Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 34 of 356
Found at i:11438669 original size:150 final size:148
Alignment explanation
Indices: 11438216--11438952 Score: 606
Period size: 153 Copynumber: 4.8 Consensus size: 148
11438206 CTACTTTTTC
* * ** *
11438216 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCGATTCACATGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-A-AGACACGCTGAGGTATTTTCAATTT
* * *
11438281 CTGTCTTTCAAAAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTG
64 CTGTTTTTC----AAAAAAA-TCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTG
11438346 AGGTAATTTCAATTTCTGTTT-C-A
124 AGGTAATTTCAATTTCTGTTTCCAA
* ** * * *
11438369 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGCTGAGGTATTTTCAATTTCT
* * * * *
11438434 G-TTTTC--AAAATTCAACTCATATTGCGAGAAATTAGTTGAGCCTCAAGACATGCTGAGGTATT
66 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAAT
* *
11438496 TTCAATTTCTATTTTTCAAAAAA
131 TTCAATTTC--TGTTTC---CAA
* ** **
11438519 AAAATCAACTCATATTGTGAGAAATGAGTTGAGCTTCAAGACATTCTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGCTGAGGTATTTTCAATTTCT
* * *
11438584 GTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTAAT
66 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAAT
*
11438649 TTCAATTTCTGTTGCCAA
131 TTCAATTTCTGTTTCCAA
* * * * *
11438667 AAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTT-AGGTCACACGCCGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAAG--ACACGCTGAGGTATTTTCAA--
* *
11438731 TCCGTTTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
61 ------TTTC--TGT-T---TTTC--AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC-
** * * * *
11438796 TGGC-TCACGCGCTGAGCTATTTTCAATTTCTGTCTTTCAAA
111 T--CAAGACACGCTGAGGTAATTTCAATTTCTG--TTTCCAA
* * *
11438837 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCA-A-GACACGCTGAGGTA--TTTTCAAT
* * * * *
11438902 TTATATTTTTCAAAGAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTC
62 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
11438953 GGGTCACATG
Statistics
Matches: 480, Mismatches: 65, Indels: 78
0.77 0.10 0.13
Matches are distributed among these distances:
143 56 0.12
144 4 0.01
145 4 0.01
148 33 0.07
149 3 0.01
150 81 0.17
151 32 0.07
152 1 0.00
153 91 0.19
155 1 0.00
156 35 0.07
158 8 0.02
160 2 0.00
161 2 0.00
162 2 0.00
164 7 0.01
166 38 0.08
167 1 0.00
168 22 0.05
169 4 0.01
170 46 0.10
172 7 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (148 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGCTGAGGTATTTTCAATTTCT
GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAAT
TTCAATTTCTGTTTCCAA
Found at i:11438817 original size:93 final size:93
Alignment explanation
Indices: 11438665--11438835 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
11438655 TTCTGTTGCC
* * *
11438665 AAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTTAGGTCACACGCCGAGGTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTTAGGTCACACGCCGAGCTATTTTCAAT
*
11438730 TTCCGTTTTTCAATTTCTGCCTTTCAAA
66 TTCCGTCTTTCAATTTCTGCCTTTCAAA
* * *
11438758 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCTCACGCGCTGAGCTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTTAGG-TCACACGCCGAGCTATTTTCAA
*
11438822 TTTCTGTCTTTCAA
65 TTTCCGTCTTTCAA
11438836 AAAAATCAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (93 bp):
AAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTTAGGTCACACGCCGAGCTATTTTCAAT
TTCCGTCTTTCAATTTCTGCCTTTCAAA
Found at i:11438865 original size:77 final size:77
Alignment explanation
Indices: 11438736--11439330 Score: 360
Period size: 88 Copynumber: 7.2 Consensus size: 77
11438726 CAATTTCCGT
**
11438736 TTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
1 TTTTCAATTTCTGTTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
*
11438801 CACGCGCTGAGCTA
64 CACACGCTGAGCTA
* * * *
11438815 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAG-CTTCAGATC
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCTC
* *
11438879 ACACACTGAGGTA
65 ACACGCTGAGCTA
* * * * * * *
11438892 TTTTTTCAATTTATATTTTTCAAAGAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGT
1 --TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
* *
11438957 CACATG-TCGAGGTA
64 CACACGCT-GAGCTA
** *
11438971 TTTTCAAAATCTGTTTTTCAGATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1 TTTTCAATTTCTGTTTTTCA-A----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
**
11439036 GCCTTGGCTCACGTGCTGAGCTA
55 GCCTTGGCTCACACGCTGAGCTA
* *
11439059 TTTTCAATTTCTGTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGCTGAGCTTTT
1 TTTTCAATTTCTG----TTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC---C
** * * *
11439124 TAATTTCTGCGAGA-GTTGAGTTGA
58 T--TGGCT-C-ACACGCTGAGCT-A
* * * *
11439148 GTCTTTTAATTTCTGTTTTTC--AAAAATCAACTTATATTGCGAGAGGTGAGTTGAACCTTCAG-
1 -T-TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGC
** *
11439210 TCACA-TATCGAGGTA
63 TCACACGCT-GAGCTA
*
11439225 TTTTCAAAATCTGCTTTTCAAGTTAAGTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTG
1 TTTTC--AA------TTTC-TGTT---TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
**
11439289 AGCCTTGGCTCACGTGCTGAGCTA
54 AGCCTTGGCTCACACGCTGAGCTA
11439313 TTTTCAATTTCTGTTTTT
1 TTTTCAATTTCTGTTTTT
11439331 AATGTCTGTT
Statistics
Matches: 405, Mismatches: 62, Indels: 101
0.71 0.11 0.18
Matches are distributed among these distances:
75 3 0.01
76 7 0.02
77 70 0.17
78 7 0.02
79 83 0.20
80 6 0.01
81 6 0.01
82 28 0.07
83 4 0.01
84 30 0.07
85 6 0.01
86 2 0.00
87 14 0.03
88 115 0.28
89 4 0.01
90 1 0.00
91 12 0.03
92 7 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (77 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
CACGCTGAGCTA
Found at i:11438898 original size:79 final size:77
Alignment explanation
Indices: 11438735--11438949 Score: 261
Period size: 79 Copynumber: 2.7 Consensus size: 77
11438725 TCAATTTCCG
* * *
11438735 TTTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC
1 TTTTTCAATTTCTGTCTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTAGA
* *
11438800 TCACGCGCTGAGCTA
63 TCACACACTGAGCTA
*
11438815 -TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTCAGATC
1 TTTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTT-AGATC
*
11438879 ACACACTGAGGTA
65 ACACACTGAGCTA
* * * * * *
11438892 TTTTTTCAATTTATATTTTTCAAAGAAATCAACTCACATTGCGAGATGTGAGTTGAGC
1 -TTTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
11438950 CTCGGGTCAC
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
76 3 0.03
77 48 0.41
79 67 0.57
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (77 bp):
TTTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTAGATCA
CACACTGAGCTA
Found at i:11438960 original size:79 final size:77
Alignment explanation
Indices: 11438757--11439119 Score: 260
Period size: 79 Copynumber: 4.5 Consensus size: 77
11438747 TGCCTTTCAA
* * * *
11438757 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTATTTTCAA
* *
11438822 TTTCTGTCTTTC
66 TTTATATCTTTC
* * * *
11438834 AAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTA--TTTTC
*
11438899 AATTTATATTTTTC
64 AATTTATATCTTTC
* * * * ** *
11438913 AAAGAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTCACA-TGTCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACT-GAGCTATTTTC-
* *
11438977 AAATCTGTTTTTCAGATTCTGTTT
64 -AA------TTT-ATA-TCT-TTC
** * * * ***
11439001 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTATTTTCAA
* * *
11439066 TTTCTGTTTTTTTTTC
66 --T-T-TATATCTTTC
*
11439082 AAAAAAATTCAACTCATATTGCGAGAGGTGAGCTGAGC
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
11439120 TTTTTAATTT
Statistics
Matches: 225, Mismatches: 43, Indels: 31
0.75 0.14 0.10
Matches are distributed among these distances:
77 55 0.24
78 1 0.00
79 65 0.29
81 7 0.03
82 33 0.15
83 1 0.00
84 1 0.00
85 3 0.01
86 4 0.02
87 2 0.01
88 52 0.23
89 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (77 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACACACTGAGCTATTTTCAA
TTTATATCTTTC
Found at i:11439111 original size:249 final size:240
Alignment explanation
Indices: 11438517--11439330 Score: 867
Period size: 254 Copynumber: 3.3 Consensus size: 240
11438507 TTTTTCAAAA
* * ** * * *
11438517 AAAAAATCAACTCATATTGTGAGAAATGAGTTGAG-CTT--CAAGACATTCTGAGGTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGC-TCACGTGCTGAGCTATTTTCAA
* * * *
11438579 TTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCTA
65 TTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTG
* * ** * * * *
11438642 AGGTA-ATTTCAATTTCTGTTGCCAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTTAG
130 AGGTATTTTTCAATTTCTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCG
* * ** * *
11438706 GTCACACGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTC
194 GTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTCTG--TTTC
* *
11438755 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTC
1 ---AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTC
* *
11438820 AATTTCTGTCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTCAGATCACACAC
63 AATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACAC
* * *
11438885 TGAGGTATTTTTTCAATTTATATTTTTCAAAGAAATCAACTCACATTGCGAGATGTGAGTTGAGC
128 TGAGGTA-TTTTTCAATTTCT-TTTTTCAAA-AAATCAACTCATATTGCGAGAGGTGAGTTGAGC
11438950 CTCGGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTC-AGATTCTGTTTTC
190 CTC-GGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAG-TTCTG-TTTC
11439003 -AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
* *
11439067 TTCTGTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGCTGAGCTTTTTA-ATTTC
66 TTCTG----TTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCAGA--TC
* * * * *
11439131 TGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTTATATTGCGAGAGG
122 -AC-ACA-CTGAGGT-A-T-TTTTCAATTTCT-TTTTTCAAAAAATCAACTCATATTGCGAGAGG
* * * * **
11439194 TGAGTTGAACCTTCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAAGTTTC
180 TGAGTTGAGCC-TCGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTCTGTTTC
*
11439256 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
11439321 TTCTGTTTTT
66 TTCTGTTTTT
11439331 AATGTCTGTT
Statistics
Matches: 489, Mismatches: 56, Indels: 47
0.83 0.09 0.08
Matches are distributed among these distances:
241 32 0.07
242 3 0.01
243 67 0.14
244 68 0.14
245 11 0.02
247 10 0.02
248 24 0.05
249 93 0.19
250 6 0.01
251 3 0.01
252 2 0.00
253 5 0.01
254 136 0.28
255 11 0.02
256 14 0.03
257 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (240 bp):
AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGA
GGTATTTTTCAATTTCTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGT
CACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTCTGTTTC
Found at i:11439137 original size:30 final size:30
Alignment explanation
Indices: 11439101--11439162 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
11439091 CAACTCATAT
11439101 TGCGAGAGGTGAGCTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGCTGAGTC-TTTTAATTTC
* *
11439131 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGCTGAGTCTTTTAATTTC
11439161 TG
1 TG
11439163 TTTTTCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.11, G:0.29, T:0.40
Consensus pattern (30 bp):
TGCGAGAGGTGAGCTGAGTCTTTTAATTTC
Found at i:11454321 original size:46 final size:45
Alignment explanation
Indices: 11454268--11454442 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
11454258 TATTTGGGCA
11454268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
11454314 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
11454361 TCCGAGCTCGTTGAGTTGAGTCCG-GTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
11454406 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11454443 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 1 0.01
45 26 0.24
46 44 0.41
47 27 0.25
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:11454422 original size:92 final size:93
Alignment explanation
Indices: 11454264--11454435 Score: 292
Period size: 92 Copynumber: 1.9 Consensus size: 93
11454254 AGGATATTTG
* *
11454264 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
11454329 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
11454357 GGCATCCGAGCTCGTTGAGTTGAGTCCG-GTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
11454421 TTGAGTCTGAGTTCG
66 TTGAGTCCGAGTTCG
11454436 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 47 0.64
93 27 0.36
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:11457377 original size:15 final size:15
Alignment explanation
Indices: 11457355--11457423 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 15
11457345 GTTTCTTGGG
11457355 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* * *
11457370 TCTCTTTATTCTAGA
1 TTTCTTTATCCTGGA
* *
11457385 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
11457400 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
11457415 TTTCTTTAT
1 TTTCTTTAT
11457424 TCGGTTTTCT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.13, C:0.17, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:11457417 original size:30 final size:30
Alignment explanation
Indices: 11457348--11457433 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
11457338 TAGTATCGTT
* * * *
11457348 TCTTGGGTTTCTTTATCCTGGATCTCTTTA
1 TCTTGGATTTCTTTATTCTGGATTTCTCTA
* *
11457378 T-TCTAGATTTCTTTATTCTGGGTTTCTCTA
1 TCT-TGGATTTCTTTATTCTGGATTTCTCTA
*
11457408 TCTTGGATTTCTTTATTC-GGTTTTCT
1 TCTTGGATTTCTTTATTCTGGATTTCT
11457434 TGTTATCTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 8 0.17
30 37 0.80
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.15, T:0.57
Consensus pattern (30 bp):
TCTTGGATTTCTTTATTCTGGATTTCTCTA
Found at i:11457434 original size:14 final size:14
Alignment explanation
Indices: 11457355--11457434 Score: 61
Period size: 15 Copynumber: 5.4 Consensus size: 14
11457345 GTTTCTTGGG
*
11457355 TTTCTTTATCCTGGA
1 TTTCTTTATTC-GGA
* *
11457370 TCTCTTTATTCTAGA
1 TTTCTTTATTC-GGA
*
11457385 TTTCTTTATTCTGGG
1 TTTCTTTATTC-GGA
* *
11457400 TTTCTCTATCTTGGA
1 TTTCTTTAT-TCGGA
*
11457415 TTTCTTTATTCGGT
1 TTTCTTTATTCGGA
11457429 TTTCTT
1 TTTCTT
11457435 GTTATCTTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
14 9 0.17
15 42 0.81
16 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.12, T:0.59
Consensus pattern (14 bp):
TTTCTTTATTCGGA
Found at i:11459998 original size:46 final size:45
Alignment explanation
Indices: 11459945--11460120 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
11459935 TATTTGTGCA
11459945 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
11459991 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * *
11460038 TCCGAGCTTGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
11460084 CCCGAGCTCGTTAAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11460121 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.62
47 30 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:11460101 original size:93 final size:93
Alignment explanation
Indices: 11459942--11460113 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
11459932 GGATATTTGT
* * *
11459942 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAGT
11460007 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * * *
11460035 GCATCCGAGCTTGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTAAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAGT
11460100 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
11460114 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:11462658 original size:25 final size:25
Alignment explanation
Indices: 11462602--11462661 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
11462592 TATAGCTCTT
* * **
11462602 ATGAGCTCCCCGTTATACAGCTCGG
1 ATGAGCTTCCCGTTATACAACTCAC
* *
11462627 ATAAGCTTCCCGTTATACAACTTAC
1 ATGAGCTTCCCGTTATACAACTCAC
11462652 ATGAGCTTCC
1 ATGAGCTTCC
11462662 TATTATATGG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATACAACTCAC
Found at i:11464248 original size:49 final size:50
Alignment explanation
Indices: 11464195--11464297 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 50
11464185 CCCTACACAA
* * *
11464195 CCTACCTGATTTACCCATGTAATTGCACATGCATGTGTGCCT-CACACGG
1 CCTACCTGATTTACCCATGTAATCGCACACGCACGTGTGCCTCCACACGG
* * * *
11464244 CCTACTTGATTTACTCATGTAATCGCACACGCCCGTGTGCCTCCACATGG
1 CCTACCTGATTTACCCATGTAATCGCACACGCACGTGTGCCTCCACACGG
11464294 CCTA
1 CCTA
11464298 ACATACGACT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 36 0.78
50 10 0.22
ACGTcount: A:0.21, C:0.33, G:0.17, T:0.28
Consensus pattern (50 bp):
CCTACCTGATTTACCCATGTAATCGCACACGCACGTGTGCCTCCACACGG
Found at i:11465318 original size:22 final size:22
Alignment explanation
Indices: 11465290--11465333 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11465280 TGATCAAAGT
11465290 TCATCAGAATCTCTATTTATAG
1 TCATCAGAATCTCTATTTATAG
11465312 TCATCAGAATCTCTATTTATAG
1 TCATCAGAATCTCTATTTATAG
11465334 GCATAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (22 bp):
TCATCAGAATCTCTATTTATAG
Found at i:11467552 original size:48 final size:47
Alignment explanation
Indices: 11467495--11467588 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 47
11467485 GTTCTGTAAG
*
11467495 ATTGGTTTTGGGTACGGCTTTTTCTTCTTCTTCTTCTTTTCTCTGAA
1 ATTGGTTTTGGGTACGGCTTTTTCTTCTTCTTCTTCTTTTCCCTGAA
11467542 ATTGGTTTTTGGGTACGGCTTTTTCTTCTTCTTCTTCTTTTCCCTGA
1 ATTGG-TTTTGGGTACGGCTTTTTCTTCTTCTTCTTCTTTTCCCTGA
11467589 CTGATCTGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 5 0.11
48 40 0.89
ACGTcount: A:0.07, C:0.20, G:0.17, T:0.55
Consensus pattern (47 bp):
ATTGGTTTTGGGTACGGCTTTTTCTTCTTCTTCTTCTTTTCCCTGAA
Found at i:11468315 original size:18 final size:18
Alignment explanation
Indices: 11468270--11468333 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
11468260 ATGAAATAAG
11468270 TTATATGTTGTTGTTC-T
1 TTATATGTTGTTGTTCAT
*
11468287 TTAGGGA-GTTGTTGTTCAT
1 TTA--TATGTTGTTGTTCAT
11468306 TTATATGTTGTTGTTCAT
1 TTATATGTTGTTGTTCAT
*
11468324 TTATAAGTTG
1 TTATATGTTG
11468334 AAGTTTCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.10
18 31 0.77
19 5 0.12
ACGTcount: A:0.17, C:0.05, G:0.22, T:0.56
Consensus pattern (18 bp):
TTATATGTTGTTGTTCAT
Found at i:11470371 original size:14 final size:15
Alignment explanation
Indices: 11470321--11470372 Score: 74
Period size: 14 Copynumber: 3.7 Consensus size: 15
11470311 CCAGAAAAGT
11470321 AAATCATTTTTCAG-
1 AAATCATTTTTCAGA
*
11470335 AAATCATTTTCCA-A
1 AAATCATTTTTCAGA
11470349 AAATCATTTTTCAGA
1 AAATCATTTTTCAGA
11470364 AAAT-ATTTT
1 AAATCATTTT
11470373 ACCTGCAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 29 0.85
15 5 0.15
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (15 bp):
AAATCATTTTTCAGA
Found at i:11472177 original size:23 final size:23
Alignment explanation
Indices: 11472151--11472248 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
11472141 ATAAGTGCCA
*
11472151 CACTGATATGTAGCCGAAGATAC
1 CACTGATATGTAGCCGAAGCTAC
11472174 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
11472197 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
11472219 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
11472242 CACTGAT
1 CACTGAT
11472249 CAATAACACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:11472207 original size:45 final size:45
Alignment explanation
Indices: 11472158--11472246 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
11472148 CCACACTGAT
* *
11472158 ATGTAGCCGAAGATACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGATACCACTGAAATGTAGCCGAAGCTACCACTGG
*
11472203 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGATACCACTGAAATGTAGCCGAAGCTACCACTG
11472247 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGATACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:11472484 original size:74 final size:75
Alignment explanation
Indices: 11472397--11472543 Score: 278
Period size: 75 Copynumber: 2.0 Consensus size: 75
11472387 CTATTCCTAA
11472397 GTTCAACCGGGAATTTACACTTAACACTTTA-TTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
11472461 CAACTTTCAT
66 CAACTTTCAT
*
11472471 GTTCAACCGGGAATTTAGACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
11472536 CAACTTTC
66 CAACTTTC
11472544 CTTCCACATT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 30 0.42
75 41 0.58
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (75 bp):
GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
CAACTTTCAT
Found at i:11478373 original size:23 final size:23
Alignment explanation
Indices: 11478347--11478444 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
11478337 ATAAGTGCCA
*
11478347 CACTGATATGTAGCCGAAGATAC
1 CACTGATATGTAGCCGAAGCTAC
11478370 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
11478393 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
11478415 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
11478438 CACTGAT
1 CACTGAT
11478445 CAATAACACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:11478403 original size:45 final size:45
Alignment explanation
Indices: 11478354--11478442 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
11478344 CCACACTGAT
* *
11478354 ATGTAGCCGAAGATACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGATACCACTGAAATGTAGCCGAAGCTACCACTGG
*
11478399 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGATACCACTGAAATGTAGCCGAAGCTACCACTG
11478443 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGATACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:11478679 original size:75 final size:75
Alignment explanation
Indices: 11478593--11478740 Score: 287
Period size: 75 Copynumber: 2.0 Consensus size: 75
11478583 CTATTCCTAA
11478593 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
11478658 CAACTTTCAT
66 CAACTTTCAT
*
11478668 GTTCAACCGGGAATTTAGACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
11478733 CAACTTTC
66 CAACTTTC
11478741 CTTCCACATT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (75 bp):
GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
CAACTTTCAT
Found at i:11483247 original size:5 final size:5
Alignment explanation
Indices: 11483237--11483264 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
11483227 ATATATATAT
11483237 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
11483265 GCATGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:11491560 original size:5 final size:5
Alignment explanation
Indices: 11491550--11491574 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11491540 CCGTAGCTTG
11491550 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
11491575 TTTAAAGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:11492762 original size:21 final size:21
Alignment explanation
Indices: 11492732--11492772 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11492722 TAAGTACTAG
11492732 TTGATCTTAG-CTTTCTTGGGA
1 TTGATCTTAGAC-TTCTTGGGA
*
11492753 TTGATGTTAGACTTCTTGGG
1 TTGATCTTAGACTTCTTGGG
11492773 TTCTTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.46
Consensus pattern (21 bp):
TTGATCTTAGACTTCTTGGGA
Found at i:11501559 original size:6 final size:6
Alignment explanation
Indices: 11501548--11501573 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11501538 ATAGTGAACT
11501548 GAGCGA GAGCGA GAGCGA GAGCGA GA
1 GAGCGA GAGCGA GAGCGA GAGCGA GA
11501574 AAACAGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.50, T:0.00
Consensus pattern (6 bp):
GAGCGA
Found at i:11515680 original size:17 final size:18
Alignment explanation
Indices: 11515660--11515694 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
11515650 GCAAAAAATC
11515660 ATTTAAAAT-TAAAAAAA
1 ATTTAAAATGTAAAAAAA
11515677 ATTTAAAATGTAAAAAAA
1 ATTTAAAATGTAAAAAAA
11515695 GTAGAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTTAAAATGTAAAAAAA
Found at i:11515751 original size:19 final size:18
Alignment explanation
Indices: 11515737--11515787 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
11515727 TTAAATTTTT
11515737 AAAATATTGAAAAATTATA
1 AAAATATT-AAAAATTATA
* *
11515756 AAAATATTAAAATAATATT
1 AAAATATTAAAA-ATTATA
11515775 AAAATAATTAAAA
1 AAAAT-ATTAAAA
11515788 CTTGTGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 17 0.61
20 7 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATATTAAAAATTATA
Found at i:11515772 original size:11 final size:11
Alignment explanation
Indices: 11515758--11515782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11515748 AAATTATAAA
11515758 AATATTAAAAT
1 AATATTAAAAT
11515769 AATATTAAAAT
1 AATATTAAAAT
11515780 AAT
1 AAT
11515783 TAAAACTTGT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:11525293 original size:14 final size:14
Alignment explanation
Indices: 11525274--11525304 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11525264 TGTGATTAAT
11525274 GTGTAACTAGCTTA
1 GTGTAACTAGCTTA
*
11525288 GTGTAAGTAGCTTA
1 GTGTAACTAGCTTA
11525302 GTG
1 GTG
11525305 GTTAGGCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (14 bp):
GTGTAACTAGCTTA
Found at i:11532835 original size:6 final size:6
Alignment explanation
Indices: 11532824--11532893 Score: 108
Period size: 6 Copynumber: 11.7 Consensus size: 6
11532814 CCAATCTTTG
11532824 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTATTT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA
11532872 TCTTTTA TTTTTA -TTTTA TTTT
1 T-TTTTA TTTTTA TTTTTA TTTT
11532894 AGTTAAATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.08
6 50 0.83
7 5 0.08
ACGTcount: A:0.16, C:0.01, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:11533090 original size:43 final size:42
Alignment explanation
Indices: 11533001--11533093 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
11532991 TATCCATGCT
* * * * *
11533001 GCCAAACAGTTCTATTCCAGCCCAGAATGCCATATCTCTGTA
1 GCCAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCA
*
11533043 GCCAAACAGTCCTATTCCAGCCTTAGAATCCCCAAAAC-CTGCA
1 GCCAAACAGTCCTATTCCAGCC-CAGAAT-CCCAAAACTCTGCA
11533086 GCCAAACA
1 GCCAAACA
11533094 CCCCTTTTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 21 0.49
43 17 0.40
44 5 0.12
ACGTcount: A:0.32, C:0.34, G:0.13, T:0.20
Consensus pattern (42 bp):
GCCAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCA
Found at i:11534087 original size:118 final size:118
Alignment explanation
Indices: 11533857--11534069 Score: 390
Period size: 118 Copynumber: 1.8 Consensus size: 118
11533847 GTTTTTCCAT
* *
11533857 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
11533922 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
11533975 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
11534040 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
11534070 TTGGGTAAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 91 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:11534221 original size:22 final size:21
Alignment explanation
Indices: 11534191--11534231 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11534181 TATTCCTAAG
* *
11534191 TAAATAAATAATAATAAAATTT
1 TAAAAAAAT-ATAAAAAAATTT
11534213 TAAAAAAATATAAAAAAAT
1 TAAAAAAATATAAAAAAAT
11534232 CAAAAAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAAATATAAAAAAATTT
Found at i:11534263 original size:15 final size:14
Alignment explanation
Indices: 11534233--11534265 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11534223 TAAAAAAATC
11534233 AAAAAAGGAAAGAA
1 AAAAAAGGAAAGAA
11534247 AAAAAA-GAGAAGAA
1 AAAAAAGGA-AAGAA
11534261 AAAAA
1 AAAAA
11534266 TAAGTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAAGGAAAGAA
Found at i:11536775 original size:19 final size:19
Alignment explanation
Indices: 11536753--11536791 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11536743 TTTTAAATAG
*
11536753 ATACACATGTATTAATAAT
1 ATACACATGTATAAATAAT
11536772 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
11536791 A
1 A
11536792 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:11537689 original size:15 final size:15
Alignment explanation
Indices: 11537641--11537690 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
11537631 TTTATCAAAT
11537641 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
11537656 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
11537671 TTATATTGATTGAAA
1 TTATATTGATTGAAA
11537686 TTATA
1 TTATA
11537691 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:11538348 original size:18 final size:19
Alignment explanation
Indices: 11538325--11538365 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
11538315 AATGAAATGA
11538325 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
11538343 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
11538362 GAAA
1 GAAA
11538366 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:11538363 original size:13 final size:13
Alignment explanation
Indices: 11538313--11538352 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11538303 TTGAGCTATT
11538313 AGAA-TGAAA-TG
1 AGAATTGAAATTG
11538324 AGAAATTG-AATTG
1 AG-AATTGAAATTG
11538337 AGAATTGAAATTG
1 AGAATTGAAATTG
11538350 AGA
1 AGA
11538353 TATGAGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 14 0.56
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (13 bp):
AGAATTGAAATTG
Found at i:11556884 original size:43 final size:43
Alignment explanation
Indices: 11556836--11556990 Score: 131
Period size: 43 Copynumber: 3.6 Consensus size: 43
11556826 TGCTCTCATA
11556836 TAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTTCGAG
1 TAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTTCGAG
* * * * * *
11556879 GAAGACCATGTCTGCGACATCGGCATCG-TAATTGTGA-TTCGTG
1 TAAGACCACGTCTGGGACGTTGGCATCGAT-A-TGTGATTTCGAG
* * * *
11556922 TAAAACC-CTGTCTGGGACAG-TGGAATCGACATGTGATTAC-ATG
1 TAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTTCGA-G
*
11556965 TAAGACCACGTCTAGGACGTTGGCAT
1 TAAGACCACGTCTGGGACGTTGGCAT
11556991 TGTACGATAT
Statistics
Matches: 84, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
42 7 0.08
43 71 0.85
44 6 0.07
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
TAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTTCGAG
Found at i:11558752 original size:27 final size:27
Alignment explanation
Indices: 11558717--11558770 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
11558707 AAGAATTCAA
11558717 ATATCACACAATATGGAATTCTTTTTC
1 ATATCACACAATATGGAATTCTTTTTC
11558744 ATATCACACAATATGGAATTCTTTTTC
1 ATATCACACAATATGGAATTCTTTTTC
11558771 TTCTCCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATCACACAATATGGAATTCTTTTTC
Found at i:11559289 original size:46 final size:46
Alignment explanation
Indices: 11559222--11559396 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
11559212 TGTAACCCAC
11559222 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
11559268 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * ** *
11559318 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
11559361 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
11559397 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.58
47 25 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:11559338 original size:93 final size:93
Alignment explanation
Indices: 11559230--11559400 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
11559220 ACCCATAAGT
* ** *
11559230 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
11559295 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
11559323 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
11559388 CGAGTTCGGATGC
66 CGAGCTCGGATGC
11559401 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:11559977 original size:19 final size:19
Alignment explanation
Indices: 11559951--11559987 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
11559941 GCAACTCATA
11559951 ATTTCAACT-ATTTTACAT
1 ATTTCAACTCATTTTACAT
11559969 ATTTACAACTCATTTTACA
1 ATTT-CAACTCATTTTACA
11559988 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTCAACTCATTTTACAT
Found at i:11562487 original size:24 final size:23
Alignment explanation
Indices: 11562430--11562487 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
11562420 TCGTTTTTGA
*
11562430 TTTTATTAA-AAATTTTAGAAGT
1 TTTTATTAATAAATATTAGAAGT
* * *
11562452 TTTCATTGATAAATATTAGATGTT
1 TTTTATTAATAAATATTAGAAG-T
11562476 TTTTATTAATAA
1 TTTTATTAATAA
11562488 CATGGATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 7 0.25
23 10 0.36
24 11 0.39
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (23 bp):
TTTTATTAATAAATATTAGAAGT
Found at i:11563945 original size:103 final size:104
Alignment explanation
Indices: 11563701--11563966 Score: 410
Period size: 103 Copynumber: 2.6 Consensus size: 104
11563691 GTTGTACATA
** *
11563701 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* ** *
11563766 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCAC
*
11563805 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
11563869 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCAC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCAC
* * *
11563908 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
11563967 AATAACGGTT
Statistics
Matches: 148, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 82 0.55
104 66 0.45
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCAC
Found at i:11587557 original size:46 final size:46
Alignment explanation
Indices: 11587490--11587582 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
11587480 CTCGGAGCTC
11587490 TCCCATGTATGCTCTTTCCATGAATAAGAAACTAATTAAATCTATT
1 TCCCATGTATGCTCTTTCCATGAATAAGAAACTAATTAAATCTATT
11587536 TCCCATGTATGCTCTTTCCATGAATAAGAAACTAATTAAATCTATT
1 TCCCATGTATGCTCTTTCCATGAATAAGAAACTAATTAAATCTATT
11587582 T
1 T
11587583 TGCCAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (46 bp):
TCCCATGTATGCTCTTTCCATGAATAAGAAACTAATTAAATCTATT
Found at i:11588509 original size:51 final size:50
Alignment explanation
Indices: 11588437--11588549 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 50
11588427 CCCTTTTAAA
* * ** *
11588437 ATTAAAAAAAATGGATGTTGGGACATTGATGGCCGACACCCTTATACTAG
1 ATTAAAAAAATTGGATGTTGGGACACTGATGGCCGACACCCCAATACCAG
* *
11588487 ATTAAAAAAATTAGGGTGTTGGGACACTGATGGCCGGCACCCCAATACCAG
1 ATTAAAAAAATT-GGATGTTGGGACACTGATGGCCGACACCCCAATACCAG
11588538 ATTTAAAAAAAT
1 A-TTAAAAAAAT
11588550 AATGTTGAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 11 0.20
51 33 0.61
52 10 0.19
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (50 bp):
ATTAAAAAAATTGGATGTTGGGACACTGATGGCCGACACCCCAATACCAG
Found at i:11593938 original size:13 final size:13
Alignment explanation
Indices: 11593922--11593951 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
11593912 ATTGTCATGT
11593922 AATTGTTTTTCTG
1 AATTGTTTTTCTG
11593935 AATTGTTTTTCTG
1 AATTGTTTTTCTG
11593948 AATT
1 AATT
11593952 TAGCTGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (13 bp):
AATTGTTTTTCTG
Found at i:11594921 original size:82 final size:80
Alignment explanation
Indices: 11594830--11595079 Score: 175
Period size: 82 Copynumber: 3.1 Consensus size: 80
11594820 CATATAAGAA
*
11594830 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATG
1 TATTTATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATATA-TTAATAATAATTATG
11594895 TTTAAATATGATTAAAT
64 TTTAAATATGATTAAAT
* * * * * * * * *
11594912 TATTTATTATT---CATATTAATAATCTTATCAAAATTTAA-ATAACA-A-TAACAATAA-TA-A
1 TATTTATTATTAAGAATTTTATTAA-ATTAT-ATATTTTAATATAATATATTAATAATAATTATG
*
11594969 TTTACCAA-A--A-CAAAT
64 TTTA--AATATGATTAAAT
* *
11594984 T-TCTGGTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGGTTAATAATAAT
1 TAT-T--T-ATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATAT-ATTAATAATAAT
*
11595048 TATGTTTAAATATGATTAAAA
60 TATGTTTAAATATGATTAAAT
11595069 TATTTATTATT
1 TATTTATTATT
11595080 GATAATAATA
Statistics
Matches: 121, Mismatches: 24, Indels: 46
0.63 0.13 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 5 0.04
75 9 0.07
76 17 0.14
77 4 0.03
78 13 0.11
79 13 0.11
80 4 0.03
81 17 0.14
82 19 0.16
83 5 0.04
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (80 bp):
TATTTATTATTAAGAATTTTATTAAATTATATATTTTAATATAATATATTAATAATAATTATGTT
TAAATATGATTAAAT
Found at i:11595003 original size:157 final size:157
Alignment explanation
Indices: 11594833--11595142 Score: 530
Period size: 157 Copynumber: 2.0 Consensus size: 157
11594823 ATAAGAATAT
* *
11594833 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATAGTTAATAATAATTATGTTT
* *
11594898 AAATATGATTAAATTATTTATTATTCATATTAATAATCTTATCAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
11594963 TAATAATTTACCAAAACAAATTTCTGG
131 TAATAATTTACCAAAACAAATTTCTGG
* *
11594990 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGGTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATAGTTAATAATAATTATGTTT
* *
11595055 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
* *
11595120 TAATCATTTACCAAAATAAATTT
131 TAATAATTTACCAAAACAAATTT
11595143 ATGCTAAGGG
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
157 143 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATAGTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTCTGG
Found at i:11595293 original size:16 final size:16
Alignment explanation
Indices: 11595272--11595339 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
11595262 GATTTGCTAT
11595272 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11595288 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
11595304 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
*
11595320 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
11595336 TACA
1 TACA
11595340 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:11595932 original size:17 final size:17
Alignment explanation
Indices: 11595896--11595929 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
11595886 TTCTTTTTTA
11595896 TATGTTATCTGTTATAT
1 TATGTTATCTGTTATAT
11595913 TATGTTA-CTGTTATAT
1 TATGTTATCTGTTATAT
11595929 T
1 T
11595930 TATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
TATGTTATCTGTTATAT
Found at i:11598337 original size:47 final size:47
Alignment explanation
Indices: 11598263--11598356 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
11598253 AATTAAGGAA
*
11598263 AAGGGTGAGAGTAAGTGCGTTCTGTGGGGAGCTTTGAAAGATTTGAT
1 AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
11598310 AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
1 AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
11598357 CCAGACACAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.07, G:0.38, T:0.29
Consensus pattern (47 bp):
AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
Found at i:11608250 original size:206 final size:206
Alignment explanation
Indices: 11607889--11608783 Score: 1320
Period size: 206 Copynumber: 4.4 Consensus size: 206
11607879 CATTTGACAC
* * * * *
11607889 ACATAGCAGATCTGGCCTTCAGATGATTAGACTGAAGTAGATCCAAGATGATTTGGCATTCTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
*
11607954 GTTTACAAGCAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
66 GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
*
11608019 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAATTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
* *
11608084 GGAGAGTAGAT
196 GAAGAGCAGAT
* * *
11608095 ACATAGTAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTAT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
*
11608160 GCTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
66 GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
* * *
11608225 TAAGATGATTTGGCATCTTTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCCAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
11608290 GAAGAGCAGAT
196 GAAGAGCAGAT
* * * *
11608301 ACATAGCAGATCTGATCTTCAGATGTTTATACTAAAGCAGAACCAAGATGGTTTGGCATCCTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
* * * *
11608366 GCTTACAAGGAACAAATCGAAATCATAGCTGAATTGGCTTTCACGTGTTTACGATGAAGCAAATA
66 GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
11608431 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
*
11608496 -AGAGAGTAGAT
196 GA-AGAGCAGAT
* *
11608507 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGTAGATCTAAGATGATTTGGCATCCTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
* * *
11608572 GTTTATAAGGAACAAATC-AAAGACATAGCTGATTTGAC-TT----T-C--ACG-T-----AAAT
66 GTTTACAAGGAACAAATCGAAA-TCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAAT
* *
11608622 CTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCAT-TTCGA
130 CTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGA
*
11608686 TGAAGAGCAGAT
195 CGAAGAGCAGAT
*** *
11608698 ACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATACTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
11608763 GTTTACAAGGAACAAATCGAA
66 GTTTACAAGGAACAAATCGAA
11608784 GAAGCAGATT
Statistics
Matches: 633, Mismatches: 52, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
191 89 0.14
192 63 0.10
197 1 0.00
198 3 0.00
201 1 0.00
205 6 0.01
206 470 0.74
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (206 bp):
ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
GAAGAGCAGAT
Found at i:11610604 original size:17 final size:17
Alignment explanation
Indices: 11610568--11610601 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11610558 TTCTTTTTCA
*
11610568 TATGTTATCTGTTATAT
1 TATGTTATCTATTATAT
11610585 TATGTTA-CTATTATAT
1 TATGTTATCTATTATAT
11610601 T
1 T
11610602 TATAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (17 bp):
TATGTTATCTATTATAT
Found at i:11612565 original size:29 final size:28
Alignment explanation
Indices: 11612533--11612604 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
11612523 GAGATTTTTA
* *
11612533 ATTTATTTTATTTATTTAAATATTTCTTT
1 ATTTACTTTAATTATTTAAATA-TTCTTT
* *
11612562 ATTTACTTTAATTCTTTAATTATTCTTT
1 ATTTACTTTAATTATTTAAATATTCTTT
* * *
11612590 TTTTAATTAAATTAT
1 ATTTACTTTAATTAT
11612605 ATTCTTTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTTACTTTAATTATTTAAATATTCTTT
Found at i:11612602 original size:28 final size:29
Alignment explanation
Indices: 11612547--11612602 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
11612537 ATTTTATTTA
* *
11612547 TTTAAATATTTCTTTATTTACTTTAATTC
1 TTTAAATATTTCTTTATTTAATTAAATTC
* *
11612576 TTTAATTA-TTCTTTTTTTAATTAAATT
1 TTTAAATATTTCTTTATTTAATTAAATT
11612603 ATATTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTAAATATTTCTTTATTTAATTAAATTC
Found at i:11612752 original size:14 final size:15
Alignment explanation
Indices: 11612723--11612758 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
11612713 ATTTTTTAAA
*
11612723 TTAAATTCTGTTCAT
1 TTAAATTCTATTCAT
11612738 TTAAATT-TATTCAT
1 TTAAATTCTATTCAT
11612752 TTAAATT
1 TTAAATT
11612759 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (15 bp):
TTAAATTCTATTCAT
Found at i:11612829 original size:118 final size:122
Alignment explanation
Indices: 11612596--11612842 Score: 267
Period size: 118 Copynumber: 2.1 Consensus size: 122
11612586 CTTTTTTTAA
* * * * * *
11612596 TTAAATTATATTCTTTTAAATTTAAATTTATTCCTTTATATTATTCTTTTAATTAAATTCGATTG
1 TTAAATTAAATTCTGTTAAATTTAAATTTATTCATTTAAATTATTCTTTTAATTAAACTCAATTG
* * *
11612661 TTTATTTTTTTATTTCTTTAAATATTTCTTTACTTAGTTTATTTCTTTAATTATTTT
66 TTTATTTTTTTATTTCTTTAAATATGTCTTTACTTACTTTATTACTTTAATTATTTT
*
11612718 TTAAATTAAATTCTGTT-CATTTAAATTTATTCATTTAAATTA-T-TTTT-ATTAAACTCAATTG
1 TTAAATTAAATTCTGTTAAATTTAAATTTATTCATTTAAATTATTCTTTTAATTAAACTCAATTG
* * * *
11612779 TTTATTTTCTTT-TTT-TTTCACT-TGTCTATATA-TTTCTTTAATTACTTTAATTCTTTT
66 TTTATTTT-TTTATTTCTTTAAATATGTCT-T-TACTTACTTT-ATTACTTTAATTATTTT
*
11612836 TTTAATT
1 TTAAATT
11612843 GATGAGATTT
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
116 4 0.04
117 11 0.10
118 46 0.43
119 7 0.07
120 1 0.01
121 22 0.21
122 15 0.14
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (122 bp):
TTAAATTAAATTCTGTTAAATTTAAATTTATTCATTTAAATTATTCTTTTAATTAAACTCAATTG
TTTATTTTTTTATTTCTTTAAATATGTCTTTACTTACTTTATTACTTTAATTATTTT
Found at i:11614816 original size:53 final size:51
Alignment explanation
Indices: 11614736--11614887 Score: 160
Period size: 53 Copynumber: 2.9 Consensus size: 51
11614726 CCATGGCAAC
* * * * **
11614736 AAGTGATAAGCGATATCCGTATAAGACCATAGTTGGGCTATGGCTTCAGATTA
1 AAGTGATAAGTG--ATCCGTATAAGACCATAGCTAGGCTATGGCATCAGAGAA
*
11614789 AAGTGATACAAGTGATCCGTATAAGACCATAGCTAGGCTATGGCATCGGAGAA
1 AAGTGAT--AAGTGATCCGTATAAGACCATAGCTAGGCTATGGCATCAGAGAA
* * * *
11614842 AAGTGATAAGTGCTCTCGTGTAAGACCATATCTAGGATATGGCATC
1 AAGTGATAAGTGATC-CGTATAAGACCATAGCTAGGCTATGGCATC
11614888 GGTATGATAT
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
51 7 0.08
52 27 0.32
53 47 0.55
55 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (51 bp):
AAGTGATAAGTGATCCGTATAAGACCATAGCTAGGCTATGGCATCAGAGAA
Found at i:11618268 original size:22 final size:23
Alignment explanation
Indices: 11618243--11618288 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11618233 CAACCAAACT
11618243 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
11618265 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
11618288 A
1 A
11618289 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:11618294 original size:23 final size:23
Alignment explanation
Indices: 11618250--11618294 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11618240 ACTAATTCAA
*
11618250 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
11618273 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
11618295 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:11625993 original size:22 final size:23
Alignment explanation
Indices: 11625968--11626013 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11625958 CAACCAAACC
11625968 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
11625990 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
11626013 A
1 A
11626014 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:11626019 original size:23 final size:23
Alignment explanation
Indices: 11625975--11626019 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11625965 ACCAATTCAA
*
11625975 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
11625998 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
11626020 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:11627766 original size:18 final size:18
Alignment explanation
Indices: 11627743--11627777 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
11627733 CTACTGCTGC
11627743 TGTCCAATATTGTTTTAA
1 TGTCCAATATTGTTTTAA
11627761 TGTCCAATATTGTTTTA
1 TGTCCAATATTGTTTTA
11627778 GTGCAAGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (18 bp):
TGTCCAATATTGTTTTAA
Found at i:11629595 original size:25 final size:25
Alignment explanation
Indices: 11629454--11629601 Score: 138
Period size: 25 Copynumber: 6.0 Consensus size: 25
11629444 AAGCTCTTTA
* * **
11629454 ATGAGCTTCCTGATATATGGCTTTC
1 ATGAGCTTCCCGTTATATGGCTCAC
* *
11629479 -TGGAGCTTCTCGATAT-TGGCTCAC
1 AT-GAGCTTCCCGTTATATGGCTCAC
* ** *
11629503 ATGAGCTTCCTGTTATACAGCTCAA
1 ATGAGCTTCCCGTTATATGGCTCAC
* ** *
11629528 ATGAGCTTCCTGTTATACAGCTCAA
1 ATGAGCTTCCCGTTATATGGCTCAC
*
11629553 ATGAGCTTCTCGTTATATGGCTCAC
1 ATGAGCTTCCCGTTATATGGCTCAC
11629578 ATGAGCTTCCCGTTATATGGCTCA
1 ATGAGCTTCCCGTTATATGGCTCA
11629602 AGAGAGAGCT
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
24 18 0.17
25 86 0.83
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCAC
Found at i:11629601 original size:50 final size:50
Alignment explanation
Indices: 11629481--11629633 Score: 141
Period size: 50 Copynumber: 3.0 Consensus size: 50
11629471 TGGCTTTCTG
* * * **
11629481 GAGCTTCTCGATAT-TGGCTCACATGAGCTTC-CTGTTATACAGCTCAAAT
1 GAGCTTCCCGTTATATGGCTCAAATGAGCTTCTC-GTTATATGGCTCAAAT
* ** *
11629530 GAGCTTCCTGTTATACAGCTCAAATGAGCTTCTCGTTATATGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCAAATGAGCTTCTCGTTATATGGCTCAAAT
* * *
11629580 GAGCTTCCCGTTATATGGCTCAAGAGAGAGCTTCTTGTT-TATGTGCTCATAT
1 GAGCTTCCCGTTATATGGCTCAA-A-TGAGCTTCTCGTTATATG-GCTCAAAT
11629632 GA
1 GA
11629634 ACATTCCTGA
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
49 11 0.13
50 47 0.56
51 6 0.07
52 20 0.24
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (50 bp):
GAGCTTCCCGTTATATGGCTCAAATGAGCTTCTCGTTATATGGCTCAAAT
Found at i:11631768 original size:18 final size:18
Alignment explanation
Indices: 11631745--11631780 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11631735 TCCCCATAGT
11631745 CTCCTTGTGATCTTTCTC
1 CTCCTTGTGATCTTTCTC
11631763 CTCCTTGTGATCTTTCTC
1 CTCCTTGTGATCTTTCTC
11631781 TCTTGATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.33, G:0.11, T:0.50
Consensus pattern (18 bp):
CTCCTTGTGATCTTTCTC
Found at i:11633643 original size:46 final size:46
Alignment explanation
Indices: 11633370--11633642 Score: 377
Period size: 46 Copynumber: 5.9 Consensus size: 46
11633360 TTTGACATGA
* * ** * *
11633370 TGCCATAGTGTCTTTCAATTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* * *
11633416 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
11633462 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
11633508 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * *
11633554 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
11633600 TGCCATGGTATCTTTCAACCGTGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCA
11633643 GAGAGCACAC
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 205 0.98
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:11635790 original size:11 final size:11
Alignment explanation
Indices: 11635774--11635820 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
11635764 CTTTATATAC
11635774 TAATAAAATAA
1 TAATAAAATAA
11635785 TAATAAAATATA
1 TAATAAAATA-A
* *
11635797 TTATTAAAATAT
1 -TAATAAAATAA
11635809 TAATAAAA-AA
1 TAATAAAATAA
11635819 TA
1 TA
11635821 TTTATCTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
10 3 0.10
11 17 0.57
12 1 0.03
13 9 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:11635804 original size:24 final size:24
Alignment explanation
Indices: 11635768--11635822 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
11635758 TTCTTTCTTT
*
11635768 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* *
11635792 ATATATTATTAAAATATTAATAAA
1 ATATATTAATAAAATAATAATAAA
*
11635816 AAATATT
1 ATATATT
11635823 TATCTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:11639575 original size:14 final size:15
Alignment explanation
Indices: 11639553--11639585 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
11639543 ACAAGGTGAC
11639553 TAAAAATTTAAT-AT
1 TAAAAATTTAATAAT
*
11639567 TAAACATTTAATAAT
1 TAAAAATTTAATAAT
11639582 TAAA
1 TAAA
11639586 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAATTTAATAAT
Found at i:11640059 original size:17 final size:17
Alignment explanation
Indices: 11639985--11640059 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
11639975 ATTCGAAAAG
11639985 ATTTAAATAAA-AATATTAA
1 ATTTAAA-AAATAA-ATT-A
11640004 ATTTAAAAAATAAATTTA
1 ATTTAAAAAATAAA-TTA
*
11640022 ATTAAAAAAATAAATCT-
1 ATTTAAAAAATAAAT-TA
* *
11640039 ATTTAAAATATGAATTA
1 ATTTAAAAAATAAATTA
11640056 ATTT
1 ATTT
11640060 TAAGTTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
16 1 0.02
17 17 0.35
18 19 0.40
19 11 0.23
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
ATTTAAAAAATAAATTA
Found at i:11648347 original size:21 final size:21
Alignment explanation
Indices: 11648323--11648366 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11648313 CGATGACGTG
11648323 ATTATTGAGAAATTATA-AAAA
1 ATTATT-AGAAATTATATAAAA
**
11648344 ATTATTTTAAATTATATAAAA
1 ATTATTAGAAATTATATAAAA
11648365 AT
1 AT
11648367 GTAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTATTAGAAATTATATAAAA
Found at i:11648375 original size:20 final size:21
Alignment explanation
Indices: 11648352--11648397 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
11648342 AAATTATTTT
11648352 AAATTATATAAA-AATGTAAA
1 AAATTATATAAATAATGTAAA
* * *
11648372 AAA-TATTTAAATTATTTAAA
1 AAATTATATAAATAATGTAAA
11648392 AAATTA
1 AAATTA
11648398 AATGTTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 7 0.33
20 12 0.57
21 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATTATATAAATAATGTAAA
Found at i:11648399 original size:28 final size:30
Alignment explanation
Indices: 11648338--11648393 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
11648328 TGAGAAATTA
11648338 TAAAAAATTATTTTAAATTATATAAAAATG
1 TAAAAAATTATTTTAAATTATATAAAAATG
*
11648368 TAAAAAA-TA-TTTAAATTATTTAAAAA
1 TAAAAAATTATTTTAAATTATATAAAAA
11648394 ATTAAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 16 0.64
29 2 0.08
30 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAAAATTATTTTAAATTATATAAAAATG
Found at i:11648427 original size:10 final size:10
Alignment explanation
Indices: 11648405--11648489 Score: 52
Period size: 10 Copynumber: 8.5 Consensus size: 10
11648395 TTAAATGTTG
11648405 TAAATAGTTAT
1 TAAATA-TTAT
11648416 TAAATATTAT
1 TAAATATTAT
11648426 TAAAATATT-T
1 T-AAATATTAT
*
11648436 TGAA-ATTAT
1 TAAATATTAT
* *
11648445 TAAAAATCAT
1 TAAATATTAT
* *
11648455 AAAAGATTATT
1 TAAATATTA-T
11648466 TAAA-ATT-T
1 TAAATATTAT
*
11648474 GTAAAAATTAT
1 -TAAATATTAT
11648485 TAAAT
1 TAAAT
11648490 GTTGTGAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
8 4 0.07
9 10 0.17
10 27 0.46
11 18 0.31
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (10 bp):
TAAATATTAT
Found at i:11648795 original size:20 final size:20
Alignment explanation
Indices: 11648770--11648814 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
11648760 AATAATTTGT
*
11648770 TAATTATTTAT-ATTTTTTAA
1 TAATTATTTATGA-TATTTAA
11648790 TAATTATTTATGATATTTAA
1 TAATTATTTATGATATTTAA
11648810 TAATT
1 TAATT
11648815 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TAATTATTTATGATATTTAA
Found at i:11648910 original size:9 final size:9
Alignment explanation
Indices: 11648896--11648954 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
11648886 ACATATTTAT
11648896 TTTTTACAA
1 TTTTTACAA
*
11648905 TTTTTATATA
1 TTTTTACA-A
11648915 TTTTTA-AA
1 TTTTTACAA
*
11648923 TATTTTACTA
1 T-TTTTACAA
*
11648933 TTTTTA-AT
1 TTTTTACAA
11648941 TTTTTACAA
1 TTTTTACAA
11648950 TTTTT
1 TTTTT
11648955 TTATTTGGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 8 0.20
9 24 0.59
10 9 0.22
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTACAA
Found at i:11648920 original size:19 final size:18
Alignment explanation
Indices: 11648837--11648938 Score: 68
Period size: 19 Copynumber: 5.6 Consensus size: 18
11648827 AATTTTATAA
*
11648837 TAATTTTTTTACAATTTT
1 TAATATTTTTACAATTTT
* * * *
11648855 AAAACATTTTAACAATATT
1 -TAATATTTTTACAATTTT
*
11648874 TAATAATTATTTAC-ATATT
1 TAAT-ATT-TTTACAATTTT
11648893 T-AT-TTTTTACAATTTT
1 TAATATTTTTACAATTTT
11648909 TATATATTTTTA-AATATTT
1 TA-ATATTTTTACAAT-TTT
*
11648928 TACTATTTTTA
1 TAATATTTTTA
11648939 ATTTTTTACA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
15 5 0.08
16 7 0.11
18 17 0.26
19 33 0.50
20 4 0.06
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATATTTTTACAATTTT
Found at i:11648945 original size:17 final size:18
Alignment explanation
Indices: 11648896--11648954 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
11648886 ACATATTTAT
11648896 TTTTTACAATTTTTATA-TA
1 TTTTTA-AATTTTT-TACTA
*
11648915 TTTTTAAATATTTTACTA
1 TTTTTAAATTTTTTACTA
*
11648933 TTTTT-AATTTTTTACAA
1 TTTTTAAATTTTTTACTA
11648950 TTTTT
1 TTTTT
11648955 TTATTTGGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 17 0.47
18 13 0.36
19 6 0.17
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAAATTTTTTACTA
Found at i:11648955 original size:18 final size:18
Alignment explanation
Indices: 11648894--11648960 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 18
11648884 TTACATATTT
* *
11648894 ATTTTTTACAATTTTTATA
1 ATTTTTTA-ATTTTTTACA
* * *
11648913 TATTTTTAAATATTTTACT
1 -ATTTTTTAATTTTTTACA
11648932 A-TTTTTAATTTTTTACA
1 ATTTTTTAATTTTTTACA
*
11648949 ATTTTTTTATTT
1 ATTTTTTAATTT
11648961 GGCCAACAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
17 14 0.38
18 10 0.27
19 6 0.16
20 7 0.19
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTAATTTTTTACA
Found at i:11649513 original size:15 final size:17
Alignment explanation
Indices: 11649479--11649515 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
11649469 GTCTGTCTCC
*
11649479 TTATTTATTCACTTTTT
1 TTATTTATTCACTTTAT
11649496 TTATTT-TTC-CTTTAT
1 TTATTTATTCACTTTAT
11649511 TTATT
1 TTATT
11649516 ATTTGAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTATTCACTTTAT
Found at i:11651223 original size:40 final size:40
Alignment explanation
Indices: 11651137--11651227 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 40
11651127 TGTTATCTAT
* * *
11651137 CAGGCTTTGTGTCGGTGTATTTATCGGGCTTTATACCTAG
1 CAGGCTTTGTGCCAGTATATTTATCGGGCTTTATACCTAG
* * * **
11651177 CGGGCTTTGTGCCAGTATGTTTATCGGGCTTTGTGTCTAG
1 CAGGCTTTGTGCCAGTATATTTATCGGGCTTTATACCTAG
*
11651217 TAGGCTTTGTG
1 CAGGCTTTGTG
11651228 TCGGTGTTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.12, C:0.16, G:0.31, T:0.41
Consensus pattern (40 bp):
CAGGCTTTGTGCCAGTATATTTATCGGGCTTTATACCTAG
Found at i:11651246 original size:25 final size:25
Alignment explanation
Indices: 11651231--11651288 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
11651221 CTTTGTGTCG
11651231 GTGTTATCTATCAGGCCTTGAGCTA
1 GTGTTATCTATCAGGCCTTGAGCTA
** *
11651256 GTGTTATCTATCAAACCTTGAGCTG
1 GTGTTATCTATCAGGCCTTGAGCTA
11651281 GTGATTAT
1 GTG-TTAT
11651289 TTAGTAGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (25 bp):
GTGTTATCTATCAGGCCTTGAGCTA
Found at i:11654102 original size:11 final size:11
Alignment explanation
Indices: 11654086--11654110 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11654076 TTCAGCTGAT
11654086 GAAAATGAAGA
1 GAAAATGAAGA
11654097 GAAAATGAAGA
1 GAAAATGAAGA
11654108 GAA
1 GAA
11654111 TTCTCGACAT
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:11656708 original size:18 final size:19
Alignment explanation
Indices: 11656670--11656708 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
11656660 TGGTTCAAGC
*
11656670 TTTTAATCTCATATCTCAA
1 TTTTAATCTCACATCTCAA
*
11656689 TTTTAAT-TCACATTTCAA
1 TTTTAATCTCACATCTCAA
11656707 TT
1 TT
11656709 CATAATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTAATCTCACATCTCAA
Found at i:11657239 original size:16 final size:17
Alignment explanation
Indices: 11657209--11657241 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
11657199 TTCATAAGTA
11657209 TATATCAATTATTTCAT
1 TATATCAATTATTTCAT
11657226 TATATCAA-TATTTCAT
1 TATATCAATTATTTCAT
11657242 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATCAATTATTTCAT
Found at i:11657587 original size:46 final size:46
Alignment explanation
Indices: 11657522--11657978 Score: 598
Period size: 46 Copynumber: 10.0 Consensus size: 46
11657512 TTATCTTTGA
* * * * * *
11657522 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* * *** *
11657568 CAGGTAGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* ** * ** * *
11657614 TACATTGCCATAGTATCTTTCAACCATGGTCTTATTCATTCCCGT-T
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT-TCATAT
*
11657660 -ATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11657705 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * * *
11657751 CATGTAGCCATGGTATCTTACAACCATGGTTTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11657797 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
11657843 CATGTTGCCATGG-AGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTA-TCTTTCAACCATGGTCTTACACATTTCATAT
*
11657889 CATTTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11657935 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACATATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
11657979 TTCAGAAAGT
Statistics
Matches: 365, Mismatches: 40, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
44 1 0.00
45 39 0.11
46 322 0.88
47 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:11660695 original size:38 final size:39
Alignment explanation
Indices: 11660645--11660894 Score: 261
Period size: 46 Copynumber: 5.9 Consensus size: 39
11660635 CTGATATGAA
11660645 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
11660684 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* *
11660722 ATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGTCAACTTG
1 -------ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
11660768 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----T--G
*
11660813 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
11660852 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
11660895 ATGACAGAAA
Statistics
Matches: 182, Mismatches: 6, Indels: 39
0.80 0.03 0.17
Matches are distributed among these distances:
38 72 0.40
39 1 0.01
41 4 0.02
43 1 0.01
44 1 0.01
45 1 0.01
46 102 0.56
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (39 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:11660751 original size:46 final size:46
Alignment explanation
Indices: 11660684--11660938 Score: 303
Period size: 46 Copynumber: 5.7 Consensus size: 46
11660674 TGGCAACCTG
11660684 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
* *
11660730 TGTGTAAGACCATGGTTGAAAGATACCATGTCAA-C---T-T---G
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
* *
11660768 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
* *
11660814 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATAT-AAAA
** * * *
11660861 -GAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
* * * *
11660906 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
11660939 TCACGTCAAA
Statistics
Matches: 183, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
38 33 0.18
39 1 0.01
41 1 0.01
42 2 0.01
43 1 0.01
45 5 0.03
46 138 0.75
47 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
Found at i:11660775 original size:84 final size:84
Alignment explanation
Indices: 11660634--11660938 Score: 412
Period size: 84 Copynumber: 3.5 Consensus size: 84
11660624 GAGTGTGCTC
*
11660634 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
11660699 TTGAAAGATACCATGGCAA
66 TTGAAAGATACCATGGCAA
* *
11660718 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGTCAACTTGTGTGTAAGACCATGG
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
11660783 TTGAAAGATACCATGGCAA
66 TTGAAAGATACCATGGCAA
* * * *
11660802 CCTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---TG--TAA
11660867 GACCATGGTTGAAAGATACCATGGCAA
58 GACCATGGTTGAAAGATACCATGGCAA
* * * * * * *
11660894 CATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
11660939 TCACGTCAAA
Statistics
Matches: 196, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
84 127 0.65
87 2 0.01
90 1 0.01
92 66 0.34
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (84 bp):
CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
TTGAAAGATACCATGGCAA
Found at i:11661244 original size:23 final size:25
Alignment explanation
Indices: 11661199--11661245 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
11661189 AATAAATATA
*
11661199 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
11661224 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
11661246 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:11665173 original size:18 final size:17
Alignment explanation
Indices: 11665145--11665178 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11665135 GGCTTTAACC
11665145 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
11665162 CATTATCAGAATCAGAA
1 CATTA-CAGAATAAGAA
11665179 TCAGAATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.21
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:11665175 original size:6 final size:6
Alignment explanation
Indices: 11665166--11665281 Score: 146
Period size: 6 Copynumber: 19.3 Consensus size: 6
11665156 AAGAAACATT
11665166 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * *
11665214 ATCAGA ATCAGA ATCAG- GTGACA ATCAGA ATCAGA ATTAGT ATCAGGTA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
*
11665263 A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
11665282 GTGAATGCAA
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
5 4 0.04
6 86 0.91
7 3 0.03
8 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:11665696 original size:27 final size:28
Alignment explanation
Indices: 11665634--11665697 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
11665624 TAGTCACTTG
*
11665634 CCCACAAGGGCAAAACAGTCATTTAACA
1 CCCACAAGGGCAAAACAGTAATTTAACA
* ** *
11665662 CCC-TAAGGGCAAAATGGTAATTTTAC-
1 CCCACAAGGGCAAAACAGTAATTTAACA
11665688 CCCACAAGGG
1 CCCACAAGGG
11665698 TATCTCGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.79
28 3 0.10
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (28 bp):
CCCACAAGGGCAAAACAGTAATTTAACA
Found at i:11665818 original size:27 final size:27
Alignment explanation
Indices: 11665677--11665810 Score: 178
Period size: 27 Copynumber: 5.0 Consensus size: 27
11665667 AGGGCAAAAT
* ** * *
11665677 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCTTACAGGGGTATTTC
*
11665704 GGTAATTCTACCTTACAGGAGTATTTC
1 GGTAATTCTACCTTACAGGGGTATTTC
11665731 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCTTACAGGGGTATTTC
* *
11665758 GGTATTTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCTTACAGGGGTATTTC
* *
11665785 GGTAATTCTACCCTATAGGGGTATTT
1 GGTAATTCTACCTTACAGGGGTATTT
11665811 TGATAATTTC
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCTTACAGGGGTATTTC
Found at i:11665831 original size:81 final size:81
Alignment explanation
Indices: 11665691--11665842 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 81
11665681 ATTTTACCCC
* * **
11665691 ACAAGGGTATCTCGGTAATTCTACCTTACAGGAGTATTTCGGTAATTCTACCTTACAGGGGTATT
1 ACAAGGGTATCTCGGTAATTCTACCCTACAGGAGTATTTCGATAATTCTACAATACAGGGGTATT
11665756 TCGGTATTTCTACCTT
66 TCGGTATTTCTACCTT
* * * *
11665772 ACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTGATAATT-TCACAA-ATCAGGGGTA
1 ACAAGGGTATCTCGGTAATTCTACCCTACAGGAGTATTTCGATAATTCT-ACAATA-CAGGGGTA
*
11665835 TTTTGGTA
64 TTTCGGTA
11665843 ATTTTACAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
80 2 0.03
81 58 0.97
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (81 bp):
ACAAGGGTATCTCGGTAATTCTACCCTACAGGAGTATTTCGATAATTCTACAATACAGGGGTATT
TCGGTATTTCTACCTT
Found at i:11665834 original size:54 final size:54
Alignment explanation
Indices: 11665677--11665845 Score: 153
Period size: 54 Copynumber: 3.1 Consensus size: 54
11665667 AGGGCAAAAT
* * * * * * ** *
11665677 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCTTACAGGAGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACAATACAGGGGTATTTC
* * ** *
11665731 GGTAATTCTACCTTACAGGGGTATTTCGGTATTTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACAATACAGGGGTATTTC
* * *
11665785 GGTAATTCTACCCTATAGGGGTATTTTGATAATTTC-ACAA-ATCAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTCGAT-ATTTCTACAATA-CAGGGGTATTTC
11665839 GGTAATT
1 GGTAATT
11665846 TTACAAACCA
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 91 0.94
55 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (54 bp):
GGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACAATACAGGGGTATTTC
Found at i:11665928 original size:27 final size:27
Alignment explanation
Indices: 11665803--11666341 Score: 279
Period size: 27 Copynumber: 20.3 Consensus size: 27
11665793 TACCCTATAG
* * * * *
11665803 GGGTATTTTGATAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11665830 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
** *
11665857 GGGTATTTTGGTAATTTTATTGATCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11665884 AGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * *
11665911 GGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*** * * ***
11665938 GGGTAAAATGGTAATTCTGTAAATTGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*** * * * * *
11665965 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*** *
11665992 GGGTAAAATGATAATTTTAT----C--
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * * * *
11666013 --TTATTTCGATAATTTTACAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * **
11666038 GGATATTTGGGTAATTTTATAAATCGG
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * ** *
11666065 GGGTACTTTGATAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
** * * ** *
11666092 GGGTATTTCAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11666119 GGGTATTTTGGTAATTTTATAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11666146 GGGTATTTTGATAATTTTACAAA-C-A
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
11666171 GTGGTATTTTGGTAATTTTACAAACTAG
1 G-GGTATTTTGGTAATTTTATAAACCAA
* *
11666199 GGGTATTTTGATAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11666226 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
11666253 GGGTATTTTGGTGATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
11666280 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11666307 GGGTATTTTGGTAATTTTGTAAATCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
*
11666334 AGGTATTT
1 GGGTATTT
11666342 AACCCAATAT
Statistics
Matches: 415, Mismatches: 86, Indels: 22
0.79 0.16 0.04
Matches are distributed among these distances:
19 12 0.03
23 2 0.00
25 1 0.00
26 21 0.05
27 378 0.91
28 1 0.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAA
Found at i:11666083 original size:54 final size:54
Alignment explanation
Indices: 11666014--11666324 Score: 315
Period size: 54 Copynumber: 5.8 Consensus size: 54
11666004 AATTTTATCT
* * * * * *
11666014 TATTTCGATAATTTTACAAATC-GAGGATATTTGGGTAATTTTATAAATCGGGGG
1 TATTTTGATAATTTTACAAACCAG-GGGTATTTTGGTAATTTTACAAATCAGGGG
* ** ** * *
11666068 TACTTTGATAATTTTACAAGTC-GAGGGTATTTCAGTAATTTCACAAATTAGGGG
1 TATTTTGATAATTTTACAAACCAG-GGGTATTTTGGTAATTTTACAAATCAGGGG
* * * * *
11666122 TATTTTGGTAATTTTATAAACTAGGGGTATTTTGATAATTTTACAAA-CAGTGG
1 TATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAATCAGGGG
* * * ** * *
11666175 TATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTGTAAACCAAGGG
1 TATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAATCAGGGG
* * *
11666229 TATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTACAAACCAGGGG
1 TATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAATCAGGGG
11666283 TATTTT-AGTAATTTTACAAACCAGGGGTATTTTGGTAATTTT
1 TATTTTGA-TAATTTTACAAACCAGGGGTATTTTGGTAATTTT
11666325 GTAAATCAAA
Statistics
Matches: 219, Mismatches: 35, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
53 48 0.22
54 170 0.78
55 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (54 bp):
TATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAATCAGGGG
Found at i:11666126 original size:81 final size:79
Alignment explanation
Indices: 11666022--11666324 Score: 356
Period size: 81 Copynumber: 3.8 Consensus size: 79
11666012 CTTATTTCGA
* * * * * *
11666022 TAATTTTACAAA-TCGAGGATATTTGGGTAATTTTATAAATCGGGGGTACTTTGATAATTTTACA
1 TAATTTTACAAACTAG-GGGTATTTTGGTAATTTTATAAACCAGGGGTATTTTGATAATTTTACA
* **
11666086 AGTCGAGGGTATTTCAG
65 A-AC-AGGGTATTTTGG
* * *
11666103 TAATTTCACAAATTAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGATAATTTTACAA
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAGGGGTATTTTGATAATTTTACAA
11666168 ACAGTGGTATTTTGG
66 ACAG-GGTATTTTGG
* * * *
11666183 TAATTTTACAAACTAGGGGTATTTTGATAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAA
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAGGGGTATTTTGATAATTTTACAA
11666248 ACCAGGGGTATTTTGG
66 A-CA-GGGTATTTTGG
* * * * *
11666264 TGATTTTACAAACCAGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTT
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAGGGGTATTTTGATAATTTT
11666325 GTAAATCAAA
Statistics
Matches: 193, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
79 2 0.01
80 68 0.35
81 120 0.62
82 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (79 bp):
TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAGGGGTATTTTGATAATTTTACAA
ACAGGGTATTTTGG
Found at i:11672532 original size:14 final size:14
Alignment explanation
Indices: 11672513--11672543 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
11672503 AACCTTATAA
11672513 AGATTTTAGGGCCT
1 AGATTTTAGGGCCT
11672527 AGATTTTAGGGCCT
1 AGATTTTAGGGCCT
11672541 AGA
1 AGA
11672544 GTGGTGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (14 bp):
AGATTTTAGGGCCT
Found at i:11684473 original size:9 final size:9
Alignment explanation
Indices: 11684405--11684472 Score: 77
Period size: 9 Copynumber: 7.6 Consensus size: 9
11684395 TTTATACAAA
11684405 TAATTCGGT
1 TAATTCGGT
11684414 TAATTCGGT
1 TAATTCGGT
*
11684423 TAATTTGCG-
1 TAATTCG-GT
11684432 TAATTCGAG-
1 TAATTCG-GT
11684441 TAATTCGGT
1 TAATTCGGT
*
11684450 TAATTCGAT
1 TAATTCGGT
*
11684459 TAATTTGGT
1 TAATTCGGT
11684468 TAATT
1 TAATT
11684473 TTATACTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
8 1 0.02
9 49 0.96
10 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:11684890 original size:20 final size:20
Alignment explanation
Indices: 11684862--11684936 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 20
11684852 CAACATAGGG
11684862 GTATCGATACCTAAGCCTAT
1 GTATCGATACCTAAGCCTAT
* * * * *
11684882 GTATTGATATCAATACAACATAGG
1 GTATCGATA-C-CTA-AGCCTA-T
11684906 GGTATCGATACCTAAGCCTAT
1 G-TATCGATACCTAAGCCTAT
*
11684927 GTATTGATAC
1 GTATCGATAC
11684937 ATTAGTGCTA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
20 16 0.41
21 2 0.05
22 6 0.15
23 6 0.15
24 2 0.05
25 7 0.18
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (20 bp):
GTATCGATACCTAAGCCTAT
Found at i:11684908 original size:45 final size:45
Alignment explanation
Indices: 11684844--11684935 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
11684834 ACTCGTATGG
11684844 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
1 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
11684889 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
1 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
11684934 TA
1 TA
11684936 CATTAGTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (45 bp):
TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
Found at i:11687202 original size:46 final size:47
Alignment explanation
Indices: 11687136--11687231 Score: 124
Period size: 48 Copynumber: 2.1 Consensus size: 47
11687126 ATAGAGCAAA
* * * *
11687136 AATGAGCATGTAAGTCCATATCA-GT-TATATGGCTTTGGAGACAGG
1 AATGAGCATGTAAGCCCATATCATATATATATGGCATTGAAGACAGG
*
11687181 AATGAGCCATGTAAGCCCATATTATATATATATGGCATTGAAGACAGG
1 AATGAG-CATGTAAGCCCATATCATATATATATGGCATTGAAGACAGG
11687229 AAT
1 AAT
11687232 AATTCATGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 6 0.14
46 15 0.35
47 1 0.02
48 21 0.49
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (47 bp):
AATGAGCATGTAAGCCCATATCATATATATATGGCATTGAAGACAGG
Found at i:11693538 original size:93 final size:93
Alignment explanation
Indices: 11693379--11693564 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
11693369 AAGGGTCCAC
*
11693379 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTAGATG
1 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTACATG
*
11693444 GATATGATATTTAGACTACTAATACATT
66 GATATGAAATTTAGACTACTAATACATT
* * *
11693472 AAAAAATACAAGATAGCTTAAGTACTTATGACGCTTACATGTACAAGTTTAATTATTATTACATG
1 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTACATG
11693537 GATATGAAATTTAGACTACTAATACATT
66 GATATGAAATTTAGACTACTAATACATT
11693565 GAGAAAGCAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (93 bp):
AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTACATG
GATATGAAATTTAGACTACTAATACATT
Found at i:11700237 original size:24 final size:24
Alignment explanation
Indices: 11700169--11700250 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
11700159 CGAGCAATAA
**
11700169 AATGGGAAGCTCATGTGAGCCATGT
1 AATGGGAAGCTCATAAGAGCCAT-T
**
11700194 AACAGGAAGCTC-TAGAGAGCCATT
1 AATGGGAAGCTCATA-AGAGCCATT
* *
11700218 AATGGGAAGCTCATACGAGCCAAT
1 AATGGGAAGCTCATAAGAGCCATT
11700242 AATGGGAAG
1 AATGGGAAG
11700251 GTTCAAGCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
24 28 0.60
25 19 0.40
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.18
Consensus pattern (24 bp):
AATGGGAAGCTCATAAGAGCCATT
Found at i:11700267 original size:25 final size:24
Alignment explanation
Indices: 11700169--11700278 Score: 80
Period size: 25 Copynumber: 4.5 Consensus size: 24
11700159 CGAGCAATAA
** *
11700169 AATGGGAAGCTCATGTGAGCCATGT
1 AATGGGAAGCTCATACGAGCCA-AT
** * *
11700194 AACAGGAAGCTC-TAGAGAGCCATT
1 AATGGGAAGCTCATA-CGAGCCAAT
11700218 AATGGGAAGCTCATACGAGCCAAT
1 AATGGGAAGCTCATACGAGCCAAT
*
11700242 AATGGGAAGGTTCA-AGCGAGCCAAT
1 AATGGGAA-GCTCATA-CGAGCCAAT
* *
11700267 ATTGGAAAGCTC
1 AATGGGAAGCTC
11700279 CGAAGAGCTT
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
24 31 0.46
25 37 0.54
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (24 bp):
AATGGGAAGCTCATACGAGCCAAT
Found at i:11700301 original size:25 final size:24
Alignment explanation
Indices: 11700273--11700338 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 24
11700263 CAATATTGGA
*
11700273 AAGCTCCGAAGAGCTTTTAATCGGG
1 AAGCTCCGAAGAGCTTTT-ATCGAG
*
11700298 AAGCTCATGAAAGAGCCTTTTATCGAG
1 AAGCTC-CG-AAGAG-CTTTTATCGAG
*
11700325 AAGCTTCGAAGAGC
1 AAGCTCCGAAGAGC
11700339 CATATATCGG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
24 1 0.03
25 11 0.32
26 2 0.06
27 15 0.44
28 5 0.15
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (24 bp):
AAGCTCCGAAGAGCTTTTATCGAG
Found at i:11704064 original size:43 final size:43
Alignment explanation
Indices: 11704002--11704124 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
11703992 CTGAACTCAT
* * ** * *
11704002 TCACTGGCATT-TCGCCTGCTAGGCTTGAAGCCCGATATCATT
1 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATAATC
*
11704044 TCACCGGTATTATAGCCTGCTAGGCCCGAAGCCCGATATAATC
1 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATAATC
* * *
11704087 TCACCGGCATTATAGCCTACAAGGCCCAAAGCCCGATA
1 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
11704125 ATATTATTCA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 9 0.13
43 60 0.87
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATAATC
Found at i:11706077 original size:14 final size:15
Alignment explanation
Indices: 11706048--11706077 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11706038 AAAAATTTAG
11706048 ACATGATACTTTCAC
1 ACATGATACTTTCAC
11706063 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
11706077 A
1 A
11706078 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:11711529 original size:55 final size:55
Alignment explanation
Indices: 11711390--11711533 Score: 146
Period size: 55 Copynumber: 2.6 Consensus size: 55
11711380 TCGGACATGG
** * **
11711390 CCGTGGGTGAACCTGTCAAAACAACACGAACGTGCAACACGCTCGTACCTTGAAA
1 CCGTGGGTGAACCTGTCAAAACAACACGGGCGTGCAACACGCCCGTACCAAGAAA
** * ** * * *
11711445 CTAT-GGTCGAACCTGTTAAATTAAAACGGGCGTGCAACACGCCCGTGCCAAGCAA
1 CCGTGGGT-GAACCTGTCAAAACAACACGGGCGTGCAACACGCCCGTACCAAGAAA
*
11711500 CCGTGGGTGAACCTGCCAAAACAACACGGGCGTG
1 CCGTGGGTGAACCTGTCAAAACAACACGGGCGTG
11711534 GACCTTCATA
Statistics
Matches: 67, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
54 3 0.04
55 61 0.91
56 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (55 bp):
CCGTGGGTGAACCTGTCAAAACAACACGGGCGTGCAACACGCCCGTACCAAGAAA
Found at i:11712689 original size:3 final size:3
Alignment explanation
Indices: 11712681--11712720 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
11712671 GTGTTCTTAA
*
11712681 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11712721 CATATTAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Done.