Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 6 of 136
Found at i:1531699 original size:21 final size:21
Alignment explanation
Indices: 1531675--1531715 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1531665 TTGACATTGA
*
1531675 GTCTCGAGACAATAAAAACAT
1 GTCTCAAGACAATAAAAACAT
* *
1531696 GTCTCAAGACCATAAGAACA
1 GTCTCAAGACAATAAAAACA
1531716 AAATTTACCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (21 bp):
GTCTCAAGACAATAAAAACAT
Found at i:1532072 original size:19 final size:18
Alignment explanation
Indices: 1532050--1532111 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
1532040 AATTACAAAA
1532050 AAAAAATTTAAAATAATTC
1 AAAAAATTTAAAA-AATTC
**
1532069 AAAATAATTTCTAAAATTC
1 AAAA-AATTTAAAAAATTC
*
1532088 AAAATATTTATAAAAATTTC
1 AAAAAATTTA-AAAAA-TTC
1532108 AAAA
1 AAAA
1532112 TTTATATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.11
19 17 0.49
20 14 0.40
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAAATTTAAAAAATTC
Found at i:1532110 original size:20 final size:19
Alignment explanation
Indices: 1532049--1532112 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
1532039 AAATTACAAA
* *
1532049 AAAAAAATTTAAAATAATTC
1 AAAATAATTTATAA-AATTC
*
1532069 AAAATAATTTCTAAAATTC
1 AAAATAATTTATAAAATTC
1532088 AAAAT-ATTTATAAAAATTTC
1 AAAATAATTTAT-AAAA-TTC
1532108 AAAAT
1 AAAAT
1532113 TTATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 5 0.13
19 14 0.37
20 19 0.50
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATAATTTATAAAATTC
Found at i:1532154 original size:19 final size:18
Alignment explanation
Indices: 1532122--1532162 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1532112 TTTATATTTT
*
1532122 TAAAAATTGTAAAATAAA
1 TAAAAATTCTAAAATAAA
1532140 TAAAAATTCTAAAAATAAA
1 TAAAAATTCT-AAAATAAA
1532159 TAAA
1 TAAA
1532163 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
TAAAAATTCTAAAATAAA
Found at i:1532438 original size:21 final size:21
Alignment explanation
Indices: 1532396--1532438 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1532386 ACTTGATTTG
*
1532396 AATTTCATTTCACCCGATTCA
1 AATTTCATTTCACCCGAATCA
*
1532417 AATTTC-TTTACACTCGAATCA
1 AATTTCATTT-CACCCGAATCA
1532438 A
1 A
1532439 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (21 bp):
AATTTCATTTCACCCGAATCA
Found at i:1533656 original size:76 final size:76
Alignment explanation
Indices: 1533565--1533705 Score: 282
Period size: 76 Copynumber: 1.9 Consensus size: 76
1533555 ATATATTATT
1533565 GTACGGATTTTTAAAACTTTTATTAAATTCAAATATAAAAATTAAAATATTTTGTATTATTTTTA
1 GTACGGATTTTTAAAACTTTTATTAAATTCAAATATAAAAATTAAAATATTTTGTATTATTTTTA
1533630 TTCTTTATGTA
66 TTCTTTATGTA
1533641 GTACGGATTTTTAAAACTTTTATTAAATTCAAATATAAAAATTAAAATATTTTGTATTATTTTTA
1 GTACGGATTTTTAAAACTTTTATTAAATTCAAATATAAAAATTAAAATATTTTGTATTATTTTTA
1533706 AATCATTATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 65 1.00
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (76 bp):
GTACGGATTTTTAAAACTTTTATTAAATTCAAATATAAAAATTAAAATATTTTGTATTATTTTTA
TTCTTTATGTA
Found at i:1541512 original size:2 final size:2
Alignment explanation
Indices: 1541505--1541529 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1541495 TTTGATAGAC
1541505 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1541530 TTAAGCGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1542598 original size:20 final size:21
Alignment explanation
Indices: 1542573--1542612 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1542563 AATACTATAT
1542573 TAATTATA-TATGTTAAATAA
1 TAATTATATTATGTTAAATAA
1542593 TAATTATATTTATGTTAAAT
1 TAATTATA-TTATGTTAAAT
1542613 CACTAACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TAATTATATTATGTTAAATAA
Found at i:1542790 original size:39 final size:40
Alignment explanation
Indices: 1542704--1542790 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
1542694 ATTTTTAAAA
* *
1542704 AATATATTTAATACAATAAAATATTTATTATATTTATTTGT
1 AATATTTTTAATACAATAAAATATTTAATATATTTA-TTGT
*
1542745 -GT-TTTTTAATACAATAAAAT-TTTAATATATTTA-TGAT
1 AATATTTTTAATACAATAAAATATTTAATATATTTATTG-T
1542782 AATATTTTT
1 AATATTTTT
1542791 TTTAATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
36 2 0.05
37 1 0.03
38 13 0.33
39 22 0.56
40 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (40 bp):
AATATTTTTAATACAATAAAATATTTAATATATTTATTGT
Found at i:1544088 original size:30 final size:30
Alignment explanation
Indices: 1544053--1544121 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
1544043 AACATGGCAA
1544053 AAAACTCTCAAATTTCTCCTTAAATTTCTC
1 AAAACTCTCAAATTTCTCCTTAAATTTCTC
1544083 AAAACTCTCAAATTTCTCCTTAAATTTCTC
1 AAAACTCTCAAATTTCTCCTTAAATTTCTC
*
1544113 AAAGCTCTC
1 AAAACTCTC
1544122 TTTAATGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.33, C:0.28, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAACTCTCAAATTTCTCCTTAAATTTCTC
Found at i:1547903 original size:127 final size:127
Alignment explanation
Indices: 1547677--1548203 Score: 736
Period size: 127 Copynumber: 4.2 Consensus size: 127
1547667 AAGGCCAAAT
* * *
1547677 AGGAACTACTGTAG-AAAAAGAGCGCCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAATGC
1 AGGAACTACTGTAGAAAAAAAAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGC
* * * *
1547741 ATCCTGCTTGAAGTATTTTTGACACTTTTTGTTCAGGATCGTCTTCTCAAAATTATTTTTTC
66 ATCCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTC
* *
1547803 AGGAACTACTGTAGAAAAAAAAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
1 AGGAACTACTGTAGAAAAAAAAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGC
** * * * *
1547868 ATCCTGCTTGAAGTGTTTTTGACATTATTTATTCAGAACCATCTTCTCAAAATCATTTTTTC
66 ATCCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTC
* * * * * * * *
1547930 AAGAACTACTGTAG-AAAAAGAGCATCCACCTAGGAGC-TTTTTCATCAATTTTGTTAACAGTGC
1 AGGAACTACTGTAGAAAAAAAAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGC
* * * *
1547993 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAAAACTGTTTTCTCAAAATTATTTTTTC
66 ATCCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTC
*
1548055 AGGAACTACTGTAGAAAAAAAAGCGTCCATGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGC
1 AGGAACTACTGTAGAAAAAAAAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGC
* * * *
1548120 ATCCTACTTGAAGCATTTTTTATACTATTTGTTCAGAACCGTTTTCTCAAAATTATTTTTTC
66 ATCCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTC
*
1548182 AGGAACTACTATAGAAAAAAAA
1 AGGAACTACTGTAGAAAAAAAA
1548204 TCCTTATTGT
Statistics
Matches: 354, Mismatches: 44, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
125 91 0.26
126 51 0.14
127 212 0.60
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (127 bp):
AGGAACTACTGTAGAAAAAAAAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGC
ATCCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTC
Found at i:1548132 original size:252 final size:253
Alignment explanation
Indices: 1547679--1548200 Score: 778
Period size: 252 Copynumber: 2.1 Consensus size: 253
1547669 GGCCAAATAG
* * * *
1547679 GAACTACTGTAGAAAAAGAGCGCCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAATGCATC
1 GAACTACTGTAGAAAAAGAGCACCCACCTAGGAGCTTTTTTCATCAATTTTGTTAACAATGCATC
* * **
1547744 CTGCTTGAAGTATTTTTGACACTTTTTGTTCAGGATCGTCTTCTCAAAATTATTTTTTCAGGAAC
66 CTGCTTGAAGCATTTTTGACACTATTTGTTCAAAATCGTCTTCTCAAAATTATTTTTTCAGGAAC
* *
1547809 TACTGTAGAAAAAAAAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTG
131 TACTGTAGAAAAAAAAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAATGCATCCTA
** *
1547874 CTTGAAGTGTTTTTGACATTATTTATTCAGAACCATCTTCTCAAAATCATTTTTTCAA
196 CTTGAAGCATTTTTGACACTATTTATTCAGAACCATCTTCTCAAAATCATTTTTTCAA
* *
1547932 GAACTACTGTAGAAAAAGAGCATCCACCTAGGAGC-TTTTTCATCAATTTTGTTAACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCACCCACCTAGGAGCTTTTTTCATCAATTTTGTTAACAATGCATC
* *
1547996 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAAAA-CTGTTTTCTCAAAATTATTTTTTCAGGAA
66 CTGCTTGAAGCATTTTTGACACTATTTGTTCAAAATC-GTCTTCTCAAAATTATTTTTTCAGGAA
**
1548060 CTACTGTAGAAAAAAAAGCGTCCATGTGGGAGCTTTTTTCATCAATTTTGCTGACAATGCATCCT
130 CTACTGTAGAAAAAAAAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAATGCATCCT
* * * * * * *
1548125 ACTTGAAGCATTTTTTATACTATTTGTTCAGAACCGTTTTCTCAAAATTATTTTTTCAG
195 ACTTGAAGCATTTTTGACACTATTTATTCAGAACCATCTTCTCAAAATCATTTTTTCAA
*
1548184 GAACTACTATAGAAAAA
1 GAACTACTGTAGAAAAA
1548201 AAATCCTTAT
Statistics
Matches: 241, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
251 1 0.00
252 209 0.87
253 31 0.13
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (253 bp):
GAACTACTGTAGAAAAAGAGCACCCACCTAGGAGCTTTTTTCATCAATTTTGTTAACAATGCATC
CTGCTTGAAGCATTTTTGACACTATTTGTTCAAAATCGTCTTCTCAAAATTATTTTTTCAGGAAC
TACTGTAGAAAAAAAAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAATGCATCCTA
CTTGAAGCATTTTTGACACTATTTATTCAGAACCATCTTCTCAAAATCATTTTTTCAA
Found at i:1548307 original size:34 final size:33
Alignment explanation
Indices: 1548257--1548384 Score: 152
Period size: 34 Copynumber: 3.8 Consensus size: 33
1548247 ACAAAGTTAT
1548257 TTTTTTAAAAA-A-TAAACCCTAATTTAATTAA
1 TTTTTTAAAAACACTAAACCCTAATTTAATTAA
* *
1548288 TTTTCTTAAAAACTCTAAACCCTAATTTAATTTA
1 TTTT-TTAAAAACACTAAACCCTAATTTAATTAA
* * *
1548322 TTTATTTAAAACCCCTAAAACCTAATTTAATTAA
1 TTT-TTTAAAAACACTAAACCCTAATTTAATTAA
* *
1548356 TTTTTAAAAAAACACTAAACCCTACTTTA
1 TTTTT-TAAAAACACTAAACCCTAATTTA
1548385 TTTTTTAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
31 4 0.05
32 7 0.09
33 2 0.02
34 67 0.83
35 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (33 bp):
TTTTTTAAAAACACTAAACCCTAATTTAATTAA
Found at i:1549123 original size:17 final size:17
Alignment explanation
Indices: 1549084--1549122 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1549074 TAGAAGATTG
1549084 TAAAAATTTAAAAAAAA
1 TAAAAATTTAAAAAAAA
*
1549101 TAAAAATTT-AAGAAAA
1 TAAAAATTTAAAAAAAA
1549117 TAAAAA
1 TAAAAA
1549123 AAGTATTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAAATTTAAAAAAAA
Found at i:1550608 original size:34 final size:33
Alignment explanation
Indices: 1550558--1550685 Score: 152
Period size: 34 Copynumber: 3.8 Consensus size: 33
1550548 ACAAAGTTAT
1550558 TTTTTTAAAAA-A-TAAACCCTAATTTAATTAA
1 TTTTTTAAAAACACTAAACCCTAATTTAATTAA
* *
1550589 TTTTCTTAAAAACTCTAAACCCTAATTTAATTTA
1 TTTT-TTAAAAACACTAAACCCTAATTTAATTAA
* * *
1550623 TTTATTTAAAACCCCTAAAACCTAATTTAATTAA
1 TTT-TTTAAAAACACTAAACCCTAATTTAATTAA
* *
1550657 TTTTTAAAAAAACACTAAACCCTACTTTA
1 TTTTT-TAAAAACACTAAACCCTAATTTA
1550686 TTTTTTAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
31 4 0.05
32 7 0.09
33 2 0.02
34 67 0.83
35 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (33 bp):
TTTTTTAAAAACACTAAACCCTAATTTAATTAA
Found at i:1551424 original size:17 final size:17
Alignment explanation
Indices: 1551385--1551423 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1551375 TAGAAGATTG
1551385 TAAAAATTTAAAAAAAA
1 TAAAAATTTAAAAAAAA
*
1551402 TAAAAATTT-AAGAAAA
1 TAAAAATTTAAAAAAAA
1551418 TAAAAA
1 TAAAAA
1551424 AAGTATTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAAATTTAAAAAAAA
Found at i:1561140 original size:66 final size:65
Alignment explanation
Indices: 1561033--1561203 Score: 227
Period size: 66 Copynumber: 2.6 Consensus size: 65
1561023 GAGCAAATTA
* * * *
1561033 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
1561097 G
65 G
*
1561098 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
1561163 G
65 G
* * * *
1561164 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
1561204 CGGCAACTAG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.02
66 88 0.94
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:1561200 original size:21 final size:21
Alignment explanation
Indices: 1561174--1561218 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1561164 CAGCAGCTTA
* *
1561174 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAACAAGAG
*
1561195 AAGCAGAGGCGGCAACTAGAG
1 AAGCAGAGGCGGCAACAAGAG
1561216 AAG
1 AAG
1561219 TACAGGCTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.18, G:0.38, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACAAGAG
Found at i:1561225 original size:21 final size:21
Alignment explanation
Indices: 1561182--1561225 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1561172 TAAAGCAGAT
* *
1561182 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAACAAGAGAAGCACAG
* *
1561203 GCGGCAACTAGAGAAGTACAG
1 GCGGCAACAAGAGAAGCACAG
1561224 GC
1 GC
1561226 TGCAGTGAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.39, T:0.05
Consensus pattern (21 bp):
GCGGCAACAAGAGAAGCACAG
Found at i:1561239 original size:21 final size:21
Alignment explanation
Indices: 1561215--1561286 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1561205 GGCAACTAGA
* *
1561215 GAAGTACAGGCTGCAGTGAGG
1 GAAGTAGAGGCTGCAGCGAGG
* **
1561236 GAAGCAGAGGCTATAGCGAGG
1 GAAGTAGAGGCTGCAGCGAGG
*
1561257 CAAGTAGAGGCTGCAGCGAGG
1 GAAGTAGAGGCTGCAGCGAGG
*
1561278 GAAGAAGAG
1 GAAGTAGAG
1561287 CAGCGTCAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.43, T:0.10
Consensus pattern (21 bp):
GAAGTAGAGGCTGCAGCGAGG
Found at i:1561751 original size:43 final size:42
Alignment explanation
Indices: 1561688--1561796 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 42
1561678 AAAGGTCAGT
* *
1561688 GACCCTAATCTTTAGCGGCGCTTTGCGCAAAAACGCCGCTAAA
1 GACCCTGATCTTTAGAGGCGCTTTGC-CAAAAACGCCGCTAAA
* * *
1561731 GACCCTGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAA
1 GACCCTGATCTTTAGAGGCGC-TTTGCCAAAAACGCCGCTAAA
1561774 GACCCTGATCTTTAGAGGCGCTT
1 GACCCTGATCTTTAGAGGCGCTT
1561797 ACACTAAAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
42 2 0.03
43 54 0.90
44 4 0.07
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (42 bp):
GACCCTGATCTTTAGAGGCGCTTTGCCAAAAACGCCGCTAAA
Found at i:1562434 original size:26 final size:25
Alignment explanation
Indices: 1562407--1562456 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 25
1562397 GTTTTGAATC
1562407 TTTA-TTTTTTATTCTTGATTTTCTTCT
1 TTTAGTTTTTT-TT-TTG-TTTTCTTCT
1562434 TTTAGTTTTTTTTTTGTTTTCTT
1 TTTAGTTTTTTTTTTGTTTTCTT
1562457 TGTTTCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 6 0.27
28 6 0.27
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.78
Consensus pattern (25 bp):
TTTAGTTTTTTTTTTGTTTTCTTCT
Found at i:1575710 original size:18 final size:18
Alignment explanation
Indices: 1575671--1575710 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1575661 GATTTTTTAT
* *
1575671 TTTTTAAAATTATTAATT
1 TTTTTAAAATTATAAATA
*
1575689 TTTTTATAATTATAAATA
1 TTTTTAAAATTATAAATA
1575707 TTTT
1 TTTT
1575711 CATCCTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTAAAATTATAAATA
Found at i:1576228 original size:18 final size:19
Alignment explanation
Indices: 1576205--1576244 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1576195 AATAATGTAG
* *
1576205 TATATTATTTTATT-TTTA
1 TATATTATGTAATTCTTTA
1576223 TATATTATGTAATTCTTTA
1 TATATTATGTAATTCTTTA
1576242 TAT
1 TAT
1576245 CACATAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TATATTATGTAATTCTTTA
Found at i:1583392 original size:38 final size:39
Alignment explanation
Indices: 1583341--1583416 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 39
1583331 TTTTAGATGC
*
1583341 AATCTTAGTTGGTATATCATTCAAAATATAGC-ATTCAA
1 AATCTTAGTTGGTACATCATTCAAAATATAGCAATTCAA
1583379 AATCTTAGTTGGTACATCATTCAAAATATAGCAATTCA
1 AATCTTAGTTGGTACATCATTCAAAATATAGCAATTCA
1583417 TTATTAAGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (39 bp):
AATCTTAGTTGGTACATCATTCAAAATATAGCAATTCAA
Found at i:1588839 original size:116 final size:114
Alignment explanation
Indices: 1588542--1588857 Score: 339
Period size: 116 Copynumber: 2.7 Consensus size: 114
1588532 GATTATCCAT
* * * *
1588542 TTTCACTAGGGAGATCATATCTTTACCTAAGTGAAGTAAA-TTACTCAAACCCTATATATAACTT
1 TTTCACTAGGGAGATCACATCTCTACCTAAGTGAAGTAAATTTA-TTAAACCCTGTATATAA-TT
* * * * * * *
1588606 AATAGTGGCCAAAATTTGAACAATCATGCTATGGCTAGGGGAGTTATTCAC
64 ATTAGTGGCCAAATTTTGAGCAAGCAAGCTATAGCTAAGGGAGTTATTCAC
* * * ** * *
1588657 TTTCACT-GCGAAGATCACATCTCTACCTAAGTGAAATAAATTTCTTAGGCCTTGTATATGGATT
1 TTTCACTAG-GGAGATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGTATAT-AATT
* ** *
1588721 ATTAGTGGCCAAGTTTTGAGTGAGCACAGCTATAGTTAAGGGAGTTATTCAC
64 ATTAGTGGCCAAATTTTGAGCAAGCA-AGCTATAGCTAAGGGAGTTATTCAC
* *
1588773 TTTCACTAGGGATATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGCATATAATTTA
1 TTTCACTAGGGAGATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGTATATAA-TTA
*
1588838 TTAGCGGCCAAATTTTGAGC
65 TTAGTGGCCAAATTTTGAGC
1588858 TATCATAATT
Statistics
Matches: 161, Mismatches: 34, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
114 1 0.01
115 66 0.41
116 93 0.58
117 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (114 bp):
TTTCACTAGGGAGATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGTATATAATTAT
TAGTGGCCAAATTTTGAGCAAGCAAGCTATAGCTAAGGGAGTTATTCAC
Found at i:1588880 original size:116 final size:113
Alignment explanation
Indices: 1588542--1588922 Score: 321
Period size: 116 Copynumber: 3.4 Consensus size: 113
1588532 GATTATCCAT
* * * *
1588542 TTTCACTAGGGAGATCATATCTTTACCTAAGTGAAGTAAA-TTACTCAAACCCTATATATAACTT
1 TTTCACTAGGGAGATCACATCTCTACCTAAGTGAAGTAAATTTA-TTAAACCCTGTATATAA-TT
* * * * **
1588606 AATAGTGGCCAAAATTTGAACAATCATGCTATGGCTAGGGGAGTTATTCAC
64 ATTAGTGGCCAAATTTTGAGCTATCATAAT-TGGCTAGGGGAGTTATTCAC
* * * ** * *
1588657 TTTCACT-GCGAAGATCACATCTCTACCTAAGTGAAATAAATTTCTTAGGCCTTGTATATGGATT
1 TTTCACTAG-GGAGATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGTATAT-AATT
* * * * * * *
1588721 ATTAGTGGCCAAGTTTTGAG-TGAGCACAGCTATAGTTAAGGGAGTTATTCAC
64 ATTAGTGGCCAAATTTTGAGCT-ATCATA-AT-TGGCTAGGGGAGTTATTCAC
* *
1588773 TTTCACTAGGGATATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGCATATAATTTA
1 TTTCACTAGGGAGATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGTATATAA-TTA
* *
1588838 TTAGCGGCCAAATTTTGAGCTATCATAATTGCGGCTAGGGGAGCTA-T--C
65 TTAGTGGCCAAATTTTGAGCTATCATAATT--GGCTAGGGGAGTTATTCAC
* * *
1588886 --T-AATAGGGAGATCATATCTCTACCTAAGTGAAATAAA
1 TTTCACTAGGGAGATCACATCTCTACCTAAGTGAAGTAAA
1588923 GTACTCAAAC
Statistics
Matches: 212, Mismatches: 44, Indels: 25
0.75 0.16 0.09
Matches are distributed among these distances:
110 32 0.15
111 1 0.00
113 1 0.00
114 2 0.01
115 68 0.32
116 106 0.50
117 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (113 bp):
TTTCACTAGGGAGATCACATCTCTACCTAAGTGAAGTAAATTTATTAAACCCTGTATATAATTAT
TAGTGGCCAAATTTTGAGCTATCATAATTGGCTAGGGGAGTTATTCAC
Found at i:1592489 original size:22 final size:22
Alignment explanation
Indices: 1592464--1592505 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1592454 AATTATACAA
1592464 TATCAAAACAATAACAAAATAG
1 TATCAAAACAATAACAAAATAG
* *
1592486 TATCAATATAATAACAAAAT
1 TATCAAAACAATAACAAAAT
1592506 GGCAACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (22 bp):
TATCAAAACAATAACAAAATAG
Found at i:1594744 original size:32 final size:32
Alignment explanation
Indices: 1594669--1594751 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
1594659 TGTCCAATAG
* *
1594669 TAAGTAGTAAGCAACAGTTCCCTGGAAGATGA
1 TAAGAAGTAAGCAACAGTTACCTGGAAGATGA
*
1594701 TAAGAAATAAGCAACAGTTACCTGGAAGAT-A
1 TAAGAAGTAAGCAACAGTTACCTGGAAGATGA
*
1594732 CTCAA-CAGTAAGCAACAGTT
1 -T-AAGAAGTAAGCAACAGTT
1594752 CCATCAAGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 1 0.02
32 41 0.93
33 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (32 bp):
TAAGAAGTAAGCAACAGTTACCTGGAAGATGA
Found at i:1598769 original size:18 final size:19
Alignment explanation
Indices: 1598746--1598788 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1598736 TATGTATGAT
1598746 ATTAAAATGAAA-AAATAG
1 ATTAAAATGAAACAAATAG
* * *
1598764 ATTAAATTTAAACACATAG
1 ATTAAAATGAAACAAATAG
1598783 ATTAAA
1 ATTAAA
1598789 TGAGTACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (19 bp):
ATTAAAATGAAACAAATAG
Found at i:1598936 original size:14 final size:14
Alignment explanation
Indices: 1598909--1598944 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1598899 AATTGTATAA
1598909 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
1598923 ATATAAAA-AAAAAT
1 AT-TAAAATAAAAAT
1598937 ATTAAAAT
1 ATTAAAAT
1598945 GTTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:1601534 original size:76 final size:77
Alignment explanation
Indices: 1601407--1601561 Score: 222
Period size: 76 Copynumber: 2.0 Consensus size: 77
1601397 TAAGATTCTC
* * * * * *
1601407 TTGTTCCGAAGGGATATCACATCTAGCACGTTAGGACACGACACTTTAAACCGCCGAAACCAAGG
1 TTGTTCCGAAGGAATATCACATCCAGCACGTTAGGACACAACACTCTAAACCACCGAAACCAAGA
1601472 TCACCTTATAGT
66 TCACCTTATAGT
* * *
1601484 TTGTTCCGAA-GAATATCACATCCAGCACGTTAGGACACAATACTCTAAACCATCGAAATCAAGA
1 TTGTTCCGAAGGAATATCACATCCAGCACGTTAGGACACAACACTCTAAACCACCGAAACCAAGA
1601548 TCACCTTATAGT
66 TCACCTTATAGT
1601560 TT
1 TT
1601562 AATGAAACCA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
76 59 0.86
77 10 0.14
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (77 bp):
TTGTTCCGAAGGAATATCACATCCAGCACGTTAGGACACAACACTCTAAACCACCGAAACCAAGA
TCACCTTATAGT
Found at i:1601791 original size:107 final size:107
Alignment explanation
Indices: 1601589--1601799 Score: 323
Period size: 107 Copynumber: 2.0 Consensus size: 107
1601579 AAGTTTTAAG
*
1601589 AGGATATTTGGCTATTTAGTCGAATAAGAAATCGAAACCCAGCACGTTAGAGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACAAGAAATCGAAACCCAGCACGTTAGAGCACGTTTTCTCGA
*
1601654 ACTTCCAAACGCAAAACATTGCCTCGTTTAGAAAATCTTGAA
66 ACTTCCAAACGCAAAACATTGCCTCATTTAGAAAATCTTGAA
* * *
1601696 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACAAGAAATCGAAACCCAGCACGTTAGAGCACGTTTTCTCGA
* * * * * *
1601761 ATTTCTAAACGCGAAATATTGGCTTATTTAGAAAATCTT
66 ACTTCCAAACGCAAAACATTGCCTCATTTAGAAAATCTT
1601800 TTTGGATAGT
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 93 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (107 bp):
AGGATATTTGGCTATTTAGTCGAACAAGAAATCGAAACCCAGCACGTTAGAGCACGTTTTCTCGA
ACTTCCAAACGCAAAACATTGCCTCATTTAGAAAATCTTGAA
Found at i:1602788 original size:6 final size:6
Alignment explanation
Indices: 1602777--1602803 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1602767 GAACCAAGGA
1602777 TGGAAT TGGAAT TGGAAT TGGAAT TGG
1 TGGAAT TGGAAT TGGAAT TGGAAT TGG
1602804 GCTAGAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (6 bp):
TGGAAT
Found at i:1606557 original size:21 final size:23
Alignment explanation
Indices: 1606516--1606560 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
1606506 AAAGAACCCT
*
1606516 AGAAAAGTGTAGAGAAAAACTAA
1 AGAAAAGTCTAGAGAAAAACTAA
1606539 AGAAAA-TCTAGAG-AAAACTAA
1 AGAAAAGTCTAGAGAAAAACTAA
1606560 A
1 A
1606561 CCTAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 6 0.29
23 6 0.29
ACGTcount: A:0.62, C:0.07, G:0.18, T:0.13
Consensus pattern (23 bp):
AGAAAAGTCTAGAGAAAAACTAA
Found at i:1606842 original size:21 final size:22
Alignment explanation
Indices: 1606804--1606844 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1606794 TCTTCCTTGG
**
1606804 GAGGTGGATATCGTGATACCCA
1 GAGGTGGATATCACGATACCCA
1606826 GAGG-GGATATCACGATACC
1 GAGGTGGATATCACGATACC
1606845 ACTGAATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20
Consensus pattern (22 bp):
GAGGTGGATATCACGATACCCA
Found at i:1608991 original size:42 final size:42
Alignment explanation
Indices: 1608932--1609015 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
1608922 CTACGAGTAT
* *
1608932 GATTAATGATTAAATTGGTTAATTGTTCTATTATGTTTTAAA
1 GATTAATAATTAAATTGGTTAATTGTTATATTATGTTTTAAA
1608974 GATTAATAATTAAATTGGTTAATTGTTATATTATGTTTTAAA
1 GATTAATAATTAAATTGGTTAATTGTTATATTATGTTTTAAA
1609016 TTTTATGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (42 bp):
GATTAATAATTAAATTGGTTAATTGTTATATTATGTTTTAAA
Found at i:1610622 original size:12 final size:12
Alignment explanation
Indices: 1610605--1610629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1610595 TAGACTCAAT
1610605 AAGGATTCCAGG
1 AAGGATTCCAGG
1610617 AAGGATTCCAGG
1 AAGGATTCCAGG
1610629 A
1 A
1610630 TATAAATTTC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (12 bp):
AAGGATTCCAGG
Found at i:1611966 original size:14 final size:15
Alignment explanation
Indices: 1611937--1611968 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1611927 AAAAACATCA
1611937 TAATTTTATCTATTT
1 TAATTTTATCTATTT
1611952 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
1611966 TAA
1 TAA
1611969 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:1612709 original size:24 final size:24
Alignment explanation
Indices: 1612681--1612728 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1612671 TATGTTGACA
1612681 AACATGAATACAAATTATCTTTAT
1 AACATGAATACAAATTATCTTTAT
1612705 AACATGAATACAAATTATCTTTAT
1 AACATGAATACAAATTATCTTTAT
1612729 GTTTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (24 bp):
AACATGAATACAAATTATCTTTAT
Found at i:1615434 original size:58 final size:60
Alignment explanation
Indices: 1615372--1615487 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 60
1615362 ATCACTTTAA
*
1615372 TATTAAATTAATATAATACTTA-T-CAGGATAAATA-TTAGA-TTATATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTACTACAGGATAAATATTTA-ATTTA-ATTTAATATTAAATC
1615430 TATTAAATTAATAGAATACTTATCTACAGGATAAATATTTAATTTAATTTAATATTAA
1 TATTAAATTAATAGAATACTTA-CTACAGGATAAATATTTAATTTAATTTAATATTAA
1615488 GATAATCACT
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
58 21 0.40
60 1 0.02
61 24 0.46
62 6 0.12
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTACTACAGGATAAATATTTAATTTAATTTAATATTAAATC
Found at i:1617062 original size:22 final size:22
Alignment explanation
Indices: 1617030--1617072 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1617020 TTATGAAACA
1617030 TATAAGGGACTCTATCACCACC
1 TATAAGGGACTCTATCACCACC
*
1617052 TATAAGTGACTCTATCACCAC
1 TATAAGGGACTCTATCACCAC
1617073 ATATTGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.26
Consensus pattern (22 bp):
TATAAGGGACTCTATCACCACC
Found at i:1617609 original size:18 final size:18
Alignment explanation
Indices: 1617586--1617620 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1617576 CACAATACAT
1617586 AGTTTGGCAAATTAATAA
1 AGTTTGGCAAATTAATAA
* *
1617604 AGTTTGTCATATTAATA
1 AGTTTGGCAAATTAATA
1617621 CAGATCACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (18 bp):
AGTTTGGCAAATTAATAA
Found at i:1622239 original size:16 final size:18
Alignment explanation
Indices: 1622204--1622247 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1622194 TGACCAAATG
*
1622204 TAAAATAAATATTGTTAT
1 TAAAATAGATATTGTTAT
1622222 TAAAATAGATA-T-TTAT
1 TAAAATAGATATTGTTAT
1622238 TAAGAATAGA
1 TAA-AATAGA
1622248 AACAGAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (18 bp):
TAAAATAGATATTGTTAT
Found at i:1622291 original size:12 final size:12
Alignment explanation
Indices: 1622274--1622304 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1622264 GAAGCTGGGG
1622274 AGAAAAAGCGAA
1 AGAAAAAGCGAA
*
1622286 AGAAAAAGGGAA
1 AGAAAAAGCGAA
1622298 AGAAAAA
1 AGAAAAA
1622305 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGCGAA
Found at i:1632692 original size:22 final size:22
Alignment explanation
Indices: 1632630--1632694 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
1632620 GTATTATCGT
*
1632630 AACAATTCAGATAC-GATGCAG
1 AACAAATCAGATACAGATGCAG
* *
1632651 AACAGATCAGATACATATGCAG
1 AACAAATCAGATACAGATGCAG
1632673 AACAAATCAGA-ATCAGATGCAG
1 AACAAATCAGATA-CAGATGCAG
1632695 TTTCCTACCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.35
22 24 0.65
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (22 bp):
AACAAATCAGATACAGATGCAG
Found at i:1634922 original size:25 final size:23
Alignment explanation
Indices: 1634878--1634974 Score: 62
Period size: 24 Copynumber: 4.1 Consensus size: 23
1634868 ATTTTAATTC
*
1634878 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
1634902 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
1634926 ATATAAATTATATTTAAATATCAT-TA
1 AT-TTAATTATA--T-AATATCATATA
1634952 A-TT-A-TATATATATAT-ATATA
1 ATTTAATTATATA-ATATCATATA
1634972 ATT
1 ATT
1634975 AAACAAATAA
Statistics
Matches: 60, Mismatches: 3, Indels: 23
0.70 0.03 0.27
Matches are distributed among these distances:
19 3 0.05
20 8 0.13
21 1 0.02
22 4 0.07
23 1 0.02
24 18 0.30
25 14 0.23
26 4 0.07
27 6 0.10
28 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:1634927 original size:35 final size:33
Alignment explanation
Indices: 1634886--1634974 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 33
1634876 TCATTTAATA
*
1634886 ATATAATATCATTATAATTTAATTATCATAAATT
1 ATATAATAT-ATTATAATTTAAATATCATAAATT
*
1634920 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATAT--ATTATAATTTAAATATCATAAATT
1634955 ATATATATATATATATAATT
1 ATATA-ATATAT-TATAATT
1634975 AAACAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
33 2 0.04
34 8 0.17
35 32 0.68
36 5 0.11
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATAATATATTATAATTTAAATATCATAAATT
Found at i:1634966 original size:20 final size:20
Alignment explanation
Indices: 1634926--1634975 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1634916 AATTCATATA
*
1634926 ATATA-AATTATATTTAAAT
1 ATATATAATTATATATAAAT
*
1634945 ATCAT-TAATTATATATATAT
1 AT-ATATAATTATATATAAAT
1634965 ATATATAATTA
1 ATATATAATTA
1634976 AACAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATAATTATATATAAAT
Found at i:1636805 original size:13 final size:12
Alignment explanation
Indices: 1636775--1636834 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
1636765 AAAAGATTAG
1636775 GAAAATAAAGAAA
1 GAAAATAAA-AAA
*
1636788 TAAAATAAAATAA
1 GAAAATAAAA-AA
* *
1636801 GAAAATGAAAAT
1 GAAAATAAAAAA
* *
1636813 GAAAGTTAAAAA
1 GAAAATAAAAAA
1636825 GAAAATAAAA
1 GAAAATAAAA
1636835 GAAAAAGAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
12 19 0.51
13 18 0.49
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (12 bp):
GAAAATAAAAAA
Found at i:1636806 original size:18 final size:17
Alignment explanation
Indices: 1636776--1636840 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
1636766 AAAGATTAGG
1636776 AAAATAAAGAAATAAAAT
1 AAAATAAA-AAATAAAAT
1636794 AAAATAAGAAAATGAAAAT
1 AAAATAA-AAAAT-AAAAT
* * *
1636813 GAAAGTTAAAAAGAAAAT
1 -AAAATAAAAAATAAAAT
*
1636831 AAAAGAAAAA
1 AAAATAAAAA
1636841 GAATTAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
17 7 0.18
18 16 0.42
19 10 0.26
20 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:1642197 original size:43 final size:43
Alignment explanation
Indices: 1642150--1642251 Score: 141
Period size: 43 Copynumber: 2.4 Consensus size: 43
1642140 GTCAGGATAT
* * *
1642150 TATTATGGGATATTATCTTTTAGCAAATTGATTCTTAATAGGA
1 TATTATAGGATATTATCTCTTAGCAAATTGATTCCTAATAGGA
* * * *
1642193 TATTATAAGATTTTATCTCTTAGCAATTTGATTCCTGATAGGA
1 TATTATAGGATATTATCTCTTAGCAAATTGATTCCTAATAGGA
1642236 TATTATAGGATATTAT
1 TATTATAGGATATTAT
1642252 TACGGGATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (43 bp):
TATTATAGGATATTATCTCTTAGCAAATTGATTCCTAATAGGA
Found at i:1643045 original size:49 final size:49
Alignment explanation
Indices: 1642973--1643073 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
1642963 GATTATTAAA
*
1642973 TTATTTTTAGGATAATATCTCATTTGGTACTTGTACTTTCATAAAATGT
1 TTATTTTTAGGATAATATCTCATTTAGTACTTGTACTTTCATAAAATGT
1643022 TTATTTTTAGGATAATATCTCATTTAGTACTTGTACTTTCATAAAATGT
1 TTATTTTTAGGATAATATCTCATTTAGTACTTGTACTTTCATAAAATGT
1643071 TTA
1 TTA
1643074 ATGCGGTACT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.50
Consensus pattern (49 bp):
TTATTTTTAGGATAATATCTCATTTAGTACTTGTACTTTCATAAAATGT
Found at i:1643119 original size:29 final size:29
Alignment explanation
Indices: 1643064--1643120 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1643054 GTACTTTCAT
* * **
1643064 AAAATGTTTAATGCGGTACTTGTATTTTG
1 AAAATGTTCAATGCGATACTTAAATTTTG
*
1643093 AAAATGTTCAGTGCGATACTTAAATTTT
1 AAAATGTTCAATGCGATACTTAAATTTT
1643121 CAATATGTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.42
Consensus pattern (29 bp):
AAAATGTTCAATGCGATACTTAAATTTTG
Found at i:1651767 original size:28 final size:28
Alignment explanation
Indices: 1651735--1651791 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1651725 ATCACTTGTC
**
1651735 ACTTGTCATTGATCAGATAAGTGTAGCT
1 ACTTGTCACCGATCAGATAAGTGTAGCT
*
1651763 ACTTGTCACCGATTAGATAAGTGTAGCT
1 ACTTGTCACCGATCAGATAAGTGTAGCT
1651791 A
1 A
1651792 AGCTACCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (28 bp):
ACTTGTCACCGATCAGATAAGTGTAGCT
Found at i:1651883 original size:51 final size:50
Alignment explanation
Indices: 1651805--1652028 Score: 369
Period size: 50 Copynumber: 4.5 Consensus size: 50
1651795 TACCACTTAT
*
1651805 CACTTGTCACTTGTCAC-TATCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAA-CTAC
*
1651855 CACTTATCACTTGTCACTTATCATTGATCAGATAAGTGTAGCTAAACTAC
1 CACTTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAACTAC
*
1651905 CACTTATCACTTGTCATTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAA-CTAC
1651956 CACTTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAACTAC
1 CACTTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAACTAC
** *
1652006 TGCTTATCACTTGTCACTGATCA
1 CACTTATCACTTGTCACTTATCA
1652029 AAAGTACTCA
Statistics
Matches: 164, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
50 88 0.54
51 76 0.46
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (50 bp):
CACTTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAACTAC
Found at i:1651968 original size:101 final size:104
Alignment explanation
Indices: 1651763--1652024 Score: 413
Period size: 101 Copynumber: 2.5 Consensus size: 104
1651753 AAGTGTAGCT
* * * *
1651763 ACTTGTCACCGATTAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCACTTGTCACTATCAC
1 ACTTATCACTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGTCAC-TGT--CTATCAC
1651828 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTC
63 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTC
*
1651870 ACTTATCATTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGTCA-T-T-TATCACTGA
1 ACTTATCACTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGTCACTGTCTATCACTGA
1651932 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTC
66 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTC
**
1651971 ACTTATCACTGATCAGATAAGTGTAGCTAAACTACTGCTTATCACTTGTCACTG
1 ACTTATCACTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGTCACTG
1652025 ATCAAAAGTA
Statistics
Matches: 145, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
101 96 0.66
102 1 0.01
104 1 0.01
105 1 0.01
107 46 0.32
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (104 bp):
ACTTATCACTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGTCACTGTCTATCACTGA
TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTC
Found at i:1652124 original size:17 final size:17
Alignment explanation
Indices: 1652102--1652134 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1652092 TATTCTCAAT
1652102 TCATCA-ACAAATATATC
1 TCATCATAC-AATATATC
1652119 TCATCATACAATATAT
1 TCATCATACAATATAT
1652135 AATTCATGAA
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:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:1656482 original size:23 final size:23
Alignment explanation
Indices: 1656448--1656497 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
1656438 CGATTCAATT
1656448 AAAT-AAAATAAAAAAATT-ATAA
1 AAATAAAAATAAAAAAATTCA-AA
1656470 AAATAAAAATAAAAAAATTCAAA
1 AAATAAAAATAAAAAAATTCAAA
1656493 AAATA
1 AAATA
1656498 GAGAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.15
23 21 0.81
24 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAAAATAAAAAAATTCAAA
Found at i:1658639 original size:18 final size:18
Alignment explanation
Indices: 1658611--1658655 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1658601 CGTTCGTTTC
*
1658611 CAAAACATTATTC-ATTT
1 CAAAACGTTATTCAATTT
*
1658628 ACAAATCGTTATTCAATTT
1 -CAAAACGTTATTCAATTT
1658647 CAAAACGTT
1 CAAAACGTT
1658656 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCAATTT
Found at i:1663003 original size:32 final size:32
Alignment explanation
Indices: 1662962--1663029 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
1662952 GTTATGCGTC
1662962 AGATAATTTGCCTCATGGGTCTTAAGCTGACG
1 AGATAATTTGCCTCATGGGTCTTAAGCTGACG
1662994 AGATAATTTGCCTCATGGGTCTTAAGCTGACG
1 AGATAATTTGCCTCATGGGTCTTAAGCTGACG
1663026 AGAT
1 AGAT
1663030 GCATAGGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (32 bp):
AGATAATTTGCCTCATGGGTCTTAAGCTGACG
Found at i:1664502 original size:9 final size:9
Alignment explanation
Indices: 1664488--1664524 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1664478 TATAGTTTGA
1664488 TATTCGAAT
1 TATTCGAAT
1664497 TATTCGAAT
1 TATTCGAAT
*
1664506 TATTCGAGT
1 TATTCGAAT
*
1664515 TGTTCGAAT
1 TATTCGAAT
1664524 T
1 T
1664525 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1664595 original size:9 final size:9
Alignment explanation
Indices: 1664578--1664608 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1664568 TCGAGTTGAT
1664578 TCGAATAAC
1 TCGAATAAC
*
1664587 TCGATTAAC
1 TCGAATAAC
1664596 TCGAATAAC
1 TCGAATAAC
1664605 TCGA
1 TCGA
1664609 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1666240 original size:25 final size:25
Alignment explanation
Indices: 1666212--1666260 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1666202 TATAGTCTAT
* *
1666212 CTATAGTAGTATCAATATATACTAC
1 CTATAGCAGTATCAAGATATACTAC
* *
1666237 CTATAGCAGTTTCAGGATATACTA
1 CTATAGCAGTATCAAGATATACTA
1666261 TCAAAGACAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (25 bp):
CTATAGCAGTATCAAGATATACTAC
Found at i:1666640 original size:18 final size:18
Alignment explanation
Indices: 1666588--1666640 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1666578 AATCATGTCG
* *
1666588 TTCATTTCCAAAACATTA
1 TTCATTTACAAAACGTTA
*
1666606 TTCATTTACAAATCGTTA
1 TTCATTTACAAAACGTTA
1666624 TTCAATTT-CAAAACGTT
1 TTC-ATTTACAAAACGTT
1666641 TTCTTATTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.42
Consensus pattern (18 bp):
TTCATTTACAAAACGTTA
Found at i:1669383 original size:42 final size:42
Alignment explanation
Indices: 1669351--1669447 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
1669341 CGAGCGTGTC
1669351 TCTCAGCCACACGGCCATGTATCTCAGCCACACGACTATGTA
1 TCTCAGCCACACGGCCATGTATCTCAGCCACACGACTATGTA
* * * * * * *
1669393 TCTCAGTCACACGGTCGTGTCTCTCAGCTACACAACCATGTA
1 TCTCAGCCACACGGCCATGTATCTCAGCCACACGACTATGTA
*
1669435 TCTCAGTCACACG
1 TCTCAGCCACACG
1669448 ATCGTGTACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (42 bp):
TCTCAGCCACACGGCCATGTATCTCAGCCACACGACTATGTA
Found at i:1669453 original size:42 final size:42
Alignment explanation
Indices: 1669372--1669454 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1669362 CGGCCATGTA
* * *
1669372 TCTCAGCCACACGACTATGTATCTCAGTCACACGGTCGTGTC
1 TCTCAGCCACACAACCATGTATCTCAGTCACACGATCGTGTC
*
1669414 TCTCAGCTACACAACCATGTATCTCAGTCACACGATCGTGT
1 TCTCAGCCACACAACCATGTATCTCAGTCACACGATCGTGT
1669455 ACCCTGTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.27
Consensus pattern (42 bp):
TCTCAGCCACACAACCATGTATCTCAGTCACACGATCGTGTC
Found at i:1669455 original size:21 final size:21
Alignment explanation
Indices: 1669323--1669448 Score: 110
Period size: 21 Copynumber: 6.0 Consensus size: 21
1669313 CCTGGCACAG
* *
1669323 CCATGTACCCCAGTCACACGA
1 CCATGTATCTCAGTCACACGA
* * * * *
1669344 GCGTGTCTCTCAGCCACACGG
1 CCATGTATCTCAGTCACACGA
*
1669365 CCATGTATCTCAGCCACACGA
1 CCATGTATCTCAGTCACACGA
* *
1669386 CTATGTATCTCAGTCACACGG
1 CCATGTATCTCAGTCACACGA
* * * *
1669407 TCGTGTCTCTCAG-CTACACAA
1 CCATGTATCTCAGTC-ACACGA
1669428 CCATGTATCTCAGTCACACGA
1 CCATGTATCTCAGTCACACGA
1669449 TCGTGTACCC
Statistics
Matches: 79, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 1 0.01
21 77 0.97
22 1 0.01
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.22
Consensus pattern (21 bp):
CCATGTATCTCAGTCACACGA
Found at i:1678005 original size:21 final size:23
Alignment explanation
Indices: 1677958--1678008 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1677948 ATTTATAGGG
*
1677958 TTTTTATAACAATTTTTAATTTA
1 TTTTTATAACAATTTTAAATTTA
1677981 TTTTTA-AAC-ATTTTAAATATT-
1 TTTTTATAACAATTTTAAAT-TTA
1678002 TTTTTAT
1 TTTTTAT
1678009 TTTAAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 14 0.56
22 5 0.20
23 6 0.24
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTTATAACAATTTTAAATTTA
Found at i:1684928 original size:19 final size:19
Alignment explanation
Indices: 1684892--1684930 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1684882 AATTTATTGT
*
1684892 AATATTATTCATATTTTTA
1 AATATTATTCATAATTTTA
1684911 AATATCTATTC-TAATTTTA
1 AATAT-TATTCATAATTTTA
1684930 A
1 A
1684931 TAGTGTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTCATAATTTTA
Found at i:1685242 original size:39 final size:38
Alignment explanation
Indices: 1685162--1685242 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
1685152 AAATTAACAA
* *
1685162 TTAACAATTTATCTAAAAAATTAAAAAAAATCAATAGT
1 TTAACAATTTATATAAAAAATTAAAAAAAATCAATAAT
* * *
1685200 TTAACAATTTATATATAATAATTAATAAATATC-ATCAAT
1 TTAACAATTTATATA-AAAAATTAAAAAAAATCAAT-AAT
1685239 TTAA
1 TTAA
1685243 ATTCATTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 16 0.44
39 20 0.56
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (38 bp):
TTAACAATTTATATAAAAAATTAAAAAAAATCAATAAT
Found at i:1686256 original size:3 final size:3
Alignment explanation
Indices: 1686250--1686311 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
1686240 CTACAACAAC
1686250 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1686297 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
1686312 GCAGAAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1689502 original size:15 final size:14
Alignment explanation
Indices: 1689482--1689511 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1689472 TAAATCTATA
1689482 ATAATATATAATATT
1 ATAATATA-AATATT
1689497 ATAATATAAATATT
1 ATAATATAAATATT
1689511 A
1 A
1689512 AAAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATATAAATATT
Found at i:1706822 original size:7 final size:7
Alignment explanation
Indices: 1706810--1706838 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1706800 TCAATTGTAT
1706810 AAAGAAA
1 AAAGAAA
1706817 AAAGAAA
1 AAAGAAA
1706824 AAAGAAA
1 AAAGAAA
1706831 AAAGAAA
1 AAAGAAA
1706838 A
1 A
1706839 GAGATTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:1713366 original size:20 final size:22
Alignment explanation
Indices: 1713320--1713368 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
1713310 ATTCTATTTC
1713320 AAAAATCTTATAAGCAATTAAA
1 AAAAATCTTATAAGCAATTAAA
*
1713342 AAAAATCTTATAA-CCATTAAA
1 AAAAATCTTATAAGCAATTAAA
1713363 AAAAAT
1 AAAAAT
1713369 TCTAGTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATCTTATAAGCAATTAAA
Found at i:1715137 original size:12 final size:13
Alignment explanation
Indices: 1715120--1715148 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1715110 ACCTTAGTCC
1715120 CAAACACTA-CTT
1 CAAACACTAGCTT
1715132 CAAACACTAGCTT
1 CAAACACTAGCTT
1715145 CAAA
1 CAAA
1715149 TATAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.45, C:0.31, G:0.03, T:0.21
Consensus pattern (13 bp):
CAAACACTAGCTT
Found at i:1715198 original size:28 final size:29
Alignment explanation
Indices: 1715150--1715206 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1715140 AGCTTCAAAT
**
1715150 ATAAATTTAATTTATTTTAATT-TTAATA
1 ATAAATTTAATTTATAGTAATTCTTAATA
1715178 ATAAATTTAAATTTA-AGTAATTCTTAATA
1 ATAAATTT-AATTTATAGTAATTCTTAATA
1715207 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
ATAAATTTAATTTATAGTAATTCTTAATA
Found at i:1727657 original size:21 final size:21
Alignment explanation
Indices: 1727633--1727672 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1727623 AAAACCTGAT
1727633 AGTATCAATATTTTTTAAATG
1 AGTATCAATATTTTTTAAATG
**
1727654 AGTATTGATATTTTTTAAA
1 AGTATCAATATTTTTTAAA
1727673 ACTTGTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (21 bp):
AGTATCAATATTTTTTAAATG
Found at i:1729538 original size:63 final size:63
Alignment explanation
Indices: 1729436--1729558 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
1729426 GTACATGCAC
* * *
1729436 TTTCATAACATGTCCAATGTGGTATCTAAACTATGAATATGTGTTTTATTATAG-TACCTATAT
1 TTTCATAAAATGTCCAATATGGTATCTAAACTATCAATATGTGTTTTATTAT-GTTACCTATAT
1729499 TTTCATAAAATGTCCAATATGGTATCTAAACTATCAATATGTGTTTTATTATGTTACCTA
1 TTTCATAAAATGTCCAATATGGTATCTAAACTATCAATATGTGTTTTATTATGTTACCTA
1729559 GTGTTAACAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 1 0.02
63 55 0.98
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (63 bp):
TTTCATAAAATGTCCAATATGGTATCTAAACTATCAATATGTGTTTTATTATGTTACCTATAT
Found at i:1731412 original size:44 final size:44
Alignment explanation
Indices: 1731349--1731876 Score: 359
Period size: 44 Copynumber: 11.7 Consensus size: 44
1731339 TATTATGGTG
*
1731349 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACA
* * **
1731393 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CGACA
* * * * * *
1731438 AATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAATCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACA
* * ** * *
1731482 AATCTTATCTCTCTGAAGTTGTAGTGGAAAAGATTAAAGATGA-G
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CGACA
* * * * * *
1731526 AATCTTA-CTTCCCTGAATTTGCAATGAAACAAATTAAAGCTACAA
1 AATCTTATC-TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGAC-A
* * ** *
1731571 GTTACAGACATTATCTCCCTGAAGTTGCAGTGGAGCAGAATTGAAGATAGCG
1 ---A-A-TC-TTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCGA-CA
* * *
1731623 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACA
* * **
1731667 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CGACA
* *
1731712 ACTCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACA
* * * * * * *
1731756 AATCCTATAC-CTCTAAAGTTACAATGG-GTCGGACTAAATTTG-GTTACA
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTAAA---GCG--ACA
* * *
1731804 AATCTTATCTCTCTAAAGTTGCAGTGGAGTAGATTAAAGTC-ATC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CGA-CA
* * *
1731848 GATCTCATCTCCCTAAAGTTGCAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
1731877 TGGATTGAAG
Statistics
Matches: 380, Mismatches: 77, Indels: 54
0.74 0.15 0.11
Matches are distributed among these distances:
43 3 0.01
44 193 0.51
45 86 0.23
46 27 0.07
47 3 0.01
48 33 0.09
49 3 0.01
50 1 0.00
51 21 0.06
52 9 0.02
53 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACA
Found at i:1731472 original size:89 final size:89
Alignment explanation
Indices: 1731349--1731876 Score: 456
Period size: 89 Copynumber: 5.8 Consensus size: 89
1731339 TATTATGGTG
* *
1731349 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACAAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
* *
1731414 CAGTGGAGCAGACTGAAGATAACA
66 CAGTGGAGCAGATTAAAGATAACA
* * * * * *
1731438 AATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAATCTATAAATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
* ** * *
1731503 TAGTGGAAAAGATTAAAGATGA-G
66 CAGTGGAGCAGATTAAAGATAACA
* * * * * *
1731526 AATCTTA-CTTCCCTGAATTTGCAATGAAACAAATTAAAGCTACAAGTTACAGACATTATCTCCC
1 AATCTTATC-TCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-A---A-A-TC-TTATCTCCC
* * *
1731590 TGAAGTTGCAGTGGAGCAGAATTGAAGATAGCG
58 TGAAGTTGCAGTGGAGCAG-ATTAAAGATAACA
* * *
1731623 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
*
1731688 CAGTGGAGCAGGTTAAAGATAACA
66 CAGTGGAGCAGATTAAAGATAACA
* * * * * *
1731712 ACTCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCGACAAATCCTATAC-CTCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTAT-CTCCCTGAAGTT
* * * * * *
1731776 ACAATGG-GTCGGACTAAATTTGGTTACA
65 GCAGTGGAG-CAGATTAAA---GATAACA
* * * * * *
1731804 AATCTTATCTCTCTAAAGTTGCAGTGGAGTAGATTAAAG-T-CATCGATCTCATCTCCCTAAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA--AATCTTATCTCCCTGAAGT
1731867 TGCAGTGGAG
64 TGCAGTGGAG
1731877 TGGATTGAAG
Statistics
Matches: 346, Mismatches: 73, Indels: 36
0.76 0.16 0.08
Matches are distributed among these distances:
87 1 0.00
88 32 0.09
89 147 0.42
90 31 0.09
91 2 0.01
92 60 0.17
93 3 0.01
94 1 0.00
95 24 0.07
96 9 0.03
97 35 0.10
98 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAGATAACA
Found at i:1732168 original size:18 final size:18
Alignment explanation
Indices: 1732145--1732180 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1732135 AGTCCAGTCC
* *
1732145 AAAAATTATAGACCCAAA
1 AAAAATTACAAACCCAAA
1732163 AAAAATTACAAACCCAAA
1 AAAAATTACAAACCCAAA
1732181 TACAAAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.19, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAATTACAAACCCAAA
Found at i:1750918 original size:29 final size:29
Alignment explanation
Indices: 1750886--1750943 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1750876 TATCTACAAG
*
1750886 ATAATTAGTAAATTAAATTTAATATTAAA
1 ATAAGTAGTAAATTAAATTTAATATTAAA
*
1750915 ATAAGTATTAAATTAAATTTAATATTAAA
1 ATAAGTAGTAAATTAAATTTAATATTAAA
1750944 TCTATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
ATAAGTAGTAAATTAAATTTAATATTAAA
Found at i:1760788 original size:129 final size:130
Alignment explanation
Indices: 1760546--1760806 Score: 443
Period size: 129 Copynumber: 2.0 Consensus size: 130
1760536 CAAGCGCCCC
* *
1760546 TCCACTAGCAGCGTCAATCATCTTCATTTCCATAGGGAGCAAACCCTCGTAGAAATATTGAAAAA
1 TCCACTAGCAGAGTCAATCATCTTCATTTCCATAGGGAGCAAACCCTCGTAGAAATACTGAAAAA
*
1760611 GTGATTGCACGGTCAAACTGTGTTGAGGACAACTTGCACACAGTTTTTTATACCGCTCCCAATAG
66 GTGATTGCACGGTCAAACCGTGTTGAGGACAACTTGCACACAGTTTTTTATACCGCTCCCAATAG
* *
1760676 TCCACTAGCA-AGTCAATCATTTTCATTTCCATAGGGAGCAAACCCTCGTAGAAATACTGAAGAA
1 TCCACTAGCAGAGTCAATCATCTTCATTTCCATAGGGAGCAAACCCTCGTAGAAATACTGAAAAA
* * *
1760740 GTGATTGCTCGGTCAAACCGTGTTGAGGGCAACTTGCACACAGTTTTTTGTACCGCTCCCAATAG
66 GTGATTGCACGGTCAAACCGTGTTGAGGACAACTTGCACACAGTTTTTTATACCGCTCCCAATAG
1760805 TC
1 TC
1760807 ATAGAGCGAT
Statistics
Matches: 123, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
129 113 0.92
130 10 0.08
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (130 bp):
TCCACTAGCAGAGTCAATCATCTTCATTTCCATAGGGAGCAAACCCTCGTAGAAATACTGAAAAA
GTGATTGCACGGTCAAACCGTGTTGAGGACAACTTGCACACAGTTTTTTATACCGCTCCCAATAG
Found at i:1774923 original size:3 final size:3
Alignment explanation
Indices: 1774915--1774944 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1774905 TATCTCTATT
1774915 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1774945 CAGTAGCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1775101 original size:30 final size:28
Alignment explanation
Indices: 1775059--1775127 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 28
1775049 ATGGTTGTTG
* *
1775059 GTGACTAGTTTGTTATTTTTCTAAAGTTTA
1 GTGACTA-TTTGTAACTTTTC-AAAGTTTA
1775089 GTGACTGATTTGTAACTTTTCAAAGTTTA
1 GTGACT-ATTTGTAACTTTTCAAAGTTTA
1775118 GTGACTATTT
1 GTGACTATTT
1775128 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 4 0.11
29 14 0.39
30 17 0.47
31 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (28 bp):
GTGACTATTTGTAACTTTTCAAAGTTTA
Found at i:1776103 original size:3 final size:3
Alignment explanation
Indices: 1776095--1776131 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1776085 GTGCATCCAT
1776095 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1776132 CTGTCGTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1784258 original size:29 final size:29
Alignment explanation
Indices: 1784209--1784267 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
1784199 GCTTGATCAA
* *
1784209 TAGATAGCTACGAAGGTGTCCA-ATTAACT
1 TAGATAGCCACGAAGGCGTCCATA-TAACT
1784238 TAGATAGCCAC-AAGGGCGTCCATATAACT
1 TAGATAGCCACGAA-GGCGTCCATATAACT
1784267 T
1 T
1784268 TTGGAAGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 2 0.08
29 23 0.88
30 1 0.04
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (29 bp):
TAGATAGCCACGAAGGCGTCCATATAACT
Found at i:1784621 original size:67 final size:67
Alignment explanation
Indices: 1784543--1784673 Score: 199
Period size: 67 Copynumber: 2.0 Consensus size: 67
1784533 CAAAGAACAT
**
1784543 CCACAAAGGCTTTCACATTTCGGTAAATGATGCTTTCGTTGATAGGGATTTCCCTAAACTCAACG
1 CCACAAAGGCTTTCACATTTCGGTAAATGATGCTTTCGACGATAGGGATTTCCCTAAACTCAACG
1784608 TC
66 TC
* * * * *
1784610 CCACAAAGGCTTTCACATTTTGGTAAATGATGTTTTTGACGATAGGGATTTGCCTACACTCAAC
1 CCACAAAGGCTTTCACATTTCGGTAAATGATGCTTTCGACGATAGGGATTTCCCTAAACTCAAC
1784674 ATATTAAGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (67 bp):
CCACAAAGGCTTTCACATTTCGGTAAATGATGCTTTCGACGATAGGGATTTCCCTAAACTCAACG
TC
Found at i:1785872 original size:3 final size:3
Alignment explanation
Indices: 1785864--1785900 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1785854 TAATCGCTAG
1785864 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1785901 ATTAGTAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1797593 original size:42 final size:42
Alignment explanation
Indices: 1797455--1798101 Score: 935
Period size: 42 Copynumber: 15.5 Consensus size: 42
1797445 TTTAAACAGA
* * * *
1797455 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTGAT-TCAG-
1 TTCACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGATAT-TGT
* * *
1797496 TACACCGGCACTT-AGCCTGCTAGACATATAGTCTGA-AATGT
1 TTCACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGATATTGT
*
1797537 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797579 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797621 TTCACCGGCATTAAGTCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797663 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797705 TTCACCGGCATTAAGTCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797747 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797789 TTCACCGGCATTAAGTCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797831 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797873 TTCACCGGCATTAAGTCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797915 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797957 TTCACCGGCATTAAGTCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1797999 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
* *
1798041 TTCACCGGCATTAAGTCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
*
1798083 TTCACCGGCATTAAACCTG
1 TTCACCGGCATTAAGCCTG
1798102 ATAGGCACTG
Statistics
Matches: 542, Mismatches: 60, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
40 3 0.01
41 61 0.11
42 478 0.88
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGT
Found at i:1797653 original size:84 final size:84
Alignment explanation
Indices: 1797498--1798101 Score: 1149
Period size: 84 Copynumber: 7.2 Consensus size: 84
1797488 TGATTCAGTA
* * *
1797498 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAA-TGTTTCACCGGCATTAAGCCTGCTAGA
1 CACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGA
1797561 CGTAAAGTCTGATATTGTTT
65 CGTAAAGTCTGATATTGTTT
1797581 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1797646 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
1797665 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1797730 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
1797749 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1797814 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
1797833 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1797898 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
1797917 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1797982 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
1798001 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
1798066 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
*
1798085 CACCGGCATTAAACCTG
1 CACCGGCATTAAGCCTG
1798102 ATAGGCACTG
Statistics
Matches: 515, Mismatches: 4, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
82 2 0.00
83 32 0.06
84 481 0.93
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (84 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCGGCATTAAGTCTGCTAGAC
GTAAAGTCTGATATTGTTT
Found at i:1799693 original size:16 final size:16
Alignment explanation
Indices: 1799650--1799702 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1799640 ATTTGTTTTT
* *
1799650 ATTTTATGTTCAATTAA
1 ATTTTATTTTAAATT-A
*
1799667 AATTTATTTTTAAATTA
1 ATTTTA-TTTTAAATTA
*
1799684 ATTTTATTTTAATTTA
1 ATTTTATTTTAAATTA
1799700 ATT
1 ATT
1799703 CTTGAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 12 0.40
17 11 0.37
18 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTTATTTTAAATTA
Found at i:1805149 original size:25 final size:25
Alignment explanation
Indices: 1805121--1805216 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
1805111 GTATGGCCAT
* *
1805121 ACGAGCTATAAATCAGTATGCTCTC
1 ACGAGCTATAAATCGGTAAGCTCTC
* *
1805146 ACGAGTTGTAAATCGGTAAG--CTC
1 ACGAGCTATAAATCGGTAAGCTCTC
*
1805169 ATCGAGCTA-AGAATCGGTAAGCTCTT
1 A-CGAGCTATA-AATCGGTAAGCTCTC
*
1805195 ACGAGCTGA-ATATCGGTAAGCT
1 ACGAGCT-ATAAATCGGTAAGCT
1805217 TATACGAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
23 5 0.09
24 15 0.26
25 33 0.57
26 5 0.09
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (25 bp):
ACGAGCTATAAATCGGTAAGCTCTC
Found at i:1805199 original size:49 final size:50
Alignment explanation
Indices: 1805118--1805234 Score: 141
Period size: 49 Copynumber: 2.4 Consensus size: 50
1805108 CATGTATGGC
* * *
1805118 CATACGAGCTATA-AATCAGTATGCTCTCACGAGTTGTAA-ATCGGTAAGCT
1 CATACGAGCTA-AGAATCGGTAAGCTCTCACGAGCTG-AATATCGGTAAGCT
*
1805168 CAT-CGAGCTAAGAATCGGTAAGCTCTTACGAGCTGAATATCGGTAAGCT
1 CATACGAGCTAAGAATCGGTAAGCTCTCACGAGCTGAATATCGGTAAGCT
* *
1805217 TATACGAGCTGAGAATCG
1 CATACGAGCTAAGAATCG
1805235 ATAATCCCTA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
48 3 0.05
49 39 0.67
50 16 0.28
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (50 bp):
CATACGAGCTAAGAATCGGTAAGCTCTCACGAGCTGAATATCGGTAAGCT
Found at i:1805222 original size:25 final size:26
Alignment explanation
Indices: 1805156--1805234 Score: 96
Period size: 25 Copynumber: 3.2 Consensus size: 26
1805146 ACGAGTTGTA
*
1805156 AATCGGTAAGCTCAT-CGAGCT-AAG
1 AATCGGTAAGCTTATACGAGCTGAAG
1805180 AATCGGTAAGCTCT-TACGAGCTGAA-
1 AATCGGTAAGCT-TATACGAGCTGAAG
*
1805205 TATCGGTAAGCTTATACGAGCTG-AG
1 AATCGGTAAGCTTATACGAGCTGAAG
1805230 AATCG
1 AATCG
1805235 ATAATCCCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
24 15 0.32
25 30 0.64
26 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (26 bp):
AATCGGTAAGCTTATACGAGCTGAAG
Found at i:1812481 original size:23 final size:23
Alignment explanation
Indices: 1812438--1812482 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1812428 TGAATTAAAT
* * *
1812438 TAAAATTTTATTATTTTTAAAAG
1 TAAAATTTTATAAATTATAAAAG
1812461 TAAAATTTTATAAATTATAAAA
1 TAAAATTTTATAAATTATAAAA
1812483 AATTTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAATTTTATAAATTATAAAAG
Found at i:1822256 original size:23 final size:20
Alignment explanation
Indices: 1822209--1822265 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 20
1822199 AAATTGTAGC
1822209 AAAATAGTGAAAAACAACAAG
1 AAAATAGT-AAAAACAACAAG
1822230 AAAATAGTAAAAACAAGAGCAAG
1 AAAATAGTAAAAAC-A-A-CAAG
*
1822253 AAAACAGTAAAAA
1 AAAATAGTAAAAA
1822266 AAATAACAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 6 0.19
21 9 0.28
22 1 0.03
23 16 0.50
ACGTcount: A:0.68, C:0.09, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAATAGTAAAAACAACAAG
Found at i:1822981 original size:21 final size:23
Alignment explanation
Indices: 1822955--1823008 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 23
1822945 TTATATGATG
1822955 TAAATTTATTATATATA-TTTTA
1 TAAATTTATTATATATATTTTTA
*
1822977 T-AA-TTATT-TATGTATTTTTA
1 TAAATTTATTATATATATTTTTA
*
1822997 TAAATTTTTTAT
1 TAAATTTATTAT
1823009 TTTTTAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 5 0.19
20 11 0.42
21 4 0.15
22 5 0.19
23 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TAAATTTATTATATATATTTTTA
Found at i:1822983 original size:20 final size:20
Alignment explanation
Indices: 1822963--1823020 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1822953 TGTAAATTTA
1822963 TTATATATATTTTATAATTAT
1 TTATATAT-TTTTATAATTAT
*
1822984 TTATGTATTTTTATAAATT-T
1 TTATATATTTTTAT-AATTAT
*
1823004 TT-TAT-TTTTTAGAATTA
1 TTATATATTTTTATAATTA
1823021 GGATCAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.12
18 6 0.19
19 2 0.06
20 9 0.28
21 11 0.34
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TTATATATTTTTATAATTAT
Found at i:1823520 original size:23 final size:23
Alignment explanation
Indices: 1823494--1823558 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 23
1823484 ATTTTATTCG
1823494 AAAAATTAAATAATATTTATAAT
1 AAAAATTAAATAATATTTATAAT
* *
1823517 AAAATATT-TATACTAATTT-TAAT
1 AAAA-ATTAAATAAT-ATTTATAAT
* *
1823540 -AAAATCACATAATATTTAT
1 AAAAATTAAATAATATTTAT
1823559 TACTAATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
21 6 0.18
22 8 0.24
23 12 0.36
24 7 0.21
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAAATTAAATAATATTTATAAT
Found at i:1827457 original size:24 final size:24
Alignment explanation
Indices: 1827390--1827458 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
1827380 TCATTTAACT
1827390 TAATCAAACATGTTCACGAACAT-
1 TAATCAAACATGTTCACGAACATA
* * * * *
1827413 TAAACGAACACGTTTATGAACATA
1 TAATCAAACATGTTCACGAACATA
*
1827437 TAATTAAACATGTTCACGAACA
1 TAATCAAACATGTTCACGAACA
1827459 ATATTAATGA
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (24 bp):
TAATCAAACATGTTCACGAACATA
Found at i:1836355 original size:18 final size:17
Alignment explanation
Indices: 1836327--1836361 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1836317 ATTTTTAAGA
*
1836327 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1836344 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1836362 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:1836615 original size:16 final size:16
Alignment explanation
Indices: 1836594--1836632 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1836584 TTGATTTGCT
*
1836594 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
1836610 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
1836626 ATTACAC
1 ATTACAC
1836633 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:1836633 original size:16 final size:16
Alignment explanation
Indices: 1836607--1836663 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
1836597 ACACAGCTTT
* *
1836607 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
1836623 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
1836639 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
1836655 TCCAATACA
1 TCCAATACA
1836664 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:1839655 original size:18 final size:19
Alignment explanation
Indices: 1839618--1839655 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1839608 TTCACGAAAG
* *
1839618 AAGATATAATAGTTATCAT
1 AAGATAAAATAGTGATCAT
1839637 AAGATAAAATAG-GATCAT
1 AAGATAAAATAGTGATCAT
1839655 A
1 A
1839656 TTGGGAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.29
Consensus pattern (19 bp):
AAGATAAAATAGTGATCAT
Found at i:1848677 original size:112 final size:111
Alignment explanation
Indices: 1848417--1848692 Score: 277
Period size: 112 Copynumber: 2.5 Consensus size: 111
1848407 AAAATGCATC
* * * * *
1848417 GTTTTGGTCTTGATGTATACTAGAATTAGTGGCGTTTATGAAAAAACGCCGCTAAAGGAAGTATT
1 GTTTT-GTCTAGAGGTATATTAGAATTA-TGGCGCTTACGAAAAAACGCCGCTAAAGGAAGTATT
* ** * **
1848482 AGCGGCGCATTGCCGAAAGCGCCGCAAAAATCTTAACGAAAACGCATT
64 AGCGGCGCATTACAAAAAGCGCCGCAAAAATCTTAACCAAAACGCAGA
* ** ** **
1848530 GTTTTGTCTCGCTGTATATTAGCGTTA-GCGACGCTTACGAAAACCCGCCGCTAAAGGAAGTATT
1 GTTTTGTCTAGAGGTATATTAGAATTATG-G-CGCTTACGAAAAAACGCCGCTAAAGGAAGTATT
* *
1848594 AGCGGCGC-TTACAAAAAGCGCCGCAACATATGTTAACCAAAACGCAGA
64 AGCGGCGCATTACAAAAAGCGCCGCAA-AAATCTTAACCAAAACGCAGA
* * *
1848642 GTTTTGTCTAGAGGTATGTTAGAATTTATGGCGCTTATGGAAAAACGCCGC
1 GTTTTGTCTAGAGGTATATTAGAA-TTATGGCGCTTACGAAAAAACGCCGC
1848693 AAACTATCCT
Statistics
Matches: 131, Mismatches: 27, Indels: 11
0.78 0.16 0.07
Matches are distributed among these distances:
110 1 0.01
111 16 0.12
112 104 0.79
113 9 0.07
114 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (111 bp):
GTTTTGTCTAGAGGTATATTAGAATTATGGCGCTTACGAAAAAACGCCGCTAAAGGAAGTATTAG
CGGCGCATTACAAAAAGCGCCGCAAAAATCTTAACCAAAACGCAGA
Found at i:1849207 original size:210 final size:209
Alignment explanation
Indices: 1848799--1849263 Score: 472
Period size: 210 Copynumber: 2.2 Consensus size: 209
1848789 GTTTTTTGGG
*
1848799 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCATGAGGTATACTAGAATTAGTGGC
* * * * *
1848864 ACAAAGGGAACACGCCGCTAAGGTATACTATTAGCGGCGTTTTCAGAGAAGCGCCGCAACATTTG
66 ACAAAGGGAACACGCCGCTAAAGCATACTATTAGCGGCGTTTTCAGAGAAGCGCCGCAAAATATA
* ** * ** *
1848929 GTAACCAAAACGCAACGTTTTTGTCTTGATGTGTACAGTTATTAGTGGCGCATATCAAAAAACGC
131 GTAACAAAAACGCAACGTTTAAGTCTTGATGTATACAGGAATTAGTGGCGCACATCAAAAAACGC
1848994 CGCTAAATCATGCC
196 CGCTAAATCATGCC
* ** * *
1849008 AAGCGCCGCAAAATATGC-TCACCAAAACGCAGAGTTTTTTCATGAGGTATATTAGACTTAGTGG
1 AAGCGCCGCAAAATAT-CTTAACCAAAACGCAGAGTTTGGTCATGAGGTATACTAGAATTAGTGG
* ** * * * * *
1849072 CGCTTATGGGGGA-ACGCCGCTAAAGCATATTATTTGCGGCGCTTTT-TGAGAAGCGTCGCAAAA
65 CAC--AAAGGGAACACGCCGCTAAAGCATACTATTAGCGGCG-TTTTCAGAGAAGCGCCGCAAAA
* * * *
1849135 TATATTAACAAAAACGCAGCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCGTC-CA-CGAGA
127 TATAGTAACAAAAACGCAACGTTTAAGTCTTGATGTATACAGGAATTAGTGGCG-CACATC-AAA
* * **
1849198 AATCGCCGCTAAAGCATAGTATTA
190 AAACGCCGCTAAATCAT-G---CC
* *
1849222 AAGCGCCGGAAAATATCTTAACCAAAATGCAGAGTTTTGGTC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTC
1849264 TTAACCGTGC
Statistics
Matches: 205, Mismatches: 39, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
209 59 0.29
210 100 0.49
211 11 0.05
213 1 0.00
214 29 0.14
215 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (209 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCATGAGGTATACTAGAATTAGTGGC
ACAAAGGGAACACGCCGCTAAAGCATACTATTAGCGGCGTTTTCAGAGAAGCGCCGCAAAATATA
GTAACAAAAACGCAACGTTTAAGTCTTGATGTATACAGGAATTAGTGGCGCACATCAAAAAACGC
CGCTAAATCATGCC
Found at i:1855688 original size:16 final size:17
Alignment explanation
Indices: 1855663--1855702 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1855653 GCCCAAATGC
1855663 CAAA-CCCAAAT-AAAA
1 CAAAGCCCAAATCAAAA
*
1855678 CAAAGCCCAAATCCAAA
1 CAAAGCCCAAATCAAAA
1855695 C-AAGCCCA
1 CAAAGCCCA
1855703 TTACAGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.55, C:0.35, G:0.05, T:0.05
Consensus pattern (17 bp):
CAAAGCCCAAATCAAAA
Found at i:1857831 original size:18 final size:18
Alignment explanation
Indices: 1857808--1857844 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1857798 ATTTTGGGCG
1857808 TATCGAGGGTGCTAATCC
1 TATCGAGGGTGCTAATCC
1857826 TATCGAGGGTGCTAATCC
1 TATCGAGGGTGCTAATCC
1857844 T
1 T
1857845 TCCTCGTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (18 bp):
TATCGAGGGTGCTAATCC
Found at i:1861326 original size:17 final size:15
Alignment explanation
Indices: 1861292--1861338 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1861282 GTTCAGACTC
* *
1861292 AAAAAA-AAAAGAAG
1 AAAAAATAAAAAAAA
1861306 AAAAAATCAAAAATAAA
1 AAAAAAT-AAAAA-AAA
1861323 AAAAAATAAAAAAAA
1 AAAAAATAAAAAAAA
1861338 A
1 A
1861339 TCAATCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.21
15 4 0.14
16 9 0.32
17 9 0.32
ACGTcount: A:0.87, C:0.02, G:0.04, T:0.06
Consensus pattern (15 bp):
AAAAAATAAAAAAAA
Found at i:1861328 original size:11 final size:10
Alignment explanation
Indices: 1861314--1861339 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1861304 AGAAAAAATC
1861314 AAAAATAAAA
1 AAAAATAAAA
1861324 AAAAATAAAA
1 AAAAATAAAA
1861334 AAAAAT
1 AAAAAT
1861340 CAATCAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:1861373 original size:6 final size:6
Alignment explanation
Indices: 1861364--1861401 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
1861354 CAAAAATAGG
1861364 AGAAAA AGAAAGA AGAAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA
1861402 GGAGAGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.70
7 6 0.20
8 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:1862244 original size:7 final size:7
Alignment explanation
Indices: 1862232--1862271 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
1862222 TGAGTCAAAA
1862232 AAAAATG
1 AAAAATG
1862239 AAAAATG
1 AAAAATG
1862246 -AAAATG
1 AAAAATG
1862252 AAAAATG
1 AAAAATG
1862259 AAAAA-G
1 AAAAATG
1862265 AAAAATG
1 AAAAATG
1862272 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:1862251 original size:13 final size:13
Alignment explanation
Indices: 1862233--1862271 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1862223 GAGTCAAAAA
1862233 AAAATGAAAAATG
1 AAAATGAAAAATG
1862246 AAAATGAAAAATG
1 AAAATGAAAAATG
*
1862259 AAAAAGAAAAATG
1 AAAATGAAAAATG
1862272 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:1862271 original size:20 final size:20
Alignment explanation
Indices: 1862232--1862268 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1862222 TGAGTCAAAA
1862232 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
1862252 AAAAATGAAAAA-GAAAA
1 AAAAATGAAAAATGAAAA
1862269 ATGGAGAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:1866666 original size:21 final size:21
Alignment explanation
Indices: 1866640--1866704 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1866630 AACTTAAAGT
*
1866640 AGAGGCGACAGCGAGGGAAGC
1 AGAGGCGACAGCGAGAGAAGC
*
1866661 AGAGGCTACAGCGAGAGAAGC
1 AGAGGCGACAGCGAGAGAAGC
1866682 AGAGGCCG-CAGCGAGAGAAGC
1 AGAGG-CGACAGCGAGAGAAGC
1866703 AG
1 AG
1866705 CGATAGAAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.43, T:0.02
Consensus pattern (21 bp):
AGAGGCGACAGCGAGAGAAGC
Found at i:1881322 original size:52 final size:52
Alignment explanation
Indices: 1881263--1881379 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 52
1881253 AAAAGATAAT
* ** *
1881263 ATTCGCTGTCTTCAACTTTAATCTGTTCCGCTGTAACG-CCGGAGAAAAGAAG
1 ATTCGCTGTCTTCAACTTTAATCTGCTCCGCTACAACGTCAGG-GAAAAGAAG
* * * *
1881315 ATTCGCTGCCTTCAATTTTAATCTGCTCTGCTACAATGTCAGGGAAAAGAAG
1 ATTCGCTGTCTTCAACTTTAATCTGCTCCGCTACAACGTCAGGGAAAAGAAG
*
1881367 ACTCGCTGTCTTC
1 ATTCGCTGTCTTC
1881380 TGTCTTAACG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 51 0.94
53 3 0.06
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (52 bp):
ATTCGCTGTCTTCAACTTTAATCTGCTCCGCTACAACGTCAGGGAAAAGAAG
Found at i:1891357 original size:52 final size:52
Alignment explanation
Indices: 1891298--1891414 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 52
1891288 AAAAGATAAT
* ** *
1891298 ATTCGCTGTCTTCAACTTTAATCTGTTCCGCTGTAACG-CCGGAGAAAAGAAG
1 ATTCGCTGTCTTCAACTTTAATCTGCTCCGCTACAACGTCAGG-GAAAAGAAG
* * * *
1891350 ATTCGCTGCCTTCAATTTTAATCTGCTCTGCTACAATGTCAGGGAAAAGAAG
1 ATTCGCTGTCTTCAACTTTAATCTGCTCCGCTACAACGTCAGGGAAAAGAAG
*
1891402 ACTCGCTGTCTTC
1 ATTCGCTGTCTTC
1891415 TGTCTTAACG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 51 0.94
53 3 0.06
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (52 bp):
ATTCGCTGTCTTCAACTTTAATCTGCTCCGCTACAACGTCAGGGAAAAGAAG
Found at i:1898082 original size:3 final size:3
Alignment explanation
Indices: 1898061--1898178 Score: 74
Period size: 3 Copynumber: 39.3 Consensus size: 3
1898051 AATGAGTAAC
* * * ** *
1898061 TAA TAA TGA TGA TAT TAA TAA TAA TAA TAA CGA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
1898109 TAA TAG TAG TAA AAA TAA AAA TAA TAA TAC GAG TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1898157 TAG TAA TAG GAG TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
1898179 GATTAAAATT
Statistics
Matches: 86, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.30
Consensus pattern (3 bp):
TAA
Done.