Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_pilon, whole genome shotgun sequence
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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 42
Found at i:4871031 original size:16 final size:16
Alignment explanation
Indices: 4871007--4871038 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4870997 TATCGCCGAC
*
4871007 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
4871023 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
4871039 TATGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:4871058 original size:12 final size:12
Alignment explanation
Indices: 4871041--4871065 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4871031 ACTATTCATA
4871041 TGAATAGTAACC
1 TGAATAGTAACC
4871053 TGAATAGTAACC
1 TGAATAGTAACC
4871065 T
1 T
4871066 CGCAAAAAAT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TGAATAGTAACC
Found at i:4871521 original size:36 final size:38
Alignment explanation
Indices: 4871449--4871534 Score: 124
Period size: 37 Copynumber: 2.3 Consensus size: 38
4871439 ATCCCATTAT
*
4871449 CATTTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
4871486 TA-TTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
4871522 CATTTTTTCAAAG
1 CATTTTTTCAAAG
4871535 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 12 0.28
37 31 0.72
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.34
Consensus pattern (38 bp):
CATTTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:4875907 original size:17 final size:17
Alignment explanation
Indices: 4875885--4876134 Score: 77
Period size: 17 Copynumber: 14.9 Consensus size: 17
4875875 AAGAAAAGAC
4875885 ATAAAAATAAAATAAAG
1 ATAAAAATAAAATAAAG
4875902 ATAAAAA-ACTAAATAAA-
1 ATAAAAATA--AAATAAAG
* *
4875919 AT--AAAGAACATAAA-
1 ATAAAAATAAAATAAAG
*
4875933 A-AATAAA-AAAATGAAG
1 ATAA-AAATAAAATAAAG
4875949 --AAAAAT-AAATAAA-
1 ATAAAAATAAAATAAAG
*
4875962 ATAATCAAAATAAAGATAACG
1 AT-A--AAAATAAA-ATAAAG
** *
4875983 AGCAAAATAAAATAAAA
1 ATAAAAATAAAATAAAG
*
4876000 ATAAGAATAAAATAAAG
1 ATAAAAATAAAATAAAG
* * * *
4876017 -GAAAAACATAATAAAT
1 ATAAAAATAAAATAAAG
* *
4876033 A-AATAAATAACAAGAGGAAA
1 ATAA-AAATAA-AATA--AAG
* *
4876053 ATACAAATGAAAATAAAT
1 ATAAAAAT-AAAATAAAG
*
4876071 ATAAAAATAAAACT-AAT
1 ATAAAAATAAAA-TAAAG
4876088 ATAAAAAATAAAAT-AAG
1 AT-AAAAATAAAATAAAG
*
4876105 A-AAAGAATAAAA-AGA-
1 ATAAA-AATAAAATAAAG
4876120 ATAAAAATAAAATAA
1 ATAAAAATAAAATAA
4876135 GCAAAATAAA
Statistics
Matches: 175, Mismatches: 29, Indels: 59
0.67 0.11 0.22
Matches are distributed among these distances:
14 16 0.09
15 22 0.13
16 31 0.18
17 43 0.25
18 43 0.25
19 2 0.01
20 14 0.08
21 4 0.02
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (17 bp):
ATAAAAATAAAATAAAG
Found at i:4875932 original size:18 final size:18
Alignment explanation
Indices: 4875888--4875977 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 18
4875878 AAAAGACATA
4875888 AAAATAAAATAAAGATAAA-
1 AAAAT-AAATAAA-ATAAAG
*
4875907 AAACTAAATAAAATAAAG
1 AAAATAAATAAAATAAAG
*
4875925 AACAT-AA-AAAATAAA-
1 AAAATAAATAAAATAAAG
*
4875940 AAAATGAAGA-AAAATAAAT
1 AAAAT-AA-ATAAAATAAAG
4875959 AAAAT-AATCAAAATAAAG
1 AAAATAAAT-AAAATAAAG
4875977 A
1 A
4875978 TAACGAGCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
15 4 0.07
16 9 0.15
17 9 0.15
18 28 0.47
19 9 0.15
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.16
Consensus pattern (18 bp):
AAAATAAATAAAATAAAG
Found at i:4875956 original size:25 final size:26
Alignment explanation
Indices: 4875889--4875977 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 26
4875879 AAAGACATAA
4875889 AAATAAAATAAAG---ATAAAAAACT
1 AAATAAAATAAAGAAAATAAAAAACT
*
4875912 AAATAAAATAAAGAACATAAAAAA-T
1 AAATAAAATAAAGAAAATAAAAAACT
* *
4875937 AAA-AAAATGAAGAAAAATAAATAAAAT
1 AAATAAAATAAAG-AAAATAAA-AAACT
4875964 -AATCAAAATAAAGA
1 AAAT-AAAATAAAGA
4875978 TAACGAGCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
23 13 0.24
24 8 0.15
25 11 0.20
26 13 0.24
27 2 0.04
28 8 0.15
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (26 bp):
AAATAAAATAAAGAAAATAAAAAACT
Found at i:4875958 original size:43 final size:41
Alignment explanation
Indices: 4875846--4875965 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 41
4875836 AGAGAAAAAT
*
4875846 AAAAT-AAATGAAAAAAGAAAAATAAGATAAAGA-AAAGACATA
1 AAAATAAAAT-AAAGAAGAAAAATAA-ATAAA-ATAAAGACATA
4875888 AAAATAAAATAAAGATA-AAAAACTAAATAAAATAAAGAACATAA
1 AAAATAAAATAAAGA-AGAAAAA-TAAATAAAATAAAG-ACAT-A
4875932 AAAATAAAA-AAATGAAGAAAAATAAATAAAATAA
1 AAAATAAAATAAA-GAAGAAAAATAAATAAAATAA
4875966 TCAAAATAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
41 1 0.01
42 23 0.33
43 28 0.41
44 17 0.25
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (41 bp):
AAAATAAAATAAAGAAGAAAAATAAATAAAATAAAGACATA
Found at i:4875975 original size:43 final size:44
Alignment explanation
Indices: 4875887--4875975 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 44
4875877 GAAAAGACAT
* *
4875887 AAAAATAAAATAAAGATAAAAAACTAAATAAAATAAAGAACATA
1 AAAAATAAAATAAAGATAAAAAACTAAATAAAATAAACAAAATA
*
4875931 AAAAATAAAA-AAATGA-AGAAAAA-TAAATAAAATAATCAAAATA
1 AAAAATAAAATAAA-GATA-AAAAACTAAATAAAATAAACAAAATA
4875974 AA
1 AA
4875976 GATAACGAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
43 23 0.57
44 17 0.43
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.16
Consensus pattern (44 bp):
AAAAATAAAATAAAGATAAAAAACTAAATAAAATAAACAAAATA
Found at i:4876002 original size:6 final size:6
Alignment explanation
Indices: 4875986--4876131 Score: 54
Period size: 6 Copynumber: 23.5 Consensus size: 6
4875976 GATAACGAGC
* *
4875986 AAAAT- AAAATA AAAATA AGAAT- AAAATA AAGGAA-A AACATA ATAAATAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA--AATA AAAATA A-AAAT-A
** * * * *
4876035 ATAAATA ACAAGAGG AAAATA CAAATG AAAATA AATATA AAAATA AAACT-
1 A-AAATA A-AA-ATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
4876085 AATATA AAAA-A TAAAATA AGAAA-A GAATAA-A AAGAATA AAAATA AAA
1 AAAATA AAAATA -AAAATA A-AAATA -AA-AATA AA-AATA AAAATA AAA
4876132 TAAGCAAAAT
Statistics
Matches: 106, Mismatches: 20, Indels: 29
0.68 0.13 0.19
Matches are distributed among these distances:
5 14 0.13
6 58 0.55
7 23 0.22
8 11 0.10
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:4876008 original size:12 final size:11
Alignment explanation
Indices: 4875840--4876134 Score: 97
Period size: 12 Copynumber: 25.2 Consensus size: 11
4875830 TAAACTAGAG
4875840 AAAAATAAAAT
1 AAAAATAAAAT
*
4875851 AAATGAA-AAAAG
1 AAA--AATAAAAT
*
4875863 AAAAATAAGAT
1 AAAAATAAAAT
4875874 AAAGAA-AAGACAT
1 AAA-AATAA-A-AT
4875887 AAAAATAAAAT
1 AAAAATAAAAT
*
4875898 AAAGATAAAA-
1 AAAAATAAAAT
4875908 AACTAAATAAAAT
1 AA--AAATAAAAT
4875921 AAAGAACATAAAA-
1 -AA-AA-ATAAAAT
4875934 AATAAA-AAAAT
1 AA-AAATAAAAT
*
4875945 GAAGAAAAATAAAT
1 -AA-AAATA-AAAT
4875959 AAAATAATCAAAAT
1 -AAA-AAT-AAAAT
* * *
4875973 AAAGATAACGAG
1 AAAAATAA-AAT
*
4875985 CAAAATAAAAT
1 AAAAATAAAAT
4875996 AAAAATAAGAAT
1 AAAAATAA-AAT
**
4876008 -AAAATAAAGG
1 AAAAATAAAAT
* *
4876018 AAAAACATAAT
1 AAAAATAAAAT
4876029 AAATAA-ATAAAT
1 AAA-AATA-AAAT
*
4876041 AACAAGAGGAAAAT
1 AA-AA-A-TAAAAT
*
4876055 ACAAATGAAAAT
1 AAAAAT-AAAAT
*
4876067 AAATATAAAAAT
1 AAAAAT-AAAAT
* *
4876079 AAAACTAATAT
1 AAAAATAAAAT
4876090 AAAAAATAAAAT
1 -AAAAATAAAAT
*
4876102 AAGAAA-AGAAT
1 AA-AAATAAAAT
*
4876113 -AAAA-AGAAT
1 AAAAATAAAAT
4876122 AAAAATAAAAT
1 AAAAATAAAAT
4876133 AA
1 AA
4876135 GCAAAATAAA
Statistics
Matches: 214, Mismatches: 38, Indels: 64
0.68 0.12 0.20
Matches are distributed among these distances:
9 8 0.04
10 14 0.07
11 66 0.31
12 79 0.37
13 20 0.09
14 25 0.12
15 2 0.01
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:4876108 original size:14 final size:14
Alignment explanation
Indices: 4876091--4876145 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
4876081 AACTAATATA
4876091 AAAAATAAAATAAG
1 AAAAATAAAATAAG
* *
4876105 AAAAGAATAAAAAGAAT
1 -AAA-AAT-AAAATAAG
4876122 AAAAATAAAATAAG
1 AAAAATAAAATAAG
*
4876136 CAAAATAAAA
1 AAAAATAAAA
4876146 AATAAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 15 0.45
15 6 0.18
16 6 0.18
17 6 0.18
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAAATAAAATAAG
Found at i:4876142 original size:20 final size:21
Alignment explanation
Indices: 4876057--4876165 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 21
4876047 AGGAAAATAC
*
4876057 AAATGAAAATAAATAT---AA
1 AAATAAAAATAAATATAAGAA
* * *
4876075 AAATAAAACTAATATAAAAAATA
1 AAATAAAAATAA-ATATAAGA-A
4876098 AAATAAGAAA-AGAATA-AA-AA
1 AAATAA-AAATA-AATATAAGAA
* *
4876118 GAATAAAAATAAA-ATAAGCA
1 AAATAAAAATAAATATAAGAA
*
4876138 AAATAAAAAATAAATATATGAA
1 AAAT-AAAAATAAATATAAGAA
4876160 AAATAA
1 AAATAA
4876166 TGATAAGGGT
Statistics
Matches: 70, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
18 11 0.16
19 10 0.14
20 11 0.16
21 12 0.17
22 12 0.17
23 11 0.16
24 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (21 bp):
AAATAAAAATAAATATAAGAA
Found at i:4876145 original size:5 final size:5
Alignment explanation
Indices: 4875841--4876134 Score: 62
Period size: 5 Copynumber: 56.4 Consensus size: 5
4875831 AAACTAGAGA
* * *
4875841 AAAAT AAAAT -AAAT GAAAA- AAGA- AAAAT AAGAT AAAGAA AAGACAT
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAA-AT AA-A-AT
* * *
4875887 AAAAAT AAAAT AAAGAT AAAAA ACTAAAT AAAAT -AAAG AACAT AAAA-
1 -AAAAT AAAAT AAA-AT AAAAT A--AAAT AAAAT AAAAT AAAAT AAAAT
* *
4875934 AATAAA AAAAT GAAGA- AAAAT -AAAT AAAAT --AAT CAAAAT AAAGAT
1 AA-AAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA-AT
** * *
4875979 AACGAGC AAAAT AAAAT AAAAAT AAGAAT AAAAT AAAGGA- AAAAC ATAAT
1 AA--AAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAA--AT AAAAT AAAAT
* * **
4876029 -AAAT -AAAT -AAAT AACA- AGAGG AAAAT ACAAAT GAAAAT AAATAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT -AAAAT AAA-AT
* *
4876073 AAAAAT AAAACT AATATAA AAAAT AAAAT AAGAA- AAGAAT AAAA- AGAAT
1 -AAAAT AAAA-T AA-A-AT AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT
4876122 AAAAAT AAAAT AA
1 -AAAAT AAAAT AA
4876135 GCAAAATAAA
Statistics
Matches: 216, Mismatches: 34, Indels: 78
0.66 0.10 0.24
Matches are distributed among these distances:
3 3 0.01
4 38 0.18
5 92 0.43
6 62 0.29
7 17 0.08
8 4 0.02
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:4876148 original size:21 final size:22
Alignment explanation
Indices: 4876122--4876165 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4876112 TAAAAAGAAT
*
4876122 AAAAATAAA-ATAAGCAAAATA
1 AAAAATAAATATAAGAAAAATA
*
4876143 AAAAATAAATATATGAAAAATA
1 AAAAATAAATATAAGAAAAATA
4876165 A
1 A
4876166 TGATAAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (22 bp):
AAAAATAAATATAAGAAAAATA
Found at i:4876162 original size:22 final size:21
Alignment explanation
Indices: 4876097--4876165 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
4876087 TATAAAAAAT
* *
4876097 AAAATAAGAAA-AGAATAA-A
1 AAAATAAAAAATAAAATAAGA
*
4876116 AAGAAT-AAAAATAAAATAAGC
1 AA-AATAAAAAATAAAATAAGA
*
4876137 AAAATAAAAAATAAATATATGA
1 AAAATAAAAAATAAA-ATAAGA
4876159 AAAATAA
1 AAAATAA
4876166 TGATAAGGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.15
20 12 0.30
21 11 0.28
22 11 0.28
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAATAAAAAATAAAATAAGA
Found at i:4877353 original size:33 final size:35
Alignment explanation
Indices: 4877327--4877404 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 35
4877317 AACCTGACCT
*
4877327 GACCTGAATATCACACTTAAAAAAACCCGACTTGACTC
1 GACCCGAATATCACACTTAAAAAAACCCGAC-T--CTC
*
4877365 GACCCGAATATCACACTT-AAAAAATCCGA-TC-C
1 GACCCGAATATCACACTTAAAAAAACCCGACTCTC
4877397 GACCCGAA
1 GACCCGAA
4877405 CAAAATAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 9 0.24
33 1 0.03
35 1 0.03
37 10 0.26
38 17 0.45
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.18
Consensus pattern (35 bp):
GACCCGAATATCACACTTAAAAAAACCCGACTCTC
Found at i:4877518 original size:2 final size:2
Alignment explanation
Indices: 4877511--4877537 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4877501 GACTTAATTA
4877511 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
4877538 AAGGGGTATT
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:4882569 original size:2 final size:2
Alignment explanation
Indices: 4882562--4882616 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
4882552 ATGTATATGC
4882562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4882604 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
4882617 CTGTTATAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4882895 original size:18 final size:18
Alignment explanation
Indices: 4882872--4882906 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4882862 AGGGATTATC
4882872 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
4882890 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
4882907 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:4889871 original size:18 final size:18
Alignment explanation
Indices: 4889837--4889871 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4889827 ATATTTTTAA
*
4889837 ATTTTTAATAATAAAAAT
1 ATTTTTAATAAAAAAAAT
*
4889855 ATTTTTATTAAAAAAAA
1 ATTTTTAATAAAAAAAA
4889872 CCCCTCTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTTTAATAAAAAAAAT
Found at i:4890258 original size:23 final size:23
Alignment explanation
Indices: 4890199--4890258 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 23
4890189 AATTTTAGGG
4890199 TTTT-TTTTAAATTAAAAAAAAGT
1 TTTTATTTTAAA-TAAAAAAAAGT
* * *
4890222 TTTAATTTT-GATAAAAATATA-T
1 TTTTATTTTAAATAAAAA-AAAGT
4890244 TTTTATTTTAAATAA
1 TTTTATTTTAAATAA
4890259 CAATCCTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
22 15 0.52
23 10 0.34
24 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTTATTTTAAATAAAAAAAAGT
Found at i:4893857 original size:165 final size:161
Alignment explanation
Indices: 4893579--4894006 Score: 550
Period size: 165 Copynumber: 2.7 Consensus size: 161
4893569 CCAGAAACTT
* * **
4893579 GTATCCTCTTAACAGAATCAACCCCATTAATCCCCAAACAATGATCTTCGATTGACCCCTCATTC
1 GTATCCT-TTAACTGAATCAACTCCATTAATCCCCAAACAATGATCTTCCTTTGACCCCTCATTC
* * *
4893644 TTAGCATGTTCTACAACCACATTGTCCTCACTTCCACTAT-TCACTCTTACTTTCAACCTCTCAT
65 TTATCATTTTCTACAACCACATTGTCCTCACTTCCACTATCTCACTCTTACTTCCAACCTCTCAT
* *
4893708 CTGATCCGGCCACTA-TGACAGCAATA-AGATCCTCTC
130 CTGATCCAGCCACTACT-ACACCAATACA-A---TC-C
* *
4893744 GTATCCTATTAACTGAATCAACTCCATTAATCCCCGATCAATGATCTTCCTTTGACCCCTCATTC
1 GTATCCT-TTAACTGAATCAACTCCATTAATCCCCAAACAATGATCTTCCTTTGACCCCTCATTC
*
4893809 TTATCATTTTCTACAACCACATTGCCCTCACTTCCACTATCT-ACTCTTACTTCCAACCTCTCAT
65 TTATCATTTTCTACAACCACATTGTCCTCACTTCCACTATCTCACTCTTACTTCCAACCTCTCAT
* *
4893873 CTGATCCAGCCCCTACTACACCGATACAATCC
130 CTGATCCAGCCACTACTACACCAATACAATCC
* *
4893905 ---T-C-TTAACTGAATCAACTCCATTAATCCCCAAACAATGATCTTCCTTCGATCCCTCATTCT
1 GTATCCTTTAACTGAATCAACTCCATTAATCCCCAAACAATGATCTTCCTTTGACCCCTCATTCT
* * *
4893965 TATCATTTCCTATAGCCACATTGTCCTCACTTCCACTATCTC
66 TATCATTTTCTACAACCACATTGTCCTCACTTCCACTATCTC
4894007 CTTTGACCTC
Statistics
Matches: 236, Mismatches: 23, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
155 91 0.39
157 1 0.00
158 1 0.00
161 1 0.00
162 2 0.01
165 137 0.58
166 3 0.01
ACGTcount: A:0.26, C:0.35, G:0.07, T:0.32
Consensus pattern (161 bp):
GTATCCTTTAACTGAATCAACTCCATTAATCCCCAAACAATGATCTTCCTTTGACCCCTCATTCT
TATCATTTTCTACAACCACATTGTCCTCACTTCCACTATCTCACTCTTACTTCCAACCTCTCATC
TGATCCAGCCACTACTACACCAATACAATCC
Found at i:4900318 original size:17 final size:17
Alignment explanation
Indices: 4900296--4900331 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4900286 GACGTATGTA
4900296 AAAAGAAACGATCTTCC
1 AAAAGAAACGATCTTCC
4900313 AAAAGAAACGATCTTCC
1 AAAAGAAACGATCTTCC
4900330 AA
1 AA
4900332 CACGGTTACG
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:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAAGAAACGATCTTCC
Found at i:4902039 original size:20 final size:20
Alignment explanation
Indices: 4902011--4902125 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
4902001 AATTGGGAAA
4902011 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
4902031 ATTGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
4902051 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
4902072 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
4902092 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
4902112 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
4902126 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.05
20 46 0.61
21 24 0.32
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:4902073 original size:61 final size:62
Alignment explanation
Indices: 4902008--4902125 Score: 161
Period size: 61 Copynumber: 1.9 Consensus size: 62
4901998 GTGAATTGGG
* * *
4902008 AAAATCGCAATGCGATACTGACTATT-GCAATGCGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACT-TTCGCAACGCGATA-ATACATAATCGCAATGCGATAATAC
*
4902069 AAAATCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
4902126 TTTCAAAGCG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
60 5 0.10
61 32 0.64
62 13 0.26
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (62 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGATAATAC
Found at i:4902077 original size:21 final size:20
Alignment explanation
Indices: 4902051--4902125 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
4902041 GATACTTACT
*
4902051 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
** *
4902072 ATCGCAACGCGATTCTGAC-T
1 ATCGCAACGCGATAAT-ACAA
*
4902092 TTCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACA-A
*
4902113 ATCGCAATGCGAT
1 ATCGCAACGCGAT
4902126 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:4902097 original size:41 final size:41
Alignment explanation
Indices: 4902034--4902126 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
4902024 ACTGACTATT
* * *
4902034 GCAATGCGATACTTACTATCGCAATGCGATAATACAAAATC
1 GCAATGCGATTCTGACTATCGCAACGCGATAATACAAAATC
* * *
4902075 GCAACGCGATTCTGACTTTCGCAACGCGATAATACATAATC
1 GCAATGCGATTCTGACTATCGCAACGCGATAATACAAAATC
4902116 GCAATGCGATT
1 GCAATGCGATT
4902127 TTCAAAGCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
GCAATGCGATTCTGACTATCGCAACGCGATAATACAAAATC
Found at i:4902321 original size:22 final size:22
Alignment explanation
Indices: 4902293--4902336 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4902283 CACTCTCTCA
*
4902293 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
4902315 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
4902337 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:4902599 original size:20 final size:20
Alignment explanation
Indices: 4902570--4902613 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4902560 GCGATTTTAG
4902570 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
4902590 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
4902610 TTTC
1 TTTC
4902614 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:4903954 original size:18 final size:18
Alignment explanation
Indices: 4903933--4903977 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4903923 TCCACTTTGG
**
4903933 GAGCCATCACCTTGCCCA
1 GAGCCATCACCTCACCCA
*
4903951 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
4903969 GAGCCATCA
1 GAGCCATCA
4903978 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:4904513 original size:19 final size:20
Alignment explanation
Indices: 4904470--4904525 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
4904460 AGCAACAAGA
4904470 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
4904490 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
4904509 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
4904526 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:4904540 original size:33 final size:33
Alignment explanation
Indices: 4904498--4904589 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
4904488 GGAAATGGCT
4904498 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
4904531 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
4904564 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
4904590 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:4904552 original size:19 final size:19
Alignment explanation
Indices: 4904498--4904594 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
4904488 GGAAATGGCT
4904498 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4904517 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
4904531 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4904550 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
4904564 ATCGCAACGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
4904583 ATCGCAATGCGA
1 ATCGCAATGCGA
4904595 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 3 0.05
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4904578 original size:13 final size:14
Alignment explanation
Indices: 4904514--4904578 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 14
4904504 ATGCGAAATG
4904514 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4904528 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
4904547 AAAATCGCAACGAC
1 AAAATCGCAACGAC
4904561 AAAATCGCAACG-C
1 AAAATCGCAACGAC
4904574 AAAAT
1 AAAAT
4904579 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.14
14 22 0.50
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4904625 original size:14 final size:14
Alignment explanation
Indices: 4904606--4904729 Score: 86
Period size: 14 Copynumber: 7.9 Consensus size: 14
4904596 TTGTGTTTCG
4904606 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4904620 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4904636 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
4904652 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TT--TTGT
*
4904670 GCATTGCGATTTTGT
1 -CGTTGCGATTTTGT
*
4904685 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
4904702 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4904718 CGTTGCGATTTT
1 CGTTGCGATTTT
4904730 CATTTCGCAT
Statistics
Matches: 88, Mismatches: 8, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
14 34 0.39
15 6 0.07
16 14 0.16
17 6 0.07
18 15 0.17
19 13 0.15
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4904674 original size:33 final size:33
Alignment explanation
Indices: 4904601--4904745 Score: 265
Period size: 33 Copynumber: 4.4 Consensus size: 33
4904591 GCGATTTGTG
*
4904601 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
4904633 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
4904666 TTTTGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
4904699 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
4904732 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
4904746 AGCCATTTCC
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 26 0.24
33 83 0.76
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:4904682 original size:19 final size:19
Alignment explanation
Indices: 4904654--4904715 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
4904644 GATTTTGTCG
4904654 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTTGCA
* *
4904673 TTGCGA--TT--TTGT-CG
1 TTGCGATTTTCATTTTGCA
*
4904687 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTTGCA
4904706 TTGCGATTTT
1 TTGCGATTTT
4904716 GTCGTTGCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
14 7 0.21
15 3 0.09
16 2 0.06
17 2 0.06
18 2 0.06
19 17 0.52
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (19 bp):
TTGCGATTTTCATTTTGCA
Found at i:4904764 original size:20 final size:19
Alignment explanation
Indices: 4904730--4904785 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
4904720 TTGCGATTTT
*
4904730 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4904749 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
4904769 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
4904786 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4905247 original size:41 final size:42
Alignment explanation
Indices: 4905151--4905238 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
4905141 GACTCACCTG
* *
4905151 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
4905193 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
4905234 TCATC
1 TCATC
4905239 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:4906677 original size:14 final size:14
Alignment explanation
Indices: 4906658--4906693 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4906648 ATTGTTTAAT
4906658 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4906672 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4906686 TGATTTGT
1 TGATTTGT
4906694 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4906839 original size:14 final size:14
Alignment explanation
Indices: 4906820--4906872 Score: 61
Period size: 14 Copynumber: 3.4 Consensus size: 14
4906810 GAAACTGACT
4906820 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
4906834 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
4906853 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
4906867 ATCGCA
1 ATCGCA
4906873 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:4906866 original size:19 final size:19
Alignment explanation
Indices: 4906830--4906866 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4906820 ATCGCAACGA
* *
4906830 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
4906849 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
4906867 ATCGCATTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:4906965 original size:20 final size:20
Alignment explanation
Indices: 4906886--4906973 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
4906876 CGATTTTCTA
*
4906886 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCAGTTTCGC
*** *
4906906 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCAGTTTCGC
* *
4906926 ATTGCAATAGCCAGTTTCGC
1 GTTGCGATAGCCAGTTTCGC
4906946 GTTGCGATAGCCAGTTTCGC
1 GTTGCGATAGCCAGTTTCGC
4906966 GTTGCGAT
1 GTTGCGAT
4906974 TTTTCCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 48 0.89
21 3 0.06
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATAGCCAGTTTCGC
Found at i:4907387 original size:12 final size:12
Alignment explanation
Indices: 4907368--4907401 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4907358 CTCTCCGGCG
4907368 ACATCCGTTCCT
1 ACATCCGTTCCT
*
4907380 ATATCCGTTCCT
1 ACATCCGTTCCT
4907392 ACATCC-TTCC
1 ACATCCGTTCC
4907402 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:4908002 original size:24 final size:24
Alignment explanation
Indices: 4907942--4908009 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
4907932 GTGAGTACTA
* * *
4907942 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATATTG
* *
4907966 GTCAATACCCGGACTTTGATATTG
1 GTCAATACTCGGAATTTGATATTG
*
4907990 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
4908010 GATGTTTCAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATATTG
Found at i:4908201 original size:12 final size:12
Alignment explanation
Indices: 4908184--4908220 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
4908174 ATATAATCCT
4908184 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4908196 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4908208 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4908220 G
1 G
4908221 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4910554 original size:33 final size:33
Alignment explanation
Indices: 4910512--4910638 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
4910502 GGAAATTACT
4910512 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
4910545 ATCGCAATGCGAAATGAAAATCACAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
4910577 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4910611 ATCGCAACGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4910639 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4910623 original size:66 final size:66
Alignment explanation
Indices: 4910513--4910645 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
4910503 GAAATTACTA
* *
4910513 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCACAACGCGAAT
4910578 T
66 T
* *
4910579 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCACAACGCGAAT
4910644 T
66 T
4910645 T
1 T
4910646 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCACAACGCGAAT
T
Found at i:4910653 original size:19 final size:19
Alignment explanation
Indices: 4910492--4910642 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
4910482 CTTAATGTCT
* **
4910492 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
*
4910512 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
4910531 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
4910545 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
4910564 ATCACAACGC----T-AAT
1 ATCGCAACGCGAAATGAAA
* *
4910578 TTCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
4910597 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
4910611 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
4910630 ATCGCAACGCGAA
1 ATCGCAACGCGAA
4910643 TTTAATTTCG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 28 0.29
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 47 0.48
20 9 0.09
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:4910689 original size:33 final size:33
Alignment explanation
Indices: 4910638--4910765 Score: 175
Period size: 33 Copynumber: 3.7 Consensus size: 33
4910628 AAATCGCAAC
* *
4910638 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
4910671 GCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTTGCGA--TTC---TCTCGTT
4910709 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
4910742 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
4910766 AGTACTTTTT
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
33 50 0.59
35 3 0.04
36 3 0.04
38 29 0.34
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:4910691 original size:19 final size:19
Alignment explanation
Indices: 4910667--4910765 Score: 145
Period size: 19 Copynumber: 5.5 Consensus size: 19
4910657 GCGATTCTCT
4910667 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
4910686 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
4910705 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4910724 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
4910738 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4910757 CATTGCGAT
1 CGTTGCGAT
4910766 AGTACTTTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 56 0.78
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4912316 original size:21 final size:21
Alignment explanation
Indices: 4912250--4912316 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4912240 GTGAATCGGG
*
4912250 CTCTTGAATGGTGGGAGA-GA
1 CTCTTGAACGGTGGGAGAGGA
* * ** * *
4912270 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGAGGA
4912292 CTCTTGAACGGTGGGAGAGGA
1 CTCTTGAACGGTGGGAGAGGA
4912313 CTCT
1 CTCT
4912317 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGAGGA
Found at i:4912767 original size:91 final size:90
Alignment explanation
Indices: 4912590--4912774 Score: 284
Period size: 91 Copynumber: 2.0 Consensus size: 90
4912580 ATTTCAAACT
4912590 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGC
4912655 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
4912683 TTCAACCAACAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGC
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGC
*
4912746 AGTATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
4912774 T
1 T
4912775 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
91 36 0.41
93 18 0.21
95 32 0.37
96 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:4914526 original size:19 final size:19
Alignment explanation
Indices: 4914462--4914626 Score: 152
Period size: 19 Copynumber: 9.1 Consensus size: 19
4914452 TCTTTTGGTT
*
4914462 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
4914481 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
4914501 GGAAATGACTATCGCAACAC
1 -GAAATGAAAATCGCAACGC
**
4914521 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
4914538 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4914554 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4914573 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
4914590 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4914606 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
4914625 GA
1 GA
4914627 TTTTGGTTTC
Statistics
Matches: 123, Mismatches: 11, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
14 19 0.15
15 2 0.02
16 4 0.03
17 4 0.03
18 2 0.02
19 61 0.50
20 29 0.24
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4914570 original size:52 final size:52
Alignment explanation
Indices: 4914487--4914621 Score: 216
Period size: 52 Copynumber: 2.6 Consensus size: 52
4914477 ACGAGATAAT
** **
4914487 GAGAATCGCAACGCGGAAATGACTATCGCAACACGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGA
*
4914540 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACACGAAATGAAAATCGCAACGA
4914592 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
4914622 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 63 0.82
53 14 0.18
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACACGAAATGAAAATCGCAACGA
Found at i:4914638 original size:19 final size:19
Alignment explanation
Indices: 4914622--4914668 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
4914612 AAAATCGCAA
*
4914622 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
4914641 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
4914660 TGCGATTTT
1 TGCGATTTT
4914669 CATTCTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:4915211 original size:20 final size:20
Alignment explanation
Indices: 4915186--4915238 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4915176 GCGCTATGTA
4915186 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
4915206 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
4915226 TATCTCGTTGCGA
1 AATCGCGTTGCGA
4915239 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:4915299 original size:41 final size:41
Alignment explanation
Indices: 4915207--4915301 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
4915197 GAAAGTCAGA
* * * * ** *
4915207 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCCAAT
*
4915248 ATCGCATTGCGATAGTCAATATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAATATCGCATTGCGATTTT-CCAAT
4915290 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
4915302 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCCAAT
Found at i:4918678 original size:19 final size:19
Alignment explanation
Indices: 4918637--4918679 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
4918627 TTAAAAGAAT
* *
4918637 CATAGTTTATTGTCAGATT
1 CATAGTTTATTGTCAAATC
*
4918656 CATAGTTTATTTTCAAATC
1 CATAGTTTATTGTCAAATC
4918675 CATAG
1 CATAG
4918680 CCCTATGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (19 bp):
CATAGTTTATTGTCAAATC
Found at i:4919955 original size:57 final size:57
Alignment explanation
Indices: 4919495--4919944 Score: 738
Period size: 57 Copynumber: 7.9 Consensus size: 57
4919485 CATAACCATA
* * * * * *
4919495 CAACCCCGTCATGAATAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
4919552 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
4919609 CAACCTCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
**
4919666 CTTCCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
4919723 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
** * *
4919780 CTTCCCCGTCACGAACAGTAAGGCTCTCAACACAAAGCCGAGGAACCCGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
4919837 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
** *
4919894 CTTCCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAGCCTGCA
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCA
4919945 GATAATCTTC
Statistics
Matches: 366, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 366 1.00
ACGTcount: A:0.33, C:0.32, G:0.21, T:0.15
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:4920035 original size:24 final size:24
Alignment explanation
Indices: 4920008--4920116 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
4919998 AAACGGAGAT
*
4920008 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
4920032 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
4920056 ATCAGAAACCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
4920080 GTAATG-AATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
4920103 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
4920117 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.01
24 67 0.97
25 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:4920037 original size:12 final size:12
Alignment explanation
Indices: 4920010--4920102 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
4920000 ACGGAGATAT
* *
4920010 CAGAAATCAAAA
1 CAGAATTCAGAA
*
4920022 CAGAATTCAGAT
1 CAGAATTCAGAA
*
4920034 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
4920046 CAGAATCCAGAT
1 CAGAATTCAGAA
**
4920058 CAGAAACCAGAA
1 CAGAATTCAGAA
4920070 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
4920084 -TGAA-TCAGAA
1 CAGAATTCAGAA
4920094 CAGAATTCA
1 CAGAATTCA
4920103 AGTCGGAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
10 2 0.03
11 6 0.10
12 45 0.74
13 6 0.10
14 2 0.03
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:4929479 original size:31 final size:31
Alignment explanation
Indices: 4929426--4929486 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
4929416 GAGAAAGACA
*
4929426 CCAGCCATTACAACCAGACAATAACCCCACC
1 CCAGCCATTACAACCAGACAATAAACCCACC
* *
4929457 CCAGCCATTACTACGA-ACCAATAAACCCAC
1 CCAGCCATTACAACCAGA-CAATAAACCCAC
4929487 ACAAACAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.39, C:0.43, G:0.07, T:0.11
Consensus pattern (31 bp):
CCAGCCATTACAACCAGACAATAAACCCACC
Found at i:4930641 original size:24 final size:24
Alignment explanation
Indices: 4930604--4930650 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4930594 TATCAAACTT
*
4930604 ACTAATGAGCACAATAAAATATTC
1 ACTAACGAGCACAATAAAATATTC
* *
4930628 ACTAACGAGTACAATAAATTATT
1 ACTAACGAGCACAATAAAATATT
4930651 TCTTACTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.28
Consensus pattern (24 bp):
ACTAACGAGCACAATAAAATATTC
Found at i:4931995 original size:22 final size:23
Alignment explanation
Indices: 4931952--4931996 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4931942 ATATTTAAAA
* *
4931952 TTGGAGTTATAGGGTTTGAGATT
1 TTGGAGTTATAGAGTTTAAGATT
4931975 TTGGAGTT-TAGAGTTTAAGATT
1 TTGGAGTTATAGAGTTTAAGATT
4931997 ATAAATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (23 bp):
TTGGAGTTATAGAGTTTAAGATT
Found at i:4937506 original size:32 final size:31
Alignment explanation
Indices: 4937453--4937619 Score: 128
Period size: 32 Copynumber: 5.2 Consensus size: 31
4937443 ACAATACGTA
*
4937453 AGTTTT-AAAGCA-TTTGAAAAATATAATATAT
1 AGTTTTAAAAACATTTTG-AAAATAT-ATATAT
* *
4937484 AGTTTTGAAATCATTTTGAAAATATAATATAT
1 AGTTTTAAAAACATTTTGAAAATAT-ATATAT
*
4937516 AGTTTAAAAAAAACA-TTTGAAAA-ACTTATATAT
1 AGTTT--TAAAAACATTTTGAAAATA--TATATAT
*
4937549 ATTTTTAAAAATCATTTTTGAAAACTATATGATAT
1 AGTTTTAAAAA-CA-TTTTGAAAA-TATAT-ATAT
* *
4937584 AGTTTTGAAAACATGTTTTAAAA-ATATATAT
1 AGTTTTAAAAACAT-TTTGAAAATATATATAT
4937615 AGTTT
1 AGTTT
4937620 AATTTTTTTT
Statistics
Matches: 114, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
31 20 0.18
32 31 0.27
33 23 0.20
34 26 0.23
35 13 0.11
36 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.41
Consensus pattern (31 bp):
AGTTTTAAAAACATTTTGAAAATATATATAT
Found at i:4937533 original size:34 final size:31
Alignment explanation
Indices: 4937465--4937621 Score: 113
Period size: 34 Copynumber: 4.8 Consensus size: 31
4937455 TTTTAAAGCA
** *
4937465 TTTGAAAAATATAATATATAGTTTTGAAATCAT
1 TTTG-AAAATAT-ATATATAGTTTAAAAAACAT
4937498 TTTGAAAATATAATATATAGTTTAAAAAAAACA-
1 TTTGAAAATAT-ATATATAGTTT--AAAAAACAT
* *
4937531 TTTGAAAA-ACTTATATATATTTTTAAAAATCATT
1 TTTGAAAATA--TATATATA-GTTTAAAAAACA-T
**
4937565 TTTGAAAACTATATGATATAGTTTTGAAAACAT
1 TTTGAAAA-TATAT-ATATAGTTTAAAAAACAT
*
4937598 GTTTTAAAA-ATATATATAGTTTAA
1 -TTTGAAAATATATATATAGTTTAA
4937622 TTTTTTTTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
31 9 0.09
32 31 0.31
33 20 0.20
34 35 0.35
35 5 0.05
36 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (31 bp):
TTTGAAAATATATATATAGTTTAAAAAACAT
Found at i:4938972 original size:103 final size:103
Alignment explanation
Indices: 4938793--4938998 Score: 412
Period size: 103 Copynumber: 2.0 Consensus size: 103
4938783 TCCCCTTTTC
4938793 AATTTTGGTTTTAATGGCGATCCTAGTATGACATTAGGGTCATGTTCTCGTATTTCCATTCTTTC
1 AATTTTGGTTTTAATGGCGATCCTAGTATGACATTAGGGTCATGTTCTCGTATTTCCATTCTTTC
4938858 CTCTGATTCTTTTGATTCAAAAGAGACCCCAGTCACAG
66 CTCTGATTCTTTTGATTCAAAAGAGACCCCAGTCACAG
4938896 AATTTTGGTTTTAATGGCGATCCTAGTATGACATTAGGGTCATGTTCTCGTATTTCCATTCTTTC
1 AATTTTGGTTTTAATGGCGATCCTAGTATGACATTAGGGTCATGTTCTCGTATTTCCATTCTTTC
4938961 CTCTGATTCTTTTGATTCAAAAGAGACCCCAGTCACAG
66 CTCTGATTCTTTTGATTCAAAAGAGACCCCAGTCACAG
4938999 CTGGATATAT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (103 bp):
AATTTTGGTTTTAATGGCGATCCTAGTATGACATTAGGGTCATGTTCTCGTATTTCCATTCTTTC
CTCTGATTCTTTTGATTCAAAAGAGACCCCAGTCACAG
Found at i:4944821 original size:2 final size:2
Alignment explanation
Indices: 4944814--4944865 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4944804 AGCTGGTTCG
4944814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4944856 AT AT AT AT AT
1 AT AT AT AT AT
4944866 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4950844 original size:14 final size:14
Alignment explanation
Indices: 4950807--4950846 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
4950797 TTTTTAGTAT
*
4950807 TATTTTTTTTTCAA
1 TATTTTATTTTCAA
*
4950821 AATATTTATTTTCAA
1 TAT-TTTATTTTCAA
4950836 TATTTTATTTT
1 TATTTTATTTT
4950847 AGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTATTTTCAA
Found at i:4953793 original size:15 final size:15
Alignment explanation
Indices: 4953773--4953839 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
4953763 TTCCAGAAAA
4953773 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
4953788 TGAATTACTGAAATT
1 TGAATTACTGGAATT
4953803 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
4953818 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
4953832 TGAATTAC
1 TGAATTAC
4953840 ATTTCTGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 12 0.26
15 35 0.74
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:4953880 original size:14 final size:14
Alignment explanation
Indices: 4953841--4953881 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4953831 ATGAATTACA
* *
4953841 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
4953855 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
4953869 TTTCCGTAAAATG
1 TTTCCGGAAAATG
4953882 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:4954027 original size:19 final size:19
Alignment explanation
Indices: 4954005--4954078 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
4953995 ATTAAATACA
*
4954005 ATAAATAATATTATTTATC
1 ATAAATAATATTATTTATT
* *
4954024 ATAAA-AAAATTTTATTATT
1 ATAAATAATATTAT-TTATT
*
4954043 AAAAATAAT-TTATTTATT
1 ATAAATAATATTATTTATT
*
4954061 ATTAAATAGTATT-TTTAT
1 A-TAAATAATATTATTTAT
4954079 AATTTTATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
18 12 0.28
19 27 0.63
20 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
ATAAATAATATTATTTATT
Found at i:4954054 original size:17 final size:18
Alignment explanation
Indices: 4954015--4954061 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
4954005 ATAAATAATA
4954015 TTATTTATCATAAAAAAATT
1 TTATTTAT--TAAAAAAATT
4954035 TTA-TTATTAAAAATAA-T
1 TTATTTATTAAAAA-AATT
4954052 TTATTTATTA
1 TTATTTATTA
4954062 TTAAATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 10 0.40
18 8 0.32
19 4 0.16
20 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTTATTAAAAAAATT
Found at i:4954059 original size:18 final size:18
Alignment explanation
Indices: 4954007--4954061 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
4953997 TAAATACAAT
4954007 AAATAATATTATTTATCATAA
1 AAATAAT-TTATTTAT--TAA
4954028 AAA-AATTT-TATTATTAA
1 AAATAATTTAT-TTATTAA
4954045 AAATAATTTATTTATTA
1 AAATAATTTATTTATTA
4954062 TTAAATAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 7 0.23
20 3 0.10
21 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATTTATTTATTAA
Found at i:4954074 original size:21 final size:21
Alignment explanation
Indices: 4954007--4954066 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
4953997 TAAATACAAT
*
4954007 AAATAATATTATTTATCA-TAA
1 AAATAAT-TTATTTATTATTAA
4954028 AAA-AA--T-TTTATTATTAA
1 AAATAATTTATTTATTATTAA
4954045 AAATAATTTATTTATTATTAA
1 AAATAATTTATTTATTATTAA
4954066 A
1 A
4954067 TAGTATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 2 0.06
20 3 0.09
21 15 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATAATTTATTTATTATTAA
Found at i:4954201 original size:15 final size:16
Alignment explanation
Indices: 4954170--4954205 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
4954160 TAATAGTGTT
4954170 ATATTATATTTTAAAA
1 ATATTATATTTTAAAA
4954186 ATATTA-ATTTTTAAAA
1 ATATTATA-TTTTAAAA
4954202 ATAT
1 ATAT
4954206 ATAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTATATTTTAAAA
Found at i:4954326 original size:31 final size:33
Alignment explanation
Indices: 4954280--4954359 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 33
4954270 ATAATATCTT
* *
4954280 ATATTATTATAATATAATTGATTATTTTA-TAT-A
1 ATATTAATA-AATATAATT-ATTATATTATTATAA
4954313 ATATTAA-AAATATAA-TATTATATTATTATAA
1 ATATTAATAAATATAATTATTATATTATTATAA
4954344 ATATTAATAAAT-TAAT
1 ATATTAATAAATATAAT
4954360 AAATAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 8 0.20
30 4 0.10
31 18 0.44
32 5 0.12
33 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
ATATTAATAAATATAATTATTATATTATTATAA
Found at i:4954330 original size:59 final size:62
Alignment explanation
Indices: 4954196--4954341 Score: 144
Period size: 59 Copynumber: 2.4 Consensus size: 62
4954186 ATATTAATTT
* * *
4954196 TTAAAAATAT-ATA-AATAATATTATTCATTATTAAATATATAATTTTTTTTATTATATATTA
1 TTAAAAATATAATATAAT-ATATTATTCATTATTAAATATATAATTATTATTATTATATAATA
* * *
4954257 TT-AAAATAAAAATATAATATCTTA-T-ATTATTATA-ATATAATTGATTATT-TTATATAATA
1 TTAAAAAT-ATAATATAATATATTATTCATTATTAAATATATAATT-ATTATTATTATATAATA
*
4954316 TTAAAAATATAATATTATATTATTAT
1 TTAAAAATATAATATAATA-TATTAT
4954342 AAATATTAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
59 28 0.41
60 26 0.38
61 4 0.06
62 8 0.12
63 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (62 bp):
TTAAAAATATAATATAATATATTATTCATTATTAAATATATAATTATTATTATTATATAATA
Found at i:4954334 original size:22 final size:23
Alignment explanation
Indices: 4954309--4954352 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4954299 GATTATTTTA
4954309 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
4954331 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
4954353 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:4954366 original size:52 final size:52
Alignment explanation
Indices: 4954263--4954369 Score: 128
Period size: 52 Copynumber: 2.0 Consensus size: 52
4954253 ATTATTAAAA
** * *
4954263 TAAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATAT
1 TAAAAATATAATA-CTTATATTATTATAATATAATAAATTA-TATAAATAATAT
4954317 TAAAAATATAATA-TTATATTATTATAAATATTAATAAATTA-ATAAATAATAT
1 TAAAAATATAATACTTATATTATTAT-AATA-TAATAAATTATATAAATAATAT
4954369 T
1 T
4954370 TTGATGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
52 22 0.47
53 4 0.09
54 21 0.45
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (52 bp):
TAAAAATATAATACTTATATTATTATAATATAATAAATTATATAAATAATAT
Found at i:4954608 original size:42 final size:41
Alignment explanation
Indices: 4954547--4954659 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 41
4954537 ATTACGTTCA
*
4954547 GAAAAACCAATTACGTGAAACAAACACTGGAAAACATTTTCC
1 GAAAAACAAATTACGTGAAACAAACAC-GGAAAACATTTTCC
* *
4954589 GGAAAACAAATTACATGAAACAAACACGGAAAAACATTTTCC
1 GAAAAACAAATTACGTGAAACAAACACGG-AAAACATTTTCC
*
4954631 GAAAAACGAATTACGTGAAACAAACACGG
1 GAAAAACAAATTACGTGAAACAAACACGG
4954660 GAATTCGGGG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 2 0.03
42 62 0.97
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.16
Consensus pattern (41 bp):
GAAAAACAAATTACGTGAAACAAACACGGAAAACATTTTCC
Found at i:4960840 original size:17 final size:18
Alignment explanation
Indices: 4960801--4960847 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
4960791 TGTTTCTGAG
*
4960801 GGAATTGGAATCTGTGAA
1 GGAATTGAAATCTGTGAA
*
4960819 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
4960836 GGAATTGAAATC
1 GGAATTGAAATC
4960848 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:4960936 original size:43 final size:43
Alignment explanation
Indices: 4960838--4960962 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 43
4960828 ATCTGTCAGG
* *
4960838 AATTGAAATCCAATTCCATATTCTGTTTGGTTGGCAGGAAATGA
1 AATTGGAATCCAATTCCATATTCTGTTTGGTTAGCA-GAAATGA
*
4960882 AATTGGAATCCAATTCCATATTCTGTTTTGTTAGCAGAAATGA
1 AATTGGAATCCAATTCCATATTCTGTTTGGTTAGCAGAAATGA
* *
4960925 AATTGGAATCCAATTCTATATTCTGTTTGGTTCGCAGA
1 AATTGGAATCCAATTCCATATTCTGTTTGGTTAGCAGA
4960963 CATGTCAGAT
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
43 42 0.56
44 33 0.44
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (43 bp):
AATTGGAATCCAATTCCATATTCTGTTTGGTTAGCAGAAATGA
Found at i:4962436 original size:21 final size:21
Alignment explanation
Indices: 4962410--4962465 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
4962400 GCAAATAAGT
4962410 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
4962431 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
*
4962452 AAATCGCAACGCGA
1 AAATCGCAATGCGA
4962466 TATTGACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:4962478 original size:41 final size:41
Alignment explanation
Indices: 4962451--4962548 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
4962441 GCGAATTTGG
*
4962451 AAAATCGCAACGCGATATTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
4962492 AAAATCGCAACGCGATACTGACTTTTGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
4962533 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
4962549 TTTCAAAGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:4962479 original size:20 final size:20
Alignment explanation
Indices: 4962454--4962548 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
4962444 AATTTGGAAA
*
4962454 ATCGCAACGCGATATTGACT
1 ATCGCAACGCGATAATGACT
*
4962474 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
4962495 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* * *
4962515 TTTGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
4962535 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
4962549 TTTCAAAGTG
Statistics
Matches: 58, Mismatches: 12, Indels: 9
0.73 0.15 0.11
Matches are distributed among these distances:
19 4 0.07
20 28 0.48
21 24 0.41
22 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:4962500 original size:21 final size:22
Alignment explanation
Indices: 4962451--4962513 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 22
4962441 GCGAATTTGG
*
4962451 AAAATCGCAACGCGATATTGAC
1 AAAATCGCAACGCGATAATGAC
*
4962473 --TATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATAATGAC
*
4962492 AAAATCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
4962514 TTTTGCAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 15 0.44
22 2 0.06
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAATCGCAACGCGATAATGAC
Found at i:4962744 original size:22 final size:22
Alignment explanation
Indices: 4962716--4962759 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4962706 ACTCTCTCAC
4962716 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
4962738 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
4962760 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:4963054 original size:20 final size:20
Alignment explanation
Indices: 4963037--4963099 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
4963027 GATAGTCAAA
4963037 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
*
4963057 TTCGTGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
4963077 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
4963097 TTC
1 TTC
4963100 AGAAACTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:4964423 original size:18 final size:18
Alignment explanation
Indices: 4964402--4964449 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
4964392 TCCACTTCGG
4964402 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
4964420 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
4964438 GAGCCATCACCT
1 GAGCCATCACCT
4964450 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:4965019 original size:19 final size:19
Alignment explanation
Indices: 4965003--4965085 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
4964993 GAAAATGACT
4965003 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4965022 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4965041 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
4965055 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4965074 ATCGCAATGCGA
1 ATCGCAATGCGA
4965086 TTTGTGTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4965097 original size:19 final size:19
Alignment explanation
Indices: 4965092--4965196 Score: 76
Period size: 19 Copynumber: 5.7 Consensus size: 19
4965082 GCGATTTGTG
*
4965092 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
4965111 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
4965127 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
* ***
4965144 TTTCGTATTGCGATAGCCA
1 TTTCGCATTGCGATTTTCA
**
4965163 TTTCCGCATTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
*
4965183 TTTTCGCGTTGCGA
1 -TTTCGCATTGCGA
4965197 AAGTAAGTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 3 0.04
19 24 0.34
20 23 0.33
21 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:4965175 original size:20 final size:20
Alignment explanation
Indices: 4965150--4965196 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4965140 TTCATTTCGT
4965150 ATTGCGATAGCCATTTCCGC
1 ATTGCGATAGCCATTTCCGC
* *
4965170 ATTGCGATAGTCATTTTCGC
1 ATTGCGATAGCCATTTCCGC
*
4965190 GTTGCGA
1 ATTGCGA
4965197 AAGTAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (20 bp):
ATTGCGATAGCCATTTCCGC
Found at i:4965207 original size:20 final size:20
Alignment explanation
Indices: 4965184--4965222 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4965174 CGATAGTCAT
4965184 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
4965204 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
4965223 ACTATTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:4965597 original size:21 final size:20
Alignment explanation
Indices: 4965571--4965639 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
4965561 CTGTCATCCC
4965571 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
4965592 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
4965613 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
4965633 TCAAGAG
1 TCAAGAG
4965640 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:4965651 original size:41 final size:42
Alignment explanation
Indices: 4965561--4965651 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
4965551 CCCGACTCAC
* *
4965561 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
4965603 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
4965644 CTGTCATC
1 CTGTCATC
4965652 GTTGAAGATG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:4967095 original size:14 final size:14
Alignment explanation
Indices: 4967061--4967099 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4967051 TTGATTGTTT
4967061 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
4967075 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
4967089 TGTTGATTTGT
1 AATTGATTTGT
4967100 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:4967263 original size:19 final size:19
Alignment explanation
Indices: 4967239--4967303 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
4967229 GCAACGAGAG
4967239 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
4967258 AATCGCAATGCAAAATAAA
1 AATCGCAATGCGAAATGAA
4967277 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
4967291 AATCGCAATGCGA
1 AATCGCAATGCGA
4967304 TTTTCATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 1 0.03
19 25 0.64
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4967347 original size:20 final size:20
Alignment explanation
Indices: 4967322--4967382 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
4967312 TCGCATTGCG
*
4967322 ATTTTCTCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
4967342 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
4967362 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
4967382 A
1 A
4967383 AATGAATGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGTC
Found at i:4970938 original size:48 final size:48
Alignment explanation
Indices: 4970867--4970963 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
4970857 AAAAATAATT
* *
4970867 CCATTATACTTCCTAATCAGATAATAGTTTCTATTACTCTTGTTGGCA
1 CCATTATACTTCCTAATCAGATAATAGTTTCCATGACTCTTGTTGGCA
4970915 CCATTATACTTCCTAATCAGATAATAGTTTCCATGACTCTTGTTGGCA
1 CCATTATACTTCCTAATCAGATAATAGTTTCCATGACTCTTGTTGGCA
4970963 C
1 C
4970964 AGTTCGTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (48 bp):
CCATTATACTTCCTAATCAGATAATAGTTTCCATGACTCTTGTTGGCA
Found at i:4971275 original size:28 final size:28
Alignment explanation
Indices: 4971235--4971290 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4971225 CATGTAACTA
*
4971235 AACAGTACTCTGTGAAGAATACTGGAAG
1 AACAATACTCTGTGAAGAATACTGGAAG
* *
4971263 AACAATACTCTGTGAGGAATGCTGGAAG
1 AACAATACTCTGTGAAGAATACTGGAAG
4971291 TCATGCTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (28 bp):
AACAATACTCTGTGAAGAATACTGGAAG
Found at i:4972636 original size:88 final size:89
Alignment explanation
Indices: 4972533--4972695 Score: 301
Period size: 88 Copynumber: 1.8 Consensus size: 89
4972523 ACTCAATACG
4972533 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTAT-GTTACATCAGTTGTAACCCACTCCT
1 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTATGGTTACATCAGTTGTAACCCACTCCT
4972597 ATGAGTGTTTTTTGGGCCCCTTTA
66 ATGAGTGTTTTTTGGGCCCCTTTA
* *
4972621 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTATTATGGTTACTTCAGTTGTAACCCACTCCT
1 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTATGGTTACATCAGTTGTAACCCACTCCT
4972686 ATGAGTGTTT
66 ATGAGTGTTT
4972696 CCTGGGCCTC
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
88 38 0.53
89 34 0.47
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (89 bp):
TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTATGGTTACATCAGTTGTAACCCACTCCT
ATGAGTGTTTTTTGGGCCCCTTTA
Found at i:4972702 original size:89 final size:88
Alignment explanation
Indices: 4972533--4972708 Score: 298
Period size: 89 Copynumber: 2.0 Consensus size: 88
4972523 ACTCAATACG
4972533 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTATGTTACATCAGTTGTAACCCACTCCTA
1 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTATGTTACATCAGTTGTAACCCACTCCTA
**
4972598 TGAGTGTTTTTTGGGCCCCTTTA
66 TGAGTGTTTCCTGGGCCCCTTTA
* *
4972621 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTATTATGGTTACTTCAGTTGTAACCCACTCCT
1 TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTAT-GTTACATCAGTTGTAACCCACTCCT
*
4972686 ATGAGTGTTTCCTGGGCCTCTTT
65 ATGAGTGTTTCCTGGGCCCCTTT
4972709 GGCCATTTAT
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
88 38 0.46
89 44 0.54
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (88 bp):
TGTTCAATTGAAGATACTTGGAAGTATTTCATCTAGTATGTTACATCAGTTGTAACCCACTCCTA
TGAGTGTTTCCTGGGCCCCTTTA
Found at i:4973035 original size:20 final size:20
Alignment explanation
Indices: 4973012--4973049 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4973002 AATCGACCCA
4973012 GTTCAACCAATATCGATATT
1 GTTCAACCAATATCGATATT
* *
4973032 GTTCATCCAATATTGATA
1 GTTCAACCAATATCGATA
4973050 CCTTAACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
GTTCAACCAATATCGATATT
Found at i:4978783 original size:30 final size:30
Alignment explanation
Indices: 4978748--4978826 Score: 158
Period size: 30 Copynumber: 2.6 Consensus size: 30
4978738 TTTTGCCTCC
4978748 TAAAATTTTATAAATTCAAATTCATCCCTA
1 TAAAATTTTATAAATTCAAATTCATCCCTA
4978778 TAAAATTTTATAAATTCAAATTCATCCCTA
1 TAAAATTTTATAAATTCAAATTCATCCCTA
4978808 TAAAATTTTATAAATTCAA
1 TAAAATTTTATAAATTCAA
4978827 GTCACCTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAAATTTTATAAATTCAAATTCATCCCTA
Found at i:4980797 original size:3 final size:3
Alignment explanation
Indices: 4980789--4980827 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
4980779 AATAATTCAT
4980789 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
4980828 TTTAGTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4987110 original size:15 final size:16
Alignment explanation
Indices: 4987090--4987121 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4987080 GATACACTAA
4987090 TAACCTGAAA-CCTTT
1 TAACCTGAAACCCTTT
4987105 TAACCTGAAACCCTTT
1 TAACCTGAAACCCTTT
4987121 T
1 T
4987122 GCCAACGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (16 bp):
TAACCTGAAACCCTTT
Found at i:4989496 original size:76 final size:76
Alignment explanation
Indices: 4989370--4989676 Score: 515
Period size: 76 Copynumber: 4.0 Consensus size: 76
4989360 TGGTAATGCT
* ** * *
4989370 GATGACCCGAAGATTTTGCAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
4989435 TATGACTTACA
66 CAGGACTTACA
*
4989446 GATGACCCTAAGGCTTTGAAAACTTCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
4989511 CAGGACTTACA
66 CAGGACTTACA
*
4989522 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCACGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
4989587 TAGGACTTACA
66 CAGGACTTACA
*
4989598 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
4989663 CAGGACTTACA
66 CAGGACTTACA
4989674 GAT
1 GAT
4989677 ATGGGAAATA
Statistics
Matches: 217, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 217 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
CAGGACTTACA
Found at i:4989980 original size:164 final size:165
Alignment explanation
Indices: 4989680--4990003 Score: 501
Period size: 164 Copynumber: 2.0 Consensus size: 165
4989670 TACAGATATG
* * *
4989680 GGAAATAGTTTACTAAGTAAGAAACTATGGAAATCGTTTTCTTATTATTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTATTATTCAACAATTTCATTTTC
** * *
4989745 AGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAATATCTTAAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTGTTCAAAATAATATCTTAAC
*
4989810 TGGGTAACATGCCCCAATCTCAAGATAATGTTGTT
131 TGGGTAACATGACCCAATCTCAAGATAATGTTGTT
4989845 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTT-TTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTA-TTATTCAACAATTTCATTTT
* * *
4989909 C-GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTGTTCAAAAT-ATCATGTTG
65 CAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTGTTCAAAATAAT-ATCTTA
*
4989972 ACTGGGTAATATGACCCAATCTCAAGATAATG
129 ACTGGGTAACATGACCCAATCTCAAGATAATG
4990004 CTCATTCTTG
Statistics
Matches: 145, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
163 2 0.01
164 82 0.57
165 59 0.41
166 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTATTATTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTGTTCAAAATAATATCTTAAC
TGGGTAACATGACCCAATCTCAAGATAATGTTGTT
Found at i:4990538 original size:22 final size:22
Alignment explanation
Indices: 4990513--4990567 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4990503 AATAAAGCTT
4990513 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
* *
4990535 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
4990557 TCATCTTTGAA
1 TCATCTTTGAA
4990568 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:4997090 original size:12 final size:12
Alignment explanation
Indices: 4997075--4997124 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
4997065 GTAAAAATGA
4997075 AAATGTAAATAC
1 AAATGTAAATAC
*
4997087 AAATGTAAAAAATGC
1 AAATGT---AAATAC
*
4997102 AAATGTAAATGC
1 AAATGTAAATAC
4997114 AAATGTAAATA
1 AAATGTAAATA
4997125 TGTGAATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 22 0.67
15 11 0.33
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:4997097 original size:27 final size:27
Alignment explanation
Indices: 4997063--4997122 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
4997053 AAATGTAATT
4997063 ATGT-AAAAATGAAAATGTAAATACAA
1 ATGTAAAAAATGAAAATGTAAATACAA
* *
4997089 ATGTAAAAAATGCAAATGTAAATGCAA
1 ATGTAAAAAATGAAAATGTAAATACAA
4997116 ATGTAAA
1 ATGTAAA
4997123 TATGTGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.23
Consensus pattern (27 bp):
ATGTAAAAAATGAAAATGTAAATACAA
Found at i:4997200 original size:7 final size:8
Alignment explanation
Indices: 4997182--4997220 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
4997172 ATAAAAGTAT
4997182 AAATGCAA
1 AAATGCAA
4997190 AAATG-AA
1 AAATGCAA
4997197 AAATGCAA
1 AAATGCAA
*
4997205 AGATGC-A
1 AAATGCAA
4997212 AAATGCAA
1 AAATGCAA
4997220 A
1 A
4997221 TGTATGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (8 bp):
AAATGCAA
Found at i:4997200 original size:15 final size:15
Alignment explanation
Indices: 4997182--4997220 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
4997172 ATAAAAGTAT
4997182 AAATGCAAAAATGAA
1 AAATGCAAAAATGAA
* *
4997197 AAATGCAAAGATGCA
1 AAATGCAAAAATGAA
4997212 AAATGCAAA
1 AAATGCAAA
4997221 TGTATGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (15 bp):
AAATGCAAAAATGAA
Found at i:4999470 original size:21 final size:22
Alignment explanation
Indices: 4999444--4999494 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
4999434 GATATTGAAA
*
4999444 AATAAATATATATTAA-AATAT
1 AATAAATATATAATAATAATAT
4999465 AATAAATA-ATAATAATAATAT
1 AATAAATATATAATAATAATAT
*
4999486 -TTAAATATA
1 AATAAATATA
4999495 AACAAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATAAATATATAATAATAATAT
Found at i:5000823 original size:3 final size:3
Alignment explanation
Indices: 5000815--5000839 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5000805 CTTGTAATTT
5000815 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5000840 ATATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5000848 original size:3 final size:3
Alignment explanation
Indices: 5000842--5000894 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
5000832 ATTATTATAT
* *
5000842 ATA ATA ATA ATA ATA TATA ATA ATA ATA ATA ATT ATT ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5000888 ATA ATA A
1 ATA ATA A
5000895 ATAAATAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:5003224 original size:18 final size:18
Alignment explanation
Indices: 5003201--5003236 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5003191 TTTTTTAAAA
5003201 TTATATTTAATATTTAGT
1 TTATATTTAATATTTAGT
**
5003219 TTATATTTTTTATTTAGT
1 TTATATTTAATATTTAGT
5003237 CATATACTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TTATATTTAATATTTAGT
Found at i:5004585 original size:12 final size:13
Alignment explanation
Indices: 5004554--5004587 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5004544 AAATTAGATG
*
5004554 CACTTAATTAAAT
1 CACTTAAATAAAT
5004567 CACTTAAATAAAT
1 CACTTAAATAAAT
5004580 -ACTTAAAT
1 CACTTAAAT
5004588 TACATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (13 bp):
CACTTAAATAAAT
Done.