Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 170 of 208
Found at i:54557916 original size:91 final size:91
Alignment explanation
Indices: 54557777--54557984 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
54557767 TTGATTTTAG
* * *
54557777 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGGAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
54557842 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
54557869 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
54557934 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
54557960 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
54557985 GTTATAATTA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 91 0.85
92 16 0.15
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:54557953 original size:26 final size:28
Alignment explanation
Indices: 54557899--54557959 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
54557889 TATTATCAAG
* *
54557899 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
54557927 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
54557953 AATTATA
1 AATTATA
54557960 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:54557959 original size:44 final size:43
Alignment explanation
Indices: 54557818--54557959 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
54557808 AATTTTATGG
* *
54557818 AATTATATATCATTATTAAATTATATTTAATATTAATTATTTTA
1 AATTATATATTATTATTAAATTATA-TTAATAATAATTATTTTA
* ** * *
54557862 AATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATGA
1 AA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TTA
54557909 AATTATATATTATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTATATATTATTATTAAATTATAT-TAATAATAATTATTTTA
54557953 AATTATA
1 AATTATA
54557960 CAAATTCATA
Statistics
Matches: 75, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 20 0.27
45 12 0.16
46 11 0.15
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (43 bp):
AATTATATATTATTATTAAATTATATTAATAATAATTATTTTA
Found at i:54558077 original size:59 final size:57
Alignment explanation
Indices: 54558011--54558199 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
54558001 ATTTTATTAA
54558011 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
54558070 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
54558131 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
54558190 ATCATATATT
1 ATCATATATT
54558200 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:54558108 original size:66 final size:64
Alignment explanation
Indices: 54558038--54558236 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
54558028 AAATATATTT
54558038 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
54558103 G
64 G
* * * * * **
54558104 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
54558158 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
54558223 G
64 G
*
54558224 AATATTGATTATT
1 AATATTAATTATT
54558237 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:54558124 original size:120 final size:120
Alignment explanation
Indices: 54558000--54558297 Score: 517
Period size: 120 Copynumber: 2.5 Consensus size: 120
54557990 AATTATTTTA
* * *
54558000 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
54558064 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
54558120 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
54558185 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54558240 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
54558298 ATGATTAAAT
Statistics
Matches: 168, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 161 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:54558140 original size:61 final size:61
Alignment explanation
Indices: 54558073--54558260 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
54558063 TTATAGTATC
54558073 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
54558134 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
54558192 C
61 T
*
54558193 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
54558254 ATATATT
1 ATATATT
54558261 TTAATTAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:54558160 original size:15 final size:15
Alignment explanation
Indices: 54558125--54558176 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54558115 TTAAGAATTT
*
54558125 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54558139 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54558153 TATTTAATAATAAT-
1 TATTTAATTATAATA
54558167 TATGTTAATT
1 TAT-TTAATT
54558177 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54558269 original size:18 final size:17
Alignment explanation
Indices: 54558241--54558275 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54558231 ATTATTAAGA
*
54558241 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54558258 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54558276 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54558491 original size:44 final size:45
Alignment explanation
Indices: 54558441--54558530 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
54558431 CCTCTATTCT
* * * *
54558441 ATTCAACCAATCACAAGATTA-CTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATAC
***
54558485 ATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATAC
1 ATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATAC
54558530 A
1 A
54558531 CCTCTAATCC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 17 0.45
45 21 0.55
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.29
Consensus pattern (45 bp):
ATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATAC
Found at i:54558532 original size:16 final size:16
Alignment explanation
Indices: 54558511--54558559 Score: 89
Period size: 16 Copynumber: 3.0 Consensus size: 16
54558501 GATTAGCTAT
54558511 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54558527 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
54558544 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54558560 CACAGCGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 16 0.50
17 16 0.50
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:54558545 original size:17 final size:17
Alignment explanation
Indices: 54558511--54558557 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
54558501 GATTAGCTAT
54558511 TACACCTCTAAT-CCAA
1 TACACCTCTAATCCCAA
54558527 TACACCTCTAATCCCAA
1 TACACCTCTAATCCCAA
54558544 TACACCTCTAATCC
1 TACACCTCTAATCC
54558558 AACACAGCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.34, C:0.40, G:0.00, T:0.26
Consensus pattern (17 bp):
TACACCTCTAATCCCAA
Found at i:54572554 original size:21 final size:20
Alignment explanation
Indices: 54572528--54572575 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
54572518 TTCTCTTCTC
*
54572528 TTCTCTTTTTTTCTCCCTCTT
1 TTCTCTTATTTTCTCCCTC-T
*
54572549 TTCTCTTATTTTCTTCCTCT
1 TTCTCTTATTTTCTCCCTCT
54572569 TTCTCTT
1 TTCTCTT
54572576 CCTCTTCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTCTTATTTTCTCCCTCT
Found at i:54572588 original size:6 final size:6
Alignment explanation
Indices: 54572560--54572590 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
54572550 TCTCTTATTT
*
54572560 TCTTCC TCTTTC TCTTCC TCTTCC TCTTCC T
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC T
54572591 ACATTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TCTTCC
Found at i:54575166 original size:20 final size:19
Alignment explanation
Indices: 54575115--54575167 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
54575105 TAACAAAGGC
* **
54575115 AAGTATCGATACTTTTGTA
1 AAGTATCAATACTTTTAAA
**
54575134 AAGTATCCGTACTTTTAAA
1 AAGTATCAATACTTTTAAA
54575153 TAAGTATCAATACTT
1 -AAGTATCAATACTT
54575168 AAGTCTAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (19 bp):
AAGTATCAATACTTTTAAA
Found at i:54576939 original size:15 final size:15
Alignment explanation
Indices: 54576919--54576948 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54576909 AGAGATTGGA
54576919 TGCAGTTACTAATTC
1 TGCAGTTACTAATTC
54576934 TGCAGTTACTAATTC
1 TGCAGTTACTAATTC
54576949 ATGATCTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
TGCAGTTACTAATTC
Found at i:54583595 original size:30 final size:30
Alignment explanation
Indices: 54583560--54583654 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
54583550 TATCGCTGTA
54583560 ATATTTAATTTCATTGTCATCGCTATTTTT
1 ATATTTAATTTCATTGTCATCGCTATTTTT
* *
54583590 ATATTT-ATCTT-AGGTTAGGGT-ATCGC---TGTA
1 ATATTTAAT-TTCA--TT---GTCATCGCTATTTTT
54583620 ATATTTAATTTCATTGTCATCGCTATTTTT
1 ATATTTAATTTCATTGTCATCGCTATTTTT
54583650 ATATT
1 ATATT
54583655 AATCGCAGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 24
0.64 0.05 0.31
Matches are distributed among these distances:
26 2 0.04
27 5 0.10
29 5 0.10
30 25 0.51
31 5 0.10
33 5 0.10
34 2 0.04
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (30 bp):
ATATTTAATTTCATTGTCATCGCTATTTTT
Found at i:54583616 original size:60 final size:60
Alignment explanation
Indices: 54583533--54583654 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
54583523 TAGTTTATTT
54583533 TTTATCTTAGGTTAGGGTATCGCTGTAATATTTAATTTCATTGTCATCGCTATTTTTATA
1 TTTATCTTAGGTTAGGGTATCGCTGTAATATTTAATTTCATTGTCATCGCTATTTTTATA
54583593 TTTATCTTAGGTTAGGGTATCGCTGTAATATTTAATTTCATTGTCATCGCTATTTTTATA
1 TTTATCTTAGGTTAGGGTATCGCTGTAATATTTAATTTCATTGTCATCGCTATTTTTATA
54583653 TT
1 TT
54583655 AATCGCAGGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (60 bp):
TTTATCTTAGGTTAGGGTATCGCTGTAATATTTAATTTCATTGTCATCGCTATTTTTATA
Found at i:54593040 original size:83 final size:83
Alignment explanation
Indices: 54592901--54593150 Score: 428
Period size: 83 Copynumber: 3.0 Consensus size: 83
54592891 AACATTAGGC
*
54592901 TATCTTTTGTAGTATTTCAGTATTTCAATTCATTAACTCTCTCTGATAAACATGATGTATGAACT
1 TATCTTTTGTAGTATTTCAGTATTTCAATTCATTAACTCTTTCTGATAAACATGATGTATGAACT
54592966 CATACTTCTCCATTTGCA
66 CATACTTCTCCATTTGCA
* *
54592984 TATCTTTTGTAGTATTTCAGTATTTCTATTCATTAACTCTTTCTGATTAACATGATGTATGAACT
1 TATCTTTTGTAGTATTTCAGTATTTCAATTCATTAACTCTTTCTGATAAACATGATGTATGAACT
54593049 CATACTTCTCCATTTGCA
66 CATACTTCTCCATTTGCA
* * *
54593067 TATCTTTTGTCGTATTTCAGTATTTCAATTCATTAACTTTTTCTGATAAACATGCTGTATGAACT
1 TATCTTTTGTAGTATTTCAGTATTTCAATTCATTAACTCTTTCTGATAAACATGATGTATGAACT
**
54593132 CATACTTCTTGATTTGCA
66 CATACTTCTCCATTTGCA
54593150 T
1 T
54593151 TCGAAGTATA
Statistics
Matches: 157, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 157 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (83 bp):
TATCTTTTGTAGTATTTCAGTATTTCAATTCATTAACTCTTTCTGATAAACATGATGTATGAACT
CATACTTCTCCATTTGCA
Found at i:54604676 original size:21 final size:23
Alignment explanation
Indices: 54604646--54604694 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
54604636 GAGTATGTTA
*
54604646 AAATTATTTTAATTAT-A-ATTT
1 AAATTATTTTAACTATAATATTT
* *
54604667 AAATTTTTTTTACTATAATATTT
1 AAATTATTTTAACTATAATATTT
54604690 AAATT
1 AAATT
54604695 GATAAGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 1 0.04
23 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATTATTTTAACTATAATATTT
Found at i:54617052 original size:30 final size:29
Alignment explanation
Indices: 54617016--54617072 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
54617006 TTCATGCATC
* *
54617016 AATTAATATATAAATATTAGGTATTAAAAA
1 AATTAATACATAAATATTA-ATATTAAAAA
54617046 AATTAATACATAAATATTAATATTAAA
1 AATTAATACATAAATATTAATATTAAA
54617073 TAATATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (29 bp):
AATTAATACATAAATATTAATATTAAAAA
Found at i:54617357 original size:43 final size:41
Alignment explanation
Indices: 54617269--54617354 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 41
54617259 TTGAATTTAA
*
54617269 TTTAATTGTTTATTTTATTTTGAAACAAATAATATTATATT
1 TTTAATTGTTTATTTTATTTTGAAACAAATAAAATTATATT
* *
54617310 TTTAATTATTTTATTTTTATTTT-AAAGTAAATAAAATTA-ATT
1 TTTAATT-GTTTA-TTTTATTTTGAAA-CAAATAAAATTATATT
54617352 TTT
1 TTT
54617355 TAAAATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
41 7 0.18
42 13 0.33
43 19 0.49
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (41 bp):
TTTAATTGTTTATTTTATTTTGAAACAAATAAAATTATATT
Found at i:54623559 original size:18 final size:18
Alignment explanation
Indices: 54623536--54623573 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54623526 TTCAATTAAG
*
54623536 TCTTTCATT-AAGTGTTTT
1 TCTTTC-TTCAAGTATTTT
54623554 TCTTTCTTCAAGTATTTT
1 TCTTTCTTCAAGTATTTT
54623572 TC
1 TC
54623574 ATCTAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTTTCTTCAAGTATTTT
Found at i:54623622 original size:13 final size:13
Alignment explanation
Indices: 54623561--54623624 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
54623551 TTTTCTTTCT
*
54623561 TCAAGTATTTTTCA
1 TCAAGT-TTTTTTA
* *
54623575 TCTAGTTCTTTTA
1 TCAAGTTTTTTTA
54623588 TCAAGTTTTTAATTA
1 TCAAGTTTTT--TTA
*
54623603 CCAAGTTTTTTTA
1 TCAAGTTTTTTTA
54623616 TCAAGTTTT
1 TCAAGTTTT
54623625 GCAGCAAGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
13 24 0.59
14 5 0.12
15 12 0.29
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (13 bp):
TCAAGTTTTTTTA
Found at i:54623664 original size:13 final size:12
Alignment explanation
Indices: 54623568--54623684 Score: 58
Period size: 12 Copynumber: 9.2 Consensus size: 12
54623558 TCTTCAAGTA
*
54623568 TTTTTCATCTAG
1 TTTTTCATCAAG
*
54623580 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
54623593 TTTTTAATTACCAAG
1 TTTTTCA-T--CAAG
*
54623608 TTTTTTTATCAAG
1 -TTTTTCATCAAG
* *
54623621 TTTTGCAGCAAG
1 TTTTTCATCAAG
*
54623633 ATCTTTT--TAAAG
1 -T-TTTTCATCAAG
54623645 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
54623657 TCTTTTCATAAAA
1 T-TTTTCATCAAG
*
54623670 TTTTCCATCAAG
1 TTTTTCATCAAG
54623682 TTT
1 TTT
54623685 AATAATTTTG
Statistics
Matches: 79, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
10 4 0.05
11 1 0.01
12 34 0.43
13 26 0.33
14 3 0.04
15 5 0.06
16 6 0.08
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (12 bp):
TTTTTCATCAAG
Found at i:54623668 original size:25 final size:24
Alignment explanation
Indices: 54623568--54623682 Score: 79
Period size: 25 Copynumber: 4.5 Consensus size: 24
54623558 TCTTCAAGTA
* *
54623568 TTTTTCATCTAGTTCTTTTATCAAG
1 TTTTTCATCAAG-TCTTTTATAAAG
* * *
54623593 TTTTTAATTACCAAGTTTTTTTATCAAG
1 TTTTTCA-T--CAAG-TCTTTTATAAAG
* *
54623621 TTTTGCAGCAAGATCTTTT-TAAAG
1 TTTTTCATCAAG-TCTTTTATAAAG
*
54623645 TTTTTCATCAAGTCTTTTCATAAAA
1 TTTTTCATCAAGTCTTTT-ATAAAG
*
54623670 TTTTCCATCAAGT
1 TTTTTCATCAAGT
54623683 TTAATAATTT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
23 6 0.08
24 14 0.19
25 31 0.43
26 1 0.01
28 20 0.28
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.50
Consensus pattern (24 bp):
TTTTTCATCAAGTCTTTTATAAAG
Found at i:54627012 original size:18 final size:19
Alignment explanation
Indices: 54626991--54627028 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
54626981 GATTAAATTT
54626991 ATATTAAATTTTATA-AAC
1 ATATTAAATTTTATATAAC
54627009 ATATTAAATTTTATATAAC
1 ATATTAAATTTTATATAAC
54627028 A
1 A
54627029 CGGACTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATTAAATTTTATATAAC
Found at i:54629605 original size:27 final size:29
Alignment explanation
Indices: 54629575--54629630 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
54629565 GAGTCATCAA
* *
54629575 ATTAAATT-AATTAATGAATC-ATAAGTT
1 ATTAAATTAAAGTAATCAATCTATAAGTT
54629602 ATTAAATTAAAGTAATCAATCTATAAGTT
1 ATTAAATTAAAGTAATCAATCTATAAGTT
54629631 TATGATGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 10 0.40
29 7 0.28
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (29 bp):
ATTAAATTAAAGTAATCAATCTATAAGTT
Found at i:54631295 original size:11 final size:11
Alignment explanation
Indices: 54631279--54631343 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
54631269 AATATATATT
54631279 TATTATTAAAA
1 TATTATTAAAA
54631290 TATTATTATAAA
1 TATTATTA-AAA
*
54631302 T-TTTTTAATAA
1 TATTATTAA-AA
*
54631313 CATT-TTAATAA
1 TATTATTAA-AA
54631324 TATTATTTAAAA
1 TATTA-TTAAAA
54631336 TTATTATT
1 -TATTATT
54631344 GTTGAAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
10 1 0.02
11 25 0.56
12 10 0.22
13 9 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:54631414 original size:31 final size:31
Alignment explanation
Indices: 54631354--54631414 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
54631344 GTTGAAATTT
* *
54631354 ATTTATTAAAATAAATTTGTAATATTAAATA
1 ATTTATTAAAATAAATTTATAATAATAAATA
*
54631385 ATTTATTAAAAT-AATATTATATTAATAAAT
1 ATTTATTAAAATAAAT-TTATAATAATAAAT
54631415 TAATAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (31 bp):
ATTTATTAAAATAAATTTATAATAATAAATA
Found at i:54631475 original size:10 final size:9
Alignment explanation
Indices: 54631442--54631474 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
54631432 ATAATATTGA
54631442 TTTTAATA-
1 TTTTAATAT
54631450 TTTTAATAT
1 TTTTAATAT
54631459 TTTTAAATAT
1 TTTT-AATAT
54631469 TTTTAA
1 TTTTAA
54631475 AAAGTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTAATAT
Found at i:54631575 original size:21 final size:20
Alignment explanation
Indices: 54631551--54631591 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54631541 GTTCCTTTTT
54631551 TTTTTCGAAAAATGACCTACA
1 TTTTT-GAAAAATGACCTACA
*
54631572 TTTTTTAAAAATGACCTACA
1 TTTTTGAAAAATGACCTACA
54631592 CAAAGAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (20 bp):
TTTTTGAAAAATGACCTACA
Found at i:54634492 original size:27 final size:27
Alignment explanation
Indices: 54634455--54634583 Score: 188
Period size: 27 Copynumber: 4.8 Consensus size: 27
54634445 ATAACATTAA
*
54634455 GCAT-ATAGTCATTTTATAACATAGGA
1 GCATAATAGTCATTTTATAACATAGGG
54634481 GCATAATAGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
* *
54634508 GCATAACAGTCACTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
***
54634535 GCATAGCCGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
*
54634562 GCATAATAGTTATTTTATAACA
1 GCATAATAGTCATTTTATAACA
54634584 GTTTGGGGGT
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 4 0.04
27 88 0.96
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (27 bp):
GCATAATAGTCATTTTATAACATAGGG
Found at i:54636533 original size:492 final size:492
Alignment explanation
Indices: 54635609--54636590 Score: 1892
Period size: 492 Copynumber: 2.0 Consensus size: 492
54635599 GTAATATTCG
54635609 GCAAAGGGAACAACTCAACAAAGCAAAACCAAAAAGAATGAGAAGCCCCCTCTAGCCGAATTCTT
1 GCAAAGGGAACAACTCAACAAAGCAAAACCAAAAAGAATGAGAAGCCCCCTCTAGCCGAATTCTT
*
54635674 GAGTGCCACAAAGTCCACTTTCGGTACTACATTCCCTCTCCCCTCATCCCTTGGTTTTCTCCTAA
66 GAGTGCCACAAAGTCCACTTTCGGCACTACATTCCCTCTCCCCTCATCCCTTGGTTTTCTCCTAA
*
54635739 AATCCCTCCTCAAATCTCTCCACCTAATCACACCTCCCCTCAACCACTTCATTATCAGAATTTTA
131 AATCCCTCCTCAAATCTCTCCACCTAATCACACCTCCCCTCAACCACTTCACTATCAGAATTTTA
* *
54635804 GTCCAACACAAACTCACACATGTTACAAGTAATAAAATAACACCCCTTTTTTGCACAGATATTTG
196 GTCCAACACAAACTCACACATGGTACAAGCAATAAAATAACACCCCTTTTTTGCACAGATATTTG
54635869 AACTCAATACCCCCAGCACACTAACACTCCACTTAACCACTAGACCAGTAGGTCCATTCTGATAT
261 AACTCAATACCCCCAGCACACTAACACTCCACTTAACCACTAGACCAGTAGGTCCATTCTGATAT
54635934 AAATAAATCCACTAACTTTAAAATATAAGCATATTGAACCCAGTTAAGGCTTTATTTAATTAAAA
326 AAATAAATCCACTAACTTTAAAATATAAGCATATTGAACCCAGTTAAGGCTTTATTTAATTAAAA
54635999 CAAAAAAATTCTGCCCAAGTCAAGGCTTGAACTTGGGACCTCTCAAACACTTCCGAGAACACTTA
391 CAAAAAAATTCTGCCCAAGTCAAGGCTTGAACTTGGGACCTCTCAAACACTTCCGAGAACACTTA
54636064 ACCACTGAAGCAGACATGTATTTATATTACAAACAAA
456 ACCACTGAAGCAGACATGTATTTATATTACAAACAAA
54636101 GCAAAGGGAACAACTCAACAAAGCAAAACCAAAAAGAATGAGAAGCCCCCTCTAGCCGAATTCTT
1 GCAAAGGGAACAACTCAACAAAGCAAAACCAAAAAGAATGAGAAGCCCCCTCTAGCCGAATTCTT
54636166 GAGTGCCACAAAGTCCACTTTCGGCACTACATTCCCTCTCCCCTCATCCCTTGGTTTTCTCCTAA
66 GAGTGCCACAAAGTCCACTTTCGGCACTACATTCCCTCTCCCCTCATCCCTTGGTTTTCTCCTAA
*
54636231 AATCCCTCCTCAAATCTCTCCACCTGATCACACCTCCCCTCAACCACTTCACTATCAGAATTTTA
131 AATCCCTCCTCAAATCTCTCCACCTAATCACACCTCCCCTCAACCACTTCACTATCAGAATTTTA
*
54636296 GTCCAACACAAACTCACACATGGTACAAGCAATAAAATAACACCCCTTTTTTGCACAGGTATTTG
196 GTCCAACACAAACTCACACATGGTACAAGCAATAAAATAACACCCCTTTTTTGCACAGATATTTG
*
54636361 AACTCAATACCCCCAGCACATTAACACTCCACTTAACCACTAGACCAGTAGGTCCATTCTGATAT
261 AACTCAATACCCCCAGCACACTAACACTCCACTTAACCACTAGACCAGTAGGTCCATTCTGATAT
54636426 AAATAAATCCACTAACTTTAAAATATAAGCATATTGAACCCAGTTAAGGCTTTATTTAATTAAAA
326 AAATAAATCCACTAACTTTAAAATATAAGCATATTGAACCCAGTTAAGGCTTTATTTAATTAAAA
54636491 CAAAAAAATTCTGCCCAAGTCAAGGCTTGAACTTGGGACCTCTCAAACACTTCCGAGAACACTTA
391 CAAAAAAATTCTGCCCAAGTCAAGGCTTGAACTTGGGACCTCTCAAACACTTCCGAGAACACTTA
*
54636556 ACCACTGAAGCAGACATGTATTTATGTTACAAACA
456 ACCACTGAAGCAGACATGTATTTATATTACAAACA
54636591 TGCAAAAATA
Statistics
Matches: 482, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
492 482 1.00
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.25
Consensus pattern (492 bp):
GCAAAGGGAACAACTCAACAAAGCAAAACCAAAAAGAATGAGAAGCCCCCTCTAGCCGAATTCTT
GAGTGCCACAAAGTCCACTTTCGGCACTACATTCCCTCTCCCCTCATCCCTTGGTTTTCTCCTAA
AATCCCTCCTCAAATCTCTCCACCTAATCACACCTCCCCTCAACCACTTCACTATCAGAATTTTA
GTCCAACACAAACTCACACATGGTACAAGCAATAAAATAACACCCCTTTTTTGCACAGATATTTG
AACTCAATACCCCCAGCACACTAACACTCCACTTAACCACTAGACCAGTAGGTCCATTCTGATAT
AAATAAATCCACTAACTTTAAAATATAAGCATATTGAACCCAGTTAAGGCTTTATTTAATTAAAA
CAAAAAAATTCTGCCCAAGTCAAGGCTTGAACTTGGGACCTCTCAAACACTTCCGAGAACACTTA
ACCACTGAAGCAGACATGTATTTATATTACAAACAAA
Found at i:54637898 original size:14 final size:14
Alignment explanation
Indices: 54637879--54637905 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54637869 CATGATAAAA
54637879 TAAAATACAAGTGG
1 TAAAATACAAGTGG
54637893 TAAAATACAAGTG
1 TAAAATACAAGTG
54637906 TGCAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:54642765 original size:18 final size:18
Alignment explanation
Indices: 54642734--54642775 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
54642724 GTAAAAGTTG
54642734 TATTTTTAATTTAAATAT
1 TATTTTTAATTTAAATAT
*
54642752 TATTATTTAA-TTAAATCT
1 TATT-TTTAATTTAAATAT
54642770 TATTTT
1 TATTTT
54642776 AACATAACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 15 0.68
19 5 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTAATTTAAATAT
Found at i:54645201 original size:12 final size:12
Alignment explanation
Indices: 54645184--54645208 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54645174 CTGAATACTT
54645184 TCAACCCTCTCA
1 TCAACCCTCTCA
54645196 TCAACCCTCTCA
1 TCAACCCTCTCA
54645208 T
1 T
54645209 GGTTTGACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (12 bp):
TCAACCCTCTCA
Found at i:54646210 original size:14 final size:16
Alignment explanation
Indices: 54646181--54646213 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
54646171 ATAAACACTA
54646181 AAAATTTAAGATAGTT
1 AAAATTTAAGATAGTT
54646197 AAAA-TTAA-ATAGTT
1 AAAATTTAAGATAGTT
54646211 AAA
1 AAA
54646214 TAATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAATTTAAGATAGTT
Found at i:54647488 original size:13 final size:13
Alignment explanation
Indices: 54647454--54647490 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
54647444 TTTCCATTTA
54647454 AAATAATATTTTT
1 AAATAATATTTTT
*
54647467 -AATTA-ATTTTT
1 AAATAATATTTTT
54647478 AAATAATATTTTT
1 AAATAATATTTTT
54647491 TATTATTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AAATAATATTTTT
Found at i:54664163 original size:3 final size:3
Alignment explanation
Indices: 54664157--54664194 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54664147 TTAAAAAAGC
54664157 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54664195 CAGAACTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54665443 original size:312 final size:308
Alignment explanation
Indices: 54664918--54665555 Score: 727
Period size: 312 Copynumber: 2.1 Consensus size: 308
54664908 ATCGTTTTTA
* * * * * * *
54664918 TAATTAGTTTCGAATCACATGTTTCATTGTTTGTTGTATGTTACTTTTAAATAAGCATTTGTGTT
1 TAATTAGTTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACAAGCATTTATGTT
* * ** *
54664983 TTTAAATTTGTGATTTCCACACACATATGTGTGTGATAGAATTTTTAATATATATTAATAATATT
66 TTTAAATTAGTGATTTCCACACACATACGCATGTAATAGAA-TTTTAATATATATTAATAATATT
* * * * * *
54665048 GTTAATTGAGTTGGAGCACAAATCAACTCGATACTAACTCAAAATTGTTGACAAAGCCATGATTA
130 GCTAATTGAGTTGGAGCACAAATAAACTCAACACTAACTCAAAATTGTTGACAAAACCATGATAA
* * * * * * *
54665113 ATAATTGTAGTACATTTAGTATTGTTTATTTGATGTATTTATGTGCTTT-ATTTTTGTTTTACTC
195 ATAATTGAAGTACATTTAGTATTATTTATCTAATGTATTTATGTG-TTTAAATCTAGTTTTACT-
* *
54665177 ACAATCTAATATATATTTTTATTTTAATATCATACATATTTCATATGTTATTATAAT
258 -C-A--TAATATA-ATCTTT-TTTTAATATCATACATATTTCATATGTAATTATAAT
*
54665234 TAATTAATTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACACA-CATTTATG-
1 TAATTAGTTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACA-AGCATTTATGT
* * * *
54665297 TTTTAAATTAGT-AGTTTCCACACGCATACGCATGTAATAGGA-TTT-CTA-GTATTAATAA-AG
65 TTTTAAATTAGTGA-TTTCCACACACATACGCATGTAATAGAATTTTAATATATATTAATAATA-
* * *
54665357 TTGCTAATTGAGTTGGTGACACAAATAAACTCAACACTAACTCATAGTTGTTGACAAAACCATGA
128 TTGCTAATTGAGTTGGAG-CACAAATAAACTCAACACTAACTCAAAATTGTTGACAAAACCATGA
*
54665422 TAAAT-ATATGAAGTGCATTTAGTATTATTTATCTAATGTATTTATGTGTTTAAATCTAGTTTTA
192 TAAATAAT-TGAAGTACATTTAGTATTATTTATCTAATGTATTTATGTGTTTAAATCTAGTTTTA
* * *
54665486 CTCATAATTTAATCTTTTTTTAATATTATACATATTTCATATGTAATTATGAT
256 CTCATAATATAATCTTTTTTTAATATCATACATATTTCATATGTAATTATAAT
*
54665539 TAATTAGTTTTAAACCA
1 TAATTAGTTTCAAACCA
54665556 AGGGCGAAGC
Statistics
Matches: 275, Mismatches: 41, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
305 48 0.17
306 5 0.02
307 6 0.02
309 1 0.00
310 2 0.01
311 30 0.11
312 92 0.33
313 3 0.01
314 1 0.00
315 33 0.12
316 53 0.19
317 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (308 bp):
TAATTAGTTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACAAGCATTTATGTT
TTTAAATTAGTGATTTCCACACACATACGCATGTAATAGAATTTTAATATATATTAATAATATTG
CTAATTGAGTTGGAGCACAAATAAACTCAACACTAACTCAAAATTGTTGACAAAACCATGATAAA
TAATTGAAGTACATTTAGTATTATTTATCTAATGTATTTATGTGTTTAAATCTAGTTTTACTCAT
AATATAATCTTTTTTTAATATCATACATATTTCATATGTAATTATAAT
Found at i:54675144 original size:43 final size:43
Alignment explanation
Indices: 54675031--54675215 Score: 161
Period size: 43 Copynumber: 4.3 Consensus size: 43
54675021 ACGTCGCTAA
* * *
54675031 CTTTTGCGGCGCTTATAGAAAAAACGCCGCT-AACGATCA-TTTT
1 CTTTAGCGGCGCTTATAGAAAAAACGCCGCTAAAAG-T-AGTGTT
* * *
54675074 CTTTAGCGGCAC-TA-AGGAAATACACGCCACT-AAAGATCA-TGTT
1 CTTTAGCGGCGCTTATA-GAAA-AAACGCCGCTAAAAG-T-AGTGTT
*
54675117 CTTTAGCGGCGCTT-TAGAAGAAAACGCCTCTAAAAGTAGTGTT
1 CTTTAGCGGCGCTTATAGAA-AAAACGCCGCTAAAAGTAGTGTT
* **
54675160 CTTTAGCGGCGCTTGT-TCAAAAACGCCGCTAAAAGTAGTGTT
1 CTTTAGCGGCGCTTATAGAAAAAACGCCGCTAAAAGTAGTGTT
54675202 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
54675216 GTTTCACAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 43 0.35
43 70 0.57
44 8 0.07
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGCTTATAGAAAAAACGCCGCTAAAAGTAGTGTT
Found at i:54675196 original size:42 final size:43
Alignment explanation
Indices: 54675113--54675218 Score: 162
Period size: 42 Copynumber: 2.5 Consensus size: 43
54675103 CTAAAGATCA
* *
54675113 TGTTCTTTAGCGGCGCTT-TAGAAGAAAACGCCTCTAAAAGTAG
1 TGTTCTTTAGCGGCGCTTGT-TAAGAAAACGCCGCTAAAAGTAG
*
54675156 TGTTCTTTAGCGGCGCTTGTTCA-AAAACGCCGCTAAAAGTAG
1 TGTTCTTTAGCGGCGCTTGTTAAGAAAACGCCGCTAAAAGTAG
54675198 TGTTCTTTAGCGGCGCTTGTT
1 TGTTCTTTAGCGGCGCTTGTT
54675219 TCACAAATGC
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
42 39 0.66
43 19 0.32
44 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTTCTTTAGCGGCGCTTGTTAAGAAAACGCCGCTAAAAGTAG
Found at i:54675666 original size:12 final size:12
Alignment explanation
Indices: 54675651--54675677 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54675641 TTTCTATCGT
54675651 TGCTTCTCTCGC
1 TGCTTCTCTCGC
54675663 TGCTTCTCTCGC
1 TGCTTCTCTCGC
54675675 TGC
1 TGC
54675678 GGCCTCTGCT
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:0.00, C:0.41, G:0.19, T:0.41
Consensus pattern (12 bp):
TGCTTCTCTCGC
Found at i:54675686 original size:21 final size:21
Alignment explanation
Indices: 54675662--54675730 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
54675652 GCTTCTCTCG
*
54675662 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
54675683 CTGCTTCTCTCACTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
54675704 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
54675725 GTGCTT
1 CTGCTT
54675731 TAAGTTGTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.42, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:54681211 original size:9 final size:9
Alignment explanation
Indices: 54681197--54681447 Score: 194
Period size: 9 Copynumber: 29.8 Consensus size: 9
54681187 AAGTTATTTA
54681197 TTATGTAAG
1 TTATGTAAG
54681206 TTATGTAAG
1 TTATGTAAG
*
54681215 TTGTGTAAG
1 TTATGTAAG
54681224 TTATGTAAG
1 TTATGTAAG
* *
54681233 CTGTGTAAG
1 TTATGTAAG
*
54681242 TTGTGT-A-
1 TTATGTAAG
* *
54681249 TTATGAAAC
1 TTATGTAAG
54681258 TTATGTAAG
1 TTATGTAAG
*
54681267 TTGTGT-A-
1 TTATGTAAG
54681274 TTATGTAAG
1 TTATGTAAG
*
54681283 TTATGTCAG
1 TTATGTAAG
*
54681292 TTGTGT-A-
1 TTATGTAAG
* *
54681299 TTATGAAAC
1 TTATGTAAG
54681308 TTATGTAAG
1 TTATGTAAG
*
54681317 TTATGT--C
1 TTATGTAAG
54681324 TTATGTAAG
1 TTATGTAAG
*
54681333 TTATGTAAA
1 TTATGTAAG
54681342 TTATGT-A-
1 TTATGTAAG
54681349 TTATGTAAG
1 TTATGTAAG
*
54681358 TTATGTCAG
1 TTATGTAAG
*
54681367 TTGTGT-A-
1 TTATGTAAG
*
54681374 TTATGTAAA
1 TTATGTAAG
54681383 TTATGT-A-
1 TTATGTAAG
54681390 TTATGTAAG
1 TTATGTAAG
*
54681399 TTATGTAAT
1 TTATGTAAG
*
54681408 TTGTGT-A-
1 TTATGTAAG
*
54681415 TTATGTAAC
1 TTATGTAAG
* *
54681424 TTATTTAAT
1 TTATGTAAG
54681433 TTATGTAAG
1 TTATGTAAG
54681442 -TATGTA
1 TTATGTA
54681448 TTATTATGTA
Statistics
Matches: 196, Mismatches: 30, Indels: 33
0.76 0.12 0.13
Matches are distributed among these distances:
7 41 0.21
8 20 0.10
9 135 0.69
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:54681215 original size:25 final size:25
Alignment explanation
Indices: 54681186--54681494 Score: 261
Period size: 25 Copynumber: 12.2 Consensus size: 25
54681176 GATTTAGGAA
* *
54681186 TAAGTTATTTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
54681211 TAAGTTGTGTAAGTTATGTAAGCTGTG
1 TAAGTTGTGT-A-TTATGTAAGTTATG
* *
54681238 TAAGTTGTGTATTATGAAACTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
54681263 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* * *
54681288 TCAGTTGTGTATTATGAAACTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
54681313 TAAGTTATGTCTTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
54681338 TAAATTATGTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
54681363 TCAGTTGTGTATTATGTAAATTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* * *
54681388 T-A-TTATGTAAGTTATGTAATTTGTG
1 TAAGTTGTGT-A-TTATGTAAGTTATG
* * *
54681413 T-A-TTATGTAACTTATTTAATTTATG
1 TAAGTTGTGT-A-TTATGTAAGTTATG
* *
54681438 TAAGTATGTATTATTATGTAATTTAT-
1 TAAGT-TGT-GTATTATGTAAGTTATG
* * *
54681464 TATGTAG-GATATTATCTAAGTTATG
1 TAAGTTGTG-TATTATGTAAGTTATG
54681489 TAAGTT
1 TAAGTT
54681495 TTTTTTTTGG
Statistics
Matches: 234, Mismatches: 40, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
23 5 0.02
24 15 0.06
25 168 0.72
26 7 0.03
27 35 0.15
28 3 0.01
29 1 0.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (25 bp):
TAAGTTGTGTATTATGTAAGTTATG
Found at i:54681277 original size:16 final size:16
Alignment explanation
Indices: 54681186--54681405 Score: 138
Period size: 16 Copynumber: 13.7 Consensus size: 16
54681176 GATTTAGGAA
*
54681186 TAAGTTATTTATTATG
1 TAAGTTATGTATTATG
*
54681202 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-A-TTATG
* *
54681220 TAAGTTATGTAAGCTGTG
1 TAAGTTATGT-A-TTATG
*
54681238 TAAGTTGTGTATTATG
1 TAAGTTATGTATTATG
*
54681254 -AA---A---CTTATG
1 TAAGTTATGTATTATG
*
54681263 TAAGTTGTGTATTATG
1 TAAGTTATGTATTATG
*
54681279 TAAGTTATGTCAGTTGTG
1 TAAGTTATGT-A-TTATG
*
54681297 T-A-TTATGAAACTTATG
1 TAAGTTATG-TA-TTATG
*
54681313 TAAGTTATGTCTTATG
1 TAAGTTATGTATTATG
54681329 TAAGTTATGTAAATTATG
1 TAAGTTATGT--ATTATG
54681347 T-A-TTATGTAAGTTATG
1 TAAGTTATGT-A-TTATG
* *
54681363 TCAGTTGTGTATTATG
1 TAAGTTATGTATTATG
*
54681379 TAAATTATGTATTATG
1 TAAGTTATGTATTATG
54681395 TAAGTTATGTA
1 TAAGTTATGTA
54681406 ATTTGTGTAT
Statistics
Matches: 162, Mismatches: 23, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
9 5 0.03
10 2 0.01
15 4 0.02
16 92 0.57
17 8 0.05
18 51 0.31
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:54681303 original size:41 final size:41
Alignment explanation
Indices: 54681258--54681446 Score: 200
Period size: 41 Copynumber: 4.8 Consensus size: 41
54681248 ATTATGAAAC
* *
54681258 TTATGTAAGTTGTGTATTATGTAAGTTATGTCAGTTGTGTA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
54681299 TTATG--AA--A---CTTATGTAAGTTATGTC--TTATGTAA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGT-A
54681332 GTTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
1 -TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
54681374 TTATGTAAATTATGTATTATGTAAGTTATGTAATTTGTGTA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
54681415 TTATGTAACTTATTTAATTTATGTAAG-TATGT
1 TTATGTAAATTATGT-A-TTATGTAAGTTATGT
54681447 ATTATTATGT
Statistics
Matches: 125, Mismatches: 10, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
32 5 0.04
33 1 0.01
34 21 0.17
36 2 0.02
38 1 0.01
39 1 0.01
41 73 0.58
42 7 0.06
43 14 0.11
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (41 bp):
TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
Found at i:54681580 original size:24 final size:26
Alignment explanation
Indices: 54681537--54681591 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
54681527 TTATGTACGG
* *
54681537 TATGTGTTATTATGTAAGTTCTTTAT
1 TATGTGTTATTATGTAAGTTATGTAT
*
54681563 TATGT-TTGTTATGT-AGTTATGTAT
1 TATGTGTTATTATGTAAGTTATGTAT
54681587 TATGT
1 TATGT
54681592 AGGATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 8 0.31
26 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.58
Consensus pattern (26 bp):
TATGTGTTATTATGTAAGTTATGTAT
Found at i:54681785 original size:15 final size:15
Alignment explanation
Indices: 54681765--54681797 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54681755 ATAATTATTT
*
54681765 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
54681780 ATAAATTTAATACTA
1 ATAAATTTAATACTA
54681795 ATA
1 ATA
54681798 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:54684263 original size:266 final size:264
Alignment explanation
Indices: 54683846--54684622 Score: 1267
Period size: 266 Copynumber: 3.0 Consensus size: 264
54683836 ATATTTTGCT
* *
54683846 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATATATCGAGACCAAAACGGTGCATT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
*
54683911 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACAAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
*
54683976 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTGAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGC-GCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
*
54684041 CGACGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
195 CGGCGTTTTCTAGTAAGCGCCACTAATATAA-TATACATCAAAATTAAAACTACGCGTTTTAGTT
54684106 AAGATA
259 AAGATA
54684112 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
*
54684177 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTGAGACCAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
54684242 ACACTGCGTTTTGTTAAGATA-------CG--TT--A-C--G-G-CGCTAAAGCTATTCTTTAAC
131 ACACTGCGTTTTGTTAAGATACGTTGCGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAAC
54684291 GGCGTTTTCTAGTAAGCGCCAC-----TAATATA-ATCAAAATTAAAACTACGCGTTTTAGTTAA
196 GGCGTTTTCTAGTAAGCGCCACTAATATAATATACATCAAAATTAAAACTACGCGTTTTAGTTAA
54684350 GATA
261 GATA
*
54684354 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGATGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
54684419 TTGGTTCAGAT-TTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
*
54684483 ACACTGCGTTTTGTTAAGATACGTTGCCGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTG-CGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
* *
54684548 CGGCGTTTTCTAGTAAGCGCCAGTAATATAAATATACATCAAAATTAAAACTACGCGTTTTAGTA
195 CGGCGTTTTCTAGTAAGCGCCACTAATAT-AATATACATCAAAATTAAAACTACGCGTTTTAGTT
54684613 AAGATA
259 AAGATA
54684619 TTTT
1 TTTT
54684623 ACGGCGCTTT
Statistics
Matches: 476, Mismatches: 11, Indels: 49
0.89 0.02 0.09
Matches are distributed among these distances:
241 73 0.15
242 109 0.23
243 4 0.01
244 3 0.01
249 42 0.09
250 1 0.00
251 3 0.01
253 1 0.00
254 2 0.00
256 3 0.01
257 1 0.00
258 43 0.09
263 1 0.00
264 6 0.01
265 37 0.08
266 147 0.31
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (264 bp):
TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
ACACTGCGTTTTGTTAAGATACGTTGCGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAAC
GGCGTTTTCTAGTAAGCGCCACTAATATAATATACATCAAAATTAAAACTACGCGTTTTAGTTAA
GATA
Found at i:54684356 original size:242 final size:244
Alignment explanation
Indices: 54684022--54684507 Score: 870
Period size: 242 Copynumber: 2.0 Consensus size: 244
54684012 GATCAAGCGC
*
54684022 CGCTGAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATT
1 CGCTAAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCAC----ATAAGTATACATCAAAATT
54684087 AAAACTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTA
62 AAAACTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTA
*
54684152 TACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCAC
127 TACATCGAGACCAAAACGATGCGTTTTGGTTCAGAT-TTTTGCGGCGTTTTCCTATAAGCGCCAC
*
54684217 TAAATGTAACATAGCTTGAGACCAAACACTGCGTTTTGTTAAGATACGTTACGG
191 TAAATGTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTTACGG
*
54684271 CGCTAAAGCTATTCTTTAACGGCGTTTTCTAGTAAGCGCCAC-TAA-TATA-ATCAAAATTAAAA
1 CGCTAAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCACATAAGTATACATCAAAATTAAAA
54684333 CTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACA
66 CTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACA
54684398 TCGAGACCAAAACGATGCGTTTTGGTTCAGATTTTTGCGGCGTTTTCCTATAAGCGCCACTAAAT
131 TCGAGACCAAAACGATGCGTTTTGGTTCAGATTTTTGCGGCGTTTTCCTATAAGCGCCACTAAAT
54684463 GTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTT
196 GTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTT
54684508 GCCGCGCTTT
Statistics
Matches: 233, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
241 77 0.33
242 109 0.47
243 4 0.02
244 3 0.01
249 40 0.17
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (244 bp):
CGCTAAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCACATAAGTATACATCAAAATTAAAA
CTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACA
TCGAGACCAAAACGATGCGTTTTGGTTCAGATTTTTGCGGCGTTTTCCTATAAGCGCCACTAAAT
GTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTTACGG
Found at i:54684973 original size:113 final size:113
Alignment explanation
Indices: 54684677--54684992 Score: 377
Period size: 114 Copynumber: 2.8 Consensus size: 113
54684667 GCATATCACA
* * *
54684677 AAGCGCCACTAAATCTAGGATACATCAACACCAAAAACGATGCGTTTTGGTTAAGATATTTTGCG
1 AAGCGCCACTAATTCTAGGATACATCAACA-CAAAAACGATGCGTTTTGGTTAGGAAATTTTGCG
* * * * * * *
54684742 GCGC-ATATCGTAAAACGCCGCTAAGACGCTTTCGGGGCCTTTTTTTTAG
65 GCGCGTTGTTGT-AAACGCCGCTAAGACACTTTAGCGGCCTGTTTTTTAG
* *
54684791 AAGCGCCACTAATTCTAGGATACATCAACACTAAAAACGATGCGTTTTGGTTAGGAGAA-ATTAC
1 AAGCGCCACTAATTCTAGGATACATCAACAC-AAAAACGATGCGTTTTGGTTAGGA-AATTTTGC
*
54684855 GGCGCGTTGTTGTAAAGCGCCGCTAAGACACTTTAGCGGCGTGTTTTTT-G
64 GGCGCGTTGTTGTAAA-CGCCGCTAAGACACTTTAGCGGCCTGTTTTTTAG
* * * * * * *
54684905 AAGCGCCACTAATTCTTGCATACATAAAGACGAAAACGTTGCGTTTTGGATAGGAAATTTTGCGG
1 AAGCGCCACTAATTCTAGGATACATCAACACAAAAACGATGCGTTTTGGTTAGGAAATTTTGCGG
*
54684970 CGCGTGGTTGTAAACGCCGCTAA
66 CGCGTTGTTGTAAACGCCGCTAA
54684993 TGATGTTCTT
Statistics
Matches: 174, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
112 11 0.06
113 40 0.23
114 91 0.52
115 32 0.18
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (113 bp):
AAGCGCCACTAATTCTAGGATACATCAACACAAAAACGATGCGTTTTGGTTAGGAAATTTTGCGG
CGCGTTGTTGTAAACGCCGCTAAGACACTTTAGCGGCCTGTTTTTTAG
Found at i:54685167 original size:16 final size:18
Alignment explanation
Indices: 54685140--54685172 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54685130 TAGAATTGGG
54685140 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
54685157 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
54685173 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:54688203 original size:6 final size:6
Alignment explanation
Indices: 54688192--54688217 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54688182 CTACGCCGCT
54688192 GGCGGA GGCGGA GGCGGA GGCGGA GG
1 GGCGGA GGCGGA GGCGGA GGCGGA GG
54688218 AGGAAGGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.69, T:0.00
Consensus pattern (6 bp):
GGCGGA
Found at i:54694816 original size:3 final size:3
Alignment explanation
Indices: 54694808--54694833 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54694798 GCTTCCTCTC
54694808 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
54694834 CGACCACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:54700114 original size:9 final size:9
Alignment explanation
Indices: 54700100--54700193 Score: 129
Period size: 9 Copynumber: 10.6 Consensus size: 9
54700090 AGTCCTTTTG
54700100 TTATT-TTA
1 TTATTATTA
*
54700108 TTTATT-TTC
1 -TTATTATTA
*
54700117 TTATTCTTA
1 TTATTATTA
* *
54700126 TTCTTATTC
1 TTATTATTA
54700135 TTATTATTA
1 TTATTATTA
54700144 TTATTATTA
1 TTATTATTA
54700153 TTATTATTA
1 TTATTATTA
54700162 TTATTATTA
1 TTATTATTA
54700171 TTATTATTA
1 TTATTATTA
54700180 TTATTATTA
1 TTATTATTA
54700189 TTATT
1 TTATT
54700194 GCTAACATTG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
8 5 0.06
9 72 0.94
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTATTA
Found at i:54700125 original size:6 final size:6
Alignment explanation
Indices: 54700100--54700193 Score: 129
Period size: 6 Copynumber: 15.8 Consensus size: 6
54700090 AGTCCTTTTG
* * * *
54700100 TTATT- TTATTTA TT-TTC TTATTC TTATTC TTATTC TTATTA TTATTA
1 TTATTA TTA-TTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
54700147 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATT
54700194 GCTAACATTG
Statistics
Matches: 84, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
5 7 0.08
6 75 0.89
7 2 0.02
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATTA
Found at i:54700377 original size:17 final size:17
Alignment explanation
Indices: 54700357--54700389 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54700347 TTCTTTCATT
54700357 TTTATTT-TTATTATTTA
1 TTTATTTATT-TTATTTA
54700374 TTTATTTATTTTATTT
1 TTTATTTATTTTATTT
54700390 TTTCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTATTTTATTTA
Found at i:54700542 original size:24 final size:24
Alignment explanation
Indices: 54700491--54700546 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
54700481 ATCTTTATAT
54700491 TTTATTTTTTTTATATATAGACATA
1 TTTATTTTTTTTATATATA-ACATA
54700516 TTTATGTTTTTTTATAT-T-ACATAA
1 TTTAT-TTTTTTTATATATAACAT-A
54700540 TTTATTT
1 TTTATTT
54700547 ACCTACACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.21
24 6 0.21
25 6 0.21
26 11 0.38
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTATTTTTTTTATATATAACATA
Found at i:54702162 original size:16 final size:16
Alignment explanation
Indices: 54702141--54702171 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54702131 TGAATTACTG
54702141 ATTACAGTTCTATTAT
1 ATTACAGTTCTATTAT
*
54702157 ATTACAGTTTTATTA
1 ATTACAGTTCTATTA
54702172 CTATCAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTACAGTTCTATTAT
Found at i:54706438 original size:43 final size:43
Alignment explanation
Indices: 54706373--54706639 Score: 392
Period size: 43 Copynumber: 6.2 Consensus size: 43
54706363 CGCCATTGTC
* *
54706373 AACGCCGCTATAGATCAGGACCTTTAGCGGCACTTTTTCCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACA
* *
54706416 AACGCCGCTATAGATCATGACCTTTAGCGGCAC-TTTTACACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACA
* *
54706458 AACGCCGCTATAAATCATGACCTTTAGCGGCGCTTTTTACACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACA
* * * *
54706501 AACGCCGCTATAGATCAAGATCTTTAGCGGTGCTTTTTTCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACA
* *
54706544 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACA
* * *
54706587 AACGCCGCTATAAATCATGATCTTTAGCGACGCTTTTTCCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACA
54706630 AACGCCGCTA
1 AACGCCGCTA
54706640 AAAATACCAT
Statistics
Matches: 205, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
42 39 0.19
43 166 0.81
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (43 bp):
AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACA
Found at i:54706654 original size:129 final size:128
Alignment explanation
Indices: 54706373--54706644 Score: 400
Period size: 128 Copynumber: 2.1 Consensus size: 128
54706363 CGCCATTGTC
* * * * *
54706373 AACGCCGCTATAGATCAGGACCTTTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCATGACC
1 AACGCCGCTAAAAATCAAGATCTTTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGACC
*
54706438 TTTAGCGGCACTTTTACACAAACGCCGCTATAAATCATGACCTTTAGCGGCGCTTTTTACACA
66 TTTAGCGGCACTTTTACACAAACGCCGCTATAAATCATGACCTTTAGCGACGCTTTTTACACA
* * ** *
54706501 AACGCCGCTATAGATCAAGATCTTTAGCGGTGCTTTTTTCACAAACGCCGCTATAGATCAAGACC
1 AACGCCGCTAAAAATCAAGATCTTTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGACC
* * * *
54706566 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAAATCATGATCTTTAGCGACGCTTTTTCCACA
66 TTTAGCGGCACTTTT-ACACAAACGCCGCTATAAATCATGACCTTTAGCGACGCTTTTTACACA
54706630 AACGCCGCTAAAAAT
1 AACGCCGCTAAAAAT
54706645 ACCATTCTTT
Statistics
Matches: 130, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
128 73 0.56
129 57 0.44
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (128 bp):
AACGCCGCTAAAAATCAAGATCTTTAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGACC
TTTAGCGGCACTTTTACACAAACGCCGCTATAAATCATGACCTTTAGCGACGCTTTTTACACA
Found at i:54706740 original size:22 final size:20
Alignment explanation
Indices: 54706701--54706740 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
54706691 ACACATTTAA
*
54706701 AAATATTAAATATTAAAATC
1 AAATATTAAATATAAAAATC
54706721 AAATATTATTAATATAAAAA
1 AAATATTA--AATATAAAAA
54706741 ATTAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATTAAATATAAAAATC
Found at i:54706741 original size:23 final size:24
Alignment explanation
Indices: 54706704--54706760 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
54706694 CATTTAAAAA
* *
54706704 TATTAAATAT-TAAAATCAAATAT
1 TATTAAATATAAAAAATCAAATAG
* *
54706727 TATT-AATATAAAAAATTAATTAG
1 TATTAAATATAAAAAATCAAATAG
54706750 TATTAAATATA
1 TATTAAATATA
54706761 TACTTTTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.18
23 17 0.61
24 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
TATTAAATATAAAAAATCAAATAG
Found at i:54715188 original size:16 final size:17
Alignment explanation
Indices: 54715152--54715193 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
54715142 CACTATAATC
54715152 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
54715170 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
54715186 ATTATTTA
1 ATTATTTA
54715194 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:54715316 original size:7 final size:7
Alignment explanation
Indices: 54715300--54715482 Score: 68
Period size: 7 Copynumber: 26.0 Consensus size: 7
54715290 ATTAATTAAT
54715300 CTAAACC
1 CTAAACC
*
54715307 CTAAATC
1 CTAAACC
54715314 CTAAACCC
1 CTAAA-CC
*
54715322 CT-AACT
1 CTAAACC
*
54715328 CTTAACC
1 CTAAACC
*
54715335 CTCAACCC
1 CT-AAACC
54715343 CT-AACC
1 CTAAACC
54715349 ACTAAACC
1 -CTAAACC
*
54715357 TTAAACC
1 CTAAACC
*
54715364 C-CAACC
1 CTAAACC
* * *
54715370 TTTAA-T
1 CTAAACC
54715376 CTATAACC
1 CTA-AACC
*
54715384 TTAAACC
1 CTAAACC
* *
54715391 ATAAACT
1 CTAAACC
* *
54715398 GTAACCC
1 CTAAACC
54715405 CTAAACC
1 CTAAACC
*
54715412 CTAAACT
1 CTAAACC
*
54715419 GTAAACC
1 CTAAACC
* *
54715426 ATAACCC
1 CTAAACC
54715433 CTAAACC
1 CTAAACC
*
54715440 CATAATCC
1 C-TAAACC
*
54715448 ATAAACC
1 CTAAACC
* *
54715455 TTAAACT
1 CTAAACC
*
54715462 CTATACC
1 CTAAACC
* *
54715469 ATATACC
1 CTAAACC
54715476 CTAAACC
1 CTAAACC
54715483 AAAAACCTTA
Statistics
Matches: 125, Mismatches: 42, Indels: 18
0.68 0.23 0.10
Matches are distributed among these distances:
6 11 0.09
7 95 0.76
8 19 0.15
ACGTcount: A:0.40, C:0.37, G:0.01, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:54715434 original size:21 final size:21
Alignment explanation
Indices: 54715380--54715481 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
54715370 TTTAATCTAT
* *
54715380 AACCTTAAACCATAAACTGTA
1 AACCATAAACCCTAAACTGTA
* *
54715401 ACCCCTAAACCCTAAACTGTA
1 AACCATAAACCCTAAACTGTA
* **
54715422 AACCATAACCCCTAAACCCATA
1 AACCATAAACCCTAAA-CTGTA
* * *
54715444 ATCCATAAACCTTAAACTCTA
1 AACCATAAACCCTAAACTGTA
* *
54715465 TACCATATACCCTAAAC
1 AACCATAAACCCTAAAC
54715482 CAAAAACCTT
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
21 47 0.75
22 16 0.25
ACGTcount: A:0.43, C:0.33, G:0.02, T:0.22
Consensus pattern (21 bp):
AACCATAAACCCTAAACTGTA
Found at i:54715437 original size:14 final size:14
Alignment explanation
Indices: 54715380--54715495 Score: 70
Period size: 14 Copynumber: 8.2 Consensus size: 14
54715370 TTTAATCTAT
* *
54715380 AACCTTAAACCATA
1 AACCATAAACCCTA
** *
54715394 AACTGTAACCCCTA
1 AACCATAAACCCTA
* **
54715408 AACCCTAAACTGTA
1 AACCATAAACCCTA
*
54715422 AACCATAACCCCTA
1 AACCATAAACCCTA
* *
54715436 AACCCATAATCCATA
1 AA-CCATAAACCCTA
* *
54715451 AACCTTAAACTCTA
1 AACCATAAACCCTA
* *
54715465 TACCATATACCCTA
1 AACCATAAACCCTA
* *
54715479 AACCAAAAACCTTA
1 AACCATAAACCCTA
54715493 AAC
1 AAC
54715496 TATAGAGATA
Statistics
Matches: 74, Mismatches: 27, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
14 62 0.84
15 12 0.16
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.21
Consensus pattern (14 bp):
AACCATAAACCCTA
Found at i:54715495 original size:7 final size:7
Alignment explanation
Indices: 54715380--54715495 Score: 54
Period size: 7 Copynumber: 16.4 Consensus size: 7
54715370 TTTAATCTAT
*
54715380 AACCTTA
1 AACCATA
54715387 AACCATA
1 AACCATA
**
54715394 AACTGTA
1 AACCATA
* *
54715401 ACCCCTA
1 AACCATA
*
54715408 AACCCTA
1 AACCATA
**
54715415 AACTGTA
1 AACCATA
54715422 AACCATA
1 AACCATA
* *
54715429 ACCCCTA
1 AACCATA
54715436 AACCCATA
1 AA-CCATA
*
54715444 ATCCATA
1 AACCATA
*
54715451 AACCTTA
1 AACCATA
54715458 AACTC-TA
1 AAC-CATA
*
54715465 TACCATA
1 AACCATA
* *
54715472 TACCCTA
1 AACCATA
*
54715479 AACCAAA
1 AACCATA
*
54715486 AACCTTA
1 AACCATA
54715493 AAC
1 AAC
54715496 TATAGAGATA
Statistics
Matches: 81, Mismatches: 25, Indels: 6
0.72 0.22 0.05
Matches are distributed among these distances:
6 1 0.01
7 74 0.91
8 6 0.07
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.21
Consensus pattern (7 bp):
AACCATA
Found at i:54715888 original size:41 final size:41
Alignment explanation
Indices: 54715802--54715958 Score: 271
Period size: 41 Copynumber: 3.9 Consensus size: 41
54715792 AAATGTTTTT
*
54715802 GCGGCGCTTTTACAAAAACGTCGCTAAAG-CCTGAGCATTA
1 GCGGCGCTTTTACAAAAACGCCGCTAAAGCCCTGAGCATTA
*
54715842 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTACAAAAACGCCGCTAAAGCCCTGAGCATTA
*
54715883 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTACAAAAACGCCGCTAAAGCCCTGAGCATTA
*
54715924 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGA
1 GCGGCGCTTTTACAAAAACGCCGCTAAAGCCCTGA
54715959 AAGGTAAGAA
Statistics
Matches: 111, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 27 0.24
41 84 0.76
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTTACAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:54716097 original size:40 final size:40
Alignment explanation
Indices: 54716049--54716143 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
54716039 GCGTTTTCCT
*
54716049 TAAAGCGCCACTAATACTCGATCTTTAGTGGCATTTTATA
1 TAAAGCGCCACTAATACTCGATCTTTAGCGGCATTTTATA
* * * * *
54716089 TAAAGCGCCGCTAATGCTCGATTTTTAGCGGCGTTTTTTA
1 TAAAGCGCCACTAATACTCGATCTTTAGCGGCATTTTATA
54716129 TGCAAA-CGCCACTAA
1 T--AAAGCGCCACTAA
54716144 AAATGCCGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 35 0.76
41 8 0.17
42 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (40 bp):
TAAAGCGCCACTAATACTCGATCTTTAGCGGCATTTTATA
Found at i:54723631 original size:21 final size:21
Alignment explanation
Indices: 54723605--54723645 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54723595 ATCTGCTCAA
* *
54723605 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54723626 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54723646 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54729232 original size:5 final size:5
Alignment explanation
Indices: 54729224--54729248 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54729214 TTATATATCC
54729224 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
54729249 GGTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:54730563 original size:24 final size:24
Alignment explanation
Indices: 54730535--54730582 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54730525 GGGTTACAAT
*
54730535 AAGATAAAATGTGAAGA-GTTAAGG
1 AAGATAAAAGGTGAA-ATGTTAAGG
*
54730559 AAGATGAAAGGTGAAATGTTAAGG
1 AAGATAAAAGGTGAAATGTTAAGG
54730583 GTTGATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (24 bp):
AAGATAAAAGGTGAAATGTTAAGG
Found at i:54730987 original size:9 final size:9
Alignment explanation
Indices: 54730961--54731002 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
54730951 ATATTTAGTC
54730961 ATATAA-TA
1 ATATAATTA
*
54730969 A-ATTATTA
1 ATATAATTA
54730977 ATATAATTA
1 ATATAATTA
54730986 ATATAATTA
1 ATATAATTA
54730995 ATATAATT
1 ATATAATT
54731003 TATTTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 3 0.10
8 4 0.13
9 23 0.77
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATAATTA
Found at i:54731109 original size:15 final size:15
Alignment explanation
Indices: 54731072--54731110 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
54731062 TAATTTTAAA
54731072 TAATATTATTCAATAC
1 TAATATT-TTCAATAC
54731088 TAATATTTT-AATAC
1 TAATATTTTCAATAC
54731102 TAAATATTT
1 T-AATATTT
54731111 ATTACAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATATTTTCAATAC
Found at i:54731109 original size:28 final size:27
Alignment explanation
Indices: 54731035--54731109 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 27
54731025 ATTTAAATTT
*
54731035 TATTTTAATAGTAAAT-TTTAAAAATAA
1 TATTTTAATA-TAAATATTCAAAAATAA
* *
54731062 TAATTTTAA-ATAATATTATTCAATACTAA
1 T-ATTTTAATATAA-A-TATTCAAAAATAA
54731091 TATTTTAATACTAAATATT
1 TATTTTAATA-TAAATATT
54731110 TATTACAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 19 0.49
29 11 0.28
30 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTTTAATATAAATATTCAAAAATAA
Found at i:54731591 original size:14 final size:14
Alignment explanation
Indices: 54731569--54731607 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
54731559 TCGGAAAAGT
54731569 AAGTCATTTTCCAGA
1 AAGTCATTTTCC-GA
54731584 AA-TCATTTTCCGA
1 AAGTCATTTTCCGA
54731597 AAGTCATTTTC
1 AAGTCATTTTC
54731608 AGTGAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 17 0.74
15 2 0.09
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (14 bp):
AAGTCATTTTCCGA
Found at i:54731968 original size:26 final size:27
Alignment explanation
Indices: 54731935--54731991 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
54731925 CAGGTTTGAT
54731935 AAAATAAATTA-TTAAAAATTCAAA-AA
1 AAAATAAATTATTTAAAAATT-AAATAA
54731961 AAAATAAATTATTTAAAAATTAAATAA
1 AAAATAAATTATTTAAAAATTAAATAA
54731988 AAAA
1 AAAA
54731992 CCGGTTCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAATAAATTATTTAAAAATTAAATAA
Found at i:54739376 original size:17 final size:17
Alignment explanation
Indices: 54739350--54739384 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54739340 CAATTTTACT
54739350 ATAATGACAAAAGAATGA
1 ATAATGACAAAAG-ATGA
54739368 ATAAT-ACAAAAGATGA
1 ATAATGACAAAAGATGA
54739384 A
1 A
54739385 GACAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (17 bp):
ATAATGACAAAAGATGA
Found at i:54739559 original size:24 final size:24
Alignment explanation
Indices: 54739532--54739583 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
54739522 TTTGTAGGTG
*
54739532 AAATAAATTATACA-AATAAATGCT
1 AAATAAATTATA-ATAATAAATACT
*
54739556 AAATATATTATAATAATAAATACT
1 AAATAAATTATAATAATAAATACT
54739580 AAAT
1 AAAT
54739584 CTTCTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATAATAATAAATACT
Found at i:54744860 original size:26 final size:26
Alignment explanation
Indices: 54744810--54744860 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
54744800 TAAAATTAGC
* * *
54744810 ATTATACAATCATTCATATTTAATAT
1 ATTATACAATCACTCAAATTAAATAT
*
54744836 ATTATATAATCACTCAAATTAAATA
1 ATTATACAATCACTCAAATTAAATA
54744861 AATCTCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTATACAATCACTCAAATTAAATAT
Found at i:54755117 original size:26 final size:26
Alignment explanation
Indices: 54755088--54755137 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
54755078 TTATTTTATT
*
54755088 TTTAAAAAATATATTTTCTAATTCGA
1 TTTAAAAAATATATTCTCTAATTCGA
***
54755114 TTTATTTAATATATTCTCTAATTC
1 TTTAAAAAATATATTCTCTAATTC
54755138 AACTTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAAAAAATATATTCTCTAATTCGA
Found at i:54758661 original size:12 final size:12
Alignment explanation
Indices: 54758644--54758669 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54758634 AAATCACCAT
54758644 ATCCTCTCTTAA
1 ATCCTCTCTTAA
54758656 ATCCTCTCTTAA
1 ATCCTCTCTTAA
54758668 AT
1 AT
54758670 GAACAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (12 bp):
ATCCTCTCTTAA
Found at i:54759548 original size:18 final size:18
Alignment explanation
Indices: 54759479--54759553 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
54759469 ATAATAGTTC
* *
54759479 TATTTTTAAATAAATAAAA
1 TATTTTTAAATATAT-AAT
*
54759498 TATTTTTAACTA-ATAAT
1 TATTTTTAAATATATAAT
* **
54759515 TGTAAATTAAAT-TATAAT
1 TAT-TTTTAAATATATAAT
54759533 TATTTTTAAATATATAAT
1 TATTTTTAAATATATAAT
54759551 TAT
1 TAT
54759554 CACAACTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 10 0.23
18 23 0.52
19 11 0.25
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TATTTTTAAATATATAAT
Found at i:54764281 original size:19 final size:18
Alignment explanation
Indices: 54764257--54764294 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54764247 ATATCTCTCA
54764257 GGCAAAGTAGAGTGATAAT
1 GGCAAA-TAGAGTGATAAT
*
54764276 GGCAAATGGAGTGATAAT
1 GGCAAATAGAGTGATAAT
54764294 G
1 G
54764295 TCCGGCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.39, C:0.05, G:0.34, T:0.21
Consensus pattern (18 bp):
GGCAAATAGAGTGATAAT
Found at i:54771365 original size:114 final size:114
Alignment explanation
Indices: 54771191--54771846 Score: 524
Period size: 113 Copynumber: 5.7 Consensus size: 114
54771181 AAATCTCAAG
* * * * *
54771191 ACCAACACGCAGCA-TTCTGGTATTGATGTATATTAGAATTAGTGGCGCTTACGAA-CAAACGCT
1 ACCAAAACGCAG-AGTT-TGGTCTTGATGTATATTAGAATTAGTGGCGCTTA-TAAGAAAACGCC
* * * *
54771254 GGTAATGCATAGTATTAGCGGCGCTTAGCGG-AAGTGCCGCAAAAGATGTTA
63 GCTAATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAGATCTTA
* *
54771305 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTACAAGTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTAT-AAGAAAACGCCGC
* * * * *
54771370 TAATGTATAGTATTAGCGGCGCTGAGTGTTAAA-CACCGCAAAACATCTTA
65 TAATGCATAGTATTAGCGGCGCTTAGTG-GAAAGCGCCGCAAAAGATCTTA
* * * * *
54771420 ACCAAAACGTAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCG-TT-TAAGGAAAACGCCA
1 ACCAAAACGCAGAG-TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAA-GAAAACGCCG
* * * ** * * * *
54771483 CTAAAGCATAGTAATAGCAGCATTTGGTGGTAAGCGCCTCAAAATATCTTA
64 CTAATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAGATCTTA
* * **
54771534 ACCAAAACGCGGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATTGGAAAACGCCGCT
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGAAAACGCCGCT
* * * * *
54771599 AA-ACTATAGTAGTAGTGGCG-TTTGTGGAAAGCGCCGC-AAAGTATCCTA
66 AATGC-ATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAG-ATCTTA
* * *** *
54771647 ACCAAAACGCAGAGTTTGGCCTTGACGTATATTA-AAGTTAGTGGCGCTTATTTCAAAACGCTGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAA-TTAGTGGCGCTTATAAGAAAACGCCGC
* * * * * * * *
54771711 TAATGCTTACTATTTGCGGCGCTTTGTGGTAAGCGCCACCAAAAGGTATTA
65 TAATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCC-GCAAAAGATCTTA
* ** * * * * ** * * *
54771762 ACGAAAATACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGGCGCACACAGGAAAACGCTGC
1 ACCAAAACGCAGAGTTT-GGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGAAAACGCCGC
*
54771827 TGAA-ACATAGTATTAGCGGC
65 T-AATGCATAGTATTAGCGGC
54771847 ACTTTTCCCG
Statistics
Matches: 432, Mismatches: 90, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
112 5 0.01
113 155 0.36
114 142 0.33
115 45 0.10
116 81 0.19
117 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (114 bp):
ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGAAAACGCCGCT
AATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAGATCTTA
Found at i:54771975 original size:18 final size:18
Alignment explanation
Indices: 54771954--54771989 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
54771944 TCATTTTATA
54771954 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
54771972 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
54771990 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:54772394 original size:12 final size:14
Alignment explanation
Indices: 54772355--54772400 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
54772345 ATATGGTTTA
*
54772355 AGGGTTAGGG-GTT
1 AGGGTTAGGGATTT
54772368 AGGGGTTAGGGATTT
1 A-GGGTTAGGGATTT
54772383 -GGGTTA-GGATTT
1 AGGGTTAGGGATTT
54772395 AGGGTT
1 AGGGTT
54772401 TTGATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 6 0.21
13 12 0.41
14 9 0.31
15 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.35
Consensus pattern (14 bp):
AGGGTTAGGGATTT
Found at i:54772396 original size:20 final size:20
Alignment explanation
Indices: 54772363--54772403 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54772353 TAAGGGTTAG
*
54772363 GGGTTAGGGGTTAGGGATTT
1 GGGTTAGGAGTTAGGGATTT
* *
54772383 GGGTTAGGATTTAGGGTTTT
1 GGGTTAGGAGTTAGGGATTT
54772403 G
1 G
54772404 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.39
Consensus pattern (20 bp):
GGGTTAGGAGTTAGGGATTT
Found at i:54773705 original size:44 final size:44
Alignment explanation
Indices: 54773628--54773715 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
54773618 GAGCGACTGC
*
54773628 GTTTTGACTTATAGTTAGTGGCGCTTAGTTTAAAACGCCGCAAA
1 GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
* * *
54773672 GTTTTGACTTATAGTTTGTGGTGCTTTGCTTAAAACGCCGCAAA
1 GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
54773716 AATGTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (44 bp):
GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
Found at i:54775185 original size:16 final size:16
Alignment explanation
Indices: 54775164--54775199 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
54775154 GTATTTATAA
*
54775164 TTATCGATTTTCAATT
1 TTATCGATTTACAATT
54775180 TTATCGATTTACAATT
1 TTATCGATTTACAATT
54775196 TTAT
1 TTAT
54775200 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:54776000 original size:18 final size:18
Alignment explanation
Indices: 54775979--54776052 Score: 50
Period size: 18 Copynumber: 4.3 Consensus size: 18
54775969 CGATTTGACT
54775979 TGTTTTAGTTATTTATAG
1 TGTTTTAGTTATTTATAG
54775997 TG-TTTA-TT-TTCTA-A-
1 TGTTTTAGTTATT-TATAG
* * * **
54776011 TGGTTTAATTCATTGATCT
1 TGTTTTAGTT-ATTTATAG
54776030 TGTTTTAGTTATTTATAG
1 TGTTTTAGTTATTTATAG
54776048 TGTTT
1 TGTTT
54776053 ATTTTCTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.05
15 7 0.17
16 6 0.14
17 5 0.12
18 14 0.33
19 8 0.19
ACGTcount: A:0.20, C:0.04, G:0.15, T:0.61
Consensus pattern (18 bp):
TGTTTTAGTTATTTATAG
Found at i:54776038 original size:51 final size:51
Alignment explanation
Indices: 54775973--54776078 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
54775963 TTAATACGAT
*
54775973 TTGA-CTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTCA
1 TTGATCTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTAA
54776023 TTGATCTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTAA
1 TTGATCTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTAA
54776074 TTGAT
1 TTGAT
54776079 TGTAATGCGA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 4 0.07
51 50 0.93
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.58
Consensus pattern (51 bp):
TTGATCTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTAA
Found at i:54776489 original size:21 final size:21
Alignment explanation
Indices: 54776459--54776508 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
54776449 CTACAAATTA
* *
54776459 AAGCAAAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*
54776480 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
*
54776501 AAGTAGAG
1 AAGCAGAG
54776509 CAGAGCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:54776916 original size:42 final size:42
Alignment explanation
Indices: 54776829--54777068 Score: 331
Period size: 42 Copynumber: 5.7 Consensus size: 42
54776819 TGTATAAAAG
** *
54776829 CGCCGCTAAAGATAATGTTCTTTAGCGG-GCTTAGAAAAAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAA
* * *
54776870 CGCCGCTAAAGACCATGCTCTTCAGCGGCGCTTAGAAAGAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAA
*
54776912 CGCCGCTAAAGACCATGTTCTTTAGCGGCCCTTAGAAAATAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AAATAAA
* * * *
54776955 TGCCCCGAAAGACCATGTTCTTTAGTGGCGCTTAGTAAA-AAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AAATAAA
*
54776997 CGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAATAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAA
*
54777039 CGCCGCTAAAGACCATGTTCTTTAGAGGCG
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCG
54777069 TTTCTTTCTA
Statistics
Matches: 174, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
41 27 0.16
42 108 0.62
43 39 0.22
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (42 bp):
CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAA
Found at i:54777000 original size:85 final size:84
Alignment explanation
Indices: 54776824--54777068 Score: 343
Period size: 85 Copynumber: 2.9 Consensus size: 84
54776814 GTTTTTGTAT
* **
54776824 AAAAGCGCCGCTAAAGATAATGTTCTTTAGCGG-GCTTAGAAAA-AAACGCCGCTAAAGACCATG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAATAAACGCCGCTAAAGACCATG
* * *
54776887 CTCTTCAGCGGCGCTTAGA
66 TTCTTTAGAGGCGCTTAGA
* * * *
54776906 AAGAAACGCCGCTAAAGACCATGTTCTTTAGCGGCCCTTAGAAAATAAATGCCCCGAAAGACCAT
1 AA-AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAATAAACGCCGCTAAAGACCAT
*
54776971 GTTCTTTAGTGGCGCTTAGTA
65 GTTCTTTAGAGGCGCTTAG-A
*
54776992 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAG-AAATAAACGCCGCTAAAGACCATG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAATAAACGCCGCTAAAGACCATG
54777056 TTCTTTAGAGGCG
66 TTCTTTAGAGGCG
54777069 TTTCTTTCTA
Statistics
Matches: 143, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
82 2 0.01
83 28 0.20
84 42 0.29
85 68 0.48
86 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAATAAACGCCGCTAAAGACCATG
TTCTTTAGAGGCGCTTAGA
Found at i:54777113 original size:42 final size:42
Alignment explanation
Indices: 54776829--54777113 Score: 268
Period size: 42 Copynumber: 6.8 Consensus size: 42
54776819 TGTATAAAAG
** * * *
54776829 CGCCGCTAAAGATAATGTTCTTTAGCG-GGCTTAGAAAAAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGACGTTTAGAAATAAA
* * * * *
54776870 CGCCGCTAAAGACCATGCTCTTCAGCGGCGCTTAGAAAGAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGACGTTTAGAAATAAA
* **
54776912 CGCCGCTAAAGACCATGTTCTTTAGCGGCCCTTAGAAAATAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGACGTTTAG-AAATAAA
* * * * * *
54776955 TGCCCCGAAAGACCATGTTCTTTAGTGGCGCTTAGTAAA-AAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGACGTTTAG-AAATAAA
*
54776997 CGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAATAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGACGTTTAGAAATAAA
* * ***** *
54777039 CGCCGCTAAAGACCATGTTCTTTAGAGGCGTTTCTTTCTAAG
1 CGCCGCTAAAGACCATGTTCTTTAGCGACGTTTAGAAATAAA
* *
54777081 CGCCGCTAAAGAACATGGTCTTTAGCGACGTTT
1 CGCCGCTAAAGACCATGTTCTTTAGCGACGTTT
54777114 TTGTTTGTAA
Statistics
Matches: 207, Mismatches: 34, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
41 26 0.13
42 142 0.69
43 39 0.19
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (42 bp):
CGCCGCTAAAGACCATGTTCTTTAGCGACGTTTAGAAATAAA
Found at i:54777494 original size:17 final size:17
Alignment explanation
Indices: 54777466--54777500 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54777456 TAATTTTACT
54777466 ATAATGACAAAAGACTGA
1 ATAATGACAAAAGA-TGA
54777484 ATAAT-ACAAAAGATGA
1 ATAATGACAAAAGATGA
54777500 A
1 A
54777501 GACAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (17 bp):
ATAATGACAAAAGATGA
Found at i:54783564 original size:50 final size:50
Alignment explanation
Indices: 54783487--54783653 Score: 169
Period size: 50 Copynumber: 3.3 Consensus size: 50
54783477 GTAATGCCGT
* * * *
54783487 GGAAGCAAGATTTGCCGTTGTGACTTCAATCTTTTCCACTGCATCGTCTA
1 GGAAGTAAGATTCGCTGCTGTGACTTCAATCTTTTCCACTGCATCGTCTA
** * **
54783537 GGAAGTAAGATTCGCTGCTGT-AGCTTCAATCTTTTGAACTGTAAT-GTCGG
1 GGAAGTAAGATTCGCTGCTGTGA-CTTCAATCTTTTCCACTG-CATCGTCTA
* * * *
54783587 GGAAGCAAGATTC-ATCGTTGTGACTTCAATCTATTCCACTGCATCGTCTA
1 GGAAGTAAGATTCGCT-GCTGTGACTTCAATCTTTTCCACTGCATCGTCTA
54783637 GGAAGTAAGATTCGCTG
1 GGAAGTAAGATTCGCTG
54783654 TCTTCGATCT
Statistics
Matches: 91, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
49 4 0.04
50 83 0.91
51 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (50 bp):
GGAAGTAAGATTCGCTGCTGTGACTTCAATCTTTTCCACTGCATCGTCTA
Found at i:54783613 original size:100 final size:99
Alignment explanation
Indices: 54783372--54783653 Score: 372
Period size: 99 Copynumber: 2.8 Consensus size: 99
54783362 TTTAATTTGC
* * * * * *
54783372 TTAACTGTGATGTCGGGGAAGCAAGATTCGCCATTGT-AGCTTTAATCTGTTCCCCTACA-CTGT
1 TTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGA-CTTCAATCTATTCCACTGCATC-GT
* **
54783435 C-AGGGAAGTAAGATTTGCTATTGTAGCTTCAATCTT
64 CTA-GGAAGTAAGATTCGCTGCTGTAGCTTCAATCTT
* * * *
54783471 TTAACTGTAATGCCGTGGAAGCAAGATTTGCCGTTGTGACTTCAATCTTTTCCACTGCATCGTCT
1 TTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGACTTCAATCTATTCCACTGCATCGTCT
54783536 AGGAAGTAAGATTCGCTGCTGTAGCTTCAATCTT
66 AGGAAGTAAGATTCGCTGCTGTAGCTTCAATCTT
**
54783570 TTGAACTGTAATGTCGGGGAAGCAAGATTCATCGTTGTGACTTCAATCTATTCCACTGCATCGTC
1 TT-AACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGACTTCAATCTATTCCACTGCATCGTC
54783635 TAGGAAGTAAGATTCGCTG
65 TAGGAAGTAAGATTCGCTG
54783654 TCTTCGATCT
Statistics
Matches: 161, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
99 83 0.52
100 78 0.48
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (99 bp):
TTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGACTTCAATCTATTCCACTGCATCGTCT
AGGAAGTAAGATTCGCTGCTGTAGCTTCAATCTT
Found at i:54783714 original size:44 final size:44
Alignment explanation
Indices: 54783666--54784585 Score: 198
Period size: 44 Copynumber: 21.1 Consensus size: 44
54783656 TTCGATCTGT
* *
54783666 TCCACTACTGCTTAGGGAGATAAGATCTTTAATTTTCAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * *
54783710 TCCACTACTGTTTAAGGAGATAATG-TCTACAATCTTCAACCTAT
1 TCCACTACTGCTTAGGGAGATAA-GATCTTCAATCTTCAACCTAC
** * * * **** * *
54783754 TCCACTGTTG-TCTAGAGAGATAGGGT-TTGTGGCTTAAATCTAC
1 TCCACTACTGCT-TAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * ** * * *
54783797 TTCC-CTACT-CCTGGGGAAGATAAGAT-TTGCTGTCTTCGATCTGC
1 -TCCACTACTGCTTAGGG-AGATAAGATCTT-CAATCTTCAACCTAC
* * *
54783841 TCCACTACTGCTTAGGGAGATAAGATATGCAATTTTCAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * * *
54783885 TCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTAT
1 TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * * * * **** * *
54783929 TCCATTGCTG-TCCAGAGAGATAGGGT-TTGTGGCTTAAATCTAC
1 TCCACTACTGCT-TAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * * * *
54783972 TTCC-CTACT-CCTGGGGAAGATAAGA--TTCACCGTCTTCGATCTGC
1 -TCCACTACTGCTTAGGG-AGATAAGATCTTCA--ATCTTCAACCTAC
* * *
54784016 TCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTTAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * * *
54784060 TCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTAT
1 TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * * **** * * *
54784104 TCCACTGCTG-TCCAGAGAGATAGGAT-TTGTGGCTTAAATCTGC
1 TCCACTACTGCT-TAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * ** ** *
54784147 TTCC-CTACT-CCTGGGGAAGATAAGA--TTCGAACTCTTTGATTTGC
1 -TCCACTACTGCTTAGGG-AGATAAGATCTTC-AA-TCTTCAACCTAC
* * *
54784191 TCCACTATTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * **** * *
54784235 TCCACTGCTGCTCAGAGAGAT-AGAGT-TTGTGGCTTAAATCTAC
1 TCCACTACTGCTTAGGGAGATAAGA-TCTTCAATCTTCAACCTAC
* * * ** * * *
54784278 TTCC-CTACT-CCTGGGGAAGATAAGAT-TCGCCGTCTTCGATCTGC
1 -TCCACTACTGCTTAGGG-AGATAAGATCT-TCAATCTTCAACCTAC
* *
54784322 TCCACTACTACTTAGGGAGATAAGATCTGT-AATTTTCAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCT-TCAATCTTCAACCTAC
* * * * * *
54784366 TCCACTGCTGCTCAAGGAGATAAGA-C-T-AGTCTTTAACCTAT
1 TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * * * * **** * * *
54784407 TCCAATGCTG-TCCAAGGAGATAGGAT-TTGTGGCTTAAATCTGC
1 TCCACTACTGCT-TAGGGAGATAAGATCTTCAATCTTCAACCTAC
* * ** * * *
54784450 TTCC-CTACT-CTTGGGGAAGATAAGAT-TCGCCGTCTTCGATCTGC
1 -TCCACTACTGCTTAGGG-AGATAAGATCT-TCAATCTTCAACCTAC
* * *
54784494 TCCACTACTACTTAGGGAGATAATAT-TTGCAATTTTCAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCTT-CAATCTTCAACCTAC
* * * *
54784538 TCCACTGA-TGCTCAAGGAGATAAGGTCTACAATCTTCAACCTAC
1 TCCACT-ACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
54784582 TCCA
1 TCCA
54784586 ATGTTGTCCA
Statistics
Matches: 624, Mismatches: 201, Indels: 102
0.67 0.22 0.11
Matches are distributed among these distances:
40 1 0.00
41 32 0.05
42 17 0.03
43 121 0.19
44 415 0.67
45 33 0.05
46 5 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
TCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTAC
Found at i:54783948 original size:175 final size:175
Alignment explanation
Indices: 54783637--54784256 Score: 1008
Period size: 175 Copynumber: 3.5 Consensus size: 175
54783627 GCATCGTCTA
* **
54783637 GGAAG-TAAGATTCGCTGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTTTAATTT
1 GGAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
* * * * * *
54783701 TCAACCTACTCCACTACTGTTTAAGGAGATAATGTCTACAATCTTCAACCTATTCCACTGTTGTC
66 TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
*
54783766 TAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
131 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
* *
54783811 GGAAGATAAGATTTGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGCAATTT
1 GGAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
*
54783876 TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCATTGCTGTC
66 TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
54783941 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
131 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
* *
54783986 GGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
1 GGAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
*
54784051 TTAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
66 TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
* *
54784116 CAGAGAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCTGG
131 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
*** * * *
54784161 GGAAGATAAGATTCGAACTCTTTGATTTGCTCCACTATTGCTTAGGGAGATAAGATCTGCAATTT
1 GGAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
*
54784226 TCAACCTACTCCACTGCTGCTCAGAGAGATA
66 TCAACCTACTCCACTGCTGCTCAGGGAGATA
54784257 GAGTTTGTGG
Statistics
Matches: 415, Mismatches: 30, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
174 5 0.01
175 410 0.99
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (175 bp):
GGAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
Found at i:54784145 original size:131 final size:131
Alignment explanation
Indices: 54784050--54784387 Score: 396
Period size: 131 Copynumber: 2.6 Consensus size: 131
54784040 ATCTGCAATT
* * *
54784050 TTTAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTG-
1 TTTAACCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGC
*
54784114 TCCAGAGAGATAG-GATTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGAA
66 T-CAGAGAGATAGAG-TTTGTGGCTTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGAA
54784178 CTC
129 CTC
* ** * * * * *
54784181 TTTGATTTGCTCCACTATTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGCTGC
1 TTTAACCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGC
* * *
54784246 TCAGAGAGATAGAGTTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGATTCG-CCG
66 TCAGAGAGATAGAGTTTGTGGCTTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGAAC-
54784310 TC
130 TC
** * * * * ** *
54784312 TTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGC
1 TTTAACCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGC
54784377 TCA-AGGAGATA
66 TCAGA-GAGATA
54784388 AGACTAGTCT
Statistics
Matches: 185, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
130 2 0.01
131 181 0.98
132 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (131 bp):
TTTAACCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGC
TCAGAGAGATAGAGTTTGTGGCTTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGAACT
C
Found at i:54784322 original size:175 final size:174
Alignment explanation
Indices: 54783829--54784694 Score: 575
Period size: 175 Copynumber: 5.0 Consensus size: 174
54783819 AGATTTGCTG
* *
54783829 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGCAATTTTCAACCTACTCCACTGCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGCT
* ***** * * * * ** * *
54783894 GCTCAGGGAGATA-AGGTCTACAATCTTCAACCTA-TT-CC-ATTGCTGTCCAGAGAGATAGGGT
66 GCTCAGAGAGATAGA-GT-TTGTGGCTTAAATCTACTTCCCTACTCCTG--GGGA-AGATAAGAT
* * * * * * *
54783955 TTG-TGGCTTAAATCTACTTCC-CTACT-CCTGGGGAAGATAAGATTC-ACCG
126 TCGCCGTCTTAGATCTGC-TCCACTACTACCTAGGG-AGATAAGATTCGA--A
* *
54784004 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTTAACCTACTCCACTGCT
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGCT
* ***** * * * ** *
54784069 GCTCAGGGAGATA-AGGTCTACAATCTTCAACCTA-TT-CC-ACTGCTGTCCAGAGAGATAGGAT
66 GCTCAGAGAGATAGA-GT-TTGTGGCTTAAATCTACTTCCCTACTCCTG--GGGA-AGATAAGAT
* * * * *
54784130 TTG-TGGCTTAAATCTGCTTCC-CTACT-CCTGGGGAAGATAAGATTCGAA
126 TCGCCGTCTTAGATCTGC-TCCACTACTACCTAGGG-AGATAAGATTCGAA
* *
54784178 CTCTTTGATTTGCTCCACTATTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGC
1 -TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGC
54784243 TGCTCAGAGAGATAGAGTTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGATTCGC
65 TGCTCAGAGAGATAGAGTTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGATTCGC
* *
54784308 CGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGA-TCTGTAA
130 CGTCTTAGATCTGCTCCACTACTACCTAGGGAGATAAGATTC-G-AA
* * * * * * * * *
54784354 T-TTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGA-CT--AGTCTTT-AACCTATTCCAATG
1 TCTTT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT-TTTCAACCTACTCCACTG
* *
54784414 CTG-TCCA-AGGAGATAG-GATTTGTGGCTTAAATCTGCTTCCCTACTCTTGGGGAAGATAAGAT
64 CTGCT-CAGA-GAGATAGAG-TTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGAT
* * * *
54784476 TCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAATATTTGCAA
126 TCGCCGTCTTAGATCTGCTCCACTACTACCTAGGGAGATAAGATTCG-AA
* * * * * * * * *
54784526 T-TTTCAACCTACTCCACTGA-TGCTCAAGGAGATAAGGTCTACAATCTTCAACCTACTCCAATG
1 TCTTT-GATCTGCTCCACT-ACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTG
* * * *
54784589 TTG-TCCAG-GAAGATAG-GATTTGTGGCTTAAATTTGCTTCCCTACTCCTAGGGAAGATAAGAT
64 CTGCT-CAGAG-AGATAGAG-TTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGAT
* *
54784651 TCGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGAT
126 TCGCCGTCTTAGATCTGCTCCACTACTACCTAGGGAGATAAGAT
54784695 CTACAATTCC
Statistics
Matches: 611, Mismatches: 56, Indels: 48
0.85 0.08 0.07
Matches are distributed among these distances:
171 3 0.00
172 147 0.24
173 6 0.01
174 32 0.05
175 406 0.66
176 11 0.02
177 6 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (174 bp):
TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGCT
GCTCAGAGAGATAGAGTTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGAAGATAAGATTCGCC
GTCTTAGATCTGCTCCACTACTACCTAGGGAGATAAGATTCGAA
Found at i:54784458 original size:172 final size:173
Alignment explanation
Indices: 54784225--54784702 Score: 730
Period size: 172 Copynumber: 2.8 Consensus size: 173
54784215 ATCTGCAATT
* *
54784225 TTCAACCTACTCCACTGCTG-CTCAGAGAGATA-GAGTTTGTGGCTTAAATCTACTTCCCTACTC
1 TTCAACCTACTCCAATGCTGTC-CAG-GAGATAGGA-TTTGTGGCTTAAATCTGCTTCCCTACTC
*
54784288 CTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTA
63 CTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCA
* *
54784353 ATTTTCAACCTACTCCACTGCTGCTCAAGGAGATAA-GACT-AGTC
128 ATTTTCAACCTACTCCACTGATGCTCAAGGAGATAAGGACTAAATC
* * *
54784397 TTTAACCTATTCCAATGCTGTCCAAGGAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCTT
1 TTCAACCTACTCCAATGCTGTCC-AGGAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCT
* *
54784462 GGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAATATTTGCAAT
65 GGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAAT
*
54784527 TTTCAACCTACTCCACTGATGCTCAAGGAGATAAGGTCTACAATC
130 TTTCAACCTACTCCACTGATGCTCAAGGAGATAAGGACTA-AATC
* *
54784572 TTCAACCTACTCCAATGTTGTCCAGGAAGATAGGATTTGTGGCTTAAATTTGCTTCCCTACTCCT
1 TTCAACCTACTCCAATGCTGTCCAGG-AGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCT
* * *
54784637 AGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAAT
65 GGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAAT
54784702 T
130 T
54784703 CCATTGATCT
Statistics
Matches: 278, Mismatches: 21, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
172 147 0.53
173 8 0.03
174 3 0.01
175 120 0.43
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (173 bp):
TTCAACCTACTCCAATGCTGTCCAGGAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCTG
GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATT
TTCAACCTACTCCACTGATGCTCAAGGAGATAAGGACTAAATC
Found at i:54792526 original size:21 final size:21
Alignment explanation
Indices: 54792487--54792526 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54792477 ATTGCCCTAA
* *
54792487 ATTTCTCTTCAATCCATTTCC
1 ATTTCTCCTCAAACCATTTCC
*
54792508 ATTTCTCCTCAAACTATTT
1 ATTTCTCCTCAAACCATTT
54792527 TGGCAATTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTCTCCTCAAACCATTTCC
Found at i:54798580 original size:5 final size:5
Alignment explanation
Indices: 54798564--54798652 Score: 115
Period size: 5 Copynumber: 17.8 Consensus size: 5
54798554 TTCATACTAG
* * * *
54798564 TCATA TCTTA TCATA TCATA ACGTA TCATA ACATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
* * *
54798614 TCATA CCAAA TCATA TCATA TCATA TTATA TCATA TCAT
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCAT
54798653 TACATGTCCT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 70 1.00
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.38
Consensus pattern (5 bp):
TCATA
Found at i:54799326 original size:49 final size:50
Alignment explanation
Indices: 54799181--54799327 Score: 138
Period size: 49 Copynumber: 3.0 Consensus size: 50
54799171 TACCCATACG
* *
54799181 GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACATGGCTAAGACACACAA
1 GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAA
**** * * * ** *
54799231 G-CTGTAAAAACACACACGG-CTGTGTGCTCTACACGGCCTACCCACAC-T
1 GTCTGTAAAGTTTCACACGGCCT-TGTGCTCCACAAGGCCAAGACACACAA
* *
54799279 GTCTGCAAAGTTTTACACGGCCTTGTGCTCCACAAGGCCAAGACACACA
1 GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACA
54799328 GGTTGCAAAA
Statistics
Matches: 71, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
48 3 0.04
49 65 0.92
50 3 0.04
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (50 bp):
GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAA
Found at i:54799344 original size:98 final size:98
Alignment explanation
Indices: 54799170--54799367 Score: 261
Period size: 98 Copynumber: 2.0 Consensus size: 98
54799160 TCCATATGGA
* * * *
54799170 CTACCCATACGGTCTGTAAAGTTTCACACGGCCTTGTGCTCCACATGGCTAAGACACACAAGCTG
1 CTACCCACACGGTCTGCAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAAGCTG
* * * * *
54799235 TAAAAACACACACGGCTGTGTGCTCTACACGGC
66 CAAAAAAACACACGACCGTGTGCTCCACACGGC
* * * *
54799268 CTACCCACACTGTCTGCAAAGTTTTACACGGCCTTGTGCTCCACAAGGCCAAGACACACAGGTTG
1 CTACCCACACGGTCTGCAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAAGCTG
* *
54799333 CAAAAAAACACATGACCGTGTGCTCCGCACGGC
66 CAAAAAAACACACGACCGTGTGCTCCACACGGC
54799366 CT
1 CT
54799368 GACACACGGC
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
98 85 1.00
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (98 bp):
CTACCCACACGGTCTGCAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAAGCTG
CAAAAAAACACACGACCGTGTGCTCCACACGGC
Found at i:54806410 original size:17 final size:16
Alignment explanation
Indices: 54806390--54806439 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
54806380 TTATTTTTAA
54806390 AATTTTTATATTATTTT
1 AATTTTTATATT-TTTT
*
54806407 AA-TTTAATATTTTTT
1 AATTTTTATATTTTTT
54806422 -ATTTATTGATATTTTTT
1 AATTT-TT-ATATTTTTT
54806439 A
1 A
54806440 TATAGTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 1 0.04
15 6 0.22
16 9 0.33
17 11 0.41
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
AATTTTTATATTTTTT
Found at i:54814744 original size:12 final size:12
Alignment explanation
Indices: 54814727--54814752 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54814717 CAAAATAGGC
54814727 TTTTAGCGGCGT
1 TTTTAGCGGCGT
54814739 TTTTAGCGGCGT
1 TTTTAGCGGCGT
54814751 TT
1 TT
54814753 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:54814800 original size:41 final size:39
Alignment explanation
Indices: 54814741--54814873 Score: 135
Period size: 40 Copynumber: 3.3 Consensus size: 39
54814731 AGCGGCGTTT
* *
54814741 TTAGCGGCGTTTGGATAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGTTT-TAT-AAAAACGCCGCTAAAAATCAAGCA
* ** *
54814782 TTAGCGGCGCTTTTATAAAAACGCTGCTAAAGGTCGAGCA
1 TTAGCGGCG-TTTTATAAAAACGCCGCTAAAAATCAAGCA
*
54814822 TTAGCGGCGCTTTT-TGGAAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCG-TTTTAT-AAAAACGCCGCTAAAAATCAAGCA
*
54814861 TTACCGGCGTTTT
1 TTAGCGGCGTTTT
54814874 CCAAAAAGTG
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
38 4 0.05
39 13 0.17
40 47 0.60
41 11 0.14
42 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (39 bp):
TTAGCGGCGTTTTATAAAAACGCCGCTAAAAATCAAGCA
Found at i:54814984 original size:41 final size:41
Alignment explanation
Indices: 54814927--54815129 Score: 334
Period size: 41 Copynumber: 5.0 Consensus size: 41
54814917 CTGAGTTTTG
* *
54814927 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
54814968 GGGCCTTTAGCGGCGTTTGTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
54815009 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
54815050 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
54815091 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
54815130 CCGCTTTTGA
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 152 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:54815800 original size:21 final size:21
Alignment explanation
Indices: 54815763--54815807 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54815753 TAAATAAGAT
* *
54815763 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAGAAGTTAGAGG
54815784 TTAGGGGTTA-AAGGTTAGAGG
1 TTAGGGGTTAGAA-GTTAGAGG
54815805 TTA
1 TTA
54815808 AGAGTTAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGAAGTTAGAGG
Found at i:54820010 original size:43 final size:43
Alignment explanation
Indices: 54819950--54820040 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
54819940 CTTTGAGTTC
* * * *
54819950 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
54819992 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
54820035 ATTACC
1 ATTACC
54820041 TTGCATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:54820392 original size:42 final size:43
Alignment explanation
Indices: 54820313--54820473 Score: 220
Period size: 42 Copynumber: 3.8 Consensus size: 43
54820303 ACGATATATT
*
54820313 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
54820356 TTTAGCGACGTTTGTGGG-GAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
54820398 TTTAGTGGCATTTGTAGGG--AAGCGCCGCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
54820440 TTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
54820474 TTAGCGACGC
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.03
42 67 0.64
43 34 0.33
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:54820576 original size:22 final size:21
Alignment explanation
Indices: 54820544--54820588 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
54820534 TTAGTGGCGT
*
54820544 TAAAAAACGCCGCTAAAGGCC
1 TAAAAAACGCCGCTAAAAGCC
54820565 TAAAAAAGCGCCGCTAAAAGCC
1 TAAAAAA-CGCCGCTAAAAGCC
54820587 TA
1 TA
54820589 TTTTGGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.44, C:0.27, G:0.18, T:0.11
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAAGCC
Done.