Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 84 of 193
Found at i:27807920 original size:146 final size:145
Alignment explanation
Indices: 27807661--27808378 Score: 738
Period size: 146 Copynumber: 5.0 Consensus size: 145
27807651 ATTTTACTTC
* *
27807661 AAAATCAAAACTTTATTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGATTTTATT
1 AAAATCAAAACTTTATTTAAAAATTTAAA-CTTTTCTTTAAAATAACT-AAAAACAGATTTT-TA
** * * * * *
27807726 TTTTTTTAAATCTAAACTCTCTTTTTTTTTTAAAAGAAAATCAGTACTTTATTTAAAAATCTAAA
63 TTTTTAAAAATATAAA----CTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAA
27807791 CTTTTATTTCGAAATAGTTAAA
124 CTTTTATTTCGAAATAGTTAAA
*
27807813 AAAATCAAAATTTTATTTAAAAATTTAAACTTTTCTTTAAAATAACT-AAAACAGATTTTTATTT
1 AAAATCAAAACTTTATTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAACAGATTTTTA--T
*
27807877 TTTTAAAAATATAAACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAATTTTT
64 TTTTAAAAATATAAACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAACTTTT
27807942 ATTTCGAAATAGTTAAA
129 ATTTCGAAATAGTTAAA
* * *
27807959 AAAATCAAAATTTTATTTAAAAATTTAAAC--TT-TTT---CT---TAAAAACAGATTGTTATTT
1 AAAATCAAAACTTTATTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAACAGATTTTTATTT
*
27808015 TAAAAAATATAAACTTTCTCCCTTTTT-AATGAAAATCACTACTTT-CTTAAAAATCTAAACTTT
66 TTAAAAATATAAACTTTCT---TTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAACTTT
* *
27808078 TATTTCGATATAGTTTAA
128 TATTTCGAAATAGTTAAA
* * * *
27808096 AAAATTAAAAATTTATTTAAAAATTTAAACTTTTTCCTTAAAATAACTAAAAAAAGATTTTTA-T
1 AAAATCAAAACTTTATTTAAAAATTTAAAC-TTTTCTTTAAAATAACTAAAAACAGATTTTTATT
* * *
27808160 TTT-AAAATAGAAACTTTCTTTTTTTAAA-GATAATCATTACTTTACTTAAAAATCTAAACTTTT
65 TTTAAAAATATAAACTTTC-TTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAACTTTT
* *
27808223 ATTTCAAAATAGTTTAA
129 ATTTCGAAATAGTTAAA
** *
27808240 AAAATCAAAACTTTGCTTAAAAATTTAAAATTTTC--T---A-AA--AAAAACAGA--TTT-TTT
1 AAAATCAAAACTTTATTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAACAGATTTTTATTT
** * * * *
27808294 AAAAAAATTTAAACTTTCTCGTGTTTAAA--AAAATCATTATTTTACTTAAAAATC-AAAGCTTT
66 TTAAAAATATAAACTTTCT--TTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAA-C-TT
* *
27808356 TTATTTCAAAATTGTTAAA
127 TTATTTCGAAATAGTTAAA
27808375 AAAA
1 AAAA
27808379 CAACACCAAA
Statistics
Matches: 497, Mismatches: 44, Indels: 67
0.82 0.07 0.11
Matches are distributed among these distances:
133 9 0.02
134 37 0.07
135 38 0.08
136 21 0.04
137 64 0.13
138 32 0.06
139 5 0.01
140 3 0.01
141 3 0.01
143 26 0.05
144 64 0.13
145 14 0.03
146 96 0.19
147 14 0.03
148 1 0.00
149 12 0.02
150 13 0.03
151 17 0.03
152 28 0.06
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (145 bp):
AAAATCAAAACTTTATTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAACAGATTTTTATTT
TTAAAAATATAAACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAACTTTTAT
TTCGAAATAGTTAAA
Found at i:27808247 original size:281 final size:277
Alignment explanation
Indices: 27807759--27808378 Score: 820
Period size: 281 Copynumber: 2.2 Consensus size: 277
27807749 TTTTTTTTAA
* * *
27807759 AAGAAAATCAGTACTTTATTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAT
1 AAGAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAA
* * *
27807824 TTTATTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAACAGATTTTTATTTTTTTAAAAATAT
66 TTTATTTAAAAATTTAAACTTTTCCTTAAAATAACTAAAAAAGATTTTTA--TTTTTAAAAATAG
* *
27807889 AAACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAATTTTTATTTCGAAATAG
129 AAACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCAAAATAG
* * * * *
27807954 TTAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTCT-TAAAAACAGATTGTTATTTTAA
194 TTAAAAAAATCAAAACTTTACTTAAAAATTTAAA-ATTTTCTAAAAAAACAGA-T-TT-TTTAAA
27808018 AAAATATAAACTTTCTCCCTTTTT
255 AAAATATAAACTTTCT-CCTTTTT
* * *
27808042 AATGAAAATCACTACTTT-CTTAAAAATCTAAACTTTTATTTCGATATAGTTTAAAAAATTAAAA
1 AA-GAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAA
27808106 ATTTATTTAAAAATTTAAACTTTTTCCTTAAAATAACTAAAAAAAGATTTTTA-TTTT-AAAATA
65 ATTTATTTAAAAATTTAAAC-TTTTCCTTAAAATAACT-AAAAAAGATTTTTATTTTTAAAAATA
* *
27808169 GAAACTTTCTTTTTTTAAA-GATAATCATTACTTTACTTAAAAATCTAAACTTTTATTTCAAAAT
128 GAAACTTTC-TTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCAAAAT
* *
27808233 AGTTTAAAAAATCAAAACTTTGCTTAAAAATTTAAAATTTTCTAAAAAAAACAGATTTTTTAAAA
192 AGTTAAAAAAATCAAAACTTTACTTAAAAATTTAAAATTTTCT-AAAAAAACAGATTTTTTAAAA
* * *
27808298 AAATTTAAACTTTCTCGTGTTT
256 AAATATAAACTTTCTCCTTTTT
* * * * *
27808320 AAAAAAATCATTATTTTACTTAAAAATC-AAAGCTTTTTATTTCAAAATTGTTAAAAAAA
1 AAGAAAATCACTACTTTACTTAAAAATCTAAA-C-TTTTATTTCGAAATAGTTAAAAAAA
27808379 CAACACCAAA
Statistics
Matches: 298, Mismatches: 30, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
277 15 0.05
278 18 0.06
279 41 0.14
280 8 0.03
281 88 0.30
282 22 0.07
283 63 0.21
284 30 0.10
285 13 0.04
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.42
Consensus pattern (277 bp):
AAGAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAA
TTTATTTAAAAATTTAAACTTTTCCTTAAAATAACTAAAAAAGATTTTTATTTTTAAAAATAGAA
ACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCAAAATAGTT
AAAAAAATCAAAACTTTACTTAAAAATTTAAAATTTTCTAAAAAAACAGATTTTTTAAAAAAATA
TAAACTTTCTCCTTTTT
Found at i:27809243 original size:42 final size:41
Alignment explanation
Indices: 27809210--27809743 Score: 484
Period size: 41 Copynumber: 12.5 Consensus size: 41
27809200 TCTATGCTTA
**
27809210 GGCCTCTATTTGCAATGAAAAGTAAATGGACCTCCACACCT
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
** *
27809251 AGGCCTCCGAATGCAA-GGAAAGTAAAATGGACCTCCACA-CT
1 -GGCCTCTAAATGCAATGAAAAGT-AAATGGACCTCCACACCT
* * *
27809292 AGCCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACACCT
1 -GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
* * *
27809334 GGCCTCTAAATTAAATGCAATGAAAAGTAAAGGGGCCTCCACACTT
1 GGCCTC-----TAAATGCAATGAAAAGTAAATGGACCTCCACACCT
*
27809380 GGCCTCTAAATGCAATGAAAAGTAAAATGGACCTCCACACTT
1 GGCCTCTAAATGCAATGAAAAGT-AAATGGACCTCCACACCT
27809422 GGCCATCTAAA-GCAATGAAAAGTAAATGGACCTCCACACCT
1 GGCC-TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
* *
27809463 GCGCCTCTAAAATGCAATGAAAAGTAAATGGACCTCTACACAT
1 G-GCCTCT-AAATGCAATGAAAAGTAAATGGACCTCCACACCT
* * * *
27809506 GGGCTCCACACATGGGCTCTGAATGCAAAGATAAGTAAATGGGCCTCCACACAT
1 GGCCTCTA-A-AT--G--C--AATG---A-A-AAGTAAATGGACCTCCACACCT
* ** * *
27809560 -GCCTCTGAATGCGGTGAAAAGCAAATGGACCTTCACACCT
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
**
27809600 GGCCTCTAAATGTGATGAAAAGTAAATGGACCTCCACACCT
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
* * *
27809641 GAGCCTCTAAATGAAATGAAAAGTAAATGGGCCTCCACATCT
1 G-GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
* * *
27809683 GGGCCTTTGAATGCGATG-AAAGTAAATGGACCTCCACACCT
1 -GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
* *
27809724 GGGCTTCTAAATGTAATGAA
1 -GGCCTCTAAATGCAATGAA
27809744 TGCTTTCCTT
Statistics
Matches: 409, Mismatches: 53, Indels: 60
0.78 0.10 0.11
Matches are distributed among these distances:
40 18 0.04
41 148 0.36
42 127 0.31
43 38 0.09
45 3 0.01
46 39 0.10
47 2 0.00
49 5 0.01
51 2 0.00
52 2 0.00
53 5 0.01
54 20 0.05
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (41 bp):
GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
Found at i:27809313 original size:83 final size:81
Alignment explanation
Indices: 27809211--27809721 Score: 427
Period size: 83 Copynumber: 6.0 Consensus size: 81
27809201 CTATGCTTAG
** * *
27809211 GCCTCTATTTGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCCGAATGCAA-GGAAAGTA
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT-GGCCTCCAAATGCAATGAAAAGT-
27809275 AAATGGACCTCCACACTA
64 AAATGGACCTCCACACTA
* * *
27809293 GCCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGCCTCTAAATTAAATGCAATGAA
1 G-CCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGCCTC-----CAAATGCAATGAA
* * *
27809358 AAGTAAAGGGGCCTCCACACTTG
60 AAGTAAATGGACCTCCACAC-TA
* *
27809381 GCCTCTAAATGCAATGAAAAGTAAAATGGACCTCCACACTTGGCCATCTAAA-GCAATGAAAAGT
1 GCCTCTAAATGCAATGAAAAGT-AAATGGACCTCCACACCTGGCC-TCCAAATGCAATGAAAAGT
*
27809445 AAATGGACCTCCACACCTGC
64 AAATGGACCTCCACA-CT-A
* * *
27809465 GCCTCTAAAATGCAATGAAAAGTAAATGGACCTCTACACATGGGCTCCACACATGGGCTCTGAAT
1 GCCTCT-AAATGCAATGAAAAGTAAATGGACCTCCACACCTGGCCTCCA-A-AT--G--C--AAT
*
27809530 GCAAAGATAAGTAAATGGGCCTCCACAC-A
57 G---A-A-AAGTAAATGGACCTCCACACTA
* ** * * * **
27809559 TGCCTCTGAATGCGGTGAAAAGCAAATGGACCTTCACACCTGGCCTCTAAATGTGATGAAAAGTA
1 -GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGCCTCCAAATGCAATGAAAAGTA
27809624 AATGGACCTCCACACCTGA
65 AATGGACCTCCACA-CT-A
* * * *** *
27809643 GCCTCTAAATGAAATGAAAAGTAAATGGGCCTCCACATCTGGGCCTTTGAATGCGATG-AAAGTA
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT-GGCCTCCAAATGCAATGAAAAGTA
27809707 AATGGACCTCCACAC
65 AATGGACCTCCACAC
27809722 CTGGGCTTCT
Statistics
Matches: 352, Mismatches: 45, Indels: 64
0.76 0.10 0.14
Matches are distributed among these distances:
81 18 0.05
82 10 0.03
83 117 0.33
84 46 0.13
85 17 0.05
86 3 0.01
87 41 0.12
88 29 0.08
89 2 0.01
90 2 0.01
92 6 0.02
93 1 0.00
94 33 0.09
95 7 0.02
96 2 0.01
97 18 0.05
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (81 bp):
GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGCCTCCAAATGCAATGAAAAGTAA
ATGGACCTCCACACTA
Found at i:27809373 original size:129 final size:126
Alignment explanation
Indices: 27809220--27809743 Score: 426
Period size: 129 Copynumber: 4.1 Consensus size: 126
27809210 GGCCTCTATT
* * *
27809220 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCCGAATGCAA-GGAAAGTAAAATGGACC
1 TGCAATGAAAAGTAAAGGGACCTCCACA-CTAGGCCTCCAAATGCAATGAAAAGTAAAATGGACC
* * *
27809284 TCCACAC-TAGCCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG-GCCTCTAAATTA
65 TCCACACTTAGCCATCTAAA-GCAATGAAAAGTAAATGGACCTCCACACCTGCGCCTCT--A--A
27809347 AA
125 AA
* * *
27809349 TGCAATGAAAAGTAAAGGGGCCTCCACACTTGGCCTCTAAATGCAATGAAAAGTAAAATGGACCT
1 TGCAATGAAAAGTAAAGGGACCTCCACACTAGGCCTCCAAATGCAATGAAAAGTAAAATGGACCT
*
27809414 CCACACTTGGCCATCTAAAGCAATGAAAAGTAAATGGACCTCCACACCTGCGCCTCTAAAA
66 CCACACTTAGCCATCTAAAGCAATGAAAAGTAAATGGACCTCCACACCTGCGCCTCTAAAA
* * * *
27809475 TGCAATGAAAAGTAAATGGACCTCTACAC-ATGGGCTCCACACATGGGCTCTGAATGCAAAGATA
1 TGCAATGAAAAGTAAAGGGACCTCCACACTA-GGCCTCCA-A-AT--G--C--AATGAAAAG-T-
* * * ** * *
27809539 AGTAAATGGGCCTCCACACAT-GCC-TCTGAATGCGGTGAAAAGCAAATGGACCTTCACACCTG-
55 A--AAATGGACCTCCACACTTAGCCATCT-AAAGCAATGAAAAGTAAATGGACCTCCACACCTGC
27809601 GCCTCT-AAA
117 GCCTCTAAAA
** * * * *
27809610 TGTGATGAAAAGTAAATGGACCTCCACACCT-GAGCCTCTAAATGAAATGAAAAGT-AAATGGGC
1 TGCAATGAAAAGTAAAGGGACCTCCACA-CTAG-GCCTCCAAATGCAATGAAAAGTAAAATGGAC
** * * * * *
27809673 CTCCACATCTGGGCC-TTTGAATGCGATG-AAAGTAAATGGACCTCCACACCTGGGCTTCT-AAA
64 CTCCACA-CTTAGCCATCT-AAAGCAATGAAAAGTAAATGGACCTCCACACCTGCGCCTCTAAAA
*
27809735 TGTAATGAA
1 TGCAATGAA
27809744 TGCTTTCCTT
Statistics
Matches: 333, Mismatches: 39, Indels: 50
0.79 0.09 0.12
Matches are distributed among these distances:
123 15 0.05
124 23 0.07
125 30 0.09
126 35 0.11
127 2 0.01
128 26 0.08
129 79 0.24
130 16 0.05
132 2 0.01
134 10 0.03
135 31 0.09
136 16 0.05
137 32 0.10
138 16 0.05
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (126 bp):
TGCAATGAAAAGTAAAGGGACCTCCACACTAGGCCTCCAAATGCAATGAAAAGTAAAATGGACCT
CCACACTTAGCCATCTAAAGCAATGAAAAGTAAATGGACCTCCACACCTGCGCCTCTAAAA
Found at i:27809518 original size:13 final size:13
Alignment explanation
Indices: 27809500--27809524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27809490 ATGGACCTCT
27809500 ACACATGGGCTCC
1 ACACATGGGCTCC
27809513 ACACATGGGCTC
1 ACACATGGGCTC
27809525 TGAATGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (13 bp):
ACACATGGGCTCC
Found at i:27810236 original size:129 final size:129
Alignment explanation
Indices: 27810006--27810262 Score: 446
Period size: 129 Copynumber: 2.0 Consensus size: 129
27809996 ATCGAAAGTT
* *
27810006 AACTCGTTAATTCTTGTAAAGCCGAATTTCCTTTTCTGACTTGACCGTTTCGACTGTGAACCCTG
1 AACTCGTTAATTCTTGTAAAGCCGAATTTCCTTTTCTGACTTGACCATTTCGACTATGAACCCTG
27810071 TACCATGGTCTTTTGAAAAATTGCGTCTTAAAGTAGATATTCTTTAATATAGTTTCTTTCTCTC
66 TACCATGGTCTTTTGAAAAATTGCGTCTTAAAGTAGATATTCTTTAATATAGTTTCTTTCTCTC
*
27810135 AACTCGTTAATTCTTGT-AAGCCGAATTTCC-TTTCTGACTTTGGACTATTTCGACTATGAACCC
1 AACTCGTTAATTCTTGTAAAGCCGAATTTCCTTTTCTGAC-TT-GACCATTTCGACTATGAACCC
*
27810198 TGTACCATGGTCTTTTGCAAAATTGCGTCTTAAAGTAGATATTCTTTAATATAGTTTCTTTCTCT
64 TGTACCATGGTCTTTTGAAAAATTGCGTCTTAAAGTAGATATTCTTTAATATAGTTTCTTTCTCT
27810263 TGCTCTCTCT
Statistics
Matches: 122, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
127 8 0.07
128 15 0.12
129 99 0.81
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (129 bp):
AACTCGTTAATTCTTGTAAAGCCGAATTTCCTTTTCTGACTTGACCATTTCGACTATGAACCCTG
TACCATGGTCTTTTGAAAAATTGCGTCTTAAAGTAGATATTCTTTAATATAGTTTCTTTCTCTC
Found at i:27810287 original size:16 final size:16
Alignment explanation
Indices: 27810266--27810300 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
27810256 TTTCTCTTGC
27810266 TCTCTCTTTCTATTTTTT
1 TCTCT-TTTCT-TTTTTT
27810284 TCTCTTTTCTTTTTTT
1 TCTCTTTTCTTTTTTT
27810300 T
1 T
27810301 GTATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTCTTTTCTTTTTTT
Found at i:27818242 original size:4 final size:4
Alignment explanation
Indices: 27818235--27818298 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
27818225 AGCGAAGGAG
* * * * *
27818235 TGAA TGAA TGAA TGAA TGAG TGAG TGAA TGAG TGAA TGAA TGAG TGAG
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
27818283 TGAA TGAA TGAA TGAA
1 TGAA TGAA TGAA TGAA
27818299 ATTGGGACAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (4 bp):
TGAA
Found at i:27818252 original size:12 final size:12
Alignment explanation
Indices: 27818235--27818298 Score: 92
Period size: 12 Copynumber: 5.3 Consensus size: 12
27818225 AGCGAAGGAG
*
27818235 TGAATGAATGAA
1 TGAATGAGTGAA
*
27818247 TGAATGAGTGAG
1 TGAATGAGTGAA
27818259 TGAATGAGTGAA
1 TGAATGAGTGAA
*
27818271 TGAATGAGTGAG
1 TGAATGAGTGAA
*
27818283 TGAATGAATGAA
1 TGAATGAGTGAA
27818295 TGAA
1 TGAA
27818299 ATTGGGACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (12 bp):
TGAATGAGTGAA
Found at i:27818259 original size:24 final size:24
Alignment explanation
Indices: 27818232--27818298 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
27818222 ATGAGCGAAG
27818232 GAGTGAATGAATGAATGAATGAGT
1 GAGTGAATGAATGAATGAATGAGT
*
27818256 GAGTGAATGAGTGAATGAATGAGT
1 GAGTGAATGAATGAATGAATGAGT
27818280 GAGTGAATGAATGAATGAA
1 GAGTGAATGAATGAATGAA
27818299 ATTGGGACAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.24
Consensus pattern (24 bp):
GAGTGAATGAATGAATGAATGAGT
Found at i:27822888 original size:84 final size:84
Alignment explanation
Indices: 27822797--27822962 Score: 300
Period size: 84 Copynumber: 2.0 Consensus size: 84
27822787 AAAAGAGATA
27822797 TTTTTCATAAATTTAAAAAA-TTTGGGGTGGGAATAAAATACTCATTTTTG-CACTTATAAATAG
1 TTTTTCATAAA-TTAAAAAATTTTGGGGTGGGAATAAAATACTCA-TTTTGACACTTATAAATAG
27822860 GGAATATATATATATATATTT
64 GGAATATATATATATATATTT
27822881 TTTTTCATAAATTAAAAAATTTTGGGGTGGGAATAAAATACTCATTTTGACACTTATAAATAGGG
1 TTTTTCATAAATTAAAAAATTTTGGGGTGGGAATAAAATACTCATTTTGACACTTATAAATAGGG
27822946 AATATATATATATATAT
66 AATATATATATATATAT
27822963 ATATTCTCTC
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
83 13 0.16
84 67 0.84
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (84 bp):
TTTTTCATAAATTAAAAAATTTTGGGGTGGGAATAAAATACTCATTTTGACACTTATAAATAGGG
AATATATATATATATATTT
Found at i:27823465 original size:147 final size:147
Alignment explanation
Indices: 27823116--27823756 Score: 685
Period size: 148 Copynumber: 4.4 Consensus size: 147
27823106 TGATTAAAAC
* * * *
27823116 AAAATCACTATTTTACTTCAAAAATCAAAATTTTTATTTCGAAATAATTAAAAAAAATCAAAACT
1 AAAATCACTACTTTACTT-AAAAATCTAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAAC-
* * * * *
27823181 TTGTTTAAAAATTTAAATTTTTTTCTTTAAAATCACTAAAAAATAGATTTTATTTTTTAAAAATC
63 TTATTTAAAAATTTAAA-ATTTTTCTTTAAAATAACTAAAAAACAGATTTT-TTTTTTAAAAATA
27823246 TAAACTTTCTTTCTTTTTTAATG
126 TAAACTTTC-TTCTTTTTTAATG
* * * *
27823269 AAAAT-ATTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATACTTAAAAAAATCATAACTTA
1 AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTA
* * * * *
27823333 TTTCAAAATTCAAACTTTTTCTTTATAATAACTAAAAAGCAGATTTTTGTTTTTAAAAATATAAA
66 TTTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAACAGATTTTT-TTTTTAAAAATATAAA
27823398 CTTTCTTCTTTTTTAATG
130 CTTTCTTCTTTTTTAATG
* *
27823416 AAAATCACTACTTT-CTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATTAAAAATTT
1 AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAA-TCAAAACTT
*
27823480 ATTTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATATAA
65 ATTTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAACAGATTTTT-TTTTTAAAAATATAA
* *
27823545 ACTTTC-T-ATTTTTAAAG
129 ACTTTCTTCTTTTTTAATG
* * * *
27823562 AAAATCACTACTTTACTTAAAAATCCAAACTATTATTTCTAAATTGTTAAAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAC-TT
* * *
27823627 GTTTAAAAA--T-AAACTTTTC-------T-A--AAAAAACAGA-TTTTTTTTTAAAAATCT-AA
65 ATTTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAACAGATTTTTTTTTTAAAAATATAAA
* * *
27823677 TTTTC-CCGTTTTTTAAAG
130 CTTTCTTC-TTTTTTAATG
* * * *
27823695 AAAATCACTATTTTACTTAAAAATC-AAAGCTTTTATTTTGAAATTGTTTAAAAAAACCAAAA
1 AAAATCACTACTTTACTTAAAAATCTAAA-CTTTTATTTCGAAATAG-TTAAAAAAATCAAAA
27823757 TTTTTCCAAA
Statistics
Matches: 432, Mismatches: 47, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
131 6 0.01
132 15 0.03
133 51 0.12
134 23 0.05
136 1 0.00
137 1 0.00
144 8 0.02
145 1 0.00
146 27 0.06
147 105 0.24
148 124 0.29
149 14 0.03
150 13 0.03
151 27 0.06
152 11 0.03
153 5 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (147 bp):
AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTA
TTTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAACAGATTTTTTTTTTAAAAATATAAAC
TTTCTTCTTTTTTAATG
Found at i:27825903 original size:41 final size:39
Alignment explanation
Indices: 27825847--27825971 Score: 142
Period size: 41 Copynumber: 3.1 Consensus size: 39
27825837 AGGTTTATGA
* * *
27825847 GAAAGCGCCGTTAAAGGTCAAAGCATTAGCGACGCTTACT
1 GAAAGCACCGCTAAAGGTCAGAGCATTAGCGACGCTTA-T
** *
27825887 GAAAGGCGTCGCTAAAGATCAGAGCATTAGCGACGCTTATT
1 GAAA-GCACCGCTAAAGGTCAGAGCATTAGCGACGCTTA-T
* *
27825928 GGGAAGCACCGCTAAAGGTCAGAGCATTAGCGGCGCTTAT
1 -GAAAGCACCGCTAAAGGTCAGAGCATTAGCGACGCTTAT
27825968 GAAA
1 GAAA
27825972 AAGTACCACT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 5 0.07
41 61 0.85
42 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (39 bp):
GAAAGCACCGCTAAAGGTCAGAGCATTAGCGACGCTTAT
Found at i:27826101 original size:26 final size:26
Alignment explanation
Indices: 27826072--27826148 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 26
27826062 CAATTATTTT
27826072 AAAACTTATATAAACTTAAAAAATTC
1 AAAACTTATATAAACTTAAAAAATTC
* * * ** * *
27826098 AAAAATTTTAAAAAAATAAAAATTTT
1 AAAACTTATATAAACTTAAAAAATTC
* *
27826124 AATACTTATATAAACTAAAAAAATT
1 AAAACTTATATAAACTTAAAAAATT
27826149 AAATTATTTT
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAACTTATATAAACTTAAAAAATTC
Found at i:27826110 original size:17 final size:17
Alignment explanation
Indices: 27826087--27826125 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
27826077 TTATATAAAC
*
27826087 TTAAAAAATTCAAAAATT
1 TTAAAAAAAT-AAAAATT
27826105 TTAAAAAAATAAAAATT
1 TTAAAAAAATAAAAATT
27826122 TTAA
1 TTAA
27826126 TACTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAAAATAAAAATT
Found at i:27826150 original size:25 final size:25
Alignment explanation
Indices: 27826070--27826151 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
27826060 AACAATTATT
*
27826070 TTAAAACTTATATAAACTTAAAAAA
1 TTAAAACTTATATAAACTAAAAAAA
* * * * **
27826095 TTCAAAAATTTTAAAAAAATAAAAATT
1 TT-AAAACTTAT-ATAAACTAAAAAAA
*
27826122 TTAATACTTATATAAACTAAAAAAA
1 TTAAAACTTATATAAACTAAAAAAA
27826147 TTAAA
1 TTAAA
27826152 TTATTTTGAT
Statistics
Matches: 40, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
25 16 0.40
26 13 0.32
27 11 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (25 bp):
TTAAAACTTATATAAACTAAAAAAA
Found at i:27830255 original size:44 final size:42
Alignment explanation
Indices: 27830090--27830425 Score: 318
Period size: 44 Copynumber: 7.9 Consensus size: 42
27830080 TTTGTTAATA
* ** * *
27830090 TTAGCGGTGTTTGTGGGAAAAATGCAGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGGTCT
* * *
27830133 TTAGCGGTGTTTGTGGGAAAAGCGCCGTTAAAGATCATGGTCT
1 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGGTCT
* * * * *
27830176 TTAGTGGCGTTTG-GGGAAAGCGCTGTTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGGTCT
** *
27830217 TTAGTAGCGTTTGTGGAAAAAAGCGCTGCTAAAGACCATGGTCT
1 TTAGCGGCGTTTGTGG--AAAAGCGCCGCTAAAGACCATGGTCT
* ** * * *
27830261 ATAGCATCGTTTGTGGAAAAGCACCGCTAAAGATCATGGTCA
1 TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGGTCT
* *
27830303 TTAGCGGCGTTTATGGCAAAAAGCGCCGCTAAAGACCATGGTCA
1 TTAGCGGCGTTTGTGG--AAAAGCGCCGCTAAAGACCATGGTCT
* * *
27830347 TTAGCGGCGTTTTTGG-AAAGCGCCGCTAAAGACCA-CGTTT
1 TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGGTCT
* * *
27830387 TATAGAGGCGTTTTTGGGAAAGCGCCGCTAAAGACCATG
1 T-TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATG
27830426 TTCTATAACA
Statistics
Matches: 250, Mismatches: 35, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
40 3 0.01
41 69 0.28
42 55 0.22
43 48 0.19
44 75 0.30
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGGTCT
Found at i:27830327 original size:86 final size:84
Alignment explanation
Indices: 27830116--27830432 Score: 343
Period size: 86 Copynumber: 3.8 Consensus size: 84
27830106 GAAAAATGCA
* * * * * *
27830116 GCTAAAGACCATGTTCTTTAGCGGTGTTTGTGGGAAAAGCGCCGTTAAAGATCATGGTCTTTAGT
1 GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGGTCTATAGC
* *
27830181 GGCGTTTGGGGAAAGCGCT
66 GGCGTTTGTGGAAAGCGCC
* ** *
27830200 GTTAAAGACCATGTTCTTTAGTAGCGTTTGTGGAAAAAAGCGCTGCTAAAGACCATGGTCTATAG
1 GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGG-AAAAAGCGCCGCTAAAGACCATGGTCTATAG
** *
27830265 CATCGTTTGTGGAAAAGCACC
65 CGGCGTTTGTGG-AAAGCGCC
* * * *
27830286 GCTAAAGATCATGGTCATTAGCGGCGTTTATGGCAAAAAGCGCCGCTAAAGACCATGGTC-ATTA
1 GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGG-AAAAAGCGCCGCTAAAGACCATGGTCTA-TA
*
27830350 GCGGCGTTTTTGGAAAGCGCC
64 GCGGCGTTTGTGGAAAGCGCC
* * * * *
27830371 GCTAAAGACCACGTT-TTATAGAGGCGTTTTTGG-GAAAGCGCCGCTAAAGACCATGTTCTATA
1 GCTAAAGACCATGTTCTT-TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGGTCTATA
27830433 ACAAGGTTTT
Statistics
Matches: 192, Mismatches: 36, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
83 25 0.13
84 31 0.16
85 67 0.35
86 69 0.36
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (84 bp):
GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGGTCTATAGC
GGCGTTTGTGGAAAGCGCC
Found at i:27830367 original size:127 final size:125
Alignment explanation
Indices: 27830089--27830425 Score: 320
Period size: 127 Copynumber: 2.6 Consensus size: 125
27830079 ATTTGTTAAT
* * ** * * *
27830089 ATTAGCGGTGTTTGTGGGAAAAATGCAGCTAAAGACCATGTTCTTTAGCGGT-GTTTGTGGGAAA
1 ATTAGCAGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCTATAGC-ATCGTTTGT-GGAAA
* * * ** * * *
27830153 AGCGCCGTTAAAGATCATGGTCTTTAGTGGCGTTTGGGGAAAGCGCTGTTAAAGACCATGTTC
63 AGCGCCGCTAAAGATCATGGTCATTAGCGGCGTTTGGAAAAAGCGCCGCTAAAGACCATGGTC
* * * *
27830216 TTTAGTAGCGTTTGTGGAAAAAAGCGCTGCTAAAGACCATGGTCTATAGCATCGTTTGTGGAAAA
1 ATTAGCAGCGTTTGTGG--AAAAGCGCCGCTAAAGACCATGTTCTATAGCATCGTTTGTGGAAAA
*
27830281 GCACCGCTAAAGATCATGGTCATTAGCGGCGTTTATGGCAAAAAGCGCCGCTAAAGACCATGGTC
64 GCGCCGCTAAAGATCATGGTCATTAGCGGCG-TT-TGG-AAAAAGCGCCGCTAAAGACCATGGTC
* * * * * * *
27830346 ATTAGCGGCGTTTTTGG-AAAGCGCCGCTAAAGACCACGTTTTATAG-AGGCGTTTTTGGGAAAG
1 ATTAGCAGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCA-TCGTTTGTGGAAAAG
*
27830409 CGCCGCTAAAGACCATG
65 CGCCGCTAAAGATCATG
27830426 TTCTATAACA
Statistics
Matches: 171, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
126 3 0.02
127 97 0.57
128 34 0.20
129 3 0.02
130 34 0.20
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (125 bp):
ATTAGCAGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCATCGTTTGTGGAAAAGC
GCCGCTAAAGATCATGGTCATTAGCGGCGTTTGGAAAAAGCGCCGCTAAAGACCATGGTC
Found at i:27834343 original size:17 final size:17
Alignment explanation
Indices: 27834323--27834370 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
27834313 CACATTCCCT
27834323 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTTAA
* * *
27834340 TTGTCACTGCATCTTCA
1 TTGTCATTGCATTTTAA
27834357 TTGTCATTGCATTT
1 TTGTCATTGCATTT
27834371 CCATGTGTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (17 bp):
TTGTCATTGCATTTTAA
Found at i:27839276 original size:40 final size:40
Alignment explanation
Indices: 27839175--27839439 Score: 298
Period size: 40 Copynumber: 6.7 Consensus size: 40
27839165 TAGTATAGTT
** * * **
27839175 GTGTTTACAGTGTCACGGCTAGTTCAATAATAATATTGCA
1 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
* * * ** * *
27839215 GTGTTT-CAGTGCCACTGCCAGTTCAGTAGTAGCATCGTA
1 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
*
27839254 GTATTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
1 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
*
27839294 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTACA
1 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
* * * * **
27839334 ATATTTACAGTGTCACTGCCAGTTCAATGGTAATATTATA
1 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
* * *
27839374 GTGTTTACAGTGTCACTACTAGTTCAGTTGTAATATCGCA
1 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
*
27839414 GTGTTTACAGTGTCACTGCCAGTTCA
1 GTGTTTACAGTGTCACTACCAGTTCA
27839440 CACAATCCAG
Statistics
Matches: 189, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 29 0.15
40 160 0.85
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (40 bp):
GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
Found at i:27839348 original size:80 final size:80
Alignment explanation
Indices: 27839178--27839439 Score: 337
Period size: 80 Copynumber: 3.3 Consensus size: 80
27839168 TATAGTTGTG
* * ** * *
27839178 TTTACAGTGTCACGGCTAGTTCAATAATAATATTGCAGTGTTT-CAGTGCCACTGCCAGTTCAGT
1 TTTACAGTGTCACTGCCAGTTCAATGGTAATATTGCAGTGTTTACAGTGTCACTACCAGTTCAGT
** *
27839242 AGTAGCATCGTAGTA
66 AGTAATATCGCAGTA
* *
27839257 TTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCAGTGTTTACAGTGTCACTACCAGTTCAGT
1 TTTACAGTGTCACTGCCAGTTCAATGGTAATATTGCAGTGTTTACAGTGTCACTACCAGTTCAGT
* ** *
27839322 GGTAATATTACAATA
66 AGTAATATCGCAGTA
** *
27839337 TTTACAGTGTCACTGCCAGTTCAATGGTAATATTATAGTGTTTACAGTGTCACTACTAGTTCAGT
1 TTTACAGTGTCACTGCCAGTTCAATGGTAATATTGCAGTGTTTACAGTGTCACTACCAGTTCAGT
* *
27839402 TGTAATATCGCAGTG
66 AGTAATATCGCAGTA
27839417 TTTACAGTGTCACTGCCAGTTCA
1 TTTACAGTGTCACTGCCAGTTCA
27839440 CACAATCCAG
Statistics
Matches: 157, Mismatches: 25, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
79 37 0.24
80 120 0.76
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (80 bp):
TTTACAGTGTCACTGCCAGTTCAATGGTAATATTGCAGTGTTTACAGTGTCACTACCAGTTCAGT
AGTAATATCGCAGTA
Found at i:27839392 original size:120 final size:119
Alignment explanation
Indices: 27839175--27839439 Score: 341
Period size: 120 Copynumber: 2.2 Consensus size: 119
27839165 TAGTATAGTT
* * * * *
27839175 GTGTTTACAGTGTCACGGCTAGTTCAATAATAATATTGCAGTGTTTCAGTGCCACTGCCAGTTCA
1 GTGTTTACAGTGTCACTGCCAGTTCAATAATAATATTACAATATTTCAGTGCCACTGCCAGTTCA
* * * *
27839240 GTAGTAGCATCGTAGTATTTACAGTGTCACTACCAGTTCAGTGGTAATATTGCA
66 ATAGTAACATCATAGTATTTACAGTGTCACTACCAGTTCAGTGGTAATATCGCA
* * ** *
27839294 GTGTTTACAGTGTCACTACCAGTTCAGTGGTAATATTACAATATTTACAGTGTCACTGCCAGTTC
1 GTGTTTACAGTGTCACTGCCAGTTCAATAATAATATTACAATATTT-CAGTGCCACTGCCAGTTC
* * * * * *
27839359 AATGGTAATATTATAGTGTTTACAGTGTCACTACTAGTTCAGTTGTAATATCGCA
65 AATAGTAACATCATAGTATTTACAGTGTCACTACCAGTTCAGTGGTAATATCGCA
27839414 GTGTTTACAGTGTCACTGCCAGTTCA
1 GTGTTTACAGTGTCACTGCCAGTTCA
27839440 CACAATCCAG
Statistics
Matches: 124, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
119 37 0.30
120 87 0.70
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (119 bp):
GTGTTTACAGTGTCACTGCCAGTTCAATAATAATATTACAATATTTCAGTGCCACTGCCAGTTCA
ATAGTAACATCATAGTATTTACAGTGTCACTACCAGTTCAGTGGTAATATCGCA
Found at i:27846248 original size:39 final size:40
Alignment explanation
Indices: 27846201--27846285 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
27846191 AGTGTCACGG
*
27846201 CTAGTTCAGTAATAATATTGCAGTGTTT-CAGTGCCACTA
1 CTAGTTCAGTAATAATATCGCAGTGTTTACAGTGCCACTA
* * * *
27846240 CTAGTTCAGTAGTAGTATCGTAGTGTTTACAGTGTCACTA
1 CTAGTTCAGTAATAATATCGCAGTGTTTACAGTGCCACTA
*
27846280 CCAGTT
1 CTAGTT
27846286 TAGTGGTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 24 0.62
40 15 0.38
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (40 bp):
CTAGTTCAGTAATAATATCGCAGTGTTTACAGTGCCACTA
Found at i:27856841 original size:17 final size:16
Alignment explanation
Indices: 27856799--27856841 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
27856789 GTCATCACAT
27856799 TTTTATTGTCACAGCA
1 TTTTATTGTCACAGCA
27856815 TTTTATTTGTCA-ATGCA
1 TTTTA-TTGTCACA-GCA
27856832 TTTGTATTGT
1 TTT-TATTGT
27856842 AGTTGCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.25
17 16 0.67
18 2 0.08
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTTATTGTCACAGCA
Found at i:27859826 original size:25 final size:25
Alignment explanation
Indices: 27859791--27859838 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
27859781 GAAATAAATT
27859791 TTAGATGTGAAAATATGGATAAAGGA
1 TTAGATGTGAAAATATGGA-AAAGGA
*
27859817 TTAGAT-TGAAAATTTGGAAAAG
1 TTAGATGTGAAAATATGGAAAAG
27859839 TATGAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (25 bp):
TTAGATGTGAAAATATGGAAAAGGA
Found at i:27859848 original size:25 final size:25
Alignment explanation
Indices: 27859793--27859844 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
27859783 AATAAATTTT
*
27859793 AGATGTGAAAATATGGATAAAGGATT
1 AGAT-TGAAAATATGGATAAAGGATG
* *
27859819 AGATTGAAAATTTGGA-AAAGTATG
1 AGATTGAAAATATGGATAAAGGATG
27859843 AG
1 AG
27859845 GATTAAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 11 0.48
26 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (25 bp):
AGATTGAAAATATGGATAAAGGATG
Found at i:27862095 original size:40 final size:40
Alignment explanation
Indices: 27862051--27862128 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
27862041 CAAACGAACT
* *
27862051 ATGTTTTTATTAATTAATCTCAAGATTAAAGTTTGGTGAC
1 ATGTTTTTATTAATTAATCCCAAGACTAAAGTTTGGTGAC
27862091 ATGTTTTTATTAATTAATCCCAAGACTAAAGTTTGGTG
1 ATGTTTTTATTAATTAATCCCAAGACTAAAGTTTGGTG
27862129 GCTTAAGACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (40 bp):
ATGTTTTTATTAATTAATCCCAAGACTAAAGTTTGGTGAC
Found at i:27862233 original size:20 final size:20
Alignment explanation
Indices: 27862208--27862292 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 20
27862198 GACTAAAACC
27862208 ATTGTTGCTTCTTTGAATCG
1 ATTGTTGCTTCTTTGAATCG
* *
27862228 ATTGTTTG-TTGTTTTAAATCG
1 ATTG-TTGCTT-CTTTGAATCG
*
27862249 ATTATTTGCTTCTTTGAATCG
1 ATT-GTTGCTTCTTTGAATCG
* * *
27862270 AATCTT-CATTGTTTGAATCG
1 ATTGTTGC-TTCTTTGAATCG
27862290 ATT
1 ATT
27862293 CATTATTGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 21 0.41
21 27 0.53
22 2 0.04
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (20 bp):
ATTGTTGCTTCTTTGAATCG
Found at i:27862249 original size:21 final size:20
Alignment explanation
Indices: 27862223--27862333 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 20
27862213 TGCTTCTTTG
*
27862223 AATCGATTGTTTGTTGTTTTA
1 AATCGATTCTTTGTTG-TTTA
* * *
27862244 AATCGATTATTTGCTTCTTTG
1 AATCGATTCTTTG-TTGTTTA
* ** *
27862265 AATCGAATCTTCATTGTTTG
1 AATCGATTCTTTGTTGTTTA
* *
27862285 AATCGATTCATTATTGTTTA
1 AATCGATTCTTTGTTGTTTA
*
27862305 AATCGATTCTTTGTTGTTTT
1 AATCGATTCTTTGTTGTTTA
*
27862325 ACTCGATTC
1 AATCGATTC
27862334 AAACTCCAAT
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
20 47 0.64
21 24 0.33
22 2 0.03
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.51
Consensus pattern (20 bp):
AATCGATTCTTTGTTGTTTA
Found at i:27862282 original size:42 final size:41
Alignment explanation
Indices: 27862212--27862292 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 41
27862202 AAAACCATTG
* * **
27862212 TTGCTTCTTTGAATCGATTGTTTGTTGTTTTAAATCGATTAT
1 TTGCTTCTTTGAATCGAATCTTCATTG-TTTAAATCGATTAT
*
27862254 TTGCTTCTTTGAATCGAATCTTCATTGTTTGAATCGATT
1 TTGCTTCTTTGAATCGAATCTTCATTGTTTAAATCGATT
27862293 CATTATTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 11 0.32
42 23 0.68
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (41 bp):
TTGCTTCTTTGAATCGAATCTTCATTGTTTAAATCGATTAT
Found at i:27862322 original size:40 final size:42
Alignment explanation
Indices: 27862216--27862334 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 42
27862206 CCATTGTTGC
* * *
27862216 TTCTTTGAATCGATTGTTTGTTGTTTTAAATCGATT-ATTTGC
1 TTCTTTAAATCGATTCTTTGTTG-TTTAAATCGATTCATTTGA
* * ** *
27862258 TTCTTTGAATCGAATCTTCATTGTTTGAATCGATTCA-TT-A
1 TTCTTTAAATCGATTCTTTGTTGTTTAAATCGATTCATTTGA
* * *
27862298 TTGTTTAAATCGATTCTTTGTTGTTTTACTCGATTCA
1 TTCTTTAAATCGATTCTTTGTTGTTTAAATCGATTCA
27862335 AACTCCAATA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
40 30 0.48
41 13 0.21
42 20 0.32
ACGTcount: A:0.21, C:0.13, G:0.14, T:0.52
Consensus pattern (42 bp):
TTCTTTAAATCGATTCTTTGTTGTTTAAATCGATTCATTTGA
Found at i:27863475 original size:2 final size:2
Alignment explanation
Indices: 27863468--27863507 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
27863458 TGTTTTATTC
* *
27863468 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TG TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27863508 TTGGTGTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (2 bp):
TA
Found at i:27863494 original size:19 final size:19
Alignment explanation
Indices: 27863470--27863508 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27863460 TTTTATTCTA
27863470 TATATATATATATATATAT
1 TATATATATATATATATAT
* *
27863489 TATATATATGTATTTATAT
1 TATATATATATATATATAT
27863508 T
1 T
27863509 TGGTGTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:27870542 original size:2 final size:2
Alignment explanation
Indices: 27870535--27870582 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
27870525 TCATAGAAGC
27870535 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27870577 GA GA GA
1 GA GA GA
27870583 TGCATGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27872341 original size:21 final size:21
Alignment explanation
Indices: 27872303--27872342 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27872293 AAATATTATG
* * *
27872303 AAATTTTTTATAATTTATAAA
1 AAATTTTATAAAAGTTATAAA
27872324 AAATTTTATAAAAGTTATA
1 AAATTTTATAAAAGTTATA
27872343 CATTATAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATTTTATAAAAGTTATAAA
Found at i:27882494 original size:31 final size:29
Alignment explanation
Indices: 27882425--27882497 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
27882415 ACAAAATACT
* *
27882425 AACATAAGTGACTAAAACGTAACATATCA
1 AACAAAAGTGACTAAAACGTAACATAGCA
* * *
27882454 AACACAAGTGACTAAAATGTAACCTGAGGCA
1 AACAAAAGTGACTAAAACGTAACAT-A-GCA
27882485 AACAAAAGTGACT
1 AACAAAAGTGACT
27882498 GTTTTTGTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 22 0.59
30 1 0.03
31 14 0.38
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (29 bp):
AACAAAAGTGACTAAAACGTAACATAGCA
Found at i:27889669 original size:267 final size:267
Alignment explanation
Indices: 27889194--27889728 Score: 1025
Period size: 267 Copynumber: 2.0 Consensus size: 267
27889184 GACTGAGTCT
27889194 TAAAATTGAGATATTTATGTGATCATATCACTATGTGCTCATGGGTTAGGATTGTATGGTGGAAA
1 TAAAATTGAGATATTTATGTGATCATATCACTATGTGCTCATGGGTTAGGATTGTATGGTGGAAA
27889259 ACGTGATAATCACCCCTTTAAACGGTTGATACTAAAACCAAACTGGGATTGGTGACGACTGGTTG
66 ACGTGATAATCACCCCTTTAAACGGTTGATACTAAAACCAAACTGGGATTGGTGACGACTGGTTG
*
27889324 GAAAAGGGTTCTGGGGAACCTTTTCACTGTGTTGGTGTGTTGGAGTATGGGTATATTGCATTGTG
131 GAAAAGGGTTCTGGGGAACCTTTTCACTGTGTTGGTGTGTTAGAGTATGGGTATATTGCATTGTG
27889389 CATGTGATTGAAACATGATTTGTAGTTACTTTTTGCGTTATGAATTGTTGTGATATTATATACTA
196 CATGTGATTGAAACATGATTTGTAGTTACTTTTTGCGTTATGAATTGTTGTGATATTATATACTA
27889454 GGTTGTA
261 GGTTGTA
*
27889461 TAAAATTGAGATATTTATGTGATCATATCACTATGTGCTCATGGGTTAGGATTGTATGGTGGAAG
1 TAAAATTGAGATATTTATGTGATCATATCACTATGTGCTCATGGGTTAGGATTGTATGGTGGAAA
27889526 ACGTGATAATCACCCCTTTAAACGGTTGATACTAAAACCAAACTGGGATTGGTGACGACTGGTTG
66 ACGTGATAATCACCCCTTTAAACGGTTGATACTAAAACCAAACTGGGATTGGTGACGACTGGTTG
* *
27889591 GAAAAGGGTTTTGGGGAACTTTTTCACTGTGTTGGTGTGTTAGAGTATGGGTATATTGCATTGTG
131 GAAAAGGGTTCTGGGGAACCTTTTCACTGTGTTGGTGTGTTAGAGTATGGGTATATTGCATTGTG
*
27889656 CATGTGATTGAAACATGATTTGTAGTTACTTTTTGCGTTATGAATTGTTTTGATATTATATACTA
196 CATGTGATTGAAACATGATTTGTAGTTACTTTTTGCGTTATGAATTGTTGTGATATTATATACTA
27889721 GGTTGTA
261 GGTTGTA
27889728 T
1 T
27889729 GTACTTTAGA
Statistics
Matches: 263, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
267 263 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (267 bp):
TAAAATTGAGATATTTATGTGATCATATCACTATGTGCTCATGGGTTAGGATTGTATGGTGGAAA
ACGTGATAATCACCCCTTTAAACGGTTGATACTAAAACCAAACTGGGATTGGTGACGACTGGTTG
GAAAAGGGTTCTGGGGAACCTTTTCACTGTGTTGGTGTGTTAGAGTATGGGTATATTGCATTGTG
CATGTGATTGAAACATGATTTGTAGTTACTTTTTGCGTTATGAATTGTTGTGATATTATATACTA
GGTTGTA
Found at i:27890897 original size:8 final size:7
Alignment explanation
Indices: 27890870--27890934 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
27890860 GATTGAGGAC
27890870 TGAAAAT
1 TGAAAAT
27890877 TCG-AAAT
1 T-GAAAAT
27890884 TGAAAAT
1 TGAAAAT
27890891 TGAAAAAT
1 TG-AAAAT
*
27890899 T-AAATT
1 TGAAAAT
*
27890905 TGAAGAT
1 TGAAAAT
27890912 TGAAAAT
1 TGAAAAT
27890919 AT-AAAAT
1 -TGAAAAT
*
27890926 TGGAAAT
1 TGAAAAT
27890933 TG
1 TG
27890935 GGGATTGAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
6 7 0.15
7 32 0.68
8 8 0.17
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (7 bp):
TGAAAAT
Found at i:27891410 original size:31 final size:30
Alignment explanation
Indices: 27891344--27891420 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
27891334 AAATAAAAGT
* *
27891344 ATATATATTCATATATAAAGATGGAAAATA
1 ATATATATTCATATATAAAGATGAAAAAAA
27891374 ATATATATT-ATATATATAAGA-GAAAAGAAA
1 ATATATATTCATATATA-AAGATGAAAA-AAA
*
27891404 ATTATATAACTCATATA
1 A-TATAT-ATTCATATA
27891421 ACCCGTATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 11 0.28
30 16 0.41
31 5 0.13
32 2 0.05
33 5 0.13
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.34
Consensus pattern (30 bp):
ATATATATTCATATATAAAGATGAAAAAAA
Found at i:27899628 original size:25 final size:25
Alignment explanation
Indices: 27899594--27899641 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
27899584 TAAATAAAAG
*
27899594 ATTTAATATA-ATATCTAGTATATGA
1 ATTTAATATATATATATA-TATATGA
27899619 ATTTAATATATATATATATATAT
1 ATTTAATATATATATATATATAT
27899642 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
ATTTAATATATATATATATATATGA
Found at i:27899631 original size:2 final size:2
Alignment explanation
Indices: 27899624--27899655 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27899614 TATGAATTTA
27899624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27899656 TTCTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27900527 original size:36 final size:37
Alignment explanation
Indices: 27900440--27900530 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 37
27900430 GCAAAACTGC
* *
27900440 TCATTGATGATATAAAATGCAAGAAGTGTAGACCAGA
1 TCATTGATGATATAAAATGAAAGAAGTGTAAACCAGA
* * ** * *
27900477 T-GTTAACCACATAAAATGAAAGAAGTGTAAACCA-T
1 TCATTGATGATATAAAATGAAAGAAGTGTAAACCAGA
27900512 TCATTGATGATATAAAATG
1 TCATTGATGATATAAAATG
27900531 TAAGCAATGC
Statistics
Matches: 40, Mismatches: 13, Indels: 3
0.71 0.23 0.05
Matches are distributed among these distances:
35 1 0.03
36 38 0.95
37 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (37 bp):
TCATTGATGATATAAAATGAAAGAAGTGTAAACCAGA
Found at i:27901112 original size:24 final size:23
Alignment explanation
Indices: 27901085--27901164 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
27901075 ACATTTTTTG
*
27901085 TGAACGTGTTCAATTATATGTTCA
1 TGAACATGTTCAATTA-ATGTTCA
** *
27901109 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCAATTAATGTTCA
* * *
27901132 TGAACACGTTCGATTAA-GTTAAA
1 TGAACATGTTCAATTAATGTT-CA
27901155 TGAACATGTT
1 TGAACATGTT
27901165 TGTGAACATT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 3 0.07
23 30 0.65
24 13 0.28
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (23 bp):
TGAACATGTTCAATTAATGTTCA
Found at i:27901135 original size:23 final size:23
Alignment explanation
Indices: 27901084--27901148 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
27901074 AACATTTTTT
* *
27901084 GTGAACGTGTTCAATTATATGTTC
1 GTGAACATGTTCGATTA-ATGTTC
* *
27901108 ATGAACATGTTCGTTTAATGTTC
1 GTGAACATGTTCGATTAATGTTC
*
27901131 GTGAACACGTTCGATTAA
1 GTGAACATGTTCGATTAA
27901149 GTTAAATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (23 bp):
GTGAACATGTTCGATTAATGTTC
Found at i:27901523 original size:16 final size:17
Alignment explanation
Indices: 27901487--27901524 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
27901477 AATGTTTTTT
* *
27901487 AAAAGTATTTTTGAGCC
1 AAAAGCATTTTTGAGCA
27901504 AAAAGCATTTTTGAG-A
1 AAAAGCATTTTTGAGCA
27901520 AAAAG
1 AAAAG
27901525 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (17 bp):
AAAAGCATTTTTGAGCA
Found at i:27901652 original size:18 final size:18
Alignment explanation
Indices: 27901629--27901668 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
27901619 TTTAGTAATA
*
27901629 TTTTTATCTCAAAAGTGT
1 TTTTTATCTCAAAAGTAT
27901647 TTTTTATCTCAAAAGTAT
1 TTTTTATCTCAAAAGTAT
27901665 TTTT
1 TTTT
27901669 GAGAAGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (18 bp):
TTTTTATCTCAAAAGTAT
Found at i:27902366 original size:20 final size:19
Alignment explanation
Indices: 27902341--27902395 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
27902331 TTAACTTTTT
27902341 AAAATTCAAAATAATA-TATA
1 AAAATT-AAAA-AATATTATA
*
27902361 AAAATTGAAAAATATTATA
1 AAAATTAAAAAATATTATA
*
27902380 AAAATAAAAAAATATT
1 AAAATTAAAAAATATT
27902396 TCATGTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.13
19 21 0.68
20 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATTAAAAAATATTATA
Found at i:27902743 original size:20 final size:21
Alignment explanation
Indices: 27902706--27902744 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
27902696 TTAATCTTTG
* *
27902706 TTACAATTTTTTTTATAATTT
1 TTACAATTTTTGTAATAATTT
27902727 TTAC-ATTTTTGTAATAAT
1 TTACAATTTTTGTAATAAT
27902745 ATTATTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TTACAATTTTTGTAATAATTT
Found at i:27902810 original size:22 final size:23
Alignment explanation
Indices: 27902760--27902811 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
27902750 TAATTTCACC
*
27902760 TAATTTCTTTTCAATTTTTTGTA
1 TAATTTATTTTCAATTTTTTGTA
*
27902783 T-CTTTATTTT-AATTTGTTT-TA
1 TAATTTATTTTCAATTT-TTTGTA
27902804 TAATTTAT
1 TAATTTAT
27902812 GTTTTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 8 0.33
22 15 0.62
23 1 0.04
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.67
Consensus pattern (23 bp):
TAATTTATTTTCAATTTTTTGTA
Found at i:27905807 original size:16 final size:16
Alignment explanation
Indices: 27905785--27905826 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
27905775 ACCGACCAGT
**
27905785 ACAAAATAAACCAAAA
1 ACAAAATAAAAAAAAA
*
27905801 CCAAAATAAAAAAAAA
1 ACAAAATAAAAAAAAA
27905817 ACAAAATAAA
1 ACAAAATAAA
27905827 TAATAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (16 bp):
ACAAAATAAAAAAAAA
Found at i:27907068 original size:28 final size:29
Alignment explanation
Indices: 27906988--27907086 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
27906978 CTTGAATATT
* ** *
27906988 TTTTTTTAAATTTGACCCCTTTATTTAGT-
1 TTTTTTCAAATTAAACCCCTTTATTT-TTA
*
27907017 TTTTTTAAAATTAAACCCCTTTATTTTTCA
1 TTTTTTCAAATTAAACCCCTTTATTTTT-A
* *
27907047 -TTTTTCAAATTAAA-TCTTTTATTTTTA
1 TTTTTTCAAATTAAACCCCTTTATTTTTA
27907074 TTCTTTTCAAATT
1 TT-TTTTCAAATT
27907087 TTCCCTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 12 0.20
29 46 0.78
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTTTCAAATTAAACCCCTTTATTTTTA
Found at i:27907142 original size:6 final size:5
Alignment explanation
Indices: 27907093--27907158 Score: 53
Period size: 5 Copynumber: 12.2 Consensus size: 5
27907083 AATTTTCCCT
* *
27907093 TTTTA TTTTT TTTTT TTTTAA TTTAATA TTTTA -TTTA CTTTTA TTATTA
1 TTTTA TTTTA TTTTA TTTT-A TTT--TA TTTTA TTTTA -TTTTA TT-TTA
27907142 TTTTA TTTTA TATTTA T
1 TTTTA TTTTA T-TTTA T
27907159 ACTTATATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 26 0.50
6 17 0.33
7 4 0.08
8 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:27911189 original size:23 final size:23
Alignment explanation
Indices: 27911158--27911201 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
27911148 ATTTATTAAA
27911158 AATAAATTTTAAACTGATTTTTT
1 AATAAATTTTAAACTGATTTTTT
* *
27911181 AATATATTTTTAACTGATTTT
1 AATAAATTTTAAACTGATTTT
27911202 ATTGTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (23 bp):
AATAAATTTTAAACTGATTTTTT
Found at i:27930574 original size:21 final size:21
Alignment explanation
Indices: 27930536--27930579 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
27930526 ATTTTAAATA
27930536 TAATTTATTTATTATTATTTT
1 TAATTTATTTATTATTATTTT
27930557 TAATATTATTTATT-TTATTTT
1 TAAT-TTATTTATTATTATTTT
27930578 TA
1 TA
27930580 CTCATAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TAATTTATTTATTATTATTTT
Found at i:27933496 original size:25 final size:23
Alignment explanation
Indices: 27933468--27933513 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
27933458 GTTGGATCCA
27933468 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
27933493 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
27933514 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:27935570 original size:17 final size:18
Alignment explanation
Indices: 27935548--27935593 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
27935538 ATAAATATAC
27935548 TAATTTTTTGAAA-TTTT
1 TAATTTTTTGAAATTTTT
*
27935565 TAATTTTTTAAAATTTTT
1 TAATTTTTTGAAATTTTT
*
27935583 TTATTTTTTGA
1 TAATTTTTTGA
27935594 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TAATTTTTTGAAATTTTT
Found at i:27935572 original size:8 final size:8
Alignment explanation
Indices: 27935548--27935599 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
27935538 ATAAATATAC
27935548 TAATTTTT
1 TAATTTTT
*
27935556 TGAAATTTT
1 T-AATTTTT
27935565 TAATTTTT
1 TAATTTTT
27935573 TAAAATTTTT
1 T--AATTTTT
*
27935583 TTATTTTT
1 TAATTTTT
*
27935591 TGATTTTT
1 TAATTTTT
27935599 T
1 T
27935600 TTTTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 22 0.59
9 7 0.19
10 8 0.22
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (8 bp):
TAATTTTT
Found at i:27935598 original size:17 final size:17
Alignment explanation
Indices: 27935550--27935606 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
27935540 AAATATACTA
* *
27935550 ATTTTTTGAAATTTTTA
1 ATTTTTTGAATTTTTTT
*
27935567 ATTTTTTAAAATTTTTTT
1 ATTTTTT-GAATTTTTTT
27935585 ATTTTTTG-ATTTTTTT
1 ATTTTTTGAATTTTTTT
27935601 -TTTTTT
1 ATTTTTT
27935607 TTAAAAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
17 7 0.20
18 14 0.40
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (17 bp):
ATTTTTTGAATTTTTTT
Found at i:27935607 original size:16 final size:16
Alignment explanation
Indices: 27935577--27935606 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27935567 ATTTTTTAAA
27935577 ATTTTTTTATTTTTTG
1 ATTTTTTTATTTTTTG
27935593 ATTTTTTT-TTTTTT
1 ATTTTTTTATTTTTT
27935607 TTAAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (16 bp):
ATTTTTTTATTTTTTG
Found at i:27941620 original size:25 final size:23
Alignment explanation
Indices: 27941592--27941637 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
27941582 GTTTGATCCA
27941592 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAA-TCT-AAAAAATAATTAG
*
27941617 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
27941638 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:27957747 original size:34 final size:34
Alignment explanation
Indices: 27957709--27957780 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
27957699 AGTAAACAAC
*
27957709 ATTTGGGTAAGGTAAAAGATAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
*
27957743 ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
27957777 ATTT
1 ATTT
27957781 TCGTTTAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (34 bp):
ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
Found at i:27960308 original size:55 final size:56
Alignment explanation
Indices: 27960235--27960343 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 56
27960225 CCTCGCAATG
** * *
27960235 ATAGTCTTGGTGGTCTTTCCACATATCAGATAATCCTTACGGACTTC-CACATAAC
1 ATAGTCTTGGTGAACTTTCCACATATCAGATAATCCTAACGAACTTCTCACATAAC
* * *
27960290 ATAGTCTTGTTGAACTTTCCACATATTAGATAGTCCTAACGAACTTCTCACATA
1 ATAGTCTTGGTGAACTTTCCACATATCAGATAATCCTAACGAACTTCTCACATA
27960344 TCAGATTGTC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
55 40 0.87
56 6 0.13
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (56 bp):
ATAGTCTTGGTGAACTTTCCACATATCAGATAATCCTAACGAACTTCTCACATAAC
Found at i:27960333 original size:29 final size:28
Alignment explanation
Indices: 27960251--27960452 Score: 171
Period size: 29 Copynumber: 7.2 Consensus size: 28
27960241 TTGGTGGTCT
* * *
27960251 TTCCACATATCAGATAATCCTTACGGAC
1 TTCCACATATCAGATAGTCCTCACGAAC
* * ***
27960279 TTCCACATA--ACATAGTCTTGTTGAAC
1 TTCCACATATCAGATAGTCCTCACGAAC
* *
27960305 TTTCCACATATTAGATAGTCCTAACGAAC
1 -TTCCACATATCAGATAGTCCTCACGAAC
* **
27960334 TTCTCACATATCAGATTGTCCTCACGGGC
1 TTC-CACATATCAGATAGTCCTCACGAAC
*
27960363 TTCCACATA--AGATAGTCCT-ATCGAAAT
1 TTCCACATATCAGATAGTCCTCA-CG-AAC
* *
27960390 TTCCACATATCAGATAGTCCTCATGGAC
1 TTCCACATATCAGATAGTCCTCACGAAC
*
27960418 TTCCCACATATCAGATAGTCCTCACAAAC
1 TT-CCACATATCAGATAGTCCTCACGAAC
27960447 TTCCAC
1 TTCCAC
27960453 GTATTCGGTA
Statistics
Matches: 137, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
25 1 0.01
26 21 0.15
27 18 0.13
28 25 0.18
29 71 0.52
30 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (28 bp):
TTCCACATATCAGATAGTCCTCACGAAC
Found at i:27960366 original size:84 final size:84
Alignment explanation
Indices: 27960253--27960452 Score: 256
Period size: 84 Copynumber: 2.4 Consensus size: 84
27960243 GGTGGTCTTT
* * * * * * *
27960253 CCACATATCAGATAATCCTTACGGACTTCCACATAACATAGTCTTGTTGAACTTTCCACATATTA
1 CCACATATCAGATAGTCCTCACGGACTTCCACATAACATAGTCCTATCGAAATTTCCACATATCA
27960318 GATAGTCCTAACGAACTTC
66 GATAGTCCTAACGAACTTC
* * * *
27960337 TCACATATCAGATTGTCCTCACGGGCTTCCACATAAGATAGTCCTATCGAAATTTCCACATATCA
1 CCACATATCAGATAGTCCTCACGGACTTCCACATAACATAGTCCTATCGAAATTTCCACATATCA
* * *
27960402 GATAGTCCTCATGGACTTC
66 GATAGTCCTAACGAACTTC
**
27960421 CCACATATCAGATAGTCCTCACAAACTTCCAC
1 CCACATATCAGATAGTCCTCACGGACTTCCAC
27960453 GTATTCGGTA
Statistics
Matches: 97, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 97 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (84 bp):
CCACATATCAGATAGTCCTCACGGACTTCCACATAACATAGTCCTATCGAAATTTCCACATATCA
GATAGTCCTAACGAACTTC
Found at i:27960376 original size:55 final size:57
Alignment explanation
Indices: 27960306--27960449 Score: 177
Period size: 55 Copynumber: 2.5 Consensus size: 57
27960296 TTGTTGAACT
* *
27960306 TTCCACATATTAGATAGTCCTAACGAACTTCT-CACATATCAGATTGTCCTCACGGGC
1 TTCCACATA-TAGATAGTCCTAACGAACTTCTCCACATATCAGATAGTCCTCACGGAC
* * *
27960363 TTCCACATA-AGATAGTCCTATCGAAATT-TCCACATATCAGATAGTCCTCATGGAC
1 TTCCACATATAGATAGTCCTAACGAACTTCTCCACATATCAGATAGTCCTCACGGAC
* *
27960418 TTCCCACATATCAGATAGTCCTCACAAACTTC
1 TT-CCACATAT-AGATAGTCCTAACGAACTTC
27960450 CACGTATTCG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
54 1 0.01
55 41 0.56
56 7 0.10
57 9 0.12
58 15 0.21
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (57 bp):
TTCCACATATAGATAGTCCTAACGAACTTCTCCACATATCAGATAGTCCTCACGGAC
Found at i:27963150 original size:22 final size:21
Alignment explanation
Indices: 27963125--27963168 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
27963115 GCCTCCTTAG
27963125 TCAATA-CAACATAACGACCATT
1 TCAATACCAAC-TAA-GACCATT
27963147 TCAATATCCAACTAAGACCATT
1 TCAATA-CCAACTAAGACCATT
27963169 CATTATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 3 0.15
24 4 0.20
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (21 bp):
TCAATACCAACTAAGACCATT
Found at i:27971058 original size:16 final size:16
Alignment explanation
Indices: 27971046--27971080 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27971036 GTATATTTAT
27971046 ATAAAACTATATTAAA
1 ATAAAACTATATTAAA
*
27971062 ATAAAATTATATTAAA
1 ATAAAACTATATTAAA
27971078 ATA
1 ATA
27971081 TTAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAAACTATATTAAA
Found at i:27972637 original size:31 final size:31
Alignment explanation
Indices: 27972602--27972664 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
27972592 AATTATCATA
*
27972602 AAGTCTGATCCAAACCTTTTTATAAAAATAC
1 AAGTCAGATCCAAACCTTTTTATAAAAATAC
27972633 AAGTCAGATCCAAACCTTTTTATAAAAATAC
1 AAGTCAGATCCAAACCTTTTTATAAAAATAC
27972664 A
1 A
27972665 TGGACAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.30
Consensus pattern (31 bp):
AAGTCAGATCCAAACCTTTTTATAAAAATAC
Found at i:27982910 original size:18 final size:16
Alignment explanation
Indices: 27982878--27982921 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
27982868 ATGGGATGAG
27982878 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
27982894 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
27982908 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
27982922 ACCTAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:27983871 original size:31 final size:31
Alignment explanation
Indices: 27983836--27983930 Score: 127
Period size: 31 Copynumber: 3.1 Consensus size: 31
27983826 AACAACCTAG
27983836 TGACTTAAATAAAAACTTTCGAATAATTCAA
1 TGACTTAAATAAAAACTTTCGAATAATTCAA
* * *
27983867 TGACTTCAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTCGAATAATTCAA
* * * *
27983898 TGCCTTAAATGAAAACTTTCAAATTATTCAA
1 TGACTTAAATAAAAACTTTCGAATAATTCAA
27983929 TG
1 TG
27983931 GCCATTTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAATAATTCAA
Found at i:27986057 original size:23 final size:23
Alignment explanation
Indices: 27986023--27986089 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
27986013 TTAGCGCCTT
27986023 ACTG-TTCAGCACTGTGTGTGCTA
1 ACTGATTC-GCACTGTGTGTGCTA
* * *
27986046 ACTGATTCGCACTATATGTGCTT
1 ACTGATTCGCACTGTGTGTGCTA
*
27986069 ACTGATTTGCACTGTGTGTGC
1 ACTGATTCGCACTGTGTGTGC
27986090 CTACTGTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 34 0.92
24 3 0.08
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (23 bp):
ACTGATTCGCACTGTGTGTGCTA
Found at i:27996250 original size:2 final size:2
Alignment explanation
Indices: 27996243--27996288 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
27996233 CTTCCCCAGG
* *
27996243 GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27996285 GA GA
1 GA GA
27996289 AGCTCTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28003795 original size:7 final size:7
Alignment explanation
Indices: 28003783--28003815 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28003773 CTATTGGTAA
28003783 TGGTGAG
1 TGGTGAG
28003790 TGGTGAG
1 TGGTGAG
28003797 TGGTGAG
1 TGGTGAG
28003804 TGGTGAG
1 TGGTGAG
28003811 TGGTG
1 TGGTG
28003816 TTGGTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.58, T:0.30
Consensus pattern (7 bp):
TGGTGAG
Found at i:28009576 original size:96 final size:96
Alignment explanation
Indices: 28009460--28009640 Score: 308
Period size: 96 Copynumber: 1.9 Consensus size: 96
28009450 GTCAATGAGG
* *
28009460 CACTGGGTGCCAAATTACTTCGGTTTAACCGATGAGACACTGGGTGTCAACCTTATTATAGCGTT
1 CACTGGGTGCCAAATTACTTCAGTTTAACCGATGAGACACTGGGTGTCAACCTTATTATAGCATT
*
28009525 GGGGCGCGTTTTATTACTTCAGACGATAAGA
66 GGGGCGCATTTTATTACTTCAGACGATAAGA
* **
28009556 CACTGGGTGCCGAATTACTTCAGTTTAATTGATGAGACACTGGGTGTCAACCTTATTATAGCATT
1 CACTGGGTGCCAAATTACTTCAGTTTAACCGATGAGACACTGGGTGTCAACCTTATTATAGCATT
28009621 GGGGCGCATTTTATTACTTC
66 GGGGCGCATTTTATTACTTC
28009641 GGATGTATCC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (96 bp):
CACTGGGTGCCAAATTACTTCAGTTTAACCGATGAGACACTGGGTGTCAACCTTATTATAGCATT
GGGGCGCATTTTATTACTTCAGACGATAAGA
Found at i:28010676 original size:21 final size:21
Alignment explanation
Indices: 28010652--28010698 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
28010642 CTTGGGAAAG
* *
28010652 TTCTACTGATACAAGTGTA-AC
1 TTCTACCGAAACAAGT-TATAC
28010673 TTCTACCGAAACAAGTTATAC
1 TTCTACCGAAACAAGTTATAC
28010694 TTCTA
1 TTCTA
28010699 TCGATACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (21 bp):
TTCTACCGAAACAAGTTATAC
Found at i:28019931 original size:52 final size:52
Alignment explanation
Indices: 28019852--28020037 Score: 309
Period size: 52 Copynumber: 3.6 Consensus size: 52
28019842 TAAATGAAAA
* * *
28019852 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
* *
28019904 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGAATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
* *
28019956 AGGTCCGATAACTATGTGTCATTGTGAGTATATGATTCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
28020008 AGGTCCGATGACTATGTGTCATCGTGAGTA
1 AGGTCCGATGACTATGTGTCATCGTGAGTA
28020038 CTAAATGAAA
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 123 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTATG
Found at i:28028375 original size:3 final size:3
Alignment explanation
Indices: 28028369--28028393 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28028359 CTTCTTTTTC
28028369 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
28028394 GTAGTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28030738 original size:22 final size:23
Alignment explanation
Indices: 28030697--28030740 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
28030687 TTGGATTGGT
28030697 ATAATATAAATTTAAAATTTAAA
1 ATAATATAAATTTAAAATTTAAA
*
28030720 ATAATATAAA-TTAATATTTAA
1 ATAATATAAATTTAAAATTTAA
28030741 TTTATTCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATATAAATTTAAAATTTAAA
Found at i:28030780 original size:23 final size:24
Alignment explanation
Indices: 28030753--28030799 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28030743 TATTCGAATT
*
28030753 ATTTAAATT-ATTTAAATTTAAAA
1 ATTTAAATTGATTCAAATTTAAAA
* *
28030776 ATTTAATTTGATTCGAATTTAAAA
1 ATTTAAATTGATTCAAATTTAAAA
28030800 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
ATTTAAATTGATTCAAATTTAAAA
Found at i:28038975 original size:18 final size:18
Alignment explanation
Indices: 28038940--28038982 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
28038930 AATAAATATA
28038940 AATACAATTTAAATTTAAT
1 AATA-AATTTAAATTTAAT
28038959 AATAAATTGTAAA-TTAAT
1 AATAAATT-TAAATTTAAT
28038977 AA-AAAT
1 AATAAAT
28038983 AAATAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTTAAATTTAAT
Found at i:28041852 original size:19 final size:19
Alignment explanation
Indices: 28041828--28041870 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28041818 AAACATAAAT
28041828 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
28041847 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
28041866 TAAAT
1 TAAAT
28041871 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:28043412 original size:16 final size:16
Alignment explanation
Indices: 28043373--28043420 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 16
28043363 TTTCCTAGAC
28043373 AAATAAAAT--AAAT-
1 AAATAAAATAGAAATA
28043386 AAATAAAATAGAAA-A
1 AAATAAAATAGAAATA
28043401 AAATAGAAATAGAAATA
1 AAATA-AAATAGAAATA
28043418 AAA
1 AAA
28043421 ATAATTGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.30
15 8 0.27
16 9 0.30
17 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAAATAGAAATA
Found at i:28043422 original size:18 final size:17
Alignment explanation
Indices: 28043373--28043424 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
28043363 TTTCCTAGAC
28043373 AAATA-AAATAAATAAATA
1 AAATAGAAAT-AA-AAATA
28043391 AAATAG-AA-AAAAATA
1 AAATAGAAATAAAAATA
28043406 GAAATAGAAATAAAAATA
1 -AAATAGAAATAAAAATA
28043424 A
1 A
28043425 TTGGGTTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.17
16 8 0.27
17 3 0.10
18 14 0.47
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AAATAGAAATAAAAATA
Found at i:28044619 original size:21 final size:21
Alignment explanation
Indices: 28044593--28044633 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28044583 ATAGATGCCT
28044593 CAGTTTGCTTTTGAAAATCTG
1 CAGTTTGCTTTTGAAAATCTG
28044614 CAGTTTGCTTTTGAAAATCT
1 CAGTTTGCTTTTGAAAATCT
28044634 ATAGATTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCTG
Found at i:28044642 original size:21 final size:21
Alignment explanation
Indices: 28044597--28044643 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28044587 ATGCCTCAGT
* *
28044597 TTGCTTTTGAAAATCTGCAGT
1 TTGCTTTTGAAAATCTACAGA
*
28044618 TTGCTTTTGAAAATCTATAGA
1 TTGCTTTTGAAAATCTACAGA
28044639 TTGCT
1 TTGCT
28044644 GCTGAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TTGCTTTTGAAAATCTACAGA
Found at i:28051268 original size:40 final size:40
Alignment explanation
Indices: 28051224--28051299 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
28051214 CATAAGTCTT
28051224 CTTTAATCATATTCTCATTCTCATCCCGAGACATGAGTTC
1 CTTTAATCATATTCTCATTCTCATCCCGAGACATGAGTTC
* *
28051264 CTTTAATCATATTCTCATTCTTATCTCGAGACATGA
1 CTTTAATCATATTCTCATTCTCATCCCGAGACATGA
28051300 ATCTTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.39
Consensus pattern (40 bp):
CTTTAATCATATTCTCATTCTCATCCCGAGACATGAGTTC
Found at i:28058857 original size:21 final size:21
Alignment explanation
Indices: 28058819--28058858 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28058809 GGTTGACTCC
*
28058819 AAGGACAATAAAAGAAAGAGG
1 AAGGACAATAAAAAAAAGAGG
28058840 AAGGACAA-AAAGAAAAAGA
1 AAGGACAATAAA-AAAAAGA
28058859 AGCACAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.03
Consensus pattern (21 bp):
AAGGACAATAAAAAAAAGAGG
Found at i:28058860 original size:18 final size:19
Alignment explanation
Indices: 28058828--28058866 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28058818 CAAGGACAAT
* *
28058828 AAAAGAAAGAGGAAGGACA
1 AAAAGAAAGAAGAAGCACA
28058847 AAAAGAAA-AAGAAGCACA
1 AAAAGAAAGAAGAAGCACA
28058865 AA
1 AA
28058867 GGGGAGCGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAAAGAAGAAGCACA
Found at i:28059010 original size:17 final size:16
Alignment explanation
Indices: 28058966--28059010 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
28058956 GCATGCATAT
*
28058966 CATTTTATTGTCATTG
1 CATTTTATTTTCATTG
*
28058982 CATTTTAGTTTTCGTTG
1 CATTTTA-TTTTCATTG
28058999 CATTTTCATTTT
1 CATTTT-ATTTT
28059011 TAGTTCGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 17 0.68
18 1 0.04
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (16 bp):
CATTTTATTTTCATTG
Found at i:28062521 original size:21 final size:20
Alignment explanation
Indices: 28062492--28062530 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28062482 ATCATATTAG
*
28062492 GAGAACAAATATTATCCTAAA
1 GAGAACAAAGA-TATCCTAAA
*
28062513 GAGATCAAAGATATCCTA
1 GAGAACAAAGATATCCTA
28062531 TAAGGGTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (20 bp):
GAGAACAAAGATATCCTAAA
Found at i:28077713 original size:240 final size:238
Alignment explanation
Indices: 28077270--28077749 Score: 820
Period size: 240 Copynumber: 2.0 Consensus size: 238
28077260 TAAAAAATGC
*
28077270 CTCCAATTTACTTGTAACTTGACCAAGACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
1 CTCCAATTTACTTGTAACTTGACCAAAACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
*
28077335 AAAGATTTTTATTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACTTTCAA
66 AAAGATTTTTATTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACCTTCAA
* *
28077400 TTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAAAATTTACTAATGAATTAAGA
131 TTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCT--AAAAAGTTACTAATGAATTAACA
28077465 GAAATATTAAAATTCATCTACAACTTATTTGATCTTTTATCATTA
194 GAAATATTAAAATTCATCTACAACTTATTTGATCTTTTATCATTA
* * *
28077510 CTCCGATTTATTTGTAACTTGACTAAAACGTGTTCACCAAACTTATCTAATTT-AAACTTAAATT
1 CTCCAATTTACTTGTAACTTGACCAAAACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
*
28077574 AAAGATTTTTATTCCTAATAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCAA
66 AAAGATTTTTATTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACCTTCAA
28077639 TTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAAAAAGCCT-AAAAGTTACTAATGAATTAA
131 TTCTTAAAATTAATTCTATTTTAGAATCCT---AAAAAAA-CCTAAAAAGTTACTAATGAATTAA
28077703 CAGAAATATTAAAATTCATCTACAACTTATTTGATCTTTTATCATTA
192 CAGAAATATTAAAATTCATCTACAACTTATTTGATCTTTTATCATTA
28077750 TTATGATCTT
Statistics
Matches: 228, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
239 104 0.46
240 114 0.50
242 7 0.03
243 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (238 bp):
CTCCAATTTACTTGTAACTTGACCAAAACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
AAAGATTTTTATTCCTAATAAGAACCCTAAAAGATACCTAAATAATTCTAGTAAAATACCTTCAA
TTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAAGTTACTAATGAATTAACAGA
AATATTAAAATTCATCTACAACTTATTTGATCTTTTATCATTA
Found at i:28078920 original size:96 final size:96
Alignment explanation
Indices: 28078787--28078965 Score: 270
Period size: 96 Copynumber: 1.9 Consensus size: 96
28078777 TGATTAAACA
*
28078787 AAAATCACTACTTTACTTAAAAATCCAAAATTTTATTTTGAAATAGTT-AAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
28078851 GTTAAAAATCTAAACTTTCTCTTTTTTGAAG
66 GTTAAAAATCTAAACTTTCTCTTTTTTGAAG
* * * ** *
28078882 AAAATCACTATTTTTATTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATTTAAATTT
1 AAAATCACTA-CTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
*
28078947 TGTTAAAAGTCTAAACTTT
65 TGTTAAAAATCTAAACTTT
28078966 TTCTCTAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 10 0.14
96 34 0.46
97 30 0.41
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (96 bp):
AAAATCACTACTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATCTAAACTTTCTCTTTTTTGAAG
Found at i:28079399 original size:159 final size:154
Alignment explanation
Indices: 28078872--28079403 Score: 596
Period size: 156 Copynumber: 3.4 Consensus size: 154
28078862 AAACTTTCTC
* *
28078872 TTTTTTGAAGAAAATCACTATTTTTA-TTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAA
1 TTTTTTAAAGAAAATCACTATTTTTACTTAAAAAAT-CAAACTTTTATTTCGAAATAGTTAAAAA
** ** * *
28078936 AATTTAAATTTTGTTAAAAGTCTAAACTTTTTCTCTAAAATAACTAAGAAAACAGATTTTTATTT
65 AATAAAAAAATTGTTAAAAATCTAAACTTTTTCTCAAAAATAACTAAGAAAACAGATTTTTA---
*
28079001 TTTTTTAAAAAATATAAGCTTTTTCTGTTT
127 -TTTTTAAAAAATATAAGC-TTTTCTTTTT
* * *
28079031 TTTTTTAAAGAAAATCACTATTTTTACTTAAAATATC-CA-TTTT-TTTCAAAATAGTTAAAAAA
1 TTTTTTAAAGAAAATCACTATTTTTACTTAAAAAATCAAACTTTTATTTCGAAATAGTTAAAAAA
* ** * *
28079093 ATCAAAACTTTGTTAAAAATCTAAACTTTTTCTCGAAAATGACTAAGAAAACAGATTTTTATTTT
66 ATAAAAAAATTGTTAAAAATCTAAACTTTTTCTCAAAAATAACTAAGAAAACAGATTTTTATTTT
*
28079158 TAAAAAATATAAGC-TTT-TTCTT
131 TAAAAAATATAAGCTTTTCTTTTT
* * ** *
28079180 TTTTTAAAAAAAAATCACTAGATTT-CTTAAAAATTCAAACTTTTATTTCGAAATAGTT-AAAAA
1 TTTTTTAAAGAAAATCACTATTTTTACTTAAAAAATCAAACTTTTATTTCGAAATAGTTAAAAAA
* ** * *
28079243 ATAAAAAAATTGTTAAAAATCTAAACTTTCTCTCAAATAACTAAAAAAAAAAACAGAATTTTATT
66 ATAAAAAAATTGTTAAAAATCTAAACTTTTTCTCAAA-AA-TAACTAAGAAAACAGATTTTTATT
*
28079308 TTT-AAAAATATAAACTTTCTCCTTTTT
129 TTTAAAAAATATAAGCTTT-T-CTTTTT
* * *
28079335 TTTTTTAAAGAAAATCATTATTTTTACTTCAAAAAAATCAAAATTTTTATTTCGAAATTGTTAAA
1 TTTTTTAAAGAAAATCACTATTTTTACTT--AAAAAATC-AAACTTTTATTTCGAAATAGTTAAA
28079400 AAAA
63 AAAA
28079404 ACAAAAACTT
Statistics
Matches: 317, Mismatches: 41, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
148 9 0.03
149 25 0.08
150 44 0.14
151 25 0.08
152 42 0.13
153 1 0.00
155 24 0.08
156 76 0.24
157 4 0.01
158 8 0.03
159 46 0.15
160 13 0.04
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.42
Consensus pattern (154 bp):
TTTTTTAAAGAAAATCACTATTTTTACTTAAAAAATCAAACTTTTATTTCGAAATAGTTAAAAAA
ATAAAAAAATTGTTAAAAATCTAAACTTTTTCTCAAAAATAACTAAGAAAACAGATTTTTATTTT
TAAAAAATATAAGCTTTTCTTTTT
Found at i:28079825 original size:3 final size:3
Alignment explanation
Indices: 28079817--28079870 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
28079807 TGAAACCTTA
* * * *
28079817 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAG AAT AAT GAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28079865 AAT AAT
1 AAT AAT
28079871 TTGGGGCCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:28079905 original size:11 final size:11
Alignment explanation
Indices: 28079889--28079913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28079879 CAAAAAGCCC
28079889 AAAGAAAAATA
1 AAAGAAAAATA
28079900 AAAGAAAAATA
1 AAAGAAAAATA
28079911 AAA
1 AAA
28079914 ACCTCTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:28080282 original size:42 final size:42
Alignment explanation
Indices: 28080236--28080511 Score: 403
Period size: 42 Copynumber: 6.6 Consensus size: 42
28080226 TCTACGCCTA
* *
28080236 GGCCTCTAAATGCAATAAAAAGTAAATGGGCCTCCACACCTG
1 GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * *
28080278 GGCCTCTAAATACAATGAAAAGTAAATGGACCTCCACACCTG
1 GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
*
28080320 GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACTTG
1 GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* ** *
28080362 GGCCTCTAAATGCAAAT-AAAAGTAAATGAACCTTCACACCTG
1 GGCCTCTGAATGC-AATGAAAAGTAAATGGGCCTCCACACCTG
*
28080404 GGCCTTTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
1 GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
*
28080446 GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACTTG
1 GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
*
28080488 GACCTCTGAATGCGAA-GAAAAGTA
1 GGCCTCTGAATGC-AATGAAAAGTA
28080512 CACCTGGGCC
Statistics
Matches: 211, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 3 0.01
42 203 0.96
43 5 0.02
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (42 bp):
GGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
Found at i:28080372 original size:126 final size:126
Alignment explanation
Indices: 28080236--28080830 Score: 757
Period size: 126 Copynumber: 4.8 Consensus size: 126
28080226 TCTACGCCTA
* *
28080236 GGCCTCTAAATGCAATAAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATACAATGAAAAGT
1 GGCCTCTAAATGCAATAAAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
*
28080301 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACTTG
66 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
** * *
28080362 GGCCTCTAAATGCAA-ATAAAAGTAAATGAACCTTCACACCTGGGCCTTTGAATGCAATGAAAAG
1 GGCCTCTAAATGCAATA-AAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAAAG
* *
28080426 TAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACTTG
65 TAAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * * * * *
28080488 GACCTCTGAATGC-----GAAG-AAA--AG--T--ACACCTGGGCCTCTGAATGTAATGAAATGT
1 GGCCTCTAAATGCAATAAAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
* * *
28080541 AAATGGGCCTCCACACCTGGGCCTTTGAATGCAATGAAAAGTAAATGAGCCTCCACACCTG
66 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * * * * *
28080602 GGCCTTTGAATGCAATGAAAAGTAAATGGGCCTTCACATCTGGGCCTCTGAATGCGATGAAAAGT
1 GGCCTCTAAATGCAATAAAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
* * * *
28080667 AAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTATATGGACCTCCACGCCTG
66 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
* * * * * *
28080728 GTCTTCTAAATGCAATGAAAAGTAAACGGGCCTCCACACTTGGGCCTCTGAATGCGATGAAAAGT
1 GGCCTCTAAATGCAATAAAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
* * *
28080793 AAATGGACCTCCACACTTAGGCCTCTAAATGCAATGAA
66 AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAA
28080831 TGCTTTCCTT
Statistics
Matches: 414, Mismatches: 42, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
114 96 0.23
116 1 0.00
118 1 0.00
119 3 0.01
120 6 0.01
121 3 0.01
122 1 0.00
124 1 0.00
125 1 0.00
126 301 0.73
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (126 bp):
GGCCTCTAAATGCAATAAAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAAAGT
AAATGGACCTCCACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
Found at i:28080522 original size:72 final size:72
Alignment explanation
Indices: 28080439--28080583 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 72
28080429 ATGGGCCTCC
*
28080439 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACTTGGACCTCTGAATGCGAA
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGACCTCTGAATGC-AA
28080504 -GAAAAGT
65 TGAAAAGT
* * * *
28080511 ACACCTGGGCCTCTGAATGTAATGAAATGTAAATGGGCCTCCACACCTGGGCCTTTGAATGCAAT
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGACCTCTGAATGCAAT
28080576 GAAAAGT
66 GAAAAGT
28080583 A
1 A
28080584 AATGAGCCTC
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
71 2 0.03
72 65 0.97
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (72 bp):
ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGACCTCTGAATGCAAT
GAAAAGT
Found at i:28080560 original size:42 final size:42
Alignment explanation
Indices: 28080511--28080830 Score: 433
Period size: 42 Copynumber: 7.6 Consensus size: 42
28080501 GAAGAAAAGT
* *
28080511 ACACCTGGGCCTCTGAATGTAATGAAATGTAAATGGGCCTCC
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
* *
28080553 ACACCTGGGCCTTTGAATGCAATGAAAAGTAAATGAGCCTCC
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
* *
28080595 ACACCTGGGCCTTTGAATGCAATGAAAAGTAAATGGGCCTTC
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
* * *
28080637 ACATCTGGGCCTCTGAATGCGATGAAAAGTAAATGGACCTCC
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
* * *
28080679 ACACCTGGGCCTCTAAATGCAATGAAAAGTATATGGACCTCC
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
* * * * *
28080721 ACGCCTGGTCTTCTAAATGCAATGAAAAGTAAACGGGCCTCC
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
* * *
28080763 ACACTTGGGCCTCTGAATGCGATGAAAAGTAAATGGACCTCC
1 ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
* * *
28080805 ACACTTAGGCCTCTAAATGCAATGAA
1 ACACCTGGGCCTCTGAATGCAATGAA
28080831 TGCTTTCCTT
Statistics
Matches: 246, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 246 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (42 bp):
ACACCTGGGCCTCTGAATGCAATGAAAAGTAAATGGGCCTCC
Found at i:28080700 original size:240 final size:240
Alignment explanation
Indices: 28080271--28080722 Score: 717
Period size: 240 Copynumber: 1.9 Consensus size: 240
28080261 ATGGGCCTCC
28080271 ACACCTGGGCCTCTAAATACAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTGAATGCAAT
1 ACACCTGGGCCTCTAAATACAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTGAATGCAAT
* *
28080336 GAAAAGTAAATGGGCCTCCACACTTGGGCCTCTAAATGCAAATAAAAGTAAATGAACCTTCACAC
66 GAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAAATAAAAGTAAATGAACCTTCACAC
* * *
28080401 CTGGGCCTTTGAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGCAATGAAA
131 CTGGGCCTCTGAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAA
*
28080466 AGTAAATGGGCCTCCACACTTGGACCTCTGAATGCGAAGAAAAGT
196 AGTAAATGGACCTCCACACTTGGACCTCTGAATGCGAAGAAAAGT
* ** * * *
28080511 ACACCTGGGCCTCTGAATGTAATGAAATGTAAATGGGCCTCCACACCTGGGCCTTTGAATGCAAT
1 ACACCTGGGCCTCTAAATACAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTGAATGCAAT
* * **
28080576 GAAAAGTAAATGAGCCTCCACACCTGGGCCTTTGAATGC-AATGAAAAGTAAATGGGCCTTCACA
66 GAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAAAT-AAAAGTAAATGAACCTTCACA
* *
28080640 TCTGGGCCTCTGAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
130 CCTGGGCCTCTGAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
*
28080705 AAGTATATGGACCTCCAC
195 AAGTAAATGGACCTCCAC
28080723 GCCTGGTCTT
Statistics
Matches: 192, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
239 3 0.02
240 189 0.98
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (240 bp):
ACACCTGGGCCTCTAAATACAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTGAATGCAAT
GAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAAATAAAAGTAAATGAACCTTCACAC
CTGGGCCTCTGAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAA
AGTAAATGGACCTCCACACTTGGACCTCTGAATGCGAAGAAAAGT
Found at i:28089324 original size:4 final size:4
Alignment explanation
Indices: 28089293--28089339 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
28089283 TAAATAAACA
* * *
28089293 AATG AGTG AATG AGTG AATG AGTG AATG AATG AATG AATG AATG AAT
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AAT
28089340 ATGGGGCACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:28095911 original size:234 final size:237
Alignment explanation
Indices: 28095453--28095924 Score: 688
Period size: 234 Copynumber: 2.0 Consensus size: 237
28095443 AATGCCTCAA
*
28095453 ATTTACTTGTAACTTGACTAAGACGTGTTCACTAAACTTATCTAATTTAAAACTTAAATTAAAGA
1 ATTTACTTGTAACTTGACTAAGACGTGTTCAC---ACTTATCTAATGTAAAACTTAAATTAAAGA
* *
28095518 TTTTTACTCCTATAAGAAGACCCTAAAAAAAATACCTAAATAATTCTAGTAAAATACTTTCAATT
63 TTTTTACTCCTATAAGAAGACCCTAAAAAAAATA-C-AAATAATTCTAGTAAAATACCTCCAATT
*
28095583 CTTAAAATTAATTCTATTTTAGAATCCTAAAAAAGACCAAAAAAAATTACTAATGAATTAAGAGA
126 CTTAAAATTAATTCTATTTTAGAATCCTAAAAAAAACC-AAAAAAATTACTAATGAATTAAGAGA
*
28095648 AATATTAAAATTCATCTATAACTTATTCGATCTTTTATCATTACTCCG
190 AATATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTACTCCG
28095696 ATTTACTTGTAACTTGACTAA-ACCGTGTTCAC-CGTTATCTAATGTAAAACTTAAATTAAAGAT
1 ATTTACTTGTAACTTGACTAAGA-CGTGTTCACAC-TTATCTAATGTAAAACTTAAATTAAAGAT
* * ***
28095759 TTTTATTCCTAT-ATAAGAACCCT-AAAGGTATA-AAATAATTCTAGTAAAATACCTCCAATTCT
64 TTTTACTCCTATAAGAAG-ACCCTAAAAAAAATACAAATAATTCTAGTAAAATACCTCCAATTCT
* * *
28095821 T-AAATTAATTTTATTTTAGAATCCTAAAAAAAAGCC-TAAAAGTTACTAATGAATTAAGAGAAA
128 TAAAATTAATTCTATTTTAGAATCCTAAAAAAAA-CCAAAAAAATTACTAATGAATTAAGAGAAA
28095884 TATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
192 TATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
28095925 TTATGATCTT
Statistics
Matches: 212, Mismatches: 13, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
234 65 0.31
235 30 0.14
236 31 0.15
239 11 0.05
240 44 0.21
242 1 0.00
243 30 0.14
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (237 bp):
ATTTACTTGTAACTTGACTAAGACGTGTTCACACTTATCTAATGTAAAACTTAAATTAAAGATTT
TTACTCCTATAAGAAGACCCTAAAAAAAATACAAATAATTCTAGTAAAATACCTCCAATTCTTAA
AATTAATTCTATTTTAGAATCCTAAAAAAAACCAAAAAAATTACTAATGAATTAAGAGAAATATT
AAAATTCATCTACAACTTATTCGATCTTTTATCATTACTCCG
Found at i:28096334 original size:16 final size:17
Alignment explanation
Indices: 28096315--28096367 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
28096305 ACCTAAATAC
28096315 AAATGTAAAAAAATAT-
1 AAATGTAAAAAAATATG
* * *
28096331 AAATATAAATAAACATG
1 AAATGTAAAAAAATATG
*
28096348 AAA-GTAAACAAATATG
1 AAATGTAAAAAAATATG
28096364 AAAT
1 AAAT
28096368 AATAATAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 26 0.90
17 3 0.10
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.23
Consensus pattern (17 bp):
AAATGTAAAAAAATATG
Found at i:28097300 original size:151 final size:147
Alignment explanation
Indices: 28096944--28097301 Score: 459
Period size: 151 Copynumber: 2.4 Consensus size: 147
28096934 TTGATTAGAC
* * *
28096944 AAAAATCACTACTTTACTTAAAAATCTAAAATTTTATTTTGAAATAGTTAAAAAAAAAT-AAAAC
1 AAAAATCACTATTTTACTTAAAATTC-AAAATTTTATTTCGAAATAGTT--AAAAAAATCAAAAC
* * * * *
28097008 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAATAGATTTTATTTTTTAAAAATC
63 CTTGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTATTTTTTAAAAATA
*
28097073 TAAACTTTCTCTTTTTTTAA
128 TAAACTTTCTCTTTCTTTAA
* * *
28097093 GAATATCACTATTTTACTTAAAAATTCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACCT
1 AAAAATCACTATTTTACTT-AAAATTCAAAATTTTATTTCGAAATAGTTAAAAAAATCAAAACCT
* *
28097158 TGTTAAAAATCTAATCTTTTTCTCT-AAATAACTAAGAAAACAGATTTTTATTTTTTTAAAAAAA
65 TGTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGA-TTTTA-TTTTTT--AAAAA
* *
28097222 TATAAGCTTTTTCTTTCTTTAA
126 TATAAACTTTCTCTTTCTTTAA
* *
28097244 AAAAATCACTATTTTTCCTTAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATC
1 AAAAATCACTA-TTTTACTTAAAATTCAAAATTTTATTTCGAAATAGTTAAAAAAATC
28097302 TAAATTTTTT
Statistics
Matches: 182, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
147 25 0.14
148 33 0.18
149 42 0.23
150 6 0.03
151 69 0.38
152 7 0.04
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (147 bp):
AAAAATCACTATTTTACTTAAAATTCAAAATTTTATTTCGAAATAGTTAAAAAAATCAAAACCTT
GTTAAAAATCTAAACTTTTTCTCTAAAATAACTAAAAAAACAGATTTTATTTTTTAAAAATATAA
ACTTTCTCTTTCTTTAA
Found at i:28097322 original size:133 final size:135
Alignment explanation
Indices: 28097162--28097443 Score: 382
Period size: 133 Copynumber: 2.1 Consensus size: 135
28097152 AAACCTTGTT
*
28097162 AAAAATCT-AATCTTTTTCTCTAAATAACTAAGAAAACAGATTTTTATTTTT-TTAAAAAAATAT
1 AAAAATCTAAATCTTTTTCTCAAAATAACTAAGAAAACAGATTTTTATTTTTCTT---AAAATAT
* *
28097225 AAGCTTTTTCTTTCT-TTAAA-AAAATCACTATTTTTCCT-TAAAATTCAAACTTTTATTTCGAA
63 AAGCTTTTTCTTTCTGTTAAAGAAAATCACTA-TTTTACTGAAAAATTCAAACTTTTATTTCGAA
28097287 ATAGTT-AA
127 ATAGTTAAA
* *
28097295 AAAAATCTAAATTTTTTTC-CAAAATAACTAAGAAAATAGATTTTTATTTTTCTTAAAATATAAG
1 AAAAATCTAAATCTTTTTCTCAAAATAACTAAGAAAACAGATTTTTATTTTTCTTAAAATATAAG
* * * * *
28097359 TTTTTTTTTTTTGTTAAAGAAAATCACTATTTTACTGAAAAATTTAAACTTTTATTTTGAAATAG
66 CTTTTTCTTTCTGTTAAAGAAAATCACTATTTTACTGAAAAATTCAAACTTTTATTTCGAAATAG
28097424 TTAAA
131 TTAAA
28097429 AAAAATCTAAA-CTTT
1 AAAAATCTAAATCTTT
28097444 GTTAAAAATC
Statistics
Matches: 132, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
131 19 0.14
132 11 0.08
133 78 0.59
134 24 0.18
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.44
Consensus pattern (135 bp):
AAAAATCTAAATCTTTTTCTCAAAATAACTAAGAAAACAGATTTTTATTTTTCTTAAAATATAAG
CTTTTTCTTTCTGTTAAAGAAAATCACTATTTTACTGAAAAATTCAAACTTTTATTTCGAAATAG
TTAAA
Found at i:28097566 original size:153 final size:152
Alignment explanation
Indices: 28097295--28097596 Score: 371
Period size: 153 Copynumber: 2.0 Consensus size: 152
28097285 AAATAGTTAA
* * * * * *
28097295 AAAAATCTAAATTTTTTTCCAAAATAACTAAGAAAATAGATTTTTATTTTTCTTAAAATATAAGT
1 AAAAATCTAAAATTTTCTCCAAAATAACTAAAAAAACAGATTTTTATTTTTCTAAAAATATAACT
* * * * *
28097360 TTTTTTTTTTTGTTAAAGAAAATCACTATTTTACTGAAAAATTTAAACTTTTATTTTGAAATAGT
66 TTTTTTCTTTTGTAAAAGAAAATCACTATTTTACTGAAAAATTCAAAATTTTATTTCGAAATAGT
*
28097425 TAAAAAAAATCTAAACTTTGTT
131 TAAAAAAAATCAAAACTTTGTT
*
28097447 AAAAATCTAAAATTTTCTCTAAAATAACTAAAAAAACAGATTTTTA-TTTT-TAAAAATATAAAA
1 AAAAATCTAAAATTTTCTCCAAAATAACTAAAAAAACAGATTTTTATTTTTCTAAAAATAT--AA
*
28097510 CTTTCTTCCTTCTTTT-TAAAAG-AAATCACTATTTTTACTTAAAAA-TCAAAATTTTATTTCGA
64 CTTT-TT--TTCTTTTGTAAAAGAAAATCACTA-TTTTACTGAAAAATTCAAAATTTTATTTCGA
* *
28097572 AATTGTTTAAAAAAATCAAAACTTT
125 AATAGTTAAAAAAAATCAAAACTTT
28097597 TCCCAAAATC
Statistics
Matches: 128, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
150 8 0.06
151 4 0.03
152 46 0.36
153 47 0.37
154 17 0.13
155 6 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (152 bp):
AAAAATCTAAAATTTTCTCCAAAATAACTAAAAAAACAGATTTTTATTTTTCTAAAAATATAACT
TTTTTTCTTTTGTAAAAGAAAATCACTATTTTACTGAAAAATTCAAAATTTTATTTCGAAATAGT
TAAAAAAAATCAAAACTTTGTT
Found at i:28099265 original size:23 final size:24
Alignment explanation
Indices: 28099226--28099275 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
28099216 TATTTCTATC
28099226 TTTTTAATTCTGTTTTCTTTTATT
1 TTTTTAATTCTGTTTTCTTTTATT
*
28099250 TTTTTAATTTTG-TTTCTTTTATT
1 TTTTTAATTCTGTTTTCTTTTATT
28099273 TTT
1 TTT
28099276 CTCACATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTTAATTCTGTTTTCTTTTATT
Found at i:28108354 original size:22 final size:22
Alignment explanation
Indices: 28108297--28108354 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
28108287 GACACATCTA
* *
28108297 TTTTCTATTACTTTTAATTCTG
1 TTTTCTTTTATTTTTAATTCTG
*
28108319 TTTTCTTTTATTTTTAATTTTG
1 TTTTCTTTTATTTTTAATTCTG
28108341 -TTTCTTTTATTTTT
1 TTTTCTTTTATTTTT
28108355 CATCAGATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTCTTTTATTTTTAATTCTG
Found at i:28115390 original size:18 final size:18
Alignment explanation
Indices: 28115367--28115418 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
28115357 AAAATGCAAG
*
28115367 AAATGATGTTAACATTTT
1 AAATGATGTTAACATTTC
28115385 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACATTTC
*
28115403 AAATAATGTTAACATT
1 AAATGATGTTAACATT
28115419 AATGGAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (18 bp):
AAATGATGTTAACATTTC
Found at i:28116089 original size:72 final size:72
Alignment explanation
Indices: 28115972--28116109 Score: 222
Period size: 72 Copynumber: 1.9 Consensus size: 72
28115962 TGAATTTATG
* *
28115972 TTGAATTTATGTTCTACTTATTTATGTGCAATCTAGTTTTATCAATAATTGTTTATGTTTGGTTT
1 TTGAATTTATGTTCTACTTATTTATGTGCAATCTAGTTTTATCAATAATTGTTTATATTTGATTT
28116037 TTAGATA
66 TTAGATA
* * * *
28116044 TTGAATTTATGTTTTACTTATTTATGTGTAATTTAGTTTTATCAATAGTTGTTTATATTTGATTT
1 TTGAATTTATGTTCTACTTATTTATGTGCAATCTAGTTTTATCAATAATTGTTTATATTTGATTT
28116109 T
66 T
28116110 GGATATAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (72 bp):
TTGAATTTATGTTCTACTTATTTATGTGCAATCTAGTTTTATCAATAATTGTTTATATTTGATTT
TTAGATA
Found at i:28117111 original size:3 final size:3
Alignment explanation
Indices: 28117103--28117134 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28117093 ATGGAGAAAG
28117103 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
28117135 GTGGTGGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:28118421 original size:40 final size:41
Alignment explanation
Indices: 28118377--28118469 Score: 120
Period size: 40 Copynumber: 2.3 Consensus size: 41
28118367 TATTTTCATT
* *
28118377 AAAAGGTTGAAAAA-GATATTATCC-AGAAGGATAATATATG
1 AAAAGGTTGAAAAAGGATATTATCCGA-AAGGATAACAAATG
* *
28118417 AAAAGGTT-AAAAAGGATGTTATTCGAAAGGATAACAAATG
1 AAAAGGTTGAAAAAGGATATTATCCGAAAGGATAACAAATG
28118457 AAAAGGTTGAAAA
1 AAAAGGTTGAAAA
28118470 CGTAAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 5 0.11
40 36 0.78
41 5 0.11
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.23
Consensus pattern (41 bp):
AAAAGGTTGAAAAAGGATATTATCCGAAAGGATAACAAATG
Found at i:28119230 original size:13 final size:13
Alignment explanation
Indices: 28119214--28119271 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
28119204 AAATCGAAAC
28119214 GGTTATATGCAAT
1 GGTTATATGCAAT
* *
28119227 GGTTATAAGAAAT
1 GGTTATATGCAAT
* *
28119240 GGTTATAGGGAAT
1 GGTTATATGCAAT
* *
28119253 GATTACATGCAAT
1 GGTTATATGCAAT
28119266 GGTTAT
1 GGTTAT
28119272 GTGAGTTGGT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (13 bp):
GGTTATATGCAAT
Found at i:28122136 original size:41 final size:43
Alignment explanation
Indices: 28122058--28122138 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
28122048 TTTTTTTATA
*
28122058 ATTATTAATATAATTTATAAATTCTATTTTGGTTTAATTTTGTT
1 ATTATTAATATAATTTATAAATTCTATTTT-GATTAATTTTGTT
*
28122102 ATTATTAATATAATTT-TATATTC-ATTCTT-ATTAATTT
1 ATTATTAATATAATTTATAAATTCTATT-TTGATTAATTT
28122139 ATATGTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 7 0.21
42 3 0.09
43 8 0.24
44 16 0.47
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (43 bp):
ATTATTAATATAATTTATAAATTCTATTTTGATTAATTTTGTT
Found at i:28132234 original size:25 final size:23
Alignment explanation
Indices: 28132206--28132251 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
28132196 GTTGGATCCA
28132206 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
28132231 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
28132252 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:28137600 original size:21 final size:19
Alignment explanation
Indices: 28137574--28137646 Score: 83
Period size: 21 Copynumber: 3.6 Consensus size: 19
28137564 CGGTGCAGAT
28137574 TTCTACCGATACAAGTGACAG
1 TTCTACCGATACAAGT-A-AG
* *
28137595 TTCTACCAATACAAGTAAC
1 TTCTACCGATACAAGTAAG
*
28137614 TTCTACCGAAACAAGTCAAG
1 TTCTACCGATACAAGT-AAG
28137634 CTTCTACCGATAC
1 -TTCTACCGATAC
28137647 TAAAAACTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.34
20 3 0.07
21 26 0.59
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (19 bp):
TTCTACCGATACAAGTAAG
Found at i:28150272 original size:15 final size:16
Alignment explanation
Indices: 28150247--28150279 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
28150237 TAATAACAAG
28150247 ATAAATAAAAAATTAA
1 ATAAATAAAAAATTAA
28150263 ATAAAT-AAAAATTAA
1 ATAAATAAAAAATTAA
28150278 AT
1 AT
28150280 GCTAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAATAAAAAATTAA
Found at i:28150357 original size:22 final size:25
Alignment explanation
Indices: 28150332--28150385 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 25
28150322 ATTAGGCATG
*
28150332 AAAATAAAT-GATAAA-TAAAT-AC
1 AAAATAAATCAATAAATTAAATGAC
*
28150354 AAAA-AAATCAATAAATTAAATGTC
1 AAAATAAATCAATAAATTAAATGAC
28150378 AAAATAAA
1 AAAATAAA
28150386 CAACAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 9 0.35
23 5 0.19
24 5 0.19
25 3 0.12
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (25 bp):
AAAATAAATCAATAAATTAAATGAC
Done.