Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 191 of 199
Found at i:55330564 original size:14 final size:14
Alignment explanation
Indices: 55330527--55330578 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
55330517 ACACAATCCT
55330527 TAAACCTTAAA-TA
1 TAAACCTTAAACTA
* * *
55330540 TAAATCATAAACTT
1 TAAACCTTAAACTA
55330554 TAAACCTTAAACTA
1 TAAACCTTAAACTA
*
55330568 TAAACTTTAAA
1 TAAACCTTAAA
55330579 ATCATAAACA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAACCTTAAACTA
Found at i:55330587 original size:15 final size:14
Alignment explanation
Indices: 55330527--55330587 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
55330517 ACACAATCCT
55330527 TAAACCTT-AAATA
1 TAAACCTTAAAATA
* * * *
55330540 TAAATCATAAACTT
1 TAAACCTTAAAATA
*
55330554 TAAACCTTAAACTA
1 TAAACCTTAAAATA
*
55330568 TAAACTTTAAAATCA
1 TAAACCTTAAAAT-A
55330583 TAAAC
1 TAAAC
55330588 AATAAAACCC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
13 6 0.16
14 25 0.68
15 6 0.16
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAACCTTAAAATA
Found at i:55330607 original size:36 final size:36
Alignment explanation
Indices: 55330534--55330615 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
55330524 CCTTAAACCT
* * *
55330534 TAAATA-T-AAATCATAAACTTTAAACCTTAAACTA
1 TAAATATTAAAATCATAAACATAAAACCCTAAACTA
55330568 TAAACT-TTAAAATCATAAACAATAAAACCCTAAAC-A
1 TAAA-TATTAAAATCATAAAC-ATAAAACCCTAAACTA
55330604 TAAATATTAAAA
1 TAAATATTAAAA
55330616 CCCTAAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
34 4 0.10
35 3 0.08
36 22 0.55
37 11 0.28
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (36 bp):
TAAATATTAAAATCATAAACATAAAACCCTAAACTA
Found at i:55330651 original size:44 final size:44
Alignment explanation
Indices: 55330575--55330749 Score: 119
Period size: 44 Copynumber: 4.1 Consensus size: 44
55330565 CTATAAACTT
*
55330575 TAAAATCATAAACAATAAAACCCTAAACATAAATATTAAAACCC
1 TAAAATCATAAACAATAAAACCCTAAACATAAACATTAAAACCC
* * * * *
55330619 TAAAATCATAAGCCATAAAA-CCTTAACTATAAACCTTAAAA-CT
1 TAAAATCATAAACAATAAAACCCTAAAC-ATAAACATTAAAACCC
* ** * * * * *
55330662 TTAACCCAT--A-ATTTAAACCCTAAACACAAAC-TTTAAACTC
1 TAAAATCATAAACAATAAAACCCTAAACATAAACATTAAAACCC
* ** * * *
55330702 TAAAATTATAAACCCTAAAACCCAAAACATAAACTTTAAAATCC
1 TAAAATCATAAACAATAAAACCCTAAACATAAACATTAAAACCC
55330746 TAAA
1 TAAA
55330750 CTTTAAAACC
Statistics
Matches: 94, Mismatches: 30, Indels: 14
0.68 0.22 0.10
Matches are distributed among these distances:
39 5 0.05
40 14 0.15
41 6 0.06
42 1 0.01
43 29 0.31
44 39 0.41
ACGTcount: A:0.53, C:0.22, G:0.01, T:0.24
Consensus pattern (44 bp):
TAAAATCATAAACAATAAAACCCTAAACATAAACATTAAAACCC
Found at i:55330742 original size:36 final size:34
Alignment explanation
Indices: 55330671--55330743 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 34
55330661 TTTAACCCAT
*
55330671 AATTTAAACCCTAAACACAAACTTTAAACTCTAA
1 AATTTAAACCCTAAACACAAACTATAAACTCTAA
* *
55330705 AATTATAAACCCTAAAACCCAAAAC-ATAAACTTTAA
1 AATT-TAAACCCT-AAACAC-AAACTATAAACTCTAA
55330741 AAT
1 AAT
55330744 CCTAAACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 4 0.12
35 8 0.24
36 17 0.52
37 4 0.12
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (34 bp):
AATTTAAACCCTAAACACAAACTATAAACTCTAA
Found at i:55330750 original size:21 final size:21
Alignment explanation
Indices: 55330540--55330750 Score: 88
Period size: 21 Copynumber: 10.2 Consensus size: 21
55330530 ACCTTAAATA
*
55330540 TAAATCATAAACTTT-AAACCT
1 TAAA-CATAAACTTTAAAACCC
55330561 TAAACTATAAACTTTAAAA---
1 TAAAC-ATAAACTTTAAAACCC
**
55330580 T---CATAAACAATAAAACCC
1 TAAACATAAACTTTAAAACCC
55330598 TAAACATAAA-TATTAAAACCC
1 TAAACATAAACT-TTAAAACCC
* **
55330619 TAAAATCATAAGCCATAAAA-CC
1 T-AAA-CATAAACTTTAAAACCC
* * **
55330641 TTAACTATAAACCTTAAAACTT
1 TAAAC-ATAAACTTTAAAACCC
*
55330663 TAACCCAT-AA-TTT-AAACCC
1 TAA-ACATAAACTTTAAAACCC
* *
55330682 TAAACACAAACTTT-AAACTC
1 TAAACATAAACTTTAAAACCC
* **
55330702 TAAAATTATAAACCCTAAAACCC
1 T-AAA-CATAAACTTTAAAACCC
* *
55330725 AAAACATAAACTTTAAAATCC
1 TAAACATAAACTTTAAAACCC
55330746 TAAAC
1 TAAAC
55330751 TTTAAAACCA
Statistics
Matches: 139, Mismatches: 31, Indels: 40
0.66 0.15 0.19
Matches are distributed among these distances:
15 11 0.08
16 1 0.01
18 3 0.02
19 10 0.07
20 13 0.09
21 63 0.45
22 22 0.16
23 16 0.12
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACATAAACTTTAAAACCC
Found at i:55330751 original size:15 final size:14
Alignment explanation
Indices: 55330725--55330779 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 14
55330715 CCTAAAACCC
*
55330725 AAAACATAAACTTT
1 AAAACCTAAACTTT
55330739 AAAATCCTAAACTTT
1 AAAA-CCTAAACTTT
55330754 AAAACCATAAACTTT
1 AAAACC-TAAACTTT
55330769 AAAACCCTAAA
1 AAAA-CCTAAA
55330780 ACACTAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 6 0.16
15 29 0.78
16 2 0.05
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAACCTAAACTTT
Found at i:55330880 original size:19 final size:20
Alignment explanation
Indices: 55330833--55330881 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
55330823 ACAAATTTTT
*
55330833 AAACCTTAAACCCTAAATAC
1 AAACCTTAAACCCTAAACAC
*
55330853 AACCCTTAAACCCT-AACAC
1 AAACCTTAAACCCTAAACAC
*
55330872 AAACTTTAAA
1 AAACCTTAAA
55330882 ACCTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (20 bp):
AAACCTTAAACCCTAAACAC
Found at i:55330886 original size:27 final size:25
Alignment explanation
Indices: 55330856--55330913 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
55330846 TAAATACAAC
55330856 CCTTAAACCCTAACACAAACTTTAAAA
1 CCTTAAACCCTAACACAAA-TTT-AAA
* *
55330883 CCTTAAACCCTAACCCTAATTTAAA
1 CCTTAAACCCTAACACAAATTTAAA
55330908 CCTTAA
1 CCTTAA
55330914 CCCCAATGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 9 0.31
26 3 0.10
27 17 0.59
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (25 bp):
CCTTAAACCCTAACACAAATTTAAA
Found at i:55338531 original size:99 final size:99
Alignment explanation
Indices: 55338407--55338596 Score: 283
Period size: 99 Copynumber: 1.9 Consensus size: 99
55338397 AAGCAGCAAC
* * * * *
55338407 AATACAAGCTAAGCAGCAGTAAAAGCAAGTTTCCTTTAAGGTCCAAAAACCGATGCCTACCTATG
1 AATACAAGCTAAACAGCAGTAAAAGCAAGTTTCCTTTAAAGTCCAAAAAACAATGCCTACCGATG
55338472 TATGCTTTCAAAAGCAAGCAGGAGCAATGTAACT
66 TATGCTTTCAAAAGCAAGCAGGAGCAATGTAACT
* *
55338506 AATACAAGCTAAACAGCAG-ATAAAGCAAGTTTCCTTTAAAGTTCAAAAAACAATGCCTGCCGAT
1 AATACAAGCTAAACAGCAGTA-AAAGCAAGTTTCCTTTAAAGTCCAAAAAACAATGCCTACCGAT
* *
55338570 GTATGCTTTCAGAAGCAAGCAGTAGCA
65 GTATGCTTTCAAAAGCAAGCAGGAGCA
55338597 GAAAGAACAA
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 1 0.01
99 80 0.99
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (99 bp):
AATACAAGCTAAACAGCAGTAAAAGCAAGTTTCCTTTAAAGTCCAAAAAACAATGCCTACCGATG
TATGCTTTCAAAAGCAAGCAGGAGCAATGTAACT
Found at i:55349275 original size:39 final size:39
Alignment explanation
Indices: 55349201--55349277 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
55349191 AATTGGTTAA
* * *
55349201 TAAATCATATTTTATAAATAATGGATAGGATTTTTTTAT
1 TAAAACATATTTTATAAATAATGGATAGCAATTTTTTAT
*
55349240 TAAAACATATTTTATAATTAATGGAT-GCCAATTTTTTA
1 TAAAACATATTTTATAAATAATGGATAG-CAATTTTTTA
55349278 GCTTTACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (39 bp):
TAAAACATATTTTATAAATAATGGATAGCAATTTTTTAT
Found at i:55350443 original size:48 final size:49
Alignment explanation
Indices: 55350349--55350445 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
55350339 TGAGGGAATT
* * * *
55350349 CTGTTGAATCCTTTATCTTTGCGAGATTAGGCTGACTTCGGTGTTTTTA
1 CTGTTGAATCCATTATCATTGCGAGATTAGGCTGACTTAGGCGTTTTTA
*
55350398 CTGTTGAATCCATTATCATTGTGAG-TTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCATTATCATTGCGAGATTAGGCTGACTTAGGCGTTTTTA
55350446 AGCAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 21 0.49
49 22 0.51
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (49 bp):
CTGTTGAATCCATTATCATTGCGAGATTAGGCTGACTTAGGCGTTTTTA
Found at i:55355528 original size:49 final size:48
Alignment explanation
Indices: 55355456--55355552 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 48
55355446 TAAAGGAATT
* * *
55355456 CTGTTGAATCCTTTATCGTTGCGAGATTAGGCTAACTTAGGTGTTTTTA
1 CTGTTGAATCCATTATCATTGCGAG-TTAGGCTAACTTAGGCGTTTTTA
*
55355505 CTGTTGAATCCATTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCATTATCATTGCGAGTTAGGCTAACTTAGGCGTTTTTA
55355553 AGCAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 21 0.48
49 23 0.52
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCATTATCATTGCGAGTTAGGCTAACTTAGGCGTTTTTA
Found at i:55355824 original size:2 final size:2
Alignment explanation
Indices: 55355817--55355859 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
55355807 AAAATAGAAA
55355817 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
55355859 A
1 A
55355860 TAAAAAATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55356196 original size:11 final size:11
Alignment explanation
Indices: 55356182--55356207 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55356172 ATTTTTTTAA
55356182 TTTTAAAATAC
1 TTTTAAAATAC
55356193 TTTTAAAATAC
1 TTTTAAAATAC
55356204 TTTT
1 TTTT
55356208 TTTAAAAAAT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:55359243 original size:27 final size:27
Alignment explanation
Indices: 55359211--55359278 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
55359201 ATGCACTTCG
55359211 GTGCTTACTGCTACGTGATTAAACTAT
1 GTGCTTACTGCTACGTGATTAAACTAT
* * ** *
55359238 GTGCTTACCGTTACGTGATTGCACTTT
1 GTGCTTACTGCTACGTGATTAAACTAT
*
55359265 GTTCTTACTGCTAC
1 GTGCTTACTGCTAC
55359279 ATGAAATGCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (27 bp):
GTGCTTACTGCTACGTGATTAAACTAT
Found at i:55360069 original size:20 final size:20
Alignment explanation
Indices: 55360013--55360069 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
55360003 AAAATATTGA
*
55360013 TACTTTGAAG-AAAGTAGAGG
1 TACTTTG-AGCAAAGTATAGG
55360033 TACTTTGAGCAAAGTATAGG
1 TACTTTGAGCAAAGTATAGG
55360053 TACTTTGAGCAAAGTAT
1 TACTTTGAGCAAAGTAT
55360070 CGATACTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 2 0.06
20 33 0.94
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.30
Consensus pattern (20 bp):
TACTTTGAGCAAAGTATAGG
Found at i:55360076 original size:20 final size:20
Alignment explanation
Indices: 55360011--55360077 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
55360001 GTAAAATATT
*
55360011 GATACTTTGAAG-AAAGTAGA
1 GATACTTTG-AGCAAAGTATA
*
55360031 GGTACTTTGAGCAAAGTATA
1 GATACTTTGAGCAAAGTATA
* *
55360051 GGTACTTTGAGCAAAGTATC
1 GATACTTTGAGCAAAGTATA
55360071 GATACTT
1 GATACTT
55360078 ATGACTTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 2 0.05
20 40 0.95
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (20 bp):
GATACTTTGAGCAAAGTATA
Found at i:55363506 original size:19 final size:19
Alignment explanation
Indices: 55363473--55363526 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
55363463 TATTTTAGAA
55363473 AATTTTT-TAAA-ATTTAT
1 AATTTTTATAAATATTTAT
* *
55363490 ATTTTTTATAAATATTTTT
1 AATTTTTATAAATATTTAT
*
55363509 AATTTTTAAAAATTATTT
1 AATTTTTATAAA-TATTT
55363527 TGAATTACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 6 0.20
18 4 0.13
19 15 0.50
20 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTTATAAATATTTAT
Found at i:55363525 original size:20 final size:19
Alignment explanation
Indices: 55363492--55363532 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
55363482 AAATTTATAT
* *
55363492 TTTTTATAAATATTTTTAA
1 TTTTTAAAAATATTTTGAA
55363511 TTTTTAAAAATTATTTTGAA
1 TTTTTAAAAA-TATTTTGAA
55363531 TT
1 TT
55363533 ACTTTGTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAAATATTTTGAA
Found at i:55363527 original size:19 final size:20
Alignment explanation
Indices: 55363492--55363532 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
55363482 AAATTTATAT
*
55363492 TTTTTATAAATATTTTT-AA
1 TTTTTAAAAATATTTTTGAA
55363511 TTTTTAAAAAT-TATTTTGAA
1 TTTTTAAAAATAT-TTTTGAA
55363531 TT
1 TT
55363533 ACTTTGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 1 0.05
19 14 0.74
20 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTAAAAATATTTTTGAA
Found at i:55377499 original size:27 final size:25
Alignment explanation
Indices: 55377465--55377540 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 25
55377455 AAAAGTGTAC
55377465 AAAATATATACATGTACATATATATA
1 AAAATATATACAT-TACATATATATA
* *
55377491 AAAATTATATACATTATATAGATTATA
1 AAAA-TATATACATTACATATA-TATA
*
55377518 AAAA-AGATA-ATTACATATATATA
1 AAAATATATACATTACATATATATA
55377541 TATATAAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
23 4 0.09
24 8 0.19
25 4 0.09
26 10 0.23
27 17 0.40
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (25 bp):
AAAATATATACATTACATATATATA
Found at i:55377536 original size:28 final size:29
Alignment explanation
Indices: 55377482--55377556 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
55377472 ATACATGTAC
* *
55377482 ATATATATAAAAATTATATACATTATATAG
1 ATATATAAAAAAATAAT-TACATTATATAG
*
55377512 AT-TATAAAAAAGATAATTACA-TATATAT
1 ATATATAAAAAA-ATAATTACATTATATAG
*
55377540 ATATATAAACAAATAAT
1 ATATATAAAAAAATAAT
55377557 AATAATTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 13 0.33
29 20 0.51
30 6 0.15
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (29 bp):
ATATATAAAAAAATAATTACATTATATAG
Found at i:55377731 original size:17 final size:17
Alignment explanation
Indices: 55377709--55377743 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55377699 TAGGAAATAA
*
55377709 AAAATGTATATGTATAT
1 AAAATGTAAATGTATAT
55377726 AAAATGTAAATGTATAT
1 AAAATGTAAATGTATAT
55377743 A
1 A
55377744 TACGTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAATGTAAATGTATAT
Found at i:55378255 original size:23 final size:24
Alignment explanation
Indices: 55378225--55378271 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
55378215 AAATTAAATC
55378225 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
55378248 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
55378272 AAGATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:55378296 original size:14 final size:12
Alignment explanation
Indices: 55378263--55378288 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55378253 GATTGCATAT
55378263 ATCATATCTAAG
1 ATCATATCTAAG
55378275 ATCATATCTAAG
1 ATCATATCTAAG
55378287 AT
1 AT
55378289 TGCATATCCT
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:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:55381809 original size:26 final size:26
Alignment explanation
Indices: 55381761--55381819 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
55381751 ACATATTTTC
* * **
55381761 TCAAAATTTTTCCTAGGGCAAAATTG
1 TCAAAATATTACCTAGGGCAAAATCA
* *
55381787 TCAAAATATTACCTGGGGTAAAATCA
1 TCAAAATATTACCTAGGGCAAAATCA
55381813 TCAAAAT
1 TCAAAAT
55381820 TTTGCTGAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (26 bp):
TCAAAATATTACCTAGGGCAAAATCA
Found at i:55384557 original size:13 final size:14
Alignment explanation
Indices: 55384523--55384564 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
55384513 ATTAGGGTTC
* *
55384523 TTTTCTTCTTCTTC
1 TTTTCTTCTTATTT
55384537 TTTT-TTCTT-TTT
1 TTTTCTTCTTATTT
55384549 TTTTCTTCTTATTT
1 TTTTCTTCTTATTT
55384563 TT
1 TT
55384565 AGATTAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 6 0.24
13 10 0.40
14 9 0.36
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTCTTATTT
Found at i:55384750 original size:23 final size:23
Alignment explanation
Indices: 55384707--55384750 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
55384697 TTCTTATCCT
* *
55384707 TACATTTAAATTCTTGGCCCATC
1 TACATTTAAATTCCTGACCCATC
55384730 TACATTTAAATTCCTGACCCA
1 TACATTTAAATTCCTGACCCA
55384751 AGCAGCTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (23 bp):
TACATTTAAATTCCTGACCCATC
Found at i:55387616 original size:23 final size:24
Alignment explanation
Indices: 55387579--55387627 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
55387569 TTAAGCTTTT
* *
55387579 AATAGGATTTATTTAGGTAAAAAG
1 AATAGGATCTATTTAAGTAAAAAG
*
55387603 AATAGG-TCTATTTAAGTACAAAG
1 AATAGGATCTATTTAAGTAAAAAG
55387626 AA
1 AA
55387628 ATGAAATGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (24 bp):
AATAGGATCTATTTAAGTAAAAAG
Found at i:55387856 original size:21 final size:21
Alignment explanation
Indices: 55387817--55387856 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55387807 GTATTAAAAA
* *
55387817 CAAATTTAAAAATACAAAGTT
1 CAAATTAAAAAAAACAAAGTT
*
55387838 CAAATTAAAAAAAATAAAG
1 CAAATTAAAAAAAACAAAG
55387857 GAAAACAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (21 bp):
CAAATTAAAAAAAACAAAGTT
Found at i:55392375 original size:62 final size:57
Alignment explanation
Indices: 55392299--55392446 Score: 181
Period size: 57 Copynumber: 2.5 Consensus size: 57
55392289 AATTGACGGT
*
55392299 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCGGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC--T--TGATATAGCCCTCCCGAAGAATATGTG-G
*
55392362 AAAAAGATCTAGCCCGAACGGGTGAT-CTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCTTGATATAGCCCTCCCGAAGAATATGTGG
* * *
55392418 AAAATAGATTTAGCCCGGATGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
55392447 GAATTAGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
56 5 0.06
57 44 0.57
58 1 0.01
59 1 0.01
61 1 0.01
62 20 0.26
63 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCTTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:55392677 original size:67 final size:67
Alignment explanation
Indices: 55392569--55392699 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
55392559 TTTATATTAT
* *
55392569 AGGGGATTTAGCCTGGACTGGTAATCCTGCTGTAAGAAATGAAGTTTGCGGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAAGTTCGCGGGAGTGTGCTCTCTT
55392634 GC
66 GC
* *
55392636 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGGTCTCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAAGTTCGCGGGAGTGTGCTCTCT
55392700 GAATTGAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAAGTTCGCGGGAGTGTGCTCTCTT
GC
Found at i:55394321 original size:49 final size:49
Alignment explanation
Indices: 55394243--55394364 Score: 181
Period size: 49 Copynumber: 2.4 Consensus size: 49
55394233 ATGTGAAAAT
* *
55394243 GTGATTATGTGATTTCCGTGTAAGGCCATAGTTGGGCTATGGCATCAGTAA
1 GTGA-TATGTGA-TTCCGTGTAAGACCATAGCTGGGCTATGGCATCAGTAA
* *
55394294 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCAGTAA
*
55394343 GTGATATGTGATTACGTGTAAG
1 GTGATATGTGATTCCGTGTAAG
55394365 TGTCACGGAC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 55 0.83
50 7 0.11
51 4 0.06
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCAGTAA
Found at i:55396740 original size:13 final size:13
Alignment explanation
Indices: 55396722--55396748 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55396712 ATAATTTATA
55396722 TGTGTGAAAATTT
1 TGTGTGAAAATTT
55396735 TGTGTGAAAATTT
1 TGTGTGAAAATTT
55396748 T
1 T
55396749 ATCGTCTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:55397942 original size:32 final size:31
Alignment explanation
Indices: 55397897--55397992 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
55397887 CTTAGATAAT
55397897 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
55397928 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
55397960 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
55397991 TT
1 TT
55397993 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:55398666 original size:41 final size:41
Alignment explanation
Indices: 55398621--55398705 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
55398611 GTAATGAACA
55398621 ATGAAAAGTTTGGTATATGAAACATAGGTTAAATAATGGTT
1 ATGAAAAGTTTGGTATATGAAACATAGGTTAAATAATGGTT
55398662 ATGAAAAGTTTGGTATATGAAACATAGGTTAAATAATGGTT
1 ATGAAAAGTTTGGTATATGAAACATAGGTTAAATAATGGTT
55398703 ATG
1 ATG
55398706 TCATTATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (41 bp):
ATGAAAAGTTTGGTATATGAAACATAGGTTAAATAATGGTT
Found at i:55400357 original size:18 final size:19
Alignment explanation
Indices: 55400311--55400364 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
55400301 ATGATCATTT
55400311 TTATTTTTAATATTAATATAA
1 TTATTTTT-AT-TTAATATAA
55400332 TTATTTTTATTTAATATTAA
1 TTATTTTTATTTAATA-TAA
55400352 -TA-TTTTATTTAAT
1 TTATTTTTATTTAAT
55400365 TAGATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.34
19 8 0.25
20 5 0.16
21 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTTTTATTTAATATAA
Found at i:55401759 original size:29 final size:30
Alignment explanation
Indices: 55401717--55401773 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
55401707 TTAAATAAAA
*
55401717 AATTTATAAATAAAACAAATAACATAATTT
1 AATTTATAAATAAAAAAAATAACATAATTT
* *
55401747 AATTTA-AACTAAAAAAAATATCATAAT
1 AATTTATAAATAAAAAAAATAACATAAT
55401774 AAAACTTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (30 bp):
AATTTATAAATAAAAAAAATAACATAATTT
Found at i:55403502 original size:41 final size:40
Alignment explanation
Indices: 55403457--55403542 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
55403447 AAACAGGCTT
*
55403457 TTAGCAGCG-TTTGAATTAAAAACGCCACTAAAAATCAAGCA
1 TTAGCAGCGCTTT-AA-CAAAAACGCCACTAAAAATCAAGCA
* * * * *
55403498 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGATCGAGCA
1 TTAGCAGCGCTTTAACAAAAACGCCACTAAAAATCAAGCA
55403538 TTAGC
1 TTAGC
55403543 GGTGAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 26 0.68
41 9 0.24
42 3 0.08
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (40 bp):
TTAGCAGCGCTTTAACAAAAACGCCACTAAAAATCAAGCA
Found at i:55403518 original size:40 final size:38
Alignment explanation
Indices: 55403474--55403609 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 38
55403464 CGTTTGAATT
*
55403474 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-TTTT-C
* * * *
55403514 AAAAACGCCGCTAAAGATCGAGCATTAGCGGTGAATTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG--TTTTC
* *
55403554 GAAAACGCCGCCAAAAAT-AAGCATTAGCGGCGTTTTCC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTT-C
*
55403592 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
55403610 CCTAAGCCCA
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 4 0.05
38 4 0.05
39 23 0.29
40 44 0.56
41 4 0.05
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTC
Found at i:55403706 original size:41 final size:41
Alignment explanation
Indices: 55403657--55403925 Score: 350
Period size: 41 Copynumber: 6.6 Consensus size: 41
55403647 CATTTAGTGA
* *
55403657 CGTTTTTGAAAAAGCGCCACTAAGGCTCTGACCTTTAGCGG
1 CGTTTTTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGG
* *
55403698 TGTTTTTGAAAAAGCGCCGCTAATGCT-TGTGCCTTTAGCGG
1 CGTTTTTGAAAAAGCGCCGCTAATGCTCTG-ACCTTTAGCGG
*
55403739 CTTTTTTGAAAAAGCGCCGCTAATGCTCTTG-CCTTTAGCGG
1 CGTTTTTGAAAAAGCGCCGCTAATGCTC-TGACCTTTAGCGG
* *
55403780 CGTTTTTAAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGA
1 CGTTTTTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGG
* *
55403821 CGTTTTTGATAAAGAGCCGCTAATGCTCGTG-CCTTTAGCGG
1 CGTTTTTGAAAAAGCGCCGCTAATGCTC-TGACCTTTAGCGG
* ** *
55403862 CATTTCTAAAAAAAGCGCCGTTAATG--CTGACCTTTAGCGG
1 CGTTT-TTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGG
55403902 CGTTTTTGAAAAAGCGCCGCTAAT
1 CGTTTTTGAAAAAGCGCCGCTAAT
55403926 AATAAAATCT
Statistics
Matches: 198, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
39 18 0.09
40 19 0.10
41 142 0.72
42 17 0.09
43 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
CGTTTTTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGG
Found at i:55403874 original size:123 final size:122
Alignment explanation
Indices: 55403657--55403925 Score: 389
Period size: 123 Copynumber: 2.2 Consensus size: 122
55403647 CATTTAGTGA
* * ** *
55403657 CGTTTTTGAAAAAGCGCCACTAAGGCTCTGACCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAAT
1 CGTTTTTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGACGTTTTTGAAAAAGAGCCGCTAAT
* * **
55403722 GCTTGTGCCTTTAGCGGC-TTTTTTGAAAAAGCGCCGCTAATGCTCTTG-CCTTTAGCGG
66 GCTCGTGCCTTTAGCGGCATTTCTAAAAAAAGCGCCGCTAATG--C-TGACCTTTAGCGG
* *
55403780 CGTTTTTAAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGACGTTTTTGATAAAGAGCCGCTAAT
1 CGTTTTTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGACGTTTTTGAAAAAGAGCCGCTAAT
*
55403845 GCTCGTGCCTTTAGCGGCATTTCTAAAAAAAGCGCCGTTAATGCTGACCTTTAGCGG
66 GCTCGTGCCTTTAGCGGCATTTCTAAAAAAAGCGCCGCTAATGCTGACCTTTAGCGG
55403902 CGTTTTTGAAAAAGCGCCGCTAAT
1 CGTTTTTGAAAAAGCGCCGCTAAT
55403926 AATAAAATCT
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
121 2 0.02
122 34 0.26
123 75 0.57
124 20 0.15
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (122 bp):
CGTTTTTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGACGTTTTTGAAAAAGAGCCGCTAAT
GCTCGTGCCTTTAGCGGCATTTCTAAAAAAAGCGCCGCTAATGCTGACCTTTAGCGG
Found at i:55405442 original size:134 final size:134
Alignment explanation
Indices: 55405170--55405416 Score: 404
Period size: 134 Copynumber: 1.8 Consensus size: 134
55405160 AAAAATGCTT
* *
55405170 TTATATTTAAAAATATTTAATCTAAACTATTTGATATATTTAAATATTAGATTTAAAAAAATTGA
1 TTATATTTAAAAATATTTAATCTAAACCATTTGATATATTTAAATACTAGATTTAAAAAAATTGA
* * *
55405235 TAAATGAATAAAAAAAAGTAACATATTGATATGAATAGGCAACTAAAGTAGTTCTTCAAATTAAT
66 TAAATAAATAAAAAAAAGCAACATATTGATATGAATAGGCAACTAAACTAGTTCTTCAAATTAAT
**
55405300 GCTT
131 GCAA
55405304 TTATATTTAAAAATATTTAATCTAAACCATTTGATATATTTAAATACTAGATTTAAAAAAAACAT
1 TTATATTTAAAAATATTTAATCTAAACCATTTGATATATTTAAATACTAGATTT--AAAAAA-AT
55405369 TGATAAATAAATAAAAAAAAGCAACATATTGATATGAATAGGCAACTA
63 TGATAAATAAATAAAAAAAAGCAACATATTGATATGAATAGGCAACTA
55405417 TCTATTTTAG
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
134 52 0.49
136 6 0.06
137 48 0.45
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (134 bp):
TTATATTTAAAAATATTTAATCTAAACCATTTGATATATTTAAATACTAGATTTAAAAAAATTGA
TAAATAAATAAAAAAAAGCAACATATTGATATGAATAGGCAACTAAACTAGTTCTTCAAATTAAT
GCAA
Found at i:55408909 original size:24 final size:24
Alignment explanation
Indices: 55408877--55408930 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
55408867 GGGAAAAGTA
* *
55408877 AGTTC-TTTCTGTATGTGTTGAAC
1 AGTTCATTTCTGCATGTATTGAAC
* *
55408900 GGTTCATTTCTGCATGTATTTAAC
1 AGTTCATTTCTGCATGTATTGAAC
55408924 AGTTCAT
1 AGTTCAT
55408931 CTTTCATTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (24 bp):
AGTTCATTTCTGCATGTATTGAAC
Found at i:55410339 original size:42 final size:42
Alignment explanation
Indices: 55410128--55410438 Score: 462
Period size: 42 Copynumber: 7.3 Consensus size: 42
55410118 GTTATGTTTC
* * * *
55410128 TAGCGGCGTTTTTGTGAGAAGCGCCGCTAAAGGT-TTGATCTA
1 TAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCTTGGTCTT
* * *
55410170 TAGCGGCGTTTTTGACGAAAAGCGCCGCTAAAGGTCATGTTCTT
1 TAGCGGCGTTTGTG--GAAAAGCGCCGCTAAAGGTCTTGGTCTT
* *
55410214 TAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGGTCTT
*
55410257 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGGTCTT
*
55410300 TAGCGGCGTTTGTGGACAAGCGCCGCTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
*
55410342 TAGCGGCGTTTGTGGAAAAGCGCTGCTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
55410384 TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
55410426 TAGCGGCGTTTGT
1 TAGCGGCGTTTGT
55410439 TTCTAAAAAT
Statistics
Matches: 252, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
42 135 0.54
43 99 0.39
44 17 0.07
45 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGGTCTT
Found at i:55411662 original size:14 final size:14
Alignment explanation
Indices: 55411647--55411819 Score: 58
Period size: 14 Copynumber: 12.4 Consensus size: 14
55411637 TCTCACATGT
*
55411647 GGATTCATAAATGT
1 GGATTCATAAATGC
* *
55411661 GGATTTATACATGC
1 GGATTCATAAATGC
* *
55411675 AGATTCATAGATGC
1 GGATTCATAAATGC
* ** *
55411689 GGATCCATATGTGT
1 GGATTCATAAATGC
* * *
55411703 TGATTTATAGATGC
1 GGATTCATAAATGC
* ** *
55411717 AGATTTGTACATGC
1 GGATTCATAAATGC
* *
55411731 GGATTCATAGATGT
1 GGATTCATAAATGC
* *
55411745 GGATCCATAGATGC
1 GGATTCATAAATGC
* * * *
55411759 GAATTAATACATGT
1 GGATTCATAAATGC
* * *
55411773 AGATTTATAGATGC
1 GGATTCATAAATGC
* *
55411787 AGATTCATAAATAC
1 GGATTCATAAATGC
* *
55411801 AGATTCATAGATGC
1 GGATTCATAAATGC
*
55411815 AGATT
1 GGATT
55411820 GTCCTGCAGA
Statistics
Matches: 117, Mismatches: 42, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 117 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (14 bp):
GGATTCATAAATGC
Found at i:55411681 original size:28 final size:28
Alignment explanation
Indices: 55411648--55411795 Score: 100
Period size: 28 Copynumber: 5.3 Consensus size: 28
55411638 CTCACATGTG
*
55411648 GATTCATAAATGTGGATTTATACATGCA
1 GATTCATAGATGTGGATTTATACATGCA
* ** ** **
55411676 GATTCATAGATGCGGATCCATATGTGTT
1 GATTCATAGATGTGGATTTATACATGCA
* ** * *
55411704 GATTTATAGATGCAGATTTGTACATGCG
1 GATTCATAGATGTGGATTTATACATGCA
** *
55411732 GATTCATAGATGTGGATCCATAGATGC-
1 GATTCATAGATGTGGATTTATACATGCA
* * * *
55411759 GAATTAATACATGTAGATTTATAGATGCA
1 G-ATTCATAGATGTGGATTTATACATGCA
55411788 GATTCATA
1 GATTCATA
55411796 AATACAGATT
Statistics
Matches: 88, Mismatches: 30, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
27 1 0.01
28 86 0.98
29 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.34
Consensus pattern (28 bp):
GATTCATAGATGTGGATTTATACATGCA
Found at i:55411755 original size:42 final size:42
Alignment explanation
Indices: 55411641--55411819 Score: 137
Period size: 42 Copynumber: 4.3 Consensus size: 42
55411631 GCAGACTCTC
* * *
55411641 ACATGTGGATTCATAAATGTGGATTTATACATGCAGATTCAT
1 ACATGCGGATTCATAGATGTGGATTTATAGATGCAGATTCAT
* * * **
55411683 AGATGCGGATCCATATG-TGTTGATTTATAGATGCAGATTTGT
1 ACATGCGGATTCATA-GATGTGGATTTATAGATGCAGATTCAT
** *
55411725 ACATGCGGATTCATAGATGTGGATCCATAGATGC-GAATTAAT
1 ACATGCGGATTCATAGATGTGGATTTATAGATGCAG-ATTCAT
** * ** * * *
55411767 ACATGTAGATTTATAGATGCAGATTCATAAATACAGATTCAT
1 ACATGCGGATTCATAGATGTGGATTTATAGATGCAGATTCAT
* *
55411809 AGATGCAGATT
1 ACATGCGGATT
55411820 GTCCTGCAGA
Statistics
Matches: 107, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
41 2 0.02
42 104 0.97
43 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (42 bp):
ACATGCGGATTCATAGATGTGGATTTATAGATGCAGATTCAT
Found at i:55414155 original size:20 final size:19
Alignment explanation
Indices: 55414131--55414181 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
55414121 AGGTTAATTA
*
55414131 ACTTAATTAAT-TATCTTTT
1 ACTTAATTAATCT-TATTTT
55414150 ATCTTAATTAATCTTATTTT
1 A-CTTAATTAATCTTATTTT
55414170 ACTTAATTAATC
1 ACTTAATTAATC
55414182 AACATATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.41
20 16 0.55
21 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (19 bp):
ACTTAATTAATCTTATTTT
Found at i:55415983 original size:44 final size:44
Alignment explanation
Indices: 55415933--55416024 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
55415923 TTTTTACGCT
* * * *
55415933 TTGACACTTGAAATTGACAACTAGTTTCATTTTGATATTTGAAC
1 TTGACACTTGAAATTGAAAACTAGGTCCATTCTGATATTTGAAC
55415977 TTGACACTTGAAATTGAAAACTAGGTCCATTCTGATATTTGAAC
1 TTGACACTTGAAATTGAAAACTAGGTCCATTCTGATATTTGAAC
55416021 TTGA
1 TTGA
55416025 AAATATAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (44 bp):
TTGACACTTGAAATTGAAAACTAGGTCCATTCTGATATTTGAAC
Found at i:55418497 original size:140 final size:138
Alignment explanation
Indices: 55418321--55418678 Score: 352
Period size: 140 Copynumber: 2.6 Consensus size: 138
55418311 AAAATTTAAT
* *
55418321 GAGCTTC-TTTCCATTTTTAAACATCGATTTTGATTCCTTTCTCACCTCAATTCAAAACT-TATG
1 GAGCTTCTTTTCCATTTTTAAACCTCGATTTCGATTCCTTTCTCACCTCAATTCAAAACTATATG
* * * *
55418384 TATTATTTTTCGTTAAAGCAACCCATCAAAAAACTGATCCAAACCCTATTTTCGACAACAAAACT
66 TATT-TTTTTC-TTAAAACAACCCATC--AAAACTCATACAAACCCTATTTTCGACAACAAAACC
* *
55418449 CTAATTCC-GAC
127 CAAATTCCAAAC
* * * * ** * * *
55418460 TAGCTTCTTTTCCATTTTTAAACCTTGATTTCAATTCCTTTCTCACATTGATAC-AAATTCTATG
1 GAGCTTCTTTTCCATTTTTAAACCTCGATTTCGATTCCTTTCTCACCTCAATTCAAAACTATATG
* * * * ***
55418524 TACTGTTTTTCTTAAAAATAACCCATCAAAACTCATACAAACCTTATTTTTGGTGACAAAACCCA
66 TA-TTTTTTTCTT-AAAACAACCCATCAAAACTCATACAAACCCTATTTTCGACAACAAAACCCA
55418589 AATTCCAAAC
129 AATTCCAAAC
* * *
55418599 GAACTTCTTTTCCATTTTTAAATCTCGATTTCGATTCC--T-TCACCCCAATTCAAAACCTATAT
1 GAGCTTCTTTTCCATTTTTAAACCTCGATTTCGATTCCTTTCTCACCTCAATTCAAAA-CTATA-
55418661 TGTATTTTTTTCTTAAAA
64 TGTATTTTTTTCTTAAAA
55418679 ATAACTTTCT
Statistics
Matches: 175, Mismatches: 36, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
136 7 0.04
137 8 0.05
138 47 0.27
139 51 0.29
140 61 0.35
141 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.39
Consensus pattern (138 bp):
GAGCTTCTTTTCCATTTTTAAACCTCGATTTCGATTCCTTTCTCACCTCAATTCAAAACTATATG
TATTTTTTTCTTAAAACAACCCATCAAAACTCATACAAACCCTATTTTCGACAACAAAACCCAAA
TTCCAAAC
Found at i:55418638 original size:139 final size:138
Alignment explanation
Indices: 55418273--55418638 Score: 328
Period size: 139 Copynumber: 2.6 Consensus size: 138
55418263 ACTTGTCAAA
* * ** * * * * *
55418273 AAAAACTCATCCTAACCCTATTTTTTACGACAAAAACCAAAATT-TAATGAGCTTC-TTTCCATT
1 AAAAACTCATACAAACCCTATTTTCGACAAC-AAAACCCAAATTCCAACGAACTTCTTTTCCATT
* * * *
55418336 TTTAAACATCGATTTTGATTCCTTTCTCACCTCAATTCAAAACTTATGTATTATTTTTCGTTAAA
65 TTTAAAC-TCGATTTCGATTCCTTTCTCACATCAATACAAAACTTATGTACTATTTTTCGTTAAA
*
55418401 GCAACCCATC
129 ACAACCCATC
* * * * * * *
55418411 AAAAAACTGATCCAAACCCTATTTTCGACAACAAAACTCTAATTCCGACTAGCTTCTTTTCCATT
1 -AAAAACTCATACAAACCCTATTTTCGACAACAAAACCCAAATTCCAACGAACTTCTTTTCCATT
* * ** * *
55418476 TTTAAACCTTGATTTCAATTCCTTTCTCACATTGATAC-AAATTCTATGTACTGTTTTTC-TTAA
65 TTTAAA-CTCGATTTCGATTCCTTTCTCACATCAATACAAAACT-TATGTACTATTTTTCGTT-A
*
55418539 AAATAACCCATC
127 AAACAACCCATC
* * ***
55418551 -AAAACTCATACAAACCTTATTTTTGGTGACAAAACCCAAATTCCAAACGAACTTCTTTTCCATT
1 AAAAACTCATACAAACCCTATTTTCGACAACAAAACCCAAATTCC-AACGAACTTCTTTTCCATT
55418615 TTTAAATCTCGATTTCGATTCCTT
65 TTTAAA-CTCGATTTCGATTCCTT
55418639 CACCCCAATT
Statistics
Matches: 182, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
138 44 0.24
139 76 0.42
140 61 0.34
141 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (138 bp):
AAAAACTCATACAAACCCTATTTTCGACAACAAAACCCAAATTCCAACGAACTTCTTTTCCATTT
TTAAACTCGATTTCGATTCCTTTCTCACATCAATACAAAACTTATGTACTATTTTTCGTTAAAAC
AACCCATC
Found at i:55422865 original size:17 final size:18
Alignment explanation
Indices: 55422843--55422876 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55422833 CAAATGGATT
*
55422843 ATTTCCTTTTCC-TTTTC
1 ATTTCCATTTCCATTTTC
55422860 ATTTCCATTTCCATTTT
1 ATTTCCATTTCCATTTT
55422877 TAGAAACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTCCATTTCCATTTTC
Found at i:55425431 original size:65 final size:65
Alignment explanation
Indices: 55425327--55425454 Score: 211
Period size: 65 Copynumber: 2.0 Consensus size: 65
55425317 GTAATTGTTC
55425327 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTTA
1 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTTA
* * * * *
55425392 AAAAAGATTGTCTTGACATCTATTTTCTAGATCTTGTAATCGAGAGTCGCCATAATGGATAGT
1 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGT
55425455 AATTTATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (65 bp):
AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTTA
Found at i:55427948 original size:49 final size:49
Alignment explanation
Indices: 55427876--55427995 Score: 159
Period size: 49 Copynumber: 2.4 Consensus size: 49
55427866 TAACCACATT
* *
55427876 TATCTGGCAGTTTATTTGGAATTTCTAGTGGCTTGTCCACATATATCTG
1 TATCTGGCAGTTTGTTTGCAATTTCTAGTGGCTTGTCCACATATATCTG
* * * *
55427925 TATCTGGCAGTTTGTTTGCAATTTTTGGTGGCTTGTTCATATATATCTG
1 TATCTGGCAGTTTGTTTGCAATTTCTAGTGGCTTGTCCACATATATCTG
* * *
55427974 TATTTGGCAGCTTGTCTGCAAT
1 TATCTGGCAGTTTGTTTGCAAT
55427996 ATCCGGTGGG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (49 bp):
TATCTGGCAGTTTGTTTGCAATTTCTAGTGGCTTGTCCACATATATCTG
Found at i:55428004 original size:49 final size:49
Alignment explanation
Indices: 55427903--55428015 Score: 136
Period size: 49 Copynumber: 2.3 Consensus size: 49
55427893 GGAATTTCTA
* * * **
55427903 GTGGCTTGTCCACATATATCTGTATCTGGCAGTTTGTTTGCAATTTTTG
1 GTGGCTTGTCCACATATATCTGTATCTGGCAGCTTGTCTGCAATATCCG
* * *
55427952 GTGGCTTGTTCATATATATCTGTATTTGGCAGCTTGTCTGCAATATCCG
1 GTGGCTTGTCCACATATATCTGTATCTGGCAGCTTGTCTGCAATATCCG
* *
55428001 GTGGGTTGTCTACAT
1 GTGGCTTGTCCACAT
55428016 TGTGGTGTGT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (49 bp):
GTGGCTTGTCCACATATATCTGTATCTGGCAGCTTGTCTGCAATATCCG
Found at i:55428562 original size:27 final size:30
Alignment explanation
Indices: 55428506--55428563 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 30
55428496 ACTTAAATCT
*
55428506 ATTTATTCAATTAAGTGATATTTTATCAAA
1 ATTTATTCAATTAAGTGATATTTTAGCAAA
*
55428536 ATTTATTGAA-TAA-TGAT-TTTTAGCAAA
1 ATTTATTCAATTAAGTGATATTTTAGCAAA
55428563 A
1 A
55428564 ACATGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 4 0.15
29 3 0.12
30 9 0.35
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (30 bp):
ATTTATTCAATTAAGTGATATTTTAGCAAA
Found at i:55433667 original size:210 final size:210
Alignment explanation
Indices: 55433305--55433729 Score: 814
Period size: 210 Copynumber: 2.0 Consensus size: 210
55433295 TATGTGAAGA
55433305 TGATAGTCCACGGTCTATTTCCTAAGAACCACAACCTTGGCAAAAAATAATAATTATATAACAAA
1 TGATAGTCCACGGTCTATTTCCTAAGAACCACAACCTTGGCAAAAAATAATAATTATATAACAAA
55433370 TATATATTATTGCATTTTTTTCACATCCATTTCCCTAAACATGTGAATAATTACAAGTATGTCAC
66 TATATATTATTGCATTTTTTTCACATCCATTTCCCTAAACATGTGAATAATTACAAGTATGTCAC
55433435 ATCTTATCAAATATTAATCAAATAGATAAAAAGAGAGATTTAGTCTCAGTTTACAACATAATCAT
131 ATCTTATCAAATATTAATCAAATAGATAAAAAGAGAGATTTAGTCTCAGTTTACAACATAATCAT
*
55433500 AGCACAACATGGCTC
196 AGCACAACATGACTC
55433515 TGATAGTCCACGGTCTATTTCCTAAGAACCACAACCTTGGCAAAAAATAATAATTATATAACAAA
1 TGATAGTCCACGGTCTATTTCCTAAGAACCACAACCTTGGCAAAAAATAATAATTATATAACAAA
55433580 TATATATTATTGCATTTTTTTCACATCCATTTCCCTAAACATGTGAATAATTACAAGTATGTCAC
66 TATATATTATTGCATTTTTTTCACATCCATTTCCCTAAACATGTGAATAATTACAAGTATGTCAC
* * *
55433645 ATCTTATCAAATATTAATCAAATAGATGAAGAGAGAGATTTAGTCTTAGTTTACAACATAATCAT
131 ATCTTATCAAATATTAATCAAATAGATAAAAAGAGAGATTTAGTCTCAGTTTACAACATAATCAT
55433710 AGCACAACATGACTC
196 AGCACAACATGACTC
55433725 TGATA
1 TGATA
55433730 CCAATTGTTA
Statistics
Matches: 211, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
210 211 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (210 bp):
TGATAGTCCACGGTCTATTTCCTAAGAACCACAACCTTGGCAAAAAATAATAATTATATAACAAA
TATATATTATTGCATTTTTTTCACATCCATTTCCCTAAACATGTGAATAATTACAAGTATGTCAC
ATCTTATCAAATATTAATCAAATAGATAAAAAGAGAGATTTAGTCTCAGTTTACAACATAATCAT
AGCACAACATGACTC
Found at i:55434518 original size:26 final size:26
Alignment explanation
Indices: 55434444--55434519 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
55434434 TCTCATCCCT
* * *
55434444 ATTTTTCCTCCAGTAAAATTTTAACA
1 ATTTTACCTCTAGTAAAATTTTGACA
* *
55434470 ATTTTACC-CTTGGTAAAATTTTGACG
1 ATTTTACCTC-TAGTAAAATTTTGACA
*
55434496 ATTTTGCCTCTAGTAAAATTTTGA
1 ATTTTACCTCTAGTAAAATTTTGA
55434520 GAAAATATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.02
26 39 0.95
27 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (26 bp):
ATTTTACCTCTAGTAAAATTTTGACA
Found at i:55448567 original size:22 final size:19
Alignment explanation
Indices: 55448518--55448573 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
55448508 TATTATAATT
*
55448518 ATTTAAATTTAAAATATTA
1 ATTTAAATTTAAAATATCA
55448537 ATTTAAAATGTTAAAATCATCA
1 ATTT-AAAT-TTAAAAT-ATCA
*
55448559 ATTCTAAATTCAAAA
1 ATT-TAAATTTAAAA
55448574 ACCATAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 12 0.39
22 10 0.32
23 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTTAAATTTAAAATATCA
Found at i:55455105 original size:27 final size:27
Alignment explanation
Indices: 55455057--55455121 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
55455047 ATAGAGGAAG
*
55455057 TACTG-TACTGGTGGTTCTGCCACA-A
1 TACTGTTACTGGTGGTTCGGCCACATA
55455082 TCACTGTTACTGGTGGCTT-GGCCACATA
1 T-ACTGTTACTGGTGG-TTCGGCCACATA
*
55455110 TACTATTACTGG
1 TACTGTTACTGG
55455122 CAGCTTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.12
27 25 0.74
28 4 0.12
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (27 bp):
TACTGTTACTGGTGGTTCGGCCACATA
Found at i:55455127 original size:27 final size:26
Alignment explanation
Indices: 55455075--55455153 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 26
55455065 TGGTGGTTCT
* *
55455075 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAAT-ACTATTACTGGTAGCTTG
* *
55455102 GCCACATATACTATTACTGGCAGCTTT
1 GCCACA-ATACTATTACTGGTAGCTTG
** *
55455129 GCTGCAATACTATTGCTGGTAGCTT
1 GCCACAATACTATTACTGGTAGCTT
55455154 TGCTACGATG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 17 0.40
27 24 0.56
28 2 0.05
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (26 bp):
GCCACAATACTATTACTGGTAGCTTG
Found at i:55455258 original size:32 final size:32
Alignment explanation
Indices: 55455201--55455332 Score: 102
Period size: 32 Copynumber: 4.1 Consensus size: 32
55455191 TACCGTTACC
** * * * *
55455201 GATGGCTGTGTGTCGGTCATTTCACTATTATT
1 GATGGCTGTGTACCGATCATATCACTACTACT
* *
55455233 GATGGCTGTGTACCTATCATATCACTGCTACT
1 GATGGCTGTGTACCGATCATATCACTACTACT
* * * ***
55455265 GATGGCTTTGTACCGATCATGTTACCGTTACT
1 GATGGCTGTGTACCGATCATATCACTACTACT
* * **
55455297 GATGGTTGTCTATAGATCATATCACTACTACT
1 GATGGCTGTGTACCGATCATATCACTACTACT
55455329 GATG
1 GATG
55455333 ACTTTGTGCC
Statistics
Matches: 76, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 76 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (32 bp):
GATGGCTGTGTACCGATCATATCACTACTACT
Found at i:55455402 original size:22 final size:22
Alignment explanation
Indices: 55455359--55455405 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55455349 ATTATTATAC
* *
55455359 TTATAGCTTGTAGCCATTCTGT
1 TTATAGCTTATAGCCATCCTGT
**
55455381 TTATAGCTTATAGTTATCCTGT
1 TTATAGCTTATAGCCATCCTGT
55455403 TTA
1 TTA
55455406 CGGCTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTGT
Found at i:55460946 original size:54 final size:53
Alignment explanation
Indices: 55460763--55460938 Score: 228
Period size: 54 Copynumber: 3.3 Consensus size: 53
55460753 TTTGCTCCTA
* * * *
55460763 GCCTGTCAATGGCCACCACCAAATACAAAAAAAAAATCAAATTTTTTTGTCCTA
1 GCCTGTCAATGACCACCACCAAGTAC-AAAAAAAAATCAAATTTTTTTGTGCTG
* * *
55460817 GCCTGTCAATGGCCACCACCAAGTACAAAAAAAAAT-AATTTTTTTTTTGTGTTG
1 GCCTGTCAATGACCACCACCAAGTACAAAAAAAAATCAA--ATTTTTTTGTGCTG
*
55460871 GCCTGTCAATGACCACCACCAAGTACAAAAAAAAATCACATTTTTTTGGTGCTG
1 GCCTGTCAATGACCACCACCAAGTACAAAAAAAAATCAAATTTTTTT-GTGCTG
*
55460925 GCTTGTCAATGACC
1 GCCTGTCAATGACC
55460939 GGCACCAAAG
Statistics
Matches: 108, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
52 2 0.02
53 17 0.16
54 88 0.81
55 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (53 bp):
GCCTGTCAATGACCACCACCAAGTACAAAAAAAAATCAAATTTTTTTGTGCTG
Found at i:55461044 original size:52 final size:55
Alignment explanation
Indices: 55460914--55461056 Score: 175
Period size: 59 Copynumber: 2.6 Consensus size: 55
55460904 AATCACATTT
*
55460914 TTTTGGTGCTGGCTTGTCAATGACCGGCACCAAAGCACGAGTTTTAGAAAAAAAATTC
1 TTTTGGTGCTGGCTTGTCAATGGCCGGCACCAAAGCACGAGTTTT--AAAAAAAA-TC
* * * *
55460972 TTTTTGGTGCTGGCCTGTCAATGGTCGGCACCAAAGTACGTGTTTT-AAAAAAA-C
1 -TTTTGGTGCTGGCTTGTCAATGGCCGGCACCAAAGCACGAGTTTTAAAAAAAATC
*
55461026 -TTTGGTACTGGCTTGTCAATGGCCGGCACCA
1 TTTTGGTGCTGGCTTGTCAATGGCCGGCACCA
55461057 GACTCAGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
52 28 0.37
54 1 0.01
56 7 0.09
59 40 0.53
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (55 bp):
TTTTGGTGCTGGCTTGTCAATGGCCGGCACCAAAGCACGAGTTTTAAAAAAAATC
Found at i:55461074 original size:52 final size:54
Alignment explanation
Indices: 55460914--55461074 Score: 148
Period size: 52 Copynumber: 2.9 Consensus size: 54
55460904 AATCACATTT
* * *
55460914 TTTTGGTGCTGGCTTGTCAATGACCGGCACCAAAGCACGAGTTTTAGAAAAAAAATTC
1 TTTTGGTGCTGGCTTGTCAATGGCCGGCACCAAA-CTC-AGTATTA-AAAAAAAA-TC
* * * * **
55460972 TTTTTGGTGCTGGCCTGTCAATGGTCGGCACCAAAGT-ACGTGTTTTAAAAAAA-C
1 -TTTTGGTGCTGGCTTGTCAATGGCCGGCACCAAACTCA-GTATTAAAAAAAAATC
* *
55461026 -TTTGGTACTGGCTTGTCAATGGCCGGCACCAGACTCAGTATTAAAAAAA
1 TTTTGGTGCTGGCTTGTCAATGGCCGGCACCAAACTCAGTATTAAAAAAA
55461075 TTTGTTTTAG
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
52 39 0.46
53 1 0.01
54 1 0.01
56 8 0.10
57 4 0.05
59 31 0.37
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (54 bp):
TTTTGGTGCTGGCTTGTCAATGGCCGGCACCAAACTCAGTATTAAAAAAAAATC
Found at i:55465275 original size:20 final size:20
Alignment explanation
Indices: 55465250--55465292 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
55465240 GAATGGTACA
* * *
55465250 GAGTTGAGCAGAGCAGAGCG
1 GAGTTGAACAGAACAGAACG
55465270 GAGTTGAACAGAACAGAACG
1 GAGTTGAACAGAACAGAACG
55465290 GAG
1 GAG
55465293 CAGAACATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.40, T:0.09
Consensus pattern (20 bp):
GAGTTGAACAGAACAGAACG
Found at i:55466216 original size:63 final size:63
Alignment explanation
Indices: 55466117--55466247 Score: 190
Period size: 63 Copynumber: 2.1 Consensus size: 63
55466107 CACATAGCCA
** *
55466117 GGGCACACACCCATGTCGTCTACCTGTGTGGTTCTAAACCATAAACAGTGAGTTACACGGCCT
1 GGGCACACACCCATGTCGTCTACCCATGTGGTTCTAAACCATAAACAGTGAGTTACAAGGCCT
* * * **
55466180 GGGCACACGCCCATGTCGTCTGCCCATGTGGTTCTAAATCATAAATTGTGAGTTACAAGGCCT
1 GGGCACACACCCATGTCGTCTACCCATGTGGTTCTAAACCATAAACAGTGAGTTACAAGGCCT
55466243 GGGCA
1 GGGCA
55466248 TGATGCGGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (63 bp):
GGGCACACACCCATGTCGTCTACCCATGTGGTTCTAAACCATAAACAGTGAGTTACAAGGCCT
Found at i:55478259 original size:316 final size:316
Alignment explanation
Indices: 55477680--55478312 Score: 1140
Period size: 316 Copynumber: 2.0 Consensus size: 316
55477670 ATGCATAGTC
*
55477680 ATTCAATTTCAATAAACAATTGTATAATCAAAATTTCAGTCTAAAATTGTCAGATAGCAGTCATA
1 ATTCAATTTCAATAAACAATTGTATAATCAAAATTTCAGTCTAAAATTGTCAAATAGCAGTCATA
*
55477745 CAGTCTAAACAGATCATACATATACACTACGAATGCCCTACAGTCGCGTTAACAATGCTTACGGC
66 CAGTCTAAACAGATCATACATATACACTACGAATGCCCTACAGTCGCGTTAACAATGCTTACAGC
55477810 CCCAAGGATGAATTCCAAACCTGACCCAGACGCCTGTGTGGTTCCACATGACCGAGCACACGCTC
131 CCCAAGGATGAATTCCAAACCTGACCCAGACGCCTGTGTGGTTCCACATGACCGAGCACACGCTC
* *
55477875 GTGTGCCCAGTCGTGTGTTTCACACGGCTTGACATATGCTCGTATAGTCCTAAATCACAAACAGT
196 GTGTGCCCAGCCGTGTGTTTCACACGGCTTGACATATGCCCGTATAGTCCTAAATCACAAACAGT
*
55477940 GTGTTACACGGCCTAGACACATGCCCGTGTCTTTAGTCTGTGTTAACCCAGCACTA
261 GTGTTACACGGCCTAGACACATGCCCGTGTCTTTAGTCCGTGTTAACCCAGCACTA
* *
55477996 ATTCAGTTTCAATAAACATTTGTATAATCAAAATTTCAGTCTAAAATTGTCAAATAGCAGTCATA
1 ATTCAATTTCAATAAACAATTGTATAATCAAAATTTCAGTCTAAAATTGTCAAATAGCAGTCATA
* * *
55478061 CAGTCTAATCAGATCATACATATACACTACGGATGCCCTACATTCGCGTTAACAATGCTTACAGC
66 CAGTCTAAACAGATCATACATATACACTACGAATGCCCTACAGTCGCGTTAACAATGCTTACAGC
*
55478126 CCCAAGGATGAATTCCAAACCTGACCCAGACGCCTGTGTGGTTCCACATGACCTAGCACACGCTC
131 CCCAAGGATGAATTCCAAACCTGACCCAGACGCCTGTGTGGTTCCACATGACCGAGCACACGCTC
* * *
55478191 GTGTTCCTAGCCGTGTGTTTCACACGGCTTGACATATGCCCGTGTAGTCCTAAATCACAAACAGT
196 GTGTGCCCAGCCGTGTGTTTCACACGGCTTGACATATGCCCGTATAGTCCTAAATCACAAACAGT
55478256 GTGTTACACGGCCTAGACACATGCCCGTGTCTTTAGTCCGTGTTAACCCAGCACTA
261 GTGTTACACGGCCTAGACACATGCCCGTGTCTTTAGTCCGTGTTAACCCAGCACTA
55478312 A
1 A
55478313 CATGCCGTGT
Statistics
Matches: 303, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
316 303 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (316 bp):
ATTCAATTTCAATAAACAATTGTATAATCAAAATTTCAGTCTAAAATTGTCAAATAGCAGTCATA
CAGTCTAAACAGATCATACATATACACTACGAATGCCCTACAGTCGCGTTAACAATGCTTACAGC
CCCAAGGATGAATTCCAAACCTGACCCAGACGCCTGTGTGGTTCCACATGACCGAGCACACGCTC
GTGTGCCCAGCCGTGTGTTTCACACGGCTTGACATATGCCCGTATAGTCCTAAATCACAAACAGT
GTGTTACACGGCCTAGACACATGCCCGTGTCTTTAGTCCGTGTTAACCCAGCACTA
Found at i:55478941 original size:26 final size:24
Alignment explanation
Indices: 55478900--55478970 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 24
55478890 GGTAGTGATC
55478900 AAAATAAAGAGGAAAGAAAAAGAATCAA
1 AAAATAAAGA--AAAGAAAAAGAA--AA
55478928 AAAATAAAGAAAAG-AAAAGAAAA
1 AAAATAAAGAAAAGAAAAAGAAAA
* *
55478951 AAAAGAAAGAAGAGGAAAAA
1 AAAATAAAGAA-AAGAAAAA
55478971 AATAGAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 12 0.31
24 2 0.05
25 11 0.28
26 4 0.10
28 10 0.26
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAATAAAGAAAAGAAAAAGAAAA
Found at i:55478955 original size:19 final size:20
Alignment explanation
Indices: 55478927--55478986 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
55478917 AAAAGAATCA
55478927 AAAAATAAAGAAAAGAA-AAG
1 AAAAA-AAAGAAAAGAAGAAG
*
55478947 AAAAAAAAG-AAAGAAGAGG
1 AAAAAAAAGAAAAGAAGAAG
55478966 AAAAAAATAGAAGAAGAAGAA
1 AAAAAAA-AGAA-AAGAAGAA
55478987 CTAATGTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.18
19 13 0.38
20 7 0.21
21 1 0.03
22 7 0.21
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (20 bp):
AAAAAAAAGAAAAGAAGAAG
Found at i:55487382 original size:85 final size:85
Alignment explanation
Indices: 55487289--55487506 Score: 253
Period size: 85 Copynumber: 2.6 Consensus size: 85
55487279 AAAAACATTA
*
55487289 CTATAGAACATGAAATTTAGC-GACGCTTTTCCCAAAAACACCACTAAAGAACATGA-CATTTAG
1 CTATAGAACATGAAATTTAGCTG-CGCTTTCCCCAAAAACACCACTAAAGAACATGAGC-TTTAG
** *
55487352 CGGCGCTTTCCCACAAACGCCG
64 CAACGCTTTCCCACAAACACCG
** * *
55487374 CTATAGAACATGATGTTTAGCTGCGCTTTCCCCACAAACGCCACTAAAGAACATGAGCTTTAGCA
1 CTATAGAACATGAAATTTAGCTGCGCTTTCCCCAAAAACACCACTAAAGAACATGAGCTTTAGCA
*
55487439 ACGCTTTTCCACAAACACCG
66 ACGCTTTCCCACAAACACCG
* ** * * *
55487459 CTAAAGAACATGACCTTTCA-TTGCGCTTTCCCCAGAAACACCGCTAAA
1 CTATAGAACATGAAATTT-AGCTGCGCTTTCCCCAAAAACACCACTAAA
55487507 AGTCATGTTA
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
85 111 0.97
86 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.22
Consensus pattern (85 bp):
CTATAGAACATGAAATTTAGCTGCGCTTTCCCCAAAAACACCACTAAAGAACATGAGCTTTAGCA
ACGCTTTCCCACAAACACCG
Found at i:55487486 original size:42 final size:42
Alignment explanation
Indices: 55487293--55487506 Score: 207
Period size: 43 Copynumber: 5.0 Consensus size: 42
55487283 ACATTACTAT
** * *
55487293 AGAACATGAAATTTAGC-GACGCTTTTCCCAAAAACACCACTAA
1 AGAACATGACCTTTAGCTG-CGC-TTTCCCACAAACACCGCTAA
* * * *
55487336 AGAACATGACATTTAGCGGCGCTTTCCCACAAACGCCGCTAT
1 AGAACATGACCTTTAGCTGCGCTTTCCCACAAACACCGCTAA
** * *
55487378 AGAACATGATGTTTAGCTGCGCTTTCCCCACAAACGCCACTAA
1 AGAACATGACCTTTAGCTGCGCTTT-CCCACAAACACCGCTAA
* ** *
55487421 AGAACATGAGCTTTAGCAACGCTTTTCCACAAACACCGCTAA
1 AGAACATGACCTTTAGCTGCGCTTTCCCACAAACACCGCTAA
* *
55487463 AGAACATGACCTTTCA-TTGCGCTTTCCCCAGAAACACCGCTAA
1 AGAACATGACCTTT-AGCTGCGCTTT-CCCACAAACACCGCTAA
55487506 A
1 A
55487507 AGTCATGTTA
Statistics
Matches: 144, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 71 0.49
43 72 0.50
44 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (42 bp):
AGAACATGACCTTTAGCTGCGCTTTCCCACAAACACCGCTAA
Found at i:55487652 original size:11 final size:13
Alignment explanation
Indices: 55487636--55487669 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
55487626 AATTTTACGG
55487636 AAAAATTTCG-T-
1 AAAAATTTCGTTC
55487647 AAAAATTTCGTTC
1 AAAAATTTCGTTC
55487660 AAAAATTTCG
1 AAAAATTTCG
55487670 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:55488847 original size:33 final size:32
Alignment explanation
Indices: 55488778--55488857 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 32
55488768 ATATAAAGGG
* *
55488778 GGTTGCTAAGTTCTGATTCCCC---CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATCATTGGT
55488805 GGTTGCTAAGTGCTGATTCCCCGATCCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAT-CATTGGT
55488838 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
55488858 ACCGTATCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 21 0.47
31 2 0.04
32 2 0.04
33 20 0.44
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.33
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCGATCATTGGT
Found at i:55488916 original size:103 final size:103
Alignment explanation
Indices: 55488737--55489003 Score: 446
Period size: 103 Copynumber: 2.6 Consensus size: 103
55488727 TATGAAGGGA
* * *
55488737 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATATAAAGGGGGTTGCTAAGTTCTGATTCCCCCA
1 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCA
55488802 AGGGGTTGCTAAGTGCTGATTCCCCG-ATCCATTGGTGG
66 AGGGGTTGCTAAGTGCTGATTCCCCGAAT-CATTGGTGG
*
55488840 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCTA
1 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCA
55488905 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGG
66 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGG
* * * *
55488943 TTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAAGTGGTTGCTAAGTGCTGATTCC
1 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCC
55489004 TCGAATCACT
Statistics
Matches: 155, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
103 153 0.99
104 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (103 bp):
TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCA
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGG
Found at i:55488950 original size:33 final size:33
Alignment explanation
Indices: 55488881--55489041 Score: 129
Period size: 33 Copynumber: 4.7 Consensus size: 33
55488871 ATGTGAAGGG
*
55488881 GGTTGCTAAGTGCTGATTCCCC---T-A-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
55488908 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
55488941 GGTTGCTAAGTGCTGATTCCACC-ATATCTTTGAATGTGAAAGT
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATC-----AT-TG---GT
* *
55488984 GGTTGCTAAGTGCTGATTCCTCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
55489017 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
55489042 TAACGGTTAA
Statistics
Matches: 110, Mismatches: 5, Indels: 31
0.75 0.03 0.21
Matches are distributed among these distances:
27 22 0.20
30 1 0.01
31 1 0.01
32 2 0.02
33 42 0.38
34 8 0.07
36 2 0.02
37 1 0.01
39 2 0.02
40 2 0.02
42 4 0.04
43 23 0.21
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:55496058 original size:9 final size:9
Alignment explanation
Indices: 55496046--55496111 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
55496036 TGATATATAT
55496046 TTATGTAAG
1 TTATGTAAG
55496055 TTATGTAAG
1 TTATGTAAG
*
55496064 TTATGATATG
1 TTATG-TAAG
* * *
55496074 ATATAT-AT
1 TTATGTAAG
55496082 TTATGT-A-
1 TTATGTAAG
55496089 TTATGTAAG
1 TTATGTAAG
55496098 TTATGTAAG
1 TTATGTAAG
55496107 TTATG
1 TTATG
55496112 ATCCAAAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 29 0.62
10 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55496060 original size:36 final size:34
Alignment explanation
Indices: 55496019--55496102 Score: 150
Period size: 36 Copynumber: 2.4 Consensus size: 34
55496009 ATCCAAAGTT
55496019 TTATGTAAGTTATGATATGATATATATTTATGTAA
1 TTATGTAAGTTATGATATGATATATATTTATGT-A
55496054 GTTATGTAAGTTATGATATGATATATATTTATGTA
1 -TTATGTAAGTTATGATATGATATATATTTATGTA
55496089 TTATGTAAGTTATG
1 TTATGTAAGTTATG
55496103 TAAGTTATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 14 0.29
35 1 0.02
36 33 0.69
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.49
Consensus pattern (34 bp):
TTATGTAAGTTATGATATGATATATATTTATGTA
Found at i:55496183 original size:13 final size:13
Alignment explanation
Indices: 55496165--55496191 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55496155 TGATTATCAT
55496165 CTTTAAATTTTAA
1 CTTTAAATTTTAA
55496178 CTTTAAATTTTAA
1 CTTTAAATTTTAA
55496191 C
1 C
55496192 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:55498590 original size:22 final size:22
Alignment explanation
Indices: 55498547--55498590 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55498537 AACATATAAT
*
55498547 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
55498569 TAAA-TAATCTAAAAATTGCAAA
1 TAAATTAATC-AAAAATTACAAA
55498591 CAACAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:55499951 original size:24 final size:24
Alignment explanation
Indices: 55499919--55499980 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
55499909 CATAAATTTT
* *
55499919 GCTAATGCTTGACCTTTTGCGGCA
1 GCTAGTGCTTTACCTTTTGCGGCA
55499943 GCTAGTGCTTTACC-TTTGCGGCA
1 GCTAGTGCTTTACCTTTTGCGGCA
55499966 GCTAGTGCTTTACCT
1 GCTAGTGCTTTACCT
55499981 ATTGTGGCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.66
24 12 0.34
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (24 bp):
GCTAGTGCTTTACCTTTTGCGGCA
Found at i:55501325 original size:31 final size:31
Alignment explanation
Indices: 55501290--55501385 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
55501280 TGTTTGCCCA
55501290 TTTAATTTGATGCACAATTTCATGCAATAAC
1 TTTAATTTGATGCACAATTTCATGCAATAAC
* * ** **
55501321 TTTAATATGTCTG-ATTATGACATGTC-A-AAC
1 TTTAATTTG-ATGCACAATTTCATG-CAATAAC
*
55501351 ATT--TTTGATGCACAATTTCATGCAATAAC
1 TTTAATTTGATGCACAATTTCATGCAATAAC
55501380 TTTAAT
1 TTTAAT
55501386 ATGTCTGATT
Statistics
Matches: 44, Mismatches: 14, Indels: 14
0.61 0.19 0.19
Matches are distributed among these distances:
27 3 0.07
28 11 0.25
29 5 0.11
30 5 0.11
31 17 0.39
32 3 0.07
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (31 bp):
TTTAATTTGATGCACAATTTCATGCAATAAC
Found at i:55501361 original size:59 final size:59
Alignment explanation
Indices: 55501295--55501414 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
55501285 GCCCATTTAA
55501295 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
1 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
*
55501354 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATTACATGTCAAACATT
1 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
55501413 TT
1 TT
55501415 GTCTAGAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (59 bp):
TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
Found at i:55514333 original size:26 final size:27
Alignment explanation
Indices: 55514264--55514337 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
55514254 TATTTTCTCG
*
55514264 AAATTTTACTAGGGGTAAAATCATCAA
1 AAATTTTACTAAGGGTAAAATCATCAA
*
55514291 AAATTTTA-TCAAAGGTAAAATCATC-A
1 AAATTTTACT-AAGGGTAAAATCATCAA
55514317 AAATTTTACTAAGGGTAAAAT
1 AAATTTTACTAAGGGTAAAAT
55514338 AGTGATGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 20 0.48
27 22 0.52
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATTTTACTAAGGGTAAAATCATCAA
Found at i:55527421 original size:6 final size:6
Alignment explanation
Indices: 55527410--55527446 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
55527400 AGTTGTAAAG
55527410 TTTTAT TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
55527447 ATTTATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:55527426 original size:11 final size:11
Alignment explanation
Indices: 55527410--55527450 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
55527400 AGTTGTAAAG
55527410 TTTTATTTTTA
1 TTTTATTTTTA
55527421 TTTTATTTTTA
1 TTTTATTTTTA
55527432 TTTTTATTTTTA
1 -TTTTATTTTTA
55527444 -TTTATTT
1 TTTTATTT
55527451 ATTTATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.24
11 11 0.38
12 11 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:55527432 original size:17 final size:16
Alignment explanation
Indices: 55527410--55527450 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
55527400 AGTTGTAAAG
55527410 TTTTATTTTTATTTTAT
1 TTTTATTTTTATTTT-T
55527427 TTTTATTTTTATTTTT
1 TTTTATTTTTATTTTT
*
55527443 ATTTATTT
1 TTTTATTT
55527451 ATTTATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTTTATTTTT
Found at i:55537341 original size:13 final size:13
Alignment explanation
Indices: 55537323--55537362 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
55537313 TCGACCTAAA
55537323 TAATTACAAA-AGT
1 TAATTACAAATA-T
55537336 TAATTACAAATAT
1 TAATTACAAATAT
*
55537349 TAGTTACAAATAT
1 TAATTACAAATAT
55537362 T
1 T
55537363 TTGTCAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 24 0.96
14 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (13 bp):
TAATTACAAATAT
Found at i:55537778 original size:17 final size:19
Alignment explanation
Indices: 55537758--55537794 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55537748 AATTATAAAA
55537758 ATAA-ATAAAAA-ATAATT
1 ATAATATAAAAATATAATT
55537775 ATAATTATAAAAATATAATT
1 ATAA-TATAAAAATATAATT
55537795 TAACATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAATATAAAAATATAATT
Found at i:55540261 original size:41 final size:39
Alignment explanation
Indices: 55540178--55540300 Score: 165
Period size: 40 Copynumber: 3.0 Consensus size: 39
55540168 TAAAAATTCA
*
55540178 CGGTGTTTATGAGAAAAACGCCGCTATTGTCTTACCTTTG
1 CGGTGTTTATGAG-AAAACGCCGCTATTGCCTTACCTTTG
55540218 CGGTGTTTATGGAGAAAACGCCGCTATTGCCTTACCTTCTG
1 CGGTGTTTAT-GAGAAAACGCCGCTATTGCCTTACCTT-TG
* * *
55540259 CGGCGTTTATGAGAGAAACACCGCTATTACCTTACCATTTG
1 CGGTGTTTATGAGA-AAACGCCGCTATTGCCTTACC-TTTG
55540300 C
1 C
55540301 AGCGATTTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
40 37 0.49
41 36 0.48
42 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (39 bp):
CGGTGTTTATGAGAAAACGCCGCTATTGCCTTACCTTTG
Found at i:55540319 original size:41 final size:41
Alignment explanation
Indices: 55540182--55540321 Score: 117
Period size: 41 Copynumber: 3.4 Consensus size: 41
55540172 AATTCACGGT
* * ** * *
55540182 GTTTATGAGAAAAACGCCGCTATTGTCTTACCTT-TGCGGT
1 GTTTATAAGAAAAACACCGCTATTACCTTACCTTCTGCAGC
* * * *
55540222 GTTTAT-GGAGAAAACGCCGCTATTGCCTTACCTTCTGCGGC
1 GTTTATAAGA-AAAACACCGCTATTACCTTACCTTCTGCAGC
* *
55540263 GTTTATGAGAGAAACACCGCTATTACCTTACCATT-TGCAGC
1 GTTTATAAGAAAAACACCGCTATTACCTTACC-TTCTGCAGC
55540304 GATTT-TAAGAAAAACACC
1 G-TTTATAAGAAAAACACC
55540322 ACTAATGGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
39 2 0.02
40 29 0.34
41 47 0.55
42 7 0.08
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
GTTTATAAGAAAAACACCGCTATTACCTTACCTTCTGCAGC
Found at i:55549361 original size:42 final size:42
Alignment explanation
Indices: 55549314--55549395 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
55549304 CTGACTTGGG
55549314 TCACACGACCAAGCCACACG-TCCGTGTGTCAGGCCGTGTGTC
1 TCACACGACCAAGCCACACGCT-CGTGTGTCAGGCCGTGTGTC
** *
55549356 TCACACGACCAAGTTACACGCTCGTGTGTCTGGCCGTGTG
1 TCACACGACCAAGCCACACGCTCGTGTGTCAGGCCGTGTG
55549396 GACCTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (42 bp):
TCACACGACCAAGCCACACGCTCGTGTGTCAGGCCGTGTGTC
Found at i:55552005 original size:45 final size:46
Alignment explanation
Indices: 55551934--55552051 Score: 139
Period size: 45 Copynumber: 2.5 Consensus size: 46
55551924 AAAATAATAT
* * * **
55551934 TATTTTAATAATTTTAATATTTAATTTAATTTAATTCTTATCTTG-G
1 TATTTTATTAA-TTTAATATTAAATTTAATCTAATAATTATCTTGAG
55551980 TATTTTATTAATTTAATATTAAATTTAATCTAATAATTATCTTGATAAG
1 TATTTTATTAATTTAATATTAAATTTAATCTAATAATTATCTTG---AG
*
55552029 TATTGTATTAATTTAATATTAAA
1 TATTTTATTAATTTAATATTAAA
55552052 ATGATTAAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 29 0.47
46 10 0.16
49 23 0.37
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (46 bp):
TATTTTATTAATTTAATATTAAATTTAATCTAATAATTATCTTGAG
Found at i:55562990 original size:77 final size:76
Alignment explanation
Indices: 55562826--55563233 Score: 431
Period size: 77 Copynumber: 5.3 Consensus size: 76
55562816 CGAAGAAATT
* * * ***
55562826 AGTGAACTGTTAGAATATCGAAGGTTGCGATCTTAAATCAACGAACCGTAAAAATTATAGAAACG
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACAGCCGCG
55562891 ATATTAAATCA
66 ATATTAAATCA
* * * * *
55562902 AGTGAACTGTTAAAATATCGAAGGTTGCGATCTTAAGTGTAACGAACCGTAAAAATGACAGCTGC
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAAT-CAACGAACCGTAAAAATGACAGCCGC
55562967 GATATTAAATCA
65 GATATTAAATCA
* * * * * *
55562979 ATTGAATTGTTAAAATATTGAAGGTCGCGATCTTAAATCGAGCGAACCGTAAAAATGACAGCCAC
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AACGAACCGTAAAAATGACAGCCGC
* *
55563044 AATATTAAATCG
65 GATATTAAATCA
** * * * * * * **
55563056 AGCAAACTATTAGAATATCAAAGGTCGCAATCTTAAATTAAGTGGACCGTAAAAATGACAATCGC
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAA-CGAACCGTAAAAATGACAGCCGC
* *
55563121 AATATTGAATCA
65 GATATTAAATCA
* * *
55563133 AGCGAACTGCTAGAATATCGAAGGTCGCGATCTTAAAATCAAGCGAACCGTAAAAATGACAACCG
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTT-AAATCAA-CGAACCGTAAAAATGACAGCCG
55563198 CTG-TATTAAATCA
64 C-GATATTAAATCA
* *
55563211 AGCGAACTATTAGAATATCGAAG
1 AGTGAACTGTTAGAATATCGAAG
55563234 ATCATGATAG
Statistics
Matches: 277, Mismatches: 50, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
76 37 0.13
77 183 0.66
78 57 0.21
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (76 bp):
AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACAGCCGCG
ATATTAAATCA
Found at i:55563034 original size:40 final size:39
Alignment explanation
Indices: 55562839--55563034 Score: 118
Period size: 40 Copynumber: 5.1 Consensus size: 39
55562829 GAACTGTTAG
55562839 AATATCGAAGGTTGCGATCTTAAATC-AACGAACCGTAAA
1 AATATCGAAGG-TGCGATCTTAAATCAAACGAACCGTAAA
* * * ** * *
55562878 AATTATAGAA---ACGATATTAAATCAAGTGAACTGTTAA
1 AA-TATCGAAGGTGCGATCTTAAATCAAACGAACCGTAAA
* **
55562915 AATATCGAAGGTTGCGATCTTAAGTGTAACGAACCGT-AA
1 AATATCGAAGG-TGCGATCTTAAATCAAACGAACCGTAAA
* * ** ** *
55562954 AA-AT-GACAGCTGCGATATTAAATCAATTGAATTGTTAA
1 AATATCGA-AGGTGCGATCTTAAATCAAACGAACCGTAAA
* * *
55562992 AATATTGAAGGTCGCGATCTTAAATCGAGCGAACCGTAAA
1 AATATCGAAGGT-GCGATCTTAAATCAAACGAACCGTAAA
55563032 AAT
1 AAT
55563035 GACAGCCACA
Statistics
Matches: 113, Mismatches: 33, Indels: 21
0.68 0.20 0.13
Matches are distributed among these distances:
36 17 0.15
37 30 0.27
38 8 0.07
39 11 0.10
40 47 0.42
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (39 bp):
AATATCGAAGGTGCGATCTTAAATCAAACGAACCGTAAA
Found at i:55571920 original size:21 final size:21
Alignment explanation
Indices: 55571884--55571946 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
55571874 TTAAATATAA
* *
55571884 ATTATAAAATTCATAAAAACTT
1 ATTAT-AAATTTATAAAAAATT
55571906 ATTATAAATTTATAAAAAATT
1 ATTATAAATTTATAAAAAATT
* * *
55571927 ATAAAAAATTT-TAGAAAATT
1 ATTATAAATTTATAAAAAATT
55571947 TTTAGAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 8 0.22
21 23 0.64
22 5 0.14
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTATAAATTTATAAAAAATT
Found at i:55571925 original size:11 final size:11
Alignment explanation
Indices: 55571889--55571958 Score: 56
Period size: 10 Copynumber: 6.5 Consensus size: 11
55571879 TATAAATTAT
*
55571889 AAAATTCAT-A
1 AAAATTTATAA
* *
55571899 AAAACTTATTA
1 AAAATTTATAA
*
55571910 TAAATTTATAA
1 AAAATTTATAA
55571921 AAAA-TTATAA
1 AAAATTTATAA
*
55571931 AAAATTT-TAG
1 AAAATTTATAA
*
55571941 AAAATTTTTAGA
1 AAAATTTATA-A
55571953 AAAATT
1 AAAATT
55571959 ATTGAAACAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
10 26 0.54
11 16 0.33
12 6 0.12
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:55571930 original size:10 final size:10
Alignment explanation
Indices: 55571889--55571960 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 10
55571879 TATAAATTAT
55571889 AAAATTCATAA
1 AAAATT-ATAA
* *
55571900 AAACTTATTAT
1 AAAATTA-TAA
*
55571911 AAATTTATAA
1 AAAATTATAA
55571921 AAAATTATAA
1 AAAATTATAA
*
55571931 AAAATTTTAGA
1 AAAATTATA-A
* *
55571942 AAATTTTTAGA
1 AAAATTATA-A
55571953 AAAATTAT
1 AAAATTAT
55571961 TGAAACATCA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
10 20 0.40
11 30 0.60
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
AAAATTATAA
Found at i:55572068 original size:31 final size:30
Alignment explanation
Indices: 55572010--55572076 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
55572000 TATAAATTTT
* *
55572010 TAAAATTTTTAAAAATTACAAATAAGTTAGA
1 TAAAATTTTAAAAAATTACAAAGAAGTT-GA
* *
55572041 TAAAATTATTAAAAAATTA-ATAGAAGTTTA
1 TAAAATT-TTAAAAAATTACAAAGAAGTTGA
55572071 TAAAAT
1 TAAAAT
55572077 AAAAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 7 0.23
31 14 0.45
32 10 0.32
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (30 bp):
TAAAATTTTAAAAAATTACAAAGAAGTTGA
Found at i:55572554 original size:16 final size:17
Alignment explanation
Indices: 55572533--55572574 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
55572523 CGTTTGGTTC
55572533 GCTGTAATAGAATAGA-
1 GCTGTAATAGAATAGAG
*
55572549 GCTGTAATGGAATAGAG
1 GCTGTAATAGAATAGAG
55572566 GC-GTAATAG
1 GCTGTAATAG
55572575 TAATTCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.24
Consensus pattern (17 bp):
GCTGTAATAGAATAGAG
Found at i:55572923 original size:120 final size:118
Alignment explanation
Indices: 55572786--55573024 Score: 442
Period size: 120 Copynumber: 2.0 Consensus size: 118
55572776 TTAATCATAT
*
55572786 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
55572851 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
55572906 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
*
55572971 ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
55573024 T
1 T
55573025 ATATAATCTA
Statistics
Matches: 117, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
118 5 0.04
119 50 0.43
120 62 0.53
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (118 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
Found at i:55572958 original size:59 final size:60
Alignment explanation
Indices: 55572778--55572960 Score: 194
Period size: 59 Copynumber: 3.0 Consensus size: 60
55572768 TAAATAATTT
* *
55572778 AATCATATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
1 AATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
* * * * * ** * * *
55572838 AATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATCATAATATATAATACT-ATAA
1 AA-TCATAAT-TTAAAATAATTATTAT-TAAATATAATTTAATAAAAATATATAAT-TTAATAA
55572899 AAT-ATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
1 AATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
55572958 AAT
1 AAT
55572961 TCTTAATATA
Statistics
Matches: 94, Mismatches: 22, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
58 3 0.03
59 36 0.38
60 17 0.18
61 35 0.37
62 3 0.03
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (60 bp):
AATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
Found at i:55573335 original size:15 final size:15
Alignment explanation
Indices: 55573311--55573348 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
55573301 AAGACATCAG
55573311 ATTCGCAGTCATAGA
1 ATTCGCAGTCATAGA
*
55573326 ATTCGTAGTCATAGA
1 ATTCGCAGTCATAGA
55573341 ATTCGCAG
1 ATTCGCAG
55573349 AAACATCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (15 bp):
ATTCGCAGTCATAGA
Found at i:55574074 original size:49 final size:49
Alignment explanation
Indices: 55574017--55574120 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
55574007 AAAAAAAAAC
* * * *
55574017 AAATTAAAATTAAGTTTAATATCATGAATTAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
55574066 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
55574115 AAATTA
1 AAATTA
55574121 TAACACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:55577642 original size:19 final size:19
Alignment explanation
Indices: 55577618--55577671 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
55577608 AATCATATCT
55577618 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55577637 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
55577656 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55577672 CTTAAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55577667 original size:38 final size:40
Alignment explanation
Indices: 55577595--55577671 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
55577585 AAATTAAATC
55577595 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
55577637 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
55577672 CTTAAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:55578269 original size:44 final size:45
Alignment explanation
Indices: 55578221--55578598 Score: 204
Period size: 44 Copynumber: 8.7 Consensus size: 45
55578211 TTGTTTATTT
* * * *
55578221 AGTCTGCCCCACTGCAATTTTAGGG-GATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* *
55578265 AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * *
55578310 GGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * * *
55578352 A-TCTG-TTCTCTACAACTTCAGAGAGATAAGA-TCTATGATT-TT-
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGAT--TTCTTG
* ** * * * * *
55578394 AATCCACTCCACTGCAATTTCAGGGAGATAGGA-T-TATTGGCTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTG
* * * *
55578438 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * *
55578480 A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGATATGTGA-TT-TT-
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-CGATTTCTTG
* * * * * * * *
55578522 AATCCGCTCCACTGCGACTTCAGAGAGATAGGA-T-TATTGGCTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTG
*
55578566 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
55578599 TTCGCCATCT
Statistics
Matches: 262, Mismatches: 49, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
39 2 0.01
40 45 0.17
41 13 0.05
42 9 0.03
43 14 0.05
44 125 0.48
45 53 0.20
46 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:55578599 original size:128 final size:128
Alignment explanation
Indices: 55578312--55578600 Score: 479
Period size: 128 Copynumber: 2.3 Consensus size: 128
55578302 CTTTCTTGGG
*** *
55578312 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGATCTGTTCTCTACAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTACAACTTCAGAGAG
* * *
55578377 ATAAGATCTATGATTTTAATCCACTCCACTGCAATTTCAGGGAGATAGGATTATTGGCTTTAA
66 ATAAGATATATGATTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
*
55578440 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTACAACTTCAGAGAG
* * *
55578505 ATAAGATATGTGATTTTAATCCGCTCCACTGCGACTTCAGAGAGATAGGATTATTGGCTTTAA
66 ATAAGATATATGATTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
55578568 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT
55578601 CGCCATCTTC
Statistics
Matches: 150, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 150 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (128 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTACAACTTCAGAGAG
ATAAGATATATGATTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
Found at i:55579039 original size:44 final size:44
Alignment explanation
Indices: 55578976--55579084 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
55578966 ATTCTACTCC
55578976 ACTGTTGCTCAGGGAGATAGGA-TTCACAATCTTCAACCTATTCT
1 ACTGTTGCTCAGGGAGATAGGACTT-ACAATCTTCAACCTATTCT
*
55579020 ACTGTTGAC-CAGGGAGATAGGACTTACAATCTTCAACCTATTCC
1 ACTGTTG-CTCAGGGAGATAGGACTTACAATCTTCAACCTATTCT
**
55579064 ACTACTG-TCTAGGGAGATAGG
1 ACTGTTGCTC-AGGGAGATAGG
55579085 GCTGGGGTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
43 1 0.02
44 54 0.93
45 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (44 bp):
ACTGTTGCTCAGGGAGATAGGACTTACAATCTTCAACCTATTCT
Found at i:55579172 original size:44 final size:44
Alignment explanation
Indices: 55579117--55579694 Score: 115
Period size: 44 Copynumber: 13.3 Consensus size: 44
55579107 GCTGTCGATG
55579117 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * ** * * * ****
55579161 CAGGGAGGCAAG-GCTGGTGTCTTCGATCC-GGTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTAT-TTTTAACCTGCTCCGCTG-CAACC
* *
55579205 CAGGAAGGCAAGATCTGCTA-TTTTAACCTACTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * ** * ** ****
55579248 CAGGGAGGCAAGGT-T--TGTCTTCGATCTGCTTTGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* *
55579290 CAGGAAGGCAAGATCTGCAATTTTTAACTTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * * ** * * * ****
55579334 TAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGTTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* * * *
55579378 CAAGAAGGCAAGATCTGCTATTTTTAACATGTTCCGCTGTAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * ** * * * * ****
55579422 CATG-AGGCAAG-GCTGGTGTCTTCGATCC-GGTTCGTTGTCGGTG
1 CAGGAAGGCAAGATCTGCTAT-TTTTAACCTGCTCCGCTG-CAACC
*
55579465 CAGGAAGGCAAGATCTGCTA-TTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * ****
55579508 CA-AAAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* * *
55579551 TAGGAAGGCAAGATCTGCAATTTTTAACTTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * * * *
55579595 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGTTGTCGACG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* * *
55579639 CAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
55579683 CAAGG-AGGCAAG
1 C-AGGAAGGCAAG
55579695 GTTGGTGTCT
Statistics
Matches: 325, Mismatches: 186, Indels: 46
0.58 0.33 0.08
Matches are distributed among these distances:
40 1 0.00
41 14 0.04
42 45 0.14
43 85 0.26
44 112 0.34
45 68 0.21
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
Found at i:55579207 original size:88 final size:88
Alignment explanation
Indices: 55579084--55579743 Score: 936
Period size: 88 Copynumber: 7.6 Consensus size: 88
55579074 AGGGAGATAG
* * * *
55579084 GGCTGGGGTCATCGATTTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
55579149 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
55579172 GGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTAACCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
55579236 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
55579259 GG-T-TTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACTTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
55579322 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
55579345 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACATGT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
55579410 TCCGCTGTAACCCA-TGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
55579432 GGCTGGTGTCTTCGATCCGGTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* **
55579496 TCCGCTACAACCCA-AAAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
55579518 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCAATTTTTAACTTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
55579583 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* ** *
55579606 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGACGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * *
55579671 TCCACTACAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
55579694 GGTTGGTGTCTTCGAACTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
55579744 TTATCTTCAC
Statistics
Matches: 505, Mismatches: 62, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
85 43 0.09
86 108 0.21
87 115 0.23
88 239 0.47
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:55579315 original size:173 final size:176
Alignment explanation
Indices: 55579084--55579743 Score: 936
Period size: 173 Copynumber: 3.8 Consensus size: 176
55579074 AGGGAGATAG
* * *
55579084 GGCTGGGGTCATCGATTTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * *
55579149 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGC
66 TCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGC
* * *
55579214 AAGATCTGCTA-TTTTAACCTACTCCGCTACAACCCAGGGAGGCAA
131 AAGATCTGCTATTTTTAACATGCTCCGCTGCAACCCAGGGAGGCAA
* * * * *
55579259 GG-T-TTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACTTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * * *
55579322 TCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAAGAAGGC
66 TCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGC
* * *
55579387 AAGATCTGCTATTTTTAACATGTTCCGCTGTAACCCA-TGAGGCAA
131 AAGATCTGCTATTTTTAACATGCTCCGCTGCAACCCAGGGAGGCAA
* * * *
55579432 GGCTGGTGTCTTCGATCCGGTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
** *
55579496 TCCGCTACAACCCA-AAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGC
66 TCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGC
* *
55579560 AAGATCTGCAATTTTTAACTTGCTCCGCTGCAACCCAGGGAGGCAA
131 AAGATCTGCTATTTTTAACATGCTCCGCTGCAACCCAGGGAGGCAA
* * *
55579606 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGACGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * * * *
55579671 TCCACTACAACCCAAGGAGGCAAGGTTGGTGTCTTCGAACTGCTTCGCTGTTGGTGCAGGAAGGC
66 TCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGC
55579736 AAGATCTG
131 AAGATCTG
55579744 TTATCTTCAC
Statistics
Matches: 429, Mismatches: 50, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
173 210 0.49
174 99 0.23
175 68 0.16
176 52 0.12
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (176 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGC
AAGATCTGCTATTTTTAACATGCTCCGCTGCAACCCAGGGAGGCAA
Found at i:55579400 original size:261 final size:261
Alignment explanation
Indices: 55579084--55579743 Score: 1045
Period size: 261 Copynumber: 2.5 Consensus size: 261
55579074 AGGGAGATAG
* * * * *
55579084 GGCTGGGGTCATCGATTTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGATGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
55579149 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGC
66 TCCGCTGCAACCCA-GGAGGCAAGGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGC
** *
55579214 AAGATCTGCTATTTTAACCTACTCCGCTACAACCCAGGGAGGCAAGG-T-TTGTCTTCGATCTGC
130 AAGATCTGCTATTTTAACCTACTCCGCTACAACCCA-AAAGGCAAGGCTGGTGTCTTCGATCTGC
* *
55579277 TTTGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACTTGCTCCGCTGCAACCTAGGGAGG
194 TTCGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACTTGCTCCGCTGCAACCCAGGGAGG
55579342 CAA
259 CAA
* * *
55579345 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACATGT
1 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGATGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
* * *
55579410 TCCGCTGTAACCCATGAGGCAAGGCTGGTGTCTTCGATCCGGTTCGTTGTCGGTGCAGGAAGGCA
66 TCCGCTGCAACCCAGGAGGCAAGGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGCA
*
55579475 AGATCTGCTATTTTAACCTGCTCCGCTACAACCCAAAAGGCAAGGCTGGTGTCTTCGATCTGCTT
131 AGATCTGCTATTTTAACCTACTCCGCTACAACCCAAAAGGCAAGGCTGGTGTCTTCGATCTGCTT
*
55579540 CGCTGTCGGTGTAGGAAGGCAAGATCTGCAATTTTTAACTTGCTCCGCTGCAACCCAGGGAGGCA
196 CGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACTTGCTCCGCTGCAACCCAGGGAGGCA
55579605 A
261 A
*
55579606 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGACGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGATGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
* * * * * * *
55579671 TCCACTACAACCCAAGGAGGCAAGGTTGGTGTCTTCGAACTGCTTCGCTGTTGGTGCAGGAAGGC
66 TCCGCTGCAACCC-AGGAGGCAAGGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGC
55579736 AAGATCTG
130 AAGATCTG
55579744 TTATCTTCAC
Statistics
Matches: 364, Mismatches: 32, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
259 8 0.02
260 84 0.23
261 220 0.60
262 52 0.14
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (261 bp):
GGCTGGTGTCTTCGATCTGCTTCGTTGTCGATGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGAGGCAAGGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGCA
AGATCTGCTATTTTAACCTACTCCGCTACAACCCAAAAGGCAAGGCTGGTGTCTTCGATCTGCTT
CGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACTTGCTCCGCTGCAACCCAGGGAGGCA
A
Found at i:55586160 original size:23 final size:22
Alignment explanation
Indices: 55586102--55586160 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
55586092 AATAAAAATA
*
55586102 AAAACATATGTATAATATATAT
1 AAAACATATATATAATATATAT
* * *
55586124 ATAAGCATACATATACTATATAT
1 A-AAACATATATATAATATATAT
55586147 AAAACAATATATAT
1 AAAAC-ATATATAT
55586161 TACATAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (22 bp):
AAAACATATATATAATATATAT
Found at i:55586690 original size:23 final size:22
Alignment explanation
Indices: 55586647--55586742 Score: 71
Period size: 19 Copynumber: 4.6 Consensus size: 22
55586637 AAAATGTATC
* *
55586647 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
55586668 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
55586691 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
55586710 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
55586729 TACATATCATATCT
1 TACAAATCATATCT
55586743 AAGATTGCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
19 37 0.57
21 3 0.05
22 15 0.23
23 10 0.15
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:55586707 original size:19 final size:19
Alignment explanation
Indices: 55586683--55586755 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
55586673 AATCATATCT
55586683 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
55586702 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55586721 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
55586740 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55586756 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55587357 original size:30 final size:29
Alignment explanation
Indices: 55587319--55587381 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
55587309 TAGGTATATG
*
55587319 TATAATTGAGCTAAAATTAAGATTT-CATT
1 TATAATTGAACTAAAATTAA-ATTTACATT
* *
55587348 TATATATTGAATTAAAATTAAATTTATATT
1 TATA-ATTGAACTAAAATTAAATTTACATT
55587378 TATA
1 TATA
55587382 CAATTGCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (29 bp):
TATAATTGAACTAAAATTAAATTTACATT
Done.