Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 6 of 11
Found at i:1864533 original size:18 final size:18
Alignment explanation
Indices: 1864512--1864546 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1864502 TTTTTATTTT
1864512 AAATTAAATAAATATTAA
1 AAATTAAATAAATATTAA
* *
1864530 AAATTAATTAATTATTA
1 AAATTAAATAAATATTA
1864547 TTAATTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTAAATAAATATTAA
Found at i:1867197 original size:11 final size:11
Alignment explanation
Indices: 1867181--1867211 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1867171 AAAACACTTA
1867181 TAATTAATTAT
1 TAATTAATTAT
1867192 TAATTAATTAT
1 TAATTAATTAT
1867203 T-ATTAATTA
1 TAATTAATTA
1867212 AAATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATTAATTAT
Found at i:1868643 original size:2 final size:2
Alignment explanation
Indices: 1868636--1868691 Score: 85
Period size: 2 Copynumber: 27.0 Consensus size: 2
1868626 CATATCTTCA
*
1868636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
1868679 AT AT AT AGT AT AT
1 AT AT AT A-T AT AT
1868692 TAATTATGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 47 0.94
3 3 0.06
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1870916 original size:3 final size:3
Alignment explanation
Indices: 1870910--1870952 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1870900 GATGGAAGCC
*
1870910 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CCT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1870953 ATTATGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:1874953 original size:17 final size:16
Alignment explanation
Indices: 1874930--1874971 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
1874920 TTCGTAAAGT
*
1874930 TTTTTTTAAAAAATTT
1 TTTTTTTAAAAAATTA
1874946 TATTTTTTAAAAAATTA
1 T-TTTTTTAAAAAATTA
1874963 TTTTTTTAA
1 TTTTTTTAA
1874972 TTTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTTAAAAAATTA
Found at i:1876777 original size:16 final size:16
Alignment explanation
Indices: 1876756--1876788 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1876746 AATTAATATA
1876756 TTAAGTATTAACATTT
1 TTAAGTATTAACATTT
*
1876772 TTAAGTATTAATATTT
1 TTAAGTATTAACATTT
1876788 T
1 T
1876789 ATTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (16 bp):
TTAAGTATTAACATTT
Found at i:1881507 original size:34 final size:34
Alignment explanation
Indices: 1881469--1881590 Score: 138
Period size: 35 Copynumber: 3.5 Consensus size: 34
1881459 TTAATAGATT
* * * *
1881469 CAAGCACAACCTTCACTATACCTTTTTATGAAAG
1 CAAGCACAACCTTCACAATGCCTTTTCATGGAAG
* *
1881503 CAAGCACAACCTTCAACAATGCATTTTCATGGGAG
1 CAAGCACAACCTTC-ACAATGCCTTTTCATGGAAG
*
1881538 CAAGCACAATCC-TCACAAATGTCTTTTCATGGAAG
1 CAAGCACAA-CCTTCAC-AATGCCTTTTCATGGAAG
*
1881573 CAAGCACAACCCTCACAA
1 CAAGCACAACCTTCACAA
1881591 ATAGCTTTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
34 20 0.27
35 53 0.71
36 2 0.03
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (34 bp):
CAAGCACAACCTTCACAATGCCTTTTCATGGAAG
Found at i:1895503 original size:3 final size:3
Alignment explanation
Indices: 1895495--1895562 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
1895485 ATGTTGCTAT
*
1895495 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1895543 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
1895563 TCAAAATTCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1906160 original size:58 final size:57
Alignment explanation
Indices: 1906071--1906190 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 57
1906061 AAGGTCTCAT
* * *
1906071 CTTTGCATGCATTGCATTTATTAAATCGCATAAAATAAATCTATCATATGCATACTA
1 CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
* *
1906128 CTTTGCATTGCATAGCATTTATTAAATTGCATAAAATAAATCTATTACATGCAAACTA
1 CTTTGCA-TGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
1906186 CTTTG
1 CTTTG
1906191 GATGATTATG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 7 0.12
58 50 0.88
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (57 bp):
CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
Found at i:1917780 original size:29 final size:28
Alignment explanation
Indices: 1917733--1917853 Score: 143
Period size: 29 Copynumber: 4.2 Consensus size: 28
1917723 TGGTAGCTTT
1917733 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
1917761 AACATGTTTGGTCTTAATTTAGACAAAAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
1917790 AATATGTTTGCCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * *
1917820 AATATTTTTTATCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
1917849 AACAT
1 AACAT
1917854 ATTAGTCTCA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
28 19 0.24
29 37 0.46
30 13 0.16
31 11 0.14
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:1918154 original size:18 final size:18
Alignment explanation
Indices: 1918114--1918146 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1918104 ATAGTAATAA
1918114 AATAA-GAGTTATTATTC
1 AATAAGGAGTTATTATTC
1918131 AATAAGGAGTT-TTATT
1 AATAAGGAGTTATTATT
1918147 TCATTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (18 bp):
AATAAGGAGTTATTATTC
Found at i:1919647 original size:15 final size:16
Alignment explanation
Indices: 1919619--1919653 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1919609 TAAAAAACTT
1919619 TAAAATAAAATTAAAC
1 TAAAATAAAATTAAAC
*
1919635 TAAAAT-AACTTAAAC
1 TAAAATAAAATTAAAC
1919650 TAAA
1 TAAA
1919654 CTACTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATAAAATTAAAC
Found at i:1925262 original size:68 final size:68
Alignment explanation
Indices: 1925150--1925299 Score: 203
Period size: 68 Copynumber: 2.2 Consensus size: 68
1925140 CATCTTTGGT
* * * * * *
1925150 ATGATAAATACCATAAGATTGTGTATATGATGTAAATTCTATATACCATGTGA-GATGATTAAGT
1 ATGATGAATGCCATAAGATTGTGTACATGATGCAAATTCCATATACCATATGATG-TGATTAAGT
*
1925214 GTAC
65 ATAC
*
1925218 ATGATGAATGCCATAAGATTGTGTACATGATGCAAATTCCATATACCATATGATGTGATTAGGTA
1 ATGATGAATGCCATAAGATTGTGTACATGATGCAAATTCCATATACCATATGATGTGATTAAGTA
*
1925283 TGC
66 TAC
1925286 ATGATGAATGCCAT
1 ATGATGAATGCCAT
1925300 GAGAATATGC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
68 71 0.99
69 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (68 bp):
ATGATGAATGCCATAAGATTGTGTACATGATGCAAATTCCATATACCATATGATGTGATTAAGTA
TAC
Found at i:1925316 original size:68 final size:66
Alignment explanation
Indices: 1925150--1925328 Score: 189
Period size: 68 Copynumber: 2.6 Consensus size: 66
1925140 CATCTTTGGT
* * * * * *
1925150 ATGATAAATACCATAAGATTGTGTATATGATGTAAATTCTATATACCATGTGAGATGATTAAGTG
1 ATGATGAATGCCATAAGATTGCG--TATGATGTAAATTCCATATACCATATGAGATGATTAAGTA
1925215 TAC
64 TAC
* * *
1925218 ATGATGAATGCCATAAGATTGTGTACATGATGCAAATTCCATATACCATATGATG-TGATTAGGT
1 ATGATGAATGCCATAAGATTGCGT--ATGATGTAAATTCCATATACCATATGA-GATGATTAAGT
*
1925282 ATGC
63 ATAC
*
1925286 ATGATGAATGCCATGAGAATATGCGTATGATGTAAATTCCATA
1 ATGATGAATGCCATAAG-AT-TGCGTATGATGTAAATTCCATA
1925329 CACTACATGA
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
66 1 0.01
68 87 0.92
69 3 0.03
70 4 0.04
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (66 bp):
ATGATGAATGCCATAAGATTGCGTATGATGTAAATTCCATATACCATATGAGATGATTAAGTATA
C
Found at i:1925529 original size:32 final size:31
Alignment explanation
Indices: 1925493--1925594 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 31
1925483 TTATAAATGT
1925493 CCAAGGTGCAATGGGGTTCATACATTACCAAC
1 CCAAGGTGCAATGGGG-TCATACATTACCAAC
* * * **
1925525 CCAAGGTGCAATAGGGCTCGTATATTACCAGT
1 CCAAGGTGCAAT-GGGGTCATACATTACCAAC
* * *
1925557 CTAAGGTGCAATGGGGTCAAACATTGCCAAC
1 CCAAGGTGCAATGGGGTCATACATTACCAAC
*
1925588 TCAAGGT
1 CCAAGGT
1925595 TAATGGGCGT
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
31 17 0.31
32 34 0.63
33 3 0.06
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (31 bp):
CCAAGGTGCAATGGGGTCATACATTACCAAC
Found at i:1930145 original size:5 final size:5
Alignment explanation
Indices: 1930123--1930183 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
1930113 ATATTATAAT
* *
1930123 TAAAA TAAAA -ATAT TAAAA TAAATA TATAATA TAAGAA TAAAA TTAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAA-A TA-AA-A TAA-AA TAAAA -TAAAA
1930172 TAAAA TAAAA TA
1 TAAAA TAAAA TA
1930184 TAAAAATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
4 2 0.04
5 25 0.53
6 13 0.28
7 7 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (5 bp):
TAAAA
Found at i:1930207 original size:56 final size:54
Alignment explanation
Indices: 1930127--1930795 Score: 130
Period size: 54 Copynumber: 11.9 Consensus size: 54
1930117 TATAATTAAA
*
1930127 ATAAAAATATTAAAATAAATATATAATATAAGAATAAAATTAAAATAAAATA-A-AAT
1 ATAAAAATATTAAAATAAATATAT-AGAT-A-AA-AAAATTAAAATAAAATATATAAT
* * * *
1930183 ATAAAAAT-TTAACATTAATAATATAGGTAAACAAATTAAAATAAAATATATAAT
1 ATAAAAATATTAAAATAAAT-ATATAGATAAAAAAATTAAAATAAAATATATAAT
* * *
1930237 ATAAAAATATATTAAAAAATAAAAATA-AAATATAATAAATTATAAATAATAA-ATA-AAT
1 AT-AAAA-ATATT--AAAATAAATATATAGATA-AAAAAATTA-AAATAA-AATATATAAT
* * * * * ** *
1930295 A-AAATATATGACATTAAAAATATATTTAAAATATGATATT-ATATAAAATTATAATAAAAAT
1 ATAAAAATATTAAAATAAATATATAGATAAAA-A--A-ATTAAAATAAAA-TAT-AT---AAT
* * * *
1930356 ATAAATATATTAAAATAAAATATAAATATTAAATAATAAATAAAATAAAATATAATGACAT
1 ATAAAAATATTAAAAT-AAATATATAGA-TAAA-AA-AATTAAAATAAAATAT-AT-A-AT
** * * *
1930417 -TAAAAATATATTTAAGAAATGATAT-TATATAAAAATTAATAATAAAA-AT-TAA-
1 ATAAAAATAT-TAAAATAAAT-ATATAGATAAAAAAATTAA-AATAAAATATATAAT
* * *
1930469 AT----ATATTAAAAATAAATATATAAAATTTAATAATAAATAAAAATAAAATAT-TATGT
1 ATAAAAATATT-AAAATAAATATAT-AGA--TAA-AA-AAATTAAAATAAAATATATA-AT
** * *
1930525 ATAAAATATATTTTAA-AAATGA-ATA-TTATAAAAATTAATAATATAAATATA-AAT
1 ATAAAA-ATATTAAAATAAAT-ATATAGATAAAAAAATTAA-AATA-AAATATATAAT
* *
1930579 ATATAAAA-A-TAAAATATAAAATATTATGAT-AATAAA-TAAAATAAAATATATGACAT
1 ATA-AAAATATTAAAATA-AATATA-TA-GATAAAAAAATTAAAATAAAATATAT-A-AT
** * * *
1930635 -TAAAAATATATTTAAGAAATGATAT-TATATAAAAATTAATAATATAAATATA-AAT
1 ATAAAAATAT-TAAAATAAAT-ATATAGATAAAAAAATTAA-AATA-AAATATATAAT
* * *
1930690 ATATTAAAATA--AAATATAAAATATTATA-AT-AATAAATAAAAATAAAATATATGAT
1 ATA--AAAATATTAAA-AT-AAATA-TATAGATAAAAAAATTAAAATAAAATATATAAT
** * * *
1930745 ATTAAAAATATTTTAAGAAATGATAT-TAT-AATAAATTAATAATAAAATATA
1 A-TAAAAATATTAAAATAAAT-ATATAGATAAAAAAATTAA-AATAAAATATA
1930796 ATATATTAAA
Statistics
Matches: 456, Mismatches: 73, Indels: 169
0.65 0.10 0.24
Matches are distributed among these distances:
48 5 0.01
49 10 0.02
50 1 0.00
52 21 0.05
53 42 0.09
54 78 0.17
55 73 0.16
56 49 0.11
57 37 0.08
58 38 0.08
59 24 0.05
60 20 0.04
61 17 0.04
62 19 0.04
63 16 0.04
64 5 0.01
65 1 0.00
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (54 bp):
ATAAAAATATTAAAATAAATATATAGATAAAAAAATTAAAATAAAATATATAAT
Found at i:1930256 original size:32 final size:32
Alignment explanation
Indices: 1930220--1930395 Score: 112
Period size: 32 Copynumber: 5.2 Consensus size: 32
1930210 TAAACAAATT
1930220 AAAATAAAATATATAATATAAAAATATATTAA
1 AAAATAAAATATATAATATAAAAATATATTAA
*
1930252 AAAATAAAA-ATAAAATATAATAAATTATAAATAATAA
1 AAAATAAAATATATAATATAA-AAA-TAT--AT--TAA
*
1930289 ATAAATAAAATATATGACAT-TAAAAATATATT-T
1 A-AAATAAAATATAT-A-ATATAAAAATATATTAA
** * *
1930322 AAAATATGATAT-T-ATATAAAATTATAAT-A
1 AAAATAAAATATATAATATAAAAATATATTAA
*
1930351 AAAATATAAATATATTAAAATAAAATATAAATATTAA
1 AAAATA-AAATATA-TAATATAAAA-AT--ATATTAA
*
1930388 ATAATAAA
1 AAAATAAA
1930396 TAAAATAAAA
Statistics
Matches: 111, Mismatches: 14, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
28 2 0.02
29 16 0.14
30 4 0.04
31 11 0.10
32 22 0.20
33 11 0.10
34 2 0.02
35 2 0.02
36 8 0.07
37 10 0.09
38 11 0.10
39 6 0.05
40 4 0.04
41 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (32 bp):
AAAATAAAATATATAATATAAAAATATATTAA
Found at i:1930266 original size:23 final size:24
Alignment explanation
Indices: 1930222--1930410 Score: 84
Period size: 25 Copynumber: 7.5 Consensus size: 24
1930212 AACAAATTAA
*
1930222 AATAAAATATATAAT-ATAAAAATAT
1 AATAAAAAATA-AATAAT-AAAATAT
*
1930247 ATTAAAAAATAAA-AATAAAATAT
1 AATAAAAAATAAATAATAAAATAT
**
1930270 AATAAATTATAAATAAT-AAATA-
1 AATAAAAAATAAATAATAAAATAT
* *
1930292 AATAAAATATATGACATTA-AAAATAT
1 AATAAAA-A-AT-AAATAATAAAATAT
* * *
1930318 ATTTAAAATATGATATTATATAAAATTAT
1 A-ATAAAAAAT-A-AATA-ATAAAA-TAT
*
1930347 AATAAAAATATAAATATATTAAAATAA
1 AATAAAAA-ATAAATA-A-TAAAATAT
* *
1930374 AATATAAATATTAAATAAT-AAATAA
1 AATA-AAA-AATAAATAATAAAATAT
*
1930399 AATAAAATATAA
1 AATAAAAAATAA
1930411 TGACATTAAA
Statistics
Matches: 127, Mismatches: 21, Indels: 34
0.70 0.12 0.19
Matches are distributed among these distances:
22 6 0.05
23 25 0.20
24 12 0.09
25 32 0.25
26 3 0.02
27 18 0.14
28 24 0.19
29 7 0.06
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (24 bp):
AATAAAAAATAAATAATAAAATAT
Found at i:1930298 original size:38 final size:38
Alignment explanation
Indices: 1930128--1930270 Score: 119
Period size: 41 Copynumber: 3.6 Consensus size: 38
1930118 ATAATTAAAA
* * *
1930128 TAAAAATATTAAAAT-AAATATATAATATAAGAATAAAAT
1 TAAAAA-ATAAAAATAAAATATATAATATAAAAAT-ATAT
* * * *
1930167 TAAAATAAAATAAAATATAAAA-ATTTAACATTAATAATATAGG
1 T--AA-AAAATAAAA-ATAAAATATATAATA-TAAAAATATA-T
*
1930210 TAAACAAATTAAAATAAAATATATAATATAAAAATATAT
1 TAAA-AAATAAAAATAAAATATATAATATAAAAATATAT
1930249 TAAAAAATAAAAATAAAATATA
1 TAAAAAATAAAAATAAAATATA
1930271 ATAAATTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
38 17 0.20
39 5 0.06
40 16 0.19
41 22 0.27
42 13 0.16
43 10 0.12
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (38 bp):
TAAAAAATAAAAATAAAATATATAATATAAAAATATAT
Found at i:1930301 original size:95 final size:95
Alignment explanation
Indices: 1930120--1930709 Score: 264
Period size: 108 Copynumber: 5.7 Consensus size: 95
1930110 ATAATATTAT
* * * *
1930120 AATTAAAATAAAA-ATATTAAAATAAATATATAATATAAGAATAAAATTAAAATAAAATAAAATA
1 AATTAAAATAAAATATA-TAATATAAAAATATAATA-AAAAATAAAAATAAAATAAAATAAAATA
*
1930184 TAAA-AAT--TTAACATTAATAATATAGGTA-A-ACA
64 TAAATAATAAATAA-A-TAA-AATATAGG-ACATA-A
* * *
1930216 AATTAAAATAAAATATATAATATAAAAATATATTAAAAAATAAAAATAAAATATAATAAATTATA
1 AATTAAAATAAAATATATAATATAAAAATATAATAAAAAATAAAAATAAAATAAAATAAAATATA
*
1930281 AATAATAAATAAATAAAATATATGACATTAA
66 AATAATAAATAAATAAAATATAGGACA-TAA
* ** *
1930312 AAATATATTTAAAATATGATATTATATAAAATTATAATAAAAATATAAATATATTAAAATAAAAT
1 AATTA-AAATAAAATAT-ATA--ATATAAAAATATAATAAAAA-ATAAA-A-A-TAAAATAAAAT
*
1930377 ATAAATATTAAATAATAAATAAAATAAAATATAATGACATTAA
58 A-AAATA-TAAATAATAAAT-AAATAAAATAT-AGGACA-TAA
* ** * *
1930420 AAATATATTTAAGAAATGATATTATATAAAAATTAATAATAAAAATTAAATATATTAAAAATAAA
1 AATTA-AAAT-A-AAAT-ATATAATATAAAAA-T-ATAATAAAAAATAAA-A-A-T-AAAATAAA
* * *
1930485 TATATAAA-ATTTAATAATAAATAAAAATAAAATATTATG-TATAA
56 -ATA-AAATA-TAAATAATAAAT--AAATAAAATA-TAGGACATAA
*** * *
1930529 AATATATTTTAAAA-ATGAATATTATAAAAATTAATAATATAAATATAAATATATAAAAATAAAA
1 AAT-TAAAATAAAATAT--ATAATATAAAAA-T-ATAATA-AAAAATAAA-A-AT-AAAAT-AAA
* *
1930593 TATAAAATATTATGATAATAAATAAAATAAAATATATGACATTAA
56 -ATAAAATA-TA-AATAATAAAT-AAATAAAATATAGGACA-TAA
* ** * * * *
1930638 AAATATATTTAAGAAATGATATTATATAAAAAT-TAATAATATAAATATAAATATATTAAAATAA
1 AATTA-AAAT-A-AAAT-ATATAATATAAAAATATAATAA-A-AAATAAAAATAAAATAAAATAA
1930702 AATATAAA
60 AATATAAA
1930710 ATATTATAAT
Statistics
Matches: 411, Mismatches: 39, Indels: 82
0.77 0.07 0.15
Matches are distributed among these distances:
94 1 0.00
95 36 0.09
96 39 0.09
97 14 0.03
98 6 0.01
100 18 0.04
101 5 0.01
102 2 0.00
103 3 0.01
104 19 0.05
105 9 0.02
106 15 0.04
107 50 0.12
108 71 0.17
109 42 0.10
110 42 0.10
111 36 0.09
112 1 0.00
113 2 0.00
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (95 bp):
AATTAAAATAAAATATATAATATAAAAATATAATAAAAAATAAAAATAAAATAAAATAAAATATA
AATAATAAATAAATAAAATATAGGACATAA
Found at i:1930352 original size:111 final size:109
Alignment explanation
Indices: 1930233--1930801 Score: 767
Period size: 111 Copynumber: 5.2 Consensus size: 109
1930223 ATAAAATATA
* *
1930233 TAAT-ATAAAAATATATTAAAAAATAAAAATAAAATATAATAAATTATAAATAATAAAT-AAATA
1 TAATAATAAAAATATA--AATATATAAAAATAAAATATAA-AAATTAT-AATAATAAATAAAATA
1930296 AAATATATGACATTAAAAATATATTTAA-AATATGATATTATATAAAAT
62 AAATATATGACATTAAAAATATATTTAAGAA-ATGATATTATATAAAAT
* *
1930344 T-ATAATAAAAATATAAATATATTAAAATAAAATATAAATATTA-AATAATAAATAAAATAAAAT
1 TAATAATAAAAATATAAATATATAAAAATAAAATATAAAAATTATAATAATAAATAAAATAAAAT
1930407 ATAATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
66 AT-ATGACATTAAAAATATATTTAAGAAATGATATTATAT-AAAAT
1930453 TAATAATAAAAAT-TAAATATATTAAAAAT-AAATATATAAAATT-TAATAATAAATAAAAATAA
1 TAATAATAAAAATATAAATATA-TAAAAATAAAATATA-AAAATTATAATAATAAAT-AAAATAA
*
1930515 AATATTATG-TA-T-AAAATATATTTTAA-AAATGAATATTATA-AAAAT
63 AATA-TATGACATTAAAAATATA-TTTAAGAAATG-ATATTATATAAAAT
* *
1930560 TAATAATATAAATATAAATATATAAAAATAAAATATAAAATATTATGATAATAAATAAAATAAAA
1 TAATAATAAAAATATAAATATATAAAAATAAAATATAAAA-ATTATAATAATAAATAAAATAAAA
1930625 TATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
65 TATATGACATTAAAAATATATTTAAGAAATGATATTATAT-AAAAT
* *
1930671 TAATAATATAAATATAAATATATTAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAA
1 TAATAATAAAAATATAAATATATAAAAATAAAATATAAAA-ATTATAATAATAAAT-AAAATAAA
*
1930736 ATATATGATATTAAAAATAT-TTTAAGAAATGATATTATA-ATAAAT
64 ATATATGACATTAAAAATATATTTAAGAAATGATATTATATA-AAAT
1930781 TAATAAT-AAAATAT-AATATAT
1 TAATAATAAAAATATAAATATAT
1930802 TAAACTTATA
Statistics
Matches: 419, Mismatches: 14, Indels: 53
0.86 0.03 0.11
Matches are distributed among these distances:
106 10 0.02
107 42 0.10
108 89 0.21
109 87 0.21
110 59 0.14
111 104 0.25
112 28 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (109 bp):
TAATAATAAAAATATAAATATATAAAAATAAAATATAAAAATTATAATAATAAATAAAATAAAAT
ATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAT
Found at i:1930357 original size:19 final size:19
Alignment explanation
Indices: 1930335--1930401 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 19
1930325 ATATGATATT
1930335 ATATAAAATTATAATAAAA
1 ATATAAAATTATAATAAAA
*
1930354 ATAT-AAATATATTAAAATAAA
1 ATATAAAAT-TA-TAATA-AAA
*
1930375 ATATAAATATTA-AATAATA
1 ATATAAA-ATTATAATAAAA
1930394 A-ATAAAAT
1 ATATAAAAT
1930402 AAAATATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
17 2 0.05
18 9 0.22
19 9 0.22
20 7 0.17
21 7 0.17
22 4 0.10
23 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAAAATTATAATAAAA
Found at i:1930361 original size:6 final size:6
Alignment explanation
Indices: 1930347--1930410 Score: 57
Period size: 5 Copynumber: 11.2 Consensus size: 6
1930337 ATAAAATTAT
* *
1930347 AATAAA AATATA AATAT- ATTA-A AATA-A AATATA AATATTA AATAATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATA-TA AAT-ATA
1930394 AATA-A AATA-A AATATA A
1 AATATA AATATA AATATA A
1930411 TGACATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
5 21 0.42
6 18 0.36
7 10 0.20
8 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AATATA
Found at i:1930377 original size:77 final size:68
Alignment explanation
Indices: 1930216--1930410 Score: 182
Period size: 70 Copynumber: 2.7 Consensus size: 68
1930206 TAGGTAAACA
*
1930216 AATTAAAATAAAATATATAATATAAAAATATATTAAAAAATAAAAATAAAATATAATAAATTATA
1 AATTAAAATAAAATATATAATATAAAAATATATTAAAAAATAAAAATAAAATATAATAAAATATA
1930281 AAT
66 AAT
* * *
1930284 AATAAATAAATAAAATATATGACAT-TAAAAATATATTTAAAATATGATATTATATAAAATTATA
1 AAT-TA-AAATAAAATATAT-A-ATATAAAAATATA-TTAAAA-A--ATA-AAAATAAAA-TATA
1930348 ATAAAAATATAAAT
56 AT-AAAATATAAAT
* *
1930362 ATATTAAAATAAAATATA-AATAT-TAAATA-ATAAATAAAATAAAATATAA
1 A-ATTAAAATAAAATATATAATATAAAAATATATTAA-AAAATAAAA-ATAA
1930411 TGACATTAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
68 3 0.03
69 2 0.02
70 20 0.19
71 11 0.11
72 12 0.12
73 4 0.04
74 7 0.07
75 5 0.05
76 7 0.07
77 18 0.17
78 12 0.12
79 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (68 bp):
AATTAAAATAAAATATATAATATAAAAATATATTAAAAAATAAAAATAAAATATAATAAAATATA
AAT
Found at i:1930402 original size:19 final size:20
Alignment explanation
Indices: 1930335--1930402 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
1930325 ATATGATATT
1930335 ATATAAA-ATTATAATAA-AA
1 ATATAAATATTA-AATAATAA
*
1930354 ATATAAATATATTAA-AATAAA
1 ATATAAATAT-TAAATAAT-AA
1930375 ATATAAATATTAAATAATAA
1 ATATAAATATTAAATAATAA
1930395 ATA-AAATA
1 ATATAAATA
1930403 AAATATAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
19 14 0.33
20 12 0.29
21 16 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATAAATATTAAATAATAA
Found at i:1930463 original size:13 final size:14
Alignment explanation
Indices: 1930442--1930715 Score: 111
Period size: 15 Copynumber: 19.9 Consensus size: 14
1930432 GAAATGATAT
1930442 TATATAAAAATTAA
1 TATATAAAAATTAA
1930456 TA-ATAAAAATTAAA
1 TATATAAAAATT-AA
*
1930470 TATATTAAAAATAAA
1 TATA-TAAAAATTAA
*
1930485 TATATAAAATTTAA
1 TATATAAAAATTAA
1930499 TA-ATAAATAA--AA
1 TATATAAA-AATTAA
*
1930511 -ATA-AAATATT-A
1 TATATAAAAATTAA
*
1930522 TGTAT-AAAA-T-A
1 TATATAAAAATTAA
* *
1930533 TATTTTAAAAATGAA
1 TA-TATAAAAATTAA
1930548 TATTATAAAAATTAA
1 TA-TATAAAAATTAA
* *
1930563 TAATATAAATATAAA
1 T-ATATAAAAATTAA
1930578 TATATAAAAA-TAA
1 TATATAAAAATTAA
*
1930591 AATATAAAATATT-A
1 TATATAAAA-ATTAA
*
1930605 TGATA-ATAAA-TAA
1 T-ATATAAAAATTAA
*
1930618 -A-ATAAAATATATGA
1 TATATAAAA-AT-TAA
*
1930632 CAT-TAAAAA-T-A
1 TATATAAAAATTAA
* *
1930643 TATTTAAGAAATGATAT
1 TATATAA-AAAT--TAA
1930660 TATATAAAAATTAA
1 TATATAAAAATTAA
* *
1930674 TAATATAAATATAAA
1 T-ATATAAAAATTAA
*
1930689 TATATTAAAA-TAA
1 TATATAAAAATTAA
*
1930702 AATATAAAATATTA
1 TATATAAAA-ATTA
1930716 TAATAATAAA
Statistics
Matches: 195, Mismatches: 32, Indels: 65
0.67 0.11 0.22
Matches are distributed among these distances:
10 2 0.01
11 15 0.08
12 16 0.08
13 42 0.22
14 44 0.23
15 57 0.29
16 13 0.07
17 6 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
TATATAAAAATTAA
Found at i:1930465 original size:29 final size:30
Alignment explanation
Indices: 1930381--1930710 Score: 93
Period size: 29 Copynumber: 10.8 Consensus size: 30
1930371 TAAAATATAA
*
1930381 ATATTAAATAATAAATA-AAATAAAAT-ATAAT
1 ATATTAAA-AATAAATATATA-AAAATGA-AAT
* * *
1930412 GACATTAAAAAT--ATATTTAAGAAATGATAT
1 -ATATTAAAAATAAATATATAA-AAATGAAAT
* *
1930442 -TATATAAAAATTAATA-ATAAAAATTAAAT
1 ATAT-TAAAAATAAATATATAAAAATGAAAT
**
1930471 ATATTAAAAATAAATATAT-AAAATTTAAT
1 ATATTAAAAATAAATATATAAAAATGAAAT
* *** *
1930500 AATAAATAAAAATAAA-ATATTATGTATAAAAT
1 -AT-ATTAAAAATAAATATA-TAAAAATGAAAT
* *
1930532 ATATTTTAAAAATGAATATTATAAAAAT-TAAT
1 ATA--TTAAAAATAAATA-TATAAAAATGAAAT
*
1930564 A-ATATAAATATAAATATATAAAAAT-AAA-
1 ATAT-TAAAAATAAATATATAAAAATGAAAT
* * *
1930592 ATA-TAAAATATTATGATAATAAATAAAATAAAAT
1 ATATTAAAA-A-TA-AAT-ATATA-AAAATGAAAT
* * *
1930626 ATATGACATTAAA-AATATATTTAAGAAATGATAT
1 ATATTA-A--AAATAA-ATATATAA-AAATGAAAT
* *
1930660 -TATATAAAAATTAATAATATAAATAT-AAAT
1 ATAT-TAAAAATAAAT-ATATAAAAATGAAAT
1930690 ATATT-AAAATAAA-ATATAAAA
1 ATATTAAAAATAAATATATAAAA
1930711 TATTATAATA
Statistics
Matches: 222, Mismatches: 41, Indels: 75
0.66 0.12 0.22
Matches are distributed among these distances:
27 11 0.05
28 4 0.02
29 60 0.27
30 37 0.17
31 37 0.17
32 36 0.16
33 13 0.06
34 16 0.07
35 4 0.02
36 1 0.00
37 1 0.00
38 2 0.01
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
ATATTAAAAATAAATATATAAAAATGAAAT
Found at i:1930528 original size:27 final size:25
Alignment explanation
Indices: 1930457--1930739 Score: 118
Period size: 28 Copynumber: 10.6 Consensus size: 25
1930447 AAAAATTAAT
*
1930457 AATAAAAATTAAATA-TA-T-TAAA
1 AATAAAAATAAAATATTATTATAAA
1930479 AATAAATATATAAAAT-TTA--ATAATA
1 AATAAA-A-ATAAAATATTATTATAA-A
1930504 AATAAAAATAAAATATTATGTAT-AA
1 AATAAAAATAAAATATTAT-TATAAA
*** *
1930529 AATATATTTTAAAAATGAATATTATAAA
1 AATA-AAAAT-AAAAT-ATTATTATAAA
* *
1930557 AATTAATAATATAAATATAAATATATAAA
1 AA-TAAAAATA-AAATAT-TAT-TATAAA
*
1930586 AATAAAATATAAAATATTATGATAATA
1 AATAAAA-ATAAAATATTATTATAA-A
1930613 AAT-AAAATAAAATATATGACATTA-AAA
1 AATAAAAATAAAATAT-T---ATTATAAA
** *
1930640 ATATATTTAAGAAATGATATTA-TATAAA
1 A-ATA-AAAATAAA--ATATTATTATAAA
* * *
1930668 AATTAATAATATAAATATAAATATATTAA
1 AA-TAAAAATA-AAATAT-TAT-TATAAA
*
1930697 AATAAAATATAAAATATTATAATAATA
1 AATAAAA-ATAAAATATTATTATAA-A
1930724 AATAAAAATAAAATAT
1 AATAAAAATAAAATAT
1930740 ATGATATTAA
Statistics
Matches: 201, Mismatches: 24, Indels: 68
0.69 0.08 0.23
Matches are distributed among these distances:
22 6 0.03
23 8 0.04
24 15 0.07
25 21 0.10
26 27 0.13
27 38 0.19
28 50 0.25
29 26 0.13
30 5 0.02
31 1 0.00
32 4 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
AATAAAAATAAAATATTATTATAAA
Found at i:1930645 original size:218 final size:217
Alignment explanation
Indices: 1930256--1930801 Score: 835
Period size: 218 Copynumber: 2.5 Consensus size: 217
1930246 TATTAAAAAA
*
1930256 TAAAAATAAAATATAATAAATTATAAATAATAAAT--AAATAAAATATATGACATTAAAAATATA
1 TAAAAATAAAATATAA-AAATTAT-AATAATAAATAAAAATAAAATATATGATATTAAAAATAT-
*
1930319 TTTAAAATATGATATTATATAAAATT-ATAATAAAAATATAAATATATTAAAATAAAATATAAAT
63 TTTAAAA-ATGATATTATA-AAAATTAATAAT-AAAATATAAATATATAAAAATAAAATATAAAT
1930383 ATTAAATAATAAATAAAATAAAATATAATGACATTAAAAATATATTTAAGAAATGATATTATATA
125 ATTAAATAATAAATAAAATAAAATATAATGACATTAAAAATATATTTAAGAAATGATATTATATA
1930448 AAAATTAATAATAAAAAT-TAAATATAT
190 AAAATTAATAATAAAAATATAAATATAT
1930475 TAAAAAT-AAATATATAAAATT-TAATAATAAATAAAAATAAAATATTATG-TA-TAAAATATAT
1 TAAAAATAAAATATA-AAAATTATAATAATAAATAAAAATAAAATA-TATGATATTAAAA-ATAT
1930536 TTTAAAAATGAATATTATAAAAATTAATAATATAAATATAAATATATAAAAATAAAATATAAAAT
63 TTTAAAAATG-ATATTATAAAAATTAATAATA-AAATATAAATATATAAAAATAAAATAT-AAAT
*
1930601 ATTATGATAATAAATAAAATAAAATAT-ATGACATTAAAAATATATTTAAGAAATGATATTATAT
125 ATTA-AATAATAAATAAAATAAAATATAATGACATTAAAAATATATTTAAGAAATGATATTATAT
*
1930665 AAAAATTAATAATATAAATATAAATATAT
189 AAAAATTAATAATAAAAATATAAATATAT
1930694 T-AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATTT
1 TAAAAATAAAATATAAAA-ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATTT
1930758 TAAGAAATGATATTATAATAAATTAATAATAAAATAT-AATATAT
65 TAA-AAATGATATTATAA-AAATTAATAATAAAATATAAATATAT
1930802 TAAACTTATA
Statistics
Matches: 305, Mismatches: 4, Indels: 36
0.88 0.01 0.10
Matches are distributed among these distances:
216 20 0.07
217 52 0.17
218 98 0.32
219 64 0.21
220 49 0.16
221 22 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (217 bp):
TAAAAATAAAATATAAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATTTT
AAAAATGATATTATAAAAATTAATAATAAAATATAAATATATAAAAATAAAATATAAATATTAAA
TAATAAATAAAATAAAATATAATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAATT
AATAATAAAAATATAAATATAT
Found at i:1930686 original size:6 final size:6
Alignment explanation
Indices: 1930675--1930740 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
1930665 AAAAATTAAT
*
1930675 AATATA AATATA AATAT- ATTA-A AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
1930724 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
1930741 TGATATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
5 16 0.32
6 18 0.36
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:1931003 original size:15 final size:15
Alignment explanation
Indices: 1930950--1931008 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
1930940 TGTTATTTTC
* *
1930950 CCTGTAATCACATTG
1 CCTGCAATCACATTA
* *
1930965 CTTACAATCACATTA
1 CCTGCAATCACATTA
*
1930980 CTTGCAATCACATTA
1 CCTGCAATCACATTA
*
1930995 CCTGTAATCACATT
1 CCTGCAATCACATT
1931009 GCATTGTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:1937393 original size:41 final size:42
Alignment explanation
Indices: 1937333--1937441 Score: 98
Period size: 41 Copynumber: 2.6 Consensus size: 42
1937323 TGATTTATTT
** * **
1937333 TATTTTATTTTATTTTTTAAATATTAACA-TCTTTAAATATTAA
1 TATTTTA-TTTATAATTTAAATATTAACAGT-TTAAAATACCAA
* *
1937376 TATTTT-TTTATAATTT-AATCATTAATAGTTTAAAATACCGA
1 TATTTTATTTATAATTTAAAT-ATTAACAGTTTAAAATACCAA
*
1937417 TATTTTATTTGTAATTTAAATATTA
1 TATTTTATTTATAATTTAAATATTA
1937442 TTCTGATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
40 3 0.06
41 28 0.52
42 14 0.26
43 9 0.17
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (42 bp):
TATTTTATTTATAATTTAAATATTAACAGTTTAAAATACCAA
Found at i:1937467 original size:17 final size:16
Alignment explanation
Indices: 1937418--1937469 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1937408 AAATACCGAT
1937418 ATTTTATTTGTAATTTAA
1 ATTTTA-TTGTAA-TTAA
* * *
1937436 ATATTATTCTGATTAA
1 ATTTTATTGTAATTAA
1937452 AGTTTTATTGTAATTAA
1 A-TTTTATTGTAATTAA
1937469 A
1 A
1937470 ATATTAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 5 0.19
17 17 0.63
18 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (16 bp):
ATTTTATTGTAATTAA
Found at i:1937816 original size:16 final size:15
Alignment explanation
Indices: 1937757--1937816 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
1937747 ATTTTCATCA
*
1937757 AAAATTTAATATATT
1 AAAATTTAATATTTT
**
1937772 AATAATTTAATAAGTT
1 AA-AATTTAATATTTT
*
1937788 AAACTTTAATATTTT
1 AAAATTTAATATTTT
1937803 AAAATATTAATATT
1 AAAAT-TTAATATT
1937817 CTTATTTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 16 0.43
16 21 0.57
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AAAATTTAATATTTT
Found at i:1937920 original size:25 final size:23
Alignment explanation
Indices: 1937865--1937920 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
1937855 AAAATAATAA
*
1937865 TATTTT-TTAAATATTAATTTTT
1 TATTTTATAAAATATTAATTTTT
1937887 TATAATTTATAAAATATTTAACTTTTT
1 TAT--TTTATAAAATA-TTAA-TTTTT
1937914 TATTTTA
1 TATTTTA
1937921 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 3 0.11
24 3 0.11
25 10 0.36
26 4 0.14
27 8 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTATAAAATATTAATTTTT
Found at i:1939838 original size:24 final size:24
Alignment explanation
Indices: 1939811--1939860 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1939801 AATAATATGA
*
1939811 TTAGACACTAATGATTGGAAATGT
1 TTAGACACTAATGATCGGAAATGT
1939835 TTAGACACTAATGATCGGAAATGT
1 TTAGACACTAATGATCGGAAATGT
1939859 TT
1 TT
1939861 TGTTATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (24 bp):
TTAGACACTAATGATCGGAAATGT
Found at i:1942487 original size:40 final size:39
Alignment explanation
Indices: 1942440--1942557 Score: 113
Period size: 40 Copynumber: 3.1 Consensus size: 39
1942430 AATATAGGTA
*
1942440 AAAGAAATTAAAATAAAATATATAACATAAAAAATATATT
1 AAAGAAATAAAAATAAAATATATAACAT-AAAAATATATT
* * * *
1942480 AAAGAAATGAAAACAAAATATATAAGAT-----TATAAT
1 AAAGAAATAAAAATAAAATATATAACATAAAAATATATT
*
1942514 -AAGAAATAAAAATAAAATATATGACATTAAAAATATATT
1 AAAGAAATAAAAATAAAATATATAACA-TAAAAATATATT
*
1942553 TAAGA
1 AAAGA
1942558 GATGATATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
33 22 0.35
34 6 0.10
39 5 0.08
40 29 0.47
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (39 bp):
AAAGAAATAAAAATAAAATATATAACATAAAAATATATT
Found at i:1943722 original size:93 final size:93
Alignment explanation
Indices: 1943617--1943804 Score: 349
Period size: 93 Copynumber: 2.0 Consensus size: 93
1943607 AAAGCCAACC
1943617 ATATATAAGTGACATTGAACTGAAGGATAAAATGTACTTCCAAATAGAAAGGTGTAGCACCTCGT
1 ATATATAAGTGACATTGAACTGAAGGATAAAATGTACTTCCAAATAGAAAGGTGTAGCACCTCGT
*
1943682 ATCCTCGTAGAGGAGTCAATAAAATTGT
66 ACCCTCGTAGAGGAGTCAATAAAATTGT
1943710 ATATATAAGTGACATTGAACTGAAGGATAAAATGTACTTCCAAATAGAAAGGTGTAGCACCTCGT
1 ATATATAAGTGACATTGAACTGAAGGATAAAATGTACTTCCAAATAGAAAGGTGTAGCACCTCGT
* *
1943775 ACCCTTGTATAGGAGTCAATAAAATTGT
66 ACCCTCGTAGAGGAGTCAATAAAATTGT
1943803 AT
1 AT
1943805 TGGTAAGACG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (93 bp):
ATATATAAGTGACATTGAACTGAAGGATAAAATGTACTTCCAAATAGAAAGGTGTAGCACCTCGT
ACCCTCGTAGAGGAGTCAATAAAATTGT
Found at i:1944065 original size:19 final size:19
Alignment explanation
Indices: 1944022--1944067 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1944012 AGAATTTTGA
** *
1944022 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
1944041 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
*
1944060 ATTAAAAT
1 AATAAAAT
1944068 TTTATCTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:1959811 original size:2 final size:2
Alignment explanation
Indices: 1959804--1959833 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1959794 TGTGGCTGAG
1959804 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
1959834 CACACACACA
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):
TA
Found at i:1959838 original size:2 final size:2
Alignment explanation
Indices: 1959833--1959857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1959823 ATATATATAT
1959833 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1959858 TATATATAAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1975863 original size:21 final size:18
Alignment explanation
Indices: 1975829--1975870 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 18
1975819 AAGCCATTCA
1975829 ATATAATTTCAGCATATAT
1 ATATAATTTCAGCATA-AT
1975848 ATATAATATCTCAGCATAAT
1 ATATAAT-T-TCAGCATAAT
1975868 ATA
1 ATA
1975871 AACCACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 8 0.38
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (18 bp):
ATATAATTTCAGCATAAT
Found at i:1983732 original size:20 final size:20
Alignment explanation
Indices: 1983705--1983752 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1983695 TACACAACAA
1983705 TCTTCCTTTAATTGGTTAGC
1 TCTTCCTTTAATTGGTTAGC
* *
1983725 TTTTCCTTTAATTGGTTTGC
1 TCTTCCTTTAATTGGTTAGC
1983745 TCTTCCTT
1 TCTTCCTT
1983753 AAACTGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.10, C:0.21, G:0.12, T:0.56
Consensus pattern (20 bp):
TCTTCCTTTAATTGGTTAGC
Found at i:1988737 original size:11 final size:11
Alignment explanation
Indices: 1988708--1988757 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1988698 GGCTAGGCTT
*
1988708 TTCTTTTTCTC
1 TTCTTTTTTTC
1988719 TT-TATTTTTT-
1 TTCT-TTTTTTC
1988729 TTCTTTTTTTC
1 TTCTTTTTTTC
*
1988740 TTCTTATTCTTC
1 TTCTT-TTTTTC
1988752 TTCTTT
1 TTCTTT
1988758 CATCTCCAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 9 0.27
11 14 0.42
12 10 0.30
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:1988746 original size:23 final size:21
Alignment explanation
Indices: 1988709--1988757 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
1988699 GCTAGGCTTT
*
1988709 TCTTTTTCTCTTTATTTTTTT
1 TCTTTTTCTCTTTATTCTTTT
* *
1988730 TCTTTTTTTCTTCTTATTCTTCT
1 TCTTTTTCTC-T-TTATTCTTTT
1988753 TCTTT
1 TCTTT
1988758 CATCTCCAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.39
22 1 0.04
23 13 0.57
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (21 bp):
TCTTTTTCTCTTTATTCTTTT
Found at i:1994732 original size:12 final size:12
Alignment explanation
Indices: 1994702--1994735 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1994692 ACATTGATAT
* *
1994702 TTTTAGGTTCAG
1 TTTTAGTTTCAA
1994714 TTTTAGTTTCAA
1 TTTTAGTTTCAA
1994726 TTTTAGTTTC
1 TTTTAGTTTC
1994736 TTCAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.59
Consensus pattern (12 bp):
TTTTAGTTTCAA
Found at i:1996719 original size:11 final size:11
Alignment explanation
Indices: 1996703--1996729 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1996693 AACAAATGCA
1996703 AGTAATATAGT
1 AGTAATATAGT
1996714 AGTAATATAGT
1 AGTAATATAGT
1996725 AGTAA
1 AGTAA
1996730 GAAAAGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (11 bp):
AGTAATATAGT
Found at i:1999823 original size:18 final size:18
Alignment explanation
Indices: 1999800--1999834 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1999790 TAATTGGTTT
*
1999800 CTTTAGCTTGTTTTCATC
1 CTTTAGCTTGTTCTCATC
*
1999818 CTTTAGGTTGTTCTCAT
1 CTTTAGCTTGTTCTCAT
1999835 TTTAGTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.54
Consensus pattern (18 bp):
CTTTAGCTTGTTCTCATC
Found at i:2001975 original size:19 final size:16
Alignment explanation
Indices: 2001946--2001991 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 16
2001936 ACTCAATTTC
*
2001946 AAATGATTAATTAAACT
1 AAATAATTAATT-AACT
2001963 AATAATAATTAATTAACT
1 -A-AATAATTAATTAACT
2001981 AAATAATTAAT
1 AAATAATTAAT
2001992 AAAGAACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 5 0.19
19 10 0.38
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (16 bp):
AAATAATTAATTAACT
Found at i:2006965 original size:33 final size:31
Alignment explanation
Indices: 2006924--2007022 Score: 99
Period size: 33 Copynumber: 3.1 Consensus size: 31
2006914 GTTTTAGATG
2006924 CTTTATATTTGTTTCGACTTTGGTGTTTGGA
1 CTTTATATTTGTTTCGACTTTGGTGTTTGGA
* * **
2006955 CTCTTGATATTCGTTTCGACATAAGTGTTTGGA
1 CT-TT-ATATTTGTTTCGACTTTGGTGTTTGGA
* * * *
2006988 CTTTTTTTGTTGTTTCGACTTTGGTATTTAGA
1 CTTTATAT-TTGTTTCGACTTTGGTGTTTGGA
2007020 CTT
1 CTT
2007023 GATGTATTAG
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
31 4 0.08
32 24 0.45
33 25 0.47
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53
Consensus pattern (31 bp):
CTTTATATTTGTTTCGACTTTGGTGTTTGGA
Found at i:2012519 original size:14 final size:15
Alignment explanation
Indices: 2012482--2012522 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
2012472 CAAAAAATTG
2012482 AAAAGAAAATAACAT
1 AAAAGAAAATAACAT
* *
2012497 AATACAAAA-AACAT
1 AAAAGAAAATAACAT
2012511 AAAAGAAAATAA
1 AAAAGAAAATAA
2012523 AAGCATTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAAGAAAATAACAT
Found at i:2013689 original size:12 final size:11
Alignment explanation
Indices: 2013659--2013700 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
2013649 GAACTTGATG
*
2013659 AAATCATTA-A
1 AAATAATTATA
2013669 AAATAATTATA
1 AAATAATTATA
*
2013680 CAATTAATTATA
1 -AAATAATTATA
2013692 AAATAATTA
1 AAATAATTA
2013701 ATTTATTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.30
11 9 0.33
12 10 0.37
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATAATTATA
Found at i:2014358 original size:54 final size:53
Alignment explanation
Indices: 2014232--2014381 Score: 176
Period size: 54 Copynumber: 2.8 Consensus size: 53
2014222 AGAAGATTTC
*
2014232 TGAAGACGAAGTTCTCAAGTCTAGTACGTGATCAAGATCAAGTCCCAAGACCCT
1 TGAAG-CGAAGTTCTCAAGTCTAGTTCGTGATCAAGATCAAGTCCCAAGACCCT
* * * *
2014286 TGAAGCAAAGTTCTCAAGTTTAGTTCATGATCAAGATCAAGTCATCCTA-ACCCT
1 TGAAGCGAAGTTCTCAAGTCTAGTTCGTGATCAAGATCAAGTC--CCAAGACCCT
* * * * *
2014340 TGAAGTGAAGTTCCCAAGTCCAGTTTGCGATCAAGATCAAGT
1 TGAAGCGAAGTTCTCAAGTCTAGTTCGTGATCAAGATCAAGT
2014382 TGCTTAGAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 34 0.42
54 44 0.54
55 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (53 bp):
TGAAGCGAAGTTCTCAAGTCTAGTTCGTGATCAAGATCAAGTCCCAAGACCCT
Found at i:2017437 original size:16 final size:16
Alignment explanation
Indices: 2017413--2017443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2017403 GTGTGAGCTT
2017413 GCAGCGATAGTGGTAA
1 GCAGCGATAGTGGTAA
*
2017429 GCAGGGATAGTGGTA
1 GCAGCGATAGTGGTA
2017444 TTAGTCCTAT
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:0.29, C:0.10, G:0.42, T:0.19
Consensus pattern (16 bp):
GCAGCGATAGTGGTAA
Found at i:2018384 original size:11 final size:11
Alignment explanation
Indices: 2018368--2018399 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
2018358 ACCCAATGAT
2018368 TAGCCTATGTG
1 TAGCCTATGTG
2018379 TAGCCTTATGTG
1 TAGCC-TATGTG
2018391 TAGCCTATG
1 TAGCCTATG
2018400 ATACGAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (11 bp):
TAGCCTATGTG
Found at i:2029994 original size:15 final size:15
Alignment explanation
Indices: 2029971--2030012 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2029961 CACACCTTAA
* *
2029971 TTAATTTAAATATTT
1 TTAAATTAAATAATT
*
2029986 TTAAATTAAACAATT
1 TTAAATTAAATAATT
2030001 TTAAATTAAATA
1 TTAAATTAAATA
2030013 GTATTACTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAATTAAATAATT
Found at i:2034680 original size:2 final size:2
Alignment explanation
Indices: 2034673--2034700 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2034663 AAAGATTTTC
2034673 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
2034701 CAAACAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2036753 original size:26 final size:26
Alignment explanation
Indices: 2036713--2036767 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
2036703 TAGGTTAAGG
2036713 TATCCATCCACTTCTAATGGTAAAAT
1 TATCCATCCACTTCTAATGGTAAAAT
* *
2036739 TATCCATCCATTTCTGATGGTAAAAT
1 TATCCATCCACTTCTAATGGTAAAAT
2036765 TAT
1 TAT
2036768 TCATAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (26 bp):
TATCCATCCACTTCTAATGGTAAAAT
Found at i:2037558 original size:16 final size:17
Alignment explanation
Indices: 2037537--2037573 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2037527 TAGATTAAAT
2037537 TCTAATCTT-CATCC-AA
1 TCTAAT-TTACATCCAAA
2037553 TCTAATTTACATCCAAA
1 TCTAATTTACATCCAAA
2037570 TCTA
1 TCTA
2037574 GGTATACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 11 0.58
17 6 0.32
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTAATTTACATCCAAA
Found at i:2039878 original size:26 final size:26
Alignment explanation
Indices: 2039839--2039891 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2039829 TTGAGGTATC
2039839 CATCCACTTATGGTGACAAAATTATT
1 CATCCACTTATGGTGACAAAATTATT
* * **
2039865 CATCTACTTTTGGTGGTAAAATTATT
1 CATCCACTTATGGTGACAAAATTATT
2039891 C
1 C
2039892 TTAGAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (26 bp):
CATCCACTTATGGTGACAAAATTATT
Found at i:2043925 original size:26 final size:25
Alignment explanation
Indices: 2043891--2043941 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2043881 TCAAAAGCAC
*
2043891 AACCAATCAAAACAACAAGACTCCACA
1 AACCAATCAAAA-AACAAAAC-CCACA
2043918 AACC-ATCAAAAAACAAAACCCACA
1 AACCAATCAAAAAACAAAACCCACA
2043942 GCTCAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 7 0.30
26 7 0.30
27 4 0.17
ACGTcount: A:0.59, C:0.33, G:0.02, T:0.06
Consensus pattern (25 bp):
AACCAATCAAAAAACAAAACCCACA
Found at i:2048005 original size:12 final size:13
Alignment explanation
Indices: 2047986--2048021 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
2047976 CCAGAATAGT
2047986 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
2047999 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
2048010 TCTTGCTGCCTC
1 TCTTGCTGCCTC
2048022 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:2048708 original size:21 final size:22
Alignment explanation
Indices: 2048673--2048716 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2048663 CTCTTAAAGT
2048673 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
2048695 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
2048716 A
1 A
2048717 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:2068876 original size:2 final size:2
Alignment explanation
Indices: 2068869--2068919 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2068859 GCTGTTGTGT
2068869 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
2068911 TA TA TA TA T
1 TA TA TA TA T
2068920 GCAGTTTTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2071839 original size:23 final size:24
Alignment explanation
Indices: 2071786--2071840 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
2071776 CTTTTTTTTA
**
2071786 TTTTTTTATTCTTCAAAATTCTAT
1 TTTTTTTATTCTTCAAAATTAAAT
*
2071810 TTATTTTATTCTT-AAAATTAAAT
1 TTTTTTTATTCTTCAAAATTAAAT
2071833 TTTTTTTA
1 TTTTTTTA
2071841 AAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTTTTATTCTTCAAAATTAAAT
Found at i:2072853 original size:15 final size:15
Alignment explanation
Indices: 2072826--2072871 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2072816 AACGGTAAAA
2072826 TTTTTATTT-TATTT
1 TTTTTATTTATATTT
*
2072840 TTTTTATTTATATTA
1 TTTTTATTTATATTT
* *
2072855 TTATTATTTATGTTT
1 TTTTTATTTATATTT
2072870 TT
1 TT
2072872 CAATTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTTATTTATATTT
Found at i:2073032 original size:15 final size:16
Alignment explanation
Indices: 2073012--2073041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2073002 CAGTTATGTA
2073012 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
2073027 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
2073042 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:2074501 original size:2 final size:2
Alignment explanation
Indices: 2074494--2074521 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2074484 TAGAACGTGT
2074494 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
2074522 GGTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2075772 original size:21 final size:23
Alignment explanation
Indices: 2075748--2075791 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
2075738 AAAACAAAAA
*
2075748 GTATCAATATATG-A-TTCAAAT
1 GTATCAATACATGCATTTCAAAT
*
2075769 GTATCGATACATGCATTTCAAAT
1 GTATCAATACATGCATTTCAAAT
2075792 TTCAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (23 bp):
GTATCAATACATGCATTTCAAAT
Found at i:2077402 original size:2 final size:2
Alignment explanation
Indices: 2077395--2077420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2077385 CAAGCATTTG
2077395 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
2077421 TAATAAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2081503 original size:35 final size:32
Alignment explanation
Indices: 2081464--2081529 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 32
2081454 AATCAAAAAA
2081464 TAAAATATAA-AAAATTAAAATTTATATAATATAGG
1 TAAAATA-AATAAAA-TAAAA--TATATAATATAGG
2081499 TAAAATAAATTAAAATAAAATATATAATATA
1 TAAAATAAA-TAAAATAAAATATATAATATA
2081530 AAAATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 11 0.38
34 2 0.07
35 12 0.41
36 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (32 bp):
TAAAATAAATAAAATAAAATATATAATATAGG
Found at i:2081530 original size:24 final size:23
Alignment explanation
Indices: 2081420--2081564 Score: 54
Period size: 26 Copynumber: 6.2 Consensus size: 23
2081410 TATAATTAAA
*
2081420 ATAAAAAATATTAAAATAAAATAT
1 ATAATAAA-ATTAAAATAAAATAT
* *
2081444 ATAATATAAGAATCAAAA-AATAAAAT
1 AT-A-ATAA-AATTAAAATAA-AATAT
*
2081470 ATAA-AAAATTAAAAT---TTAT
1 ATAATAAAATTAAAATAAAATAT
* **
2081489 ATAATATAGGTAAAAT-AAAT-T
1 ATAATAAAATTAAAATAAAATAT
*
2081510 AAAATAAAATATATAATATAAAAATAT
1 ATAATAAAAT-TA-AA-AT-AAAATAT
*
2081537 ATTAA-AGAAATAAAAATAAAATAT
1 A-TAATA-AAATTAAAATAAAATAT
2081561 ATAA
1 ATAA
2081565 GATTATAATA
Statistics
Matches: 89, Mismatches: 16, Indels: 33
0.64 0.12 0.24
Matches are distributed among these distances:
19 6 0.07
20 8 0.09
21 7 0.08
22 10 0.11
23 7 0.08
24 13 0.15
25 6 0.07
26 21 0.24
27 5 0.06
28 6 0.07
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (23 bp):
ATAATAAAATTAAAATAAAATAT
Found at i:2081548 original size:33 final size:34
Alignment explanation
Indices: 2081511--2081660 Score: 102
Period size: 33 Copynumber: 4.4 Consensus size: 34
2081501 AAATAAATTA
*
2081511 AAATAAAATATATAATATAAAAAT-ATATTAAAG
1 AAATAAAATATATAATATAAAAATAATAATAAAG
*
2081544 AAATAAAA-ATAAAATATATAAGATTATAATAATAAATG
1 AAATAAAATATATAATATA-AA-A--ATAATAATAAA-G
* *
2081582 AAAATAAAATATATGACAT-TAAAAAT-ATATTTAAG
1 -AAATAAAATATAT-A-ATATAAAAATAATAATAAAG
*
2081617 AAAT--GATAT-T-ATATAAAAATTAATAATAAA-
1 AAATAAAATATATAATATAAAAA-TAATAATAAAG
2081647 AAATATAAATATAT
1 AAATA-AAATATAT
2081661 TAAACTTGTA
Statistics
Matches: 91, Mismatches: 9, Indels: 33
0.68 0.07 0.25
Matches are distributed among these distances:
28 2 0.02
29 6 0.07
30 5 0.05
31 7 0.08
32 13 0.14
33 14 0.15
34 6 0.07
35 1 0.01
36 8 0.09
37 9 0.10
38 1 0.01
39 9 0.10
40 5 0.05
41 3 0.03
42 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (34 bp):
AAATAAAATATATAATATAAAAATAATAATAAAG
Found at i:2081548 original size:78 final size:73
Alignment explanation
Indices: 2081420--2081620 Score: 191
Period size: 78 Copynumber: 2.7 Consensus size: 73
2081410 TATAATTAAA
* * *
2081420 ATAAAA-AATATTAAAATAAAATATATAATATAAGAATCA-A-AAAATAAAATATAAAAAATTAA
1 ATAAAATAA-ATTAAAATAAAATATATAATATAAAAAT-ATATTAAA-GAAATAT-AAAAA-TAA
*
2081482 AATTTATATA-ATAT
61 AATATATA-AGAT-T
2081496 AGGTAAAATAAATTAAAATAAAATATATAATATAAAAATATATTAAAG-AA-ATAAAAATAAAAT
1 A--TAAAATAAATTAAAATAAAATATATAATATAAAAATATATTAAAGAAATATAAAAATAAAAT
2081559 ATATAAGATT
64 ATATAAGATT
* *
2081569 ATAATAATAAATGAAAATAAAATATATGACAT-TAAAAATATATTTAAGAAAT
1 ATAA-AATAAATTAAAATAAAATATAT-A-ATATAAAAATATATTAAAGAAAT
2081621 GATATTATAT
Statistics
Matches: 108, Mismatches: 6, Indels: 23
0.79 0.04 0.17
Matches are distributed among these distances:
71 3 0.03
72 21 0.19
73 19 0.18
74 16 0.15
75 5 0.05
76 3 0.03
77 3 0.03
78 33 0.31
79 5 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (73 bp):
ATAAAATAAATTAAAATAAAATATATAATATAAAAATATATTAAAGAAATATAAAAATAAAATAT
ATAAGATT
Found at i:2081561 original size:39 final size:38
Alignment explanation
Indices: 2081505--2081620 Score: 109
Period size: 39 Copynumber: 3.1 Consensus size: 38
2081495 TAGGTAAAAT
*
2081505 AAATTAAAATAAAATATATAATATAAAAATATATTAAAG
1 AAATAAAAATAAAATATATAATATAAAAATATATT-AAG
* * *
2081544 AAATAAAAATAAAATATATAAGAT-----TATAATAAT
1 AAATAAAAATAAAATATATAATATAAAAATATATTAAG
*
2081577 AAATGAAAATAAAATATATGACAT-TAAAAATATATTTAAG
1 AAATAAAAATAAAATATAT-A-ATATAAAAATATA-TTAAG
2081617 AAAT
1 AAAT
2081621 GATATTATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
33 20 0.33
34 7 0.11
35 1 0.02
39 26 0.43
40 7 0.11
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (38 bp):
AAATAAAAATAAAATATATAATATAAAAATATATTAAG
Found at i:2081597 original size:15 final size:14
Alignment explanation
Indices: 2081416--2081595 Score: 93
Period size: 15 Copynumber: 12.1 Consensus size: 14
2081406 CTATTATAAT
*
2081416 TAAAATAAAAAATA
1 TAAAATAAAATATA
2081430 TTAAAATAAAATATA
1 -TAAAATAAAATATA
*
2081445 TAATATAAGAATCA-A
1 TAAAATAA-AAT-ATA
2081460 -AAAATAAAATATA
1 TAAAATAAAATATA
*
2081473 AAAAATTAAAATTTATA
1 TAAAA-TAAAA--TATA
*
2081490 TAATATAGGTAAAATAAA
1 TAA-A-A--TAAAATATA
2081508 TTAAAATAAAATATA
1 -TAAAATAAAATATA
*
2081523 TAATATAAAA-ATA
1 TAAAATAAAATATA
* *
2081536 T--ATTAAAGAAATA
1 TAAAATAAA-ATATA
2081549 -AAAATAAAATATA
1 TAAAATAAAATATA
*
2081562 TAAGATTATAATAATAAA
1 TAA-A--ATAA-AATATA
2081580 TGAAAATAAAATATA
1 T-AAAATAAAATATA
2081595 T
1 T
2081596 GACATTAAAA
Statistics
Matches: 130, Mismatches: 14, Indels: 42
0.70 0.08 0.23
Matches are distributed among these distances:
11 4 0.03
12 2 0.02
13 15 0.12
14 33 0.25
15 37 0.28
16 5 0.04
17 11 0.08
18 12 0.09
19 6 0.05
20 5 0.04
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAAATAAAATATA
Found at i:2081831 original size:15 final size:15
Alignment explanation
Indices: 2081810--2081854 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
2081800 GTTATTTTCT
2081810 CTGCAATCACATTAC
1 CTGCAATCACATTAC
*
2081825 TTGCAATCACATTAC
1 CTGCAATCACATTAC
*
2081840 CTGTAATCACATTAC
1 CTGCAATCACATTAC
2081855 ATTGTAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (15 bp):
CTGCAATCACATTAC
Found at i:2085077 original size:2 final size:2
Alignment explanation
Indices: 2085070--2085094 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2085060 TCACATTATC
2085070 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
2085095 CACACTTATA
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:2097806 original size:2 final size:2
Alignment explanation
Indices: 2097799--2097829 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2097789 GAACGAAATA
2097799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2097830 ATTTGATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2098954 original size:19 final size:17
Alignment explanation
Indices: 2098930--2098969 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
2098920 CTTAAGTCTC
2098930 AATATTTTATAATCTAAAT
1 AATATTTTA-AAT-TAAAT
*
2098949 AATATTTTAAATTAATT
1 AATATTTTAAATTAAAT
2098966 AATA
1 AATA
2098970 AAAAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTTTAAATTAAAT
Found at i:2099332 original size:30 final size:30
Alignment explanation
Indices: 2099276--2099339 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
2099266 GAAAGGACAT
*
2099276 TAATAAAATAGAAAAAGCCTAAAATAAAAA
1 TAATAAAATAGAAAAAGCATAAAATAAAAA
* *
2099306 TAATAAAATAGAAAATG-ATAATAATAATAA
1 TAATAAAATAGAAAAAGCATAA-AATAAAAA
2099336 TAAT
1 TAAT
2099340 GAACATAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.23
Consensus pattern (30 bp):
TAATAAAATAGAAAAAGCATAAAATAAAAA
Found at i:2104128 original size:20 final size:20
Alignment explanation
Indices: 2104072--2104120 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
2104062 TAACTCTAAT
2104072 GCTTTAATCAGTTAAAGTAA
1 GCTTTAATCAGTTAAAGTAA
2104092 GCTTTAATCAGTTAAAGTAA
1 GCTTTAATCAGTTAAAGTAA
2104112 GCTTTAATC
1 GCTTTAATC
2104121 GATTAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (20 bp):
GCTTTAATCAGTTAAAGTAA
Found at i:2110348 original size:20 final size:20
Alignment explanation
Indices: 2110292--2110358 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
2110282 CTAACTCAAT
*
2110292 AATAA-TTAAACTAAAAGTAA
1 AATAACTTAAACTAAAA-CAA
* *
2110312 ATTATCATTAAACTAAAACAA
1 AATAAC-TTAAACTAAAACAA
* *
2110333 AATAACTTAAATTAAATCAA
1 AATAACTTAAACTAAAACAA
*
2110353 CATAAC
1 AATAAC
2110359 ATGATTTACT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 20 0.54
21 6 0.16
22 11 0.30
ACGTcount: A:0.60, C:0.12, G:0.01, T:0.27
Consensus pattern (20 bp):
AATAACTTAAACTAAAACAA
Found at i:2113156 original size:13 final size:13
Alignment explanation
Indices: 2113115--2113156 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2113105 GATAAGCAAA
2113115 GAGGAATTTAATT
1 GAGGAATTTAATT
**
2113128 GAGG-ATCGAATAT
1 GAGGAATTTAAT-T
2113141 GAGGAATTTAATT
1 GAGGAATTTAATT
2113154 GAG
1 GAG
2113157 TACCAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 5 0.22
13 13 0.57
14 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (13 bp):
GAGGAATTTAATT
Found at i:2113165 original size:26 final size:26
Alignment explanation
Indices: 2113115--2113167 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2113105 GATAAGCAAA
* *
2113115 GAGGAATTTAATTGAGGATCGAATAT
1 GAGGAATTTAATTGAGGACCAAATAT
*
2113141 GAGGAATTTAATTGAGTACCAAATAT
1 GAGGAATTTAATTGAGGACCAAATAT
2113167 G
1 G
2113168 TCTAAATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.30
Consensus pattern (26 bp):
GAGGAATTTAATTGAGGACCAAATAT
Found at i:2116324 original size:86 final size:86
Alignment explanation
Indices: 2115869--2116323 Score: 740
Period size: 86 Copynumber: 5.3 Consensus size: 86
2115859 TGTGAATTAT
* *
2115869 TAAAAGTAAAATAAATTTATATTACTTGAACTATGA---AAATTTAAATATATAAAATTTTTATA
1 TAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATA
2115931 TTAGTTGAACTTGTAAACTAA
66 TTAGTTGAACTTGTAAACTAA
2115952 TAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATA
1 TAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATA
*
2116017 TTAGTTGAACTTGTAAATTAA
66 TTAGTTGAACTTGTAAACTAA
* * *
2116038 TAAATG-CAAATAAATTTATATTACTTAAACTATTATGCAAACTTAAATATATAAAATTTTTATA
1 TAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATA
* **
2116102 TTAGTTG-ACTTTTAATTTAA
66 TTAGTTGAACTTGTAAACTAA
* * *
2116122 TAAATGTAAAATAAATTTATATTACCTGGACTATGATGCAAACTTAAATATATAAAATTTTTGTA
1 TAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATA
2116187 TTAGTTGAACTTGTAAACTAA
66 TTAGTTGAACTTGTAAACTAA
*
2116208 TAAATGTAAAATAAATTTATATTACTTGAATTATGATGCAAACTTAAATATATAAAATTTTTATA
1 TAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATA
* *
2116273 TTAGTTGGACTTGTAAACTAT
66 TTAGTTGAACTTGTAAACTAA
2116294 TAAATGTAAAATAAATTTATATTACTTGAA
1 TAAATGTAAAATAAATTTATATTACTTGAA
2116324 TATATATATA
Statistics
Matches: 344, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
83 35 0.10
84 17 0.05
85 121 0.35
86 171 0.50
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (86 bp):
TAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATA
TTAGTTGAACTTGTAAACTAA
Found at i:2119912 original size:8 final size:8
Alignment explanation
Indices: 2119891--2119961 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 8
2119881 CTCTTTTCTT
2119891 CTTTCT-C
1 CTTTCTCC
*
2119898 CTCTCTCC
1 CTTTCTCC
2119906 CTTTCTCC
1 CTTTCTCC
*
2119914 CTTTCTTC
1 CTTTCTCC
*
2119922 CTTTCTTCTTT
1 CTTTC-TC--C
*
2119933 CTTTCTTC
1 CTTTCTCC
*
2119941 CTTTCTTC
1 CTTTCTCC
2119949 CTTTCT-C
1 CTTTCTCC
2119956 CTTTCT
1 CTTTCT
2119962 TTCTTGCTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
7 12 0.23
8 34 0.64
9 1 0.02
10 1 0.02
11 5 0.09
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (8 bp):
CTTTCTCC
Found at i:2119930 original size:19 final size:19
Alignment explanation
Indices: 2119908--2119948 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2119898 CTCTCTCCCT
2119908 TTCTCCCTTTCTTCCTTTC
1 TTCTCCCTTTCTTCCTTTC
**
2119927 TTCTTTCTTTCTTCCTTTC
1 TTCTCCCTTTCTTCCTTTC
2119946 TTC
1 TTC
2119949 CTTTCTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (19 bp):
TTCTCCCTTTCTTCCTTTC
Found at i:2119936 original size:27 final size:27
Alignment explanation
Indices: 2119871--2119965 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 27
2119861 CTAAGCGGAA
*
2119871 CCTTATCTTTCT-CTTTTCTT-CTTTCT
1 CCTT-TCTTTCTCCCTTTCTTCCTTTCT
2119897 CCTCTCTCCCTTTCTCCCTTTCTTCCTTTCT
1 CCT-T-T--CTTTCTCCCTTTCTTCCTTTCT
* *
2119928 TCTTTCTTTCTTCCTTTCTTCCTTTCT
1 CCTTTCTTTCTCCCTTTCTTCCTTTCT
2119955 CCTTTCTTTCT
1 CCTTTCTTTCT
2119966 TGCTTCTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 3 0.05
27 33 0.56
29 7 0.12
30 8 0.14
31 8 0.14
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.61
Consensus pattern (27 bp):
CCTTTCTTTCTCCCTTTCTTCCTTTCT
Found at i:2119963 original size:19 final size:20
Alignment explanation
Indices: 2119914--2119990 Score: 88
Period size: 19 Copynumber: 3.9 Consensus size: 20
2119904 CCCTTTCTCC
2119914 CTTTCTTCCTTTCTT-CTTT
1 CTTTCTTCCTTTCTTCCTTT
2119933 CTTTCTTCCTTTCTTCCTTT
1 CTTTCTTCCTTTCTTCCTTT
* * *
2119953 C-TCCTTTCTTTCTTGC-TT
1 CTTTCTTCCTTTCTTCCTTT
2119971 CTTTTCTTCCTTTGCTTCCT
1 C-TTTCTTCCTTT-CTTCCT
2119991 AACCGAATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.06
19 27 0.57
20 13 0.28
21 4 0.09
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.64
Consensus pattern (20 bp):
CTTTCTTCCTTTCTTCCTTT
Found at i:2119965 original size:11 final size:12
Alignment explanation
Indices: 2119914--2119983 Score: 65
Period size: 11 Copynumber: 6.0 Consensus size: 12
2119904 CCCTTTCTCC
2119914 CTTTCTTCCTTT
1 CTTTCTTCCTTT
*
2119926 C-TTCTTTCTTT
1 CTTTCTTCCTTT
* * *
2119937 CTTCCTTTCTTC
1 CTTTCTTCCTTT
2119949 CTTTC-TCCTTT
1 CTTTCTTCCTTT
*
2119960 CTTTCTTGC-TT
1 CTTTCTTCCTTT
2119971 CTTTTCTTCCTTT
1 C-TTTCTTCCTTT
2119984 GCTTCCTAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
11 22 0.48
12 22 0.48
13 2 0.04
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (12 bp):
CTTTCTTCCTTT
Found at i:2119965 original size:31 final size:31
Alignment explanation
Indices: 2119876--2119983 Score: 111
Period size: 31 Copynumber: 3.7 Consensus size: 31
2119866 CGGAACCTTA
* * *
2119876 TCTTTC-TCTTTTCTT-CTTTCTCCTCTCTC
1 TCTTTCTTCCTTTCTTCCTTTCTCCTTTCTT
* *
2119905 CCTTTCTCCCTTTCTTCC-TT-T-C-TTCTT
1 TCTTTCTTCCTTTCTTCCTTTCTCCTTTCTT
2119932 TCTTTCTTCCTTTCTTCCTTTCTCCTTTCTT
1 TCTTTCTTCCTTTCTTCCTTTCTCCTTTCTT
* *
2119963 TCTTGCTTCTTTTCTTCCTTT
1 TCTTTCTTCCTTTCTTCCTTT
2119984 GCTTCCTAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
27 19 0.30
28 3 0.05
29 7 0.11
30 10 0.16
31 25 0.39
ACGTcount: A:0.00, C:0.36, G:0.01, T:0.63
Consensus pattern (31 bp):
TCTTTCTTCCTTTCTTCCTTTCTCCTTTCTT
Found at i:2136471 original size:49 final size:49
Alignment explanation
Indices: 2136316--2136550 Score: 169
Period size: 49 Copynumber: 4.9 Consensus size: 49
2136306 CCATGAACAA
* * * * ** *
2136316 AACATACATACCTCACATAATATCATCGTCT-AGAATCATCTACGGATGG
1 AACATACATATCTCGCATCATATCATCATCTGA-AATCATCTACAAATAG
* ** * ** *
2136365 AATATACATATCTCATATCATATCATCATTTG--A--ATCTATGAACAG
1 AACATACATATCTCGCATCATATCATCATCTGAAATCATCTACAAATAG
* * * * * * *
2136410 AACATGCATATCTTGCATCGTATCATCGT-TCGGAATCATTTACAAATGG
1 AACATACATATCTCGCATCATATCATCATCT-GAAATCATCTACAAATAG
* *
2136459 AATATACATATCTCGTATCATATCATCATCTGAAATCATCTACAAATAG
1 AACATACATATCTCGCATCATATCATCATCTGAAATCATCTACAAATAG
* *
2136508 AACATACATAATC-CACATCATATCATCATTTGAAATCATCTAC
1 AACATACAT-ATCTCGCATCATATCATCATCTGAAATCATCTAC
2136551 GGACAGACCA
Statistics
Matches: 143, Mismatches: 35, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
44 1 0.01
45 31 0.22
47 2 0.01
49 105 0.73
50 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (49 bp):
AACATACATATCTCGCATCATATCATCATCTGAAATCATCTACAAATAG
Found at i:2146599 original size:15 final size:15
Alignment explanation
Indices: 2146579--2146608 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2146569 TGTTGAATAG
2146579 TTTAGTTTAAGTTAT
1 TTTAGTTTAAGTTAT
*
2146594 TTTAGTTTAATTTAT
1 TTTAGTTTAAGTTAT
2146609 GTTAACTTGC
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:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (15 bp):
TTTAGTTTAAGTTAT
Found at i:2155853 original size:182 final size:182
Alignment explanation
Indices: 2155546--2155895 Score: 513
Period size: 182 Copynumber: 1.9 Consensus size: 182
2155536 ATAGTATGTT
* * * * * *
2155546 GGTGCTTGTTAAGGAATAAGTTCATTGAACATGACTCGCTATGAGAGTTCCATTTGATATTTCAC
1 GGTGCTTATTAAGGAACAAGTTCACTAAACATGACTCGCTATGAGAGTTCAATTTGAAATTTCAC
*
2155611 TCAAGGGTCTATGGAAATACTTTCATATGTTACTAGCGTAAATAATTTTTAGACTTGTGATACCA
66 TCAAGGGTCTATGGAAATACTTTCATATGTTAATAGCGTAAATAATTTTTAGACTTGTGATACCA
**
2155676 AGTCATCTTGTATGTGAATTGTCATGCTTTGATTTCACACCTATGGTATATA
131 AGTCATCTTGTATGTGAAAGGTCATGCTTTGATTTCACACCTATGGTATATA
* *
2155728 GGTGCTTATTAAGGAACAAGTTCACTAAACATGATTTGCTATGAGAGTTCAATTTGGAAATTT-A
1 GGTGCTTATTAAGGAACAAGTTCACTAAACATGACTCGCTATGAGAGTTCAATTT-GAAATTTCA
* * * * * *
2155792 CTCAAGTGTTTATGGAAATACTTTCATGTGTTAATAGTGTAAGTAATTTTTAGACTTGTGATATC
65 CTCAAGGGTCTATGGAAATACTTTCATATGTTAATAGCGTAAATAATTTTTAGACTTGTGATACC
* *
2155857 TAGTCATCTTGTATGTGAAAGGTCATGCTTTGCTTTCAC
130 AAGTCATCTTGTATGTGAAAGGTCATGCTTTGATTTCAC
2155896 CTTTATTGGT
Statistics
Matches: 148, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
182 142 0.96
183 6 0.04
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (182 bp):
GGTGCTTATTAAGGAACAAGTTCACTAAACATGACTCGCTATGAGAGTTCAATTTGAAATTTCAC
TCAAGGGTCTATGGAAATACTTTCATATGTTAATAGCGTAAATAATTTTTAGACTTGTGATACCA
AGTCATCTTGTATGTGAAAGGTCATGCTTTGATTTCACACCTATGGTATATA
Found at i:2171556 original size:11 final size:11
Alignment explanation
Indices: 2171540--2171576 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2171530 TAAGTTAATA
2171540 ATGTTAGTTTT
1 ATGTTAGTTTT
2171551 ATGTTA-TTTAT
1 ATGTTAGTTT-T
2171562 AT-TTAGTTTT
1 ATGTTAGTTTT
2171572 ATGTT
1 ATGTT
2171577 TTTGTTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.65
Consensus pattern (11 bp):
ATGTTAGTTTT
Found at i:2171556 original size:20 final size:21
Alignment explanation
Indices: 2171520--2171576 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
2171510 TCATATTTAA
*
2171520 ATATTTA-TTTTAAGTTA-AT
1 ATATTTAGTTTTATGTTATAT
*
2171539 A-ATGTTAGTTTTATGTTATTT
1 ATAT-TTAGTTTTATGTTATAT
2171560 ATATTTAGTTTTATGTT
1 ATATTTAGTTTTATGTT
2171577 TTTGTTGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 9 0.28
21 15 0.47
22 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (21 bp):
ATATTTAGTTTTATGTTATAT
Found at i:2172991 original size:21 final size:20
Alignment explanation
Indices: 2172958--2172996 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2172948 TCGGTCTAAA
* *
2172958 TTCAATATTTTTATTTTATT
1 TTCAATACTTTTAGTTTATT
2172978 TTCAAGTACTTTTAGTTTA
1 TTCAA-TACTTTTAGTTTA
2172997 GTTGATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (20 bp):
TTCAATACTTTTAGTTTATT
Found at i:2192712 original size:29 final size:28
Alignment explanation
Indices: 2192665--2192805 Score: 129
Period size: 28 Copynumber: 4.9 Consensus size: 28
2192655 TGGTAGTTTT
*
2192665 AACATGTTTATCTTAATTTAGACAAAAA
1 AACATGTTTGTCTTAATTTAGACAAAAA
* *
2192693 AACATGTTTGGTCTTAATTTAGATAACAA
1 AACATGTTT-GTCTTAATTTAGACAAAAA
* *
2192722 AATATGTTTGACTTAATTTAAGACAAAAA
1 AACATGTTTGTCTTAATTT-AGACAAAAA
* * * *
2192751 GAATAGTTTTTGTCTTAATCTAGACAAGAA
1 -AACA-TGTTTGTCTTAATTTAGACAAAAA
* * * *
2192781 AGCATATTTGTCTCAATTAAGACAA
1 AACATGTTTGTCTTAATTTAGACAA
2192806 GATAAAATAT
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
28 35 0.38
29 33 0.36
30 12 0.13
31 12 0.13
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAAAA
Found at i:2192792 original size:28 final size:28
Alignment explanation
Indices: 2192759--2192828 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
2192749 AAGAATAGTT
*
2192759 TTTGTCTTAATCT-AGACAAGA-AAGCATA
1 TTTGTCTTAAT-TAAGACAAGATAA-AATA
*
2192787 TTTGTCTCAATTAAGACAAGATAAAATA
1 TTTGTCTTAATTAAGACAAGATAAAATA
*
2192815 TTTGTCCTAATTAA
1 TTTGTCTTAATTAA
2192829 AGATAAGAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.03
28 33 0.92
29 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (28 bp):
TTTGTCTTAATTAAGACAAGATAAAATA
Found at i:2193000 original size:17 final size:17
Alignment explanation
Indices: 2192978--2193010 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2192968 ATAATAATTA
2192978 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
2192995 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
2193011 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:2194064 original size:16 final size:17
Alignment explanation
Indices: 2194032--2194065 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2194022 AAATATATAC
*
2194032 ATATTTTTTCTATTAAA
1 ATATTTTTTCTAATAAA
2194049 ATATTTTTT-TAATAAA
1 ATATTTTTTCTAATAAA
2194065 A
1 A
2194066 AAAAGTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTTTTCTAATAAA
Found at i:2200653 original size:57 final size:56
Alignment explanation
Indices: 2200568--2200725 Score: 192
Period size: 57 Copynumber: 2.7 Consensus size: 56
2200558 TGTTTGTCCT
* * * * *
2200568 AATTTAGACAAGAAAACATGTTTGGTCTTAATTTAGATAAGAAAATATGTTTGGCTTC
1 AATTTAGACAAGAAAA-ATATTTTGTCTTAATTTAGACAAGAAAACATATTTGGC-TC
*
2200626 -ATTTAAGACAAGAAAAATATTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTC
1 AATTT-AGACAAGAAAAATATTTTGTCTTAATTTAGACAAGAAAACATATTTGGCTC
*
2200682 AATTTAGACAAGATAAAATACTTTTGTCTTAATTAAAGACAAGA
1 AATTTAGACAAGA-AAAATA-TTTTGTCTTAATT-TAGACAAGA
2200726 GTTGTCTTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
56 10 0.11
57 46 0.52
58 24 0.27
59 8 0.09
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (56 bp):
AATTTAGACAAGAAAAATATTTTGTCTTAATTTAGACAAGAAAACATATTTGGCTC
Found at i:2200677 original size:28 final size:28
Alignment explanation
Indices: 2200555--2200725 Score: 175
Period size: 28 Copynumber: 5.9 Consensus size: 28
2200545 GGCAGCTTTG
* *
2200555 ACATGTTTGTCCTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAA
* *
2200583 ACATGTTTGGTCTTAATTTAGATAAGAAA
1 ACATATTT-GTCTTAATTTAGACAAGAAA
* * * *
2200612 ATATGTTTGGCTTCATTTAAGACAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAA
2200641 A-ATATTTTGTCTTAATTTAGACAAGAAA
1 ACATA-TTTGTCTTAATTTAGACAAGAAA
*
2200669 ACATATTTGTCTCAATTTAGACAAGATAA
1 ACATATTTGTCTTAATTTAGACAAGA-AA
*
2200698 A-ATACTTTTGTCTTAATTAAAGACAAGA
1 ACATA--TTTGTCTTAATT-TAGACAAGA
2200726 GTTGTCTTAA
Statistics
Matches: 123, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
28 52 0.42
29 52 0.42
30 11 0.09
31 8 0.07
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (28 bp):
ACATATTTGTCTTAATTTAGACAAGAAA
Found at i:2209167 original size:10 final size:11
Alignment explanation
Indices: 2209152--2209196 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
2209142 ATTTGGGATG
2209152 AAAAAAA-AAC
1 AAAAAAAGAAC
2209162 AAAAAAAG-AC
1 AAAAAAAGAAC
2209172 AAAGAAAAGAA-
1 AAA-AAAAGAAC
2209183 AAAAAAAGAAC
1 AAAAAAAGAAC
2209194 AAA
1 AAA
2209197 GTGTTGGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 19 0.61
11 11 0.35
12 1 0.03
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAC
Found at i:2209187 original size:22 final size:23
Alignment explanation
Indices: 2209154--2209197 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2209144 TTGGGATGAA
2209154 AAAAAAACAAAAAAAG-ACAAAG
1 AAAAAAACAAAAAAAGAACAAAG
*
2209176 AAAAGAA-AAAAAAAGAACAAAG
1 AAAAAAACAAAAAAAGAACAAAG
2209198 TGTTGGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (23 bp):
AAAAAAACAAAAAAAGAACAAAG
Found at i:2212806 original size:36 final size:36
Alignment explanation
Indices: 2212746--2212843 Score: 88
Period size: 36 Copynumber: 2.7 Consensus size: 36
2212736 GGCCACTAAC
* * **
2212746 CATCCTCATTCACATCATCTTAGGTGAGCAAATAAT
1 CATCCACATTCATATCATAATAGGTGAGCAAATAAT
** * ** *
2212782 CATCCATGTTCATATCATAATAGGTGGGTTACTAAT
1 CATCCACATTCATATCATAATAGGTGAGCAAATAAT
* *
2212818 CATCCACATTCATATCGTAGTAGGTG
1 CATCCACATTCATATCATAATAGGTG
2212844 GGCATACATT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (36 bp):
CATCCACATTCATATCATAATAGGTGAGCAAATAAT
Found at i:2212857 original size:36 final size:36
Alignment explanation
Indices: 2212778--2212859 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
2212768 GGTGAGCAAA
** *
2212778 TAATCATCCATGTTCATATCATAATAGGTGGGTTAC
1 TAATCATCCACATTCATATCATAATAGGTGGGATAC
* *
2212814 TAATCATCCACATTCATATCGTAGTAGGTGGGCATAC
1 TAATCATCCACATTCATATCATAATAGGTGGG-ATAC
*
2212851 -ATTCATCCA
1 TAATCATCCA
2212860 TAAAGGCAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 36 0.92
37 3 0.08
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (36 bp):
TAATCATCCACATTCATATCATAATAGGTGGGATAC
Found at i:2220652 original size:18 final size:18
Alignment explanation
Indices: 2220631--2220667 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2220621 GGCCTACCTA
2220631 GGCTACCTAACTTGCTTG
1 GGCTACCTAACTTGCTTG
* *
2220649 GGCTACTTAGCTTGCTTG
1 GGCTACCTAACTTGCTTG
2220667 G
1 G
2220668 ATTGGTCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.35
Consensus pattern (18 bp):
GGCTACCTAACTTGCTTG
Found at i:2231593 original size:25 final size:25
Alignment explanation
Indices: 2231554--2231611 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
2231544 GTCGCAACTG
*
2231554 CATATATC-ACTTGTGGCCTAGCCA
1 CATATATCAACCTGTGGCCTAGCCA
* *
2231578 CATATATCAACCTGTGGCCTTGCCG
1 CATATATCAACCTGTGGCCTAGCCA
*
2231603 CGTATATCA
1 CATATATCA
2231612 CAAACCATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (25 bp):
CATATATCAACCTGTGGCCTAGCCA
Found at i:2232015 original size:2 final size:2
Alignment explanation
Indices: 2232008--2232032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2231998 AATTAAGTTG
2232008 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
2232033 GATCAAGACA
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:2232867 original size:8 final size:8
Alignment explanation
Indices: 2232854--2232914 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
2232844 TTTTTCTTCC
2232854 TCCTTTCT
1 TCCTTTCT
2232862 TCCTTTC-
1 TCCTTTCT
*
2232869 TCGCTTTGGT
1 TC-CTTT-CT
2232879 TCCTTTC-
1 TCCTTTCT
2232886 TCCTTTCT
1 TCCTTTCT
*
2232894 TTCTTTCT
1 TCCTTTCT
2232902 TCCTTTGCT
1 TCCTTT-CT
2232911 TCCT
1 TCCT
2232915 ACCTGAATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 9 0.20
8 23 0.52
9 10 0.23
10 2 0.05
ACGTcount: A:0.00, C:0.34, G:0.07, T:0.59
Consensus pattern (8 bp):
TCCTTTCT
Found at i:2232893 original size:32 final size:32
Alignment explanation
Indices: 2232853--2232914 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
2232843 TTTTTTCTTC
*
2232853 CTCCTTTCTTCCTTTC-TCGCTTTGGTTCCTTT
1 CTCCTTTCTTCCTTTCTTC-CTTTGCTTCCTTT
*
2232885 CTCCTTTCTTTCTTTCTTCCTTTGCTTCCT
1 CTCCTTTCTTCCTTTCTTCCTTTGCTTCCT
2232915 ACCTGAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.00, C:0.35, G:0.06, T:0.58
Consensus pattern (32 bp):
CTCCTTTCTTCCTTTCTTCCTTTGCTTCCTTT
Found at i:2236204 original size:29 final size:29
Alignment explanation
Indices: 2236107--2236494 Score: 358
Period size: 29 Copynumber: 13.4 Consensus size: 29
2236097 GTTTTTATAT
*
2236107 TTTTGTCTTAATTTAGACAAGAAAATAT-
1 TTTTGTCTTAATTTAGACAAGAAAACATG
** * *
2236135 AATTG-CTTAAATTTGGACAAAAAAACCATG
1 TTTTGTCTT-AATTTAGACAAGAAAA-CATG
* *
2236165 -TCTGTCTTAATATTAGATAAGAAAACAT-
1 TTTTGTCTTAAT-TTAGACAAGAAAACATG
*
2236193 CTTTGTCTTAATTTAGACAAGAAAACATG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
* * *
2236222 TTTTGTCTTAGTTTTGACAATAAAACAT-
1 TTTTGTCTTAATTTAGACAAGAAAACATG
* * *
2236250 TTTTTTCTTAATTTGGAGAAGAAAACATG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
*
2236279 TTTTGTCTTAATTTCGACAAGAAAACATG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
* *
2236308 TTTTATCTTAATTTAGATAAGAAAACATG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
* *
2236337 TTTTATCTTAATTTAGATAAGAAAACATG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
* * * *
2236366 TTTTATCTTAATTAAGACAAGAAAATACG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
* * *
2236395 TTTTGTCTTAATATAGAAAAGAAAA-ATACT
1 TTTTGTCTTAATTTAGACAAGAAAACAT--G
* * **
2236425 TTTTATCTTAATTTAGACAAGAAGACGCG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
* * * * * *
2236454 -TTTGCCTCAATTTAAACAAGATAGCAAG
1 TTTTGTCTTAATTTAGACAAGAAAACATG
2236482 TTTTGTCTTAATT
1 TTTTGTCTTAATT
2236495 AAAAATAAGA
Statistics
Matches: 293, Mismatches: 55, Indels: 23
0.79 0.15 0.06
Matches are distributed among these distances:
27 3 0.01
28 75 0.26
29 181 0.62
30 34 0.12
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TTTTGTCTTAATTTAGACAAGAAAACATG
Found at i:2249954 original size:22 final size:22
Alignment explanation
Indices: 2249926--2249969 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2249916 AATTTCCAGA
*
2249926 GAGAAGTAGCGCTGCAGCGCTG
1 GAGAAGTAGCGCCGCAGCGCTG
2249948 GAGAAGTAGCGCCGCAGCGCTG
1 GAGAAGTAGCGCCGCAGCGCTG
2249970 CACAACGTTC
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:0.23, C:0.25, G:0.41, T:0.11
Consensus pattern (22 bp):
GAGAAGTAGCGCCGCAGCGCTG
Found at i:2256243 original size:30 final size:30
Alignment explanation
Indices: 2256187--2256268 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
2256177 CGATAGATGG
2256187 TTTGTTCTTTGGGAAAAGAG--CTCTTACT
1 TTTGTTCTTTGGGAAAAGAGCTCTCTTACT
2256215 TTTGTTCTTTGGGAAAAGAGCTCTCTTACT
1 TTTGTTCTTTGGGAAAAGAGCTCTCTTACT
2256245 TTTGTTCTTTGGGAAAAGAGCTCT
1 TTTGTTCTTTGGGAAAAGAGCTCT
2256269 TGCTTGCTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 20 0.38
30 32 0.62
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.43
Consensus pattern (30 bp):
TTTGTTCTTTGGGAAAAGAGCTCTCTTACT
Found at i:2261605 original size:20 final size:19
Alignment explanation
Indices: 2261580--2261639 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
2261570 AATCGAAATT
2261580 AATTAATTAATTAAACTAAA
1 AATTAA-TAATTAAACTAAA
*
2261600 AATT-A-AATAAAACTAAA
1 AATTAATAATTAAACTAAA
* *
2261617 TCATAAATAATTAAACTAAA
1 -AATTAATAATTAAACTAAA
2261637 AAT
1 AAT
2261640 CATAGAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 11 0.34
18 2 0.06
19 4 0.12
20 15 0.47
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAATAATTAAACTAAA
Found at i:2268364 original size:17 final size:17
Alignment explanation
Indices: 2268337--2268369 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2268327 TTTTCAAAAT
2268337 CCTTCAAAAGTTCTTCAA
1 CCTTCAAAAGTT-TTCAA
2268355 CCTT-AAAAGTTTTCA
1 CCTTCAAAAGTTTTCA
2268370 TCAAATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (17 bp):
CCTTCAAAAGTTTTCAA
Found at i:2270449 original size:21 final size:21
Alignment explanation
Indices: 2270405--2270449 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2270395 TATTTATGTG
* *
2270405 AATATGAGAAAATGAATTTGA
1 AATATAAGAAAATGAATTTAA
2270426 AATATAAGAAAATG-ATTTCAA
1 AATATAAGAAAATGAATTT-AA
2270447 AAT
1 AAT
2270450 TTAATGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (21 bp):
AATATAAGAAAATGAATTTAA
Done.