 ATCCGCAGAG
*
3652852 GCACTGTCGTCGACC
1 GCACCGTCGTCGACC
3652867 GCACCGTCGTCGACC
1 GCACCGTCGTCGACC
3652882 GC
1 GC
3652884 TGCACCGCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.44, G:0.28, T:0.16
Consensus pattern (15 bp):
GCACCGTCGTCGACC
Found at i:3658695 original size:2 final size:2
Alignment explanation
Indices: 3658688--3658720 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3658678 AGTTATTTTC
*
3658688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3658721 GTTATTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3658701 original size:24 final size:24
Alignment explanation
Indices: 3658655--3658702 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3658645 ACATCATGAT
*
3658655 GTTAATTTCATATGCTATAATATA
1 GTTAATTTCATATGATATAATATA
*
3658679 GTTATTTTCATAT-ATATATATATA
1 GTTAATTTCATATGATATA-ATATA
3658703 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (24 bp):
GTTAATTTCATATGATATAATATA
Found at i:3660754 original size:44 final size:43
Alignment explanation
Indices: 3660686--3660834 Score: 174
Period size: 44 Copynumber: 3.4 Consensus size: 43
3660676 GAGATAATAT
* *
3660686 TGATCCAGCTCCTTATCCGATGGAATCGAACGAAATGTTGATGC
1 TGATCCAACTCCTTATGCGATGGAAT-GAACGAAATGTTGATGC
* *
3660730 TGATCCAACTCCTTATGCGGTGGAATGAAGCGAAATGTTGATAC
1 TGATCCAACTCCTTATGCGATGGAATGAA-CGAAATGTTGATGC
* ** *
3660774 TGGTCCAACTCCTTATGTTATGGAATTGAGA-GAAATGTTGATGT
1 TGATCCAACTCCTTATGCGATGGAA-TGA-ACGAAATGTTGATGC
*
3660818 TGATCCAACTTCTTATG
1 TGATCCAACTCCTTATG
3660835 TGATAAAATC
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
43 3 0.03
44 83 0.92
45 3 0.03
46 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (43 bp):
TGATCCAACTCCTTATGCGATGGAATGAACGAAATGTTGATGC
Found at i:3661034 original size:42 final size:42
Alignment explanation
Indices: 3660971--3661121 Score: 114
Period size: 42 Copynumber: 3.6 Consensus size: 42
3660961 CACCCTTCTT
* *
3660971 GAAAGACTTA-TAGA-GGACCCGGAGGATTTAAACATCACGCTA
1 GAAAGACTTACT-GATGG-CCCGAAGGATTTAATCATCACGCTA
* * * *
3661013 GAAAGACTTACTGATGGCCCGGAGAACTT-ATCACTCTACTC-A
1 GAAAGACTTACTGATGGCCCGAAGGATTTAATCA-TC-ACGCTA
* * * * * *
3661055 -AAAGACTTACAGATGACCCAAAAGATTTAATCATCATGCTC
1 GAAAGACTTACTGATGGCCCGAAGGATTTAATCATCACGCTA
*
3661096 GAAATACTTACTGATGGCCCGAAGGA
1 GAAAGACTTACTGATGGCCCGAAGGA
3661122 CTTATCACTC
Statistics
Matches: 83, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
40 2 0.02
41 26 0.31
42 49 0.59
43 6 0.07
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
GAAAGACTTACTGATGGCCCGAAGGATTTAATCATCACGCTA
Found at i:3661060 original size:83 final size:83
Alignment explanation
Indices: 3660972--3661215 Score: 294
Period size: 83 Copynumber: 3.0 Consensus size: 83
3660962 ACCCTTCTTG
* * * * *
3660972 AAAGACTTATAGAGGACCCGGAGGATTTAAACATCACGCTAGAAAGACTTACTGATGGCCCGGAG
1 AAAGACTTACAGAGGACCCGAAAGATTTAATCATCATGCTAGAAAGACTTACTGATGGCCCGGAG
*
3661037 AACTTATCACTCTACTCA
66 GACTTATCACTCTACTCA
* * * * *
3661055 AAAGACTTACAGATGACCCAAAAGATTTAATCATCATGCTCGAAATACTTACTGATGGCCCGAAG
1 AAAGACTTACAGAGGACCCGAAAGATTTAATCATCATGCTAGAAAGACTTACTGATGGCCCGGAG
*
3661120 GACTTATCACTCTGCTCA
66 GACTTATCACTCTACTCA
* * * * * * *
3661138 AAAGATTTACAAAGGACCTGAAAGATTTAATCATCATGCTCA-AATGACTTATTAATGGTCCGGA
1 AAAGACTTACAGAGGACCCGAAAGATTTAATCATCATGCT-AGAAAGACTTACTGATGGCCCGGA
3661202 GGACTTATCA-TCTA
65 GGACTTATCACTCTA
3661216 GAAACCTTTG
Statistics
Matches: 135, Mismatches: 25, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
82 3 0.02
83 132 0.98
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (83 bp):
AAAGACTTACAGAGGACCCGAAAGATTTAATCATCATGCTAGAAAGACTTACTGATGGCCCGGAG
GACTTATCACTCTACTCA
Found at i:3661064 original size:41 final size:41
Alignment explanation
Indices: 3661014--3661147 Score: 137
Period size: 41 Copynumber: 3.2 Consensus size: 41
3661004 ATCACGCTAG
* *
3661014 AAAGACTTACTGATGGCCCGGAGAACTTATCACTCTACTCA
1 AAAGACTTACTGATGGCCCGAAGAACTTATCACTCTGCTCA
* * * * *
3661055 AAAGACTTACAGATGACCC-AAAAGATTTAATCA-TCATGCTCG
1 AAAGACTTACTGATGGCCCGAAGA-ACTT-ATCACTC-TGCTCA
* *
3661097 AAATACTTACTGATGGCCCGAAGGACTTATCACTCTGCTCA
1 AAAGACTTACTGATGGCCCGAAGAACTTATCACTCTGCTCA
*
3661138 AAAGATTTAC
1 AAAGACTTAC
3661148 AAAGGACCTG
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
40 2 0.03
41 39 0.54
42 29 0.40
43 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (41 bp):
AAAGACTTACTGATGGCCCGAAGAACTTATCACTCTGCTCA
Found at i:3667297 original size:4 final size:4
Alignment explanation
Indices: 3667288--3667319 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
3667278 TTCCTCTTCT
3667288 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG
3667320 GAATTGGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (4 bp):
TTTG
Found at i:3668213 original size:13 final size:13
Alignment explanation
Indices: 3668195--3668220 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3668185 CATCTTTGAT
3668195 CACCTTCGATTCA
1 CACCTTCGATTCA
3668208 CACCTTCGATTCA
1 CACCTTCGATTCA
3668221 AGTTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (13 bp):
CACCTTCGATTCA
Found at i:3669321 original size:37 final size:38
Alignment explanation
Indices: 3669260--3669620 Score: 168
Period size: 36 Copynumber: 9.9 Consensus size: 38
3669250 CACAAAATGG
3669260 TTTTTGAAAAATACGTATATAATATATGATTTAAAAAATCA
1 TTTTTG-AAAATA--TATATAATATATGATTTAAAAAATCA
* *
3669301 -TTTTGAAAATGTATATAATATATAGTTTTTTAAAAAAAT-A
1 TTTTTGAAAATATATATAATATAT-G--ATTT-AAAAAATCA
** * **
3669341 CCTTT-AAAA-ACTATATAATATATAATTTTTAAAA-CA
1 TTTTTGAAAATA-TATATAATATATGATTTAAAAAATCA
* **
3669377 TTTTTAGAAAACATATATAATATAT-AGTTTTTAAAATCA
1 TTTTT-GAAAATATATATAATATATGA-TTTAAAAAATCA
* *
3669416 -TTTTGAAAACT-TATATAACATAT-AGTTT-TAAAATCA
1 TTTTTGAAAA-TATATATAATATATGA-TTTAAAAAATCA
* *
3669452 -TTTTG-AAATTTATATAATATATAGTTTTAAAAAA-CA
1 TTTTTGAAAATATATATAATATAT-GATTTAAAAAATCA
* *
3669488 TTTTTGAAAATATATAT--TATA-G-TTT-TAAAA-CG
1 TTTTTGAAAATATATATAATATATGATTTAAAAAATCA
* *
3669520 TTTTTGAAAACTATA-A-CATATA-G-TTT-GAAAA-CA
1 TTTTTGAAAA-TATATATAATATATGATTTAAAAAATCA
* **
3669553 TTTTT-AAAAT-TATATAATATATGGTTTTGAAAAT-A
1 TTTTTGAAAATATATATAATATATGATTTAAAAAATCA
* * * *
3669588 TCTTTG-AAATATATATTATATATAATTTTAAAA
1 TTTTTGAAAATATATATAATATATGATTTAAAAA
3669621 CAATTTTTTA
Statistics
Matches: 264, Mismatches: 26, Indels: 65
0.74 0.07 0.18
Matches are distributed among these distances:
30 2 0.01
31 2 0.01
32 25 0.09
33 26 0.10
34 5 0.02
35 28 0.11
36 48 0.18
37 46 0.17
38 39 0.15
39 8 0.03
40 25 0.09
41 10 0.04
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (38 bp):
TTTTTGAAAATATATATAATATATGATTTAAAAAATCA
Found at i:3669551 original size:33 final size:32
Alignment explanation
Indices: 3669353--3669628 Score: 162
Period size: 35 Copynumber: 7.9 Consensus size: 32
3669343 TTTAAAAACT
* *
3669353 ATATAATATATAATTTTTAAAACATTTTTAGAAAACA
1 ATATAACATAT-AGTTTTAAAACATTTTT-G--AA-A
*
3669390 TATATAATATATAGTTTTTAAAATCA-TTTTGAAAA
1 -ATATAACATATAG-TTTTAAAA-CATTTTTG-AAA
3669425 CTTATATAACATATAGTTTTAAAATCA-TTTTGAAA
1 ---ATATAACATATAGTTTTAAAA-CATTTTTGAAA
*
3669460 TTTATATAATATATAGTTTTAAAAAACATTTTTGAAA
1 ---ATATAACATATAGTTTT--AAAACATTTTTGAAA
* *
3669497 ATATATA-TTATAGTTTTAAAACGTTTTTGAAA
1 ATATA-ACATATAGTTTTAAAACATTTTTGAAA
* *
3669529 ACTATAACATATAGTTTGAAAACATTTTTAAAA
1 A-TATAACATATAGTTTTAAAACATTTTTGAAA
* * * *
3669562 TTATATAATATATGGTTTTGAAAATATCTTTGAAA
1 --ATATAACATATAGTTTT-AAAACATTTTTGAAA
* *
3669597 TATATATTATATATAATTTTAAAACAATTTTT
1 -ATATA--ACATATAGTTTTAAAAC-ATTTTT
3669629 TATATATATT
Statistics
Matches: 202, Mismatches: 20, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
32 16 0.08
33 25 0.12
34 33 0.16
35 40 0.20
36 36 0.18
37 27 0.13
38 23 0.11
39 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (32 bp):
ATATAACATATAGTTTTAAAACATTTTTGAAA
Found at i:3669608 original size:34 final size:33
Alignment explanation
Indices: 3669352--3669643 Score: 234
Period size: 36 Copynumber: 8.3 Consensus size: 33
3669342 CTTTAAAAAC
*
3669352 TATATAATATATAATTTTTAAAACATTTTTAGAAAACA
1 TATATAATATAT-AGTTTTAAAACATTTTT-G--AA-A
3669390 TATATAATATATAGTTTTTAAAATCA-TTTTGAAAA
1 TATATAATATATAG-TTTTAAAA-CATTTTTG-AAA
*
3669425 CTTATATAACATATAGTTTTAAAATCA-TTTTGAAA
1 --TATATAATATATAGTTTTAAAA-CATTTTTGAAA
3669460 TTTATATAATATATAGTTTTAAAAAACATTTTTGAAA
1 --TATATAATATATAGTTTT--AAAACATTTTTGAAA
*
3669497 -ATAT-ATATTATAGTTTTAAAACGTTTTTGAAA
1 TATATAATA-TATAGTTTTAAAACATTTTTGAAA
* * *
3669529 -ACTATAACATATAGTTTGAAAACATTTTTAAAA
1 TA-TATAATATATAGTTTTAAAACATTTTTGAAA
* * *
3669562 TTATATAATATATGGTTTTGAAAATATCTTTGAAA
1 -TATATAATATATAGTTTT-AAAACATTTTTGAAA
* * *
3669597 TATATATTATATATAATTTTAAAACAATTTTTTATA
1 TATATA--ATATATAGTTTTAAAAC-ATTTTTGAAA
*
3669633 TATATTATATA
1 TATATAATATA
3669644 GTATATTCTT
Statistics
Matches: 216, Mismatches: 22, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
32 15 0.07
33 27 0.12
34 39 0.18
35 39 0.18
36 43 0.20
37 27 0.12
38 24 0.11
39 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (33 bp):
TATATAATATATAGTTTTAAAACATTTTTGAAA
Found at i:3669682 original size:26 final size:26
Alignment explanation
Indices: 3669653--3669725 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
3669643 AGTATATTCT
3669653 TTTATTTTATTCTTTTTTATTTATTA
1 TTTATTTTATTCTTTTTTATTTATTA
*
3669679 TTTATTTT-TGTGTTTTGTT-TTTATTA
1 TTTATTTTAT-TCTTTT-TTATTTATTA
* *
3669705 TTTA-TTTAATCGTTTTTATTT
1 TTTATTTTATTCTTTTTTATTT
3669726 TGGTTAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 2 0.05
25 11 0.28
26 24 0.62
27 2 0.05
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.75
Consensus pattern (26 bp):
TTTATTTTATTCTTTTTTATTTATTA
Found at i:3670889 original size:4 final size:4
Alignment explanation
Indices: 3670880--3670947 Score: 93
Period size: 4 Copynumber: 17.0 Consensus size: 4
3670870 TTGATTTAAC
* **
3670880 ATTT ATTT ATTT -TATT CTTT ATCA ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3670928 ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT
3670948 CTAACATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
3 1 0.02
4 55 0.96
5 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:3672907 original size:3 final size:3
Alignment explanation
Indices: 3672899--3672982 Score: 89
Period size: 3 Copynumber: 28.0 Consensus size: 3
3672889 ATTTATAATT
* * * *
3672899 TAA TAA TAA TTA TAA -AA TAA TGA TAA TAA TAT TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
3672946 TAA AAA TAT TAA TAA TAA TAA TAAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
3672983 ATGGACAAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3672911 original size:17 final size:17
Alignment explanation
Indices: 3672891--3672939 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 17
3672881 TTGTAATTAT
3672891 TTATAATTTAATAATAA
1 TTATAATTTAATAATAA
*
3672908 TTATAA---AATAATGA
1 TTATAATTTAATAATAA
*
3672922 TAATAATATTAATAATAA
1 TTATAAT-TTAATAATAA
3672940 AAATAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
14 12 0.48
17 6 0.24
18 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TTATAATTTAATAATAA
Found at i:3673385 original size:137 final size:138
Alignment explanation
Indices: 3673230--3673709 Score: 468
Period size: 139 Copynumber: 3.6 Consensus size: 138
3673220 AAGGTTAAAC
* *
3673230 AACAAGTTCTTTTCATTATAAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
* * * * * *
3673295 TTCTGGAAATGCTGATCCTCAAAAGAGG-TGTT-GTTGATTCAGCTTCATATG-TGATGAATTAA
66 TTCTGGAAATGTTGATCCTCAAAAGAGGTTATTCGTTCATTCAACTCCATA-GATGATGAATCAA
* *
3673357 GGC-AAGGTTG
130 -GCTAAAG-TA
*
3673367 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-TC
* * ** *
3673432 C-TCTGAAAATATTGATCCTCAAGTGAGGTTATTCTTTCATTCAACTCCATAGATGATGAATCAA
65 CTTCTGGAAATGTTGATCCTCAAAAGAGGTTATTCGTTCATTCAACTCCATAGATGATGAATCAA
3673496 GCTAAAGTA
130 GCTAAAGTA
*
3673505 AAGCAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACT-
1 AA-CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
* ** * * *
3673569 CTATCTGGAAATGTTGATGCT-----GA--TCTA-TC-TTC-TT-TTCT-GATAGA-G-TCAAGC
65 CT-TCTGGAAATGTTGATCCTCAAAAGAGGT-TATTCGTTCATTCAACTCCATAGATGATGAATC
* *
3673620 AA---AAGGTTG
128 AAGCTAAAG-TA
*
3673629 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT-C
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
*
3673693 TCTCTAGAAATGTTGAT
66 T-TCTGGAAATGTTGAT
3673710 GATGATCTAT
Statistics
Matches: 301, Mismatches: 32, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
123 78 0.26
124 3 0.01
126 6 0.02
127 1 0.00
128 5 0.02
129 2 0.01
130 2 0.01
131 3 0.01
132 3 0.01
133 2 0.01
134 2 0.01
137 82 0.27
138 13 0.04
139 99 0.33
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (138 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
TTCTGGAAATGTTGATCCTCAAAAGAGGTTATTCGTTCATTCAACTCCATAGATGATGAATCAAG
CTAAAGTA
Found at i:3673586 original size:139 final size:136
Alignment explanation
Indices: 3673230--3673816 Score: 481
Period size: 123 Copynumber: 4.5 Consensus size: 136
3673220 AAGGTTAAAC
* *
3673230 AACAAGTTCTTTTCATTATAAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT-C
* * * * * *
3673295 TTCTGGAAATGCTGATCCTCAAAAGAGGTGTTGTTGATTCAGCTTCATATGTGATGAATTAAGGC
65 TTCTGGAAATGTTGATCCTCAAAAGAGGTATTGTTCATTCAACTCCATATGTGATGAATCAAGGC
* *
3673360 AAGGTTG
130 AAAGTTA
*
3673367 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-TC
* * * ** *
3673432 CTCTGAAAATATTGATCCTCAAGTGAGGTTATTCTTTCATTCAACTCCATA-GATGATGAATCAA
65 TTCTGGAAATGTTGATCCTCAAAAGAGG-TATT-GTTCATTCAACTCCATATG-TGATGAATCAA
3673496 -GCTAAAG-TA
127 GGC-AAAGTTA
*
3673505 AAGCAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTC
1 AA-CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
* ** * ** *
3673570 TATCTGGAAATGTTGATGCT-----GATCTA-TCTTC-TT-TTCT-GATA---GA-G--TCAA-G
65 T-TCTGGAAATGTTGATCCTCAAAAGAGGTATTGTTCATTCAACTCCATATGTGATGAATCAAGG
*
3673619 CAAAAGGTTG
129 C-AAA-GTTA
*
3673629 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * * * * * *
3673694 CTCTAGAAATGTTGA---T--------G-A-TGATC--T-ATCTCCTTCTGTGATAGAGTCAA-A
66 -TCTGGAAATGTTGATCCTCAAAAGAGGTATTGTTCATTCAACTCCATATGTGAT-GAATCAAGG
*
3673742 CAAAAGGTTG
129 C-AAA-GTTA
3673752 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
3673817 ACCCTGCAAT
Statistics
Matches: 389, Mismatches: 44, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
115 4 0.01
116 5 0.01
119 2 0.01
120 1 0.00
121 1 0.00
122 9 0.02
123 153 0.39
124 4 0.01
125 2 0.01
128 3 0.01
129 2 0.01
130 2 0.01
131 3 0.01
132 1 0.00
133 2 0.01
134 2 0.01
137 82 0.21
138 12 0.03
139 99 0.25
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (136 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
TCTGGAAATGTTGATCCTCAAAAGAGGTATTGTTCATTCAACTCCATATGTGATGAATCAAGGCA
AAGTTA
Found at i:3673733 original size:123 final size:124
Alignment explanation
Indices: 3673508--3674077 Score: 927
Period size: 123 Copynumber: 4.6 Consensus size: 124
3673498 TAAAGTAAAG
*
3673508 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTCTA-
1 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * *
3673572 TCTGGAAATGTTGATGCTGATCTATCTTCTTTTCTGATAGAGTCAAGCAAAAGGTTGAA
66 TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAA
*
3673631 CAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT-C
1 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * *
3673695 TCTAGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCAAACAAAAGGTTGAA
66 TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAA
3673754 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
1 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * * *
3673819 CCT-GCAATGTTGATGCTGATCTATCTCCTTATGTGATAGAGTCGAGCAAAAGGTTGAA
66 TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAA
*
3673877 CAAGTTCTTCTCATTATGAACTTCTGCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
1 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * *
3673942 -CTGGCAATGTTGATGCTGATCTATCTCTTTCTGTGATAGAGTCGAGCAAAAGGTTGAA
66 TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAA
* *
3674000 CAAGTTCTTTTCATTATGAACTTCTTCTTCCTCTCCAGATGAGTTCTTCTCATTATGAACTCTAC
1 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
*
3674065 -CT-GCAATGTTGAT
66 TCTGGAAATGTTGAT
3674078 CCATCGAGTG
Statistics
Matches: 423, Mismatches: 21, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
122 13 0.03
123 407 0.96
124 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (124 bp):
CAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAA
Found at i:3674521 original size:2 final size:2
Alignment explanation
Indices: 3674514--3674548 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3674504 AAAAATGAAG
3674514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3674549 TTGTATAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3674726 original size:4 final size:4
Alignment explanation
Indices: 3674717--3674741 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3674707 TGACTAAAAC
3674717 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
3674742 GTACTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:3676007 original size:3 final size:3
Alignment explanation
Indices: 3675999--3676044 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
3675989 ATTTATAATT
* *
3675999 TAA TAA TAA TAA -AA AAA AAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3676045 AAAAAAAACG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:3676029 original size:23 final size:23
Alignment explanation
Indices: 3675999--3676044 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3675989 ATTTATAATT
3675999 TAATAATAATAAAAAAAAAATAA
1 TAATAATAATAAAAAAAAAATAA
* *
3676022 TAATAATAATAATAATAAAATAA
1 TAATAATAATAAAAAAAAAATAA
3676045 AAAAAAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
TAATAATAATAAAAAAAAAATAA
Found at i:3676281 original size:22 final size:22
Alignment explanation
Indices: 3676253--3676294 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3676243 TCTTGTTAGA
3676253 CGTTTGATGTGCATGGGTGTGG
1 CGTTTGATGTGCATGGGTGTGG
3676275 CGTTTGATGTGCATGGGTGT
1 CGTTTGATGTGCATGGGTGT
3676295 TATGTAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.43, T:0.38
Consensus pattern (22 bp):
CGTTTGATGTGCATGGGTGTGG
Found at i:3676650 original size:32 final size:29
Alignment explanation
Indices: 3676576--3676664 Score: 133
Period size: 30 Copynumber: 2.9 Consensus size: 29
3676566 ATAACTAATG
*
3676576 TTTACTTTTTGTTTCATTTTAGTACCAACA
1 TTTACTTTTTGTTTCATTTTAGTACC-TCA
3676606 TTTACTTTTTGTTTCATTTTAGTACCTCA
1 TTTACTTTTTGTTTCATTTTAGTACCTCA
3676635 TTATTAACTTTTTGTTTCATTTTAGTACCT
1 -T-TT-ACTTTTTGTTTCATTTTAGTACCT
3676665 AAATTTTTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
29 2 0.04
30 27 0.49
31 2 0.04
32 24 0.44
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.57
Consensus pattern (29 bp):
TTTACTTTTTGTTTCATTTTAGTACCTCA
Found at i:3676855 original size:2 final size:2
Alignment explanation
Indices: 3676848--3676881 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3676838 ATCCTAGCTT
3676848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3676882 ATTAGTATGC
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):
TA
Found at i:3677031 original size:17 final size:17
Alignment explanation
Indices: 3677009--3677049 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
3676999 AGTCTGTCTT
3677009 TCCGCTATGAAGCTTCC
1 TCCGCTATGAAGCTTCC
3677026 TCCGCTATGAAGCTTCC
1 TCCGCTATGAAGCTTCC
3677043 TCCGCTA
1 TCCGCTA
3677050 AGACAGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.17, C:0.37, G:0.17, T:0.29
Consensus pattern (17 bp):
TCCGCTATGAAGCTTCC
Found at i:3697516 original size:132 final size:133
Alignment explanation
Indices: 3697287--3697525 Score: 335
Period size: 132 Copynumber: 1.8 Consensus size: 133
3697277 GTATAAATAA
* *
3697287 GATATTTATTTATTTAGAAATATCAGAAAAAGGCTTCTAGGTGCTTTAAGATAGCTCTTTTCTTC
1 GATATTTATTTATTTAGAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACAGCTCTTTTCTTC
* *
3697352 GATATTAAAAAAAATAACTAAAAAACATTTTTTC-TAAAAATAATTAATATATAATTTATAAAAA
66 GATATTAAAAAAAAAAAATAAAAAACATTTTTTCATAAAAATAATTAATATATAATTTATAAAAA
3697416 CAG
131 CAG
*
3697419 GATATTTATTTATTTA-AGAATATCA-AAAAAGAACTTCTAGGTGTTTTAAGACAGCTCTTTTCT
1 GATATTTATTTATTTAGA-AATATCAGAAAAAG-ACTTCTAGGTGCTTTAAGACAGCTCTTTTCT
** *
3697482 TCGATATTAATAAATAAAAAAATGTAATA-A-TTTTTCATAAAAAT
64 TCGATATTAA-AAA-AAAAAAATAAAAAACATTTTTTCATAAAAAT
3697526 GATTTAAATA
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
131 7 0.07
132 67 0.71
133 11 0.12
134 9 0.10
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (133 bp):
GATATTTATTTATTTAGAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACAGCTCTTTTCTTC
GATATTAAAAAAAAAAAATAAAAAACATTTTTTCATAAAAATAATTAATATATAATTTATAAAAA
CAG
Found at i:3698892 original size:20 final size:19
Alignment explanation
Indices: 3698867--3698921 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
3698857 TTGGGTTTTT
3698867 TAATATTAATAAATAATATA
1 TAATATTAAT-AATAATATA
3698887 TAATATTAATAATAATA-A
1 TAATATTAATAATAATATA
*
3698905 TTATTATT-ATAATAATA
1 -TAATATTAATAATAATA
3698922 AATTTAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 10 0.30
19 13 0.39
20 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTAATAATAATATA
Found at i:3698895 original size:26 final size:27
Alignment explanation
Indices: 3698866--3698918 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3698856 TTTGGGTTTT
*
3698866 TTAATATTAATAAATAATA-TATAATA
1 TTAATAATAATAAATAATATTATAATA
* *
3698892 TTAATAATAATAATTATTATTATAATA
1 TTAATAATAATAAATAATATTATAATA
3698919 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAATAATAATAAATAATATTATAATA
Found at i:3699675 original size:227 final size:228
Alignment explanation
Indices: 3699056--3699770 Score: 1270
Period size: 227 Copynumber: 3.1 Consensus size: 228
3699046 GATGAAAATG
* * * * * * *
3699056 TTTGAAAACATCATGTACTGAAGGGCTTAGAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
*
3699121 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAA
*
3699186 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATTATGCACTGCAGGACTTACAGATGACCCTAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAA
*
3699251 GGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
195 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
3699285 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
3699350 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
3699415 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATTCACTGCAGGACTTACAGATGACCCTAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
3699480 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
3699513 TTTGGAAACATCATGCACTGCAGGACTTACATATGA-CCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
3699577 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
3699642 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
*
3699707 GCTTTGAAAACATCAAAAAGCTCCCAAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
3699740 TTTAGAAACATCATGCACTGCAGGACTTACA
1 TTTGGAAACATCATGCACTGCAGGACTTACA
3699771 AATGTAGGAA
Statistics
Matches: 468, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
227 217 0.46
228 213 0.46
229 38 0.08
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (228 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:3699801 original size:76 final size:76
Alignment explanation
Indices: 3699056--3699770 Score: 1270
Period size: 76 Copynumber: 9.4 Consensus size: 76
3699046 GATGAAAATG
* * * * * * *
3699056 TTTGAAAACATCATGTACTGAAGGGCTTAGAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
3699121 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
3699133 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
3699198 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
3699209 TTTGGAAACATTATGCACTGCAGGACTTACAGATGACCCTAAGGGTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
3699274 CCCGAAGGCTT
66 CCCGAAGGCTT
3699285 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
3699350 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3699361 TTTGGAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
3699426 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3699437 TTTGGAAACATCATTCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
3699502 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3699513 TTTGGAAACATCATGCACTGCAGGACTTACATATGA-CCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
3699577 CCCGAAGGCTT
66 CCCGAAGGCTT
*
3699588 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
3699653 CCCGAAGGCTT
66 CCCGAAGGCTT
3699664 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
3699729 CCCAAAGGCTT
66 CCCGAAGGCTT
*
3699740 TTTAGAAACATCATGCACTGCAGGACTTACA
1 TTTGGAAACATCATGCACTGCAGGACTTACA
3699771 AATGTAGGAA
Statistics
Matches: 615, Mismatches: 22, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
75 74 0.12
76 503 0.82
77 38 0.06
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:3700438 original size:22 final size:22
Alignment explanation
Indices: 3700410--3700461 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3700400 GATAAAGCTT
* *
3700410 TCATCTTTTAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
3700432 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
3700454 TCATCTTT
1 TCATCTTT
3700462 GAAGAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:3703314 original size:115 final size:115
Alignment explanation
Indices: 3703113--3703688 Score: 1012
Period size: 115 Copynumber: 5.0 Consensus size: 115
3703103 GCAGTTCTTT
* * * * *
3703113 TTTCAATTCCAATGATTGG-TTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACACT
1 TTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACACT
3703177 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
66 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
*
3703227 TTTCAAATCCAATGATTGGTTTTTGGGGTTTATACCAAACCAAATCAGATAACTCAAAGAACACT
1 TTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACACT
*
3703292 TACAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
66 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
*
3703342 TTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACACT
1 TTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACACT
3703407 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
66 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
*
3703457 TTTCAAATCCAATGATTGGTTTTTGGGGTTCCTACCAAACCAAATCAGATAACTCAAAGAACACT
1 TTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACACT
*
3703522 TCTAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
66 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
* * *
3703572 TTTCAAATCTAATGATTGGTTTTTGGAGTTTATACCAAACCAAATCAGATAACTCAAAGAACACT
1 TTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACACT
3703637 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAG-AATATTCATC
66 TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAA-ATTCATC
3703687 TT
1 TT
3703689 GCTCCAGTTA
Statistics
Matches: 442, Mismatches: 18, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
114 20 0.05
115 422 0.95
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (115 bp):
TTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCATC
Found at i:3710005 original size:19 final size:21
Alignment explanation
Indices: 3709963--3710011 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
3709953 CTAACAGACA
3709963 AATAAAAT-AAAAAATACTTG
1 AATAAAATAAAAAAATACTTG
3709983 AATAAAATAAAAAAATA-TT-
1 AATAAAATAAAAAAATACTTG
*
3710002 AATAGAATAA
1 AATAAAATAA
3710012 TATAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.33
20 10 0.37
21 8 0.30
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
AATAAAATAAAAAAATACTTG
Found at i:3712174 original size:3 final size:3
Alignment explanation
Indices: 3712142--3712212 Score: 106
Period size: 3 Copynumber: 23.0 Consensus size: 3
3712132 TTGGGTTTTG
* *
3712142 TAA TAT TAA TAAA TAA TATA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
3712189 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
3712213 ATTTAAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3713777 original size:20 final size:20
Alignment explanation
Indices: 3713752--3713844 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
3713742 TTTTCCCAAT
3713752 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
3713772 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
3713792 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
3713813 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
3713834 TCGCAATGCGA
1 TCGCAATGCGA
3713845 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:3713794 original size:41 final size:41
Alignment explanation
Indices: 3713749--3713844 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
3713739 CGATTTTCCC
3713749 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
3713790 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
3713831 AAATCGCAATGCGA
1 AATTCGCAATGCGA
3713845 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:3713798 original size:21 final size:20
Alignment explanation
Indices: 3713752--3713844 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
3713742 TTTTCCCAAT
*
3713752 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
3713772 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
3713792 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
3713813 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
3713834 TCGCAATGCGA
1 TCGCAATGCGA
3713845 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:3713858 original size:20 final size:20
Alignment explanation
Indices: 3713833--3713926 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
3713823 AATTGGGAAA
*
3713833 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
3713853 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* * *
3713874 ATCGCAACGAGTTACTTACT
1 ATCGCAACGCGATACTGACT
*
3713894 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3713914 TTCGCAACGCGAT
1 ATCGCAACGCGAT
3713927 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3713875 original size:41 final size:41
Alignment explanation
Indices: 3713830--3713907 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
3713820 GCGAATTGGG
* * *
3713830 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
3713871 AAAATCGCAACGAGTTACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
3713908 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:3714486 original size:19 final size:19
Alignment explanation
Indices: 3714448--3714514 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
3714438 TTCGAGAATG
*
3714448 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
3714468 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
3714487 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
3714506 AAAATCGCA
1 AAAATCGCA
3714515 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:3714532 original size:19 final size:19
Alignment explanation
Indices: 3714510--3714560 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
3714500 GAAACCAAAA
*
3714510 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3714529 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3714548 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3714561 CTCTCATCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3714580 original size:33 final size:33
Alignment explanation
Indices: 3714543--3714630 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
3714533 GTTGCGATTT
3714543 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
3714576 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
3714609 TCATTTCCGCGTTGCAATTCTC
1 TCATTT-CGCGTTGCGATTCTC
3714631 ATTATCTCGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 38 0.73
34 14 0.27
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:3714632 original size:20 final size:20
Alignment explanation
Indices: 3714609--3714655 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3714599 ATTGCGATAG
3714609 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
3714629 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
3714649 TCATTTC
1 TCATTTC
3714656 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:3716716 original size:42 final size:42
Alignment explanation
Indices: 3716656--3716778 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
3716646 GCCCGACTCG
* * *
3716656 CCTATCATCCATCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
3716698 CCTATCATTCC-TCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCA-TCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
3716740 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCATCAAGA-GTCCACTCCCACCGTTCAAGAG
3716779 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.03
42 58 0.87
43 7 0.10
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:3716736 original size:21 final size:21
Alignment explanation
Indices: 3716712--3716778 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3716702 TCATTCCTCG
3716712 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3716733 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3716754 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3716775 AGAG
1 AGAG
3716779 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3718156 original size:14 final size:14
Alignment explanation
Indices: 3718137--3718172 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3718127 ATTGTTTAAT
3718137 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3718151 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3718165 TGATTTGT
1 TGATTTGT
3718173 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3718353 original size:19 final size:19
Alignment explanation
Indices: 3718331--3718448 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
3718321 CGAAATTAAA
3718331 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3718350 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
3718365 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3718383 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
3718398 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
3718416 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
3718435 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
3718449 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3718377 original size:33 final size:33
Alignment explanation
Indices: 3718335--3718428 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
3718325 ATTAAATTCG
3718335 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
3718368 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
3718401 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3718429 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:3722239 original size:14 final size:14
Alignment explanation
Indices: 3722220--3722256 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3722210 CATCAATTAA
3722220 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3722234 ACAAATCATCTTTT
1 ACAAATCAACATTT
3722248 ACAAATCAA
1 ACAAATCAA
3722257 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3722828 original size:14 final size:14
Alignment explanation
Indices: 3722809--3722845 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3722799 CATCAATTAA
3722809 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3722823 ACAAATCATCTTTT
1 ACAAATCAACATTT
3722837 ACAAATCAA
1 ACAAATCAA
3722846 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3723414 original size:14 final size:14
Alignment explanation
Indices: 3723395--3723431 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3723385 CATCAATTAA
3723395 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3723409 ACAAATCATCTTTT
1 ACAAATCAACATTT
3723423 ACAAATCAA
1 ACAAATCAA
3723432 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3724339 original size:590 final size:590
Alignment explanation
Indices: 3721844--3727271 Score: 9845
Period size: 589 Copynumber: 9.1 Consensus size: 590
3721834 TTTAACAATT
*
3721844 ATTATTGAATTCTAGGTACTTAACCAAATATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3721909 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3721974 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
3722039 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGTGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
*
3722104 TCGTTGCGATAGCCATTTCGCGTTGCGATAGGCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3722169 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
3722234 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3722299 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
3722364 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
3722429 AGCAA
586 AGCAA
3722434 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3722499 CTTGCATTATGTGTATTTTATGTGTGCAC-TTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3722563 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
3722628 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
3722693 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3722758 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
3722823 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAT-ATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3722887 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
3722952 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
3723017 AGCAA
586 AGCAA
3723022 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAA-G-G-ATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3723084 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3723149 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
3723214 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
3723279 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3723344 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
3723409 ACAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3723473 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
3723538 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
3723603 AGCAA
586 AGCAA
3723608 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3723673 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
*
3723738 GAGTTTGAACATTTCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
3723803 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
3723868 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3723933 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
*
3723998 ATAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3724063 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
*
3724128 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTATAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
3724193 AGCAA
586 AGCAA
3724198 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3724263 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3724328 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
3724393 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
3724458 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3724523 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
3724588 ACAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3724652 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
3724717 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
*
3724782 AACAA
586 AGCAA
3724787 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3724852 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3724917 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
3724982 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
3725047 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3725112 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
3725177 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3725242 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
3725307 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
3725372 AGCAA
586 AGCAA
3725377 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAAC-AAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3725441 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3725506 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
3725571 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
3725636 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3725701 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
*
3725766 ATAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAAT-ATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3725830 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCA-TTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
3725894 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTAC-AAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
3725958 AGCAA
586 AGCAA
3725963 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3726028 CTTGCATTATGTGTA-TTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3726092 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
3726157 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
3726222 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
3726287 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
3726352 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
3726417 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
3726482 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
3726547 AGC-A
586 AGCAA
3726551 A--ATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
3726614 CTTGCATTA--TGTATTTTATGTGTGCACTTTTAACATTTTCAGTCAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
3726677 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTAT--C
*
3726742 AATGCGAAAATGGTTATCGCAACGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATG
194 ---GC----A-----AT------GCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACG
*** * *
3726807 -AAATCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
241 AAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATTTCGCGTTGCGA---T-A-GT--C--T--
* * * *** *
3726871 GATTTT-CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTG-CCTTCAACATAAAGCA
295 G-TTTTGC-C-TT-C-A-A--CA--------T---AAAG-CAG-ATTGAAAATCAAC--AAATCA
* * * *
3726934 GATTGAAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
337 -ACT----AT-TAC-ATTTCA----AC-ACAAATTATGTACACATCAATTAAACAAATCAACATT
3726999 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
390 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
* **
3727064 AATTATTGAATCAA-GAATCAACAACTTTGTGACCCTGTACATCCATTTCATGCAGCTCACTTAA
455 AATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAA
3727128 GGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAA
520 GGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAA
3727193 CAGCAA
585 CAGCAA
*
3727199 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATGTGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
3727264 CTTGCATT
66 CTTGCATT
3727272 TGACTTACCA
Statistics
Matches: 4722, Mismatches: 35, Indels: 102
0.97 0.01 0.02
Matches are distributed among these distances:
584 4 0.00
585 161 0.03
586 1026 0.22
587 164 0.03
588 349 0.07
589 1671 0.35
590 907 0.19
594 1 0.00
599 2 0.00
604 43 0.01
605 41 0.01
607 1 0.00
608 1 0.00
609 1 0.00
611 1 0.00
613 1 0.00
615 2 0.00
616 5 0.00
617 2 0.00
618 1 0.00
619 1 0.00
620 1 0.00
622 2 0.00
630 1 0.00
633 3 0.00
634 7 0.00
635 3 0.00
636 5 0.00
637 2 0.00
641 2 0.00
642 2 0.00
643 5 0.00
647 117 0.02
648 118 0.02
650 69 0.01
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (590 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
AGCAA
Found at i:3724593 original size:14 final size:14
Alignment explanation
Indices: 3724574--3724610 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3724564 CATCAATTAA
3724574 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3724588 ACAAATCATCTTTT
1 ACAAATCAACATTT
3724602 ACAAATCAA
1 ACAAATCAA
3724611 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3725182 original size:14 final size:14
Alignment explanation
Indices: 3725163--3725199 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3725153 CATCAATTAA
3725163 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3725177 ACAAATCATCTTTT
1 ACAAATCAACATTT
3725191 ACAAATCAA
1 ACAAATCAA
3725200 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3726357 original size:14 final size:14
Alignment explanation
Indices: 3726338--3726374 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3726328 CATCAATTAA
3726338 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3726352 ACAAATCATCTTTT
1 ACAAATCAACATTT
3726366 ACAAATCAA
1 ACAAATCAA
3726375 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3726761 original size:20 final size:20
Alignment explanation
Indices: 3726736--3726792 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3726726 TTCATTTGAC
*
3726736 TATCGCAATGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
3726756 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
*
3726776 TATCGCAACGAGAAAAT
1 TATCGCAACGCGAAAAT
3726793 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGT
Found at i:3726834 original size:14 final size:16
Alignment explanation
Indices: 3726814--3726887 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
3726804 ATGAAATCGC
3726814 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
3726829 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
3726846 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
3726865 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
3726881 -TTGCGAT
1 ATTGCGAT
3726888 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:3726851 original size:19 final size:19
Alignment explanation
Indices: 3726810--3726877 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
3726800 CGAAATGAAA
3726810 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3726826 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3726843 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3726862 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
3726878 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3727005 original size:14 final size:14
Alignment explanation
Indices: 3726986--3727022 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3726976 CATCAATTAA
3726986 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3727000 ACAAATCATCTTTT
1 ACAAATCAACATTT
3727014 ACAAATCAA
1 ACAAATCAA
3727023 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3728922 original size:20 final size:19
Alignment explanation
Indices: 3728887--3728952 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 19
3728877 GAAACTTAAA
3728887 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3728906 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
3728926 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
3728944 ATCGCAACG
1 ATCGCAACG
3728953 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.39
20 17 0.41
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3728961 original size:14 final size:14
Alignment explanation
Indices: 3728942--3729030 Score: 88
Period size: 14 Copynumber: 5.8 Consensus size: 14
3728932 ATGCGAAATG
3728942 AAATCGCAACGACA
1 AAATCGCAACGACA
*
3728956 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
3728972 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
*
3728988 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
3729004 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
3729020 AAATCGCAACG
1 AAATCGCAACG
3729031 CGAAACACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 29 0.46
16 16 0.25
18 18 0.29
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:3728970 original size:32 final size:32
Alignment explanation
Indices: 3728926--3729035 Score: 211
Period size: 32 Copynumber: 3.4 Consensus size: 32
3728916 GGAAATGGCT
*
3728926 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3728958 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3728990 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3729022 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3729036 CACAAATCGC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:3729064 original size:19 final size:17
Alignment explanation
Indices: 3729042--3729136 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
3729032 GAAACACAAA
3729042 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
3729061 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
3729077 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
3729093 TCGCGTTGCGA-TT--TG
1 TCGC-TTGCGATTTCATT
3729108 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
3729125 TCGCATTGCGAT
1 TCGC-TTGCGAT
3729137 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
13 6 0.10
14 9 0.15
15 6 0.10
16 8 0.13
17 6 0.10
18 10 0.16
19 16 0.26
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:3729094 original size:32 final size:33
Alignment explanation
Indices: 3729047--3729136 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
3729037 ACAAATCGCA
3729047 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
3729080 TTGCGA-TTTCATTTCGCGTTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
3729111 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
3729137 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 13 0.24
32 35 0.65
33 6 0.11
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:3729155 original size:20 final size:19
Alignment explanation
Indices: 3729121--3729175 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3729111 TTGCGATTTT
*
3729121 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3729140 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3729160 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3729176 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3729666 original size:18 final size:18
Alignment explanation
Indices: 3729640--3729684 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3729630 GTCGATCAGA
*
3729640 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
3729658 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
3729676 TGATGGCTC
1 TGATGGCTC
3729685 CGAAGTGGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:3734365 original size:20 final size:20
Alignment explanation
Indices: 3734322--3734365 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3734312 TGTTTTTAAT
*
3734322 AAATTTTTATCTATAAAATT
1 AAATTTTTATCTATAAAATA
*
3734342 AAATTTTTAT-TTTCAAAATA
1 AAATTTTTATCTAT-AAAATA
3734362 AAAT
1 AAAT
3734366 ATTAAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTTTTATCTATAAAATA
Done.