Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 31 of 82
Found at i:11085128 original size:61 final size:61
Alignment explanation
Indices: 11085062--11085291 Score: 307
Period size: 61 Copynumber: 3.8 Consensus size: 61
11085052 CAGCTCATGT
* *
11085062 ACATCATCACCAGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCATGACA
1 ACATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCATGACA
* * * ***
11085123 ACATCATTACCGACATGTGCATTGCCCACTCCACACATGCGTAGTTGTAATTATCATGACA
1 ACATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCATGACA
* * * ** * * *
11085184 TCATCATTATCGGCATGTGCACTGCCCATTTTGCACATGCATGGTTGTAATTATTAAGACA
1 ACATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCATGACA
*
11085245 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTG
1 ACATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTG
11085292 CATTTGTCAC
Statistics
Matches: 143, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 143 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (61 bp):
ACATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCATGACA
Found at i:11088322 original size:2 final size:2
Alignment explanation
Indices: 11088315--11088340 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11088305 CATTACAACC
11088315 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11088341 CAATCATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11088433 original size:41 final size:42
Alignment explanation
Indices: 11088381--11088504 Score: 178
Period size: 41 Copynumber: 3.0 Consensus size: 42
11088371 CATCTCATAT
* *
11088381 GCAACGGCTTATGTGCACTCCCATTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
11088423 -CAACGACTTATGTGCACTCCCACTCGCACATAGCCGAGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* **
11088464 GCAACGGCTTATTTGCACTCTTACTCGCACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
11088505 CACATCAACA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 37 0.51
42 35 0.49
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:11097776 original size:61 final size:61
Alignment explanation
Indices: 11097689--11097905 Score: 256
Period size: 61 Copynumber: 3.6 Consensus size: 61
11097679 TCATCACCGG
* *** * * *
11097689 CATGTGCACTGCCTACTCTACACATGCATGGTTGTAATTACCAAGACAACATCATTATCGA
1 CATGTGCACTGCCCACTCCGTACATGCACGGTTGTAATTATCAAGACAGCATCATTATCGA
* * * * *
11097750 CATGCGCACTGCCCACTCCGTGCATGCACGGTTGTAATTATCAGGACAGCATCATTACCGG
1 CATGTGCACTGCCCACTCCGTACATGCACGGTTGTAATTATCAAGACAGCATCATTATCGA
* * *
11097811 CCTGTGCACTACCCACTCCGTACATGCACGGTTGTAATTATCACGACAGCATCATTATCGGA
1 CATGTGCACTGCCCACTCCGTACATGCACGGTTGTAATTATCAAGACAGCATCATTATC-GA
* * *
11097873 -ATATGCACTGCCCACTCTGCACATGCACGGTTG
1 CATGTGCACTGCCCACTCCGTACATGCACGGTTG
11097906 CATTTGTCAC
Statistics
Matches: 131, Mismatches: 24, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
61 130 0.99
62 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (61 bp):
CATGTGCACTGCCCACTCCGTACATGCACGGTTGTAATTATCAAGACAGCATCATTATCGA
Found at i:11097898 original size:122 final size:122
Alignment explanation
Indices: 11097677--11097905 Score: 298
Period size: 122 Copynumber: 1.9 Consensus size: 122
11097667 AGCTCATGTA
* * * *
11097677 CATCATCACCGGCATGTGCACTGCCTACTCTACACATGCATGGTTGTAATTACCAAGACAACATC
1 CATCATCACCGGCATGTGCACTACCCACTCCACACATGCACGGTTGTAATTACCAAGACAACATC
* **
11097742 ATTATCGACATGCGCACTGCCCACTCCGTGCATGCACGGTTGTAATTATCAGGACAG
66 ATTATCGACATACGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCAGGACAG
* * ** * * *
11097799 CATCATTACCGGCCTGTGCACTACCCACTCCGTACATGCACGGTTGTAATTATCACGACAGCATC
1 CATCATCACCGGCATGTGCACTACCCACTCCACACATGCACGGTTGTAATTACCAAGACAACATC
* *
11097864 ATTATCGGA-ATATGCACTGCCCACTCTGCACATGCACGGTTG
66 ATTATC-GACATACGCACTGCCCACTCCGCACATGCACGGTTG
11097906 CATTTGTCAC
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
122 88 0.98
123 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (122 bp):
CATCATCACCGGCATGTGCACTACCCACTCCACACATGCACGGTTGTAATTACCAAGACAACATC
ATTATCGACATACGCACTGCCCACTCCGCACATGCACGGTTGTAATTATCAGGACAG
Found at i:11099977 original size:19 final size:20
Alignment explanation
Indices: 11099953--11099990 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11099943 CTATAAATAC
11099953 CTTGAA-TTTCCAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
11099972 CTTGAATTTTCCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
11099991 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:11100815 original size:43 final size:43
Alignment explanation
Indices: 11100727--11100845 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 43
11100717 GTAATTATAT
* * * *
11100727 TGACTCGGCTATGTGAGAGTAGGGAGTGCGCATAAGATGAGGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACACGAGGA
* * *
11100770 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGATGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACACGAGGA
** * *
11100813 TGACCCAACCATGTGCGAGTAGGGAATGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
11100846 GAGCTGGTGA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACACGAGGA
Found at i:11103367 original size:35 final size:35
Alignment explanation
Indices: 11103328--11103471 Score: 191
Period size: 35 Copynumber: 4.1 Consensus size: 35
11103318 GAGAATGCGT
11103328 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
1 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
*
11103363 ATGATGATATTGAAATGTGCGAGT-AGGAAGTGAAC
1 ATGATGATATTGAAATGTGCGAGTAAGG-AGTGCAC
** * *
11103398 ATGATGATATTGAAATGTATGAATAGGGAGTGCAC
1 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
* * * *
11103433 ATGATGATATTGAAATGTGTGTGTAGGGAGTGTAC
1 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
11103468 ATGA
1 ATGA
11103472 ATTGACTGAA
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
34 3 0.03
35 92 0.95
36 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (35 bp):
ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
Found at i:11103403 original size:70 final size:70
Alignment explanation
Indices: 11103328--11103471 Score: 216
Period size: 70 Copynumber: 2.1 Consensus size: 70
11103318 GAGAATGCGT
* *
11103328 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCACATGATGATATTGAAATGTGCGAGTAGGAAG
1 ATGATGATATTGAAATGTACGAATAAGGAGTGCACATGATGATATTGAAATGTGCGAGTAGGAAG
11103393 TGAAC
66 TGAAC
* * * * *
11103398 ATGATGATATTGAAATGTATGAATAGGGAGTGCACATGATGATATTGAAATGTGTGTGTAGGGAG
1 ATGATGATATTGAAATGTACGAATAAGGAGTGCACATGATGATATTGAAATGTGCGAGTAGGAAG
*
11103463 TGTAC
66 TGAAC
11103468 ATGA
1 ATGA
11103472 ATTGACTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (70 bp):
ATGATGATATTGAAATGTACGAATAAGGAGTGCACATGATGATATTGAAATGTGCGAGTAGGAAG
TGAAC
Found at i:11104726 original size:36 final size:36
Alignment explanation
Indices: 11104686--11104754 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
11104676 ATAACCGTGC
** * *
11104686 GTGTGCAGTGTGGGAGTGCACATGATGGTGATGGTG
1 GTGTGCAAAGTGGGAGTGCACACGATGATGATGGTG
11104722 GTGTGCAAAGTGGGAGTGCACACGATGATGATG
1 GTGTGCAAAGTGGGAGTGCACACGATGATGATG
11104755 ATATTTGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.43, T:0.25
Consensus pattern (36 bp):
GTGTGCAAAGTGGGAGTGCACACGATGATGATGGTG
Found at i:11104777 original size:42 final size:38
Alignment explanation
Indices: 11104731--11104824 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 38
11104721 GGTGTGCAAA
* *
11104731 GTGGGAGTGCACACGATGATGATGATATTTGCCATGTGTAGT
1 GTGGGAGTGCACAC----ATGATGACATTTGCCATGTGCAGT
11104773 GTGGGAGTG--CACATGATGACATTTGCCATGTGCAGT
1 GTGGGAGTGCACACATGATGACATTTGCCATGTGCAGT
11104809 GTGGGAGT--ACACATGA
1 GTGGGAGTGCACACATGA
11104825 GCTGAGTTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
36 37 0.76
40 3 0.06
42 9 0.18
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (38 bp):
GTGGGAGTGCACACATGATGACATTTGCCATGTGCAGT
Found at i:11104789 original size:36 final size:36
Alignment explanation
Indices: 11104749--11104824 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
11104739 GCACACGATG
* * *
11104749 ATGATGATATTTGCCATGTGTAGTGTGGGAGTGCAC
1 ATGATGACATTTGCCATGTGCAGTGTGGGAGTACAC
11104785 ATGATGACATTTGCCATGTGCAGTGTGGGAGTACAC
1 ATGATGACATTTGCCATGTGCAGTGTGGGAGTACAC
11104821 ATGA
1 ATGA
11104825 GCTGAGTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.13, G:0.32, T:0.30
Consensus pattern (36 bp):
ATGATGACATTTGCCATGTGCAGTGTGGGAGTACAC
Found at i:11111145 original size:14 final size:14
Alignment explanation
Indices: 11111126--11111154 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11111116 AATGACATTC
11111126 TACACACATCCTTA
1 TACACACATCCTTA
11111140 TACACACATCCTTA
1 TACACACATCCTTA
11111154 T
1 T
11111155 GGTCTTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (14 bp):
TACACACATCCTTA
Found at i:11118361 original size:10 final size:11
Alignment explanation
Indices: 11118343--11118371 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
11118333 CCTAGGGTTC
11118343 TTGTTCTTCCT
1 TTGTTCTTCCT
11118354 TT-TTCTTCCT
1 TTGTTCTTCCT
11118364 TTGTTCTT
1 TTGTTCTT
11118372 GTTTTGGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.69
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:11122831 original size:42 final size:42
Alignment explanation
Indices: 11122764--11122888 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 42
11122754 TGTTGATGTG
* * * *
11122764 GACCCGAG-TATGTGCAAGT-AGGAGTGCCCATAAGCCGTTGTT
1 GACCCG-GCTATGTGCGAGTGA-GAGTGCACATAAGTCGTTGCT
11122806 GACCCGGCTATGTGCGAGTGAGAGTGCACATAAGTCGTTGCT
1 GACCCGGCTATGTGCGAGTGAGAGTGCACATAAGTCGTTGCT
* * *
11122848 GACCCGACTATGTGCGAGTGGGAGTGCGCATAAGTCGTTGC
1 GACCCGGCTATGTGCGAGTGAGAGTGCACATAAGTCGTTGC
11122889 ATATGAGATG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 72 0.97
43 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGAGAGTGCACATAAGTCGTTGCT
Found at i:11123236 original size:21 final size:21
Alignment explanation
Indices: 11123191--11123236 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
11123181 GTACTGCAGC
*
11123191 TTCTAGCTACAGCGAGAATCG
1 TTCTAGCTACAGCGAGAAACG
* * *
11123212 TTCTCGCTACAGTGAGAAACT
1 TTCTAGCTACAGCGAGAAACG
11123233 TTCT
1 TTCT
11123237 GTTTTATGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (21 bp):
TTCTAGCTACAGCGAGAAACG
Found at i:11130499 original size:2 final size:2
Alignment explanation
Indices: 11130492--11130517 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11130482 ATGATGATTG
11130492 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11130518 GGTATATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11133754 original size:40 final size:37
Alignment explanation
Indices: 11133710--11133813 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 37
11133700 ACCTGGCTCA
*
11133710 TGTGCATCCCCCCACATTGTGCACATAACCGGCGCCATCG
1 TGTGCATCCCCCCACATCGTGCACATAA---GCGCCATCG
* *
11133750 TGTGCATCCCCCCACATCGTGCACAATTAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCAC-ATAAGCGCCATCG
* * *
11133788 TGTACATCCCCTCACATGGTGCACAT
1 TGTGCATCCCCCCACATCGTGCACAT
11133814 GGGCACTATC
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
37 2 0.04
38 29 0.51
40 23 0.40
41 3 0.05
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (37 bp):
TGTGCATCCCCCCACATCGTGCACATAAGCGCCATCG
Found at i:11133937 original size:2 final size:2
Alignment explanation
Indices: 11133930--11133956 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11133920 CATGCACAAC
11133930 AT 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 AT A
11133957 AATCATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11137002 original size:39 final size:37
Alignment explanation
Indices: 11136950--11137025 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 37
11136940 ACCCGAGAGG
*
11136950 AAGAAAAAGAGAAAGGAGGGAAAGGCTCGA-GTTGTGA
1 AAGAAAAAGAGAAAGGAAGGAAAGGCTC-ATGTTGTGA
11136987 AAGAAAAAGAAAGAAAGGAAGGAAAGGCTCATGTTGTGA
1 AAGAAAAAG--AGAAAGGAAGGAAAGGCTCATGTTGTGA
11137026 GGATTTAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 9 0.26
38 1 0.03
39 25 0.71
ACGTcount: A:0.49, C:0.05, G:0.34, T:0.12
Consensus pattern (37 bp):
AAGAAAAAGAGAAAGGAAGGAAAGGCTCATGTTGTGA
Found at i:11138089 original size:55 final size:55
Alignment explanation
Indices: 11138018--11138234 Score: 301
Period size: 55 Copynumber: 3.9 Consensus size: 55
11138008 ATCTATACAA
* * *
11138018 CCACCGGCTTATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCATCAT
1 CCACCGG-TCATCAGCTCATGTGCACTCCCACACTACACATAGCTGGAATCATCAT
* *
11138074 CCACCGGTCATCAGCTCATGTGCACTCCCACA-TAGCACATAGCTGGATTTATCAT
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACTA-CACATAGCTGGAATCATCAT
* * *
11138129 CCACCGGTCATCAGCTTATGTGCACTCCCACACCACACATAGTTGGAATCATCAT
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACTACACATAGCTGGAATCATCAT
** * *
11138184 CCACTAGTCATCAGCTCGTGTGCACTCCCACACTACACATAGCTGGGATCA
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACTACACATAGCTGGAATCA
11138235 CCCATCATCA
Statistics
Matches: 142, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
54 1 0.01
55 133 0.94
56 8 0.06
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (55 bp):
CCACCGGTCATCAGCTCATGTGCACTCCCACACTACACATAGCTGGAATCATCAT
Found at i:11138223 original size:110 final size:111
Alignment explanation
Indices: 11138018--11138229 Score: 338
Period size: 110 Copynumber: 1.9 Consensus size: 111
11138008 ATCTATACAA
* ** *
11138018 CCACCGGCTTATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCATCATCCACCGGTC
1 CCACCGGCTCATCAGCTCATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACCAGTC
11138083 ATCAGCTCATGTGCACTCCCACATAGCACATAGCTGGATTTATCAT
66 ATCAGCTCATGTGCACTCCCACATAGCACATAGCTGGATTTATCAT
* *
11138129 CCACCGG-TCATCAGCTTATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACTAGTC
1 CCACCGGCTCATCAGCTCATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACCAGTC
*
11138193 ATCAGCTCGTGTGCACTCCCACACTA-CACATAGCTGG
66 ATCAGCTCATGTGCACTCCCACA-TAGCACATAGCTGG
11138230 GATCACCCAT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
110 84 0.90
111 9 0.10
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.24
Consensus pattern (111 bp):
CCACCGGCTCATCAGCTCATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACCAGTC
ATCAGCTCATGTGCACTCCCACATAGCACATAGCTGGATTTATCAT
Found at i:11138276 original size:110 final size:107
Alignment explanation
Indices: 11138030--11138265 Score: 282
Period size: 110 Copynumber: 2.2 Consensus size: 107
11138020 ACCGGCTTAT
** *
11138030 CAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCATCATCCACCGGTCATCAGCTCATGT
1 CAGCT-ATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACCAGTCATCAGCTCATGT
* * * *
11138095 GCACTCCCACATAGCACATAGCTGGATTTATCATCCACCGGTCAT
65 GCACTCCCACATAGCACATAGCTGG--TGATCACCCACCGATCAC
* *
11138140 CAGCTTATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACTAGTCATCAGCTCGTGT
1 CAGC-TATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACCAGTCATCAGCTCATGT
*
11138205 GCACTCCCACACTA-CACATAGCTGG-GATCACCCATC-ATCAC
65 GCACTCCCACA-TAGCACATAGCTGGTGATCACCCACCGATCAC
* * *
11138246 CGGC-ATGTGCGCTTCCACAC
1 CAGCTATGTGCACTCCCACAC
11138266 TGAACGCACA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
104 14 0.13
106 6 0.05
107 8 0.07
110 80 0.72
111 3 0.03
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.23
Consensus pattern (107 bp):
CAGCTATGTGCACTCCCACACCACACATAGTTGGAATCATCATCCACCAGTCATCAGCTCATGTG
CACTCCCACATAGCACATAGCTGGTGATCACCCACCGATCAC
Found at i:11139054 original size:14 final size:14
Alignment explanation
Indices: 11139019--11139045 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11139009 AAAGAAAGGA
11139019 AAGGAAAAGAAAAC
1 AAGGAAAAGAAAAC
11139033 AAGGAAAAGAAAA
1 AAGGAAAAGAAAA
11139046 TGAAGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGGAAAAGAAAAC
Found at i:11141573 original size:25 final size:25
Alignment explanation
Indices: 11141545--11141592 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
11141535 ATACATTGCA
*
11141545 AGGCCACAGGTTGATATATGTGGCT
1 AGGCCACAAGTTGATATATGTGGCT
*
11141570 AGGCTACAAGTTGATATATGTGG
1 AGGCCACAAGTTGATATATGTGG
11141593 TTCGACCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.29
Consensus pattern (25 bp):
AGGCCACAAGTTGATATATGTGGCT
Found at i:11160333 original size:2 final size:2
Alignment explanation
Indices: 11160326--11160356 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11160316 TTTCTATGAC
11160326 AT AT AT 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 AT AT AT A
11160357 CACACNAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11160370 original size:69 final size:68
Alignment explanation
Indices: 11160285--11160431 Score: 276
Period size: 69 Copynumber: 2.1 Consensus size: 68
11160275 CAATGCCAAC
11160285 ATACAACACAATCACAAATATTTTCATAAACTTTCTATGACATATATATATATATATATATATAT
1 ATAC-ACACAATCACAAATATTTTCATAAACTTTCTATGACATATATATATATATATATATATAT
11160350 ATAT
65 ATAT
11160354 ATACACACNAATCACAAATATTTTCATAAACTTTCTATGACATATATATATATATATATATATAT
1 ATACACAC-AATCACAAATATTTTCATAAACTTTCTATGACATATATATATATATATATATATAT
11160419 ATAT
65 ATAT
11160423 ATACACACA
1 ATACACACA
11160432 TTATCATGTA
Statistics
Matches: 77, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
68 5 0.06
69 72 0.94
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.37
Consensus pattern (68 bp):
ATACACACAATCACAAATATTTTCATAAACTTTCTATGACATATATATATATATATATATATATA
TAT
Found at i:11160402 original size:2 final size:2
Alignment explanation
Indices: 11160395--11160425 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11160385 TTTCTATGAC
11160395 AT AT AT 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 AT AT AT A
11160426 CACACATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11160539 original size:42 final size:43
Alignment explanation
Indices: 11160461--11160543 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
11160451 ACCACACTAT
* *
11160461 GCTCATGTGCACTCCCTACTCACACATAGCTGGGTCATCATCA
1 GCTCATGTGCACTCCCTACACACACATAACTGGGTCATCATCA
* *
11160504 GCTCATGTGCACTCTC-ACACGCACATAACTGGGTCATCAT
1 GCTCATGTGCACTCCCTACACACACATAACTGGGTCATCAT
11160544 TATCACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 21 0.58
43 15 0.42
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (43 bp):
GCTCATGTGCACTCCCTACACACACATAACTGGGTCATCATCA
Found at i:11165762 original size:42 final size:42
Alignment explanation
Indices: 11165642--11165764 Score: 174
Period size: 43 Copynumber: 2.9 Consensus size: 42
11165632 ATACTCCACT
* * * * *
11165642 CATGTGCACTCCCTACTCGCACATAGTTGGGTCATCATTAGCC
1 CATGTGCACTCCC-ACACGCACATAGCTGGGTCATCATCAACA
11165685 CATGTGCACTCCCACACTGCACATAGCTGGGTCATCATCAACA
1 CATGTGCACTCCCACAC-GCACATAGCTGGGTCATCATCAACA
*
11165728 CATGTGCATTCCCACACGCACATAGCTGGGTCATCAT
1 CATGTGCACTCCCACACGCACATAGCTGGGTCATCAT
11165765 TATCACACAA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
42 23 0.32
43 50 0.68
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (42 bp):
CATGTGCACTCCCACACGCACATAGCTGGGTCATCATCAACA
Found at i:11166251 original size:29 final size:30
Alignment explanation
Indices: 11166214--11166270 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
11166204 GTCACACTAA
*
11166214 AAATGATTAAACAATCTCAACAA-TAAATC
1 AAATGATTAAACAATATCAACAACTAAATC
* * *
11166243 AAATTATTAGACATTATCAACAACTAAA
1 AAATGATTAAACAATATCAACAACTAAA
11166271 AATATCAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (30 bp):
AAATGATTAAACAATATCAACAACTAAATC
Found at i:11176754 original size:54 final size:54
Alignment explanation
Indices: 11176678--11176842 Score: 231
Period size: 54 Copynumber: 3.1 Consensus size: 54
11176668 TTTCTAGCAA
* *
11176678 ACATCCCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACCTAGCCGG
1 ACATCCCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGG
** * *
11176732 ATGTCCCATCTCACCCAGCTCATGTGCATCCCACCACATTGTTCACATAGCCGG
1 ACATCCCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGG
* * * * *
11176786 ACATCCCATCTTAGCCAGCTCATGTGCATCCTACCACATCATGCACATAGACGG
1 ACATCCCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGG
11176840 ACA
1 ACA
11176843 GTATCACCAT
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.21
Consensus pattern (54 bp):
ACATCCCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGG
Found at i:11179501 original size:19 final size:19
Alignment explanation
Indices: 11179473--11179510 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11179463 CCATTTGACT
* *
11179473 TATTGGAGTATGATTTGAG
1 TATTGAAGTATGATATGAG
11179492 TATTGAAGTATGATATGAG
1 TATTGAAGTATGATATGAG
11179511 ATTTAGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGAAGTATGATATGAG
Found at i:11182130 original size:15 final size:15
Alignment explanation
Indices: 11182091--11182134 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
11182081 AGATCAGAGA
11182091 TTTTGGTTTTAAAGC
1 TTTTGGTTTTAAAGC
*
11182106 -TTTGAATTTTAAAGC
1 TTTTG-GTTTTAAAGC
11182121 TTTTGGTTTTAAAG
1 TTTTGGTTTTAAAG
11182135 TTGTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (15 bp):
TTTTGGTTTTAAAGC
Found at i:11192494 original size:42 final size:42
Alignment explanation
Indices: 11192372--11192498 Score: 191
Period size: 43 Copynumber: 3.0 Consensus size: 42
11192362 CCACACTCCA
* * * *
11192372 CTCATGTGCACTCACTACTCGCACATAGTTGGGTCATCATCAG
1 CTCATGTGCACTC-CCACACGCACATAGCTGGGTCATCATTAG
*
11192415 CTCATATGCACTCCCACACTGCACATAGCTGGGTCATCATTAG
1 CTCATGTGCACTCCCACAC-GCACATAGCTGGGTCATCATTAG
11192458 CTCATGTGCACTCCCACACGCACATAGCTGGGTCATCATTA
1 CTCATGTGCACTCCCACACGCACATAGCTGGGTCATCATTA
11192499 TCATACAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
42 26 0.34
43 51 0.66
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.26
Consensus pattern (42 bp):
CTCATGTGCACTCCCACACGCACATAGCTGGGTCATCATTAG
Found at i:11196759 original size:19 final size:21
Alignment explanation
Indices: 11196737--11196776 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11196727 AAATCATTCC
11196737 TTCATC-TT-ACATCTAACTT
1 TTCATCATTGACATCTAACTT
*
11196756 TTCATCATTGACATTTAACTT
1 TTCATCATTGACATCTAACTT
11196777 GCCCTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.47
Consensus pattern (21 bp):
TTCATCATTGACATCTAACTT
Found at i:11197599 original size:18 final size:17
Alignment explanation
Indices: 11197576--11197615 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
11197566 CTTAAAGAAG
11197576 AAGAAGAAAAAGACAAGA
1 AAGAAGAAAAAGA-AAGA
*
11197594 AAGAAGCAAAAGAAAGA
1 AAGAAGAAAAAGAAAGA
11197611 AAGAA
1 AAGAA
11197616 AAGCATTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAGAAAGA
Found at i:11201836 original size:42 final size:41
Alignment explanation
Indices: 11201789--11201921 Score: 149
Period size: 42 Copynumber: 3.2 Consensus size: 41
11201779 AATGTTGTGT
11201789 GCATAAGTTGATACTGACCTAGCTATGTGCGAGTAGGAGTGC
1 GCATAAGTTGATACTGACCT-GCTATGTGCGAGTAGGAGTGC
** * * * *
11201831 GCATAAGCCGATGCTGACCCTGCTATGTGTGAGTGGGAGTGT
1 GCATAAGTTGATACTGA-CCTGCTATGTGCGAGTAGGAGTGC
* * *
11201873 GCATAAGTTGATACTGACCCGGCTGTGTACGAGTAGGAGTGC
1 GCATAAGTTGATACTGA-CCTGCTATGTGCGAGTAGGAGTGC
*
11201915 GAATAAG
1 GCATAAG
11201922 CCAATGATGA
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 71 0.96
43 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (41 bp):
GCATAAGTTGATACTGACCTGCTATGTGCGAGTAGGAGTGC
Found at i:11201933 original size:42 final size:42
Alignment explanation
Indices: 11201810--11201973 Score: 132
Period size: 42 Copynumber: 3.9 Consensus size: 42
11201800 TACTGACCTA
* * *
11201810 GCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTGACCCT
1 GCTATGTACGAGTAGGAGTGCGCATAAGCCGATGATGACCCG
** * * **
11201852 GCTATGTGTGAGTGGGAGTGTGCATAAGTTGAT-ACTGACCCG
1 GCTATGTACGAGTAGGAGTGCGCATAAGCCGATGA-TGACCCG
* * * *
11201894 GCTGTGTACGAGTAGGAGTGCGAATAAGCCAATGATGACCCA
1 GCTATGTACGAGTAGGAGTGCGCATAAGCCGATGATGACCCG
* * * * ** *
11201936 GCCATGTGCTAGTGGGAGTGCATATAAGCTGATGATGA
1 GCTATGTACGAGTAGGAGTGCGCATAAGCCGATGATGA
11201974 TGGGAAGGTG
Statistics
Matches: 94, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
42 93 0.99
43 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.24
Consensus pattern (42 bp):
GCTATGTACGAGTAGGAGTGCGCATAAGCCGATGATGACCCG
Found at i:11201933 original size:84 final size:84
Alignment explanation
Indices: 11201785--11201955 Score: 245
Period size: 84 Copynumber: 2.0 Consensus size: 84
11201775 GAATAATGTT
* * * * *
11201785 GTGTGCATAAGTTGATACTGACCTAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTGACC
1 GTGTGCATAAGTTGATACTGACCCAGCTATGTACGAGTAGGAGTGCGAATAAGCCAATGATGACC
* *
11201850 CTGCTATGTG-TGAGTGGGA
66 CAGCCATGTGCT-AGTGGGA
* *
11201869 GTGTGCATAAGTTGATACTGACCCGGCTGTGTACGAGTAGGAGTGCGAATAAGCCAATGATGACC
1 GTGTGCATAAGTTGATACTGACCCAGCTATGTACGAGTAGGAGTGCGAATAAGCCAATGATGACC
11201934 CAGCCATGTGCTAGTGGGA
66 CAGCCATGTGCTAGTGGGA
11201953 GTG
1 GTG
11201956 CATATAAGCT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 76 0.99
85 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (84 bp):
GTGTGCATAAGTTGATACTGACCCAGCTATGTACGAGTAGGAGTGCGAATAAGCCAATGATGACC
CAGCCATGTGCTAGTGGGA
Found at i:11202004 original size:2 final size:2
Alignment explanation
Indices: 11201997--11202026 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11201987 ATGATGATTG
11201997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11202027 TTCCNGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11202043 original size:57 final size:56
Alignment explanation
Indices: 11201975--11202085 Score: 213
Period size: 57 Copynumber: 2.0 Consensus size: 56
11201965 TGATGATGAT
11201975 GGGAAGGTGTGCATGATGATTGATATATATATATATATATATATATATATATTTCC
1 GGGAAGGTGTGCATGATGATTGATATATATATATATATATATATATATATATTTCC
11202031 NGGGAAGGTGTGCATGATGATTGATATATATATATATATATATATATATATATTT
1 -GGGAAGGTGTGCATGATGATTGATATATATATATATATATATATATATATATTT
11202086 TCATACATAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.41
Consensus pattern (56 bp):
GGGAAGGTGTGCATGATGATTGATATATATATATATATATATATATATATATTTCC
Found at i:11202061 original size:2 final size:2
Alignment explanation
Indices: 11202054--11202083 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11202044 ATGATGATTG
11202054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11202084 TTTCATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11205869 original size:22 final size:22
Alignment explanation
Indices: 11205843--11205884 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
11205833 AGGGAGATAG
11205843 AAAGTAGAA-TAAATTTAGGGAA
1 AAAGTAGAAGT-AATTTAGGGAA
11205865 AAAGTAGAAGTAATTTAGGG
1 AAAGTAGAAGTAATTTAGGG
11205885 GTAATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (22 bp):
AAAGTAGAAGTAATTTAGGGAA
Found at i:11207796 original size:20 final size:20
Alignment explanation
Indices: 11207771--11207808 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11207761 TATCTCATTT
11207771 CTTCCAGCACCTTCTTCTCA
1 CTTCCAGCACCTTCTTCTCA
*
11207791 CTTCCAGCAGCTTCTTCT
1 CTTCCAGCACCTTCTTCT
11207809 TCTTCTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.42, G:0.08, T:0.37
Consensus pattern (20 bp):
CTTCCAGCACCTTCTTCTCA
Found at i:11208748 original size:35 final size:35
Alignment explanation
Indices: 11208709--11208816 Score: 162
Period size: 35 Copynumber: 3.1 Consensus size: 35
11208699 GGAGTTCGTG
*
11208709 TGATGATATTGAAATATGCATGTAGGGAGTGCACA
1 TGATGATATTGAAATATGCGTGTAGGGAGTGCACA
* *
11208744 TGATGATATTGAAATGTTCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATATGCGTGTAGGGAGTGCACA
***
11208779 TGATGATATTGCCTTATGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATATGCGTGTAGGGAGTGCACA
11208814 TGA
1 TGA
11208817 GCTGAGTAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.31
Consensus pattern (35 bp):
TGATGATATTGAAATATGCGTGTAGGGAGTGCACA
Found at i:11208854 original size:2 final size:2
Alignment explanation
Indices: 11208847--11208871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11208837 TTTTCATGTG
11208847 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11208872 GCTATAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11220028 original size:55 final size:55
Alignment explanation
Indices: 11219933--11220085 Score: 229
Period size: 55 Copynumber: 2.8 Consensus size: 55
11219923 AACCACCGGC
* * ** * *
11219933 TCATCAACTCATGTGCACTCCCACACCT-CAAATAACTGGAATCATCATCCACTGG
1 TCATCAGCTCATGTGCACTCCCACA-CTGCACATAGTTGGAATCATCATCAACAGG
11219988 TCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCATCATCAACAGG
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCATCATCAACAGG
11220043 TCATCAGCTCATGTGCACTCCCACAC-GCACATAGTTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCA
11220086 CCCATCATCA
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 19 0.21
55 72 0.79
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCATCATCAACAGG
Found at i:11224601 original size:38 final size:40
Alignment explanation
Indices: 11224503--11224611 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 40
11224493 CACATCCAGC
* * *
11224503 TCATGTACATCCCCCCACATCCTGCACATAGTCGGAGTCA
1 TCATGTACATCCCCCCACATCGTGCACATAGTCAGAGCCA
* ** * *
11224543 TCATGTGCATCCCCTTACATCGTGTACA-A-TCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGTCAGAGCCA
*
11224581 T-AGTGTACATCCCCCCACATCGTGCATATAG
1 TCA-TGTACATCCCCCCACATCGTGCACATAG
11224612 CACTATCATC
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
37 1 0.02
38 27 0.51
39 2 0.04
40 23 0.43
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.26
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGTCAGAGCCA
Found at i:11247607 original size:43 final size:43
Alignment explanation
Indices: 11247537--11247655 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
11247527 GTAATTATAT
* *
11247537 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
11247580 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* * *
11247623 TGACCCAGCCATGTGTGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
11247656 GAGCTGGTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:11247665 original size:43 final size:43
Alignment explanation
Indices: 11247547--11247668 Score: 165
Period size: 43 Copynumber: 2.8 Consensus size: 43
11247537 TGACTCGGCT
* **
11247547 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
11247590 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* * *
11247633 ATGTGTGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
11247669 TGATGATGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 69 0.99
ACGTcount: A:0.23, C:0.18, G:0.39, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:11251140 original size:2 final size:2
Alignment explanation
Indices: 11251135--11251169 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11251125 TATATATATA
11251135 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
11251170 ATACGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:11251349 original size:42 final size:42
Alignment explanation
Indices: 11251196--11251337 Score: 203
Period size: 42 Copynumber: 3.4 Consensus size: 42
11251186 GTAATGATAT
* *
11251196 TGACCCGGCTATGTGCTAGGGGGAGTGCGCATAAGCCGATGC
1 TGACCCAGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGC
* * *
11251238 TAACCCAGCTATGTGCGAGGGGGAGTGTGCATAAGTCGATGC
1 TGACCCAGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGC
** *
11251280 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATTAGCCGATGC
1 TGACCCAGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGC
*
11251322 TGACCCAGCCATGTGC
1 TGACCCAGCTATGTGC
11251338 TAGTGGAAGT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.20
Consensus pattern (42 bp):
TGACCCAGCTATGTGCGAGGGGGAGTGCGCATAAGCCGATGC
Found at i:11263749 original size:20 final size:20
Alignment explanation
Indices: 11263719--11263776 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
11263709 ATTCATGGGA
11263719 AGAGTAAAGTCTCGAGACTTT
1 AGAG-AAAGTCTCGAGACTTT
*
11263740 AGAGAAAGTCTAGAGACTTT
1 AGAGAAAGTCTCGAGACTTT
* *
11263760 AGAGGAAGTCTCTAGAC
1 AGAGAAAGTCTCGAGAC
11263777 ATGTTACCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (20 bp):
AGAGAAAGTCTCGAGACTTT
Found at i:11284840 original size:3 final size:3
Alignment explanation
Indices: 11284832--11284865 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11284822 ACACAGTAGC
11284832 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
11284866 ATTGTTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:11292311 original size:12 final size:11
Alignment explanation
Indices: 11292291--11292327 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
11292281 TTAAAGGAAT
11292291 AAAAAAATAAA
1 AAAAAAATAAA
11292302 AAATAAAATAAA
1 AAA-AAAATAAA
11292314 AAAATAAATAAA
1 AAAA-AAATAAA
11292326 AA
1 AA
11292328 GGGTGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:11300829 original size:130 final size:128
Alignment explanation
Indices: 11300595--11300854 Score: 502
Period size: 130 Copynumber: 2.0 Consensus size: 128
11300585 CCCCTCTGAC
11300595 TAAGCTGACACATAAGGATACAAAATTTGAGTGGTTTGATGCTTGTGAGGATAGCTTTGAGAAGC
1 TAAGCTGACACATAAGGATACAAAATTTGAGTGGTTTGATGCTTGTGAGGATAGCTTTGAGAAGC
11300660 TTAAGGCATGTCTCACCGCAGCTCCAGTGTTAAGCCTACCGCAAGGCACACGGGGGTTATACGG
66 TTAAGGCATGTCTCACCGCAGCTCCAGTGTTAAGCCTACCGCAAGGCACA-GGGGGTTATACGG
11300724 TNAAGCTGACACATAAGGATACAAAATTTGAGTGGTTTGATGCTTGTGAGGATAGCTTTGAGAAG
1 T-AAGCTGACACATAAGGATACAAAATTTGAGTGGTTTGATGCTTGTGAGGATAGCTTTGAGAAG
11300789 CTTAAGGCATGTCTCACCGCAGCTCCAGTGTTAAGCCTACCGCAAGGCACAGGGGGTTATACGG
65 CTTAAGGCATGTCTCACCGCAGCTCCAGTGTTAAGCCTACCGCAAGGCACAGGGGGTTATACGG
11300853 TA
1 TA
11300855 TTCTGTGATG
Statistics
Matches: 130, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
128 1 0.01
129 15 0.12
130 114 0.88
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (128 bp):
TAAGCTGACACATAAGGATACAAAATTTGAGTGGTTTGATGCTTGTGAGGATAGCTTTGAGAAGC
TTAAGGCATGTCTCACCGCAGCTCCAGTGTTAAGCCTACCGCAAGGCACAGGGGGTTATACGG
Found at i:11313652 original size:11 final size:12
Alignment explanation
Indices: 11313625--11313657 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
11313615 CTTCTTGTAT
*
11313625 TTATTATTGTCA
1 TTATTATTATCA
11313637 TTATTATTAT-A
1 TTATTATTATCA
11313648 TTATTATTAT
1 TTATTATTAT
11313658 TATTTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (12 bp):
TTATTATTATCA
Found at i:11313659 original size:20 final size:19
Alignment explanation
Indices: 11313622--11313661 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
11313612 TTCCTTCTTG
*
11313622 TATTTATTATTGTCATTAT
1 TATTTATTATTATCATTAT
*
11313641 TATTATATTATTATTATTAT
1 TATT-TATTATTATCATTAT
11313661 T
1 T
11313662 TTGTTTCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TATTTATTATTATCATTAT
Found at i:11318897 original size:28 final size:29
Alignment explanation
Indices: 11318856--11318915 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
11318846 GTCTATGGGC
*
11318856 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
11318884 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
11318914 AA
1 AA
11318916 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:11377381 original size:8 final size:8
Alignment explanation
Indices: 11377368--11377392 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11377358 AAGAGATATT
11377368 AGAAAAGA
1 AGAAAAGA
11377376 AGAAAAGA
1 AGAAAAGA
11377384 AGAAAAGA
1 AGAAAAGA
11377392 A
1 A
11377393 AAAGGCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:11390291 original size:19 final size:19
Alignment explanation
Indices: 11390257--11390297 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11390247 ATTAAAGTTG
11390257 AGAAGAATTTGAAAGATTCA
1 AGAAGAATTTGAAAGA-TCA
*
11390277 AGAAG-ATTTGGAAGATCA
1 AGAAGAATTTGAAAGATCA
11390295 AGA
1 AGA
11390298 TTATAGTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 9 0.45
20 5 0.25
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (19 bp):
AGAAGAATTTGAAAGATCA
Found at i:11395433 original size:43 final size:43
Alignment explanation
Indices: 11395380--11395466 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
11395370 TGATAATTAG
* * * *
11395380 GACCTAGCTATGCGCGGTGTGGGAGTGCACATGAGTTGATGAT
1 GACCCAGCTATGCGCGATGGGGGAGTGCACATGAGCTGATGAT
*
11395423 GACCCAGCTATGTGCGATGGGGGAGTGCACATGAGCTGATGAT
1 GACCCAGCTATGCGCGATGGGGGAGTGCACATGAGCTGATGAT
11395466 G
1 G
11395467 CTATTGCATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (43 bp):
GACCCAGCTATGCGCGATGGGGGAGTGCACATGAGCTGATGAT
Found at i:11395544 original size:2 final size:2
Alignment explanation
Indices: 11395537--11395620 Score: 78
Period size: 2 Copynumber: 41.5 Consensus size: 2
11395527 ATGATGTATG
** ** **
11395537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NNN NN NN
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
** *
11395580 NN NA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11395621 GTTATAGAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11398326 original size:31 final size:31
Alignment explanation
Indices: 11398285--11398343 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
11398275 CACTATTACG
*
11398285 TCCACGACCAAATTTAGTTGCGAGAAATACC
1 TCCACAACCAAATTTAGTTGCGAGAAATACC
11398316 TCCACAACCAAATTTAGTTGCGAGAAAT
1 TCCACAACCAAATTTAGTTGCGAGAAAT
11398344 GTTGATCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TCCACAACCAAATTTAGTTGCGAGAAATACC
Found at i:11402650 original size:78 final size:77
Alignment explanation
Indices: 11402555--11402788 Score: 389
Period size: 78 Copynumber: 3.0 Consensus size: 77
11402545 GCTAAAAACA
11402555 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGTTCATGTTTATATATCCATGA
1 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGG-TCATGTTTATATATCCATGA
11402620 CTCATCTCATTTC
65 CTCATCTCATTTC
* *
11402633 AATTTAAACATTTAAGGATTTAAAAATAAATAAGTGGTAAAAGACTCATGTTTATATATCCATGA
1 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAG-GTCATGTTTATATATCCATGA
11402698 CTCATCTCATTTC
65 CTCATCTCATTTC
* *
11402711 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGTCGATATTTATATATCCAAGA
1 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGTC-ATGTTTATATATCCATGA
11402776 C-CTATCTCATTTC
65 CTC-ATCTCATTTC
11402789 TTACATGTGT
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
77 3 0.02
78 144 0.98
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (77 bp):
AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGTCATGTTTATATATCCATGAC
TCATCTCATTTC
Found at i:11404305 original size:23 final size:24
Alignment explanation
Indices: 11404275--11404340 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
11404265 TGTTGGACAG
11404275 ATTTTCAACAGAATTTTTTCAA-AA
1 ATTTTCAAC-GAATTTTTTCAACAA
* *
11404299 A-TTTCAACTAATTTTTACAACAA
1 ATTTTCAACGAATTTTTTCAACAA
11404322 ATTTTCAACGGAATTTTTT
1 ATTTTCAAC-GAATTTTTT
11404341 TGTTGGAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.29
23 10 0.29
24 8 0.23
25 7 0.20
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.44
Consensus pattern (24 bp):
ATTTTCAACGAATTTTTTCAACAA
Found at i:11404538 original size:14 final size:14
Alignment explanation
Indices: 11404519--11404586 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
11404509 TAAGCTATTA
11404519 CCAACGGAAATTTT
1 CCAACGGAAATTTT
11404533 CCAACGG-AATATTT
1 CCAACGGAAAT-TTT
**
11404547 -CATTGGAAAAGTTATT
1 CCAACGG-AAA-TT-TT
*
11404563 ACCAACAGAAATTTT
1 -CCAACGGAAATTTT
11404578 CCAACGGAA
1 CCAACGGAA
11404587 TATTCCGTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
13 7 0.17
14 18 0.44
15 5 0.12
16 5 0.12
17 3 0.07
18 3 0.07
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (14 bp):
CCAACGGAAATTTT
Found at i:11404574 original size:45 final size:46
Alignment explanation
Indices: 11404493--11404590 Score: 162
Period size: 45 Copynumber: 2.2 Consensus size: 46
11404483 GGTTTTAACA
* *
11404493 GAATTTTTCATTGGAATAAGCTATTACCAACGGAAATTTTCCAACG
1 GAATATTTCATTGGAATAAGCTATTACCAACAGAAATTTTCCAACG
*
11404539 GAATATTTCATTGGAA-AAGTTATTACCAACAGAAATTTTCCAACG
1 GAATATTTCATTGGAATAAGCTATTACCAACAGAAATTTTCCAACG
11404584 GAATATT
1 GAATATT
11404591 CCGTTGGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 34 0.69
46 15 0.31
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (46 bp):
GAATATTTCATTGGAATAAGCTATTACCAACAGAAATTTTCCAACG
Found at i:11405141 original size:2 final size:2
Alignment explanation
Indices: 11405134--11405158 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11405124 NNNNNNNNNN
11405134 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
11405159 GATAAACCTG
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:11405556 original size:18 final size:17
Alignment explanation
Indices: 11405516--11405556 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
11405506 TATATTGAGT
11405516 AATATTAAAAAATTTAA
1 AATATTAAAAAATTTAA
**
11405533 TTTATTAATAAAATTTAA
1 AATATTAA-AAAATTTAA
11405551 AATATT
1 AATATT
11405557 CAAATATGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTAAAAAATTTAA
Found at i:11411960 original size:30 final size:30
Alignment explanation
Indices: 11411921--11411984 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
11411911 ATCTCTTGAT
* * *
11411921 TGAAGATGAAGAAGATGACATGCAAAGAGA
1 TGAAAATGAAAAAGATAACATGCAAAGAGA
*
11411951 TGAAAATGAAAAAGATAACATGGAAAGAGA
1 TGAAAATGAAAAAGATAACATGCAAAGAGA
11411981 TGAA
1 TGAA
11411985 GATCAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.05, G:0.27, T:0.14
Consensus pattern (30 bp):
TGAAAATGAAAAAGATAACATGCAAAGAGA
Found at i:11413290 original size:2 final size:2
Alignment explanation
Indices: 11413283--11413319 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11413273 ACTTTCTATA
11413283 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
11413320 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11413787 original size:2 final size:2
Alignment explanation
Indices: 11413780--11413805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11413770 NNNNNNNNNN
11413780 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11413806 CAACACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11416455 original size:2 final size:2
Alignment explanation
Indices: 11416448--11416484 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11416438 TTGTGTTATC
11416448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11416485 GTGGTTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11427417 original size:42 final size:42
Alignment explanation
Indices: 11427318--11427428 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
11427308 AGCTCATATG
* * * * * *
11427318 CACTCCCACTAGCACATGGCTGGGTCCGCATCGGCTTATGCA
1 CACTCCTACTCGCACATAGCCGGGTCAGCATCAGCTTATGCA
* * * *
11427360 CACTCTTATTGGCACATAGTCGGGTCAGCATCAGCTTATGCA
1 CACTCCTACTCGCACATAGCCGGGTCAGCATCAGCTTATGCA
11427402 CACTCCTACTCGCACATAGCCGGGTCA
1 CACTCCTACTCGCACATAGCCGGGTCA
11427429 ATATCATTAC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (42 bp):
CACTCCTACTCGCACATAGCCGGGTCAGCATCAGCTTATGCA
Found at i:11433684 original size:12 final size:12
Alignment explanation
Indices: 11433667--11433704 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11433657 CTTGGGTAAG
11433667 ATACGTGAGGAA
1 ATACGTGAGGAA
11433679 ATACGTG-GAGAA
1 ATACGTGAG-GAA
*
11433691 ATACGTGAAGAA
1 ATACGTGAGGAA
11433703 AT
1 AT
11433705 TAAGAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.96
ACGTcount: A:0.45, C:0.08, G:0.29, T:0.18
Consensus pattern (12 bp):
ATACGTGAGGAA
Found at i:11434851 original size:78 final size:78
Alignment explanation
Indices: 11434719--11434874 Score: 255
Period size: 78 Copynumber: 2.0 Consensus size: 78
11434709 GCTAAAAACA
*
11434719 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGCTCATGTTTATATATCC-ATG
1 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGCTCATATTTATATATCCAAT-
11434783 A-CTCATCTCATTTC
65 ACCT-ATCTCATTTC
11434797 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGC-CGATATTTATATATCCAAT
1 AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGCTC-ATATTTATATATCCAAT
11434861 ACCTATCTCATTTC
65 ACCTATCTCATTTC
11434875 TTACATGTGT
Statistics
Matches: 74, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
77 1 0.01
78 69 0.93
79 4 0.05
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (78 bp):
AATTTAAACATTTAAGGACTTAAAAATAAATAAGTGGTAAAAGGCTCATATTTATATATCCAATA
CCTATCTCATTTC
Found at i:11442355 original size:2 final size:2
Alignment explanation
Indices: 11442348--11442388 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11442338 AGCATGAAAA
11442348 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
11442389 GAAAAGAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11443212 original size:22 final size:22
Alignment explanation
Indices: 11443180--11443226 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
11443170 ACTAACTATT
11443180 ATTAATCAAAATATCATTTGTC
1 ATTAATCAAAATATCATTTGTC
*
11443202 ATTAATTAAAATATCATTTGTC
1 ATTAATCAAAATATCATTTGTC
11443224 ATT
1 ATT
11443227 TTATGTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTAATCAAAATATCATTTGTC
Found at i:11443811 original size:36 final size:36
Alignment explanation
Indices: 11443761--11443833 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
11443751 CTAAATCAAT
*
11443761 TTAAAATCAATTACAAAACTTATAAATGTATTTTTG
1 TTAAAATCAATTACAAAACTTATAAAGGTATTTTTG
*
11443797 TTAAAATCACTTACAAAACTTATAAAGGTATTTTTG
1 TTAAAATCAATTACAAAACTTATAAAGGTATTTTTG
11443833 T
1 T
11443834 ATCAGTACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (36 bp):
TTAAAATCAATTACAAAACTTATAAAGGTATTTTTG
Found at i:11452521 original size:24 final size:23
Alignment explanation
Indices: 11452468--11452521 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
11452458 TTAAAGTTTT
* *
11452468 TGAATTACCAAAACAATAAAAAA
1 TGAAATACCAAAACAAAAAAAAA
11452491 TGAAAATACCAACAA-AAAAAAAATA
1 TG-AAATACCAA-AACAAAAAAAA-A
11452516 TGAAAT
1 TGAAAT
11452522 CTTCTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.08
24 19 0.73
25 5 0.19
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (23 bp):
TGAAATACCAAAACAAAAAAAAA
Found at i:11453735 original size:18 final size:18
Alignment explanation
Indices: 11453712--11453769 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
11453702 TTTCGTCTAA
11453712 AAATTTCTTCATTGATTC
1 AAATTTCTTCATTGATTC
* * *
11453730 AAATTTTTTCGTCT-A--A
1 AAATTTCTTCAT-TGATTC
11453746 AAATTTCTTCATTGATTC
1 AAATTTCTTCATTGATTC
11453764 AAATTT
1 AAATTT
11453770 TGAGATATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 1 0.03
16 11 0.37
18 17 0.57
19 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (18 bp):
AAATTTCTTCATTGATTC
Found at i:11453745 original size:34 final size:34
Alignment explanation
Indices: 11453702--11453770 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
11453692 TGATCATTCC
11453702 TTTCGTCTAAAAATTTCTTCATTGATTCAAATTT
1 TTTCGTCTAAAAATTTCTTCATTGATTCAAATTT
11453736 TTTCGTCTAAAAATTTCTTCATTGATTCAAATTT
1 TTTCGTCTAAAAATTTCTTCATTGATTCAAATTT
11453770 T
1 T
11453771 GAGATATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (34 bp):
TTTCGTCTAAAAATTTCTTCATTGATTCAAATTT
Found at i:11454568 original size:34 final size:34
Alignment explanation
Indices: 11454525--11454591 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
11454515 ATAAATGATA
11454525 ATTTGTTAAAAGTAAAATCTTATATAACAATGTC
1 ATTTGTTAAAAGTAAAATCTTATATAACAATGTC
11454559 ATTTGTTAAAAGTAAAATCTTATATAACAATGT
1 ATTTGTTAAAAGTAAAATCTTATATAACAATGT
11454592 AAGAATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (34 bp):
ATTTGTTAAAAGTAAAATCTTATATAACAATGTC
Found at i:11454809 original size:19 final size:19
Alignment explanation
Indices: 11454785--11454823 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11454775 TATGGCCATT
11454785 TGGGTTGAATGTTGTAGCA
1 TGGGTTGAATGTTGTAGCA
11454804 TGGGTTGAATGTTGTAGCA
1 TGGGTTGAATGTTGTAGCA
11454823 T
1 T
11454824 ATGCAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.36, T:0.38
Consensus pattern (19 bp):
TGGGTTGAATGTTGTAGCA
Found at i:11454998 original size:28 final size:28
Alignment explanation
Indices: 11454911--11454983 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
11454901 GGGGTGTAAG
* **
11454911 AAAATAGAAATTAGTA-AAAGCATGTTAC
1 AAAATAGAAATTA-TACAAGGCATGCAAC
11454939 AAAATAGAAATTATACAAGGCATGCAAC
1 AAAATAGAAATTATACAAGGCATGCAAC
*
11454967 AAAATAGAGATTATACA
1 AAAATAGAAATTATACA
11454984 GGATGTGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 2 0.05
28 38 0.95
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.22
Consensus pattern (28 bp):
AAAATAGAAATTATACAAGGCATGCAAC
Found at i:11457112 original size:29 final size:29
Alignment explanation
Indices: 11457080--11457163 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
11457070 GGTCGCACTT
*
11457080 GTAATTGACAAAATATAGAAGGTTGGAGC
1 GTAATTGACAATATATAGAAGGTTGGAGC
* * *
11457109 GTAATTGACAATATATATAAGGTTGGCGT
1 GTAATTGACAATATATAGAAGGTTGGAGC
* *
11457138 GTAACTAACAATATATAGAAGGTTGG
1 GTAATTGACAATATATAGAAGGTTGG
11457164 CATGTCATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (29 bp):
GTAATTGACAATATATAGAAGGTTGGAGC
Found at i:11475776 original size:35 final size:35
Alignment explanation
Indices: 11475709--11475777 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
11475699 AACCACTTTG
*
11475709 GGTTTTAGTTGAGCCTGTGAAAAACTAGTGTAAAA
1 GGTTTTAGTTGAGCCTGTGAAAAACCAGTGTAAAA
* * *
11475744 GGTTTTGGTTGAGCCTG-GTAAAAGCCATTGTAAA
1 GGTTTTAGTTGAGCCTGTG-AAAAACCAGTGTAAA
11475778 GCTTGGTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (35 bp):
GGTTTTAGTTGAGCCTGTGAAAAACCAGTGTAAAA
Found at i:11477327 original size:20 final size:19
Alignment explanation
Indices: 11477302--11477357 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
11477292 TGGTCTATGG
11477302 AATTGAATTAGTTAATTTAA
1 AATTGAATTAGTTAATTT-A
*
11477322 AATTGAA-TATGATTCATTTA
1 AATTGAATTA-G-TTAATTTA
11477342 AATT-AATTAGTTAATT
1 AATTGAATTAGTTAATT
11477358 AATAATATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 15 0.48
21 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (19 bp):
AATTGAATTAGTTAATTTA
Found at i:11477732 original size:17 final size:17
Alignment explanation
Indices: 11477703--11477735 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11477693 TTTAATTAGA
11477703 AATTGGTTAAATATTAT
1 AATTGGTTAAATATTAT
11477720 AATT-GTTATAATATTA
1 AATTGGTTA-AATATTA
11477736 AGGACTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
AATTGGTTAAATATTAT
Found at i:11479728 original size:43 final size:43
Alignment explanation
Indices: 11479651--11479781 Score: 185
Period size: 43 Copynumber: 3.1 Consensus size: 43
11479641 TTGTGTGGTA
*
11479651 ATGATGACCCAGCTATGTG-TGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
* * *
11479693 ATGATGACTCAACTATGTGCGGTGTGGGAGTGCACATGAGTTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
11479736 ATGATGACCCAGTTATGTGCGAGT-AGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCG-GTGTGGGAGTGCACATGAGCTG
11479779 ATG
1 ATG
11479782 TGGTGGGATG
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
42 17 0.22
43 59 0.76
44 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
Found at i:11479814 original size:2 final size:2
Alignment explanation
Indices: 11479807--11479856 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
11479797 TATGATGATG
11479807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11479849 TA TA TA TA
1 TA TA TA TA
11479857 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11479941 original size:2 final size:2
Alignment explanation
Indices: 11479934--11479988 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
11479924 NNNNNNNNNN
11479934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11479976 TA TA TA TA AA TA T
1 TA TA TA TA TA TA T
11479989 GTGCATTATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11483755 original size:298 final size:296
Alignment explanation
Indices: 11483205--11483756 Score: 664
Period size: 298 Copynumber: 1.9 Consensus size: 296
11483195 CAGGGTTGGT
* * ** *
11483205 GTGTTGTATAATCAACTGTCAGGCATGGTGCATCTCATACTCATCTGTTGTATGTTATGGTGTGT
1 GTGTTGCATAATCAACTGTCAGGAATGGCACATCTCATACTCATCTATTGTATGTTATGGTGTGT
* * *
11483270 TGCATATAACCCTGTCAGTCATGGTGTGTATGATGGTTGTAGGTCAAGGTTCGTACGTCGCATAT
66 TGCATATAACCCTATCAGTCATGGAGTGTATGATGGTTGCAGGTCAA-GTTCGTACGTCGCATAT
* *
11483335 AACCTGTCATGCATGGCATGTTGCATTTTACCATATCAGCCACTAGTCTAACGCATTTTCCCATT
130 AACCTGTCATGCATGGCATGTGGCATTTTACCATATAAGCCAC-AGTCTAACGCATTTTCCCATT
* * * *
11483400 TAATGCATGCCGTGTCACGTATTTGGTTGTTAAGGTTGGCATCTCGCATACTCACCTATTATTGA
194 TAATGCATGCCATGTCACGTATTGGGATGTTAAGGTTGGCATCTCGCATAATCACCTATTATTGA
11483465 ATCCATGGGGTGTCGACTAATCACCTGTTATGGTTGAC
259 ATCCATGGGGTGTCGACTAATCACCTGTTATGGTTGAC
* * * *
11483503 GTGTTGCATAATCATCTGTCAGGAATTGCACATCTCATACTCTTTTATTGTATGTTATGGCT-TG
1 GTGTTGCATAATCAACTGTCAGGAATGGCACATCTCATACTCATCTATTGTATGTTATGG-TGTG
* * * *
11483567 TTGCATGTAACCTTATCAGTCATGGAGTGTATGATGGTTGCAGTTCAA-TTACGTGCATGTCGCA
65 TTGCATATAACCCTATCAGTCATGGAGTGTATGATGGTTGCAGGTCAAGTT-CGT--ACGTCGCA
* * ** * **
11483631 TTTAACCTGTCATGCATTGCTATGTGGTGTTTTACCATATAAGGCA-AGGT-TAGTGGCATTTTC
127 TATAACCTGTCATGCATGGC-ATGTGGCATTTTACCATATAAGCCACA-GTCTA-ACGCATTTTC
* ** * * * *
11483694 CCATTTCATGCATGCCATGTTGCGTA-TGGGATGTTAGGGTTGGCGTGTTGCATAATCACCTAT
189 CCATTTAATGCATGCCATGTCACGTATTGGGATGTTAAGGTTGGCATCTCGCATAATCACCTAT
11483757 CAAGCATGGC
Statistics
Matches: 211, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
296 2 0.01
297 3 0.01
298 128 0.61
299 58 0.27
300 20 0.09
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.37
Consensus pattern (296 bp):
GTGTTGCATAATCAACTGTCAGGAATGGCACATCTCATACTCATCTATTGTATGTTATGGTGTGT
TGCATATAACCCTATCAGTCATGGAGTGTATGATGGTTGCAGGTCAAGTTCGTACGTCGCATATA
ACCTGTCATGCATGGCATGTGGCATTTTACCATATAAGCCACAGTCTAACGCATTTTCCCATTTA
ATGCATGCCATGTCACGTATTGGGATGTTAAGGTTGGCATCTCGCATAATCACCTATTATTGAAT
CCATGGGGTGTCGACTAATCACCTGTTATGGTTGAC
Found at i:11487287 original size:20 final size:20
Alignment explanation
Indices: 11487264--11487306 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
11487254 AGTTTAGGAC
11487264 AGAAACAACTTAATCGACTA
1 AGAAACAACTTAATCGACTA
** * *
11487284 AGAAGGAAGTTAGTCGACTA
1 AGAAACAACTTAATCGACTA
11487304 AGA
1 AGA
11487307 GCTCACTGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.19
Consensus pattern (20 bp):
AGAAACAACTTAATCGACTA
Found at i:11489434 original size:10 final size:11
Alignment explanation
Indices: 11489407--11489441 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
11489397 TATGGCCGGC
*
11489407 CAAAGCAAGAA
1 CAAAGGAAGAA
11489418 CAAAGGAAGAA
1 CAAAGGAAGAA
11489429 -AAAGGAAGAA
1 CAAAGGAAGAA
11489439 CAA
1 CAA
11489442 GAACCCTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:11494714 original size:134 final size:135
Alignment explanation
Indices: 11494491--11495061 Score: 654
Period size: 134 Copynumber: 4.2 Consensus size: 135
11494481 ATTCATATTT
* * * *
11494491 TGTACCATCTTAAGATAGTGAGGATTTATCTTTCTATAAATGGTGTGTCACAATTGTCTATATAG
1 TGTACCATTTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAG
* * * *
11494556 GGTAGGACTGTAAGATCATTATGTGTTCCATGGATGGCGTGTATCACCATCTATTATTGAATCCA
66 GGTAAGACTATAACAACATTATGTGTTCCATGGATGGCGTGTATCACCATCTATTATTGAATCCA
11494621 TGGCA
131 TGGCA
* * *
11494626 TGTACCATTTTAAGATAATGAGGATTT-TCTTTCTATAAATGGCATGTCACAACTGACTGTATAG
1 TGTACCATTTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAG
* * ***
11494690 GGTAAGACTATAACATCATTATGTGTTCTATGGATAAAGTGTATCACCATCTATTATTGAATCCA
66 GGTAAGACTATAACAACATTATGTGTTCCATGGATGGCGTGTATCACCATCTATTATTGAATCCA
*
11494755 TGGCG
131 TGGCA
* * *
11494760 TGTACCTTTTTAAAATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAA
1 TGTACCATTTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAG
* * ** * * * * * ** * *
11494825 GGCAGGACTATAGGAACAACTCTATGTTCTATGGATGGCATGTATCACTTTCTGTTATTGAATCT
66 GGTAAGACTATAACAAC-ATTATGTGTTCCATGGATGGCGTGTATCACCATCTATTATTGAATCC
11494890 ATGGCA
130 ATGGCA
* *
11494896 TGTACCATTTTAAGATAGTGAGGATTTATCTTTCTATAAATGGTGTGTCACAATTGACTATATAG
1 TGTACCATTTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAG
* * **
11494961 AGT-AGCACTGTAGGAACAAC-TCTAT-TGGTGACAT-GA---CGTGTATCACCATCTATTATTG
66 GGTAAG-AC--TA-TAACAACAT-TATGT-GTTCCATGGATGGCGTGTATCACCATCTATTATTG
*
11495019 AATCCATGGCG
125 AATCCATGGCA
*
11495030 TGTACCATCTTAAGATAGTGAGGATTTATCTT
1 TGTACCATTTTAAGATAGTGAGGATTTATCTT
11495062 ATGTATCCAT
Statistics
Matches: 367, Mismatches: 61, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
134 176 0.48
135 72 0.20
136 104 0.28
137 3 0.01
138 8 0.02
139 4 0.01
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (135 bp):
TGTACCATTTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAG
GGTAAGACTATAACAACATTATGTGTTCCATGGATGGCGTGTATCACCATCTATTATTGAATCCA
TGGCA
Found at i:11495004 original size:270 final size:268
Alignment explanation
Indices: 11494491--11495061 Score: 738
Period size: 270 Copynumber: 2.1 Consensus size: 268
11494481 ATTCATATTT
* * * *
11494491 TGTACCATCTTAAGATAGTGAGGATTTATCTTTCTATAAATGGTGTGTCACAATTGTCTATATAG
1 TGTACCATCTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAA
* * * * * *
11494556 GGTAGGACTGTAAGATCATTATGTGTTCCATGGATGGCGTGTATCACCATCTATTATTGAATCCA
66 GGCAGGACTATAAGAACACTATATGTTCCATGGATGGCATGTATCACCATCTATTATTGAATCCA
*
11494621 TGGCATGTACCATTTTAAGATAATGAGGATTTTCTTTCTATAAATGGCATGTCACAACTGACTGT
131 TGGCATGTACCATTTTAAGATAATGAGGATTTTCTTTCTATAAATGGCATGTCACAACTGACTAT
* * * * * *
11494686 ATAGGGTAAGACTATAACATCATTATGTGTTCTATGGATAAAGTGTATCACCATCTATTATTGAA
196 ATAGAGTAAGACTAGAACAACATTATGTGGTCGA-GCATAAAGTGTATCACCATCTATTATTGAA
11494751 TCCATGGCG
260 TCCATGGCG
* * *
11494760 TGTACCTTTTTAAAATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAA
1 TGTACCATCTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAA
* * * ** * *
11494825 GGCAGGACTATAGGAACAACTCTATGTTCTATGGATGGCATGTATCACTTTCTGTTATTGAATCT
66 GGCAGGACTATAAGAAC-ACTATATGTTCCATGGATGGCATGTATCACCATCTATTATTGAATCC
* ** *
11494890 ATGGCATGTACCATTTTAAGATAGTGAGGATTTATCTTTCTATAAATGGTGTGTCACAATTGACT
130 ATGGCATGTACCATTTTAAGATAATGAGGATTT-TCTTTCTATAAATGGCATGTCACAACTGACT
* *
11494955 ATATAGAGT-AGCACTGTAGGAACAAC-TCTAT-TGGT-GA-CATGACGTGTATCACCATCTATT
194 ATATAGAGTAAG-AC--TA-GAACAACAT-TATGTGGTCGAGCATAAAGTGTATCACCATCTATT
11495015 ATTGAATCCATGGCG
254 ATTGAATCCATGGCG
11495030 TGTACCATCTTAAGATAGTGAGGATTTATCTT
1 TGTACCATCTTAAGATAGTGAGGATTTATCTT
11495062 ATGTATCCAT
Statistics
Matches: 259, Mismatches: 36, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
269 71 0.27
270 136 0.53
271 37 0.14
272 1 0.00
273 6 0.02
274 8 0.03
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (268 bp):
TGTACCATCTTAAGATAGTGAGGATTTATCTTTCTATAAATGGCGTGTCACAACTGACTATATAA
GGCAGGACTATAAGAACACTATATGTTCCATGGATGGCATGTATCACCATCTATTATTGAATCCA
TGGCATGTACCATTTTAAGATAATGAGGATTTTCTTTCTATAAATGGCATGTCACAACTGACTAT
ATAGAGTAAGACTAGAACAACATTATGTGGTCGAGCATAAAGTGTATCACCATCTATTATTGAAT
CCATGGCG
Found at i:11500028 original size:35 final size:35
Alignment explanation
Indices: 11499965--11500211 Score: 274
Period size: 35 Copynumber: 7.1 Consensus size: 35
11499955 CACTTGATTA
* *
11499965 AAATTGTTT-ATTAAGT-A--GTGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
11499996 AAATTGTTTAATTGAA-TCATTGGGCCTAATTAATT
1 AAATTGTTTAATT-AAGTCATTGGGCCTAATTAATT
11500031 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
**** *
11500066 AAATTAAACAATTAAGGT-ATTGGGCCTAATTGATT
1 AAATTGTTTAATTAA-GTCATTGGGCCTAATTAATT
* *
11500101 AAATTAGTTTAATTAAGTCATTAGGCCTAGTT-ATT
1 AAATT-GTTTAATTAAGTCATTGGGCCTAATTAATT
* ** *
11500136 AAATTTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
11500172 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
11500207 AAATT
1 AAATT
11500212 AAACAATTAA
Statistics
Matches: 182, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
31 9 0.05
32 4 0.02
33 3 0.02
34 2 0.01
35 137 0.75
36 27 0.15
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:11500144 original size:106 final size:106
Alignment explanation
Indices: 11499984--11500212 Score: 302
Period size: 106 Copynumber: 2.2 Consensus size: 106
11499974 ATTAAGTAGT
* * * *
11499984 GCCTAATTAACTAAATT-GTTTAATTGAATCATTGGGCCTAATTAATTAAATTGTTTAATTAAGT
1 GCCTAATTGATTAAATTAGTTTAATTGAATCATTAGGCCTAATTAATTAAATTGTTTAATTAAAT
11500048 CATTGGGCCTAATTAATTAAATTAAACAATTAAGGTATTGG
66 CATTGGGCCTAATTAATTAAATTAAACAATTAAGGTATTGG
*
11500089 GCCTAATTGATTAAATTAGTTTAATT-AAGTCATTAGGCCTAGTT-ATTAAATTTGTTTAATTAA
1 GCCTAATTGATTAAATTAGTTTAATTGAA-TCATTAGGCCTAATTAATTAAA-TTGTTTAATTAA
** * **** *
11500152 ATTGTTGGGCTTAATTAATTAAATTGTTTAATTAAGTTATTGG
64 ATCATTGGGCCTAATTAATTAAATTAAACAATTAAGGTATTGG
11500195 GCCTAATTGATTAAATTA
1 GCCTAATTGATTAAATTA
11500213 AACAATTAAG
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
105 23 0.21
106 85 0.79
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (106 bp):
GCCTAATTGATTAAATTAGTTTAATTGAATCATTAGGCCTAATTAATTAAATTGTTTAATTAAAT
CATTGGGCCTAATTAATTAAATTAAACAATTAAGGTATTGG
Found at i:11507448 original size:62 final size:62
Alignment explanation
Indices: 11507341--11507536 Score: 221
Period size: 62 Copynumber: 3.2 Consensus size: 62
11507331 TTCGAAGCAA
* * * * * * *
11507341 CCAACTTGATTTTTGCTGCGACGAGGAACTTTCTGCCTTAAGAGTTACTGTTCTTGCCGTAG
1 CCAAATTGATTTTTGCCGCGGCGAGAAACTTTCTGCCTTAGGAGTTACTATTCTCGCCGTAG
* * *
11507403 CCAAATTGATTTTTGCCGCGGCGAGAAACTTTCTACCTTAGGAGTTACTATTCTGGCAGTAG
1 CCAAATTGATTTTTGCCGCGGCGAGAAACTTTCTGCCTTAGGAGTTACTATTCTCGCCGTAG
* *** * * * **
11507465 CCAAATTGATATTCATCGCGGTGAGAAACTTTCTGTCTTAGGAATTACTATTCTCGCCACAG
1 CCAAATTGATTTTTGCCGCGGCGAGAAACTTTCTGCCTTAGGAGTTACTATTCTCGCCGTAG
11507527 CCAAATTGAT
1 CCAAATTGAT
11507537 ATAGCAAAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 113 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (62 bp):
CCAAATTGATTTTTGCCGCGGCGAGAAACTTTCTGCCTTAGGAGTTACTATTCTCGCCGTAG
Found at i:11526714 original size:42 final size:42
Alignment explanation
Indices: 11526655--11526738 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
11526645 GTATTGATAT
*
11526655 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTGC
* *
11526697 TGACCTGGCTATGTGCGAGTGGGAGTGCGCATAAGCCATTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTGC
11526739 ATATGAGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.23
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTGC
Found at i:11533445 original size:43 final size:43
Alignment explanation
Indices: 11533327--11533448 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
11533317 TGACTCGACT
* **
11533327 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
11533370 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
11533413 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
11533449 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:11533459 original size:20 final size:20
Alignment explanation
Indices: 11533434--11533496 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
11533424 GGGAGTGCGC
11533434 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
11533454 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
11533474 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
11533493 ATGA
1 ATGA
11533497 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:11533514 original size:2 final size:2
Alignment explanation
Indices: 11533509--11533541 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11533499 GGTATATACG
*
11533509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11533542 GTAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11535678 original size:22 final size:19
Alignment explanation
Indices: 11535636--11535684 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
11535626 CATCTTCCCA
*
11535636 ATGCCATTTTCATGCTTCC
1 ATGCCATTTTCATGCTACC
11535655 ATGCCATTTTCACCTTGCTACC
1 ATGCCATTTTCA---TGCTACC
11535677 ATG-CATTT
1 ATGCCATTT
11535685 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 12 0.46
21 5 0.19
22 9 0.35
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (19 bp):
ATGCCATTTTCATGCTACC
Found at i:11535776 original size:16 final size:15
Alignment explanation
Indices: 11535753--11535829 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 15
11535743 GAGATCAGTT
11535753 GGAAGAAAGGAGAAA
1 GGAAGAAAGGAGAAA
11535768 GGAA-AGAA--AGAAA
1 GGAAGA-AAGGAGAAA
11535781 GG-AGAAA-G-GAAA
1 GGAAGAAAGGAGAAA
*
11535793 GAAAGAAAGGAGAAA
1 GGAAGAAAGGAGAAA
11535808 -GAA-AAAGAGAGAAA
1 GGAAGAAAG-GAGAAA
11535822 GGAAGAAA
1 GGAAGAAA
11535830 AAGCTTGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
12 8 0.16
13 17 0.33
14 10 0.20
15 13 0.25
16 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GGAAGAAAGGAGAAA
Found at i:11535778 original size:4 final size:4
Alignment explanation
Indices: 11535763--11535829 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
11535753 GGAAGAAAGG
* *
11535763 AGAA AGGAA AGAA AGAA AG-G AGAA AGGAA AGAA AGAA AG-G AGAA AG-A
1 AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA
* *
11535810 A-AA AGAG AGAA AGGA AGAA A
1 AGAA AGAA AGAA AGAA AGAA A
11535830 AAGCTTGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
3 8 0.16
4 33 0.67
5 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:11535810 original size:24 final size:20
Alignment explanation
Indices: 11535755--11535829 Score: 114
Period size: 20 Copynumber: 3.6 Consensus size: 20
11535745 GATCAGTTGG
11535755 AAGAAAGGAGAAAGGAAAGA
1 AAGAAAGGAGAAAGGAAAGA
11535775 AAGAAAGGAGAAAGGAAAGA
1 AAGAAAGGAGAAAGGAAAGA
*
11535795 AAGAAAGGAGAAAGAAAAAGA
1 AAGAAAGGAGAAAG-GAAAGA
*
11535816 GAGAAAGGAAGAAA
1 AAGAAAGG-AGAAA
11535830 AAGCTTGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 34 0.67
21 12 0.24
22 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGAAAGGAGAAAGGAAAGA
Found at i:11538513 original size:62 final size:62
Alignment explanation
Indices: 11538402--11538638 Score: 235
Period size: 62 Copynumber: 3.8 Consensus size: 62
11538392 AACATCATTT
* * * *
11538402 TTGCCGTAGCCAAATTGATTTTTGCCATAGTGAGAAACTTTATGCCTTAGGAGTTACTGTTC
1 TTGCCGCAGCCAAATTGATTTTCGCCATAGCGAGAAACTTTTTGCCTTAGGAGTTACTGTTC
* * * *
11538464 TCGCCGCAGCCAAATTGATTTTCGCCATGGCGAGAAACTTTTTGTCTTAGAAGTTACTGTTC
1 TTGCCGCAGCCAAATTGATTTTCGCCATAGCGAGAAACTTTTTGCCTTAGGAGTTACTGTTC
* * * * * * * *
11538526 TTGTCC-CAGCGAAGTTGATTTTCACCGT-TCTGAGAAACTTTCTACCTTGAGGAGTCACTGTTC
1 TTG-CCGCAGCCAAATTGATTTTCGCCATAGC-GAGAAACTTTTTGCCTT-AGGAGTTACTGTTC
* * * * *
11538589 TTGCCGCAGCCAAATTTGATTCTCGTCGTAGCGAGAAACTCTTTGTCTTA
1 TTGCCGCAGCCAAA-TTGATTTTCGCCATAGCGAGAAACTTTTTGCCTTA
11538639 TTTGGAAATC
Statistics
Matches: 140, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
61 1 0.01
62 90 0.64
63 24 0.17
64 24 0.17
65 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (62 bp):
TTGCCGCAGCCAAATTGATTTTCGCCATAGCGAGAAACTTTTTGCCTTAGGAGTTACTGTTC
Found at i:11541423 original size:37 final size:37
Alignment explanation
Indices: 11541381--11541499 Score: 168
Period size: 37 Copynumber: 3.2 Consensus size: 37
11541371 TAATGGTGTG
* * *
11541381 TGATGATGTTGAAGTATACGAGTAGGGATTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
11541418 TGATGATGTT-AGAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACA
* * *
11541455 TGATGATGTGGAAGTGTGTGAGTAGGGAGTACACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
11541492 TGATGATG
1 TGATGATG
11541500 CTATTACATT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.01
37 72 0.97
38 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.35, T:0.26
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:11543117 original size:43 final size:43
Alignment explanation
Indices: 11543070--11543231 Score: 166
Period size: 43 Copynumber: 3.8 Consensus size: 43
11543060 ATCATCATGT
* ** *
11543070 GCACTCCCTACACGCACATAATCGGGTCATCATTGGCTTATGC
1 GCACTCCCTACACACACATAGCCGGGTCATCATCGGCTTATGC
* *
11543113 GCACTCCCTACTCACACATAGCCTGGTCATCATCGGCTTATGC
1 GCACTCCCTACACACACATAGCCGGGTCATCATCGGCTTATGC
* * * * *
11543156 ACACTCCCTACTA-ACACATAGCCGAGTCATCATCAGCTCATGT
1 GCACTCCCTAC-ACACACATAGCCGGGTCATCATCGGCTTATGC
* * *
11543199 GCACTCCC-ACATCGCACATAGCTGAGTCATCAT
1 GCACTCCCTACA-CACACATAGCCGGGTCATCAT
11543232 TATCACACAA
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 97 0.97
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.24
Consensus pattern (43 bp):
GCACTCCCTACACACACATAGCCGGGTCATCATCGGCTTATGC
Found at i:11543253 original size:20 final size:21
Alignment explanation
Indices: 11543228--11543281 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
11543218 AGCTGAGTCA
11543228 TCATT-ATCACACAACAT-TAT
1 TCATTAAT-ACACAACATATAT
*
11543248 TCATTAATGCACAACATATAT
1 TCATTAATACACAACATATAT
11543269 TCATATATATACA
1 TCAT-TA-ATACA
11543282 TACCAACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 13 0.46
21 9 0.32
22 2 0.07
23 4 0.14
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (21 bp):
TCATTAATACACAACATATAT
Found at i:11549241 original size:29 final size:28
Alignment explanation
Indices: 11549198--11549399 Score: 206
Period size: 29 Copynumber: 6.9 Consensus size: 28
11549188 CAGCTTTGAC
11549198 ATGTTTGTCTTAATTTAGACAAGAAAAA
1 ATGTTTGTCTTAATTTAGACAAGAAAAA
*
11549226 ATGTTTGGTCTTAATTTAGACAAGAAAAC
1 ATGTTT-GTCTTAATTTAGACAAGAAAAA
*
11549255 ATGTTTGGTCTTAATTTAGACAAGAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAA
*
11549284 ATGTTTGCCTTAATTTAAGACAAGAAAAA
1 ATGTTTGTCTTAATTT-AGACAAGAAAAA
* * * *
11549313 TATTTTTTTTCTTAATTTAGTCAAGAAAAC
1 -A-TGTTTGTCTTAATTTAGACAAGAAAAA
* * *
11549343 ATATTTGTCTCAATTTAGGCAAGATAAAA
1 ATGTTTGTCTTAATTTAGACAAGA-AAAA
* *
11549372 TATTTTTTTGTCTTAATTACAGACAAGA
1 -A--TGTTTGTCTTAATT-TAGACAAGA
11549400 GTTGTCTTAG
Statistics
Matches: 147, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
28 34 0.23
29 70 0.48
30 12 0.08
31 12 0.08
32 12 0.08
33 7 0.05
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAA
Found at i:11549340 original size:59 final size:58
Alignment explanation
Indices: 11549205--11549399 Score: 230
Period size: 59 Copynumber: 3.3 Consensus size: 58
11549195 GACATGTTTG
* * **
11549205 TCTTAATTTAGACAAGAAAAAATGTTTGGTCTTAATTTAGACAAG-AAAACATGTTTGG
1 TCTTAATTTAGACAAGAAAAAATGTTT-GTCTTAATTTAGACAAGAAAAATATTTTTTT
* *
11549263 TCTTAATTTAGACAAGAAAATATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTTT
1 TCTTAATTTAGACAAGAAAAAATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTT
* * * * *
11549322 TCTTAATTTAGTCAAGAAAACATATTTGTCTCAATTTAGGCAAGATAAAATATTTTTTT
1 TCTTAATTTAGACAAGAAAAAATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTTT
*
11549381 GTCTTAATTACAGACAAGA
1 -TCTTAATT-TAGACAAGA
11549400 GTTGTCTTAG
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
57 9 0.08
58 40 0.34
59 54 0.46
60 8 0.07
61 7 0.06
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (58 bp):
TCTTAATTTAGACAAGAAAAAATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTT
Found at i:11560408 original size:22 final size:22
Alignment explanation
Indices: 11560369--11560417 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
11560359 CCAAATTACA
11560369 CTGCAGCAAAAATACCTTTCCG
1 CTGCAGCAAAAATACCTTTCCG
* * *
11560391 CTGCAGTAAGAATGCCTTTCCG
1 CTGCAGCAAAAATACCTTTCCG
11560413 CTGCA
1 CTGCA
11560418 ACGAGGACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (22 bp):
CTGCAGCAAAAATACCTTTCCG
Found at i:11563094 original size:4 final size:4
Alignment explanation
Indices: 11563085--11563123 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
11563075 AAAGCCGAAC
*
11563085 AAGA AAGA AAGA AAGA GAGA AAG- AAGA AAGGA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AAGA AAG
11563124 GGAGAAGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:11563199 original size:34 final size:35
Alignment explanation
Indices: 11563151--11563218 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
11563141 TAAGGGGGTA
*
11563151 GTTTTGCTGCCA-TTTAGGGAGGAAAGGAGAGCTG
1 GTTTTGCTGCCATTTTAAGGAGGAAAGGAGAGCTG
*
11563185 GTTTTGCTGTCATTTTAAGGAGGAAAGGAGAGCT
1 GTTTTGCTGCCATTTTAAGGAGGAAAGGAGAGCT
11563219 ATTTTTTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.35
35 20 0.65
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.29
Consensus pattern (35 bp):
GTTTTGCTGCCATTTTAAGGAGGAAAGGAGAGCTG
Found at i:11563237 original size:33 final size:35
Alignment explanation
Indices: 11563152--11563237 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
11563142 AAGGGGGTAG
* * *
11563152 TTTTGCTGCCA-TTTAGGGAGGAAAGGAGAGCTGG
1 TTTTGCTACCATTTTAAGGAGGAAAGGAGAGCTGA
**
11563186 TTTTGCTGTCATTTTAAGGAGGAAAGGAGAGCT-A
1 TTTTGCTACCATTTTAAGGAGGAAAGGAGAGCTGA
*
11563220 TTTT-TTACCATTTTAAGG
1 TTTTGCTACCATTTTAAGG
11563238 GAAAGAAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 11 0.24
34 14 0.31
35 20 0.44
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (35 bp):
TTTTGCTACCATTTTAAGGAGGAAAGGAGAGCTGA
Done.