Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014306.1 Kokia drynarioides strain JFW-HI SEQ_129342, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 546136
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4315 original size:65 final size:65
Alignment explanation
Indices: 4211--4340 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
4201 TTGGAAATTT
4211 TCATATGATATTATGTTATGTTATTGTATGATTTGGTTATCGTGAACTCATCTTACTATTGCAAA
1 TCATATGATATTATGTTATGTTATTGTATGATTTGGTTATCGTGAACTCATCTTACTATTGCAAA
* *
4276 TCATATGATGTTATGTTATGTTATTGTATGATTTGGTTATCGTGAACTCATCTTACTGTTGCAAA
1 TCATATGATATTATGTTATGTTATTGTATGATTTGGTTATCGTGAACTCATCTTACTATTGCAAA
4341 ATGTGATGGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (65 bp):
TCATATGATATTATGTTATGTTATTGTATGATTTGGTTATCGTGAACTCATCTTACTATTGCAAA
Found at i:6826 original size:23 final size:22
Alignment explanation
Indices: 6799--6857 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
6789 AAATACAATT
*
6799 AATAACAATTAATAACACAATAA
1 AATAAAAATTAATAACA-AATAA
**
6822 AATAATAAA-TAATAGTAAATAA
1 AATAA-AAATTAATAACAAATAA
6844 AATAAAAATATAAT
1 AATAAAAAT-TAAT
6858 CATGGTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 3 0.10
22 10 0.33
23 15 0.50
24 2 0.07
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (22 bp):
AATAAAAATTAATAACAAATAA
Found at i:7054 original size:24 final size:25
Alignment explanation
Indices: 7001--7055 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
6991 ATGAAATTAA
7001 ATAAAAAATGCAAATTAAATAAAAG
1 ATAAAAAATGCAAATTAAATAAAAG
*
7026 GTAAAAAATG-AAA-TAAA-AAATAG
1 ATAAAAAATGCAAATTAAATAAA-AG
7049 CATAAAA
1 -ATAAAA
7056 TACAACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.12
23 6 0.23
24 8 0.31
25 9 0.35
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (25 bp):
ATAAAAAATGCAAATTAAATAAAAG
Found at i:7057 original size:36 final size:37
Alignment explanation
Indices: 6998--7083 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 37
6988 GGCATGAAAT
* **
6998 TAAATAAAAAAT-GCAAATTAAATAAAAGGTA-AAAAA
1 TAAATAAAAAATAGC-AATAAAATAAAACATATAAAAA
*
7034 TGAAATAAAAAATAGC-ATAAAATACAACATATAAAAA
1 T-AAATAAAAAATAGCAATAAAATAAAACATATAAAAA
*
7071 TAAATAAACAATA
1 TAAATAAAAAATA
7084 AATAAATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
36 23 0.55
37 17 0.40
38 2 0.05
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (37 bp):
TAAATAAAAAATAGCAATAAAATAAAACATATAAAAA
Found at i:7152 original size:11 final size:11
Alignment explanation
Indices: 7064--7155 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 11
7054 AATACAACAT
7064 ATAAA-AATAA
1 ATAAATAATAA
*
7074 ATAAACAATAA
1 ATAAATAATAA
7085 ATAAAT-ATAA
1 ATAAATAATAA
* *
7095 TTAAATAAGACA
1 ATAAATAATA-A
*
7107 A-AAAT-GTAA
1 ATAAATAATAA
*
7116 ATAATATAAAAAA
1 ATAA-AT-AATAA
* * *
7129 ATGAGTAACAA
1 ATAAATAATAA
7140 ATAAATAATAA
1 ATAAATAATAA
7151 ATAAA
1 ATAAA
7156 ACAATAATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
9 2 0.03
10 17 0.28
11 35 0.57
12 2 0.03
13 5 0.08
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (11 bp):
ATAAATAATAA
Found at i:8928 original size:48 final size:48
Alignment explanation
Indices: 8739--9154 Score: 467
Period size: 48 Copynumber: 8.8 Consensus size: 48
8729 TTTCTGTAAT
* * *
8739 TTTAAGGGTATAAGAGTT-G-TGT-GT-GACTTCAATTTGCCCATCTAGA
1 TTTAAGGGTATAAGA-TTGGATGTGGTAG-CTTCAATCTGCCCCTCTGGA
* * *
8785 TTTAAGGGTATAGGAGTT-G-TGT-GTGGCTTCAATATGCCCCCTCTGGA
1 TTTAAGGGTATAAGA-TTGGATGTGGTAGCTTCAATCTG-CCCCTCTGGA
*
8832 TTTAAGGGTATAGGAGTT-G-TGT-GTAGCTTCAATCTGCCCCTCTGGA
1 TTTAAGGGTATAAGA-TTGGATGTGGTAGCTTCAATCTGCCCCTCTGGA
* * * * *
8878 TTT-AGGAGTATAAGATTGGATGTTGTAGTTTTAACCTGCCCCTCTAGA
1 TTTAAGG-GTATAAGATTGGATGTGGTAGCTTCAATCTGCCCCTCTGGA
*
8926 TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTTCCCCTCTGGA
1 TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTGCCCCTCTGGA
* ** * * *
8974 TTTAAGGGTATAAGATTAGATGTGGTAGCTAAAATTTGCCCCTTTGAA
1 TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTGCCCCTCTGGA
* * ** *
9022 TTTAGGGGTATAAAATTATATGTGGTAGCTTCAATCTACCCCTCTGGA
1 TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTGCCCCTCTGGA
*
9070 TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATTTGCCCCTCTGGA
1 TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTGCCCCTCTGGA
*
9118 TTTAAGGGTATAAGATTGAATGTGGTAGCTTCAATCT
1 TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCT
9155 ATTCCTCTTG
Statistics
Matches: 322, Mismatches: 41, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
45 5 0.02
46 53 0.16
47 46 0.14
48 215 0.67
49 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (48 bp):
TTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTGCCCCTCTGGA
Found at i:9033 original size:144 final size:142
Alignment explanation
Indices: 8773--9357 Score: 470
Period size: 144 Copynumber: 4.0 Consensus size: 142
8763 GACTTCAATT
* * * *
8773 TGCCCATCTAGATTTAAGGGTATAGGAGTT-G-TGT-GTGGCTTCAATATGCCCCCTCTGGATTT
1 TGCCCCTCTAGATTTAAGGGTATAAGA-TTGGATGTGGTAGCTTCAAT-T-TCCCCTCTGGATTT
* ** * * *
8835 AAGGGTATAGGAGTTG-TGT-GTAGCTTCAATCTGCCCCTCTGGATTTAGGAGTATAAGATTGGA
63 AAGGGTATAAGA-TTGATGTGGTAGCTAAAATCTGCCCCTCTGAATTTAGGAGTATAAAATTAGA
* * *
8898 TGTTGTAGTTTTAACC
127 TGTGGTAGCTTCAACC
8914 TGCCCCTCTAGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTTCCCCTCTGGATTTAA
1 TGCCCCTCTAGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAAT-TTCCCCTCTGGATTTAA
* * * *
8979 GGGTATAAGATTAGATGTGGTAGCTAAAATTTGCCCCTTTGAATTTAGGGGTATAAAATTATATG
65 GGGTATAAGATT-GATGTGGTAGCTAAAATCTGCCCCTCTGAATTTAGGAGTATAAAATTAGATG
*
9044 TGGTAGCTTCAATC
129 TGGTAGCTTCAACC
* *
9058 TACCCCTCTGGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATTTGCCCCTCTGGATTTAA
1 TGCCCCTCTAGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATTT-CCCCTCTGGATTTAA
* *
9123 GGGTATAAGATTGAATGTGGTAGCTTCAATCTATTCCTCTTGAATCTACCCCTCTGGATTTATGG
65 GGGTATAAGATTG-ATGTGGTAGC-T--A---A---------AATCTGCCCCTCTGAATTTA-GG
* * ** *
9188 -GTATAAGA-TGGATGTGGTATATTCAATC
113 AGTATAAAATTAGATGTGGTAGCTTCAACC
* * * * * *
9216 TGTCGCTTTAGATTTAAGGGTATAAGATTGGATGTGGTAGCTTTAA--TCCGTCCTTTTAGATTT
1 TGCCCCTCTAGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATTTCC--CC-TCTGGATTT
** ** * * *
9279 TGGAGGTATAAGATTGGATGTGGTAGCTTCAATCCGCCCCTCT-AGATTTAGGGGTATAAGATTA
63 AAG-GGTATAAGATT-GATGTGGTAGCTAAAATCTGCCCCTCTGA-ATTTAGGAGTATAAAATTA
9343 GATGTGGTAGCTTCA
125 GATGTGGTAGCTTCA
9358 CTCCATTCCA
Statistics
Matches: 364, Mismatches: 48, Indels: 60
0.77 0.10 0.13
Matches are distributed among these distances:
140 2 0.01
141 28 0.08
142 28 0.08
143 19 0.05
144 153 0.42
145 15 0.04
147 1 0.00
150 1 0.00
155 2 0.01
156 1 0.00
157 2 0.01
158 65 0.18
159 44 0.12
160 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (142 bp):
TGCCCCTCTAGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATTTCCCCTCTGGATTTAAG
GGTATAAGATTGATGTGGTAGCTAAAATCTGCCCCTCTGAATTTAGGAGTATAAAATTAGATGTG
GTAGCTTCAACC
Found at i:9251 original size:110 final size:111
Alignment explanation
Indices: 9054--9366 Score: 327
Period size: 110 Copynumber: 3.0 Consensus size: 111
9044 TGGTAGCTTC
* * *
9054 AATCTACCCCTCTGGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATTTGCCCCTCTGGAT
1 AATCTACCCCTCTGGATTTAAGGGTATAAGATTGGATGTGGTAGATTCAATCTGCCCCTCTAGAT
9119 TTAAGGGTATAAGATTGAATGTGGTAGCTTCAATCTATTCCTCTTG
66 TTAAGGGTATAAGATTGAATGTGGTAGCTTCAATCTATTCCTCTTG
* * * * *
9165 AATCTACCCCTCTGGATTTATGGGTATAAGA-TGGATGTGGTATATTCAATCTGTCGCTTTAGAT
1 AATCTACCCCTCTGGATTTAAGGGTATAAGATTGGATGTGGTAGATTCAATCTGCCCCTCTAGAT
* * ** *
9229 TTAAGGGTATAAGATTGGATGTGGTAGCTTTAATC-CGTCCT-TTT
66 TTAAGGGTATAAGATTGAATGTGGTAGCTTCAATCTATTCCTCTTG
* *
9273 AGAT-T-----T-TGG-----A-GGTATAAGATTGGATGTGGTAGCTTCAATCCGCCCCTCTAGA
1 A-ATCTACCCCTCTGGATTTAAGGGTATAAGATTGGATGTGGTAGATTCAATCTGCCCCTCTAGA
* * *
9325 TTTAGGGGTATAAGATT-AGATGTGGTAGCTTCACTCCATTCC
65 TTTAAGGGTATAAGATTGA-ATGTGGTAGCTTCAATCTATTCC
9367 ACTACAACTT
Statistics
Matches: 172, Mismatches: 26, Indels: 21
0.79 0.12 0.10
Matches are distributed among these distances:
96 9 0.05
97 57 0.33
98 3 0.02
102 3 0.02
103 1 0.01
108 4 0.02
109 6 0.03
110 59 0.34
111 30 0.17
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (111 bp):
AATCTACCCCTCTGGATTTAAGGGTATAAGATTGGATGTGGTAGATTCAATCTGCCCCTCTAGAT
TTAAGGGTATAAGATTGAATGTGGTAGCTTCAATCTATTCCTCTTG
Found at i:9302 original size:49 final size:47
Alignment explanation
Indices: 9179--9357 Score: 225
Period size: 48 Copynumber: 3.7 Consensus size: 47
9169 TACCCCTCTG
* ** *
9179 GATTTATGGGTATAAGA-TGGATGTGGTATATTCAATCTGTCGCTTTA
1 GATTTAGGGGTATAAGATTGGATGTGGTAGCTTCAATCCGTC-CTTTA
* *
9226 GATTTAAGGGTATAAGATTGGATGTGGTAGCTTTAATCCGTCCTTTTA
1 GATTTAGGGGTATAAGATTGGATGTGGTAGCTTCAATCCGTCC-TTTA
* * *
9274 GATTTTGGAGGTATAAGATTGGATGTGGTAGCTTCAATCCGCCCCTCTA
1 GATTTAGG-GGTATAAGATTGGATGTGGTAGCTTCAATCCG-TCCTTTA
*
9323 GATTTAGGGGTATAAGATTAGATGTGGTAGCTTCA
1 GATTTAGGGGTATAAGATTGGATGTGGTAGCTTCA
9358 CTCCATTCCA
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
47 17 0.15
48 56 0.48
49 41 0.35
50 2 0.02
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (47 bp):
GATTTAGGGGTATAAGATTGGATGTGGTAGCTTCAATCCGTCCTTTA
Found at i:16318 original size:34 final size:34
Alignment explanation
Indices: 16280--16345 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
16270 TTGTAGTATA
*
16280 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* * *
16314 ATTGTCGCTGTATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
16346 CCATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 25 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:16941 original size:19 final size:19
Alignment explanation
Indices: 16899--16945 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
16889 AGTCACTTGA
16899 AAAAGGAAAATGAGAAAAAG
1 AAAA-GAAAATGAGAAAAAG
16919 -AAAGAAAA-GAGAAAAGAG
1 AAAAGAAAATGAGAAAA-AG
16937 AAAAGAAAA
1 AAAAGAAAA
16946 AAAAATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
19 11 0.44
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (19 bp):
AAAAGAAAATGAGAAAAAG
Found at i:16950 original size:24 final size:24
Alignment explanation
Indices: 16898--16949 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
16888 CAGTCACTTG
16898 AAAAAGGAAAATGAGAAAAAGAAA
1 AAAAAGGAAAATGAGAAAAAGAAA
*
16922 GAAAAGAGAAAA-GAG-AAAAGAAA
1 AAAAAG-GAAAATGAGAAAAAGAAA
16945 AAAAA
1 AAAAA
16950 ATGTTTGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.48
24 8 0.32
25 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (24 bp):
AAAAAGGAAAATGAGAAAAAGAAA
Found at i:41727 original size:12 final size:12
Alignment explanation
Indices: 41710--41739 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41700 CCTCGGTAGG
41710 TTCTTCTTCTTT
1 TTCTTCTTCTTT
41722 TTCTTCTTCTTT
1 TTCTTCTTCTTT
*
41734 CTCTTC
1 TTCTTC
41740 CTCATCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:53912 original size:17 final size:17
Alignment explanation
Indices: 53877--53937 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
53867 CATTAATTTA
*
53877 CAATGACACATGGAAATG
1 CAATGACA-ATGAAAATG
*
53895 CAATGACAATGCAAATG
1 CAATGACAATGAAAATG
* *
53912 CAGTGACAATTAAAATG
1 CAATGACAATGAAAATG
*
53929 AAATGACAA
1 CAATGACAA
53938 AAGGAATGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 29 0.78
18 8 0.22
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:67205 original size:39 final size:37
Alignment explanation
Indices: 67162--67236 Score: 89
Period size: 38 Copynumber: 1.9 Consensus size: 37
67152 TTTAGTTGAT
67162 GGCTTAAATTTTGGTCTTTGTA-TTGGGTTGTAAAAATTG
1 GGCTT-AATTTT-GTCTTTGTATTTGGGTT-TAAAAATTG
* *
67201 GGCTTTATTTTGTTTTTGTATTTTGGGTTTAAAAAT
1 GGCTTAATTTTGTCTTTGTA-TTTGGGTTTAAAAAT
67237 ATAAGAGCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 8 0.25
38 12 0.38
39 12 0.38
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.52
Consensus pattern (37 bp):
GGCTTAATTTTGTCTTTGTATTTGGGTTTAAAAATTG
Found at i:68953 original size:21 final size:21
Alignment explanation
Indices: 68909--68982 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
68899 AGTGTAGACC
* * *
68909 TCTACCAATACAAGTAATAAT
1 TCTACCGATACAAGTAGTACT
68930 TCTACCGATACAAGTGAGT-CT
1 TCTACCGATACAAGT-AGTACT
**
68951 TCTACCGGA-ACAAGTCTTACT
1 TCTACC-GATACAAGTAGTACT
68972 TCTACCGATAC
1 TCTACCGATAC
68983 TAAAAACTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.07
21 37 0.84
22 4 0.09
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTAGTACT
Found at i:69760 original size:53 final size:53
Alignment explanation
Indices: 69644--69939 Score: 282
Period size: 53 Copynumber: 5.7 Consensus size: 53
69634 CGCATTTGAT
* * * * * **
69644 AACTCACGATGACACGGAGTCATC-GACCTTTAATCTGTGAT-GGATTCGTGT
1 AACTCACAATGACACAGAGTCATCAGACCTTTAATCCGTAATAGGATTCATAA
* * * * * *
69695 AACTCACGATGACACAAAGTCATCAGACCCTTAATCCATAATAGAATTCATAC
1 AACTCACAATGACACAGAGTCATCAGACCTTTAATCCGTAATAGGATTCATAA
* * * *
69748 AACTCACAATGACACAGAGCCATCGGACCTTTAATCCGTGATAGGATTCATAT
1 AACTCACAATGACACAGAGTCATCAGACCTTTAATCCGTAATAGGATTCATAA
* *
69801 AACTCA-AGATGACACAGAGTTATCAGACCTTTAATCCGTTATAGGATTCATAA
1 AACTCACA-ATGACACAGAGTCATCAGACCTTTAATCCGTAATAGGATTCATAA
* * * * * **
69854 AACTCACGATGACATAGAG---TCA-ACCTTAAATCCGTGATAAGATTCATGT
1 AACTCACAATGACACAGAGTCATCAGACCTTTAATCCGTAATAGGATTCATAA
* *
69903 AACTCACAGTGACACAGAGTCATCGGACCTTTAATCC
1 AACTCACAATGACACAGAGTCATCAGACCTTTAATCC
69940 TTGGAATAAG
Statistics
Matches: 201, Mismatches: 36, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
49 38 0.19
50 3 0.01
51 22 0.11
52 16 0.08
53 122 0.61
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (53 bp):
AACTCACAATGACACAGAGTCATCAGACCTTTAATCCGTAATAGGATTCATAA
Found at i:69827 original size:106 final size:104
Alignment explanation
Indices: 69644--69939 Score: 366
Period size: 106 Copynumber: 2.8 Consensus size: 104
69634 CGCATTTGAT
* * * *
69644 AACTCACGATGACACGGAGTCATCGACCTTTAATCTGTGAT-GGATTCGTGTAACTCACGATGAC
1 AACTCACGATGACACAGAG-CATCGACCTTTAATCCGTGATAGGATTCATGTAACTCAAGATGAC
* * *
69708 ACAAAGTCATCAGACCCTTAATCCATAATAGAATTCATAC
65 ACAGAGTCATCAGACCTTTAATCCATAATAGAATTCATAA
* *
69748 AACTCACAATGACACAGAGCCATCGGACCTTTAATCCGTGATAGGATTCATATAACTCAAGATGA
1 AACTCACGATGACACAGAG-CATC-GACCTTTAATCCGTGATAGGATTCATGTAACTCAAGATGA
* * * *
69813 CACAGAGTTATCAGACCTTTAATCCGTTATAGGATTCATAA
64 CACAGAGTCATCAGACCTTTAATCCATAATAGAATTCATAA
* * * *
69854 AACTCACGATGACATAGAG--TCAACCTTAAATCCGTGATAAGATTCATGTAACTCACAG-TGAC
1 AACTCACGATGACACAGAGCATCGACCTTTAATCCGTGATAGGATTCATGTAACTCA-AGATGAC
*
69916 ACAGAGTCATCGGACCTTTAATCC
65 ACAGAGTCATCAGACCTTTAATCC
69940 TTGGAATAAG
Statistics
Matches: 167, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
102 56 0.34
103 4 0.02
104 21 0.13
105 16 0.10
106 70 0.42
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (104 bp):
AACTCACGATGACACAGAGCATCGACCTTTAATCCGTGATAGGATTCATGTAACTCAAGATGACA
CAGAGTCATCAGACCTTTAATCCATAATAGAATTCATAA
Found at i:70804 original size:21 final size:20
Alignment explanation
Indices: 70780--70823 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
70770 ACTTTCATCA
* *
70780 TTAAGCTTTAATTAACCCTTT
1 TTAAGC-TTAATTAAACCTAT
*
70801 TTAATCTTAATTAAACCTAT
1 TTAAGCTTAATTAAACCTAT
70821 TTA
1 TTA
70824 TAATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAGCTTAATTAAACCTAT
Found at i:78400 original size:2 final size:2
Alignment explanation
Indices: 78393--78418 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78383 CAAGTGTGAG
78393 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
78419 GAAAACTCAC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79122 original size:50 final size:50
Alignment explanation
Indices: 79062--79234 Score: 217
Period size: 47 Copynumber: 3.5 Consensus size: 50
79052 TCAAATCTTG
* *
79062 TTTATCTAAATTGTTTTGTTCAGATATGGTGTTTTATATAAAAATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTAAATAAAAATAAATA
* * *
79112 TTTATTTAAA-T-TATT-TTCAGATATGATGTTTTAAATAAATATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTAAATAAAAATAAATA
* * * * *
79159 TTTATTTAAATTGTTTTGTTTAAATTTGGTGTTTTACATAAACATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTAAATAAAAATAAATA
*
79209 TTTACTTTATATTGTTTTGTTCAGAT
1 TTTA-TTTAAATTGTTTTGTTCAGAT
79235 CTTATATTTT
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
47 39 0.38
48 4 0.04
49 4 0.04
50 39 0.38
51 18 0.17
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (50 bp):
TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTAAATAAAAATAAATA
Found at i:80008 original size:71 final size:72
Alignment explanation
Indices: 79931--80087 Score: 172
Period size: 76 Copynumber: 2.1 Consensus size: 72
79921 ATTTTATTCT
* * * * *
79931 ATTTTTATTTTGTTTCCAAACAAGAATTAATTGAATAATTCTATTTCGAGATTTATTCCCGCCGT
1 ATTTTTATTTTGATTCCAAACAAGAATTAATTGAATAATTCTATTTCAAGACTTATTCACACCGT
*
79996 TCAATAG
66 TCAACAG
* * * * *
80003 ATTTTATTCTATTTTGATTCCAAACAAGGATTAATTGAATAATTTTGTTTCAAGACTTATTTATA
1 A--TT-TT-TATTTTGATTCCAAACAAGAATTAATTGAATAATTCTATTTCAAGACTTATTCACA
80068 CCGTTCAACAG
62 CCGTTCAACAG
80079 A-TTTTATTT
1 ATTTTTATTT
80088 CATTTTGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
71 5 0.07
72 3 0.04
73 1 0.01
74 2 0.03
75 2 0.03
76 57 0.81
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.45
Consensus pattern (72 bp):
ATTTTTATTTTGATTCCAAACAAGAATTAATTGAATAATTCTATTTCAAGACTTATTCACACCGT
TCAACAG
Found at i:80157 original size:82 final size:82
Alignment explanation
Indices: 79714--80146 Score: 463
Period size: 82 Copynumber: 5.4 Consensus size: 82
79704 AAAAAATTAA
* * * * * *
79714 AATTGAATAAATCTGTTTCAGGATTTATTCCTGCCGTTCAATAAAATTTTATTTTATTTTTATTT
1 AATTGAATAATTCTATTTCAGGATTTATTCCTGCCGTTCAA-CAGATTTTATTTCATTTTGATTT
*
79779 TGTTTCTAAACAAGAATT
65 TGTTTCCAAACAAGAATT
* * * ** *
79797 AATTGAATAATTATGTTTC-GGA-TTATTCTTGTTGTTCAACAGATTTTATTTTATTTTGATTTT
1 AATTGAATAATTCTATTTCAGGATTTATTCCTGCCGTTCAACAGATTTTATTTCATTTTGATTTT
* *
79860 GTTTGCAAACAAGGATT
66 GTTTCCAAACAAGAATT
* ** ** *
79877 AATTGAATAATTTTATTTTGGGATTTATTCCTGCTATTCAACAGATTTTA-TTCTATTTTTATTT
1 AATTGAATAATTCTATTTCAGGATTTATTCCTGCCGTTCAACAGATTTTATTTC-ATTTTGATTT
79941 TGTTTCCAAACAAGAATT
65 TGTTTCCAAACAAGAATT
* *
79959 AATTGAATAATTCTATTTC-GAGATTTATTCCCGCCGTTCAATAGATTTTA-TTC----T-ATTT
1 AATTGAATAATTCTATTTCAG-GATTTATTCCTGCCGTTCAACAGATTTTATTTCATTTTGATTT
* *
80017 TGATTCCAAACAAGGATT
65 TGTTTCCAAACAAGAATT
* * * * ** *
80035 AATTGAATAATTTTGTTTCAAGACTTATTTATACCGTTCAACAGATTTTATTTCATTTTGATTTT
1 AATTGAATAATTCTATTTCAGGATTTATTCCTGCCGTTCAACAGATTTTATTTCATTTTGATTTT
*
80100 GTTTCCAAACAATAATT
66 GTTTCCAAACAAGAATT
*
80117 AATTAAATAATTCTATTTCAGGATTTATTC
1 AATTGAATAATTCTATTTCAGGATTTATTC
80147 TTGTCATTCA
Statistics
Matches: 292, Mismatches: 47, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
76 60 0.21
77 4 0.01
80 51 0.17
81 21 0.07
82 139 0.48
83 17 0.06
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (82 bp):
AATTGAATAATTCTATTTCAGGATTTATTCCTGCCGTTCAACAGATTTTATTTCATTTTGATTTT
GTTTCCAAACAAGAATT
Found at i:80157 original size:158 final size:158
Alignment explanation
Indices: 79714--80161 Score: 533
Period size: 158 Copynumber: 2.8 Consensus size: 158
79704 AAAAAATTAA
* * * * *
79714 AATTGAATAAATCTGTTTCAGGATTTATTCCTGCCGTTCAATAAAATTTTATTTTATTTTTATTT
1 AATTGAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAA-CAGATTTTATTTCATTTTTATTT
* * * * *
79779 TGTTTCTAAACAAGAATTAATTGAATAATTATGTTTCGGA-TTATTCTTGTTGTTCAACAGATTT
65 TGTTTCCAAACAAGAATTAATTGAATAATTCTATTTCGGATTTATTCTTGTCGTTCAATAGATTT
* *
79843 TATTTTATTTTGATTTTGTTTGCAAACAAGGATT
130 TATTCTATTTTGA-----TTTCCAAACAAGGATT
* ** **
79877 AATTGAATAATTTTATTTTGGGATTTATTCCTGCTATTCAACAGATTTTA-TTCTATTTTTATTT
1 AATTGAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAGATTTTATTTC-ATTTTTATTT
** *
79941 TGTTTCCAAACAAGAATTAATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAATAGATT
65 TGTTTCCAAACAAGAATTAATTGAATAATTCTATTTCG-GATTTATTCTTGTCGTTCAATAGATT
80006 TTATTCTATTTTGA-TTCCAAACAAGGATT
129 TTATTCTATTTTGATTTCCAAACAAGGATT
* * ** * *
80035 AATTGAATAATTTTGTTTCAAGACTTATTTATACCGTTCAACAGATTTTATTTCATTTTGATTTT
1 AATTGAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAGATTTTATTTCATTTTTATTTT
* * *
80100 GTTTCCAAACAATAATTAATTAAATAATTCTATTTCAGGATTTATTCTTGTCATTCAATAGA
66 GTTTCCAAACAAGAATTAATTGAATAATTCTATTTC-GGATTTATTCTTGTCGTTCAATAGA
80162 ATTGATTTTG
Statistics
Matches: 243, Mismatches: 37, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
158 118 0.49
159 4 0.02
161 2 0.01
162 52 0.21
163 36 0.15
164 31 0.13
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (158 bp):
AATTGAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAGATTTTATTTCATTTTTATTTT
GTTTCCAAACAAGAATTAATTGAATAATTCTATTTCGGATTTATTCTTGTCGTTCAATAGATTTT
ATTCTATTTTGATTTCCAAACAAGGATT
Found at i:82569 original size:25 final size:26
Alignment explanation
Indices: 82510--82569 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
82500 CCCTAGTGCA
*
82510 CTCTCCGTTACTTAGCACGTATTGTG
1 CTCTCCGTTACTTAGCACGTATAGTG
* * *
82536 CTCTACGTTA-TTAGCATGTGTAGTG
1 CTCTCCGTTACTTAGCACGTATAGTG
*
82561 CTTTCCGTT
1 CTCTCCGTT
82570 TAGCACATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (26 bp):
CTCTCCGTTACTTAGCACGTATAGTG
Found at i:82589 original size:22 final size:22
Alignment explanation
Indices: 82558--82630 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
82548 AGCATGTGTA
* * *
82558 GTGCTTTCCGTTTAGCACATT-T
1 GTGCTCTCCGATTAGCAC-TTCG
82580 GTGCTCTCCGATTAGCACTTCG
1 GTGCTCTCCGATTAGCACTTCG
82602 GTGCTCTCCGATTAGCACTTCG
1 GTGCTCTCCGATTAGCACTTCG
82624 GTGCTCT
1 GTGCTCT
82631 TTGTTCCTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 2 0.04
22 45 0.96
ACGTcount: A:0.12, C:0.29, G:0.22, T:0.37
Consensus pattern (22 bp):
GTGCTCTCCGATTAGCACTTCG
Found at i:85379 original size:50 final size:50
Alignment explanation
Indices: 85321--85489 Score: 191
Period size: 47 Copynumber: 3.4 Consensus size: 50
85311 CTTGTTTAGC
*
85321 TAAATTGTTTTGTTCAGATCTGGTGTTTTATATAAAAATAAATATTTATT
1 TAAATTGTTTTGTTCAGATCTGGTGTTTTAAATAAAAATAAATATTTATT
* * ** *
85371 TAAATTG--TT-TTCATATATAATGTTTTAAATAAATATAAATATTTATT
1 TAAATTGTTTTGTTCAGATCTGGTGTTTTAAATAAAAATAAATATTTATT
* * * * *
85418 TAAATTGTTTTGTTTAGACCTGGTATTTTACATAAACATAAATATTTATTT
1 TAAATTGTTTTGTTCAGATCTGGTGTTTTAAATAAAAATAAATATTTA-TT
* *
85469 TATATTTTTTTGTTCAGATCT
1 TAAATTGTTTTGTTCAGATCT
85490 TAAATAGTTT
Statistics
Matches: 96, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
47 39 0.41
48 2 0.02
49 2 0.02
50 34 0.35
51 19 0.20
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.51
Consensus pattern (50 bp):
TAAATTGTTTTGTTCAGATCTGGTGTTTTAAATAAAAATAAATATTTATT
Found at i:90537 original size:23 final size:22
Alignment explanation
Indices: 90501--90544 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
90491 TAAATATTTC
*
90501 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
90524 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
90545 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:108283 original size:2 final size:2
Alignment explanation
Indices: 108276--108303 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
108266 TAAAAGAAGA
108276 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
108304 TATTATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112766 original size:15 final size:15
Alignment explanation
Indices: 112748--112787 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
112738 TAAATGTTGG
112748 ATTCCAAAGTAACAA
1 ATTCCAAAGTAACAA
* **
112763 ATTCCAAAGCAACGG
1 ATTCCAAAGTAACAA
112778 ATTCCAAAGT
1 ATTCCAAAGT
112788 TGCGTTCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (15 bp):
ATTCCAAAGTAACAA
Found at i:113244 original size:28 final size:28
Alignment explanation
Indices: 113195--113291 Score: 115
Period size: 28 Copynumber: 3.5 Consensus size: 28
113185 AAATAAAGAT
* * **
113195 GAAGTGCGGGCTATCATTGTGAAGCTGC
1 GAAGTGCGAGCTATTACAGTGAAGCTGC
*
113223 GAAGTGCGAGCTGTTACAGTGAAGCTGC
1 GAAGTGCGAGCTATTACAGTGAAGCTGC
* * *
113251 GAAGTGCAAGTTATTACAGTGAA-CTAC
1 GAAGTGCGAGCTATTACAGTGAAGCTGC
113278 GAAGTGCGAGCTAT
1 GAAGTGCGAGCTAT
113292 CGAAGTCTCG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
27 15 0.26
28 43 0.74
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (28 bp):
GAAGTGCGAGCTATTACAGTGAAGCTGC
Found at i:122117 original size:11 final size:11
Alignment explanation
Indices: 122101--122126 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
122091 AGTAAAAGAT
122101 AATATTAAAAA
1 AATATTAAAAA
122112 AATATTAAAAA
1 AATATTAAAAA
122123 AATA
1 AATA
122127 CCAAACAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATATTAAAAA
Found at i:128321 original size:19 final size:20
Alignment explanation
Indices: 128290--128341 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
128280 TTAGACCTTT
128290 TAGTT-TTTTATTT-TGGG-
1 TAGTTGTTTTATTTATGGGC
128307 TAGTTGTTTTGATTTATGGGC
1 TAGTTGTTTT-ATTTATGGGC
*
128328 TAG-TGTTTTCTTTA
1 TAGTTGTTTTATTTA
128342 AAGTTTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.17
18 4 0.13
19 8 0.27
20 10 0.33
21 3 0.10
ACGTcount: A:0.13, C:0.04, G:0.23, T:0.60
Consensus pattern (20 bp):
TAGTTGTTTTATTTATGGGC
Found at i:138957 original size:24 final size:23
Alignment explanation
Indices: 138926--138971 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
138916 ATCAATTACC
*
138926 TAAAAAAACAAAAGATTAAATTG
1 TAAAAAAACAAAAGATGAAATTG
*
138949 TAAATAAAACAAAATATGAAATT
1 TAAA-AAAACAAAAGATGAAATT
138972 AACAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (23 bp):
TAAAAAAACAAAAGATGAAATTG
Found at i:139256 original size:71 final size:71
Alignment explanation
Indices: 139168--139313 Score: 292
Period size: 71 Copynumber: 2.1 Consensus size: 71
139158 GACTATCAAA
139168 TTGATGCCCAATAAGATCTCCTCTCGGTTTCACTTATCTTAATTTTTCTTTAAGATCTTCAATCC
1 TTGATGCCCAATAAGATCTCCTCTCGGTTTCACTTATCTTAATTTTTCTTTAAGATCTTCAATCC
139233 TAAGTT
66 TAAGTT
139239 TTGATGCCCAATAAGATCTCCTCTCGGTTTCACTTATCTTAATTTTTCTTTAAGATCTTCAATCC
1 TTGATGCCCAATAAGATCTCCTCTCGGTTTCACTTATCTTAATTTTTCTTTAAGATCTTCAATCC
139304 TAAGTT
66 TAAGTT
139310 TTGA
1 TTGA
139314 AGTTTATTCG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (71 bp):
TTGATGCCCAATAAGATCTCCTCTCGGTTTCACTTATCTTAATTTTTCTTTAAGATCTTCAATCC
TAAGTT
Found at i:139346 original size:19 final size:19
Alignment explanation
Indices: 139314--139350 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
139304 TAAGTTTTGA
*
139314 AGTTTATTCGATTTAGTCT
1 AGTTTATTCAATTTAGTCT
*
139333 AGTTTTTTCAATTTAGTC
1 AGTTTATTCAATTTAGTC
139351 CTTAAACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.54
Consensus pattern (19 bp):
AGTTTATTCAATTTAGTCT
Found at i:150507 original size:27 final size:26
Alignment explanation
Indices: 150466--150517 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
150456 AACTTAGACC
* *
150466 CGTTGACTTTGACTTTGACCGTTGAT
1 CGTTGACATTGACTTTAACCGTTGAT
150492 CGTTGACCATTGACTTTAACCGTTGA
1 CGTTGA-CATTGACTTTAACCGTTGA
150518 CTTTTTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (26 bp):
CGTTGACATTGACTTTAACCGTTGAT
Found at i:150519 original size:13 final size:13
Alignment explanation
Indices: 150474--150521 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
150464 CCCGTTGACT
150474 TTGACTTTGACCG
1 TTGACTTTGACCG
* *
150487 TTGATCGTTGACCA
1 TTGA-CTTTGACCG
*
150501 TTGACTTTAACCG
1 TTGACTTTGACCG
150514 TTGACTTT
1 TTGACTTT
150522 TTTGAGAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:151716 original size:6 final size:6
Alignment explanation
Indices: 151705--151733 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
151695 AATTATAGAC
151705 TTTATA TTTATA TTTATA TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTAT
151734 GAATGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:156431 original size:25 final size:25
Alignment explanation
Indices: 156398--156456 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
156388 TCTCAAAATC
* * * *
156398 TCTTCCTTCAAGTCTGCCTTTATTT
1 TCTTTCTTCAAGTCAGCATTTAGTT
*
156423 TCTTTCTTCAATTCAGCATTTAGTT
1 TCTTTCTTCAAGTCAGCATTTAGTT
*
156448 TCTCTCTTC
1 TCTTTCTTC
156457 TAACAAGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.14, C:0.27, G:0.07, T:0.53
Consensus pattern (25 bp):
TCTTTCTTCAAGTCAGCATTTAGTT
Found at i:162319 original size:39 final size:39
Alignment explanation
Indices: 162276--162361 Score: 100
Period size: 42 Copynumber: 2.1 Consensus size: 39
162266 TCTGAAGTAC
* *
162276 TTCCTTGTTATTGAAGTAGCTAGAACATAGAATGATATT
1 TTCCTTGGTATTGAAGTAGCTAGAACAAAGAATGATATT
* * *
162315 TTCCTAATTGGTATTGAAGTAGGTAGATCAAAGAATGGTATT
1 TTCC---TTGGTATTGAAGTAGCTAGAACAAAGAATGATATT
162357 TTCCT
1 TTCCT
162362 ATCTTAACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
39 5 0.13
42 34 0.87
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.38
Consensus pattern (39 bp):
TTCCTTGGTATTGAAGTAGCTAGAACAAAGAATGATATT
Found at i:163485 original size:16 final size:15
Alignment explanation
Indices: 163464--163507 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
163454 ATTTGAATTC
*
163464 AAAATATAAATAGATA
1 AAAATA-AAATAAATA
163480 AAAATAATAATGAAATA
1 AAAATAA-AAT-AAATA
163497 AAAATAAAATA
1 AAAATAAAATA
163508 TGATTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 12 0.48
17 11 0.44
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (15 bp):
AAAATAAAATAAATA
Found at i:167076 original size:17 final size:18
Alignment explanation
Indices: 167045--167078 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
167035 GCTTCGGGGA
167045 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
*
167063 ATAT-CCAAAGTCTTCA
1 ATATGCCAAAATCTTCA
167079 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:168283 original size:129 final size:129
Alignment explanation
Indices: 168125--168383 Score: 473
Period size: 129 Copynumber: 2.0 Consensus size: 129
168115 CGATCATCTC
*
168125 CCATGACTATTATTATAGTCCTATTTACTACATCCATGTCAAAGATTATATCTTTTGAATTTATC
1 CCATGACTATTATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCTTTTGAATTTATC
*
168190 ACATAATGTTACATTCTCTTCAGGGAATGATTAGGTTTCGTGATTAAAATTTTTTGTTCAACCA
66 ACATAATGTTACATTCTCTTCAGGGAATGATTAGGTTTCGTGATTAAAAATTTTTGTTCAACCA
*
168254 CCATTACTATTATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCTTTTGAATTTATC
1 CCATGACTATTATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCTTTTGAATTTATC
* *
168319 ACATAATGTTACATTCTCTTCAGGGAATGTTTAGGTTTTGTGATTAAAAATTTTTGTTCAACCA
66 ACATAATGTTACATTCTCTTCAGGGAATGATTAGGTTTCGTGATTAAAAATTTTTGTTCAACCA
168383 C
1 C
168384 AAGTAAATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (129 bp):
CCATGACTATTATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCTTTTGAATTTATC
ACATAATGTTACATTCTCTTCAGGGAATGATTAGGTTTCGTGATTAAAAATTTTTGTTCAACCA
Found at i:171746 original size:22 final size:22
Alignment explanation
Indices: 171721--171771 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
171711 GGTTAAAAAG
171721 GAGTGAGTGAGCTTAACAAGCT
1 GAGTGAGTGAGCTTAACAAGCT
171743 GAGTGAGTGAGCTTAACAAGCT
1 GAGTGAGTGAGCTTAACAAGCT
*
171765 CAGTGAG
1 GAGTGAG
171772 AGCCTAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.22
Consensus pattern (22 bp):
GAGTGAGTGAGCTTAACAAGCT
Found at i:176049 original size:17 final size:17
Alignment explanation
Indices: 176027--176069 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
176017 AATTGTCGGC
*
176027 GCAATGAACAAGTAAAT
1 GCAATGAAAAAGTAAAT
176044 GCAATGAAAAAGTAAAT
1 GCAATGAAAAAGTAAAT
176061 GCAAT-AAAA
1 GCAATGAAAA
176070 TTGTGAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.16
Consensus pattern (17 bp):
GCAATGAAAAAGTAAAT
Found at i:183566 original size:94 final size:94
Alignment explanation
Indices: 183410--183718 Score: 419
Period size: 94 Copynumber: 3.3 Consensus size: 94
183400 TTCTCGTCAT
* *
183410 CTTAGTGTGAGCAGCATCGT-TA-AGG-AACAATTATATGTACAGATA-CATTATTGATGGCTGA
1 CTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCA-TATCGATGGCTGA
183471 GGTACCGCATATGTTGCGAGTCCTCATCAG
65 GGTACCGCATATGTTGCGAGTCCTCATCAG
* *
183501 CTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACATATACCATATCGATGGTTGAG
1 CTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCATATCGATGGCTGAG
** ** * *
183566 GTACAACATATGTTGTAAGTCCTCGTTAG
66 GTACCGCATATGTTGCGAGTCCTCATCAG
** * *
183595 CTTAAAGTGAGCAACATCGTATACTGGTAACAATTATATGTACAGATACCGTATCGATGGCTGAG
1 CTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCATATCGATGGCTGAG
* *
183660 GTACCGCATATGTCGCGAGTCCTCATCAA
66 GTACCGCATATGTTGCGAGTCCTCATCAG
* *
183689 CTTAGTGTGAGCAGTATCTTATACTGGTAA
1 CTTAGTGTGAGCAGCATCGTATACTGGTAA
183719 TAGAGACAAT
Statistics
Matches: 185, Mismatches: 29, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
91 20 0.11
92 2 0.01
93 2 0.01
94 159 0.86
95 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (94 bp):
CTTAGTGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACCATATCGATGGCTGAG
GTACCGCATATGTTGCGAGTCCTCATCAG
Found at i:184507 original size:21 final size:21
Alignment explanation
Indices: 184481--184529 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
184471 CTGGAGTTTG
184481 TTGTATCGGTAGAAGTAATAA
1 TTGTATCGGTAGAAGTAATAA
* * * *
184502 TTGTATTGGTAGTAGTCATAC
1 TTGTATCGGTAGAAGTAATAA
184523 TTGTATC
1 TTGTATC
184530 AATAGAACCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTAATAA
Found at i:188113 original size:94 final size:94
Alignment explanation
Indices: 187978--188288 Score: 484
Period size: 94 Copynumber: 3.3 Consensus size: 94
187968 AATTCTTGTT
* *
187978 AGCTTAGTGTGAGCAACATCGT-TA-AGG-AACAGTTATATGTACAAATACCGTATCGATGGCTG
1 AGCTTAGTGTGAGCAACATCGTATACTGGTAACAGTTATATGTACAGATACCGTATCGATGGCTG
* *
188040 AGGTATCGCATATGTTACGAGTCCTCATC
66 AGGTATCACATATGTTGCGAGTCCTCATC
* *
188069 AGCTTAGTGTGAGCAGCATTGTATACTGGTAACAGTTATATGTACAGATACCGTATCGATGGCTG
1 AGCTTAGTGTGAGCAACATCGTATACTGGTAACAGTTATATGTACAGATACCGTATCGATGGCTG
* * *
188134 AGGTACCATATATGTTGCGAGTCCTCGTC
66 AGGTATCACATATGTTGCGAGTCCTCATC
* *
188163 AGCTTAGTGTGAGAAACATCGTATATTGGTAACAGTTATATGTACAGATACCGTATCGATGGCTG
1 AGCTTAGTGTGAGCAACATCGTATACTGGTAACAGTTATATGTACAGATACCGTATCGATGGCTG
* *
188228 AGGTATCACATATGTGGTGAGTCCTCATC
66 AGGTATCACATATGTTGCGAGTCCTCATC
188257 AGCTTAGTGTGAGCAACATCGTATACTGGTAA
1 AGCTTAGTGTGAGCAACATCGTATACTGGTAA
188289 TATAGATAGT
Statistics
Matches: 197, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
91 20 0.10
92 2 0.01
93 2 0.01
94 173 0.88
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (94 bp):
AGCTTAGTGTGAGCAACATCGTATACTGGTAACAGTTATATGTACAGATACCGTATCGATGGCTG
AGGTATCACATATGTTGCGAGTCCTCATC
Found at i:218769 original size:44 final size:44
Alignment explanation
Indices: 218719--218806 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
218709 AATCCATACA
*
218719 AAGAAGGCACGACATTTTGAGCTATTCATGCTAAAAAGGAGGAG
1 AAGAAGGCACGACATTTTGAGCTATTCACGCTAAAAAGGAGGAG
*
218763 AAGAAGGCACGGCATTTTGAGCTATTCACGCTAAAAAGGAGGAG
1 AAGAAGGCACGACATTTTGAGCTATTCACGCTAAAAAGGAGGAG
218807 GAACCTATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (44 bp):
AAGAAGGCACGACATTTTGAGCTATTCACGCTAAAAAGGAGGAG
Found at i:220671 original size:21 final size:21
Alignment explanation
Indices: 220641--220702 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
220631 CTGCTTACCA
*
220641 TGTCGTGACATGGCTCCTGTG
1 TGTCGCGACATGGCTCCTGTG
* *
220662 TGTCGCGACATGGCTTCTATG
1 TGTCGCGACATGGCTCCTGTG
* *
220683 TGTCGCAACATCGACTCCTG
1 TGTCGCGACAT-GGCTCCTG
220703 AATGCAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 28 0.85
22 5 0.15
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (21 bp):
TGTCGCGACATGGCTCCTGTG
Found at i:220901 original size:25 final size:26
Alignment explanation
Indices: 220873--220923 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
220863 CTTCTTGTAA
* *
220873 TTTAGGTTTTAGTTATTTT-ATTTTC
1 TTTAAGTTTAAGTTATTTTCATTTTC
220898 TTTAAGTTTAAGTTATTTTCATTTTC
1 TTTAAGTTTAAGTTATTTTCATTTTC
220924 ATTTTACTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.65
Consensus pattern (26 bp):
TTTAAGTTTAAGTTATTTTCATTTTC
Found at i:223933 original size:322 final size:323
Alignment explanation
Indices: 223347--224317 Score: 1644
Period size: 324 Copynumber: 3.0 Consensus size: 323
223337 TAAAGTATTA
* *
223347 TACAAAATAACATCATCCTAGTACATGTCATATAACCAAGTGCTATAAAAACTACCAAACGAGCT
1 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
* * * *
223412 CCGCGATAGTGTGAC-TCTGTCAAGATGATTCGGTCTTTAAGCAGCAAAATAATCTACAAAACAA
66 CCGAGATAGTGTGACTTC-GTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAA
*
223476 CAATAACATCA-CTAGTAAGCTTCACAGCTTAGTAAGTTCGAAGAGTCTAAAAGAGTTACCAAAC
130 CAATAACATCATC-AGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAAC
*
223540 ATATGCATAGAGCAGTTTATAACTCAATTGAATGAGGATAAATCTTTGCTTCCTCAAGCCATATT
194 ATATGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATT
*
223605 TAGCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCCGATGCTACTCACATAGCTG
259 TAGCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACATAGCTG
*
223670 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGACCT
1 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
*
223735 CCG-GATAGTGTGACTTCATCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAAC
66 CCGAGATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAAC
223799 AATAACATCATCAGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACAT
131 AATAACATCATCAGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACAT
*
223864 ATGCATAGAGCAGTTTATAACTCAATTAAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTTA
196 ATGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTTA
* *
223929 GCATTTCAACTTTCTTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACACAAGCTG
261 GCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACA-TAGCTG
223993 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
1 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
* * *
224058 CCGAGATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGAAGCAAAATAATCAACAAAACAAT
66 CCGAGATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAAC
* * *
224123 AACAACATCACTC-GTAAGTTTCACAACTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACA
131 AATAACATCA-TCAGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACA
*
224187 TATGCATAGAGCAGTTTATAACTCAATTGAACAAGGATAAATCTTTGCTTCCTCAAGCCATATTT
195 TATGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTT
* * **
224252 AGCATTTCAACTTTCCTGCCTGTATCATCTCTATTACCAGTACTTGATGCTACTCACATGAGCTG
260 AGCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACAT-AGCTG
224317 T
1 T
224318 CAAGAACTCG
Statistics
Matches: 613, Mismatches: 29, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
322 234 0.38
323 140 0.23
324 237 0.39
325 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (323 bp):
TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
CCGAGATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAAC
AATAACATCATCAGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACAT
ATGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTTA
GCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACATAGCTG
Found at i:224212 original size:324 final size:322
Alignment explanation
Indices: 223347--224309 Score: 1642
Period size: 322 Copynumber: 3.0 Consensus size: 322
223337 TAAAGTATTA
* *
223347 TACAAAATAACATCATCCTAGTACATGTCATATAACCAAGTGCTATAAAAACTACCAAACGAGCT
1 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
* * *
223412 CCGCGATAGTGTGAC-TCTGTCAAGATGATTCGGTCTTTAAGCAGCAAAATAATCTACAAAACAA
66 CCG-GATAGTGTGACTTC-GTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAA
* *
223476 CAATAACATCACTAGTAAGCTTCACAGCTTAGTAAGTTCGAAGAGTCTAAAAGAGTTACCAAACA
129 CAATAACATCACTCGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACA
*
223541 TATGCATAGAGCAGTTTATAACTCAATTGAATGAGGATAAATCTTTGCTTCCTCAAGCCATATTT
194 TATGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTT
* *
223606 AGCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCCGATGCTACTCACATAGCTG
259 AGCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACAAAGCTG
*
223670 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGACCT
1 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
*
223735 CCGGATAGTGTGACTTCATCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAACA
66 CCGGATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAACA
223800 ATAACATCA-TCAGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACAT
131 ATAACATCACTC-GTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACAT
*
223864 ATGCATAGAGCAGTTTATAACTCAATTAAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTTA
195 ATGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTTA
*
223929 GCATTTCAACTTTCTTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACACAAGCTG
260 GCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACA-AAGCTG
223993 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
1 TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
* * *
224058 CCGAGATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGAAGCAAAATAATCAACAAAACAAT
66 CCG-GATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAAC
* * *
224123 AACAACATCACTCGTAAGTTTCACAACTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACAT
130 AATAACATCACTCGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACAT
*
224188 ATGCATAGAGCAGTTTATAACTCAATTGAACAAGGATAAATCTTTGCTTCCTCAAGCCATATTTA
195 ATGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTTA
* * **
224253 GCATTTCAACTTTCCTGCCTGTATCATCTCTATTACCAGTACTTGATGCTACTCACA
260 GCATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACA
224310 TGAGCTGTCA
Statistics
Matches: 606, Mismatches: 29, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
321 1 0.00
322 233 0.38
323 139 0.23
324 231 0.38
325 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (322 bp):
TACAAAATAACATCATCCTAGTACATGCCATATAACCAAGTGCTGTAAAAACTACCAAACGAGCT
CCGGATAGTGTGACTTCGTCAAGATGATCCGATCTTCAAGCAGCAAAATAATCTACAAAACAACA
ATAACATCACTCGTAAGCTTCACAGCTTAGTAAGTTTGAAGAGTCTAAAAGAGTTACCAAACATA
TGCATAGAGCAGTTTATAACTCAATTGAACGAGGATAAATCTTTGCTTCCTCAAGCCATATTTAG
CATTTCAACTTTCCTGTCTGTATCATCTCTATTACTAGTACCAGATGCTACTCACAAAGCTG
Found at i:229679 original size:3 final size:3
Alignment explanation
Indices: 229671--229708 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
229661 GGCTCAAATT
229671 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
229709 TAATATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:230526 original size:151 final size:151
Alignment explanation
Indices: 230156--230671 Score: 640
Period size: 152 Copynumber: 3.4 Consensus size: 151
230146 GATTTTGGGA
* * * * * *
230156 AAAGTTTTGTTTTTTTTAAATAATATGGAAATAAAAGTTTTTATTTTTAAGTAAAATAGTGA--T
1 AAAGTTTTGATTTTTTTAACTAATTTCGAAATAAAA-TTTTGATTTTTAAGTAAACTAGTGATTT
* *
230219 T-TTT-AAAAAAAAAGAGAGTTTATATTTTTAAAAAT-AAAAATCTGTTTTTTAGTTATTTTAAA
65 TCTTTAAAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAAATATGTTTTTTAGTTATTTTAAA
*
230281 GAAAAAGTTTAAAATTTTAAAC
130 GAAAAAGTTTAAATTTTTAAAC
* * *
230303 AAAGTTTTGATTTTTTTAACT-ATTTTGACATAAAAGTTTGGATTTTTAAGTAAAAC-AGTGATT
1 AAAGTTTTGATTTTTTTAACTAATTTCGAAATAAAA-TTTTGATTTTTAAGT-AAACTAGTGATT
*
230366 TTCTTTAAAAAAAAAAGAAAGTTTATATTTTTAAAAAATAAAAAAAATGTTTTTTAGTTATTTTA
64 TTCTTTAAAAAAAAAAGAAAGTTTATATTTTT-AAAAATAAAAAATATGTTTTTTAGTTATTTTA
* * *
230431 AGGAAAAAGTTCAAATTTTTAAAT
128 AAGAAAAAGTTTAAATTTTTAAAC
*
230455 AAAGTTTTGATTTTTTTAACT-TTTTCGAAATAAAATTTTGGA-TTTTAAGTAAACTAGTGATTT
1 AAAGTTTTGATTTTTTTAACTAATTTCGAAATAAAATTTT-GATTTTTAAGTAAACTAGTGATTT
* * * * *
230518 TCTTTAAAAAAAAAAGAGAAAGTTTAGA-TTTTAAAAATATATATATATGTTTTTTAATGATTTT
65 TCTTT-AAAAAAAAA-AGAAAGTTTATATTTTTAAAAATA-AAAAATATGTTTTTTAGTTATTTT
*
230582 AAAGAAAAAGTTTAATTTTTTAAAC
127 AAAGAAAAAGTTTAAATTTTTAAAC
* * *
230607 AAAGTTTTGATTTTTTTAGCT-ATTTCGAAATACAAATTTTGATTTTAAAGTAAAGTAGTGATTT
1 AAAGTTTTGATTTTTTTAACTAATTTCGAAATA-AAATTTTGATTTTTAAGTAAACTAGTGATTT
230671 T
65 T
230672 ATTTTAATCA
Statistics
Matches: 322, Mismatches: 33, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
146 30 0.09
147 22 0.07
148 2 0.01
149 3 0.01
150 28 0.09
151 37 0.11
152 162 0.50
153 38 0.12
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (151 bp):
AAAGTTTTGATTTTTTTAACTAATTTCGAAATAAAATTTTGATTTTTAAGTAAACTAGTGATTTT
CTTTAAAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAAATATGTTTTTTAGTTATTTTAAAG
AAAAAGTTTAAATTTTTAAAC
Found at i:232063 original size:239 final size:237
Alignment explanation
Indices: 231641--232111 Score: 748
Period size: 239 Copynumber: 2.0 Consensus size: 237
231631 AAAATAATAA
* * * * * *
231641 TAATGATAAAAGATAGAATAAGTTGTAGATGGATTTTAATATTTTTCTTAATTCATTAGTAATTT
1 TAATAATAAAAGATAGAATAAGTTGGAGATGAACTTTAATATTTCTCTTAATTCATTAGAAATTT
231706 TTAGGTTTTTATAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTTACTAGAATTA
66 TTAGGTTTTTATAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTTACTAGAATTA
*
231771 TTTAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAAATCTCTAATTCAAGTTTTAAATTAGATAA
131 TTTAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAAAACTCTAATTCAAGTTTTAAATTAGATAA
* *
231836 GTTTGGTAAACACGTCTTAATCAAGTTACAAGTAAATCAGAG
196 ATTTGGTAAACACGTCTTAATCAAATTACAAGTAAATCAGAG
231878 TAATAATAAAAGATCA-AATAAGTTGGAGATGAACTTTAATATTTCTCTTAATTCATTAGAAATT
1 TAATAATAAAAGAT-AGAATAAGTTGGAGATGAACTTTAATATTTCTCTTAATTCATTAGAAA--
*
231942 TTTTTAGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAA-GTATTTTACTAGA
63 TTTTTAGG-TTTTTATAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTTACTAGA
* *
232006 ATTATTTAGGTATTCTTTAGGGTTCTTGTTAGAAGTAAAAAACTCTAATTTAAGTTTTAAATTAG
127 ATTATTTAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAAAACTCTAATTCAAGTTTTAAATTAG
* * * *
232071 ATAAATTTGGTGAATACGTCTTAGTCAAATTATAAGTAAAT
192 ATAAATTTGGTAAACACGTCTTAATCAAATTACAAGTAAAT
232112 TGGAGGCATT
Statistics
Matches: 214, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
237 54 0.25
238 1 0.00
239 118 0.55
240 41 0.19
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (237 bp):
TAATAATAAAAGATAGAATAAGTTGGAGATGAACTTTAATATTTCTCTTAATTCATTAGAAATTT
TTAGGTTTTTATAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTTACTAGAATTA
TTTAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAAAACTCTAATTCAAGTTTTAAATTAGATAA
ATTTGGTAAACACGTCTTAATCAAATTACAAGTAAATCAGAG
Found at i:232564 original size:23 final size:20
Alignment explanation
Indices: 232537--232581 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
232527 GGTTTTTTAG
232537 TATTTATGCATATTAGATTTATT
1 TATTTATGC--ATTA-ATTTATT
*
232560 TATTTGTGCATTAATTTATT
1 TATTTATGCATTAATTTATT
232580 TA
1 TA
232582 GTTGTCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
23 8 0.38
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (20 bp):
TATTTATGCATTAATTTATT
Found at i:232578 original size:20 final size:21
Alignment explanation
Indices: 232548--232586 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
232538 ATTTATGCAT
*
232548 ATTAGATTTATTTATTTGTGC
1 ATTAGATTTATTTAGTTGTGC
232569 ATTA-ATTTATTTAGTTGT
1 ATTAGATTTATTTAGTTGT
232587 CTAATGTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.59
Consensus pattern (21 bp):
ATTAGATTTATTTAGTTGTGC
Found at i:233166 original size:22 final size:23
Alignment explanation
Indices: 233129--233171 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
233119 TTTAAATTTG
*
233129 TTCGCAATGTTTTATATTTTAAT
1 TTCGCAATGTTTTATACTTTAAT
*
233152 TTCGC-ATTTTTTATACTTTA
1 TTCGCAATGTTTTATACTTTA
233172 TTTGACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (23 bp):
TTCGCAATGTTTTATACTTTAAT
Found at i:238598 original size:12 final size:12
Alignment explanation
Indices: 238581--238606 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
238571 CCCCATCACT
238581 TAAAGAAAATTA
1 TAAAGAAAATTA
238593 TAAAGAAAATTA
1 TAAAGAAAATTA
238605 TA
1 TA
238607 TTCCTTGCTA
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:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
TAAAGAAAATTA
Found at i:239812 original size:14 final size:14
Alignment explanation
Indices: 239789--239818 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
239779 GCATTTAGAA
*
239789 GCCCATGTGTGGAG
1 GCCCAGGTGTGGAG
239803 GCCCAGGTGTGGAG
1 GCCCAGGTGTGGAG
239817 GC
1 GC
239819 TCATTTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (14 bp):
GCCCAGGTGTGGAG
Found at i:239847 original size:42 final size:42
Alignment explanation
Indices: 239800--240053 Score: 334
Period size: 42 Copynumber: 6.1 Consensus size: 42
239790 CCCATGTGTG
*
239800 GAGGCCCAGGTGTGGAGGCTCATTTACTTTTCACTGCATTTA
1 GAGGCCCAGGTGTGGAGGCTCATTTACTTTTCATTGCATTTA
* * *
239842 GAGGCCTAGGTGTGGAGGCCCATTTACTTTTCATTACATTTA
1 GAGGCCCAGGTGTGGAGGCTCATTTACTTTTCATTGCATTTA
*
239884 GAGGCCCAGGTGTAGAGGCTCATTTACTTTTCATTGCATTTA
1 GAGGCCCAGGTGTGGAGGCTCATTTACTTTTCATTGCATTTA
* * * *
239926 AAGGCTCATGTTTGGAGGCTCATTTAC-TTTCATTGCATTTA
1 GAGGCCCAGGTGTGGAGGCTCATTTACTTTTCATTGCATTTA
* *
239967 GAGTCCCAGGTGTGGAGG-TCTATTTACTTTTCATTGCACTTA
1 GAGGCCCAGGTGTGGAGGCTC-ATTTACTTTTCATTGCATTTA
* * * *
240009 GAGACCTAGGTGTGGAGG-TCCATTTACTTTTCATTACATTCA
1 GAGGCCCAGGTGTGGAGGCT-CATTTACTTTTCATTGCATTTA
240051 GAG
1 GAG
240054 ACCTAGGCGC
Statistics
Matches: 185, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.01
41 33 0.18
42 149 0.81
43 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
GAGGCCCAGGTGTGGAGGCTCATTTACTTTTCATTGCATTTA
Found at i:240035 original size:125 final size:126
Alignment explanation
Indices: 239812--240048 Score: 352
Period size: 125 Copynumber: 1.9 Consensus size: 126
239802 GGCCCAGGTG
*
239812 TGGAGGCTCATTTACTTTTCACTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTTTTCATT
1 TGGAGGCTCATTTACTTTTCACTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATT
* * *
239877 ACATTTAGAGGCCCAGGTGTAGAGGCTCATTTACTTTTCATTGCATTTAAAGGCTCATGTT
66 ACACTTAGAGACCCAGGTGTAGAGGCTCATTTACTTTTCATTACATTTAAAGGCTCATGTT
* * * *
239938 TGGAGGCTCATTTAC-TTTCATTGCATTTAGAGTCCCAGGTGTGGAGGTCTATTTACTTTTCATT
1 TGGAGGCTCATTTACTTTTCACTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATT
* * *
240002 GCACTTAGAGACCTAGGTGTGGAGG-TCCATTTACTTTTCATTACATT
66 ACACTTAGAGACCCAGGTGTAGAGGCT-CATTTACTTTTCATTACATT
240049 CAGAGACCTA
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
124 1 0.01
125 83 0.84
126 15 0.15
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (126 bp):
TGGAGGCTCATTTACTTTTCACTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATT
ACACTTAGAGACCCAGGTGTAGAGGCTCATTTACTTTTCATTACATTTAAAGGCTCATGTT
Found at i:241998 original size:52 final size:51
Alignment explanation
Indices: 241831--242018 Score: 175
Period size: 52 Copynumber: 3.6 Consensus size: 51
241821 TTTCATTTAA
* ** * * *
241831 TACTCACAATGACA-TATAGTCATCGGATCTCTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGATC-CTTAATCCGTAAATG-ATTCATT
* * * * *
241884 TACTCATGATGACACTAAGCCATCGGA-CCTTTAATCCAT-CATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGATCC-TTAATCCGTAAAT-GATTCATT
*
241935 TACTCATGATGACACTTAGTCATCGGATCCTTCAATCCGTAAATGATTCATT
1 TACTCACGATGACACTTAGTCATCGGATCCTT-AATCCGTAAATGATTCATT
* *
241987 TACTCACGATGACACTTAGTTATCGGACCCTT
1 TACTCACGATGACACTTAGTCATCGGATCCTT
242019 TCGTTTATAG
Statistics
Matches: 112, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
51 35 0.31
52 53 0.47
53 23 0.21
54 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGATCCTTAATCCGTAAATGATTCATT
Found at i:247583 original size:52 final size:52
Alignment explanation
Indices: 247428--247668 Score: 276
Period size: 52 Copynumber: 4.6 Consensus size: 52
247418 GTTCATTTAA
* *
247428 TACTCACGATGACA-TATAGTCATCGGACCTCTTGT--TCCGA-ATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACC-CTT-TAATCC-ATAAAGG-ATTCATT
* * * *
247481 TACTCACGATGACACTGAGTCATCAGA-CCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
*
247532 TACTCACGATGACACTTAATCATCGGACCCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
* * * * *
247584 TACTCATGATGACACCTAGTCATCAGACCCTTTAATCCGTAAAGAATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
* *
247636 TACTCACAATGACACTTAGTCATCGAACCCTTT
1 TACTCACGATGACACTTAGTCATCGGACCCTTT
247669 CGTTTATAGC
Statistics
Matches: 161, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.01
51 34 0.21
52 102 0.63
53 23 0.14
54 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (52 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
Found at i:250944 original size:230 final size:234
Alignment explanation
Indices: 250529--250994 Score: 735
Period size: 230 Copynumber: 2.0 Consensus size: 234
250519 AAAATAATAA
* *
250529 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTATCTTAATTCATTAGTAATTT
1 TAATGATAAAAGATCGAATAAGTTGGAGATGAACTTTAATATTTATCTTAATTCATTA-TAA-TT
*
250594 TTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATATATTTTACTAGAACTA
64 TTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATATATTTTACTAAAACTA
250659 TTTAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAATCTCTAATTCAAGTTTTAAATTAGATAAG
129 TTTAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAATCTCTAATTCAAGTTTTAAATTAGATAAG
250724 TTTGATGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
194 TTTGATGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
* *
250765 TAATGATAAAAGATCGAATAAGTTGGAGATGAACTTTAATATTTCTTTTAATTCA-T-T-A-TTT
1 TAATGATAAAAGATCGAATAAGTTGGAGATGAACTTTAATATTTATCTTAATTCATTATAATTTT
* * * *
250826 AGGTTTTTTTAGGATTTTAAAATAGAATTAATTTTAAGATTTGAA-GTATTTTACTAAAATTATT
66 AGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATATATTTTACTAAAACTATT
* *
250890 TAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAAATCTCTAATTTAATTTTTAAATTAGATAAGT
131 TAGGTATCCTTTAGGGTTCTTGTTAGAAGT-AAAATCTCTAATTCAAGTTTTAAATTAGATAAGT
* * * *
250955 TTGGTGAATACGTCTTAGTCAAGTTATAAGTAAATTGGAG
195 TTGATGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
250995 GCATTTTTTT
Statistics
Matches: 214, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
229 46 0.21
230 114 0.53
232 1 0.00
233 1 0.00
235 1 0.00
236 51 0.24
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (234 bp):
TAATGATAAAAGATCGAATAAGTTGGAGATGAACTTTAATATTTATCTTAATTCATTATAATTTT
AGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATATATTTTACTAAAACTATT
TAGGTATCCTTTAGGGTTCTTGTTAGAAGTAAAATCTCTAATTCAAGTTTTAAATTAGATAAGTT
TGATGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
Found at i:260555 original size:18 final size:18
Alignment explanation
Indices: 260534--260568 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
260524 GCATTCGAGC
*
260534 ATGTGGTTACATCTGATT
1 ATGTGATTACATCTGATT
*
260552 ATGTGATTGCATCTGAT
1 ATGTGATTACATCTGAT
260569 CAGGATGTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (18 bp):
ATGTGATTACATCTGATT
Found at i:264795 original size:31 final size:31
Alignment explanation
Indices: 264757--264826 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
264747 TTAAAATGAA
264757 AAAATTTTCATTCAGGCTCTTAAAATTTTTT
1 AAAATTTTCATTCAGGCTCTTAAAATTTTTT
264788 AAAATTTTCATTCAGGCTCTTAAAATTTTTT
1 AAAATTTTCATTCAGGCTCTTAAAATTTTTT
264819 AAAATTTT
1 AAAATTTT
264827 AAATTAGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (31 bp):
AAAATTTTCATTCAGGCTCTTAAAATTTTTT
Found at i:268692 original size:16 final size:16
Alignment explanation
Indices: 268660--268702 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 16
268650 AAATATATAC
268660 AAAAATATAATAATAAATTT
1 AAAAATA-AATAA-AAA--T
268680 AAAAATAAATAAAAAT
1 AAAAATAAATAAAAAT
268696 AAAAATA
1 AAAAATA
268703 TTATTGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
18 3 0.13
19 5 0.22
20 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:272395 original size:29 final size:29
Alignment explanation
Indices: 272364--272556 Score: 150
Period size: 28 Copynumber: 6.7 Consensus size: 29
272354 GGGTGAATGG
*
272364 GTAATTTTTGGATGTTCGAGGG-AAAAAT
1 GTAATTTTTGGAAGTTCGAGGGTAAAAAT
* * * **
272392 GGTAAGTTTT-GATGTTTG-GGGGCAAAAT
1 -GTAATTTTTGGAAGTTCGAGGGTAAAAAT
* * *
272420 GGTAA-TTGTGGATGTTCGAGGGTTAAAAT
1 -GTAATTTTTGGAAGTTCGAGGGTAAAAAT
* *
272449 GT-ATTTTTGGAAGTT-TAGGGGTTAAAAT
1 GTAATTTTTGGAAGTTCGA-GGGTAAAAAT
272477 GTAATTTTTGGAAGTTCGAGGGTCAAAAA-
1 GTAATTTTTGGAAGTTCGAGGGT-AAAAAT
* *
272506 GTAA-TTATGGAAAGTTCGAGGGTCAAAAT
1 GTAATTTTTGG-AAGTTCGAGGGTAAAAAT
*
272535 GTAATTTTTGAAAAGTTCGAGG
1 GTAATTTTTG-GAAGTTCGAGG
272557 ATCTCTTAAG
Statistics
Matches: 136, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
27 8 0.06
28 56 0.41
29 53 0.39
30 19 0.14
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTCGAGGGTAAAAAT
Found at i:272459 original size:28 final size:29
Alignment explanation
Indices: 272364--272556 Score: 166
Period size: 29 Copynumber: 6.7 Consensus size: 29
272354 GGGTGAATGG
* *
272364 GTAATTTTTGGATGTTCGAGGG-AAAAAT
1 GTAATTTTTGGAAGTTCGAGGGTCAAAAT
* * * *
272392 GGTAAGTTTT-GATGTTTG-GGGGCAAAAT
1 -GTAATTTTTGGAAGTTCGAGGGTCAAAAT
* * *
272420 GGTAA-TTGTGGATGTTCGAGGGTTAAAAT
1 -GTAATTTTTGGAAGTTCGAGGGTCAAAAT
* *
272449 GT-ATTTTTGGAAGTT-TAGGGGTTAAAAT
1 GTAATTTTTGGAAGTTCGA-GGGTCAAAAT
*
272477 GTAATTTTTGGAAGTTCGAGGGTCAAAAA
1 GTAATTTTTGGAAGTTCGAGGGTCAAAAT
*
272506 GTAA-TTATGGAAAGTTCGAGGGTCAAAAT
1 GTAATTTTTGG-AAGTTCGAGGGTCAAAAT
*
272535 GTAATTTTTGAAAAGTTCGAGG
1 GTAATTTTTG-GAAGTTCGAGG
272557 ATCTCTTAAG
Statistics
Matches: 137, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
27 8 0.06
28 52 0.38
29 62 0.45
30 15 0.11
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTCGAGGGTCAAAAT
Found at i:272499 original size:57 final size:57
Alignment explanation
Indices: 272310--272556 Score: 173
Period size: 57 Copynumber: 4.3 Consensus size: 57
272300 AAAATCGAAC
* * * * * ***
272310 TTTTGGAAAATTCGA-GGTTGAAAATGCGATTTTTTGAAATTTAGGGGTGAATGGGTAAT
1 TTTTGG-AAGTTCGAGGGTT-AAAATG-TATTTTTGGAAGTTTAGGGGTCAAAATGTAAT
* * * * *
272369 TTTTGGATGTTCGAGGG-AAAAATGGTAAGTTTT-GATGTTT-GGGGGCAAAATGGTAA-
1 TTTTGGAAGTTCGAGGGTTAAAAT-GT-ATTTTTGGAAGTTTAGGGGTCAAAAT-GTAAT
* * *
272425 TTGTGGATGTTCGAGGGTTAAAATGTATTTTTGGAAGTTTAGGGGTTAAAATGTAAT
1 TTTTGGAAGTTCGAGGGTTAAAATGTATTTTTGGAAGTTTAGGGGTCAAAATGTAAT
* * * * *
272482 TTTTGGAAGTTCGAGGGTCAAAAAGTAATTATGGAAAG-TTCGAGGGTCAAAATGTAAT
1 TTTTGGAAGTTCGAGGGTTAAAATGTATTTTTGG-AAGTTTAG-GGGTCAAAATGTAAT
*
272540 TTTTGAAAAGTTCGAGG
1 TTTTG-GAAGTTCGAGG
272557 ATCTCTTAAG
Statistics
Matches: 150, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
55 5 0.03
56 34 0.23
57 59 0.39
58 34 0.23
59 18 0.12
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (57 bp):
TTTTGGAAGTTCGAGGGTTAAAATGTATTTTTGGAAGTTTAGGGGTCAAAATGTAAT
Found at i:274302 original size:43 final size:43
Alignment explanation
Indices: 274239--274321 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
274229 GGGTTTAGGT
274239 ATTTTAAAATTTAAACAAATTTAAACTTAAAATGTATTTGGAC
1 ATTTTAAAATTTAAACAAATTTAAACTTAAAATGTATTTGGAC
* * *
274282 ATTTT-AAATTTAAAATAAATTTAAATTTAAAATTTATTTG
1 ATTTTAAAATTT-AAACAAATTTAAACTTAAAATGTATTTG
274322 TTTCTTAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 6 0.17
43 30 0.83
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (43 bp):
ATTTTAAAATTTAAACAAATTTAAACTTAAAATGTATTTGGAC
Found at i:274760 original size:48 final size:49
Alignment explanation
Indices: 274691--274810 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 49
274681 CTTGATCTTT
* * * * *
274691 TTCTCTATATCTCATCTGGAAGATGATCGCTTCA-TTGCTTCGA-CCTAC
1 TTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGCTTCAATCC-AC
* * *
274739 TTCTCTGTATCCCATCAGGAAGATGACCGCATCACTTGTTTTAATCCAC
1 TTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGCTTCAATCCAC
*
274788 TTCTTTGTATCTCATCAGGAAGA
1 TTCTCTGTATCTCATCAGGAAGA
274811 CGGATTTGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 29 0.48
49 29 0.48
50 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (49 bp):
TTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGCTTCAATCCAC
Found at i:275283 original size:207 final size:208
Alignment explanation
Indices: 274736--275284 Score: 852
Period size: 208 Copynumber: 2.6 Consensus size: 208
274726 TGCTTCGACC
* *
274736 TACTTCTCTGTATCCCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTTTGTATCTC
1 TACTTCTCTGTATCTCATCAGGAAGATGACCGCATCAC-TGTTTCAATCCACTTCTTTGTATCTC
* ** **
274801 ATCAGGAAGACGGATTTGGTCCACTTCTCTGTGTCTCATCAAGAAGACGACTGCTTTATTGCTTC
65 ATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGTGACTATTTTATTGCTTC
* *
274866 GACCTGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCAAAGTTTTGCTCACATTGAGCTTTGTT
130 GACCAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCAAAGTTTTGCTCACATTAAGCTTTGTT
274931 TCATTGATTTGGTA
195 TCATTGATTTGGTA
* *
274945 TACTTCCCTGTATCTCATCAGGAAGATGATCGCATCACTGTTTCAATCCACTTCTTTGTATCTCA
1 TACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTGTTTCAATCCACTTCTTTGTATCTCA
*
275010 TCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGTGACTATTTTATTTCTTCG
66 TCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGTGACTATTTTATTGCTTCG
* *
275075 ACCAGTTTCTCAGTATCTCATCAGGAAGCT-GGGATTCGAAA-TTTTGCTCACATTAAGCTTTGT
131 ACCAGCTTCTCAATATCTCATCAGGAAGCTAGGG-TTC-AAAGTTTTGCTCACATTAAGCTTTGT
275138 TTCATTGATTTGGTA
194 TTCATTGATTTGGTA
** *
275153 TACTTCTCTGTATCTCATCAGGAAGATGA-CATATCACTGTTTCAATCCACTTCTCTGTATCTCA
1 TACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTGTTTCAATCCACTTCTTTGTATCTCA
* * * * *
275217 TTAGGAAGACGGATTTAGTCCACTTCTCTGTATCTCATTAGGAAGGTGACCATTTTATTGCTTCG
66 TCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGTGACTATTTTATTGCTTCG
275282 ACC
131 ACC
275285 TGATTCTTTT
Statistics
Matches: 314, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
207 97 0.31
208 179 0.57
209 38 0.12
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (208 bp):
TACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTGTTTCAATCCACTTCTTTGTATCTCA
TCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGTGACTATTTTATTGCTTCG
ACCAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCAAAGTTTTGCTCACATTAAGCTTTGTTT
CATTGATTTGGTA
Found at i:276094 original size:44 final size:43
Alignment explanation
Indices: 276042--276124 Score: 139
Period size: 44 Copynumber: 1.9 Consensus size: 43
276032 TTTGGTTTTA
*
276042 AGACGCCCTTTGTGGGTTTTCATCTCGATCTCTTTTTTTTAATG
1 AGACGCCCTTTGTGGGTTTTCATCTCAATC-CTTTTTTTTAATG
*
276086 AGACGCCCTTTTTGGGTTTTCATCTCAATCCTTTTTTTT
1 AGACGCCCTTTGTGGGTTTTCATCTCAATCCTTTTTTTT
276125 GTTTTTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
43 9 0.24
44 28 0.76
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.49
Consensus pattern (43 bp):
AGACGCCCTTTGTGGGTTTTCATCTCAATCCTTTTTTTTAATG
Found at i:287128 original size:29 final size:29
Alignment explanation
Indices: 287096--287186 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
287086 GAAATAATAG
* *
287096 TTTTTGGGTGTTTG-GGAGCAAAATGGTAA
1 TTTTTGGATGTTCGAGG-GCAAAATGGTAA
*
287125 TTTTTGGATGTTCGAGGGTAAAATGGTAA
1 TTTTTGGATGTTCGAGGGCAAAATGGTAA
* *
287154 TTTTT-GATGTTCGGGGGTCAAAAT-GTGA
1 TTTTTGGATGTTCGAGGG-CAAAATGGTAA
287182 TTTTT
1 TTTTT
287187 TGAAACTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 19 0.35
29 33 0.61
30 2 0.04
ACGTcount: A:0.23, C:0.04, G:0.31, T:0.42
Consensus pattern (29 bp):
TTTTTGGATGTTCGAGGGCAAAATGGTAA
Found at i:287166 original size:28 final size:30
Alignment explanation
Indices: 287114--287219 Score: 112
Period size: 29 Copynumber: 3.6 Consensus size: 30
287104 TGTTTGGGAG
287114 CAAAATGGTAATTTTTGGATGTTCGAGGGT
1 CAAAATGGTAATTTTTGGATGTTCGAGGGT
*
287144 -AAAATGGTAATTTTT-GATGTTCGGGGGT
1 CAAAATGGTAATTTTTGGATGTTCGAGGGT
* * ** * *
287172 CAAAAT-GTGATTTTTTGAAACTTTGGGGGT
1 CAAAATGGT-AATTTTTGGATGTTCGAGGGT
287202 CAAAAT-GTAATTTTTGGA
1 CAAAATGGTAATTTTTGGA
287220 AAGTTTAGAG
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 14 0.22
29 34 0.52
30 17 0.26
ACGTcount: A:0.28, C:0.06, G:0.27, T:0.39
Consensus pattern (30 bp):
CAAAATGGTAATTTTTGGATGTTCGAGGGT
Found at i:287187 original size:29 final size:29
Alignment explanation
Indices: 287114--287216 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 29
287104 TGTTTGGGAG
* *
287114 CAAAATGGTAATTTTTGGATGTTCGAGGGT
1 CAAAAT-GTAATTTTTTGATGTTCGGGGGT
287144 -AAAATGGTAA-TTTTTGATGTTCGGGGGT
1 CAAAAT-GTAATTTTTTGATGTTCGGGGGT
* ** *
287172 CAAAATGTGATTTTTTGAAACTTTGGGGGT
1 CAAAATGTAATTTTTTG-ATGTTCGGGGGT
287202 CAAAATGTAATTTTT
1 CAAAATGTAATTTTT
287217 GGAAAGTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
28 19 0.30
29 21 0.33
30 23 0.37
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (29 bp):
CAAAATGTAATTTTTTGATGTTCGGGGGT
Found at i:291994 original size:86 final size:86
Alignment explanation
Indices: 291855--292012 Score: 237
Period size: 86 Copynumber: 1.8 Consensus size: 86
291845 AATGAAGGAC
* * **
291855 TCATGTCTCGGGATGAGCATGAGATTATGTATAAATGGAAGACTCACATCTCGGGGTGAGCATGA
1 TCATGTCTCGGGACGAGAATGAGATTATGTATAAATGGAAGACTCACATCTCGGAATGAGCATGA
291920 GATTATGTAGAAATGGAAGAT
66 GATTATGTAGAAATGGAAGAT
* **
291941 TCATGTCTCGGGACGAGAATGAGATTATGTATTAATGGAAGACTCGTGA-CTCGGAATGAGCATG
1 TCATGTCTCGGGACGAGAATGAGATTATGTATAAATGGAAGACTC-ACATCTCGGAATGAGCATG
292005 AGATTATG
65 AGATTATG
292013 GTTAAGGAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
86 63 0.98
87 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (86 bp):
TCATGTCTCGGGACGAGAATGAGATTATGTATAAATGGAAGACTCACATCTCGGAATGAGCATGA
GATTATGTAGAAATGGAAGAT
Found at i:292033 original size:41 final size:42
Alignment explanation
Indices: 291852--292091 Score: 211
Period size: 43 Copynumber: 5.7 Consensus size: 42
291842 ATAAATGAAG
*
291852 GACTCATGTCTCGGGATGAGCATGAGATTAT-GTATAAATGGAA
1 GACTCATGACTCGGGATGAGCATGAGATTATGGT-T-AATGGAA
* * *
291895 GACTCA-CATCTCGGGGTGAGCATGAGATTAT-GTAGAAATGGAA
1 GACTCATGA-CTCGGGATGAGCATGAGATTATGGT--TAATGGAA
* * * * *
291938 GATTCATGTCTCGGGACGAGAATGAGATTATGTATTAATGGAA
1 GACTCATGACTCGGGATGAGCATGAGATTATG-GTTAATGGAA
* *
291981 GACTCGTGACTCGGAATGAGCATGAGATTATGGTTAA-GGAA
1 GACTCATGACTCGGGATGAGCATGAGATTATGGTTAATGGAA
* ** * * *
292022 GACTCGTGACTCGAAATGAGTATGAGATTATGTTTAAAGGAA
1 GACTCATGACTCGGGATGAGCATGAGATTATGGTTAATGGAA
* * *
292064 GACTTATGACTCGGTA-GAGCATAAGATT
1 GACTCATGACTCGGGATGAGCATGAGATT
292092 GTTTAAAAAG
Statistics
Matches: 162, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
41 48 0.30
42 20 0.12
43 93 0.57
45 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (42 bp):
GACTCATGACTCGGGATGAGCATGAGATTATGGTTAATGGAA
Found at i:292774 original size:21 final size:21
Alignment explanation
Indices: 292748--292798 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
292738 GGAGTTTCTA
292748 GTATCGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTCAT-ACTT
*
292769 GTATCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTCATACTT
*
292790 GTAACGGTA
1 GTATCGGTA
292799 AAACTAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:298224 original size:24 final size:24
Alignment explanation
Indices: 298185--298253 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
298175 AATTTGATTC
*
298185 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
298209 AAAGAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
298233 AAACAAATAAACAGAGTTTAA
1 AAACAAATAAACAGAGTTTAA
298254 CTAAAAGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:299470 original size:20 final size:20
Alignment explanation
Indices: 299445--299484 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
299435 GAAGCTCACC
299445 TTCGTTCATGCGAAACGTAA
1 TTCGTTCATGCGAAACGTAA
299465 TTCGTTCATGCGAAACGTAA
1 TTCGTTCATGCGAAACGTAA
299485 ATAGACGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
TTCGTTCATGCGAAACGTAA
Found at i:300275 original size:29 final size:24
Alignment explanation
Indices: 300218--300283 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
300208 AATTTGACTC
*
300218 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
300242 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
300266 --A-AAATAAACAGAATTTAA
1 AAACAAATAAACAGAGTTTAA
300284 CAAAAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.40
22 1 0.03
24 23 0.57
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:300291 original size:20 final size:21
Alignment explanation
Indices: 300246--300291 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
300236 TAATTGAAAC
* **
300246 AAATAAACAGAGTTTAATTGA
1 AAATAAACAGAATTTAATCAA
300267 AAATAAACAGAATTTAA-CAA
1 AAATAAACAGAATTTAATCAA
300287 AAATA
1 AAATA
300292 TAATTTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (21 bp):
AAATAAACAGAATTTAATCAA
Found at i:300938 original size:31 final size:31
Alignment explanation
Indices: 300901--300971 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
300891 TGAAATTTTC
*
300901 TCGAATCGAGCCGAGTGAGATGAAATTCAAA
1 TCGAATCGAGCCGAGTGAGAGGAAATTCAAA
* *
300932 TCGAATCGAGCTGAGTGAGAGGAAATTCGAA
1 TCGAATCGAGCCGAGTGAGAGGAAATTCAAA
300963 TCGAATCGA
1 TCGAATCGA
300972 ATATATTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (31 bp):
TCGAATCGAGCCGAGTGAGAGGAAATTCAAA
Found at i:301233 original size:18 final size:17
Alignment explanation
Indices: 301165--301235 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
301155 TGTCATTATG
* *
301165 TATTTTGAAATTAAAAAA
1 TATTTT-AAAATAAAAAT
*
301183 TATATTAAATATAAAAAT
1 TATTTTAAA-ATAAAAAT
**
301201 GTGATTTTTTAATAAAAAT
1 -T-ATTTTAAAATAAAAAT
301220 TATTTTAAAGATAAAA
1 TATTTTAAA-ATAAAA
301236 TGTAAAACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
17 9 0.22
18 18 0.44
19 9 0.22
20 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TATTTTAAAATAAAAAT
Found at i:304645 original size:41 final size:41
Alignment explanation
Indices: 304588--304704 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 41
304578 AAAATGCCGT
* *
304588 AAAAGGTAAAGCAATAGCGGTGTTTTTTCCATAAACGCTTC
1 AAAAGATAAAGCAATAGCGGTGTTTTTTCCATAAACGCTGC
*
304629 AAAAGATAAAGCAATAGCGGCG-TTTTTCCATAAACGCTGC
1 AAAAGATAAAGCAATAGCGGTGTTTTTTCCATAAACGCTGC
* * *
304669 AAAA-AGTAAAGAAATAGCGGTGTTTTTGCTATAAAC
1 AAAAGA-TAAAGCAATAGCGGTGTTTTTTCCATAAAC
304705 CCGCTAAAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 35 0.52
41 31 0.46
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (41 bp):
AAAAGATAAAGCAATAGCGGTGTTTTTTCCATAAACGCTGC
Found at i:304752 original size:41 final size:41
Alignment explanation
Indices: 304707--305016 Score: 272
Period size: 41 Copynumber: 7.6 Consensus size: 41
304697 CTATAAACCC
* * *
304707 GCTAAAGGTTAGAGCATTAGCGATGTTTATGAGAAAACGCA
1 GCTAAAGGTCAAAGCATTAGCGACGTTTATGAGAAAACGCA
* * * *
304748 GCTAAAGGTCTAAGCATTAGTGGCATTTATGAGAAAACGCA
1 GCTAAAGGTCAAAGCATTAGCGACGTTTATGAGAAAACGCA
* * *
304789 GCTAAAGGTCAAAGCATTAGCAGA-GTTTATGAGACAATGCT
1 GCTAAAGGTCAAAGCATTAGC-GACGTTTATGAGAAAACGCA
* * *
304830 GCTCAAGGTCAAAGCATTAGCAATGTTTATGAGAAAACGCCA
1 GCTAAAGGTCAAAGCATTAGCGACGTTTATGAGAAAACG-CA
* * * * *
304872 -CTAAAGGTCAGAGCATTAGAGGCATTATTTGA-AAATAC-C-
1 GCTAAAGGTCAAAGCATTAGCGACGTT-TATGAGAAA-ACGCA
* * * * *
304911 GCTAAAGGTCAGAGCAGTAGCGGCGTTTATTAGAAAACGCC
1 GCTAAAGGTCAAAGCATTAGCGACGTTTATGAGAAAACGCA
* * * *
304952 GCTAAAGGTCAAAGCATTAGCGGCGTTTATGGGAAAAACACT
1 GCTAAAGGTCAAAGCATTAGCGACGTTTATGAG-AAAACGCA
* *
304994 GCTAAAGGT-TAAGCAATAGCGAC
1 GCTAAAGGTCAAAGCATTAGCGAC
305017 ATTTTTCCCA
Statistics
Matches: 218, Mismatches: 41, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
39 5 0.02
40 29 0.13
41 161 0.74
42 23 0.11
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (41 bp):
GCTAAAGGTCAAAGCATTAGCGACGTTTATGAGAAAACGCA
Found at i:309050 original size:12 final size:12
Alignment explanation
Indices: 309033--309061 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
309023 GCTCTGTTGG
309033 ATTTTAACATTT
1 ATTTTAACATTT
309045 ATTTTAACATTT
1 ATTTTAACATTT
309057 ATTTT
1 ATTTT
309062 CATCAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTAACATTT
Found at i:313425 original size:58 final size:58
Alignment explanation
Indices: 313355--313471 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
313345 AACCCAAATA
313355 TTAAAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAAC-CTAAATATTTAAT
1 TTAAAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAACTC-AAATATTTAAT
313413 TTAAAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAACTCAAATATTTAAT
1 TTAAAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAACTCAAATATTTAAT
313471 T
1 T
313472 ATTTAATTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (58 bp):
TTAAAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAACTCAAATATTTAAT
Found at i:313504 original size:58 final size:58
Alignment explanation
Indices: 313355--313507 Score: 148
Period size: 58 Copynumber: 2.6 Consensus size: 58
313345 AACCCAAATA
* ** * *
313355 TTAAAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAACCTAAATATTTAAT
1 TTAAAATATATAATTAAATAAATAGTTAATTATTAAACCCTAAACCTAAATATTTAAT
* ** * *
313413 TTAAAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAA-CTCAAATATTTAAT
1 TTAAAATATATAATTAAATAAATAGTTAATTATTAAACCCTAAACCT-AAATATTTAAT
** * *
313471 TATTTAAT-TATATTTAAATAAATATTTAATTATTAAA
1 T-TAAAATATATAATTAAATAAATAGTTAATTATTAAA
313508 AACAATCCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.02
58 78 0.93
59 4 0.05
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (58 bp):
TTAAAATATATAATTAAATAAATAGTTAATTATTAAACCCTAAACCTAAATATTTAAT
Found at i:313585 original size:14 final size:14
Alignment explanation
Indices: 313566--313607 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
313556 GACCCTAAAC
*
313566 CCAAATATGTAATT
1 CCAAATATTTAATT
313580 CCAAATATTTAATT
1 CCAAATATTTAATT
*
313594 CAAAATATTTAATT
1 CCAAATATTTAATT
313608 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (14 bp):
CCAAATATTTAATT
Found at i:313612 original size:8 final size:8
Alignment explanation
Indices: 313599--313627 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
313589 TAATTCAAAA
313599 TATTTAAT
1 TATTTAAT
313607 TATTTAAT
1 TATTTAAT
313615 TATTTAAT
1 TATTTAAT
313623 TATTT
1 TATTT
313628 GCAACTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTTAAT
Found at i:319764 original size:43 final size:43
Alignment explanation
Indices: 319697--319912 Score: 213
Period size: 43 Copynumber: 5.1 Consensus size: 43
319687 TACTGTTAGT
* * *
319697 GGCGTTTGT-AGAAAAACGCTGCTAAAGAACATGTTCTATAGC
1 GGCGTTTGTGAGAAAAGCGCAGCTAAAGACCATGTTCTATAGC
* * *
319739 GGCATTTGTGAGAAAAGCGCAGCTAAAGATCATGTTCTTTAGC
1 GGCGTTTGTGAGAAAAGCGCAGCTAAAGACCATGTTCTATAGC
* * * * * * * * *
319782 GGCGTTTTTGGGAAAAGCACCGGTAAATACCTTTTTCTTTAGC
1 GGCGTTTGTGAGAAAAGCGCAGCTAAAGACCATGTTCTATAGC
* * *
319825 GGCGTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTATAGC
1 GGCGTTTGTGAGAAAAGCGCAGCTAAAGACCATGTTCTATAGC
* * *
319868 GACGTTTTTG-GCAAAGCGCCA-CTAAAGACCATGTTCTATAGC
1 GGCGTTTGTGAGAAAAGCG-CAGCTAAAGACCATGTTCTATAGC
319910 GGC
1 GGC
319913 ATTTTCCCTC
Statistics
Matches: 143, Mismatches: 29, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
42 37 0.26
43 106 0.74
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
GGCGTTTGTGAGAAAAGCGCAGCTAAAGACCATGTTCTATAGC
Found at i:324592 original size:21 final size:21
Alignment explanation
Indices: 324568--324621 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
324558 CTTGTGACAG
*
324568 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* *
324589 TTCTACCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
324610 TTCTACCGATAC
1 TTCTACCGATAC
324622 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:334286 original size:9 final size:9
Alignment explanation
Indices: 334263--334322 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
334253 TTATAGGTAC
334263 TATTTTATT
1 TATTTTATT
334272 TA-TTTATT
1 TATTTTATT
334280 TATTTTATT
1 TATTTTATT
*
334289 TTTGTTTATT
1 TAT-TTTATT
*
334299 T-TTCATATT
1 TATT-TTATT
*
334308 TTTCTTTATT
1 TAT-TTTATT
334318 TATTT
1 TATTT
334323 AAAAATGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 9 0.21
9 18 0.43
10 14 0.33
11 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (9 bp):
TATTTTATT
Found at i:334298 original size:19 final size:19
Alignment explanation
Indices: 334274--334322 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
334264 ATTTTATTTA
*
334274 TTTATTTATTTTATTTTTG
1 TTTATTTATTTTATTTTTC
*
334293 TTTATTT-TTCATATTTTTC
1 TTTATTTATT-TTATTTTTC
334312 TTTATTTATTT
1 TTTATTTATTT
334323 AAAAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 21 0.84
20 2 0.08
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTATTTATTTTATTTTTC
Found at i:341540 original size:26 final size:26
Alignment explanation
Indices: 341483--341545 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
341473 TATAGCTCAT
* *
341483 ACGAGCTCAGT-CAGTAATTTGCTCTT
1 ACGAGCT-AGTACAATAATTTGCTCTC
* *
341509 ATGAGCTAGTACAATATTTTGCTCTC
1 ACGAGCTAGTACAATAATTTGCTCTC
*
341535 ACGAGCCAGTA
1 ACGAGCTAGTA
341546 TTGCTCTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (26 bp):
ACGAGCTAGTACAATAATTTGCTCTC
Found at i:341551 original size:19 final size:19
Alignment explanation
Indices: 341527--341567 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
341517 GTACAATATT
341527 TTGCTCTCACGAGCCAGTA
1 TTGCTCTCACGAGCCAGTA
*
341546 TTGCTCTTACGAGCCAGTA
1 TTGCTCTCACGAGCCAGTA
341565 TTG
1 TTG
341568 TTTATTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (19 bp):
TTGCTCTCACGAGCCAGTA
Found at i:345268 original size:20 final size:20
Alignment explanation
Indices: 345230--345268 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
345220 GTCAAATATA
* *
345230 TGCAGTCGAGCCACTATAAT
1 TGCAGTCAAGCCACCATAAT
*
345250 TGCAGTCAAGCTACCATAA
1 TGCAGTCAAGCCACCATAA
345269 CAAATATTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
TGCAGTCAAGCCACCATAAT
Found at i:347710 original size:40 final size:39
Alignment explanation
Indices: 347653--347745 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
347643 AGATTTTCTT
* * * *
347653 ACTCTTTCTTTCACTTTATCGAG-AAAAAATTGGTAAGAG
1 ACTCTTTCTTGCTCTTTATCG-GTAAAAAATTAGTAAAAG
*
347692 ACTCTTCTCTTGCTCTTTATTGGTAAAAAATTAGTAAAAG
1 ACTCTT-TCTTGCTCTTTATCGGTAAAAAATTAGTAAAAG
347732 -CT-TTTCTTGCTCTT
1 ACTCTTTCTTGCTCTT
347746 GCTCTTGCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
37 10 0.21
38 2 0.04
39 9 0.19
40 26 0.55
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (39 bp):
ACTCTTTCTTGCTCTTTATCGGTAAAAAATTAGTAAAAG
Found at i:351496 original size:59 final size:59
Alignment explanation
Indices: 351422--351556 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 59
351412 GATTTTTTTT
*
351422 AATTCATATTTTAATAATAATTACT-TTAAGA-ATGTTAATAAATTATATATTATTT-TTATCA
1 AATT-ATA-TTTAATAATAATTA-TGTTAAAATATGTT--TAAATTATATATTATTTATTATCA
* * *
351483 AATTGTATTTAATAATAATTATGTTAAAATATGTTTAAATTATTTATTATTTATTATTA
1 AATTATATTTAATAATAATTATGTTAAAATATGTTTAAATTATATATTATTTATTATCA
351542 AATTATATTTAATAA
1 AATTATATTTAATAA
351557 CTATCTTATT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
58 17 0.26
59 38 0.58
60 7 0.11
61 4 0.06
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (59 bp):
AATTATATTTAATAATAATTATGTTAAAATATGTTTAAATTATATATTATTTATTATCA
Found at i:351713 original size:44 final size:45
Alignment explanation
Indices: 351663--351749 Score: 117
Period size: 44 Copynumber: 1.9 Consensus size: 45
351653 CATCTATTTT
351663 ATTCAACCAAACACAAT-AA-TGCTT-TTACAACTCTATTCCATTCC
1 ATTCAACCAAACA-AATGAATTG-TTATTACAACTCTATTCCATTCC
*
351707 ATTCAACCAAACAATTGAATTGTTGATTACAACTCTATTCCAT
1 ATTCAACCAAACAAATGAATTGTT-ATTACAACTCTATTCCAT
351750 CACAGTCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
43 2 0.05
44 17 0.45
45 2 0.05
46 17 0.45
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (45 bp):
ATTCAACCAAACAAATGAATTGTTATTACAACTCTATTCCATTCC
Found at i:353398 original size:105 final size:104
Alignment explanation
Indices: 353212--353450 Score: 381
Period size: 105 Copynumber: 2.3 Consensus size: 104
353202 TTCTCATTTA
* * *
353212 ATACTCACAATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATATACTCACGATGA
1 ATACTCACGATGACACATAGTCATCGGACCCCATAATCCGTAAAGGATTCATATACTCACGATGA
*
353277 CACATAGTCATTAGACCTCGA-AATCCGTAAAAAGATTCAT
66 CACATAGTCATCAGACCT-GATAATCCGT-AAAAGATTCAT
353317 ATACTCACGATGACACATAGTCATCGGACCCCATAATCCGTAAAGGATTCATATACTCACGATGA
1 ATACTCACGATGACACATAGTCATCGGACCCCATAATCCGTAAAGGATTCATATACTCACGATGA
* * *
353382 CACATAGTCATCAGACCTTATAATTCGTAAAGGATTCAT
66 CACATAGTCATCAGACCTGATAATCCGTAAAAGATTCAT
*
353421 ATACTCACGATGACATATAGTCATCGGACC
1 ATACTCACGATGACACATAGTCATCGGACC
353451 TTTTGCATTT
Statistics
Matches: 125, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
104 40 0.32
105 85 0.68
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCGGACCCCATAATCCGTAAAGGATTCATATACTCACGATGA
CACATAGTCATCAGACCTGATAATCCGTAAAAGATTCAT
Found at i:353452 original size:52 final size:52
Alignment explanation
Indices: 353212--353451 Score: 374
Period size: 52 Copynumber: 4.6 Consensus size: 52
353202 TTCTCATTTA
*
353212 ATACTCACAATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
353264 ATACTCACGATGACACATAGTCATTAGACCTCGA-AATCCGTAAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTC-ATAATCCGT-AAAGGATTCAT
* *
353317 ATACTCACGATGACACATAGTCATCGGACCCCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
353369 ATACTCACGATGACACATAGTCATCAGACCTTATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
353421 ATACTCACGATGACATATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
353452 TTTGCATTTA
Statistics
Matches: 172, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
52 125 0.73
53 47 0.27
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:354955 original size:13 final size:14
Alignment explanation
Indices: 354937--354965 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
354927 AAATTAAATT
354937 AAAGTCC-AATTAC
1 AAAGTCCAAATTAC
354950 AAAGTCCAAATTAC
1 AAAGTCCAAATTAC
354964 AA
1 AA
354966 TGGCCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAGTCCAAATTAC
Found at i:355656 original size:24 final size:24
Alignment explanation
Indices: 355627--355672 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
355617 TTATATATTA
355627 AATAATTTCATTAATA-ATAATAAT
1 AATAATTTCATTAA-AGATAATAAT
*
355651 AATAATTTTATTAAAGATAATA
1 AATAATTTCATTAAAGATAATA
355673 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AATAATTTCATTAAAGATAATAAT
Found at i:355689 original size:18 final size:17
Alignment explanation
Indices: 355648--355690 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
355638 TAATAATAAT
355648 AATAATAAT-TTTATTA
1 AATAATAATATTTATTA
*
355664 AA-GATAATATTTATTA
1 AATAATAATATTTATTA
355680 AATAATTAATA
1 AATAA-TAATA
355691 ATATTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 1 0.05
18 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATAATAATATTTATTA
Found at i:356444 original size:29 final size:29
Alignment explanation
Indices: 356411--357056 Score: 568
Period size: 30 Copynumber: 22.2 Consensus size: 29
356401 TGAAAATTAT
*
356411 ATTTTTACCCCTGAACTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCC
* * *
356440 ATTTTCGACCTCGAAACTTCCAAAAATTCC
1 ATTTT-TACCCCTAAACTTCCAAAAATTCC
* * *
356470 ATTTTCGACCCCAAAACCTCCAAAAATTCC
1 ATTTT-TACCCCTAAACTTCCAAAAATTCC
* *
356500 ATTTTTACCCCAAAATTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCC
* *
356529 TTTTTTAACCAC-ATAACTTCCAAAAATTCC
1 ATTTTT-ACCCCTA-AACTTCCAAAAATTCC
* *
356559 ATTTTTACCCCCAAACTTCTAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCC
* *
356588 A-TTTT----C--GAC-CCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCC
* * **
356609 ACTTTTACCCTC-AAATTTCCAAATTTTCC
1 ATTTTTACCC-CTAAACTTCCAAAAATTCC
* *
356638 ATTTTTAACCCTAAAACTTCCAAAAATTTC
1 ATTTTTACCCCT-AAACTTCCAAAAATTCC
356668 ATTTTTACCCCTAAACTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCC
* *
356697 ATTTTTGA-CACTAAACTTTCAAAAATTCC
1 ATTTTT-ACCCCTAAACTTCCAAAAATTCC
* *
356726 ATTTTTGA-CACTAAACTTTCAAAAATTCC
1 ATTTTT-ACCCCTAAACTTCCAAAAATTCC
* *
356755 ATTTTTAACCCCAAAACTTCTAAAAATTCC
1 ATTTTT-ACCCCTAAACTTCCAAAAATTCC
* *
356785 ATTTTTGACCCCAAAACTTTCAAAAATTCC
1 ATTTTT-ACCCCTAAACTTCCAAAAATTCC
* * * *
356815 ATTTTTGACCTCGAAACTTCAAAAAAATCC
1 ATTTTT-ACCCCTAAACTTCCAAAAATTCC
*
356845 AATTTTACCCC-AAACTTCCAAAAATTCC
1 ATTTTTACCCCTAAACTTCCAAAAATTCC
** *
356873 ATTTTTGGCCTTGAAACTTCCAAAAATTCC
1 ATTTTTACCCCT-AAACTTCCAAAAATTCC
** *
356903 ATTTTTGGCCTTGAAACTTCCAAAAATTCC
1 ATTTTTACCCCT-AAACTTCCAAAAATTCC
*
356933 ATTTTTA-CCCTCGAACTTCCAAAAATTCC
1 ATTTTTACCCCT-AAACTTCCAAAAATTCC
* *
356962 ATTTTTAGCCCCGAAACTTCAAAAAATTCC
1 ATTTTTA-CCCCTAAACTTCCAAAAATTCC
* *
356992 ATTTTTA-CCCTCGAA-TGTCTAAAAATTCC
1 ATTTTTACCCCT-AAACT-TCCAAAAATTCC
* * ** *
357021 ATTTTAACCCCGAATTTTCCCAAAATTACC
1 ATTTTTACCCCTAAACTTCCAAAAATT-CC
357051 ATTTTT
1 ATTTTT
357057 CCCTCGAAAA
Statistics
Matches: 520, Mismatches: 72, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
21 11 0.02
22 6 0.01
24 1 0.00
27 1 0.00
28 32 0.06
29 204 0.39
30 262 0.50
31 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTTTTACCCCTAAACTTCCAAAAATTCC
Found at i:356523 original size:59 final size:59
Alignment explanation
Indices: 356411--357056 Score: 592
Period size: 59 Copynumber: 11.1 Consensus size: 59
356401 TGAAAATTAT
** * *
356411 ATTTTT-ACCCCTGAACTTCCAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTT-TACCCCGAAACTTCCAAAAATTCC
* * * *
356470 ATTTTCGACCCCAAAACCTCCAAAAATTCCATTTTTACCCCAAAATTTCCAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCC
* * * * * *
356529 TTTTTTAACCACATAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCC
* * * **
356588 ATTTTCGA---C----C--CCAAAAATTCCACTTTTACCCTC-AAATTTCCAAATTTTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCC-CGAAACTTCCAAAAATTCC
* * * *
356638 ATTTTTAACCCTAAAACTTCCAAAAATTTCATTTTTACCCCTAAACTTCCAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCC
* * * * * *
356697 ATTTTTGA-CACTAAACTTTCAAAAATTCCATTTTTGA-CACTAAACTTTCAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAATTCC
* * * *
356755 ATTTTTAACCCCAAAACTTCTAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAATTCC
* * * * *
356815 ATTTTTGACCTCGAAACTTCAAAAAAATCCAATTTTACCCC-AAACTTCCAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCC
* *** * **
356873 ATTTTTGGCCTTGAAACTTCCAAAAATTCCATTTTTGGCCTTGAAACTTCCAAAAATTCC
1 ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAATTCC
* *
356933 ATTTTT-ACCCTC-GAACTTCCAAAAATTCCATTTTTAGCCCCGAAACTTCAAAAAATTCC
1 ATTTTTGACCC-CAAAACTTCCAAAAATTCCATTTTTA-CCCCGAAACTTCCAAAAATTCC
* * * ** *
356992 ATTTTT-ACCCTC-GAA-TGTCTAAAAATTCCATTTTAACCCCGAATTTTCCCAAAATTACC
1 ATTTTTGACCC-CAAAACT-TCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATT-CC
357051 ATTTTT
1 ATTTTT
357057 CCCTCGAAAA
Statistics
Matches: 489, Mismatches: 77, Indels: 42
0.80 0.13 0.07
Matches are distributed among these distances:
50 39 0.08
51 1 0.00
52 1 0.00
56 1 0.00
57 1 0.00
58 113 0.23
59 236 0.48
60 97 0.20
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (59 bp):
ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCC
Found at i:356607 original size:50 final size:50
Alignment explanation
Indices: 356548--356642 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
356538 CACATAACTT
* *
356548 CCAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATTCCATTTTCGACC
1 CCAAAAATTCCACTTTTACCCCCAAACTTCCAAAAATTCCATTTTCGACC
* * **
356598 CCAAAAATTCCACTTTTACCCTCAAATTTCCAAATTTTCCATTTT
1 CCAAAAATTCCACTTTTACCCCCAAACTTCCAAAAATTCCATTTT
356643 TAACCCTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.33, C:0.31, G:0.01, T:0.36
Consensus pattern (50 bp):
CCAAAAATTCCACTTTTACCCCCAAACTTCCAAAAATTCCATTTTCGACC
Found at i:356618 original size:20 final size:21
Alignment explanation
Indices: 356579--356623 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
356569 CCAAACTTCT
356579 AAAAATTCCATTTTCGACCC-C
1 AAAAATTCCATTTTC-ACCCTC
356600 AAAAATTCCACTTTT-ACCCTC
1 AAAAATTCCA-TTTTCACCCTC
356621 AAA
1 AAA
356624 TTTCCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATTCCATTTTCACCCTC
Found at i:356659 original size:50 final size:50
Alignment explanation
Indices: 356548--356659 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 50
356538 CACATAACTT
* * *
356548 CCAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATTCCATTTTCGACC
1 CCAAAAATTCCACTTTTACCCCCAAACTTCCAAAAATTCCATTTTCAACC
* * ** *
356598 CCAAAAATTCCACTTTTACCCTCAAATTTCCAAATTTTCCATTTTTAACC
1 CCAAAAATTCCACTTTTACCCCCAAACTTCCAAAAATTCCATTTTCAACC
* *
356648 CTAAAACTTCCA
1 CCAAAAATTCCA
356660 AAAATTTCAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.34
Consensus pattern (50 bp):
CCAAAAATTCCACTTTTACCCCCAAACTTCCAAAAATTCCATTTTCAACC
Found at i:360393 original size:24 final size:24
Alignment explanation
Indices: 360375--360473 Score: 162
Period size: 24 Copynumber: 4.1 Consensus size: 24
360365 AGTTTTACTC
*
360375 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
360399 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
360423 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* * *
360447 AAACAATTAAATAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
360471 AAA
1 AAA
360474 GATTATTTCT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:360427 original size:48 final size:48
Alignment explanation
Indices: 360363--360473 Score: 168
Period size: 48 Copynumber: 2.3 Consensus size: 48
360353 TAGACTAATA
* *
360363 AGAGTTTTACTCAAACAAATAAACAAAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAACAAAGTTTAATTGAAACAAATAAAC
* * * *
360411 AGAGTTTAATTGAAACAAATAAACAGAGTTTAATTGAAACAATTAAAT
1 AGAGTTTAACTGAAACAAATAAACAAAGTTTAATTGAAACAAATAAAC
360459 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
360474 GATTATTTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (48 bp):
AGAGTTTAACTGAAACAAATAAACAAAGTTTAATTGAAACAAATAAAC
Found at i:362465 original size:24 final size:24
Alignment explanation
Indices: 362404--362466 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
362394 TAGACTAATA
* *
362404 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
362428 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
362452 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
362467 TATTATTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:364127 original size:20 final size:21
Alignment explanation
Indices: 364094--364159 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 21
364084 TCTTTTTCAA
364094 CAAAAATTACAAAATAATTTT
1 CAAAAATTACAAAATAATTTT
*
364115 CAAAAATT-TAAAATAATTTT
1 CAAAAATTACAAAATAATTTT
* *
364135 -TAAAA-TCCAAAAT-ATTTT
1 CAAAAATTACAAAATAATTTT
*
364153 TAAAAAT
1 CAAAAAT
364160 CCAAAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.16
19 13 0.34
20 11 0.29
21 8 0.21
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (21 bp):
CAAAAATTACAAAATAATTTT
Done.