Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 185 of 230
Found at i:55532636 original size:16 final size:16
Alignment explanation
Indices: 55532615--55532647 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55532605 TTCGCTGTAT
55532615 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
55532631 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
55532647 T
1 T
55532648 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:55532859 original size:16 final size:16
Alignment explanation
Indices: 55532822--55532889 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
55532812 TTAATCATAT
*
55532822 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
55532838 TT-AAATATATTATAA
1 TTAAAATATATTATAA
*
55532853 TTAAAATATATAATTTAA
1 TTAAAATATAT--TATAA
55532871 -TAAAAT-TATTAATAA
1 TTAAAATATATT-ATAA
55532886 TTAA
1 TTAA
55532890 TATTCTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.09
15 13 0.30
16 16 0.37
17 6 0.14
18 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:55532863 original size:18 final size:18
Alignment explanation
Indices: 55532842--55532889 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
55532832 TTATTATTAA
55532842 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
55532860 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
55532877 -TAT-TAATAATTAA
1 ATATATTATAATTAA
55532890 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:55532870 original size:14 final size:15
Alignment explanation
Indices: 55532831--55532872 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55532821 TTTAAACATA
*
55532831 ATTATTATTAAATAT
1 ATTATAATTAAATAT
55532846 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
55532860 A-TATAATTTAATA
1 ATTATAATTAAATA
55532873 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:55532983 original size:18 final size:17
Alignment explanation
Indices: 55532960--55532996 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
55532950 AATTATTATT
55532960 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
55532976 AAATATATGATTTAATA
1 AAATATATGATTTAATA
55532993 AAAT
1 AAAT
55532997 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:55532994 original size:59 final size:58
Alignment explanation
Indices: 55532825--55533001 Score: 164
Period size: 59 Copynumber: 3.0 Consensus size: 58
55532815 ATCATATTTA
* * *
55532825 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-TATAAAT
* * * * * *
55532884 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAATATAAATT
1 AACATAATTATTATTAAAT-ATATTT--T--AATTAAAATATATGAT-TTAATAAAATATAAA-T
*
55532945 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATATAAA
55533002 ATAATTATAA
Statistics
Matches: 91, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
57 12 0.13
58 5 0.05
59 28 0.31
60 5 0.05
61 23 0.25
62 5 0.05
63 13 0.14
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (58 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATATAAAT
Found at i:55533045 original size:47 final size:46
Alignment explanation
Indices: 55532979--55533146 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
55532969 TTAATTAAAA
*
55532979 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * **
55533026 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATA-ATA-AATTTTCT
* * *
55533074 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
55533117 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
55533147 ATATTAAATA
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
42 2 0.02
43 8 0.09
44 18 0.19
45 5 0.05
46 5 0.05
47 40 0.43
48 14 0.15
49 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:55533055 original size:101 final size:93
Alignment explanation
Indices: 55532936--55533220 Score: 328
Period size: 91 Copynumber: 3.0 Consensus size: 93
55532926 ATACTATAAA
* * * * *
55532936 ATATAAATTAACATAATTATTATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTA
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT-
*
55533000 AAATAATTATAACTAATAAATTTTCTTATATGAATTT
64 ---T--CT-TAA-TAATAAATTTTCTTATATGAATTT
* *
55533037 GTATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTC
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
*
55533100 TTGATAATAAATTTTCTTATATGAATTT
66 TTAATAATAAATTTTCTTATATGAATTT
* * *
55533128 ATACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTC
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
*
55533191 TTAATAATAAAATGTTCTTATATGAATTT
66 TTAATAAT-AAATTTTCTTATATGAATTT
55533220 A
1 A
55533221 CTAAAATCAA
Statistics
Matches: 166, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
91 89 0.54
92 22 0.13
93 1 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 49 0.30
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
TTAATAATAAATTTTCTTATATGAATTT
Found at i:55533068 original size:26 final size:28
Alignment explanation
Indices: 55533038--55533098 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
55533028 TATGAATTTG
*
55533038 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
55533064 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
55533092 TAAAATT
1 TATAATT
55533099 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:55533108 original size:91 final size:91
Alignment explanation
Indices: 55533013--55533220 Score: 344
Period size: 91 Copynumber: 2.3 Consensus size: 91
55533003 TAATTATAAC
* * * *
55533013 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
55533078 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
55533104 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
55533169 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
55533195 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
55533221 CTAAAATCAA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 89 0.82
92 20 0.18
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:55533180 original size:44 final size:43
Alignment explanation
Indices: 55533038--55533180 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
55533028 TATGAATTTG
* *
55533038 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
55533082 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
55533129 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
55533173 TATAATTT
1 TATAATTT
55533181 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:55533195 original size:47 final size:47
Alignment explanation
Indices: 55533063--55533201 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
55533053 TTATTATTAC
* *
55533063 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
55533110 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
55533154 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
55533201 A
1 A
55533202 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:55536285 original size:15 final size:15
Alignment explanation
Indices: 55536265--55536300 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
55536255 GGTATATGTA
55536265 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
55536280 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
55536295 TAATTG
1 TAATTG
55536301 TTGTTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (15 bp):
TAATTGACCTAAAAT
Found at i:55536522 original size:6 final size:6
Alignment explanation
Indices: 55536511--55536536 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55536501 TAGTTTGAAC
55536511 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
55536537 ATAATTTCGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:55536997 original size:13 final size:13
Alignment explanation
Indices: 55536979--55537003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55536969 ATCAAATTTG
55536979 TATGTACTCTTTA
1 TATGTACTCTTTA
55536992 TATGTACTCTTT
1 TATGTACTCTTT
55537004 CACTAATAAA
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:55537525 original size:29 final size:29
Alignment explanation
Indices: 55537492--55537559 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 29
55537482 AACAAATGCA
55537492 ACAATTTCCAGTTTCATTGAAAAC-AGCAG
1 ACAATTTCCAGTTTCATTGAAAACTA-CAG
55537521 ACAATTTCCAGTTTCATTGAAAACTACAG
1 ACAATTTCCAGTTTCATTGAAAACTACAG
55537550 ACAATTTCCA
1 ACAATTTCCA
55537560 TTGCAACAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 37 0.97
30 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (29 bp):
ACAATTTCCAGTTTCATTGAAAACTACAG
Found at i:55538667 original size:15 final size:15
Alignment explanation
Indices: 55538647--55538675 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55538637 GCAATACAAA
55538647 CATACAAAACAGAAC
1 CATACAAAACAGAAC
55538662 CATACAAAACAGAA
1 CATACAAAACAGAA
55538676 ACCACAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.24, G:0.07, T:0.07
Consensus pattern (15 bp):
CATACAAAACAGAAC
Found at i:55543025 original size:21 final size:21
Alignment explanation
Indices: 55543000--55543040 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55542990 GGACTTGAGA
55543000 AATTTTAGATTAGGGATTTTC
1 AATTTTAGATTAGGGATTTTC
* *
55543021 AATTTTGGGTTAGGGATTTT
1 AATTTTAGATTAGGGATTTT
55543041 TGAGTCTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (21 bp):
AATTTTAGATTAGGGATTTTC
Found at i:55545054 original size:39 final size:39
Alignment explanation
Indices: 55544934--55545142 Score: 296
Period size: 39 Copynumber: 5.3 Consensus size: 39
55544924 CTCCTCGTTA
* *
55544934 AAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCAC
1 AAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCAC
* * * * *
55544974 AAATGCCTTCGGGACTTAACTCGGATTTAGTAACTAGCAC
1 AAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCAC
*
55545014 AAATACCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
55545053 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
55545092 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
55545131 AAATGCCTTCGG
1 AAATGCCTTCGG
55545143 ATCTTAGTCC
Statistics
Matches: 155, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 111 0.72
40 42 0.27
41 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCAC
Found at i:55545114 original size:78 final size:79
Alignment explanation
Indices: 55544934--55545192 Score: 298
Period size: 78 Copynumber: 3.3 Consensus size: 79
55544924 CTCCTCGTTA
* * *
55544934 AAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACTCG
1 AAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGGACTTAACCCG
*
55544997 GATTTAGTAACTAGCAC
63 GAATTAGTAACTAGCAC
* *
55545014 AAATACCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGAA
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGAA
* *
55545078 TTAGTATCTCGCAC
66 TTAGTAACTAGCAC
**
55545092 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC-GA
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* *
55545155 ATATTGTCACTTAGCAC
65 AT-TAGTAAC-TAGCAC
55545172 -AA-GCCTTCGGGACTTAGCCCG
1 AAATGCCTTCGGG-CTTAGCCCG
55545193 AACATCATTC
Statistics
Matches: 158, Mismatches: 14, Indels: 15
0.84 0.07 0.08
Matches are distributed among these distances:
77 2 0.01
78 84 0.53
79 54 0.34
80 18 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGAA
TTAGTAACTAGCAC
Found at i:55552999 original size:40 final size:40
Alignment explanation
Indices: 55552955--55553215 Score: 319
Period size: 39 Copynumber: 6.7 Consensus size: 40
55552945 GCTCCTCGTT
* *
55552955 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
55552995 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
55553035 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
55553074 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
55553113 CAAATGCCTTCGGG-CTTAG-CCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
55553151 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
55553192 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55553216 CATCATTCAA
Statistics
Matches: 202, Mismatches: 10, Indels: 19
0.87 0.04 0.08
Matches are distributed among these distances:
37 2 0.01
38 30 0.15
39 101 0.50
40 58 0.29
41 11 0.05
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:55555911 original size:24 final size:23
Alignment explanation
Indices: 55555864--55555906 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
55555854 ACATATATTC
55555864 TTTTTTAAAGTATTTGTTTTTGT
1 TTTTTTAAAGTATTTGTTTTTGT
*
55555887 TTTTTTATAGTATTT-TTTTT
1 TTTTTTAAAGTATTTGTTTTT
55555907 ATGTTATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (23 bp):
TTTTTTAAAGTATTTGTTTTTGT
Found at i:55570706 original size:3 final size:3
Alignment explanation
Indices: 55570698--55570722 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55570688 ATGCTTTTAA
55570698 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
55570723 GAGAGTGTGT
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:55572599 original size:20 final size:17
Alignment explanation
Indices: 55572565--55572603 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
55572555 ATTCTGTAGT
55572565 TAAAAAAAAAAAGAGAG
1 TAAAAAAAAAAAGAGAG
55572582 TAAATAAAACAAATAGAGAG
1 TAAA-AAAA-AAA-AGAGAG
55572602 TA
1 TA
55572604 TAGAAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 3 0.16
20 8 0.42
ACGTcount: A:0.69, C:0.03, G:0.15, T:0.13
Consensus pattern (17 bp):
TAAAAAAAAAAAGAGAG
Found at i:55586482 original size:17 final size:18
Alignment explanation
Indices: 55586452--55586485 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
55586442 TTAAATATAT
55586452 TTTTATCTTTTGGGCCCC
1 TTTTATCTTTTGGGCCCC
55586470 TTTTATC-TTTGGGCCC
1 TTTTATCTTTTGGGCCC
55586486 TGGGCTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (18 bp):
TTTTATCTTTTGGGCCCC
Found at i:55588686 original size:13 final size:13
Alignment explanation
Indices: 55588649--55588689 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
55588639 TTTTGCTTTA
55588649 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
55588662 CT--TTGTGCCTCTG
1 CTGCTT-TG-CTCTG
55588675 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
55588688 CT
1 CT
55588690 TTGCTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 16 0.67
14 2 0.08
15 2 0.08
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (13 bp):
CTGCTTTGCTCTG
Found at i:55588864 original size:12 final size:12
Alignment explanation
Indices: 55588847--55588871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55588837 TATTTTAGAG
55588847 TTTACTAATTGC
1 TTTACTAATTGC
55588859 TTTACTAATTGC
1 TTTACTAATTGC
55588871 T
1 T
55588872 AGATCCCCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTACTAATTGC
Found at i:55592234 original size:72 final size:72
Alignment explanation
Indices: 55592134--55592305 Score: 242
Period size: 72 Copynumber: 2.4 Consensus size: 72
55592124 AAAAACAATG
* * *
55592134 CTAAA-CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACTT
55592198 ATTTAT-
66 ATTTATA
* * * *
55592204 GTGTAATCTAGTTTTATCAATGGTTGTTTATGTTTTCTTTTTAGATATTGAATTTATGTTCTACT
1 CT-AAATCTAGTTTTATCAATAGTTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACT
55592269 TATTTATA
65 TATTTATA
*
55592277 CTAAAT-TAATTTTATCAATAGTTGTTTAT
1 CTAAATCTAGTTTTATCAATAGTTGTTTAT
55592306 ATATGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
70 1 0.01
71 23 0.26
72 63 0.72
73 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (72 bp):
CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACTT
ATTTATA
Found at i:55598350 original size:22 final size:23
Alignment explanation
Indices: 55598320--55598366 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
55598310 AAGTGGGTTA
55598320 TTTACATGTTTAGGG-CTTAGGG
1 TTTACATGTTTAGGGTCTTAGGG
* *
55598342 TTTAGATGTTTAGGGTTTTAGGG
1 TTTACATGTTTAGGGTCTTAGGG
55598365 TT
1 TT
55598367 AGGATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.17, C:0.04, G:0.32, T:0.47
Consensus pattern (23 bp):
TTTACATGTTTAGGGTCTTAGGG
Found at i:55598477 original size:28 final size:28
Alignment explanation
Indices: 55598424--55598525 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 28
55598414 GATTTTGGAG
* * *
55598424 AAAATAAATTGGGTTTTAGGAATTTTAA
1 AAAATAAATTAGGTTTTATGATTTTTAA
55598452 AAAATAAATTAGGTTTTATGATTTTTTTTAAA
1 AAAATAAATTAGGTTTTATGA---TTTTT-AA
* *
55598484 ATAAATTAAATTAGGATTTATTG-TTTATAA
1 A-AAA-TAAATTAGGTTTTA-TGATTTTTAA
55598514 AAAATAAATTAG
1 AAAATAAATTAG
55598526 AGCCTAGGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
28 27 0.44
29 3 0.05
30 3 0.05
31 8 0.13
32 3 0.05
33 3 0.05
34 13 0.21
35 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (28 bp):
AAAATAAATTAGGTTTTATGATTTTTAA
Found at i:55598802 original size:125 final size:127
Alignment explanation
Indices: 55598638--55598907 Score: 372
Period size: 125 Copynumber: 2.2 Consensus size: 127
55598628 TTTTGTTCAG
** *
55598638 TCAGCAAAAGTACT-AAAAAAGCTCCCAGCTGGATGCTATTTTTCTAAAGTAGTTTCTGAAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTATTTTTCTAAAGTAGTTTCTAAAAAAA
* * *
55598702 TAATTTTGAGAAGATGATTCTGAAAAA-TAGGGTCAAAAA-TGCTTTAAGCATGATGCACT-T
66 TAATTTTGAGAAGATGATTCTAAAAAATTAGGGT-AAAAAGTGCTTCAAGCAGGATGCACTGT
* * *
55598762 TCAGCAAAAATATTGAAAAAAGCTCCCA-CATGGACACTATTTTTCTATAGTAGTTTCTAAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGC-TGGACACTATTTTTCTAAAGTAGTTTCTAAAAAA
* * *
55598826 ATAATTTTGAGAAGATGGTTCTAAAAAATTAGTGTAAAAAGTGCTTCAAGCAGGATGTACTGT
65 ATAATTTTGAGAAGATGATTCTAAAAAATTAGGGTAAAAAGTGCTTCAAGCAGGATGCACTGT
55598889 T-AGCAAAAGTACTGAAAAA
1 TCAGCAAAAGTACTGAAAAA
55598908 TGGAAGAGTG
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
124 13 0.10
125 74 0.58
126 38 0.30
127 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (127 bp):
TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTATTTTTCTAAAGTAGTTTCTAAAAAAA
TAATTTTGAGAAGATGATTCTAAAAAATTAGGGTAAAAAGTGCTTCAAGCAGGATGCACTGT
Found at i:55599930 original size:58 final size:59
Alignment explanation
Indices: 55599819--55599947 Score: 158
Period size: 58 Copynumber: 2.2 Consensus size: 59
55599809 TCTATTACCT
* * *
55599819 TATTTAAAACAACTTCTATTTTATTAAATAGGACAAAATATAAAAATAATTTGTATAAATA
1 TATTTAAAA-AAATTCTATTTTATTAAATA-GACAAAATATAAAAACAATTTGTACAAATA
*
55599880 TATTTAAAAAAATT-TGATTTTATTAAAT-GA-AATAATATAAAAACAGTTTGTACAAATA
1 TATTTAAAAAAATTCT-ATTTTATTAAATAGACAA-AATATAAAAACAATTTGTACAAATA
55599938 TA-TTAAAAAA
1 TATTTAAAAAA
55599948 TCAATACATG
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
57 10 0.16
58 26 0.42
59 1 0.02
60 16 0.26
61 9 0.15
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (59 bp):
TATTTAAAAAAATTCTATTTTATTAAATAGACAAAATATAAAAACAATTTGTACAAATA
Found at i:55602432 original size:29 final size:30
Alignment explanation
Indices: 55602374--55602434 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
55602364 TTTTGGCCCA
** *
55602374 TTCCGATAAATAAAGTTTAAAGTGGCCCAT
1 TTCCGATAAATAAAGTGGAAAGTGGACCAT
55602404 TTCCG-TAAATAAAGTAGGAAA-TGGACCAT
1 TTCCGATAAATAAAGT-GGAAAGTGGACCAT
55602433 TT
1 TT
55602435 TTAGTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (30 bp):
TTCCGATAAATAAAGTGGAAAGTGGACCAT
Found at i:55604268 original size:16 final size:16
Alignment explanation
Indices: 55604247--55604293 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
55604237 TTTAACTGCC
55604247 AAATTAAATTAATTCA
1 AAATTAAATTAATTCA
55604263 AAATTAAATTAATTCA
1 AAATTAAATTAATTCA
*
55604279 AAATTAATTTAATTC
1 AAATTAAATTAATTC
55604294 TTGTGACAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTAAATTAATTCA
Found at i:55614928 original size:19 final size:19
Alignment explanation
Indices: 55614895--55615026 Score: 201
Period size: 19 Copynumber: 6.8 Consensus size: 19
55614885 AATCATATAT
*
55614895 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
55614914 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
55614933 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
55614952 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
55614973 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55614992 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55615011 TCTAAGATTGAATATC
1 TCTAAGATTGCATATC
55615027 CTCAAAATTA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 84 0.82
21 19 0.18
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55614945 original size:38 final size:38
Alignment explanation
Indices: 55614872--55615026 Score: 202
Period size: 38 Copynumber: 3.9 Consensus size: 38
55614862 AAATTAAATC
* *
55614872 TCTAAGATTATAAAATCATATATTCTAATATTGCATATCATA
1 TCTAAGATTAT-ATATC--ATA-TCTAAGATTGCATATCATA
55614914 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
55614952 TCTAAGATTGCATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATT--ATATATCATATCTAAGATTGCATATCATA
* ** *
55614992 TCTAGGATTGCATATCATATCTAAGATTGAATATC
1 TCTAAGATTATATATCATATCTAAGATTGCATATC
55615027 CTCAAAATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
38 50 0.48
39 3 0.03
40 37 0.35
41 4 0.04
42 11 0.10
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (38 bp):
TCTAAGATTATATATCATATCTAAGATTGCATATCATA
Found at i:55614978 original size:59 final size:59
Alignment explanation
Indices: 55614906--55615025 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
55614896 CTAATATTGC
* *
55614906 ATATCATATCTAAGATTATATATCATATCTAAGATTGCATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTGAAT
* *
55614965 ATATCATATCTAAGATTGCATATCATATCTAGGATTGCATATCATATCTAAGATTGAAT
1 ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTGAAT
55615024 AT
1 AT
55615026 CCTCAAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (59 bp):
ATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTGAAT
Found at i:55616378 original size:22 final size:21
Alignment explanation
Indices: 55616339--55616379 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
55616329 TTTATTTTCA
55616339 TATTTTTTAATATATTATACT
1 TATTTTTTAATATATTATACT
* *
55616360 TATTTTATTTATATTTTATA
1 TATTTT-TTAATATATTATA
55616380 AAGTACATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTTTAATATATTATACT
Found at i:55629205 original size:13 final size:13
Alignment explanation
Indices: 55629189--55629218 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
55629179 ATTGTCATGT
55629189 AATTGTTTTTCTG
1 AATTGTTTTTCTG
55629202 AATTGTTTTTCTG
1 AATTGTTTTTCTG
55629215 AATT
1 AATT
55629219 TAGCTGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (13 bp):
AATTGTTTTTCTG
Found at i:55631459 original size:13 final size:13
Alignment explanation
Indices: 55631441--55631470 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
55631431 CAATCAGCTA
55631441 AATTCAGAAAAAC
1 AATTCAGAAAAAC
55631454 AATTCAGAAAAAC
1 AATTCAGAAAAAC
55631467 AATT
1 AATT
55631471 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:55636954 original size:27 final size:26
Alignment explanation
Indices: 55636916--55637092 Score: 103
Period size: 27 Copynumber: 6.6 Consensus size: 26
55636906 GCTTGGGCCA
*
55636916 AAAATTATCAAAATACTCATATAGGAT
1 AAAATTACCAAAATACTCATA-AGGAT
55636943 AAAATTACCAAAATACCCTCA-AAGGAT
1 AAAATTACCAAAATA--CTCATAAGGAT
* * * *
55636970 -AAATTACCGAAATACCCCTGAAGGGT
1 AAAATTACCAAAATACTCAT-AAGGAT
* *
55636996 AAAATTACTAAAATACCCTCA-AAGGGT
1 AAAATTACCAAAATA--CTCATAAGGAT
* * *
55637023 AAAATTATCGAAATACCTTCA-AAGGGT
1 AAAATTACCAAAATA-C-TCATAAGGAT
* * *
55637050 AAAATTATCGAAATACCCCCATAAGG-T
1 AAAATTACCAAAATA--CTCATAAGGAT
*
55637077 AAAATTACCGAAATAC
1 AAAATTACCAAAATAC
55637093 ACTCGAAGGG
Statistics
Matches: 126, Mismatches: 14, Indels: 22
0.78 0.09 0.14
Matches are distributed among these distances:
24 2 0.02
25 1 0.01
26 20 0.16
27 90 0.71
28 7 0.06
29 6 0.05
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (26 bp):
AAAATTACCAAAATACTCATAAGGAT
Found at i:55637052 original size:54 final size:52
Alignment explanation
Indices: 55636942--55637175 Score: 233
Period size: 54 Copynumber: 4.4 Consensus size: 52
55636932 TCATATAGGA
* *
55636942 TAAAATTACCAAAATACCCTCAAAGG-ATAAATTACCGAAATACCCCTGAAGGG
1 TAAAATTACTAAAATACCCTCAAAGGTA-AAATTACCGAAATACCTC-GAAGGG
* *
55636995 TAAAATTACTAAAATACCCTCAAAGGGTAAAATTATCGAAATACCTTCAAAGGG
1 TAAAATTACTAAAATACCCTCAAA-GGTAAAATTACCGAAATACC-TCGAAGGG
* *
55637049 TAAAATTA-TCGAAATACCCCCATAAGGTAAAATTACCGAAATACACTCGAAGGG
1 TAAAATTACT-AAAATACCCTCA-AAGGTAAAATTACCGAAATAC-CTCGAAGGG
** * * * *
55637103 TAAAATTTTTGAAATACCCTTGAAAGGTAAAATGACCAAAATACGGC-CGAAGGG
1 TAAAATTACTAAAATACCC-TCAAAGGTAAAATTACCGAAATAC--CTCGAAGGG
55637157 TAAAA-TACCTAAAATACCC
1 TAAAATTA-CTAAAATACCC
55637176 CCATAGGGCA
Statistics
Matches: 154, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
53 25 0.16
54 121 0.79
55 8 0.05
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.21
Consensus pattern (52 bp):
TAAAATTACTAAAATACCCTCAAAGGTAAAATTACCGAAATACCTCGAAGGG
Found at i:55637091 original size:81 final size:81
Alignment explanation
Indices: 55636916--55637173 Score: 244
Period size: 81 Copynumber: 3.2 Consensus size: 81
55636906 GCTTGGGCCA
* * * * * *
55636916 AAAATTATCAAAAT--ACTCATATAGGATAAAATTACCAAAATACCCTCAAAGGAT-AAATTACC
1 AAAATTACCAAAATACACTCA-A-AGGGTAAAATTATCGAAATACCTTCAAAGGGTAAAATTACC
55636978 GAAATACCCCTGAAGGGT
64 GAAATACCCCTGAAGGGT
* * *
55636996 AAAATTACTAAAATACCCTCAAAGGGTAAAATTATCGAAATACCTTCAAAGGGTAAAATTATCGA
1 AAAATTACCAAAATACACTCAAAGGGTAAAATTATCGAAATACCTTCAAAGGGTAAAATTACCGA
55637061 AATACCCCCAT-AA-GGT
66 AATA-CCCC-TGAAGGGT
* * * * * * *
55637077 AAAATTACCGAAATACACTCGAAGGGTAAAATTTTTGAAATACCCTTGAAA-GGTAAAATGACCA
1 AAAATTACCAAAATACACTCAAAGGGTAAAATTATCGAAATA-CCTTCAAAGGGTAAAATTACCG
*
55637141 AAATACGGCC-GAAGGGT
65 AAATAC-CCCTGAAGGGT
55637158 AAAA-TACCTAAAATAC
1 AAAATTACC-AAAATAC
55637174 CCCCATAGGG
Statistics
Matches: 147, Mismatches: 21, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
80 46 0.31
81 83 0.56
82 17 0.12
83 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (81 bp):
AAAATTACCAAAATACACTCAAAGGGTAAAATTATCGAAATACCTTCAAAGGGTAAAATTACCGA
AATACCCCTGAAGGGT
Found at i:55637104 original size:27 final size:26
Alignment explanation
Indices: 55636942--55637162 Score: 167
Period size: 27 Copynumber: 8.2 Consensus size: 26
55636932 TCATATAGGA
* * *
55636942 TAAAATTACCAAAATACCCTCAAAGGA
1 TAAAATTACCGAAATA-CCTCGAAGGG
*
55636969 T-AAATTACCGAAATACCCCTGAAGGG
1 TAAAATTACCGAAATACCTC-GAAGGG
** *
55636995 TAAAATTACTAAAATACCCTCAAAGGG
1 TAAAATTACCGAAATA-CCTCGAAGGG
* *
55637022 TAAAATTATCGAAATACCTTCAAAGGG
1 TAAAATTACCGAAATACC-TCGAAGGG
* * * *
55637049 TAAAATTATCGAAATACCCCCATAAGG
1 TAAAATTACCGAAATACCTCGA-AGGG
55637076 TAAAATTACCGAAATACACTCGAAGGG
1 TAAAATTACCGAAATAC-CTCGAAGGG
*** * *
55637103 TAAAATTTTTGAAATACCCTTGAAAGG
1 TAAAATTACCGAAATA-CCTCGAAGGG
* *
55637130 TAAAATGACCAAAATACGGC-CGAAGGG
1 TAAAATTACCGAAATAC--CTCGAAGGG
55637157 TAAAAT
1 TAAAAT
55637163 ACCTAAAATA
Statistics
Matches: 155, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.02
26 23 0.15
27 121 0.78
28 8 0.05
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (26 bp):
TAAAATTACCGAAATACCTCGAAGGG
Found at i:55637183 original size:27 final size:26
Alignment explanation
Indices: 55636942--55637188 Score: 156
Period size: 27 Copynumber: 9.2 Consensus size: 26
55636932 TCATATAGGA
* * *
55636942 TAAAATTACCAAAATACCCTCAAAGG
1 TAAAATTACCGAAATACCCCCAAGGG
*
55636968 -ATAAATTACCGAAATACCCCTGAAGGG
1 TA-AAATTACCGAAATACCCC-CAAGGG
** *
55636995 TAAAATTACTAAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCC-CCAAGGG
* * *
55637022 TAAAATTATCGAAATACCTTCAAAGGG
1 TAAAATTACCGAAATACC-CCCAAGGG
* *
55637049 TAAAATTATCGAAATACCCCCATAAGG
1 TAAAATTACCGAAATACCCCCA-AGGG
* *
55637076 TAAAATTACCGAAATACACTCGAAGGG
1 TAAAATTACCGAAATAC-CCCCAAGGG
*** ** *
55637103 TAAAATTTTTGAAATACCCTTGAAAGG
1 TAAAATTACCGAAATACCC-CCAAGGG
* * * *
55637130 TAAAATGACCAAAATACGGCCGAAGGG
1 TAAAATTACCGAAATAC-CCCCAAGGG
*
55637157 TAAAA-TACCTAAAATACCCCCATAGGG
1 TAAAATTACC-GAAATACCCCCA-AGGG
*
55637184 CAAAA
1 TAAAA
55637189 GGACTGATAT
Statistics
Matches: 174, Mismatches: 36, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
25 1 0.01
26 25 0.14
27 142 0.82
28 6 0.03
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (26 bp):
TAAAATTACCGAAATACCCCCAAGGG
Found at i:55637427 original size:26 final size:26
Alignment explanation
Indices: 55637367--55637442 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
55637357 TTACCACAAA
* **
55637367 TACTGTTACTGGCAGCTTTGCTGTGC
1 TACTATTACTGGCAGCTTTGCTGCAC
* *
55637393 TACTGTTACTGGCAGCTTTGCTGCAT
1 TACTATTACTGGCAGCTTTGCTGCAC
*
55637419 TA-TCATTACTAGCAGCTTTGCTGC
1 TACT-ATTACTGGCAGCTTTGCTGC
55637443 GATATTGGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 1 0.02
26 43 0.98
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCAC
Found at i:55637596 original size:28 final size:28
Alignment explanation
Indices: 55637549--55637642 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 28
55637539 ACTGCATTGT
*
55637549 ACTGTTTACTGTACTGGGCTAAGGCCCAC
1 ACTG-TTACTGTAATGGGCTAAGGCCCAC
* * *
55637578 ATTGTTACTGTATTAGGCTAAGGCCCAC
1 ACTGTTACTGTAATGGGCTAAGGCCCAC
* *
55637606 GCTGATACTGTAATGGGCTAAGGCCCAC
1 ACTGTTACTGTAATGGGCTAAGGCCCAC
55637634 ACTG-TACTG
1 ACTGTTACTG
55637643 ACACTGTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.09
28 48 0.86
29 3 0.05
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.28
Consensus pattern (28 bp):
ACTGTTACTGTAATGGGCTAAGGCCCAC
Found at i:55648191 original size:21 final size:22
Alignment explanation
Indices: 55648167--55648220 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
55648157 AGTGCAAATT
55648167 CTAAGTTAAGA-TGAAA-TAAAA
1 CTAAGTTAA-ACTGAAACTAAAA
* *
55648188 CTAA-TTAAACTTAAACTAAAT
1 CTAAGTTAAACTGAAACTAAAA
55648209 CTAAGTTAAACT
1 CTAAGTTAAACT
55648221 ATCAGAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 8 0.29
21 12 0.43
22 7 0.25
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (22 bp):
CTAAGTTAAACTGAAACTAAAA
Found at i:55660477 original size:44 final size:44
Alignment explanation
Indices: 55660280--55660477 Score: 168
Period size: 45 Copynumber: 4.5 Consensus size: 44
55660270 GCAGGTTGAA
*
55660280 AGATAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAG
1 AGATACCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAG
* * ** *
55660324 AGATACCAGATCTTGTCTCCCTGTACAGGCGGTGGAGTAGATC-G
1 AGATACCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCAG
* * * * * * *
55660368 AAGAAAGCAGATCTTGCCTTCCCATACTAGTGGCG-G-AGCAGATCAA
1 -AGATACCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATCAG
* * *
55660414 AGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAG
1 AGATACCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAG
* *
55660458 AGATACCAGATTTTATCTTC
1 AGATACCAGATCTTGTCTTC
55660478 CCATATTGGT
Statistics
Matches: 119, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
42 7 0.06
43 4 0.03
44 49 0.41
45 50 0.42
46 1 0.01
47 3 0.03
48 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
AGATACCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAG
Found at i:55660691 original size:44 final size:45
Alignment explanation
Indices: 55660628--55660725 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 45
55660618 CAGTAGAATC
* *
55660628 GATCGAAGAAAGCAGATCTTGTCTTCAT-GTATTGG-CGTGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTC-TCATACTGGTCGTGAAGTA
*
55660672 GATCGAAGAAAGCAGATCTTGTCTTCTCATACTGGTGGTGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCTCATACTGGTCGTGAAGTA
55660717 GATCGAAGA
1 GATCGAAGA
55660726 TACAAGTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
43 1 0.02
44 31 0.63
45 17 0.35
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (45 bp):
GATCGAAGAAAGCAGATCTTGTCTTCTCATACTGGTCGTGAAGTA
Found at i:55660802 original size:44 final size:43
Alignment explanation
Indices: 55660746--55660890 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 43
55660736 ATCTCCCTGA
*
55660746 AGTTGCAGTGGAGCAGACAGAAATAATCGGTCCTATCTCCCAAG
1 AGTTGCAATGGAGCAGACA-AAATAATCGGTCCTATCTCCCAAG
* ** * * *
55660790 AGTTGCAATGGAGTAGACTAAAACCA-CAGAT-CTCATCTCTC-TG
1 AGTTGCAATGGAGCAGAC-AAAATAATC-GGTCCT-ATCTCCCAAG
** *
55660833 AAGTTGCAGCGGAGCAGACAAAAATAATCGGTCCTATCTCCCAGG
1 -AGTTGCAATGGAGCAGAC-AAAATAATCGGTCCTATCTCCCAAG
55660878 AGTTGCAATGGAG
1 AGTTGCAATGGAG
55660891 TGGACTAAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
43 4 0.05
44 67 0.88
45 5 0.07
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.21
Consensus pattern (43 bp):
AGTTGCAATGGAGCAGACAAAATAATCGGTCCTATCTCCCAAG
Found at i:55660862 original size:88 final size:88
Alignment explanation
Indices: 55660736--55660938 Score: 352
Period size: 88 Copynumber: 2.3 Consensus size: 88
55660726 TACAAGTCTT
* *
55660736 ATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAATAATCGGTCCTATCTCCCAAGAGTTGCAATGG
1 ATCTCTCTGAAGTTGCAGTGGAGCAGACAAAAATAATCGGTCCTATCTCCCAAGAGTTGCAATGG
55660801 AGTAGACTAAAACCACAGATCTC
66 AGTAGACTAAAACCACAGATCTC
* *
55660824 ATCTCTCTGAAGTTGCAGCGGAGCAGACAAAAATAATCGGTCCTATCTCCCAGGAGTTGCAATGG
1 ATCTCTCTGAAGTTGCAGTGGAGCAGACAAAAATAATCGGTCCTATCTCCCAAGAGTTGCAATGG
*
55660889 AGTGGACTAAAACCACAGATCTC
66 AGTAGACTAAAACCACAGATCTC
*
55660912 ATCTCTCTGAAGTTGCAGTAGAGCAGA
1 ATCTCTCTGAAGTTGCAGTGGAGCAGA
55660939 TCACATTAGA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 108 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (88 bp):
ATCTCTCTGAAGTTGCAGTGGAGCAGACAAAAATAATCGGTCCTATCTCCCAAGAGTTGCAATGG
AGTAGACTAAAACCACAGATCTC
Found at i:55660926 original size:44 final size:44
Alignment explanation
Indices: 55660790--55660928 Score: 147
Period size: 44 Copynumber: 3.2 Consensus size: 44
55660780 ATCTCCCAAG
55660790 AGTTGCAATGGAGTAGACTAAAACCACAGATCTCATCTCTCTGA
1 AGTTGCAATGGAGTAGACTAAAACCACAGATCTCATCTCTCTGA
** * * ** * * * *
55660834 AGTTGCAGCGGAGCAGACAAAAATAATC-GGTC-CTATCTCCCAGG
1 AGTTGCAATGGAGTAGACTAAAACCA-CAGATCTC-ATCTCTCTGA
*
55660878 AGTTGCAATGGAGTGGACTAAAACCACAGATCTCATCTCTCTGA
1 AGTTGCAATGGAGTAGACTAAAACCACAGATCTCATCTCTCTGA
55660922 AGTTGCA
1 AGTTGCA
55660929 GTAGAGCAGA
Statistics
Matches: 70, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
43 2 0.03
44 66 0.94
45 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (44 bp):
AGTTGCAATGGAGTAGACTAAAACCACAGATCTCATCTCTCTGA
Found at i:55661343 original size:44 final size:44
Alignment explanation
Indices: 55661276--55661361 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
55661266 GGCCCAATCG
* * *
55661276 GCCCAAAACAGTTCCTAGTCCAACATTACAAAATTAAACAGACA
1 GCCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGACA
* * *
55661320 GCCCAAAACGGTCCCTAGCCCAACACTACAAAGTTAAGCAGA
1 GCCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGA
55661362 AAAACCCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.42, C:0.30, G:0.13, T:0.15
Consensus pattern (44 bp):
GCCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGACA
Found at i:55662522 original size:22 final size:22
Alignment explanation
Indices: 55662496--55662537 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55662486 TTTATTTTCA
55662496 TATTTT-TTTAATATATTATACT
1 TATTTTATTT-ATATATTATACT
*
55662518 TATTTTATTTATATTTTATA
1 TATTTTATTTATATATTATA
55662538 AAGTACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTATTTATATATTATACT
Found at i:55665379 original size:98 final size:98
Alignment explanation
Indices: 55665205--55665401 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
55665195 GTACAATAAA
* *
55665205 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
55665270 CCTCTAGAATCCCAAATTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
55665303 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
55665368 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
55665401 A
1 A
55665402 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:55666098 original size:24 final size:26
Alignment explanation
Indices: 55666069--55666117 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
55666059 ATATAAATAT
55666069 GAAAATATTC-ATT-AAAAAATATAG
1 GAAAATATTCGATTAAAAAAATATAG
*
55666093 GAAAATATTCGTTTAAAAAAATATA
1 GAAAATATTCGATTAAAAAAATATA
55666118 TACATGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 2 0.09
26 10 0.45
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (26 bp):
GAAAATATTCGATTAAAAAAATATAG
Found at i:55666782 original size:57 final size:57
Alignment explanation
Indices: 55666700--55666810 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
55666690 AGCCACCTTT
* * *
55666700 AAAAAACTGCCAATCGTTCTTTTTTTTATTCCTCCCTTTTCTTCCTTTTTTTTTAAA
1 AAAAAACTACCAATCGTTCTCTTTTTTATTCCTCCCCTTTCTTCCTTTTTTTTTAAA
55666757 AAAAAACTACCAATCGTTCTCTTTTTTATTCCTCCCCTTTCTTCCTTTTTTTTT
1 AAAAAACTACCAATCGTTCTCTTTTTTATTCCTCCCCTTTCTTCCTTTTTTTTT
55666811 CCTTTTACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.20, C:0.25, G:0.03, T:0.52
Consensus pattern (57 bp):
AAAAAACTACCAATCGTTCTCTTTTTTATTCCTCCCCTTTCTTCCTTTTTTTTTAAA
Found at i:55666978 original size:19 final size:19
Alignment explanation
Indices: 55666947--55667076 Score: 197
Period size: 19 Copynumber: 6.7 Consensus size: 19
55666937 TCATATATTT
55666947 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
* ** *
55666966 TAAGTTTATATATAATATC
1 TAAGATTGCATATCATATC
55666985 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
55667004 TAAGATTGCATATATCATATC
1 TAAGATTGC--ATATCATATC
55667025 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
*
55667044 TAGGATTGCATATCATATC
1 TAAGATTGCATATCATATC
55667063 TAAGATTGCATATC
1 TAAGATTGCATATC
55667077 CTCAAAAATT
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
19 80 0.81
21 19 0.19
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:55667027 original size:59 final size:59
Alignment explanation
Indices: 55666947--55667075 Score: 199
Period size: 59 Copynumber: 2.2 Consensus size: 59
55666937 TCATATATTT
* *
55666947 TAAGATTGC--ATATCATATCTAAGTTTATATATAATATCTAAGATTGCATATCATATC
1 TAAGATTGCATATATCATATCTAAGATTACATATAATATCTAAGATTGCATATCATATC
* * *
55667004 TAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTGCATATCATATC
1 TAAGATTGCATATATCATATCTAAGATTACATATAATATCTAAGATTGCATATCATATC
55667063 TAAGATTGCATAT
1 TAAGATTGCATAT
55667076 CCTCAAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 9 0.14
59 56 0.86
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (59 bp):
TAAGATTGCATATATCATATCTAAGATTACATATAATATCTAAGATTGCATATCATATC
Found at i:55668600 original size:13 final size:13
Alignment explanation
Indices: 55668571--55668604 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
55668561 TAAACTCGTT
*
55668571 AGAAAAAGAAAAG
1 AGAAAAAAAAAAG
55668584 -GAAAAAAAAAAG
1 AGAAAAAAAAAAG
55668596 AGAAAAAAA
1 AGAAAAAAA
55668605 GAAGGTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:55670443 original size:21 final size:21
Alignment explanation
Indices: 55670387--55670467 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
55670377 TGATCAGTAT
*
55670387 ACGACACAT-AAGTGCCTGTA
1 ACGACACATAAAGTGCCTGAA
* ** *
55670407 ATGACACACGAGGTGCCTGAA
1 ACGACACATAAAGTGCCTGAA
55670428 ACGACACATAAAGTGCCTGAGA
1 ACGACACATAAAGTGCCTGA-A
* *
55670450 TACAAGACATAAAGTGCC
1 -ACGACACATAAAGTGCC
55670468 GGATCGGCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 7 0.15
21 25 0.52
22 1 0.02
23 15 0.31
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.16
Consensus pattern (21 bp):
ACGACACATAAAGTGCCTGAA
Found at i:55671677 original size:15 final size:16
Alignment explanation
Indices: 55671659--55671690 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55671649 TTAATTAATA
55671659 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
55671674 TAATTTAATAATATTT
1 TAATTTAATAATATTT
55671690 T
1 T
55671691 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:55671681 original size:25 final size:26
Alignment explanation
Indices: 55671646--55671698 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
55671636 TATTATCTTA
55671646 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
55671670 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
55671697 AT
1 AT
55671699 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:55672314 original size:18 final size:19
Alignment explanation
Indices: 55672284--55672325 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
55672274 TATTCCACTA
*
55672284 AAGTT-GTTAATTATATTT
1 AAGTTAGTTAATTATAGTT
55672302 AAGTTAGTT-ATTATAGTT
1 AAGTTAGTTAATTATAGTT
55672320 AA-TTAG
1 AAGTTAG
55672326 ACCAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 15 0.68
19 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (19 bp):
AAGTTAGTTAATTATAGTT
Found at i:55680215 original size:54 final size:54
Alignment explanation
Indices: 55680157--55680277 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
55680147 CATGTAACAA
*
55680157 ACTGTG-TCTGTGTAACTCAAAGTCACACGACCGCGTCGCCAGGCCATGTACCTC
1 ACTGTGATC-GTGTAACTCAAAGTCACACGACCGCGTCACCAGGCCATGTACCTC
* ** * * *
55680211 ACTGTGATCGTGTAATTCAGGGTCACACGACCGTGTCACCAGGTCATGTAACTC
1 ACTGTGATCGTGTAACTCAAAGTCACACGACCGCGTCACCAGGCCATGTACCTC
**
55680265 TTTGTGATCGTGT
1 ACTGTGATCGTGT
55680278 GGACTACCCT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 55 0.96
55 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (54 bp):
ACTGTGATCGTGTAACTCAAAGTCACACGACCGCGTCACCAGGCCATGTACCTC
Found at i:55681169 original size:83 final size:83
Alignment explanation
Indices: 55680993--55681162 Score: 340
Period size: 83 Copynumber: 2.0 Consensus size: 83
55680983 AAACTTATCG
55680993 TATAAACATATCAATCACACAAAAATAATTAATAAACAATAATCCCGTCAACCACAATCATTCAA
1 TATAAACATATCAATCACACAAAAATAATTAATAAACAATAATCCCGTCAACCACAATCATTCAA
55681058 CAGGTGAGTCTTTAAGTT
66 CAGGTGAGTCTTTAAGTT
55681076 TATAAACATATCAATCACACAAAAATAATTAATAAACAATAATCCCGTCAACCACAATCATTCAA
1 TATAAACATATCAATCACACAAAAATAATTAATAAACAATAATCCCGTCAACCACAATCATTCAA
55681141 CAGGTGAGTCTTTAAGTT
66 CAGGTGAGTCTTTAAGTT
55681159 TATA
1 TATA
55681163 CTCATATTGT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (83 bp):
TATAAACATATCAATCACACAAAAATAATTAATAAACAATAATCCCGTCAACCACAATCATTCAA
CAGGTGAGTCTTTAAGTT
Found at i:55687324 original size:27 final size:27
Alignment explanation
Indices: 55687263--55687547 Score: 196
Period size: 27 Copynumber: 10.6 Consensus size: 27
55687253 ATTTTGTTAG
** *
55687263 CCTCTGTGGCAAACTCTGAAAGAATAG
1 CCTCTGTGGTGAACTCTGAAAGAATAT
* * * * * *
55687290 ACTTTATGGTAAACTTTGAAATAATAT
1 CCTCTGTGGTGAACTCTGAAAGAATAT
* * *
55687317 CCTCTATGGCGAACTCTGAAAGAATAG
1 CCTCTGTGGTGAACTCTGAAAGAATAT
* * * * *
55687344 CCGCTGTAGCT-AACTTTGAAATAATAG
1 CCTCTGT-GGTGAACTCTGAAAGAATAT
** * *
55687371 GATTTGTGGCT-AACTCTGAAAGAATAG
1 CCTCTGTGG-TGAACTCTGAAAGAATAT
** * ** *
55687398 GATTTGTGGCAAACTTTGAAAGAATAT
1 CCTCTGTGGTGAACTCTGAAAGAATAT
* * * *
55687425 CCTTTGTGGCGAACTTTGAAAGAATAA
1 CCTCTGTGGTGAACTCTGAAAGAATAT
55687452 CCTCTGTGGTGAACTCTGAAAGAATAT
1 CCTCTGTGGTGAACTCTGAAAGAATAT
* *
55687479 CCTCTATGATGAACTCTGAAAGAATAT
1 CCTCTGTGGTGAACTCTGAAAGAATAT
* * * *
55687506 CCTCTATTGTGAACTCTAAAAGAATAG
1 CCTCTGTGGTGAACTCTGAAAGAATAT
*
55687533 CCTTTGTGGTGAACT
1 CCTCTGTGGTGAACT
55687548 ATAACATACC
Statistics
Matches: 208, Mismatches: 47, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
26 1 0.00
27 206 0.99
28 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (27 bp):
CCTCTGTGGTGAACTCTGAAAGAATAT
Found at i:55687499 original size:81 final size:81
Alignment explanation
Indices: 55687263--55687547 Score: 259
Period size: 81 Copynumber: 3.5 Consensus size: 81
55687253 ATTTTGTTAG
* * * * *
55687263 CCTCTGTGGCAAACTCTGAAAGAATAGA-CTTTATGGTAAACTTTGAAATAATATCCTCTATGGC
1 CCTCTGTGGCGAACTCTGAAAGAATA-ACCTTTGTGGTGAACTCTGAAAGAATATCCTCTATGGC
*
55687327 GAACTCTGAAAGAATAG
65 GAACTCTGAAAGAATAT
* * * * * *** *** * *
55687344 CCGCTGTAGCTAACTTTGAAATAATAGGATTTGTGGCT-AACTCTGAAAGAATAGGATTTGTGGC
1 CCTCTGTGGCGAACTCTGAAAGAATAACCTTTGTGG-TGAACTCTGAAAGAATATCCTCTATGGC
* *
55687408 AAACTTTGAAAGAATAT
65 GAACTCTGAAAGAATAT
* * * **
55687425 CCTTTGTGGCGAACTTTGAAAGAATAACCTCTGTGGTGAACTCTGAAAGAATATCCTCTATGATG
1 CCTCTGTGGCGAACTCTGAAAGAATAACCTTTGTGGTGAACTCTGAAAGAATATCCTCTATGGCG
55687490 AACTCTGAAAGAATAT
66 AACTCTGAAAGAATAT
* * * * *
55687506 CCTCTATTGTGAACTCTAAAAGAATAGCCTTTGTGGTGAACT
1 CCTCTGTGGCGAACTCTGAAAGAATAACCTTTGTGGTGAACT
55687548 ATAACATACC
Statistics
Matches: 157, Mismatches: 44, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
80 1 0.01
81 155 0.99
82 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (81 bp):
CCTCTGTGGCGAACTCTGAAAGAATAACCTTTGTGGTGAACTCTGAAAGAATATCCTCTATGGCG
AACTCTGAAAGAATAT
Found at i:55690254 original size:31 final size:32
Alignment explanation
Indices: 55690201--55690265 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
55690191 ATAAGTATTA
*
55690201 TTAAGTATTTATTGGTTTTGGCTT-GTAATTT
1 TTAAGTATTTATTGGTTTTGGCTTGGTAACTT
*
55690232 TTAATTATTT-TTGGTTTGTGGCTTGGTAACTT
1 TTAAGTATTTATTGGTTT-TGGCTTGGTAACTT
55690264 TT
1 TT
55690266 CTTTTGGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 7 0.23
31 15 0.50
32 8 0.27
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.58
Consensus pattern (32 bp):
TTAAGTATTTATTGGTTTTGGCTTGGTAACTT
Found at i:55690917 original size:81 final size:81
Alignment explanation
Indices: 55690777--55691103 Score: 361
Period size: 81 Copynumber: 4.0 Consensus size: 81
55690767 CAAAGCCCTT
* * * * * * *
55690777 AACTTTGAAAGACTAACCTTTGTGGTGAACTTTGAAAGAATAACCTCTATGGTGAACTCTAAAAG
1 AACTCTGAAAGAATAACCTCTGTGGTGAACTATGAAAGAATATCCTCTATGGCGAACTCTGAAAG
*
55690842 AATAACCTCTATGGTG
66 AATAACCTCTATGGCG
* **
55690858 AACTCTGAAAGAATAACCTCTATGGTGAACTATGAAAGAATATCCTCTATGATGAACTCTGAAAG
1 AACTCTGAAAGAATAACCTCTGTGGTGAACTATGAAAGAATATCCTCTATGGCGAACTCTGAAAG
* * *
55690923 AATATCCTCTATAGCA
66 AATAACCTCTATGGCG
* * * * * *
55690939 AACTCTGAAAGAATAACCTTTGTGGCGAACTATGAAAGAATAGCCT-TCGTGGCGAATTCTTAAA
1 AACTCTGAAAGAATAACCTCTGTGGTGAACTATGAAAGAATATCCTCT-ATGGCGAACTCTGAAA
* * *
55691003 GAATAGCCTTTGTGGCG
65 GAATAACCTCTATGGCG
* * * *
55691020 AATTCTGAAAGAATAACCTCTGTGGTGAACTCTAAAAGAATAGT-CTTTATGGCGAACTCTGAAA
1 AACTCTGAAAGAATAACCTCTGTGGTGAACTATGAAAGAATA-TCCTCTATGGCGAACTCTGAAA
* *
55691084 GAATAACCTTTGTGGCG
65 GAATAACCTCTATGGCG
55691101 AAC
1 AAC
55691104 CTTGAATGGA
Statistics
Matches: 206, Mismatches: 37, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.00
81 204 0.99
82 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (81 bp):
AACTCTGAAAGAATAACCTCTGTGGTGAACTATGAAAGAATATCCTCTATGGCGAACTCTGAAAG
AATAACCTCTATGGCG
Found at i:55691109 original size:27 final size:27
Alignment explanation
Indices: 55690777--55691103 Score: 314
Period size: 27 Copynumber: 12.1 Consensus size: 27
55690767 CAAAGCCCTT
* * * * *
55690777 AACTTTGAAAGACTAACCTTTGTGGTG
1 AACTCTGAAAGAATAACCTCTATGGCG
* *
55690804 AACTTTGAAAGAATAACCTCTATGGTG
1 AACTCTGAAAGAATAACCTCTATGGCG
* *
55690831 AACTCTAAAAGAATAACCTCTATGGTG
1 AACTCTGAAAGAATAACCTCTATGGCG
*
55690858 AACTCTGAAAGAATAACCTCTATGGTG
1 AACTCTGAAAGAATAACCTCTATGGCG
* * **
55690885 AACTATGAAAGAATATCCTCTATGATG
1 AACTCTGAAAGAATAACCTCTATGGCG
* * *
55690912 AACTCTGAAAGAATATCCTCTATAGCA
1 AACTCTGAAAGAATAACCTCTATGGCG
* *
55690939 AACTCTGAAAGAATAACCTTTGTGGCG
1 AACTCTGAAAGAATAACCTCTATGGCG
* * *
55690966 AACTATGAAAGAATAGCCT-TCGTGGCG
1 AACTCTGAAAGAATAACCTCT-ATGGCG
* * * * *
55690993 AATTCTTAAAGAATAGCCTTTGTGGCG
1 AACTCTGAAAGAATAACCTCTATGGCG
* * *
55691020 AATTCTGAAAGAATAACCTCTGTGGTG
1 AACTCTGAAAGAATAACCTCTATGGCG
* ** *
55691047 AACTCTAAAAGAATAGTCTTTATGGCG
1 AACTCTGAAAGAATAACCTCTATGGCG
* *
55691074 AACTCTGAAAGAATAACCTTTGTGGCG
1 AACTCTGAAAGAATAACCTCTATGGCG
55691101 AAC
1 AAC
55691104 CTTGAATGGA
Statistics
Matches: 259, Mismatches: 39, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 1 0.00
27 257 0.99
28 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (27 bp):
AACTCTGAAAGAATAACCTCTATGGCG
Found at i:55693573 original size:124 final size:124
Alignment explanation
Indices: 55693407--55693634 Score: 357
Period size: 124 Copynumber: 1.8 Consensus size: 124
55693397 TTACAATTTG
* *
55693407 ATTACCAACTGTCATCTAAGTAAAGCTAACATGGTAGCTAATGCATTAAGCCAGAAATCTTTGTT
1 ATTACCAACTATCATCTAAGTAAACCTAACATGGTAGCTAATGCATTAAGCCAGAAATCTTTGTT
* * *
55693472 TTTTTAAAGCAATGAACACTCATCTGACTTTGCAACGTGCTGGGAAATGTTACGATCTA
66 TTTTTAAAGCAATGAACACTCATCTAAATTTGAAACGTGCTGGGAAATGTTACGATCTA
** * *
55693531 ATTACCAACTATCATCTGGGTAAACCTAACATGGTAGCTAATGCATTAAGCCATAAATCTTTTTT
1 ATTACCAACTATCATCTAAGTAAACCTAACATGGTAGCTAATGCATTAAGCCAGAAATCTTTGTT
* *
55693596 TTTTTGAAGCAATGAACACTTATCTAAATTTGAAACGTG
66 TTTTTAAAGCAATGAACACTCATCTAAATTTGAAACGTG
55693635 ATGATTCTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
124 93 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (124 bp):
ATTACCAACTATCATCTAAGTAAACCTAACATGGTAGCTAATGCATTAAGCCAGAAATCTTTGTT
TTTTTAAAGCAATGAACACTCATCTAAATTTGAAACGTGCTGGGAAATGTTACGATCTA
Found at i:55697133 original size:18 final size:19
Alignment explanation
Indices: 55697106--55697148 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
55697096 GTACTCTTGA
* *
55697106 ATAAACAATCAATT-TCAG
1 ATAAATAATCAATTAACAG
*
55697124 ATAAATAATCACTTAACAG
1 ATAAATAATCAATTAACAG
55697143 ATAAAT
1 ATAAAT
55697149 TGATTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (19 bp):
ATAAATAATCAATTAACAG
Found at i:55701066 original size:25 final size:25
Alignment explanation
Indices: 55701006--55701055 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
55700996 TTGGGAGTCA
* *
55701006 TCCACTTCGATGCCCAAGACAAAGC
1 TCCACTCCAATGCCCAAGACAAAGC
55701031 TCCACTCCAATGCCCAAGACAAAGC
1 TCCACTCCAATGCCCAAGACAAAGC
55701056 ATTTCCCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.38, G:0.14, T:0.14
Consensus pattern (25 bp):
TCCACTCCAATGCCCAAGACAAAGC
Found at i:55704696 original size:20 final size:19
Alignment explanation
Indices: 55704673--55704725 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
55704663 ATTTTGTACT
55704673 TTTTAAAATAAATTTAATAA
1 TTTTAAAATAAATTTAA-AA
* *
55704693 TTTTAAATTTAAATTTTAAA
1 TTTTAAA-ATAAATTTAAAA
*
55704713 TTTTTAAA-AAATT
1 TTTTAAAATAAATT
55704726 AATTAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.18
20 15 0.54
21 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTAAAATAAATTTAAAA
Found at i:55704696 original size:21 final size:20
Alignment explanation
Indices: 55704672--55704721 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
55704662 AATTTTGTAC
55704672 TTTTTAAAATAAATTTAATAA
1 TTTTTAAAATAAATTTAA-AA
* *
55704693 -TTTTAAATTTAAATTTTAAA
1 TTTTTAAA-ATAAATTTAAAA
55704713 TTTTTAAAA
1 TTTTTAAAA
55704722 AATTAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTAAAATAAATTTAAAA
Found at i:55704709 original size:13 final size:15
Alignment explanation
Indices: 55704681--55704715 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
55704671 CTTTTTAAAA
55704681 TAAATTTAATAATTT
1 TAAATTTAATAATTT
55704696 TAAATTT-A-AATTT
1 TAAATTTAATAATTT
55704709 TAAATTT
1 TAAATTT
55704716 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
14 1 0.05
15 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATTTAATAATTT
Found at i:55708603 original size:44 final size:46
Alignment explanation
Indices: 55708540--55708634 Score: 142
Period size: 44 Copynumber: 2.1 Consensus size: 46
55708530 TATTACAACA
*
55708540 CCATTCCATTCAACCAAACACA-AGAA-TA-TTATTACAGTTCTATT
1 CCATTCCATTCAACCAAACA-ATAGAATTACTTATTACAGCTCTATT
*
55708584 CCATTCCATTCAACCAAACAATTGAATTACTTATTACAGCTCTATT
1 CCATTCCATTCAACCAAACAATAGAATTACTTATTACAGCTCTATT
55708630 CCATT
1 CCATT
55708635 ACAGCTCTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 2 0.04
46 20 0.43
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (46 bp):
CCATTCCATTCAACCAAACAATAGAATTACTTATTACAGCTCTATT
Found at i:55708637 original size:16 final size:16
Alignment explanation
Indices: 55708616--55708687 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
55708606 TGAATTACTT
55708616 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
55708632 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
* *
55708648 ATTACAGCTTTATTCA
1 ATTACAGCTCTATTCC
*
55708664 ATTACATCTCTATTCC
1 ATTACAGCTCTATTCC
55708680 ATTACAGC
1 ATTACAGC
55708688 GAACCAAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:55718175 original size:35 final size:35
Alignment explanation
Indices: 55718117--55718211 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
55718107 ATAAATTTAG
* **
55718117 TATAAATACAATTTAATTTATATTTT-ATTATTTGAT
1 TATAAATATAATTTAA-AAATATTTTGA-TATTTGAT
* *
55718153 T-TAAATATAATTTGTAAAATATTTTGATATTTTAT
1 TATAAATATAATTT-AAAAATATTTTGATATTTGAT
*
55718188 TATGAATATAATTTAAAAATATTT
1 TATAAATATAATTTAAAAATATTT
55718212 AAATTTTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
35 35 0.71
36 14 0.29
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (35 bp):
TATAAATATAATTTAAAAATATTTTGATATTTGAT
Found at i:55720062 original size:6 final size:6
Alignment explanation
Indices: 55720023--55720053 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
55720013 TATAAAGGAA
*
55720023 AGAAAG AAAAAG AGAAAG AGAAAG AGAAAG A
1 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG A
55720054 AAGATAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:55720216 original size:5 final size:5
Alignment explanation
Indices: 55720188--55720229 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
55720178 CACTTTGATT
* *
55720188 ATTGA ATTGA TTTAA AGTTG- ATTGA ATTGA ATTGA ATTGA AT
1 ATTGA ATTGA ATTGA A-TTGA ATTGA ATTGA ATTGA ATTGA AT
55720230 ATATGTGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 3 0.10
5 26 0.84
6 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (5 bp):
ATTGA
Found at i:55724497 original size:43 final size:43
Alignment explanation
Indices: 55724435--55724517 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
55724425 GTACAGGTTA
*
55724435 TGCTTCAGTTTATTAGATGATGCACTATGTATGCCAGTATAGT
1 TGCTTCAGTATATTAGATGATGCACTATGTATGCCAGTATAGT
* * *
55724478 TGCTTCAGTATATTTGATGATGCACTGTGTGTGCCAGTAT
1 TGCTTCAGTATATTAGATGATGCACTATGTATGCCAGTAT
55724518 GCACTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (43 bp):
TGCTTCAGTATATTAGATGATGCACTATGTATGCCAGTATAGT
Found at i:55725432 original size:9 final size:9
Alignment explanation
Indices: 55725403--55725439 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55725393 TGAGTTTTCG
55725403 AATTCGAAT
1 AATTCGAAT
*
55725412 AACTCGAAT
1 AATTCGAAT
55725421 AATTCGAAT
1 AATTCGAAT
*
55725430 AATTTGAAT
1 AATTCGAAT
55725439 A
1 A
55725440 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55727971 original size:24 final size:24
Alignment explanation
Indices: 55727932--55727982 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
55727922 TCAAAGTAAG
** *
55727932 TTTTAAATGTTGTCCAAAATATGT
1 TTTTAAATGTCATCCAAAACATGT
*
55727956 TTTTAAATGTCATCCAAAGCATGT
1 TTTTAAATGTCATCCAAAACATGT
55727980 TTT
1 TTT
55727983 AAGAATTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (24 bp):
TTTTAAATGTCATCCAAAACATGT
Found at i:55728770 original size:35 final size:34
Alignment explanation
Indices: 55728654--55728790 Score: 130
Period size: 35 Copynumber: 3.9 Consensus size: 34
55728644 CATTTGTCTA
* * *
55728654 TTATACCAACCAGTGTTGGGCACATCTATTGTCGG
1 TTATACCGACCAGTGCT-GGCACATCTATTGTTGG
* *
55728689 TTATACCGACCAGTGCTTGGTACATCTATTATTGG
1 TTATACCGACCAGTGC-TGGCACATCTATTGTTGG
* *
55728724 TTTTACCGACCAGTGCTGGACACATCTATTGTTGA
1 TTATACCGACCAGTGCTGG-CACATCTATTGTTGG
** * * *
55728759 TTATATTGACCAATGCTACGCATATCTATTGT
1 TTATACCGACCAGTGCT-GGCACATCTATTGT
55728791 CAATTTTACC
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
34 3 0.04
35 79 0.94
36 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (34 bp):
TTATACCGACCAGTGCTGGCACATCTATTGTTGG
Found at i:55728786 original size:70 final size:70
Alignment explanation
Indices: 55728657--55728788 Score: 156
Period size: 70 Copynumber: 1.9 Consensus size: 70
55728647 TTGTCTATTA
* * * * ** *
55728657 TACCAACCAGTGTTGGGCACATCTATTGTCGGTTATACCGACCAGTGCTTGGTACATCTATTATT
1 TACCAACCAGTGCTGGACACATCTATTGTCGATTATACCGACCAATGCTACGCACATCTATTATT
55728722 GGTTT
66 GGTTT
* * ** *
55728727 TACCGACCAGTGCTGGACACATCTATTGTTGATTATATTGACCAATGCTACGCATATCTATT
1 TACCAACCAGTGCTGGACACATCTATTGTCGATTATACCGACCAATGCTACGCACATCTATT
55728789 GTCAATTTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
70 50 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (70 bp):
TACCAACCAGTGCTGGACACATCTATTGTCGATTATACCGACCAATGCTACGCACATCTATTATT
GGTTT
Found at i:55736150 original size:17 final size:15
Alignment explanation
Indices: 55736100--55736154 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 15
55736090 AGTACCATTG
*
55736100 AATAAATAATCAATTT
1 AATAAATAAT-TATTT
55736116 CAGATAAATAATTATTT
1 -A-ATAAATAATTATTT
55736133 AATAAATAAATTAGTTT
1 AATAAAT-AATTA-TTT
55736150 AATAA
1 AATAA
55736155 TCGAAGCATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 6 0.18
16 6 0.18
17 13 0.38
18 9 0.26
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (15 bp):
AATAAATAATTATTT
Found at i:55738473 original size:24 final size:23
Alignment explanation
Indices: 55738446--55738505 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
55738436 TTATTAACAT
55738446 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* ***
55738470 TGTTCATGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
55738493 TGTTCGTGAACAT
1 TGTTCGTGAACAT
55738506 TAAACAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:55743793 original size:17 final size:18
Alignment explanation
Indices: 55743771--55743807 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55743761 CCTAATACAC
55743771 TAGGTA-CCTTGAAAAAA
1 TAGGTACCCTTGAAAAAA
55743788 TAGGTACCCTTGAAAAAA
1 TAGGTACCCTTGAAAAAA
55743806 TA
1 TA
55743808 ATTAACTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (18 bp):
TAGGTACCCTTGAAAAAA
Found at i:55757115 original size:8 final size:8
Alignment explanation
Indices: 55757048--55757117 Score: 63
Period size: 8 Copynumber: 8.4 Consensus size: 8
55757038 ATTACTATGA
55757048 AAATATAT
1 AAATATAT
55757056 AAA-ATAT
1 AAATATAT
55757063 AAA-ATAT
1 AAATATAT
55757070 AAATATAT
1 AAATATAT
*
55757078 AGAATCCTAT
1 A-AAT-ATAT
*
55757088 AACATATGT
1 AA-ATATAT
55757097 AAAACTATAT
1 -AAA-TATAT
55757107 AAATATAT
1 AAATATAT
55757115 AAA
1 AAA
55757118 AGCGTATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
7 14 0.27
8 16 0.31
9 10 0.19
10 12 0.23
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (8 bp):
AAATATAT
Found at i:55757126 original size:18 final size:17
Alignment explanation
Indices: 55757047--55757118 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 17
55757037 TATTACTATG
*
55757047 AAAATATATAAA-ATAT
1 AAAACATATAAATATAT
55757063 -AAA-ATATAAATATAT
1 AAAACATATAAATATAT
* * *
55757078 AGAATCCTATAACATATGT
1 A-AAACATATAA-ATATAT
55757097 AAAACTATATAAATATAT
1 AAAAC-ATATAAATATAT
55757115 AAAA
1 AAAA
55757119 GCGTATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 7 0.16
15 7 0.16
17 2 0.05
18 17 0.39
19 11 0.25
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAACATATAAATATAT
Found at i:55761663 original size:29 final size:30
Alignment explanation
Indices: 55761603--55761665 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
55761593 TTTTTTCATG
* * *
55761603 TTCTTTGAACTTTCTTTTTTTTCTTTTATC
1 TTCTTTAAACTTTCTCTTTTTTCTATTATC
*
55761633 TTCTTTAAACTTTCTCTTTTTT-TATTCTC
1 TTCTTTAAACTTTCTCTTTTTTCTATTATC
55761662 TTCT
1 TTCT
55761666 CCTTCTCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (30 bp):
TTCTTTAAACTTTCTCTTTTTTCTATTATC
Found at i:55764119 original size:33 final size:33
Alignment explanation
Indices: 55764082--55764144 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
55764072 TATACACTCA
55764082 GGATTAGAGGCGTATTGGATTAGAGGTGTATTG
1 GGATTAGAGGCGTATTGGATTAGAGGTGTATTG
* *
55764115 GGATTAGATGTGTATTGGATTAGAGGTGTA
1 GGATTAGAGGCGTATTGGATTAGAGGTGTA
55764145 ATAGCTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.38, T:0.35
Consensus pattern (33 bp):
GGATTAGAGGCGTATTGGATTAGAGGTGTATTG
Found at i:55764120 original size:17 final size:16
Alignment explanation
Indices: 55764082--55764144 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
55764072 TATACACTCA
*
55764082 GGATTAGAGGCGTATT
1 GGATTAGAGGTGTATT
55764098 GGATTAGAGGTGTATT
1 GGATTAGAGGTGTATT
*
55764114 GGGATTAGATGTGTATT
1 -GGATTAGAGGTGTATT
55764131 GGATTAGAGGTGTA
1 GGATTAGAGGTGTA
55764145 ATAGCTAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
16 28 0.65
17 15 0.35
ACGTcount: A:0.25, C:0.02, G:0.38, T:0.35
Consensus pattern (16 bp):
GGATTAGAGGTGTATT
Found at i:55764209 original size:44 final size:45
Alignment explanation
Indices: 55764125--55764215 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
55764115 GGATTAGATG
* * *
55764125 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
55764170 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
55764214 TG
1 TG
55764216 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:55764401 original size:18 final size:17
Alignment explanation
Indices: 55764380--55764414 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55764370 TTATTATTGA
*
55764380 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55764398 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55764415 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55764642 original size:18 final size:17
Alignment explanation
Indices: 55764621--55764655 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55764611 TTATTATTAA
*
55764621 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55764639 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55764656 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55764743 original size:120 final size:120
Alignment explanation
Indices: 55764363--55764866 Score: 911
Period size: 120 Copynumber: 4.2 Consensus size: 120
55764353 ATCATATTTA
*
55764363 AACATAATTATTATTGAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
55764428 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * *
55764483 AACATAATTATTATTAAATTTATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAA-T-AATT
*
55764547 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
55764604 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
55764669 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
55764724 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
55764789 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
55764844 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
55764867 AACTTGAAAA
Statistics
Matches: 371, Mismatches: 10, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
119 1 0.00
120 254 0.68
121 115 0.31
122 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:55767929 original size:33 final size:33
Alignment explanation
Indices: 55767890--55767999 Score: 127
Period size: 33 Copynumber: 3.3 Consensus size: 33
55767880 ATTATAAAGC
55767890 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
55767923 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
55767956 AATGT-T-ATTGTCCCTAAAA-AACATTGTTGGTGT
1 -ATGTATAATTG-ACCTAAAATTA-ATTGTTGGTGT
*
55767989 ACGTATAATTG
1 ATGTATAATTG
55768000 TTGGTTTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 8 0.12
33 49 0.75
34 8 0.12
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:55768006 original size:51 final size:51
Alignment explanation
Indices: 55767946--55768060 Score: 205
Period size: 51 Copynumber: 2.3 Consensus size: 51
55767936 CTAAAATTAC
55767946 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGTTGGTGTACGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTACGTATAA
*
55767997 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTACGTATAA
55768048 TTGTTGGTTTAAT
1 TTGTTGGTTTAAT
55768061 TGTTGGTTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 1 0.02
51 61 0.98
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (51 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTACGTATAA
Found at i:55768062 original size:12 final size:12
Alignment explanation
Indices: 55768045--55768072 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
55768035 GGTGTATGTA
55768045 TAATTGTTGGTT
1 TAATTGTTGGTT
55768057 TAATTGTTGGTT
1 TAATTGTTGGTT
55768069 TAAT
1 TAAT
55768073 GTTATTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (12 bp):
TAATTGTTGGTT
Found at i:55772951 original size:16 final size:16
Alignment explanation
Indices: 55772930--55772965 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
55772920 TAAATAATTT
*
55772930 TTATATTTAAAAAAAC
1 TTATATTTAAAAAAAA
55772946 TTATATTTAAAAAAAA
1 TTATATTTAAAAAAAA
55772962 TTAT
1 TTAT
55772966 GCACTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTATATTTAAAAAAAA
Found at i:55772995 original size:16 final size:16
Alignment explanation
Indices: 55772974--55773013 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
55772964 ATGCACTTTT
55772974 ATTTTAAATATATATA
1 ATTTTAAATATATATA
* *
55772990 ATTTTAAATTTTTATA
1 ATTTTAAATATATATA
*
55773006 TTTTTAAA
1 ATTTTAAA
55773014 ATTGACAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAAATATATATA
Found at i:55773154 original size:9 final size:9
Alignment explanation
Indices: 55773142--55773193 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 9
55773132 GTTGAACCAG
55773142 TTTTTATAA
1 TTTTTATAA
55773151 TTTTTATAA
1 TTTTTATAA
55773160 TTTATTGACTTAA
1 TTT-TT-A--TAA
55773173 -TTTTATAA
1 TTTTTATAA
55773181 TTTTATATAA
1 TTTT-TATAA
55773191 TTT
1 TTT
55773194 ATTTTCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 3 0.08
9 15 0.41
10 11 0.30
11 3 0.08
12 2 0.05
13 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:55773193 original size:31 final size:31
Alignment explanation
Indices: 55773143--55773217 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 31
55773133 TTGAACCAGT
55773143 TTTTATAATTTTTATAATTTATTGAC-TTAA
1 TTTTATAATTTTTATAATTTATTGACTTTAA
** *
55773173 TTTTATAATTTTATATAATTTATTTTCTTTTA
1 TTTTATAATTTT-TATAATTTATTGACTTTAA
55773205 TTTTATAATTTTT
1 TTTTATAATTTTT
55773218 GTATATATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 12 0.30
31 13 0.32
32 15 0.38
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (31 bp):
TTTTATAATTTTTATAATTTATTGACTTTAA
Found at i:55773718 original size:103 final size:103
Alignment explanation
Indices: 55773539--55773745 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
55773529 AAGGAGACCT
55773539 AATATTTGCTAGACCTTTAAATGAGAGCTACGATTTAATGGTGAATCTTAGTTTTCAAGGCGAGT
1 AATATTTGCTAGACCTTTAAATGAGAGCTACGATTTAATGGTGAATCTTAGTTTTCAAGGCGAGT
*
55773604 TAAGAGATCAAGAGGGACTAGGATTAGTCATAAAATTG
66 TAAGAGATCAAGAAGGACTAGGATTAGTCATAAAATTG
*
55773642 AATATTTGCTAGACCTTTAAATGAGAGCTACGATTTAGTGGTGAATCTTAGTTTTCAAGGCGAGT
1 AATATTTGCTAGACCTTTAAATGAGAGCTACGATTTAATGGTGAATCTTAGTTTTCAAGGCGAGT
*
55773707 TGAGAGATCAAGAAGGACTAGGATTAGTCATAAAATTG
66 TAAGAGATCAAGAAGGACTAGGATTAGTCATAAAATTG
55773745 A
1 A
55773746 GGATGAGTAA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (103 bp):
AATATTTGCTAGACCTTTAAATGAGAGCTACGATTTAATGGTGAATCTTAGTTTTCAAGGCGAGT
TAAGAGATCAAGAAGGACTAGGATTAGTCATAAAATTG
Found at i:55775679 original size:37 final size:38
Alignment explanation
Indices: 55775630--55775702 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
55775620 TCCTTTTTTG
55775630 TTTCCCTTTTTCC-CTTTCTTTCCC-TTGTTTTTTCAT
1 TTTCCCTTTTTCCTCTTTCTTTCCCATTGTTTTTTCAT
* *
55775666 TTTCCCGTTTTTCCTTTTTCTTTCCCATTTTTTTTTC
1 TTTCCC-TTTTTCCTCTTTCTTTCCCATTGTTTTTTC
55775703 TTCTCAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 6 0.19
37 7 0.22
38 10 0.31
39 9 0.28
ACGTcount: A:0.03, C:0.29, G:0.03, T:0.66
Consensus pattern (38 bp):
TTTCCCTTTTTCCTCTTTCTTTCCCATTGTTTTTTCAT
Found at i:55775706 original size:20 final size:19
Alignment explanation
Indices: 55775645--55775706 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
55775635 CTTTTTCCCT
*
55775645 TTCTTTCCCTTGTTTTTTC
1 TTCTTTCCCTTTTTTTTTC
* *
55775664 AT-TTTCCCGTTTTTCCTTT-
1 TTCTTTCCC-TTTTT-TTTTC
55775683 TTCTTTCCCATTTTTTTTTC
1 TTCTTTCCC-TTTTTTTTTC
55775703 TTCT
1 TTCT
55775707 CAACCAAGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.18
19 9 0.27
20 18 0.55
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.68
Consensus pattern (19 bp):
TTCTTTCCCTTTTTTTTTC
Found at i:55777913 original size:23 final size:23
Alignment explanation
Indices: 55777865--55777913 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
55777855 GTTATTGATC
* *
55777865 GTGGTAGCTTCGGCTACATTTTA
1 GTGGTAGCTTCGGCTACATATCA
55777888 GTGGTAGCTTCGGCTACATATCA
1 GTGGTAGCTTCGGCTACATATCA
55777911 GTG
1 GTG
55777914 TGGCACTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (23 bp):
GTGGTAGCTTCGGCTACATATCA
Found at i:55783779 original size:21 final size:21
Alignment explanation
Indices: 55783753--55783830 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
55783743 AAAAAAGAAA
*
55783753 AAAAGAAAAAAAATAAAATGGG
1 AAAAGAAAAAAAA-AAAAGGGG
* *
55783775 -AAAGAGAAAGAAAAAAGGGG
1 AAAAGAAAAAAAAAAAAGGGG
*
55783795 AAAAGGAAAAAAAAAGAAAGGGA
1 AAAA-GAAAAAAAAA-AAAGGGG
* *
55783818 AAAATAGAAAAAA
1 AAAAGAAAAAAAA
55783831 TATTAATTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 7 0.16
21 13 0.29
22 15 0.33
23 10 0.22
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (21 bp):
AAAAGAAAAAAAAAAAAGGGG
Found at i:55783807 original size:19 final size:19
Alignment explanation
Indices: 55783761--55783810 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
55783751 AAAAAAGAAA
*
55783761 AAAAATAAAATGGGAAAGAG
1 AAAAA-AAAAGGGGAAAGAG
55783781 AAAGAAAAAAGGGGAAA-AGG
1 AAA-AAAAAAGGGGAAAGA-G
55783801 AAAAAAAAAG
1 AAAAAAAAAG
55783811 AAAGGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.30
20 17 0.63
21 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAGGGGAAAGAG
Found at i:55796373 original size:22 final size:24
Alignment explanation
Indices: 55796337--55796380 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
55796327 TGTTATAGGA
55796337 AGGGCACGACGGTGGAG-GGTGTT
1 AGGGCACGACGGTGGAGAGGTGTT
*
55796360 AGGGC-CGATGGTGGAGAGGTG
1 AGGGCACGACGGTGGAGAGGTG
55796381 ATGGTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.18, C:0.11, G:0.55, T:0.16
Consensus pattern (24 bp):
AGGGCACGACGGTGGAGAGGTGTT
Found at i:55807599 original size:152 final size:152
Alignment explanation
Indices: 55807262--55807599 Score: 350
Period size: 147 Copynumber: 2.2 Consensus size: 152
55807252 GTTTTAGGAG
* *
55807262 AAAAAAATTGTTTGTGTTGGAGTTTTAAGG-GAGATATTGTGATAGTTTTAAGGTAGATTTTTAT
1 AAAAAAATTGTTTGTGTTGGAGTTTT--GGAGAGATATTATGATAATTTTAAGGTA-ATTTTTAT
* * * * * *
55807326 TGTTTGTAATAATAATTTGTATGTTGTATGTTTATATTTTAATTTATTATTAATCTTTAGATTTA
63 TGTTTATAATAATAATATGTATATTATATGTTTATATTTTAA-TTATTATTAATATTTAGAATTA
*
55807391 ATATTTAAGATTATATTTTTGTTTGT
127 ATATTTAAGAATATATTTTTGTTTGT
** * * * *
55807417 AAAAAAATTGTTTGAATTCGAGTTTTAGAGATAGATTATGATAATTTTAAGGT-ATTTTTAGTT-
1 AAAAAAATTGTTTGTGTTGGAGTTTTGGAGAGATATTATGATAATTTTAAGGTAATTTTTA-TTG
55807480 TTTATAATAATAATAAT-TATATTATATGTTTATATTTT-A-T-TT-TTAATATTTAGAATTAAT
65 TTTATAATAATAAT-ATGTATATTATATGTTTATATTTTAATTATTATTAATATTTAGAATTAAT
* *
55807540 GTTTTAGAATATATTTTTGTTTGT
129 ATTTAAGAATATATTTTTGTTTGT
****
55807564 AAATTTTTTTTTGTTTGTGTTGGAGTTTTGGAGAGA
1 AAA---AAAATTGTTTGTGTTGGAGTTTTGGAGAGA
55807600 AAAAAGGTTG
Statistics
Matches: 151, Mismatches: 26, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
147 40 0.26
148 2 0.01
149 1 0.01
150 21 0.14
151 1 0.01
152 39 0.26
153 4 0.03
154 20 0.13
155 23 0.15
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.53
Consensus pattern (152 bp):
AAAAAAATTGTTTGTGTTGGAGTTTTGGAGAGATATTATGATAATTTTAAGGTAATTTTTATTGT
TTATAATAATAATATGTATATTATATGTTTATATTTTAATTATTATTAATATTTAGAATTAATAT
TTAAGAATATATTTTTGTTTGT
Found at i:55811182 original size:14 final size:15
Alignment explanation
Indices: 55811149--55811182 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55811139 ATTTTCTGTT
55811149 ATTTAATTTAGTGAA
1 ATTTAATTTAGTGAA
55811164 ATTTAATTTA-TGAA
1 ATTTAATTTAGTGAA
*
55811178 TTTTA
1 ATTTA
55811183 TCTCTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
ATTTAATTTAGTGAA
Found at i:55818196 original size:15 final size:16
Alignment explanation
Indices: 55818170--55818200 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55818160 ATAAGTGAGA
55818170 GATGATGGGATGATTG
1 GATGATGGGATGATTG
55818186 GATGA-GGGATGATTG
1 GATGATGGGATGATTG
55818201 AAAAAGTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.26, C:0.00, G:0.45, T:0.29
Consensus pattern (16 bp):
GATGATGGGATGATTG
Found at i:55827475 original size:34 final size:34
Alignment explanation
Indices: 55827437--55827515 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
55827427 TGATGAATGG
55827437 GTGAGAGATGATGAGATGAGGGATGATTGAAAAA
1 GTGAGAGATGATGAGATGAGGGATGATTGAAAAA
*
55827471 GTGAGAGATGATGGGATGAGGGATGATTGAAAAA
1 GTGAGAGATGATGAGATGAGGGATGATTGAAAAA
*
55827505 GTGAGAAATGA
1 GTGAGAGATGA
55827516 GCTTTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (34 bp):
GTGAGAGATGATGAGATGAGGGATGATTGAAAAA
Found at i:55827480 original size:19 final size:19
Alignment explanation
Indices: 55827453--55827515 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
55827443 GATGATGAGA
*
55827453 TGAGGGATGATTGAAAAAG
1 TGAGAGATGATTGAAAAAG
**
55827472 TGAGAGATGA-TG--GGA-
1 TGAGAGATGATTGAAAAAG
*
55827487 TGAGGGATGATTGAAAAAG
1 TGAGAGATGATTGAAAAAG
*
55827506 TGAGAAATGA
1 TGAGAGATGA
55827516 GCTTTTATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
15 9 0.28
16 3 0.09
18 3 0.09
19 17 0.53
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATTGAAAAAG
Found at i:55836037 original size:17 final size:17
Alignment explanation
Indices: 55836005--55836036 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55835995 TTTTCCTCTT
55836005 TTTCTTCGATTTTTTTC
1 TTTCTTCGATTTTTTTC
55836022 TTTCTTC-ATTTTTTT
1 TTTCTTCGATTTTTTT
55836037 TTCGATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTCTTCGATTTTTTTC
Done.