Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 82 of 126
Found at i:16607961 original size:22 final size:21
Alignment explanation
Indices: 16607928--16607972 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
16607918 TTTTTAAAAA
*
16607928 TTTTTAAATTTTTAAATTTTT
1 TTTTTAAATTTTAAAATTTTT
*
16607949 TTTTTGAATTTTTAAAATTTTT
1 TTTTT-AAATTTTAAAATTTTT
16607971 TT
1 TT
16607973 AATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTAAATTTTAAAATTTTT
Found at i:16608113 original size:21 final size:20
Alignment explanation
Indices: 16608084--16608127 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
16608074 ATTTAGAATG
* *
16608084 TTTTTAAGTTTTTTAATTTT
1 TTTTTAAGTTTTTAAAATTT
16608104 TTTTTGAAGTTTTTAAAATTT
1 TTTTT-AAGTTTTTAAAATTT
16608125 TTT
1 TTT
16608128 AGAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTTTAAGTTTTTAAAATTT
Found at i:16608169 original size:28 final size:26
Alignment explanation
Indices: 16608123--16608187 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
16608113 TTTTTAAAAT
* * * *
16608123 TTTTTAGAAAATTTTAAAATATTTATG
1 TTTTTA-AAAATTTAAAAAAATTAAAG
16608150 ATTTTTAAAAATTTAAAAAAAATTAAAG
1 -TTTTTAAAAATTT-AAAAAAATTAAAG
16608178 TTTTTAAAAA
1 TTTTTAAAAA
16608188 AATTAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (26 bp):
TTTTTAAAAATTTAAAAAAATTAAAG
Found at i:16608175 original size:18 final size:18
Alignment explanation
Indices: 16608154--16608193 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16608144 TTTATGATTT
16608154 TTAAAAATTTAAAAAAAA
1 TTAAAAATTTAAAAAAAA
** *
16608172 TTAAAGTTTTTAAAAAAA
1 TTAAAAATTTAAAAAAAA
16608190 TTAA
1 TTAA
16608194 TATTTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TTAAAAATTTAAAAAAAA
Found at i:16610767 original size:10 final size:9
Alignment explanation
Indices: 16610741--16610779 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
16610731 GTTTATTTTT
16610741 TTATTAAAA
1 TTATTAAAA
16610750 TT-TTAAAA
1 TTATTAAAA
16610758 TTAATTAAAA
1 TT-ATTAAAA
16610768 CTTATTAAAA
1 -TTATTAAAA
16610778 TT
1 TT
16610780 TTTTTTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.30
9 4 0.15
10 13 0.48
11 2 0.07
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (9 bp):
TTATTAAAA
Found at i:16610956 original size:29 final size:30
Alignment explanation
Indices: 16610924--16610980 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
16610914 GTAATCTTAA
*
16610924 TTTTAATATTTA-AAATAATCTCTTTAATT
1 TTTTAATATTTACAAAAAATCTCTTTAATT
* * *
16610953 TTTTATTTTTTACAAAAAATCTTTTTAA
1 TTTTAATATTTACAAAAAATCTCTTTAA
16610981 AACTTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTTAATATTTACAAAAAATCTCTTTAATT
Found at i:16611327 original size:20 final size:20
Alignment explanation
Indices: 16611304--16611342 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16611294 AATACAAACA
*
16611304 CAAATTAAAAGATGCAAATT
1 CAAACTAAAAGATGCAAATT
* *
16611324 CAAACTGAAATATGCAAAT
1 CAAACTAAAAGATGCAAAT
16611343 GATCAATGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (20 bp):
CAAACTAAAAGATGCAAATT
Found at i:16611913 original size:32 final size:30
Alignment explanation
Indices: 16611835--16611891 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16611825 AAAAAAATTT
16611835 ACAATTCAAT-AAAC-TACA-AATAAAATAC
1 ACAATTCAATAAAACATA-ATAATAAAATAC
16611863 ACAATTCAATAAAACATAATAATAAAATA
1 ACAATTCAATAAAACATAATAATAAAATA
16611892 ATCACAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 10 0.38
29 5 0.19
30 11 0.42
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (30 bp):
ACAATTCAATAAAACATAATAATAAAATAC
Found at i:16613092 original size:6 final size:7
Alignment explanation
Indices: 16613072--16613099 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
16613062 AACTAAATAC
16613072 AATAAAA
1 AATAAAA
16613079 AATAAAA
1 AATAAAA
16613086 AATAAAA
1 AATAAAA
16613093 AATAAAA
1 AATAAAA
16613100 TAGAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:16615141 original size:13 final size:14
Alignment explanation
Indices: 16615111--16615153 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
16615101 TTGAATTGTC
16615111 AAATTTTGAACTTT
1 AAATTTTGAACTTT
*
16615125 AAATTTTGATC-TT
1 AAATTTTGAACTTT
*
16615138 AAATTTTGAATTTT
1 AAATTTTGAACTTT
16615152 AA
1 AA
16615154 GCTCATATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (14 bp):
AAATTTTGAACTTT
Found at i:16621911 original size:19 final size:18
Alignment explanation
Indices: 16621867--16621933 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 18
16621857 CATATAAATT
*
16621867 TTAATAAAATT-TATATAA
1 TTAATTAAATTATA-ATAA
16621885 TT--TTAAATTATAATTAA
1 TTAATTAAATTATAA-TAA
16621902 TTAATTAAATTATAATAA
1 TTAATTAAATTATAATAA
16621920 TT-A-TAAATTA-AATA
1 TTAATTAAATTATAATA
16621934 CTCTCTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
15 4 0.09
16 14 0.32
17 8 0.18
18 7 0.16
19 11 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATTAAATTATAATAA
Found at i:16621920 original size:14 final size:14
Alignment explanation
Indices: 16621890--16621933 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
16621880 TATAATTTTA
*
16621890 AATTATAATTAATT
1 AATTATAATTAAAT
16621904 AATTA-AATTATAAT
1 AATTATAATTA-AAT
16621918 AATTATAAATTAAAT
1 AATTAT-AATTAAAT
16621933 A
1 A
16621934 CTCTCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 4 0.15
16 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATAATTAAAT
Found at i:16622222 original size:16 final size:17
Alignment explanation
Indices: 16622195--16622257 Score: 76
Period size: 16 Copynumber: 3.7 Consensus size: 17
16622185 AATATTATTT
16622195 TTAATATAAATATAAAA
1 TTAATATAAATATAAAA
16622212 TTAAT-TAAATATAAAAAA
1 TTAATATAAATAT--AAAA
**
16622230 TGCATATAAATATAAAA
1 TTAATATAAATATAAAA
16622247 TTAA-ATAAATA
1 TTAATATAAATA
16622258 ATATTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 14 0.36
17 11 0.28
18 7 0.18
19 7 0.18
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TTAATATAAATATAAAA
Found at i:16622260 original size:19 final size:19
Alignment explanation
Indices: 16622203--16622266 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 19
16622193 TTTTAATATA
*
16622203 AATATAAAATTAATTAAAT
1 AATATAAAATTAAATAAAT
* ** *
16622222 -ATA-AAAAATGCATATA-
1 AATATAAAATTAAATAAAT
16622238 AATATAAAATTAAATAAAT
1 AATATAAAATTAAATAAAT
16622257 AATATTAAAA
1 AATA-TAAAA
16622267 ATAATTATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 7
0.67 0.19 0.15
Matches are distributed among these distances:
17 11 0.34
18 12 0.38
19 4 0.12
20 5 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AATATAAAATTAAATAAAT
Found at i:16624214 original size:35 final size:35
Alignment explanation
Indices: 16624168--16624239 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
16624158 CAACAAAGCA
* *
16624168 AAACAATTAATTTATTTCTTGTATGGAAATATGCT
1 AAACAATTAATTTATTTCTTGCATGGAAAGATGCT
16624203 AAACAATTAATTTATTTCTTGCATGGAAAGATGCT
1 AAACAATTAATTTATTTCTTGCATGGAAAGATGCT
16624238 AA
1 AA
16624240 CTTCTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (35 bp):
AAACAATTAATTTATTTCTTGCATGGAAAGATGCT
Found at i:16646129 original size:4 final size:4
Alignment explanation
Indices: 16646120--16646226 Score: 57
Period size: 4 Copynumber: 27.0 Consensus size: 4
16646110 GAGCCCAATA
* *
16646120 ATTT ATTT ATTT ATTT ACATTT -TTT ATGT ATAT ATTT -TTT ATTT ATTT
1 ATTT ATTT ATTT ATTT --ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * *
16646168 ATCCT ATTT A-TT ATTTT ATTT -TATT A-TT ATTTT ATGT -TTT ATGT
1 AT-TT ATTT ATTT A-TTT ATTT AT-TT ATTT A-TTT ATTT ATTT ATTT
*
16646212 -TTT ATTT TTTT ATTT
1 ATTT ATTT ATTT ATTT
16646227 GGTTTGTTAC
Statistics
Matches: 79, Mismatches: 11, Indels: 26
0.68 0.09 0.22
Matches are distributed among these distances:
3 17 0.22
4 49 0.62
5 9 0.11
6 4 0.05
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:16646178 original size:32 final size:32
Alignment explanation
Indices: 16646120--16646199 Score: 76
Period size: 32 Copynumber: 2.5 Consensus size: 32
16646110 GAGCCCAATA
* *
16646120 ATTTATTTATTTATTTACATTTTTTATGTA-TAT
1 ATTT-TTTATTTATTTACACTATTTAT-TATTAT
*
16646153 ATTTTTTATTTATTTATC-CTATTTATTATTTT
1 ATTTTTTATTTATTTA-CACTATTTATTATTAT
16646185 ATTTTATTA-TTATTT
1 ATTTT-TTATTTATTT
16646200 TATGTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 2 0.05
32 31 0.76
33 8 0.20
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (32 bp):
ATTTTTTATTTATTTACACTATTTATTATTAT
Found at i:16648038 original size:18 final size:16
Alignment explanation
Indices: 16647990--16648021 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16647980 TCTATTTATG
16647990 TAAAAGAAACATAAAA
1 TAAAAGAAACATAAAA
16648006 TAAAAGAAACATAAAA
1 TAAAAGAAACATAAAA
16648022 AATAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
TAAAAGAAACATAAAA
Found at i:16649436 original size:14 final size:14
Alignment explanation
Indices: 16649417--16649446 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16649407 CTTGTAACTG
16649417 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
*
16649431 TTTTTTTTTTTCTT
1 TTTTTTTTCTTCTT
16649445 TT
1 TT
16649447 CAAGAGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:16651144 original size:4 final size:4
Alignment explanation
Indices: 16651135--16651159 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
16651125 TTAGGTAAAT
16651135 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
16651160 CTTTATTTTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:16651523 original size:16 final size:16
Alignment explanation
Indices: 16651512--16651542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16651502 ATTAAATTAT
16651512 AAAAATAATAAATAAC
1 AAAAATAATAAATAAC
*
16651528 AAAAATAATGAATAA
1 AAAAATAATAAATAA
16651543 TGAGCAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATAATAAATAAC
Found at i:16652991 original size:20 final size:20
Alignment explanation
Indices: 16652966--16653005 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16652956 TTCCTTAAAA
16652966 TTTTA-TTTATGAAAATTATT
1 TTTTATTTTATG-AAATTATT
16652986 TTTTATTTTATGAAATTATT
1 TTTTATTTTATGAAATTATT
16653006 ATTATTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATTTTATGAAATTATT
Found at i:16652997 original size:21 final size:19
Alignment explanation
Indices: 16652966--16653013 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
16652956 TTCCTTAAAA
16652966 TTTTA-TTTATGAAAATTATT
1 TTTTATTTTATG-AAATTA-T
16652986 TTTTATTTTATGAAATTAT
1 TTTTATTTTATGAAATTAT
*
16653005 TATTATTTT
1 TTTTATTTT
16653014 TGCATTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.35
20 11 0.42
21 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTATTTTATGAAATTAT
Found at i:16653292 original size:7 final size:7
Alignment explanation
Indices: 16653280--16653306 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
16653270 AATATTTAAT
16653280 TTATTTA
1 TTATTTA
16653287 TTATTTA
1 TTATTTA
16653294 TTATTTA
1 TTATTTA
16653301 TTATTT
1 TTATTT
16653307 TCATCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:16653397 original size:2 final size:2
Alignment explanation
Indices: 16653390--16653421 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16653380 GTGAAATCCA
16653390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16653422 ATAATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16653753 original size:3 final size:3
Alignment explanation
Indices: 16653747--16653803 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
16653737 TTTCACTTTC
16653747 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16653795 ATT ATT ATT
1 ATT ATT ATT
16653804 TTGTTTATCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16656327 original size:59 final size:58
Alignment explanation
Indices: 16656252--16656776 Score: 712
Period size: 60 Copynumber: 8.9 Consensus size: 58
16656242 GGAAAGAATG
*
16656252 AATTT-TTTT-TAGGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
1 AATTTATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
* *
16656308 AATTTCGATTTTC-AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTGAA
1 AATTT--ATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAA---TATTTTTTGGA
* *
16656369 AATTTA-TTTCTAAGGAAAATTGATACTTTCAACTCTTCCCCAAAAATATTTTTTTTGA
1 AATTTATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGA
16656427 AATTTTGATTTTC-AAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTGGA
1 AA-TTT-ATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGA
* *
16656488 AATTTATTTTTCTTTTAAGGAAAATTGATAATTTCAACTTTTCCCTAAAAATATTTTTTGGA
1 AATTTA-TTTTC---TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
* *
16656550 AATTTATTCT-TAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTGGA
1 AATTTATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
*
16656606 AATTTATTCT-TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
1 AATTTATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
*
16656663 AATTTA-TTTCTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTATTTTGGA
1 AATTTATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TT-TTTTGGA
*
16656723 AATTTA-TTTCTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 AATTTATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
16656777 TAGAATTTTT
Statistics
Matches: 429, Mismatches: 16, Indels: 47
0.87 0.03 0.10
Matches are distributed among these distances:
56 63 0.15
57 92 0.21
58 15 0.03
59 77 0.18
60 100 0.23
61 31 0.07
62 16 0.04
64 35 0.08
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (58 bp):
AATTTATTTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
Found at i:16656877 original size:8 final size:8
Alignment explanation
Indices: 16656857--16656895 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
16656847 CTAATCTAAT
16656857 AAATAAA-
1 AAATAAAC
16656864 AAATAAAC
1 AAATAAAC
16656872 AAAT--A-
1 AAATAAAC
16656877 AAATAAAC
1 AAATAAAC
16656885 AAATAAAC
1 AAATAAAC
16656893 AAA
1 AAA
16656896 GAAAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.14
6 1 0.04
7 8 0.29
8 15 0.54
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATAAAC
Found at i:16656881 original size:13 final size:13
Alignment explanation
Indices: 16656863--16656891 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16656853 TAATAAATAA
16656863 AAAATAAACAAAT
1 AAAATAAACAAAT
16656876 AAAATAAACAAAT
1 AAAATAAACAAAT
16656889 AAA
1 AAA
16656892 CAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAATAAACAAAT
Found at i:16656890 original size:21 final size:20
Alignment explanation
Indices: 16656857--16656900 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
16656847 CTAATCTAAT
*
16656857 AAATAAAAAATAAACAAATA
1 AAATAAAAAATAAACAAAGA
16656877 AAATAAACAAATAAACAAAGA
1 AAATAAA-AAATAAACAAAGA
16656898 AAA
1 AAA
16656901 AAAGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (20 bp):
AAATAAAAAATAAACAAAGA
Found at i:16657275 original size:19 final size:20
Alignment explanation
Indices: 16657232--16657276 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
16657222 AACACCGGTG
* *
16657232 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCA
*
16657252 TCGGAATCTGGAAA-TTTCA
1 CCGGAATCTGGAAATTTTCA
16657271 CCGGAA
1 CCGGAA
16657277 GTTGGCCGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCA
Found at i:16658189 original size:1 final size:1
Alignment explanation
Indices: 16658185--16658275 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
16658175 TTATTTTTGA
* * * * ** ** * *
16658185 TTTTTTTTATTTTTGTTTTTATTTTTTTTATTTTTTTGATTTTTTTGATTTTTTTGTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
16658250 TTTTGTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
16658276 GGCCGAAGCT
Statistics
Matches: 68, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (1 bp):
T
Found at i:16658329 original size:41 final size:41
Alignment explanation
Indices: 16658283--16658976 Score: 817
Period size: 41 Copynumber: 17.0 Consensus size: 41
16658273 TTTGGCCGAA
* * *
16658283 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGAC-TTTGAAAAATAAATT
* * * *
16658324 ACTCCTCTAAAGAGAGG--CAACGGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAAC-GACTTTGAAAAATAAATT
* *
16658364 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTT-GAAAAATAAATT
* * *
16658406 GCTCCTCTCAACAGAGGCACCACGACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
* *
16658446 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
* *
16658487 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
* * * * *
16658528 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
* * * *
16658569 GCTCCTCTCAACAGAGGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
* * *
16658610 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
* *
16658651 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
* * * * * *
16658692 GCTCCTCTCAATAGAGGTACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
*
16658733 GCTCCTCTAAACAGAGG--CAACGGAACTTTAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAAC-G-ACTTTGAAAAATAAATT
16658774 GCTCCTCTAAACAGAGG--CAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAAC-G-ACTTTGAAAAATAAATT
16658815 GCTCCTCTAAACAGAGG--CAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAAC-G-ACTTTGAAAAATAAATT
16658856 GCTCCTCTAAACAGAGG--CAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAAC-G-ACTTTGAAAAATAAATT
16658897 GCTCCTCTAAACAGAGG--CAACGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAACG-ACTTTGAAAAATAAATT
16658937 GCTCCTCTAAACAGAGG--CAACGAACTTTGAAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACAACG-ACTTTGAAAAA-TAAAT
16658977 ACTCCTAGAC
Statistics
Matches: 607, Mismatches: 37, Indels: 18
0.92 0.06 0.03
Matches are distributed among these distances:
39 11 0.02
40 119 0.20
41 435 0.72
42 42 0.07
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAATT
Found at i:16660019 original size:7 final size:8
Alignment explanation
Indices: 16660000--16660121 Score: 141
Period size: 8 Copynumber: 15.8 Consensus size: 8
16659990 ACTTTTTCCT
16660000 TTTTTTCCA
1 TTTTTT-CA
*
16660009 TTTTTTCT
1 TTTTTTCA
16660017 TTTTTTCA
1 TTTTTTCA
16660025 TTTTTTCA
1 TTTTTTCA
16660033 TTTTTTTTCA
1 --TTTTTTCA
16660043 TTTTTTCA
1 TTTTTTCA
16660051 -TTTTTCA
1 TTTTTTCA
*
16660058 TTTTTCCA
1 TTTTTTCA
16660066 TTTTTTCA
1 TTTTTTCA
16660074 --TTTT--
1 TTTTTTCA
16660078 TTTTTT-A
1 TTTTTTCA
16660085 TTTTTTCA
1 TTTTTTCA
16660093 -TTTTTCA
1 TTTTTTCA
*
16660100 TTTTTCCA
1 TTTTTTCA
16660108 TTTTTTCA
1 TTTTTTCA
16660116 TTTTTT
1 TTTTTT
16660122 TCAAGCATAG
Statistics
Matches: 99, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
6 8 0.08
7 20 0.20
8 57 0.58
9 6 0.06
10 8 0.08
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:16660030 original size:34 final size:33
Alignment explanation
Indices: 16659987--16660124 Score: 140
Period size: 34 Copynumber: 4.1 Consensus size: 33
16659977 GTCCTCCTTG
16659987 TTCACTTTTTCCTTTTTTTCCATTTTTTCTTTTT
1 TTCA-TTTTTCCTTTTTTTCCATTTTTTCTTTTT
* * *
16660021 TTCATTTTTTCATTTTTTTTCATTTTTTC-ATTT
1 TTCA-TTTTTCCTTTTTTTCCATTTTTTCTTTTT
* *
16660054 TTCATTTTTCCATTTTTT-CATTTTTTTTTTATTTT
1 TTCATTTTTCCTTTTTTTCCA--TTTTTTCT-TTTT
*
16660089 TTCATTTTT-C-ATTTTTCCATTTTTTCATTTTT
1 TTCATTTTTCCTTTTTTTCCATTTTTTC-TTTTT
16660121 TTCA
1 TTCA
16660125 AGCATAGTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
31 2 0.02
32 26 0.30
33 19 0.22
34 29 0.33
35 12 0.14
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (33 bp):
TTCATTTTTCCTTTTTTTCCATTTTTTCTTTTT
Found at i:16660038 original size:42 final size:40
Alignment explanation
Indices: 16659987--16660123 Score: 175
Period size: 42 Copynumber: 3.3 Consensus size: 40
16659977 GTCCTCCTTG
* * * *
16659987 TTCACTTTTTCCTTTTTTTCCATTTTTTCTTTTTTTCATTTT
1 TTCATTTTTTTCTTTTTTT-CA-TTTTTCATTTTTCCATTTT
*
16660029 TTCATTTTTTTTCATTTTTTCATTTTTCATTTTTCCATTTT
1 TTCA-TTTTTTTCTTTTTTTCATTTTTCATTTTTCCATTTT
*
16660070 TTCATTTTTTTTTTATTTTTTCATTTTTCATTTTTCCATTTT
1 TTCA-TTTTTTTCT-TTTTTTCATTTTTCATTTTTCCATTTT
16660112 TTCATTTTTTTC
1 TTCATTTTTTTC
16660124 AAGCATAGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
41 36 0.42
42 37 0.44
43 12 0.14
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (40 bp):
TTCATTTTTTTCTTTTTTTCATTTTTCATTTTTCCATTTT
Found at i:16660103 original size:6 final size:7
Alignment explanation
Indices: 16660036--16660120 Score: 95
Period size: 7 Copynumber: 11.7 Consensus size: 7
16660026 TTTTTCATTT
16660036 TTTTTCA
1 TTTTTCA
16660043 TTTTTTCA
1 -TTTTTCA
16660051 TTTTTCA
1 TTTTTCA
16660058 TTTTTCCA
1 TTTTT-CA
16660066 TTTTTTCA
1 -TTTTTCA
16660074 TTTTT--
1 TTTTTCA
16660079 TTTTT-A
1 TTTTTCA
16660085 TTTTTTCA
1 -TTTTTCA
16660093 TTTTTCA
1 TTTTTCA
16660100 TTTTTCCA
1 TTTTT-CA
16660108 TTTTTTCA
1 -TTTTTCA
16660116 TTTTT
1 TTTTT
16660121 TTCAAGCATA
Statistics
Matches: 70, Mismatches: 0, Indels: 15
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.07
7 39 0.56
8 16 0.23
9 10 0.14
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:16667871 original size:58 final size:57
Alignment explanation
Indices: 16667690--16667958 Score: 431
Period size: 56 Copynumber: 4.7 Consensus size: 57
16667680 TTTTTTTTAG
*
16667690 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTT-TGA
1 GGAAAATTGATACTTTCAACTTTT-CCTAAAAATATTTTTTTTGAAATTTATTTCTAA
*
16667747 GGAAAATTGATACTTTCAACTTTTCCCAAAAATA--TTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
*
16667802 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCC-TAAAAATATTTTTTTTGAAATTTATTTCTAA
*
16667860 GGAAAATTGATACTTTCAACTTTTCCCAAAAAGTA--TTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTAAAAA-TATTTTTTTTGAAATTTATTTCTAA
16667916 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTT-CCTAAAAATATTTTTTTT
16667959 TGGAACTTTT
Statistics
Matches: 197, Mismatches: 7, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
54 17 0.09
55 28 0.14
56 62 0.31
57 36 0.18
58 54 0.27
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
Found at i:16667932 original size:114 final size:112
Alignment explanation
Indices: 16667690--16667958 Score: 511
Period size: 114 Copynumber: 2.4 Consensus size: 112
16667680 TTTTTTTTAG
16667690 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTGAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTGAGGAAAATT
16667755 GATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTATTTCTAA
66 GATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTATTTCTAA
*
16667802 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAATTTATTTCTGAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTT-TGAGGAAAAT
16667867 TGATACTTTCAACTTTTCCCAAAAAGTATTTTTTGAAATTTATTTCTAA
65 TGATACTTTCAACTTTTCCCAAAAA-TATTTTTTGAAATTTATTTCTAA
16667916 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
16667959 TGGAACTTTT
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
112 53 0.35
113 35 0.23
114 65 0.42
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (112 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTGAGGAAAATT
GATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTATTTCTAA
Found at i:16668010 original size:11 final size:11
Alignment explanation
Indices: 16667994--16668049 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
16667984 AGAAAAATAG
16667994 AAAAATAAAAA
1 AAAAATAAAAA
16668005 AAAAATAAAAAA
1 AAAAAT-AAAAA
*
16668017 AGAAAAGTAAAAC
1 A-AAAA-TAAAAA
*
16668030 AAAACTAAAAA
1 AAAAATAAAAA
*
16668041 TAAAATAAA
1 AAAAATAAA
16668050 GATAAAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
11 18 0.49
12 9 0.24
13 9 0.24
14 1 0.03
ACGTcount: A:0.82, C:0.04, G:0.04, T:0.11
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:16668020 original size:25 final size:25
Alignment explanation
Indices: 16667986--16668040 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
16667976 TTATTTAAAG
*
16667986 AAAAATAGAAAAATAAAAAAAAAAT
1 AAAAAAAGAAAAATAAAAAAAAAAT
* * *
16668011 AAAAAAAGAAAAGTAAAACAAAACT
1 AAAAAAAGAAAAATAAAAAAAAAAT
16668036 AAAAA
1 AAAAA
16668041 TAAAATAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.82, C:0.04, G:0.05, T:0.09
Consensus pattern (25 bp):
AAAAAAAGAAAAATAAAAAAAAAAT
Found at i:16668028 original size:19 final size:19
Alignment explanation
Indices: 16667982--16668033 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
16667972 TTTTTTATTT
* *
16667982 AAAGAAAAATAGAAAAATA
1 AAAGAAAAATAAAAAAAGA
*
16668001 AAAAAAAAATAAAAAAAGA
1 AAAGAAAAATAAAAAAAGA
* *
16668020 AAAGTAAAACAAAA
1 AAAGAAAAATAAAA
16668034 CTAAAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.83, C:0.02, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAGAAAAATAAAAAAAGA
Found at i:16668040 original size:7 final size:6
Alignment explanation
Indices: 16667994--16668138 Score: 54
Period size: 6 Copynumber: 23.8 Consensus size: 6
16667984 AGAAAAATAG
* * *
16667994 AAAAAT AAAAA- AAAAAT AAAAAA AGAAAAGT -AAAAC AAAACT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAA-T AAAAAT AAAAAT AAAAAT
* * * * * **
16668042 -AAAAT AAAGAT AAAAA- GAATAT -TAAAT AAACAT -AATCT AATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT
16668087 AAAAAT AATAAAT AAACAAAT AAACAAAT AAAAATT CAAAAA- AAAAA-
1 AAAAAT AA-AAAT -AA-AAAT -AA-AAAT AAAAA-T -AAAAAT AAAAAT
16668134 AAAAA
1 AAAAA
16668139 CCTGGAGCGG
Statistics
Matches: 107, Mismatches: 19, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
5 29 0.27
6 44 0.41
7 15 0.14
8 19 0.18
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:16668054 original size:11 final size:11
Alignment explanation
Indices: 16667994--16668102 Score: 55
Period size: 11 Copynumber: 9.8 Consensus size: 11
16667984 AGAAAAATAG
*
16667994 AAAAATAAAAA
1 AAAAATAAAAT
16668005 AAAAATAAAA-
1 AAAAATAAAAT
* *
16668015 AAAGA-AAAGT
1 AAAAATAAAAT
*
16668025 AAAACA-AAACT
1 AAAA-ATAAAAT
16668036 AAAAATAAAAT
1 AAAAATAAAAT
*
16668047 AAAGATAAAA-
1 AAAAATAAAAT
* *
16668057 AGAATATTAAAT
1 A-AAAATAAAAT
* **
16668069 AAACATAATCT
1 AAAAATAAAAT
16668080 AATAAATAAAAAT
1 AA-AAAT-AAAAT
16668093 AATAAATAAA
1 AA-AAATAAA
16668103 CAAATAAACA
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
9 3 0.04
10 9 0.12
11 47 0.62
12 7 0.09
13 10 0.13
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:16668101 original size:31 final size:29
Alignment explanation
Indices: 16668051--16668121 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
16668041 TAAAATAAAG
* * *
16668051 ATAAA-AAGAATATTAAATAAACATAATCTA
1 ATAAATAAAAATAATAAATAAACA-AAT-AA
16668081 ATAAATAAAAATAATAAATAAACAAATAA
1 ATAAATAAAAATAATAAATAAACAAATAA
*
16668110 ACAAATAAAAAT
1 ATAAATAAAAAT
16668122 TCAAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 12 0.33
30 8 0.22
31 16 0.44
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.23
Consensus pattern (29 bp):
ATAAATAAAAATAATAAATAAACAAATAA
Found at i:16668500 original size:19 final size:20
Alignment explanation
Indices: 16668465--16668508 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
16668455 GGTGCCAGAT
16668465 TCTGGAAAATTCACCGGAA-
1 TCTGGAAAATTCACCGGAAG
*
16668484 TCTGG-AAATTTAGCCGGAAG
1 TCTGGAAAATTCA-CCGGAAG
16668504 TCTGG
1 TCTGG
16668509 GATATCGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 11 0.50
20 5 0.23
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (20 bp):
TCTGGAAAATTCACCGGAAG
Found at i:16668608 original size:16 final size:16
Alignment explanation
Indices: 16668580--16668613 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
16668570 TTGGCCGGAG
16668580 ATTTGCCGAAAATTCA
1 ATTTGCCGAAAATTCA
16668596 ATTTCGCCG-AAATTCA
1 ATTT-GCCGAAAATTCA
16668612 AT
1 AT
16668614 CGGAAATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (16 bp):
ATTTGCCGAAAATTCA
Found at i:16669128 original size:29 final size:30
Alignment explanation
Indices: 16669092--16669167 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
16669082 ATTACACAAA
*
16669092 AAAAAAATAATAATAATATATAA-CTGTAT
1 AAAAAAATAATAATAATATATAATCTGAAT
* *
16669121 AAATAAATACAT-ATAA-ATCTAATCTGAAT
1 AAAAAAATA-ATAATAATATATAATCTGAAT
16669150 AAAAAAATAAATAA-AATA
1 AAAAAAAT-AATAATAATA
16669168 AGATATACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
28 5 0.13
29 28 0.74
30 5 0.13
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (30 bp):
AAAAAAATAATAATAATATATAATCTGAAT
Found at i:16669195 original size:16 final size:17
Alignment explanation
Indices: 16669176--16669219 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
16669166 TAAGATATAC
16669176 ATAATAATAATAAT-GA
1 ATAATAATAATAATAGA
16669192 ATAAT-ATAATAATAGA
1 ATAATAATAATAATAGA
16669208 ATACATAA-AATA
1 ATA-ATAATAATA
16669220 CAAAAGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.32
16 10 0.40
17 6 0.24
18 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
ATAATAATAATAATAGA
Found at i:16669867 original size:2 final size:2
Alignment explanation
Indices: 16669860--16669888 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16669850 ACAGCTCACT
16669860 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 T
16669889 TAGTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16671192 original size:50 final size:50
Alignment explanation
Indices: 16671131--16671225 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
16671121 CATTATTTTT
16671131 AATATAATTTTAATCA-GGATATAAATTTTATAATTCATGACTGAAAGTAA
1 AATATAATTTTAATCACGG-TATAAATTTTATAATTCATGACTGAAAGTAA
* *
16671181 AATATAATTTTAATCACGGTATAAATTTTATAATTTATGATTGAA
1 AATATAATTTTAATCACGGTATAAATTTTATAATTCATGACTGAA
16671226 TGTTACACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.41
Consensus pattern (50 bp):
AATATAATTTTAATCACGGTATAAATTTTATAATTCATGACTGAAAGTAA
Found at i:16671337 original size:83 final size:83
Alignment explanation
Indices: 16671237--16671405 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
16671227 GTTACACATG
16671237 CAACAGTATTAATAAATATATTAAAAAGTAATAAATAAAAAAAGTAAAAGATTTTTGGAGGGTCA
1 CAACAGTATTAATAAATATATTAAAAAGTAATAAATAAAAAAAGTAAAAGATTTTTGGAGGGTCA
16671302 AATCCCAAATTAACTCAT
66 AATCCCAAATTAACTCAT
16671320 CAACAGTATTAATAAATATATTAAAAAGTAATAAATAAAAAAAGTAAAAGATTTTTGGAGGGTCA
1 CAACAGTATTAATAAATATATTAAAAAGTAATAAATAAAAAAAGTAAAAGATTTTTGGAGGGTCA
16671385 AATCCCAAATTAACTCAT
66 AATCCCAAATTAACTCAT
16671403 CAA
1 CAA
16671406 GGATTCCAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (83 bp):
CAACAGTATTAATAAATATATTAAAAAGTAATAAATAAAAAAAGTAAAAGATTTTTGGAGGGTCA
AATCCCAAATTAACTCAT
Found at i:16672995 original size:14 final size:15
Alignment explanation
Indices: 16672976--16673004 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16672966 AGCTGGTTAG
16672976 AGTCTTT-AGTGTTT
1 AGTCTTTCAGTGTTT
16672990 AGTCTTTCAGTGTTT
1 AGTCTTTCAGTGTTT
16673005 TGAAGCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.10, G:0.21, T:0.55
Consensus pattern (15 bp):
AGTCTTTCAGTGTTT
Found at i:16675136 original size:41 final size:41
Alignment explanation
Indices: 16675073--16675168 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
16675063 TAAAAAGATG
*
16675073 AAAA-TAATATATAAATATTTATAAGAGTATAT-ATTTTTAA
1 AAAATTAATATATAAATAATTATAAGAGTATATAATTTTT-A
* * ** *
16675113 AAAATTAATTTATAGATAATTATATTATTATATAATTTTTA
1 AAAATTAATATATAAATAATTATAAGAGTATATAATTTTTA
16675154 AAAATTAATA-ATAAA
1 AAAATTAATATATAAA
16675169 GTTAATTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
40 8 0.17
41 32 0.70
42 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (41 bp):
AAAATTAATATATAAATAATTATAAGAGTATATAATTTTTA
Found at i:16676138 original size:3 final size:3
Alignment explanation
Indices: 16676130--16676174 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
16676120 AATTAATCTC
16676130 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16676175 TTAAATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16678111 original size:21 final size:23
Alignment explanation
Indices: 16678076--16678121 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
16678066 TTAATTTTGT
*
16678076 TTTTGTTTTCTCATC-AAACCAG
1 TTTTGTTTGCTCATCTAAACCAG
*
16678098 TTTTG-TTGCTCATCTAAATCAG
1 TTTTGTTTGCTCATCTAAACCAG
16678120 TT
1 TT
16678122 CCCTTTCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (23 bp):
TTTTGTTTGCTCATCTAAACCAG
Found at i:16681605 original size:2 final size:2
Alignment explanation
Indices: 16681600--16681646 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
16681590 TATTATATTC
*
16681600 TG TG TG TG TG TG TG TG -G TG TG TG GG TG TG TG -G T- TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16681639 -G T- TG TG TG
1 TG TG TG TG TG
16681647 AAAGTGGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
TG
Found at i:16684973 original size:60 final size:60
Alignment explanation
Indices: 16684905--16685019 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
16684895 TTATTCGTAC
* * *
16684905 TAAAATGTATATCAAATTACATAACTTTTAGCCGACAAAACCTTGTTATTATGTTCAATT
1 TAAAATGTAAATCAAATTACATAACTCTTAGCCGACAAAACCTTATTATTATGTTCAATT
*
16684965 TAAAATGTAAATCAAATTGCATAACTCTTAGCCGACAAAACCTTATTATTATGTT
1 TAAAATGTAAATCAAATTACATAACTCTTAGCCGACAAAACCTTATTATTATGTT
16685020 AATAACAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (60 bp):
TAAAATGTAAATCAAATTACATAACTCTTAGCCGACAAAACCTTATTATTATGTTCAATT
Found at i:16686004 original size:2 final size:2
Alignment explanation
Indices: 16685991--16686030 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
16685981 GTGCCCATCC
* * *
16685991 AT AT AT AA AT AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16686031 CATGAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:16686247 original size:17 final size:17
Alignment explanation
Indices: 16686221--16686254 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16686211 TGTAAATTTT
16686221 TTTTAATTTTAAGAAAA
1 TTTTAATTTTAAGAAAA
* *
16686238 TTTTATTTTTATGAAAA
1 TTTTAATTTTAAGAAAA
16686255 ACTTATGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTTAATTTTAAGAAAA
Found at i:16686427 original size:20 final size:19
Alignment explanation
Indices: 16686404--16686481 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 19
16686394 AAGTTATTTT
16686404 GAATTTTTAGAACATTTTCA
1 GAATTTTTAGAA-ATTTTCA
16686424 GAATTTTTA-AAATTTTTCA
1 GAATTTTTAGAAA-TTTTCA
* * *
16686443 TAATTTTTCTGAAATTTTGA
1 GAATTTTT-AGAAATTTTCA
*
16686463 GAATTTTTTAGAAAATTTC
1 GAA-TTTTTAGAAATTTTC
16686482 TTTTAGTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.02
19 15 0.32
20 23 0.49
21 8 0.17
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (19 bp):
GAATTTTTAGAAATTTTCA
Found at i:16686431 original size:10 final size:10
Alignment explanation
Indices: 16686404--16686475 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
16686394 AAGTTATTTT
16686404 GAATTTTT-A
1 GAATTTTTCA
*
16686413 GAACATTTTCA
1 GAA-TTTTTCA
16686424 GAATTTTT-A
1 GAATTTTTCA
*
16686433 AAATTTTTCA
1 GAATTTTTCA
* *
16686443 TAATTTTTCT
1 GAATTTTTCA
* *
16686453 GAAATTTTGA
1 GAATTTTTCA
*
16686463 GAATTTTTTA
1 GAATTTTTCA
16686473 GAA
1 GAA
16686476 AATTTCTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
9 11 0.22
10 34 0.69
11 4 0.08
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (10 bp):
GAATTTTTCA
Found at i:16687881 original size:27 final size:27
Alignment explanation
Indices: 16687814--16687893 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
16687804 TTTTATTAAA
* **
16687814 ATTAAAAT-TAAAATAGCATATTTATT
1 ATTAAAATATAAAAAATAATATTTATT
*
16687840 ATTAAAATATTAAAAATAATATTTATT
1 ATTAAAATATAAAAAATAATATTTATT
* * *
16687867 ATT-AAGTCATAAAAAGTATTATTTATT
1 ATTAAAAT-ATAAAAAATAATATTTATT
16687894 TTTATTATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 11 0.25
27 33 0.75
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTAAAATATAAAAAATAATATTTATT
Found at i:16690043 original size:256 final size:257
Alignment explanation
Indices: 16689581--16690073 Score: 826
Period size: 256 Copynumber: 1.9 Consensus size: 257
16689571 AGCAAGGATC
*
16689581 AATCAAGTCATCTTATTTTCCACAAACATAAAAGCAAAGAAAGAAATATTAAAATAAGAAAAACT
1 AATCAAGTCATCTTATTTTCCAAAAACATAAAAGCAAAGAAAGAAATATTAAAATAAGAAAAACT
* * * *
16689646 AGCAACCGTGTTTCAAGTGCAGGGATCAATCATGTCATCTTGCTTTCCACATATCAAAGCATATT
66 AGCAACCGTGTTTCAAGTGCAAGGATCAATCATGTCATCTTACTATCCACATATCAAAGCACATT
* * *
16689711 TTAAGTCAAGAAAGCTATCGAGCGTGTTCTACGTGCATGGATAATCAAGTCATGCTGCATTTCAC
131 TTAAGTCAAGAAAGCTATCGAACGTGTTCTAAGTGCATGGATAATCAAGTCATCCTGCATTTCAC
*
16689776 AAACATCAAAGCACACTAAGAAATTTTAAGTCATGAAAGCTAACGACAGTTTTCTAAACGTA
196 AAACATCAAAGCACACTAAGAAATTTTAAGTCAAGAAAGCTAACGACAGTTTTCTAAACGTA
*
16689838 AATCAA-TCATCTTATTTTCCAAAAACATAAAAGCAGAGAAAGAAATATTAAAATAAGAAAAACT
1 AATCAAGTCATCTTATTTTCCAAAAACATAAAAGCAAAGAAAGAAATATTAAAATAAGAAAAACT
* *
16689902 AGCAACCGTGTTTCACGTGCAAGGATCAATCATGTCATCTTACTATCTACATATCAAAGCACATT
66 AGCAACCGTGTTTCAAGTGCAAGGATCAATCATGTCATCTTACTATCCACATATCAAAGCACATT
* *
16689967 TTAAGTCAAGAAAGCTATCGAACGTGTTCTAAGTGCATGGATAATCCAGTCATCCTGCTTTTCAC
131 TTAAGTCAAGAAAGCTATCGAACGTGTTCTAAGTGCATGGATAATCAAGTCATCCTGCATTTCAC
* * *
16690032 AAACGTCAAAGCAGACTAAGAACTTTTAAGTCAAGAAAGCTA
196 AAACATCAAAGCACACTAAGAAATTTTAAGTCAAGAAAGCTA
16690074 TCGTGTTCTA
Statistics
Matches: 219, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
256 213 0.97
257 6 0.03
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (257 bp):
AATCAAGTCATCTTATTTTCCAAAAACATAAAAGCAAAGAAAGAAATATTAAAATAAGAAAAACT
AGCAACCGTGTTTCAAGTGCAAGGATCAATCATGTCATCTTACTATCCACATATCAAAGCACATT
TTAAGTCAAGAAAGCTATCGAACGTGTTCTAAGTGCATGGATAATCAAGTCATCCTGCATTTCAC
AAACATCAAAGCACACTAAGAAATTTTAAGTCAAGAAAGCTAACGACAGTTTTCTAAACGTA
Found at i:16690096 original size:86 final size:87
Alignment explanation
Indices: 16689964--16690155 Score: 296
Period size: 86 Copynumber: 2.2 Consensus size: 87
16689954 ATCAAAGCAC
* *
16689964 ATTTTAAGTCAAGAAAGCTATCGAACGTGTTCTAAGTGCATGGATAATCCAGTCATCCTGCTTTT
1 ATTTTAAGTCAAGAAAGCTAT---ACGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTT
*
16690029 CACAAACGTCAAAGCAGACTAAGAA
63 CACAAACATCAAAGCAGACTAAGAA
*
16690054 CTTTTAAGTCAAGAAAGCTAT-CGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTTCAC
1 ATTTTAAGTCAAGAAAGCTATACGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTTCAC
* *
16690118 AAACATCGAAGCGGACTAAGAA
66 AAACATCAAAGCAGACTAAGAA
16690140 ATTTTAAGTCAAGAAA
1 ATTTTAAGTCAAGAAA
16690156 ACTAATCACC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
86 75 0.79
90 20 0.21
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (87 bp):
ATTTTAAGTCAAGAAAGCTATACGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTTCAC
AAACATCAAAGCAGACTAAGAA
Found at i:16690382 original size:13 final size:14
Alignment explanation
Indices: 16690358--16690387 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
16690348 AGTTCATTTT
16690358 TTTAATGTATTTAA
1 TTTAATGTATTTAA
16690372 TTTAATG-ATTTAA
1 TTTAATGTATTTAA
16690385 TTT
1 TTT
16690388 TATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAATGTATTTAA
Found at i:16690389 original size:14 final size:15
Alignment explanation
Indices: 16690357--16690389 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
16690347 GAGTTCATTT
16690357 TTTTAATGTATTTAA
1 TTTTAATGTATTTAA
16690372 -TTTAATG-ATTTAA
1 TTTTAATGTATTTAA
16690385 TTTTA
1 TTTTA
16690390 TTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTAATGTATTTAA
Found at i:16691259 original size:15 final size:17
Alignment explanation
Indices: 16691239--16691282 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
16691229 ATGATTATGT
16691239 AAATAACTTAA-TCAA-
1 AAATAACTTAAGTCAAC
* *
16691254 AAATAAATTAAGTTAAC
1 AAATAACTTAAGTCAAC
16691271 AAATAACTTAAG
1 AAATAACTTAAG
16691283 ATATGGTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.42
16 3 0.12
17 11 0.46
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (17 bp):
AAATAACTTAAGTCAAC
Found at i:16692623 original size:12 final size:13
Alignment explanation
Indices: 16692607--16692639 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
16692597 CAATTTTTGT
*
16692607 TTTTATTTGTTTA
1 TTTTATTTATTTA
16692620 -TTTATTTATTTA
1 TTTTATTTATTTA
16692632 TTTTATTT
1 TTTTATTT
16692640 TATCTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:16693615 original size:27 final size:24
Alignment explanation
Indices: 16693551--16693622 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 24
16693541 TGTTTCGAAA
* * *
16693551 TTTTATATTTTTTAATATCTAAAAT
1 TTTTAT-TTTTTTATTTTTTAAAAT
16693576 TTTTATTTTTTTATTTTTTAAAAT
1 TTTTATTTTTTTATTTTTTAAAAT
16693600 TATTTATTATTATTTATTTTTTA
1 T-TTTATT-TT-TTTATTTTTTA
16693623 CATTAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
24 16 0.39
25 12 0.29
26 2 0.05
27 11 0.27
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTATTTTTTTATTTTTTAAAAT
Found at i:16698426 original size:29 final size:29
Alignment explanation
Indices: 16698376--16698432 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
16698366 TGGAGAATTT
* * *
16698376 AAAAGAAATTGCTTATCTAAAAATTTTTG
1 AAAAGAAATTCCTTATCAAAAAAATTTTG
16698405 AAAAGTAAATTCCTTA-CAAAAAAATTTT
1 AAAAG-AAATTCCTTATCAAAAAAATTTT
16698433 CACTTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAAGAAATTCCTTATCAAAAAAATTTTG
Found at i:16699673 original size:21 final size:21
Alignment explanation
Indices: 16699647--16699687 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
16699637 TTTTTAAGGA
16699647 AAATTGATACTTTCAACTTTC
1 AAATTGATACTTTCAACTTTC
16699668 AAATTGATACTTTCAACTTT
1 AAATTGATACTTTCAACTTT
16699688 TCCTCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (21 bp):
AAATTGATACTTTCAACTTTC
Found at i:16699678 original size:78 final size:79
Alignment explanation
Indices: 16699590--16699745 Score: 278
Period size: 79 Copynumber: 2.0 Consensus size: 79
16699580 TGTGTGAGGA
* *
16699590 AAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTGTTTTTAAGGAAAATTGA
1 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
16699654 TACTTTCAACTTTC
66 TACTTTCAACTTTC
*
16699668 AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
1 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
16699733 TACTTTCAACTTT
66 TACTTTCAACTTT
16699746 TCCTCAAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 31 0.42
79 43 0.58
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (79 bp):
AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
TACTTTCAACTTTC
Found at i:16699793 original size:60 final size:59
Alignment explanation
Indices: 16699668--16700008 Score: 489
Period size: 59 Copynumber: 5.8 Consensus size: 59
16699658 TTCAACTTTC
16699668 AAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTGAAAATTTATTTTTAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
*
16699726 AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTATTTTTAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTTGAAAATTTATTTTTAAGGA
** * *
16699786 AAATTGATACTTTCAACTTTTCCTCAAAAATACCTTTTTTGAAAATGTATTTATAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
* *
16699845 AAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTT--TAATTTATTTTCAAGGA
1 AAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
* * *
16699902 AAATTGATACTTTCAACTTTTTCCT-AAAAATA-TTTTTTGGAAATTTTGATTTTCAAGGA
1 AAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTTGAAAATTT-ATTTTTAAGGA
*
16699961 AAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTTGGAAATTT
1 AAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTTGAAAATTT
16700009 TGATTTTTTT
Statistics
Matches: 254, Mismatches: 18, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
56 6 0.02
57 37 0.15
58 49 0.19
59 93 0.37
60 69 0.27
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (59 bp):
AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
Found at i:16699960 original size:116 final size:115
Alignment explanation
Indices: 16699668--16700000 Score: 512
Period size: 116 Copynumber: 2.8 Consensus size: 115
16699658 TTCAACTTTC
16699668 AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTGAAAATTTA-TTTTAAGGAAAATTGA
*
16699733 TACTTTCAACTTTT-CCTCAAAAATATTTTTTTTTGAAACTTTATTTTTAAGGA
64 TACTTTCAACTTTTCCCT-AAAAATATTTTTTTTT-AAACTTTATTTTCAAGGA
*
16699786 AAATTGATACTTTCAACTTTTCCTCAAAAATACCTTTTTTGAAAATGTATTTATAAGGAAAATTG
1 AAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTGAAAATTTATTT-TAAGGAAAATTG
16699851 ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTT-AA-TTTATTTTCAAGGA
63 ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTAAACTTTATTTTCAAGGA
*
16699902 AAATTGATACTTTCAACTTTTTCCT-AAAAATATTTTTTGGAAATTTTGATTTTCAAGGAAAATT
1 AAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT-GAAAATTT-ATTTT-AAGGAAAATT
16699966 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
62 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
16700001 GGAAATTTTG
Statistics
Matches: 203, Mismatches: 5, Indels: 16
0.91 0.02 0.07
Matches are distributed among these distances:
114 6 0.03
115 7 0.03
116 86 0.42
117 9 0.04
118 35 0.17
119 57 0.28
120 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (115 bp):
AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTATTTTAAGGAAAATTGATA
CTTTCAACTTTTCCCTAAAAATATTTTTTTTTAAACTTTATTTTCAAGGA
Found at i:16700047 original size:17 final size:17
Alignment explanation
Indices: 16700022--16700069 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
16700012 TTTTTTTATT
*
16700022 TAAAGAAAATAGAAT-AA
1 TAAAAAAAATA-AATAAA
16700039 TAAAAAAAATAAATAAA
1 TAAAAAAAATAAATAAA
16700056 TAATAAAAAATAAA
1 TAA-AAAAAATAAA
16700070 GAAACGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 3 0.11
17 15 0.54
18 10 0.36
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
TAAAAAAAATAAATAAA
Found at i:16700096 original size:17 final size:17
Alignment explanation
Indices: 16700049--16700109 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
16700039 TAAAAAAAAT
16700049 AAATAAATAATAAAA-AA
1 AAATAAA-AATAAAACAA
* **
16700066 TAAAGAAACGTAAAACAA
1 -AAATAAAAATAAAACAA
*
16700084 AAATAAAAATAAAACTA
1 AAATAAAAATAAAACAA
*
16700101 AGATAAAAA
1 AAATAAAAA
16700110 GAATATTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
17 26 0.76
18 8 0.24
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (17 bp):
AAATAAAAATAAAACAA
Found at i:16700751 original size:26 final size:23
Alignment explanation
Indices: 16700712--16700763 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
16700702 AATCTGGAAA
*
16700712 TTTCCCAGAAATTTCCAAAAAAATT
1 TTTCCCAAAAATTT--AAAAAAATT
*
16700737 TTTCGCCAAAAATTTATAAAAATT
1 TTTC-CCAAAAATTTAAAAAAATT
16700761 TTT
1 TTT
16700764 TCTCACTCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 4 0.17
26 9 0.38
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.38
Consensus pattern (23 bp):
TTTCCCAAAAATTTAAAAAAATT
Found at i:16701162 original size:3 final size:3
Alignment explanation
Indices: 16701154--16701186 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
16701144 TATTATAAAA
16701154 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16701187 CATATATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16701175 original size:14 final size:14
Alignment explanation
Indices: 16701158--16701186 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16701148 ATAAAAAATA
16701158 ATAATAATAATAAT
1 ATAATAATAATAAT
16701172 ATAATAATAATAAT
1 ATAATAATAATAAT
16701186 A
1 A
16701187 CATATATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:16701175 original size:17 final size:18
Alignment explanation
Indices: 16701155--16701192 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
16701145 ATTATAAAAA
16701155 ATAATAATAATAATA-AT
1 ATAATAATAATAATACAT
16701172 ATAATAATAATAATACAT
1 ATAATAATAATAATACAT
16701190 ATA
1 ATA
16701193 TAACTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATAATAATAATACAT
Found at i:16701177 original size:20 final size:20
Alignment explanation
Indices: 16701154--16701282 Score: 70
Period size: 20 Copynumber: 6.1 Consensus size: 20
16701144 TATTATAAAA
16701154 AATAATAATAATAATAATAT
1 AATAATAATAATAATAATAT
16701174 AATAATAATAATACAT-ATAT
1 AATAATAATAATA-ATAATAT
*
16701194 AACTATATAAATAA-ATTACATAT
1 AA-TA-AT-AATAATAATA-ATAT
* * *
16701217 AAATATTAACAAAAATAA-AT
1 -AATAATAATAATAATAATAT
16701237 AAATCAATCAATCAATATATACATAT
1 -AAT-AAT-AAT-AATA-ATA-ATAT
*
16701263 GATAATAATAA-AATAA-AT
1 AATAATAATAATAATAATAT
16701281 AA
1 AA
16701283 AACACAAAAG
Statistics
Matches: 86, Mismatches: 9, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
18 3 0.03
19 1 0.01
20 28 0.33
21 13 0.15
22 11 0.13
23 17 0.20
24 8 0.09
25 3 0.03
26 2 0.02
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (20 bp):
AATAATAATAATAATAATAT
Found at i:16701195 original size:11 final size:10
Alignment explanation
Indices: 16701154--16701207 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 10
16701144 TATTATAAAA
16701154 AATAATA-AT
1 AATAATATAT
16701163 AATAATAATAT
1 AATAAT-ATAT
16701174 AATAATA-AT
1 AATAATATAT
16701183 AATACATATAT
1 AATA-ATATAT
16701194 AACT-ATATA-
1 AA-TAATATAT
16701203 AATAA
1 AATAA
16701208 ATTACATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 15 0.38
10 10 0.26
11 12 0.31
12 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AATAATATAT
Found at i:16701312 original size:13 final size:14
Alignment explanation
Indices: 16701288--16701317 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
16701278 AATAAAACAC
16701288 AAAAGAAGAAAAGA
1 AAAAGAAGAAAAGA
16701302 AAAAGAA-AAAAGA
1 AAAAGAAGAAAAGA
16701315 AAA
1 AAA
16701318 TAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:16701385 original size:20 final size:21
Alignment explanation
Indices: 16701360--16701398 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16701350 TTACCCCATT
16701360 TGGGCCAGG-CCCAATTGGTC
1 TGGGCCAGGACCCAATTGGTC
*
16701380 TGGGCCTGGACCCAATTGG
1 TGGGCCAGGACCCAATTGG
16701399 GTGTCTACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (21 bp):
TGGGCCAGGACCCAATTGGTC
Found at i:16701514 original size:10 final size:9
Alignment explanation
Indices: 16701499--16701561 Score: 65
Period size: 10 Copynumber: 6.4 Consensus size: 9
16701489 TCATTTTTTA
16701499 TTTTTTGTAT
1 TTTTTTGT-T
16701509 TTTTTTGTT
1 TTTTTTGTT
16701518 GTTTTTTGTTGT
1 -TTTTTTG-T-T
16701530 TTTTTTGTT
1 TTTTTTGTT
16701539 TTTATTAT-TT
1 TTT-TT-TGTT
16701549 TTTTTTGTT
1 TTTTTTGTT
16701558 TTTT
1 TTTT
16701562 AACCAAAGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.02
9 13 0.28
10 23 0.49
11 9 0.19
12 1 0.02
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:16701524 original size:20 final size:19
Alignment explanation
Indices: 16701492--16701561 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
16701482 AACATTGTCA
*
16701492 TTTTTTATTTTTTGTATTT
1 TTTTTTGTTTTTTGTATTT
*
16701511 TTTTGTTGTTTTTTGT-TGT
1 TTTT-TTGTTTTTTGTATTT
16701530 TTTTTTGTTTTTAT-TATTT
1 TTTTTTGTTTTT-TGTATTT
16701549 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
16701562 AACCAAAGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
18 10 0.22
19 25 0.56
20 10 0.22
ACGTcount: A:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (19 bp):
TTTTTTGTTTTTTGTATTT
Found at i:16701540 original size:27 final size:27
Alignment explanation
Indices: 16701510--16701561 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
16701500 TTTTTGTATT
* *
16701510 TTTTTGTTGTTTTTTGTTGTTTTTTTG
1 TTTTTATTATTTTTTGTTGTTTTTTTG
*
16701537 TTTTTATTATTTTTTTTTGTTTTTT
1 TTTTTATTATTTTTTGTTGTTTTTT
16701562 AACCAAAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.04, C:0.00, G:0.12, T:0.85
Consensus pattern (27 bp):
TTTTTATTATTTTTTGTTGTTTTTTTG
Found at i:16701692 original size:41 final size:40
Alignment explanation
Indices: 16701594--16702015 Score: 597
Period size: 41 Copynumber: 10.3 Consensus size: 40
16701584 ACTTTGGAAC
16701594 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAG
*
16701634 TAAATTGCTCCTCTAAACAGAGGCAACGAAC-TTGAAAAAAA
1 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTG--AAAAG
*
16701675 AAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTG-AAAAG
*
16701717 TAAATTGCTCCTCTAAACAGATGCAACGAACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAG
16701757 TAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAG
16701798 TAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGGAAAA-
1 TAAATTGCTCCTCTAAACAGAGGCAAC-GAACTTT-GAAAAG
16701839 TAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAG
16701880 TAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCA--ACGAAC-TTTGAAAAG
* *
16701922 TAAATTGCTCCTCTAAACAGAGGC-ACCATGACTTTGGAAAG
1 TAAATTGCTCCTCTAAACAGAGGCAACGA--ACTTTGAAAAG
16701963 TAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCAAC-GAACTTTGAAAAG
16702004 TAAATTGCTCCT
1 TAAATTGCTCCT
16702016 TGACAATCAT
Statistics
Matches: 352, Mismatches: 10, Indels: 39
0.88 0.02 0.10
Matches are distributed among these distances:
39 7 0.02
40 69 0.20
41 191 0.54
42 76 0.22
43 9 0.03
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (40 bp):
TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAG
Found at i:16701777 original size:82 final size:81
Alignment explanation
Indices: 16701594--16702015 Score: 674
Period size: 82 Copynumber: 5.1 Consensus size: 81
16701584 ACTTTGGAAC
16701594 TAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 TAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
*
16701657 CAACGAAC-TTGAAAAAAA
65 CAACGAACTTTG--AAAAG
* *
16701675 AAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGATG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGG
16701740 CAACGAACTTTGAAAAG
65 CAACGAACTTTGAAAAG
16701757 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
16701822 AACGGAACTTTGGAAAA-
66 AAC-GAACTTT-GAAAAG
16701839 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
16701904 ACCACG-ACTTTTGAAAAG
66 A--ACGAAC-TTTGAAAAG
* *
16701922 TAAATTGCTCCTCTAAACAGAGGCACCATGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGC
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
16701987 AACGGAACTTTGAAAAG
66 AAC-GAACTTTGAAAAG
16702004 TAAATTGCTCCT
1 TAAATTGCTCCT
16702016 TGACAATCAT
Statistics
Matches: 322, Mismatches: 7, Indels: 23
0.91 0.02 0.07
Matches are distributed among these distances:
81 57 0.18
82 147 0.46
83 113 0.35
84 5 0.02
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (81 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
AACGAACTTTGAAAAG
Found at i:16701803 original size:123 final size:122
Alignment explanation
Indices: 16701572--16702015 Score: 661
Period size: 123 Copynumber: 3.6 Consensus size: 122
16701562 AACCAAAGCT
* * *
16701572 AGAGGCACCATGACTTTG-GAACTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTA
1 AGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTA
**
16701636 AATTGCTCCTCTAAACAGAGGCA--ACGAAC-TTGAAAAAAAAAAATTGCTCCTCTAAAC
66 AATTGCTCCTCTAAACAGAGGCACCACG-ACTTTG--AAAAGTAAATTGCTCCTCTAAAC
*
16701693 AGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGATGCAACGAACTTTGAAAAGT
1 AGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGT
16701758 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAAC
65 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAAC
16701816 AGAGGCA--ACGGAACTTTGGAAAA-TAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAA
1 AGAGGCACCAC-G-ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGAA
16701877 AAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAAC
61 AAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAAC
* *
16701940 AGAGGCACCATGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAGT
1 AGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAAC-GAACTTTGAAAAGT
16702005 AAATTGCTCCT
65 AAATTGCTCCT
16702016 TGACAATCAT
Statistics
Matches: 298, Mismatches: 9, Indels: 29
0.89 0.03 0.09
Matches are distributed among these distances:
121 19 0.06
122 27 0.09
123 151 0.51
124 93 0.31
125 7 0.02
126 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (122 bp):
AGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTA
AATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAAC
Found at i:16703230 original size:28 final size:28
Alignment explanation
Indices: 16703198--16703266 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
16703188 TCAATCTCAA
*
16703198 TCTTTTTTCATTTTCTTTCTTC-T-TTCTT
1 TCTTTTTT--TTTTCTTTCTTCATCATCTT
*
16703226 TCTTTTTTTTTTCTTTTTTCATCATCTT
1 TCTTTTTTTTTTCTTTCTTCATCATCTT
16703254 TCTTTTTTTTTTC
1 TCTTTTTTTTTTC
16703267 ATCATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 11 0.30
27 1 0.03
28 25 0.68
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (28 bp):
TCTTTTTTTTTTCTTTCTTCATCATCTT
Found at i:16703238 original size:22 final size:23
Alignment explanation
Indices: 16703224--16703294 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
16703214 TTCTTCTTTC
*
16703224 TTTCTTT-TTTTTTTCTTTTTTCA
1 TTTCTTTCTTTTTTT-TTTCTTCA
* *
16703247 TCATCTTTCTTTTTTTTTTCATCA
1 T-TTCTTTCTTTTTTTTTTCTTCA
*
16703271 TTT-TTTCTTTTTTTTTTATTCA
1 TTTCTTTCTTTTTTTTTTCTTCA
16703293 TT
1 TT
16703295 GTTGATATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 19 0.47
23 2 0.05
24 12 0.30
25 7 0.17
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTCTTTCTTTTTTTTTTCTTCA
Found at i:16703242 original size:39 final size:39
Alignment explanation
Indices: 16703198--16703283 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
16703188 TCAATCTCAA
** * **
16703198 TCTTTTTTCATTTTCTTTCTTCTTTCTTTCTTTTTTTTT
1 TCTTTTTTCATCATCTTTCTTCTTTCTTTCATCATTTTT
* *
16703237 TCTTTTTTCATCATCTTTCTTTTTTTTTTCATCATTTTT
1 TCTTTTTTCATCATCTTTCTTCTTTCTTTCATCATTTTT
16703276 TCTTTTTT
1 TCTTTTTT
16703284 TTTTATTCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (39 bp):
TCTTTTTTCATCATCTTTCTTCTTTCTTTCATCATTTTT
Found at i:16703265 original size:21 final size:22
Alignment explanation
Indices: 16703234--16703287 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
16703224 TTTCTTTTTT
16703234 TTTTCTTTTTTCATCA-TCTTTC
1 TTTT-TTTTTTCATCATTCTTTC
*
16703256 TTTTTTTTTTCATCATTTTTTC
1 TTTTTTTTTTCATCATTCTTTC
16703278 TTTTTTTTTT
1 TTTTTTTTTT
16703288 ATTCATTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTTTTCATCATTCTTTC
Found at i:16703694 original size:14 final size:13
Alignment explanation
Indices: 16703670--16703700 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
16703660 TTGTAGTGTC
16703670 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
16703683 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
16703696 TTTTC
1 TTTTC
16703701 AAAAACTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:16707103 original size:59 final size:59
Alignment explanation
Indices: 16707040--16707396 Score: 418
Period size: 58 Copynumber: 5.9 Consensus size: 59
16707030 TTTTGTGTGG
* ** *
16707040 GGAAAATTGATACTTTCAACTTTTTTCC-AAAAAATATTTTTTGGAAATTTTAACTTCGA
1 GGAAAATTGATACTTTCAAC-TTTTCCCTAAAAAATATTTTTTGGAAATTTTATTTTCAA
* *** * *
16707099 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAATATTTTTTGGAAATTTTATTTTCAA
*
16707157 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA-A---TATTTTTTGGAAATTTT-ATTTTCAA
*
16707221 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAATA-TTTTTTGGAAATTTT-ATTTTCAA
* * * *
16707281 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAATCCTTTTTT-GAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAAT-ATTTTTTGGAAATTTTATTTTCAA
* *
16707339 GGATAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTGAAAATTTTGATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA-ATATTTTTTGGAAATTTT-ATTTT
16707397 TTTATTTAAA
Statistics
Matches: 258, Mismatches: 26, Indels: 26
0.83 0.08 0.08
Matches are distributed among these distances:
58 75 0.29
59 58 0.22
60 67 0.26
61 5 0.02
62 11 0.04
63 7 0.03
64 35 0.14
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAAATATTTTTTGGAAATTTTATTTTCAA
Found at i:16707349 original size:182 final size:178
Alignment explanation
Indices: 16707040--16707396 Score: 547
Period size: 182 Copynumber: 2.0 Consensus size: 178
16707030 TTTTGTGTGG
* * *
16707040 GGAAAATTGATACTTTCAACTTTTTTCCAAAAAATATTTTTTGGAAATTTTAACTTCGAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAAATATTTTTTGAAAATTTTAACTTCAAGGAAAA
16707105 TTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAATTTATTTTTAAGGAAAATTGATAC
66 TTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAATTTATTTTTAAGGAAAATTGATAC
* *
16707170 TTTCAACTTTTCCCTAAAAATATTTTTTTTTTTGGAAATTTTGATTTTCAA
131 TTTCAACTTTTCCCTAAAAATA---TATTTTTTGAAAATTTTGATTTTCAA
* **
16707221 GGAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAAATA-TTTTTTGAAAATTTT-AACTTCAAGGAA
* * *
16707285 AATTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTTGAAAATTTATTTTTAAGGATAATTGA
64 AATTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTG-AAATTTATTTTTAAGGAAAATTGA
16707349 TACTTTCAACTTTTCCCTAAAAATATATTTTTTGAAAATTTTGATTTT
128 TACTTTCAACTTTTCCCTAAAAATATATTTTTTGAAAATTTTGATTTT
16707397 TTTATTTAAA
Statistics
Matches: 162, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
179 21 0.13
180 13 0.08
181 41 0.25
182 87 0.54
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (178 bp):
GGAAAATTGATACTTTCAACTTTTTCCCAAAAAATATTTTTTGAAAATTTTAACTTCAAGGAAAA
TTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAATTTATTTTTAAGGAAAATTGATAC
TTTCAACTTTTCCCTAAAAATATATTTTTTGAAAATTTTGATTTTCAA
Found at i:16707541 original size:23 final size:23
Alignment explanation
Indices: 16707498--16707540 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
16707488 AACCTAATCT
16707498 AATAAATAAAAAATAAAAAAACA
1 AATAAATAAAAAATAAAAAAACA
*
16707521 AATAAAT-GAAAATAAAAAAA
1 AATAAATAAAAAATAAAAAAA
16707541 AATTCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (23 bp):
AATAAATAAAAAATAAAAAAACA
Found at i:16707551 original size:11 final size:11
Alignment explanation
Indices: 16707535--16707564 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
16707525 AATGAAAATA
16707535 AAAAAAAATTC
1 AAAAAAAATTC
16707546 AAAAAAAATTC
1 AAAAAAAATTC
16707557 AAAAAAAA
1 AAAAAAAA
16707565 AAAAACCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:16707943 original size:19 final size:19
Alignment explanation
Indices: 16707890--16707944 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
16707880 AGAACACCGG
* *
16707890 TGGAATTTTCGCCGGATTC
1 TGGAAATTTCGCCGGAATC
* *
16707909 TGGAAAATGTCACCGGAATC
1 TGG-AAATTTCGCCGGAATC
16707929 TGGAAATTTCGCCGGA
1 TGGAAATTTCGCCGGA
16707945 GGTTCACCGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (19 bp):
TGGAAATTTCGCCGGAATC
Found at i:16708683 original size:9 final size:10
Alignment explanation
Indices: 16708644--16708684 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
16708634 AAACAAAGAT
16708644 ATACATAATA
1 ATACATAATA
16708654 ATA-ATAATA
1 ATACATAATA
16708663 ATA-ATAA-A
1 ATACATAATA
16708671 ATACATAA-A
1 ATACATAATA
16708680 ATACA
1 ATACA
16708685 AAAGAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 4 0.13
9 23 0.77
10 3 0.10
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (10 bp):
ATACATAATA
Found at i:16708926 original size:1 final size:1
Alignment explanation
Indices: 16708922--16709027 Score: 86
Period size: 1 Copynumber: 106.0 Consensus size: 1
16708912 ATTTTTTGAA
** ** * ** * * *
16708922 TTTTTTTTGATTTTTTTGATTTTTTGTTTTTTTTTTTTTTGGTTTTTGTTTTTTTGTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
16708987 TTTTTGTTTTTTTTGTTTTGTTTTGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16709028 GCCGAAGCTC
Statistics
Matches: 81, Mismatches: 24, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (1 bp):
T
Found at i:16708927 original size:41 final size:41
Alignment explanation
Indices: 16708866--16708999 Score: 145
Period size: 41 Copynumber: 3.3 Consensus size: 41
16708856 AACTCAACAT
**
16708866 TTTTTGATTTTTTTTATTTTTTTGATTTTTTTGA-TTTTTG
1 TTTTTGATTTTTTGAATTTTTTTGATTTTTTTGATTTTTTG
16708906 TTTTTGATTTTTTGAATTTTTTTTGATTTTTTTGATTTTTTG
1 TTTTTGATTTTTTGAA-TTTTTTTGATTTTTTTGATTTTTTG
* *
16708948 TTTTT--TTTTTT--TTTGGTTTTTG-TTTTTTTGTTTTTTTG
1 TTTTTGATTTTTTGAATT--TTTTTGATTTTTTTGATTTTTTG
*
16708986 TTTTTTGTTTTTTT
1 -TTTTTGATTTTTT
16709000 TGTTTTGTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
37 2 0.02
38 15 0.18
39 11 0.13
40 20 0.24
41 24 0.29
42 11 0.13
ACGTcount: A:0.07, C:0.00, G:0.11, T:0.82
Consensus pattern (41 bp):
TTTTTGATTTTTTGAATTTTTTTGATTTTTTTGATTTTTTG
Found at i:16708999 original size:8 final size:8
Alignment explanation
Indices: 16708874--16709025 Score: 138
Period size: 8 Copynumber: 18.9 Consensus size: 8
16708864 ATTTTTTGAT
*
16708874 TTTTTTTA
1 TTTTTTTG
16708882 TTTTTTTG
1 TTTTTTTG
16708890 ATTTTTTTG
1 -TTTTTTTG
*
16708899 -ATTTTTG
1 TTTTTTTG
16708906 --TTTTTG
1 TTTTTTTG
*
16708912 ATTTTTTG
1 TTTTTTTG
16708920 AATTTTTTTTG
1 ---TTTTTTTG
16708931 ATTTTTTTG
1 -TTTTTTTG
*
16708940 ATTTTTTG
1 TTTTTTTG
16708948 TTTTTTT-
1 TTTTTTTG
16708955 TTTTTTTG
1 TTTTTTTG
*
16708963 -GTTTTTG
1 TTTTTTTG
16708970 TTTTTTTG
1 TTTTTTTG
16708978 TTTTTTTG
1 TTTTTTTG
16708986 -TTTTTTG
1 TTTTTTTG
16708993 TTTTTTTTG
1 -TTTTTTTG
16709002 TTTTGTTTTG
1 -TTT-TTTTG
16709012 TTTTTTT-
1 TTTTTTTG
16709019 TTTTTTT
1 TTTTTTT
16709026 TTGCCGAAGC
Statistics
Matches: 125, Mismatches: 8, Indels: 23
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.05
7 33 0.26
8 44 0.35
9 30 0.24
10 5 0.04
11 7 0.06
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:16709162 original size:42 final size:41
Alignment explanation
Indices: 16709034--16709452 Score: 580
Period size: 42 Copynumber: 10.1 Consensus size: 41
16709024 TTTTGCCGAA
* * *
16709034 GCTCCTCTAAACAGAGGCTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* * *
16709075 GCTCCTCTAAACAGAGGCAACA-GACTTTGGAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
16709115 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTG-AAAAGTAAATT
* *
16709157 GCTCCTCTCAACAGAGGCACCACGACTTTTGGAAATTAAATT
1 GCTCCTCTCAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
16709199 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATT
16709241 GCTCCTCTCAACAGAGGCACCACGACTTTTG-AAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
16709282 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATT
16709324 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
16709365 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAGAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCAC-G-ACTTTGA-AAAGTAAATT
* *
16709407 GCTCCTCTCAACAGAGGCACC-GGACTTTGGAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
16709447 ACTCCT
1 GCTCCT
16709453 TGACAATCAT
Statistics
Matches: 346, Mismatches: 19, Indels: 27
0.88 0.05 0.07
Matches are distributed among these distances:
39 6 0.02
40 52 0.15
41 107 0.31
42 174 0.50
43 7 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:16709299 original size:125 final size:124
Alignment explanation
Indices: 16709034--16709452 Score: 600
Period size: 125 Copynumber: 3.4 Consensus size: 124
16709024 TTTTGCCGAA
* * * * * *
16709034 GCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCAACA-G
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACG
*
16709098 ACTTTGG-AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGAC-TTTGAAAAAATAAATT
66 ACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTTG--AAAGTAAATT
*
16709157 GCTCCTCTCAACAGAGGCACCACGACTTTTGGAAATTAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTCAACAGAGGCACCACGAC-TTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCAC
*
16709222 GACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGACTTTTGAAAGTAAATT
65 GACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTTGAAAGTAAATT
*
16709282 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTCAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTCAACAGAGGCACCAC
* *
16709347 GACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGGAACTTTGAGAAAGTAAATT
65 GACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGCACCAC-G-ACTTT-TGAAAGTAAATT
* *
16709407 GCTCCTCTCAACAGAGGCACC-GGACTTTGGAAAGTAAATTACTCCT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCT
16709453 TGACAATCAT
Statistics
Matches: 272, Mismatches: 16, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
122 2 0.01
123 38 0.14
124 80 0.29
125 113 0.42
126 35 0.13
127 4 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (124 bp):
GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACG
ACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTTGAAAGTAAATT
Found at i:16709317 original size:83 final size:83
Alignment explanation
Indices: 16709034--16709452 Score: 609
Period size: 83 Copynumber: 5.1 Consensus size: 83
16709024 TTTTGCCGAA
* * * * * * *
16709034 GCTCCTCTAAACAGAGGCTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACA-
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
*
16709097 GACTTTGGAAAGTAAATT
66 GACTTTTGAAAGTAAATT
*
16709115 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
*
16709180 GACTTTTGGAAATTAAATT
66 GACTTTT-GAAAGTAAATT
16709199 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
16709264 GACTTTTGAAAGTAAATT
66 GACTTTTGAAAGTAAATT
16709282 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
16709347 GAC-TTTGAAAAGTAAATT
66 GACTTTTG-AAAGTAAATT
* *
16709365 GCTCCTCTAAACAGAGGCA--ACGGAACTTT-GAGAAAGTAAATTGCTCCTCTCAACAGAGGCAC
1 GCTCCTCTCAACAGAGGCACCAC-G-ACTTTGGA-AAAATAAATTGCTCCTCTCAACAGAGGCAC
* *
16709427 C-GGACTTTGGAAAGTAAATT
63 CACGACTTTTGAAAGTAAATT
*
16709447 ACTCCT
1 GCTCCT
16709453 TGACAATCAT
Statistics
Matches: 313, Mismatches: 17, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
81 28 0.09
82 54 0.17
83 150 0.48
84 81 0.26
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (83 bp):
GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
GACTTTTGAAAGTAAATT
Found at i:16710716 original size:21 final size:20
Alignment explanation
Indices: 16710690--16710735 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
16710680 TATTTTCTCA
16710690 TTTTTTCCTTCTTTCTTTCTT
1 TTTTTTCCTTCTTTCTTT-TT
*
16710711 TTTTTTCCTTTTTTCTTTTT
1 TTTTTTCCTTCTTTCTTTTT
16710731 TTTTT
1 TTTTT
16710736 CTTTTCATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTCCTTCTTTCTTTTT
Found at i:16710770 original size:24 final size:24
Alignment explanation
Indices: 16710723--16710772 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
16710713 TTTTCCTTTT
*
16710723 TTCTTTTTTTTTTCTTTTCATCATC
1 TTCTTTTTTTTCTCTTTT-ATCATC
16710748 TTCTTTTTTTTCTCATTTT-TCATC
1 TTCTTTTTTTTCTC-TTTTATCATC
16710772 T
1 T
16710773 ATTGTTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 13 0.57
26 4 0.17
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (24 bp):
TTCTTTTTTTTCTCTTTTATCATC
Found at i:16714642 original size:25 final size:25
Alignment explanation
Indices: 16714614--16714695 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 25
16714604 TTGTGTAGGG
16714614 AAAATTGATACTTTCAACTTTTCCC
1 AAAATTGATACTTTCAACTTTTCCC
* ** * * * *
16714639 AAAAAT-ATTTTTTGAAATTTTTTCG
1 AAAATTGATACTTT-CAACTTTTCCC
16714664 AGGAAAATTGATACTTTCAACTTTTCCC
1 A---AAATTGATACTTTCAACTTTTCCC
16714692 AAAA
1 AAAA
16714696 ATTTTTTTGA
Statistics
Matches: 38, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
24 5 0.13
25 16 0.42
28 12 0.32
29 5 0.13
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (25 bp):
AAAATTGATACTTTCAACTTTTCCC
Found at i:16714643 original size:26 final size:26
Alignment explanation
Indices: 16714614--16714698 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
16714604 TTGTGTAGGG
16714614 AAAATTGATACTTTCAACTTTTCCCA
1 AAAATTGATACTTTCAACTTTTCCCA
** * * * *
16714640 AAAA-T-ATTTTTTGAAATTTTTTCGA
1 AAAATTGATACTTT-CAACTTTTCCCA
16714665 GGAAAATTGATACTTTCAACTTTTCCCA
1 --AAAATTGATACTTTCAACTTTTCCCA
16714693 AAAATT
1 AAAATT
16714699 TTTTTGAAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 10
0.66 0.19 0.16
Matches are distributed among these distances:
24 5 0.12
25 9 0.21
26 10 0.24
27 4 0.10
28 9 0.21
29 5 0.12
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.41
Consensus pattern (26 bp):
AAAATTGATACTTTCAACTTTTCCCA
Found at i:16714669 original size:53 final size:53
Alignment explanation
Indices: 16714612--16714998 Score: 415
Period size: 53 Copynumber: 6.9 Consensus size: 53
16714602 TTTTGTGTAG
*
16714612 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTTTTCAA
*
16714665 GGAAAATTGATACTTTCAACTTTTCCCAAAAAT-TTTTTTGAAATTTATTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTT-TTTCAA
*
16714718 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTG-AATTTTATT--T
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATA-TTTTTTGAAATTTT-TTCAA
* * * * *
16714770 TGAAAATTTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTAAATTTATT
1 GGAAAA----TT---GATACTT--T-C----AACTTTTCC-CAAAAATATTTTTTGAAA-TT-TT
16714835 TTCAA
49 TTCAA
*
16714840 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTGAAATTTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTGAAA-TT-TTTTCAA
*
16714896 GGAAAATTGATACTTTCAACTTTTCCCAAAAAT-TTTTTTGAAATTTATTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTT-TTTCAA
16714949 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTT-GAAATTTT
16714999 GATTTTTTTA
Statistics
Matches: 291, Mismatches: 14, Indels: 56
0.81 0.04 0.16
Matches are distributed among these distances:
52 19 0.07
53 105 0.36
54 23 0.08
55 21 0.07
56 72 0.25
59 5 0.02
60 1 0.00
61 2 0.01
62 1 0.00
63 5 0.02
66 17 0.06
67 9 0.03
68 4 0.01
69 2 0.01
70 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (53 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTTTTCAA
Found at i:16714788 original size:66 final size:67
Alignment explanation
Indices: 16714709--16714836 Score: 215
Period size: 66 Copynumber: 1.9 Consensus size: 67
16714699 TTTTTGAAAT
*
16714709 TTATTTTAAGGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTGAATTTTATTTTGA
1 TTATTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTTGAAATTTATTTTGA
16714773 AAA
65 AAA
*
16714776 TT-TTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTAAATTTATTTT
1 TTATTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTGAAATTTATTTT
16714837 CAAGGAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 49 0.84
67 9 0.16
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (67 bp):
TTATTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTGAA
AA
Found at i:16714843 original size:56 final size:55
Alignment explanation
Indices: 16714760--16714997 Score: 376
Period size: 56 Copynumber: 4.3 Consensus size: 55
16714750 TATTTTTTTG
*
16714760 AATTTTATTTTGAAAATT-TTTTAAGGAAAATTGATACTTTCAACTTTT-CCTCAAA
1 AATTTT-TTTTGAAATTTATTTTAAGGAAAATTGATACTTTCAACTTTTCCCT-AAA
*
16714815 AATTTTTTTTTAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCTAAA
1 AATTTTTTTTGAAATTTATTTT-AAGGAAAATTGATACTTTCAACTTTTCCCTAAA
16714871 AATTTTTTTTGAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCC-AAA
1 AATTTTTTTTGAAATTTATTTT-AAGGAAAATTGATACTTTCAACTTTTCCCTAAA
16714926 AA-TTTTTTTGAAATTTATTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAA
1 AATTTTTTTTGAAATTTATTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAA
*
16714980 AATATTTTTTGGAAATTT
1 AAT-TTTTTTTGAAATTT
16714998 TGATTTTTTT
Statistics
Matches: 173, Mismatches: 4, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
53 29 0.17
54 33 0.19
55 15 0.09
56 93 0.54
57 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (55 bp):
AATTTTTTTTGAAATTTATTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAA
Found at i:16714967 original size:109 final size:110
Alignment explanation
Indices: 16714612--16714998 Score: 529
Period size: 122 Copynumber: 3.4 Consensus size: 110
16714602 TTTTGTGTAG
* **
16714612 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTGAAATTTTTTCGAGGAAAATTGAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTGAAATTTTTTTAAGGAAAATTGAT
16714676 ACTTTCAACTTTTCC-CAAAAA-TTTTTTTGAAATTTATTTT-AA
66 ACTTTCAACTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTCAA
16714718 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTGAATTTTATTTTGAAAATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-TTTTTTTGAA----A---T-----TTTTTT
*
16714782 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTAAATTTATTTTCAA
53 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTCAA
16714840 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTGAAATTTATTTTCAAGGAAAATTG
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTGAAATTT-TTTT-AAGGAAAATTG
16714905 ATACTTTCAACTTTTCC-CAAAAA-TTTTTTTGAAATTTATTTT-AA
64 ATACTTTCAACTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTCAA
*
16714949 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-TTTTTTTGAAATTTT
16714999 GATTTTTTTA
Statistics
Matches: 255, Mismatches: 6, Indels: 37
0.86 0.02 0.12
Matches are distributed among these distances:
106 33 0.13
107 9 0.04
109 37 0.15
110 33 0.13
111 11 0.04
112 28 0.11
114 1 0.00
115 1 0.00
118 1 0.00
119 32 0.13
120 6 0.02
121 18 0.07
122 39 0.15
123 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (110 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATTTTTTTTGAAATTTTTTTAAGGAAAATTGAT
ACTTTCAACTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTCAA
Found at i:16715037 original size:12 final size:13
Alignment explanation
Indices: 16715016--16715044 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16715006 TTATTTAAAG
16715016 AAAATAGAAAATA
1 AAAATAGAAAATA
16715029 AAAAT-GAAAATA
1 AAAATAGAAAATA
16715041 AAAA
1 AAAA
16715045 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAATAGAAAATA
Found at i:16715126 original size:22 final size:22
Alignment explanation
Indices: 16715101--16715157 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
16715091 AACCTAATCT
*
16715101 AATAAATAAAAAATAAAAAACA
1 AATAAATAAAAAATAAAAAAAA
*
16715123 AATAAAT-GAAAATAAAAAAAA
1 AATAAATAAAAAATAAAAAAAA
*
16715144 AATCAAAAAAAAAA
1 AAT-AAATAAAAAA
16715158 ACCTGGAGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 15 0.52
22 10 0.34
23 4 0.14
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (22 bp):
AATAAATAAAAAATAAAAAAAA
Found at i:16715153 original size:12 final size:11
Alignment explanation
Indices: 16715101--16715157 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
16715091 AACCTAATCT
*
16715101 AATAAATAAAA
1 AATAAAAAAAA
*
16715112 AATAAAAAACA
1 AATAAAAAAAA
**
16715123 AAT-AAATGAA
1 AATAAAAAAAA
16715133 AATAAAAAAAA
1 AATAAAAAAAA
16715144 AATCAAAAAAAA
1 AAT-AAAAAAAA
16715156 AA
1 AA
16715158 ACCTGGAGCG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
10 7 0.19
11 20 0.54
12 10 0.27
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:16715188 original size:5 final size:5
Alignment explanation
Indices: 16715178--16715203 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16715168 GCTCGGATCG
16715178 CGGCT CGGCT CGGCT CGGCT CGGCT C
1 CGGCT CGGCT CGGCT CGGCT CGGCT C
16715204 AAGGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.38, T:0.19
Consensus pattern (5 bp):
CGGCT
Done.