Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 55
Found at i:5259349 original size:27 final size:27
Alignment explanation
Indices: 5259319--5259374 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 27
5259309 GTTTTGAATT
* *
5259319 TTTTTTGAATATATATAT-ATAATATAG
1 TTTTTTGAAAACATATATAAT-ATATAG
5259346 --TTTTGAAAACATATATAATATATAG
1 TTTTTTGAAAACATATATAATATATAG
5259371 TTTT
1 TTTT
5259375 CTATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
25 20 0.83
26 2 0.08
27 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (27 bp):
TTTTTTGAAAACATATATAATATATAG
Found at i:5259508 original size:19 final size:19
Alignment explanation
Indices: 5259484--5259532 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
5259474 ATTATACAAT
5259484 TTTATTTTATTATCAT-TTA
1 TTTATTTTATTAT-ATATTA
*
5259503 TTTATTTTTGTTATATATTA
1 TTTA-TTTTATTATATATTA
5259523 -TTATTTTATT
1 TTTATTTTATT
5259533 TTTTGGGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 6 0.23
19 9 0.35
20 11 0.42
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTATATATTA
Found at i:5259510 original size:24 final size:20
Alignment explanation
Indices: 5259482--5259534 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 20
5259472 ATATTATACA
5259482 ATTTTATTTTATTATCATTTATTT
1 ATTTTATTTTA-TAT-A-TTA-TT
*
5259506 ATTTT-TGTTATATATTATT
1 ATTTTATTTTATATATTATT
5259525 ATTTTATTTT
1 ATTTTATTTT
5259535 TTGGGTCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 7 0.27
20 6 0.23
21 1 0.04
22 3 0.12
23 4 0.15
24 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
ATTTTATTTTATATATTATT
Found at i:5264572 original size:21 final size:21
Alignment explanation
Indices: 5264529--5264572 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5264519 GGTAACTATG
* **
5264529 CCACCCCAAGAATTGGATGTA
1 CCACCCCAAGAATTCGACATA
*
5264550 CCACCCCAAGCATTCGACATA
1 CCACCCCAAGAATTCGACATA
5264571 CC
1 CC
5264573 TCATCCATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.39, G:0.14, T:0.16
Consensus pattern (21 bp):
CCACCCCAAGAATTCGACATA
Found at i:5271288 original size:112 final size:111
Alignment explanation
Indices: 5271165--5271448 Score: 349
Period size: 112 Copynumber: 2.5 Consensus size: 111
5271155 ATATACATAG
5271165 CATATATAATATATAGTTTTGAAAACATTTTTTTAAATTATATATAGTATATAGTTTT-AAAACA
1 CATATATAATATATAGTTTTGAAAACA-TTTTTTAAATTATATATAGTATATAGTTTTGAAAAC-
* * *** *
5271229 AATTTGAAAAAATATATATATTGTATAATTTT-AAATTTTTTTTG-AAAT
64 AATTTG--AAAATATATATAGTATATAATTTTGAAAACATTTTTGAAAAA
* * * * * *
5271277 TATATATAATATATAGTTTTAAAAACATTTTTTAAAATATATATAATATATAATTTTGAAAACAT
1 CATATATAATATATAGTTTTGAAAACATTTTTTAAATTATATATAGTATATAGTTTTGAAAACAA
* *
5271342 TTTGAAATTATATATAGTATATAGTTTTGAAAACATTTTTGAAAAAA
66 TTTGAAAATATATATAGTATATAATTTTGAAAACATTTTTG-AAAAA
* * *
5271389 CATATATAATATATAGTTTTGAAAACATTTTTGAAATTGTATATAGTATGTAGTTTTGAA
1 CATATATAATATATAGTTTTGAAAACATTTTTTAAATTATATATAGTATATAGTTTTGAA
5271449 TTTTTTTTTT
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
109 20 0.14
110 9 0.06
111 32 0.22
112 85 0.58
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (111 bp):
CATATATAATATATAGTTTTGAAAACATTTTTTAAATTATATATAGTATATAGTTTTGAAAACAA
TTTGAAAATATATATAGTATATAATTTTGAAAACATTTTTGAAAAA
Found at i:5271318 original size:37 final size:37
Alignment explanation
Indices: 5271166--5271510 Score: 295
Period size: 37 Copynumber: 9.5 Consensus size: 37
5271156 TATACATAGC
*
5271166 ATATATAATATATAGTTTTGAAAACATTTTTTTAAATT
1 ATATATAATATATAGTTTTGAAAACA-TTTTTTAAAAT
* ***
5271204 ATATATAGTATATAGTTTT-AAAACAAATTTGAAAAAAT
1 ATATATAATATATAGTTTTGAAAAC--ATTTTTTAAAAT
* * * ** *
5271242 ATATATATTGTATAATTTT--AAATTTTTTTTGAAATT
1 ATATATAATATATAGTTTTGAAAACATTTTTT-AAAAT
*
5271278 ATATATAATATATAGTTTTAAAAACATTTTTTAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTAAAAT
* * *
5271315 ATATATAATATATAATTTTGAAAACA-TTTTGAAATT
1 ATATATAATATATAGTTTTGAAAACATTTTTTAAAAT
* * *
5271351 ATATATAGTATATAGTTTTGAAAACATTTTTGAAAAAAC
1 ATATATAATATATAGTTTTGAAAACATTTTT--TAAAAT
* *
5271390 ATATATAATATATAGTTTTGAAAACATTTTTGAAATT
1 ATATATAATATATAGTTTTGAAAACATTTTTTAAAAT
* * *
5271427 GTATATAGTATGTAGTTTTG---A-ATTTTTT----T
1 ATATATAATATATAGTTTTGAAAACATTTTTTAAAAT
* *
5271456 -T-TTTGAATATATAGTTTTGAAAACATTTTTGAAAAT
1 ATATAT-AATATATAGTTTTGAAAACATTTTTTAAAAT
*
5271492 AAATATAATATATAGTTTT
1 ATATATAATATATAGTTTT
5271511 CTAAAAAAAT
Statistics
Matches: 245, Mismatches: 43, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
27 2 0.01
28 13 0.05
29 1 0.00
31 1 0.00
32 6 0.02
33 6 0.02
34 1 0.00
35 3 0.01
36 53 0.22
37 73 0.30
38 52 0.21
39 34 0.14
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTTAAAAT
Found at i:5271330 original size:73 final size:74
Alignment explanation
Indices: 5271166--5271445 Score: 332
Period size: 73 Copynumber: 3.8 Consensus size: 74
5271156 TATACATAGC
* *
5271166 ATATATAATATATAGTTTTGAAAACATTTTTTT-AAATTATATATAGTATATAGTTTTAAAACAA
1 ATATATAATATATAATTTTG-AAA-ATTTTTTTGAAATTATATATAGTATATAGTTTTAAAA-AC
**
5271230 ATTTGAAAAAAT
63 ATTTTTAAAAAT
* * * *
5271242 ATATATATTGTATAATTTT-AAATTTTTTTTGAAATTATATATAATATATAGTTTTAAAAACATT
1 ATATATAATATATAATTTTGAAAATTTTTTTGAAATTATATATAGTATATAGTTTTAAAAACATT
*
5271306 TTTTAAAAT
66 TTTAAAAAT
** *
5271315 ATATATAATATATAATTTTGAAAA-CATTTTGAAATTATATATAGTATATAGTTTTGAAAACATT
1 ATATATAATATATAATTTTGAAAATTTTTTTGAAATTATATATAGTATATAGTTTTAAAAACATT
*
5271379 TTTGAAAAAAC
66 TTT--AAAAAT
* ** * *
5271390 ATATATAATATATAGTTTTGAAAACATTTTTGAAATTGTATATAGTATGTAGTTTT
1 ATATATAATATATAATTTTGAAAATTTTTTTGAAATTATATATAGTATATAGTTTT
5271446 GAATTTTTTT
Statistics
Matches: 176, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
73 73 0.41
74 33 0.19
75 27 0.15
76 43 0.24
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (74 bp):
ATATATAATATATAATTTTGAAAATTTTTTTGAAATTATATATAGTATATAGTTTTAAAAACATT
TTTAAAAAT
Found at i:5271547 original size:104 final size:104
Alignment explanation
Indices: 5271359--5271549 Score: 264
Period size: 104 Copynumber: 1.8 Consensus size: 104
5271349 TTATATATAG
*
5271359 TATATAGTTTTGAAAACATTTTTGAAAAAACATATATAATATATAGTTTTGAAAACATTTTTGAA
1 TATATAGTTTTGAAAACATTTTTGAAAAAACATATATAATATATAGTTTTAAAAACATTTTTGAA
** *
5271424 ATTGTATATAGTATGTAGTTTTGAATTTTTTTTTTTGAA
66 AACGTATATAGTATATAGTTTTGAATTTTTTTTTTTGAA
* *
5271463 TATATAGTTTTGAAAACATTTTTGAAAATA-A-ATATAATATATAGTTTTCTAAAAAAATATTTT
1 TATATAGTTTTGAAAACATTTTTGAAAAAACATATATAATATATAG-TTT-T--AAAAACATTTT
5271526 TGAAAACGTATA-A-TATATAGTTTT
62 TGAAAACGTATATAGTATATAGTTTT
5271550 CTTAATGGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
102 13 0.17
103 4 0.05
104 40 0.52
105 1 0.01
106 19 0.25
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (104 bp):
TATATAGTTTTGAAAACATTTTTGAAAAAACATATATAATATATAGTTTTAAAAACATTTTTGAA
AACGTATATAGTATATAGTTTTGAATTTTTTTTTTTGAA
Found at i:5271641 original size:19 final size:18
Alignment explanation
Indices: 5271617--5271666 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5271607 TATAATATTA
*
5271617 TTTTATTTTATTATCATTT
1 TTTTATTTTATTAT-ATAT
*
5271636 TTTTATTTTTGTTATATAT
1 TTTTA-TTTTATTATATAT
*
5271655 TATTATTTTATT
1 TTTTATTTTATT
5271667 TTTTTGTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTATTTTATTATATAT
Found at i:5271663 original size:24 final size:23
Alignment explanation
Indices: 5271614--5271669 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
5271604 TAATATAATA
* *
5271614 TTATTTTATTTTATTATCATTTTT
1 TTATTTT-TGTTATTATCATTATT
*
5271638 TTATTTTTGTTATATATTATTATT
1 TTATTTTTGTTAT-TATCATTATT
5271662 TTATTTTT
1 TTATTTTT
5271670 TTGTCTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (23 bp):
TTATTTTTGTTATTATCATTATT
Found at i:5272811 original size:19 final size:19
Alignment explanation
Indices: 5272787--5272830 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5272777 ATTTAGTCCT
5272787 TTATTTATTTATTTATTTC
1 TTATTTATTTATTTATTTC
* *
5272806 TTATTTGTTTATTTTTTTC
1 TTATTTATTTATTTATTTC
5272825 TT-TTTA
1 TTATTTA
5272831 GCATTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (19 bp):
TTATTTATTTATTTATTTC
Found at i:5273096 original size:6 final size:6
Alignment explanation
Indices: 5273085--5273111 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5273075 GAATCAAGTT
5273085 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
5273112 GTTGAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5273526 original size:64 final size:63
Alignment explanation
Indices: 5273396--5273553 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
5273386 ATGCACACCC
* * * *
5273396 AACATCGAA-GCCATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTATTTTATTGA
1 AACATCGAATG-CATTTTGTGTACCGATACACAACCATGCATCGATACACTCCTACTTTATTAA
* * * *
5273459 AACATCGAATGCATTTTGTGTACCGATACACATTCTATTCATCGATACACT-CTGGCTTTATTAA
1 AACATCGAATGCATTTTGTGTACCGATACACA-ACCATGCATCGATACACTCCT-ACTTTATTAA
* * * *
5273523 AACATCAAATGCAATTAGTGTATCGATACAC
1 AACATCGAATGCATTTTGTGTACCGATACAC
5273554 CCCAAGTGTA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
63 30 0.38
64 50 0.62
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (63 bp):
AACATCGAATGCATTTTGTGTACCGATACACAACCATGCATCGATACACTCCTACTTTATTAA
Found at i:5279356 original size:21 final size:21
Alignment explanation
Indices: 5279330--5279386 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
5279320 TATCGATACA
5279330 TATGTATCGATACACCTTCGC
1 TATGTATCGATACACCTTCGC
5279351 TATGTATCGATACACCTTCGC
1 TATGTATCGATACACCTTCGC
5279372 TATGTATCGATACAC
1 TATGTATCGATACAC
5279387 TATGATAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (21 bp):
TATGTATCGATACACCTTCGC
Found at i:5282154 original size:63 final size:63
Alignment explanation
Indices: 5282076--5282233 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 63
5282066 ATGCACACCC
*
5282076 AACATCGAAGTCATTTTATGTACCGATGCACAACC-ATGCATCGATACACTCATAT-TCTATTAA
1 AACATCGAA-TCATTTTATGTACCGATACACAACCTATGCATCGATACACTC-TATCTCTATTAA
* ** * * * *
5282139 AACATCGAATACATTTTGTGTGTCGATACATATCCTATGCATCGATACACTCTGTCTTTATTAA
1 AACATCGAAT-CATTTTATGTACCGATACACAACCTATGCATCGATACACTCTATCTCTATTAA
* *
5282203 AACATTGAATGCA-ATTAGTGTACCGATACAC
1 AACATCGAAT-CATTTTA-TGTACCGATACAC
5282234 CCCAAGTGTA
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
62 1 0.01
63 31 0.41
64 44 0.58
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (63 bp):
AACATCGAATCATTTTATGTACCGATACACAACCTATGCATCGATACACTCTATCTCTATTAA
Found at i:5290308 original size:32 final size:27
Alignment explanation
Indices: 5290272--5290349 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 27
5290262 AGCAACAAGA
5290272 TTAACGAGCAACGAGTCGAGCAACAAGTTTT
1 TTAACGAGCAACGAGTCGAGCAA-AA---TT
5290303 CTTAACGAGCAA-GAGTCGAGCAAAATT
1 -TTAACGAGCAACGAGTCGAGCAAAATT
*
5290330 TTAACGAGCAACAAGTCGAG
1 TTAACGAGCAACGAGTCGAG
5290350 TCGAGCAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
26 11 0.25
27 9 0.20
30 2 0.05
31 11 0.25
32 11 0.25
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (27 bp):
TTAACGAGCAACGAGTCGAGCAAAATT
Found at i:5292061 original size:23 final size:23
Alignment explanation
Indices: 5292034--5292078 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5292024 AAATATTTAT
* *
5292034 TTATTTTTTTAAAATTAAATTAA
1 TTATTTATTTAAAATAAAATTAA
*
5292057 TTATTTATTTGAAATAAAATTA
1 TTATTTATTTAAAATAAAATTA
5292079 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATTTATTTAAAATAAAATTAA
Found at i:5292280 original size:24 final size:23
Alignment explanation
Indices: 5292197--5292283 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
5292187 GATAATTTAA
* *
5292197 AAATAATATTATTTCAAGTAAAT
1 AAATAATATTATTTTAAATAAAT
* *
5292220 AATTAATATTATTTAAAATAAAT
1 AAATAATATTATTTTAAATAAAT
* *
5292243 AAATAATATGATTTTAAA-AATT
1 AAATAATATTATTTTAAATAAAT
5292265 AAATAATATTTTATTTTAA
1 AAATAATA--TTATTTTAA
5292284 TTTATCAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 11 0.20
23 35 0.65
24 8 0.15
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATAATATTATTTTAAATAAAT
Found at i:5300488 original size:29 final size:29
Alignment explanation
Indices: 5300454--5300512 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5300444 CCTAAATTAA
5300454 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
*
5300483 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
5300512 T
1 T
5300513 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:5305176 original size:29 final size:29
Alignment explanation
Indices: 5305142--5305200 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5305132 CCTAAATTAA
5305142 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
5305171 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
5305200 T
1 T
5305201 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:5307951 original size:12 final size:12
Alignment explanation
Indices: 5307934--5307958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5307924 ATGTTCGTTC
5307934 ATTTAAATGATA
1 ATTTAAATGATA
5307946 ATTTAAATGATA
1 ATTTAAATGATA
5307958 A
1 A
5307959 ACGAACATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTAAATGATA
Found at i:5307981 original size:20 final size:20
Alignment explanation
Indices: 5307956--5307995 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5307946 ATTTAAATGA
*
5307956 TAAACGAACATAAACAAACG
1 TAAACGAACACAAACAAACG
*
5307976 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACAAACG
5307996 AACATAAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACAAACG
Found at i:5308012 original size:10 final size:10
Alignment explanation
Indices: 5307955--5307994 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5307945 AATTTAAATG
5307955 ATAAACGAAC
1 ATAAACGAAC
*
5307965 ATAAACAAAC
1 ATAAACGAAC
*
5307975 GTAAACGAAC
1 ATAAACGAAC
*
5307985 ACAAACGAAC
1 ATAAACGAAC
5307995 GAACATAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:5308319 original size:14 final size:13
Alignment explanation
Indices: 5308300--5308349 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
5308290 ATATAAATGA
5308300 ACATAAATGAACGG
1 ACATAAATGAAC-G
5308314 ACATAAAT-AA--
1 ACATAAATGAACG
5308324 ACATAAATGAACG
1 ACATAAATGAACG
*
5308337 AACATAAACGAAC
1 -ACATAAATGAAC
5308350 ATATAATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 8 0.26
11 2 0.06
13 2 0.06
14 19 0.61
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (13 bp):
ACATAAATGAACG
Found at i:5308326 original size:24 final size:24
Alignment explanation
Indices: 5308287--5308386 Score: 98
Period size: 24 Copynumber: 4.2 Consensus size: 24
5308277 GACTTCTGTT
*
5308287 CGAATATAAATGAACATAAATGAA
1 CGAACATAAATGAACATAAATGAA
* *
5308311 CGGACATAAATAAACATAAATGAA
1 CGAACATAAATGAACATAAATGAA
*
5308335 CGAACATAAACGAACAT--AT-AA
1 CGAACATAAATGAACATAAATGAA
* ** *
5308356 TCGAACGTTCACGAACATAAATGAA
1 -CGAACATAAATGAACATAAATGAA
5308381 CGAACA
1 CGAACA
5308387 AACCATTTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.03
22 16 0.26
24 42 0.68
25 2 0.03
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (24 bp):
CGAACATAAATGAACATAAATGAA
Found at i:5330014 original size:14 final size:14
Alignment explanation
Indices: 5329995--5330022 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5329985 AAGTGAAAGA
5329995 ATAGTTATATAATT
1 ATAGTTATATAATT
5330009 ATAGTTATATAATT
1 ATAGTTATATAATT
5330023 TTGTTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:5331862 original size:24 final size:24
Alignment explanation
Indices: 5331830--5331886 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
5331820 GCATGCATCT
5331830 CTTCCAATCTTATCCCTATTCAAC
1 CTTCCAATCTTATCCCTATTCAAC
5331854 CTTCCAATCTTATCCCTATTCAAC
1 CTTCCAATCTTATCCCTATTCAAC
5331878 CTTCCAATC
1 CTTCCAATC
5331887 AAACCAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.39, G:0.00, T:0.37
Consensus pattern (24 bp):
CTTCCAATCTTATCCCTATTCAAC
Found at i:5334491 original size:12 final size:12
Alignment explanation
Indices: 5334474--5334500 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5334464 TTAATCGTGA
5334474 AAATCAAAATTT
1 AAATCAAAATTT
5334486 AAATCAAAATTT
1 AAATCAAAATTT
5334498 AAA
1 AAA
5334501 AATTCAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATCAAAATTT
Found at i:5334642 original size:27 final size:25
Alignment explanation
Indices: 5334598--5334656 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
5334588 GAGAAAAAAA
*
5334598 TAATAAAAAATATTAATATAATAATAT
1 TAATAAAAAATATAAATA-AATAA-AT
5334625 TAATAAAAAA-ATGAAATAAATAAAT
1 TAATAAAAAATAT-AAATAAATAAAT
*
5334650 AAATAAA
1 TAATAAA
5334657 TATAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 8 0.28
26 7 0.24
27 14 0.48
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (25 bp):
TAATAAAAAATATAAATAAATAAAT
Found at i:5334647 original size:4 final size:4
Alignment explanation
Indices: 5334595--5334658 Score: 51
Period size: 4 Copynumber: 15.2 Consensus size: 4
5334585 CATGAGAAAA
* *
5334595 AAAT -AAT AAA- AAAT ATTAAT ATAAT AATAT TAAT AAAA AAAT GAAAT
1 AAAT AAAT AAAT AAAT A--AAT A-AAT AA-AT AAAT AAAT AAAT -AAAT
5334642 AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT A
5334659 TAAAACAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 6 0.12
4 28 0.56
5 12 0.24
6 4 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:5335077 original size:33 final size:33
Alignment explanation
Indices: 5335036--5335106 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
5335026 AGAATGCTTC
5335036 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
*
5335069 GGTTTTAGTGTTTCAATAGGATTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
5335102 GGTTT
1 GGTTT
5335107 ATTTTCTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
Found at i:5335178 original size:3 final size:3
Alignment explanation
Indices: 5335155--5335230 Score: 79
Period size: 3 Copynumber: 25.3 Consensus size: 3
5335145 GGCTTGCAAA
*
5335155 AAT AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5335201 AAAT AAAT AAAT ATAT AAT -AT AAT AA- AAT A
1 -AAT -AAT -AAT A-AT AAT AAT AAT AAT AAT A
5335231 TTTTTGTAGA
Statistics
Matches: 65, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
2 8 0.12
3 43 0.66
4 14 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5336823 original size:24 final size:25
Alignment explanation
Indices: 5336764--5336839 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 25
5336754 AATTTATTTT
* *
5336764 ATTAAATTTAAA-TTACATACTCTCTA
1 ATTAAATTTAAATTTATAAACT-T-TA
* *
5336790 ATTAAATTTATATTT-TAAATTTTA
1 ATTAAATTTAAATTTATAAACTTTA
*
5336814 ATTAATTTTAAATTTATAAACTTTA
1 ATTAAATTTAAATTTATAAACTTTA
5336839 A
1 A
5336840 GCATAAAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
24 15 0.37
25 10 0.24
26 14 0.34
27 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTAAATTTAAATTTATAAACTTTA
Found at i:5337392 original size:24 final size:25
Alignment explanation
Indices: 5337349--5337400 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
5337339 TATTTTCTGT
* *
5337349 TTAAAGTTTAAAAATTTAAAATTAA
1 TTAAAATTTAAAAATATAAAATTAA
*
5337374 TTAAAATTT-AAAATATAAATTTAA
1 TTAAAATTTAAAAATATAAAATTAA
5337398 TTA
1 TTA
5337401 GAGAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TTAAAATTTAAAAATATAAAATTAA
Found at i:5337421 original size:26 final size:24
Alignment explanation
Indices: 5337359--5337440 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
5337349 TTAAAGTTTA
* *
5337359 AAAATTTAAAATTAATTAAAATTT
1 AAAATTTAAATTTAATTAAAATAT
*
5337383 AAAATATAAATTTAATTAGAGAATAT
1 AAAATTTAAATTTAATTA-A-AATAT
* *
5337409 ATAATTTAAATTTAA-TAAAAAAT
1 AAAATTTAAATTTAATTAAAATAT
5337432 -AAATTTAAA
1 AAAATTTAAA
5337441 ATAAATGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 8 0.16
23 4 0.08
24 17 0.35
25 3 0.06
26 17 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATTTAAATTTAATTAAAATAT
Found at i:5338284 original size:16 final size:16
Alignment explanation
Indices: 5338263--5338302 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
5338253 ATAAGTTGAC
5338263 AAATGCTATCATGTTG
1 AAATGCTATCATGTTG
*
5338279 AAATGCTATTATGTTG
1 AAATGCTATCATGTTG
5338295 AAATGCTA
1 AAATGCTA
5338303 CTAAACATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (16 bp):
AAATGCTATCATGTTG
Found at i:5338806 original size:89 final size:89
Alignment explanation
Indices: 5338655--5338832 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
5338645 CCTATACCCT
5338655 AAGTTAACTTTAGATACCTAAATAATTTTTCGCTAAGAATAGGTGAATAGAGTTTTCGACGTTAC
1 AAGTTAACTTTAGATACCTAAATAATTTTTCGCTAAGAATAGGTGAATAGAGTTTTCGACGTTAC
5338720 ACTTTTAAGTTCCTAGGTTATAAC
66 ACTTTTAAGTTCCTAGGTTATAAC
5338744 AAGTTAACTTTAGATACCTAAATAATTTTTCGCTAAGAATAGGTGAATAGAGTTTTCGACGTTAC
1 AAGTTAACTTTAGATACCTAAATAATTTTTCGCTAAGAATAGGTGAATAGAGTTTTCGACGTTAC
5338809 ACTTTTAAGTTCCTAGGTTATAAC
66 ACTTTTAAGTTCCTAGGTTATAAC
5338833 GACAATTAAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (89 bp):
AAGTTAACTTTAGATACCTAAATAATTTTTCGCTAAGAATAGGTGAATAGAGTTTTCGACGTTAC
ACTTTTAAGTTCCTAGGTTATAAC
Found at i:5342447 original size:18 final size:18
Alignment explanation
Indices: 5342423--5342465 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5342413 AGTTTGATTA
* *
5342423 AAAGTAGAGAATTTTATT
1 AAAGTAGAAAACTTTATT
*
5342441 GAAGTAGAAAACTTTATT
1 AAAGTAGAAAACTTTATT
5342459 AAAGTAG
1 AAAGTAG
5342466 TTTTTTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (18 bp):
AAAGTAGAAAACTTTATT
Found at i:5349790 original size:31 final size:31
Alignment explanation
Indices: 5349752--5349810 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5349742 TTTGAAAGAT
* *
5349752 CAAACGCCGCTAATTCTCTTGTTTTTAGCTC
1 CAAACGCCGCTAATTATCTTATTTTTAGCTC
*
5349783 CAAACGCCGTTAATTATCTTATTTTTAG
1 CAAACGCCGCTAATTATCTTATTTTTAG
5349811 TGGCATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (31 bp):
CAAACGCCGCTAATTATCTTATTTTTAGCTC
Found at i:5349836 original size:73 final size:77
Alignment explanation
Indices: 5349752--5349934 Score: 203
Period size: 82 Copynumber: 2.4 Consensus size: 77
5349742 TTTGAAAGAT
* * * *
5349752 CAAACGCCGCTAATTCTCTTGTTTTTAG-C-T-CCA-AACGCCGTTAATTATCTTATTTTTAGTG
1 CAAACGACGCTAATTATCTTGTTTTTAGCCTTACCACAACGCCGCTAATTATCTTATCTTTAGTG
**
5349813 GCATTTTTGTCA
66 GCATTTTTACCA
*
5349825 CAAACGACGCTAATTATCTTGTTTTTAGTGCCTTTTAGCCACAACGCCGCTAATTCTCTTATCTT
1 CAAACGACGCTAATTATCTTGTTTTTA--GCC--TTA-CCACAACGCCGCTAATTATCTTATCTT
*
5349890 TAGTGGCGTTTTTACCA
61 TAGTGGCATTTTTACCA
* *
5349907 CAAACGACGCTAATTTTGTTGTTTTTAG
1 CAAACGACGCTAATTATCTTGTTTTTAG
5349935 TGGCGTTTGT
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
73 25 0.27
75 1 0.01
76 1 0.01
79 1 0.01
80 1 0.01
81 3 0.03
82 59 0.65
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (77 bp):
CAAACGACGCTAATTATCTTGTTTTTAGCCTTACCACAACGCCGCTAATTATCTTATCTTTAGTG
GCATTTTTACCA
Found at i:5349929 original size:82 final size:82
Alignment explanation
Indices: 5349785--5349936 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 82
5349775 TTTAGCTCCA
* * **
5349785 AACGCCGTTAATTATCTTATTTTTAGTGGCATTTTTGTCACAAACGACGCTAATTATCTTGTTTT
1 AACGCCGCTAATTATCTTATCTTTAGTGGCATTTTTACCACAAACGACGCTAATTATCTTGTTTT
5349850 TAGTGCCTTTTAGCCAC
66 TAGTGCCTTTTAGCCAC
* * * *
5349867 AACGCCGCTAATTCTCTTATCTTTAGTGGCGTTTTTACCACAAACGACGCTAATTTTGTTGTTTT
1 AACGCCGCTAATTATCTTATCTTTAGTGGCATTTTTACCACAAACGACGCTAATTATCTTGTTTT
5349932 TAGTG
66 TAGTG
5349937 GCGTTTGTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 62 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (82 bp):
AACGCCGCTAATTATCTTATCTTTAGTGGCATTTTTACCACAAACGACGCTAATTATCTTGTTTT
TAGTGCCTTTTAGCCAC
Found at i:5349939 original size:42 final size:42
Alignment explanation
Indices: 5349783--5349942 Score: 173
Period size: 42 Copynumber: 3.9 Consensus size: 42
5349773 TTTTTAGCTC
* * * * **
5349783 CAAACGCCGTTAATTATCTTATTTTTAGTGGCATTTTTGTCA
1 CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTTTTACCA
*
5349825 CAAACGACGCTAATTATCTTGTTTTTAGT-GC-CTTTTAGCCA
1 CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTTTTA-CCA
* * * *
5349866 C-AACGCCGCTAATTCTCTTATCTTTAGTGGCGTTTTTACCA
1 CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTTTTACCA
* *
5349907 CAAACGACGCTAATTTTGTTGTTTTTAGTGGCGTTT
1 CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTT
5349943 GTAATACAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 27 0.28
41 11 0.11
42 60 0.61
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (42 bp):
CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTTTTACCA
Found at i:5349952 original size:42 final size:41
Alignment explanation
Indices: 5349783--5349961 Score: 146
Period size: 42 Copynumber: 4.3 Consensus size: 41
5349773 TTTTTAGCTC
* * * * **
5349783 CAAACGCCGTTAATTATCTTATTTTTAGTGGCATTTTTGTCA
1 CAAACGACGCTAATTATCTTGTTTTTAGTGGC-GTTTTAACA
* *
5349825 CAAACGACGCTAATTATCTTGTTTTTAGT-GCCTTTTAGC-
1 CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTTTAACA
* * * * *
5349864 CACAACGCCGCTAATTCTCTTATCTTTAGTGGCGTTTTTACCA
1 CA-AACGACGCTAATTATCTTGTTTTTAGTGGCG-TTTTAACA
* * *
5349907 CAAACGACGCTAATTTTGTTGTTTTTAGTGGCGTTTGTAATA
1 CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTT-TAACA
*
5349949 CAAAACGCCGCTA
1 C-AAACGACGCTA
5349962 TATATTATGA
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.02
40 28 0.25
41 7 0.06
42 62 0.56
43 12 0.11
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (41 bp):
CAAACGACGCTAATTATCTTGTTTTTAGTGGCGTTTTAACA
Found at i:5352952 original size:36 final size:36
Alignment explanation
Indices: 5352902--5352990 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
5352892 CATAAGTGAG
*
5352902 GAATG-TAACTAAATTCCACTTGAACAGCAGCAGTA
1 GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
5352937 GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
1 GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
*
5352973 GAATGTTGATTAAATTCC
1 GAATGTTAATTAAATTCC
5352991 CAACCGTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 5 0.10
36 46 0.90
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (36 bp):
GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
Found at i:5354418 original size:56 final size:59
Alignment explanation
Indices: 5354327--5354445 Score: 147
Period size: 56 Copynumber: 2.1 Consensus size: 59
5354317 GCGGCGTTTG
* ** * *
5354327 TAAACATAAACGCCACTAAAGTATGACTCTTTAGCGGCGTTTAT-AA-A-AAACGCCAC
1 TAAACACAAACGCCACTAAAGTACAACTCTATAGCGACGTTTATAAATACAAACGCCAC
*
5354383 TAAACACAAACGCCACTAAAGTACAAGC-CTATAGCGACGTTTGTAAATACAAACGCCAC
1 TAAACACAAACGCCACTAAAGTACAA-CTCTATAGCGACGTTTATAAATACAAACGCCAC
5354442 TAAA
1 TAAA
5354446 GTACAAGTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
56 36 0.68
57 3 0.06
58 1 0.02
59 13 0.25
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.20
Consensus pattern (59 bp):
TAAACACAAACGCCACTAAAGTACAACTCTATAGCGACGTTTATAAATACAAACGCCAC
Found at i:5354496 original size:41 final size:40
Alignment explanation
Indices: 5354390--5354686 Score: 301
Period size: 41 Copynumber: 7.2 Consensus size: 40
5354380 CACTAAACAC
* * *
5354390 AAACGCCACTAAAGTACAAGCCTATAGCGACGTTTGTAAATA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATA
*
5354432 CAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTA-A
1 -AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
5354472 CAAACCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
1 -AAA-CGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* * * * * *
5354514 AAATGCCACTAAAGTACTACTTTATCGCGGCGTTTTATATA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTGTATA
*
5354555 TAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAA
1 -AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT-A
* * * *
5354597 AAACGTCGA-TAAAGTACTACTCTATCGCGGCGTTTTGTATAA
1 AAACG-CCACTAAAGTACGAGTCTATAGCGGCG-TTTGTAT-A
* * * *
5354639 AAACACCATTAAAGTACGAGTCTATAGCGGCATTTGTTTAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT-A
5354680 AAACGCC
1 AAACGCC
5354687 GCTATAGTTA
Statistics
Matches: 219, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
40 29 0.13
41 93 0.42
42 62 0.28
43 35 0.16
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (40 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
Found at i:5354660 original size:83 final size:83
Alignment explanation
Indices: 5354390--5354686 Score: 368
Period size: 83 Copynumber: 3.6 Consensus size: 83
5354380 CACTAAACAC
* * * * * *
5354390 AAACGCCACTAAAGTACAAGCCTATAGCGACGTTTGTAAATACAAACGCCACTAAAGTACAAGTC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATAAAAACGCCACTAAAGTACTACTC
*
5354455 TATAGCGGCG-TTTGTA-ACA
64 TATCGCGGCGTTTTGTATA-A
* * *
5354474 AACCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT-AAAATGCCACTAAAGTACTACTTTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTA
* *
5354538 TCGCGGCGTTTTATATAT
66 TCGCGGCGTTTTGTATAA
* *
5354556 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAAAAACGTCGA-TAAAGTACTACTCT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACG-CCACTAAAGTACTACTCT
5354620 ATCGCGGCGTTTTGTATAA
65 ATCGCGGCGTTTTGTATAA
* * * *
5354639 AAACACCATTAAAGTACGAGTCTATAGCGGCATTTGTTTAAAAACGCC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
5354687 GCTATAGTTA
Statistics
Matches: 184, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
81 27 0.15
82 45 0.24
83 77 0.42
84 35 0.19
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (83 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTA
TCGCGGCGTTTTGTATAA
Found at i:5359979 original size:34 final size:30
Alignment explanation
Indices: 5359940--5360008 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
5359930 TCGATATAAC
*
5359940 AATTTAAGGCAAAATAGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
5359974 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
5360003 AATTTA
1 AATTTA
5360009 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:5360015 original size:31 final size:31
Alignment explanation
Indices: 5359949--5360008 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
5359939 CAATTTAAGG
*
5359949 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
5359980 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
5360009 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATAGTATTTGGACTTGAATTGAATTTA
Found at i:5360195 original size:21 final size:21
Alignment explanation
Indices: 5360169--5360210 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5360159 ATTTGAATAT
5360169 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
5360190 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
5360211 CCCATTCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:5360533 original size:34 final size:32
Alignment explanation
Indices: 5360494--5360563 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5360484 TTTTGTAAAG
*
5360494 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
5360528 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
5360560 GGGA
1 GGGA
5360564 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:5362786 original size:31 final size:31
Alignment explanation
Indices: 5362720--5362779 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
5362710 CAATTTAAGG
*
5362720 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
5362751 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
5362780 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATAGTATTTGGACTTGAATTGAATTTA
Found at i:5363023 original size:21 final size:21
Alignment explanation
Indices: 5362997--5363038 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5362987 ATTTGAATAT
*
5362997 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5363018 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5363039 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:5365979 original size:12 final size:12
Alignment explanation
Indices: 5365964--5366020 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
5365954 TAGAAATCAA
5365964 AACAGAATTCAG
1 AACAGAATTCAG
5365976 AACAG-ATATCAG
1 AACAGAAT-TCAG
* *
5365988 AACAGAATCCAT
1 AACAGAATTCAG
* * *
5366000 ATCAGAAATCAA
1 AACAGAATTCAG
5366012 AACAGAATT
1 AACAGAATT
5366021 TAGGTCATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 2 0.06
12 31 0.89
13 2 0.06
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:5365986 original size:24 final size:24
Alignment explanation
Indices: 5365959--5366046 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
5365949 GATATTAGAA
*
5365959 ATCAAAACAGAATTCAGAACAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
5365983 ATCAGAACAGAATCCATATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
* *
5366007 ATCAAAACAGAATTTAGGTCATG-T
1 ATCAAAACAGAATTCAGATCA-GAT
*
5366031 ATCAGAACAGAATTCA
1 ATCAAAACAGAATTCA
5366047 AGTCGAAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
24 49 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:5366058 original size:48 final size:48
Alignment explanation
Indices: 5365950--5366043 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
5365940 GTAAACGGAG
*
5365950 ATATTAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
* **
5365998 ATATCAGAAATCAAAACAGAATTTAGGTCATG-TATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAATTCAGAACA-GATATCAGAACAGAAT
5366044 TCAAGTCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
Found at i:5367818 original size:36 final size:36
Alignment explanation
Indices: 5367762--5367843 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
5367752 CTTTATTGAG
* *
5367762 ATAAATTATAATCTATATATCCATGGCTGATTCTTTT
1 ATAACTTA-AATCTACATATCCATGGCTGATTCTTTT
*
5367799 ATAACTTAAATCTACATATCCATGGTTGATTCTTTT
1 ATAACTTAAATCTACATATCCATGGCTGATTCTTTT
*
5367835 ATCACTTAA
1 ATAACTTAA
5367844 TTCCAGAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 34 0.83
37 7 0.17
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (36 bp):
ATAACTTAAATCTACATATCCATGGCTGATTCTTTT
Found at i:5368507 original size:8 final size:7
Alignment explanation
Indices: 5368481--5368510 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
5368471 GGTCAACTTT
5368481 GGTCAAC
1 GGTCAAC
5368488 GGTCAAC
1 GGTCAAC
5368495 GGTCAACC
1 GGTCAA-C
5368503 GGTCAAC
1 GGTCAAC
5368510 G
1 G
5368511 TGTCGGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:5368507 original size:15 final size:14
Alignment explanation
Indices: 5368481--5368510 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5368471 GGTCAACTTT
5368481 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
5368495 GGTCAACCGGTCAAC
1 GGTCAA-CGGTCAAC
5368510 G
1 G
5368511 TGTCGGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:5368547 original size:23 final size:22
Alignment explanation
Indices: 5368520--5368566 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 22
5368510 GTGTCGGATC
5368520 AACGGGACGGGTCAGGTTGGGT
1 AACGGGACGGGTCAGGTTGGGT
5368542 AA----ACGGGTCAGGTTGGGT
1 AACGGGACGGGTCAGGTTGGGT
5368560 AAACGGG
1 -AACGGG
5368567 TTAGGTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 9
0.69 0.00 0.31
Matches are distributed among these distances:
18 16 0.80
19 2 0.10
22 2 0.10
ACGTcount: A:0.23, C:0.13, G:0.47, T:0.17
Consensus pattern (22 bp):
AACGGGACGGGTCAGGTTGGGT
Found at i:5368573 original size:23 final size:18
Alignment explanation
Indices: 5368526--5368572 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
5368516 GATCAACGGG
5368526 ACGGGTCAGGTTGGGTAA
1 ACGGGTCAGGTTGGGTAA
5368544 ACGGGTCAGGTTGGGTAA
1 ACGGGTCAGGTTGGGTAA
*
5368562 ACGGGTTAGGT
1 ACGGGTCAGGT
5368573 CTGGTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.45, T:0.23
Consensus pattern (18 bp):
ACGGGTCAGGTTGGGTAA
Found at i:5372614 original size:7 final size:7
Alignment explanation
Indices: 5372599--5372628 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5372589 AACTTACCAA
*
5372599 ATTATAT
1 ATTAAAT
5372606 ATTAAAT
1 ATTAAAT
5372613 ATTAAAT
1 ATTAAAT
5372620 ATTAAAT
1 ATTAAAT
5372627 AT
1 AT
5372629 AATATTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATTAAAT
Found at i:5375489 original size:21 final size:21
Alignment explanation
Indices: 5375465--5375558 Score: 170
Period size: 21 Copynumber: 4.4 Consensus size: 21
5375455 ACCTGTCTAT
5375465 ACAACAATCATACAAACGAAA
1 ACAACAATCATACAAACGAAA
*
5375486 ACAACAATCTTACAAACGAAA
1 ACAACAATCATACAAACGAAA
5375507 ACAACAATCATACAAACGAAA
1 ACAACAATCATACAAACGAAA
5375528 ACAACAATCATACAAACGAAA
1 ACAACAATCATACAAACGAAA
5375549 ACTAACAATC
1 AC-AACAATC
5375559 TCCTTAATGC
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
21 63 0.90
22 7 0.10
ACGTcount: A:0.60, C:0.24, G:0.04, T:0.12
Consensus pattern (21 bp):
ACAACAATCATACAAACGAAA
Found at i:5382789 original size:15 final size:15
Alignment explanation
Indices: 5382769--5382799 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5382759 CAACAAATAG
5382769 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
5382784 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
5382799 A
1 A
5382800 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:5388890 original size:44 final size:44
Alignment explanation
Indices: 5388787--5389114 Score: 477
Period size: 44 Copynumber: 7.5 Consensus size: 44
5388777 ACCGTTACAG
* *
5388787 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTT-CCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
5388830 CAGGTCCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
5388874 CAGGTGCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
5388918 CAGGTCCCTTTGTTATGTGCAAGGGTAAGCGTTACAGTTTCCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* *
5388962 CATGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
5389006 CAAGTCCCTTTACTGTGTGCAATGGTAAGCCTTACAGTTT--CC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
5389048 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* *
5389091 CAGG-CTCTTTTGCTATGTGCAAGG
1 CAGGTC-CCTTTGCTGTGTGCAAGG
5389115 ACAAAACTTT
Statistics
Matches: 257, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
42 38 0.15
43 59 0.23
44 160 0.62
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (44 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
Found at i:5402477 original size:53 final size:53
Alignment explanation
Indices: 5402364--5402994 Score: 858
Period size: 53 Copynumber: 11.7 Consensus size: 53
5402354 TGGGTTCGCT
* * *
5402364 CCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTCAACAAACTT--GTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-TCACA--ATCTTCATC-AA-TTGCGTCTGCC
* *
5402419 CCCTATTTCTTCAGAGAGTATAAGAAC-CATAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCACAATCTTCATCAATTGCGTCTGCC
* * * *
5402472 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATTGCGTCTGCC
* * *
5402527 CCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
5402580 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATTGCGTCTGCC
* *
5402635 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGCCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
5402688 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
5402741 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATTGCGTCTGCC
*
5402796 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
*
5402849 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
* *
5402902 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCA-CGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTT-CATCAATTGCGTCTGCC
* *
5402957 CCCTATTTCTTCAGGGAGTATAAGACCCACAATCTTCA
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCA
5402995 ACAAATGGGT
Statistics
Matches: 524, Mismatches: 38, Indels: 31
0.88 0.06 0.05
Matches are distributed among these distances:
51 1 0.00
52 6 0.01
53 295 0.56
54 1 0.00
55 217 0.41
56 4 0.01
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (53 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATTGCGTCTGCC
Found at i:5403014 original size:108 final size:107
Alignment explanation
Indices: 5402364--5403051 Score: 955
Period size: 108 Copynumber: 6.4 Consensus size: 107
5402354 TGGGTTCGCT
* * *
5402364 CCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT--GTCTGCCCCCTATT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAAC-GA-TTGCGTCTGCCCCCTATT
* *
5402426 TCTTCAGAGAGTATAAGAACCATAATCTTCATCAATCGCGTCTGCC
63 TCTTCAGAGAGTATAAGACCCACAATCTTCATCAAT-GCGTCTGCC
* * *
5402472 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
5402537 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAAT-GCGTCTGCC
5402580 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
*
5402645 TCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGCCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAA-TGCGTCTGCC
5402688 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
* * *
5402751 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
66 TCAGAGAGTATAAGAC-C-CACAATCTTCATC-AATGCGTCTGCC
* * *
5402796 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
*
5402859 TCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAAT-GCGTCTGCC
* *
5402902 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
* * * *
5402967 TCAGGGAGTATAAGACCCACAATCTTCAACAAATGGGT-TCGCT
66 TCAGAGAGTATAAGACCCACAATCTTCATC-AATGCGTCT-GCC
* *
5403010 CCCTATTTC-TCTAGGGAGTAT-AGAACTCGAACATTTCTTCAA
1 CCCTATTTCTTC-AGAGAGTATAAG-ACTCGAACA-ATCTTCAA
5403052 ACGGGTTCGC
Statistics
Matches: 531, Mismatches: 33, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
105 2 0.00
106 99 0.19
107 10 0.02
108 409 0.77
109 11 0.02
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (107 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCATCAATGCGTCTGCC
Found at i:5403031 original size:161 final size:161
Alignment explanation
Indices: 5402364--5402998 Score: 963
Period size: 161 Copynumber: 3.9 Consensus size: 161
5402354 TGGGTTCGCT
* * * **
5402364 CCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTCAACAAACTTGTCTGCCCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAGAC-TCACA--ATCTTCAACAATCGCGTCTGCCCCCTATTTC
* * *
5402428 TTCAGAGAGTATAAGAAC-C--ATAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
63 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * *
5402490 TATAAGACTCGAACGATCTTCAACGATTGTGTCTGCC
127 TATAAGAC-C-CACAATCTTCAACAATTGCGTCTGCC
* * *
5402527 CCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
*
5402592 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
* *
5402657 AGACCCACAATCTTCATCAATTGCGCCTGCC
131 AGACCCACAATCTTCAACAATTGCGTCTGCC
* *
5402688 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
*
5402753 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
*
5402818 AGACCCACAATCTTCATCAATTGCGTCTGCC
131 AGACCCACAATCTTCAACAATTGCGTCTGCC
*
5402849 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
* *
5402914 AGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCTTCAGGGAGTATA
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
5402979 AGACCCACAATCTTCAACAA
131 AGACCCACAATCTTCAACAA
5402999 ATGGGTTCGC
Statistics
Matches: 437, Mismatches: 31, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
160 2 0.00
161 361 0.83
162 2 0.00
163 72 0.16
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (161 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTC
AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
AGACCCACAATCTTCAACAATTGCGTCTGCC
Found at i:5403117 original size:51 final size:50
Alignment explanation
Indices: 5402996--5403449 Score: 523
Period size: 51 Copynumber: 8.8 Consensus size: 50
5402986 CAATCTTCAA
* * * * *
5402996 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACATTTCTT
1 CAAACGGGTTCGCTCCTTCTTT-TTTAAGGAGTATAGAACTCGAACA--TCTT
* * *
5403049 CAAACGGGTTCGCTCCTTATTCTTTTCAGGGGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTT-TTTTAAGGAGTATAGAACTCGAACATCTT
*
5403100 CAAACGGGTTCGCTCCTTCCTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTT-CTTTTTTAAGGAGTATAGAACTCGAACATCTT
5403151 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTT-TTTAAGGAGTATAGAACTCGAACATCTT
* * * *
5403202 CAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTC-AGACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTT-TTTAAGGAGTATAGAACTCGA-ACA--TCTT
* *
5403255 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTTGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTT-TTTAAGGAGTATAGAACTCGAACATCTT
* * *
5403306 TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTT
1 CAAACGGGTTCGCTCCTTCTTT-TTTAAGGAGTATAGAACTCGAACATCTT
* * * * * *
5403357 CACACGGGTTCGCTCATTCTTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCTTCTTT-TTTAAGGAGTATAGAACTCGAACATCTT
* * * *
5403408 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 CAAACGGGTTCGCTCCTTCTTT-TTTAAGGAGTATAGAACTC
5403450 AAATAATCTT
Statistics
Matches: 359, Mismatches: 35, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
50 4 0.01
51 267 0.74
52 2 0.01
53 84 0.23
54 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (50 bp):
CAAACGGGTTCGCTCCTTCTTTTTTAAGGAGTATAGAACTCGAACATCTT
Found at i:5403218 original size:206 final size:206
Alignment explanation
Indices: 5402996--5403450 Score: 698
Period size: 206 Copynumber: 2.2 Consensus size: 206
5402986 CAATCTTCAA
* * *
5402996 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTC-GAACATTTCTTCAAACGGGTTC
1 CAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAG-ACATCTCTTCAAACGGGTTC
* *
5403060 GCTCCTTA-TTCTTTTCAGGGGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCCTTCT
65 GCTCCTTATTTC-TTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCCTTCT
* *
5403124 TTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGA
129 TTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCATTCTTTCTCTAAGGAGTATAGA
5403189 ACTCGAACATCTT
194 ACTCGAACATCTT
*
5403202 CAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCAGACATCTCTTCAAACGGGTTCG
1 CAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACATCTCTTCAAACGGGTTCG
* * * * *
5403267 CTCCTTCTTTCTTTAAGGAGTATGGAACTTGAACATCTTTAAACGGGTTCGCTCCTTCTTTCTTT
66 CTCCTTATTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCCTTCTTT
* * * * *
5403332 AAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCTCATTCTTTCTCTAGGGAGTATGGAAC
131 AAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCATTCTTTCTCTAAGGAGTATAGAAC
*
5403397 TCGGACATCTT
196 TCGAACATCTT
*
5403408 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
1 CAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
5403451 AATAATCTTC
Statistics
Matches: 226, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
206 222 0.98
207 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (206 bp):
CAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACATCTCTTCAAACGGGTTCG
CTCCTTATTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCCTTCTTT
AAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCATTCTTTCTCTAAGGAGTATAGAAC
TCGAACATCTT
Found at i:5403283 original size:155 final size:153
Alignment explanation
Indices: 5402996--5403449 Score: 612
Period size: 155 Copynumber: 2.9 Consensus size: 153
5402986 CAATCTTCAA
* * * * *
5402996 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACATTTCTTCAAACGGGTTCG
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCG
* *
5403061 CT-CCT-TATTCTTTTCAGGG-GTATAGAACTCGA-ACATCTTCAAACGGGTTCGCTCCTTCCTT
64 CTCCCTCT-TTC-TTT-AGGGAGTATGGAACTCGACAC-TCTTCAAACGGGTTCGCTCCTTCTTT
*
5403122 CTTTAAGGAGTATAGAACTCGAACATCTT
125 CTTTAAGGAGTATGGAACTCGAACATCTT
*
5403151 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAATGGGTTCGCT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
5403216 CCCTCTTTCTTTAGGGAGTATGGAACTCAGACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTT
66 CCCTCTTTCTTTAGGGAGTATGGAACTC-GACA-CTCTTCAAACGGGTTCGCTCCTTCTTTCTTT
*
5403281 AAGGAGTATGGAACTTGAACATCTT
129 AAGGAGTATGGAACTCGAACATCTT
* * * *
5403306 TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
** * * *
5403371 CATTCTTTCTCTAGGGAGTATGGAACTCGGACA-TCTTCAAACGGGTTCGCTCCCTCTTTCTCTA
66 CCCTCTTTCTTTAGGGAGTATGGAACTC-GACACTCTTCAAACGGGTTCGCTCCTTCTTTCTTTA
*
5403435 GGGAGTATGGAACTC
130 AGGAGTATGGAACTC
5403450 AAATAATCTT
Statistics
Matches: 270, Mismatches: 23, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
152 4 0.01
153 72 0.27
154 8 0.03
155 185 0.69
156 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (153 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
CCCTCTTTCTTTAGGGAGTATGGAACTCGACACTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAA
GGAGTATGGAACTCGAACATCTT
Found at i:5403889 original size:36 final size:36
Alignment explanation
Indices: 5403865--5404091 Score: 339
Period size: 36 Copynumber: 6.3 Consensus size: 36
5403855 ACTACTTTTT
* * * *
5403865 GGTGAAGACTTAAGATGGTTTGCTTCACTACTCTCT
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
*
5403901 GGTGAAGACTT-ATGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGGCTTCA-GATGGTTTGCTTCACTATTCTCC
* * *
5403937 GGTGAAGGCTTCAGATTGATTGCTTCCCTATTCTCC
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
*
5403973 GATGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
* *
5404009 GGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCC
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
5404045 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
5404081 GGTGAAGGCTT
1 GGTGAAGGCTT
5404092 AGGATTGACT
Statistics
Matches: 174, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
35 1 0.01
36 172 0.99
37 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (36 bp):
GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
Found at i:5403999 original size:108 final size:108
Alignment explanation
Indices: 5403831--5404092 Score: 339
Period size: 108 Copynumber: 2.4 Consensus size: 108
5403821 ACTCTTCTGA
* * ** * *
5403831 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGTGAAGACTTAAGATGGTTTGCTTCACTA
1 GAAGGCTTCAGATGGAT-TGCTTCACTA-TTCTCCGATGAAGGCTTAAGATGGTTTGCTTCACTA
* *
5403895 CTCTCTGGTGAAGACTT-ATGATGGTTTGCTTCACTATTCTCCGGT
64 CTCTCCGGTGAAGACTTCA-GATGGATTGCTTCACTATTCTCCGGT
* * * *
5403940 GAAGGCTTCAGATTGATTGCTTCCCTATTCTCCGATGAAGGCTTCAGATGGTTTGCTTCACTATT
1 GAAGGCTTCAGATGGATTGCTTCACTATTCTCCGATGAAGGCTTAAGATGGTTTGCTTCACTACT
* *
5404005 CTCCGGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
66 CTCCGGTGAAGACTTCAGATGGATTGCTTCACTATTCTCCGGT
* *
5404048 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTA
1 GAAGGCTTCAGATGGATTGCTTCACTATTCTCCGATGAAGGCTTA
5404093 GGATTGACTT
Statistics
Matches: 132, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
107 2 0.02
108 115 0.87
109 15 0.11
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (108 bp):
GAAGGCTTCAGATGGATTGCTTCACTATTCTCCGATGAAGGCTTAAGATGGTTTGCTTCACTACT
CTCCGGTGAAGACTTCAGATGGATTGCTTCACTATTCTCCGGT
Found at i:5418603 original size:57 final size:57
Alignment explanation
Indices: 5418515--5418631 Score: 207
Period size: 57 Copynumber: 2.1 Consensus size: 57
5418505 AGATGGAACC
*
5418515 TCCAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTATGAAGA
1 TCCAGCACATCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTATGAAGA
* *
5418572 TCCAGCACATCTGCAGCAAAACCAAGAATCTGATCCTGGTCCAAGATCTTGTGAAGA
1 TCCAGCACATCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTATGAAGA
5418629 TCC
1 TCC
5418632 TTTAGGTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.21
Consensus pattern (57 bp):
TCCAGCACATCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTATGAAGA
Found at i:5424682 original size:13 final size:14
Alignment explanation
Indices: 5424650--5424686 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5424640 ATAAAGAAAA
5424650 TAAT-AAATTAAAG
1 TAATGAAATTAAAG
5424663 TAATGAAATTAAAG
1 TAATGAAATTAAAG
*
5424677 -ACTGAAATTA
1 TAATGAAATTA
5424687 TATAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.30
Consensus pattern (14 bp):
TAATGAAATTAAAG
Found at i:5424888 original size:15 final size:16
Alignment explanation
Indices: 5424863--5424892 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5424853 TTTCAAACAT
5424863 AAAATAAATAAATAAG
1 AAAATAAATAAATAAG
5424879 AAAA-AAATAAATAA
1 AAAATAAATAAATAA
5424893 AAATTAGCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAATAAATAAATAAG
Found at i:5425111 original size:130 final size:129
Alignment explanation
Indices: 5424975--5425272 Score: 463
Period size: 129 Copynumber: 2.3 Consensus size: 129
5424965 GCGGGTTGTA
* *
5424975 CCCGGATCGGGTCACCGCAA-AGTTGTATAATAATTCGAACATAAAATAAAATACATAAATAAAA
1 CCCGGATCGGGTCACCACAAGA-TCGTATAATAATTCGAACATAAAATAAAATACATAAATAAAA
* * *
5425039 GGTTAATAGTTAAAAGTTAACGGTTAGATGTTAACAGAGTCCATAACATAATAATTTGGATCGTA
65 -GTTAATAGTTAAAAGTTAACGATTAGATGTTAACAGAGTCCAGAACATAATAATGTGGATCGTA
5425104 C
129 C
*
5425105 CCCGGATCGGGTCACCACAAGATCGTATAATAATTCAAACATAAAATAAAATACATAAATAAAAG
1 CCCGGATCGGGTCACCACAAGATCGTATAATAATTCGAACATAAAATAAAATACATAAATAAAAG
* * * *
5425170 TTATTGGTTAAAAGTTAGCGATTAGATGTTAACAGAGTCCAGACCATAATAATGTGGATCGTAC
66 TTAATAGTTAAAAGTTAACGATTAGATGTTAACAGAGTCCAGAACATAATAATGTGGATCGTAC
* *
5425234 CTCGGATCGGGTCACCACAAGATCGTATAATAATCCGAA
1 CCCGGATCGGGTCACCACAAGATCGTATAATAATTCGAA
5425273 AACTAATAAC
Statistics
Matches: 154, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
129 94 0.61
130 59 0.38
131 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (129 bp):
CCCGGATCGGGTCACCACAAGATCGTATAATAATTCGAACATAAAATAAAATACATAAATAAAAG
TTAATAGTTAAAAGTTAACGATTAGATGTTAACAGAGTCCAGAACATAATAATGTGGATCGTAC
Found at i:5429361 original size:18 final size:16
Alignment explanation
Indices: 5429324--5429362 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
5429314 GTGCAATGTA
*
5429324 AAAATAAAAACAAAAT
1 AAAATAAAAACAAAAG
5429340 AAAATAAAAAGGCAAAAG
1 AAAATAAAAA--CAAAAG
5429358 AAAAT
1 AAAAT
5429363 TAGTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (16 bp):
AAAATAAAAACAAAAG
Found at i:5450106 original size:6 final size:7
Alignment explanation
Indices: 5450097--5450144 Score: 53
Period size: 8 Copynumber: 6.4 Consensus size: 7
5450087 AAATTAAATT
5450097 TATTA-A
1 TATTATA
5450103 TATTATA
1 TATTATA
5450110 TATATATA
1 TAT-TATA
5450118 TATATATA
1 TAT-TATA
5450126 TATATATA
1 TAT-TATA
5450134 TATATATA
1 TAT-TATA
5450142 TAT
1 TAT
5450145 AAAATAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 5 0.12
7 4 0.10
8 31 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TATTATA
Found at i:5450113 original size:2 final size:2
Alignment explanation
Indices: 5450102--5450145 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5450092 AAATTTATTA
5450102 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5450143 AT A
1 AT A
5450146 AAATAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5450286 original size:35 final size:36
Alignment explanation
Indices: 5450240--5450308 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
5450230 AAACTCGTCC
5450240 CGTCCCCGTTTAACATAAACGG-TTTTCCCCATCAT
1 CGTCCCCGTTTAACATAAACGGTTTTTCCCCATCAT
*
5450275 CGTCCCCGTTTAGCATAAACGGTTTTTCCCCATC
1 CGTCCCCGTTTAACATAAACGGTTTTTCCCCATC
5450309 CCGTTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.66
36 11 0.34
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (36 bp):
CGTCCCCGTTTAACATAAACGGTTTTTCCCCATCAT
Found at i:5451677 original size:2 final size:2
Alignment explanation
Indices: 5451670--5451699 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5451660 ACGGATCTTT
5451670 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
5451700 AAAGCAAGGT
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:5452451 original size:38 final size:39
Alignment explanation
Indices: 5452393--5452470 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
5452383 CCGGAATAAA
*
5452393 TATAAAGTAATACCGATTTAAAAATAACACTAAATTATT
1 TATAAAGTAATACCGATTTAAAAATAACACTAAATCATT
** *
5452432 TATAAA-TAATATTGATTTAAAAATAACTCTAAATCATT
1 TATAAAGTAATACCGATTTAAAAATAACACTAAATCATT
5452470 T
1 T
5452471 TATTTCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 29 0.83
39 6 0.17
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (39 bp):
TATAAAGTAATACCGATTTAAAAATAACACTAAATCATT
Found at i:5452470 original size:21 final size:20
Alignment explanation
Indices: 5452408--5452470 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
5452398 AGTAATACCG
*
5452408 ATTTAAAAATAACACTAAATT
1 ATTTAAAAATAAC-CTAAATC
* * *
5452429 ATTTATAAATAA--T-ATTG
1 ATTTAAAAATAACCTAAATC
5452446 ATTTAAAAATAACTCTAAATC
1 ATTTAAAAATAAC-CTAAATC
5452467 ATTT
1 ATTT
5452471 TATTTCATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 13 0.41
18 1 0.03
20 1 0.03
21 17 0.53
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTAAAAATAACCTAAATC
Found at i:5452486 original size:13 final size:13
Alignment explanation
Indices: 5452468--5452494 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5452458 CTCTAAATCA
5452468 TTTTATTTCATAT
1 TTTTATTTCATAT
5452481 TTTTATTTCATAT
1 TTTTATTTCATAT
5452494 T
1 T
5452495 GAACGCCGAG
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:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATTTCATAT
Found at i:5452658 original size:33 final size:33
Alignment explanation
Indices: 5452616--5452680 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5452606 CTGTTTCACC
* *
5452616 ATTGAAAAACATCCT-TCCTCTTTTGAAGGAAAG
1 ATTGAAAAACAACCTCT-CTCTTTTAAAGGAAAG
5452649 ATTGAAAAACAACCTCTCTCTTTTAAAGGAAA
1 ATTGAAAAACAACCTCTCTCTTTTAAAGGAAA
5452681 TATAATCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (33 bp):
ATTGAAAAACAACCTCTCTCTTTTAAAGGAAAG
Found at i:5454166 original size:29 final size:32
Alignment explanation
Indices: 5454109--5454168 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
5454099 ATTTCAAAAT
5454109 TATAATTATGAAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAAATATATTAATTTATA
* *
5454141 TATATTTAT-AAATAAAATAT-TT-ATTTAT
1 TATAATTATGAAAAAAAATATATTAATTTAT
5454169 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.23
30 2 0.08
31 10 0.38
32 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
TATAATTATGAAAAAAAATATATTAATTTATA
Found at i:5454263 original size:20 final size:19
Alignment explanation
Indices: 5454224--5454265 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5454214 TTTCTTCGAT
5454224 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
5454243 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
5454263 ATT
1 ATT
5454266 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:5454448 original size:3 final size:3
Alignment explanation
Indices: 5454440--5454469 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5454430 TTTATGGCTA
*
5454440 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5454470 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5455774 original size:3 final size:3
Alignment explanation
Indices: 5455766--5455834 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
5455756 TAAAATTATT
* * * *
5455766 TAA TAA TAA TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5455813 TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
5455835 TTCAAATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.85
4 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5455833 original size:38 final size:37
Alignment explanation
Indices: 5455743--5455833 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 37
5455733 TTAGGTTTGT
*
5455743 AATAGTAAATAAATAAAATTATTTAATAATAATAATAA
1 AATA-TAAATAATTAAAATTATTTAATAATAATAATAA
* *
5455781 TATAATAATTATAATTATAATTATAATT-ATAATAATAATAA
1 AAT-ATAA--ATAATTAAAATTAT--TTAATAATAATAATAA
5455822 AATATAAATAAT
1 AATATAAATAAT
5455834 ATTCAAATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
38 10 0.23
39 1 0.02
40 16 0.36
41 15 0.34
42 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (37 bp):
AATATAAATAATTAAAATTATTTAATAATAATAATAA
Found at i:5456431 original size:113 final size:113
Alignment explanation
Indices: 5456175--5456849 Score: 982
Period size: 113 Copynumber: 6.0 Consensus size: 113
5456165 ATAGAGTTAT
* *
5456175 GCAAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * **
5456240 ATTATGAACACT-TCTGGCAATA-CTGATCCATCAAATGATGAATTCAA
66 ATTATGAACTTTCTCTGG-AAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
5456287 ACAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
5456352 ATTATGAACTTTCTCTGGAAATGCTGATCCATCAGGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
5456400 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
5456465 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
5456513 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * **
5456578 ATTATGAAC-TT-TCTGGCAATA-TTGATCCATCAAATGATGAATTCAA
66 ATTATGAACTTTCTCTGG-AAAAGCTGATCCATCAAGTGATGGATTTGA
* *
5456624 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
5456689 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * * * * *
5456737 GTAAAAGGTTGAACAAGCTATTCTCATTATAAACTTCTTCTTTCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
5456802 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
5456850 ATCTTTGCTA
Statistics
Matches: 513, Mismatches: 44, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
111 97 0.19
112 84 0.16
113 332 0.65
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:5456677 original size:337 final size:338
Alignment explanation
Indices: 5456175--5456849 Score: 1185
Period size: 337 Copynumber: 2.0 Consensus size: 338
5456165 ATAGAGTTAT
* *
5456175 GCAAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
5456240 ATTATGAACACTTCTGGCAATACTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 ATTATGAACACTTCTGGCAATACTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
*
5456305 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * *
5456370 AAATGCTGATCCATC-AGGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
196 AAAAGCTGATCCATCGA-GTGATGGATTTGAGCAAAAGGTTGAACAAGCTATTCTCATTATAAAC
* *
5456434 TTCTTC-TTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATC
260 TTCTTCTTTC-TTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
5456498 AAGTGATGGATTTGA
324 AAGTGATGGATTTGA
*
5456513 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
5456578 ATTATGAAC-TTTCTGGCAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 ATTATGAACACTTCTGGCAATACTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
5456642 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
5456707 AAAAGTTGATCCATCGAGTGATGGATTTGAGTAAAAGGTTGAACAAGCTATTCTCATTATAAACT
196 AAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTATTCTCATTATAAACT
*
5456772 TCTTCTTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGA
261 TCTTCTTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
5456837 GTGATGGATTTGA
326 GTGATGGATTTGA
5456850 ATCTTTGCTA
Statistics
Matches: 321, Mismatches: 14, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
337 246 0.77
338 75 0.23
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (338 bp):
GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACACTTCTGGCAATACTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTATTCTCATTATAAACT
TCTTCTTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
GTGATGGATTTGA
Found at i:5456697 original size:224 final size:224
Alignment explanation
Indices: 5456176--5456834 Score: 964
Period size: 224 Copynumber: 2.9 Consensus size: 224
5456166 TAGAGTTATG
*
5456176 CAAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * * * ** * *
5456241 TTATGAACACT-TCTGGCAATA-CTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
66 TTATGAACTTTCTCTGG-AAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
* *
5456304 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
130 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TT-TCTG
* ** * ** *
5456369 GAAATGCTGATCCATCAGGTGATGGATTTGAG
193 GAAATACTGATCCATCAAATGATGAATTCAAA
** *
5456401 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
5456466 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
5456531 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGCA
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAA
*
5456596 ATATTGATCCATCAAATGATGAATTCAAA
196 ATACTGATCCATCAAATGATGAATTCAAA
5456625 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
5456690 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGATTTGAGTAAAAGGTTGAACAAGC
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
* * * *
5456755 TATTCTCATTATAAACTTCTTCTTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TT-TCTGG
5456820 AAA-AGCTGATCCATC
194 AAATA-CTGATCCATC
5456835 GAGTGATGGA
Statistics
Matches: 393, Mismatches: 36, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
224 204 0.52
225 78 0.20
226 111 0.28
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (224 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAA
ATACTGATCCATCAAATGATGAATTCAAA
Found at i:5458386 original size:16 final size:15
Alignment explanation
Indices: 5458365--5458421 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
5458355 TTGACCCTCC
5458365 TTTTTTTTCTTTTCT
1 TTTTTTTTCTTTTCT
5458380 TTTTTTTTCTTTT-T
1 TTTTTTTTCTTTTCT
5458394 CTTTTTTTTC-TTTCT
1 -TTTTTTTTCTTTTCT
*
5458409 TCTTTTTTCTTTT
1 TTTTTTTTCTTTT
5458422 TTCATTTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTTCTTTTCT
Found at i:5458424 original size:30 final size:30
Alignment explanation
Indices: 5458364--5458422 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
5458354 CTTGACCCTC
*
5458364 CTTTTTTTTCTTTTCTTTTTTTTTCTTTTT
1 CTTTTTTTTCTTTTCTTCTTTTTTCTTTTT
5458394 CTTTTTTTTC-TTTCTTCTTTTTTCTTTTT
1 CTTTTTTTTCTTTTCTTCTTTTTTCTTTTT
5458423 TCATTTCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (30 bp):
CTTTTTTTTCTTTTCTTCTTTTTTCTTTTT
Found at i:5458438 original size:30 final size:28
Alignment explanation
Indices: 5458374--5458440 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
5458364 CTTTTTTTTC
* **
5458374 TTTTCTTTTTTTTTCTTTTTCTTTTTTT
1 TTTTCTTCTTTTTTCTTTTTCTTTCATT
5458402 TCTTTCTTCTTTTTTCTTTTTTCATTTCATT
1 T-TTTCTTCTTTTTTC-TTTTTC-TTTCATT
5458433 TTTTCTTC
1 TTTTCTTC
5458441 AAGCATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 13 0.39
30 13 0.39
31 6 0.18
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTTCTTCTTTTTTCTTTTTCTTTCATT
Found at i:5461977 original size:9 final size:9
Alignment explanation
Indices: 5461954--5461984 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5461944 GAAAAATAAT
5461954 GAATGTAAA
1 GAATGTAAA
5461963 -AATGTAAA
1 GAATGTAAA
5461971 GAATGTAAA
1 GAATGTAAA
5461980 GAATG
1 GAATG
5461985 ATTGCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:5465766 original size:15 final size:15
Alignment explanation
Indices: 5465743--5465774 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5465733 TGCAATGAAT
5465743 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
5465758 AATGCATGTATGCAA
1 AATGAATGTATGCAA
5465773 AA
1 AA
5465775 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:5469669 original size:29 final size:32
Alignment explanation
Indices: 5469612--5469671 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
5469602 ATTTCAAAAT
5469612 TATAATTATGAAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAAATATATTAATTTATA
* *
5469644 TATATTTAT-AAATAAAATAT-TT-ATTTAT
1 TATAATTATGAAAAAAAATATATTAATTTAT
5469672 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.23
30 2 0.08
31 10 0.38
32 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
TATAATTATGAAAAAAAATATATTAATTTATA
Found at i:5469766 original size:20 final size:19
Alignment explanation
Indices: 5469727--5469768 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5469717 TTTCTTCGAT
5469727 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
5469746 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
5469766 ATT
1 ATT
5469769 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:5469879 original size:120 final size:120
Alignment explanation
Indices: 5469640--5469872 Score: 294
Period size: 120 Copynumber: 2.0 Consensus size: 120
5469630 TATATTAATT
* * *
5469640 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAAGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCT
* * *
5469705 TAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAATAATTAA
66 TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * * *
5469760 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGACATCCAGGTGC
* * *
5469824 TTTAAGACTGC-CCTTTCTT-AATATTCAAAAATAAATAAAT-ATTAAAACA
64 CTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
5469873 GGATTAAAAT
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 8 0.08
119 25 0.26
120 46 0.47
121 18 0.19
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCT
TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:5471277 original size:3 final size:3
Alignment explanation
Indices: 5471262--5471330 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
5471252 TAAAATTATT
* * * * *
5471262 TAA TAA TAC TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5471309 TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
5471331 TTCAAATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
2 6 0.12
3 44 0.85
4 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5472882 original size:60 final size:60
Alignment explanation
Indices: 5472760--5472873 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
5472750 CGGATGATCA
* *
5472760 TTTTAATAGTTGAGGGACTTAACAAAGTAACATTCTATAGTTAGAGGACCATTTTGTAAC
1 TTTTAATAGTCGAAGGACTTAACAAAGTAACATTCTATAGTTAGAGGACCATTTTGTAAC
* * * * *
5472820 TTTTAATAGTCGAATGACTTAATAAAGTAATATTTTATAGTCTAG-GGATCATTT
1 TTTTAATAGTCGAAGGACTTAACAAAGTAACATTCTATAGT-TAGAGGACCATTT
5472874 GTGCACTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (60 bp):
TTTTAATAGTCGAAGGACTTAACAAAGTAACATTCTATAGTTAGAGGACCATTTTGTAAC
Found at i:5473253 original size:28 final size:29
Alignment explanation
Indices: 5473204--5473271 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
5473194 ATTATTTTGA
*
5473204 TAAAAAAAATATTAAGTTAAAT-ATT-TT
1 TAAAAAAAATATGAAGTTAAATAATTATT
5473231 TAAAAAATAATATGAA-TTAAAATAATTATT
1 TAAAAAA-AATATGAAGTT-AAATAATTATT
*
5473261 TAAACAAAATA
1 TAAAAAAAATA
5473272 AAAGTAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.26
28 11 0.31
29 7 0.20
30 8 0.23
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (29 bp):
TAAAAAAAATATGAAGTTAAATAATTATT
Found at i:5473644 original size:26 final size:26
Alignment explanation
Indices: 5473608--5473659 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5473598 TAAAATTAAT
* *
5473608 ATATTTAATTTT-TGATAATATTATAA
1 ATATATAATTTTATAAT-ATATTATAA
5473634 ATATATAATTTTATAATATATTATAA
1 ATATATAATTTTATAATATATTATAA
5473660 TTTAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
ATATATAATTTTATAATATATTATAA
Found at i:5473647 original size:16 final size:18
Alignment explanation
Indices: 5473622--5473662 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
5473612 TTAATTTTTG
*
5473622 ATAATATTATAA-ATA-T
1 ATAATTTTATAATATATT
5473638 ATAATTTTATAATATATT
1 ATAATTTTATAATATATT
5473656 ATAATTT
1 ATAATTT
5473663 AATTAATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAATTTTATAATATATT
Found at i:5474384 original size:2 final size:2
Alignment explanation
Indices: 5474377--5474424 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5474367 TCTTATTCTT
5474377 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
5474419 TA TA TA
1 TA TA TA
5474425 ATTGGTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5474862 original size:5 final size:5
Alignment explanation
Indices: 5474852--5474880 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5474842 AACTAACTGA
5474852 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
5474881 AGAGATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:5489315 original size:29 final size:28
Alignment explanation
Indices: 5489282--5489345 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
5489272 ATTGTATTGT
5489282 TTATACTACTGAACTTTTAATT-TTATCAA
1 TTATAC-ACTGAAC-TTTAATTGTTATCAA
* *
5489311 TTATAGCATTGAACTTTAATTGTTTTCAA
1 TTATA-CACTGAACTTTAATTGTTATCAA
5489340 TTATAC
1 TTATAC
5489346 CACTTGACCG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 8 0.26
29 22 0.71
30 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (28 bp):
TTATACACTGAACTTTAATTGTTATCAA
Found at i:5491348 original size:16 final size:16
Alignment explanation
Indices: 5491314--5491354 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5491304 TAAATAAATA
5491314 AAAATTAAA-GGGTAG
1 AAAATTAAATGGGTAG
* *
5491329 AAAATTAAATGTGTAT
1 AAAATTAAATGGGTAG
5491345 AAAATTAAAT
1 AAAATTAAAT
5491355 AACAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (16 bp):
AAAATTAAATGGGTAG
Found at i:5492263 original size:2 final size:2
Alignment explanation
Indices: 5492258--5492299 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5492248 TCACTCTCTT
5492258 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
5492300 CACATACGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5492630 original size:15 final size:15
Alignment explanation
Indices: 5492610--5492647 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
5492600 AAAGATAGAG
5492610 AAATGGAGCCAAAGA
1 AAATGGAGCCAAAGA
5492625 AAATGGAGCCAAAGA
1 AAATGGAGCCAAAGA
5492640 AAATGGAG
1 AAATGGAG
5492648 TAAAAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.53, C:0.11, G:0.29, T:0.08
Consensus pattern (15 bp):
AAATGGAGCCAAAGA
Found at i:5493888 original size:242 final size:236
Alignment explanation
Indices: 5493398--5494168 Score: 985
Period size: 242 Copynumber: 3.2 Consensus size: 236
5493388 TCTTTTATCC
* * * * ** * * *
5493398 TGCTCGAAGGTCTTACAGATGACCCGAAAGATCTGGGCATCATGCTCAAAAGACTTATTAATGGC
1 TGCTCGAAAGACTTATAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTAATGATGG-
* * *
5493463 CCGAAAGAATAACTAAGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATCAATTTTTT
65 CCGAAAGACTTACTAAGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATCAA-TTTTC
* * *
5493528 ATAAAAGGTTTAAATGAGAAACTTTGGAAATTGA-TTT-TTCATTTTTTGAAAATCATGTGAAAA
129 AGAAAAGATTTAAATGAGAAACTTTGGAAA-TCACTTTCTT-ATTTTTTGAAAATCATGTGAAAA
5493591 CATCCTGCCAGAAGGTCTTATGGAT-GACCCGAATGACTTATCATCT
192 CATCCTGCC-GAAGGTCTTATGGATGGA-CCGAATGACTTATCATCT
* * * *
5493637 TGCTCGAAAGACTTATAGATGGCCCGAAAGATTTAGGAATCATGCTTGAAAGACTTAATGATGGC
1 TGCTCGAAAGACTTATAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTAATGATGGC
* *
5493702 TCGAAGGACTTACTAAGTAAGAAACTTT-AGAAATCGTTTTCTTATTTTTTTCAAAAATCAATTT
66 -CGAAAGACTTACTAAGTAAGAAACTTTGA-AAATCGTTTTCTTA--CTTTTCAAAAATCAATTT
* *
5493766 TCAGAAAAGATTTAAATGGGAAATTTTGGAAATCACTTTCTTATTTTTTTTGAAAATCATGTGAA
127 TCAGAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTTA--TTTTTTGAAAATCATGTGAA
* *
5493831 AACATCCTGCACGAAGCTCTTATAGATGGACCGAATGACTTATCATCT
190 AACATCCTGC-CGAAGGTCTTATGGATGGACCGAATGACTTATCATCT
* * *
5493879 TGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTAATGATGAC
1 TGCTCGAAAGACTTATAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTAATGATGGC
* * * * *
5493944 CTGAATGACTTACTAAGTAAGAAGCTTTGTAAATCATTTTCTTACTTTTCAAGAATCAATTTTCA
66 C-GAAAGACTTACTAAGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATCAATTTTCA
* *
5494009 GAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCA-TTTTTGAAAATCACGTGAAAACAT
130 GAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTTATTTTTTGAAAATCATGTGAAAACAT
* * * * *
5494073 CATGCCCGAAGGTATTATGGATGGCCCAAAGGACTTATCATCT
195 CCTG-CCGAAGGTCTTATGGATGGACCGAATGACTTATCATCT
* * *
5494116 TACTCGAAAGACTTATAGATTACCCGAAAGATTTAAGCATCATGCTTGAAAGA
1 TGCTCGAAAGACTTATAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGA
5494169 TATAAGCATC
Statistics
Matches: 467, Mismatches: 52, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
237 105 0.22
238 3 0.01
239 93 0.20
240 90 0.19
241 17 0.04
242 156 0.33
243 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (236 bp):
TGCTCGAAAGACTTATAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTAATGATGGC
CGAAAGACTTACTAAGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATCAATTTTCAG
AAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTTATTTTTTGAAAATCATGTGAAAACATC
CTGCCGAAGGTCTTATGGATGGACCGAATGACTTATCATCT
Found at i:5493895 original size:41 final size:40
Alignment explanation
Indices: 5493849--5493955 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 40
5493839 GCACGAAGCT
* * *
5493849 CTTATAGATGGACCGAATGACTTATCATCTTGCTCGAAAGA
1 CTTATAGAT-GACCGAATGACTTAGCACCATGCTCGAAAGA
* *
5493890 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGA
1 CTTATAGATGA-CCGAATGACTT-AGCACCATGCTCGAAAGA
5493932 CTTA-ATGATGACCTGAATGACTTA
1 CTTATA-GATGACC-GAATGACTTA
5493956 CTAAGTAAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
40 2 0.04
41 22 0.40
42 31 0.56
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (40 bp):
CTTATAGATGACCGAATGACTTAGCACCATGCTCGAAAGA
Found at i:5494169 original size:22 final size:22
Alignment explanation
Indices: 5494140--5494188 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
5494130 ATAGATTACC
*
5494140 CGAAAGATTTAAGCATCATGCT
1 CGAAAGATATAAGCATCATGCT
*
5494162 TGAAAGATATAAGCATCATGCT
1 CGAAAGATATAAGCATCATGCT
5494184 CGAAA
1 CGAAA
5494189 AACTTACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (22 bp):
CGAAAGATATAAGCATCATGCT
Found at i:5494396 original size:55 final size:55
Alignment explanation
Indices: 5494325--5494904 Score: 652
Period size: 55 Copynumber: 10.6 Consensus size: 55
5494315 ATTCATCATG
* * * ** *
5494325 TCAAGAAACCTT-TGAAAATCATACTTACTTTCTTTGAAAGGTCGTTTAAAAATCA
1 TCAAGAAA-CTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * *
5494380 TCAAGAAACTTCTGAAAATGAGACTTAGTTTCTTTAAAAGCTCGTTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * *
5494435 TTAAGAAACTTCTGAAAATGAGACTTAGTTTCTTTAAAAACTCATTTGAAAATCG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
*
5494490 TCAAGAAACTTCTGAAAATCAGACTTAGATTCTTTAAAAACTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* *
5494545 TCAAGAAACTTC-GAAAAATCAGAC--AGTTTCTTTGAAAGCTCATTTAAAAAT-A
1 TCAAGAAACTTCTG-AAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * *
5494597 GTTAAGAAACTTCTGAAAATCAGACTTAATTTCTTTAAAAACTCATTTGAAAATCA
1 -TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * *
5494653 ACAAGAAACTTATGAAAATCAGATTTAGTTTCTTTAAAAACTCATTTTAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * *
5494708 TCAAGAAACTTCTAAAAATCAGACTTAGTTTTTTTTAAAACTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* ** * * * * *
5494763 TCAAGAATCTTCCAAAAATCGGACTTAGCTTCTTTCAAAATTCATTTAAAAATAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * * * * * * *
5494818 TCAAGAAACTT-TCGAATATCAAACCTAGATTCTTTTAAAATTCACTT-ACAATTA
1 TCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
** * *
5494872 TCAAGAAACCCCTGAAAATTAGGCTTAGTTTCT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
5494905 AAAAAATCGT
Statistics
Matches: 452, Mismatches: 64, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.00
53 45 0.10
54 33 0.07
55 372 0.82
56 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
Found at i:5494609 original size:218 final size:218
Alignment explanation
Indices: 5494339--5494828 Score: 676
Period size: 218 Copynumber: 2.2 Consensus size: 218
5494329 GAAACCTTTG
* * * * *
5494339 AAAATCATACTTACTTTCTTTGAAAGGTCGTTTAAAAATCATCAAGAAACTTCTGAAAATGAGAC
1 AAAATCAGAC-TAGTTTCTTTGAAAGCTCATTTAAAAAT-ATCAAGAAACTTCTGAAAATCAGAC
* * * ** * *
5494404 TTAGTTTCTTTAAAAGCTCGTTTAAAAATCATTAAGAAACTTCTGAAAATGAGACTTAGTTTCTT
64 TTAATTTCTTTAAAAACTCATTTAAAAATCAACAAGAAACTTATGAAAATCAGACTTAGTTTCTT
* *
5494469 TAAAAACTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGACTTAGATTCTTTAAAAACTCA
129 TAAAAACTCATTTGAAAATCATCAAGAAACTTCTAAAAATCAGACTTAGATTCTTTAAAAACTCA
*
5494534 TTTAAAAATCATCAAGAAACTTCGA
194 TTTAAAAATCATCAAGAAACTTCCA
*
5494559 AAAATCAGAC-AGTTTCTTTGAAAGCTCATTTAAAAATAGTTAAGAAACTTCTGAAAATCAGACT
1 AAAATCAGACTAGTTTCTTTGAAAGCTCATTTAAAAATA-TCAAGAAACTTCTGAAAATCAGACT
* *
5494623 TAATTTCTTTAAAAACTCATTTGAAAATCAACAAGAAACTTATGAAAATCAGATTTAGTTTCTTT
65 TAATTTCTTTAAAAACTCATTTAAAAATCAACAAGAAACTTATGAAAATCAGACTTAGTTTCTTT
* * * *
5494688 AAAAACTCATTTTAAAATCATCAAGAAACTTCTAAAAATCAGACTTAGTTTTTTTTAAAACTCAT
130 AAAAACTCATTTGAAAATCATCAAGAAACTTCTAAAAATCAGACTTAGATTCTTTAAAAACTCAT
*
5494753 TTAAAAATCATCAAGAATCTTCCA
195 TTAAAAATCATCAAGAAACTTCCA
* * * **
5494777 AAAATCGGACTTAGCTTCTTTCAAAATTCATTTAAAAATAATCAAGAAACTT
1 AAAATCAGAC-TAGTTTCTTTGAAAGCTCATTTAAAAAT-ATCAAGAAACTT
5494829 TCGAATATCA
Statistics
Matches: 237, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
217 1 0.00
218 193 0.81
220 42 0.18
221 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (218 bp):
AAAATCAGACTAGTTTCTTTGAAAGCTCATTTAAAAATATCAAGAAACTTCTGAAAATCAGACTT
AATTTCTTTAAAAACTCATTTAAAAATCAACAAGAAACTTATGAAAATCAGACTTAGTTTCTTTA
AAAACTCATTTGAAAATCATCAAGAAACTTCTAAAAATCAGACTTAGATTCTTTAAAAACTCATT
TAAAAATCATCAAGAAACTTCCA
Found at i:5494707 original size:273 final size:274
Alignment explanation
Indices: 5494327--5494833 Score: 730
Period size: 273 Copynumber: 1.9 Consensus size: 274
5494317 TCATCATGTC
* * * ** * * *
5494327 AAGAAACCTTTGAAAATCATACTTACTTTCTTTGAAAGGTCGTTTAAAAATCATCAAGAAACTTC
1 AAGAAACCTTTGAAAATCAGACTTAATTTCTTTAAAAACTCATTTAAAAATCAACAAGAAACTTA
* * * * * *
5494392 TGAAAATGAGACTTAGTTTCTTTAAAAGCTCGTTTAAAAATCATTAAGAAACTTCTGAAAATGAG
66 TGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCTAAAAATCAG
* * **
5494457 ACTTAGTTTCTTTAAAAACTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGACTTAGATTC
131 ACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAATCAGACTTAGATTC
*
5494522 TTTAAAAACTCATTTAAAAATCATCAAGAAAC-TTCGAAAAATCAGACAGTTTCTTTGAAAGCTC
196 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTTCGAAAAATCAGACAGTTTCTTTGAAAGCTC
5494586 ATTTAAAAATAGTT
261 ATTTAAAAATAGTT
*
5494600 AAGAAA-CTTCTGAAAATCAGACTTAATTTCTTTAAAAACTCATTTGAAAATCAACAAGAAACTT
1 AAGAAACCTT-TGAAAATCAGACTTAATTTCTTTAAAAACTCATTTAAAAATCAACAAGAAACTT
* *
5494664 ATGAAAATCAGATTTAGTTTCTTTAAAAACTCATTTTAAAATCATCAAGAAACTTCTAAAAATCA
65 ATGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCTAAAAATCA
* * * * *
5494729 GACTTAGTTTTTTTTAAAACTCATTTAAAAATCATCAAGAATCTTCCAAAAATCGGACTTAGCTT
130 GACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAATCAGACTTAGATT
* *
5494794 CTTTCAAAATTCATTTAAAAATAATCAAGAAACTTTCGAA
195 CTTTAAAAACTCATTTAAAAATAATCAAGAAACTTTCGAA
5494834 TATCAAACCT
Statistics
Matches: 203, Mismatches: 29, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
272 3 0.01
273 194 0.96
274 6 0.03
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (274 bp):
AAGAAACCTTTGAAAATCAGACTTAATTTCTTTAAAAACTCATTTAAAAATCAACAAGAAACTTA
TGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCTAAAAATCAG
ACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAATCAGACTTAGATTC
TTTAAAAACTCATTTAAAAATAATCAAGAAACTTTCGAAAAATCAGACAGTTTCTTTGAAAGCTC
ATTTAAAAATAGTT
Found at i:5496679 original size:12 final size:11
Alignment explanation
Indices: 5496664--5496793 Score: 50
Period size: 12 Copynumber: 10.6 Consensus size: 11
5496654 CTCATTTCAA
5496664 TTTTCTTTTCTC
1 TTTTCTTTT-TC
*
5496676 TTTTTTTTATTCC
1 TTTTCTTT-TT-C
5496689 TTTTTCTTCTTT-
1 -TTTTCTT-TTTC
5496701 TTCTTC-TTTTC
1 TT-TTCTTTTTC
5496712 ATTTTCATTTTT-
1 -TTTTC-TTTTTC
*
5496724 ATTTCATTTTTC
1 TTTTC-TTTTTC
*
5496736 TTTTCTCTTTCTTT
1 -TTT-TCTTT-TTC
*
5496750 TTTTCTTTTTA
1 TTTTCTTTTTC
*
5496761 TTTTCCTTATTC
1 TTTT-CTTTTTC
5496773 TTTTCTTCATTCTC
1 TTTTCTT--TT-TC
5496787 TTTTCTT
1 TTTTCTT
5496794 CGAGTGTAGT
Statistics
Matches: 92, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
10 3 0.03
11 25 0.27
12 27 0.29
13 15 0.16
14 21 0.23
15 1 0.01
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTTTTTC
Done.