Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397287.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_302.0, 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: 796134
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1883 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:910 original size:17 final size:17
Alignment explanation
Indices: 888--923 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
878 AGAATAAAGA
888 ATGGCAATAAATGCTTC
1 ATGGCAATAAATGCTTC
905 ATGGCAATAAATGCTTC
1 ATGGCAATAAATGCTTC
922 AT
1 AT
924 CCATCTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (17 bp):
ATGGCAATAAATGCTTC
Found at i:9585 original size:90 final size:90
Alignment explanation
Indices: 9421--9595 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 90
9411 AAGTTTTGAA
* * *
9421 ATTATTTTGTTTTCATTATCGTCAAGTTTCAAAAGGATTTCAATAATTTGGTTTTAATTTATAGT
1 ATTATTTTGTTTTCATCATCGTCAAGTTTCAAAAAGATTTCAATAAGTTGGTTTTAATTTATAGT
* * * *
9486 TTTAGCAAATTAAGTAAGTGTTGCT
66 TGTAACAAATAAAATAAGTGTTGCT
* * *
9511 ATTATTTTGTTTTCATCATC-TCCAAGCTTT-AAAAAGATTTCAAT-GGTTGATTTTTAATTTTT
1 ATTATTTTGTTTTCATCATCGT-CAAG-TTTCAAAAAGATTTCAATAAGTTG-GTTTTAATTTAT
*
9573 GGTTGTAACAAATAAAATAAGTG
63 AGTTGTAACAAATAAAATAAGTG
9596 ACTTAAAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
89 4 0.06
90 64 0.90
91 3 0.04
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (90 bp):
ATTATTTTGTTTTCATCATCGTCAAGTTTCAAAAAGATTTCAATAAGTTGGTTTTAATTTATAGT
TGTAACAAATAAAATAAGTGTTGCT
Found at i:10131 original size:26 final size:24
Alignment explanation
Indices: 10088--10144 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
10078 AGATACTTTA
*
10088 ATATGTTCTTATTATATTTAAATG
1 ATATATTCTTATTATATTTAAATG
* *
10112 ATATATTCTTATTATGTATTTTAATT
1 ATATATTCTTATTA--TATTTAAATG
10138 ATATATT
1 ATATATT
10145 TAATGTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 13 0.46
26 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (24 bp):
ATATATTCTTATTATATTTAAATG
Found at i:10140 original size:24 final size:22
Alignment explanation
Indices: 10084--10141 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
10074 ATGAAGATAC
*
10084 TTTAA-TATGTTCTTATTATAT
1 TTTAATTATATTCTTATTATAT
*
10105 TTAAATGATATATTCTTATTATGTAT
1 TTTAAT--TATATTCTTATTA--TAT
10131 TTTAATTATAT
1 TTTAATTATAT
10142 ATTTAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.14
24 17 0.59
26 8 0.28
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTAATTATATTCTTATTATAT
Found at i:13484 original size:90 final size:89
Alignment explanation
Indices: 13313--13486 Score: 217
Period size: 90 Copynumber: 1.9 Consensus size: 89
13303 AAGTTTTGAA
13313 ATTATTTTATTTTCATCATCTTCAAGCTTAAAAGGATTTCAATTATTCGGTTTTAAATTATAGTT
1 ATTATTTTATTTTCATCATCTTCAAGCTTAAAAGGATTTCAATTATTCGGTTTTAAATTATAGTT
** * * *
13378 TTAGCAAATTAGGTAAGTGTTTCT
66 GGAACAAATCAAGTAAGTGTTTCT
* * * * *
13402 ATTATTTTGTTTTCATCATCTTTAAGCTTTAAAAGGATTTCAA-TAGTT-GGTCTTTAATTTTTG
1 ATTATTTTATTTTCATCATCTTCAAGC-TTAAAAGGATTTCAATTA-TTCGGT-TTTAAATTATA
13465 GTTGGAACAAATCAAGTAAGTG
63 GTTGGAACAAATCAAGTAAGTG
13487 AATTAAAAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
89 30 0.42
90 42 0.58
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (89 bp):
ATTATTTTATTTTCATCATCTTCAAGCTTAAAAGGATTTCAATTATTCGGTTTTAAATTATAGTT
GGAACAAATCAAGTAAGTGTTTCT
Found at i:21968 original size:7 final size:7
Alignment explanation
Indices: 21956--21982 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
21946 ATTAAACATG
21956 TCCATAC
1 TCCATAC
21963 TCCATAC
1 TCCATAC
21970 TCCATAC
1 TCCATAC
21977 TCCATA
1 TCCATA
21983 TGCATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (7 bp):
TCCATAC
Found at i:23451 original size:13 final size:13
Alignment explanation
Indices: 23433--23461 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
23423 GTTTACATAG
23433 TTTCCAACAGAAT
1 TTTCCAACAGAAT
23446 TTTCCAACAGAAT
1 TTTCCAACAGAAT
23459 TTT
1 TTT
23462 TCGTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (13 bp):
TTTCCAACAGAAT
Found at i:28014 original size:2 final size:2
Alignment explanation
Indices: 28007--28046 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27997 TGGTGATTCA
28007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28047 CTCAGCCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28907 original size:21 final size:22
Alignment explanation
Indices: 28881--28922 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28871 AAGCCATAAA
28881 AAGGAAG-GAAGTATGGGGAAG
1 AAGGAAGAGAAGTATGGGGAAG
28902 AAGGAAGAGAAGTATGGGGAA
1 AAGGAAGAGAAGTATGGGGAA
28923 AAGTATGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.10
Consensus pattern (22 bp):
AAGGAAGAGAAGTATGGGGAAG
Found at i:38156 original size:2 final size:2
Alignment explanation
Indices: 38149--38173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38139 GAGTTTTTAT
38149 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38174 GACTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44071 original size:14 final size:15
Alignment explanation
Indices: 44052--44091 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
44042 ACTCACAACT
44052 TTTTGTTTTTTTGG-
1 TTTTGTTTTTTTGGC
*
44066 TTTTGTTTCTTTGGC
1 TTTTGTTTTTTTGGC
44081 TTTT-TTTTTTT
1 TTTTGTTTTTTT
44092 ACTTCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (15 bp):
TTTTGTTTTTTTGGC
Found at i:49251 original size:3 final size:3
Alignment explanation
Indices: 49243--49269 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49233 ACATCATTTA
49243 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
49270 GTTTACCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55676 original size:2 final size:2
Alignment explanation
Indices: 55669--55704 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
55659 CAAGACTTTC
55669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55705 ATAGAACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60579 original size:2 final size:2
Alignment explanation
Indices: 60574--60601 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60564 AACAAAAAAC
60574 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
60602 GGAGGGAGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61887 original size:3 final size:3
Alignment explanation
Indices: 61879--61903 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
61869 ATTTGTTTGG
61879 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
61904 TTGTAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:68976 original size:15 final size:15
Alignment explanation
Indices: 68956--68988 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
68946 AAAAATTGAA
68956 AAGATAGCACTTTTT
1 AAGATAGCACTTTTT
68971 AAGATAGCACTTTTT
1 AAGATAGCACTTTTT
68986 AAG
1 AAG
68989 GTTTTAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (15 bp):
AAGATAGCACTTTTT
Found at i:75112 original size:20 final size:21
Alignment explanation
Indices: 75087--75125 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
75077 ATTGAGATTA
*
75087 TTTTT-AATAAATAAAAATAT
1 TTTTTAAATAAAAAAAAATAT
75107 TTTTTAAATAAAAAAAAAT
1 TTTTTAAATAAAAAAAAAT
75126 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTTAAATAAAAAAAAATAT
Found at i:75171 original size:23 final size:24
Alignment explanation
Indices: 75128--75174 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
75118 AAAAAAATTT
*
75128 AAAAAATAAAACATGTTTTCTTTA
1 AAAAAAGAAAACATGTTTTCTTTA
75152 AAAAAAGAAAA-A-GTTCTTCTTTA
1 AAAAAAGAAAACATGTT-TTCTTTA
75175 GAGCTTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 8 0.38
24 10 0.48
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (24 bp):
AAAAAAGAAAACATGTTTTCTTTA
Found at i:94216 original size:2 final size:2
Alignment explanation
Indices: 94211--94261 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
94201 TTGAACTTAC
94211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94253 AT AT AT AT A
1 AT AT AT AT A
94262 AATGGTTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:102845 original size:55 final size:55
Alignment explanation
Indices: 102761--102872 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
102751 TTGCTTACTA
102761 ATAAGATTTTCTTGTAAGTTAAAGCTAATTTGGGAGTTGGTATAGGAGATGGATC
1 ATAAGATTTTCTTGTAAGTTAAAGCTAATTTGGGAGTTGGTATAGGAGATGGATC
* *
102816 ATAAGATTTTCTTGTAAGTTAAAGCTAATTTGGGAGTTGTTATAGGTGATGGATC
1 ATAAGATTTTCTTGTAAGTTAAAGCTAATTTGGGAGTTGGTATAGGAGATGGATC
102871 AT
1 AT
102873 CTATTTCATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.38
Consensus pattern (55 bp):
ATAAGATTTTCTTGTAAGTTAAAGCTAATTTGGGAGTTGGTATAGGAGATGGATC
Found at i:103135 original size:26 final size:26
Alignment explanation
Indices: 103099--103152 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
103089 GTAAGAGATT
*
103099 CAAGGATGAAATAATATGGATAGCTA
1 CAAGGATGAAATAATATGGAAAGCTA
103125 CAAGGATGAAATAATATGGAAAGCTA
1 CAAGGATGAAATAATATGGAAAGCTA
103151 CA
1 CA
103153 CCTAGTACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.20
Consensus pattern (26 bp):
CAAGGATGAAATAATATGGAAAGCTA
Found at i:117912 original size:2 final size:2
Alignment explanation
Indices: 117905--117938 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
117895 GTGGCAGTAG
117905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117939 GAAAGTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:125766 original size:20 final size:20
Alignment explanation
Indices: 125741--125803 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
125731 CTCCACCTAT
125741 TTTCCAACACCTTGAACAAC
1 TTTCCAACACCTTGAACAAC
*
125761 TTTCCAAGCA---T-AAGAA-
1 TTTCCAA-CACCTTGAACAAC
*
125777 TTTCCAATACCTTGAACAAC
1 TTTCCAACACCTTGAACAAC
*
125797 TCTCCAA
1 TTTCCAA
125804 ACACAAGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
15 1 0.03
16 7 0.21
17 4 0.12
18 2 0.06
19 4 0.12
20 13 0.39
21 2 0.06
ACGTcount: A:0.37, C:0.30, G:0.06, T:0.27
Consensus pattern (20 bp):
TTTCCAACACCTTGAACAAC
Found at i:127556 original size:12 final size:12
Alignment explanation
Indices: 127535--127569 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
127525 TTACTCATAT
*
127535 ATATATATATAC
1 ATATACATATAC
127547 ATATACATATAC
1 ATATACATATAC
*
127559 TTATACATATA
1 ATATACATATA
127570 TGTAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATACATATAC
Found at i:128288 original size:47 final size:47
Alignment explanation
Indices: 128220--128320 Score: 193
Period size: 47 Copynumber: 2.1 Consensus size: 47
128210 AATTGTATAT
128220 AAAAAAATTTATTATAACTTAGAATAATTTGTGTCTTTAGGTGAGGA
1 AAAAAAATTTATTATAACTTAGAATAATTTGTGTCTTTAGGTGAGGA
*
128267 AAAAAAATTTGTTATAACTTAGAATAATTTGTGTCTTTAGGTGAGGA
1 AAAAAAATTTATTATAACTTAGAATAATTTGTGTCTTTAGGTGAGGA
128314 AAAAAAA
1 AAAAAAA
128321 AAGAGAGAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.36
Consensus pattern (47 bp):
AAAAAAATTTATTATAACTTAGAATAATTTGTGTCTTTAGGTGAGGA
Found at i:131979 original size:20 final size:19
Alignment explanation
Indices: 131954--131997 Score: 79
Period size: 20 Copynumber: 2.3 Consensus size: 19
131944 AAATAAACAA
131954 TGAAATGTTGTATTTCATG
1 TGAAATGTTGTATTTCATG
131973 TTGAAATGTTGTATTTCATG
1 -TGAAATGTTGTATTTCATG
131993 TGAAA
1 TGAAA
131998 AAGTGTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (19 bp):
TGAAATGTTGTATTTCATG
Found at i:132120 original size:12 final size:12
Alignment explanation
Indices: 132103--132134 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
132093 TTAATTTGGA
132103 TCTCTCTCTCTG
1 TCTCTCTCTCTG
132115 TCTCTCTCTCTG
1 TCTCTCTCTCTG
132127 TCTCTCTC
1 TCTCTCTC
132135 ATTGGCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (12 bp):
TCTCTCTCTCTG
Found at i:137352 original size:14 final size:15
Alignment explanation
Indices: 137313--137345 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
137303 TATACAAACT
*
137313 TTGTAATATATAACA
1 TTGTAACATATAACA
137328 TTGTAACATATAA-A
1 TTGTAACATATAACA
137342 TTGT
1 TTGT
137346 GTCATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (15 bp):
TTGTAACATATAACA
Found at i:140880 original size:54 final size:54
Alignment explanation
Indices: 140723--140880 Score: 169
Period size: 53 Copynumber: 2.9 Consensus size: 54
140713 TTTTCAATCA
** * * * *
140723 TTGGAAAATTATTTCCAA-TGGAAAATTCCATTGGAAATATCCAACGGAATTCTG
1 TTGGAAAAGAATTTCCAACT-GAAAATTTCGTTGGAAATTTCCAACGGAATTCCG
* * * *
140777 TTTGAAAAGAATTTGCAAC--AAAATTTTTGTTGAAAATTTCCAACGGAATTCCG
1 TTGGAAAAGAATTTCCAACTGAAAA-TTTCGTTGGAAATTTCCAACGGAATTCCG
* *
140830 TTGGAAAAGCATTTCCAACTGAAAATTTCGTTGGAAATTTCCAACAGAATT
1 TTGGAAAAGAATTTCCAACTGAAAATTTCGTTGGAAATTTCCAACGGAATT
140881 ACTACGAGAT
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
52 4 0.05
53 39 0.46
54 37 0.44
55 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (54 bp):
TTGGAAAAGAATTTCCAACTGAAAATTTCGTTGGAAATTTCCAACGGAATTCCG
Found at i:146655 original size:25 final size:25
Alignment explanation
Indices: 146627--146721 Score: 84
Period size: 25 Copynumber: 3.7 Consensus size: 25
146617 TGACTGTAAT
* *
146627 ATTTTTTGAATATGATGTGTAATAA
1 ATTTTTTTAATATAATGTGTAATAA
* **
146652 ATTTTTTAAATATAACATGTAATAA
1 ATTTTTTTAATATAATGTGTAATAA
* *
146677 TTTGTTTTCTATTATAATGTGTAAT-A
1 ATT-TTTT-TAATATAATGTGTAATAA
*
146703 ATTTTTCTTAATATGATGT
1 ATTTTT-TTAATATAATGT
146722 AAAATAATAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
25 35 0.64
26 8 0.15
27 12 0.22
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.52
Consensus pattern (25 bp):
ATTTTTTTAATATAATGTGTAATAA
Found at i:146684 original size:27 final size:27
Alignment explanation
Indices: 146644--146706 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
146634 GAATATGATG
* *
146644 TGTAATAAATT-TTTT-AAATATAACA
1 TGTAATAATTTGTTTTCTAATATAACA
* **
146669 TGTAATAATTTGTTTTCTATTATAATG
1 TGTAATAATTTGTTTTCTAATATAACA
146696 TGTAATAATTT
1 TGTAATAATTT
146707 TTCTTAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 10 0.32
26 4 0.13
27 17 0.55
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (27 bp):
TGTAATAATTTGTTTTCTAATATAACA
Found at i:156693 original size:175 final size:174
Alignment explanation
Indices: 156394--156744 Score: 569
Period size: 175 Copynumber: 2.0 Consensus size: 174
156384 TTACCATCTA
* * *
156394 TTTTGTTCTTATTTGGACTTCTTTAGTGTCTGAGTTTTGAAACTGTAAATTTCATGATGGAAAAA
1 TTTTGTTCTTATTTGGACTTCTATAGTGTCTAAGTTTTGAAACTGTAAATTTCATGAAGGAAAAA
* *
156459 GGGGCCGCTAAATGATAACTCAATGAAGCACAAACTAATGGCTGTATATTAATCAAATATGCCCC
66 GGGGCCACTAAATGACAACTCAATGAAGCACAAACTAATGGCTGTATATTAATCAAATATGCCCC
* *
156524 AAAAGTCAAATTTGTAGGC-ATTCAAAAGTTAGTGAAGTTAAGAG
131 AAAAGTCAAATTTGTAGGCGA-TCAAAACTTAGTGAAGTTAACAG
*
156568 TTTTGTTCTTTATTTGGACTTCTATAGTGTCTAAGTTTTGAAACTGTAAATTTCATGAAGGATAA
1 TTTTGTTC-TTATTTGGACTTCTATAGTGTCTAAGTTTTGAAACTGTAAATTTCATGAAGGAAAA
* * *
156633 GGGGGCCACTAAATGACAACTCAATGAAGCACAAACTAATTGCTTTATATTAATCAAATATGCCC
65 AGGGGCCACTAAATGACAACTCAATGAAGCACAAACTAATGGCTGTATATTAATCAAATATGCCC
*
156698 CAAAAGTCAAATTTGTAGGCGATCAAAACTTGGTGAAGTTAACAG
130 CAAAAGTCAAATTTGTAGGCGATCAAAACTTAGTGAAGTTAACAG
156743 TT
1 TT
156745 GCAATGCTAG
Statistics
Matches: 163, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
174 8 0.05
175 154 0.94
176 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (174 bp):
TTTTGTTCTTATTTGGACTTCTATAGTGTCTAAGTTTTGAAACTGTAAATTTCATGAAGGAAAAA
GGGGCCACTAAATGACAACTCAATGAAGCACAAACTAATGGCTGTATATTAATCAAATATGCCCC
AAAAGTCAAATTTGTAGGCGATCAAAACTTAGTGAAGTTAACAG
Found at i:158748 original size:21 final size:21
Alignment explanation
Indices: 158718--158760 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
158708 TTGGTGTAAT
* *
158718 TTGACTGTTAAGAAGATGATG
1 TTGACCGTTAAAAAGATGATG
158739 TTGACCGTTAAAAAGATGATG
1 TTGACCGTTAAAAAGATGATG
158760 T
1 T
158761 GGTAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGACCGTTAAAAAGATGATG
Found at i:177256 original size:19 final size:21
Alignment explanation
Indices: 177224--177266 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
177214 AATGTGTAAA
*
177224 ATATAAATAGTTAAAAATGAT
1 ATATAAATAGTTAAAAATAAT
*
177245 ATATAAA-A-TTAATAATAAT
1 ATATAAATAGTTAAAAATAAT
177264 ATA
1 ATA
177267 AATTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 1 0.05
21 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
ATATAAATAGTTAAAAATAAT
Found at i:179295 original size:2 final size:2
Alignment explanation
Indices: 179288--179318 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
179278 GAACGAATGT
179288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
179319 GTTTGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:179677 original size:81 final size:80
Alignment explanation
Indices: 179590--179771 Score: 186
Period size: 81 Copynumber: 2.2 Consensus size: 80
179580 AACAAATCAA
* * * * **
179590 GGTTAAAAAAAGTTGTTACATATTATGTT-GAAATAATATATTATTGTTATACGTCATGTACAAA
1 GGTTAAAAAAA-TTGTTACATATCATATTAAAAAAAATATATTATTGTTATACACCAT-TACAAA
***
179654 AACATATTACATGTCAT
64 AACATATTACACACCAT
* * * * *
179671 GGTTAAAAAAAATTATTAAATGTCATATTAAAAAAAATATATTGTTGTTATACACCATTATAAAA
1 GGTT-AAAAAAATTGTTACATATCATATTAAAAAAAATATATTATTGTTATACACCATTACAAAA
* *
179736 ACATGTTATACACCAT
65 ACATATTACACACCAT
179752 GGTTAAAAAAATTGTTACAT
1 GGTTAAAAAAATTGTTACAT
179772 GCTATTTTAA
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
80 14 0.17
81 37 0.46
82 30 0.37
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (80 bp):
GGTTAAAAAAATTGTTACATATCATATTAAAAAAAATATATTATTGTTATACACCATTACAAAAA
CATATTACACACCAT
Found at i:179701 original size:25 final size:27
Alignment explanation
Indices: 179651--179713 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
179641 CGTCATGTAC
* * *
179651 AAAAACATATTACATGTCATGGTTAAA
1 AAAAATATATTAAATGTCATGATTAAA
179678 AAAAAT-TATTAAATGTCAT-ATTAAA
1 AAAAATATATTAAATGTCATGATTAAA
179703 AAAAATATATT
1 AAAAATATATT
179714 GTTGTTATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.34
26 16 0.50
27 5 0.16
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (27 bp):
AAAAATATATTAAATGTCATGATTAAA
Found at i:179767 original size:25 final size:24
Alignment explanation
Indices: 179715--179768 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
179705 AAATATATTG
*
179715 TTGTTATACACCATTATAAAAACA
1 TTGTTATACACCATTATAAAAAAA
179739 -TGTTATACACCATGGT-TAAAAAAA
1 TTGTTATACACCAT--TATAAAAAAA
179763 TTGTTA
1 TTGTTA
179769 CATGCTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 13 0.50
24 7 0.27
25 6 0.23
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (24 bp):
TTGTTATACACCATTATAAAAAAA
Found at i:180144 original size:2 final size:2
Alignment explanation
Indices: 180137--180163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
180127 GTTAATTGAA
180137 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
180164 GTGTTAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:183557 original size:18 final size:18
Alignment explanation
Indices: 183515--183550 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
183505 TCAAGTGCAA
183515 AAAAAAAAAATGATTTTT
1 AAAAAAAAAATGATTTTT
183533 AAAAAAAAAATGATTTTT
1 AAAAAAAAAATGATTTTT
183551 TTTAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
AAAAAAAAAATGATTTTT
Found at i:184503 original size:34 final size:34
Alignment explanation
Indices: 184451--184549 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 34
184441 TGCTACACAC
* * *
184451 CAAAACTTCAGCAGCAAATGTTACATGCCAAGGT
1 CAAAACTTTAGCACCAAATGTTACATGCCAAAGT
* *
184485 CAAAACTTTAACACCAAATGTTACATACCAAAGT
1 CAAAACTTTAGCACCAAATGTTACATGCCAAAGT
* * *
184519 C-AAAGTTTCAGCATCAGATGTTACATGCCAA
1 CAAAACTTT-AGCACCAAATGTTACATGCCAA
184550 TGCCATAGCT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 6 0.11
34 48 0.89
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (34 bp):
CAAAACTTTAGCACCAAATGTTACATGCCAAAGT
Found at i:188763 original size:17 final size:18
Alignment explanation
Indices: 188740--188781 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
188730 TTGAACGTAA
188740 AAAATAA-TAATTTTTTT
1 AAAATAATTAATTTTTTT
*
188757 GAAATAATTTAATTTTTTT
1 AAAATAA-TTAATTTTTTT
188776 AAAATA
1 AAAATA
188782 GTATGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
19 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AAAATAATTAATTTTTTT
Found at i:189028 original size:21 final size:23
Alignment explanation
Indices: 188998--189042 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
188988 GGTAATATTA
*
188998 AAAAAATATT-TTTTA-AATTTT
1 AAAAAATATTATTATATAATTTT
*
189019 AAAAATTATTATTATATAATTTT
1 AAAAAATATTATTATATAATTTT
189042 A
1 A
189043 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAAAATATTATTATATAATTTT
Found at i:205852 original size:21 final size:22
Alignment explanation
Indices: 205818--205864 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
205808 AATTATAAAC
*
205818 TTTATGTTATATAAAAATATT-T
1 TTTATATTATATAAAAAT-TTGT
205840 TTTATATT-TATAAAAATTTGT
1 TTTATATTATATAAAAATTTGT
205861 TTTA
1 TTTA
205865 AATAGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 2 0.09
21 14 0.61
22 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTATATTATATAAAAATTTGT
Found at i:206475 original size:20 final size:20
Alignment explanation
Indices: 206450--206487 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
206440 AATCGATGAA
*
206450 ATCTATCAATAGATTTGGTC
1 ATCTATCAATAAATTTGGTC
*
206470 ATCTATCGATAAATTTGG
1 ATCTATCAATAAATTTGG
206488 CAATGTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (20 bp):
ATCTATCAATAAATTTGGTC
Found at i:208291 original size:4 final size:4
Alignment explanation
Indices: 208282--208308 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
208272 GCTATTGAAT
208282 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
208309 TACCATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:210076 original size:2 final size:2
Alignment explanation
Indices: 210069--210106 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
210059 AAGTTCATAC
210069 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
210107 ATGTTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215076 original size:20 final size:20
Alignment explanation
Indices: 215048--215089 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
215038 AAAGTAATTA
**
215048 TATTCAACAGTTCATAATATG
1 TATTCAACAAATCA-AATATG
215069 TATT-AACAAATCAAATATG
1 TATTCAACAAATCAAATATG
215088 TA
1 TA
215090 ACACTAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 7 0.37
21 4 0.21
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (20 bp):
TATTCAACAAATCAAATATG
Found at i:217419 original size:7 final size:7
Alignment explanation
Indices: 217407--217437 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
217397 AAAAGGTTTT
217407 GAGCAGA
1 GAGCAGA
217414 GAGCAGA
1 GAGCAGA
217421 GAGCAGA
1 GAGCAGA
217428 GAGCAGA
1 GAGCAGA
217435 GAG
1 GAG
217438 AGGAAGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.45, T:0.00
Consensus pattern (7 bp):
GAGCAGA
Found at i:225730 original size:36 final size:36
Alignment explanation
Indices: 225683--225758 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
225673 CTTGCATTTA
* *
225683 GCTTAGGAAAATATTTTACCTTGATTCATTATTTTT
1 GCTTAGGAAAATATTATACCTTGATTCATTATTTGT
*
225719 GCTTAGGAAAATATTATATCTTGATTCATTATTTGT
1 GCTTAGGAAAATATTATACCTTGATTCATTATTTGT
225755 GCTT
1 GCTT
225759 GTACTTAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.49
Consensus pattern (36 bp):
GCTTAGGAAAATATTATACCTTGATTCATTATTTGT
Found at i:225811 original size:47 final size:47
Alignment explanation
Indices: 225720--225901 Score: 233
Period size: 47 Copynumber: 3.9 Consensus size: 47
225710 ATTATTTTTG
* * * * *
225720 CTTAGGAAAATA-TTATA-TCTTGATTCATTATTTGTGCTTGTACTTAA
1 CTTAGGAAAATATTTTTACT-TTGATTTATTATTTGTTCAT-TACTTGA
*
225767 CCTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATTACTTGA
1 CTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATTACTTGA
* **
225814 CTTGGGAAAATATTTTTACTTTGATTTATTATTTGCCCATTACTTGA
1 CTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATTACTTGA
* *
225861 CTTAAGAAAATATCTTTACTTTGATTTATTATTTGTTCATT
1 CTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATT
225902 TCAATTTATT
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
47 96 0.81
48 21 0.18
49 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (47 bp):
CTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCATTACTTGA
Found at i:226119 original size:19 final size:19
Alignment explanation
Indices: 226095--226132 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
226085 TCATTTTCAC
226095 ATTTG-CTTTCTCTCTACTT
1 ATTTGCCTTTCTC-CTACTT
226114 ATTTGCCTTTCTCCTACTT
1 ATTTGCCTTTCTCCTACTT
226133 TCTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.11, C:0.29, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTGCCTTTCTCCTACTT
Found at i:226873 original size:20 final size:20
Alignment explanation
Indices: 226823--226873 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
226813 TTAATAAATG
226823 ATAAATAAATAAATATTTAAA
1 ATAAAT-AATAAATATTTAAA
*
226844 ATTAAA-AATAAA-ATCTTATA
1 A-TAAATAATAAATAT-TTAAA
226864 ATAAATAATA
1 ATAAATAATA
226874 TTTTTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.23
20 15 0.58
21 1 0.04
22 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATAATAAATATTTAAA
Found at i:228385 original size:21 final size:21
Alignment explanation
Indices: 228361--228420 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
228351 ATGCGAGGGC
*
228361 AGTTTAAAACTAATTTAAACA
1 AGTTTAAAACTAATTCAAACA
* * *
228382 AGTTCAAAAATAATTCAAGCA
1 AGTTTAAAACTAATTCAAACA
* *
228403 ATTTTAAAACTTATTCAA
1 AGTTTAAAACTAATTCAA
228421 GTAATTTGAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (21 bp):
AGTTTAAAACTAATTCAAACA
Found at i:228494 original size:21 final size:21
Alignment explanation
Indices: 228470--228544 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
228460 CAAAACTTAC
*
228470 AAGTTTAAAAACTATTCAAAT
1 AAGTTCAAAAACTATTCAAAT
* *
228491 AAGTTCAAAACCTTATTCAAAC
1 AAGTTCAAAAAC-TATTCAAAT
* *
228513 AAGTTCAAAGA-TCAATCAAAT
1 AAGTTCAAAAACT-ATTCAAAT
228534 AAGTTCAAAAA
1 AAGTTCAAAAA
228545 TCATTGAAGC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.02
21 26 0.59
22 17 0.39
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.27
Consensus pattern (21 bp):
AAGTTCAAAAACTATTCAAAT
Found at i:228510 original size:22 final size:20
Alignment explanation
Indices: 228477--228543 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 20
228467 TACAAGTTTA
*
228477 AAAACTATTCAAATAAGTTC
1 AAAATTATTCAAATAAGTTC
*
228497 AAAACCTTATTCAAACAAGTTC
1 AAAA--TTATTCAAATAAGTTC
* *
228519 AAAGATCAATCAAATAAGTTC
1 AAA-ATTATTCAAATAAGTTC
228540 AAAA
1 AAAA
228544 ATCATTGAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 5 0.13
21 16 0.41
22 17 0.44
23 1 0.03
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.25
Consensus pattern (20 bp):
AAAATTATTCAAATAAGTTC
Found at i:231489 original size:33 final size:32
Alignment explanation
Indices: 231452--231514 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
231442 TATTTTTAAA
231452 TTATTTAAATAA-TAAAATAAAAATAGTTTTTTG
1 TTATTTAAATAACT-AAATAAAAATA-TTTTTTG
* *
231485 TTATTTAGATAACTCAATAAAAATATTTTT
1 TTATTTAAATAACTAAATAAAAATATTTTT
231515 CATTATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 5 0.19
33 21 0.78
34 1 0.04
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (32 bp):
TTATTTAAATAACTAAATAAAAATATTTTTTG
Found at i:234949 original size:39 final size:38
Alignment explanation
Indices: 234835--234949 Score: 119
Period size: 39 Copynumber: 3.0 Consensus size: 38
234825 CAGCTGGAAC
*
234835 CCCAATCAAATA-TAAGCCTGATGGAGCAGCAGTTGCAAA
1 CCCAATCAAATATTAA-CCTGATGGATCAGCAGTTGC-AA
* * *
234874 CCCAGTCTAAT-TTAAACCTGATGGATCAGCAATTGCAA
1 CCCAATCAAATATT-AACCTGATGGATCAGCAGTTGCAA
*
234912 CTCCAATCAAATATTAATCTGATGGATCCA-CAGTTGCA
1 C-CCAATCAAATATTAACCTGATGGAT-CAGCAGTTGCA
234950 GCCGCAATTG
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.05
39 54 0.86
40 6 0.10
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (38 bp):
CCCAATCAAATATTAACCTGATGGATCAGCAGTTGCAA
Found at i:235002 original size:39 final size:39
Alignment explanation
Indices: 234942--235055 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 39
234932 GATGGATCCA
* * *
234942 CAGTTGCAGCCGCAATTGAATGCCTTTGGGGTTAATCAG
1 CAGTTGCAGCCTCAGTTGAATGCCTTTGGGGATAATCAG
* * **
234981 CATTTTCAGCCTCAGTTGAATGCCACTGGGGATAATCAG
1 CAGTTGCAGCCTCAGTTGAATGCCTTTGGGGATAATCAG
*
235020 CGGTTGCAGCCTCAGTTGAATGCCTTTGGGGATAAT
1 CAGTTGCAGCCTCAGTTGAATGCCTTTGGGGATAAT
235056 ATGTTAAATC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (39 bp):
CAGTTGCAGCCTCAGTTGAATGCCTTTGGGGATAATCAG
Found at i:239984 original size:26 final size:26
Alignment explanation
Indices: 239955--240004 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
239945 AGTTAAAATA
239955 AAATTTATAAAATAAAAAAAGTTTGT
1 AAATTTATAAAATAAAAAAAGTTTGT
* *
239981 AAATTTATAAAATTAAACAAGTTT
1 AAATTTATAAAATAAAAAAAGTTT
240005 ACTTCTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (26 bp):
AAATTTATAAAATAAAAAAAGTTTGT
Found at i:240499 original size:2 final size:2
Alignment explanation
Indices: 240492--240520 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
240482 GCGTTTTCGG
240492 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
240521 TATTGCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:248571 original size:22 final size:20
Alignment explanation
Indices: 248516--248577 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
248506 TTAAATTATT
*
248516 TAAATAAATTTTTATTTTTT
1 TAAATAAATTTTTATTTTTC
* *
248536 TAATTATATTTTTATTTTGATC
1 TAAATAAATTTTTATTTT--TC
248558 TAAATAAATTTTTATATTTT
1 TAAATAAATTTTTAT-TTTT
248578 TATTTTGAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 16 0.47
21 1 0.03
22 14 0.41
23 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TAAATAAATTTTTATTTTTC
Found at i:248573 original size:30 final size:30
Alignment explanation
Indices: 248539--248603 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
248529 ATTTTTTTAA
* * *
248539 TTATATTTTTATTTTGATCTAAATAAATTT
1 TTATATTTTTATTTTGAACCAAATAAACTT
248569 TTATATTTTTATTTTGAACCAAATAAACTT
1 TTATATTTTTATTTTGAACCAAATAAACTT
248599 TTATA
1 TTATA
248604 ATTAATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATATTTTTATTTTGAACCAAATAAACTT
Found at i:249674 original size:2 final size:2
Alignment explanation
Indices: 249667--249713 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
249657 ATTCTGACTT
249667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
249709 TA TA T
1 TA TA T
249714 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:249718 original size:2 final size:2
Alignment explanation
Indices: 249713--249739 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
249703 TATATATATA
249713 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
249740 CAACCTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:251910 original size:64 final size:65
Alignment explanation
Indices: 251791--251913 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 65
251781 CAAGAGCTTC
* * * * **
251791 TTTTGACAAAAAGGGCTTGTTTACTGTTAGAAAAACCCATGAGTTTAATGCTTGGCTTAACTTAT
1 TTTTGACAAAAAGGACTTATTTACTGTTAGAAAAACCCATGAATATAACACTTGGCTTAACTTAT
*
251856 TTTTGACAAAAAGGACTTATTTGCTGTT-GAAAAACCCATGAATATAACACTTGGCTTA
1 TTTTGACAAAAAGGACTTATTTACTGTTAGAAAAACCCATGAATATAACACTTGGCTTA
251914 CAAAGAGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 26 0.51
65 25 0.49
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (65 bp):
TTTTGACAAAAAGGACTTATTTACTGTTAGAAAAACCCATGAATATAACACTTGGCTTAACTTAT
Found at i:263121 original size:2 final size:2
Alignment explanation
Indices: 263114--263140 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
263104 GGTTAACATA
263114 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
263141 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:266275 original size:30 final size:30
Alignment explanation
Indices: 266223--266281 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
266213 TTACGTTCAA
*
266223 TTATACTTTTATTTTGAGTTAAAGAAATTT
1 TTATACTTTTATTTTGAATTAAAGAAATTT
* *
266253 TTATATTTTTA-TTTGAAATTAAATAAATT
1 TTATACTTTTATTTTG-AATTAAAGAAATT
266282 CTTTTGACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (30 bp):
TTATACTTTTATTTTGAATTAAAGAAATTT
Found at i:267273 original size:10 final size:10
Alignment explanation
Indices: 267266--267338 Score: 92
Period size: 10 Copynumber: 7.0 Consensus size: 10
267256 TTACTCTTCT
267266 AAACTCTTTC
1 AAACTCTTTC
*
267276 AAACTCTTTG
1 AAACTCTTTC
267286 AAACTTCTTTC
1 AAAC-TCTTTC
*
267297 AAACTCTTTG
1 AAACTCTTTC
267307 AAACTTCTTTC
1 AAAC-TCTTTC
*
267318 AAACTCTTTG
1 AAACTCTTTC
267328 AAACTTCTTTC
1 AAAC-TCTTTC
267339 TATCAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
10 31 0.57
11 23 0.43
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.42
Consensus pattern (10 bp):
AAACTCTTTC
Found at i:267296 original size:21 final size:21
Alignment explanation
Indices: 267258--267338 Score: 139
Period size: 21 Copynumber: 3.9 Consensus size: 21
267248 GAAAGTTTTT
267258 ACTCTTCT-AAAC-TCTTTCAA
1 ACTCTT-TGAAACTTCTTTCAA
267278 ACTCTTTGAAACTTCTTTCAA
1 ACTCTTTGAAACTTCTTTCAA
267299 ACTCTTTGAAACTTCTTTCAA
1 ACTCTTTGAAACTTCTTTCAA
267320 ACTCTTTGAAACTTCTTTC
1 ACTCTTTGAAACTTCTTTC
267339 TATCAATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
19 1 0.02
20 10 0.17
21 48 0.81
ACGTcount: A:0.27, C:0.26, G:0.04, T:0.43
Consensus pattern (21 bp):
ACTCTTTGAAACTTCTTTCAA
Found at i:278108 original size:80 final size:79
Alignment explanation
Indices: 277956--278261 Score: 339
Period size: 80 Copynumber: 3.8 Consensus size: 79
277946 GTAACATCTG
* * * * * *
277956 TGCCATCAGATGTATGCGTTAAGCATA-TCATGTACATTATGGGCTAAACATGTGAATAATTTTT
1 TGCCATGAGATGTATGTGTTGAG-ATAGTCATATACATTATGGGCTAAGCATGTGAATAATTTAT
**
278020 GATATTATGAAATACA
65 GAGGTTATGAAATA-A
* * * * *
278036 TACCATGAGATGTATGTGTTGAGATAGTCATATATATTATGGGATAAGTATGTGAATGATTTATG
1 TGCCATGAGATGTATGTGTTGAGATAGTCATATACATTATGGGCTAAGCATGTGAATAATTTATG
*
278101 AGGTTATGAGATATA
66 AGGTTATGAAATA-A
* * * *
278116 TGCCATGAGATATATGTGTTGAAATAGTCATATACATTATAGGCTAAGCATGTGAGTAATTTATG
1 TGCCATGAGATGTATGTGTTGAGATAGTCATATACATTATGGGCTAAGCATGTGAATAATTTATG
278181 AGGTTATGAGAAGT-A
66 AGGTTATGA-AA-TAA
* * * *
278196 TGCCATGAGATTTATGTGTTGATATAGTCATATACACTATGGGCTAAGCATGATG-ATGATTTAT
1 TGCCATGAGATGTATGTGTTGAGATAGTCATATACATTATGGGCTAAGCATG-TGAATAATTTAT
278260 GA
65 GA
278262 AAATGTTATA
Statistics
Matches: 191, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
79 3 0.02
80 184 0.96
81 3 0.02
82 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (79 bp):
TGCCATGAGATGTATGTGTTGAGATAGTCATATACATTATGGGCTAAGCATGTGAATAATTTATG
AGGTTATGAAATAA
Found at i:279540 original size:23 final size:23
Alignment explanation
Indices: 279514--279559 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
279504 ACATGTAAAT
279514 ATTATAGTGCATTAAAGATGTGG
1 ATTATAGTGCATTAAAGATGTGG
*
279537 ATTATAGTGCATTAGAGATGTGG
1 ATTATAGTGCATTAAAGATGTGG
279560 CACTCTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (23 bp):
ATTATAGTGCATTAAAGATGTGG
Found at i:284880 original size:25 final size:25
Alignment explanation
Indices: 284852--284912 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
284842 CTGGACTTCT
*
284852 TATAAGCGGGTGTGCTACACACCCC
1 TATAAGCCGGTGTGCTACACACCCC
284877 TATAAGCCGGTGTGCTACACACCCC
1 TATAAGCCGGTGTGCTACACACCCC
284902 TATAAGCCGGT
1 TATAAGCCGGT
284913 TTATGGGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (25 bp):
TATAAGCCGGTGTGCTACACACCCC
Found at i:286666 original size:19 final size:18
Alignment explanation
Indices: 286626--286666 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
286616 TAAATATATA
286626 ATTAAAAAAAATTACTTT
1 ATTAAAAAAAATTACTTT
286644 -TTAAACAAATAATTA-TTT
1 ATTAAA-AAA-AATTACTTT
286662 ATTAA
1 ATTAA
286667 TTACTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAAAAAAAATTACTTT
Found at i:291237 original size:10 final size:10
Alignment explanation
Indices: 291222--291296 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
291212 ATATCCAAAT
291222 AATAATATTA
1 AATAATATTA
*
291232 AATAATATTCTT
1 AATAATA-T-TA
*
291244 TATAATATT-
1 AATAATATTA
* *
291253 TATTATAGTTA
1 AATAATA-TTA
291264 AATAATATT-
1 AATAATATTA
291273 AAT-ATATTA
1 AATAATATTA
291282 AATAATATTTA
1 AATAATA-TTA
291293 AATA
1 AATA
291297 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 12 0.23
10 15 0.28
11 14 0.26
12 7 0.13
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (10 bp):
AATAATATTA
Found at i:291284 original size:18 final size:19
Alignment explanation
Indices: 291245--291290 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
291235 AATATTCTTT
*
291245 ATAATATTTATTATAGTTAA
1 ATAATA-TTAATATAGTTAA
291265 ATAATATTAATATA-TTAA
1 ATAATATTAATATAGTTAA
291283 ATAATATT
1 ATAATATT
291291 TAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 7 0.28
20 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATAATATTAATATAGTTAA
Found at i:291289 original size:12 final size:11
Alignment explanation
Indices: 291222--291296 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
291212 ATATCCAAAT
291222 AATAATA-TTA
1 AATAATATTTA
*
291232 AATAATATTCTT
1 AATAATATT-TA
*
291244 TATAATATTT-
1 AATAATATTTA
* *
291254 -ATTATAGTTA
1 AATAATATTTA
291264 AATAATA-TT-
1 AATAATATTTA
291273 AAT-ATA-TTA
1 AATAATATTTA
291282 AATAATATTTA
1 AATAATATTTA
291293 AATA
1 AATA
291297 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 13 0.25
10 12 0.23
11 14 0.26
12 9 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
AATAATATTTA
Found at i:291297 original size:18 final size:18
Alignment explanation
Indices: 291245--291298 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
291235 AATATTCTTT
*
291245 ATAATATTTATTATAGTTAA
1 ATAATATTTA-AATA-TTAA
291265 ATAATA-TTAATATATTAA
1 ATAATATTTAA-ATATTAA
291283 ATAATATTTAAATATT
1 ATAATATTTAAATATT
291299 TTCATTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAATATTTAAATATTAA
Found at i:294079 original size:15 final size:15
Alignment explanation
Indices: 294059--294113 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
294049 TTTACAATAC
294059 AATGTGATTACAAGT
1 AATGTGATTACAAGT
**
294074 AATGTGATTGTAAGT
1 AATGTGATTACAAGT
* *
294089 AATGTGATTGCAAGC
1 AATGTGATTACAAGT
294104 AATGTGATTA
1 AATGTGATTA
294114 TAGGGAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:294467 original size:20 final size:20
Alignment explanation
Indices: 294422--294469 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
294412 AATGTGAGAG
* *
294422 GAAGAAAGAAAAGAAGGAAAA
1 GAAGAAA-AAAAAAAAGAAAA
*
294443 G-AGAAAAAAAAAAAGAAGA
1 GAAGAAAAAAAAAAAGAAAA
294462 GAAGAAAA
1 GAAGAAAA
294470 GAACAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 11 0.48
20 11 0.48
21 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
GAAGAAAAAAAAAAAGAAAA
Found at i:295730 original size:20 final size:20
Alignment explanation
Indices: 295707--295750 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
295697 TTAATTAAGT
295707 TGATTACTAATTAGGTGATA
1 TGATTACTAATTAGGTGATA
*
295727 TGATTACTGATTAGGTGATA
1 TGATTACTAATTAGGTGATA
295747 TGAT
1 TGAT
295751 CATATTTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (20 bp):
TGATTACTAATTAGGTGATA
Found at i:298715 original size:104 final size:104
Alignment explanation
Indices: 298535--298745 Score: 350
Period size: 104 Copynumber: 2.0 Consensus size: 104
298525 CACATATTCG
* *
298535 ATACATTATGTGCTTGTAGTATTGTAATAATTAGCCAATTTCAATTTCAATGATTTACTGTGTTT
1 ATACATTATGTGCTTGTAGTATTGTAATAATTAGCCAATTTCAAGTTCAATGATATACTGTGTTT
* *
298600 AGGACATAATTAATTATTTAGTTGTGATTTATTAGATGT
66 AGGACATAATTAATTATTTAATTGTGATTTATTAGACGT
* * *
298639 ATACATTATGTGCTTGTAGTGTTGTAATAATTGGTCAATTTCAAGTTCAATGATATACTGTGTTT
1 ATACATTATGTGCTTGTAGTATTGTAATAATTAGCCAATTTCAAGTTCAATGATATACTGTGTTT
*
298704 AGGACATAATTATTTATTTAATTGTGATTTATTAGACGT
66 AGGACATAATTAATTATTTAATTGTGATTTATTAGACGT
298743 ATA
1 ATA
298746 GTTAAAATTC
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (104 bp):
ATACATTATGTGCTTGTAGTATTGTAATAATTAGCCAATTTCAAGTTCAATGATATACTGTGTTT
AGGACATAATTAATTATTTAATTGTGATTTATTAGACGT
Found at i:306464 original size:31 final size:29
Alignment explanation
Indices: 306429--306495 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
306419 ATCATTAGTA
*
306429 ATAAAGGTTTATTTGACTTAAAATAAAAAAT
1 ATAAAGATTTATTT-ACTTAAAAT-AAAAAT
* *
306460 ATAAAAATTTATTTATTTAAAATAAAAAT
1 ATAAAGATTTATTTACTTAAAATAAAAAT
306489 ATAAAGA
1 ATAAAGA
306496 CTTAATTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.38
30 8 0.25
31 12 0.38
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (29 bp):
ATAAAGATTTATTTACTTAAAATAAAAAT
Found at i:306482 original size:30 final size:30
Alignment explanation
Indices: 306436--306533 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 30
306426 GTAATAAAGG
306436 TTTATTTGACTTAAAATAAAAAATATAAAAA
1 TTTATTTGACTTAAAAT-AAAAATATAAAAA
* *
306467 TTTATTT-ATTTAAAATAAAAATATAAAGA
1 TTTATTTGACTTAAAATAAAAATATAAAAA
* * * * *
306496 CTTAATTGAAC--ATAATAAAAATATAAGAG
1 TTTATTTG-ACTTAAAATAAAAATATAAAAA
306525 TTTATTTGA
1 TTTATTTGA
306534 ATTTTCTTGA
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 1 0.02
29 37 0.69
30 8 0.15
31 8 0.15
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTATTTGACTTAAAATAAAAATATAAAAA
Found at i:314287 original size:18 final size:18
Alignment explanation
Indices: 314248--314287 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
314238 CGTGTTAAAT
* *
314248 TTTTTTATTTTTAAATGA
1 TTTTTAATTTTTAAAAGA
*
314266 TTTTTAATTTTTAAAAGC
1 TTTTTAATTTTTAAAAGA
314284 TTTT
1 TTTT
314288 ACAACTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTAATTTTTAAAAGA
Found at i:314337 original size:22 final size:21
Alignment explanation
Indices: 314307--314349 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
314297 TATACATATC
314307 TTAATATATTCTAATAAAAAT
1 TTAATATATTCTAATAAAAAT
* *
314328 TTAATTATATTTTGATAAAAAT
1 TTAA-TATATTCTAATAAAAAT
314350 GATCATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAATATATTCTAATAAAAAT
Found at i:315355 original size:27 final size:27
Alignment explanation
Indices: 315307--315631 Score: 141
Period size: 27 Copynumber: 11.9 Consensus size: 27
315297 AAAAATATAG
* *
315307 TGTTACATACCATATTCTAAAATTTAAT
1 TGTTACATACCATGTT-AAAAATTTAAT
*
315335 TGTTACGTACCATGTTAAAAA--TAAT
1 TGTTACATACCATGTTAAAAATTTAAT
* * * *
315360 TATTACATGCCATGCTAAAAATATAAT
1 TGTTACATACCATGTTAAAAATTTAAT
*** * * *
315387 TGTTACATGTTATGTTGAAAACTTAGT
1 TGTTACATACCATGTTAAAAATTTAAT
*** * * *
315414 TGTTACATGTTATATTGAAAAATGTAGT
1 TGTTACATACCATGTT-AAAAATTTAAT
* *** * * *
315442 TATTACACGTCATGTTGAAATTTTAGT
1 TGTTACATACCATGTTAAAAATTTAAT
* **
315469 TGTTACATATCATGTTAAAAAATGAAAT
1 TGTTACATACCATGTT-AAAAATTTAAT
* * *
315497 TGTTACACACTATGTTAAAAATTTAGT
1 TGTTACATACCATGTTAAAAATTTAAT
* * *
315524 TGTTACACACCATGTTAAAAAATATAAC
1 TGTTACATACCATGTT-AAAAATTTAAT
* *** * * *
315552 TATTACACGTCATGTTGAAGATTTAGT
1 TGTTACATACCATGTTAAAAATTTAAT
*** *
315579 TGTTACACGTCATATTGAAAAATTTAAT
1 TGTTACATACCATGTT-AAAAATTTAAT
* * *
315607 TGTTACACATCATGATGAAAAATTT
1 TGTTACATACCATG-TTAAAAATTT
315632 GTTATACACC
Statistics
Matches: 230, Mismatches: 60, Indels: 14
0.76 0.20 0.05
Matches are distributed among these distances:
25 21 0.09
27 106 0.46
28 102 0.44
29 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (27 bp):
TGTTACATACCATGTTAAAAATTTAAT
Found at i:315365 original size:25 final size:25
Alignment explanation
Indices: 315331--315382 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
315321 TTCTAAAATT
* * *
315331 TAATTGTTACGTACCATGTTAAAAA
1 TAATTATTACATACCATGCTAAAAA
*
315356 TAATTATTACATGCCATGCTAAAAA
1 TAATTATTACATACCATGCTAAAAA
315381 TA
1 TA
315383 TAATTGTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (25 bp):
TAATTATTACATACCATGCTAAAAA
Found at i:315448 original size:55 final size:55
Alignment explanation
Indices: 315376--315627 Score: 236
Period size: 55 Copynumber: 4.6 Consensus size: 55
315366 ATGCCATGCT
* * * * * ** * *
315376 AAAAATATAATTGTTACATGTTATGTTGAAAACTTAGTTGTTACATGTTATATTG
1 AAAAATGTAATTATTACACGTCATGTTGAAAATTTAGTTGTTACACATCATATTA
* * * *
315431 AAAAATGTAGTTATTACACGTCATGTTGAAATTTTAGTTGTTACATATCATGTTA
1 AAAAATGTAATTATTACACGTCATGTTGAAAATTTAGTTGTTACACATCATATTA
* * * * * *
315486 AAAAATGAAATTGTTACAC-ACTATGTTAAAAATTTAGTTGTTACACACCATGTTA
1 AAAAATGTAATTATTACACGTC-ATGTTGAAAATTTAGTTGTTACACATCATATTA
* * * * *
315541 AAAAATATAACTATTACACGTCATGTTGAAGATTTAGTTGTTACACGTCATATTG
1 AAAAATGTAATTATTACACGTCATGTTGAAAATTTAGTTGTTACACATCATATTA
* * * *
315596 AAAAATTTAATTGTTACACATCATGATGAAAA
1 AAAAATGTAATTATTACACGTCATGTTGAAAA
315628 ATTTGTTATA
Statistics
Matches: 159, Mismatches: 36, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
54 1 0.01
55 157 0.99
56 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (55 bp):
AAAAATGTAATTATTACACGTCATGTTGAAAATTTAGTTGTTACACATCATATTA
Found at i:315523 original size:110 final size:110
Alignment explanation
Indices: 315397--315615 Score: 269
Period size: 110 Copynumber: 2.0 Consensus size: 110
315387 TGTTACATGT
* **** * * **
315397 TATGTTGAAAACTTAGTTGTTACATGTTATATTGAAAAATGTAGTTATTACACGTCATGTTGAA-
1 TATGTTAAAAACTTAGTTGTTACACACCATATTAAAAAATATAACTATTACACGTCATGTTGAAG
* *
315461 ATTTTAGTTGTTACATATCATGTTAAAAAATGAAATTGTTACACAC
66 A-TTTAGTTGTTACACATCATATTAAAAAATGAAATTGTTACACAC
* *
315507 TATGTTAAAAATTTAGTTGTTACACACCATGTTAAAAAATATAACTATTACACGTCATGTTGAAG
1 TATGTTAAAAACTTAGTTGTTACACACCATATTAAAAAATATAACTATTACACGTCATGTTGAAG
* * **
315572 ATTTAGTTGTTACACGTCATATTGAAAAATTTAATTGTTACACA
66 ATTTAGTTGTTACACATCATATTAAAAAATGAAATTGTTACACA
315616 TCATGATGAA
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
110 90 0.99
111 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (110 bp):
TATGTTAAAAACTTAGTTGTTACACACCATATTAAAAAATATAACTATTACACGTCATGTTGAAG
ATTTAGTTGTTACACATCATATTAAAAAATGAAATTGTTACACAC
Found at i:315630 original size:28 final size:28
Alignment explanation
Indices: 315398--315631 Score: 190
Period size: 28 Copynumber: 8.5 Consensus size: 28
315388 GTTACATGTT
* ** *
315398 ATGTTG-AAAACTTAGTTGTTACATGTT
1 ATGTTGAAAAATTTAGTTGTTACACATC
* * * *
315425 ATATTGAAAAATGTAGTTATTACACGTC
1 ATGTTGAAAAATTTAGTTGTTACACATC
* *
315453 ATGTTG-AAATTTTAGTTGTTACATATC
1 ATGTTGAAAAATTTAGTTGTTACACATC
* ** *
315480 ATGTTAAAAAATGAAATTGTTACACA-C
1 ATGTTGAAAAATTTAGTTGTTACACATC
*
315507 TATGTT-AAAAATTTAGTTGTTACACACC
1 -ATGTTGAAAAATTTAGTTGTTACACATC
* * ** * *
315535 ATGTTAAAAAATATAACTATTACACGTC
1 ATGTTGAAAAATTTAGTTGTTACACATC
* *
315563 ATGTTG-AAGATTTAGTTGTTACACGTC
1 ATGTTGAAAAATTTAGTTGTTACACATC
* *
315590 ATATTGAAAAATTTAATTGTTACACATC
1 ATGTTGAAAAATTTAGTTGTTACACATC
*
315618 ATGATGAAAAATTT
1 ATGTTGAAAAATTT
315632 GTTATACACC
Statistics
Matches: 162, Mismatches: 39, Indels: 11
0.76 0.18 0.05
Matches are distributed among these distances:
27 70 0.43
28 92 0.57
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (28 bp):
ATGTTGAAAAATTTAGTTGTTACACATC
Found at i:316873 original size:7 final size:7
Alignment explanation
Indices: 316861--316887 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
316851 CAATGCTATG
316861 TGTGTAT
1 TGTGTAT
316868 TGTGTAT
1 TGTGTAT
316875 TGTGTAT
1 TGTGTAT
316882 TGTGTA
1 TGTGTA
316888 AAGTGTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (7 bp):
TGTGTAT
Found at i:318741 original size:26 final size:27
Alignment explanation
Indices: 318689--318742 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
318679 CAATCTCATA
318689 TATTATTATTTTGAAAAATTACGCCTATG
1 TATTATTATTTTGAAAAATTA--CCTATG
318718 TATTATTATTTTGAAAAATT-CCTAT
1 TATTATTATTTTGAAAAATTACCTAT
318743 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.20
29 20 0.80
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (27 bp):
TATTATTATTTTGAAAAATTACCTATG
Found at i:319078 original size:20 final size:20
Alignment explanation
Indices: 319041--319079 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
319031 TTAAAAACTA
* *
319041 TTTTTAAATTTTTTAAAATT
1 TTTTTAAATTTCTAAAAATT
*
319061 TTTTTGAATTTCTAAAAAT
1 TTTTTAAATTTCTAAAAAT
319080 AATATATATT
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:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTAAATTTCTAAAAATT
Found at i:322190 original size:2 final size:2
Alignment explanation
Indices: 322183--322221 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
322173 TTTAAGCCAA
322183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
322222 CACACACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:322622 original size:24 final size:25
Alignment explanation
Indices: 322590--322637 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
322580 AATTATTAGA
*
322590 TTATTTTTAA-AAAATTTTCTTTTG
1 TTATGTTTAATAAAATTTTCTTTTG
* *
322614 TTATGTTTAATTAAATTTTTTTTT
1 TTATGTTTAATAAAATTTTCTTTT
322638 ATTTTAAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (25 bp):
TTATGTTTAATAAAATTTTCTTTTG
Found at i:322651 original size:22 final size:22
Alignment explanation
Indices: 322609--322651 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
322599 AAAAATTTTC
*
322609 TTTTGTTATGTTTAATTAAATT
1 TTTTGTTATGTTTAATCAAATT
*
322631 TTTTTTTAT-TTTAAGTCAAAT
1 TTTTGTTATGTTTAA-TCAAAT
322652 AAGCTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTTGTTATGTTTAATCAAATT
Found at i:327921 original size:20 final size:19
Alignment explanation
Indices: 327896--327945 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
327886 TTAAATTGTC
*
327896 ATTTTATTTTAATTCGTTCA
1 ATTTTATTTT-ATACGTTCA
*
327916 ATTTTATTATTATACTTTCA
1 ATTTTATT-TTATACGTTCA
*
327936 ATTTCATTTT
1 ATTTTATTTT
327946 TTTTATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTATTTTATACGTTCA
Found at i:333545 original size:2 final size:2
Alignment explanation
Indices: 333538--333568 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
333528 CCTATCTCGT
333538 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
333569 TTCACTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:334962 original size:3 final size:3
Alignment explanation
Indices: 334954--334987 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
334944 TCTTAAATCC
*
334954 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
334988 CCTTGGTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:335312 original size:11 final size:10
Alignment explanation
Indices: 335280--335356 Score: 53
Period size: 11 Copynumber: 8.1 Consensus size: 10
335270 CATAAAAAAT
335280 AAATAAAGT-A
1 AAATAAA-TAA
335290 AAAT-AA-AA
1 AAATAAATAA
335298 AAATAAATGAA
1 AAATAAAT-AA
335309 AAATAAAT--
1 AAATAAATAA
335317 -AATAAATAA
1 AAATAAATAA
335326 AAA-AAATTAA
1 AAATAAA-TAA
*
335336 AAATTAA-AA
1 AAATAAATAA
335345 AAATAGAATAA
1 AAATA-AATAA
335356 A
1 A
335357 CCACTCCGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 21
0.70 0.03 0.27
Matches are distributed among these distances:
7 7 0.13
8 5 0.09
9 13 0.24
10 14 0.26
11 15 0.28
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AAATAAATAA
Found at i:335343 original size:17 final size:17
Alignment explanation
Indices: 335273--335347 Score: 73
Period size: 18 Copynumber: 4.3 Consensus size: 17
335263 CTTTTTGCAT
*
335273 AAAAAATAAATAAAGTAA
1 AAAAAAT-AATAAATTAA
* *
335291 AATAAAAAAATAAATGAA
1 AA-AAAATAATAAATTAA
335309 AAATAAATAATAAA-TAA
1 AAA-AAATAATAAATTAA
335326 AAAAAATTAA-AAATTAA
1 AAAAAA-TAATAAATTAA
335343 AAAAA
1 AAAAA
335348 TAGAATAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 6 0.12
17 17 0.35
18 21 0.44
19 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAAAATAATAAATTAA
Found at i:340266 original size:96 final size:96
Alignment explanation
Indices: 340076--340249 Score: 240
Period size: 96 Copynumber: 1.8 Consensus size: 96
340066 TAACCCTCAC
*** * * * * *
340076 AATGGCTTTTTCATGGGATCAAGCGATAACCCTTGGTTTTTAATGAGCTCAACTATAAACCCATA
1 AATGGCTTTTTCACAAGATCAAGCGATAAACCATAGTTTTTAATGAGCTCAACCACAAACCCATA
340141 TAATGGCCTTTTTCAAGATCAATCATAACCT
66 TAATGGCCTTTTTCAAGATCAATCATAACCT
* * *
340172 AATGGCTTTTTCACAAGATCAAGTGATAAACCATAGTTTTTAATGGGCTCAACCACAAACCTATA
1 AATGGCTTTTTCACAAGATCAAGCGATAAACCATAGTTTTTAATGAGCTCAACCACAAACCCATA
*
340237 TAATGGCTTTTTT
66 TAATGGCCTTTTT
340250 TGAGATTAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 66 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (96 bp):
AATGGCTTTTTCACAAGATCAAGCGATAAACCATAGTTTTTAATGAGCTCAACCACAAACCCATA
TAATGGCCTTTTTCAAGATCAATCATAACCT
Found at i:340995 original size:20 final size:20
Alignment explanation
Indices: 340970--341008 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
340960 TGTTGAGTTA
340970 AGAATGAACTTCTTAGCTTG
1 AGAATGAACTTCTTAGCTTG
*
340990 AGAATGAACTTCTTGGCTT
1 AGAATGAACTTCTTAGCTT
341009 AAGATAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
AGAATGAACTTCTTAGCTTG
Found at i:343099 original size:5 final size:5
Alignment explanation
Indices: 343082--343120 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
343072 TTAAATTAAG
* *
343082 TTATT TTAGTT TTATT TTATT TTATT TTAAT TTACT TTA
1 TTATT TTA-TT TTATT TTATT TTATT TTATT TTATT TTA
343121 AGAAAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:344799 original size:11 final size:11
Alignment explanation
Indices: 344783--344820 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
344773 TTACCTAGTG
*
344783 AGTAAAGAGTA
1 AGTAAAGAGAA
344794 AGTAAAGAGAA
1 AGTAAAGAGAA
344805 AGTAAA-AGAA
1 AGTAAAGAGAA
*
344815 ATTAAA
1 AGTAAA
344821 ATGAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (11 bp):
AGTAAAGAGAA
Found at i:345661 original size:21 final size:22
Alignment explanation
Indices: 345619--345674 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
345609 AAGTTGTTTT
345619 ATTTTAGTTTTATGTTAAATTG
1 ATTTTAGTTTTATGTTAAATTG
*
345641 ATTTTAG-TTTA-GTTAGTATTG
1 ATTTTAGTTTTATGTTA-AATTG
*
345662 A-TTTAGTCTTATG
1 ATTTTAGTTTTATG
345675 CGTTTGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 9 0.31
21 12 0.41
22 8 0.28
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (22 bp):
ATTTTAGTTTTATGTTAAATTG
Found at i:352414 original size:19 final size:19
Alignment explanation
Indices: 352383--352427 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
352373 ATTAATGTAT
352383 TTCACAACATCCAAGTGTC
1 TTCACAACATCCAAGTGTC
* *
352402 TTTACAACGTCCAAGTGTC
1 TTCACAACATCCAAGTGTC
352421 TTCACAA
1 TTCACAA
352428 TGCTCCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (19 bp):
TTCACAACATCCAAGTGTC
Found at i:360697 original size:16 final size:16
Alignment explanation
Indices: 360678--360711 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
360668 TGAATGCAAC
360678 AAAA-AATAAAATATAA
1 AAAAGAATAAAA-ATAA
360694 AAAAGAATAAAAATAA
1 AAAAGAATAAAAATAA
360710 AA
1 AA
360712 GATAAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAGAATAAAAATAA
Found at i:360710 original size:6 final size:6
Alignment explanation
Indices: 360679--360747 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
360669 GAATGCAACA
* *
360679 AAAAAT -AAAAT ATAAAA- AAGAAT AAAAAT AAAAGAT AAATAGT AAAAATT
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAA-AT AAA-AAT AAAAA-T
360729 AAAAA- ATAAAAT AAAAAT A
1 AAAAAT A-AAAAT AAAAAT A
360748 TCAACCAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
5 9 0.18
6 21 0.41
7 20 0.39
8 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:360731 original size:21 final size:19
Alignment explanation
Indices: 360699--360746 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
360689 TATAAAAAAG
*
360699 AATAAAAA-TAAAAGATAA
1 AATAAAAATTAAAAAATAA
360717 ATAGTAAAAATTAAAAAATAA
1 A-A-TAAAAATTAAAAAATAA
360738 AATAAAAAT
1 AATAAAAAT
360747 ATCAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 8 0.31
20 7 0.27
21 10 0.38
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (19 bp):
AATAAAAATTAAAAAATAA
Found at i:360735 original size:8 final size:7
Alignment explanation
Indices: 360678--360739 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
360668 TGAATGCAAC
360678 AAAAAAT
1 AAAAAAT
*
360685 AAAATAT
1 AAAAAAT
*
360692 AAAAAAGA
1 AAAAAA-T
360700 ATAAAAAT
1 A-AAAAAT
*
360708 AAAAGAT
1 AAAAAAT
* *
360715 AAATAGT
1 AAAAAAT
*
360722 AAAAATT
1 AAAAAAT
360729 AAAAAAT
1 AAAAAAT
360736 AAAA
1 AAAA
360740 TAAAAATATC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
7 35 0.83
8 2 0.05
9 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (7 bp):
AAAAAAT
Found at i:362634 original size:24 final size:24
Alignment explanation
Indices: 362602--362658 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
362592 GTGGTGAGAG
362602 AAAGAGGGGGAAACTATGATAGCA
1 AAAGAGGGGGAAACTATGATAGCA
362626 AAAGAGGGGGAAACTATGATAGCA
1 AAAGAGGGGGAAACTATGATAGCA
362650 AAAGAGGGG
1 AAAGAGGGG
362659 AAAAAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.37, T:0.11
Consensus pattern (24 bp):
AAAGAGGGGGAAACTATGATAGCA
Found at i:367412 original size:29 final size:29
Alignment explanation
Indices: 367366--367440 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
367356 TCACGCAAGT
* *
367366 TCAACTTAAAGGTTAATTAAAGATAAAGA
1 TCAACTTAAAAGTAAATTAAAGATAAAGA
367395 TCAACTTAAAAGTAAATTAAAGATAAAGA
1 TCAACTTAAAAGTAAATTAAAGATAAAGA
367424 TCAACTTAAAAGTAAAT
1 TCAACTTAAAAGTAAAT
367441 CTGTTCATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.27
Consensus pattern (29 bp):
TCAACTTAAAAGTAAATTAAAGATAAAGA
Found at i:368171 original size:22 final size:22
Alignment explanation
Indices: 368132--368173 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
368122 ACATTGCAAA
**
368132 AATATATACATTTTATTATATT
1 AATATATACATTACATTATATT
*
368154 AATATGTACATTACATTATA
1 AATATATACATTACATTATA
368174 ATGACTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
AATATATACATTACATTATATT
Found at i:378010 original size:13 final size:13
Alignment explanation
Indices: 377992--378016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
377982 ATACTTAAAA
377992 ATATAAAATATTG
1 ATATAAAATATTG
378005 ATATAAAATATT
1 ATATAAAATATT
378017 TAATATACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATAAAATATTG
Found at i:380124 original size:2 final size:2
Alignment explanation
Indices: 380119--380151 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
380109 CTCTCTCTAA
*
380119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
380152 GTGATCGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:383012 original size:2 final size:2
Alignment explanation
Indices: 383005--383032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
382995 AAGTTCGAAT
383005 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
383033 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:389369 original size:14 final size:14
Alignment explanation
Indices: 389350--389382 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
389340 AATAAAATCT
389350 ATATAACAGAA-AAA
1 ATATAACA-AATAAA
389364 ATATAACAAATAAA
1 ATATAACAAATAAA
389378 ATATA
1 ATATA
389383 GAAGGTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (14 bp):
ATATAACAAATAAA
Found at i:391310 original size:12 final size:12
Alignment explanation
Indices: 391295--391320 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
391285 AAAATATTAA
391295 AAAAATATTTTT
1 AAAAATATTTTT
391307 AAAAATATTTTT
1 AAAAATATTTTT
391319 AA
1 AA
391321 TTTTACACTT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAAATATTTTT
Done.