Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 4 of 117
Found at i:930378 original size:57 final size:56
Alignment explanation
Indices: 930264--930378 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 56
930254 CTCTTTTGCA
* *
930264 ATTTTTAAAATTTTCACCATTTGGGCCTATTTAGAATTTTTTTTAATTTTTTGTTGG
1 ATTTTTAAAATTTTCACCATTTGGACCAATTTAGAATTTTTTTT-ATTTTTTGTTGG
* *
930321 ATTTTTAAATTTTTCACCATTTGGATCAATTTAGAAATATTTTTTT-TTTGTTT-TTGG
1 ATTTTTAAAATTTTCACCATTTGGACCAATTTAG-AAT-TTTTTTTATTT-TTTGTTGG
930378 A
1 A
930379 AAGAAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
57 38 0.75
58 6 0.12
59 7 0.14
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.57
Consensus pattern (56 bp):
ATTTTTAAAATTTTCACCATTTGGACCAATTTAGAATTTTTTTTATTTTTTGTTGG
Found at i:932149 original size:44 final size:43
Alignment explanation
Indices: 932047--932153 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
932037 ATTTTTAGAG
* *
932047 AATAAACAAAACTCCTATAAACAAAGGCTAAACAACTTTTGAA
1 AATAAACAAAGCTCCTCTAAACAAAGGCTAAACAACTTTTGAA
* *
932090 AATAAACAAAGCTCCTCTAAACAGAGGC-ACAACGACTTTTGAAA
1 AATAAACAAAGCTCCTCTAAACAAAGGCTA-AACAACTTTTG-AA
*
932134 AATAAACAAGGCTCCTCTAA
1 AATAAACAAAGCTCCTCTAA
932154 TTAGAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
42 1 0.02
43 35 0.61
44 21 0.37
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.20
Consensus pattern (43 bp):
AATAAACAAAGCTCCTCTAAACAAAGGCTAAACAACTTTTGAA
Found at i:932181 original size:73 final size:73
Alignment explanation
Indices: 932088--932227 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 73
932078 ACAACTTTTG
*
932088 AAAATAAACAAAGCTCCTCTAAACAGAGGCACAACGACTTTTG-AAAAATAAACAAGGCTCCTCT
1 AAAATAAACAAAGCTCCTCTAAACAGAGGCACAACGAC-TTTGAAAAAAAAAACAAGGCTCCTCT
932152 AATTAGAAA
65 AATTAGAAA
* * * * * *
932161 AAAATAAGCAAGGCTTCTCTAATCAGAGGCTCAACGACTTTGAAAAAAAAAATAAGGCTCCTCTA
1 AAAATAAACAAAGCTCCTCTAAACAGAGGCACAACGACTTTGAAAAAAAAAACAAGGCTCCTCTA
932226 AT
66 AT
932228 CAGAGGTTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 4 0.07
73 55 0.93
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.21
Consensus pattern (73 bp):
AAAATAAACAAAGCTCCTCTAAACAGAGGCACAACGACTTTGAAAAAAAAAACAAGGCTCCTCTA
ATTAGAAA
Found at i:932225 original size:44 final size:44
Alignment explanation
Indices: 932157--932310 Score: 200
Period size: 44 Copynumber: 3.4 Consensus size: 44
932147 CCTCTAATTA
* *
932157 GAAAAAAATAAGCAAGGCTTCTCTAATCAGAGGCTCAACGACTTT
1 GAAAAAAA-AAACAAGGCTCCTCTAATCAGAGGCTCAACGACTTT
* * *
932202 GAAAAAAAAAATAAGGCTCCTCTAATCAGAGGTTCAACAACTTT
1 GAAAAAAAAAACAAGGCTCCTCTAATCAGAGGCTCAACGACTTT
* * *
932246 GAAAAAAAATAAACAAGGCTTCTTTAATCAGAGGCTCAACGATTTT
1 G-AAAAAAA-AAACAAGGCTCCTCTAATCAGAGGCTCAACGACTTT
*
932292 GAAAAAATAAACAAGGCTC
1 GAAAAAAAAAACAAGGCTC
932311 ATCGACAATC
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
44 42 0.45
45 21 0.22
46 31 0.33
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (44 bp):
GAAAAAAAAAACAAGGCTCCTCTAATCAGAGGCTCAACGACTTT
Found at i:932254 original size:46 final size:46
Alignment explanation
Indices: 932158--932298 Score: 187
Period size: 46 Copynumber: 3.1 Consensus size: 46
932148 CTCTAATTAG
* *
932158 AAAAAAATAAGCAAGGCTTCTCTAATCAGAGGCTCAACGACTTTG-
1 AAAAAAAAAAACAAGGCTTCTCTAATCAGAGGCTCAACGACTTTGA
* * * *
932203 -AAAAAAAAAATAAGGCTCCTCTAATCAGAGGTTCAACAACTTTGA
1 AAAAAAAAAAACAAGGCTTCTCTAATCAGAGGCTCAACGACTTTGA
* * *
932248 AAAAAAATAAACAAGGCTTCTTTAATCAGAGGCTCAACGATTTTGA
1 AAAAAAAAAAACAAGGCTTCTCTAATCAGAGGCTCAACGACTTTGA
932294 AAAAA
1 AAAAA
932299 TAAACAAGGC
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
44 38 0.47
46 43 0.53
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (46 bp):
AAAAAAAAAAACAAGGCTTCTCTAATCAGAGGCTCAACGACTTTGA
Found at i:943969 original size:109 final size:110
Alignment explanation
Indices: 943718--943977 Score: 325
Period size: 109 Copynumber: 2.4 Consensus size: 110
943708 AAATATATCT
* ** * * *
943718 AATTATTCTACCATTTAGGCCAAATTAGAAATATTCTC-TTTTGAAATTTCTAAATTTTTCATCA
1 AATTTTTC-ACCATTTAGATCAATTTAGAAATATTTTCTTTTTGAAATTTCTAAATTTTTCACCA
** *
943782 TTTGGGCCTATTTAGAAATTCTTTTTGTTCATTTTTTTGGGTTTCTA
65 TTTGAACCTATTTAG-AATTCTTTTTGTTCATTTTTTTGGATTTCTA
* *
943829 AATTTTTCACTATTTAGGTCAATTTAGAAATATTTTCTTTTTCGAAATTTCTAAATTTTTCACCA
1 AATTTTTCACCATTTAGATCAATTTAGAAATATTTTCTTTTT-GAAATTTCTAAATTTTTCACCA
943894 TTTGAACCTATTTAG-ATT-TTTTT-TT-ATTTTTTGTTGGATTTCTA
65 TTTGAACCTATTTAGAATTCTTTTTGTTCA-TTTTT-TTGGATTTCTA
*
943938 AATTTTTCACCATTTTGATCAATTTAGAAATATTTT-TTTT
1 AATTTTTCACCATTTAGATCAATTTAGAAATATTTTCTTTT
943978 ATTTTGGAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
107 1 0.01
108 11 0.08
109 48 0.36
110 28 0.21
111 11 0.08
112 34 0.26
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.53
Consensus pattern (110 bp):
AATTTTTCACCATTTAGATCAATTTAGAAATATTTTCTTTTTGAAATTTCTAAATTTTTCACCAT
TTGAACCTATTTAGAATTCTTTTTGTTCATTTTTTTGGATTTCTA
Found at i:944515 original size:189 final size:187
Alignment explanation
Indices: 944152--944515 Score: 454
Period size: 189 Copynumber: 1.9 Consensus size: 187
944142 TCAATTAAAA
*
944152 TTTTATTTGAAAAAAAATACAATTACTTTTATTAAAATTTCATCTAAATTATTCTACCATTTTAG
1 TTTTATTTGAAAAAAAATACAATTACTTTTATTAAAATTTCATCTAAATTATTCCACCATTTTAG
944217 ACAAATTTAGAGAAAATTTCTCACCTAAAAACCTTTTAAGAATTTAACATTTAAAATTTCTAAGA
66 ACAAATTTAGAGAAAATTTCTCACCTAAAAA-CTTTTAAGAATTTAACATTTAAAATTTCTAAGA
* * * *
944282 ATTTCATCATTTGGTAATTTGTATTTAATTCCAAAAATTTTTATTAATTTTTTTATTT
130 ATTTCATCATTAGATAATTTGTATTTAATTCAAAAAAATTTTATTAATTTTTTTATTT
* * * ** *
944340 TTTTGTTTGAAAATAAATATTAATTA-TTGTTATTGCAATTTTATCTAAATTATTCCACCA-TTT
1 TTTTATTTGAAAAAAAATA-CAATTACTT-TTATTAAAATTTCATCTAAATTATTCCACCATTTT
* * * *
944403 ATGATAAATTTAGATAAAATTTCTCACCTAAAAA-TTTTATAGAAATTTACCATTTGAAATTTCT
64 A-GACAAATTTAGAGAAAATTTCTCACCTAAAAACTTTTA-AG-AATTTAACATTTAAAATTTCT
944467 ACA-AA-TTCAATCATTAGATAATTAT-TATTT-ATTCTAAAAAAATTTTATT
126 A-AGAATTTC-ATCATTAGATAATT-TGTATTTAATTC-AAAAAAATTTTATT
944516 TTAAATTTTT
Statistics
Matches: 152, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
187 5 0.03
188 32 0.21
189 113 0.74
190 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (187 bp):
TTTTATTTGAAAAAAAATACAATTACTTTTATTAAAATTTCATCTAAATTATTCCACCATTTTAG
ACAAATTTAGAGAAAATTTCTCACCTAAAAACTTTTAAGAATTTAACATTTAAAATTTCTAAGAA
TTTCATCATTAGATAATTTGTATTTAATTCAAAAAAATTTTATTAATTTTTTTATTT
Found at i:950191 original size:20 final size:20
Alignment explanation
Indices: 950166--950244 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 20
950156 TGCAAGAATG
950166 TCATGCAAATATATTAATTA
1 TCATGCAAATATATTAATTA
* *
950186 TCATGCAATAATAATAATAATAA
1 TCATGC-A-AAT-ATATTAATTA
**
950209 TCATATAAATATA-TAA-TA
1 TCATGCAAATATATTAATTA
* *
950227 TCATGTAAATACATTAAT
1 TCATGCAAATATATTAAT
950245 AATTATGTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 12 0.26
19 6 0.13
20 9 0.19
21 4 0.09
22 4 0.09
23 12 0.26
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (20 bp):
TCATGCAAATATATTAATTA
Found at i:950372 original size:24 final size:23
Alignment explanation
Indices: 950317--950372 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
950307 AATATCATTC
*
950317 AAATATAATATTAATCATGCAGT
1 AAATATAATATTAATCATGCAAT
*
950340 AACAAATAATATTATATCATGCAAT
1 AA-ATATAATATTA-ATCATGCAAT
950365 AAATATAA
1 AAATATAA
950373 AATCATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 15 0.54
25 11 0.39
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (23 bp):
AAATATAATATTAATCATGCAAT
Found at i:950478 original size:20 final size:20
Alignment explanation
Indices: 950455--950544 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
950445 AAATAAATTA
950455 ATAATCATGCAATTAAATAT
1 ATAATCATGCAATTAAATAT
950475 ATAATCATGCAATT-AATAAT
1 ATAATCATGCAATTAAAT-AT
* *
950495 GTAA--AT-C-ATTCAA-AT
1 ATAATCATGCAATTAAATAT
*
950510 A-AA-CATGTAATTAAATAT
1 ATAATCATGCAATTAAATAT
*
950528 ATAATCATGCAAATAAA
1 ATAATCATGCAATTAAA
950545 AAAACATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
14 2 0.04
15 4 0.07
16 3 0.05
17 8 0.14
18 5 0.09
19 5 0.09
20 29 0.52
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (20 bp):
ATAATCATGCAATTAAATAT
Found at i:950593 original size:32 final size:31
Alignment explanation
Indices: 950556--950805 Score: 160
Period size: 32 Copynumber: 8.4 Consensus size: 31
950546 AAACATAAAC
950556 CATGCAAATAAATATGCAATTAAATATATAAT
1 CATGCAAATAAATAT-CAATTAAATATATAAT
* *
950588 CATGC-AATCACACAAAT-AAATAAAT-TAATAAT
1 CATGCAAAT-A-A-ATATCAATTAAATAT-ATAAT
* *
950620 CATGCAATTGAACT-TACAATTAAATATATAAT
1 CATGCAAAT-AAATAT-CAATTAAATATATAAT
*
950652 CATGCAAAT--A-AT-AA-T-ATTA-ATAAT
1 CATGCAAATAAATATCAATTAAATATATAAT
* *
950676 CATGTAAATAAACATACAATTAAATATATAAT
1 CATGCAAATAAATAT-CAATTAAATATATAAT
* *
950708 TATGCAAAT-AA-A--AA-T--ATATA-AAC
1 CATGCAAATAAATATCAATTAAATATATAAT
* *
950731 CAGGCAAATAAATATGTAATTAAATATATAAT
1 CATGCAAATAAATAT-CAATTAAATATATAAT
*
950763 CATGCAAATAAACATACAATTAAATATATAAT
1 CATGCAAATAAATAT-CAATTAAATATATAAT
*
950795 CATTCAAATAA
1 CATGCAAATAA
950806 TAATATATAA
Statistics
Matches: 169, Mismatches: 23, Indels: 52
0.69 0.09 0.21
Matches are distributed among these distances:
23 9 0.05
24 20 0.12
25 4 0.02
26 3 0.02
27 6 0.04
28 2 0.01
29 4 0.02
30 3 0.02
31 14 0.08
32 96 0.57
33 5 0.03
34 3 0.02
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (31 bp):
CATGCAAATAAATATCAATTAAATATATAAT
Found at i:950671 original size:56 final size:55
Alignment explanation
Indices: 950600--950773 Score: 192
Period size: 56 Copynumber: 3.1 Consensus size: 55
950590 TGCAATCACA
*
950600 CAAATAAATAA-ATTAATAATCATGCAATTGAACTTACAATTAAATATATAATCATG
1 CAAAT-AATAATATTAATAATCATGCAAAT-AACTTACAATTAAATATATAATCATG
* * *
950656 CAAATAATAATATTAATAATCATGTAAATAAACATACAATTAAATATATAATTATG
1 CAAATAATAATATTAATAATCATGCAAAT-AACTTACAATTAAATATATAATCATG
* * * * **
950712 CAAATAAAAATA-T-ATAAACCAGGCAAATAAATATGTAATTAAATATATAATCATG
1 CAAATAATAATATTAAT-AATCATGCAAATAACT-TACAATTAAATATATAATCATG
950767 CAAATAA
1 CAAATAA
950774 ACATACAATT
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
54 4 0.04
55 41 0.41
56 56 0.55
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.30
Consensus pattern (55 bp):
CAAATAATAATATTAATAATCATGCAAATAACTTACAATTAAATATATAATCATG
Found at i:950793 original size:20 final size:22
Alignment explanation
Indices: 950770--950818 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
950760 AATCATGCAA
*
950770 ATAAACATAC-AATTA-AATAT
1 ATAAACATACAAATAATAATAT
* *
950790 ATAATCATTCAAATAATAATAT
1 ATAAACATACAAATAATAATAT
950812 ATAAACA
1 ATAAACA
950819 ATGCAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 4 0.17
22 11 0.48
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAACATACAAATAATAATAT
Found at i:950796 original size:175 final size:172
Alignment explanation
Indices: 950464--950797 Score: 476
Period size: 175 Copynumber: 1.9 Consensus size: 172
950454 AATAATCATG
* **
950464 CAATTAAATATATAATCATGCAATTAATAATGTAAATCATTCAAATAAACATGTAATTAAATATA
1 CAATTAAATATATAATCATGCAAATAATAATGTAAATCATTCAAATAAACATACAATTAAATATA
*
950529 TAATCATGCAAATAAAAAAACATAAACCATGCAAATAAATATGCAATTAAATATATAATCATGCA
66 TAATCATGCAAATAAAAAAACATAAACCAGGCAAATAAATATGCAATTAAATATATAATCATGCA
* *
950594 ATCACACAAATAAATAAATTAATAATCATGCAATTGAACTTA
131 ATCAAACAAACAAATAAATTAATAATCATGCAATTGAACTTA
*
950636 CAATTAAATATATAATCATGCAAATAATAATATTAATAATCATGT-AAATAAACATACAATTAAA
1 CAATTAAATATATAATCATGCAAATAATAAT-GT-A-AATCAT-TCAAATAAACATACAATTAAA
* * * *
950700 TATATAATTATGCAAATAAAAATATATAAACCAGGCAAATAAATATGTAATTAAATATATAATCA
62 TATATAATCATGCAAATAAAAAAACATAAACCAGGCAAATAAATATGCAATTAAATATATAATCA
* *
950765 TGCAAAT-AAACATACAATTAAA-TATATAATCAT
127 TGC-AATCAAACAAACAAATAAATTA-ATAATCAT
950798 TCAAATAATA
Statistics
Matches: 143, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
172 30 0.21
173 1 0.01
174 3 0.02
175 105 0.73
176 4 0.03
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (172 bp):
CAATTAAATATATAATCATGCAAATAATAATGTAAATCATTCAAATAAACATACAATTAAATATA
TAATCATGCAAATAAAAAAACATAAACCAGGCAAATAAATATGCAATTAAATATATAATCATGCA
ATCAAACAAACAAATAAATTAATAATCATGCAATTGAACTTA
Found at i:950949 original size:24 final size:24
Alignment explanation
Indices: 950848--950983 Score: 81
Period size: 24 Copynumber: 5.8 Consensus size: 24
950838 ATATATAACT
*
950848 ATGTAAATGAATATATTAATAATC
1 ATGTAAATAAATATATTAATAATC
* * * *
950872 AAGCAATTAAATGTATTAATAATC
1 ATGTAAATAAATATATTAATAATC
*
950896 A--TACAATCAAAT-TA-AATATAATC
1 ATGTA-AAT-AAATATATTA-ATAATC
* *
950919 ATATAAATAAATATATTAATAATT
1 ATGTAAATAAATATATTAATAATC
950943 ATG----TAAATATATTAATAAATC
1 ATGTAAATAAATATATTAAT-AATC
***
950964 ACACAAATAAATATATTAAT
1 ATGTAAATAAATATATTAAT
950984 CATGCAAACA
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
20 13 0.15
21 4 0.05
22 2 0.02
23 15 0.17
24 36 0.42
25 16 0.19
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (24 bp):
ATGTAAATAAATATATTAATAATC
Found at i:950984 original size:21 final size:21
Alignment explanation
Indices: 950960--951002 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
950950 TATATTAATA
*
950960 AATCACACAAATAAATATATT
1 AATCACACAAACAAATATATT
**
950981 AATCATGCAAACAAATATATT
1 AATCACACAAACAAATATATT
951002 A
1 A
951003 GGCAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (21 bp):
AATCACACAAACAAATATATT
Found at i:951048 original size:17 final size:17
Alignment explanation
Indices: 951022--951056 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
951012 ATTATCATGC
951022 AAATCCATACAA-AAAT
1 AAATCCATACAATAAAT
951038 AAATACCATACAATAAAT
1 AAAT-CCATACAATAAAT
951056 A
1 A
951057 TAAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATCCATACAATAAAT
Found at i:951628 original size:12 final size:12
Alignment explanation
Indices: 951608--951637 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
951598 TTTTGATTAA
951608 AAAAATTAAATT
1 AAAAATTAAATT
*
951620 AAAAGTTAAATT
1 AAAAATTAAATT
951632 AAAAAT
1 AAAAAT
951638 ACAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:954771 original size:69 final size:69
Alignment explanation
Indices: 954647--954777 Score: 199
Period size: 69 Copynumber: 1.9 Consensus size: 69
954637 GGGTGTGAAC
* * * *
954647 CGTGGTAGGTAGGCTGATTTGGGATGCCAGATGAGTGTATGTCCGGATCTCAGAGCGACGCGTGC
1 CGTGGTAGATAAGCTGATCTGGGATGCCAGATGAGTGTATGCCCGGATCTCAGAGCGACGCGTGC
954712 GAAT
66 GAAT
* * *
954716 CGTGGTAGATAAGCTGATCTGGGATGCCAGATGAGTGTATGCCCGGGTCTTAGAGCGGCGCG
1 CGTGGTAGATAAGCTGATCTGGGATGCCAGATGAGTGTATGCCCGGATCTCAGAGCGACGCG
954778 GGTTCGAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.24
Consensus pattern (69 bp):
CGTGGTAGATAAGCTGATCTGGGATGCCAGATGAGTGTATGCCCGGATCTCAGAGCGACGCGTGC
GAAT
Found at i:958961 original size:40 final size:41
Alignment explanation
Indices: 958901--958989 Score: 146
Period size: 40 Copynumber: 2.2 Consensus size: 41
958891 TAGAGAAGGC
* *
958901 ATTTTTAT-TTATATTTATTAGATATTTTATA-TTATTTTT
1 ATTTTTATATTATATTCATTAGATATTTTAAATTTATTTTT
958940 ATTTTTATATTATATTCATTAGATATTTTAAATTTATTTTT
1 ATTTTTATATTATATTCATTAGATATTTTAAATTTATTTTT
958981 ATTTTTATA
1 ATTTTTATA
958990 AATATTTAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 8 0.17
40 21 0.46
41 17 0.37
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (41 bp):
ATTTTTATATTATATTCATTAGATATTTTAAATTTATTTTT
Found at i:961286 original size:3 final size:3
Alignment explanation
Indices: 961278--961333 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
961268 ACAAAATTTA
961278 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
961326 AAT AAT AA
1 AAT AAT AA
961334 AAGAAAACAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:964141 original size:2 final size:2
Alignment explanation
Indices: 964130--964158 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
964120 AACAAACAGC
964130 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
964159 TTACAATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:966290 original size:22 final size:22
Alignment explanation
Indices: 966248--966292 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
966238 AAAAGATAAA
* *
966248 ATCTTATTATTATTATTATTTT
1 ATCTTATTATTATCATAATTTT
*
966270 ATCTTATTA-TATCATAAATTT
1 ATCTTATTATTATCATAATTTT
966291 AT
1 AT
966293 GCACCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
ATCTTATTATTATCATAATTTT
Found at i:975788 original size:14 final size:14
Alignment explanation
Indices: 975769--975796 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
975759 TAACAAGGAA
975769 ACTTTCAAGCTAGC
1 ACTTTCAAGCTAGC
975783 ACTTTCAAGCTAGC
1 ACTTTCAAGCTAGC
975797 TCTTCAGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
ACTTTCAAGCTAGC
Found at i:977060 original size:5 final size:5
Alignment explanation
Indices: 977050--977076 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
977040 TGTTGCCATA
977050 ATGGG ATGGG ATGGG ATGGG ATGGG AT
1 ATGGG ATGGG ATGGG ATGGG ATGGG AT
977077 ACAAGGATTC
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:0.22, C:0.00, G:0.56, T:0.22
Consensus pattern (5 bp):
ATGGG
Found at i:978044 original size:20 final size:19
Alignment explanation
Indices: 978004--978051 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
977994 TTATATATAT
*
978004 TTATATATTTAATAAATAAA
1 TTAT-TATTAAATAAATAAA
*
978024 TTTTTATTAAATAATATAAA
1 TTATTATTAAATAA-ATAAA
978044 TTATTATT
1 TTATTATT
978052 TTAGATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTATTAAATAAATAAA
Found at i:980175 original size:22 final size:21
Alignment explanation
Indices: 980150--980195 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
980140 ATATATTTAT
*
980150 TATTTAATATAAATAATAAATA
1 TATTTAATAAAAATAAT-AATA
*
980172 TATTTTATAAAAATAATAATA
1 TATTTAATAAAAATAATAATA
980193 TAT
1 TAT
980196 CAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATTTAATAAAAATAATAATA
Found at i:980175 original size:25 final size:23
Alignment explanation
Indices: 980132--980195 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 23
980122 TGGAAATGGT
* * *
980132 TATAAAAAATATATTTATTATTTAA
1 TATAAATAATAAATATATT-TTT-A
980157 TATAAATAATAAATATA-TTTTA
1 TATAAATAATAAATATATTTTTA
*
980179 TAAAAATAAT-AATATAT
1 TATAAATAATAAATATAT
980196 CAAAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 6 0.18
22 10 0.29
23 3 0.09
24 1 0.03
25 14 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAAATAATAAATATATTTTTA
Found at i:980591 original size:46 final size:47
Alignment explanation
Indices: 980506--980615 Score: 136
Period size: 46 Copynumber: 2.4 Consensus size: 47
980496 TGTATAATTT
* *
980506 ATTAATAATATTTTAATACTGAATATTATTTTGAAAATATTTTAATA
1 ATTAATAATATTTTAATACTAAATATTATTTAGAAAATATTTTAATA
* * * *
980553 TTTAATAATCTTTT-ATACTAAATATTAATTTAG-TAATATTTTAGTA
1 ATTAATAATATTTTAATACTAAATATT-ATTTAGAAAATATTTTAATA
980599 ATTAAT-ATATTTTAATA
1 ATTAATAATATTTTAATA
980616 ATTTTTTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
45 6 0.11
46 30 0.57
47 17 0.32
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (47 bp):
ATTAATAATATTTTAATACTAAATATTATTTAGAAAATATTTTAATA
Found at i:980612 original size:28 final size:29
Alignment explanation
Indices: 980553--980655 Score: 95
Period size: 28 Copynumber: 3.6 Consensus size: 29
980543 TATTTTAATA
* * * *
980553 TTTAATAATCTTTT-ATACTAAATATTAA
1 TTTAATAATATTTTAATATTACATATTAT
* *
980581 TTTAGTAATATTTTAGTAATTA-ATA-TAT
1 TTTAATAATATTTTAAT-ATTACATATTAT
*
980609 TTTAATAATTTTTTAATATTACATATTAT
1 TTTAATAATATTTTAATATTACATATTAT
* *
980638 TTTAATATTAATTTAATA
1 TTTAATAATATTTTAATA
980656 ATATTTTGCA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.07
28 31 0.52
29 22 0.37
30 3 0.05
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTAATAATATTTTAATATTACATATTAT
Found at i:980652 original size:29 final size:27
Alignment explanation
Indices: 980599--980655 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
980589 TATTTTAGTA
*
980599 ATTAATATATTTTAATAATTTTTTAAT
1 ATTAATATATTTTAATAATTATTTAAT
980626 ATTACATATTATTTTAAT-ATTAATTTAAT
1 ATTA-ATA-TATTTTAATAATT-ATTTAAT
980655 A
1 A
980656 ATATTTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 6 0.23
29 16 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTAATATATTTTAATAATTATTTAAT
Found at i:983015 original size:3 final size:3
Alignment explanation
Indices: 983007--983045 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
982997 AATAAAGAAG
983007 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
983046 AAGATATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:984342 original size:16 final size:17
Alignment explanation
Indices: 984323--984362 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
984313 TAAAAGTTTA
984323 AAATATAATTTAAT-TT
1 AAATATAATTTAATATT
*
984339 AAATAT-ATTTATTATT
1 AAATATAATTTAATATT
984355 AAAT-TAAT
1 AAATATAAT
984363 CAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATATAATTTAATATT
Found at i:987017 original size:19 final size:20
Alignment explanation
Indices: 986958--987022 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 20
986948 CTATAATGCT
986958 TTATTAA-ATTACATATTAAA
1 TTATTAACA-TACATATTAAA
*
986978 TT-TTATCATA-ATA-TAAA
1 TTATTAACATACATATTAAA
986995 --ATTAAC-TACATATTAAA
1 TTATTAACATACATATTAAA
987012 TTATTAA-ATAC
1 TTATTAACATAC
987023 TCTTGTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
15 2 0.06
16 7 0.19
17 8 0.22
18 3 0.08
19 13 0.36
20 3 0.08
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATTAACATACATATTAAA
Found at i:987558 original size:16 final size:16
Alignment explanation
Indices: 987537--987584 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
987527 TACTCCTAGA
987537 AATTACATATTAAATT
1 AATTACATATTAAATT
*
987553 AATTACATA--AGATTT
1 AATTACATATTA-AATT
*
987568 AACTACATATTAAATT
1 AATTACATATTAAATT
987584 A
1 A
987585 TTATAAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.04
15 11 0.42
16 13 0.50
17 1 0.04
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (16 bp):
AATTACATATTAAATT
Found at i:988054 original size:29 final size:29
Alignment explanation
Indices: 988022--988131 Score: 82
Period size: 29 Copynumber: 3.8 Consensus size: 29
988012 TTTAATACCA
* *
988022 AATATTATTTTAATATTTAATATCATTTT
1 AATAATATTTTAATATTTAATATAATTTT
* *
988051 AATAATATTTT-ATACTAAATATTAATTTT
1 AATAATATTTTAATATTTAATA-TAATTTT
* * ** *
988080 -GTAATATTGTAGCATTTAATATTATTTTT
1 AATAATATTTTAATATTTAATA-TAATTTT
* *
988109 AA-ATTATTTTAAAATTTAATATA
1 AATAATATTTTAATATTTAATATA
988132 GTTTAACATT
Statistics
Matches: 62, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
28 18 0.29
29 44 0.71
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
AATAATATTTTAATATTTAATATAATTTT
Found at i:989031 original size:35 final size:35
Alignment explanation
Indices: 988986--989053 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
988976 CATAAATTCA
* * * *
988986 TTAATAATTAAGTTCATGAAAATAGTTATATTTTT
1 TTAATAATTAAATCCATAAAAATAGTTAGATTTTT
*
989021 TTAATGATTAAATCCATAAAAATAGTTAGATTT
1 TTAATAATTAAATCCATAAAAATAGTTAGATTT
989054 ATATAACCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (35 bp):
TTAATAATTAAATCCATAAAAATAGTTAGATTTTT
Found at i:989450 original size:36 final size:32
Alignment explanation
Indices: 989396--989495 Score: 89
Period size: 36 Copynumber: 3.0 Consensus size: 32
989386 GAATTTATTG
**
989396 TAATAAAT-AAAACCTATTATTATATAATAAA
1 TAATAAATAAAAATATATTATTATATAATAAA
*
989427 TAAATAAA-AAAATATTTAGTATTA-TATTATGAATTAA
1 T-AATAAATAAAA-A--TA-TATTATTA-TAT-AATAAA
989464 TAATAAATAAAAATATATTATTATATAATAAA
1 TAATAAATAAAAATATATTATTATATAATAAA
989496 CTATTTATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
31 1 0.02
32 14 0.25
33 9 0.16
34 4 0.07
35 2 0.04
36 15 0.27
37 10 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (32 bp):
TAATAAATAAAAATATATTATTATATAATAAA
Found at i:989575 original size:19 final size:18
Alignment explanation
Indices: 989551--989601 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
989541 TCACAAAAAT
*
989551 AATTTAATAATTTTTTAA
1 AATTTAATAATTTTATAA
*
989569 CAATTTATTAATTTTATAA
1 -AATTTAATAATTTTATAA
*
989588 ATATTAAATAATTT
1 A-ATTTAATAATTT
989602 CAAAGTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTAATAATTTTATAA
Found at i:994454 original size:14 final size:14
Alignment explanation
Indices: 994386--994473 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
994376 TTCAATTCAA
994386 TTAATTAATTTTTAAAT
1 TTAATTAA--TTT-AAT
* *
994403 TTTATAAATTTAAT
1 TTAATTAATTTAAT
* * *
994417 TTGATTAA-TAAAA
1 TTAATTAATTTAAT
* *
994430 TAAAATAATTTAAT
1 TTAATTAATTTAAT
994444 TTAATTAATTTAATT
1 TTAATTAATTTAA-T
*
994459 TTAAATAATTTAAT
1 TTAATTAATTTAAT
994473 T
1 T
994474 CAAAATTAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
13 8 0.15
14 25 0.45
15 16 0.29
17 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (14 bp):
TTAATTAATTTAAT
Found at i:994467 original size:15 final size:15
Alignment explanation
Indices: 994432--994473 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
994422 TAATAAAATA
994432 AAATAATTTAA-TTT
1 AAATAATTTAATTTT
*
994446 AATTAATTTAATTTT
1 AAATAATTTAATTTT
994461 AAATAATTTAATT
1 AAATAATTTAATT
994474 CAAAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATAATTTAATTTT
Found at i:994479 original size:15 final size:14
Alignment explanation
Indices: 994430--994479 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
994420 ATTAATAAAA
994430 TAAAATAATTTAAT
1 TAAAATAATTTAAT
* *
994444 TTAATTAATTTAATT
1 TAAAATAATTTAA-T
*
994459 TTAAATAATTTAAT
1 TAAAATAATTTAAT
994473 TCAAAAT
1 T-AAAAT
994480 TAATCAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATAATTTAAT
Found at i:995360 original size:20 final size:20
Alignment explanation
Indices: 995332--995375 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
995322 GTTTAATGAT
* *
995332 TTTATTAATATAAATTAAAA
1 TTTAATAATATAAATGAAAA
* *
995352 TTTAATAATTTGAATGAAAA
1 TTTAATAATATAAATGAAAA
995372 TTTA
1 TTTA
995376 GTTAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTAATAATATAAATGAAAA
Found at i:995970 original size:30 final size:28
Alignment explanation
Indices: 995909--995981 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
995899 CGTTATTTAG
**
995909 ATAAATTTTTATATTTTTATTATATTTAA
1 ATAAATTTTTAT-TTTTTATTATATCAAA
995938 ATAAATTTTTATTTTTTGATTTATATCAAA
1 ATAAATTTTTATTTTTT-A-TTATATCAAA
* *
995968 ATATATTATTATTT
1 ATAAATTTTTATTT
995982 CAAATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 5 0.13
29 13 0.34
30 20 0.53
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (28 bp):
ATAAATTTTTATTTTTTATTATATCAAA
Found at i:1000765 original size:14 final size:14
Alignment explanation
Indices: 1000745--1000780 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1000735 TGCTGAAATC
1000745 CTCTCTGTCTCTCT
1 CTCTCTGTCTCTCT
* *
1000759 GTCTCTGTCTCTGT
1 CTCTCTGTCTCTCT
1000773 CTCTCTGT
1 CTCTCTGT
1000781 GTGTGTGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.14, T:0.50
Consensus pattern (14 bp):
CTCTCTGTCTCTCT
Found at i:1002943 original size:22 final size:22
Alignment explanation
Indices: 1002897--1002947 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
1002887 ATTTTGCTTG
* *
1002897 TTTTTTGGATTATTTTGAACTT
1 TTTTTTGAATTATTTTAAACTT
1002919 TTTTTTCGAATTATTTTAAACTT
1 TTTTTT-GAATTATTTTAAACTT
1002942 TTTTTT
1 TTTTTT
1002948 TCTTTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.67
Consensus pattern (22 bp):
TTTTTTGAATTATTTTAAACTT
Found at i:1006792 original size:10 final size:10
Alignment explanation
Indices: 1006761--1006793 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1006751 AATGCCCAAA
*
1006761 TTTTCTTTTC
1 TTTTCTTTTT
1006771 TTTTCTTTTT
1 TTTTCTTTTT
1006781 TTTT-TTTTT
1 TTTTCTTTTT
1006790 TTTT
1 TTTT
1006794 AAGTAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:1010753 original size:15 final size:15
Alignment explanation
Indices: 1010729--1010758 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1010719 AGAAATTGAA
*
1010729 GAAGAGGAAGAGGAG
1 GAAGAAGAAGAGGAG
1010744 GAAGAAGAAGAGGAG
1 GAAGAAGAAGAGGAG
1010759 AGAGGCGACG
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAGGAG
Found at i:1019339 original size:2 final size:2
Alignment explanation
Indices: 1019332--1019364 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1019322 TGAAACCATT
1019332 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1019365 AGGATAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1020009 original size:16 final size:15
Alignment explanation
Indices: 1019984--1020034 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
1019974 ATTTTTAATT
1019984 TAAATATAAATTTAAA
1 TAAATATAAA-TTAAA
* * *
1020000 TAAATTTAAACATATA
1 TAAATATAAA-TTAAA
1020016 TAAATATAAATTAAA
1 TAAATATAAATTAAA
1020031 TAAA
1 TAAA
1020035 AAATTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATATAAATTAAA
Found at i:1020149 original size:15 final size:15
Alignment explanation
Indices: 1020131--1020160 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1020121 TACTCAATTT
*
1020131 AAAATTAATTTTAAA
1 AAAAATAATTTTAAA
1020146 AAAAATAATTTTAAA
1 AAAAATAATTTTAAA
1020161 TAATTGAATC
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAATAATTTTAAA
Found at i:1024861 original size:19 final size:19
Alignment explanation
Indices: 1024825--1024865 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1024815 ATTTTTAAAA
*
1024825 ATTTTGAAAACTTTATTTT
1 ATTTTGAAAACTTAATTTT
1024844 ATTTTGAAAA-TTAAATTTT
1 ATTTTGAAAACTT-AATTTT
1024863 ATT
1 ATT
1024866 AAGAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTTTGAAAACTTAATTTT
Found at i:1026088 original size:2 final size:2
Alignment explanation
Indices: 1026081--1026125 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1026071 CGGCACCAAC
1026081 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1026123 TA T
1 TA T
1026126 TGCCTCATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1026228 original size:2 final size:2
Alignment explanation
Indices: 1026221--1026245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1026211 TTAGCATGTG
1026221 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1026246 TCATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1028586 original size:2 final size:2
Alignment explanation
Indices: 1028579--1028608 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1028569 TTCACGCGTG
*
1028579 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1028609 AGCTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1031997 original size:209 final size:212
Alignment explanation
Indices: 1031637--1032062 Score: 768
Period size: 209 Copynumber: 2.0 Consensus size: 212
1031627 TGTTCCGAAA
1031637 TTTACGAGGAAATTAGTAGTAAAATATTATGATTAAATATTAATGATTATGGTGGCTATCGGACG
1 TTTACGAGGAAATTAGTAGTAAAATATTATGATTAAATATTAATGATTATGGTGGCTATCGGACG
* * *
1031702 TCGTTGTTTGTGTCAGAGGGATGATGTTACGTTTCGCGCGTCATAACCTTTGTCGCAGCCAAAAG
66 TCGTTGGTTGTGACAAAGGGATGATGTTACGTTTCGCGCGTCATAACCTTTGTCGCAGCCAAAAG
*
1031767 GACTATCGACAACGTAAAAGATTC-G-CCCC-CCCCCCCCACTCTGTAAAGTCTTTTGCGGCGCT
131 GACTATCGACAACCTAAAAGATTCGGCCCCCGCCCCCCCCACTCTGTAAAGTCTTTTGCGGCGCT
*
1031829 ACCGACCGCTTCTCATT
196 ACCGACCACTTCTCATT
1031846 TTTACGAGGAAATTAGTAGTAAAATATTATGATTAAATATTAATGATTATGGTGGCTATCGGACG
1 TTTACGAGGAAATTAGTAGTAAAATATTATGATTAAATATTAATGATTATGGTGGCTATCGGACG
1031911 TCGTTGGTTGTGACAAAGGGATGATGTTACGTTTCGCGCGTCATAACCTTTGTCGCAGCCAAAAG
66 TCGTTGGTTGTGACAAAGGGATGATGTTACGTTTCGCGCGTCATAACCTTTGTCGCAGCCAAAAG
1031976 GACTATCGACAACCTAAAAGATTCGGCCCCCCGCCCCCCCCACTCTGTAAAGTCTTTTGCGGCGC
131 GACTATCGACAACCTAAAAGATTCGG-CCCCCGCCCCCCCCACTCTGTAAAGTCTTTTGCGGCGC
*
1032041 TACCGGCCACTTCTCATT
195 TACCGACCACTTCTCATT
1032059 TTTA
1 TTTA
1032063 AAAACGTAAT
Statistics
Matches: 207, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
209 150 0.72
210 1 0.00
212 4 0.02
213 52 0.25
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (212 bp):
TTTACGAGGAAATTAGTAGTAAAATATTATGATTAAATATTAATGATTATGGTGGCTATCGGACG
TCGTTGGTTGTGACAAAGGGATGATGTTACGTTTCGCGCGTCATAACCTTTGTCGCAGCCAAAAG
GACTATCGACAACCTAAAAGATTCGGCCCCCGCCCCCCCCACTCTGTAAAGTCTTTTGCGGCGCT
ACCGACCACTTCTCATT
Found at i:1032080 original size:15 final size:14
Alignment explanation
Indices: 1032058--1032084 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1032048 CACTTCTCAT
1032058 TTTTAAAAACGTAA
1 TTTTAAAAACGTAA
1032072 TTTTAAAAACGTA
1 TTTTAAAAACGTA
1032085 CGTACCTGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
TTTTAAAAACGTAA
Found at i:1032370 original size:12 final size:12
Alignment explanation
Indices: 1032341--1032376 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1032331 AGATTTTATT
* *
1032341 TATATACGTGTA
1 TATATATGTATA
1032353 TATATATGTATA
1 TATATATGTATA
1032365 TATATATGTATA
1 TATATATGTATA
1032377 ACTTTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (12 bp):
TATATATGTATA
Found at i:1042868 original size:34 final size:34
Alignment explanation
Indices: 1042823--1042890 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1042813 AGGCTCATCC
* *
1042823 TTAAGCCCAGATGAAGGTTAAGAAAAGTTCGAAT
1 TTAAACCCAGATGAAGGTGAAGAAAAGTTCGAAT
* *
1042857 TTAAACCCAGATGAAGGTGAAGACAAGTTTGAAT
1 TTAAACCCAGATGAAGGTGAAGAAAAGTTCGAAT
1042891 CTGACAGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (34 bp):
TTAAACCCAGATGAAGGTGAAGAAAAGTTCGAAT
Found at i:1046649 original size:16 final size:15
Alignment explanation
Indices: 1046603--1046659 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1046593 AAGAATAAAG
1046603 AAAAAAAAATCAAGAT
1 AAAAAAAAATCAA-AT
* *
1046619 CAAAATCAAAGTCAAAT
1 -AAAA-AAAAATCAAAT
1046636 AAAAAAAAATTCAAA-
1 AAAAAAAAA-TCAAAT
1046651 AAAAAAAAA
1 AAAAAAAAA
1046660 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.35
16 9 0.26
17 6 0.18
18 7 0.21
ACGTcount: A:0.75, C:0.09, G:0.04, T:0.12
Consensus pattern (15 bp):
AAAAAAAAATCAAAT
Found at i:1046660 original size:16 final size:16
Alignment explanation
Indices: 1046630--1046660 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1046620 AAAATCAAAG
*
1046630 TCAAATAAAAAAAAAT
1 TCAAAAAAAAAAAAAT
1046646 TCAAAAAAAAAAAAA
1 TCAAAAAAAAAAAAA
1046661 AAAAAAAAAC
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:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (16 bp):
TCAAAAAAAAAAAAAT
Found at i:1046955 original size:19 final size:19
Alignment explanation
Indices: 1046931--1046975 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1046921 GAACGCCGGT
*
1046931 GCCGGATTCTGGAAAATTC
1 GCCGGAATCTGGAAAATTC
* *
1046950 GCCGGAATCTGGGAATTTC
1 GCCGGAATCTGGAAAATTC
1046969 GCCGGAA
1 GCCGGAA
1046976 ATTGGCCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (19 bp):
GCCGGAATCTGGAAAATTC
Found at i:1047066 original size:31 final size:31
Alignment explanation
Indices: 1047028--1047098 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1047018 ACTGGGTCTG
*
1047028 TCGCCGGAAACTTC-AAAGTTCGCCGGAATTA
1 TCGCCGGAAAATTCAAAAG-TCGCCGGAATTA
*
1047059 TCGCCGGAAAATTCAAAAGTCGCCGGAATTT
1 TCGCCGGAAAATTCAAAAGTCGCCGGAATTA
1047090 TCGCCGGAA
1 TCGCCGGAA
1047099 TCTGGAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAAAGTCGCCGGAATTA
Found at i:1047685 original size:6 final size:7
Alignment explanation
Indices: 1047669--1047696 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1047659 AGAGAAAAAG
1047669 AAAAATA
1 AAAAATA
1047676 AAAAATA
1 AAAAATA
1047683 AAAAATA
1 AAAAATA
1047690 AAAAATA
1 AAAAATA
1047697 CGGGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:1047760 original size:20 final size:20
Alignment explanation
Indices: 1047737--1047791 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1047727 TTGGGGCAGA
* *
1047737 CCCAAATGATCTGGGTCAGG
1 CCCAATTGATCCGGGTCAGG
1047757 CCCAATTGATCCGGGTCAGG
1 CCCAATTGATCCGGGTCAGG
1047777 CCCAATTGATCCGGG
1 CCCAATTGATCCGGG
1047792 CTCGGACCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (20 bp):
CCCAATTGATCCGGGTCAGG
Found at i:1047824 original size:2 final size:2
Alignment explanation
Indices: 1047817--1047841 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1047807 GTGTCTACAC
1047817 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 A
1047842 AGAATCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1048607 original size:20 final size:20
Alignment explanation
Indices: 1048582--1048620 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1048572 TATCTAAAAA
*
1048582 TAATTTTTTAATTATTTATT
1 TAATTTTATAATTATTTATT
1048602 TAATTTTATAATTATTTAT
1 TAATTTTATAATTATTTAT
1048621 ATATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TAATTTTATAATTATTTATT
Found at i:1048625 original size:14 final size:12
Alignment explanation
Indices: 1048604--1048640 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1048594 TATTTATTTA
1048604 ATTTTATA-ATT
1 ATTTTATATATT
1048615 ATTTATATATATT
1 ATTT-TATATATT
1048628 ATTTTATAT-TT
1 ATTTTATATATT
1048639 AT
1 AT
1048641 ATTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 9 0.38
13 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTATATATT
Found at i:1048643 original size:16 final size:16
Alignment explanation
Indices: 1048593--1048644 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 16
1048583 AATTTTTTAA
*
1048593 TTAT-TTATTTAAT-T
1 TTATATTATTTTATAT
1048607 TTATAATTA-TTTATA-
1 TTAT-ATTATTTTATAT
1048622 -TATATTATTTTATAT
1 TTATATTATTTTATAT
1048637 TTATATTA
1 TTATATTA
1048645 AAAATAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 4 0.13
14 13 0.42
15 4 0.13
16 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTATTTTATAT
Found at i:1048659 original size:25 final size:24
Alignment explanation
Indices: 1048604--1048664 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
1048594 TATTTATTTA
* * *
1048604 ATTTTATAATTATTTATATATATT
1 ATTTTATAATTATTTAAAAATAAT
*
1048628 ATTTTATATTTATATTAAAAATAAT
1 ATTTTATAATTAT-TTAAAAATAAT
1048653 ATTTTATTAATT
1 ATTTTA-TAATT
1048665 TCGAGTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 12 0.40
25 14 0.47
26 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTATAATTATTTAAAAATAAT
Found at i:1051098 original size:143 final size:142
Alignment explanation
Indices: 1050783--1051090 Score: 367
Period size: 143 Copynumber: 2.1 Consensus size: 142
1050773 TAACACATAT
* * * *
1050783 ATGACTGTTTA--GAAGGGAAGATTGAATTAAATTTCGAGTTGAATTTATGAGTATCTTGATTCA
1 ATGACTGTTTATGGAAGGG-AGATT-CATTAAATTTAGAGTTCAATTTATGAGTATCTTAATTCA
** * * *
1050846 AGTATAATTATTAAAGAAAAAGATATATTTTATTTTTGAAAATTAATAGTCAAATTAACACACAT
64 AGTATAATTACAAAAAAAAAAGATATATTTTACTTTTGAAAATTAAGAGTCAAATTAACACACAT
1050911 ATACTTGTGAGAAA
129 ATACTTGTGAGAAA
*
1050925 ATGACTGTTTATGGACGGGAGATTGCATTAAATTTAGAGTTCAATTTAT-ATGTATCTTAATTCA
1 ATGACTGTTTATGGAAGGGAGATT-CATTAAATTTAGAGTTCAATTTATGA-GTATCTTAATTCA
* * *
1050989 CA-TATAGTTACAAAAAAAAAAGATATATTTTACTTTTGAAAATTAAGAGTGAGAA-TAACGCAT
64 -AGTATAATTACAAAAAAAAAAGATATATTTTACTTTTGAAAATTAAGAGTCA-AATTAA--CAC
*
1051052 ATATATACTTGTGAGAAA
125 ACATATACTTGTGAGAAA
1051070 ATGAC-GATTTATGGAAGGGAG
1 ATGACTG-TTTATGGAAGGGAG
1051091 CATATTAATT
Statistics
Matches: 143, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
142 12 0.08
143 85 0.59
144 9 0.06
145 37 0.26
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (142 bp):
ATGACTGTTTATGGAAGGGAGATTCATTAAATTTAGAGTTCAATTTATGAGTATCTTAATTCAAG
TATAATTACAAAAAAAAAAGATATATTTTACTTTTGAAAATTAAGAGTCAAATTAACACACATAT
ACTTGTGAGAAA
Found at i:1051980 original size:46 final size:46
Alignment explanation
Indices: 1051926--1052017 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 46
1051916 TTTTTTACTA
1051926 CAAAATTATGAGAATC-AATTAGTTTTAAAATTATCTTTAATTAAG
1 CAAAATTATGAGAATCTAATTAGTTTTAAAATTATCTTTAATTAAG
*
1051971 CAAATATTATGAGAATCTAATTAGTTTTGAAATTATCTTTAATTAAG
1 CAAA-ATTATGAGAATCTAATTAGTTTTAAAATTATCTTTAATTAAG
1052018 TTATTATTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 4 0.09
46 12 0.27
47 28 0.64
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (46 bp):
CAAAATTATGAGAATCTAATTAGTTTTAAAATTATCTTTAATTAAG
Found at i:1056122 original size:17 final size:19
Alignment explanation
Indices: 1056100--1056134 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1056090 CAATTTTTTA
1056100 TTTTATTT-T-TAATAAAT
1 TTTTATTTATATAATAAAT
1056117 TTTTATTTATATAATAAA
1 TTTTATTTATATAATAAA
1056135 AAGCTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATTTATATAATAAAT
Found at i:1064480 original size:2 final size:2
Alignment explanation
Indices: 1064473--1064497 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1064463 TCGTTATCTT
1064473 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1064498 TTTGAGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1067076 original size:19 final size:20
Alignment explanation
Indices: 1067047--1067090 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1067037 TAATTTTTTA
1067047 GTAATATATT-ATATATAAAT
1 GTAATATATTAAT-TATAAAT
*
1067067 GTAATA-ATTAATTATAACT
1 GTAATATATTAATTATAAAT
1067086 GTAAT
1 GTAAT
1067091 TTTTTTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
GTAATATATTAATTATAAAT
Found at i:1069364 original size:114 final size:111
Alignment explanation
Indices: 1069202--1069602 Score: 290
Period size: 114 Copynumber: 3.5 Consensus size: 111
1069192 TTTTTATCAC
* * * * ** *
1069202 TTTTAGACTTACGGTATCATCCCAATCATCCAATCCCGG-TTCATGCCAGATCATTTCCAAACTT
1 TTTTAGACTT-CAGCATCATCTCAGTCATCCAATCTTGGCTT-AGGCCAGATCATTTCCAAACTT
* * *
1069266 GCAGCATCATCTCAATCATTCATTTATGATATTGACTAAGTCTTTGTCA
64 ACAGCATCATCTCGATCATTCATTTATGAT-TCGACTAAGTCTTTGTCA
* *
1069315 TTTTCAGACTTGCAGCATCATCTCAGTCATCCAATCTTGACTTAGGCCAGATCATTTTCAAACTT
1 TTTT-AGACTT-CAGCATCATCTCAGTCATCCAATCTTGGCTTAGGCCAGATCATTTCCAAACTT
** * * * * *
1069380 ATGGCCTCATCCCGATTATTTATTTATGACTTCGACTTAGT-TTTGGTCA
64 ACAGCATCATCTCGATCATTCATTTATGA-TTCGACTAAGTCTTT-GTCA
* ** * * * * * * * * *
1069429 TTTTTAGACTCTCGGCATTGTCTTAGTTATTCAATCTCGGCTTAGGTCAGATTATTTTCAGATTT
1 -TTTTAGACT-TCAGCATCATCTCAGTCATCCAATCTTGGCTTAGGCCAGATCATTTCCAAACTT
* * *
1069494 ACAACATCATCTCGATCATTCATTTATGATCTCGACTAGGTC-TTGATCG
64 ACAGCATCATCTCGATCATTCATTTATGAT-TCGACTAAGTCTTTG-TCA
* * ** * *
1069543 CTTTAAACCCACAGCATCATC-CAGTCATCCGATCTTGGCAT-GGTCCAGATCATTTCCAAA
1 TTTTAGA-CTTCAGCATCATCTCAGTCATCCAATCTTGGCTTAGG-CCAGATCATTTCCAAA
1069603 TTCGTGGTTC
Statistics
Matches: 218, Mismatches: 59, Indels: 23
0.73 0.20 0.08
Matches are distributed among these distances:
111 2 0.01
112 26 0.12
113 21 0.10
114 161 0.74
115 8 0.04
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (111 bp):
TTTTAGACTTCAGCATCATCTCAGTCATCCAATCTTGGCTTAGGCCAGATCATTTCCAAACTTAC
AGCATCATCTCGATCATTCATTTATGATTCGACTAAGTCTTTGTCA
Found at i:1069891 original size:16 final size:15
Alignment explanation
Indices: 1069870--1069899 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1069860 TTTTCTCTAA
1069870 AAAAAATAATAATAAT
1 AAAAAATAA-AATAAT
1069886 AAAAAATAAAATAA
1 AAAAAATAAAATAA
1069900 ATTCTTATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAATAAAATAAT
Found at i:1071419 original size:31 final size:32
Alignment explanation
Indices: 1071362--1071430 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 32
1071352 AAAAAAAAAA
1071362 TTATGAAACATCATTCCCATAGACGTGATGTT
1 TTATGAAACATCATTCCCATAGACGTGATGTT
*
1071394 TTATGAAACATCATT-CCGTAGACGTGATGTT
1 TTATGAAACATCATTCCCATAGACGTGATGTT
1071425 TTATGA
1 TTATGA
1071431 CCCATAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 21 0.58
32 15 0.42
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (32 bp):
TTATGAAACATCATTCCCATAGACGTGATGTT
Found at i:1072997 original size:89 final size:89
Alignment explanation
Indices: 1072841--1073019 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 89
1072831 CGTTTCTTCT
* * *
1072841 TATAAACCAAATGCACGTCTAGATTCAATTCTATAGTTTATTAATTGGACAGTCATTTTCATCAT
1 TATAAACCAAATGCACGGCTACATTCAATTCTATAGTTTATTAATTGGACAGTCATTTTCATAAT
*
1072906 TTCGGTTTCAATTGTACAAGCTTG
66 TTCGGTTTCAATTGCACAAGCTTG
* *
1072930 TATAAACCAAATGCACGGCTACCTTCAATTCTATAGTTTATTTATTGGACAGTCATTTTCATAAT
1 TATAAACCAAATGCACGGCTACATTCAATTCTATAGTTTATTAATTGGACAGTCATTTTCATAAT
*
1072995 TTCGGTTTCAATTGCACGAGCTTG
66 TTCGGTTTCAATTGCACAAGCTTG
1073019 T
1 T
1073020 TTTATAAAGT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (89 bp):
TATAAACCAAATGCACGGCTACATTCAATTCTATAGTTTATTAATTGGACAGTCATTTTCATAAT
TTCGGTTTCAATTGCACAAGCTTG
Found at i:1073702 original size:10 final size:10
Alignment explanation
Indices: 1073687--1073711 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1073677 TAGTTATATA
1073687 TATTTTAATT
1 TATTTTAATT
1073697 TATTTTAATT
1 TATTTTAATT
1073707 TATTT
1 TATTT
1073712 ATTAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTAATT
Found at i:1073769 original size:18 final size:20
Alignment explanation
Indices: 1073731--1073771 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1073721 TTTTTTTAGT
1073731 AATATATTATATATAAATGC
1 AATATATTATATATAAATGC
*
1073751 AATA-ATTAT-TATAACTGC
1 AATATATTATATATAAATGC
1073769 AAT
1 AAT
1073772 TTTTTGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 5 0.25
20 4 0.20
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (20 bp):
AATATATTATATATAAATGC
Found at i:1080779 original size:12 final size:12
Alignment explanation
Indices: 1080762--1080786 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1080752 GGAAAAATAT
1080762 CTCAAGATAAAG
1 CTCAAGATAAAG
1080774 CTCAAGATAAAG
1 CTCAAGATAAAG
1080786 C
1 C
1080787 ATTCTAAATA
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:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (12 bp):
CTCAAGATAAAG
Found at i:1081575 original size:12 final size:12
Alignment explanation
Indices: 1081560--1081584 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1081550 ATAATATAAA
1081560 ATATTTAAATTT
1 ATATTTAAATTT
1081572 ATATTTAAATTT
1 ATATTTAAATTT
1081584 A
1 A
1081585 AATTATATAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTAAATTT
Found at i:1084653 original size:27 final size:23
Alignment explanation
Indices: 1084604--1084658 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 23
1084594 ATCATTTTAA
*
1084604 TTTTTATATTATATTTTTTAACT
1 TTTTTATATTATATTTTTAAACT
1084627 TTTTTATATATATTATTTTTAAAAACT
1 TTTTTATAT-TA-TATTTTT--AAACT
1084654 TTTTT
1 TTTTT
1084659 GTGGGACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 9 0.33
24 2 0.07
25 7 0.26
27 9 0.33
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTATATTATATTTTTAAACT
Found at i:1086475 original size:282 final size:283
Alignment explanation
Indices: 1085961--1086523 Score: 1060
Period size: 282 Copynumber: 2.0 Consensus size: 283
1085951 AAAAAAGATA
1085961 TAGTTAAAGATATTGACATAACACTCACATTTTTTTGCTTTTTTTAAGTTTTAATTATTTTAATT
1 TAGTTAAAGATATTGACATAACACTCACATTTTTTTGCTTTTTTTAAGTTTTAATTATTTTAATT
*
1086026 TATATATTAAATTTTGTAAGAAAATAAAGTCAATTGAAATATCACGTGACAGACTTATTTGACTG
66 TATATATTAAATTCTGTAAGAAAATAAAGTCAATTGAAATATCACGTGACAGACTTATTTGACTG
*
1086091 ATTTTTTTTCTCTTACTTTTTTTTTATTTTTTAAAATTAAATAAATTTTGTAAAAATAAATCGAT
131 ATCTTTTTTCTCTTACTTTTTTTTTATTTTTTAAAATTAAATAAATTTTGTAAAAATAAATCGAT
*
1086156 AAAAGTAAAAATAAAAAATTAATCGATTTTTAGAGGTTTGGACTGTCATAATCT-ATATGAATTT
196 AAAAGTAAAAATAAAAAATTAATCCATTTTTAGAGGTTTGGACTGTCATAATCTAATATGAA--T
1086220 TTTTTTTTTTATAATCAATAGTTGG
259 TTTTTTTTTTATAATCAATAGTTGG
1086245 TAGTTAAAGATATTGACATAACACTCACATTTTTTTGC-TTTTTTAAGTTTTAATTATTTTAATT
1 TAGTTAAAGATATTGACATAACACTCACATTTTTTTGCTTTTTTTAAGTTTTAATTATTTTAATT
1086309 TATATATTAAATTCTGTAAGAAAATAAAGTCAATTGAAATATCACGTGACAGACTTATTTGACTG
66 TATATATTAAATTCTGTAAGAAAATAAAGTCAATTGAAATATCACGTGACAGACTTATTTGACTG
1086374 A-CTTTTTTCTCTTACTTTTTTTTTATTTTTTAAAATTAAATAAATTTTGTAAAAATAAATCGAT
131 ATCTTTTTTCTCTTACTTTTTTTTTATTTTTTAAAATTAAATAAATTTTGTAAAAATAAATCGAT
1086438 AAAAGTAAAAATAAAAAATTAATCCATTTTTAGAGGTTTGGACTGTCATAATCTAATATGAATTT
196 AAAAGTAAAAATAAAAAATTAATCCATTTTTAGAGGTTTGGACTGTCATAATCTAATATGAATTT
1086503 TTTTTTTTATAATCAATAGTT
261 TTTTTTTTATAATCAATAGTT
1086524 CGTTGAGATA
Statistics
Matches: 275, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
281 24 0.09
282 115 0.42
283 98 0.36
284 38 0.14
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (283 bp):
TAGTTAAAGATATTGACATAACACTCACATTTTTTTGCTTTTTTTAAGTTTTAATTATTTTAATT
TATATATTAAATTCTGTAAGAAAATAAAGTCAATTGAAATATCACGTGACAGACTTATTTGACTG
ATCTTTTTTCTCTTACTTTTTTTTTATTTTTTAAAATTAAATAAATTTTGTAAAAATAAATCGAT
AAAAGTAAAAATAAAAAATTAATCCATTTTTAGAGGTTTGGACTGTCATAATCTAATATGAATTT
TTTTTTTTATAATCAATAGTTGG
Found at i:1086807 original size:28 final size:28
Alignment explanation
Indices: 1086775--1086834 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
1086765 TTAAATTTAA
1086775 ATTTATATATTAT-A-TTAATAAAATAATT
1 ATTTA-ATATTATGATTTAATAAAATAA-T
* *
1086803 ATTTAATATTTTGATTTAATAAATTAAT
1 ATTTAATATTATGATTTAATAAAATAAT
1086831 ATTT
1 ATTT
1086835 TAAATTGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.21
28 11 0.39
29 11 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTAATATTATGATTTAATAAAATAAT
Found at i:1086918 original size:12 final size:12
Alignment explanation
Indices: 1086887--1086917 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1086877 TCGCTTGTAC
1086887 TTATTTTTATTT
1 TTATTTTTATTT
1086899 TTATTTTTA-TT
1 TTATTTTTATTT
1086910 TTATTTTT
1 TTATTTTT
1086918 TGATATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:1086933 original size:7 final size:6
Alignment explanation
Indices: 1086887--1086917 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1086877 TCGCTTGTAC
1086887 TTATTT TTATTT TTATTT TTA-TT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
1086918 TGATATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:1087211 original size:25 final size:24
Alignment explanation
Indices: 1087183--1087246 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
1087173 TTTAACCACC
1087183 TTATATATATATATAAGTATATAT
1 TTATATATATATATAAGTATATAT
* * *
1087207 TT-TATTAATATATTTAATTTTATAT
1 TTATA-T-ATATATATAAGTATATAT
1087232 TTATATATATTATAT
1 TTATATATA-TATAT
1087247 TAATAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
23 2 0.06
24 6 0.19
25 22 0.69
26 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATATATATATATAAGTATATAT
Found at i:1097370 original size:3 final size:3
Alignment explanation
Indices: 1097364--1097395 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1097354 CACCAAAAAA
1097364 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1097396 AGCACATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1098309 original size:2 final size:2
Alignment explanation
Indices: 1098302--1098344 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1098292 TGCACTGAAA
* *
1098302 AT AT AT AT GT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1098344 A
1 A
1098345 AAGATGCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1108769 original size:29 final size:29
Alignment explanation
Indices: 1108737--1108795 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
1108727 TATATTGTCC
*
1108737 TAAAAAAATAAAATC-ATTATATATTATAA
1 TAAAAAAATAAAATCAATTATA-ATAATAA
** *
1108766 TAAATTAATAAATTCAATTATAATAATAA
1 TAAAAAAATAAAATCAATTATAATAATAA
1108795 T
1 T
1108796 GGATTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAAAAAATAAAATCAATTATAATAATAA
Found at i:1119022 original size:2 final size:2
Alignment explanation
Indices: 1119015--1119058 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
1119005 ATTTTCTTTC
1119015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
1119058 T
1 T
1119059 TCGTATTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1124334 original size:12 final size:12
Alignment explanation
Indices: 1124319--1124344 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1124309 ATGAAAGTCG
1124319 ATACAATATTAA
1 ATACAATATTAA
1124331 ATACAATATTAA
1 ATACAATATTAA
1124343 AT
1 AT
1124345 TCGATGTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
ATACAATATTAA
Found at i:1124423 original size:12 final size:12
Alignment explanation
Indices: 1124406--1124431 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1124396 ATTAAAGTCG
1124406 ATACAATATTAA
1 ATACAATATTAA
1124418 ATACAATATTAA
1 ATACAATATTAA
1124430 AT
1 AT
1124432 TCGATGTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
ATACAATATTAA
Found at i:1125577 original size:21 final size:19
Alignment explanation
Indices: 1125543--1125581 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
1125533 TGAAAGTTTT
1125543 TAAATTTGAATTTTAAAAC
1 TAAATTTGAATTTTAAAAC
1125562 TAAACTTTGAGATTTTAAAA
1 TAAA-TTTGA-ATTTTAAAA
1125582 ATCACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
TAAATTTGAATTTTAAAAC
Found at i:1130040 original size:13 final size:14
Alignment explanation
Indices: 1130012--1130072 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
1130002 AAATTGTAAA
1130012 ATATTAAAATTTAT
1 ATATTAAAATTTAT
*
1130026 ATATTTAAATTATATT
1 ATATTAAAATT-TA-T
* *
1130042 TTTTATAAAATTTAT
1 ATAT-TAAAATTTAT
* *
1130057 ATGTTATAATTTAT
1 ATATTAAAATTTAT
1130071 AT
1 AT
1130073 TGATATAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
14 21 0.57
15 5 0.14
16 5 0.14
17 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATATTAAAATTTAT
Found at i:1130080 original size:31 final size:31
Alignment explanation
Indices: 1130016--1130082 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1130006 TGTAAAATAT
**
1130016 TAAAATTTATATATTTAAATTATATTTTTTA
1 TAAAATTTATATATTTAAATTATATTTGATA
* *
1130047 TAAAATTTATATGTTATAATTTATA-TTGATA
1 TAAAATTTATATATT-TAAATTATATTTGATA
1130078 TAAAA
1 TAAAA
1130083 ATATAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
TAAAATTTATATATTTAAATTATATTTGATA
Found at i:1130084 original size:32 final size:30
Alignment explanation
Indices: 1130012--1130084 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 30
1130002 AAATTGTAAA
*
1130012 ATATTAAAATTTATATATTTAAATTATATT
1 ATATAAAAATTTATATATTTAAATTATATT
* * * *
1130042 TTTTATAAAATTTATATGTTATAATTTATATT
1 ATATA-AAAATTTATATATT-TAAATTATATT
1130074 GATATAAAAAT
1 -ATATAAAAAT
1130085 ATAAAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
30 2 0.06
31 13 0.39
32 15 0.45
33 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATAAAAATTTATATATTTAAATTATATT
Found at i:1130122 original size:24 final size:23
Alignment explanation
Indices: 1130083--1130132 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1130073 TGATATAAAA
**
1130083 ATATAAAATATAATATTTTTATT
1 ATATAAAATATAATATAATTATT
*
1130106 ATATTAAATATATATATAATTATT
1 ATATAAAATATA-ATATAATTATT
1130130 ATA
1 ATA
1130133 ATTTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATAAAATATAATATAATTATT
Found at i:1130148 original size:12 final size:14
Alignment explanation
Indices: 1130126--1130159 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1130116 TATATATAAT
1130126 TATTATAATTTT-A
1 TATTATAATTTTAA
1130139 TATT-TAATTTTAA
1 TATTATAATTTTAA
1130152 TATTATAA
1 TATTATAA
1130160 ATCATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.37
13 9 0.47
14 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATAATTTTAA
Found at i:1131273 original size:11 final size:12
Alignment explanation
Indices: 1131257--1131289 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1131247 CTAATATATA
1131257 TAATTATTT-TT
1 TAATTATTTATT
1131268 TAATTATTTATT
1 TAATTATTTATT
1131280 TAATT-TTTAT
1 TAATTATTTAT
1131290 ATTTACATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TAATTATTTATT
Found at i:1131312 original size:18 final size:20
Alignment explanation
Indices: 1131286--1131331 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1131276 TATTTAATTT
1131286 TTATATTTACATTA-AAAAA
1 TTATATTTACATTATAAAAA
*
1131305 TTAT-TTTATATTATAAAAA
1 TTATATTTACATTATAAAAA
*
1131324 TAATATTT
1 TTATATTT
1131332 TATTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 3 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATTTACATTATAAAAA
Found at i:1131335 original size:19 final size:18
Alignment explanation
Indices: 1131291--1131337 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1131281 AATTTTTATA
* *
1131291 TTTACATTAAAAAATTAT
1 TTTATATTAAAAAATAAT
1131309 TTTATATTATAAAAATAAT
1 TTTATATTA-AAAAATAAT
1131328 ATTT-TATTAA
1 -TTTATATTAA
1131338 TTTTGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
19 13 0.52
20 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATATTAAAAAATAAT
Found at i:1131374 original size:22 final size:21
Alignment explanation
Indices: 1131322--1131374 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1131312 ATATTATAAA
*
1131322 AATAATATTTTATTAATTTTG
1 AATAATATTATATTAATTTTG
*
1131343 AATCAA-ATTATATGTAATTTTT
1 AAT-AATATTATAT-TAATTTTG
*
1131365 CATAATATTA
1 AATAATATTA
1131375 AATCAGATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (21 bp):
AATAATATTATATTAATTTTG
Found at i:1135897 original size:24 final size:24
Alignment explanation
Indices: 1135833--1135897 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
1135823 CTCTCCCACT
* *
1135833 TCATCATCATCGCC-TCCATCTTCA
1 TCATCATCACCGCCGT-CATCGTCA
* ** *
1135857 TTATCATCTGCGTCGTCATCGTCA
1 TCATCATCACCGCCGTCATCGTCA
1135881 TCATCATCACCGCCGTC
1 TCATCATCACCGCCGTC
1135898 TTCACAGCTT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.18, C:0.38, G:0.11, T:0.32
Consensus pattern (24 bp):
TCATCATCACCGCCGTCATCGTCA
Found at i:1137549 original size:5 final size:5
Alignment explanation
Indices: 1137539--1137567 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1137529 ATATTGATGA
1137539 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1137568 ACAAATGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:1153535 original size:2 final size:2
Alignment explanation
Indices: 1153528--1153557 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1153518 ACACAACTGC
1153528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1153558 GTATGTATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1162609 original size:3 final size:3
Alignment explanation
Indices: 1162601--1162625 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1162591 CTAAAATCAC
1162601 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1162626 ATAAATTGTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1173619 original size:12 final size:12
Alignment explanation
Indices: 1173604--1173637 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1173594 TTCATTTCAT
*
1173604 ATAAATAAAAAA
1 ATAAAGAAAAAA
1173616 ATAAAGAAAAAA
1 ATAAAGAAAAAA
1173628 ATAAAAGAAA
1 AT-AAAGAAA
1173638 TTCGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
ATAAAGAAAAAA
Found at i:1193901 original size:15 final size:15
Alignment explanation
Indices: 1193883--1193917 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1193873 TTCTTGACCC
*
1193883 TCTTTTTCTTCATTT
1 TCTTTTTCCTCATTT
1193898 TCTTTTTCCTCATTT
1 TCTTTTTCCTCATTT
1193913 TCTTT
1 TCTTT
1193918 ATCATCACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTTTTCCTCATTT
Found at i:1194130 original size:12 final size:12
Alignment explanation
Indices: 1194115--1194147 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1194105 TCTTCCCGCA
1194115 CTTCTTCTTGCT
1 CTTCTTCTTGCT
1194127 CTTCTTCTTGCT
1 CTTCTTCTTGCT
*
1194139 CCTCTTCTT
1 CTTCTTCTT
1194148 CATGTTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.36, G:0.06, T:0.58
Consensus pattern (12 bp):
CTTCTTCTTGCT
Found at i:1194165 original size:33 final size:33
Alignment explanation
Indices: 1194127--1194217 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 33
1194117 TCTTCTTGCT
*
1194127 CTTCTTCTTGCTCCTCTTCTTCATGTTTGCTTG
1 CTTCTTCTTGCTCCTCTTCTTCATGTTTGCTAG
* *
1194160 CTTCTTCCTGCCCCTCTTCTTCATGTTTGCTAG
1 CTTCTTCTTGCTCCTCTTCTTCATGTTTGCTAG
* *
1194193 CTCCTTCTTGCTTCTCTTCTTCATG
1 CTTCTTCTTGCTCCTCTTCTTCATG
1194218 CCTCTTAGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.04, C:0.34, G:0.11, T:0.51
Consensus pattern (33 bp):
CTTCTTCTTGCTCCTCTTCTTCATGTTTGCTAG
Found at i:1207374 original size:17 final size:16
Alignment explanation
Indices: 1207336--1207374 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1207326 ATCTTACATT
1207336 TAAATAACTCGATAAA
1 TAAATAACTCGATAAA
*
1207352 TCAAATAACTTGATAGAA
1 T-AAATAACTCGATA-AA
1207370 TAAAT
1 TAAAT
1207375 TCATCAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.80
18 3 0.15
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (16 bp):
TAAATAACTCGATAAA
Found at i:1210334 original size:38 final size:39
Alignment explanation
Indices: 1210278--1210355 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
1210268 GTTAAGGGTT
*
1210278 TTTTGCTAAAACCAAAAGATCGCTAGTCTTCCTCTTGGC
1 TTTTGCTAAAACCAAAAGATCGCTAGTCTCCCTCTTGGC
* *
1210317 TTTT-CTAAAACGAAAAGATCGTTAGTCTCCCTCTTGGC
1 TTTTGCTAAAACCAAAAGATCGCTAGTCTCCCTCTTGGC
1210355 T
1 T
1210356 CATGTCTGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 32 0.89
39 4 0.11
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (39 bp):
TTTTGCTAAAACCAAAAGATCGCTAGTCTCCCTCTTGGC
Found at i:1212088 original size:22 final size:22
Alignment explanation
Indices: 1212063--1212106 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1212053 TGTATATTTA
*
1212063 TATTTGTATATCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
*
1212085 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
1212107 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATACCTAGAATTAAG
Found at i:1215979 original size:22 final size:22
Alignment explanation
Indices: 1215953--1215996 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1215943 TGTATATTTA
*
1215953 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1215975 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1215997 AAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:1218328 original size:20 final size:20
Alignment explanation
Indices: 1218303--1218341 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1218293 TCCTACCGAT
1218303 AGATAGCTTACTATATATAC
1 AGATAGCTTACTATATATAC
1218323 AGATAGCTTACTATATATA
1 AGATAGCTTACTATATATA
1218342 GATTGATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (20 bp):
AGATAGCTTACTATATATAC
Found at i:1218344 original size:18 final size:18
Alignment explanation
Indices: 1218301--1218344 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 18
1218291 TATCCTACCG
1218301 ATAGATAGCTTACTATAT
1 ATAGATAGCTTACTATAT
1218319 ATACAGATAGCTTACTATAT
1 AT--AGATAGCTTACTATAT
1218339 ATAGAT
1 ATAGAT
1218345 TGATGCATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
20 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (18 bp):
ATAGATAGCTTACTATAT
Found at i:1219527 original size:2 final size:2
Alignment explanation
Indices: 1219515--1219556 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1219505 CAAAACAGCA
*
1219515 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1219557 ACACACACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Done.