Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006927.1 Hibiscus syriacus cultivar Beakdansim tig00017771_pilon, 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: 330415
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:205072 original size:13 final size:13
Alignment explanation
Indices: 205054--205083 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
205044 GAGAGCTAGT
*
205054 GAGATCAAGATGA
1 GAGATCAAAATGA
205067 GAGATCAAAATGA
1 GAGATCAAAATGA
205080 GAGA
1 GAGA
205084 AATGAGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.30, T:0.13
Consensus pattern (13 bp):
GAGATCAAAATGA
Found at i:206214 original size:14 final size:14
Alignment explanation
Indices: 206195--206245 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
206185 CCCTTTGTTC
206195 GAACATAAATGAAT
1 GAACATAAATGAAT
206209 GAACATAAATGAAT
1 GAACATAAATGAAT
*
206223 GAACATAAATGAAC
1 GAACATAAATGAAT
206237 GAACATAAA
1 GAACATAAA
206246 GGAACATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.18
Consensus pattern (14 bp):
GAACATAAATGAAT
Found at i:206250 original size:14 final size:14
Alignment explanation
Indices: 206194--206250 Score: 87
Period size: 14 Copynumber: 4.1 Consensus size: 14
206184 GCCCTTTGTT
206194 CGAACATAAATGAA
1 CGAACATAAATGAA
*
206208 TGAACATAAATGAA
1 CGAACATAAATGAA
*
206222 TGAACATAAATGAA
1 CGAACATAAATGAA
*
206236 CGAACATAAAGGAA
1 CGAACATAAATGAA
206250 C
1 C
206251 ATATAATCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:206881 original size:20 final size:19
Alignment explanation
Indices: 206854--206950 Score: 88
Period size: 20 Copynumber: 4.7 Consensus size: 19
206844 TATAGGTTAC
206854 ATATATAGTTTATATAACAT
1 ATATATAGTTTATAT-ACAT
*
206874 ATAAATAGATTGTATATATTCAT
1 ATATATAG-TT-TATATA--CAT
*
206897 ATACTATA-TGTTATATATAT
1 ATA-TATAGT-TTATATACAT
206917 ATATATAGTTTATATACACT
1 ATATATAGTTTATATACA-T
*
206937 ATACATAGTTTATA
1 ATATATAGTTTATA
206951 CATACATGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
19 12 0.19
20 27 0.42
21 3 0.05
22 12 0.19
23 7 0.11
24 3 0.05
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (19 bp):
ATATATAGTTTATATACAT
Found at i:206930 original size:17 final size:18
Alignment explanation
Indices: 206895--206939 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
206885 GTATATATTC
206895 ATATACTATATGTTATAT
1 ATATACTATATGTTATAT
206913 ATATA-TATATAGTT-TAT
1 ATATACTATAT-GTTATAT
*
206930 ATACACTATA
1 ATATACTATA
206940 CATAGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (18 bp):
ATATACTATATGTTATAT
Found at i:207015 original size:24 final size:23
Alignment explanation
Indices: 206982--207026 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
206972 AAGTTACATA
*
206982 TATAGTTTACATGTATACATATAT
1 TATAGGTTACAT-TATACATATAT
*
207006 TATAGGTTACATTATATATAT
1 TATAGGTTACATTATACATAT
207027 TAACTATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TATAGGTTACATTATACATATAT
Found at i:207106 original size:28 final size:28
Alignment explanation
Indices: 207036--207142 Score: 94
Period size: 28 Copynumber: 3.9 Consensus size: 28
207026 TTAACTATTC
207036 TTTAT-GTTTAGGGTTTAGGGTTTATGA-
1 TTTATGGTTTAGGGTTTAGGGTTTA-GAT
* * * * * *
207063 TGTAAGGGTTAAGGTTTAGGATTTAAAT
1 TTTATGGTTTAGGGTTTAGGGTTTAGAT
207091 TTTATGGTTTAGGGTTTAGGGTTTAGAT
1 TTTATGGTTTAGGGTTTAGGGTTTAGAT
* * *
207119 TATCA-AGTTTAGGGTTTAGAGTTT
1 T-TTATGGTTTAGGGTTTAGGGTTT
207143 TTTTATATAA
Statistics
Matches: 62, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
27 4 0.06
28 56 0.90
29 2 0.03
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (28 bp):
TTTATGGTTTAGGGTTTAGGGTTTAGAT
Found at i:207135 original size:7 final size:7
Alignment explanation
Indices: 207041--207116 Score: 55
Period size: 7 Copynumber: 10.9 Consensus size: 7
207031 TATTCTTTAT
207041 GTTTAGG
1 GTTTAGG
207048 GTTTAGG
1 GTTTAGG
*
207055 GTTTATG
1 GTTTAGG
* *
207062 ATGTAAGG
1 GT-TTAGG
*
207070 G-TTAAG
1 GTTTAGG
207076 GTTTAGG
1 GTTTAGG
* **
207083 ATTTAAA
1 GTTTAGG
* *
207090 TTTTATG
1 GTTTAGG
207097 GTTTAGG
1 GTTTAGG
207104 GTTTAGG
1 GTTTAGG
207111 GTTTAG
1 GTTTAG
207117 ATTATCAAGT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
6 4 0.08
7 44 0.86
8 3 0.06
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:207307 original size:42 final size:42
Alignment explanation
Indices: 207261--207370 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
207251 TAGTTTATAC
* *
207261 ATACATGTATTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
*
207303 ATACATACACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
*
207345 ATACACATACTATAAGTTACATATAT
1 ATACATATACTATAAGTTACATATAT
207371 TAACTATTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (42 bp):
ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
Found at i:207708 original size:15 final size:15
Alignment explanation
Indices: 207688--207723 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
207678 CTATATATTT
*
207688 TATATAGTTTATACA
1 TATATAGTATATACA
*
207703 TATATAGTATATATA
1 TATATAGTATATACA
207718 TATATA
1 TATATA
207724 TAGTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
TATATAGTATATACA
Found at i:207734 original size:77 final size:77
Alignment explanation
Indices: 207640--207799 Score: 221
Period size: 77 Copynumber: 2.1 Consensus size: 77
207630 TTATGCATAC
*
207640 ATATATATACTATATTAATATAAATTATAACATATAAACTATATATTTTATATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATACATA
207705 TATAGTATATAT
66 TATAGTATATAT
* * *** * * *
207717 ATATATATAGTATATTAATATATATAATATTTTATAAACTATATATTTTTTGTAGTTTATACCTA
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATACATA
*
207782 TATAGTTTATAT
66 TATAGTATATAT
*
207794 ACATAT
1 ATATAT
207800 TTTATATATA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (77 bp):
ATATATATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATACATA
TATAGTATATAT
Found at i:207741 original size:17 final size:17
Alignment explanation
Indices: 207584--207742 Score: 81
Period size: 17 Copynumber: 9.6 Consensus size: 17
207574 TATTTCTTTA
207584 ATATATATATA-TATAT
1 ATATATATATAGTATAT
**
207600 ATATATATATTCTATAT
1 ATATATATATAGTATAT
207617 ACT-TACT-TATTAGTTATGCAT
1 A-TATA-TATA-TAG-TAT--AT
* *
207638 ACATATATATACTATAT
1 ATATATATATAGTATAT
*
207655 -TA-ATATA-AAT-TAT
1 ATATATATATAGTATAT
* * *
207668 A-ACATATAAACTATAT
1 ATATATATATAGTATAT
*
207684 AT-TTTATATAGT-T-T
1 ATATATATATAGTATAT
*
207698 ATACATATATAGTATAT
1 ATATATATATAGTATAT
207715 ATATATATATAGTATAT
1 ATATATATATAGTATAT
207732 -TAATATATATA
1 AT-ATATATATA
207743 ATATTTTATA
Statistics
Matches: 110, Mismatches: 15, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
13 4 0.04
14 10 0.09
15 16 0.15
16 23 0.21
17 38 0.35
18 3 0.03
19 6 0.05
20 3 0.03
21 7 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATATATATAGTATAT
Found at i:207746 original size:15 final size:16
Alignment explanation
Indices: 207696--207752 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
207686 TTTATATAGT
* *
207696 TTATACATATATAGTA
1 TTATATATATATAATA
207712 TATATATATATATAGTATA
1 T-TATATATATATA--ATA
207731 TTA-ATATATATAATA
1 TTATATATATATAATA
*
207746 TTTTATA
1 TTATATA
207753 AACTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 5 0.15
16 4 0.12
17 20 0.59
18 2 0.06
19 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (16 bp):
TTATATATATATAATA
Found at i:207761 original size:2 final size:2
Alignment explanation
Indices: 207584--207746 Score: 73
Period size: 2 Copynumber: 84.0 Consensus size: 2
207574 TATTTCTTTA
*
207584 AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT AT AT ACT -T ACT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT
** * *
207625 AT -T AGT -T AT GC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * * *
207665 -T AT A- AC AT AT AA ACT AT AT AT -T TT AT AT AGT TT AT AC AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
207706 AT AGT AT AT AT AT AT AT AT AGT AT AT -T A- AT AT AT AT A- AT AT
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
207747 TTTATAAACT
Statistics
Matches: 123, Mismatches: 17, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
1 13 0.11
2 99 0.80
3 11 0.09
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:207808 original size:77 final size:78
Alignment explanation
Indices: 207636--207813 Score: 216
Period size: 77 Copynumber: 2.3 Consensus size: 78
207626 TTAGTTATGC
*
207636 ATACATATATATACTATATTAATATAAATTATAACATATAAACTATATATTTTATATAGTTTATA
1 ATACATAT-TATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATA
207701 CATATATAGTATAT
65 CATATATAGTATAT
* * * *** * *
207715 ATATATA-TATAGTATATTAATATATATAATATTTTATAAACTATATATTTTTTGTAGTTTATAC
1 ATACATATTATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATAC
* *
207779 CTATATAGTTTAT
66 ATATATAGTATAT
*
207792 ATACATATTTTA-TATATATAAT
1 ATACATATTATACTATAT-TAAT
207814 TCACATAAAC
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
77 71 0.85
78 7 0.08
79 6 0.07
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (78 bp):
ATACATATTATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATAC
ATATATAGTATAT
Found at i:207874 original size:18 final size:18
Alignment explanation
Indices: 207830--208064 Score: 122
Period size: 18 Copynumber: 12.2 Consensus size: 18
207820 AAACATAATT
*
207830 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
207848 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
207866 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
*
207884 TTTTATATACATAGTTTATATA
1 ---TATATATATAGTTTATA-A
* ***
207906 TATAGTTCACATA-AACATAA
1 TATA--T-ATATAGTTTATAA
*
207926 TTTATATATATAGCTTATAA
1 --TATATATATAGTTTATAA
207946 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
207964 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
*
207982 TTTTATATACATAGTTTATATA
1 ---TATATATATAGTTTATA-A
* **
208004 TATAGTGCACATA-AATATAA
1 TATA-T--ATATAGTTTATAA
208024 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
208044 TA-ATTATATAGTTTAT-A
1 TATA-TATATAGTTTATAA
208061 TATA
1 TATA
208065 ATTTTATATT
Statistics
Matches: 171, Mismatches: 20, Indels: 52
0.70 0.08 0.21
Matches are distributed among these distances:
17 6 0.04
18 75 0.44
19 18 0.11
20 13 0.08
21 39 0.23
22 20 0.12
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:207915 original size:98 final size:98
Alignment explanation
Indices: 207787--208065 Score: 506
Period size: 98 Copynumber: 2.9 Consensus size: 98
207777 ACCTATATAG
* *
207787 TTTATATACATATTTTATATATATAATTCACATAAACATAATTTATATATATAGCTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
207852 TATATAGTTTATAATATAAATATAGTTTATAAT
66 TATATAGTTTATAATATAAATATAGTTTATAAT
207885 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
207950 TATATAGTTTATAATATAAATATAGTTTATAAT
66 TATATAGTTTATAATATAAATATAGTTTATAAT
* * *
207983 TTTATATACATAGTTTATATATATAGTGCACATAAATATAATTTATATATATAGTTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
208048 TATATAGTTTAT-ATATAA
66 TATATAGTTTATAATATAA
208066 TTTTATATTA
Statistics
Matches: 176, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
97 6 0.03
98 170 0.97
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (98 bp):
TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
TATATAGTTTATAATATAAATATAGTTTATAAT
Found at i:208040 original size:13 final size:13
Alignment explanation
Indices: 207688--208089 Score: 112
Period size: 13 Copynumber: 29.5 Consensus size: 13
207678 CTATATATTT
207688 TATATAGTTTATACA
1 TATATAGTTTAT--A
*
207703 TATATAGTATATA
1 TATATAGTTTATA
*
207716 TATATA-TATAGTA
1 TATATAGTTTA-TA
* *
207729 TAT-TAATATATA
1 TATATAGTTTATA
*
207741 TA-ATATTTTATAAA
1 TATATAGTTTAT--A
207755 CTATATA-TTT-T-
1 -TATATAGTTTATA
*
207766 T-TGTAGTTTATA
1 TATATAGTTTATA
207778 CCTATATAGTTTATA
1 --TATATAGTTTATA
* *
207793 TACATATTTTATA
1 TATATAGTTTATA
* *
207806 TATATAATTCACATA
1 TATATAGTT--TATA
* * *
207821 AACATAATTTATA
1 TATATAGTTTATA
207834 TATATAGCTTATAATAA
1 TATATAG-TT-T-AT-A
207851 TTATATAGTTTATA
1 -TATATAGTTTATA
**
207865 -ATATA-AATATA
1 TATATAGTTTATA
* *
207876 GTTTATAATTTTATA
1 -TATAT-AGTTTATA
*
207891 TACATAGTTTATA
1 TATATAGTTTATA
*
207904 TATATAGTTCACATA
1 TATATAGTT--TATA
* * *
207919 AACATAATTTATA
1 TATATAGTTTATA
207932 TATATAGCTTATAATAA
1 TATATAG-TT-T-AT-A
207949 TTATATAGTTTATA
1 -TATATAGTTTATA
**
207963 -ATATA-AATATA
1 TATATAGTTTATA
* *
207974 GTTTATAATTTTATA
1 -TATAT-AGTTTATA
*
207989 TACATAGTTTATA
1 TATATAGTTTATA
**
208002 TATATAGTGCACATA
1 TATATAGT--TTATA
* *
208017 AATATAATTTATA
1 TATATAGTTTATA
208030 TATATAGTTTATAATAA
1 TATATAG-TT-T-AT-A
208047 TTATATAGTTTATA
1 -TATATAGTTTATA
*
208061 TATA-ATTTTATA
1 TATATAGTTTATA
*
208073 T-TATA-TATATA
1 TATATAGTTTATA
208084 TATATA
1 TATATA
208090 TTTTTTTCAT
Statistics
Matches: 291, Mismatches: 52, Indels: 91
0.67 0.12 0.21
Matches are distributed among these distances:
9 3 0.01
10 4 0.01
11 17 0.06
12 39 0.13
13 95 0.33
14 20 0.07
15 71 0.24
16 12 0.04
17 9 0.03
18 21 0.07
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:208060 original size:29 final size:25
Alignment explanation
Indices: 208027--208094 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
208017 AATATAATTT
*
208027 ATATATATAGTTTATAATAATTATATAGT
1 ATATATATAATTT-T-AT-ATTATATA-T
*
208056 TTATATATAATTTTATATTATATAT
1 ATATATATAATTTTATATTATATAT
*
208081 ATATATATATTTTT
1 ATATATATAATTTT
208095 TTCATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 13 0.37
26 8 0.23
27 2 0.06
28 1 0.03
29 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
ATATATATAATTTTATATTATATAT
Found at i:208078 original size:17 final size:18
Alignment explanation
Indices: 208030--208081 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
208020 ATAATTTATA
208030 TATATAGTT-TATAATAAT
1 TATATAGTTATAT-ATAAT
208048 TATATAGTTTATATATAAT
1 TATATAG-TTATATATAAT
*
208067 TTTATA-TTATATATA
1 TATATAGTTATATATA
208082 TATATATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 12 0.39
20 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATATAGTTATATATAAT
Found at i:214377 original size:14 final size:14
Alignment explanation
Indices: 214358--214396 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
214348 TAATGGGGAG
214358 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
214372 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
214386 GAATCTCTGCA
1 TAATCCCTGCA
214397 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:225022 original size:13 final size:13
Alignment explanation
Indices: 225004--225030 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
224994 ATGAAAAAAT
225004 AATAAAAGATAAA
1 AATAAAAGATAAA
225017 AATAAAAGATAAA
1 AATAAAAGATAAA
225030 A
1 A
225031 CAAAATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (13 bp):
AATAAAAGATAAA
Found at i:225261 original size:10 final size:10
Alignment explanation
Indices: 225220--225266 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
225210 ACATATATAT
225220 AAATAATAAA
1 AAATAATAAA
*
225230 ACAAAAATAAA
1 A-AATAATAAA
*
225241 ATAATATTAAA
1 A-AATAATAAA
225252 AAATAATAAA
1 AAATAATAAA
225262 AAATA
1 AAATA
225267 TATACATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 14 0.45
11 17 0.55
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAATAAA
Found at i:225279 original size:22 final size:21
Alignment explanation
Indices: 225221--225267 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
225211 CATATATATA
* *
225221 AATAATAAAACAAAAATAAAAT
1 AATATTAAAA-AATAATAAAAT
225243 AATATTAAAAAATAATAAAA-
1 AATATTAAAAAATAATAAAAT
225263 AATAT
1 AATAT
225268 ATACATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 9 0.39
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AATATTAAAAAATAATAAAAT
Found at i:227074 original size:31 final size:31
Alignment explanation
Indices: 227039--227108 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
227029 ACTGAACTCG
* *
227039 AAGGTTTGATGTTTCAAGAGAAACATTTTCA
1 AAGGTTTCATGTTTCAAGAGAAACAATTTCA
* *
227070 AAGGTTTTCTTTTTTCAAGAGAAACAATTTCA
1 AAGG-TTTCATGTTTCAAGAGAAACAATTTCA
227102 AAGGTTT
1 AAGGTTT
227109 TTTGTGCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 7 0.21
32 27 0.79
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (31 bp):
AAGGTTTCATGTTTCAAGAGAAACAATTTCA
Found at i:227126 original size:33 final size:32
Alignment explanation
Indices: 227051--227127 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
227041 GGTTTGATGT
* *
227051 TTCAAGAGAAACATTTTCAAAGGTTTTCTTTT
1 TTCAAGAGAAACAATTTCAAAGGTTTTCTTTC
227083 TTCAAGAGAAACAATTTCAAAGGTTTT-TTGTGC
1 TTCAAGAGAAACAATTTCAAAGGTTTTCTT-T-C
*
227116 TTCAAAAGAAAC
1 TTCAAGAGAAAC
227128 TGTCTCAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.05
32 27 0.68
33 11 0.28
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (32 bp):
TTCAAGAGAAACAATTTCAAAGGTTTTCTTTC
Found at i:227272 original size:21 final size:21
Alignment explanation
Indices: 227213--227278 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
227203 AGGAACTGTC
227213 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAA-TTTGTT
*
227235 TCAAG-G-G---AAA-CTGTT
1 TCAAGAGAGACAAAATTTGTT
227250 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
227271 TCAAGAGA
1 TCAAGAGA
227279 AACTGTCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 9 0.25
16 1 0.03
17 4 0.11
20 4 0.11
21 13 0.36
22 5 0.14
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:227281 original size:36 final size:36
Alignment explanation
Indices: 227197--227655 Score: 378
Period size: 36 Copynumber: 13.1 Consensus size: 36
227187 AGATTGGTGC
*
227197 TTCAAGAGGAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* *
227234 TTCAAGGGAAACTGTTTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
**
227270 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCAGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* * * *
227307 TTTAAAAGAAACTGTCTCGAGAGAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
227343 TTAAAG-GAAAACATAT-TC-A-A-AG----ATTTTAT
1 TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTTGT
* * *
227372 TTCAAGGGAAACAGTCCCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * **
227408 TTCAAGAAAAACTATCTCAAAAGAGACAAAATTTAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * ** *
227444 TTCTAAAAGAAACTGTCTCGAGAGAGATGAAATTTAT
1 TTC-AAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
227481 TTAAAG-GAAAACAGAT-TC-----A-A-ATATTTTGT
1 TTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATTTGT
* *
227510 TTCAAGGGAAACTGTCTCAAGAGAGAGAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
227546 TTTAAGAGAAAATGTTTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
227582 TTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
227618 TTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
227654 TT
1 TT
227656 TGAGATAAAT
Statistics
Matches: 339, Mismatches: 59, Indels: 49
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.01
29 32 0.09
30 4 0.01
31 2 0.01
32 2 0.01
33 2 0.01
34 2 0.01
35 4 0.01
36 201 0.59
37 88 0.26
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:227290 original size:73 final size:73
Alignment explanation
Indices: 227197--227655 Score: 377
Period size: 73 Copynumber: 6.5 Consensus size: 73
227187 AGATTGGTGC
* * *
227197 TTCAAGAGGAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTTTCAAGAGAGACA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
227262 AAATTTGT
66 AAATTTGT
** * * * *
227270 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCAGTTTTAAAAGAAACTGTCTCGAGAGAGACG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
227335 AAATTTGT
66 AAATTTGT
* * * * * * *
227343 TTAAAG-GAAAACATAT-TC-A-A-AG-----ATTTTATTTCAAGGGAAACAGTCCCAAGAGAGA
1 TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
227398 CAAAATTTGT
64 CAAAATTTGT
* * * ** * * *
227408 TTCAAGAAAAACTATCTCAAAAGAGACAAAA-TTTAATTCTAAAAGAAACTGTCTCGAGAGAGAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTC-AAGAGAAACTGTCTCAAGAGAGAC
* *
227472 GAAATTTAT
65 AAAATTTGT
* * ** * * *
227481 TT-AA-AGGAA-------AACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAA-ACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
227537 AAAATTTGT
65 AAAATTTGT
* * * * *
227546 TTTAAGAGAAAATGTTTCAAGAGAGACAAAA-TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
227610 AAATTTGT
66 AAATTTGT
*
227618 TTTAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
227656 TGAGATAAAT
Statistics
Matches: 305, Mismatches: 56, Indels: 51
0.74 0.14 0.12
Matches are distributed among these distances:
64 12 0.04
65 73 0.24
66 9 0.03
67 5 0.02
68 2 0.01
70 2 0.01
71 4 0.01
72 83 0.27
73 104 0.34
74 11 0.04
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (73 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
AAATTTGT
Found at i:227398 original size:138 final size:137
Alignment explanation
Indices: 227233--227628 Score: 549
Period size: 138 Copynumber: 2.9 Consensus size: 137
227223 CAAAACTTTG
*
227233 TTTCAAGGGAAACTGTTTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
* *
227298 AAACTCAGTTTTAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACATATTCAA
66 AAA-TTAGTTTTAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAA
227363 AGATTTTA
130 AGATTTTA
* * * * *
227371 TTTCAAGGGAAACAGTCCCAAGAGAGACAAAATTTGTTTCAAGAAAAACTATCTCAAAAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
* * * *
227436 AAATTTAATTCTAAAAGAAACTGTCTCGAGAGAGATGAAATTTATTTAAAGGAAAACAGATTCAA
66 AAA-TTAGTTTTAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAA
* *
227501 ATATTTTG
130 AGATTTTA
* * * *
227509 TTTCAAGGGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGAGAAAATGTTTCAAGAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
* * * * * *
227574 AAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAA
66 AAATTAGTTTTAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAG-GAAA
227629 CTGTCTCAAG
Statistics
Matches: 223, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
137 37 0.17
138 186 0.83
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (137 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
AAATTAGTTTTAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAA
GATTTTA
Found at i:227419 original size:65 final size:65
Alignment explanation
Indices: 227314--227557 Score: 211
Period size: 65 Copynumber: 3.6 Consensus size: 65
227304 AGTTTTAAAA
* * *
227314 GAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACATATTCAAAGATTTTATTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAAAAACATATTCAAAGATTTTATTTCAAGG
* * * *
227379 GAAACAGTCCCAAGAGAGACAAAATTTGTTTCAAGAAAAAC-TATCTCAAAAGAGACAAAATTTA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAAAAACATAT-TC--AA-AG----ATTTTA
* **
227443 ATTCTAAAA
58 TTTC-AAGG
* ** * * * * *
227452 GAAACTGTCTCGAGAGAGATGAAATTTATTTAAAGGAAAACAGATTCAAATATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAAAAACATATTCAAAGATTTTATTTCAAGG
* *
227517 GAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGAGAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA-AAAA
227558 TGTTTCAAGA
Statistics
Matches: 137, Mismatches: 31, Indels: 21
0.72 0.16 0.11
Matches are distributed among these distances:
64 3 0.02
65 69 0.50
66 11 0.08
67 2 0.01
68 2 0.01
70 1 0.01
71 2 0.01
72 8 0.06
73 37 0.27
74 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (65 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAAAAACATATTCAAAGATTTTATTTCAAGG
Found at i:227553 original size:19 final size:19
Alignment explanation
Indices: 227531--227626 Score: 73
Period size: 17 Copynumber: 5.3 Consensus size: 19
227521 CTGTCTCAAG
227531 AGAGAGAAAATTTGTTTT-
1 AGAGAGAAAATTTGTTTTA
*
227549 A-AGAGAAAA--TGTTTCA
1 AGAGAGAAAATTTGTTTTA
227565 AGAGAGACAAAATTTGTTTT-
1 AGAGAG--AAAATTTGTTTTA
* *
227585 A-AGAGAAAA--TGTCTCA
1 AGAGAGAAAATTTGTTTTA
227601 AGAGAGACAAAATTTGTTTTA
1 AGAGAG--AAAATTTGTTTTA
227622 AGAGA
1 AGAGA
227627 AACTGTCTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
15 9 0.15
16 2 0.03
17 20 0.33
18 1 0.02
19 12 0.20
20 1 0.02
21 15 0.25
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (19 bp):
AGAGAGAAAATTTGTTTTA
Found at i:227586 original size:102 final size:102
Alignment explanation
Indices: 227403--227593 Score: 231
Period size: 102 Copynumber: 1.9 Consensus size: 102
227393 AGAGACAAAA
* *
227403 TTTGTTTCAAGAAAAACTATCTCAAAAGAGACAAAATTTAATTCTAAAAGAAACTGTCTCGAGAG
1 TTTGTTTCAAGAAAAACTATCTCAAAAGAGACAAAATTTAATTCTAAAAGAAAATGTCTCAAGAG
**
227468 AGATGAAATTTATTTAAAGGAAAACAGATTCAAATAT
66 AGACAAAATTTATTTAAAGGAAAACAGATTCAAATAT
** * * * * * * *
227505 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAGAAAATTT-GTTTTAAGAGAAAATGTTTCAAGAG
1 TTTGTTTCAAGAAAAACTATCTCAAAAGAGACAAAATTTAATTCTAAAAGAAAATGTCTCAAGAG
* *
227569 AGACAAAATTTGTTTTAAGAGAAAA
66 AGACAAAATTTATTTAAAG-GAAAA
227594 TGTCTCAAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
101 34 0.47
102 39 0.53
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAGAAAAACTATCTCAAAAGAGACAAAATTTAATTCTAAAAGAAAATGTCTCAAGAG
AGACAAAATTTATTTAAAGGAAAACAGATTCAAATAT
Found at i:227672 original size:72 final size:71
Alignment explanation
Indices: 227524--227673 Score: 221
Period size: 72 Copynumber: 2.1 Consensus size: 71
227514 AGGGAAACTG
* * *
227524 TCTCAAGAGAGAGAAAATTTGTTTTAAGAGAAAATGTTTCAAGAGAGACAAAATTTGTTTTAAGA
1 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTGTTTT-AGA
*
227589 GAAAATG
65 GAAAATA
*
227596 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTT-GAG
1 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTGTTTTAGAG
227660 ATAAATAA
66 A-AAAT-A
227668 TCTCAA
1 TCTCAA
227674 AGGTGATCGA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
70 4 0.06
71 4 0.06
72 63 0.89
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (71 bp):
TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTGTTTTAGAG
AAAATA
Found at i:229123 original size:95 final size:95
Alignment explanation
Indices: 228952--229133 Score: 285
Period size: 95 Copynumber: 1.9 Consensus size: 95
228942 AAATGTAAAT
* * * * *
228952 ACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCAAAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
*
229017 ACAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
229047 ACCTTTATCAGGCTAGCTGAATATTATCCAAAAAGCCGGGGCATTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCAAAAAGCCGGGGCATTTAACCAATTGCCT-TAGAGG
*
229111 GACAACTTAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
229134 TAAATAATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 2 0.03
95 77 0.97
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCAAAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:233439 original size:41 final size:36
Alignment explanation
Indices: 233390--233480 Score: 85
Period size: 36 Copynumber: 2.4 Consensus size: 36
233380 CGTGTAAAGA
* *
233390 AATATAAAATATACATATATATATAAATAAATAAAAAAAT
1 AATATAAAAAATA-ATAT-TA-AAAAAT-AATAAAAAAAT
*
233430 AATATTAAAAAATAATATTAAAAAATAATAAATAAAT
1 AATA-TAAAAAATAATATTAAAAAATAATAAAAAAAT
*
233467 -ATATACATAAATAA
1 AATATA-AAAAATAA
233481 ATATGCATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
35 2 0.04
36 10 0.22
37 10 0.22
38 5 0.11
39 2 0.04
40 8 0.18
41 8 0.18
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (36 bp):
AATATAAAAAATAATATTAAAAAATAATAAAAAAAT
Found at i:233441 original size:13 final size:13
Alignment explanation
Indices: 233414--233459 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
233404 ATATATATAT
*
233414 AAATAA-ATAAAA
1 AAATAATATTAAA
233426 AAATAATATTAAA
1 AAATAATATTAAA
233439 AAATAATATTAAA
1 AAATAATATTAAA
233452 AAATAATA
1 AAATAATA
233460 AATAAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 6 0.19
13 26 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAATATTAAA
Found at i:233477 original size:26 final size:25
Alignment explanation
Indices: 233423--233483 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 25
233413 TAAATAAATA
*
233423 AAAAAATAATATTAAAAAATAATATT
1 AAAAAATAATA-TAAAAAATAATAAT
*
233449 AAAAAATAATA-AATAAATATATACAT
1 AAAAAATAATATAAAAAATA-ATA-AT
233475 AAATAAATA
1 AAA-AAATA
233484 TGCATTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.23
25 3 0.10
26 15 0.50
27 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAAATAATATAAAAAATAATAAT
Found at i:233499 original size:4 final size:4
Alignment explanation
Indices: 233412--233483 Score: 60
Period size: 4 Copynumber: 17.8 Consensus size: 4
233402 ACATATATAT
*
233412 ATAA ATAA ATAA AAAA ATAA TATTAA A-AA ATAA TATTAA A-AA AT-A
1 ATAA ATAA ATAA ATAA ATAA -A-TAA ATAA ATAA -A-TAA ATAA ATAA
* *
233457 ATAA ATAA ATAT ATAC ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
233484 TGCATTGTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
3 9 0.16
4 37 0.66
5 4 0.07
6 6 0.11
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:241537 original size:14 final size:14
Alignment explanation
Indices: 241518--241563 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
241508 ACATGAAAAG
*
241518 GTGATATAAGTTAT
1 GTGATATAAGCTAT
* *
241532 GTGATATTGACCTAT
1 GTGATA-TAAGCTAT
241547 GTGATATAAGCTAT
1 GTGATATAAGCTAT
241561 GTG
1 GTG
241564 GCATTGATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (14 bp):
GTGATATAAGCTAT
Found at i:241614 original size:22 final size:22
Alignment explanation
Indices: 241545--241614 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
241535 ATATTGACCT
*
241545 ATGTGATATAAGCTATGTGGC-
1 ATGTGATATAAGCTATGTGACA
* * *
241566 AT-TGATCTACGTAGCTATATGAAA
1 ATGTGATATA---AGCTATGTGACA
241590 ATGTGATATAAGCTATGTGACA
1 ATGTGATATAAGCTATGTGACA
241612 ATG
1 ATG
241615 AGCTATGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 6 0.16
21 2 0.05
22 13 0.35
23 8 0.22
24 2 0.05
25 6 0.16
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (22 bp):
ATGTGATATAAGCTATGTGACA
Found at i:241793 original size:23 final size:23
Alignment explanation
Indices: 241739--241817 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
241729 GGTTCTACGC
*
241739 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTATGT
* * *
241762 GATCATTCGGGACAATACTATGT
1 GGTCCTTCGGGACAATTCTATGT
** *
241785 GGTCCTTCGAAACATTTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
*
241808 GGTACTTCGG
1 GGTCCTTCGG
241818 TGCAATTTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:242021 original size:6 final size:6
Alignment explanation
Indices: 241935--242017 Score: 112
Period size: 6 Copynumber: 13.8 Consensus size: 6
241925 TTGAATAGTG
*
241935 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT ACTGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
* * * * *
241983 AATGAC AATGAC AATGAC AATGAC AATGAC AATGA
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGA
242018 CAATTATCGT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (6 bp):
AATGAT
Found at i:242514 original size:11 final size:12
Alignment explanation
Indices: 242493--242525 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
242483 AATAAATATT
242493 ATAATAATTTAA
1 ATAATAATTTAA
242505 ATAA-AATTTAA
1 ATAATAATTTAA
*
242516 ATTATAATTT
1 ATAATAATTT
242526 TTTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATAATTTAA
Found at i:242640 original size:20 final size:22
Alignment explanation
Indices: 242599--242645 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
242589 TCTTTGATAT
242599 TAATAAATATTATAATAATTTA
1 TAATAAATATTATAATAATTTA
**
242621 -AATAAA-ATTATAATTTTTTA
1 TAATAAATATTATAATAATTTA
242641 TAATA
1 TAATA
242646 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATAAATATTATAATAATTTA
Found at i:242683 original size:110 final size:113
Alignment explanation
Indices: 242469--242717 Score: 407
Period size: 110 Copynumber: 2.2 Consensus size: 113
242459 AAGACATCTC
*
242469 TTTTCTTCGATATTAATAAATATTATAATAATTTAAATAAAATTTAAATTATAATTTTTTTATAA
1 TTTTCTTTGATATTAATAAATATTATAATAATTTAAAT--AA--TAAATTATAATTTTTTTATAA
242534 TATTTAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCCA
62 TATTTAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCCA
242586 TTTTCTTTGATATTAATAAATATTATAATAATTTAAAT-A-AAATTATAA-TTTTTTATAATATT
1 TTTTCTTTGATATTAATAAATATTATAATAATTTAAATAATAAATTATAATTTTTTTATAATATT
*
242648 TAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCCC
66 TAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCCA
242696 TTTTCTTTGATATTGAA-AAATA
1 TTTTCTTTGATATT-AATAAATA
242718 AATAAATATT
Statistics
Matches: 129, Mismatches: 2, Indels: 9
0.92 0.01 0.06
Matches are distributed among these distances:
110 80 0.62
111 11 0.09
114 1 0.01
117 37 0.29
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (113 bp):
TTTTCTTTGATATTAATAAATATTATAATAATTTAAATAATAAATTATAATTTTTTTATAATATT
TAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCCA
Found at i:242886 original size:21 final size:21
Alignment explanation
Indices: 242815--242886 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 21
242805 ATGACTATAT
*
242815 AATAATAATAAAT-ATAATATA
1 AATAA-AATAAATAATAATAAA
* * *
242836 AATATAAACAAGTGAA-ATTAAA
1 AATA-AAATAAAT-AATAATAAA
242858 ACAT-AAATAAATAATAATAAA
1 A-ATAAAATAAATAATAATAAA
242879 AATAAAAT
1 AATAAAAT
242887 TAGAACTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 4 0.11
21 25 0.66
22 6 0.16
23 3 0.08
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (21 bp):
AATAAAATAAATAATAATAAA
Found at i:244245 original size:3 final size:3
Alignment explanation
Indices: 244237--244298 Score: 99
Period size: 3 Copynumber: 20.3 Consensus size: 3
244227 TTAATTTTTT
244237 ATA ATA ATA ATA AT- ATA TATA TATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA
244283 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
244299 AAATGGGTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.84
4 7 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:244558 original size:17 final size:17
Alignment explanation
Indices: 244536--244594 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
244526 TTGAACAAGC
244536 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
244553 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
244572 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
244589 TCTTCT
1 TCTTCT
244595 GAAGATGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 4 0.12
19 10 0.29
20 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:244601 original size:33 final size:34
Alignment explanation
Indices: 244536--244602 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
244526 TTGAACAAGC
**
244536 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTGTGAA--TCTTCTTCTGAAGATGAGT
244572 TCTTCTCATTGTGAA-CTTCTTCTGAAGATGA
1 TCTTCTCATTGTGAATCTTCTTCTGAAGATGA
244603 TGATATATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 14 0.48
36 15 0.52
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (34 bp):
TCTTCTCATTGTGAATCTTCTTCTGAAGATGAGT
Found at i:245155 original size:3 final size:3
Alignment explanation
Indices: 245147--245210 Score: 101
Period size: 3 Copynumber: 20.3 Consensus size: 3
245137 TTAATTTTTT
245147 ATA ATA ATA ATA ATA ATA TATA TATA TATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA -ATA -ATA ATA ATA ATA ATA ATA ATA
245195 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
245211 ATAAAATGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 49 0.82
4 11 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:245473 original size:17 final size:17
Alignment explanation
Indices: 245451--245509 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
245441 TTGAACAAGC
245451 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
245468 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
245487 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
245504 TCTTCT
1 TCTTCT
245510 GAAGATGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 4 0.12
19 10 0.29
20 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:245516 original size:33 final size:34
Alignment explanation
Indices: 245451--245517 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
245441 TTGAACAAGC
**
245451 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTGTGAA--TCTTCTTCTGAAGATGAGT
245487 TCTTCTCATTGTGAA-CTTCTTCTGAAGATGA
1 TCTTCTCATTGTGAATCTTCTTCTGAAGATGA
245518 TGATATATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 14 0.48
36 15 0.52
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (34 bp):
TCTTCTCATTGTGAATCTTCTTCTGAAGATGAGT
Found at i:245588 original size:114 final size:115
Alignment explanation
Indices: 245410--245734 Score: 318
Period size: 113 Copynumber: 2.8 Consensus size: 115
245400 GATGACAATT
* * *
245410 TATCTCCTTCTGTGATGTAATCTAGCAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTT
1 TATCTCCTTCTGTGATGTAATATAGCAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTT
*
245475 C-TTC-AGATGAGTTCTTCTCATTGTGAACTTCTTCTGAAGATGATGATA
66 CTTTCTAGATGAGTTCTTCTCATTATGAACTTCTTCTGAAGATGATGATA
* * *
245523 TATCTCCTTCTGTGATAG-AGTATTGCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTTTTC
1 TATCTCCTTCTGTGAT-GTAATATAGC-AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTC
245587 TTCTTTCTTTAGATGAGTTCTTCTCATTATGAAC-TCTCTCTGGAA-A--A-G-T-
64 TTCTTTC--TAGATGAGTTCTTCTCATTATGAACTTCT-TCT-GAAGATGATGATA
* * * * *
245636 TGA--TCCATCGAGTGATG-AAT-TCGAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
1 T-ATCTCCTTC-TGTGATGTAATAT--AGC-AAAGGTCGAACAAGCTCTTCTCATTATGAACTTC
*
245697 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
61 TTCTTCTTTC-T-AGATGAGTTCTTCTCATTATGAACT
245735 CTTTCACTGG
Statistics
Matches: 181, Mismatches: 17, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
111 1 0.01
112 10 0.06
113 92 0.51
114 40 0.22
115 4 0.02
116 1 0.01
117 3 0.02
118 27 0.15
119 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (115 bp):
TATCTCCTTCTGTGATGTAATATAGCAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTT
CTTTCTAGATGAGTTCTTCTCATTATGAACTTCTTCTGAAGATGATGATA
Found at i:245694 original size:113 final size:113
Alignment explanation
Indices: 245548--246105 Score: 716
Period size: 113 Copynumber: 4.9 Consensus size: 113
245538 TAGAGTATTG
* ** * * *
245548 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTTTTCTTCTTTCTTTAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
245613 TTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAG
66 TTATGAACTCTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
*
245661 CGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** *
245725 ATTATGAACTCTTTCACTGGGGATGCTGATCCATCAAATGATGAATTCAAA
65 ATTATGAACTC--TCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
245776 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * ** *
245841 TTATGAACTTTTTCTGGAAAAGTTGATCCATCAAATGATGGATTTGAG
66 TTATGAACTCTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
245889 CAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * *
245950 TCATTAGGAACTTTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
63 TCATTATGAACTCT-CTCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
246001 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * **
246066 TTAAGAACT-TCTACTGGTACTGTTGATCCATTGAATGATG
66 TTATGAACTCTCT-CTGGAAATGTTGATCCATCAAATGATG
246106 GATTTAAATC
Statistics
Matches: 392, Mismatches: 39, Indels: 28
0.85 0.08 0.06
Matches are distributed among these distances:
109 11 0.03
110 5 0.01
111 2 0.01
112 84 0.21
113 168 0.43
114 9 0.02
115 102 0.26
116 11 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
Found at i:246034 original size:225 final size:227
Alignment explanation
Indices: 245548--246110 Score: 814
Period size: 225 Copynumber: 2.5 Consensus size: 227
245538 TAGAGTATTG
* ** * * *
245548 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTTTTCTTCTTTCTTTAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
245613 TTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGT
66 TTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGGATTTGAGCGAAAAGTTGAACAAAT
* *
245678 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACT
131 TCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCTTACACT
**
245743 GGGGATGCTGATCCATCAAATGATGAATTCAAA
195 GGCAATGCTGATCCATCAAATGATGAATTCAAA
245776 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
245841 TTATGAACTTTTTCTGGAAAAGTTGATCCATCAAATGATGGATTTGAGC-AAAAGGTTGAACAAA
66 TTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGGATTTGAGCGAAAA-GTTGAACAAA
245905 TTCTTCTCATTATGAA-T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTAGGAACT-TTAC
130 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAGGAACTCTTAC
*
245966 -CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
192 ACTGGCAATGCTGATCCATCAAATGATGAATTCAAA
246001 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * ** *
246066 TTAAGAACTTCTACTGGTACTGTTGATCCATTGAATGATGGATTT
66 TTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGGATTT
246111 AAATCTTTGT
Statistics
Matches: 305, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
224 11 0.04
225 139 0.46
226 4 0.01
227 24 0.08
228 127 0.42
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (227 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGGATTTGAGCGAAAAGTTGAACAAAT
TCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCTTACACTG
GCAATGCTGATCCATCAAATGATGAATTCAAA
Found at i:246961 original size:114 final size:114
Alignment explanation
Indices: 246796--247249 Score: 755
Period size: 114 Copynumber: 4.0 Consensus size: 114
246786 ACGATCATGC
* * * * * * * * * *
246796 AATTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTAACGAACCAGATCAGATGACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
* * *
246861 GAAAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCA
246910 AATTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
*
246975 GAATACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCA
*
247024 AATTCATCTTTCAAATGCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
247089 GAACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCA
*
247138 AATTCATCTTTCAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
*
247203 GAACACTTCCAAAAGATGCTATTGGGTCTTCGTATTCCTACTATGAG
66 GAACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAG
247250 AACGTAGCAC
Statistics
Matches: 322, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 322 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCA
Found at i:247571 original size:19 final size:17
Alignment explanation
Indices: 247543--247591 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
247533 AAAATAAAAG
*
247543 AATAAGTTGAATTTTCAAA
1 AATAAATTGAATTTTC--A
*
247562 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
247578 AATAAATTGAATTT
1 AATAAATTGAATTT
247592 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:247967 original size:19 final size:19
Alignment explanation
Indices: 247945--248081 Score: 110
Period size: 19 Copynumber: 7.2 Consensus size: 19
247935 TTGACCACCC
247945 TTTTTTCTTCTTCTTTTTT
1 TTTTTTCTTCTTCTTTTTT
*
247964 TTTTCTT-TT-TTTTTCTTTT
1 TTTT-TTCTTCTTCTT-TTTT
247983 TTTTTTCTTCTTCTCTTTTT
1 TTTTTTCTTCTTCT-TTTTT
*
248003 TCTTTTCTT-TT-TTCTTTT
1 TTTTTTCTTCTTCTT-TTTT
248021 TTCTTTTCTTC-TCTTTTTT
1 TT-TTTTCTTCTTCTTTTTT
*
248040 TCTTTTCTTTCTT-TTTTTCT
1 TTTTTTC-TTCTTCTTTTT-T
248060 CTTTTTT-TTC-TCTTTTTAT
1 -TTTTTTCTTCTTCTTTTT-T
248079 TTT
1 TTT
248082 CATCATTTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 29
0.73 0.05 0.22
Matches are distributed among these distances:
17 1 0.01
18 21 0.22
19 48 0.49
20 21 0.22
21 6 0.06
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTCTTCTTCTTTTTT
Found at i:247988 original size:27 final size:27
Alignment explanation
Indices: 247945--248068 Score: 133
Period size: 27 Copynumber: 4.6 Consensus size: 27
247935 TTGACCACCC
* *
247945 TTTTTTCTTCTTCTTTTTTTTTTCTTT
1 TTTTTTCTTTTTTTTTTTTTTTTCTTT
* * *
247972 TTTTTTCTTTTTTTTTTCTTCTTC-TC
1 TTTTTTCTTTTTTTTTTTTTTTTCTTT
247998 TTTTTTCTTTTCTTTTTTCTTTTTTCTTT
1 TTTTTTCTTTT-TTTTTT-TTTTTTCTTT
* * * *
248027 TCTTCTCTTTTTTTCTTTTCTTTCTTT
1 TTTTTTCTTTTTTTTTTTTTTTTCTTT
*
248054 TTTTCTCTTTTTTTT
1 TTTTTTCTTTTTTTT
248069 CTCTTTTTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
26 12 0.15
27 48 0.60
28 10 0.12
29 10 0.12
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTTCTTTTTTTTTTTTTTTTCTTT
Found at i:247996 original size:38 final size:38
Alignment explanation
Indices: 247945--248070 Score: 157
Period size: 38 Copynumber: 3.2 Consensus size: 38
247935 TTGACCACCC
247945 TTTTTTCTTCTTCTTTTTTTTTTCTTTTTTTTTCTTTT
1 TTTTTTCTTCTTCTTTTTTTTTTCTTTTTTTTTCTTTT
* *
247983 TTTTTTCTTCTTCTCTTTTTTCTT-TTCTTTTTTCTTTT
1 TTTTTTCTTCTTCT-TTTTTTTTTCTTTTTTTTTCTTTT
*
248021 TTCTTTTCTTC-TCTTTTTTTCTTTTCTTTCTTTTTTTCTCTT
1 TT-TTTTCTTCTTC-TTTTTT-TTTTC-TT-TTTTTTTCTTTT
248063 TTTTTTCT
1 TTTTTTCT
248071 CTTTTTATTT
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
38 36 0.47
39 20 0.26
41 8 0.11
42 12 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (38 bp):
TTTTTTCTTCTTCTTTTTTTTTTCTTTTTTTTTCTTTT
Found at i:248015 original size:53 final size:53
Alignment explanation
Indices: 247944--248097 Score: 158
Period size: 53 Copynumber: 2.9 Consensus size: 53
247934 CTTGACCACC
*
247944 CTTTTTTCTTCTTC-TTTTTTTTTTCTTTTTTTTTCTTTTTTTTTTCTTCTTCT
1 CTTTTTTCTT-TTCTTTTTTTTTTTCTTTTTTTTTCTTATTTTTTTCTTCTTCT
* * *
247997 CTTTTTTCTTTTCTTTTTTCTTTTT-TCTTTTCTTC-TCTTTTTTTCTT-TTCT
1 CTTTTTTCTTTTCTTTTTT-TTTTTCTTTTTTTTTCTTATTTTTTTCTTCTTCT
* * *
248048 -TTCTTT-TTTTCTCTTTTTTTTCTCTTTTTATTTTCATCATTTTTTTCTTC
1 CTTTTTTCTTTTCT-TTTTTTTTTTCTTTTT-TTTTC-TTATTTTTTTCTTC
248098 AAACATAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
49 10 0.12
50 14 0.17
51 8 0.10
52 14 0.17
53 33 0.39
54 5 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (53 bp):
CTTTTTTCTTTTCTTTTTTTTTTTCTTTTTTTTTCTTATTTTTTTCTTCTTCT
Found at i:248076 original size:1 final size:1
Alignment explanation
Indices: 247958--248068 Score: 60
Period size: 1 Copynumber: 111.0 Consensus size: 1
247948 TTTCTTCTTC
* * * * * * * * *
247958 TTTTTTTTTTCTTTTTTTTTCTTTTTTTTTTCTTCTTCTCTTTTTTCTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
248023 CTTTTCTTCTCTTTTTTTCTTTTCTTTCTTTTTTTCTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
248069 CTCTTTTTAT
Statistics
Matches: 74, Mismatches: 36, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:248082 original size:36 final size:35
Alignment explanation
Indices: 247946--248095 Score: 125
Period size: 36 Copynumber: 4.3 Consensus size: 35
247936 TGACCACCCT
*
247946 TTTTTCTTCTTCTTTTTTTTTTCTTTTTTTTTCTTT-
1 TTTTT-TTC-TCTTTTTTTTCTCTTTTTTTTTCTTTC
*
247982 TTTTTTTCTTCTTCTCTTTTT-TC-TTTTCTTT-TTTC
1 TTTTTTTC-TCTT-T-TTTTTCTCTTTTTTTTTCTTTC
* * *
248017 -TTTTTTCT-TTTCTTCTCTTTTTTTCTTTTCTTTC
1 TTTTTTTCTCTTTTTTTTCTCTTTTT-TTTTCTTTC
*
248051 TTTTTTTCTCTTTTTTTTCTCTTTTTATTTTC-ATC
1 TTTTTTTCTCTTTTTTTTCTCTTTTT-TTTTCTTTC
248086 ATTTTTTTCT
1 -TTTTTTTCT
248096 TCAAACATAA
Statistics
Matches: 94, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
30 3 0.03
31 2 0.02
32 6 0.06
33 4 0.04
34 14 0.15
35 25 0.27
36 35 0.37
37 5 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (35 bp):
TTTTTTTCTCTTTTTTTTCTCTTTTTTTTTCTTTC
Found at i:248091 original size:27 final size:24
Alignment explanation
Indices: 247944--248093 Score: 119
Period size: 26 Copynumber: 5.9 Consensus size: 24
247934 CTTGACCACC
*
247944 CTTTTTTCTTCTTCTTTTTTTTT-T
1 CTTTTTTTTTC-TCTTTTTTTTTCT
247968 CTTTTTTTTTCT-TTTTTTTTTCTT
1 CTTTTTTTTTCTCTTTTTTTTTC-T
247992 CTTCTCTTTTTTCT-TTTCTTTTTTCTT
1 CTT-T-TTTTTTCTCTTT-TTTTTTC-T
* *
248019 TTTTCTTTTCTTCTCTTTTTTTCTTTT
1 CTTT-TTTT-TTCTCTTTTTTT-TTCT
248046 CTTTCTTTTTT-TCTCTTTTTTTTCT
1 CTTT-TTTTTTCTCT-TTTTTTTTCT
*
248071 CTTTTTATTTTCATCATTTTTTT
1 CTTTTT-TTTTC-TCTTTTTTTT
248094 CTTCAAACAT
Statistics
Matches: 108, Mismatches: 6, Indels: 22
0.79 0.04 0.16
Matches are distributed among these distances:
22 9 0.08
23 1 0.01
24 16 0.15
25 15 0.14
26 32 0.30
27 30 0.28
28 5 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (24 bp):
CTTTTTTTTTCTCTTTTTTTTTCT
Found at i:248093 original size:55 final size:58
Alignment explanation
Indices: 247947--248082 Score: 97
Period size: 56 Copynumber: 2.4 Consensus size: 58
247937 GACCACCCTT
* * * *
247947 TTTTCTTCTTCTTTTTTTTTTCTTTTTTTTTCTTTT-TTTTTTC-TTCTTCTCTTTTTTC
1 TTTTCTTCTTCTTTTTCTTTTC-TTTCTTCTCTTTTCTCTTTTCTTTCTT-TCTTTTTTC
* * *
248005 TTTTCTT-TT-TTCTT-TTTTCTTTTCTTCTCTTTTTTTCTTTTCTTTCTTT-TTTTCTC
1 TTTTCTTCTTCTTTTTCTTTTC-TTTCTTCTC-TTTTCTCTTTTCTTTCTTTCTTTTTTC
* *
248061 TTTT-TTTTCTCTTTTTATTTTC
1 TTTTCTTCT-TCTTTTTCTTTTC
248083 ATCATTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
55 15 0.23
56 19 0.29
57 10 0.15
58 16 0.25
59 5 0.08
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.82
Consensus pattern (58 bp):
TTTTCTTCTTCTTTTTCTTTTCTTTCTTCTCTTTTCTCTTTTCTTTCTTTCTTTTTTC
Found at i:255433 original size:15 final size:15
Alignment explanation
Indices: 255410--255446 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
255400 TGCAATGAAT
*
255410 AATGAATGTATGCAA
1 AATGTATGTATGCAA
255425 AATGTATGTATGCAA
1 AATGTATGTATGCAA
*
255440 AAGGTAT
1 AATGTAT
255447 TGATCCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (15 bp):
AATGTATGTATGCAA
Found at i:259338 original size:11 final size:12
Alignment explanation
Indices: 259317--259349 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
259307 AATAAATATT
259317 ATAATAATTTAA
1 ATAATAATTTAA
259329 ATAA-AATTTAA
1 ATAATAATTTAA
*
259340 ATTATAATTT
1 ATAATAATTT
259350 TTTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATAATTTAA
Found at i:259505 original size:111 final size:113
Alignment explanation
Indices: 259292--259542 Score: 391
Period size: 111 Copynumber: 2.2 Consensus size: 113
259282 TAAGATAGCT
*
259292 CTTTTCTTCGATATTAATAAATATTATAATAATTTAAATAAAATTTAAATTATAATTTTTTTATA
1 CTTTTCTTTGATATTAATAAATATTATAATAATTTAAAT--AA--TAAATTATAATTTTTTTATA
* * *
259357 ATATTTAATTTTAAAATATCAGAATATGACATCCAGTTTTATTAAGACTGCC
62 ATATTTAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCC
259409 CTTTTCTTTGATATTAATAAATATTATAATAATTTAAAT-A-AAATTATAATTTTTTTATAATAT
1 CTTTTCTTTGATATTAATAAATATTATAATAATTTAAATAATAAATTATAATTTTTTTATAATAT
*
259472 TTAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTATGACTGCC
66 TTAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCC
259520 CTTTTCTTTGATATTGAA-AAATA
1 CTTTTCTTTGATATT-AATAAATA
259543 AATAAATATT
Statistics
Matches: 128, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
111 87 0.68
112 2 0.02
114 1 0.01
117 38 0.30
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (113 bp):
CTTTTCTTTGATATTAATAAATATTATAATAATTTAAATAATAAATTATAATTTTTTTATAATAT
TTAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCC
Found at i:259577 original size:111 final size:111
Alignment explanation
Indices: 259292--259577 Score: 308
Period size: 111 Copynumber: 2.5 Consensus size: 111
259282 TAAGATAGCT
* * * **
259292 CTTTTCTTCGATATTAATAAATATTATAATAATTTAAATAAAATTTAAATTATAATTTTTTTATA
1 CTTTTCTTTGATATTAATAAATAATATAATAATTAAAATAAAA--TAAA--A-AA-TAATTTATA
* * *
259357 ATATTTAATTTTAAAATATCAGAATATGACATCCAGTTTTATTAAGACTGCC
60 ATATTTAATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCC
* * * * * **
259409 CTTTTCTTTGATATTAATAAATATTATAATAATTTAAATAAAATTATAATTTTTTTATAATATTT
1 CTTTTCTTTGATATTAATAAATAATATAATAATTAAAATAAAATAAAAAATAATTTATAATATTT
*
259474 AATTTTAAAATACCAGAATAGGACATCCAGTTGTATTATGACTGCC
66 AATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCC
**
259520 CTTTTCTTTGATATTGAA-AAATAA-ATAA-ATATTAAAATATGATAAAAAAATAATTTAT
1 CTTTTCTTTGATATT-AATAAATAATATAATA-ATTAAAATAAAAT-AAAAAATAATTTAT
259578 GTAAAATCAA
Statistics
Matches: 149, Mismatches: 17, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
109 1 0.01
110 14 0.09
111 86 0.58
112 3 0.02
113 1 0.01
115 2 0.01
117 42 0.28
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (111 bp):
CTTTTCTTTGATATTAATAAATAATATAATAATTAAAATAAAATAAAAAATAATTTATAATATTT
AATTTTAAAATACCAGAATAGGACATCCAGTTGTATTAAGACTGCC
Found at i:261075 original size:3 final size:3
Alignment explanation
Indices: 261067--261126 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
261057 AATTATTTTT
* * * *
261067 TAA TAA TAA TAA TAA T-T TATA TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
261112 TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
261127 ATAAATAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 48 0.94
4 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:261093 original size:21 final size:24
Alignment explanation
Indices: 261056--261126 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 24
261046 ATTGGACCTG
*
261056 TAATTATT-TTTTAATAATAATAA
1 TAATTATTATTATAATAATAATAA
261079 TAA-T-TTA-TATAATAATAATAA
1 TAATTATTATTATAATAATAATAA
*
261100 TAATTATTATTATTATAATAATAA
1 TAATTATTATTATAATAATAATAA
261124 TAA
1 TAA
261127 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 18 0.43
22 2 0.05
23 6 0.14
24 16 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTATTATTATAATAATAATAA
Found at i:262527 original size:31 final size:31
Alignment explanation
Indices: 262484--262550 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
262474 TATACTATTG
*
262484 ATAA-AATTTAATAAATTTAATAAATATTTT
1 ATAATAATATAATAAATTTAATAAATATTTT
* *
262514 ATAATAATATAATAATTTTAATAATTATTTT
1 ATAATAATATAATAAATTTAATAAATATTTT
262545 ATAATA
1 ATAATA
262551 TCAATATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATAATAATATAATAAATTTAATAAATATTTT
Found at i:262535 original size:17 final size:17
Alignment explanation
Indices: 262501--262538 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
262491 TTAATAAATT
*
262501 TAATAAATATTTTATAA
1 TAATAAATAATTTATAA
262518 TAATATAATAATTT-TAA
1 TAATA-AATAATTTATAA
262535 TAAT
1 TAAT
262539 TATTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATAAATAATTTATAA
Found at i:265397 original size:20 final size:20
Alignment explanation
Indices: 265372--265416 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
265362 CCCATTTGAG
265372 AAAGAAATCGTTCCAGAAAA
1 AAAGAAATCGTTCCAGAAAA
* * *
265392 AAAGAACTCGTTCGAGAAAC
1 AAAGAAATCGTTCCAGAAAA
265412 AAAGA
1 AAAGA
265417 GGTTGTGTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAGAAATCGTTCCAGAAAA
Found at i:265471 original size:23 final size:23
Alignment explanation
Indices: 265445--265513 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
265435 CACCACAGCT
* *
265445 CGTATAAATGCGCCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
265468 CGTAGAATTGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
*
265491 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
265514 TATATATAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:272368 original size:23 final size:23
Alignment explanation
Indices: 272342--272401 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
272332 CACCATAGCT
*
272342 CGTATAAATGCACCGAAGTG-CTA
1 CGTAGAAATGCACCGAAGTGTC-A
* *
272365 CGTAGAATTGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGTCA
272388 CGTAGAAATGCACC
1 CGTAGAAATGCACC
272402 ATAGTGACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGTCA
Found at i:277239 original size:38 final size:39
Alignment explanation
Indices: 277188--277262 Score: 118
Period size: 38 Copynumber: 1.9 Consensus size: 39
277178 TTTAAGAAAT
*
277188 TAAAAAATATATATATATTTA-ATAAGTTAAGACAAAGA
1 TAAAAAATATATATATATTTATATAAATTAAGACAAAGA
277226 TAAAATAA-ATATATATATTTATATAAATTAAGACAAA
1 TAAAA-AATATATATATATTTATATAAATTAAGACAAA
277263 TAATAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 18 0.53
39 16 0.47
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (39 bp):
TAAAAAATATATATATATTTATATAAATTAAGACAAAGA
Found at i:284296 original size:118 final size:119
Alignment explanation
Indices: 284138--284379 Score: 378
Period size: 118 Copynumber: 2.0 Consensus size: 119
284128 GTCTCGTTTA
* * *
284138 ATTTAGTCCAAAGTTCTAGAAACTGTACATTTACGAACCAAAAATGGTGTAGGCTGCCATTTTTG
1 ATTTAGTCCAAAGTCCTAGAAACTGTACATTTACGAACCAAAAATAGCGTAGGCTGCCATTTTTG
*
284203 CTTCTCAAGCTGAATAAATTTCA-TTGACAAGCAATAAAACTATTTTCAATATG
66 CTCCTCAAGCTGAATAAATTTCACTTGACAAGCAATAAAACTATTTTCAATATG
**
284256 ATTTAGTCCCGAGTCCTAGAAACTGTACATTTACGAACCAAAAATAGCGTAGGCTGCCATTTTTG
1 ATTTAGTCCAAAGTCCTAGAAACTGTACATTTACGAACCAAAAATAGCGTAGGCTGCCATTTTTG
* *
284321 CTCCTCAAGCTGAATAAATTTCATCCTTTGACATGCAATGAAACTATTTTCAATATG
66 CTCCTCAAGCTGAATAAATTTCA--C-TTGACAAGCAATAAAACTATTTTCAATATG
284378 AT
1 AT
284380 GAGGTAACCA
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
118 82 0.73
122 30 0.27
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (119 bp):
ATTTAGTCCAAAGTCCTAGAAACTGTACATTTACGAACCAAAAATAGCGTAGGCTGCCATTTTTG
CTCCTCAAGCTGAATAAATTTCACTTGACAAGCAATAAAACTATTTTCAATATG
Found at i:287121 original size:284 final size:287
Alignment explanation
Indices: 286628--287291 Score: 796
Period size: 284 Copynumber: 2.3 Consensus size: 287
286618 ACAAGTTACA
* * **
286628 ATAATTTCATGTTTATTCAATTTAGTCCTTAAAATTATA-TTTTATTTGGAATTGACTCATACTT
1 ATAATTTCATATTTATTCAATTTAGTCCTTAAAATTATATTTTTATCTAAAATTGAC-CATACTT
* * *
286692 ATTTATATTTTTATAGTTTAATCCAAACCCTATAAATCACATCAAAAACATCATTTCAAATCCTA
65 ATTTATATTTTTGTAATTTACTCCAAACCCTATAAATCACATCAAAAACATCATTTCAAATCCTA
* * * * *
286757 TAAATTATATCACAATCTCTAAAACCTTATAAATTTTTGTTCATCAAGTTTTTAAATGAATGCAA
130 TAAATTATATCACAATCTCCAAAACCTTATAAACTTTTGTTCACCAACTTTATAAATGAATG-AA
* **
286822 TTTAGTCCATTTTATATTAATTTC-ATCTTCACACTTTATAATTATTTTGATTTGATCC-C-T-A
194 TTTAGTCAATTTTATATTAATTTCAAT-TTCACACTTTATAATTATTTCAATTTGATCCACATCA
286883 -CGTGTTGTTTAATTT-TTT-TTTTCAATTT
258 GCGTGTTGTTTAATTTATTTATTTT-AATTT
* * * *
286911 GTAATTTCATATTTATTCAA-CTAGGGCCTTAAAATTATATTTTTATCTAAAATTAATCCATACT
1 ATAATTTCATATTTATTCAATTTA-GTCCTTAAAATTATATTTTTATCTAAAATTGA-CCATACT
* *
286975 TATTTATATTTTTGTAATTTACTCCAAACCCTATAAATCACATCATAAACTTCATTTCAAA-CAC
64 TATTTATATTTTTGTAATTTACTCCAAACCCTATAAATCACATCAAAAACATCATTTCAAATC-C
* * *
287039 TATAAATTATATCATAATCTCCAAAGCC-TATAAACTTTTGTTCACCAACTTTATAGATGGATAT
128 TATAAATTATATCACAATCTCCAAAACCTTATAAACTTTTGTTCACCAACTTTATAAAT-GA-AT
* *
287103 G-ATTTAGTCAATTTTTATATTAATTTCAATTTCACATTTTATAATTGTTTCAATTTGATCCATC
191 GAATTTAGTCAA-TTTTATATTAATTTCAATTTCACACTTTATAATTATTTCAATTTGATCCA-C
* *
287167 ATCCATGTGTGTTGTTTAATTTATTTAAATTTTAGTTT
254 AT-CA-GCGTGTTGTTTAATTTATTT--ATTTTAATTT
* * *
287205 ATAATTTTATATTTATTCAATTTAGTCCTTAAAATTATATTTTTATC-AAAATTGACCCATAATC
1 ATAATTTCATATTTATTCAATTTAGTCCTTAAAATTATATTTTTATCTAAAATTGA-CCATACTT
*
287269 ATTTCTATTTTTTGTAATTTACT
65 ATTTATA-TTTTTGTAATTTACT
287292 TAAAATCCTA
Statistics
Matches: 323, Mismatches: 37, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
282 2 0.01
283 67 0.21
284 144 0.45
285 6 0.02
286 1 0.00
287 1 0.00
289 1 0.00
291 14 0.04
292 3 0.01
293 19 0.06
294 59 0.18
295 6 0.02
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (287 bp):
ATAATTTCATATTTATTCAATTTAGTCCTTAAAATTATATTTTTATCTAAAATTGACCATACTTA
TTTATATTTTTGTAATTTACTCCAAACCCTATAAATCACATCAAAAACATCATTTCAAATCCTAT
AAATTATATCACAATCTCCAAAACCTTATAAACTTTTGTTCACCAACTTTATAAATGAATGAATT
TAGTCAATTTTATATTAATTTCAATTTCACACTTTATAATTATTTCAATTTGATCCACATCAGCG
TGTTGTTTAATTTATTTATTTTAATTT
Found at i:288596 original size:18 final size:19
Alignment explanation
Indices: 288573--288614 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
288563 TTCGGATCAG
*
288573 AAAAAAATA-AAACATTAT
1 AAAAAAATATAAACAATAT
288591 -AAAAAATATAAACAATAT
1 AAAAAAATATAAACAATAT
288609 AAAAAA
1 AAAAAA
288615 TCATAAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAAATATAAACAATAT
Found at i:288602 original size:9 final size:9
Alignment explanation
Indices: 288573--288621 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
288563 TTCGGATCAG
288573 AAAAAA-AT
1 AAAAAATAT
*
288581 AAAACATTAT
1 AAAA-AATAT
288591 AAAAAATAT
1 AAAAAATAT
*
288600 AAACAATAT
1 AAAAAATAT
288609 AAAAAATCAT
1 AAAAAAT-AT
288619 AAA
1 AAA
288622 TCGAGTGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 4 0.12
9 19 0.56
10 11 0.32
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATAT
Found at i:288615 original size:18 final size:18
Alignment explanation
Indices: 288574--288621 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
288564 TCGGATCAGA
*
288574 AAAAAATA-AAACATTAT
1 AAAAAATATAAACAATAT
288591 AAAAAATATAAACAATAT
1 AAAAAATATAAACAATAT
288609 AAAAAATCATAAA
1 AAAAAAT-ATAAA
288622 TCGAGTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 8 0.29
18 15 0.54
19 5 0.18
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAATATAAACAATAT
Found at i:290705 original size:17 final size:17
Alignment explanation
Indices: 290683--290727 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
290673 CCCAATAAAG
290683 ACTAAAT-TATTATAA-A
1 ACTAAATGTATT-TAACA
290699 ACATAAATGTATTTAACA
1 AC-TAAATGTATTTAACA
290717 ACTAAATGTAT
1 ACTAAATGTAT
290728 CATACCCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.08
17 17 0.65
18 7 0.27
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (17 bp):
ACTAAATGTATTTAACA
Found at i:292564 original size:17 final size:17
Alignment explanation
Indices: 292542--292586 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
292532 CCCAATAAAG
292542 ACTAAAT-TATTATAA-A
1 ACTAAATGTATT-TAACA
292558 ACATAAATGTATTTAACA
1 AC-TAAATGTATTTAACA
292576 ACTAAATGTAT
1 ACTAAATGTAT
292587 CATACCCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.08
17 17 0.65
18 7 0.27
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (17 bp):
ACTAAATGTATTTAACA
Found at i:296897 original size:17 final size:16
Alignment explanation
Indices: 296866--296896 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
296856 TCAAATGAGT
296866 TGATTTAAAAAAAAAC
1 TGATTTAAAAAAAAAC
296882 TGATTTAAAAAAAAA
1 TGATTTAAAAAAAAA
296897 AATTAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
TGATTTAAAAAAAAAC
Found at i:297802 original size:27 final size:28
Alignment explanation
Indices: 297748--297800 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
297738 AGTTTGATCC
*
297748 GGTTGGGATGGAGGGTGTATAATATTTG
1 GGTTGGGATGGAGGGCGTATAATATTTG
*
297776 GGTTGGG-TGGAGTGCGTATAA-ATTT
1 GGTTGGGATGGAGGGCGTATAATATTT
297801 TGAGTCAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 7 0.30
ACGTcount: A:0.21, C:0.02, G:0.42, T:0.36
Consensus pattern (28 bp):
GGTTGGGATGGAGGGCGTATAATATTTG
Found at i:300102 original size:17 final size:17
Alignment explanation
Indices: 300080--300120 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
300070 CCCAATAATG
300080 ACTAAAT-TATTATAA-A
1 ACTAAATGTATT-TAACA
300096 ACATAAATGTATTTAACA
1 AC-TAAATGTATTTAACA
300114 ACTAAAT
1 ACTAAAT
300121 ATATCATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (17 bp):
ACTAAATGTATTTAACA
Found at i:304432 original size:16 final size:15
Alignment explanation
Indices: 304403--304431 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
304393 TCAAATGAGT
304403 TGATTTAAAAAAAAC
1 TGATTTAAAAAAAAC
304418 TGATTTAAAAAAAA
1 TGATTTAAAAAAAA
304432 ATTAAAACAA
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:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
TGATTTAAAAAAAAC
Found at i:305337 original size:27 final size:28
Alignment explanation
Indices: 305283--305335 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
305273 AGTTTGATCC
*
305283 GGTTGGGATGGAGGGTGTATAATATTTG
1 GGTTGGGATGGAGGGCGTATAATATTTG
*
305311 GGTTGGG-TGGAGTGCGTATAA-ATTT
1 GGTTGGGATGGAGGGCGTATAATATTT
305336 TGAGTCAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 7 0.30
ACGTcount: A:0.21, C:0.02, G:0.42, T:0.36
Consensus pattern (28 bp):
GGTTGGGATGGAGGGCGTATAATATTTG
Found at i:307633 original size:17 final size:17
Alignment explanation
Indices: 307611--307651 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
307601 CCCAATAAAG
307611 ACTAAAT-TATTATAA-A
1 ACTAAATGTATT-TAACA
307627 ACATAAATGTATTTAACA
1 AC-TAAATGTATTTAACA
307645 ACTAAAT
1 ACTAAAT
307652 ATATCATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (17 bp):
ACTAAATGTATTTAACA
Found at i:309725 original size:12 final size:12
Alignment explanation
Indices: 309708--309733 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
309698 CAATTTTCAA
309708 AAAAAATAAAAT
1 AAAAAATAAAAT
309720 AAAAAATAAAAT
1 AAAAAATAAAAT
309732 AA
1 AA
309734 CATTAAACCT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:311190 original size:8 final size:8
Alignment explanation
Indices: 311177--311208 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
311167 TCCTCCCCTT
311177 ATCTCTCC
1 ATCTCTCC
311185 ATCTCTCC
1 ATCTCTCC
311193 ATCTCTCC
1 ATCTCTCC
311201 ATCTCTCC
1 ATCTCTCC
311209 TCCACCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (8 bp):
ATCTCTCC
Found at i:315513 original size:64 final size:64
Alignment explanation
Indices: 315444--315622 Score: 161
Period size: 64 Copynumber: 2.8 Consensus size: 64
315434 TTGGAACCTT
** *
315444 AGTGCATCGGTGCACT-CTTAGTGCACCGATGCATCATGTGTATTCGATGTT-TTA-AAATAGCC
1 AGTGCATCGGTGCA-TGC-TAGTGCACCGATGCATCAAATGCATTCGATGTTCTTATAAA-AGCC
315506 -C
63 TC
* * * *
315507 GAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAAATCCT
1 -AGTGCATCGGTGCAT-GCTAGTGCACCGATGCATCAAATGCATTCGATGTTCTTATAAAAGCCT
315572 C
64 C
* * * ** *
315573 AGTGCATCGGTGCATGGT-GTGCATCGATCCATGGAATGCATTTGATGTTC
1 AGTGCATCGGTGCATGCTAGTGCACCGATGCATCAAATGCATTCGATGTTC
315623 AATTTAATTC
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
63 29 0.30
64 43 0.44
65 21 0.22
66 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (64 bp):
AGTGCATCGGTGCATGCTAGTGCACCGATGCATCAAATGCATTCGATGTTCTTATAAAAGCCTC
Found at i:322246 original size:22 final size:21
Alignment explanation
Indices: 322204--322243 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
322194 GAGTTTGTTT
*
322204 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
322225 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
322244 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:325078 original size:17 final size:17
Alignment explanation
Indices: 325033--325079 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
325023 TTTCACCCCA
325033 ATAAAGACTAAA-TTATT
1 ATAAA-ACTAAATTTATT
325050 ATAAAACATAAATTTATT
1 ATAAAAC-TAAATTTATT
325068 -TAACAACTAAAT
1 ATAA-AACTAAAT
325080 GTATCATACC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.07
17 17 0.63
18 8 0.30
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAAAACTAAATTTATT
Done.