Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 192 of 193
Found at i:60075343 original size:2 final size:2
Alignment explanation
Indices: 60075338--60075365 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60075328 AAAAAATTAA
60075338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60075366 TTATTACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60076200 original size:17 final size:17
Alignment explanation
Indices: 60076178--60076307 Score: 93
Period size: 17 Copynumber: 7.1 Consensus size: 17
60076168 ATTGGGTTTC
* *
60076178 AATTTATAATAATTTTA
1 AATTTAAAATAAATTTA
60076195 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
*
60076212 AACTTAAATTAAATTCAAATTTAA
1 AA--T---TTAAAAT-AAATTT-A
*
60076236 AATTTAAAATTTAAATTTG
1 AATTTAAAA--TAAATTTA
* *
60076255 AATTTAAAATAAGTCTA
1 AATTTAAAATAAATTTA
60076272 AATTT-AAATCAAATTT-
1 AATTTAAAAT-AAATTTA
60076288 AATCTTAAAATAAATTTA
1 AAT-TTAAAATAAATTTA
60076306 AA
1 AA
60076308 GGGGCCCGGT
Statistics
Matches: 90, Mismatches: 10, Indels: 25
0.72 0.08 0.20
Matches are distributed among these distances:
16 7 0.08
17 39 0.43
18 6 0.07
19 15 0.17
20 6 0.07
21 1 0.01
22 7 0.08
23 6 0.07
24 3 0.03
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:60076204 original size:7 final size:6
Alignment explanation
Indices: 60076191--60076307 Score: 84
Period size: 6 Copynumber: 20.0 Consensus size: 6
60076181 TTATAATAAT
* * *
60076191 TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA -TTAAA TTCAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
* * * * *
60076238 TTTAAAA TTTAAA TTTGAA TTTAAA -ATAAG TCTAAA TTTAAA -TCAAA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
60076285 TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA
60076308 GGGGCCCGGT
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
5 23 0.26
6 49 0.56
7 15 0.17
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:60076221 original size:12 final size:11
Alignment explanation
Indices: 60076192--60076307 Score: 74
Period size: 11 Copynumber: 10.0 Consensus size: 11
60076182 TATAATAATT
60076192 TTAAATTTAAA
1 TTAAATTTAAA
*
60076203 ATAAATTTAAA
1 TTAAATTTAAA
60076214 CTTAAA-TTAAA
1 -TTAAATTTAAA
60076225 TTCAAATTTAAAA
1 TT-AAATTT-AAA
60076238 TTTAAAATTTAAA
1 -TT-AAATTTAAA
*
60076251 TTTGAATTTAAA
1 -TTAAATTTAAA
* * *
60076263 ATAAGTCTAAA
1 TTAAATTTAAA
*
60076274 TTTAAA-TCAAA
1 -TTAAATTTAAA
*
60076285 TTTAATCTTAAA
1 TTAAAT-TTAAA
*
60076297 ATAAATTTAAA
1 TTAAATTTAAA
60076308 GGGGCCCGGT
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
10 6 0.07
11 33 0.41
12 25 0.31
13 9 0.11
14 8 0.10
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:60076891 original size:17 final size:17
Alignment explanation
Indices: 60076861--60076925 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
60076851 TTTTTTGGAC
*
60076861 TTTTAATATT-AAATAAT
1 TTTTAAT-TTAAAATAAA
60076878 TTTTAATTTAAAATAAA
1 TTTTAATTTAAAATAAA
**
60076895 TTCGAATTTAAAATAAA
1 TTTTAATTTAAAATAAA
**
60076912 TTAAAATTTAAAAT
1 TTTTAATTTAAAAT
60076926 TAAAAGTTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
16 2 0.05
17 40 0.95
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTTAATTTAAAATAAA
Found at i:60077392 original size:20 final size:21
Alignment explanation
Indices: 60077367--60077406 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
60077357 ATTTTGATTA
60077367 ACTGTTGATTGA-TGTTGACC
1 ACTGTTGATTGATTGTTGACC
60077387 ACTGTTGATTGATTGTTGAC
1 ACTGTTGATTGATTGTTGAC
60077407 AAGTATTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (21 bp):
ACTGTTGATTGATTGTTGACC
Found at i:60077415 original size:21 final size:20
Alignment explanation
Indices: 60077366--60077415 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
60077356 GATTTTGATT
*
60077366 AACTGTTGATTGATGTTGAC
1 AACTATTGATTGATGTTGAC
* *
60077386 CACTGTTGATTGATTGTTGAC
1 AACTATTGATTGA-TGTTGAC
*
60077407 AAGTATTGA
1 AACTATTGA
60077416 CCACCGTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (20 bp):
AACTATTGATTGATGTTGAC
Found at i:60077862 original size:23 final size:24
Alignment explanation
Indices: 60077822--60077868 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
60077812 TGTAATTTTG
*
60077822 TATATATTATTTTGAATTTTTATAA
1 TATATATTATTATGAA-TTTTATAA
60077847 TATATA-TATTAT-AATTTTATAA
1 TATATATTATTATGAATTTTATAA
60077869 AAGTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 2 0.10
24 5 0.24
25 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATATATTATTATGAATTTTATAA
Found at i:60077867 original size:22 final size:21
Alignment explanation
Indices: 60077814--60077868 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
60077804 ATAAAAATTG
* *
60077814 TAATTTTGT-ATATATTATTT
1 TAATTTTATAATATATTATTA
60077834 TGAATTTTTATAATATATATATTA
1 T-AA-TTTTATAATATAT-TATTA
60077858 TAATTTTATAA
1 TAATTTTATAA
60077869 AAGTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 2 0.07
22 13 0.45
23 8 0.28
24 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TAATTTTATAATATATTATTA
Found at i:60079016 original size:102 final size:102
Alignment explanation
Indices: 60078870--60079160 Score: 348
Period size: 102 Copynumber: 2.9 Consensus size: 102
60078860 TATTAACGGG
* * * **
60078870 GGAGCAGAGGATGGTGGGCATGGCAACAGGACAGAGCCTGAAATAGACGAAGATGTAGGAGCTGA
1 GGAGCAGAGGATGGTGGCCATGGCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCCCA
* * *
60078935 GCTCATCGGAGTCGCGCTTTATAACTATATTAACACA
66 ACTCATCGGAATCGAGCTTTATAACTATATTAACACA
* * * * * * *
60078972 GGTGTAGAGGATGGCGGCCATGGGAACACGAGGGAGCCTGAAATAGAGGAAGATGAAGGAGCCCA
1 GGAGCAGAGGATGGTGGCCATGGCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCCCA
* * *
60079037 ACTTATCGGAATCGAGCTTTATAACTATATTAACGCT
66 ACTCATCGGAATCGAGCTTTATAACTATATTAACACA
* * * **
60079074 GGAGCAGAGGATGGTGGTCATGGCAACAGGACGGATCCTGAAGTAGACGAAGGCGAAGGAGCCCA
1 GGAGCAGAGGATGGTGGCCATGGCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCCCA
* * *
60079139 TCTCATCGGAATCCAGCCTTAT
66 ACTCATCGGAATCGAGCTTTAT
60079161 CACGTTATTC
Statistics
Matches: 155, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
102 155 1.00
ACGTcount: A:0.31, C:0.19, G:0.32, T:0.18
Consensus pattern (102 bp):
GGAGCAGAGGATGGTGGCCATGGCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCCCA
ACTCATCGGAATCGAGCTTTATAACTATATTAACACA
Found at i:60081583 original size:23 final size:23
Alignment explanation
Indices: 60081559--60081604 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
60081549 AAATGTGTAT
60081559 AACAATTATCTAATTTAAAAAATA
1 AACAATTATCTAA-TTAAAAAATA
* *
60081583 AATAATTATTTAATTAAAAAAT
1 AACAATTATCTAATTAAAAAAT
60081605 TAAAACCCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
AACAATTATCTAATTAAAAAATA
Found at i:60087071 original size:19 final size:18
Alignment explanation
Indices: 60087029--60087072 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
60087019 TAACGAAAAG
60087029 ATTAGAAAAGGATGAACA
1 ATTAGAAAAGGATGAACA
*
60087047 AATAGAAAAGGATGAAACA
1 ATTAGAAAAGGATG-AACA
60087066 ATTAGAA
1 ATTAGAA
60087073 TGTTAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.16
Consensus pattern (18 bp):
ATTAGAAAAGGATGAACA
Found at i:60092487 original size:8 final size:8
Alignment explanation
Indices: 60092474--60092548 Score: 53
Period size: 8 Copynumber: 8.5 Consensus size: 8
60092464 TAATTTTTTT
60092474 AAAATATA
1 AAAATATA
60092482 AAAATATA
1 AAAATATA
60092490 AAAATTATA
1 AAAA-TATA
*
60092499 TAAACTTATA
1 -AAA-ATATA
60092509 AAAA-AGTTA
1 AAAATA--TA
60092518 AAAACTTATA
1 AAAA--TATA
*
60092528 AATATTATA
1 AA-AATATA
60092537 AAAATATA
1 AAAATATA
60092545 AAAA
1 AAAA
60092549 ATCTAATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
7 1 0.02
8 21 0.39
9 19 0.35
10 11 0.20
11 1 0.02
12 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (8 bp):
AAAATATA
Found at i:60092501 original size:19 final size:19
Alignment explanation
Indices: 60092478--60092548 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
60092468 TTTTTTAAAA
60092478 TATAAAAATATAAAAATTA-
1 TATAAAAATATAAAAA-TAG
**
60092497 TATAAACTTATAAAAA-AG
1 TATAAAAATATAAAAATAG
* *
60092515 T-TAAAAACT-TATAAATAT
1 TATAAAAA-TATAAAAATAG
60092533 TATAAAAATATAAAAA
1 TATAAAAATATAAAAA
60092549 ATCTAATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 10 0.25
18 5 0.12
19 25 0.62
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (19 bp):
TATAAAAATATAAAAATAG
Found at i:60092508 original size:27 final size:27
Alignment explanation
Indices: 60092478--60092548 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
60092468 TTTTTTAAAA
60092478 TATAAAAATATAAAAA-TTATATAA-ACT
1 TATAAAAATATAAAAACTTATA-AATA-T
60092505 TATAAAAA-AGTTAAAAACTTATAAATAT
1 TATAAAAATA--TAAAAACTTATAAATAT
60092533 TATAAAAATATAAAAA
1 TATAAAAATATAAAAA
60092549 ATCTAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
26 1 0.03
27 14 0.36
28 17 0.44
29 7 0.18
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (27 bp):
TATAAAAATATAAAAACTTATAAATAT
Found at i:60092913 original size:61 final size:61
Alignment explanation
Indices: 60092834--60092961 Score: 150
Period size: 61 Copynumber: 2.1 Consensus size: 61
60092824 ATATTTAAAA
* * * * * *
60092834 TTTTTAGAGTTAAGACTAAATTGATAAATTTTGTAAATAATGAGGGTCAAATTTATTGAAT
1 TTTTTAGAATTAAGACTAAATTGACAAAATTTATAAACAATGAGGGTCAAATTTATAGAAT
* * * *
60092895 TTTTTAGAATT-AGAACTAAATTGACAAAATTTATAAACATTGAGGGTTAATTTTGTAGAAT
1 TTTTTAGAATTAAG-ACTAAATTGACAAAATTTATAAACAATGAGGGTCAAATTTATAGAAT
60092956 TTTTTA
1 TTTTTA
60092962 TATTTAGGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 2 0.04
61 54 0.96
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (61 bp):
TTTTTAGAATTAAGACTAAATTGACAAAATTTATAAACAATGAGGGTCAAATTTATAGAAT
Found at i:60097673 original size:20 final size:19
Alignment explanation
Indices: 60097636--60097673 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
60097626 AAAGTGTATG
60097636 ATAAAGAGAGGGAGAGGTT
1 ATAAAGAGAGGGAGAGGTT
60097655 ATAAATGAGAAGGGA-AGGT
1 ATAAA-GAG-AGGGAGAGGT
60097674 ATTCAGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.39, T:0.16
Consensus pattern (19 bp):
ATAAAGAGAGGGAGAGGTT
Found at i:60099144 original size:35 final size:36
Alignment explanation
Indices: 60099091--60099164 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 36
60099081 AAGGTCGACC
*
60099091 TTTAGAAAAGATTAGGATAGACCCGTCTAAGACAAT
1 TTTAGAAAAGATTAGGATAAACCCGTCTAAGACAAT
* *
60099127 TTTA-AAAAGATTGGGATAAACCCGTCTAAGTCAAT
1 TTTAGAAAAGATTAGGATAAACCCGTCTAAGACAAT
60099162 TTT
1 TTT
60099165 TTTTCTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (36 bp):
TTTAGAAAAGATTAGGATAAACCCGTCTAAGACAAT
Found at i:60101064 original size:19 final size:18
Alignment explanation
Indices: 60101020--60101067 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
60101010 GTTTTTTTTT
*
60101020 ATTATAAAAATACATAAGA
1 ATTAT-AAAATACATAAAA
*
60101039 TTCTATAAAATACATATAAA
1 AT-TATAAAATACATA-AAA
60101059 ATTATAAAA
1 ATTATAAAA
60101068 AAATATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (18 bp):
ATTATAAAATACATAAAA
Found at i:60101220 original size:10 final size:10
Alignment explanation
Indices: 60101207--60101348 Score: 91
Period size: 10 Copynumber: 14.7 Consensus size: 10
60101197 AAAAAACTGC
60101207 AAAAAATTAT
1 AAAAAATTAT
*
60101217 --AAAATAAT
1 AAAAAATTAT
*
60101225 AAATAATTAT
1 AAAAAATTAT
* *
60101235 AGAAAATTAC
1 AAAAAATTAT
*
60101245 AAAGAAACTAT
1 AAA-AAATTAT
*
60101256 AGAAAATTAT
1 AAAAAATTAT
*
60101266 AAAAACTTAT
1 AAAAAATTAT
** *
60101276 GGAAAATCATT
1 AAAAAATTA-T
60101287 AAAAAA-TAT
1 AAAAAATTAT
* *
60101296 ACATAATTAT
1 AAAAAATTAT
*
60101306 -AAAAATGAT
1 AAAAAATTAT
60101315 AAAAAA-T-T
1 AAAAAATTAT
60101323 AAAAAATTAT
1 AAAAAATTAT
60101333 AAAAAA-TAT
1 AAAAAATTAT
*
60101342 GAAAAAT
1 AAAAAAT
60101349 AGAATTTTTA
Statistics
Matches: 96, Mismatches: 27, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
8 14 0.15
9 20 0.21
10 50 0.52
11 12 0.12
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:60101349 original size:9 final size:9
Alignment explanation
Indices: 60101184--60101349 Score: 61
Period size: 10 Copynumber: 17.4 Consensus size: 9
60101174 GAAATTTATG
60101184 AATATTAAAA
1 AATA-TAAAA
60101194 AATA-AAAA
1 AATATAAAA
* **
60101202 ACTGCAAAA
1 AATATAAAA
60101211 AATTATAAAA
1 AA-TATAAAA
*
60101221 TAATA-AATA
1 -AATATAAAA
*
60101230 ATTATAGAAA
1 AATATA-AAA
* *
60101240 ATTACAAAGA
1 AATATAAA-A
60101250 AACTATAGAAA
1 AA-TATA-AAA
*
60101261 ATTATAAAA
1 AATATAAAA
* **
60101270 ACTTATGGAA
1 A-ATATAAAA
60101280 AATCATTAAAA
1 AAT-A-TAAAA
* *
60101291 AATATACAT
1 AATATAAAA
60101300 AAT-TATAAA
1 AATATA-AAA
60101309 AATGATAAAA
1 AAT-ATAAAA
60101319 AAT-TAAAA
1 AATATAAAA
60101327 AATTATAAAA
1 AA-TATAAAA
*
60101337 AATATGAAA
1 AATATAAAA
60101346 AATA
1 AATA
60101350 GAATTTTTAT
Statistics
Matches: 118, Mismatches: 22, Indels: 33
0.68 0.13 0.19
Matches are distributed among these distances:
8 18 0.15
9 37 0.31
10 46 0.39
11 15 0.13
12 2 0.02
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (9 bp):
AATATAAAA
Found at i:60101993 original size:15 final size:15
Alignment explanation
Indices: 60101973--60102010 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
60101963 TCCCGTCAGT
60101973 CACATGTCTTCCAGC
1 CACATGTCTTCCAGC
60101988 CACATGTCTTCCAGC
1 CACATGTCTTCCAGC
60102003 CACCATGT
1 CA-CATGT
60102011 GCTGGCGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.21, C:0.39, G:0.13, T:0.26
Consensus pattern (15 bp):
CACATGTCTTCCAGC
Found at i:60104303 original size:6 final size:6
Alignment explanation
Indices: 60104273--60104370 Score: 75
Period size: 6 Copynumber: 17.0 Consensus size: 6
60104263 TTTTATATTT
* * *
60104273 TTTAAA -TTAAT TTTAAA TTT-TA TTTAGA TTTAAA TTT--A TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
* *
60104318 TTTAAA TTTATTTA TTTAAA TTT-AC TTTAAA TTTAAA TTT-AA -TTAAA
1 TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
60104365 TTTAAA
1 TTTAAA
60104371 AATAATATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 20
0.72 0.09 0.20
Matches are distributed among these distances:
4 4 0.05
5 18 0.25
6 44 0.60
7 2 0.03
8 5 0.07
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:60104306 original size:17 final size:16
Alignment explanation
Indices: 60104279--60104370 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
60104269 ATTTTTTAAA
*
60104279 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
*
60104296 TTAGATTTAAATTTAT
1 TTAAATTTAAATTTAT
60104312 CTTAAATTTAAATTTAT
1 -TTAAATTTAAATTTAT
60104329 TT--ATTTAAATTTACT
1 TTAAATTTAAATTTA-T
*
60104344 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
60104360 TTAAATTTAAA
1 TTAAATTTAAA
60104371 AATAATATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.16
15 3 0.04
16 18 0.27
17 35 0.52
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:60104361 original size:11 final size:11
Alignment explanation
Indices: 60104273--60104370 Score: 65
Period size: 11 Copynumber: 8.5 Consensus size: 11
60104263 TTTTATATTT
60104273 TTTAAA-TTAA
1 TTTAAATTTAA
*
60104283 TTTTAAATTTTA
1 -TTTAAATTTAA
*
60104295 TTTAGATTTAAA
1 TTTAAATTT-AA
** *
60104307 TTTATCTTAAA
1 TTTAAATTTAA
60104318 TTTAAATTTATTTA
1 TTTAAATTTA---A
*
60104332 TTTAAATTTAC
1 TTTAAATTTAA
60104343 TTTAAATTTAAA
1 TTTAAATTT-AA
*
60104355 TTT-AATTAAA
1 TTTAAATTTAA
60104365 TTTAAA
1 TTTAAA
60104371 AATAATATTA
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
10 5 0.07
11 38 0.56
12 14 0.21
14 11 0.16
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:60104533 original size:18 final size:18
Alignment explanation
Indices: 60104510--60104548 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
60104500 AGACAGCCCA
* *
60104510 ATTACAAATTCATAACCC
1 ATTACAAATTAAAAACCC
*
60104528 ATTACATATTAAAAACCC
1 ATTACAAATTAAAAACCC
60104546 ATT
1 ATT
60104549 TCAGCCCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTACAAATTAAAAACCC
Found at i:60105099 original size:15 final size:15
Alignment explanation
Indices: 60105079--60105108 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60105069 ATAATTTCAT
60105079 AAATATCATTAATAA
1 AAATATCATTAATAA
*
60105094 AAATATTATTAATAA
1 AAATATCATTAATAA
60105109 TCATAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATCATTAATAA
Found at i:60105122 original size:16 final size:15
Alignment explanation
Indices: 60105101--60105187 Score: 61
Period size: 16 Copynumber: 5.7 Consensus size: 15
60105091 TAAAAATATT
60105101 ATTAATAATCATAATA
1 ATTAATAAT-ATAATA
*
60105117 ATTAATAATTGTAATA
1 ATTAATAA-TATAATA
* * * *
60105133 AATATTTATGATTATA
1 ATTAATAAT-ATAATA
60105149 ATTAAT-AT-TAATA
1 ATTAATAATATAATA
*
60105162 ATTAATAATATCAAAA
1 ATTAATAATAT-AATA
*
60105178 AATAATAATA
1 ATTAATAATA
60105188 ATAAAAAAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
13 10 0.18
14 2 0.04
15 4 0.07
16 38 0.69
17 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAATAATATAATA
Found at i:60105133 original size:19 final size:19
Alignment explanation
Indices: 60105111--60105171 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
60105101 ATTAATAATC
*
60105111 ATAATAATTAATAATTGTA
1 ATAATAATTAATAATTATA
* *
60105130 ATAA-ATATTTATGATTATA
1 ATAATA-ATTAATAATTATA
60105149 ATTAAT-ATTAATAATTAATA
1 A-TAATAATTAATAATT-ATA
60105169 ATA
1 ATA
60105172 TCAAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.03
19 25 0.76
20 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAATAATTAATAATTATA
Found at i:60106331 original size:30 final size:30
Alignment explanation
Indices: 60106278--60106563 Score: 256
Period size: 30 Copynumber: 9.4 Consensus size: 30
60106268 AGTTGTCCAG
* * * *
60106278 AAATTATATTTTTGACCCCAAAACCTTCTAA
1 AAATTACA-TTTTAACCCTAAAACTTTCTAA
* * *
60106309 AAAATGCATTTTAACCCTAAAACTTT-TCCA
1 AAATTACATTTTAACCCTAAAACTTTCT-AA
* **
60106339 AAATTATATTTTAACCCCGAAACTTTCTAA
1 AAATTACATTTTAACCCTAAAACTTTCTAA
* *
60106369 AAATTACATTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTAACCCTAAAACTTTCTAA
* * *
60106399 AAATTACATTTTGACTCTAAAACTTT-TCCA
1 AAATTACATTTTAACCCTAAAACTTTCT-AA
* * * * * *
60106429 AAATTATATTTTGACCTTAAATCTTTTTGA
1 AAATTACATTTTAACCCTAAAACTTTCTAA
*
60106459 AAATTACATTTTAACCCTAAAACTTT-TCCA
1 AAATTACATTTTAACCCTAAAACTTTCT-AA
60106489 AAATTACATTTTAACCCTAAAACTTTCCT-A
1 AAATTACATTTTAACCCTAAAACTTT-CTAA
* *
60106519 AAATTACATTTTAACCATAAAACTTTGCCAA
1 AAATTACATTTTAACCCTAAAACTTT-CTAA
*
60106550 AATTTACCATTTTA
1 AAATTA-CATTTTA
60106564 TTCCTTGAAC
Statistics
Matches: 213, Mismatches: 33, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
29 3 0.01
30 189 0.89
31 13 0.06
32 8 0.04
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (30 bp):
AAATTACATTTTAACCCTAAAACTTTCTAA
Found at i:60106379 original size:60 final size:59
Alignment explanation
Indices: 60106273--60106590 Score: 246
Period size: 60 Copynumber: 5.3 Consensus size: 59
60106263 CCTTAAGTTG
* * * * *
60106273 TCCAGAAATTATATTTTTGACCCCAAAAC-CTTCTAAAAAATGCATTTTAACCCTAAAACTTT
1 TCCA-AAATTACA-TTTTAACCCCAAAACTTTTC-AAAAATTACATTTTAACCCTAAAAC-TT
* * * *
60106335 TCCAAAATTATATTTTAACCCCGAAAC-TTTCTAAAAATTACATTTTGACCCCAAAACTT
1 TCCAAAATTACATTTTAACCCCAAAACTTTTC-AAAAATTACATTTTAACCCTAAAACTT
* * * * * * * * *
60106394 TCTAAAAATTACATTTTGACTCTAAAACTTTTCCAAAATTATATTTTGACCTTAAATCTTT
1 TC-CAAAATTACATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAAC-TT
** * *
60106455 TTGAAAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTT
1 TCCAAAATTACATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTT
** * * ** **
60106514 TCCTAAAATTACATTTTAACCATAAAACTTTGCCAAAATTTACCATTTTATTCCTTGAACTT
1 TCC-AAAATTACATTTTAACCCCAAAACTTT-TCAAAAATTA-CATTTTAACCCTAAAACTT
*
60106576 TCC-AAATTCCATTTT
1 TCCAAAATTACATTTT
60106591 TAGCCTCGAT
Statistics
Matches: 213, Mismatches: 37, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
59 7 0.03
60 162 0.76
61 22 0.10
62 22 0.10
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.38
Consensus pattern (59 bp):
TCCAAAATTACATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTT
Found at i:60106432 original size:90 final size:91
Alignment explanation
Indices: 60106278--60106534 Score: 324
Period size: 90 Copynumber: 2.8 Consensus size: 91
60106268 AGTTGTCCAG
* * * *
60106278 AAATTATATTTTTGACCCCAAAACCTTCTAAAAAATGCATTTTAACCCTAAAACTTTTCCAAAAT
1 AAATTACA-TTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCAAAAT
60106343 TATATTTTAACCCCGAAA-CTTTCTAA
65 TATATTTTAACCCCGAAATCTTTCTAA
* *
60106369 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACTCTAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCAAAATT
* ** * *
60106434 ATATTTTGA-CCTTAAATCTTTTTGA
66 ATATTTTAACCCCGAAATCTTTCTAA
* * *
60106459 AAATTACATTTTAACCCTAAAACTTT-TCCAAAATTACATTTTAACCCTAAAAC-TTTCCTAAAA
1 AAATTACATTTTGACCCCAAAACTTTCT-AAAAATTACATTTTAACCCTAAAACTTTTCC-AAAA
*
60106522 TTACATTTTAACC
64 TTATATTTTAACC
60106535 ATAAAACTTT
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
89 11 0.08
90 125 0.87
91 8 0.06
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.38
Consensus pattern (91 bp):
AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCAAAATT
ATATTTTAACCCCGAAATCTTTCTAA
Found at i:60106552 original size:90 final size:89
Alignment explanation
Indices: 60106278--60106563 Score: 306
Period size: 90 Copynumber: 3.1 Consensus size: 89
60106268 AGTTGTCCAG
* * * * *
60106278 AAATTATATTTTTGACCCCAAAACCTTCTAAAAAATGCATTTTAACCCTAAAACTTTTCCAAAAT
1 AAATTACA-TTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCAAAAT
***
60106343 TATATTTTAACCCCGAAACTTTCTAA
65 TATATTTTAACCATAAAACTTTC-AA
* * *
60106369 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACTCTAAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCAAAATT
* * * **
60106434 ATATTTTGACCTTAAATCTTTTTGA
66 ATATTTTAACCATAAAAC-TTTCAA
* *
60106459 AAATTACATTTTAACCCTAAAACTTT-TCCAAAATTACATTTTAACCCTAAAAC-TTTCCTAAAA
1 AAATTACATTTTAACCCCAAAACTTTCT-AAAAATTACATTTTAACCCTAAAACTTTTCC-AAAA
*
60106522 TTACATTTTAACCATAAAACTTTGCCAA
64 TTATATTTTAACCATAAAACTTT--CAA
*
60106550 AATTTACCATTTTA
1 AAATTA-CATTTTA
60106564 TTCCTTGAAC
Statistics
Matches: 164, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
89 9 0.05
90 132 0.80
91 16 0.10
92 7 0.04
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (89 bp):
AAATTACATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCCAAAATT
ATATTTTAACCATAAAACTTTCAA
Found at i:60110072 original size:4 final size:4
Alignment explanation
Indices: 60110065--60110093 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
60110055 CTTTCTTTTG
60110065 CATT CATT CATT CATT CATT CATT CATT C
1 CATT CATT CATT CATT CATT CATT CATT C
60110094 GCATCAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:60110669 original size:21 final size:22
Alignment explanation
Indices: 60110644--60110685 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
60110634 TAGAGGTATC
60110644 CAAATAGATGGAAGA-AAGGTA
1 CAAATAGATGGAAGACAAGGTA
* *
60110665 CAAATGGTTGGAAGACAAGGT
1 CAAATAGATGGAAGACAAGGT
60110686 TAGAGCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.45, C:0.07, G:0.31, T:0.17
Consensus pattern (22 bp):
CAAATAGATGGAAGACAAGGTA
Found at i:60115043 original size:12 final size:12
Alignment explanation
Indices: 60115026--60115050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60115016 CTTTTGATAA
60115026 GATGTGTCTTGG
1 GATGTGTCTTGG
60115038 GATGTGTCTTGG
1 GATGTGTCTTGG
60115050 G
1 G
60115051 TCAACATGAC
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:0.08, C:0.08, G:0.44, T:0.40
Consensus pattern (12 bp):
GATGTGTCTTGG
Found at i:60118184 original size:68 final size:67
Alignment explanation
Indices: 60118073--60118469 Score: 600
Period size: 68 Copynumber: 5.9 Consensus size: 67
60118063 ATTTCCAATC
*
60118073 CCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC
1 CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC
60118138 AT
66 AT
* *
60118140 CCTCTTGAAGTTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGT
1 CC-CTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGT
*
60118205 CTT
65 CAT
*
60118208 CCCCTTGAAATTGAAGTAGAGTGGA-AACACGTCTTTATCTCTTAAATTGAAGTAAGAGCAACGT
1 -CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGT
*
60118272 CTT
65 CAT
60118275 CCCTTGAAATTGAAGTAGAGTGGA-AACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC
1 CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC
60118339 AT
66 AT
* * *
60118341 CCCTTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATCGAAGTAAGAGTAACAT
1 CCC-TTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGT
60118406 CAT
65 CAT
* * * *
60118409 CCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGA
1 CC-CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTAT--CTCTGAAATTGAAGTAAGA
60118470 ATAAGATGAA
Statistics
Matches: 305, Mismatches: 17, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
66 67 0.22
67 63 0.21
68 139 0.46
69 18 0.06
71 18 0.06
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (67 bp):
CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC
AT
Found at i:60118419 original size:201 final size:206
Alignment explanation
Indices: 60117995--60118469 Score: 667
Period size: 201 Copynumber: 2.3 Consensus size: 206
60117985 ATCATTTCCA
* *
60117995 ATCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGCAAAG
1 ATCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAAG
*
60118060 ATCATTTCCAATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAG
66 ATC--TT---ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
* * *
60118125 TAAGAGCAACGTCATCCTCTTGAAGTTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTG
126 TAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATCG
*
60118190 AAGTAAGAGCAACGTC
191 AAGTAAGAGCAACATC
* * * *
60118206 TTCCCCTTGAAATTGAAGTAGAGTGGA-AACACGTCTTTATCTCTTAAATTGAAGTAAGAGCAAC
1 AT-CCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAA
60118270 G-TC-T-T-CCCTTGAAATTGAAGTAGAGTGGA-AACACGTCTTTATCTCTGAAATTGAAGTAAG
65 GATCTTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAG
60118330 AGCAACGTCATCC-CTTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATCGAAG
130 AGCAACGTCATCCTC-TTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATCGAAG
*
60118394 TAAGAGTAACATC
194 TAAGAGCAACATC
* * *
60118407 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGA
1 ATCC-CTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTAT--CTCTGAAATTGAAGTAAGA
60118470 ATAAGATGAA
Statistics
Matches: 239, Mismatches: 18, Indels: 20
0.86 0.06 0.07
Matches are distributed among these distances:
200 3 0.01
201 118 0.49
202 28 0.12
203 11 0.05
205 18 0.08
207 1 0.00
210 2 0.01
211 34 0.14
212 24 0.10
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (206 bp):
ATCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAAG
ATCTTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGA
GCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATCGAAGTA
AGAGCAACATC
Found at i:60118465 original size:40 final size:41
Alignment explanation
Indices: 60118409--60118551 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 41
60118399 GTAACATCAT
60118409 CCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTC
1 CCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTC
* * * ***
60118450 CCTC-TGAAATTGAAGT-AAGAATAAGAT--GAAGCACTAACATC
1 CCTCTTGAAATTGAAGTAAAG-CT-GGATAACAAGC-CT-TTGTC
60118491 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTC
1 --CCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTC
*
60118534 CCTC-TCAAATTGAAGTAA
1 CCTCTTGAAATTGAAGTAA
60118552 GAATAAGATG
Statistics
Matches: 79, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
39 7 0.09
40 28 0.35
41 13 0.16
43 9 0.11
44 15 0.19
45 7 0.09
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (41 bp):
CCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTC
Found at i:60118544 original size:84 final size:84
Alignment explanation
Indices: 60118400--60118576 Score: 336
Period size: 84 Copynumber: 2.1 Consensus size: 84
60118390 GAAGTAAGAG
*
60118400 TAACATCATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAG
1 TAACATCATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCCTCTCAAATTGAAG
60118465 TAAGAATAAGATGAAGCAC
66 TAAGAATAAGATGAAGCAC
60118484 TAACATCATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCCTCTCAAATTGAAG
1 TAACATCATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCCTCTCAAATTGAAG
60118549 TAAGAATAAGATGAAGCAC
66 TAAGAATAAGATGAAGCAC
*
60118568 TGACATCAT
1 TAACATCAT
60118577 TTTCGTCCCT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (84 bp):
TAACATCATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCCTCTCAAATTGAAG
TAAGAATAAGATGAAGCAC
Found at i:60118907 original size:6 final size:6
Alignment explanation
Indices: 60118883--60118974 Score: 70
Period size: 6 Copynumber: 15.8 Consensus size: 6
60118873 TTTTTTAATA
* * *
60118883 TTAATT TTAAAT TT-TAT TTAGAT TTAAAT TT--AT CTTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT
* *
60118929 TTATTTAT TTAAAT TT-ACT TTAAAT TTAAAT TT-AAT TT-AAT TTAAA
1 TTA--AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
60118975 ATAATATTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.03
5 20 0.29
6 41 0.59
7 2 0.03
8 5 0.07
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (6 bp):
TTAAAT
Found at i:60118908 original size:17 final size:15
Alignment explanation
Indices: 60118883--60118974 Score: 105
Period size: 17 Copynumber: 5.7 Consensus size: 15
60118873 TTTTTTAATA
60118883 TTAATTTTAAATTTTAT
1 TTAA-TTTAAA-TTTAT
60118900 TTAGATTTAAATTTAT
1 TTA-ATTTAAATTTAT
60118916 CTTAAATTTAAATTTAT
1 -TT-AATTTAAATTTAT
60118933 TT-ATTTAAATTTACT
1 TTAATTTAAATTTA-T
60118948 TTAAATTTAAATTTAAT
1 TT-AATTTAAATTT-AT
60118965 TTAATTTAAA
1 TTAATTTAAA
60118975 ATAATATTAA
Statistics
Matches: 68, Mismatches: 0, Indels: 15
0.82 0.00 0.18
Matches are distributed among these distances:
14 11 0.16
15 3 0.04
16 15 0.22
17 36 0.53
18 3 0.04
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (15 bp):
TTAATTTAAATTTAT
Found at i:60118965 original size:11 final size:11
Alignment explanation
Indices: 60118876--60118974 Score: 75
Period size: 11 Copynumber: 9.0 Consensus size: 11
60118866 TTGATTTTTT
*
60118876 TTTAATATTAAT
1 TTTAAT-TTAAA
*
60118888 TTTAAATTT-TA
1 TTT-AATTTAAA
60118899 TTTAGATTTAAA
1 TTTA-ATTTAAA
60118911 TTT-ATCTTAAA
1 TTTAAT-TTAAA
60118922 TTTAAATTT--A
1 TTT-AATTTAAA
60118932 TTT-ATTTAAA
1 TTTAATTTAAA
*
60118942 TTTACTTTAAA
1 TTTAATTTAAA
60118953 TTTAAATTT-AA
1 TTT-AATTTAAA
60118964 TTTAATTTAAA
1 TTTAATTTAAA
60118975 ATAATATTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
8 4 0.06
10 16 0.23
11 31 0.44
12 15 0.21
13 5 0.07
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:60119725 original size:16 final size:15
Alignment explanation
Indices: 60119690--60119788 Score: 71
Period size: 16 Copynumber: 6.7 Consensus size: 15
60119680 CATAAATATC
* *
60119690 ATTAATAAAAT-ATT
1 ATTAATAATATAATA
60119704 ATTAATAATCATAATA
1 ATTAATAAT-ATAATA
*
60119720 ATTAATAATTGTAATA
1 ATTAATAA-TATAATA
* * * *
60119736 AATATTTATGATTATA
1 ATTAATAAT-ATAATA
60119752 ATTAAT-AT-TAATA
1 ATTAATAATATAATA
60119765 ATTAATAATATAA-A
1 ATTAATAATATAATA
*
60119779 AATAATAATA
1 ATTAATAATA
60119789 AACAAATATG
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
13 10 0.15
14 20 0.30
15 8 0.12
16 28 0.42
17 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTAATAATATAATA
Found at i:60119736 original size:19 final size:19
Alignment explanation
Indices: 60119714--60119774 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
60119704 ATTAATAATC
*
60119714 ATAATAATTAATAATTGTA
1 ATAATAATTAATAATTATA
* *
60119733 ATAA-ATATTTATGATTATA
1 ATAATA-ATTAATAATTATA
60119752 ATTAAT-ATTAATAATTAATA
1 A-TAATAATTAATAATT-ATA
60119772 ATA
1 ATA
60119775 TAAAAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.03
19 25 0.76
20 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAATAATTAATAATTATA
Found at i:60120382 original size:13 final size:13
Alignment explanation
Indices: 60120364--60120388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60120354 TGGGGGATTT
60120364 GAGAGAAAAAAAA
1 GAGAGAAAAAAAA
60120377 GAGAGAAAAAAA
1 GAGAGAAAAAAA
60120389 TAGTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAGAGAAAAAAAA
Found at i:60120923 original size:30 final size:30
Alignment explanation
Indices: 60120873--60121096 Score: 213
Period size: 30 Copynumber: 7.4 Consensus size: 30
60120863 AGTTGTTCAG
* **
60120873 AAATTATATTTTTGACCCCAAAACTTTTTAA
1 AAATTACA-TTTTGACCCCAAAACTTTCCAA
* *
60120904 AAATTGCATTTTAACCCCAAAACTTTTCC-A
1 AAATTACATTTTGACCCCAAAAC-TTTCCAA
* ** *
60120934 AAATTATATTTTGACCTTAAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTCCAA
* * *
60120964 AAATTATATTTTGACCCCGAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTCCAA
60120994 AAATTACATTTTGA-CCCAAAACTTTTCC-A
1 AAATTACATTTTGACCCCAAAAC-TTTCCAA
* * *
60121023 AAATTACACTTTAACCCCTAAAA-TTTCCCA
1 AAATTACATTTTGACCCC-AAAACTTTCCAA
*
60121053 AAATTACATTTTAACCCCAAAACTTTGCCAA
1 AAATTACATTTTGACCCCAAAACTTT-CCAA
*
60121084 AATTTACCATTTT
1 AAATTA-CATTTT
60121097 ATTCCCCGAA
Statistics
Matches: 162, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
29 33 0.20
30 102 0.63
31 21 0.13
32 6 0.04
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTCCAA
Found at i:60121070 original size:89 final size:90
Alignment explanation
Indices: 60120873--60121097 Score: 274
Period size: 89 Copynumber: 2.5 Consensus size: 90
60120863 AGTTGTTCAG
* *
60120873 AAATTATATTTTTGACCCCAAAACTTTTTAAAAATTGCATTTTAACCCCAAAACTTTTCCAAAAT
1 AAATTATA-TTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCCAAAACTTTTCCAAAAT
* * * * *
60120938 TATATTTTGACCTTAAAACTTTCTAA
65 TACACTTTAACCCTAAAACTTTCCAA
* *
60120964 AAATTATATTTTGACCCCGAAACTTTCTAAAAATTACATTTTGA-CCCAAAACTTTTCCAAAATT
1 AAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCCAAAACTTTTCCAAAATT
*
60121028 ACACTTTAACCCCTAAAA-TTTCCCA
66 ACACTTTAA-CCCTAAAACTTTCCAA
* * * *
60121053 AAATTACATTTTAACCCCAAAACTTTGCCAAAATTTACCATTTTA
1 AAATTATATTTTGACCCCAAAACTTT-CTAAAAATTA-CATTTTA
60121098 TTCCCCGAAC
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
89 54 0.47
90 47 0.41
91 14 0.12
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (90 bp):
AAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCCAAAACTTTTCCAAAATT
ACACTTTAACCCTAAAACTTTCCAA
Found at i:60124428 original size:30 final size:30
Alignment explanation
Indices: 60124371--60124428 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
60124361 TTTAACAACT
*
60124371 ATTTTCATTTTAGTCACTCAGTTTTAATAA
1 ATTTTCATTTTAGTCACTCAGTATTAATAA
* *
60124401 ATTTTTATTTTGGTCACTC-GTCATTAAT
1 ATTTTCATTTTAGTCACTCAGT-ATTAAT
60124429 TCAATGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.52
Consensus pattern (30 bp):
ATTTTCATTTTAGTCACTCAGTATTAATAA
Found at i:60128193 original size:17 final size:17
Alignment explanation
Indices: 60128168--60128202 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
60128158 GTTTTTTTAT
60128168 TAAAATAATTAAAAAAA
1 TAAAATAATTAAAAAAA
* *
60128185 TAAATTAATTACAAAAA
1 TAAAATAATTAAAAAAA
60128202 T
1 T
60128203 GAGATAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATAATTAAAAAAA
Found at i:60128788 original size:30 final size:31
Alignment explanation
Indices: 60128754--60128827 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
60128744 CATTTAACAC
60128754 AACAGTCACTCAA-CTT-T-GAAAATGTGACAA
1 AACAGTCACT-AATCTTATCGAAAA-GTGACAA
*
60128784 AACAGTCACTAATGTTATCGAAAAGTGACAA
1 AACAGTCACTAATCTTATCGAAAAGTGACAA
60128815 AACAGTCACTAAT
1 AACAGTCACTAAT
60128828 TAACAGTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 2 0.05
30 12 0.30
31 21 0.52
32 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.23
Consensus pattern (31 bp):
AACAGTCACTAATCTTATCGAAAAGTGACAA
Found at i:60128957 original size:6 final size:6
Alignment explanation
Indices: 60128948--60129015 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
60128938 AAACAATAGC
* * * *
60128948 AATCAA AATC-C AATCAA AATCAA AAT--A ACTCTA AATCAAA AATGAA
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA AATC-AA AATCAA
* *
60128994 AATCAG AATCCA AATCAA AATC
1 AATCAA AATCAA AATCAA AATC
60129016 GAATAAACCC
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
4 3 0.06
5 4 0.09
6 36 0.77
7 4 0.09
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (6 bp):
AATCAA
Found at i:60129029 original size:47 final size:46
Alignment explanation
Indices: 60128948--60129080 Score: 126
Period size: 47 Copynumber: 2.8 Consensus size: 46
60128938 AAACAATAGC
* * * *
60128948 AATCAAAATCC-AATCAAAATC-AAAATAACTCTAAATCAAAAATGAA
1 AATC-AAATCCAAATCAAAATCGAATA-AACCCTAAATAAAAAATCAA
*
60128994 AATCAGAATCCAAATCAAAATCGAATAAACCCTAAATAAAAAATCAT
1 AATCA-AATCCAAATCAAAATCGAATAAACCCTAAATAAAAAATCAA
* * * * *
60129041 AATCAATATCGACATCAAATTCGAATAAACACAAAATAAA
1 AATCAA-ATCCAAATCAAAATCGAATAAACCCTAAATAAA
60129081 CCTAAATACA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.01
46 10 0.14
47 59 0.81
48 3 0.04
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.20
Consensus pattern (46 bp):
AATCAAATCCAAATCAAAATCGAATAAACCCTAAATAAAAAATCAA
Found at i:60132729 original size:58 final size:58
Alignment explanation
Indices: 60132660--60132992 Score: 228
Period size: 58 Copynumber: 5.7 Consensus size: 58
60132650 CTCGATGGAA
*
60132660 AAAATG-TAATTTCGAGA-AAATTCGGGTTAAAAATGGAATCTTGAAAAGTTTAGGGGT
1 AAAATGATAATTTTGAGATAAATTCGGGTTAAAAATGGAAT-TTGAAAAGTTTAGGGGT
* * * **
60132717 AAAATGATAATTTTTG-G-TAAATTTGGAGTTAAAAATGGGATTTGGGAAAGTTCGGGGGT
1 AAAATGATAA-TTTTGAGATAAATTCGG-GTTAAAAATGGAATTT-GAAAAGTTTAGGGGT
* * *
60132776 AAAAT-AGTAATTTT-AGATGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTT-GGGGT
1 AAAATGA-TAATTTTGAGAT-AAATTCGGGTTAAAAAT-GGAATTTGAAAAGTTTAGGGGT
* * * * *
60132834 AAAATGGTAATTTTTA-ATAAAATCAGGGTT-AAAATGGAATTTTAGGAAGTTTAGGGGT
1 AAAATGATAATTTTGAGATAAATTC-GGGTTAAAAATGGAATTTGA-AAAGTTTAGGGGT
* * * * * *
60132892 AAAATGGTAATTTTTG-G-TAAAATCGAGG-TAAAACTAGAATTTTGGAAAGTTT-GGGCAT
1 AAAATGATAA-TTTTGAGATAAATTCG-GGTTAAAAATGGAA-TTTGAAAAGTTTAGGG-GT
* *
60132950 AAAATGGTAATTTTG-GGTGAAA-TCGGGGTTAAAAATGGAATTT
1 AAAATGATAATTTTGAGAT-AAATTC-GGGTTAAAAATGGAATTT
60132993 TGGAAAGTCT
Statistics
Matches: 225, Mismatches: 26, Indels: 49
0.75 0.09 0.16
Matches are distributed among these distances:
56 6 0.03
57 32 0.14
58 99 0.44
59 76 0.34
60 12 0.05
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.33
Consensus pattern (58 bp):
AAAATGATAATTTTGAGATAAATTCGGGTTAAAAATGGAATTTGAAAAGTTTAGGGGT
Found at i:60132754 original size:59 final size:57
Alignment explanation
Indices: 60132677--60133025 Score: 346
Period size: 59 Copynumber: 6.0 Consensus size: 57
60132667 AATTTCGAGA
* * *
60132677 AAATTCGGGTTAAAAATGGAATCTTGAAAAGTTTAGGGGTAAAATGATAATTTTTGGT-
1 AAATT-GGGTTAAAAATGGAATTTTGGAAAGTTT-GGGGTAAAATGGTAATTTTTGGTG
* * * * * *
60132735 AAATTTGGAGTTAAAAATGGGATTTGGGAAAGTTCGGGGGTAAAATAGTAATTTTAGATG
1 AAA-TTGG-GTTAAAAATGGAATTTTGGAAAGTT-TGGGGTAAAATGGTAATTTTTGGTG
* ** *
60132795 AAATTGGGGTTAAAAATGGGATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTAATA
1 AAATT-GGGTTAAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGGTG
* *
60132853 AAATCAGGGTT-AAAATGGAATTTTAGG-AAGTTTAGGGGTAAAATGGTAATTTTTGGTA
1 AAAT-TGGGTTAAAAATGGAATTTT-GGAAAGTTT-GGGGTAAAATGGTAATTTTTGGTG
* * * * *
60132911 AAATCGAGG-TAAAACTAGAATTTTGGAAAGTTTGGGCATAAAATGGTAATTTTGGGTG
1 AAATTG-GGTTAAAAATGGAATTTTGGAAAGTTTGGG-GTAAAATGGTAATTTTTGGTG
* * *
60132969 AAATCGGGGTTAAAAATGGAATTTTGGAAAGTCTGGAGGTAAAACGGTAATTTTTGG
1 AAAT-TGGGTTAAAAATGGAATTTTGGAAAGTTTGG-GGTAAAATGGTAATTTTTGG
60133026 AATTTTCATG
Statistics
Matches: 244, Mismatches: 32, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
57 25 0.10
58 105 0.43
59 108 0.44
60 6 0.02
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (57 bp):
AAATTGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGGTG
Found at i:60132830 original size:29 final size:29
Alignment explanation
Indices: 60132683--60133000 Score: 130
Period size: 29 Copynumber: 10.9 Consensus size: 29
60132673 GAGAAAATTC
* *
60132683 GGGTTAAAAATGGAATCTTGAAAAGTTTAG
1 GGGTTAAAAATGGAATTTTGGAAAGTTT-G
*
60132713 GGG-T-AAAATGATAATTTTTGGTAAA-TTTG
1 GGGTTAAAAATG-GAA-TTTTGG-AAAGTTTG
* * * *
60132742 GAGTTAAAAATGGGATTTGGGAAAGTTCG
1 GGGTTAAAAATGGAATTTTGGAAAGTTTG
* *
60132771 GGGGT-AAAATAGTAATTTTAGATGAAA--TTG
1 GGGTTAAAAAT-GGAATTTT-G--GAAAGTTTG
*
60132801 GGGTTAAAAATGGGATTTTGGAAAGTTTG
1 GGGTTAAAAATGGAATTTTGGAAAGTTTG
** ** **
60132830 GGG-T-AAAATGGTAATTTTTAATAAAATCA
1 GGGTTAAAAATGG-AATTTTGGA-AAGTTTG
60132859 GGGTT-AAAATGGAATTTTAGG-AAGTTTAG
1 GGGTTAAAAATGGAATTTT-GGAAAGTTT-G
* *
60132888 GGG-T-AAAATGGTAATTTTTGGTAAA-ATCG
1 GGGTTAAAAATGG-AA-TTTTGG-AAAGTTTG
* * *
60132917 AGG-TAAAACTAGAATTTTGGAAAGTTTG
1 GGGTTAAAAATGGAATTTTGGAAAGTTTG
** *
60132945 GGCAT-AAAATGGTAATTTTGGGTGAAA--TCG
1 GGGTTAAAAATGG-AATTTT--G-GAAAGTTTG
60132975 GGGTTAAAAATGGAATTTTGGAAAGT
1 GGGTTAAAAATGGAATTTTGGAAAGT
60133001 CTGGAGGTAA
Statistics
Matches: 212, Mismatches: 44, Indels: 65
0.66 0.14 0.20
Matches are distributed among these distances:
27 18 0.08
28 47 0.22
29 61 0.29
30 54 0.25
31 24 0.11
32 8 0.04
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (29 bp):
GGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:60134832 original size:27 final size:27
Alignment explanation
Indices: 60134798--60134867 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
60134788 CATTGGGCCT
*
60134798 ATTTGGGCCATTGTAATTGAG-CCTTCA
1 ATTTGGGCCTTTGTAATTGAGCCCTT-A
*
60134825 ATTTGGGCCTTTGTAATTGGGCCCTTA
1 ATTTGGGCCTTTGTAATTGAGCCCTTA
60134852 ATTTGGGCCTTTGTAA
1 ATTTGGGCCTTTGTAA
60134868 ATGAACTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (27 bp):
ATTTGGGCCTTTGTAATTGAGCCCTTA
Found at i:60134955 original size:17 final size:18
Alignment explanation
Indices: 60134933--60134973 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
60134923 TTTCAAATAT
*
60134933 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
60134950 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
60134968 TTTAAA
1 TTTAAA
60134974 CCTAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:60135870 original size:200 final size:200
Alignment explanation
Indices: 60135515--60136505 Score: 1547
Period size: 200 Copynumber: 5.0 Consensus size: 200
60135505 GAGCGTTGAG
* * ** * * * * *
60135515 TATCTCATCAGGAAGATGACTGCCTCTTTTATTTTAATTTGCTTCTCTAGATCCCCTCAAGAAGA
1 TATCTCATCAGAAAGATAACTGCCTCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGA
* * * * *
60135580 CAAATTTGGTCCACTTCTCTATATCTCATCAGGAAACTAACCATGTTATTGTTTCGACCTACTTC
66 CGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTC
* *
60135645 TCAGTATCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGATTTGGTATTCTT
131 TCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCTT
60135710 CTCTA
196 CTCTA
* * * * *
60135715 TGTCTCATTAGAAAGATGACTGCCTCGCTTGTTTTAATTCGCTTCTCTGGATCTCCTCAAGAAGA
1 TATCTCATCAGAAAGATAACTGCCTCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGA
* *
60135780 CGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTTCTTC
66 CGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTC
* *
60135845 TCAGTGTCTCACCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTTAGCGTTGAGTTGGTATTCTT
131 TCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCTT
*
60135910 CTCTG
196 CTCTA
* * *
60135915 TATCTCATCAGAAAGATAACCGCATCACTTGTTTTAATTCACTTCTCTGGATCTCCTCAGGAAGA
1 TATCTCATCAGAAAGATAACTGCCTCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGA
* * * *
60135980 TGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTTCTGC
66 CGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTC
60136045 TCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCTT
131 TCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCTT
*
60136110 CTCTG
196 CTCTA
*
60136115 TATCTCATCAGAAAGATAACTGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGA
1 TATCTCATCAGAAAGATAACTGCCTCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGA
* *
60136180 TGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATGTTATTGTTTCGACCTGCTTC
66 CGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTC
*
60136245 TCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCTT
131 TCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCTT
60136310 CTCTA
196 CTCTA
* *
60136315 TATCTCATCAGGAAGATAA-T-CACATCACTTGTTTTAATTCACTTCTCTGGATCTCCTCAGGAA
1 TATCTCATCAGAAAGATAACTGC-C-TCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAA
*
60136378 GACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGGT
64 GACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCT
* *
60136443 TTTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCG-TGTTGAGCGTTGAGTTGGTAT
129 TCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCT-TTGAGCGTTGAGTTGGTAT
60136506 ATGTATCTCA
Statistics
Matches: 739, Mismatches: 49, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
198 1 0.00
199 2 0.00
200 736 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (200 bp):
TATCTCATCAGAAAGATAACTGCCTCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGA
CGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTC
TCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCTT
CTCTA
Found at i:60136496 original size:600 final size:585
Alignment explanation
Indices: 60135315--60136505 Score: 1690
Period size: 600 Copynumber: 2.0 Consensus size: 585
60135305 TTCATTGACC
* * * * **
60135315 TGGTCTTCTTCTCTGTGTCTGATCAGGAAGATAACCACAATCATCTGTTTTAATTTGCTTCTCTG
1 TGGTATTCTTCTCTGTATCTCATCAGAAAGATAACCACAATCATCTGTTTTAATTCACTTCTCTG
* ** * * *
60135380 GATCTCCTCAGGAAGACGAATTTGGTCTACTTCTCTGTGTCTTATTAGGAAGCTAACCTTTTTAT
66 GATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTAT
* *
60135445 TGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGTTCGAAGATTTGCTCGCGTTGAGCG
131 TGCTTCGACCTGCTGCTCAGTATCTCATCAAGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGCG
* * * ** *
60135510 TTGAGTATCTCATCAGGAAGATGACTGCCTCTTTTATTTTAATTTGCTTCTCTAGATCCCCTCAA
196 TTGAGTATCTCATCAGAAAGATAACTGCATCACTTATTTTAATTCGCTTCTCTAGATCCCCTCAA
60135575 GAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAACTAACCATGTTATTGTTTCGACCT
261 GAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAACTAACCATGTTATTGTTTCGACCT
* *
60135640 ACTTCTCAGTATCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGATTTGGTA
326 ACTTCTCAGTATCTCATCAGGAAGCTAGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTA
* * * * *
60135705 TTCTTCTCTATGTCTCATTAGAAAGATGACTGCCTCGCTTGTTTTAATTCGCTTCTCTGGATCTC
391 TTCTTCTCTATATCTCATCAGAAAGATGAATGCCTCACTTGTTTTAATTCACTTCTCTGGATCTC
60135770 CTCAAGAAGACGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTATTGTTTC
456 CTCAAGAAGACGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTATTGTTTC
* * *
60135835 GACCTTCTTCTCAGTGTCTCACCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTTAGCGTTGAGT
521 GACCTGCTTCTCAGTGTCTCACCAGGAAGCTGGGTACGAAGATTGGCTCGCTTTGAGCGTTGAGT
*
60135900 TGGTATTCTTCTCTGTATCTCATCAGAAAGATAACCGC-ATCA-CTTGTTTTAATTCACTTCTCT
1 TGGTATTCTTCTCTGTATCTCATCAGAAAGATAACCACAATCATC-TGTTTTAATTCACTTCTCT
*
60135963 GGATCTCCTCAGGAAGATGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTA
65 GGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTA
* * * * *
60136028 TTGTTTCGACCTTCTGCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGC
130 TTGCTTCGACCTGCTGCTCAGTATCTCATCAAGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGC
*
60136093 GTTGAGTTGGTATTCTTCTCTGTATCTCATCAGAAAGATAACTGCATCACTTGTTTTAATTCGCT
195 -----GTT-G-A---------GTATCTCATCAGAAAGATAACTGCATCACTTATTTTAATTCGCT
* * * ** * *
60136158 TCTCTGGATCTCCTCAGGAAGATGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCA
244 TCTCTAGATCCCCTCAAGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAACTAACCA
* *
60136223 TGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTTGCTCGCTT
309 TGTTATTGTTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTAGGTACGAAGATTTGCTCGCTT
*
60136288 TGAGCGTTGAGTTGGTATTCTTCTCTATATCTCATCAGGAAGAT-AAT-CACATCACTTGTTTTA
374 TGAGCGTTGAGTTGGTATTCTTCTCTATATCTCATCAGAAAGATGAATGC-C-TCACTTGTTTTA
* *
60136351 ATTCACTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAG
437 ATTCACTTCTCTGGATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAG
* * *
60136416 CTAACCATTTTATTGTTTCGACCTGGTTTTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGG
502 CTAACCATTTTATTGTTTCGACCTGCTTCTCAGTGTCTCACCAGGAAGCTGGGTACGAAGATTGG
60136481 CTCG-TGTTGAGCGTTGAGT
567 CTCGCT-TTGAGCGTTGAGT
60136500 TGGTAT
1 TGGTAT
60136506 ATGTATCTCA
Statistics
Matches: 533, Mismatches: 53, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
583 1 0.00
584 137 0.26
585 33 0.06
589 3 0.01
590 1 0.00
591 1 0.00
598 1 0.00
599 4 0.01
600 352 0.66
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (585 bp):
TGGTATTCTTCTCTGTATCTCATCAGAAAGATAACCACAATCATCTGTTTTAATTCACTTCTCTG
GATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTAT
TGCTTCGACCTGCTGCTCAGTATCTCATCAAGAAGCTGGGTACGAAGATTTGCTCGCGTTGAGCG
TTGAGTATCTCATCAGAAAGATAACTGCATCACTTATTTTAATTCGCTTCTCTAGATCCCCTCAA
GAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAACTAACCATGTTATTGTTTCGACCT
ACTTCTCAGTATCTCATCAGGAAGCTAGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTA
TTCTTCTCTATATCTCATCAGAAAGATGAATGCCTCACTTGTTTTAATTCACTTCTCTGGATCTC
CTCAAGAAGACGAATTTGGTCCACTTCTCTGCATCTCATCAGGAAGCTAACCATTTTATTGTTTC
GACCTGCTTCTCAGTGTCTCACCAGGAAGCTGGGTACGAAGATTGGCTCGCTTTGAGCGTTGAGT
Found at i:60148578 original size:30 final size:29
Alignment explanation
Indices: 60148490--60148582 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
60148480 AATTTGAGGT
*
60148490 TAAAAATG-GAATCTTGGAAAGTTTAGGGG
1 TAAAAATGAG-ATTTTGGAAAGTTTAGGGG
* * *
60148519 T-AAAATGATAATTTTTGGTGAAG--TCGGGG
1 TAAAAATGA-GA-TTTTGG-AAAGTTTAGGGG
60148548 TTAAAAATGAGATTTTGGAAAGTTTAGGGG
1 -TAAAAATGAGATTTTGGAAAGTTTAGGGG
60148578 TAAAA
1 TAAAA
60148583 TGGTAATGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
28 9 0.18
29 18 0.37
30 12 0.24
31 10 0.20
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (29 bp):
TAAAAATGAGATTTTGGAAAGTTTAGGGG
Found at i:60148594 original size:28 final size:28
Alignment explanation
Indices: 60148563--60148645 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
60148553 AATGAGATTT
60148563 TGGAAAGTTTAGGGGTAAAATGGTAATG
1 TGGAAAGTTTAGGGGTAAAATGGTAATG
* ** * *
60148591 TGGATGAAATCGA-GGTTAAAATGG-AATT
1 TGGA--AAGTTTAGGGGTAAAATGGTAATG
* *
60148619 TGGGAAGTTTGGGGGTAAAATGGTAAT
1 TGGAAAGTTTAGGGGTAAAATGGTAAT
60148646 TTTTAGTGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
26 3 0.08
27 10 0.25
28 13 0.32
29 10 0.25
30 4 0.10
ACGTcount: A:0.35, C:0.01, G:0.35, T:0.29
Consensus pattern (28 bp):
TGGAAAGTTTAGGGGTAAAATGGTAATG
Found at i:60148729 original size:58 final size:57
Alignment explanation
Indices: 60148483--60148765 Score: 295
Period size: 59 Copynumber: 4.9 Consensus size: 57
60148473 TTAAGAAAAT
* * * *
60148483 TTGAGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGTAAAATGATAATTTTTGGTGAAG
1 TTGAGGTT-AAAATGGAATTTTGGAAAGTTTA-GGGTAAAATGGTAATTTTGGGTGAAA
* * * *
60148542 TCGGGGTTAAAAAT-GAGATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TGTGGATGAAA
1 TTGAGGTT-AAAATGGA-ATTTTGGAAAGTTTA-GGGTAAAATGGTAATTTTGGGTGAAA
* * * **
60148600 TCGAGGTTAAAATGGAA-TTTGGGAAGTTTGGGGGTAAAATGGTAATTTTTAGTGAAA
1 TTGAGGTTAAAATGGAATTTTGGAAAGTTT-AGGGTAAAATGGTAATTTTGGGTGAAA
* *
60148657 TTGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGTTAAAATGGTAATTTTGGGTGAAA
1 TTGAGGT-TAAAATGGAATTTTGGAAAGTTT-AGGGTAAAATGGTAATTTTGGGTGAAA
* *
60148716 TT-AGGGTTAAAATGGAATTTTGGAAAGTTTAAGGGTAAAACGATAATTTT
1 TTGA-GGTTAAAATGGAATTTTGGAAAGTTT-AGGGTAAAATGGTAATTTT
60148766 TAAAAGTTTC
Statistics
Matches: 190, Mismatches: 27, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
56 25 0.13
57 19 0.10
58 66 0.35
59 80 0.42
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (57 bp):
TTGAGGTTAAAATGGAATTTTGGAAAGTTTAGGGTAAAATGGTAATTTTGGGTGAAA
Found at i:60148763 original size:29 final size:29
Alignment explanation
Indices: 60148739--60148803 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
60148729 GGAATTTTGG
*
60148739 AAAGTTT-AAGGGTAAAACGATAATTTTTA
1 AAAGTTTCAAGGGTAAAACG-TAATTTTCA
* * *
60148768 AAAGTTTCAAGGTTAAAATGTAATTTTCT
1 AAAGTTTCAAGGGTAAAACGTAATTTTCA
60148797 AAAGTTT
1 AAAGTTT
60148804 TGGGATCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (29 bp):
AAAGTTTCAAGGGTAAAACGTAATTTTCA
Found at i:60148782 original size:58 final size:56
Alignment explanation
Indices: 60148478--60148803 Score: 250
Period size: 58 Copynumber: 5.6 Consensus size: 56
60148468 TAATTTTAAG
* * *
60148478 AAAATTTGAGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGTAAAATGATAATTTTT
1 AAAATTCGAGGTT-AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
** * * **
60148535 GGTGAAGTCGGGGTTAAAAAT-GAGATTTTGGAAAGTTTAGGGGTAAAATGGTAATGTGGAT
1 --AAAATTCGAGGTT-AAAATGGA-ATTTTGGAAAGTTTAGGGGTAAAATGGTAAT-T-TTT
* * *
60148596 GAAA-TCGAGGTTAAAATGGAA-TTTGGGAAGTTTGGGGGTAAAATGGTAATTTTT
1 AAAATTCGAGGTTAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
* *
60148650 AGTGAAATT-GAGGTCAAAAATGGAATTTTGGAAAGTTT-GAGGTTAAAATGGTAATTTTGGGT
1 A---AAATTCGAGGT-TAAAATGGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTT---T
* * * * *
60148712 GAAATTAG-GGTTAAAATGGAATTTTGGAAAGTTTAAGGGTAAAACGATAATTTTT
1 AAAATTCGAGGTTAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
* * **
60148767 AAAAGTTTCAAGGTTAAAATGTAATTTTCTAAAGTTT
1 AAAA--TTCGAGGTTAAAATGGAATTTTGGAAAGTTT
60148804 TGGGATCACA
Statistics
Matches: 216, Mismatches: 32, Indels: 39
0.75 0.11 0.14
Matches are distributed among these distances:
54 1 0.00
55 5 0.02
56 27 0.12
57 16 0.07
58 82 0.38
59 81 0.38
60 2 0.01
61 1 0.00
62 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (56 bp):
AAAATTCGAGGTTAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
Found at i:60150640 original size:14 final size:13
Alignment explanation
Indices: 60150621--60150688 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
60150611 TTGGGCCTAT
60150621 TTGGGCCATTGTAA
1 TTGGGCC-TTGTAA
*
60150635 TTGGGCCTT-CAA
1 TTGGGCCTTGTAA
60150647 TTTGGGCCTTTGTAA
1 -TTGGGCC-TTGTAA
* *
60150662 CTGGGCCCT-TAA
1 TTGGGCCTTGTAA
60150674 TTTGGGCCTTTGTAA
1 -TTGGGCC-TTGTAA
60150689 ATGGACTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 5 0.12
13 16 0.38
14 16 0.38
15 5 0.12
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (13 bp):
TTGGGCCTTGTAA
Found at i:60150654 original size:27 final size:27
Alignment explanation
Indices: 60150619--60150688 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
60150609 CATTGGGCCT
* *
60150619 ATTTGGGCCATTGTAATTGGG-CCTTCA
1 ATTTGGGCCTTTGTAACTGGGCCCTT-A
60150646 ATTTGGGCCTTTGTAACTGGGCCCTTA
1 ATTTGGGCCTTTGTAACTGGGCCCTTA
60150673 ATTTGGGCCTTTGTAA
1 ATTTGGGCCTTTGTAA
60150689 ATGGACTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (27 bp):
ATTTGGGCCTTTGTAACTGGGCCCTTA
Found at i:60150786 original size:18 final size:17
Alignment explanation
Indices: 60150754--60150794 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 17
60150744 TTTCAAATAT
60150754 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
60150771 TTTAAATTTAATAATAAA
1 TTTAAATTTAA-AATAAA
60150789 TTTAAA
1 TTTAAA
60150795 CCTAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:60151043 original size:23 final size:23
Alignment explanation
Indices: 60150998--60151044 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
60150988 TTATCGGCTC
* * *
60150998 AAACTTGATTTTTGAAGTAAAAA
1 AAACTTGATTTCTAAAATAAAAA
*
60151021 AAACTTGATTTCTAAAATGAAAA
1 AAACTTGATTTCTAAAATAAAAA
60151044 A
1 A
60151045 TAAATATTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (23 bp):
AAACTTGATTTCTAAAATAAAAA
Found at i:60153378 original size:39 final size:39
Alignment explanation
Indices: 60153293--60153427 Score: 126
Period size: 39 Copynumber: 3.5 Consensus size: 39
60153283 TATCAGTCTG
* * * * * * *
60153293 GTAGTGTTTACAGTCTCACTACCTACTCAGTATAGCATT
1 GTAGTGTTTACAGTGTCACCATCAATTCAGTATTGTATT
* * *
60153332 ATGGTGTTTGCAGTGTCACCATCAATTCAGTATTGTATT
1 GTAGTGTTTACAGTGTCACCATCAATTCAGTATTGTATT
* * ** *
60153371 GTAGTGTTTACAATTTCACTGTCAATTTAGTATTGTATT
1 GTAGTGTTTACAGTGTCACCATCAATTCAGTATTGTATT
*
60153410 GTAGTGTTTCCAGTGTCA
1 GTAGTGTTTACAGTGTCA
60153428 TTGCCAGTTC
Statistics
Matches: 75, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (39 bp):
GTAGTGTTTACAGTGTCACCATCAATTCAGTATTGTATT
Found at i:60153695 original size:73 final size:74
Alignment explanation
Indices: 60153571--60153765 Score: 293
Period size: 74 Copynumber: 2.6 Consensus size: 74
60153561 CGTGTGTGTC
* * * *
60153571 ACACGGTCTGACACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTTTCTGATTTC-AGAAAAT
1 ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTTTCTGATGTCAAAAAAAT
60153635 AGAATATCT
66 AGAATATCT
* * *
60153644 ACACAGTCTGGCACACGCCCATGTGTCCAACACATGTAACTCACTGTTTCTGATGTCAAAAAAAT
1 ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTTTCTGATGTCAAAAAAAT
60153709 AGAATATCT
66 AGAATATCT
* * *
60153718 ACACAGTCTGGCACACGCTCGTGTGTCCAGCCCGTGTAACTAACTGTT
1 ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTT
60153766 GCTAGTTTCC
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
73 51 0.47
74 57 0.53
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (74 bp):
ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTTTCTGATGTCAAAAAAAT
AGAATATCT
Found at i:60159246 original size:25 final size:25
Alignment explanation
Indices: 60159218--60159269 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
60159208 TAAATCTCAG
*
60159218 TAATTTATT-ATTTTAAAAATATAAT
1 TAATTTATTAAATTTAAAAATA-AAT
*
60159243 TAATTTTTTAAATTTAAAAATAAAT
1 TAATTTATTAAATTTAAAAATAAAT
60159268 TA
1 TA
60159270 TAGTTAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATTTATTAAATTTAAAAATAAAT
Found at i:60159571 original size:131 final size:131
Alignment explanation
Indices: 60159433--60159692 Score: 439
Period size: 131 Copynumber: 2.0 Consensus size: 131
60159423 CTACAATTCA
60159433 TTTTTTTCATTAAATTGCTGCGAACATCATGAATTTAAGAACCAAAAGCAAAACAATTTTCTTCT
1 TTTTTTTCATTAAATTGCTGCGAACATCATGAATTTAAGAACCAAAAGCAAAACAATTTTCTTCT
* *
60159498 TTGATCTCCGACATTGACCATCAAATTGATTTGGATCTAAGATATGTTCTTCTGCTCATCAATGA
66 CTGATCTCCGACATTGACCATCAAATTGATTTGGATCTAAGATATGTTCTTCTACTCATCAATGA
60159563 G
131 G
** * * * *
60159564 TTTTTTTCATTAAATTGCTTTGAACGTCATGAATTTACGAACCAAAATCTAAACAATTTTCTTCT
1 TTTTTTTCATTAAATTGCTGCGAACATCATGAATTTAAGAACCAAAAGCAAAACAATTTTCTTCT
*
60159629 CTGATCTCCGACATTGACCATCAAATTGATTTGGATCTAAGGTATGTTCTTCTACTCATCAATG
66 CTGATCTCCGACATTGACCATCAAATTGATTTGGATCTAAGATATGTTCTTCTACTCATCAATG
60159693 GGCACTGAGC
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 120 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (131 bp):
TTTTTTTCATTAAATTGCTGCGAACATCATGAATTTAAGAACCAAAAGCAAAACAATTTTCTTCT
CTGATCTCCGACATTGACCATCAAATTGATTTGGATCTAAGATATGTTCTTCTACTCATCAATGA
G
Found at i:60162538 original size:11 final size:11
Alignment explanation
Indices: 60162522--60162600 Score: 62
Period size: 11 Copynumber: 7.6 Consensus size: 11
60162512 AATTAATCAT
60162522 ATTAATATTAA
1 ATTAATATTAA
60162533 ATTAATA--AA
1 ATTAATATTAA
*
60162542 A-TATTATTAA
1 ATTAATATTAA
*
60162552 GATAAATATTAA
1 -ATTAATATTAA
*
60162564 ATTAA-ATTTA
1 ATTAATATTAA
* *
60162574 A-T-ATCTTAT
1 ATTAATATTAA
60162583 ATTAATATTAA
1 ATTAATATTAA
60162594 ATTAATA
1 ATTAATA
60162601 AAATACTATC
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
8 5 0.10
9 7 0.14
10 8 0.16
11 24 0.47
12 7 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:60172969 original size:19 final size:20
Alignment explanation
Indices: 60172927--60172978 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
60172917 TAAAATATTT
*
60172927 TTAT-TTATT-AATTTATAG
1 TTATATTATTAAATTTATAA
60172945 TT-TATTATTAAATTTA-AA
1 TTATATTATTAAATTTATAA
60172963 TTATA-T-TTAAATTTAT
1 TTATATTATTAAATTTAT
60172979 TTTATACTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.34
18 11 0.38
19 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATATTATTAAATTTATAA
Found at i:60173305 original size:15 final size:15
Alignment explanation
Indices: 60173286--60173321 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
60173276 TATACTACAT
*
60173286 AACCCAATCCGACCC
1 AACCCAATCCAACCC
*
60173301 GACCCAATCCAACCC
1 AACCCAATCCAACCC
60173316 AACCCA
1 AACCCA
60173322 TTTTTCTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.53, G:0.06, T:0.06
Consensus pattern (15 bp):
AACCCAATCCAACCC
Found at i:60174284 original size:35 final size:35
Alignment explanation
Indices: 60174245--60174313 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
60174235 ATTTAGGAAT
*
60174245 GAATATGAATATTTTCTTTATATTTACATTCAATA
1 GAATATGAATATTTTCTTGATATTTACATTCAATA
60174280 GAATATGAATATTTTCTTGATATTTACATTCAAT
1 GAATATGAATATTTTCTTGATATTTACATTCAAT
60174314 TATCTTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (35 bp):
GAATATGAATATTTTCTTGATATTTACATTCAATA
Found at i:60174832 original size:15 final size:15
Alignment explanation
Indices: 60174812--60174843 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60174802 ACTTACACAC
60174812 TTAGTCCAATTTTAT
1 TTAGTCCAATTTTAT
*
60174827 TTAGTCCAGTTTTAT
1 TTAGTCCAATTTTAT
60174842 TT
1 TT
60174844 TTTTTCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.56
Consensus pattern (15 bp):
TTAGTCCAATTTTAT
Found at i:60175327 original size:28 final size:27
Alignment explanation
Indices: 60175296--60175358 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
60175286 TTTTGGTTTT
*
60175296 TTTTTTGCTGTTTTGATTTTTTTTACTG
1 TTTTTTGCT-TTTTGATTGTTTTTACTG
* *
60175324 TTTTGGTGCTTTTTTATTGTTTTTACTG
1 TTTT-TTGCTTTTTGATTGTTTTTACTG
60175352 TTATTTT
1 TT-TTTT
60175359 TGTTGCTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.08, C:0.06, G:0.14, T:0.71
Consensus pattern (27 bp):
TTTTTTGCTTTTTGATTGTTTTTACTG
Found at i:60175336 original size:19 final size:19
Alignment explanation
Indices: 60175264--60175346 Score: 96
Period size: 18 Copynumber: 4.3 Consensus size: 19
60175254 ATTATATTGT
60175264 TGTTTTGGTGTTTTTTTCAC
1 TGTTTTGGTGTTTTTTT-AC
* *
60175284 TGTTTTGGTTTTTTTTTTGC
1 TGTTTTGG-TGTTTTTTTAC
*
60175304 TGTTTTGAT-TTTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
* *
60175322 TGTTTTGGTGCTTTTTTAT
1 TGTTTTGGTGTTTTTTTAC
60175341 TGTTTT
1 TGTTTT
60175347 TACTGTTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
18 16 0.30
19 14 0.26
20 16 0.30
21 8 0.15
ACGTcount: A:0.05, C:0.06, G:0.18, T:0.71
Consensus pattern (19 bp):
TGTTTTGGTGTTTTTTTAC
Found at i:60175337 original size:38 final size:40
Alignment explanation
Indices: 60175264--60175338 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 40
60175254 ATTATATTGT
* **
60175264 TGTTTTGGTGTTTTTTTCACTGTTTTGGTTTTTTTTTTGC
1 TGTTTTGATGTTTTTTTCACTGTTTTGGTGCTTTTTTTGC
60175304 TGTTTTGAT-TTTTTTT-ACTGTTTTGGTGCTTTTTT
1 TGTTTTGATGTTTTTTTCACTGTTTTGGTGCTTTTTT
60175339 ATTGTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 17 0.53
39 7 0.22
40 8 0.25
ACGTcount: A:0.04, C:0.07, G:0.19, T:0.71
Consensus pattern (40 bp):
TGTTTTGATGTTTTTTTCACTGTTTTGGTGCTTTTTTTGC
Found at i:60176138 original size:27 final size:25
Alignment explanation
Indices: 60176080--60176132 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
60176070 AAATTTTACA
60176080 AATATTATATAATTTTTTAATAATAT
1 AATA-TATATAATTTTTTAATAATAT
60176106 AATATATATAATATATTTTAATTAATA
1 AATATATATAAT-T-TTTTAA-TAATA
60176133 CATATAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 8 0.33
26 5 0.21
27 6 0.25
28 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATATATATAATTTTTTAATAATAT
Found at i:60178042 original size:21 final size:21
Alignment explanation
Indices: 60178016--60178056 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60178006 TGACAGCGAG
60178016 TCACAC-GGTCGTGTATCTCAA
1 TCACACAGGT-GTGTATCTCAA
*
60178037 TCACACAGGTGTGTCTCTCA
1 TCACACAGGTGTGTATCTCA
60178057 GCCACACGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
TCACACAGGTGTGTATCTCAA
Found at i:60181382 original size:41 final size:41
Alignment explanation
Indices: 60181324--60181445 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 41
60181314 TTTTCAACGT
* *
60181324 GTTTTTGTCTCAGTCAAGGAAAAATGCTCCTACGTAGAAGCA
1 GTTTTTGTCTCATTCAAGGAAAAGTGCTCC-ACGTAGAAGCA
60181366 -TTTTTGTCTCATTCAAGG-AAAGTGCTTCCACGTAG-AG-A
1 GTTTTTGTCTCATTCAAGGAAAAGTGC-TCCACGTAGAAGCA
* *
60181404 TGTTTTTGTCTCATTCAAGGAAGAGTGCTCCCACGTGGAAGC
1 -GTTTTTGTCTCATTCAAGGAAAAGTGCT-CCACGTAGAAGC
60181446 GCTTTTTTAC
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
38 1 0.01
39 2 0.03
40 31 0.45
41 33 0.48
42 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
GTTTTTGTCTCATTCAAGGAAAAGTGCTCCACGTAGAAGCA
Found at i:60181410 original size:40 final size:39
Alignment explanation
Indices: 60181323--60181439 Score: 139
Period size: 40 Copynumber: 2.9 Consensus size: 39
60181313 TTTTTCAACG
* *
60181323 TGTTTTTGTCTCAGTCAAGGAAAAATGC-TCCTACGTAGAA
1 TGTTTTTGTCTCATTCAAGG-AAAGTGCTTCC-ACGTAGAA
60181363 -GCATTTTTGTCTCATTCAAGGAAAGTGCTTCCACGTAGAGA
1 TG--TTTTTGTCTCATTCAAGGAAAGTGCTTCCACGTAGA-A
*
60181404 TGTTTTTGTCTCATTCAAGGAAGAGTGCTCCCACGT
1 TGTTTTTGTCTCATTCAAGGAA-AGTGCTTCCACGT
60181440 GGAAGCGCTT
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
39 1 0.01
40 33 0.49
41 33 0.49
42 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (39 bp):
TGTTTTTGTCTCATTCAAGGAAAGTGCTTCCACGTAGAA
Found at i:60182326 original size:3 final size:3
Alignment explanation
Indices: 60182320--60182355 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
60182310 AGAAGAAGAA
* *
60182320 GAT GAT GAT GAT GAT GAT GAT GGT GAT AAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
60182356 TCTAGAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:60185864 original size:19 final size:20
Alignment explanation
Indices: 60185842--60185886 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
60185832 TTTTTTCTAA
* *
60185842 TTTTTAATAAATTTTGA-AT
1 TTTTTAATAAAATTTAATAT
*
60185861 TTTTTATTAAAATTTAATAT
1 TTTTTAATAAAATTTAATAT
60185881 TTTTTA
1 TTTTTA
60185887 TTGATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTAATAAAATTTAATAT
Found at i:60186176 original size:90 final size:89
Alignment explanation
Indices: 60186016--60186290 Score: 338
Period size: 90 Copynumber: 3.1 Consensus size: 89
60186006 GTCAAATGAT
* ** * * * *
60186016 TTTTTTGATGTA-TTTGACGGTTCAAGTACCCAATTGAGTGTAAAAACAATCGAGGGCTTAATTG
1 TTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAGCAAGGGCTTAATTG
60186080 CTTTTTTTTTAAAAAGTTTGAGGGC
66 C-TTTTTTTTAAAAAGTTTGAGGGC
*
60186105 TTTTTTGATGCATTTTGAAAGTTCAAGTACTCAATTGAGTGCAAAATAAAAGCAAGGGCTTAATT
1 TTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAA-AAAAGCAAGGGCTTAATT
* *
60186170 GCTTTTTTTGAAATAGTTTGAGGGC
65 GCTTTTTTTTAAAAAGTTTGAGGGC
* * * *
60186195 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAGTGAGTGCAAAAAAAAG-TAGAGGATTAATT
1 TTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAGCAAG-GGCTTAATT
** *
60186259 ATTATTTTTTTGAAAAAATTTGAGGGC
65 GCT-TTTTTTT-AAAAAGTTTGAGGGC
60186286 TTTTT
1 TTTTT
60186291 ACACCCTTAA
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
88 2 0.01
89 25 0.16
90 99 0.62
91 34 0.21
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (89 bp):
TTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAGCAAGGGCTTAATTG
CTTTTTTTTAAAAAGTTTGAGGGC
Found at i:60186513 original size:31 final size:31
Alignment explanation
Indices: 60186478--60186542 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
60186468 TGGCCAAGTT
*
60186478 AGGCTCAAAACTTGACAATTATTT-CTCATTG
1 AGGCT-AAAACTTGACAATTATTTCCACATTG
** *
60186509 AGGCTTGAATTTGACAATTATTTCCACATTG
1 AGGCTAAAACTTGACAATTATTTCCACATTG
60186540 AGG
1 AGG
60186543 GTCTGAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (31 bp):
AGGCTAAAACTTGACAATTATTTCCACATTG
Found at i:60186523 original size:30 final size:32
Alignment explanation
Indices: 60186489--60186552 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 32
60186479 GGCTCAAAAC
*
60186489 TTGACAATTATTT-CTCATTGAGGCT-TGAAT
1 TTGACAATTATTTCCACATTGAGGCTCTGAAT
*
60186519 TTGACAATTATTTCCACATTGAGGGTCTGAAT
1 TTGACAATTATTTCCACATTGAGGCTCTGAAT
60186551 TT
1 TT
60186553 TAGGATTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.43
31 10 0.33
32 7 0.23
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (32 bp):
TTGACAATTATTTCCACATTGAGGCTCTGAAT
Found at i:60187859 original size:19 final size:19
Alignment explanation
Indices: 60187835--60187872 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60187825 TGATTTTCTG
60187835 TGCCACCGTTCTCATTGGT
1 TGCCACCGTTCTCATTGGT
60187854 TGCCACCGTTCTCATTGGT
1 TGCCACCGTTCTCATTGGT
60187873 GGCACAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.32, G:0.21, T:0.37
Consensus pattern (19 bp):
TGCCACCGTTCTCATTGGT
Found at i:60188781 original size:17 final size:17
Alignment explanation
Indices: 60188759--60188847 Score: 90
Period size: 17 Copynumber: 5.2 Consensus size: 17
60188749 TTATTTTTTT
* *
60188759 AATTTACTTTAAGTTTG
1 AATTTACTTTAAATTTA
60188776 AATTTA-TTCTAAATTTA
1 AATTTACTT-TAAATTTA
* * * *
60188793 AATTCATTTTGAGTTTA
1 AATTTACTTTAAATTTA
60188810 AATTTACTTTAAATTTA
1 AATTTACTTTAAATTTA
* *
60188827 AATTTATTTTAAATTAA
1 AATTTACTTTAAATTTA
60188844 AATT
1 AATT
60188848 AATTAAAAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
16 2 0.03
17 55 0.93
18 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTACTTTAAATTTA
Found at i:60188814 original size:34 final size:34
Alignment explanation
Indices: 60188770--60188836 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
60188760 ATTTACTTTA
*
60188770 AGTTTGAATTTA-TTCTAAATTTAAATTCATTTTG
1 AGTTTAAATTTACTT-TAAATTTAAATTCATTTTG
*
60188804 AGTTTAAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTAAATTTACTTTAAATTTAAATTCATTTT
60188837 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (34 bp):
AGTTTAAATTTACTTTAAATTTAAATTCATTTTG
Found at i:60189593 original size:10 final size:10
Alignment explanation
Indices: 60189559--60189605 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
60189549 ATAATGACCC
*
60189559 TAATAATAA-
1 TAATATTAAT
60189568 TAATATT-AT
1 TAATATTAAT
*
60189577 TATTATTAAT
1 TAATATTAAT
60189587 TAATATTAAT
1 TAATATTAAT
*
60189597 AAATATTAA
1 TAATATTAA
60189606 ATAAAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 1 0.03
9 12 0.38
10 19 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATATTAAT
Found at i:60190799 original size:28 final size:28
Alignment explanation
Indices: 60190714--60191060 Score: 228
Period size: 29 Copynumber: 12.0 Consensus size: 28
60190704 CCAAGAAGGT
* *
60190714 CCCT-GAACTGTCCAAAAATCATATTTTGA
1 CCCTCGAACT-TCCAAAAATTACATTTT-A
* * * *
60190743 CCCTCAAAGTTTTCAAAAATTATCGTTTTA
1 CCCTCGAA-CTTCCAAAAATTA-CATTTTA
*
60190773 CCCTCGAACTTCCAAAAATTTCATTTTGA
1 CCCTCGAACTTCCAAAAATTACATTTT-A
60190802 CCC-CGAACTTTCCAAAAATTACAATTTTA
1 CCCTCGAAC-TTCCAAAAATTAC-ATTTTA
**
60190831 CCCTTAAAC-TCCAAAAATTACATTTTTA
1 CCCTCGAACTTCCAAAAATTACA-TTTTA
*
60190859 TCC-CGAAACTTCCAAAAATTACATTTTTA
1 CCCTCG-AACTTCCAAAAATTACA-TTTTA
* *
60190888 ACCTCGAAATTTCCAAAAATTACATTTTA
1 CCCTCG-AACTTCCAAAAATTACATTTTA
* *
60190917 CCCCCAAACTTCCAAAAATTACCA-TTTA
1 CCCTCGAACTTCCAAAAATTA-CATTTTA
*
60190945 CCCCCGAA-TGTCCAAAAATT-CTATTTTTGA
1 CCCTCGAACT-TCCAAAAATTAC-A-TTTT-A
* *
60190975 -CCTCGAAATTTCCAAAAAATTATCGTTTTA
1 CCCTCG-AACTTCC-AAAAATTA-CATTTTA
*
60191005 CCC-CTGAAGTGTCC-AAAATTACAATTTTA
1 CCCTC-GAACT-TCCAAAAATTAC-ATTTTA
* * * *
60191034 CCCCCGAGCATCCAAAAATCACATTTT
1 CCCTCGAACTTCCAAAAATTACATTTT
60191061 TTTTTGACTC
Statistics
Matches: 258, Mismatches: 32, Indels: 57
0.74 0.09 0.16
Matches are distributed among these distances:
26 1 0.00
27 3 0.01
28 76 0.29
29 96 0.37
30 58 0.22
31 23 0.09
33 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.33
Consensus pattern (28 bp):
CCCTCGAACTTCCAAAAATTACATTTTA
Found at i:60190869 original size:86 final size:86
Alignment explanation
Indices: 60190724--60191061 Score: 294
Period size: 86 Copynumber: 3.9 Consensus size: 86
60190714 CCCTGAACTG
* * * * * ** *
60190724 TCCAAAAATCATATTTTGACCCTCAAAGTTTTCAAAAATTATCGTTTTACCCTCGAACTTCCAAA
1 TCCAAAAATTACATTTT-ACCCCCAAA-CTTCCAAAAATTA-CCATTTACCCCCGAACTTCCAAA
* *
60190789 AATTTCA-TTTTGACCCCGAACTT
63 AATTTCATTTTTGACCTCGAAATT
** *
60190812 TCCAAAAATTACAATTTTACCCTTAAAC-TCCAAAAATTA-CATTTTTA-TCCCGAAACTTCCAA
1 TCCAAAAATTAC-ATTTTACCCCCAAACTTCCAAAAATTACCA--TTTACCCCCG-AACTTCCAA
* *
60190874 AAATTACATTTTTAACCTCGAAATT
62 AAATTTCATTTTTGACCTCGAAATT
60190899 TCCAAAAATTACATTTTACCCCCAAACTTCCAAAAATTACCATTTACCCCCGAA-TGTCCAAAAA
1 TCCAAAAATTACATTTTACCCCCAAACTTCCAAAAATTACCATTTACCCCCGAACT-TCCAAAAA
60190963 -TTCTATTTTTGACCTCGAAATT
65 TTTC-ATTTTTGACCTCGAAATT
* ** * * * *
60190985 TCCAAAAAATTATCGTTTTACCCCTGAAGTGTCC-AAAATTACAATTTTACCCCCGAGCATCCAA
1 TCC-AAAAATTA-CATTTTACCCCCAAACT-TCCAAAAATTACCA-TTTACCCCCGAACTTCCAA
**
60191049 AAATCACATTTTT
62 AAATTTCATTTTT
60191062 TTTTGACTCC
Statistics
Matches: 207, Mismatches: 27, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
85 6 0.03
86 77 0.37
87 48 0.23
88 42 0.20
89 33 0.16
90 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (86 bp):
TCCAAAAATTACATTTTACCCCCAAACTTCCAAAAATTACCATTTACCCCCGAACTTCCAAAAAT
TTCATTTTTGACCTCGAAATT
Found at i:60204044 original size:2 final size:2
Alignment explanation
Indices: 60204031--60204060 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
60204021 TCTATGTATC
*
60204031 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60204061 TCGTATCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:60204242 original size:20 final size:20
Alignment explanation
Indices: 60204217--60204278 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
60204207 AAATTTTGAT
60204217 TATTTTAAAATATATATATA
1 TATTTTAAAATATATATATA
60204237 TATTTTATAAAT-TAT-TACTCA
1 TATTTTA-AAATATATATA-T-A
*
60204258 TATTTATAAAAAATATATATA
1 TATTT-TAAAATATATATATA
60204279 GTTTTTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 14 0.40
22 6 0.17
23 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTTTAAAATATATATATA
Found at i:60207050 original size:18 final size:17
Alignment explanation
Indices: 60207022--60207115 Score: 82
Period size: 17 Copynumber: 5.4 Consensus size: 17
60207012 TAAACCCATT
60207022 TTAAGATTTATTTTAAAGA
1 TTAA-ATTTATTTTAAA-A
* *
60207041 TTAAATTTA-TTTGAAT
1 TTAAATTTATTTTAAAA
**
60207057 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
60207074 TTAAATTTGTTTTAAAA
1 TTAAATTTATTTTAAAA
* * *
60207091 TTTAGATTTAATTTAAAT
1 -TTAAATTTATTTTAAAA
60207109 TTAAATT
1 TTAAATT
60207116 CATATTTAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
16 9 0.15
17 30 0.49
18 18 0.30
19 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:60207063 original size:6 final size:6
Alignment explanation
Indices: 60207041--60207130 Score: 55
Period size: 6 Copynumber: 15.7 Consensus size: 6
60207031 ATTTTAAAGA
* * * **
60207041 TTAAAT TT--AT TTGAAT TTAAAT TT-ATT TTAAGT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
60207085 TTAAAAT TTAGAT TT-AAT TTAAAT TTAAAT TCATAT TTAAGT TTAA
1 TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
60207131 GACTTAATAA
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
4 4 0.06
5 11 0.17
6 45 0.71
7 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:60207093 original size:35 final size:33
Alignment explanation
Indices: 60207021--60207130 Score: 103
Period size: 35 Copynumber: 3.2 Consensus size: 33
60207011 TTAAACCCAT
* *
60207021 TTTAAGATTTATTTTAAAGATTAAATTTATTTGAA
1 TTTAA-ATTTATTTT-AAGTTTAAATTTATTTAAA
*
60207056 TTTAAATTTATTTTAAGTTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGTTTAAATTT-ATTT-AAA
* * * *
60207091 TTTAGATTTAATTTAAATTTAAATTCATATTTAAG
1 TTTAAATTTATTTTAAGTTTAAATT--TATTTAAA
60207126 TTTAA
1 TTTAA
60207131 GACTTAATAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
33 11 0.18
34 12 0.19
35 35 0.56
36 3 0.05
37 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (33 bp):
TTTAAATTTATTTTAAGTTTAAATTTATTTAAA
Found at i:60208782 original size:30 final size:30
Alignment explanation
Indices: 60208739--60208856 Score: 100
Period size: 30 Copynumber: 3.9 Consensus size: 30
60208729 TAAACTGTCC
* *
60208739 AAAAATTATATTTTAAACCCTAAAATTTTCT
1 AAAAATTACATTTT-ACCCCTAAAATTTTCT
*
60208770 AAAAA-TACATTTTGACCCCTAAACTTATT-T
1 AAAAATTACATTTT-ACCCCTAAAATT-TTCT
* ** *
60208800 -AAAATTATATTTT-GGCCTCAAAACTTTCT
1 AAAAATTACATTTTACCCCT-AAAATTTTCT
60208829 AAAAATTACATTTTTACCCCTAAAATTT
1 AAAAATTACA-TTTTACCCCTAAAATTT
60208857 CCAAAATTCT
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
28 5 0.07
29 9 0.13
30 33 0.49
31 17 0.25
32 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAAATTACATTTTACCCCTAAAATTTTCT
Found at i:60208907 original size:58 final size:58
Alignment explanation
Indices: 60208830--60209169 Score: 258
Period size: 58 Copynumber: 5.8 Consensus size: 58
60208820 AAACTTTCTA
* * *
60208830 AAAATTA-CATTTTTACCCCTAAAATTTCCAAAATTCTATTTTTGACTTC-GATTTCACC
1 AAAATTACCA-TTTTACCCCTAAACTTTCCAAAATTCCATTTTTGAC-CCAGATTTCACC
60208888 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTA-ATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCC-AGATTTCACC
* *
60208946 AAATTACCATTTTACCATTTTACCCTCGAAA-TTTCCAAAATTCCATTTTT-ACCCTGATTTCAC
1 -AA--A--A--TTACCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTTGACCCAGATTTCAC
*
60209009 TA
58 -C
* * * *
60209011 AAAATTACCATTTTA-CCCTATACTTTCTAAAATTCTA-TTTTGACCCCAAAACTTTCTA--
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGA-CCC-AGA-TTTC-ACC
* * * *
60209069 AAAATT-GCATTTTTGCCCC-AAACTTTCC-AAATTCCA-TTTTAACCTC-GATCTCACC
1 AAAATTACCA-TTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACC-CAGATTTCACC
* *
60209124 AAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTG
1 --AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTG
60209170 CCCTCGAAAG
Statistics
Matches: 228, Mismatches: 24, Indels: 58
0.74 0.08 0.19
Matches are distributed among these distances:
53 1 0.00
54 3 0.01
55 1 0.00
56 9 0.04
57 45 0.20
58 91 0.40
59 15 0.07
60 9 0.04
61 2 0.01
62 1 0.00
63 1 0.00
64 13 0.06
65 33 0.14
66 4 0.02
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCAGATTTCACC
Found at i:60208918 original size:29 final size:28
Alignment explanation
Indices: 60208886--60209167 Score: 109
Period size: 29 Copynumber: 9.5 Consensus size: 28
60208876 TTCGATTTCA
60208886 CCAAAATTACCATTTTACCCCTAAACTTT
1 CCAAAATT-CCATTTTACCCCTAAACTTT
60208915 CCAAAATTCCATTTTTGA-CCCT-AA-TTT
1 CCAAAATTCCA-TTTT-ACCCCTAAACTTT
*
60208942 CACCAAATTACCATTTTACCATTTTACCCTCGAAA-TTT
1 --CC-AA--A--A--TT-CCATTTTACCC-CTAAACTTT
*
60208980 CCAAAATTCCATTTTTA-CCCT-GA-TTT
1 CCAAAATTCCA-TTTTACCCCTAAACTTT
*
60209006 CACTAAAAATTACCATTTTA-CCCTATACTTT
1 C-C--AAAATT-CCATTTTACCCCTAAACTTT
* * *
60209037 CTAAAATTCTATTTTGACCCCAAAACTTT
1 CCAAAATTCCATTTT-ACCCCTAAACTTT
* * *
60209066 CTAAAAATTGCATTTTTGCCCC-AAACTTT
1 C-CAAAATTCCA-TTTTACCCCTAAACTTT
* * * **
60209095 CC-AAATTCCATTTTA-ACCTCGATCTCA
1 CCAAAATTCCATTTTACCCCT-AAACTTT
*
60209122 CCAAAAAATTACCATTTTACCCCCAAACTTT
1 CC--AAAATT-CCATTTTACCCCTAAACTTT
*
60209153 CCAAAATTCTATTTT
1 CCAAAATTCCATTTT
60209168 TGCCCTCGAA
Statistics
Matches: 193, Mismatches: 27, Indels: 67
0.67 0.09 0.23
Matches are distributed among these distances:
25 2 0.01
26 9 0.05
27 23 0.12
28 23 0.12
29 64 0.33
30 23 0.12
31 22 0.11
32 3 0.02
33 1 0.01
34 1 0.01
35 3 0.02
36 10 0.05
37 4 0.02
38 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (28 bp):
CCAAAATTCCATTTTACCCCTAAACTTT
Found at i:60208949 original size:28 final size:30
Alignment explanation
Indices: 60208831--60208958 Score: 87
Period size: 29 Copynumber: 4.4 Consensus size: 30
60208821 AACTTTCTAA
*
60208831 AAATTA-CATTTTTACCCCTAAAATTTC-CA
1 AAATTACCATTTTTACCCCT-AAATTTCACC
* * **
60208860 AAATT-CTATTTTTGA--CTTCGATTTCACC
1 AAATTACCATTTTT-ACCCCTAAATTTCACC
*
60208888 AAAATTACCA-TTTTACCCCTAAACTTTC-CA
1 -AAATTACCATTTTTACCCCTAAA-TTTCACC
60208918 AAATT-CCATTTTTGA-CCCT-AATTTCACC
1 AAATTACCATTTTT-ACCCCTAAATTTCACC
60208946 AAATTACCATTTT
1 AAATTACCATTTT
60208959 ACCATTTTAC
Statistics
Matches: 76, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
27 9 0.12
28 15 0.20
29 40 0.53
30 8 0.11
31 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (30 bp):
AAATTACCATTTTTACCCCTAAATTTCACC
Found at i:60208967 original size:65 final size:65
Alignment explanation
Indices: 60208892--60209027 Score: 204
Period size: 65 Copynumber: 2.1 Consensus size: 65
60208882 TTCACCAAAA
* *
60208892 TTACCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTTGACCCTAATTTCAC-CAAATTACCA
1 TTACCATTTTACCCTCGAAA-TTTCCAAAATTCCATTTTT-ACCCTAATTTCACAAAAATTACCA
60208955 TT
64 TT
*
60208957 TTACCATTTTACCCTCGAAATTTCCAAAATTCCATTTTTACCCTGATTTCACTAAAAATTACCAT
1 TTACCATTTTACCCTCGAAATTTCCAAAATTCCATTTTTACCCTAATTTCAC-AAAAATTACCAT
60209022 T
65 T
60209023 TTACC
1 TTACC
60209028 CTATACTTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
64 12 0.18
65 33 0.51
66 20 0.31
ACGTcount: A:0.31, C:0.28, G:0.02, T:0.39
Consensus pattern (65 bp):
TTACCATTTTACCCTCGAAATTTCCAAAATTCCATTTTTACCCTAATTTCACAAAAATTACCATT
Found at i:60209185 original size:58 final size:57
Alignment explanation
Indices: 60208957--60209202 Score: 175
Period size: 57 Copynumber: 4.3 Consensus size: 57
60208947 AATTACCATT
* *
60208957 TTACCATTTTACCCTCGAAA-TTTCCAAAATTCCATTTTTACCCT-G-ATTTCACTAAAAA
1 TTACCATTTTACCC-CCAAACTTTCCAAAATTCCA-TTTTACCCTCGAAATTCA--AAAAA
* * * * * *
60209015 TTACCATTTTA-CCCTATACTTTCTAAAATTCTATTTTGACCC-CAAAACTTTCTAAAAA
1 TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTT-ACCCTCGAAA--TTCAAAAAA
* ** * ** *
60209073 TT-GCATTTTTGCCCCAAACTTTCC-AAATTCCATTTTAACCTCGATCTCACCAAAAAA
1 TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTACCCTCGAAAT--TCAAAAAA
* * *
60209130 TTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTGCCCTCGAAAGTC-AAAAA
1 TTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTACCCTCGAAATTCAAAAAA
*
60209187 TTACCATTTTGCCCCC
1 TTACCATTTTACCCCC
60209203 GGATATCCAA
Statistics
Matches: 145, Mismatches: 30, Indels: 27
0.72 0.15 0.13
Matches are distributed among these distances:
55 1 0.01
56 10 0.07
57 65 0.45
58 49 0.34
59 7 0.05
60 13 0.09
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (57 bp):
TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTACCCTCGAAATTCAAAAAA
Found at i:60214215 original size:29 final size:29
Alignment explanation
Indices: 60214081--60214227 Score: 145
Period size: 30 Copynumber: 5.0 Consensus size: 29
60214071 CTAAATTATC
* *
60214081 CAAAAATTACATTTTGACACTAAAACTTT
1 CAAAAATTACATTTTGACCCCAAAACTTT
* *
60214110 CTGAAAATTACATTTTAACCCCAAAACTTTT
1 C-AAAAATTACATTTTGACCCCAAAAC-TTT
* *
60214141 CCAAAATTATATTTTGACCCCAAAA-TTT
1 CAAAAATTACATTTTGACCCCAAAACTTT
* * *
60214169 CCAAAAAATTGCATTTTTACCCCGAAACTTT
1 -C-AAAAATTACATTTTGACCCCAAAACTTT
*
60214200 CAAAAATTACCATTTT-ACCCCCAAACTT
1 CAAAAATTA-CATTTTGACCCCAAAACTT
60214228 CCCTAAATCC
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
28 3 0.03
29 20 0.20
30 68 0.69
31 7 0.07
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.33
Consensus pattern (29 bp):
CAAAAATTACATTTTGACCCCAAAACTTT
Found at i:60214215 original size:60 final size:60
Alignment explanation
Indices: 60214081--60214229 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
60214071 CTAAATTATC
* * **
60214081 CAAAAATTACATTTTGACACTAAAACTTT-CTGAAAATTACATTTTAACCCCAAAACTTTT
1 CAAAAATTACATTTTGACCCCAAAA-TTTCCAAAAAATTACATTTTAACCCCAAAACTTTT
* * * * *
60214141 CCAAAATTATATTTTGACCCCAAAATTTCCAAAAAATTGCATTTTTACCCCGAAAC-TTT
1 CAAAAATTACATTTTGACCCCAAAATTTCCAAAAAATTACATTTTAACCCCAAAACTTTT
* *
60214200 CAAAAATTACCATTTT-ACCCCCAAACTTCC
1 CAAAAATTA-CATTTTGACCCCAAAATTTCC
60214230 CTAAATCCCA
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
59 26 0.35
60 48 0.65
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (60 bp):
CAAAAATTACATTTTGACCCCAAAATTTCCAAAAAATTACATTTTAACCCCAAAACTTTT
Found at i:60214235 original size:29 final size:29
Alignment explanation
Indices: 60214183--60214293 Score: 82
Period size: 29 Copynumber: 3.8 Consensus size: 29
60214173 AAAATTGCAT
* * **
60214183 TTTTACCCCGAAACTTTCAAAAATTACCA
1 TTTTACCCCCAAACTTCCCTAAATTACCA
*
60214212 TTTTACCCCCAAACTTCCCTAAA-TCCCA
1 TTTTACCCCCAAACTTCCCTAAATTACCA
* * * * *
60214240 TTTTAAACCTC-GATTTCACTAAAGTTACCA
1 TTTT-ACCCCCAAACTTCCCTAAA-TTACCA
* *
60214270 TTTTACCCTCAAACTTCCTTAAAT
1 TTTTACCCCCAAACTTCCCTAAAT
60214294 CTCATTTTAA
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
28 17 0.27
29 29 0.47
30 16 0.26
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTACCCCCAAACTTCCCTAAATTACCA
Found at i:60214269 original size:58 final size:57
Alignment explanation
Indices: 60214202--60214337 Score: 191
Period size: 58 Copynumber: 2.4 Consensus size: 57
60214192 GAAACTTTCA
* *
60214202 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTAAACCTCGATTTCACT
1 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTT-AACCCCGATTTCACC
* * * *
60214260 AAAGTTACCATTTTACCCTCAAACTTCCTTAAATCTCATTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTAACCCCGATTTCACC
*
60214317 AAAATCTACCATTTTGCCCCC
1 AAAAT-TACCATTTTACCCCC
60214338 GGGTATCCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 17 0.25
58 51 0.75
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTAACCCCGATTTCACC
Found at i:60215290 original size:13 final size:13
Alignment explanation
Indices: 60215272--60215347 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 13
60215262 TAATTACTAA
60215272 TTAAATATTGATT
1 TTAAATATTGATT
* *
60215285 TTAAATATAGATAAAG
1 TTAAATATTGAT---T
60215301 TTAAACTA--GATT
1 TTAAA-TATTGATT
**
60215313 TTAAATATTTTTT
1 TTAAATATTGATT
60215326 TTAAAATATTGATT
1 TT-AAATATTGATT
60215340 TTAAATAT
1 TTAAATAT
60215348 AGATAAAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
11 2 0.04
12 5 0.10
13 21 0.43
14 11 0.22
15 3 0.06
16 5 0.10
17 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (13 bp):
TTAAATATTGATT
Found at i:60219838 original size:28 final size:28
Alignment explanation
Indices: 60219747--60219962 Score: 130
Period size: 28 Copynumber: 7.5 Consensus size: 28
60219737 ATTGGGGTCA
* * *
60219747 AAAATGAAATTTTGGAAAGTTCGAGGGT
1 AAAATGGAATTTTGGAAAATTCGGGGGT
* * * *
60219775 AAAATGGTAATTTTTTGATAAAATCGAGGTT
1 AAAATGG-AA-TTTTGGA-AAATTCGGGGGT
60219806 AAAATGGAATTTTGGAAAATTCGGGGGT
1 AAAATGGAATTTTGGAAAATTCGGGGGT
* * * *
60219834 GAAATGACAATTTTGGTGAAA-TCGGGGGC
1 AAAATG-GAATTTTGG-AAAATTCGGGGGT
* * *
60219863 AAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGAAAATTCGGGGGT
** **
60219891 -AAATGGTAATTTTGGTGAATTCGGTGGCA
1 AAAATGG-AATTTTGGAAAATTCGG-GGGT
* * * *
60219920 AAAATGAAATTTTGTAGAACTTGGGGGGTT
1 AAAATGGAATTTTGGA-AAATTCGGGGG-T
*
60219950 AAAATGTAATTTT
1 AAAATGGAATTTT
60219963 TAAAAGTTTT
Statistics
Matches: 141, Mismatches: 36, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
27 8 0.06
28 45 0.32
29 39 0.28
30 33 0.23
31 16 0.11
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAATTCGGGGGT
Found at i:60219873 original size:57 final size:57
Alignment explanation
Indices: 60219712--60219933 Score: 214
Period size: 57 Copynumber: 3.8 Consensus size: 57
60219702 TTGGATACCC
* * *
60219712 GGGGTAAAATAGTAATTTTGATGAAATTGGGGTCAAAAATGAAATTTTGGAAAGTTCG
1 GGGGT-AAATGGTAATTTTGATGAAATCGGGGGCAAAAATGAAATTTTGGAAAGTTCG
* * * ** * *
60219770 AGGGTAAAATGGTAATTTTTTGATAAAATC-GAGGTTAAAATGGAATTTTGGAAAATTCG
1 GGGGT-AAATGGTAA--TTTTGATGAAATCGGGGGCAAAAATGAAATTTTGGAAAGTTCG
** * * * *
60219829 GGGGTGAAATGACAATTTTGGTGAAATCGGGGGC-AAAATGGAATTTTAGAAAGTTTG
1 GGGGT-AAATGGTAATTTTGATGAAATCGGGGGCAAAAATGAAATTTTGGAAAGTTCG
* * *
60219886 GGGGTAAATGGTAATTTTGGTGAATTCGGTGGCAAAAATGAAATTTTG
1 GGGGTAAATGGTAATTTTGATGAAATCGGGGGCAAAAATGAAATTTTG
60219934 TAGAACTTGG
Statistics
Matches: 133, Mismatches: 27, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
56 24 0.18
57 48 0.36
58 16 0.12
59 34 0.26
60 11 0.08
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (57 bp):
GGGGTAAATGGTAATTTTGATGAAATCGGGGGCAAAAATGAAATTTTGGAAAGTTCG
Found at i:60219944 original size:57 final size:57
Alignment explanation
Indices: 60219806--60219946 Score: 155
Period size: 56 Copynumber: 2.5 Consensus size: 57
60219796 AATCGAGGTT
*
60219806 AAAATGGAATTTTGGA-AAATTCGGGGGTGAAATGACAATTTTGGTGAAATCGGGGGC
1 AAAATGGAATTTTGTAGAAATT-GGGGGTGAAATGACAATTTTGGTGAAATCGGGGGC
** * *
60219863 AAAATGGAA-TTT-TAGAAAGTTTGGGGGT-AAATGGTAATTTTGGTGAATTCGGTGGC
1 AAAATGGAATTTTGTAGAAA--TTGGGGGTGAAATGACAATTTTGGTGAAATCGGGGGC
* *
60219919 AAAAATGAAATTTTGTAGAACTTGGGGG
1 -AAAATGGAATTTTGTAGAAATTGGGGG
60219947 GTTAAAATGT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
55 1 0.01
56 30 0.42
57 30 0.42
58 5 0.07
59 5 0.07
ACGTcount: A:0.33, C:0.05, G:0.32, T:0.30
Consensus pattern (57 bp):
AAAATGGAATTTTGTAGAAATTGGGGGTGAAATGACAATTTTGGTGAAATCGGGGGC
Found at i:60220134 original size:60 final size:60
Alignment explanation
Indices: 60219944--60220305 Score: 392
Period size: 60 Copynumber: 6.0 Consensus size: 60
60219934 TAGAACTTGG
* * * *
60219944 GGGGTTAAAATGTAATTTTTA-AAAGTTTTGAGGTTAACATATAATTTTGAAGAAGTTTA
1 GGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAGAAGTTTA
* * * * ** * *
60220003 AGGGTGAAAATGTAATTTTTAGAAAGCTTTGGGGTTAAAAATATAATTTTAAAGATGTTTG
1 GGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGG-TCAAAATATAATTTTGGAGAAGTTTA
* * * *
60220064 GGGGTCAAAATGTTATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAGAAGTTTA
1 GGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAGAAGTTTA
* * * *
60220124 GGGGTTAAAATGTAATTTTAAGAAATTTTTAGGGTCAAAATATAATTTTGGAGAAG-TTC
1 GGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAGAAGTTTA
* * * * * *
60220183 GAGGG-TCAAATGTGATTTTCA-AAATGTTGTGGGGTCAACATATAATTTTGGAAAAGTTTA
1 G-GGGTTAAAATGTAATTTTTAGAAA-GTTTTGGGGTCAAAATATAATTTTGGAGAAGTTTA
* * *
60220243 GGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAACACTATTTTTGGA-TAGTTTA
1 GGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATA-TAATTTTGGAGAAGTTTA
60220303 GGG
1 GGG
60220306 ACTTTTAGGG
Statistics
Matches: 253, Mismatches: 42, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
58 3 0.01
59 64 0.25
60 124 0.49
61 62 0.25
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.38
Consensus pattern (60 bp):
GGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAGAAGTTTA
Found at i:60220240 original size:119 final size:119
Alignment explanation
Indices: 60219945--60220282 Score: 428
Period size: 119 Copynumber: 2.8 Consensus size: 119
60219935 AGAACTTGGG
* * * *
60219945 GGGTTAAAATGTAATTTTTAAAAGTTTTGAGGTTAACATATAATTTT-GAAGAAGTTTAAGGGTG
1 GGGTCAAAATGTAATTTTTAAAAGTTTTGGGGTTAACATATAATTTTGGAA-AAGTTTAGGGGTT
* * * * *
60220009 AAAATGTAATTTTTAGAAAGCTTTGGGGTTAAAAATATAATTTTAAAGATGTTTGG
65 AAAATGTAATTTTTAGAAAGTTTTGGGG-TCAAAATATAATTTTAAAGAAGTTCGA
* * * *
60220065 GGGTCAAAATGTTATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAGAAGTTTAGGGGTT
1 GGGTCAAAATGTAATTTTTA-AAAGTTTTGGGGTTAACATATAATTTTGGAAAAGTTTAGGGGTT
* * * **
60220130 AAAATGTAATTTTAAGAAATTTTTAGGGTCAAAATATAATTTTGGAGAAGTTCGA
65 AAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTAAAGAAGTTCGA
* * * *
60220185 GGGTC-AAATGTGATTTTCAAAATGTTGTGGGGTCAACATATAATTTTGGAAAAGTTTAGGGGTT
1 GGGTCAAAATGTAATTTTTAAAA-GTTTTGGGGTTAACATATAATTTTGGAAAAGTTTAGGGGTT
60220249 AAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAA
65 AAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAA
60220283 CACTATTTTT
Statistics
Matches: 187, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
118 3 0.02
119 79 0.42
120 44 0.24
121 59 0.32
122 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (119 bp):
GGGTCAAAATGTAATTTTTAAAAGTTTTGGGGTTAACATATAATTTTGGAAAAGTTTAGGGGTTA
AAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTAAAGAAGTTCGA
Found at i:60220269 original size:30 final size:30
Alignment explanation
Indices: 60219944--60220282 Score: 211
Period size: 30 Copynumber: 11.3 Consensus size: 30
60219934 TAGAACTTGG
*
60219944 GGGGTTAAAATGTAATTTTTA-AAAGTTTT
1 GGGGTTAAAATGTAATTTTTAGAAAGTTTA
* * * *
60219973 GAGGTTAACATATAATTTTGA-AGAAGTTTA
1 GGGGTTAAAATGTAATTTTTAGA-AAGTTTA
* *
60220003 AGGGTGAAAATGTAATTTTTAGAAAGCTTT-
1 GGGGTTAAAATGTAATTTTTAGAAAG-TTTA
* *
60220033 GGGGTTAAAAATATAA-TTTTA-AAGATGTTTG
1 GGGGTT-AAAATGTAATTTTTAGAA-A-GTTTA
* *
60220064 GGGGTCAAAATGTTATTTTTAGAAAGTTTTA
1 GGGGTTAAAATGTAATTTTTAGAAAG-TTTA
* *
60220095 -GGGTTAAAATATAA-TTTTGGAGAAGTTTA
1 GGGGTTAAAATGTAATTTTTAGA-AAGTTTA
* *
60220124 GGGGTTAAAATGTAATTTTAAGAAATTTTTA
1 GGGGTTAAAATGTAATTTTTAGAAA-GTTTA
* * * *
60220155 -GGGTCAAAATATAA-TTTTGGAGAAG-TTC
1 GGGGTTAAAATGTAATTTTTAGA-AAGTTTA
* * *
60220183 GAGGG-TCAAATGTGATTTTCA-AAATGTTGT-
1 G-GGGTTAAAATGTAATTTTTAGAAA-GTT-TA
* * * *
60220213 GGGGTCAACATATAA-TTTTGGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTTAG-AAAGTTTA
*
60220243 GGGGTTAAAATGTAATTTTTAGAAAGTTTT
1 GGGGTTAAAATGTAATTTTTAGAAAGTTTA
*
60220273 GGGGTCAAAA
1 GGGGTTAAAA
60220283 CACTATTTTT
Statistics
Matches: 233, Mismatches: 51, Indels: 51
0.70 0.15 0.15
Matches are distributed among these distances:
28 4 0.02
29 50 0.21
30 132 0.57
31 45 0.19
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTTAGAAAGTTTA
Found at i:60232675 original size:60 final size:61
Alignment explanation
Indices: 60232577--60232706 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 61
60232567 TGTTCATGGG
* * * * * *
60232577 TAAATTTATTAATTTTTTTAGAATTAGAATTAAATGATAAATTTTGTAAGCATTGAAAT-T
1 TAAATTTATTAATATTTTTAGAATTAAAATTAAATGATAAAATGTGTAAACATTAAAATAT
* *
60232637 TAAATTTGTTAA-ATTTTTA-AATTTAAAATTAAATTGATAAAATGTGTAAATATTAAAATAT
1 TAAATTTATTAATATTTTTAGAA-TTAAAATTAAA-TGATAAAATGTGTAAACATTAAAATAT
60232698 TAAATTTAT
1 TAAATTTAT
60232707 CATTGGGCCA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.03
59 16 0.28
60 31 0.53
61 9 0.16
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (61 bp):
TAAATTTATTAATATTTTTAGAATTAAAATTAAATGATAAAATGTGTAAACATTAAAATAT
Found at i:60232679 original size:29 final size:28
Alignment explanation
Indices: 60232591--60232695 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 28
60232581 TTTATTAATT
*
60232591 TTTTTAGAA-TTAGAATTAAA-TGATAAA
1 TTTTTA-AATTTAAAATTAAATTGATAAA
* * *
60232618 TTTTGTAAGCATTGAAATTTAAATTTGTTAAA
1 TTTT-TAA--ATTTAAAATTAAA-TTGATAAA
60232650 TTTTTAAATTTAAAATTAAATTGATAAAA
1 TTTTTAAATTTAAAATTAAATTGAT-AAA
* *
60232679 TGTGTAAATATTAAAAT
1 TTTTTAAAT-TTAAAAT
60232696 ATTAAATTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
27 5 0.08
28 6 0.10
29 22 0.36
30 15 0.25
31 3 0.05
32 10 0.16
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.44
Consensus pattern (28 bp):
TTTTTAAATTTAAAATTAAATTGATAAA
Done.