Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 14 of 322
Found at i:3820498 original size:9 final size:9
Alignment explanation
Indices: 3820439--3820499 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
3820429 AATTTTATAT
3820439 TTTTAAAAAA
1 TTTT-AAAAA
*
3820449 TTATAAAAA
1 TTTTAAAAA
*
3820458 TTCTAAAATA
1 TTTTAAAA-A
3820468 TATATTAAAAA
1 T-T-TTAAAAA
*
3820479 ATTT-AAAA
1 TTTTAAAAA
3820487 TTTTAAAAA
1 TTTTAAAAA
3820496 TTTT
1 TTTT
3820500 CTAAAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 7 0.17
9 22 0.52
10 6 0.14
11 2 0.05
12 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:3821893 original size:31 final size:31
Alignment explanation
Indices: 3821858--3821922 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3821848 CAAAATGGTC
**
3821858 ATTAAATTATTCGAATGTTTTTATTTAAGTT
1 ATTAAATTATTCGAAAATTTTTATTTAAGTT
* * *
3821889 ATTAACTTGTTTGAAAATTTTTATTTAAGTT
1 ATTAAATTATTCGAAAATTTTTATTTAAGTT
3821920 ATT
1 ATT
3821923 GAGCTGTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.55
Consensus pattern (31 bp):
ATTAAATTATTCGAAAATTTTTATTTAAGTT
Found at i:3826466 original size:26 final size:27
Alignment explanation
Indices: 3826409--3826467 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
3826399 CAAAAAGTCA
3826409 AACTATGCCCTTTTTTTAAGGAAATCG
1 AACTATGCCCTTTTTTTAAGGAAATCG
3826436 AACTATGCCCTTTTTTTAAGGAAATCG
1 AACTATGCCCTTTTTTTAAGGAAATCG
3826463 -ACTAT
1 AACTAT
3826468 ATGGAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (27 bp):
AACTATGCCCTTTTTTTAAGGAAATCG
Found at i:3830854 original size:31 final size:31
Alignment explanation
Indices: 3830800--3830864 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3830790 TTAATAATTA
* *
3830800 TTTTATAATTTTTAAAAGGTTAAATTA-AAT
1 TTTTATAATTTTTAAAAGATTAAAATATAAT
* *
3830830 TTTTATCATTTTTTGAAAGATTAAAATATAAT
1 TTTTAT-AATTTTTAAAAGATTAAAATATAAT
3830862 TTT
1 TTT
3830865 ATTTTTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.21
31 17 0.59
32 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (31 bp):
TTTTATAATTTTTAAAAGATTAAAATATAAT
Found at i:3833037 original size:21 final size:21
Alignment explanation
Indices: 3832972--3833039 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
3832962 ACCGGTTAAT
* *
3832972 TTATATTTATTTAAGTTTACCTA
1 TTATTTTTATTTAA-TATA-CTA
* **
3832995 -TATTTTTTTTTAA-ATAAAA
1 TTATTTTTATTTAATATACTA
3833014 TTATTTTTATTTAATATACTA
1 TTATTTTTATTTAATATACTA
3833035 TTATT
1 TTATT
3833040 ATATGTTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 1 0.03
20 14 0.40
21 9 0.26
22 11 0.31
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (21 bp):
TTATTTTTATTTAATATACTA
Found at i:3833772 original size:24 final size:24
Alignment explanation
Indices: 3833728--3833773 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3833718 CGCGACACCC
*
3833728 CCACCTACTGCTGCTATTGCCGCT
1 CCACCTACTGCTGCTACTGCCGCT
*
3833752 CCACCTACTGCTGCTGCTGCCG
1 CCACCTACTGCTGCTACTGCCG
3833774 TTGCTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.43, G:0.20, T:0.26
Consensus pattern (24 bp):
CCACCTACTGCTGCTACTGCCGCT
Found at i:3834525 original size:220 final size:216
Alignment explanation
Indices: 3834213--3834754 Score: 824
Period size: 220 Copynumber: 2.4 Consensus size: 216
3834203 TTTTATAGTT
*
3834213 GATTAGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTGCATTACTGTATTGTGA-TTTTTTTA
1 GATTAGGTTATATAAATTGTTAGTGTTTAGT-G--T-GT--ATTAGTGTATTGTGATTTTTTTTA
3834277 GTAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAA
60 GTAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAA
3834342 ATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAGTAATATATTTT-AAA
125 ATTGTTAGTGTTTAGTGGTTTAGTGTATT-GTG-A---T--TTTTTTTAGTAATATATTTTAAAA
3834406 AAATATTTTTATAGCTATTTTATTAGTAATTTAA
183 AAATATTTTTATAGCTATTTTATTAGTAATTTAA
3834440 GATTAGGTTATATAAATTGTTAGTGTTTAGTG-GT-TTAGTGTATTGTGATTTTTTTTAGTAATA
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGTGTATTAGTGTATTGTGATTTTTTTTAGTAATA
*
3834503 TATTTTAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTGTT
66 TATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTGTT
3834568 AGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTATA
131 AGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTATA
3834633 GCTATTTTATTAGTAATTTAA
196 GCTATTTTATTAGTAATTTAA
* *
3834654 GATTAGGTTATATATTGTTAGTGTTTAGTGGTTTAGTGTGTATTAGTGTATTGTGATTTTTTTTA
1 GATTAGGTTATATA----AATTG-TTAGT-GTTTAGTGTGTATTAGTGTATTGTGATTTTTTTTA
* *
3834719 GTAATGTA-TTTAAAAAAATAATTTTATAGTTATTTT
60 GTAATATATTTTAAAAAAATAATTTTATAGCTATTTT
3834755 GTGTTAGTAT
Statistics
Matches: 298, Mismatches: 7, Indels: 26
0.90 0.02 0.08
Matches are distributed among these distances:
213 20 0.07
214 51 0.17
215 1 0.00
218 4 0.01
219 21 0.07
220 109 0.37
221 28 0.09
222 32 0.11
226 1 0.00
227 31 0.10
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.52
Consensus pattern (216 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTGTGTATTAGTGTATTGTGATTTTTTTTAGTAATA
TATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTGTT
AGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTATA
GCTATTTTATTAGTAATTTAA
Found at i:3834569 original size:107 final size:107
Alignment explanation
Indices: 3834239--3834754 Score: 786
Period size: 107 Copynumber: 4.7 Consensus size: 107
3834229 TTGTTAGTGT
** * *
3834239 TTAGTAGTTTAGTGCATTACTGTATTGTGA-TTTTTTTAGTAATATATTTTAAAAAAATAATTTT
1 TTAGT-GTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTT
3834303 ATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTG
65 ATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTG
3834346 TTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAGTAATATATTTT-AAAAAAT
1 TTAGTGTTTAGTGGTTTAGTGTATT-GTG-A---T--TTTTTTTAGTAATATATTTTAAAAAAAT
3834410 ATTTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTG
59 ATTTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTG
3834459 TTAGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTA
1 TTAGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTA
3834524 TAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTG
66 TAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTG
3834566 TTAGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTA
1 TTAGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTA
* *
3834631 TAGCTATTTTATTAGTAATTTAAGATTAGGTTATATATTGTTAGTG
66 TAGCTATTTTATTAGTAATTTAAGATTAGGTTATATA----AATTG
* *
3834677 TTTAGTGGTTTAGTGTGTATTAGTGTATTGTGATTTTTTTTAGTAATGTA-TTTAAAAAAATAAT
1 -TTAGT-GTTTAGTG-GT-TTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATT
*
3834741 TTTATAGTTATTTT
62 TTTATAGCTATTTT
3834755 GTGTTAGTAT
Statistics
Matches: 383, Mismatches: 9, Indels: 27
0.91 0.02 0.06
Matches are distributed among these distances:
106 37 0.10
107 166 0.43
108 2 0.01
111 4 0.01
112 8 0.02
113 88 0.23
114 48 0.13
115 30 0.08
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.52
Consensus pattern (107 bp):
TTAGTGTTTAGTGGTTTAGTGTATTGTGATTTTTTTTAGTAATATATTTTAAAAAAATATTTTTA
TAGCTATTTTATTAGTAATTTAAGATTAGGTTATATAAATTG
Found at i:3834841 original size:15 final size:16
Alignment explanation
Indices: 3834812--3834843 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3834802 TGTGATTTTT
3834812 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
3834828 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
3834843 T
1 T
3834844 TATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:3835605 original size:96 final size:96
Alignment explanation
Indices: 3835441--3835632 Score: 357
Period size: 96 Copynumber: 2.0 Consensus size: 96
3835431 GCGATATGAC
3835441 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCGGAGACCCACACATTTCATTTGCCGTGCGGGGA
1 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCGGAGACCCACACATTTCATTTGCCGTGCGGGGA
*
3835506 GTGCACCATCACTCTAGAAGACGTTGCAGTA
66 GTGCACCATCACTCTAGAAGACGTCGCAGTA
*
3835537 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCGGAGACCTACACATTTCATTTGCCGTGCGGGGA
1 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCGGAGACCCACACATTTCATTTGCCGTGCGGGGA
*
3835602 GTGCATCATCACTCTAGAAGACGTCGCAGTA
66 GTGCACCATCACTCTAGAAGACGTCGCAGTA
3835633 CAGCTCGGGC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.27
Consensus pattern (96 bp):
TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCGGAGACCCACACATTTCATTTGCCGTGCGGGGA
GTGCACCATCACTCTAGAAGACGTCGCAGTA
Found at i:3838986 original size:27 final size:27
Alignment explanation
Indices: 3838924--3838986 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3838914 CCTACCAAGA
*
3838924 AGGCACAACTAGTCGTGCCTGTCAGAT
1 AGGCACAACTAGTCGAGCCTGTCAGAT
* * * *
3838951 ATGCTCAACTAGTTGAGCTTGTCAGAT
1 AGGCACAACTAGTCGAGCCTGTCAGAT
*
3838978 AGGCGCAAC
1 AGGCACAAC
3838987 ATGTATGTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (27 bp):
AGGCACAACTAGTCGAGCCTGTCAGAT
Found at i:3840025 original size:17 final size:18
Alignment explanation
Indices: 3839993--3840026 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3839983 ATATTATTTT
*
3839993 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
3840011 TAAAA-TTAATATTAAA
1 TAAAATTTAATATTAAA
3840027 TACTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:3840052 original size:13 final size:13
Alignment explanation
Indices: 3840034--3840058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3840024 AAATACTTTA
3840034 TTAAATTAATAAT
1 TTAAATTAATAAT
3840047 TTAAATTAATAA
1 TTAAATTAATAA
3840059 ATTATTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATTAATAAT
Found at i:3840063 original size:29 final size:29
Alignment explanation
Indices: 3840001--3840125 Score: 76
Period size: 29 Copynumber: 4.1 Consensus size: 29
3839991 TTTAAAATTT
* *
3840001 ATTATTAAAATAAAATTAATATTAAATAC
1 ATTATTAAATTAAAATTAATATTAAATAA
*
3840030 TTTATTAAATTAATAATTTAA-ATT-AATAA
1 ATTATTAAATTAA-AA-TTAATATTAAATAA
* *
3840059 ATTATTATATTATTAAATATATATATTTAATAA
1 ATTATTAAATTA--AAAT-TA-ATATTAAATAA
* *
3840092 TATTA-AAAATTATAATATTTAATATTAATTAA
1 -ATTATTAAATTA-AA-A-TTAATATTAAATAA
3840124 AT
1 AT
3840126 ATATATTATT
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
29 26 0.34
30 9 0.12
31 8 0.11
32 15 0.20
33 13 0.17
34 5 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTATTAAATTAAAATTAATATTAAATAA
Found at i:3840075 original size:16 final size:16
Alignment explanation
Indices: 3840051--3840131 Score: 53
Period size: 16 Copynumber: 5.0 Consensus size: 16
3840041 AATAATTTAA
3840051 ATTAATAAAT-TATTAT
1 ATTAATAAATATA-TAT
*
3840067 ATTATTAAATATATAT
1 ATTAATAAATATATAT
* *
3840083 ATTTAAT-AATATTAAAA
1 A-TTAATAAATA-TATAT
*
3840100 ATT-AT-AATATTTAAT
1 ATTAATAAATATAT-AT
3840115 ATTAATTAAATATATAT
1 ATTAA-TAAATATATAT
3840132 TATTTAAGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
14 1 0.02
15 10 0.20
16 20 0.40
17 13 0.26
18 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAATAAATATATAT
Found at i:3840109 original size:25 final size:25
Alignment explanation
Indices: 3840073--3840138 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
3840063 TTATATTATT
3840073 AAATATATATATTTAATAAT-ATTAA
1 AAATATA-ATATTTAATAATAATTAA
*
3840098 AAATTATAATATTTAATATTAATTAA
1 AAA-TATAATATTTAATAATAATTAA
* *
3840124 ATATATATTATTTAA
1 AAATATAATATTTAA
3840139 GTTAATTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 25 0.69
26 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATATAATATTTAATAATAATTAA
Found at i:3840114 original size:22 final size:24
Alignment explanation
Indices: 3840065--3840138 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
3840055 ATAAATTATT
*
3840065 ATATTATTAAATATAT-ATATTTA
1 ATATTAATAAATATATAATATTTA
* * *
3840088 ATAATATTAAAAATTATAATATTTA
1 ATATTAATAAATA-TATAATATTTA
*
3840113 ATATTAATTAAATATATATTATTTA
1 ATATTAA-TAAATATATAATATTTA
3840138 A
1 A
3840139 GTTAATTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
23 11 0.26
24 3 0.07
25 23 0.55
26 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTAATAAATATATAATATTTA
Found at i:3841316 original size:23 final size:23
Alignment explanation
Indices: 3841271--3841316 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3841261 TCATTAACAT
* *
3841271 TGTTCGTGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
* *
3841294 TGTTTGTGAGCATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
3841317 GTTAAATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.46
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:3845197 original size:6 final size:6
Alignment explanation
Indices: 3845188--3845212 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3845178 AAAAAGAAAG
3845188 AAGTGA AAGTGA AAGTGA AAGTGA A
1 AAGTGA AAGTGA AAGTGA AAGTGA A
3845213 TTCTTTGCTA
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
AAGTGA
Found at i:3855764 original size:15 final size:15
Alignment explanation
Indices: 3855744--3855774 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3855734 AAAAAAAAAA
*
3855744 AAGCAGAGTTCTTTC
1 AAGCAGAGTTCCTTC
3855759 AAGCAGAGTTCCTTC
1 AAGCAGAGTTCCTTC
3855774 A
1 A
3855775 CTGTAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (15 bp):
AAGCAGAGTTCCTTC
Found at i:3856390 original size:24 final size:22
Alignment explanation
Indices: 3856357--3856432 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 22
3856347 TCAAATTTAA
3856357 TTTAAA-TTTTTTATTTTAATT
1 TTTAAATTTTTTTATTTTAATT
*
3856378 TTTAAATTCTTTTTTATTTTTAATAA
1 TTTAAA-T-TTTTTTA-TTTTAAT-T
* *
3856404 TTGATAATTTTTTTAATTTAATT
1 TTTA-AATTTTTTTATTTTAATT
3856427 TTTAAA
1 TTTAAA
3856433 GTTGAGATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
21 6 0.14
22 2 0.05
23 3 0.07
24 13 0.30
25 14 0.32
26 4 0.09
27 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTAAATTTTTTTATTTTAATT
Found at i:3857323 original size:13 final size:13
Alignment explanation
Indices: 3857305--3857330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3857295 TAAGATCTTT
3857305 TTTAAAATTAAAA
1 TTTAAAATTAAAA
3857318 TTTAAAATTAAAA
1 TTTAAAATTAAAA
3857331 GGTTTTTAAG
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAATTAAAA
Found at i:3862503 original size:10 final size:10
Alignment explanation
Indices: 3862486--3862524 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
3862476 TGTAAAGAAA
3862486 ACTATTTTTT
1 ACTATTTTTT
*
3862496 ATTATTTTTT
1 ACTATTTTTT
*
3862506 ACTATTTTGCT
1 ACTATTTT-TT
3862517 ACTATTTT
1 ACTATTTT
3862525 ACAATATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (10 bp):
ACTATTTTTT
Found at i:3862983 original size:14 final size:14
Alignment explanation
Indices: 3862964--3862991 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3862954 ATACATCCAT
3862964 GTCAAAAAGCTTAA
1 GTCAAAAAGCTTAA
3862978 GTCAAAAAGCTTAA
1 GTCAAAAAGCTTAA
3862992 CTAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
GTCAAAAAGCTTAA
Found at i:3863997 original size:18 final size:18
Alignment explanation
Indices: 3863974--3864011 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3863964 AATATATATT
*
3863974 AACCCAAGTACCTAACCC
1 AACCCAAGTACCCAACCC
*
3863992 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
3864010 AA
1 AA
3864012 TCATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.45, G:0.03, T:0.11
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:3864004 original size:13 final size:13
Alignment explanation
Indices: 3863988--3864012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3863978 CAAGTACCTA
3863988 ACCCAACCCAATT
1 ACCCAACCCAATT
3864001 ACCCAACCCAAT
1 ACCCAACCCAAT
3864013 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:3864050 original size:5 final size:6
Alignment explanation
Indices: 3864037--3864076 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
3864027 ATAATTTAAT
*
3864037 AAATAA AAATAA AATTCTAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AA--ATAA AAATAA AAATAA AAATAA AA
3864077 CATATAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 25 0.83
8 5 0.17
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:3865272 original size:2 final size:2
Alignment explanation
Indices: 3865267--3865293 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3865257 ATTCTCTCCA
3865267 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3865294 TTTTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3871833 original size:19 final size:18
Alignment explanation
Indices: 3871811--3871846 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3871801 TATCTAGTTT
3871811 ATATCATATAAAAAATATA
1 ATATCATA-AAAAAATATA
*
3871830 ATATTATAAAAAAATAT
1 ATATCATAAAAAAATAT
3871847 TAAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATCATAAAAAAATATA
Found at i:3882362 original size:12 final size:11
Alignment explanation
Indices: 3882345--3882386 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
3882335 AAAAGGCAAG
3882345 ATTATTAAATAA
1 ATTATTAAA-AA
3882357 ATTATTAAAAA
1 ATTATTAAAAA
*
3882368 A-T-TTATAAA
1 ATTATTAAAAA
3882377 ATTATTAAAA
1 ATTATTAAAA
3882387 TAGAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 8 0.31
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTATTAAAAA
Found at i:3895492 original size:15 final size:15
Alignment explanation
Indices: 3895472--3895579 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
3895462 TTTATGGAAA
3895472 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
3895487 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
*
3895501 AGTCAAAGATATGAGT
1 A-TCAAAGATATGGGT
* **
3895517 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3895531 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
3895547 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3895561 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
3895577 ATC
1 ATC
3895580 GAGATATTAG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:3895501 original size:30 final size:30
Alignment explanation
Indices: 3895465--3895579 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
3895455 ATCCATATTT
*
3895465 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3895495 ATGGAAAGTCAAAGATATGAGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3895525 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3895555 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
3895580 GAGATATTAG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 81 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:3900186 original size:15 final size:15
Alignment explanation
Indices: 3900166--3900273 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
3900156 TTTATGGAAA
3900166 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
3900181 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
3900195 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
3900211 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3900225 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
3900241 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3900255 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
3900271 ATC
1 ATC
3900274 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:3900195 original size:30 final size:30
Alignment explanation
Indices: 3900159--3900273 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
3900149 ATCCATATTT
*
3900159 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
3900189 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3900219 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3900249 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
3900274 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:3914410 original size:15 final size:17
Alignment explanation
Indices: 3914390--3914422 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3914380 CAATATTTTA
3914390 TTTTC-TTC-TCTTATT
1 TTTTCTTTCATCTTATT
3914405 TTTTCTTTCATCTTATT
1 TTTTCTTTCATCTTATT
3914422 T
1 T
3914423 CATTCGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 3 0.19
17 8 0.50
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTCTTTCATCTTATT
Found at i:3915225 original size:15 final size:16
Alignment explanation
Indices: 3915196--3915227 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3915186 TATATGATAA
3915196 AATTTTATGTTTTATT
1 AATTTTATGTTTTATT
3915212 AATTTTAT-TTTTATT
1 AATTTTATGTTTTATT
3915227 A
1 A
3915228 TATATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
AATTTTATGTTTTATT
Found at i:3919677 original size:19 final size:19
Alignment explanation
Indices: 3919655--3919695 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3919645 AATAAAATAA
3919655 AAAATAATTTCCAAAATTC
1 AAAATAATTTCCAAAATTC
**
3919674 AAAATAATTTTTAAAATTC
1 AAAATAATTTCCAAAATTC
3919693 AAA
1 AAA
3919696 TTATTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATAATTTCCAAAATTC
Found at i:3924441 original size:42 final size:40
Alignment explanation
Indices: 3924343--3924459 Score: 155
Period size: 42 Copynumber: 2.9 Consensus size: 40
3924333 TGTGTTTTTA
*
3924343 GTCTGCTCCACTACTATTTAGGGAGATAAGACTG-GATGT
1 GTCTGCTCCACTACTACTTAGGGAGATAAGACTGTGATGT
* * *
3924382 GACCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTT
1 G-TCTGCTCCACTACTACTTAGGGAGATAAGA-CTGTGATGT
*
3924424 CGTCTGCTCCGCTACTACTTAGGGAGATAAGACTGT
1 -GTCTGCTCCACTACTACTTAGGGAGATAAGACTGT
3924460 AATCTTCGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
39 1 0.01
40 28 0.41
41 7 0.10
42 31 0.46
43 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (40 bp):
GTCTGCTCCACTACTACTTAGGGAGATAAGACTGTGATGT
Found at i:3924764 original size:44 final size:44
Alignment explanation
Indices: 3924715--3925237 Score: 457
Period size: 44 Copynumber: 11.9 Consensus size: 44
3924705 TCCACTGCCA
* * * *
3924715 AATACAGGAAGGCAAGATCTGCAATCTTCGACCTACTTCACGCC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* * * * *
3924759 AATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACC
* ** * *
3924804 AGTATGGGAAGACAAGATCTGC-ATCGTCGATCCACTTC-CTACC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACC
* * * *
3924847 AATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* * * *
3924891 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACC
** *
3924936 AATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACC
* * * * *
3924979 AATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* * * * * * *
3925023 AATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCGCT
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* * * *
3925067 AATACATGAAGACAAGATCTGATTTCTTCGATCTACTTCGCCACC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACC
* * *
3925112 AATA-TGGAAAGATAAGATCTGC-ATCTTCGATCCACTTC-CTACC
1 AATACAGG-AAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACC
* * * * * *
3925155 AATATAGGAAAATAGGATCTGCTACCTTCGATCTACTTCACGCC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
* * *
3925199 AATACATGAAGACAAGACCTGCTTTCTTCGATCTACTTC
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTC
3925238 GCCACCAGTA
Statistics
Matches: 384, Mismatches: 81, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
42 3 0.01
43 62 0.16
44 256 0.67
45 63 0.16
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (44 bp):
AATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACC
Found at i:3924957 original size:132 final size:132
Alignment explanation
Indices: 3924715--3925149 Score: 608
Period size: 132 Copynumber: 3.3 Consensus size: 132
3924705 TCCACTGCCA
* * * * *
3924715 AATACAGGAAGGCAAGATCTGCAATCTTCGACCTACTTCACGCCAATACATGAAGATAAGATCTG
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* *
3924780 CTTTCTGCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTA
66 CTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTA
3924845 CC
131 CC
* *
3924847 AATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
3924912 CTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTA
66 CTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTA
3924977 CC
131 CC
* * * *
3924979 AATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTA
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* * *** *
3925044 CTTTCTGCGATCTACTTCG-CGCTAATACATGAAGACAAGATCTG-ATTTCTTCGATCTACTTCG
66 CTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA--TCTTCGATCCACTTC-
*
3925107 CCACC
128 CTACC
* *
3925112 AATAT-GGAAAGATAAGATCTGC-ATCTTCGATCCACTTC
1 AATATAGG-AAGACAAGATCTGCTATCTTCGATCTACTTC
3925150 CTACCAATAT
Statistics
Matches: 276, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
130 1 0.00
131 20 0.07
132 233 0.84
133 22 0.08
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (132 bp):
AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
CTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTA
CC
Found at i:3925157 original size:132 final size:132
Alignment explanation
Indices: 3924728--3925253 Score: 580
Period size: 132 Copynumber: 4.0 Consensus size: 132
3924718 ACAGGAAGGC
* *
3924728 AAGATCTGCAATCTTCGA-CCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTGCGATC
1 AAGATCTGCTATCTTCGATCC-ACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATC
* ** * *
3924792 TACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAA
65 TACTTCGCCACCAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCCCACCAATATAGGAA
*
3924857 GAC
130 GAT
* * *
3924860 AGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCT
1 AAGATCTGCTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCT
** *
3924925 ACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAG
66 ACTTCGCCACCAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCCCACCAATATAGGAAG
3924990 AT
131 AT
* * * *
3924992 AGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTGCGATCT
1 AAGATCTGCTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCT
* * * *
3925057 ACTTCG-CGCTAATACATGAAGACAAGATCTG-ATTTCTTCGATCTACTTCGCCACCAATAT-GG
66 ACTTCGCCACCAATACAGGAAGACAAGATCTGCA--TCTTCGATCCACTTC-CCACCAATATAGG
3925119 AAAGAT
128 -AAGAT
* * * * * * ** *
3925125 AAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAAATAGGATCTGCTACCTTCGATC
1 AAGATCTGCTATCTTCGATCCACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTGCGATC
* * * * * * * *
3925188 TACTTC-ACGCCAATACATGAAGACAAGACCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGG
65 TACTTCGCCACCAATACAGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CCACCAATATAGG
3925252 AA
128 AA
3925254 CAGGGAGGTA
Statistics
Matches: 349, Mismatches: 35, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
130 1 0.00
131 21 0.06
132 302 0.87
133 25 0.07
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (132 bp):
AAGATCTGCTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCT
ACTTCGCCACCAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCCCACCAATATAGGAAG
AT
Found at i:3925238 original size:176 final size:176
Alignment explanation
Indices: 3924845--3925239 Score: 664
Period size: 176 Copynumber: 2.2 Consensus size: 176
3924835 CCACTTCCTA
* * * * *
3924845 CCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
1 CCAATACATGAAGACAAGACCTGCTTTCTTCGATCTACTTCGCGCCAATACATGAAGACAAGATC
* *
3924910 TGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCC
66 TGATTTCTGCGATCTACTTCGCCACCAATATGGAAAGACAAGATCTGCATCTTCGATCCACTTCC
*
3924975 TACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACG
131 TACCAATATAGGAAAATAGGATCTGCTACCTTCGATCTACTTCACG
* * * *
3925021 CCAATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCGCTAATACATGAAGACAAGATC
1 CCAATACATGAAGACAAGACCTGCTTTCTTCGATCTACTTCGCGCCAATACATGAAGACAAGATC
* *
3925086 TGATTTCTTCGATCTACTTCGCCACCAATATGGAAAGATAAGATCTGCATCTTCGATCCACTTCC
66 TGATTTCTGCGATCTACTTCGCCACCAATATGGAAAGACAAGATCTGCATCTTCGATCCACTTCC
3925151 TACCAATATAGGAAAATAGGATCTGCTACCTTCGATCTACTTCACG
131 TACCAATATAGGAAAATAGGATCTGCTACCTTCGATCTACTTCACG
3925197 CCAATACATGAAGACAAGACCTGCTTTCTTCGATCTACTTCGC
1 CCAATACATGAAGACAAGACCTGCTTTCTTCGATCTACTTCGC
3925240 CACCAGTATG
Statistics
Matches: 202, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
176 202 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (176 bp):
CCAATACATGAAGACAAGACCTGCTTTCTTCGATCTACTTCGCGCCAATACATGAAGACAAGATC
TGATTTCTGCGATCTACTTCGCCACCAATATGGAAAGACAAGATCTGCATCTTCGATCCACTTCC
TACCAATATAGGAAAATAGGATCTGCTACCTTCGATCTACTTCACG
Found at i:3925408 original size:86 final size:86
Alignment explanation
Indices: 3925274--3925537 Score: 384
Period size: 86 Copynumber: 3.1 Consensus size: 86
3925264 AAATCTGCCA
* * * *
3925274 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGATATCTTTAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTA
*
3925339 CAAACGAGAGAGGTAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* * *
3925361 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
*
3925426 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* *
3925447 TGTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
* * * *
3925512 GACCAAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
3925533 TCTTC
1 TCTTC
3925538 AATTTTTACT
Statistics
Matches: 157, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 137 0.87
87 20 0.13
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:3935268 original size:3 final size:3
Alignment explanation
Indices: 3935260--3935313 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
3935250 CTTTATTAAA
* * * *
3935260 TAT TAT TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT CAA TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
3935305 TAT TAT TAT
1 TAT TAT TAT
3935314 ATATATTAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3935274 original size:9 final size:9
Alignment explanation
Indices: 3935252--3935313 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
3935242 TTTTGTTTCT
3935252 TTATTAAATA
1 TTATT-AATA
*
3935262 TTATTATTA
1 TTATTAATA
3935271 TTATTTCTAATA
1 TTA--T-TAATA
3935283 TTATTAATA
1 TTATTAATA
*
3935292 TTATCAATA
1 TTATTAATA
*
3935301 TTATTATTA
1 TTATTAATA
3935310 TTAT
1 TTAT
3935314 ATATATTAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 30 0.68
10 6 0.14
11 1 0.02
12 7 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTAATA
Found at i:3935286 original size:18 final size:18
Alignment explanation
Indices: 3935263--3935313 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
3935253 TATTAAATAT
3935263 TATTATTATTATT-TCTAA
1 TATTATTATTATTATC-AA
*
3935281 TATTATTAATATTATCAA
1 TATTATTATTATTATCAA
3935299 TATTATTATTATTAT
1 TATTATTATTATTAT
3935314 ATATATTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 28 0.93
19 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATTATTATTATCAA
Found at i:3935319 original size:18 final size:18
Alignment explanation
Indices: 3935252--3935321 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
3935242 TTTTGTTTCT
*
3935252 TTATTAAATATTATTATTA
1 TTATTATATA-TATTATTA
*
3935271 TTATT-TCTAATATTATTA
1 TTATTATAT-ATATTATTA
*
3935289 ATATTATCA-ATATTATTA
1 TTATTAT-ATATATTATTA
3935307 TTATTATATATATTA
1 TTATTATATATATTA
3935322 GTGTATGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 1 0.02
18 34 0.81
19 7 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTATATATATTATTA
Found at i:3935469 original size:24 final size:23
Alignment explanation
Indices: 3935442--3935525 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 23
3935432 TTAATATTGG
3935442 TATATATTTTATTATATATGTAT
1 TATATATTTTATTATATATGTAT
*
3935465 ATATATACTTT-TTATATA-GTAT
1 -TATATATTTTATTATATATGTAT
* *
3935487 TATCAT-TTCTATTATTATATTTAT
1 TAT-ATATTTTATTA-TATATGTAT
3935511 TAT-TATGTTTATTAT
1 TATATAT-TTTATTAT
3935526 TTTCACTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
21 5 0.10
22 10 0.20
23 13 0.27
24 21 0.43
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TATATATTTTATTATATATGTAT
Found at i:3935526 original size:12 final size:12
Alignment explanation
Indices: 3935400--3935526 Score: 65
Period size: 12 Copynumber: 10.7 Consensus size: 12
3935390 TTTCATATTG
3935400 TTATTATTAGTAT
1 TTATTATTA-TAT
*
3935413 TATAATATTATAT
1 T-TATTATTATAT
*
3935426 TTATTTTTAATAT
1 TTATTATT-ATAT
3935439 TGGTA-TA-TAT-T
1 T--TATTATTATAT
3935450 TTATTA-TATAT
1 TTATTATTATAT
*
3935461 GTA-TATATATACT
1 TTATTAT-TATA-T
3935474 TT-TTA-TATA-
1 TTATTATTATAT
* *
3935483 GTATTATCAT-T
1 TTATTATTATAT
3935494 TCTATTATTATAT
1 T-TATTATTATAT
*
3935507 TTATTATTATGT
1 TTATTATTATAT
3935519 TTATTATT
1 TTATTATT
3935527 TTCACTATTA
Statistics
Matches: 88, Mismatches: 11, Indels: 31
0.68 0.08 0.24
Matches are distributed among these distances:
9 3 0.03
10 10 0.11
11 11 0.12
12 37 0.42
13 17 0.19
14 8 0.09
15 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:3935535 original size:21 final size:21
Alignment explanation
Indices: 3935498--3935537 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3935488 ATCATTTCTA
*
3935498 TTATTATATTTATTATTATGT
1 TTATTATATTTACTATTATGT
3935519 TTATTAT-TTTCACTATTAT
1 TTATTATATTT-ACTATTAT
3935538 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATTATATTTACTATTATGT
Found at i:3935728 original size:26 final size:26
Alignment explanation
Indices: 3935699--3935770 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
3935689 CATATATTTT
3935699 ATTATGTATATATTTTTAATAACTAC
1 ATTATGTATATATTTTTAATAACTAC
* * * *
3935725 ATTATGTATGTATTTGTAA-CACTAT
1 ATTATGTATATATTTTTAATAACTAC
* *
3935750 ATTATGTACATACTTTTAATA
1 ATTATGTATATATTTTTAATA
3935771 TTATTATGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (26 bp):
ATTATGTATATATTTTTAATAACTAC
Found at i:3935754 original size:25 final size:26
Alignment explanation
Indices: 3935698--3935792 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 26
3935688 TCATATATTT
*
3935698 TATTATGTATATATTTTTAATAACTA
1 TATTATGTATATATTTGTAATAACTA
* * *
3935724 CATTATGTATGTATTTGTAA-CACTA
1 TATTATGTATATATTTGTAATAACTA
*
3935749 TATTATGTACATACTTT-TAAT-A-T-
1 TATTATGTATATA-TTTGTAATAACTA
*
3935772 TATTATGTATTTATTT-TAATA
1 TATTATGTATATATTTGTAATA
3935793 TATATGTACA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
22 7 0.12
23 11 0.19
24 1 0.02
25 18 0.32
26 20 0.35
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (26 bp):
TATTATGTATATATTTGTAATAACTA
Found at i:3935806 original size:20 final size:21
Alignment explanation
Indices: 3935747--3935807 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
3935737 TTTGTAACAC
3935747 TATATTATGTACATACTTTTAA
1 TATATTATGTACATA-TTTTAA
**
3935769 TATTATTATGTATTTATTTTAA
1 TA-TATTATGTACATATTTTAA
3935791 TATA-TATGTACATATTT
1 TATATTATGTACATATTT
3935808 ATGTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.32
21 2 0.06
22 10 0.29
23 11 0.32
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TATATTATGTACATATTTTAA
Found at i:3935806 original size:24 final size:22
Alignment explanation
Indices: 3935763--3935840 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
3935753 ATGTACATAC
**
3935763 TTTTAATATTATTATGTATTTA
1 TTTTAATATTATTACATATTTA
3935785 TTTTAATATATATGTACATATTTA
1 TTTTAATAT-TAT-TACATATTTA
* *
3935809 -TGTAGTATTATTA-ATATATATA
1 TTTTAATATTATTACATAT-T-TA
3935831 TTTTAATATT
1 TTTTAATATT
3935841 TCTAATATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 3 0.07
22 14 0.31
23 16 0.36
24 8 0.18
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTTAATATTATTACATATTTA
Found at i:3935874 original size:26 final size:26
Alignment explanation
Indices: 3935768--3935890 Score: 76
Period size: 26 Copynumber: 4.7 Consensus size: 26
3935758 CATACTTTTA
*
3935768 ATATTAT-TATGTATTTATTT-TAAT
1 ATATTATGTATATATTTATTTCTAAT
* ** *
3935792 ATA-TATGTACATATTTATGTAGTATT
1 ATATTATGTATATATTTAT-TTCTAAT
* * *
3935818 ATTAATATATATATTTTAATATTTCTAAT
1 A-TATTATGTATATATT--TATTTCTAAT
*
3935847 ATA-TATTGTATATGTTTATTT-TATAT
1 ATATTA-TGTATATATTTATTTCTA-AT
3935873 ATATTATGTATATATTTA
1 ATATTATGTATATATTTA
3935891 ATATTATTAT
Statistics
Matches: 76, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
23 3 0.04
24 12 0.16
25 3 0.04
26 25 0.33
27 6 0.08
28 19 0.25
29 5 0.07
30 3 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (26 bp):
ATATTATGTATATATTTATTTCTAAT
Found at i:3935898 original size:21 final size:22
Alignment explanation
Indices: 3935863--3935905 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3935853 TGTATATGTT
*
3935863 TATTTTATATATATTATGTATA
1 TATTTAATATATATTATGTATA
3935885 TATTTAATAT-TATTATGTATA
1 TATTTAATATATATTATGTATA
3935906 CACTTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TATTTAATATATATTATGTATA
Found at i:3938808 original size:15 final size:16
Alignment explanation
Indices: 3938779--3938810 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3938769 TATATGATAA
3938779 AATTTTATGTTTTATT
1 AATTTTATGTTTTATT
3938795 AATTTTAT-TTTTATT
1 AATTTTATGTTTTATT
3938810 A
1 A
3938811 TATATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
AATTTTATGTTTTATT
Found at i:3944616 original size:21 final size:21
Alignment explanation
Indices: 3944590--3944641 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
3944580 CGCTATTTCT
*
3944590 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
3944611 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
3944632 AATCTCACCG
1 AATCTCACCG
3944642 TCACCGCTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.37, G:0.10, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:3945086 original size:22 final size:22
Alignment explanation
Indices: 3945061--3945105 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3945051 TACATATATA
3945061 TATTACATA-TAATATTTGATTT
1 TATTA-ATATTAATATTTGATTT
* *
3945083 TATTAATATTTATGTTTGATTT
1 TATTAATATTAATATTTGATTT
3945105 T
1 T
3945106 TTTGAAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TATTAATATTAATATTTGATTT
Found at i:3945907 original size:25 final size:23
Alignment explanation
Indices: 3945879--3945936 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
3945869 TTGCAAAGAT
*
3945879 ATTACTTTTTAGTTTTATTTTTTTA
1 ATTA-TTTTT-GTTTTATTTTTTAA
3945904 ATTATTTAGTTGTTTTATTTTTTAA
1 ATTATTT--TTGTTTTATTTTTTAA
3945929 ATTATTTT
1 ATTATTTT
3945937 AGGAATCATC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 24 0.80
26 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (23 bp):
ATTATTTTTGTTTTATTTTTTAA
Found at i:3949702 original size:18 final size:18
Alignment explanation
Indices: 3949675--3949711 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3949665 AAATTTTGAG
* *
3949675 TTAATTAAATTGAGTTAT
1 TTAATCAAATCGAGTTAT
3949693 TTAATCAAATCGAGTTAT
1 TTAATCAAATCGAGTTAT
3949711 T
1 T
3949712 CAAATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAATCAAATCGAGTTAT
Found at i:3949925 original size:19 final size:20
Alignment explanation
Indices: 3949884--3949931 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3949874 AATTACAAAA
3949884 AAAATT-AAAAAAAATTTCC
1 AAAATTCAAAAAAAATTTCC
* *
3949903 AAAATTCAAAATAAATTT-T
1 AAAATTCAAAAAAAATTTCC
3949922 AAAATTCAAA
1 AAAATTCAAA
3949932 TTATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATTCAAAAAAAATTTCC
Found at i:3954762 original size:153 final size:153
Alignment explanation
Indices: 3954465--3954766 Score: 408
Period size: 153 Copynumber: 2.0 Consensus size: 153
3954455 TCTAAGGGAC
* * * * * *
3954465 TGCAATCTTTGTGAAGGAGATATTCCACGTGATATTTCTGGTCTATCCTCTTTGACAGATCTTGA
1 TGCAATCTTGGTGAAGCAGATATTCAAAGTGATATTTCTGGTCTATCCTCTTTGACACATCTTAA
* * * * *
3954530 TCTTAGTGGTAACAATTTCAGCAGCATACCTGCATCTCTTATTGGACTCTCGAAGCTTGGGTTTC
66 TCTTAGTGGTAACAATTTCAGCAACATACCTGCATCTCTTACTAGACTCTCCAAGCTTGAGTTTC
*
3954595 TTACGTTGTCAAATTGCAACATG
131 TTACATTGTCAAATTGCAACATG
* * **
3954618 TGCACTCTTGGTGAAGCAGATATTCAAAGTTATATTTCTGGTCTATCCTCTTTGGTACATCTTAA
1 TGCAATCTTGGTGAAGCAGATATTCAAAGTGATATTTCTGGTCTATCCTCTTTGACACATCTTAA
* * *
3954683 TCTTAGTGTTAACAATTTCATCAACATACCTGCATCTCTTACTAGACTCTCCAAGCTTTAGTTTC
66 TCTTAGTGGTAACAATTTCAGCAACATACCTGCATCTCTTACTAGACTCTCCAAGCTTGAGTTTC
*
3954748 TTGCATTGGT-AAATTGCAA
131 TTACATT-GTCAAATTGCAA
3954767 GATGCTTAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
153 126 0.98
154 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (153 bp):
TGCAATCTTGGTGAAGCAGATATTCAAAGTGATATTTCTGGTCTATCCTCTTTGACACATCTTAA
TCTTAGTGGTAACAATTTCAGCAACATACCTGCATCTCTTACTAGACTCTCCAAGCTTGAGTTTC
TTACATTGTCAAATTGCAACATG
Found at i:3959752 original size:18 final size:18
Alignment explanation
Indices: 3959729--3959803 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
3959719 CCCAACTACT
*
3959729 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
**
3959747 GTATACGTGAATAGTATT
1 GTATACGTGAATAGTACC
*
3959765 GTATAAGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
3959783 ATATACATGAATAGTACC
1 GTATACGTGAATAGTACC
3959801 GTA
1 GTA
3959804 AACGGTCGTA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3959775 original size:36 final size:36
Alignment explanation
Indices: 3959728--3959798 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
3959718 TCCCAACTAC
* * *
3959728 TGTATACGTGAACAGTACCGTATACGTGAATAGTAT
1 TGTATAAGTGAACAGTACCATATACATGAATAGTAT
*
3959764 TGTATAAGTGAATAGTACCATATACATGAATAGTA
1 TGTATAAGTGAACAGTACCATATACATGAATAGTA
3959799 CCGTAAACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (36 bp):
TGTATAAGTGAACAGTACCATATACATGAATAGTAT
Found at i:3967894 original size:86 final size:86
Alignment explanation
Indices: 3967749--3968090 Score: 670
Period size: 86 Copynumber: 4.0 Consensus size: 86
3967739 AAAGTCAAAG
3967749 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
1 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
3967814 TCTAAAGAACCTGGAAAACGT
66 TCTAAAGAACCTGGAAAACGT
3967835 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
1 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
3967900 TCTAAAGAACCTGGAAAACGT
66 TCTAAAGAACCTGGAAAACGT
3967921 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
1 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
3967986 TCTAAAGAACCTGGAAAACGT
66 TCTAAAGAACCTGGAAAACGT
3968007 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
1 ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
3968072 TCTAAAGAA-C-GGAAAACGT
66 TCTAAAGAACCTGGAAAACGT
3968091 TGTAGATTGT
Statistics
Matches: 256, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
84 9 0.04
85 1 0.00
86 246 0.96
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.24
Consensus pattern (86 bp):
ACAACAAATATTTGTGGATGCATGATTTGTTGAAAGAGATGGGAAGAAAAATTGTTAGGGAAAAA
TCTAAAGAACCTGGAAAACGT
Found at i:3969059 original size:13 final size:13
Alignment explanation
Indices: 3969041--3969065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3969031 GAATATGCAT
3969041 TAGATATAAGTAC
1 TAGATATAAGTAC
3969054 TAGATATAAGTA
1 TAGATATAAGTA
3969066 TTTAATACTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
TAGATATAAGTAC
Found at i:3969103 original size:81 final size:81
Alignment explanation
Indices: 3969001--3969292 Score: 584
Period size: 81 Copynumber: 3.6 Consensus size: 81
3968991 AAGATTTTGT
3969001 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAAGTACTAGATATAAGTA
1 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAAGTACTAGATATAAGTA
3969066 TTTAATACTCATGTAC
66 TTTAATACTCATGTAC
3969082 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAAGTACTAGATATAAGTA
1 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAAGTACTAGATATAAGTA
3969147 TTTAATACTCATGTAC
66 TTTAATACTCATGTAC
3969163 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAAGTACTAGATATAAGTA
1 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAAGTACTAGATATAAGTA
3969228 TTTAATACTCATGTAC
66 TTTAATACTCATGTAC
3969244 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAA
1 TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAA
3969293 CAACATAGCT
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 211 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (81 bp):
TTAAAAGATCATACCTTAATACCTATATTCGAATATGCATTAGATATAAGTACTAGATATAAGTA
TTTAATACTCATGTAC
Found at i:3969140 original size:13 final size:13
Alignment explanation
Indices: 3969122--3969146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3969112 GAATATGCAT
3969122 TAGATATAAGTAC
1 TAGATATAAGTAC
3969135 TAGATATAAGTA
1 TAGATATAAGTA
3969147 TTTAATACTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
TAGATATAAGTAC
Found at i:3969221 original size:13 final size:13
Alignment explanation
Indices: 3969203--3969227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3969193 GAATATGCAT
3969203 TAGATATAAGTAC
1 TAGATATAAGTAC
3969216 TAGATATAAGTA
1 TAGATATAAGTA
3969228 TTTAATACTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
TAGATATAAGTAC
Found at i:3970646 original size:153 final size:153
Alignment explanation
Indices: 3970360--3970647 Score: 353
Period size: 153 Copynumber: 1.9 Consensus size: 153
3970350 CACGGTCTTT
* * * * * *
3970360 GTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCTTTGAGACGTCTTAATCTTAGCGGT
1 GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTATTTGAAAAGTCTTAATCTTAGAGGT
** * * * * * * *
3970425 AACAATTTCATCAACATGCCTGCCCCTCTTACTCGACTTTACAAGCTTGAATTTCTTATATTGGC
66 AACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAGC
3970490 AAATTGCGGCTTATGCCATTTTG
131 AAATTGCGGCTTATGCCATTTTG
* *
3970513 GTGAAGGAGATATTACTAATGATATTTCTTGTCTATCCTATTTGAAAAGTCTTGATCTTAGAGAG
1 GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTATTTGAAAAGTCTTAATCTTAGAG-G
* * * * * *
3970578 -AACAATTTCGTCAGCACACCTGCATCTCTTACTCGACTATCCAACCTTCAATTCCTTGGATTAT
65 TAACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAG
3970642 CAAATT
130 CAAATT
3970648 CCAGGGAGCT
Statistics
Matches: 111, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
153 110 0.99
154 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (153 bp):
GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTATTTGAAAAGTCTTAATCTTAGAGGT
AACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAGC
AAATTGCGGCTTATGCCATTTTG
Found at i:3972525 original size:36 final size:36
Alignment explanation
Indices: 3972478--3972550 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
3972468 GATTGGTCTG
3972478 ACTGATTGGATCGAGAATCGATTAGTATACTAGTCC
1 ACTGATTGGATCGAGAATCGATTAGTATACTAGTCC
3972514 ACTGATTGGATCGAGAATCGATTAGTATACTAGTCC
1 ACTGATTGGATCGAGAATCGATTAGTATACTAGTCC
3972550 A
1 A
3972551 AACAAAGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (36 bp):
ACTGATTGGATCGAGAATCGATTAGTATACTAGTCC
Found at i:3977820 original size:18 final size:18
Alignment explanation
Indices: 3977797--3977831 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3977787 TAATAGATAT
3977797 ACTTAAAATCTAATTGGC
1 ACTTAAAATCTAATTGGC
*
3977815 ACTTAAAATCTAGTTGG
1 ACTTAAAATCTAATTGG
3977832 ACTGCAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
ACTTAAAATCTAATTGGC
Found at i:3983712 original size:26 final size:26
Alignment explanation
Indices: 3983674--3983783 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
3983664 TGATACAAAT
3983674 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
3983700 TGATAATATGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3983726 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3983752 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3983778 TGATAA
1 TGATAA
3983784 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:3985288 original size:26 final size:26
Alignment explanation
Indices: 3985225--3985300 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
3985215 AAAAGTAGCT
* * * *
3985225 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-GTGCA
3985253 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGGTGCA
3985279 AAATTACTGTTATACCCCTAGG
1 AAATTACTGTTATACCCCTAGG
3985301 GTTAATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 25 0.57
27 1 0.02
28 18 0.41
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGGTGCA
Found at i:3985444 original size:27 final size:27
Alignment explanation
Indices: 3985403--3985523 Score: 170
Period size: 27 Copynumber: 4.4 Consensus size: 27
3985393 GAGGAAGCGT
*
3985403 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
3985430 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
3985457 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
3985484 TCTGGTGGCTCTGCCACGATTATCTATA
1 TCTGGTGGCTCTGCCACAAATATCT-GA
*
3985512 TCTGGTGACTCT
1 TCTGGTGGCTCT
3985524 ATCACATTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 73 0.87
28 11 0.13
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:3985488 original size:54 final size:55
Alignment explanation
Indices: 3985403--3985542 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 55
3985393 GAGGAAGCGT
* * *
3985403 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCT-GA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTAGA
* * *
3985457 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTATA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTAGA
* **
3985512 TCTGGTGACTCTATCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
3985543 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 59 0.78
55 17 0.22
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTAGA
Found at i:3985628 original size:19 final size:22
Alignment explanation
Indices: 3985604--3985643 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
3985594 CTCCCCACAC
3985604 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
3985623 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
3985644 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:3999618 original size:11 final size:11
Alignment explanation
Indices: 3999598--3999631 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3999588 TGCATTTAGT
3999598 TTTATTCTTGA
1 TTTATTCTTGA
*
3999609 TTTGTTCTTGA
1 TTTATTCTTGA
3999620 TTTATTCTTGA
1 TTTATTCTTGA
3999631 T
1 T
3999632 AATTTGGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTATTCTTGA
Found at i:4002820 original size:21 final size:21
Alignment explanation
Indices: 4002790--4002853 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
4002780 ACAAACTGTT
*
4002790 GATTTTCAAAAGAGAACAGAG
1 GATTTTCAAAAGAAAACAGAG
* *
4002811 GATTTCCAAAAGAAAATAGAG
1 GATTTTCAAAAGAAAACAGAG
*
4002832 GATTTTCAATAGAAAACAGAG
1 GATTTTCAAAAGAAAACAGAG
4002853 G
1 G
4002854 CATCTATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.20
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACAGAG
Found at i:4005414 original size:7 final size:7
Alignment explanation
Indices: 4005396--4005437 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
4005386 AAATTAATAA
4005396 AATAAA-
1 AATAAAT
4005402 AATAAAT
1 AATAAAT
4005409 AATAAAT
1 AATAAAT
4005416 AATAAAT
1 AATAAAT
4005423 AATAAA-
1 AATAAAT
*
4005429 ACTAAAT
1 AATAAAT
4005436 AA
1 AA
4005438 AACAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:4005446 original size:27 final size:27
Alignment explanation
Indices: 4005396--4005447 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4005386 AAATTAATAA
*
4005396 AATAAAAATAAATAATAAATAATAAAT
1 AATAAAAATAAATAATAAAAAATAAAT
*
4005423 AATAAAACTAAATAA-AACAAAATAA
1 AATAAAAATAAATAATAA-AAAATAA
4005448 TATCTTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (27 bp):
AATAAAAATAAATAATAAAAAATAAAT
Found at i:4007912 original size:27 final size:27
Alignment explanation
Indices: 4007854--4007912 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
4007844 TTAATTAAAT
* *
4007854 ATTAAATAAGGAGATATGATTTTGTTA
1 ATTAAATAAGGAGATATGATTATATTA
* *
4007881 TTTAACTAAGGAGATATGATTATATTA
1 ATTAAATAAGGAGATATGATTATATTA
4007908 ATTAA
1 ATTAA
4007913 TTGTTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41
Consensus pattern (27 bp):
ATTAAATAAGGAGATATGATTATATTA
Found at i:4012740 original size:153 final size:153
Alignment explanation
Indices: 4012462--4012760 Score: 334
Period size: 153 Copynumber: 2.0 Consensus size: 153
4012452 ACTAAGGGAC
* * * * **
4012462 TGCAATCTTGGTGAAGGAGATATTCCTAGTGCTATTTCTTGTATATCCTCTTTGACACATCTTGA
1 TGCAATATTGGTGAAGGAGATAATCCTAGTGATATTTCTGGTATATCCTCACTGACACATCTTGA
* * *
4012527 TCTTCACAGTAACAATTTCAACAGCATACCTGTATCTCTTACTCGACTCTCGAAACTTGAATATC
66 GCTTCACAGTAACAATTTCAACAGCATACCTGTACCTCTTACTCGACTCTCCAAACTTGAATATC
*
4012592 TTAGG-TTGTCAAATTGTGGCCTG
131 TT-GGAGTGTCAAATTGTGGCCTG
* * **
4012615 TGCAATATTGGTGAAGGAGATAATCCTAGTGATATTTCTGGTCTATCCTCACTGAGAGTTCTTGA
1 TGCAATATTGGTGAAGGAGATAATCCTAGTGATATTTCTGGTATATCCTCACTGACACATCTTGA
**** * * * * * *
4012680 GCTTGGTGGTAACAATTTCACCAGCATAGCTACGT-CCT-TTACTCGTCTTTCCAATCTTGAATT
66 GCTTCACAGTAACAATTTCAACAGCATACCT--GTACCTCTTACTCGACTCTCCAAACTTGAATA
4012743 TCTTGGAGTGTCAAATTG
129 TCTTGGAGTGTCAAATTG
4012761 CTGTGAGCTT
Statistics
Matches: 119, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
152 2 0.02
153 113 0.95
154 2 0.02
155 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (153 bp):
TGCAATATTGGTGAAGGAGATAATCCTAGTGATATTTCTGGTATATCCTCACTGACACATCTTGA
GCTTCACAGTAACAATTTCAACAGCATACCTGTACCTCTTACTCGACTCTCCAAACTTGAATATC
TTGGAGTGTCAAATTGTGGCCTG
Found at i:4023319 original size:19 final size:19
Alignment explanation
Indices: 4023271--4023325 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
4023261 ATAATCTTCA
4023271 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4023290 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4023308 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
4023326 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:4023351 original size:22 final size:22
Alignment explanation
Indices: 4023271--4023348 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 22
4023261 ATAATCTTCA
4023271 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4023290 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4023308 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
4023330 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
4023349 GATTTAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.35
19 14 0.27
22 8 0.15
23 12 0.23
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:4023360 original size:23 final size:23
Alignment explanation
Indices: 4023317--4023359 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4023307 TATGATATGC
*
4023317 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATAATTTTGT
*
4023340 AATCTTAG-AGATTTAATTTT
1 AATCTTAGAAGATATAATTTT
4023360 TAGATACCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
AATCTTAGAAGATATAATTTTGT
Found at i:4023639 original size:17 final size:17
Alignment explanation
Indices: 4023615--4023649 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4023605 TGTTTCCCTG
*
4023615 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
4023633 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
4023650 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:4027984 original size:6 final size:6
Alignment explanation
Indices: 4027971--4028016 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
4027961 GTGAATTGTT
* *
4027971 ATTG-A ATTGAA ATTGAA ATTGAA ATTAAA ATT-AA AATGTAA ATTGA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTG-AA ATTGA
4028017 TTGGAAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
5 8 0.23
6 22 0.63
7 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (6 bp):
ATTGAA
Found at i:4028793 original size:45 final size:45
Alignment explanation
Indices: 4028729--4028856 Score: 238
Period size: 45 Copynumber: 2.8 Consensus size: 45
4028719 TACTACTACT
4028729 GTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
1 GTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
*
4028774 GTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTATTGTTACC
1 GTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
*
4028819 GTTACCGATTCGGCACTTTGTGTGTCGGATATTGTTAC
1 GTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTAC
4028857 CGTACTGTTA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (45 bp):
GTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
Found at i:4029288 original size:18 final size:19
Alignment explanation
Indices: 4029265--4029303 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4029255 TGGAACTAAG
*
4029265 AATTGAAATGTGA-ATTGA
1 AATTGAAATATGAGATTGA
*
4029283 AATTGATATATGAGATTGA
1 AATTGAAATATGAGATTGA
4029302 AA
1 AA
4029304 GCTTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (19 bp):
AATTGAAATATGAGATTGA
Found at i:4033477 original size:16 final size:16
Alignment explanation
Indices: 4033452--4033483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4033442 AAAAGAAAAG
4033452 ATATCGGATAAATGAA
1 ATATCGGATAAATGAA
*
4033468 ATATCTGATAAATGAA
1 ATATCGGATAAATGAA
4033484 TCGGTAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (16 bp):
ATATCGGATAAATGAA
Found at i:4035943 original size:22 final size:22
Alignment explanation
Indices: 4035917--4035960 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4035907 ATAGAAAATG
4035917 TAGCCCTAGAGGAAGGGAAAGA
1 TAGCCCTAGAGGAAGGGAAAGA
*
4035939 TAGCCCTAGAGGAGGGGAAAGA
1 TAGCCCTAGAGGAAGGGAAAGA
4035961 GGTGAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.39, T:0.09
Consensus pattern (22 bp):
TAGCCCTAGAGGAAGGGAAAGA
Found at i:4040596 original size:78 final size:78
Alignment explanation
Indices: 4040494--4040787 Score: 455
Period size: 78 Copynumber: 3.8 Consensus size: 78
4040484 CGAAGAAACA
** * * *
4040494 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGTAGATCTGACTTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACTTTCATTGAA
4040559 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * *
4040572 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGTCCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACTTTCATTGAA
4040637 GCAGATCCAAGAT
66 GCAGATCCAAGAT
*
4040650 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGAT-TGGACTTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACTTTCATTGA
4040714 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
* * * *
4040728 GGTTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGACATAGCAGATTTGGCTTTCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACTTTCA
4040788 CGTGTTTACG
Statistics
Matches: 198, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
77 1 0.01
78 196 0.99
79 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACTTTCATTGAA
GCAGATCCAAGAT
Found at i:4040681 original size:41 final size:41
Alignment explanation
Indices: 4040558--4040689 Score: 112
Period size: 41 Copynumber: 3.3 Consensus size: 41
4040548 CTTTCATTGA
4040558 AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
* * ** ** * * ** *
4040599 AGCAGATCGAAGA-CA--CAGCAGATCTGTCCTT-CA-TTGA
1 AGCAGATCCAAGATGATTTGGCATCTCTGT-ATTAGACGGGG
4040636 AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
*
4040677 AGCAGATCGAAGA
1 AGCAGATCCAAGA
4040690 CATAACAGAT
Statistics
Matches: 62, Mismatches: 23, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
37 13 0.21
38 10 0.16
39 4 0.06
40 10 0.16
41 25 0.40
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (41 bp):
AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
Found at i:4040988 original size:78 final size:78
Alignment explanation
Indices: 4040859--4041231 Score: 577
Period size: 78 Copynumber: 4.8 Consensus size: 78
4040849 CGAAGAAACA
** * * * *
4040859 GATTTGGCATCTCCATATTCGACGGGAAGCAAATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTAAA
4040924 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * *
4040937 GATTTGGCATCTCTGTATTAGACGGGGAGTAGATCGAAGACACAGCAGATCTTACCTTCATTAAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTAAA
4041002 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
4041015 GATTTGGCATCTCTGTATTAGACGGGGAGTAGATCGAAGACACAGCAGATCTGACCTTCATTAAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTAAA
4041080 GCAGATCCAAGAT
66 GCAGATCCAAGAT
*** * *
4041093 GATTTGGCATCTCTGTATTAGACGAATAGCAGATCGAAGACATAACAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTAA
4041157 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
*
4041171 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGTAGATCTGACCTTCAT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
4041232 GTGTTTACAT
Statistics
Matches: 271, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
77 1 0.00
78 269 0.99
79 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTAAA
GCAGATCCAAGAT
Found at i:4041084 original size:365 final size:365
Alignment explanation
Indices: 4040353--4041143 Score: 1290
Period size: 365 Copynumber: 2.2 Consensus size: 365
4040343 ACATCGAAGT
*
4040353 AGATCCAAGATGATTTGGCATC-CT-TACGTT-GAC-AATGAGCATATCGAAGACATAGCAGATT
1 AGATCCAAGATGATTTGGCATCTCTGTA--TTAGACGAA-GAGCAAATCGAAGACATAGCAGATT
*
4040414 TGGCTTTCACATGTTTACACTGAAGCAGATCTAAGATGATTTGGAATCTCTGTACTTTCAGAGAA
63 TGGCTTTCACATGTTTACACTGAAGCAGATCTAAGATGATTTGGAATCTCTGTACTATCAGAGAA
* *
4040479 CAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGTAGAT
128 CAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAAATCGAAGACATAGCAGAT
*
4040544 CTGACTTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGA
193 CTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGA
*
4040609 AGACACAGCAGATCTGTCCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACG
258 AGACACAGCAGATCTGTCCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACG
* * *
4040674 GGGAGCAGATCGAAGACATAACAGATTGGACTTTCATTGAAGC
323 GGGAGCAGATCGAAGACACAACAGATTGGACCTTCATTAAAGC
* **
4040717 AGATCCAAGATGGTTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGACATAGCAGATTTGG
1 AGATCCAAGATGATTTGGCATCTCTGTATTAGACGAAGAGCAAATCGAAGACATAGCAGATTTGG
* * *
4040782 CTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTATCAGAGAACAA
66 CTTTCACATGTTTACACTGAAGCAGATCTAAGATGATTTGGAATCTCTGTACTATCAGAGAACAA
4040847 ATCGAAGAAACAGATTTGGCATCTCCATATTCGACGG-GAAGCAAATCGAAGACATAGCAGATCT
131 ATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAG-AGCAAATCGAAGACATAGCAGATCT
*
4040911 GACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGTAGATCGAAG
195 GACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG
4040976 ACACAGCAGATCT-TACCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG
260 ACACAGCAGATCTGT-CCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG
* *
4041040 GGAGTAGATCGAAGACACAGCAGATCT-GACCTTCATTAAAGC
324 GGAGCAGATCGAAGACACAACAGAT-TGGACCTTCATTAAAGC
* * *
4041082 AGATCCAAGATGATTTGGCATCTCTGTATTAGACGAATAGCAGATCGAAGACATAACAGATT
1 AGATCCAAGATGATTTGGCATCTCTGTATTAGACGAAGAGCAAATCGAAGACATAGCAGATT
4041144 GGACCTTCAT
Statistics
Matches: 396, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
364 25 0.06
365 368 0.93
366 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (365 bp):
AGATCCAAGATGATTTGGCATCTCTGTATTAGACGAAGAGCAAATCGAAGACATAGCAGATTTGG
CTTTCACATGTTTACACTGAAGCAGATCTAAGATGATTTGGAATCTCTGTACTATCAGAGAACAA
ATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAAATCGAAGACATAGCAGATCTG
ACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGA
CACAGCAGATCTGTCCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
AGCAGATCGAAGACACAACAGATTGGACCTTCATTAAAGC
Found at i:4041369 original size:44 final size:45
Alignment explanation
Indices: 4041171--4041438 Score: 283
Period size: 45 Copynumber: 5.9 Consensus size: 45
4041161 GATCCAAGAT
* **
4041171 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC-AA-AGATAACA
* * * * * * * *
4041218 GATCTGACCT-TCATGTGTTTACATC--GAAGCAGATCCAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCAAAGATAACA
* *
4041263 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACA
* *
4041308 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTAAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACA
** *
4041352 GATTTGGTGTCTCTGTATTAGACAGGGAGCAGATCAAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACA
* *
4041397 GATTTGGCGTCTCTATATTAGACGGGGAGCAGATCAAAGATA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATA
4041439 GTAGATATAA
Statistics
Matches: 181, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.01
44 43 0.24
45 108 0.60
46 5 0.03
47 19 0.10
48 4 0.02
49 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.26
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACA
Found at i:4041416 original size:89 final size:89
Alignment explanation
Indices: 4041245--4041436 Score: 285
Period size: 89 Copynumber: 2.1 Consensus size: 89
4041235 TTTACATCGA
* * * *
4041245 AGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAGAGATAACAGA
1 AGCAGATCAAAGAAG-CAGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCAAAGATAACAGA
*
4041310 TTTGGCATCTCTGTATTAGACGGGG
65 TTTGGCATCTCTATATTAGACGGGG
* ** *
4041335 AGCAGATTAAAGAAGCAGATTTGGTGTCTCTGTATTAGACAGGGAGCAGATCAAAGATAACAGAT
1 AGCAGATCAAAGAAGCAGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCAAAGATAACAGAT
*
4041400 TTGGCGTCTCTATATTAGACGGGG
66 TTGGCATCTCTATATTAGACGGGG
4041424 AGCAGATCAAAGA
1 AGCAGATCAAAGA
4041437 TAGTAGATAT
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
89 79 0.87
90 12 0.13
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (89 bp):
AGCAGATCAAAGAAGCAGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCAAAGATAACAGAT
TTGGCATCTCTATATTAGACGGGG
Found at i:4041689 original size:20 final size:22
Alignment explanation
Indices: 4041640--4041689 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
4041630 GCCCAGAAAT
*
4041640 AAGTCCAAAAACAAAAATAATA
1 AAGTCCAAAAACAAAAATAACA
**
4041662 AACCCCAAAAA-AAAAA-AACA
1 AAGTCCAAAAACAAAAATAACA
4041682 AAGTCCAA
1 AAGTCCAA
4041690 GTTCAGTCCA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 9 0.39
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.08
Consensus pattern (22 bp):
AAGTCCAAAAACAAAAATAACA
Found at i:4041819 original size:14 final size:15
Alignment explanation
Indices: 4041800--4041855 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
4041790 AATCTTCAAT
4041800 GATATG-CAATCTTA
1 GATATGACAATCTTA
4041814 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
4041831 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
4041849 GATATGA
1 GATATGA
4041856 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:4041844 original size:35 final size:37
Alignment explanation
Indices: 4041798--4041876 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
4041788 ATAATCTTCA
4041798 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
4041834 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
4041870 A-GATATG
1 ATGATATG
4041877 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:4041876 original size:17 final size:19
Alignment explanation
Indices: 4041798--4041869 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
4041788 ATAATCTTCA
4041798 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4041817 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4041834 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4041852 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
4041870 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:4041895 original size:22 final size:22
Alignment explanation
Indices: 4041798--4041895 Score: 69
Period size: 17 Copynumber: 5.0 Consensus size: 22
4041788 ATAATCTTCA
4041798 ATGATATGCAATC-T--TAGAT
1 ATGATATGCAATCTTAGTAGAT
4041817 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGTAGAT
4041834 ATGAT-TGCAATC-T--TAGAT
1 ATGATATGCAATCTTAGTAGAT
*
4041852 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGTAGAT
* *
4041874 ATGATTTTGTAATCTTA-TAGAT
1 ATGA-TATGCAATCTTAGTAGAT
4041896 TTAATTTGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
17 15 0.23
18 15 0.23
19 13 0.20
20 1 0.02
22 12 0.18
23 10 0.15
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
ATGATATGCAATCTTAGTAGAT
Found at i:4054004 original size:26 final size:26
Alignment explanation
Indices: 4053968--4054075 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
4053958 TGAAATTCTC
*
4053968 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
* *
4053994 ATCATGGAACATTTACCAAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
4054020 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
4054046 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
4054072 ATCA
1 ATCA
4054076 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:4055306 original size:26 final size:28
Alignment explanation
Indices: 4055250--4055307 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
4055240 CTAAGGTCGG
4055250 ATAATATCTATCCATATCCAAGATTTAT
1 ATAATATCTATCCATATCCAAGATTTAT
* *
4055278 ATAATCTCTCTCCATATCCAAGATTTAT
1 ATAATATCTATCCATATCCAAGATTTAT
4055306 AT
1 AT
4055308 CACAGAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (28 bp):
ATAATATCTATCCATATCCAAGATTTAT
Found at i:4059699 original size:21 final size:21
Alignment explanation
Indices: 4059668--4059727 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
4059658 TGCGTATAAC
* *
4059668 AAAATACATATACTAATATTA
1 AAAATAAATATACTAATAATA
* **
4059689 ATAATAAATATACTAGGAATA
1 AAAATAAATATACTAATAATA
*
4059710 AAAATAAATATAATAATA
1 AAAATAAATATACTAATA
4059728 GTATATATAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAATAAATATACTAATAATA
Found at i:4059774 original size:27 final size:28
Alignment explanation
Indices: 4059729--4059786 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
4059719 ATAATAATAG
* *
4059729 TATATATATGATATGGTATTTAA-AAGA
1 TATATATATGATATAGTATTCAAGAAGA
4059756 TATATATATG-TAATAGTATTCAAGAAGA
1 TATATATATGAT-ATAGTATTCAAGAAGA
4059784 TAT
1 TAT
4059787 GAAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 19 0.70
28 7 0.26
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.40
Consensus pattern (28 bp):
TATATATATGATATAGTATTCAAGAAGA
Found at i:4060545 original size:25 final size:25
Alignment explanation
Indices: 4060465--4060546 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
4060455 ATATAACATT
4060465 AAAAATATATATGT-GTA-ATATACA
1 AAAAATATATA-GTAGTATATATACA
*
4060489 AAAACATATATAGTAGTAT-TA-AGA
1 AAAA-ATATATAGTAGTATATATACA
4060513 ATATAAATATA-AGATAGTATATATACA
1 A-A-AAATATATAG-TAGTATATATACA
4060540 AAAAATA
1 AAAAATA
4060547 AGTAATGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
24 11 0.23
25 29 0.60
26 5 0.10
27 3 0.06
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (25 bp):
AAAAATATATAGTAGTATATATACA
Found at i:4067098 original size:13 final size:13
Alignment explanation
Indices: 4067080--4067104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4067070 TAGTTTAGAT
4067080 TTGATTATGTAAA
1 TTGATTATGTAAA
4067093 TTGATTATGTAA
1 TTGATTATGTAA
4067105 TCTTGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:4075594 original size:14 final size:15
Alignment explanation
Indices: 4075575--4075605 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4075565 CAAGAAATGG
4075575 GAAGAAAAAT-TGTT
1 GAAGAAAAATGTGTT
4075589 GAAGAAAAATGTGTT
1 GAAGAAAAATGTGTT
4075604 GA
1 GA
4075606 TGAACCTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (15 bp):
GAAGAAAAATGTGTT
Found at i:4078529 original size:153 final size:153
Alignment explanation
Indices: 4078245--4078529 Score: 372
Period size: 153 Copynumber: 1.9 Consensus size: 153
4078235 ACTAAGGGAC
* * * * * *
4078245 TGCAATCTTGGTGAAGGAGATATTCCTAGTGCTATTTCTTGTTTATCCTCTTTGACAAATCTTGA
1 TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCATTGACAAATCTTGA
* * * * *
4078310 TCTTAGCGGTAATAATTTCAGCAGCATACCGGCATCTCTTACTCGACTCTCCAAACTTGAAGATC
66 TCTTAACGGTAACAATTTCACCAGCATACCGGCATCTCTTACTCGACTCTCCAAACTTCAACATC
4078375 TTCGGTTGTCAAATTGCGGCCTG
131 TTCGGTTGTCAAATTGCGGCCTG
* * *
4078398 TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCATTGAGATATCTTGT
1 TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCATTGACAAATCTTGA
* * * * * * * *
4078463 TCTTAATGGTAACAATTTCACCAGCATAGCTGCGTCTCTTACTTGTCTTTCCAATCTTCAACATC
66 TCTTAACGGTAACAATTTCACCAGCATACCGGCATCTCTTACTCGACTCTCCAAACTTCAACATC
4078528 TT
131 TT
4078530 GGAGTGTCAG
Statistics
Matches: 110, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
153 110 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (153 bp):
TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCATTGACAAATCTTGA
TCTTAACGGTAACAATTTCACCAGCATACCGGCATCTCTTACTCGACTCTCCAAACTTCAACATC
TTCGGTTGTCAAATTGCGGCCTG
Found at i:4080420 original size:23 final size:23
Alignment explanation
Indices: 4080371--4080420 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
4080361 TAAGCAATAA
** *
4080371 TCATTCATTTACAGTATACTTTT
1 TCATTCATTTACAGTATAAATTC
* *
4080394 TCATTCATTTTCAGTCTAAATTC
1 TCATTCATTTACAGTATAAATTC
4080417 TCAT
1 TCAT
4080421 ATACTTACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (23 bp):
TCATTCATTTACAGTATAAATTC
Found at i:4080880 original size:20 final size:20
Alignment explanation
Indices: 4080855--4080901 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
4080845 GTTTACACAA
4080855 GCCAGAAGCTTCTGGAACGT
1 GCCAGAAGCTTCTGGAACGT
4080875 GCCAGAAGCTTCTGGAACGT
1 GCCAGAAGCTTCTGGAACGT
4080895 GCCAGAA
1 GCCAGAA
4080902 CAACGCCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.17
Consensus pattern (20 bp):
GCCAGAAGCTTCTGGAACGT
Found at i:4088558 original size:16 final size:16
Alignment explanation
Indices: 4088537--4088568 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4088527 GATGCTATTT
*
4088537 ATATAATTTTTTATAA
1 ATATAACTTTTTATAA
4088553 ATATAACTTTTTATAA
1 ATATAACTTTTTATAA
4088569 GCACCATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATAACTTTTTATAA
Found at i:4092790 original size:11 final size:11
Alignment explanation
Indices: 4092774--4092798 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4092764 TTTTTGAAAT
4092774 TTTTATTTTAA
1 TTTTATTTTAA
4092785 TTTTATTTTAA
1 TTTTATTTTAA
4092796 TTT
1 TTT
4092799 AAAATTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:4096008 original size:13 final size:13
Alignment explanation
Indices: 4095969--4096020 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
4095959 CGTTTAACAA
4095969 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
4095982 TGCTATGGAAAAG
1 TGCTTTTGAAAAG
*
4095995 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
4096008 TGTTTTTTAAAAG
1 TGCTTTTGAAAAG
4096021 ATTGGTTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:4099627 original size:18 final size:18
Alignment explanation
Indices: 4099601--4099729 Score: 150
Period size: 18 Copynumber: 7.2 Consensus size: 18
4099591 TACGACCGTT
* *
4099601 TACGATACTATTCATGTA
1 TACGGTACTATTCACGTA
4099619 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
**
4099637 TATAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
4099655 TACGGCACTATTCATGTA
1 TACGGTACTATTCACGTA
** *
4099673 TACGACACTATTCGCGTA
1 TACGGTACTATTCACGTA
* *
4099691 TACGATACTATTCATGTA
1 TACGGTACTATTCACGTA
*
4099709 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
4099727 TAC
1 TAC
4099730 AGTAGTTGGG
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 94 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:4107442 original size:30 final size:30
Alignment explanation
Indices: 4107386--4107443 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
4107376 TAGGCACTTC
* *
4107386 CACACGGGTGATCCACATGCCTGTGTGTGA
1 CACACGGGTGATCCACACGCCCGTGTGTGA
*
4107416 CACACGGGTAGA-CCATACGCCCGTGTGT
1 CACACGGGT-GATCCACACGCCCGTGTGT
4107444 CATGGCCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (30 bp):
CACACGGGTGATCCACACGCCCGTGTGTGA
Found at i:4113063 original size:11 final size:12
Alignment explanation
Indices: 4113033--4113092 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
4113023 CTTTGAGCCC
*
4113033 TTTTATTTTA-C
1 TTTTATTTTATT
*
4113044 TATTATATTTATT
1 TTTTAT-TTTATT
4113057 TTTTATTTTA-T
1 TTTTATTTTATT
*
4113068 TTTAATTTTATT
1 TTTTATTTTATT
* *
4113080 TTGTCTTTTATT
1 TTTTATTTTATT
4113092 T
1 T
4113093 CTTTTTGAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 15 0.38
12 19 0.49
13 5 0.13
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTATTTTATT
Done.