Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 146 of 150
Found at i:44090237 original size:20 final size:20
Alignment explanation
Indices: 44090212--44090251 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
44090202 AAAGTAAATA
44090212 GAAGAGCAAGAACCGTAGGT
1 GAAGAGCAAGAACCGTAGGT
44090232 GAAGAGCAAGAACCGTAGGT
1 GAAGAGCAAGAACCGTAGGT
44090252 TGCTTGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.35, T:0.10
Consensus pattern (20 bp):
GAAGAGCAAGAACCGTAGGT
Found at i:44097250 original size:21 final size:21
Alignment explanation
Indices: 44097226--44097278 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
44097216 ATAATTACGT
44097226 TTATTTTCTTTAAATT-AAGAA
1 TTATTTT-TTTAAATTCAAGAA
* *
44097247 TTATTTTTTTAACTTCATGAA
1 TTATTTTTTTAAATTCAAGAA
*
44097268 TTATTTATTTA
1 TTATTTTTTTA
44097279 TTTTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (21 bp):
TTATTTTTTTAAATTCAAGAA
Found at i:44097359 original size:14 final size:13
Alignment explanation
Indices: 44097332--44097364 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
44097322 ATAATAAATT
44097332 ATATCTCATTAAAA
1 ATAT-TCATTAAAA
44097346 ATATTCATTAAAA
1 ATATTCATTAAAA
44097359 ATATTC
1 ATATTC
44097365 CACGTATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATTCATTAAAA
Found at i:44101567 original size:31 final size:32
Alignment explanation
Indices: 44101532--44101596 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
44101522 AAATATTCAT
44101532 TAAACTATTC-AAAAGTTTTCATTTAACT-CAC
1 TAAACTATTCGAAAA-TTTTCATTTAACTGCAC
* * *
44101563 TAAACTTTTCGAAAATTTTTATTTTACTGCAC
1 TAAACTATTCGAAAATTTTCATTTAACTGCAC
44101595 TA
1 TA
44101597 TTAAGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (32 bp):
TAAACTATTCGAAAATTTTCATTTAACTGCAC
Found at i:44114427 original size:5 final size:5
Alignment explanation
Indices: 44114417--44114483 Score: 61
Period size: 5 Copynumber: 13.8 Consensus size: 5
44114407 AACGATGAGC
* *
44114417 AAAAG AAAAG -AAAG -AAAG AAAAAG AAAAG GAAAG -GAAG AAAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG
*
44114466 -AGAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAA
44114484 AAATGGAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 14 0.27
5 31 0.60
6 7 0.13
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:44114455 original size:20 final size:20
Alignment explanation
Indices: 44114417--44114483 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 20
44114407 AACGATGAGC
44114417 AAAAGAAAA-GAAAGAAAGA
1 AAAAGAAAAGGAAAGAAAGA
*
44114436 AAAAGAAAAGGAAAGGAAGA
1 AAAAGAAAAGGAAAGAAAGA
*
44114456 AAAAGAAAA-GAGAGAAA-A
1 AAAAGAAAAGGAAAGAAAGA
44114474 GAAAAGAAAA
1 -AAAAGAAAA
44114484 AAATGGAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.02
19 24 0.56
20 18 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAGGAAAGAAAGA
Found at i:44114459 original size:15 final size:14
Alignment explanation
Indices: 44114417--44114486 Score: 69
Period size: 14 Copynumber: 5.3 Consensus size: 14
44114407 AACGATGAGC
44114417 AAAAGAAAAGAA-A
1 AAAAGAAAAGAAGA
*
44114430 GAAAG-AAA-AAGA
1 AAAAGAAAAGAAGA
* *
44114442 AAAGGAAAGGAAGA
1 AAAAGAAAAGAAGA
44114456 AAAAGAAAAG-AGA
1 AAAAGAAAAGAAGA
44114469 GAAAAGAAAAGAA-A
1 -AAAAGAAAAGAAGA
44114483 AAAA
1 AAAA
44114487 TGGAAAGAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 2 0.04
12 7 0.15
13 13 0.28
14 23 0.50
15 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAGA
Found at i:44114484 original size:20 final size:19
Alignment explanation
Indices: 44114417--44114484 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
44114407 AACGATGAGC
44114417 AAAAG-AAAAGAAAGAAAG
1 AAAAGAAAAAGAAAGAAAG
* *
44114435 AAAAAGAAAAGGAAAGGAAG
1 -AAAAGAAAAAGAAAGAAAG
*
44114455 AAAA-AGAAAAGAGAGAAAAG
1 AAAAGA-AAAAGAAAG-AAAG
44114475 AAAAGAAAAA
1 AAAAGAAAAA
44114485 AATGGAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.03
19 16 0.40
20 22 0.55
21 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAAGAAAG
Found at i:44117400 original size:21 final size:21
Alignment explanation
Indices: 44117376--44117421 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
44117366 CGAGAGAAGC
*
44117376 AGAGGTTGAAGCGAGGGAAAT
1 AGAGGCTGAAGCGAGGGAAAT
* *
44117397 AGAGGCTGCAGCGAGGGAAGT
1 AGAGGCTGAAGCGAGGGAAAT
44117418 AGAG
1 AGAG
44117422 CAGTGTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.46, T:0.11
Consensus pattern (21 bp):
AGAGGCTGAAGCGAGGGAAAT
Found at i:44117942 original size:86 final size:85
Alignment explanation
Indices: 44117807--44118009 Score: 223
Period size: 86 Copynumber: 2.4 Consensus size: 85
44117797 GCGATAAAAA
** * *
44117807 CGCCGCTAAAGATCAGGGACTTTAGCGGCGTTTGTTGGAAAGGTACCGCTAAAGATCAGGGTTTT
1 CGCCGCTAAAGATCAGGGACTTTAGCGGCGTTTGTCAGAAAGG-ACCGCTAAAGATCAGGATCTT
44117872 TAGCGGCGTTT-TCTGGAGAAG
65 TAGCGGCGTTTGTCTGG-GAAG
* * * **
44117893 CGCCACTAAAGATCAGGGTCTTTAGCGGCGTTTGTCAGAGAAGCG-CCGCTAAAGGTCATTATCT
1 CGCCGCTAAAGATCAGGGACTTTAGCGGCGTTTGTCAGA-AAG-GACCGCTAAAGATCAGGATCT
* *
44117957 TTAGCGGCGTTTGTTTGGTAAG
64 TTAGCGGCGTTTGTCTGGGAAG
* *
44117979 CGCCGCTAAAGACCA-TGACCTTTAGCGGCGT
1 CGCCGCTAAAGATCAGGGA-CTTTAGCGGCGT
44118010 CTTTCCATGG
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
85 1 0.01
86 89 0.91
87 7 0.07
88 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.27
Consensus pattern (85 bp):
CGCCGCTAAAGATCAGGGACTTTAGCGGCGTTTGTCAGAAAGGACCGCTAAAGATCAGGATCTTT
AGCGGCGTTTGTCTGGGAAG
Found at i:44117970 original size:43 final size:43
Alignment explanation
Indices: 44117742--44118009 Score: 197
Period size: 43 Copynumber: 6.2 Consensus size: 43
44117732 TCTATCAAAA
* ** * * *
44117742 TTAGTGGCGTTTGTGGGAAAAGCGCTGCTAAAGATCACGATCT
1 TTAGCGGCGTTTGTCAGAGAAGCGCCGCTAAAGATCATGATCT
** * * * *
44117785 TCCGCGGCGTTTG-CGATAAAAACGCCGCTAAAGATCAGGGA-CT
1 TTAGCGGCGTTTGTC-AGAGAAGCGCCGCTAAAGATCA-TGATCT
** * * *
44117828 TTAGCGGCGTTTGTTGGA-AAG-GTACCGCTAAAGATCAGGGTTT
1 TTAGCGGCGTTTGTCAGAGAAGCG--CCGCTAAAGATCATGATCT
* * * *
44117871 TTAGCGGCGTTT-TCTGGAGAAGCGCCACTAAAGATCAGGGTCT
1 TTAGCGGCGTTTGTC-AGAGAAGCGCCGCTAAAGATCATGATCT
* *
44117914 TTAGCGGCGTTTGTCAGAGAAGCGCCGCTAAAGGTCATTATCT
1 TTAGCGGCGTTTGTCAGAGAAGCGCCGCTAAAGATCATGATCT
** * *
44117957 TTAGCGGCGTTTGTTTG-GTAAGCGCCGCTAAAGACCATGACCT
1 TTAGCGGCGTTTGTCAGAG-AAGCGCCGCTAAAGATCATGATCT
44118000 TTAGCGGCGT
1 TTAGCGGCGT
44118010 CTTTCCATGG
Statistics
Matches: 182, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
41 1 0.01
42 6 0.03
43 167 0.92
44 7 0.04
45 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (43 bp):
TTAGCGGCGTTTGTCAGAGAAGCGCCGCTAAAGATCATGATCT
Found at i:44120270 original size:27 final size:28
Alignment explanation
Indices: 44120223--44120278 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
44120213 TTTTATGTTT
44120223 AATAAATATAATTAATATTTATTTTTAA
1 AATAAATATAATTAATATTTATTTTTAA
* *
44120251 AATAAAT-TTATTTATATTTATTTTTAA
1 AATAAATATAATTAATATTTATTTTTAA
44120278 A
1 A
44120279 TCCTTCAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATAAATATAATTAATATTTATTTTTAA
Found at i:44121377 original size:10 final size:10
Alignment explanation
Indices: 44121364--44121388 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44121354 CTAAAAGTTC
44121364 TAAAAAATTT
1 TAAAAAATTT
44121374 TAAAAAATTT
1 TAAAAAATTT
44121384 TAAAA
1 TAAAA
44121389 TTCCAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:44121405 original size:28 final size:29
Alignment explanation
Indices: 44121347--44121410 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
44121337 AGAAAAAAAT
* *
44121347 AAAAATTCTAAAAGTTCTAAAAAATTTTA
1 AAAAATTCTAAAAGTTCCAAAAAATTCTA
*
44121376 AAAAATTTTAAAA-TTCCAAAATAA-TCTA
1 AAAAATTCTAAAAGTTCCAAAA-AATTCTA
*
44121404 AACAATT
1 AAAAATT
44121411 GAGATTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATTCTAAAAGTTCCAAAAAATTCTA
Found at i:44136171 original size:28 final size:28
Alignment explanation
Indices: 44136131--44136185 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
44136121 ATCAACTGTG
44136131 AGACAGGGGCAACAAACAAAGTAGAATA
1 AGACAGGGGCAACAAACAAAGTAGAATA
44136159 AGACAGGGGCAACAAACAAAGTAGAAT
1 AGACAGGGGCAACAAACAAAGTAGAAT
44136186 CAACCCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.15, G:0.25, T:0.07
Consensus pattern (28 bp):
AGACAGGGGCAACAAACAAAGTAGAATA
Found at i:44139258 original size:27 final size:26
Alignment explanation
Indices: 44139215--44139274 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
44139205 AAGTACATGA
44139215 AAAAATAGATTAAAAAATCAAAAATAT
1 AAAAATAGATTAAAAAAT-AAAAATAT
*
44139242 AAAAATA-ATTCATAAAATAAAAATAT
1 AAAAATAGATT-AAAAAATAAAAATAT
44139268 AATAAAT
1 AA-AAAT
44139275 TTTAGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAATAGATTAAAAAATAAAAATAT
Found at i:44139769 original size:20 final size:20
Alignment explanation
Indices: 44139744--44139788 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
44139734 TTTATAAATT
44139744 ATTTTTGAATTATTTTTATA
1 ATTTTTGAATTATTTTTATA
* *
44139764 ATTTTTTATTTATTTTTATA
1 ATTTTTGAATTATTTTTATA
44139784 ATTTT
1 ATTTT
44139789 AATCTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTTGAATTATTTTTATA
Found at i:44139798 original size:18 final size:20
Alignment explanation
Indices: 44139744--44139802 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
44139734 TTTATAAATT
44139744 ATTTTTGAAT-TATTTTTATA
1 ATTTTT-AATCTATTTTTATA
* *
44139764 ATTTTTTATTTATTTTTATA
1 ATTTTTAATCTATTTTTATA
44139784 A-TTTTAATCTA-TTTTATA
1 ATTTTTAATCTATTTTTATA
44139802 A
1 A
44139803 AGTTTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.23
19 10 0.29
20 17 0.49
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTAATCTATTTTTATA
Found at i:44152701 original size:42 final size:42
Alignment explanation
Indices: 44152642--44152778 Score: 184
Period size: 42 Copynumber: 3.5 Consensus size: 42
44152632 ACCCCTCGGG
44152642 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
* *
44152684 GGAATCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
*
44152717 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
44152759 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
44152779 ACCAATGAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 18 0.22
34 5 0.06
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 6 0.07
42 38 0.47
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
Found at i:44152753 original size:75 final size:75
Alignment explanation
Indices: 44152536--44152813 Score: 442
Period size: 75 Copynumber: 3.8 Consensus size: 75
44152526 TATCCGTTAT
* * *
44152536 CGGTGGATTCAGCACTTAGCAACCACCAATTAGTCGGGGAATTAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
44152601 ATTTAAGATA
66 ATTTAAGATA
* * *
44152611 CGGTGGGATCAGCACTTAGCAACC-CC--T-CG--GGGGAATCAGCACTTAGCAACCCCCTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
44152670 ATTTAAGATA
66 ATTTAAGATA
44152680 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
44152745 ATTTAAGATA
66 ATTTAAGATA
* *
44152755 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCC
44152814 CTTTATATTC
Statistics
Matches: 187, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
69 61 0.33
70 2 0.01
71 1 0.01
72 2 0.01
73 1 0.01
74 2 0.01
75 118 0.63
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTTAAGATA
Found at i:44156984 original size:12 final size:12
Alignment explanation
Indices: 44156969--44156998 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44156959 CCTATTTCAT
*
44156969 TTATTTGAATCC
1 TTATTTGAATAC
44156981 TTATTTGAATAC
1 TTATTTGAATAC
44156993 TTATTT
1 TTATTT
44156999 TATGAGGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (12 bp):
TTATTTGAATAC
Found at i:44162448 original size:2 final size:2
Alignment explanation
Indices: 44162393--44162438 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
44162383 ACCTATGTCA
44162393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44162435 AT AT
1 AT AT
44162439 TTCTTATATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44167484 original size:164 final size:164
Alignment explanation
Indices: 44167213--44167543 Score: 662
Period size: 164 Copynumber: 2.0 Consensus size: 164
44167203 TACTTCGGTT
44167213 ATACCAATGAGTGTTTGGCACAATGTATACTTCAGACGTTCTGATGAGGCACTAGGTGTCAGATT
1 ATACCAATGAGTGTTTGGCACAATGTATACTTCAGACGTTCTGATGAGGCACTAGGTGTCAGATT
44167278 GGTGTGTTGGCCGGATGATCCACGTATCTATCCCGAGTCTGAGTTAGGTTAATAGGGATTATAAA
66 GGTGTGTTGGCCGGATGATCCACGTATCTATCCCGAGTCTGAGTTAGGTTAATAGGGATTATAAA
44167343 ATATGAACTTGATAAATGATAGTGAATTGAGATG
131 ATATGAACTTGATAAATGATAGTGAATTGAGATG
44167377 ATACCAATGAGTGTTTGGCACAATGTATACTTCAGACGTTCTGATGAGGCACTAGGTGTCAGATT
1 ATACCAATGAGTGTTTGGCACAATGTATACTTCAGACGTTCTGATGAGGCACTAGGTGTCAGATT
44167442 GGTGTGTTGGCCGGATGATCCACGTATCTATCCCGAGTCTGAGTTAGGTTAATAGGGATTATAAA
66 GGTGTGTTGGCCGGATGATCCACGTATCTATCCCGAGTCTGAGTTAGGTTAATAGGGATTATAAA
44167507 ATATGAACTTGATAAATGATAGTGAATTGAGATG
131 ATATGAACTTGATAAATGATAGTGAATTGAGATG
44167541 ATA
1 ATA
44167544 ATATGAAACA
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 167 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (164 bp):
ATACCAATGAGTGTTTGGCACAATGTATACTTCAGACGTTCTGATGAGGCACTAGGTGTCAGATT
GGTGTGTTGGCCGGATGATCCACGTATCTATCCCGAGTCTGAGTTAGGTTAATAGGGATTATAAA
ATATGAACTTGATAAATGATAGTGAATTGAGATG
Found at i:44169560 original size:21 final size:22
Alignment explanation
Indices: 44169536--44169589 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
44169526 TTTTTCAAAT
*
44169536 TAATTAAATAATATATTTTTA-
1 TAATTAAATAATATATATTTAC
*
44169557 TAATTTTAA-AATATATATTTAC
1 TAA-TTAAATAATATATATTTAC
44169579 TAATTAAATAA
1 TAATTAAATAA
44169590 GAATTTGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATTAAATAATATATATTTAC
Found at i:44170582 original size:2 final size:2
Alignment explanation
Indices: 44170575--44170609 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
44170565 CCCGTGCTTT
44170575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44170610 AATTAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44170904 original size:20 final size:20
Alignment explanation
Indices: 44170868--44170935 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
44170858 ATTTAAATTT
44170868 AATTCAACCAGTTTTTTATCC
1 AATTCAACCAGTTTTTTAT-C
* *
44170889 AATTCAACTATTTTTTTATC
1 AATTCAACCAGTTTTTTATC
* * *
44170909 AATTCAATCAGTTTTATGTC
1 AATTCAACCAGTTTTTTATC
44170929 AATTCAA
1 AATTCAA
44170936 TCTTCTTCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (20 bp):
AATTCAACCAGTTTTTTATC
Found at i:44182880 original size:14 final size:15
Alignment explanation
Indices: 44182863--44182899 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
44182853 TATTTCATTT
*
44182863 ATATTA-AATCTATA
1 ATATTATAATATATA
44182877 ATA-TATAATATATA
1 ATATTATAATATATA
44182891 ATATTATAA
1 ATATTATAA
44182900 GGCATACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 13 0.65
15 5 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTATAATATATA
Found at i:44186426 original size:9 final size:9
Alignment explanation
Indices: 44186409--44186445 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44186399 TGAGTTTTCG
44186409 AATTCGAAT
1 AATTCGAAT
*
44186418 AACTCGAAT
1 AATTCGAAT
44186427 AATTCGAAT
1 AATTCGAAT
44186436 AATTCGAAT
1 AATTCGAAT
44186445 A
1 A
44186446 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:44188477 original size:110 final size:110
Alignment explanation
Indices: 44188283--44188516 Score: 308
Period size: 110 Copynumber: 2.1 Consensus size: 110
44188273 TGATATATGT
* ** * * **
44188283 CCAAGGCAACTAATCAGTGTATGGAATTGGGGTTTCAAGAATGAAACGATGATTCCTTATGGAAA
1 CCAAGGCAACTAATCAGTATACAGAAATGGGGTTTCAAGAATGAAAAGATGATTCCCAATGGAAA
44188348 AATCAACAAATCGAAATAAATAAGCAATTGCATGACAGCATAAGC
66 AATCAACAAATCGAAATAAATAAGCAATTGCATGACAGCATAAGC
* *
44188393 CCAAGGCATCTAATCGGTATACAGAAATGGGGTTTCAAGAATGAAAAGATGATTCCCAATGGAAA
1 CCAAGGCAACTAATCAGTATACAGAAATGGGGTTTCAAGAATGAAAAGATGATTCCCAATGGAAA
* * *** * *
44188458 AATCAACAAA-CGGATATAAATTAGCAATTGCATGGTGGCATATGT
66 AATCAACAAATC-GAAATAAATAAGCAATTGCATGACAGCATAAGC
44188503 CCAAGGCAACTAAT
1 CCAAGGCAACTAAT
44188517 TTCAAAAATG
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
109 1 0.01
110 105 0.99
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.23
Consensus pattern (110 bp):
CCAAGGCAACTAATCAGTATACAGAAATGGGGTTTCAAGAATGAAAAGATGATTCCCAATGGAAA
AATCAACAAATCGAAATAAATAAGCAATTGCATGACAGCATAAGC
Found at i:44188693 original size:203 final size:201
Alignment explanation
Indices: 44188315--44188719 Score: 541
Period size: 203 Copynumber: 2.0 Consensus size: 201
44188305 GGAATTGGGG
* *
44188315 TTTCAAGAATGAAACGATGATTCCTTATGGAAAAATCAACAAATCGAAATAAATAAGCAATTGCA
1 TTTCAAAAATGAAACGATAATTCCTTATGGAAAAATCAACAAATCGAAATAAATAAGCAATTGCA
*
44188380 TGACAGCATAAGCCCAAGGCATCTAATCGGTATACAGAAATGGGGTTTCAAGAATGAAAAGATGA
66 TGACAGCATAAGCCCAAGGCAACTAATCGGTATACAGAAATGGGGTTTCAAGAATGAAAAGATGA
* * * **** *
44188445 TTCCCAATGGAAAAATCAACAAACGGATATAAATTAGCAATTGCATGGTGGCATATGTCCAAGGC
131 CTCCCAATGGAAAAATCAACAAACGGAAATAAATAAGCAATTGCATGACACCATACGTCCAAGGC
44188510 AACTAA
196 AACTAA
* *
44188516 TTTCAAAAATGCAACGATAATTCCTTATGGAAAAAATCAACAAATGGAAATAAATAAGCAATTGC
1 TTTCAAAAATGAAACGATAATTCCTTATGG-AAAAATCAACAAATCGAAATAAATAAGCAATTGC
* * * * *
44188581 ATGACGCGGCA-CA-TCCAAGGCAAACTAATTGGTATA-TGTAAATGGGGTTTCAAGAATGAAAC
65 ATGA--CAGCATAAGCCCAAGGC-AACTAATCGGTATACAG-AAATGGGGTTTCAAGAATGAAA-
*
44188643 A-ATGACTCCCAATGGAAAAATCAACAAATC-GAAATGAATAAGCAATTGCATGACACCATACGT
125 AGATGACTCCCAATGGAAAAATCAACAAA-CGGAAATAAATAAGCAATTGCATGACACCATACGT
44188706 CCAAGGCAACTAA
189 CCAAGGCAACTAA
44188719 T
1 T
44188720 CGGTACACGG
Statistics
Matches: 178, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
201 27 0.15
202 45 0.25
203 100 0.56
204 6 0.03
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (201 bp):
TTTCAAAAATGAAACGATAATTCCTTATGGAAAAATCAACAAATCGAAATAAATAAGCAATTGCA
TGACAGCATAAGCCCAAGGCAACTAATCGGTATACAGAAATGGGGTTTCAAGAATGAAAAGATGA
CTCCCAATGGAAAAATCAACAAACGGAAATAAATAAGCAATTGCATGACACCATACGTCCAAGGC
AACTAA
Found at i:44191827 original size:27 final size:27
Alignment explanation
Indices: 44191770--44191832 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
44191760 CAAAGAAGAA
* * *
44191770 ACTCTCCCTTAGTTGTAGCATCAACAT
1 ACTCTCACTTAGTAGTAGCATCAACAC
*
44191797 ACTCTCACTTAGTAGTAGCATCAATAC
1 ACTCTCACTTAGTAGTAGCATCAACAC
*
44191824 ACTCCCACT
1 ACTCTCACT
44191833 CAATAAGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.30
Consensus pattern (27 bp):
ACTCTCACTTAGTAGTAGCATCAACAC
Found at i:44195911 original size:26 final size:26
Alignment explanation
Indices: 44195882--44195933 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
44195872 ATTACTTAGT
44195882 ATAATTTCCATAATTCATCATTAATC
1 ATAATTTCCATAATTCATCATTAATC
44195908 ATAATTTCCATAATTCATCATTAATC
1 ATAATTTCCATAATTCATCATTAATC
44195934 CTTATTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAATTTCCATAATTCATCATTAATC
Found at i:44208771 original size:32 final size:31
Alignment explanation
Indices: 44208712--44208771 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
44208702 TTAAAAGGAA
*
44208712 TAATAAAAATTTTCAAAAGTTTTGAAAGATT
1 TAATAAAAATTTTCAAAACTTTTGAAAGATT
* **
44208743 TAATTAAAATTTTCAGTACTTTTAGAAAG
1 TAATAAAAATTTTCAAAACTTTT-GAAAG
44208772 CTTAACTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 19 0.79
32 5 0.21
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (31 bp):
TAATAAAAATTTTCAAAACTTTTGAAAGATT
Found at i:44211009 original size:6 final size:6
Alignment explanation
Indices: 44210998--44211031 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
44210988 AATTAGTTTG
* *
44210998 AAATAT AAATAT AAATCT AAATCT AAATCT AAAT
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAAT
44211032 TTGAATTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:44213576 original size:2 final size:2
Alignment explanation
Indices: 44213569--44213630 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
44213559 AGAATTTTAT
44213569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44213611 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
44213631 AAGCTTGTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44224241 original size:2 final size:2
Alignment explanation
Indices: 44224234--44224258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44224224 ATGATTCGAG
44224234 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 T
44224259 TTCACGTCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44230323 original size:119 final size:119
Alignment explanation
Indices: 44230112--44230349 Score: 309
Period size: 119 Copynumber: 2.0 Consensus size: 119
44230102 TGTCTAGGAC
* * * ** *
44230112 AAATGACTACTCATTTACTATTGCAAGTAATGATCATTTTCATCATAGAAGATACAATGATGACG
1 AAATGACTAATCATTTACTATTGCAAGTAATGATCATTTTCATCACAAAAGATACAATGACAACC
44230177 ACAAGATAAAAATAGATCAAATTAGGAAAACA-AGTTTAATATAAAGGAATCATG
66 ACAAGATAAAAATAGATCAAATTAGGAAAACAGAG-TTAATATAAAGGAATCATG
* * *
44230231 AAATGACTAATCATTTACTATTTCAAGTAATGGTCATTTTTATCACAAAAGATACAATGACAACC
1 AAATGACTAATCATTTACTATTGCAAGTAATGATCATTTTCATCACAAAAGATACAATGACAACC
** * * * *
44230296 ATGAGA-AAAAGATGGATCGAATTAGGAAAATAGAGTTAATATAAATGAATCATG
66 ACAAGATAAAA-ATAGATCAAATTAGGAAAACAGAGTTAATATAAAGGAATCATG
44230350 GATATCCTAT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
118 4 0.04
119 96 0.94
120 2 0.02
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (119 bp):
AAATGACTAATCATTTACTATTGCAAGTAATGATCATTTTCATCACAAAAGATACAATGACAACC
ACAAGATAAAAATAGATCAAATTAGGAAAACAGAGTTAATATAAAGGAATCATG
Found at i:44236214 original size:16 final size:17
Alignment explanation
Indices: 44236201--44236238 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
44236191 TTTTAAATAT
44236201 TTAAAATTTGAAATAAC
1 TTAAAATTTGAAATAAC
* *
44236218 TTAAAA-TTAAAATTAC
1 TTAAAATTTGAAATAAC
44236234 TTAAA
1 TTAAA
44236239 TCCAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
TTAAAATTTGAAATAAC
Found at i:44249210 original size:14 final size:15
Alignment explanation
Indices: 44249178--44249210 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
44249168 AAGTGATTTT
44249178 AAAATATAAGCCCGA
1 AAAATATAAGCCCGA
44249193 AAAATATAAGCCCGA
1 AAAATATAAGCCCGA
44249208 AAA
1 AAA
44249211 GTGAAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAATATAAGCCCGA
Found at i:44263630 original size:28 final size:29
Alignment explanation
Indices: 44263568--44263631 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
44263558 CAATGACTTG
* *
44263568 ATTA-TATTAATACAAAAGTATTTATAAT
1 ATTATTATAAATACAAAAGTATTTATAAA
44263596 ATATATTATAAATA-AAAAGT-TTTATAAGA
1 AT-TATTATAAATACAAAAGTATTTATAA-A
44263625 ATTATTA
1 ATTATTA
44263632 GCCGTTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 14 0.45
29 10 0.32
30 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
ATTATTATAAATACAAAAGTATTTATAAA
Found at i:44265600 original size:29 final size:26
Alignment explanation
Indices: 44265532--44265600 Score: 66
Period size: 31 Copynumber: 2.4 Consensus size: 26
44265522 GAAAGTTTCA
*
44265532 TATGTATAATTGTACAAAATCAAAAT
1 TATGTATAATTGCACAAAATCAAAAT
*
44265558 TCATGTATCAAATTGCACATTAAATCAACAGT
1 T-ATGTAT--AATTGCACA--AAATCAA-AAT
44265590 TATGTATAATT
1 TATGTATAATT
44265601 TTAAGATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
29 12 0.34
31 13 0.37
32 3 0.09
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (26 bp):
TATGTATAATTGCACAAAATCAAAAT
Found at i:44271390 original size:2 final size:2
Alignment explanation
Indices: 44271385--44271412 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44271375 GAAAAAAACA
44271385 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
44271413 GTACCAGAGT
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:44275207 original size:7 final size:7
Alignment explanation
Indices: 44275195--44275222 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
44275185 TATTTTAACC
44275195 TATTATT
1 TATTATT
44275202 TATTATT
1 TATTATT
44275209 TATTATT
1 TATTATT
44275216 TATTATT
1 TATTATT
44275223 ATAGTGTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:44277844 original size:36 final size:36
Alignment explanation
Indices: 44277804--44277881 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
44277794 TTAAATATGT
*
44277804 TCAACATCAGATTCAAGCTAACATTTAACACCTAAA
1 TCAACATCAAATTCAAGCTAACATTTAACACCTAAA
44277840 TCAACATCAAATTCAAGCTAACATTTAACACCTAAA
1 TCAACATCAAATTCAAGCTAACATTTAACACCTAAA
*
44277876 TTAACA
1 TCAACA
44277882 CCAATATGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (36 bp):
TCAACATCAAATTCAAGCTAACATTTAACACCTAAA
Found at i:44278927 original size:17 final size:17
Alignment explanation
Indices: 44278886--44278933 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
44278876 TCAAACTCAA
44278886 ACCCAAACCCAAAA-TG
1 ACCCAAACCCAAAATTG
* *
44278902 A-CTAGAACCTAAAATTG
1 ACCCA-AACCCAAAATTG
44278919 ACCCAAACCCAAAAT
1 ACCCAAACCCAAAAT
44278934 GATCGGACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 12 0.48
18 2 0.08
ACGTcount: A:0.50, C:0.31, G:0.06, T:0.12
Consensus pattern (17 bp):
ACCCAAACCCAAAATTG
Found at i:44283123 original size:31 final size:31
Alignment explanation
Indices: 44283065--44283123 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
44283055 TATACACATG
**
44283065 AAACTTTAATTATAATTTAAATGTATACTTA
1 AAACTTTAATTATAATTTAAACATATACTTA
* * *
44283096 AAACTTTAATTTTGATTTAACCATATAC
1 AAACTTTAATTATAATTTAAACATATAC
44283124 ATTTAGAGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.44
Consensus pattern (31 bp):
AAACTTTAATTATAATTTAAACATATACTTA
Found at i:44292051 original size:8 final size:8
Alignment explanation
Indices: 44292038--44292068 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
44292028 CAATGCATCT
44292038 TAATTTAA
1 TAATTTAA
44292046 TAATTTAA
1 TAATTTAA
44292054 TAATTTAA
1 TAATTTAA
44292062 TAATTTA
1 TAATTTA
44292069 TTTAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TAATTTAA
Found at i:44297485 original size:17 final size:17
Alignment explanation
Indices: 44297463--44297517 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
44297453 TTTTTATGTT
44297463 TTATATATATTATTTTA
1 TTATATATATTATTTTA
*
44297480 TTATATAATATATATTATA
1 TTATAT-ATAT-TATTTTA
*
44297499 TTATATTATATTGTTTTA
1 TTATA-TATATTATTTTA
44297517 T
1 T
44297518 ATTATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.19
18 10 0.31
19 15 0.47
20 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATATATATTATTTTA
Found at i:44297490 original size:5 final size:5
Alignment explanation
Indices: 44297463--44297524 Score: 69
Period size: 5 Copynumber: 13.2 Consensus size: 5
44297453 TTTTTATGTT
*
44297463 TTATA -TATA TTAT- TT-TA TTATA TAATA -TATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
44297509 TTGTT TTATA TTATA T
1 TTATA TTATA TTATA T
44297525 AAATTAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
3 1 0.02
4 11 0.23
5 35 0.74
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:44297491 original size:24 final size:24
Alignment explanation
Indices: 44297465--44297509 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
44297455 TTTATGTTTT
44297465 ATATATATTAT-TT-TATTATATA
1 ATATATATTATATTATATTATATA
44297487 ATATATATTATATTATATTATAT
1 ATATATATTATATTATATTATAT
44297510 TGTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 2 0.10
24 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATATATTATATTATATTATATA
Found at i:44298581 original size:5 final size:5
Alignment explanation
Indices: 44298573--44298634 Score: 78
Period size: 5 Copynumber: 13.2 Consensus size: 5
44298563 TATTTAATTT
* *
44298573 ATATA ATATA AAATA ATATA ATATA ATATA ATAT- ATATT ATATA ATA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
44298621 A-ATA ATAT- ATATA A
1 ATATA ATATA ATATA A
44298635 AACATAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
3 1 0.02
4 12 0.24
5 37 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:44307625 original size:15 final size:15
Alignment explanation
Indices: 44307605--44307636 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
44307595 TGGGTCGTCA
44307605 AACTTCTAAGCCTAC
1 AACTTCTAAGCCTAC
44307620 AACTTCTAAGCCTAC
1 AACTTCTAAGCCTAC
44307635 AA
1 AA
44307637 ACCCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (15 bp):
AACTTCTAAGCCTAC
Found at i:44329617 original size:27 final size:27
Alignment explanation
Indices: 44329576--44329633 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
44329566 AAAGTGGGTT
44329576 ATTTATACATACTGTAGTGGGTCTGTA
1 ATTTATACATACTGTAGTGGGTCTGTA
*
44329603 ATTTATACATGCTGTAGTGGGTCTGTA
1 ATTTATACATACTGTAGTGGGTCTGTA
44329630 ATTT
1 ATTT
44329634 GTTTTCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (27 bp):
ATTTATACATACTGTAGTGGGTCTGTA
Found at i:44330033 original size:49 final size:48
Alignment explanation
Indices: 44329949--44330047 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 48
44329939 TCCGTTAGGC
44329949 TGTTTTTGTTTCTTTCAAAACAATTTCAAAAAGTTTATTTTTAAAGAA
1 TGTTTTTGTTTCTTTCAAAACAATTTCAAAAAGTTTATTTTTAAAGAA
44329997 TGTTTTTGTTTCTTTCAAAAACAATTTCAAAAAGTTTATTTTTAAAGAA
1 TGTTTTTGTTTCTTTC-AAAACAATTTCAAAAAGTTTATTTTTAAAGAA
44330046 TG
1 TG
44330048 CTAATTTTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 16 0.32
49 34 0.68
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.47
Consensus pattern (48 bp):
TGTTTTTGTTTCTTTCAAAACAATTTCAAAAAGTTTATTTTTAAAGAA
Found at i:44333389 original size:48 final size:48
Alignment explanation
Indices: 44333318--44333453 Score: 157
Period size: 48 Copynumber: 3.0 Consensus size: 48
44333308 ACTCGAATAC
*
44333318 TTTATCAGTTTTAAACAAATTATTCTTTGCATCAACAAATCTTTTCCA
1 TTTATCAGTCTTAAACAAATTATTCTTTGCATCAACAAATCTTTTCCA
* * *
44333366 TTTATCAGTCTTAAACAACTTATTCTTCGCAT---CAAA-----TAC-
1 TTTATCAGTCTTAAACAAATTATTCTTTGCATCAACAAATCTTTTCCA
44333405 TTTATCAGTCTTAAACAAATTATT-TTTCGCATCAACAAATCTTTTCCA
1 TTTATCAGTCTTAAACAAATTATTCTTT-GCATCAACAAATCTTTTCCA
44333453 T
1 T
44333454 GACATTGCAC
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
38 2 0.03
39 27 0.38
40 2 0.03
42 4 0.06
45 4 0.06
47 2 0.03
48 30 0.42
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (48 bp):
TTTATCAGTCTTAAACAAATTATTCTTTGCATCAACAAATCTTTTCCA
Found at i:44333710 original size:33 final size:34
Alignment explanation
Indices: 44333655--44333723 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
44333645 AAGAAAATGA
*
44333655 TAGCCAATGATATTAGTGTAGTGAAATATGGATT
1 TAGCCAATGATATTAGTGTAGTGAAATATGAATT
*
44333689 TAGCCAGTGATA-TAGTGTAGTGAAATATGAATT
1 TAGCCAATGATATTAGTGTAGTGAAATATGAATT
44333722 TA
1 TA
44333724 AAGTGAGGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (34 bp):
TAGCCAATGATATTAGTGTAGTGAAATATGAATT
Found at i:44340352 original size:2 final size:2
Alignment explanation
Indices: 44340345--44340372 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44340335 ATATGTGTAG
44340345 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
44340373 GCTGGAACCT
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:44369647 original size:2 final size:2
Alignment explanation
Indices: 44369640--44369688 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
44369630 ACATAAAGGA
* * *
44369640 AT AT AT AT AT AT AC AC AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
44369682 AT GT AT A
1 AT AT AT A
44369689 ATGTGTCGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:44370227 original size:15 final size:15
Alignment explanation
Indices: 44370207--44370236 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44370197 GGTGCTCAAC
44370207 ATTTTTAATAAAAAT
1 ATTTTTAATAAAAAT
44370222 ATTTTTAATAAAAAT
1 ATTTTTAATAAAAAT
44370237 GTTTAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTTTAATAAAAAT
Found at i:44371102 original size:55 final size:55
Alignment explanation
Indices: 44371009--44371160 Score: 207
Period size: 55 Copynumber: 2.8 Consensus size: 55
44370999 ACTTCTTCTT
* *
44371009 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACT-
1 CTTCTTTTGAATCGATTGTTTATATGTTCAAATCGATTGTTATGTTGAAATACTA
* * * *
44371063 GTTGCTTTTGAATCAACTGTTTATATGTTCAAATTGATTGTTATGTTGAAATACTA
1 CTT-CTTTTGAATCGATTGTTTATATGTTCAAATCGATTGTTATGTTGAAATACTA
* * *
44371119 CTTCTTTTGAATCGATTGTTTATATGTTTAGATCAATTGTTA
1 CTTCTTTTGAATCGATTGTTTATATGTTCAAATCGATTGTTA
44371161 CGTAGCACAT
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
54 2 0.02
55 79 0.95
56 2 0.02
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (55 bp):
CTTCTTTTGAATCGATTGTTTATATGTTCAAATCGATTGTTATGTTGAAATACTA
Found at i:44374528 original size:31 final size:30
Alignment explanation
Indices: 44374493--44374579 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
44374483 TTTTATTATG
*
44374493 CCAATATCTCGGTACCCATATATTTGACTTT
1 CCAATAT-TCGATACCCATATATTTGACTTT
* *
44374524 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTCGATACCCATATATTTGACTTT
* * ** *
44374554 CTATTATTTAATACCCATATCTTTGA
1 CCAATATTCGATACCCATATATTTGA
44374580 TATGGATGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 43 0.86
31 7 0.14
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.43
Consensus pattern (30 bp):
CCAATATTCGATACCCATATATTTGACTTT
Found at i:44374541 original size:30 final size:30
Alignment explanation
Indices: 44374505--44374579 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
44374495 AATATCTCGG
* *
44374505 TACCCATATATTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTAA
* *
44374535 TACCCATATCTTTGACTTTCTATTATTTAA
1 TACCCATATCTTTGACTTTCCAATATTTAA
44374565 TACCCATATCTTTGA
1 TACCCATATCTTTGA
44374580 TATGGATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.45
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTAA
Found at i:44379199 original size:30 final size:30
Alignment explanation
Indices: 44379146--44379239 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
44379136 TTTTATTATG
* *
44379146 CCAATATCTTGGTACCCTTATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
44379177 CCAATATTTGATACCCACATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
44379207 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
44379237 CCA
1 CCA
44379240 TAAATATGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 48 0.87
31 7 0.13
ACGTcount: A:0.23, C:0.24, G:0.07, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:44379769 original size:16 final size:16
Alignment explanation
Indices: 44379744--44379774 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44379734 ACACGAAAAT
*
44379744 ACATAGGTATATATGA
1 ACATACGTATATATGA
44379760 ACATACGTATATATG
1 ACATACGTATATATG
44379775 TATATAACCA
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:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (16 bp):
ACATACGTATATATGA
Found at i:44380285 original size:3 final size:3
Alignment explanation
Indices: 44380207--44380265 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
44380197 AAATGAAAAT
* * * *
44380207 ATA ATTA ATA ACA ATA ATA TTA ATA CTA ATA ATA ATA GTA A-A GATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
44380253 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
44380266 CCTAACTAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 1 0.02
3 40 0.89
4 4 0.09
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:44381808 original size:45 final size:44
Alignment explanation
Indices: 44381759--44381869 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 44
44381749 TGATTTTAGT
*
44381759 CTACTCCACTGCAACTTCAGGGAGATAAGACTCGCTATCTTCAGC
1 CTACTCCACTGCAACTTCAGGGAGATAAGACTCG-TATCTTCAAC
* * * ** *
44381804 CTACTCTACTGCAACCTCAGAGAGATAAGGTTTGTATCTTCAAC
1 CTACTCCACTGCAACTTCAGGGAGATAAGACTCGTATCTTCAAC
* * *
44381848 CTGCCCCACTACAACTTCAGGG
1 CTACTCCACTGCAACTTCAGGG
44381870 GGGATGAGAT
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
44 25 0.47
45 28 0.53
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (44 bp):
CTACTCCACTGCAACTTCAGGGAGATAAGACTCGTATCTTCAAC
Found at i:44382062 original size:46 final size:46
Alignment explanation
Indices: 44381987--44382365 Score: 571
Period size: 46 Copynumber: 8.2 Consensus size: 46
44381977 ATTTGCTTTA
* * * * *
44381987 CTGCCAGATACAGGAAGACAATATTTGCTATCTTCGATCTACTTTG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
* *
44382033 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCCCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
44382079 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
* *
44382125 CTGCCAAATACAGAAAGACAAGATCTGCTATCTTCGATCTCCTCCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
*
44382171 CTACCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
* *
44382217 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATATCCTCTA
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
*
44382263 CTGCCAAATACAGAAAGACAAGATCTGCTATCTTCGATCTCCT-TCG
1 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCT-G
* * * *
44382309 CTGCCAAATACAGAAAGACAAAGATCTACTATCTTCGATCTCTTCCG
1 CTGCCAAATACAGGAAGAC-AAGATCTGCTATCTTCGATCTCCTCTG
*
44382356 TTGCCAAATA
1 CTGCCAAATA
44382366 TATCTTTGAA
Statistics
Matches: 306, Mismatches: 24, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 273 0.89
47 32 0.10
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTG
Found at i:44382383 original size:28 final size:28
Alignment explanation
Indices: 44382338--44382393 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
44382328 AAAGATCTAC
* * **
44382338 TATCTTCGATCTCTTCCGTTGCCAAATA
1 TATCTTCGAACTCCTCCGCAGCCAAATA
*
44382366 TATCTTTGAACTCCTCCGCAGCCAAATA
1 TATCTTCGAACTCCTCCGCAGCCAAATA
44382394 CAGGAAGACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (28 bp):
TATCTTCGAACTCCTCCGCAGCCAAATA
Found at i:44382433 original size:74 final size:75
Alignment explanation
Indices: 44382291--44382439 Score: 228
Period size: 74 Copynumber: 2.0 Consensus size: 75
44382281 CAAGATCTGC
* * * *
44382291 TATCTTCGATCTCCTTCGCTGCCAAATACAGAAAGACAAAGATCTACTATCTTCGATCTCTTCCG
1 TATCTTCGAACTCCTCCGCAGCCAAATACAGAAAGACAAAGATCTACTATCTTCGATCTCCTCCG
44382356 TTGCCAAATA
66 TTGCCAAATA
* * *
44382366 TATCTTTGAACTCCTCCGCAGCCAAATACAGGAAGAC-AAGATCTTCTATCTTCGATCTCCTCCG
1 TATCTTCGAACTCCTCCGCAGCCAAATACAGAAAGACAAAGATCTACTATCTTCGATCTCCTCCG
44382430 TTGCCAAATA
66 TTGCCAAATA
44382440 CAGGAAGACA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
74 35 0.52
75 32 0.48
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.30
Consensus pattern (75 bp):
TATCTTCGAACTCCTCCGCAGCCAAATACAGAAAGACAAAGATCTACTATCTTCGATCTCCTCCG
TTGCCAAATA
Found at i:44382436 original size:46 final size:46
Alignment explanation
Indices: 44382379--44382651 Score: 451
Period size: 46 Copynumber: 5.9 Consensus size: 46
44382369 CTTTGAACTC
* *
44382379 CTCCGCAGCCAAATACAGGAAGACAAGATCTTCTATCTTCGATCTC-
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATC-CA
*
44382425 CTCCGTTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCA
*
44382471 CTCTGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATC-CA
*
44382517 CTCCGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCCA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCA
*
44382563 CTCTGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCA
*
44382609 CTCTGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGAT
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGAT
44382652 TGAATACTTT
Statistics
Matches: 215, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
45 2 0.01
46 212 0.99
47 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (46 bp):
CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCA
Found at i:44382496 original size:167 final size:166
Alignment explanation
Indices: 44382199--44382531 Score: 499
Period size: 167 Copynumber: 2.0 Consensus size: 166
44382189 CAAGATCTGC
* * * *
44382199 TATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATATCCTCTAC
1 TATCTTCGAACTCCTCCGCAGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATATCCTCCAC
44382264 TGCCAAATACAGAAAGACAAGATCTGCTATCTTCGATCTCCTTCGCTGCCAAATACAGAAAGACA
66 TGCCAAATACAGAAAGACAAGATCTGCTATCTTCGATCTCCTTCGCTGCCAAATACAGAAAGAC-
* *
44382329 AAGATCTACTATCTTCGATCTCTTCCGTTGCCAAATA
130 AAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATA
* * * **
44382366 TATCTTTGAACTCCTCCGCAGCCAAATACAGGAAGACAAGATCTTCTATCTTCGATCTCCTCCGT
1 TATCTTCGAACTCCTCCGCAGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATATCCTCCAC
* *
44382431 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATC-CAC-TCTGCTGCCAAATACAGGAAGA
66 TGCCAAATACAGAAAGACAAGATCTGCTATCTTCGATCTC-CTTC-GCTGCCAAATACAGAAAGA
*
44382494 CAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATA
129 CAAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATA
44382532 CAGGAAGACA
Statistics
Matches: 150, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
166 37 0.25
167 113 0.75
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (166 bp):
TATCTTCGAACTCCTCCGCAGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATATCCTCCAC
TGCCAAATACAGAAAGACAAGATCTGCTATCTTCGATCTCCTTCGCTGCCAAATACAGAAAGACA
AGATCTACTATCTTCGATCTCCTCCGCTGCCAAATA
Found at i:44382530 original size:213 final size:212
Alignment explanation
Indices: 44382153--44382560 Score: 685
Period size: 213 Copynumber: 1.9 Consensus size: 212
44382143 CAAGATCTGC
* *
44382153 TATCTTCGATCTCCTCCGCTACCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTGC
1 TATCTTCGAACTCCTCCGCTACCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGC
*
44382218 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATATCCTCTACTGCCAAATACAGAAAGACA
66 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATACCCTCTACTGCCAAATACAGAAAGACA
*
44382283 AGATCTGCTATCTTCGATCTCCTTCGCTGCCAAATACAGAAAGACAAAGATCTACTATCTTCGAT
131 AGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGAAAGAC-AAGATCTACTATCTTCGAT
44382348 CTCTTCCGTTGCCAAATA
195 CTCTTCCGTTGCCAAATA
* *
44382366 TATCTTTGAACTCCTCCGC-AGCCAAATACAGGAAGACAAGATCTTCTATCTTCGATCTCCTCCG
1 TATCTTCGAACTCCTCCGCTA-CCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCG
* * *
44382430 TTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGAT-CCACTCTGCTGCCAAATACAGGAAGA
65 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATACC-CTCTACTGCCAAATACAGAAAGA
*
44382494 CAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGA
129 CAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGAAAGACAAGATCTACTATCTTCGA
44382559 TC
194 TC
44382561 CACTCTGCTG
Statistics
Matches: 183, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
212 22 0.12
213 161 0.88
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (212 bp):
TATCTTCGAACTCCTCCGCTACCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGC
TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATACCCTCTACTGCCAAATACAGAAAGACA
AGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGAAAGACAAGATCTACTATCTTCGATC
TCTTCCGTTGCCAAATA
Found at i:44382614 original size:138 final size:138
Alignment explanation
Indices: 44382366--44382651 Score: 502
Period size: 138 Copynumber: 2.1 Consensus size: 138
44382356 TTGCCAAATA
* * * *
44382366 TATCTTTGAACTCCTCCGCAGCCAAATACAGGAAGACAAGATCTTCTATCTTCGATCTCCTCCGT
1 TATCTTCGATCTCCTCCGCAGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGC
44382431 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTCTGCTGCCAAATACAGGAAGACA
66 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTCTGCTGCCAAATACAGGAAGACA
44382496 AGATCTGC
131 AGATCTGC
* *
44382504 TATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATC-CACTCTG
1 TATCTTCGATCTCCTCCGCAGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTC-CTCCG
44382568 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTCTGCTGCCAAATACAGGAAGAC
65 CTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTCTGCTGCCAAATACAGGAAGAC
44382633 AAGATCTGC
130 AAGATCTGC
44382642 TATCTTCGAT
1 TATCTTCGAT
44382652 TGAATACTTT
Statistics
Matches: 141, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
137 1 0.01
138 140 0.99
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (138 bp):
TATCTTCGATCTCCTCCGCAGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGC
TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTCTGCTGCCAAATACAGGAAGACA
AGATCTGC
Found at i:44387733 original size:87 final size:87
Alignment explanation
Indices: 44387587--44387939 Score: 562
Period size: 87 Copynumber: 4.1 Consensus size: 87
44387577 AAGAAGTAGT
* * * *
44387587 TCGAAAACAAAGCCTAGCCTCTATTGGTTGCAGTGGAGCTGGTTGAAGATAACAGATCTTGCCTT
1 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
44387652 CCTGCGTTAACAGCGAAGCAGA
66 CCTGCGTTAACAGCGAAGCAGA
*
44387674 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCATATCTTGCCTT
1 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
44387739 CCTGCGTTAACAGCGAAGCAGA
66 CCTGCGTTAACAGCGAAGCAGA
* * * * *
44387761 TTGGAAACGAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAAATCTTGCCTT
1 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
44387826 CCTGCGTTAACAGCGAAGCAGA
66 CCTGCGTTAACAGCGAAGCAGA
* * *
44387848 TCGAAAACAAAGCCTTGCCTCCATTGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCCT
1 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
** *
44387913 CCTGCGTCGACAGTGAAGCAGA
66 CCTGCGTTAACAGCGAAGCAGA
44387935 TCGAA
1 TCGAA
44387940 GATTATAAGT
Statistics
Matches: 245, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 245 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (87 bp):
TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
CCTGCGTTAACAGCGAAGCAGA
Found at i:44388173 original size:129 final size:129
Alignment explanation
Indices: 44387994--44388241 Score: 293
Period size: 129 Copynumber: 1.9 Consensus size: 129
44387984 AATTACAAGT
* * ** ** *
44387994 CTTATCTCCCTGATGTCACAGTGGAGCAGATTGAAGCTAGTAATCCTATC-TCCTTGAAGTTGCA
1 CTTATCTCCCTAAAGTCACAGTGGAGCAGATTGAAGAAACCAATCCTATCTTCC-TGAAGTTACA
* *
44388058 GTGGAGT-GGATTAAAACCACAGATCTTATCACTCTGAAGTTGCAGTAGAGCAGATCGTATCCAA
65 GT-GAATCGGATTAAAACCACAGAACTTATCACTCTGAAGTTGCAGTAGAGCAGATCGTATCCAA
44388122 A
129 A
** *
44388123 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCTTATCTTCCTGAAGTTACAG
1 CTTATCTCCCTAAAGTCACAGTGGAGCAGATTGAAGAAACCAATCCTATCTTCCTGAAGTTACAG
* ** ** * *
44388188 TGAATCGGATTAGAATGATGGAACTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
66 TGAATCGGATTAAAACCACAGAACTTATCACTCTGAAGTTGCAGTAGAGCAGAT
44388242 AGCATCAGAC
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
128 3 0.03
129 92 0.94
130 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (129 bp):
CTTATCTCCCTAAAGTCACAGTGGAGCAGATTGAAGAAACCAATCCTATCTTCCTGAAGTTACAG
TGAATCGGATTAAAACCACAGAACTTATCACTCTGAAGTTGCAGTAGAGCAGATCGTATCCAAA
Found at i:44388189 original size:44 final size:43
Alignment explanation
Indices: 44387993--44388189 Score: 139
Period size: 44 Copynumber: 4.6 Consensus size: 43
44387983 AAATTACAAG
* ** ** **
44387993 TCTTATCTCCCTGATGTCACAGTGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAGAAACCAA
* * ** *
44388037 TCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTAA-AACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAAAC-CA-A
* * * * * *
44388081 TCTTATCACTCTGAAGTTGCAGTAGAGCAGA-T-CGTATCCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAAACCAA
* *
44388122 ACTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAGAAACCAA
* *
44388166 TCTTATCTTCCTGAAGTTACAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
44388190 AATCGGATTA
Statistics
Matches: 113, Mismatches: 34, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
41 27 0.24
42 3 0.03
43 6 0.05
44 77 0.68
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAAACCAA
Found at i:44388992 original size:13 final size:13
Alignment explanation
Indices: 44388974--44388998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44388964 TAGGGGGGCC
44388974 CTCATTTTTTTCT
1 CTCATTTTTTTCT
44388987 CTCATTTTTTTC
1 CTCATTTTTTTC
44388999 ATCTTTTCTT
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:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
CTCATTTTTTTCT
Found at i:44397726 original size:20 final size:20
Alignment explanation
Indices: 44397701--44397742 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
44397691 CTTACAACGG
*
44397701 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
44397721 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
44397741 TA
1 TA
44397743 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:44401260 original size:18 final size:18
Alignment explanation
Indices: 44401227--44401261 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44401217 ACCAGCAGAT
* *
44401227 GGCATACTGACTTGTTGG
1 GGCATACTAACCTGTTGG
44401245 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
44401262 TGGAGAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGG
Found at i:44402516 original size:15 final size:15
Alignment explanation
Indices: 44402496--44402526 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44402486 CTATCATCTT
44402496 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
44402511 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
44402526 T
1 T
44402527 TACAACGGTA
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:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:44402560 original size:20 final size:20
Alignment explanation
Indices: 44402535--44402576 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
44402525 CTTACAACGG
*
44402535 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
44402555 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
44402575 TA
1 TA
44402577 ACTCTAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:44404563 original size:21 final size:21
Alignment explanation
Indices: 44404538--44404578 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44404528 ACCCTTAAAT
44404538 CCCTAAAT-CTTAACCCCTAAC
1 CCCTAAATAC-TAACCCCTAAC
*
44404559 CCCTAACTACTAACCCCTAA
1 CCCTAAATACTAACCCCTAA
44404579 ACCTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCTAAATACTAACCCCTAAC
Found at i:44409372 original size:2 final size:2
Alignment explanation
Indices: 44409367--44409391 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44409357 ACATACATAA
44409367 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
44409392 CACATACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44415572 original size:22 final size:22
Alignment explanation
Indices: 44415530--44415572 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
44415520 AGAATATATC
* *
44415530 TCTTTTTGATTTGGTTGATTTT
1 TCTTTTTCATTTGGCTGATTTT
44415552 TCTTTTTCATTTCGGCT-ATTT
1 TCTTTTTCATTT-GGCTGATTT
44415573 AAAGCCGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.09, C:0.12, G:0.14, T:0.65
Consensus pattern (22 bp):
TCTTTTTCATTTGGCTGATTTT
Found at i:44415706 original size:16 final size:16
Alignment explanation
Indices: 44415681--44415718 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
44415671 GTTCTGTTTT
44415681 TCTT-TTTTTTTACTG
1 TCTTGTTTTTTTACTG
* *
44415696 TCTTGTTTTTTTATTT
1 TCTTGTTTTTTTACTG
44415712 TCTTGTT
1 TCTTGTT
44415719 CTTTAAAACA
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:0.05, C:0.11, G:0.08, T:0.76
Consensus pattern (16 bp):
TCTTGTTTTTTTACTG
Found at i:44416203 original size:3 final size:3
Alignment explanation
Indices: 44416195--44416265 Score: 54
Period size: 3 Copynumber: 22.7 Consensus size: 3
44416185 TGTCTTTCTA
* * *
44416195 TAT TAT TAT CAT T-T TAT TATT TATT TATT TAT TAT TAA TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT
* *
44416242 TAT TATT TAT TAT CAA TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TA
44416266 ATATATTCCT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
2 2 0.04
3 39 0.71
4 14 0.25
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:44416238 original size:9 final size:9
Alignment explanation
Indices: 44416224--44416269 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
44416214 TTTATTTATT
44416224 TATTATTAA
1 TATTATTAA
44416233 TATTATTAA
1 TATTATTAA
44416242 TATTATT--
1 TATTATTAA
*
44416249 TATTATCAA
1 TATTATTAA
44416258 TATTATTAA
1 TATTATTAA
44416267 TAT
1 TAT
44416270 ATTCCTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 6 0.18
9 27 0.82
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTATTAA
Found at i:44416259 original size:25 final size:25
Alignment explanation
Indices: 44416209--44416269 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
44416199 ATTATCATTT
* *
44416209 TATTATTTAT-TTATTTATTATTAA
1 TATTATTAATATTATTTATTATCAA
44416233 TATTATTAATATTATTTATTATCAA
1 TATTATTAATATTATTTATTATCAA
44416258 TATTATTAATAT
1 TATTATTAATAT
44416270 ATTCCTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 9 0.26
25 25 0.74
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTATTAATATTATTTATTATCAA
Found at i:44417726 original size:32 final size:31
Alignment explanation
Indices: 44417679--44417751 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
44417669 TCGACAATGA
44417679 GTATATATATATATTATAGAAAAAAT-ATGTAC
1 GTATATATATATATTAT--AAAAAATCATGTAC
* *
44417711 GTGTATATATGTATTATAAAAAATGCATGTAC
1 GTATATATATATATTATAAAAAAT-CATGTAC
44417743 GTATATATA
1 GTATATATA
44417752 ATGACTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 7 0.19
32 29 0.81
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.38
Consensus pattern (31 bp):
GTATATATATATATTATAAAAAATCATGTAC
Found at i:44418599 original size:18 final size:19
Alignment explanation
Indices: 44418578--44418625 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
44418568 AATGGATTTG
*
44418578 AAAGAAAAAAAAGAAA-AA
1 AAAGAAAAAAAACAAATAA
44418596 AAAGAGAAAAAAACAAATAA
1 AAAGA-AAAAAAACAAATAA
*
44418616 ATAGAAAAAA
1 AAAGAAAAAA
44418626 TATCAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 5 0.19
19 15 0.58
20 6 0.23
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.04
Consensus pattern (19 bp):
AAAGAAAAAAAACAAATAA
Found at i:44418626 original size:9 final size:9
Alignment explanation
Indices: 44418578--44418625 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
44418568 AATGGATTTG
44418578 AAAGAAAAA
1 AAAGAAAAA
44418587 AAAGAAAAA
1 AAAGAAAAA
44418596 AAAGAGAAAA
1 AAAGA-AAAA
*
44418606 AAACAAATAA
1 AAAGAAA-AA
*
44418616 ATAGAAAAA
1 AAAGAAAAA
44418625 A
1 A
44418626 TATCAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.04
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:44419630 original size:128 final size:128
Alignment explanation
Indices: 44419479--44420240 Score: 1202
Period size: 128 Copynumber: 6.0 Consensus size: 128
44419469 GTTATGGCGT
* *
44419479 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTAATCCGCTCCACTGCAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCCACTGCAACTTC
* ** * * *
44419544 AGGGAGATAGGATTAGTAGCTT-TAGTCTACTCCACTACTGCTTAGGGAGATAAAACTTGATGC
66 AGGGAGATAGGATTGGTTTCTTCT-GTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC
* * * * * *
44419607 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATATGTGGTTTTAATCCACTCCACTGTAATTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCCACTGCAACTTC
* * * *
44419672 AGGGAGATAGGATTGGTTTCTTCTGTCTGCCCCACTACTGCTTAGAGAGATAAGACTGAATAC
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC
* * * * *
44419735 GATCTACTCTACTGCAGCTTCAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCATTGCAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCCACTGCAACTTC
*
44419800 AGGGAGATAGGATTGGTTTCTTCTGTCTGTTCCACTACTGCTTAGGGAGATAAGACTGGATGC
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC
* * *
44419863 GATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCAACTACAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCCACTGCAACTTC
44419928 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC
* * *
44419991 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCTATTACAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCCACTGCAACTTC
*
44420056 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGT
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC
* *
44420119 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGTTCCACTGCAACTTT
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCCACTGCAACTTC
*
44420184 AGGGAGATAGGATTGCTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
44420241 TGCTATCTTT
Statistics
Matches: 586, Mismatches: 47, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
128 585 1.00
129 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (128 bp):
GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCCACTGCAACTTC
AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC
Found at i:44419880 original size:84 final size:84
Alignment explanation
Indices: 44419780--44420152 Score: 249
Period size: 84 Copynumber: 4.4 Consensus size: 84
44419770 TGTGGTTTTA
* * *
44419780 ATCTGCTCCATTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGTTCCACTACTGCTTAG
1 ATCTGCTCTATTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAG
44419845 GGAGATAAGACTGGATGCG
66 GGAGATAAGACTGGATGCG
* * ** * * **
44419864 ATCTGCTCTATTGCAACTTCAGAGAGATAAGATCT-GTGGT-TTCAATCCGCTCAACTACAACTT
1 ATCTGCTCTATTGCAACTTCAGGGAGATAAGAT-TGGT-TTCTTCTGTCTGCTCCACTACTGCTT
* * * *
44419927 CAGGGAGATAGGATTGGTTTC-
64 -AGGGAGATAAGACTGGATGCG
* ** * * * * * * * *
44419948 TTCTG-TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCA--ACT
1 ATCTGCTCTATTGCA--ACT--TCAGGGAGATAAGATTGGTTTC-TTCTG-TCTGCTCCACTACT
* * * * *
44420010 --TCAGAGAGATAAGATCTGTGGTTTCA
60 GCTTAGGGAGATAAGA-C--TGGATGCG
* * *
44420036 ATCCGCTCTATTACAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAG
1 ATCTGCTCTATTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAG
*
44420101 GGAGATAAGACTGGATGTG
66 GGAGATAAGACTGGATGCG
* *
44420120 ATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
1 ATCTGCTCTATTGCAACTTCAGGGAGATAAGAT
44420153 CTGTGGTTTC
Statistics
Matches: 208, Mismatches: 61, Indels: 40
0.67 0.20 0.13
Matches are distributed among these distances:
83 13 0.06
84 98 0.47
85 42 0.20
86 2 0.01
87 37 0.18
88 5 0.02
89 11 0.05
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (84 bp):
ATCTGCTCTATTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAG
GGAGATAAGACTGGATGCG
Found at i:44420174 original size:84 final size:85
Alignment explanation
Indices: 44419830--44420192 Score: 240
Period size: 84 Copynumber: 4.3 Consensus size: 85
44419820 TTCTGTCTGT
** * *
44419830 TCCACTACTGCTT-AGGGAGATAAGACTGGATGCGATCTGCTCTATTGCAACTTCAGAGAGATAA
1 TCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAA
44419894 GATCTGTGGTTTCAATCCGC
66 GATCTGTGGTTTCAATCCGC
* * * * ** * * * *
44419914 TCAACTACAACTTCAGGGAGATAGGATTGG-TTTCTTCTG-TCTGCTCCACTACTGCTTAGGGAG
1 TCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCA--ACT--TCAGAGAG
* * * *
44419977 ATAAGA-C--TGGATGCGATCTGC
62 ATAAGATCTGTGGTTTCAATCCGC
* * * * * * * * * *
44419998 TCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTCAATCCGCTCTATTACAACTTCAGGGAGA
1 TCCACTACAACTTCAGGGAGATAAGA-CTG-GATGT-GATCTGCTCTACTGCAACTTCAGAGAGA
* * ** *
44420063 TAGGAT-TG-GTTTCTTCTGTCTGC
63 TAAGATCTGTG-GT-TTCAATCCGC
**
44420086 TCCACTACTGCTT-AGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAA
1 TCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAA
*
44420150 GATCTGTGGTTTCAATCCGT
66 GATCTGTGGTTTCAATCCGC
* *
44420170 TCCACTGCAACTTTAGGGAGATA
1 TCCACTACAACTTCAGGGAGATA
44420193 GGATTGCTTT
Statistics
Matches: 204, Mismatches: 57, Indels: 35
0.69 0.19 0.12
Matches are distributed among these distances:
83 6 0.03
84 91 0.45
85 46 0.23
86 7 0.03
87 29 0.14
88 19 0.09
89 6 0.03
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (85 bp):
TCCACTACAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAA
GATCTGTGGTTTCAATCCGC
Found at i:44420427 original size:90 final size:90
Alignment explanation
Indices: 44420235--44420480 Score: 390
Period size: 90 Copynumber: 2.7 Consensus size: 90
44420225 TTAGGGAGAT
*
44420235 AAGACTTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT-AGTC
1 AAGACTTGCTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTCAGTC
* *
44420299 TACTTTGCTGCCAATACAGGAAGAC
66 TACTTCGCTGCCAATACAGAAAGAC
* *
44420324 AAGACTTGCTATC-TTCAGTCTACTTTGCTGCCAATATAGGAAGACAAGA-CTTGCTATCTTCAG
1 AAGACTTGCTATCTTTGA-TCTACTTCGCTGCCAATATAGGAAGACAAGATC-TGCTATCTTCAG
44420387 TCTACTTCGCTGCCAATACAGAAAGAC
64 TCTACTTCGCTGCCAATACAGAAAGAC
* *
44420414 AAGACTTGCTATCTTTGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGCCATCTTCAGTC
1 AAGACTTGCTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTCAGTC
44420479 TA
66 TA
44420481 ATTAACTGCA
Statistics
Matches: 143, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
88 4 0.03
89 51 0.36
90 84 0.59
91 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (90 bp):
AAGACTTGCTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTCAGTC
TACTTCGCTGCCAATACAGAAAGAC
Found at i:44420489 original size:45 final size:45
Alignment explanation
Indices: 44420235--44420480 Score: 340
Period size: 45 Copynumber: 5.5 Consensus size: 45
44420225 TTAGGGAGAT
*
44420235 AAGACTTGCTATCTT-TGATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGACTTGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
*
44420280 AAGA-TCTGCTATCTT-AGTCTACTTTGCTGCCAATACAGGAAGAC
1 AAGACT-TGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
* *
44420324 AAGACTTGCTATCTTCAGTCTACTTTGCTGCCAATATAGGAAGAC
1 AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
*
44420369 AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGAAAGAC
1 AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
* * *
44420414 AAGACTTGCTATCTT-TGATCTACTTCACTGCCAATATAGGAAGAC
1 AAGACTTGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
*
44420459 AAGA-TCTGCCATCTTCAGTCTA
1 AAGACT-TGCTATCTTCAGTCTA
44420481 ATTAACTGCA
Statistics
Matches: 183, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
44 42 0.23
45 140 0.77
46 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
Found at i:44421328 original size:108 final size:107
Alignment explanation
Indices: 44421137--44421345 Score: 289
Period size: 108 Copynumber: 1.9 Consensus size: 107
44421127 GAAAAATGCT
* * **
44421137 TGAAAAAGGTTATCAAAATGGACAAGATGAAATTTTGTTGAGAGCAAAGCTATAAATGAATGAAT
1 TGAAAAAGATTATCAAAATGGACAAGATGAAATTTTATTGAGAGCAAAGCTATAAATGAACAAAT
44421202 TAATCAAGATAGCAAATTTTGCTA-AGATACAAGATGAATAAGA
66 TAATCAAGATAGCAAATTTTGCTAGA-ATACAA-ATGAATAAGA
* * *
44421245 TGAAAAAGATTATCACAAA-GGATAATATGGAAA-TTTATTGAGAGCAAAGCTCTAAATGAACAA
1 TGAAAAAGATTATCA-AAATGGACAAGAT-GAAATTTTATTGAGAGCAAAGCTATAAATGAACAA
*
44421308 ATTAATCAAGATAGCCAATTTTGCTAGAATACAAATGA
64 ATTAATCAAGATAGCAAATTTTGCTAGAATACAAATGA
44421346 GAATAAATTA
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
107 4 0.04
108 78 0.87
109 8 0.09
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (107 bp):
TGAAAAAGATTATCAAAATGGACAAGATGAAATTTTATTGAGAGCAAAGCTATAAATGAACAAAT
TAATCAAGATAGCAAATTTTGCTAGAATACAAATGAATAAGA
Found at i:44421696 original size:10 final size:10
Alignment explanation
Indices: 44421681--44421722 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
44421671 TTTTTCGTTC
44421681 TTCTTTTATT
1 TTCTTTTATT
44421691 TTCTTTTATT
1 TTCTTTTATT
*
44421701 TT-TTGTTTTT
1 TTCTT-TTATT
44421711 TTCTTTT-TT
1 TTCTTTTATT
44421720 TTC
1 TTC
44421723 AAGTGAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 7 0.24
10 20 0.69
11 2 0.07
ACGTcount: A:0.05, C:0.10, G:0.02, T:0.83
Consensus pattern (10 bp):
TTCTTTTATT
Found at i:44422228 original size:23 final size:23
Alignment explanation
Indices: 44422178--44422234 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
44422168 CATTCTCGTT
* *
44422178 TTCTGTTTTGTTTTATTTTTTTGC
1 TTCTCTTTT-TTTTACTTTTTTGC
44422202 --CTCTTTTTTTTACTTTTTTGC
1 TTCTCTTTTTTTTACTTTTTTGC
44422223 TTCTCTTTTTTT
1 TTCTCTTTTTTT
44422235 GCCTCCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 13 0.45
22 6 0.21
23 10 0.34
ACGTcount: A:0.04, C:0.14, G:0.07, T:0.75
Consensus pattern (23 bp):
TTCTCTTTTTTTTACTTTTTTGC
Found at i:44425931 original size:32 final size:32
Alignment explanation
Indices: 44425863--44425932 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
44425853 TGTATATGAG
*
44425863 TATATATATATTATAGAAAAAATATGTACGTG
1 TATATATATATTATAGAAAAAATATGTACGTA
*
44425895 TATATATATATTATA-AAAAACGCT-TGTACGTA
1 TATATATATATTATAGAAAAA--ATATGTACGTA
44425927 TATATA
1 TATATA
44425933 ATGACTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.15
32 28 0.82
33 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (32 bp):
TATATATATATTATAGAAAAAATATGTACGTA
Found at i:44426762 original size:11 final size:11
Alignment explanation
Indices: 44426741--44426774 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
44426731 AAATGGATTT
44426741 GAAAGAAAAAAA
1 GAAA-AAAAAAA
44426753 GAAAAAAAAAA
1 GAAAAAAAAAA
*
44426764 GAGAAAAAAAA
1 GAAAAAAAAAA
44426775 CAAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:44426764 original size:19 final size:20
Alignment explanation
Indices: 44426742--44426791 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
44426732 AATGGATTTG
44426742 AAAGAAAAAAAGAA-AAA-AA
1 AAAGAAAAAAA-AACAAATAA
44426761 AAAGAGAAAAAAAACAAATAA
1 AAAGA-AAAAAAAACAAATAA
*
44426782 ATAGAAAAAA
1 AAAGAAAAAA
44426792 TATCAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 7 0.26
20 14 0.52
21 6 0.22
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAAAAACAAATAA
Found at i:44426768 original size:13 final size:12
Alignment explanation
Indices: 44426741--44426774 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
44426731 AAATGGATTT
*
44426741 GAAAGAAAAAAA
1 GAAAAAAAAAAA
44426753 GAAAAAAAAAAGA
1 GAAAAAAAAAA-A
44426766 GAAAAAAAA
1 GAAAAAAAA
44426775 CAAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:44432002 original size:27 final size:26
Alignment explanation
Indices: 44431951--44432003 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
44431941 ACTCTCTCTT
*
44431951 TTTCTCTTTATTTTCCATTATCTTCTG
1 TTTCTCTTTATTTTCCA-TACCTTCTG
44431978 TTTCTCCTTCTATTTTCC-TACCTTCT
1 TTTCT-CTT-TATTTTCCATACCTTCT
44432004 CCATGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
28 3 0.13
29 8 0.35
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCTCTTTATTTTCCATACCTTCTG
Found at i:44437206 original size:28 final size:29
Alignment explanation
Indices: 44437174--44437245 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
44437164 AACTAATGCA
* *
44437174 ACATTTCAACAT-ATATGATAGAATTATT
1 ACATTTCAAAATCAAATGATAGAATTATT
*
44437202 ACA-TTCAAAATCAAATTATAGAATTATT
1 ACATTTCAAAATCAAATGATAGAATTATT
44437230 AC-TTTCAAAATCAAAT
1 ACATTTCAAAATCAAAT
44437246 TAAATCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.36
Consensus pattern (29 bp):
ACATTTCAAAATCAAATGATAGAATTATT
Found at i:44437246 original size:28 final size:28
Alignment explanation
Indices: 44437191--44437247 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
44437181 AACATATATG
44437191 ATAGAATTATTACATTCAAAATCAAATT
1 ATAGAATTATTACATTCAAAATCAAATT
*
44437219 ATAGAATTATTACTTTCAAAATCAAATT
1 ATAGAATTATTACATTCAAAATCAAATT
44437247 A
1 A
44437248 AATCAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (28 bp):
ATAGAATTATTACATTCAAAATCAAATT
Found at i:44438916 original size:74 final size:74
Alignment explanation
Indices: 44438792--44438944 Score: 261
Period size: 74 Copynumber: 2.1 Consensus size: 74
44438782 CGTAAGTATC
* * *
44438792 TGGTGTGGAAAATAGTGGCAGTAGAAAACGCGTTTCAATCGCTTTTCATTTCGGAGTCATGCTTA
1 TGGTGTGGAAAATAGCGGCACTAGAAAACGCGTTTCAATCGCTTTCCATTTCGGAGTCATGCTTA
44438857 CGGTCCATT
66 CGGTCCATT
* *
44438866 TGGTGTGGAAAATAGCGGTACTAGAAAACGCGTTTCAATCGCTTTCCATTTTGGAGTCATGCTTA
1 TGGTGTGGAAAATAGCGGCACTAGAAAACGCGTTTCAATCGCTTTCCATTTCGGAGTCATGCTTA
44438931 CGGTCCATT
66 CGGTCCATT
44438940 TGGTG
1 TGGTG
44438945 CTCAACATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (74 bp):
TGGTGTGGAAAATAGCGGCACTAGAAAACGCGTTTCAATCGCTTTCCATTTCGGAGTCATGCTTA
CGGTCCATT
Found at i:44439492 original size:7 final size:7
Alignment explanation
Indices: 44439475--44439522 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
44439465 TTTTATTTTT
44439475 ATTTTAAA
1 ATTTT-AA
44439483 ATTTTTAA
1 A-TTTTAA
* *
44439491 TTTTTAT
1 ATTTTAA
*
44439498 ATTTCAA
1 ATTTTAA
44439505 ATTTTAA
1 ATTTTAA
44439512 ATTTTAA
1 ATTTTAA
44439519 ATTT
1 ATTT
44439523 AATTATTAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
7 26 0.79
8 3 0.09
9 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:44439495 original size:22 final size:22
Alignment explanation
Indices: 44439462--44439524 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
44439452 TTTGAAATTT
*
44439462 ATTTTTTATTTTTAT-TTTAAA
1 ATTTTTAATTTTTATATTTAAA
*
44439483 ATTTTTAATTTTTATATTTCAA
1 ATTTTTAATTTTTATATTTAAA
* *
44439505 A-TTTTAAATTTTAAATTTAA
1 ATTTTTAATTTTTATATTTAA
44439525 TTATTAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 30 0.83
22 6 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTAATTTTTATATTTAAA
Found at i:44441980 original size:55 final size:55
Alignment explanation
Indices: 44441896--44442124 Score: 253
Period size: 55 Copynumber: 4.2 Consensus size: 55
44441886 CTTCTTTTGG
* * * * * * * *
44441896 ATCGATTATCACGTTGGAATAGTGCTTCTTTTGAGTCAATTCTTTATATGTTTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
* * *
44441951 ATCGATTGTCAAGTTGGAACACTACTTCTTTTGAATCGATTGTGTATATGATTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
* * * * * *
44442006 ATTGATTGTTATGTTGGAATACTGCTTCTTTTTAATTGATTGTGTATATGATTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
* * * *
44442061 ATCGATTATTATGTTGGAATATTACTTCTTTTGAATCGATTGCT-TATATGTTTAA
1 ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATT-CTGTATATGATTAA
44442116 ATCGATTGT
1 ATCGATTGT
44442125 TACATAACAC
Statistics
Matches: 147, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
55 146 0.99
56 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (55 bp):
ATCGATTGTCATGTTGGAATACTACTTCTTTTGAATCGATTCTGTATATGATTAA
Found at i:44442101 original size:110 final size:110
Alignment explanation
Indices: 44441908--44442126 Score: 287
Period size: 110 Copynumber: 2.0 Consensus size: 110
44441898 CGATTATCAC
* * * * *
44441908 GTTGGAATAGTGCTTCTTTTGAGTCAATTCTTTATATGTTTAAATCGATTGTCAAGTTGGAACAC
1 GTTGGAATACTGCTTCTTTTGAATCAATTCTGTATATGATTAAATCGATTATCAAGTTGGAACAC
*
44441973 TACTTCTTTTGAATCGATTG-TGTATATGATTAAATTGATTGTTAT
66 TACTTCTTTTGAATCGATTGCT-TATATGATTAAATCGATTGTTAT
* ** * * * * *
44442018 GTTGGAATACTGCTTCTTTTTAATTGATTGTGTATATGATTAAATCGATTATTATGTTGGAATAT
1 GTTGGAATACTGCTTCTTTTGAATCAATTCTGTATATGATTAAATCGATTATCAAGTTGGAACAC
*
44442083 TACTTCTTTTGAATCGATTGCTTATATGTTTAAATCGATTGTTA
66 TACTTCTTTTGAATCGATTGCTTATATGATTAAATCGATTGTTA
44442127 CATAACACAT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
110 92 0.99
111 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.47
Consensus pattern (110 bp):
GTTGGAATACTGCTTCTTTTGAATCAATTCTGTATATGATTAAATCGATTATCAAGTTGGAACAC
TACTTCTTTTGAATCGATTGCTTATATGATTAAATCGATTGTTAT
Found at i:44456289 original size:55 final size:55
Alignment explanation
Indices: 44456214--44456434 Score: 235
Period size: 55 Copynumber: 4.0 Consensus size: 55
44456204 ATCTATTATC
* * * * * * * *
44456214 ATGTTGGAATAGTGCTTCTTTTGAGTCAATTCTTTACATGTTTAAATCGATTGTC
1 ATGTTGGAATACTACTTCTTTTGAATCAATTGTGTATATGATTAAATCGATTGTT
* * * * *
44456269 AAGTTGGAACACTACGTCTTTTGAATAAATTGTGTATATGATTAAATTGATTGTT
1 ATGTTGGAATACTACTTCTTTTGAATCAATTGTGTATATGATTAAATCGATTGTT
* * ** *
44456324 ATGTTGGAATACTGCTTCTTTTTAATTGATTGTGTATATGATTAAATCGATTATT
1 ATGTTGGAATACTACTTCTTTTGAATCAATTGTGTATATGATTAAATCGATTGTT
* * * * *
44456379 ATGTTGGAATATTACTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTGTT
1 ATGTTGGAATACTACTTCTTTTGAATCAATTGTGTATATGATTAAATCGATTGTT
44456434 A
1 A
44456435 CATAACACAT
Statistics
Matches: 136, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 136 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.47
Consensus pattern (55 bp):
ATGTTGGAATACTACTTCTTTTGAATCAATTGTGTATATGATTAAATCGATTGTT
Found at i:44457662 original size:55 final size:55
Alignment explanation
Indices: 44457575--44457770 Score: 288
Period size: 55 Copynumber: 3.6 Consensus size: 55
44457565 AACTTGTGAG
* *
44457575 TACTGCTT-TTTTCGAATAGATTGTTTATATGTTTAAATTGATTGTCATGTTGGAA
1 TACTGCTTCTTTT-GAATCGATTGTTTATATGTTTAAATTGATTGTTATGTTGGAA
* *
44457630 TATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAA
1 TACTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTTATGTTGGAA
* * * *
44457685 TACTG-TTGCTTTTGAATCAACTGATTATATGTTCAAATTGATTGTTATGTTGGAA
1 TACTGCTT-CTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTTATGTTGGAA
44457740 TACTGCTTCTTTTGAATCGATTGTTTATATG
1 TACTGCTTCTTTTGAATCGATTGTTTATATG
44457771 CTTAGATCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
54 2 0.02
55 117 0.94
56 6 0.05
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (55 bp):
TACTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTTATGTTGGAA
Found at i:44459789 original size:74 final size:75
Alignment explanation
Indices: 44459619--44459804 Score: 284
Period size: 74 Copynumber: 2.5 Consensus size: 75
44459609 ACACAGTACG
**
44459619 TATCTTCAGTTCATAAACATCCCAATAAACCATTGGGATTCAAACACAAAACCATCACACAAACA
1 TATCTTCAGTTCATAAACATCCCAATAAACCATTGACATTCAAACAC-AAACCATCACACAAACA
* * **
44459684 CATATTGTCTG
65 CATACTGACAA
**
44459695 TATCTTCAGTTCATAAACATCCCAATAAACCATTGACATTCAAACAC-AACCATCACACAAATGC
1 TATCTTCAGTTCATAAACATCCCAATAAACCATTGACATTCAAACACAAACCATCACACAAACAC
44459759 ATACTGACAA
66 ATACTGACAA
44459769 TATCTTCAGTTCATAAACATCCCAATAAACCATTGA
1 TATCTTCAGTTCATAAACATCCCAATAAACCATTGA
44459805 GACTGTATTT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 57 0.56
76 45 0.44
ACGTcount: A:0.41, C:0.27, G:0.06, T:0.25
Consensus pattern (75 bp):
TATCTTCAGTTCATAAACATCCCAATAAACCATTGACATTCAAACACAAACCATCACACAAACAC
ATACTGACAA
Found at i:44459922 original size:42 final size:42
Alignment explanation
Indices: 44459861--44459997 Score: 211
Period size: 42 Copynumber: 3.3 Consensus size: 42
44459851 CAACCTGGCT
** * *
44459861 AGCTTCAGTTGGTTTTCTTTTAACTCAGCTTCGTCCTGATCC
1 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
44459903 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
1 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
* **
44459945 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCATCCTTCTCC
1 AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
44459987 AGCTTCAGTTT
1 AGCTTCAGTTT
44459998 GTCTTTTCTA
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.15, C:0.28, G:0.14, T:0.44
Consensus pattern (42 bp):
AGCTTCAGTTTCTTCTCTTTTAAGTCAGCTTCGTCCTGATCC
Found at i:44465863 original size:59 final size:59
Alignment explanation
Indices: 44465788--44465907 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
44465778 AAACCCAAGG
44465788 CCCCTCAAGACCTAAGCTAACAAATGGACTCCCAATCTACTTTTGGATGCCCAGCAGAA
1 CCCCTCAAGACCTAAGCTAACAAATGGACTCCCAATCTACTTTTGGATGCCCAGCAGAA
44465847 CCCCTCAAGACCTAAGCTAACAAATGGACTCCCAATCTACTTTTGGATGCCCAGCAGAA
1 CCCCTCAAGACCTAAGCTAACAAATGGACTCCCAATCTACTTTTGGATGCCCAGCAGAA
44465906 CC
1 CC
44465908 ACCCCAAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.32, C:0.33, G:0.15, T:0.20
Consensus pattern (59 bp):
CCCCTCAAGACCTAAGCTAACAAATGGACTCCCAATCTACTTTTGGATGCCCAGCAGAA
Found at i:44467017 original size:30 final size:31
Alignment explanation
Indices: 44466963--44467024 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
44466953 AGCAAAGTTT
44466963 AAGAATCCATGCAAAAACCCACGTTGCATGC
1 AAGAATCCATGCAAAAACCCACGTTGCATGC
*
44466994 AAGAATCCATGC-AAAACCTACGTTGCATGC
1 AAGAATCCATGCAAAAACCCACGTTGCATGC
44467024 A
1 A
44467025 CGAAACCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (31 bp):
AAGAATCCATGCAAAAACCCACGTTGCATGC
Found at i:44470944 original size:26 final size:26
Alignment explanation
Indices: 44470888--44470949 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
44470878 TTTAAGTATA
44470888 AATATTTTTTA-AAAAAATTTATTTT
1 AATATTTTTTAGAAAAAATTTATTTT
* * *
44470913 CA-ATTTTTTAGGAAACATTTATTTT
1 AATATTTTTTAGAAAAAATTTATTTT
44470938 AATATTTTTTAG
1 AATATTTTTTAG
44470950 TGTATCTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 8 0.26
25 14 0.45
26 9 0.29
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (26 bp):
AATATTTTTTAGAAAAAATTTATTTT
Found at i:44481309 original size:48 final size:47
Alignment explanation
Indices: 44481247--44481340 Score: 161
Period size: 48 Copynumber: 2.0 Consensus size: 47
44481237 TGCCAAATAC
*
44481247 TTTATCAGTCTTAAACAAATTATTCTTTGCATCAACAAATCTTTTTCA
1 TTTATCAGTCTTAAACAAATTATTCTTCGCATCAAC-AATCTTTTTCA
*
44481295 TTTATCAGTCTTAAACAAATTATTCTTCGCATCAACAATTTTTTTC
1 TTTATCAGTCTTAAACAAATTATTCTTCGCATCAACAATCTTTTTC
44481341 CATGACATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 9 0.20
48 35 0.80
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (47 bp):
TTTATCAGTCTTAAACAAATTATTCTTCGCATCAACAATCTTTTTCA
Found at i:44483130 original size:14 final size:14
Alignment explanation
Indices: 44483111--44483137 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44483101 TAACTGTGAA
44483111 CAAAATATGTTTAG
1 CAAAATATGTTTAG
44483125 CAAAATATGTTTA
1 CAAAATATGTTTA
44483138 ACATGCATTA
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:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (14 bp):
CAAAATATGTTTAG
Done.