Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 20 of 97
Found at i:8881987 original size:15 final size:15
Alignment explanation
Indices: 8881967--8881996 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8881957 CCAGCATTTA
8881967 TTTTTTTTGTTTTTT
1 TTTTTTTTGTTTTTT
8881982 TTTTTTTTGTTTTTT
1 TTTTTTTTGTTTTTT
8881997 GTAGATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (15 bp):
TTTTTTTTGTTTTTT
Found at i:8887311 original size:47 final size:47
Alignment explanation
Indices: 8887242--8887336 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
8887232 AAAGAATGTA
8887242 TATGCAAATCCTTCTCCCTCTTTCTCTCTCTCTGTGTCTCTGTGTCT
1 TATGCAAATCCTTCTCCCTCTTTCTCTCTCTCTGTGTCTCTGTGTCT
8887289 TATGCAAATCCTTCTCCCTCTTTCTCTCTCTCTGTGTCTCTGTGTCT
1 TATGCAAATCCTTCTCCCTCTTTCTCTCTCTCTGTGTCTCTGTGTCT
8887336 T
1 T
8887337 TCTTGCTTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.08, C:0.34, G:0.11, T:0.47
Consensus pattern (47 bp):
TATGCAAATCCTTCTCCCTCTTTCTCTCTCTCTGTGTCTCTGTGTCT
Found at i:8890166 original size:18 final size:18
Alignment explanation
Indices: 8890143--8890179 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
8890133 TCTCTTTTCA
8890143 TCTCTTTCTTTTTCTCTT
1 TCTCTTTCTTTTTCTCTT
*
8890161 TCTCTTTCTTTTTGTCTT
1 TCTCTTTCTTTTTCTCTT
8890179 T
1 T
8890180 TCATTGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTCTTTCTTTTTCTCTT
Found at i:8890463 original size:29 final size:26
Alignment explanation
Indices: 8890431--8890484 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
8890421 TTATAATTAA
*
8890431 TTATAAATTTTATATTATATAAAAAAATT
1 TTAT-AATTTT-TA-TAAATAAAAAAATT
*
8890460 TTATACTTTTTATAAATAAAAAAAT
1 TTATAATTTTTATAAATAAAAAAAT
8890485 AAAATTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 12 0.52
27 2 0.09
28 5 0.22
29 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TTATAATTTTTATAAATAAAAAAATT
Found at i:8894295 original size:12 final size:12
Alignment explanation
Indices: 8894257--8894298 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
8894247 CCATCGATAA
8894257 CATTA-CATCAT
1 CATTATCATCAT
*
8894268 CATCATCATCAT
1 CATTATCATCAT
*
8894280 CATTTTCATCAT
1 CATTATCATCAT
8894292 CATTATC
1 CATTATC
8894299 GTTCATTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (12 bp):
CATTATCATCAT
Found at i:8909175 original size:27 final size:26
Alignment explanation
Indices: 8909145--8909242 Score: 115
Period size: 27 Copynumber: 3.7 Consensus size: 26
8909135 TATTATGACA
* *
8909145 TATAAAAACTAAATTTTCAATATAACG
1 TATAACAATTAAATTTTCAA-ATAACG
* * *
8909172 TATAATAATTAAATCTTCAAAATGACG
1 TATAACAATTAAATTTTC-AAATAACG
8909199 TATAACAATTAAATTTTCAAAGTAACG
1 TATAACAATTAAATTTTCAAA-TAACG
*
8909226 TGTAACAATTAAATTTT
1 TATAACAATTAAATTTT
8909243 TAACATAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.05
27 56 0.92
28 2 0.03
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (26 bp):
TATAACAATTAAATTTTCAAATAACG
Found at i:8909289 original size:26 final size:26
Alignment explanation
Indices: 8909225--8909325 Score: 69
Period size: 27 Copynumber: 3.8 Consensus size: 26
8909215 TCAAAGTAAC
* * * *
8909225 GTGTAACAATTAAATTTTTAACATAAT
1 GTGTAACAACT-AATTTTCAATATGAT
** *
8909252 GTGTAATGACT-ATTTTGTAATATGAT
1 GTGTAACAACTAATTTT-CAATATGAT
8909278 GTGTAACAACTAAATTTTCAATATGAT
1 GTGTAACAACT-AATTTTCAATATGAT
* * *
8909305 GTATAATAATTATATTTTCAA
1 GTGTAACAACTA-ATTTTCAA
8909326 CGCGATTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
25 5 0.08
26 17 0.29
27 32 0.54
28 5 0.08
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.43
Consensus pattern (26 bp):
GTGTAACAACTAATTTTCAATATGAT
Found at i:8909818 original size:21 final size:20
Alignment explanation
Indices: 8909781--8909822 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
8909771 TAAATTAAAA
* *
8909781 TAAAAATTTAAATTTTTTTT
1 TAAAAATTAAAACTTTTTTT
8909801 TAAATAATTAAAACTTTTTTT
1 TAAA-AATTAAAACTTTTTTT
8909822 T
1 T
8909823 TTAAGTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TAAAAATTAAAACTTTTTTT
Found at i:8909908 original size:2 final size:2
Alignment explanation
Indices: 8909901--8909941 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
8909891 CTGCCCCTCA
* * *
8909901 CT CT CT CT CT TT CT CT CT CT CC CT CT CT CT CT CT GT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
8909942 ACACACACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:8912695 original size:15 final size:15
Alignment explanation
Indices: 8912675--8912705 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8912665 TTTTATGACA
8912675 CGTGGGAACCACGTG
1 CGTGGGAACCACGTG
8912690 CGTGGGAACCACGTG
1 CGTGGGAACCACGTG
8912705 C
1 C
8912706 TTGCATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.29, G:0.39, T:0.13
Consensus pattern (15 bp):
CGTGGGAACCACGTG
Found at i:8918599 original size:2 final size:2
Alignment explanation
Indices: 8918589--8918656 Score: 104
Period size: 2 Copynumber: 34.5 Consensus size: 2
8918579 AAAATATGAT
*
8918589 TA TA T- TA TA TA TA TA TA TA TA TA TA GTT TA T- 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
8918630 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 T
8918657 CGTAAAAACC
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 2 0.03
2 58 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8922379 original size:46 final size:46
Alignment explanation
Indices: 8922326--8922414 Score: 153
Period size: 46 Copynumber: 1.9 Consensus size: 46
8922316 TTCATCATTG
8922326 AGCATACTCCTTGAAACTCTT-GATCAACTTTTACTCAATGTTTTGT
1 AGCATACTCCTTGAAACTCTTAG-TCAACTTTTACTCAATGTTTTGT
*
8922372 AGCATACTCCTTGAAAGTCTTAGTCAACTTTTACTCAATGTTT
1 AGCATACTCCTTGAAACTCTTAGTCAACTTTTACTCAATGTTT
8922415 GATAGTGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
46 40 0.98
47 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.40
Consensus pattern (46 bp):
AGCATACTCCTTGAAACTCTTAGTCAACTTTTACTCAATGTTTTGT
Found at i:8932966 original size:29 final size:30
Alignment explanation
Indices: 8932934--8933000 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
8932924 ATATGTCGTG
8932934 TAACAACA-ATATTTTTTCAACATGGCGTA
1 TAACAACAGATATTTTTTCAACATGGCGTA
* *
8932963 TAACAACAGTATTTTTTTTCAACATGGCGTG
1 TAACAACAG-ATATTTTTTCAACATGGCGTA
8932994 TAACAAC
1 TAACAAC
8933001 CTTTTTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 8 0.24
31 26 0.76
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (30 bp):
TAACAACAGATATTTTTTCAACATGGCGTA
Found at i:8933124 original size:45 final size:45
Alignment explanation
Indices: 8933065--8933159 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
8933055 TTTTTTTTCA
* * ** *
8933065 ACATGGCGTGTAACAACCTAACCATGGCTTGTCACAGGTTTTTGT
1 ACATGACGTATAACAACCTAACCATAACCTGTCACAGGTTTTTGT
*
8933110 ACATGACGTATAACAAGCTAACCATAACCTGTCACAGGTTTTTGT
1 ACATGACGTATAACAACCTAACCATAACCTGTCACAGGTTTTTGT
8933155 ACATG
1 ACATG
8933160 GTTTGTCACA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (45 bp):
ACATGACGTATAACAACCTAACCATAACCTGTCACAGGTTTTTGT
Found at i:8933199 original size:69 final size:69
Alignment explanation
Indices: 8933087--8933229 Score: 196
Period size: 69 Copynumber: 2.1 Consensus size: 69
8933077 ACAACCTAAC
* **
8933087 CATGGCTTGTCACAGGTTTTTGTACATGACGTATAACAAGCTAACCATAACCTGTCACAGGTTTT
1 CATGGCTTGTCACAGATTTTTGTACACAACGTATAACAAGCTAACCATAACCTGTCACAGGTTTT
8933152 TGTA
66 TGTA
* * * * ** *
8933156 CATGGTTTGTCACATATTTTTGTACACAACGTGTAACATGCTAACCATGGCTTGTCACAGGTTTT
1 CATGGCTTGTCACAGATTTTTGTACACAACGTATAACAAGCTAACCATAACCTGTCACAGGTTTT
8933221 TGTA
66 TGTA
8933225 CATGG
1 CATGG
8933230 AGTGTAACAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (69 bp):
CATGGCTTGTCACAGATTTTTGTACACAACGTATAACAAGCTAACCATAACCTGTCACAGGTTTT
TGTA
Found at i:8933214 original size:114 final size:114
Alignment explanation
Indices: 8933065--8933627 Score: 644
Period size: 114 Copynumber: 4.8 Consensus size: 114
8933055 TTTTTTTTCA
* * ** *
8933065 ACATGGCGTGTAACAACCTAACCATGGCTTGTCACAGGTTTTTGTACATGACGTATAACAAGCTA
1 ACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGACATGCAACACGCTA
* * * ** **
8933130 ACCATAACCTGTCACAGGTTTTTGTACATGGTTTGTCACATATTTTTGT
66 ACCATGACTTATCACAGGTTTTTGTACATGGCGTGTCACAGGTTTTTGT
*** * * *
8933179 ACACAACGTGTAACATGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGA-GTGTAACACGCT
1 ACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACAT-GACATGCAACACGCT
* *
8933243 AATCATGGCTTATCACAGGTTTTTGTACATGGCGTGTCACAGGTTTTTGT
65 AACCATGACTTATCACAGGTTTTTGTACATGGCGTGTCACAGGTTTTTGT
* *
8933293 ACATGGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCATGCAACACGCTA
1 ACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGACATGCAACACGCTA
*
8933358 ACCATGGCTTATCACAGGTTTTTTGTACATGGCGTGTCACAGGTTTTTGT
66 ACCATGACTTATCACAGG-TTTTTGTACATGGCGTGTCACAGGTTTTTGT
* *
8933408 ACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGGTTTTGTACATGGCATGCAACACGCTA
1 ACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGACATGCAACACGCTA
* * * *
8933473 ACCATGGA-TTGTCACAGGTTTTTGTATATGGCGTGCAACACGCTAACCATAGGGTTTTGT
66 ACCAT-GACTTATCACAGGTTTTTGTACATGGCGT-------G-T---CACAGGTTTTTGT
* * * * * * *
8933533 ACATGGCGTGCAACACGCTAACCATAGCTTGTCACAGGGTTTTGTACATGGCGTGTAACACGCTA
1 ACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGACATGCAACACGCTA
* *
8933598 ACCATGGCTTGTCACAGGTTTTTGTACATG
66 ACCATGACTTATCACAGGTTTTTGTACATG
8933628 ATATGTAACA
Statistics
Matches: 395, Mismatches: 38, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
113 1 0.00
114 183 0.46
115 110 0.28
116 1 0.00
121 1 0.00
122 1 0.00
124 1 0.00
125 97 0.25
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (114 bp):
ACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGACATGCAACACGCTA
ACCATGACTTATCACAGGTTTTTGTACATGGCGTGTCACAGGTTTTTGT
Found at i:8933221 original size:45 final size:45
Alignment explanation
Indices: 8933156--8933272 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 45
8933146 GGTTTTTGTA
* ** *
8933156 CATGGTTTGTCACATATTTTTGTACA-CAACGTGTAACATGCTAAC
1 CATGGCTTGTCACAGGTTTTTGTACATCAA-GTGTAACACGCTAAC
** *
8933201 CATGGCTTGTCACAGGTTTTTGTACATGGAGTGTAACACGCTAAT
1 CATGGCTTGTCACAGGTTTTTGTACATCAAGTGTAACACGCTAAC
*
8933246 CATGGCTTATCACAGGTTTTTGTACAT
1 CATGGCTTGTCACAGGTTTTTGTACAT
8933273 GGCGTGTCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 62 0.98
46 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (45 bp):
CATGGCTTGTCACAGGTTTTTGTACATCAAGTGTAACACGCTAAC
Found at i:8933273 original size:45 final size:45
Alignment explanation
Indices: 8933186--8933279 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
8933176 TGTACACAAC
* *
8933186 GTGTAACATGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGA
1 GTGTAACACGCTAACCATGGCTTATCACAGGTTTTTGTACATGGA
* *
8933231 GTGTAACACGCTAATCATGGCTTATCACAGGTTTTTGTACATGGC
1 GTGTAACACGCTAACCATGGCTTATCACAGGTTTTTGTACATGGA
8933276 GTGT
1 GTGT
8933280 CACAGGTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (45 bp):
GTGTAACACGCTAACCATGGCTTATCACAGGTTTTTGTACATGGA
Found at i:8933274 original size:69 final size:69
Alignment explanation
Indices: 8933201--8933344 Score: 252
Period size: 69 Copynumber: 2.1 Consensus size: 69
8933191 ACATGCTAAC
* *
8933201 CATGGCTTGTCACAGGTTTTTGTACATGGAGTGTAACACGCTAATCATGGCTTATCACAGGTTTT
1 CATGGCGTGTCACAGGTTTTTGTACATGGAGTGTAACACGCTAACCATGGCTTATCACAGGTTTT
8933266 TGTA
66 TGTA
* *
8933270 CATGGCGTGTCACAGGTTTTTGTACATGGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTT
1 CATGGCGTGTCACAGGTTTTTGTACATGGAGTGTAACACGCTAACCATGGCTTATCACAGGTTTT
8933335 TGTA
66 TGTA
8933339 CATGGC
1 CATGGC
8933345 ATGCAACACG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (69 bp):
CATGGCGTGTCACAGGTTTTTGTACATGGAGTGTAACACGCTAACCATGGCTTATCACAGGTTTT
TGTA
Found at i:8933320 original size:45 final size:45
Alignment explanation
Indices: 8933270--8933394 Score: 205
Period size: 45 Copynumber: 2.8 Consensus size: 45
8933260 GGTTTTTGTA
*
8933270 CATGGCGTGTCACAGGTTTTTGTACATGGCGTGTAACACGCTAAC
1 CATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACACGCTAAC
* *
8933315 CATGGCTTGTCACAGGTTTTTGTACATGGCATGCAACACGCTAAC
1 CATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACACGCTAAC
*
8933360 CATGGCTTATCACAGGTTTTTTGTACATGGCGTGT
1 CATGGCTTGTCACAGG-TTTTTGTACATGGCGTGT
8933395 CACAGGTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 57 0.78
46 16 0.22
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (45 bp):
CATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACACGCTAAC
Found at i:8933397 original size:25 final size:24
Alignment explanation
Indices: 8933360--8933418 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
8933350 ACACGCTAAC
* *
8933360 CATGGCTTATCACAGGTTTTTTGTA
1 CATGGCGTGTCACAGG-TTTTTGTA
8933385 CATGGCGTGTCACAGGTTTTTGTA
1 CATGGCGTGTCACAGGTTTTTGTA
8933409 CATGGCGTGT
1 CATGGCGTGT
8933419 AACAAGCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (24 bp):
CATGGCGTGTCACAGGTTTTTGTA
Found at i:8933406 original size:70 final size:69
Alignment explanation
Indices: 8933315--8933459 Score: 227
Period size: 70 Copynumber: 2.1 Consensus size: 69
8933305 ACACGCTAAC
* * *
8933315 CATGGCTTGTCACAGGTTTTTGTACATGGCATGCAACACGCTAACCATGGCTTATCACAGGTTTT
1 CATGGCGTGTCACAGGTTTTTGTACATGGCATGCAACAAGCTAACCATGGCTTATCACAGG-GTT
8933380 TTGTA
65 TTGTA
* * *
8933385 CATGGCGTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATGGCTTGTCACAGGGTTT
1 CATGGCGTGTCACAGGTTTTTGTACATGGCATGCAACAAGCTAACCATGGCTTATCACAGGGTTT
8933450 TGTA
66 TGTA
8933454 CATGGC
1 CATGGC
8933460 ATGCAACACG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 13 0.19
70 56 0.81
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (69 bp):
CATGGCGTGTCACAGGTTTTTGTACATGGCATGCAACAAGCTAACCATGGCTTATCACAGGGTTT
TGTA
Found at i:8933441 original size:45 final size:45
Alignment explanation
Indices: 8933385--8933627 Score: 317
Period size: 45 Copynumber: 5.6 Consensus size: 45
8933375 GTTTTTTGTA
* * * *
8933385 CATGGCGTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAAC
1 CATGGCTTGTCACAGGGTTTTGTACATGGCGTGCAACACGCTAAC
*
8933430 CATGGCTTGTCACAGGGTTTTGTACATGGCATGCAACACGCTAAC
1 CATGGCTTGTCACAGGGTTTTGTACATGGCGTGCAACACGCTAAC
* * *
8933475 CATGGATTGTCACAGGTTTTTGTATATGGCGTGCAACACGCTAAC
1 CATGGCTTGTCACAGGGTTTTGTACATGGCGTGCAACACGCTAAC
8933520 CA-------T---AGGGTTTTGTACATGGCGTGCAACACGCTAAC
1 CATGGCTTGTCACAGGGTTTTGTACATGGCGTGCAACACGCTAAC
* *
8933555 CATAGCTTGTCACAGGGTTTTGTACATGGCGTGTAACACGCTAAC
1 CATGGCTTGTCACAGGGTTTTGTACATGGCGTGCAACACGCTAAC
*
8933600 CATGGCTTGTCACAGGTTTTTGTACATG
1 CATGGCTTGTCACAGGGTTTTGTACATG
8933628 ATATGTAACA
Statistics
Matches: 174, Mismatches: 14, Indels: 20
0.84 0.07 0.10
Matches are distributed among these distances:
35 32 0.18
38 1 0.01
42 1 0.01
45 140 0.80
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (45 bp):
CATGGCTTGTCACAGGGTTTTGTACATGGCGTGCAACACGCTAAC
Found at i:8933539 original size:35 final size:35
Alignment explanation
Indices: 8933492--8933559 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
8933482 TGTCACAGGT
*
8933492 TTTTGTATATGGCGTGCAACACGCTAACCATAGGG
1 TTTTGTACATGGCGTGCAACACGCTAACCATAGGG
8933527 TTTTGTACATGGCGTGCAACACGCTAACCATAG
1 TTTTGTACATGGCGTGCAACACGCTAACCATAG
8933560 CTTGTCACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (35 bp):
TTTTGTACATGGCGTGCAACACGCTAACCATAGGG
Found at i:8933576 original size:80 final size:80
Alignment explanation
Indices: 8933443--8933602 Score: 266
Period size: 80 Copynumber: 2.0 Consensus size: 80
8933433 GGCTTGTCAC
* * *
8933443 AGGGTTTTGTACATGGCATGCAACACGCTAACCATGGATTGTCACAGGTTTTTGTATATGGCGTG
1 AGGGTTTTGTACATGGCATGCAACACGCTAACCATAGATTGTCACAGGGTTTTGTACATGGCGTG
8933508 CAACACGCTAACCAT
66 CAACACGCTAACCAT
* *
8933523 AGGGTTTTGTACATGGCGTGCAACACGCTAACCATAGCTTGTCACAGGGTTTTGTACATGGCGTG
1 AGGGTTTTGTACATGGCATGCAACACGCTAACCATAGATTGTCACAGGGTTTTGTACATGGCGTG
*
8933588 TAACACGCTAACCAT
66 CAACACGCTAACCAT
8933603 GGCTTGTCAC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (80 bp):
AGGGTTTTGTACATGGCATGCAACACGCTAACCATAGATTGTCACAGGGTTTTGTACATGGCGTG
CAACACGCTAACCAT
Found at i:8937398 original size:24 final size:24
Alignment explanation
Indices: 8937366--8937419 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
8937356 GCACACGGTC
* *
8937366 CTCTTTCTACCTGTTTTTTTCTTT
1 CTCTTTCTACCTCTCTTTTTCTTT
*
8937390 CTCTTTCTACTTCTCTTTTTCTTT
1 CTCTTTCTACCTCTCTTTTTCTTT
*
8937414 TTCTTT
1 CTCTTT
8937420 TTTTATTGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.69
Consensus pattern (24 bp):
CTCTTTCTACCTCTCTTTTTCTTT
Found at i:8939812 original size:69 final size:72
Alignment explanation
Indices: 8939729--8939866 Score: 178
Period size: 69 Copynumber: 2.0 Consensus size: 72
8939719 TAATATCATC
* *
8939729 TCTTAAATATATTTTAATGTTATATATTTTATTTTTATTT-TTTAT-TATA-ATACTATATATTT
1 TCTTAAATATATTTTAATATTATATATTTTATTTTAATTTCTTTATATATATATA-TATA-ATTT
8939791 T-TTTTCTT
64 TATTTTCTT
* * *
8939799 TCTTTAATA-ATTTTTATATTATATATTTTGTTTTAATTTCTTTATATATATATATATAATTTTA
1 TCTTAAATATATTTTAATATTATATATTTTATTTTAATTTCTTTATATATATATATATAATTTTA
8939863 TTTT
66 TTTT
8939867 TTATATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
69 26 0.44
70 18 0.31
71 12 0.20
72 3 0.05
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (72 bp):
TCTTAAATATATTTTAATATTATATATTTTATTTTAATTTCTTTATATATATATATATAATTTTA
TTTTCTT
Found at i:8940043 original size:11 final size:12
Alignment explanation
Indices: 8940015--8940044 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
8940005 AAGTGAAAAG
*
8940015 TAAAAATATCTT
1 TAAAAATACCTT
8940027 TAAAAATACCTT
1 TAAAAATACCTT
8940039 TAAAAA
1 TAAAAA
8940045 CATTGCAGAG
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:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAAATACCTT
Found at i:8940790 original size:19 final size:19
Alignment explanation
Indices: 8940766--8940815 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
8940756 AAAAGATCAA
8940766 AAACCGAATCTATACTAGT
1 AAACCGAATCTATACTAGT
8940785 AAACCGAATCTATACTAGT
1 AAACCGAATCTATACTAGT
8940804 AAACCGAATCTA
1 AAACCGAATCTA
8940816 AGTAGCCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (19 bp):
AAACCGAATCTATACTAGT
Found at i:8953716 original size:21 final size:20
Alignment explanation
Indices: 8953676--8953716 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
8953666 AATAATGTGT
* *
8953676 AGTAATGTAAAATGACTAAC
1 AGTAATGTAAAAAGAATAAC
8953696 AGTAATGTAAAAAAGAATAAC
1 AGTAATGT-AAAAAGAATAAC
8953717 CTTCAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (20 bp):
AGTAATGTAAAAAGAATAAC
Found at i:8957045 original size:5 final size:5
Alignment explanation
Indices: 8957035--8957061 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
8957025 GGGAGAGCAA
8957035 AGAAG AGAAG AGAAG AGAAG AGAAG AG
1 AGAAG AGAAG AGAAG AGAAG AGAAG AG
8957062 CAAGTATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:8958198 original size:15 final size:16
Alignment explanation
Indices: 8958178--8958208 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8958168 TAAAAAATAT
8958178 ATAA-TTTTATTTATA
1 ATAATTTTTATTTATA
8958193 ATAATTTTTATTTATA
1 ATAATTTTTATTTATA
8958209 TGAAATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATAATTTTTATTTATA
Found at i:8960316 original size:20 final size:21
Alignment explanation
Indices: 8960293--8960350 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
8960283 ATTCATTCAA
8960293 TTTTACTCAAATTTTTAA-TT
1 TTTTACTCAAATTTTTAAGTT
** *
8960313 TTTTTTTTAAATTTTTAAGTT
1 TTTTACTCAAATTTTTAAGTT
* *
8960334 TCTCTACTCATATTTTT
1 T-TTTACTCAAATTTTT
8960351 CTTTTTTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 15 0.54
21 3 0.11
22 10 0.36
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTACTCAAATTTTTAAGTT
Found at i:8960425 original size:3 final size:3
Alignment explanation
Indices: 8960417--8960441 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8960407 TTTCTATTTA
8960417 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
8960442 TATATTTATT
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:8960450 original size:19 final size:19
Alignment explanation
Indices: 8960428--8960471 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8960418 ATTATTATTA
*
8960428 TTATTATTATTATTTATAT
1 TTATTATTATTAATTATAT
* *
8960447 TTATTTTTTTTAATTATAT
1 TTATTATTATTAATTATAT
8960466 TCTATT
1 T-TATT
8960472 TGCTAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTATTATTAATTATAT
Found at i:8960619 original size:15 final size:16
Alignment explanation
Indices: 8960601--8960635 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
8960591 CTGTTATGTG
*
8960601 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
8960616 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
8960632 AATT
1 AATT
8960636 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:8962633 original size:28 final size:28
Alignment explanation
Indices: 8962584--8962639 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
8962574 GAAGATGTAA
8962584 AAAATATACATTTGATCAATTAA-AAAT
1 AAAATATACATTTGATCAATTAAGAAAT
* * *
8962611 AAAATATATATTTTTATTAATTAAGAAAT
1 AAAATATACA-TTTGATCAATTAAGAAAT
8962640 TTACAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 11 0.46
29 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATATACATTTGATCAATTAAGAAAT
Found at i:8963006 original size:19 final size:21
Alignment explanation
Indices: 8962959--8963008 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
8962949 TTCTATTCAA
8962959 TTAT-ATTTTAA-ATTATTTT
1 TTATAATTTTAATATTATTTT
*
8962978 TTATCA-TTTAATA-TATTTT
1 TTATAATTTTAATATTATTTT
8962997 TT-TAATTTTAAT
1 TTATAATTTTAAT
8963009 TTAATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATAATTTTAATATTATTTT
Found at i:8988700 original size:21 final size:21
Alignment explanation
Indices: 8988655--8988700 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
8988645 TCATCCGTGA
* *
8988655 TGGACTGACTCCCCTTGGAGT
1 TGGACTGACTCCCCTTGCAGG
8988676 TGGACTGACTCCCCTTGCAGG
1 TGGACTGACTCCCCTTGCAGG
8988697 TGGA
1 TGGA
8988701 GTGGAAGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.26
Consensus pattern (21 bp):
TGGACTGACTCCCCTTGCAGG
Found at i:8992318 original size:20 final size:21
Alignment explanation
Indices: 8992290--8992328 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
8992280 TTATTTAATT
8992290 TTAAATAAAAAT-ATAAAAAA
1 TTAAATAAAAATAATAAAAAA
* *
8992310 TTAATTAAATATAATAAAA
1 TTAAATAAAAATAATAAAA
8992329 GAATAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAATAAAAATAATAAAAAA
Found at i:8992690 original size:2 final size:2
Alignment explanation
Indices: 8992627--8992671 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
8992617 TTTAAATTAA
*
8992627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8992668 AT AT
1 AT AT
8992672 TACGTTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8992696 original size:19 final size:19
Alignment explanation
Indices: 8992664--8992702 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8992654 TATATATATT
8992664 GTATATATTACGTTTTATA
1 GTATATATTACGTTTTATA
8992683 GNTATATA-TACGTTTTATA
1 G-TATATATTACGTTTTATA
8992702 G
1 G
8992703 ATTGAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.49
Consensus pattern (19 bp):
GTATATATTACGTTTTATA
Found at i:9001359 original size:2 final size:2
Alignment explanation
Indices: 9001354--9001379 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9001344 TTCCATGGGC
9001354 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
9001380 GTAGAGGAGC
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:9004464 original size:25 final size:24
Alignment explanation
Indices: 9004436--9004487 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
9004426 GTTAACCAAT
9004436 TTATAGAGAAAAGCCAAAAATGAGG
1 TTATAGAG-AAAGCCAAAAATGAGG
* * *
9004461 TTATGGAGTATGCCAAAAATGAGG
1 TTATAGAGAAAGCCAAAAATGAGG
9004485 TTA
1 TTA
9004488 CGAAATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.44, C:0.08, G:0.25, T:0.23
Consensus pattern (24 bp):
TTATAGAGAAAGCCAAAAATGAGG
Found at i:9004496 original size:24 final size:24
Alignment explanation
Indices: 9004448--9004496 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9004438 ATAGAGAAAA
* * *
9004448 GCCAAAAATGAGGTTATGGAGTAT
1 GCCAAAAATGAGGTTACGAAATAT
9004472 GCCAAAAATGAGGTTACGAAATAT
1 GCCAAAAATGAGGTTACGAAATAT
9004496 G
1 G
9004497 AGAAGCAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (24 bp):
GCCAAAAATGAGGTTACGAAATAT
Found at i:9008828 original size:580 final size:580
Alignment explanation
Indices: 9007721--9008880 Score: 1957
Period size: 580 Copynumber: 2.0 Consensus size: 580
9007711 CTCAGTACCC
9007721 CCATGAAATGACAATGAAAATTCTGCAATATCCAGTAGACCATTGGAGCCAAAACTTGGAAGAAA
1 CCATGAAATGACAATGAAAATTCTGCAATATCCAGTAGACCATTGGAGCCAAAACTTGGAAGAAA
* * *
9007786 AGAAAAGGAAAACGCGATTGAGAATTTAGAAGAGAGAAATGAACTATCAGCAACTCAAGAAAACT
66 AGAAAAGGAAAAAGCGATTGAGAATTGAGAAGAGAGAAATGAACCATCAGCAACTCAAGAAAACT
*
9007851 GTTAAAAACTGTGTTTCACACAGCATCATATGTCTGAGCTTACCTATGTGTGCATGTATTCAGAT
131 GTTAAAAACTGTGTTTCACACAGCATCATATGTCTGAGCTTACCCATGTGTGCATGTATTCAGAT
* *
9007916 GGTTTTATAGGTGTCTCCTCTAATGTGCGTCTATATAAGAGATAAATTTGGAGAATTCAAACAAC
196 GGTTTTATAGGTGTCTCCTCTAATGTGCATCTATATAAGAGATAAATTTGGAGAATTCAAAAAAC
*
9007981 TAAAAAAACGAAGTAATCTCTGTTATAATATCTTAGGAAGGTGAGTAAAAGAACGAAAGCTGTAG
261 TAAAAAAACGAAGTAATCTCCGTTATAATATCTTAGGAAGGTGAGTAAAAGAACGAAAGCTGTAG
* ** * * *
9008046 TGGCTAACAGATTGGTCTGTCCGAATGCCCCACACTAGGACAAAATAGCTACCCTTGGAATTCGT
326 TGGCTAACAGAGTGGTCCATCCGAATGCCCCACACTAAGACAAAATAGCTACCCCTGGAATTCAT
* * *
9008111 TTTCCCAGAGCACAATATAAACTATTCATGTTTTTCAAAAATGCAAGTTCACATATTTCAATTAT
391 TTTCCCAGAGCACAATATAAACTATTCATGTGTTTCAAAAATGCAAGTTCACATACTTCAATCAT
**
9008176 GGGATAATGCTCACAACAACTGTTTTGATAATTTTAGGATCACACTAGCTGTAAGTGATGTTGGT
456 GGGATAATGCTCACAACAACTGTTTTGATAATTTTAGGATCACACTAGCTGTAAGTGATGTCAGT
*
9008241 TGATGCTGGGCAACATTGGTAAAGTGACAAAAGTTGGAAATGCAGGGGAATGTGCTTTCA
521 TGATGCTGGGCAACATTGATAAAGTGACAAAAGTTGGAAATGCAGGGGAATGTGCTTTCA
* * *
9008301 CCATGAGATGACAATGAAAATTCTGCAATTTCCAGTAGACCATTGGCA-CCAACACTTGGAAGAA
1 CCATGAAATGACAATGAAAATTCTGCAATATCCAGTAGACCATTGG-AGCCAAAACTTGGAAGAA
* *
9008365 AAGAAAAGGAAAAAGCGATTGAGGATTGAGAAGAGTGAAATGAACCAT-AGGCAACTCAAGAAAA
65 AAGAAAAGGAAAAAGCGATTGAGAATTGAGAAGAGAGAAATGAACCATCA-GCAACTCAAGAAAA
*
9008429 CTGTTAAAAACTGTGTTTCACACAGCATCATATGTCTGAGCTTACCCATGTGTGCGTGTATTCAG
129 CTGTTAAAAACTGTGTTTCACACAGCATCATATGTCTGAGCTTACCCATGTGTGCATGTATTCAG
9008494 ATGGTTTTATAGGTGTCTCCTCTAATGTGCATCTATATAAGAGATAAATTTGGAGAATTCAAAAA
194 ATGGTTTTATAGGTGTCTCCTCTAATGTGCATCTATATAAGAGATAAATTTGGAGAATTCAAAAA
* *
9008559 ACTAAAACAAA-GAAGTAATCTCCGTTATAATATCTTAGGTAGGTGAGTAAAAGAATGAAAGCTG
259 ACTAAAA-AAACGAAGTAATCTCCGTTATAATATCTTAGGAAGGTGAGTAAAAGAACGAAAGCTG
*
9008623 TAGTGGCTAATAGAGTGGTCCATCCGAATGCCCCACACTAAGACAAAATAGCTACCCCTGGAATT
323 TAGTGGCTAACAGAGTGGTCCATCCGAATGCCCCACACTAAGACAAAATAGCTACCCCTGGAATT
* ** **
9008688 CATTTTCCCAGATCATGATATAAACTATTCATGTGTTTCACCAATGCAAGTTCACATACTTCAAT
388 CATTTTCCCAGAGCACAATATAAACTATTCATGTGTTTCAAAAATGCAAGTTCACATACTTCAAT
**
9008753 CATGGGATAATGCTCACAACAACTGTTTTGATGCTTTTAGGATCACACTAGCTGTAAGTGATGTC
453 CATGGGATAATGCTCACAACAACTGTTTTGATAATTTTAGGATCACACTAGCTGTAAGTGATGTC
9008818 AGTTGATGCTGGGCAACATTGATAAAGTGACAAAAGTTGGAAATGCAGGGGAATGTGCTTTCA
518 AGTTGATGCTGGGCAACATTGATAAAGTGACAAAAGTTGGAAATGCAGGGGAATGTGCTTTCA
9008881 GGAAATGATA
Statistics
Matches: 542, Mismatches: 35, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
579 1 0.00
580 537 0.99
581 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (580 bp):
CCATGAAATGACAATGAAAATTCTGCAATATCCAGTAGACCATTGGAGCCAAAACTTGGAAGAAA
AGAAAAGGAAAAAGCGATTGAGAATTGAGAAGAGAGAAATGAACCATCAGCAACTCAAGAAAACT
GTTAAAAACTGTGTTTCACACAGCATCATATGTCTGAGCTTACCCATGTGTGCATGTATTCAGAT
GGTTTTATAGGTGTCTCCTCTAATGTGCATCTATATAAGAGATAAATTTGGAGAATTCAAAAAAC
TAAAAAAACGAAGTAATCTCCGTTATAATATCTTAGGAAGGTGAGTAAAAGAACGAAAGCTGTAG
TGGCTAACAGAGTGGTCCATCCGAATGCCCCACACTAAGACAAAATAGCTACCCCTGGAATTCAT
TTTCCCAGAGCACAATATAAACTATTCATGTGTTTCAAAAATGCAAGTTCACATACTTCAATCAT
GGGATAATGCTCACAACAACTGTTTTGATAATTTTAGGATCACACTAGCTGTAAGTGATGTCAGT
TGATGCTGGGCAACATTGATAAAGTGACAAAAGTTGGAAATGCAGGGGAATGTGCTTTCA
Found at i:9016597 original size:33 final size:33
Alignment explanation
Indices: 9016554--9016626 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
9016544 GATCAAAATT
*
9016554 ACCTCCAATATTAAGTGGGCTGTCAGTGGTCCA
1 ACCTCCAATATTAAGTGGGCTGTCACTGGTCCA
* *
9016587 ACCTCTAATATTAGGTGGGCTGTCACTGGTCCA
1 ACCTCCAATATTAAGTGGGCTGTCACTGGTCCA
9016620 ACCTCCA
1 ACCTCCA
9016627 GCCAAAGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (33 bp):
ACCTCCAATATTAAGTGGGCTGTCACTGGTCCA
Found at i:9018432 original size:16 final size:17
Alignment explanation
Indices: 9018413--9018450 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
9018403 AAATGAATTA
*
9018413 AAAAAATAAAAATAAT-
1 AAAAAATAAAAAAAATG
*
9018429 AAAAATTAAAAAAAATG
1 AAAAAATAAAAAAAATG
9018446 AAAAA
1 AAAAA
9018451 GGGTGGAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAAATAAAAAAAATG
Found at i:9019524 original size:21 final size:22
Alignment explanation
Indices: 9019479--9019529 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
9019469 TTATTTGTTC
*
9019479 TAAATTATTTTAGTATAACATTT
1 TAAATT-TTTTAGTATAACAGTT
*
9019502 TAAATTTTTTAG-ATGACAGTT
1 TAAATTTTTTAGTATAACAGTT
9019523 TAAATTT
1 TAAATTT
9019530 AGGAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.54
22 6 0.23
23 6 0.23
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (22 bp):
TAAATTTTTTAGTATAACAGTT
Found at i:9020046 original size:17 final size:18
Alignment explanation
Indices: 9020017--9020054 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
9020007 CATGACATTA
9020017 AATAAATAAAAAATAAAT
1 AATAAATAAAAAATAAAT
*
9020035 AATAAA-AAAAAATAACT
1 AATAAATAAAAAATAAAT
9020052 AAT
1 AAT
9020055 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AATAAATAAAAAATAAAT
Found at i:9020202 original size:14 final size:14
Alignment explanation
Indices: 9020183--9020226 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
9020173 TTGCTTATGA
*
9020183 AAAAATATAATAAT
1 AAAAATATAAAAAT
9020197 AAAAATATAAAAAT
1 AAAAATATAAAAAT
9020211 ATATAAA-ATAAAAAT
1 A-A-AAATATAAAAAT
9020226 A
1 A
9020227 GTATGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 14 0.52
15 10 0.37
16 3 0.11
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATATAAAAAT
Found at i:9020220 original size:23 final size:23
Alignment explanation
Indices: 9020182--9020226 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9020172 ATTGCTTATG
9020182 AAAAAATATAATAATAAAAATAT
1 AAAAAATATAATAATAAAAATAT
9020205 AAAAATATATAA-AATAAAAATA
1 AAAAA-ATATAATAATAAAAATA
9020227 GTATGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAAAATATAATAATAAAAATAT
Found at i:9020391 original size:15 final size:16
Alignment explanation
Indices: 9020360--9020412 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
9020350 AATAATAAGA
9020360 AATAAGAATAGAAAATAT
1 AATAA-AATA-AAAATAT
* *
9020378 GATAACA-AAAAATAT
1 AATAAAATAAAAATAT
9020393 AATAAAATAAAAATAAT
1 AATAAAATAAAAAT-AT
9020410 AAT
1 AAT
9020413 TAATTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 12 0.41
16 7 0.24
17 6 0.21
18 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (16 bp):
AATAAAATAAAAATAT
Found at i:9020399 original size:12 final size:13
Alignment explanation
Indices: 9020343--9020435 Score: 62
Period size: 14 Copynumber: 6.6 Consensus size: 13
9020333 GTAAAGTATA
9020343 AAAAAATAATAAT
1 AAAAAATAATAAT
* *
9020356 AAGAAATAAGAAT
1 AAAAAATAATAAT
* *
9020369 AGAAAATATGATAAC
1 A-AAAA-ATAATAAT
9020384 AAAAAAT-ATAAT
1 AAAAAATAATAAT
*
9020396 AAAATAAAAATAAT
1 AAAA-AATAATAAT
9020410 AATTAATTAATAATAACT
1 AA--AA--AATAATAA-T
9020428 AAAAAATA
1 AAAAAATA
9020436 TAGATAATTG
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
12 8 0.13
13 16 0.25
14 18 0.29
15 6 0.10
16 4 0.06
17 8 0.13
18 3 0.05
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:9021395 original size:16 final size:16
Alignment explanation
Indices: 9021374--9021404 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9021364 TATTTATAAA
9021374 AATTAATAAATAAATT
1 AATTAATAAATAAATT
9021390 AATTAATAAATAAAT
1 AATTAATAAATAAAT
9021405 ATATGACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTAATAAATAAATT
Found at i:9022886 original size:30 final size:30
Alignment explanation
Indices: 9022852--9022929 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
9022842 ATAAACTTTC
*
9022852 AAAATTTGATAGAAATTTTTATAAAATACA
1 AAAATTTAATAGAAATTTTTATAAAATACA
9022882 AAAATTTAATAGAAATTTTTATAAAATACA
1 AAAATTTAATAGAAATTTTTATAAAATACA
9022912 AAAATTTAATAGAAATTT
1 AAAATTTAATAGAAATTT
9022930 GTAGTGAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATTTAATAGAAATTTTTATAAAATACA
Found at i:9026386 original size:28 final size:29
Alignment explanation
Indices: 9026328--9026391 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
9026318 GCAAATTTTT
** *
9026328 AAAAATTACACTTTTACCCCTGTAAAGTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
* *
9026357 AAAAATTATATTTTTACCCC-AAAAACTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
9026385 AAAAATT
1 AAAAATT
9026392 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCTAAAAACTG
Found at i:9030614 original size:16 final size:17
Alignment explanation
Indices: 9030576--9030616 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
9030566 AATATGATTA
*
9030576 AAATTTAAATATGAGTG
1 AAATTTAAATATCAGTG
9030593 --ATTTAAATATCA-TG
1 AAATTTAAATATCAGTG
9030607 AAATTTAAAT
1 AAATTTAAAT
9030617 TTGAATACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (17 bp):
AAATTTAAATATCAGTG
Found at i:9031193 original size:11 final size:11
Alignment explanation
Indices: 9031163--9031195 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9031153 AGCTATTATT
*
9031163 TTTCATAAGAG
1 TTTCATAATAG
9031174 TTTCATAATAG
1 TTTCATAATAG
9031185 TTTCATAATAG
1 TTTCATAATAG
9031196 ATTTTAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (11 bp):
TTTCATAATAG
Found at i:9033756 original size:20 final size:19
Alignment explanation
Indices: 9033733--9033785 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
9033723 TTTTTAGATT
9033733 ATATTTCCTTTTTCTTTATA
1 ATATTT-CTTTTTCTTTATA
* *
9033753 ATATTGTTTTTTTTCTTTCTA
1 ATA-T-TTCTTTTTCTTTATA
9033774 ATATTTCTTTTT
1 ATATTTCTTTTT
9033786 ATTGCTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.25
20 4 0.14
21 15 0.54
22 2 0.07
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (19 bp):
ATATTTCTTTTTCTTTATA
Found at i:9033784 original size:21 final size:20
Alignment explanation
Indices: 9033741--9033818 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 20
9033731 TTATATTTCC
*
9033741 TTTTTCTTTATAATATTGTTT
1 TTTTTCTTTCTAATATT-TTT
9033762 TTTTTCTTTCTAATATTTCTT
1 TTTTTCTTTCTAATATTT-TT
9033783 TTTATTGCTTTC--ATATTTTT
1 TTT-TT-CTTTCTAATATTTTT
*
9033803 CATTTTTCTTTTTAAT
1 --TTTTTCTTTCTAAT
9033819 CTCAATTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
20 7 0.15
21 29 0.60
22 7 0.15
23 5 0.10
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTCTTTCTAATATTTTT
Found at i:9049248 original size:40 final size:40
Alignment explanation
Indices: 9049200--9049346 Score: 186
Period size: 40 Copynumber: 3.6 Consensus size: 40
9049190 AAAGATCTTC
*
9049200 AACATAAACTTAAATAACTAAAAATAAATATCCATACAAT
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAT
* * * * * *
9049240 GATATAAACTTAAATAACTATACATTAATATCCAAATAAT
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAT
* * *
9049280 AACATAAACTTAAATAACTAAACACAAAGATCCAAACAAAT
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAAC-AAT
*
9049321 AACATAAACTTAAATAACAAAAAATA
1 AACATAAACTTAAATAACTAAAAATA
9049347 TAATTTTATT
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 63 0.71
41 26 0.29
ACGTcount: A:0.60, C:0.15, G:0.01, T:0.24
Consensus pattern (40 bp):
AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAT
Found at i:9049297 original size:15 final size:15
Alignment explanation
Indices: 9049277--9049339 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 15
9049267 ATATCCAAAT
9049277 AATAACATAAACTTA
1 AATAACATAAACTTA
**
9049292 AATAAC-TAAACACA
1 AATAACATAAACTTA
* * *
9049306 AAGATC-CAAAC--A
1 AATAACATAAACTTA
9049318 AATAACATAAACTTA
1 AATAACATAAACTTA
9049333 AATAACA
1 AATAACA
9049340 AAAAATATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
14 14 0.38
15 14 0.38
ACGTcount: A:0.62, C:0.17, G:0.02, T:0.19
Consensus pattern (15 bp):
AATAACATAAACTTA
Found at i:9049440 original size:23 final size:25
Alignment explanation
Indices: 9049413--9049461 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
9049403 TTATATTTAA
*
9049413 AGTATATATACTAAA-AGT-ATTAT
1 AGTATATATACAAAATAGTAATTAT
9049436 AGTATATATACAAAATAGTAATTAT
1 AGTATATATACAAAATAGTAATTAT
9049461 A
1 A
9049462 TTCTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.61
24 3 0.13
25 6 0.26
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (25 bp):
AGTATATATACAAAATAGTAATTAT
Found at i:9053469 original size:13 final size:13
Alignment explanation
Indices: 9053451--9053475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9053441 TTCCAAAAAA
9053451 TTTATAAAATCAT
1 TTTATAAAATCAT
9053464 TTTATAAAATCA
1 TTTATAAAATCA
9053476 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:9054727 original size:19 final size:19
Alignment explanation
Indices: 9054703--9054740 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9054693 ACTTTTAAAC
9054703 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9054722 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9054741 AGTCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:9059137 original size:11 final size:11
Alignment explanation
Indices: 9059121--9059151 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
9059111 TTAAAATATT
9059121 AATAATTAACA
1 AATAATTAACA
*
9059132 AATAATTAATA
1 AATAATTAACA
9059143 AATAATTAA
1 AATAATTAA
9059152 AATAATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATTAACA
Found at i:9059963 original size:35 final size:35
Alignment explanation
Indices: 9059917--9059987 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
9059907 AACGATTTCT
* *
9059917 TTGTTCTCGTTGTTATGGAGCAGCTCCTAGAGTCC
1 TTGTTCTCGTTGTTATGAAGCAGCTACTAGAGTCC
* * *
9059952 TTGTTGTCGTTGTTATGAAGTAGCTATTAGAGTCC
1 TTGTTCTCGTTGTTATGAAGCAGCTACTAGAGTCC
9059987 T
1 T
9059988 CCATGAGGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (35 bp):
TTGTTCTCGTTGTTATGAAGCAGCTACTAGAGTCC
Found at i:9060204 original size:21 final size:21
Alignment explanation
Indices: 9060178--9060250 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
9060168 GGATATCTCT
9060178 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
* ** *
9060199 TTTAAATGT-AATTAATCCT-TA
1 TTTAAATTTAAACAAAT--TAAA
9060220 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
*
9060241 TTGAAATTTA
1 TTTAAATTTA
9060251 TATCCTATCA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 6 0.15
21 27 0.69
22 6 0.15
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (21 bp):
TTTAAATTTAAACAAATTAAA
Found at i:9071872 original size:13 final size:13
Alignment explanation
Indices: 9071855--9071893 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
9071845 AAATTAACAG
9071855 AAAAAAACCCTAT
1 AAAAAAACCCTAT
*
9071868 TAAAAAA-CCTAT
1 AAAAAAACCCTAT
*
9071880 AAAAAAACCATAT
1 AAAAAAACCCTAT
9071893 A
1 A
9071894 TCATGGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAACCCTAT
Found at i:9072849 original size:3 final size:3
Alignment explanation
Indices: 9072843--9072882 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9072833 GAGTGGTGTT
9072843 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9072883 ATATGTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9084945 original size:18 final size:18
Alignment explanation
Indices: 9084922--9084959 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
9084912 TACTGTTCAT
9084922 GATATATTTGAAGTCCCA
1 GATATATTTGAAGTCCCA
*
9084940 GATATATTTGAAGTTCCA
1 GATATATTTGAAGTCCCA
9084958 GA
1 GA
9084960 AACCAGTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (18 bp):
GATATATTTGAAGTCCCA
Found at i:9094555 original size:24 final size:25
Alignment explanation
Indices: 9094528--9094643 Score: 92
Period size: 25 Copynumber: 4.5 Consensus size: 25
9094518 CACCATATAC
*
9094528 AAAAACATGTTACACGTCATGTTAAA
1 AAAAACATATTACACGTCATGTT-AA
* *
9094554 AAAATATTATTATTACACGTCATG-TAC
1 AAAA-A-CA-TATTACACGTCATGTTAA
9094581 AAAAACATATTACACGTCATGGTTAA
1 AAAAACATATTACACGTCAT-GTTAA
* * * *
9094607 AAAGA-TTCTTACACTTCATGTTGAA
1 AAAAACATATTACACGTCATGTT-AA
*
9094632 AAAAAAATATTA
1 AAAAACATATTA
9094644 TTGTTACATG
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
24 16 0.23
25 19 0.27
26 15 0.21
27 6 0.08
28 2 0.03
29 13 0.18
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (25 bp):
AAAAACATATTACACGTCATGTTAA
Found at i:9094752 original size:80 final size:82
Alignment explanation
Indices: 9094551--9094914 Score: 346
Period size: 81 Copynumber: 4.4 Consensus size: 82
9094541 ACGTCATGTT
* * *
9094551 AAAAAAATATTATTATTACACGTCATGTACAAAAACATATTACACGTCATGGTT--AAAAAGATT
1 AAAAAAATATTATTGTTACACGTCATATACAAAAACATATTACACGTCATAGTTAAAAAAAGATT
* *
9094614 CTTACACTTCATGTTGAA
66 CTTACACATCATATT-AA
* * *
9094632 AAAAAAATATTATTGTTACATGTCATATACAAAAACATGTTACACCTCATAGTT-AAAAAAGATT
1 AAAAAAATATTATTGTTACACGTCATATACAAAAACATATTACACGTCATAGTTAAAAAAAGATT
* *
9094696 TTTACACACCATATT-A
66 CTTACACATCATATTAA
* * * * * * *
9094712 AAAAAAATGA-TGTTGTTATACGTCATGTACAAAAATATGTTATACGTCATAGTTAAAAAAAAAG
1 AAAAAAAT-ATTATTGTTACACGTCATATACAAAAACATATTACACGTCATAGTTAAAAAAAGA-
* *
9094776 TTGTTACACGTCATATTAA
64 TTCTTACACATCATATTAA
* * * *
9094795 AAAAAAATATTATTGTCACACGTTATATACAAAAATATATTACACGTCAT-GTTGAAAAAATATT
1 AAAAAAATATTATTGTTACACGTCATATACAAAAACATATTACACGTCATAGTT-AAAAAA-A-G
* * *
9094859 ATTATTACACGTCATGTTTAA
63 ATTCTTACACATCAT-ATTAA
* * *
9094880 AAAATATTATTATTATTACACGTCATA-ATCAAAAA
1 AAAAAAATATTATTGTTACACGTCATATA-CAAAAA
9094915 AAATTTGTTA
Statistics
Matches: 236, Mismatches: 36, Indels: 18
0.81 0.12 0.06
Matches are distributed among these distances:
80 46 0.19
81 56 0.24
82 38 0.16
83 48 0.20
84 15 0.06
85 33 0.14
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (82 bp):
AAAAAAATATTATTGTTACACGTCATATACAAAAACATATTACACGTCATAGTTAAAAAAAGATT
CTTACACATCATATTAA
Found at i:9094891 original size:55 final size:56
Alignment explanation
Indices: 9094755--9094891 Score: 129
Period size: 55 Copynumber: 2.4 Consensus size: 56
9094745 AATATGTTAT
* * * *
9094755 ACGTCATAGTTAAAAAAAAAGTTGTTACACGTCATATTAAAAAAAAATATTATTGTCAC
1 ACGTCAT-GTTTAAAAAATA-TTATTACACGTCATATT-AAAAAAAATATTATTATCAC
* * * * *
9094814 ACGT--TATATACAAAAATA-TATTACACGTCATGTT-GAAAAAATATTATTATTAC
1 ACGTCATGTTTA-AAAAATATTATTACACGTCATATTAAAAAAAATATTATTATCAC
9094867 ACGTCATGTTTAAAAAATATTATTA
1 ACGTCATGTTTAAAAAATATTATTA
9094892 TTATTACACG
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
53 20 0.32
54 7 0.11
55 23 0.37
56 2 0.03
57 7 0.11
59 4 0.06
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (56 bp):
ACGTCATGTTTAAAAAATATTATTACACGTCATATTAAAAAAAATATTATTATCAC
Found at i:9094896 original size:32 final size:29
Alignment explanation
Indices: 9094537--9094905 Score: 122
Period size: 24 Copynumber: 13.4 Consensus size: 29
9094527 CAAAAACATG
9094537 TTACACGTCATGTTAAAAAAATATTATTA
1 TTACACGTCATGTTAAAAAAATATTATTA
* *
9094566 TTACACGTCATG-T-ACAAAA-A-CA-TA
1 TTACACGTCATGTTAAAAAAATATTATTA
* *
9094590 TTACACGTCATGGTT---AAAA-A-GATTC
1 TTACACGTCAT-GTTAAAAAAATATTATTA
* *
9094615 TTACACTTCATGTTGAAAAAAAAATATTATTG
1 TTACACGTCATGTT---AAAAAAATATTATTA
* * * * *
9094647 TTACATGTCAT-AT-ACAAAA-A-CA-TG
1 TTACACGTCATGTTAAAAAAATATTATTA
*
9094671 TTACACCTCATAGTTAAAAAAGAT-TT-TTA
1 TTACACGTCAT-GTTAAAAAA-ATATTATTA
* * * *
9094700 -CACAC--CATATTAAAAAAA-ATGATGTTG
1 TTACACGTCATGTTAAAAAAATAT--TATTA
* * *
9094727 TTATACGTCATG-TACAAAAATA-TGTTA
1 TTACACGTCATGTTAAAAAAATATTATTA
*
9094754 -T--ACGTCATAGTTAAAAAAA-A--AGTTG
1 TTACACGTCAT-GTTAAAAAAATATTA-TTA
* *
9094779 TTACACGTCATATTAAAAAAAAATATTATTG
1 TTACACGTCATGTT--AAAAAAATATTATTA
* * * *
9094810 TCACACGTTAT-AT-ACAAAA-A-TA-TA
1 TTACACGTCATGTTAAAAAAATATTATTA
*
9094834 TTACACGTCATGTTGAAAAAATATTATTA
1 TTACACGTCATGTTAAAAAAATATTATTA
9094863 TTACACGTCATGTTTAAAAAATATTATTATTA
1 TTACACGTCATG-TTAAAAAA-A-TATTATTA
9094895 TTACACGTCAT
1 TTACACGTCAT
9094906 AATCAAAAAA
Statistics
Matches: 255, Mismatches: 40, Indels: 87
0.67 0.10 0.23
Matches are distributed among these distances:
24 52 0.20
25 29 0.11
26 23 0.09
27 28 0.11
28 18 0.07
29 41 0.16
30 17 0.07
31 15 0.06
32 32 0.13
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (29 bp):
TTACACGTCATGTTAAAAAAATATTATTA
Found at i:9094914 original size:32 final size:32
Alignment explanation
Indices: 9094855--9094915 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
9094845 GTTGAAAAAA
** *
9094855 TATTATTATTACACGTCATGTTTAAAAAATAT
1 TATTATTATTACACGTCATAATCAAAAAATAT
9094887 TATTATTATTACACGTCATAATCAAAAAA
1 TATTATTATTACACGTCATAATCAAAAAA
9094916 AATTTGTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.39
Consensus pattern (32 bp):
TATTATTATTACACGTCATAATCAAAAAATAT
Found at i:9097470 original size:11 final size:13
Alignment explanation
Indices: 9097449--9097491 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
9097439 GTATTTTGAT
9097449 ATTATATTGAAAA
1 ATTATATTGAAAA
9097462 ATTA-A-TGAAAA
1 ATTATATTGAAAA
9097473 ACTTATATTGAAAA
1 A-TTATATTGAAAA
9097487 ATTAT
1 ATTAT
9097492 TGATATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.26
12 4 0.15
13 9 0.33
14 7 0.26
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (13 bp):
ATTATATTGAAAA
Found at i:9099308 original size:22 final size:23
Alignment explanation
Indices: 9099283--9099330 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
9099273 ATTTCTTCTC
*
9099283 TTTAATTATTC-TTTCAGTTATT
1 TTTAATTATTCTTTTAAGTTATT
*
9099305 TTTATTTATTCTTTTAAGTTATT
1 TTTAATTATTCTTTTAAGTTATT
9099328 TTT
1 TTT
9099331 CATAACACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTAATTATTCTTTTAAGTTATT
Found at i:9099820 original size:59 final size:59
Alignment explanation
Indices: 9099740--9099857 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
9099730 AATAAAAAAA
* *
9099740 TTATAAATTTATTTATTCCCTGAAGTGAATGCAATATCATTTAATAATTACGATCATGG
1 TTATAAATCTATCTATTCCCTGAAGTGAATGCAATATCATTTAATAATTACGATCATGG
* * *
9099799 TTATAAATCTATCTATTCCCTGAAGTGAATGCTATATTATTTAATAATTATGATCATGG
1 TTATAAATCTATCTATTCCCTGAAGTGAATGCAATATCATTTAATAATTACGATCATGG
9099858 ATATGGAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (59 bp):
TTATAAATCTATCTATTCCCTGAAGTGAATGCAATATCATTTAATAATTACGATCATGG
Found at i:9100089 original size:18 final size:18
Alignment explanation
Indices: 9100036--9100092 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
9100026 TAAAAAATGT
* *
9100036 ATAATCCACCAGAAGTGG
1 ATAACCCACCAAAAGTGG
* * *
9100054 ATAACCCATCATATGTGG
1 ATAACCCACCAAAAGTGG
*
9100072 ATCACCCACCAAAAGTGG
1 ATAACCCACCAAAAGTGG
9100090 ATA
1 ATA
9100093 TATACTTGTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (18 bp):
ATAACCCACCAAAAGTGG
Found at i:9105644 original size:14 final size:14
Alignment explanation
Indices: 9105627--9105674 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
9105617 TTCTCTACAC
9105627 CTTTTTCTCTTTTT
1 CTTTTTCTCTTTTT
*
9105641 CTTTTTCTC-TTCT
1 CTTTTTCTCTTTTT
*
9105654 CTTTTGTGTCTTTTT
1 CTTTT-TCTCTTTTT
*
9105669 ATTTTT
1 CTTTTT
9105675 ATTTCTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 8 0.29
14 13 0.46
15 7 0.25
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (14 bp):
CTTTTTCTCTTTTT
Found at i:9110242 original size:53 final size:53
Alignment explanation
Indices: 9110177--9110337 Score: 286
Period size: 53 Copynumber: 3.0 Consensus size: 53
9110167 TTCAAAAGCA
* **
9110177 TATGGGGTTGTATAACTCTTCATGGACTAGAACCTCTTAGATGGAAATATTTG
1 TATGGGGATGTATAGTTCTTCATGGACTAGAACCTCTTAGATGGAAATATTTG
*
9110230 TATGGGGATGTATAGTTCTTCATGGACTAGAACCTCTTAAATGGAAATATTTG
1 TATGGGGATGTATAGTTCTTCATGGACTAGAACCTCTTAGATGGAAATATTTG
9110283 TATGGGGATGTATAGTTCTTCATGGACTAGAACCTCTTAGATGGAAATATTTG
1 TATGGGGATGTATAGTTCTTCATGGACTAGAACCTCTTAGATGGAAATATTTG
9110336 TA
1 TA
9110338 CGGTTGATTG
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 103 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (53 bp):
TATGGGGATGTATAGTTCTTCATGGACTAGAACCTCTTAGATGGAAATATTTG
Found at i:9123031 original size:61 final size:60
Alignment explanation
Indices: 9122936--9123058 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 60
9122926 TTTAGCTCAC
9122936 TTGCACTCCCTTCAAAATCGGATATGTAAGTTTCTTCAAGTACTTTAATCCAAGTTTCATT
1 TTGCACTCCCTTCAAAATCGGATATGTAAGTTTCTTCAAGTACTTTAATCCAAGTTTC-TT
* *
9122997 TTGCACTCCCTTCAACATCGGATATGTAAGTTTCTTCAAGTTCTTTAATCCAAGTTTCTT
1 TTGCACTCCCTTCAAAATCGGATATGTAAGTTTCTTCAAGTACTTTAATCCAAGTTTCTT
9123057 TT
1 TT
9123059 AGCTTCATGA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 4 0.07
61 56 0.93
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.41
Consensus pattern (60 bp):
TTGCACTCCCTTCAAAATCGGATATGTAAGTTTCTTCAAGTACTTTAATCCAAGTTTCTT
Found at i:9133220 original size:2 final size:2
Alignment explanation
Indices: 9133213--9133240 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9133203 GCATGCGCAC
9133213 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9133241 TCTACTAAAC
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):
CT
Found at i:9140537 original size:15 final size:15
Alignment explanation
Indices: 9140504--9140551 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9140494 GTTTGGTATT
*
9140504 TTATAATATAATATAA
1 TTATAA-ATAATATGA
*
9140520 TTATAAATAATGTGA
1 TTATAAATAATATGA
* *
9140535 TTACAAGTAATATGA
1 TTATAAATAATATGA
9140550 TT
1 TT
9140552 GTAGAAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 21 0.78
16 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (15 bp):
TTATAAATAATATGA
Found at i:9144481 original size:24 final size:24
Alignment explanation
Indices: 9144449--9144804 Score: 320
Period size: 24 Copynumber: 14.8 Consensus size: 24
9144439 TATTTTCACT
* *
9144449 ATGTACAGAAACATGTGACACGTC
1 ATGTACAAAAACATGTGACACGCC
* *
9144473 ATGTACAGAAATATGTGACACGCC
1 ATGTACAAAAACATGTGACACGCC
* *
9144497 ATGTACAAAAATATGTAACACGCC
1 ATGTACAAAAACATGTGACACGCC
* * *
9144521 ATGTA-AAGGAACATATGACATGCC
1 ATGTACAA-AAACATGTGACACGCC
* * * *
9144545 ATGTACAGAAATATGTAACACGTC
1 ATGTACAAAAACATGTGACACGCC
* * *
9144569 ATGTATAAAAATATGTGACACGTC
1 ATGTACAAAAACATGTGACACGCC
* *
9144593 ATGTACAAAAATATGTGACTCGCC
1 ATGTACAAAAACATGTGACACGCC
* *
9144617 ATGTACAAAAACATGTGACTCGTC
1 ATGTACAAAAACATGTGACACGCC
* *
9144641 ATGTACAAAAACATGTGACTCACC
1 ATGTACAAAAACATGTGACACGCC
* *
9144665 ATGTACAAAAACATGTGACTCACC
1 ATGTACAAAAACATGTGACACGCC
*
9144689 ATGTACAAAAACATATGACACGCC
1 ATGTACAAAAACATGTGACACGCC
* * * * *
9144713 ATATACAGAAATATGTGACATGTC
1 ATGTACAAAAACATGTGACACGCC
* *
9144737 ATGTA-AAGGAATATGTGACACGCC
1 ATGTACAA-AAACATGTGACACGCC
* * * * * *
9144761 ATATATAGAAACATATAACACGCT
1 ATGTACAAAAACATGTGACACGCC
* *
9144785 ATATATAAAAACATGTGACA
1 ATGTACAAAAACATGTGACA
9144805 AGTCATGGTT
Statistics
Matches: 278, Mismatches: 50, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
23 3 0.01
24 273 0.98
25 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (24 bp):
ATGTACAAAAACATGTGACACGCC
Found at i:9144947 original size:32 final size:32
Alignment explanation
Indices: 9144902--9144965 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
9144892 AAAAAGGTTG
9144902 TTACACGCAATGTTGAAAAAAAAATATTGTTA
1 TTACACGCAATGTTGAAAAAAAAATATTGTTA
* *
9144934 TTACACGTC-ATGTTGAAAAAATATTATTGTTA
1 TTACACG-CAATGTTGAAAAAAAAATATTGTTA
9144966 CACGACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (32 bp):
TTACACGCAATGTTGAAAAAAAAATATTGTTA
Found at i:9144981 original size:29 final size:28
Alignment explanation
Indices: 9144920--9144994 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
9144910 AATGTTGAAA
* * * *
9144920 AAAAAATATTGTTATTACACGTCATGTTG
1 AAAAAATATT-TTGTTACACGACATATTC
9144949 AAAAAATATTATTGTTACACGACATATTC
1 AAAAAATATT-TTGTTACACGACATATTC
*
9144978 -AAAAACATTTTGTTACA
1 AAAAAATATTTTGTTACA
9144995 TGTTAATACT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 8 0.20
28 8 0.20
29 24 0.60
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (28 bp):
AAAAAATATTTTGTTACACGACATATTC
Found at i:9145176 original size:15 final size:15
Alignment explanation
Indices: 9145156--9145185 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9145146 GGGAACAAAA
*
9145156 ACCAAAAATTGCAAC
1 ACCAAAAATTACAAC
9145171 ACCAAAAATTACAAC
1 ACCAAAAATTACAAC
9145186 CAAACACGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.27, G:0.03, T:0.13
Consensus pattern (15 bp):
ACCAAAAATTACAAC
Found at i:9147127 original size:6 final size:7
Alignment explanation
Indices: 9147108--9147134 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
9147098 ATATTCAATC
9147108 TATTTTT
1 TATTTTT
9147115 TATTTTT
1 TATTTTT
9147122 TATTTTT
1 TATTTTT
9147129 TATTTT
1 TATTTT
9147135 AAATCAAATG
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:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:9149763 original size:30 final size:30
Alignment explanation
Indices: 9149720--9149777 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
9149710 AGCACAAGGG
** *
9149720 TTTATTTGGATATAAATCAAAAA-ATAAAAA
1 TTTATTTAAATAT-AATAAAAAAGATAAAAA
9149750 TTTATTTAAATATAATAAAAAAGATAAA
1 TTTATTTAAATATAATAAAAAAGATAAA
9149778 TCAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (30 bp):
TTTATTTAAATATAATAAAAAAGATAAAAA
Found at i:9150429 original size:13 final size:15
Alignment explanation
Indices: 9150398--9150433 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
9150388 TTAAATAAAA
9150398 AATA-TAATTTATAT
1 AATATTAATTTATAT
9150412 AATATTAATTT-T-T
1 AATATTAATTTATAT
9150425 AATATTAAT
1 AATATTAAT
9150434 AAAAAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 5 0.24
15 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTAATTTATAT
Found at i:9150547 original size:17 final size:18
Alignment explanation
Indices: 9150525--9150564 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
9150515 ATATCTAACG
9150525 AAATATTT-TTTAAAAAT
1 AAATATTTATTTAAAAAT
9150542 AAATATTTATTTAAAAAT
1 AAATATTTATTTAAAAAT
*
9150560 TAATA
1 AAATA
9150565 AATTAATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATTTATTTAAAAAT
Found at i:9151421 original size:30 final size:30
Alignment explanation
Indices: 9151387--9151445 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
9151377 AGTCAATGTG
* *
9151387 TTTTTATTTTTAGTCAAATAAGTTTTTATA
1 TTTTTATTATGAGTCAAATAAGTTTTTATA
9151417 TTTTTATTATGAGTCAAATAAGTTTTTAT
1 TTTTTATTATGAGTCAAATAAGTTTTTAT
9151446 GACTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTTTATTATGAGTCAAATAAGTTTTTATA
Found at i:9153476 original size:28 final size:26
Alignment explanation
Indices: 9153404--9153476 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 26
9153394 AATAAATATT
*
9153404 ATATATTTTTATTAAATTTTAATATTAAA
1 ATATA-TTTTATTAAA--TTAAAATTAAA
**
9153433 ATATATTTTAAAAAATTAAAATTAAA
1 ATATATTTTATTAAATTAAAATTAAA
9153459 ATATATTATTATTTAAAT
1 ATATATT-TTA-TTAAAT
9153477 AATAAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 17 0.46
27 3 0.08
28 12 0.32
29 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATATTTTATTAAATTAAAATTAAA
Found at i:9155347 original size:6 final size:6
Alignment explanation
Indices: 9155336--9155361 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9155326 ATAAGGCTAT
9155336 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
9155362 GCTGATTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:9177165 original size:30 final size:30
Alignment explanation
Indices: 9177131--9177189 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9177121 TGCTATAAGA
*
9177131 AAGCAAGTCTTATCACT-GTCATTAATTACT
1 AAGCAAGGCTTATCACTAG-CATTAATTACT
9177161 AAGCAAGGCTTATCACTAGCATTAATTAC
1 AAGCAAGGCTTATCACTAGCATTAATTAC
9177190 AAACCCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (30 bp):
AAGCAAGGCTTATCACTAGCATTAATTACT
Found at i:9181682 original size:12 final size:11
Alignment explanation
Indices: 9181657--9181690 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
9181647 ATAGTTTCCA
9181657 TATAAAAA-AT
1 TATAAAAATAT
9181667 TATAAAAATTAT
1 TATAAAAA-TAT
9181679 TATAAAAATAT
1 TATAAAAATAT
9181690 T
1 T
9181691 GAAAGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.36
11 4 0.18
12 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:9181788 original size:38 final size:36
Alignment explanation
Indices: 9181718--9181788 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
9181708 ATACATGCCT
*
9181718 AAAATAGAAAAATGAATTAATTTTAAAACAAATTTA
1 AAAAAAGAAAAATGAATTAATTTTAAAACAAATTTA
*
9181754 AAAAAAGAAAAATAGATATTTAA-TTTGAAACAAAT
1 AAAAAAGAAAAAT-GA-A-TTAATTTTAAAACAAAT
9181789 AGAATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 12 0.40
37 2 0.07
38 12 0.40
39 4 0.13
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (36 bp):
AAAAAAGAAAAATGAATTAATTTTAAAACAAATTTA
Found at i:9192976 original size:2 final size:2
Alignment explanation
Indices: 9192969--9192995 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9192959 TTATCCAAAA
9192969 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
9192996 GACAATAAAA
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:9194133 original size:23 final size:23
Alignment explanation
Indices: 9194090--9194134 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9194080 TATACTTCCG
*
9194090 ATTTCTCTCTTCTGCATTTTCAT
1 ATTTCTCTCTTCTGCACTTTCAT
*
9194113 ATTTCTCT-TTCTTGCGCTTTCA
1 ATTTCTCTCTTC-TGCACTTTCA
9194135 AGATACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.11, C:0.27, G:0.07, T:0.56
Consensus pattern (23 bp):
ATTTCTCTCTTCTGCACTTTCAT
Found at i:9200558 original size:3 final size:3
Alignment explanation
Indices: 9200550--9200584 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9200540 ATGCATTTGT
9200550 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
9200585 TTATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:9200589 original size:3 final size:3
Alignment explanation
Indices: 9200583--9200622 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9200573 CTACTACTAC
9200583 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9200623 GGGGGTTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9217446 original size:35 final size:36
Alignment explanation
Indices: 9217407--9217555 Score: 178
Period size: 35 Copynumber: 4.2 Consensus size: 36
9217397 AAATGTTTAA
* * *
9217407 TTTAATCAATT-GGACCCAATAACTTAATTAAAC-AG
1 TTTAATCAATTAAG-CCCAACAACTTAATTAAACAAT
* *
9217442 TTTAATTAATTAAGCACAACAACTTAATTAAACAAT
1 TTTAATCAATTAAGCCCAACAACTTAATTAAACAAT
* * *
9217478 TTTAATCAATTAGGTCCAATAACTTAATTAAACAA-
1 TTTAATCAATTAAGCCCAACAACTTAATTAAACAAT
* *
9217513 TTTAATTAATTAAGCTCAACAACTTAATTAAACAAT
1 TTTAATCAATTAAGCCCAACAACTTAATTAAACAAT
9217549 TTTAATC
1 TTTAATC
9217556 TAGTACTTAA
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
35 57 0.60
36 38 0.40
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.35
Consensus pattern (36 bp):
TTTAATCAATTAAGCCCAACAACTTAATTAAACAAT
Found at i:9217497 original size:71 final size:71
Alignment explanation
Indices: 9217407--9217555 Score: 255
Period size: 71 Copynumber: 2.1 Consensus size: 71
9217397 AAATGTTTAA
*
9217407 TTTAATCAATTGGACCCAATAACTTAATTAAACAGTTTAATTAATTAAGCACAACAACTTAATTA
1 TTTAATCAATTGGACCCAATAACTTAATTAAACAATTTAATTAATTAAGCACAACAACTTAATTA
9217472 AACAAT
66 AACAAT
* *
9217478 TTTAATCAATTAGG-TCCAATAACTTAATTAAACAATTTAATTAATTAAGCTCAACAACTTAATT
1 TTTAATCAATT-GGACCCAATAACTTAATTAAACAATTTAATTAATTAAGCACAACAACTTAATT
9217542 AAACAAT
65 AAACAAT
9217549 TTTAATC
1 TTTAATC
9217556 TAGTACTTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
71 72 0.97
72 2 0.03
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.35
Consensus pattern (71 bp):
TTTAATCAATTGGACCCAATAACTTAATTAAACAATTTAATTAATTAAGCACAACAACTTAATTA
AACAAT
Found at i:9217857 original size:15 final size:15
Alignment explanation
Indices: 9217839--9217882 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
9217829 ATAGTTTGAC
*
9217839 TCAACTTTTCAGTGA
1 TCAACCTTTCAGTGA
9217854 TCAACCTTTCAGTGA
1 TCAACCTTTCAGTGA
*
9217869 TTAACCTTTCAGTG
1 TCAACCTTTCAGTG
9217883 TAATTCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (15 bp):
TCAACCTTTCAGTGA
Found at i:9222463 original size:20 final size:20
Alignment explanation
Indices: 9222446--9222483 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9222436 CCTCAAATCT
9222446 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
9222466 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
9222484 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:9224904 original size:23 final size:22
Alignment explanation
Indices: 9224862--9224906 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
9224852 ATTAGCATAA
*
9224862 TATTTAAAAAAAGTTCATAAAC
1 TATTTAAAAAAAGTTAATAAAC
*
9224884 TATTTAAAAAAATTTAAATAAAC
1 TATTTAAAAAAAGTT-AATAAAC
9224907 CCTTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
TATTTAAAAAAAGTTAATAAAC
Found at i:9224942 original size:29 final size:29
Alignment explanation
Indices: 9224909--9224980 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
9224899 AAATAAACCC
*
9224909 TTATATTTTTATTACATTCAA-TCAAGTTT
1 TTATATTTTTATTACAATCAAGT-AAGTTT
* **
9224938 TTATACTTTTATTTTGAATCAAGTAAGTTT
1 TTATATTTTTA-TTACAATCAAGTAAGTTT
9224968 TTATATTTTTATT
1 TTATATTTTTATT
9224981 TTGAGTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 12 0.33
30 23 0.64
31 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.58
Consensus pattern (29 bp):
TTATATTTTTATTACAATCAAGTAAGTTT
Found at i:9224968 original size:30 final size:30
Alignment explanation
Indices: 9224932--9224989 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
9224922 ACATTCAATC
9224932 AAGTTTTTATACTTTTATTTTGAATCAAGT
1 AAGTTTTTATACTTTTATTTTGAATCAAGT
* *
9224962 AAGTTTTTATATTTTTATTTTGAGTCAA
1 AAGTTTTTATACTTTTATTTTGAATCAA
9224990 ATAATCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.55
Consensus pattern (30 bp):
AAGTTTTTATACTTTTATTTTGAATCAAGT
Found at i:9230462 original size:29 final size:30
Alignment explanation
Indices: 9230421--9230479 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
9230411 CATGGCGTGC
* *
9230421 AATAACATTTTTTTTAAATATGGCGTGTAAT
1 AATAACA-TTTTTTTAAACATGACGTGTAAT
9230452 AATAACA-TTTTTTAAACATGACGTGTAA
1 AATAACATTTTTTTAAACATGACGTGTAA
9230480 CTTGGTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 19 0.73
31 7 0.27
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (30 bp):
AATAACATTTTTTTAAACATGACGTGTAAT
Found at i:9231005 original size:75 final size:75
Alignment explanation
Indices: 9230881--9231023 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 75
9230871 CTCCTGATTC
* * * ***
9230881 CTTTCTTCGACATCCGTCTGCTATGCTTTCGATTTCTCTCTCTTGCCATCCAGCTCTCTCTAATT
1 CTTTCTCCCACATCCATCTGCTATGCTTTCGATTTCTCTCTCCCACCATCCAGCTCTCTCTAATT
9230946 TTATCCATTT
66 TTATCCATTT
* * *
9230956 CTTTCTCCCACATCCATCTGCTGTGCTTTCGATTTTTCTCTCCCACCATCCAGCTCTCTTTAATT
1 CTTTCTCCCACATCCATCTGCTATGCTTTCGATTTCTCTCTCCCACCATCCAGCTCTCTCTAATT
9231021 TTA
66 TTA
9231024 CCACCATTGC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.14, C:0.34, G:0.08, T:0.44
Consensus pattern (75 bp):
CTTTCTCCCACATCCATCTGCTATGCTTTCGATTTCTCTCTCCCACCATCCAGCTCTCTCTAATT
TTATCCATTT
Found at i:9232743 original size:23 final size:23
Alignment explanation
Indices: 9232694--9232745 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
9232684 GTACATATTC
*
9232694 TAATTTAATCATTTTTTAAAGTTT
1 TAATTTAATCA-TTTTTAAAGTGT
*
9232718 TAATTTAATCA-TTTTAATTGTGT
1 TAATTTAATCATTTTTAA-AGTGT
9232741 TAATT
1 TAATT
9232746 GTGTAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 8 0.32
24 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (23 bp):
TAATTTAATCATTTTTAAAGTGT
Found at i:9234369 original size:19 final size:16
Alignment explanation
Indices: 9234325--9234374 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
9234315 AATTTTATTC
9234325 AAATAATTAAAATAAAA
1 AAAT-ATTAAAATAAAA
9234342 AAA-ATTAAAACTAAAA
1 AAATATTAAAA-TAAAA
9234358 TTAAATATT-AAATAAAA
1 --AAATATTAAAATAAAA
9234375 CTCACTTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.24
16 5 0.17
17 8 0.28
18 6 0.21
19 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATATTAAAATAAAA
Found at i:9240303 original size:14 final size:14
Alignment explanation
Indices: 9240286--9240353 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
9240276 TATTTTATTT
9240286 TTTAATATTAATAA
1 TTTAATATTAATAA
9240300 TTT-ATATTAATTAAAA
1 TTTAATATTAA-T--AA
9240316 TATTAATAATTAATAA
1 T-TTAAT-ATTAATAA
* * *
9240332 TTTAAAATCAATAT
1 TTTAATATTAATAA
9240346 TTTAATAT
1 TTTAATAT
9240354 AATTTAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 7 0.16
14 17 0.39
15 4 0.09
16 6 0.14
17 2 0.05
18 3 0.07
19 5 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTAATATTAATAA
Found at i:9240470 original size:16 final size:16
Alignment explanation
Indices: 9240445--9240475 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9240435 TTTTATATTC
9240445 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
*
9240461 ATTAATAATTTAATA
1 ATTAAAAATTTAATA
9240476 AAAAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:9240583 original size:28 final size:28
Alignment explanation
Indices: 9240498--9240583 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 28
9240488 AAAAAATTTA
9240498 TATTAATATTTTAATATATTT-T-AAT-ATT
1 TATTAATA-TTTAA-AT-TTTATAAATAATT
* * *
9240526 TAATAATGTTTAAATTATATATAA-AA--
1 TATTAATATTTAAATTTTATA-AATAATT
9240552 TATTAATATTTAAATTTTATAAATAATT
1 TATTAATATTTAAATTTTATAAATAATT
9240580 TATT
1 TATT
9240584 CTTTTTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
25 4 0.09
26 23 0.51
27 5 0.11
28 13 0.29
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TATTAATATTTAAATTTTATAAATAATT
Found at i:9240873 original size:21 final size:21
Alignment explanation
Indices: 9240849--9240900 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
9240839 GCCGTCGCAA
* *
9240849 TCGTCGTCGCTTCCGCTGCCG
1 TCGTCGTCGCTTCCACCGCCG
9240870 TCGTCGTCGCTTCCACCGCCG
1 TCGTCGTCGCTTCCACCGCCG
*
9240891 TCGCCGTCGC
1 TCGTCGTCGC
9240901 CACTAACATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.46, G:0.27, T:0.25
Consensus pattern (21 bp):
TCGTCGTCGCTTCCACCGCCG
Found at i:9241305 original size:4 final size:4
Alignment explanation
Indices: 9241298--9241323 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
9241288 TATATATATA
9241298 TAGG TAGG TAGG TAGG TAGG TAGG TA
1 TAGG TAGG TAGG TAGG TAGG TAGG TA
9241324 AGAAGGCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.46, T:0.27
Consensus pattern (4 bp):
TAGG
Done.