Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008979.1 Hibiscus syriacus cultivar Beakdansim tig00112339_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1115631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:160109 original size:30 final size:31
Alignment explanation
Indices: 160073--160174 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
160063 TAGTTAATTT
160073 TTAATTTAATTCCTAAATTTTAAAT-AAATA
1 TTAATTTAATTCCTAAATTTTAAATAAAATA
* * *
160103 TTAATTTAACTCCTAAAATTTAGATAAAATA
1 TTAATTTAATTCCTAAATTTTAAATAAAATA
* * * * *
160134 TCATTTTTA-TCTTTGAATTTTAAATAAAATA
1 TTAATTTAATTC-CTAAATTTTAAATAAAATA
*
160165 TAAATTTAAT
1 TTAATTTAAT
160175 CCTTGAATCC
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
30 24 0.43
31 32 0.57
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (31 bp):
TTAATTTAATTCCTAAATTTTAAATAAAATA
Found at i:160134 original size:31 final size:30
Alignment explanation
Indices: 160073--160130 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
160063 TAGTTAATTT
* *
160073 TTAATTTAATTCCTAAATTTTAAATAAATA
1 TTAATTTAACTCCTAAAATTTAAATAAATA
*
160103 TTAATTTAACTCCTAAAATTTAGATAAA
1 TTAATTTAACTCCTAAAATTTAAATAAA
160131 ATATCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (30 bp):
TTAATTTAACTCCTAAAATTTAAATAAATA
Found at i:162926 original size:41 final size:40
Alignment explanation
Indices: 162868--163177 Score: 188
Period size: 41 Copynumber: 7.5 Consensus size: 40
162858 TAACATTAAC
* * *
162868 GGCGTTTCTCAACAAACGCCGCTAAAACTCGTACTTTAGT
1 GGCGTTTTTTAACAAACGCCGCTAAAACTAGTACTTTAGT
*
162908 GGCGTTTATTTAACAAACGCCGCTAAATA-TCAGTACATTAGT
1 GGCGTTT-TTTAACAAACGCCGCTAAA-ACT-AGTACTTTAGT
* * *
162950 GGCGTTTGTTAACAAACG-CGCCATAGAA-TAGTTCTTTAGT
1 GGCGTTTTTTAACAAACGCCG-C-TAAAACTAGTACTTTAGT
* * * * ** *
162990 GGTG-TTTTTAGAAAAACACCG-TAATA-GGGTACATATATCGT
1 GGCGTTTTTTA-ACAAACGCCGCTAAAACTAGTAC-T-T-TAGT
* * *
163031 GGCG-TTTTTAGAAAAACGCCGCTAAAACATAATACTTTAAT
1 GGCGTTTTTTA-ACAAACGCCGCTAAAAC-TAGTACTTTAGT
* * * *
163072 GGC-ATTTTGAGCAAAAACGCCG-TCAAATACTCGTACTTTAGT
1 GGCGTTTTTTA--ACAAACGCCGCT-AAA-ACTAGTACTTTAGT
* *
163114 GGTGTTTTTAAACAAACGCCGCTAAAACATAGTACTTTAGT
1 GGCGTTTTTTAACAAACGCCGCTAAAAC-TAGTACTTTAGT
*
163155 GGCGTTTTTTGAATAAACGCCGC
1 GGCGTTTTTT-AACAAACGCCGC
163178 AATTTATCAG
Statistics
Matches: 210, Mismatches: 39, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
38 6 0.03
39 6 0.03
40 29 0.14
41 97 0.46
42 61 0.29
43 8 0.04
44 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (40 bp):
GGCGTTTTTTAACAAACGCCGCTAAAACTAGTACTTTAGT
Found at i:163173 original size:83 final size:81
Alignment explanation
Indices: 162868--163204 Score: 273
Period size: 83 Copynumber: 4.1 Consensus size: 81
162858 TAACATTAAC
* * * *
162868 GGCGTTTCTCAACAAACGCCGCTAAAAC-TCGTACTTTAGTGGCGTTTATTTA-ACAAACGCCG-
1 GGCGTTTTTAAACAAACGCCGCTAAAACATAGTACTTTAGTGGCG-TT-TTTAGAAAAACGCCGT
*
162930 CTAAATATCAGTACATTAGT
64 C-AAATATC-GTACTTTAGT
* * * * *
162950 GGCGTTTGTT-AACAAACG-CGCCATAGA-ATAGTTCTTTAGTGGTGTTTTTAGAAAAACACCGT
1 GGCGTTT-TTAAACAAACGCCGCTA-AAACATAGTACTTTAGTGGCGTTTTTAGAAAAACGCCGT
** *
163012 --AATAGGGTACATATATCGT
64 CAAATATCGTAC-T-T-TAGT
* * * *
163031 GGCGTTTTTAGAA-AAACGCCGCTAAAACATAATACTTTAATGGCATTTTGAGCAAAAACGCCGT
1 GGCGTTTTTA-AACAAACGCCGCTAAAACATAGTACTTTAGTGGCGTTTTTAG-AAAAACGCCGT
163095 CAAATACTCGTACTTTAGT
64 CAAATA-TCGTACTTTAGT
* *
163114 GGTGTTTTTAAACAAACGCCGCTAAAACATAGTACTTTAGTGGCGTTTTTTGAATAAACGCCG-C
1 GGCGTTTTTAAACAAACGCCGCTAAAACATAGTACTTTAGTGGCGTTTTTAGAA-AAACGCCGTC
*
163178 AATTTATCAGTACATTTAGT
65 AA-ATATC-GTAC-TTTAGT
163198 GGC-TTTT
1 GGCGTTTT
163205 CTATTTACAA
Statistics
Matches: 202, Mismatches: 32, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
78 4 0.02
79 4 0.02
80 7 0.03
81 31 0.15
82 63 0.31
83 75 0.37
84 9 0.04
85 5 0.02
86 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (81 bp):
GGCGTTTTTAAACAAACGCCGCTAAAACATAGTACTTTAGTGGCGTTTTTAGAAAAACGCCGTCA
AATATCGTACTTTAGT
Found at i:163273 original size:25 final size:25
Alignment explanation
Indices: 163245--163293 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
163235 CTAAGTCCCA
* *
163245 CCCCTTTAACCCTTTTTTCATTTTT
1 CCCCTTCAACCATTTTTTCATTTTT
* *
163270 CCCCTTCATCTATTTTTTCATTTT
1 CCCCTTCAACCATTTTTTCATTTT
163294 CGCCGTTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.12, C:0.31, G:0.00, T:0.57
Consensus pattern (25 bp):
CCCCTTCAACCATTTTTTCATTTTT
Found at i:164516 original size:29 final size:29
Alignment explanation
Indices: 164484--164631 Score: 143
Period size: 29 Copynumber: 5.0 Consensus size: 29
164474 ACTCTTATGC
*
164484 ATATGGATGTTTGTACTTGTTGGGGCTTT
1 ATATGGATGTTTGTACCTGTTGGGGCTTT
*
164513 ATATGGATGTTTGTACCTGTTGGAGCTTT
1 ATATGGATGTTTGTACCTGTTGGGGCTTT
** * *
164542 ATACAGATGTTTGAACCTGTTGGTGCTTT
1 ATATGGATGTTTGTACCTGTTGGGGCTTT
* * *
164571 ACATGGATGTGTATACCTGTTGGTGCTCGCTTT
1 ATATGGATGTTTGTACCTGTTGG-G---GCTTT
* * * *
164604 ATATGGATCTCTGTACATGTTGGTGCTT
1 ATATGGATGTTTGTACCTGTTGGGGCTT
164632 AGTCTTGCTT
Statistics
Matches: 96, Mismatches: 19, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
29 73 0.76
33 23 0.24
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (29 bp):
ATATGGATGTTTGTACCTGTTGGGGCTTT
Found at i:164610 original size:33 final size:33
Alignment explanation
Indices: 164566--164630 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
164556 ACCTGTTGGT
* * *
164566 GCTTTACATGGATGTGTATACCTGTTGGTGCTC
1 GCTTTACATGGATCTCTATACATGTTGGTGCTC
* *
164599 GCTTTATATGGATCTCTGTACATGTTGGTGCT
1 GCTTTACATGGATCTCTATACATGTTGGTGCT
164631 TAGTCTTGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.42
Consensus pattern (33 bp):
GCTTTACATGGATCTCTATACATGTTGGTGCTC
Found at i:166833 original size:21 final size:21
Alignment explanation
Indices: 166809--166867 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
166799 TGATTTATTA
*
166809 TTATGAATTTCAAGTTTCTTG
1 TTATGAATTTCAAGTTTCATG
*
166830 TTATGAATTTCAAGTTTGATG
1 TTATGAATTTCAAGTTTCATG
* *
166851 TTATGGATGTCAAGTTT
1 TTATGAATTTCAAGTTT
166868 ATTGGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (21 bp):
TTATGAATTTCAAGTTTCATG
Found at i:167119 original size:43 final size:43
Alignment explanation
Indices: 166973--167297 Score: 296
Period size: 43 Copynumber: 7.6 Consensus size: 43
166963 AAAAAATGTT
* *
166973 GCTATAGAT-GTGACCGTTTGCGGCGTTTGTTCCAAAAACGCC
1 GCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
* * * **
167015 GCTATAGAT-CTGACCTATTGTGGCGTTTGTATAAAAAAACGCC
1 GCTATAGATATTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCC
* * *
167058 TCTATAGA-ACTGACCTTTTGCGGCGTTTGTATCTAAAAACGCC
1 GCTATAGATATTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCC
* * * * * * *
167101 GCTATATATATTGACTTTTTGCGGTGTTTATTCTAAAAGCGTC
1 GCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
** * * **
167144 GCTATAGATATCAACCTTTTGCAGCGTTTGTTCCAAAAATGTT
1 GCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
* * *
167187 GCTATAGATATCGACCTTTTGCGGTGTTTGTTCCAAAAATGCC
1 GCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
* * * ** * *
167230 GCTATAGATGTCGACCTTTTACGATGTTTGTTTCAGAAACGCC
1 GCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
* *
167273 GCTATAGATCTTGACCTGTTGCGGC
1 GCTATAGATATTGACCTTTTGCGGC
167298 ATTTTTTGTT
Statistics
Matches: 233, Mismatches: 47, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
42 26 0.11
43 189 0.81
44 18 0.08
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (43 bp):
GCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
Found at i:169042 original size:3 final size:3
Alignment explanation
Indices: 169034--169116 Score: 89
Period size: 3 Copynumber: 26.7 Consensus size: 3
169024 CACCATTTTC
169034 TAT TAT TAT TATT TAT TAT TAT TAT TAT T-T TAT ATAT ATAT ATAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TAT TAT
* *
169082 TAT TAT T-T TATT TAT TAT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
169117 CAAACGGGCC
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 50 0.70
4 17 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:169079 original size:26 final size:23
Alignment explanation
Indices: 169034--169104 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 23
169024 CACCATTTTC
169034 TATTATTATTATTTATTATTATTAT
1 TATT-TTATTA-TTATTATTATTAT
169059 TATTTTATATATATATATATTATTAT
1 TATTTTAT-TAT-TAT-TATTATTAT
169085 TATTTTATTTATTATTATTA
1 TATTTTA-TTATTATTATTA
169105 AAATTATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
24 10 0.24
25 12 0.29
26 19 0.45
27 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTTATTATTATTATTATTAT
Found at i:170516 original size:27 final size:27
Alignment explanation
Indices: 170429--170516 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
170419 TGCTTTTAAA
*
170429 TATATAGTTTTAATTTTATTTTTATTAT
1 TATATA-TTTAAATTTTATTTTTATTAT
** * *
170457 TGAT-TATTTATGTTTTAATTTTACTTGT
1 T-ATATATTTAAATTTTATTTTTA-TTAT
*
170485 T-TATATTTAAATATTATTTTTATTAT
1 TATATATTTAAATTTTATTTTTATTAT
170511 TATATA
1 TATATA
170517 GTCATATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
26 5 0.11
27 32 0.70
28 7 0.15
29 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.65
Consensus pattern (27 bp):
TATATATTTAAATTTTATTTTTATTAT
Found at i:181944 original size:10 final size:10
Alignment explanation
Indices: 181929--181971 Score: 77
Period size: 10 Copynumber: 4.2 Consensus size: 10
181919 ATGCTTGAAG
181929 AAAAAGAAAA
1 AAAAAGAAAA
181939 AAAAAGAAAA
1 AAAAAGAAAA
181949 AAAGAAGAAAA
1 AAA-AAGAAAA
181960 AAAAAGAAAA
1 AAAAAGAAAA
181970 AA
1 AA
181972 GGGGTCAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 22 0.69
11 10 0.31
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:181958 original size:21 final size:21
Alignment explanation
Indices: 181932--181971 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
181922 CTTGAAGAAA
181932 AAGAAAAAAAAAGAAAAAAAG
1 AAGAAAAAAAAAGAAAAAAAG
181953 AAGAAAAAAAAAGAAAAAA
1 AAGAAAAAAAAAGAAAAAA
181972 GGGGTCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAAAAAAG
Found at i:182366 original size:19 final size:17
Alignment explanation
Indices: 182324--182372 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
182314 TATTTTCTCT
182324 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
182340 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
182358 AAAATTCAATTTATT
1 -AAATTCAATTTATT
182373 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 1 0.04
19 13 0.46
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:182871 original size:114 final size:114
Alignment explanation
Indices: 182666--182888 Score: 383
Period size: 114 Copynumber: 2.0 Consensus size: 114
182656 TGCCACGTTA
* *
182666 TCATGGTAGAAATAAGGAGGCCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * *
182731 TTTGGTATAAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGC
66 TTCGGTATAAACCACAAAACCAATCATTAGAATTGAAAGATGAATTTGC
*
182780 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
182845 TTCGGTATGAACCACAAAACCAATCATTAGAATTGAAAGATGAA
66 TTCGGTATAAACCACAAAACCAATCATTAGAATTGAAAGATGAA
182889 CTGCATGATT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTCGGTATAAACCACAAAACCAATCATTAGAATTGAAAGATGAATTTGC
Found at i:184018 original size:116 final size:116
Alignment explanation
Indices: 183836--184366 Score: 771
Period size: 116 Copynumber: 4.7 Consensus size: 116
183826 TCCCAGAGAA
* * *
183836 AGTTCTTAATGAGAAGAA--C-TCATTTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* *
183898 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
66 TTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
*
183949 AGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* *
184014 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
66 TTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
*
184065 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAAAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
*
184129 TTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
66 TTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
* *
184180 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * * * * *
184245 TTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AA
66 TTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAG-GTAG
* **
184296 AGTTCATAATGAGAAGAA--C-TCATCT---GAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
184354 TTCAACCTTTTGC
66 TTCAACCTTTTGC
184367 ATAATTCTAT
Statistics
Matches: 388, Mismatches: 25, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
109 38 0.10
110 3 0.01
113 23 0.06
114 1 0.00
115 112 0.29
116 210 0.54
117 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (116 bp):
AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
Found at i:184161 original size:231 final size:227
Alignment explanation
Indices: 183818--184366 Score: 807
Period size: 231 Copynumber: 2.4 Consensus size: 227
183808 ATAGATCAAC
* * * * *
183818 ATCAACTTTCCCAGAGAAAGTTCTTAATGAGAAGAACTCATTTGAAGAAGGAAGAATAAGTTCAT
1 ATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAA-AAGAAGTTCAT
* *
183883 AATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTA
64 AATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTA
* *
183948 GAGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
129 GAGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTT
* ** * *
184013 GTTCAACCTTTTGTTTGAATTCATCATTTGATGG
194 GTTCAACCTTTTGCTCAAATCCATCACTTGATGG
*
184047 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAAAGAAGTT
1 ATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG-AAAAGAAGTT
*
184111 CATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAG
61 CATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAG
*
184176 GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAA
126 GTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGAAAGAAGAAATTCATAATGAGAAGAA
184241 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGG
191 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGG
* * * *
184278 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG--AAGAAGTTCACAA
1 ATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAGAAGTTCATAA
**
184341 TGAGAAGAGCTTGTTCAACCTTTTGC
66 TGAGAAGAATTTGTTCAACCTTTTGC
184367 ATAATTCTAT
Statistics
Matches: 289, Mismatches: 25, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
225 35 0.12
228 14 0.05
229 31 0.11
231 195 0.67
232 14 0.05
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (227 bp):
ATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
GTTCATAATGAGAAGAACTCGTCATCTAAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGT
TCAACCTTTTGCTCAAATCCATCACTTGATGG
Found at i:184725 original size:3 final size:3
Alignment explanation
Indices: 184717--184795 Score: 101
Period size: 3 Copynumber: 26.7 Consensus size: 3
184707 CCACATTTTC
184717 TAT TAT TAT TATT TAT TAT TAT TAT T-T TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
184761 TAT TAT T-T TATT TAT TAT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
184796 CAAACGGGCC
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 6 0.09
3 55 0.82
4 6 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:184735 original size:13 final size:13
Alignment explanation
Indices: 184717--184782 Score: 91
Period size: 13 Copynumber: 5.0 Consensus size: 13
184707 CCACATTTTC
184717 TATTATTATTATT
1 TATTATTATTATT
184730 TATTATTATTATT
1 TATTATTATTATT
184743 T-TATATTATTA-T
1 TAT-TATTATTATT
184755 TATTATTATTATTT
1 TATTATTATTA-TT
184769 TATTTATTATTATT
1 TA-TTATTATTATT
184783 AAAATTATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
12 11 0.23
13 23 0.48
14 5 0.10
15 9 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:184999 original size:16 final size:16
Alignment explanation
Indices: 184978--185018 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
184968 CCAACAGCAA
184978 ACCCTAGGGTTATGAT
1 ACCCTAGGGTTATGAT
184994 ACCCTAGGGTTATGAT
1 ACCCTAGGGTTATGAT
185010 ACCCTAGGG
1 ACCCTAGGG
185019 CCACGACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (16 bp):
ACCCTAGGGTTATGAT
Found at i:187740 original size:90 final size:92
Alignment explanation
Indices: 187536--187741 Score: 249
Period size: 90 Copynumber: 2.3 Consensus size: 92
187526 CCCTCATTTT
* * * *
187536 GTTGAAA-ATCATTTGTTATATAAAAGAAGTGGTGAAATCGAGATTTTATGTAAATGTTAGAGGA
1 GTTGAAAGTTCATTCGTTATATAAAAGAAGCGGTGAAATCGAGATTTTATGTAAATGCTAGAGGA
*
187600 ACGAGAATAGATTTGTTAGATTTGAAG
66 ACGAGAATAGATTTGTTAGATTGGAAG
* * * ** *
187627 GTTGAAAGTTCATTTGTTGTATAAAAGAAGCGTTGAAATCTCGA-TTTGTGTAAATGCTAGTA-G
1 GTTGAAAGTTCATTCGTTATATAAAAGAAGCGGTGAAATCGAGATTTTATGTAAATGCTAG-AGG
* *
187690 AACGGGAATAGA-TTGTTGGATTGGAAG
65 AACGAGAATAGATTTGTTAGATTGGAAG
*
187717 GTTGAAAGTTCCTTCGTTATATAAA
1 GTTGAAAGTTCATTCGTTATATAAA
187742 TTTTTTAATT
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
90 35 0.35
91 33 0.33
92 31 0.31
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (92 bp):
GTTGAAAGTTCATTCGTTATATAAAAGAAGCGGTGAAATCGAGATTTTATGTAAATGCTAGAGGA
ACGAGAATAGATTTGTTAGATTGGAAG
Found at i:187805 original size:22 final size:22
Alignment explanation
Indices: 187780--187857 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
187770 GTTAATGTAT
187780 AATTTAAAATTAAATTGAATCG
1 AATTTAAAATTAAATTGAATCG
* * * *
187802 AATTTAAATTTACATTAATTAGTTG
1 AATTTAAAATTAAATTGA--A-TCG
*
187827 AGTCTTAAAATTAAATTGAATCG
1 AAT-TTAAAATTAAATTGAATCG
187850 AATTTAAA
1 AATTTAAA
187858 TTTACATTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
22 20 0.48
23 4 0.10
24 2 0.05
25 4 0.10
26 12 0.29
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (22 bp):
AATTTAAAATTAAATTGAATCG
Found at i:187836 original size:48 final size:49
Alignment explanation
Indices: 187783--187884 Score: 188
Period size: 48 Copynumber: 2.1 Consensus size: 49
187773 AATGTATAAT
187783 TTAAAATTAAATTGAATCGAATTTAAATTTACATTAA-TTAGTTGAGTC
1 TTAAAATTAAATTGAATCGAATTTAAATTTACATTAATTTAGTTGAGTC
*
187831 TTAAAATTAAATTGAATCGAATTTAAATTTACATTAATTTAGTTGAGTG
1 TTAAAATTAAATTGAATCGAATTTAAATTTACATTAATTTAGTTGAGTC
187880 TTAAA
1 TTAAA
187885 CTTGAACTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 37 0.71
49 15 0.29
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (49 bp):
TTAAAATTAAATTGAATCGAATTTAAATTTACATTAATTTAGTTGAGTC
Found at i:188637 original size:21 final size:20
Alignment explanation
Indices: 188611--188649 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
188601 TAAAACGTCC
188611 AATAATAAATTTCCAATAAAA
1 AATAAT-AATTTCCAATAAAA
*
188632 AATAATATTTTCCAATAA
1 AATAATAATTTCCAATAA
188650 TTTTTATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAATTTCCAATAAAA
Found at i:194184 original size:2 final size:2
Alignment explanation
Indices: 194177--194202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
194167 CACATTTGAT
194177 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
194203 CTGAGTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:199567 original size:40 final size:40
Alignment explanation
Indices: 199521--199597 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
199511 AGTTATCTAA
* * *
199521 GGATGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGG
1 GGATGACACGACTCATACGCGATGAAGAGATCTGGTCGGG
* * *
199561 GGATGACACGACTCATATGTGATGAAGAGTTCTGGTC
1 GGATGACACGACTCATACGCGATGAAGAGATCTGGTC
199598 ATCTTTAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.22
Consensus pattern (40 bp):
GGATGACACGACTCATACGCGATGAAGAGATCTGGTCGGG
Found at i:199600 original size:134 final size:134
Alignment explanation
Indices: 199399--199742 Score: 474
Period size: 134 Copynumber: 2.6 Consensus size: 134
199389 GTGATACAGT
* * * * * *
199399 TCCTACGTGATTAGGAAATCTGGTCGGGGAATGACACGGCTCAAACGTGATGAAGAGTTCTGGTC
1 TCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGAAGAGTTCTGGTC
* * *
199464 ATCTTTAGGAAGGGTAATAACTTGGTT-CTAACGCGATAAGGACGACTAGTTATCTAAGGATGAC
66 ATCTTTAGGAAGGGTAATAACTCGATTCCT-ACACGATAAGGACGACTAGTTATCTAAGGATGAC
199528 ACGGC
130 ACGGC
*
199533 TCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATATGTGATGAAGAGTTCTGGTC
1 TCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGAAGAGTTCTGGTC
* * * * * * *
199598 ATCTTTAGGAAGGGTGATAACTCGATTCCTACATGATGAGGACGGCTGGTTATCTAGGGGTGACA
66 ATCTTTAGGAAGGGTAATAACTCGATTCCTACACGATAAGGACGACTAGTTATCTAAGGATGACA
*
199663 CGGT
131 CGGC
* * **
199667 TCCTATGCGATGAGGAGATCTGGTCAGGGGATGACATTACTCATACGTGATGAAGAGTTCTGGTC
1 TCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGAAGAGTTCTGGTC
199732 ATCTTTAGGAA
66 ATCTTTAGGAA
199743 TTATGGTTTC
Statistics
Matches: 186, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
134 184 0.99
135 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (134 bp):
TCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGAAGAGTTCTGGTC
ATCTTTAGGAAGGGTAATAACTCGATTCCTACACGATAAGGACGACTAGTTATCTAAGGATGACA
CGGC
Found at i:199788 original size:28 final size:28
Alignment explanation
Indices: 199748--199827 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
199738 AGGAATTATG
** *
199748 GTTTCAAGGGAAACTGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
199776 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
* *
199804 GTTTTAAGAA-AAACAAACTCAAAG
1 GTTTCAA-AAGAAACAGACTCAAAG
199828 GTGATGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 44 0.96
29 2 0.04
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:200563 original size:65 final size:66
Alignment explanation
Indices: 200400--200616 Score: 165
Period size: 66 Copynumber: 3.3 Consensus size: 66
200390 TTTATTTCAG
* * *
200400 AGAAACAAACTCAAAGATTTTGTATT-TCTAGAGAAACTGTC-TCAAGGGAGACAAAA-TTTGTT
1 AGAAACAAACTCAAAGATTTT-T-TTCTCAAAAGAAATTGTCTTCAA--GAGACAAAATTTTGTT
* *
200462 TTAAT
62 TCAAA
** * * * * * * *
200467 AGAAATGATCTCAAAGGTGGGTATTT-TCAAAAGAATTTGTC-TCGAGAGGCAAAATTTTGTTTC
1 AGAAACAAACTCAAAGAT--TTTTTTCTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTC
200530 AAA
64 AAA
* * * * *
200533 TGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTTTAAGAGATAATATTTTGTTTTAA
1 AGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAA
200598 A
66 A
*
200599 AGAAACAGACTCAAAGAT
1 AGAAACAAACTCAAAGAT
200617 AAATTACCTC
Statistics
Matches: 115, Mismatches: 30, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
64 4 0.03
65 22 0.19
66 57 0.50
67 30 0.26
68 1 0.01
69 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (66 bp):
AGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAA
A
Found at i:201114 original size:36 final size:35
Alignment explanation
Indices: 201069--201180 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 35
201059 CATAATTTGG
*
201069 AAAATTGTCTCAAGTGAGACAACATTTGTTTTTAGA
1 AAAATTGTCTCAAGCGAGACAA-ATTTGTTTTTAGA
* *
201105 AAAATTGTCTCAAACGAGACAAAAATTGTTTTTAGA
1 AAAATTGTCTCAAGCGAGAC-AAATTTGTTTTTAGA
* * *
201141 GAAATTGTCTCAAGCGAGGCAAAGTTTGTTTATGAGA
1 AAAATTGTCTCAAGCGAGACAAA-TTTGTTT-TTAGA
201178 AAA
1 AAA
201181 CGATCTCAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 3 0.05
36 53 0.83
37 8 0.12
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (35 bp):
AAAATTGTCTCAAGCGAGACAAATTTGTTTTTAGA
Found at i:201558 original size:153 final size:153
Alignment explanation
Indices: 201304--201582 Score: 350
Period size: 153 Copynumber: 1.8 Consensus size: 153
201294 AAGTGAGATT
*
201304 AATTTTATTTCAAGTTAATCAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAGCAAGA
1 AATTTTATTTCAAGTTAAACAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAGCAAGA
* * * * *
201369 CGAAGTTGTTTTAAGAGAATTACCTTAAATGAGACAAGATTTGTTTTAAAATTCTCAAAATGTAT
66 CGAAGTTGTTTGAAGAGAATTACCTCAAACGAGACAAAATTCGTTTTAAAATTCTCAAAATGTAT
201434 CGGAAATGTCTCAAGCGAGAAAG
131 CGGAAATGTCTCAAGCGAGAAAG
* * * * * *
201457 AATTTTGTTTCAAG-TACAACAAATT-TAAATTTGTATCTTAGA-GAAAAAATGTCTCAAGCAAT
1 AATTTTATTTCAAGTTA-AACAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAGCAAG
* ** *
201519 ACGAAATTTGCTTTGATAGA-AATTGTCTCAAGCGAGACAAAATTCGTTTTAAAATTCTCAAAAT
65 ACG-AAGTTG-TTTGA-AGAGAATTACCTCAAACGAGACAAAATTCGTTTTAAAATTCTCAAAAT
201583 TTGTGGAAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
151 22 0.21
152 20 0.19
153 61 0.58
154 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (153 bp):
AATTTTATTTCAAGTTAAACAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAGCAAGA
CGAAGTTGTTTGAAGAGAATTACCTCAAACGAGACAAAATTCGTTTTAAAATTCTCAAAATGTAT
CGGAAATGTCTCAAGCGAGAAAG
Found at i:201595 original size:33 final size:33
Alignment explanation
Indices: 201557--201626 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
201547 CAAGCGAGAC
201557 AAAATTCGTTTTAAAATTCTCAAAATTTGTGGA
1 AAAATTCGTTTTAAAATTCTCAAAATTTGTGGA
201590 AAAATTCGTTTTAAAATTCTCAAAATTTGTGGA
1 AAAATTCGTTTTAAAATTCTCAAAATTTGTGGA
201623 AAAA
1 AAAA
201627 ATGTATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (33 bp):
AAAATTCGTTTTAAAATTCTCAAAATTTGTGGA
Found at i:201636 original size:4 final size:4
Alignment explanation
Indices: 201627--202404 Score: 1278
Period size: 4 Copynumber: 197.8 Consensus size: 4
201617 TGTGGAAAAA
*
201627 ATGT ATGT ATGG ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
201675 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
201723 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
201771 A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- ATGT ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
201816 ATG- ATGT ATG- ATGT ATGT ATGT ATGT ATGT ATGT -CGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
201861 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
201909 ATGT A-GT -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
201955 ATGT ATG- A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
202001 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
202049 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
202097 A--T ATGT ATGT ATGT ATGT ATGT ATGGT ATGG ATG- ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT
* * * * * * *
202143 ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGC ATGC ATGC ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
202191 ATGC ATGC ATGC ATGT ATGC ATG- ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
202238 ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
202286 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
202334 ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAT GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
202382 ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATG
202405 CTTTTCTCGA
Statistics
Matches: 742, Mismatches: 17, Indels: 30
0.94 0.02 0.04
Matches are distributed among these distances:
2 5 0.01
3 23 0.03
4 710 0.96
5 4 0.01
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:203989 original size:21 final size:20
Alignment explanation
Indices: 203964--204003 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
203954 TGAAAATAAA
*
203964 ATGCAGGTGCAAAATGCAAAG
1 ATGCAGATGC-AAATGCAAAG
203985 ATGCAGATGCAAATGCAAA
1 ATGCAGATGCAAATGCAAA
204004 AATATTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (20 bp):
ATGCAGATGCAAATGCAAAG
Found at i:204750 original size:28 final size:28
Alignment explanation
Indices: 204719--204775 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
204709 TGAAAAATGA
*
204719 TATAAACAAAACAAAAG-AAATAAGTTAG
1 TATAAAC-AAACAAAAGAAAATAAATTAG
* *
204747 TATACACAAACAAAGGAAAATAAATTAG
1 TATAAACAAACAAAAGAAAATAAATTAG
204775 T
1 T
204776 TAATACATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (28 bp):
TATAAACAAACAAAAGAAAATAAATTAG
Found at i:207259 original size:48 final size:45
Alignment explanation
Indices: 207184--207309 Score: 166
Period size: 48 Copynumber: 2.8 Consensus size: 45
207174 TATAAAATCT
*
207184 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACTAAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA-TAAAAATA
* * *
207230 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTATAAAAATA
*
207277 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
207310 GCATACTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
46 11 0.15
47 11 0.15
48 26 0.36
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATAAAAATA
Found at i:210045 original size:27 final size:30
Alignment explanation
Indices: 210015--210070 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 30
210005 AACAAATATA
210015 ATAAAACAAAGAT-GA-CT-AAAATGAAAT
1 ATAAAACAAAGATAGAGCTCAAAATGAAAT
*
210042 ATAAAACAAATATAGAGCTCAAAATGAAA
1 ATAAAACAAAGATAGAGCTCAAAATGAAA
210071 AGTAAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 12 0.48
28 2 0.08
29 2 0.08
30 9 0.36
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (30 bp):
ATAAAACAAAGATAGAGCTCAAAATGAAAT
Found at i:211155 original size:3 final size:3
Alignment explanation
Indices: 211147--211195 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
211137 AATGTAATGT
211147 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
211195 T
1 T
211196 TTAAAATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:214929 original size:26 final size:28
Alignment explanation
Indices: 214862--214923 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
214852 TATATATATA
*
214862 TTACAAGCCCAAAGGACCCGAAGGCCCATT
1 TTACAAGCCCAAA--ACCCGAAGGCCCAGT
214892 TTACAAGCCCAAAACCCGAA-GCCC-GT
1 TTACAAGCCCAAAACCCGAAGGCCCAGT
214918 TTACAA
1 TTACAA
214924 TTCCAATCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.23
27 4 0.13
28 7 0.23
30 13 0.42
ACGTcount: A:0.35, C:0.34, G:0.16, T:0.15
Consensus pattern (28 bp):
TTACAAGCCCAAAACCCGAAGGCCCAGT
Found at i:216623 original size:17 final size:17
Alignment explanation
Indices: 216601--216638 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
216591 ATATTTTATT
216601 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
216618 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
216635 TATA
1 TATA
216639 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:217142 original size:28 final size:27
Alignment explanation
Indices: 217111--217164 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
217101 TAATTCTTTC
* *
217111 TTTTCAAAATTTTTATATTTATTTATTA
1 TTTTCAAAATATTTATATGT-TTTATTA
*
217139 TTTTCATAATATTTATATGTTTTATT
1 TTTTCAAAATATTTATATGTTTTATT
217165 TTATTTGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTCAAAATATTTATATGTTTTATTA
Found at i:217169 original size:18 final size:18
Alignment explanation
Indices: 217119--217170 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
217109 TCTTTTCAAA
217119 ATTTTTATATTTATTTATT
1 ATTTTTAT-TTTATTTATT
* **
217138 ATTTTCATAATATTTA-T
1 ATTTTTATTTTATTTATT
217155 ATGTTTTATTTTATTT
1 AT-TTTTATTTTATTT
217171 GCAAGTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 3 0.12
18 16 0.62
19 7 0.27
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATTTTATTTATT
Found at i:219271 original size:36 final size:36
Alignment explanation
Indices: 219190--219284 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 36
219180 CATACATGCA
* *
219190 TTTACTTTTTACATCTTTGCATTTCCATCTTGTATT
1 TTTACTTTTTACATCTTTGCATTACCATCTTGCATT
*
219226 CTTACTTTTTACATCTTTGCATTACACAGT-TTGCATT
1 TTTACTTTTTACATCTTTGCATTAC-CA-TCTTGCATT
*
219263 TTTA-TTTTTGCAT-TTATGCATT
1 TTTACTTTTTACATCTT-TGCATT
219285 TTCGTATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.04
36 37 0.73
37 11 0.22
38 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.07, T:0.56
Consensus pattern (36 bp):
TTTACTTTTTACATCTTTGCATTACCATCTTGCATT
Found at i:224169 original size:93 final size:92
Alignment explanation
Indices: 224010--224284 Score: 414
Period size: 93 Copynumber: 3.0 Consensus size: 92
224000 ACCCAATAAT
* *
224010 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCACAGAACCAATCATT
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTATGAAACCACAGAATCAATCATT
224075 GAATTTGGAAGATGAATGTGCTCATAGC
65 GAATTTGGAAGATGAATGTGCTCATAGC
*
224103 ATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAAACCACAGAATCAATCATT
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTATGAAACCACAGAATCAATCATT
224168 GAATTTGGAAGATGAATGTGCTCATAGC
65 GAATTTGGAAGATGAATGTGCTCATAGC
*
224196 ATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CA-AATTCAATCA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTTGGTATGAAAC-CACAGAA-TCAATCA
* *
224258 TT-AGATTTGAAAGATGAATTTGCTCAT
63 TTGA-ATTTGGAAGATGAATGTGCTCAT
224285 GGTAGAAATA
Statistics
Matches: 170, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
91 3 0.02
92 36 0.21
93 131 0.77
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (92 bp):
ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGTATGAAACCACAGAATCAATCATTG
AATTTGGAAGATGAATGTGCTCATAGC
Found at i:224391 original size:114 final size:115
Alignment explanation
Indices: 224187--224504 Score: 496
Period size: 115 Copynumber: 2.8 Consensus size: 115
224177 AGATGAATGT
* *
224187 GCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAT
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
*
224251 TCAATCATTAGATTTGAAAGATGAA-TTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTAGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
224300 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
*
224365 TCAATCATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
66 TCAATCATTAGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
* * * * * *
224415 ACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAGAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
* * * *
224480 CCGATCATTTGAATTGAAAGATGAA
66 TCAATCATTAGATTTGAAAGATGAA
224505 CTTCATGATC
Statistics
Matches: 189, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 4 0.02
114 82 0.43
115 103 0.54
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (115 bp):
GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
TCAATCATTAGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
Found at i:227042 original size:22 final size:22
Alignment explanation
Indices: 227015--227069 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
227005 ATCTACACTC
227015 TTTAAAGATGATAGATTCTCTT
1 TTTAAAGATGATAGATTCTCTT
227037 TTTAAAGATGATAGATTCTCTT
1 TTTAAAGATGATAGATTCTCTT
* *
227059 TTCAAAAATGA
1 TTTAAAGATGA
227070 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTAAAGATGATAGATTCTCTT
Found at i:227747 original size:77 final size:77
Alignment explanation
Indices: 227516--228084 Score: 1061
Period size: 77 Copynumber: 7.4 Consensus size: 77
227506 CTATTTCCCA
227516 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
227581 AAGCCTTAGGGT
66 AAGCCTTAGGGT
227593 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
227657 AAGCCTTAGGGT
66 AAGCCTTAGGGT
*
227669 CATCTGTAAGTTCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
227734 AAGCCTTAGGGT
66 AAGCCTTAGGGT
*
227746 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
227811 AAGCCTTAGGGT
66 AAGCCTTAGGGT
*
227823 CATCTGTAAGTCATTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
227888 AAGCCTTAGGGT
66 AAGCCTTAGGGT
227900 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
227965 AAGCCTTAGGGT
66 AAGCCTTAGGGT
*
227977 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
228041 AAGCCTTCGGGT
66 AAGCCTTAGGGT
* *
228053 CATCTATAAGCCCTTCAGTGCATGATGTTTTC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC
228085 AAACATTTCC
Statistics
Matches: 480, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
76 147 0.31
77 333 0.69
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (77 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGGT
Found at i:228222 original size:3 final size:3
Alignment explanation
Indices: 228214--228265 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
228204 CATTTAAATT
* * *
228214 TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
228260 TTA TTA
1 TTA TTA
228266 ATATAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 1 0.03
3 36 0.90
4 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:229801 original size:23 final size:22
Alignment explanation
Indices: 229775--229824 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
229765 ATATATAATA
* *
229775 AATAATAATTTATATTTTTTTTC
1 AATAATAATTT-TAATATTTTTC
*
229798 AATAAATTATTTTAATATTTTTC
1 AAT-AATAATTTTAATATTTTTC
229821 AATA
1 AATA
229825 TCGAAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 15 0.65
24 7 0.30
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
AATAATAATTTTAATATTTTTC
Found at i:230032 original size:29 final size:29
Alignment explanation
Indices: 229999--230054 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
229989 TCATTTTCTG
*
229999 ATATTTCTAAATAAATAAATATTTTATTT
1 ATATTTATAAATAAATAAATATTTTATTT
* * *
230028 ATATTTATATATAAATATATTTTTTAT
1 ATATTTATAAATAAATAAATATTTTAT
230055 ATAATTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTTATAAATAAATAAATATTTTATTT
Found at i:230057 original size:27 final size:25
Alignment explanation
Indices: 230013--230063 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
230003 TTCTAAATAA
*
230013 ATAAATATTTTATTTATATTTATAT
1 ATAAATATTTTATTTATAATTATAT
*
230038 ATAAATATATTTTTTATATAATTATA
1 ATAAATAT-TTTATT-TATAATTATA
230064 ACTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 5 0.23
27 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATAAATATTTTATTTATAATTATAT
Found at i:230063 original size:25 final size:25
Alignment explanation
Indices: 230013--230064 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
230003 TTCTAAATAA
*
230013 ATAAATATTTTATTTATATTTATAT
1 ATAAATATTTTATTTATATATATAT
230038 ATAAATATATTT-TTTATATA-AT-T
1 ATAAATAT-TTTATTTATATATATAT
230061 ATAA
1 ATAA
230065 CTTTGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 2 0.08
25 15 0.60
26 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATAAATATTTTATTTATATATATAT
Found at i:236001 original size:21 final size:21
Alignment explanation
Indices: 235975--236063 Score: 115
Period size: 21 Copynumber: 4.2 Consensus size: 21
235965 CTGACTATCA
235975 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
*
235996 CATTGCAATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
* *
236017 CGTTGCGATTTTCCGAATTCG
1 CATTGCGATTTTCCAAATTCG
* ** *
236038 CAATGCGATAGTCCAAAATCG
1 CATTGCGATTTTCCAAATTCG
236059 CATTG
1 CATTG
236064 TGATAGCACT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCG
Found at i:236808 original size:21 final size:21
Alignment explanation
Indices: 236779--236892 Score: 174
Period size: 21 Copynumber: 5.4 Consensus size: 21
236769 ATTTTGATCA
* *
236779 CTATTGCAATGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
236800 CTATCGCAACGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
*
236821 CTATCGCAACGGTGAACAATG
1 CTATCGCAACGGTGAACAGTG
* *
236842 TTATCGCAACGGTGAACAGTA
1 CTATCGCAACGGTGAACAGTG
*
236863 CTATCGTAACGGTGAACAGTG
1 CTATCGCAACGGTGAACAGTG
236884 CTATCGCAA
1 CTATCGCAA
236893 TGCGATTTTG
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (21 bp):
CTATCGCAACGGTGAACAGTG
Found at i:236908 original size:21 final size:21
Alignment explanation
Indices: 236884--236940 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
236874 GTGAACAGTG
236884 CTATCGCAATGCGATTTTGGA
1 CTATCGCAATGCGATTTTGGA
* *
236905 CTATCGCATTGCGAATTTGGA
1 CTATCGCAATGCGATTTTGGA
**
236926 AAATCGCAATGCGAT
1 CTATCGCAATGCGAT
236941 AGTCAGAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (21 bp):
CTATCGCAATGCGATTTTGGA
Found at i:237527 original size:13 final size:13
Alignment explanation
Indices: 237494--237553 Score: 75
Period size: 13 Copynumber: 4.6 Consensus size: 13
237484 GCACAATCTT
*
237494 AGACACAACTTTA
1 AGACACAACTTTG
* *
237507 AGAAACAAATTTG
1 AGACACAACTTTG
*
237520 AGACACAATTTTG
1 AGACACAACTTTG
*
237533 AGAGACAACTTTG
1 AGACACAACTTTG
237546 AGACACAA
1 AGACACAA
237554 TTCACGAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.22
Consensus pattern (13 bp):
AGACACAACTTTG
Found at i:237554 original size:26 final size:26
Alignment explanation
Indices: 237494--237555 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
237484 GCACAATCTT
*
237494 AGACACAACTTTAAGAAACAAATTTG
1 AGACACAATTTTAAGAAACAAATTTG
* * *
237520 AGACACAATTTTGAGAGACAACTTTG
1 AGACACAATTTTAAGAAACAAATTTG
237546 AGACACAATT
1 AGACACAATT
237556 CACGAAGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (26 bp):
AGACACAATTTTAAGAAACAAATTTG
Found at i:237901 original size:3 final size:3
Alignment explanation
Indices: 237895--237925 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
237885 ATAATAATAT
237895 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
237926 CTTGGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:238764 original size:2 final size:2
Alignment explanation
Indices: 238757--238807 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
238747 CTTTTAAAAC
238757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238799 AT AT AT AT A
1 AT AT AT AT A
238808 CCCCCATCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:239002 original size:24 final size:24
Alignment explanation
Indices: 238968--239038 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
238958 AAACGGAGAT
* *
238968 ATCAGAAATCAAAACAGAATTCATA
1 ATCAGATATCATAACAGAATTCA-A
* *
238993 AT-AGATATCATAACAGAATCCAG
1 ATCAGATATCATAACAGAATTCAA
239016 ATCAGATATCATAACAGAATTCA
1 ATCAGATATCATAACAGAATTCA
239039 GGTCATGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.23
Consensus pattern (24 bp):
ATCAGATATCATAACAGAATTCAA
Found at i:239033 original size:12 final size:11
Alignment explanation
Indices: 238974--239035 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
238964 AGATATCAGA
*
238974 AATCAAAACAG
1 AATCATAACAG
*
238985 AATTCATAATAG
1 AA-TCATAACAG
238997 ATATCATAACAG
1 A-ATCATAACAG
* *
239009 AATCCAGATCAG
1 AAT-CATAACAG
239021 ATATCATAACAG
1 A-ATCATAACAG
239033 AAT
1 AAT
239036 TCAGGTCATG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 6 0.15
12 31 0.77
13 3 0.08
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.23
Consensus pattern (11 bp):
AATCATAACAG
Found at i:239049 original size:24 final size:24
Alignment explanation
Indices: 238969--239067 Score: 85
Period size: 24 Copynumber: 4.1 Consensus size: 24
238959 AACGGAGATA
* * **
238969 TCAGAAATCAAAACAGAATTCATAA
1 TCAGATATCATAACAGAATTCA-GG
* *
238994 T-AGATATCATAACAGAATCCAGA
1 TCAGATATCATAACAGAATTCAGG
239017 TCAGATATCATAACAGAATTCAGG
1 TCAGATATCATAACAGAATTCAGG
* * *
239041 TCATG-TATCAGAACATAATTCAAG
1 TCA-GATATCATAACAGAATTCAGG
239065 TCA
1 TCA
239068 AAAATCAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.03
24 59 0.94
25 2 0.03
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.24
Consensus pattern (24 bp):
TCAGATATCATAACAGAATTCAGG
Found at i:242392 original size:13 final size:13
Alignment explanation
Indices: 242372--242440 Score: 93
Period size: 13 Copynumber: 5.3 Consensus size: 13
242362 AATCTTAGAC
242372 ACAACTTTGAGAA
1 ACAACTTTGAGAA
*
242385 ATAACTTTGAGAA
1 ACAACTTTGAGAA
*
242398 ACAACTTTGAGAC
1 ACAACTTTGAGAA
* *
242411 ATAACTTTGAGAG
1 ACAACTTTGAGAA
*
242424 ACAACTTTGAGAC
1 ACAACTTTGAGAA
242437 ACAA
1 ACAA
242441 TTCACAAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (13 bp):
ACAACTTTGAGAA
Found at i:242436 original size:26 final size:26
Alignment explanation
Indices: 242372--242437 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
242362 AATCTTAGAC
*
242372 ACAACTTTGAGAAATAACTTTGAGAA
1 ACAACTTTGAGACATAACTTTGAGAA
*
242398 ACAACTTTGAGACATAACTTTGAGAG
1 ACAACTTTGAGACATAACTTTGAGAA
242424 ACAACTTTGAGACA
1 ACAACTTTGAGACA
242438 CAATTCACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (26 bp):
ACAACTTTGAGACATAACTTTGAGAA
Found at i:243991 original size:28 final size:29
Alignment explanation
Indices: 243955--244028 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
243945 GAAACTTATT
243955 AAATATATTTTATTCTTAACTTAA-TTGA
1 AAATATATTTTATTCTTAACTTAATTTGA
* * ** *
243983 AAATCTATTTTATTATTATTTTAATTTTA
1 AAATATATTTTATTCTTAACTTAATTTGA
*
244012 AAATTGTATTTTATTCT
1 AAA-TATATTTTATTCT
244029 CCATATAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 20 0.54
29 6 0.16
30 11 0.30
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (29 bp):
AAATATATTTTATTCTTAACTTAATTTGA
Found at i:244121 original size:18 final size:19
Alignment explanation
Indices: 244098--244136 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
244088 ATTTATTAAA
244098 TAAATTATATT-AT-TATTT
1 TAAATTAT-TTAATATATTT
244116 TAAATTATTTAATATATTT
1 TAAATTATTTAATATATTT
244135 TA
1 TA
244137 TTTTTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 10 0.53
19 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAAATTATTTAATATATTT
Found at i:244223 original size:31 final size:31
Alignment explanation
Indices: 244127--244259 Score: 100
Period size: 31 Copynumber: 4.5 Consensus size: 31
244117 AAATTATTTA
* *
244127 ATATATTTTATTTTTATCTTAACTT--AAA-
1 ATATATTTTATTCTTATCATAACTTAAAAAC
** ** *
244155 A-ATATTTTAAACTTATTTTAA-TTTAAAA-
1 ATATATTTTATTCTTATCATAACTTAAAAAC
*
244183 A-ATATTTTATTCTTATCATAACTTAAAAAT
1 ATATATTTTATTCTTATCATAACTTAAAAAC
* * * **
244213 GTGTATTTTATTTTTATTTTAACTTAAAAAC
1 ATATATTTTATTCTTATCATAACTTAAAAAC
244244 ATATATTTTATTCTTA
1 ATATATTTTATTCTTA
244260 ACTTTACTTA
Statistics
Matches: 82, Mismatches: 18, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
26 2 0.02
27 16 0.20
28 21 0.26
29 6 0.07
31 37 0.45
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (31 bp):
ATATATTTTATTCTTATCATAACTTAAAAAC
Found at i:244269 original size:31 final size:31
Alignment explanation
Indices: 244184--244269 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
244174 AATTTAAAAA
* * * **
244184 ATATTTTATTCTTATCATAACTTAAAAATGT
1 ATATTTTATTCTTAACTTTACTTAAAAACAT
* * *
244215 GTATTTTATT-TTTATTTTAACTTAAAAACAT
1 ATATTTTATTCTTAACTTT-ACTTAAAAACAT
244246 ATATTTTATTCTTAACTTTACTTA
1 ATATTTTATTCTTAACTTTACTTA
244270 TATATATATA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
30 3 0.07
31 33 0.79
32 6 0.14
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (31 bp):
ATATTTTATTCTTAACTTTACTTAAAAACAT
Found at i:245536 original size:21 final size:21
Alignment explanation
Indices: 245510--245564 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
245500 GATTTACATA
*
245510 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCAAAG
245531 TTCGCATTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCAAAG
*
245552 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
245565 TTTCCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCAAAG
Found at i:245651 original size:21 final size:21
Alignment explanation
Indices: 245621--245694 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
245611 GATTTACATA
*
245621 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** * *
245642 TTCGCGTTGCGATTTTTCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
245663 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
245682 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
245695 TTATTCCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 14 0.34
21 27 0.66
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:245675 original size:40 final size:42
Alignment explanation
Indices: 245627--245722 Score: 160
Period size: 40 Copynumber: 2.3 Consensus size: 42
245617 CATATTCGCA
245627 TTGCGATAGTCCAAGTTCGCGTTGCGATTT-TT-CAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
245667 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
245709 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
245723 AATCGCAACG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 29 0.57
41 2 0.04
42 20 0.39
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:246463 original size:21 final size:21
Alignment explanation
Indices: 246434--246545 Score: 92
Period size: 19 Copynumber: 5.4 Consensus size: 21
246424 ATTTTGGACT
246434 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
246455 ATTGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
246476 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
246497 ATCGCAATGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
246518 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
246537 ATCGCAACG
1 ATCGCAACG
246546 CGAACTTCGA
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
19 26 0.37
21 26 0.37
23 19 0.27
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:246486 original size:42 final size:42
Alignment explanation
Indices: 246430--246566 Score: 233
Period size: 42 Copynumber: 3.3 Consensus size: 42
246420 TGCGATTTTG
* *
246430 GACTATCGCAACGAATTTGGAATAAATTGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
246472 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
246514 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
246554 GACTATCGCAACG
1 GACTATCGCAACG
246567 CGAACTTCGA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 31 0.34
41 1 0.01
42 59 0.65
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:246561 original size:21 final size:21
Alignment explanation
Indices: 246427--246654 Score: 184
Period size: 21 Copynumber: 11.0 Consensus size: 21
246417 CGTTGCGATT
*
246427 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
246446 TTGGAATAAATTGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
246469 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
246488 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
246511 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
246530 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
246551 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* * *
246572 TTCGACTATCACAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
246591 TTGGAATAAATCGCAACGCAAAC
1 TTGGACT--ATCGCAACGCGAAC
*
246614 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
246635 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
246655 TATGTAAATC
Statistics
Matches: 165, Mismatches: 30, Indels: 26
0.75 0.14 0.12
Matches are distributed among these distances:
19 40 0.24
21 98 0.59
23 27 0.16
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:246628 original size:63 final size:61
Alignment explanation
Indices: 246497--246644 Score: 242
Period size: 63 Copynumber: 2.4 Consensus size: 61
246487 TTTGGAATAA
* * *
246497 ATCGCAATGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAAATCGCAACGCAAACTTCGACT
246558 ATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAATAAATCGCAACGCAAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCACAACGAATTTGG-A-AAATCGCAACGCAAACTTCGACT
*
246621 ATCGCAACGCGAACTTGGACTATC
1 ATCGCAACGCGAACTTCGACTATC
246645 GCAATGCGAA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
61 35 0.43
62 1 0.01
63 45 0.56
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAAATCGCAACGCAAACTTCGACT
Found at i:247575 original size:21 final size:20
Alignment explanation
Indices: 247543--247581 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
247533 TTAACTTATT
247543 AAATATTTTTTTATTTTAAA
1 AAATATTTTTTTATTTTAAA
247563 AAATATATTTTTTATTTTA
1 AAATAT-TTTTTTATTTTA
247582 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AAATATTTTTTTATTTTAAA
Found at i:247611 original size:29 final size:28
Alignment explanation
Indices: 247504--247631 Score: 88
Period size: 28 Copynumber: 4.6 Consensus size: 28
247494 AATTCACATC
* *
247504 TTAACATTAAAAA-ATATATTATTTTTATC
1 TTAA-ATTAAAAATATATTTTA-TTTTATT
* **
247533 TTAACTTATTAA-ATA-TTT-TTTTATT
1 TTAAATTAAAAATATATTTTATTTTATT
* *
247558 TTAAA--AAATATATTTTTTATTTTATT
1 TTAAATTAAAAATATATTTTATTTTATT
*
247584 TTAAATTAAAAATATATTTTATTCTTATA
1 TTAAATTAAAAATATATTTTATT-TTATT
*
247613 TTAACTTTTAAAAATATAT
1 TTAA--ATTAAAAATATAT
247632 CTTAAATTAA
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
23 2 0.03
24 2 0.03
25 13 0.17
26 12 0.16
27 2 0.03
28 22 0.29
29 12 0.16
31 12 0.16
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (28 bp):
TTAAATTAAAAATATATTTTATTTTATT
Found at i:247624 original size:31 final size:29
Alignment explanation
Indices: 247555--247631 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 29
247545 ATATTTTTTT
*
247555 ATTTTAAAAAATATATTTTTTATTTTATTTTA
1 ATTTT-AAAAATATA--TTTTATTTTATATTA
*
247587 A-ATTAAAAATATATTTTATTCTTATATTA
1 ATTTTAAAAATATATTTTATT-TTATATTA
247616 ACTTTTAAAAATATAT
1 A-TTTTAAAAATATAT
247632 CTTAAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 7 0.18
29 8 0.21
30 9 0.23
31 14 0.36
32 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTTAAAAATATATTTTATTTTATATTA
Found at i:247712 original size:32 final size:30
Alignment explanation
Indices: 247669--247733 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
247659 TTTCATAAGT
247669 TAAGATAAAAATAAAGTAT-TTTTAAGATAAAA
1 TAAGATAAAAAT--A-TATGTTTTAAGATAAAA
* *
247701 TAAGATTAAAATATATGTTTTAAGTTAAAA
1 TAAGATAAAAATATATGTTTTAAGATAAAA
247731 TAA
1 TAA
247734 ATTTTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.10
30 16 0.53
32 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.35
Consensus pattern (30 bp):
TAAGATAAAAATATATGTTTTAAGATAAAA
Found at i:247741 original size:18 final size:19
Alignment explanation
Indices: 247701--247752 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
247691 TAAGATAAAA
*
247701 TAAGATTAAAATATATGTTT
1 TAAG-TTAAAATAAATGTTT
247721 TAAGTTAAAATAAAT-TTT
1 TAAGTTAAAATAAATGTTT
*
247739 TAAGTTAAGATAAA
1 TAAGTTAAAATAAA
247753 AAATAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 16 0.53
19 10 0.33
20 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (19 bp):
TAAGTTAAAATAAATGTTT
Found at i:247760 original size:30 final size:29
Alignment explanation
Indices: 247726--247806 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
247716 TGTTTTAAGT
247726 TAAAATAAATTTTTAAGTTAAGATAAAAAA
1 TAAAATAAATTTTTAAGTTAAGAT-AAAAA
** * *
247756 TAAAATATAATTAATAAGTTAAGGTAAACA
1 TAAAATA-AATTTTTAAGTTAAGATAAAAA
247786 TAAAAT--ATTTTTAATGTTAAG
1 TAAAATAAATTTTTAA-GTTAAG
247807 TGTGAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.14
28 6 0.14
30 17 0.40
31 14 0.33
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (29 bp):
TAAAATAAATTTTTAAGTTAAGATAAAAA
Found at i:256973 original size:35 final size:38
Alignment explanation
Indices: 256927--257006 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 38
256917 ACGTTAATCT
*
256927 CATGCATTTCTTAA-TGAG-ATTA-TATGCATTAAACA
1 CATGCATTTCTTAAGTGAGCATTATTATACATTAAACA
256962 CATGCATTTCTTAATGTGAGCATTATTATACATTAAACA
1 CATGCATTTCTTAA-GTGAGCATTATTATACATTAAACA
*
257001 CGTGCA
1 CATGCA
257007 CTATTCTAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 14 0.36
37 4 0.10
38 4 0.10
39 17 0.44
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (38 bp):
CATGCATTTCTTAAGTGAGCATTATTATACATTAAACA
Found at i:258464 original size:21 final size:22
Alignment explanation
Indices: 258424--258464 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
258414 TAGAATTTTA
258424 TTATTTCAGATTAATTAAATCT
1 TTATTTCAGATTAATTAAATCT
258446 TTATTT-A-ATTAATTTAAAT
1 TTATTTCAGATTAA-TTAAAT
258465 TAAATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (22 bp):
TTATTTCAGATTAATTAAATCT
Found at i:259702 original size:30 final size:29
Alignment explanation
Indices: 259642--259714 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 29
259632 GTTCTTCTTT
259642 TAATATAATGTCTAAATTACCTCAAAAAAA
1 TAATATAATGTCTAAATTA-CTCAAAAAAA
259672 TAATATAATGTCTAAATTA-TCAAAATAAAA
1 TAATATAATGTCTAAATTACTC-AAA-AAAA
259702 TAAAATATAATGT
1 T--AATATAATGT
259715 TTAAGTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
28 2 0.05
29 3 0.08
30 24 0.62
32 10 0.26
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (29 bp):
TAATATAATGTCTAAATTACTCAAAAAAA
Found at i:269939 original size:21 final size:24
Alignment explanation
Indices: 269885--269934 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
269875 ATAAACATCA
*
269885 AATACAATAAATAAAATTATTTATT
1 AATAAAAT-AATAAAATTATTTATT
*
269910 AATAAAATAATAATATTATTT-TT
1 AATAAAATAATAAAATTATTTATT
269933 AA
1 AA
269935 AAATATTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATAAAATAATAAAATTATTTATT
Found at i:270043 original size:30 final size:29
Alignment explanation
Indices: 269987--270061 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
269977 ATTCTTAAAT
*
269987 TATTATATAT-ATAATTTTATAAATAAAAA
1 TATTATAAATAAT-ATTTTATAAATAAAAA
*
270016 TATTA-AAATAATATTTTATTAAAATAAAAT
1 TATTATAAATAATATTTTA-T-AAATAAAAA
*
270046 TATTATAAATTATATT
1 TATTATAAATAATATT
270062 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 9 0.23
29 8 0.21
30 13 0.33
31 9 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TATTATAAATAATATTTTATAAATAAAAA
Found at i:270054 original size:16 final size:16
Alignment explanation
Indices: 269983--270054 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 16
269973 TATTATTCTT
*
269983 AAATTATTAT-ATATA
1 AAATTATTATAAAATA
*
269998 TAATT-TTAT-AAATA
1 AAATTATTATAAAATA
*
270012 AAAATA-T-TAAAATA
1 AAATTATTATAAAATA
*
270026 ATATT-TTATTAAAATA
1 AAATTATTA-TAAAATA
270042 AAATTATTATAAA
1 AAATTATTATAAA
270055 TTATATTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
13 1 0.02
14 21 0.48
15 4 0.09
16 15 0.34
17 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTATTATAAAATA
Found at i:270274 original size:25 final size:25
Alignment explanation
Indices: 270248--270297 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
270238 CAATTACTTA
* *
270248 TTCAAATAATAATATTATTAAAATAT
1 TTCAAAAAAT-ATAATATTAAAATAT
*
270274 TTGAAAAAATATAATATTAAAATA
1 TTCAAAAAATATAATATTAAAATA
270298 AAAATGATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
TTCAAAAAATATAATATTAAAATAT
Found at i:270517 original size:18 final size:17
Alignment explanation
Indices: 270494--270527 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
270484 TTTATTAAAA
270494 TAATATTAAATAATATAT
1 TAATATTAAA-AATATAT
270512 TAATATTAAAAATATA
1 TAATATTAAAAATATA
270528 AAGTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATTAAAAATATAT
Found at i:271738 original size:2 final size:2
Alignment explanation
Indices: 271731--271764 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
271721 CGAAACATAC
271731 AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271765 TATGTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:271765 original size:12 final size:13
Alignment explanation
Indices: 271731--271767 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
271721 CGAAACATAC
271731 ATATATATA-TAT
1 ATATATATATTAT
271743 ATATATATATTAT
1 ATATATATATTAT
271756 AT-TATATATTAT
1 ATATATATATTAT
271768 GTATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:273017 original size:2 final size:2
Alignment explanation
Indices: 273010--273037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
273000 CAAGTATTCA
273010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
273038 TCTTTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273175 original size:16 final size:16
Alignment explanation
Indices: 273155--273232 Score: 75
Period size: 16 Copynumber: 4.5 Consensus size: 16
273145 TAATTCCATT
273155 TTTTTATTGTTGTTTTA
1 TTTTTATT-TTGTTTTA
273172 TTTTTATTTTGTTTTA
1 TTTTTATTTTGTTTTA
* *
273188 TCTTTATTTATGTTCTCATT
1 TTTTTATTT-TGTT-T--TA
*
273208 TTATTTAATTTGTTTTA
1 TT-TTTATTTTGTTTTA
273225 TTTTTATT
1 TTTTTATT
273233 CTTAGTTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 21 0.42
17 15 0.30
18 1 0.02
19 1 0.02
20 6 0.12
21 6 0.12
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTTATTTTGTTTTA
Found at i:273210 original size:17 final size:16
Alignment explanation
Indices: 273173--273214 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
273163 GTTGTTTTAT
*
273173 TTTTATTT-TGTTTTA
1 TTTTATTTATGTTTCA
273188 TCTTTATTTATGTTCTCA
1 T-TTTATTTATGTT-TCA
273206 TTTTATTTA
1 TTTTATTTA
273215 ATTTGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 1 0.04
16 7 0.30
17 12 0.52
18 3 0.13
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTTATTTATGTTTCA
Found at i:277089 original size:15 final size:15
Alignment explanation
Indices: 277069--277099 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
277059 AAGACCAGAT
277069 GAATATGGTCAAAGG
1 GAATATGGTCAAAGG
277084 GAATATGGTCAAAGG
1 GAATATGGTCAAAGG
277099 G
1 G
277100 GACCATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.19
Consensus pattern (15 bp):
GAATATGGTCAAAGG
Found at i:278140 original size:54 final size:54
Alignment explanation
Indices: 278058--278165 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
278048 TTGGATCCGT
278058 TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
1 TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
*
278112 TTCAATTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
1 TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
278166 CTATAATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (54 bp):
TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
Found at i:285668 original size:2 final size:2
Alignment explanation
Indices: 285661--285702 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
285651 TGACCGAATC
285661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
285703 TATTTTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:286879 original size:6 final size:6
Alignment explanation
Indices: 286864--286920 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
286854 ATATTTTACT
* * * *
286864 TATATG TATACA TATACA TACATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
286912 TATATA TAT
1 TATATA TAT
286921 TTACTCTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (6 bp):
TATATA
Found at i:286884 original size:10 final size:10
Alignment explanation
Indices: 286864--286920 Score: 78
Period size: 10 Copynumber: 5.7 Consensus size: 10
286854 ATATTTTACT
*
286864 TATATGTATA
1 TATATATATA
* *
286874 CATATACATA
1 TATATATATA
*
286884 CATATATATA
1 TATATATATA
286894 TATATATATA
1 TATATATATA
286904 TATATATATA
1 TATATATATA
286914 TATATAT
1 TATATAT
286921 TTACTCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (10 bp):
TATATATATA
Found at i:286892 original size:4 final size:4
Alignment explanation
Indices: 286864--286920 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
286854 ATATTTTACT
* * * *
286864 TATA TGTA TACA TATA CATA CATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
286912 TATA TATA T
1 TATA TATA T
286921 TTACTCTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (4 bp):
TATA
Found at i:287005 original size:50 final size:48
Alignment explanation
Indices: 286904--287018 Score: 126
Period size: 50 Copynumber: 2.4 Consensus size: 48
286894 TATATATATA
* *
286904 TATATATATATATATATTTACTCTTTTTGTTTTATTTTACCAAGTATT
1 TATATATATATATATATTTACTCTTTTTGTTTTATTTAACCAAGTAAT
* * *
286952 TATATATATATATATATTATTCTTTTTACTTGTTTTA-TTAACC-ATTGAAT
1 TATATATATATATATATT-TACTCTTT--TTGTTTTATTTAACCAAGT-AAT
*
287002 TATACATATATATATAT
1 TATATATATATATATAT
287019 ATATATATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
48 18 0.32
49 8 0.14
50 23 0.40
51 8 0.14
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (48 bp):
TATATATATATATATATTTACTCTTTTTGTTTTATTTAACCAAGTAAT
Found at i:287014 original size:2 final size:2
Alignment explanation
Indices: 287002--287094 Score: 177
Period size: 2 Copynumber: 46.5 Consensus size: 2
286992 ACCATTGAAT
*
287002 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
287044 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
287086 TA TA TA TA T
1 TA TA TA TA T
287095 TATTTTTACC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:287132 original size:16 final size:17
Alignment explanation
Indices: 287097--287132 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
287087 ATATATATTA
287097 TTTTTACCTTATTTGTT
1 TTTTTACCTTATTTGTT
287114 TTTTTACCTTATTTGTT
1 TTTTTACCTTATTTGTT
287131 TT
1 TT
287133 ATTTTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTTACCTTATTTGTT
Found at i:287154 original size:27 final size:26
Alignment explanation
Indices: 287122--287204 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 26
287112 TTTTTTTACC
287122 TTATTTGTTTTATTTTTTTGTTGTTTT
1 TTATTTGTTTTATTTTTTT-TTGTTTT
287149 TTATTTGTTTTATTTAATTTAATTT-TTTT
1 TTATTTGTTTTATTT--TTT--TTTGTTTT
287178 ATT-TTTGTTTTATTTTTATTTTGTTTT
1 -TTATTTGTTTTATTTTT-TTTTGTTTT
287205 ATCTTTATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
26 3 0.06
27 21 0.43
28 1 0.02
29 19 0.39
30 4 0.08
31 1 0.02
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (26 bp):
TTATTTGTTTTATTTTTTTTTGTTTT
Found at i:287182 original size:5 final size:5
Alignment explanation
Indices: 287147--287277 Score: 51
Period size: 5 Copynumber: 25.8 Consensus size: 5
287137 TTTTGTTGTT
* * * *
287147 TTTTA -TTTG TTTTA -TTTA ATTTA ATTT- TTTTA TTTTTG TTTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA -TTTTA
* * * *
287196 TTTTG TTTTA TCTTTA -TTTA TGTTCCCA TTTTA -TTTA ATTTG TTTTA
1 TTTTA TTTTA T-TTTA TTTTA T-TT--TA TTTTA TTTTA TTTTA TTTTA
*
287243 TTTTTA TTCTTA -GTTA TTTTA TTATTA TTTT- TTTT
1 -TTTTA TT-TTA TTTTA TTTTA TT-TTA TTTTA TTTT
287278 GCTTTAATCA
Statistics
Matches: 97, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
4 25 0.26
5 40 0.41
6 28 0.29
7 2 0.02
8 2 0.02
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:287194 original size:45 final size:45
Alignment explanation
Indices: 287105--287215 Score: 122
Period size: 45 Copynumber: 2.5 Consensus size: 45
287095 TATTTTTACC
** *
287105 TTATTTGTTTT-TTTACCTT-ATTTGTTTTATTTTTTTGTTGTTTT
1 TTATTTGTTTTATTTAATTTAATTTGTTTTATTTTTTTGTT-ATTT
287149 TTATTTGTTTTATTTAATTTAATTT-TTTTATTTTTGTT-TTATTT
1 TTATTTGTTTTATTTAATTTAATTTGTTTTATTTTT-TTGTTATTT
*
287193 TTATTTTGTTTTATCTTTATTTA
1 TTA-TTTGTTTTAT-TTAATTTA
287216 TGTTCCCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
44 17 0.29
45 28 0.48
46 13 0.22
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (45 bp):
TTATTTGTTTTATTTAATTTAATTTGTTTTATTTTTTTGTTATTT
Found at i:287227 original size:45 final size:43
Alignment explanation
Indices: 287136--287227 Score: 96
Period size: 45 Copynumber: 2.1 Consensus size: 43
287126 TTGTTTTATT
* ***
287136 TTTTTGTTGTTTTTTATTTGTTTTATTTAATTTAATTTTTTTA
1 TTTTTGTTGTTTTTTATTTGTTTTATTTAATTTAATGTTCCCA
* *
287179 TTTTTGTTTTATTTTTATTTTGTTTTATCTTTATTT-ATGTTCCCA
1 TTTTTGTTGT-TTTTTA-TTTGTTTTAT-TTAATTTAATGTTCCCA
287224 TTTT
1 TTTT
287228 ATTTAATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
43 9 0.22
44 6 0.15
45 19 0.47
46 6 0.15
ACGTcount: A:0.14, C:0.04, G:0.07, T:0.75
Consensus pattern (43 bp):
TTTTTGTTGTTTTTTATTTGTTTTATTTAATTTAATGTTCCCA
Found at i:292948 original size:6 final size:6
Alignment explanation
Indices: 292937--292961 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
292927 GGTTTTTTTC
292937 TTTCCT TTTCCT TTTCCT TTTCCT T
1 TTTCCT TTTCCT TTTCCT TTTCCT T
292962 GTATATACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCCT
Found at i:293209 original size:117 final size:117
Alignment explanation
Indices: 293003--293233 Score: 462
Period size: 117 Copynumber: 2.0 Consensus size: 117
292993 ATCCCTTTGT
293003 TCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGCTTGC
1 TCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGCTTGC
293068 CCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTATTGC
66 CCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTATTGC
293120 TCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGCTTGC
1 TCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGCTTGC
293185 CCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTAT
66 CCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTAT
293234 GTACCAAATG
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (117 bp):
TCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGCTTGC
CCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTATTGC
Found at i:295824 original size:19 final size:20
Alignment explanation
Indices: 295800--295850 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
295790 AATGACCAAT
295800 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* * *
295819 AAAATCGCAATGCGATTTAG
1 AAAATCGCAACGCGATATAC
295839 AAAATCGCAACG
1 AAAATCGCAACG
295851 TTAAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:295860 original size:20 final size:20
Alignment explanation
Indices: 295837--295890 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
295827 AATGCGATTT
*
295837 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
295857 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
295877 AGAAAATCGCAACG
1 AGAAAATCGCAACG
295891 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:296846 original size:16 final size:17
Alignment explanation
Indices: 296806--296847 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
296796 ATATTCTTCT
296806 TTTCTTCTTCTTCTTCAC
1 TTTC-TCTTCTTCTTCAC
*
296824 TTT-TCTTCTTCTT-TC
1 TTTCTCTTCTTCTTCAC
296839 TTTCTCTTC
1 TTTCTCTTC
296848 ACTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 15 0.68
18 3 0.14
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTCTCTTCTTCTTCAC
Found at i:296846 original size:26 final size:27
Alignment explanation
Indices: 296799--296853 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
296789 CATTCCCATA
*
296799 TTCTTCTTTTCTTCTTCTTCTTCACTT
1 TTCTTCTTCTCTTCTTCTTCTTCACTT
296826 TTCTTCTTCT-TTCTT-TCTCTTCACTT
1 TTCTTCTTCTCTTCTTCT-TCTTCACTT
296852 TT
1 TT
296854 ATTTCTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 1 0.04
26 16 0.62
27 9 0.35
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (27 bp):
TTCTTCTTCTCTTCTTCTTCTTCACTT
Found at i:298946 original size:20 final size:20
Alignment explanation
Indices: 298905--298947 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
298895 AATAAATTTG
* *
298905 TTAATATAATTATTTTTTTA
1 TTAATATAATTATTTATATA
298925 TTAATATAATT-TATTATATA
1 TTAATATAATTAT-TTATATA
298945 TTA
1 TTA
298948 TTTTAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATATAATTATTTATATA
Found at i:300215 original size:3 final size:3
Alignment explanation
Indices: 300202--300242 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
300192 TATTTTAATA
300202 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
300243 GTAACGCCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:301521 original size:22 final size:22
Alignment explanation
Indices: 301452--301511 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
301442 ACTAATACTC
301452 AAGAGAGTATCGATACCTAAGT
1 AAGAGAGTATCGATACCTAAGT
301474 AAGAGAGTATCGATACCTAAGT
1 AAGAGAGTATCGATACCTAAGT
301496 AAGAGAGTATCGATAC
1 AAGAGAGTATCGATAC
301512 TCCTAGAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (22 bp):
AAGAGAGTATCGATACCTAAGT
Found at i:311306 original size:17 final size:18
Alignment explanation
Indices: 311273--311307 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
311263 TTTTAAAAAA
311273 TTAATTCTTAAATAATTT
1 TTAATTCTTAAATAATTT
*
311291 TTAATT-TTACATAATTT
1 TTAATTCTTAAATAATTT
311308 AATCATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTCTTAAATAATTT
Found at i:312542 original size:6 final size:6
Alignment explanation
Indices: 312531--312574 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
312521 ACTGTTTTTA
* *
312531 TTATTT TTATTT TTATGT TTATTT GT-TTT TTATTT TCTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT T-TATTT TT
312575 TATTAACCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 4 0.12
6 22 0.69
7 6 0.19
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:312694 original size:11 final size:11
Alignment explanation
Indices: 312674--312710 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
312664 GGGACCCATG
312674 TTATTATTATT
1 TTATTATTATT
*
312685 TTATTTTTATT
1 TTATTATTATT
312696 TT-TTATTATT
1 TTATTATTATT
312706 TTATT
1 TTATT
312711 TAATTAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTATTATT
Done.