Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 159 of 320
Found at i:52491856 original size:12 final size:12
Alignment explanation
Indices: 52491841--52491880 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
52491831 AAAAGAAAAA
*
52491841 GAAAATGAGATT
1 GAAAAAGAGATT
*
52491853 GAAAAAGAGAAT
1 GAAAAAGAGATT
*
52491865 GAAAAAGAGTTT
1 GAAAAAGAGATT
52491877 GAAA
1 GAAA
52491881 GAGAAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:52491856 original size:24 final size:24
Alignment explanation
Indices: 52491811--52491891 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
52491801 AAAAGCCTTT
* * **
52491811 GAAAAACAAAAAGAAAAAGAAAAA
1 GAAAAAGAAAAAGAGATTGAAAAA
*
52491835 GAAAAAGAAAATGAGATTGAAAAA
1 GAAAAAGAAAAAGAGATTGAAAAA
* * * *
52491859 GAGAATGAAAAAGAGTTTGAAAGA
1 GAAAAAGAAAAAGAGATTGAAAAA
52491883 GAAAAAGAA
1 GAAAAAGAA
52491892 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.69, C:0.01, G:0.21, T:0.09
Consensus pattern (24 bp):
GAAAAAGAAAAAGAGATTGAAAAA
Found at i:52496147 original size:46 final size:46
Alignment explanation
Indices: 52496078--52496208 Score: 190
Period size: 46 Copynumber: 2.8 Consensus size: 46
52496068 GATATTTGGG
* *
52496078 CATCCGAGCTTGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
**
52496124 TGTCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** * *
52496170 CATTTGAGCTCGATGAGTTGAGTCCTAGTTCACTTATGG
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52496209 GCGGGTTACA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:52500416 original size:19 final size:20
Alignment explanation
Indices: 52500380--52500417 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52500370 TATCTTGCTC
*
52500380 AATTCAGCTCATTTGAGCTT
1 AATTCAGCTCAGTTGAGCTT
52500400 AATTCAGCTC-GTTGAGCT
1 AATTCAGCTCAGTTGAGCT
52500418 AGATTTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
AATTCAGCTCAGTTGAGCTT
Found at i:52507864 original size:27 final size:27
Alignment explanation
Indices: 52507833--52507884 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
52507823 ACAAGTGAGG
52507833 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
52507860 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
52507885 ATGTGAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:52514006 original size:17 final size:17
Alignment explanation
Indices: 52513986--52514021 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52513976 ACCTATAAGC
52513986 ATAATTAAACAAGTTAA
1 ATAATTAAACAAGTTAA
52514003 ATAATTAAACAAGTTAA
1 ATAATTAAACAAGTTAA
52514020 AT
1 AT
52514022 GGCTGTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
ATAATTAAACAAGTTAA
Found at i:52514804 original size:24 final size:23
Alignment explanation
Indices: 52514751--52514827 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
52514741 ATTAATTAGA
**
52514751 AAATGGTATTTGGTTTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
** *
52514774 ATTTGGTATTTGGGAATTGGTACT
1 AAATGGTATTT-GGAATTGGTACG
** *
52514798 AAATGGTA-AAGGATTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
52514820 AAATGGTA
1 AAATGGTA
52514828 ATGGTTCAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 18 0.43
23 9 0.21
24 15 0.36
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.38
Consensus pattern (23 bp):
AAATGGTATTTGGAATTGGTACG
Found at i:52516599 original size:18 final size:17
Alignment explanation
Indices: 52516578--52516634 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
52516568 TTTTTCAAAC
52516578 TCATTTTCTTTTCTTTCT
1 TCATTTTCTTTTCTTT-T
* * *
52516596 TCATTCTCACTCTCTTTT
1 TCATTTTC-TTTTCTTTT
*
52516614 TCAATTTTCTTTTCTTGT
1 TC-ATTTTCTTTTCTTTT
52516632 TCA
1 TCA
52516635 CATTCTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
17 1 0.03
18 18 0.60
19 11 0.37
ACGTcount: A:0.11, C:0.25, G:0.02, T:0.63
Consensus pattern (17 bp):
TCATTTTCTTTTCTTTT
Found at i:52521714 original size:25 final size:25
Alignment explanation
Indices: 52521668--52521715 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
52521658 CTATATATTG
* **
52521668 AAAAAAATAAAAGAATTCAAAAATT
1 AAAAAAATAAAAAAAAACAAAAATT
*
52521693 AAAAAAATAAAAAAAAAGAAAAA
1 AAAAAAATAAAAAAAAACAAAAA
52521716 GAAGTGATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.12
Consensus pattern (25 bp):
AAAAAAATAAAAAAAAACAAAAATT
Found at i:52522115 original size:10 final size:10
Alignment explanation
Indices: 52522102--52522147 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
52522092 AGCTCACTTG
52522102 AGCTCGTTTT
1 AGCTCGTTTT
* *
52522112 AGCTTGTTTG
1 AGCTCGTTTT
*
52522122 AGCTCGAATTT
1 AGCTCG-TTTT
52522133 AGCTCGTTTT
1 AGCTCGTTTT
52522143 AGCTC
1 AGCTC
52522148 ATTCCTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:52522135 original size:21 final size:20
Alignment explanation
Indices: 52522099--52522147 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
52522089 ATCAGCTCAC
* *
52522099 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGATTTAGCTCGT
52522119 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
52522140 TTTAGCTC
1 TTGAGCTC
52522148 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:52524861 original size:15 final size:15
Alignment explanation
Indices: 52524825--52524866 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
52524815 TTTTTAACTT
*
52524825 GATTTTTTTTTGGTC
1 GATTTTTTTTTGCTC
52524840 -ACCTTTTTTTTTGCTC
1 GA--TTTTTTTTTGCTC
52524856 GATTTTTTTTT
1 GATTTTTTTTT
52524867 CACTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 1 0.04
15 9 0.39
16 12 0.52
17 1 0.04
ACGTcount: A:0.07, C:0.12, G:0.12, T:0.69
Consensus pattern (15 bp):
GATTTTTTTTTGCTC
Found at i:52524875 original size:14 final size:14
Alignment explanation
Indices: 52524858--52524923 Score: 71
Period size: 15 Copynumber: 4.6 Consensus size: 14
52524848 TTTTGCTCGA
*
52524858 TTTTTTTTTC-ACT
1 TTTTTTTTTCAATT
*
52524871 TTTTTTTTTGAATT
1 TTTTTTTTTCAATT
*
52524885 TTTTTTTCAATCAATT
1 TTTTTTT--TTCAATT
52524901 TTTTTTTTTCGAATT
1 TTTTTTTTTC-AATT
52524916 TTTTTTTT
1 TTTTTTTT
52524924 GATTTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 9 0.20
14 11 0.25
15 12 0.27
16 12 0.27
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCAATT
Found at i:52524928 original size:12 final size:12
Alignment explanation
Indices: 52524858--52524933 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 12
52524848 TTTTGCTCGA
*
52524858 TTTTTTTTTCACT
1 TTTTTTTTTGA-T
52524871 TTTTTTTTTGAAT
1 TTTTTTTTTG-AT
*
52524884 TTTTTTTTCAATCAATT
1 TTTTTTTT---T-GA-T
52524901 TTTTTTTTTCGAAT
1 TTTTTTTTT-G-AT
52524915 TTTTTTTTTGAT
1 TTTTTTTTTGAT
52524927 TTTTTTT
1 TTTTTTT
52524934 GTTACTCCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
12 9 0.17
13 19 0.36
14 13 0.25
15 1 0.02
16 2 0.04
17 9 0.17
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTGAT
Found at i:52526558 original size:20 final size:19
Alignment explanation
Indices: 52526535--52526599 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
52526525 AAGCTCAAAC
52526535 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
52526555 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
52526575 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
52526595 GAGCT
1 GAGCT
52526600 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:52527044 original size:20 final size:21
Alignment explanation
Indices: 52526990--52527037 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
52526980 AAATGAAATG
*
52526990 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTAAAATCA
52527011 AGCTCAAACGAGCTAAAA-CA
1 AGCTCAAACGAGCTAAAATCA
52527031 AGCTCAA
1 AGCTCAA
52527038 GTGAGCTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (21 bp):
AGCTCAAACGAGCTAAAATCA
Found at i:52528693 original size:20 final size:20
Alignment explanation
Indices: 52528670--52528716 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
52528660 GGGTTAAGAT
*
52528670 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
52528690 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
52528710 TGAGCTG
1 TGAGCTG
52528717 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:52530441 original size:48 final size:48
Alignment explanation
Indices: 52530386--52530491 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
52530376 TTGTCTTTTC
*
52530386 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
52530434 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
52530482 TTTCTTTTTC
1 TTTCTTTTTC
52530492 TATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:52531739 original size:30 final size:30
Alignment explanation
Indices: 52531705--52531801 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
52531695 AGCTCACTCC
52531705 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
52531735 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
52531765 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
52531795 TAGCTCA
1 TAGCTCA
52531802 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:52534922 original size:20 final size:20
Alignment explanation
Indices: 52534899--52534945 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
52534889 GGGTTAAGAT
*
52534899 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
52534919 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
52534939 TGAGCTG
1 TGAGCTG
52534946 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:52536912 original size:95 final size:94
Alignment explanation
Indices: 52536813--52536987 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 94
52536803 CTCATTTCTG
* **
52536813 TGCCGATGCCATGACCCAGACATCGTCTTACACTGGCTCTCATAATA-TGGCTGAAGCATGTTCA
1 TGCCGATGCCATGACCCAGACATCGTCTTACACTAGCTCTCATAA-AGTGGCAAAAGCATG-TCA
*
52536877 GAGACATGTCTTACACTAGCCCTCGTCTGGA
64 CAGACATGTCTTACACTAGCCCTCGTCTGGA
* * *
52536908 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAAGTGGCAAAAGCATGTCCCA
1 TGCCGATGCCATGACCCAGACATCGTCTTACACTAGCTCTCATAAAGTGGCAAAAGCATGTCACA
52536973 GACATGTCTTACACT
66 GACATGTCTTACACT
52536988 GGCGCACAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
94 19 0.26
95 53 0.74
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (94 bp):
TGCCGATGCCATGACCCAGACATCGTCTTACACTAGCTCTCATAAAGTGGCAAAAGCATGTCACA
GACATGTCTTACACTAGCCCTCGTCTGGA
Found at i:52538022 original size:29 final size:30
Alignment explanation
Indices: 52537984--52538051 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
52537974 GCCTCAAGTA
52537984 GCCAAAGCTAG-TTAAATCACACACTTAGC
1 GCCAAAGCTAGTTTAAATCACACACTTAGC
** *
52538013 GCCAAAGCTAGTTTAAATTGCACACTTAGT
1 GCCAAAGCTAGTTTAAATCACACACTTAGC
52538043 GCCAAAGCT
1 GCCAAAGCT
52538052 TCCGATTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (30 bp):
GCCAAAGCTAGTTTAAATCACACACTTAGC
Found at i:52538662 original size:30 final size:30
Alignment explanation
Indices: 52538567--52538663 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
52538557 AGCTCACTCC
* * *
52538567 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
52538597 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
52538627 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
52538657 TAGCTCA
1 TAGCTCA
52538664 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:52540521 original size:12 final size:10
Alignment explanation
Indices: 52540517--52540566 Score: 73
Period size: 10 Copynumber: 4.7 Consensus size: 10
52540507 TTTTGAAACT
52540517 TTTTTTTGAA
1 TTTTTTTGAA
52540527 TTTTTTTCGAA
1 TTTTTTT-GAA
52540538 TTTTTTTTCGAA
1 -TTTTTTT-GAA
52540550 TTTTTTTGAA
1 TTTTTTTGAA
52540560 TTTTTTT
1 TTTTTTT
52540567 TATACTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 17 0.45
11 10 0.26
12 11 0.29
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:52540567 original size:12 final size:11
Alignment explanation
Indices: 52540502--52540567 Score: 89
Period size: 11 Copynumber: 5.8 Consensus size: 11
52540492 TGCACAAATC
52540502 ATTTTTTTTGAA
1 ATTTTTTTTG-A
52540514 ACTTTTTTTTGA
1 A-TTTTTTTTGA
*
52540526 ATTTTTTTCGA
1 ATTTTTTTTGA
52540537 ATTTTTTTTCGA
1 ATTTTTTTT-GA
52540549 A-TTTTTTTGA
1 ATTTTTTTTGA
52540559 ATTTTTTTT
1 ATTTTTTTT
52540568 ATACTTGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
10 3 0.06
11 31 0.63
12 6 0.12
13 9 0.18
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.70
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:52542023 original size:10 final size:10
Alignment explanation
Indices: 52542008--52542073 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 10
52541998 AATGTCATAT
52542008 TTCAAAAAAA
1 TTCAAAAAAA
52542018 TTCAAAAAAA
1 TTCAAAAAAA
*
52542028 TTTGAAAAAAAAAA
1 -TT---CAAAAAAA
52542042 TTCGAAAAAAAA
1 TTC--AAAAAAA
52542054 TTCAAAAAAAA
1 TTC-AAAAAAA
52542065 TTCAAAAAA
1 TTCAAAAAA
52542074 CAAGTAACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
10 16 0.33
11 13 0.27
12 10 0.21
13 2 0.04
14 7 0.15
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.20
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:52542027 original size:11 final size:11
Alignment explanation
Indices: 52542011--52542073 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
52542001 GTCATATTTC
52542011 AAAAAAATTCA
1 AAAAAAATTCA
* *
52542022 AAAAAATTTGAAA
1 AAAAAAATT--CA
52542035 AAAAAAATTCGA
1 AAAAAAATTC-A
52542047 AAAAAAATTCA
1 AAAAAAATTCA
52542058 AAAAAAATTCA
1 AAAAAAATTCA
52542069 AAAAA
1 AAAAA
52542074 CAAGTAACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
11 25 0.56
12 11 0.24
13 9 0.20
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:52542040 original size:14 final size:14
Alignment explanation
Indices: 52542021--52542064 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 14
52542011 AAAAAAATTC
*
52542021 AAAAAAATTTGAAA
1 AAAAAAATTCGAAA
52542035 AAAAAAATTCG--A
1 AAAAAAATTCGAAA
52542047 AAAAAAATTC-AAA
1 AAAAAAATTCGAAA
52542060 AAAAA
1 AAAAA
52542065 TTCAAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 11 0.41
13 6 0.22
14 10 0.37
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:52542454 original size:46 final size:46
Alignment explanation
Indices: 52542387--52542557 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
52542377 AACCCGCCCC
** *
52542387 TAAGTGAACTCGGACTCAACTCAACGAACTCGAGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCATTTGCATCCA
* *
52542433 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GA-G-C-ATTTGCATCCA
* * * *
52542481 TCA-CGAACTCAGACTCAACTCAACGAGTTCG-GACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAG-CATTTGCATCCA
*
52542526 TAGGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
52542558 GATGCTCAAC
Statistics
Matches: 102, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 5 0.05
44 3 0.03
45 1 0.01
46 56 0.55
47 27 0.26
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCATTTGCATCCA
Found at i:52542500 original size:93 final size:93
Alignment explanation
Indices: 52542392--52542562 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
52542382 GCCCCTAAGT
* * *
52542392 GAACTCGGACTCAACTCAACGAACTC-GAGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAGACTCAACTCAACGAACTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52542456 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
** *
52542485 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52542550 CGAGTTCGGATGC
66 CGAGTTCGGATGC
52542563 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 69 0.97
94 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:52547870 original size:10 final size:10
Alignment explanation
Indices: 52547857--52547905 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
52547847 AGCTCACTTG
52547857 AGCTCGTTTT
1 AGCTCGTTTT
*
52547867 AGCTCGTTTG
1 AGCTCGTTTT
*
52547877 AGCTCGAATTT
1 AGCTCG-TTTT
*
52547888 AGCTCGTTTC
1 AGCTCGTTTT
52547898 AGCTCGTT
1 AGCTCGTT
52547906 CCTTTTTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:52547890 original size:21 final size:20
Alignment explanation
Indices: 52547854--52547903 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
52547844 ATCAGCTCAC
*
52547854 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
52547874 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
52547895 TTCAGCTCG
1 TTGAGCTCG
52547904 TTCCTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:52552348 original size:20 final size:21
Alignment explanation
Indices: 52552294--52552341 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
52552284 AAATGAAATG
*
52552294 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTAAAATCA
52552315 AGCTCAAACGAGCTAAAA-CA
1 AGCTCAAACGAGCTAAAATCA
52552335 AGCTCAA
1 AGCTCAA
52552342 GTGAGCTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (21 bp):
AGCTCAAACGAGCTAAAATCA
Found at i:52553868 original size:10 final size:10
Alignment explanation
Indices: 52553853--52553914 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
52553843 TTTGAACCAT
*
52553853 TACCAATTCG
1 TACCAATTCA
*
52553863 TACCAAATACCA
1 TACC-AAT-TCA
*
52553875 TACCATTTCA
1 TACCAATTCA
52553885 TACCAATTCCA
1 TACCAATT-CA
* *
52553896 TACCATTTCG
1 TACCAATTCA
52553906 TACCAATTC
1 TACCAATTC
52553915 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:52553898 original size:21 final size:21
Alignment explanation
Indices: 52553853--52553915 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
52553843 TTTGAACCAT
* *
52553853 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
52553875 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
52553896 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
52553916 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:52556139 original size:47 final size:44
Alignment explanation
Indices: 52555845--52556200 Score: 180
Period size: 47 Copynumber: 7.6 Consensus size: 44
52555835 TTGCCAATAC
* **
52555845 CATGTCCCAGACATGGTCTTACACTGGCTCTCATACATGCGTGCTAATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTC-T-C-TG-ATGCCGATG
* * * *
52555894 CATGTCCCAGACATGTCTTACACTAGCACAACTCTTA-GCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTC-TCTCTGATGCCGATG
* * * * * *
52555938 CGTGTCCCAAACACGTCTTTCACTGGCTATCTCTGTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGC--TCTCTCT-GATGCCGATG
* * * *
52555985 CATGTCCTAGACATATCTTACTCTGGCACTCATTTCTG-TGCCGATG
1 CATGTCCCAGACATGTCTTACACTGG--CTC-TCTCTGATGCCGATG
* * * *
52556031 CCATGACCCAGACATCGTCTTACACTGGCTCTCATAAT-ATGGCTGAAG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTC-T-CTGAT-GCCGATG
** * *
52556079 CATGTTCAGAGACATGTCTTACACTAGCCCTCGTCTGGATGCCGATG
1 CATG-TCCCAGACATGTCTTACACTGGCTCTC-TCT-GATGCCGATG
* ** ** *
52556126 CCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-AAAGTGGCAAAAG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTC-TCTGA-T-GCCGATG
52556174 CATGTCCCAGACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
52556201 GCACAAATCA
Statistics
Matches: 233, Mismatches: 53, Indels: 45
0.70 0.16 0.14
Matches are distributed among these distances:
44 27 0.12
45 4 0.02
46 28 0.12
47 92 0.39
48 66 0.28
49 16 0.07
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCTCTGATGCCGATG
Found at i:52556175 original size:95 final size:94
Alignment explanation
Indices: 52556023--52556197 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 94
52556013 CTCATTTCTG
* ** *
52556023 TGCCGATGCCATGACCCAGACATCGTCTTACACTGGCTCTCATAATATGGCTGAAGCATGTTCAG
1 TGCCGATGCCATGACCCAGACATCGTCTTACACTAGCTCTCATAATATGGCAAAAGCATG-TCAC
52556088 AGACATGTCTTACACTAGCCCTCGTCTGGA
65 AGACATGTCTTACACTAGCCCTCGTCTGGA
* * *
52556118 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAA-AGTGGCAAAAGCATGTCCC
1 TGCCGATGCCATGACCCAGACATCGTCTTACACTAGCTCTCATAATA-TGGCAAAAGCATGTCAC
52556182 AGACATGTCTTACACT
65 AGACATGTCTTACACT
52556198 GGCGCACAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
94 19 0.26
95 53 0.74
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (94 bp):
TGCCGATGCCATGACCCAGACATCGTCTTACACTAGCTCTCATAATATGGCAAAAGCATGTCACA
GACATGTCTTACACTAGCCCTCGTCTGGA
Found at i:52559842 original size:23 final size:22
Alignment explanation
Indices: 52559791--52559842 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
52559781 CCTCGTCTTT
*
52559791 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
52559813 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
52559836 TTCTTTT
1 TTCTTTT
52559843 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:52564952 original size:30 final size:29
Alignment explanation
Indices: 52564900--52564967 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 29
52564890 GCCTCAAGTA
52564900 GCCAAAGCTAGTTAAATCGCACACTTAGT
1 GCCAAAGCTAGTTAAATCGCACACTTAGT
*
52564929 GCCAAAGCTAGTTTAAATTGCACACTTAGT
1 GCCAAAGCTAG-TTAAATCGCACACTTAGT
52564959 GCCAAAGCT
1 GCCAAAGCT
52564968 TCCGATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (29 bp):
GCCAAAGCTAGTTAAATCGCACACTTAGT
Found at i:52565578 original size:30 final size:30
Alignment explanation
Indices: 52565483--52565579 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
52565473 AGCTCACTCC
* * *
52565483 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
52565513 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
52565543 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
52565573 TAGCTCA
1 TAGCTCA
52565580 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:52567447 original size:13 final size:12
Alignment explanation
Indices: 52567416--52567485 Score: 81
Period size: 13 Copynumber: 5.6 Consensus size: 12
52567406 GCACAAATCA
52567416 TTTTTTTTGAAACT
1 TTTTTTTTG-AA-T
52567430 TTTTTTTTGAAT
1 TTTTTTTTGAAT
52567442 TGTTTTTTTCGAAT
1 T-TTTTTTT-GAAT
52567456 TTTTTTTCTGAA-
1 TTTTTTT-TGAAT
52567468 -TTTTTTTGAAT
1 TTTTTTTTGAAT
52567479 TTTTTTT
1 TTTTTTT
52567486 ATACTTGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.08
11 6 0.12
12 8 0.16
13 18 0.35
14 15 0.29
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.71
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:52567447 original size:14 final size:13
Alignment explanation
Indices: 52567416--52567485 Score: 74
Period size: 14 Copynumber: 5.5 Consensus size: 13
52567406 GCACAAATCA
*
52567416 TTTTTTTTGAAACT
1 TTTTTTTTG-AATT
52567430 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
52567443 GTTTTTTTCGAATT
1 -TTTTTTTTGAATT
*
52567457 TTTTTTCTGAA--
1 TTTTTTTTGAATT
52567468 -TTTTTTTGAATT
1 TTTTTTTTGAATT
52567480 TTTTTT
1 TTTTTT
52567486 ATACTTGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.19
13 17 0.36
14 21 0.45
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.71
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:52569190 original size:30 final size:30
Alignment explanation
Indices: 52569104--52569201 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
52569094 TTAAACTAAA
* *
52569104 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
52569134 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
52569164 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
52569194 ATGAGCTA
1 ATGAGCTA
52569202 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:52570493 original size:20 final size:20
Alignment explanation
Indices: 52570470--52570517 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
52570460 AGCTTCGTCT
*
52570470 AGCTCAACTCAGCTTATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
52570490 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
52570510 AGCTCAAC
1 AGCTCAAC
52570518 CTAGCTTACC
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:52573044 original size:24 final size:23
Alignment explanation
Indices: 52573011--52573091 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
52573001 AAGAAATGAA
52573011 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAA-AGATTGAGAG
* *
52573035 TGAAAAAGAAAATAAGATTGA-AA
1 AGAAAAAGAAAA-AAGATTGAGAG
* * *
52573058 AGAGAATGAAAAAAAGTTTGAGAG
1 AGAAAAAG-AAAAAAGATTGAGAG
52573082 AGAAAAAGAA
1 AGAAAAAGAA
52573092 TGTGACAAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
23 15 0.33
24 29 0.64
25 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.12
Consensus pattern (23 bp):
AGAAAAAGAAAAAAGATTGAGAG
Found at i:52579209 original size:33 final size:33
Alignment explanation
Indices: 52579171--52579233 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
52579161 GATTACTCAC
52579171 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
52579204 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
52579234 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:52579260 original size:21 final size:21
Alignment explanation
Indices: 52579231--52579286 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
52579221 CAAGCTCTCT
*
52579231 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
52579252 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
52579273 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
52579287 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:52579279 original size:14 final size:14
Alignment explanation
Indices: 52579230--52579286 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
52579220 TCAAGCTCTC
52579230 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
52579243 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
52579257 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
52579271 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
52579285 TT
1 TT
52579287 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:52579323 original size:41 final size:39
Alignment explanation
Indices: 52579228--52579367 Score: 124
Period size: 41 Copynumber: 3.5 Consensus size: 39
52579218 TTTCAAGCTC
* *
52579228 TCTTTCAATTTCTTTTTTCGCTTTTTCTTTTTCAATTTTCTTT
1 TCTTTCAATTTC-TTTTT--CTTCTACTTTTTC-ATTTTCTTT
*
52579271 TC-TTCATTTTCTTTTTC-TCTCACTTTTTCGATTTT-TTT
1 TCTTTCAATTTCTTTTTCTTCT-ACTTTTTC-ATTTTCTTT
* * * *
52579309 TCTTTTGCAATTTCTTTTTCTTCTTCGTTTTCTTTTTGTTT
1 TC-TTT-CAATTTCTTTTTCTTCTACTTTTTCATTTTCTTT
52579350 TCTTTCAATTTCTTTTTC
1 TCTTTCAATTTCTTTTTC
52579368 AATCTCTTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
38 7 0.08
39 26 0.31
40 9 0.11
41 28 0.34
42 11 0.13
43 2 0.02
ACGTcount: A:0.08, C:0.19, G:0.04, T:0.69
Consensus pattern (39 bp):
TCTTTCAATTTCTTTTTCTTCTACTTTTTCATTTTCTTT
Found at i:52579367 original size:6 final size:6
Alignment explanation
Indices: 52579248--52579354 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
52579238 TCTTTTTTCG
* * * **
52579248 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
52579299 CGATTT -TTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
52579346 -GTTTT CTTT
1 CTTTTT CTTT
52579355 CAATTTCTTT
Statistics
Matches: 70, Mismatches: 27, Indels: 8
0.67 0.26 0.08
Matches are distributed among these distances:
5 7 0.10
6 51 0.73
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:52579385 original size:39 final size:41
Alignment explanation
Indices: 52579302--52579386 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 41
52579292 ACTTTTTCGA
* *
52579302 TTTT-TTTTCTTTTGCAATTTCTTTTTCTTCTTCGTTTTCT
1 TTTTGTTTTCTTTTGCAATTTCTTTTTCATCTTCGTTTTCC
52579342 TTTTGTTTTC-TTT-CAATTTCTTTTTCAATC-TC-TTTCTCC
1 TTTTGTTTTCTTTTGCAATTTCTTTTTC-ATCTTCGTTT-TCC
52579381 TTTTGT
1 TTTTGT
52579387 CGCTCAATGG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 3 0.08
39 23 0.57
40 9 0.22
41 5 0.12
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.69
Consensus pattern (41 bp):
TTTTGTTTTCTTTTGCAATTTCTTTTTCATCTTCGTTTTCC
Found at i:52584514 original size:24 final size:25
Alignment explanation
Indices: 52584487--52584540 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
52584477 ATGAGTGATA
*
52584487 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
52584511 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
52584535 AAAAAA
1 AAAAAA
52584541 AGAATTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:52599733 original size:47 final size:46
Alignment explanation
Indices: 52599526--52599832 Score: 216
Period size: 47 Copynumber: 6.5 Consensus size: 46
52599516 TTGCCGATTC
* *
52599526 CATGTCCCAGACATGGTCTTACACTTGCTATCATCATCGAGGCCAATG
1 CATGTCCCAGACAT-GTCTTACACTGGC-ATCATCATCGAGGCCGATG
* * * * **
52599574 CCATGTCCGAGACATGGTCTTACACTAGCTCTCGTAT-ATACG-TGATGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGC-ATC--ATCAT-CGAGGCCGATG
* * ** * *
52599624 CATGTCCCAAACATGTCTTACACTAGCA-CAATTTTC-A-GCCAATA
1 CATGTCCCAGACATGTCTTACACTGGCATC-ATCATCGAGGCCGATG
* * **
52599668 CATGTCCC-GAACAAGTCTTACACTGGCTATCATCGTCGAGGTTGATG
1 CATGTCCCAG-ACATGTCTTACACTGGC-ATCATCATCGAGGCCGATG
* *
52599715 CATGTCCCAGACATGTCTTACACTGGCACTCATC-TCTACGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCA-TCATCATCGAGGCCGATG
* * *
52599761 CCATGTCCCAGACATGGTCTTACACTGGCACTCATAAT-GTGGTCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCA-TCATCATCGAGGCCGATG
52599809 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
52599833 AGCACACAAG
Statistics
Matches: 208, Mismatches: 35, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
44 26 0.12
45 8 0.04
46 23 0.11
47 60 0.29
48 39 0.19
49 42 0.20
50 6 0.03
51 4 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCATCATCATCGAGGCCGATG
Found at i:52599814 original size:94 final size:93
Alignment explanation
Indices: 52599526--52599837 Score: 298
Period size: 94 Copynumber: 3.3 Consensus size: 93
52599516 TTGCCGATTC
* * * *
52599526 CATGTCCCAGACATGGTCTTACACTTGCTA-TCATCATCGAGGCCAATGCCATGTCCGAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATC-TCTACGCCAATGCCATGTCCCAGACATG
* * * *
52599590 GTCTTACACTAGCTCTCGTATATACGTGATGATG
63 GTCTTACACTGGCACTC--ATA-ATGTGGTGATG
* * * * *
52599624 CATGTCCCAAACATGTCTTACACTAGCAC-AAT-T-TTCAGCCAAT-ACATGTCCC-GAACA-AG
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTAC-GCCAATGCCATGTCCCAG-ACATGG
** *
52599683 TCTTACACTGGCTA-TCATCGTCGAGGTTGATG
64 TCTTACACTGGC-ACTCATAAT-GTGG-TGATG
* *
52599715 CATGTCCCAGACATGTCTTACACTGGCACTCATCTCTACGCCGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTACGCCAATGCCATGTCCCAGACATGGTC
52599780 TTACACTGGCACTCATAATGTGGTCGATG
66 TTACACTGGCACTCATAATGTGGT-GATG
52599809 CATGTCCCAGACATGTCTTACACTAGCAC
1 CATGTCCCAGACATGTCTTACACTAGCAC
52599838 ACAAGTAATC
Statistics
Matches: 173, Mismatches: 27, Indels: 32
0.75 0.12 0.14
Matches are distributed among these distances:
90 4 0.02
91 32 0.18
92 17 0.10
93 17 0.10
94 56 0.32
95 19 0.11
96 3 0.02
97 12 0.07
98 13 0.08
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTACGCCAATGCCATGTCCCAGACATGGTC
TTACACTGGCACTCATAATGTGGTGATG
Found at i:52600571 original size:12 final size:12
Alignment explanation
Indices: 52600554--52600578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52600544 CAAAAATGTA
52600554 AAAATCATCAAG
1 AAAATCATCAAG
52600566 AAAATCATCAAG
1 AAAATCATCAAG
52600578 A
1 A
52600579 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:52603926 original size:48 final size:48
Alignment explanation
Indices: 52603805--52603978 Score: 233
Period size: 48 Copynumber: 3.5 Consensus size: 48
52603795 TAAGGTCGCA
* * * * *
52603805 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCA-G
52603856 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCAG
52603904 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTC-G
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCAG
* *
52603951 CATGTGTAGTACTATGTGCACGCTACTA
1 --TGTGTAGTACTAAGTGCAGGCTACTA
52603979 TGCATATCAG
Statistics
Matches: 114, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
47 1 0.01
48 47 0.41
49 29 0.25
50 1 0.01
51 36 0.32
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCAG
Found at i:52608551 original size:8 final size:9
Alignment explanation
Indices: 52608529--52608558 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
52608519 ACTGAGGAAT
52608529 TGGGGGAGG
1 TGGGGGAGG
52608538 TGGGGGAGG
1 TGGGGGAGG
52608547 TGGGGGAGG
1 TGGGGGAGG
52608556 TGG
1 TGG
52608559 AGTGTTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.77, T:0.13
Consensus pattern (9 bp):
TGGGGGAGG
Found at i:52611422 original size:3 final size:3
Alignment explanation
Indices: 52611414--52611439 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52611404 TTATAACCTC
52611414 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
52611440 TTCCCCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:52612963 original size:44 final size:43
Alignment explanation
Indices: 52612883--52612979 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 43
52612873 TCCCAGACAG
* *
52612883 GGTCTTACAC-TAAATCAAGTATGATGCCAACATCCCAAAGGT
1 GGTCTTACACGTAAATCAAGTACGATGCCAACATCCCAAACGT
* *
52612925 GGTCTTACACGTAAATCATAAGT-CGATGCCAACGTCCCAGACGT
1 GGTCTTACACGTAAATC--AAGTACGATGCCAACATCCCAAACGT
52612969 GGTCTTACACG
1 GGTCTTACACG
52612980 ATAACACATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 10 0.21
43 6 0.12
44 28 0.58
45 4 0.08
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAAGTACGATGCCAACATCCCAAACGT
Found at i:52614555 original size:27 final size:27
Alignment explanation
Indices: 52614525--52614611 Score: 108
Period size: 27 Copynumber: 3.2 Consensus size: 27
52614515 GTGACGAAGT
52614525 CACCAGATACAAATATTGTGGCAGAGC
1 CACCAGATACAAATATTGTGGCAGAGC
*
52614552 CACCA-AAACAGATATATT-TGGCAGAGC
1 CACCAGATACA-A-ATATTGTGGCAGAGC
*
52614579 CACCAGAT-CAAATAATTGTGGCATAGC
1 CACCAGATACAAAT-ATTGTGGCAGAGC
52614606 CACCAG
1 CACCAG
52614612 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.04
26 8 0.15
27 36 0.69
28 6 0.12
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (27 bp):
CACCAGATACAAATATTGTGGCAGAGC
Found at i:52619051 original size:27 final size:26
Alignment explanation
Indices: 52619013--52619090 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 26
52619003 GCGAGGCTGC
*
52619013 CAGATATTGTGGC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
52619039 ACAGATATTGTGGCAGAGCCACCAGAT
1 -CAGATATTGTGGCAGAGCCACCAGAT
*
52619066 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
52619091 GATGCTTCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
26 5 0.11
27 41 0.87
28 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:52623826 original size:21 final size:22
Alignment explanation
Indices: 52623778--52623836 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
52623768 ATTAATAAAG
52623778 TAGATTATATATTAT--TTTTA
1 TAGATTATATATTATAATTTTA
*
52623798 TAGTATTATATATTATAATTTTT
1 TAG-ATTATATATTATAATTTTA
*
52623821 TA-ATTA-ATATAATAAT
1 TAGATTATATATTATAAT
52623837 AATTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 12 0.35
21 16 0.47
23 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TAGATTATATATTATAATTTTA
Found at i:52623868 original size:58 final size:57
Alignment explanation
Indices: 52623802--52623966 Score: 190
Period size: 58 Copynumber: 2.9 Consensus size: 57
52623792 TTTTTATAGT
* * *
52623802 ATTATATATTATAATTT-TTTAATTA-ATATAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTATTAAATTATATATAATAATAATTATATTAA-AATATGATTAA
* *
52623860 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
1 ATTATATATTATTTTATTAAATTATATATAATAATAATTATATTAAAATATGATTAA
* * * **
52623917 ATTATTTATTATTTTTATTAAATTATTTTTAATAATAATCCTATTAAAAT
1 ATTATATATTA-TTTTATTAAATTATATATAATAATAATTATATTAAAAT
52623967 TTAATAACAA
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
56 3 0.03
57 26 0.28
58 65 0.69
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTATATATAATAATAATTATATTAAAATATGATTAA
Found at i:52625060 original size:7 final size:8
Alignment explanation
Indices: 52625043--52625069 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
52625033 AAAAGGTGCA
52625043 TTTTTATT
1 TTTTTATT
52625051 TTTTTATT
1 TTTTTATT
52625059 TTTTTATT
1 TTTTTATT
52625067 TTT
1 TTT
52625070 CAAGTGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:52627792 original size:20 final size:21
Alignment explanation
Indices: 52627759--52627801 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
52627749 GTATCTTCAG
*
52627759 CTTGATTTAGAA-TTAAGATTA
1 CTTGATTTAAAATTTAA-ATTA
52627780 CTTG-TTTAAAATTTAAATTA
1 CTTGATTTAAAATTTAAATTA
52627800 CT
1 CT
52627802 CTTTAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (21 bp):
CTTGATTTAAAATTTAAATTA
Found at i:52629823 original size:20 final size:20
Alignment explanation
Indices: 52629795--52629837 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
52629785 ACATATATTT
* *
52629795 GATGTGATATCTGTTAAGTA
1 GATGCGATATCTGTTAAATA
52629815 GATGCGATATCTGTTAAATA
1 GATGCGATATCTGTTAAATA
52629835 GAT
1 GAT
52629838 ATGTTCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (20 bp):
GATGCGATATCTGTTAAATA
Found at i:52629972 original size:2 final size:2
Alignment explanation
Indices: 52629965--52630004 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
52629955 GTGGCTAAGC
52629965 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
52630005 TATATACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:52633538 original size:45 final size:45
Alignment explanation
Indices: 52633488--52633575 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
52633478 AAACATGTGC
* *
52633488 CACATACATCATGAACTCAGACCACAACTCAATGAGTTTAGATGT
1 CACATACATCAAGAACTCAGACCACAACTCAATGAGTTCAGATGT
*
52633533 CACATATATCAAGAACTCAGACCACAACTCAATGAGTTCAGAT
1 CACATACATCAAGAACTCAGACCACAACTCAATGAGTTCAGAT
52633576 CACATGGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (45 bp):
CACATACATCAAGAACTCAGACCACAACTCAATGAGTTCAGATGT
Found at i:52633573 original size:21 final size:21
Alignment explanation
Indices: 52633504--52633579 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
52633494 CATCATGAAC
52633504 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
* * * **
52633525 TTAGATGTCACATATATCAA-GAAC
1 TCAGA--CCACA-A-CTCAATGAGT
52633549 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
*
52633570 TCAGATCACA
1 TCAGACCACA
52633580 TGGTTTCTAG
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
20 4 0.10
21 16 0.41
22 4 0.10
23 4 0.10
24 7 0.18
25 4 0.10
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.22
Consensus pattern (21 bp):
TCAGACCACAACTCAATGAGT
Found at i:52638656 original size:14 final size:15
Alignment explanation
Indices: 52638637--52638669 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
52638627 ATATTTAACT
52638637 TGTTCTTAA-TTATG
1 TGTTCTTAACTTATG
*
52638651 TGTTCTTAACTTTTG
1 TGTTCTTAACTTATG
52638666 TGTT
1 TGTT
52638670 GGTATCCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.61
Consensus pattern (15 bp):
TGTTCTTAACTTATG
Found at i:52648309 original size:43 final size:43
Alignment explanation
Indices: 52648149--52648319 Score: 134
Period size: 43 Copynumber: 4.0 Consensus size: 43
52648139 ATAGGATTTT
* * * * *
52648149 GATATGTGATTTCATGTAAAACCATGTCTGGGATGTTGGCATC
1 GATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCATC
* * * * ** *
52648192 GAT-TTGAGATTTACGTGTAAGACCATGTCTGGGACATCCGCACC
1 GATATT-TGA-TTACATGTAAGACCACGTCTGGGACGTTGGCATC
*** *
52648236 G-TATTTGATTTTGTGTAAGACTCTAC--CTGGGACGGTGGCATC
1 GATATTTGATTACATGTAAGAC-C-ACGTCTGGGACGTTGGCATC
52648278 GATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
52648320 TGTACGGGTT
Statistics
Matches: 97, Mismatches: 23, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
41 2 0.02
42 25 0.26
43 40 0.41
44 30 0.31
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
GATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:52648533 original size:42 final size:43
Alignment explanation
Indices: 52648480--52648568 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 43
52648470 AGAAAATATG
52648480 CTATATGTGCAAATGAATTGGGAATATGGGAAATGTATATGAA
1 CTATATGTGCAAATGAATTGGGAATATGGGAAATGTATATGAA
*
52648523 CTATA-GTGCAAATGAATTGGGAATATGTGAAATGTATATGAA
1 CTATATGTGCAAATGAATTGGGAATATGGGAAATGTATATGAA
52648565 CTAT
1 CTAT
52648569 GTGATTTGTG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 40 0.89
43 5 0.11
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (43 bp):
CTATATGTGCAAATGAATTGGGAATATGGGAAATGTATATGAA
Found at i:52648569 original size:20 final size:20
Alignment explanation
Indices: 52648504--52648572 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
52648494 GAATTGGGAA
*
52648504 TATGGGAAATGTATATGAAC
1 TATGTGAAATGTATATGAAC
*
52648524 TATAGTGCAAATGAAT-TGGGAA-
1 TAT-GTG-AAATGTATAT--GAAC
52648546 TATGTGAAATGTATATGAAC
1 TATGTGAAATGTATATGAAC
52648566 TATGTGA
1 TATGTGA
52648573 TTTGTGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
19 3 0.08
20 17 0.43
21 7 0.17
22 10 0.25
23 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (20 bp):
TATGTGAAATGTATATGAAC
Found at i:52652910 original size:35 final size:35
Alignment explanation
Indices: 52652871--52652991 Score: 145
Period size: 35 Copynumber: 3.5 Consensus size: 35
52652861 TAGGTATGTA
*
52652871 CATATGTGATGTTATATCTAACTTGTATATTTGGC
1 CATATGTGATGATATATCTAACTTGTATATTTGGC
* * *
52652906 CATATGTGATGATGTAT-TGAATTTGTAAATTTGGC
1 CATATGTGATGATATATCT-AACTTGTATATTTGGC
* * * * *
52652941 TACATGTGATGTTCTATCTAACTTGTATATTCGGC
1 CATATGTGATGATATATCTAACTTGTATATTTGGC
52652976 CATATGTGATGATATA
1 CATATGTGATGATATA
52652992 ATGAACCTTA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.97
36 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (35 bp):
CATATGTGATGATATATCTAACTTGTATATTTGGC
Found at i:52653073 original size:50 final size:50
Alignment explanation
Indices: 52652978--52653079 Score: 114
Period size: 50 Copynumber: 2.0 Consensus size: 50
52652968 TATTCGGCCA
* * * *
52652978 TATGTGATGATATAATGAACCTTATGTATTCAGCCATACATGTAAGTCTT
1 TATGAGATGATATAATGAACCTTATATATTCAGCCATACAGGTAAGTATT
* * * ** *
52653028 TATGAGATGATATATTGGACCTTGTATATTCAGTTATATAGGTAAGTATT
1 TATGAGATGATATAATGAACCTTATATATTCAGCCATACAGGTAAGTATT
52653078 TA
1 TA
52653080 CATGGTGTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (50 bp):
TATGAGATGATATAATGAACCTTATATATTCAGCCATACAGGTAAGTATT
Found at i:52654279 original size:20 final size:18
Alignment explanation
Indices: 52654249--52654291 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
52654239 TTTGTAAAGT
*
52654249 TTGTAAAATAAGTTGTAAA
1 TTGTGAAATAA-TTGTAAA
52654268 TGTGTGAAATAATTG-AAA
1 T-TGTGAAATAATTGTAAA
52654286 TTGTGA
1 TTGTGA
52654292 GTTGTTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 4 0.18
20 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (18 bp):
TTGTGAAATAATTGTAAA
Found at i:52658407 original size:48 final size:48
Alignment explanation
Indices: 52658336--52658449 Score: 165
Period size: 48 Copynumber: 2.4 Consensus size: 48
52658326 GGTGTTACAA
* * *
52658336 TAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCCAGTG
1 TAAGACATGTCTGAGACAAGCATCGGCCTCGAGATACACAAGCCAGTG
* *
52658384 TAAGACATGTTTGAGACAAGCATCGGCCTCGAGATACACAAGCTAGTG
1 TAAGACATGTCTGAGACAAGCATCGGCCTCGAGATACACAAGCCAGTG
* *
52658432 TAAGACCTGTCTGGGACA
1 TAAGACATGTCTGAGACA
52658450 TGACGTCAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (48 bp):
TAAGACATGTCTGAGACAAGCATCGGCCTCGAGATACACAAGCCAGTG
Found at i:52658648 original size:97 final size:97
Alignment explanation
Indices: 52658469--52658648 Score: 211
Period size: 97 Copynumber: 1.9 Consensus size: 97
52658459 CTTGTTGTGT
* * * *
52658469 GTCAGTGTAAGACCTATCTGGGACATGGCATTGACACTGATAGATGAGAGCCAGTGTAAGACTTG
1 GTCAGTGTAAGACCTATCTAGGACATGGCATCGACACTGATAGATGAGAGCCAGCGTAAGACATG
**
52658534 TCTGGGACAGGTGTCGGCCTCGAGATATGAAA
66 TCTGGGACAGGCATCGGCCTCGAGATATGAAA
* ** ** * *
52658566 GTCAGTGTAAGACCTGTCTAGGACATGGCATCGACTTTGAT-G-TGCTAGCTAGCGTAAGCCCAT
1 GTCAGTGTAAGACCTATCTAGGACATGGCATCGACACTGATAGATGAGAGCCAGCGTAAG-ACAT
52658629 GTCTGGGACATGGCATCGGC
65 GTCTGGGACA-GGCATCGGC
52658649 ATTGTATCCC
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
95 12 0.18
96 13 0.19
97 43 0.63
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (97 bp):
GTCAGTGTAAGACCTATCTAGGACATGGCATCGACACTGATAGATGAGAGCCAGCGTAAGACATG
TCTGGGACAGGCATCGGCCTCGAGATATGAAA
Found at i:52671967 original size:40 final size:40
Alignment explanation
Indices: 52671873--52672097 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
52671863 TATTCGAATG
* *
52671873 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
52671914 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
52671954 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
52671994 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * * *
52672034 ATATCCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
52672074 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
52672098 CTTGCGCAAG
Statistics
Matches: 157, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 127 0.81
41 29 0.18
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:52672087 original size:120 final size:121
Alignment explanation
Indices: 52671873--52672097 Score: 312
Period size: 120 Copynumber: 1.9 Consensus size: 121
52671863 TATTCGAATG
** * *
52671873 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * *
52671938 ATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
66 ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
* *
52671994 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCCTGAAGG
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCC-GAAGG
* *
52672057 CATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGC
65 CATTCATGCGAGTTG-CCACATCCGGGCTAAGACCCGAAGGC
52672098 CTTGCGCAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
119 5 0.05
120 55 0.60
121 31 0.34
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (121 bp):
ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
Found at i:52680145 original size:40 final size:40
Alignment explanation
Indices: 52680051--52680275 Score: 240
Period size: 40 Copynumber: 5.6 Consensus size: 40
52680041 TATTCGAATG
* *
52680051 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GCGACT
* * * * *
52680092 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-CGACT
* *
52680132 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* *
52680172 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * * *
52680212 ATATCCGGGCTAAG-TCCTGAAGGCATATATGCTAGTGACC
1 ATATCCGGGCTAAGATCC-GAAGGCATTTGTGCTAGCGACT
* *
52680252 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
52680276 CTTGCGCAAG
Statistics
Matches: 157, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
39 3 0.02
40 122 0.78
41 31 0.20
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
Found at i:52680234 original size:80 final size:80
Alignment explanation
Indices: 52680051--52680275 Score: 281
Period size: 80 Copynumber: 2.8 Consensus size: 80
52680041 TATTCGAATG
* * * *
52680051 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
*
52680116 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * *
52680132 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
52680197 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * * *
52680212 ATATCCGGGCTAAGTCCTGAAGGCATATATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGC
52680276 CTTGCGCAAG
Statistics
Matches: 123, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
79 1 0.01
80 90 0.73
81 32 0.26
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:52680265 original size:120 final size:121
Alignment explanation
Indices: 52680051--52680275 Score: 305
Period size: 120 Copynumber: 1.9 Consensus size: 121
52680041 TATTCGAATG
** * *
52680051 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * *
52680116 ATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
66 ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
* *
52680172 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCCTGAAGG
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCC-GAAGG
*
52680235 CATAT-ATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGC
65 CAT-TCATGCGAGTTG-CCACATCCGGGCTAAGACCCGAAGGC
52680276 CTTGCGCAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
119 5 0.05
120 54 0.59
121 32 0.35
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (121 bp):
ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
Found at i:52686821 original size:18 final size:18
Alignment explanation
Indices: 52686798--52686837 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52686788 GGCAATTTTT
52686798 GGGCGTCGTGGG-CCACAC
1 GGGCGT-GTGGGACCACAC
*
52686816 GGGCGTGTGGGACCACAT
1 GGGCGTGTGGGACCACAC
52686834 GGGC
1 GGGC
52686838 CCGTATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.12, C:0.28, G:0.47, T:0.12
Consensus pattern (18 bp):
GGGCGTGTGGGACCACAC
Found at i:52686979 original size:27 final size:27
Alignment explanation
Indices: 52686941--52687065 Score: 178
Period size: 27 Copynumber: 4.6 Consensus size: 27
52686931 ACGTGCCTGA
* *
52686941 ACCCTCATGTGATAAAATGACAATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
52686968 ACTCTTATGTGATAAAATGATGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
52686995 GCCCTTATGTGATAAAATAACGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
52687022 ACCCTTATGTGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
52687049 TCCCTCATGTGATAAAA
1 ACCCTTATGTGATAAAA
52687066 GGATCGAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (27 bp):
ACCCTTATGTGATAAAATGACGATTTT
Found at i:52687097 original size:27 final size:27
Alignment explanation
Indices: 52687061--52687133 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
52687051 CCTCATGTGA
*
52687061 TAAAAGGATCGAAATACCTCC-ATAGGG
1 TAAAATGATCGAAATACC-CCTATAGGG
* * *
52687088 TAGAATGATCAAAATACCCCTGTAGGG
1 TAAAATGATCGAAATACCCCTATAGGG
* *
52687115 TAAAATGATTGTAATACCC
1 TAAAATGATCGAAATACCC
52687134 TGGTAAGGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 2 0.05
27 35 0.95
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCCTATAGGG
Found at i:52694845 original size:40 final size:40
Alignment explanation
Indices: 52694747--52694861 Score: 169
Period size: 39 Copynumber: 2.9 Consensus size: 40
52694737 GGACTAAGAT
* * * *
52694747 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
*
52694787 CCG-AGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
*
52694826 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTA
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTA
52694862 CGTCNNNNNN
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.51
40 33 0.49
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:52712081 original size:23 final size:23
Alignment explanation
Indices: 52712041--52712085 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
52712031 TTCAGTCGCA
52712041 ATTTCTCACATTTTCAATTCAATC
1 ATTTCTCACATTTTCAA-TCAATC
*
52712065 ATTTTTCAC-TTTTCAATCAAT
1 ATTTCTCACATTTTCAATCAAT
52712086 TTTCAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTCTCACATTTTCAATCAATC
Found at i:52712379 original size:15 final size:15
Alignment explanation
Indices: 52712337--52712379 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52712327 TACTTACTAT
* *
52712337 AAAATAAATAAATTT
1 AAAATAAATAACTTA
*
52712352 AAAATTAAT-ACTTA
1 AAAATAAATAACTTA
52712366 AAAATAAATAACTT
1 AAAATAAATAACTT
52712380 GAATTAGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAAATAACTTA
Found at i:52715193 original size:34 final size:35
Alignment explanation
Indices: 52715150--52715227 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 35
52715140 CTTAAGGTTT
52715150 TTTA-GGTTTAGGGTTTTGCTAAAATA-ATTTA-GG
1 TTTAGGGTTTAGGGTTTTGCTAAAATACA-TTAGGG
* *
52715183 TTTAGGGTTTAGGTTTTTGTTAAAATACATTAGGG
1 TTTAGGGTTTAGGGTTTTGCTAAAATACATTAGGG
52715218 TTTAGGGTTT
1 TTTAGGGTTT
52715228 TAGTGGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 4 0.10
34 23 0.57
35 13 0.32
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (35 bp):
TTTAGGGTTTAGGGTTTTGCTAAAATACATTAGGG
Found at i:52715630 original size:126 final size:126
Alignment explanation
Indices: 52715396--52715773 Score: 528
Period size: 126 Copynumber: 3.0 Consensus size: 126
52715386 ATTGACTATT
* * * *
52715396 TTTCCTTACAAAAATAATTTTGAGAAGAAGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGTA
1 TTTCCTGA-AAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCA
* * * * * *
52715461 GGATGCACTG-CGTGCAAAATTACTGAAAAAAGCTCCAATGTGGACGCTCTTTTTTTACAGTA
65 GGATGCAATGTC-AGCAAAATTATTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTA
* *
52715523 TTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAATGCTTCAAGCAG
1 TTTCCTGAAAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAG
* * *
52715588 AATGCAATGTCAACAAAATTATTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATA
66 GATGCAATGTCAGCAAAATTATTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTA
* * *
52715649 TTTCCTGAAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACACTTCAATCAG
1 TTTCCTGAAAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAG
* *
52715714 GATGCAATATCAGCAAAATT-TCTGAAAAAA-CTCCCACGTGGACGTTCTTTTTCTACAGTA
66 GATGCAATGTCAGCAAAATTAT-TGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTA
52715774 GTTCATGTTT
Statistics
Matches: 225, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
125 29 0.13
126 188 0.84
127 8 0.04
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (126 bp):
TTTCCTGAAAAAATAATTTTGAGAAGAAGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAG
GATGCAATGTCAGCAAAATTATTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTA
Found at i:52718875 original size:24 final size:23
Alignment explanation
Indices: 52718819--52718875 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
52718809 AAGAACTTTT
*
52718819 ATTTTATTAAAAATATAAAATTA
1 ATTTTATTAAAAATATAAAACTA
52718842 ATTTACTATT-AAAATATTAAAACTA
1 ATTT--TATTAAAAATA-TAAAACTA
52718867 ACTTTTATT
1 A-TTTTATT
52718876 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAACTA
Found at i:52719911 original size:7 final size:7
Alignment explanation
Indices: 52719892--52719925 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
52719882 AAATATTAGT
52719892 TAAATAC
1 TAAATAC
52719899 -ATAATAC
1 TA-AATAC
52719906 TAAATAC
1 TAAATAC
52719913 TAAATAC
1 TAAATAC
52719920 TAAATA
1 TAAATA
52719926 TGAAACAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 23 0.92
8 1 0.04
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (7 bp):
TAAATAC
Found at i:52720884 original size:26 final size:25
Alignment explanation
Indices: 52720855--52720944 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 25
52720845 ATAAAAAATT
52720855 ATAAATTACAAATTAATTAAAATTAC
1 ATAAATTA-AAATTAATTAAAATTAC
* * *
52720881 ATAAATGAAAA-AATATTAAATAATATTC
1 ATAAATTAAAATTA-ATT-AA-AAT-TAC
* *
52720909 AAAAATTAAAATTAATTAGAATTAC
1 ATAAATTAAAATTAATTAAAATTAC
*
52720934 ATAAATGAAAA
1 ATAAATTAAAA
52720945 AAATATTAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
24 1 0.02
25 17 0.35
26 12 0.24
27 4 0.08
28 14 0.29
29 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (25 bp):
ATAAATTAAAATTAATTAAAATTAC
Found at i:52720921 original size:53 final size:54
Alignment explanation
Indices: 52720857--52720977 Score: 217
Period size: 54 Copynumber: 2.2 Consensus size: 54
52720847 AAAAAATTAT
52720857 AAATTACAAATTAATTAAAATTACATAAATG-AAAAAATATTAAATAATATTCAA
1 AAATTA-AAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCAA
*
52720911 AAATTAAAATTAATTAGAATTACATAAATGAAAAAAATATTAAATAATATTCAA
1 AAATTAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCAA
52720965 AAATTAAAATTAA
1 AAATTAAAATTAA
52720978 CCTTTACCAT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
53 23 0.35
54 42 0.65
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (54 bp):
AAATTAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTCAA
Found at i:52720945 original size:26 final size:25
Alignment explanation
Indices: 52720855--52720945 Score: 69
Period size: 26 Copynumber: 3.5 Consensus size: 25
52720845 ATAAAAAATT
* *
52720855 ATAAATTACAAATTAATTAAAATTAC
1 ATAAATGAAAAATTAATT-AAATTAC
*
52720881 ATAAATGAAAAAAT-ATTAAATAATATTC
1 ATAAATGAAAAATTAATTAAAT--TA--C
* *
52720909 AAAAAT-TAAAATTAATTAGAATTAC
1 ATAAATGAAAAATTAATTA-AATTAC
52720934 ATAAATGAAAAA
1 ATAAATGAAAAA
52720946 AATATTAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
24 4 0.08
25 9 0.18
26 17 0.34
27 7 0.14
28 10 0.20
29 3 0.06
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (25 bp):
ATAAATGAAAAATTAATTAAATTAC
Found at i:52720952 original size:26 final size:25
Alignment explanation
Indices: 52720874--52720955 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
52720864 AAATTAATTA
52720874 AAATTACATAAATG-AAAAAATATT
1 AAATTACATAAATGAAAAAAATATT
* * **
52720898 AAATAATATTCAAAAATTAAAATTA-ATT
1 AAAT--TA--CATAAATGAAAAAAATATT
52720926 AGAATTACATAAATGAAAAAAATATT
1 A-AATTACATAAATGAAAAAAATATT
52720952 AAAT
1 AAAT
52720956 AATATTCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 13
0.67 0.12 0.20
Matches are distributed among these distances:
24 4 0.09
25 14 0.33
26 6 0.14
27 2 0.05
28 10 0.23
29 7 0.16
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (25 bp):
AAATTACATAAATGAAAAAAATATT
Found at i:52721182 original size:21 final size:21
Alignment explanation
Indices: 52721133--52721182 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
52721123 TAAAGAAAGC
** *
52721133 TTTGAGAAATTTAATGAGAAA
1 TTTGAGAGCTTTAAGGAGAAA
52721154 TTTGAGAGCTTTAAGGAGAAA
1 TTTGAGAGCTTTAAGGAGAAA
*
52721175 TTTTAGAG
1 TTTGAGAG
52721183 TTTTTTTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (21 bp):
TTTGAGAGCTTTAAGGAGAAA
Found at i:52726703 original size:24 final size:22
Alignment explanation
Indices: 52726655--52726706 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
52726645 ATAGTTTTAA
* *
52726655 ATTTTTATAATATTTATTCAAT
1 ATTTTTATAATATTCATGCAAT
52726677 ATTTTTATAATATATCATGCAATT
1 ATTTTTATAATAT-TCATGCAA-T
52726701 ATTTTT
1 ATTTTT
52726707 TTATTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 13 0.50
23 6 0.23
24 7 0.27
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTTATAATATTCATGCAAT
Found at i:52730200 original size:2 final size:2
Alignment explanation
Indices: 52730193--52730217 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52730183 TTAAATATCA
52730193 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52730218 GATTTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52730521 original size:16 final size:16
Alignment explanation
Indices: 52730500--52730533 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
52730490 TAATAATTTT
52730500 TTTGAA-AATAATAAAA
1 TTTGAATAATAA-AAAA
52730516 TTTGAATAATAAAAAA
1 TTTGAATAATAAAAAA
52730532 TT
1 TT
52730534 AATCAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TTTGAATAATAAAAAA
Found at i:52749358 original size:51 final size:51
Alignment explanation
Indices: 52749290--52749497 Score: 319
Period size: 51 Copynumber: 4.1 Consensus size: 51
52749280 ATCACATTTA
52749290 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * *
52749341 TCACTTGTCACTGATCAGATAAGTGTAGCTAAA-CTACCACTTATTATTTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
52749391 TCACTCGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * * * *
52749442 TCACTTATCATTGATCAAATAAGTGTAGCTGAGGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
52749493 TCACT
1 TCACT
52749498 GATCAGAAGT
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
50 45 0.32
51 96 0.68
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:52749390 original size:101 final size:102
Alignment explanation
Indices: 52749285--52749486 Score: 334
Period size: 101 Copynumber: 2.0 Consensus size: 102
52749275 CACTGATCAC
* *
52749285 ATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTC
1 ATTTATCACTCGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATC
*
52749350 ACTGATCAGATAAGTGTAGCT-AAACTACCACTTATT
66 ACTGATCAAATAAGTGTAGCTGAAACTACCACTTATT
*
52749386 ATTTATCACTCGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATC
1 ATTTATCACTCGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATC
* **
52749451 ATTGATCAAATAAGTGTAGCTGAGGCTACCACTTAT
66 ACTGATCAAATAAGTGTAGCTGAAACTACCACTTAT
52749487 CACTTGTCAC
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 81 0.87
102 12 0.13
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (102 bp):
ATTTATCACTCGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATC
ACTGATCAAATAAGTGTAGCTGAAACTACCACTTATT
Found at i:52755153 original size:30 final size:30
Alignment explanation
Indices: 52755113--52755175 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
52755103 ACTTAACAAG
*
52755113 CAAATGTCTTTAAAATAATAATAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
*
52755143 CAAATTTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
52755173 CAA
1 CAA
52755176 CAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.32
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAACAAAATTAA
Found at i:52755260 original size:22 final size:22
Alignment explanation
Indices: 52755213--52755260 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
52755203 CTATAACAAC
* * * *
52755213 AAAATAGTAGTAACATAATAAT
1 AAAATAGTAGCAAAATAAGAAG
52755235 AAAATAGTAGCAAAATAAGAAG
1 AAAATAGTAGCAAAATAAGAAG
52755257 AAAA
1 AAAA
52755261 CAATAAGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAAG
Found at i:52758560 original size:25 final size:25
Alignment explanation
Indices: 52758484--52758565 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
52758474 AAAACCAAAC
* * *
52758484 AAAGCCTTTGTAGCGAA-TATTCGT
1 AAAGCCTTTGTGGCGAACTCTTTGT
* * *
52758508 AAAGCCTTTGTGGCAAACTCTCTAT
1 AAAGCCTTTGTGGCGAACTCTTTGT
52758533 AAAGCCTTTGTGGCGAACTCTTTGT
1 AAAGCCTTTGTGGCGAACTCTTTGT
*
52758558 AAAACCTT
1 AAAGCCTT
52758566 CTTGGCGTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 15 0.32
25 32 0.68
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (25 bp):
AAAGCCTTTGTGGCGAACTCTTTGT
Found at i:52760260 original size:38 final size:38
Alignment explanation
Indices: 52760210--52760344 Score: 189
Period size: 40 Copynumber: 3.4 Consensus size: 38
52760200 CCTGCGAAAC
* * *
52760210 TTTAAGCCCGGATATAGTACCAGCACTAAGCCTGTGGGA
1 TTTAA-CCCGGATATATTACCAGCACGAAGCCTGCGGGA
52760249 TTTAACCCGGATATATATTACCAGCACGAAGCCTGCGGGA
1 TTTAACCCGG--ATATATTACCAGCACGAAGCCTGCGGGA
*
52760289 TTTAACCCGAATATATATTACCAGCACGAAGCCTGCGGGA
1 TTTAACCCG--GATATATTACCAGCACGAAGCCTGCGGGA
52760329 TTTAACCCGGATATAT
1 TTTAACCCGGATATAT
52760345 GATATATCAA
Statistics
Matches: 87, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
38 11 0.13
39 5 0.06
40 71 0.82
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (38 bp):
TTTAACCCGGATATATTACCAGCACGAAGCCTGCGGGA
Found at i:52768386 original size:38 final size:38
Alignment explanation
Indices: 52768337--52768430 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 38
52768327 CCTTCGAAAC
*
52768337 TTTAAGCCCGGATATAGTACCAGCACTAAGCCTGCGGGA
1 TTTAA-CCCGGATATAGTACCAGCACAAAGCCTGCGGGA
*
52768376 TTTAACCCGGATATATATTACCAGCACAAAGCCTGCGGGA
1 TTTAACCCGG--ATATAGTACCAGCACAAAGCCTGCGGGA
52768416 TTTAACCCGGATATA
1 TTTAACCCGGATATA
52768431 TAATATATCA
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
38 10 0.20
39 5 0.10
40 36 0.71
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (38 bp):
TTTAACCCGGATATAGTACCAGCACAAAGCCTGCGGGA
Found at i:52768431 original size:40 final size:40
Alignment explanation
Indices: 52768348--52768432 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
52768338 TTAAGCCCGG
*
52768348 ATATAGTACCAGCACTAAGCCTGCGGGATTTAACCCGGAT
1 ATATAGTACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
*
52768388 ATATATTACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
1 ATATAGTACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
52768428 ATATA
1 ATATA
52768433 ATATATCAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (40 bp):
ATATAGTACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
Found at i:52771099 original size:15 final size:15
Alignment explanation
Indices: 52771079--52771116 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
52771069 TGGAATTCTG
52771079 TTTAGATTAATCAGA
1 TTTAGATTAATCAGA
*
52771094 TTTAGA-AAATCAGA
1 TTTAGATTAATCAGA
*
52771108 TTTACATTA
1 TTTAGATTA
52771117 TATATCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (15 bp):
TTTAGATTAATCAGA
Found at i:52773335 original size:18 final size:18
Alignment explanation
Indices: 52773312--52773365 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
52773302 ACAAGTGGTG
52773312 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
52773330 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
52773342 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
52773360 GTGGAG
1 GTGGAG
52773366 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:52773348 original size:30 final size:30
Alignment explanation
Indices: 52773312--52773375 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
52773302 ACAAGTGGTG
52773312 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
* *
52773342 GTGGAGCAAGTGTGGCTAGTGGAGTTGGTG
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
52773372 GTGG
1 GTGG
52773376 CAAAGGCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.50, T:0.25
Consensus pattern (30 bp):
GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
Found at i:52774303 original size:91 final size:91
Alignment explanation
Indices: 52774115--52774510 Score: 350
Period size: 91 Copynumber: 4.4 Consensus size: 91
52774105 ACGTGAGCCA
* * * * * *
52774115 AGGCTTAACTCACTTCTCGCAATATGAGTTGATTT-TTA-AAACA-AAATATG--TAAAACAGAT
1 AGGCTAAACTCACCTCTCGCAATATGAGTTGATTTCTGACAAACATAAAT-TGAAAAAAAAAGAA
* ** ** *
52774175 TTTGAAAATACCTCGGTATGTGACCCG
65 ATTGAAAATACCTTAGCGTGTGACCTG
* **
52774202 AGGCTAAACTCACCTCTCGTAATATGAGTTGATTTCTG-CAAAGCATAAATT-AGAAAAAAAATC
1 AGGCTAAACTCACCTCTCGCAATATGAGTTGATTTCTGACAAA-CATAAATTGA-AAAAAAAAGA
52774265 AATTGAAAATACCTTAGCGTGTGACCTG
64 AATTGAAAATACCTTAGCGTGTGACCTG
* *
52774293 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAAAAAAAAGA
1 AGGCTAAACTCACCTCTCGCAATATGAGTTGA--TTTCTGACAAACATAAATTGAAAAAAAAAGA
52774358 AATTGAAAATACCTTAGCGTGT--CCTG
64 AATTGAAAATACCTTAGCGTGTGACCTG
* * * *
52774384 AGGCTGAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACA-AAATTTG--AAAAACA
1 AGGCTAAACTCACCTCTCGCAATATGAGTTGA--TTTCT-GACAAACATAAA-TTGAAAAAAAAA
* * * * *
52774446 GAATTTGAAAATACCTCAGCATGTGA-GTCA
62 GAAATTGAAAATACCTTAGCGTGTGACCT-G
* * *
52774476 AGGCTCAACTCACCACTCGCAATATGAGCTGATTT
1 AGGCTAAACTCACCTCTCGCAATATGAGTTGATTT
52774511 TTTTGAAACA
Statistics
Matches: 262, Mismatches: 31, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
87 32 0.12
88 4 0.02
89 3 0.01
90 34 0.13
91 102 0.39
92 39 0.15
93 43 0.16
94 5 0.02
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (91 bp):
AGGCTAAACTCACCTCTCGCAATATGAGTTGATTTCTGACAAACATAAATTGAAAAAAAAAGAAA
TTGAAAATACCTTAGCGTGTGACCTG
Found at i:52774456 original size:13 final size:14
Alignment explanation
Indices: 52774424--52774456 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
52774414 GATTTTTTTG
52774424 GAAAAACAAAATTT
1 GAAAAACAAAATTT
*
52774438 GAAAAACAGAATTT
1 GAAAAACAAAATTT
52774452 GAAAA
1 GAAAA
52774457 TACCTCAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
GAAAAACAAAATTT
Found at i:52774497 original size:183 final size:177
Alignment explanation
Indices: 52774042--52774620 Score: 531
Period size: 183 Copynumber: 3.3 Consensus size: 177
52774032 TCAACTCATT
* * * * * * * *
52774042 TCTCGCAATATGAATTGA-CTCTTT-AAAAACAGACA-TT-AAAATAGAAATTGAACATAGCTCA
1 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTGAAAAAAGAATTTGAAAATACCTCA
* * *
52774103 GCACGTGAGCCAAGGCTTAACTCACTTCTCGCAATATGAGTTGA--TTTTT-AAAACAAAATATG
66 GCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAAAAT-TG
* * ** * *
52774165 -TAAAACAGATTTTGAAAATACCTCGGTATGTGACCCGAGGCTAAACTCACC
130 AAAAAAAAGAAATTGAAAATACCT---TA-GTGTCCTGAGGCTAAACTCACC
* * * * * *
52774216 TCTCGTAATATGAGTTGA--TTTCTGCAAAGCATAAATTAGAAAAAA-AATCAATTGAAAATACC
1 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTGAAAAAAGAAT---TTGAAAATACC
* * *
52774278 TTAGCGTGTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATA
63 TCAGCATGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAACA-A
*
52774342 AATTGAAAAAAAAAGAAATTGAAAATACCTTAGCGTGTCCTGAGGCTGAACTCACC
125 AATTG-AAAAAAAAGAAATTGAAAATACCTTA--GTGTCCTGAGGCTAAACTCACC
52774398 TCTCGCAATATGAGTTGATTTTTTTGGAAAAACA-AAATTTGAAAAACAGAATTTGAAAATACCT
1 TCTCGCAATATGAGTTGATTTTTTT-GAAAAACAGAAATTTGAAAAA-AGAATTTGAAAATACCT
* * *
52774462 CAGCATGTGAGTCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTGAAACACAGAAA
64 CAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACA-AAA
* * * * * * * *
52774527 TTGAAGAACAA-AAATGGAAAACACCTCAGTGTCTTGAGGTTTAACTCACC
127 TTGAAAAAAAAGAAATTGAAAATACCTTAGTGTCCTGAGGCTAAACTCACC
* *
52774577 TCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA-TTGAAAA
1 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTGAAAA
52774621 TACCTCAACG
Statistics
Matches: 333, Mismatches: 49, Indels: 42
0.79 0.12 0.10
Matches are distributed among these distances:
173 3 0.01
174 23 0.07
175 3 0.01
176 5 0.02
177 2 0.01
178 61 0.18
179 46 0.14
180 5 0.02
181 17 0.05
182 51 0.15
183 72 0.22
184 35 0.11
185 7 0.02
186 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (177 bp):
TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTGAAAAAAGAATTTGAAAATACCTCA
GCATGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAAAATTGA
AAAAAAAGAAATTGAAAATACCTTAGTGTCCTGAGGCTAAACTCACC
Found at i:52774512 original size:91 final size:91
Alignment explanation
Indices: 52774030--52774620 Score: 500
Period size: 87 Copynumber: 6.6 Consensus size: 91
52774020 GTGATCGTGA
** * * * * *
52774030 GCTCAACTCATTTCTCGCAATATGAATTGA-CTCTTT-AAAAACAGACATT--AAAATAGAAATT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAACAGAAATT
* * * * *
52774091 GAACATAGCTCAGCACGTGAGCCAAG
66 GAAAATACCTCAGCATGTGACCCGAG
* * * **
52774117 GCTTAACTCACTTCTCGCAATATGAGTTGA--TTTTT--AAAACA-AAATATGTAAAACAGATTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT-TGAAAAACAGAAAT
* *
52774177 TGAAAATACCTCGGTATGTGACCCGAG
65 TGAAAATACCTCAGCATGTGACCCGAG
* * * * * * *
52774204 GCTAAACTCACCTCTCGTAATATGAGTTGA--TTTCTGCAAAGCATAAATTAGAAAAA-AAATCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT-GAAAAACAGA--A
* * *
52774266 ATTGAAAATACCTTAGCGTGTGACCTGAG
63 ATTGAAAATACCTCAGCATGTGACCCGAG
* * *
52774295 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAAAAAAAAGAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG--AAAAACAGAAA
* * *
52774360 TTGAAAATACCTTAGC--GTGTCCTGAG
64 TTGAAAATACCTCAGCATGTGACCCGAG
* *
52774386 GCTGAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACA-AAATTTGAAAAACAGAAT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-GAAAAACAGAAA-TTGAAAAACAGAAA
** *
52774450 TTGAAAATACCTCAGCATGTGAGTCAAG
64 TTGAAAATACCTCAGCATGTGACCCGAG
* * * * * *
52774478 GCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTGAAACACAGAAATTGAAGAACAAAAATG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAACAGAAATT
* **
52774543 GAAAACACCTCAG--TGT--CTTGAG
66 GAAAATACCTCAGCATGTGACCCGAG
* * * *
52774565 GTTTAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA
52774621 TACCTCAACG
Statistics
Matches: 421, Mismatches: 64, Indels: 38
0.80 0.12 0.07
Matches are distributed among these distances:
84 3 0.01
85 7 0.02
86 4 0.01
87 140 0.33
89 11 0.03
90 33 0.08
91 130 0.31
92 53 0.13
93 33 0.08
94 5 0.01
95 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (91 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAACAGAAATT
GAAAATACCTCAGCATGTGACCCGAG
Found at i:52774981 original size:146 final size:146
Alignment explanation
Indices: 52774533--52774967 Score: 735
Period size: 147 Copynumber: 3.0 Consensus size: 146
52774523 GAAATTGAAG
* ** * *
52774533 AACAAAAATGGAAAACACCTCAGTGTCTTGAGGTTTAACTCACCTCTCGCAATATGAGCTGATTT
1 AACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTT
52774598 TTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
66 TTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
52774663 GAGTTGATTTTTAACA
131 GAGTTGATTTTTAACA
* * *
52774679 AACAAAAATTGAAGTTACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAACATGAGTTGATTT
1 AACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGA-TT
*
52774744 TTTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTTTCGCAATA
65 TTTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATA
*
52774809 TGAGTTGATTTTTGACA
130 TGAGTTGATTTTTAACA
52774826 AACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTT
1 AACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTT
* * *
52774891 TTTTGGAAGACAGAAATTGAAAATACATCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATAT
66 TTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
*
52774956 GAGTCGATTTTT
131 GAGTTGATTTTT
52774968 TTTAAACATA
Statistics
Matches: 270, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
146 129 0.48
147 141 0.52
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (146 bp):
AACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTT
TTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTAACA
Found at i:52775191 original size:14 final size:13
Alignment explanation
Indices: 52775156--52775200 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
52775146 TTGATTTTTG
52775156 AAAAACAGAAATT
1 AAAAACAGAAATT
*
52775169 AAAAGCAGAAATT
1 AAAAACAGAAATT
52775182 GAAAAACAGAAATT
1 -AAAAACAGAAATT
52775196 AAAAA
1 AAAAA
52775201 TACCTCGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:52775221 original size:100 final size:101
Alignment explanation
Indices: 52774992--52775272 Score: 408
Period size: 100 Copynumber: 2.8 Consensus size: 101
52774982 AAAAAAATGA
*
52774992 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTG
1 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * * *
52775055 AAAAGCAGAATTTGGAAGGAAAAAATTGAAAAACAG
66 AAAAACAGAAATTGAAAAGAAAAAATTGAAAAACAG
*
52775091 AAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* *
52775156 AAAAACAGAAATT-AAAAGCAGAAATTGAAAAACAG
66 AAAAACAGAAATTGAAAAGAAAAAATTGAAAAACAG
* * * *
52775191 AAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTT-
1 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
*
52775255 AAAAAGCATAAATTGAAA
66 AAAAA-CAGAAATTGAAA
52775273 TTACCTCAGC
Statistics
Matches: 164, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
99 62 0.38
100 84 0.51
101 18 0.11
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (101 bp):
AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
AAAAACAGAAATTGAAAAGAAAAAATTGAAAAACAG
Found at i:52775310 original size:73 final size:73
Alignment explanation
Indices: 52775183--52775419 Score: 368
Period size: 73 Copynumber: 3.2 Consensus size: 73
52775173 GCAGAAATTG
* * * * * * *
52775183 AAAAA-CAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGT
1 AAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
52775247 TGATTTTT
66 TGATTTTT
52775255 AAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
52775320 TGATTTTT
66 TGATTTTT
**
52775328 AAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAATCTCAACTCACCTCTCGCAATATGAGT
1 AAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
52775393 TGATTTTTT
66 TGA-TTTTT
*
52775402 GAAAAGCATAAATTGAAA
1 AAAAAGCATAAATTGAAA
52775420 AAACAGAAAT
Statistics
Matches: 153, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
72 5 0.03
73 126 0.82
74 22 0.14
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (73 bp):
AAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTT
Done.