Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold396
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: 560635
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 4
Found at i:124106 original size:3 final size:3
Alignment explanation
Indices: 124098--124126 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
124088 ATGTTGCTGA
124098 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
124127 GCACATGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:124422 original size:57 final size:62
Alignment explanation
Indices: 124324--124447 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 62
124314 TTTTTGTTAT
* *
124324 TAATAAGATTTATCATATTTATCTAATTGTATTAAAAGA-TTT-GGTTAAAT-AATTTATTGGA
1 TAATAAGATTTAT-ATATGTATCTAATTCTATTAAAAGATTTTAGG-TAAATAAATTTATTGGA
* *
124385 TAATAAGATTTAT-TATGT-T-TAATTCTATTCAATGATTTTAGGTAAATAAAATTTATTGGA
1 TAATAAGATTTATATATGTATCTAATTCTATTAAAAGATTTTAGGTAAAT-AAATTTATTGGA
124445 TAA
1 TAA
124448 AAAATAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
57 13 0.24
58 9 0.16
59 6 0.11
60 14 0.25
61 13 0.24
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (62 bp):
TAATAAGATTTATATATGTATCTAATTCTATTAAAAGATTTTAGGTAAATAAATTTATTGGA
Found at i:125878 original size:14 final size:15
Alignment explanation
Indices: 125859--125893 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
125849 TATTTTTTTA
125859 ATTTAAATTA-ATTT
1 ATTTAAATTATATTT
125873 ATTTAAATTATTATTT
1 ATTTAAATTA-TATTT
125889 ATTTA
1 ATTTA
125894 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
16 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAAATTATATTT
Found at i:125892 original size:20 final size:19
Alignment explanation
Indices: 125869--125912 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
125859 ATTTAAATTA
* *
125869 ATTTATTTAAATTATTATTT
1 ATTTATTAAAAATATT-TTT
125889 ATTTATTAAAAATATTTTT
1 ATTTATTAAAAATATTTTT
125908 ATTTA
1 ATTTA
125913 AATTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTATTAAAAATATTTTT
Found at i:127083 original size:20 final size:20
Alignment explanation
Indices: 127026--127083 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
127016 AATATATTAA
127026 AAAATTA-TATATAAA-ATT
1 AAAATTATTATATAAATATT
*
127044 ATAAATTATTATAATTAATA-T
1 A-AAATTATTAT-ATAAATATT
127065 AAAATTATTACTATAAATA
1 AAAATTATTA-TATAAATA
127084 GATCAAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 1 0.03
19 6 0.18
20 18 0.55
21 7 0.21
22 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTATTATATAAATATT
Found at i:127228 original size:32 final size:33
Alignment explanation
Indices: 127145--127234 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 33
127135 TATTAAAATC
* *
127145 ATATTTAAGATATTATATAATTATATAAATTTTGAT
1 ATATTT-ATATATT-TAT-ATTATATAAATTTTAAT
* * *
127181 ACATTAATA-AATTATATTATATAAA-TTTAAT
1 ATATTTATATATTTATATTATATAAATTTTAAT
*
127212 ATATTTATATATTTATATCATAT
1 ATATTTATATATTTATATTATAT
127235 TTGTATTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
31 12 0.27
32 21 0.48
33 3 0.07
34 2 0.05
35 2 0.05
36 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (33 bp):
ATATTTATATATTTATATTATATAAATTTTAAT
Found at i:127229 original size:27 final size:27
Alignment explanation
Indices: 127147--127229 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 27
127137 TTAAAATCAT
* *
127147 ATTTAAGATA-TTATATAATTATATAA
1 ATTTAATATATTTATATATTTATATAA
* * *
127173 ATTTTGATACATTAATAAATTATATTATATAA
1 A-TTTAATATATT--TATA-TAT-TTATATAA
127205 ATTTAATATATTTATATATTTATAT
1 ATTTAATATATTTATATATTTATAT
127230 CATATTTGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
26 1 0.02
27 12 0.28
28 4 0.09
29 3 0.07
30 3 0.07
31 11 0.26
32 9 0.21
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (27 bp):
ATTTAATATATTTATATATTTATATAA
Found at i:127234 original size:19 final size:17
Alignment explanation
Indices: 127193--127236 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
127183 ATTAATAAAT
127193 TATATTATATAAATTTAA
1 TATATT-TATAAATTTAA
*
127211 TATATTTATATATTTATA
1 TATATTTATAAATTTA-A
127229 TCATATTT
1 T-ATATTT
127237 GTATTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 8 0.35
19 6 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTATAAATTTAA
Found at i:127382 original size:2 final size:2
Alignment explanation
Indices: 127375--127490 Score: 137
Period size: 2 Copynumber: 57.5 Consensus size: 2
127365 AATCTTTAGG
* *
127375 AT AT AT AT AT AT AT AG AT GA- AT GAG A- AT AT AT CAT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT -AT AT AT AT
* * *
127416 AT AT AC AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
127458 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127491 GATGAATGAG
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
1 2 0.02
2 92 0.94
3 4 0.04
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:129147 original size:24 final size:22
Alignment explanation
Indices: 129112--129155 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
129102 TCAACACGAC
129112 ATGAAAAAAATAATATAATATAAA
1 ATGAAAAAAAT-ATA-AATATAAA
*
129136 ATGAAAATAATATAAATATA
1 ATGAAAAAAATATAAATATA
129156 TTAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (22 bp):
ATGAAAAAAATATAAATATAAA
Found at i:129189 original size:32 final size:33
Alignment explanation
Indices: 129142--129207 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
129132 TAAAATGAAA
129142 ATAATATAAATATATTAATATATAAAAAATTTAT
1 ATAATATAAATATATTAATATAT-AAAAATTTAT
* *
129176 ATAATAT-AA-ATATTAATTTATTAAAATTTAT
1 ATAATATAAATATATTAATATATAAAAATTTAT
129207 A
1 A
129208 AAAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 10 0.33
32 11 0.37
33 2 0.07
34 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATAATATAAATATATTAATATATAAAAATTTAT
Found at i:129214 original size:32 final size:33
Alignment explanation
Indices: 129144--129215 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
129134 AAATGAAAAT
*
129144 AATATAAATATATTAATATATAAAAAATTTATAT
1 AATAT-AATATATTAATATATAAAAAATTTATAA
* *
129178 AATATAA-ATATTAATTTAT-TAAAATTTATAAA
1 AATATAATATATTAATATATAAAAAATTTAT-AA
129210 AATATA
1 AATATA
129216 TTCACCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 9 0.26
32 18 0.53
33 2 0.06
34 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATAATATATTAATATATAAAAAATTTATAA
Found at i:129276 original size:4 final size:4
Alignment explanation
Indices: 129267--129292 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
129257 ACGGCTGGAG
129267 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
129293 GAAGCTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:131339 original size:16 final size:16
Alignment explanation
Indices: 131309--131368 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
131299 AATCAAGTTG
* *
131309 ATTAATTTAATTTTAA
1 ATTATTTTAAATTTAA
*
131325 ATTGTTTTAAATTTAA
1 ATTATTTTAAATTTAA
*
131341 ATTATTTTAAATTTGA
1 ATTATTTTAAATTTAA
*
131357 GTTATATTTAAA
1 ATTAT-TTTAAA
131369 ATTTGAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
16 31 0.84
17 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:131365 original size:27 final size:26
Alignment explanation
Indices: 131318--131368 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
131308 GATTAATTTA
**
131318 ATTTTAAATTGTTTTAAATTTAAATT
1 ATTTTAAATTGAGTTAAATTTAAATT
*
131344 ATTTTAAATTTGAGTTATATTTAAA
1 ATTTTAAA-TTGAGTTAAATTTAAA
131369 ATTTGAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (26 bp):
ATTTTAAATTGAGTTAAATTTAAATT
Found at i:131370 original size:18 final size:18
Alignment explanation
Indices: 131343--131377 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
131333 AAATTTAAAT
*
131343 TATTTTAAATTTGAGTTA
1 TATTTAAAATTTGAGTTA
131361 TATTTAAAATTTGAGTT
1 TATTTAAAATTTGAGTT
131378 TTAATTATAT
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:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
TATTTAAAATTTGAGTTA
Found at i:134071 original size:10 final size:11
Alignment explanation
Indices: 134050--134074 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
134040 GATACAAATA
134050 TTTTTAATTTT
1 TTTTTAATTTT
134061 TTTTTAATTTT
1 TTTTTAATTTT
134072 TTT
1 TTT
134075 AATAATTTTA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTAATTTT
Found at i:140888 original size:2 final size:2
Alignment explanation
Indices: 140881--140915 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
140871 GTAAACATTA
140881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
140916 AACACAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:141660 original size:16 final size:16
Alignment explanation
Indices: 141635--141665 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
141625 TTATTTGAAT
*
141635 AATATTATTTTTAAAA
1 AATATAATTTTTAAAA
141651 AATATAATTTTTAAA
1 AATATAATTTTTAAA
141666 TATAAATTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATAATTTTTAAAA
Found at i:141707 original size:14 final size:14
Alignment explanation
Indices: 141684--141734 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
141674 AAATGATAAG
*
141684 AAATATTAATTTTT
1 AAATAATAATTTTT
141698 AAATAATAATTTTTTT
1 AAATAATAA--TTTTT
*
141714 AAA-AAAAATATTTT
1 AAATAATAAT-TTTT
141728 AAATAAT
1 AAATAAT
141735 TTTCATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.03
14 15 0.50
15 6 0.20
16 8 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATAATAATTTTT
Found at i:141727 original size:15 final size:16
Alignment explanation
Indices: 141692--141733 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
141682 AGAAATATTA
*
141692 ATTTTTAAATAATAAT
1 ATTTTTAAATAAAAAT
*
141708 TTTTTTAAA-AAAAAT
1 ATTTTTAAATAAAAAT
141723 A-TTTTAAATAA
1 ATTTTTAAATAA
141734 TTTTCATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.32
15 7 0.32
16 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTTAAATAAAAAT
Found at i:142160 original size:24 final size:25
Alignment explanation
Indices: 142094--142161 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
142084 TTAAAATATG
142094 AAATAACAATAAATATAAATATTAAAAT
1 AAATAA-AATAAA-A-AAATATTAAAAT
* *
142122 AAATAAAGT-AAAAAATATTATAAT
1 AAATAAAATAAAAAAATATTAAAAT
142146 AAA-AAAATAAAAAAAT
1 AAATAAAATAAAAAAAT
142162 GGATCAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 4 0.11
24 21 0.58
25 1 0.03
26 2 0.06
27 2 0.06
28 6 0.17
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (25 bp):
AAATAAAATAAAAAAATATTAAAAT
Found at i:142897 original size:20 final size:21
Alignment explanation
Indices: 142841--142898 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
142831 ATTTTTTATA
*
142841 TAATTTATATTTATT-TAATT
1 TAATTTATATATATTATAATT
* * *
142861 TAATTAACATATTTTATAA-T
1 TAATTTATATATATTATAATT
142881 TAATTTATATATATTATA
1 TAATTTATATATATTATA
142899 TATATTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTTATATATATTATAATT
Found at i:147119 original size:2 final size:2
Alignment explanation
Indices: 147112--147140 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
147102 GATTTCAACA
147112 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
147141 TTTAGAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:153844 original size:18 final size:18
Alignment explanation
Indices: 153799--153846 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
153789 ATGAATGCCA
*
153799 TATATATTTTAATTATTTTT
1 TATATA-TTTAA-AATTTTT
153819 TAT-T-TTTAAAATTTTT
1 TATATATTTAAAATTTTT
153835 TATATATTTAAA
1 TATATATTTAAA
153847 TAATATTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 6 0.24
19 1 0.04
20 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATATTTAAAATTTTT
Found at i:154097 original size:22 final size:23
Alignment explanation
Indices: 154054--154097 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
154044 ACATACCTAT
154054 CATATTTATATTTAAAATTTTAA
1 CATATTTATATTTAAAATTTTAA
154077 CATATTTA-A-TTAATAATTTTA
1 CATATTTATATTTAA-AATTTTA
154098 GTGATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
CATATTTATATTTAAAATTTTAA
Found at i:154387 original size:9 final size:9
Alignment explanation
Indices: 154357--154404 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
154347 GAAGAATATT
154357 TAATAAATA
1 TAATAAATA
*
154366 TAAAAATAATA
1 T-AATA-AATA
154377 TAATAAATA
1 TAATAAATA
154386 TAATAAGATA
1 TAATAA-ATA
*
154396 TATTAAATA
1 TAATAAATA
154405 ATTAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 14 0.42
10 14 0.42
11 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
TAATAAATA
Found at i:154475 original size:32 final size:33
Alignment explanation
Indices: 154412--154477 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
154402 ATAATTAAAA
*
154412 TAAAATATTTAATATACGTATCATATTTATATT
1 TAAAATATTTAATATACGTATCATATATATATT
**
154445 TAAAAT-TTTAATATATTTAATCATTATATATAT
1 TAAAATATTTAATATACGT-ATCA-TATATATAT
154478 AGTTTTAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 10 0.36
33 10 0.36
34 8 0.29
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (33 bp):
TAAAATATTTAATATACGTATCATATATATATT
Found at i:154683 original size:386 final size:385
Alignment explanation
Indices: 153974--154866 Score: 1179
Period size: 386 Copynumber: 2.3 Consensus size: 385
153964 TAATTATGAT
* *
153974 ATATTTAATGAATATAAAAATTATATAATAAATATGATAAATACATTAAATAATTAAAATAAAAT
1 ATATTTAATAAATATAAAAATAATATAATAAATATGATAAATACATTAAATAATTAAAATAAAAT
* * * *
154039 ATTTCACATACCTATCATATTTATATTTAAAATTTTAACATATTT-A--A-T-TA-ATA-ATTTT
66 ATTTAATATACATATCATATTTATATTTAAAATTTTAATATATTTAATCATTATATATATATTTT
* * * *
154097 AGTGATTAAAAAAATACAATATGGGCACTAATTATGTCTAACTTTTTATGTTGGGTTTGTTGTCC
131 AGTGATTAAAAAAATACAATATAGGCACTAATTAAGTCTAACTTTTTATGTTGGGTTTATTCTCC
154162 TTTTCTTTCAAGTTTTGATCTGTCATTAATAATTTTTTTTTTCAAAAAATTCATTTATCAAATCA
196 TTTTCTTTCAAGTTTTGATCTGTCATTAATAATTTTTTTTTTCAAAAAATTCATTTATCAAATCA
* * * * *
154227 ATGCAACAAAGGTTTGCTATTCATAAAAATAGGAATTCAGATATGATAACTTTAAAATTGGTGGA
261 ATGCAACAAAGGCTTGCTATTCATAAAAAAAAGAATCCAGATATGATAACTTTAAAATTGGTGAA
*
154292 ATTGAATCTGAAAATGGTTGCAGAGATGATGTGAAATTATATTATTACCAAAATGGAAGA
326 ATTGAATCTGAAAATGGTTGCAGAGATGATGTGAAATTATAGTATTACCAAAATGGAAGA
* *
154352 ATATTTAATAAATATAAAAATAATATAATAAATATAATAAGATATATTAAATAATTAAAATAAAA
1 ATATTTAATAAATATAAAAATAATATAATAAATATGATAA-ATACATTAAATAATTAAAATAAAA
*
154417 TATTTAATATACGTATCATATTTATATTTAAAATTTTAATATATTTAATCATTATATATATAGTT
65 TATTTAATATACATATCATATTTATATTTAAAATTTTAATATATTTAATCATTATATATATA-TT
* * * * *
154482 TTAGT-ATTTAAAAAATGCAAT-TAGGTACTAATTAAGTCT-ATTTTTTCATGTTTGGTTTATTC
129 TTAGTGATTAAAAAAATACAATATAGGCACTAATTAAGTCTAACTTTTT-ATGTTGGGTTTATTC
* * *
154544 TCCATTTT-TTTAAGTAAGTTTTGGTCTGTCATTAAT-A-TTTTTTTTTGAAAAAATTCATTTAT
193 TCC-TTTTCTTT---CAAGTTTTGATCTGTCATTAATAATTTTTTTTTTCAAAAAATTCATTTAT
* * *
154606 TAAATCAATGCAACAAAGGCTTGTTATTCATAAAAAAAAGAATCCAGATTTGATATA-TTTAAAA
254 CAAATCAATGCAACAAAGGCTTGCTATTCATAAAAAAAAGAATCCAGATATGATA-ACTTTAAAA
* * * * * * *
154670 TTGGTGAAATTGAATTTGACAATGTTTGCATAGATGATGTGAAATTATAGTATTATCAATATGTA
318 TTGGTGAAATTGAATCTGAAAATGGTTGCAGAGATGATGTGAAATTATAGTATTACCAAAATGGA
154735 AGA
383 AGA
* * * *
154738 ATATTTATTTAATGTAAAAATATTATATAATAAATATGATATAATACATT-AGTAGATTAAAAT-
1 ATATTTAATAAATATAAAAATA--ATATAATAAATATGATA-AATACATTAAATA-ATTAAAATA
* *
154801 AAATATTTATTATACATATTATATTTATATTTAAAATTTTAATATATTTAATCATTATATATATA
62 AAATATTTAATATACATATCATATTTATATTTAAAATTTTAATATATTTAATCATTATATATATA
154866 T
127 T
154867 ATATATATAT
Statistics
Matches: 451, Mismatches: 45, Indels: 30
0.86 0.09 0.06
Matches are distributed among these distances:
378 37 0.08
379 65 0.14
380 1 0.00
382 1 0.00
383 1 0.00
384 8 0.02
385 36 0.08
386 177 0.39
387 74 0.16
388 50 0.11
389 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (385 bp):
ATATTTAATAAATATAAAAATAATATAATAAATATGATAAATACATTAAATAATTAAAATAAAAT
ATTTAATATACATATCATATTTATATTTAAAATTTTAATATATTTAATCATTATATATATATTTT
AGTGATTAAAAAAATACAATATAGGCACTAATTAAGTCTAACTTTTTATGTTGGGTTTATTCTCC
TTTTCTTTCAAGTTTTGATCTGTCATTAATAATTTTTTTTTTCAAAAAATTCATTTATCAAATCA
ATGCAACAAAGGCTTGCTATTCATAAAAAAAAGAATCCAGATATGATAACTTTAAAATTGGTGAA
ATTGAATCTGAAAATGGTTGCAGAGATGATGTGAAATTATAGTATTACCAAAATGGAAGA
Found at i:154768 original size:18 final size:19
Alignment explanation
Indices: 154730--154768 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
154720 TATTATCAAT
* *
154730 ATGTAAGAATATTTATTTA
1 ATGTAAAAATATTTATATA
154749 ATGTAAAAATA-TTATATA
1 ATGTAAAAATATTTATATA
154767 AT
1 AT
154769 AAATATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
ATGTAAAAATATTTATATA
Found at i:155948 original size:39 final size:39
Alignment explanation
Indices: 155905--156083 Score: 122
Period size: 39 Copynumber: 4.8 Consensus size: 39
155895 TTAAAATCCA
* *
155905 AAAAATGTGATTAATGTATAAATTTTTTATTGAAATTTT
1 AAAAATGTGATTAATATATAAATTTTTTATTGAAATTTG
* * * * * *
155944 AAAAATGTTAATAATATATAGATTATTTATTGGAATATG
1 AAAAATGTGATTAATATATAAATTTTTTATTGAAATTTG
* * * * *
155983 GAAGATATGA-TAACATAT-AATTTTTTATTGAAATTCG
1 AAAAATGTGATTAATATATAAATTTTTTATTGAAATTTG
* * ** *
156020 AAATATGAGATTAATGCATGAATTCTTTT-TTGAAA--T-
1 AAAAATGTGATTAATATATAAATT-TTTTATTGAAATTTG
*
156056 --ATATGTGATTAATATATAAATTTTTTAT
1 AAAAATGTGATTAATATATAAATTTTTTAT
156084 GAGAATTAGA
Statistics
Matches: 106, Mismatches: 30, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
33 4 0.04
34 19 0.18
37 20 0.19
38 12 0.11
39 47 0.44
40 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (39 bp):
AAAAATGTGATTAATATATAAATTTTTTATTGAAATTTG
Found at i:156512 original size:12 final size:12
Alignment explanation
Indices: 156495--156520 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
156485 TAAAAGTTCA
156495 TCATTGTCATTT
1 TCATTGTCATTT
156507 TCATTGTCATTT
1 TCATTGTCATTT
156519 TC
1 TC
156521 GTTTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (12 bp):
TCATTGTCATTT
Found at i:158657 original size:5 final size:5
Alignment explanation
Indices: 158647--158673 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
158637 TTTTTATCTC
158647 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
158674 GGTAAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:159616 original size:74 final size:74
Alignment explanation
Indices: 159462--159747 Score: 335
Period size: 74 Copynumber: 3.9 Consensus size: 74
159452 CTATTCTTAT
* * * * *
159462 AAATAAAAATAAATCAT-CGCTTAAAAAACTTTTAACTCCTATAGTCAAACCAAAAAAATAAATT
1 AAATAAAAATAAATCATAC-CTTAAAAAA-TTTAAACTCGTATAATCATACCTAAAAAATAAATT
159526 TAAACTTCTAC
64 TAAACTTCTAC
* * * *
159537 AAATAAAAATAAATCATACCTTAAAAAATATAAACTCGTATAATCATACCTAGAAAACAAATCTA
1 AAATAAAAATAAATCATACCTTAAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATTTA
*
159602 AACTTTTAC
66 AACTTCTAC
* * * * *
159611 AAATAAAAATAAATAAAACTTTAAAAAATTTAAACTCGTATAATTA-AACTAAAAAATAAATTTA
1 AAATAAAAATAAATCATACCTTAAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATTTA
*
159675 AACTTCTAT
66 AACTTCTAC
* * * * * *
159684 AAATAAAAATAAATTATACTTTAAAAAATTTAAACCCGAATAATCATA-CTCAAAAATAATTTTA
1 AAATAAAAATAAATCATACCTTAAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATTTA
159748 TAAATAAAAA
Statistics
Matches: 181, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
73 76 0.42
74 78 0.43
75 26 0.14
76 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.29
Consensus pattern (74 bp):
AAATAAAAATAAATCATACCTTAAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATTTA
AACTTCTAC
Found at i:159696 original size:73 final size:72
Alignment explanation
Indices: 159462--159747 Score: 302
Period size: 73 Copynumber: 3.9 Consensus size: 72
159452 CTATTCTTAT
* * * * * *
159462 AAATAAAAATAAATCATCGCTTAAAAAACTTTTAACTCCTATAGTCAAACCAAAAAAATAAATTT
1 AAATAAAAATAAATAAAC-CTTAAAAAA-TTTAAACTCGTATAATCAAA-CTAAAAAATAAATTT
159527 AAACTTCTAC
63 AAACTTCTAC
* * * * * *
159537 AAATAAAAATAAATCATACCTTAAAAAATATAAACTCGTATAATCATACCTAGAAAACAAATCTA
1 AAATAAAAATAAAT-AAACCTTAAAAAATTTAAACTCGTATAATCA-AACTAAAAAATAAATTTA
*
159602 AACTTTTAC
64 AACTTCTAC
* *
159611 AAATAAAAATAAATAAAACTTTAAAAAATTTAAACTCGTATAATTAAACTAAAAAATAAATTTAA
1 AAATAAAAATAAAT-AAACCTTAAAAAATTTAAACTCGTATAATCAAACTAAAAAATAAATTTAA
*
159676 ACTTCTAT
65 ACTTCTAC
* * * * * * *
159684 AAATAAAAATAAATTATACTTTAAAAAATTTAAACCCGAATAATCATACTCAAAAATAATTTTA
1 AAATAAAAATAAA-TAAACCTTAAAAAATTTAAACTCGTATAATCAAACTAAAAAATAAATTTA
159748 TAAATAAAAA
Statistics
Matches: 177, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
73 76 0.43
74 76 0.43
75 24 0.14
76 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.29
Consensus pattern (72 bp):
AAATAAAAATAAATAAACCTTAAAAAATTTAAACTCGTATAATCAAACTAAAAAATAAATTTAAA
CTTCTAC
Found at i:159712 original size:25 final size:26
Alignment explanation
Indices: 159662--159710 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
159652 AATTAAACTA
*
159662 AAAAATAAATTTAAACTTCTATAAAT
1 AAAAATAAATTTAAACTTCTAAAAAT
*
159688 AAAAATAAA-TTATACTT-TAAAAA
1 AAAAATAAATTTAAACTTCTAAAAA
159711 ATTTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 7 0.33
26 9 0.43
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAATAAATTTAAACTTCTAAAAAT
Found at i:160025 original size:74 final size:72
Alignment explanation
Indices: 159868--160064 Score: 270
Period size: 73 Copynumber: 2.7 Consensus size: 72
159858 CAAACTAATC
* * * *
159868 TTATAAATAAAAATAAATTACACCTCAAAAAATTTTTAACTCCTATAATC-AATCAAAAAATAAA
1 TTATAAATAAAAATAAATTATACCTTAAAAAA-TTTAAACTCCTATAATCAAACCAAAAAATAAA
159932 TTTAAATT
65 TTTAAATT
* * * *
159940 TCTATAGATAAAAATAAATCATACCTTAAAAGAATTTAAATTCGTATAATCAAACCAAAAAATAA
1 T-TATAAATAAAAATAAATTATACCTTAAAA-AATTTAAACTCCTATAATCAAACCAAAAAATAA
160005 ATTTAAACTT
64 ATTTAAA-TT
*
160015 TTATAAATAAAAATAAATTATACTTTAAAAAATTTAAACTCCTATAATCA
1 TTATAAATAAAAATAAATTATACCTTAAAAAATTTAAACTCCTATAATCA
160065 TACCCCAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
72 1 0.01
73 57 0.53
74 47 0.44
75 3 0.03
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (72 bp):
TTATAAATAAAAATAAATTATACCTTAAAAAATTTAAACTCCTATAATCAAACCAAAAAATAAAT
TTAAATT
Found at i:160047 original size:25 final size:26
Alignment explanation
Indices: 159997--160047 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
159987 AATCAAACCA
* *
159997 AAAAATAAATTTAAACTTTTATAAAT
1 AAAAATAAATTTAAACTTTAAAAAAT
*
160023 AAAAATAAA-TTATACTTTAAAAAAT
1 AAAAATAAATTTAAACTTTAAAAAAT
160048 TTAAACTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAATAAATTTAAACTTTAAAAAAT
Found at i:160350 original size:70 final size:72
Alignment explanation
Indices: 160270--160428 Score: 198
Period size: 70 Copynumber: 2.2 Consensus size: 72
160260 CAAATTAATC
** * ** * *
160270 TTATAAATAAAAATAAATAATACTTTAAAATAATTTATACTCTTATAATC-AAC-CACAA-AAAT
1 TTATAAATAAAAATAAATAATACCATAAAA-AATTTAAACTAGTATAATCAAACTAAAAATAAAT
160332 TTAAACTT
65 TTAAACTT
*
160340 TTATAAATAAAAATAAATCATACCATAAAAAATTTAAACTAGTATAATCAAACTAAAAATAAATT
1 TTATAAATAAAAATAAATAATACCATAAAAAATTTAAACTAGTATAATCAAACTAAAAATAAATT
*
160405 TAAATTT
66 TAAACTT
*
160412 TTACAAATAAAAATAAA
1 TTATAAATAAAAATAAA
160429 ATTACACAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
69 16 0.21
70 30 0.39
71 3 0.04
72 27 0.36
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (72 bp):
TTATAAATAAAAATAAATAATACCATAAAAAATTTAAACTAGTATAATCAAACTAAAAATAAATT
TAAACTT
Found at i:161009 original size:31 final size:32
Alignment explanation
Indices: 160948--161009 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
160938 AAAATAATAA
* * *
160948 CACTTAAATATTTTTTTAATTTATCATTTTTT
1 CACTTAAATATTTTATAAATATATCATTTTTT
160980 CACTTAAATATTTTATAAATAT-TCATTTTT
1 CACTTAAATATTTTATAAATATATCATTTTT
161010 AACTTAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (32 bp):
CACTTAAATATTTTATAAATATATCATTTTTT
Found at i:161015 original size:30 final size:32
Alignment explanation
Indices: 160949--161016 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
160939 AAATAATAAC
* * * *
160949 ACTTAAATATTTTTTTAATTTATCATTTTTTC
1 ACTTAAATATTTTATAAATATATCATTTTTTA
160981 ACTTAAATATTTTATAAATAT-TCA-TTTTTA
1 ACTTAAATATTTTATAAATATATCATTTTTTA
161011 ACTTAA
1 ACTTAA
161017 TACTAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 11 0.34
31 3 0.09
32 18 0.56
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (32 bp):
ACTTAAATATTTTATAAATATATCATTTTTTA
Found at i:161604 original size:10 final size:10
Alignment explanation
Indices: 161572--161609 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
161562 ATTAATTTAA
161572 TTTTATATAT
1 TTTTATATAT
161582 TTTTA-AGTAT
1 TTTTATA-TAT
161592 TTTTATAT-T
1 TTTTATATAT
161601 TTTTATATA
1 TTTTATATA
161610 ATTTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 10 0.40
10 14 0.56
11 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTATATAT
Found at i:162476 original size:15 final size:15
Alignment explanation
Indices: 162447--162496 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
162437 TATTAATTTT
162447 TTAATTAAA-TTAAA
1 TTAATTAAATTTAAA
162461 TTAATTAAATTTAAA
1 TTAATTAAATTTAAA
* *
162476 -TATTTTATATTTAAA
1 TTA-ATTAAATTTAAA
162491 TTAATT
1 TTAATT
162497 TTCTCAAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.37
15 17 0.57
16 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATTAAATTTAAA
Found at i:162730 original size:21 final size:22
Alignment explanation
Indices: 162706--162747 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
162696 AAATTTATTA
*
162706 TTAACTTAAAT-TGAATAAAAT
1 TTAACTTAAATATAAATAAAAT
*
162727 TTAATTTAAATATAAATAAAA
1 TTAACTTAAATATAAATAAAA
162748 AATTTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAACTTAAATATAAATAAAAT
Found at i:162742 original size:27 final size:24
Alignment explanation
Indices: 162693--162754 Score: 63
Period size: 27 Copynumber: 2.5 Consensus size: 24
162683 ATATTAATAA
* *
162693 AAAAAATTTATTATTAACTTAAATT
1 AAAAAATTTAATATTAAATTAAA-T
162718 GAATAAAATTTAAT-TTAAATATAAAT
1 -AA-AAAATTTAATATTAAAT-TAAAT
162744 AAAAAATTTAA
1 AAAAAATTTAA
162755 ATCACGACGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 9 0.28
25 2 0.06
26 8 0.25
27 13 0.41
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
AAAAAATTTAATATTAAATTAAAT
Found at i:162827 original size:20 final size:20
Alignment explanation
Indices: 162802--162841 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
162792 GATTTCATAT
162802 ATATATATATATATTAATAA
1 ATATATATATATATTAATAA
* * *
162822 ATATATTTTTATATTTATAA
1 ATATATATATATATTAATAA
162842 TATTTGAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATATATATATTAATAA
Found at i:164340 original size:26 final size:27
Alignment explanation
Indices: 164302--164354 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
164292 GTTAATTTTA
*
164302 AAATTATTTTTAA-TTAT-TATTAAATT
1 AAATTATTATTAAGTTATAT-TTAAATT
164328 AAATTATTATTAAGTTATATTTAAATT
1 AAATTATTATTAAGTTATATTTAAATT
164355 CAAGTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 12 0.50
27 11 0.46
28 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
AAATTATTATTAAGTTATATTTAAATT
Found at i:164795 original size:25 final size:25
Alignment explanation
Indices: 164770--164816 Score: 71
Period size: 23 Copynumber: 1.9 Consensus size: 25
164760 CTAAATTTTA
164770 AAAATAAATAAT-TAT-TTTTAAATT
1 AAAA-AAATAATATATATTTTAAATT
164794 AAAAAAATAATATATATTTTAAA
1 AAAAAAATAATATATATTTTAAA
164817 ATTTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAAAATAATATATATTTTAAATT
Found at i:164805 original size:26 final size:27
Alignment explanation
Indices: 164769--164819 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
164759 TCTAAATTTT
*
164769 AAAAATAAATA-ATTATTTTTAAATTAA
1 AAAAATAAATATA-TATTTTAAAATTAA
164796 AAAAAT-AATATATATTTTAAAATT
1 AAAAATAAATATATATTTTAAAATT
164820 TTAATCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAAATAAATATATATTTTAAAATTAA
Found at i:165401 original size:17 final size:18
Alignment explanation
Indices: 165379--165419 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
165369 ATTCAAACTT
* *
165379 AAAATAAT-TTAATTTTA
1 AAAATAATCTAAAATTTA
165396 AAAATAATCTAAAATTTA
1 AAAATAATCTAAAATTTA
165414 AAAATA
1 AAAATA
165420 TGATTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATAATCTAAAATTTA
Found at i:165771 original size:11 final size:10
Alignment explanation
Indices: 165752--165809 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 10
165742 TGAGTTTAAT
165752 TTAATTTTATA
1 TTAA-TTTATA
165763 TTCAATTTAT-
1 TT-AATTTATA
165773 TTAATTATATA
1 TTAATT-TATA
165784 TTAATTTAT-
1 TTAATTTATA
*
165793 TTATTTTAT-
1 TTAATTTATA
165802 TTAATTTA
1 TTAATTTA
165810 GTGACATGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 19 0.45
10 8 0.19
11 13 0.31
12 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTAATTTATA
Found at i:165774 original size:21 final size:20
Alignment explanation
Indices: 165750--165809 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
165740 TGTGAGTTTA
165750 ATTTAATTTTATATTCAATTT
1 ATTTAATTTTATATT-AATTT
*
165771 ATTTAATTATATATTAATTT
1 ATTTAATTTTATATTAATTT
165791 ATTT-ATTTTAT-TTAATTT
1 ATTTAATTTTATATTAATTT
165809 A
1 A
165810 GTGACATGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.22
19 6 0.16
20 9 0.24
21 14 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTAATTTTATATTAATTT
Found at i:172080 original size:15 final size:15
Alignment explanation
Indices: 172046--172101 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
172036 GATAATATAT
* *
172046 TAAAATTTATATAATT
1 TAAATTTTATA-AATA
172062 TAAATTATTA-AAATA
1 TAAATT-TTATAAATA
172077 TAAAAATTTTATAAATA
1 T--AAATTTTATAAATA
172094 TAAATTTT
1 TAAATTTT
172102 TTTTAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 11 0.32
16 9 0.26
17 14 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAATTTTATAAATA
Found at i:172103 original size:17 final size:16
Alignment explanation
Indices: 172051--172102 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
172041 TATATTAAAA
*
172051 TTTATATAATTTAAATT
1 TTTATA-AATATAAATT
* *
172068 ATTA-AAATATAAAAAT
1 TTTATAAATAT-AAATT
172084 TTTATAAATATAAATT
1 TTTATAAATATAAATT
172100 TTT
1 TTT
172103 TTTAAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 4 0.14
16 15 0.54
17 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTATAAATATAAATT
Found at i:172109 original size:17 final size:17
Alignment explanation
Indices: 172063--172097 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
172053 TATATAATTT
172063 AAATTATTA-AAATATAA
1 AAATT-TTATAAATATAA
172080 AAATTTTATAAATATAA
1 AAATTTTATAAATATAA
172097 A
1 A
172098 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTTTATAAATATAA
Found at i:172541 original size:18 final size:19
Alignment explanation
Indices: 172505--172543 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
172495 TTATAATGCG
*
172505 TAAAAAAATACATTTAAAT
1 TAAAAAAATACATTAAAAT
*
172524 TAAAAAAAT-TATTAAAAT
1 TAAAAAAATACATTAAAAT
172542 TA
1 TA
172544 TAATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAAATACATTAAAAT
Found at i:172837 original size:28 final size:28
Alignment explanation
Indices: 172805--172877 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 28
172795 GATTAATAAT
172805 AATTTATTATATATTTTTAATAATTTTA
1 AATTTATTATATATTTTTAATAATTTTA
172833 AATTTATT-TA-ATATTTTAA-AATTTTA
1 AATTTATTATATAT-TTTTAATAATTTTA
* *
172859 AA--TATTAAATATTTATAAT
1 AATTTATTATATATTTTTAAT
172878 TAAAAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 4 0.10
25 6 0.15
26 13 0.33
27 8 0.21
28 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTTATTATATATTTTTAATAATTTTA
Found at i:172858 original size:16 final size:17
Alignment explanation
Indices: 172819--172877 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 17
172809 TATTATATAT
*
172819 TTTTAATAATTTTAAATT
1 TTTTAAT-ATTTTAAATA
172837 TATTTAATATTTTAAA-A
1 T-TTTAATATTTTAAATA
*
172854 TTTTAA-ATATTAAATA
1 TTTTAATATTTTAAATA
172870 TTTATAAT
1 TTT-TAAT
172878 TAAAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 7 0.20
16 9 0.26
17 4 0.11
18 9 0.26
19 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATATTTTAAATA
Found at i:179242 original size:26 final size:26
Alignment explanation
Indices: 179198--179247 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
179188 ATATATTGAT
*
179198 TTTTATAATTAAATTTAAATAAAATA
1 TTTTATAATTAAATATAAATAAAATA
179224 TTTT-TAATTAAATAATAAATAAAA
1 TTTTATAATTAAAT-ATAAATAAAA
179248 ACAGATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTTTATAATTAAATATAAATAAAATA
Found at i:179974 original size:16 final size:16
Alignment explanation
Indices: 179953--179983 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
179943 ATAAAAAAAA
179953 TTATTTTATTATAATT
1 TTATTTTATTATAATT
179969 TTATTTTATTATAAT
1 TTATTTTATTATAAT
179984 AAATCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTATTATAATT
Found at i:179986 original size:39 final size:39
Alignment explanation
Indices: 179912--179986 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
179902 TTAATACTAC
* * * *
179912 AATTATTCTATTTTATTTTTATTTTATTTTCATAAAAAA
1 AATTATTCTATTATAATTTTATTTTATTATAATAAAAAA
*
179951 AATTATTTTATTATAATTTTATTTTATTATAATAAA
1 AATTATTCTATTATAATTTTATTTTATTATAATAAA
179987 TCAAATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (39 bp):
AATTATTCTATTATAATTTTATTTTATTATAATAAAAAA
Found at i:189704 original size:244 final size:243
Alignment explanation
Indices: 189221--189706 Score: 740
Period size: 244 Copynumber: 2.0 Consensus size: 243
189211 GCTGCATTCA
* *
189221 TATGGCCCATATTTGAGCTGTGAATTTTTGATGAAAATCATTTACAAACAATCGAATTGACCAAA
1 TATGGCCCATATTTGAGCTGTGAATGTTTGAT---AATCATGTACAAACAATCGAATTGACCAAA
*
189286 CCTTGTCTTTCAACGCCAGAGGAGAATGTTCCTTACAGCTGATAAATGAAACTTGTGTCCTATTC
63 CCTTGTCTTTCAACGCCAGAGGAGAATGTTCCTTACAGCTGATAAATCAAACTTGTGTCCTATTC
** ** * **
189351 TATGGTTTCCCTTGCTTCCTTAGTGTCATTTGCTGCATGGGAATATGATAACAAATTATGTGCCA
128 TATGACTTCCCTTGCTTCCTTACCGTCATTTGCTGCATGGGAATATAATAACAAATTACCTGCCA
*
189416 AAATAAATGAAGATGTAGCCTTCTAATCCCATCTCCTGGAAAAAAATGGAC
193 AAATAAATGAAGATGCAGCCTTCTAATCCCATCTCCTGGAAAAAAATGGAC
* * *
189467 TATGGCCCATATGTTGAGCTTTGAATGTTTGAT-ATCATGTATAAACAATCGAATTGGCCAAACC
1 TATGGCCCATAT-TTGAGCTGTGAATGTTTGATAATCATGTACAAACAATCGAATTGACCAAACC
*
189531 TTGTCTTTCCAACTCCAGAGGAGAATGTTCCTTACAGCTGATAAATCAAACTTGTGTCCTATTCT
65 TTGTCTTT-CAACGCCAGAGGAGAATGTTCCTTACAGCTGATAAATCAAACTTGTGTCCTATTCT
* *
189596 ATGACTTCCCTTGCTTCCTTACCGTCATTTGCTGCATGGTAATATAATTACAAATTACCTGCCAA
129 ATGACTTCCCTTGCTTCCTTACCGTCATTTGCTGCATGGGAATATAATAACAAATTACCTGCCAA
* *
189661 AATAAATGAAGATGCAGCCTTCCTGATCCCATCTCCTGAAAAAAAA
194 AATAAATGAAGATGCAGCCTT-CTAATCCCATCTCCTGGAAAAAAA
189707 AAGGAGTGCC
Statistics
Matches: 218, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
243 36 0.17
244 130 0.60
245 22 0.10
246 12 0.06
247 18 0.08
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (243 bp):
TATGGCCCATATTTGAGCTGTGAATGTTTGATAATCATGTACAAACAATCGAATTGACCAAACCT
TGTCTTTCAACGCCAGAGGAGAATGTTCCTTACAGCTGATAAATCAAACTTGTGTCCTATTCTAT
GACTTCCCTTGCTTCCTTACCGTCATTTGCTGCATGGGAATATAATAACAAATTACCTGCCAAAA
TAAATGAAGATGCAGCCTTCTAATCCCATCTCCTGGAAAAAAATGGAC
Found at i:192300 original size:28 final size:29
Alignment explanation
Indices: 192268--192330 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
192258 AAGGTTTACA
*
192268 ATTTAAAGATTAACG-TTAGAGTTTTAA-G
1 ATTTAAAGATTAACGTTTAAAG-TTTAAGG
* *
192296 ATTTAAAGTTTAGCGTTTAAAGTTTAAGG
1 ATTTAAAGATTAACGTTTAAAGTTTAAGG
192325 ATTTAA
1 ATTTAA
192331 TGTAACAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.41
Consensus pattern (29 bp):
ATTTAAAGATTAACGTTTAAAGTTTAAGG
Found at i:192321 original size:21 final size:20
Alignment explanation
Indices: 192269--192322 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
192259 AGGTTTACAA
* *
192269 TTTAAAGATTAACGTTAGAG
1 TTTAAAGTTTAAAGTTAGAG
* *
192289 TTTTAAGATTTAAAGTTTAGCG
1 TTTAAAG-TTTAAAG-TTAGAG
192311 TTTAAAGTTTAA
1 TTTAAAGTTTAA
192323 GGATTTAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.43
Consensus pattern (20 bp):
TTTAAAGTTTAAAGTTAGAG
Found at i:199651 original size:13 final size:13
Alignment explanation
Indices: 199633--199658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
199623 CATATCATGG
199633 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
199646 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
199659 GAAGAGTGCC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:200947 original size:15 final size:15
Alignment explanation
Indices: 200929--200958 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
200919 TCAATGTACT
200929 TTGATTGTCTGAAAG
1 TTGATTGTCTGAAAG
200944 TTGATTGTCTGAAAG
1 TTGATTGTCTGAAAG
200959 CAGACGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
TTGATTGTCTGAAAG
Found at i:204762 original size:24 final size:24
Alignment explanation
Indices: 204734--204781 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
204724 TTACATTTGT
204734 TACCATGGAGTTTAATCATAAAAA
1 TACCATGGAGTTTAATCATAAAAA
204758 TACCATGGAGTTTAATCATAAAAA
1 TACCATGGAGTTTAATCATAAAAA
204782 CGCCCTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (24 bp):
TACCATGGAGTTTAATCATAAAAA
Found at i:209289 original size:2 final size:2
Alignment explanation
Indices: 209284--209310 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
209274 GCAACAATGT
209284 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
209311 TACCATCTAC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:209887 original size:22 final size:21
Alignment explanation
Indices: 209844--209927 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 21
209834 ATTTGATTAT
* **
209844 TTTTTAATTT-TTTAAAATTA
1 TTTTTATTTTATTTAATTTTA
209864 TTTTTATTTTATTTAATTTATA
1 TTTTTATTTTATTTAATTT-TA
*
209886 TTTTTATTTTAATTAAATTTTA
1 TTTTTATTTT-ATTTAATTTTA
*
209908 TTATTATTTTTATTTTAATT
1 TTTTTA-TTTTA-TTTAATT
209928 AAAATTTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.17
21 6 0.11
22 20 0.38
23 18 0.34
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTATTTTATTTAATTTTA
Found at i:209905 original size:17 final size:16
Alignment explanation
Indices: 209870--209942 Score: 57
Period size: 17 Copynumber: 4.6 Consensus size: 16
209860 ATTATTTTTA
*
209870 TTTTATTTAATTTATAT
1 TTTTATTTAA-TTAAAT
209887 TTTTATTTTAATTAAA-
1 TTTTA-TTTAATTAAAT
209903 TTTTA-TT-ATT--AT
1 TTTTATTTAATTAAAT
209915 TTTTATTTTAATTAAAAT
1 TTTTA-TTTAATT-AAAT
*
209933 TTTAATTTAA
1 TTTTATTTAA
209943 ATTTAGGTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
11 1 0.02
12 5 0.11
13 3 0.07
14 4 0.09
15 3 0.07
16 5 0.11
17 14 0.30
18 11 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATTTAATTAAAT
Found at i:209905 original size:28 final size:29
Alignment explanation
Indices: 209874--209946 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 29
209864 TTTTTATTTT
209874 ATTTAATTTATATTTTTATTTTAATT-AA
1 ATTTAATTTATATTTTTATTTTAATTAAA
*
209902 ATTTTA-TTATTATTTTTATTTTAATTAAA
1 ATTTAATTTA-TATTTTTATTTTAATTAAA
*
209931 ATTTTAATTTAAATTT
1 A-TTTAATTTATATTT
209947 AGGTAGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.08
28 21 0.55
29 3 0.08
30 8 0.21
31 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
ATTTAATTTATATTTTTATTTTAATTAAA
Found at i:212125 original size:25 final size:26
Alignment explanation
Indices: 212106--212152 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
212096 ATTAATAGTA
*
212106 ATTTTTTT-TTAT-TTTTTTAA-AAT
1 ATTTTTTTATTATACTTTTTAATAAT
212129 ATTTTTTTATTATACTTTTTAATA
1 ATTTTTTTATTATACTTTTTAATA
212153 CTTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 4 0.20
25 7 0.35
26 1 0.05
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (26 bp):
ATTTTTTTATTATACTTTTTAATAAT
Found at i:213007 original size:2 final size:2
Alignment explanation
Indices: 213000--213044 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
212990 GTCCCATTCC
*
213000 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
213041 TA TA
1 TA TA
213045 AAATATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:213558 original size:22 final size:21
Alignment explanation
Indices: 213525--213570 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
213515 ATTTTCTTAT
*
213525 TTTTTAAGATTTTTT-ATTACA
1 TTTTTAAAATTTTTTAATTA-A
213546 TTTTTAATAATTTTTTAATTAA
1 TTTTTAA-AATTTTTTAATTAA
213568 TTT
1 TTT
213571 GTGCTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTAAAATTTTTTAATTAA
Found at i:214095 original size:2 final size:2
Alignment explanation
Indices: 214088--214132 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
214078 TTTATAATTG
214088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
214130 AT A
1 AT A
214133 AAGATGAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:216421 original size:10 final size:10
Alignment explanation
Indices: 216392--216422 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
216382 TTTACAATTG
*
216392 ATATATATAT
1 ATATATATAA
216402 ATATATATAA
1 ATATATATAA
216412 ATATATATAA
1 ATATATATAA
216422 A
1 A
216423 GAGATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAA
Found at i:227213 original size:16 final size:17
Alignment explanation
Indices: 227184--227216 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
227174 TATGATCTAA
227184 TTTTTTGTAAAAATTTTT
1 TTTTTTGT-AAAATTTTT
227202 TTTTTTGT-AAATTTT
1 TTTTTTGTAAAATTTT
227217 CAAATAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTTTTGTAAAATTTTT
Found at i:228572 original size:2 final size:2
Alignment explanation
Indices: 228565--228608 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
228555 TGTTTCGAGA
228565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
228607 AT
1 AT
228609 TCAAAAAAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:233738 original size:45 final size:45
Alignment explanation
Indices: 233674--233772 Score: 182
Period size: 45 Copynumber: 2.2 Consensus size: 45
233664 GCAATTTTGG
*
233674 ACTGCTTTTGTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
1 ACTGCTTTTTTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
233719 ACTGCTTTTTTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
1 ACTGCTTTTTTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
233764 ACTG-TTTTT
1 ACTGCTTTTT
233773 GCCTAATATG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 5 0.09
45 48 0.91
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (45 bp):
ACTGCTTTTTTTAGGGAAAGATTTAACAAGTACACTGACGTTGCA
Found at i:237118 original size:15 final size:16
Alignment explanation
Indices: 237098--237130 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
237088 ACATATTATT
*
237098 TTTTTGTTATATA-AA
1 TTTTTGATATATATAA
237113 TTTTTGATATATATAA
1 TTTTTGATATATATAA
237129 TT
1 TT
237131 GTATCATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTTGATATATATAA
Found at i:240322 original size:15 final size:15
Alignment explanation
Indices: 240279--240325 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
240269 CTTTTATTAG
*
240279 AAAAATAAAAATTTA
1 AAAAATAAAAATATA
*
240294 AAAAATATTAAATATA
1 AAAAATA-AAAATATA
240310 AAAAATAAAAATATA
1 AAAAATAAAAATATA
240325 A
1 A
240326 TATATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAAAAATATA
Found at i:241067 original size:16 final size:18
Alignment explanation
Indices: 241048--241088 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
241038 AGAGAAAAAG
241048 AAAATAATAAT-AGTA-C
1 AAAATAATAATAAGTATC
*
241064 AAAATAA-AATAAGTATG
1 AAAATAATAATAAGTATC
241081 AAAATAAT
1 AAAATAAT
241089 TCTTTTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.24
Consensus pattern (18 bp):
AAAATAATAATAAGTATC
Found at i:241371 original size:110 final size:110
Alignment explanation
Indices: 241208--241425 Score: 427
Period size: 110 Copynumber: 2.0 Consensus size: 110
241198 ATATTTTAAA
241208 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
1 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
*
241273 TAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACTAT
66 CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACTAT
241318 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
1 CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
241383 CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACT
66 CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACT
241426 GCCTTTTGAT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (110 bp):
CTAAAACTTAAATTTAAAAGACTAAAAATTATTTACATATTAATATTTGAATAAGTATTGGGAAG
CAAAAGTAATGGCTATTTAAGAATTCAAGGATACCAATACACTAT
Found at i:243224 original size:19 final size:20
Alignment explanation
Indices: 243202--243252 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
243192 TATTTTAATT
243202 TTTTTAATTTTTTCTTTT-A
1 TTTTTAATTTTTTCTTTTCA
*
243221 TTTTT-ATATTTTCTTTTCA
1 TTTTTAATTTTTTCTTTTCA
243240 TTTCTTAATTTTT
1 TTT-TTAATTTTT
243253 AGCAACTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
19 9 0.33
20 2 0.07
21 5 0.19
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTAATTTTTTCTTTTCA
Found at i:243591 original size:2 final size:2
Alignment explanation
Indices: 243584--243618 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
243574 TTTATAATTA
*
243584 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
243619 AAGAGATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:244754 original size:15 final size:15
Alignment explanation
Indices: 244734--244767 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
244724 AACAAAAAAC
244734 AAAGGGGAGAAAGGA
1 AAAGGGGAGAAAGGA
**
244749 AAAGGGTCGAAAGGA
1 AAAGGGGAGAAAGGA
244764 AAAG
1 AAAG
244768 AAAAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.41, T:0.03
Consensus pattern (15 bp):
AAAGGGGAGAAAGGA
Found at i:248958 original size:2 final size:2
Alignment explanation
Indices: 248951--248990 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
248941 TTGCAAGATC
248951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
248991 CACTAAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:251102 original size:589 final size:588
Alignment explanation
Indices: 250305--251460 Score: 1615
Period size: 590 Copynumber: 2.0 Consensus size: 588
250295 TCCGTACACA
* * *
250305 CAAAAAGTTTAAAAAATATAACGGAAGGTTTTCACTTTTTTTTTTTTTTGCCCAACGCTGAAAAT
1 CAAAAAGTTTAAAAAATATAACAGAAGGTTTTCACTTTTTTTTTTTTTTGCCCAACACTGAAAAG
** * * *
250370 GATACTTATTACCGTTTTATCAAAACTAATTAAATTATGTTTGGCTTTATAAGATGGTTTATTTA
66 GATACCCATAACCGTTTTATCAAAACTAATTAAACTATCTTTGGCTTTATAAGATGGTTTATTTA
* *
250435 AGCTTCAAATTAAAAAATAATTAATAATTAAGATTTATTTTTTTATTATTTTTATTTATTATTAA
131 AGCTTCAAATTAAAAAATAATTAACAATTAAGATTTATTTTTTAATTATTTTTATTTATTATTAA
250500 TGATAAAATATCTAAATGATGAGTTTTGTATTATAGACCAAGTAAAATAAATTAAATT-AAAAAA
196 TGATAAAATATCTAAATGATGAGTTTTGTATTATAGACCAAGTAAAATAAATTAAATTAAAAAAA
* * * **
250564 TTATTTGAAATTTTATATAATAAAATAAAAATATATAAATTTTGAAAACATCTTTATCTTTTAAC
261 TTATTTGAAAATTTATATAATAAAATAAAAATATATAAATGTT-AAAAAAAATTTATCTTTTAAC
* * *
250629 -TTTTTTTAAAAAAATAAAACTCCAGTTAAATACTTTTAACCAGAATGCTCTTA-TGAAAGTTGC
325 TTTTTTTTAAAAAAATAAAACTCCAGTTAAATACTTTCAACCAGAATACTCTCATTG-AAGTTGC
* **
250692 TCATCTCATGAAACCGATGGAACTCTGAAAACCCATATATAATAAATTAAAAGAGGAA-AAAAA-
389 TCATCTCATAAAACCGATGGAACTCTGAAAACCCATATATAATAAACCAAAAGA--AAGAAAAAC
* * * ** *
250755 ATTTCAACCTTCACATATGTTTTATAGACGAATAAGATTGCAGGT-AAAAAAATGCTTATGTTTT
452 ATTTCAACCATCACATATGTTTTAAAGACGAATAAGATGGCAGGTAAAAAAAAAACTTATATTTT
250819 GGTCGAGTGTGGAGATCGC-TTGTAATACGC-ATTCCAATAAAAAAATTAAAAAACTTTTACTTG
517 GGTCGAGTGTGGAGA-C-CTTTGTAATAC-CAATTCCAAT-AAAAAATTAAAAAACTTTTACTTG
250882 TCACCTTTTAT
578 TCACCTTTTAT
* *
250893 CAAAAGGTTTAAAGAATATAACAGAAGG-TTTCTA-TTTTTTATTTTTTTT-CCCAACACTGAAA
1 CAAAAAGTTTAAAAAATATAACAGAAGGTTTTC-ACTTTTTT-TTTTTTTTGCCCAACACTGAAA
* ** *
250955 AGGATACCCA-AAGCCTTTTTATCAAAACTTGTTTAACTATACTTAAT-GCGTTTATAAGATGGT
64 AGGATACCCATAA-CCGTTTTATCAAAACTAATTAAACTAT-CTT--TGGC-TTTATAAGATGGT
*
251018 TTATTTAAGCTTCAAATTTGAAAAACT-ATTAACAATTAA-ATTTA-TTTTTAATTATTTTTATT
124 TTATTTAAGCTTCAAA-TT-AAAAAATAATTAACAATTAAGATTTATTTTTTAATTATTTTTATT
* * *
251080 TATTGTTAATGATAAAATATCTAAATGATGAGTTTTGTATTATAGACCAAGTAATATCAATTAAA
187 TATTATTAATGATAAAATATCTAAATGATGAGTTTTGTATTATAGACCAAGTAAAATAAATTAAA
*
251145 TTAAAAAAATTATTTGAAAATTTATATAATAAAATAAAAATATATAAATGTTAAAAAAAATTTGT
252 TTAAAAAAATTATTTGAAAATTTATATAATAAAATAAAAATATATAAATGTTAAAAAAAATTTAT
*
251210 CTTTTAACTTTTTTTTAAAAAAATAAAACTCGAGTTAAATACTTTCAACCAGAATACTCTCATTG
317 CTTTTAACTTTTTTTTAAAAAAATAAAACTCCAGTTAAATACTTTCAACCAGAATACTCTCATTG
* ** **
251275 AAGTTGCTTATCTCATAAAATTGATTTAACTCTGAAAACCCATATATAATAAACCAAAAGAAAGA
382 AAGTTGCTCATCTCATAAAACCGATGGAACTCTGAAAACCCATATATAATAAACCAAAAGAAAGA
*
251340 AAAACATTTCAACCATCACATATGTTTTAAAGACGAATAAGATGGCTGGTAAAAAAAAAAACTTA
447 AAAACATTTCAACCATCACATATGTTTTAAAGACGAATAAGATGGCAGGT-AAAAAAAAAACTTA
* *
251405 TATTTTGGTCGGGTGTGGAGACCTTTGTAATACCAATTCCAATAAAATATTAAAAA
511 TATTTTGGTCGAGTGTGGAGACCTTTGTAATACCAATTCCAATAAAAAATTAAAAA
251461 GTTTTCACTT
Statistics
Matches: 503, Mismatches: 47, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
586 1 0.00
587 51 0.10
588 38 0.08
589 105 0.21
590 239 0.48
591 33 0.07
592 36 0.07
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (588 bp):
CAAAAAGTTTAAAAAATATAACAGAAGGTTTTCACTTTTTTTTTTTTTTGCCCAACACTGAAAAG
GATACCCATAACCGTTTTATCAAAACTAATTAAACTATCTTTGGCTTTATAAGATGGTTTATTTA
AGCTTCAAATTAAAAAATAATTAACAATTAAGATTTATTTTTTAATTATTTTTATTTATTATTAA
TGATAAAATATCTAAATGATGAGTTTTGTATTATAGACCAAGTAAAATAAATTAAATTAAAAAAA
TTATTTGAAAATTTATATAATAAAATAAAAATATATAAATGTTAAAAAAAATTTATCTTTTAACT
TTTTTTTAAAAAAATAAAACTCCAGTTAAATACTTTCAACCAGAATACTCTCATTGAAGTTGCTC
ATCTCATAAAACCGATGGAACTCTGAAAACCCATATATAATAAACCAAAAGAAAGAAAAACATTT
CAACCATCACATATGTTTTAAAGACGAATAAGATGGCAGGTAAAAAAAAAACTTATATTTTGGTC
GAGTGTGGAGACCTTTGTAATACCAATTCCAATAAAAAATTAAAAAACTTTTACTTGTCACCTTT
TAT
Found at i:252790 original size:650 final size:650
Alignment explanation
Indices: 251546--253459 Score: 2237
Period size: 650 Copynumber: 2.9 Consensus size: 650
251536 GTAGAGAGAC
* * * * *
251546 AACCCATATATAATAAACTAAAAGAGAGAAAAAAATTTTAGCCTTCACATAAGTTTTAAAGACGA
1 AACCCATATATAATAAACCAAAAGAGA-AAAAAAAATTCAGCCTTCACATATGTTTTACAGACGA
* * * * *
251611 AGAAGATGACAAGTAAAAAAAAGCTTATGTTTTGGTTGGGTGTGAAGACCCTTGTAATACCCGTT
65 AGAAGATGGCAGGTAAAAAAAAGCTTATGTTTTGGTTGGGTGTGGAGACGCTTGTAATA-CCATT
* * *
251676 CCTAA-AAAAAATATTAAAAAAAACTTTTACTTACTTATCACCTATTTGAT-CTAAGAAAG-AGG
129 ACTAATAAAAAA-ATT--AAAAAACTTTTACTTACTTATCGCCTATTTGATCCTAA-AAAGAAAG
* * * * * * *
251738 CTTGAATCGGCATTTTTTAATATGGTCAAAAATAGTAGAGTGTAT-GTACGC-AAAAGATTTAAA
190 CTTGAATCGGCATTATTGAATAAGGTCAGAAATAGTAAAATGT-TCGTACACAAAAAGATTTAAA
* ** * *
251801 AAATATAACATA-ATATTTTTACTTT-TTTTTTGCCCAACACT-AAAAAGGATACCAATGGCCGT
254 AAATATAAC-TAGATGTTTTTACTTTATTTTTTTTCCAACACTGAAAAA-GATACCAATTGCCAT
251863 TTTATTAAAACTTGTTTAACTATGCTTAATTCTTTCATAAGATAGTTTATTTAAGTTTCAAATTT
317 TTTATTAAAACTTGTTTAACTATGCTT-A---TTT-ATAAGAT-GTTTATTTAAGTTTCAAATTT
* * * *
251928 AAAAAATAATTAATAATTAAGATTTA-TTTTTTATTATTTTTATTTATTAATAATGATAAAATAT
376 AAAAAAAAATTAACAATTAGGATTTATTTTTTTATTATTTTTATTTATTATTAATGATAAAATAT
* * * *
251992 CT-AATGATGAGTTTTGTATTATAGACCAATTAACATCAATTAAATGAAAAATTATTTGAAATTT
441 CTAAATGATGAGTTTTGTATTATAGACCAAGTAATATCAATTAAATTAAAAATTATTTAAAATTT
252056 TATATAATAAAATAAAAATATATAAATTTTAAAAACA-CTTTTATCTTTTAAC--TTTTTTAAAA
506 TATATAATAAAATAAAAATATATAAATTTTAAAAACATC-TTTATCTTTTAACTTTTTTTTAAAA
* ** * * * *
252118 AAATAAAAATTTAGTTAAATACTTTCAACTAGAATGCTCTCATGGAAGTCACTTATCTTATTAAA
570 AAATAAAACTCAAGTTAAATACTTTCAACTAGAATGCTCTCATGAAAATCACTTATCTCATGAAA
*
252183 TCGATGGAATTCTAAA
635 TCGATGGAACTCTAAA
* * * *
252199 AACCCATATATAATAAGCCAAAAGAGAAAAAAAAATTCAACCTTTACATATGTTTTACAGACAAA
1 AACCCATATATAATAAACCAAAAGAGAAAAAAAAATTCAGCCTTCACATATGTTTTACAGACGAA
* * * **
252264 AAAGATGGCAGGTACAAAAAAGCTTATATTTTGGCCGGGTGTGGAGACTGCTTGTAATACTCATT
66 GAAGATGGCAGGTAAAAAAAAGCTTATGTTTTGGTTGGGTGTGGAGAC-GCTTGTAATAC-CATT
* * *
252329 -CTAATAAAAAAATTAAAAAACTTTTGCTTACTTATCGCCTATTTAATCCCAAAAAGAAAGCTTG
129 ACTAATAAAAAAATTAAAAAACTTTTACTTACTTATCGCCTATTTGATCCTAAAAAGAAAGCTTG
* * * * **
252393 AATCGCCATTGTTGAATAAAGCCAGAAACCGTAAAATGTTCGTACACAAAAAGGATTTAAAAAAT
194 AATCGGCATTATTGAATAAGGTCAGAAATAGTAAAATGTTCGTACACAAAAA-GATTTAAAAAAT
* *
252458 AT-ACTAGGAGGTTTTTACTTTATTTTTTTTCCAACACTGAAAAAGATACCAATTGTCATTTTAT
258 ATAACTA-GATGTTTTTACTTTATTTTTTTTCCAACACTGAAAAAGATACCAATTGCCATTTTAT
*
252522 CAAAACTTGTTTAACTATGCTT-TTTATAAGATGGTTTATTTAAGTTTCAAATTTTAAAAAAAAA
322 TAAAACTTGTTTAACTATGCTTATTTATAAGAT-GTTTATTTAAGTTTCAAA-TTTAAAAAAAAA
*
252586 TTAACAATTAGGATTTATTTTTTTATTA-TTTTAATTATTATTAATGATAAAATATCTAAATGAT
385 TTAACAATTAGGATTTATTTTTTTATTATTTTTATTTATTATTAATGATAAAATATCTAAATGAT
*
252650 GAGTTTTGTACTATAGACCAAGTAATATCAATTAAATTAAAAATTATTTAAAATTTTATATAAT-
450 GAGTTTTGTATTATAGACCAAGTAATATCAATTAAATTAAAAATTATTTAAAATTTTATATAATA
252714 AAAT-AAAATATATAAATTTTAAAAACATCTTTATCTTTTAACTTTTTTTTAAAAAAATAAAACT
515 AAATAAAAATATATAAATTTTAAAAACATCTTTATCTTTTAACTTTTTTTTAAAAAAATAAAACT
* * *
252778 CGAGTTAAATACTTTCAACTATAATGCTCTCATGAAAATCGCTTATCTCATGAAATCGATGGAAC
580 CAAGTTAAATACTTTCAACTAGAATGCTCTCATGAAAATCACTTATCTCATGAAATCGATGGAAC
*
252843 TCTGAA
645 TCTAAA
* * * * * *
252849 AACCTATATATAATAAACCAAAGGAAAAAAAATAAATTCAGCCTTCACTTATGTTTTACAAATGA
1 AACCCATATATAATAAACCAAAAGAGAAAAAA-AAATTCAGCCTTCACATATGTTTTACAGACGA
* * ***
252914 AGAAGATCGCAGGTAAAAAAAAAGTTTATGTTTTGGTTAAATGTGGAGACCGCTTGTAATACCTA
65 AGAAGATGGCAGGT-AAAAAAAAGCTTATGTTTTGGTTGGGTGTGGAGA-CGCTTGTAATACC-A
* * * * * *
252979 TTAC-AATCAAAGAAATTAAAAAGCTTTTACTTACTTGTCGCCTGTTTGATCTTAAGAAGAAAGC
127 TTACTAAT-AAAAAAATTAAAAAACTTTTACTTACTTATCGCCTATTTGATCCTAAAAAGAAAGC
* * * * * * * *
253043 TCGAATTGGTATAATTGAATAAGGTTAGAAATAGTAAAATATCCATACACACAAAA-AGTTTAAA
191 TTGAATCGGCATTATTGAATAAGGTCAGAAATAGTAAAATGTTCGTACACA-AAAAGA-TTTAAA
* * * * *
253107 GAATATAAC-AGAATGTTTTTATTTATTTATTTTTTTTTTGCTCAATACTGAAAAGGATACCCAT
254 AAATATAACTAG-ATGTTTTTA---CTTTA--TTTTTTTT-C-CAACACTGAAAAAGATACCAAT
* *
253171 TGCCATTTTATTAAAACTTGTTTAACTACT-CTTAATGCCTT-T-ATATGTTTATTTAAGCTTCA
311 TGCCATTTTATTAAAACTTGTTTAACTA-TGCTT-AT---TTATAAGATGTTTATTTAAGTTTCA
* * *
253233 AATTTGAAAAACAATTAACAATTAGCATTTATTTTTTTATTATTTTTATTTATTATTAATGATAA
371 AATTTAAAAAAAAATTAACAATTAGGATTTATTTTTTTATTATTTTTATTTATTATTAATGATAA
* * * *
253298 AAAATCTAAATTATGAGTTTTGTATTACAGACTAAGTAATATCAATTAAATTATAAAATTATTTA
436 AATATCTAAATGATGAGTTTTGTATTATAGACCAAGTAATATCAATTAAATTA-AAAATTATTTA
* *
253363 AAATTTTATATAATAAAATAAAAATATATAAATTTTAAAAA-AT-TTTACCTTATAACTTTTCTT
500 AAATTTTATATAATAAAATAAAAATATATAAATTTTAAAAACATCTTTATCTTTTAACTTTT-TT
* *
253426 TT-AAAAAATAAAACTCAACTTAAATACTTCCAAC
564 TTAAAAAAATAAAACTCAAGTTAAATACTTTCAAC
253460 CTATGAGAAA
Statistics
Matches: 1082, Mismatches: 133, Indels: 82
0.83 0.10 0.06
Matches are distributed among these distances:
648 61 0.06
649 61 0.06
650 218 0.20
651 83 0.08
652 130 0.12
653 174 0.16
654 58 0.05
655 5 0.00
656 4 0.00
658 8 0.01
659 1 0.00
660 48 0.04
661 38 0.04
662 87 0.08
663 72 0.07
664 11 0.01
665 23 0.02
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (650 bp):
AACCCATATATAATAAACCAAAAGAGAAAAAAAAATTCAGCCTTCACATATGTTTTACAGACGAA
GAAGATGGCAGGTAAAAAAAAGCTTATGTTTTGGTTGGGTGTGGAGACGCTTGTAATACCATTAC
TAATAAAAAAATTAAAAAACTTTTACTTACTTATCGCCTATTTGATCCTAAAAAGAAAGCTTGAA
TCGGCATTATTGAATAAGGTCAGAAATAGTAAAATGTTCGTACACAAAAAGATTTAAAAAATATA
ACTAGATGTTTTTACTTTATTTTTTTTCCAACACTGAAAAAGATACCAATTGCCATTTTATTAAA
ACTTGTTTAACTATGCTTATTTATAAGATGTTTATTTAAGTTTCAAATTTAAAAAAAAATTAACA
ATTAGGATTTATTTTTTTATTATTTTTATTTATTATTAATGATAAAATATCTAAATGATGAGTTT
TGTATTATAGACCAAGTAATATCAATTAAATTAAAAATTATTTAAAATTTTATATAATAAAATAA
AAATATATAAATTTTAAAAACATCTTTATCTTTTAACTTTTTTTTAAAAAAATAAAACTCAAGTT
AAATACTTTCAACTAGAATGCTCTCATGAAAATCACTTATCTCATGAAATCGATGGAACTCTAAA
Found at i:257956 original size:5 final size:5
Alignment explanation
Indices: 257946--257970 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
257936 CGCGGCCCGC
257946 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
257971 TTTGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:258137 original size:16 final size:15
Alignment explanation
Indices: 258087--258138 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
258077 ATTAATGATT
258087 ATATAAATATAATAC
1 ATATAAATATAATAC
*
258102 ATATAAA-ATATTA-
1 ATATAAATATAATAC
258115 A-AT--ATATAATAC
1 ATATAAATATAATAC
258127 GATATAAATATA
1 -ATATAAATATA
258139 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 11
0.69 0.05 0.26
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 2 0.07
13 2 0.07
14 7 0.24
15 7 0.24
16 5 0.17
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (15 bp):
ATATAAATATAATAC
Found at i:258207 original size:22 final size:22
Alignment explanation
Indices: 258182--258246 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
258172 TATTAAAATC
258182 AATATAAATATAAAATATTTTA
1 AATATAAATATAAAATATTTTA
* * **
258204 AATACT-ATTAT-AAATAATAAA
1 AATA-TAAATATAAAATATTTTA
258225 ATATATAAATATAAAAT-TTTTA
1 A-ATATAAATATAAAATATTTTA
258247 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
21 9 0.29
22 17 0.55
23 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATAAATATAAAATATTTTA
Found at i:258233 original size:16 final size:15
Alignment explanation
Indices: 258183--258241 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
258173 ATTAAAATCA
258183 ATATAAATATAAAAT
1 ATATAAATATAAAAT
* * **
258198 ATTTTAA-ATACTAT
1 ATATAAATATAAAAT
258212 -TATAAATAATAAAAT
1 ATATAAAT-ATAAAAT
258227 ATATAAATATAAAAT
1 ATATAAATATAAAAT
258242 TTTTATTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 17 0.52
16 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAAATATAAAAT
Found at i:258322 original size:18 final size:17
Alignment explanation
Indices: 258221--258325 Score: 54
Period size: 18 Copynumber: 6.1 Consensus size: 17
258211 TTATAAATAA
*
258221 TAAAA-TATATAA-ATA
1 TAAAATTATATAATATT
* *
258236 TAAAATT-TTTATTATT
1 TAAAATTATATAATATT
* *
258252 TAAAATTTTATCATATT
1 TAAAATTATATAATATT
* * **
258269 TAATACGTAATATTTTCATT
1 TAA-A-ATTATATAAT-ATT
* *
258289 TAAAATTTTATCATATT
1 TAAAATTATATAATATT
258306 TAATAATTATATAATATT
1 TAA-AATTATATAATATT
258324 TA
1 TA
258326 TTTTTATATT
Statistics
Matches: 65, Mismatches: 18, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
15 8 0.12
16 10 0.15
17 15 0.23
18 20 0.31
19 6 0.09
20 6 0.09
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (17 bp):
TAAAATTATATAATATT
Found at i:258484 original size:2 final size:2
Alignment explanation
Indices: 258479--258510 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
258469 ACATGCATAC
*
258479 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
258511 CCCTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:258978 original size:18 final size:18
Alignment explanation
Indices: 258955--258989 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
258945 CAAAAATTAT
258955 ATTTTTCAAACTTGAATA
1 ATTTTTCAAACTTGAATA
258973 ATTTTTCAAACTTGAAT
1 ATTTTTCAAACTTGAAT
258990 GTAAATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTTTTCAAACTTGAATA
Found at i:259972 original size:35 final size:35
Alignment explanation
Indices: 259926--259997 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
259916 TTCTTGCCAT
259926 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
1 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
259961 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
1 AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
259996 AA
1 AA
259998 CACAGCCAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (35 bp):
AATAGCTCATCCACGGCTACTATTTAGTGTAGAGC
Found at i:262633 original size:79 final size:80
Alignment explanation
Indices: 262528--262681 Score: 226
Period size: 79 Copynumber: 1.9 Consensus size: 80
262518 CCAAAAAAAA
*
262528 ACAAATTCCTACTACAGCAATTGTAGCCAATAAAACCCCAGTTACTGCCAAATCTGTGT-AA-CA
1 ACAAATTCCTACTACAGCAATGGTAGCCAATAAAACCCCAGTTACTGCCAAA--TGTGTCAAGCA
262591 AAGCAAACAACTTTTCC
64 AAGCAAACAACTTTTCC
* *
262608 ACAAATTCCTA-TACAGCACA-GGTAGCCAATAAAACCCCAGTTATTGCCAAATGTGTCAAGGAA
1 ACAAATTCCTACTACAGCA-ATGGTAGCCAATAAAACCCCAGTTACTGCCAAATGTGTCAAGCAA
262671 AGCAAACAACT
65 AGCAAACAACT
262682 CTTAGCCAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
77 5 0.07
78 2 0.03
79 49 0.72
80 12 0.18
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (80 bp):
ACAAATTCCTACTACAGCAATGGTAGCCAATAAAACCCCAGTTACTGCCAAATGTGTCAAGCAAA
GCAAACAACTTTTCC
Found at i:268525 original size:15 final size:16
Alignment explanation
Indices: 268498--268542 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
268488 CAATTTGGGT
*
268498 TTTTTGGTTAATTTTGA
1 TTTTT-GTTAATTTTAA
*
268515 TTTTT-TTAATTATAA
1 TTTTTGTTAATTTTAA
268530 TTTTTGTTAATTT
1 TTTTTGTTAATTT
268543 GATACTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 13 0.54
16 6 0.25
17 5 0.21
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (16 bp):
TTTTTGTTAATTTTAA
Found at i:269806 original size:16 final size:16
Alignment explanation
Indices: 269785--269825 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
269775 TACTTTTTAC
*
269785 TTTAATTAATAGGGTT
1 TTTAATTAATAGGATT
*
269801 TTTAATTAGTAGGATT
1 TTTAATTAATAGGATT
*
269817 TTTATTTAA
1 TTTAATTAA
269826 ACTTTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (16 bp):
TTTAATTAATAGGATT
Found at i:270852 original size:14 final size:14
Alignment explanation
Indices: 270833--270880 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
270823 CTGATAATTT
270833 TAAATATAATTATA
1 TAAATATAATTATA
270847 TAAATATAATATATA
1 TAAATATAAT-TATA
*
270862 TAAAATAGTAAATATA
1 T-AAATA-TAATTATA
270878 TAA
1 TAA
270881 TAAGATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.33
15 7 0.23
16 10 0.33
17 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:270876 original size:16 final size:15
Alignment explanation
Indices: 270834--270953 Score: 80
Period size: 16 Copynumber: 7.4 Consensus size: 15
270824 TGATAATTTT
*
270834 AAATATAATTATAT-
1 AAATATAAATATATA
270848 AAATATAATATATATA
1 AAATATAA-ATATATA
270864 AAATAGTAAATATATAA
1 AAATA-TAAATATAT-A
270881 TAAGATATAAATATATATAA
1 -AA-ATAT-AA-ATATAT-A
* *
270901 AAATTTATATAATATA
1 AAATATAAAT-ATATA
* *
270917 AATTATTAATATATTA
1 AAATATAAATATA-TA
* *
270933 AAATTTAAATAAATA
1 AAATATAAATATATA
270948 AAATAT
1 AAATAT
270954 TTTAAATATT
Statistics
Matches: 84, Mismatches: 12, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
14 8 0.10
15 15 0.18
16 31 0.37
17 9 0.11
18 6 0.07
19 7 0.08
20 8 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AAATATAAATATATA
Found at i:270911 original size:34 final size:31
Alignment explanation
Indices: 270846--270949 Score: 95
Period size: 34 Copynumber: 3.2 Consensus size: 31
270836 ATATAATTAT
**
270846 ATAAATATAATATATATAAAATAGTAAATATATA
1 ATAAATATAATATATATAAAA-A-TTTATATA-A
270880 ATAAGATATAAATATATATAAAAATTTATATAA
1 ATAA-ATAT-AATATATATAAAAATTTATATAA
*
270913 TATAAATTATTAATATAT-T-AAAATTTAAATAA
1 -ATAAA-TA-TAATATATATAAAAATTTATATAA
270945 ATAAA
1 ATAAA
270950 ATATTTTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
31 5 0.08
32 12 0.19
33 3 0.05
34 23 0.37
35 6 0.10
36 13 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
ATAAATATAATATATATAAAAATTTATATAA
Found at i:270942 original size:50 final size:45
Alignment explanation
Indices: 270875--270981 Score: 117
Period size: 50 Copynumber: 2.3 Consensus size: 45
270865 AATAGTAAAT
* *
270875 ATATAATAAGATATAAATATATATAAAA-ATTTATATAATATAAATTATTA
1 ATATAATAAAATTTAAATA-A-ATAAAATATTT-TA-AATAT-AATTA-TA
* *
270925 ATATATTAAAATTTAAATAAATAAAATATTTTAAATATTATTATA
1 ATATAATAAAATTTAAATAAATAAAATATTTTAAATATAATTATA
270970 ATATAATAAAAT
1 ATATAATAAAAT
270982 ATATAGATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
45 13 0.25
46 4 0.08
47 5 0.10
48 8 0.16
49 5 0.10
50 16 0.31
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (45 bp):
ATATAATAAAATTTAAATAAATAAAATATTTTAAATATAATTATA
Found at i:270958 original size:25 final size:30
Alignment explanation
Indices: 270851--270985 Score: 85
Period size: 28 Copynumber: 4.7 Consensus size: 30
270841 ATTATATAAA
*
270851 TATAATAT-ATATAAA-ATAGTAAATA-TAT
1 TATAATATAATA-AAATATATTAAATATTAT
* * *
270879 AATAAGAT-AT-AAATATATATAAAAATT-T
1 TATAATATAATAAAATATAT-TAAATATTAT
*
270907 ATATAATATAAATTATTAATATATTAAA-A-T-T
1 -TATAATAT-AA-TA-AAATATATTAAATATTAT
*
270938 TA-AATA-AATAAAATATTTTAAATATTAT
1 TATAATATAATAAAATATATTAAATATTAT
270966 TATAATATAATAAAATATAT
1 TATAATATAATAAAATATAT
270986 AGATATAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
25 10 0.12
26 6 0.07
27 6 0.07
28 17 0.20
29 15 0.18
30 13 0.16
31 3 0.04
32 2 0.02
33 4 0.05
34 7 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
TATAATATAATAAAATATATTAAATATTAT
Found at i:274491 original size:24 final size:24
Alignment explanation
Indices: 274437--274491 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
274427 AAAAGCAAAA
274437 TTAA-TAAAAAAAATTTAAAACTT
1 TTAATTAAAAAAAATTTAAAACTT
* *
274460 TTATATTAAAAAACATTT-ACACTTT
1 TTA-ATTAAAAAAAATTTAAAAC-TT
274485 TTAATTA
1 TTAATTA
274492 GTATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 3 0.11
24 8 0.30
25 16 0.59
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAATTAAAAAAAATTTAAAACTT
Found at i:280586 original size:27 final size:29
Alignment explanation
Indices: 280532--280586 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
280522 TTTCTGGTTT
*
280532 AAGGAAAGATCAAGAAGCATTTTTAGTTC
1 AAGGAAAGATCAAGAAGCATTTTGAGTTC
* *
280561 AAGGAAATAT-AAGAATC-TTTTGAGTT
1 AAGGAAAGATCAAGAAGCATTTTGAGTT
280587 TTCATTCCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 8 0.35
28 6 0.26
29 9 0.39
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (29 bp):
AAGGAAAGATCAAGAAGCATTTTGAGTTC
Found at i:290750 original size:6 final size:6
Alignment explanation
Indices: 290736--290857 Score: 138
Period size: 6 Copynumber: 20.5 Consensus size: 6
290726 GCAGGCTCAC
* * *
290736 CTTCTT CTTCCT CTTTTT CCTCTT CTTCTT CTTC-T CTTCTT CTTCTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * *
290783 CTCCTT CTTCTT CTTCTT CTTCTT CTCCTT CTCCTT CTCCTT CTCCTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * *
290831 CTCCTT CTCCTT CTCCTT CTTCTT CTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTT
290858 TAGATTCTCC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
5 5 0.05
6 100 0.95
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (6 bp):
CTTCTT
Found at i:290755 original size:9 final size:9
Alignment explanation
Indices: 290738--290807 Score: 70
Period size: 9 Copynumber: 7.9 Consensus size: 9
290728 AGGCTCACCT
290738 TCTTCTTCC
1 TCTTCTTCC
*
290747 TCTTTTTCC
1 TCTTCTTCC
*
290756 TCTTCTTCT
1 TCTTCTTCC
*
290765 TCTTC-TCT
1 TCTTCTTCC
*
290773 TCTTCTTCT
1 TCTTCTTCC
* *
290782 TCTCCTTCT
1 TCTTCTTCC
*
290791 TCTTCTTCT
1 TCTTCTTCC
290800 TCTTCTTC
1 TCTTCTTC
290808 TCCTTCTCCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
8 8 0.15
9 47 0.85
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (9 bp):
TCTTCTTCC
Found at i:294963 original size:20 final size:20
Alignment explanation
Indices: 294935--294982 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
294925 ATATCAAATA
*
294935 TCAAATAAACAATAAAAAAG
1 TCAAATAAACAACAAAAAAG
* * *
294955 TCAATTAAAGAACAAAAAAA
1 TCAAATAAACAACAAAAAAG
294975 T-AAATAAA
1 TCAAATAAA
294983 AATCGGCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.17
Consensus pattern (20 bp):
TCAAATAAACAACAAAAAAG
Found at i:296089 original size:10 final size:11
Alignment explanation
Indices: 296073--296109 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
296063 AACGAAAATA
296073 AATTTTATTTT
1 AATTTTATTTT
296084 -ATTTTATTTT
1 AATTTTATTTT
*
296094 AATTTTA-ATT
1 AATTTTATTTT
296104 AATTTT
1 AATTTT
296110 TAATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
AATTTTATTTT
Found at i:296149 original size:23 final size:23
Alignment explanation
Indices: 296083--296150 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
296073 AATTTTATTT
* *
296083 TATTTTA-TTTTAATTTTAATTAA
1 TATTTTATTTTTAA-ATTAATAAA
296106 T-TTTTAATTTTT--ATTATATAAA
1 TATTTT-ATTTTTAAATTA-ATAAA
296128 TATTTTATTTTTAAATTAATAAA
1 TATTTTATTTTTAAATTAATAAA
296151 AACTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
21 3 0.08
22 15 0.41
23 11 0.30
24 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTATTTTTAAATTAATAAA
Found at i:296636 original size:31 final size:31
Alignment explanation
Indices: 296564--296641 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
296554 TCGAATTTGA
*
296564 TTAA-AAATAAA-TTAAATTTATTTAGTTAT
1 TTAATAAATAAATTTAAATTTATTTAATTAT
* *
296593 TT-TTGAATTAAATTTAAA-TTATTTAAATTAT
1 TTAAT-AAATAAATTTAAATTTATTT-AATTAT
296624 TTAATAAATAAATTTAAA
1 TTAATAAATAAATTTAAA
296642 ATATCATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
29 2 0.05
30 12 0.31
31 24 0.62
32 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (31 bp):
TTAATAAATAAATTTAAATTTATTTAATTAT
Found at i:296723 original size:18 final size:18
Alignment explanation
Indices: 296675--296723 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
296665 AATTTACGAG
* *
296675 TTTAATTTAATTTTTTATT
1 TTTAA-TTAATATATTATT
296694 TTTAA-TATATATATTATT
1 TTTAATTA-ATATATTATT
296712 TTTAATTAATAT
1 TTTAATTAATAT
296724 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.08
18 17 0.65
19 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTAATTAATATATTATT
Found at i:296740 original size:6 final size:6
Alignment explanation
Indices: 296729--296753 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
296719 AATATTTAAA
296729 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
296754 TCGAGTTTAA
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:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:297642 original size:21 final size:20
Alignment explanation
Indices: 297616--297655 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
297606 TAAATAACGT
*
297616 GTTTGTTAATAATATATTAAC
1 GTTTGTTAAT-ATAAATTAAC
297637 GTTTGTTAATATAAATTAA
1 GTTTGTTAATATAAATTAA
297656 TGCTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
GTTTGTTAATATAAATTAAC
Found at i:298430 original size:2 final size:2
Alignment explanation
Indices: 298423--298448 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
298413 GTGTTGTGAA
298423 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
298449 ATAAGTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:298711 original size:14 final size:14
Alignment explanation
Indices: 298692--298719 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
298682 ATATTTGAAC
298692 GTATCTAAAAGATT
1 GTATCTAAAAGATT
298706 GTATCTAAAAGATT
1 GTATCTAAAAGATT
298720 ATATTCTCGT
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:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
GTATCTAAAAGATT
Found at i:300650 original size:6 final size:6
Alignment explanation
Indices: 300641--300668 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
300631 ATGGTAGGGG
300641 TTGGGT TTGGGT TTGGGT TTGGGT TTGG
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGG
300669 AGGAGAGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
TTGGGT
Found at i:301390 original size:20 final size:20
Alignment explanation
Indices: 301342--301402 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
301332 TTTTTAACAG
* *
301342 TAATGATAAAATTAACT-TT
1 TAATAATAAAATTAAATATT
301361 TATGATAATAAAATTAAATATT
1 TA--ATAATAAAATTAAATATT
301383 TAATAATAAAATTAAA-ATT
1 TAATAATAAAATTAAATATT
301402 T
1 T
301403 CTCTCTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 6 0.16
20 14 0.38
21 13 0.35
22 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (20 bp):
TAATAATAAAATTAAATATT
Done.