Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 67 of 216
Found at i:20103555 original size:13 final size:13
Alignment explanation
Indices: 20103534--20103584 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
20103524 ATAATACACC
*
20103534 ACTTACATAAATA
1 ACTTGCATAAATA
*
20103547 ACTTGCATAATACA
1 ACTTGCATAA-ATA
20103561 CCACTT-CATAAATA
1 --ACTTGCATAAATA
20103575 ACTTGCATAA
1 ACTTGCATAA
20103585 TACATAGCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 4 0.13
13 14 0.45
14 4 0.13
15 5 0.16
16 4 0.13
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.29
Consensus pattern (13 bp):
ACTTGCATAAATA
Found at i:20103579 original size:28 final size:29
Alignment explanation
Indices: 20103515--20103588 Score: 132
Period size: 28 Copynumber: 2.6 Consensus size: 29
20103505 CATAGCGTAC
*
20103515 ATAACTTACATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
20103544 ATAACTTGCATAATACACCACTT-CATAA
1 ATAACTTGCATAATACACCACTTACATAA
20103572 ATAACTTGCATAATACA
1 ATAACTTGCATAATACA
20103589 TAGCCTACGT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 22 0.50
29 22 0.50
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAACTTGCATAATACACCACTTACATAA
Found at i:20103791 original size:12 final size:12
Alignment explanation
Indices: 20103774--20103818 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
20103764 TACATAACCA
*
20103774 ACATAATGACTT
1 ACATAATAACTT
*
20103786 ACATAATAACCT
1 ACATAATAACTT
*
20103798 AAATAATAACTT
1 ACATAATAACTT
20103810 ACATAATAA
1 ACATAATAA
20103819 TACATAACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (12 bp):
ACATAATAACTT
Found at i:20103803 original size:24 final size:24
Alignment explanation
Indices: 20103767--20103818 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
20103757 CACAACTTAC
*
20103767 ATAACCAACATAATGACTTACATA
1 ATAACCAACATAATAACTTACATA
20103791 ATAACCTAA-ATAATAACTTACATA
1 ATAACC-AACATAATAACTTACATA
20103815 ATAA
1 ATAA
20103819 TACATAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (24 bp):
ATAACCAACATAATAACTTACATA
Found at i:20103881 original size:9 final size:9
Alignment explanation
Indices: 20103867--20103986 Score: 121
Period size: 9 Copynumber: 14.2 Consensus size: 9
20103857 CAAAAACAAA
20103867 AACTTACAT
1 AACTTACAT
20103876 AACTTACAT
1 AACTTACAT
*
20103885 AA--GACAT
1 AACTTACAT
*
20103892 AAATTACAT
1 AACTTACAT
* *
20103901 AACCTACTT
1 AACTTACAT
20103910 AA--TACAT
1 AACTTACAT
20103917 AACTTACAT
1 AACTTACAT
*
20103926 AATTTACAT
1 AACTTACAT
20103935 AA--TACAT
1 AACTTACAT
20103942 AACTTACAT
1 AACTTACAT
* *
20103951 AATTTACTT
1 AACTTACAT
20103960 AA--TACAT
1 AACTTACAT
20103967 AACTTACAT
1 AACTTACAT
20103976 AACTTACAT
1 AACTTACAT
20103985 AA
1 AA
20103987 ATATCCCTTC
Statistics
Matches: 93, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
7 25 0.27
9 68 0.73
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:20103893 original size:16 final size:17
Alignment explanation
Indices: 20103871--20103986 Score: 100
Period size: 16 Copynumber: 6.9 Consensus size: 17
20103861 AACAAAAACT
20103871 TACATAACTTACATAA-
1 TACATAACTTACATAAC
* *
20103887 GACATAAATTACATAACC
1 TACATAACTTACATAA-C
*
20103905 TACTTAA--TACATAAC
1 TACATAACTTACATAAC
*
20103920 TTACATAATTTACATAA-
1 -TACATAACTTACATAAC
*
20103937 TACATAACTTACATAATT
1 TACATAACTTACATAA-C
*
20103955 TACTTAA--TACATAAC
1 TACATAACTTACATAAC
20103970 TTACATAACTTACATAA
1 -TACATAACTTACATAA
20103987 ATATCCCTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.01
16 55 0.68
18 25 0.31
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (17 bp):
TACATAACTTACATAAC
Found at i:20103898 original size:25 final size:25
Alignment explanation
Indices: 20103867--20103986 Score: 177
Period size: 25 Copynumber: 4.8 Consensus size: 25
20103857 CAAAAACAAA
*
20103867 AACTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* * *
20103892 AAATTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
*
20103917 AACTTACATAATTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
20103942 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
20103967 AACTTACATAACTTACATAA
1 AACTTACATAACTTACATAA
20103987 ATATCCCTTC
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 84 1.00
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:20103902 original size:50 final size:49
Alignment explanation
Indices: 20103840--20103986 Score: 161
Period size: 50 Copynumber: 2.9 Consensus size: 49
20103830 ATCAAATTAA
* * * *
20103840 ATAAGTTACATAATACACAAAAACAAAAACTTACATAACTTACATAAGAC
1 ATAAATTACATAATACACTAATAC-ATAACTTACATAACTTACATAAGAC
* * *
20103890 ATAAATTACATAACCTAC-TTAATACATAACTTACATAATTTACATAATAC
1 ATAAATTACATAA--TACACTAATACATAACTTACATAACTTACATAAGAC
* **
20103940 ATAACTTACATAATTTACTTAATACATAACTTACATAACTTACATAA
1 ATAAATTACATAATACAC-TAATACATAACTTACATAACTTACATAA
20103987 ATATCCCTTC
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
48 1 0.01
50 73 0.90
51 4 0.05
52 3 0.04
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (49 bp):
ATAAATTACATAATACACTAATACATAACTTACATAACTTACATAAGAC
Found at i:20109547 original size:66 final size:66
Alignment explanation
Indices: 20109464--20109599 Score: 193
Period size: 66 Copynumber: 2.1 Consensus size: 66
20109454 GACCACAGTT
* * * *
20109464 GAGGTTCAAAGGAAATATGAAGAACTCCAGCT-ACAATTTAAAGCAGAGGCGGCAACGAGAGAAG
1 GAGGTTCAAAAGAAATATGAAGAACTCCAG-TAACAACTTAAAGCAGAGGCGGCAACCAGAAAAG
20109528 CA
65 CA
* * *
20109530 GAGGTTCAAAAGAAATATGAAGAACTCCAGTAACAACTTAAAGCTGATGCGGCATCCAGAAAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGTAACAACTTAAAGCAGAGGCGGCAACCAGAAAAGC
20109595 A
66 A
20109596 GAGG
1 GAGG
20109600 CTGCAGCGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 61 0.98
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.15
Consensus pattern (66 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGTAACAACTTAAAGCAGAGGCGGCAACCAGAAAAGC
A
Found at i:20111945 original size:13 final size:13
Alignment explanation
Indices: 20111924--20111953 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20111914 AAACTAGATT
*
20111924 TTAATTAAGAAAA
1 TTAACTAAGAAAA
20111937 TTAACTAAGAAAA
1 TTAACTAAGAAAA
20111950 TTAA
1 TTAA
20111954 AAGGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACTAAGAAAA
Found at i:20128097 original size:48 final size:48
Alignment explanation
Indices: 20128022--20128113 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
20128012 TTAGGAGGTA
* ** *
20128022 GCTGATTATTTTGATTATCACTTATCTCTACAAAAATATCCTTTTCTT
1 GCTGATTATCTTGATTATCACCCATCTCCACAAAAATATCCTTTTCTT
*
20128070 GCTGATTATCTTGATTATCACCCATCTCCACAATAATATCCTTT
1 GCTGATTATCTTGATTATCACCCATCTCCACAAAAATATCCTTT
20128114 CTTCTTGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (48 bp):
GCTGATTATCTTGATTATCACCCATCTCCACAAAAATATCCTTTTCTT
Found at i:20128319 original size:20 final size:19
Alignment explanation
Indices: 20128290--20128334 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
20128280 ATTAGAATAT
*
20128290 AAAAATTAAATTAAAAACA
1 AAAAATTAAAATAAAAACA
*
20128309 AAAATATTAAAATAAAAATA
1 AAAA-ATTAAAATAAAAACA
20128329 AAAAAT
1 AAAAAT
20128335 GGCTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATTAAAATAAAAACA
Found at i:20131590 original size:27 final size:27
Alignment explanation
Indices: 20131534--20131597 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
20131524 ATCCTGTCAG
*
20131534 CCTTTGTGGCATACTCTGAATGAATCA
1 CCTTTGTGGCATACTCTGAATGAATAA
*
20131561 CCTTTGTGGCATACTCTGTAT-ATATAA
1 CCTTTGTGGCATACTCTGAATGA-ATAA
*
20131588 CCTTTATGGC
1 CCTTTGTGGC
20131598 GTACACTACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (27 bp):
CCTTTGTGGCATACTCTGAATGAATAA
Found at i:20133479 original size:33 final size:33
Alignment explanation
Indices: 20133437--20133505 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
20133427 AATCAAAATC
20133437 TTAGTGAGTCGATTGCTGAAGAAACCTTTTCGA
1 TTAGTGAGTCGATTGCTGAAGAAACCTTTTCGA
* *
20133470 TTAGTGAGTCGATTGCTGAAGAGACCTTTTTGA
1 TTAGTGAGTCGATTGCTGAAGAAACCTTTTCGA
20133503 TTA
1 TTA
20133506 CCAGACGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (33 bp):
TTAGTGAGTCGATTGCTGAAGAAACCTTTTCGA
Found at i:20134250 original size:25 final size:25
Alignment explanation
Indices: 20134218--20134402 Score: 131
Period size: 25 Copynumber: 6.9 Consensus size: 25
20134208 GTATGTTTTT
20134218 TATG-TATGTATATTACTATTTATG
1 TATGTTATGTATATTACTATTTATG
*
20134242 TATGTTATGTTTTATATTTCTATTTATG
1 TATGTTATG---TATATTACTATTTATG
* * *
20134270 TATTTTATGCATATTACTTTTTATG
1 TATGTTATGTATATTACTATTTATG
* *
20134295 TATGTTATATATATTACTGTTTATATCATG
1 TATGTTATGTATATTAC----TAT-TTATG
* *
20134325 TATGTTATATATATTACTATTTATAT
1 TATGTTATGTATATTACTATTTAT-G
*
20134351 TATG-TATGTATATTAATGTTGATATTATG
1 TATGTTATGTATATT-A--CT-AT-TTATG
* *
20134380 TATGTTATGTATACTACTGTTTA
1 TATGTTATGTATATTACTATTTA
20134403 CATTATTTAT
Statistics
Matches: 127, Mismatches: 18, Indels: 31
0.72 0.10 0.18
Matches are distributed among these distances:
24 4 0.03
25 46 0.36
26 9 0.07
27 1 0.01
28 24 0.19
29 9 0.07
30 34 0.27
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (25 bp):
TATGTTATGTATATTACTATTTATG
Found at i:20134320 original size:16 final size:16
Alignment explanation
Indices: 20134299--20134350 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
20134289 TTTATGTATG
20134299 TTATATATATTACTGT
1 TTATATATATTACTGT
*
20134315 TTATATCAT-GTA-TG-
1 TTATAT-ATATTACTGT
*
20134329 TTATATATATTACTAT
1 TTATATATATTACTGT
20134345 TTATAT
1 TTATAT
20134351 TATGTATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 2 0.07
14 8 0.28
15 3 0.10
16 14 0.48
17 2 0.07
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATATATATTACTGT
Found at i:20134326 original size:30 final size:30
Alignment explanation
Indices: 20134290--20134440 Score: 186
Period size: 30 Copynumber: 5.2 Consensus size: 30
20134280 ATATTACTTT
20134290 TTATGTATGTTATATATATTACTGTTTATA
1 TTATGTATGTTATATATATTACTGTTTATA
* *
20134320 TCATGTATGTTATATATATTACTATTTATA
1 TTATGTATGTTATATATATTACTGTTTATA
*
20134350 TTATGTATG-TATAT-TA--A-TGTTGATA
1 TTATGTATGTTATATATATTACTGTTTATA
* * *
20134375 TTATGTATGTTATGTATACTACTGTTTACA
1 TTATGTATGTTATATATATTACTGTTTATA
* * *
20134405 TTATTTATGTTATGTATATTAATGTTTATA
1 TTATGTATGTTATATATATTACTGTTTATA
20134435 TTATGT
1 TTATGT
20134441 CACTCACTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
25 15 0.15
26 5 0.05
27 2 0.02
28 2 0.02
29 6 0.06
30 73 0.71
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (30 bp):
TTATGTATGTTATATATATTACTGTTTATA
Found at i:20134342 original size:55 final size:55
Alignment explanation
Indices: 20134218--20134440 Score: 226
Period size: 55 Copynumber: 4.0 Consensus size: 55
20134208 GTATGTTTTT
*
20134218 TATG-TATGTATATTACTATTTATGTATGTTATGT-T-TTATAT-TTCTAT-TTATG
1 TATGTTATGTATATTACTTTTTATGTATGTTATGTATATTA-ATGTT-TATATTATG
* * * * *
20134270 TATTTTATGCATATTACTTTTTATGTATGTTATATATATTACTGTTTATATCATG
1 TATGTTATGTATATTACTTTTTATGTATGTTATGTATATTAATGTTTATATTATG
* *
20134325 TATGTTATATATATTACTATTTATAT-TATG-TATGTATATTAATGTTGATATTATG
1 TATGTTATGTATATTACT-TTT-TATGTATGTTATGTATATTAATGTTTATATTATG
* *
20134380 TATGTTATGTATACTACTGTTTACATTATTTATGTTATGTATATTAATGTTTATATTATG
1 TATGTTATGTATATTAC--TTT---TTATGTATGTTATGTATATTAATGTTTATATTATG
20134440 T
1 T
20134441 CACTCACTTT
Statistics
Matches: 141, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
52 3 0.02
53 27 0.19
54 5 0.04
55 60 0.43
56 9 0.06
57 4 0.03
58 3 0.02
59 5 0.04
60 25 0.18
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (55 bp):
TATGTTATGTATATTACTTTTTATGTATGTTATGTATATTAATGTTTATATTATG
Found at i:20134349 original size:14 final size:14
Alignment explanation
Indices: 20134297--20134350 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
20134287 TTTTTATGTA
20134297 TGTTATATATATTAC
1 TGTT-TATATATTAC
20134312 TGTTTATATCATGTA-
1 TGTTTATAT-AT-TAC
20134327 TGTTATATATATTAC
1 TGTT-TATATATTAC
*
20134342 TATTTATAT
1 TGTTTATAT
20134351 TATGTATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 12 0.35
15 15 0.44
16 7 0.21
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (14 bp):
TGTTTATATATTAC
Found at i:20134379 original size:21 final size:19
Alignment explanation
Indices: 20134290--20134440 Score: 64
Period size: 21 Copynumber: 7.8 Consensus size: 19
20134280 ATATTACTTT
* *
20134290 TTATG-TATGTTATATATA
1 TTATGTTATATTATGTATA
* *
20134308 TTACTGTTTATATCATGTATG
1 TTA-TG-TTATATTATGTATA
* *
20134329 TTAT-ATATATTA-CTAT-
1 TTATGTTATATTATGTATA
* *
20134345 TTATATTAT-GTATGTATA
1 TTATGTTATATTATGTATA
*
20134363 TTAATGTTGATATTATGTATG
1 TT-ATGTT-ATATTATGTATA
* *
20134384 TTATG-TATACTACTGTTTACA
1 TTATGTTATATTA-TG--TATA
*
20134405 TTAT-TTATGTTATGTATA
1 TTATGTTATATTATGTATA
20134423 TTAATGTTTATATTATGT
1 TT-ATG-TTATATTATGT
20134441 CACTCACTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 29
0.66 0.14 0.20
Matches are distributed among these distances:
16 6 0.06
17 9 0.09
18 21 0.22
19 11 0.11
20 8 0.08
21 42 0.43
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (19 bp):
TTATGTTATATTATGTATA
Found at i:20134433 original size:25 final size:25
Alignment explanation
Indices: 20134211--20134440 Score: 124
Period size: 25 Copynumber: 8.5 Consensus size: 25
20134201 TATATTAGTA
20134211 TGTTT-TTTATG-TATGTATATTAC
1 TGTTTATTTATGTTATGTATATTAC
* * *
20134234 TATTTATGTATGTTATGTTTTATATTTC
1 TGTTTATTTATGTTATG---TATATTAC
* * * *
20134262 TATTTATGTATTTTATGCATATTAC
1 TGTTTATTTATGTTATGTATATTAC
* * *
20134287 TTTTTATGTATGTTATATATATTAC
1 TGTTTATTTATGTTATGTATATTAC
*
20134312 TGTTTATATCATGTATGTTATATATATTAC
1 TG-TT-TAT--T-TATGTTATGTATATTAC
* *
20134342 TATTTATATTATG-TATGTATATTAA
1 TGTTTAT-TTATGTTATGTATATTAC
*
20134367 TGTTGATATTATGTATGTTATGTATACTAC
1 TGTT--TA-T-T-TATGTTATGTATATTAC
*
20134397 TGTTTACATTATTTATGTTATGTATATTAA
1 TG--T---TTATTTATGTTATGTATATTAC
20134427 TGTTTATATTATGT
1 TGTTTAT-TTATGT
20134441 CACTCACTTT
Statistics
Matches: 166, Mismatches: 20, Indels: 39
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.02
24 5 0.03
25 49 0.30
26 12 0.07
27 7 0.04
28 30 0.18
29 6 0.04
30 47 0.28
31 1 0.01
32 2 0.01
33 2 0.01
35 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.11, T:0.57
Consensus pattern (25 bp):
TGTTTATTTATGTTATGTATATTAC
Found at i:20148944 original size:20 final size:21
Alignment explanation
Indices: 20148911--20148950 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20148901 CAAACCATAC
* *
20148911 AAAACCCTAGAAAACCTAATG
1 AAAACACTAGAAAAACTAATG
20148932 AAAACACTA-AAAAACTAAT
1 AAAACACTAGAAAAACTAAT
20148951 AAGCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.20, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAACACTAGAAAAACTAATG
Found at i:20149213 original size:29 final size:27
Alignment explanation
Indices: 20149170--20149230 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
20149160 AATTAACTAC
20149170 ATTAAAATATAAAATTTAA-TCCTTATTTA
1 ATTAAAATATAAAA-TTAACT-C-TATTTA
20149199 ATTAAAATA-ATAAATTAACTCTATTTA
1 ATTAAAATATA-AAATTAACTCTATTTA
20149226 ATTAA
1 ATTAA
20149231 GTAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 11 0.37
28 6 0.20
29 13 0.43
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (27 bp):
ATTAAAATATAAAATTAACTCTATTTA
Found at i:20149254 original size:31 final size:31
Alignment explanation
Indices: 20149196--20149255 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
20149186 TAATCCTTAT
* * *
20149196 TTAATTAAAATAATAAATTAACTCTATTTAA
1 TTAAGTAAAATAATAAACTAACCCTATTTAA
20149227 TTAAGTAAAAT-ATCAAACTAACCCTATTT
1 TTAAGTAAAATAAT-AAACTAACCCTATTT
20149256 TCATCCCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (31 bp):
TTAAGTAAAATAATAAACTAACCCTATTTAA
Found at i:20155771 original size:42 final size:42
Alignment explanation
Indices: 20155700--20155783 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
20155690 CAACACACCA
*
20155700 ATCTAGCACCTCAGTGCATCATCGAAAAGT-TCAAAGTAATAT
1 ATCTAGCACCTCAGTGCATCATAGAAAAGTAT-AAAGTAATAT
*
20155742 ATCTGGCACCTCAGTGCATCATTAG-AAAGTATAAAGTAATAT
1 ATCTAGCACCTCAGTGCATCA-TAGAAAAGTATAAAGTAATAT
20155784 GTGCTTAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (42 bp):
ATCTAGCACCTCAGTGCATCATAGAAAAGTATAAAGTAATAT
Found at i:20162904 original size:17 final size:17
Alignment explanation
Indices: 20162882--20162979 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
20162872 AATTCAATAC
20162882 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
20162899 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
20162918 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
* * *
20162936 TTATGTAGTGATTTAAATAT
1 TTATGTAATG-TTT--TTAA
*
20162956 TTATGTAATGCTTTTAA
1 TTATGTAATGTTTTTAA
20162973 TTATGTA
1 TTATGTA
20162980 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 26 0.45
18 7 0.12
19 6 0.10
20 19 0.33
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:20162961 original size:20 final size:19
Alignment explanation
Indices: 20162896--20162989 Score: 72
Period size: 17 Copynumber: 5.1 Consensus size: 19
20162886 GTAATGTTTT
*
20162896 TAATTATGTAGTGATTCAA
1 TAATTATGTAGTGATTTAA
* *
20162915 -AGACTTATGTAAT-ATTT-T
1 TA-A-TTATGTAGTGATTTAA
20162933 TAATTATGTAGTGATTTAAA
1 TAATTATGTAGTGATTT-AA
* * *
20162953 TATTTATGTAATGCTTT--
1 TAATTATGTAGTGATTTAA
20162970 TAATTATGTAGTGATTTAA
1 TAATTATGTAGTGATTTAA
20162989 T
1 T
20162990 TTGGGTAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 16
0.67 0.13 0.19
Matches are distributed among these distances:
17 22 0.39
18 6 0.11
19 6 0.11
20 22 0.39
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (19 bp):
TAATTATGTAGTGATTTAA
Found at i:20162986 original size:37 final size:37
Alignment explanation
Indices: 20162877--20162988 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
20162867 GTGTTAATTC
*
20162877 AATACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AATACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
20162914 AAGACTTATGTAATATTTTTAATTATGTAGTGATTTA
1 AATACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
20162951 AATATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AATACTTATGTAATGTTTTTAATTATGTAGTGATTTA
20162988 A
1 A
20162989 TTTGGGTAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (37 bp):
AATACTTATGTAATGTTTTTAATTATGTAGTGATTTA
Found at i:20163018 original size:20 final size:20
Alignment explanation
Indices: 20162993--20163039 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20162983 ATTTAATTTG
20162993 GGTAATTCGGGTAATTTTCA
1 GGTAATTCGGGTAATTTTCA
*
20163013 GGTAATTCGGGTATTTTTCA
1 GGTAATTCGGGTAATTTTCA
20163033 GGTAATT
1 GGTAATT
20163040 TGAGTTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.43
Consensus pattern (20 bp):
GGTAATTCGGGTAATTTTCA
Found at i:20164309 original size:51 final size:51
Alignment explanation
Indices: 20164249--20164363 Score: 203
Period size: 51 Copynumber: 2.3 Consensus size: 51
20164239 TCCTCTCTAA
20164249 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
* *
20164300 TCCTCTCAATTTCTTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
20164351 TCCCCTCAATTTC
1 TCCTCTCAATTTC
20164364 ATTTTTGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:20166190 original size:18 final size:18
Alignment explanation
Indices: 20166163--20166202 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20166153 CAGGTGTGTT
* *
20166163 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTACATGTA
*
20166181 TCCTAACCCTTACATGTT
1 TCCTAACCCTTACATGTA
20166199 TCCT
1 TCCT
20166203 TTTCCGAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTACATGTA
Found at i:20166481 original size:21 final size:21
Alignment explanation
Indices: 20166457--20166506 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
20166447 CAGATGTCGA
*
20166457 ATCGGAAGAACCACAATCACC
1 ATCGGAAGAACAACAATCACC
* * *
20166478 ATCGGAGGAAGAACAATCGCC
1 ATCGGAAGAACAACAATCACC
*
20166499 ACCGGAAG
1 ATCGGAAG
20166507 CTAGAGGAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.28, G:0.24, T:0.08
Consensus pattern (21 bp):
ATCGGAAGAACAACAATCACC
Found at i:20166666 original size:26 final size:25
Alignment explanation
Indices: 20166602--20166670 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
20166592 TTTAAATTTA
* *
20166602 TTATCTGATGCAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* * *
20166627 TTATTTAATATAATAAAATAGAATT
1 TTATTTGATGTAATAAAATAGAAGT
20166652 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
20166671 ACCCTAACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 21 0.58
26 15 0.42
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:20166689 original size:18 final size:18
Alignment explanation
Indices: 20166666--20167189 Score: 219
Period size: 18 Copynumber: 31.8 Consensus size: 18
20166656 TTTGATGTAA
20166666 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
20166684 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
20166702 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
20166720 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
*
20166738 TAAAAACCCTAAGTTAAT
1 TAAAAACCCTAACTTAAT
* **
20166756 TAAAAATCCTAAC---CC
1 TAAAAACCCTAACTTAAT
*
20166771 T---AA-CCTAATTTAAT
1 TAAAAACCCTAACTTAAT
**
20166785 TAAAAACCCTAAC---CC
1 TAAAAACCCTAACTTAAT
20166800 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTAAT
**
20166814 TAAAAACCCTAAC---CC
1 TAAAAACCCTAACTTAAT
20166829 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTAAT
**
20166843 TAAAAACCCTAACCCAAT
1 TAAAAACCCTAACTTAAT
*
20166861 TAAAAACCCTAAC-T--C
1 TAAAAACCCTAACTTAAT
*
20166876 T---AA-CCTAATTTAAT
1 TAAAAACCCTAACTTAAT
*
20166890 TAAAACCCTAACCTAACTTAAT
1 TAAAA----ACCCTAACTTAAT
*
20166912 TAAAAACCCTAACCTTAAC
1 TAAAAACCCTAA-CTTAAT
** *
20166931 T-CTAA-CCTAATTTAAT
1 TAAAAACCCTAACTTAAT
20166947 TAAAAACCCTAACCTAACTTAAT
1 TAAAAA--C---CCTAACTTAAT
*
20166970 TAAAAACCCTAAC-T--C
1 TAAAAACCCTAACTTAAT
*
20166985 T---AA-CCTAATTTAAT
1 TAAAAACCCTAACTTAAT
* **
20166999 TAAAAACCCAAAC---CC
1 TAAAAACCCTAACTTAAT
*
20167014 T---AA-CCTAATTTAAT
1 TAAAAACCCTAACTTAAT
*
20167028 TAAAAGCCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
* **
20167046 TAAAAACCCAAAC---CC
1 TAAAAACCCTAACTTAAT
20167061 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTAAT
* *
20167075 TACAAACCCGAACTTAAT
1 TAAAAACCCTAACTTAAT
*
20167093 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
20167111 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
* * **
20167129 TAAAAACACAAAC---CC
1 TAAAAACCCTAACTTAAT
20167144 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTAAT
20167158 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
20167176 TAAAAACCCTAACT
1 TAAAAACCCTAACT
20167190 CTAACCCTAA
Statistics
Matches: 369, Mismatches: 69, Indels: 136
0.64 0.12 0.24
Matches are distributed among these distances:
11 40 0.11
12 18 0.05
14 8 0.02
15 8 0.02
16 5 0.01
17 22 0.06
18 229 0.62
19 6 0.02
21 2 0.01
22 15 0.04
23 16 0.04
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:20166787 original size:29 final size:29
Alignment explanation
Indices: 20166745--20167040 Score: 285
Period size: 29 Copynumber: 9.8 Consensus size: 29
20166735 AATTAAAAAC
* *
20166745 CCTAAGTTAATTAAAAATCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
20166774 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
20166803 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
20166832 CCTAACTTAATTAAAAACCCTAACCCAATTAAAAA
1 CCTAACTTAATTAAAAACCCTAACCC---T---AA
* * ****
20166867 CCCTAACTCTAACCTAATTTAATTAAAACCCTAA
1 -CCTAACT-TAA-TTAA--AAACCCTAACCCTAA
*
20166901 CCTAACTTAATTAAAAACCCTAACCTTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
20166930 CTCTAACCTAATTTAATTAAA----AACCCTAA
1 C-CTAACTTAA-TTAA--AAACCCTAACCCTAA
*
20166959 CCTAACTTAATTAAAAACCCTAACTCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* *
20166988 CCTAATTTAATTAAAAACCCAAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* *
20167017 CCTAATTTAATTAAAAGCCCTAAC
1 CCTAACTTAATTAAAAACCCTAAC
20167041 TTAATTAAAA
Statistics
Matches: 223, Mismatches: 25, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
25 3 0.01
27 4 0.02
28 8 0.04
29 154 0.69
30 8 0.04
31 7 0.03
32 4 0.02
33 10 0.04
34 2 0.01
35 2 0.01
36 7 0.03
37 4 0.02
38 3 0.01
40 7 0.03
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (29 bp):
CCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:20166854 original size:76 final size:73
Alignment explanation
Indices: 20166782--20166925 Score: 215
Period size: 76 Copynumber: 2.0 Consensus size: 73
20166772 AACCTAATTT
20166782 AATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAA
1 AATTAAAAACCCTAACCCTAACCTAACTTAATT-AAAACCCTAA-CCTAACCTAA-TTAATTAAA
20166847 AACCCTAACCC
63 AACCCTAACCC
* *
20166858 AATTAAAAACCCTAACTCTAACCTAATTTAATTAAAACCCTAACCTAA-C---TTAATTAAAAAC
1 AATTAAAAACCCTAACCCTAACCTAACTTAATTAAAACCCTAACCTAACCTAATTAATTAAAAAC
20166919 CCTAACC
66 CCTAACC
20166926 TTAACTCTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
69 19 0.29
73 1 0.02
74 5 0.08
75 10 0.15
76 31 0.47
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (73 bp):
AATTAAAAACCCTAACCCTAACCTAACTTAATTAAAACCCTAACCTAACCTAATTAATTAAAAAC
CCTAACCC
Found at i:20166979 original size:185 final size:185
Alignment explanation
Indices: 20166691--20167170 Score: 585
Period size: 185 Copynumber: 2.6 Consensus size: 185
20166681 AATTAAAAAC
* * * * * *
20166691 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAAGTTAAT
1 CCTAACTTAATTACAAACCCGAACTTAATTAAAAACCCTAACTTAACTAAAAACCCTAACTTAAT
* * *
20166756 TAAAAATCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
66 T-AACA--CAAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
* * *
20166821 CCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCAATTAAAAACCCTAACTCTAA
128 CCAAACCCTAACCTAACTTAATTAAAAACCCTAACCCAATTAAAAACCCAAACCCTAA
* * **
20166879 CCTAATTTAATTA-AAACCCTAACCTAACTTAATTAAAAACCCTAACCTTAACT-CTAA-CCTAA
1 CCTAACTTAATTACAAA--C---CCGAACTTAATTAAAAACCCTAA-CTTAACTAAAAACCCTAA
* * *
20166941 TTTAATT-A-A-AAACCCTAACCTAACTTAATTAAAAACCCTAACTCTAACCTAATTTAATTAAA
60 CTTAATTAACACAAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAA
* * **
20167003 AACCCAAACCCTAACCTAATTTAATTAAAAGCCCTAACTTAATTAAAAACCCAAACCCTAA
125 AACCCAAACCCTAACCTAACTTAATTAAAAACCCTAACCCAATTAAAAACCCAAACCCTAA
* *
20167064 CCTAACTTAATTACAAACCCGAACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAACTTAAT
1 CCTAACTTAATTACAAACCCGAACTTAATTAAAAACCCTAACTTAACTAAAAACCCTAACTTAAT
20167129 TAAAAACACAAACCCTAACCTAACTTAATTAAAAACCCTAAC
66 T---AACACAAACCCTAACCTAACTTAATTAAAAACCCTAAC
20167171 TTAATTAAAA
Statistics
Matches: 254, Mismatches: 23, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
180 5 0.02
181 24 0.09
182 11 0.04
184 1 0.00
185 115 0.45
186 4 0.02
187 4 0.02
188 47 0.19
189 2 0.01
191 11 0.04
192 25 0.10
193 5 0.02
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.27
Consensus pattern (185 bp):
CCTAACTTAATTACAAACCCGAACTTAATTAAAAACCCTAACTTAACTAAAAACCCTAACTTAAT
TAACACAAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCA
AACCCTAACCTAACTTAATTAAAAACCCTAACCCAATTAAAAACCCAAACCCTAA
Found at i:20167075 original size:47 final size:47
Alignment explanation
Indices: 20166988--20167200 Score: 268
Period size: 47 Copynumber: 4.7 Consensus size: 47
20166978 CTAACTCTAA
* * *
20166988 CCTAATTTAATTAAAAACCCAAACCCTAACCTAATTTAATTAAAAGC
1 CCTAACTTAATTAAAAACCCAAACCCTAACCTAACTTAATTAAAAAC
*
20167035 CCTAACTTAATTAAAAACCCAAACCCTAACCTAACTTAATTACAAAC
1 CCTAACTTAATTAAAAACCCAAACCCTAACCTAACTTAATTAAAAAC
*
20167082 CCGAACTTAATT---AA---AAACCCTAA--T---TTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCAAACCCTAACCTAACTTAATTAAAAAC
*
20167118 CCTAACTTAATTAAAAACACAAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCAAACCCTAACCTAACTTAATTAAAAAC
* *
20167165 CCTAACTTAATTAAAAACCCTAACTCTAACCCTAAC
1 CCTAACTTAATTAAAAACCCAAACCCTAA-CCTAAC
20167201 CCTAACCCAA
Statistics
Matches: 144, Mismatches: 10, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
36 22 0.15
39 3 0.02
41 9 0.06
42 9 0.06
44 3 0.02
47 92 0.64
48 6 0.04
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.25
Consensus pattern (47 bp):
CCTAACTTAATTAAAAACCCAAACCCTAACCTAACTTAATTAAAAAC
Found at i:20167121 original size:83 final size:83
Alignment explanation
Indices: 20166835--20167187 Score: 348
Period size: 83 Copynumber: 4.2 Consensus size: 83
20166825 ACCCTAACCT
*** * **
20166835 AACTTAATTAAAAACCCTAACCCAATTAAAAACCCTAACTCTAACCTAATTTAATTA-AAACCCT
1 AACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAACT-TAA-TTAA---AAACACAAACCCT
*
20166899 AACCTAACTTAATTAAAAACCCT
61 AACCTAACTTAATTAAAAACCCG
* ** * * *
20166922 AACCTTAACT-CTAA-CCTAATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACTC
1 AA-CTTAATTAAAAACCCTAATTTAATTAAAAA--C---CCTAACTTAATTAAAAACACAAACCC
* *
20166985 TAACCTAATTTAATTAAAAACCCA
60 TAACCTAACTTAATTAAAAACCCG
** * *
20167009 AAC---CCT---AA-CCTAATTTAATTAAAAGCCCTAACTTAATTAAAAACCCAAACCCTAACCT
1 AACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAACTTAATTAAAAACACAAACCCTAACCT
*
20167067 AACTTAATTACAAACCCG
66 AACTTAATTAAAAACCCG
20167085 AACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAACTTAATTAAAAACACAAACCCTAACCT
1 AACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAACTTAATTAAAAACACAAACCCTAACCT
*
20167150 AACTTAATTAAAAACCCT
66 AACTTAATTAAAAACCCG
20167168 AACTTAATTAAAAACCCTAA
1 AACTTAATTAAAAACCCTAA
20167188 CTCTAACCCT
Statistics
Matches: 225, Mismatches: 27, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
76 48 0.21
79 2 0.01
81 18 0.08
82 2 0.01
83 86 0.38
86 17 0.08
87 32 0.14
88 7 0.03
89 3 0.01
90 3 0.01
91 7 0.03
ACGTcount: A:0.48, C:0.25, G:0.01, T:0.26
Consensus pattern (83 bp):
AACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAACTTAATTAAAAACACAAACCCTAACCT
AACTTAATTAAAAACCCG
Found at i:20167199 original size:6 final size:6
Alignment explanation
Indices: 20167180--20167219 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
20167170 CTTAATTAAA
* * *
20167180 AACCCT AACTCT AACCCT AACCCT AACCCA AACCCA AACC
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACC
20167220 TTTGTACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.12
Consensus pattern (6 bp):
AACCCT
Found at i:20168673 original size:124 final size:124
Alignment explanation
Indices: 20168453--20168678 Score: 418
Period size: 124 Copynumber: 1.8 Consensus size: 124
20168443 CCCAAACTTG
*
20168453 CTACTGTAGCAAAATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
20168518 TAGAAGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
*
20168577 CTACTGTAGCAAAATCGCGTCCGCGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
20168642 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTT-ACTCAGAAACGTCAA
20168679 CTCGAAATAA
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
124 97 0.98
125 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
Found at i:20183404 original size:38 final size:38
Alignment explanation
Indices: 20183352--20183426 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
20183342 TCATTTGTTA
* * *
20183352 ATCCTTGACTAACATTCCACTTAAGATAATCCTTGGCG
1 ATCCTTGACGAACATCCCACTTAAGATAATCCCTGGCG
*
20183390 ATCCTTGGCGAACATCCCACTTAAGATAATCCCTGGC
1 ATCCTTGACGAACATCCCACTTAAGATAATCCCTGGC
20183427 TTACTTTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (38 bp):
ATCCTTGACGAACATCCCACTTAAGATAATCCCTGGCG
Found at i:20195551 original size:43 final size:42
Alignment explanation
Indices: 20195485--20195601 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 42
20195475 GCTCGTACAG
* ***
20195485 TGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATAACGA
1 TGCCAATGTCCCAGACAAAGTCTTACACGTAATCAAAT-ACGA
* * *
20195528 TGCCACTGTCCCAGACAAAGTCTTACACGAAATCATATACGA
1 TGCCAATGTCCCAGACAAAGTCTTACACGTAATCAAATACGA
* **
20195570 TGCTAATGTCCCAGACATGGTCTTACACGTAA
1 TGCCAATGTCCCAGACAAAGTCTTACACGTAA
20195602 ATCTCAAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 31 0.50
43 31 0.50
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
TGCCAATGTCCCAGACAAAGTCTTACACGTAATCAAATACGA
Found at i:20195583 original size:42 final size:43
Alignment explanation
Indices: 20195485--20195604 Score: 134
Period size: 43 Copynumber: 2.8 Consensus size: 43
20195475 GCTCGTACAG
* *** *
20195485 TGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATAACGA
1 TGCCAATGTCCCAGACAAAGTCTTACACGAAATCAAATAACGA
* *
20195528 TGCCACTGTCCCAGACAAAGTCTTACACGAAATCATAT-ACGA
1 TGCCAATGTCCCAGACAAAGTCTTACACGAAATCAAATAACGA
* **
20195570 TGCTAATGTCCCAGACATGGTCTTACACGTAAATC
1 TGCCAATGTCCCAGACAAAGTCTTACACG-AAATC
20195605 TCAAATTGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 29 0.45
43 36 0.55
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (43 bp):
TGCCAATGTCCCAGACAAAGTCTTACACGAAATCAAATAACGA
Found at i:20206658 original size:20 final size:20
Alignment explanation
Indices: 20206633--20206670 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20206623 ACCCCCTTTA
20206633 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
20206653 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
20206671 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:20213542 original size:17 final size:16
Alignment explanation
Indices: 20213520--20213554 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
20213510 AGAGAGTTGA
20213520 GAGAGAGGATGAGAGAT
1 GAGAGAGG-TGAGAGAT
*
20213537 GAGAGAGGTGAGGGAT
1 GAGAGAGGTGAGAGAT
20213553 GA
1 GA
20213555 TTGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (16 bp):
GAGAGAGGTGAGAGAT
Found at i:20217579 original size:20 final size:20
Alignment explanation
Indices: 20217554--20217599 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
20217544 ATCGTGGTCT
20217554 TTACTTCTTTACTTACTCT-C
1 TTACTTCTTTACTTACT-TGC
*
20217574 TTACTTGTTTACTTACTTGC
1 TTACTTCTTTACTTACTTGC
20217594 TTACTT
1 TTACTT
20217600 AAATAACTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (20 bp):
TTACTTCTTTACTTACTTGC
Found at i:20217944 original size:50 final size:50
Alignment explanation
Indices: 20217867--20217996 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 50
20217857 TGTCATATCT
* * ** * * *
20217867 CAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTCC
1 CAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCC
*
20217917 CAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCC
1 CAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCC
*
20217967 CAAACATGGTCTTAC-GTGGGACCTCTCATA
1 CAGACATGGTCTTACAG-GGGACCTCTCATA
20217997 ACCCCAATAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
CAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCC
Found at i:20223952 original size:42 final size:41
Alignment explanation
Indices: 20223839--20223956 Score: 112
Period size: 43 Copynumber: 2.8 Consensus size: 41
20223829 CAAAAAGCTC
* * *
20223839 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACA-GAAATCAA
* * * * *
20223881 ATAACAATGCCACTATCCCAAACAGGGTCTTATGCA-AAATCAT
1 AT-ACAATGCCAATGTCCCAGACATGGTCTTA--CAGAAATCAA
*
20223924 ATACGATGCCAATGTCCCAGACATGGTCTTACA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACA
20223957 CATAAATCTC
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
40 2 0.03
42 26 0.43
43 30 0.50
45 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (41 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACAGAAATCAA
Found at i:20226186 original size:24 final size:24
Alignment explanation
Indices: 20226142--20226187 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20226132 TTTCATCCTA
*
20226142 AAAATTAAATATTATTATAAAATT
1 AAAATTAAATATTAATATAAAATT
*
20226166 AAAATTAAA-ATTACATGTAAAA
1 AAAATTAAATATTA-ATATAAAA
20226188 GAGAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAATTAAATATTAATATAAAATT
Found at i:20232661 original size:19 final size:20
Alignment explanation
Indices: 20232637--20232683 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
20232627 TGGAGGTGTA
*
20232637 TTTTAAGTTTT-AAGATAAT
1 TTTTAAATTTTAAAGATAAT
*
20232656 TTTTAAATTTTAAATATAAT
1 TTTTAAATTTTAAAGATAAT
20232676 TTTATAAA
1 TTT-TAAA
20232684 AATAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 10 0.42
21 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTAAATTTTAAAGATAAT
Found at i:20236107 original size:22 final size:22
Alignment explanation
Indices: 20236079--20236123 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
20236069 TCTGTCATAG
*
20236079 TCACACGGTCGTGTGCCTCCTT
1 TCACACGGGCGTGTGCCTCCTT
20236101 TCACACGGGCGTGTGCCTCCTT
1 TCACACGGGCGTGTGCCTCCTT
20236123 T
1 T
20236124 ACATAGGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.36, G:0.24, T:0.31
Consensus pattern (22 bp):
TCACACGGGCGTGTGCCTCCTT
Found at i:20254846 original size:17 final size:17
Alignment explanation
Indices: 20254826--20254861 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20254816 AACCACATAT
*
20254826 AATTTAGTCATTATCAC
1 AATTTACTCATTATCAC
*
20254843 AATTTACTCCTTATCAC
1 AATTTACTCATTATCAC
20254860 AA
1 AA
20254862 ACATCCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTACTCATTATCAC
Found at i:20255637 original size:6 final size:6
Alignment explanation
Indices: 20255626--20255672 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
20255616 ACAATCTTAT
20255626 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
20255673 TTTACACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:20256849 original size:58 final size:59
Alignment explanation
Indices: 20256776--20256916 Score: 164
Period size: 59 Copynumber: 2.4 Consensus size: 59
20256766 GTTGAAGTCC
* * *
20256776 CAATGT-GAGAACAATTG-TCAAGTTTAGTGCCTAACTT-GA-ACAAAAAATGTTCATACCT
1 CAATGTGGA-AACAATTGCT-AAGTTTAGGGCCTAACTTGGATA-AAAAAAAGTTCAGACCT
*
20256834 CAATGTGGAAACAATTGCTAAGTTTAGGGCCTAACTTGGATAAAAAAAAGTTTAGACCT
1 CAATGTGGAAACAATTGCTAAGTTTAGGGCCTAACTTGGATAAAAAAAAGTTCAGACCT
* * *
20256893 CAATATGGAAAAAATTACTAAGTT
1 CAATGTGGAAACAATTGCTAAGTT
20256917 GAAGTCCCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
58 31 0.43
59 40 0.56
60 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (59 bp):
CAATGTGGAAACAATTGCTAAGTTTAGGGCCTAACTTGGATAAAAAAAAGTTCAGACCT
Found at i:20258529 original size:19 final size:20
Alignment explanation
Indices: 20258487--20258530 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
20258477 ATTATTATAC
*
20258487 AATA-ATATTTTAATTTTAG
1 AATATATATTTTAATTTTAA
*
20258506 GATATATATTTT-ATTTTAA
1 AATATATATTTTAATTTTAA
20258525 AATATA
1 AATATA
20258531 ATTATATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
AATATATATTTTAATTTTAA
Found at i:20259045 original size:40 final size:40
Alignment explanation
Indices: 20259001--20259100 Score: 98
Period size: 40 Copynumber: 2.5 Consensus size: 40
20258991 AAAGAATACA
* *
20259001 AAAATTTCTAAGAGCATATTCTTA-AATATTTTGATATTTC
1 AAAATTTCTAAGAGCATATACATAGAA-ATTTTGATATTTC
* *
20259041 AAAATATCT-A-AGCATACGTACATAGAAATTTTGGTATTTC
1 AAAATTTCTAAGAGCATA--TACATAGAAATTTTGATATTTC
*
20259081 AAAATTTGTAAAGAGCATAT
1 AAAATTTCT-AAGAGCATAT
20259101 CATTAGCTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
38 6 0.12
39 1 0.02
40 31 0.65
41 3 0.06
42 1 0.02
43 6 0.12
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (40 bp):
AAAATTTCTAAGAGCATATACATAGAAATTTTGATATTTC
Found at i:20263542 original size:3 final size:3
Alignment explanation
Indices: 20263534--20263568 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20263524 ATTAGTTTAA
20263534 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20263569 GGTCTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20269989 original size:16 final size:18
Alignment explanation
Indices: 20269955--20269997 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
20269945 AGGCGGCACC
20269955 ATTATTTTTTTTAATAAAT
1 ATTA-TTTTTTTAATAAAT
*
20269974 TTTATTTTTTT-A-AAAT
1 ATTATTTTTTTAATAAAT
20269990 ATTATTTT
1 ATTATTTT
20269998 ATTAGTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 11 0.50
17 1 0.05
18 7 0.32
19 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTATTTTTTTAATAAAT
Found at i:20270358 original size:5 final size:5
Alignment explanation
Indices: 20270348--20270405 Score: 73
Period size: 5 Copynumber: 11.4 Consensus size: 5
20270338 TTGAAGTTTT
* *
20270348 ATCGA ATCGA ATCGA GT-GA GATAGAA ATCGA ATCGA ATCGA ATCGA ATCGA
1 ATCGA ATCGA ATCGA ATCGA -ATCG-A ATCGA ATCGA ATCGA ATCGA ATCGA
20270399 ATCGA AT
1 ATCGA AT
20270406 TATTTGTTCG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
4 2 0.04
5 40 0.85
6 4 0.09
7 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (5 bp):
ATCGA
Found at i:20270576 original size:19 final size:19
Alignment explanation
Indices: 20270552--20270595 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
20270542 TAAAAGTAAC
20270552 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
**
20270571 ACAACATCATTCCAAATAA
1 ACAACATCAACCCAAATAA
20270590 ACAACA
1 ACAACA
20270596 AAAATAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:20273632 original size:29 final size:29
Alignment explanation
Indices: 20273600--20273658 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
20273590 TAATTTTTAA
*
20273600 ATGTAGTGTTTTTTAAAAATAAAAAATAT
1 ATGTAGTGTATTTTAAAAATAAAAAATAT
*
20273629 ATGTGGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTGTATTTTAAAAATAAAAAATAT
20273658 A
1 A
20273659 GTTTATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (29 bp):
ATGTAGTGTATTTTAAAAATAAAAAATAT
Found at i:20273676 original size:9 final size:9
Alignment explanation
Indices: 20273664--20273700 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20273654 ATATAGTTTA
20273664 TATTCGAAT
1 TATTCGAAT
20273673 TATTCGAAT
1 TATTCGAAT
*
20273682 TATTCGAGT
1 TATTCGAAT
20273691 TATTCGAAT
1 TATTCGAAT
20273700 T
1 T
20273701 CAAAAATTCA
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:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20273958 original size:23 final size:23
Alignment explanation
Indices: 20273913--20273963 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20273903 AAAGAATAGG
*
20273913 GAAAGAAAGGAGAGGAAGGAGAA
1 GAAAGAAAGGAGAGGAAGAAGAA
* *
20273936 GAAAGAAAGGAGATGTAGAAGAA
1 GAAAGAAAGGAGAGGAAGAAGAA
*
20273959 AAAAG
1 GAAAG
20273964 GAAAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.37, T:0.04
Consensus pattern (23 bp):
GAAAGAAAGGAGAGGAAGAAGAA
Found at i:20274368 original size:101 final size:101
Alignment explanation
Indices: 20274099--20274531 Score: 507
Period size: 101 Copynumber: 4.2 Consensus size: 101
20274089 TGGTTTAATT
* * * *
20274099 TTTTTTATGAATGTAAATTTTTTTTATAATTATTTTAAAATTATTTTGTTAGTAATTTATGATTA
1 TTTTTTATGAATGT-AA-TTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTA
* * *
20274164 TGTT-TAATTTGTTTGTGTTTTAGTTTAGTGTTTTGTGA
64 GGTTATAAATTGATTGTG-TTTAGTTTAGTGTTTTGTGA
* * * * * * *
20274202 -ATTTCATGTAAATTTTTTTATTTTTT-AAAATTATTTTATAGTTATTTTGTTAATAACTTAAGA
1 TTTTTTATG--AA---TGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGA
* *
20274265 TTAGGTCATAAATTG-TTGTGCTTAGTTTAGTGTTTTGTGA
61 TTAGGTTATAAATTGATTGTGTTTAGTTTAGTGTTTTGTGA
* *
20274305 TTTTTTATTAATGTAATTTTTTAAAAGATTATTTTATAGTTATTTTGCTAGTAATTTATGATTAG
1 TTTTTTATGAATGTAATTTTTTAAAA-ATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAG
* * *
20274370 GTTATAAGTTGATAGTGTTTAGTTTAGTGTTTTGTAA
65 GTTATAAATTGATTGTGTTTAGTTTAGTGTTTTGTGA
* * *
20274407 TTTTTTATGAATGTAAATTTTTAAAATTTATTTTATAGTTATTTTGTTATTAATTTATGATTAGG
1 TTTTTTATGAATGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGG
20274472 TTATAAATTG-TTAGTGTTTAGTTTAGTGTTTTGTGA
66 TTATAAATTGATT-GTGTTTAGTTTAGTGTTTTGTGA
*
20274508 TTTTTTATGAAAGTAAATTTTTTA
1 TTTTTTATGAATGT-AATTTTTTA
20274532 TAATGTAATT
Statistics
Matches: 280, Mismatches: 38, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
99 9 0.03
100 4 0.01
101 123 0.44
102 62 0.22
103 19 0.07
104 48 0.17
105 12 0.04
106 1 0.00
107 2 0.01
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (101 bp):
TTTTTTATGAATGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGG
TTATAAATTGATTGTGTTTAGTTTAGTGTTTTGTGA
Found at i:20280934 original size:24 final size:26
Alignment explanation
Indices: 20280907--20280955 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
20280897 ATAAACATTA
*
20280907 AACTAAC-AAATAA-TTTATAATAAT
1 AACTAACAAAATAACTTTAAAATAAT
20280931 AACTAACAAAATAACTTTAAAATAA
1 AACTAACAAAATAACTTTAAAATAA
20280956 ATTAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AACTAACAAAATAACTTTAAAATAAT
Found at i:20282290 original size:21 final size:21
Alignment explanation
Indices: 20282236--20282290 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
20282226 TACTTTAAAT
20282236 ATATTAACTTTGTTAAACAGTAA
1 ATATTAA-TTT-TTAAACAGTAA
* * *
20282259 ATAATATTTTTTAAATAGTAA
1 ATATTAATTTTTAAACAGTAA
*
20282280 ATGTTAATTTT
1 ATATTAATTTT
20282291 ATTTCAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 18 0.69
22 3 0.12
23 5 0.19
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (21 bp):
ATATTAATTTTTAAACAGTAA
Found at i:20284236 original size:6 final size:6
Alignment explanation
Indices: 20284227--20284254 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20284217 TCCAACTCAA
20284227 CAAAAT CAAAAT CAAAAT CAAAAT CAAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAA
20284255 CCGAACAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.14
Consensus pattern (6 bp):
CAAAAT
Found at i:20284308 original size:6 final size:6
Alignment explanation
Indices: 20284297--20284324 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20284287 AGAGCAATTT
20284297 AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAA
20284325 AGAACTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:20286108 original size:23 final size:23
Alignment explanation
Indices: 20286082--20286138 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
20286072 TTTTTTTGGC
20286082 TTTTAGGGTTTAGGGTTCAAGCT
1 TTTTAGGGTTTAGGGTTCAAGCT
*
20286105 TTTTAGGGTTTAGGGTTCAGGCT
1 TTTTAGGGTTTAGGGTTCAAGCT
20286128 TTTTAGGGTTT
1 TTTTAGGGTTT
20286139 TTAGGTTCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.07, G:0.32, T:0.47
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTTCAAGCT
Found at i:20286481 original size:123 final size:124
Alignment explanation
Indices: 20286166--20286514 Score: 601
Period size: 124 Copynumber: 2.8 Consensus size: 124
20286156 TTATTTCGAG
20286166 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
20286231 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAGTAATTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* * * *
20286290 TTGATGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGTTATTTCAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
20286355 AAATCATGCCCTCGTGGACGCGATTTTGCTATAGTTGGTCATGTAAGAAATAA-TTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
*
20286413 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
20286478 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAG
20286515 CAAGTTTGGG
Statistics
Matches: 208, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
123 99 0.48
124 109 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:20288811 original size:23 final size:26
Alignment explanation
Indices: 20288785--20288917 Score: 141
Period size: 29 Copynumber: 5.0 Consensus size: 26
20288775 TTAGGGCAGT
20288785 GGGTTTTTAATTAAAATAGGTTAGGGTTA
1 GGGTTTTTAATT-AAATA-G-TAGGGTTA
20288814 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAA-TA-G-TAGGGTTA
20288843 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAA-TA-G-TAGGGTTA
20288872 GGGTTTTTAATTAAAT--TA-GGTTA
1 GGGTTTTTAATTAAATAGTAGGGTTA
*
20288895 GGATTTTTAATTAAAT--TAGGGTT
1 GGGTTTTTAATTAAATAGTAGGGTT
20288918 TTTATTACAT
Statistics
Matches: 101, Mismatches: 1, Indels: 9
0.91 0.01 0.08
Matches are distributed among these distances:
23 22 0.22
24 6 0.06
28 4 0.04
29 69 0.68
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (26 bp):
GGGTTTTTAATTAAATAGTAGGGTTA
Found at i:20288845 original size:35 final size:29
Alignment explanation
Indices: 20288785--20288896 Score: 215
Period size: 29 Copynumber: 3.9 Consensus size: 29
20288775 TTAGGGCAGT
*
20288785 GGGTTTTTAATTAAAATAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGTTA
20288814 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGTTA
20288843 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGTTA
20288872 GGGTTTTTAATTAAATTAGGTTAGG
1 GGGTTTTTAATTAAATTAGGTTAGG
20288897 ATTTTTAATT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 82 1.00
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.44
Consensus pattern (29 bp):
GGGTTTTTAATTAAATTAGGTTAGGGTTA
Found at i:20289000 original size:36 final size:36
Alignment explanation
Indices: 20288960--20289074 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
20288950 ATATCAAATA
*
20288960 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
20288996 ATATC-AAATAAACTTCTATTTTATTAC-AT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
20289031 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
20289067 ACATCAAA
1 ATATCAAA
20289075 TAAACTTCTA
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 7 0.13
35 17 0.31
36 24 0.44
37 7 0.13
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:20289026 original size:25 final size:25
Alignment explanation
Indices: 20288992--20289102 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
20288982 TTTCTATGCC
*
20288992 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
20289017 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
20289038 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
20289063 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
20289088 TATTACATCAAATAA
1 TATTACATCAAATAA
20289103 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:20289027 original size:71 final size:71
Alignment explanation
Indices: 20288920--20289104 Score: 325
Period size: 71 Copynumber: 2.6 Consensus size: 71
20288910 TTAGGGTTTT
* *
20288920 TATTACATCAAATAGAACTTCTATGTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTT
20288985 CTATGCC
65 CTATGCC
*
20288992 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
20289057 TATGCG
66 TATGCC
20289063 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
20289105 AATTTAAATA
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 95 0.88
72 13 0.12
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:20290201 original size:7 final size:7
Alignment explanation
Indices: 20290191--20290215 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20290181 TTATATACAT
20290191 AATACTA
1 AATACTA
20290198 AATACTA
1 AATACTA
20290205 AATACTA
1 AATACTA
20290212 AATA
1 AATA
20290216 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:20291388 original size:40 final size:40
Alignment explanation
Indices: 20291341--20291427 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
20291331 GAAATTGAGG
20291341 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
*
20291381 GGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
20291421 GGAAATT
1 GGAAATT
20291428 TGGAAGGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (40 bp):
GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
Found at i:20291431 original size:12 final size:12
Alignment explanation
Indices: 20291414--20291439 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20291404 TTGAGAGAAT
20291414 TTTGGAAGGAAA
1 TTTGGAAGGAAA
20291426 TTTGGAAGGAAA
1 TTTGGAAGGAAA
20291438 TT
1 TT
20291440 GAGAGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGGAAGGAAA
Found at i:20292370 original size:13 final size:13
Alignment explanation
Indices: 20292352--20292383 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20292342 ATGTACCTGG
20292352 ATTTAATAGAGAA
1 ATTTAATAGAGAA
20292365 ATTTAATAGAGAA
1 ATTTAATAGAGAA
*
20292378 TTTTAA
1 ATTTAA
20292384 CAGTGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (13 bp):
ATTTAATAGAGAA
Found at i:20293394 original size:86 final size:86
Alignment explanation
Indices: 20293249--20293421 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
20293239 CTATATAGAG
20293249 ATGATGCTAATATGAGAAATCTTTTGTTTAGAATAAGAAATGTCCTCTTAATTACAATTCAAAGC
1 ATGATGCTAATATGAGAAATCTTTTGTTTAGAATAAGAAATGTCCTCTTAATTACAATTCAAAGC
20293314 TTTGAGTGTTAGAACCGTAAA
66 TTTGAGTGTTAGAACCGTAAA
20293335 ATGATGCTAATATGAGAAATCTTTTGTTTAGAATAAGAAATGTCCTCTTAATTACAATTCAAAGC
1 ATGATGCTAATATGAGAAATCTTTTGTTTAGAATAAGAAATGTCCTCTTAATTACAATTCAAAGC
20293400 TTTGAGTGTTAGAACCGTAAA
66 TTTGAGTGTTAGAACCGTAAA
20293421 A
1 A
20293422 ACAAGATTTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (86 bp):
ATGATGCTAATATGAGAAATCTTTTGTTTAGAATAAGAAATGTCCTCTTAATTACAATTCAAAGC
TTTGAGTGTTAGAACCGTAAA
Found at i:20298411 original size:46 final size:46
Alignment explanation
Indices: 20298332--20298539 Score: 368
Period size: 46 Copynumber: 4.6 Consensus size: 46
20298322 TACGTATGAT
* *
20298332 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
20298376 CACTTATCACTTTGTCACTTGATTAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
20298422 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
20298467 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
20298513 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
20298540 AGTACTCAAA
Statistics
Matches: 157, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
44 10 0.06
45 50 0.32
46 97 0.62
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:20298478 original size:91 final size:92
Alignment explanation
Indices: 20298332--20298539 Score: 377
Period size: 91 Copynumber: 2.3 Consensus size: 92
20298322 TACGTATGAT
*
20298332 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
*
20298395 TGATTAGATAAGTGTAGCTAAAGCTAC
66 TGATCAGATAAGTGTAGCTAAAGCTAC
20298422 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA-GCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
20298486 TGATCAGATAAGTGTAGCTAAAGCTAC
66 TGATCAGATAAGTGTAGCTAAAGCTAC
20298513 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
20298540 AGTACTCAAA
Statistics
Matches: 114, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
90 10 0.09
91 82 0.72
92 22 0.19
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (92 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
TGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:20304621 original size:20 final size:20
Alignment explanation
Indices: 20304596--20304639 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
20304586 TAAGGTAATA
20304596 AAATAGTAAGTTCATACTTG
1 AAATAGTAAGTTCATACTTG
20304616 AAATAGTAAGTTCATACTTG
1 AAATAGTAAGTTCATACTTG
20304636 AAAT
1 AAAT
20304640 GGAAAGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (20 bp):
AAATAGTAAGTTCATACTTG
Found at i:20304646 original size:20 final size:20
Alignment explanation
Indices: 20304596--20304646 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
20304586 TAAGGTAATA
*
20304596 AAATAGTAAGTTCATACTTG
1 AAATAGAAAGTTCATACTTG
*
20304616 AAATAGTAAGTTCATACTTG
1 AAATAGAAAGTTCATACTTG
*
20304636 AAATGGAAAGT
1 AAATAGAAAGT
20304647 GATGAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (20 bp):
AAATAGAAAGTTCATACTTG
Found at i:20311653 original size:2 final size:2
Alignment explanation
Indices: 20311646--20311674 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20311636 TTATTTCAAA
20311646 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20311675 TGCAAGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20313578 original size:15 final size:16
Alignment explanation
Indices: 20313552--20313581 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20313542 TTTCTTAATA
20313552 TATTACTTTATTTTAT
1 TATTACTTTATTTTAT
20313568 TATTA-TTTATTTTA
1 TATTACTTTATTTTA
20313582 ACATATAAAA
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:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTACTTTATTTTAT
Found at i:20319048 original size:11 final size:11
Alignment explanation
Indices: 20319019--20319047 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20319009 ACATATTTTT
20319019 ATTATTTTAAA
1 ATTATTTTAAA
20319030 ATTATTTTAAA
1 ATTATTTTAAA
20319041 A-TATTTT
1 ATTATTTT
20319048 TTTGATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATTTTAAA
Found at i:20322345 original size:18 final size:17
Alignment explanation
Indices: 20322293--20322334 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
20322283 ATGTTGAATG
*
20322293 TGGAAATAAATATGTTT
1 TGGAAAGAAATATGTTT
20322310 TGGAAAGAAATATGTTT
1 TGGAAAGAAATATGTTT
20322327 TGGAAAGA
1 TGGAAAGA
20322335 CTACTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (17 bp):
TGGAAAGAAATATGTTT
Found at i:20322499 original size:12 final size:12
Alignment explanation
Indices: 20322484--20322524 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
20322474 TGCAAAAAAT
20322484 AATTGAAAATTC
1 AATTGAAAATTC
*
20322496 AATTGGAAAAAT-
1 AATT-GAAAATTC
20322508 AATTGAAAATTC
1 AATTGAAAATTC
20322520 AATTG
1 AATTG
20322525 GACACCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 13 0.52
13 6 0.24
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (12 bp):
AATTGAAAATTC
Found at i:20322510 original size:24 final size:24
Alignment explanation
Indices: 20322478--20322526 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20322468 TTATGATGCA
20322478 AAAAATAATTGAAAATTCAATTGG
1 AAAAATAATTGAAAATTCAATTGG
20322502 AAAAATAATTGAAAATTCAATTGG
1 AAAAATAATTGAAAATTCAATTGG
20322526 A
1 A
20322527 CACCCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (24 bp):
AAAAATAATTGAAAATTCAATTGG
Found at i:20323526 original size:21 final size:21
Alignment explanation
Indices: 20323502--20323550 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
20323492 AGCATAGAAG
20323502 ACTGTTATCCCAATAGGGCAA
1 ACTGTTATCCCAATAGGGCAA
*
20323523 ACTGATATCCCAATAGGGCAA
1 ACTGTTATCCCAATAGGGCAA
20323544 ACTGTTA
1 ACTGTTA
20323551 GTGCAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (21 bp):
ACTGTTATCCCAATAGGGCAA
Found at i:20325432 original size:145 final size:145
Alignment explanation
Indices: 20325264--20325555 Score: 476
Period size: 145 Copynumber: 2.0 Consensus size: 145
20325254 ATCAAAGGTG
* * *
20325264 ACAGAACGAAATGTATTTTACCAAAATTATTCTTTACCCATGATCTTGAGAAAAGAGGTGATATA
1 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATA
* * *
20325329 AATGTTTAAAAAAATCATTTTAGTGAGAATTTAGTAGATTTTTTTACTAAGGCATTGCCAACTTC
66 AATGTTCAAAAAAATCATTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
*
20325394 AACCTTTGAAAGACT
131 AACATTTGAAAGACT
* *
20325409 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCTATGATCTTGCGAAAAGAGGTGATATA
1 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATA
* **
20325474 AATGTTCAAAAAATTTGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
66 AATGTTCAAAAAAATCATTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
20325539 AACATTTGAAAGACT
131 AACATTTGAAAGACT
20325554 AC
1 AC
20325556 TACACAAGAT
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
145 135 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (145 bp):
ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATA
AATGTTCAAAAAAATCATTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
AACATTTGAAAGACT
Found at i:20329525 original size:18 final size:20
Alignment explanation
Indices: 20329488--20329529 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20329478 AATATGGGAA
*
20329488 ATGTATGTGTATTCTAAAAT
1 ATGTATGTATATTCTAAAAT
20329508 ATGTATGTATATT-TAAATAT
1 ATGTATGTATATTCTAAA-AT
20329528 AT
1 AT
20329530 ATACATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (20 bp):
ATGTATGTATATTCTAAAAT
Found at i:20329668 original size:3 final size:3
Alignment explanation
Indices: 20329660--20329718 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
20329650 TGTACATGAA
* * *
20329660 AAT AAT AAT TAC AAT -AT CAAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
20329705 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
20329719 GGAGAAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20332056 original size:32 final size:32
Alignment explanation
Indices: 20332017--20332111 Score: 163
Period size: 32 Copynumber: 2.9 Consensus size: 32
20332007 TTAGATATTG
20332017 ATTATGTTTTAAGCTTGTTAGATATTAAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTAAATTT
* *
20332049 ATTATGTTTTAAGCTTGTTGGATATTCAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTAAATTT
20332081 ATTATGTTTTAAGCTTGTTAGATATTGAAAT
1 ATTATGTTTTAAGCTTGTTAGATATT-AAAT
20332112 GATTGACAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 55 0.95
33 3 0.05
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTAAATTT
Found at i:20340655 original size:73 final size:72
Alignment explanation
Indices: 20340536--20340682 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 72
20340526 TGGAGATTTG
*
20340536 ATCTTCCAAATTAGTACACAAAATTTCAGAGAATATTTACTTTCTTTCCTAAGGATGGGATATTA
1 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTT-CTAAGGATGGGATATTA
20340601 GAAAAGAT
65 GAAAAGAT
* *
20340609 ATCTTCCAAATTAGCACACAAAATTTTAGAGAATATTTGCTTTCTTTCTAAGGATGGGATATTAG
1 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTTCTAAGGATGGGATATTAG
20340674 AAAAGAT
66 AAAAGAT
20340681 AT
1 AT
20340683 TTTGTGTGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 27 0.38
73 44 0.62
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (72 bp):
ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTTCTAAGGATGGGATATTAG
AAAAGAT
Found at i:20341281 original size:19 final size:19
Alignment explanation
Indices: 20341257--20341294 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20341247 AAGTGAGGTC
20341257 AGTATCAAAATAATAAACA
1 AGTATCAAAATAATAAACA
20341276 AGTATCAAAATAATAAACA
1 AGTATCAAAATAATAAACA
20341295 GAGTGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (19 bp):
AGTATCAAAATAATAAACA
Found at i:20349023 original size:48 final size:48
Alignment explanation
Indices: 20348952--20349048 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
20348942 TACCTTCAAA
*
20348952 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCTATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
*
20349000 GCACACACCACCACTACTATTCAATTTAAATCTAGTTGCCTTTCCATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
20349048 G
1 G
20349049 TTCAATTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (48 bp):
GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
Found at i:20356114 original size:20 final size:19
Alignment explanation
Indices: 20356089--20356131 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
20356079 AATACATTTA
* *
20356089 AAAACATGAAAACAAATATT
1 AAAACAAGAAAAAAAATA-T
20356109 AAAACAAGAAAAAAAATAT
1 AAAACAAGAAAAAAAATAT
20356128 AAAA
1 AAAA
20356132 TGATACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAACAAGAAAAAAAATAT
Found at i:20356353 original size:34 final size:34
Alignment explanation
Indices: 20356315--20356386 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
20356305 AAAGAACAAT
* *
20356315 AAAACACCACAAAAAGTA-A-CACCAAAACAACATA
1 AAAACAACACAAAAA-TACAGCACC-AAACAACACA
*
20356349 AAAACAACATAAAAATACAGCACCAAACAACACA
1 AAAACAACACAAAAATACAGCACCAAACAACACA
20356383 AAAA
1 AAAA
20356387 ATAGCATCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.06
34 27 0.82
35 4 0.12
ACGTcount: A:0.67, C:0.25, G:0.03, T:0.06
Consensus pattern (34 bp):
AAAACAACACAAAAATACAGCACCAAACAACACA
Found at i:20356362 original size:10 final size:11
Alignment explanation
Indices: 20356338--20356363 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20356328 AAGTAACACC
20356338 AAAACAACATA
1 AAAACAACATA
20356349 AAAACAACATA
1 AAAACAACATA
20356360 AAAA
1 AAAA
20356364 TACAGCACCA
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:0.77, C:0.15, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAACAACATA
Found at i:20359459 original size:20 final size:20
Alignment explanation
Indices: 20359434--20359551 Score: 58
Period size: 24 Copynumber: 5.3 Consensus size: 20
20359424 TTTTATGATT
20359434 TATATATTTATTACCTTATA
1 TATATATTTATTACCTTATA
* * *
20359454 TATATATGTACGTATACTTTCTA
1 TATATATTTA--T-TACCTTATA
*
20359477 TACATATTT-TATACTTTCTATATA
1 TATATATTTAT-TAC---CT-TATA
* * *
20359501 TATATAATCATTATCTTTATGA
1 TATATATTTATTA-CCTTAT-A
20359523 TTTATATATTTATTACCTTATA
1 --TATATATTTATTACCTTATA
20359545 TATATAT
1 TATATAT
20359552 GTACGTATAC
Statistics
Matches: 72, Mismatches: 14, Indels: 24
0.65 0.13 0.22
Matches are distributed among these distances:
20 21 0.29
21 3 0.04
22 4 0.06
23 20 0.28
24 22 0.31
25 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (20 bp):
TATATATTTATTACCTTATA
Found at i:20359521 original size:91 final size:91
Alignment explanation
Indices: 20359406--20359651 Score: 429
Period size: 91 Copynumber: 2.7 Consensus size: 91
20359396 TTTTTAAGTT
* * * *
20359406 TATATATGTAATTATCATTTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
1 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
*
20359471 TTTCTATACATATTTTATACTTTCTA
66 TTTCTATACATATTTTATAATTTCTA
20359497 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
1 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
20359562 TTTCTATACATATTTTATAATTTCTA
66 TTTCTATACATATTTTATAATTTCTA
* *
20359588 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATA
1 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATA
20359652 TATGTATTAT
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 148 1.00
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.52
Consensus pattern (91 bp):
TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
TTTCTATACATATTTTATAATTTCTA
Found at i:20359537 original size:24 final size:23
Alignment explanation
Indices: 20359495--20359642 Score: 99
Period size: 24 Copynumber: 6.5 Consensus size: 23
20359485 TTATACTTTC
* *
20359495 TATATATATATAATCATTATCTT
1 TATATATATATATTTATTATCTT
* *
20359518 TATGATTTATATATTTATTACCTT
1 TAT-ATATATATATTTATTATCTT
* **
20359542 ATATATATATGTACGTA-TA-CTT
1 -TATATATATATATTTATTATCTT
* * *
20359564 TCTATACATAT-TTTATAAT-TT
1 TATATATATATATTTATTATCTT
* *
20359585 CTATATATATATAATCATTATCTT
1 -TATATATATATATTTATTATCTT
* *
20359609 TATGATCTATATATTTATTAAC-T
1 TAT-ATATATATATTTATTATCTT
20359632 TATATATATAT
1 TATATATATAT
20359643 GTACGTATAT
Statistics
Matches: 93, Mismatches: 24, Indels: 17
0.69 0.18 0.13
Matches are distributed among these distances:
20 2 0.02
21 11 0.12
22 19 0.20
23 17 0.18
24 41 0.44
25 3 0.03
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (23 bp):
TATATATATATATTTATTATCTT
Found at i:20359585 original size:20 final size:20
Alignment explanation
Indices: 20359557--20359594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20359547 TATATGTACG
*
20359557 TATACTTTCTATACATATTT
1 TATAATTTCTATACATATTT
*
20359577 TATAATTTCTATATATAT
1 TATAATTTCTATACATAT
20359595 ATAATCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTTCTATACATATTT
Found at i:20361995 original size:24 final size:24
Alignment explanation
Indices: 20361968--20362013 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20361958 AGAACAGTCC
* *
20361968 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
20361992 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
20362014 AAAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:20364603 original size:12 final size:12
Alignment explanation
Indices: 20364586--20364680 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
20364576 GTTCAGATTC
20364586 AAAAAAAAAAAG
1 AAAAAAAAAAAG
**
20364598 AAAAAAAAAGGG
1 AAAAAAAAAAAG
* ** *
20364610 TCAAAATCAAAAT
1 -AAAAAAAAAAAG
**
20364623 AAAAAATGAAAG
1 AAAAAAAAAAAG
**
20364635 TGAAAAAAAAAG
1 AAAAAAAAAAAG
*
20364647 AAAAAGAAAAAG
1 AAAAAAAAAAAG
*
20364659 AAAAAGAAAAAG
1 AAAAAAAAAAAG
20364671 AAAAGAAAAA
1 AAAA-AAAAA
20364681 GGAGAGGCCA
Statistics
Matches: 60, Mismatches: 21, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
12 50 0.83
13 10 0.17
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:20364650 original size:6 final size:6
Alignment explanation
Indices: 20364637--20364681 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
20364627 AATGAAAGTG
20364637 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAG- AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAG
20364682 GAGAGGCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 9 0.24
6 29 0.76
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:20364652 original size:18 final size:18
Alignment explanation
Indices: 20364637--20364681 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
20364627 AATGAAAGTG
20364637 AAAA-AAAAAGAAAAAGA
1 AAAAGAAAAAGAAAAAGA
20364654 AAAAGAAAAAGAAAAAG-
1 AAAAGAAAAAGAAAAAGA
20364671 AAAAGAAAAAG
1 AAAAGAAAAAG
20364682 GAGAGGCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAAGA
Found at i:20365981 original size:43 final size:42
Alignment explanation
Indices: 20365928--20366069 Score: 106
Period size: 43 Copynumber: 3.3 Consensus size: 42
20365918 CCTACACCGA
20365928 CAGCGAAGCAGATCGAAGAAACCAGCCTTGCCTCCTTGGGTTG
1 CAGCGAAGCAGATCGAAGAAACCAGCCTTGCCTCC-TGGGTTG
* * * * ** * * **
20365971 CAGCGGAGCAGGT-TAAAAATAGTAGATCTTGCCTTCCTGCGCCG
1 CAGCGAAGCAGATCGAAGAA-ACCAG-CCTTGCC-TCCTGGGTTG
*
20366015 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 -CAGCGAAGCAGATCGAAGAAACCAGCCTTGCCT-CCTGGGTTG
* *
20366059 TAGCGGAGCAG
1 CAGCGAAGCAG
20366070 GTTAAAAAAA
Statistics
Matches: 70, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
42 4 0.06
43 24 0.34
44 22 0.31
45 17 0.24
46 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.18
Consensus pattern (42 bp):
CAGCGAAGCAGATCGAAGAAACCAGCCTTGCCTCCTGGGTTG
Found at i:20366046 original size:44 final size:44
Alignment explanation
Indices: 20365910--20366053 Score: 114
Period size: 44 Copynumber: 3.3 Consensus size: 44
20365900 AATAGCAGAT
* *
20365910 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGAAACCAGC
1 CTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGAAACCAGC
* ** * * * * ** *
20365954 CTTGCC-TCCTTGGGTTG-CAGCGGAGCAGGT-TAAAAATAGTAGAT
1 CTTGCCTTCC-TGCGCCGACAGCGAAGCAGATCGAAGAA-ACCAG-C
*
20365998 CTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGAAACCAGC
*
20366042 CTTGCCTCCCTG
1 CTTGCCTTCCTG
20366054 GGTTGTAGCG
Statistics
Matches: 70, Mismatches: 24, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
42 4 0.06
43 17 0.24
44 29 0.41
45 17 0.24
46 3 0.04
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.19
Consensus pattern (44 bp):
CTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGAAACCAGC
Found at i:20366047 original size:88 final size:89
Alignment explanation
Indices: 20365898--20366124 Score: 366
Period size: 88 Copynumber: 2.6 Consensus size: 89
20365888 CAGATCAGTG
*
20365898 AAAATAGCAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGAAACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGAAACCAGCCTTGCCTCC
*
20365963 TTGGGTTGCAGCGGAGCAGGTT-A
66 CTGGGTTGCAGCGGAGCAGGTTAA
* * *
20365986 AAAATAGTAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGAAACCAGCCTTGCCTCC
*
20366051 CTGGGTTGTAGCGGAGCAGGTTAAA
66 CTGGGTTGCAGCGGAGCAGGTT-AA
* *
20366076 AAAATAGCAGATATTGCCTTCCTACGCCGACAGCGAAGCAGATCAAAGA
1 AAAATAGCAGATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGA
20366125 TGGCAAATTT
Statistics
Matches: 127, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
88 81 0.64
90 46 0.36
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (89 bp):
AAAATAGCAGATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGAAACCAGCCTTGCCTCC
CTGGGTTGCAGCGGAGCAGGTTAA
Found at i:20366349 original size:132 final size:132
Alignment explanation
Indices: 20366107--20366628 Score: 733
Period size: 132 Copynumber: 3.9 Consensus size: 132
20366097 CTACGCCGAC
* * * *
20366107 AGCGAAGCAGATCAAAGATGGCAAATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCA
1 AGCGGAGCAGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
20366172 GTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAA
66 GTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAA
20366237 GT
131 GT
* *
20366239 AGCGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAACCA
1 AGCGGAGCAGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
* * ** *
20366304 ATAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCGCCCTAAGTA
66 GTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAG-A
20366369 A-T
130 AGT
* * * *
20366371 AGCGGAGTAGATTGAAGATGGCGAATTTTACCTCCCTGCGGTTACAGTGGAATACATTGAAGCCA
1 AGCGGAGCAGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
* * * *
20366436 GTAATTCTACTTTCCTAGACAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
66 GTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAA
20366501 GT
131 GT
* * * * *
20366503 AGCGGAGTAAATCGAAGATGGCGGATTTTAACCTCCCTGTGGTTTCAGCGGAGTACATTGAAGCC
1 AGCGGAGCAGATCGAAGATGGCGAATTTT-ACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* * * * * *
20366568 AGTAATCCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGT-GAATCCTATCTCCCT
65 AGTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATT-TCAAATCTTATCTCCCT
20366629 TGTCAGCAGT
Statistics
Matches: 346, Mismatches: 40, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
131 1 0.00
132 261 0.75
133 83 0.24
134 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (132 bp):
AGCGGAGCAGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
GTAATTCTACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAA
GT
Found at i:20366619 original size:44 final size:44
Alignment explanation
Indices: 20366571--20366739 Score: 234
Period size: 44 Copynumber: 3.8 Consensus size: 44
20366561 TGAAGCCAGT
*
20366571 AATCCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTG
1 AATCCTATC-TCCCTGGTCAGCAGTGGAATAGATTGAAGATTGTG
* * *
20366615 AATCCTATCTCCCTTGTCAGCAGTGGAATAGGTTGAAGATTGTA
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTGTG
* *
20366659 AATCCTATCTCCCTGGTCAACAGTGGAATA-AGTTGAAGATTGAG
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGA-TTGAAGATTGTG
* *
20366703 AATCCTATCTCCCTGGTCAGCGGTGGAATAGGTTGAA
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAA
20366740 AGTAAACAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
44 109 0.99
45 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTGTG
Found at i:20366663 original size:88 final size:88
Alignment explanation
Indices: 20366571--20366739 Score: 261
Period size: 88 Copynumber: 1.9 Consensus size: 88
20366561 TGAAGCCAGT
* * *
20366571 AATCCTA-CTTCCCTGGGCAGCAGTGGAAT-AGATTGAAGATTGTGAATCCTATCTCCCTTGTCA
1 AATCCTATC-TCCCTGGGCAACAGTGGAATAAG-TTGAAGATTGAGAATCCTATCTCCCTGGTCA
20366634 GCAGTGGAATAGGTTGAAGATTGTA
64 GCAGTGGAATAGGTTGAAGATTGTA
*
20366659 AATCCTATCTCCCTGGTCAACAGTGGAATAAGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGC
1 AATCCTATCTCCCTGGGCAACAGTGGAATAAGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGC
*
20366724 GGTGGAATAGGTTGAA
66 AGTGGAATAGGTTGAA
20366740 AGTAAACAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
88 71 0.96
89 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (88 bp):
AATCCTATCTCCCTGGGCAACAGTGGAATAAGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGC
AGTGGAATAGGTTGAAGATTGTA
Found at i:20366684 original size:264 final size:263
Alignment explanation
Indices: 20366121--20366696 Score: 737
Period size: 264 Copynumber: 2.2 Consensus size: 263
20366111 AAGCAGATCA
** * * * *
20366121 AAGATGGCAAATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTACTTCC
1 AAGATGGCAAATCCTACCTCCCT-CGGTAACAGTGGAATACATTGAAGCCAGTAATTCTACTTCC
*
20366186 CTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAAGTAGCGGAGCAGAT
65 CTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAAGTAGCGGAGCAAAT
* *
20366251 CGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAACCAATAATTCTACTT
130 CGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGCGGAGTACATTGAAACCAATAATCCTACTT
* * * *
20366316 CCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCGCCCTAAGTAATAGCGGAGTAG
195 CCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCCTATCGCCCTAAGTAACAGCGGAATAG
20366381 ATTG
260 ATTG
* ** * *
20366385 AAGATGGCGAATTTTACCTCCCTGCGGTTACAGTGGAATACATTGAAGCCAGTAATTCTACTTTC
1 AAGATGGCAAATCCTACCTCCCT-CGGTAACAGTGGAATACATTGAAGCCAGTAATTCTACTTCC
* * * *
20366450 CTAGACAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGCGGAGTAAAT
65 CTAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAAGTAGCGGAGCAAAT
* * *
20366515 CGAAGATGGCGGATTTTAACCTCCCTGTGGTTTCAGCGGAGTACATTGAAGCCAGTAATCCTACT
130 CGAAGATGGCGGATTTT-ACCTCCCTGTGGTTACAGCGGAGTACATTGAAACCAATAATCCTACT
* * * * * * *
20366580 TCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTGA-ATCCTATCTCCCT-TGTCAGCAGTGGAA
194 TCCCTGGACAACAGTGGAATAGATTGAAGATT-TCAGATCCTATCGCCCTAAGT-AACAGCGGAA
*
20366643 TAGGTTG
257 TAGATTG
* * *
20366650 AAGATTGTAAATCCTATCTCCCT-GGTCAACAGTGGAATA-AGTTGAAG
1 AAGATGGCAAATCCTACCTCCCTCGGT-AACAGTGGAATACA-TTGAAG
20366697 ATTGAGAATC
Statistics
Matches: 273, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
263 4 0.01
264 156 0.57
265 111 0.41
266 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (263 bp):
AAGATGGCAAATCCTACCTCCCTCGGTAACAGTGGAATACATTGAAGCCAGTAATTCTACTTCCC
TAGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAAGTAGCGGAGCAAATC
GAAGATGGCGGATTTTACCTCCCTGTGGTTACAGCGGAGTACATTGAAACCAATAATCCTACTTC
CCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCCTATCGCCCTAAGTAACAGCGGAATAGA
TTG
Found at i:20368337 original size:48 final size:48
Alignment explanation
Indices: 20368283--20368530 Score: 159
Period size: 48 Copynumber: 5.1 Consensus size: 48
20368273 TTTTTAAGTT
20368283 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATA
** * * * **
20368331 TATATATGTACGTA-TACTTTCTAT-A--CATAT-TTTATAATTTCTATA
1 TATATATGTAATTATTA-TTTTTATGATTTATATATTTATTACCT-TATA
* * *
20368376 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATA
** * * **
20368424 TATATATGTACGTA-TATATATTAT-ACTTTCTATACATATTTTATAATTTCTATA
1 TATATATGTAATTATTAT-TTTTATGA--TT-TAT--ATA-TTTATTACCT-TATA
* * * * *
20368478 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATA
*
20368526 CATAT
1 TATAT
20368531 GTACGTATAT
Statistics
Matches: 146, Mismatches: 37, Indels: 34
0.67 0.17 0.16
Matches are distributed among these distances:
44 7 0.05
45 23 0.16
46 3 0.02
47 7 0.05
48 48 0.33
49 16 0.11
50 6 0.04
52 6 0.04
53 8 0.05
54 18 0.12
55 4 0.03
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.53
Consensus pattern (48 bp):
TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATA
Found at i:20368371 original size:20 final size:20
Alignment explanation
Indices: 20368343--20368380 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20368333 TATATGTACG
*
20368343 TATACTTTCTATACATATTT
1 TATAATTTCTATACATATTT
*
20368363 TATAATTTCTATATATAT
1 TATAATTTCTATACATAT
20368381 ATATAATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTTCTATACATATTT
Found at i:20368393 original size:93 final size:93
Alignment explanation
Indices: 20368283--20368539 Score: 365
Period size: 102 Copynumber: 2.7 Consensus size: 93
20368273 TTTTTAAGTT
* * *
20368283 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
1 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
20368348 TTTCTATACATATTTTATAATTTCTATA
66 TTTCTATACATATTTTATAATTTCTATA
20368376 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACG-----
20368441 ATATTATACTTTCTATACATATTTTATAATTTCTATA
61 ----TATACTTTCTATACATATTTTATAATTTCTATA
* * *
20368478 TATATATATAATCATTATCTTTATGATCTATATATTTATTAAC-T-TATACATATGTACGTATA
1 TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATA
20368540 TATGTATTAT
Statistics
Matches: 149, Mismatches: 6, Indels: 20
0.85 0.03 0.11
Matches are distributed among these distances:
91 4 0.03
93 57 0.38
100 13 0.09
101 1 0.01
102 74 0.50
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (93 bp):
TATATATATAATCATTATCTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAC
TTTCTATACATATTTTATAATTTCTATA
Done.