Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 128 of 132
Found at i:39603058 original size:6 final size:6
Alignment explanation
Indices: 39603013--39603066 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
39603003 TATATATATG
* * * *
39603013 TATGTA TATATA CATATA TATATA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
39603061 TGATGT
1 T-ATGT
39603067 GTTTCAGTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 39 0.91
7 4 0.09
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (6 bp):
TATGTA
Found at i:39603061 original size:12 final size:12
Alignment explanation
Indices: 39603005--39603057 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
39602995 AAAAACTGTA
*
39603005 TATATATGTATG
1 TATATATATATG
* *
39603017 TATATATACATA
1 TATATATATATG
39603029 TATATATATATG
1 TATATATATATG
*
39603041 TATATGTATATG
1 TATATATATATG
39603053 TATAT
1 TATAT
39603058 GTATGATGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (12 bp):
TATATATATATG
Found at i:39606576 original size:50 final size:50
Alignment explanation
Indices: 39606501--39606600 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
39606491 TACTAAGTAT
39606501 GCTTTAAACTTAAAATGTATGGTTTGAATGTTATCAATGCATGTGAATAA
1 GCTTTAAACTTAAAATGTATGGTTTGAATGTTATCAATGCATGTGAATAA
39606551 GCTTTAAACTTAAAATGTATGGTTTGAATGTTATCAATGCATGTGAATAA
1 GCTTTAAACTTAAAATGTATGGTTTGAATGTTATCAATGCATGTGAATAA
39606601 AAATTGTACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (50 bp):
GCTTTAAACTTAAAATGTATGGTTTGAATGTTATCAATGCATGTGAATAA
Found at i:39608749 original size:15 final size:14
Alignment explanation
Indices: 39608703--39608751 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
39608693 TAATAATGGA
39608703 TTTAATTTATTTAT
1 TTTAATTTATTTAT
**
39608717 TTTAATTTGGTTATT
1 TTTAATTTATTTA-T
*
39608732 TTTAATTTTTTGTAT
1 TTTAATTTATT-TAT
39608747 TTTAA
1 TTTAA
39608752 AATTTTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 11 0.38
15 16 0.55
16 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTAATTTATTTAT
Found at i:39615814 original size:15 final size:16
Alignment explanation
Indices: 39615788--39615817 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39615778 GAGATGAATG
39615788 ATTAGACTTCAAATCC
1 ATTAGACTTCAAATCC
39615804 ATTAG-CTTCAAATC
1 ATTAGACTTCAAATC
39615818 ACCTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (16 bp):
ATTAGACTTCAAATCC
Found at i:39616716 original size:33 final size:33
Alignment explanation
Indices: 39616655--39616717 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
39616645 TCATAGTTTA
* *
39616655 ATAAACAGAAAAAGGAAAAAAAAGTATTAAATC
1 ATAAAAAGAAAAAGGAAAAAAAACTATTAAATC
*
39616688 ATAAAAAGAAAAA-GAAATAATAACTATTAA
1 ATAAAAAGAAAAAGGAAA-AAAAACTATTAA
39616718 GTTATTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (33 bp):
ATAAAAAGAAAAAGGAAAAAAAACTATTAAATC
Found at i:39621234 original size:13 final size:13
Alignment explanation
Indices: 39621216--39621242 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39621206 TGACAAAATA
39621216 TAAATATATATTT
1 TAAATATATATTT
39621229 TAAATATATATTT
1 TAAATATATATTT
39621242 T
1 T
39621243 GAAGTTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATATATTT
Found at i:39622777 original size:22 final size:20
Alignment explanation
Indices: 39622737--39622803 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
39622727 TCCTCTATTT
39622737 TAAAAAT-AGAAATAAATATA
1 TAAAAATCAGAAA-AAATATA
39622757 TAAAAATTCAGAAAAACATATA
1 TAAAAA-TCAGAAAAA-ATATA
*
39622779 TGTAAAATCTAGAAAAAA-ATA
1 T-AAAAATC-AGAAAAAATATA
39622800 TAAA
1 TAAA
39622804 GTATGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 8 0.20
21 7 0.17
22 14 0.35
23 11 0.28
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (20 bp):
TAAAAATCAGAAAAAATATA
Found at i:39622784 original size:24 final size:23
Alignment explanation
Indices: 39622743--39622801 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
39622733 ATTTTAAAAA
*
39622743 TAGAAATAAATATATA-AAAAT-
1 TAGAAAAAAATATATATAAAATC
* *
39622764 TCAGAAAAACATATATGTAAAATC
1 T-AGAAAAAAATATATATAAAATC
39622788 TAGAAAAAAATATA
1 TAGAAAAAAATATA
39622802 AAGTATGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 12 0.39
23 17 0.55
24 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.25
Consensus pattern (23 bp):
TAGAAAAAAATATATATAAAATC
Found at i:39622978 original size:18 final size:19
Alignment explanation
Indices: 39622944--39622998 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
39622934 TAAAAAATAT
39622944 TTAATAAATCTAAAATTTA
1 TTAATAAATCTAAAATTTA
*
39622963 TTAA-AAATTTAAAATTTA
1 TTAATAAATCTAAAATTTA
**
39622981 AGAATAACAT-TAAAATTT
1 TTAATAA-ATCTAAAATTT
39622999 TATATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 15 0.48
19 14 0.45
20 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAATAAATCTAAAATTTA
Found at i:39623010 original size:9 final size:9
Alignment explanation
Indices: 39622996--39623020 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39622986 AACATTAAAA
39622996 TTTTATATT
1 TTTTATATT
39623005 TTTTATATT
1 TTTTATATT
39623014 TTTTATA
1 TTTTATA
39623021 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATATT
Found at i:39623032 original size:27 final size:27
Alignment explanation
Indices: 39622993--39623101 Score: 100
Period size: 27 Copynumber: 4.1 Consensus size: 27
39622983 AATAACATTA
*
39622993 AAATTTTATATTTTTTATATTTTTTAT
1 AAATTTTAAATTTTTTATATTTTTTAT
* *
39623020 AAATTTTAAA---TTTAAATTTTTTAC
1 AAATTTTAAATTTTTTATATTTTTTAT
**
39623044 AAATTATTAAATATTTTTATATTTTAAAT
1 AAATT-TTAAAT-TTTTTATATTTTTTAT
* *
39623073 AAATTTT-AATTTTTAAATAATTTTTAT
1 AAATTTTAAATTTTT-TATATTTTTTAT
39623100 AA
1 AA
39623102 TATTATTATT
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
24 17 0.26
25 5 0.08
26 4 0.06
27 22 0.34
28 2 0.03
29 15 0.23
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
AAATTTTAAATTTTTTATATTTTTTAT
Found at i:39623038 original size:24 final size:25
Alignment explanation
Indices: 39623006--39623055 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
39622996 TTTTATATTT
* *
39623006 TTTATATTTTTTATAAATT-TTAAA
1 TTTAAATTTTTTACAAATTATTAAA
39623030 TTTAAATTTTTTACAAATTATTAAA
1 TTTAAATTTTTTACAAATTATTAAA
39623055 T
1 T
39623056 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAAATTTTTTACAAATTATTAAA
Found at i:39623061 original size:53 final size:56
Alignment explanation
Indices: 39623004--39623109 Score: 146
Period size: 53 Copynumber: 1.9 Consensus size: 56
39622994 AATTTTATAT
**
39623004 TTTTTATATTTTTTATAAATTTTAA-ATTTAAAT-TTTTTACAA-ATTATTAAATA
1 TTTTTATATTTTAAATAAATTTTAATATTTAAATATTTTTACAATATTATTAAATA
* *
39623057 TTTTTATATTTTAAATAAATTTTAATTTTTAAATAATTTTTATAATATTATTA
1 TTTTTATATTTTAAATAAATTTTAATATTTAAAT-ATTTTTACAATATTATTA
39623110 TTGATTTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 23 0.51
54 7 0.16
56 8 0.18
57 7 0.16
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (56 bp):
TTTTTATATTTTAAATAAATTTTAATATTTAAATATTTTTACAATATTATTAAATA
Found at i:39623072 original size:17 final size:19
Alignment explanation
Indices: 39623050--39623100 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
39623040 TTACAAATTA
39623050 TTAAAT-ATTTTTATA-TT
1 TTAAATAATTTTTATATTT
*
39623067 TTAAATAAATTTTA-ATTT
1 TTAAATAATTTTTATATTT
39623085 TTAAATAATTTTTATA
1 TTAAATAATTTTTATA
39623101 ATATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.24
18 21 0.72
19 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAAATAATTTTTATATTT
Found at i:39623202 original size:2 final size:2
Alignment explanation
Indices: 39623195--39623238 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
39623185 TTTTCTAATT
*
39623195 TA TA TA TA TA T- TA TGA -A TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
39623236 TA T
1 TA T
39623239 TTATTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.92
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39632869 original size:31 final size:31
Alignment explanation
Indices: 39632831--39632889 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
39632821 TGAATCGATA
39632831 TTTCTATTAAAAATTTCATCTCC-ATTAAGTG
1 TTTCTATTAAAAATTTCATC-CCAATTAAGTG
39632862 TTTCTATTAAAAATTTCATCCCAATTAA
1 TTTCTATTAAAAATTTCATCCCAATTAA
39632890 AAATTAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTCTATTAAAAATTTCATCCCAATTAAGTG
Found at i:39640372 original size:5 final size:5
Alignment explanation
Indices: 39640362--39640392 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
39640352 GAAAAAAAAG
39640362 TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA T
1 TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA T
39640393 CTCTTTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TGTCA
Found at i:39640990 original size:24 final size:24
Alignment explanation
Indices: 39640962--39641010 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39640952 TTAAATCTTG
* *
39640962 AAAAAAACGACATATTTGACCAATT
1 AAAAAAA-AACATATATGACCAATT
*
39640987 AAAAAAAAACATATATGCCCAATT
1 AAAAAAAAACATATATGACCAATT
39641011 TAATCAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.22
Consensus pattern (24 bp):
AAAAAAAAACATATATGACCAATT
Found at i:39641337 original size:26 final size:26
Alignment explanation
Indices: 39641284--39641337 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
39641274 TAAAAAATAT
* *
39641284 TTTTTAACAAAAAACTATTAATATAA
1 TTTTTAACAAAAAACTATTAACAAAA
39641310 TTTTTAACAAAAAACTATTAACAAAA
1 TTTTTAACAAAAAACTATTAACAAAA
39641336 TT
1 TT
39641338 GAATTATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (26 bp):
TTTTTAACAAAAAACTATTAACAAAA
Found at i:39656814 original size:27 final size:26
Alignment explanation
Indices: 39656747--39656816 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
39656737 ACGTGAACCA
*
39656747 TTAAAAAATATTAAA-AAATATAATT
1 TTAAAAAATATTAAATAAAAATAATT
* *
39656772 TTATAATTAATTTTAAATAAAAATATATT
1 TTA-AA-AAATATTAAATAAAAATA-ATT
39656801 TTAAAAAATATTAAAT
1 TTAAAAAATATTAAAT
39656817 CGGGATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 3 0.08
26 2 0.06
27 17 0.47
28 8 0.22
29 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAAAAATATTAAATAAAAATAATT
Found at i:39658645 original size:23 final size:23
Alignment explanation
Indices: 39658619--39658665 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
39658609 TGAATTGATT
39658619 ATTTCAT-ATTTAATTATTTAAAA
1 ATTTCATAATTT-ATTATTTAAAA
*
39658642 ATTTGATAATTTATTATTTAAAA
1 ATTTCATAATTTATTATTTAAAA
39658665 A
1 A
39658666 AAAATTGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTCATAATTTATTATTTAAAA
Found at i:39660452 original size:2 final size:2
Alignment explanation
Indices: 39660445--39660469 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39660435 AAGTAAGATA
39660445 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39660470 AAGTATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39662330 original size:19 final size:17
Alignment explanation
Indices: 39662306--39662340 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
39662296 TTAATATTTA
39662306 CATTATTTATTTATTTGAT
1 CATTA-TTATTT-TTTGAT
39662325 CATTATTATTTTTTGA
1 CATTATTATTTTTTGA
39662341 ATTAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (17 bp):
CATTATTATTTTTTGAT
Found at i:39662344 original size:15 final size:18
Alignment explanation
Indices: 39662300--39662344 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39662290 TAGTCCTTAA
39662300 TATTT-ACATTATTTATT
1 TATTTGACATTATTTATT
39662317 TATTTGATCATTA-TTATT
1 TATTTGA-CATTATTTATT
39662335 T-TTTGA-ATTA
1 TATTTGACATTA
39662345 AATTTGTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.15
17 10 0.38
18 7 0.27
19 5 0.19
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (18 bp):
TATTTGACATTATTTATT
Found at i:39663617 original size:17 final size:16
Alignment explanation
Indices: 39663588--39663638 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
39663578 TCTAAAGTTT
39663588 TTTTTTA-AAAATTTGA
1 TTTTTTATAAAATTT-A
*
39663604 TTTTTTATAGAATTTA
1 TTTTTTATAAAATTTA
39663620 TATTTTTATGATAAATTTA
1 T-TTTTTAT-A-AAATTTA
39663639 GTAATACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 9 0.31
17 13 0.45
18 1 0.03
19 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTTTTATAAAATTTA
Found at i:39671488 original size:26 final size:26
Alignment explanation
Indices: 39671433--39671492 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
39671423 ACTCTCTTTT
* * *
39671433 AAAAAAAATAATGATTAAATTTAGTTA
1 AAAAAAAATAAAGATCAAATTGAG-TA
*
39671460 AAAAAGAATAAAGATCAAATTGA-TA
1 AAAAAAAATAAAGATCAAATTGAGTA
39671485 AAAAAAAA
1 AAAAAAAA
39671493 ATGTAAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 9 0.32
27 19 0.68
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (26 bp):
AAAAAAAATAAAGATCAAATTGAGTA
Found at i:39671732 original size:19 final size:19
Alignment explanation
Indices: 39671694--39671732 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39671684 AATGTTTTTC
* **
39671694 AAAAATATTTTTTAGTAAA
1 AAAAATACTTTTTAAAAAA
39671713 AAAAATACTTTTTAAAAAA
1 AAAAATACTTTTTAAAAAA
39671732 A
1 A
39671733 GTTAAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAAATACTTTTTAAAAAA
Found at i:39678287 original size:53 final size:52
Alignment explanation
Indices: 39678155--39678289 Score: 175
Period size: 53 Copynumber: 2.6 Consensus size: 52
39678145 AATGAAAAAG
* *
39678155 GGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCACAGATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTCACAGAATATAA
* * *
39678207 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATTCTTTTACGGAATA-AGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAA-TCCTTCACAGAATATA-A
*
39678260 GGTCCGATGACTATA-TGTCATCATGAGTAT
1 GGTCCGATGACTA-AGTGTCATCGTGAGTAT
39678290 TAAATGAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
52 35 0.47
53 38 0.51
54 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTCACAGAATATAA
Found at i:39678937 original size:22 final size:24
Alignment explanation
Indices: 39678887--39678942 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
39678877 TGAATTGTGA
*
39678887 GTATCGGTAGTTATATGCATAGAT
1 GTATCGGTAGTTATATGCATACAT
39678911 GTATCGGTAG-T-T-TGCATGACAT
1 GTATCGGTAGTTATATGCAT-ACAT
*
39678933 GTATCCGTAG
1 GTATCGGTAG
39678943 AAATTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 5 0.17
22 13 0.45
23 1 0.03
24 10 0.34
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (24 bp):
GTATCGGTAGTTATATGCATACAT
Found at i:39679581 original size:16 final size:16
Alignment explanation
Indices: 39679556--39679594 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
39679546 TGTGATTGTA
39679556 TTAT-TATATA-ATGAT
1 TTATATATATATAT-AT
39679571 TTATATATATATATAT
1 TTATATATATATATAT
39679587 TTATATAT
1 TTATATAT
39679595 CCAAATTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 16 0.73
17 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTATATATATATATAT
Found at i:39686515 original size:22 final size:23
Alignment explanation
Indices: 39686487--39686532 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
39686477 CATTTTACTT
* *
39686487 ATTATATATTAATA-GTTTTTTA
1 ATTATATATAAATATATTTTTTA
39686509 ATTATATATAAATATATTTTTTA
1 ATTATATATAAATATATTTTTTA
39686532 A
1 A
39686533 AGTTTACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTATATATAAATATATTTTTTA
Found at i:39692295 original size:19 final size:19
Alignment explanation
Indices: 39692281--39692328 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
39692271 GAAATTTATT
39692281 CAATTTAGTCTAATTTTTA
1 CAATTTAGTCTAATTTTTA
*
39692300 CAATTTAGTCTAGTTTTTA
1 CAATTTAGTCTAATTTTTA
39692319 CAATTTAGTC
1 CAATTTAGTC
39692329 CCTGACCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (19 bp):
CAATTTAGTCTAATTTTTA
Found at i:39694177 original size:2 final size:2
Alignment explanation
Indices: 39694172--39694199 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39694162 TTATTCATCC
39694172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39694200 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39696419 original size:16 final size:16
Alignment explanation
Indices: 39696400--39696434 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39696390 TGAATAAATT
39696400 ATTAAAAATAA-AAAAA
1 ATTAAAAA-AAGAAAAA
39696416 ATTAAAAAAAGAAAAA
1 ATTAAAAAAAGAAAAA
39696432 ATT
1 ATT
39696435 GATTCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
ATTAAAAAAAGAAAAA
Found at i:39699687 original size:34 final size:34
Alignment explanation
Indices: 39699644--39699710 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
39699634 TGTGAAGTTA
39699644 CTAATAATAACAACTATTTCTCATGGTAGATAGT
1 CTAATAATAACAACTATTTCTCATGGTAGATAGT
*
39699678 CTAATAATAACAACTATTTTTCATGGTAGATAG
1 CTAATAATAACAACTATTTCTCATGGTAGATAG
39699711 ACTTCCCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (34 bp):
CTAATAATAACAACTATTTCTCATGGTAGATAGT
Found at i:39714056 original size:10 final size:11
Alignment explanation
Indices: 39714041--39714066 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39714031 ATTAGCTAAT
39714041 AAAAAAACAAA
1 AAAAAAACAAA
39714052 AAAAAAACAAA
1 AAAAAAACAAA
39714063 AAAA
1 AAAA
39714067 GGGTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:39719249 original size:32 final size:32
Alignment explanation
Indices: 39719208--39719282 Score: 150
Period size: 32 Copynumber: 2.3 Consensus size: 32
39719198 CCAAGATTGA
39719208 AAGGGGTCCAAAATATTATTTTTCGATTTTTT
1 AAGGGGTCCAAAATATTATTTTTCGATTTTTT
39719240 AAGGGGTCCAAAATATTATTTTTCGATTTTTT
1 AAGGGGTCCAAAATATTATTTTTCGATTTTTT
39719272 AAGGGGTCCAA
1 AAGGGGTCCAA
39719283 TTTTTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (32 bp):
AAGGGGTCCAAAATATTATTTTTCGATTTTTT
Found at i:39719300 original size:29 final size:29
Alignment explanation
Indices: 39719236--39719336 Score: 75
Period size: 32 Copynumber: 3.4 Consensus size: 29
39719226 TTTTTCGATT
**
39719236 TTTTAAGGGGTCCAAAATATTATTTTT-CGATT
1 TTTTAAGGGG-CCAAAAT-TT-TTTTTAC-AAC
**
39719268 TTTTAAGGGGTCCAATTTTTTTTTTA-AAC
1 TTTTAAGGGG-CCAAAATTTTTTTTACAAC
39719297 TTTTATA--GGCCAAAATTTTTTTTACCAAC
1 TTTTA-AGGGGCCAAAATTTTTTTTA-CAAC
39719326 TTTTAAGGGGC
1 TTTTAAGGGGC
39719337 TTAAAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 13 0.23
28 3 0.05
29 14 0.25
30 9 0.16
31 2 0.04
32 16 0.28
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (29 bp):
TTTTAAGGGGCCAAAATTTTTTTTACAAC
Found at i:39720916 original size:27 final size:27
Alignment explanation
Indices: 39720876--39720960 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 27
39720866 TTAGTAAAAC
* *
39720876 AAAATTTTGAGCCCTTTAAAAGCTGAA
1 AAAAATTTGAGCCCCTTAAAAGCTGAA
* **
39720903 AAAAATTTGGGCCCCTTAAAATTTG-A
1 AAAAATTTGAGCCCCTTAAAAGCTGAA
* * **
39720929 AAAAATTTCAGACCCTTAAAAATTGAA
1 AAAAATTTGAGCCCCTTAAAAGCTGAA
39720956 AAAAA
1 AAAAA
39720961 AATTAAAACT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
26 22 0.46
27 26 0.54
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (27 bp):
AAAAATTTGAGCCCCTTAAAAGCTGAA
Found at i:39721274 original size:27 final size:27
Alignment explanation
Indices: 39721225--39721280 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
39721215 TTTTATGTTT
*
39721225 AATAAATATAATTAATATTTATTTTTAA
1 AATAAATATAATTAATATATA-TTTTAA
* *
39721253 AATAAAT-TTATTTATATATATTTTAA
1 AATAAATATAATTAATATATATTTTAA
39721279 AA
1 AA
39721281 CCTTTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.32
27 10 0.40
28 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATAAATATAATTAATATATATTTTAA
Found at i:39724172 original size:2 final size:2
Alignment explanation
Indices: 39724167--39724212 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
39724157 ATATAATAGA
39724167 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39724209 AG AG
1 AG AG
39724213 TATAAAACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39725156 original size:16 final size:16
Alignment explanation
Indices: 39725135--39725204 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
39725125 CTCTCCTGGA
* *
39725135 AGAATATTTTTTATTT
1 AGAATAATTTTTGTTT
* *
39725151 AGAATAGTTGTTGTTT
1 AGAATAATTTTTGTTT
39725167 AGAATAATTTTTGTTT
1 AGAATAATTTTTGTTT
* *
39725183 GAGAAT-AGTTATGTTT
1 -AGAATAATTTTTGTTT
39725199 AGAATA
1 AGAATA
39725205 GCTATGTTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
15 5 0.11
16 35 0.78
17 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (16 bp):
AGAATAATTTTTGTTT
Found at i:39725178 original size:32 final size:32
Alignment explanation
Indices: 39725135--39725204 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
39725125 CTCTCCTGGA
* *
39725135 AGAATATTTTTTATTT-AGAATAGTTGTTGTTT
1 AGAATAATTTTTATTTGAGAATAGTT-ATGTTT
*
39725167 AGAATAATTTTTGTTTGAGAATAGTTATGTTT
1 AGAATAATTTTTATTTGAGAATAGTTATGTTT
39725199 AGAATA
1 AGAATA
39725205 GCTATGTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 25 0.74
33 9 0.26
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (32 bp):
AGAATAATTTTTATTTGAGAATAGTTATGTTT
Found at i:39725204 original size:15 final size:15
Alignment explanation
Indices: 39725148--39725212 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 15
39725138 ATATTTTTTA
*
39725148 TTTAGAATAGTTGTTG
1 TTTAGAATAGTT-ATG
* *
39725164 TTTAGAATAATTTTTG
1 TTTAGAAT-AGTTATG
39725180 TTTGAGAATAGTTATG
1 TTT-AGAATAGTTATG
*
39725196 TTTAGAATAGCTATG
1 TTTAGAATAGTTATG
39725211 TT
1 TT
39725213 CAAACCAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
15 13 0.30
16 22 0.51
17 8 0.19
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (15 bp):
TTTAGAATAGTTATG
Found at i:39725283 original size:16 final size:16
Alignment explanation
Indices: 39725258--39725295 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39725248 AGTGTAATTA
*
39725258 TCAT-TTGAGAATAAC
1 TCATGTTGAGAACAAC
39725273 TCATGTTGAGAACAAC
1 TCATGTTGAGAACAAC
*
39725289 TCTTGTT
1 TCATGTT
39725296 TAGTATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (16 bp):
TCATGTTGAGAACAAC
Found at i:39725508 original size:23 final size:22
Alignment explanation
Indices: 39725476--39725521 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
39725466 TTTTAGAGGG
**
39725476 ACGAAGTAAATTTGTAATTTTT
1 ACGAAGTAAAAATGTAATTTTT
39725498 ACGATAGTAAAAATGTAATTTTT
1 ACGA-AGTAAAAATGTAATTTTT
39725521 A
1 A
39725522 AAAAGATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (22 bp):
ACGAAGTAAAAATGTAATTTTT
Found at i:39739387 original size:22 final size:21
Alignment explanation
Indices: 39739345--39739387 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39739335 TATTTCGATG
* *
39739345 AGTGTTGGGCACACTTTTACT
1 AGTGTTGGGCACAATTATACT
*
39739366 AGTGTTTGGCACAATGTATACT
1 AGTGTTGGGCACAAT-TATACT
39739388 TCGGAGGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (21 bp):
AGTGTTGGGCACAATTATACT
Found at i:39748975 original size:40 final size:40
Alignment explanation
Indices: 39748920--39749001 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
39748910 AGGACTAAAA
39748920 TCTCAAACTTCGAAAAGTACAAAAACTAGAGTTAACCAAT
1 TCTCAAACTTCGAAAAGTACAAAAACTAGAGTTAACCAAT
39748960 TCTCAAACTTCGAAAAGTACAAAAACTAGAGTTAACCAAT
1 TCTCAAACTTCGAAAAGTACAAAAACTAGAGTTAACCAAT
39749000 TC
1 TC
39749002 AAAAAATACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (40 bp):
TCTCAAACTTCGAAAAGTACAAAAACTAGAGTTAACCAAT
Found at i:39750545 original size:21 final size:22
Alignment explanation
Indices: 39750521--39750576 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
39750511 ATTTTATTTT
39750521 TATATATTATA-AGGATAAAAA
1 TATATATTATATAGGATAAAAA
* **
39750542 TATA-ATAATATATTATAAAAA
1 TATATATTATATAGGATAAAAA
*
39750563 TCATATATTTTATA
1 T-ATATATTATATA
39750577 TTTAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 5 0.19
21 13 0.48
22 3 0.11
23 6 0.22
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
TATATATTATATAGGATAAAAA
Found at i:39755465 original size:3 final size:3
Alignment explanation
Indices: 39755440--39755493 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
39755430 TTCCATTTTG
* *
39755440 TTA TTA -TA TTA CTA CTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39755486 TTA TTA TT
1 TTA TTA TT
39755494 TGAGTATTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39755531 original size:12 final size:12
Alignment explanation
Indices: 39755457--39755540 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
39755447 ATTACTACTA
39755457 TTTTATTATTAT
1 TTTTATTATTAT
*
39755469 TATTATTATTAT
1 TTTTATTATTAT
*
39755481 TATTATTATTA-
1 TTTTATTATTAT
* * *
39755492 TTTGAGTATT-G
1 TTTTATTATTAT
* *
39755503 TATAACTT-TTA-
1 TTTTA-TTATTAT
39755514 TTTTATTATTAT
1 TTTTATTATTAT
*
39755526 TTTTATTACTAT
1 TTTTATTATTAT
39755538 TTT
1 TTT
39755541 AAAGATATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
10 2 0.04
11 18 0.32
12 37 0.65
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:39755533 original size:9 final size:9
Alignment explanation
Indices: 39755457--39755533 Score: 52
Period size: 9 Copynumber: 8.9 Consensus size: 9
39755447 ATTACTACTA
39755457 TTTTATTAT
1 TTTTATTAT
*
39755466 TATTATTAT
1 TTTTATTAT
*
39755475 TATTATTAT
1 TTTTATTAT
*
39755484 TATTATTA-
1 TTTTATTAT
* *
39755492 TTTGAGTA-
1 TTTTATTAT
* * *
39755500 TTGTATAAC
1 TTTTATTAT
39755509 TTTTATT-T
1 TTTTATTAT
*
39755517 TATTATTAT
1 TTTTATTAT
39755526 TTTTATTA
1 TTTTATTA
39755534 CTATTTTAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
8 15 0.28
9 38 0.72
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (9 bp):
TTTTATTAT
Found at i:39756968 original size:94 final size:94
Alignment explanation
Indices: 39756781--39756969 Score: 265
Period size: 95 Copynumber: 2.0 Consensus size: 94
39756771 ACGGCATACG
* **
39756781 TCCAAGGCAACTAATCAGTATACAGAAATGGGGTTTCAAGAATGAAACGATAATTCCTTATGGAA
1 TCCAAGGCAACTAATCAGTATACAGAAATGGGGTTTCAAGAATGAAACAATAATTCCCAATGGAA
*
39756846 AAAATCAACAAATGGAAATAAATAAGCAA
66 AAAATCAACAAATCGAAATAAATAAGCAA
** * *
39756875 TCCAAGGCAAACTAATTGGTATA-TGTAAATGGGGTTTCAAGAATGAAACAATGATTCCCAATGG
1 TCCAAGGC-AACTAATCAGTATACAG-AAATGGGGTTTCAAGAATGAAACAATAATTCCCAATGG
*
39756939 -AAAAATCAACATATCGAAATAAATAAGCAA
64 AAAAAATCAACAAATCGAAATAAATAAGCAA
39756969 T
1 T
39756970 TGCAAGACAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 38 0.45
95 46 0.55
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.23
Consensus pattern (94 bp):
TCCAAGGCAACTAATCAGTATACAGAAATGGGGTTTCAAGAATGAAACAATAATTCCCAATGGAA
AAAATCAACAAATCGAAATAAATAAGCAA
Found at i:39761516 original size:383 final size:375
Alignment explanation
Indices: 39760549--39761651 Score: 1190
Period size: 383 Copynumber: 3.0 Consensus size: 375
39760539 TTTTTTATTA
* * * * *
39760549 TATGC-AGAATTAGATTTGTAGGAATTAAAATTGTTGTAAACAATACTAATCCAGTGTGTAGAAT
1 TATGCAAG-ATTAGATTTGTAGGAACTAAAATTGTTGTAAATAATACTAATCTAGTGTATAGAAA
* * *
39760613 TTGGGT-CATATG-TGTTTTTGTGTTTTAGTTGCAATTTTTTTTTTATTTGTGAGTTCGAACCTC
65 TTGAGTGCATA-GATGTTATTGTGTTATAGTTGCAA--TTTTTTTTATTTGTGAGTTCGAACCTC
* **** * * * *
39760676 TCAACCAACATTTT-AAAATAATTTTTTATTATGTGCAGGATATATTTGTAGGAACTAAAATTAT
127 TCAACCAACATTTTAAAAAAAAAAAATTATTATGTGCAAGATAGATTTGTGGGAACTAAAATTGT
** ** * * ** * * *
39760740 TATAAATAATCTTGACTTGAATAGAG-GGATGGCT-AAAGTTTTTGTTAAACACTTG-TTT-C--
192 CGTAAATACCCTTGACTTGAAGAGAGCGG-TGG-TAAAACTCCTTATCAAACACCTGCTTTGCAA
** * * * *
39760799 GTATT-----G---TTATCCCCATCCCTTATCCTTAATATTGTTTTGAAAAACATTATCGTTAAT
255 CAATTCAAACGATATTATCCCCATCCCTTACCCCTAATATTGTATT-AAAAAAATTATCGTTAAT
*
39760856 AATATTAATTCAACGTGTAGAAATTGAGTTTTGTGTGCATTTTAGAAGAATATTTTT
319 AATACTAATTCAACGTGTAGAAATTGAGTTTTGTGTGCATTTTAGAAGAATATTTTT
* *
39760913 TATGCAATATTAGATTTGTAGGAACTAAAATTGTTGTAAATAATACTAATCTAGTGTGTAGAAAT
1 TATGCAAGATTAGATTTGTAGGAACTAAAATTGTTGTAAATAATACTAATCTAGTGTATAGAAAT
* *
39760978 TGAGTGCATATATGTTATTGTGTTATAGTTGCAATTTTTTTTATTTGTGAGTTCGAATCTCTCAA
66 TGAGTGCATAGATGTTATTGTGTTATAGTTGCAATTTTTTTTATTTGTGAGTTCGAACCTCTCAA
* *
39761043 TCAACATTTTAAAAAAAAAAAATTATTATGTGCAAGATAGATTTGTGGGAACTAAAATTGTTGTA
131 CCAACATTTTAAAAAAAAAAAATTATTATGTGCAAGATAGATTTGTGGGAACTAAAATTGTCGTA
* * * * * * *
39761108 AATAGCTTTGACTTTAAGGGAGCGGTGGATAAAACT-CTTGTCAAACACTTG-TTTCGCATCAAT
196 AATACCCTTGACTTGAAGAGAGCGGTGG-TAAAACTCCTTATCAAACACCTGCTTT-GCAACAAT
39761171 TCAAACCG-TATTATCCCCATCCCTTACCCCTAATATTGTATTAAAAAAAATTATCGTTAATAAT
259 TCAAA-CGATATTATCCCCATCCCTTACCCCTAATATTGTATT-AAAAAAATTATCGTTAATAAT
* *
39761235 ACTAATTCAACGTATAGAAATTGAGTTTTGTGTGCATTTTAGAAGGATATTTTTTTAAT
322 ACTAATTCAACGTGTAGAAATTGAGTTTTGTGTGCATTTTAGAA-GA-A-TATTTT--T
**
39761294 TATGTGCGGGATTAGATTTGTAGGAACTAAAATTGTTGTAAATAATACTAATCTAGTGTATAGAA
1 TA--TGCAAGATTAGATTTGTAGGAACTAAAATTGTTGTAAATAATACTAATCTAGTGTATAGAA
* *
39761359 ATTGGGTGCATAGGTGTTATTGTGTTATAGTTGCAATTTTTTTTATTTGTGAGTTCGAACCTCTC
64 ATTGAGTGCATAGATGTTATTGTGTTATAGTTGCAATTTTTTTTATTTGTGAGTTCGAACCTCTC
* * ***** * **
39761424 AACCAGCATTTTAAAAGAATTTTTTTATTATGTGCAAGTTAGATTTGTGGGATTTAAAATTGTCG
129 AACCAACATTTTAAAAAAAAAAAATTATTATGTGCAAGATAGATTTGTGGGAACTAAAATTGTCG
* * * * *
39761489 TAAATACCCTTGACTTGAATAGAGCGGTGGTTAAAGTCCTTATCAAACACCTGCTTTGCAAGAGT
194 TAAATACCCTTGACTTGAAGAGAGCGGTGGTAAAACTCCTTATCAAACACCTGCTTTGCAACAAT
* * * * *
39761554 TCGAACGATGTTATCTCCATCCCTCACCCCTAATATTGTATT-AAAAAA-TATCATTAATAATAC
259 TCAAACGATATTATCCCCATCCCTTACCCCTAATATTGTATTAAAAAAATTATCGTTAATAATAC
** *
39761617 TAATTCAATATGTAGAAATTGGGTTTTGTGTGCAT
324 TAATTCAACGTGTAGAAATTGAGTTTTGTGTGCAT
39761652 AGATGTTATT
Statistics
Matches: 629, Mismatches: 82, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
363 39 0.06
364 142 0.23
365 31 0.05
366 1 0.00
368 3 0.00
374 1 0.00
376 91 0.14
377 2 0.00
378 1 0.00
379 5 0.01
380 45 0.07
381 9 0.01
382 7 0.01
383 249 0.40
384 3 0.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (375 bp):
TATGCAAGATTAGATTTGTAGGAACTAAAATTGTTGTAAATAATACTAATCTAGTGTATAGAAAT
TGAGTGCATAGATGTTATTGTGTTATAGTTGCAATTTTTTTTATTTGTGAGTTCGAACCTCTCAA
CCAACATTTTAAAAAAAAAAAATTATTATGTGCAAGATAGATTTGTGGGAACTAAAATTGTCGTA
AATACCCTTGACTTGAAGAGAGCGGTGGTAAAACTCCTTATCAAACACCTGCTTTGCAACAATTC
AAACGATATTATCCCCATCCCTTACCCCTAATATTGTATTAAAAAAATTATCGTTAATAATACTA
ATTCAACGTGTAGAAATTGAGTTTTGTGTGCATTTTAGAAGAATATTTTT
Found at i:39768928 original size:7 final size:7
Alignment explanation
Indices: 39768918--39769004 Score: 52
Period size: 7 Copynumber: 12.7 Consensus size: 7
39768908 CCTAAACCTC
39768918 ATTCAAG
1 ATTCAAG
39768925 ATTCAAG
1 ATTCAAG
* *
39768932 GTTCGAG
1 ATTCAAG
*
39768939 -TTC-GG
1 ATTCAAG
* *
39768944 GTTCAAA
1 ATTCAAG
39768951 ATTCAAG
1 ATTCAAG
* *
39768958 GTTCAGG
1 ATTCAAG
*
39768965 ATTCGAG
1 ATTCAAG
*
39768972 GTTCAAG
1 ATTCAAG
*
39768979 TTTCAAG
1 ATTCAAG
39768986 ATTCAAG
1 ATTCAAG
* *
39768993 GTTGAAG
1 ATTCAAG
39769000 ATTCA
1 ATTCA
39769005 TGGTATAAGG
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
5 1 0.02
6 6 0.10
7 51 0.88
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (7 bp):
ATTCAAG
Found at i:39768976 original size:21 final size:21
Alignment explanation
Indices: 39768952--39769004 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
39768942 GGGTTCAAAA
* * *
39768952 TTCAAGGTTCAGGATTCGAGG
1 TTCAAGATTCAAGATTCAAGG
*
39768973 TTCAAGTTTCAAGATTCAAGG
1 TTCAAGATTCAAGATTCAAGG
*
39768994 TTGAAGATTCA
1 TTCAAGATTCA
39769005 TGGTATAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCAAGATTCAAGATTCAAGG
Found at i:39768983 original size:28 final size:27
Alignment explanation
Indices: 39768919--39768990 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
39768909 CTAAACCTCA
39768919 TTCAAGATTCAAGGTTC-GAGTTCGGG
1 TTCAAGATTCAAGGTTCAGAGTTCGGG
*
39768945 TTCAAAATTCAAGGTTCAG-GATTCGAGG
1 TTCAAGATTCAAGGTTCAGAG-TTCG-GG
* *
39768973 TTCAAGTTTCAAGATTCA
1 TTCAAGATTCAAGGTTCA
39768991 AGGTTGAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 17 0.44
27 5 0.13
28 17 0.44
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (27 bp):
TTCAAGATTCAAGGTTCAGAGTTCGGG
Found at i:39769004 original size:14 final size:14
Alignment explanation
Indices: 39768919--39768992 Score: 71
Period size: 14 Copynumber: 5.4 Consensus size: 14
39768909 CTAAACCTCA
39768919 TTCAAGATTCAAGG
1 TTCAAGATTCAAGG
* *
39768933 TTCGAG-TTC-GGG
1 TTCAAGATTCAAGG
*
39768945 TTCAAAATTCAAGG
1 TTCAAGATTCAAGG
* *
39768959 TTCAGGATTCGAGG
1 TTCAAGATTCAAGG
* *
39768973 TTCAAGTTTCAAGA
1 TTCAAGATTCAAGG
39768987 TTCAAG
1 TTCAAG
39768993 GTTGAAGATT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
12 6 0.13
13 6 0.13
14 34 0.74
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (14 bp):
TTCAAGATTCAAGG
Found at i:39769079 original size:21 final size:20
Alignment explanation
Indices: 39769041--39769090 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
39769031 AGAGTTTGGG
*
39769041 TTTAAAATTTAAGATTTATGA
1 TTTAAAATTCAAGATTTA-GA
* *
39769062 TTTAAAATTCGAGGTTTAGA
1 TTTAAAATTCAAGATTTAGA
*
39769082 GTTAAAATT
1 TTTAAAATT
39769091 TTAGGATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (20 bp):
TTTAAAATTCAAGATTTAGA
Found at i:39771800 original size:21 final size:21
Alignment explanation
Indices: 39771771--39771814 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
39771761 AATTGGGTGC
39771771 TTAATAAGAATATTAA-AAAAAT
1 TTAATAAGAA-A-TAATAAAAAT
39771793 TTAA-AAGAAATAATAAAAAT
1 TTAATAAGAAATAATAAAAAT
39771813 TT
1 TT
39771815 TCAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 9 0.43
21 5 0.24
22 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TTAATAAGAAATAATAAAAAT
Found at i:39771862 original size:32 final size:31
Alignment explanation
Indices: 39771803--39771862 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
39771793 TTAAAAGAAA
* *
39771803 TAATAAAAATTTTCAAATTTTTTGAAAGATT
1 TAATAAAAATTTTCAAACTTTTAGAAAGATT
* *
39771834 TAATTAAAATTTTCAGCACTTTTAGAAAG
1 TAATAAAAATTTTCA-AACTTTTAGAAAG
39771863 CTTAACTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
TAATAAAAATTTTCAAACTTTTAGAAAGATT
Found at i:39780235 original size:40 final size:40
Alignment explanation
Indices: 39780191--39780273 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
39780181 CAATCCAATA
*
39780191 AAAATGACTCAAAATTTTTAAATATTAATTAATTAAACTC
1 AAAATGACTCAAAATTTTTAAATATTAATTAATTAAACCC
*
39780231 AAAATGATTCAAAATTTTTAAATATTAATTAATTAAACCC
1 AAAATGACTCAAAATTTTTAAATATTAATTAATTAAACCC
39780271 AAA
1 AAA
39780274 TTAATTGTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (40 bp):
AAAATGACTCAAAATTTTTAAATATTAATTAATTAAACCC
Found at i:39782297 original size:12 final size:12
Alignment explanation
Indices: 39782280--39782306 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39782270 GTTCAAAGAT
39782280 GTAACAATCTTG
1 GTAACAATCTTG
39782292 GTAACAATCTTG
1 GTAACAATCTTG
39782304 GTA
1 GTA
39782307 TAGAAGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (12 bp):
GTAACAATCTTG
Found at i:39793535 original size:14 final size:15
Alignment explanation
Indices: 39793508--39793537 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
39793498 TGACATGTTC
39793508 ATGAACATTAAACAA
1 ATGAACATTAAACAA
39793523 ATGAACA-TAAACAA
1 ATGAACATTAAACAA
39793537 A
1 A
39793538 ACATTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (15 bp):
ATGAACATTAAACAA
Found at i:39801344 original size:16 final size:15
Alignment explanation
Indices: 39801297--39801346 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
39801287 TTTGATTAAT
39801297 TTTGAGTTTAAATTA
1 TTTGAGTTTAAATTA
* * *
39801312 TTTTAATTTCAAGTTA
1 TTTGAGTTT-AAATTA
39801328 TTTGAGTTTGAAATTA
1 TTTGAGTTT-AAATTA
39801344 TTT
1 TTT
39801347 TTTTATATGA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (15 bp):
TTTGAGTTTAAATTA
Found at i:39822120 original size:16 final size:16
Alignment explanation
Indices: 39822099--39822129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39822089 AAATTTGAAA
*
39822099 AAAAAGGGGCAAATAG
1 AAAAAGGGGAAAATAG
39822115 AAAAAGGGGAAAATA
1 AAAAAGGGGAAAATA
39822130 AGTACAAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.29, T:0.06
Consensus pattern (16 bp):
AAAAAGGGGAAAATAG
Found at i:39824840 original size:15 final size:15
Alignment explanation
Indices: 39824820--39824850 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39824810 TTCAAGTTCG
39824820 ACTCGATATATAATT
1 ACTCGATATATAATT
39824835 ACTCGATATATAATT
1 ACTCGATATATAATT
39824850 A
1 A
39824851 AGTCATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
ACTCGATATATAATT
Found at i:39829982 original size:31 final size:32
Alignment explanation
Indices: 39829947--39830014 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 32
39829937 AAATGCAATG
* *
39829947 TAAGAAATAAAATAAAC-ATCAATTCATAGTA
1 TAAGAAATAAAATAAACTATAAATTCATAATA
* * **
39829978 TAAGACATGAAATTCACTATAAATTCATAATA
1 TAAGAAATAAAATAAACTATAAATTCATAATA
39830010 TAAGA
1 TAAGA
39830015 TGTGATTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.28
Consensus pattern (32 bp):
TAAGAAATAAAATAAACTATAAATTCATAATA
Found at i:39834436 original size:30 final size:29
Alignment explanation
Indices: 39834391--39834471 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
39834381 ATTTAGGTCA
* *
39834391 TTTAATAAATGTAAAATTATATTTTAATTCT
1 TTTAA-AAATATAAAAATATATTTTAATT-T
*
39834422 TTTAAAAATATAAAAATGTGA-TTTAATTT
1 TTTAAAAATATAAAAATAT-ATTTTAATTT
*
39834451 TTTAAAATTATAAAAATATAT
1 TTTAAAAATATAAAAATATAT
39834472 GTTATTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 18 0.42
30 18 0.42
31 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (29 bp):
TTTAAAAATATAAAAATATATTTTAATTT
Found at i:39840179 original size:22 final size:22
Alignment explanation
Indices: 39840137--39840179 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39840127 GAATGAATCT
*
39840137 TTTTTGAGCTTTTTCTGCATTG
1 TTTTTGAGCTTTTACTGCATTG
*
39840159 TTTTTGTA-CTTTTACTTCATT
1 TTTTTG-AGCTTTTACTGCATT
39840180 TTCCCTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTTGAGCTTTTACTGCATTG
Found at i:39850793 original size:15 final size:15
Alignment explanation
Indices: 39850773--39850822 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
39850763 ATTTAATCGA
39850773 TTTAATATATATTAT
1 TTTAATATATATTAT
39850788 TTTAAT-TA-ATATAT
1 TTTAATATATAT-TAT
*
39850802 TTATAATATATAAT-T
1 TT-TAATATATATTAT
39850817 TTTAAT
1 TTTAAT
39850823 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 2 0.07
14 11 0.37
15 13 0.43
16 3 0.10
17 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATATATATTAT
Found at i:39850834 original size:25 final size:29
Alignment explanation
Indices: 39850775--39850834 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
39850765 TTAATCGATT
*
39850775 TAATATATATTATTTTAATTAATATATTTA
1 TAATATATAATATTTTAATT-ATATATTTA
39850805 TAATATATAAT-TTTTAATT-TAT-TTTA
1 TAATATATAATATTTTAATTATATATTTA
39850831 -AATA
1 TAATA
39850835 AAATAGGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.14
26 4 0.14
27 3 0.10
29 8 0.28
30 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TAATATATAATATTTTAATTATATATTTA
Found at i:39851470 original size:26 final size:24
Alignment explanation
Indices: 39851422--39851471 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
39851412 TTACTTCGAA
*
39851422 TAATTTAAAATTATTAATGTATTT
1 TAATTTAAAATTAATAATGTATTT
*
39851446 TAATTTAATAATTTAATAATTTATTT
1 TAATTTAA-AA-TTAATAATGTATTT
39851472 AATGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 2 0.09
26 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TAATTTAAAATTAATAATGTATTT
Found at i:39859757 original size:16 final size:16
Alignment explanation
Indices: 39859736--39859766 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39859726 AATGTATGTT
*
39859736 TAAAAATAACATATAA
1 TAAAAATAAAATATAA
39859752 TAAAAATAAAATATA
1 TAAAAATAAAATATA
39859767 TGGTTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATAAAATATAA
Found at i:39874147 original size:112 final size:112
Alignment explanation
Indices: 39873964--39874168 Score: 329
Period size: 112 Copynumber: 1.8 Consensus size: 112
39873954 CATATAAACC
*
39873964 ATTACTTCAGTTAATATTGATATTATTATTAATATAAGAGGATATAAGTTCGAGTGCGTTGAAAC
1 ATTACTTCAGTTAATATTGATATTATTATTAATATAAGAGGATATAAGTTCGAGTACGTTGAAAC
* *
39874029 GCATTATTTTCTTATTTAAGGGTTGAGGTCAAGCTTTCATATTGAGT
66 GCATTATTCTCTTATTTAAGAGTTGAGGTCAAGCTTTCATATTGAGT
* * * * *
39874076 ATTAGTTCAGTTAATATTTATATTATTGTTAATATAAGAGGATGTAAGTTCGAGTACGTTGAAAT
1 ATTACTTCAGTTAATATTGATATTATTATTAATATAAGAGGATATAAGTTCGAGTACGTTGAAAC
*
39874141 GTATTATTCTCTTATTTAAGAGTTGAGG
66 GCATTATTCTCTTATTTAAGAGTTGAGG
39874169 AAGGGCTATG
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 84 1.00
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (112 bp):
ATTACTTCAGTTAATATTGATATTATTATTAATATAAGAGGATATAAGTTCGAGTACGTTGAAAC
GCATTATTCTCTTATTTAAGAGTTGAGGTCAAGCTTTCATATTGAGT
Found at i:39881003 original size:2 final size:2
Alignment explanation
Indices: 39880998--39881036 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39880988 TATATAGTGC
39880998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39881037 GCAGATTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39886025 original size:23 final size:23
Alignment explanation
Indices: 39885999--39886044 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
39885989 CTTACTTTAA
39885999 CCCATAAATGTTTTATAGCAGTT
1 CCCATAAATGTTTTATAGCAGTT
39886022 CCCATAAATGTTTTATAGCAGTT
1 CCCATAAATGTTTTATAGCAGTT
39886045 AAATCGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
CCCATAAATGTTTTATAGCAGTT
Found at i:39888793 original size:14 final size:14
Alignment explanation
Indices: 39888774--39888800 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39888764 TATTATTCTC
39888774 TGATCCAACTATGG
1 TGATCCAACTATGG
39888788 TGATCCAACTATG
1 TGATCCAACTATG
39888801 TTAGGCAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
TGATCCAACTATGG
Found at i:39889288 original size:21 final size:22
Alignment explanation
Indices: 39889259--39889304 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
39889249 GTTGACGATT
*
39889259 ATTCTCTCTTTGATGAGATGAC
1 ATTCTCTCTTTGACGAGATGAC
39889281 ATTC-CTCTTTGACGAGATGAC
1 ATTCTCTCTTTGACGAGATGAC
39889302 ATT
1 ATT
39889305 TTTCTGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
ATTCTCTCTTTGACGAGATGAC
Found at i:39889774 original size:98 final size:97
Alignment explanation
Indices: 39889666--39889954 Score: 476
Period size: 96 Copynumber: 3.0 Consensus size: 97
39889656 TATACTTTAA
39889666 TTTTTAAGATAATAAAAAAAAACATTTCAAATTATTTCACATTATAATTTTTTGTTTATTAAAAC
1 TTTTTAAGATAAT-AAAAAAAACATTTCAAATTATTTCACATTATAATTTTTTGTTTATTAAAAC
*
39889731 ATATTTACATTTTCAGATGTCATATAATATTAT
65 ATATTTACATTTTCAGATGTCATATGATATTAT
*
39889764 TTTTTAAGATAATAAAAAAAACATTTCAAATTATTTCACATTATAATTTTTTTTGTTTATTAAGA
1 TTTTTAAGATAATAAAAAAAACATTTCAAATTATTTCACATTATAA--TTTTTTGTTTATTAAAA
*
39889829 CATATTTTCATTTTCAGATG-CATATGATATTAT
64 CATATTTACATTTTCAGATGTCATATGATATTAT
* *
39889862 TTTTTAAGATAAT--AAAAAATATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAAC
1 TTTTTAAGATAATAAAAAAAACATTTCAAATTATTTCACATTATA-ATTTTTTGTTTATTAAAAC
39889925 ATATTTACATTTTCAGATGTCATATGATAT
65 ATATTTACATTTTCAGATGTCATATGATAT
39889955 ATCATTTTGG
Statistics
Matches: 180, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
95 35 0.19
96 39 0.22
97 33 0.18
98 38 0.21
99 35 0.19
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (97 bp):
TTTTTAAGATAATAAAAAAAACATTTCAAATTATTTCACATTATAATTTTTTGTTTATTAAAACA
TATTTACATTTTCAGATGTCATATGATATTAT
Found at i:39889865 original size:49 final size:48
Alignment explanation
Indices: 39889713--39889954 Score: 129
Period size: 49 Copynumber: 5.0 Consensus size: 48
39889703 CACATTATAA
* *
39889713 TTTTTTGTTTATTAAAACATATTTACATTTTCAGATGTCATATAATATT
1 TTTTTTGTTTATTAAAACATATTTTCATTTTCAGATG-CATATGATATT
* * * * * ** * * * *
39889762 ATTTTTTAAG-ATAATAAAAAAAACATTTCAAATT-A-TTTCACATTATAATT
1 -TTTTTT--GTTTATTAAAACATA-TTTTCATTTTCAGATGCATATGAT-ATT
*
39889812 TTTTTTGTTTATTAAGACATATTTTCATTTTCAGATGCATATGATATT
1 TTTTTTGTTTATTAAAACATATTTTCATTTTCAGATGCATATGATATT
* * * ** * * * *
39889860 ATTTTTTAAG-ATAATAAAAAATA-TTTCAAATT-A-TTTCACATTATATT
1 -TTTTTT--GTTTATTAAAACATATTTTCATTTTCAGATGCATATGATATT
*
39889907 TTTTTTGTTTATTAAAACATATTTACATTTTCAGATGTCATATGATAT
1 TTTTTTGTTTATTAAAACATATTTTCATTTTCAGATG-CATATGATAT
39889955 ATCATTTTGG
Statistics
Matches: 133, Mismatches: 44, Indels: 31
0.64 0.21 0.15
Matches are distributed among these distances:
44 1 0.01
45 10 0.08
46 12 0.09
47 19 0.14
48 14 0.11
49 40 0.30
50 19 0.14
51 11 0.08
52 7 0.05
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.50
Consensus pattern (48 bp):
TTTTTTGTTTATTAAAACATATTTTCATTTTCAGATGCATATGATATT
Found at i:39889949 original size:96 final size:97
Alignment explanation
Indices: 39889666--39889954 Score: 476
Period size: 98 Copynumber: 3.0 Consensus size: 97
39889656 TATACTTTAA
*
39889666 TTTTTAAGATAATAAAAAAAAACATTTCAAATTATTTCACATTATA-ATTTTTTGTTTATTAAAA
1 TTTTTAAGATAAT--AAAAAAACATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAA
*
39889730 CATATTTACATTTTCAGATGTCATATAATATTAT
64 CATATTTACATTTTCAGATGTCATATGATATTAT
*
39889764 TTTTTAAGATAATAAAAAAAACATTTCAAATTATTTCACATTATAATTTTTTTTGTTTATTAAGA
1 TTTTTAAGATAAT-AAAAAAACATTTCAAATTATTTCACATTAT-ATTTTTTTTGTTTATTAAAA
*
39889829 CATATTTTCATTTTCAGATG-CATATGATATTAT
64 CATATTTACATTTTCAGATGTCATATGATATTAT
*
39889862 TTTTTAAGATAAT-AAAAAATATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAACA
1 TTTTTAAGATAATAAAAAAACATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAACA
39889926 TATTTACATTTTCAGATGTCATATGATAT
66 TATTTACATTTTCAGATGTCATATGATAT
39889955 ATCATTTTGG
Statistics
Matches: 181, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
95 38 0.21
96 38 0.21
97 31 0.17
98 39 0.22
99 35 0.19
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (97 bp):
TTTTTAAGATAATAAAAAAACATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAACA
TATTTACATTTTCAGATGTCATATGATATTAT
Found at i:39889978 original size:96 final size:95
Alignment explanation
Indices: 39889680--39889968 Score: 395
Period size: 97 Copynumber: 3.0 Consensus size: 95
39889670 TAAGATAATA
* *
39889680 AAAAAAAACATTTCAAATTATTTCACATTATA-ATTTTTTGTTTATTAAAACATATTTACATTTT
1 AAAAAAAATATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAACATATTTACATTTT
* * *
39889744 CAGATGTCATATAATATTATTTTTTAAGATAAT
66 CAGATGTCATATGATA-TATATTTT--GATGAT
* * *
39889777 AAAAAAAACATTTCAAATTATTTCACATTATAATTTTTTTTGTTTATTAAGACATATTTTCATTT
1 AAAAAAAATATTTCAAATTATTTCACATTAT-ATTTTTTTTGTTTATTAAAACATATTTACATTT
* *
39889842 TCAGATG-CATATGATAT-TATTTTTTAAGAT
65 TCAGATGTCATATGATATATA-TTTTGATGAT
39889872 AATAAAAAATATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAACATATTTACATTT
1 AA-AAAAAATATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAACATATTTACATTT
*
39889937 TCAGATGTCATATGATATATCATTTTGGTGAT
65 TCAGATGTCATATGATATAT-ATTTTGATGAT
39889969 CGCATAAATA
Statistics
Matches: 171, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
95 43 0.25
96 39 0.23
97 44 0.26
98 10 0.06
99 35 0.20
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (95 bp):
AAAAAAAATATTTCAAATTATTTCACATTATATTTTTTTTGTTTATTAAAACATATTTACATTTT
CAGATGTCATATGATATATATTTTGATGAT
Found at i:39893186 original size:11 final size:11
Alignment explanation
Indices: 39893172--39893219 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
39893162 TTTTGTTGTC
39893172 ATTTTACTATT
1 ATTTTACTATT
* *
39893183 ATTTTCCTATC
1 ATTTTACTATT
*
39893194 ATTTTGCTATT
1 ATTTTACTATT
*
39893205 ATATTA-TATT
1 ATTTTACTATT
39893215 ATTTT
1 ATTTT
39893220 GTTGTTATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 8 0.27
11 22 0.73
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.62
Consensus pattern (11 bp):
ATTTTACTATT
Found at i:39895900 original size:105 final size:105
Alignment explanation
Indices: 39895790--39895997 Score: 416
Period size: 105 Copynumber: 2.0 Consensus size: 105
39895780 GTGATTTTAT
39895790 TTTTGAAAAAAGTTTTGGGTCTATTTTGGAATTCCAGTCAATATCATCGATATACAAATCTGTTG
1 TTTTGAAAAAAGTTTTGGGTCTATTTTGGAATTCCAGTCAATATCATCGATATACAAATCTGTTG
39895855 CATTACTTGACAACTTAATCTCGCAAGAAAAATCATGAGA
66 CATTACTTGACAACTTAATCTCGCAAGAAAAATCATGAGA
39895895 TTTTGAAAAAAGTTTTGGGTCTATTTTGGAATTCCAGTCAATATCATCGATATACAAATCTGTTG
1 TTTTGAAAAAAGTTTTGGGTCTATTTTGGAATTCCAGTCAATATCATCGATATACAAATCTGTTG
39895960 CATTACTTGACAACTTAATCTCGCAAGAAAAATCATGA
66 CATTACTTGACAACTTAATCTCGCAAGAAAAATCATGA
39895998 TAAATTTCTC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (105 bp):
TTTTGAAAAAAGTTTTGGGTCTATTTTGGAATTCCAGTCAATATCATCGATATACAAATCTGTTG
CATTACTTGACAACTTAATCTCGCAAGAAAAATCATGAGA
Found at i:39897934 original size:28 final size:26
Alignment explanation
Indices: 39897903--39897963 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
39897893 GAATAAAAAA
39897903 ATCTTTTATATAAATACAAAATAGATGT
1 ATCTTTTATATAAA-ACAAAATA-ATGT
* * *
39897931 ATCTTTT-TGTAAAATAAAATATTGT
1 ATCTTTTATATAAAACAAAATAATGT
39897956 ATCTTTTA
1 ATCTTTTA
39897964 ACGAAATATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 10 0.34
26 7 0.24
27 5 0.17
28 7 0.24
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (26 bp):
ATCTTTTATATAAAACAAAATAATGT
Found at i:39899002 original size:17 final size:17
Alignment explanation
Indices: 39898977--39899040 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
39898967 AATAAGTTTG
*
39898977 AATTTATTTTAAATTCA
1 AATTTATTTTAAATTTA
* * *
39898994 AATTCATTTTGAATTTG
1 AATTTATTTTAAATTTA
*
39899011 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
39899028 AATTTATTTTAAA
1 AATTTATTTTAAA
39899041 AAAAAATAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:39899011 original size:34 final size:34
Alignment explanation
Indices: 39898973--39899037 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
39898963 TTTAAATAAG
*
39898973 TTTGAATTTATTTTAAATTCAAATTCATTTTGAA
1 TTTGAATTTACTTTAAATTCAAATTCATTTTGAA
* *
39899007 TTTGAATTTACTTTAAATTTAAATTTATTTT
1 TTTGAATTTACTTTAAATTCAAATTCATTTT
39899038 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (34 bp):
TTTGAATTTACTTTAAATTCAAATTCATTTTGAA
Found at i:39903376 original size:16 final size:16
Alignment explanation
Indices: 39903355--39903387 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39903345 TTTGCCTCAG
39903355 GATTCAAAAAAATAAA
1 GATTCAAAAAAATAAA
*
39903371 GATTCAAAACAATAAA
1 GATTCAAAAAAATAAA
39903387 G
1 G
39903388 TCTACTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (16 bp):
GATTCAAAAAAATAAA
Found at i:39905845 original size:30 final size:29
Alignment explanation
Indices: 39905809--39905899 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 29
39905799 CCTTGGAGGT
39905809 CCTTAAACTATCCAAAAATCATATTTTGAC
1 CCTTAAACT-TCCAAAAATCATATTTTGAC
*
39905839 CCTTAAACTTTCCAAAATTCCAT-TTTTGAC
1 CCTTAAAC-TTCCAAAAAT-CATATTTTGAC
* *
39905869 CC-TAAACGTTCCAAAAATCACATTTTTAC
1 CCTTAAAC-TTCCAAAAATCATATTTTGAC
39905898 CC
1 CC
39905900 CGAAATTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.04
29 22 0.42
30 25 0.47
31 4 0.08
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CCTTAAACTTCCAAAAATCATATTTTGAC
Found at i:39905874 original size:29 final size:28
Alignment explanation
Indices: 39905812--39906336 Score: 236
Period size: 29 Copynumber: 18.0 Consensus size: 28
39905802 TGGAGGTCCT
* *
39905812 TAAACTATCCAAAAAT-CATATTTTGACCC
1 TAAACTTTCCAAAATTCCAT-TTTT-ACCC
39905841 TTAAACTTTCCAAAATTCCATTTTTGACCC
1 -TAAACTTTCCAAAATTCCATTTTT-ACCC
* *
39905871 TAAACGTTCCAAAAATCACATTTTTACCCC
1 TAAACTTTCCAAAATTC-CATTTTTA-CCC
* * *
39905901 GAAATTTTCCAAACTTCCATTTTTAACCC
1 TAAACTTTCCAAAATTCCATTTTT-ACCC
* ** * *
39905930 TAAATTTTTTGAAAATTACATTTTAACCC
1 TAAA-CTTTCCAAAATTCCATTTTTACCC
* * *
39905959 TTGAACTTTCCAAAACTCCA-TTTTAACC
1 -TAAACTTTCCAAAATTCCATTTTTACCC
* * *
39905987 TCAAATTTTCTAAAAATTACATTTTTACCCC
1 T-AAACTTTC-CAAAATTCCATTTTTA-CCC
* *
39906018 TAAACTTTCCAAAATTCCATTTTAATCAC
1 TAAACTTTCCAAAATTCCATTTTTA-CCC
* ** *
39906047 -AAATTTTTTGAAAATTACATTTTTACACC
1 TAAA-CTTTCCAAAATTCCATTTTTAC-CC
* *
39906076 TAAA-ATTCCAAAAATTCCATTTTTAAGCTC
1 TAAACTTTCC-AAAATTCCATTTTT-A-CCC
* * *
39906106 AAAAC-TTCTAAAAATTACATTTTTACCC
1 TAAACTTTC-CAAAATTCCATTTTTACCC
* *
39906134 TCGAAC-TTCCAAAAATTCTATTTTTAACCC
1 T-AAACTTTCC-AAAATTCCATTTTT-ACCC
* * *
39906164 TAAAAC-TTCAAAAAATTACA-TGTTACCC
1 T-AAACTTTC-CAAAATTCCATTTTTACCC
*
39906192 CAAAC-TTCCAAAATTTCCATTTTTGATCCC
1 TAAACTTTCCAAAA-TTCCATTTTT-A-CCC
* *
39906222 AAAAC-TTCCAAAAATTACATTTTTACCCCC
1 TAAACTTTCC-AAAATTCCATTTTTA--CCC
*
39906252 T-AAC-TTCCAAAAATTCCATTTTGACCC
1 TAAACTTTCC-AAAATTCCATTTTTACCC
*
39906279 TGAAGC-TTCCAAAAATTACCA-TTTTACCGC
1 T-AAACTTTCC-AAAATT-CCATTTTTACC-C
* *
39906309 -GAA-TGTCCAAAAATTCCATTTTTGACCC
1 TAAACTTTCC-AAAATTCCATTTTT-ACCC
39906337 CGATGCTTTC
Statistics
Matches: 384, Mismatches: 76, Indels: 72
0.72 0.14 0.14
Matches are distributed among these distances:
26 4 0.01
27 19 0.05
28 43 0.11
29 162 0.42
30 145 0.38
31 11 0.03
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (28 bp):
TAAACTTTCCAAAATTCCATTTTTACCC
Found at i:39905910 original size:59 final size:57
Alignment explanation
Indices: 39905812--39906538 Score: 412
Period size: 59 Copynumber: 12.4 Consensus size: 57
39905802 TGGAGGTCCT
* * * ** *
39905812 TAAACTATCCAAAAATCATATTTTGACCCTTAAACTTTCCAAAATTCCATTTTTGACCC
1 TAAACT-TCCAAAAATTACATTTTTACCCCGAAA-TTTCCAAAATTCCATTTTTAACCC
* *
39905871 TAAACGTTCCAAAAATCACATTTTTACCCCGAAATTTTCCAAACTTCCATTTTTAACCC
1 TAAAC-TTCCAAAAATTACATTTTTACCCCGAAA-TTTCCAAAATTCCATTTTTAACCC
* *** * * * *
39905930 TAAATTTTTTGAAAATTACATTTTAACCCTTGAACTTTCCAAAACTCCA-TTTTAA-CC
1 TAAA-CTTCCAAAAATTACATTTTTACCC-CGAAATTTCCAAAATTCCATTTTTAACCC
* * * *
39905987 TCAAATTTTCTAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAATCAC
1 T-AAA-CTTCCAAAAATTACATTTTTACCCCGAAA-TTTCCAAAATTCCATTTTTAA-CCC
* *** * * * *
39906047 -AAATTTTTTGAAAATTACATTTTTACACCTAAAATTCCAAAAATTCCATTTTTAAGCTC
1 TAAA-CTTCCAAAAATTACATTTTTACCCCGAAATTTCC-AAAATTCCATTTTTAA-CCC
* * * *
39906106 AAAACTTCTAAAAATTACATTTTTACCCTCG-AACTTCCAAAAATTCTATTTTTAACCC
1 TAAACTTCCAAAAATTACATTTTTACCC-CGAAATTTCC-AAAATTCCATTTTTAACCC
* * * *
39906164 TAAAACTTCAAAAAATTACA-TGTTACCCC-AAACTTCCAAAATTTCCATTTTTGATCCC
1 T-AAACTTCCAAAAATTACATTTTTACCCCGAAATTTCCAAAA-TTCCATTTTT-AACCC
* ** * *
39906222 AAAACTTCCAAAAATTACATTTTTACCCCCTAACTTCCAAAAATTCCA-TTTTGACCC
1 TAAACTTCCAAAAATTACATTTTTACCCCGAAATTTCC-AAAATTCCATTTTTAACCC
* * * *
39906279 TGAAGCTTCCAAAAATTACCA-TTTTACCGCG-AATGTCCAAAAATTCCATTTTTGACCCC
1 T-AAACTTCCAAAAATTA-CATTTTTACCCCGAAATTTCC-AAAATTCCATTTTT-AACCC
* ** * * * *
39906338 GATGCTTTCAAAAATTACCA-TTTTACCCCCG-GATGTCCAAAAATTCCATTTTTTGATCCC
1 TAAACTTCCAAAAATTA-CATTTTTA-CCCCGAAATTTCC-AAAATTCCA-TTTTT-AACCC
* *
39906398 -AAAGCTTTCAAAAA-T-CAGTATTTTACCCTCG--ATTGTCGTAAAATTCCATTTTTAACCCC
1 TAAA-CTTCCAAAAATTACA-T-TTTTACCC-CGAAATT-TC-CAAAATTCCATTTTTAA-CCC
* * * * *
39906457 GAACCTTCCAAAAATTACCA-TTTTACCCTCG-AATGTCTTAAAATTCCATTTTTGACCC
1 TAAACTTCCAAAAATTA-CATTTTTACCC-CGAAATTTC-CAAAATTCCATTTTTAACCC
* * *
39906515 CAAAATTCCAAATATTACCATTTT
1 TAAACTTCCAAAAATTA-CATTTT
39906539 GGCCCCAAGT
Statistics
Matches: 552, Mismatches: 78, Indels: 76
0.78 0.11 0.11
Matches are distributed among these distances:
56 4 0.01
57 63 0.11
58 183 0.33
59 244 0.44
60 56 0.10
62 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (57 bp):
TAAACTTCCAAAAATTACATTTTTACCCCGAAATTTCCAAAATTCCATTTTTAACCC
Found at i:39906365 original size:29 final size:29
Alignment explanation
Indices: 39906196--39906389 Score: 150
Period size: 29 Copynumber: 6.7 Consensus size: 29
39906186 TTACCCCAAA
* * * **
39906196 CTTCCAAAATTTCCATTTTTGATCCCAAAA
1 CTTCCAAAAATTCCA-TTTTGACCCCGATG
* * * *
39906226 CTTCCAAAAATTACATTTTTACCCC-CTAA
1 CTTCCAAAAATTCCATTTTGACCCCGAT-G
* *
39906255 CTTCCAAAAATTCCATTTTGACCCTGAAG
1 CTTCCAAAAATTCCATTTTGACCCCGATG
*
39906284 CTTCCAAAAATTACCATTTT-ACCGCGAATG
1 CTTCCAAAAATT-CCATTTTGACCCCG-ATG
39906314 --TCCAAAAATTCCATTTTTGACCCCGATG
1 CTTCCAAAAATTCCA-TTTTGACCCCGATG
*
39906342 CTTTCAAAAATTACCATTTT-ACCCCCGGATG
1 CTTCCAAAAATT-CCATTTTGA-CCCC-GATG
39906373 --TCCAAAAATTCCATTTT
1 CTTCCAAAAATTCCATTTT
39906390 TTGATCCCAA
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.02
28 24 0.18
29 62 0.46
30 39 0.29
31 7 0.05
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.34
Consensus pattern (29 bp):
CTTCCAAAAATTCCATTTTGACCCCGATG
Found at i:39906450 original size:29 final size:30
Alignment explanation
Indices: 39906418--39906514 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
39906408 AAAATCAGTA
* *
39906418 TTTT-ACCCTCGATTGTCGTAAAATTCCAT
1 TTTTAACCCTCGAATGTCCTAAAATTCCAT
*
39906447 TTTTAACCC-CGAACCT-TCCAAAAATTACCA-
1 TTTTAACCCTCGAA--TGTCCTAAAATT-CCAT
*
39906477 TTTT-ACCCTCGAATGTCTTAAAATTCCAT
1 TTTTAACCCTCGAATGTCCTAAAATTCCAT
*
39906506 TTTTGACCC
1 TTTTAACCC
39906515 CAAAATTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
28 4 0.07
29 23 0.42
30 24 0.44
31 4 0.07
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTTAACCCTCGAATGTCCTAAAATTCCAT
Found at i:39909759 original size:15 final size:16
Alignment explanation
Indices: 39909739--39909768 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39909729 TTATTATTTT
39909739 ATTTATTT-TTTAAAA
1 ATTTATTTCTTTAAAA
39909754 ATTTATTTCTTTAAA
1 ATTTATTTCTTTAAA
39909769 TAAGACTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTATTTCTTTAAAA
Found at i:39917686 original size:22 final size:22
Alignment explanation
Indices: 39917661--39917704 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39917651 TAGCAAATAA
*
39917661 TTTTAAAATTATTAAAATTATTT
1 TTTTAAAA-TAATAAAATTATTT
*
39917684 TTTTGAAATAATAAAATTATT
1 TTTTAAAATAATAAAATTATT
39917705 AAAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTAAAATAATAAAATTATTT
Found at i:39919073 original size:19 final size:18
Alignment explanation
Indices: 39919039--39919078 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
39919029 TTTTTAAATG
*
39919039 TTTTTTAATTTTAATTAA
1 TTTTTTAATTTAAATTAA
*
39919057 TTTTTTAAGTTTAAATTTA
1 TTTTTTAA-TTTAAATTAA
39919076 TTT
1 TTT
39919079 GCTGACGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTTAATTTAAATTAA
Found at i:39921736 original size:100 final size:99
Alignment explanation
Indices: 39921617--39921815 Score: 301
Period size: 100 Copynumber: 2.0 Consensus size: 99
39921607 AAGTACGAGG
* * * *
39921617 TCCTTAGTGAATGAATGTGAAGTCAAATTTTGATTCGA-CCGGAATAATTGAGAGATATGAGCAT
1 TCCTTAGTGAATGAATGTGAAGTCAAATTTTGATTCAATCAGGAA-AATTAAGAGATACGAGCAT
* *
39921681 TTCATATATTATGGTTTGAAAGGGGACTTAATTGTA
65 TTCAGATATTATGGTTT-AAAAGGGACTTAATTGTA
* *
39921717 TCCTTAGTGAATGAATGTGAATTCGAATTTTGATTCAATCAGGAAAATTAAGAGATACGAGCATT
1 TCCTTAGTGAATGAATGTGAAGTCAAATTTTGATTCAATCAGGAAAATTAAGAGATACGAGCATT
39921782 TCAGATATTATGGTTTAAAAGGGACTTAATTGTA
66 TCAGATATTATGGTTTAAAAGGGACTTAATTGTA
39921816 AAAATACAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
99 17 0.19
100 68 0.76
101 5 0.06
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (99 bp):
TCCTTAGTGAATGAATGTGAAGTCAAATTTTGATTCAATCAGGAAAATTAAGAGATACGAGCATT
TCAGATATTATGGTTTAAAAGGGACTTAATTGTA
Found at i:39930664 original size:18 final size:18
Alignment explanation
Indices: 39930641--39930677 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39930631 AAAATACAGT
39930641 CTTACTATGATGTAATAA
1 CTTACTATGATGTAATAA
39930659 CTTACTATGATGTAATAA
1 CTTACTATGATGTAATAA
39930677 C
1 C
39930678 CTCATAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
CTTACTATGATGTAATAA
Found at i:39933679 original size:11 final size:11
Alignment explanation
Indices: 39933649--39933673 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39933639 GACACACACA
39933649 AAAAAAAAAAG
1 AAAAAAAAAAG
39933660 AAAAAAAAAAG
1 AAAAAAAAAAG
39933671 AAA
1 AAA
39933674 GGAAAATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:39936472 original size:18 final size:18
Alignment explanation
Indices: 39936435--39936473 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39936425 TTAATGCCGG
* * *
39936435 AATAATTTTTTTTGTTAA
1 AATAATATTTTTTATAAA
39936453 AATAATATTTTTTATAAA
1 AATAATATTTTTTATAAA
39936471 AAT
1 AAT
39936474 TCATATCAAT
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:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AATAATATTTTTTATAAA
Found at i:39937704 original size:2 final size:2
Alignment explanation
Indices: 39937697--39937734 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
39937687 TTCCAGTGCG
39937697 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39937735 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:39942939 original size:100 final size:99
Alignment explanation
Indices: 39942828--39943026 Score: 292
Period size: 100 Copynumber: 2.0 Consensus size: 99
39942818 AAGTACGAGG
* * * *
39942828 TCCTTAGTGAATGAATGTGAAGTTAAATTTTGATTCGATC-GAAAAAATTGAGAGATATGAGCAT
1 TCCTTAGTGAATGAATGTGAAGTCAAATTTTGATTCAATCAG-AAAAATTAAGAGATACGAGCAT
* *
39942892 TTCATATATTATGGTTTGAAAGGGGACTTAATTGTA
65 TTCAGATATTATGGTTT-AAAAGGGACTTAATTGTA
** *
39942928 TCCTTAGTGAATGAATGTGAAGTCGGATTTTGATTCAATCAGGAAAATTAAGAGATACGAGCATT
1 TCCTTAGTGAATGAATGTGAAGTCAAATTTTGATTCAATCAGAAAAATTAAGAGATACGAGCATT
39942993 TCAGATATTATGGTTTAAAAGGGACTTAATTGTA
66 TCAGATATTATGGTTTAAAAGGGACTTAATTGTA
39943027 AAATACAAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
99 17 0.19
100 71 0.80
101 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (99 bp):
TCCTTAGTGAATGAATGTGAAGTCAAATTTTGATTCAATCAGAAAAATTAAGAGATACGAGCATT
TCAGATATTATGGTTTAAAAGGGACTTAATTGTA
Found at i:39947691 original size:5 final size:5
Alignment explanation
Indices: 39947683--39947727 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
39947673 TAAATTTATT
39947683 TTTAA TTTAAA TTTAA TTTAA GTTTGAA TTTAA TTTAAA TTTAA T
1 TTTAA TTT-AA TTTAA TTTAA -TTT-AA TTTAA TTT-AA TTTAA T
39947728 ATTATTGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 18 0.50
6 16 0.44
7 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (5 bp):
TTTAA
Found at i:39947691 original size:11 final size:11
Alignment explanation
Indices: 39947675--39947727 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
39947665 TTTGAAATTA
*
39947675 AATTTATTTTT
1 AATTTAATTTT
*
39947686 AATTTAAATTT
1 AATTTAATTTT
*
39947697 AATTTAAGTTTG
1 AATTTAA-TTTT
*
39947709 AATTTAATTTA
1 AATTTAATTTT
39947720 AATTTAAT
1 AATTTAAT
39947728 ATTATTGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 27 0.75
12 9 0.25
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (11 bp):
AATTTAATTTT
Found at i:39947712 original size:17 final size:16
Alignment explanation
Indices: 39947658--39947744 Score: 77
Period size: 17 Copynumber: 5.2 Consensus size: 16
39947648 AATCATTTTA
* *
39947658 AATTTACTTTGAAATTA
1 AATTTAATTT-AAATTT
* *
39947675 AATTTATTTTTAATTT
1 AATTTAATTTAAATTT
*
39947691 AAATTTAATTTAAGTTT
1 -AATTTAATTTAAATTT
39947708 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
39947725 AATATT-ATTGTAAATTT
1 AAT-TTAATT-TAAATTT
39947742 AAT
1 AAT
39947745 AAAACCCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
16 10 0.17
17 49 0.83
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:39947740 original size:28 final size:28
Alignment explanation
Indices: 39947683--39947744 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
39947673 TAAATTTATT
*
39947683 TTTAATTTAAATTTAATTTAAGTTTGAA
1 TTTAATTTAAATTTAATTTAAGTTTAAA
39947711 TTTAATTTAAATTTAATATT-A-TTGTAAA
1 TTTAATTTAAATTTAAT-TTAAGTT-TAAA
39947739 TTTAAT
1 TTTAAT
39947745 AAAACCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 2 0.06
28 27 0.87
29 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTAATTTAAATTTAATTTAAGTTTAAA
Found at i:39948837 original size:30 final size:30
Alignment explanation
Indices: 39948785--39949226 Score: 197
Period size: 30 Copynumber: 15.0 Consensus size: 30
39948775 GAAAGTCCCT
**
39948785 AAACTATC-CAAAAATTGTATTTTGACCCCC
1 AAACT-TCTCAAAAATTACATTTTGACCCCC
* * ***
39948815 AAACTTCTCTAAAATTACATTTTTAACCTTG
1 AAACTTCTCAAAAATTACA-TTTTGACCCCC
* * *
39948846 AAACTTCT-AAAAATTACATTTTTACGCCT
1 AAACTTCTCAAAAATTACATTTTGACCCCC
* * * *
39948875 AAACTTC-CAAAATTTCCAATTTTGGCCCCA
1 AAACTTCTCAAAAATTAC-ATTTTGACCCCC
*
39948905 AAACTTCTC-AAAATTACATTTTTA-CCCC
1 AAACTTCTCAAAAATTACATTTTGACCCCC
* * **
39948933 GAACTTC-CAAAAATTCCAATTTTGACCCTG
1 AAACTTCTCAAAAATTAC-ATTTTGACCCCC
* *
39948963 AAACTTCAC-AAAATTACATTTTTACCCCC
1 AAACTTCTCAAAAATTACATTTTGACCCCC
** * * * * ***
39948992 TGACTT-TAAAAAAATTCCAATTTTAATCAAG
1 AAACTTCT-CAAAAATTAC-ATTTTGACCCCC
* *
39949023 AAAATT-TCAAAAATTACATTTT-ACCCTC
1 AAACTTCTCAAAAATTACATTTTGACCCCC
* * *
39949051 GAACTTC-CCAAAATTACATTTTGACCCCG
1 AAACTTCTCAAAAATTACATTTTGACCCCC
*
39949080 AAACTT-TCAAAAATTTCTATTTT-ACCCCC
1 AAACTTCTCAAAAATTAC-ATTTTGACCCCC
* * * * *
39949109 AAA-TACCCAAAAATT-CTATTTTTAACCTCG
1 AAACTTCTCAAAAATTAC-A-TTTTGACCCCC
*
39949139 AAAC-TCTCAAAGATTACCATTTTGA-CCCC
1 AAACTTCTCAAAAATTA-CATTTTGACCCCC
* * * * *
39949168 GAA-TGTC-CAAAAACTCCATTTTTGACCTCG
1 AAACT-TCTCAAAAATTACA-TTTTGACCCCC
39949198 AAACTT-TCAAAAATTACCATTTT-ACCCCC
1 AAACTTCTCAAAAATTA-CATTTTGACCCCC
39949227 GAGAGTCCAT
Statistics
Matches: 300, Mismatches: 83, Indels: 59
0.68 0.19 0.13
Matches are distributed among these distances:
27 1 0.00
28 42 0.14
29 108 0.36
30 116 0.39
31 32 0.11
32 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (30 bp):
AAACTTCTCAAAAATTACATTTTGACCCCC
Found at i:39949106 original size:29 final size:29
Alignment explanation
Indices: 39948793--39949225 Score: 224
Period size: 29 Copynumber: 14.7 Consensus size: 29
39948783 CTAAACTATC
** *
39948793 CAAAAATTGTATTTTGACCCCCAAACTTCT
1 CAAAAATTACATTTTGACCCCGAAACTT-T
* * **
39948823 CTAAAATTACATTTTTAACCTTGAAAC-TT
1 CAAAAATTACA-TTTTGACCCCGAAACTTT
* * * *
39948852 CTAAAAATTACATTTTTACGCCTAAACTTC
1 C-AAAAATTACATTTTGACCCCGAAACTTT
* * * *
39948882 CAAAATTTCCAATTTTGGCCCCAAAACTTCT
1 CAAAAATTAC-ATTTTGACCCCGAAACTT-T
* *
39948913 C-AAAATTACATTTTTACCCCG-AACTTC
1 CAAAAATTACATTTTGACCCCGAAACTTT
* *
39948940 CAAAAATTCCAATTTTGACCCTGAAAC-TT
1 CAAAAATTAC-ATTTTGACCCCGAAACTTT
* ***
39948969 CACAAAATTACATTTTTACCCCCTGACTTT
1 CA-AAAATTACATTTTGACCCCGAAACTTT
* * * * ** *
39948999 AAAAAAATTCCAATTTTAATCAAGAAAATTT
1 -CAAAAATTAC-ATTTTGACCCCGAAACTTT
*
39949030 CAAAAATTACATTTT-ACCCTCG-AACTTC
1 CAAAAATTACATTTTGACCC-CGAAACTTT
*
39949058 CCAAAATTACATTTTGACCCCGAAACTTT
1 CAAAAATTACATTTTGACCCCGAAACTTT
* * **
39949087 CAAAAATTTCTATTTT-ACCCCCAAA-TACC
1 CAAAAATTAC-ATTTTGACCCCGAAACT-TT
* * *
39949116 CAAAAATT-CTATTTTTAACCTCGAAACTCT
1 CAAAAATTAC-A-TTTTGACCCCGAAACTTT
* *
39949146 CAAAGATTACCATTTTGACCCCG-AA-TGTC
1 CAAAAATTA-CATTTTGACCCCGAAACT-TT
* * *
39949175 CAAAAACTCCATTTTTGACCTCGAAACTTT
1 CAAAAATTACA-TTTTGACCCCGAAACTTT
39949205 CAAAAATTACCATTTT-ACCCC
1 CAAAAATTA-CATTTTGACCCC
39949226 CGAGAGTCCA
Statistics
Matches: 299, Mismatches: 77, Indels: 55
0.69 0.18 0.13
Matches are distributed among these distances:
27 1 0.00
28 41 0.14
29 117 0.39
30 110 0.37
31 29 0.10
32 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (29 bp):
CAAAAATTACATTTTGACCCCGAAACTTT
Found at i:39949227 original size:59 final size:57
Alignment explanation
Indices: 39948793--39949228 Score: 301
Period size: 59 Copynumber: 7.4 Consensus size: 57
39948783 CTAAACTATC
** * * * * * *
39948793 CAAAAATTGTATTTTGACCCCCAAACTTCTCTAAAATTACATTTTTAACCTTGAAAC-TT
1 CAAAAATTACATTTT-ACCCCCGAA-TTC-CAAAAATTCCAATTTTGACCTCGAAACTTT
* ** * * * *
39948852 CTAAAAATTACATTTTTACGCCTAAACTTCCAAAATTTCCAATTTTGGCCCCAAAACTTCT
1 C-AAAAATTACA-TTTTACCCCCGAA-TTCCAAAAATTCCAATTTTGACCTCGAAACTT-T
39948913 C-AAAATTACATTTTTA-CCCCGAACTTCCAAAAATTCCAATTTTGACC-CTGAAAC-TT
1 CAAAAATTACA-TTTTACCCCCGAA-TTCCAAAAATTCCAATTTTGACCTC-GAAACTTT
* ** * * ** *
39948969 CACAAAATTACATTTTTACCCCCTGACTTTAAAAAAATTCCAATTTTAATCAAGAAAATTT
1 CA-AAAATTACA-TTTTACCCCC-GA-ATTCCAAAAATTCCAATTTTGACCTCGAAACTTT
* * * *
39949030 CAAAAATTACATTTTACCCTCGAACTTCCCAAAATTAC-ATTTTGACCCCGAAACTTT
1 CAAAAATTACATTTTACCCCCGAA-TTCCAAAAATTCCAATTTTGACCTCGAAACTTT
* * * * * * *
39949087 CAAAAATTTCTATTTTACCCCCAAATACCCAAAAATTCTATTTTTAACCTCGAAACTCT
1 CAAAAATTAC-ATTTTACCCCCGAAT-TCCAAAAATTCCAATTTTGACCTCGAAACTTT
* * *
39949146 CAAAGATTACCATTTTGA-CCCCGAATGTCCAAAAACTCCATTTTTGACCTCGAAACTTT
1 CAAAAATTA-CATTTT-ACCCCCGAAT-TCCAAAAATTCCAATTTTGACCTCGAAACTTT
39949205 CAAAAATTACCATTTTACCCCCGA
1 CAAAAATTA-CATTTTACCCCCGA
39949229 GAGTCCATAA
Statistics
Matches: 300, Mismatches: 58, Indels: 38
0.76 0.15 0.10
Matches are distributed among these distances:
56 2 0.01
57 26 0.09
58 77 0.26
59 129 0.43
60 56 0.19
61 10 0.03
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (57 bp):
CAAAAATTACATTTTACCCCCGAATTCCAAAAATTCCAATTTTGACCTCGAAACTTT
Found at i:39952435 original size:25 final size:31
Alignment explanation
Indices: 39952392--39952468 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
39952382 ATTTTGAACA
39952392 AAATAATTAATTTACATTTTGATCTAACATAC
1 AAAT-ATTAATTTACATTTTGATCTAACATAC
39952424 AAATATTAATTTACATTTTGATCTAACATAC
1 AAATATTAATTTACATTTTGATCTAACATAC
39952455 AAATATTAATTTAC
1 AAATATTAATTTAC
39952469 TGTAGAGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 41 0.91
32 4 0.09
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.42
Consensus pattern (31 bp):
AAATATTAATTTACATTTTGATCTAACATAC
Found at i:39957463 original size:17 final size:17
Alignment explanation
Indices: 39957427--39957464 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39957417 CTTAAGGCCG
* *
39957427 AAATAATTTTTTTGTCA
1 AAATAATTTTTTTATAA
39957444 AAATAATTTTTTTATAA
1 AAATAATTTTTTTATAA
39957461 AAAT
1 AAAT
39957465 TCATATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
AAATAATTTTTTTATAA
Found at i:39959196 original size:36 final size:36
Alignment explanation
Indices: 39959122--39959196 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
39959112 TTAATTTGGC
* *
39959122 CAACACGTAATATAAACATCACCTAAACATCGTCTT
1 CAACAAGTAATATAAACATCACCTAAACATCATCTT
* *
39959158 CAACAAGTAATATAGACATCACCTAAACATCATGTT
1 CAACAAGTAATATAAACATCACCTAAACATCATCTT
39959194 CAA
1 CAA
39959197 ACTAATATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (36 bp):
CAACAAGTAATATAAACATCACCTAAACATCATCTT
Found at i:39960114 original size:24 final size:24
Alignment explanation
Indices: 39960087--39960169 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 24
39960077 TAATTTTCTA
39960087 AAAATTATAAATATATAGATTATT
1 AAAATTATAAATATATAGATTATT
* * *
39960111 AAAATAATAAA-AT-TATATTTTT
1 AAAATTATAAATATATAGATTATT
** *
39960133 ATTATGATAAAAATTATATAGATTATT
1 AAAAT--TATAAA-TATATAGATTATT
39960160 AAAAATTATA
1 -AAAATTATA
39960170 CAATTTAACT
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
22 10 0.24
23 2 0.05
24 14 0.34
26 5 0.12
27 7 0.17
28 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AAAATTATAAATATATAGATTATT
Found at i:39961976 original size:15 final size:16
Alignment explanation
Indices: 39961949--39961978 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39961939 GTTAGTCTTA
39961949 TTTAAAGAAATAAATT
1 TTTAAAGAAATAAATT
39961965 TTTAAA-AAATAAAT
1 TTTAAAGAAATAAAT
39961979 AAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TTTAAAGAAATAAATT
Found at i:39963482 original size:89 final size:90
Alignment explanation
Indices: 39963389--39963553 Score: 253
Period size: 89 Copynumber: 1.8 Consensus size: 90
39963379 AAATCTGAAT
* *
39963389 ATAATATAATGGCCAAAACAATAATTTGATTAAAAATA-AAA-TTAATTTATTTACGTATGCGAC
1 ATAATATAATGACCAAAACAATAATTTGATTAAAAA-ACAAATTTAATTTATTTACCTATGCGAC
39963452 AACCAAAATGATTATATCATAACATC
65 AACCAAAATGATTATATCATAACATC
* *
39963478 ATAATATAATGACCAAAACAATAATTTGATTAAAAAACAAATTTTATTTATTTACCTATGTGACA
1 ATAATATAATGACCAAAACAATAATTTGATTAAAAAACAAATTTAATTTATTTACCTATGCGACA
**
39963543 GTCAAAATGAT
66 ACCAAAATGAT
39963554 GTGGAATAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
88 1 0.01
89 38 0.56
90 29 0.43
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.33
Consensus pattern (90 bp):
ATAATATAATGACCAAAACAATAATTTGATTAAAAAACAAATTTAATTTATTTACCTATGCGACA
ACCAAAATGATTATATCATAACATC
Found at i:39971418 original size:15 final size:16
Alignment explanation
Indices: 39971392--39971421 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39971382 ATGCCTGCAA
39971392 ATTTTAAAAAATATAT
1 ATTTTAAAAAATATAT
39971408 ATTTT-AAAAATATA
1 ATTTTAAAAAATATA
39971422 ACTCAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTTAAAAAATATAT
Found at i:39980523 original size:24 final size:24
Alignment explanation
Indices: 39980485--39980554 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 24
39980475 ATTTGAAAAA
* *
39980485 TAATT-TTTCAGTTAAACTTTGGT
1 TAATTGTTTCAATTAAACTCTGGT
*
39980508 TAATTGTTTCAATTAAACTCTGTT
1 TAATTGTTTCAATTAAACTCTGGT
39980532 TATATTTGTTTCAATTAAACTCT
1 TA-A-TTGTTTCAATTAAACTCT
39980555 ATTTATTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 5 0.12
24 17 0.41
25 1 0.02
26 18 0.44
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (24 bp):
TAATTGTTTCAATTAAACTCTGGT
Found at i:39980543 original size:26 final size:25
Alignment explanation
Indices: 39980490--39980566 Score: 95
Period size: 24 Copynumber: 3.1 Consensus size: 25
39980480 AAAAATAATT
* * *
39980490 TTTCAGTTAAACTTTGGTTA-ATTG
1 TTTCAATTAAACTCTGTTTATATTG
39980514 TTTCAATTAAACTCTGTTTATATTTG
1 TTTCAATTAAACTCTGTTTATA-TTG
*
39980540 TTTCAATTAAACTCTATTTAT-TTG
1 TTTCAATTAAACTCTGTTTATATTG
39980564 TTT
1 TTT
39980567 GAGTCAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
24 23 0.49
25 1 0.02
26 23 0.49
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.55
Consensus pattern (25 bp):
TTTCAATTAAACTCTGTTTATATTG
Done.