Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 23 of 325
Found at i:5371178 original size:33 final size:32
Alignment explanation
Indices: 5371141--5371227 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 32
5371131 GTTTTTTTAG
5371141 TTTTTTTTTT-GTTAGGTTTTTCTTTTTTCTT
1 TTTTTTTTTTGGTTAGGTTTTTCTTTTTTCTT
5371172 CTTTTTTTTTTGGTTAGGTTTTTCTTTTTTCTT
1 -TTTTTTTTTTGGTTAGGTTTTTCTTTTTTCTT
5371205 TTTTTTTTTTGGGTTAGGTTTTT
1 TTTTTTTTTT-GGTTAGGTTTTT
5371228 TTTGGGGGGC
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
32 20 0.38
33 33 0.62
ACGTcount: A:0.03, C:0.06, G:0.14, T:0.77
Consensus pattern (32 bp):
TTTTTTTTTTGGTTAGGTTTTTCTTTTTTCTT
Found at i:5371976 original size:21 final size:20
Alignment explanation
Indices: 5371929--5371976 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
5371919 CAATGTATTT
5371929 TAATATTTAGATTATAATAA
1 TAATATTTAGATTATAATAA
*
5371949 TATATATTTA-ATTTTATATATA
1 TA-ATATTTAGATTATA-ATA-A
5371971 TAATAT
1 TAATAT
5371977 AAATTACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.29
21 14 0.58
22 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATATTTAGATTATAATAA
Found at i:5372335 original size:16 final size:17
Alignment explanation
Indices: 5372309--5372342 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5372299 ATTCCTTTTT
*
5372309 TTATATTTTTTTCTTCC
1 TTATATTTTTTTCATCC
5372326 TTAT-TTTTTTTCATCC
1 TTATATTTTTTTCATCC
5372342 T
1 T
5372343 CCTCCTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATTTTTTTCATCC
Found at i:5379844 original size:3 final size:3
Alignment explanation
Indices: 5379836--5379864 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5379826 TTTGAATTTG
5379836 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5379865 ATGTTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5380879 original size:37 final size:38
Alignment explanation
Indices: 5380779--5380880 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 38
5380769 ATATATTTGG
5380779 TAATAATAATA--TAAAATAATAA-TATGTACATAAAAA
1 TAATAATAATATCTAAAATAA-AAGTATGTACATAAAAA
* *
5380815 TACATATATATATATGCATATAATAAAAGTATGTA-ATAATAA
1 TA-ATA-ATA-ATAT-C-TAAAATAAAAGTATGTACATAAAAA
*
5380857 TAATAATAATATCTACAATAAAAG
1 TAATAATAATATCTAAAATAAAAG
5380881 AAAATATTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 7 0.13
40 3 0.05
41 3 0.05
42 10 0.18
43 13 0.24
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (38 bp):
TAATAATAATATCTAAAATAAAAGTATGTACATAAAAA
Found at i:5381155 original size:23 final size:24
Alignment explanation
Indices: 5381113--5381165 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
5381103 GAATATATAC
*
5381113 ATAAGAAATATATAACTAATAGAT
1 ATAAAAAATATATAACTAATAGAT
*
5381137 -TAAAAAATATAT-ACATAATATAT
1 ATAAAAAATATATAAC-TAATAGAT
5381160 ATAAAA
1 ATAAAA
5381166 TACTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 2 0.08
23 18 0.72
24 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
ATAAAAAATATATAACTAATAGAT
Found at i:5381162 original size:38 final size:37
Alignment explanation
Indices: 5381064--5381162 Score: 100
Period size: 38 Copynumber: 2.7 Consensus size: 37
5381054 AATATGGTAT
*
5381064 TTAAAAAATATAT--AT-ATATGTATATATAATAGTA
1 TTAAAAAATATATACATAATATATATATATAATAGTA
* * *
5381098 TCT-AAGAATATATACATAAGAAATATATAACTAATAG-A
1 T-TAAAAAATATATACATAATATATATAT-A-TAATAGTA
5381136 TTAAAAAATATATACATAATATATATA
1 TTAAAAAATATATACATAATATATATA
5381163 AAATACTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
34 10 0.20
35 1 0.02
36 2 0.04
37 8 0.16
38 24 0.47
39 6 0.12
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (37 bp):
TTAAAAAATATATACATAATATATATATATAATAGTA
Found at i:5381303 original size:76 final size:77
Alignment explanation
Indices: 5381177--5381318 Score: 277
Period size: 76 Copynumber: 1.9 Consensus size: 77
5381167 ACTTAAAAAA
5381177 AAGAAGGGGGAAAGAAGAGAGAAGAGAGGGGGAAAGGAAATCCGGCCAA-GGGGCCGATCACCGG
1 AAGAAGGGGGAAAGAAGAGAGAAGAGAGGGGGAAAGGAAATCCGGCCAAGGGGGCCGATCACCGG
5381241 CGACGAGCGGCG
66 CGACGAGCGGCG
5381253 AAGAAGGGGGAAAGAAGAGAGAAGAGAGGGGGAAAGGAAATCCGGCCAAGGGGGCCGATCACCGG
1 AAGAAGGGGGAAAGAAGAGAGAAGAGAGGGGGAAAGGAAATCCGGCCAAGGGGGCCGATCACCGG
5381318 C
66 C
5381319 CGATCGTCGG
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
76 49 0.75
77 16 0.25
ACGTcount: A:0.37, C:0.16, G:0.44, T:0.03
Consensus pattern (77 bp):
AAGAAGGGGGAAAGAAGAGAGAAGAGAGGGGGAAAGGAAATCCGGCCAAGGGGGCCGATCACCGG
CGACGAGCGGCG
Found at i:5381764 original size:22 final size:22
Alignment explanation
Indices: 5381739--5381788 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
5381729 TTTTTTCTTC
*
5381739 TTTTTTTTTTGGGGGGTTAGGT
1 TTTTTTTTTTGGAGGGTTAGGT
**
5381761 TTTTTTTTTTTTAGGGTTAGGT
1 TTTTTTTTTTGGAGGGTTAGGT
5381783 TTTTTT
1 TTTTTT
5381789 GGGGGGCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.06, C:0.00, G:0.26, T:0.68
Consensus pattern (22 bp):
TTTTTTTTTTGGAGGGTTAGGT
Found at i:5382986 original size:77 final size:78
Alignment explanation
Indices: 5382818--5383034 Score: 276
Period size: 77 Copynumber: 2.7 Consensus size: 78
5382808 ATGTGACCCG
* * * * *
5382818 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--AAAATACCT
* * * *
5382883 CAGTGTGTGATCTGA
64 CAGCGCGTGAGCTCA
*
5382898 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
5382962 GCGCGTGAGC-CA
66 GCGCGTGAGCTCA
*
5382974 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAGGCAGAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAGACAGAAATTGAAAA
5383035 ACGGAAATTG
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
76 2 0.02
77 47 0.39
79 47 0.39
80 26 0.21
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
GCGCGTGAGCTCA
Found at i:5383048 original size:250 final size:244
Alignment explanation
Indices: 5382443--5383277 Score: 899
Period size: 250 Copynumber: 3.4 Consensus size: 244
5382433 AACAGACATT
*
5382443 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGTTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** * * * *
5382508 TTGATTTTTTG-AAACTTAACTTGAAAAGCAGATTTTGAAAATATCTCGATATGTGA-CTGAAGG
66 TTGATTTTTTGAAAACAGAAATTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCTG-AGG
* * *
5382571 TTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAGACTCAACTC
130 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA-AAT-ACCTC
* * * ***
5382633 AACTCTCGCAGAAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTG
193 -AGTGT-G-TGACTGAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG
* *
5382689 AAAAAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGTAATA
1 ----AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATA
* *
5382754 TGAGTTGA-TTTTTGAAAACAG-AATCTGAAAAATAGATTTTGAAAATACCTCGACATGTGACCC
62 TGAGTTGATTTTTTGAAAACAGAAAT-TGAAAAACAGATTTTGAAAATACCTCGACATGTGACCT
* * * *
5382817 GAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACC
126 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACC
5382882 TCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
191 TCAGTGTGTGA-CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* *
5382937 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * ** * * *
5383002 TTGATTTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTTTGACCT
66 TTGA----TTTTTTGAAA-ACAGAAATTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCT
* * * * * *
5383067 GAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG--AAATTACT
126 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACC
* * *
5383129 TCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
191 TCAGTGTGTGACTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * * ** ** *
5383182 AAAAACAGAAATTAAAAATACCTCAGCA--TG-TCTTGAGGCTCAACTCATTTCTCACAATATGA
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
5383244 GTTGAATTTTTTTTTGAAAGACAGAAATT-AAAAA
65 GTTG-A---TTTTTTGAAA-ACAGAAATTGAAAAA
5383278 TACCTCAGCA
Statistics
Matches: 508, Mismatches: 61, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
242 6 0.01
243 52 0.10
244 66 0.13
245 66 0.13
247 14 0.03
248 11 0.02
249 59 0.12
250 202 0.40
251 9 0.02
252 19 0.04
253 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (244 bp):
AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAAACAGAAATTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCTGAGGC
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACCTCAGT
GTGTGACTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:5383097 original size:94 final size:94
Alignment explanation
Indices: 5382934--5383106 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 94
5382924 GTTGATTTTT
* * * *
5382934 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
5382999 GAGTTGATTTTTTTTTTGAAAGGCAGAAA
66 GAGTTGATTTTTTTTTTGAAAGGCAGAAA
* * ** * *
5383028 TTGAAAAACGGAAATTGAAAATACCTCGGCGTTTGA-CCTGAGGCTCAACTCGCCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCACAATA
5383092 CGAGTTGATTTTTTT
65 CGAGTTGATTTTTTT
5383107 GACAACAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
93 2 0.03
94 66 0.97
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (94 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
GAGTTGATTTTTTTTTTGAAAGGCAGAAA
Found at i:5383223 original size:75 final size:75
Alignment explanation
Indices: 5383028--5383332 Score: 353
Period size: 75 Copynumber: 4.0 Consensus size: 75
5383018 AAGGCAGAAA
* * * * * * *
5383028 TTGAAAAACGGAAATTGAAAATACCTCGGCGTTTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTAAAAATACCTCAGC--ATGTCCTGAGGCTCAACTCACCTCTCACAATAT
5383093 GAGTTGATTTTT
64 GAGTTGATTTTT
* * * * * *
5383105 TTG-ACAACAGAAATTGAAATTACTTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
5383169 GTTGATTTTT
66 GTTGATTTTT
* **
5383179 TTGAAAAACAGAAATTAAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
5383244 GTTGAATTTTTTT
66 GTTG-A--TTTTT
* *
5383257 TTGAAAGACAGAAATTAAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCATGT---CCTGAGGCTCAACTCACCTCTCACAATA
*
5383321 TGAGCTGATTTT
63 TGAGTTGATTTT
5383333 GAAAAAGTAG
Statistics
Matches: 196, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
74 43 0.22
75 56 0.29
76 22 0.11
77 7 0.04
78 38 0.19
79 1 0.01
80 28 0.14
81 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (75 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
GTTGATTTTT
Found at i:5383401 original size:54 final size:54
Alignment explanation
Indices: 5383301--5383406 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5383291 GAACCGAGGC
*
5383301 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5383355 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5383407 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5383441 original size:220 final size:209
Alignment explanation
Indices: 5383183--5383588 Score: 544
Period size: 220 Copynumber: 1.9 Consensus size: 209
5383173 ATTTTTTTGA
* * **
5383183 AAAACAGAAATTAAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTG
1 AAAACAGAAATTAAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
* * *
5383248 AATTTTTTTTTGAAAGACAGAAATTAAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTC
66 AA-------TTAAAACACAAAAATTAAAAATACCTCAGC--GTGAACCGAGGCTCAACTCACCTC
* *
5383313 TCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGG-TTCAACCCACCTCTCGCAATATG
122 TAGCAATATGAGCTGATTTTGAAAAA-CA-AAATTAAAAGGCTT-AACCCACCTCTCGCAATATG
5383377 AGTTGATTCTTGAACAACGTAAATTG
184 AGTTGATTCTTGAACAACGTAAATTG
* * *
5383403 AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTAAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
* **
5383468 AATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATAT
66 AATTAAAACACAAAAATTAAAAATACCTCAGCGTGAACCGAGGCTCAACTCACCTCTAGCAATAT
* *
5383533 GAGTTGATTTTGAAAAACAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGT
131 GAGCTGATTTTGAAAAACAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGT
5383589 CAATTTAAAA
Statistics
Matches: 168, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
209 33 0.20
210 3 0.02
211 46 0.27
213 26 0.15
220 60 0.36
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (209 bp):
AAAACAGAAATTAAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
AATTAAAACACAAAAATTAAAAATACCTCAGCGTGAACCGAGGCTCAACTCACCTCTAGCAATAT
GAGCTGATTTTGAAAAACAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGTTGATTCTTG
AACAACGTAAATTG
Found at i:5383707 original size:70 final size:69
Alignment explanation
Indices: 5383560--5383821 Score: 334
Period size: 70 Copynumber: 3.8 Consensus size: 69
5383550 CAAAATTAAA
* * * * *
5383560 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACA-AAAATTAAAATACCTCAACGT
5383623 GCCCG
65 GCCCG
*
5383628 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCAACGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCAACGTG
**
5383693 TCTTG
66 -CCCG
* * *
5383698 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATT-AAAATACCTCAACG
5383761 TGCCCCG
64 TG-CCCG
*
5383768 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
5383822 GGCTTAACTC
Statistics
Matches: 168, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
68 31 0.18
69 34 0.20
70 85 0.51
71 4 0.02
72 11 0.07
73 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (69 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCAACGTG
CCCG
Found at i:5383880 original size:261 final size:263
Alignment explanation
Indices: 5383400--5384250 Score: 1508
Period size: 262 Copynumber: 3.3 Consensus size: 263
5383390 ACAACGTAAA
* * * * * *
5383400 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5383465 TTGAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAA
66 TTG-ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAA
5383530 TATGAGTTGATTTTGAAAAAC-AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATT
130 TATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATT
5383594 TAAAAC-ATAAACTAAAAATACCTCAACGTG-CCCGAGGCTCAACTCACTTCTCGCAATATGAGT
195 TAAAACTA-AAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
5383657 TGATT
259 TGATT
5383662 TTGAAAACAAAAATT-AAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5383726 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
5383791 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
131 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
5383856 AAAACTAAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCACAATATGAGTTG
196 AAAACTAAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
5383921 ATT
261 ATT
5383924 TTGAAAAC-AAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5383988 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
5384053 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA-TT
131 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
* *
5384117 -----TAAAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
196 AAAACTAAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
5384177 ATT
261 ATT
* *
5384180 TTGAAAACAACAATTAAAAACACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5384245 TTGATT
66 TTGATT
5384251 TTCCTTGAAA
Statistics
Matches: 573, Mismatches: 11, Indels: 15
0.96 0.02 0.03
Matches are distributed among these distances:
256 68 0.12
257 60 0.10
260 82 0.14
261 127 0.22
262 236 0.41
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (263 bp):
TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
AAAACTAAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
ATT
Found at i:5383899 original size:192 final size:192
Alignment explanation
Indices: 5383628--5383993 Score: 497
Period size: 192 Copynumber: 1.9 Consensus size: 192
5383618 AACGTGCCCG
* * * *
5383628 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCAACGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTGAAAACAAAAATAAAAATACCTCAACGTG
* ** * *
5383693 TCTTGAGGCTCAACTCA-TCTCTCGCAATATGAGTTGA-TTAAAACACAAAAATTGAAAATACCT
66 CCCCGAGGCTCAACTCACT-TCTCACAATATGAGTTGATTTAAAA-AC-AAAATTAAAAATACCT
*
5383756 CAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
128 CAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
* *
5383821 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACTAAAACTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTGAAAAC-AAAAATAAAAATACCTCAACGT
*
5383884 GCCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATTTTGAAAACAAAATTAAAAATACCTC
65 GCCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGA-TTTAAAAACAAAATTAAAAATACCTC
* ** * *
5383949 AACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATT
129 AACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATT
5383994 AAAACACAAA
Statistics
Matches: 151, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
191 5 0.03
192 112 0.74
193 29 0.19
194 5 0.03
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (192 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTGAAAACAAAAATAAAAATACCTCAACGTG
CCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATTTAAAAACAAAATTAAAAATACCTCAA
CGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:5383963 original size:70 final size:71
Alignment explanation
Indices: 5383821--5384083 Score: 322
Period size: 70 Copynumber: 3.7 Consensus size: 71
5383811 AAAAATTAAA
* * * * * *
5383821 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACTAAAACTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
5383884 GCCCCG
66 GCCCCG
*
5383890 AGGCTCAACTCACTTCTCACAATATGAGTTGATTTTGAAAAC-AAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
* **
5383954 GTCTTG
66 GCCCCG
* * * * *
5383960 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAACG
5384023 TGCCCCG
65 TGCCCCG
5384030 AGGCTCAACTCACCTCT-AGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCA-CAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
5384084 GGCTTAACTC
Statistics
Matches: 164, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
68 5 0.03
69 27 0.16
70 110 0.67
71 5 0.03
72 14 0.09
73 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
GCCCCG
Found at i:5384053 original size:140 final size:141
Alignment explanation
Indices: 5383821--5384083 Score: 397
Period size: 140 Copynumber: 1.9 Consensus size: 141
5383811 AAAAATTAAA
* * *
5383821 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACTAAAACTAAAAATACCTCAACGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAAACAAAAACTAAAAATACCTCAACGTGC
*
5383886 CCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATTTTG-AAAAC-AAAATTAAAAATACCTC
66 CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTGAAAAACAAAAATTAAAAATACCTC
5383949 AACGTGTCTTG
131 AACGTGTCTTG
* ** * * *
5383960 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAA-ACAAAAACTAAAAATACCTCAACGTG
5384025 CCCCGAGGCTCAACTCACCTCT-AGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
65 CCCCGAGGCTCAACTCACCTCTCA-CAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
5384084 GGCTTAACTC
Statistics
Matches: 110, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
139 34 0.31
140 61 0.55
141 5 0.05
142 10 0.09
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (141 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAAACAAAAACTAAAAATACCTCAACGTGC
CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTGAAAAACAAAAATTAAAAATACCTC
AACGTGTCTTG
Found at i:5389268 original size:12 final size:12
Alignment explanation
Indices: 5389248--5389283 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5389238 ATGGATATGC
*
5389248 AATGTATGAATG
1 AATGCATGAATG
5389260 AATGCATGAATG
1 AATGCATGAATG
5389272 AATGCATGAATG
1 AATGCATGAATG
5389284 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:5390977 original size:27 final size:27
Alignment explanation
Indices: 5390930--5390982 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
5390920 TAAAATAGGA
* * *
5390930 AAAATGATAATTTGGTAATAATAATAT
1 AAAATAATAATATGGTAATAAAAATAT
5390957 AAAATAATAATAT-GTACATAAAAATA
1 AAAATAATAATATGGTA-ATAAAAATA
5390983 CTATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATAATAATATGGTAATAAAAATAT
Found at i:5394806 original size:38 final size:39
Alignment explanation
Indices: 5394722--5394856 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
5394712 ACCAATATGG
*
5394722 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
5394761 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
5394799 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
5394840 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5394857 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:5396429 original size:5 final size:5
Alignment explanation
Indices: 5396411--5396461 Score: 93
Period size: 5 Copynumber: 10.0 Consensus size: 5
5396401 TTTCTTTTAT
5396411 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
5396462 TTAATTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 40 0.89
6 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:5401775 original size:10 final size:9
Alignment explanation
Indices: 5401754--5401786 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5401744 CGTATTCCAA
5401754 ATTTTTTTT
1 ATTTTTTTT
*
5401763 -TTTTTTTA
1 ATTTTTTTT
5401771 ATTTTTTTT
1 ATTTTTTTT
5401780 ATTTTTT
1 ATTTTTT
5401787 ATAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:5401775 original size:17 final size:17
Alignment explanation
Indices: 5401753--5401787 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5401743 GCGTATTCCA
*
5401753 AATTTTTTTTTTTTTTT
1 AATTTTTTTTATTTTTT
5401770 AATTTTTTTTATTTTTT
1 AATTTTTTTTATTTTTT
5401787 A
1 A
5401788 TAAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
AATTTTTTTTATTTTTT
Found at i:5402609 original size:38 final size:39
Alignment explanation
Indices: 5402525--5402659 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
5402515 ACCAATATGG
*
5402525 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
5402564 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
5402602 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
5402643 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5402660 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:5404238 original size:5 final size:5
Alignment explanation
Indices: 5404220--5404270 Score: 93
Period size: 5 Copynumber: 10.0 Consensus size: 5
5404210 TTTCTTTTAT
5404220 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
5404271 CTTAATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 40 0.89
6 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:5408441 original size:18 final size:19
Alignment explanation
Indices: 5408406--5408441 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5408396 GATATTTAAA
*
5408406 GAAAATCGTTTGCATTTAG
1 GAAAAACGTTTGCATTTAG
5408425 GAAAAACGTTT-CATTTA
1 GAAAAACGTTTGCATTTA
5408442 ATAAAACCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (19 bp):
GAAAAACGTTTGCATTTAG
Found at i:5408447 original size:18 final size:19
Alignment explanation
Indices: 5408399--5408447 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5408389 TAATCGTGAT
*
5408399 ATTTAAAGAAAATCGTTTGC
1 ATTT-AAGAAAAACGTTTGC
*
5408419 ATTTAGGAAAAACGTTT-C
1 ATTTAAGAAAAACGTTTGC
*
5408437 ATTTAATAAAA
1 ATTTAAGAAAA
5408448 CCGAGTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 11 0.44
20 4 0.16
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (19 bp):
ATTTAAGAAAAACGTTTGC
Found at i:5411841 original size:24 final size:23
Alignment explanation
Indices: 5411805--5411860 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
5411795 ATTAAGATGG
* *
5411805 TTCTTCCTTATTATTATTATT-TT
1 TTCTTTCTT-TTATTATTTTTCTT
5411828 TTC-TTCTTTTATTATTTTTCTT
1 TTCTTTCTTTTATTATTTTTCTT
5411850 TTCTTTCTTTT
1 TTCTTTCTTTT
5411861 TTTTCGAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 10 0.34
22 9 0.31
23 10 0.34
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (23 bp):
TTCTTTCTTTTATTATTTTTCTT
Found at i:5411863 original size:18 final size:17
Alignment explanation
Indices: 5411818--5411865 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
5411808 TTCCTTATTA
5411818 TTATTATTTTTTCTTCTT
1 TTATT-TTTTTTCTTCTT
* *
5411836 TTATTATTTTTCTTTTCT
1 TTATTTTTTTTCTTCT-T
*
5411854 TTCTTTTTTTTC
1 TTATTTTTTTTC
5411866 GAAGCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTTTTTCTTCTT
Found at i:5412557 original size:3 final size:3
Alignment explanation
Indices: 5412549--5412599 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
5412539 TAATTTTAAC
* * * *
5412549 ATT ATT ATT TTT ATT ATT ATC ACT ATT ATT ATT ATTT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
5412595 ATT AT
1 ATT AT
5412600 ACTATTAAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5412593 original size:13 final size:14
Alignment explanation
Indices: 5412559--5412606 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 14
5412549 ATTATTATTT
5412559 TTATTATTATCACTA
1 TTATTATTAT-ACTA
5412574 TTATTATTATTTACTA
1 TTATTATTA--TACTA
5412590 TTATTATTATACTA
1 TTATTATTATACTA
5412604 TTA
1 TTA
5412607 AACTGATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.26
15 9 0.29
16 13 0.42
17 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATTATTATACTA
Found at i:5413138 original size:23 final size:23
Alignment explanation
Indices: 5413094--5413138 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5413084 TTATATTAAA
**
5413094 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAAAATAAATATG
*
5413117 ATTAAAAATAAAAAATATATAT
1 ATTAAAAATAAAAAATAAATAT
5413139 TTAGTATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTAAAAATAAAAAATAAATATG
Found at i:5413481 original size:11 final size:11
Alignment explanation
Indices: 5413467--5413502 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5413457 CTTATCACCA
5413467 TTTTATTTCAT
1 TTTTATTTCAT
5413478 TTTTA-TT-AT
1 TTTTATTTCAT
5413487 TTTTATTTCAT
1 TTTTATTTCAT
5413498 TTTTA
1 TTTTA
5413503 CTTAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.30
10 4 0.17
11 12 0.52
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTCAT
Found at i:5415065 original size:34 final size:34
Alignment explanation
Indices: 5415022--5415086 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
5415012 CTTCTACTAA
*
5415022 ACCCTCATTTAAATTTTCAGGACCATCTACCCCT
1 ACCCACATTTAAATTTTCAGGACCATCTACCCCT
* **
5415056 ACCCACATTTAACTTTTCATTACCATCTACC
1 ACCCACATTTAAATTTTCAGGACCATCTACC
5415087 ACACCTCTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.34
Consensus pattern (34 bp):
ACCCACATTTAAATTTTCAGGACCATCTACCCCT
Found at i:5416178 original size:16 final size:17
Alignment explanation
Indices: 5416159--5416191 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5416149 TTGATTTTTT
5416159 ATAAAAT-AAATTTAAA
1 ATAAAATCAAATTTAAA
*
5416175 ATAATATCAAATTTAAA
1 ATAAAATCAAATTTAAA
5416192 TTTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATCAAATTTAAA
Found at i:5422731 original size:32 final size:34
Alignment explanation
Indices: 5422685--5422749 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
5422675 TAACAGTGGT
*
5422685 ACTGGGCCAGAG-CCCTT-TTCAAATTACAATAA
1 ACTGGGCCAGAGCCCCTTATTCAAATAACAATAA
** *
5422717 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAGAGCCCCTTATTCAAATAACAATA
5422750 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 10 0.37
33 5 0.19
34 12 0.44
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAAATAACAATAA
Found at i:5423091 original size:25 final size:27
Alignment explanation
Indices: 5423054--5423103 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
5423044 TCAAACATGC
5423054 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
5423080 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
5423104 ATAAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:5424625 original size:26 final size:26
Alignment explanation
Indices: 5424589--5424698 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5424579 CATGAAATTC
5424589 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5424615 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
5424641 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5424667 TTGTCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5424693 TTATCA
1 TTATCA
5424699 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5425040 original size:49 final size:50
Alignment explanation
Indices: 5424968--5425188 Score: 223
Period size: 49 Copynumber: 4.5 Consensus size: 50
5424958 TGGGGCGTTA
* *
5424968 CAGGCTACTACGTGTACCAGATAATT-GGTCGCATGTGTAGTACTAAGTG
1 CAGGCTACTATGTGTACCAGATAATTAGGTCACATGTGTAGTACTAAGTG
* * * * ** *
5425017 CAGGCTACTATGCGTACCTGATAACTTCGATCATGTGTGTAGTATTAAGTG
1 CAGGCTACTATGTGTACCAGATAA-TTAGGTCACATGTGTAGTACTAAGTG
* * ** * **
5425068 CAAGCTACTATGTGTATCAGATGGTTAGGTCACGTACGTAGTACTAAGTG
1 CAGGCTACTATGTGTACCAGATAATTAGGTCACATGTGTAGTACTAAGTG
** *
5425118 CAGGCTA-TACATGTACCAGATAATT-GGTCGCATGTGTAGTACTAAGTG
1 CAGGCTACTATGTGTACCAGATAATTAGGTCACATGTGTAGTACTAAGTG
* *
5425166 CAGGCTACTATGCGTACTAGATA
1 CAGGCTACTATGTGTACCAGATA
5425189 GCCTTGTCTA
Statistics
Matches: 135, Mismatches: 34, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
48 26 0.19
49 45 0.33
50 28 0.21
51 36 0.27
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (50 bp):
CAGGCTACTATGTGTACCAGATAATTAGGTCACATGTGTAGTACTAAGTG
Found at i:5433363 original size:46 final size:46
Alignment explanation
Indices: 5433291--5433563 Score: 350
Period size: 46 Copynumber: 5.9 Consensus size: 46
5433281 CTTTCTGAAA
** * * *
5433291 TGAAATGCGTAAGACCATGGTAGAAAGATACCATAGCAACATGATG
1 TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
**
5433337 TGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACG
1 TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
* * * *
5433383 GGAAATGAATAAGACCATGGTTGAAAGATACCATTGCAACGTGACA
1 TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
5433429 TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
1 TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
* *
5433475 GGAAATGAATAAGACAATGGTTGAAAGATACCATGGCAACATGACAG
1 TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC-G
* * * * * * *
5433522 -AAAATGAGTAAGACTATAGTTGAAAGACACTATGGCATCATG
1 TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
5433564 TCGAAGATAA
Statistics
Matches: 203, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
46 202 1.00
47 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
Found at i:5433449 original size:92 final size:92
Alignment explanation
Indices: 5433300--5433563 Score: 386
Period size: 92 Copynumber: 2.9 Consensus size: 92
5433290 ATGAAATGCG
* ** *
5433300 TAAGACCATGGTAGAAAGATACCATAGCAACATGATGTGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATAGCAACATGACATGAAATGAGTAAGACCATGGTTGAAAGA
5433365 TACCATGGCAACATGACGGGAAATGAA
66 TACCATGGCAACATGACGGGAAATGAA
* * *
5433392 TAAGACCATGGTTGAAAGATACCATTGCAACGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATAGCAACATGACATGAAATGAGTAAGACCATGGTTGAAAGA
5433457 TACCATGGCAACATGACGGGAAATGAA
66 TACCATGGCAACATGACGGGAAATGAA
* * * *
5433484 TAAGACAATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACTATAGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATAGCAACATGACATG-AAATGAGTAAGACCATGGTTGAAAG
* * *
5433548 ACACTATGGCATCATG
65 ATACCATGGCAACATG
5433564 TCGAAGATAA
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
91 1 0.01
92 154 0.99
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATAGCAACATGACATGAAATGAGTAAGACCATGGTTGAAAGA
TACCATGGCAACATGACGGGAAATGAA
Found at i:5433544 original size:138 final size:138
Alignment explanation
Indices: 5433290--5433548 Score: 392
Period size: 138 Copynumber: 1.9 Consensus size: 138
5433280 GCTTTCTGAA
** * * ** *
5433290 ATGAAATGCGTAAGACCATGGTAGAAAGATACCATAGCAACATGATGTGAAATGTGTAAGACCAT
1 ATGAAATGAATAAGACCATGGTAGAAAGATACCATAGCAACATGACGGGAAATGAATAAGACAAT
* * *
5433355 GGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATTGC
66 GGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGATACCATTGC
5433420 AACGTGAC
131 AACGTGAC
* *
5433428 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGACAAT
1 ATGAAATGAATAAGACCATGGTAGAAAGATACCATAGCAACATGACGGGAAATGAATAAGACAAT
* *
5433493 GGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACTATAGTTGAAAGA
66 GGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGA
5433549 CACTATGGCA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 107 1.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (138 bp):
ATGAAATGAATAAGACCATGGTAGAAAGATACCATAGCAACATGACGGGAAATGAATAAGACAAT
GGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGATACCATTGC
AACGTGAC
Found at i:5434454 original size:34 final size:33
Alignment explanation
Indices: 5434396--5434502 Score: 128
Period size: 34 Copynumber: 3.1 Consensus size: 33
5434386 TAAGCCCCCC
5434396 AAAA-AAAAACCTAACCCAAAAAAAAAAAGAAAAAGA
1 AAAAGAAAAACCTAA-CC--AAAAAAAAAGAAAAA-A
*
5434432 AAAAGAAAAACCTAACCTAAAAAAAAAGAAGAAA
1 AAAAGAAAAACCTAACC-AAAAAAAAAGAAAAAA
*
5434466 AAAAGAAAAACCTAACCAAAAAATAAA-AATAAA
1 AAAAGAAAAACCTAACCAAAAAA-AAAGAAAAAA
5434499 AAAA
1 AAAA
5434503 CCTAGCCACC
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
33 15 0.23
34 21 0.32
35 14 0.21
36 6 0.09
37 10 0.15
ACGTcount: A:0.77, C:0.12, G:0.06, T:0.06
Consensus pattern (33 bp):
AAAAGAAAAACCTAACCAAAAAAAAAGAAAAAA
Found at i:5434486 original size:19 final size:19
Alignment explanation
Indices: 5434431--5434494 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 19
5434421 AAAGAAAAAG
5434431 AAAAAGAAAAACCTAACC-
1 AAAAAGAAAAACCTAACCA
* * **
5434449 TAAAA-AAAAA--GAAGAA
1 AAAAAGAAAAACCTAACCA
5434465 AAAAAGAAAAACCTAACCA
1 AAAAAGAAAAACCTAACCA
*
5434484 AAAAATAAAAA
1 AAAAAGAAAAA
5434495 TAAAAAAACC
Statistics
Matches: 33, Mismatches: 9, Indels: 7
0.67 0.18 0.14
Matches are distributed among these distances:
15 2 0.06
16 4 0.12
17 10 0.30
18 4 0.12
19 13 0.39
ACGTcount: A:0.75, C:0.12, G:0.06, T:0.06
Consensus pattern (19 bp):
AAAAAGAAAAACCTAACCA
Found at i:5434738 original size:18 final size:17
Alignment explanation
Indices: 5434699--5434737 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5434689 CCTAAAGGTG
*
5434699 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
5434716 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
5434733 ATTTT
1 ATTTT
5434738 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:5434803 original size:13 final size:13
Alignment explanation
Indices: 5434785--5434833 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
5434775 TATATACATC
5434785 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
5434798 ATAATAAAAATAT
1 ATAATAAAAAAAT
5434811 AT-ATACAAACAAAT
1 ATAATA-AAA-AAAT
5434825 ATAA-AAAAA
1 ATAATAAAAA
5434834 TTACAGGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 4 0.13
13 20 0.65
14 6 0.19
15 1 0.03
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:5434992 original size:29 final size:29
Alignment explanation
Indices: 5434936--5434992 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
5434926 TCTCTTCTTT
* *
5434936 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
5434965 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
5434993 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:5435253 original size:11 final size:11
Alignment explanation
Indices: 5435235--5435264 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5435225 GTGTATATTG
5435235 TATATATTATA
1 TATATATTATA
*
5435246 TTTATATTATA
1 TATATATTATA
5435257 TATATATT
1 TATATATT
5435265 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:5435973 original size:26 final size:26
Alignment explanation
Indices: 5435937--5436124 Score: 322
Period size: 26 Copynumber: 7.2 Consensus size: 26
5435927 TGATACAAAT
5435937 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5435963 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5435989 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5436015 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5436041 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5436067 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5436093 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5436119 TGATAA
1 TGATAA
5436125 GAATTTCATG
Statistics
Matches: 156, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 156 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5436066 original size:78 final size:78
Alignment explanation
Indices: 5435937--5436124 Score: 358
Period size: 78 Copynumber: 2.4 Consensus size: 78
5435927 TGATACAAAT
5435937 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
5436002 GGTAAATGTTTCA
66 GGTAAATGTTTCA
5436015 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
5436080 GGTAAATGTTTCA
66 GGTAAATGTTTCA
* *
5436093 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAA
5436125 GAATTTCATG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 108 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (78 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
GGTAAATGTTTCA
Found at i:5438194 original size:136 final size:136
Alignment explanation
Indices: 5437910--5438183 Score: 539
Period size: 136 Copynumber: 2.0 Consensus size: 136
5437900 GAGTAGTCTC
5437910 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
*
5437975 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGACCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
5438040 CTGTTA
131 CTGTTA
5438046 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
5438111 GTTATCTGAATAAGGGGCTAAGACCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGACCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
5438176 CTGTTA
131 CTGTTA
5438182 CC
1 CC
5438184 TGAGTGGGCT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGACCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:5439913 original size:48 final size:48
Alignment explanation
Indices: 5439769--5439990 Score: 160
Period size: 48 Copynumber: 4.6 Consensus size: 48
5439759 CGTTGCTACA
* ** * * * *
5439769 CCCGTATAAGACCATATCTGGGATATAACATTGGCATCA-AGATGTGAT
1 CCCGTATAAGACCATGTCTGGGATATGGCATCGACAT-AGATATGAGAT
* * * ** * **
5439817 CCCGTGTAAGACTATGTCTAGGATATGGCATCGGTATCGATAAAAGAT
1 CCCGTATAAGACCATGTCTGGGATATGGCATCGACATAGATATGAGAT
*
5439865 CCCGTATAAGACCACGTCTGGGATATGGCATCGACATTAG-TATGAGAT
1 CCCGTATAAGACCATGTCTGGGATATGGCATCGACA-TAGATATGAGAT
** * * * * * * * * *
5439913 CCAATGTAAGACCATATCTTGGATATGACGTTGGCATCGATATGAGGT
1 CCCGTATAAGACCATGTCTGGGATATGGCATCGACATAGATATGAGAT
*
5439961 CCCGTATAAGACCATGTCTGGGACATGGCA
1 CCCGTATAAGACCATGTCTGGGATATGGCA
5439991 CCAGCATCGT
Statistics
Matches: 129, Mismatches: 42, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
47 2 0.02
48 125 0.97
49 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (48 bp):
CCCGTATAAGACCATGTCTGGGATATGGCATCGACATAGATATGAGAT
Found at i:5447775 original size:18 final size:17
Alignment explanation
Indices: 5447752--5447795 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5447742 AAAAATATTT
5447752 TTTAAATATAATGATAAA
1 TTTAAATATAAT-ATAAA
* *
5447770 TTTAAATTTTATATAAA
1 TTTAAATATAATATAAA
5447787 TATTAAATA
1 T-TTAAATA
5447796 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATATAATATAAA
Found at i:5448383 original size:148 final size:151
Alignment explanation
Indices: 5448091--5448385 Score: 490
Period size: 148 Copynumber: 2.0 Consensus size: 151
5448081 GGGACGTGGC
* * *
5448091 AGGGCAGGGAGGGGTAAGAGGTAGACGGGGAGAGTTTTTATTTGATATTAATATAAAATTTTAAT
1 AGGGCAGGGAGAGATAAGAGGTAGACGGGGAGAGTTTTTATTTAATATTAATATAAAATTTTAAT
*
5448156 ATATTATTATTTGTTTGAATTTTTTATGTATTTTTTTATTTTCTTTGAATTTTTTAAAATTAAGA
66 ATATTATTATTTGTTTGAATTTTTTATGTATTTTTTTATTTTCTTTGAATTTTTTAAAATTAAAA
5448221 TTAAATTGAGATTATTTATAT
131 TTAAATTGAGATTATTTATAT
*
5448242 AGGGGAGGGAGAGATAAGAGGTAGACGGGGAGAGTTTTTATTTAATATTAATATAAAATTTT-A-
1 AGGGCAGGGAGAGATAAGAGGTAGACGGGGAGAGTTTTTATTTAATATTAATATAAAATTTTAAT
**
5448305 AT-TTATTATTTGTTTGAATTTTTTATGTA-TTTTTTATTTTCTTTGAAATTTTTTTGAATTAAA
66 ATATTATTATTTGTTTGAATTTTTTATGTATTTTTTTATTTTCTTTG-AATTTTTTAAAATTAAA
5448368 ATTAAATTGAGATTATTT
130 ATTAAATTGAGATTATTT
5448386 GTAACTTTTG
Statistics
Matches: 136, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
147 16 0.12
148 59 0.43
149 2 0.01
150 1 0.01
151 58 0.43
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (151 bp):
AGGGCAGGGAGAGATAAGAGGTAGACGGGGAGAGTTTTTATTTAATATTAATATAAAATTTTAAT
ATATTATTATTTGTTTGAATTTTTTATGTATTTTTTTATTTTCTTTGAATTTTTTAAAATTAAAA
TTAAATTGAGATTATTTATAT
Found at i:5449574 original size:4 final size:4
Alignment explanation
Indices: 5449565--5449591 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5449555 TGAGTTATCA
5449565 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
5449592 CATTTGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:5449952 original size:16 final size:16
Alignment explanation
Indices: 5449930--5449971 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
5449920 TATGGATATT
5449930 ATTGTTATAGCGAAATG
1 ATTGTTATAGCG-AATG
*
5449947 -TTGTTATAGCGAGTG
1 ATTGTTATAGCGAATG
5449962 ATTGTTATAG
1 ATTGTTATAG
5449972 AGTGGATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (16 bp):
ATTGTTATAGCGAATG
Found at i:5454366 original size:30 final size:30
Alignment explanation
Indices: 5454330--5454388 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5454320 CTTGAAAGGT
* *
5454330 ATATATAT-AAAATAGTTTAAGATAAATAAC
1 ATATATATGAAAATA-TTGAAAATAAATAAC
5454360 ATATATATGAAAATATTGAAAATAAATAA
1 ATATATATGAAAATATTGAAAATAAATAA
5454389 TACGTCGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (30 bp):
ATATATATGAAAATATTGAAAATAAATAAC
Found at i:5454548 original size:25 final size:26
Alignment explanation
Indices: 5454486--5454548 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 26
5454476 ACTTGAAGTA
5454486 AATAATAGAACAGTTTAAAATAAGTAAT
1 AATAATA-AA-AGTTTAAAATAAGTAAT
*
5454514 -ATAAACAAAAG-TTAAAATATA-TAAT
1 AAT-AATAAAAGTTTAAAATA-AGTAAT
5454539 AATAATAAAA
1 AATAATAAAA
5454549 TAGTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
25 18 0.60
26 5 0.17
27 4 0.13
28 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (26 bp):
AATAATAAAAGTTTAAAATAAGTAAT
Found at i:5454874 original size:3 final size:3
Alignment explanation
Indices: 5454866--5454944 Score: 90
Period size: 3 Copynumber: 26.3 Consensus size: 3
5454856 AAAAATAGGT
*
5454866 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
5454913 GTCA ATA ATA AGA ATG ATA ATTA A-A ATA ATA A
1 AT-A ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
5454945 CATAAATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.05
3 57 0.89
4 4 0.06
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5455056 original size:3 final size:3
Alignment explanation
Indices: 5455050--5455118 Score: 50
Period size: 3 Copynumber: 22.0 Consensus size: 3
5455040 CTGCTACTAC
* * * * *
5455050 TAA TAA TAA TGAGA CAA TAG TAA TAA -AA GAA TAA TGACA TAC TAA TAC
1 TAA TAA TAA T-A-A TAA TAA TAA TAA TAA TAA TAA T-A-A TAA TAA TAA
5455098 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
5455119 AATTAAAAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
2 2 0.04
3 43 0.83
4 4 0.08
5 3 0.06
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:5455165 original size:27 final size:27
Alignment explanation
Indices: 5455115--5455166 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5455105 AATAATAATA
* *
5455115 ATAAAATTAAAAGAAATTTGTACAACG
1 ATAAAATTAAAAGAAATATATACAACG
5455142 ATAAAA-TAAAAGAAAATATATACAA
1 ATAAAATTAAAAG-AAATATATACAA
5455167 AAAAACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (27 bp):
ATAAAATTAAAAGAAATATATACAACG
Found at i:5455214 original size:17 final size:17
Alignment explanation
Indices: 5455142--5455206 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
5455132 TTGTACAACG
*
5455142 ATAAAATAAAAGAAAATA
1 ATAAAA-AAAACAAAATA
*
5455160 TATACAAAAAAACAATTATA
1 -ATA-AAAAAAACAA-AATA
*
5455180 ATAAAGAAAACAAAATA
1 ATAAAAAAAACAAAATA
5455197 ATAAAAAAAA
1 ATAAAAAAAA
5455207 TTAAATAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.31
18 9 0.23
19 12 0.31
20 6 0.15
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (17 bp):
ATAAAAAAAACAAAATA
Found at i:5458312 original size:47 final size:47
Alignment explanation
Indices: 5458245--5458375 Score: 156
Period size: 47 Copynumber: 2.8 Consensus size: 47
5458235 CACATCTTTA
* * *
5458245 CACAATGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATAT
1 CACACTGATGCCATATCCCAGATATGGTCTTACACAGTAAT-ACATAT
* * * * *
5458292 CTCACTGATGTCATATCCCAGATATGGTCTTATACAGTAGTATATAT
1 CACACTGATGCCATATCCCAGATATGGTCTTACACAGTAATACATAT
* *
5458339 CACACCGATGCCATATCCCAGATATGGTCTTATACAG
1 CACACTGATGCCATATCCCAGATATGGTCTTACACAG
5458376 AAATCACTTG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
47 68 0.94
48 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
CACACTGATGCCATATCCCAGATATGGTCTTACACAGTAATACATAT
Found at i:5458391 original size:7 final size:7
Alignment explanation
Indices: 5458379--5458407 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5458369 TATACAGAAA
5458379 TCACTTG
1 TCACTTG
5458386 TCACTTG
1 TCACTTG
5458393 TCACTTG
1 TCACTTG
5458400 TCACTTG
1 TCACTTG
5458407 T
1 T
5458408 AGCCAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:5458441 original size:31 final size:30
Alignment explanation
Indices: 5458406--5458583 Score: 221
Period size: 31 Copynumber: 5.7 Consensus size: 30
5458396 CTTGTCACTT
* *
5458406 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAA-CTACCACTTTTCACTGATCAG
* ** *
5458437 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGC-CGAACTACCACTTTTCACTGATCAG
5458468 GTAGCCGGAACTACCACTTTTCACTGATCAG
1 GTAGCC-GAACTACCACTTTTCACTGATCAG
*
5458499 GTAGCCGGAACTACCACTTTTCACTAATCAG
1 GTAGCC-GAACTACCACTTTTCACTGATCAG
*
5458530 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCG-AACTACCACTTTTCACTGATCAG
*
5458561 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAA-CTACCACTTTTCA
5458584 GTTGTCATTT
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
30 3 0.02
31 127 0.98
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (30 bp):
GTAGCCGAACTACCACTTTTCACTGATCAG
Found at i:5458503 original size:62 final size:62
Alignment explanation
Indices: 5458406--5458583 Score: 259
Period size: 62 Copynumber: 2.9 Consensus size: 62
5458396 CTTGTCACTT
* * * *
5458406 GTAGCC-AAAGCTACCACTATTCACTGATCAGGTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAA-CTACCACTTTTCACTGATCAGGTAGCTGGAGCTACCACTTTTCACTAATCAG
* * *
5458468 GTAGCCGGAACTACCACTTTTCACTGATCAGGTAGCCGGAACTACCACTTTTCACTAATCAG
1 GTAGCCGAAACTACCACTTTTCACTGATCAGGTAGCTGGAGCTACCACTTTTCACTAATCAG
* *
5458530 GTAGCTGAAACTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAACTACCACTTTTCACTGATCAGGTAGCTGGAGCTACCACTTTTCA
5458584 GTTGTCATTT
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
62 101 0.98
63 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (62 bp):
GTAGCCGAAACTACCACTTTTCACTGATCAGGTAGCTGGAGCTACCACTTTTCACTAATCAG
Found at i:5458667 original size:50 final size:50
Alignment explanation
Indices: 5458561--5458737 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
5458551 CACTGATCAG
* * * *
5458561 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
5458612 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
5458662 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
5458712 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
5458738 GTTTCCATGG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:5463574 original size:19 final size:19
Alignment explanation
Indices: 5463550--5463603 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
5463540 ATTAAAAATA
* *
5463550 TATTTTTATATTTTTTAAT
1 TATTTTAATAGTTTTTAAT
5463569 TATTTTAATAGTTTTTAAT
1 TATTTTAATAGTTTTTAAT
* *
5463588 T-TTTAAATAATTTTTA
1 TATTTTAATAGTTTTTA
5463604 CAACTTTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTAATAGTTTTTAAT
Found at i:5463583 original size:18 final size:18
Alignment explanation
Indices: 5463561--5463603 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5463551 ATTTTTATAT
* *
5463561 TTTTTAATTATTTTAATAG
1 TTTTTAATT-TTTAAATAA
5463580 TTTTTAATTTTTAAATAA
1 TTTTTAATTTTTAAATAA
5463598 TTTTTA
1 TTTTTA
5463604 CAACTTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTAATTTTTAAATAA
Found at i:5468234 original size:25 final size:25
Alignment explanation
Indices: 5468200--5468250 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5468190 AAATTTTAGG
5468200 TTGAAATCTTACCGTATGCAAGTTC
1 TTGAAATCTTACCGTATGCAAGTTC
5468225 TTGAAATCTTACCGTATGCAAGTTC
1 TTGAAATCTTACCGTATGCAAGTTC
5468250 T
1 T
5468251 CTCTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (25 bp):
TTGAAATCTTACCGTATGCAAGTTC
Found at i:5482138 original size:21 final size:21
Alignment explanation
Indices: 5482095--5482138 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5482085 TACACTATAT
* ** *
5482095 TTTATATTTTTTTACTTAGAG
1 TTTAAATTTTTTTACAAAAAG
5482116 TTTAAATTTTTTTACAAAAAG
1 TTTAAATTTTTTTACAAAAAG
5482137 TT
1 TT
5482139 AACATTTGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAAATTTTTTTACAAAAAG
Found at i:5482235 original size:15 final size:15
Alignment explanation
Indices: 5482215--5482244 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5482205 GAGTATGATA
5482215 AAATATTAAAAAAAT
1 AAATATTAAAAAAAT
*
5482230 AAATATTTAAAAAAT
1 AAATATTAAAAAAAT
5482245 TACCAATAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATTAAAAAAAT
Found at i:5485396 original size:16 final size:17
Alignment explanation
Indices: 5485365--5485398 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5485355 TGATAAGTAG
*
5485365 ATAAAAATTATCATTTA
1 ATAAAAAATATCATTTA
5485382 ATAAAAAATAT-ATTTA
1 ATAAAAAATATCATTTA
5485398 A
1 A
5485399 CTTCTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAAATATCATTTA
Found at i:5485888 original size:26 final size:27
Alignment explanation
Indices: 5485841--5485896 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
5485831 TTTATAATTT
*
5485841 TTTATAATTTTTGAACTTTTTTTTAAA
1 TTTATAATTTTTGAACTATTTTTTAAA
*
5485868 TTTA-AATTTTTGAA-TAATTTTTTGAA
1 TTTATAATTTTTGAACT-ATTTTTTAAA
5485894 TTT
1 TTT
5485897 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 21 0.81
27 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.62
Consensus pattern (27 bp):
TTTATAATTTTTGAACTATTTTTTAAA
Found at i:5489723 original size:33 final size:33
Alignment explanation
Indices: 5489667--5489757 Score: 136
Period size: 32 Copynumber: 2.8 Consensus size: 33
5489657 TAAGCCCCCC
5489667 AAAA-AAAACCTAACCCCAAAAAAAAAAGAAGAA
1 AAAAGAAAACCTAA-CCCAAAAAAAAAAGAAGAA
5489700 AAAAGAAAACCTAACCC-AAAAAAAAAGAAGAA
1 AAAAGAAAACCTAACCCAAAAAAAAAAGAAGAA
5489732 AAAAGAAAAACCTAA--CAAAAAAAAAA
1 AAAAG-AAAACCTAACCCAAAAAAAAAA
5489758 CTAAAAAAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
31 1 0.02
32 29 0.53
33 16 0.29
34 9 0.16
ACGTcount: A:0.75, C:0.15, G:0.07, T:0.03
Consensus pattern (33 bp):
AAAAGAAAACCTAACCCAAAAAAAAAAGAAGAA
Found at i:5489813 original size:12 final size:12
Alignment explanation
Indices: 5489796--5489825 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5489786 TCCCACTTGC
5489796 CCCATTTTTCCT
1 CCCATTTTTCCT
5489808 CCCATTTTTCCT
1 CCCATTTTTCCT
5489820 CCCATT
1 CCCATT
5489826 GTCTACCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (12 bp):
CCCATTTTTCCT
Found at i:5490305 original size:29 final size:29
Alignment explanation
Indices: 5490249--5490305 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
5490239 TCTCTTCTTT
* *
5490249 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
5490278 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
5490306 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:5490566 original size:11 final size:11
Alignment explanation
Indices: 5490548--5490577 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5490538 GTGTATATTG
5490548 TATATATTATA
1 TATATATTATA
*
5490559 TTTATATTATA
1 TATATATTATA
5490570 TATATATT
1 TATATATT
5490578 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:5497044 original size:25 final size:25
Alignment explanation
Indices: 5496951--5497044 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 25
5496941 TGACTCTTTG
* *
5496951 GAGCTACCCGTTAT-TGGCTCACAT
1 GAGCTTCCTGTTATATGGCTCACAT
** **
5496975 GAGCTTCCT-AAATATGGCTCTTAT
1 GAGCTTCCTGTTATATGGCTCACAT
* * **
5496999 CAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCTGTTATATGGCTCACAT
*
5497024 GAACTTCCTGTTATATGGCTC
1 GAGCTTCCTGTTATATGGCTC
5497045 GAGAAAGGAC
Statistics
Matches: 49, Mismatches: 19, Indels: 3
0.69 0.27 0.04
Matches are distributed among these distances:
23 2 0.04
24 22 0.45
25 25 0.51
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCACAT
Found at i:5497577 original size:40 final size:43
Alignment explanation
Indices: 5497533--5497621 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 43
5497523 TGCATTTATT
*
5497533 TAAAAATTTAAAGTTAA-A-ATATATTATAAT-ATTATAAT-AA
1 TAAAAATTAAAAGTTAAGATATATATTATAATAATTA-AATAAA
*
5497573 TAAAACTTAAAAGTTAAGTATATATATTATAATAATTAAATAAA
1 TAAAAATTAAAAGTTAAG-ATATATATTATAATAATTAAATAAA
5497617 TAAAA
1 TAAAA
5497622 TAAATAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 15 0.36
42 1 0.02
43 15 0.36
44 11 0.26
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (43 bp):
TAAAAATTAAAAGTTAAGATATATATTATAATAATTAAATAAA
Found at i:5498557 original size:42 final size:38
Alignment explanation
Indices: 5498510--5498620 Score: 107
Period size: 37 Copynumber: 2.8 Consensus size: 38
5498500 TGTCTTCGAG
5498510 TCGATGAGAACACTGGGTGTCATTTTATTACTTTGGATTAA
1 TCGATGAG-ACACTGGGTGTCA--TTATTACTTTGGATTAA
* ** * *
5498551 TTCGATGAGGCACTGGGTACCAAT-TTACTTTGGTTTAA
1 -TCGATGAGACACTGGGTGTCATTATTACTTTGGATTAA
*
5498589 TCAATGAGACACTGGGTGTCAACTTATTACTT
1 TCGATGAGACACTGGGTGTC-A-TTATTACTT
5498621 CGAATTATCC
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
37 16 0.29
38 14 0.25
39 2 0.04
40 6 0.11
41 10 0.18
42 8 0.14
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (38 bp):
TCGATGAGACACTGGGTGTCATTATTACTTTGGATTAA
Found at i:5498855 original size:14 final size:15
Alignment explanation
Indices: 5498836--5498864 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5498826 TAATTGAATA
5498836 TGTTATGAA-TGATT
1 TGTTATGAACTGATT
5498850 TGTTATGAACTGATT
1 TGTTATGAACTGATT
5498865 AATTGAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TGTTATGAACTGATT
Found at i:5500542 original size:3 final size:3
Alignment explanation
Indices: 5500527--5500586 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
5500517 TGAAAATGAC
* * * * *
5500527 AAT AAT GAT AAT AAT AAT ACT AAT AAA AAT AAT AA- AAA AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5500574 AAT AAT AAAT AAT
1 AAT AAT -AAT AAT
5500587 CTAATTTTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:5500545 original size:15 final size:15
Alignment explanation
Indices: 5500507--5500545 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5500497 TAATACGATG
*
5500507 ATAACAATAATGAAA
1 ATAACAATAATGATA
*
5500522 ATGACAATAATGATA
1 ATAACAATAATGATA
*
5500537 ATAATAATA
1 ATAACAATA
5500546 CTAATAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (15 bp):
ATAACAATAATGATA
Found at i:5502582 original size:44 final size:44
Alignment explanation
Indices: 5502350--5503515 Score: 502
Period size: 44 Copynumber: 25.6 Consensus size: 44
5502340 TCTTTATAAC
* * * *
5502350 CCACTGCAACTTCA--GAGGTATAGAATTTGTTGTTTCAATCTACA
1 CCACTGCAACTTCAGGGAGATA-AG-ATTTGTAGCTTCAATCTACT
* * * *
5502394 CTACTGCAA-TCTCAGGGAGATAAGATTTTTAACTTCAATCTGCT
1 CCACTGCAACT-TCAGGGAGATAAGATTTGTAGCTTCAATCTACT
** * * * * *
5502438 CCACAACAA-TTCAAGGAGATAAGGTTTATAGCTTTAATCTATT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * ** *
5502481 CCACTGCAACTTCAAGGTGATAAAATTTGCTATTTTCGATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTACT
* *
5502526 CCACTGCAACTTCAGGGAGATAACATTTGTGGCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
** * * *
5502570 CCACTATAACTTCAGGGAGATAAGATCTGTGGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * *
5502614 CCACTGCAACTTTAGGGAGATAATATTAGTGGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * * *
5502658 CTATTGCAACTTTAGGGAGATAAGATTTCCCATAATGATTTCAATCCA-T
1 CCACTGCAACTTCAGGGAGATAAGATTT---GT-A-G-CTTCAATCTACT
* * *
5502707 CCCACTGCAACTTTAGGG-GAATAAGACTCATAACTTGTAGCTTTAATCTATT
1 -CCACTGCAACTTCAGGGAG-ATAAG----AT---TTGTAGCTTCAATCTACT
* * * ** *
5502759 CCACTGCAACTTCAGGGAAATAAGATTAGCATTTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * *
5502803 CCACTGTAACTTTAGGGAGATAAAATTTGTAGCTTGTAGCTTTAGTCTATT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGC-T-T--C---AATCTACT
* * * *
5502854 CCACTGCAACCTT-AGAGAGATAAGACTCGTATCTTCAATC-ATCT
1 CCACTGCAA-CTTCAGGGAGATAAGATTTGTAGCTTCAATCTA-CT
* ** * * * *
5502898 TCACTGCAACTTCAGAAAGATAAGATTTTTGGTTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * * **
5502942 ACTCTGCAACTTTAGGGAGATAAGATTTGTAATTTGTAGCTTTAATTTGTT
1 CCACTGCAACTTCAGGGAGAT-A-A---G--ATTTGTAGCTTCAATCTACT
* * * **
5502993 CCACTGCAACTTCAGAGAGATAATATTCGCTATATTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTACT
* * ** *
5503038 CCATTGCAACTTCAAGGAGATAAGATTCACTATCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATT-TGTAGCTTCAATCTACT
* * * * * *
5503083 CCACTGCAACTTCACGGAGGTAAGACTTGTAACTTCAACCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * *
5503127 CCACTGTAACTTCAGGAAGATAA-AGTTTATAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTTGTAGCTTCAATCTACT
** * ** * *
5503171 CTGCTACAACTTCAAAGAGATAAGATTTGCTATCCTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTACT
* ** * * * * *
5503216 CCACTGCAACTTTAGGGAGAGCAGATCTATAACTTCAATTTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
*
5503260 CCACTGCAACTTCAGGGAGATCAGATTTGTAATTTGTAGCCTT-AATCTGCT
1 CCACTGCAACTTCAGGGAGAT-A-A---G--ATTTGTAG-CTTCAATCTACT
* * * * * ** * * * * *
5503311 ACATTGCAACCTCAAGGAAATAAGATTCACTATCCTCAGTTTGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-TGTAGCTTCAATCTACT
* ** * * * *
5503356 CTACTATAACTTCAGGGATATAAGACTTGTAACTTCAA-CCAGC-
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTA-CT
* * * * *
5503399 CCTACTGCAACTTCAGGGAGATAAGGTTTATAGGTTTAATCTGCT
1 CC-ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * ** * * ** * *
5503444 CTATTATAACTTCAGAGAGATAAGATTTTCTATTTTCGATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTTGTAGCTTCAATCTACT
*
5503489 CCACTGCAACTTCAGAGAGATAAGATT
1 CCACTGCAACTTCAGGGAGATAAGATT
5503516 CGCCACGATT
Statistics
Matches: 827, Mismatches: 235, Indels: 120
0.70 0.20 0.10
Matches are distributed among these distances:
43 40 0.05
44 403 0.49
45 203 0.25
46 9 0.01
47 4 0.00
48 1 0.00
49 8 0.01
50 30 0.04
51 115 0.14
52 8 0.01
53 1 0.00
54 3 0.00
57 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
Found at i:5502919 original size:95 final size:95
Alignment explanation
Indices: 5502740--5502925 Score: 223
Period size: 95 Copynumber: 2.0 Consensus size: 95
5502730 AGACTCATAA
* * *
5502740 CTTGTAGCTTTAATCTATTCCACTGCAACTTCAGGGAAATAAGATTAGCATTTTCAATCTGCTCC
1 CTTGTAGCTTTAATCTATTCCACTGCAACTTCAGAGAAATAAGACTAGCATCTTCAATCTGCTCC
* * **
5502805 ACTGTAACTTTAGGGAGATAAAATTTGTAG
66 ACTGCAACTTCAGAAAGATAAAATTTGTAG
* * * *
5502835 CTTGTAGCTTTAGTCTATTCCACTGCAACCTT-AGAGAGATAAGACTCGTATCTTCAATCAT-CT
1 CTTGTAGCTTTAATCTATTCCACTGCAA-CTTCAGAGAAATAAGACTAGCATCTTCAATC-TGCT
* *
5502898 TCACTGCAACTTCAGAAAGATAAGATTT
64 CCACTGCAACTTCAGAAAGATAAAATTT
5502926 TTGGTTTCAA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
95 72 0.95
96 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (95 bp):
CTTGTAGCTTTAATCTATTCCACTGCAACTTCAGAGAAATAAGACTAGCATCTTCAATCTGCTCC
ACTGCAACTTCAGAAAGATAAAATTTGTAG
Found at i:5502935 original size:139 final size:140
Alignment explanation
Indices: 5502751--5503064 Score: 359
Period size: 139 Copynumber: 2.2 Consensus size: 140
5502741 TTGTAGCTTT
* * ***** * *
5502751 AATCTATTCCACTGCAACTTCAGGGAA-ATAAGATTAGCATTTTCAATCTGCTCCACTGTAACTT
1 AATCTACTCCACTGCAACTTCA-AGAAGATAAGATTTTTGGTTTCAATCTGCTACACTGCAACTT
* *
5502815 TAGGGAGATAAAATTTGTAGCTTGTAGCTTTAGTCTATTCCACTGCAACCTT-AGAGAGATAAGA
65 TAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTATTCCACTGCAA-CTTCAGAGAGATAAGA
*
5502879 CTCG-TATCTTC
129 CTCGCTATATTC
* *
5502890 AATC-ATCTTCACTGCAACTTC-AGAAAGATAAGATTTTTGGTTTCAATCTGCTACTCTGCAACT
1 AATCTA-CTCCACTGCAACTTCAAG-AAGATAAGATTTTTGGTTTCAATCTGCTACACTGCAACT
* * * * *
5502953 TTAGGGAGATAAGATTTGTAATTTGTAGCTTTAATTTGTTCCACTGCAACTTCAGAGAGATAATA
64 TTAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTATTCCACTGCAACTTCAGAGAGATAAGA
*
5503018 TTCGCTATATTC
129 CTCGCTATATTC
* *
5503030 AATCTACTCCATTGCAACTTCAAGGAGATAAGATT
1 AATCTACTCCACTGCAACTTCAAGAAGATAAGATT
5503065 CACTATCTTC
Statistics
Matches: 145, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
137 1 0.01
138 6 0.04
139 102 0.70
140 33 0.23
141 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (140 bp):
AATCTACTCCACTGCAACTTCAAGAAGATAAGATTTTTGGTTTCAATCTGCTACACTGCAACTTT
AGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTATTCCACTGCAACTTCAGAGAGATAAGACT
CGCTATATTC
Found at i:5503204 original size:133 final size:131
Alignment explanation
Indices: 5503044--5503513 Score: 415
Period size: 133 Copynumber: 3.5 Consensus size: 131
5503034 TACTCCATTG
* * *
5503044 CAACTTCAAGGAGATAAGATTCACTATCTTCAATCTACTCCACTGCAACTTCACGGAGGTAAGAC
1 CAACTTCAAAGAGATAAGATTCACTATCCTCAATCTACTCCACTGCAACTTCAGGGAGGTAAGAC
* *
5503109 TTGTAACTTCAACCTGCTCCACTGTAACTTCAGGAAGATAAAGTTTATAGCTTTAATCTGCTCTG
66 TTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAAGTTTATAGCTTTAATCTGCTCT-
5503174 CTA
130 -TA
** * *
5503177 CAACTTCAAAGAGATAAGATTTGCTATCCTCAATCTACTCCACTGCAACTTTAGGGAGAG-CAGA
1 CAACTTCAAAGAGATAAGATTCACTATCCTCAATCTACTCCACTGCAACTTCAGGGAG-GTAAGA
* ** * * *
5503241 -TCTATAACTTCAATTTGCTCCACTGCAACTTCAGGGAGATCAGATTTGTAATTTGTAGCCTTAA
65 CT-TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGAT-A-A-----AGTTTATAGCTTTAA
*
5503305 TCTGCTACATTG
122 TCTGCT-C-TTA
* * * * * * * ** **
5503317 CAACCTCAAGGAAATAAGATTCACTATCCTCAGTTTGCTCTACTATAACTTCAGGGATATAAGAC
1 CAACTTCAAAGAGATAAGATTCACTATCCTCAATCTACTCCACTGCAACTTCAGGGAGGTAAGAC
* * *
5503382 TTGTAACTTCAACCAGC-CCTACTGCAACTTCAGGGAGATAAGGTTTATAGGTTTAATCTGCTCT
66 TTGTAACTTCAACCTGCTCC-ACTGCAACTTCAGGGAGATAAAGTTTATAGCTTTAATCTGCTC-
5503446 ATTA
129 -TTA
* * ** ** * * * *
5503450 TAACTTCAGAGAGATAAGATTTTCTATTTTCGATCTGCTCCACTGCAACTTCAGAGAGATAAGA
1 CAACTTCAAAGAGATAAGATTCACTATCCTCAATCTACTCCACTGCAACTTCAGGGAGGTAAGA
5503514 TTCGCCACGA
Statistics
Matches: 264, Mismatches: 58, Indels: 30
0.75 0.16 0.09
Matches are distributed among these distances:
132 2 0.01
133 154 0.58
134 2 0.01
135 1 0.00
138 1 0.00
139 3 0.01
140 98 0.37
141 2 0.01
142 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (131 bp):
CAACTTCAAAGAGATAAGATTCACTATCCTCAATCTACTCCACTGCAACTTCAGGGAGGTAAGAC
TTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAAGTTTATAGCTTTAATCTGCTCTT
A
Found at i:5503270 original size:89 final size:87
Alignment explanation
Indices: 5502992--5503515 Score: 268
Period size: 89 Copynumber: 5.8 Consensus size: 87
5502982 TTTAATTTGT
* * * * *
5502992 TCCACTGCAACTTCAGAGAGATAATATTCGCTATATTCAATCTACTCCATTGCAACTTCAAGGAG
1 TCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTCAGGGAG
* *
5503057 ATAAGATTCACTATCTTCAATCTAC
66 A-AAGATT-A-TAACTTCAATCTGC
* * * * * *
5503082 TCCACTGCAACTTCACG-GAGGTAAGACTTG-TAACTTCAACCTGCTCCACTGTAACTTCAGGAA
1 TCCACTGCAACTTCA-GAGAGATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTCAGG--
* * * *
5503145 GATAAAGTTTATAGCTTTAATCTGC
63 GAGAAAGATTATAACTTCAATCTGC
** * * * *
5503170 TCTGCTACAACTTCAAAGAGATAAGATTTGCTATCCTCAATCTACTCCACTGCAACTTTAGGGAG
1 TCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTCAGGGAG
* *
5503235 AGCAGATCTATAACTTCAATTTGC
66 A-AAGAT-TATAACTTCAATCTGC
* * * * * * *
5503259 TCCACTGCAACTTCAGGGAGATCAGATTTG-TAATTTGTAGCCTTAATCTGCTACATTGCAACCT
1 TCCACTGCAACTTCAGAGAGATAAGATTTGCT-ATCT-T---C--AATCTACTCCACTGCAACTT
* * * * * *
5503323 CAAGGAAATAAGATTCACTATCCTCAGTTTGC
59 CAGGGAGA-AAGATT-A-TAACTTCAATCTGC
* ** * * * * *
5503355 TCTACTATAACTTCAGGGATATAAGACTTG-TAACTTCAA-CCAGC-CCTACTGCAACTTCAGGG
1 TCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTA-CTCC-ACTGCAACTTCAGGG
* ** *
5503417 AGATAAGGTTTATAGGTTTAATCTGC
64 AGA-AA-GATTATAACTTCAATCTGC
* * ** * * * * *
5503443 TCTATTATAACTTCAGAGAGATAAGATTTTCTATTTTCGATCTGCTCCACTGCAACTTCAGAGAG
1 TCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTCAGGGAG
5503508 ATAAGATT
66 A-AAGATT
5503516 CGCCACGATT
Statistics
Matches: 324, Mismatches: 88, Indels: 46
0.71 0.19 0.10
Matches are distributed among these distances:
87 3 0.01
88 76 0.23
89 137 0.42
90 36 0.11
91 5 0.02
93 1 0.00
94 2 0.01
95 28 0.09
96 36 0.11
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (87 bp):
TCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTCAGGGAG
AAAGATTATAACTTCAATCTGC
Found at i:5510639 original size:64 final size:64
Alignment explanation
Indices: 5510559--5510738 Score: 177
Period size: 67 Copynumber: 2.8 Consensus size: 64
5510549 TGACATTATG
* ** *
5510559 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAAAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAAAGCTACAAGATAA
* * * * * *
5510623 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACAAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAAAGCTACAAGAT
5510688 AA
63 AA
* * *
5510690 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGA
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGA
5510739 GAGCCGAACT
Statistics
Matches: 93, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 15 0.16
64 25 0.27
66 21 0.23
67 31 0.33
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAAAGCTACAAGATAA
Found at i:5513740 original size:15 final size:15
Alignment explanation
Indices: 5513720--5513750 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5513710 GAGGGTGATA
5513720 GTGGCTGAGTCGATG
1 GTGGCTGAGTCGATG
5513735 GTGGCTGAGTCGATG
1 GTGGCTGAGTCGATG
5513750 G
1 G
5513751 GTCCTCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.48, T:0.26
Consensus pattern (15 bp):
GTGGCTGAGTCGATG
Found at i:5515875 original size:25 final size:25
Alignment explanation
Indices: 5515820--5515875 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
5515810 ATTTGTAATA
*
5515820 ATAATATATACACAATATGGTATTT
1 ATAATATATACACAATATGGTATAT
* * *
5515845 AAAATATATATATATATAT-GTATAT
1 ATAATATATACACA-ATATGGTATAT
5515870 ATAATA
1 ATAATA
5515876 GTATTTAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (25 bp):
ATAATATATACACAATATGGTATAT
Found at i:5515944 original size:39 final size:39
Alignment explanation
Indices: 5515845--5515944 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
5515835 TATGGTATTT
* * * *
5515845 AAAATATATATAT-ATATATGTATATATAATAGTATTTA
1 AAAATATATACATAATATATATATATATAATAGCATTAA
* * * *
5515883 AGAATATATACATAAGAAATATATA-ACTAATGGCATTAA
1 AAAATATATACATAATATATATATATA-TAATAGCATTAA
5515922 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
5515945 AAATACCTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
38 12 0.24
39 37 0.76
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATATATACATAATATATATATATATAATAGCATTAA
Found at i:5516484 original size:34 final size:34
Alignment explanation
Indices: 5516400--5516490 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
5516390 AGGTTTTTTA
* *
5516400 TTTTTTATTT-GGTTAGCTTTTTCTTTTTTCTTC
1 TTTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTC
5516433 TTTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTT-
1 TTTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTC
5516466 TTTTTTTTTTAGGGTTAGGGTTTTT
1 TTTTTTTTTT-GGGTTA-GGTTTTT
5516491 TTTGGGGGGC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 19 0.36
34 27 0.51
35 7 0.13
ACGTcount: A:0.05, C:0.07, G:0.15, T:0.73
Consensus pattern (34 bp):
TTTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTC
Found at i:5517253 original size:88 final size:85
Alignment explanation
Indices: 5517137--5517568 Score: 282
Period size: 88 Copynumber: 5.0 Consensus size: 85
5517127 GACTCTCTAA
* * *
5517137 AAACAGACATTAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCT
1 AAACAGA-ATTAAAAGCAGATATTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCT
5517202 CGCAATATGAGTTGATTTTTTG
64 CGCAATATGAGTTGATTTTTTG
** * * * * *
5517224 AAACTTAACTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGAAGGTTCAACTCACCT
1 AAACAGAA-TT-AAAAGCAGATATTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCT
*
5517288 CTCGTAATATGAGTTGA-TTTTTG
62 CTCGCAATATGAGTTGATTTTTTG
** * * * ** *** * * *
5517311 AAAAACAGAAATTAAAAGACTCA-ACT-CAACT--CTCGCA-GAAATTAAAAAGCTCGACTCATC
1 --AAACAG-AATTAAAAG-CAGATATTGAAAATACCTCGCACGTGA-GCCAAGGCTCAACTCACC
5517371 TCTCGCAATATGAGTTGAATTTTTTTG
61 TCTCGCAATATGAGTTG-A-TTTTTTG
* * *
5517398 --A-A-AA--AAAA-CAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTC
1 AAACAGAATTAAAAGCAGATATTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTC
5517456 GCAATATGAGTTGA-TTTTTG
65 GCAATATGAGTTGATTTTTTG
* * * * * *
5517476 AAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACAT
1 -AAACAGAAT-T-AAAAGCAGATATTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCT
*
5517541 CTCGCAATGTGAGTTGATTTTTTTG
62 CTCGCAATATGAGTTGA-TTTTTTG
5517566 AAA
1 AAA
5517569 AATATAAATT
Statistics
Matches: 262, Mismatches: 51, Indels: 62
0.70 0.14 0.17
Matches are distributed among these distances:
76 2 0.01
77 2 0.01
78 13 0.05
80 6 0.02
81 32 0.12
82 4 0.02
83 5 0.02
84 28 0.11
85 5 0.02
86 1 0.00
87 29 0.11
88 116 0.44
89 11 0.04
90 8 0.03
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (85 bp):
AAACAGAATTAAAAGCAGATATTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCG
CAATATGAGTTGATTTTTTG
Found at i:5517352 original size:30 final size:30
Alignment explanation
Indices: 5517316--5517377 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
5517306 TTTTGAAAAA
5517316 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
* *
5517346 CAGAAATTAAAAAGCTCGACTCATCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
5517376 CA
1 CA
5517378 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.21
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:5517810 original size:92 final size:94
Alignment explanation
Indices: 5517642--5517812 Score: 240
Period size: 92 Copynumber: 1.8 Consensus size: 94
5517632 GTTGATTTTT
* * * * *
5517642 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGAGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
5517707 GAGTTGATTTTTTTTTTGAAAGGCAGAAA
66 GAGTTGATTTTTTTTTTGAAAGGCAGAAA
* * *
5517736 TTGAAAAAC-GAAATTGAAAATACCTCAGC-ATTGA-CCTGAGGCTCAACTCGCCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGAGTGAGCC-AAGGCTCAACTCACCTCTCACAATA
5517798 CGAGTTGATTTTTTT
65 CGAGTTGATTTTTTT
5517813 GACAACAGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 2 0.03
92 39 0.57
93 19 0.28
94 8 0.12
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (94 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGAGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
GAGTTGATTTTTTTTTTGAAAGGCAGAAA
Found at i:5517895 original size:75 final size:76
Alignment explanation
Indices: 5517736--5518038 Score: 400
Period size: 75 Copynumber: 4.0 Consensus size: 76
5517726 AAGGCAGAAA
* * *
5517736 TTGAAAAAC-GAAATTGAAAATACCTCAGCATTGACCTGAGGCTCAACTCGCCTCTCACAATACG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCACAATATG
5517800 AGTTGATTTTT
66 AGTTGATTTTT
* * * *
5517811 TTG-ACAACAGAAATTGAAATTACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCACAATATG
5517874 AGTTGATTTTT
66 AGTTGATTTTT
* * **
5517885 TTGAAAAACAGAAATTGAAAATACCTCAGCA-TGTCTTGAGGCTCAACTCATTTCTCACAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCACAATATG
5517949 AGTTGAATTTTTTT
66 AGTTG-A--TTTTT
* *
5517963 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCA-GTG-ACCTGAGGCTCAACTCACCTCTCACAATA
*
5518027 TGAGCTGATTTT
64 TGAGTTGATTTT
5518039 GAAAAAGTAG
Statistics
Matches: 199, Mismatches: 20, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
74 47 0.24
75 80 0.40
76 1 0.01
77 4 0.02
78 35 0.18
79 1 0.01
80 30 0.15
81 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (76 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCACAATATG
AGTTGATTTTT
Found at i:5517963 original size:243 final size:245
Alignment explanation
Indices: 5517148--5517983 Score: 834
Period size: 253 Copynumber: 3.4 Consensus size: 245
5517138 AACAGACATT
*
5517148 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCA--TGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
** * * ** * *
5517213 TTGA---TTTTTTG-AA-ACTTAACTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTG
64 TTGATTTTTTTTTGAAAGACAGAAATTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCG
* * ** *
5517272 AAGGTTCAACTCACCTCTCGTAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAGACTCA
129 -AGGCTCAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA-A-T-A
* * * * ** * * *
5517334 ACTCAACTCTCGCAGAAATTAAAAAGCTCGACTCATCTCTCGCAATATGAGTTGAATTTTTTTG
190 CCTC-A---GCG-TGTACCT--GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG
5517398 AAAAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATAT
1 ---AAAAACAGAAATTGAAAATAGCTCAGCA--TGAGCCAAGGCTCAACTCACTTCTCGCAATAT
**
5517463 GAGTTGA----TTTTTGAAA-ACAG-AATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGA
61 GAGTTGATTTTTTTTTGAAAGACAGAAAT-TGAAAAACAGAAATTGAAAATACCTCGACATGTGA
* ** * *
5517522 CCCGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAAT
125 CCCGAGGCTCAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAAAT
* *
5517587 ACCTCAGCGTGTGATCTGAAGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTG
189 ACCTCAGCGTGT-ACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * *
5517645 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCA--GCATGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
*
5517710 TTGATTTTTTTTTTGAAAGGCAGAAATTGAAAAAC-GAAATTGAAAATACCTC-AGCAT-TGACC
64 TTGA-TTTTTTTTTGAAAGACAGAAATTGAAAAACAGAAATTGAAAATACCTCGA-CATGTGACC
* * * * *
5517772 TGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG-AAATTACC
127 CGAGGCTCAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACC
*
5517835 TCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
192 TCAGCGTGTACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * ** * *
5517888 AAAAACAGAAATTGAAAATACCTCAGCATG-TCTTGAGGCTCAACTCATTTCTCACAATATGAGT
1 AAAAACAGAAATTGAAAATAGCTCAGCATGAGC-CAAGGCTCAACTCACTTCTCGCAATATGAGT
5517952 TGAATTTTTTTTTGAAAGACAGAAATTGAAAA
65 TG-ATTTTTTTTTGAAAGACAGAAATTGAAAA
5517984 TACCTCAGCA
Statistics
Matches: 511, Mismatches: 52, Indels: 52
0.83 0.08 0.08
Matches are distributed among these distances:
240 1 0.00
241 59 0.12
242 1 0.00
243 64 0.13
244 62 0.12
245 16 0.03
246 2 0.00
247 19 0.04
248 70 0.14
249 28 0.05
250 15 0.03
251 3 0.01
252 8 0.02
253 134 0.26
254 6 0.01
255 18 0.04
256 1 0.00
257 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (245 bp):
AAAAACAGAAATTGAAAATAGCTCAGCATGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTT
GATTTTTTTTTGAAAGACAGAAATTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAG
GCTCAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
CGTGTACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:5518107 original size:54 final size:54
Alignment explanation
Indices: 5518007--5518112 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5517997 GAACCGAGGC
*
5518007 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5518061 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5518113 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5518147 original size:220 final size:209
Alignment explanation
Indices: 5517889--5518294 Score: 562
Period size: 220 Copynumber: 1.9 Consensus size: 209
5517879 ATTTTTTTGA
* * **
5517889 AAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
* * *
5517954 AATTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTC
66 AA------ATTAAAACACA-AAATTGAAAATACCTCAGC--GTG-ACCGAGGCTCAACTCACCTC
* * *
5518019 TCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGG-TTCAACCCACCTCTCGCAATATG
121 TAGCAATATGAGCTGATTTTGAAAAA-CAAAAATTAAAAGGCTT-AACCCACCTCTCGCAATATG
5518083 AGTTGATTCTTGAACAACGTAAATTG
184 AGTTGATTCTTGAACAACGTAAATTG
* *
5518109 AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
*
5518174 AAATTAAAACACAAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTAGCAATATG
66 AAATTAAAACACAAAATTGAAAATACCTCAGCGTGACCGAGGCTCAACTCACCTCTAGCAATATG
* *
5518239 AGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGT
131 AGCTGATTTTGAAAAACAAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGT
5518295 CAATTTAAAA
Statistics
Matches: 170, Mismatches: 15, Indels: 13
0.86 0.08 0.07
Matches are distributed among these distances:
209 34 0.20
210 45 0.26
211 3 0.02
213 19 0.11
214 8 0.05
220 61 0.36
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (209 bp):
AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
AAATTAAAACACAAAATTGAAAATACCTCAGCGTGACCGAGGCTCAACTCACCTCTAGCAATATG
AGCTGATTTTGAAAAACAAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGTTGATTCTTG
AACAACGTAAATTG
Found at i:5518229 original size:70 final size:71
Alignment explanation
Indices: 5518103--5518266 Score: 244
Period size: 70 Copynumber: 2.3 Consensus size: 71
5518093 TGAACAACGT
* * *
5518103 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTGAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
5518168 GAGTTG
66 GAGTTG
5518174 AAATT-AAAACACAAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTGAAAACA-AAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
5518237 TGAGTTG
65 TGAGTTG
**
5518244 ATTTTGAAAAACAAAAATT-AAAA
1 AAATTG-AAAACAAAAATTGAAAA
5518267 GGCTTAACTC
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
70 46 0.54
71 33 0.39
72 6 0.07
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (71 bp):
AAATTGAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:5518341 original size:121 final size:121
Alignment explanation
Indices: 5518143--5518642 Score: 498
Period size: 121 Copynumber: 4.0 Consensus size: 121
5518133 GCGTGACCTG
* * * *
5518143 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAATTGAAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAG-TCAATTTAAAACA-AAAACTAAAAATACCTCAGCGT
5518208 G-CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
64 GCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* *
5518266 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTG-
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAAAAACTAAAAATACCTCAGCGTGC
* *
5518330 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATT-AAA
** * * * * * *
5518386 ATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAAT-ATGAGTTGATTAAAACACAAAAA
1 A-GGCTCAAC---TC---A-CCTC-TCGCA-ATAT-G-AGTCA--A--T--TTAAA--ACAAAAA
* *
5518450 TTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA
46 CTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAA
5518515 ACAAAAATTAAA
110 ACAAAAATTAAA
* *
5518527 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTT------AAAACTAAAAATACCTCAGCGTGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAAAAACTAAAAATACCTCAGCGTGC
* * *
5518586 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAACAATTAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
5518642 A
1 A
5518643 ATACCTCAAC
Statistics
Matches: 315, Mismatches: 37, Indels: 58
0.77 0.09 0.14
Matches are distributed among these distances:
115 15 0.05
116 60 0.19
119 7 0.02
120 8 0.03
121 64 0.20
122 11 0.03
123 27 0.09
124 4 0.01
126 1 0.00
127 1 0.00
128 4 0.01
129 5 0.02
130 4 0.01
131 4 0.01
132 5 0.02
133 4 0.01
134 1 0.00
135 1 0.00
137 7 0.02
139 23 0.07
140 44 0.14
141 8 0.03
142 7 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (121 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAAAAACTAAAAATACCTCAGCGTGC
CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:5518422 original size:70 final size:70
Alignment explanation
Indices: 5518266--5518527 Score: 336
Period size: 70 Copynumber: 3.8 Consensus size: 70
5518256 AAAAATTAAA
* * * * *
5518266 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
5518329 GCCCG
66 GCCCG
* *
5518334 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
**
5518398 GTCTTG
66 G-CCCG
* * *
5518404 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAGCG
5518467 TGCCCCG
65 TG-CCCG
*
5518474 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
5518528 GGCTTAACTC
Statistics
Matches: 165, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
68 31 0.19
69 27 0.16
70 90 0.55
72 14 0.08
73 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (70 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
GCCCG
Found at i:5518476 original size:261 final size:255
Alignment explanation
Indices: 5518106--5518693 Score: 1002
Period size: 261 Copynumber: 2.3 Consensus size: 255
5518096 ACAACGTAAA
* * * * * *
5518106 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5518171 TTGAAATTAAAACACAAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTG--ATTAAAACACAAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTAGCAAT
5518236 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
129 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
5518301 AAAACATAAACTAAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
194 -----A-AAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
5518365 ATT
253 ATT
5518368 TTGAAAA-AAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5518432 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATTAAAACAC-AAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTAGCAAT
5518497 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
129 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
5518562 AAAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
194 AAAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
*
5518624 TTGAAAACAACAATTAAAAATACCTCAACGTGT-TTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5518688 TTGATT
66 TTGATT
5518694 TTCCTTGAAA
Statistics
Matches: 315, Mismatches: 7, Indels: 14
0.94 0.02 0.04
Matches are distributed among these distances:
255 22 0.07
256 83 0.26
257 24 0.08
259 10 0.03
260 23 0.07
261 146 0.46
262 7 0.02
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (255 bp):
TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
TTGATTAAAACACAAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAA
AACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
Found at i:5518501 original size:140 final size:140
Alignment explanation
Indices: 5518266--5518527 Score: 402
Period size: 140 Copynumber: 1.9 Consensus size: 140
5518256 AAAAATTAAA
* * *
5518266 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAAACAAAAACTAAAAATACCTCAGCGTGC
* *
5518331 CCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTG-AAAA-AAAAATTAAAAATACCTCA
66 CCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAATACCTCA
5518394 ACGTGTCTTG
131 ACGTGTCTTG
* ** * *
5518404 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAA-ACAAAAACTAAAAATACCTCAGCGTG
5518469 CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
65 -CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
5518528 GGCTTAACTC
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
138 33 0.30
139 23 0.21
140 39 0.35
141 4 0.04
142 11 0.10
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (140 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAAACAAAAACTAAAAATACCTCAGCGTGC
CCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAATACCTCA
ACGTGTCTTG
Found at i:5527221 original size:37 final size:37
Alignment explanation
Indices: 5527121--5527221 Score: 91
Period size: 43 Copynumber: 2.6 Consensus size: 37
5527111 ATATATTTGG
5527121 TAATAATAATA--TAAAATAATAATATGTACATAAAAA
1 TAATAATAATATCTAAAATAA-AATATGTACATAAAAA
* *
5527157 TACATATATATATATGCATATAATAAAAGTATGTA-ATAATAA
1 TA-ATA-ATA-ATAT-C-TAAAATAAAA-TATGTACATAAAAA
*
5527199 TAATAATAATATCTACAATAAAA
1 TAATAATAATATCTAAAATAAAA
5527222 AAAATATTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 12 0.22
38 4 0.07
39 7 0.13
40 3 0.06
41 3 0.06
42 10 0.19
43 13 0.24
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (37 bp):
TAATAATAATATCTAAAATAAAATATGTACATAAAAA
Found at i:5527465 original size:33 final size:33
Alignment explanation
Indices: 5527403--5527465 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5527393 ACACAATATG
* * *
5527403 GTATTTAAAATATATATATATGTATATATAATA
1 GTATTTAAAATATATACATAAGTAAATATAATA
5527436 GTATTTAAGAATATATACATAAG-AAATATA
1 GTATTTAA-AATATATACATAAGTAAATATA
5527466 TAACTAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (33 bp):
GTATTTAAAATATATACATAAGTAAATATAATA
Found at i:5528000 original size:32 final size:32
Alignment explanation
Indices: 5527955--5528051 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
5527945 GGTGGCTAGG
* *
5527955 TTTTTT-TATTTTTTATTT-GGTTAGCTTTTTC
1 TTTTTTCT-TTTTTTTTTTGGGTTAGGTTTTTC
5527986 TTTTTTCTTCTTTTTTTTTTTGGGTTAGGTTTTTC
1 --TTTT-TTCTTTTTTTTTTTGGGTTAGGTTTTTC
*
5528021 TTTTTTCTTTTTTTTTTAGGGTTAGGTTTTT
1 TTTTTTCTTTTTTTTTTTGGGTTAGGTTTTT
5528052 TTGGGGGGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
32 26 0.45
33 8 0.14
34 11 0.19
35 13 0.22
ACGTcount: A:0.06, C:0.06, G:0.13, T:0.74
Consensus pattern (32 bp):
TTTTTTCTTTTTTTTTTTGGGTTAGGTTTTTC
Found at i:5528008 original size:34 final size:34
Alignment explanation
Indices: 5527957--5528037 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 34
5527947 TGGCTAGGTT
*
5527957 TTTTTATTTTTTATTTGGTTAGCTTTTTCTTTTTTC
1 TTTTT-TTTTTT-TTGGGTTAGCTTTTTCTTTTTTC
*
5527993 TTCTTTTTTTTTTTGGGTTAGGTTTTTCTTTTTTC
1 TT-TTTTTTTTTTTGGGTTAGCTTTTTCTTTTTTC
5528028 TTTTTTTTTT
1 TTTTTTTTTT
5528038 AGGGTTAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 8 0.19
35 23 0.55
36 8 0.19
37 3 0.07
ACGTcount: A:0.05, C:0.07, G:0.10, T:0.78
Consensus pattern (34 bp):
TTTTTTTTTTTTTGGGTTAGCTTTTTCTTTTTTC
Found at i:5540241 original size:32 final size:35
Alignment explanation
Indices: 5540199--5540284 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
5540189 ATGTTTCTTG
*
5540199 GATTATTATGTAAT-TG-TCACAACATTA-CAT-GT
1 GATTAATATGTAATATGATCAC-ACATTACCATAGT
5540231 GATTAATATGT-ATATGATCACACATTACTCATAGT
1 GATTAATATGTAATATGATCACACATTAC-CATAGT
5540266 GATTAATATGT-ATATGATC
1 GATTAATATGTAATATGATC
5540285 CTCATACTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
31 2 0.04
32 18 0.38
33 4 0.08
34 3 0.06
35 21 0.44
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (35 bp):
GATTAATATGTAATATGATCACACATTACCATAGT
Found at i:5546189 original size:3 final size:3
Alignment explanation
Indices: 5546174--5546237 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
5546164 TGAAAATGAC
* * * * *
5546174 AAT AAT GAT AAT AAT AAT ACT AAT AAC GAT AAT AA- AA- AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5546220 AAT AAT AAAT AAT -AT AAT
1 AAT AAT -AAT AAT AAT AAT
5546238 TTTTAAAAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 6 0.12
3 39 0.81
4 3 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:5546395 original size:17 final size:18
Alignment explanation
Indices: 5546355--5546428 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 18
5546345 AGTAGAAGTA
* *
5546355 ATAAATAAATAATATGAAC
1 ATAAACAAATAA-ATAAAC
5546374 AATAAACAAATAAAT-AAC
1 -ATAAACAAATAAATAAAC
* *
5546392 ATAAAAAAATGAATAAATC
1 ATAAACAAATAAATAAA-C
*
5546411 ATTAAAACAAGTAAATAA
1 A-T-AAACAAATAAATAA
5546429 CATTAAGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 12 0.27
18 5 0.11
19 4 0.09
20 12 0.27
21 11 0.25
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.22
Consensus pattern (18 bp):
ATAAACAAATAAATAAAC
Found at i:5550088 original size:40 final size:40
Alignment explanation
Indices: 5550044--5550120 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
5550034 ACGATACCAT
* * *
5550044 TTGGTGTGTAGGGTTGAATGGGTTGATTTTATCCCCATAC
1 TTGGTGTGTAGGGCTGAATGGGTCGATTCTATCCCCATAC
**
5550084 TTGGTGTGTAGGGCTGGGTGGGTCGATTCTATCCCCA
1 TTGGTGTGTAGGGCTGAATGGGTCGATTCTATCCCCA
5550121 CAAGGTGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.14, C:0.16, G:0.34, T:0.36
Consensus pattern (40 bp):
TTGGTGTGTAGGGCTGAATGGGTCGATTCTATCCCCATAC
Found at i:5555534 original size:8 final size:8
Alignment explanation
Indices: 5555521--5555546 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5555511 GGAAGAATGA
5555521 GGTAGCTT
1 GGTAGCTT
5555529 GGTAGCTT
1 GGTAGCTT
5555537 GGTAGCTT
1 GGTAGCTT
5555545 GG
1 GG
5555547 CGAATCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.42, T:0.35
Consensus pattern (8 bp):
GGTAGCTT
Found at i:5555914 original size:39 final size:40
Alignment explanation
Indices: 5555871--5556023 Score: 109
Period size: 41 Copynumber: 4.1 Consensus size: 40
5555861 ATTAGTGGCA
5555871 TTTTTGCAAAAACGCCGTT-AAAAACAGAGCAAT-GCGGCG
1 TTTTTGCAAAAACGCC-TTAAAAAACAGAGCAATAGCGGCG
** *
5555910 TTTTTGGTAAAATGCCTTAAAAAAACAGAGCAATAGCGGCG
1 TTTTTGCAAAAACGCCTT-AAAAAACAGAGCAATAGCGGCG
* *
5555951 ---TT-C-----C-AC-TAAAAACCAGAGCAATAGCGGCG
1 TTTTTGCAAAAACGCCTTAAAAAACAGAGCAATAGCGGCG
**
5555980 TTTTTGGTAAAACGTCGC-TAAAAAACAGAGCAATAGCGGCG
1 TTTTTGCAAAAACG-C-CTTAAAAAACAGAGCAATAGCGGCG
5556021 TTT
1 TTT
5556024 GTGGTCAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 28
0.70 0.08 0.22
Matches are distributed among these distances:
29 21 0.24
30 1 0.01
31 1 0.01
32 2 0.02
38 5 0.06
39 13 0.15
40 14 0.16
41 32 0.36
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (40 bp):
TTTTTGCAAAAACGCCTTAAAAAACAGAGCAATAGCGGCG
Found at i:5555986 original size:70 final size:68
Alignment explanation
Indices: 5555889--5556022 Score: 209
Period size: 70 Copynumber: 1.9 Consensus size: 68
5555879 AAAACGCCGT
*
5555889 TAAAAACAGAGCAATGCGGCGTTTTTGGTAAAATG-C-CTTAAAAAAACAGAGCAATAGCGGCGT
1 TAAAAACAGAGCAATGCGGCGTTTTTGGTAAAACGTCGC-T-AAAAAACAGAGCAATAGCGGCGT
5555952 TCCAC
64 TCCAC
5555957 TAAAAACCAGAGCAATAGCGGCGTTTTTGGTAAAACGTCGCTAAAAAACAGAGCAATAGCGGCGT
1 TAAAAA-CAGAGCAAT-GCGGCGTTTTTGGTAAAACGTCGCTAAAAAACAGAGCAATAGCGGCGT
5556022 T
64 T
5556023 TGTGGTCAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
68 6 0.10
69 9 0.15
70 43 0.70
71 2 0.03
72 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (68 bp):
TAAAAACAGAGCAATGCGGCGTTTTTGGTAAAACGTCGCTAAAAAACAGAGCAATAGCGGCGTTC
CAC
Done.